Multiple sequence alignment - TraesCS6D01G252300

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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 TraesCS6D01G252300 chr6D 100.000 5012 0 0 1 5012 356592655 356597666 0.000000e+00 9256.0
1 TraesCS6D01G252300 chr6D 96.990 764 23 0 1 764 20945255 20944492 0.000000e+00 1284.0
2 TraesCS6D01G252300 chr6B 95.483 3808 121 13 773 4571 537553196 537556961 0.000000e+00 6032.0
3 TraesCS6D01G252300 chr6B 92.763 152 11 0 4861 5012 537578096 537578247 2.350000e-53 220.0
4 TraesCS6D01G252300 chr6A 96.068 2747 78 11 1913 4642 499004167 499006900 0.000000e+00 4447.0
5 TraesCS6D01G252300 chr6A 97.340 639 15 2 773 1409 499003531 499004169 0.000000e+00 1085.0
6 TraesCS6D01G252300 chr6A 86.752 234 14 5 4788 5012 499007065 499007290 1.390000e-60 244.0
7 TraesCS6D01G252300 chr1D 97.375 762 19 1 3 764 75856644 75857404 0.000000e+00 1295.0
8 TraesCS6D01G252300 chr1D 82.945 686 92 18 6 680 204311108 204310437 3.340000e-166 595.0
9 TraesCS6D01G252300 chr5D 97.120 764 22 0 1 764 28457087 28456324 0.000000e+00 1290.0
10 TraesCS6D01G252300 chr5D 83.728 676 90 12 3 669 41836360 41837024 5.510000e-174 621.0
11 TraesCS6D01G252300 chr2D 97.120 764 22 0 1 764 386709884 386709121 0.000000e+00 1290.0
12 TraesCS6D01G252300 chr2D 91.772 158 10 2 1410 1564 79056162 79056319 3.040000e-52 217.0
13 TraesCS6D01G252300 chr7A 92.349 745 51 5 25 765 462902684 462901942 0.000000e+00 1055.0
14 TraesCS6D01G252300 chr3A 81.991 683 104 11 7 680 455635767 455636439 3.390000e-156 562.0
15 TraesCS6D01G252300 chr3A 85.870 92 8 1 4775 4866 497296384 497296298 5.340000e-15 93.5
16 TraesCS6D01G252300 chr4B 95.219 251 12 0 1 251 270528850 270528600 1.010000e-106 398.0
17 TraesCS6D01G252300 chr4B 92.829 251 18 0 1 251 270630798 270630548 1.030000e-96 364.0
18 TraesCS6D01G252300 chr5B 84.653 404 51 8 286 680 178392150 178392551 4.700000e-105 392.0
19 TraesCS6D01G252300 chr5B 75.943 212 29 13 4775 4971 680682521 680682317 6.910000e-14 89.8
20 TraesCS6D01G252300 chr1A 84.406 404 52 8 286 680 27197460 27197861 2.190000e-103 387.0
21 TraesCS6D01G252300 chr4A 93.506 154 8 1 1414 1565 460230649 460230802 1.400000e-55 228.0
22 TraesCS6D01G252300 chr3D 92.857 154 9 1 1414 1565 441388667 441388820 6.530000e-54 222.0
23 TraesCS6D01G252300 chr3D 89.286 56 6 0 4908 4963 579597095 579597150 2.500000e-08 71.3
24 TraesCS6D01G252300 chr3B 93.377 151 6 2 1413 1559 328715443 328715593 2.350000e-53 220.0
25 TraesCS6D01G252300 chr3B 91.195 159 12 1 1408 1564 396271873 396272031 1.090000e-51 215.0
26 TraesCS6D01G252300 chr7B 92.208 154 10 1 1413 1564 44939553 44939706 3.040000e-52 217.0
27 TraesCS6D01G252300 chr7B 86.567 67 6 3 4792 4858 561282566 561282629 2.500000e-08 71.3
28 TraesCS6D01G252300 chr7B 77.778 117 22 4 4658 4773 479873109 479873222 9.000000e-08 69.4
29 TraesCS6D01G252300 chr7B 77.778 117 22 4 4658 4773 479896320 479896433 9.000000e-08 69.4
30 TraesCS6D01G252300 chr4D 92.258 155 9 2 1414 1565 74079351 74079505 3.040000e-52 217.0
31 TraesCS6D01G252300 chr2A 90.184 163 14 1 1414 1574 141506470 141506308 1.410000e-50 211.0
