Multiple sequence alignment - TraesCS6B01G216600

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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 TraesCS6B01G216600 chr6B 100.000 1620 0 0 612 2231 297475555 297477174 0.000000e+00 2992
1 TraesCS6B01G216600 chr6B 96.000 675 21 5 1559 2230 388024289 388023618 0.000000e+00 1092
2 TraesCS6B01G216600 chr6B 100.000 383 0 0 1 383 297474944 297475326 0.000000e+00 708
3 TraesCS6B01G216600 chr6B 97.382 382 8 1 1371 1750 388068249 388067868 0.000000e+00 649
4 TraesCS6B01G216600 chr6B 95.567 203 6 2 1554 1753 592197317 592197115 2.760000e-84 322
5 TraesCS6B01G216600 chr7A 98.608 934 12 1 612 1544 60281593 60282526 0.000000e+00 1652
6 TraesCS6B01G216600 chrUn 98.501 934 13 1 612 1544 186206141 186205208 0.000000e+00 1646
7 TraesCS6B01G216600 chrUn 97.586 497 10 1 1735 2231 229492413 229492907 0.000000e+00 850
8 TraesCS6B01G216600 chrUn 97.384 497 11 1 1735 2231 296250265 296249771 0.000000e+00 845
9 TraesCS6B01G216600 chrUn 96.867 383 12 0 1 383 434805443 434805825 1.870000e-180 641
10 TraesCS6B01G216600 chr7D 98.296 939 10 2 612 1544 382052359 382053297 0.000000e+00 1640
11 TraesCS6B01G216600 chr7D 97.128 383 11 0 1 383 382051952 382052334 0.000000e+00 647
12 TraesCS6B01G216600 chr7D 96.867 383 12 0 1 383 381925874 381926256 1.870000e-180 641
13 TraesCS6B01G216600 chr7D 96.867 383 12 0 1 383 381971897 381971515 1.870000e-180 641
14 TraesCS6B01G216600 chr7B 98.394 934 14 1 612 1544 742991726 742992659 0.000000e+00 1640
15 TraesCS6B01G216600 chr7B 98.180 934 16 1 612 1544 716876501 716875568 0.000000e+00 1629
16 TraesCS6B01G216600 chr7B 97.128 383 11 0 1 383 716836697 716836315 0.000000e+00 647
17 TraesCS6B01G216600 chr7B 96.867 383 12 0 1 383 742991318 742991700 1.870000e-180 641
18 TraesCS6B01G216600 chr5A 98.296 939 10 2 612 1544 19246563 19245625 0.000000e+00 1640
19 TraesCS6B01G216600 chr5A 97.128 383 11 0 1 383 19246970 19246588 0.000000e+00 647
20 TraesCS6B01G216600 chr1A 98.394 934 14 1 612 1544 498688947 498688014 0.000000e+00 1640
21 TraesCS6B01G216600 chr2B 98.289 935 14 2 612 1544 112843482 112844416 0.000000e+00 1637
22 TraesCS6B01G216600 chr2B 98.287 934 15 1 612 1544 391163289 391164222 0.000000e+00 1635
23 TraesCS6B01G216600 chr1B 96.889 675 17 3 1559 2231 471873007 471872335 0.000000e+00 1127
24 TraesCS6B01G216600 chr1B 96.889 675 16 4 1559 2231 135102477 135103148 0.000000e+00 1125
25 TraesCS6B01G216600 chr1B 96.047 683 23 3 1551 2231 135061433 135062113 0.000000e+00 1109
26 TraesCS6B01G216600 chr1B 95.900 683 24 3 1551 2231 135107052 135107732 0.000000e+00 1103
27 TraesCS6B01G216600 chr1B 97.389 383 7 2 1371 1750 135015885 135015503 0.000000e+00 649
28 TraesCS6B01G216600 chr4D 97.183 497 12 1 1735 2231 123441992 123441498 0.000000e+00 839
29 TraesCS6B01G216600 chr4D 96.867 383 12 0 1 383 123337344 123337726 1.870000e-180 641
30 TraesCS6B01G216600 chr5B 96.781 497 14 1 1735 2231 567250992 567251486 0.000000e+00 828
31 TraesCS6B01G216600 chr2D 96.850 381 12 0 3 383 39532900 39533280 2.420000e-179 638
32 TraesCS6B01G216600 chr3D 97.423 194 3 2 1559 1750 399710462 399710269 1.650000e-86 329


