Multiple sequence alignment - TraesCS6A01G169800

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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 TraesCS6A01G169800 chr6A 100.000 2192 0 0 1 2192 179186875 179189066 0.000000e+00 4048.0
1 TraesCS6A01G169800 chr6A 97.218 683 18 1 1511 2192 179198386 179199068 0.000000e+00 1155.0
2 TraesCS6A01G169800 chr7B 90.466 1458 125 8 46 1489 474552787 474554244 0.000000e+00 1910.0
3 TraesCS6A01G169800 chr7B 97.072 683 19 1 1511 2192 382005045 382004363 0.000000e+00 1149.0
4 TraesCS6A01G169800 chr7B 96.476 681 21 1 1511 2191 539634591 539635268 0.000000e+00 1122.0
5 TraesCS6A01G169800 chr2A 88.948 1502 124 11 1 1489 113096177 113094705 0.000000e+00 1816.0
6 TraesCS6A01G169800 chr2A 96.774 682 19 2 1511 2192 154040841 154041519 0.000000e+00 1134.0
7 TraesCS6A01G169800 chr2A 96.334 682 22 2 1511 2192 154028408 154029086 0.000000e+00 1118.0
8 TraesCS6A01G169800 chr2A 92.676 710 45 3 1 710 260836687 260837389 0.000000e+00 1016.0
9 TraesCS6A01G169800 chr2A 87.788 737 75 7 766 1488 475921710 475920975 0.000000e+00 848.0
10 TraesCS6A01G169800 chr2A 96.275 510 19 0 88 597 475922598 475922089 0.000000e+00 837.0
11 TraesCS6A01G169800 chr5A 88.235 1411 113 18 83 1488 310424976 310426338 0.000000e+00 1637.0
12 TraesCS6A01G169800 chr5A 88.148 1409 104 31 86 1488 199299430 199298079 0.000000e+00 1618.0
13 TraesCS6A01G169800 chr4B 87.544 1413 136 23 83 1488 279024295 279025674 0.000000e+00 1598.0
14 TraesCS6A01G169800 chr4B 85.897 78 9 2 1411 1487 149037148 149037224 5.020000e-12 82.4
15 TraesCS6A01G169800 chr2B 87.553 1414 135 19 83 1490 303246111 303247489 0.000000e+00 1598.0
16 TraesCS6A01G169800 chr5B 96.921 682 21 0 1511 2192 119310358 119311039 0.000000e+00 1144.0
17 TraesCS6A01G169800 chr5B 96.041 682 24 1 1511 2192 115794865 115794187 0.000000e+00 1107.0
18 TraesCS6A01G169800 chr3D 89.043 940 55 22 83 1017 306830653 306831549 0.000000e+00 1122.0
19 TraesCS6A01G169800 chr1A 96.064 686 23 2 1507 2192 332933556 332934237 0.000000e+00 1114.0
20 TraesCS6A01G169800 chr6D 94.685 715 38 0 1 715 259462374 259463088 0.000000e+00 1110.0
21 TraesCS6A01G169800 chr6D 94.406 715 40 0 1 715 259464796 259465510 0.000000e+00 1099.0
22 TraesCS6A01G169800 chr6D 91.217 649 56 1 841 1488 259465499 259466147 0.000000e+00 881.0
23 TraesCS6A01G169800 chr6D 90.431 627 59 1 841 1466 259463077 259463703 0.000000e+00 824.0
24 TraesCS6A01G169800 chr4D 94.818 714 33 1 1 710 126518396 126517683 0.000000e+00 1110.0
