Multiple sequence alignment - TraesCS6B01G405900

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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 TraesCS6B01G405900 chr6B 100.000 3656 0 0 1 3656 680769054 680765399 0.000000e+00 6752.0
1 TraesCS6B01G405900 chr6B 94.387 1728 72 15 1024 2744 680894298 680896007 0.000000e+00 2630.0
2 TraesCS6B01G405900 chr6B 96.838 917 25 4 2742 3656 680896132 680897046 0.000000e+00 1530.0
3 TraesCS6B01G405900 chr6B 88.344 489 25 18 506 982 680893835 680894303 3.190000e-155 558.0
4 TraesCS6B01G405900 chr6B 74.925 335 80 4 2011 2343 6681928 6681596 2.270000e-32 150.0
5 TraesCS6B01G405900 chr6B 92.308 91 3 2 731 817 680768284 680768194 3.830000e-25 126.0
6 TraesCS6B01G405900 chr6B 92.308 91 3 2 771 861 680768324 680768238 3.830000e-25 126.0
7 TraesCS6B01G405900 chr6B 73.860 329 78 7 2019 2343 6605231 6605555 1.380000e-24 124.0
8 TraesCS6B01G405900 chr6B 87.692 65 5 3 2819 2880 43280234 43280170 5.060000e-09 73.1
9 TraesCS6B01G405900 chr6A 91.779 1861 92 35 811 2662 595004720 595002912 0.000000e+00 2532.0
10 TraesCS6B01G405900 chr6A 83.394 277 28 10 515 777 595004946 595004674 1.310000e-59 241.0
11 TraesCS6B01G405900 chr6A 89.773 176 11 5 520 694 595005736 595005567 6.150000e-53 219.0
12 TraesCS6B01G405900 chr6D 92.086 1769 98 22 979 2718 449161993 449160238 0.000000e+00 2453.0
13 TraesCS6B01G405900 chr6D 91.363 521 36 4 3144 3656 448917142 448916623 0.000000e+00 704.0
14 TraesCS6B01G405900 chr6D 87.500 360 36 4 3293 3646 449154489 449154133 1.220000e-109 407.0
15 TraesCS6B01G405900 chr6D 96.939 196 6 0 1583 1778 449271456 449271261 2.720000e-86 329.0
16 TraesCS6B01G405900 chr6D 79.098 488 69 19 3199 3656 449285895 449286379 4.590000e-79 305.0
17 TraesCS6B01G405900 chr6D 95.946 148 5 1 1192 1338 449271122 449271269 4.720000e-59 239.0
18 TraesCS6B01G405900 chr6D 80.422 332 19 18 838 1164 449269858 449270148 1.030000e-50 211.0
19 TraesCS6B01G405900 chr6D 89.308 159 11 4 537 694 449158444 449158291 1.040000e-45 195.0
20 TraesCS6B01G405900 chr6D 80.723 249 33 10 538 776 449162320 449162077 2.900000e-41 180.0
21 TraesCS6B01G405900 chr6D 80.913 241 26 11 3199 3420 448917327 448917088 4.850000e-39 172.0
22 TraesCS6B01G405900 chr6D 74.702 336 77 7 2011 2342 3317525 3317856 3.810000e-30 143.0
23 TraesCS6B01G405900 chr6D 83.186 113 9 4 838 950 449256717 449256819 1.080000e-15 95.3
24 TraesCS6B01G405900 chr6D 81.356 118 6 8 587 694 449269663 449269774 8.410000e-12 82.4
25 TraesCS6B01G405900 chr6D 100.000 31 0 0 1157 1187 449271099 449271129 1.420000e-04 58.4
26 TraesCS6B01G405900 chr4D 82.464 1266 196 17 1028 2282 381737441 381738691 0.000000e+00 1085.0
27 TraesCS6B01G405900 chr4D 80.357 168 30 2 2490 2657 381747005 381747169 1.380000e-24 124.0
28 TraesCS6B01G405900 chrUn 93.347 496 24 4 3168 3656 227613875 227613382 0.000000e+00 725.0
29 TraesCS6B01G405900 chrUn 93.347 496 24 4 3168 3656 253545413 253545906 0.000000e+00 725.0
30 TraesCS6B01G405900 chr4A 80.777 515 81 15 3 508 568875294 568875799 1.590000e-103 387.0
