Multiple sequence alignment - TraesCS2D01G023600

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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 TraesCS2D01G023600 chr2D 100.000 4444 0 0 1 4444 10532491 10528048 0.000000e+00 8207.0
1 TraesCS2D01G023600 chr2D 93.704 2827 124 29 996 3796 10435061 10432263 0.000000e+00 4185.0
2 TraesCS2D01G023600 chr2D 87.844 946 61 14 1 944 10435968 10435075 0.000000e+00 1061.0
3 TraesCS2D01G023600 chr2D 90.506 158 13 2 3640 3796 61763905 61763749 1.620000e-49 207.0
4 TraesCS2D01G023600 chr2D 93.878 49 3 0 55 103 55403695 55403743 1.710000e-09 75.0
5 TraesCS2D01G023600 chr2B 91.296 2022 117 27 1570 3572 15462593 15464574 0.000000e+00 2704.0
6 TraesCS2D01G023600 chr2B 90.358 1929 140 22 1568 3489 14619098 14617209 0.000000e+00 2490.0
7 TraesCS2D01G023600 chr2B 92.176 1457 98 9 996 2444 14351479 14350031 0.000000e+00 2045.0
8 TraesCS2D01G023600 chr2B 89.497 1590 143 14 903 2486 14506390 14504819 0.000000e+00 1989.0
9 TraesCS2D01G023600 chr2B 92.320 1276 69 13 2524 3795 14477591 14476341 0.000000e+00 1786.0
10 TraesCS2D01G023600 chr2B 92.241 1276 69 13 2524 3795 14504825 14503576 0.000000e+00 1781.0
11 TraesCS2D01G023600 chr2B 88.193 1533 113 26 73 1569 14620665 14619165 0.000000e+00 1766.0
12 TraesCS2D01G023600 chr2B 82.886 2010 254 47 213 2179 14408019 14406057 0.000000e+00 1724.0
13 TraesCS2D01G023600 chr2B 84.784 1275 156 26 2189 3451 14405956 14404708 0.000000e+00 1245.0
14 TraesCS2D01G023600 chr2B 84.173 1270 157 28 2189 3454 14212971 14211742 0.000000e+00 1192.0
15 TraesCS2D01G023600 chr2B 87.721 961 71 13 1 944 14462934 14462004 0.000000e+00 1077.0
16 TraesCS2D01G023600 chr2B 87.721 961 71 13 1 944 14491731 14490801 0.000000e+00 1077.0
17 TraesCS2D01G023600 chr2B 83.557 1192 117 25 384 1569 15461429 15462547 0.000000e+00 1042.0
18 TraesCS2D01G023600 chr2B 91.534 756 51 6 996 1744 14490785 14490036 0.000000e+00 1029.0
19 TraesCS2D01G023600 chr2B 91.402 756 52 6 996 1744 14461988 14461239 0.000000e+00 1024.0
20 TraesCS2D01G023600 chr2B 92.786 707 34 11 2866 3570 14336903 14336212 0.000000e+00 1007.0
21 TraesCS2D01G023600 chr2B 92.846 657 43 4 1789 2444 14460377 14459724 0.000000e+00 950.0
22 TraesCS2D01G023600 chr2B 86.179 738 62 13 1 707 14345561 14344833 0.000000e+00 761.0
23 TraesCS2D01G023600 chr2B 82.309 944 75 29 1 912 14352381 14351498 0.000000e+00 734.0
24 TraesCS2D01G023600 chr2B 90.647 556 33 9 3016 3570 13912273 13912810 0.000000e+00 721.0
25 TraesCS2D01G023600 chr2B 92.143 420 28 2 2492 2909 13911863 13912279 4.950000e-164 588.0
26 TraesCS2D01G023600 chr2B 82.550 298 17 13 3511 3792 14615082 14614804 3.460000e-56 230.0
27 TraesCS2D01G023600 chr2B 92.258 155 7 1 778 932 13908090 13908239 9.680000e-52 215.0
28 TraesCS2D01G023600 chr2B 96.094 128 5 0 828 955 14344836 14344709 4.500000e-50 209.0
29 TraesCS2D01G023600 chr2A 88.021 1728 163 23 754 2465 10846158 10844459 0.000000e+00 2004.0
30 TraesCS2D01G023600 chr2A 87.228 1425 125 27 2173 3572 10735681 10734289 0.000000e+00 1570.0