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 TraesCS6B01G216600 chr6B 297474944 297477174 2230 False 1850.0 2992 100.0000 1 2231 2 chr6B.!!$F1 2230
1 TraesCS6B01G216600 chr6B 388023618 388024289 671 True 1092.0 1092 96.0000 1559 2230 1 chr6B.!!$R1 671
2 TraesCS6B01G216600 chr7A 60281593 60282526 933 False 1652.0 1652 98.6080 612 1544 1 chr7A.!!$F1 932
3 TraesCS6B01G216600 chrUn 186205208 186206141 933 True 1646.0 1646 98.5010 612 1544 1 chrUn.!!$R1 932
4 TraesCS6B01G216600 chr7D 382051952 382053297 1345 False 1143.5 1640 97.7120 1 1544 2 chr7D.!!$F2 1543
5 TraesCS6B01G216600 chr7B 716875568 716876501 933 True 1629.0 1629 98.1800 612 1544 1 chr7B.!!$R2 932
6 TraesCS6B01G216600 chr7B 742991318 742992659 1341 False 1140.5 1640 97.6305 1 1544 2 chr7B.!!$F1 1543
7 TraesCS6B01G216600 chr5A 19245625 19246970 1345 True 1143.5 1640 97.7120 1 1544 2 chr5A.!!$R1 1543
8 TraesCS6B01G216600 chr1A 498688014 498688947 933 True 1640.0 1640 98.3940 612 1544 1 chr1A.!!$R1 932
9 TraesCS6B01G216600 chr2B 112843482 112844416 934 False 1637.0 1637 98.2890 612 1544 1 chr2B.!!$F1 932
10 TraesCS6B01G216600 chr2B 391163289 391164222 933 False 1635.0 1635 98.2870 612 1544 1 chr2B.!!$F2 932
11 TraesCS6B01G216600 chr1B 471872335 471873007 672 True 1127.0 1127 96.8890 1559 2231 1 chr1B.!!$R2 672
12 TraesCS6B01G216600 chr1B 135102477 135107732 5255 False 1114.0 1125 96.3945 1551 2231 2 chr1B.!!$F2 680
13 TraesCS6B01G216600 chr1B 135061433 135062113 680 False 1109.0 1109 96.0470 1551 2231 1 chr1B.!!$F1 680

