Multiple sequence alignment - TraesCS1B01G385100

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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 TraesCS1B01G385100 chr1B 100.000 3407 0 0 1 3407 618541997 618545403 0.000000e+00 6292.0
1 TraesCS1B01G385100 chr1B 88.407 1708 153 27 729 2411 618316577 618318264 0.000000e+00 2015.0
2 TraesCS1B01G385100 chr1B 87.456 1435 128 24 992 2411 618196966 618198363 0.000000e+00 1605.0
3 TraesCS1B01G385100 chr1B 84.668 1311 171 23 952 2246 618698970 618697674 0.000000e+00 1280.0
4 TraesCS1B01G385100 chr1B 84.918 789 109 9 2625 3407 52779796 52779012 0.000000e+00 789.0
5 TraesCS1B01G385100 chr1B 83.666 802 111 5 2625 3407 94577627 94578427 0.000000e+00 737.0
6 TraesCS1B01G385100 chr1B 96.657 359 11 1 2625 2983 618549666 618550023 2.260000e-166 595.0
7 TraesCS1B01G385100 chr1B 93.785 177 6 1 371 542 618196418 618196594 9.380000e-66 261.0
8 TraesCS1B01G385100 chr1B 87.719 228 17 6 138 364 618196011 618196228 4.360000e-64 255.0
9 TraesCS1B01G385100 chr1B 85.057 174 15 7 2465 2628 618318410 618318582 2.100000e-37 167.0
10 TraesCS1B01G385100 chr1B 93.694 111 2 4 798 905 618196802 618196910 9.780000e-36 161.0
11 TraesCS1B01G385100 chr1B 82.065 184 22 6 2451 2628 618198490 618198668 2.740000e-31 147.0
12 TraesCS1B01G385100 chr1B 84.956 113 6 5 1 104 618194491 618194601 1.670000e-18 104.0
13 TraesCS1B01G385100 chr1B 93.220 59 3 1 718 776 618196744 618196801 6.060000e-13 86.1
14 TraesCS1B01G385100 chr1B 100.000 36 0 0 112 147 618195950 618195985 2.190000e-07 67.6
15 TraesCS1B01G385100 chr1D 85.989 2077 210 51 369 2411 450738625 450740654 0.000000e+00 2148.0
16 TraesCS1B01G385100 chr1D 86.937 1822 170 36 623 2408 450578830 450580619 0.000000e+00 1984.0
17 TraesCS1B01G385100 chr1D 85.383 1252 149 20 1009 2246 451035700 451034469 0.000000e+00 1267.0
18 TraesCS1B01G385100 chr1D 81.084 1586 231 44 578 2129 451044382 451042832 0.000000e+00 1203.0
19 TraesCS1B01G385100 chr1D 87.417 1057 107 16 948 1990 451063174 451062130 0.000000e+00 1192.0
20 TraesCS1B01G385100 chr1D 88.406 207 20 3 138 341 450738346 450738551 2.630000e-61 246.0
21 TraesCS1B01G385100 chr1D 88.462 182 9 4 138 317 450576333 450576504 3.450000e-50 209.0
22 TraesCS1B01G385100 chr1D 93.662 142 6 1 369 510 450578559 450578697 3.450000e-50 209.0
23 TraesCS1B01G385100 chr1D 97.030 101 3 0 2523 2623 450740824 450740924 1.630000e-38 171.0
24 TraesCS1B01G385100 chr1D 86.607 112 9 3 1 108 450738153 450738262 5.970000e-23 119.0
25 TraesCS1B01G385100 chr1D 90.667 75 5 1 34 108 450576176 450576248 7.780000e-17 99.0
26 TraesCS1B01G385100 chr1D 100.000 29 0 0 119 147 450576279 450576307 2.000000e-03 54.7
27 TraesCS1B01G385100 chr1A 86.785 1922 186 37 519 2411 545751549 545753431 0.000000e+00 2080.0
28 TraesCS1B01G385100 chr1A 81.858 1604 210 56 582 2147 545764349 545762789 0.000000e+00 1275.0