31 TraesCS2D01G023600 chr2A 90.158 1077 79 19 2498 3570 10844459 10843406 0.000000e+00 1376.0
32 TraesCS2D01G023600 chr2A 86.345 1223 82 21 1 1201 10737695 10736536 0.000000e+00 1254.0
33 TraesCS2D01G023600 chr2A 89.375 160 15 2 3638 3796 206441975 206441817 2.710000e-47 200.0
34 TraesCS2D01G023600 chrUn 89.497 1590 143 14 903 2486 353663478 353661907 0.000000e+00 1989.0
35 TraesCS2D01G023600 chrUn 93.092 883 36 12 2917 3795 461723465 461722604 0.000000e+00 1269.0
36 TraesCS2D01G023600 chrUn 88.105 950 93 11 903 1847 349801010 349801944 0.000000e+00 1110.0
37 TraesCS2D01G023600 chrUn 87.721 961 71 20 1 944 345005604 345006534 0.000000e+00 1077.0
38 TraesCS2D01G023600 chrUn 91.402 756 52 6 996 1744 329540181 329539432 0.000000e+00 1024.0
39 TraesCS2D01G023600 chrUn 92.846 657 43 4 1789 2444 329538570 329537917 0.000000e+00 950.0
40 TraesCS2D01G023600 chrUn 96.154 78 3 0 2492 2569 329537898 329537821 1.300000e-25 128.0
41 TraesCS2D01G023600 chr7B 82.182 550 46 20 3858 4404 217786348 217785848 4.110000e-115 425.0
42 TraesCS2D01G023600 chr5A 82.768 354 48 9 4060 4406 601173045 601173392 2.010000e-78 303.0
43 TraesCS2D01G023600 chr5A 90.164 61 6 0 3796 3856 399463406 399463346 3.680000e-11 80.5
44 TraesCS2D01G023600 chr7D 86.063 287 33 6 4097 4381 143712617 143712336 7.220000e-78 302.0
45 TraesCS2D01G023600 chr6A 82.371 329 46 11 4120 4443 143011005 143010684 4.380000e-70 276.0
46 TraesCS2D01G023600 chr6A 77.210 509 77 27 3950 4430 615180336 615179839 1.230000e-65 261.0
47 TraesCS2D01G023600 chr6A 84.109 258 31 9 4120 4374 143010924 143010674 1.600000e-59 241.0
48 TraesCS2D01G023600 chr4D 79.784 371 60 12 4078 4444 219268388 219268747 5.700000e-64 255.0
49 TraesCS2D01G023600 chr4A 80.286 350 56 11 4101 4441 627727904 627727559 7.380000e-63 252.0
50 TraesCS2D01G023600 chr7A 83.150 273 37 8 4101 4369 403199095 403198828 1.600000e-59 241.0
51 TraesCS2D01G023600 chr6B 81.605 299 44 11 4101 4395 720872664 720872955 2.070000e-58 237.0
52 TraesCS2D01G023600 chr1D 92.157 51 4 0 56 106 416109715 416109765 6.170000e-09 73.1


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 TraesCS2D01G023600 chr2D 10528048 10532491 4443 True 8207.000000 8207 100.000000 1 4444 1 chr2D.!!$R1 4443
1 TraesCS2D01G023600 chr2D 10432263 10435968 3705 True 2623.000000 4185 90.774000 1 3796 2 chr2D.!!$R3 3795
2 TraesCS2D01G023600 chr2B 14503576 14506390 2814 True 1885.000000 1989 90.869000 903 3795 2 chr2B.!!$R9 2892
3 TraesCS2D01G023600 chr2B 15461429 15464574 3145 False 1873.000000 2704 87.426500 384 3572 2 chr2B.!!$F2 3188
4 TraesCS2D01G023600 chr2B 14476341 14477591 1250 True 1786.000000 1786 92.320000 2524 3795 1 chr2B.!!$R3 1271
5 TraesCS2D01G023600 chr2B 14614804 14620665 5861 True 1495.333333 2490 87.033667 73 3792 3 chr2B.!!$R10 3719
6 TraesCS2D01G023600 chr2B 14404708 14408019 3311 True 1484.500000 1724 83.835000 213 3451 2 chr2B.!!$R6 3238
7 TraesCS2D01G023600 chr2B 14350031 14352381 2350 True 1389.500000 2045 87.242500 1 2444 2 chr2B.!!$R5 2443
8 TraesCS2D01G023600 chr2B 14211742 14212971 1229 True 1192.000000 1192 84.173000 2189 3454 1 chr2B.!!$R1 1265