25 TraesCS6A01G169800 chr3A 95.773 686 29 0 1507 2192 233404980 233405665 0.000000e+00 1107.0
26 TraesCS6A01G169800 chr7A 86.898 748 76 12 764 1496 308449771 308449031 0.000000e+00 819.0
27 TraesCS6A01G169800 chr6B 84.076 314 35 9 454 766 169138817 169138518 2.750000e-74 289.0


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 TraesCS6A01G169800 chr6A 179186875 179189066 2191 False 4048.0 4048 100.00000 1 2192 1 chr6A.!!$F1 2191
1 TraesCS6A01G169800 chr6A 179198386 179199068 682 False 1155.0 1155 97.21800 1511 2192 1 chr6A.!!$F2 681
2 TraesCS6A01G169800 chr7B 474552787 474554244 1457 False 1910.0 1910 90.46600 46 1489 1 chr7B.!!$F1 1443
3 TraesCS6A01G169800 chr7B 382004363 382005045 682 True 1149.0 1149 97.07200 1511 2192 1 chr7B.!!$R1 681
4 TraesCS6A01G169800 chr7B 539634591 539635268 677 False 1122.0 1122 96.47600 1511 2191 1 chr7B.!!$F2 680
5 TraesCS6A01G169800 chr2A 113094705 113096177 1472 True 1816.0 1816 88.94800 1 1489 1 chr2A.!!$R1 1488
6 TraesCS6A01G169800 chr2A 154040841 154041519 678 False 1134.0 1134 96.77400 1511 2192 1 chr2A.!!$F2 681
7 TraesCS6A01G169800 chr2A 154028408 154029086 678 False 1118.0 1118 96.33400 1511 2192 1 chr2A.!!$F1 681
8 TraesCS6A01G169800 chr2A 260836687 260837389 702 False 1016.0 1016 92.67600 1 710 1 chr2A.!!$F3 709
9 TraesCS6A01G169800 chr2A 475920975 475922598 1623 True 842.5 848 92.03150 88 1488 2 chr2A.!!$R2 1400
10 TraesCS6A01G169800 chr5A 310424976 310426338 1362 False 1637.0 1637 88.23500 83 1488 1 chr5A.!!$F1 1405
11 TraesCS6A01G169800 chr5A 199298079 199299430 1351 True 1618.0 1618 88.14800 86 1488 1 chr5A.!!$R1 1402
12 TraesCS6A01G169800 chr4B 279024295 279025674 1379 False 1598.0 1598 87.54400 83 1488 1 chr4B.!!$F2 1405
13 TraesCS6A01G169800 chr2B 303246111 303247489 1378 False 1598.0 1598 87.55300 83 1490 1 chr2B.!!$F1 1407
14 TraesCS6A01G169800 chr5B 119310358 119311039 681 False 1144.0 1144 96.92100 1511 2192 1 chr5B.!!$F1 681
15 TraesCS6A01G169800 chr5B 115794187 115794865 678 True 1107.0 1107 96.04100 1511 2192 1 chr5B.!!$R1 681
16 TraesCS6A01G169800 chr3D 306830653 306831549 896 False 1122.0 1122 89.04300 83 1017 1 chr3D.!!$F1 934
17 TraesCS6A01G169800 chr1A 332933556 332934237 681 False 1114.0 1114 96.06400 1507 2192 1 chr1A.!!$F1 685
18 TraesCS6A01G169800 chr6D 259462374 259466147 3773 False 978.5 1110 92.68475 1 1488 4 chr6D.!!$F1 1487
19 TraesCS6A01G169800 chr4D 126517683 126518396 713 True 1110.0 1110 94.81800 1 710 1 chr4D.!!$R1 709
20 TraesCS6A01G169800 chr3A 233404980 233405665 685 False 1107.0 1107 95.77300 1507 2192 1 chr3A.!!$F1 685