32 TraesCS6D01G252300 chr2B 85.526 76 2 8 4701 4773 770566132 770566201 2.500000e-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 TraesCS6D01G252300 chr6D 356592655 356597666 5011 False 9256.000000 9256 100.000000 1 5012 1 chr6D.!!$F1 5011
1 TraesCS6D01G252300 chr6D 20944492 20945255 763 True 1284.000000 1284 96.990000 1 764 1 chr6D.!!$R1 763
2 TraesCS6D01G252300 chr6B 537553196 537556961 3765 False 6032.000000 6032 95.483000 773 4571 1 chr6B.!!$F1 3798
3 TraesCS6D01G252300 chr6A 499003531 499007290 3759 False 1925.333333 4447 93.386667 773 5012 3 chr6A.!!$F1 4239
4 TraesCS6D01G252300 chr1D 75856644 75857404 760 False 1295.000000 1295 97.375000 3 764 1 chr1D.!!$F1 761
5 TraesCS6D01G252300 chr1D 204310437 204311108 671 True 595.000000 595 82.945000 6 680 1 chr1D.!!$R1 674
6 TraesCS6D01G252300 chr5D 28456324 28457087 763 True 1290.000000 1290 97.120000 1 764 1 chr5D.!!$R1 763
7 TraesCS6D01G252300 chr5D 41836360 41837024 664 False 621.000000 621 83.728000 3 669 1 chr5D.!!$F1 666
8 TraesCS6D01G252300 chr2D 386709121 386709884 763 True 1290.000000 1290 97.120000 1 764 1 chr2D.!!$R1 763
9 TraesCS6D01G252300 chr7A 462901942 462902684 742 True 1055.000000 1055 92.349000 25 765 1 chr7A.!!$R1 740
10 TraesCS6D01G252300 chr3A 455635767 455636439 672 False 562.000000 562 81.991000 7 680 1 chr3A.!!$F1 673

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
682 692 1.344438 AGATGACGACACTGAAGCCAA 59.656 47.619 0.0 0.0 0.00 4.52 F
1400 1418 0.933097 CTGCCAATGTCGATTCCTCG 59.067 55.000 0.0 0.0 46.41 4.63 F
2528 2551 1.305201 TCTTTCTGTTCCACAACGCC 58.695 50.000 0.0 0.0 34.95 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1734 0.683828 TCGGCGTGTATCCCCAGTAA 60.684 55.0 6.85 0.00 0.00 2.24 R
2946 2970 1.073177 GGTCAATTGCATGCAAGCAC 58.927 50.0 34.15 27.40 45.61 4.40 R
4172 4196 0.108615 GACACAGTACCGCATGCTCT 60.109 55.0 17.13 5.97 0.00 4.09 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
69 70 3.005897 GCACAGATAAGGAGCGGATAGAA 59.994 47.826 0.00 0.00 0.00 2.10
252 254 4.261801 CCTTTCGGTTCAATACATGGTCT 58.738 43.478 0.00 0.00 0.00 3.85
375 379 7.282224 GGGCAAGCATATATCAACCGAATTATA 59.718 37.037 0.00 0.00 0.00 0.98
526 535 5.413499 ACATGAAGCATTAGTTTGAATGGC 58.587 37.500 0.00 0.00 37.31 4.40
536 545 7.712205 GCATTAGTTTGAATGGCCTGATTAATT 59.288 33.333 3.32 0.00 37.31 1.40
584 594 4.202040 GCACACCTAAATATGAGCATTGCA 60.202 41.667 11.91 0.00 33.25 4.08
645 655 8.439971 ACACTAACATACCATGTCATATTGGAT 58.560 33.333 0.00 0.00 44.07 3.41
682 692 1.344438 AGATGACGACACTGAAGCCAA 59.656 47.619 0.00 0.00 0.00 4.52
684 694 2.031258 TGACGACACTGAAGCCAAAA 57.969 45.000 0.00 0.00 0.00 2.44
765 778 1.666189 GCACGGGAAATCAGCTAGTTC 59.334 52.381 0.00 0.00 0.00 3.01
990 1005 1.560860 GCCGACAGTCACTGAAGCAC 61.561 60.000 13.14 0.00 35.18 4.40
1048 1063 2.037367 TCGTCCTCTCCACCCCTG 59.963 66.667 0.00 0.00 0.00 4.45
1267 1282 3.703556 GGGTTCTACTAGTAGTGGGGTTC 59.296 52.174 25.58 11.64 34.84 3.62
1295 1310 8.963130 TGTATTTGTTCGAAATTGATTTGACAC 58.037 29.630 0.00 0.00 30.88 3.67
1362 1380 2.911926 GCTTCCAGGGCTCCCAGTT 61.912 63.158 7.82 0.00 38.92 3.16
