Multiple sequence alignment - TraesCS2A01G219500

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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 TraesCS2A01G219500 chr2A 100.000 2393 0 0 1 2393 206909661 206912053 0.000000e+00 4420.0
1 TraesCS2A01G219500 chr2A 87.078 681 81 7 895 1573 303844208 303844883 0.000000e+00 763.0
2 TraesCS2A01G219500 chr2A 91.446 491 35 7 1 486 449884334 449884822 0.000000e+00 667.0
3 TraesCS2A01G219500 chr2A 92.857 42 3 0 1567 1608 706108230 706108189 7.140000e-06 62.1
4 TraesCS2A01G219500 chr2A 92.857 42 3 0 1567 1608 706116264 706116223 7.140000e-06 62.1
5 TraesCS2A01G219500 chr2A 100.000 32 0 0 1567 1598 101346817 101346848 2.570000e-05 60.2
6 TraesCS2A01G219500 chr5A 93.005 1501 81 9 151 1649 96331315 96332793 0.000000e+00 2169.0
7 TraesCS2A01G219500 chr5A 92.355 484 28 9 1 479 528518780 528518301 0.000000e+00 680.0
8 TraesCS2A01G219500 chr5A 81.608 821 95 34 1612 2393 29804690 29805493 1.560000e-176 628.0
9 TraesCS2A01G219500 chr5A 90.816 98 8 1 844 941 484415502 484415406 1.930000e-26 130.0
10 TraesCS2A01G219500 chr5A 84.848 99 14 1 844 942 438828290 438828193 5.440000e-17 99.0
11 TraesCS2A01G219500 chr3A 94.240 1389 57 9 154 1541 220015204 220016570 0.000000e+00 2100.0
12 TraesCS2A01G219500 chr3A 93.466 1408 65 12 154 1557 220023279 220024663 0.000000e+00 2065.0
13 TraesCS2A01G219500 chr3A 88.611 1001 84 15 559 1554 263720887 263719912 0.000000e+00 1190.0
14 TraesCS2A01G219500 chr3A 88.000 1000 94 12 559 1554 263712859 263711882 0.000000e+00 1158.0
15 TraesCS2A01G219500 chr3A 93.204 103 6 1 817 918 626412362 626412464 1.480000e-32 150.0
16 TraesCS2A01G219500 chr3A 86.765 136 16 2 807 941 626415080 626414946 1.480000e-32 150.0
17 TraesCS2A01G219500 chr7A 93.495 907 36 6 154 1059 394424150 394425034 0.000000e+00 1327.0
18 TraesCS2A01G219500 chr7A 93.164 907 40 12 154 1059 394402650 394403535 0.000000e+00 1312.0
19 TraesCS2A01G219500 chr7A 92.449 490 36 1 1162 1650 394425025 394425514 0.000000e+00 699.0
20 TraesCS2A01G219500 chr7A 82.988 241 18 7 686 925 295070999 295070781 1.880000e-46 196.0
21 TraesCS2A01G219500 chr7A 91.228 114 8 1 686 799 295092596 295092485 1.150000e-33 154.0
22 TraesCS2A01G219500 chr7A 94.000 100 4 2 470 567 458627928 458627829 1.480000e-32 150.0
23 TraesCS2A01G219500 chr7A 92.553 94 5 2 459 551 493167157 493167249 1.490000e-27 134.0
24 TraesCS2A01G219500 chr7A 97.015 67 1 1 470 536 478045874 478045939 6.990000e-21 111.0
25 TraesCS2A01G219500 chr7A 84.158 101 15 1 814 914 583011915 583011816 1.960000e-16 97.1
26 TraesCS2A01G219500 chr7A 94.118 51 3 0 630 680 186227067 186227017 7.090000e-11 78.7
27 TraesCS2A01G219500 chr6A 96.292 782 28 1 1612 2393 334576265 334575485 0.000000e+00 1282.0
28 TraesCS2A01G219500 chr6A 96.164 782 30 0 1612 2393 160277228 160278009 0.000000e+00 1279.0
29 TraesCS2A01G219500 chr6A 96.164 782 30 0 1612 2393 334568331 334567550 0.000000e+00 1279.0
30 TraesCS2A01G219500 chr6A 95.780 782 33 0 1612 2393 160284914 160285695 0.000000e+00 1262.0
31 TraesCS2A01G219500 chr6A 94.696 773 38 2 1612 2381 228211385 228210613 0.000000e+00 1197.0
32 TraesCS2A01G219500 chr6A 93.806 775 41 5 1612 2381 228204206 228203434 0.000000e+00 1158.0
33 TraesCS2A01G219500 chr6A 95.211 710 34 0 1684 2393 160303640 160304349 0.000000e+00 1123.0
