Multiple sequence alignment - TraesCS2D01G525400

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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 TraesCS2D01G525400 chr2D 100.000 2975 0 0 1 2975 613419063 613422037 0.000000e+00 5494.0
1 TraesCS2D01G525400 chr2D 96.118 1520 50 1 714 2224 260867194 260865675 0.000000e+00 2471.0
2 TraesCS2D01G525400 chr2D 96.319 1494 35 3 725 2218 451467953 451469426 0.000000e+00 2436.0
3 TraesCS2D01G525400 chr2D 93.733 1500 74 4 720 2218 520043084 520044564 0.000000e+00 2231.0
4 TraesCS2D01G525400 chr2D 96.224 715 17 4 2220 2924 241271527 241272241 0.000000e+00 1162.0
5 TraesCS2D01G525400 chr2D 93.718 780 25 9 2220 2975 260865598 260864819 0.000000e+00 1147.0
6 TraesCS2D01G525400 chr2D 95.671 462 10 6 2524 2975 451487533 451487994 0.000000e+00 734.0
7 TraesCS2D01G525400 chr2D 91.786 487 21 6 2498 2975 520044984 520045460 0.000000e+00 660.0
8 TraesCS2D01G525400 chr2D 89.876 484 30 6 2501 2975 35330052 35329579 3.280000e-169 604.0
9 TraesCS2D01G525400 chr2D 92.661 327 9 1 2220 2531 451469509 451469835 9.720000e-125 457.0
10 TraesCS2D01G525400 chr2D 90.751 346 22 1 2220 2555 520044663 520045008 1.260000e-123 453.0
11 TraesCS2D01G525400 chr2D 91.489 282 23 1 2274 2555 35330344 35330064 1.290000e-103 387.0
12 TraesCS2D01G525400 chr2D 99.495 198 1 0 1 198 613400446 613400643 7.840000e-96 361.0
13 TraesCS2D01G525400 chr2D 94.643 56 3 0 2220 2275 35330354 35330299 1.470000e-13 87.9
14 TraesCS2D01G525400 chr5B 91.416 1864 118 27 720 2555 260234931 260236780 0.000000e+00 2518.0
15 TraesCS2D01G525400 chr5B 90.719 334 21 4 2498 2821 260236756 260237089 1.270000e-118 436.0
16 TraesCS2D01G525400 chr6D 95.947 1505 59 2 721 2224 114017560 114016057 0.000000e+00 2440.0
17 TraesCS2D01G525400 chr5D 96.307 1381 51 0 844 2224 26959808 26958428 0.000000e+00 2268.0
18 TraesCS2D01G525400 chr5D 94.744 780 14 6 2220 2975 26958351 26957575 0.000000e+00 1188.0
19 TraesCS2D01G525400 chr7D 92.786 1497 83 7 725 2218 151511976 151513450 0.000000e+00 2143.0
20 TraesCS2D01G525400 chr7D 90.965 487 25 6 2498 2975 151513858 151514334 3.230000e-179 638.0
21 TraesCS2D01G525400 chr7A 92.507 1428 105 2 718 2145 471263893 471262468 0.000000e+00 2043.0
22 TraesCS2D01G525400 chr7A 90.936 342 20 6 2220 2555 471262322 471261986 1.630000e-122 449.0
23 TraesCS2D01G525400 chr6A 92.491 1425 101 5 721 2145 144491473 144492891 0.000000e+00 2034.0
