Multiple sequence alignment - TraesCS2D01G328400

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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 TraesCS2D01G328400 chr2D 100.000 3907 0 0 1 3907 421792353 421796259 0.000000e+00 7215.0
1 TraesCS2D01G328400 chr2D 90.000 270 16 3 84 352 421477144 421477403 4.840000e-89 339.0
2 TraesCS2D01G328400 chr2D 93.137 102 4 3 1458 1558 174430742 174430841 3.150000e-31 147.0
3 TraesCS2D01G328400 chr2D 94.792 96 2 3 1457 1551 367218189 367218096 3.150000e-31 147.0
4 TraesCS2D01G328400 chr2A 96.295 2375 68 8 1546 3907 568284975 568287342 0.000000e+00 3880.0
5 TraesCS2D01G328400 chr2A 85.940 761 36 19 1 741 568283457 568284166 0.000000e+00 747.0
6 TraesCS2D01G328400 chr2A 94.363 479 15 1 998 1464 568284498 568284976 0.000000e+00 725.0
7 TraesCS2D01G328400 chr2A 86.111 216 9 2 148 363 546771556 546771362 3.060000e-51 213.0
8 TraesCS2D01G328400 chr2A 87.634 186 13 7 779 959 568284243 568284423 1.420000e-49 207.0
9 TraesCS2D01G328400 chr2A 95.604 91 4 0 1463 1553 464445178 464445088 3.150000e-31 147.0
10 TraesCS2D01G328400 chr2A 94.681 94 3 2 1463 1555 659614675 659614583 1.130000e-30 145.0
11 TraesCS2D01G328400 chr2A 92.208 77 4 2 109 185 567734294 567734368 1.480000e-19 108.0
12 TraesCS2D01G328400 chr2A 94.444 36 2 0 5 40 546773758 546773723 5.450000e-04 56.5
13 TraesCS2D01G328400 chr2A 94.444 36 2 0 5 40 567734262 567734297 5.450000e-04 56.5
14 TraesCS2D01G328400 chr2B 96.266 1446 31 6 2464 3907 494265522 494266946 0.000000e+00 2350.0
15 TraesCS2D01G328400 chr2B 89.138 1114 42 30 396 1464 494263336 494264415 0.000000e+00 1314.0
16 TraesCS2D01G328400 chr2B 94.651 673 32 3 1544 2213 494264415 494265086 0.000000e+00 1040.0
17 TraesCS2D01G328400 chr2B 91.623 382 18 8 1 381 494260793 494261161 2.080000e-142 516.0
18 TraesCS2D01G328400 chr2B 95.276 254 9 2 2212 2465 494265168 494265418 2.190000e-107 399.0
19 TraesCS2D01G328400 chr2B 84.921 378 19 11 1 372 493986524 493986869 8.030000e-92 348.0
20 TraesCS2D01G328400 chr2B 89.441 161 12 4 2327 2485 288939766 288939923 8.560000e-47 198.0
21 TraesCS2D01G328400 chr2B 89.172 157 11 4 2331 2484 91043233 91043386 1.430000e-44 191.0
22 TraesCS2D01G328400 chr6B 90.968 155 12 1 2333 2485 530129117 530128963 1.420000e-49 207.0
23 TraesCS2D01G328400 chr4A 83.913 230 23 7 5 227 147567041 147566819 1.420000e-49 207.0
24 TraesCS2D01G328400 chr1A 90.446 157 13 1 2331 2485 395177604 395177448 5.120000e-49 206.0
25 TraesCS2D01G328400 chr5D 88.820 161 14 2 2326 2484 204323226 204323384 1.110000e-45 195.0
26 TraesCS2D01G328400 chr1D 88.535 157 16 1 2331 2485 314705761 314705605 5.150000e-44 189.0
27 TraesCS2D01G328400 chr1D 79.283 251 22 12 32 275 376281702 376281475 8.750000e-32 148.0
28 TraesCS2D01G328400 chr1D 90.654 107 6 4 1446 1550 471289923 471290027 5.260000e-29 139.0
29 TraesCS2D01G328400 chr1B 88.679 159 13 2 2334 2487 390622293 390622451 5.150000e-44 189.0
30 TraesCS2D01G328400 chr1B 84.259 108 8 3 19 123 502815555 502815454 3.210000e-16 97.1
31 TraesCS2D01G328400 chr1B 85.567 97 5 3 30 123 502854153 502854063 4.160000e-15 93.5
32 TraesCS2D01G328400 chr1B 94.118 51 0 1 32 79 502897801 502897751 1.510000e-09 75.0
33 TraesCS2D01G328400 chr4D 80.632 253 30 14 128 366 323927750 323927997 1.120000e-40 178.0
34 TraesCS2D01G328400 chr4D 100.000 28 0 0 3155 3182 292300278 292300251 7.000000e-03 52.8
35 TraesCS2D01G328400 chr4B 87.500 160 11 6 128 279 404513394 404513552 4.010000e-40 176.0
