Multiple sequence alignment - TraesCS1A01G004400

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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 TraesCS1A01G004400 chr1A 100.000 7141 0 0 1 7141 2648820 2641680 0.000000e+00 13188.0
1 TraesCS1A01G004400 chr1A 81.232 1071 127 22 3719 4755 2656917 2655887 0.000000e+00 797.0
2 TraesCS1A01G004400 chr1A 88.732 568 49 9 6315 6867 2695342 2694775 0.000000e+00 680.0
3 TraesCS1A01G004400 chr1A 84.862 687 67 10 3722 4391 2840997 2840331 0.000000e+00 658.0
4 TraesCS1A01G004400 chr1A 79.556 900 130 32 1734 2622 2843035 2842179 1.720000e-165 593.0
5 TraesCS1A01G004400 chr1A 84.452 566 49 21 5018 5575 2839469 2838935 8.210000e-144 521.0
6 TraesCS1A01G004400 chr1A 84.632 462 43 11 1000 1453 2843855 2843414 1.100000e-117 435.0
7 TraesCS1A01G004400 chr1A 85.680 419 50 8 4750 5163 2655670 2655257 3.960000e-117 433.0
8 TraesCS1A01G004400 chr1A 78.303 613 83 18 2882 3446 2657983 2657373 4.100000e-92 350.0
9 TraesCS1A01G004400 chr1A 84.127 378 33 9 2632 2991 2842049 2841681 2.470000e-89 340.0
10 TraesCS1A01G004400 chr1A 88.511 235 26 1 5993 6226 2653338 2653104 4.220000e-72 283.0
11 TraesCS1A01G004400 chr1A 87.568 185 19 2 5815 5999 2837470 2837290 2.020000e-50 211.0
12 TraesCS1A01G004400 chr1A 86.047 172 21 3 3439 3610 2841370 2841202 1.580000e-41 182.0
13 TraesCS1A01G004400 chr1A 82.069 145 15 6 3583 3716 2841203 2841059 5.850000e-21 113.0
14 TraesCS1A01G004400 chr6D 97.537 2883 63 5 3438 6318 472499637 472496761 0.000000e+00 4924.0
15 TraesCS1A01G004400 chr6D 92.972 1921 104 15 703 2622 472502566 472500676 0.000000e+00 2771.0
16 TraesCS1A01G004400 chr6D 96.057 837 14 3 2621 3441 472500580 472499747 0.000000e+00 1345.0
17 TraesCS1A01G004400 chr6D 93.407 455 16 4 6701 7141 472495714 472495260 0.000000e+00 662.0
18 TraesCS1A01G004400 chr6D 84.884 688 64 11 3722 4391 472427259 472426594 0.000000e+00 658.0
19 TraesCS1A01G004400 chr6D 95.396 391 18 0 6314 6704 472496406 472496016 2.190000e-174 623.0
20 TraesCS1A01G004400 chr6D 78.586 976 109 51 492 1453 472430534 472429645 2.910000e-153 553.0
21 TraesCS1A01G004400 chr6D 84.303 567 50 13 5018 5576 472425767 472425232 1.060000e-142 518.0
22 TraesCS1A01G004400 chr6D 92.778 360 20 4 156 515 472504665 472504312 3.820000e-142 516.0
23 TraesCS1A01G004400 chr6D 83.377 379 34 11 2632 2991 472428311 472427943 2.480000e-84 324.0
24 TraesCS1A01G004400 chr6D 90.426 188 15 1 5815 5999 472423749 472423562 1.990000e-60 244.0
25 TraesCS1A01G004400 chr6D 91.503 153 13 0 2 154 472504962 472504810 2.020000e-50 211.0
26 TraesCS1A01G004400 chr6D 78.979 333 44 14 5993 6313 472423514 472423196 3.380000e-48 204.0
27 TraesCS1A01G004400 chr6D 99.048 105 1 0 552 656 472502666 472502562 9.460000e-44 189.0
28 TraesCS1A01G004400 chr6D 86.628 172 20 2 3439 3610 472427632 472427464 3.400000e-43 187.0
29 TraesCS1A01G004400 chr6D 93.333 90 6 0 4666 4755 472426448 472426359 4.490000e-27 134.0
30 TraesCS1A01G004400 chr6D 82.069 145 15 7 3583 3716 472427465 472427321 5.850000e-21 113.0
31 TraesCS1A01G004400 chr6B 89.417 1956 166 26 675 2622 717420724 717418802 0.000000e+00 2427.0
32 TraesCS1A01G004400 chr6B 86.907 1138 78 21 3514 4604 717418026 717416913 0.000000e+00 1210.0
33 TraesCS1A01G004400 chr6B 91.322 749 36 5 4751 5499 717416512 717415793 0.000000e+00 996.0
34 TraesCS1A01G004400 chr6B 90.230 696 45 7 2621 3294 717418727 717418033 0.000000e+00 887.0
35 TraesCS1A01G004400 chr6B 82.249 1076 110 21 3719 4748 717401333 717400293 0.000000e+00 854.0
36 TraesCS1A01G004400 chr6B 85.007 687 66 10 3722 4391 717140208 717139542 0.000000e+00 664.0
37 TraesCS1A01G004400 chr6B 87.189 562 58 9 6320 6867 717414495 717413934 1.690000e-175 627.0
38 TraesCS1A01G004400 chr6B 78.359 975 113 49 492 1449 717143582 717142689 6.300000e-150 542.0