9 TraesCS2D01G023600 chr2B 14490036 14491731 1695 True 1053.000000 1077 89.627500 1 1744 2 chr2B.!!$R8 1743
10 TraesCS2D01G023600 chr2B 14459724 14462934 3210 True 1017.000000 1077 90.656333 1 2444 3 chr2B.!!$R7 2443
11 TraesCS2D01G023600 chr2B 14336212 14336903 691 True 1007.000000 1007 92.786000 2866 3570 1 chr2B.!!$R2 704
12 TraesCS2D01G023600 chr2B 13908090 13912810 4720 False 508.000000 721 91.682667 778 3570 3 chr2B.!!$F1 2792
13 TraesCS2D01G023600 chr2B 14344709 14345561 852 True 485.000000 761 91.136500 1 955 2 chr2B.!!$R4 954
14 TraesCS2D01G023600 chr2A 10843406 10846158 2752 True 1690.000000 2004 89.089500 754 3570 2 chr2A.!!$R3 2816
15 TraesCS2D01G023600 chr2A 10734289 10737695 3406 True 1412.000000 1570 86.786500 1 3572 2 chr2A.!!$R2 3571
16 TraesCS2D01G023600 chrUn 353661907 353663478 1571 True 1989.000000 1989 89.497000 903 2486 1 chrUn.!!$R1 1583
17 TraesCS2D01G023600 chrUn 461722604 461723465 861 True 1269.000000 1269 93.092000 2917 3795 1 chrUn.!!$R2 878
18 TraesCS2D01G023600 chrUn 349801010 349801944 934 False 1110.000000 1110 88.105000 903 1847 1 chrUn.!!$F2 944
19 TraesCS2D01G023600 chrUn 345005604 345006534 930 False 1077.000000 1077 87.721000 1 944 1 chrUn.!!$F1 943
20 TraesCS2D01G023600 chrUn 329537821 329540181 2360 True 700.666667 1024 93.467333 996 2569 3 chrUn.!!$R3 1573
21 TraesCS2D01G023600 chr7B 217785848 217786348 500 True 425.000000 425 82.182000 3858 4404 1 chr7B.!!$R1 546

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
57 62 0.108615 CGAGAGGAACATCCACGCTT 60.109 55.0 0.00 0.0 39.61 4.68 F
1446 3494 0.179073 CTTAGCTCCATCCACCACCG 60.179 60.0 0.00 0.0 0.00 4.94 F
1847 4798 0.174845 CATACCTTGCGTTCGGAGGA 59.825 55.0 8.47 0.0 34.61 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 3545 0.178992 CAACCTGAACCTCAAGGCCA 60.179 55.000 5.01 0.0 39.32 5.36 R
2624 5880 2.045926 GCCACCTCAGCGGATGTT 60.046 61.111 0.00 0.0 36.31 2.71 R
3799 9210 0.102120 CTGAAGGCGCTGACTAGGAG 59.898 60.000 7.64 0.0 0.00 3.69 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
46 51 0.681733 AGCAACTTCAGCGAGAGGAA 59.318 50.000 0.00 0.00 37.01 3.36
48 53 1.873903 GCAACTTCAGCGAGAGGAACA 60.874 52.381 0.00 0.00 0.00 3.18
57 62 0.108615 CGAGAGGAACATCCACGCTT 60.109 55.000 0.00 0.00 39.61 4.68
140 158 2.438795 GTCGGAGGAGACGGCTCT 60.439 66.667 19.83 3.79 41.06 4.09
150 168 1.185618 AGACGGCTCTGGCAGTGTAA 61.186 55.000 15.27 0.00 46.03 2.41
215 234 1.065491 CGATTGGACCAGTGGGATGAA 60.065 52.381 15.21 0.77 38.05 2.57
264 283 6.454795 TGGCAATTTGAAGAGGAACAATTAC 58.545 36.000 0.00 0.00 0.00 1.89
328 349 9.129532 TGAATTTTAATTCCAACCATGCTTTTT 57.870 25.926 11.54 0.00 43.19 1.94
431 471 9.098355 GGAATTTTGCTAGAAAAACAGAAAGTT 57.902 29.630 10.95 0.00 43.89 2.66
501 543 2.796032 GCGTGAGGATGGCAAAATTAGC 60.796 50.000 0.00 0.00 0.00 3.09
580 624 4.455877 CACCAACTAAACTTGTCATCCTCC 59.544 45.833 0.00 0.00 0.00 4.30
596 640 3.815809 TCCTCCACGAACACAAATTTCT 58.184 40.909 0.00 0.00 0.00 2.52
759 808 8.857098 AGAAATACTACTAGCAATTCGGTATGA 58.143 33.333 0.00 0.00 0.00 2.15