36 TraesCS2D01G328400 chr4B 100.000 29 0 0 3152 3180 156923804 156923776 2.000000e-03 54.7
37 TraesCS2D01G328400 chr7A 94.898 98 3 2 1461 1556 558288811 558288714 6.760000e-33 152.0
38 TraesCS2D01G328400 chr7A 95.699 93 3 1 1462 1553 238816496 238816404 8.750000e-32 148.0
39 TraesCS2D01G328400 chr3A 95.604 91 4 0 1463 1553 61924371 61924281 3.150000e-31 147.0
40 TraesCS2D01G328400 chr5B 93.000 100 4 3 1462 1559 158045819 158045721 4.070000e-30 143.0


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 TraesCS2D01G328400 chr2D 421792353 421796259 3906 False 7215.00 7215 100.0000 1 3907 1 chr2D.!!$F3 3906
1 TraesCS2D01G328400 chr2A 568283457 568287342 3885 False 1389.75 3880 91.0580 1 3907 4 chr2A.!!$F2 3906
2 TraesCS2D01G328400 chr2B 494260793 494266946 6153 False 1123.80 2350 93.3908 1 3907 5 chr2B.!!$F4 3906

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
662 2872 0.178068 CGCCACTACTTACCTGCCAT 59.822 55.0 0.00 0.0 0.00 4.40 F
1446 3757 0.035056 AGAGCAAACCTCGGGATTGG 60.035 55.0 12.51 0.0 45.54 3.16 F
1479 3790 0.040646 TCTACTCCCTCGGCTCCAAA 59.959 55.0 0.00 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 4404 0.032678 CTGGATTGATAGGAGCGCGT 59.967 55.000 8.43 0.0 0.00 6.01 R
2825 5330 0.038166 AGCCATGCGGGAGAAAAAGA 59.962 50.000 0.00 0.0 40.01 2.52 R
3159 5664 1.067000 AGCAGCAGCAACAACAACAAA 60.067 42.857 3.17 0.0 45.49 2.83 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
33 35 0.458025 GAGTCGTCCGGCCAAGTAAG 60.458 60.000 2.24 0.00 0.00 2.34
67 72 7.172342 AGTTGGCAAGATGTAATAAGTGGTAA 58.828 34.615 0.00 0.00 0.00 2.85
68 73 6.995511 TGGCAAGATGTAATAAGTGGTAAC 57.004 37.500 0.00 0.00 0.00 2.50
69 74 5.883673 TGGCAAGATGTAATAAGTGGTAACC 59.116 40.000 0.00 0.00 0.00 2.85
70 75 5.007332 GGCAAGATGTAATAAGTGGTAACCG 59.993 44.000 0.00 0.00 0.00 4.44
71 76 5.503520 GCAAGATGTAATAAGTGGTAACCGC 60.504 44.000 0.00 0.00 0.00 5.68
72 77 5.347620 AGATGTAATAAGTGGTAACCGCA 57.652 39.130 0.00 0.00 36.32 5.69
73 78 5.114081 AGATGTAATAAGTGGTAACCGCAC 58.886 41.667 0.00 0.00 36.32 5.34
74 79 4.540359 TGTAATAAGTGGTAACCGCACT 57.460 40.909 0.00 0.00 36.32 4.40
75 80 4.897140 TGTAATAAGTGGTAACCGCACTT 58.103 39.130 9.75 9.75 41.41 3.16
76 81 4.691685 TGTAATAAGTGGTAACCGCACTTG 59.308 41.667 13.53 0.00 39.24 3.16
77 82 2.914695 TAAGTGGTAACCGCACTTGT 57.085 45.000 13.53 0.00 39.24 3.16
78 83 1.305201 AAGTGGTAACCGCACTTGTG 58.695 50.000 4.81 0.00 37.71 3.33
79 84 0.179468 AGTGGTAACCGCACTTGTGT 59.821 50.000 0.00 0.00 36.32 3.72
80 85 1.018910 GTGGTAACCGCACTTGTGTT 58.981 50.000 2.61 0.00 33.65 3.32
81 86 1.018148 TGGTAACCGCACTTGTGTTG 58.982 50.000 2.61 0.00 0.00 3.33
82 87 1.018910 GGTAACCGCACTTGTGTTGT 58.981 50.000 2.61 0.00 0.00 3.32
113 118 0.248377 GCTTGTCTGATGATTGCGCC 60.248 55.000 4.18 0.00 0.00 6.53
116 121 2.896854 TCTGATGATTGCGCCGCC 60.897 61.111 6.63 0.00 0.00 6.13
188 211 1.570803 AGACCATTCTGAGCTGAGCT 58.429 50.000 6.69 6.69 43.88 4.09
189 212 1.207570 AGACCATTCTGAGCTGAGCTG 59.792 52.381 13.71 0.00 39.88 4.24
190 213 1.206610 GACCATTCTGAGCTGAGCTGA 59.793 52.381 13.71 0.99 39.88 4.26
191 214 1.207570 ACCATTCTGAGCTGAGCTGAG 59.792 52.381 13.71 14.45 41.09 3.35
192 215 1.292061 CATTCTGAGCTGAGCTGAGC 58.708 55.000 18.32 18.32 39.63 4.26
353 376 2.570135 TGTGTGCAATTCTGTGCTGTA 58.430 42.857 0.00 0.00 45.17 2.74
478 2673 6.096141 TGGCTTTCAGACATTTCAACAGTTTA 59.904 34.615 0.00 0.00 0.00 2.01
540 2744 0.245539 AGCTAAGCCGTTACGCAAGA 59.754 50.000 0.00 0.00 43.62 3.02
