Multiple sequence alignment - TraesCS7A01G024900

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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 TraesCS7A01G024900 chr7A 100.000 4018 0 0 1 4018 9753570 9757587 0.000000e+00 7420
1 TraesCS7A01G024900 chr7A 79.123 479 67 24 1612 2088 639220820 639221267 2.350000e-77 300
2 TraesCS7A01G024900 chr7D 91.659 3069 153 43 1 3039 10713790 10716785 0.000000e+00 4154
3 TraesCS7A01G024900 chr7D 88.729 905 53 19 3145 4004 10716868 10717768 0.000000e+00 1061
4 TraesCS7A01G024900 chr7D 79.332 479 65 24 1612 2088 63071061 63071507 5.050000e-79 305
5 TraesCS7A01G024900 chr7D 80.658 243 27 14 3772 4013 10719092 10719315 1.920000e-38 171
6 TraesCS7A01G024900 chr4A 88.503 2044 116 43 2034 4009 728086328 728084336 0.000000e+00 2362
7 TraesCS7A01G024900 chr4A 88.481 1363 97 28 699 2038 728087856 728086531 0.000000e+00 1592
8 TraesCS7A01G024900 chr4A 93.926 675 29 3 1 673 728088518 728087854 0.000000e+00 1009
9 TraesCS7A01G024900 chr6D 79.541 479 64 22 1612 2088 435556737 435557183 1.080000e-80 311
10 TraesCS7A01G024900 chr4D 78.675 483 67 24 1612 2091 452006859 452006410 5.080000e-74 289
11 TraesCS7A01G024900 chr2B 90.850 153 13 1 2542 2693 510167747 510167595 1.890000e-48 204


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 TraesCS7A01G024900 chr7A 9753570 9757587 4017 False 7420.000000 7420 100.000000 1 4018 1 chr7A.!!$F1 4017
1 TraesCS7A01G024900 chr7D 10713790 10719315 5525 False 1795.333333 4154 87.015333 1 4013 3 chr7D.!!$F2 4012
2 TraesCS7A01G024900 chr4A 728084336 728088518 4182 True 1654.333333 2362 90.303333 1 4009 3 chr4A.!!$R1 4008

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
878 881 0.247775 GTGTGCGAAAACGAAACCGT 60.248 50.0 0.0 0.0 42.82 4.83 F
1863 1892 0.384309 TACGGACCACATCGATCAGC 59.616 55.0 0.0 0.0 0.00 4.26 F
2497 2767 0.323087 TCCATCCGTCGACTCCTGAA 60.323 55.0 14.7 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 2734 0.101399 CTTCAGGAGTCGACGGATGG 59.899 60.0 10.46 0.41 0.0 3.51 R
2954 3229 0.108615 CTGCTACCTCCACCGTCTTG 60.109 60.0 0.00 0.00 0.0 3.02 R
3392 3740 0.249489 GCCATGCTACCTCGATCGTT 60.249 55.0 15.94 3.47 0.0 3.85 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
76 77 9.071276 GGATAAGGAGAAGCAAATCAAATCATA 57.929 33.333 0.00 0.00 0.00 2.15
85 86 6.870769 AGCAAATCAAATCATAAGGACCAAG 58.129 36.000 0.00 0.00 0.00 3.61
86 87 5.521372 GCAAATCAAATCATAAGGACCAAGC 59.479 40.000 0.00 0.00 0.00 4.01
87 88 6.628844 GCAAATCAAATCATAAGGACCAAGCT 60.629 38.462 0.00 0.00 0.00 3.74
88 89 7.416664 GCAAATCAAATCATAAGGACCAAGCTA 60.417 37.037 0.00 0.00 0.00 3.32
89 90 8.636213 CAAATCAAATCATAAGGACCAAGCTAT 58.364 33.333 0.00 0.00 0.00 2.97
90 91 7.756395 ATCAAATCATAAGGACCAAGCTATG 57.244 36.000 0.00 0.00 0.00 2.23
136 138 9.965902 CTATGGCATATATTCCTCCTTAGTTTT 57.034 33.333 7.81 0.00 0.00 2.43
141 143 9.998106 GCATATATTCCTCCTTAGTTTTCTACA 57.002 33.333 0.00 0.00 31.46 2.74
167 169 7.397192 ACCTACGTAGTTTAACCAAGAGGAATA 59.603 37.037 20.73 0.00 37.78 1.75
248 250 1.169661 ACGTCGGGCAAATTTCTGCA 61.170 50.000 4.59 0.00 44.52 4.41
249 251 0.454957 CGTCGGGCAAATTTCTGCAG 60.455 55.000 7.63 7.63 44.52 4.41
250 252 0.733909 GTCGGGCAAATTTCTGCAGC 60.734 55.000 9.47 0.00 44.52 5.25
251 253 0.895100 TCGGGCAAATTTCTGCAGCT 60.895 50.000 9.47 0.00 44.52 4.24