817 866 2.735772 GCTGCTGGGTGCCTAGCTA 61.736 63.158 23.59 11.69 42.00 3.32
1168 1247 2.993471 CCCAACAATGGCGGACAGC 61.993 63.158 0.00 0.00 46.09 4.40
1188 1267 3.693085 AGCTGGCAGATCAAGTACATTTG 59.307 43.478 20.86 0.00 0.00 2.32
1237 1326 5.163478 ACCGGCAAGTAGTACATAAAGTAGG 60.163 44.000 0.00 0.00 32.19 3.18
1293 1402 3.897505 TGGATGATGTCACAGGTCGATAT 59.102 43.478 0.00 0.00 0.00 1.63
1445 3493 0.181350 CCTTAGCTCCATCCACCACC 59.819 60.000 0.00 0.00 0.00 4.61
1446 3494 0.179073 CTTAGCTCCATCCACCACCG 60.179 60.000 0.00 0.00 0.00 4.94
1447 3495 2.252072 TTAGCTCCATCCACCACCGC 62.252 60.000 0.00 0.00 0.00 5.68
1492 3540 0.604578 ACAATGCCAGTGATGTTGCC 59.395 50.000 0.00 0.00 0.00 4.52
1497 3545 0.607489 GCCAGTGATGTTGCCTCTGT 60.607 55.000 0.00 0.00 0.00 3.41
1622 3740 7.041848 GCTGTAAGAAAAACCTAAAACTACGGA 60.042 37.037 0.00 0.00 34.07 4.69
1635 3758 7.593644 CCTAAAACTACGGACAAAATTTTGGAG 59.406 37.037 29.37 22.05 42.34 3.86
1640 3763 8.575649 ACTACGGACAAAATTTTGGAGATTAT 57.424 30.769 29.37 11.02 42.34 1.28
1671 3799 2.768833 CCAAATGCATGGTCGAGATG 57.231 50.000 0.00 0.00 35.65 2.90
1847 4798 0.174845 CATACCTTGCGTTCGGAGGA 59.825 55.000 8.47 0.00 34.61 3.71
2023 5133 9.176460 CATAGATCACTATGCTAGAGATGAGAA 57.824 37.037 0.00 0.00 45.85 2.87
2623 5879 4.045104 GCACTCTATTCCGTGATGTACAG 58.955 47.826 0.33 0.00 33.04 2.74
2624 5880 4.202020 GCACTCTATTCCGTGATGTACAGA 60.202 45.833 0.33 0.00 33.04 3.41
2793 6051 1.159285 TGATTTTGCAGTGGCGAGAG 58.841 50.000 0.00 0.00 45.35 3.20
2925 6183 2.937873 GCAACATACGTTTCCCCTGCTA 60.938 50.000 0.00 0.00 31.13 3.49
2972 6230 6.239008 CCAATGTCTCTTGCTAAAGTTGGAAA 60.239 38.462 0.00 0.00 36.99 3.13
3531 8919 7.765819 TGTAGGTATTGATTCTGATTCTGTGTG 59.234 37.037 1.76 0.00 0.00 3.82
3549 8937 8.874744 TCTGTGTGGTACTACTAAAACTCTAT 57.125 34.615 10.95 0.00 0.00 1.98
3550 8938 9.305555 TCTGTGTGGTACTACTAAAACTCTATT 57.694 33.333 10.95 0.00 0.00 1.73
3761 9172 1.745653 GGTATGCCAGCTCCAGTTTTC 59.254 52.381 0.00 0.00 34.09 2.29
3808 9219 4.543590 CTTTTTCAGGAGCTCCTAGTCA 57.456 45.455 34.67 16.54 46.65 3.41
3809 9220 4.502962 CTTTTTCAGGAGCTCCTAGTCAG 58.497 47.826 34.67 21.64 46.65 3.51
3810 9221 1.479709 TTCAGGAGCTCCTAGTCAGC 58.520 55.000 34.67 4.45 46.65 4.26
3811 9222 0.749818 TCAGGAGCTCCTAGTCAGCG 60.750 60.000 34.67 20.17 46.65 5.18
3812 9223 2.124693 AGGAGCTCCTAGTCAGCGC 61.125 63.158 34.40 0.00 46.48 5.92
3813 9224 2.415426 GAGCTCCTAGTCAGCGCC 59.585 66.667 2.29 0.00 42.14 6.53
3814 9225 2.043450 AGCTCCTAGTCAGCGCCT 60.043 61.111 2.29 0.00 42.14 5.52
3815 9226 1.671901 GAGCTCCTAGTCAGCGCCTT 61.672 60.000 2.29 0.00 42.14 4.35
3816 9227 1.227118 GCTCCTAGTCAGCGCCTTC 60.227 63.158 2.29 0.00 0.00 3.46
3817 9228 1.949847 GCTCCTAGTCAGCGCCTTCA 61.950 60.000 2.29 0.00 0.00 3.02
3818 9229 0.102120 CTCCTAGTCAGCGCCTTCAG 59.898 60.000 2.29 0.00 0.00 3.02
3819 9230 1.520342 CCTAGTCAGCGCCTTCAGC 60.520 63.158 2.29 0.00 38.52 4.26
3820 9231 1.216444 CTAGTCAGCGCCTTCAGCA 59.784 57.895 2.29 0.00 44.04 4.41
3821 9232 1.079819 TAGTCAGCGCCTTCAGCAC 60.080 57.895 2.29 0.00 44.04 4.40
3822 9233 2.507110 TAGTCAGCGCCTTCAGCACC 62.507 60.000 2.29 0.00 44.04 5.01