1400 1418 0.933097 CTGCCAATGTCGATTCCTCG 59.067 55.000 0.00 0.00 46.41 4.63
1588 1608 1.667724 CTAGCAGCGCACAAAGCTTAT 59.332 47.619 11.47 0.00 44.06 1.73
1598 1618 5.316770 CGCACAAAGCTTATAGTCTCAAAC 58.683 41.667 0.00 0.00 42.61 2.93
1610 1630 6.803154 ATAGTCTCAAACAGCTTTTGGTAC 57.197 37.500 16.28 14.45 0.00 3.34
1619 1639 5.695851 ACAGCTTTTGGTACAGAATGAAG 57.304 39.130 0.00 0.00 42.39 3.02
1622 1642 3.193479 GCTTTTGGTACAGAATGAAGGGG 59.807 47.826 0.00 0.00 42.39 4.79
1653 1673 9.745018 CCAAATATAAGACCCACTATGATTGAT 57.255 33.333 0.00 0.00 0.00 2.57
1664 1684 6.539103 CCCACTATGATTGATCATCAGCTATG 59.461 42.308 9.61 0.00 45.52 2.23
1670 1690 8.637196 ATGATTGATCATCAGCTATGTCAAAT 57.363 30.769 0.00 9.64 45.52 2.32
1671 1691 8.459911 TGATTGATCATCAGCTATGTCAAATT 57.540 30.769 0.00 8.20 38.22 1.82
1672 1692 8.909923 TGATTGATCATCAGCTATGTCAAATTT 58.090 29.630 0.00 0.00 38.22 1.82
1676 1696 9.346005 TGATCATCAGCTATGTCAAATTTATGT 57.654 29.630 0.00 0.00 36.89 2.29
1678 1698 9.961265 ATCATCAGCTATGTCAAATTTATGTTG 57.039 29.630 0.00 0.00 36.89 3.33
1679 1699 9.176460 TCATCAGCTATGTCAAATTTATGTTGA 57.824 29.630 0.00 0.00 36.89 3.18
1680 1700 9.961265 CATCAGCTATGTCAAATTTATGTTGAT 57.039 29.630 0.00 0.00 37.34 2.57
1682 1702 9.176460 TCAGCTATGTCAAATTTATGTTGATCA 57.824 29.630 0.00 0.00 37.34 2.92
1683 1703 9.961265 CAGCTATGTCAAATTTATGTTGATCAT 57.039 29.630 0.00 0.00 37.34 2.45
1714 1734 8.408043 TGTGACACTGGATGAGAAATTATTTT 57.592 30.769 7.20 0.00 0.00 1.82
1749 1769 2.656085 GCCGAGAGATCACACTAATCG 58.344 52.381 0.00 0.00 0.00 3.34
1777 1797 6.545666 TGGTGATCAAACAAGAAATGTACAGT 59.454 34.615 0.33 0.00 42.99 3.55
1778 1798 7.068103 TGGTGATCAAACAAGAAATGTACAGTT 59.932 33.333 8.54 8.54 42.99 3.16
1879 1899 1.347707 GTTCCTCACCTGTCATCACCA 59.652 52.381 0.00 0.00 0.00 4.17
1880 1900 1.728323 TCCTCACCTGTCATCACCAA 58.272 50.000 0.00 0.00 0.00 3.67
1881 1901 2.269023 TCCTCACCTGTCATCACCAAT 58.731 47.619 0.00 0.00 0.00 3.16
1882 1902 2.026915 TCCTCACCTGTCATCACCAATG 60.027 50.000 0.00 0.00 36.65 2.82
1883 1903 2.026915 CCTCACCTGTCATCACCAATGA 60.027 50.000 0.00 0.00 42.21 2.57
1884 1904 3.268330 CTCACCTGTCATCACCAATGAG 58.732 50.000 0.00 0.00 45.06 2.90
1885 1905 1.741706 CACCTGTCATCACCAATGAGC 59.258 52.381 0.00 0.00 45.06 4.26
1886 1906 1.352017 ACCTGTCATCACCAATGAGCA 59.648 47.619 0.00 0.00 45.06 4.26
1887 1907 2.224843 ACCTGTCATCACCAATGAGCAA 60.225 45.455 0.00 0.00 45.06 3.91
1888 1908 2.422479 CCTGTCATCACCAATGAGCAAG 59.578 50.000 0.00 0.00 45.06 4.01
1889 1909 3.340928 CTGTCATCACCAATGAGCAAGA 58.659 45.455 0.00 0.00 45.06 3.02
1890 1910 3.340928 TGTCATCACCAATGAGCAAGAG 58.659 45.455 0.00 0.00 45.06 2.85
1891 1911 3.244665 TGTCATCACCAATGAGCAAGAGT 60.245 43.478 0.00 0.00 45.06 3.24
1892 1912 3.755378 GTCATCACCAATGAGCAAGAGTT 59.245 43.478 0.00 0.00 45.06 3.01
1893 1913 4.005650 TCATCACCAATGAGCAAGAGTTC 58.994 43.478 0.00 0.00 39.52 3.01
1894 1914 3.777106 TCACCAATGAGCAAGAGTTCT 57.223 42.857 0.00 0.00 0.00 3.01
1895 1915 4.090761 TCACCAATGAGCAAGAGTTCTT 57.909 40.909 0.00 0.00 36.45 2.52
1896 1916 4.067896 TCACCAATGAGCAAGAGTTCTTC 58.932 43.478 0.00 0.00 33.11 2.87