39 TraesCS1A01G004400 chr6B 89.831 354 32 2 5645 5998 717415601 717415252 1.090000e-122 451.0
40 TraesCS1A01G004400 chr6B 86.158 419 49 8 4749 5163 717400070 717399657 1.830000e-120 444.0
41 TraesCS1A01G004400 chr6B 87.599 379 26 2 5018 5396 717138671 717138314 3.080000e-113 420.0
42 TraesCS1A01G004400 chr6B 88.450 329 36 2 2295 2622 717402859 717402532 5.190000e-106 396.0
43 TraesCS1A01G004400 chr6B 88.657 335 17 1 6005 6318 717415191 717414857 8.690000e-104 388.0
44 TraesCS1A01G004400 chr6B 78.170 623 75 29 2882 3446 717402466 717401847 2.470000e-89 340.0
45 TraesCS1A01G004400 chr6B 87.500 280 26 2 2712 2991 717141162 717140892 1.500000e-81 315.0
46 TraesCS1A01G004400 chr6B 84.802 329 32 7 2296 2622 717141661 717141349 1.500000e-81 315.0
47 TraesCS1A01G004400 chr6B 79.464 448 73 15 6415 6850 717389198 717388758 4.190000e-77 300.0
48 TraesCS1A01G004400 chr6B 85.069 288 40 3 172 458 717143854 717143569 2.520000e-74 291.0
49 TraesCS1A01G004400 chr6B 90.411 219 20 1 4748 4966 717138892 717138675 3.260000e-73 287.0
50 TraesCS1A01G004400 chr6B 88.285 239 27 1 5993 6230 717389724 717389486 1.170000e-72 285.0
51 TraesCS1A01G004400 chr6B 90.426 188 15 1 5815 5999 717137670 717137483 1.990000e-60 244.0
52 TraesCS1A01G004400 chr6B 76.994 326 43 20 6003 6313 717137425 717137117 2.670000e-34 158.0
53 TraesCS1A01G004400 chr6B 76.752 314 37 15 3439 3716 717140583 717140270 7.470000e-30 143.0
54 TraesCS1A01G004400 chr6B 94.444 90 5 0 4666 4755 717416819 717416730 9.660000e-29 139.0
55 TraesCS1A01G004400 chr6B 94.318 88 5 0 4666 4753 717139366 717139279 1.250000e-27 135.0
56 TraesCS1A01G004400 chr6B 90.000 80 5 2 5529 5606 717415787 717415709 4.560000e-17 100.0
57 TraesCS1A01G004400 chr6B 97.826 46 1 0 6229 6274 717389462 717389417 5.940000e-11 80.5
58 TraesCS1A01G004400 chr6A 91.776 1374 98 10 4629 5999 617322028 617323389 0.000000e+00 1897.0
59 TraesCS1A01G004400 chr6A 94.000 1050 58 5 1573 2622 617318791 617319835 0.000000e+00 1585.0
60 TraesCS1A01G004400 chr6A 91.232 844 46 11 2621 3441 617319913 617320751 0.000000e+00 1123.0
61 TraesCS1A01G004400 chr6A 90.476 777 30 11 3719 4479 617321190 617321938 0.000000e+00 985.0
62 TraesCS1A01G004400 chr6A 89.466 712 38 17 859 1544 617318092 617318792 0.000000e+00 865.0
63 TraesCS1A01G004400 chr6A 87.225 681 54 24 675 1335 617217205 617217872 0.000000e+00 745.0
64 TraesCS1A01G004400 chr6A 77.168 1476 208 72 1125 2536 617234888 617236298 0.000000e+00 739.0
65 TraesCS1A01G004400 chr6A 78.737 1124 147 39 3513 4581 617224108 617225194 0.000000e+00 667.0
66 TraesCS1A01G004400 chr6A 82.754 806 78 25 3977 4755 617350455 617351226 0.000000e+00 662.0
67 TraesCS1A01G004400 chr6A 84.805 691 67 9 3719 4391 617555544 617556214 0.000000e+00 660.0
68 TraesCS1A01G004400 chr6A 79.902 1020 107 43 3466 4410 617237438 617238434 0.000000e+00 658.0
69 TraesCS1A01G004400 chr6A 79.088 899 127 35 1734 2622 617553236 617554083 4.840000e-156 562.0
70 TraesCS1A01G004400 chr6A 83.025 648 67 23 4968 5576 617351536 617352179 1.350000e-151 547.0
71 TraesCS1A01G004400 chr6A 84.629 566 47 14 5019 5576 617557081 617557614 1.760000e-145 527.0
72 TraesCS1A01G004400 chr6A 89.234 418 38 5 6315 6730 617324139 617324551 3.820000e-142 516.0
73 TraesCS1A01G004400 chr6A 77.218 992 110 59 493 1453 617551950 617552856 2.330000e-129 473.0
74 TraesCS1A01G004400 chr6A 87.896 347 21 3 5993 6318 617323437 617323783 8.690000e-104 388.0
75 TraesCS1A01G004400 chr6A 75.176 995 160 44 1143 2099 617348294 617349239 8.690000e-104 388.0
76 TraesCS1A01G004400 chr6A 92.251 271 20 1 5205 5475 617239443 617239712 4.040000e-102 383.0
77 TraesCS1A01G004400 chr6A 88.629 299 24 7 3438 3726 617320861 617321159 8.810000e-94 355.0
78 TraesCS1A01G004400 chr6A 81.757 444 56 12 5571 5999 617239798 617240231 1.470000e-91 348.0
