Multiple sequence alignment - TraesCS5D01G216800

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 TraesCS5D01G216800 chr5D 100.000 3666 0 0 1 3666 326117108 326120773 0.000000e+00 6770.0
1 TraesCS5D01G216800 chr5D 87.512 1009 103 9 2638 3643 325664861 325665849 0.000000e+00 1144.0
2 TraesCS5D01G216800 chr5D 89.831 767 66 9 2544 3302 325648104 325648866 0.000000e+00 974.0
3 TraesCS5D01G216800 chr5D 100.000 477 0 0 3920 4396 326121027 326121503 0.000000e+00 881.0
4 TraesCS5D01G216800 chr5D 86.892 740 67 19 934 1672 325646758 325647468 0.000000e+00 802.0
5 TraesCS5D01G216800 chr5D 91.411 489 37 4 941 1426 325663603 325664089 0.000000e+00 665.0
6 TraesCS5D01G216800 chr5D 86.564 521 47 16 1136 1654 325422824 325423323 1.790000e-153 553.0
7 TraesCS5D01G216800 chr5D 85.524 525 44 15 1746 2266 325664331 325664827 1.810000e-143 520.0
8 TraesCS5D01G216800 chr5D 86.005 443 51 9 1987 2421 325647610 325648049 8.610000e-127 464.0
9 TraesCS5D01G216800 chr5D 86.379 301 29 8 3340 3637 325652098 325652389 7.090000e-83 318.0
10 TraesCS5D01G216800 chr5D 89.474 247 15 3 1472 1718 325664098 325664333 7.150000e-78 302.0
11 TraesCS5D01G216800 chr5D 97.619 42 1 0 799 840 325646666 325646707 6.100000e-09 73.1
12 TraesCS5D01G216800 chr5B 95.348 3676 131 18 1 3666 378509566 378513211 0.000000e+00 5805.0
13 TraesCS5D01G216800 chr5B 85.281 2772 261 65 922 3643 378068231 378070905 0.000000e+00 2723.0
14 TraesCS5D01G216800 chr5B 82.162 1665 165 69 798 2432 377978009 377979571 0.000000e+00 1308.0
15 TraesCS5D01G216800 chr5B 89.944 716 67 4 2630 3341 377979595 377980309 0.000000e+00 918.0
16 TraesCS5D01G216800 chr5B 93.388 484 17 3 3920 4396 378513235 378513710 0.000000e+00 702.0
17 TraesCS5D01G216800 chr5B 86.320 519 49 15 1136 1654 377698698 377699194 2.990000e-151 545.0
18 TraesCS5D01G216800 chr5B 86.818 220 20 5 416 635 377976204 377976414 2.040000e-58 237.0
19 TraesCS5D01G216800 chr5B 86.250 80 5 3 799 873 378068140 378068218 1.010000e-11 82.4
20 TraesCS5D01G216800 chr5A 93.998 3682 134 41 5 3661 430509431 430505812 0.000000e+00 5494.0
21 TraesCS5D01G216800 chr5A 85.016 1882 190 47 1777 3642 430957990 430956185 0.000000e+00 1829.0
22 TraesCS5D01G216800 chr5A 89.596 990 86 14 2654 3636 431029495 431028516 0.000000e+00 1242.0
23 TraesCS5D01G216800 chr5A 86.635 838 76 20 807 1637 431045269 431044461 0.000000e+00 894.0