1897 1917 4.070716 CACCAATGAGCAAGAGTTCTTCT 58.929 43.478 0.00 0.00 37.93 2.85
1898 1918 6.971250 ATCACCAATGAGCAAGAGTTCTTCTT 60.971 38.462 0.00 0.00 41.80 2.52
1899 1919 5.702670 CACCAATGAGCAAGAGTTCTTCTTA 59.297 40.000 0.00 0.00 44.34 2.10
1900 1920 6.373774 CACCAATGAGCAAGAGTTCTTCTTAT 59.626 38.462 0.00 0.00 44.34 1.73
1901 1921 6.373774 ACCAATGAGCAAGAGTTCTTCTTATG 59.626 38.462 0.00 0.00 44.34 1.90
1902 1922 6.183360 CCAATGAGCAAGAGTTCTTCTTATGG 60.183 42.308 0.00 0.00 44.34 2.74
1903 1923 5.489792 TGAGCAAGAGTTCTTCTTATGGT 57.510 39.130 0.00 0.00 44.34 3.55
2039 2059 2.490509 TGCATCAGAGCAATGTTGAAGG 59.509 45.455 0.00 0.00 42.46 3.46
2300 2323 2.800250 ACAGGATTCTTCTTGCTTGGG 58.200 47.619 0.00 0.00 32.39 4.12
2528 2551 1.305201 TCTTTCTGTTCCACAACGCC 58.695 50.000 0.00 0.00 34.95 5.68
2690 2713 7.276658 GCATCAACCATGATAGTGTAGCTATAC 59.723 40.741 12.38 12.38 44.53 1.47
2892 2916 3.544684 TGAACTCACTTGCACACAATCT 58.455 40.909 0.00 0.00 34.61 2.40
3212 3236 5.941555 GGGACCAATTCTCTCTCTCTTAA 57.058 43.478 0.00 0.00 0.00 1.85
3661 3685 6.039382 GGAAATGTCCATATTGTTGGTCTACC 59.961 42.308 0.00 0.00 44.26 3.18
3694 3718 7.841915 ACAAACTTGTTCCTTTTATGTTTGG 57.158 32.000 16.41 3.48 43.72 3.28
3731 3755 6.769512 TGATGAACTTTACTAGAAGTTGCCT 58.230 36.000 12.84 0.30 46.73 4.75
3736 3760 8.540388 TGAACTTTACTAGAAGTTGCCTGATAT 58.460 33.333 12.84 0.00 46.73 1.63
3778 3802 0.321387 TCGCAGTCAGTAGTCTCGGT 60.321 55.000 0.00 0.00 0.00 4.69
3785 3809 0.817654 CAGTAGTCTCGGTGCATGGA 59.182 55.000 0.00 0.00 0.00 3.41
3794 3818 1.686800 GGTGCATGGATTGGCCCTT 60.687 57.895 0.00 0.00 34.97 3.95
3804 3828 0.995024 ATTGGCCCTTAGCTGACACT 59.005 50.000 0.00 0.00 43.05 3.55
3903 3927 2.279073 CCTGCGGAGAGAGGGGTA 59.721 66.667 5.10 0.00 0.00 3.69
3912 3936 2.574450 GAGAGAGGGGTAGAGGTAACG 58.426 57.143 0.00 0.00 46.39 3.18
3975 3999 0.445436 CAGAGAACAGAATGCACGCC 59.555 55.000 0.00 0.00 42.53 5.68
3981 4005 0.968405 ACAGAATGCACGCCCAAAAT 59.032 45.000 0.00 0.00 42.53 1.82
4040 4064 6.098679 CCTATCATTGTATGCTAGACTGCTC 58.901 44.000 0.00 0.00 32.22 4.26
4052 4076 1.966354 AGACTGCTCAGTGTCACATCA 59.034 47.619 7.33 0.00 42.66 3.07
4172 4196 5.810587 GTCTAGATTACTTTGGATTGTCGCA 59.189 40.000 0.00 0.00 0.00 5.10
4300 4324 3.512033 ACGGTGCTCTCTTAGAATCAC 57.488 47.619 0.00 0.00 31.25 3.06
4303 4327 3.526534 GGTGCTCTCTTAGAATCACCAC 58.473 50.000 16.76 6.17 42.57 4.16
4571 4597 4.339439 ACTCTTCTTAGAACGACGCTAC 57.661 45.455 0.00 0.00 0.00 3.58
4578 4616 0.656785 AGAACGACGCTACGAGGATC 59.343 55.000 6.42 0.00 37.03 3.36
4600 4638 4.952957 TCCACAATCCAAGAGACTAGAGAG 59.047 45.833 0.00 0.00 0.00 3.20
4601 4639 4.952957 CCACAATCCAAGAGACTAGAGAGA 59.047 45.833 0.00 0.00 0.00 3.10
4642 4680 0.250513 ATCCAGGAGTGAGGCGTTTC 59.749 55.000 0.00 0.00 0.00 2.78
4643 4681 1.738099 CCAGGAGTGAGGCGTTTCG 60.738 63.158 0.00 0.00 0.00 3.46
4644 4682 1.738099 CAGGAGTGAGGCGTTTCGG 60.738 63.158 0.00 0.00 0.00 4.30
4653 4691 2.890961 GCGTTTCGGCTCCTAGGC 60.891 66.667 2.96 0.00 37.44 3.93
4654 4692 2.893398 CGTTTCGGCTCCTAGGCT 59.107 61.111 2.96 0.00 38.85 4.58
4655 4693 1.227002 CGTTTCGGCTCCTAGGCTC 60.227 63.158 2.96 0.00 38.85 4.70
