Multiple sequence alignment - TraesCS2A01G194700

Loading Multiple Alignment...

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 TraesCS2A01G194700 chr2A 100.000 2813 0 0 1 2813 163856477 163853665 0.000000e+00 5195.0
1 TraesCS2A01G194700 chr2A 84.034 119 16 3 202 317 20898363 20898245 8.240000e-21 111.0
2 TraesCS2A01G194700 chr2A 82.400 125 19 3 202 323 20868207 20868083 3.830000e-19 106.0
3 TraesCS2A01G194700 chr2A 100.000 39 0 0 456 494 163855954 163855916 3.890000e-09 73.1
4 TraesCS2A01G194700 chr2A 100.000 39 0 0 524 562 163856022 163855984 3.890000e-09 73.1
5 TraesCS2A01G194700 chr2B 90.390 2362 93 42 512 2813 196010868 196013155 0.000000e+00 2981.0
6 TraesCS2A01G194700 chr2B 84.835 455 49 13 5 444 196009736 196010185 9.250000e-120 440.0
7 TraesCS2A01G194700 chr2D 92.557 1760 71 22 512 2249 138162346 138164067 0.000000e+00 2470.0
8 TraesCS2A01G194700 chr2D 94.580 572 24 2 2243 2813 138174555 138175120 0.000000e+00 878.0
9 TraesCS2A01G194700 chr2D 90.291 309 23 7 5 310 138159286 138159590 5.650000e-107 398.0
10 TraesCS2A01G194700 chr2D 93.137 102 7 0 342 443 138160511 138160612 1.750000e-32 150.0
11 TraesCS2A01G194700 chr6B 85.684 468 46 10 1118 1576 492822288 492821833 9.120000e-130 473.0
12 TraesCS2A01G194700 chr6B 74.286 210 33 13 110 314 142226503 142226310 5.030000e-08 69.4
13 TraesCS2A01G194700 chr4A 82.870 216 33 4 107 319 338746018 338746232 1.030000e-44 191.0
14 TraesCS2A01G194700 chr3A 82.741 197 23 8 110 302 705225134 705225323 6.230000e-37 165.0
15 TraesCS2A01G194700 chrUn 82.320 181 23 6 125 302 132298461 132298287 6.280000e-32 148.0
16 TraesCS2A01G194700 chr5D 80.628 191 28 7 107 295 377147660 377147843 3.780000e-29 139.0
17 TraesCS2A01G194700 chr5D 83.607 122 16 4 202 319 499237335 499237456 8.240000e-21 111.0
18 TraesCS2A01G194700 chr6A 81.875 160 25 4 110 267 84917903 84917746 6.320000e-27 132.0


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 TraesCS2A01G194700 chr2A 163853665 163856477 2812 True 1780.4 5195 100.0000 1 2813 3 chr2A.!!$R3 2812
1 TraesCS2A01G194700 chr2B 196009736 196013155 3419 False 1710.5 2981 87.6125 5 2813 2 chr2B.!!$F1 2808
2 TraesCS2A01G194700 chr2D 138159286 138164067 4781 False 1006.0 2470 91.9950 5 2249 3 chr2D.!!$F2 2244
3 TraesCS2A01G194700 chr2D 138174555 138175120 565 False 878.0 878 94.5800 2243 2813 1 chr2D.!!$F1 570

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
608 3260 0.110419 GCATGCGCTACGAAACAACA 60.110 50.000 9.73 0.0 34.3 3.33 F
878 3556 1.064611 TCCCGTCCTCTACTCCTCTTG 60.065 57.143 0.00 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 4455 1.063942 TCGAGCCAGTTCAGGATCCTA 60.064 52.381 15.67 0.0 40.96 2.94 R
