Multiple sequence alignment - TraesCS5D01G344000

Loading Multiple Alignment...

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 TraesCS5D01G344000 chr5D 100.000 4204 0 0 1 4204 431722928 431727131 0.000000e+00 7764.0
1 TraesCS5D01G344000 chr6B 94.832 2206 50 30 1559 3715 712387745 712385555 0.000000e+00 3384.0
2 TraesCS5D01G344000 chr6B 96.334 1091 20 9 1 1084 712388823 712387746 0.000000e+00 1775.0
3 TraesCS5D01G344000 chr6B 98.039 51 1 0 4154 4204 712385540 712385490 5.790000e-14 89.8
4 TraesCS5D01G344000 chr6B 97.368 38 1 0 404 441 134811019 134810982 9.760000e-07 65.8
5 TraesCS5D01G344000 chr7A 90.489 1798 113 30 1742 3495 675267432 675265649 0.000000e+00 2320.0
6 TraesCS5D01G344000 chr7A 88.864 889 57 18 370 1228 675268731 675267855 0.000000e+00 1055.0
7 TraesCS5D01G344000 chr7A 92.011 363 18 7 3846 4204 675265613 675265258 2.260000e-137 499.0
8 TraesCS5D01G344000 chr7A 90.446 314 23 7 1385 1692 675267848 675267536 1.410000e-109 407.0
9 TraesCS5D01G344000 chr2B 90.385 1768 123 31 1742 3489 725139972 725141712 0.000000e+00 2279.0
10 TraesCS5D01G344000 chr2B 91.828 673 41 8 567 1235 725138719 725139381 0.000000e+00 926.0
11 TraesCS5D01G344000 chr2B 89.744 468 32 9 1 460 725138181 725138640 6.060000e-163 584.0
12 TraesCS5D01G344000 chr2B 89.709 447 34 11 1249 1692 725139433 725139870 1.020000e-155 560.0
13 TraesCS5D01G344000 chr2B 89.503 362 21 10 3846 4204 725141748 725142095 3.860000e-120 442.0
14 TraesCS5D01G344000 chr1B 90.162 1789 119 36 1742 3491 26969144 26967374 0.000000e+00 2276.0
15 TraesCS5D01G344000 chr1B 88.810 1269 84 29 1 1228 26970817 26969566 0.000000e+00 1504.0
16 TraesCS5D01G344000 chr1B 89.937 318 25 7 1381 1692 26969563 26969247 1.820000e-108 403.0
17 TraesCS5D01G344000 chr3D 85.472 413 39 15 1289 1692 61313816 61314216 1.090000e-110 411.0
18 TraesCS5D01G344000 chr3D 93.204 103 6 1 1742 1843 61314314 61314416 2.620000e-32 150.0
19 TraesCS5D01G344000 chr5B 90.650 246 16 6 3840 4084 63615735 63615496 1.890000e-83 320.0
20 TraesCS5D01G344000 chr3B 91.262 103 8 1 1742 1843 97079088 97079190 5.670000e-29 139.0
21 TraesCS5D01G344000 chr6A 77.143 140 18 4 389 528 77287468 77287593 7.540000e-08 69.4


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 TraesCS5D01G344000 chr5D 431722928 431727131 4203 False 7764.000000 7764 100.000000 1 4204 1 chr5D.!!$F1 4203
1 TraesCS5D01G344000 chr6B 712385490 712388823 3333 True 1749.600000 3384 96.401667 1 4204 3 chr6B.!!$R2 4203
2 TraesCS5D01G344000 chr7A 675265258 675268731 3473 True 1070.250000 2320 90.452500 370 4204 4 chr7A.!!$R1 3834
3 TraesCS5D01G344000 chr2B 725138181 725142095 3914 False 958.200000 2279 90.233800 1 4204 5 chr2B.!!$F1 4203
4 TraesCS5D01G344000 chr1B 26967374 26970817 3443 True 1394.333333 2276 89.636333 1 3491 3 chr1B.!!$R1 3490
5 TraesCS5D01G344000 chr3D 61313816 61314416 600 False 280.500000 411 89.338000 1289 1843 2 chr3D.!!$F1 554

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
112 113 1.005630 GCTGTTCAGCGAGGTCAGT 60.006 57.895 9.04 0.0 0.00 3.41 F
1248 1340 1.002134 AGGCAAGCCATTGTACGCT 60.002 52.632 14.40 0.0 38.76 5.07 F
2258 2416 0.107508 GGCAGCATCAGCAAGTAGGA 60.108 55.000 0.00 0.0 45.49 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 1462 0.111061 TGACAATGAGCACTGCCCTT 59.889 50.0 0.0 0.0 0.00 3.95 R
2774 2952 2.503869 AGAGAGCCCTGACCCATTAT 57.496 50.0 0.0 0.0 0.00 1.28 R
3959 4178 0.249615 GCGACTGAGCATGGCATCTA 60.250 55.0 0.0 0.0 37.05 1.98 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