24 TraesCS2D01G525400 chr6A 91.919 495 21 7 2490 2975 596357344 596357828 0.000000e+00 675.0
25 TraesCS2D01G525400 chr6A 89.754 488 28 8 2498 2975 144493351 144493826 3.280000e-169 604.0
26 TraesCS2D01G525400 chr6A 91.789 341 21 4 2220 2555 144493037 144493375 4.490000e-128 468.0
27 TraesCS2D01G525400 chr6A 96.721 61 2 0 2158 2218 596356915 596356975 5.250000e-18 102.0
28 TraesCS2D01G525400 chr6B 90.166 1505 118 12 714 2218 494076428 494077902 0.000000e+00 1932.0
29 TraesCS2D01G525400 chr6B 93.252 489 22 7 2498 2975 28119329 28119817 0.000000e+00 710.0
30 TraesCS2D01G525400 chr6B 92.262 336 26 0 2220 2555 494077985 494078320 7.460000e-131 477.0
31 TraesCS2D01G525400 chr2A 91.185 726 54 6 3 720 745020531 745021254 0.000000e+00 977.0
32 TraesCS2D01G525400 chr2A 78.756 193 37 4 474 665 51597390 51597201 3.110000e-25 126.0
33 TraesCS2D01G525400 chr2A 96.721 61 2 0 2158 2218 673358975 673359035 5.250000e-18 102.0
34 TraesCS2D01G525400 chr3B 76.580 269 40 9 336 596 413964889 413964636 3.110000e-25 126.0
35 TraesCS2D01G525400 chr5A 96.721 61 2 0 2158 2218 407701250 407701310 5.250000e-18 102.0
36 TraesCS2D01G525400 chr7B 85.567 97 13 1 564 660 15715442 15715347 1.890000e-17 100.0
37 TraesCS2D01G525400 chr3D 74.729 277 45 12 336 604 307834046 307834305 1.890000e-17 100.0
38 TraesCS2D01G525400 chr3A 74.007 277 46 13 336 604 427098509 427098767 4.080000e-14 89.8


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 TraesCS2D01G525400 chr2D 613419063 613422037 2974 False 5494.000000 5494 100.000000 1 2975 1 chr2D.!!$F4 2974
1 TraesCS2D01G525400 chr2D 260864819 260867194 2375 True 1809.000000 2471 94.918000 714 2975 2 chr2D.!!$R2 2261
2 TraesCS2D01G525400 chr2D 451467953 451469835 1882 False 1446.500000 2436 94.490000 725 2531 2 chr2D.!!$F5 1806
3 TraesCS2D01G525400 chr2D 241271527 241272241 714 False 1162.000000 1162 96.224000 2220 2924 1 chr2D.!!$F1 704
4 TraesCS2D01G525400 chr2D 520043084 520045460 2376 False 1114.666667 2231 92.090000 720 2975 3 chr2D.!!$F6 2255
5 TraesCS2D01G525400 chr2D 35329579 35330354 775 True 359.633333 604 92.002667 2220 2975 3 chr2D.!!$R1 755
6 TraesCS2D01G525400 chr5B 260234931 260237089 2158 False 1477.000000 2518 91.067500 720 2821 2 chr5B.!!$F1 2101
7 TraesCS2D01G525400 chr6D 114016057 114017560 1503 True 2440.000000 2440 95.947000 721 2224 1 chr6D.!!$R1 1503
8 TraesCS2D01G525400 chr5D 26957575 26959808 2233 True 1728.000000 2268 95.525500 844 2975 2 chr5D.!!$R1 2131