29 TraesCS1B01G385100 chr1A 85.425 789 106 8 2624 3407 593754522 593755306 0.000000e+00 811.0
30 TraesCS1B01G385100 chr1A 87.898 157 7 5 1 147 545750959 545751113 1.260000e-39 174.0
31 TraesCS1B01G385100 chr1A 90.991 111 6 1 2522 2628 545753570 545753680 2.740000e-31 147.0
32 TraesCS1B01G385100 chr1A 95.890 73 3 0 371 443 545751445 545751517 5.970000e-23 119.0
33 TraesCS1B01G385100 chr1A 97.561 41 1 0 469 509 545751514 545751554 1.700000e-08 71.3
34 TraesCS1B01G385100 chr1A 94.286 35 1 1 1 34 545765241 545765207 6.000000e-03 52.8
35 TraesCS1B01G385100 chr4D 86.929 788 95 6 2625 3407 226964688 226963904 0.000000e+00 878.0
36 TraesCS1B01G385100 chr7B 86.058 789 101 8 2625 3407 733822954 733823739 0.000000e+00 839.0
37 TraesCS1B01G385100 chr7B 84.752 787 114 6 2625 3407 245628140 245627356 0.000000e+00 784.0
38 TraesCS1B01G385100 chr6B 84.071 791 115 10 2623 3407 165868015 165868800 0.000000e+00 752.0
39 TraesCS1B01G385100 chr5D 80.952 672 110 17 2745 3407 525143671 525143009 1.810000e-142 516.0
40 TraesCS1B01G385100 chrUn 84.922 451 65 3 2959 3407 333016293 333015844 1.440000e-123 453.0


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 TraesCS1B01G385100 chr1B 618541997 618545403 3406 False 6292.0000 6292 100.000000 1 3407 1 chr1B.!!$F2 3406
1 TraesCS1B01G385100 chr1B 618697674 618698970 1296 True 1280.0000 1280 84.668000 952 2246 1 chr1B.!!$R2 1294
2 TraesCS1B01G385100 chr1B 618316577 618318582 2005 False 1091.0000 2015 86.732000 729 2628 2 chr1B.!!$F5 1899
3 TraesCS1B01G385100 chr1B 52779012 52779796 784 True 789.0000 789 84.918000 2625 3407 1 chr1B.!!$R1 782
4 TraesCS1B01G385100 chr1B 94577627 94578427 800 False 737.0000 737 83.666000 2625 3407 1 chr1B.!!$F1 782
5 TraesCS1B01G385100 chr1B 618194491 618198668 4177 False 335.8375 1605 90.361875 1 2628 8 chr1B.!!$F4 2627
6 TraesCS1B01G385100 chr1D 451034469 451035700 1231 True 1267.0000 1267 85.383000 1009 2246 1 chr1D.!!$R1 1237
7 TraesCS1B01G385100 chr1D 451042832 451044382 1550 True 1203.0000 1203 81.084000 578 2129 1 chr1D.!!$R2 1551
8 TraesCS1B01G385100 chr1D 451062130 451063174 1044 True 1192.0000 1192 87.417000 948 1990 1 chr1D.!!$R3 1042
9 TraesCS1B01G385100 chr1D 450738153 450740924 2771 False 671.0000 2148 89.508000 1 2623 4 chr1D.!!$F2 2622
10 TraesCS1B01G385100 chr1D 450576176 450580619 4443 False 511.1400 1984 91.945600 34 2408 5 chr1D.!!$F1 2374
11 TraesCS1B01G385100 chr1A 593754522 593755306 784 False 811.0000 811 85.425000 2624 3407 1 chr1A.!!$F1 783
12 TraesCS1B01G385100 chr1A 545762789 545765241 2452 True 663.9000 1275 88.072000 1 2147 2 chr1A.!!$R1 2146
13 TraesCS1B01G385100 chr1A 545750959 545753680 2721 False 518.2600 2080 91.825000 1 2628 5 chr1A.!!$F2 2627
14 TraesCS1B01G385100 chr4D 226963904 226964688 784 True 878.0000 878 86.929000 2625 3407 1 chr4D.!!$R1 782
15 TraesCS1B01G385100 chr7B 733822954 733823739 785 False 839.0000 839 86.058000 2625 3407 1 chr7B.!!$F1 782