3823 9234 3.939939 TCAGCGCCTTCAGCACCA 61.940 61.111 2.29 0.00 44.04 4.17
3824 9235 2.979676 CAGCGCCTTCAGCACCAA 60.980 61.111 2.29 0.00 44.04 3.67
3825 9236 2.980233 AGCGCCTTCAGCACCAAC 60.980 61.111 2.29 0.00 44.04 3.77
3826 9237 2.980233 GCGCCTTCAGCACCAACT 60.980 61.111 0.00 0.00 44.04 3.16
3827 9238 1.671054 GCGCCTTCAGCACCAACTA 60.671 57.895 0.00 0.00 44.04 2.24
3828 9239 1.639298 GCGCCTTCAGCACCAACTAG 61.639 60.000 0.00 0.00 44.04 2.57
3829 9240 1.021390 CGCCTTCAGCACCAACTAGG 61.021 60.000 0.00 0.00 44.04 3.02
3830 9241 0.324943 GCCTTCAGCACCAACTAGGA 59.675 55.000 0.00 0.00 42.97 2.94
3831 9242 1.677217 GCCTTCAGCACCAACTAGGAG 60.677 57.143 0.00 0.00 42.97 3.69
3832 9243 1.625818 CCTTCAGCACCAACTAGGAGT 59.374 52.381 0.00 0.00 41.22 3.85
3833 9244 2.039084 CCTTCAGCACCAACTAGGAGTT 59.961 50.000 0.00 0.00 39.39 3.01
3834 9245 3.330267 CTTCAGCACCAACTAGGAGTTC 58.670 50.000 0.00 0.00 36.03 3.01
3835 9246 1.623811 TCAGCACCAACTAGGAGTTCC 59.376 52.381 0.00 0.00 36.03 3.62
3836 9247 0.608640 AGCACCAACTAGGAGTTCCG 59.391 55.000 0.00 0.00 36.03 4.30
3837 9248 0.320697 GCACCAACTAGGAGTTCCGT 59.679 55.000 0.00 0.00 36.03 4.69
3838 9249 1.672145 GCACCAACTAGGAGTTCCGTC 60.672 57.143 0.00 0.00 36.03 4.79
3839 9250 0.886563 ACCAACTAGGAGTTCCGTCG 59.113 55.000 0.00 0.00 36.03 5.12
3840 9251 0.458025 CCAACTAGGAGTTCCGTCGC 60.458 60.000 0.00 0.00 36.03 5.19
3841 9252 0.458025 CAACTAGGAGTTCCGTCGCC 60.458 60.000 0.00 0.00 36.03 5.54
3842 9253 1.602327 AACTAGGAGTTCCGTCGCCC 61.602 60.000 0.00 0.00 42.08 6.13
3843 9254 2.036098 TAGGAGTTCCGTCGCCCA 59.964 61.111 0.00 0.00 42.08 5.36
3844 9255 2.280823 CTAGGAGTTCCGTCGCCCAC 62.281 65.000 0.00 0.00 42.08 4.61
3862 9273 3.258290 GCTGCCGCGCTAAGACTC 61.258 66.667 5.56 0.00 0.00 3.36
3869 9280 1.872679 GCGCTAAGACTCGAACCGG 60.873 63.158 0.00 0.00 0.00 5.28
3875 9286 1.313812 AAGACTCGAACCGGCGATCT 61.314 55.000 9.30 6.04 39.85 2.75
3876 9287 1.298488 GACTCGAACCGGCGATCTC 60.298 63.158 9.30 0.00 39.85 2.75
3877 9288 1.716826 GACTCGAACCGGCGATCTCT 61.717 60.000 9.30 0.00 39.85 3.10
3908 9319 1.517257 CAGCGCTCTAACCACGAGG 60.517 63.158 7.13 0.00 42.21 4.63
3912 9323 1.448013 GCTCTAACCACGAGGCCAC 60.448 63.158 5.01 0.00 39.06 5.01
3933 9344 2.597510 GGCACGCCTTGGAGGTTT 60.598 61.111 0.00 0.00 37.80 3.27
3943 9354 4.498241 GCCTTGGAGGTTTGATCATTTTC 58.502 43.478 0.00 0.00 37.80 2.29
3945 9356 5.418840 GCCTTGGAGGTTTGATCATTTTCTA 59.581 40.000 0.00 0.00 37.80 2.10
3948 9359 6.455360 TGGAGGTTTGATCATTTTCTATGC 57.545 37.500 0.00 0.00 0.00 3.14
3953 9364 7.550712 AGGTTTGATCATTTTCTATGCTTTCC 58.449 34.615 0.00 0.00 0.00 3.13
3954 9365 7.398332 AGGTTTGATCATTTTCTATGCTTTCCT 59.602 33.333 0.00 0.00 0.00 3.36
3955 9366 8.037166 GGTTTGATCATTTTCTATGCTTTCCTT 58.963 33.333 0.00 0.00 0.00 3.36
3956 9367 9.428097 GTTTGATCATTTTCTATGCTTTCCTTT 57.572 29.630 0.00 0.00 0.00 3.11
4123 9535 9.258826 TGAAATTTGACAAAGTCCACATATTTG 57.741 29.630 6.77 0.00 39.32 2.32
4124 9536 9.474920 GAAATTTGACAAAGTCCACATATTTGA 57.525 29.630 6.77 0.00 37.37 2.69
4321 9734 9.868389 GTTCATCAAAATTGGAAAAAGTTCATC 57.132 29.630 0.00 0.00 35.25 2.92
