Multiple sequence alignment - TraesCS6D01G329300

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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 TraesCS6D01G329300 chr6D 100.000 3510 0 0 1 3510 433533045 433536554 0.000000e+00 6482.0
1 TraesCS6D01G329300 chr6D 83.175 1682 229 30 885 2540 433259192 433257539 0.000000e+00 1489.0
2 TraesCS6D01G329300 chr6D 83.105 1681 231 26 885 2540 432914522 432912870 0.000000e+00 1482.0
3 TraesCS6D01G329300 chr6D 81.779 1833 260 49 728 2510 433592555 433594363 0.000000e+00 1467.0
4 TraesCS6D01G329300 chr6D 82.370 1679 238 35 893 2540 433155401 433153750 0.000000e+00 1408.0
5 TraesCS6D01G329300 chr6A 93.609 3505 182 20 12 3510 579510462 579513930 0.000000e+00 5193.0
6 TraesCS6D01G329300 chr6A 82.480 1661 236 32 885 2519 579124994 579123363 0.000000e+00 1404.0
7 TraesCS6D01G329300 chr6A 81.866 1726 258 38 795 2486 579794923 579796627 0.000000e+00 1402.0
8 TraesCS6D01G329300 chr6B 83.273 1650 228 32 885 2519 653788844 653787228 0.000000e+00 1474.0
9 TraesCS6D01G329300 chr6B 82.840 1655 229 31 885 2510 653856617 653854989 0.000000e+00 1432.0
10 TraesCS6D01G329300 chr6B 95.897 780 31 1 2619 3398 654874765 654875543 0.000000e+00 1262.0
11 TraesCS6D01G329300 chr6B 91.164 713 47 12 11 716 654832159 654832862 0.000000e+00 953.0
12 TraesCS6D01G329300 chr6B 93.333 285 17 2 2193 2476 654836495 654836778 1.510000e-113 420.0
13 TraesCS6D01G329300 chr6B 93.902 246 7 3 710 950 654835043 654835285 7.160000e-97 364.0
14 TraesCS6D01G329300 chr6B 92.086 139 9 1 2475 2613 654874463 654874599 9.940000e-46 195.0
15 TraesCS6D01G329300 chr7D 85.455 110 13 2 392 501 550684596 550684702 1.030000e-20 111.0
16 TraesCS6D01G329300 chr5A 82.203 118 15 5 392 507 582637267 582637380 2.880000e-16 97.1
17 TraesCS6D01G329300 chr5D 82.301 113 15 5 395 506 203822844 203822736 3.730000e-15 93.5
18 TraesCS6D01G329300 chr3A 80.833 120 18 4 395 513 296442018 296441903 4.830000e-14 89.8
19 TraesCS6D01G329300 chr1D 81.416 113 18 2 395 507 487298600 487298491 4.830000e-14 89.8
20 TraesCS6D01G329300 chr1D 80.870 115 17 2 395 508 211960662 211960552 6.240000e-13 86.1
21 TraesCS6D01G329300 chr3D 81.081 111 18 2 390 500 398823118 398823225 6.240000e-13 86.1


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 TraesCS6D01G329300 chr6D 433533045 433536554 3509 False 6482.0 6482 100.000000 1 3510 1 chr6D.!!$F1 3509
1 TraesCS6D01G329300 chr6D 433257539 433259192 1653 True 1489.0 1489 83.175000 885 2540 1 chr6D.!!$R3 1655
