Multiple sequence alignment - TraesCS2B01G099200

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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 TraesCS2B01G099200 chr2B 100.000 2811 0 0 1 2811 58790524 58793334 0.000000e+00 5192.0
1 TraesCS2B01G099200 chr2B 85.666 593 53 14 997 1573 58826203 58826779 1.860000e-166 595.0
2 TraesCS2B01G099200 chr2B 93.979 382 19 2 1000 1380 58773405 58773783 2.430000e-160 575.0
3 TraesCS2B01G099200 chr2B 83.615 592 66 23 997 1573 58689431 58690006 6.900000e-146 527.0
4 TraesCS2B01G099200 chr2B 82.992 488 59 12 2088 2565 58774935 58775408 1.200000e-113 420.0
5 TraesCS2B01G099200 chr2B 80.695 518 70 22 2074 2573 58692477 58692982 2.640000e-100 375.0
6 TraesCS2B01G099200 chr2B 84.574 188 18 5 767 944 58826011 58826197 2.880000e-40 176.0
7 TraesCS2B01G099200 chr2B 90.000 110 11 0 1652 1761 58835048 58835157 2.920000e-30 143.0
8 TraesCS2B01G099200 chr2B 88.776 98 8 3 772 866 58773229 58773326 1.770000e-22 117.0
9 TraesCS2B01G099200 chr2B 93.651 63 4 0 1510 1572 58834989 58835051 8.290000e-16 95.3
10 TraesCS2B01G099200 chr2D 90.400 750 39 19 608 1337 35563977 35564713 0.000000e+00 955.0
11 TraesCS2B01G099200 chr2D 90.376 665 47 9 2154 2810 35640243 35640898 0.000000e+00 857.0
12 TraesCS2B01G099200 chr2D 82.893 1023 104 38 587 1573 35638651 35639638 0.000000e+00 854.0
13 TraesCS2B01G099200 chr2D 89.127 653 53 12 2168 2810 35668321 35668965 0.000000e+00 797.0
14 TraesCS2B01G099200 chr2D 89.262 596 45 6 997 1573 35531831 35532426 0.000000e+00 728.0
15 TraesCS2B01G099200 chr2D 86.464 591 47 17 997 1573 35677847 35678418 3.980000e-173 617.0
16 TraesCS2B01G099200 chr2D 79.420 724 108 24 2074 2786 35534764 35535457 9.110000e-130 473.0
17 TraesCS2B01G099200 chr2D 94.595 222 11 1 1044 1264 42076260 42076039 2.680000e-90 342.0
18 TraesCS2B01G099200 chr2D 79.572 514 69 19 2074 2571 42064631 42064138 4.490000e-88 335.0
19 TraesCS2B01G099200 chr2D 90.551 254 23 1 198 451 395940444 395940192 4.490000e-88 335.0
20 TraesCS2B01G099200 chr2D 90.438 251 23 1 198 448 455942236 455942485 2.090000e-86 329.0
21 TraesCS2B01G099200 chr2D 89.844 256 24 2 198 452 380694301 380694555 7.510000e-86 327.0
22 TraesCS2B01G099200 chr2D 89.535 258 24 1 197 454 194818860 194819114 9.710000e-85 324.0
23 TraesCS2B01G099200 chr2D 82.353 340 47 10 2124 2458 35565550 35565881 1.650000e-72 283.0
24 TraesCS2B01G099200 chr2D 90.090 222 15 3 1359 1573 35564705 35564926 5.930000e-72 281.0
25 TraesCS2B01G099200 chr2D 90.594 202 18 1 1 201 35559457 35559658 1.660000e-67 267.0
26 TraesCS2B01G099200 chr2D 88.837 215 22 1 2574 2786 35566169 35566383 2.150000e-66 263.0
27 TraesCS2B01G099200 chr2D 80.923 325 31 14 1653 1977 35564923 35565216 7.830000e-56 228.0
28 TraesCS2B01G099200 chr2D 84.332 217 31 2 2573 2786 42061297 42061081 2.840000e-50 209.0
29 TraesCS2B01G099200 chr2D 77.752 427 36 19 1652 2065 35532422 35532802 1.020000e-49 207.0
30 TraesCS2B01G099200 chr2D 84.305 223 16 7 492 698 35531341 35531560 1.710000e-47 200.0
31 TraesCS2B01G099200 chr2D 81.818 253 23 11 1829 2077 35639772 35640005 1.030000e-44 191.0
32 TraesCS2B01G099200 chr2D 82.432 222 32 6 2571 2786 42064100 42063880 1.330000e-43 187.0
33 TraesCS2B01G099200 chr2D 84.656 189 25 4 3 190 35674903 35675088 4.780000e-43 185.0