112 113 1.005630 GCTGTTCAGCGAGGTCAGT 60.006 57.895 9.04 0.00 0.00 3.41
299 307 2.158971 ACAAAACAAGCACCAATCCCAC 60.159 45.455 0.00 0.00 0.00 4.61
565 580 4.225942 TCATAGCTGGACAGTCCTGAAATT 59.774 41.667 26.58 12.55 37.65 1.82
716 762 7.012894 TCGTTGATATCAGTCCAACAAGTTTTT 59.987 33.333 5.39 0.00 39.90 1.94
722 768 4.082463 TCAGTCCAACAAGTTTTTGTGTCC 60.082 41.667 1.33 0.00 46.54 4.02
727 773 1.134175 ACAAGTTTTTGTGTCCGGCAG 59.866 47.619 0.00 0.00 45.54 4.85
730 776 2.306847 AGTTTTTGTGTCCGGCAGATT 58.693 42.857 0.00 0.00 0.00 2.40
753 799 8.921353 ATTGAATTAGCTAAGAATGCAGATCT 57.079 30.769 12.54 0.00 0.00 2.75
754 800 8.743085 TTGAATTAGCTAAGAATGCAGATCTT 57.257 30.769 18.32 18.32 40.18 2.40
755 801 8.151141 TGAATTAGCTAAGAATGCAGATCTTG 57.849 34.615 21.62 14.56 37.67 3.02
756 802 7.772292 TGAATTAGCTAAGAATGCAGATCTTGT 59.228 33.333 21.62 11.97 37.67 3.16
757 803 9.265901 GAATTAGCTAAGAATGCAGATCTTGTA 57.734 33.333 21.62 11.24 37.67 2.41
758 804 9.790344 AATTAGCTAAGAATGCAGATCTTGTAT 57.210 29.630 21.62 12.34 37.67 2.29
760 806 9.920133 TTAGCTAAGAATGCAGATCTTGTATAG 57.080 33.333 21.62 14.30 37.67 1.31
991 1037 5.930837 TGAAAAGTTCCCTGTGTCAAATT 57.069 34.783 0.00 0.00 0.00 1.82
1228 1275 2.551459 CAAAACTCTCTGCCTCCAACAG 59.449 50.000 0.00 0.00 36.44 3.16
1246 1338 1.137404 GCAGGCAAGCCATTGTACG 59.863 57.895 14.40 0.00 38.76 3.67
1247 1339 1.137404 CAGGCAAGCCATTGTACGC 59.863 57.895 14.40 0.00 38.76 4.42
1248 1340 1.002134 AGGCAAGCCATTGTACGCT 60.002 52.632 14.40 0.00 38.76 5.07
1249 1341 1.137404 GGCAAGCCATTGTACGCTG 59.863 57.895 6.14 0.00 38.76 5.18
1250 1342 1.586154 GGCAAGCCATTGTACGCTGT 61.586 55.000 6.14 0.00 38.76 4.40
1251 1343 1.083489 GCAAGCCATTGTACGCTGTA 58.917 50.000 0.00 0.00 38.76 2.74
1252 1344 1.202031 GCAAGCCATTGTACGCTGTAC 60.202 52.381 10.61 10.61 38.76 2.90
1253 1345 4.661383 GCAAGCCATTGTACGCTGTACG 62.661 54.545 12.11 0.00 42.56 3.67
1278 1370 1.318576 ACAAGGCTGTGGCAGTTAAC 58.681 50.000 0.00 0.00 40.87 2.01
1286 1378 3.005791 GCTGTGGCAGTTAACCATCTTTT 59.994 43.478 0.88 0.00 39.95 2.27
1327 1420 1.311651 TGTGTGTGTGTTGCTGGTGG 61.312 55.000 0.00 0.00 0.00 4.61
1342 1435 1.281577 TGGTGGCTCATGCTCAACATA 59.718 47.619 0.00 0.00 36.64 2.29
1369 1462 2.230508 GTCAGATCGATTGCCCCGTATA 59.769 50.000 0.00 0.00 0.00 1.47
1399 1492 2.663119 GCTCATTGTCATTGGCGTTTTC 59.337 45.455 0.00 0.00 0.00 2.29
1455 1553 9.814899 AAAATCATGTGTATTTGTGTTCTTTCA 57.185 25.926 0.00 0.00 0.00 2.69
1456 1554 9.467258 AAATCATGTGTATTTGTGTTCTTTCAG 57.533 29.630 0.00 0.00 0.00 3.02
1457 1555 6.437928 TCATGTGTATTTGTGTTCTTTCAGC 58.562 36.000 0.00 0.00 0.00 4.26
1459 1557 4.887071 TGTGTATTTGTGTTCTTTCAGCCT 59.113 37.500 0.00 0.00 0.00 4.58
1460 1558 5.215160 GTGTATTTGTGTTCTTTCAGCCTG 58.785 41.667 0.00 0.00 0.00 4.85
1461 1559 4.887071 TGTATTTGTGTTCTTTCAGCCTGT 59.113 37.500 0.00 0.00 0.00 4.00
1462 1560 3.781079 TTTGTGTTCTTTCAGCCTGTG 57.219 42.857 0.00 0.00 0.00 3.66
1489 1589 1.981256 TCCCAGTGTTCTTTTGGCTC 58.019 50.000 0.00 0.00 0.00 4.70
1507 1607 3.365364 GGCTCTCTCGTTGTTGATTTTGG 60.365 47.826 0.00 0.00 0.00 3.28
1582 1682 9.749340 ATGTTAGTACAAGTTTAGGGCTTTTAT 57.251 29.630 0.00 0.00 37.91 1.40
1724 1853 5.500234 ACTTGAATAGCTCATGGTAAGCAA 58.500 37.500 7.54 0.00 42.35 3.91
1726 1855 5.357742 TGAATAGCTCATGGTAAGCAAGA 57.642 39.130 7.54 0.00 42.35 3.02
1727 1856 5.933617 TGAATAGCTCATGGTAAGCAAGAT 58.066 37.500 7.54 0.00 42.35 2.40
1729 1858 3.641434 AGCTCATGGTAAGCAAGATGT 57.359 42.857 7.54 0.00 42.35 3.06
1730 1859 3.960571 AGCTCATGGTAAGCAAGATGTT 58.039 40.909 7.54 0.00 42.35 2.71
