Multiple sequence alignment - TraesCS6B01G418900

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 TraesCS6B01G418900 chr6B 100.000 2602 0 0 1 2602 690893454 690896055 0.000000e+00 4806
1 TraesCS6B01G418900 chr6B 94.476 525 20 7 2084 2602 695494793 695495314 0.000000e+00 800
2 TraesCS6B01G418900 chr6B 78.360 744 134 21 873 1602 690047638 690046908 8.490000e-125 457
3 TraesCS6B01G418900 chr6A 94.882 1778 67 11 320 2088 600565714 600567476 0.000000e+00 2758
4 TraesCS6B01G418900 chr6A 79.739 765 130 19 869 1623 600376485 600375736 4.930000e-147 531
5 TraesCS6B01G418900 chr6A 92.918 353 23 2 1 352 600565352 600565703 1.790000e-141 512
6 TraesCS6B01G418900 chr6A 85.227 264 35 2 1390 1649 600565236 600565499 4.270000e-68 268
7 TraesCS6B01G418900 chr6D 91.859 1474 97 13 609 2073 454404454 454405913 0.000000e+00 2036
8 TraesCS6B01G418900 chr6D 78.312 770 134 21 869 1623 454017183 454016432 1.410000e-127 466
9 TraesCS6B01G418900 chr3B 81.533 1083 145 30 583 1653 160676557 160677596 0.000000e+00 841
10 TraesCS6B01G418900 chrUn 95.127 513 22 3 2089 2600 215043228 215042718 0.000000e+00 806
11 TraesCS6B01G418900 chrUn 95.127 513 22 3 2089 2600 268445429 268445939 0.000000e+00 806
12 TraesCS6B01G418900 chr1B 94.961 516 19 5 2089 2602 123974225 123974735 0.000000e+00 802
13 TraesCS6B01G418900 chr1B 94.231 520 25 5 2085 2602 497982592 497983108 0.000000e+00 789
14 TraesCS6B01G418900 chr7A 94.434 521 24 4 2083 2601 34304925 34304408 0.000000e+00 797
15 TraesCS6B01G418900 chr5A 94.747 514 23 3 2089 2600 617245074 617245585 0.000000e+00 797
16 TraesCS6B01G418900 chr4A 94.253 522 26 3 2082 2601 507568662 507568143 0.000000e+00 795
17 TraesCS6B01G418900 chr4A 94.574 516 25 3 2089 2602 703254170 703254684 0.000000e+00 795
18 TraesCS6B01G418900 chr3A 79.267 1119 178 27 544 1653 121216851 121215778 0.000000e+00 732
19 TraesCS6B01G418900 chr3A 79.478 575 83 19 544 1114 121248991 121248448 2.440000e-100 375


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 TraesCS6B01G418900 chr6B 690893454 690896055 2601 False 4806.000000 4806 100.000 1 2602 1 chr6B.!!$F1 2601
1 TraesCS6B01G418900 chr6B 695494793 695495314 521 False 800.000000 800 94.476 2084 2602 1 chr6B.!!$F2 518
2 TraesCS6B01G418900 chr6B 690046908 690047638 730 True 457.000000 457 78.360 873 1602 1 chr6B.!!$R1 729
3 TraesCS6B01G418900 chr6A 600565236 600567476 2240 False 1179.333333 2758 91.009 1 2088 3 chr6A.!!$F1 2087
