Multiple sequence alignment - TraesCS1D01G265500

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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 TraesCS1D01G265500 chr1D 100.000 2059 0 0 1 2059 361204135 361206193 0.000000e+00 3803.0
1 TraesCS1D01G265500 chr1D 82.060 1126 158 31 951 2059 361213312 361214410 0.000000e+00 920.0
2 TraesCS1D01G265500 chr1D 78.157 1085 182 42 971 2034 361487831 361488881 7.720000e-180 640.0
3 TraesCS1D01G265500 chr1D 100.000 311 0 0 2248 2558 361206382 361206692 2.210000e-160 575.0
4 TraesCS1D01G265500 chr1D 86.047 215 23 4 432 645 361487599 361487807 9.210000e-55 224.0
5 TraesCS1D01G265500 chr1D 83.333 228 31 6 58 280 441287067 441287292 1.200000e-48 204.0
6 TraesCS1D01G265500 chr1D 82.843 204 26 7 446 645 361213109 361213307 9.410000e-40 174.0
7 TraesCS1D01G265500 chr1B 92.982 1596 94 10 432 2015 483865743 483867332 0.000000e+00 2311.0
8 TraesCS1D01G265500 chr1B 81.412 694 114 14 951 1635 484217441 484218128 1.030000e-153 553.0
9 TraesCS1D01G265500 chr1B 80.692 694 108 19 951 1635 484150455 484151131 1.360000e-142 516.0
10 TraesCS1D01G265500 chr1B 95.273 275 12 1 43 317 483858719 483858992 3.910000e-118 435.0
11 TraesCS1D01G265500 chr1B 93.785 177 10 1 2383 2558 483867463 483867639 5.430000e-67 265.0
12 TraesCS1D01G265500 chr1B 95.413 109 5 0 301 409 483864738 483864846 9.410000e-40 174.0
13 TraesCS1D01G265500 chr1B 90.411 73 7 0 2296 2368 11916443 11916371 2.090000e-16 97.1
14 TraesCS1D01G265500 chr1B 92.308 52 2 1 2 53 483856737 483856786 3.530000e-09 73.1
15 TraesCS1D01G265500 chr1B 100.000 30 0 0 2030 2059 483867331 483867360 3.560000e-04 56.5
16 TraesCS1D01G265500 chr1A 83.769 1109 164 14 959 2059 460967270 460968370 0.000000e+00 1037.0
17 TraesCS1D01G265500 chr1A 79.695 852 133 25 971 1809 461047681 461048505 1.710000e-161 579.0
18 TraesCS1D01G265500 chr1A 82.018 228 34 5 58 280 536688713 536688488 1.210000e-43 187.0
19 TraesCS1D01G265500 chrUn 78.967 271 50 7 676 943 11816427 11816693 7.270000e-41 178.0
20 TraesCS1D01G265500 chrUn 78.832 274 51 7 676 946 405641576 405641307 7.270000e-41 178.0
21 TraesCS1D01G265500 chrUn 76.254 299 37 19 676 959 18805026 18804747 7.430000e-26 128.0
22 TraesCS1D01G265500 chrUn 85.897 78 11 0 2293 2370 37322514 37322437 1.630000e-12 84.2
23 TraesCS1D01G265500 chr3B 94.872 78 4 0 2293 2370 74761455 74761378 3.460000e-24 122.0
24 TraesCS1D01G265500 chr3B 83.784 111 13 3 832 941 537574871 537574977 1.620000e-17 100.0
25 TraesCS1D01G265500 chr3D 85.345 116 11 3 832 946 411007869 411007979 5.780000e-22 115.0
26 TraesCS1D01G265500 chr2D 83.065 124 16 4 826 947 96801339 96801459 9.680000e-20 108.0
27 TraesCS1D01G265500 chr2B 91.139 79 7 0 2292 2370 764915170 764915092 9.680000e-20 108.0
28 TraesCS1D01G265500 chr5D 83.051 118 17 3 676 791 445804202 445804318 1.250000e-18 104.0
29 TraesCS1D01G265500 chr5B 89.873 79 8 0 2292 2370 606930341 606930263 4.500000e-18 102.0
30 TraesCS1D01G265500 chr3A 79.195 149 22 9 813 956 547482171 547482315 7.530000e-16 95.3
31 TraesCS1D01G265500 chr6D 81.308 107 14 4 843 946 394928223 394928120 5.870000e-12 82.4


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 TraesCS1D01G265500 chr1D 361204135 361206692 2557 False 2189.000 3803 100.0000 1 2558 2 chr1D.!!$F2 2557