34 TraesCS2B01G099200 chr2D 83.500 200 28 2 4 201 35525122 35525318 6.190000e-42 182.0
35 TraesCS2B01G099200 chr2D 83.158 190 32 0 3 192 42098144 42097955 1.040000e-39 174.0
36 TraesCS2B01G099200 chr2D 90.909 121 11 0 1652 1772 35639634 35639754 2.240000e-36 163.0
37 TraesCS2B01G099200 chr2D 95.506 89 4 0 2074 2162 35640113 35640201 2.920000e-30 143.0
38 TraesCS2B01G099200 chr2D 75.174 431 38 35 1652 2065 42075080 42074702 3.780000e-29 139.0
39 TraesCS2B01G099200 chr2D 74.541 436 48 26 513 925 35677342 35677737 6.320000e-27 132.0
40 TraesCS2B01G099200 chr2A 90.175 743 50 13 2074 2810 38814499 38815224 0.000000e+00 946.0
41 TraesCS2B01G099200 chr2A 83.056 962 73 31 1002 1948 38878970 38879856 0.000000e+00 791.0
42 TraesCS2B01G099200 chr2A 86.815 584 50 15 997 1573 38812155 38812718 6.610000e-176 627.0
43 TraesCS2B01G099200 chr2A 86.575 581 47 13 997 1573 38755037 38755590 1.850000e-171 612.0
44 TraesCS2B01G099200 chr2A 84.276 566 49 17 997 1537 38908633 38909183 1.490000e-142 516.0
45 TraesCS2B01G099200 chr2A 89.916 238 11 3 1652 1888 38812714 38812939 7.610000e-76 294.0
46 TraesCS2B01G099200 chr2A 88.318 214 22 2 2569 2780 38888914 38889126 1.290000e-63 254.0
47 TraesCS2B01G099200 chr2A 77.662 385 50 17 587 944 38908252 38908627 4.750000e-48 202.0
48 TraesCS2B01G099200 chr2A 85.340 191 28 0 3 193 38809555 38809745 6.140000e-47 198.0
49 TraesCS2B01G099200 chr2A 75.460 489 64 25 494 942 38878485 38878957 1.330000e-43 187.0
50 TraesCS2B01G099200 chr2A 84.324 185 26 3 9 193 38741189 38741370 8.000000e-41 178.0
51 TraesCS2B01G099200 chr2A 83.237 173 25 4 19 190 38868378 38868547 3.750000e-34 156.0
52 TraesCS2B01G099200 chr2A 91.045 67 5 1 2011 2077 38814323 38814388 3.860000e-14 89.8
53 TraesCS2B01G099200 chr5D 90.157 254 23 2 197 449 9234373 9234121 2.090000e-86 329.0
54 TraesCS2B01G099200 chr5D 90.476 252 21 3 198 449 269336491 269336243 2.090000e-86 329.0
55 TraesCS2B01G099200 chr7D 90.119 253 21 4 198 450 28399591 28399343 2.700000e-85 326.0
56 TraesCS2B01G099200 chr3B 90.079 252 23 2 198 448 73604176 73604426 2.700000e-85 326.0
57 TraesCS2B01G099200 chr4A 89.494 257 26 1 198 454 674617043 674616788 9.710000e-85 324.0
58 TraesCS2B01G099200 chr6B 89.855 69 7 0 1389 1457 720673869 720673801 3.860000e-14 89.8


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 TraesCS2B01G099200 chr2B 58790524 58793334 2810 False 5192.000000 5192 100.000000 1 2811 1 chr2B.!!$F1 2810
1 TraesCS2B01G099200 chr2B 58689431 58692982 3551 False 451.000000 527 82.155000 997 2573 2 chr2B.!!$F2 1576
2 TraesCS2B01G099200 chr2B 58826011 58826779 768 False 385.500000 595 85.120000 767 1573 2 chr2B.!!$F4 806
3 TraesCS2B01G099200 chr2B 58773229 58775408 2179 False 370.666667 575 88.582333 772 2565 3 chr2B.!!$F3 1793
4 TraesCS2B01G099200 chr2D 35668321 35668965 644 False 797.000000 797 89.127000 2168 2810 1 chr2D.!!$F3 642
5 TraesCS2B01G099200 chr2D 35638651 35640898 2247 False 441.600000 857 88.300400 587 2810 5 chr2D.!!$F9 2223
6 TraesCS2B01G099200 chr2D 35531341 35535457 4116 False 402.000000 728 82.684750 492 2786 4 chr2D.!!$F7 2294
7 TraesCS2B01G099200 chr2D 35563977 35566383 2406 False 402.000000 955 86.520600 608 2786 5 chr2D.!!$F8 2178