4656 4694 1.898154 GTTTCGGCTCCTAGGCTCA 59.102 57.895 2.96 0.00 38.85 4.26
4657 4695 0.466124 GTTTCGGCTCCTAGGCTCAT 59.534 55.000 2.96 0.00 38.85 2.90
4658 4696 0.465705 TTTCGGCTCCTAGGCTCATG 59.534 55.000 2.96 0.00 38.85 3.07
4659 4697 1.402896 TTCGGCTCCTAGGCTCATGG 61.403 60.000 2.96 0.00 38.85 3.66
4662 4700 1.479368 GGCTCCTAGGCTCATGGGAG 61.479 65.000 2.96 16.33 45.71 4.30
4734 4772 4.897509 TTTGTGTGTGGAGAGAGATGAT 57.102 40.909 0.00 0.00 0.00 2.45
4739 4777 3.118847 TGTGTGGAGAGAGATGATGAAGC 60.119 47.826 0.00 0.00 0.00 3.86
4749 4787 1.328680 GATGATGAAGCGCGTGATGTT 59.671 47.619 8.43 0.00 0.00 2.71
4779 4817 7.486802 CAAATTTCAGAGCATTTGGAAGTTT 57.513 32.000 8.42 0.00 36.93 2.66
4780 4818 7.349711 CAAATTTCAGAGCATTTGGAAGTTTG 58.650 34.615 0.00 0.00 39.14 2.93
4781 4819 3.648339 TCAGAGCATTTGGAAGTTTGC 57.352 42.857 0.00 0.00 35.34 3.68
4782 4820 2.297033 TCAGAGCATTTGGAAGTTTGCC 59.703 45.455 0.00 0.00 35.71 4.52
4783 4821 1.270550 AGAGCATTTGGAAGTTTGCCG 59.729 47.619 0.00 0.00 35.71 5.69
4784 4822 1.000274 GAGCATTTGGAAGTTTGCCGT 60.000 47.619 0.00 0.00 35.71 5.68
4785 4823 1.412343 AGCATTTGGAAGTTTGCCGTT 59.588 42.857 0.00 0.00 35.71 4.44
4786 4824 1.526464 GCATTTGGAAGTTTGCCGTTG 59.474 47.619 0.00 0.00 0.00 4.10
4801 4887 1.498865 CGTTGGTGCACTGTCTGGAC 61.499 60.000 17.98 4.54 40.47 4.02
4822 4908 7.957002 TGGACCTGATTTTGTTTATTTTGCTA 58.043 30.769 0.00 0.00 0.00 3.49
4859 4945 7.716123 AGATGTCCAAATGCTTTGAAATTTGAA 59.284 29.630 9.16 0.00 43.41 2.69
4881 4974 3.851098 ACGCACTAAGTCATCTTTCTCC 58.149 45.455 0.00 0.00 35.36 3.71
4944 5039 0.033503 TCAGGTGTAGATGAGCCCGA 60.034 55.000 0.00 0.00 0.00 5.14
4948 5043 1.753078 TGTAGATGAGCCCGAGCGT 60.753 57.895 0.00 0.00 46.67 5.07
4961 5056 3.864921 GCCCGAGCGTAGAATTGGATATT 60.865 47.826 0.00 0.00 0.00 1.28
4962 5057 3.927142 CCCGAGCGTAGAATTGGATATTC 59.073 47.826 0.00 0.00 0.00 1.75
4963 5058 4.556233 CCGAGCGTAGAATTGGATATTCA 58.444 43.478 0.00 0.00 0.00 2.57
4964 5059 4.623167 CCGAGCGTAGAATTGGATATTCAG 59.377 45.833 0.00 0.00 0.00 3.02
4965 5060 5.223382 CGAGCGTAGAATTGGATATTCAGT 58.777 41.667 0.00 0.00 0.00 3.41
4966 5061 5.692204 CGAGCGTAGAATTGGATATTCAGTT 59.308 40.000 0.00 0.00 0.00 3.16
4977 5072 6.813293 TGGATATTCAGTTCATCCAGAGAA 57.187 37.500 0.00 0.00 42.55 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.144297 TGTTTCTCATGCTTGGCTACTTT 58.856 39.130 0.00 0.00 0.00 2.66
584 594 6.276847 TGTCATTTGCTTTTTGTACGGATTT 58.723 32.000 0.00 0.00 0.00 2.17
645 655 6.605995 TCGTCATCTACTTCCTTCCATAAAGA 59.394 38.462 0.00 0.00 37.12 2.52
684 694 6.354938 ACGTTACTCTTCCTTCTTCCTTTTT 58.645 36.000 0.00 0.00 0.00 1.94
699 712 3.181483 ACCGACAAGACAAACGTTACTCT 60.181 43.478 0.00 1.10 0.00 3.24
738 751 1.131826 GATTTCCCGTGCGTTGTCG 59.868 57.895 0.00 0.00 40.37 4.35
740 753 1.852067 GCTGATTTCCCGTGCGTTGT 61.852 55.000 0.00 0.00 0.00 3.32
990 1005 3.207669 GCAGCCATCGCAAGGAGG 61.208 66.667 0.00 0.00 37.52 4.30
1267 1282 9.993881 GTCAAATCAATTTCGAACAAATACAAG 57.006 29.630 0.00 0.00 0.00 3.16
1295 1310 7.970061 CCATGTCACAACTTATTATTTCCTGTG 59.030 37.037 0.00 0.00 35.21 3.66
1362 1380 3.561313 GCAGAGGATTGGAAACTACCCAA 60.561 47.826 0.00 0.00 46.48 4.12