16 TraesCS1B01G385100 chr7B 245627356 245628140 784 True 784.0000 784 84.752000 2625 3407 1 chr7B.!!$R1 782
17 TraesCS1B01G385100 chr6B 165868015 165868800 785 False 752.0000 752 84.071000 2623 3407 1 chr6B.!!$F1 784
18 TraesCS1B01G385100 chr5D 525143009 525143671 662 True 516.0000 516 80.952000 2745 3407 1 chr5D.!!$R1 662

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
965 4763 0.967380 GGAAGCCACCACAATCCCTG 60.967 60.0 0.00 0.0 0.00 4.45 F
2105 5949 0.248498 TTCGGCGCTCTCGACATTAG 60.248 55.0 7.64 0.0 46.08 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 6229 0.110373 GAACAATCGTGTCCCAACGC 60.110 55.0 0.00 0.0 43.26 4.84 R
3305 7322 0.546122 CCTGGGTCCCGAATCAATGA 59.454 55.0 2.65 0.0 0.00 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 51 3.047877 CACCACCCGCTCCGTTTC 61.048 66.667 0.00 0.00 0.00 2.78
153 1566 4.697756 CAGCCGGCGTCTGGGAAA 62.698 66.667 23.20 0.00 0.00 3.13
233 1656 1.676014 GGGATCGAATATTCCCTGCCG 60.676 57.143 13.63 0.00 46.91 5.69
260 1684 3.452755 TCCTATTCCTATGTGCGTGTG 57.547 47.619 0.00 0.00 0.00 3.82
261 1685 2.102420 TCCTATTCCTATGTGCGTGTGG 59.898 50.000 0.00 0.00 0.00 4.17
262 1686 2.102420 CCTATTCCTATGTGCGTGTGGA 59.898 50.000 0.00 0.00 0.00 4.02
263 1687 2.779755 ATTCCTATGTGCGTGTGGAA 57.220 45.000 0.00 0.00 40.49 3.53
320 1763 1.279840 GCGCGCCAGATATTTCACC 59.720 57.895 23.24 0.00 0.00 4.02
321 1764 1.160329 GCGCGCCAGATATTTCACCT 61.160 55.000 23.24 0.00 0.00 4.00
575 4229 2.159156 ACACTCGCGCCATTAGATACAA 60.159 45.455 0.00 0.00 0.00 2.41
628 4357 1.446907 TTCCGACTCCTACACGAGAC 58.553 55.000 0.00 0.00 33.83 3.36
720 4463 1.074248 ACCGTCCAACCCAATCCAC 59.926 57.895 0.00 0.00 0.00 4.02
871 4639 1.547901 CCCAACTTTTCCTCTCCCACC 60.548 57.143 0.00 0.00 0.00 4.61
898 4673 2.416244 ATATACGCTCACCCGCCACG 62.416 60.000 0.00 0.00 0.00 4.94
905 4682 1.153127 TCACCCGCCACGAAAAAGT 60.153 52.632 0.00 0.00 0.00 2.66
907 4684 1.161843 CACCCGCCACGAAAAAGTAT 58.838 50.000 0.00 0.00 0.00 2.12
925 4702 9.659830 AAAAAGTATAACTCGTCAACAATTCAC 57.340 29.630 0.00 0.00 0.00 3.18
946 4735 3.344904 CTTGGACACAAGCAACAGAAG 57.655 47.619 0.00 0.00 46.67 2.85
964 4762 1.142688 AGGAAGCCACCACAATCCCT 61.143 55.000 0.00 0.00 0.00 4.20
965 4763 0.967380 GGAAGCCACCACAATCCCTG 60.967 60.000 0.00 0.00 0.00 4.45
974 4772 1.203050 CCACAATCCCTGTTCCCAACT 60.203 52.381 0.00 0.00 35.47 3.16
990 4792 4.838423 TCCCAACTCAGATTACACAAGAGA 59.162 41.667 0.00 0.00 0.00 3.10
1080 4882 4.814294 GTGTTCCTCGCGGCGGAT 62.814 66.667 23.46 0.00 0.00 4.18
1153 4958 2.500815 TACGCTGAGGAGGGAGCAGT 62.501 60.000 0.00 0.00 34.69 4.40
1403 5208 2.158959 CGAGGAACGTGGTGATCGC 61.159 63.158 0.00 0.00 37.22 4.58
1678 5486 1.384643 GTCCCCCAGTGGCTATCCT 60.385 63.158 2.61 0.00 0.00 3.24
1770 5578 4.625800 GAGCATCCGTTCTTGGCT 57.374 55.556 0.00 0.00 37.56 4.75
1821 5638 0.770499 TGGAGAGCAAATGGGTGTCA 59.230 50.000 0.00 0.00 38.92 3.58