9 TraesCS2D01G525400 chr7D 151511976 151514334 2358 False 1390.500000 2143 91.875500 725 2975 2 chr7D.!!$F1 2250
10 TraesCS2D01G525400 chr7A 471261986 471263893 1907 True 1246.000000 2043 91.721500 718 2555 2 chr7A.!!$R1 1837
11 TraesCS2D01G525400 chr6A 144491473 144493826 2353 False 1035.333333 2034 91.344667 721 2975 3 chr6A.!!$F1 2254
12 TraesCS2D01G525400 chr6A 596356915 596357828 913 False 388.500000 675 94.320000 2158 2975 2 chr6A.!!$F2 817
13 TraesCS2D01G525400 chr6B 494076428 494078320 1892 False 1204.500000 1932 91.214000 714 2555 2 chr6B.!!$F2 1841
14 TraesCS2D01G525400 chr2A 745020531 745021254 723 False 977.000000 977 91.185000 3 720 1 chr2A.!!$F2 717

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
162 163 0.167689 AAGCGACCGTAGACGAGAAC 59.832 55.0 3.07 0.0 43.02 3.01 F
770 779 0.250597 GTGGGTGGTTCGCTTTACCT 60.251 55.0 0.00 0.0 36.60 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1650 0.255890 AGCCACGCCATTACCTCAAT 59.744 50.0 0.0 0.0 0.00 2.57 R
2581 2919 0.106419 AAGAGTAGGAGGGAGAGCCG 60.106 60.0 0.0 0.0 33.83 5.52 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
26 27 3.119209 AGGGGAAAATCTACGACGAGTTC 60.119 47.826 0.00 0.00 0.00 3.01
32 33 0.441533 TCTACGACGAGTTCACGAGC 59.558 55.000 0.00 0.00 37.03 5.03
38 39 1.226156 CGAGTTCACGAGCGAGGAG 60.226 63.158 0.00 0.00 35.09 3.69
79 80 1.605058 GAGGCGGGCACTCTACAAGA 61.605 60.000 3.78 0.00 32.28 3.02
114 115 2.406401 GCAAGCTGCGATGCGATT 59.594 55.556 15.59 0.00 38.13 3.34
115 116 1.937846 GCAAGCTGCGATGCGATTG 60.938 57.895 15.59 4.74 38.13 2.67
131 132 4.916293 TGCGATGGAGGCGGATGC 62.916 66.667 0.00 0.00 41.71 3.91
162 163 0.167689 AAGCGACCGTAGACGAGAAC 59.832 55.000 3.07 0.00 43.02 3.01
163 164 1.579626 GCGACCGTAGACGAGAACG 60.580 63.158 3.07 4.99 43.02 3.95
186 187 2.436646 AGCTCCCCGTCATTTGCG 60.437 61.111 0.00 0.00 0.00 4.85
187 188 4.179579 GCTCCCCGTCATTTGCGC 62.180 66.667 0.00 0.00 0.00 6.09
193 194 4.817063 CGTCATTTGCGCCGGCTG 62.817 66.667 26.68 19.05 40.82 4.85
246 251 3.083997 GGGCCTCACCTCGACCAT 61.084 66.667 0.84 0.00 39.10 3.55
256 261 2.099263 CACCTCGACCATCAACGTCTAT 59.901 50.000 0.00 0.00 0.00 1.98
263 268 4.291783 GACCATCAACGTCTATAGAGCAC 58.708 47.826 1.64 0.00 0.00 4.40
296 301 2.166907 AGAGTAGGAGGTGGGACATG 57.833 55.000 0.00 0.00 44.52 3.21
299 304 2.168728 GAGTAGGAGGTGGGACATGAAC 59.831 54.545 0.00 0.00 44.52 3.18
300 305 1.134788 GTAGGAGGTGGGACATGAACG 60.135 57.143 0.00 0.00 44.52 3.95
