Multiple sequence alignment - TraesCS6B01G212500

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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 TraesCS6B01G212500 chr6B 100.000 2264 0 0 1 2264 281223416 281221153 0.000000e+00 4181.0
1 TraesCS6B01G212500 chr2D 93.487 2165 107 12 1 2138 632766136 632768293 0.000000e+00 3186.0
2 TraesCS6B01G212500 chr2D 95.155 1548 70 3 1 1544 476789247 476790793 0.000000e+00 2438.0
3 TraesCS6B01G212500 chr1D 91.355 2221 158 12 1 2198 14674870 14672661 0.000000e+00 3007.0
4 TraesCS6B01G212500 chr4A 91.244 2147 158 19 59 2183 564697244 564699382 0.000000e+00 2896.0
5 TraesCS6B01G212500 chr5B 90.140 2221 181 19 1 2189 89726814 89729028 0.000000e+00 2854.0
6 TraesCS6B01G212500 chr5B 88.939 2206 200 29 1 2170 584816933 584814736 0.000000e+00 2682.0
7 TraesCS6B01G212500 chr5B 92.773 1785 121 5 1 1779 64293427 64295209 0.000000e+00 2575.0
8 TraesCS6B01G212500 chr2A 91.094 1965 139 18 1 1939 48624240 48622286 0.000000e+00 2627.0
9 TraesCS6B01G212500 chr2A 77.660 188 37 4 2009 2194 770002888 770003072 2.380000e-20 110.0
10 TraesCS6B01G212500 chr4B 92.022 1805 102 20 432 2198 467349624 467347824 0.000000e+00 2497.0
11 TraesCS6B01G212500 chr3A 88.742 1972 171 32 233 2168 497386154 497388110 0.000000e+00 2364.0
12 TraesCS6B01G212500 chr7D 89.117 1507 126 21 708 2184 131690098 131691596 0.000000e+00 1840.0
13 TraesCS6B01G212500 chr7D 91.415 827 45 5 1256 2057 72155657 72156482 0.000000e+00 1110.0
14 TraesCS6B01G212500 chr7D 80.513 195 33 5 2009 2201 131691680 131691489 6.520000e-31 145.0
15 TraesCS6B01G212500 chr3B 87.474 1461 142 17 744 2184 103209533 103210972 0.000000e+00 1646.0
16 TraesCS6B01G212500 chrUn 82.166 757 100 23 1470 2198 86408368 86409117 3.190000e-173 617.0
17 TraesCS6B01G212500 chr2B 95.308 341 16 0 1 341 15222345 15222005 1.980000e-150 542.0
18 TraesCS6B01G212500 chr4D 88.542 192 19 3 2009 2198 495818443 495818633 1.750000e-56 230.0
19 TraesCS6B01G212500 chr4D 78.246 285 37 14 1793 2056 495818326 495818606 2.330000e-35 159.0
20 TraesCS6B01G212500 chr6D 82.386 176 26 4 2009 2182 377214448 377214276 5.040000e-32 148.0
21 TraesCS6B01G212500 chr5D 96.875 32 1 0 1895 1926 390419474 390419443 1.000000e-03 54.7


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 TraesCS6B01G212500 chr6B 281221153 281223416 2263 True 4181 4181 100.000 1 2264 1 chr6B.!!$R1 2263
1 TraesCS6B01G212500 chr2D 632766136 632768293 2157 False 3186 3186 93.487 1 2138 1 chr2D.!!$F2 2137