252 254 0.810648 CGGGCAAATTTCTGCAGCTA 59.189 50.000 9.47 0.00 44.52 3.32
253 255 1.406539 CGGGCAAATTTCTGCAGCTAT 59.593 47.619 9.47 1.33 44.52 2.97
254 256 2.618241 CGGGCAAATTTCTGCAGCTATA 59.382 45.455 9.47 0.00 44.52 1.31
255 257 3.254166 CGGGCAAATTTCTGCAGCTATAT 59.746 43.478 9.47 0.00 44.52 0.86
256 258 4.553323 GGGCAAATTTCTGCAGCTATATG 58.447 43.478 9.47 6.56 44.52 1.78
257 259 3.985925 GGCAAATTTCTGCAGCTATATGC 59.014 43.478 9.47 15.74 44.52 3.14
345 347 4.220821 ACGTTAGAAGGTCACATCTGTCAT 59.779 41.667 0.00 0.00 0.00 3.06
347 349 6.096987 ACGTTAGAAGGTCACATCTGTCATAT 59.903 38.462 0.00 0.00 0.00 1.78
479 481 8.087750 TGCGATTTGATTTGGACTTAAAGAAAT 58.912 29.630 0.00 0.00 0.00 2.17
519 521 2.435805 GAGACAGTGGGCATTGGATCTA 59.564 50.000 0.00 0.00 0.00 1.98
529 531 4.035675 GGGCATTGGATCTAAGAACTTTCG 59.964 45.833 0.00 0.00 0.00 3.46
532 534 5.563842 CATTGGATCTAAGAACTTTCGCAC 58.436 41.667 0.00 0.00 0.00 5.34
721 724 4.312443 CCTTACTTTGTTCCTTCGCACTA 58.688 43.478 0.00 0.00 0.00 2.74
784 787 3.398954 TTGCTCGATACGGCAAATTTC 57.601 42.857 7.29 0.00 44.01 2.17
878 881 0.247775 GTGTGCGAAAACGAAACCGT 60.248 50.000 0.00 0.00 42.82 4.83
1060 1074 2.431771 CGATGGTGGCGACGAACA 60.432 61.111 0.00 0.00 0.00 3.18
1241 1255 3.118884 AGGCAAAAACAGATCATCATGGC 60.119 43.478 0.00 0.00 0.00 4.40
1414 1436 4.237207 GGAATCCTCGGCCCGGTC 62.237 72.222 1.90 0.00 0.00 4.79
1534 1556 3.385079 CTCGCTTTCGGGTAAATGTTC 57.615 47.619 0.00 0.00 36.13 3.18
1535 1557 2.739913 CTCGCTTTCGGGTAAATGTTCA 59.260 45.455 0.00 0.00 36.13 3.18
1539 1561 4.142687 CGCTTTCGGGTAAATGTTCATTCT 60.143 41.667 0.00 0.00 0.00 2.40
1540 1562 5.332707 GCTTTCGGGTAAATGTTCATTCTC 58.667 41.667 0.00 0.00 0.00 2.87
1541 1563 5.123979 GCTTTCGGGTAAATGTTCATTCTCT 59.876 40.000 0.00 0.00 0.00 3.10
1544 1571 6.737254 TCGGGTAAATGTTCATTCTCTTTC 57.263 37.500 0.00 0.00 0.00 2.62
1550 1577 5.972107 AATGTTCATTCTCTTTCCTGTGG 57.028 39.130 0.00 0.00 0.00 4.17
1553 1580 3.507162 TCATTCTCTTTCCTGTGGCAA 57.493 42.857 0.00 0.00 0.00 4.52
1559 1586 4.023291 TCTCTTTCCTGTGGCAAAAAGTT 58.977 39.130 0.00 0.00 32.03 2.66
1560 1587 4.114794 CTCTTTCCTGTGGCAAAAAGTTG 58.885 43.478 0.00 0.00 37.83 3.16
1567 1594 4.093261 CCTGTGGCAAAAAGTTGTTTTCTG 59.907 41.667 0.00 0.00 34.64 3.02
1568 1595 4.636249 TGTGGCAAAAAGTTGTTTTCTGT 58.364 34.783 0.00 0.00 34.64 3.41
1569 1596 4.450419 TGTGGCAAAAAGTTGTTTTCTGTG 59.550 37.500 0.00 0.00 34.64 3.66
1571 1598 5.178438 GTGGCAAAAAGTTGTTTTCTGTGAA 59.822 36.000 0.00 0.00 34.64 3.18
1572 1599 5.760253 TGGCAAAAAGTTGTTTTCTGTGAAA 59.240 32.000 0.00 0.00 34.64 2.69
1573 1600 6.260936 TGGCAAAAAGTTGTTTTCTGTGAAAA 59.739 30.769 1.85 1.85 34.64 2.29
1574 1601 6.796552 GGCAAAAAGTTGTTTTCTGTGAAAAG 59.203 34.615 5.81 0.00 34.64 2.27
1575 1602 7.307692 GGCAAAAAGTTGTTTTCTGTGAAAAGA 60.308 33.333 5.81 2.66 34.64 2.52
1576 1603 8.067189 GCAAAAAGTTGTTTTCTGTGAAAAGAA 58.933 29.630 10.06 10.06 34.64 2.52
1577 1604 9.584839 CAAAAAGTTGTTTTCTGTGAAAAGAAG 57.415 29.630 13.19 1.40 37.48 2.85
1578 1605 7.889589 AAAGTTGTTTTCTGTGAAAAGAAGG 57.110 32.000 13.19 0.00 37.48 3.46
1579 1606 6.590234 AGTTGTTTTCTGTGAAAAGAAGGT 57.410 33.333 13.19 4.51 37.48 3.50
1581 1608 7.441836 AGTTGTTTTCTGTGAAAAGAAGGTTT 58.558 30.769 13.19 1.68 37.48 3.27
1582 1609 7.598869 AGTTGTTTTCTGTGAAAAGAAGGTTTC 59.401 33.333 13.19 4.71 37.48 2.78