31 TraesCS6B01G405900 chr4A 74.426 305 52 21 219 508 27663187 27662894 1.390000e-19 108.0
32 TraesCS6B01G405900 chr4A 91.935 62 4 1 458 519 165830342 165830282 6.500000e-13 86.1
33 TraesCS6B01G405900 chr4A 76.344 186 19 19 344 508 476496215 476496034 3.910000e-10 76.8
34 TraesCS6B01G405900 chr1D 79.727 513 91 11 3 507 460976309 460976816 3.470000e-95 359.0
35 TraesCS6B01G405900 chr1D 90.909 44 3 1 1372 1415 492537589 492537547 1.420000e-04 58.4
36 TraesCS6B01G405900 chr5A 77.132 516 99 17 4 508 306506160 306506667 7.730000e-72 281.0
37 TraesCS6B01G405900 chr2B 75.651 538 111 15 2016 2543 727221831 727221304 2.180000e-62 250.0
38 TraesCS6B01G405900 chr2B 75.978 179 26 12 344 508 263914113 263914288 3.910000e-10 76.8
39 TraesCS6B01G405900 chr2B 74.586 181 29 11 344 509 110090284 110090106 3.050000e-06 63.9
40 TraesCS6B01G405900 chr2D 76.149 457 97 11 2019 2469 598729002 598728552 2.840000e-56 230.0
41 TraesCS6B01G405900 chr5D 76.596 329 53 20 196 507 292136177 292135856 3.780000e-35 159.0
42 TraesCS6B01G405900 chr5D 77.193 228 32 17 295 507 322397212 322397434 8.300000e-22 115.0
43 TraesCS6B01G405900 chr7A 86.111 108 9 5 404 507 113034393 113034498 1.070000e-20 111.0
44 TraesCS6B01G405900 chr7A 85.149 101 14 1 2443 2543 157153514 157153415 6.460000e-18 102.0
45 TraesCS6B01G405900 chr7D 83.495 103 15 2 2443 2543 155305417 155305315 1.080000e-15 95.3
46 TraesCS6B01G405900 chr7D 86.747 83 11 0 2781 2863 510397709 510397791 3.890000e-15 93.5
47 TraesCS6B01G405900 chr7D 76.243 181 27 9 344 509 529471287 529471108 8.410000e-12 82.4
48 TraesCS6B01G405900 chr7D 95.833 48 2 0 461 508 334398064 334398017 1.090000e-10 78.7
49 TraesCS6B01G405900 chr7B 83.158 95 10 3 421 509 324399433 324399527 8.410000e-12 82.4
50 TraesCS6B01G405900 chr7B 94.118 34 2 0 2881 2914 324550873 324550906 7.000000e-03 52.8
51 TraesCS6B01G405900 chr3D 81.250 96 17 1 2873 2967 557653747 557653842 3.910000e-10 76.8
52 TraesCS6B01G405900 chr3D 97.500 40 1 0 2826 2865 459078919 459078880 6.550000e-08 69.4
53 TraesCS6B01G405900 chr3D 95.238 42 1 1 2825 2865 495804864 495804905 8.470000e-07 65.8
54 TraesCS6B01G405900 chr3D 93.182 44 3 0 2822 2865 495804962 495804919 8.470000e-07 65.8
55 TraesCS6B01G405900 chr3A 95.455 44 2 0 2820 2863 18825605 18825562 1.820000e-08 71.3
56 TraesCS6B01G405900 chr3A 91.837 49 4 0 2817 2865 456381667 456381715 6.550000e-08 69.4
57 TraesCS6B01G405900 chr1B 71.000 300 75 11 1120 1415 685233345 685233054 1.100000e-05 62.1
58 TraesCS6B01G405900 chr3B 85.965 57 4 4 2809 2863 654335530 654335584 1.420000e-04 58.4
59 TraesCS6B01G405900 chr1A 90.909 44 3 1 1372 1415 590997060 590997018 1.420000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G405900 chr6B 680765399 680769054 3655 True 2334.666667 6752 94.872000 1 3656 3 chr6B.!!$R3 3655
1 TraesCS6B01G405900 chr6B 680893835 680897046 3211 False 1572.666667 2630 93.189667 506 3656 3 chr6B.!!$F2 3150
2 TraesCS6B01G405900 chr6A 595002912 595005736 2824 True 997.333333 2532 88.315333 515 2662 3 chr6A.!!$R1 2147