2 TraesCS6B01G212500 chr2D 476789247 476790793 1546 False 2438 2438 95.155 1 1544 1 chr2D.!!$F1 1543
3 TraesCS6B01G212500 chr1D 14672661 14674870 2209 True 3007 3007 91.355 1 2198 1 chr1D.!!$R1 2197
4 TraesCS6B01G212500 chr4A 564697244 564699382 2138 False 2896 2896 91.244 59 2183 1 chr4A.!!$F1 2124
5 TraesCS6B01G212500 chr5B 89726814 89729028 2214 False 2854 2854 90.140 1 2189 1 chr5B.!!$F2 2188
6 TraesCS6B01G212500 chr5B 584814736 584816933 2197 True 2682 2682 88.939 1 2170 1 chr5B.!!$R1 2169
7 TraesCS6B01G212500 chr5B 64293427 64295209 1782 False 2575 2575 92.773 1 1779 1 chr5B.!!$F1 1778
8 TraesCS6B01G212500 chr2A 48622286 48624240 1954 True 2627 2627 91.094 1 1939 1 chr2A.!!$R1 1938
9 TraesCS6B01G212500 chr4B 467347824 467349624 1800 True 2497 2497 92.022 432 2198 1 chr4B.!!$R1 1766
10 TraesCS6B01G212500 chr3A 497386154 497388110 1956 False 2364 2364 88.742 233 2168 1 chr3A.!!$F1 1935
11 TraesCS6B01G212500 chr7D 131690098 131691596 1498 False 1840 1840 89.117 708 2184 1 chr7D.!!$F2 1476
12 TraesCS6B01G212500 chr7D 72155657 72156482 825 False 1110 1110 91.415 1256 2057 1 chr7D.!!$F1 801
13 TraesCS6B01G212500 chr3B 103209533 103210972 1439 False 1646 1646 87.474 744 2184 1 chr3B.!!$F1 1440
14 TraesCS6B01G212500 chrUn 86408368 86409117 749 False 617 617 82.166 1470 2198 1 chrUn.!!$F1 728

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
461 462 0.325933 CCTTGATGCCTCACAGTGGA 59.674 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1531 1566 0.415429 TTCTTGCCCTCTCCTCCTCT 59.585 55.0 0.0 0.0 0.0 3.69 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
22 23 3.307410 CCTTGCTGGTGACCACAATACTA 60.307 47.826 16.18 0.00 29.49 1.82
105 106 2.098117 GGATTGGCGAAAAGATGGACTG 59.902 50.000 0.00 0.00 0.00 3.51
127 128 5.139727 TGTCCATTCAAGGTTCAAGATTGT 58.860 37.500 0.00 0.00 0.00 2.71
152 153 1.695893 GCATCAAGCGCGCAAGTCTA 61.696 55.000 35.10 12.45 41.68 2.59
341 342 1.467883 CGCATTTGATGACCGCAACAT 60.468 47.619 0.00 0.00 0.00 2.71
423 424 1.099689 CAAACAAGGTTGACGTGGGT 58.900 50.000 0.00 0.00 32.45 4.51
430 431 3.228017 TTGACGTGGGTGCCTCGA 61.228 61.111 0.00 0.00 42.19 4.04
461 462 0.325933 CCTTGATGCCTCACAGTGGA 59.674 55.000 0.00 0.00 0.00 4.02
575 576 4.093011 GGATGATCTAGCTGGATACACCT 58.907 47.826 13.16 0.00 46.17 4.00
627 628 0.798776 GAGGCATCGGACAACAACAG 59.201 55.000 0.00 0.00 0.00 3.16
756 775 2.285368 TGGCCGTGGAGGAAGGAT 60.285 61.111 0.00 0.00 45.00 3.24
807 827 1.003051 GGACTAGCCTTGGAGGGGA 59.997 63.158 0.00 0.00 35.37 4.81