1 TraesCS1D01G265500 chr1D 361213109 361214410 1301 False 547.000 920 82.4515 446 2059 2 chr1D.!!$F3 1613
2 TraesCS1D01G265500 chr1D 361487599 361488881 1282 False 432.000 640 82.1020 432 2034 2 chr1D.!!$F4 1602
3 TraesCS1D01G265500 chr1B 483864738 483867639 2901 False 701.625 2311 95.5450 301 2558 4 chr1B.!!$F4 2257
4 TraesCS1D01G265500 chr1B 484217441 484218128 687 False 553.000 553 81.4120 951 1635 1 chr1B.!!$F2 684
5 TraesCS1D01G265500 chr1B 484150455 484151131 676 False 516.000 516 80.6920 951 1635 1 chr1B.!!$F1 684
6 TraesCS1D01G265500 chr1B 483856737 483858992 2255 False 254.050 435 93.7905 2 317 2 chr1B.!!$F3 315
7 TraesCS1D01G265500 chr1A 460967270 460968370 1100 False 1037.000 1037 83.7690 959 2059 1 chr1A.!!$F1 1100
8 TraesCS1D01G265500 chr1A 461047681 461048505 824 False 579.000 579 79.6950 971 1809 1 chr1A.!!$F2 838

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
125 2069 0.250038 CTAGATGGTGGGGCACGATG 60.250 60.0 0.00 0.00 33.22 3.84 F
1026 3849 0.106669 TGGAGGCGCTTCTAGCTCTA 60.107 55.0 19.65 5.27 39.60 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 4157 0.251165 GGGGAAGTAGTTGGCTGCAA 60.251 55.0 0.5 0.0 0.0 4.08 R
2333 5196 0.034863 TCCCAGGCCGTAATCAAACC 60.035 55.0 0.0 0.0 0.0 3.27 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
41 42 2.892852 AGTGCAATGTGGTACATGCTTT 59.107 40.909 13.40 0.00 44.52 3.51
74 2018 1.000955 CCAGATGTATGCTCCCGGTAC 59.999 57.143 0.00 0.00 0.00 3.34
93 2037 3.469970 TCATGCGGATGGCTCGGT 61.470 61.111 17.41 0.00 44.05 4.69
125 2069 0.250038 CTAGATGGTGGGGCACGATG 60.250 60.000 0.00 0.00 33.22 3.84
151 2095 6.037610 GCATCCTCTATTGTTGAGTTTGTAGG 59.962 42.308 0.00 0.00 0.00 3.18
191 2135 9.225201 CTTCGGATTGTTTAATGTATGTCATTG 57.775 33.333 0.00 0.00 45.14 2.82
341 2285 7.066645 GTGATACGCCTCCTTTTTAATTAAGGT 59.933 37.037 13.62 1.60 42.29 3.50
389 2333 2.934887 TGCATACAATGTCCCAGATGG 58.065 47.619 0.00 0.00 0.00 3.51
409 2353 2.073816 GAACCCGTATCAACACCACAG 58.926 52.381 0.00 0.00 0.00 3.66
410 2354 0.323629 ACCCGTATCAACACCACAGG 59.676 55.000 0.00 0.00 0.00 4.00
411 2355 0.323629 CCCGTATCAACACCACAGGT 59.676 55.000 0.00 0.00 35.62 4.00
412 2356 1.674817 CCCGTATCAACACCACAGGTC 60.675 57.143 0.00 0.00 31.02 3.85
414 2358 2.354704 CCGTATCAACACCACAGGTCAT 60.355 50.000 0.00 0.00 31.02 3.06
416 2360 4.442893 CCGTATCAACACCACAGGTCATAT 60.443 45.833 0.00 0.00 31.02 1.78
417 2361 4.745125 CGTATCAACACCACAGGTCATATC 59.255 45.833 0.00 0.00 31.02 1.63
418 2362 4.842531 ATCAACACCACAGGTCATATCA 57.157 40.909 0.00 0.00 31.02 2.15
419 2363 3.937814 TCAACACCACAGGTCATATCAC 58.062 45.455 0.00 0.00 31.02 3.06
421 2365 4.019411 TCAACACCACAGGTCATATCACAT 60.019 41.667 0.00 0.00 31.02 3.21
422 2366 5.188751 TCAACACCACAGGTCATATCACATA 59.811 40.000 0.00 0.00 31.02 2.29
424 2368 6.252599 ACACCACAGGTCATATCACATAAT 57.747 37.500 0.00 0.00 31.02 1.28
425 2369 6.291377 ACACCACAGGTCATATCACATAATC 58.709 40.000 0.00 0.00 31.02 1.75
426 2370 6.126796 ACACCACAGGTCATATCACATAATCA 60.127 38.462 0.00 0.00 31.02 2.57
427 2371 6.938596 CACCACAGGTCATATCACATAATCAT 59.061 38.462 0.00 0.00 31.02 2.45
429 2373 7.446319 ACCACAGGTCATATCACATAATCATTG 59.554 37.037 0.00 0.00 0.00 2.82
430 2374 7.303261 CACAGGTCATATCACATAATCATTGC 58.697 38.462 0.00 0.00 0.00 3.56
509 3327 6.992063 TTTGAAAGCTTGTAGATGGAGATC 57.008 37.500 0.00 0.00 0.00 2.75
510 3328 5.682234 TGAAAGCTTGTAGATGGAGATCA 57.318 39.130 0.00 0.00 0.00 2.92