1583 1610 7.227049 TGTTTTCTGTGAAAAGAAGGTTTCT 57.773 32.000 5.81 0.00 43.15 2.52
1596 1623 6.712276 AAGAAGGTTTCTTCCATGTAGTAGG 58.288 40.000 2.88 0.00 46.62 3.18
1597 1624 6.051179 GAAGGTTTCTTCCATGTAGTAGGT 57.949 41.667 0.00 0.00 42.61 3.08
1598 1625 5.678955 AGGTTTCTTCCATGTAGTAGGTC 57.321 43.478 0.00 0.00 0.00 3.85
1599 1626 5.091552 AGGTTTCTTCCATGTAGTAGGTCA 58.908 41.667 0.00 0.00 0.00 4.02
1600 1627 5.726793 AGGTTTCTTCCATGTAGTAGGTCAT 59.273 40.000 0.00 0.00 0.00 3.06
1601 1628 5.817816 GGTTTCTTCCATGTAGTAGGTCATG 59.182 44.000 0.00 0.00 40.46 3.07
1602 1629 6.407202 GTTTCTTCCATGTAGTAGGTCATGT 58.593 40.000 0.00 0.00 39.53 3.21
1618 1645 7.701539 AGGTCATGTTGCAAAGTTTCATATA 57.298 32.000 0.00 0.00 0.00 0.86
1620 1647 7.176515 AGGTCATGTTGCAAAGTTTCATATACA 59.823 33.333 0.00 0.00 0.00 2.29
1622 1649 8.853345 GTCATGTTGCAAAGTTTCATATACAAG 58.147 33.333 0.00 0.00 0.00 3.16
1624 1651 8.641155 CATGTTGCAAAGTTTCATATACAAGTG 58.359 33.333 0.00 0.00 0.00 3.16
1649 1676 7.274904 TGTGTAGCACGACTATAAGTTTGAATC 59.725 37.037 0.00 0.00 37.14 2.52
1652 1679 5.515626 AGCACGACTATAAGTTTGAATCGAC 59.484 40.000 0.00 0.00 32.63 4.20
1669 1696 6.759356 TGAATCGACTCTGTTTGAACACTTTA 59.241 34.615 0.00 0.00 34.70 1.85
1671 1698 7.730364 ATCGACTCTGTTTGAACACTTTAAT 57.270 32.000 0.00 0.00 34.70 1.40
1672 1699 8.827177 ATCGACTCTGTTTGAACACTTTAATA 57.173 30.769 0.00 0.00 34.70 0.98
1673 1700 8.068893 TCGACTCTGTTTGAACACTTTAATAC 57.931 34.615 0.00 0.00 34.70 1.89
1674 1701 7.707464 TCGACTCTGTTTGAACACTTTAATACA 59.293 33.333 0.00 0.00 34.70 2.29
1675 1702 8.004344 CGACTCTGTTTGAACACTTTAATACAG 58.996 37.037 0.00 0.00 34.70 2.74
1676 1703 7.639945 ACTCTGTTTGAACACTTTAATACAGC 58.360 34.615 0.00 0.00 34.70 4.40
1688 1716 9.686683 ACACTTTAATACAGCTTCCATTAATCT 57.313 29.630 5.44 0.00 0.00 2.40
1696 1724 7.676683 ACAGCTTCCATTAATCTAACTAGGA 57.323 36.000 0.00 0.00 0.00 2.94
1697 1725 7.731054 ACAGCTTCCATTAATCTAACTAGGAG 58.269 38.462 0.00 0.00 0.00 3.69
1700 1728 9.084533 AGCTTCCATTAATCTAACTAGGAGTAG 57.915 37.037 0.00 0.00 0.00 2.57
1723 1751 5.945784 AGTACAATAGGAGCTTGAAATGCAA 59.054 36.000 0.00 0.00 39.85 4.08
1724 1752 5.927281 ACAATAGGAGCTTGAAATGCAAT 57.073 34.783 0.00 0.00 39.85 3.56
1725 1753 7.775093 AGTACAATAGGAGCTTGAAATGCAATA 59.225 33.333 0.00 0.00 39.85 1.90
1726 1754 7.592885 ACAATAGGAGCTTGAAATGCAATAT 57.407 32.000 0.00 0.00 39.85 1.28
1815 1844 7.501559 AGCACATAATAGCATCTTGAACTGAAT 59.498 33.333 0.00 0.00 0.00 2.57
1840 1869 5.560966 ACAGCAAAAGAAAAAGACTTCGA 57.439 34.783 0.00 0.00 0.00 3.71
1860 1889 3.114065 GACTTTACGGACCACATCGATC 58.886 50.000 0.00 0.00 0.00 3.69
1863 1892 0.384309 TACGGACCACATCGATCAGC 59.616 55.000 0.00 0.00 0.00 4.26
1865 1894 1.141881 GGACCACATCGATCAGCGT 59.858 57.895 0.00 0.00 41.80 5.07
1866 1895 0.384309 GGACCACATCGATCAGCGTA 59.616 55.000 0.00 0.00 41.80 4.42
1867 1896 1.000163 GGACCACATCGATCAGCGTAT 60.000 52.381 0.00 0.00 41.80 3.06
1881 1916 4.933330 TCAGCGTATCCTATGAACAGAAC 58.067 43.478 0.00 0.00 0.00 3.01
1891 1926 7.724305 TCCTATGAACAGAACTTTAACACAC 57.276 36.000 0.00 0.00 0.00 3.82
1892 1927 7.276658 TCCTATGAACAGAACTTTAACACACA 58.723 34.615 0.00 0.00 0.00 3.72
1893 1928 7.936847 TCCTATGAACAGAACTTTAACACACAT 59.063 33.333 0.00 0.00 0.00 3.21