24 TraesCS5D01G216800 chr5A 79.443 1148 184 38 1386 2519 666934223 666933114 0.000000e+00 765.0
25 TraesCS5D01G216800 chr5A 94.118 476 19 4 3920 4394 430505788 430505321 0.000000e+00 715.0
26 TraesCS5D01G216800 chr5A 90.467 493 45 1 934 1426 430958686 430958196 0.000000e+00 649.0
27 TraesCS5D01G216800 chr5A 84.144 637 45 26 1634 2266 431030126 431029542 2.290000e-157 566.0
28 TraesCS5D01G216800 chr5A 85.444 529 57 14 1136 1654 423745092 423745610 2.330000e-147 532.0
29 TraesCS5D01G216800 chr5A 90.196 204 15 2 1472 1674 430958187 430957988 1.210000e-65 261.0
30 TraesCS5D01G216800 chrUn 79.443 1148 185 37 1386 2519 30413676 30412566 0.000000e+00 765.0
31 TraesCS5D01G216800 chr7D 83.922 765 91 18 1765 2514 50650395 50651142 0.000000e+00 702.0
32 TraesCS5D01G216800 chr6D 82.222 765 101 19 1765 2514 36220061 36220805 1.040000e-175 627.0
33 TraesCS5D01G216800 chr6D 88.406 138 8 5 3920 4056 427226669 427226799 4.550000e-35 159.0
34 TraesCS5D01G216800 chr2A 83.086 674 83 15 1843 2513 154137113 154136468 6.340000e-163 584.0
35 TraesCS5D01G216800 chr2A 88.806 134 8 5 3920 4053 163044381 163044507 1.640000e-34 158.0
36 TraesCS5D01G216800 chr1A 83.388 307 48 3 1925 2231 50749079 50748776 9.310000e-72 281.0
37 TraesCS5D01G216800 chr2D 88.550 131 8 4 3923 4053 533094289 533094166 7.620000e-33 152.0
38 TraesCS5D01G216800 chr2D 87.023 131 10 4 3923 4053 612337045 612336922 1.650000e-29 141.0
39 TraesCS5D01G216800 chr3D 88.462 130 7 5 3925 4053 582884457 582884579 2.740000e-32 150.0
40 TraesCS5D01G216800 chr3D 86.957 138 10 5 3920 4056 341452036 341452166 9.850000e-32 148.0
41 TraesCS5D01G216800 chr6A 87.313 134 10 4 3920 4053 9360648 9360774 3.540000e-31 147.0


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 TraesCS5D01G216800 chr5D 326117108 326121503 4395 False 3825.50 6770 100.000000 1 4396 2 chr5D.!!$F4 4395
1 TraesCS5D01G216800 chr5D 325663603 325665849 2246 False 657.75 1144 88.480250 941 3643 4 chr5D.!!$F3 2702
2 TraesCS5D01G216800 chr5D 325646666 325652389 5723 False 526.22 974 89.345200 799 3637 5 chr5D.!!$F2 2838
3 TraesCS5D01G216800 chr5B 378509566 378513710 4144 False 3253.50 5805 94.368000 1 4396 2 chr5B.!!$F4 4395
4 TraesCS5D01G216800 chr5B 378068140 378070905 2765 False 1402.70 2723 85.765500 799 3643 2 chr5B.!!$F3 2844
5 TraesCS5D01G216800 chr5B 377976204 377980309 4105 False 821.00 1308 86.308000 416 3341 3 chr5B.!!$F2 2925
