Multiple sequence alignment - TraesCS6B01G427100

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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 TraesCS6B01G427100 chr6B 100.000 3681 0 0 1 3681 695812508 695808828 0.000000e+00 6798
1 TraesCS6B01G427100 chr6B 83.518 2081 296 29 1148 3209 649055614 649053562 0.000000e+00 1899
2 TraesCS6B01G427100 chr6B 82.085 1295 169 30 1201 2483 649833051 649831808 0.000000e+00 1048
3 TraesCS6B01G427100 chr6B 88.000 100 11 1 7 105 649058323 649058224 2.320000e-22 117
4 TraesCS6B01G427100 chr6D 96.744 3685 92 5 1 3681 457258618 457254958 0.000000e+00 6115
5 TraesCS6B01G427100 chr6D 84.313 1855 253 24 1372 3209 430680038 430678205 0.000000e+00 1779
6 TraesCS6B01G427100 chr6D 82.819 745 113 9 409 1146 430681527 430680791 0.000000e+00 652
7 TraesCS6B01G427100 chr6D 87.500 264 28 5 88 349 430681782 430681522 2.150000e-77 300
8 TraesCS6B01G427100 chr6D 89.583 96 10 0 7 102 430682323 430682228 4.990000e-24 122
9 TraesCS6B01G427100 chr5A 95.920 3088 118 5 1 3081 531399374 531402460 0.000000e+00 4998
10 TraesCS6B01G427100 chr5A 95.795 547 19 3 3133 3676 531402461 531403006 0.000000e+00 880
11 TraesCS6B01G427100 chr6A 96.815 1413 42 1 1672 3081 604193422 604192010 0.000000e+00 2357
12 TraesCS6B01G427100 chr6A 95.923 1447 56 3 7 1451 604194867 604193422 0.000000e+00 2342
13 TraesCS6B01G427100 chr6A 84.719 2081 261 27 1148 3209 577704345 577702303 0.000000e+00 2028
14 TraesCS6B01G427100 chr6A 84.623 2081 263 27 1148 3209 577686782 577684740 0.000000e+00 2017
15 TraesCS6B01G427100 chr6A 84.342 2082 267 29 1148 3209 577658491 577656449 0.000000e+00 1984
16 TraesCS6B01G427100 chr6A 83.818 1996 266 25 1148 3123 577475568 577473610 0.000000e+00 1844
17 TraesCS6B01G427100 chr6A 95.100 551 22 4 3133 3680 604192009 604191461 0.000000e+00 863
18 TraesCS6B01G427100 chr6A 83.931 753 105 10 409 1155 577706012 577705270 0.000000e+00 706
19 TraesCS6B01G427100 chr6A 83.798 753 106 10 409 1155 577688449 577687707 0.000000e+00 701
20 TraesCS6B01G427100 chr6A 81.806 753 122 11 409 1155 577477236 577476493 5.220000e-173 617
21 TraesCS6B01G427100 chr6A 89.015 264 25 4 88 349 577477492 577477231 1.280000e-84 324
22 TraesCS6B01G427100 chr6A 89.015 264 25 4 88 349 577688705 577688444 1.280000e-84 324
23 TraesCS6B01G427100 chr6A 89.015 264 25 4 88 349 577706268 577706007 1.280000e-84 324
24 TraesCS6B01G427100 chrUn 84.131 397 56 7 687 1081 479721702 479721311 9.650000e-101 377
25 TraesCS6B01G427100 chr7D 83.586 396 54 7 296 685 484073891 484073501 9.720000e-96 361
26 TraesCS6B01G427100 chr7D 81.633 392 50 12 296 685 489312824 489312453 4.620000e-79 305
27 TraesCS6B01G427100 chr7D 85.202 223 31 2 686 907 535508705 535508926 1.030000e-55 228


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 TraesCS6B01G427100 chr6B 695808828 695812508 3680 True 6798.000000 6798 100.000000 1 3681 1 chr6B.!!$R2 3680
