Multiple sequence alignment - TraesCS6D01G200000

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 TraesCS6D01G200000 chr6D 100.000 3026 0 0 1 3026 277856997 277853972 0.000000e+00 5589.0
1 TraesCS6D01G200000 chr6D 86.996 1638 160 28 751 2361 277849480 277847869 0.000000e+00 1796.0
2 TraesCS6D01G200000 chr6D 88.665 794 83 2 1228 2014 278630882 278631675 0.000000e+00 961.0
3 TraesCS6D01G200000 chr6A 91.825 2887 154 25 78 2951 401221122 401218305 0.000000e+00 3949.0
4 TraesCS6D01G200000 chr6A 90.892 1592 112 15 812 2390 401201797 401200226 0.000000e+00 2106.0
5 TraesCS6D01G200000 chr6A 88.917 794 81 2 1228 2014 402884741 402885534 0.000000e+00 972.0
6 TraesCS6D01G200000 chr6A 82.953 657 76 15 1730 2374 401199428 401198796 7.330000e-156 560.0
7 TraesCS6D01G200000 chr6A 90.080 373 36 1 1643 2014 402272270 402272642 1.630000e-132 483.0
8 TraesCS6D01G200000 chr6A 87.294 425 48 4 1228 1646 402271347 402271771 5.870000e-132 481.0
9 TraesCS6D01G200000 chr6A 90.415 313 22 8 2641 2951 401200042 401199736 3.630000e-109 405.0
10 TraesCS6D01G200000 chr6A 91.371 197 10 4 2429 2620 401200219 401200025 2.310000e-66 263.0
11 TraesCS6D01G200000 chr6B 93.636 2404 100 12 1 2400 439731868 439729514 0.000000e+00 3542.0
12 TraesCS6D01G200000 chr6B 86.772 1512 151 25 765 2254 439678318 439676834 0.000000e+00 1639.0
13 TraesCS6D01G200000 chr6B 93.047 676 29 12 2363 3026 439729525 439728856 0.000000e+00 972.0
14 TraesCS6D01G200000 chr6B 87.868 544 60 1 1228 1765 440757358 440757901 4.260000e-178 634.0
15 TraesCS6D01G200000 chrUn 83.662 355 36 15 2405 2744 34314099 34314446 6.300000e-82 315.0
16 TraesCS6D01G200000 chr5A 82.597 362 52 10 2 358 688524515 688524870 2.930000e-80 309.0
17 TraesCS6D01G200000 chr5A 79.042 167 28 6 2640 2804 607838963 607839124 1.150000e-19 108.0
18 TraesCS6D01G200000 chr3A 82.173 359 61 3 1 357 19566460 19566103 3.790000e-79 305.0
19 TraesCS6D01G200000 chr3A 83.857 223 32 2 1 222 642941645 642941864 3.060000e-50 209.0
20 TraesCS6D01G200000 chr3B 80.548 365 61 7 1 360 214442092 214442451 3.840000e-69 272.0
21 TraesCS6D01G200000 chr3B 81.570 293 52 2 20 310 420404392 420404684 1.080000e-59 241.0
22 TraesCS6D01G200000 chr3B 86.667 90 6 5 2419 2504 3782992 3783079 8.930000e-16 95.3
23 TraesCS6D01G200000 chr3B 86.667 90 6 5 2419 2504 4682869 4682956 8.930000e-16 95.3
24 TraesCS6D01G200000 chr3B 86.667 90 6 5 2419 2504 762456546 762456633 8.930000e-16 95.3
25 TraesCS6D01G200000 chr3D 80.870 345 56 7 19 358 147922272 147921933 2.310000e-66 263.0
26 TraesCS6D01G200000 chr3D 82.918 281 46 2 31 309 300779974 300779694 5.010000e-63 252.0
