Multiple sequence alignment - TraesCS7A01G125800

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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 TraesCS7A01G125800 chr7A 100.000 3434 0 0 1 3434 80862907 80866340 0.000000e+00 6342.0
1 TraesCS7A01G125800 chr7A 85.694 706 88 3 1 693 8591115 8591820 0.000000e+00 732.0
2 TraesCS7A01G125800 chr7A 98.000 100 2 0 2265 2364 80865141 80865240 1.270000e-39 174.0
3 TraesCS7A01G125800 chr7A 98.000 100 2 0 2235 2334 80865171 80865270 1.270000e-39 174.0
4 TraesCS7A01G125800 chr7A 97.143 70 2 0 2295 2364 80865141 80865210 6.020000e-23 119.0
5 TraesCS7A01G125800 chr7A 97.143 70 2 0 2235 2304 80865201 80865270 6.020000e-23 119.0
6 TraesCS7A01G125800 chr7A 95.000 40 2 0 2235 2274 80865231 80865270 2.860000e-06 63.9
7 TraesCS7A01G125800 chr7D 94.277 2219 102 7 1 2211 76744486 76746687 0.000000e+00 3371.0
8 TraesCS7A01G125800 chr7D 91.912 2238 140 17 1 2211 76920215 76922438 0.000000e+00 3092.0
9 TraesCS7A01G125800 chr7D 92.027 1894 129 12 394 2269 77045885 77047774 0.000000e+00 2641.0
10 TraesCS7A01G125800 chr7D 85.055 2362 306 35 1 2335 76785102 76787443 0.000000e+00 2362.0
11 TraesCS7A01G125800 chr7D 83.434 2662 286 67 287 2885 76955728 76958297 0.000000e+00 2329.0
12 TraesCS7A01G125800 chr7D 84.354 2237 308 31 1 2205 76930816 76933042 0.000000e+00 2154.0
13 TraesCS7A01G125800 chr7D 84.128 1846 247 31 13 1833 76624273 76622449 0.000000e+00 1744.0
14 TraesCS7A01G125800 chr7D 85.141 747 95 9 1 733 7561990 7562734 0.000000e+00 750.0
15 TraesCS7A01G125800 chr7D 86.882 465 46 6 2933 3388 77048424 77048882 1.100000e-139 507.0
16 TraesCS7A01G125800 chr7D 86.750 400 37 7 3000 3394 76787711 76788099 6.810000e-117 431.0
17 TraesCS7A01G125800 chr7D 83.507 479 40 16 2951 3405 76958302 76958765 8.870000e-111 411.0
18 TraesCS7A01G125800 chr7D 85.390 308 31 6 3094 3394 76923162 76923462 1.200000e-79 307.0
19 TraesCS7A01G125800 chr7D 89.529 191 9 3 2728 2907 77048244 77048434 7.410000e-57 231.0
20 TraesCS7A01G125800 chr7D 87.562 201 19 3 2287 2484 76787358 76787555 9.590000e-56 228.0
21 TraesCS7A01G125800 chr7D 92.035 113 5 2 2698 2809 77048162 77048271 4.590000e-34 156.0
22 TraesCS7A01G125800 chr7D 96.226 53 2 0 2317 2369 76957673 76957725 1.700000e-13 87.9
23 TraesCS7A01G125800 chr7D 100.000 38 0 0 2782 2819 77048192 77048229 1.710000e-08 71.3
24 TraesCS7A01G125800 chr7D 97.500 40 1 0 2235 2274 76957711 76957750 6.150000e-08 69.4
25 TraesCS7A01G125800 chr7B 87.412 2272 232 29 1 2231 23525473 23527731 0.000000e+00 2562.0
26 TraesCS7A01G125800 chr7B 87.084 2222 263 18 3 2211 23958923 23961133 0.000000e+00 2492.0
27 TraesCS7A01G125800 chr7B 86.201 2232 276 17 1 2206 23517064 23519289 0.000000e+00 2386.0
28 TraesCS7A01G125800 chr7B 85.552 2291 294 25 1 2269 23597631 23599906 0.000000e+00 2362.0
29 TraesCS7A01G125800 chr7B 83.371 2201 289 45 28 2211 23934300 23936440 0.000000e+00 1965.0
30 TraesCS7A01G125800 chr7B 86.413 1288 168 6 926 2211 23639655 23640937 0.000000e+00 1402.0
31 TraesCS7A01G125800 chr7B 87.848 395 39 6 2966 3360 23528938 23529323 4.040000e-124 455.0
32 TraesCS7A01G125800 chr7B 81.556 450 39 14 2319 2767 23585488 23585894 7.100000e-87 331.0
33 TraesCS7A01G125800 chr7B 86.306 314 19 9 2595 2907 23600088 23600378 1.540000e-83 320.0
34 TraesCS7A01G125800 chr7B 88.163 245 20 5 2319 2559 23527721 23527960 2.020000e-72 283.0