511 3329 6.244552 TGAAAGCTTGTAGATGGAGATCAT 57.755 37.500 0.00 0.00 39.13 2.45
512 3330 6.053650 TGAAAGCTTGTAGATGGAGATCATG 58.946 40.000 0.00 0.00 35.97 3.07
513 3331 5.627182 AAGCTTGTAGATGGAGATCATGT 57.373 39.130 0.00 0.00 35.97 3.21
514 3332 6.737720 AAGCTTGTAGATGGAGATCATGTA 57.262 37.500 0.00 0.00 35.97 2.29
515 3333 6.343716 AGCTTGTAGATGGAGATCATGTAG 57.656 41.667 0.00 0.00 35.97 2.74
559 3379 6.358118 TGGCTTACAAGTCTAATAATTGCG 57.642 37.500 0.00 0.00 0.00 4.85
709 3531 9.603921 ATGGTGAATTTTATTAGCTCAAAATGG 57.396 29.630 11.99 0.00 35.19 3.16
727 3549 8.689061 TCAAAATGGATCATCAAAAGGATACAG 58.311 33.333 0.00 0.00 39.75 2.74
737 3559 6.748333 TCAAAAGGATACAGAAGCAATGAG 57.252 37.500 0.00 0.00 41.41 2.90
751 3573 0.467844 AATGAGCACACAACCAGGCA 60.468 50.000 0.00 0.00 0.00 4.75
782 3604 2.334307 GATGCACACAGCCAACACT 58.666 52.632 0.00 0.00 44.83 3.55
785 3607 1.979855 TGCACACAGCCAACACTAAT 58.020 45.000 0.00 0.00 44.83 1.73
810 3632 4.211164 CACAAACACGAAAGCTACATCAGA 59.789 41.667 0.00 0.00 0.00 3.27
811 3633 4.997395 ACAAACACGAAAGCTACATCAGAT 59.003 37.500 0.00 0.00 0.00 2.90
832 3654 8.506437 TCAGATACTAGCAATGTGAAAACAAAG 58.494 33.333 3.75 0.00 0.00 2.77
833 3655 8.506437 CAGATACTAGCAATGTGAAAACAAAGA 58.494 33.333 0.00 0.00 0.00 2.52
834 3656 8.507249 AGATACTAGCAATGTGAAAACAAAGAC 58.493 33.333 0.00 0.00 0.00 3.01
841 3664 2.750166 TGTGAAAACAAAGACCGAAGCA 59.250 40.909 0.00 0.00 0.00 3.91
876 3699 9.803315 GTGGAGTAAAGAAAAATGAAAAACTCT 57.197 29.630 0.00 0.00 33.16 3.24
899 3722 6.864685 TCTGAGCAATCAAAACAATGATCAAC 59.135 34.615 0.00 0.00 39.08 3.18
914 3737 8.077991 ACAATGATCAACAATCTACAACAACAG 58.922 33.333 0.00 0.00 35.24 3.16
930 3753 2.691526 CAACAGCCATATCAGCACCAAT 59.308 45.455 0.00 0.00 0.00 3.16
939 3762 5.181433 CCATATCAGCACCAATCATCTCTTG 59.819 44.000 0.00 0.00 0.00 3.02
966 3789 0.883153 TTGTGATGTCATGCAGGCAC 59.117 50.000 0.00 13.71 32.48 5.01
1008 3831 6.435277 AGGTGCCAAATCTATGCCTATAAATG 59.565 38.462 0.00 0.00 0.00 2.32
1026 3849 0.106669 TGGAGGCGCTTCTAGCTCTA 60.107 55.000 19.65 5.27 39.60 2.43
1028 3851 1.600023 GAGGCGCTTCTAGCTCTAGA 58.400 55.000 12.94 2.65 39.60 2.43
1061 3895 6.065374 ACTACATCTACACTCCACTCCATAG 58.935 44.000 0.00 0.00 0.00 2.23
1067 3901 6.853490 TCTACACTCCACTCCATAGTCATAT 58.147 40.000 0.00 0.00 31.97 1.78
1099 3933 7.250569 AGTGATACAATTTTATGTGAAAGCCG 58.749 34.615 0.00 0.00 34.75 5.52
1121 3955 5.106555 CCGTAGAAGCAACAATGAAGAACAT 60.107 40.000 0.00 0.00 41.45 2.71
1129 3963 5.765176 CAACAATGAAGAACATCAAGCTCA 58.235 37.500 0.00 0.00 38.38 4.26
1316 4157 0.679505 GATGCCATGCCATGAATGCT 59.320 50.000 6.18 0.00 0.00 3.79
1387 4228 1.754803 GGGTGGATATCTGTGACGACA 59.245 52.381 2.05 0.00 0.00 4.35
1456 4297 1.609061 CGGGCAGTGTCAAGATGTTCT 60.609 52.381 0.00 0.00 0.00 3.01
1579 4422 8.675504 CAAAAATAAAGCTCAGATGAGATGAGT 58.324 33.333 13.98 0.00 44.92 3.41
1586 4429 4.916831 GCTCAGATGAGATGAGTATTGTCG 59.083 45.833 13.98 0.00 44.92 4.35
1757 4605 1.379527 CTCCCTGAATAAACACCCGC 58.620 55.000 0.00 0.00 0.00 6.13
1783 4631 5.705609 AATTGTGTGTCTCCGCTTAAAAT 57.294 34.783 0.00 0.00 0.00 1.82
1928 4784 5.212532 TGGCTAATTGTTTGCAACATTCT 57.787 34.783 0.00 0.00 41.79 2.40
2288 5151 5.036916 ACCAATTATCCTCCTTAGTGGACA 58.963 41.667 0.00 0.00 40.56 4.02
2289 5152 5.491078 ACCAATTATCCTCCTTAGTGGACAA 59.509 40.000 0.00 0.00 40.56 3.18