1 TraesCS6B01G427100 chr6B 649831808 649833051 1243 True 1048.000000 1048 82.085000 1201 2483 1 chr6B.!!$R1 1282
2 TraesCS6B01G427100 chr6B 649053562 649058323 4761 True 1008.000000 1899 85.759000 7 3209 2 chr6B.!!$R3 3202
3 TraesCS6B01G427100 chr6D 457254958 457258618 3660 True 6115.000000 6115 96.744000 1 3681 1 chr6D.!!$R1 3680
4 TraesCS6B01G427100 chr6D 430678205 430682323 4118 True 713.250000 1779 86.053750 7 3209 4 chr6D.!!$R2 3202
5 TraesCS6B01G427100 chr5A 531399374 531403006 3632 False 2939.000000 4998 95.857500 1 3676 2 chr5A.!!$F1 3675
6 TraesCS6B01G427100 chr6A 577656449 577658491 2042 True 1984.000000 1984 84.342000 1148 3209 1 chr6A.!!$R1 2061
7 TraesCS6B01G427100 chr6A 604191461 604194867 3406 True 1854.000000 2357 95.946000 7 3680 3 chr6A.!!$R5 3673
8 TraesCS6B01G427100 chr6A 577702303 577706268 3965 True 1019.333333 2028 85.888333 88 3209 3 chr6A.!!$R4 3121
9 TraesCS6B01G427100 chr6A 577684740 577688705 3965 True 1014.000000 2017 85.812000 88 3209 3 chr6A.!!$R3 3121
10 TraesCS6B01G427100 chr6A 577473610 577477492 3882 True 928.333333 1844 84.879667 88 3123 3 chr6A.!!$R2 3035

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
989 1457 0.616111 ATCCTCACGACCCTCAAGCT 60.616 55.000 0.0 0.0 0.0 3.74 F
1367 3039 3.412386 ACAGAGAAGGGGTTGAATTTCG 58.588 45.455 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 3735 1.470098 GATCCTGCGTGCTTCAACATT 59.530 47.619 0.0 0.0 0.00 2.71 R
2704 4406 3.033909 TCATCTCGGACTGAACATCCAT 58.966 45.455 0.0 0.0 35.83 3.41 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
23 24 1.218844 GGGCCCCATTGTTAGGTAGA 58.781 55.000 12.23 0.00 0.00 2.59
64 65 7.649306 GCCATGTGTATTGTTAAATCTTGGATC 59.351 37.037 0.00 0.00 0.00 3.36
382 844 2.100197 CAGACGGAGGGAGTATGACAA 58.900 52.381 0.00 0.00 33.08 3.18
384 846 2.695666 AGACGGAGGGAGTATGACAATG 59.304 50.000 0.00 0.00 0.00 2.82
605 1071 7.013846 AGAGGTGTGTAGTATAATCTTGAGCTC 59.986 40.741 6.82 6.82 0.00 4.09
651 1117 6.694411 GCTATGAGTGATTTGCAAATACCTTG 59.306 38.462 24.15 13.68 38.15 3.61
658 1124 6.762661 GTGATTTGCAAATACCTTGGCATTAT 59.237 34.615 24.15 0.00 35.38 1.28
762 1230 0.677288 CCGTCCAACCTACACAGACA 59.323 55.000 0.00 0.00 0.00 3.41
912 1380 9.309516 GAGAATATATGAGTTAAACGTCCACAA 57.690 33.333 0.00 0.00 0.00 3.33
989 1457 0.616111 ATCCTCACGACCCTCAAGCT 60.616 55.000 0.00 0.00 0.00 3.74
1277 2947 4.268884 GCTAGGTTGTCGATCTTGTGATTC 59.731 45.833 0.00 0.00 32.19 2.52
1367 3039 3.412386 ACAGAGAAGGGGTTGAATTTCG 58.588 45.455 0.00 0.00 0.00 3.46
1536 3210 5.848036 CCTTGATTTTGCATCGTCGATAATC 59.152 40.000 16.42 16.42 0.00 1.75
1879 3578 5.497464 TGACTACTGATTTTGATGGTCCA 57.503 39.130 0.00 0.00 0.00 4.02
2456 4158 1.571460 GCAGAACCTGTGCTTGTCG 59.429 57.895 0.00 0.00 37.96 4.35
2679 4381 6.385759 TCTGAGGGAAGCAAACCTTGTATATA 59.614 38.462 0.00 0.00 37.18 0.86
2704 4406 5.014202 GGACAAAGGGTAAGCCTTCAATTA 58.986 41.667 0.00 0.00 34.45 1.40