35 TraesCS7A01G125800 chr7B 90.452 199 17 2 2933 3129 23600368 23600566 9.450000e-66 261.0
36 TraesCS7A01G125800 chr7B 86.344 227 20 6 2319 2545 23599863 23600078 1.590000e-58 237.0
37 TraesCS7A01G125800 chr7B 86.385 213 18 6 2554 2762 23528603 23528808 4.460000e-54 222.0
38 TraesCS7A01G125800 chr7B 84.431 167 11 9 2323 2477 23640965 23641128 2.130000e-32 150.0
39 TraesCS7A01G125800 chr7B 95.181 83 4 0 2765 2847 23528855 23528937 7.730000e-27 132.0
40 TraesCS7A01G125800 chr7B 82.222 135 12 5 2355 2477 23961199 23961333 4.690000e-19 106.0
41 TraesCS7A01G125800 chr3B 86.193 746 85 8 2 733 741464085 741464826 0.000000e+00 791.0
42 TraesCS7A01G125800 chr4A 84.845 772 105 2 1 760 731615933 731615162 0.000000e+00 767.0


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 TraesCS7A01G125800 chr7A 80862907 80866340 3433 False 1165.316667 6342 97.547667 1 3434 6 chr7A.!!$F2 3433
1 TraesCS7A01G125800 chr7A 8591115 8591820 705 False 732.000000 732 85.694000 1 693 1 chr7A.!!$F1 692
2 TraesCS7A01G125800 chr7D 76744486 76746687 2201 False 3371.000000 3371 94.277000 1 2211 1 chr7D.!!$F2 2210
3 TraesCS7A01G125800 chr7D 76930816 76933042 2226 False 2154.000000 2154 84.354000 1 2205 1 chr7D.!!$F3 2204
4 TraesCS7A01G125800 chr7D 76622449 76624273 1824 True 1744.000000 1744 84.128000 13 1833 1 chr7D.!!$R1 1820
5 TraesCS7A01G125800 chr7D 76920215 76923462 3247 False 1699.500000 3092 88.651000 1 3394 2 chr7D.!!$F5 3393
6 TraesCS7A01G125800 chr7D 76785102 76788099 2997 False 1007.000000 2362 86.455667 1 3394 3 chr7D.!!$F4 3393
7 TraesCS7A01G125800 chr7D 7561990 7562734 744 False 750.000000 750 85.141000 1 733 1 chr7D.!!$F1 732
8 TraesCS7A01G125800 chr7D 76955728 76958765 3037 False 724.325000 2329 90.166750 287 3405 4 chr7D.!!$F6 3118
9 TraesCS7A01G125800 chr7D 77045885 77048882 2997 False 721.260000 2641 92.094600 394 3388 5 chr7D.!!$F7 2994
10 TraesCS7A01G125800 chr7B 23517064 23519289 2225 False 2386.000000 2386 86.201000 1 2206 1 chr7B.!!$F1 2205
11 TraesCS7A01G125800 chr7B 23934300 23936440 2140 False 1965.000000 1965 83.371000 28 2211 1 chr7B.!!$F3 2183
12 TraesCS7A01G125800 chr7B 23958923 23961333 2410 False 1299.000000 2492 84.653000 3 2477 2 chr7B.!!$F7 2474
13 TraesCS7A01G125800 chr7B 23597631 23600566 2935 False 795.000000 2362 87.163500 1 3129 4 chr7B.!!$F5 3128
14 TraesCS7A01G125800 chr7B 23639655 23641128 1473 False 776.000000 1402 85.422000 926 2477 2 chr7B.!!$F6 1551
15 TraesCS7A01G125800 chr7B 23525473 23529323 3850 False 730.800000 2562 88.997800 1 3360 5 chr7B.!!$F4 3359
16 TraesCS7A01G125800 chr3B 741464085 741464826 741 False 791.000000 791 86.193000 2 733 1 chr3B.!!$F1 731
17 TraesCS7A01G125800 chr4A 731615162 731615933 771 True 767.000000 767 84.845000 1 760 1 chr4A.!!$R1 759

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
253 255 0.963355 TTGTCTACAAATGCGGGGGC 60.963 55.0 0.00 0.0 32.11 5.80 F
1131 1186 0.464036 AGCGGATGCCTCGAAACATA 59.536 50.0 0.11 0.0 44.31 2.29 F
1715 1780 0.105246 AGTCTAGAGGGATGGGCAGG 60.105 60.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1687 0.908198 ACTGCATCCTCCACCTTCTC 59.092 55.0 0.0 0.0 0.00 2.87 R
2322 2446 0.761187 TTGTGGACTCTGCTTCTGCT 59.239 50.0 0.0 0.0 40.48 4.24 R
3219 4409 0.610232 GCCAGCATATCATCCACCCC 60.610 60.0 0.0 0.0 0.00 4.95 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
239 241 4.992319 TCACAATCGGAAAACGTATTGTCT 59.008 37.500 8.73 0.00 44.05 3.41
253 255 0.963355 TTGTCTACAAATGCGGGGGC 60.963 55.000 0.00 0.00 32.11 5.80