1731 1860 4.338879 AGCTCATGGTAAGCAAGATGTTT 58.661 39.130 7.54 0.00 42.35 2.83
1733 1862 5.244626 AGCTCATGGTAAGCAAGATGTTTTT 59.755 36.000 7.54 0.00 42.35 1.94
1734 1863 6.434028 AGCTCATGGTAAGCAAGATGTTTTTA 59.566 34.615 7.54 0.00 42.35 1.52
1736 1865 7.761249 GCTCATGGTAAGCAAGATGTTTTTAAT 59.239 33.333 0.21 0.00 39.61 1.40
1737 1866 9.643693 CTCATGGTAAGCAAGATGTTTTTAATT 57.356 29.630 0.00 0.00 0.00 1.40
1738 1867 9.421806 TCATGGTAAGCAAGATGTTTTTAATTG 57.578 29.630 0.00 0.00 0.00 2.32
1796 1954 2.135933 CAAGACCAAGAACACCGACTC 58.864 52.381 0.00 0.00 0.00 3.36
1944 2102 1.892474 GGACAAAGCCTTATGCCAACA 59.108 47.619 0.00 0.00 42.71 3.33
2142 2300 6.608808 GTGTACATTACCCTCCCTCTACTTTA 59.391 42.308 0.00 0.00 0.00 1.85
2258 2416 0.107508 GGCAGCATCAGCAAGTAGGA 60.108 55.000 0.00 0.00 45.49 2.94
2302 2460 1.754803 ACGGTGTGTTCTTCTCTGTCA 59.245 47.619 0.00 0.00 0.00 3.58
2446 2617 4.215399 CGACAACCATTGGATAGTGTTTGT 59.785 41.667 10.37 7.47 34.12 2.83
2521 2692 7.341445 AGGACTCATATCTTCACAAGTCTAC 57.659 40.000 0.00 0.00 34.85 2.59
2583 2756 8.684386 TTTGTTTCTGTCCATCACACTTTATA 57.316 30.769 0.00 0.00 0.00 0.98
2860 3055 7.889873 TTTCTGAAACATCACCTCCTTTTTA 57.110 32.000 0.00 0.00 0.00 1.52
3349 3563 3.118702 TGTTGAGGAAGTTGTCGTTGGTA 60.119 43.478 0.00 0.00 0.00 3.25
3498 3714 8.036273 TGTTCTCCCGTAATTTTCACTATTTC 57.964 34.615 0.00 0.00 0.00 2.17
3564 3780 8.773404 TCTATTCTTTCTTTTAGTTTCCCTCG 57.227 34.615 0.00 0.00 0.00 4.63
3587 3803 8.289939 TCGGTCTTATTTAGTATGTCTTCAGT 57.710 34.615 0.00 0.00 0.00 3.41
3651 3869 7.338449 GGTACCTAAAGGAATAAATTGTGCTCA 59.662 37.037 4.06 0.00 38.94 4.26
3684 3902 3.443037 CCATTCGCTTAGTCACTCTCTG 58.557 50.000 0.00 0.00 0.00 3.35
3692 3910 4.994217 GCTTAGTCACTCTCTGCTTCTTTT 59.006 41.667 0.00 0.00 0.00 2.27
3727 3945 2.772568 TTTTTCCGTGTCATGTGCAG 57.227 45.000 0.00 0.00 0.00 4.41
3728 3946 0.310543 TTTTCCGTGTCATGTGCAGC 59.689 50.000 0.00 0.00 0.00 5.25
3729 3947 0.817229 TTTCCGTGTCATGTGCAGCA 60.817 50.000 0.00 0.00 0.00 4.41
3730 3948 0.817229 TTCCGTGTCATGTGCAGCAA 60.817 50.000 0.00 0.00 0.00 3.91
3731 3949 1.081906 CCGTGTCATGTGCAGCAAC 60.082 57.895 0.00 0.00 0.00 4.17
3732 3950 1.648174 CGTGTCATGTGCAGCAACA 59.352 52.632 0.00 0.00 0.00 3.33
3733 3951 0.029167 CGTGTCATGTGCAGCAACAA 59.971 50.000 0.00 0.00 32.81 2.83
3734 3952 1.762419 GTGTCATGTGCAGCAACAAG 58.238 50.000 0.00 0.00 32.81 3.16
3735 3953 1.066002 GTGTCATGTGCAGCAACAAGT 59.934 47.619 0.00 0.00 32.81 3.16
3736 3954 1.065851 TGTCATGTGCAGCAACAAGTG 59.934 47.619 0.00 0.00 32.81 3.16
3737 3955 1.334556 GTCATGTGCAGCAACAAGTGA 59.665 47.619 0.00 0.00 32.81 3.41
3738 3956 1.605232 TCATGTGCAGCAACAAGTGAG 59.395 47.619 0.00 0.00 32.81 3.51
3739 3957 1.335810 CATGTGCAGCAACAAGTGAGT 59.664 47.619 0.00 0.00 32.81 3.41
3740 3958 1.016627 TGTGCAGCAACAAGTGAGTC 58.983 50.000 0.00 0.00 0.00 3.36
3741 3959 1.303309 GTGCAGCAACAAGTGAGTCT 58.697 50.000 0.00 0.00 0.00 3.24
3742 3960 1.672881 GTGCAGCAACAAGTGAGTCTT 59.327 47.619 0.00 0.00 36.75 3.01
3743 3961 1.942657 TGCAGCAACAAGTGAGTCTTC 59.057 47.619 0.00 0.00 33.63 2.87
3744 3962 1.942657 GCAGCAACAAGTGAGTCTTCA 59.057 47.619 0.00 0.00 33.63 3.02
3745 3963 2.551459 GCAGCAACAAGTGAGTCTTCAT 59.449 45.455 0.00 0.00 35.39 2.57
3746 3964 3.364764 GCAGCAACAAGTGAGTCTTCATC 60.365 47.826 0.00 0.00 35.39 2.92
3747 3965 4.063689 CAGCAACAAGTGAGTCTTCATCT 58.936 43.478 0.00 0.00 35.39 2.90
3748 3966 5.233225 CAGCAACAAGTGAGTCTTCATCTA 58.767 41.667 0.00 0.00 35.39 1.98
3749 3967 5.873712 CAGCAACAAGTGAGTCTTCATCTAT 59.126 40.000 0.00 0.00 35.39 1.98
