Multiple sequence alignment - TraesCS4D01G226300

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 TraesCS4D01G226300 chr4D 100.000 2879 0 0 1 2879 385631820 385634698 0.000000e+00 5317
1 TraesCS4D01G226300 chr4D 93.726 1817 94 14 1 1805 385699628 385701436 0.000000e+00 2706
2 TraesCS4D01G226300 chr4D 91.880 1133 82 7 998 2125 385518002 385519129 0.000000e+00 1574
3 TraesCS4D01G226300 chr4D 86.094 1129 107 28 719 1805 385649549 385650669 0.000000e+00 1170
4 TraesCS4D01G226300 chr4D 88.559 944 89 14 875 1805 385587303 385588240 0.000000e+00 1127
5 TraesCS4D01G226300 chr4D 87.154 794 52 21 46 827 385578971 385579726 0.000000e+00 856
6 TraesCS4D01G226300 chr4D 89.715 632 45 11 46 665 385640917 385641540 0.000000e+00 789
7 TraesCS4D01G226300 chr4B 89.120 1296 117 19 799 2081 472207025 472208309 0.000000e+00 1591
8 TraesCS4D01G226300 chr4B 86.506 1119 109 22 719 1801 472210549 472211661 0.000000e+00 1192
9 TraesCS4D01G226300 chr4A 87.937 1343 133 19 799 2125 66928242 66929571 0.000000e+00 1555
10 TraesCS4D01G226300 chr4A 85.155 1354 114 43 489 1805 66930753 66932056 0.000000e+00 1306
11 TraesCS4D01G226300 chr4A 83.355 775 110 16 2121 2879 486118549 486119320 0.000000e+00 699
12 TraesCS4D01G226300 chr2D 87.467 766 72 11 2122 2879 89905867 89906616 0.000000e+00 861
13 TraesCS4D01G226300 chr7A 84.910 782 86 15 2124 2879 663824036 663823261 0.000000e+00 761
14 TraesCS4D01G226300 chr7A 82.542 779 107 22 2124 2879 666430595 666431367 0.000000e+00 658
15 TraesCS4D01G226300 chr3D 85.046 769 83 9 2124 2879 182426707 182425958 0.000000e+00 754
16 TraesCS4D01G226300 chr7D 86.391 676 76 7 2219 2879 129821320 129821994 0.000000e+00 725
17 TraesCS4D01G226300 chr1D 84.082 779 95 13 2124 2879 489544751 489543979 0.000000e+00 725
18 TraesCS4D01G226300 chr2B 83.990 762 105 13 2122 2879 153704224 153704972 0.000000e+00 715
19 TraesCS4D01G226300 chr2B 83.093 763 103 14 2122 2879 773994849 773994108 0.000000e+00 671
20 TraesCS4D01G226300 chr5D 83.247 770 94 9 2120 2876 233014461 233013714 0.000000e+00 675
21 TraesCS4D01G226300 chr5D 81.316 760 120 13 2122 2862 72468007 72468763 5.310000e-167 597
22 TraesCS4D01G226300 chr3B 83.491 424 46 8 2121 2538 151229144 151228739 9.740000e-100 374
23 TraesCS4D01G226300 chr3B 86.957 276 29 5 2125 2393 595686904 595686629 1.300000e-78 303
24 TraesCS4D01G226300 chr2A 85.366 287 37 3 2112 2393 494922171 494922457 2.810000e-75 292