27 TraesCS6D01G200000 chr1D 80.571 350 46 15 2405 2744 100914465 100914802 1.800000e-62 250.0
28 TraesCS6D01G200000 chr1B 79.412 340 48 15 2405 2731 150770740 150770410 1.410000e-53 220.0
29 TraesCS6D01G200000 chr5D 82.222 225 23 9 2522 2744 59034085 59034294 8.620000e-41 178.0
30 TraesCS6D01G200000 chr4B 82.927 123 12 5 2614 2730 653316234 653316115 5.340000e-18 102.0


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 TraesCS6D01G200000 chr6D 277853972 277856997 3025 True 5589.0 5589 100.00000 1 3026 1 chr6D.!!$R2 3025
1 TraesCS6D01G200000 chr6D 277847869 277849480 1611 True 1796.0 1796 86.99600 751 2361 1 chr6D.!!$R1 1610
2 TraesCS6D01G200000 chr6D 278630882 278631675 793 False 961.0 961 88.66500 1228 2014 1 chr6D.!!$F1 786
3 TraesCS6D01G200000 chr6A 401218305 401221122 2817 True 3949.0 3949 91.82500 78 2951 1 chr6A.!!$R1 2873
4 TraesCS6D01G200000 chr6A 402884741 402885534 793 False 972.0 972 88.91700 1228 2014 1 chr6A.!!$F1 786
5 TraesCS6D01G200000 chr6A 401198796 401201797 3001 True 833.5 2106 88.90775 812 2951 4 chr6A.!!$R2 2139
6 TraesCS6D01G200000 chr6A 402271347 402272642 1295 False 482.0 483 88.68700 1228 2014 2 chr6A.!!$F2 786
7 TraesCS6D01G200000 chr6B 439728856 439731868 3012 True 2257.0 3542 93.34150 1 3026 2 chr6B.!!$R2 3025
8 TraesCS6D01G200000 chr6B 439676834 439678318 1484 True 1639.0 1639 86.77200 765 2254 1 chr6B.!!$R1 1489
9 TraesCS6D01G200000 chr6B 440757358 440757901 543 False 634.0 634 87.86800 1228 1765 1 chr6B.!!$F1 537

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
425 426 2.172717 AGTGTAAGGTGCAGTTTGAGGT 59.827 45.455 0.0 0.0 0.0 3.85 F
1125 1155 1.645455 CGCCATCAATGCTCTTCCG 59.355 57.895 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1519 0.104855 TCATACTCCATGTGAGCCGC 59.895 55.0 10.15 0.00 45.61 6.53 R
2954 5014 2.029918 GGTTCTTTCCATGCAAGACCAC 60.030 50.0 5.32 3.26 29.70 4.16 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
24 25 2.624838 ACACAAATTTCTCCCAGCACAG 59.375 45.455 0.00 0.00 0.00 3.66
97 98 4.022416 GGAGCATCAGTGACTACTCCATAG 60.022 50.000 23.56 0.00 42.64 2.23
121 122 5.732528 GCACCAGTTGATTGATATGCTTCAG 60.733 44.000 0.00 0.00 0.00 3.02
152 153 7.094634 GCTCTTTACATCATTTGGACTCTTTCA 60.095 37.037 0.00 0.00 0.00 2.69
291 292 3.600388 AGTCCATACACACAAGCTTAGC 58.400 45.455 0.00 0.00 0.00 3.09
308 309 4.684703 GCTTAGCAAACTTGACGAAGAGTA 59.315 41.667 0.00 0.00 32.98 2.59
425 426 2.172717 AGTGTAAGGTGCAGTTTGAGGT 59.827 45.455 0.00 0.00 0.00 3.85
435 436 5.234116 GGTGCAGTTTGAGGTGTTTAATTTG 59.766 40.000 0.00 0.00 0.00 2.32
444 445 8.477419 TTGAGGTGTTTAATTTGAAGGAATCT 57.523 30.769 0.00 0.00 0.00 2.40