3750 3968 6.370994 CAGCAACAAGTGAGTCTTCATCTATT 59.629 38.462 0.00 0.00 35.39 1.73
3751 3969 6.939163 AGCAACAAGTGAGTCTTCATCTATTT 59.061 34.615 0.00 0.00 35.39 1.40
3752 3970 7.118971 AGCAACAAGTGAGTCTTCATCTATTTC 59.881 37.037 0.00 0.00 35.39 2.17
3753 3971 7.118971 GCAACAAGTGAGTCTTCATCTATTTCT 59.881 37.037 0.00 0.00 35.39 2.52
3754 3972 8.441608 CAACAAGTGAGTCTTCATCTATTTCTG 58.558 37.037 0.00 0.00 35.39 3.02
3755 3973 7.901029 ACAAGTGAGTCTTCATCTATTTCTGA 58.099 34.615 0.00 0.00 35.39 3.27
3756 3974 8.538701 ACAAGTGAGTCTTCATCTATTTCTGAT 58.461 33.333 0.00 0.00 35.39 2.90
3757 3975 9.381033 CAAGTGAGTCTTCATCTATTTCTGATT 57.619 33.333 0.00 0.00 35.39 2.57
3758 3976 9.598517 AAGTGAGTCTTCATCTATTTCTGATTC 57.401 33.333 0.00 0.00 35.39 2.52
3759 3977 8.980596 AGTGAGTCTTCATCTATTTCTGATTCT 58.019 33.333 0.00 0.00 35.39 2.40
3760 3978 9.248291 GTGAGTCTTCATCTATTTCTGATTCTC 57.752 37.037 0.00 0.00 35.39 2.87
3761 3979 8.975295 TGAGTCTTCATCTATTTCTGATTCTCA 58.025 33.333 0.00 0.00 0.00 3.27
3762 3980 9.814899 GAGTCTTCATCTATTTCTGATTCTCAA 57.185 33.333 0.00 0.00 0.00 3.02
3768 3986 9.503399 TCATCTATTTCTGATTCTCAATGATGG 57.497 33.333 0.00 0.00 0.00 3.51
3769 3987 9.286170 CATCTATTTCTGATTCTCAATGATGGT 57.714 33.333 0.00 0.00 0.00 3.55
3770 3988 8.672823 TCTATTTCTGATTCTCAATGATGGTG 57.327 34.615 0.00 0.00 0.00 4.17
3771 3989 6.710597 ATTTCTGATTCTCAATGATGGTGG 57.289 37.500 0.00 0.00 0.00 4.61
3772 3990 5.440207 TTCTGATTCTCAATGATGGTGGA 57.560 39.130 0.00 0.00 0.00 4.02
3773 3991 5.032327 TCTGATTCTCAATGATGGTGGAG 57.968 43.478 0.00 0.00 0.00 3.86
3774 3992 4.135306 CTGATTCTCAATGATGGTGGAGG 58.865 47.826 0.00 0.00 0.00 4.30
3775 3993 3.524789 TGATTCTCAATGATGGTGGAGGT 59.475 43.478 0.00 0.00 0.00 3.85
3776 3994 4.721274 TGATTCTCAATGATGGTGGAGGTA 59.279 41.667 0.00 0.00 0.00 3.08
3777 3995 4.487714 TTCTCAATGATGGTGGAGGTAC 57.512 45.455 0.00 0.00 0.00 3.34
3778 3996 3.449918 TCTCAATGATGGTGGAGGTACA 58.550 45.455 0.00 0.00 0.00 2.90
3779 3997 4.040047 TCTCAATGATGGTGGAGGTACAT 58.960 43.478 0.00 0.00 0.00 2.29
3780 3998 4.101585 TCTCAATGATGGTGGAGGTACATC 59.898 45.833 0.00 0.00 40.96 3.06
3781 3999 4.040047 TCAATGATGGTGGAGGTACATCT 58.960 43.478 7.56 0.00 41.12 2.90
3782 4000 4.474651 TCAATGATGGTGGAGGTACATCTT 59.525 41.667 7.56 0.00 41.12 2.40
3783 4001 5.044919 TCAATGATGGTGGAGGTACATCTTT 60.045 40.000 7.56 0.00 41.12 2.52
3784 4002 6.157820 TCAATGATGGTGGAGGTACATCTTTA 59.842 38.462 7.56 0.00 41.12 1.85
3785 4003 6.770286 ATGATGGTGGAGGTACATCTTTAT 57.230 37.500 7.56 0.00 41.12 1.40
3786 4004 6.174720 TGATGGTGGAGGTACATCTTTATC 57.825 41.667 7.56 7.38 41.12 1.75
3787 4005 5.905331 TGATGGTGGAGGTACATCTTTATCT 59.095 40.000 7.56 0.00 41.12 1.98
3788 4006 7.073208 TGATGGTGGAGGTACATCTTTATCTA 58.927 38.462 7.56 0.00 41.12 1.98
3789 4007 7.567250 TGATGGTGGAGGTACATCTTTATCTAA 59.433 37.037 7.56 0.00 41.12 2.10
3790 4008 7.931015 TGGTGGAGGTACATCTTTATCTAAT 57.069 36.000 7.56 0.00 0.00 1.73
3791 4009 8.331931 TGGTGGAGGTACATCTTTATCTAATT 57.668 34.615 7.56 0.00 0.00 1.40
3792 4010 8.778059 TGGTGGAGGTACATCTTTATCTAATTT 58.222 33.333 7.56 0.00 0.00 1.82
3793 4011 9.628500 GGTGGAGGTACATCTTTATCTAATTTT 57.372 33.333 7.56 0.00 0.00 1.82
3814 4032 6.463995 TTTTTAGTGTTCTTCATTGCAGGT 57.536 33.333 0.00 0.00 0.00 4.00
3815 4033 6.463995 TTTTAGTGTTCTTCATTGCAGGTT 57.536 33.333 0.00 0.00 0.00 3.50
3816 4034 7.575414 TTTTAGTGTTCTTCATTGCAGGTTA 57.425 32.000 0.00 0.00 0.00 2.85
3817 4035 6.801539 TTAGTGTTCTTCATTGCAGGTTAG 57.198 37.500 0.00 0.00 0.00 2.34
3818 4036 4.718961 AGTGTTCTTCATTGCAGGTTAGT 58.281 39.130 0.00 0.00 0.00 2.24