838 859 1.688627 GGATCCGGTGGTTCTAGGACT 60.689 57.143 0.00 0.00 35.36 3.85
843 864 2.100197 CGGTGGTTCTAGGACTCATCA 58.900 52.381 0.01 0.00 0.00 3.07
874 895 1.405121 GGAAGGCCTATCGACGTGTTT 60.405 52.381 5.16 0.00 0.00 2.83
1010 1040 2.806434 TGTTGTAGGCATGGCTTCATT 58.194 42.857 28.30 5.01 0.00 2.57
1152 1183 2.092429 TGTTTGCAAGGTGAAGGAGTCT 60.092 45.455 0.00 0.00 0.00 3.24
1154 1185 3.685139 TTGCAAGGTGAAGGAGTCTAG 57.315 47.619 0.00 0.00 0.00 2.43
1574 1609 1.300080 GCAAAAGCTCGCAAGGCAA 60.300 52.632 0.00 0.00 36.22 4.52
1615 1651 0.786435 ACAAGAAGGGGAAATGGCCT 59.214 50.000 3.32 0.00 0.00 5.19
1620 1656 0.546598 AAGGGGAAATGGCCTCGTAG 59.453 55.000 3.32 0.00 32.06 3.51
1865 1984 1.765314 ACTGTTGTGCTGAGAAGAGGT 59.235 47.619 0.00 0.00 0.00 3.85
1873 1992 1.707632 CTGAGAAGAGGTGCAGAACG 58.292 55.000 0.00 0.00 0.00 3.95
1908 2174 1.058284 TTTTACCCTACCGCCACAGT 58.942 50.000 0.00 0.00 0.00 3.55
1935 2201 1.971357 CGGTAGGATGCTTGACCCTAT 59.029 52.381 0.00 0.00 35.28 2.57
1939 2205 0.394565 GGATGCTTGACCCTATCGCT 59.605 55.000 0.00 0.00 0.00 4.93
2110 2425 2.519013 GAGAAAAATGAGCACCCTGGT 58.481 47.619 0.00 0.00 0.00 4.00
2198 2517 7.479916 GCTCGTTTTTCTCATCATAGAAAGTTG 59.520 37.037 0.00 0.00 44.15 3.16
2199 2518 7.806690 TCGTTTTTCTCATCATAGAAAGTTGG 58.193 34.615 0.00 0.00 44.15 3.77
2200 2519 6.524586 CGTTTTTCTCATCATAGAAAGTTGGC 59.475 38.462 0.00 0.00 44.15 4.52
2201 2520 5.801350 TTTCTCATCATAGAAAGTTGGCG 57.199 39.130 0.00 0.00 39.86 5.69
2202 2521 3.797039 TCTCATCATAGAAAGTTGGCGG 58.203 45.455 0.00 0.00 0.00 6.13
2203 2522 3.197766 TCTCATCATAGAAAGTTGGCGGT 59.802 43.478 0.00 0.00 0.00 5.68
2204 2523 4.404394 TCTCATCATAGAAAGTTGGCGGTA 59.596 41.667 0.00 0.00 0.00 4.02
2205 2524 4.693283 TCATCATAGAAAGTTGGCGGTAG 58.307 43.478 0.00 0.00 0.00 3.18
2206 2525 3.536956 TCATAGAAAGTTGGCGGTAGG 57.463 47.619 0.00 0.00 0.00 3.18
2207 2526 3.101437 TCATAGAAAGTTGGCGGTAGGA 58.899 45.455 0.00 0.00 0.00 2.94
2208 2527 3.709653 TCATAGAAAGTTGGCGGTAGGAT 59.290 43.478 0.00 0.00 0.00 3.24
2209 2528 4.163458 TCATAGAAAGTTGGCGGTAGGATT 59.837 41.667 0.00 0.00 0.00 3.01
2210 2529 2.987232 AGAAAGTTGGCGGTAGGATTC 58.013 47.619 0.00 0.00 0.00 2.52
2211 2530 2.572104 AGAAAGTTGGCGGTAGGATTCT 59.428 45.455 0.00 0.00 0.00 2.40
2212 2531 3.009143 AGAAAGTTGGCGGTAGGATTCTT 59.991 43.478 0.00 0.00 0.00 2.52
2225 2544 1.070289 GGATTCTTACCCTACCGCCAG 59.930 57.143 0.00 0.00 0.00 4.85
2226 2545 0.468648 ATTCTTACCCTACCGCCAGC 59.531 55.000 0.00 0.00 0.00 4.85
2239 2558 1.725973 GCCAGCGTGCTCGTTTTTC 60.726 57.895 10.18 0.00 39.49 2.29