1824 5641 0.478072 AGAGCAAATGGGTGTCACCA 59.522 50.000 23.48 10.15 46.24 4.17
1853 5670 4.778143 GGACGCGGCATTCTGGGT 62.778 66.667 17.00 0.00 45.96 4.51
1885 5714 4.456253 CCGACGAGGTGGACGACG 62.456 72.222 0.00 0.00 44.67 5.12
1886 5715 3.417224 CGACGAGGTGGACGACGA 61.417 66.667 0.00 0.00 46.85 4.20
1887 5716 2.479650 GACGAGGTGGACGACGAG 59.520 66.667 0.00 0.00 34.70 4.18
2105 5949 0.248498 TTCGGCGCTCTCGACATTAG 60.248 55.000 7.64 0.00 46.08 1.73
2165 6012 4.456911 ACAAGAAGCACACGATGATGATTT 59.543 37.500 0.00 0.00 0.00 2.17
2166 6013 4.611310 AGAAGCACACGATGATGATTTG 57.389 40.909 0.00 0.00 0.00 2.32
2178 6031 2.172505 TGATGATTTGGTCGTAGGGCAT 59.827 45.455 0.00 0.00 0.00 4.40
2206 6068 3.501445 GCATCAGCCATTGGAGATTCTAC 59.499 47.826 6.95 0.00 33.58 2.59
2237 6099 8.855110 TCACCAATTAGTGTCATGTAAATTGTT 58.145 29.630 3.91 4.24 38.91 2.83
2240 6102 9.567848 CCAATTAGTGTCATGTAAATTGTTACC 57.432 33.333 14.03 0.00 39.16 2.85
2241 6103 9.567848 CAATTAGTGTCATGTAAATTGTTACCC 57.432 33.333 0.00 0.00 39.16 3.69
2242 6104 5.873179 AGTGTCATGTAAATTGTTACCCG 57.127 39.130 0.00 0.00 39.16 5.28
2298 6172 2.414559 CGATTTCGTTCATGCCAAAGCT 60.415 45.455 0.00 0.00 35.61 3.74
2333 6207 1.991965 CGCTGCTCTTCTGTTTCTCTC 59.008 52.381 0.00 0.00 0.00 3.20
2334 6208 2.352617 CGCTGCTCTTCTGTTTCTCTCT 60.353 50.000 0.00 0.00 0.00 3.10
2335 6209 3.253230 GCTGCTCTTCTGTTTCTCTCTC 58.747 50.000 0.00 0.00 0.00 3.20
2336 6210 3.056607 GCTGCTCTTCTGTTTCTCTCTCT 60.057 47.826 0.00 0.00 0.00 3.10
2337 6211 4.487948 CTGCTCTTCTGTTTCTCTCTCTG 58.512 47.826 0.00 0.00 0.00 3.35
2338 6212 3.253230 GCTCTTCTGTTTCTCTCTCTGC 58.747 50.000 0.00 0.00 0.00 4.26
2339 6213 3.056607 GCTCTTCTGTTTCTCTCTCTGCT 60.057 47.826 0.00 0.00 0.00 4.24
2340 6214 4.561326 GCTCTTCTGTTTCTCTCTCTGCTT 60.561 45.833 0.00 0.00 0.00 3.91
2341 6215 4.880759 TCTTCTGTTTCTCTCTCTGCTTG 58.119 43.478 0.00 0.00 0.00 4.01
2343 6217 2.632028 TCTGTTTCTCTCTCTGCTTGCT 59.368 45.455 0.00 0.00 0.00 3.91
2344 6218 2.737783 CTGTTTCTCTCTCTGCTTGCTG 59.262 50.000 0.00 0.00 0.00 4.41
2352 6229 3.800863 CTGCTTGCTGCTGCTCCG 61.801 66.667 17.00 6.12 43.37 4.63
2369 6246 2.314647 CGCGTTGGGACACGATTGT 61.315 57.895 0.00 0.00 39.29 2.71
2388 6266 7.772721 GATTGTTCGAGAAATTTCAAGACAG 57.227 36.000 19.99 4.93 0.00 3.51
2391 6269 7.496529 TGTTCGAGAAATTTCAAGACAGAAT 57.503 32.000 19.99 0.00 0.00 2.40
2401 6285 7.573968 ATTTCAAGACAGAATATAGGTTGCC 57.426 36.000 0.00 0.00 0.00 4.52
2411 6295 5.128171 AGAATATAGGTTGCCACTAACACGA 59.872 40.000 0.00 0.00 32.22 4.35
2412 6296 3.906720 ATAGGTTGCCACTAACACGAT 57.093 42.857 0.00 0.00 32.22 3.73
2417 6301 1.011968 TGCCACTAACACGATGCGTC 61.012 55.000 0.00 0.00 38.32 5.19
2418 6302 1.011968 GCCACTAACACGATGCGTCA 61.012 55.000 6.75 0.00 38.32 4.35
2420 6304 1.668919 CCACTAACACGATGCGTCAGT 60.669 52.381 6.75 0.74 38.32 3.41
2421 6305 2.058798 CACTAACACGATGCGTCAGTT 58.941 47.619 15.48 15.48 38.32 3.16