3819 4037 5.133221 AGTGTTCTTCATTGCAGGTTAGTT 58.867 37.500 0.00 0.00 0.00 2.24
3820 4038 5.239525 AGTGTTCTTCATTGCAGGTTAGTTC 59.760 40.000 0.00 0.00 0.00 3.01
3821 4039 5.008613 GTGTTCTTCATTGCAGGTTAGTTCA 59.991 40.000 0.00 0.00 0.00 3.18
3822 4040 5.769662 TGTTCTTCATTGCAGGTTAGTTCAT 59.230 36.000 0.00 0.00 0.00 2.57
3823 4041 5.885230 TCTTCATTGCAGGTTAGTTCATG 57.115 39.130 0.00 0.00 0.00 3.07
3824 4042 4.701651 TCTTCATTGCAGGTTAGTTCATGG 59.298 41.667 0.00 0.00 0.00 3.66
3825 4043 4.032960 TCATTGCAGGTTAGTTCATGGT 57.967 40.909 0.00 0.00 0.00 3.55
3826 4044 4.406456 TCATTGCAGGTTAGTTCATGGTT 58.594 39.130 0.00 0.00 0.00 3.67
3827 4045 5.565509 TCATTGCAGGTTAGTTCATGGTTA 58.434 37.500 0.00 0.00 0.00 2.85
3828 4046 5.647658 TCATTGCAGGTTAGTTCATGGTTAG 59.352 40.000 0.00 0.00 0.00 2.34
3829 4047 3.950397 TGCAGGTTAGTTCATGGTTAGG 58.050 45.455 0.00 0.00 0.00 2.69
3830 4048 3.329520 TGCAGGTTAGTTCATGGTTAGGT 59.670 43.478 0.00 0.00 0.00 3.08
3831 4049 4.202524 TGCAGGTTAGTTCATGGTTAGGTT 60.203 41.667 0.00 0.00 0.00 3.50
3832 4050 4.765339 GCAGGTTAGTTCATGGTTAGGTTT 59.235 41.667 0.00 0.00 0.00 3.27
3833 4051 5.106277 GCAGGTTAGTTCATGGTTAGGTTTC 60.106 44.000 0.00 0.00 0.00 2.78
3834 4052 6.238648 CAGGTTAGTTCATGGTTAGGTTTCT 58.761 40.000 0.00 0.00 0.00 2.52
3835 4053 6.715264 CAGGTTAGTTCATGGTTAGGTTTCTT 59.285 38.462 0.00 0.00 0.00 2.52
3836 4054 6.715264 AGGTTAGTTCATGGTTAGGTTTCTTG 59.285 38.462 0.00 0.00 0.00 3.02
3837 4055 6.489022 GGTTAGTTCATGGTTAGGTTTCTTGT 59.511 38.462 0.00 0.00 0.00 3.16
3838 4056 7.360361 GTTAGTTCATGGTTAGGTTTCTTGTG 58.640 38.462 0.00 0.00 0.00 3.33
3839 4057 4.827284 AGTTCATGGTTAGGTTTCTTGTGG 59.173 41.667 0.00 0.00 0.00 4.17
3840 4058 3.153919 TCATGGTTAGGTTTCTTGTGGC 58.846 45.455 0.00 0.00 0.00 5.01
3841 4059 2.738587 TGGTTAGGTTTCTTGTGGCA 57.261 45.000 0.00 0.00 0.00 4.92
3842 4060 3.237268 TGGTTAGGTTTCTTGTGGCAT 57.763 42.857 0.00 0.00 0.00 4.40
3843 4061 3.571590 TGGTTAGGTTTCTTGTGGCATT 58.428 40.909 0.00 0.00 0.00 3.56
3844 4062 3.964031 TGGTTAGGTTTCTTGTGGCATTT 59.036 39.130 0.00 0.00 0.00 2.32
3888 4106 5.580691 CGTAGGTGTCTAATTTCATTCTGCA 59.419 40.000 0.00 0.00 0.00 4.41
3896 4114 7.607607 TGTCTAATTTCATTCTGCAGTGTGTAT 59.392 33.333 14.67 8.96 0.00 2.29
3917 4135 6.823182 TGTATCACTTTTTCCATCGATGTGAT 59.177 34.615 23.27 22.32 43.30 3.06
3918 4136 6.764308 ATCACTTTTTCCATCGATGTGATT 57.236 33.333 23.27 6.79 39.64 2.57
3977 4196 2.288640 TGATAGATGCCATGCTCAGTCG 60.289 50.000 0.00 0.00 0.00 4.18
3987 4206 1.214062 GCTCAGTCGCACTACTGCT 59.786 57.895 6.08 0.00 45.34 4.24
4037 4256 2.766263 TCAGTCCCTGTTCGCATCTATT 59.234 45.455 0.00 0.00 32.61 1.73
4050 4269 7.914871 TGTTCGCATCTATTTCAAATAACATGG 59.085 33.333 0.00 3.05 0.00 3.66
4107 4326 9.774742 CTTTGCTTCTTATAAGGTATTTCACAC 57.225 33.333 12.54 0.00 0.00 3.82
4187 4409 8.960591 ACAATCAGAAAATGTAAATAGTCCTGG 58.039 33.333 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.306805 TGCAATCTGACCTCCAACATCT 59.693 45.455 0.00 0.00 0.00 2.90
299 307 2.193248 GGGGGAAAGATCGGCCAG 59.807 66.667 2.24 0.00 0.00 4.85
359 367 6.266131 TCCCTCATAGCCTCATAACAAAAT 57.734 37.500 0.00 0.00 0.00 1.82
360 368 5.708736 TCCCTCATAGCCTCATAACAAAA 57.291 39.130 0.00 0.00 0.00 2.44
668 714 3.239449 TGTCTGCCTTCCTCTTAGTTGA 58.761 45.455 0.00 0.00 0.00 3.18
716 762 2.198827 AATTCAATCTGCCGGACACA 57.801 45.000 5.05 0.00 0.00 3.72
722 768 5.991328 TTCTTAGCTAATTCAATCTGCCG 57.009 39.130 6.64 0.00 0.00 5.69
727 773 9.001542 AGATCTGCATTCTTAGCTAATTCAATC 57.998 33.333 6.64 3.39 0.00 2.67
730 776 7.772292 ACAAGATCTGCATTCTTAGCTAATTCA 59.228 33.333 6.64 0.00 32.27 2.57
