Multiple sequence alignment - TraesCS2A01G305800

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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 TraesCS2A01G305800 chr2A 100.000 3170 0 0 1 3170 526062856 526066025 0.000000e+00 5854.0
1 TraesCS2A01G305800 chr2D 97.005 1202 32 4 1800 2998 389277957 389279157 0.000000e+00 2017.0
2 TraesCS2A01G305800 chr2D 93.406 1016 44 8 346 1343 389276598 389277608 0.000000e+00 1483.0
3 TraesCS2A01G305800 chr2D 93.377 302 20 0 28 329 389276309 389276610 6.240000e-122 448.0
4 TraesCS2A01G305800 chr2D 93.004 243 15 2 1341 1582 389277657 389277898 1.400000e-93 353.0
5 TraesCS2A01G305800 chr2D 95.111 225 10 1 2946 3170 389279156 389279379 1.400000e-93 353.0
6 TraesCS2A01G305800 chr2B 93.393 1014 61 6 1341 2350 461092053 461093064 0.000000e+00 1496.0
7 TraesCS2A01G305800 chr2B 92.354 1007 57 8 346 1341 461091009 461092006 0.000000e+00 1415.0
8 TraesCS2A01G305800 chr2B 91.340 843 52 5 2349 3170 461093146 461093988 0.000000e+00 1133.0
9 TraesCS2A01G305800 chr2B 91.793 329 27 0 1 329 461090693 461091021 2.880000e-125 459.0
10 TraesCS2A01G305800 chr3A 90.476 42 4 0 283 324 549626768 549626809 4.420000e-04 56.5
11 TraesCS2A01G305800 chr4D 100.000 28 0 0 289 316 482372912 482372939 6.000000e-03 52.8
12 TraesCS2A01G305800 chr4B 96.875 32 0 1 286 316 185447693 185447662 6.000000e-03 52.8


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 TraesCS2A01G305800 chr2A 526062856 526066025 3169 False 5854.00 5854 100.0000 1 3170 1 chr2A.!!$F1 3169
1 TraesCS2A01G305800 chr2D 389276309 389279379 3070 False 930.80 2017 94.3806 28 3170 5 chr2D.!!$F1 3142
2 TraesCS2A01G305800 chr2B 461090693 461093988 3295 False 1125.75 1496 92.2200 1 3170 4 chr2B.!!$F1 3169

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
734 743 0.463833 GCCCGATCAGGTTTAGGTGG 60.464 60.0 0.00 0.0 38.74 4.61 F
1627 1703 0.320946 GCAATTTGCCAGCACCATGT 60.321 50.0 10.34 0.0 37.42 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1752 0.036765 TTCATCTAAGTTGCCCGCGT 60.037 50.0 4.92 0.0 0.0 6.01 R
2814 2996 0.249398 TGAAGGCCGAGGTTAGCTTC 59.751 55.0 0.00 0.0 0.0 3.86 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
77 78 1.612463 GTCCTACGAGCGAATGGGTAT 59.388 52.381 0.00 0.00 0.00 2.73
78 79 2.035576 GTCCTACGAGCGAATGGGTATT 59.964 50.000 0.00 0.00 0.00 1.89
90 91 4.407365 GAATGGGTATTGGGTTGGATAGG 58.593 47.826 0.00 0.00 0.00 2.57
116 117 4.100808 GTGAGTCTCTGATAGCTGGGAAAT 59.899 45.833 0.00 0.00 0.00 2.17
176 177 1.688735 TGGATCTGACTAATGCCCTCG 59.311 52.381 0.00 0.00 0.00 4.63
195 196 2.894765 TCGTGTGTTGGATAGTGGAGAA 59.105 45.455 0.00 0.00 0.00 2.87