4323 9736 8.140628 TCATCAAAATTGGAAAAAGTTCATCGA 58.859 29.630 0.00 0.00 35.25 3.59
4397 9810 7.755582 AAAAGTTCACCGAATTTGAAAAGAG 57.244 32.000 0.00 0.00 34.78 2.85
4398 9811 6.451064 AAGTTCACCGAATTTGAAAAGAGT 57.549 33.333 0.00 0.00 34.78 3.24
4399 9812 6.451064 AGTTCACCGAATTTGAAAAGAGTT 57.549 33.333 0.00 0.00 34.78 3.01
4400 9813 6.495706 AGTTCACCGAATTTGAAAAGAGTTC 58.504 36.000 0.00 0.00 34.78 3.01
4401 9814 6.094881 AGTTCACCGAATTTGAAAAGAGTTCA 59.905 34.615 0.00 0.00 34.78 3.18
4402 9815 6.633500 TCACCGAATTTGAAAAGAGTTCAT 57.367 33.333 0.00 0.00 0.00 2.57
4403 9816 6.668323 TCACCGAATTTGAAAAGAGTTCATC 58.332 36.000 0.00 0.00 0.00 2.92
4404 9817 6.262049 TCACCGAATTTGAAAAGAGTTCATCA 59.738 34.615 0.00 0.00 0.00 3.07
4405 9818 6.917477 CACCGAATTTGAAAAGAGTTCATCAA 59.083 34.615 0.00 0.00 0.00 2.57
4406 9819 7.434897 CACCGAATTTGAAAAGAGTTCATCAAA 59.565 33.333 2.69 2.69 43.53 2.69
4421 9834 9.922305 GAGTTCATCAAATTAGGAAATACTTCG 57.078 33.333 0.00 0.00 31.77 3.79
4422 9835 9.449719 AGTTCATCAAATTAGGAAATACTTCGT 57.550 29.630 0.00 0.00 34.20 3.85
4423 9836 9.704098 GTTCATCAAATTAGGAAATACTTCGTC 57.296 33.333 0.00 0.00 32.14 4.20
4424 9837 8.433421 TCATCAAATTAGGAAATACTTCGTCC 57.567 34.615 0.00 0.00 32.14 4.79
4431 9844 8.801882 ATTAGGAAATACTTCGTCCAATTTGA 57.198 30.769 0.00 0.00 33.57 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 36 1.205893 GGATGTTCCTCTCGCTGAAGT 59.794 52.381 0.00 0.00 32.53 3.01
57 62 1.472878 ACGATAGCTTCTCTTGCGTCA 59.527 47.619 0.00 0.00 42.67 4.35
146 164 0.392998 GCAAGCCTAGCAGCCTTACA 60.393 55.000 0.00 0.00 0.00 2.41
150 168 4.479993 CCGCAAGCCTAGCAGCCT 62.480 66.667 0.00 0.00 0.00 4.58
215 234 3.260205 TGAACAATTCTTCCTCCCTCCT 58.740 45.455 0.00 0.00 0.00 3.69
286 305 4.728102 CAACGGACCGGCGTGCTA 62.728 66.667 20.00 0.00 0.00 3.49
328 349 4.036941 ACATAAAGGGACCGCCTAAAAA 57.963 40.909 0.00 0.00 0.00 1.94
329 350 3.724732 ACATAAAGGGACCGCCTAAAA 57.275 42.857 0.00 0.00 0.00 1.52
330 351 5.376756 AATACATAAAGGGACCGCCTAAA 57.623 39.130 0.00 0.00 0.00 1.85
334 355 3.317149 GGAAAATACATAAAGGGACCGCC 59.683 47.826 0.00 0.00 0.00 6.13
431 471 4.734398 ATTTGCCATGGCTAAAAATCGA 57.266 36.364 35.53 13.29 39.04 3.59
432 472 6.312426 TGTTTATTTGCCATGGCTAAAAATCG 59.688 34.615 35.53 0.00 39.04 3.34
479 521 1.549203 AATTTTGCCATCCTCACGCT 58.451 45.000 0.00 0.00 0.00 5.07
501 543 5.751680 CCAGAATATATCCGTGTTTGCAAG 58.248 41.667 0.00 0.00 0.00 4.01
550 594 4.207165 ACAAGTTTAGTTGGTGAGCATGT 58.793 39.130 0.00 0.00 0.00 3.21
580 624 7.990499 CGTTTTTCATAGAAATTTGTGTTCGTG 59.010 33.333 0.00 0.00 0.00 4.35
667 715 4.349636 TGTACCAACATTTCTTCTGGAGGA 59.650 41.667 0.00 0.00 32.97 3.71
740 789 6.073327 TGACTCATACCGAATTGCTAGTAG 57.927 41.667 0.00 0.00 0.00 2.57
817 866 3.557264 GCCAATTTATAGGCGAGCTACCT 60.557 47.826 12.24 12.24 41.70 3.08
1168 1247 4.696877 TGACAAATGTACTTGATCTGCCAG 59.303 41.667 2.13 0.00 0.00 4.85
1169 1248 4.650734 TGACAAATGTACTTGATCTGCCA 58.349 39.130 2.13 0.00 0.00 4.92
1170 1249 4.437930 GCTGACAAATGTACTTGATCTGCC 60.438 45.833 2.13 0.00 32.20 4.85