79 TraesCS1A01G004400 chr6A 83.854 384 34 10 2626 2991 617554207 617554580 2.470000e-89 340.0
80 TraesCS1A01G004400 chr6A 84.375 352 25 4 5993 6318 617240279 617240626 1.160000e-82 318.0
81 TraesCS1A01G004400 chr6A 83.473 357 40 11 2233 2589 617222870 617223207 1.500000e-81 315.0
82 TraesCS1A01G004400 chr6A 82.152 381 53 9 5571 5946 617352203 617352573 5.380000e-81 313.0
83 TraesCS1A01G004400 chr6A 85.069 288 39 3 172 458 617234115 617234399 2.520000e-74 291.0
84 TraesCS1A01G004400 chr6A 89.732 224 23 0 6004 6227 617352697 617352920 3.260000e-73 287.0
85 TraesCS1A01G004400 chr6A 81.299 385 40 15 2882 3240 617236723 617237101 4.220000e-72 283.0
86 TraesCS1A01G004400 chr6A 86.992 246 31 1 180 424 617232684 617232929 7.060000e-70 276.0
87 TraesCS1A01G004400 chr6A 91.414 198 11 2 180 371 617317494 617317691 4.250000e-67 267.0
88 TraesCS1A01G004400 chr6A 79.515 371 58 14 2060 2425 617247114 617247471 1.540000e-61 248.0
89 TraesCS1A01G004400 chr6A 88.649 185 17 2 5815 5999 617559079 617559259 9.320000e-54 222.0
90 TraesCS1A01G004400 chr6A 84.390 205 27 5 1001 1202 617246649 617246851 5.650000e-46 196.0
91 TraesCS1A01G004400 chr6A 87.805 164 18 1 3439 3602 617555174 617555335 2.630000e-44 191.0
92 TraesCS1A01G004400 chr6A 76.647 334 45 18 5993 6313 617559307 617559620 3.450000e-33 154.0
93 TraesCS1A01G004400 chr6A 96.667 90 3 0 6229 6318 617353960 617354049 4.460000e-32 150.0
94 TraesCS1A01G004400 chr6A 93.976 83 5 0 4666 4748 617556390 617556472 7.520000e-25 126.0
95 TraesCS1A01G004400 chr6A 92.063 63 4 1 3655 3716 617555423 617555485 3.550000e-13 87.9
96 TraesCS1A01G004400 chr6A 94.118 51 3 0 6817 6867 617324604 617324654 2.140000e-10 78.7
97 TraesCS1A01G004400 chr7D 80.183 545 78 20 2063 2589 194244101 194244633 1.450000e-101 381.0
98 TraesCS1A01G004400 chr5D 90.106 283 23 3 6860 7141 413445798 413446076 5.270000e-96 363.0
99 TraesCS1A01G004400 chr5D 85.556 270 32 6 6872 7138 500869559 500869824 7.060000e-70 276.0
100 TraesCS1A01G004400 chr1B 90.217 276 24 1 6866 7138 29926910 29927185 2.450000e-94 357.0
101 TraesCS1A01G004400 chr3B 89.781 274 27 1 6866 7138 33094126 33094399 4.100000e-92 350.0
102 TraesCS1A01G004400 chr3B 88.929 280 23 6 6865 7141 556495146 556494872 8.870000e-89 339.0
103 TraesCS1A01G004400 chr1D 85.663 279 35 4 6863 7138 21818648 21818924 9.060000e-74 289.0
104 TraesCS1A01G004400 chr2D 85.294 272 35 4 6870 7138 604048273 604048542 7.060000e-70 276.0
105 TraesCS1A01G004400 chr2B 84.615 273 36 5 6866 7133 33915035 33915306 4.250000e-67 267.0
106 TraesCS1A01G004400 chr7A 80.176 227 40 4 6003 6225 203968734 203968959 1.590000e-36 165.0
107 TraesCS1A01G004400 chr7B 78.243 239 43 7 5993 6225 158173723 158173958 2.080000e-30 145.0


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 TraesCS1A01G004400 chr1A 2641680 2648820 7140 True 13188.000000 13188 100.000000 1 7141 1 chr1A.!!$R1 7140
1 TraesCS1A01G004400 chr1A 2694775 2695342 567 True 680.000000 680 88.732000 6315 6867 1 chr1A.!!$R2 552
2 TraesCS1A01G004400 chr1A 2653104 2657983 4879 True 465.750000 797 83.431500 2882 6226 4 chr1A.!!$R3 3344
3 TraesCS1A01G004400 chr1A 2837290 2843855 6565 True 381.625000 658 84.164125 1000 5999 8 chr1A.!!$R4 4999
4 TraesCS1A01G004400 chr6D 472495260 472504962 9702 True 1405.125000 4924 94.837250 2 7141 8 chr6D.!!$R2 7139
5 TraesCS1A01G004400 chr6D 472423196 472430534 7338 True 326.111111 658 84.731667 492 6313 9 chr6D.!!$R1 5821
6 TraesCS1A01G004400 chr6B 717413934 717420724 6790 True 802.777778 2427 89.777444 675 6867 9 chr6B.!!$R4 6192
7 TraesCS1A01G004400 chr6B 717399657 717402859 3202 True 508.500000 854 83.756750 2295 5163 4 chr6B.!!$R3 2868
8 TraesCS1A01G004400 chr6B 717137117 717143854 6737 True 319.454545 664 85.203364 172 6313 11 chr6B.!!$R1 6141