4 TraesCS6B01G418900 chr6A 600375736 600376485 749 True 531.000000 531 79.739 869 1623 1 chr6A.!!$R1 754
5 TraesCS6B01G418900 chr6D 454404454 454405913 1459 False 2036.000000 2036 91.859 609 2073 1 chr6D.!!$F1 1464
6 TraesCS6B01G418900 chr6D 454016432 454017183 751 True 466.000000 466 78.312 869 1623 1 chr6D.!!$R1 754
7 TraesCS6B01G418900 chr3B 160676557 160677596 1039 False 841.000000 841 81.533 583 1653 1 chr3B.!!$F1 1070
8 TraesCS6B01G418900 chrUn 215042718 215043228 510 True 806.000000 806 95.127 2089 2600 1 chrUn.!!$R1 511
9 TraesCS6B01G418900 chrUn 268445429 268445939 510 False 806.000000 806 95.127 2089 2600 1 chrUn.!!$F1 511
10 TraesCS6B01G418900 chr1B 123974225 123974735 510 False 802.000000 802 94.961 2089 2602 1 chr1B.!!$F1 513
11 TraesCS6B01G418900 chr1B 497982592 497983108 516 False 789.000000 789 94.231 2085 2602 1 chr1B.!!$F2 517
12 TraesCS6B01G418900 chr7A 34304408 34304925 517 True 797.000000 797 94.434 2083 2601 1 chr7A.!!$R1 518
13 TraesCS6B01G418900 chr5A 617245074 617245585 511 False 797.000000 797 94.747 2089 2600 1 chr5A.!!$F1 511
14 TraesCS6B01G418900 chr4A 507568143 507568662 519 True 795.000000 795 94.253 2082 2601 1 chr4A.!!$R1 519
15 TraesCS6B01G418900 chr4A 703254170 703254684 514 False 795.000000 795 94.574 2089 2602 1 chr4A.!!$F1 513
16 TraesCS6B01G418900 chr3A 121215778 121216851 1073 True 732.000000 732 79.267 544 1653 1 chr3A.!!$R1 1109
17 TraesCS6B01G418900 chr3A 121248448 121248991 543 True 375.000000 375 79.478 544 1114 1 chr3A.!!$R2 570

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
613 776 0.321671 ATGTGGCTTGCGTGTAGACT 59.678 50.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2362 1.367599 TTCGTGCGTCCGTGGTTTTT 61.368 50.0 0.0 0.0 0.0 1.94 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
33 150 4.037923 CACAAATGGTGTAGAGGCAAGTTT 59.962 41.667 0.00 0.00 42.75 2.66
34 151 4.649218 ACAAATGGTGTAGAGGCAAGTTTT 59.351 37.500 0.00 0.00 39.29 2.43
132 249 9.691362 TGAGCTATAAAATTTGAAAAAGTGGTC 57.309 29.630 0.00 0.00 0.00 4.02
151 268 6.071952 AGTGGTCTATAAAATTTGTGTGCCTG 60.072 38.462 0.00 0.00 0.00 4.85
200 317 7.047891 TGTATTAATTGTAAGGTGCCTCTCTG 58.952 38.462 0.00 0.00 0.00 3.35
237 354 7.272084 CACATCGAATTGATTTTCTTGAGAACC 59.728 37.037 0.00 0.00 34.13 3.62
251 368 5.848369 TCTTGAGAACCCATCTATCCATCAT 59.152 40.000 0.00 0.00 38.96 2.45
252 369 5.752036 TGAGAACCCATCTATCCATCATC 57.248 43.478 0.00 0.00 38.96 2.92
257 374 5.495926 ACCCATCTATCCATCATCTGAAC 57.504 43.478 0.00 0.00 0.00 3.18