2314 5023 1.068588 AGTGCAAGAGTTCACGTGCTA 59.931 47.619 11.67 0.0 43.40 3.49 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
53 54 3.242837 CCACTCACATGATTGGCGTTATG 60.243 47.826 0.00 0.00 37.92 1.90
59 60 7.661437 ACTCACATGATTGGCGTTATGTAATAT 59.339 33.333 0.00 0.00 32.86 1.28
90 91 7.037438 TCGTTCCAAAATACTACAGTGGATAC 58.963 38.462 0.00 0.00 38.16 2.24
175 176 4.050553 CCAACATCCACAACACAACATTC 58.949 43.478 0.00 0.00 0.00 2.67
271 272 9.793259 ATTCTAGAAACTTGGTCAAACATAAGA 57.207 29.630 9.71 0.00 0.00 2.10
272 273 9.793259 TTCTAGAAACTTGGTCAAACATAAGAT 57.207 29.630 1.68 0.00 0.00 2.40
273 274 9.219603 TCTAGAAACTTGGTCAAACATAAGATG 57.780 33.333 0.00 0.00 0.00 2.90
343 358 4.083431 AGCGGCGATATGTAACACTACTAG 60.083 45.833 12.98 0.00 0.00 2.57
361 1254 7.548075 CACTACTAGTCCGGTAAATCACAAATT 59.452 37.037 0.00 0.00 0.00 1.82
444 1337 2.177394 TGATAAGCTTTGCACACGGA 57.823 45.000 3.20 0.00 0.00 4.69
445 1338 1.804151 TGATAAGCTTTGCACACGGAC 59.196 47.619 3.20 0.00 0.00 4.79
448 1341 1.890876 AAGCTTTGCACACGGACATA 58.109 45.000 0.00 0.00 0.00 2.29
449 1342 1.442769 AGCTTTGCACACGGACATAG 58.557 50.000 0.00 0.00 0.00 2.23
453 1346 3.331150 CTTTGCACACGGACATAGGTTA 58.669 45.455 0.00 0.00 0.00 2.85
454 1347 3.404224 TTGCACACGGACATAGGTTAA 57.596 42.857 0.00 0.00 0.00 2.01
455 1348 3.404224 TGCACACGGACATAGGTTAAA 57.596 42.857 0.00 0.00 0.00 1.52
456 1349 3.741249 TGCACACGGACATAGGTTAAAA 58.259 40.909 0.00 0.00 0.00 1.52
460 1353 5.627172 CACACGGACATAGGTTAAAATGTG 58.373 41.667 4.56 0.00 36.48 3.21
467 1360 7.522399 CGGACATAGGTTAAAATGTGTTTTCCA 60.522 37.037 4.56 0.00 38.44 3.53
469 1362 9.535878 GACATAGGTTAAAATGTGTTTTCCAAA 57.464 29.630 4.56 0.00 38.44 3.28
507 1400 7.477144 TTCTCATAGTATGGTAAAATGTGCG 57.523 36.000 10.26 0.00 0.00 5.34
508 1401 5.465390 TCTCATAGTATGGTAAAATGTGCGC 59.535 40.000 10.26 0.00 0.00 6.09
522 3173 4.864916 ATGTGCGCAAAGTAATGAGTAG 57.135 40.909 14.00 0.00 0.00 2.57
575 3227 5.950883 TCTCATAGTAGTTTGACTCGGTTG 58.049 41.667 0.00 0.00 0.00 3.77
608 3260 0.110419 GCATGCGCTACGAAACAACA 60.110 50.000 9.73 0.00 34.30 3.33
612 3264 1.495951 CGCTACGAAACAACAGGGC 59.504 57.895 0.00 0.00 0.00 5.19
620 3272 1.734388 AAACAACAGGGCGGTCAAGC 61.734 55.000 0.00 0.00 0.00 4.01
663 3315 3.480470 CAACATCGGGATAATTGCTCCT 58.520 45.455 8.34 0.00 33.05 3.69
714 3379 4.196965 GGTAACCGAAGCCTTCCG 57.803 61.111 0.00 0.00 0.00 4.30
715 3380 2.104859 GGTAACCGAAGCCTTCCGC 61.105 63.158 0.00 0.00 37.98 5.54
716 3381 2.104859 GTAACCGAAGCCTTCCGCC 61.105 63.158 0.00 0.00 38.78 6.13
717 3382 3.652539 TAACCGAAGCCTTCCGCCG 62.653 63.158 0.00 0.00 38.78 6.46
780 3449 2.229039 CGCTAAGCACTGCGCATAT 58.771 52.632 12.24 0.00 45.50 1.78
781 3450 1.418373 CGCTAAGCACTGCGCATATA 58.582 50.000 12.24 0.00 45.50 0.86