2290 5153 6.160459 ACCAATTATCCTCCTTAGTGGACAAT 59.840 38.462 0.00 0.00 40.56 2.71
2291 5154 7.349859 ACCAATTATCCTCCTTAGTGGACAATA 59.650 37.037 0.00 0.00 40.56 1.90
2292 5155 7.661847 CCAATTATCCTCCTTAGTGGACAATAC 59.338 40.741 0.00 0.00 40.56 1.89
2293 5156 7.931015 ATTATCCTCCTTAGTGGACAATACA 57.069 36.000 0.00 0.00 40.56 2.29
2294 5157 5.615925 ATCCTCCTTAGTGGACAATACAC 57.384 43.478 0.00 0.00 40.56 2.90
2296 5159 5.834460 TCCTCCTTAGTGGACAATACACTA 58.166 41.667 0.00 0.00 46.62 2.74
2321 5184 8.556213 AGTAGAAAAATAACCTTATGTTCGCA 57.444 30.769 0.00 0.00 38.42 5.10
2322 5185 9.174166 AGTAGAAAAATAACCTTATGTTCGCAT 57.826 29.630 0.00 0.00 41.41 4.73
2323 5186 9.434559 GTAGAAAAATAACCTTATGTTCGCATC 57.565 33.333 0.00 0.00 38.94 3.91
2324 5187 8.050778 AGAAAAATAACCTTATGTTCGCATCA 57.949 30.769 0.00 0.00 38.94 3.07
2325 5188 8.686334 AGAAAAATAACCTTATGTTCGCATCAT 58.314 29.630 0.00 0.00 38.94 2.45
2326 5189 9.301153 GAAAAATAACCTTATGTTCGCATCATT 57.699 29.630 0.00 0.00 38.94 2.57
2328 5191 9.950680 AAAATAACCTTATGTTCGCATCATTAG 57.049 29.630 0.00 0.00 38.94 1.73
2329 5192 8.677148 AATAACCTTATGTTCGCATCATTAGT 57.323 30.769 0.00 0.00 38.94 2.24
2330 5193 6.604735 AACCTTATGTTCGCATCATTAGTC 57.395 37.500 0.00 0.00 38.94 2.59
2331 5194 5.057149 ACCTTATGTTCGCATCATTAGTCC 58.943 41.667 0.00 0.00 38.94 3.85
2332 5195 4.452455 CCTTATGTTCGCATCATTAGTCCC 59.548 45.833 0.00 0.00 38.94 4.46
2333 5196 1.934589 TGTTCGCATCATTAGTCCCG 58.065 50.000 0.00 0.00 0.00 5.14
2334 5197 1.217882 GTTCGCATCATTAGTCCCGG 58.782 55.000 0.00 0.00 0.00 5.73
2335 5198 0.828022 TTCGCATCATTAGTCCCGGT 59.172 50.000 0.00 0.00 0.00 5.28
2336 5199 0.828022 TCGCATCATTAGTCCCGGTT 59.172 50.000 0.00 0.00 0.00 4.44
2337 5200 1.208535 TCGCATCATTAGTCCCGGTTT 59.791 47.619 0.00 0.00 0.00 3.27
2338 5201 1.330521 CGCATCATTAGTCCCGGTTTG 59.669 52.381 0.00 0.00 0.00 2.93
2339 5202 2.639065 GCATCATTAGTCCCGGTTTGA 58.361 47.619 0.00 0.00 0.00 2.69
2340 5203 3.214328 GCATCATTAGTCCCGGTTTGAT 58.786 45.455 0.00 0.00 0.00 2.57
2341 5204 3.632145 GCATCATTAGTCCCGGTTTGATT 59.368 43.478 0.00 0.00 0.00 2.57
2342 5205 4.819630 GCATCATTAGTCCCGGTTTGATTA 59.180 41.667 0.00 0.00 0.00 1.75
2343 5206 5.277828 GCATCATTAGTCCCGGTTTGATTAC 60.278 44.000 0.00 0.00 0.00 1.89
2344 5207 4.435425 TCATTAGTCCCGGTTTGATTACG 58.565 43.478 0.00 0.00 0.00 3.18
2345 5208 2.965572 TAGTCCCGGTTTGATTACGG 57.034 50.000 0.00 0.00 46.79 4.02
2346 5209 0.392060 AGTCCCGGTTTGATTACGGC 60.392 55.000 0.00 0.00 45.93 5.68
2347 5210 1.078285 TCCCGGTTTGATTACGGCC 60.078 57.895 0.00 0.00 45.93 6.13
2348 5211 1.078001 CCCGGTTTGATTACGGCCT 60.078 57.895 0.00 0.00 45.93 5.19
2349 5212 1.373590 CCCGGTTTGATTACGGCCTG 61.374 60.000 0.00 0.00 45.93 4.85
2350 5213 1.373590 CCGGTTTGATTACGGCCTGG 61.374 60.000 0.00 0.00 41.23 4.45
2351 5214 1.373590 CGGTTTGATTACGGCCTGGG 61.374 60.000 0.00 0.00 0.00 4.45
2352 5215 0.034863 GGTTTGATTACGGCCTGGGA 60.035 55.000 0.00 0.00 0.00 4.37
2353 5216 1.092348 GTTTGATTACGGCCTGGGAC 58.908 55.000 0.00 0.00 0.00 4.46
2354 5217 0.988832 TTTGATTACGGCCTGGGACT 59.011 50.000 0.00 0.00 0.00 3.85
2355 5218 1.868713 TTGATTACGGCCTGGGACTA 58.131 50.000 0.00 0.00 0.00 2.59
2356 5219 1.868713 TGATTACGGCCTGGGACTAA 58.131 50.000 0.00 0.00 0.00 2.24
2357 5220 2.404559 TGATTACGGCCTGGGACTAAT 58.595 47.619 0.00 0.00 0.00 1.73