1188 1267 7.234187 TGAAAATACGATATGTTCAGCTGAC 57.766 36.000 18.03 12.36 0.00 3.51
1293 1402 4.243008 TCACGCCGGCCTTCAACA 62.243 61.111 23.46 0.00 0.00 3.33
1447 3495 3.052082 CTGCACCGGTGAGGCTTG 61.052 66.667 38.30 15.32 46.52 4.01
1492 3540 0.397941 TGAACCTCAAGGCCACAGAG 59.602 55.000 5.01 8.91 39.32 3.35
1497 3545 0.178992 CAACCTGAACCTCAAGGCCA 60.179 55.000 5.01 0.00 39.32 5.36
1847 4798 1.339151 GCCTCGTCCAATGTTTCCTCT 60.339 52.381 0.00 0.00 0.00 3.69
1923 4874 2.860062 ACGAACTACACTGCATCGTAC 58.140 47.619 7.44 0.00 44.08 3.67
1928 4879 3.498397 CCAAAGAACGAACTACACTGCAT 59.502 43.478 0.00 0.00 0.00 3.96
1982 5092 5.238214 GTGATCTATGAACCATCTTGCTTCC 59.762 44.000 0.00 0.00 0.00 3.46
2023 5133 0.536460 AAGCAACGGGTCGGAATTGT 60.536 50.000 0.00 0.00 0.00 2.71
2210 5414 0.421904 AGTCCCCTTCCACCACCTAT 59.578 55.000 0.00 0.00 0.00 2.57
2447 5651 4.183865 TGAATTATGAGAAGTGCACCGAG 58.816 43.478 14.63 0.00 0.00 4.63
2448 5652 4.200838 TGAATTATGAGAAGTGCACCGA 57.799 40.909 14.63 0.00 0.00 4.69
2623 5879 2.109126 GCCACCTCAGCGGATGTTC 61.109 63.158 0.00 0.00 36.31 3.18
2624 5880 2.045926 GCCACCTCAGCGGATGTT 60.046 61.111 0.00 0.00 36.31 2.71
2925 6183 3.074412 GGTGATCTTTTCATCCACACGT 58.926 45.455 0.00 0.00 36.54 4.49
2972 6230 6.627508 CGCTGACTGAACTAATTTAGGGTAGT 60.628 42.308 8.26 8.02 31.81 2.73
3579 8984 9.841295 AGTTAATCAACCAACTAGTTTCAACTA 57.159 29.630 5.07 0.00 36.59 2.24
3592 8997 5.184864 CCAATGGTGCTAGTTAATCAACCAA 59.815 40.000 0.00 0.00 35.05 3.67
3660 9066 4.203226 GGATTTCAGGATTTCCAGGAGTC 58.797 47.826 0.00 0.00 38.89 3.36
3761 9172 0.469331 ATCCCATGCATTGCCAGAGG 60.469 55.000 6.12 2.13 0.00 3.69
3796 9207 1.671901 AAGGCGCTGACTAGGAGCTC 61.672 60.000 7.64 4.71 34.03 4.09
3797 9208 1.671901 GAAGGCGCTGACTAGGAGCT 61.672 60.000 7.64 0.00 34.03 4.09
3798 9209 1.227118 GAAGGCGCTGACTAGGAGC 60.227 63.158 7.64 6.05 0.00 4.70
3799 9210 0.102120 CTGAAGGCGCTGACTAGGAG 59.898 60.000 7.64 0.00 0.00 3.69
3800 9211 1.949847 GCTGAAGGCGCTGACTAGGA 61.950 60.000 7.64 0.00 0.00 2.94
3801 9212 1.520342 GCTGAAGGCGCTGACTAGG 60.520 63.158 7.64 0.00 0.00 3.02
3802 9213 1.080995 GTGCTGAAGGCGCTGACTAG 61.081 60.000 7.64 0.92 46.82 2.57
3803 9214 1.079819 GTGCTGAAGGCGCTGACTA 60.080 57.895 7.64 0.00 46.82 2.59
3804 9215 2.358003 GTGCTGAAGGCGCTGACT 60.358 61.111 7.64 0.00 46.82 3.41
3810 9221 1.021390 CCTAGTTGGTGCTGAAGGCG 61.021 60.000 0.00 0.00 45.43 5.52
3811 9222 0.324943 TCCTAGTTGGTGCTGAAGGC 59.675 55.000 0.00 0.00 37.07 4.35
3812 9223 1.625818 ACTCCTAGTTGGTGCTGAAGG 59.374 52.381 0.00 0.00 37.07 3.46
3813 9224 3.330267 GAACTCCTAGTTGGTGCTGAAG 58.670 50.000 0.00 0.00 38.80 3.02
3814 9225 2.038557 GGAACTCCTAGTTGGTGCTGAA 59.961 50.000 0.00 0.00 38.80 3.02
3815 9226 1.623811 GGAACTCCTAGTTGGTGCTGA 59.376 52.381 0.00 0.00 38.80 4.26
3816 9227 1.673033 CGGAACTCCTAGTTGGTGCTG 60.673 57.143 0.00 0.00 38.80 4.41
3817 9228 0.608640 CGGAACTCCTAGTTGGTGCT 59.391 55.000 0.00 0.00 38.80 4.40
3818 9229 0.320697 ACGGAACTCCTAGTTGGTGC 59.679 55.000 0.00 0.00 38.80 5.01
3819 9230 1.402456 CGACGGAACTCCTAGTTGGTG 60.402 57.143 0.00 0.00 38.80 4.17