8 TraesCS2B01G099200 chr2D 35674903 35678418 3515 False 311.333333 617 81.887000 3 1573 3 chr2D.!!$F10 1570
9 TraesCS2B01G099200 chr2D 42061081 42064631 3550 True 243.666667 335 82.112000 2074 2786 3 chr2D.!!$R3 712
10 TraesCS2B01G099200 chr2D 42074702 42076260 1558 True 240.500000 342 84.884500 1044 2065 2 chr2D.!!$R4 1021
11 TraesCS2B01G099200 chr2A 38755037 38755590 553 False 612.000000 612 86.575000 997 1573 1 chr2A.!!$F2 576
12 TraesCS2B01G099200 chr2A 38878485 38879856 1371 False 489.000000 791 79.258000 494 1948 2 chr2A.!!$F6 1454
13 TraesCS2B01G099200 chr2A 38809555 38815224 5669 False 430.960000 946 88.658200 3 2810 5 chr2A.!!$F5 2807
14 TraesCS2B01G099200 chr2A 38908252 38909183 931 False 359.000000 516 80.969000 587 1537 2 chr2A.!!$F7 950

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
705 3302 0.179045 ACAAGCACGATCCCTATGCC 60.179 55.0 0.0 0.0 40.33 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 10299 0.035458 AATATGCCGGAGCTGGTAGC 59.965 55.0 5.05 0.0 42.84 3.58 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
24 25 7.609760 TCTGTTAGTATGTGCTTATTGTTGG 57.390 36.000 0.00 0.00 0.00 3.77
33 34 3.127895 GTGCTTATTGTTGGTTGGCGATA 59.872 43.478 0.00 0.00 0.00 2.92
55 56 7.149335 CGATATCACTAGAACACGTTATTGTCG 60.149 40.741 3.12 0.00 0.00 4.35
56 57 5.361135 TCACTAGAACACGTTATTGTCGA 57.639 39.130 0.00 0.00 0.00 4.20
59 60 5.508573 CACTAGAACACGTTATTGTCGAGAG 59.491 44.000 0.00 0.00 0.00 3.20
61 62 4.474113 AGAACACGTTATTGTCGAGAGTC 58.526 43.478 0.00 0.00 0.00 3.36
65 66 4.621460 ACACGTTATTGTCGAGAGTCAATG 59.379 41.667 8.74 1.32 46.45 2.82
66 67 4.621460 CACGTTATTGTCGAGAGTCAATGT 59.379 41.667 8.74 1.84 46.45 2.71
67 68 4.621460 ACGTTATTGTCGAGAGTCAATGTG 59.379 41.667 8.74 2.59 46.45 3.21
78 79 7.276658 GTCGAGAGTCAATGTGTCATTAATCTT 59.723 37.037 0.00 0.00 0.00 2.40
80 81 8.750416 CGAGAGTCAATGTGTCATTAATCTTAG 58.250 37.037 0.00 0.00 0.00 2.18
81 82 8.430801 AGAGTCAATGTGTCATTAATCTTAGC 57.569 34.615 0.00 0.00 0.00 3.09
125 126 1.358787 TCTCCAATTGGGGCTGTCAAT 59.641 47.619 24.29 0.00 35.00 2.57
132 133 2.969821 TGGGGCTGTCAATTACAACT 57.030 45.000 0.00 0.00 37.74 3.16
142 143 9.542462 GGCTGTCAATTACAACTACATATTCTA 57.458 33.333 0.00 0.00 37.74 2.10
181 182 8.989980 TCAAGTACATATAGTCATGAGTAGACG 58.010 37.037 15.30 6.57 40.84 4.18
193 194 2.029623 GAGTAGACGTTGATAGGCCCA 58.970 52.381 0.00 0.00 0.00 5.36
196 197 0.325296 AGACGTTGATAGGCCCAGGA 60.325 55.000 0.00 0.00 0.00 3.86
197 198 0.759346 GACGTTGATAGGCCCAGGAT 59.241 55.000 0.00 0.00 0.00 3.24
198 199 1.141053 GACGTTGATAGGCCCAGGATT 59.859 52.381 0.00 0.00 0.00 3.01
202 203 4.204012 CGTTGATAGGCCCAGGATTTTTA 58.796 43.478 0.00 0.00 0.00 1.52
204 205 5.301805 CGTTGATAGGCCCAGGATTTTTATT 59.698 40.000 0.00 0.00 0.00 1.40
205 206 6.183360 CGTTGATAGGCCCAGGATTTTTATTT 60.183 38.462 0.00 0.00 0.00 1.40
206 207 7.013846 CGTTGATAGGCCCAGGATTTTTATTTA 59.986 37.037 0.00 0.00 0.00 1.40
209 210 7.724061 TGATAGGCCCAGGATTTTTATTTACTC 59.276 37.037 0.00 0.00 0.00 2.59
210 211 5.208890 AGGCCCAGGATTTTTATTTACTCC 58.791 41.667 0.00 0.00 0.00 3.85
213 2332 4.261031 CCCAGGATTTTTATTTACTCCGCG 60.261 45.833 0.00 0.00 0.00 6.46
219 2338 8.985805 AGGATTTTTATTTACTCCGCGTATTAG 58.014 33.333 4.92 0.00 0.00 1.73
220 2339 7.743400 GGATTTTTATTTACTCCGCGTATTAGC 59.257 37.037 4.92 0.00 0.00 3.09