9 TraesCS1A01G004400 chr6B 717388758 717389724 966 True 221.833333 300 88.525000 5993 6850 3 chr6B.!!$R2 857
10 TraesCS1A01G004400 chr6A 617317494 617324654 7160 False 805.970000 1897 90.824100 180 6867 10 chr6A.!!$F5 6687
11 TraesCS1A01G004400 chr6A 617217205 617217872 667 False 745.000000 745 87.225000 675 1335 1 chr6A.!!$F1 660
12 TraesCS1A01G004400 chr6A 617222870 617225194 2324 False 491.000000 667 81.105000 2233 4581 2 chr6A.!!$F2 2348
13 TraesCS1A01G004400 chr6A 617232684 617240626 7942 False 412.000000 739 83.601625 172 6318 8 chr6A.!!$F3 6146
14 TraesCS1A01G004400 chr6A 617348294 617354049 5755 False 391.166667 662 84.917667 1143 6318 6 chr6A.!!$F6 5175
15 TraesCS1A01G004400 chr6A 617551950 617559620 7670 False 334.290000 660 84.873400 493 6313 10 chr6A.!!$F7 5820
16 TraesCS1A01G004400 chr6A 617246649 617247471 822 False 222.000000 248 81.952500 1001 2425 2 chr6A.!!$F4 1424
17 TraesCS1A01G004400 chr7D 194244101 194244633 532 False 381.000000 381 80.183000 2063 2589 1 chr7D.!!$F1 526

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
818 4101 0.106268 TGCCAAAAGGAGCTTGGACA 60.106 50.000 5.53 0.72 45.31 4.02 F
819 4102 0.315251 GCCAAAAGGAGCTTGGACAC 59.685 55.000 5.53 0.00 45.31 3.67 F
1640 5475 0.888619 TCTCACCTGTTGACGCCTAG 59.111 55.000 0.00 0.00 0.00 3.02 F
1644 5479 1.045407 ACCTGTTGACGCCTAGTTCA 58.955 50.000 0.00 0.00 0.00 3.18 F
1880 5805 1.272212 ACAGCCGGCAAAATTTTCGAT 59.728 42.857 31.54 0.00 0.00 3.59 F
1970 5896 1.977594 AAAGTTTATCGCCGCGCTGG 61.978 55.000 8.21 10.08 42.50 4.85 F
3016 7415 2.094539 CGTGCGACACAATCTGCG 59.905 61.111 9.95 0.00 33.40 5.18 F
4291 9637 3.711059 CTGTGCTGCCTGGGGATCC 62.711 68.421 1.92 1.92 0.00 3.36 F
5322 11620 1.606668 CCGCTGCAGGTTTCTTGTTTA 59.393 47.619 17.12 0.00 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 5876 0.179200 CAGCGCGGCGATAAACTTTT 60.179 50.000 28.54 0.0 0.00 2.27 R
1970 5896 1.146637 CTGAGTGTCAACAGCTGAGC 58.853 55.000 23.35 0.0 33.60 4.26 R
2993 7387 1.790623 AGATTGTGTCGCACGTTGTAC 59.209 47.619 5.69 0.0 37.14 2.90 R
3016 7415 2.755469 AATGCATGGTCGGGTGGC 60.755 61.111 0.00 0.0 0.00 5.01 R
3835 9156 2.629336 TGTGTGTGTGGATGCAACTA 57.371 45.000 0.00 0.0 0.00 2.24 R
3842 9163 3.897239 TCTTCCTTTTGTGTGTGTGGAT 58.103 40.909 0.00 0.0 0.00 3.41 R
4567 10331 2.949177 TTAAAGACTCTTGGCAGGCA 57.051 45.000 0.00 0.0 0.00 4.75 R
5596 12901 0.317436 GATCGTGGCGAGCTACTCAG 60.317 60.000 9.75 0.0 39.28 3.35 R
6980 17459 1.034838 GGGTGGTGTTGTTGTGCTCA 61.035 55.000 0.00 0.0 0.00 4.26 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
50 51 2.764128 CGGAGGCTCTAGGGGCAA 60.764 66.667 19.77 0.00 0.00 4.52
52 53 1.690985 GGAGGCTCTAGGGGCAAGT 60.691 63.158 19.77 0.00 0.00 3.16
68 69 1.032014 AAGTGTGCGCCAAGAATTGT 58.968 45.000 4.18 0.00 46.99 2.71
72 73 0.725784 GTGCGCCAAGAATTGTGACG 60.726 55.000 4.18 0.00 46.99 4.35
75 76 1.463528 GCGCCAAGAATTGTGACGTAC 60.464 52.381 0.00 0.00 46.99 3.67
154 155 4.375005 CGATGAACTGCGTATTAATCGTGG 60.375 45.833 0.00 0.00 32.83 4.94
331 1914 0.377554 ACGTCTATCAGCGAGGTTCG 59.622 55.000 0.00 0.00 43.89 3.95
342 1931 1.609794 GAGGTTCGTGGAGGAGGGT 60.610 63.158 0.00 0.00 0.00 4.34
356 1945 0.459759 GAGGGTCGGGTCGATTTGTC 60.460 60.000 0.00 0.00 38.42 3.18
371 1960 2.099062 GTCTTTGCGCATGGCTCG 59.901 61.111 12.75 0.00 44.05 5.03
408 1997 3.720193 CATATCGCTGGCGCTGGC 61.720 66.667 7.64 11.29 39.59 4.85
515 2104 3.377172 CGACCATGATTTGACCCCTTTAC 59.623 47.826 0.00 0.00 0.00 2.01
530 2119 7.121020 TGACCCCTTTACGTAAATTGTAAATCC 59.879 37.037 20.39 7.13 40.06 3.01
539 2128 7.430441 ACGTAAATTGTAAATCCCAATATGGC 58.570 34.615 0.00 0.00 35.79 4.40
675 3930 2.736531 CCCAAAACACCTGGCAGC 59.263 61.111 9.56 0.00 32.10 5.25
676 3931 1.833934 CCCAAAACACCTGGCAGCT 60.834 57.895 9.56 0.00 32.10 4.24