34 TraesCS2A01G219500 chr6A 91.236 696 44 12 1705 2393 433277704 433277019 0.000000e+00 931.0
35 TraesCS2A01G219500 chr6A 91.092 696 45 12 1705 2393 433266432 433265747 0.000000e+00 926.0
36 TraesCS2A01G219500 chr6A 90.099 101 10 0 816 916 347164517 347164617 5.370000e-27 132.0
37 TraesCS2A01G219500 chr6A 89.109 101 11 0 819 919 264791473 264791373 2.500000e-25 126.0
38 TraesCS2A01G219500 chr2D 84.464 811 92 26 1599 2393 249856619 249857411 0.000000e+00 769.0
39 TraesCS2A01G219500 chr2D 84.444 810 93 25 1599 2393 249848724 249849515 0.000000e+00 767.0
40 TraesCS2A01G219500 chr4A 90.688 494 34 9 1 486 398368546 398368057 0.000000e+00 647.0
41 TraesCS2A01G219500 chr4A 90.688 494 34 9 1 486 398375980 398375491 0.000000e+00 647.0
42 TraesCS2A01G219500 chr4A 95.062 162 6 1 1612 1773 319860769 319860928 1.100000e-63 254.0
43 TraesCS2A01G219500 chr4A 82.264 265 19 8 669 933 378951116 378950880 1.120000e-48 204.0
44 TraesCS2A01G219500 chr4A 93.443 122 8 0 559 680 294135015 294134894 5.250000e-42 182.0
45 TraesCS2A01G219500 chr4A 92.941 85 3 2 1567 1649 166498766 166498683 1.160000e-23 121.0
46 TraesCS2A01G219500 chr4A 92.941 85 3 2 1567 1649 166506980 166506897 1.160000e-23 121.0
47 TraesCS2A01G219500 chr4A 89.583 96 8 1 704 799 287165934 287166027 1.160000e-23 121.0
48 TraesCS2A01G219500 chr4A 94.737 38 2 0 1567 1604 169181408 169181371 2.570000e-05 60.2
49 TraesCS2A01G219500 chr1A 87.594 532 57 8 1029 1554 428859048 428859576 2.030000e-170 608.0
50 TraesCS2A01G219500 chr1A 86.225 559 68 9 1029 1582 163669334 163668780 4.400000e-167 597.0
51 TraesCS2A01G219500 chr1A 91.089 101 9 0 816 916 206350575 206350675 1.150000e-28 137.0
52 TraesCS2A01G219500 chr1A 91.250 80 5 2 470 549 60368115 60368038 9.050000e-20 108.0
53 TraesCS2A01G219500 chr1A 92.308 39 1 2 511 549 259141621 259141585 1.000000e-03 54.7


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 TraesCS2A01G219500 chr2A 206909661 206912053 2392 False 4420 4420 100.000 1 2393 1 chr2A.!!$F2 2392
1 TraesCS2A01G219500 chr2A 303844208 303844883 675 False 763 763 87.078 895 1573 1 chr2A.!!$F3 678
2 TraesCS2A01G219500 chr5A 96331315 96332793 1478 False 2169 2169 93.005 151 1649 1 chr5A.!!$F2 1498
3 TraesCS2A01G219500 chr5A 29804690 29805493 803 False 628 628 81.608 1612 2393 1 chr5A.!!$F1 781
4 TraesCS2A01G219500 chr3A 220015204 220016570 1366 False 2100 2100 94.240 154 1541 1 chr3A.!!$F1 1387
5 TraesCS2A01G219500 chr3A 220023279 220024663 1384 False 2065 2065 93.466 154 1557 1 chr3A.!!$F2 1403
6 TraesCS2A01G219500 chr3A 263719912 263720887 975 True 1190 1190 88.611 559 1554 1 chr3A.!!$R2 995
7 TraesCS2A01G219500 chr3A 263711882 263712859 977 True 1158 1158 88.000 559 1554 1 chr3A.!!$R1 995
8 TraesCS2A01G219500 chr7A 394402650 394403535 885 False 1312 1312 93.164 154 1059 1 chr7A.!!$F1 905
9 TraesCS2A01G219500 chr7A 394424150 394425514 1364 False 1013 1327 92.972 154 1650 2 chr7A.!!$F4 1496
10 TraesCS2A01G219500 chr6A 334575485 334576265 780 True 1282 1282 96.292 1612 2393 1 chr6A.!!$R5 781
11 TraesCS2A01G219500 chr6A 160277228 160278009 781 False 1279 1279 96.164 1612 2393 1 chr6A.!!$F1 781
12 TraesCS2A01G219500 chr6A 334567550 334568331 781 True 1279 1279 96.164 1612 2393 1 chr6A.!!$R4 781