224 2343 7.775397 TTATTTACTCCGCGTATTAGCTTTT 57.225 32.000 4.92 0.00 34.40 2.27
225 2344 5.459110 TTTACTCCGCGTATTAGCTTTTG 57.541 39.130 4.92 0.00 34.40 2.44
226 2345 2.968675 ACTCCGCGTATTAGCTTTTGT 58.031 42.857 4.92 0.00 34.40 2.83
228 2347 2.927477 CTCCGCGTATTAGCTTTTGTCA 59.073 45.455 4.92 0.00 34.40 3.58
426 2584 9.243637 GACTAAAGTCAACTCTAATATGCAGAG 57.756 37.037 11.37 11.37 44.18 3.35
443 2601 9.866655 ATATGCAGAGTAAATAAAAATGGAGGA 57.133 29.630 0.00 0.00 0.00 3.71
444 2602 8.593945 ATGCAGAGTAAATAAAAATGGAGGAA 57.406 30.769 0.00 0.00 0.00 3.36
480 2717 9.723601 TTTTTGCCAATTCTTTAGAGCATTTAT 57.276 25.926 0.00 0.00 0.00 1.40
484 2721 8.137437 TGCCAATTCTTTAGAGCATTTATAAGC 58.863 33.333 0.00 0.00 0.00 3.09
485 2722 8.137437 GCCAATTCTTTAGAGCATTTATAAGCA 58.863 33.333 0.18 0.00 0.00 3.91
490 2727 7.517320 TCTTTAGAGCATTTATAAGCATGGGA 58.483 34.615 0.00 0.00 0.00 4.37
491 2728 7.998383 TCTTTAGAGCATTTATAAGCATGGGAA 59.002 33.333 0.00 0.00 0.00 3.97
492 2729 8.532186 TTTAGAGCATTTATAAGCATGGGAAA 57.468 30.769 0.00 0.00 0.00 3.13
498 2997 6.573094 GCATTTATAAGCATGGGAAATCCTCC 60.573 42.308 0.00 0.00 44.54 4.30
522 3067 7.124147 TCCACATAGATTGAACACAGAGACATA 59.876 37.037 0.00 0.00 0.00 2.29
546 3091 6.887626 TTTTTGAAACACATAGTAGACCCC 57.112 37.500 0.00 0.00 0.00 4.95
555 3100 7.607615 ACACATAGTAGACCCCGTATTTATT 57.392 36.000 0.00 0.00 0.00 1.40
570 3120 9.276397 CCCGTATTTATTAAACAAAAACCTACG 57.724 33.333 7.31 7.31 0.00 3.51
599 3159 5.581085 GCCCTCAAATATATATGTGACGACC 59.419 44.000 11.02 1.05 0.00 4.79
610 3175 2.033372 TGTGACGACCCTTTCACAGTA 58.967 47.619 0.31 0.00 45.63 2.74
705 3302 0.179045 ACAAGCACGATCCCTATGCC 60.179 55.000 0.00 0.00 40.33 4.40
897 3552 2.330216 CCCATAAAACACCAACCCCAA 58.670 47.619 0.00 0.00 0.00 4.12
911 3572 1.758592 CCCAACCCGTCCTTCTCAA 59.241 57.895 0.00 0.00 0.00 3.02
923 3584 4.991056 CGTCCTTCTCAACAGAATTCAGAA 59.009 41.667 8.44 6.61 38.02 3.02
954 3699 1.004440 AGCTCACAAAGACTCGGGC 60.004 57.895 0.00 0.00 0.00 6.13
958 3703 1.302033 CACAAAGACTCGGGCAGCT 60.302 57.895 0.00 0.00 0.00 4.24
960 3705 1.302033 CAAAGACTCGGGCAGCTGT 60.302 57.895 16.64 0.00 0.00 4.40
963 3708 4.803426 GACTCGGGCAGCTGTCGG 62.803 72.222 18.99 18.99 0.00 4.79
992 3737 2.280552 GGTACAGGGGCACGTGAGA 61.281 63.158 22.23 0.00 36.39 3.27
993 3738 1.080025 GTACAGGGGCACGTGAGAC 60.080 63.158 22.23 9.06 36.39 3.36
1155 3906 1.443702 CGTCCTGCATCACGTCGAA 60.444 57.895 0.00 0.00 0.00 3.71
1167 3930 4.856607 GTCGAAGCCGAGCCCGAG 62.857 72.222 0.00 0.00 46.52 4.63
1236 3999 1.072965 CTCCTCAAGCCAAAGGACACT 59.927 52.381 0.00 0.00 36.75 3.55
1553 5050 0.318441 CAGCCAACGGAGAACAGAGA 59.682 55.000 0.00 0.00 0.00 3.10
1577 5074 0.179056 CCGCCGATCACCAGGTAATT 60.179 55.000 0.00 0.00 0.00 1.40
1581 5078 3.554129 CGCCGATCACCAGGTAATTGATA 60.554 47.826 0.00 0.00 29.93 2.15
1594 5091 0.877649 ATTGATAGCACGCTCGCCTG 60.878 55.000 0.00 0.00 0.00 4.85
1595 5092 3.333969 GATAGCACGCTCGCCTGC 61.334 66.667 0.00 4.98 0.00 4.85
1611 5114 1.871676 CCTGCGAACTCATCCATCATG 59.128 52.381 0.00 0.00 0.00 3.07
1623 5126 1.730451 CCATCATGGCAATCGCAGCA 61.730 55.000 0.00 0.00 41.24 4.41
1633 5136 1.736126 CAATCGCAGCAACTCATCTGT 59.264 47.619 0.00 0.00 33.09 3.41
1636 5139 0.671472 CGCAGCAACTCATCTGTCCA 60.671 55.000 0.00 0.00 33.09 4.02