6 TraesCS5D01G216800 chr5A 430505321 430509431 4110 True 3104.50 5494 94.058000 5 4394 2 chr5A.!!$R3 4389
7 TraesCS5D01G216800 chr5A 430956185 430958686 2501 True 913.00 1829 88.559667 934 3642 3 chr5A.!!$R4 2708
8 TraesCS5D01G216800 chr5A 431028516 431030126 1610 True 904.00 1242 86.870000 1634 3636 2 chr5A.!!$R5 2002
9 TraesCS5D01G216800 chr5A 431044461 431045269 808 True 894.00 894 86.635000 807 1637 1 chr5A.!!$R1 830
10 TraesCS5D01G216800 chr5A 666933114 666934223 1109 True 765.00 765 79.443000 1386 2519 1 chr5A.!!$R2 1133
11 TraesCS5D01G216800 chr5A 423745092 423745610 518 False 532.00 532 85.444000 1136 1654 1 chr5A.!!$F1 518
12 TraesCS5D01G216800 chrUn 30412566 30413676 1110 True 765.00 765 79.443000 1386 2519 1 chrUn.!!$R1 1133
13 TraesCS5D01G216800 chr7D 50650395 50651142 747 False 702.00 702 83.922000 1765 2514 1 chr7D.!!$F1 749
14 TraesCS5D01G216800 chr6D 36220061 36220805 744 False 627.00 627 82.222000 1765 2514 1 chr6D.!!$F1 749
15 TraesCS5D01G216800 chr2A 154136468 154137113 645 True 584.00 584 83.086000 1843 2513 1 chr2A.!!$R1 670

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
540 551 0.820482 ACCCCGGGACAAACTTTTCG 60.820 55.0 26.32 2.06 0.00 3.46 F
880 2355 0.898320 CGCCTTCTCCTTCTCTCCAA 59.102 55.0 0.00 0.00 0.00 3.53 F
1441 2947 0.997932 GCACTCTCAAGCACGATCAG 59.002 55.0 0.00 0.00 0.00 2.90 F
1858 3420 0.318120 GAGGATAGCTGAGCTGCTCC 59.682 60.0 25.61 22.86 42.97 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 3127 1.057285 GCGTTCATGAACTCGTACACG 59.943 52.381 30.45 19.41 39.08 4.49 R
1858 3420 2.430332 TGTTGTTCTTTTGGAAGGCAGG 59.570 45.455 0.00 0.00 34.23 4.85 R
2315 3917 3.007635 ACCTTTGTAGTAATTCCAGCGC 58.992 45.455 0.00 0.00 0.00 5.92 R
3398 8223 4.079327 TCCTACTCACTTCCCTACCTTAGG 60.079 50.000 0.00 0.00 45.81 2.69 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
41 42 9.715121 ACTTCTATCATGTTTACTCGGTAAAAA 57.285 29.630 9.77 6.40 39.28 1.94
48 49 8.316214 TCATGTTTACTCGGTAAAAAGGAGTAT 58.684 33.333 9.77 0.00 41.44 2.12
49 50 8.943002 CATGTTTACTCGGTAAAAAGGAGTATT 58.057 33.333 9.77 0.00 41.44 1.89
177 178 1.404851 CCAGGCCGTTCTCTTCTTCTC 60.405 57.143 0.00 0.00 0.00 2.87
202 203 7.068593 TCTGTTTGTTGATCTTGAAACTTCCAT 59.931 33.333 12.30 0.00 31.03 3.41
226 227 3.632604 CCCTCGAGCAATTCACTCTACTA 59.367 47.826 6.99 0.00 31.71 1.82
260 261 4.568956 GGCTTGCACAAAGTCCAAATTAT 58.431 39.130 0.00 0.00 38.25 1.28
280 281 6.478512 TTATAATTTCCCAAGGTGAATGGC 57.521 37.500 0.00 0.00 36.58 4.40