13 TraesCS2A01G219500 chr6A 160284914 160285695 781 False 1262 1262 95.780 1612 2393 1 chr6A.!!$F2 781
14 TraesCS2A01G219500 chr6A 228210613 228211385 772 True 1197 1197 94.696 1612 2381 1 chr6A.!!$R2 769
15 TraesCS2A01G219500 chr6A 228203434 228204206 772 True 1158 1158 93.806 1612 2381 1 chr6A.!!$R1 769
16 TraesCS2A01G219500 chr6A 160303640 160304349 709 False 1123 1123 95.211 1684 2393 1 chr6A.!!$F3 709
17 TraesCS2A01G219500 chr6A 433277019 433277704 685 True 931 931 91.236 1705 2393 1 chr6A.!!$R7 688
18 TraesCS2A01G219500 chr6A 433265747 433266432 685 True 926 926 91.092 1705 2393 1 chr6A.!!$R6 688
19 TraesCS2A01G219500 chr2D 249856619 249857411 792 False 769 769 84.464 1599 2393 1 chr2D.!!$F2 794
20 TraesCS2A01G219500 chr2D 249848724 249849515 791 False 767 767 84.444 1599 2393 1 chr2D.!!$F1 794
21 TraesCS2A01G219500 chr1A 428859048 428859576 528 False 608 608 87.594 1029 1554 1 chr1A.!!$F2 525
22 TraesCS2A01G219500 chr1A 163668780 163669334 554 True 597 597 86.225 1029 1582 1 chr1A.!!$R2 553

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
156 157 0.610785 TTTTCCCCATGCCTTCGTCC 60.611 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 1855 1.137479 ACGAGGAACTTGACGTCCAAA 59.863 47.619 14.12 0.04 44.22 3.28 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
21 22 2.077687 ATGGCATGGACCTTTGATCC 57.922 50.000 0.00 0.00 36.70 3.36
30 31 5.993748 TGGACCTTTGATCCATTTAAACC 57.006 39.130 0.00 0.00 41.47 3.27
31 32 5.398236 TGGACCTTTGATCCATTTAAACCA 58.602 37.500 0.00 0.00 41.47 3.67
32 33 5.841237 TGGACCTTTGATCCATTTAAACCAA 59.159 36.000 0.00 0.00 41.47 3.67
33 34 6.014669 TGGACCTTTGATCCATTTAAACCAAG 60.015 38.462 0.00 0.00 41.47 3.61
34 35 6.358974 ACCTTTGATCCATTTAAACCAAGG 57.641 37.500 0.00 0.00 0.00 3.61
35 36 5.248248 ACCTTTGATCCATTTAAACCAAGGG 59.752 40.000 9.21 0.00 36.98 3.95
36 37 5.483583 CCTTTGATCCATTTAAACCAAGGGA 59.516 40.000 0.00 0.00 34.09 4.20
37 38 6.013812 CCTTTGATCCATTTAAACCAAGGGAA 60.014 38.462 0.00 0.00 34.09 3.97
38 39 7.311234 CCTTTGATCCATTTAAACCAAGGGAAT 60.311 37.037 0.00 0.00 34.09 3.01
39 40 7.566658 TTGATCCATTTAAACCAAGGGAATT 57.433 32.000 0.00 0.00 0.00 2.17
40 41 7.181569 TGATCCATTTAAACCAAGGGAATTC 57.818 36.000 0.00 0.00 0.00 2.17
41 42 6.728164 TGATCCATTTAAACCAAGGGAATTCA 59.272 34.615 7.93 0.00 0.00 2.57
42 43 6.353404 TCCATTTAAACCAAGGGAATTCAC 57.647 37.500 7.93 3.01 0.00 3.18
43 44 5.247337 TCCATTTAAACCAAGGGAATTCACC 59.753 40.000 3.45 4.47 0.00 4.02
44 45 5.248248 CCATTTAAACCAAGGGAATTCACCT 59.752 40.000 3.45 6.87 40.96 4.00
45 46 5.799827 TTTAAACCAAGGGAATTCACCTG 57.200 39.130 14.10 7.67 38.63 4.00
46 47 2.309136 AACCAAGGGAATTCACCTGG 57.691 50.000 21.67 21.67 38.63 4.45
47 48 1.158007 ACCAAGGGAATTCACCTGGT 58.842 50.000 22.98 22.98 38.63 4.00
48 49 1.203050 ACCAAGGGAATTCACCTGGTG 60.203 52.381 26.87 20.86 37.79 4.17
49 50 1.075374 CCAAGGGAATTCACCTGGTGA 59.925 52.381 25.12 25.12 41.09 4.02
50 51 2.162681 CAAGGGAATTCACCTGGTGAC 58.837 52.381 28.35 17.00 42.60 3.67
51 52 1.747444 AGGGAATTCACCTGGTGACT 58.253 50.000 28.35 20.71 42.60 3.41
52 53 2.065799 AGGGAATTCACCTGGTGACTT 58.934 47.619 28.35 27.34 42.60 3.01
53 54 2.040412 AGGGAATTCACCTGGTGACTTC 59.960 50.000 34.38 34.38 45.27 3.01