543 2747 2.810650 CTAAGCCGTTACGCAAGAGAT 58.189 47.619 0.00 0.00 43.62 2.75
557 2762 2.834549 CAAGAGATATCGTAGCCCCCAT 59.165 50.000 0.00 0.00 0.00 4.00
559 2764 3.633418 AGAGATATCGTAGCCCCCATAC 58.367 50.000 0.00 0.00 0.00 2.39
656 2866 0.245539 TGCTCACGCCACTACTTACC 59.754 55.000 0.00 0.00 34.43 2.85
657 2867 0.531200 GCTCACGCCACTACTTACCT 59.469 55.000 0.00 0.00 0.00 3.08
658 2868 1.736032 GCTCACGCCACTACTTACCTG 60.736 57.143 0.00 0.00 0.00 4.00
659 2869 0.245539 TCACGCCACTACTTACCTGC 59.754 55.000 0.00 0.00 0.00 4.85
660 2870 0.739813 CACGCCACTACTTACCTGCC 60.740 60.000 0.00 0.00 0.00 4.85
661 2871 1.189524 ACGCCACTACTTACCTGCCA 61.190 55.000 0.00 0.00 0.00 4.92
662 2872 0.178068 CGCCACTACTTACCTGCCAT 59.822 55.000 0.00 0.00 0.00 4.40
663 2873 1.668419 GCCACTACTTACCTGCCATG 58.332 55.000 0.00 0.00 0.00 3.66
665 2875 1.134098 CCACTACTTACCTGCCATGGG 60.134 57.143 15.13 0.00 0.00 4.00
675 2885 2.270850 GCCATGGGCCAGTTACGA 59.729 61.111 15.13 0.00 44.06 3.43
676 2886 1.819632 GCCATGGGCCAGTTACGAG 60.820 63.158 15.13 0.00 44.06 4.18
677 2887 1.819632 CCATGGGCCAGTTACGAGC 60.820 63.158 13.78 0.00 0.00 5.03
678 2888 1.221840 CATGGGCCAGTTACGAGCT 59.778 57.895 13.78 0.00 0.00 4.09
679 2889 1.091771 CATGGGCCAGTTACGAGCTG 61.092 60.000 13.78 0.00 0.00 4.24
730 2945 1.135228 GTGCTGGTGTTGACGGTTTTT 60.135 47.619 0.00 0.00 0.00 1.94
759 3001 1.604604 CAACATGGAAACGGTGGAGT 58.395 50.000 0.00 0.00 0.00 3.85
762 3004 1.270839 ACATGGAAACGGTGGAGTGAG 60.271 52.381 0.00 0.00 0.00 3.51
795 3049 0.509929 GCACCGTTCACCGTTACTTC 59.490 55.000 0.00 0.00 33.66 3.01
1353 3664 2.165234 CGAGCTCTTCACTCCATCTTCA 59.835 50.000 12.85 0.00 0.00 3.02
1396 3707 8.615705 ACCTTCCTTCCTTAGTTAATCAAATCT 58.384 33.333 0.00 0.00 0.00 2.40
1420 3731 3.826466 TCTATGCTGCGAATCTATGTCG 58.174 45.455 0.00 0.00 41.46 4.35
1446 3757 0.035056 AGAGCAAACCTCGGGATTGG 60.035 55.000 12.51 0.00 45.54 3.16
1464 3775 8.989980 CGGGATTGGTTTTCTAATCTAATCTAC 58.010 37.037 0.00 0.00 43.97 2.59
1469 3780 8.855804 TGGTTTTCTAATCTAATCTACTCCCT 57.144 34.615 0.00 0.00 0.00 4.20
1470 3781 8.925338 TGGTTTTCTAATCTAATCTACTCCCTC 58.075 37.037 0.00 0.00 0.00 4.30
1471 3782 8.083462 GGTTTTCTAATCTAATCTACTCCCTCG 58.917 40.741 0.00 0.00 0.00 4.63
1472 3783 7.762588 TTTCTAATCTAATCTACTCCCTCGG 57.237 40.000 0.00 0.00 0.00 4.63
1473 3784 5.254901 TCTAATCTAATCTACTCCCTCGGC 58.745 45.833 0.00 0.00 0.00 5.54
1474 3785 3.818295 ATCTAATCTACTCCCTCGGCT 57.182 47.619 0.00 0.00 0.00 5.52
1475 3786 3.143211 TCTAATCTACTCCCTCGGCTC 57.857 52.381 0.00 0.00 0.00 4.70
1476 3787 2.164338 CTAATCTACTCCCTCGGCTCC 58.836 57.143 0.00 0.00 0.00 4.70
1477 3788 0.261991 AATCTACTCCCTCGGCTCCA 59.738 55.000 0.00 0.00 0.00 3.86
1478 3789 0.261991 ATCTACTCCCTCGGCTCCAA 59.738 55.000 0.00 0.00 0.00 3.53
1479 3790 0.040646 TCTACTCCCTCGGCTCCAAA 59.959 55.000 0.00 0.00 0.00 3.28
1480 3791 0.902531 CTACTCCCTCGGCTCCAAAA 59.097 55.000 0.00 0.00 0.00 2.44
1481 3792 1.486726 CTACTCCCTCGGCTCCAAAAT 59.513 52.381 0.00 0.00 0.00 1.82
1482 3793 1.580059 ACTCCCTCGGCTCCAAAATA 58.420 50.000 0.00 0.00 0.00 1.40
1483 3794 1.486726 ACTCCCTCGGCTCCAAAATAG 59.513 52.381 0.00 0.00 0.00 1.73
1484 3795 1.762957 CTCCCTCGGCTCCAAAATAGA 59.237 52.381 0.00 0.00 0.00 1.98
1485 3796 2.370189 CTCCCTCGGCTCCAAAATAGAT 59.630 50.000 0.00 0.00 0.00 1.98
1486 3797 2.104792 TCCCTCGGCTCCAAAATAGATG 59.895 50.000 0.00 0.00 0.00 2.90
1487 3798 2.104792 CCCTCGGCTCCAAAATAGATGA 59.895 50.000 0.00 0.00 0.00 2.92
1488 3799 3.134458 CCTCGGCTCCAAAATAGATGAC 58.866 50.000 0.00 0.00 0.00 3.06