1489 1509 8.367911 ACTACATACAGACTGAAATGAGTGAAA 58.632 33.333 21.47 6.21 0.00 2.69
1550 1570 4.158025 TGCTAGCAACTACTACCTCTGTTC 59.842 45.833 16.84 0.00 0.00 3.18
1551 1571 4.087182 TGCTAGCAACTACTACCTCTGTT 58.913 43.478 16.84 0.00 0.00 3.16
1552 1572 3.697045 CTGCTAGCAACTACTACCTCTGT 59.303 47.826 19.86 0.00 0.00 3.41
1588 1608 5.676552 TGTACCAAAAGCTGTTTGAGACTA 58.323 37.500 17.53 7.56 0.00 2.59
1598 1618 4.082571 CCCTTCATTCTGTACCAAAAGCTG 60.083 45.833 0.00 0.00 0.00 4.24
1622 1642 2.956333 GTGGGTCTTATATTTGGCACCC 59.044 50.000 0.00 0.00 43.47 4.61
1653 1673 9.176460 TCAACATAAATTTGACATAGCTGATGA 57.824 29.630 0.00 0.00 39.06 2.92
1673 1693 8.030692 CCAGTGTCACATAAAAATGATCAACAT 58.969 33.333 5.62 0.00 41.45 2.71
1674 1694 7.230309 TCCAGTGTCACATAAAAATGATCAACA 59.770 33.333 5.62 0.00 0.00 3.33
1675 1695 7.592938 TCCAGTGTCACATAAAAATGATCAAC 58.407 34.615 5.62 0.00 0.00 3.18
1676 1696 7.757941 TCCAGTGTCACATAAAAATGATCAA 57.242 32.000 5.62 0.00 0.00 2.57
1677 1697 7.611079 TCATCCAGTGTCACATAAAAATGATCA 59.389 33.333 5.62 0.00 0.00 2.92
1678 1698 7.988737 TCATCCAGTGTCACATAAAAATGATC 58.011 34.615 5.62 0.00 0.00 2.92
1679 1699 7.830697 TCTCATCCAGTGTCACATAAAAATGAT 59.169 33.333 5.62 0.00 0.00 2.45
1680 1700 7.167535 TCTCATCCAGTGTCACATAAAAATGA 58.832 34.615 5.62 4.91 0.00 2.57
1681 1701 7.381766 TCTCATCCAGTGTCACATAAAAATG 57.618 36.000 5.62 0.94 0.00 2.32
1682 1702 8.408043 TTTCTCATCCAGTGTCACATAAAAAT 57.592 30.769 5.62 0.00 0.00 1.82
1683 1703 7.815840 TTTCTCATCCAGTGTCACATAAAAA 57.184 32.000 5.62 0.00 0.00 1.94
1684 1704 8.408043 AATTTCTCATCCAGTGTCACATAAAA 57.592 30.769 5.62 0.00 0.00 1.52
1714 1734 0.683828 TCGGCGTGTATCCCCAGTAA 60.684 55.000 6.85 0.00 0.00 2.24
1717 1737 2.076622 CTCTCGGCGTGTATCCCCAG 62.077 65.000 6.85 0.00 0.00 4.45
1725 1745 1.213013 GTGTGATCTCTCGGCGTGT 59.787 57.895 6.85 0.00 0.00 4.49
1749 1769 8.511321 TGTACATTTCTTGTTTGATCACCATAC 58.489 33.333 0.00 0.00 39.87 2.39
1778 1798 2.360844 TGCAGTGTCGAACCAGAAAAA 58.639 42.857 0.00 0.00 0.00 1.94
1782 1802 1.668751 GTTTTGCAGTGTCGAACCAGA 59.331 47.619 0.00 0.00 0.00 3.86
1879 1899 6.479884 ACCATAAGAAGAACTCTTGCTCATT 58.520 36.000 0.00 0.00 44.47 2.57
1880 1900 6.059787 ACCATAAGAAGAACTCTTGCTCAT 57.940 37.500 0.00 0.00 44.47 2.90
1881 1901 5.489792 ACCATAAGAAGAACTCTTGCTCA 57.510 39.130 0.00 0.00 44.47 4.26
1882 1902 7.819900 TCTTTACCATAAGAAGAACTCTTGCTC 59.180 37.037 0.00 0.00 44.47 4.26
1883 1903 7.680730 TCTTTACCATAAGAAGAACTCTTGCT 58.319 34.615 0.00 0.00 44.47 3.91
1884 1904 7.907214 TCTTTACCATAAGAAGAACTCTTGC 57.093 36.000 0.00 0.00 44.47 4.01
1885 1905 9.442047 ACATCTTTACCATAAGAAGAACTCTTG 57.558 33.333 0.00 0.00 44.47 3.02
1889 1909 9.384764 GCTAACATCTTTACCATAAGAAGAACT 57.615 33.333 0.00 0.00 37.66 3.01
1890 1910 9.384764 AGCTAACATCTTTACCATAAGAAGAAC 57.615 33.333 0.00 0.00 37.66 3.01
1891 1911 9.601217 GAGCTAACATCTTTACCATAAGAAGAA 57.399 33.333 0.00 0.00 37.66 2.52
1892 1912 8.982723 AGAGCTAACATCTTTACCATAAGAAGA 58.017 33.333 0.00 0.00 37.66 2.87
1893 1913 9.039870 CAGAGCTAACATCTTTACCATAAGAAG 57.960 37.037 0.00 0.00 37.66 2.85
1894 1914 8.758829 TCAGAGCTAACATCTTTACCATAAGAA 58.241 33.333 0.00 0.00 37.66 2.52