1637 5140 0.801251 GCAGCAACTCATCTGTCCAC 59.199 55.000 0.00 0.00 33.09 4.02
1638 5141 1.446907 CAGCAACTCATCTGTCCACC 58.553 55.000 0.00 0.00 0.00 4.61
1639 5142 0.326264 AGCAACTCATCTGTCCACCC 59.674 55.000 0.00 0.00 0.00 4.61
1644 5147 1.203364 ACTCATCTGTCCACCCCTCTT 60.203 52.381 0.00 0.00 0.00 2.85
1648 5151 1.352083 TCTGTCCACCCCTCTTCTTG 58.648 55.000 0.00 0.00 0.00 3.02
1651 5154 0.771755 GTCCACCCCTCTTCTTGGTT 59.228 55.000 0.00 0.00 0.00 3.67
1680 5183 1.977293 AAGCGGCTGGAGAAGGATCC 61.977 60.000 1.81 2.48 40.03 3.36
1683 5186 2.279784 GCTGGAGAAGGATCCGCG 60.280 66.667 5.98 0.00 42.77 6.46
1820 5342 7.823310 AGAGACTCTACATGTAAACGAACTAGA 59.177 37.037 2.19 0.00 0.00 2.43
1821 5343 7.976826 AGACTCTACATGTAAACGAACTAGAG 58.023 38.462 7.06 10.46 32.28 2.43
1822 5344 7.066043 AGACTCTACATGTAAACGAACTAGAGG 59.934 40.741 16.76 4.09 31.16 3.69
1823 5345 6.658391 ACTCTACATGTAAACGAACTAGAGGT 59.342 38.462 16.76 4.55 31.16 3.85
1824 5346 7.081526 TCTACATGTAAACGAACTAGAGGTC 57.918 40.000 7.06 0.00 0.00 3.85
1825 5347 5.979288 ACATGTAAACGAACTAGAGGTCT 57.021 39.130 0.00 0.00 0.00 3.85
1826 5348 8.043113 TCTACATGTAAACGAACTAGAGGTCTA 58.957 37.037 7.06 0.00 0.00 2.59
1855 5378 6.669631 AGAAAAGTAGAAGAAGGTTTTGGGA 58.330 36.000 0.00 0.00 0.00 4.37
1860 5383 2.443255 AGAAGAAGGTTTTGGGAGAGCA 59.557 45.455 0.00 0.00 0.00 4.26
1861 5384 2.575805 AGAAGGTTTTGGGAGAGCAG 57.424 50.000 0.00 0.00 0.00 4.24
1862 5385 1.777272 AGAAGGTTTTGGGAGAGCAGT 59.223 47.619 0.00 0.00 0.00 4.40
1863 5386 1.882623 GAAGGTTTTGGGAGAGCAGTG 59.117 52.381 0.00 0.00 0.00 3.66
1901 6717 8.097038 ACATACATTAGGCGATCTGAATGTATT 58.903 33.333 18.76 12.53 46.12 1.89
1912 6729 5.022282 TCTGAATGTATTCATCGGCTTCA 57.978 39.130 7.67 0.00 44.92 3.02
1920 6737 0.532573 TCATCGGCTTCAGTCCAGTC 59.467 55.000 0.00 0.00 0.00 3.51
1956 6773 5.046950 TGGTGATACAGTAGCACACATTACA 60.047 40.000 26.26 13.48 46.29 2.41
1958 6775 5.291128 GTGATACAGTAGCACACATTACACC 59.709 44.000 21.63 0.00 44.06 4.16
1960 6777 2.290071 ACAGTAGCACACATTACACCCC 60.290 50.000 0.00 0.00 0.00 4.95
1961 6778 1.280998 AGTAGCACACATTACACCCCC 59.719 52.381 0.00 0.00 0.00 5.40
1962 6779 1.280998 GTAGCACACATTACACCCCCT 59.719 52.381 0.00 0.00 0.00 4.79
1963 6780 0.328258 AGCACACATTACACCCCCTC 59.672 55.000 0.00 0.00 0.00 4.30
1964 6781 0.679960 GCACACATTACACCCCCTCC 60.680 60.000 0.00 0.00 0.00 4.30
2227 10154 4.910458 AACAGTGGTAGTTAGCCTCATT 57.090 40.909 0.00 0.00 0.00 2.57
2268 10195 5.163754 CCGCCTAGTCAATGGTTAAGAAAAG 60.164 44.000 0.00 0.00 0.00 2.27
2345 10279 9.988815 ATCAATTTGAATATACTAGCGAGTCTT 57.011 29.630 1.52 0.00 37.10 3.01
2361 10295 5.614887 GCGAGTCTTCATTCAAACTTGTACC 60.615 44.000 0.00 0.00 0.00 3.34
2364 10298 7.307989 CGAGTCTTCATTCAAACTTGTACCATT 60.308 37.037 0.00 0.00 0.00 3.16
2365 10299 7.651808 AGTCTTCATTCAAACTTGTACCATTG 58.348 34.615 0.00 0.00 0.00 2.82
2366 10300 6.363357 GTCTTCATTCAAACTTGTACCATTGC 59.637 38.462 0.00 0.00 0.00 3.56
2367 10301 6.265196 TCTTCATTCAAACTTGTACCATTGCT 59.735 34.615 0.00 0.00 0.00 3.91
2368 10302 7.446931 TCTTCATTCAAACTTGTACCATTGCTA 59.553 33.333 0.00 0.00 0.00 3.49
2369 10303 6.908825 TCATTCAAACTTGTACCATTGCTAC 58.091 36.000 0.00 0.00 0.00 3.58
2416 10376 2.411547 GCGAGTCTCCGTTCAACATTTG 60.412 50.000 0.00 0.00 0.00 2.32
2420 10380 3.632145 AGTCTCCGTTCAACATTTGCTTT 59.368 39.130 0.00 0.00 0.00 3.51