54 55 2.040412 GGGAATTCACCTGGTGACTTCT 59.960 50.000 37.24 21.99 45.30 2.85
55 56 3.339141 GGAATTCACCTGGTGACTTCTC 58.661 50.000 37.24 29.00 45.30 2.87
56 57 3.008485 GGAATTCACCTGGTGACTTCTCT 59.992 47.826 37.24 19.27 45.30 3.10
57 58 4.505742 GGAATTCACCTGGTGACTTCTCTT 60.506 45.833 37.24 22.32 45.30 2.85
58 59 4.713792 ATTCACCTGGTGACTTCTCTTT 57.286 40.909 28.35 4.32 42.60 2.52
59 60 5.825593 ATTCACCTGGTGACTTCTCTTTA 57.174 39.130 28.35 11.50 42.60 1.85
60 61 5.825593 TTCACCTGGTGACTTCTCTTTAT 57.174 39.130 28.35 0.00 42.60 1.40
61 62 6.928348 TTCACCTGGTGACTTCTCTTTATA 57.072 37.500 28.35 7.17 42.60 0.98
62 63 6.928348 TCACCTGGTGACTTCTCTTTATAA 57.072 37.500 25.12 0.00 37.67 0.98
63 64 6.698380 TCACCTGGTGACTTCTCTTTATAAC 58.302 40.000 25.12 0.00 37.67 1.89
64 65 6.269077 TCACCTGGTGACTTCTCTTTATAACA 59.731 38.462 25.12 0.00 37.67 2.41
65 66 7.038302 TCACCTGGTGACTTCTCTTTATAACAT 60.038 37.037 25.12 0.00 37.67 2.71
66 67 8.258007 CACCTGGTGACTTCTCTTTATAACATA 58.742 37.037 22.33 0.00 35.23 2.29
67 68 8.258708 ACCTGGTGACTTCTCTTTATAACATAC 58.741 37.037 0.00 0.00 0.00 2.39
68 69 7.711339 CCTGGTGACTTCTCTTTATAACATACC 59.289 40.741 0.00 0.00 0.00 2.73
69 70 7.562135 TGGTGACTTCTCTTTATAACATACCC 58.438 38.462 0.00 0.00 0.00 3.69
70 71 7.402071 TGGTGACTTCTCTTTATAACATACCCT 59.598 37.037 0.00 0.00 0.00 4.34
71 72 7.927092 GGTGACTTCTCTTTATAACATACCCTC 59.073 40.741 0.00 0.00 0.00 4.30
72 73 7.927092 GTGACTTCTCTTTATAACATACCCTCC 59.073 40.741 0.00 0.00 0.00 4.30
73 74 7.070821 TGACTTCTCTTTATAACATACCCTCCC 59.929 40.741 0.00 0.00 0.00 4.30
74 75 6.041751 ACTTCTCTTTATAACATACCCTCCCG 59.958 42.308 0.00 0.00 0.00 5.14
75 76 5.708544 TCTCTTTATAACATACCCTCCCGA 58.291 41.667 0.00 0.00 0.00 5.14
76 77 6.320518 TCTCTTTATAACATACCCTCCCGAT 58.679 40.000 0.00 0.00 0.00 4.18
77 78 7.472741 TCTCTTTATAACATACCCTCCCGATA 58.527 38.462 0.00 0.00 0.00 2.92
78 79 7.614583 TCTCTTTATAACATACCCTCCCGATAG 59.385 40.741 0.00 0.00 0.00 2.08
79 80 7.243824 TCTTTATAACATACCCTCCCGATAGT 58.756 38.462 0.00 0.00 0.00 2.12
80 81 8.393259 TCTTTATAACATACCCTCCCGATAGTA 58.607 37.037 0.00 0.00 0.00 1.82
81 82 8.585471 TTTATAACATACCCTCCCGATAGTAG 57.415 38.462 0.00 0.00 0.00 2.57
82 83 3.453059 ACATACCCTCCCGATAGTAGG 57.547 52.381 0.00 0.00 37.16 3.18
124 125 8.993404 TCCAATTATGTGGAATTATCATCACA 57.007 30.769 0.00 0.00 44.91 3.58
125 126 8.849168 TCCAATTATGTGGAATTATCATCACAC 58.151 33.333 0.00 0.00 44.91 3.82
126 127 8.631797 CCAATTATGTGGAATTATCATCACACA 58.368 33.333 0.00 0.00 41.96 3.72
127 128 9.454585 CAATTATGTGGAATTATCATCACACAC 57.545 33.333 0.00 0.00 41.96 3.82
128 129 8.985315 ATTATGTGGAATTATCATCACACACT 57.015 30.769 0.00 0.00 41.96 3.55
129 130 8.806429 TTATGTGGAATTATCATCACACACTT 57.194 30.769 0.00 0.00 41.96 3.16
130 131 6.499234 TGTGGAATTATCATCACACACTTG 57.501 37.500 0.00 0.00 35.52 3.16
131 132 5.106197 TGTGGAATTATCATCACACACTTGC 60.106 40.000 0.00 0.00 35.52 4.01
132 133 5.008980 TGGAATTATCATCACACACTTGCA 58.991 37.500 0.00 0.00 0.00 4.08
133 134 5.476254 TGGAATTATCATCACACACTTGCAA 59.524 36.000 0.00 0.00 0.00 4.08
134 135 6.015603 TGGAATTATCATCACACACTTGCAAA 60.016 34.615 0.00 0.00 0.00 3.68
135 136 7.037438 GGAATTATCATCACACACTTGCAAAT 58.963 34.615 0.00 0.00 0.00 2.32
136 137 8.190122 GGAATTATCATCACACACTTGCAAATA 58.810 33.333 0.00 0.00 0.00 1.40