344 346 6.074648 ACCATTGAAGAAACTAACATTGGGA 58.925 36.000 0.00 0.00 37.78 4.37
836 877 4.520492 ACACTTTGTTAGCTCTTTCATGGG 59.480 41.667 0.00 0.00 0.00 4.00
1131 1186 0.464036 AGCGGATGCCTCGAAACATA 59.536 50.000 0.11 0.00 44.31 2.29
1572 1637 2.232452 CTCACCCTCACTGGAGTACTTG 59.768 54.545 0.00 0.00 39.64 3.16
1579 1644 4.081420 CCTCACTGGAGTACTTGCACTTAT 60.081 45.833 0.00 0.00 39.64 1.73
1622 1687 5.048504 AGACATTGTGTGATAACCTTTGCAG 60.049 40.000 0.00 0.00 0.00 4.41
1678 1743 3.485463 TCCCGAAGTTGAAGAACATGT 57.515 42.857 0.00 0.00 34.17 3.21
1715 1780 0.105246 AGTCTAGAGGGATGGGCAGG 60.105 60.000 0.00 0.00 0.00 4.85
1769 1834 5.986135 CAGTAATATTCCCGGTTCTTGAGAG 59.014 44.000 0.00 0.00 0.00 3.20
1795 1860 4.922206 ACAAATCAACATCTGCCCTAAGA 58.078 39.130 0.00 0.00 0.00 2.10
1918 2021 6.287525 TCCCTTGAAATTTTGTGGATTCAAC 58.712 36.000 0.00 0.00 36.99 3.18
1976 2079 1.712977 GATCTGGCAAAGCTGAGCGG 61.713 60.000 0.00 0.00 0.00 5.52
1978 2081 4.648626 TGGCAAAGCTGAGCGGCT 62.649 61.111 15.87 0.00 45.30 5.52
1991 2094 4.067896 CTGAGCGGCTTAATGGTGAATAT 58.932 43.478 2.97 0.00 0.00 1.28
2134 2237 2.767505 CCCTTGACCGCCTAATCATAC 58.232 52.381 0.00 0.00 0.00 2.39
2211 2314 3.906846 ACTTGCTCCCTATCCCAGATAAG 59.093 47.826 0.00 0.00 0.00 1.73
2247 2365 4.132999 GCTCCAGAAGCCGAATCC 57.867 61.111 0.00 0.00 45.92 3.01
2248 2366 1.221840 GCTCCAGAAGCCGAATCCA 59.778 57.895 0.00 0.00 45.92 3.41
2249 2367 1.092345 GCTCCAGAAGCCGAATCCAC 61.092 60.000 0.00 0.00 45.92 4.02
2250 2368 0.250234 CTCCAGAAGCCGAATCCACA 59.750 55.000 0.00 0.00 0.00 4.17
2251 2369 0.690192 TCCAGAAGCCGAATCCACAA 59.310 50.000 0.00 0.00 0.00 3.33
2252 2370 1.281867 TCCAGAAGCCGAATCCACAAT 59.718 47.619 0.00 0.00 0.00 2.71
2253 2371 2.094675 CCAGAAGCCGAATCCACAATT 58.905 47.619 0.00 0.00 0.00 2.32
2254 2372 3.054728 TCCAGAAGCCGAATCCACAATTA 60.055 43.478 0.00 0.00 0.00 1.40
2255 2373 3.885297 CCAGAAGCCGAATCCACAATTAT 59.115 43.478 0.00 0.00 0.00 1.28
2274 2392 2.669300 TAGCAGAAGCAGAAGCAGAG 57.331 50.000 0.00 0.00 45.49 3.35
2304 2428 2.669300 TAGCAGAAGCAGAAGCAGAG 57.331 50.000 0.00 0.00 45.49 3.35
2322 2446 5.104776 AGCAGAGTCCACAATTATAGCAGAA 60.105 40.000 0.00 0.00 0.00 3.02
2323 2447 5.236047 GCAGAGTCCACAATTATAGCAGAAG 59.764 44.000 0.00 0.00 0.00 2.85
2324 2448 5.236047 CAGAGTCCACAATTATAGCAGAAGC 59.764 44.000 0.00 0.00 42.56 3.86
2325 2449 5.102953 AGTCCACAATTATAGCAGAAGCA 57.897 39.130 0.00 0.00 45.49 3.91
2326 2450 5.121811 AGTCCACAATTATAGCAGAAGCAG 58.878 41.667 0.00 0.00 45.49 4.24
2327 2451 5.104776 AGTCCACAATTATAGCAGAAGCAGA 60.105 40.000 0.00 0.00 45.49 4.26
2328 2452 5.586243 GTCCACAATTATAGCAGAAGCAGAA 59.414 40.000 0.00 0.00 45.49 3.02
2329 2453 5.819379 TCCACAATTATAGCAGAAGCAGAAG 59.181 40.000 0.00 0.00 45.49 2.85
2330 2454 5.505324 CCACAATTATAGCAGAAGCAGAAGC 60.505 44.000 0.00 0.00 45.49 3.86
2331 2455 5.065602 CACAATTATAGCAGAAGCAGAAGCA 59.934 40.000 0.00 0.00 45.49 3.91
2332 2456 5.296283 ACAATTATAGCAGAAGCAGAAGCAG 59.704 40.000 0.00 0.00 45.49 4.24
2333 2457 4.743057 TTATAGCAGAAGCAGAAGCAGA 57.257 40.909 0.00 0.00 45.49 4.26
2334 2458 2.669300 TAGCAGAAGCAGAAGCAGAG 57.331 50.000 0.00 0.00 45.49 3.35
2335 2459 0.686224 AGCAGAAGCAGAAGCAGAGT 59.314 50.000 0.00 0.00 45.49 3.24
2336 2460 1.077915 GCAGAAGCAGAAGCAGAGTC 58.922 55.000 0.00 0.00 45.49 3.36
2337 2461 1.724429 CAGAAGCAGAAGCAGAGTCC 58.276 55.000 0.00 0.00 45.49 3.85