258 375 4.288105 ACCCATCTATCCATCATCTGAACC 59.712 45.833 0.00 0.00 0.00 3.62
276 394 4.104102 TGAACCAAATCTACAGACACCCTT 59.896 41.667 0.00 0.00 0.00 3.95
287 405 2.270352 GACACCCTTGTCCACATGAA 57.730 50.000 0.00 0.00 45.77 2.57
321 439 4.107072 TGGTCCTCTCAATGGAAATCTCT 58.893 43.478 0.00 0.00 35.10 3.10
323 441 4.880696 GGTCCTCTCAATGGAAATCTCTTG 59.119 45.833 0.00 0.00 35.10 3.02
363 524 5.915758 GTGTCTGGTTAGTCGATGATGATAC 59.084 44.000 0.00 0.00 0.00 2.24
365 526 5.009710 GTCTGGTTAGTCGATGATGATACCA 59.990 44.000 0.00 0.00 33.69 3.25
371 532 9.517609 GGTTAGTCGATGATGATACCATAATAC 57.482 37.037 0.00 0.00 32.09 1.89
375 536 7.122204 AGTCGATGATGATACCATAATACCGAA 59.878 37.037 0.00 0.00 32.09 4.30
383 544 1.354368 CCATAATACCGAATGGGCCCT 59.646 52.381 25.70 2.15 39.23 5.19
418 579 3.316308 CCATTGTCGGATGAGAAAATCCC 59.684 47.826 0.00 0.00 42.86 3.85
419 580 2.309528 TGTCGGATGAGAAAATCCCG 57.690 50.000 0.00 0.00 42.86 5.14
420 581 1.828595 TGTCGGATGAGAAAATCCCGA 59.171 47.619 0.00 0.00 42.86 5.14
451 612 5.636121 TGATTTTCTTCATGACATGCTTTGC 59.364 36.000 10.76 0.00 0.00 3.68
482 643 6.528423 CACTAGAAGTATGTGTCACTAGTTGC 59.472 42.308 4.27 0.00 38.54 4.17
484 645 5.473931 AGAAGTATGTGTCACTAGTTGCTG 58.526 41.667 4.27 0.00 0.00 4.41
497 658 2.440409 AGTTGCTGGTGATGTGGATTC 58.560 47.619 0.00 0.00 0.00 2.52
515 676 9.465199 TGTGGATTCAGATAAAGATTTCATTGA 57.535 29.630 0.00 0.00 0.00 2.57
570 733 9.494271 TGTAAATTTTGTGCTTGGCAAATATTA 57.506 25.926 0.00 0.00 41.47 0.98
613 776 0.321671 ATGTGGCTTGCGTGTAGACT 59.678 50.000 0.00 0.00 0.00 3.24
629 792 6.806739 CGTGTAGACTGTGAATAAGAATGACA 59.193 38.462 0.00 0.00 0.00 3.58
801 965 8.589701 ATGTGCATTTCCATGTATATGATCAT 57.410 30.769 13.81 13.81 36.36 2.45
808 972 9.763837 ATTTCCATGTATATGATCATTGATGGT 57.236 29.630 14.65 2.97 36.36 3.55
1071 1257 1.136252 CACCAAGATCAACAACTCGCG 60.136 52.381 0.00 0.00 0.00 5.87
1139 1325 4.081087 TGCTTATGTCCTTGGTCTTACTCC 60.081 45.833 0.00 0.00 0.00 3.85
1484 1679 9.531158 GGGTTCTAACTAGCTAAGATAGGATTA 57.469 37.037 0.00 0.00 32.74 1.75
1592 1787 8.028938 TGAATTTAGCCTTGCTTCTTGAATTAC 58.971 33.333 0.00 0.00 40.44 1.89
1870 2071 1.369625 GTTTCCGCATCCGAACTGAT 58.630 50.000 0.00 0.00 36.29 2.90
1972 2175 8.970691 AATGATTTTTACAAGTGTGCTCATAC 57.029 30.769 0.00 0.00 0.00 2.39
1973 2176 7.503521 TGATTTTTACAAGTGTGCTCATACA 57.496 32.000 0.00 0.00 0.00 2.29
2032 2235 4.249661 GCTCTGACTTTCTCCCAACTTAG 58.750 47.826 0.00 0.00 0.00 2.18