312 317 0.371301 CATGAACGTGGCACATCTCG 59.629 55.000 19.09 5.61 44.52 4.04
352 357 2.007608 TCGTGTCTCATGTCCTACTCG 58.992 52.381 0.00 0.81 0.00 4.18
363 368 2.439701 CTACTCGTCCCCTCGCCA 60.440 66.667 0.00 0.00 0.00 5.69
369 374 4.222847 GTCCCCTCGCCATCGACC 62.223 72.222 0.00 0.00 40.21 4.79
378 383 1.234615 CGCCATCGACCCACAACTTT 61.235 55.000 0.00 0.00 38.10 2.66
446 453 1.149361 GAACACAGACGTCGCCACAA 61.149 55.000 10.46 0.00 0.00 3.33
558 565 7.938563 TTTGGTCTGGTTTAAATGAAAATCG 57.061 32.000 0.00 0.00 0.00 3.34
571 578 5.594724 ATGAAAATCGTTTGGTTTGCATG 57.405 34.783 0.00 0.00 33.40 4.06
581 588 5.509771 GTTTGGTTTGCATGAAATTTGTCC 58.490 37.500 0.00 0.00 0.00 4.02
591 598 4.993029 TGAAATTTGTCCGGTTTGTTCT 57.007 36.364 0.00 0.00 0.00 3.01
611 618 5.054390 TCTAATTCCCGTTTGAAATGTGC 57.946 39.130 0.00 0.00 0.00 4.57
643 650 2.391926 TGGATAGGGTTGGATCGCTA 57.608 50.000 0.00 0.00 37.29 4.26
650 657 1.686325 GGTTGGATCGCTAGCTCCCA 61.686 60.000 17.85 15.56 31.83 4.37
658 665 3.434940 TCGCTAGCTCCCATATCACTA 57.565 47.619 13.93 0.00 0.00 2.74
664 671 5.419155 GCTAGCTCCCATATCACTATACACA 59.581 44.000 7.70 0.00 0.00 3.72
668 675 6.728164 AGCTCCCATATCACTATACACATTCT 59.272 38.462 0.00 0.00 0.00 2.40
673 680 7.030165 CCATATCACTATACACATTCTCGGAC 58.970 42.308 0.00 0.00 0.00 4.79
711 720 2.052782 ACGGGATAGTTTTGGATGCC 57.947 50.000 0.00 0.00 0.00 4.40
770 779 0.250597 GTGGGTGGTTCGCTTTACCT 60.251 55.000 0.00 0.00 36.60 3.08
1172 1192 2.438795 GGAGCTCCGTCGAGAGGT 60.439 66.667 19.06 13.05 46.91 3.85
1223 1243 2.747460 GGATGCGTTGGAGCTGCA 60.747 61.111 2.72 2.72 43.67 4.41
1429 1449 1.800586 TGCTCTTGTCGTCAATGAAGC 59.199 47.619 13.57 13.57 35.74 3.86
1461 1481 1.535462 CGGCGTTGGATTCAGTTTTCT 59.465 47.619 0.00 0.00 0.00 2.52
1575 1595 1.126846 GCGTCCGTGAAAGATGTTCTG 59.873 52.381 0.00 0.00 0.00 3.02
1751 1771 3.216800 TGGATGAGTATGAAGCAATGCC 58.783 45.455 0.00 0.00 0.00 4.40
1837 1857 2.380064 TTGCCACATGAAGGAGGTTT 57.620 45.000 12.18 0.00 0.00 3.27
1929 1950 3.198068 TCGCAAGCATATCTTCAAGACC 58.802 45.455 0.00 0.00 31.27 3.85
2156 2204 8.011106 GTGCCAAATATTTGTGTGAAATTTCTG 58.989 33.333 23.24 7.43 36.45 3.02
2218 2282 5.008613 TGGTACAATTGTGAGCTTCTTTGTC 59.991 40.000 21.42 0.00 31.92 3.18
2267 2442 7.677747 GCAGCTTAACAGTAACAAACACAAGTA 60.678 37.037 0.00 0.00 0.00 2.24
2286 2461 6.374333 ACAAGTACATGAAACACAAGTTCTGT 59.626 34.615 4.87 0.00 36.84 3.41