2 TraesCS6D01G329300 chr6D 432912870 432914522 1652 True 1482.0 1482 83.105000 885 2540 1 chr6D.!!$R1 1655
3 TraesCS6D01G329300 chr6D 433592555 433594363 1808 False 1467.0 1467 81.779000 728 2510 1 chr6D.!!$F2 1782
4 TraesCS6D01G329300 chr6D 433153750 433155401 1651 True 1408.0 1408 82.370000 893 2540 1 chr6D.!!$R2 1647
5 TraesCS6D01G329300 chr6A 579510462 579513930 3468 False 5193.0 5193 93.609000 12 3510 1 chr6A.!!$F1 3498
6 TraesCS6D01G329300 chr6A 579123363 579124994 1631 True 1404.0 1404 82.480000 885 2519 1 chr6A.!!$R1 1634
7 TraesCS6D01G329300 chr6A 579794923 579796627 1704 False 1402.0 1402 81.866000 795 2486 1 chr6A.!!$F2 1691
8 TraesCS6D01G329300 chr6B 653787228 653788844 1616 True 1474.0 1474 83.273000 885 2519 1 chr6B.!!$R1 1634
9 TraesCS6D01G329300 chr6B 653854989 653856617 1628 True 1432.0 1432 82.840000 885 2510 1 chr6B.!!$R2 1625
10 TraesCS6D01G329300 chr6B 654874463 654875543 1080 False 728.5 1262 93.991500 2475 3398 2 chr6B.!!$F2 923
11 TraesCS6D01G329300 chr6B 654832159 654836778 4619 False 579.0 953 92.799667 11 2476 3 chr6B.!!$F1 2465

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
182 184 1.483004 TGAGTTCCAACAGTTCCACGA 59.517 47.619 0.0 0.0 0.00 4.35 F
1117 3458 0.759959 TTGTAGTTCGGTCCCAGCAA 59.240 50.000 0.0 0.0 0.00 3.91 F
1604 3959 0.811915 CTACCGTGCTGCTACAGAGT 59.188 55.000 0.0 0.0 32.44 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 3545 0.320374 TCGAATCGGTGTGCCTTCTT 59.680 50.000 1.76 0.0 0.00 2.52 R
2045 4400 2.445155 GCCCCATGTTGTTCCCCT 59.555 61.111 0.00 0.0 0.00 4.79 R
3137 5710 1.202817 GTGCATGATTGATGTGTGCCA 59.797 47.619 0.00 0.0 35.03 4.92 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
42 44 1.715862 TTTTTGTAGCGTGGCGTGCA 61.716 50.000 3.56 0.00 33.85 4.57
61 63 3.075005 GTGCGGAGGCTGGGTCTA 61.075 66.667 0.00 0.00 40.82 2.59
134 136 6.145338 TGAACTTATCCTATTCGGTGACTC 57.855 41.667 0.00 0.00 0.00 3.36
141 143 3.315470 TCCTATTCGGTGACTCATTCTCG 59.685 47.826 0.00 0.00 0.00 4.04
182 184 1.483004 TGAGTTCCAACAGTTCCACGA 59.517 47.619 0.00 0.00 0.00 4.35
189 191 5.471556 TCCAACAGTTCCACGACTTATAA 57.528 39.130 0.00 0.00 0.00 0.98
204 206 6.210984 ACGACTTATAAGGGAAGAACAGTTCT 59.789 38.462 16.73 10.27 43.15 3.01
329 333 2.677875 CAGCTGGTTTGGGCCTCC 60.678 66.667 5.57 5.54 0.00 4.30
424 430 8.440059 TCAGCTGTTAATCTTTATGTTAACACG 58.560 33.333 14.67 0.20 42.59 4.49
493 502 9.555727 TGAAATCTTCCGTCCTTTATTATTAGG 57.444 33.333 0.00 0.00 0.00 2.69