3 TraesCS6B01G405900 chr6D 449154133 449162320 8187 True 808.750000 2453 87.404250 537 3646 4 chr6D.!!$R3 3109
4 TraesCS6B01G405900 chr6D 448916623 448917327 704 True 438.000000 704 86.138000 3144 3656 2 chr6D.!!$R2 512
5 TraesCS6B01G405900 chr4D 381737441 381738691 1250 False 1085.000000 1085 82.464000 1028 2282 1 chr4D.!!$F1 1254
6 TraesCS6B01G405900 chr4A 568875294 568875799 505 False 387.000000 387 80.777000 3 508 1 chr4A.!!$F1 505
7 TraesCS6B01G405900 chr1D 460976309 460976816 507 False 359.000000 359 79.727000 3 507 1 chr1D.!!$F1 504
8 TraesCS6B01G405900 chr5A 306506160 306506667 507 False 281.000000 281 77.132000 4 508 1 chr5A.!!$F1 504
9 TraesCS6B01G405900 chr2B 727221304 727221831 527 True 250.000000 250 75.651000 2016 2543 1 chr2B.!!$R2 527

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
781 1091 0.035458 ATGGTAGCTAGATTGCCGGC 59.965 55.000 22.73 22.73 0.0 6.13 F
783 1093 0.035458 GGTAGCTAGATTGCCGGCAT 59.965 55.000 33.25 20.52 0.0 4.40 F
788 1098 0.240145 CTAGATTGCCGGCATGCATG 59.760 55.000 33.25 22.70 41.7 4.06 F
803 1113 1.000739 CATGGCCACCACAGGGAAT 59.999 57.895 8.16 0.00 35.8 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2267 0.387202 ACAGCGAGGGATCGAGAATG 59.613 55.000 1.17 0.0 34.64 2.67 R
1948 2270 1.758936 TTTACAGCGAGGGATCGAGA 58.241 50.000 1.17 0.0 34.64 4.04 R
2122 2494 2.047274 CACCACGGCGTCCATCTT 60.047 61.111 10.85 0.0 0.00 2.40 R
2939 3470 8.630037 ACTCCCTCTGTTTTTAAATACAAGTTG 58.370 33.333 11.79 0.0 0.00 3.16 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
65 66 1.895131 GACCACATTCTTGCCCATTGT 59.105 47.619 0.00 0.00 0.00 2.71
66 67 1.619827 ACCACATTCTTGCCCATTGTG 59.380 47.619 0.00 0.00 37.90 3.33
67 68 1.894466 CCACATTCTTGCCCATTGTGA 59.106 47.619 3.10 0.00 39.98 3.58
77 78 2.942376 TGCCCATTGTGATTACGCTAAG 59.058 45.455 0.00 0.00 0.00 2.18
110 111 0.942410 GGTGCTTCGACGTGCTACAA 60.942 55.000 14.25 0.00 0.00 2.41
113 114 1.267533 TGCTTCGACGTGCTACAAGTA 59.732 47.619 14.25 0.00 0.00 2.24
120 121 5.090757 TCGACGTGCTACAAGTAAACATAG 58.909 41.667 0.00 0.00 0.00 2.23
131 132 1.852895 GTAAACATAGAGCTGCCGACG 59.147 52.381 0.00 0.00 0.00 5.12
132 133 0.460284 AAACATAGAGCTGCCGACGG 60.460 55.000 10.29 10.29 0.00 4.79
134 135 1.299468 CATAGAGCTGCCGACGGAC 60.299 63.158 20.50 9.82 0.00 4.79
146 147 0.453950 CGACGGACGATGAGACGTTT 60.454 55.000 0.00 0.00 46.52 3.60
162 163 2.168936 ACGTTTACTGACTGGTGGTTGA 59.831 45.455 0.00 0.00 0.00 3.18
163 164 3.199677 CGTTTACTGACTGGTGGTTGAA 58.800 45.455 0.00 0.00 0.00 2.69
168 169 1.334869 CTGACTGGTGGTTGAAGCAAC 59.665 52.381 5.31 5.31 42.89 4.17
218 219 2.617308 TGGATTCGACTCCTACGTCATC 59.383 50.000 21.08 0.95 36.20 2.92
231 232 0.740868 CGTCATCGGAACTGCATGGT 60.741 55.000 0.00 0.00 0.00 3.55
234 235 1.815421 ATCGGAACTGCATGGTCGC 60.815 57.895 0.00 0.00 31.85 5.19
268 269 3.020984 GGAACACAAGGGTCTTCAACAA 58.979 45.455 0.00 0.00 0.00 2.83
270 271 4.421058 GAACACAAGGGTCTTCAACAAAC 58.579 43.478 0.00 0.00 0.00 2.93