1894 1929 9.214957 CCTATGAACAGAACTTTAACACACATA 57.785 33.333 0.00 0.00 0.00 2.29
1968 2003 4.438744 GGTTTGTATTGCACACCTATGAGC 60.439 45.833 3.13 0.00 42.97 4.26
1977 2012 4.136796 GCACACCTATGAGCCATGATTTA 58.863 43.478 0.00 0.00 36.51 1.40
2027 2063 8.942338 ACAAATTCAAATGAATCTCATCCATG 57.058 30.769 8.96 0.00 43.41 3.66
2029 2065 9.031360 CAAATTCAAATGAATCTCATCCATGAC 57.969 33.333 8.96 0.00 43.41 3.06
2030 2066 6.704289 TTCAAATGAATCTCATCCATGACC 57.296 37.500 0.00 0.00 35.76 4.02
2171 2417 4.351054 CTCCACCACCACCTGCCC 62.351 72.222 0.00 0.00 0.00 5.36
2464 2719 1.440850 TCGTGTACTGCGTACGTGC 60.441 57.895 17.90 0.93 41.41 5.34
2482 2737 4.241555 GCGCGATCCCTGGTCCAT 62.242 66.667 12.10 0.00 0.00 3.41
2483 2738 2.029666 CGCGATCCCTGGTCCATC 59.970 66.667 0.00 0.00 0.00 3.51
2497 2767 0.323087 TCCATCCGTCGACTCCTGAA 60.323 55.000 14.70 0.00 0.00 3.02
2730 3005 1.883275 CGCCATTAAACTGAACCCACA 59.117 47.619 0.00 0.00 0.00 4.17
2732 3007 2.029380 GCCATTAAACTGAACCCACACC 60.029 50.000 0.00 0.00 0.00 4.16
2770 3045 4.454504 ACACTGTTGTTTTTCGTCAGAGTT 59.545 37.500 0.00 0.00 28.43 3.01
2772 3047 4.693566 ACTGTTGTTTTTCGTCAGAGTTCA 59.306 37.500 0.00 0.00 0.00 3.18
2773 3048 5.163854 ACTGTTGTTTTTCGTCAGAGTTCAG 60.164 40.000 0.00 0.00 0.00 3.02
2774 3049 4.693566 TGTTGTTTTTCGTCAGAGTTCAGT 59.306 37.500 0.00 0.00 0.00 3.41
2775 3050 4.857871 TGTTTTTCGTCAGAGTTCAGTG 57.142 40.909 0.00 0.00 0.00 3.66
2776 3051 3.621268 TGTTTTTCGTCAGAGTTCAGTGG 59.379 43.478 0.00 0.00 0.00 4.00
2777 3052 3.536956 TTTTCGTCAGAGTTCAGTGGT 57.463 42.857 0.00 0.00 0.00 4.16
2778 3053 2.795175 TTCGTCAGAGTTCAGTGGTC 57.205 50.000 0.00 0.00 0.00 4.02
2779 3054 1.982660 TCGTCAGAGTTCAGTGGTCT 58.017 50.000 0.00 0.00 0.00 3.85
2780 3055 3.136009 TCGTCAGAGTTCAGTGGTCTA 57.864 47.619 0.00 0.00 0.00 2.59
2781 3056 3.483421 TCGTCAGAGTTCAGTGGTCTAA 58.517 45.455 0.00 0.00 0.00 2.10
2782 3057 3.887110 TCGTCAGAGTTCAGTGGTCTAAA 59.113 43.478 0.00 0.00 0.00 1.85
2811 3086 2.896044 AGACAGTGAGCTCATTCAGTGA 59.104 45.455 21.47 0.00 46.67 3.41
2876 3151 4.394712 CTGGGGTCGGTGCTGGTC 62.395 72.222 0.00 0.00 0.00 4.02
3018 3293 0.536260 GCAGCAGGAGAGAGTGTGAT 59.464 55.000 0.00 0.00 0.00 3.06
3019 3294 1.471327 GCAGCAGGAGAGAGTGTGATC 60.471 57.143 0.00 0.00 0.00 2.92
3021 3296 0.463620 GCAGGAGAGAGTGTGATCCC 59.536 60.000 0.00 0.00 31.86 3.85
3047 3322 2.487934 GAAGTCTGAACTGCAGCAAGA 58.512 47.619 15.27 11.50 44.52 3.02
3102 3379 9.725019 AACATGATGAACTGAAACTACTAATCA 57.275 29.630 0.00 0.00 0.00 2.57
3139 3416 4.632538 CGTAGGAAATTTGGATGGGAAC 57.367 45.455 0.00 0.00 0.00 3.62
3184 3480 1.489649 AGATGCTCTGGTGAAGATGGG 59.510 52.381 0.00 0.00 33.29 4.00
3207 3503 6.429385 GGGGATGAACTATGAGATGTTGATTC 59.571 42.308 0.00 0.00 0.00 2.52
3238 3534 9.494271 TGTCACTCAAATCCATCTATAATTAGC 57.506 33.333 0.00 0.00 0.00 3.09
3239 3535 8.940952 GTCACTCAAATCCATCTATAATTAGCC 58.059 37.037 0.00 0.00 0.00 3.93
3281 3593 2.618241 TCATGTCCGAATTAGCAATGGC 59.382 45.455 0.00 0.00 41.61 4.40
3331 3675 2.547855 CCTGTGTCGTCCTTCATTGACA 60.548 50.000 0.00 0.00 38.91 3.58
3359 3704 0.030369 CCCCACGTACGAGCTCATAC 59.970 60.000 24.41 12.52 0.00 2.39
3367 3715 6.304922 CCACGTACGAGCTCATACATAAATAC 59.695 42.308 24.41 4.10 0.00 1.89
3373 3721 5.063944 CGAGCTCATACATAAATACCCATGC 59.936 44.000 15.40 0.00 0.00 4.06