451 452 9.466497 TGTTTAATTTGAAGGAATCTGCTAGAT 57.534 29.630 0.00 0.00 36.28 1.98
493 494 5.810525 AGTGTTTTCTTCTGTTGAATGTCG 58.189 37.500 0.00 0.00 0.00 4.35
496 497 3.878086 TTCTTCTGTTGAATGTCGCAC 57.122 42.857 0.00 0.00 0.00 5.34
574 575 6.536582 AGATATAGCCGATGTCATTGCATTAC 59.463 38.462 9.98 0.00 0.00 1.89
618 620 5.061311 GTCTCATTGCAATGATGGAAAAACG 59.939 40.000 35.61 22.74 43.87 3.60
619 621 4.880759 TCATTGCAATGATGGAAAAACGT 58.119 34.783 33.08 0.00 40.47 3.99
620 622 5.295950 TCATTGCAATGATGGAAAAACGTT 58.704 33.333 33.08 0.00 40.47 3.99
621 623 5.757320 TCATTGCAATGATGGAAAAACGTTT 59.243 32.000 33.08 7.96 40.47 3.60
622 624 5.649602 TTGCAATGATGGAAAAACGTTTC 57.350 34.783 15.01 2.33 42.16 2.78
623 625 3.733224 TGCAATGATGGAAAAACGTTTCG 59.267 39.130 15.01 0.00 43.56 3.46
624 626 3.733727 GCAATGATGGAAAAACGTTTCGT 59.266 39.130 15.01 5.39 43.56 3.85
799 802 8.776470 AGGAAAGAAACAACGACGAAATAAATA 58.224 29.630 0.00 0.00 0.00 1.40
800 803 9.384682 GGAAAGAAACAACGACGAAATAAATAA 57.615 29.630 0.00 0.00 0.00 1.40
870 889 3.633094 CTGGACCCAGTGAGCGACG 62.633 68.421 7.88 0.00 39.10 5.12
1125 1155 1.645455 CGCCATCAATGCTCTTCCG 59.355 57.895 0.00 0.00 0.00 4.30
1398 1428 4.202441 CCAACCTTGTTATCTGGATGGAG 58.798 47.826 0.00 0.00 43.72 3.86
1683 2221 3.141488 AGGTACGAGCTCAGCGGG 61.141 66.667 15.40 0.00 0.00 6.13
1766 3762 1.160137 GTTCAGAAGTTGGCGCATCT 58.840 50.000 10.83 0.30 0.00 2.90
2047 4043 1.485066 GGGAGATTTAGTGGCGGAGAA 59.515 52.381 0.00 0.00 0.00 2.87
2088 4088 9.455847 GAATCCTGAGTTGTTAAATAATGATGC 57.544 33.333 0.00 0.00 0.00 3.91
2134 4134 9.077885 GCTCCCTTTGAATTGTGGAATTATATA 57.922 33.333 0.00 0.00 31.58 0.86
2536 4590 6.016213 TGTATACAACTTGTCTGCGAAGTA 57.984 37.500 2.20 0.00 33.20 2.24
2612 4668 7.865889 CGTATTTCTAGCACATGTACTATTCCA 59.134 37.037 6.26 0.00 0.00 3.53
2840 4900 6.133356 AGGTTCCTTTGGACAAAATAGTGAA 58.867 36.000 0.00 0.00 0.00 3.18
2953 5013 7.649533 TCTGAATTTGCATGATAGGTGAAAT 57.350 32.000 0.00 0.00 0.00 2.17
2954 5014 7.485810 TCTGAATTTGCATGATAGGTGAAATG 58.514 34.615 0.00 0.00 0.00 2.32
2965 5026 2.880443 AGGTGAAATGTGGTCTTGCAT 58.120 42.857 0.00 0.00 0.00 3.96
2982 5043 3.364549 TGCATGGAAAGAACCTAATGGG 58.635 45.455 0.00 0.00 41.89 4.00
3011 5076 4.733850 TCTACTGAGTCAACAAGCATACG 58.266 43.478 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.401931 CGCTGTGCTGGGAGAAATTTG 60.402 52.381 0.00 0.00 0.00 2.32
24 25 0.726827 TGCGGTTCTTGATGATTCGC 59.273 50.000 0.00 0.00 42.46 4.70
74 75 2.103373 TGGAGTAGTCACTGATGCTCC 58.897 52.381 14.62 14.62 41.92 4.70
97 98 4.096833 TGAAGCATATCAATCAACTGGTGC 59.903 41.667 0.00 0.00 0.00 5.01