782 3451 1.388093 CGCTAAGCACTGCGCATATAG 59.612 52.381 12.24 10.31 45.50 1.31
869 3547 4.863548 TCTGTTTCTATTCCCGTCCTCTA 58.136 43.478 0.00 0.00 0.00 2.43
871 3549 4.607239 TGTTTCTATTCCCGTCCTCTACT 58.393 43.478 0.00 0.00 0.00 2.57
872 3550 4.643784 TGTTTCTATTCCCGTCCTCTACTC 59.356 45.833 0.00 0.00 0.00 2.59
873 3551 3.505480 TCTATTCCCGTCCTCTACTCC 57.495 52.381 0.00 0.00 0.00 3.85
874 3552 3.054576 TCTATTCCCGTCCTCTACTCCT 58.945 50.000 0.00 0.00 0.00 3.69
875 3553 2.368311 ATTCCCGTCCTCTACTCCTC 57.632 55.000 0.00 0.00 0.00 3.71
876 3554 1.296984 TTCCCGTCCTCTACTCCTCT 58.703 55.000 0.00 0.00 0.00 3.69
877 3555 1.296984 TCCCGTCCTCTACTCCTCTT 58.703 55.000 0.00 0.00 0.00 2.85
878 3556 1.064611 TCCCGTCCTCTACTCCTCTTG 60.065 57.143 0.00 0.00 0.00 3.02
966 3648 2.092699 CCATCTCTTCTTCTTCCCCACC 60.093 54.545 0.00 0.00 0.00 4.61
1545 4236 2.511600 GACGGGGCCAAGATCACG 60.512 66.667 4.39 0.00 0.00 4.35
1771 4465 0.032130 GCGTCGCATTAGGATCCTGA 59.968 55.000 25.28 17.43 0.00 3.86
1797 4491 1.256812 TCGAAGAGCTGTCCATCACA 58.743 50.000 0.00 0.00 0.00 3.58
1836 4530 7.609760 ATCTTGTGTAAAGATCGTGCATTTA 57.390 32.000 0.00 0.00 31.78 1.40
1973 4669 3.785887 TGGAGCCCACCATAACTTTCTAT 59.214 43.478 0.00 0.00 34.77 1.98
1974 4670 4.141482 TGGAGCCCACCATAACTTTCTATC 60.141 45.833 0.00 0.00 34.77 2.08
1975 4671 4.103311 GGAGCCCACCATAACTTTCTATCT 59.897 45.833 0.00 0.00 0.00 1.98
1976 4672 5.297569 AGCCCACCATAACTTTCTATCTC 57.702 43.478 0.00 0.00 0.00 2.75
1977 4673 4.058817 GCCCACCATAACTTTCTATCTCG 58.941 47.826 0.00 0.00 0.00 4.04
1978 4674 4.202223 GCCCACCATAACTTTCTATCTCGA 60.202 45.833 0.00 0.00 0.00 4.04
1979 4675 5.684030 GCCCACCATAACTTTCTATCTCGAA 60.684 44.000 0.00 0.00 0.00 3.71
1980 4676 5.986135 CCCACCATAACTTTCTATCTCGAAG 59.014 44.000 0.00 0.00 0.00 3.79
1981 4677 6.183360 CCCACCATAACTTTCTATCTCGAAGA 60.183 42.308 0.00 0.00 0.00 2.87
1982 4678 7.437748 CCACCATAACTTTCTATCTCGAAGAT 58.562 38.462 0.00 0.00 38.70 2.40
1983 4679 7.928706 CCACCATAACTTTCTATCTCGAAGATT 59.071 37.037 3.27 0.00 36.20 2.40
1984 4680 9.319143 CACCATAACTTTCTATCTCGAAGATTT 57.681 33.333 3.27 0.00 36.20 2.17
1985 4681 9.892130 ACCATAACTTTCTATCTCGAAGATTTT 57.108 29.630 3.27 0.00 36.20 1.82
2033 4729 6.500684 AGAGTATTTGATCGTGCATTTGTT 57.499 33.333 0.00 0.00 0.00 2.83
2108 4811 9.850628 TTATATTATATCGTTACGCAGCTTCTT 57.149 29.630 0.00 0.00 0.00 2.52
2146 4849 1.630369 TGTTGCTAGAATCCTGCCACT 59.370 47.619 0.00 0.00 0.00 4.00
2156 4862 2.205022 TCCTGCCACTGGAAGAAATG 57.795 50.000 4.33 0.00 37.43 2.32
2161 4867 1.738030 GCCACTGGAAGAAATGCATGC 60.738 52.381 11.82 11.82 37.43 4.06
2314 5023 5.205821 TCCATCCATGCTGAATTCATTTCT 58.794 37.500 8.96 0.00 35.23 2.52