3820 9231 0.886563 CGACGGAACTCCTAGTTGGT 59.113 55.000 0.00 0.00 38.80 3.67
3821 9232 0.458025 GCGACGGAACTCCTAGTTGG 60.458 60.000 0.00 0.00 38.80 3.77
3822 9233 0.458025 GGCGACGGAACTCCTAGTTG 60.458 60.000 0.00 0.00 38.80 3.16
3823 9234 1.602327 GGGCGACGGAACTCCTAGTT 61.602 60.000 0.00 0.00 41.95 2.24
3824 9235 2.050934 GGGCGACGGAACTCCTAGT 61.051 63.158 0.00 0.00 0.00 2.57
3825 9236 2.050350 TGGGCGACGGAACTCCTAG 61.050 63.158 0.00 0.00 0.00 3.02
3826 9237 2.036098 TGGGCGACGGAACTCCTA 59.964 61.111 0.00 0.00 0.00 2.94
3827 9238 3.692406 GTGGGCGACGGAACTCCT 61.692 66.667 0.00 0.00 0.00 3.69
3845 9256 3.258290 GAGTCTTAGCGCGGCAGC 61.258 66.667 8.83 0.00 40.74 5.25
3846 9257 2.867333 TTCGAGTCTTAGCGCGGCAG 62.867 60.000 8.83 0.00 32.71 4.85
3847 9258 2.985117 TTCGAGTCTTAGCGCGGCA 61.985 57.895 8.83 0.00 32.71 5.69
3848 9259 2.202570 TTCGAGTCTTAGCGCGGC 60.203 61.111 8.83 0.00 32.71 6.53
3849 9260 1.872679 GGTTCGAGTCTTAGCGCGG 60.873 63.158 8.83 0.00 32.71 6.46
3850 9261 2.215604 CGGTTCGAGTCTTAGCGCG 61.216 63.158 0.00 0.00 0.00 6.86
3851 9262 1.872679 CCGGTTCGAGTCTTAGCGC 60.873 63.158 0.00 0.00 0.00 5.92
3852 9263 1.872679 GCCGGTTCGAGTCTTAGCG 60.873 63.158 1.90 0.00 0.00 4.26
3853 9264 1.872679 CGCCGGTTCGAGTCTTAGC 60.873 63.158 1.90 0.00 0.00 3.09
3854 9265 0.381089 ATCGCCGGTTCGAGTCTTAG 59.619 55.000 9.98 0.00 42.14 2.18
3855 9266 0.379669 GATCGCCGGTTCGAGTCTTA 59.620 55.000 9.98 0.00 42.14 2.10
3856 9267 1.139095 GATCGCCGGTTCGAGTCTT 59.861 57.895 9.98 0.00 42.14 3.01
3862 9273 1.140407 GACAAGAGATCGCCGGTTCG 61.140 60.000 1.90 0.00 0.00 3.95
3869 9280 3.987868 TGTAACACAAGACAAGAGATCGC 59.012 43.478 0.00 0.00 0.00 4.58
3875 9286 1.864711 GCGCTGTAACACAAGACAAGA 59.135 47.619 0.00 0.00 0.00 3.02
3876 9287 1.867233 AGCGCTGTAACACAAGACAAG 59.133 47.619 10.39 0.00 0.00 3.16
3877 9288 1.864711 GAGCGCTGTAACACAAGACAA 59.135 47.619 18.48 0.00 0.00 3.18
3918 9329 0.804989 GATCAAACCTCCAAGGCGTG 59.195 55.000 0.00 0.00 39.63 5.34
3920 9331 1.755179 ATGATCAAACCTCCAAGGCG 58.245 50.000 0.00 0.00 39.63 5.52
3921 9332 4.221482 AGAAAATGATCAAACCTCCAAGGC 59.779 41.667 0.00 0.00 39.63 4.35
3922 9333 5.990120 AGAAAATGATCAAACCTCCAAGG 57.010 39.130 0.00 0.00 42.49 3.61
3923 9334 6.976925 GCATAGAAAATGATCAAACCTCCAAG 59.023 38.462 0.00 0.00 0.00 3.61
3927 9338 7.704047 GGAAAGCATAGAAAATGATCAAACCTC 59.296 37.037 0.00 0.00 0.00 3.85
3989 9400 9.460019 AAACAGAAAAGGAAAAATGGAAAATGA 57.540 25.926 0.00 0.00 0.00 2.57
4372 9785 7.817478 ACTCTTTTCAAATTCGGTGAACTTTTT 59.183 29.630 0.00 0.00 34.78 1.94
4378 9791 6.443934 TGAACTCTTTTCAAATTCGGTGAA 57.556 33.333 0.00 0.00 33.21 3.18
4380 9793 6.437928 TGATGAACTCTTTTCAAATTCGGTG 58.562 36.000 0.00 0.00 31.55 4.94
4381 9794 6.633500 TGATGAACTCTTTTCAAATTCGGT 57.367 33.333 0.00 0.00 31.55 4.69
4382 9795 7.928908 TTTGATGAACTCTTTTCAAATTCGG 57.071 32.000 0.00 0.00 34.20 4.30
4395 9808 9.922305 CGAAGTATTTCCTAATTTGATGAACTC 57.078 33.333 0.00 0.00 0.00 3.01
4396 9809 9.449719 ACGAAGTATTTCCTAATTTGATGAACT 57.550 29.630 0.00 0.00 41.94 3.01


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

AutoCloner maintained by Alex Coulton.