688 3945 2.647297 GCAGCTGGAACTTGCACC 59.353 61.111 17.12 0.00 37.75 5.01
796 4079 0.937699 GTTGCGTGCGTGTGAGTAGA 60.938 55.000 0.00 0.00 0.00 2.59
809 4092 3.135712 TGTGAGTAGAAGTGCCAAAAGGA 59.864 43.478 0.00 0.00 0.00 3.36
812 4095 2.373502 AGTAGAAGTGCCAAAAGGAGCT 59.626 45.455 0.00 0.00 0.00 4.09
813 4096 2.371658 AGAAGTGCCAAAAGGAGCTT 57.628 45.000 0.00 0.00 0.00 3.74
814 4097 1.959282 AGAAGTGCCAAAAGGAGCTTG 59.041 47.619 0.00 0.00 0.00 4.01
816 4099 0.185901 AGTGCCAAAAGGAGCTTGGA 59.814 50.000 5.53 0.00 45.31 3.53
817 4100 0.315251 GTGCCAAAAGGAGCTTGGAC 59.685 55.000 5.53 0.00 45.31 4.02
818 4101 0.106268 TGCCAAAAGGAGCTTGGACA 60.106 50.000 5.53 0.72 45.31 4.02
819 4102 0.315251 GCCAAAAGGAGCTTGGACAC 59.685 55.000 5.53 0.00 45.31 3.67
820 4103 1.691196 CCAAAAGGAGCTTGGACACA 58.309 50.000 0.00 0.00 45.31 3.72
821 4104 1.338020 CCAAAAGGAGCTTGGACACAC 59.662 52.381 0.00 0.00 45.31 3.82
827 4110 2.056906 GAGCTTGGACACACCCACCT 62.057 60.000 0.00 0.00 35.62 4.00
1134 4629 2.534298 CTCATCGATCACTTCAACGCT 58.466 47.619 0.00 0.00 0.00 5.07
1226 4726 3.864686 CGTTGCCCAAGATCCGCG 61.865 66.667 0.00 0.00 0.00 6.46
1232 4732 4.891727 CCAAGATCCGCGTCCCCG 62.892 72.222 4.92 0.00 37.07 5.73
1402 4979 1.449246 CTACTCAGGTGCTGCTGGC 60.449 63.158 0.00 0.00 42.22 4.85
1510 5235 5.005094 TGGTCTATTTGGTAAAGGTTTCGG 58.995 41.667 0.00 0.00 0.00 4.30
1563 5302 1.158466 TGCAAGGGTCCCTCTCTCA 59.842 57.895 12.07 4.11 30.89 3.27
1611 5350 3.842732 TTGCATCTCATGAAGCTTGTG 57.157 42.857 2.10 2.49 37.74 3.33
1640 5475 0.888619 TCTCACCTGTTGACGCCTAG 59.111 55.000 0.00 0.00 0.00 3.02
1644 5479 1.045407 ACCTGTTGACGCCTAGTTCA 58.955 50.000 0.00 0.00 0.00 3.18
1728 5623 3.186909 GGCAATCGAGTTAATTTTGGCC 58.813 45.455 0.00 0.00 37.01 5.36
1825 5750 6.491403 CCTTAATTTGGGATATTCCAGGACAG 59.509 42.308 2.12 0.00 38.64 3.51
1865 5790 6.099341 CCCATTACTTTTATTCACAACAGCC 58.901 40.000 0.00 0.00 0.00 4.85
1880 5805 1.272212 ACAGCCGGCAAAATTTTCGAT 59.728 42.857 31.54 0.00 0.00 3.59
1950 5876 4.390129 TCTTTGTATTTGTGGGCCCTTA 57.610 40.909 25.70 9.17 0.00 2.69
1958 5884 6.553852 TGTATTTGTGGGCCCTTAAAAGTTTA 59.446 34.615 25.70 10.20 0.00 2.01
1970 5896 1.977594 AAAGTTTATCGCCGCGCTGG 61.978 55.000 8.21 10.08 42.50 4.85
2079 6015 5.671997 GCACAATTTTCATGTTTGTCGTTTG 59.328 36.000 0.00 0.00 31.48 2.93
2080 6016 6.671879 GCACAATTTTCATGTTTGTCGTTTGT 60.672 34.615 0.00 0.00 31.48 2.83
2118 6054 8.624701 TTGTAACTGACTAAACGCATATAGTC 57.375 34.615 11.06 11.06 45.29 2.59
2547 6611 4.893608 TGTTCAAGAACATAGCTAGCACA 58.106 39.130 18.83 4.27 45.42 4.57
2548 6612 5.304778 TGTTCAAGAACATAGCTAGCACAA 58.695 37.500 18.83 1.78 45.42 3.33
2549 6613 5.762711 TGTTCAAGAACATAGCTAGCACAAA 59.237 36.000 18.83 0.00 45.42 2.83
2550 6614 6.262049 TGTTCAAGAACATAGCTAGCACAAAA 59.738 34.615 18.83 0.00 45.42 2.44
2551 6615 6.486253 TCAAGAACATAGCTAGCACAAAAG 57.514 37.500 18.83 2.87 0.00 2.27
2552 6616 5.412594 TCAAGAACATAGCTAGCACAAAAGG 59.587 40.000 18.83 0.96 0.00 3.11
2993 7387 3.550950 TGGTGTGAATGTGCAATAACG 57.449 42.857 0.00 0.00 0.00 3.18
3016 7415 2.094539 CGTGCGACACAATCTGCG 59.905 61.111 9.95 0.00 33.40 5.18
3463 8640 6.762702 TTTGTTTTAACGACCCTTTCTTCT 57.237 33.333 0.00 0.00 0.00 2.85
3835 9156 7.309316 GCAGTAGTAGTCCTGTTTTAGACTCTT 60.309 40.741 0.00 0.00 42.31 2.85
3842 9163 5.989777 GTCCTGTTTTAGACTCTTAGTTGCA 59.010 40.000 0.00 0.00 0.00 4.08
4291 9637 3.711059 CTGTGCTGCCTGGGGATCC 62.711 68.421 1.92 1.92 0.00 3.36
4491 10141 7.621102 CACTTGAAAATTCAGCTTGTTAAACC 58.379 34.615 0.00 0.00 38.61 3.27
4567 10331 6.669154 AGTGATGGGTATGTCATTTGGATTTT 59.331 34.615 0.00 0.00 0.00 1.82
4741 10517 7.257722 AGTTTTCAAACTATTGTGGTTGACAG 58.742 34.615 2.98 0.00 46.75 3.51
4936 11165 9.853555 CTGTAGCCTATCTCTTGTCATTTATAG 57.146 37.037 0.00 0.00 0.00 1.31