991 1037 5.244755 TGAGTTGTAATGCATGCACTCTTA 58.755 37.500 25.37 15.25 0.00 2.10
1212 1259 1.675801 TGCTGTTGGAGGCAGAGAG 59.324 57.895 0.00 0.00 36.12 3.20
1228 1275 1.137404 CGTACAATGGCTTGCCTGC 59.863 57.895 13.18 0.00 35.69 4.85
1246 1338 2.351726 CAGCCTTGTAAATCCGTACAGC 59.648 50.000 0.00 0.00 35.47 4.40
1247 1339 3.370978 CACAGCCTTGTAAATCCGTACAG 59.629 47.826 0.00 0.00 35.47 2.74
1248 1340 3.331150 CACAGCCTTGTAAATCCGTACA 58.669 45.455 0.00 0.00 35.25 2.90
1249 1341 2.676342 CCACAGCCTTGTAAATCCGTAC 59.324 50.000 0.00 0.00 35.25 3.67
1250 1342 2.937873 GCCACAGCCTTGTAAATCCGTA 60.938 50.000 0.00 0.00 35.25 4.02
1251 1343 1.821216 CCACAGCCTTGTAAATCCGT 58.179 50.000 0.00 0.00 35.25 4.69
1252 1344 0.451783 GCCACAGCCTTGTAAATCCG 59.548 55.000 0.00 0.00 35.25 4.18
1253 1345 1.474077 CTGCCACAGCCTTGTAAATCC 59.526 52.381 0.00 0.00 38.69 3.01
1286 1378 3.960102 ACTCCAAGAATCCAGCAACAAAA 59.040 39.130 0.00 0.00 0.00 2.44
1291 1383 2.158623 ACACACTCCAAGAATCCAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
1297 1389 3.206150 ACACACACACACTCCAAGAATC 58.794 45.455 0.00 0.00 0.00 2.52
1305 1397 0.378257 CCAGCAACACACACACACTC 59.622 55.000 0.00 0.00 0.00 3.51
1306 1398 0.322456 ACCAGCAACACACACACACT 60.322 50.000 0.00 0.00 0.00 3.55
1342 1435 2.684881 GGGCAATCGATCTGACAACAAT 59.315 45.455 13.21 0.00 0.00 2.71
1355 1448 3.226884 CCCTTATACGGGGCAATCG 57.773 57.895 6.39 0.00 40.75 3.34
1369 1462 0.111061 TGACAATGAGCACTGCCCTT 59.889 50.000 0.00 0.00 0.00 3.95
1378 1471 2.352503 AAACGCCAATGACAATGAGC 57.647 45.000 0.00 0.00 0.00 4.26
1399 1492 9.645059 TCTCAGTCAAAGAACTATGATACAAAG 57.355 33.333 0.00 0.00 0.00 2.77
1432 1529 7.086376 GCTGAAAGAACACAAATACACATGAT 58.914 34.615 0.00 0.00 34.07 2.45
1454 1552 2.031120 TGGGAACTTTTTCACAGGCTG 58.969 47.619 14.16 14.16 40.42 4.85
1455 1553 2.452600 TGGGAACTTTTTCACAGGCT 57.547 45.000 0.00 0.00 40.42 4.58
1459 1557 4.340617 AGAACACTGGGAACTTTTTCACA 58.659 39.130 0.00 0.00 43.23 3.58
1460 1558 4.983671 AGAACACTGGGAACTTTTTCAC 57.016 40.909 0.00 0.00 35.46 3.18
1461 1559 5.993748 AAAGAACACTGGGAACTTTTTCA 57.006 34.783 0.00 0.00 32.80 2.69
1462 1560 5.580691 CCAAAAGAACACTGGGAACTTTTTC 59.419 40.000 12.87 0.00 38.26 2.29
1471 1571 1.882623 GAGAGCCAAAAGAACACTGGG 59.117 52.381 0.00 0.00 0.00 4.45
1489 1589 7.117812 ACACTATACCAAAATCAACAACGAGAG 59.882 37.037 0.00 0.00 0.00 3.20
1507 1607 5.701290 AGCTTGTTTTGAGGTGACACTATAC 59.299 40.000 5.39 0.00 0.00 1.47
1582 1682 6.766997 ACCTTAGCTGGTCTATCTAGAGTA 57.233 41.667 0.00 0.00 34.86 2.59
1724 1853 9.912634 ACATTTGATCGACAATTAAAAACATCT 57.087 25.926 0.00 0.00 38.36 2.90
1727 1856 9.307121 ACAACATTTGATCGACAATTAAAAACA 57.693 25.926 0.00 0.00 38.36 2.83
1731 1860 9.521503 TGAAACAACATTTGATCGACAATTAAA 57.478 25.926 0.00 0.00 38.36 1.52
1733 1862 9.340695 GATGAAACAACATTTGATCGACAATTA 57.659 29.630 0.00 0.00 38.36 1.40
1734 1863 7.866898 TGATGAAACAACATTTGATCGACAATT 59.133 29.630 0.00 0.00 38.36 2.32
1736 1865 6.733145 TGATGAAACAACATTTGATCGACAA 58.267 32.000 0.00 0.00 36.65 3.18
1737 1866 6.204495 TCTGATGAAACAACATTTGATCGACA 59.796 34.615 0.00 0.00 0.00 4.35
1738 1867 6.602179 TCTGATGAAACAACATTTGATCGAC 58.398 36.000 0.00 0.00 0.00 4.20
1796 1954 1.948104 TGGGCGAACAGGAATAATCG 58.052 50.000 0.00 0.00 38.28 3.34
1944 2102 1.004745 AGGAAATTGTCGATGTGCCCT 59.995 47.619 0.00 0.00 0.00 5.19
2258 2416 7.201496 CGTATTTGACAAATCTAGCCGTTTACT 60.201 37.037 16.57 0.00 32.38 2.24
2446 2617 8.502387 CAAAAAGTTTCCACTTGAAATTGACAA 58.498 29.630 0.00 0.00 42.89 3.18