3385 3733 3.293714 CCATGCCGCACAACCACA 61.294 61.111 0.00 0.00 0.00 4.17
3392 3740 1.227527 CGCACAACCACACTCCTGA 60.228 57.895 0.00 0.00 0.00 3.86
3414 3762 0.244994 GATCGAGGTAGCATGGCGAT 59.755 55.000 10.31 10.31 43.48 4.58
3453 3801 4.697756 CACCACGTCCATGGCGGT 62.698 66.667 25.35 17.56 44.33 5.68
3617 3974 3.011885 CCTCCCTCTCCTCCGACT 58.988 66.667 0.00 0.00 0.00 4.18
3619 3976 1.152839 CTCCCTCTCCTCCGACTCC 60.153 68.421 0.00 0.00 0.00 3.85
4010 5928 4.796231 GCATCGCCTGACCGTCGT 62.796 66.667 0.00 0.00 0.00 4.34
4011 5929 2.579787 CATCGCCTGACCGTCGTC 60.580 66.667 0.00 0.00 39.66 4.20
4012 5930 4.175489 ATCGCCTGACCGTCGTCG 62.175 66.667 0.00 0.00 42.37 5.12
4014 5932 4.175489 CGCCTGACCGTCGTCGAT 62.175 66.667 2.98 0.00 42.37 3.59
4015 5933 2.278013 GCCTGACCGTCGTCGATC 60.278 66.667 2.98 0.00 42.37 3.69
4016 5934 2.022902 CCTGACCGTCGTCGATCG 59.977 66.667 9.36 9.36 42.37 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 3.268023 ACAACCTAAGAGTGCCATAGC 57.732 47.619 0.00 0.00 40.48 2.97
86 87 6.879458 AGTTTTACAACCTAAGAGTGCCATAG 59.121 38.462 0.00 0.00 32.70 2.23
87 88 6.775708 AGTTTTACAACCTAAGAGTGCCATA 58.224 36.000 0.00 0.00 32.70 2.74
88 89 5.631119 AGTTTTACAACCTAAGAGTGCCAT 58.369 37.500 0.00 0.00 32.70 4.40
89 90 5.043737 AGTTTTACAACCTAAGAGTGCCA 57.956 39.130 0.00 0.00 32.70 4.92
90 91 6.093633 CCATAGTTTTACAACCTAAGAGTGCC 59.906 42.308 0.00 0.00 32.70 5.01
94 95 7.865706 ATGCCATAGTTTTACAACCTAAGAG 57.134 36.000 0.00 0.00 32.70 2.85
136 138 6.714810 TCTTGGTTAAACTACGTAGGTGTAGA 59.285 38.462 25.63 13.15 43.65 2.59
141 143 5.079643 TCCTCTTGGTTAAACTACGTAGGT 58.920 41.667 25.63 17.99 34.23 3.08
167 169 9.186837 ACTGCATTACTAACAGTACTGTATACT 57.813 33.333 28.13 15.32 44.13 2.12
238 240 7.587037 TTTAGGCATATAGCTGCAGAAATTT 57.413 32.000 20.43 1.79 44.12 1.82
257 259 6.183360 CCTGAAGAATTTGGGCTACATTTAGG 60.183 42.308 0.00 0.00 0.00 2.69
311 313 7.338703 TGTGACCTTCTAACGTACTGAGATATT 59.661 37.037 0.00 0.00 0.00 1.28
479 481 5.589855 TGTCTCTTCTTTGATGAGCAAAACA 59.410 36.000 0.00 0.00 45.26 2.83
519 521 1.226746 CTTCCCGTGCGAAAGTTCTT 58.773 50.000 0.00 0.00 0.00 2.52
611 614 5.128827 CCTTCTTCTACACTGTAGGGCATTA 59.871 44.000 14.97 0.00 0.00 1.90
721 724 6.283694 TCGAATAGCTGTCTCTTTATTGCAT 58.716 36.000 0.00 0.00 0.00 3.96
784 787 8.737168 TCTCTTAATGTCTGAATAATTGTGGG 57.263 34.615 0.00 0.00 0.00 4.61
878 881 0.247460 CAAGGCATGTCTCCGACTCA 59.753 55.000 0.00 0.00 33.15 3.41
897 900 1.025041 GGTCCGGAAAATGGCATCTC 58.975 55.000 5.23 0.28 0.00 2.75
1060 1074 0.595053 GTCATGACGGCGATCACGAT 60.595 55.000 16.62 0.00 42.66 3.73
1414 1436 0.244994 AGAGCGTGTACTGAAGCAGG 59.755 55.000 0.00 0.00 35.51 4.85
1527 1549 5.279156 GCCACAGGAAAGAGAATGAACATTT 60.279 40.000 1.56 0.00 0.00 2.32
1528 1550 4.219288 GCCACAGGAAAGAGAATGAACATT 59.781 41.667 0.00 0.00 0.00 2.71
1529 1551 3.760684 GCCACAGGAAAGAGAATGAACAT 59.239 43.478 0.00 0.00 0.00 2.71
1531 1553 3.149196 TGCCACAGGAAAGAGAATGAAC 58.851 45.455 0.00 0.00 0.00 3.18
1532 1554 3.507162 TGCCACAGGAAAGAGAATGAA 57.493 42.857 0.00 0.00 0.00 2.57
1533 1555 3.507162 TTGCCACAGGAAAGAGAATGA 57.493 42.857 0.00 0.00 0.00 2.57
1534 1556 4.589216 TTTTGCCACAGGAAAGAGAATG 57.411 40.909 0.00 0.00 0.00 2.67
1535 1557 4.651045 ACTTTTTGCCACAGGAAAGAGAAT 59.349 37.500 4.93 0.00 34.20 2.40
1539 1561 3.513515 ACAACTTTTTGCCACAGGAAAGA 59.486 39.130 10.54 0.00 36.00 2.52