2246 2565 2.827555 CGTGCTCGTTTTTCTCATCAC 58.172 47.619 0.00 0.00 0.00 3.06
2247 2566 2.220824 CGTGCTCGTTTTTCTCATCACA 59.779 45.455 0.00 0.00 0.00 3.58
2248 2567 3.662713 CGTGCTCGTTTTTCTCATCACAG 60.663 47.826 0.00 0.00 0.00 3.66
2249 2568 3.494626 GTGCTCGTTTTTCTCATCACAGA 59.505 43.478 0.00 0.00 0.00 3.41
2250 2569 4.024893 GTGCTCGTTTTTCTCATCACAGAA 60.025 41.667 0.00 0.00 0.00 3.02
2251 2570 4.574421 TGCTCGTTTTTCTCATCACAGAAA 59.426 37.500 0.00 0.00 40.03 2.52
2252 2571 5.142962 GCTCGTTTTTCTCATCACAGAAAG 58.857 41.667 0.00 0.00 42.14 2.62
2253 2572 5.277538 GCTCGTTTTTCTCATCACAGAAAGT 60.278 40.000 0.00 0.00 42.14 2.66
2254 2573 6.677781 TCGTTTTTCTCATCACAGAAAGTT 57.322 33.333 0.00 0.00 42.14 2.66
2255 2574 7.083875 TCGTTTTTCTCATCACAGAAAGTTT 57.916 32.000 0.00 0.00 42.14 2.66
2256 2575 8.203937 TCGTTTTTCTCATCACAGAAAGTTTA 57.796 30.769 0.00 0.00 42.14 2.01
2257 2576 8.120465 TCGTTTTTCTCATCACAGAAAGTTTAC 58.880 33.333 0.00 0.00 42.14 2.01
2258 2577 7.376072 CGTTTTTCTCATCACAGAAAGTTTACC 59.624 37.037 0.00 0.00 42.14 2.85
2259 2578 6.877611 TTTCTCATCACAGAAAGTTTACCC 57.122 37.500 0.00 0.00 37.45 3.69
2260 2579 4.906618 TCTCATCACAGAAAGTTTACCCC 58.093 43.478 0.00 0.00 0.00 4.95
2261 2580 4.010349 CTCATCACAGAAAGTTTACCCCC 58.990 47.826 0.00 0.00 0.00 5.40
2262 2581 3.655777 TCATCACAGAAAGTTTACCCCCT 59.344 43.478 0.00 0.00 0.00 4.79
2263 2582 4.847512 TCATCACAGAAAGTTTACCCCCTA 59.152 41.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.042322 AGTGTACTTTAGTATTGTGGTCACCA 59.958 38.462 0.00 0.00 32.54 4.17
105 106 5.712152 ACAATCTTGAACCTTGAATGGAC 57.288 39.130 0.00 0.00 0.00 4.02
127 128 2.015627 GCGCGCTTGATGCAACAAA 61.016 52.632 26.67 0.00 43.06 2.83
382 383 2.503331 TCCAATGTGAACTCGTGCAAT 58.497 42.857 0.00 0.00 0.00 3.56
405 406 1.099689 CACCCACGTCAACCTTGTTT 58.900 50.000 0.00 0.00 0.00 2.83
423 424 4.503714 AGGAAAGGATTAAATCGAGGCA 57.496 40.909 0.00 0.00 0.00 4.75
430 431 6.097412 GTGAGGCATCAAGGAAAGGATTAAAT 59.903 38.462 0.92 0.00 37.14 1.40
461 462 1.279271 GTCTGGCCCAACATACTCAGT 59.721 52.381 0.00 0.00 0.00 3.41
575 576 4.832266 ACCACTACCAAATTGCTTCATTCA 59.168 37.500 0.00 0.00 0.00 2.57
627 628 1.601903 TGTCGTTGCATTCTCCACAAC 59.398 47.619 0.00 0.00 40.17 3.32
838 859 3.117888 GCCTTCCCCTATCAACTTGATGA 60.118 47.826 13.66 0.78 37.70 2.92
843 864 1.987080 AGGCCTTCCCCTATCAACTT 58.013 50.000 0.00 0.00 32.11 2.66
874 895 3.712016 TTTCAACCATCCGGATTGAGA 57.288 42.857 21.66 13.11 34.04 3.27
1010 1040 2.577059 GCCTCGTCATGGAACCGA 59.423 61.111 0.00 0.00 0.00 4.69