2430 10390 8.165428 CGTTCAACATTTGCTTTGTTTCTTTTA 58.835 29.630 0.00 0.00 35.18 1.52
2467 10428 8.890410 TTAGTACACTTTGACTACCTAATCCT 57.110 34.615 0.00 0.00 0.00 3.24
2565 13503 7.876896 TTCATTTTTACCTAAATTGTTCCGC 57.123 32.000 0.00 0.00 31.92 5.54
2591 13581 3.263937 ACCCGTGCTATGGTTTACCTTTA 59.736 43.478 0.00 0.00 36.82 1.85
2717 13711 5.103728 TGGATAATGCTGGGAAAATAGTCCA 60.104 40.000 0.00 0.00 39.70 4.02
2747 13742 8.458573 TGTTAGTTTAAAATTGAGAAGCCTCA 57.541 30.769 0.00 0.00 46.95 3.86
2762 13757 1.118838 CCTCAGAAATCGCTCTCCCT 58.881 55.000 0.00 0.00 0.00 4.20
2765 13760 3.323403 CCTCAGAAATCGCTCTCCCTAAT 59.677 47.826 0.00 0.00 0.00 1.73
2804 13799 1.079127 CCACATGTCAGGGTCGACC 60.079 63.158 27.04 27.04 40.67 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.486108 CGTGTTCTAGTGATATCGCCAAC 59.514 47.826 12.66 12.85 0.00 3.77
33 34 5.946298 TCGACAATAACGTGTTCTAGTGAT 58.054 37.500 0.00 0.00 0.00 3.06
55 56 8.547069 GCTAAGATTAATGACACATTGACTCTC 58.453 37.037 7.16 0.00 0.00 3.20
56 57 8.043113 TGCTAAGATTAATGACACATTGACTCT 58.957 33.333 7.16 4.22 0.00 3.24
59 60 7.698130 GGTTGCTAAGATTAATGACACATTGAC 59.302 37.037 7.16 0.26 0.00 3.18
61 62 7.537715 TGGTTGCTAAGATTAATGACACATTG 58.462 34.615 7.16 0.00 0.00 2.82
105 106 0.776810 TTGACAGCCCCAATTGGAGA 59.223 50.000 26.60 0.00 37.39 3.71
132 133 8.980481 TGATGGATATCTCGCTAGAATATGTA 57.020 34.615 2.05 0.00 34.73 2.29
142 143 5.991933 ATGTACTTGATGGATATCTCGCT 57.008 39.130 2.05 0.00 34.31 4.93
143 144 8.625651 ACTATATGTACTTGATGGATATCTCGC 58.374 37.037 2.05 0.00 34.31 5.03
180 181 2.348411 AAATCCTGGGCCTATCAACG 57.652 50.000 4.53 0.00 0.00 4.10
181 182 6.731292 AATAAAAATCCTGGGCCTATCAAC 57.269 37.500 4.53 0.00 0.00 3.18
193 194 7.797038 AATACGCGGAGTAAATAAAAATCCT 57.203 32.000 12.47 0.00 39.04 3.24
196 197 8.374327 AGCTAATACGCGGAGTAAATAAAAAT 57.626 30.769 12.47 0.00 39.04 1.82
197 198 7.775397 AGCTAATACGCGGAGTAAATAAAAA 57.225 32.000 12.47 0.00 39.04 1.94
198 199 7.775397 AAGCTAATACGCGGAGTAAATAAAA 57.225 32.000 12.47 0.00 39.04 1.52
202 203 5.583457 ACAAAAGCTAATACGCGGAGTAAAT 59.417 36.000 12.47 0.00 39.04 1.40
204 205 4.497300 ACAAAAGCTAATACGCGGAGTAA 58.503 39.130 12.47 0.00 39.04 2.24
205 206 4.107622 GACAAAAGCTAATACGCGGAGTA 58.892 43.478 12.47 4.11 40.03 2.59
206 207 2.928116 GACAAAAGCTAATACGCGGAGT 59.072 45.455 12.47 2.60 34.40 3.85
209 210 3.733024 TTGACAAAAGCTAATACGCGG 57.267 42.857 12.47 0.00 34.40 6.46
210 211 4.708601 ACTTTGACAAAAGCTAATACGCG 58.291 39.130 3.53 3.53 45.71 6.01
213 2332 9.516314 AAGTTTGACTTTGACAAAAGCTAATAC 57.484 29.630 1.62 0.00 45.71 1.89
219 2338 8.905103 TTACTAAGTTTGACTTTGACAAAAGC 57.095 30.769 1.62 0.00 45.71 3.51
469 2706 7.394359 GGATTTCCCATGCTTATAAATGCTCTA 59.606 37.037 0.00 0.00 34.14 2.43
470 2707 6.210185 GGATTTCCCATGCTTATAAATGCTCT 59.790 38.462 0.00 0.00 34.14 4.09
471 2708 6.210185 AGGATTTCCCATGCTTATAAATGCTC 59.790 38.462 0.00 0.00 34.41 4.26
472 2709 6.080009 AGGATTTCCCATGCTTATAAATGCT 58.920 36.000 0.00 0.00 34.60 3.79
473 2710 6.350629 AGGATTTCCCATGCTTATAAATGC 57.649 37.500 0.00 0.00 37.41 3.56
474 2711 6.494491 TGGAGGATTTCCCATGCTTATAAATG 59.506 38.462 0.00 0.00 46.19 2.32
475 2712 6.494835 GTGGAGGATTTCCCATGCTTATAAAT 59.505 38.462 0.00 0.00 46.19 1.40