313 318 1.135575 CCCTGCGCTTTCTGTCAATTC 60.136 52.381 9.73 0.00 0.00 2.17
339 344 1.213799 GGTACGGTTCGACCAGTCC 59.786 63.158 0.00 0.00 38.47 3.85
390 395 2.460757 TACACGGTCAGGGCTTAAAC 57.539 50.000 0.00 0.00 0.00 2.01
517 528 1.033746 TCCTACGTCCGATGGTCCAC 61.034 60.000 0.00 0.00 0.00 4.02
518 529 1.436336 CTACGTCCGATGGTCCACC 59.564 63.158 0.00 0.00 0.00 4.61
519 530 2.012902 CTACGTCCGATGGTCCACCC 62.013 65.000 0.00 0.00 34.29 4.61
520 531 4.508128 CGTCCGATGGTCCACCCG 62.508 72.222 0.00 0.56 35.15 5.28
521 532 3.072468 GTCCGATGGTCCACCCGA 61.072 66.667 14.98 0.00 35.15 5.14
540 551 0.820482 ACCCCGGGACAAACTTTTCG 60.820 55.000 26.32 2.06 0.00 3.46
603 614 2.347490 GGTGTGACATGCCCGTCT 59.653 61.111 0.00 0.00 36.82 4.18
643 2057 1.607148 GTTCCCACGAAGAAGGTTTGG 59.393 52.381 0.00 0.00 0.00 3.28
880 2355 0.898320 CGCCTTCTCCTTCTCTCCAA 59.102 55.000 0.00 0.00 0.00 3.53
888 2363 3.052566 TCTCCTTCTCTCCAATCCTGCTA 60.053 47.826 0.00 0.00 0.00 3.49
1441 2947 0.997932 GCACTCTCAAGCACGATCAG 59.002 55.000 0.00 0.00 0.00 2.90
1442 2948 1.403382 GCACTCTCAAGCACGATCAGA 60.403 52.381 0.00 0.00 0.00 3.27
1488 3013 1.135139 TGGTCGATGAACAGCTAGCTC 59.865 52.381 16.15 4.71 0.00 4.09
1519 3049 1.055849 TGTTCTTGCAGGCTGAGGTA 58.944 50.000 20.86 0.00 0.00 3.08
1831 3393 3.498777 GTCCCCTGAAGTTTCTTTTCTCG 59.501 47.826 0.00 0.00 0.00 4.04
1858 3420 0.318120 GAGGATAGCTGAGCTGCTCC 59.682 60.000 25.61 22.86 42.97 4.70
2021 3592 1.410004 ACTCTTGGTCAACGTGGAGA 58.590 50.000 0.00 0.00 0.00 3.71
2203 3795 1.303888 TCGACTCGGTAAGCCACCT 60.304 57.895 0.00 0.00 46.19 4.00
2315 3917 3.242413 CGAACACAACTTCACACCTCTTG 60.242 47.826 0.00 0.00 0.00 3.02
2334 3936 4.391830 TCTTGCGCTGGAATTACTACAAAG 59.608 41.667 9.73 0.00 0.00 2.77
2347 3949 9.665264 GAATTACTACAAAGGTGTCTGAAAAAG 57.335 33.333 0.00 0.00 39.30 2.27
2546 4169 7.729116 TGAGATACATTTAGCAGTCATGATCA 58.271 34.615 0.00 0.00 0.00 2.92
2551 4175 7.458409 ACATTTAGCAGTCATGATCAAGTTT 57.542 32.000 0.00 0.00 0.00 2.66
2565 4189 8.950210 CATGATCAAGTTTACAGAAACACCTAT 58.050 33.333 0.00 0.00 46.30 2.57
2671 4296 3.792956 CGCATTGTATTTCACTTCATGCC 59.207 43.478 0.00 0.00 34.69 4.40
2906 4536 0.395724 TCTCTGGGCTGCGATCAGTA 60.396 55.000 13.22 4.23 42.29 2.74
3637 8467 2.544903 CCGGTTTTGATTTTCGCAAGGT 60.545 45.455 0.00 0.00 38.47 3.50
3653 8483 4.681744 GCAAGGTTTGTTGTTCAAGATGA 58.318 39.130 0.00 0.00 37.35 2.92