2051 2254 8.402472 CAACTTAGAAAACCTATGTGTGTGAAA 58.598 33.333 0.00 0.00 36.31 2.69
2052 2255 8.691661 ACTTAGAAAACCTATGTGTGTGAAAT 57.308 30.769 0.00 0.00 35.27 2.17
2081 2284 4.696479 ACCTTCTCTGTCTTTCACACAT 57.304 40.909 0.00 0.00 0.00 3.21
2120 2326 7.464830 AATAACGAGAATAAATGAGACACGG 57.535 36.000 0.00 0.00 0.00 4.94
2196 2402 2.039480 AGGCGCAATCACTATGATGGAT 59.961 45.455 10.83 0.00 37.15 3.41
2216 2422 5.069119 TGGATGAGTATTACAAGCACGAGAT 59.931 40.000 0.00 0.00 0.00 2.75
2261 2468 4.728090 ACATGGGGTATATATGAGGGGA 57.272 45.455 0.00 0.00 0.00 4.81
2419 2629 3.273084 ACCTTGATCCAAATTCCCTCCAT 59.727 43.478 0.00 0.00 0.00 3.41
2455 2665 6.725364 AGTGAATAACTCCATCCAAATCAGT 58.275 36.000 0.00 0.00 31.64 3.41
2510 2720 7.769044 GGACTAATGAGAAATACCAACTAAGCA 59.231 37.037 0.00 0.00 0.00 3.91
2554 2764 2.206576 AGGAACTGGCTTTGTCATCC 57.793 50.000 0.00 0.00 37.18 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 167 8.762645 AGACTAAATTCACCACTCTTCATATGA 58.237 33.333 0.00 0.00 0.00 2.15
51 168 8.954950 AGACTAAATTCACCACTCTTCATATG 57.045 34.615 0.00 0.00 0.00 1.78
124 241 7.015195 AGGCACACAAATTTTATAGACCACTTT 59.985 33.333 0.00 0.00 0.00 2.66
128 245 6.007076 TCAGGCACACAAATTTTATAGACCA 58.993 36.000 0.00 0.00 0.00 4.02
200 317 0.955428 TTCGATGTGAGGTTGCAGGC 60.955 55.000 0.00 0.00 0.00 4.85
237 354 5.494390 TGGTTCAGATGATGGATAGATGG 57.506 43.478 0.00 0.00 0.00 3.51
251 368 4.262894 GGGTGTCTGTAGATTTGGTTCAGA 60.263 45.833 0.00 0.00 33.60 3.27
252 369 4.003648 GGGTGTCTGTAGATTTGGTTCAG 58.996 47.826 0.00 0.00 0.00 3.02
257 374 4.021102 ACAAGGGTGTCTGTAGATTTGG 57.979 45.455 0.00 0.00 29.49 3.28
276 394 3.270027 GGTTCGATCATTCATGTGGACA 58.730 45.455 0.00 0.00 0.00 4.02
287 405 2.366916 GAGAGGACCATGGTTCGATCAT 59.633 50.000 20.85 2.57 0.00 2.45
343 504 5.453567 TGGTATCATCATCGACTAACCAG 57.546 43.478 0.00 0.00 32.26 4.00
363 524 1.354368 AGGGCCCATTCGGTATTATGG 59.646 52.381 27.56 0.00 40.82 2.74
365 526 2.305927 CTCAGGGCCCATTCGGTATTAT 59.694 50.000 27.56 0.00 0.00 1.28
371 532 1.048724 TACTCTCAGGGCCCATTCGG 61.049 60.000 27.56 13.47 0.00 4.30
375 536 1.507300 AGAGATACTCTCAGGGCCCAT 59.493 52.381 27.56 6.34 45.73 4.00
407 568 5.429681 TCAAACCTATCGGGATTTTCTCA 57.570 39.130 0.00 0.00 38.76 3.27
418 579 7.751732 TGTCATGAAGAAAATCAAACCTATCG 58.248 34.615 0.00 0.00 32.06 2.92
419 580 9.512435 CATGTCATGAAGAAAATCAAACCTATC 57.488 33.333 7.04 0.00 32.06 2.08
420 581 7.977853 GCATGTCATGAAGAAAATCAAACCTAT 59.022 33.333 17.24 0.00 32.06 2.57