21 TraesCS6A01G169800 chr7A 308449031 308449771 740 True 819.0 819 86.89800 764 1496 1 chr7A.!!$R1 732

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
927 1199 0.547712 CCTCCTTCCCTCCTTGTCCA 60.548 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 4730 2.552315 CAGTGCAAAAGGTGACCGTTAT 59.448 45.455 2.6 0.0 0.0 1.89 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
27 28 5.508200 TTACTTGTTTTTGAACGGAGCAT 57.492 34.783 0.00 0.00 0.00 3.79
73 74 1.069358 CTTAATGTCCGAGGAGGCCTC 59.931 57.143 25.59 25.59 46.44 4.70
349 370 5.419542 CGATGATGTTTTAGTCCTTCTGGA 58.580 41.667 0.00 0.00 40.69 3.86
391 416 5.277825 TGTAACAAAAATCGCTCTTTGGTG 58.722 37.500 4.39 0.00 36.94 4.17
470 495 7.936847 GTCTTCCTCTCTTCTATGTCAGATCTA 59.063 40.741 0.00 0.00 31.77 1.98
488 513 7.870954 TCAGATCTACACACGTCAAGTTTAAAT 59.129 33.333 0.00 0.00 0.00 1.40
554 579 3.774842 AGAGGGAGAGAAAGAGTGGAT 57.225 47.619 0.00 0.00 0.00 3.41
655 680 3.496160 CAGCCATGGGAGGAGGGG 61.496 72.222 15.13 0.00 0.00 4.79
693 718 3.636231 CCTTCCCACACCGCCTGA 61.636 66.667 0.00 0.00 0.00 3.86
701 726 1.913262 ACACCGCCTGATCACCTCA 60.913 57.895 0.00 0.00 0.00 3.86
740 779 2.936032 GGGGTGGAGGCAGAGGTT 60.936 66.667 0.00 0.00 0.00 3.50
794 1053 3.749064 GCAGAGGAGGCGACGACA 61.749 66.667 2.19 0.00 0.00 4.35
809 1068 3.114647 GACACGGTGGCGCAACAAA 62.115 57.895 18.47 0.00 0.00 2.83
892 1164 2.597217 TTCCCCGCTGTTGCTTGG 60.597 61.111 0.00 0.00 36.97 3.61
901 1173 1.580845 CTGTTGCTTGGCTTCCTCGG 61.581 60.000 0.00 0.00 0.00 4.63
919 1191 3.157949 CGGCCTCCTCCTTCCCTC 61.158 72.222 0.00 0.00 0.00 4.30
920 1192 2.770475 GGCCTCCTCCTTCCCTCC 60.770 72.222 0.00 0.00 0.00 4.30
922 1194 1.307430 GCCTCCTCCTTCCCTCCTT 60.307 63.158 0.00 0.00 0.00 3.36
927 1199 0.547712 CCTCCTTCCCTCCTTGTCCA 60.548 60.000 0.00 0.00 0.00 4.02
970 3664 3.307906 ACCCGCACCGTGAAGCTA 61.308 61.111 1.65 0.00 0.00 3.32
988 3682 1.607628 CTAACCTACGTCCGATCTGGG 59.392 57.143 0.00 0.00 38.76 4.45
1017 3711 0.908198 ACATGGAAGAGGACAGGAGC 59.092 55.000 0.00 0.00 0.00 4.70
1025 3719 3.071206 GGACAGGAGCAGGCGAGA 61.071 66.667 0.00 0.00 0.00 4.04
1248 3942 3.256960 AGGTGATTGGGTGCGGGT 61.257 61.111 0.00 0.00 0.00 5.28
1347 4041 4.285807 CAGTCATTGGACAACGAAAACA 57.714 40.909 0.00 0.00 46.80 2.83
1396 4091 0.617935 TGCGAAGATCCATGGTCCAA 59.382 50.000 12.58 0.00 0.00 3.53
1403 4098 2.172505 AGATCCATGGTCCAAACGCATA 59.827 45.455 12.58 0.00 0.00 3.14
1437 4134 0.818040 ACAGCCAACGAAGGACCAAC 60.818 55.000 0.00 0.00 0.00 3.77
1490 4187 6.697019 CCAGCCTCATTATTGGTTTAAATTCG 59.303 38.462 0.00 0.00 0.00 3.34