2338 2462 1.001746 CAGAAGCAGAAGCAGAGTCCA 59.998 52.381 0.00 0.00 45.49 4.02
2339 2463 1.001860 AGAAGCAGAAGCAGAGTCCAC 59.998 52.381 0.00 0.00 45.49 4.02
2340 2464 0.761187 AAGCAGAAGCAGAGTCCACA 59.239 50.000 0.00 0.00 45.49 4.17
2341 2465 0.761187 AGCAGAAGCAGAGTCCACAA 59.239 50.000 0.00 0.00 45.49 3.33
2342 2466 1.350351 AGCAGAAGCAGAGTCCACAAT 59.650 47.619 0.00 0.00 45.49 2.71
2343 2467 2.157738 GCAGAAGCAGAGTCCACAATT 58.842 47.619 0.00 0.00 41.58 2.32
2344 2468 3.008375 AGCAGAAGCAGAGTCCACAATTA 59.992 43.478 0.00 0.00 45.49 1.40
2416 2540 2.575993 CCTCCTGTGCTCACTCGG 59.424 66.667 1.47 2.70 0.00 4.63
2478 2614 9.238368 CCTTTCCTTGTGTTATTATGGTTTAGA 57.762 33.333 0.00 0.00 0.00 2.10
2619 3420 6.442952 GTGCCACATTCTGTACACATTTTTA 58.557 36.000 0.00 0.00 36.90 1.52
2630 3432 9.135843 TCTGTACACATTTTTAGACAAGTATCG 57.864 33.333 0.00 0.00 0.00 2.92
2704 3624 3.641439 GTCTCAACGATCACCGAAATG 57.359 47.619 0.00 0.00 41.76 2.32
2720 3641 5.891551 ACCGAAATGGCATAAAGAGGTAAAT 59.108 36.000 0.00 0.00 43.94 1.40
2904 3933 1.610038 CTTTGCCACATCAACTCAGCA 59.390 47.619 0.00 0.00 0.00 4.41
2905 3934 0.953727 TTGCCACATCAACTCAGCAC 59.046 50.000 0.00 0.00 0.00 4.40
2906 3935 0.179023 TGCCACATCAACTCAGCACA 60.179 50.000 0.00 0.00 0.00 4.57
2907 3936 0.239347 GCCACATCAACTCAGCACAC 59.761 55.000 0.00 0.00 0.00 3.82
2908 3937 0.877071 CCACATCAACTCAGCACACC 59.123 55.000 0.00 0.00 0.00 4.16
2909 3938 0.877071 CACATCAACTCAGCACACCC 59.123 55.000 0.00 0.00 0.00 4.61
2910 3939 0.250901 ACATCAACTCAGCACACCCC 60.251 55.000 0.00 0.00 0.00 4.95
2911 3940 1.003355 ATCAACTCAGCACACCCCG 60.003 57.895 0.00 0.00 0.00 5.73
2912 3941 3.357079 CAACTCAGCACACCCCGC 61.357 66.667 0.00 0.00 0.00 6.13
2913 3942 3.872603 AACTCAGCACACCCCGCA 61.873 61.111 0.00 0.00 0.00 5.69
2914 3943 3.414136 AACTCAGCACACCCCGCAA 62.414 57.895 0.00 0.00 0.00 4.85
2915 3944 2.594303 CTCAGCACACCCCGCAAA 60.594 61.111 0.00 0.00 0.00 3.68
2916 3945 2.124109 TCAGCACACCCCGCAAAA 60.124 55.556 0.00 0.00 0.00 2.44
2917 3946 1.733402 CTCAGCACACCCCGCAAAAA 61.733 55.000 0.00 0.00 0.00 1.94
3038 4105 5.150683 TGTTTTCATCGTCTTTATTTGCCG 58.849 37.500 0.00 0.00 0.00 5.69
3064 4135 7.325660 TCTCTGTAATCATCAAGGAAATTGC 57.674 36.000 0.00 0.00 38.89 3.56
3072 4143 6.704289 TCATCAAGGAAATTGCTTATCAGG 57.296 37.500 0.00 0.00 38.89 3.86
3091 4280 6.406692 TCAGGCTAGATACTGATTTACCAC 57.593 41.667 7.79 0.00 38.71 4.16
3131 4320 3.518705 ACTCCTGTCAGAATTCAGATGCT 59.481 43.478 8.44 0.00 34.02 3.79
3137 4327 6.036953 CCTGTCAGAATTCAGATGCTACTTTC 59.963 42.308 8.44 0.00 34.02 2.62
3154 4344 5.330455 ACTTTCTGATGATAGAGCGTCAA 57.670 39.130 0.00 0.00 33.71 3.18
3165 4355 2.650322 AGAGCGTCAAGAAAACCCAAA 58.350 42.857 0.00 0.00 0.00 3.28
3171 4361 3.428862 CGTCAAGAAAACCCAAAGCTGTT 60.429 43.478 0.00 0.00 0.00 3.16
3214 4404 2.498441 ACCCTGGTAAATATCCCTGCA 58.502 47.619 0.00 0.00 0.00 4.41
3217 4407 4.078630 ACCCTGGTAAATATCCCTGCAAAT 60.079 41.667 0.00 0.00 0.00 2.32
3219 4409 5.221501 CCCTGGTAAATATCCCTGCAAATTG 60.222 44.000 0.00 0.00 0.00 2.32
3235 4434 3.899360 CAAATTGGGGTGGATGATATGCT 59.101 43.478 0.00 0.00 0.00 3.79
3236 4435 2.662535 TTGGGGTGGATGATATGCTG 57.337 50.000 0.00 0.00 0.00 4.41
3237 4436 0.773014 TGGGGTGGATGATATGCTGG 59.227 55.000 0.00 0.00 0.00 4.85
3238 4437 0.610232 GGGGTGGATGATATGCTGGC 60.610 60.000 0.00 0.00 0.00 4.85
3239 4438 0.111061 GGGTGGATGATATGCTGGCA 59.889 55.000 0.00 0.00 0.00 4.92
3310 4516 1.888512 GCAGGTTGGCATCTCTGAAAA 59.111 47.619 13.84 0.00 0.00 2.29