240 241 7.449704 AGAATGTTAAGATTTGAGAAAGCTGGT 59.550 33.333 0.00 0.00 37.18 4.00
241 242 6.959639 TGTTAAGATTTGAGAAAGCTGGTT 57.040 33.333 0.00 0.00 37.18 3.67
253 254 6.089249 AGAAAGCTGGTTTGAAGGTTATTG 57.911 37.500 9.87 0.00 34.40 1.90
305 306 2.677542 ACACTACTCACTCTGTCCCA 57.322 50.000 0.00 0.00 0.00 4.37
318 319 7.615403 TCACTCTGTCCCATAATATAAGATGC 58.385 38.462 0.00 0.00 0.00 3.91
319 320 7.455953 TCACTCTGTCCCATAATATAAGATGCT 59.544 37.037 0.00 0.00 0.00 3.79
320 321 8.753133 CACTCTGTCCCATAATATAAGATGCTA 58.247 37.037 0.00 0.00 0.00 3.49
321 322 9.499369 ACTCTGTCCCATAATATAAGATGCTAT 57.501 33.333 0.00 0.00 0.00 2.97
384 385 2.079925 GAGCAAGCTAGAGTTGGGTTG 58.920 52.381 0.00 0.00 43.57 3.77
385 386 1.168714 GCAAGCTAGAGTTGGGTTGG 58.831 55.000 0.00 0.00 41.76 3.77
408 409 5.003804 GTGAGGCAATTTCTAAGAGGTTGA 58.996 41.667 0.00 0.00 0.00 3.18
433 434 4.842574 TGCAAATAGACCAGTGCATAGAA 58.157 39.130 0.00 0.00 41.85 2.10
434 435 4.877823 TGCAAATAGACCAGTGCATAGAAG 59.122 41.667 0.00 0.00 41.85 2.85
435 436 4.274459 GCAAATAGACCAGTGCATAGAAGG 59.726 45.833 0.00 0.00 36.97 3.46
440 441 1.524621 CAGTGCATAGAAGGCCCGG 60.525 63.158 0.00 0.00 0.00 5.73
637 638 5.749596 TTTAGACAACACTGTTCATGTGG 57.250 39.130 0.00 0.00 39.52 4.17
640 641 4.016444 AGACAACACTGTTCATGTGGTTT 58.984 39.130 0.00 0.00 34.23 3.27
714 715 3.993584 CGACCCGAACCCGTCCAA 61.994 66.667 0.00 0.00 0.00 3.53
720 721 4.011517 GAACCCGTCCAAGCCCGA 62.012 66.667 0.00 0.00 0.00 5.14
721 722 3.325201 GAACCCGTCCAAGCCCGAT 62.325 63.158 0.00 0.00 0.00 4.18
722 723 3.325201 AACCCGTCCAAGCCCGATC 62.325 63.158 0.00 0.00 0.00 3.69
723 724 3.781307 CCCGTCCAAGCCCGATCA 61.781 66.667 0.00 0.00 0.00 2.92
724 725 2.202932 CCGTCCAAGCCCGATCAG 60.203 66.667 0.00 0.00 0.00 2.90
725 726 2.202932 CGTCCAAGCCCGATCAGG 60.203 66.667 0.00 0.00 40.63 3.86
734 743 0.463833 GCCCGATCAGGTTTAGGTGG 60.464 60.000 0.00 0.00 38.74 4.61
1134 1154 2.726351 GCGCCTAACCAGGAGAGCT 61.726 63.158 0.00 0.00 45.91 4.09
1384 1455 2.554893 GCGTTTAGGTTTGTGGATTGGA 59.445 45.455 0.00 0.00 0.00 3.53
1393 1464 2.479566 TGTGGATTGGAGCTCTGAAC 57.520 50.000 14.64 4.82 0.00 3.18
1395 1466 2.027745 TGTGGATTGGAGCTCTGAACTC 60.028 50.000 14.64 0.00 0.00 3.01
1404 1475 0.952984 GCTCTGAACTCTGTGGTGCC 60.953 60.000 0.00 0.00 0.00 5.01
1479 1550 1.281287 GAGGGGAAGGGGAGTAACAAC 59.719 57.143 0.00 0.00 0.00 3.32
1588 1664 5.278957 GCAGAGAAGAAAAAGGTAAATGCCA 60.279 40.000 0.00 0.00 0.00 4.92
1589 1665 6.152379 CAGAGAAGAAAAAGGTAAATGCCAC 58.848 40.000 0.00 0.00 0.00 5.01
1595 1671 5.128663 AGAAAAAGGTAAATGCCACAACACT 59.871 36.000 0.00 0.00 0.00 3.55
1627 1703 0.320946 GCAATTTGCCAGCACCATGT 60.321 50.000 10.34 0.00 37.42 3.21