2358 5221 2.104111 TGATTACGGCCTGGGACTAATG 59.896 50.000 0.00 0.00 0.00 1.90
2359 5222 1.575419 TTACGGCCTGGGACTAATGT 58.425 50.000 0.00 0.00 0.00 2.71
2360 5223 0.828022 TACGGCCTGGGACTAATGTG 59.172 55.000 0.00 0.00 0.00 3.21
2361 5224 0.907704 ACGGCCTGGGACTAATGTGA 60.908 55.000 0.00 0.00 0.00 3.58
2362 5225 0.469917 CGGCCTGGGACTAATGTGAT 59.530 55.000 0.00 0.00 0.00 3.06
2363 5226 1.541233 CGGCCTGGGACTAATGTGATC 60.541 57.143 0.00 0.00 0.00 2.92
2364 5227 1.490490 GGCCTGGGACTAATGTGATCA 59.510 52.381 0.00 0.00 0.00 2.92
2365 5228 2.107204 GGCCTGGGACTAATGTGATCAT 59.893 50.000 0.00 0.00 35.59 2.45
2366 5229 3.435601 GGCCTGGGACTAATGTGATCATT 60.436 47.826 0.00 0.00 45.00 2.57
2367 5230 4.202461 GGCCTGGGACTAATGTGATCATTA 60.202 45.833 0.00 0.00 43.12 1.90
2381 5244 7.939784 TGTGATCATTAGTAGACAGTACACT 57.060 36.000 0.00 0.00 0.00 3.55
2424 5287 1.735559 GAGGTGTGTCGGCGGTAAC 60.736 63.158 7.21 3.68 0.00 2.50
2440 5303 2.167398 TAACGACCTGCTGCAGACCC 62.167 60.000 30.10 16.48 32.44 4.46
2463 5326 1.991230 CTGGAAGGTAGGGTGTGGG 59.009 63.158 0.00 0.00 0.00 4.61
2470 5333 1.420532 GGTAGGGTGTGGGTGTTGGA 61.421 60.000 0.00 0.00 0.00 3.53
2472 5335 1.131303 TAGGGTGTGGGTGTTGGAGG 61.131 60.000 0.00 0.00 0.00 4.30
2473 5336 2.763645 GGGTGTGGGTGTTGGAGGT 61.764 63.158 0.00 0.00 0.00 3.85
2474 5337 1.528309 GGTGTGGGTGTTGGAGGTG 60.528 63.158 0.00 0.00 0.00 4.00
2475 5338 1.226262 GTGTGGGTGTTGGAGGTGT 59.774 57.895 0.00 0.00 0.00 4.16
2476 5339 1.101049 GTGTGGGTGTTGGAGGTGTG 61.101 60.000 0.00 0.00 0.00 3.82
2477 5340 1.226262 GTGGGTGTTGGAGGTGTGT 59.774 57.895 0.00 0.00 0.00 3.72
2478 5341 1.101049 GTGGGTGTTGGAGGTGTGTG 61.101 60.000 0.00 0.00 0.00 3.82
2479 5342 1.275421 TGGGTGTTGGAGGTGTGTGA 61.275 55.000 0.00 0.00 0.00 3.58
2503 5367 3.356529 AATCCAAGTGAGGGATGACAC 57.643 47.619 0.00 0.00 44.30 3.67
2520 5384 0.098200 CACATGCCAAGATGCTCACG 59.902 55.000 0.00 0.00 0.00 4.35
2523 5387 1.674441 CATGCCAAGATGCTCACGAAT 59.326 47.619 0.00 0.00 0.00 3.34
2525 5389 0.379669 GCCAAGATGCTCACGAATGG 59.620 55.000 0.00 0.00 0.00 3.16
2539 5403 0.037139 GAATGGCCTTGCATGCAACA 60.037 50.000 28.80 24.10 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.950836 CATGCAGGAAAACGACACCA 59.049 50.000 0.00 0.00 0.00 4.17
29 30 1.886222 GCAGACCCAAAGCATGTACCA 60.886 52.381 0.00 0.00 0.00 3.25
30 31 0.811281 GCAGACCCAAAGCATGTACC 59.189 55.000 0.00 0.00 0.00 3.34
56 2000 0.959553 CGTACCGGGAGCATACATCT 59.040 55.000 6.32 0.00 0.00 2.90
74 2018 3.333189 CGAGCCATCCGCATGACG 61.333 66.667 0.00 0.00 41.38 4.35
93 2037 3.452264 CACCATCTAGAACTGGGTCATCA 59.548 47.826 15.34 0.00 36.82 3.07
125 2069 4.702131 ACAAACTCAACAATAGAGGATGCC 59.298 41.667 0.00 0.00 37.43 4.40
151 2095 0.798776 CCGAAGCCATCACTCAACAC 59.201 55.000 0.00 0.00 0.00 3.32
247 2191 2.434774 GGTTGAAACCTCGGGCCT 59.565 61.111 0.84 0.00 45.75 5.19
322 2266 5.068723 GGGCTACCTTAATTAAAAAGGAGGC 59.931 44.000 21.00 21.22 45.41 4.70
389 2333 2.073816 CTGTGGTGTTGATACGGGTTC 58.926 52.381 0.00 0.00 0.00 3.62
409 2353 8.118607 CGTATGCAATGATTATGTGATATGACC 58.881 37.037 0.00 0.00 0.00 4.02
410 2354 8.659491 ACGTATGCAATGATTATGTGATATGAC 58.341 33.333 0.00 0.00 0.00 3.06
411 2355 8.776376 ACGTATGCAATGATTATGTGATATGA 57.224 30.769 0.00 0.00 0.00 2.15
412 2356 9.269415 CAACGTATGCAATGATTATGTGATATG 57.731 33.333 0.00 0.00 0.00 1.78