2423 6307 2.287970 ACTAACACGATGCGTCAGTTCA 60.288 45.455 14.82 4.55 38.32 3.18
2425 6309 0.249280 ACACGATGCGTCAGTTCACA 60.249 50.000 6.75 0.00 38.32 3.58
2427 6311 0.667487 ACGATGCGTCAGTTCACAGG 60.667 55.000 6.75 0.00 33.69 4.00
2428 6312 0.388520 CGATGCGTCAGTTCACAGGA 60.389 55.000 6.75 0.00 0.00 3.86
2429 6313 1.737029 CGATGCGTCAGTTCACAGGAT 60.737 52.381 6.75 0.00 0.00 3.24
2432 6316 0.798776 GCGTCAGTTCACAGGATTGG 59.201 55.000 0.00 0.00 0.00 3.16
2433 6317 0.798776 CGTCAGTTCACAGGATTGGC 59.201 55.000 0.00 0.00 0.00 4.52
2434 6318 1.877680 CGTCAGTTCACAGGATTGGCA 60.878 52.381 0.00 0.00 0.00 4.92
2435 6319 1.808945 GTCAGTTCACAGGATTGGCAG 59.191 52.381 0.00 0.00 0.00 4.85
2436 6320 0.524862 CAGTTCACAGGATTGGCAGC 59.475 55.000 0.00 0.00 0.00 5.25
2437 6321 0.610232 AGTTCACAGGATTGGCAGCC 60.610 55.000 3.66 3.66 0.00 4.85
2438 6322 0.895100 GTTCACAGGATTGGCAGCCA 60.895 55.000 11.22 11.22 0.00 4.75
2439 6323 0.895100 TTCACAGGATTGGCAGCCAC 60.895 55.000 15.89 2.97 30.78 5.01
2440 6324 2.360350 ACAGGATTGGCAGCCACG 60.360 61.111 15.89 2.90 30.78 4.94
2459 6443 3.659092 CGCGCACCAAAGCTTCCA 61.659 61.111 8.75 0.00 0.00 3.53
2462 6446 2.644992 GCACCAAAGCTTCCACGG 59.355 61.111 0.00 0.70 0.00 4.94
2483 6467 3.259425 GAAAGCACTGCTGCACGGG 62.259 63.158 3.73 0.00 46.97 5.28
2488 6472 2.186160 CACTGCTGCACGGGTCAAA 61.186 57.895 0.00 0.00 0.00 2.69
2502 6486 3.990318 GGTCAAAAACCTCTTGTCAGG 57.010 47.619 0.00 0.00 45.45 3.86
2503 6487 2.034685 GGTCAAAAACCTCTTGTCAGGC 59.965 50.000 0.00 0.00 45.45 4.85
2508 6496 2.045536 CCTCTTGTCAGGCAGGCC 60.046 66.667 0.97 0.97 0.00 5.19
2513 6501 1.078497 TTGTCAGGCAGGCCATACG 60.078 57.895 13.63 0.00 38.92 3.06
2519 6507 2.045340 GCAGGCCATACGTGGGTT 60.045 61.111 5.01 0.00 46.14 4.11
2605 6599 0.541863 ATTACTTCGCCAGGTGGAGG 59.458 55.000 13.36 1.97 37.39 4.30
2649 6643 1.663695 CGAACCACTGTCAACCAAGT 58.336 50.000 0.00 0.00 0.00 3.16
2694 6688 1.202348 CATCGACTACAGCTGGTGTCA 59.798 52.381 28.31 20.02 40.94 3.58
2726 6736 1.542915 GACAGCTACAGTACCGGAACA 59.457 52.381 9.46 0.00 0.00 3.18
2793 6803 2.125269 CCGAACTGGGCCCGTTAG 60.125 66.667 25.44 24.14 0.00 2.34
2808 6820 3.155093 CGTTAGCGGGTGTAACAGTAT 57.845 47.619 0.00 0.00 39.98 2.12
2860 6872 2.028190 CGATGGACTAGGCGGCTG 59.972 66.667 23.55 13.95 0.00 4.85
2874 6887 4.752879 GCTGCGGCCGAGGTGTAA 62.753 66.667 33.48 3.07 0.00 2.41
2875 6888 2.186903 CTGCGGCCGAGGTGTAAT 59.813 61.111 33.48 0.00 0.00 1.89
2892 6906 3.322541 TGTAATCAAACAGACGTGAGGGA 59.677 43.478 0.00 0.00 0.00 4.20
2910 6924 2.112297 GGTTGGGAGGAACACGCA 59.888 61.111 0.00 0.00 40.32 5.24
2936 6951 7.656412 TGTGAAATTCAAATTCCAGATCGAAA 58.344 30.769 0.00 0.00 0.00 3.46
2937 6952 8.140628 TGTGAAATTCAAATTCCAGATCGAAAA 58.859 29.630 0.00 0.00 0.00 2.29
2938 6953 9.143631 GTGAAATTCAAATTCCAGATCGAAAAT 57.856 29.630 0.00 0.00 0.00 1.82
2940 6955 9.578439 GAAATTCAAATTCCAGATCGAAAATCT 57.422 29.630 0.00 0.00 0.00 2.40