291 293 0.681175 GCAGCAACAAAGAACCCCAT 59.319 50.000 0.00 0.00 0.00 4.00
293 295 1.273327 CAGCAACAAAGAACCCCATCC 59.727 52.381 0.00 0.00 0.00 3.51
302 304 1.916181 AGAACCCCATCCCAACTAGTG 59.084 52.381 0.00 0.00 0.00 2.74
316 318 1.556911 ACTAGTGGAGATGGTGCTTGG 59.443 52.381 0.00 0.00 0.00 3.61
344 346 0.251077 AAGAGTGGAAGCTTGCAGGG 60.251 55.000 22.03 0.00 0.00 4.45
352 354 2.282745 GCTTGCAGGGCTTGGAGT 60.283 61.111 0.00 0.00 0.00 3.85
353 355 2.338785 GCTTGCAGGGCTTGGAGTC 61.339 63.158 0.00 0.00 0.00 3.36
388 390 6.821031 TCCTTTTGTGAGAGAGTAGACTAC 57.179 41.667 4.32 4.32 0.00 2.73
390 392 7.005296 TCCTTTTGTGAGAGAGTAGACTACTT 58.995 38.462 16.24 6.78 39.59 2.24
393 395 6.561737 TTGTGAGAGAGTAGACTACTTGTG 57.438 41.667 16.24 0.00 39.59 3.33
407 411 2.023673 ACTTGTGTCATGGTGTTGTGG 58.976 47.619 0.00 0.00 0.00 4.17
413 417 0.257328 TCATGGTGTTGTGGGTGTGT 59.743 50.000 0.00 0.00 0.00 3.72
418 422 1.519676 TGTTGTGGGTGTGTCGACG 60.520 57.895 11.62 0.00 0.00 5.12
420 424 1.519676 TTGTGGGTGTGTCGACGTG 60.520 57.895 11.62 0.00 0.00 4.49
434 438 1.898079 CGACGTGAATGTTCGCATTTG 59.102 47.619 0.00 0.00 46.84 2.32
436 440 3.296628 GACGTGAATGTTCGCATTTGTT 58.703 40.909 0.00 0.00 46.84 2.83
455 459 9.206870 CATTTGTTGTTGGCTTCTTGTAATTAT 57.793 29.630 0.00 0.00 0.00 1.28
457 461 9.685828 TTTGTTGTTGGCTTCTTGTAATTATAC 57.314 29.630 0.00 0.00 0.00 1.47
459 463 8.726988 TGTTGTTGGCTTCTTGTAATTATACTC 58.273 33.333 0.00 0.00 32.98 2.59
501 508 3.242349 ACGCTATTGTCGTACTCTCGAAG 60.242 47.826 0.00 0.00 41.47 3.79
529 806 7.750229 AAACTGTGTATGTTCATTCTCACAT 57.250 32.000 13.48 0.00 37.40 3.21
548 829 3.131478 GGCACGGCCGTTAGCAAT 61.131 61.111 33.31 9.58 46.50 3.56
574 859 2.378547 TCCCAGCCAGGTCTTTACAATT 59.621 45.455 0.00 0.00 34.66 2.32
624 909 8.954350 TCTCGTCTTAAAGTTAGTTAGCTATGT 58.046 33.333 0.00 0.00 0.00 2.29
774 1084 2.975489 CCACAGGGAATGGTAGCTAGAT 59.025 50.000 0.00 0.00 35.59 1.98
775 1085 3.392616 CCACAGGGAATGGTAGCTAGATT 59.607 47.826 0.00 0.00 35.59 2.40
776 1086 4.384056 CACAGGGAATGGTAGCTAGATTG 58.616 47.826 0.00 0.00 0.00 2.67
777 1087 3.181450 ACAGGGAATGGTAGCTAGATTGC 60.181 47.826 0.00 0.98 0.00 3.56
778 1088 2.373502 AGGGAATGGTAGCTAGATTGCC 59.626 50.000 20.45 20.45 37.73 4.52
779 1089 2.417719 GGAATGGTAGCTAGATTGCCG 58.582 52.381 0.00 0.00 0.00 5.69
780 1090 2.417719 GAATGGTAGCTAGATTGCCGG 58.582 52.381 0.00 0.00 0.00 6.13
781 1091 0.035458 ATGGTAGCTAGATTGCCGGC 59.965 55.000 22.73 22.73 0.00 6.13
782 1092 1.334384 TGGTAGCTAGATTGCCGGCA 61.334 55.000 29.03 29.03 0.00 5.69
783 1093 0.035458 GGTAGCTAGATTGCCGGCAT 59.965 55.000 33.25 20.52 0.00 4.40
784 1094 1.151668 GTAGCTAGATTGCCGGCATG 58.848 55.000 33.25 18.38 0.00 4.06
785 1095 0.603707 TAGCTAGATTGCCGGCATGC 60.604 55.000 33.25 26.32 0.00 4.06
786 1096 2.188829 GCTAGATTGCCGGCATGCA 61.189 57.895 33.25 17.27 40.07 3.96
787 1097 1.521450 GCTAGATTGCCGGCATGCAT 61.521 55.000 33.25 21.93 41.70 3.96
788 1098 0.240145 CTAGATTGCCGGCATGCATG 59.760 55.000 33.25 22.70 41.70 4.06
789 1099 1.174078 TAGATTGCCGGCATGCATGG 61.174 55.000 33.25 20.95 41.70 3.66
