Multiple sequence alignment - TraesCS6B01G030600

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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 TraesCS6B01G030600 chr6B 100.000 2231 0 0 1 2231 18241397 18243627 0.000000e+00 4120.0
1 TraesCS6B01G030600 chr6B 96.116 2240 75 5 1 2231 18400236 18398000 0.000000e+00 3644.0
2 TraesCS6B01G030600 chr6B 77.700 1278 185 51 695 1919 18431553 18432783 0.000000e+00 689.0
3 TraesCS6B01G030600 chr6B 76.716 1151 182 44 589 1709 18633204 18634298 1.500000e-156 562.0
4 TraesCS6B01G030600 chr6B 78.448 696 121 18 604 1284 18268850 18269531 5.690000e-116 427.0
5 TraesCS6B01G030600 chr6B 75.987 912 168 27 604 1495 18167406 18168286 7.360000e-115 424.0
6 TraesCS6B01G030600 chr6B 96.875 32 1 0 1 32 17727364 17727333 1.000000e-03 54.7
7 TraesCS6B01G030600 chrUn 76.566 1788 251 88 509 2229 240894098 240895784 0.000000e+00 826.0
8 TraesCS6B01G030600 chrUn 76.566 1788 251 88 509 2229 268929802 268928116 0.000000e+00 826.0
9 TraesCS6B01G030600 chrUn 75.848 1474 238 76 770 2205 71131226 71132619 1.870000e-180 641.0
10 TraesCS6B01G030600 chrUn 74.715 526 105 13 1 505 240893549 240894067 2.240000e-50 209.0
11 TraesCS6B01G030600 chrUn 74.669 529 106 13 1 508 268930351 268929830 2.240000e-50 209.0
12 TraesCS6B01G030600 chrUn 92.308 52 4 0 1635 1686 71132267 71132318 8.540000e-10 75.0
13 TraesCS6B01G030600 chr6D 77.871 1071 153 45 604 1638 10308177 10307155 2.470000e-164 588.0
14 TraesCS6B01G030600 chr6D 81.270 630 106 5 620 1243 9858101 9857478 1.190000e-137 499.0
15 TraesCS6B01G030600 chr6D 76.092 916 171 28 589 1493 9915429 9916307 3.400000e-118 435.0
16 TraesCS6B01G030600 chr6D 74.947 471 58 27 1745 2194 10307265 10306834 6.380000e-36 161.0
17 TraesCS6B01G030600 chr6A 77.795 635 96 24 682 1282 11477568 11478191 1.270000e-92 350.0
18 TraesCS6B01G030600 chr2D 97.297 37 1 0 2 38 15516505 15516469 1.850000e-06 63.9
19 TraesCS6B01G030600 chr2A 92.500 40 2 1 1 39 17413245 17413206 3.090000e-04 56.5


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 TraesCS6B01G030600 chr6B 18241397 18243627 2230 False 4120.0 4120 100.0000 1 2231 1 chr6B.!!$F2 2230
1 TraesCS6B01G030600 chr6B 18398000 18400236 2236 True 3644.0 3644 96.1160 1 2231 1 chr6B.!!$R2 2230
2 TraesCS6B01G030600 chr6B 18431553 18432783 1230 False 689.0 689 77.7000 695 1919 1 chr6B.!!$F4 1224
3 TraesCS6B01G030600 chr6B 18633204 18634298 1094 False 562.0 562 76.7160 589 1709 1 chr6B.!!$F5 1120
4 TraesCS6B01G030600 chr6B 18268850 18269531 681 False 427.0 427 78.4480 604 1284 1 chr6B.!!$F3 680