137 138 9.740239 GAATTATCATCACACACTTGCAAATAT 57.260 29.630 0.00 0.00 0.00 1.28
140 141 9.926158 TTATCATCACACACTTGCAAATATTTT 57.074 25.926 0.00 0.00 0.00 1.82
141 142 7.872163 TCATCACACACTTGCAAATATTTTC 57.128 32.000 0.00 0.00 0.00 2.29
142 143 6.867816 TCATCACACACTTGCAAATATTTTCC 59.132 34.615 0.00 0.00 0.00 3.13
143 144 5.537188 TCACACACTTGCAAATATTTTCCC 58.463 37.500 0.00 0.00 0.00 3.97
144 145 4.690280 CACACACTTGCAAATATTTTCCCC 59.310 41.667 0.00 0.00 0.00 4.81
145 146 4.346418 ACACACTTGCAAATATTTTCCCCA 59.654 37.500 0.00 0.00 0.00 4.96
146 147 5.012975 ACACACTTGCAAATATTTTCCCCAT 59.987 36.000 0.00 0.00 0.00 4.00
147 148 5.352016 CACACTTGCAAATATTTTCCCCATG 59.648 40.000 0.00 0.00 0.00 3.66
148 149 4.333372 CACTTGCAAATATTTTCCCCATGC 59.667 41.667 0.00 0.00 0.00 4.06
149 150 3.557228 TGCAAATATTTTCCCCATGCC 57.443 42.857 0.00 0.00 0.00 4.40
150 151 3.113824 TGCAAATATTTTCCCCATGCCT 58.886 40.909 0.00 0.00 0.00 4.75
151 152 3.522750 TGCAAATATTTTCCCCATGCCTT 59.477 39.130 0.00 0.00 0.00 4.35
152 153 4.129380 GCAAATATTTTCCCCATGCCTTC 58.871 43.478 0.00 0.00 0.00 3.46
153 154 4.370917 CAAATATTTTCCCCATGCCTTCG 58.629 43.478 0.00 0.00 0.00 3.79
154 155 2.818751 TATTTTCCCCATGCCTTCGT 57.181 45.000 0.00 0.00 0.00 3.85
155 156 1.474330 ATTTTCCCCATGCCTTCGTC 58.526 50.000 0.00 0.00 0.00 4.20
156 157 0.610785 TTTTCCCCATGCCTTCGTCC 60.611 55.000 0.00 0.00 0.00 4.79
157 158 2.493273 TTTCCCCATGCCTTCGTCCC 62.493 60.000 0.00 0.00 0.00 4.46
158 159 3.727258 CCCCATGCCTTCGTCCCA 61.727 66.667 0.00 0.00 0.00 4.37
159 160 2.597340 CCCATGCCTTCGTCCCAT 59.403 61.111 0.00 0.00 0.00 4.00
218 219 8.986991 CCTATAAATTCTAGACTATGCCAGGAT 58.013 37.037 0.00 0.00 0.00 3.24
246 247 5.891198 TCCTCCAATTTTCAGATCCTTTGA 58.109 37.500 0.00 0.00 0.00 2.69
727 731 1.602771 GACCCCTTTTCCTCCCGAG 59.397 63.158 0.00 0.00 0.00 4.63
763 767 3.854669 CCAGCTCCTCCCGCGAAT 61.855 66.667 8.23 0.00 0.00 3.34
839 843 2.528818 CCTTCCTCCCAGCACCACA 61.529 63.158 0.00 0.00 0.00 4.17
871 875 1.997874 GCCTCCTCACCTCCCATGT 60.998 63.158 0.00 0.00 0.00 3.21
879 883 1.685765 ACCTCCCATGTCGCTGCTA 60.686 57.895 0.00 0.00 0.00 3.49
1292 1410 2.668212 CGGCCGTCTGCAGGAAAA 60.668 61.111 19.50 0.00 43.89 2.29
1400 1521 3.846588 AGTTCTTTTCCATAGGCCTCTCA 59.153 43.478 9.68 0.00 0.00 3.27
1402 1523 4.494091 TCTTTTCCATAGGCCTCTCAAG 57.506 45.455 9.68 4.58 0.00 3.02
1445 1566 5.317733 TGTTTGTGGATTTCGTCAAGTTT 57.682 34.783 0.00 0.00 0.00 2.66
1500 1621 1.531423 TCTAGGACGCGACAAGTTCT 58.469 50.000 15.93 0.66 0.00 3.01
1532 1654 6.467723 AAAAACGTCTATATGATGATCCGC 57.532 37.500 0.00 0.00 35.71 5.54
1912 2060 5.679792 CGAATGCATGTGTTGTATGAGATTG 59.320 40.000 0.00 0.00 30.30 2.67
2017 2178 0.877649 CTAGCATGTTCCGCGCATCT 60.878 55.000 8.75 1.98 0.00 2.90
2093 2257 1.067985 TCGTGGCACCGTTATCGTTAA 60.068 47.619 12.86 0.00 35.01 2.01
2116 2280 2.494530 GCCGTGGCACCCTTTTTCA 61.495 57.895 12.86 0.00 41.49 2.69
2145 2309 4.320861 CCACGGTGACAAATGCTTCATAAA 60.321 41.667 10.28 0.00 0.00 1.40
2152 2316 5.801444 TGACAAATGCTTCATAAAATGCTCG 59.199 36.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.292389 TGGATCAAAGGTCCATGCCATT 60.292 45.455 0.00 0.00 40.72 3.16
3 4 0.703488 TGGATCAAAGGTCCATGCCA 59.297 50.000 0.00 0.00 40.72 4.92
4 5 3.594453 TGGATCAAAGGTCCATGCC 57.406 52.632 0.00 0.00 40.72 4.40