414 2358 7.094848 CCCAACGTATGCAATGATTATGTGATA 60.095 37.037 0.00 0.00 0.00 2.15
416 2360 5.008514 CCCAACGTATGCAATGATTATGTGA 59.991 40.000 0.00 0.00 0.00 3.58
417 2361 5.008514 TCCCAACGTATGCAATGATTATGTG 59.991 40.000 0.00 0.00 0.00 3.21
418 2362 5.129634 TCCCAACGTATGCAATGATTATGT 58.870 37.500 0.00 0.00 0.00 2.29
419 2363 5.469760 TCTCCCAACGTATGCAATGATTATG 59.530 40.000 0.00 0.00 0.00 1.90
421 2365 5.029807 TCTCCCAACGTATGCAATGATTA 57.970 39.130 0.00 0.00 0.00 1.75
422 2366 3.884895 TCTCCCAACGTATGCAATGATT 58.115 40.909 0.00 0.00 0.00 2.57
424 2368 3.118445 TGATCTCCCAACGTATGCAATGA 60.118 43.478 0.00 0.00 0.00 2.57
425 2369 3.205338 TGATCTCCCAACGTATGCAATG 58.795 45.455 0.00 0.00 0.00 2.82
426 2370 3.558931 TGATCTCCCAACGTATGCAAT 57.441 42.857 0.00 0.00 0.00 3.56
427 2371 3.205338 CATGATCTCCCAACGTATGCAA 58.795 45.455 0.00 0.00 0.00 4.08
429 2373 2.838736 ACATGATCTCCCAACGTATGC 58.161 47.619 0.00 0.00 0.00 3.14
430 2374 3.809832 GGAACATGATCTCCCAACGTATG 59.190 47.826 0.00 0.00 0.00 2.39
515 3333 0.676736 ATCTAGGCCTAGCTCGTTGC 59.323 55.000 31.76 0.00 43.29 4.17
559 3379 7.830940 TGTTCAATGGACATATGCAAAATTC 57.169 32.000 1.58 0.00 0.00 2.17
594 3414 0.321564 ACATGCACCACTACGCACAT 60.322 50.000 0.00 0.00 41.79 3.21
599 3419 1.069973 CACACAACATGCACCACTACG 60.070 52.381 0.00 0.00 0.00 3.51
696 3518 7.396907 TCCTTTTGATGATCCATTTTGAGCTAA 59.603 33.333 0.00 0.00 0.00 3.09
709 3531 6.932356 TGCTTCTGTATCCTTTTGATGATC 57.068 37.500 0.00 0.00 34.76 2.92
720 3542 3.064545 GTGTGCTCATTGCTTCTGTATCC 59.935 47.826 0.00 0.00 43.37 2.59
727 3549 1.337703 TGGTTGTGTGCTCATTGCTTC 59.662 47.619 0.00 0.00 43.37 3.86
737 3559 2.723746 CAGTGCCTGGTTGTGTGC 59.276 61.111 0.00 0.00 0.00 4.57
761 3583 0.467844 TGTTGGCTGTGTGCATCCTT 60.468 50.000 0.00 0.00 45.15 3.36
773 3595 2.692557 TGTTTGTGCATTAGTGTTGGCT 59.307 40.909 0.00 0.00 0.00 4.75
782 3604 3.980646 AGCTTTCGTGTTTGTGCATTA 57.019 38.095 0.00 0.00 0.00 1.90
785 3607 2.010497 TGTAGCTTTCGTGTTTGTGCA 58.990 42.857 0.00 0.00 0.00 4.57
810 3632 7.573096 CGGTCTTTGTTTTCACATTGCTAGTAT 60.573 37.037 0.00 0.00 31.06 2.12
811 3633 6.293190 CGGTCTTTGTTTTCACATTGCTAGTA 60.293 38.462 0.00 0.00 31.06 1.82
832 3654 1.244019 ACCAAGGCATTGCTTCGGTC 61.244 55.000 5.36 0.00 34.91 4.79
833 3655 1.228552 ACCAAGGCATTGCTTCGGT 60.229 52.632 5.36 2.61 34.91 4.69
834 3656 1.213537 CACCAAGGCATTGCTTCGG 59.786 57.895 5.36 1.85 34.91 4.30
841 3664 3.806949 TCTTTACTCCACCAAGGCATT 57.193 42.857 0.00 0.00 37.29 3.56
876 3699 6.514063 TGTTGATCATTGTTTTGATTGCTCA 58.486 32.000 0.00 0.00 36.48 4.26
899 3722 6.682423 TGATATGGCTGTTGTTGTAGATTG 57.318 37.500 0.00 0.00 0.00 2.67
914 3737 3.418995 AGATGATTGGTGCTGATATGGC 58.581 45.455 0.00 0.00 0.00 4.40
930 3753 5.473066 TCACAACTGATGTCAAGAGATGA 57.527 39.130 0.00 0.00 41.46 2.92
1026 3849 7.441458 GGAGTGTAGATGTAGTTGTTGTTTTCT 59.559 37.037 0.00 0.00 0.00 2.52
1028 3851 7.012044 GTGGAGTGTAGATGTAGTTGTTGTTTT 59.988 37.037 0.00 0.00 0.00 2.43
1089 3923 1.871039 GTTGCTTCTACGGCTTTCACA 59.129 47.619 0.00 0.00 0.00 3.58
1099 3933 6.902341 TGATGTTCTTCATTGTTGCTTCTAC 58.098 36.000 0.00 0.00 36.83 2.59
1121 3955 2.097036 CAAGGATTGCCATGAGCTTGA 58.903 47.619 0.00 0.00 40.39 3.02
1316 4157 0.251165 GGGGAAGTAGTTGGCTGCAA 60.251 55.000 0.50 0.00 0.00 4.08
1387 4228 3.017581 GGGGCACTGAGGATGGGT 61.018 66.667 0.00 0.00 0.00 4.51