1540 1562 3.860641 ACAACTTTTTGCCACAGGAAAG 58.139 40.909 0.00 0.00 36.00 2.62
1541 1563 3.971245 ACAACTTTTTGCCACAGGAAA 57.029 38.095 0.00 0.00 36.00 3.13
1544 1571 4.093261 CAGAAAACAACTTTTTGCCACAGG 59.907 41.667 0.00 0.00 36.00 4.00
1550 1577 7.571892 TCTTTTCACAGAAAACAACTTTTTGC 58.428 30.769 1.09 0.00 36.00 3.68
1553 1580 7.931407 ACCTTCTTTTCACAGAAAACAACTTTT 59.069 29.630 1.09 0.00 32.24 2.27
1559 1586 7.227049 AGAAACCTTCTTTTCACAGAAAACA 57.773 32.000 1.09 0.00 37.86 2.83
1573 1600 5.785940 ACCTACTACATGGAAGAAACCTTCT 59.214 40.000 0.00 0.00 43.15 2.85
1574 1601 6.051179 ACCTACTACATGGAAGAAACCTTC 57.949 41.667 0.00 0.00 39.38 3.46
1575 1602 5.546499 TGACCTACTACATGGAAGAAACCTT 59.454 40.000 0.00 0.00 0.00 3.50
1576 1603 5.091552 TGACCTACTACATGGAAGAAACCT 58.908 41.667 0.00 0.00 0.00 3.50
1577 1604 5.416271 TGACCTACTACATGGAAGAAACC 57.584 43.478 0.00 0.00 0.00 3.27
1578 1605 6.407202 ACATGACCTACTACATGGAAGAAAC 58.593 40.000 0.00 0.00 45.31 2.78
1579 1606 6.620877 ACATGACCTACTACATGGAAGAAA 57.379 37.500 0.00 0.00 45.31 2.52
1581 1608 5.626809 GCAACATGACCTACTACATGGAAGA 60.627 44.000 0.00 0.00 45.31 2.87
1582 1609 4.572389 GCAACATGACCTACTACATGGAAG 59.428 45.833 0.00 0.00 45.31 3.46
1583 1610 4.019771 TGCAACATGACCTACTACATGGAA 60.020 41.667 0.00 0.00 45.31 3.53
1584 1611 3.517500 TGCAACATGACCTACTACATGGA 59.482 43.478 0.00 0.00 45.31 3.41
1585 1612 3.872696 TGCAACATGACCTACTACATGG 58.127 45.455 0.00 0.00 45.31 3.66
1586 1613 5.412594 ACTTTGCAACATGACCTACTACATG 59.587 40.000 0.00 0.00 46.11 3.21
1587 1614 5.560724 ACTTTGCAACATGACCTACTACAT 58.439 37.500 0.00 0.00 0.00 2.29
1588 1615 4.968259 ACTTTGCAACATGACCTACTACA 58.032 39.130 0.00 0.00 0.00 2.74
1589 1616 5.941948 AACTTTGCAACATGACCTACTAC 57.058 39.130 0.00 0.00 0.00 2.73
1590 1617 6.058833 TGAAACTTTGCAACATGACCTACTA 58.941 36.000 0.00 0.00 0.00 1.82
1591 1618 4.887071 TGAAACTTTGCAACATGACCTACT 59.113 37.500 0.00 0.00 0.00 2.57
1592 1619 5.181690 TGAAACTTTGCAACATGACCTAC 57.818 39.130 0.00 0.00 0.00 3.18
1593 1620 7.701539 ATATGAAACTTTGCAACATGACCTA 57.298 32.000 0.00 0.00 0.00 3.08
1594 1621 4.942761 ATGAAACTTTGCAACATGACCT 57.057 36.364 0.00 0.00 0.00 3.85
1595 1622 7.312154 TGTATATGAAACTTTGCAACATGACC 58.688 34.615 0.00 0.00 0.00 4.02
1596 1623 8.741101 TTGTATATGAAACTTTGCAACATGAC 57.259 30.769 0.00 3.22 0.00 3.06
1597 1624 8.575589 ACTTGTATATGAAACTTTGCAACATGA 58.424 29.630 0.00 0.00 0.00 3.07
1598 1625 8.641155 CACTTGTATATGAAACTTTGCAACATG 58.359 33.333 0.00 0.00 0.00 3.21
1599 1626 8.359642 ACACTTGTATATGAAACTTTGCAACAT 58.640 29.630 0.00 1.23 0.00 2.71
1600 1627 7.647318 CACACTTGTATATGAAACTTTGCAACA 59.353 33.333 0.00 0.00 0.00 3.33
1601 1628 7.647715 ACACACTTGTATATGAAACTTTGCAAC 59.352 33.333 0.00 0.00 32.60 4.17
1602 1629 7.711846 ACACACTTGTATATGAAACTTTGCAA 58.288 30.769 0.00 0.00 32.60 4.08
1622 1649 5.860182 TCAAACTTATAGTCGTGCTACACAC 59.140 40.000 0.00 0.00 46.45 3.82
1624 1651 6.939551 TTCAAACTTATAGTCGTGCTACAC 57.060 37.500 0.00 0.00 31.59 2.90
1633 1660 8.690680 AACAGAGTCGATTCAAACTTATAGTC 57.309 34.615 10.80 0.00 0.00 2.59
1635 1662 9.140286 TCAAACAGAGTCGATTCAAACTTATAG 57.860 33.333 10.80 0.00 0.00 1.31
1649 1676 7.847487 TGTATTAAAGTGTTCAAACAGAGTCG 58.153 34.615 0.00 0.00 40.05 4.18