9 10 5.993748 TGGTTTAAATGGATCAAAGGTCC 57.006 39.130 0.00 0.00 36.26 4.46
12 13 5.483583 TCCCTTGGTTTAAATGGATCAAAGG 59.516 40.000 0.00 3.07 0.00 3.11
13 14 6.603940 TCCCTTGGTTTAAATGGATCAAAG 57.396 37.500 0.00 0.00 0.00 2.77
14 15 7.566658 ATTCCCTTGGTTTAAATGGATCAAA 57.433 32.000 0.00 0.00 0.00 2.69
15 16 7.236432 TGAATTCCCTTGGTTTAAATGGATCAA 59.764 33.333 2.27 0.00 0.00 2.57
16 17 6.728164 TGAATTCCCTTGGTTTAAATGGATCA 59.272 34.615 2.27 0.00 0.00 2.92
17 18 7.041721 GTGAATTCCCTTGGTTTAAATGGATC 58.958 38.462 2.27 0.00 0.00 3.36
18 19 6.070251 GGTGAATTCCCTTGGTTTAAATGGAT 60.070 38.462 2.27 0.00 0.00 3.41
19 20 5.247337 GGTGAATTCCCTTGGTTTAAATGGA 59.753 40.000 2.27 0.00 0.00 3.41
20 21 5.248248 AGGTGAATTCCCTTGGTTTAAATGG 59.752 40.000 2.27 0.00 0.00 3.16
21 22 6.165577 CAGGTGAATTCCCTTGGTTTAAATG 58.834 40.000 11.53 0.00 0.00 2.32
22 23 5.248248 CCAGGTGAATTCCCTTGGTTTAAAT 59.752 40.000 10.41 0.00 0.00 1.40
23 24 4.591072 CCAGGTGAATTCCCTTGGTTTAAA 59.409 41.667 10.41 0.00 0.00 1.52
24 25 4.156477 CCAGGTGAATTCCCTTGGTTTAA 58.844 43.478 10.41 0.00 0.00 1.52
25 26 3.141272 ACCAGGTGAATTCCCTTGGTTTA 59.859 43.478 17.22 0.00 32.81 2.01
26 27 2.090775 ACCAGGTGAATTCCCTTGGTTT 60.091 45.455 17.22 0.00 32.81 3.27
27 28 1.503347 ACCAGGTGAATTCCCTTGGTT 59.497 47.619 17.22 4.15 32.81 3.67
28 29 1.158007 ACCAGGTGAATTCCCTTGGT 58.842 50.000 17.22 17.22 32.24 3.67
29 30 1.075374 TCACCAGGTGAATTCCCTTGG 59.925 52.381 20.84 15.97 39.78 3.61
30 31 2.162681 GTCACCAGGTGAATTCCCTTG 58.837 52.381 24.65 11.03 44.49 3.61
31 32 2.065799 AGTCACCAGGTGAATTCCCTT 58.934 47.619 24.65 1.54 44.49 3.95
32 33 1.747444 AGTCACCAGGTGAATTCCCT 58.253 50.000 24.65 13.52 44.49 4.20
33 34 2.586648 AAGTCACCAGGTGAATTCCC 57.413 50.000 26.36 13.38 45.58 3.97
37 38 4.713792 AAAGAGAAGTCACCAGGTGAAT 57.286 40.909 24.65 20.87 44.49 2.57
38 39 5.825593 ATAAAGAGAAGTCACCAGGTGAA 57.174 39.130 24.65 5.54 44.49 3.18
39 40 6.269077 TGTTATAAAGAGAAGTCACCAGGTGA 59.731 38.462 19.21 19.21 40.50 4.02
40 41 6.464222 TGTTATAAAGAGAAGTCACCAGGTG 58.536 40.000 14.19 14.19 34.45 4.00
41 42 6.681729 TGTTATAAAGAGAAGTCACCAGGT 57.318 37.500 0.00 0.00 0.00 4.00
42 43 7.711339 GGTATGTTATAAAGAGAAGTCACCAGG 59.289 40.741 0.00 0.00 0.00 4.45
43 44 7.711339 GGGTATGTTATAAAGAGAAGTCACCAG 59.289 40.741 0.00 0.00 0.00 4.00
44 45 7.402071 AGGGTATGTTATAAAGAGAAGTCACCA 59.598 37.037 0.00 0.00 0.00 4.17
45 46 7.793036 AGGGTATGTTATAAAGAGAAGTCACC 58.207 38.462 0.00 0.00 0.00 4.02
46 47 7.927092 GGAGGGTATGTTATAAAGAGAAGTCAC 59.073 40.741 0.00 0.00 0.00 3.67
47 48 7.070821 GGGAGGGTATGTTATAAAGAGAAGTCA 59.929 40.741 0.00 0.00 0.00 3.41
48 49 7.443477 GGGAGGGTATGTTATAAAGAGAAGTC 58.557 42.308 0.00 0.00 0.00 3.01
49 50 6.041751 CGGGAGGGTATGTTATAAAGAGAAGT 59.958 42.308 0.00 0.00 0.00 3.01
50 51 6.267014 TCGGGAGGGTATGTTATAAAGAGAAG 59.733 42.308 0.00 0.00 0.00 2.85
51 52 6.138263 TCGGGAGGGTATGTTATAAAGAGAA 58.862 40.000 0.00 0.00 0.00 2.87
52 53 5.708544 TCGGGAGGGTATGTTATAAAGAGA 58.291 41.667 0.00 0.00 0.00 3.10
53 54 6.607004 ATCGGGAGGGTATGTTATAAAGAG 57.393 41.667 0.00 0.00 0.00 2.85
54 55 7.243824 ACTATCGGGAGGGTATGTTATAAAGA 58.756 38.462 0.00 0.00 0.00 2.52
55 56 7.477945 ACTATCGGGAGGGTATGTTATAAAG 57.522 40.000 0.00 0.00 0.00 1.85
56 57 7.616935 CCTACTATCGGGAGGGTATGTTATAAA 59.383 40.741 0.00 0.00 0.00 1.40