2520 2825 1.195115 CCCTCCTGTAGCTTGCTGTA 58.805 55.000 5.26 0.00 0.00 2.74
2531 2869 1.896220 CTTGCTGTAAAGACTGGGCA 58.104 50.000 0.00 0.00 0.00 5.36
2581 2919 1.297456 GCTGCCTGCTGTGAAGACTC 61.297 60.000 0.00 0.00 38.95 3.36
2586 2924 0.735632 CTGCTGTGAAGACTCGGCTC 60.736 60.000 0.00 0.00 40.96 4.70
2588 2926 0.457681 GCTGTGAAGACTCGGCTCTC 60.458 60.000 0.00 0.00 38.41 3.20
2589 2927 0.172352 CTGTGAAGACTCGGCTCTCC 59.828 60.000 0.00 0.00 0.00 3.71
2591 2929 0.968393 GTGAAGACTCGGCTCTCCCT 60.968 60.000 0.00 0.00 0.00 4.20
2592 2930 0.681564 TGAAGACTCGGCTCTCCCTC 60.682 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.934553 CGTCGTAGATTTTCCCCTTTCC 59.065 50.000 0.00 0.00 40.67 3.13
1 2 3.853475 TCGTCGTAGATTTTCCCCTTTC 58.147 45.455 0.00 0.00 40.67 2.62
26 27 3.842923 ATGGGCTCCTCGCTCGTG 61.843 66.667 0.00 0.00 44.18 4.35
32 33 4.864334 GGCACCATGGGCTCCTCG 62.864 72.222 18.09 0.00 0.00 4.63
57 58 3.075005 TAGAGTGCCCGCCTCCAC 61.075 66.667 2.70 0.00 0.00 4.02
64 65 1.153823 CGGTCTTGTAGAGTGCCCG 60.154 63.158 0.00 0.00 0.00 6.13
106 107 1.864862 CCTCCATCGCAATCGCATC 59.135 57.895 0.00 0.00 38.40 3.91
114 115 4.916293 GCATCCGCCTCCATCGCA 62.916 66.667 0.00 0.00 0.00 5.10
115 116 4.916293 TGCATCCGCCTCCATCGC 62.916 66.667 0.00 0.00 37.32 4.58
231 236 0.741221 GTTGATGGTCGAGGTGAGGC 60.741 60.000 0.00 0.00 0.00 4.70
246 251 4.457949 TGAAGTGTGCTCTATAGACGTTGA 59.542 41.667 0.00 0.00 0.00 3.18
256 261 0.528017 CCTCGCTGAAGTGTGCTCTA 59.472 55.000 0.00 0.00 0.00 2.43
263 268 2.159310 CCTACTCTTCCTCGCTGAAGTG 60.159 54.545 11.80 11.75 41.96 3.16
296 301 1.781555 CACGAGATGTGCCACGTTC 59.218 57.895 0.00 0.00 42.70 3.95
363 368 3.326880 AGGAAGTAAAGTTGTGGGTCGAT 59.673 43.478 0.00 0.00 0.00 3.59
369 374 5.153950 AGCTCTAGGAAGTAAAGTTGTGG 57.846 43.478 0.00 0.00 0.00 4.17
378 383 2.320781 GGCCATGAGCTCTAGGAAGTA 58.679 52.381 23.66 0.00 43.05 2.24
446 453 3.760684 ACCTAGTCTACATTTTCGTCGGT 59.239 43.478 0.00 0.00 0.00 4.69
524 531 5.867903 AAACCAGACCAAATTCATGACAA 57.132 34.783 0.00 0.00 0.00 3.18
537 544 7.095816 CCAAACGATTTTCATTTAAACCAGACC 60.096 37.037 0.00 0.00 0.00 3.85
558 565 5.509771 GGACAAATTTCATGCAAACCAAAC 58.490 37.500 0.00 0.00 0.00 2.93
571 578 7.115805 GGAATTAGAACAAACCGGACAAATTTC 59.884 37.037 9.46 2.72 0.00 2.17
581 588 4.023878 TCAAACGGGAATTAGAACAAACCG 60.024 41.667 0.00 0.00 44.86 4.44
591 598 3.056465 GGGCACATTTCAAACGGGAATTA 60.056 43.478 0.00 0.00 0.00 1.40
611 618 1.609208 CTATCCATCAAAAGCCCGGG 58.391 55.000 19.09 19.09 0.00 5.73