2521 2692 7.930217 TGAACAACTTACAAATTTCTCTCTGG 58.070 34.615 0.00 0.00 0.00 3.86
2583 2756 8.308931 AGCATTTAGACAAAAATGATGTGATGT 58.691 29.630 12.25 0.00 45.61 3.06
2774 2952 2.503869 AGAGAGCCCTGACCCATTAT 57.496 50.000 0.00 0.00 0.00 1.28
2840 3018 7.889873 TTCTTAAAAAGGAGGTGATGTTTCA 57.110 32.000 0.00 0.00 0.00 2.69
2860 3055 5.163426 TGCAAACACTCCACAATCATTTCTT 60.163 36.000 0.00 0.00 0.00 2.52
3349 3563 5.907207 ACAACAATATGAGATGCTCGTACT 58.093 37.500 0.00 0.00 35.21 2.73
3498 3714 8.872845 GCCAATCTGAACAATTAATAAAACTGG 58.127 33.333 0.00 0.00 0.00 4.00
3651 3869 0.831307 GCGAATGGGAGGGACTTACT 59.169 55.000 0.00 0.00 41.55 2.24
3715 3933 1.066002 ACTTGTTGCTGCACATGACAC 59.934 47.619 0.00 0.00 0.00 3.67
3717 3935 1.334556 TCACTTGTTGCTGCACATGAC 59.665 47.619 0.00 0.00 0.00 3.06
3718 3936 1.605232 CTCACTTGTTGCTGCACATGA 59.395 47.619 0.00 5.30 0.00 3.07
3719 3937 1.335810 ACTCACTTGTTGCTGCACATG 59.664 47.619 0.00 8.88 0.00 3.21
3720 3938 1.605710 GACTCACTTGTTGCTGCACAT 59.394 47.619 0.00 0.00 0.00 3.21
3724 3942 1.942657 TGAAGACTCACTTGTTGCTGC 59.057 47.619 0.00 0.00 39.13 5.25
3727 3945 6.734104 AATAGATGAAGACTCACTTGTTGC 57.266 37.500 0.00 0.00 39.13 4.17
3728 3946 8.441608 CAGAAATAGATGAAGACTCACTTGTTG 58.558 37.037 0.00 0.00 39.13 3.33
3729 3947 8.370940 TCAGAAATAGATGAAGACTCACTTGTT 58.629 33.333 0.00 0.00 39.13 2.83
3730 3948 7.901029 TCAGAAATAGATGAAGACTCACTTGT 58.099 34.615 0.00 0.00 39.13 3.16
3731 3949 8.945481 ATCAGAAATAGATGAAGACTCACTTG 57.055 34.615 0.00 0.00 39.13 3.16
3732 3950 9.598517 GAATCAGAAATAGATGAAGACTCACTT 57.401 33.333 0.00 0.00 42.03 3.16
3733 3951 8.980596 AGAATCAGAAATAGATGAAGACTCACT 58.019 33.333 0.00 0.00 33.30 3.41
3734 3952 9.248291 GAGAATCAGAAATAGATGAAGACTCAC 57.752 37.037 0.00 0.00 31.26 3.51
3735 3953 8.975295 TGAGAATCAGAAATAGATGAAGACTCA 58.025 33.333 0.00 0.00 42.56 3.41
3754 3972 4.162040 ACCTCCACCATCATTGAGAATC 57.838 45.455 0.00 0.00 0.00 2.52
3755 3973 4.474651 TGTACCTCCACCATCATTGAGAAT 59.525 41.667 0.00 0.00 0.00 2.40
3756 3974 3.843619 TGTACCTCCACCATCATTGAGAA 59.156 43.478 0.00 0.00 0.00 2.87
3757 3975 3.449918 TGTACCTCCACCATCATTGAGA 58.550 45.455 0.00 0.00 0.00 3.27
3758 3976 3.912496 TGTACCTCCACCATCATTGAG 57.088 47.619 0.00 0.00 0.00 3.02
3759 3977 4.040047 AGATGTACCTCCACCATCATTGA 58.960 43.478 0.00 0.00 37.93 2.57
3760 3978 4.428294 AGATGTACCTCCACCATCATTG 57.572 45.455 0.00 0.00 37.93 2.82
3761 3979 5.456921 AAAGATGTACCTCCACCATCATT 57.543 39.130 0.00 0.00 37.93 2.57
3762 3980 6.560304 AGATAAAGATGTACCTCCACCATCAT 59.440 38.462 0.00 0.00 37.93 2.45
3763 3981 5.905331 AGATAAAGATGTACCTCCACCATCA 59.095 40.000 0.00 0.00 37.93 3.07
3764 3982 6.426646 AGATAAAGATGTACCTCCACCATC 57.573 41.667 0.00 0.00 36.16 3.51
3765 3983 7.931015 TTAGATAAAGATGTACCTCCACCAT 57.069 36.000 0.00 0.00 0.00 3.55
3766 3984 7.931015 ATTAGATAAAGATGTACCTCCACCA 57.069 36.000 0.00 0.00 0.00 4.17
3767 3985 9.628500 AAAATTAGATAAAGATGTACCTCCACC 57.372 33.333 0.00 0.00 0.00 4.61
3791 4009 6.463995 ACCTGCAATGAAGAACACTAAAAA 57.536 33.333 0.00 0.00 0.00 1.94
3792 4010 6.463995 AACCTGCAATGAAGAACACTAAAA 57.536 33.333 0.00 0.00 0.00 1.52
3793 4011 6.770785 ACTAACCTGCAATGAAGAACACTAAA 59.229 34.615 0.00 0.00 0.00 1.85
3794 4012 6.296026 ACTAACCTGCAATGAAGAACACTAA 58.704 36.000 0.00 0.00 0.00 2.24
3795 4013 5.865085 ACTAACCTGCAATGAAGAACACTA 58.135 37.500 0.00 0.00 0.00 2.74
3796 4014 4.718961 ACTAACCTGCAATGAAGAACACT 58.281 39.130 0.00 0.00 0.00 3.55
3797 4015 5.008613 TGAACTAACCTGCAATGAAGAACAC 59.991 40.000 0.00 0.00 0.00 3.32
3798 4016 5.129634 TGAACTAACCTGCAATGAAGAACA 58.870 37.500 0.00 0.00 0.00 3.18