1895 1915 8.306313 TCAGAGCTAACATCTTTACCATAAGA 57.694 34.615 0.00 0.00 38.43 2.10
1896 1916 8.948631 TTCAGAGCTAACATCTTTACCATAAG 57.051 34.615 0.00 0.00 0.00 1.73
1897 1917 9.905713 ATTTCAGAGCTAACATCTTTACCATAA 57.094 29.630 0.00 0.00 0.00 1.90
1898 1918 9.905713 AATTTCAGAGCTAACATCTTTACCATA 57.094 29.630 0.00 0.00 0.00 2.74
1899 1919 8.814038 AATTTCAGAGCTAACATCTTTACCAT 57.186 30.769 0.00 0.00 0.00 3.55
1900 1920 7.882791 TGAATTTCAGAGCTAACATCTTTACCA 59.117 33.333 0.00 0.00 0.00 3.25
1901 1921 8.178313 GTGAATTTCAGAGCTAACATCTTTACC 58.822 37.037 0.00 0.00 0.00 2.85
1902 1922 8.940952 AGTGAATTTCAGAGCTAACATCTTTAC 58.059 33.333 0.00 0.00 0.00 2.01
1903 1923 9.507329 AAGTGAATTTCAGAGCTAACATCTTTA 57.493 29.630 0.00 0.00 0.00 1.85
2300 2323 3.031013 ACCTAAATAAACAGCATGCCCC 58.969 45.455 15.66 0.00 42.53 5.80
2690 2713 9.533253 AGAATGAAACAAACTTACATTTTCAGG 57.467 29.630 0.00 0.00 39.02 3.86
2847 2871 2.615240 GCCCAACCCCAAACATCAATTC 60.615 50.000 0.00 0.00 0.00 2.17
2892 2916 3.051081 ACAAGCAAGCCAACAAAACAA 57.949 38.095 0.00 0.00 0.00 2.83
2946 2970 1.073177 GGTCAATTGCATGCAAGCAC 58.927 50.000 34.15 27.40 45.61 4.40
3681 3705 9.981114 AAACTCTAAACATCCAAACATAAAAGG 57.019 29.630 0.00 0.00 0.00 3.11
3731 3755 9.904198 TGATTGAATTACAAGGACTTGATATCA 57.096 29.630 18.15 0.00 42.93 2.15
3736 3760 7.626240 GCGAATGATTGAATTACAAGGACTTGA 60.626 37.037 18.15 0.00 42.93 3.02
3778 3802 0.756442 GCTAAGGGCCAATCCATGCA 60.756 55.000 6.18 0.00 36.21 3.96
3785 3809 0.995024 AGTGTCAGCTAAGGGCCAAT 59.005 50.000 6.18 0.00 43.05 3.16
3804 3828 3.069443 GCAGGGACCAAGAATCACAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
3903 3927 2.643232 GGCACCGTCCGTTACCTCT 61.643 63.158 0.00 0.00 0.00 3.69
3930 3954 1.804748 GGGAATACGATCGAATTGGGC 59.195 52.381 24.34 3.96 0.00 5.36
3936 3960 1.045407 CCTGGGGGAATACGATCGAA 58.955 55.000 24.34 0.00 33.58 3.71
3997 4021 1.202698 GGGTAATCAAGCTCCGAGCAT 60.203 52.381 22.29 7.82 45.56 3.79
4040 4064 7.687445 TCAATTTCGATAATGATGTGACACTG 58.313 34.615 7.20 0.00 0.00 3.66
4093 4117 2.238646 CTCCAAGGGTTACAGTATGCCA 59.761 50.000 4.62 0.00 42.53 4.92
4172 4196 0.108615 GACACAGTACCGCATGCTCT 60.109 55.000 17.13 5.97 0.00 4.09
4286 4310 4.026744 TGGAGGTGGTGATTCTAAGAGAG 58.973 47.826 0.00 0.00 0.00 3.20
4300 4324 2.040544 GCACGGTGATTGGAGGTGG 61.041 63.158 13.29 0.00 0.00 4.61
4328 4352 6.210784 TGGAGTTATGCAGTAGTACAACTCTT 59.789 38.462 20.90 3.92 40.92 2.85
4578 4616 4.952957 TCTCTCTAGTCTCTTGGATTGTGG 59.047 45.833 0.00 0.00 0.00 4.17
4616 4654 0.743688 CTCACTCCTGGATGGTCTCG 59.256 60.000 0.00 0.00 37.07 4.04
4618 4656 0.980231 GCCTCACTCCTGGATGGTCT 60.980 60.000 0.00 0.00 37.07 3.85
4642 4680 2.739784 CCATGAGCCTAGGAGCCG 59.260 66.667 14.75 0.00 0.00 5.52
4643 4681 1.460305 TCCCATGAGCCTAGGAGCC 60.460 63.158 14.75 0.31 0.00 4.70
4644 4682 2.056985 CTCCCATGAGCCTAGGAGC 58.943 63.158 14.75 3.36 39.54 4.70
4646 4684 0.636647 TCACTCCCATGAGCCTAGGA 59.363 55.000 14.75 0.00 42.74 2.94
4647 4685 0.755686 GTCACTCCCATGAGCCTAGG 59.244 60.000 3.67 3.67 42.74 3.02
4648 4686 1.786937 AGTCACTCCCATGAGCCTAG 58.213 55.000 0.00 0.00 42.74 3.02