2332 5041 1.339929 TCTAGCACGTGAACTCTTGCA 59.660 47.619 22.23 0.00 37.44 4.08
2368 5077 3.324099 GACAACGAGCTCGGCGAGA 62.324 63.158 38.56 4.26 44.95 4.04
2416 5125 4.150454 AGGCCCCTCTCCCTCTCG 62.150 72.222 0.00 0.00 0.00 4.04
2422 5131 3.591835 CTCTCCCTCTCGCGCTCC 61.592 72.222 5.56 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.815641 TGGAATATTACATAACGCCAATCATG 58.184 34.615 0.00 0.00 0.00 3.07
59 60 6.938030 ACTGTAGTATTTTGGAACGAATGGAA 59.062 34.615 0.00 0.00 0.00 3.53
149 150 2.728007 TGTGTTGTGGATGTTGGTCAA 58.272 42.857 0.00 0.00 0.00 3.18
151 152 2.425312 TGTTGTGTTGTGGATGTTGGTC 59.575 45.455 0.00 0.00 0.00 4.02
303 306 4.628074 GCCGCTACCTCTATTTCACAATA 58.372 43.478 0.00 0.00 0.00 1.90
310 313 3.510360 ACATATCGCCGCTACCTCTATTT 59.490 43.478 0.00 0.00 0.00 1.40
313 316 2.195741 ACATATCGCCGCTACCTCTA 57.804 50.000 0.00 0.00 0.00 2.43
314 317 2.195741 TACATATCGCCGCTACCTCT 57.804 50.000 0.00 0.00 0.00 3.69
322 325 5.354054 ACTAGTAGTGTTACATATCGCCG 57.646 43.478 0.85 0.00 31.96 6.46
343 358 4.201980 GGCCTAATTTGTGATTTACCGGAC 60.202 45.833 9.46 0.00 0.00 4.79
361 1254 1.476085 CCATTTGATTTGTGCGGCCTA 59.524 47.619 0.00 0.00 0.00 3.93
437 1330 5.180492 ACACATTTTAACCTATGTCCGTGTG 59.820 40.000 0.00 0.00 39.15 3.82
444 1337 9.541143 CTTTGGAAAACACATTTTAACCTATGT 57.459 29.630 0.00 0.00 38.17 2.29
445 1338 9.757227 TCTTTGGAAAACACATTTTAACCTATG 57.243 29.630 0.00 0.00 38.17 2.23
482 1375 7.466725 GCGCACATTTTACCATACTATGAGAAA 60.467 37.037 0.30 0.00 0.00 2.52
483 1376 6.018262 GCGCACATTTTACCATACTATGAGAA 60.018 38.462 0.30 0.00 0.00 2.87
484 1377 5.465390 GCGCACATTTTACCATACTATGAGA 59.535 40.000 0.30 0.00 0.00 3.27
485 1378 5.236263 TGCGCACATTTTACCATACTATGAG 59.764 40.000 5.66 0.00 0.00 2.90
486 1379 5.119694 TGCGCACATTTTACCATACTATGA 58.880 37.500 5.66 0.00 0.00 2.15
488 1381 6.094881 ACTTTGCGCACATTTTACCATACTAT 59.905 34.615 11.12 0.00 0.00 2.12
490 1383 4.217550 ACTTTGCGCACATTTTACCATACT 59.782 37.500 11.12 0.00 0.00 2.12
492 1385 4.775058 ACTTTGCGCACATTTTACCATA 57.225 36.364 11.12 0.00 0.00 2.74
493 1386 3.658757 ACTTTGCGCACATTTTACCAT 57.341 38.095 11.12 0.00 0.00 3.55
495 1388 5.157781 TCATTACTTTGCGCACATTTTACC 58.842 37.500 11.12 0.00 0.00 2.85
496 1389 5.856455 ACTCATTACTTTGCGCACATTTTAC 59.144 36.000 11.12 0.00 0.00 2.01
498 1391 4.870363 ACTCATTACTTTGCGCACATTTT 58.130 34.783 11.12 0.00 0.00 1.82
499 1392 4.503741 ACTCATTACTTTGCGCACATTT 57.496 36.364 11.12 0.00 0.00 2.32
501 1394 4.503910 TCTACTCATTACTTTGCGCACAT 58.496 39.130 11.12 0.00 0.00 3.21
502 1395 3.920446 TCTACTCATTACTTTGCGCACA 58.080 40.909 11.12 1.28 0.00 4.57
503 1396 4.921470 TTCTACTCATTACTTTGCGCAC 57.079 40.909 11.12 0.00 0.00 5.34