57 58 7.121382 CCTACTATCGGGAGGGTATGTTATAA 58.879 42.308 0.00 0.00 0.00 0.98
58 59 6.354213 CCCTACTATCGGGAGGGTATGTTATA 60.354 46.154 4.81 0.00 44.42 0.98
59 60 5.516984 CCTACTATCGGGAGGGTATGTTAT 58.483 45.833 0.00 0.00 0.00 1.89
60 61 4.264083 CCCTACTATCGGGAGGGTATGTTA 60.264 50.000 4.81 0.00 44.42 2.41
61 62 3.501751 CCCTACTATCGGGAGGGTATGTT 60.502 52.174 4.81 0.00 44.42 2.71
62 63 2.042706 CCCTACTATCGGGAGGGTATGT 59.957 54.545 4.81 0.00 44.42 2.29
63 64 2.736347 CCCTACTATCGGGAGGGTATG 58.264 57.143 4.81 0.00 44.42 2.39
71 72 7.893124 TTTAATATAGCTCCCTACTATCGGG 57.107 40.000 0.00 0.00 43.38 5.14
99 100 8.849168 GTGTGATGATAATTCCACATAATTGGA 58.151 33.333 0.00 0.00 44.39 3.53
100 101 8.631797 TGTGTGATGATAATTCCACATAATTGG 58.368 33.333 0.00 0.00 40.94 3.16
101 102 9.454585 GTGTGTGATGATAATTCCACATAATTG 57.545 33.333 0.00 0.00 40.94 2.32
102 103 9.412460 AGTGTGTGATGATAATTCCACATAATT 57.588 29.630 0.00 0.00 40.94 1.40
103 104 8.985315 AGTGTGTGATGATAATTCCACATAAT 57.015 30.769 0.00 0.00 40.94 1.28
104 105 8.676401 CAAGTGTGTGATGATAATTCCACATAA 58.324 33.333 0.00 0.00 40.94 1.90
105 106 7.201723 GCAAGTGTGTGATGATAATTCCACATA 60.202 37.037 0.00 0.00 40.94 2.29
106 107 6.405065 GCAAGTGTGTGATGATAATTCCACAT 60.405 38.462 0.00 0.00 40.94 3.21
107 108 5.106197 GCAAGTGTGTGATGATAATTCCACA 60.106 40.000 0.00 0.00 37.21 4.17
108 109 5.106197 TGCAAGTGTGTGATGATAATTCCAC 60.106 40.000 0.00 0.00 0.00 4.02
109 110 5.008980 TGCAAGTGTGTGATGATAATTCCA 58.991 37.500 0.00 0.00 0.00 3.53
110 111 5.565592 TGCAAGTGTGTGATGATAATTCC 57.434 39.130 0.00 0.00 0.00 3.01
111 112 9.740239 ATATTTGCAAGTGTGTGATGATAATTC 57.260 29.630 4.47 0.00 0.00 2.17
114 115 9.926158 AAAATATTTGCAAGTGTGTGATGATAA 57.074 25.926 4.47 0.00 0.00 1.75
115 116 9.571810 GAAAATATTTGCAAGTGTGTGATGATA 57.428 29.630 4.47 0.00 0.00 2.15
116 117 7.546667 GGAAAATATTTGCAAGTGTGTGATGAT 59.453 33.333 8.47 0.00 0.00 2.45
117 118 6.867816 GGAAAATATTTGCAAGTGTGTGATGA 59.132 34.615 8.47 0.00 0.00 2.92
118 119 6.091169 GGGAAAATATTTGCAAGTGTGTGATG 59.909 38.462 8.47 0.00 0.00 3.07
119 120 6.165577 GGGAAAATATTTGCAAGTGTGTGAT 58.834 36.000 8.47 0.00 0.00 3.06
120 121 5.510520 GGGGAAAATATTTGCAAGTGTGTGA 60.511 40.000 8.47 0.00 0.00 3.58
121 122 4.690280 GGGGAAAATATTTGCAAGTGTGTG 59.310 41.667 8.47 0.00 0.00 3.82
122 123 4.346418 TGGGGAAAATATTTGCAAGTGTGT 59.654 37.500 8.47 0.00 0.00 3.72
123 124 4.892433 TGGGGAAAATATTTGCAAGTGTG 58.108 39.130 8.47 0.00 0.00 3.82
124 125 5.490159 CATGGGGAAAATATTTGCAAGTGT 58.510 37.500 8.47 0.00 0.00 3.55
125 126 4.333372 GCATGGGGAAAATATTTGCAAGTG 59.667 41.667 8.47 2.90 0.00 3.16
126 127 4.516323 GCATGGGGAAAATATTTGCAAGT 58.484 39.130 8.47 0.00 0.00 3.16
127 128 3.878699 GGCATGGGGAAAATATTTGCAAG 59.121 43.478 8.47 0.00 0.00 4.01
128 129 3.522750 AGGCATGGGGAAAATATTTGCAA 59.477 39.130 8.47 0.00 0.00 4.08
129 130 3.113824 AGGCATGGGGAAAATATTTGCA 58.886 40.909 8.47 0.00 0.00 4.08
130 131 3.843893 AGGCATGGGGAAAATATTTGC 57.156 42.857 0.39 0.00 0.00 3.68
131 132 4.141959 ACGAAGGCATGGGGAAAATATTTG 60.142 41.667 0.39 0.00 0.00 2.32
132 133 4.030216 ACGAAGGCATGGGGAAAATATTT 58.970 39.130 0.00 0.00 0.00 1.40
133 134 3.636764 GACGAAGGCATGGGGAAAATATT 59.363 43.478 0.00 0.00 0.00 1.28
134 135 3.222603 GACGAAGGCATGGGGAAAATAT 58.777 45.455 0.00 0.00 0.00 1.28