3949 8779 7.393234 CCCACCTGAATATTTTACTCAAAGTGA 59.607 37.037 0.00 0.00 30.49 3.41
3959 8789 5.843673 TTACTCAAAGTGACCAAAATGCA 57.156 34.783 0.00 0.00 0.00 3.96
3963 8793 4.873817 TCAAAGTGACCAAAATGCATGAG 58.126 39.130 0.00 0.00 0.00 2.90
3964 8794 3.947910 AAGTGACCAAAATGCATGAGG 57.052 42.857 0.00 5.30 0.00 3.86
3965 8795 3.159213 AGTGACCAAAATGCATGAGGA 57.841 42.857 16.58 0.00 0.00 3.71
3966 8796 3.705051 AGTGACCAAAATGCATGAGGAT 58.295 40.909 16.58 4.03 0.00 3.24
3967 8797 4.091549 AGTGACCAAAATGCATGAGGATT 58.908 39.130 16.58 0.00 37.39 3.01
3968 8798 4.081862 AGTGACCAAAATGCATGAGGATTG 60.082 41.667 16.58 9.77 35.82 2.67
3969 8799 3.833650 TGACCAAAATGCATGAGGATTGT 59.166 39.130 16.58 2.07 35.82 2.71
4002 8832 5.007332 CCAGTTTATAAGGAAAACCGGATCG 59.993 44.000 9.46 0.00 36.79 3.69
4023 8853 6.702716 TCGAAAACCTAAACAAATTGACCT 57.297 33.333 0.00 0.00 0.00 3.85
4034 8864 6.877611 AACAAATTGACCTCGTTTATGAGT 57.122 33.333 0.00 0.00 34.04 3.41
4182 9012 7.599621 TCCATTGTTTGCAAATGAAATGAGTAG 59.400 33.333 28.58 19.14 38.21 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.128322 ACATGATAGAAGTTCTACAACAGTCT 57.872 34.615 14.82 0.00 34.88 3.24
8 9 9.569167 CGAGTAAACATGATAGAAGTTCTACAA 57.431 33.333 14.82 6.77 30.79 2.41
12 13 7.171630 ACCGAGTAAACATGATAGAAGTTCT 57.828 36.000 10.87 10.87 0.00 3.01
41 42 7.571025 ACCGGTCAAAATTATACAATACTCCT 58.429 34.615 0.00 0.00 0.00 3.69
48 49 7.303998 CCGTTTTACCGGTCAAAATTATACAA 58.696 34.615 12.40 0.00 43.07 2.41
49 50 6.128063 CCCGTTTTACCGGTCAAAATTATACA 60.128 38.462 12.40 0.00 46.66 2.29
177 178 6.563422 TGGAAGTTTCAAGATCAACAAACAG 58.437 36.000 13.01 0.00 32.20 3.16
202 203 1.902508 AGAGTGAATTGCTCGAGGGAA 59.097 47.619 15.58 2.88 37.99 3.97
226 227 0.537143 TGCAAGCCGTTCTGGTGAAT 60.537 50.000 0.00 0.00 41.21 2.57
260 261 4.059773 AGCCATTCACCTTGGGAAATTA 57.940 40.909 0.00 0.00 34.66 1.40
280 281 1.017387 CGCAGGGCCTTTTAGCTAAG 58.983 55.000 1.32 0.00 0.00 2.18
313 318 3.119388 TGGTCGAACCGTACCTGAAATAG 60.119 47.826 0.00 0.00 42.58 1.73
339 344 3.250762 TCAATTTGCAGGAACGAGTGAAG 59.749 43.478 0.00 0.00 0.00 3.02
390 395 1.251251 ACAGCTGCCTTTAGCCTTTG 58.749 50.000 15.27 0.00 44.76 2.77
498 509 1.033746 GTGGACCATCGGACGTAGGA 61.034 60.000 0.00 0.00 0.00 2.94
519 530 0.820482 AAAAGTTTGTCCCGGGGTCG 60.820 55.000 23.50 0.00 0.00 4.79
520 531 0.956633 GAAAAGTTTGTCCCGGGGTC 59.043 55.000 23.50 15.12 0.00 4.46
521 532 0.820482 CGAAAAGTTTGTCCCGGGGT 60.820 55.000 23.50 0.00 0.00 4.95