3799 4017 5.689383 TGAACTAACCTGCAATGAAGAAC 57.311 39.130 0.00 0.00 0.00 3.01
3800 4018 5.183713 CCATGAACTAACCTGCAATGAAGAA 59.816 40.000 0.00 0.00 0.00 2.52
3801 4019 4.701651 CCATGAACTAACCTGCAATGAAGA 59.298 41.667 0.00 0.00 0.00 2.87
3802 4020 4.460382 ACCATGAACTAACCTGCAATGAAG 59.540 41.667 0.00 0.00 0.00 3.02
3803 4021 4.406456 ACCATGAACTAACCTGCAATGAA 58.594 39.130 0.00 0.00 0.00 2.57
3804 4022 4.032960 ACCATGAACTAACCTGCAATGA 57.967 40.909 0.00 0.00 0.00 2.57
3805 4023 4.789012 AACCATGAACTAACCTGCAATG 57.211 40.909 0.00 0.00 0.00 2.82
3806 4024 4.949856 CCTAACCATGAACTAACCTGCAAT 59.050 41.667 0.00 0.00 0.00 3.56
3807 4025 4.202524 ACCTAACCATGAACTAACCTGCAA 60.203 41.667 0.00 0.00 0.00 4.08
3808 4026 3.329520 ACCTAACCATGAACTAACCTGCA 59.670 43.478 0.00 0.00 0.00 4.41
3809 4027 3.951663 ACCTAACCATGAACTAACCTGC 58.048 45.455 0.00 0.00 0.00 4.85
3810 4028 6.238648 AGAAACCTAACCATGAACTAACCTG 58.761 40.000 0.00 0.00 0.00 4.00
3811 4029 6.449830 AGAAACCTAACCATGAACTAACCT 57.550 37.500 0.00 0.00 0.00 3.50
3812 4030 6.489022 ACAAGAAACCTAACCATGAACTAACC 59.511 38.462 0.00 0.00 0.00 2.85
3813 4031 7.360361 CACAAGAAACCTAACCATGAACTAAC 58.640 38.462 0.00 0.00 0.00 2.34
3814 4032 6.488683 CCACAAGAAACCTAACCATGAACTAA 59.511 38.462 0.00 0.00 0.00 2.24
3815 4033 6.001460 CCACAAGAAACCTAACCATGAACTA 58.999 40.000 0.00 0.00 0.00 2.24
3816 4034 4.827284 CCACAAGAAACCTAACCATGAACT 59.173 41.667 0.00 0.00 0.00 3.01
3817 4035 4.558697 GCCACAAGAAACCTAACCATGAAC 60.559 45.833 0.00 0.00 0.00 3.18
3818 4036 3.572255 GCCACAAGAAACCTAACCATGAA 59.428 43.478 0.00 0.00 0.00 2.57
3819 4037 3.153919 GCCACAAGAAACCTAACCATGA 58.846 45.455 0.00 0.00 0.00 3.07
3820 4038 2.890311 TGCCACAAGAAACCTAACCATG 59.110 45.455 0.00 0.00 0.00 3.66
3821 4039 3.237268 TGCCACAAGAAACCTAACCAT 57.763 42.857 0.00 0.00 0.00 3.55
3822 4040 2.738587 TGCCACAAGAAACCTAACCA 57.261 45.000 0.00 0.00 0.00 3.67
3823 4041 4.600692 AAATGCCACAAGAAACCTAACC 57.399 40.909 0.00 0.00 0.00 2.85
3824 4042 5.596845 TGAAAATGCCACAAGAAACCTAAC 58.403 37.500 0.00 0.00 0.00 2.34
3825 4043 5.362430 ACTGAAAATGCCACAAGAAACCTAA 59.638 36.000 0.00 0.00 0.00 2.69
3826 4044 4.892934 ACTGAAAATGCCACAAGAAACCTA 59.107 37.500 0.00 0.00 0.00 3.08
3827 4045 3.706086 ACTGAAAATGCCACAAGAAACCT 59.294 39.130 0.00 0.00 0.00 3.50
3828 4046 4.058721 ACTGAAAATGCCACAAGAAACC 57.941 40.909 0.00 0.00 0.00 3.27
3829 4047 6.756542 ACTAAACTGAAAATGCCACAAGAAAC 59.243 34.615 0.00 0.00 0.00 2.78
3830 4048 6.756074 CACTAAACTGAAAATGCCACAAGAAA 59.244 34.615 0.00 0.00 0.00 2.52
3831 4049 6.127479 ACACTAAACTGAAAATGCCACAAGAA 60.127 34.615 0.00 0.00 0.00 2.52
3832 4050 5.359576 ACACTAAACTGAAAATGCCACAAGA 59.640 36.000 0.00 0.00 0.00 3.02
3833 4051 5.591099 ACACTAAACTGAAAATGCCACAAG 58.409 37.500 0.00 0.00 0.00 3.16
3834 4052 5.359576 AGACACTAAACTGAAAATGCCACAA 59.640 36.000 0.00 0.00 0.00 3.33
3835 4053 4.887071 AGACACTAAACTGAAAATGCCACA 59.113 37.500 0.00 0.00 0.00 4.17
3836 4054 5.008613 TCAGACACTAAACTGAAAATGCCAC 59.991 40.000 0.00 0.00 39.68 5.01
3837 4055 5.129634 TCAGACACTAAACTGAAAATGCCA 58.870 37.500 0.00 0.00 39.68 4.92
3838 4056 5.689383 TCAGACACTAAACTGAAAATGCC 57.311 39.130 0.00 0.00 39.68 4.40
3844 4062 3.133362 ACGGGTTCAGACACTAAACTGAA 59.867 43.478 0.00 0.00 46.36 3.02
3896 4114 6.573664 AAATCACATCGATGGAAAAAGTGA 57.426 33.333 28.09 19.94 38.67 3.41
3959 4178 0.249615 GCGACTGAGCATGGCATCTA 60.250 55.000 0.00 0.00 37.05 1.98
4037 4256 7.950512 AGTGTGATGTTTCCATGTTATTTGAA 58.049 30.769 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.