547 556 3.488553 GCAATATTTTCTGTACGCACCCC 60.489 47.826 0.00 0.00 0.00 4.95
574 583 7.434013 ACAATTTTGTAAAGCAACGGAAGTTAG 59.566 33.333 0.00 0.00 46.44 2.34
755 2953 2.171870 TCGGATTGACACCTAAATCCCC 59.828 50.000 8.46 0.00 46.14 4.81
919 3124 2.509336 CAGCCCTACTTCACCGCG 60.509 66.667 0.00 0.00 0.00 6.46
1092 3433 2.711009 CCTTGGTATCCTTGGATGCCTA 59.289 50.000 28.31 22.51 38.04 3.93
1098 3439 3.607490 ATCCTTGGATGCCTATGCTTT 57.393 42.857 0.72 0.00 38.71 3.51
1112 3453 1.886886 TGCTTTTGTAGTTCGGTCCC 58.113 50.000 0.00 0.00 0.00 4.46
1117 3458 0.759959 TTGTAGTTCGGTCCCAGCAA 59.240 50.000 0.00 0.00 0.00 3.91
1157 3499 1.547372 CTTTTCAATGGGGCACTCCAG 59.453 52.381 0.00 0.00 40.56 3.86
1173 3515 1.270414 CCAGGAGAGCTGGATGGTGT 61.270 60.000 0.00 0.00 44.39 4.16
1203 3545 1.000060 GTGTGTACAAGGACGCCACTA 60.000 52.381 0.00 0.00 0.00 2.74
1307 3649 2.614057 GGGCATCAATCAGTTTACCGAG 59.386 50.000 0.00 0.00 0.00 4.63
1449 3792 1.228245 TGGAGACCAAAGGTGCAGC 60.228 57.895 8.11 8.11 35.25 5.25
1520 3874 9.855021 ATGATGATGTATTGCATGTATCATTTG 57.145 29.630 13.82 0.00 41.11 2.32
1587 3941 2.099427 GGTTGTTGTTGGGCGTTTTCTA 59.901 45.455 0.00 0.00 0.00 2.10
1604 3959 0.811915 CTACCGTGCTGCTACAGAGT 59.188 55.000 0.00 0.00 32.44 3.24
1700 4055 1.150536 GACCAGGGTTGTGAAGGCA 59.849 57.895 0.00 0.00 0.00 4.75
1723 4078 4.280174 AGGCTCATGGATGATGCATTTAAC 59.720 41.667 0.00 0.00 36.02 2.01
1775 4130 5.017490 CCGAGTCCAACTATCCATATACCT 58.983 45.833 0.00 0.00 0.00 3.08
1779 4134 5.014858 GTCCAACTATCCATATACCTCGGA 58.985 45.833 0.00 0.00 0.00 4.55
1795 4150 5.869579 ACCTCGGAATATGATAAGTGCAAT 58.130 37.500 0.00 0.00 0.00 3.56
1901 4256 1.065854 GCCAACATGTCTCAGTAGCCT 60.066 52.381 0.00 0.00 0.00 4.58
1987 4342 2.146342 GACCTGGATCATGGTATTGCG 58.854 52.381 0.00 0.00 36.59 4.85
2106 4461 5.011533 CAGAGAAGGATATTCCCGACAAGAT 59.988 44.000 0.00 0.00 37.19 2.40
2107 4462 5.604650 AGAGAAGGATATTCCCGACAAGATT 59.395 40.000 0.00 0.00 37.19 2.40
2187 4544 2.542205 GCACATATGTTCGCATGCACAT 60.542 45.455 22.68 22.68 38.47 3.21
2373 4773 7.068962 TCCTTCGGATATTTGTCACATGTAGTA 59.931 37.037 0.00 0.00 0.00 1.82
2401 4809 6.521162 TGTAAGTGAATTGTGCTGTCTCTTA 58.479 36.000 0.00 0.00 0.00 2.10
2613 5026 0.180406 CGCTAGTTGCCCACCCTAAT 59.820 55.000 0.00 0.00 38.78 1.73
2873 5446 7.852454 CGTTAACTGTGATTAATGATCATGTGG 59.148 37.037 9.46 0.00 46.01 4.17
2918 5491 9.384764 ACTTTGACTAATCTACATTTAGGAAGC 57.615 33.333 0.00 0.00 32.15 3.86
2984 5557 6.014242 TCGATTAGCATCATGGATCCTTAAGT 60.014 38.462 14.23 0.00 0.00 2.24