797 1107 3.383681 GCATGCATGGCCACCACA 61.384 61.111 27.34 7.20 35.80 4.17
798 1108 2.889617 CATGCATGGCCACCACAG 59.110 61.111 19.40 1.16 35.80 3.66
799 1109 2.363276 ATGCATGGCCACCACAGG 60.363 61.111 8.16 0.00 35.80 4.00
800 1110 3.968837 ATGCATGGCCACCACAGGG 62.969 63.158 8.16 0.00 35.80 4.45
801 1111 4.365111 GCATGGCCACCACAGGGA 62.365 66.667 8.16 0.00 35.80 4.20
802 1112 2.440147 CATGGCCACCACAGGGAA 59.560 61.111 8.16 0.00 35.80 3.97
803 1113 1.000739 CATGGCCACCACAGGGAAT 59.999 57.895 8.16 0.00 35.80 3.01
804 1114 1.000739 ATGGCCACCACAGGGAATG 59.999 57.895 8.16 0.00 35.80 2.67
805 1115 2.362889 GGCCACCACAGGGAATGG 60.363 66.667 0.00 0.00 43.43 3.16
812 1122 2.918712 CCACAGGGAATGGTAGCTAG 57.081 55.000 0.00 0.00 35.59 3.42
813 1123 2.398588 CCACAGGGAATGGTAGCTAGA 58.601 52.381 0.00 0.00 35.59 2.43
827 1137 1.521450 GCTAGATTGCCGGCATGCAT 61.521 55.000 33.25 21.93 41.70 3.96
1022 1335 2.097825 GGAGTCGGGAAGTGCTACTAA 58.902 52.381 0.00 0.00 0.00 2.24
1659 1972 2.040412 GGAGTTCAAGGAGATGGTGGTT 59.960 50.000 0.00 0.00 0.00 3.67
1680 1993 2.821366 CTGATGACCACTGCCGGC 60.821 66.667 22.73 22.73 0.00 6.13
1811 2124 2.511600 GTCCGAACATGAGGCGGG 60.512 66.667 19.67 6.34 44.87 6.13
1812 2125 2.682136 TCCGAACATGAGGCGGGA 60.682 61.111 19.67 8.20 44.87 5.14
1945 2267 5.385617 TCAAAGCTCTACTTAACGTACGTC 58.614 41.667 23.05 5.58 37.75 4.34
1946 2268 5.049474 TCAAAGCTCTACTTAACGTACGTCA 60.049 40.000 23.05 3.49 37.75 4.35
1948 2270 5.557891 AGCTCTACTTAACGTACGTCATT 57.442 39.130 23.05 8.99 0.00 2.57
1950 2272 5.353678 AGCTCTACTTAACGTACGTCATTCT 59.646 40.000 23.05 8.16 0.00 2.40
1951 2273 5.676310 GCTCTACTTAACGTACGTCATTCTC 59.324 44.000 23.05 2.34 0.00 2.87
1952 2274 5.789507 TCTACTTAACGTACGTCATTCTCG 58.210 41.667 23.05 8.09 0.00 4.04
1954 2276 5.227238 ACTTAACGTACGTCATTCTCGAT 57.773 39.130 23.05 4.95 0.00 3.59
1974 2296 3.536956 TCCCTCGCTGTAAATAACCAG 57.463 47.619 0.00 0.00 0.00 4.00
1983 2307 5.236263 CGCTGTAAATAACCAGACATGCATA 59.764 40.000 0.00 0.00 0.00 3.14
1984 2308 6.073058 CGCTGTAAATAACCAGACATGCATAT 60.073 38.462 0.00 0.00 0.00 1.78
1985 2309 7.080099 GCTGTAAATAACCAGACATGCATATG 58.920 38.462 0.00 0.00 40.24 1.78
2007 2342 3.181513 GCACTCATGACACATGACACATC 60.182 47.826 9.88 0.00 0.00 3.06
2172 2544 1.064296 CCTCGAGGAATCCGACGTG 59.936 63.158 28.21 15.42 37.39 4.49
2376 2748 4.790861 GCGAGGTTCGACCCCGAC 62.791 72.222 12.70 0.00 45.50 4.79
2543 2915 3.461773 CGACTGGGAGATGCCGGT 61.462 66.667 4.29 4.29 37.63 5.28
2545 2917 4.101448 ACTGGGAGATGCCGGTGC 62.101 66.667 1.90 0.00 37.63 5.01
2546 2918 4.864334 CTGGGAGATGCCGGTGCC 62.864 72.222 1.90 0.00 37.63 5.01
2841 3348 3.967203 ATAAGAACTACTCGCTCCGTC 57.033 47.619 0.00 0.00 0.00 4.79
2842 3349 1.823797 AAGAACTACTCGCTCCGTCT 58.176 50.000 0.00 0.00 0.00 4.18
2856 3363 5.031578 CGCTCCGTCTCATAATATAAGAGC 58.968 45.833 0.00 0.00 40.55 4.09
3023 6451 6.075918 GTGCATATCACAAGCGAATTGATAG 58.924 40.000 7.68 0.00 44.98 2.08
3059 6487 8.471609 ACAAATCATCATTGAGCATAATGTTGA 58.528 29.630 19.85 19.85 44.42 3.18
