Multiple sequence alignment - TraesCS4B01G243800

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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 TraesCS4B01G243800 chr4B 100.000 2503 0 0 1 2503 505038956 505036454 0 4623
1 TraesCS4B01G243800 chr2A 93.867 2511 139 12 1 2503 538635679 538633176 0 3770
2 TraesCS4B01G243800 chr2A 93.133 1631 99 8 884 2503 605771413 605773041 0 2379
3 TraesCS4B01G243800 chr2B 93.362 2516 152 11 1 2503 103776100 103773587 0 3707
4 TraesCS4B01G243800 chr2B 93.958 1837 82 14 1 1809 738353425 738351590 0 2750
5 TraesCS4B01G243800 chr2B 91.599 1345 97 13 1166 2503 780644180 780645515 0 1844
6 TraesCS4B01G243800 chr4A 92.994 2512 159 16 1 2503 694169489 694171992 0 3648
7 TraesCS4B01G243800 chr4A 92.823 2536 146 18 1 2503 694127145 694129677 0 3642
8 TraesCS4B01G243800 chr7B 92.911 2511 148 13 1 2503 610766481 610763993 0 3624
9 TraesCS4B01G243800 chr3B 92.772 2421 137 23 114 2500 787077433 787079849 0 3467
10 TraesCS4B01G243800 chr6A 92.805 1918 107 10 596 2503 529360586 529362482 0 2748
11 TraesCS4B01G243800 chr3A 92.778 1814 118 8 701 2503 579943192 579941381 0 2612
12 TraesCS4B01G243800 chr7A 94.669 1388 69 4 1 1384 734436171 734437557 0 2148
13 TraesCS4B01G243800 chr6B 93.660 1388 84 2 1 1384 152333070 152334457 0 2073


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 TraesCS4B01G243800 chr4B 505036454 505038956 2502 True 4623 4623 100.000 1 2503 1 chr4B.!!$R1 2502
1 TraesCS4B01G243800 chr2A 538633176 538635679 2503 True 3770 3770 93.867 1 2503 1 chr2A.!!$R1 2502
2 TraesCS4B01G243800 chr2A 605771413 605773041 1628 False 2379 2379 93.133 884 2503 1 chr2A.!!$F1 1619
3 TraesCS4B01G243800 chr2B 103773587 103776100 2513 True 3707 3707 93.362 1 2503 1 chr2B.!!$R1 2502
4 TraesCS4B01G243800 chr2B 738351590 738353425 1835 True 2750 2750 93.958 1 1809 1 chr2B.!!$R2 1808
5 TraesCS4B01G243800 chr2B 780644180 780645515 1335 False 1844 1844 91.599 1166 2503 1 chr2B.!!$F1 1337
6 TraesCS4B01G243800 chr4A 694169489 694171992 2503 False 3648 3648 92.994 1 2503 1 chr4A.!!$F2 2502
7 TraesCS4B01G243800 chr4A 694127145 694129677 2532 False 3642 3642 92.823 1 2503 1 chr4A.!!$F1 2502
8 TraesCS4B01G243800 chr7B 610763993 610766481 2488 True 3624 3624 92.911 1 2503 1 chr7B.!!$R1 2502
9 TraesCS4B01G243800 chr3B 787077433 787079849 2416 False 3467 3467 92.772 114 2500 1 chr3B.!!$F1 2386
10 TraesCS4B01G243800 chr6A 529360586 529362482 1896 False 2748 2748 92.805 596 2503 1 chr6A.!!$F1 1907
11 TraesCS4B01G243800 chr3A 579941381 579943192 1811 True 2612 2612 92.778 701 2503 1 chr3A.!!$R1 1802
12 TraesCS4B01G243800 chr7A 734436171 734437557 1386 False 2148 2148 94.669 1 1384 1 chr7A.!!$F1 1383
13 TraesCS4B01G243800 chr6B 152333070 152334457 1387 False 2073 2073 93.660 1 1384 1 chr6B.!!$F1 1383

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