1579 4422 3.252400 ACGAACAAATACGGCGACAATA 58.748 40.909 16.62 0.00 0.00 1.90
1586 4429 4.026310 CCTACATGTACGAACAAATACGGC 60.026 45.833 0.08 0.00 39.58 5.68
1757 4605 2.066262 AGCGGAGACACACAATTAACG 58.934 47.619 0.00 0.00 0.00 3.18
1783 4631 8.939201 AAAATTGTGTGACATGAACAAATGTA 57.061 26.923 0.00 0.00 40.87 2.29
1928 4784 3.637229 GCTACCTATAACCTGAGCACTCA 59.363 47.826 0.00 0.00 38.06 3.41
2260 5123 6.234177 CACTAAGGAGGATAATTGGTCATCC 58.766 44.000 14.80 14.80 44.66 3.51
2261 5124 6.043243 TCCACTAAGGAGGATAATTGGTCATC 59.957 42.308 0.00 0.00 43.07 2.92
2295 5158 9.656040 TGCGAACATAAGGTTATTTTTCTACTA 57.344 29.630 0.00 0.00 40.63 1.82
2296 5159 8.556213 TGCGAACATAAGGTTATTTTTCTACT 57.444 30.769 0.00 0.00 40.63 2.57
2297 5160 9.434559 GATGCGAACATAAGGTTATTTTTCTAC 57.565 33.333 0.00 0.00 40.63 2.59
2298 5161 9.168451 TGATGCGAACATAAGGTTATTTTTCTA 57.832 29.630 0.00 0.00 40.63 2.10
2299 5162 8.050778 TGATGCGAACATAAGGTTATTTTTCT 57.949 30.769 0.00 0.00 40.63 2.52
2300 5163 8.856490 ATGATGCGAACATAAGGTTATTTTTC 57.144 30.769 0.00 0.00 40.63 2.29
2302 5165 9.950680 CTAATGATGCGAACATAAGGTTATTTT 57.049 29.630 0.00 0.00 40.63 1.82
2303 5166 9.120538 ACTAATGATGCGAACATAAGGTTATTT 57.879 29.630 0.00 0.00 40.63 1.40
2304 5167 8.677148 ACTAATGATGCGAACATAAGGTTATT 57.323 30.769 0.00 0.00 40.63 1.40
2305 5168 7.387948 GGACTAATGATGCGAACATAAGGTTAT 59.612 37.037 0.00 0.00 40.63 1.89
2306 5169 6.704493 GGACTAATGATGCGAACATAAGGTTA 59.296 38.462 0.00 0.00 40.63 2.85
2307 5170 5.527582 GGACTAATGATGCGAACATAAGGTT 59.472 40.000 0.00 0.00 44.10 3.50
2308 5171 5.057149 GGACTAATGATGCGAACATAAGGT 58.943 41.667 0.00 0.00 36.35 3.50
2309 5172 4.452455 GGGACTAATGATGCGAACATAAGG 59.548 45.833 0.00 0.00 36.35 2.69
2310 5173 4.150627 CGGGACTAATGATGCGAACATAAG 59.849 45.833 0.00 0.00 36.35 1.73
2311 5174 4.055360 CGGGACTAATGATGCGAACATAA 58.945 43.478 0.00 0.00 36.35 1.90
2312 5175 3.554129 CCGGGACTAATGATGCGAACATA 60.554 47.826 0.00 0.00 36.35 2.29
2313 5176 2.483876 CGGGACTAATGATGCGAACAT 58.516 47.619 0.00 0.00 39.98 2.71
2314 5177 1.472552 CCGGGACTAATGATGCGAACA 60.473 52.381 0.00 0.00 0.00 3.18
2315 5178 1.217882 CCGGGACTAATGATGCGAAC 58.782 55.000 0.00 0.00 0.00 3.95
2316 5179 0.828022 ACCGGGACTAATGATGCGAA 59.172 50.000 6.32 0.00 0.00 4.70
2317 5180 0.828022 AACCGGGACTAATGATGCGA 59.172 50.000 6.32 0.00 0.00 5.10
2318 5181 1.330521 CAAACCGGGACTAATGATGCG 59.669 52.381 6.32 0.00 0.00 4.73
2319 5182 2.639065 TCAAACCGGGACTAATGATGC 58.361 47.619 6.32 0.00 0.00 3.91
2320 5183 5.050363 CGTAATCAAACCGGGACTAATGATG 60.050 44.000 6.32 0.00 0.00 3.07
2321 5184 5.054477 CGTAATCAAACCGGGACTAATGAT 58.946 41.667 6.32 3.28 0.00 2.45
2322 5185 4.435425 CGTAATCAAACCGGGACTAATGA 58.565 43.478 6.32 0.71 0.00 2.57
2323 5186 3.558418 CCGTAATCAAACCGGGACTAATG 59.442 47.826 6.32 0.00 38.09 1.90
2324 5187 3.800531 CCGTAATCAAACCGGGACTAAT 58.199 45.455 6.32 0.00 38.09 1.73
2325 5188 2.677613 GCCGTAATCAAACCGGGACTAA 60.678 50.000 6.32 0.00 41.96 2.24
2326 5189 1.134729 GCCGTAATCAAACCGGGACTA 60.135 52.381 6.32 0.00 41.96 2.59
2327 5190 0.392060 GCCGTAATCAAACCGGGACT 60.392 55.000 6.32 0.00 41.96 3.85
2328 5191 1.371337 GGCCGTAATCAAACCGGGAC 61.371 60.000 6.32 0.00 41.96 4.46
2329 5192 1.078285 GGCCGTAATCAAACCGGGA 60.078 57.895 6.32 0.00 41.96 5.14
2330 5193 1.078001 AGGCCGTAATCAAACCGGG 60.078 57.895 6.32 0.00 41.96 5.73