4649 4687 3.398318 TTAGTCACTCCCATGAGCCTA 57.602 47.619 0.00 0.00 42.74 3.93
4650 4688 2.254152 TTAGTCACTCCCATGAGCCT 57.746 50.000 0.00 0.00 42.74 4.58
4651 4689 3.350219 TTTTAGTCACTCCCATGAGCC 57.650 47.619 0.00 0.00 42.74 4.70
4711 4749 5.034852 TCATCTCTCTCCACACACAAAAA 57.965 39.130 0.00 0.00 0.00 1.94
4712 4750 4.687901 TCATCTCTCTCCACACACAAAA 57.312 40.909 0.00 0.00 0.00 2.44
4713 4751 4.284234 TCATCATCTCTCTCCACACACAAA 59.716 41.667 0.00 0.00 0.00 2.83
4714 4752 3.834231 TCATCATCTCTCTCCACACACAA 59.166 43.478 0.00 0.00 0.00 3.33
4715 4753 3.434309 TCATCATCTCTCTCCACACACA 58.566 45.455 0.00 0.00 0.00 3.72
4716 4754 4.431809 CTTCATCATCTCTCTCCACACAC 58.568 47.826 0.00 0.00 0.00 3.82
4717 4755 3.118847 GCTTCATCATCTCTCTCCACACA 60.119 47.826 0.00 0.00 0.00 3.72
4718 4756 3.456280 GCTTCATCATCTCTCTCCACAC 58.544 50.000 0.00 0.00 0.00 3.82
4727 4765 1.191868 CATCACGCGCTTCATCATCTC 59.808 52.381 5.73 0.00 0.00 2.75
4734 4772 1.663388 ACGAACATCACGCGCTTCA 60.663 52.632 5.73 0.00 0.00 3.02
4739 4777 2.436997 TTTGGCACGAACATCACGCG 62.437 55.000 3.53 3.53 0.00 6.01
4749 4787 1.603456 TGCTCTGAAATTTGGCACGA 58.397 45.000 0.00 0.00 0.00 4.35
4775 4813 1.752694 AGTGCACCAACGGCAAACT 60.753 52.632 14.63 0.00 43.91 2.66
4778 4816 2.439338 ACAGTGCACCAACGGCAA 60.439 55.556 14.63 0.00 43.91 4.52
4779 4817 2.899838 GACAGTGCACCAACGGCA 60.900 61.111 14.63 0.00 39.32 5.69
4780 4818 2.591715 AGACAGTGCACCAACGGC 60.592 61.111 14.63 1.60 0.00 5.68
4781 4819 2.253758 CCAGACAGTGCACCAACGG 61.254 63.158 14.63 4.29 0.00 4.44
4782 4820 1.227527 TCCAGACAGTGCACCAACG 60.228 57.895 14.63 2.17 0.00 4.10
4783 4821 1.166531 GGTCCAGACAGTGCACCAAC 61.167 60.000 14.63 4.90 0.00 3.77
4784 4822 1.148273 GGTCCAGACAGTGCACCAA 59.852 57.895 14.63 0.00 0.00 3.67
4785 4823 1.766059 AGGTCCAGACAGTGCACCA 60.766 57.895 14.63 0.00 0.00 4.17
4786 4824 1.302033 CAGGTCCAGACAGTGCACC 60.302 63.158 14.63 0.00 0.00 5.01
4822 4908 7.398024 AGCATTTGGACATCTAAGTAGTTCTT 58.602 34.615 0.00 0.00 39.89 2.52
4859 4945 4.246458 GGAGAAAGATGACTTAGTGCGTT 58.754 43.478 0.00 0.00 35.05 4.84
4938 5033 1.144057 CCAATTCTACGCTCGGGCT 59.856 57.895 5.36 0.00 36.09 5.19
4939 5034 0.249911 ATCCAATTCTACGCTCGGGC 60.250 55.000 0.00 0.00 0.00 6.13
4944 5039 6.582636 TGAACTGAATATCCAATTCTACGCT 58.417 36.000 0.02 0.00 0.00 5.07
4948 5043 8.937835 TCTGGATGAACTGAATATCCAATTCTA 58.062 33.333 6.63 0.00 46.96 2.10
4961 5056 6.071334 ACGTTTAGATTCTCTGGATGAACTGA 60.071 38.462 0.00 0.00 0.00 3.41
4962 5057 6.035435 CACGTTTAGATTCTCTGGATGAACTG 59.965 42.308 0.00 0.00 0.00 3.16
4963 5058 6.071334 TCACGTTTAGATTCTCTGGATGAACT 60.071 38.462 0.00 0.00 0.00 3.01
4964 5059 6.100004 TCACGTTTAGATTCTCTGGATGAAC 58.900 40.000 0.00 0.00 0.00 3.18
4965 5060 6.280855 TCACGTTTAGATTCTCTGGATGAA 57.719 37.500 0.00 0.00 0.00 2.57
4966 5061 5.914898 TCACGTTTAGATTCTCTGGATGA 57.085 39.130 0.00 0.00 0.00 2.92
4977 5072 5.790593 TGCTAGTTTCCTTCACGTTTAGAT 58.209 37.500 0.00 0.00 0.00 1.98
4990 5085 1.268743 GCCATCGCATTGCTAGTTTCC 60.269 52.381 7.12 0.00 34.03 3.13


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

AutoCloner maintained by Alex Coulton.