943 974 0.107703 CGGCTAGGAGCATTTCACCA 60.108 55.0 0.21 0.0 44.75 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2089 0.456482 TGCATGCTTTTTGGCGATCG 60.456 50.0 20.33 11.69 34.52 3.69 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
43 44 5.772825 TTGCACTGCTAAGATTTTCTTGT 57.227 34.783 1.98 0.00 37.29 3.16
119 121 6.657541 TGCATCATGTAATGTGATCATGCTAT 59.342 34.615 0.00 0.00 44.87 2.97
280 286 9.243637 TGTAATATTGAAACTGTTGTTTTGCTC 57.756 29.630 0.00 0.00 45.36 4.26
285 291 6.449635 TGAAACTGTTGTTTTGCTCTACAT 57.550 33.333 0.00 0.00 45.36 2.29
296 302 6.150976 TGTTTTGCTCTACATTATTGGTCCAG 59.849 38.462 0.00 0.00 0.00 3.86
358 364 6.463995 TGGTTCTGGTCAATTTATATTGCC 57.536 37.500 1.36 6.69 40.78 4.52
685 714 7.480810 TCGAGATCGTAATTGAGAAATCTTGA 58.519 34.615 1.70 0.00 40.80 3.02
733 762 8.534496 TCACTCATTTCTTTATCATCACTCTGA 58.466 33.333 0.00 0.00 0.00 3.27
781 812 0.603569 CACTACTTGACCCTCGCTGT 59.396 55.000 0.00 0.00 0.00 4.40
839 870 1.507141 CGTGAGCCCCACAAAGTGAC 61.507 60.000 7.49 0.00 45.98 3.67
845 876 1.893808 CCCACAAAGTGACGCTGCT 60.894 57.895 0.00 0.00 35.23 4.24
846 877 0.602638 CCCACAAAGTGACGCTGCTA 60.603 55.000 0.00 0.00 35.23 3.49
943 974 0.107703 CGGCTAGGAGCATTTCACCA 60.108 55.000 0.21 0.00 44.75 4.17
1054 1086 2.224402 TGTTGCATGTACTACCAGCACA 60.224 45.455 0.00 3.24 34.56 4.57
1091 1123 1.824230 GCTCTCTGCCTCTCTTCTTCA 59.176 52.381 0.00 0.00 35.15 3.02
1266 1298 2.034532 TGGCTGACGACGACCCTA 59.965 61.111 0.00 0.00 0.00 3.53
1284 1343 2.244695 CTACTATGGTGGTGGCGGATA 58.755 52.381 0.00 0.00 0.00 2.59
1307 1366 1.001020 CCTTGCTATGGTGGTGGCA 60.001 57.895 0.00 0.00 33.52 4.92
1384 1473 4.082523 CCTCGCGATGGTGGTGGT 62.083 66.667 10.36 0.00 0.00 4.16
1407 1496 2.277591 GCAATCCCACAGCTTGGCA 61.278 57.895 8.85 0.00 45.37 4.92
1538 1628 2.660189 AGTGGCAATGTTAAGCATGC 57.340 45.000 10.51 10.51 37.96 4.06
1845 1936 1.336877 GCGAAATCTGCCGGTTTTTC 58.663 50.000 1.90 6.87 0.00 2.29
1907 1998 4.340894 TGAATGCTAAAGACATGCGTTC 57.659 40.909 10.93 10.93 46.71 3.95
1917 2008 1.792949 GACATGCGTTCTTCGTGAAGT 59.207 47.619 9.29 0.00 42.13 3.01
1986 2088 5.422145 TCAAAGTAGACCCTATTTTACGGC 58.578 41.667 0.00 0.00 0.00 5.68
1987 2089 4.412796 AAGTAGACCCTATTTTACGGCC 57.587 45.455 0.00 0.00 0.00 6.13
1988 2090 2.363359 AGTAGACCCTATTTTACGGCCG 59.637 50.000 26.86 26.86 0.00 6.13
2007 2112 1.712401 GATCGCCAAAAAGCATGCAA 58.288 45.000 21.98 0.00 0.00 4.08
2019 2124 1.031571 GCATGCAATTCCGACCCTCA 61.032 55.000 14.21 0.00 0.00 3.86
2166 2272 4.458397 AGGCATTTCATCACAGAATCGAT 58.542 39.130 0.00 0.00 0.00 3.59
2201 2308 0.320374 CTCAAACCTAGCCACGGACA 59.680 55.000 0.00 0.00 0.00 4.02
2228 2335 3.622459 GATGAAATCGGCCGGTTTG 57.378 52.632 39.32 4.34 31.13 2.93
2232 2340 1.807742 TGAAATCGGCCGGTTTGTTAG 59.192 47.619 39.32 0.83 0.00 2.34
2290 2402 0.384309 GACCTCCGCGTCACATCATA 59.616 55.000 4.92 0.00 32.74 2.15
2336 2449 7.539366 GCAAAAATACTAAACTTGCAATACCGA 59.461 33.333 0.00 0.00 41.55 4.69