1489 3800 3.134458 CTCGGCTCCAAAATAGATGACC 58.866 50.000 0.00 0.00 0.00 4.02
1490 3801 2.158813 TCGGCTCCAAAATAGATGACCC 60.159 50.000 0.00 0.00 0.00 4.46
1491 3802 2.421388 CGGCTCCAAAATAGATGACCCA 60.421 50.000 0.00 0.00 0.00 4.51
1492 3803 3.631250 GGCTCCAAAATAGATGACCCAA 58.369 45.455 0.00 0.00 0.00 4.12
1493 3804 3.381590 GGCTCCAAAATAGATGACCCAAC 59.618 47.826 0.00 0.00 0.00 3.77
1494 3805 4.273318 GCTCCAAAATAGATGACCCAACT 58.727 43.478 0.00 0.00 0.00 3.16
1495 3806 4.706962 GCTCCAAAATAGATGACCCAACTT 59.293 41.667 0.00 0.00 0.00 2.66
1496 3807 5.185828 GCTCCAAAATAGATGACCCAACTTT 59.814 40.000 0.00 0.00 0.00 2.66
1497 3808 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1498 3809 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1499 3810 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1500 3811 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
1501 3812 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
1502 3813 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
1503 3814 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
1504 3815 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
1505 3816 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
1506 3817 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
1507 3818 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
1508 3819 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
1509 3820 9.227777 GATGACCCAACTTTGTACTAACTTTAT 57.772 33.333 0.00 0.00 0.00 1.40
1511 3822 9.492973 TGACCCAACTTTGTACTAACTTTATAC 57.507 33.333 0.00 0.00 0.00 1.47
1512 3823 9.492973 GACCCAACTTTGTACTAACTTTATACA 57.507 33.333 0.00 0.00 0.00 2.29
1513 3824 9.850198 ACCCAACTTTGTACTAACTTTATACAA 57.150 29.630 0.00 0.00 37.10 2.41
1533 3844 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1534 3845 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1535 3846 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1536 3847 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1537 3848 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1538 3849 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1539 3850 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1540 3851 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1541 3852 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1542 3853 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1703 4019 5.296283 GCAGTAGTAGTAGAAATCTCGACCA 59.704 44.000 0.00 0.00 0.00 4.02
1749 4065 6.426328 AGCATGCAGAAATAAGCAGTACTATC 59.574 38.462 21.98 0.00 44.94 2.08
1784 4101 2.829120 GGGCTGTTTCTAGAGTGAGAGT 59.171 50.000 0.00 0.00 0.00 3.24
1788 4105 5.337169 GGCTGTTTCTAGAGTGAGAGTTCAT 60.337 44.000 0.00 0.00 35.39 2.57
1805 4122 5.609423 AGTTCATGTGCCTCTAATCATCTC 58.391 41.667 0.00 0.00 0.00 2.75
1950 4267 3.758023 CAGCAATGTTGTAACTGGATGGA 59.242 43.478 0.00 0.00 0.00 3.41
1951 4268 4.218200 CAGCAATGTTGTAACTGGATGGAA 59.782 41.667 0.00 0.00 0.00 3.53
1984 4301 2.051334 TTTCACCCTGTGTCAAGTGG 57.949 50.000 0.00 0.00 34.79 4.00
1992 4309 1.286880 GTGTCAAGTGGTGCATGCC 59.713 57.895 16.68 6.42 0.00 4.40
2000 4317 1.283029 AGTGGTGCATGCCTATTCAGT 59.717 47.619 16.68 6.32 0.00 3.41
2008 4325 6.183360 GGTGCATGCCTATTCAGTTTAGATTT 60.183 38.462 16.68 0.00 0.00 2.17
2087 4404 0.467290 GCACTGGTTGGTGGAAAGGA 60.467 55.000 0.00 0.00 37.65 3.36
2123 4440 2.618241 TCCAGATGCAGTGTTTGTTGTC 59.382 45.455 0.00 0.00 0.00 3.18
2266 4666 7.117812 AGTGTACAGAAAACATTGATTCTACCG 59.882 37.037 0.00 2.28 34.24 4.02