135 136 2.650322 GACGAAGGCATGGGGAAAATA 58.350 47.619 0.00 0.00 0.00 1.40
136 137 1.474330 GACGAAGGCATGGGGAAAAT 58.526 50.000 0.00 0.00 0.00 1.82
137 138 0.610785 GGACGAAGGCATGGGGAAAA 60.611 55.000 0.00 0.00 0.00 2.29
138 139 1.001393 GGACGAAGGCATGGGGAAA 60.001 57.895 0.00 0.00 0.00 3.13
139 140 2.674754 GGACGAAGGCATGGGGAA 59.325 61.111 0.00 0.00 0.00 3.97
140 141 3.407967 GGGACGAAGGCATGGGGA 61.408 66.667 0.00 0.00 0.00 4.81
141 142 2.572333 AATGGGACGAAGGCATGGGG 62.572 60.000 0.00 0.00 0.00 4.96
142 143 0.684153 AAATGGGACGAAGGCATGGG 60.684 55.000 0.00 0.00 0.00 4.00
143 144 1.185315 AAAATGGGACGAAGGCATGG 58.815 50.000 0.00 0.00 0.00 3.66
144 145 2.417243 GGAAAAATGGGACGAAGGCATG 60.417 50.000 0.00 0.00 0.00 4.06
145 146 1.824852 GGAAAAATGGGACGAAGGCAT 59.175 47.619 0.00 0.00 0.00 4.40
146 147 1.253100 GGAAAAATGGGACGAAGGCA 58.747 50.000 0.00 0.00 0.00 4.75
147 148 0.530744 GGGAAAAATGGGACGAAGGC 59.469 55.000 0.00 0.00 0.00 4.35
148 149 1.182667 GGGGAAAAATGGGACGAAGG 58.817 55.000 0.00 0.00 0.00 3.46
149 150 2.215942 AGGGGAAAAATGGGACGAAG 57.784 50.000 0.00 0.00 0.00 3.79
150 151 2.109304 AGAAGGGGAAAAATGGGACGAA 59.891 45.455 0.00 0.00 0.00 3.85
151 152 1.708551 AGAAGGGGAAAAATGGGACGA 59.291 47.619 0.00 0.00 0.00 4.20
152 153 2.092323 GAGAAGGGGAAAAATGGGACG 58.908 52.381 0.00 0.00 0.00 4.79
153 154 3.458044 AGAGAAGGGGAAAAATGGGAC 57.542 47.619 0.00 0.00 0.00 4.46
154 155 5.813965 AATAGAGAAGGGGAAAAATGGGA 57.186 39.130 0.00 0.00 0.00 4.37
155 156 7.565029 ACATTAATAGAGAAGGGGAAAAATGGG 59.435 37.037 0.00 0.00 0.00 4.00
156 157 8.539117 ACATTAATAGAGAAGGGGAAAAATGG 57.461 34.615 0.00 0.00 0.00 3.16
157 158 8.633561 GGACATTAATAGAGAAGGGGAAAAATG 58.366 37.037 0.00 0.00 0.00 2.32
158 159 8.343787 TGGACATTAATAGAGAAGGGGAAAAAT 58.656 33.333 0.00 0.00 0.00 1.82
159 160 7.704727 TGGACATTAATAGAGAAGGGGAAAAA 58.295 34.615 0.00 0.00 0.00 1.94
218 219 4.324563 GGATCTGAAAATTGGAGGAGGTGA 60.325 45.833 0.00 0.00 0.00 4.02
246 247 7.751768 TTTTTGAATCCAACCAAAACAAGTT 57.248 28.000 0.00 0.00 40.60 2.66
309 310 7.872993 TGGTTTGGCGATATTTTAGAGATAGAG 59.127 37.037 0.00 0.00 0.00 2.43
355 356 2.463589 ATTCTTGGAGCGCCGGAACA 62.464 55.000 5.05 0.00 36.79 3.18
578 581 4.338710 GGTTACAGCGGGGGTGCA 62.339 66.667 0.00 0.00 37.31 4.57
988 992 4.148825 GGCCATGAGAGACGCGGT 62.149 66.667 12.47 0.00 0.00 5.68
1201 1316 1.539665 GAGGGAGGAGGTCGAGGAT 59.460 63.158 0.00 0.00 0.00 3.24
1369 1490 6.447162 CCTATGGAAAAGAACTTGGTGAAAC 58.553 40.000 0.00 0.00 0.00 2.78
1400 1521 2.826777 CTTGGCGCATCCTGGTCCTT 62.827 60.000 10.83 0.00 35.26 3.36
1402 1523 2.825836 CTTGGCGCATCCTGGTCC 60.826 66.667 10.83 0.00 35.26 4.46
1445 1566 1.945819 GCCCTCATTCAACGAAGCTCA 60.946 52.381 0.00 0.00 0.00 4.26
1532 1654 2.752322 TTCGGTGCGACGGTACTTGG 62.752 60.000 0.00 0.00 34.89 3.61
1733 1855 1.137479 ACGAGGAACTTGACGTCCAAA 59.863 47.619 14.12 0.04 44.22 3.28
1912 2060 1.579429 GGACATGGTGCAAACGGTC 59.421 57.895 0.00 0.00 0.00 4.79
2017 2178 3.493028 TGCAAAGGAGAAGTGTGCA 57.507 47.368 0.00 0.00 42.62 4.57
2116 2280 1.885887 CATTTGTCACCGTGGTGGAAT 59.114 47.619 18.47 12.94 45.43 3.01
2368 2549 2.564062 CACTCCCGGTTAGGTACTCAAA 59.436 50.000 0.00 0.00 41.75 2.69


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

AutoCloner maintained by Alex Coulton.