1491 4188 7.257722 CAGCCTCATTATTGGTTTAAATTCGT 58.742 34.615 0.00 0.00 0.00 3.85
1492 4189 7.220683 CAGCCTCATTATTGGTTTAAATTCGTG 59.779 37.037 0.00 0.00 0.00 4.35
1493 4190 7.122055 AGCCTCATTATTGGTTTAAATTCGTGA 59.878 33.333 0.00 0.00 0.00 4.35
1494 4191 7.757624 GCCTCATTATTGGTTTAAATTCGTGAA 59.242 33.333 0.00 0.00 0.00 3.18
1495 4192 9.801873 CCTCATTATTGGTTTAAATTCGTGAAT 57.198 29.630 0.00 0.00 0.00 2.57
1498 4195 9.687717 CATTATTGGTTTAAATTCGTGAATTGC 57.312 29.630 8.49 1.21 40.57 3.56
1499 4196 9.651913 ATTATTGGTTTAAATTCGTGAATTGCT 57.348 25.926 8.49 0.00 40.57 3.91
1500 4197 7.961325 ATTGGTTTAAATTCGTGAATTGCTT 57.039 28.000 8.49 0.00 40.57 3.91
1501 4198 6.761731 TGGTTTAAATTCGTGAATTGCTTG 57.238 33.333 8.49 0.00 40.57 4.01
1502 4199 6.276847 TGGTTTAAATTCGTGAATTGCTTGT 58.723 32.000 8.49 0.00 40.57 3.16
1503 4200 7.426410 TGGTTTAAATTCGTGAATTGCTTGTA 58.574 30.769 8.49 0.00 40.57 2.41
1504 4201 8.085296 TGGTTTAAATTCGTGAATTGCTTGTAT 58.915 29.630 8.49 0.00 40.57 2.29
1505 4202 8.372521 GGTTTAAATTCGTGAATTGCTTGTATG 58.627 33.333 8.49 0.00 40.57 2.39
1506 4203 9.123709 GTTTAAATTCGTGAATTGCTTGTATGA 57.876 29.630 8.49 0.00 40.57 2.15
1507 4204 8.667987 TTAAATTCGTGAATTGCTTGTATGAC 57.332 30.769 8.49 0.00 40.57 3.06
1508 4205 4.678509 TTCGTGAATTGCTTGTATGACC 57.321 40.909 0.00 0.00 0.00 4.02
1681 4378 1.898154 GTAAGAGGAGCTTGCCGGA 59.102 57.895 5.05 0.00 37.42 5.14
1714 4411 1.047034 GCCCCGGTAAGAGGAGCTTA 61.047 60.000 0.00 0.00 38.05 3.09
1819 4516 3.376935 CTGCGTCCCGGCAAGATCT 62.377 63.158 0.00 0.00 43.39 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.020839 GGTACAACTAGGTAGCAGTGGAAA 60.021 45.833 0.00 0.00 40.52 3.13
119 121 7.167302 CGACAATGATCTTTCTAGTCATGAGTC 59.833 40.741 6.25 11.88 36.23 3.36
128 130 6.690098 CCAAATTGCGACAATGATCTTTCTAG 59.310 38.462 5.95 0.00 0.00 2.43
391 416 8.457261 AGTTCAAAGAATCAGTTGATGCTATTC 58.543 33.333 3.05 0.00 39.50 1.75
444 469 6.772716 AGATCTGACATAGAAGAGAGGAAGAC 59.227 42.308 0.00 0.00 39.30 3.01
470 495 7.681939 ATGGATATTTAAACTTGACGTGTGT 57.318 32.000 0.00 0.00 0.00 3.72
514 539 6.071896 CCCTCTTTTAATTTCTTCCTCACACC 60.072 42.308 0.00 0.00 0.00 4.16
533 558 3.551635 TCCACTCTTTCTCTCCCTCTT 57.448 47.619 0.00 0.00 0.00 2.85
554 579 2.992689 TGGCGGCGAACTAGGTGA 60.993 61.111 12.98 0.00 0.00 4.02
598 623 1.656587 AGGAGGACAACATGTGCCTA 58.343 50.000 13.38 0.00 39.72 3.93
655 680 1.407258 CGAGAGGAACCAGGAGATCAC 59.593 57.143 0.00 0.00 0.00 3.06
693 718 0.034670 GGCAAGGAGCTTGAGGTGAT 60.035 55.000 0.00 0.00 43.42 3.06