2292 4692 5.136828 TGCTTTGGATTGTAAAGTCCTCAA 58.863 37.500 0.00 0.00 37.44 3.02
2342 4742 6.780198 ATCTCTCTATGAACTACTCCCTCT 57.220 41.667 0.00 0.00 0.00 3.69
2356 4756 8.012957 ACTACTCCCTCTGTTCACAAATATAG 57.987 38.462 0.00 0.00 0.00 1.31
2399 4799 8.667463 TGTGAATCAAATGTATGTAGACACATG 58.333 33.333 0.00 0.00 45.17 3.21
2428 4828 6.198966 GTGTGTTTGTTCATTCATTTCAGTCC 59.801 38.462 0.00 0.00 0.00 3.85
2453 4853 7.280876 CCGTATGGTCCATATTGAAATATCCAG 59.719 40.741 14.78 0.00 30.77 3.86
2494 4999 4.216411 TGGAGGGAGTACAAAGTAATGC 57.784 45.455 0.00 0.00 0.00 3.56
2542 5047 6.485648 ACTTTGTTGGTCTATACTTGTTGACC 59.514 38.462 0.00 0.00 46.53 4.02
2855 5360 1.155889 CGCATGGCTTGTGTGTCTTA 58.844 50.000 5.82 0.00 0.00 2.10
2940 5445 1.263217 GGTGGTGTGTTTTGCTACTCG 59.737 52.381 0.00 0.00 0.00 4.18
3113 5618 3.368236 GTCAGGAAAGTTCAGTACGATGC 59.632 47.826 0.00 0.00 0.00 3.91
3143 5648 8.710551 TGTTGTGTTACTAAATATGTTGGTACG 58.289 33.333 0.00 0.00 0.00 3.67
3159 5664 8.780846 TGTTGGTACGACTATCATTATTGTTT 57.219 30.769 0.00 0.00 0.00 2.83
3175 5680 3.802722 TGTTTTTGTTGTTGTTGCTGC 57.197 38.095 0.00 0.00 0.00 5.25
3176 5681 3.397482 TGTTTTTGTTGTTGTTGCTGCT 58.603 36.364 0.00 0.00 0.00 4.24
3177 5682 3.186001 TGTTTTTGTTGTTGTTGCTGCTG 59.814 39.130 0.00 0.00 0.00 4.41
3178 5683 1.357907 TTTGTTGTTGTTGCTGCTGC 58.642 45.000 8.89 8.89 40.20 5.25
3179 5684 0.531657 TTGTTGTTGTTGCTGCTGCT 59.468 45.000 17.00 0.00 40.48 4.24
3180 5685 0.179132 TGTTGTTGTTGCTGCTGCTG 60.179 50.000 17.00 0.77 40.48 4.41
3181 5686 0.179129 GTTGTTGTTGCTGCTGCTGT 60.179 50.000 17.00 0.00 40.48 4.40
3357 5864 2.281345 ACCTCAGCACAGCACAGC 60.281 61.111 0.00 0.00 0.00 4.40
3490 5998 4.557496 CGCTTATCATCGTCTCTCATGGAA 60.557 45.833 0.00 0.00 0.00 3.53
3493 6001 6.426328 GCTTATCATCGTCTCTCATGGAAATT 59.574 38.462 0.00 0.00 0.00 1.82
3663 6171 3.265221 ACATTTCCCTCTCTGATGAGCAA 59.735 43.478 0.00 0.00 40.03 3.91
3702 6212 9.653287 GCAAAAGGTATGTATGTATATCAGCTA 57.347 33.333 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 2.561478 TCTTGCCAACTCCCACTTAC 57.439 50.000 0.00 0.00 0.00 2.34
67 72 0.675208 TGACACAACACAAGTGCGGT 60.675 50.000 0.00 0.00 40.59 5.68
68 73 0.248054 GTGACACAACACAAGTGCGG 60.248 55.000 0.00 0.00 40.59 5.69
69 74 0.445829 TGTGACACAACACAAGTGCG 59.554 50.000 5.62 0.00 45.81 5.34
75 80 1.093972 CTTGCCTGTGACACAACACA 58.906 50.000 10.02 5.32 46.45 3.72
76 81 0.248621 GCTTGCCTGTGACACAACAC 60.249 55.000 10.02 2.68 40.68 3.32
77 82 0.394216 AGCTTGCCTGTGACACAACA 60.394 50.000 10.02 8.22 0.00 3.33
78 83 0.740737 AAGCTTGCCTGTGACACAAC 59.259 50.000 10.02 5.57 0.00 3.32
79 84 0.740149 CAAGCTTGCCTGTGACACAA 59.260 50.000 14.65 0.00 0.00 3.33
80 85 0.394216 ACAAGCTTGCCTGTGACACA 60.394 50.000 26.27 8.26 0.00 3.72
81 86 0.308993 GACAAGCTTGCCTGTGACAC 59.691 55.000 26.27 0.00 0.00 3.67
82 87 0.181114 AGACAAGCTTGCCTGTGACA 59.819 50.000 26.27 0.00 0.00 3.58
113 118 2.201732 ACATACAAACTCATAGCGGCG 58.798 47.619 0.51 0.51 0.00 6.46
116 121 7.648112 ACACTACATACATACAAACTCATAGCG 59.352 37.037 0.00 0.00 0.00 4.26
183 206 4.447989 GCCGCTCAGCTCAGCTCA 62.448 66.667 8.35 0.00 36.40 4.26
184 207 4.447989 TGCCGCTCAGCTCAGCTC 62.448 66.667 8.35 0.00 36.40 4.09
185 208 4.454319 CTGCCGCTCAGCTCAGCT 62.454 66.667 8.35 0.00 40.77 4.24
186 209 4.447989 TCTGCCGCTCAGCTCAGC 62.448 66.667 0.00 0.00 42.56 4.26
187 210 2.202770 CTCTGCCGCTCAGCTCAG 60.203 66.667 8.94 8.94 42.56 3.35
188 211 4.447989 GCTCTGCCGCTCAGCTCA 62.448 66.667 0.00 0.00 42.56 4.26