3098 6526 6.583806 AGCAACATCGTTTGAATCAAGATTTC 59.416 34.615 0.00 0.00 0.00 2.17
3122 6550 7.825681 TCACCACATATTTGACTACCAAAATG 58.174 34.615 0.00 0.00 46.64 2.32
3134 6562 5.713025 ACTACCAAAATGTTGATGCATGTC 58.287 37.500 2.46 0.00 36.83 3.06
3181 8981 7.054124 TGGAAAGAAAGGCTAATGATATCGTT 58.946 34.615 14.45 14.45 0.00 3.85
3196 8996 1.442520 CGTTGCCTTCATTGGTGCG 60.443 57.895 0.00 0.00 0.00 5.34
3353 9153 3.036091 TGTAGGCCATGGTACCTCTTAC 58.964 50.000 14.67 8.06 37.50 2.34
3525 9331 8.716909 ACAAAATTGGTGAAAACTTTTGTACTG 58.283 29.630 9.28 0.00 44.05 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.875963 CAAGAATGTGGTCCACGCC 59.124 57.895 17.27 8.52 37.14 5.68
65 66 2.167693 CCACACCTCCTTAGCGTAATCA 59.832 50.000 0.00 0.00 0.00 2.57
66 67 2.822764 CCACACCTCCTTAGCGTAATC 58.177 52.381 0.00 0.00 0.00 1.75
67 68 1.134491 GCCACACCTCCTTAGCGTAAT 60.134 52.381 0.00 0.00 0.00 1.89
90 91 2.126618 TAGCACGTCGAAGCACCG 60.127 61.111 14.72 0.00 0.00 4.94
92 93 0.435008 CTTGTAGCACGTCGAAGCAC 59.565 55.000 14.72 11.28 0.00 4.40
110 111 2.479730 CGTCGGCAGCTCTATGTTTACT 60.480 50.000 0.00 0.00 0.00 2.24
113 114 0.460284 CCGTCGGCAGCTCTATGTTT 60.460 55.000 0.00 0.00 0.00 2.83
120 121 4.194720 ATCGTCCGTCGGCAGCTC 62.195 66.667 6.34 0.00 40.32 4.09
131 132 3.119919 AGTCAGTAAACGTCTCATCGTCC 60.120 47.826 0.00 0.00 43.38 4.79
132 133 3.846896 CAGTCAGTAAACGTCTCATCGTC 59.153 47.826 0.00 0.00 43.38 4.20
134 135 3.172050 CCAGTCAGTAAACGTCTCATCG 58.828 50.000 0.00 0.00 0.00 3.84
146 147 1.765904 TGCTTCAACCACCAGTCAGTA 59.234 47.619 0.00 0.00 0.00 2.74
162 163 1.208293 GGAGAATCTCCCTCGTTGCTT 59.792 52.381 18.34 0.00 44.36 3.91
163 164 0.827368 GGAGAATCTCCCTCGTTGCT 59.173 55.000 18.34 0.00 44.36 3.91
168 169 7.633772 TAGAATTTTCTTGGAGAATCTCCCTCG 60.634 40.741 25.16 13.71 42.76 4.63
189 190 3.288964 AGGAGTCGAATCCACGTAGAAT 58.711 45.455 31.53 7.43 42.26 2.40
218 219 0.530650 ATAGCGACCATGCAGTTCCG 60.531 55.000 0.00 0.00 37.31 4.30
234 235 4.082571 CCTTGTGTTCCTTTGCTTCCATAG 60.083 45.833 0.00 0.00 0.00 2.23
252 253 2.021457 CGGTTTGTTGAAGACCCTTGT 58.979 47.619 0.00 0.00 0.00 3.16
268 269 0.102300 GGTTCTTTGTTGCTGCGGTT 59.898 50.000 0.00 0.00 0.00 4.44
270 271 1.007387 GGGTTCTTTGTTGCTGCGG 60.007 57.895 0.00 0.00 0.00 5.69
291 293 2.187958 CACCATCTCCACTAGTTGGGA 58.812 52.381 13.77 7.21 45.82 4.37
293 295 1.556911 AGCACCATCTCCACTAGTTGG 59.443 52.381 8.69 8.69 46.62 3.77
302 304 3.326006 TGATATCTCCAAGCACCATCTCC 59.674 47.826 3.98 0.00 0.00 3.71
312 314 5.526846 GCTTCCACTCTTTGATATCTCCAAG 59.473 44.000 3.98 4.23 0.00 3.61
316 318 5.007528 GCAAGCTTCCACTCTTTGATATCTC 59.992 44.000 0.00 0.00 0.00 2.75
344 346 1.549170 TCTAAACCTCCGACTCCAAGC 59.451 52.381 0.00 0.00 0.00 4.01
352 354 4.285003 TCACAAAAGGATCTAAACCTCCGA 59.715 41.667 0.00 0.00 36.67 4.55
353 355 4.575885 TCACAAAAGGATCTAAACCTCCG 58.424 43.478 0.00 0.00 36.67 4.63
388 390 1.337703 CCCACAACACCATGACACAAG 59.662 52.381 0.00 0.00 0.00 3.16
390 392 0.257328 ACCCACAACACCATGACACA 59.743 50.000 0.00 0.00 0.00 3.72