1638 1714 4.278170 GCCAGCACCATGTTATATTTGCTA 59.722 41.667 0.00 0.00 38.24 3.49
1675 1751 7.490657 TTACCATGTGTAGACATCCTACTTT 57.509 36.000 1.81 0.00 46.19 2.66
1676 1752 8.598202 TTACCATGTGTAGACATCCTACTTTA 57.402 34.615 1.81 0.00 46.19 1.85
1732 1809 5.512942 TCCTGGTTCATAACATTTCTCCA 57.487 39.130 0.00 0.00 0.00 3.86
1739 1816 7.556275 TGGTTCATAACATTTCTCCACCTTATC 59.444 37.037 0.00 0.00 0.00 1.75
1764 1841 6.506147 TCTATGTGTTTATGGCAATTGCATC 58.494 36.000 30.32 15.47 44.36 3.91
1771 1848 6.757478 TGTTTATGGCAATTGCATCTAATGTG 59.243 34.615 30.32 0.00 44.36 3.21
1774 1851 3.762823 TGGCAATTGCATCTAATGTGTCA 59.237 39.130 30.32 12.43 44.36 3.58
1812 1889 9.959721 TTATATTAAAGGTGAAAACTGAGCTCT 57.040 29.630 16.19 0.00 0.00 4.09
1886 1964 6.757897 TGGAAAAGTTCAGTGCTATATTGG 57.242 37.500 0.00 0.00 0.00 3.16
1932 2010 6.834168 TTGATTCAGGAAAGTACCAAATCC 57.166 37.500 0.00 0.00 35.46 3.01
1983 2061 2.049767 TCGCGATGGCCTGACAGTA 61.050 57.895 3.71 0.00 35.02 2.74
2001 2079 6.536224 TGACAGTATACGAAATCGAGTACTCA 59.464 38.462 22.37 10.16 43.02 3.41
2114 2192 1.204113 ACTGAGGAGAAGCCCTTGGG 61.204 60.000 0.32 0.32 36.49 4.12
2302 2380 6.635030 AGGTTACAAATGTTCTTCTCCAAC 57.365 37.500 0.00 0.00 0.00 3.77
2309 2387 6.980397 ACAAATGTTCTTCTCCAACACAATTC 59.020 34.615 0.00 0.00 36.59 2.17
2335 2413 9.559958 CGAAATGTTATTAGTTTCTTTCAGCAT 57.440 29.630 0.00 0.00 31.42 3.79
2342 2420 4.756084 AGTTTCTTTCAGCATGCTGTAC 57.244 40.909 39.08 27.12 43.96 2.90
2656 2819 3.077359 GGTTAGCTCTTCACAACATGCT 58.923 45.455 0.00 0.00 34.92 3.79
2744 2924 1.611673 CCAAGACAAGCCATCCGAAGT 60.612 52.381 0.00 0.00 0.00 3.01
2752 2932 0.394352 GCCATCCGAAGTGACCCAAT 60.394 55.000 0.00 0.00 0.00 3.16
2814 2996 1.267806 CCACAGCAACAGCTAAACCAG 59.732 52.381 0.00 0.00 36.70 4.00
3071 3304 7.647715 AGGAACATTTTAGTGTTTGAATCAACG 59.352 33.333 0.00 0.00 42.08 4.10
3116 3349 2.496070 TGAACTACCGACCTGAATCCAG 59.504 50.000 0.00 0.00 40.09 3.86
3131 3364 5.554070 TGAATCCAGTATCACATGCCTATG 58.446 41.667 0.00 0.00 40.24 2.23
3133 3366 4.607293 TCCAGTATCACATGCCTATGAC 57.393 45.455 0.00 0.00 37.73 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.715523 TTTCCCCGCCTCTTGCCG 62.716 66.667 0.00 0.00 36.24 5.69
43 44 2.748388 GTAGGACTCAAGGCCCTTAGA 58.252 52.381 0.00 0.00 0.00 2.10
77 78 1.633432 CTCACACCCTATCCAACCCAA 59.367 52.381 0.00 0.00 0.00 4.12
78 79 1.285280 CTCACACCCTATCCAACCCA 58.715 55.000 0.00 0.00 0.00 4.51
90 91 2.100584 CCAGCTATCAGAGACTCACACC 59.899 54.545 5.02 0.00 0.00 4.16
116 117 8.313944 TGTAAGTGTAGCCATAGGAAATCTAA 57.686 34.615 0.00 0.00 0.00 2.10
136 137 8.962679 AGATCCAACTCTAGTAAGAACTGTAAG 58.037 37.037 0.00 0.00 36.36 2.34
176 177 3.600388 CCTTCTCCACTATCCAACACAC 58.400 50.000 0.00 0.00 0.00 3.82