2993 7010 4.595781 TCCAAGTACCTCACAGTTGGTATT 59.404 41.667 8.40 0.13 43.92 1.89
3053 7070 1.215382 CCAGATTCAGCGACCGTCA 59.785 57.895 0.00 0.00 0.00 4.35
3127 7144 1.202114 TGCTTCGCCATGAAATCAACC 59.798 47.619 0.00 0.00 35.79 3.77
3305 7322 0.249489 AACGTCAGCAAGCTCGAGTT 60.249 50.000 15.13 4.78 0.00 3.01
3309 7326 2.072298 GTCAGCAAGCTCGAGTTCATT 58.928 47.619 15.13 1.49 0.00 2.57
3313 7330 3.126514 CAGCAAGCTCGAGTTCATTGATT 59.873 43.478 15.13 4.42 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 697 1.710013 GCTCAGCTAGCGTACAACAA 58.290 50.000 9.55 0.00 42.53 2.83
147 1515 2.280524 CCGCACACGAGTTTCCCA 60.281 61.111 0.00 0.00 43.93 4.37
233 1656 5.047235 ACGCACATAGGAATAGGAATAGGAC 60.047 44.000 0.00 0.00 0.00 3.85
260 1684 1.235281 GGCGTTCCACTTCCACTTCC 61.235 60.000 0.00 0.00 0.00 3.46
261 1685 1.566018 CGGCGTTCCACTTCCACTTC 61.566 60.000 0.00 0.00 0.00 3.01
262 1686 1.597027 CGGCGTTCCACTTCCACTT 60.597 57.895 0.00 0.00 0.00 3.16
263 1687 2.030562 CGGCGTTCCACTTCCACT 59.969 61.111 0.00 0.00 0.00 4.00
320 1763 3.084786 GGGACCTGACAGAAAATTCCAG 58.915 50.000 3.32 0.00 0.00 3.86
321 1764 2.552155 CGGGACCTGACAGAAAATTCCA 60.552 50.000 3.32 0.00 0.00 3.53
510 4158 0.615850 GAAGGTGCTAGCTTGAGGGT 59.384 55.000 17.23 0.00 35.86 4.34
522 4175 1.212616 CGATGATTCTCGGAAGGTGC 58.787 55.000 0.00 0.00 35.03 5.01
547 4200 0.602638 ATGGCGCGAGTGTTTTGAGA 60.603 50.000 12.10 0.00 0.00 3.27
598 4276 3.487372 AGGAGTCGGAAAAGGGAAAAAG 58.513 45.455 0.00 0.00 0.00 2.27
628 4357 5.349817 CCTATGATTAGCCTGCGTCAAATAG 59.650 44.000 0.00 0.00 0.00 1.73
736 4498 1.151668 CTGTTTGGGTTCTCGAGCAG 58.848 55.000 7.81 2.70 0.00 4.24
871 4639 4.669318 CGGGTGAGCGTATATATAGGTTG 58.331 47.826 12.71 0.00 0.00 3.77
898 4673 9.872757 TGAATTGTTGACGAGTTATACTTTTTC 57.127 29.630 0.00 0.00 0.00 2.29
905 4682 6.370442 CCAAGGTGAATTGTTGACGAGTTATA 59.630 38.462 0.00 0.00 0.00 0.98
907 4684 4.513692 CCAAGGTGAATTGTTGACGAGTTA 59.486 41.667 0.00 0.00 0.00 2.24
925 4702 1.679139 TCTGTTGCTTGTGTCCAAGG 58.321 50.000 4.76 0.00 46.72 3.61
937 4726 0.823356 TGGTGGCTTCCTTCTGTTGC 60.823 55.000 1.63 0.00 0.00 4.17
939 4728 0.550914 TGTGGTGGCTTCCTTCTGTT 59.449 50.000 1.63 0.00 0.00 3.16
941 4730 1.815003 GATTGTGGTGGCTTCCTTCTG 59.185 52.381 1.63 0.00 0.00 3.02
944 4733 0.251787 GGGATTGTGGTGGCTTCCTT 60.252 55.000 1.63 0.00 0.00 3.36
945 4734 1.142688 AGGGATTGTGGTGGCTTCCT 61.143 55.000 1.63 0.00 0.00 3.36
946 4735 0.967380 CAGGGATTGTGGTGGCTTCC 60.967 60.000 0.00 0.00 0.00 3.46
964 4762 4.698201 TGTGTAATCTGAGTTGGGAACA 57.302 40.909 0.00 0.00 39.83 3.18
965 4763 5.305585 TCTTGTGTAATCTGAGTTGGGAAC 58.694 41.667 0.00 0.00 0.00 3.62
974 4772 6.150318 GTCGTCTTTCTCTTGTGTAATCTGA 58.850 40.000 0.00 0.00 0.00 3.27
1134 4939 1.754621 CTGCTCCCTCCTCAGCGTA 60.755 63.158 0.00 0.00 38.59 4.42
1135 4940 3.073735 CTGCTCCCTCCTCAGCGT 61.074 66.667 0.00 0.00 38.59 5.07
1488 5296 4.028490 ACCTCCGGCGCCATGAAA 62.028 61.111 28.98 5.08 0.00 2.69