189 212 4.146075 AGCTCTGCCGCTCAGCTC 62.146 66.667 10.03 0.00 39.37 4.09
190 213 4.454319 CAGCTCTGCCGCTCAGCT 62.454 66.667 10.03 10.03 44.59 4.24
191 214 4.756458 ACAGCTCTGCCGCTCAGC 62.756 66.667 6.12 6.12 42.56 4.26
192 215 2.814341 CACAGCTCTGCCGCTCAG 60.814 66.667 0.00 0.00 44.21 3.35
233 256 2.815503 TCACACACATCCAGCAAATCTG 59.184 45.455 0.00 0.00 42.49 2.90
353 376 1.564348 CACCAAAGGTATAGGCACCCT 59.436 52.381 0.00 0.00 39.62 4.34
390 413 7.070571 TCCAAACAGGTCATTGGTTCTATTTTT 59.929 33.333 4.62 0.00 45.12 1.94
393 416 5.476945 GTCCAAACAGGTCATTGGTTCTATT 59.523 40.000 4.62 0.00 45.12 1.73
394 417 5.010282 GTCCAAACAGGTCATTGGTTCTAT 58.990 41.667 4.62 0.00 45.12 1.98
478 2673 3.010420 GACCGGCTGCTTCTAGAAAAAT 58.990 45.455 6.63 0.00 0.00 1.82
523 2725 2.273370 TCTCTTGCGTAACGGCTTAG 57.727 50.000 0.00 0.00 0.00 2.18
540 2744 3.366396 CAGTATGGGGGCTACGATATCT 58.634 50.000 0.34 0.00 0.00 1.98
557 2762 3.373226 GTGAGCACGGGTCCAGTA 58.627 61.111 0.00 0.00 0.00 2.74
659 2869 1.819632 GCTCGTAACTGGCCCATGG 60.820 63.158 4.14 4.14 0.00 3.66
660 2870 1.091771 CAGCTCGTAACTGGCCCATG 61.092 60.000 0.00 0.00 0.00 3.66
661 2871 1.221840 CAGCTCGTAACTGGCCCAT 59.778 57.895 0.00 0.00 0.00 4.00
662 2872 1.764571 AACAGCTCGTAACTGGCCCA 61.765 55.000 0.00 0.00 39.55 5.36
663 2873 1.003718 AACAGCTCGTAACTGGCCC 60.004 57.895 0.00 0.00 39.55 5.80
665 2875 1.227999 TGCAACAGCTCGTAACTGGC 61.228 55.000 6.95 0.00 39.55 4.85
667 2877 1.394917 GGATGCAACAGCTCGTAACTG 59.605 52.381 0.00 0.00 41.08 3.16
668 2878 1.276421 AGGATGCAACAGCTCGTAACT 59.724 47.619 0.00 0.00 0.00 2.24
669 2879 1.726853 AGGATGCAACAGCTCGTAAC 58.273 50.000 0.00 0.00 0.00 2.50
670 2880 2.346803 GAAGGATGCAACAGCTCGTAA 58.653 47.619 0.00 0.00 0.00 3.18
671 2881 1.405526 GGAAGGATGCAACAGCTCGTA 60.406 52.381 0.00 0.00 0.00 3.43
672 2882 0.674895 GGAAGGATGCAACAGCTCGT 60.675 55.000 0.00 0.00 0.00 4.18
673 2883 1.699656 CGGAAGGATGCAACAGCTCG 61.700 60.000 0.00 0.00 0.00 5.03
674 2884 1.986575 GCGGAAGGATGCAACAGCTC 61.987 60.000 0.00 0.00 0.00 4.09
675 2885 2.042831 GCGGAAGGATGCAACAGCT 61.043 57.895 0.00 0.00 0.00 4.24
676 2886 2.262471 CTGCGGAAGGATGCAACAGC 62.262 60.000 0.00 0.00 41.22 4.40
677 2887 0.674581 TCTGCGGAAGGATGCAACAG 60.675 55.000 0.00 0.00 41.22 3.16
678 2888 0.035152 ATCTGCGGAAGGATGCAACA 60.035 50.000 0.00 0.00 41.22 3.33
679 2889 0.379669 CATCTGCGGAAGGATGCAAC 59.620 55.000 0.00 0.00 41.22 4.17
759 3001 0.666374 TGCGTTTGAGTCGAGTCTCA 59.334 50.000 20.51 11.42 41.85 3.27
762 3004 1.606350 CGGTGCGTTTGAGTCGAGTC 61.606 60.000 13.54 13.54 0.00 3.36
800 3054 2.666862 TTTGTTCGCCGCGGTCAT 60.667 55.556 28.70 0.00 0.00 3.06
841 3095 2.032528 TGTTGGCTTCGCTCTGGG 59.967 61.111 0.00 0.00 0.00 4.45
842 3096 2.684843 GCTGTTGGCTTCGCTCTGG 61.685 63.158 0.00 0.00 38.06 3.86
843 3097 1.962822 TGCTGTTGGCTTCGCTCTG 60.963 57.895 0.00 0.00 42.39 3.35
844 3098 1.963338 GTGCTGTTGGCTTCGCTCT 60.963 57.895 0.00 0.00 42.39 4.09
845 3099 2.253758 TGTGCTGTTGGCTTCGCTC 61.254 57.895 0.00 0.00 42.39 5.03
846 3100 2.203195 TGTGCTGTTGGCTTCGCT 60.203 55.556 0.00 0.00 42.39 4.93
847 3101 2.050985 GTGTGCTGTTGGCTTCGC 60.051 61.111 0.00 0.00 42.39 4.70
920 3183 1.416401 GAGTTTGGTCAGGTCAGGTGA 59.584 52.381 0.00 0.00 0.00 4.02
1353 3664 3.277416 AGGTGGGTAAGGAGAAGAAGT 57.723 47.619 0.00 0.00 0.00 3.01
1396 3707 6.030228 CGACATAGATTCGCAGCATAGATTA 58.970 40.000 0.00 0.00 0.00 1.75
1420 3731 2.032681 AGGTTTGCTCTCGCCCAC 59.967 61.111 0.00 0.00 34.43 4.61
1430 3741 2.653557 AACCAATCCCGAGGTTTGC 58.346 52.632 7.74 0.00 45.46 3.68