3203 5776 7.639113 TTGTCAGTTCTTTTCAAATAGTGGT 57.361 32.000 0.00 0.00 0.00 4.16
3393 5966 6.878923 TGTCTAGTAAAAACCATCACATCCAG 59.121 38.462 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.935682 CGCTACAAAAAGTCATACATAAATGAT 57.064 29.630 0.00 0.00 38.13 2.45
8 9 8.941977 ACGCTACAAAAAGTCATACATAAATGA 58.058 29.630 0.00 0.00 33.48 2.57
9 10 8.998989 CACGCTACAAAAAGTCATACATAAATG 58.001 33.333 0.00 0.00 0.00 2.32
10 11 8.181573 CCACGCTACAAAAAGTCATACATAAAT 58.818 33.333 0.00 0.00 0.00 1.40
11 12 7.523219 CCACGCTACAAAAAGTCATACATAAA 58.477 34.615 0.00 0.00 0.00 1.40
12 13 6.402766 GCCACGCTACAAAAAGTCATACATAA 60.403 38.462 0.00 0.00 0.00 1.90
13 14 5.064198 GCCACGCTACAAAAAGTCATACATA 59.936 40.000 0.00 0.00 0.00 2.29
14 15 4.142687 GCCACGCTACAAAAAGTCATACAT 60.143 41.667 0.00 0.00 0.00 2.29
15 16 3.187637 GCCACGCTACAAAAAGTCATACA 59.812 43.478 0.00 0.00 0.00 2.29
16 17 3.723835 CGCCACGCTACAAAAAGTCATAC 60.724 47.826 0.00 0.00 0.00 2.39
17 18 2.413796 CGCCACGCTACAAAAAGTCATA 59.586 45.455 0.00 0.00 0.00 2.15
18 19 1.196808 CGCCACGCTACAAAAAGTCAT 59.803 47.619 0.00 0.00 0.00 3.06
61 63 6.039270 TCACCGTCAGATCAAAAGAAAACAAT 59.961 34.615 0.00 0.00 0.00 2.71
134 136 4.489810 GGTCTATATGTGGCTCGAGAATG 58.510 47.826 18.75 0.00 0.00 2.67
141 143 1.000955 CCACGGGTCTATATGTGGCTC 59.999 57.143 0.00 0.00 44.69 4.70
216 220 7.553760 TCTGGTAATATGTACGTCTGTAACAGA 59.446 37.037 12.80 12.80 38.25 3.41
224 228 8.241497 TGGTATTTCTGGTAATATGTACGTCT 57.759 34.615 0.00 0.00 0.00 4.18
229 233 8.513139 TCCCATGGTATTTCTGGTAATATGTA 57.487 34.615 11.73 0.00 0.00 2.29
263 267 5.605534 AGGAAACATGGTCTTGATATCTCG 58.394 41.667 3.98 0.00 0.00 4.04
274 278 2.627699 TGCCAAAGAAGGAAACATGGTC 59.372 45.455 0.00 0.00 0.00 4.02
276 280 3.749665 TTGCCAAAGAAGGAAACATGG 57.250 42.857 0.00 0.00 0.00 3.66
329 333 2.540101 CAGAAGCGGCCTAATAAACTCG 59.460 50.000 0.00 0.00 0.00 4.18
379 385 9.896645 ACAGCTGAGATTCAATATTTAGAAAGA 57.103 29.630 23.35 0.00 0.00 2.52
547 556 5.518487 ACTTCCGTTGCTTTACAAAATTGTG 59.482 36.000 8.99 0.00 42.31 3.33
792 2993 9.140286 GCTTTGGATTTTAGTACAAGGAAAATC 57.860 33.333 17.91 17.91 43.83 2.17
793 2994 8.094548 GGCTTTGGATTTTAGTACAAGGAAAAT 58.905 33.333 0.00 1.90 35.90 1.82
794 2995 7.289084 AGGCTTTGGATTTTAGTACAAGGAAAA 59.711 33.333 0.00 0.00 0.00 2.29
1092 3433 2.224670 TGGGACCGAACTACAAAAGCAT 60.225 45.455 0.00 0.00 0.00 3.79
1098 3439 0.759959 TTGCTGGGACCGAACTACAA 59.240 50.000 0.00 0.00 0.00 2.41
1112 3453 3.008240 CTGAGCTCACGCGTTGCTG 62.008 63.158 32.24 19.36 42.32 4.41