1652 1679 7.865707 AGCTGTATTAAAGTGTTCAAACAGAG 58.134 34.615 0.00 0.00 40.05 3.35
1671 1698 8.777578 TCCTAGTTAGATTAATGGAAGCTGTA 57.222 34.615 0.00 0.00 33.80 2.74
1672 1699 7.345914 ACTCCTAGTTAGATTAATGGAAGCTGT 59.654 37.037 0.00 0.00 33.80 4.40
1673 1700 7.731054 ACTCCTAGTTAGATTAATGGAAGCTG 58.269 38.462 0.00 0.00 33.80 4.24
1674 1701 7.922699 ACTCCTAGTTAGATTAATGGAAGCT 57.077 36.000 0.00 0.00 37.58 3.74
1675 1702 8.862085 ACTACTCCTAGTTAGATTAATGGAAGC 58.138 37.037 0.00 0.00 27.62 3.86
1687 1715 8.158789 AGCTCCTATTGTACTACTCCTAGTTAG 58.841 40.741 0.00 0.00 34.79 2.34
1688 1716 8.043429 AGCTCCTATTGTACTACTCCTAGTTA 57.957 38.462 0.00 0.00 34.79 2.24
1692 1720 6.907961 TCAAGCTCCTATTGTACTACTCCTA 58.092 40.000 0.00 0.00 0.00 2.94
1693 1721 5.767670 TCAAGCTCCTATTGTACTACTCCT 58.232 41.667 0.00 0.00 0.00 3.69
1694 1722 6.466885 TTCAAGCTCCTATTGTACTACTCC 57.533 41.667 0.00 0.00 0.00 3.85
1695 1723 7.042389 GCATTTCAAGCTCCTATTGTACTACTC 60.042 40.741 0.00 0.00 0.00 2.59
1696 1724 6.763610 GCATTTCAAGCTCCTATTGTACTACT 59.236 38.462 0.00 0.00 0.00 2.57
1697 1725 6.538742 TGCATTTCAAGCTCCTATTGTACTAC 59.461 38.462 0.00 0.00 0.00 2.73
1700 1728 5.818136 TGCATTTCAAGCTCCTATTGTAC 57.182 39.130 0.00 0.00 0.00 2.90
1709 1737 6.264067 AGGGTCTTATATTGCATTTCAAGCTC 59.736 38.462 0.00 0.00 38.22 4.09
1711 1739 6.396829 AGGGTCTTATATTGCATTTCAAGC 57.603 37.500 0.00 0.00 38.22 4.01
1726 1754 9.435570 AGAATCAAACTAGCTATTAGGGTCTTA 57.564 33.333 0.00 0.00 33.42 2.10
1815 1844 5.799936 CGAAGTCTTTTTCTTTTGCTGTTGA 59.200 36.000 0.00 0.00 0.00 3.18
1840 1869 2.494471 TGATCGATGTGGTCCGTAAAGT 59.506 45.455 0.54 0.00 0.00 2.66
1860 1889 4.938080 AGTTCTGTTCATAGGATACGCTG 58.062 43.478 0.00 0.00 46.39 5.18
1863 1892 8.592998 GTGTTAAAGTTCTGTTCATAGGATACG 58.407 37.037 0.00 0.00 46.39 3.06
1865 1894 9.431887 GTGTGTTAAAGTTCTGTTCATAGGATA 57.568 33.333 0.00 0.00 0.00 2.59
1866 1895 7.936847 TGTGTGTTAAAGTTCTGTTCATAGGAT 59.063 33.333 0.00 0.00 0.00 3.24
1867 1896 7.276658 TGTGTGTTAAAGTTCTGTTCATAGGA 58.723 34.615 0.00 0.00 0.00 2.94
1904 1939 9.683069 AAAGTGTTTAATTCTGATTCACATGAC 57.317 29.630 0.00 0.00 0.00 3.06
1947 1982 3.694072 GGCTCATAGGTGTGCAATACAAA 59.306 43.478 0.00 0.00 44.49 2.83
1951 1986 3.136260 TCATGGCTCATAGGTGTGCAATA 59.864 43.478 0.00 0.00 44.49 1.90
1996 2032 8.961294 TGAGATTCATTTGAATTTGTTTGGTT 57.039 26.923 7.20 0.00 44.14 3.67
2018 2054 2.224233 CCTAGCACAGGTCATGGATGAG 60.224 54.545 0.00 0.00 39.91 2.90
2030 2066 0.598680 GCGCCTCATACCTAGCACAG 60.599 60.000 0.00 0.00 0.00 3.66
2467 2722 2.427753 GGATGGACCAGGGATCGC 59.572 66.667 0.00 0.54 38.79 4.58
2470 2725 2.134287 CGACGGATGGACCAGGGAT 61.134 63.158 0.00 0.00 38.90 3.85
2473 2728 2.005960 GAGTCGACGGATGGACCAGG 62.006 65.000 10.46 0.00 38.90 4.45
2474 2729 1.433879 GAGTCGACGGATGGACCAG 59.566 63.158 10.46 0.00 38.90 4.00
2476 2731 1.753463 AGGAGTCGACGGATGGACC 60.753 63.158 10.46 6.49 34.24 4.46
2477 2732 1.030488 TCAGGAGTCGACGGATGGAC 61.030 60.000 10.46 0.00 33.94 4.02
2478 2733 0.323087 TTCAGGAGTCGACGGATGGA 60.323 55.000 10.46 1.75 0.00 3.41
2479 2734 0.101399 CTTCAGGAGTCGACGGATGG 59.899 60.000 10.46 0.41 0.00 3.51
2482 2737 1.835494 AATCTTCAGGAGTCGACGGA 58.165 50.000 10.46 4.08 0.00 4.69
2483 2738 3.777465 TTAATCTTCAGGAGTCGACGG 57.223 47.619 10.46 1.54 0.00 4.79
2497 2767 9.595823 CCAATCAAAATCTTGCATCTTTAATCT 57.404 29.630 0.00 0.00 32.14 2.40