478 2715 4.415179 TGTGGAGGATTTCCCATGCTTATA 59.585 41.667 0.00 0.00 46.19 0.98
480 2717 2.580322 TGTGGAGGATTTCCCATGCTTA 59.420 45.455 0.00 0.00 46.19 3.09
481 2718 1.358787 TGTGGAGGATTTCCCATGCTT 59.641 47.619 0.00 0.00 46.19 3.91
482 2719 1.002069 TGTGGAGGATTTCCCATGCT 58.998 50.000 0.00 0.00 46.19 3.79
484 2721 4.712051 TCTATGTGGAGGATTTCCCATG 57.288 45.455 0.00 0.00 46.19 3.66
485 2722 5.373555 TCAATCTATGTGGAGGATTTCCCAT 59.626 40.000 0.00 0.00 46.19 4.00
487 2724 5.310409 TCAATCTATGTGGAGGATTTCCC 57.690 43.478 0.00 0.00 46.19 3.97
490 2727 6.484288 TGTGTTCAATCTATGTGGAGGATTT 58.516 36.000 0.00 0.00 0.00 2.17
491 2728 6.065976 TGTGTTCAATCTATGTGGAGGATT 57.934 37.500 0.00 0.00 0.00 3.01
492 2729 5.426509 TCTGTGTTCAATCTATGTGGAGGAT 59.573 40.000 0.00 0.00 0.00 3.24
498 2997 8.883954 ATATGTCTCTGTGTTCAATCTATGTG 57.116 34.615 0.00 0.00 0.00 3.21
508 3007 8.958043 GTGTTTCAAAAATATGTCTCTGTGTTC 58.042 33.333 0.00 0.00 0.00 3.18
522 3067 6.150474 CGGGGTCTACTATGTGTTTCAAAAAT 59.850 38.462 0.00 0.00 0.00 1.82
526 3071 3.579586 ACGGGGTCTACTATGTGTTTCAA 59.420 43.478 0.00 0.00 0.00 2.69
537 3082 9.737844 TTTTGTTTAATAAATACGGGGTCTACT 57.262 29.630 0.00 0.00 0.00 2.57
555 3100 3.251487 GGCAGCTCGTAGGTTTTTGTTTA 59.749 43.478 0.00 0.00 0.00 2.01
570 3120 6.314896 GTCACATATATATTTGAGGGCAGCTC 59.685 42.308 11.09 0.00 0.00 4.09
599 3159 5.209818 TCTACCAACTGTACTGTGAAAGG 57.790 43.478 6.13 8.78 0.00 3.11
610 3175 1.679898 GGGCAGCTCTACCAACTGT 59.320 57.895 0.00 0.00 33.87 3.55
674 3247 0.658536 GTGCTTGTCTTCTTGCGCAC 60.659 55.000 11.12 0.00 40.53 5.34
790 3420 1.154413 CGATGCTGGTTGTTGCGAC 60.154 57.895 0.00 0.00 0.00 5.19
897 3552 1.420430 TTCTGTTGAGAAGGACGGGT 58.580 50.000 0.00 0.00 32.98 5.28
911 3572 3.265791 GCGTCTGGATTCTGAATTCTGT 58.734 45.455 9.94 0.00 0.00 3.41
923 3584 1.750780 TGAGCTCTCGCGTCTGGAT 60.751 57.895 16.19 0.00 42.32 3.41
944 3605 2.659610 GACAGCTGCCCGAGTCTT 59.340 61.111 15.27 0.00 0.00 3.01
954 3699 1.588403 CAGAGATCGCCGACAGCTG 60.588 63.158 13.48 13.48 40.39 4.24
958 3703 0.678684 TACCACAGAGATCGCCGACA 60.679 55.000 0.00 0.00 0.00 4.35
960 3705 0.678684 TGTACCACAGAGATCGCCGA 60.679 55.000 0.00 0.00 0.00 5.54
992 3737 3.256960 AGTTCCCCATGCCCACGT 61.257 61.111 0.00 0.00 0.00 4.49
993 3738 2.751436 CAGTTCCCCATGCCCACG 60.751 66.667 0.00 0.00 0.00 4.94
994 3739 3.070576 GCAGTTCCCCATGCCCAC 61.071 66.667 0.00 0.00 36.41 4.61
1236 3999 3.663815 GACCTGGCCGAGGAGGAGA 62.664 68.421 23.24 0.00 46.33 3.71
1446 4940 4.521062 GATGGCCTCGTCGCAGCT 62.521 66.667 3.32 0.00 0.00 4.24
1577 5074 2.104928 CAGGCGAGCGTGCTATCA 59.895 61.111 4.82 0.00 34.52 2.15
1594 5091 0.590195 GCCATGATGGATGAGTTCGC 59.410 55.000 17.22 0.00 40.96 4.70
1595 5092 1.957668 TGCCATGATGGATGAGTTCG 58.042 50.000 17.22 0.00 40.96 3.95
1596 5093 3.058432 CGATTGCCATGATGGATGAGTTC 60.058 47.826 17.22 1.81 40.96 3.01
1597 5094 2.882761 CGATTGCCATGATGGATGAGTT 59.117 45.455 17.22 0.00 40.96 3.01
1598 5095 2.501261 CGATTGCCATGATGGATGAGT 58.499 47.619 17.22 0.00 40.96 3.41
1599 5096 1.199327 GCGATTGCCATGATGGATGAG 59.801 52.381 17.22 2.92 40.96 2.90
1600 5097 1.241165 GCGATTGCCATGATGGATGA 58.759 50.000 17.22 0.00 40.96 2.92
1601 5098 0.955905 TGCGATTGCCATGATGGATG 59.044 50.000 17.22 0.06 40.96 3.51
1611 5114 0.248377 GATGAGTTGCTGCGATTGCC 60.248 55.000 1.50 0.00 41.78 4.52