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
678 679 0.033503 TGGAGTGATCCAGTAGCCGA 60.034 55.0 0.0 0.0 34.33 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1569 0.331278 TCAAATCGGGTTCCTGGCAT 59.669 50.0 0.0 0.0 0.0 4.4 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
39 40 2.230130 TCTCATTTGGGGCGGAAAAT 57.770 45.000 0.00 0.00 0.00 1.82
130 131 6.374333 CGAACCCTCCAATGAAGAAATAAGAA 59.626 38.462 0.00 0.00 0.00 2.52
131 132 7.468141 AACCCTCCAATGAAGAAATAAGAAC 57.532 36.000 0.00 0.00 0.00 3.01
198 199 4.041198 ACGGAGAAATAAAGAAGTGTGGGA 59.959 41.667 0.00 0.00 0.00 4.37
210 211 1.842920 TGTGGGAGAGAAGCAGCCA 60.843 57.895 0.00 0.00 0.00 4.75
298 299 4.343239 GGGGCTGATTGCAAAAGATATCTT 59.657 41.667 12.37 12.37 45.15 2.40
303 304 9.617975 GGCTGATTGCAAAAGATATCTTAATAC 57.382 33.333 18.23 9.08 45.15 1.89
678 679 0.033503 TGGAGTGATCCAGTAGCCGA 60.034 55.000 0.00 0.00 34.33 5.54
731 737 4.943705 CCACACTTGGCTCTACACATTTAT 59.056 41.667 0.00 0.00 35.56 1.40
806 812 0.319900 CGTTATCCCCATCTCAGCCG 60.320 60.000 0.00 0.00 0.00 5.52
852 858 1.413808 GGGGAGAGAGTGGAGCCTATT 60.414 57.143 0.00 0.00 0.00 1.73
1138 1144 7.414222 TTGTATAGTAAGTGATCCGAACCTT 57.586 36.000 0.00 0.00 0.00 3.50
1224 1230 0.961358 CGGTTCGGAGAGGACTCAGT 60.961 60.000 1.75 0.00 44.22 3.41
1239 1245 6.073314 AGGACTCAGTTGTTAGTTAGTACCA 58.927 40.000 0.00 0.00 0.00 3.25
1541 1548 3.031736 AGCGAGATAGGCTTTACTGGAA 58.968 45.455 0.00 0.00 37.50 3.53
1542 1549 3.643792 AGCGAGATAGGCTTTACTGGAAT 59.356 43.478 0.00 0.00 37.50 3.01
1544 1551 4.449405 GCGAGATAGGCTTTACTGGAATTC 59.551 45.833 0.00 0.00 0.00 2.17
1545 1552 4.681942 CGAGATAGGCTTTACTGGAATTCG 59.318 45.833 0.00 0.00 0.00 3.34
1546 1553 4.962155 AGATAGGCTTTACTGGAATTCGG 58.038 43.478 0.00 0.00 0.00 4.30
1547 1554 1.751437 AGGCTTTACTGGAATTCGGC 58.249 50.000 0.00 0.00 0.00 5.54
1548 1555 1.004277 AGGCTTTACTGGAATTCGGCA 59.996 47.619 0.00 0.00 0.00 5.69
1549 1556 1.401905 GGCTTTACTGGAATTCGGCAG 59.598 52.381 9.42 9.42 0.00 4.85
1552 1559 3.002759 GCTTTACTGGAATTCGGCAGATC 59.997 47.826 15.93 0.00 0.00 2.75
1557 1564 2.420022 CTGGAATTCGGCAGATCGTTTT 59.580 45.455 5.97 0.00 0.00 2.43
1609 1616 8.875604 TGGTGACACGAGGATTTTCAATCCTT 62.876 42.308 17.35 3.75 41.65 3.36
1910 6503 5.584551 AAGTTAGGTCATTCCTTTCTGGT 57.415 39.130 0.00 0.00 45.67 4.00
1958 6551 2.559705 CCCATAAGGCAAAGGGAAGGTT 60.560 50.000 0.00 0.00 44.30 3.50
2005 6598 6.040955 GGAGAGATTCCCACAGTTTTCTTTTT 59.959 38.462 0.00 0.00 40.37 1.94
2055 6648 4.771114 ATGAATATGGGGTTCGAAGTCA 57.229 40.909 0.00 0.00 0.00 3.41
2204 6798 2.422832 CACTTACTACTCAGGTCCGGTC 59.577 54.545 0.00 0.00 0.00 4.79
2205 6799 2.308275 ACTTACTACTCAGGTCCGGTCT 59.692 50.000 0.00 0.00 0.00 3.85
2216 6810 7.284074 ACTCAGGTCCGGTCTATATATATCTG 58.716 42.308 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 1.582968 CATTGGCGCTTTGCTCTGT 59.417 52.632 7.64 0.0 45.43 3.41
131 132 1.153901 CCATTGGCGCTTTGCTCTG 60.154 57.895 7.64 0.0 45.43 3.35
198 199 0.619505 ATGAGCTTGGCTGCTTCTCT 59.380 50.000 0.00 0.0 44.17 3.10
210 211 3.965888 AAGCGAAGGGAATGAGCTT 57.034 47.368 0.00 0.0 42.51 3.74
678 679 1.275421 GGCACTTCTAGGCCCCTTCT 61.275 60.000 0.00 0.0 44.53 2.85
731 737 1.361543 ACTGGACAGGGGTAAGCTCTA 59.638 52.381 4.14 0.0 0.00 2.43
1114 1120 7.414222 AAGGTTCGGATCACTTACTATACAA 57.586 36.000 0.00 0.0 0.00 2.41
1239 1245 2.079911 TCCACCCCGAAACCAAGGT 61.080 57.895 0.00 0.0 0.00 3.50
1557 1564 1.281419 TCGGGTTCCTGGCATAGAAA 58.719 50.000 2.06 0.0 0.00 2.52
1562 1569 0.331278 TCAAATCGGGTTCCTGGCAT 59.669 50.000 0.00 0.0 0.00 4.40
1574 1581 2.131972 TCGTGTCACCAGTTCAAATCG 58.868 47.619 0.00 0.0 0.00 3.34
1910 6503 7.287927 ACCCTCGATCATACTCTTTTCTGATAA 59.712 37.037 0.00 0.0 0.00 1.75
1958 6551 0.842635 GGGTAGTAGGTCGAGGGAGA 59.157 60.000 0.00 0.0 0.00 3.71
1964 6557 0.467384 CTCCGAGGGTAGTAGGTCGA 59.533 60.000 0.00 0.0 34.28 4.20
2055 6648 5.181433 GCGAATGAGAAAGGTTCTTTTAGGT 59.819 40.000 0.00 0.0 40.87 3.08


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

AutoCloner maintained by Alex Coulton.