2570 2845 3.390521 TCAGCAGCAGGTACCCGG 61.391 66.667 8.74 2.04 0.00 5.73
2616 2891 2.436646 CTGAAGGCGGCGGTGAAT 60.437 61.111 9.78 0.00 0.00 2.57
2706 2981 1.471287 GGTTCAGTTTAATGGCGGACC 59.529 52.381 0.00 0.00 0.00 4.46
2730 3005 0.399949 TGTTCAGAGAGTGGGTGGGT 60.400 55.000 0.00 0.00 0.00 4.51
2732 3007 1.051812 AGTGTTCAGAGAGTGGGTGG 58.948 55.000 0.00 0.00 0.00 4.61
2770 3045 3.578282 TCTGATGCAGTTTAGACCACTGA 59.422 43.478 4.23 0.00 43.90 3.41
2772 3047 3.324846 TGTCTGATGCAGTTTAGACCACT 59.675 43.478 15.43 0.00 38.96 4.00
2773 3048 3.664107 TGTCTGATGCAGTTTAGACCAC 58.336 45.455 15.43 0.00 38.96 4.16
2774 3049 3.324846 ACTGTCTGATGCAGTTTAGACCA 59.675 43.478 15.43 6.97 43.87 4.02
2775 3050 3.681897 CACTGTCTGATGCAGTTTAGACC 59.318 47.826 15.43 3.91 43.87 3.85
2776 3051 4.560128 TCACTGTCTGATGCAGTTTAGAC 58.440 43.478 12.72 12.72 43.87 2.59
2777 3052 4.814147 CTCACTGTCTGATGCAGTTTAGA 58.186 43.478 0.00 0.00 43.87 2.10
2778 3053 3.370366 GCTCACTGTCTGATGCAGTTTAG 59.630 47.826 0.00 2.12 43.87 1.85
2779 3054 3.007290 AGCTCACTGTCTGATGCAGTTTA 59.993 43.478 0.00 0.00 43.87 2.01
2780 3055 2.149578 GCTCACTGTCTGATGCAGTTT 58.850 47.619 0.00 0.00 43.87 2.66
2781 3056 1.347050 AGCTCACTGTCTGATGCAGTT 59.653 47.619 0.00 0.00 43.87 3.16
2782 3057 0.975135 AGCTCACTGTCTGATGCAGT 59.025 50.000 0.00 0.00 46.86 4.40
2811 3086 5.351458 TCATCAGATCAATCGACAATTCGT 58.649 37.500 0.00 0.00 46.01 3.85
2876 3151 1.467678 CGAGGTAGAGGCCCAGGATG 61.468 65.000 0.00 0.00 0.00 3.51
2952 3227 1.898154 CTACCTCCACCGTCTTGGG 59.102 63.158 0.00 0.00 44.64 4.12
2954 3229 0.108615 CTGCTACCTCCACCGTCTTG 60.109 60.000 0.00 0.00 0.00 3.02
3018 3293 0.316204 GTTCAGACTTCGGTTCGGGA 59.684 55.000 0.00 0.00 0.00 5.14
3019 3294 0.317479 AGTTCAGACTTCGGTTCGGG 59.683 55.000 0.00 0.00 29.87 5.14
3021 3296 0.784778 GCAGTTCAGACTTCGGTTCG 59.215 55.000 0.00 0.00 32.54 3.95
3047 3322 7.199766 TCTAGTTCAAAATTTCAAATGCGTGT 58.800 30.769 0.00 0.00 0.00 4.49
3102 3379 4.144297 TCCTACGGTACAGTACAGTGTTT 58.856 43.478 22.52 2.54 37.64 2.83
3135 3412 4.756642 TCATGTCAAGATCACAACTGTTCC 59.243 41.667 0.00 0.00 0.00 3.62
3139 3416 5.120363 CACTCTCATGTCAAGATCACAACTG 59.880 44.000 0.00 0.00 0.00 3.16
3184 3480 8.504815 CATGAATCAACATCTCATAGTTCATCC 58.495 37.037 0.00 0.00 34.03 3.51
3207 3503 4.267536 AGATGGATTTGAGTGACACCATG 58.732 43.478 0.84 0.00 34.46 3.66
3238 3534 1.004277 GAACGACACAGAGTGAGCGG 61.004 60.000 16.39 2.72 38.39 5.52
3239 3535 1.330779 CGAACGACACAGAGTGAGCG 61.331 60.000 3.88 9.35 39.28 5.03
3281 3593 2.507944 CCCCAAGCCGGAGATCAG 59.492 66.667 5.05 0.00 36.56 2.90
3282 3594 3.797353 GCCCCAAGCCGGAGATCA 61.797 66.667 5.05 0.00 36.56 2.92
3323 3667 0.984230 GGGTGAGGGTCTGTCAATGA 59.016 55.000 0.00 0.00 0.00 2.57
3331 3675 1.608627 GTACGTGGGGTGAGGGTCT 60.609 63.158 0.00 0.00 0.00 3.85
3359 3704 1.952990 TGTGCGGCATGGGTATTTATG 59.047 47.619 5.72 0.00 0.00 1.90
3367 3715 4.054825 GTGGTTGTGCGGCATGGG 62.055 66.667 5.72 0.00 0.00 4.00
3373 3721 2.111043 AGGAGTGTGGTTGTGCGG 59.889 61.111 0.00 0.00 0.00 5.69
3385 3733 2.290464 CTACCTCGATCGTTCAGGAGT 58.710 52.381 23.80 8.54 0.00 3.85
3392 3740 0.249489 GCCATGCTACCTCGATCGTT 60.249 55.000 15.94 3.47 0.00 3.85


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

AutoCloner maintained by Alex Coulton.