2868 4580 8.524870 AAAAATGTTGCATCACAATTCTCTAC 57.475 30.769 0.00 0.00 41.27 2.59
3334 5051 8.367156 ACAAACATTTAGTGCACCTAATTCAAT 58.633 29.630 14.63 0.00 35.59 2.57
3418 5135 6.813152 ACTTTCAATGCATTTTAATTCCCTCG 59.187 34.615 9.83 0.00 0.00 4.63
3461 5178 4.501071 ACAGGTGAACCACATATACGTTC 58.499 43.478 0.00 0.00 38.89 3.95
3477 5194 8.559536 CATATACGTTCCACTTGATTTATTGCT 58.440 33.333 0.00 0.00 0.00 3.91
3512 5229 3.623906 ATTGGAGGTCTCATGTCACTG 57.376 47.619 0.14 0.00 0.00 3.66
3677 5394 4.448210 GAGGTAGGTTTTCATTATCCGCA 58.552 43.478 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.664428 ACACATGGCTTATAAACCTTTGTT 57.336 33.333 6.47 0.82 35.82 2.83
235 697 7.221452 CACTCCATTGTTCTCAAAGAAACAAAG 59.779 37.037 4.94 1.38 35.75 2.77
384 846 8.856103 ACACACCAATAATATGGCTTTATTACC 58.144 33.333 0.00 0.00 44.75 2.85
399 861 7.333423 GCTCAAGATTGTAGTACACACCAATAA 59.667 37.037 1.43 0.00 36.69 1.40
403 865 4.283467 AGCTCAAGATTGTAGTACACACCA 59.717 41.667 1.43 0.00 36.69 4.17
762 1230 7.776107 TGTACTACTACTGTCGTACACTATCT 58.224 38.462 8.82 0.00 44.74 1.98
896 1364 3.064931 CTCCCTTGTGGACGTTTAACTC 58.935 50.000 0.00 0.00 38.61 3.01
912 1380 0.833834 CATAGTCATCGCCCCTCCCT 60.834 60.000 0.00 0.00 0.00 4.20
989 1457 2.751036 TCCGCATCACCGTCGGTA 60.751 61.111 18.38 6.32 43.35 4.02
1134 1602 5.187772 ACCTAATTCCTTGAAATTGGCCTTC 59.812 40.000 3.32 0.00 31.50 3.46
1367 3039 2.109425 AGACCTCCATACAAAACGGC 57.891 50.000 0.00 0.00 0.00 5.68
1465 3138 9.667107 AACAATTACGAGAATAATCCTTCAGAA 57.333 29.630 0.00 0.00 0.00 3.02
1482 3155 8.645487 GTTTTCTAGTAGGACTCAACAATTACG 58.355 37.037 0.00 0.00 0.00 3.18
1536 3210 3.138304 TCGACCACCTGACAAAAATCTG 58.862 45.455 0.00 0.00 0.00 2.90
1670 3366 8.480133 TCTTTAGGTTTGGGTAAAAGCATTAA 57.520 30.769 3.22 0.00 46.57 1.40
1704 3400 7.901283 ATTATGAACATTGAACCATCATGGA 57.099 32.000 11.90 0.00 40.96 3.41
1879 3578 2.159057 CCTTTTTGCTGACCTTTGTGCT 60.159 45.455 0.00 0.00 0.00 4.40
2036 3735 1.470098 GATCCTGCGTGCTTCAACATT 59.530 47.619 0.00 0.00 0.00 2.71
2456 4158 6.879458 ACCAATGAGTTGTAGGTGTTATTCTC 59.121 38.462 0.00 0.00 33.36 2.87
2679 4381 3.198784 AGGCTTACCCTTTGTCCCT 57.801 52.632 0.00 0.00 43.06 4.20
2704 4406 3.033909 TCATCTCGGACTGAACATCCAT 58.966 45.455 0.00 0.00 35.83 3.41
2868 4580 5.786264 ACTAGGTAATGGGTCGATTACAG 57.214 43.478 14.57 8.80 39.59 2.74
2999 4711 5.565439 GCACAGATTAAAGCAAACTGGACAT 60.565 40.000 0.00 0.00 40.42 3.06
3084 4797 7.870954 TCGGCTTACATAAACATGGTATCTTAG 59.129 37.037 0.00 0.00 0.00 2.18
3089 4802 5.925509 ACTCGGCTTACATAAACATGGTAT 58.074 37.500 0.00 0.00 0.00 2.73
3461 5178 8.902806 TGAAGGTTATAGCAATAAATCAAGTGG 58.097 33.333 0.00 0.00 29.41 4.00
3477 5194 6.011981 AGACCTCCAATTTGGTGAAGGTTATA 60.012 38.462 21.91 0.00 40.96 0.98
3512 5229 7.396540 AATCAAATCAAGGACCTAACATGAC 57.603 36.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.