1117 3458 1.445066 CATCACTGAGCTCACGCGT 60.445 57.895 13.74 5.58 42.32 6.01
1157 3499 1.490574 ACTACACCATCCAGCTCTCC 58.509 55.000 0.00 0.00 0.00 3.71
1173 3515 1.199789 CTTGTACACACGGCCGTACTA 59.800 52.381 33.70 20.66 39.00 1.82
1203 3545 0.320374 TCGAATCGGTGTGCCTTCTT 59.680 50.000 1.76 0.00 0.00 2.52
1417 3759 1.618837 GTCTCCAGTCTACTGTTGCCA 59.381 52.381 9.17 0.00 42.27 4.92
1449 3792 1.142465 CCTGATCCTTGATGGGAGTGG 59.858 57.143 0.00 0.00 38.92 4.00
1520 3874 7.652507 GGTAGCTACTGTAAGGATACATTCAAC 59.347 40.741 22.74 0.00 41.09 3.18
1587 3941 1.290324 CACTCTGTAGCAGCACGGT 59.710 57.895 0.00 0.00 0.00 4.83
1604 3959 4.153475 GCCAGTTTTGAGCTTAACGATACA 59.847 41.667 0.00 0.00 0.00 2.29
1700 4055 2.677542 AATGCATCATCCATGAGCCT 57.322 45.000 0.00 0.00 40.64 4.58
1723 4078 4.818546 AGACCGCCATTCTTGATTATGAAG 59.181 41.667 0.00 0.00 0.00 3.02
1775 4130 6.873605 CCACTATTGCACTTATCATATTCCGA 59.126 38.462 0.00 0.00 0.00 4.55
1779 4134 7.998383 TGGTTCCACTATTGCACTTATCATATT 59.002 33.333 0.00 0.00 0.00 1.28
1795 4150 1.886222 GCAGCACCATTGGTTCCACTA 60.886 52.381 5.34 0.00 31.02 2.74
1823 4178 4.096984 GGCTGGAACATCCTCATAACTTTG 59.903 45.833 0.00 0.00 42.15 2.77
1887 4242 4.809193 TCCATCTAAGGCTACTGAGACAT 58.191 43.478 0.00 0.00 37.03 3.06
1901 4256 7.075797 TGGAAAGTCATATCTCCTCCATCTAA 58.924 38.462 0.00 0.00 29.89 2.10
1987 4342 4.532834 TGGTCTTTCCATAACCAATAGCC 58.467 43.478 0.00 0.00 41.93 3.93
2045 4400 2.445155 GCCCCATGTTGTTCCCCT 59.555 61.111 0.00 0.00 0.00 4.79
2106 4461 2.735883 GCAAGCCACACATGCCAA 59.264 55.556 0.00 0.00 34.03 4.52
2107 4462 3.672447 CGCAAGCCACACATGCCA 61.672 61.111 0.00 0.00 36.75 4.92
2187 4544 5.503662 AGACGCATGCAATTAATTGATCA 57.496 34.783 28.33 18.61 40.14 2.92
2373 4773 7.013655 AGAGACAGCACAATTCACTTACAAAAT 59.986 33.333 0.00 0.00 0.00 1.82
2401 4809 8.353423 AGTTCAATATACAAACTTGAAGGCAT 57.647 30.769 0.00 0.00 39.00 4.40
2442 4853 3.119352 GCTCCAAGATTGCCGAGAAAAAT 60.119 43.478 3.82 0.00 0.00 1.82
2554 4967 5.793967 AGGAGATAAGGGTCAGTCCTAATT 58.206 41.667 0.00 0.00 35.80 1.40
2555 4968 5.137082 AGAGGAGATAAGGGTCAGTCCTAAT 59.863 44.000 0.00 0.00 35.80 1.73
3097 5670 7.338196 TCTTTCTATGTGGTTCACTTTGTTTCA 59.662 33.333 0.00 0.00 35.11 2.69
3137 5710 1.202817 GTGCATGATTGATGTGTGCCA 59.797 47.619 0.00 0.00 35.03 4.92
3228 5801 8.246180 AGGAATGTGTCAATGTGTATGAAATTC 58.754 33.333 0.00 0.00 0.00 2.17
3469 6042 7.854557 TTGATGAGATGAGACATGTTTAAGG 57.145 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.