2345 2458 3.059188 ACTTGCAATACCGACGTTTTCTG 60.059 43.478 0.00 0.00 0.00 3.02
2352 2465 3.409851 ACCGACGTTTTCTGGAAAAAC 57.590 42.857 9.65 4.56 41.37 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
358 364 8.873215 ATCTACTATAAATTGACCAGAACACG 57.127 34.615 0.00 0.00 0.00 4.49
565 580 6.891908 ACTGGACATAAATAGGAAACAAGCAT 59.108 34.615 0.00 0.00 0.00 3.79
622 651 0.252479 AGCCAGCCATCTCACTTCTG 59.748 55.000 0.00 0.00 0.00 3.02
685 714 9.105844 AGTGATGATAAATATACCTGCCTACTT 57.894 33.333 0.00 0.00 0.00 2.24
733 762 3.354948 TGCCAATCAAGCACTAGACAT 57.645 42.857 0.00 0.00 34.69 3.06
766 795 1.178276 CTCTACAGCGAGGGTCAAGT 58.822 55.000 0.00 0.00 0.00 3.16
781 812 1.352083 AACTTGTCAGGCAGCCTCTA 58.648 50.000 12.53 0.00 0.00 2.43
873 904 1.228124 CACCACCAACACGTCCCAT 60.228 57.895 0.00 0.00 0.00 4.00
943 974 2.503061 CTGTAGCTCATGGGCGCT 59.497 61.111 12.97 10.80 40.15 5.92
1035 1067 2.811431 GTTGTGCTGGTAGTACATGCAA 59.189 45.455 17.21 6.13 40.42 4.08
1054 1086 0.246635 AGCTTACTGGCATCGTCGTT 59.753 50.000 0.00 0.00 34.17 3.85
1091 1123 3.308473 GGTAGAGGAAGCCAAAAGGACAT 60.308 47.826 0.00 0.00 0.00 3.06
1221 1253 1.374125 CATGGTCGTCGTGAGCCAA 60.374 57.895 7.05 0.00 44.62 4.52
1227 1259 1.788886 CATCATAGCATGGTCGTCGTG 59.211 52.381 0.00 0.00 35.53 4.35
1266 1298 1.140252 GTTATCCGCCACCACCATAGT 59.860 52.381 0.00 0.00 0.00 2.12
1284 1343 0.690762 ACCACCATAGCAAGGTCGTT 59.309 50.000 0.00 0.00 37.23 3.85
1307 1366 0.456221 CCATAGCAAGGTCGTCGTCT 59.544 55.000 0.00 0.00 0.00 4.18
1384 1473 2.677524 GCTGTGGGATTGCAGGCA 60.678 61.111 0.00 0.00 33.62 4.75
1407 1496 1.619827 CACAATTGGCATGGTCCTGTT 59.380 47.619 10.83 0.00 0.00 3.16
1538 1628 9.654663 AGATTACACTAACAAGCTTAAACCTAG 57.345 33.333 0.00 0.00 0.00 3.02
1826 1917 1.335506 TGAAAAACCGGCAGATTTCGC 60.336 47.619 0.00 0.00 35.15 4.70
1907 1998 2.069273 CCTTGTAGCCACTTCACGAAG 58.931 52.381 5.24 5.24 43.79 3.79
1917 2008 1.198759 GGTGACCCTCCTTGTAGCCA 61.199 60.000 0.00 0.00 0.00 4.75
1986 2088 1.141591 GCATGCTTTTTGGCGATCGG 61.142 55.000 18.30 0.00 34.52 4.18
1987 2089 0.456482 TGCATGCTTTTTGGCGATCG 60.456 50.000 20.33 11.69 34.52 3.69
1988 2090 1.712401 TTGCATGCTTTTTGGCGATC 58.288 45.000 20.33 0.00 34.52 3.69
2007 2112 3.158676 GAGTAGCTATGAGGGTCGGAAT 58.841 50.000 0.00 0.00 0.00 3.01
2019 2124 2.037772 CTGAATTGCCGGGAGTAGCTAT 59.962 50.000 2.18 0.00 0.00 2.97
2166 2272 3.717400 TTGAGCCGTGCAAATTTGTTA 57.283 38.095 19.03 6.61 0.00 2.41
2201 2308 3.813596 GATTTCATCGTGGCGGCT 58.186 55.556 11.43 0.00 0.00 5.52
2290 2402 3.089284 GCTAGTTGGTAGGCCACATTTT 58.911 45.455 5.01 0.00 46.01 1.82
2336 2449 5.182380 TGAGAACAGTTTTTCCAGAAAACGT 59.818 36.000 5.08 1.49 43.01 3.99
2345 2458 5.287752 GGTCGTTTTTGAGAACAGTTTTTCC 59.712 40.000 0.00 0.00 0.00 3.13
2352 2465 4.124238 TGGTAGGTCGTTTTTGAGAACAG 58.876 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.