1446 3757 8.083462 CCGAGGGAGTAGATTAGATTAGAAAAC 58.917 40.741 0.00 0.00 0.00 2.43
1464 3775 1.762957 TCTATTTTGGAGCCGAGGGAG 59.237 52.381 0.00 0.00 0.00 4.30
1465 3776 1.874129 TCTATTTTGGAGCCGAGGGA 58.126 50.000 0.00 0.00 0.00 4.20
1466 3777 2.104792 TCATCTATTTTGGAGCCGAGGG 59.895 50.000 0.00 0.00 0.00 4.30
1467 3778 3.134458 GTCATCTATTTTGGAGCCGAGG 58.866 50.000 0.00 0.00 0.00 4.63
1468 3779 3.134458 GGTCATCTATTTTGGAGCCGAG 58.866 50.000 0.00 0.00 0.00 4.63
1469 3780 2.158813 GGGTCATCTATTTTGGAGCCGA 60.159 50.000 0.00 0.00 38.06 5.54
1470 3781 2.222027 GGGTCATCTATTTTGGAGCCG 58.778 52.381 0.00 0.00 38.06 5.52
1471 3782 3.297134 TGGGTCATCTATTTTGGAGCC 57.703 47.619 0.00 0.00 45.66 4.70
1472 3783 4.273318 AGTTGGGTCATCTATTTTGGAGC 58.727 43.478 0.00 0.00 0.00 4.70
1473 3784 6.209391 ACAAAGTTGGGTCATCTATTTTGGAG 59.791 38.462 0.00 0.00 0.00 3.86
1474 3785 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1475 3786 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1476 3787 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
1477 3788 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
1478 3789 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
1479 3790 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
1480 3791 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
1481 3792 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
1482 3793 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
1483 3794 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
1485 3796 9.492973 GTATAAAGTTAGTACAAAGTTGGGTCA 57.507 33.333 0.00 0.00 0.00 4.02
1486 3797 9.492973 TGTATAAAGTTAGTACAAAGTTGGGTC 57.507 33.333 0.00 0.00 0.00 4.46
1487 3798 9.850198 TTGTATAAAGTTAGTACAAAGTTGGGT 57.150 29.630 9.39 0.00 35.91 4.51
1507 3818 9.184523 CCAAAATAGATGACCCAACTTTGTATA 57.815 33.333 0.00 0.00 0.00 1.47
1508 3819 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
1509 3820 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1510 3821 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1511 3822 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1512 3823 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1513 3824 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1514 3825 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1515 3826 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1516 3827 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1517 3828 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1518 3829 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1519 3830 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1520 3831 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1521 3832 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1522 3833 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1523 3834 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1524 3835 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1525 3836 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1526 3837 5.703730 ATTACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
1527 3838 4.586306 ATTACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
1528 3839 4.376225 AATTACTCCCTCCGTTCCAAAA 57.624 40.909 0.00 0.00 0.00 2.44
1529 3840 4.533311 AGTAATTACTCCCTCCGTTCCAAA 59.467 41.667 12.50 0.00 0.00 3.28
1530 3841 4.098894 AGTAATTACTCCCTCCGTTCCAA 58.901 43.478 12.50 0.00 0.00 3.53
1531 3842 3.716431 AGTAATTACTCCCTCCGTTCCA 58.284 45.455 12.50 0.00 0.00 3.53