3349 4555 0.177141 GCAATGCCATGCAGGACAAT 59.823 50.000 0.00 0.00 43.65 2.71
3378 4584 2.092753 AGAACTCCATCATCACGGCATT 60.093 45.455 0.00 0.00 0.00 3.56
3379 4585 1.959042 ACTCCATCATCACGGCATTC 58.041 50.000 0.00 0.00 0.00 2.67
3394 4600 2.349886 GGCATTCGATGAGTGTTGTCTC 59.650 50.000 0.00 0.00 35.28 3.36
3395 4601 3.257393 GCATTCGATGAGTGTTGTCTCT 58.743 45.455 0.00 0.00 35.68 3.10
3396 4602 3.681897 GCATTCGATGAGTGTTGTCTCTT 59.318 43.478 0.00 0.00 35.68 2.85
3397 4603 4.435253 GCATTCGATGAGTGTTGTCTCTTG 60.435 45.833 0.00 0.00 35.68 3.02
3398 4604 4.584327 TTCGATGAGTGTTGTCTCTTGA 57.416 40.909 0.00 0.00 35.68 3.02
3399 4605 4.790765 TCGATGAGTGTTGTCTCTTGAT 57.209 40.909 0.00 0.00 35.68 2.57
3400 4606 4.738124 TCGATGAGTGTTGTCTCTTGATC 58.262 43.478 0.00 0.00 35.68 2.92
3401 4607 3.862267 CGATGAGTGTTGTCTCTTGATCC 59.138 47.826 0.00 0.00 35.68 3.36
3402 4608 4.619160 CGATGAGTGTTGTCTCTTGATCCA 60.619 45.833 0.00 0.00 35.68 3.41
3403 4609 4.263018 TGAGTGTTGTCTCTTGATCCAG 57.737 45.455 0.00 0.00 35.68 3.86
3404 4610 3.643320 TGAGTGTTGTCTCTTGATCCAGT 59.357 43.478 0.00 0.00 35.68 4.00
3405 4611 4.101585 TGAGTGTTGTCTCTTGATCCAGTT 59.898 41.667 0.00 0.00 35.68 3.16
3406 4612 5.041191 AGTGTTGTCTCTTGATCCAGTTT 57.959 39.130 0.00 0.00 0.00 2.66
3407 4613 5.059833 AGTGTTGTCTCTTGATCCAGTTTC 58.940 41.667 0.00 0.00 0.00 2.78
3408 4614 5.059833 GTGTTGTCTCTTGATCCAGTTTCT 58.940 41.667 0.00 0.00 0.00 2.52
3409 4615 5.178438 GTGTTGTCTCTTGATCCAGTTTCTC 59.822 44.000 0.00 0.00 0.00 2.87
3410 4616 5.070981 TGTTGTCTCTTGATCCAGTTTCTCT 59.929 40.000 0.00 0.00 0.00 3.10
3411 4617 6.267699 TGTTGTCTCTTGATCCAGTTTCTCTA 59.732 38.462 0.00 0.00 0.00 2.43
3412 4618 6.274157 TGTCTCTTGATCCAGTTTCTCTAC 57.726 41.667 0.00 0.00 0.00 2.59
3413 4619 5.775195 TGTCTCTTGATCCAGTTTCTCTACA 59.225 40.000 0.00 0.00 0.00 2.74
3414 4620 6.438741 TGTCTCTTGATCCAGTTTCTCTACAT 59.561 38.462 0.00 0.00 0.00 2.29
3415 4621 6.756074 GTCTCTTGATCCAGTTTCTCTACATG 59.244 42.308 0.00 0.00 0.00 3.21
3416 4622 6.438741 TCTCTTGATCCAGTTTCTCTACATGT 59.561 38.462 2.69 2.69 0.00 3.21
3417 4623 7.615757 TCTCTTGATCCAGTTTCTCTACATGTA 59.384 37.037 5.25 5.25 0.00 2.29
3418 4624 7.776107 TCTTGATCCAGTTTCTCTACATGTAG 58.224 38.462 24.37 24.37 34.56 2.74
3419 4625 7.615757 TCTTGATCCAGTTTCTCTACATGTAGA 59.384 37.037 29.19 29.19 39.67 2.59
3420 4626 7.904558 TGATCCAGTTTCTCTACATGTAGAT 57.095 36.000 30.76 16.32 40.97 1.98
3421 4627 7.720442 TGATCCAGTTTCTCTACATGTAGATG 58.280 38.462 30.76 24.68 40.97 2.90
3422 4628 7.343057 TGATCCAGTTTCTCTACATGTAGATGT 59.657 37.037 30.76 13.94 45.24 3.06
3423 4629 7.101652 TCCAGTTTCTCTACATGTAGATGTC 57.898 40.000 30.76 21.17 42.14 3.06
3424 4630 6.663523 TCCAGTTTCTCTACATGTAGATGTCA 59.336 38.462 30.76 15.47 42.14 3.58
3425 4631 6.977502 CCAGTTTCTCTACATGTAGATGTCAG 59.022 42.308 30.76 20.43 42.14 3.51
3426 4632 6.475076 CAGTTTCTCTACATGTAGATGTCAGC 59.525 42.308 30.76 19.50 42.14 4.26
3427 4633 4.820284 TCTCTACATGTAGATGTCAGCG 57.180 45.455 30.76 19.20 42.14 5.18
3428 4634 3.003793 TCTCTACATGTAGATGTCAGCGC 59.996 47.826 30.76 0.00 42.14 5.92
3429 4635 2.687935 TCTACATGTAGATGTCAGCGCA 59.312 45.455 27.96 5.59 42.14 6.09
3430 4636 2.385013 ACATGTAGATGTCAGCGCAA 57.615 45.000 11.47 0.00 38.53 4.85
3431 4637 2.698803 ACATGTAGATGTCAGCGCAAA 58.301 42.857 11.47 0.00 38.53 3.68
3432 4638 3.273434 ACATGTAGATGTCAGCGCAAAT 58.727 40.909 11.47 0.00 38.53 2.32