5 TraesCS6B01G030600 chr6B 18167406 18168286 880 False 424.0 424 75.9870 604 1495 1 chr6B.!!$F1 891
6 TraesCS6B01G030600 chrUn 240893549 240895784 2235 False 517.5 826 75.6405 1 2229 2 chrUn.!!$F2 2228
7 TraesCS6B01G030600 chrUn 268928116 268930351 2235 True 517.5 826 75.6175 1 2229 2 chrUn.!!$R1 2228
8 TraesCS6B01G030600 chrUn 71131226 71132619 1393 False 358.0 641 84.0780 770 2205 2 chrUn.!!$F1 1435
9 TraesCS6B01G030600 chr6D 9857478 9858101 623 True 499.0 499 81.2700 620 1243 1 chr6D.!!$R1 623
10 TraesCS6B01G030600 chr6D 9915429 9916307 878 False 435.0 435 76.0920 589 1493 1 chr6D.!!$F1 904
11 TraesCS6B01G030600 chr6D 10306834 10308177 1343 True 374.5 588 76.4090 604 2194 2 chr6D.!!$R2 1590
12 TraesCS6B01G030600 chr6A 11477568 11478191 623 False 350.0 350 77.7950 682 1282 1 chr6A.!!$F1 600

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
810 889 0.246635 CCAGGCTAGTACACGTGCTT 59.753 55.0 17.22 3.72 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1912 2.278854 GAATGCTCACTCTGCTTCCTC 58.721 52.381 0.0 0.0 0.0 3.71 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
34 35 1.318886 TGCAATATTGTGGCCACCGG 61.319 55.000 32.62 15.82 0.00 5.28
92 93 4.682778 TTAGCACCACCTCACCATATAC 57.317 45.455 0.00 0.00 0.00 1.47
160 161 2.751806 CAATCCCTCCAAGAGCAGAAAC 59.248 50.000 0.00 0.00 0.00 2.78
192 199 0.400213 AATGGCGGGTTTCTCTCACA 59.600 50.000 0.00 0.00 0.00 3.58
340 353 4.655963 AGTAGAGCATGTTCAACCACATT 58.344 39.130 12.41 0.00 35.03 2.71
810 889 0.246635 CCAGGCTAGTACACGTGCTT 59.753 55.000 17.22 3.72 0.00 3.91
838 944 1.553417 CCATATGGGGGAGAGACCGAT 60.553 57.143 14.52 0.00 40.11 4.18
1161 1327 1.203440 AGGATGTACCACCACCCTTCT 60.203 52.381 7.91 0.00 42.04 2.85
1410 1624 5.810074 ACATAACTGAACCTTGTTTGTTTGC 59.190 36.000 0.00 0.00 0.00 3.68
1432 1646 2.923121 TGCTGCAGGTAATCAATCTCC 58.077 47.619 17.12 0.00 0.00 3.71
1443 1657 6.159398 AGGTAATCAATCTCCTCTGTGGATTT 59.841 38.462 0.00 0.00 45.16 2.17
1444 1658 6.261826 GGTAATCAATCTCCTCTGTGGATTTG 59.738 42.308 12.05 12.05 45.16 2.32
1505 1723 0.895530 TGCAGTGCTACCTCCTACAC 59.104 55.000 17.60 0.00 0.00 2.90
1536 1754 1.069765 CCTGCCGTGTGACTCTGTT 59.930 57.895 0.00 0.00 0.00 3.16
1548 1770 0.748005 ACTCTGTTGCGTTGCCTTGT 60.748 50.000 0.00 0.00 0.00 3.16
1550 1772 0.380378 TCTGTTGCGTTGCCTTGTTC 59.620 50.000 0.00 0.00 0.00 3.18
1569 1791 2.676748 TCCCTGCTTGATTGGTTTGTT 58.323 42.857 0.00 0.00 0.00 2.83
1574 1796 4.202101 CCTGCTTGATTGGTTTGTTGTGTA 60.202 41.667 0.00 0.00 0.00 2.90
1588 1810 4.311606 TGTTGTGTACTCGTTGCATATGT 58.688 39.130 4.29 0.00 0.00 2.29
1598 1820 5.236478 ACTCGTTGCATATGTATTACCTTGC 59.764 40.000 4.29 6.03 0.00 4.01