5005 11236 3.377346 TGTTGGTAATTGCGCACAAAT 57.623 38.095 11.12 0.00 39.77 2.32
5070 11301 4.139786 TGACTTTGCTGCTCTTTCAAGAT 58.860 39.130 0.00 0.00 33.93 2.40
5072 11303 5.764686 TGACTTTGCTGCTCTTTCAAGATTA 59.235 36.000 0.00 0.00 33.93 1.75
5181 11460 9.672673 AGTTGTTTTAGCTGTCTCATAATGTAT 57.327 29.630 0.00 0.00 0.00 2.29
5322 11620 1.606668 CCGCTGCAGGTTTCTTGTTTA 59.393 47.619 17.12 0.00 0.00 2.01
5443 12706 5.191727 TCAGAATTAATTGAGGCTTGGGA 57.808 39.130 5.17 0.00 0.00 4.37
5502 12766 7.469181 GCCTCACAATAGAAATGGATTTTCGAT 60.469 37.037 0.00 0.00 46.89 3.59
5513 12785 5.518848 TGGATTTTCGATTTCATCCATGG 57.481 39.130 4.97 4.97 40.28 3.66
5542 12814 8.811378 GTTATTATTACAACTACGACCCAAGTC 58.189 37.037 0.00 0.00 39.83 3.01
5596 12901 3.454371 ACGTGCCTGGACATCTATAAC 57.546 47.619 0.00 0.00 0.00 1.89
5643 13017 4.326610 CCCTACCCATTAAAACCCATCCTT 60.327 45.833 0.00 0.00 0.00 3.36
5652 13026 4.670896 AAAACCCATCCTTGTTTCTGTG 57.329 40.909 0.00 0.00 33.76 3.66
5679 13053 8.942338 GGAACCAAACTTACTTCAAAATTTCT 57.058 30.769 0.00 0.00 0.00 2.52
5705 13079 6.522946 TGTGATTTCATTTCCAATCTGCAAA 58.477 32.000 0.00 0.00 31.64 3.68
5706 13080 6.990939 TGTGATTTCATTTCCAATCTGCAAAA 59.009 30.769 0.00 0.00 31.64 2.44
5707 13081 7.498239 TGTGATTTCATTTCCAATCTGCAAAAA 59.502 29.630 0.00 0.00 31.64 1.94
5753 13172 6.668541 ATCTGAATGTTCACGTAAGATTGG 57.331 37.500 0.00 0.00 43.62 3.16
5778 13197 7.282450 GGTGGGGAAGAATAGTGTAAAATACTG 59.718 40.741 0.00 0.00 0.00 2.74
5966 14609 0.469705 TGCACCAGACAGCCCAAAAT 60.470 50.000 0.00 0.00 0.00 1.82
5974 14617 0.116940 ACAGCCCAAAATCCACCCAT 59.883 50.000 0.00 0.00 0.00 4.00
6386 16502 1.139654 CGAGGAAGCAGATCCATGGAA 59.860 52.381 20.67 1.96 42.27 3.53
6396 16512 4.504514 GCAGATCCATGGAAGAAGCAGATA 60.505 45.833 20.67 0.00 0.00 1.98
6404 16520 8.535335 TCCATGGAAGAAGCAGATAGTATATTC 58.465 37.037 13.46 0.00 0.00 1.75
6576 16693 7.118496 TGTGGATAAAGGACAAACACAAAAT 57.882 32.000 0.00 0.00 34.80 1.82
6621 16739 8.971321 CAACTTTGATTTCTTTAACATGGTGAG 58.029 33.333 0.00 0.00 0.00 3.51
6647 16765 6.750660 TCATTACCATTCCCGACCTAATTA 57.249 37.500 0.00 0.00 0.00 1.40
6655 16773 6.376018 CCATTCCCGACCTAATTACAGAAAAA 59.624 38.462 0.00 0.00 0.00 1.94
6868 17346 3.639094 CCTCATCGACCTCCTTCACTTAT 59.361 47.826 0.00 0.00 0.00 1.73
6968 17447 1.007038 CACACACACCAAGGCATGC 60.007 57.895 9.90 9.90 0.00 4.06
7005 17484 3.876156 GCACAACAACACCACCCCTATAT 60.876 47.826 0.00 0.00 0.00 0.86
7007 17486 3.589735 ACAACAACACCACCCCTATATGA 59.410 43.478 0.00 0.00 0.00 2.15
7044 17523 1.793414 TGATGATCCGTGGACTCCAT 58.207 50.000 0.00 0.00 35.28 3.41
7059 17538 3.197790 CATGGCGGCGTCTTCAGG 61.198 66.667 14.51 2.54 0.00 3.86
7081 17560 1.433879 GATACGACACCAGAGCGCT 59.566 57.895 11.27 11.27 0.00 5.92
7100 17579 3.147595 CCACTGCCCGATCCGAGA 61.148 66.667 0.00 0.00 0.00 4.04
7133 17612 2.359850 GGAGCAACACGATGGGCA 60.360 61.111 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.036010 CCAGACGGTCATGCTCCTTT 60.036 55.000 11.27 0.00 0.00 3.11
50 51 0.311790 CACAATTCTTGGCGCACACT 59.688 50.000 10.83 0.00 34.12 3.55
52 53 0.310543 GTCACAATTCTTGGCGCACA 59.689 50.000 10.83 1.22 34.12 4.57
72 73 1.392589 TAGGTGGATCCGTTCGGTAC 58.607 55.000 7.39 0.00 41.99 3.34
75 76 0.750850 ACATAGGTGGATCCGTTCGG 59.249 55.000 7.39 4.74 41.99 4.30
109 110 0.322098 ACACCATTTCATCGCCGGAA 60.322 50.000 5.05 0.00 0.00 4.30
115 116 2.935849 TCATCGGAACACCATTTCATCG 59.064 45.455 0.00 0.00 0.00 3.84
145 146 6.399743 TGTGTTATAAGAGCACCACGATTAA 58.600 36.000 0.00 0.00 32.62 1.40
154 155 6.743575 AGGTCATTTGTGTTATAAGAGCAC 57.256 37.500 0.00 0.00 0.00 4.40
331 1914 3.075641 GACCCGACCCTCCTCCAC 61.076 72.222 0.00 0.00 0.00 4.02
342 1931 1.153353 GCAAAGACAAATCGACCCGA 58.847 50.000 0.00 0.00 41.13 5.14
377 1966 0.588252 GATATGCCGTCATTGCGCTT 59.412 50.000 9.73 0.00 34.22 4.68