393 395 0.667993 CACACCCACAACACCATGAC 59.332 55.000 0.00 0.00 0.00 3.06
407 411 1.191647 GAACATTCACGTCGACACACC 59.808 52.381 17.16 0.00 0.00 4.16
413 417 1.424403 AATGCGAACATTCACGTCGA 58.576 45.000 0.00 0.00 43.08 4.20
418 422 4.317980 CCAACAACAAATGCGAACATTCAC 60.318 41.667 0.00 0.00 45.90 3.18
420 424 3.362888 GCCAACAACAAATGCGAACATTC 60.363 43.478 0.00 0.00 45.90 2.67
434 438 8.947115 AGAGTATAATTACAAGAAGCCAACAAC 58.053 33.333 0.00 0.00 0.00 3.32
436 440 8.540388 AGAGAGTATAATTACAAGAAGCCAACA 58.460 33.333 0.00 0.00 0.00 3.33
456 460 9.694137 GCGTACCATATTTTTATAGAAGAGAGT 57.306 33.333 0.00 0.00 0.00 3.24
457 461 9.915629 AGCGTACCATATTTTTATAGAAGAGAG 57.084 33.333 0.00 0.00 0.00 3.20
507 514 5.578336 CGATGTGAGAATGAACATACACAGT 59.422 40.000 18.34 11.69 40.58 3.55
510 517 4.260375 GCCGATGTGAGAATGAACATACAC 60.260 45.833 0.00 0.00 37.15 2.90
548 829 0.178873 AAGACCTGGCTGGGAAGGTA 60.179 55.000 15.36 0.00 46.97 3.08
780 1090 3.365291 CTGTGGTGGCCATGCATGC 62.365 63.158 21.69 11.82 35.28 4.06
781 1091 2.717044 CCTGTGGTGGCCATGCATG 61.717 63.158 20.19 20.19 35.28 4.06
782 1092 2.363276 CCTGTGGTGGCCATGCAT 60.363 61.111 9.72 0.00 35.28 3.96
783 1093 4.682334 CCCTGTGGTGGCCATGCA 62.682 66.667 9.72 7.74 35.28 3.96
784 1094 3.884704 TTCCCTGTGGTGGCCATGC 62.885 63.158 9.72 2.53 35.28 4.06
785 1095 1.000739 ATTCCCTGTGGTGGCCATG 59.999 57.895 9.72 0.00 35.28 3.66
786 1096 1.000739 CATTCCCTGTGGTGGCCAT 59.999 57.895 9.72 0.00 35.28 4.40
787 1097 2.440147 CATTCCCTGTGGTGGCCA 59.560 61.111 0.00 0.00 0.00 5.36
788 1098 2.362889 CCATTCCCTGTGGTGGCC 60.363 66.667 0.00 0.00 31.96 5.36
793 1103 2.398588 TCTAGCTACCATTCCCTGTGG 58.601 52.381 0.00 0.00 42.55 4.17
794 1104 4.384056 CAATCTAGCTACCATTCCCTGTG 58.616 47.826 0.00 0.00 0.00 3.66
795 1105 3.181450 GCAATCTAGCTACCATTCCCTGT 60.181 47.826 0.00 0.00 0.00 4.00
796 1106 3.406764 GCAATCTAGCTACCATTCCCTG 58.593 50.000 0.00 0.00 0.00 4.45
797 1107 2.373502 GGCAATCTAGCTACCATTCCCT 59.626 50.000 0.00 0.00 34.17 4.20
798 1108 2.784347 GGCAATCTAGCTACCATTCCC 58.216 52.381 0.00 0.00 34.17 3.97
799 1109 2.417719 CGGCAATCTAGCTACCATTCC 58.582 52.381 0.00 0.00 34.17 3.01
800 1110 2.417719 CCGGCAATCTAGCTACCATTC 58.582 52.381 0.00 0.00 34.17 2.67
801 1111 1.543429 GCCGGCAATCTAGCTACCATT 60.543 52.381 24.80 0.00 34.17 3.16
802 1112 0.035458 GCCGGCAATCTAGCTACCAT 59.965 55.000 24.80 0.00 34.17 3.55
803 1113 1.334384 TGCCGGCAATCTAGCTACCA 61.334 55.000 30.74 0.00 34.17 3.25
804 1114 0.035458 ATGCCGGCAATCTAGCTACC 59.965 55.000 36.33 0.00 34.17 3.18
805 1115 1.151668 CATGCCGGCAATCTAGCTAC 58.848 55.000 36.33 0.00 34.17 3.58
806 1116 0.603707 GCATGCCGGCAATCTAGCTA 60.604 55.000 36.33 6.47 34.17 3.32
807 1117 1.895707 GCATGCCGGCAATCTAGCT 60.896 57.895 36.33 12.84 34.17 3.32
808 1118 2.188829 TGCATGCCGGCAATCTAGC 61.189 57.895 36.33 29.02 41.65 3.42
809 1119 4.146058 TGCATGCCGGCAATCTAG 57.854 55.556 36.33 21.02 41.65 2.43
827 1137 3.770040 CCCTGTCGATCGTGGCCA 61.770 66.667 15.94 0.00 0.00 5.36