1152 1183 2.416836 CCATGACTTCTTTCGGTCGCTA 60.417 50.000 0.00 0.00 35.45 4.26
1154 1185 0.721718 CCATGACTTCTTTCGGTCGC 59.278 55.000 0.00 0.00 35.45 5.19
1423 1458 5.278512 GCCTCTTTGAAACCTTTCTTCGAAT 60.279 40.000 0.00 0.00 38.02 3.34
1531 1566 0.415429 TTCTTGCCCTCTCCTCCTCT 59.585 55.000 0.00 0.00 0.00 3.69
1574 1609 2.092538 CACATGCCTCATCCTCCTCTTT 60.093 50.000 0.00 0.00 0.00 2.52
1615 1651 3.083122 AGGCTTTACTGAGTCCTACGA 57.917 47.619 0.00 0.00 0.00 3.43
1620 1656 1.360820 GCGAAGGCTTTACTGAGTCC 58.639 55.000 0.00 0.00 35.83 3.85
1759 1821 5.426504 TGCAAACATCTCCACACAAAATTT 58.573 33.333 0.00 0.00 0.00 1.82
1765 1827 1.955778 CCTTGCAAACATCTCCACACA 59.044 47.619 0.00 0.00 0.00 3.72
1865 1984 3.258372 ACAGAGTAATCCTTCGTTCTGCA 59.742 43.478 0.00 0.00 36.42 4.41
1908 2174 3.161450 GCATCCTACCGCCAGGGA 61.161 66.667 1.15 0.00 43.47 4.20
2006 2281 0.600557 CAGAGCTATGGCGTAGGGAG 59.399 60.000 15.25 0.00 44.37 4.30
2007 2282 0.827925 CCAGAGCTATGGCGTAGGGA 60.828 60.000 15.73 0.00 44.37 4.20
2018 2294 1.341285 TGTAACCTACCGCCAGAGCTA 60.341 52.381 0.00 0.00 36.60 3.32
2085 2400 2.749621 GGGTGCTCATTTTTCTCGTCAT 59.250 45.455 0.00 0.00 0.00 3.06
2198 2517 1.421480 AGGGTAAGAATCCTACCGCC 58.579 55.000 2.26 0.00 34.80 6.13
2199 2518 3.657015 GTAGGGTAAGAATCCTACCGC 57.343 52.381 3.83 0.00 45.92 5.68
2203 2522 2.091166 TGGCGGTAGGGTAAGAATCCTA 60.091 50.000 0.00 0.00 34.75 2.94
2204 2523 1.343681 TGGCGGTAGGGTAAGAATCCT 60.344 52.381 0.00 0.00 37.18 3.24
2205 2524 1.070289 CTGGCGGTAGGGTAAGAATCC 59.930 57.143 0.00 0.00 0.00 3.01
2206 2525 1.540580 GCTGGCGGTAGGGTAAGAATC 60.541 57.143 0.00 0.00 0.00 2.52
2207 2526 0.468648 GCTGGCGGTAGGGTAAGAAT 59.531 55.000 0.00 0.00 0.00 2.40
2208 2527 1.902556 GCTGGCGGTAGGGTAAGAA 59.097 57.895 0.00 0.00 0.00 2.52
2209 2528 2.420568 CGCTGGCGGTAGGGTAAGA 61.421 63.158 7.12 0.00 35.56 2.10
2210 2529 2.106332 CGCTGGCGGTAGGGTAAG 59.894 66.667 7.12 0.00 35.56 2.34
2211 2530 2.681064 ACGCTGGCGGTAGGGTAA 60.681 61.111 18.99 0.00 41.39 2.85
2212 2531 3.454573 CACGCTGGCGGTAGGGTA 61.455 66.667 18.99 0.00 41.28 3.69
2225 2544 1.194547 TGATGAGAAAAACGAGCACGC 59.805 47.619 2.62 0.00 43.96 5.34
2226 2545 2.220824 TGTGATGAGAAAAACGAGCACG 59.779 45.455 0.76 0.76 45.75 5.34
2232 2551 7.376072 GGTAAACTTTCTGTGATGAGAAAAACG 59.624 37.037 0.00 0.00 40.59 3.60
2234 2553 7.201875 GGGGTAAACTTTCTGTGATGAGAAAAA 60.202 37.037 0.00 0.00 40.59 1.94
2239 2558 4.010349 GGGGGTAAACTTTCTGTGATGAG 58.990 47.826 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.