701 726 2.437897 CCACTGGGCAAGGAGCTT 59.562 61.111 0.00 0.00 44.79 3.74
723 762 2.936032 AACCTCTGCCTCCACCCC 60.936 66.667 0.00 0.00 0.00 4.95
724 763 2.352805 CAACCTCTGCCTCCACCC 59.647 66.667 0.00 0.00 0.00 4.61
725 764 2.360475 GCAACCTCTGCCTCCACC 60.360 66.667 0.00 0.00 46.13 4.61
740 779 1.028130 CTCTGCCTATGAGAGACGCA 58.972 55.000 0.00 0.00 39.58 5.24
744 783 2.246469 GCATCCTCTGCCTATGAGAGA 58.754 52.381 0.00 0.00 45.66 3.10
794 1053 2.128853 CTGATTTGTTGCGCCACCGT 62.129 55.000 9.38 0.00 36.67 4.83
919 1191 1.909302 AGGTGTAGGATGTGGACAAGG 59.091 52.381 0.00 0.00 0.00 3.61
920 1192 2.093447 GGAGGTGTAGGATGTGGACAAG 60.093 54.545 0.00 0.00 0.00 3.16
922 1194 1.568504 GGAGGTGTAGGATGTGGACA 58.431 55.000 0.00 0.00 0.00 4.02
927 1199 1.649633 TGTAGGGGAGGTGTAGGATGT 59.350 52.381 0.00 0.00 0.00 3.06
968 3662 1.607628 CCCAGATCGGACGTAGGTTAG 59.392 57.143 5.32 0.00 36.56 2.34
970 3664 0.324091 ACCCAGATCGGACGTAGGTT 60.324 55.000 5.32 0.00 36.56 3.50
988 3682 2.047655 TTCCATGTCACCGCCGAC 60.048 61.111 0.00 0.00 36.40 4.79
992 3686 0.741221 GTCCTCTTCCATGTCACCGC 60.741 60.000 0.00 0.00 0.00 5.68
1017 3711 0.459489 CCTTCTCCTCTTCTCGCCTG 59.541 60.000 0.00 0.00 0.00 4.85
1025 3719 2.664081 CCGCCAGCCTTCTCCTCTT 61.664 63.158 0.00 0.00 0.00 2.85
1171 3865 3.111484 CCTAGCCCTCTTTCTCTTTCCT 58.889 50.000 0.00 0.00 0.00 3.36
1231 3925 3.256960 ACCCGCACCCAATCACCT 61.257 61.111 0.00 0.00 0.00 4.00
1347 4041 5.841957 AACTCAGTTTTCATCTTGCAGTT 57.158 34.783 0.00 0.00 0.00 3.16
1490 4187 5.314923 ACATGGTCATACAAGCAATTCAC 57.685 39.130 0.00 0.00 0.00 3.18
1491 4188 4.094739 CGACATGGTCATACAAGCAATTCA 59.905 41.667 0.00 0.00 32.09 2.57
1492 4189 4.496341 CCGACATGGTCATACAAGCAATTC 60.496 45.833 0.00 0.00 32.09 2.17
1493 4190 3.378112 CCGACATGGTCATACAAGCAATT 59.622 43.478 0.00 0.00 32.09 2.32
1494 4191 2.945008 CCGACATGGTCATACAAGCAAT 59.055 45.455 0.00 0.00 32.09 3.56
1495 4192 2.355197 CCGACATGGTCATACAAGCAA 58.645 47.619 0.00 0.00 32.09 3.91
1496 4193 2.022764 CCGACATGGTCATACAAGCA 57.977 50.000 0.00 0.00 32.09 3.91
1507 4204 3.564644 CCTACTCTAGTACACCGACATGG 59.435 52.174 0.00 0.00 46.41 3.66
1508 4205 3.564644 CCCTACTCTAGTACACCGACATG 59.435 52.174 0.00 0.00 0.00 3.21
1544 4241 2.970324 GCCCGTGCACGAGTTCAA 60.970 61.111 39.10 0.00 43.02 2.69
1545 4242 4.228567 TGCCCGTGCACGAGTTCA 62.229 61.111 39.10 25.24 44.23 3.18
1714 4411 3.503839 TTGGTTGGCCTTCCCGGT 61.504 61.111 3.32 0.00 35.87 5.28
2033 4730 2.552315 CAGTGCAAAAGGTGACCGTTAT 59.448 45.455 2.60 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.