1678 5486 0.836400 AAGAAGTCCTTGGCCTCCGA 60.836 55.000 3.32 0.00 32.92 4.55
1821 5638 1.598130 GTCCAGCGTGCTCTTTGGT 60.598 57.895 0.00 0.00 32.51 3.67
1824 5641 3.044305 GCGTCCAGCGTGCTCTTT 61.044 61.111 0.00 0.00 43.66 2.52
1905 5734 1.201424 ATGCTCTGATCCTGCTGACA 58.799 50.000 0.00 0.00 0.00 3.58
1907 5736 1.134189 CCAATGCTCTGATCCTGCTGA 60.134 52.381 0.00 0.00 0.00 4.26
1908 5737 1.309950 CCAATGCTCTGATCCTGCTG 58.690 55.000 0.00 0.00 0.00 4.41
1961 5790 3.518998 CGATCCAGCCCTCGTCGT 61.519 66.667 0.00 0.00 0.00 4.34
2052 5890 0.827925 ACTCCTCTTCACTGGTCGCA 60.828 55.000 0.00 0.00 0.00 5.10
2105 5949 4.961511 TGTGCTCCACGTCCACGC 62.962 66.667 0.00 0.00 44.43 5.34
2165 6012 1.991121 CCTACTATGCCCTACGACCA 58.009 55.000 0.00 0.00 0.00 4.02
2166 6013 0.602060 GCCTACTATGCCCTACGACC 59.398 60.000 0.00 0.00 0.00 4.79
2206 6068 6.808008 ACATGACACTAATTGGTGAGAAAG 57.192 37.500 26.56 14.33 40.13 2.62
2237 6099 3.957591 TGCAACATAACAGTACGGGTA 57.042 42.857 0.00 0.00 0.00 3.69
2238 6100 2.809696 GTTGCAACATAACAGTACGGGT 59.190 45.455 24.52 0.00 0.00 5.28
2239 6101 2.809119 TGTTGCAACATAACAGTACGGG 59.191 45.455 27.96 0.00 33.43 5.28
2240 6102 4.065423 CTGTTGCAACATAACAGTACGG 57.935 45.455 31.17 12.64 46.13 4.02
2311 6185 0.952984 AGAAACAGAAGAGCAGCGCC 60.953 55.000 2.29 0.00 0.00 6.53
2321 6195 3.070734 AGCAAGCAGAGAGAGAAACAGAA 59.929 43.478 0.00 0.00 0.00 3.02
2352 6229 0.110373 GAACAATCGTGTCCCAACGC 60.110 55.000 0.00 0.00 43.26 4.84
2374 6251 9.508567 GCAACCTATATTCTGTCTTGAAATTTC 57.491 33.333 11.41 11.41 0.00 2.17
2380 6257 5.189736 AGTGGCAACCTATATTCTGTCTTGA 59.810 40.000 0.00 0.00 0.00 3.02
2382 6259 5.700402 AGTGGCAACCTATATTCTGTCTT 57.300 39.130 0.00 0.00 0.00 3.01
2386 6264 5.234329 CGTGTTAGTGGCAACCTATATTCTG 59.766 44.000 0.00 0.00 0.00 3.02
2387 6265 5.128171 TCGTGTTAGTGGCAACCTATATTCT 59.872 40.000 0.00 0.00 0.00 2.40
2388 6266 5.353938 TCGTGTTAGTGGCAACCTATATTC 58.646 41.667 0.00 0.00 0.00 1.75
2391 6269 4.689071 CATCGTGTTAGTGGCAACCTATA 58.311 43.478 0.00 0.00 0.00 1.31
2401 6285 1.698165 ACTGACGCATCGTGTTAGTG 58.302 50.000 4.54 0.00 40.42 2.74
2411 6295 2.079158 CAATCCTGTGAACTGACGCAT 58.921 47.619 0.00 0.00 0.00 4.73
2412 6296 1.511850 CAATCCTGTGAACTGACGCA 58.488 50.000 0.00 0.00 0.00 5.24
2417 6301 0.524862 GCTGCCAATCCTGTGAACTG 59.475 55.000 0.00 0.00 0.00 3.16
2418 6302 0.610232 GGCTGCCAATCCTGTGAACT 60.610 55.000 15.17 0.00 0.00 3.01
2420 6304 0.895100 GTGGCTGCCAATCCTGTGAA 60.895 55.000 25.23 0.00 34.18 3.18
2421 6305 1.303561 GTGGCTGCCAATCCTGTGA 60.304 57.895 25.23 0.00 34.18 3.58
2423 6307 2.360350 CGTGGCTGCCAATCCTGT 60.360 61.111 25.23 0.00 34.18 4.00
2442 6326 3.659092 TGGAAGCTTTGGTGCGCG 61.659 61.111 0.00 0.00 38.13 6.86
2443 6327 2.050077 GTGGAAGCTTTGGTGCGC 60.050 61.111 0.00 0.00 38.13 6.09
2446 6330 2.644992 GCCGTGGAAGCTTTGGTG 59.355 61.111 0.00 0.00 0.00 4.17