3433 4639 3.691118 ACATGTAGATGTCAGCGCAAATT 59.309 39.130 11.47 0.00 38.53 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
239 241 2.044451 CAGGCCCCCGCATTTGTA 60.044 61.111 0.00 0.00 36.38 2.41
344 346 6.840705 ACCTCATATTTGCCTCCAACATTATT 59.159 34.615 0.00 0.00 0.00 1.40
612 617 6.437755 ACAATTATCCCATATGCATAGCCAT 58.562 36.000 12.79 4.35 0.00 4.40
761 793 5.841237 TGGAAGTATTTTCCAATTCAACCCA 59.159 36.000 6.18 0.00 44.90 4.51
762 794 6.353404 TGGAAGTATTTTCCAATTCAACCC 57.647 37.500 6.18 0.00 44.90 4.11
836 877 2.342910 CAGTCAAAATCCTGCTGCAC 57.657 50.000 0.00 0.00 0.00 4.57
1131 1186 2.301346 CAAAGGTTGTTCAGCTGACCT 58.699 47.619 18.03 17.41 44.11 3.85
1572 1637 6.373216 TCAGTTTACCCATGTTGTATAAGTGC 59.627 38.462 0.00 0.00 0.00 4.40
1579 1644 5.931294 TGTCTTCAGTTTACCCATGTTGTA 58.069 37.500 0.00 0.00 0.00 2.41
1622 1687 0.908198 ACTGCATCCTCCACCTTCTC 59.092 55.000 0.00 0.00 0.00 2.87
1678 1743 4.748701 AGACTAGGTAGGTGTTCCAAGAA 58.251 43.478 0.00 0.00 35.89 2.52
1715 1780 3.030652 CCACACCCGCACTGTTTC 58.969 61.111 0.00 0.00 0.00 2.78
1769 1834 2.099756 GGGCAGATGTTGATTTGTAGCC 59.900 50.000 0.00 0.00 38.84 3.93
1795 1860 2.036346 GGCTCAGTGGAAAACTTGCAAT 59.964 45.455 0.00 0.00 36.83 3.56
1849 1918 4.398319 CATAAACACTCCACCTCCAAGTT 58.602 43.478 0.00 0.00 0.00 2.66
1918 2021 2.742372 CACCAAACCTCCGGAGCG 60.742 66.667 26.87 20.57 0.00 5.03
1976 2079 5.065914 TCCTGCAGATATTCACCATTAAGC 58.934 41.667 17.39 0.00 0.00 3.09
1978 2081 5.065914 GCTCCTGCAGATATTCACCATTAA 58.934 41.667 17.39 0.00 39.41 1.40
1991 2094 1.681666 CCTTTCAGGCTCCTGCAGA 59.318 57.895 17.39 0.00 43.31 4.26
2134 2237 3.136123 CAACTCGGGGCAGCCATG 61.136 66.667 15.19 4.58 0.00 3.66
2194 2297 5.398236 TCTTGACTTATCTGGGATAGGGAG 58.602 45.833 0.00 0.00 0.00 4.30
2211 2314 3.932089 GAGCTCCAGTTCTGAATCTTGAC 59.068 47.826 0.87 0.00 0.00 3.18
2238 2356 4.067896 CTGCTATAATTGTGGATTCGGCT 58.932 43.478 0.00 0.00 0.00 5.52
2239 2357 4.065088 TCTGCTATAATTGTGGATTCGGC 58.935 43.478 0.00 0.00 0.00 5.54
2240 2358 5.334414 GCTTCTGCTATAATTGTGGATTCGG 60.334 44.000 0.00 0.00 36.03 4.30
2241 2359 5.237127 TGCTTCTGCTATAATTGTGGATTCG 59.763 40.000 0.00 0.00 40.48 3.34
2242 2360 6.484643 TCTGCTTCTGCTATAATTGTGGATTC 59.515 38.462 0.00 0.00 40.48 2.52
2243 2361 6.359804 TCTGCTTCTGCTATAATTGTGGATT 58.640 36.000 0.00 0.00 40.48 3.01
2244 2362 5.933617 TCTGCTTCTGCTATAATTGTGGAT 58.066 37.500 0.00 0.00 40.48 3.41
2245 2363 5.357742 TCTGCTTCTGCTATAATTGTGGA 57.642 39.130 0.00 0.00 40.48 4.02
2246 2364 5.505324 GCTTCTGCTTCTGCTATAATTGTGG 60.505 44.000 0.00 0.00 40.48 4.17
2247 2365 5.065602 TGCTTCTGCTTCTGCTATAATTGTG 59.934 40.000 0.00 0.00 40.48 3.33
2248 2366 5.188434 TGCTTCTGCTTCTGCTATAATTGT 58.812 37.500 0.00 0.00 40.48 2.71
2249 2367 5.526479 TCTGCTTCTGCTTCTGCTATAATTG 59.474 40.000 0.00 0.00 40.48 2.32
2250 2368 5.678583 TCTGCTTCTGCTTCTGCTATAATT 58.321 37.500 0.00 0.00 40.48 1.40
2251 2369 5.163322 ACTCTGCTTCTGCTTCTGCTATAAT 60.163 40.000 0.00 0.00 40.48 1.28
2252 2370 4.161189 ACTCTGCTTCTGCTTCTGCTATAA 59.839 41.667 0.00 0.00 40.48 0.98
2253 2371 3.703556 ACTCTGCTTCTGCTTCTGCTATA 59.296 43.478 0.00 0.00 40.48 1.31
2254 2372 2.500910 ACTCTGCTTCTGCTTCTGCTAT 59.499 45.455 0.00 0.00 40.48 2.97
2255 2373 1.898472 ACTCTGCTTCTGCTTCTGCTA 59.102 47.619 0.00 0.00 40.48 3.49
2274 2392 5.118990 TCTGCTTCTGCTATAATTGTGGAC 58.881 41.667 0.00 0.00 40.48 4.02
2304 2428 5.118990 TCTGCTTCTGCTATAATTGTGGAC 58.881 41.667 0.00 0.00 40.48 4.02