1532 3843 4.750021 AAGTAATTACTCCCTCCGTTCC 57.250 45.455 18.28 0.00 34.99 3.62
1533 3844 7.983484 TGAATTAAGTAATTACTCCCTCCGTTC 59.017 37.037 18.28 14.37 36.13 3.95
1534 3845 7.854337 TGAATTAAGTAATTACTCCCTCCGTT 58.146 34.615 18.28 3.27 36.13 4.44
1535 3846 7.427989 TGAATTAAGTAATTACTCCCTCCGT 57.572 36.000 18.28 3.97 36.13 4.69
1536 3847 6.424207 GCTGAATTAAGTAATTACTCCCTCCG 59.576 42.308 18.28 10.09 36.13 4.63
1537 3848 7.280356 TGCTGAATTAAGTAATTACTCCCTCC 58.720 38.462 18.28 8.90 36.13 4.30
1538 3849 8.732746 TTGCTGAATTAAGTAATTACTCCCTC 57.267 34.615 18.28 12.53 36.13 4.30
1539 3850 7.775561 CCTTGCTGAATTAAGTAATTACTCCCT 59.224 37.037 18.28 6.09 36.13 4.20
1540 3851 7.468768 GCCTTGCTGAATTAAGTAATTACTCCC 60.469 40.741 18.28 7.05 36.13 4.30
1541 3852 7.418408 GCCTTGCTGAATTAAGTAATTACTCC 58.582 38.462 18.28 6.75 36.13 3.85
1542 3853 7.126398 CGCCTTGCTGAATTAAGTAATTACTC 58.874 38.462 18.28 6.71 36.13 2.59
1703 4019 4.261280 GCTGCTTCCATTTTTGCAAATGTT 60.261 37.500 13.65 0.00 45.57 2.71
1749 4065 4.713792 AACAGCCCCTTCCTATTCTATG 57.286 45.455 0.00 0.00 0.00 2.23
1759 4076 2.567615 TCACTCTAGAAACAGCCCCTTC 59.432 50.000 0.00 0.00 0.00 3.46
1784 4101 4.202398 GGGAGATGATTAGAGGCACATGAA 60.202 45.833 0.00 0.00 0.00 2.57
1788 4105 2.763039 TGGGAGATGATTAGAGGCACA 58.237 47.619 0.00 0.00 0.00 4.57
1805 4122 7.331687 GGACATTAAACAAATCAGACAAATGGG 59.668 37.037 0.00 0.00 0.00 4.00
1972 4289 0.039798 GCATGCACCACTTGACACAG 60.040 55.000 14.21 0.00 0.00 3.66
1984 4301 6.382869 AATCTAAACTGAATAGGCATGCAC 57.617 37.500 21.36 9.10 0.00 4.57
2087 4404 0.032678 CTGGATTGATAGGAGCGCGT 59.967 55.000 8.43 0.00 0.00 6.01
2123 4440 2.016165 GCAAACGCAAAGAAGGCCG 61.016 57.895 0.00 0.00 0.00 6.13
2266 4666 4.706962 AGGACTTTACAATCCAAAGCATCC 59.293 41.667 0.00 0.00 36.63 3.51
2292 4692 8.814931 TCATGGTTTTGAAGAATCCAATGTTAT 58.185 29.630 0.00 0.00 0.00 1.89
2356 4756 7.648142 TGATTCACAACAAAGTTAGAACATCC 58.352 34.615 0.00 0.00 0.00 3.51
2399 4799 8.627487 TGAAATGAATGAACAAACACACTAAC 57.373 30.769 0.00 0.00 0.00 2.34
2428 4828 8.040727 TCTGGATATTTCAATATGGACCATACG 58.959 37.037 16.60 10.85 31.96 3.06
2453 4853 8.571336 CCCTCCATTCACAAATATAAGATGTTC 58.429 37.037 0.00 0.00 0.00 3.18
2542 5047 6.254157 CAGTGACATTTTGAAACTCAACTTGG 59.746 38.462 0.00 0.00 35.89 3.61
2612 5117 8.800332 AGATTTTGAACATTTAGAGAAGCACAT 58.200 29.630 0.00 0.00 0.00 3.21
2655 5160 2.740981 CAGTCACTGACTTTCCATGCTC 59.259 50.000 9.11 0.00 41.37 4.26
2825 5330 0.038166 AGCCATGCGGGAGAAAAAGA 59.962 50.000 0.00 0.00 40.01 2.52
2855 5360 8.739039 TCATTGTAATCTTTTTGGTTCATCGAT 58.261 29.630 0.00 0.00 0.00 3.59
2901 5406 7.500227 ACACCACCATATCAGACATTATCAAAG 59.500 37.037 0.00 0.00 0.00 2.77
2940 5445 4.627035 GCCAAAATGGTATTCTGCAGAAAC 59.373 41.667 31.55 26.25 40.46 2.78
3113 5618 9.393249 CCAACATATTTAGTAACACAACAACAG 57.607 33.333 0.00 0.00 0.00 3.16
3159 5664 1.067000 AGCAGCAGCAACAACAACAAA 60.067 42.857 3.17 0.00 45.49 2.83
3166 5671 3.516981 TTTTTACAGCAGCAGCAACAA 57.483 38.095 3.17 0.00 45.49 2.83
3315 5822 2.708051 ACAATCTGATGCAGTGGTGAG 58.292 47.619 0.00 0.00 32.61 3.51
3357 5864 2.364632 TCCCATGACCATGTTTAAGCG 58.635 47.619 8.93 0.00 37.11 4.68
3514 6022 1.421268 TCCATGGAGCAAGTTGTGTCT 59.579 47.619 11.44 0.00 0.00 3.41
3663 6171 2.158549 ACCTTTTGCTCTCAGGCTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
3702 6212 4.609691 ACGAAACGATCAACTGTGTTTT 57.390 36.364 0.00 0.00 34.89 2.43


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

AutoCloner maintained by Alex Coulton.