2447 6331 2.978010 CGCCGTGGAAGCTTTGGT 60.978 61.111 0.00 0.00 0.00 3.67
2448 6332 3.737172 CCGCCGTGGAAGCTTTGG 61.737 66.667 0.00 1.87 42.00 3.28
2449 6333 2.668212 TCCGCCGTGGAAGCTTTG 60.668 61.111 0.00 0.00 46.38 2.77
2459 6443 4.626081 AGCAGTGCTTTCCGCCGT 62.626 61.111 13.14 0.00 33.89 5.68
2470 6454 1.723608 TTTTGACCCGTGCAGCAGTG 61.724 55.000 0.00 0.00 0.00 3.66
2483 6467 2.687935 TGCCTGACAAGAGGTTTTTGAC 59.312 45.455 0.00 0.00 35.29 3.18
2488 6472 0.538287 GCCTGCCTGACAAGAGGTTT 60.538 55.000 0.00 0.00 35.29 3.27
2493 6477 0.253044 GTATGGCCTGCCTGACAAGA 59.747 55.000 9.97 0.00 36.94 3.02
2498 6482 2.584064 CACGTATGGCCTGCCTGA 59.416 61.111 9.97 0.00 36.94 3.86
2499 6483 2.514592 CCACGTATGGCCTGCCTG 60.515 66.667 9.97 0.00 39.82 4.85
2501 6485 3.638592 AACCCACGTATGGCCTGCC 62.639 63.158 3.32 0.00 45.76 4.85
2502 6486 2.045340 AACCCACGTATGGCCTGC 60.045 61.111 3.32 0.00 45.76 4.85
2503 6487 1.813753 CGAACCCACGTATGGCCTG 60.814 63.158 3.32 0.00 45.76 4.85
2508 6496 0.806102 CTCTGCCGAACCCACGTATG 60.806 60.000 0.00 0.00 0.00 2.39
2513 6501 2.432628 CGACTCTGCCGAACCCAC 60.433 66.667 0.00 0.00 0.00 4.61
2546 6534 3.483738 GCTTGTCGATAAAGGTTTCGCTC 60.484 47.826 11.45 0.00 35.39 5.03
2649 6643 1.328279 TCTCCTTCGTGAGCAGTCAA 58.672 50.000 0.00 0.00 33.27 3.18
2694 6688 1.241990 TAGCTGTCTCGCCGTTGTCT 61.242 55.000 0.00 0.00 0.00 3.41
2726 6736 1.004918 CGAGTCGACTTGGGCCTTT 60.005 57.895 23.06 0.00 0.00 3.11
2793 6803 4.450080 GGCTATAAATACTGTTACACCCGC 59.550 45.833 0.00 0.00 0.00 6.13
2808 6820 5.493809 AGGAAAGCAACTAACGGCTATAAA 58.506 37.500 0.00 0.00 40.01 1.40
2860 6872 1.022451 TTTGATTACACCTCGGCCGC 61.022 55.000 23.51 2.99 0.00 6.53
2874 6887 1.276421 CCTCCCTCACGTCTGTTTGAT 59.724 52.381 0.00 0.00 0.00 2.57
2875 6888 0.679505 CCTCCCTCACGTCTGTTTGA 59.320 55.000 0.00 0.00 0.00 2.69
2892 6906 1.779061 ATGCGTGTTCCTCCCAACCT 61.779 55.000 0.00 0.00 0.00 3.50
2910 6924 7.395190 TCGATCTGGAATTTGAATTTCACAT 57.605 32.000 0.00 0.00 30.87 3.21
2927 6941 5.430462 GCGAGAATTGAGATTTTCGATCTG 58.570 41.667 13.88 0.00 46.80 2.90
2936 6951 1.952296 GCCATGGCGAGAATTGAGATT 59.048 47.619 23.48 0.00 0.00 2.40
2937 6952 1.602311 GCCATGGCGAGAATTGAGAT 58.398 50.000 23.48 0.00 0.00 2.75
2938 6953 3.085208 GCCATGGCGAGAATTGAGA 57.915 52.632 23.48 0.00 0.00 3.27
2993 7010 1.271982 ACTCCAGGACGAACAGCTCTA 60.272 52.381 0.00 0.00 0.00 2.43
3127 7144 0.969894 AACTTCTGGTCCAGGTCGAG 59.030 55.000 19.11 13.35 31.51 4.04
3305 7322 0.546122 CCTGGGTCCCGAATCAATGA 59.454 55.000 2.65 0.00 0.00 2.57
3309 7326 3.407967 GGCCTGGGTCCCGAATCA 61.408 66.667 2.65 0.00 0.00 2.57
3328 7345 3.244215 TGACGAGATGACAAGCTTCCTTT 60.244 43.478 0.00 0.00 0.00 3.11
3330 7347 1.895798 TGACGAGATGACAAGCTTCCT 59.104 47.619 0.00 0.00 0.00 3.36
3333 7350 1.670087 CCGTGACGAGATGACAAGCTT 60.670 52.381 6.54 0.00 0.00 3.74
3381 7398 0.824595 TCTCGAAACCCAGTCCGTCA 60.825 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.