195 196 7.300658 ACATTCTAGATTTATTTGGCATCCCT 58.699 34.615 0.00 0.00 0.00 4.20
240 241 5.076873 AGCCACTTAGCAATAACCTTCAAA 58.923 37.500 0.00 0.00 34.23 2.69
241 242 4.662278 AGCCACTTAGCAATAACCTTCAA 58.338 39.130 0.00 0.00 34.23 2.69
277 278 6.207213 ACAGAGTGAGTAGTGTTTTACGAAG 58.793 40.000 0.00 0.00 0.00 3.79
333 334 4.390129 TGTAATAGCACCCCCTCAAAAA 57.610 40.909 0.00 0.00 0.00 1.94
334 335 4.390129 TTGTAATAGCACCCCCTCAAAA 57.610 40.909 0.00 0.00 0.00 2.44
335 336 4.601406 ATTGTAATAGCACCCCCTCAAA 57.399 40.909 0.00 0.00 0.00 2.69
336 337 4.972568 TCTATTGTAATAGCACCCCCTCAA 59.027 41.667 6.74 0.00 38.57 3.02
337 338 4.562767 TCTATTGTAATAGCACCCCCTCA 58.437 43.478 6.74 0.00 38.57 3.86
338 339 5.248477 TCATCTATTGTAATAGCACCCCCTC 59.752 44.000 6.74 0.00 38.57 4.30
339 340 5.162637 TCATCTATTGTAATAGCACCCCCT 58.837 41.667 6.74 0.00 38.57 4.79
340 341 5.499004 TCATCTATTGTAATAGCACCCCC 57.501 43.478 6.74 0.00 38.57 5.40
341 342 6.711277 TCATCATCTATTGTAATAGCACCCC 58.289 40.000 6.74 0.00 38.57 4.95
342 343 6.314896 GCTCATCATCTATTGTAATAGCACCC 59.685 42.308 6.74 0.00 38.57 4.61
343 344 6.875726 TGCTCATCATCTATTGTAATAGCACC 59.124 38.462 6.74 0.00 38.57 5.01
344 345 7.895975 TGCTCATCATCTATTGTAATAGCAC 57.104 36.000 6.74 0.00 38.57 4.40
345 346 7.118825 GCTTGCTCATCATCTATTGTAATAGCA 59.881 37.037 6.74 0.00 38.57 3.49
346 347 7.333921 AGCTTGCTCATCATCTATTGTAATAGC 59.666 37.037 6.74 0.00 38.57 2.97
384 385 3.956744 ACCTCTTAGAAATTGCCTCACC 58.043 45.455 0.00 0.00 0.00 4.02
385 386 5.003804 TCAACCTCTTAGAAATTGCCTCAC 58.996 41.667 1.51 0.00 0.00 3.51
408 409 1.073763 TGCACTGGTCTATTTGCACCT 59.926 47.619 0.00 0.00 40.01 4.00
511 512 0.938008 CTTATTTCGGGCCTTCGAGC 59.062 55.000 0.84 0.00 40.42 5.03
520 521 4.814234 TGATCATTTCGGACTTATTTCGGG 59.186 41.667 0.00 0.00 0.00 5.14
613 614 6.321181 ACCACATGAACAGTGTTGTCTAAAAT 59.679 34.615 14.57 0.00 36.23 1.82
619 620 4.104776 CAAACCACATGAACAGTGTTGTC 58.895 43.478 14.57 0.00 36.23 3.18
623 624 2.031120 CCCAAACCACATGAACAGTGT 58.969 47.619 0.00 0.00 35.24 3.55
628 629 1.288752 CGGCCCAAACCACATGAAC 59.711 57.895 0.00 0.00 0.00 3.18
669 670 2.296190 ACAAAGCCCGAAGTCAAAATCC 59.704 45.455 0.00 0.00 0.00 3.01
710 711 1.209504 CTAAACCTGATCGGGCTTGGA 59.790 52.381 21.17 0.00 36.97 3.53
713 714 1.065418 CACCTAAACCTGATCGGGCTT 60.065 52.381 21.17 17.14 36.97 4.35
714 715 0.541863 CACCTAAACCTGATCGGGCT 59.458 55.000 21.17 5.39 36.97 5.19
720 721 5.789574 TGGTATTTCCACCTAAACCTGAT 57.210 39.130 0.00 0.00 41.93 2.90
769 778 6.590292 CAGTACCAGTCTTGATTTCACGTTAT 59.410 38.462 0.00 0.00 0.00 1.89
776 785 3.326747 ACGCAGTACCAGTCTTGATTTC 58.673 45.455 0.00 0.00 41.94 2.17