1605 1827 3.652057 ATGTATTACCTTGCTGTGGCT 57.348 42.857 0.00 0.00 39.59 4.75
1619 1841 2.431683 GGCTGTGTGGCTTCCAGA 59.568 61.111 0.00 0.00 38.32 3.86
1683 1912 0.891373 TCGGAGCTCTTGAGGAACTG 59.109 55.000 14.64 0.00 41.55 3.16
1738 1971 4.019321 ACCTGCATAACTGAAGCTTTCCTA 60.019 41.667 0.00 0.00 0.00 2.94
1756 1990 2.416296 CCTACCATGTGTGCATTGCTTG 60.416 50.000 10.49 0.49 31.99 4.01
1768 2002 2.722094 CATTGCTTGCCCTACTTACCA 58.278 47.619 0.00 0.00 0.00 3.25
2137 2419 3.623510 GCTGATTGTAAGTAAGCTGGGAC 59.376 47.826 0.00 0.00 0.00 4.46
2183 2466 6.882610 TTATACATGCTCATTGTTCCATCC 57.117 37.500 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.396996 CCACCAATCGGACGACATTTC 59.603 52.381 0.00 0.00 35.59 2.17
92 93 1.419387 CCTCCCCTCCATAAGCTGAAG 59.581 57.143 0.00 0.00 0.00 3.02
160 161 2.983803 CCCGCCATTTAAAACGTTCTTG 59.016 45.455 0.00 0.00 0.00 3.02
192 199 4.078863 AGAGACCTAAGGAGCCTTGTATCT 60.079 45.833 11.94 10.64 37.47 1.98
340 353 6.884832 ACTTCGAATCCATTATGGTACTTGA 58.115 36.000 11.39 3.90 39.03 3.02
810 889 0.348730 TCCCCCATATGGACAAGGGA 59.651 55.000 25.06 25.06 44.30 4.20
838 944 2.242708 GGGTCTCCAGTCTAGAGAAGGA 59.757 54.545 0.00 0.00 41.88 3.36
1161 1327 3.057548 TGGTTCGGCTCGTAGCGA 61.058 61.111 0.00 0.00 43.62 4.93
1410 1624 3.252701 GGAGATTGATTACCTGCAGCATG 59.747 47.826 8.66 0.00 40.87 4.06
1432 1646 3.144506 AGCTCAACACAAATCCACAGAG 58.855 45.455 0.00 0.00 0.00 3.35
1505 1723 0.239347 CGGCAGGAAAGCTTCTGTTG 59.761 55.000 14.63 6.47 33.81 3.33
1536 1754 2.192861 CAGGGAACAAGGCAACGCA 61.193 57.895 0.00 0.00 46.39 5.24
1548 1770 2.676748 ACAAACCAATCAAGCAGGGAA 58.323 42.857 0.00 0.00 0.00 3.97
1550 1772 2.102925 ACAACAAACCAATCAAGCAGGG 59.897 45.455 0.00 0.00 0.00 4.45
1569 1791 6.698329 GGTAATACATATGCAACGAGTACACA 59.302 38.462 1.58 0.00 0.00 3.72
1574 1796 5.236478 GCAAGGTAATACATATGCAACGAGT 59.764 40.000 1.58 0.00 34.10 4.18
1588 1810 2.039746 ACACAGCCACAGCAAGGTAATA 59.960 45.455 0.00 0.00 43.56 0.98
1598 1820 2.263741 GGAAGCCACACAGCCACAG 61.264 63.158 0.00 0.00 0.00 3.66
1605 1827 2.885135 ATCAATCTGGAAGCCACACA 57.115 45.000 0.00 0.00 0.00 3.72
1619 1841 7.682628 ACCAAACCAAATCAGATCAAATCAAT 58.317 30.769 0.00 0.00 0.00 2.57
1683 1912 2.278854 GAATGCTCACTCTGCTTCCTC 58.721 52.381 0.00 0.00 0.00 3.71
1738 1971 3.898380 CAAGCAATGCACACATGGT 57.102 47.368 8.35 0.00 36.36 3.55
1768 2002 2.635427 ACCACAAACCAACAACCAAAGT 59.365 40.909 0.00 0.00 0.00 2.66
2183 2466 5.220739 GCTAACACATCAGCTCCAAATACAG 60.221 44.000 0.00 0.00 34.86 2.74
2210 2494 3.290948 AACCAGCCTTACAAGTGACAA 57.709 42.857 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.