378 1967 1.560004 CGATATGCCGTCATTGCGCT 61.560 55.000 9.73 0.00 34.22 5.92
425 2014 1.695114 CCATGACCGCACCTATCCCA 61.695 60.000 0.00 0.00 0.00 4.37
515 2104 6.580791 CGCCATATTGGGATTTACAATTTACG 59.419 38.462 0.00 0.00 39.18 3.18
539 2128 4.792502 TTGCAAGCGCGCGATTCG 62.793 61.111 37.18 26.95 42.97 3.34
675 3930 2.886523 TCAGAATTGGTGCAAGTTCCAG 59.113 45.455 0.00 0.00 35.05 3.86
676 3931 2.622942 GTCAGAATTGGTGCAAGTTCCA 59.377 45.455 0.00 0.00 0.00 3.53
796 4079 1.043022 CCAAGCTCCTTTTGGCACTT 58.957 50.000 0.00 0.00 38.73 3.16
809 4092 2.078665 AGGTGGGTGTGTCCAAGCT 61.079 57.895 0.00 0.00 42.63 3.74
812 4095 1.694525 TGGAGGTGGGTGTGTCCAA 60.695 57.895 0.00 0.00 38.72 3.53
813 4096 2.040359 TGGAGGTGGGTGTGTCCA 60.040 61.111 0.00 0.00 36.72 4.02
814 4097 0.834687 TACTGGAGGTGGGTGTGTCC 60.835 60.000 0.00 0.00 0.00 4.02
816 4099 1.742308 AATACTGGAGGTGGGTGTGT 58.258 50.000 0.00 0.00 0.00 3.72
817 4100 2.436417 CAAATACTGGAGGTGGGTGTG 58.564 52.381 0.00 0.00 0.00 3.82
818 4101 1.271926 GCAAATACTGGAGGTGGGTGT 60.272 52.381 0.00 0.00 0.00 4.16
819 4102 1.271871 TGCAAATACTGGAGGTGGGTG 60.272 52.381 0.00 0.00 0.00 4.61
820 4103 1.072266 TGCAAATACTGGAGGTGGGT 58.928 50.000 0.00 0.00 0.00 4.51
821 4104 2.301346 GATGCAAATACTGGAGGTGGG 58.699 52.381 0.00 0.00 0.00 4.61
827 4110 0.813610 CGGCCGATGCAAATACTGGA 60.814 55.000 24.07 0.00 40.13 3.86
884 4325 3.678548 GGAGAAGCTTACGTTACCAGTTG 59.321 47.826 0.00 0.00 0.00 3.16
1226 4726 1.153229 GATTGTACTGGGCGGGGAC 60.153 63.158 0.00 0.00 0.00 4.46
1230 4730 0.469917 ATCCTGATTGTACTGGGCGG 59.530 55.000 0.00 0.00 0.00 6.13
1232 4732 4.899352 ATAGATCCTGATTGTACTGGGC 57.101 45.455 0.00 0.00 0.00 5.36
1234 4734 6.016192 ACACGTATAGATCCTGATTGTACTGG 60.016 42.308 0.00 0.00 0.00 4.00
1236 4745 6.016192 CCACACGTATAGATCCTGATTGTACT 60.016 42.308 0.00 0.00 0.00 2.73
1237 4746 6.016527 TCCACACGTATAGATCCTGATTGTAC 60.017 42.308 0.00 0.00 0.00 2.90
1315 4829 3.117171 CTGGACTGCTGCGACTGC 61.117 66.667 0.00 0.00 43.20 4.40
1402 4979 9.965902 AGAGCTTATTAAGTTAATATGGGGATG 57.034 33.333 21.24 6.54 31.27 3.51
1549 5288 0.040499 GACACTGAGAGAGGGACCCT 59.960 60.000 14.79 14.79 36.03 4.34
1563 5302 3.326588 TGTAACAACATGCCCTAGACACT 59.673 43.478 0.00 0.00 0.00 3.55
1640 5475 1.082169 TGTCGCGCAATTGCTGAAC 60.082 52.632 26.86 20.16 39.32 3.18
1644 5479 3.345808 ACGTGTCGCGCAATTGCT 61.346 55.556 26.86 3.74 46.11 3.91
1766 5690 0.250901 AGGCAATGGACCGGCATATC 60.251 55.000 0.00 0.00 0.00 1.63
1825 5750 2.335011 GGCGCAGAAACAACCACC 59.665 61.111 10.83 0.00 0.00 4.61
1865 5790 7.333288 AGAACTTTAATCGAAAATTTTGCCG 57.667 32.000 8.47 6.91 0.00 5.69
1880 5805 3.202829 ACCTGCCAACGAGAACTTTAA 57.797 42.857 0.00 0.00 0.00 1.52
1950 5876 0.179200 CAGCGCGGCGATAAACTTTT 60.179 50.000 28.54 0.00 0.00 2.27
1970 5896 1.146637 CTGAGTGTCAACAGCTGAGC 58.853 55.000 23.35 0.00 33.60 4.26
2246 6252 8.180706 TGACATGAAAGAGGAAATGATGAAAA 57.819 30.769 0.00 0.00 0.00 2.29
2536 6600 6.325028 TCATCTCTACCTTTTGTGCTAGCTAT 59.675 38.462 17.23 0.00 0.00 2.97
2541 6605 7.044181 CAGAATCATCTCTACCTTTTGTGCTA 58.956 38.462 0.00 0.00 32.03 3.49
2542 6606 5.879223 CAGAATCATCTCTACCTTTTGTGCT 59.121 40.000 0.00 0.00 32.03 4.40
2543 6607 5.065731 CCAGAATCATCTCTACCTTTTGTGC 59.934 44.000 0.00 0.00 32.03 4.57
2544 6608 6.176183 ACCAGAATCATCTCTACCTTTTGTG 58.824 40.000 0.00 0.00 32.03 3.33
2545 6609 6.380079 ACCAGAATCATCTCTACCTTTTGT 57.620 37.500 0.00 0.00 32.03 2.83
2546 6610 7.108847 AGAACCAGAATCATCTCTACCTTTTG 58.891 38.462 0.00 0.00 32.03 2.44
2547 6611 7.264294 AGAACCAGAATCATCTCTACCTTTT 57.736 36.000 0.00 0.00 32.03 2.27
2548 6612 6.882768 AGAACCAGAATCATCTCTACCTTT 57.117 37.500 0.00 0.00 32.03 3.11
2549 6613 6.214412 ACAAGAACCAGAATCATCTCTACCTT 59.786 38.462 0.00 0.00 32.03 3.50
2550 6614 5.723887 ACAAGAACCAGAATCATCTCTACCT 59.276 40.000 0.00 0.00 32.03 3.08