1623 5126 1.203364 AGAGGGGTGGACAGATGAGTT 60.203 52.381 0.00 0.00 0.00 3.01
1633 5136 1.064825 GAACCAAGAAGAGGGGTGGA 58.935 55.000 0.00 0.00 34.51 4.02
1636 5139 1.068121 CCTGAACCAAGAAGAGGGGT 58.932 55.000 0.00 0.00 36.19 4.95
1637 5140 1.362224 TCCTGAACCAAGAAGAGGGG 58.638 55.000 0.00 0.00 0.00 4.79
1638 5141 2.784347 GTTCCTGAACCAAGAAGAGGG 58.216 52.381 0.00 0.00 35.36 4.30
1639 5142 2.417719 CGTTCCTGAACCAAGAAGAGG 58.582 52.381 4.54 0.00 38.03 3.69
1644 5147 1.542547 GCTTCCGTTCCTGAACCAAGA 60.543 52.381 15.53 4.93 38.03 3.02
1648 5151 2.033194 CCGCTTCCGTTCCTGAACC 61.033 63.158 4.54 0.00 38.03 3.62
1651 5154 3.311110 AGCCGCTTCCGTTCCTGA 61.311 61.111 0.00 0.00 0.00 3.86
1820 5342 9.457436 CTTCTTCTACTTTTCTACTCTAGACCT 57.543 37.037 0.00 0.00 33.84 3.85
1821 5343 8.680001 CCTTCTTCTACTTTTCTACTCTAGACC 58.320 40.741 0.00 0.00 33.84 3.85
1822 5344 9.234827 ACCTTCTTCTACTTTTCTACTCTAGAC 57.765 37.037 0.00 0.00 33.84 2.59
1823 5345 9.810870 AACCTTCTTCTACTTTTCTACTCTAGA 57.189 33.333 0.00 0.00 0.00 2.43
1826 5348 9.549078 CAAAACCTTCTTCTACTTTTCTACTCT 57.451 33.333 0.00 0.00 0.00 3.24
1827 5349 8.775527 CCAAAACCTTCTTCTACTTTTCTACTC 58.224 37.037 0.00 0.00 0.00 2.59
1855 5378 8.914011 TGTATGTATACATTTCTACACTGCTCT 58.086 33.333 22.90 0.00 38.28 4.09
1901 6717 0.532573 GACTGGACTGAAGCCGATGA 59.467 55.000 0.00 0.00 0.00 2.92
1912 6729 3.403038 CAAAACGGATTCAGACTGGACT 58.597 45.455 1.81 0.00 0.00 3.85
1920 6737 4.695455 ACTGTATCACCAAAACGGATTCAG 59.305 41.667 0.00 0.00 40.28 3.02
2016 6991 2.011947 GTGGCTTGGATAAACCGGTAC 58.988 52.381 8.00 0.00 42.61 3.34
2164 10087 4.744570 TCAGAAATGTATCCGTGTCAGTC 58.255 43.478 0.00 0.00 0.00 3.51
2166 10089 4.115516 CCTCAGAAATGTATCCGTGTCAG 58.884 47.826 0.00 0.00 0.00 3.51
2227 10154 2.627945 GCGGTCTCACCATACATTCAA 58.372 47.619 0.00 0.00 38.47 2.69
2361 10295 2.182842 GCCGGAGCTGGTAGCAATG 61.183 63.158 5.05 0.00 45.56 2.82
2364 10298 1.121407 ATATGCCGGAGCTGGTAGCA 61.121 55.000 5.05 0.00 45.56 3.49
2365 10299 0.035458 AATATGCCGGAGCTGGTAGC 59.965 55.000 5.05 0.00 42.84 3.58
2366 10300 1.344438 TCAATATGCCGGAGCTGGTAG 59.656 52.381 5.05 0.00 40.80 3.18
2367 10301 1.419381 TCAATATGCCGGAGCTGGTA 58.581 50.000 5.05 0.00 40.80 3.25
2368 10302 0.546122 TTCAATATGCCGGAGCTGGT 59.454 50.000 5.05 0.00 40.80 4.00
2369 10303 1.538512 CATTCAATATGCCGGAGCTGG 59.461 52.381 5.05 0.00 40.80 4.85
2416 10376 7.575332 TGTGTCTTGTTAAAAGAAACAAAGC 57.425 32.000 5.71 0.00 45.88 3.51
2430 10390 8.395633 GTCAAAGTGTACTAATTGTGTCTTGTT 58.604 33.333 0.00 0.00 0.00 2.83
2543 13479 7.883229 AAGCGGAACAATTTAGGTAAAAATG 57.117 32.000 0.00 0.00 0.00 2.32
2544 13480 9.414295 GTTAAGCGGAACAATTTAGGTAAAAAT 57.586 29.630 0.00 0.00 0.00 1.82
2545 13481 7.866898 GGTTAAGCGGAACAATTTAGGTAAAAA 59.133 33.333 6.18 0.00 0.00 1.94
2549 13487 4.943093 GGGTTAAGCGGAACAATTTAGGTA 59.057 41.667 0.00 0.00 0.00 3.08
2565 13503 3.624410 GGTAAACCATAGCACGGGTTAAG 59.376 47.826 6.39 0.00 46.33 1.85
2591 13581 4.489810 TGCAGAACGTTCACAAAATTTGT 58.510 34.783 28.78 5.41 46.75 2.83
2747 13742 7.509546 TCAAATTATTAGGGAGAGCGATTTCT 58.490 34.615 0.00 0.00 0.00 2.52
2781 13776 1.484653 CGACCCTGACATGTGGGAATA 59.515 52.381 24.46 0.00 46.15 1.75


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

AutoCloner maintained by Alex Coulton.