643 650 6.728164 AGAATGTGTATAGTGATATGGGAGCT 59.272 38.462 0.00 0.00 0.00 4.09
650 657 7.761038 TGTCCGAGAATGTGTATAGTGATAT 57.239 36.000 0.00 0.00 0.00 1.63
658 665 8.421784 ACATAGTATTTGTCCGAGAATGTGTAT 58.578 33.333 0.00 0.00 0.00 2.29
673 680 7.852971 TCCCGTAAAAAGGACATAGTATTTG 57.147 36.000 0.00 0.00 0.00 2.32
693 700 1.133792 AGGGCATCCAAAACTATCCCG 60.134 52.381 0.00 0.00 37.36 5.14
770 779 5.456921 AGGAGCCAAAATAAAGATCAGGA 57.543 39.130 0.00 0.00 0.00 3.86
833 853 2.281484 TGGAGACAAACCAGCCGC 60.281 61.111 0.00 0.00 37.44 6.53
1172 1192 1.126488 GGAGATCAGGACATGGCTCA 58.874 55.000 0.00 0.00 34.42 4.26
1223 1243 1.751349 AAGCACGTACCACCCGAAGT 61.751 55.000 0.00 0.00 0.00 3.01
1429 1449 2.542907 AACGCCGGCAACACTTGAG 61.543 57.895 28.98 9.11 0.00 3.02
1461 1481 1.234821 GAACCATTCTGCACCAACGA 58.765 50.000 0.00 0.00 0.00 3.85
1503 1523 0.539051 AGCCGAGCTTGCTCTTGTAT 59.461 50.000 18.75 3.16 33.89 2.29
1575 1595 2.281484 TCGCCACCCAACTGCTTC 60.281 61.111 0.00 0.00 0.00 3.86
1630 1650 0.255890 AGCCACGCCATTACCTCAAT 59.744 50.000 0.00 0.00 0.00 2.57
1713 1733 1.002134 CATGGACTCGGGTGGCTTT 60.002 57.895 0.00 0.00 0.00 3.51
1751 1771 4.006989 TCCGTAGTCACCCAATTCAAATG 58.993 43.478 0.00 0.00 0.00 2.32
1837 1857 0.965866 AGCAGAGGACCACGATCGAA 60.966 55.000 24.34 0.00 0.00 3.71
1904 1924 2.826428 TGAAGATATGCTTGCGAGTCC 58.174 47.619 2.14 0.00 36.83 3.85
1929 1950 1.522355 ATCGATCTTGCCCAGCACG 60.522 57.895 0.00 0.00 38.71 5.34
2156 2204 6.542852 CATAGTACCAGCACATTACACAAAC 58.457 40.000 0.00 0.00 0.00 2.93
2218 2282 6.018913 TGCATAATTTGTGTTCAGTTGCAAAG 60.019 34.615 0.00 0.00 34.85 2.77
2267 2442 5.126067 AGCTACAGAACTTGTGTTTCATGT 58.874 37.500 0.00 0.00 41.10 3.21
2286 2461 7.852971 ACTTGTGTTTGTTACTGTTAAGCTA 57.147 32.000 0.00 0.00 0.00 3.32
2531 2869 3.076092 CAAGCTGCAGGAGGGAGT 58.924 61.111 17.12 0.00 37.27 3.85
2581 2919 0.106419 AAGAGTAGGAGGGAGAGCCG 60.106 60.000 0.00 0.00 33.83 5.52
2586 2924 4.285863 ACATCTCAAAGAGTAGGAGGGAG 58.714 47.826 0.00 0.00 0.00 4.30
2588 2926 3.386402 GGACATCTCAAAGAGTAGGAGGG 59.614 52.174 0.00 0.00 0.00 4.30
2589 2927 4.285863 AGGACATCTCAAAGAGTAGGAGG 58.714 47.826 0.00 0.00 0.00 4.30
2591 2929 4.467795 CCAAGGACATCTCAAAGAGTAGGA 59.532 45.833 0.00 0.00 0.00 2.94
2592 2930 4.467795 TCCAAGGACATCTCAAAGAGTAGG 59.532 45.833 0.00 0.00 0.00 3.18
2758 3106 5.816682 ACAAGGGAAAGTACAAGAATAGGG 58.183 41.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.