504 1397 4.935205 ACATTCTACTCATTACTTTGCGCA 59.065 37.500 5.66 5.66 0.00 6.09
506 1399 6.408858 ACACATTCTACTCATTACTTTGCG 57.591 37.500 0.00 0.00 0.00 4.85
507 1400 9.118236 GAAAACACATTCTACTCATTACTTTGC 57.882 33.333 0.00 0.00 0.00 3.68
508 1401 9.612620 GGAAAACACATTCTACTCATTACTTTG 57.387 33.333 0.00 0.00 0.00 2.77
575 3227 1.419922 CATGCCTCGCGTACACAAC 59.580 57.895 5.77 0.00 0.00 3.32
612 3264 0.109132 GCTCAAATTGGGCTTGACCG 60.109 55.000 11.12 0.00 41.63 4.79
620 3272 3.499537 GCCAAAAGAAAGCTCAAATTGGG 59.500 43.478 15.67 0.00 37.04 4.12
646 3298 2.191128 GCAGGAGCAATTATCCCGAT 57.809 50.000 5.46 0.00 41.58 4.18
663 3315 5.064707 GGAGAAAATTTATGACGCTAGTGCA 59.935 40.000 2.40 3.03 39.64 4.57
667 3319 9.573133 AATTTTGGAGAAAATTTATGACGCTAG 57.427 29.630 0.00 0.00 45.51 3.42
717 3382 4.947147 TGGTCAACGGTGCCAGCC 62.947 66.667 11.85 4.67 0.00 4.85
718 3383 3.357079 CTGGTCAACGGTGCCAGC 61.357 66.667 24.41 7.59 40.10 4.85
719 3384 3.357079 GCTGGTCAACGGTGCCAG 61.357 66.667 28.76 28.76 44.94 4.85
720 3385 3.705934 TTGCTGGTCAACGGTGCCA 62.706 57.895 14.56 14.56 32.31 4.92
721 3386 2.904866 TTGCTGGTCAACGGTGCC 60.905 61.111 0.00 0.37 0.00 5.01
722 3387 1.724582 AACTTGCTGGTCAACGGTGC 61.725 55.000 0.00 0.00 0.00 5.01
723 3388 0.738389 AAACTTGCTGGTCAACGGTG 59.262 50.000 0.00 0.00 0.00 4.94
780 3449 0.691078 GGCCCTGGGATGTCAGTCTA 60.691 60.000 19.27 0.00 33.14 2.59
781 3450 1.997874 GGCCCTGGGATGTCAGTCT 60.998 63.158 19.27 0.00 33.14 3.24
782 3451 2.592308 GGCCCTGGGATGTCAGTC 59.408 66.667 19.27 0.00 33.14 3.51
869 3547 0.038159 CGAAGAACGGCAAGAGGAGT 60.038 55.000 0.00 0.00 38.46 3.85
871 3549 4.988065 CGAAGAACGGCAAGAGGA 57.012 55.556 0.00 0.00 38.46 3.71
1465 4156 2.666098 GGCGTATGACACCCCACCT 61.666 63.158 0.00 0.00 0.00 4.00
1705 4396 3.854459 CGCTCCGCTTTTCCTCGC 61.854 66.667 0.00 0.00 0.00 5.03
1761 4455 1.063942 TCGAGCCAGTTCAGGATCCTA 60.064 52.381 15.67 0.00 40.96 2.94
1797 4491 5.063880 ACACAAGATTACTTCTTCGCCTTT 58.936 37.500 0.00 0.00 42.98 3.11
1988 4684 9.218525 ACTCTATCTTCAAGATATTTCCCTCAA 57.781 33.333 7.60 0.00 36.67 3.02
1989 4685 8.789767 ACTCTATCTTCAAGATATTTCCCTCA 57.210 34.615 7.60 0.00 36.67 3.86
1999 4695 9.689976 CACGATCAAATACTCTATCTTCAAGAT 57.310 33.333 4.98 4.98 38.70 2.40
2033 4729 4.885413 GCATATCCTGGCATTAAATTGCA 58.115 39.130 3.61 0.00 44.59 4.08
2108 4811 3.728076 ACAAGTGCTAACGACAGAAGA 57.272 42.857 0.00 0.00 0.00 2.87
2314 5023 1.068588 AGTGCAAGAGTTCACGTGCTA 59.931 47.619 11.67 0.00 43.40 3.49
2332 5041 4.266070 AGTGCACGTCGTCGCAGT 62.266 61.111 18.47 18.40 39.20 4.40
2679 5402 2.579787 CGACCGCTCGACCATGTC 60.580 66.667 0.00 0.00 43.06 3.06


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

AutoCloner maintained by Alex Coulton.