2322 2446 0.761187 TTGTGGACTCTGCTTCTGCT 59.239 50.000 0.00 0.00 40.48 4.24
2323 2447 1.818642 ATTGTGGACTCTGCTTCTGC 58.181 50.000 0.00 0.00 40.20 4.26
2324 2448 5.236047 GCTATAATTGTGGACTCTGCTTCTG 59.764 44.000 0.00 0.00 0.00 3.02
2325 2449 5.104776 TGCTATAATTGTGGACTCTGCTTCT 60.105 40.000 0.00 0.00 0.00 2.85
2326 2450 5.118990 TGCTATAATTGTGGACTCTGCTTC 58.881 41.667 0.00 0.00 0.00 3.86
2327 2451 5.102953 TGCTATAATTGTGGACTCTGCTT 57.897 39.130 0.00 0.00 0.00 3.91
2328 2452 4.406972 TCTGCTATAATTGTGGACTCTGCT 59.593 41.667 0.00 0.00 0.00 4.24
2329 2453 4.697514 TCTGCTATAATTGTGGACTCTGC 58.302 43.478 0.00 0.00 0.00 4.26
2330 2454 5.236047 GCTTCTGCTATAATTGTGGACTCTG 59.764 44.000 0.00 0.00 36.03 3.35
2331 2455 5.104776 TGCTTCTGCTATAATTGTGGACTCT 60.105 40.000 0.00 0.00 40.48 3.24
2332 2456 5.118990 TGCTTCTGCTATAATTGTGGACTC 58.881 41.667 0.00 0.00 40.48 3.36
2333 2457 5.102953 TGCTTCTGCTATAATTGTGGACT 57.897 39.130 0.00 0.00 40.48 3.85
2334 2458 5.118990 TCTGCTTCTGCTATAATTGTGGAC 58.881 41.667 0.00 0.00 40.48 4.02
2335 2459 5.357742 TCTGCTTCTGCTATAATTGTGGA 57.642 39.130 0.00 0.00 40.48 4.02
2336 2460 5.505324 GCTTCTGCTTCTGCTATAATTGTGG 60.505 44.000 0.00 0.00 40.48 4.17
2337 2461 5.065602 TGCTTCTGCTTCTGCTATAATTGTG 59.934 40.000 0.00 0.00 40.48 3.33
2338 2462 5.188434 TGCTTCTGCTTCTGCTATAATTGT 58.812 37.500 0.00 0.00 40.48 2.71
2339 2463 5.526479 TCTGCTTCTGCTTCTGCTATAATTG 59.474 40.000 0.00 0.00 40.48 2.32
2340 2464 5.678583 TCTGCTTCTGCTTCTGCTATAATT 58.321 37.500 0.00 0.00 40.48 1.40
2341 2465 5.287674 TCTGCTTCTGCTTCTGCTATAAT 57.712 39.130 0.00 0.00 40.48 1.28
2342 2466 4.743057 TCTGCTTCTGCTTCTGCTATAA 57.257 40.909 0.00 0.00 40.48 0.98
2343 2467 4.743057 TTCTGCTTCTGCTTCTGCTATA 57.257 40.909 0.00 0.00 40.48 1.31
2344 2468 3.623906 TTCTGCTTCTGCTTCTGCTAT 57.376 42.857 0.00 0.00 40.48 2.97
2416 2540 4.926238 CACACCTCAGTTATTGTCAGACTC 59.074 45.833 1.31 0.00 0.00 3.36
2546 2687 6.000840 GGAATCAGAAGATCCTATGAAACCC 58.999 44.000 0.00 0.00 31.90 4.11
2699 3619 8.257306 TGGAAATTTACCTCTTTATGCCATTTC 58.743 33.333 0.00 0.00 0.00 2.17
2704 3624 7.147742 TGGATTGGAAATTTACCTCTTTATGCC 60.148 37.037 0.00 0.00 0.00 4.40
2720 3641 4.916041 AGAGATGTCACTGGATTGGAAA 57.084 40.909 0.00 0.00 0.00 3.13
2929 3958 9.930693 CTAGATAAAGTACTGTCCTGAGTTTTT 57.069 33.333 0.00 0.00 0.00 1.94
2930 3959 8.035984 GCTAGATAAAGTACTGTCCTGAGTTTT 58.964 37.037 0.00 0.00 0.00 2.43
2931 3960 7.397761 AGCTAGATAAAGTACTGTCCTGAGTTT 59.602 37.037 0.00 0.00 0.00 2.66
2932 3961 6.893005 AGCTAGATAAAGTACTGTCCTGAGTT 59.107 38.462 0.00 0.00 0.00 3.01
2933 3962 6.428295 AGCTAGATAAAGTACTGTCCTGAGT 58.572 40.000 0.00 0.00 0.00 3.41
2934 3963 6.952773 AGCTAGATAAAGTACTGTCCTGAG 57.047 41.667 0.00 0.00 0.00 3.35
2935 3964 8.684520 GTTTAGCTAGATAAAGTACTGTCCTGA 58.315 37.037 13.29 0.00 0.00 3.86
2936 3965 8.467598 TGTTTAGCTAGATAAAGTACTGTCCTG 58.532 37.037 13.29 0.00 0.00 3.86
2937 3966 8.591114 TGTTTAGCTAGATAAAGTACTGTCCT 57.409 34.615 13.29 0.00 0.00 3.85
2938 3967 9.465985 GATGTTTAGCTAGATAAAGTACTGTCC 57.534 37.037 13.29 0.72 0.00 4.02
3025 4092 3.003480 ACAGAGAGCGGCAAATAAAGAC 58.997 45.455 1.45 0.00 0.00 3.01
3038 4105 7.416022 CAATTTCCTTGATGATTACAGAGAGC 58.584 38.462 0.00 0.00 36.97 4.09
3064 4135 8.807118 TGGTAAATCAGTATCTAGCCTGATAAG 58.193 37.037 15.39 0.00 45.32 1.73
3072 4143 9.726438 ATAATTGGTGGTAAATCAGTATCTAGC 57.274 33.333 0.00 0.00 0.00 3.42
3090 4167 5.539955 AGGAGTTCAAAGCAACATAATTGGT 59.460 36.000 0.00 0.00 0.00 3.67