2331 5194 1.373590 CCAGGCCGTAATCAAACCGG 61.374 60.000 0.00 0.00 44.46 5.28
2332 5195 1.373590 CCCAGGCCGTAATCAAACCG 61.374 60.000 0.00 0.00 0.00 4.44
2333 5196 0.034863 TCCCAGGCCGTAATCAAACC 60.035 55.000 0.00 0.00 0.00 3.27
2334 5197 1.092348 GTCCCAGGCCGTAATCAAAC 58.908 55.000 0.00 0.00 0.00 2.93
2335 5198 0.988832 AGTCCCAGGCCGTAATCAAA 59.011 50.000 0.00 0.00 0.00 2.69
2336 5199 1.868713 TAGTCCCAGGCCGTAATCAA 58.131 50.000 0.00 0.00 0.00 2.57
2337 5200 1.868713 TTAGTCCCAGGCCGTAATCA 58.131 50.000 0.00 0.00 0.00 2.57
2338 5201 2.104281 ACATTAGTCCCAGGCCGTAATC 59.896 50.000 0.00 0.00 0.00 1.75
2339 5202 2.124411 ACATTAGTCCCAGGCCGTAAT 58.876 47.619 0.00 0.00 0.00 1.89
2340 5203 1.208535 CACATTAGTCCCAGGCCGTAA 59.791 52.381 0.00 0.00 0.00 3.18
2341 5204 0.828022 CACATTAGTCCCAGGCCGTA 59.172 55.000 0.00 0.00 0.00 4.02
2342 5205 0.907704 TCACATTAGTCCCAGGCCGT 60.908 55.000 0.00 0.00 0.00 5.68
2343 5206 0.469917 ATCACATTAGTCCCAGGCCG 59.530 55.000 0.00 0.00 0.00 6.13
2344 5207 1.490490 TGATCACATTAGTCCCAGGCC 59.510 52.381 0.00 0.00 0.00 5.19
2345 5208 3.498774 ATGATCACATTAGTCCCAGGC 57.501 47.619 0.00 0.00 32.21 4.85
2355 5218 8.972127 AGTGTACTGTCTACTAATGATCACATT 58.028 33.333 0.00 0.00 46.64 2.71
2356 5219 8.526667 AGTGTACTGTCTACTAATGATCACAT 57.473 34.615 0.00 0.00 38.50 3.21
2357 5220 7.939784 AGTGTACTGTCTACTAATGATCACA 57.060 36.000 0.00 0.00 0.00 3.58
2358 5221 9.111613 ACTAGTGTACTGTCTACTAATGATCAC 57.888 37.037 0.00 0.00 0.00 3.06
2362 5225 9.597170 CACTACTAGTGTACTGTCTACTAATGA 57.403 37.037 5.39 0.00 41.19 2.57
2363 5226 9.597170 TCACTACTAGTGTACTGTCTACTAATG 57.403 37.037 14.63 3.67 46.03 1.90
2365 5228 9.597170 CATCACTACTAGTGTACTGTCTACTAA 57.403 37.037 14.63 0.00 46.03 2.24
2366 5229 7.710044 GCATCACTACTAGTGTACTGTCTACTA 59.290 40.741 14.63 4.64 46.03 1.82
2367 5230 6.539464 GCATCACTACTAGTGTACTGTCTACT 59.461 42.308 14.63 2.99 46.03 2.57
2368 5231 6.238429 GGCATCACTACTAGTGTACTGTCTAC 60.238 46.154 14.63 0.00 46.03 2.59
2369 5232 5.821470 GGCATCACTACTAGTGTACTGTCTA 59.179 44.000 14.63 0.00 46.03 2.59
2370 5233 4.641094 GGCATCACTACTAGTGTACTGTCT 59.359 45.833 14.63 0.00 46.03 3.41
2371 5234 4.398358 TGGCATCACTACTAGTGTACTGTC 59.602 45.833 14.63 12.47 46.03 3.51
2372 5235 4.341487 TGGCATCACTACTAGTGTACTGT 58.659 43.478 14.63 0.00 46.03 3.55
2373 5236 4.983671 TGGCATCACTACTAGTGTACTG 57.016 45.455 14.63 11.80 46.03 2.74
2374 5237 5.262009 TCTTGGCATCACTACTAGTGTACT 58.738 41.667 14.63 0.82 46.03 2.73
2375 5238 5.578005 TCTTGGCATCACTACTAGTGTAC 57.422 43.478 14.63 6.69 46.03 2.90
2376 5239 5.394224 GCTTCTTGGCATCACTACTAGTGTA 60.394 44.000 14.63 4.06 46.03 2.90
2377 5240 4.621747 GCTTCTTGGCATCACTACTAGTGT 60.622 45.833 14.63 0.00 46.03 3.55
2378 5241 4.382470 AGCTTCTTGGCATCACTACTAGTG 60.382 45.833 5.39 9.65 39.99 2.74
2379 5242 3.772025 AGCTTCTTGGCATCACTACTAGT 59.228 43.478 0.00 0.00 34.17 2.57
2380 5243 4.399004 AGCTTCTTGGCATCACTACTAG 57.601 45.455 0.00 0.00 34.17 2.57
2381 5244 4.222810 TCAAGCTTCTTGGCATCACTACTA 59.777 41.667 0.00 0.00 34.17 1.82
2440 5303 0.108138 CACCCTACCTTCCAGCTTCG 60.108 60.000 0.00 0.00 0.00 3.79
2463 5326 3.859411 TTTTTCACACACCTCCAACAC 57.141 42.857 0.00 0.00 0.00 3.32
2503 5367 1.089112 TTCGTGAGCATCTTGGCATG 58.911 50.000 0.00 0.00 34.92 4.06


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

AutoCloner maintained by Alex Coulton.