976 1286 1.128724 GTCGATCTCGTGTCGTGCTG 61.129 60.000 0.00 0.00 39.91 4.41
977 1287 1.134901 GTCGATCTCGTGTCGTGCT 59.865 57.895 0.00 0.00 39.91 4.40
978 1288 2.209076 CGTCGATCTCGTGTCGTGC 61.209 63.158 0.00 0.00 39.91 5.34
979 1289 0.852412 GTCGTCGATCTCGTGTCGTG 60.852 60.000 0.00 0.00 39.91 4.35
980 1290 1.013005 AGTCGTCGATCTCGTGTCGT 61.013 55.000 0.00 0.00 39.91 4.34
981 1291 0.919300 TAGTCGTCGATCTCGTGTCG 59.081 55.000 0.00 4.36 40.80 4.35
982 1292 2.348685 CCATAGTCGTCGATCTCGTGTC 60.349 54.545 0.00 0.00 40.80 3.67
1011 1324 3.072476 ACATGGTGGTGTTAGTAGCACTT 59.928 43.478 15.63 0.00 45.66 3.16
1022 1335 1.956477 GCTCTTGAAACATGGTGGTGT 59.044 47.619 0.00 0.00 0.00 4.16
1212 1525 4.457496 ATCGGTCCGTGCAGCCTG 62.457 66.667 11.88 0.00 0.00 4.85
1224 1537 1.221840 GGTCAGGTGCATGATCGGT 59.778 57.895 0.00 0.00 0.00 4.69
1659 1972 1.297689 GGCAGTGGTCATCAGCTCA 59.702 57.895 0.00 0.00 0.00 4.26
1680 1993 3.691342 TCGCCGAGGTTCACCAGG 61.691 66.667 0.00 2.57 38.89 4.45
1811 2124 1.021390 CCTGTCATTGTCGGCCACTC 61.021 60.000 2.24 0.00 0.00 3.51
1812 2125 1.003355 CCTGTCATTGTCGGCCACT 60.003 57.895 2.24 0.00 0.00 4.00
1908 2230 4.284490 AGAGCTTTGATGTTGAGGTCTGTA 59.716 41.667 3.78 0.00 44.09 2.74
1945 2267 0.387202 ACAGCGAGGGATCGAGAATG 59.613 55.000 1.17 0.00 34.64 2.67
1946 2268 1.982660 TACAGCGAGGGATCGAGAAT 58.017 50.000 1.17 0.00 34.64 2.40
1948 2270 1.758936 TTTACAGCGAGGGATCGAGA 58.241 50.000 1.17 0.00 34.64 4.04
1950 2272 3.243636 GGTTATTTACAGCGAGGGATCGA 60.244 47.826 1.17 0.00 34.64 3.59
1951 2273 3.057734 GGTTATTTACAGCGAGGGATCG 58.942 50.000 0.00 0.00 0.00 3.69
1952 2274 4.058817 CTGGTTATTTACAGCGAGGGATC 58.941 47.826 0.00 0.00 0.00 3.36
1954 2276 3.101437 TCTGGTTATTTACAGCGAGGGA 58.899 45.455 0.00 0.00 34.76 4.20
1983 2307 2.745821 GTGTCATGTGTCATGAGTGCAT 59.254 45.455 11.90 0.00 34.29 3.96
1984 2308 2.145536 GTGTCATGTGTCATGAGTGCA 58.854 47.619 11.90 5.37 0.00 4.57
1985 2309 2.145536 TGTGTCATGTGTCATGAGTGC 58.854 47.619 11.90 6.84 0.00 4.40
1987 2311 3.008266 TGGATGTGTCATGTGTCATGAGT 59.992 43.478 11.90 1.08 0.00 3.41
1989 2313 3.699411 TGGATGTGTCATGTGTCATGA 57.301 42.857 8.14 8.14 0.00 3.07
2122 2494 2.047274 CACCACGGCGTCCATCTT 60.047 61.111 10.85 0.00 0.00 2.40
2939 3470 8.630037 ACTCCCTCTGTTTTTAAATACAAGTTG 58.370 33.333 11.79 0.00 0.00 3.16
3023 6451 8.119226 GCTCAATGATGATTTGTACAGTACTTC 58.881 37.037 12.07 7.01 34.37 3.01
3059 6487 1.322442 GTTGCTTCCCTGCTCTTGTT 58.678 50.000 0.00 0.00 0.00 2.83
3098 6526 7.601856 ACATTTTGGTAGTCAAATATGTGGTG 58.398 34.615 13.15 0.00 43.95 4.17
3122 6550 3.564235 TTTCTGCTGACATGCATCAAC 57.436 42.857 0.00 0.00 42.48 3.18
3134 6562 6.759356 TCCATATTTGCATGAAATTTCTGCTG 59.241 34.615 27.54 20.92 35.74 4.41
3143 6571 6.594937 GCCTTTCTTTCCATATTTGCATGAAA 59.405 34.615 0.00 0.00 0.00 2.69
3146 6574 5.667466 AGCCTTTCTTTCCATATTTGCATG 58.333 37.500 0.00 0.00 0.00 4.06
3181 8981 1.971167 GACCGCACCAATGAAGGCA 60.971 57.895 0.00 0.00 0.00 4.75
3479 9279 5.199982 TGTAGCAATCCTTTTATCCCCAA 57.800 39.130 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.