3091 4280 5.865552 CAGGAGTTCAAAGCAACATAATTGG 59.134 40.000 0.00 0.00 0.00 3.16
3099 4288 3.206150 TCTGACAGGAGTTCAAAGCAAC 58.794 45.455 1.81 0.00 0.00 4.17
3131 4320 6.318900 TCTTGACGCTCTATCATCAGAAAGTA 59.681 38.462 0.00 0.00 0.00 2.24
3137 4327 5.006165 GGTTTTCTTGACGCTCTATCATCAG 59.994 44.000 0.00 0.00 0.00 2.90
3154 4344 4.322080 GCTTAACAGCTTTGGGTTTTCT 57.678 40.909 0.00 0.00 43.51 2.52
3171 4361 2.139917 ACGTTCATGCGAGTTTGCTTA 58.860 42.857 0.00 0.00 35.36 3.09
3179 4369 1.393539 CAGGGTAAACGTTCATGCGAG 59.606 52.381 0.00 0.00 35.59 5.03
3180 4370 1.434555 CAGGGTAAACGTTCATGCGA 58.565 50.000 0.00 0.00 35.59 5.10
3212 4402 3.555586 GCATATCATCCACCCCAATTTGC 60.556 47.826 0.00 0.00 0.00 3.68
3214 4404 3.899360 CAGCATATCATCCACCCCAATTT 59.101 43.478 0.00 0.00 0.00 1.82
3217 4407 1.145531 CCAGCATATCATCCACCCCAA 59.854 52.381 0.00 0.00 0.00 4.12
3219 4409 0.610232 GCCAGCATATCATCCACCCC 60.610 60.000 0.00 0.00 0.00 4.95
3235 4434 2.457813 ACCTGAATATTGCCATGCCA 57.542 45.000 0.00 0.00 0.00 4.92
3236 4435 6.567050 CATTATACCTGAATATTGCCATGCC 58.433 40.000 0.00 0.00 0.00 4.40
3237 4436 6.038356 GCATTATACCTGAATATTGCCATGC 58.962 40.000 0.00 0.00 34.72 4.06
3238 4437 7.160547 TGCATTATACCTGAATATTGCCATG 57.839 36.000 0.00 0.00 37.67 3.66
3239 4438 7.575532 CGTTGCATTATACCTGAATATTGCCAT 60.576 37.037 0.00 0.00 37.67 4.40
3310 4516 6.403866 TTGCTTCCTTCATTTTGTGTATGT 57.596 33.333 0.00 0.00 0.00 2.29
3342 4548 4.103153 TGGAGTTCTGACTTTGATTGTCCT 59.897 41.667 0.00 0.00 35.88 3.85
3349 4555 5.240891 GTGATGATGGAGTTCTGACTTTGA 58.759 41.667 0.00 0.00 35.88 2.69
3378 4584 4.380973 GGATCAAGAGACAACACTCATCGA 60.381 45.833 0.00 0.00 39.14 3.59
3379 4585 3.862267 GGATCAAGAGACAACACTCATCG 59.138 47.826 0.00 0.00 39.14 3.84
3394 4600 7.776107 TCTACATGTAGAGAAACTGGATCAAG 58.224 38.462 27.96 2.96 37.28 3.02
3395 4601 7.718334 TCTACATGTAGAGAAACTGGATCAA 57.282 36.000 27.96 4.48 37.28 2.57
3396 4602 7.343057 ACATCTACATGTAGAGAAACTGGATCA 59.657 37.037 32.81 11.94 44.47 2.92
3397 4603 7.721402 ACATCTACATGTAGAGAAACTGGATC 58.279 38.462 32.81 0.00 44.47 3.36
3398 4604 7.343057 TGACATCTACATGTAGAGAAACTGGAT 59.657 37.037 32.81 15.60 43.79 3.41
3399 4605 6.663523 TGACATCTACATGTAGAGAAACTGGA 59.336 38.462 32.81 17.57 43.79 3.86
3400 4606 6.867550 TGACATCTACATGTAGAGAAACTGG 58.132 40.000 32.81 20.03 43.79 4.00
3401 4607 6.475076 GCTGACATCTACATGTAGAGAAACTG 59.525 42.308 32.81 27.54 43.79 3.16
3402 4608 6.568869 GCTGACATCTACATGTAGAGAAACT 58.431 40.000 32.81 18.13 43.79 2.66
3403 4609 5.457148 CGCTGACATCTACATGTAGAGAAAC 59.543 44.000 32.81 24.15 43.79 2.78
3404 4610 5.582550 CGCTGACATCTACATGTAGAGAAA 58.417 41.667 32.81 20.16 43.79 2.52
3405 4611 4.498177 GCGCTGACATCTACATGTAGAGAA 60.498 45.833 32.81 19.88 43.79 2.87
3406 4612 3.003793 GCGCTGACATCTACATGTAGAGA 59.996 47.826 32.81 19.07 43.79 3.10
3407 4613 3.243201 TGCGCTGACATCTACATGTAGAG 60.243 47.826 32.81 26.36 43.79 2.43
3408 4614 2.687935 TGCGCTGACATCTACATGTAGA 59.312 45.455 32.17 32.17 43.79 2.59
3409 4615 3.084070 TGCGCTGACATCTACATGTAG 57.916 47.619 24.37 24.37 43.79 2.74
3410 4616 3.518634 TTGCGCTGACATCTACATGTA 57.481 42.857 9.73 5.25 43.79 2.29
3411 4617 2.385013 TTGCGCTGACATCTACATGT 57.615 45.000 9.73 2.69 46.64 3.21
3412 4618 3.957671 ATTTGCGCTGACATCTACATG 57.042 42.857 9.73 0.00 35.92 3.21


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

AutoCloner maintained by Alex Coulton.