540 551 0.233848 CGGGTTCGCGTTTATATGGC 59.766 55.000 5.77 0.00 0.00 4.40
603 614 2.039746 ACGAACATGGGTGGATCAAAGA 59.960 45.455 0.00 0.00 0.00 2.52
643 2057 4.524328 AGGTTTTCATTCATGGAGTTGACC 59.476 41.667 0.00 0.00 0.00 4.02
880 2355 2.769095 GAGAAGGTCAGGTTAGCAGGAT 59.231 50.000 0.00 0.00 0.00 3.24
888 2363 1.545706 GCGAGGGAGAAGGTCAGGTT 61.546 60.000 0.00 0.00 0.00 3.50
1255 2758 3.391382 GCAGCCGAGGTAGTGGGT 61.391 66.667 0.00 0.00 36.12 4.51
1426 2932 1.931906 GCATCTGATCGTGCTTGAGA 58.068 50.000 9.50 0.00 38.30 3.27
1441 2947 3.065786 TCGAAATTGATCTGCCAAGCATC 59.934 43.478 0.00 0.00 38.13 3.91
1442 2948 3.018856 TCGAAATTGATCTGCCAAGCAT 58.981 40.909 0.00 0.00 38.13 3.79
1446 2952 2.164219 GGCTTCGAAATTGATCTGCCAA 59.836 45.455 13.98 0.00 38.99 4.52
1488 3013 4.487948 CTGCAAGAACAACCCACATAATG 58.512 43.478 0.00 0.00 34.07 1.90
1519 3049 3.160269 CCTCAGTTGCCCAAGAAAGAAT 58.840 45.455 0.00 0.00 0.00 2.40
1597 3127 1.057285 GCGTTCATGAACTCGTACACG 59.943 52.381 30.45 19.41 39.08 4.49
1831 3393 3.384467 AGCTCAGCTATCCTCTTGACTTC 59.616 47.826 0.00 0.00 36.99 3.01
1858 3420 2.430332 TGTTGTTCTTTTGGAAGGCAGG 59.570 45.455 0.00 0.00 34.23 4.85
2021 3592 4.141158 AGGATGTTTCAGGTCAGTTTCCTT 60.141 41.667 0.00 0.00 32.37 3.36
2315 3917 3.007635 ACCTTTGTAGTAATTCCAGCGC 58.992 45.455 0.00 0.00 0.00 5.92
2367 3985 8.978539 CAAAAGCTAAAGGTTGGAAATTAAGAC 58.021 33.333 0.00 0.00 35.72 3.01
2537 4160 7.041098 AGGTGTTTCTGTAAACTTGATCATGAC 60.041 37.037 15.03 4.15 44.44 3.06
2541 4164 9.653287 CTATAGGTGTTTCTGTAAACTTGATCA 57.347 33.333 0.00 0.00 44.44 2.92
2542 4165 9.871238 TCTATAGGTGTTTCTGTAAACTTGATC 57.129 33.333 0.00 0.00 44.44 2.92
2671 4296 8.326680 AGCATTGAAATTTTGTTAGGGAAATG 57.673 30.769 0.00 0.00 0.00 2.32
3398 8223 4.079327 TCCTACTCACTTCCCTACCTTAGG 60.079 50.000 0.00 0.00 45.81 2.69
3936 8766 6.214191 TGCATTTTGGTCACTTTGAGTAAA 57.786 33.333 0.00 0.00 0.00 2.01
3949 8779 3.055675 CCACAATCCTCATGCATTTTGGT 60.056 43.478 0.00 0.00 28.86 3.67
3959 8789 3.853355 GGATCAGTCCACAATCCTCAT 57.147 47.619 0.00 0.00 44.42 2.90
4002 8832 6.500910 ACGAGGTCAATTTGTTTAGGTTTTC 58.499 36.000 0.00 0.00 0.00 2.29
4023 8853 2.690786 CCCGGTTTCACTCATAAACGA 58.309 47.619 0.00 0.00 37.64 3.85
4034 8864 2.194889 GGTTTTCGGCCCGGTTTCA 61.195 57.895 1.90 0.00 0.00 2.69
4256 9086 6.481954 TTCTTAAAGAATCACGAAAGCCTC 57.518 37.500 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.