2551 6615 5.983540 ACAAGAACCAGAATCATCTCTACC 58.016 41.667 0.00 0.00 32.03 3.18
2552 6616 6.872920 AGACAAGAACCAGAATCATCTCTAC 58.127 40.000 0.00 0.00 32.03 2.59
2618 6716 8.057536 ACAAATACACAAGGTTGTTAAAGTGA 57.942 30.769 0.00 0.00 39.91 3.41
2619 6717 9.228636 GTACAAATACACAAGGTTGTTAAAGTG 57.771 33.333 0.00 0.00 39.91 3.16
2751 7024 6.135290 TCCTTTTTGAAACTCAGACATGTG 57.865 37.500 1.15 0.00 0.00 3.21
2993 7387 1.790623 AGATTGTGTCGCACGTTGTAC 59.209 47.619 5.69 0.00 37.14 2.90
3001 7398 3.422303 GGCGCAGATTGTGTCGCA 61.422 61.111 10.83 0.00 46.78 5.10
3016 7415 2.755469 AATGCATGGTCGGGTGGC 60.755 61.111 0.00 0.00 0.00 5.01
3028 7427 5.838531 TCATGATTATGACAAGCAATGCA 57.161 34.783 8.35 0.00 38.37 3.96
3463 8640 6.567687 TTTATCAACCATTTCTTCGCTTGA 57.432 33.333 0.00 0.00 0.00 3.02
3835 9156 2.629336 TGTGTGTGTGGATGCAACTA 57.371 45.000 0.00 0.00 0.00 2.24
3842 9163 3.897239 TCTTCCTTTTGTGTGTGTGGAT 58.103 40.909 0.00 0.00 0.00 3.41
4155 9501 9.681062 TTCCTGAAATTTCTCCGTAGATAAAAT 57.319 29.630 18.64 0.00 0.00 1.82
4156 9502 9.162764 CTTCCTGAAATTTCTCCGTAGATAAAA 57.837 33.333 18.64 0.00 0.00 1.52
4157 9503 8.319146 ACTTCCTGAAATTTCTCCGTAGATAAA 58.681 33.333 18.64 3.37 0.00 1.40
4158 9504 7.848128 ACTTCCTGAAATTTCTCCGTAGATAA 58.152 34.615 18.64 5.33 0.00 1.75
4291 9637 4.462483 TGGCTACCTTAAAGCAAAGAATGG 59.538 41.667 0.37 0.00 41.93 3.16
4491 10141 4.701956 AGAAAGCAACCGTGGAATAATG 57.298 40.909 0.00 0.00 0.00 1.90
4567 10331 2.949177 TTAAAGACTCTTGGCAGGCA 57.051 45.000 0.00 0.00 0.00 4.75
4741 10517 4.752661 TTTATGGTCGTTTGGTAAGTGC 57.247 40.909 0.00 0.00 0.00 4.40
4749 10525 3.986572 TGCATTGCTTTTATGGTCGTTTG 59.013 39.130 10.49 0.00 0.00 2.93
4925 11154 7.669089 TGGTGTATCCACTCTATAAATGACA 57.331 36.000 0.00 0.00 41.93 3.58
5443 12706 1.428869 ACAGAACTGAAGCTCCAGGT 58.571 50.000 4.49 0.00 38.44 4.00
5513 12785 8.931385 TGGGTCGTAGTTGTAATAATAACTTC 57.069 34.615 0.00 0.00 38.02 3.01
5542 12814 3.067742 GGGATGAATGTCTGATTTGGCAG 59.932 47.826 0.00 0.00 37.24 4.85
5596 12901 0.317436 GATCGTGGCGAGCTACTCAG 60.317 60.000 9.75 0.00 39.28 3.35
5643 13017 2.104170 GTTTGGTTCCCCACAGAAACA 58.896 47.619 0.00 0.00 41.65 2.83
5652 13026 5.601583 TTTTGAAGTAAGTTTGGTTCCCC 57.398 39.130 0.00 0.00 0.00 4.81
5679 13053 7.407393 TGCAGATTGGAAATGAAATCACATA 57.593 32.000 0.00 0.00 35.63 2.29
5708 13082 9.793252 CAGATTTCTTTCATTCGGTCATAAATT 57.207 29.630 0.00 0.00 0.00 1.82
5709 13083 9.177608 TCAGATTTCTTTCATTCGGTCATAAAT 57.822 29.630 0.00 0.00 0.00 1.40
5722 13096 6.618287 ACGTGAACATTCAGATTTCTTTCA 57.382 33.333 0.00 0.00 37.98 2.69
5753 13172 7.827729 ACAGTATTTTACACTATTCTTCCCCAC 59.172 37.037 0.00 0.00 0.00 4.61
6192 14891 1.933853 CGATTGGAAGTTCTTAGGCGG 59.066 52.381 2.25 0.00 0.00 6.13
6386 16502 8.663209 ACATCCTGAATATACTATCTGCTTCT 57.337 34.615 0.00 0.00 0.00 2.85
6596 16713 8.695456 ACTCACCATGTTAAAGAAATCAAAGTT 58.305 29.630 0.00 0.00 0.00 2.66
6598 16715 9.533253 AAACTCACCATGTTAAAGAAATCAAAG 57.467 29.630 0.00 0.00 0.00 2.77
6621 16739 3.617284 AGGTCGGGAATGGTAATGAAAC 58.383 45.455 0.00 0.00 0.00 2.78
6655 16773 7.837863 TGTACTTCCGATTTCTGTATCTCTTT 58.162 34.615 0.00 0.00 0.00 2.52
6711 17134 5.009310 TGAGACGTGAGCAGAAACTTAGTTA 59.991 40.000 0.00 0.00 0.00 2.24
6968 17447 2.097038 GTGCTCAGCGCCTGTGTAG 61.097 63.158 2.29 0.00 38.05 2.74
6980 17459 1.034838 GGGTGGTGTTGTTGTGCTCA 61.035 55.000 0.00 0.00 0.00 4.26
6985 17464 3.589735 TCATATAGGGGTGGTGTTGTTGT 59.410 43.478 0.00 0.00 0.00 3.32
7005 17484 4.198530 TCATATGCGGCTTCATCTTTTCA 58.801 39.130 0.00 0.00 0.00 2.69
7007 17486 4.823442 TCATCATATGCGGCTTCATCTTTT 59.177 37.500 0.00 0.00 0.00 2.27
7044 17523 3.589654 CTTCCTGAAGACGCCGCCA 62.590 63.158 0.45 0.00 40.79 5.69
7059 17538 1.534175 CGCTCTGGTGTCGTATCCTTC 60.534 57.143 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.