121 122 6.094603 AGTCCAAATGATGTAAAGAGCATGAC 59.905 38.462 0.00 0.00 0.00 3.06
314 315 6.520572 CGAACCCCTAAAACTTAACTCCCTAA 60.521 42.308 0.00 0.00 0.00 2.69
380 381 7.391554 ACTTTCACTTCTTATATTTGCTCAGCA 59.608 33.333 0.00 0.00 36.47 4.41
425 426 8.862325 TCTAGCAGATTCCTTCAAATTAAACA 57.138 30.769 0.00 0.00 0.00 2.83
435 436 6.071447 TCAGAGCATATCTAGCAGATTCCTTC 60.071 42.308 4.35 0.73 36.20 3.46
493 494 0.729140 GTACAAAGCATGCACCGTGC 60.729 55.000 21.98 16.93 45.65 5.34
496 497 0.447801 GGAGTACAAAGCATGCACCG 59.552 55.000 21.98 9.60 0.00 4.94
605 607 9.925268 GTATATTACGAAACGTTTTTCCATCAT 57.075 29.630 15.89 6.55 41.54 2.45
732 735 1.787847 CACAACAACGGGCGATCTC 59.212 57.895 0.00 0.00 0.00 2.75
870 889 2.051345 CAACTGGAAACCGCGTGC 60.051 61.111 4.92 0.00 0.00 5.34
1398 1428 3.181492 GGCCGTAGTACTGAGTAAACTCC 60.181 52.174 5.39 0.00 42.20 3.85
1489 1519 0.104855 TCATACTCCATGTGAGCCGC 59.895 55.000 10.15 0.00 45.61 6.53
1683 2221 1.066454 ACAAAAGTGTAAGCCGTTGGC 59.934 47.619 0.00 0.00 42.50 4.52
1692 2230 4.396790 GTGAAGTGGTCCACAAAAGTGTAA 59.603 41.667 24.02 0.00 35.72 2.41
1698 2236 2.374184 CTGGTGAAGTGGTCCACAAAA 58.626 47.619 24.02 5.64 36.74 2.44
1766 3762 3.487202 GCGATTGTTCGGCGAGCA 61.487 61.111 22.57 22.57 45.59 4.26
2038 4034 2.281484 GCAACTGGTTCTCCGCCA 60.281 61.111 0.00 0.00 36.30 5.69
2047 4043 3.446161 CAGGATTCAATCATGCAACTGGT 59.554 43.478 0.00 0.00 34.09 4.00
2088 4088 2.095059 GCTTGCCAATTGTACACCTGAG 60.095 50.000 4.43 0.00 0.00 3.35
2536 4590 8.523915 TGCATAAAACAGTATTTCCTCATGAT 57.476 30.769 0.00 0.00 0.00 2.45
2583 4639 5.348986 AGTACATGTGCTAGAAATACGTGG 58.651 41.667 15.40 0.00 36.04 4.94
2587 4643 9.712305 ATGGAATAGTACATGTGCTAGAAATAC 57.288 33.333 24.87 14.09 31.54 1.89
2840 4900 7.990886 TCACTTTGACTAGGTGTCTTTATGTTT 59.009 33.333 0.00 0.00 45.54 2.83
2860 4920 2.576648 GGGTAGAATCCCACCTCACTTT 59.423 50.000 2.25 0.00 46.30 2.66
2883 4943 5.623169 AGGTCATTTTACGACACCCTTTTA 58.377 37.500 0.00 0.00 34.97 1.52
2953 5013 2.622942 GTTCTTTCCATGCAAGACCACA 59.377 45.455 5.32 0.00 29.70 4.17
2954 5014 2.029918 GGTTCTTTCCATGCAAGACCAC 60.030 50.000 5.32 3.26 29.70 4.16
2965 5026 4.946160 ATGTCCCATTAGGTTCTTTCCA 57.054 40.909 0.00 0.00 36.75 3.53
2982 5043 6.813649 TGCTTGTTGACTCAGTAGATTATGTC 59.186 38.462 0.00 0.00 0.00 3.06
2987 5048 5.807520 CGTATGCTTGTTGACTCAGTAGATT 59.192 40.000 0.00 0.00 0.00 2.40
2988 5049 5.125578 TCGTATGCTTGTTGACTCAGTAGAT 59.874 40.000 0.00 0.00 0.00 1.98
2994 5055 4.314961 ACATTCGTATGCTTGTTGACTCA 58.685 39.130 1.46 0.00 35.03 3.41


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

AutoCloner maintained by Alex Coulton.