823 840 3.538392 GCGTGCGATTTACATCTTTTGTC 59.462 43.478 0.00 0.00 39.87 3.18
859 879 6.352526 CGTGTGTACAATTACAACTTCTGTC 58.647 40.000 0.00 0.00 40.00 3.51
860 880 5.277154 GCGTGTGTACAATTACAACTTCTGT 60.277 40.000 0.00 0.00 40.00 3.41
863 883 5.085636 TGCGTGTGTACAATTACAACTTC 57.914 39.130 0.00 0.00 40.00 3.01
1078 1098 3.197092 GCATTTGGGCGCAATGGC 61.197 61.111 17.68 18.57 43.88 4.40
1384 1455 0.034616 GCACCACAGAGTTCAGAGCT 59.965 55.000 0.00 0.00 0.00 4.09
1393 1464 0.249699 TACACAACGGCACCACAGAG 60.250 55.000 0.00 0.00 0.00 3.35
1395 1466 1.234821 ATTACACAACGGCACCACAG 58.765 50.000 0.00 0.00 0.00 3.66
1404 1475 2.227865 CACCTTCCCCAATTACACAACG 59.772 50.000 0.00 0.00 0.00 4.10
1479 1550 1.296056 GGTTGACGACGACCCCAATG 61.296 60.000 12.73 0.00 43.02 2.82
1542 1613 3.047718 TAGAAGCCTGTCCGCGACG 62.048 63.158 8.23 0.00 34.95 5.12
1548 1619 0.107945 CTGCCTGTAGAAGCCTGTCC 60.108 60.000 0.00 0.00 0.00 4.02
1595 1671 1.190833 AAATTGCAATGCCCACGGGA 61.191 50.000 13.82 0.00 37.50 5.14
1675 1751 0.818938 TCATCTAAGTTGCCCGCGTA 59.181 50.000 4.92 0.00 0.00 4.42
1676 1752 0.036765 TTCATCTAAGTTGCCCGCGT 60.037 50.000 4.92 0.00 0.00 6.01
1732 1809 7.136822 TGCCATAAACACATAGAGATAAGGT 57.863 36.000 0.00 0.00 0.00 3.50
1739 1816 5.893687 TGCAATTGCCATAAACACATAGAG 58.106 37.500 26.94 0.00 41.18 2.43
1792 1869 6.260936 CAGAAAGAGCTCAGTTTTCACCTTTA 59.739 38.462 22.02 0.00 34.18 1.85
1795 1872 4.133078 CAGAAAGAGCTCAGTTTTCACCT 58.867 43.478 22.02 5.89 34.18 4.00
1812 1889 8.584157 ACCATTCATTATAAGCAACAACAGAAA 58.416 29.630 0.00 0.00 0.00 2.52
1908 1986 6.095440 CGGATTTGGTACTTTCCTGAATCAAT 59.905 38.462 0.00 0.00 35.05 2.57
1932 2010 1.560923 CGGTAGAAATCACCTCTGCG 58.439 55.000 0.00 0.00 33.62 5.18
1983 2061 6.387041 TCCAATGAGTACTCGATTTCGTAT 57.613 37.500 17.85 0.52 40.80 3.06
2001 2079 1.143813 CTCCCCTGGTGCTATCCAAT 58.856 55.000 0.00 0.00 37.01 3.16
2043 2121 3.304057 GCTTTCTAGAAGCAACAAACGCT 60.304 43.478 16.99 0.00 42.56 5.07
2114 2192 4.531332 CAAAACAAGTCTAGTCTGCTTGC 58.469 43.478 14.22 0.00 42.20 4.01
2309 2387 8.948853 TGCTGAAAGAAACTAATAACATTTCG 57.051 30.769 0.00 0.00 37.41 3.46
2442 2605 0.307760 GTGGACACAACCTGCGAAAG 59.692 55.000 0.00 0.00 0.00 2.62
2744 2924 1.240256 GTTGCCGTGTAATTGGGTCA 58.760 50.000 0.00 0.00 0.00 4.02
2752 2932 3.350612 GGCGCTGTTGCCGTGTAA 61.351 61.111 7.64 0.00 46.75 2.41
2814 2996 0.249398 TGAAGGCCGAGGTTAGCTTC 59.751 55.000 0.00 0.00 0.00 3.86
3071 3304 6.371825 CAGTTCTCTGTACCCCTTGAAATAAC 59.628 42.308 0.00 0.00 36.97 1.89
3116 3349 4.808895 TGAAACGTCATAGGCATGTGATAC 59.191 41.667 0.00 0.00 33.57 2.24


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

AutoCloner maintained by Alex Coulton.