451 612 6.037098 GTGACACATACTTCTAGTGCCTTAG 58.963 44.000 0.00 0.00 36.76 2.18
482 643 6.351711 TCTTTATCTGAATCCACATCACCAG 58.648 40.000 0.00 0.00 0.00 4.00
484 645 7.814264 AATCTTTATCTGAATCCACATCACC 57.186 36.000 0.00 0.00 0.00 4.02
613 776 9.695526 CAAAGGAAAATGTCATTCTTATTCACA 57.304 29.630 0.00 0.00 27.74 3.58
629 792 5.010012 CACACTAGGAACTGCAAAGGAAAAT 59.990 40.000 0.00 0.00 41.52 1.82
801 965 3.448301 GGATGAGCATTCCAAACCATCAA 59.552 43.478 0.00 0.00 33.92 2.57
808 972 4.538738 TGATCATGGATGAGCATTCCAAA 58.461 39.130 3.46 0.03 46.92 3.28
1071 1257 1.282875 GGTCGTTTGTGCTGAAGGC 59.717 57.895 0.00 0.00 42.22 4.35
1139 1325 4.333913 AATGACTACCTGATGCTAGCAG 57.666 45.455 23.89 11.79 0.00 4.24
1529 1724 5.774690 TGGCTCATATGAGTGAAAAACCTTT 59.225 36.000 28.92 0.00 43.85 3.11
1630 1826 5.882557 AGTCAAGCACCCACATTTTATAGAG 59.117 40.000 0.00 0.00 0.00 2.43
1838 2037 4.451629 TGCGGAAACCAAGTAACAAAAA 57.548 36.364 0.00 0.00 0.00 1.94
1839 2038 4.500035 GGATGCGGAAACCAAGTAACAAAA 60.500 41.667 0.00 0.00 0.00 2.44
1840 2039 3.004944 GGATGCGGAAACCAAGTAACAAA 59.995 43.478 0.00 0.00 0.00 2.83
1994 2197 7.986085 AGTCAGAGCAGTACAAACATTAAAT 57.014 32.000 0.00 0.00 0.00 1.40
2032 2235 7.875971 AGAGAATTTCACACACATAGGTTTTC 58.124 34.615 0.00 0.00 0.00 2.29
2051 2254 7.875554 GTGAAAGACAGAGAAGGTTTAGAGAAT 59.124 37.037 0.00 0.00 0.00 2.40
2052 2255 7.147724 TGTGAAAGACAGAGAAGGTTTAGAGAA 60.148 37.037 0.00 0.00 0.00 2.87
2118 2324 3.063452 CACGTAAAAATCCATGTCTCCCG 59.937 47.826 0.00 0.00 0.00 5.14
2119 2325 3.377172 CCACGTAAAAATCCATGTCTCCC 59.623 47.826 0.00 0.00 0.00 4.30
2120 2326 4.258543 TCCACGTAAAAATCCATGTCTCC 58.741 43.478 0.00 0.00 0.00 3.71
2156 2362 1.367599 TTCGTGCGTCCGTGGTTTTT 61.368 50.000 0.00 0.00 0.00 1.94
2196 2402 5.105917 TGTCATCTCGTGCTTGTAATACTCA 60.106 40.000 0.00 0.00 0.00 3.41
2261 2468 6.681729 TCCTACAAGGACTCTTATGTGTTT 57.318 37.500 0.00 0.00 40.06 2.83
2419 2629 7.663827 TGGAGTTATTCACTTTCTTCGACTAA 58.336 34.615 0.00 0.00 35.01 2.24
2455 2665 4.817464 ACTTTGACGCACAAGGTGTTTATA 59.183 37.500 9.20 0.00 44.90 0.98
2532 2742 4.018050 AGGATGACAAAGCCAGTTCCTATT 60.018 41.667 0.00 0.00 30.52 1.73
2533 2743 3.525199 AGGATGACAAAGCCAGTTCCTAT 59.475 43.478 0.00 0.00 30.52 2.57
2535 2745 1.707427 AGGATGACAAAGCCAGTTCCT 59.293 47.619 0.00 0.00 0.00 3.36
2554 2764 8.065473 AGTACTCATGATAATCCTGCTGATAG 57.935 38.462 0.00 0.00 31.83 2.08


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

AutoCloner maintained by Alex Coulton.