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 TraesCS4D01G226300 chr4D 385631820 385634698 2878 False 5317.0 5317 100.000 1 2879 1 chr4D.!!$F4 2878
1 TraesCS4D01G226300 chr4D 385699628 385701436 1808 False 2706.0 2706 93.726 1 1805 1 chr4D.!!$F7 1804
2 TraesCS4D01G226300 chr4D 385518002 385519129 1127 False 1574.0 1574 91.880 998 2125 1 chr4D.!!$F1 1127
3 TraesCS4D01G226300 chr4D 385649549 385650669 1120 False 1170.0 1170 86.094 719 1805 1 chr4D.!!$F6 1086
4 TraesCS4D01G226300 chr4D 385587303 385588240 937 False 1127.0 1127 88.559 875 1805 1 chr4D.!!$F3 930
5 TraesCS4D01G226300 chr4D 385578971 385579726 755 False 856.0 856 87.154 46 827 1 chr4D.!!$F2 781
6 TraesCS4D01G226300 chr4D 385640917 385641540 623 False 789.0 789 89.715 46 665 1 chr4D.!!$F5 619
7 TraesCS4D01G226300 chr4B 472207025 472211661 4636 False 1391.5 1591 87.813 719 2081 2 chr4B.!!$F1 1362
8 TraesCS4D01G226300 chr4A 66928242 66932056 3814 False 1430.5 1555 86.546 489 2125 2 chr4A.!!$F2 1636
9 TraesCS4D01G226300 chr4A 486118549 486119320 771 False 699.0 699 83.355 2121 2879 1 chr4A.!!$F1 758
10 TraesCS4D01G226300 chr2D 89905867 89906616 749 False 861.0 861 87.467 2122 2879 1 chr2D.!!$F1 757
11 TraesCS4D01G226300 chr7A 663823261 663824036 775 True 761.0 761 84.910 2124 2879 1 chr7A.!!$R1 755
12 TraesCS4D01G226300 chr7A 666430595 666431367 772 False 658.0 658 82.542 2124 2879 1 chr7A.!!$F1 755
13 TraesCS4D01G226300 chr3D 182425958 182426707 749 True 754.0 754 85.046 2124 2879 1 chr3D.!!$R1 755
14 TraesCS4D01G226300 chr7D 129821320 129821994 674 False 725.0 725 86.391 2219 2879 1 chr7D.!!$F1 660
15 TraesCS4D01G226300 chr1D 489543979 489544751 772 True 725.0 725 84.082 2124 2879 1 chr1D.!!$R1 755
16 TraesCS4D01G226300 chr2B 153704224 153704972 748 False 715.0 715 83.990 2122 2879 1 chr2B.!!$F1 757
17 TraesCS4D01G226300 chr2B 773994108 773994849 741 True 671.0 671 83.093 2122 2879 1 chr2B.!!$R1 757
18 TraesCS4D01G226300 chr5D 233013714 233014461 747 True 675.0 675 83.247 2120 2876 1 chr5D.!!$R1 756
19 TraesCS4D01G226300 chr5D 72468007 72468763 756 False 597.0 597 81.316 2122 2862 1 chr5D.!!$F1 740

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
979 3820 0.253044 TTGCATCTGACCAGGTAGCC 59.747 55.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 4973 0.033405 TACTCTAAGCGGGGCTCAGT 60.033 55.0 0.0 0.0 38.25 3.41 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
24 25 5.205821 TCATGCAGAAATCATCCAAATCCT 58.794 37.500 0.00 0.00 0.00 3.24
28 29 5.471116 TGCAGAAATCATCCAAATCCTATCG 59.529 40.000 0.00 0.00 0.00 2.92
186 193 9.825972 AAACACATGACTTGAATACTTATTTCG 57.174 29.630 0.00 0.00 0.00 3.46
610 2636 5.435686 TTGTACAAAGCTGATAGGATGGT 57.564 39.130 5.64 0.00 0.00 3.55
625 2651 5.277857 AGGATGGTTAAGATAGTTGACCG 57.722 43.478 0.00 0.00 33.07 4.79
912 3753 1.025812 TAAAAAGCACACACCACCCG 58.974 50.000 0.00 0.00 0.00 5.28
952 3793 1.479709 CACAAACACCAGAACCCCAA 58.520 50.000 0.00 0.00 0.00 4.12
979 3820 0.253044 TTGCATCTGACCAGGTAGCC 59.747 55.000 0.00 0.00 0.00 3.93
1318 4159 3.575351 GAGTCGGAGTGCTTGGCGT 62.575 63.158 0.00 0.00 0.00 5.68
1645 4489 2.966309 GAACCAGAAGGCAACGGCG 61.966 63.158 4.80 4.80 46.39 6.46
1667 4526 2.268920 CGGTGTAGCACAGCCCAT 59.731 61.111 11.21 0.00 43.18 4.00
1706 4565 4.928140 AGGGTCCGGTGGTGTCGT 62.928 66.667 0.00 0.00 0.00 4.34
1716 4575 3.948719 GGTGTCGTTGGGCAGGGA 61.949 66.667 0.00 0.00 0.00 4.20
1825 4684 0.620030 TGGATGCAGCTTGCTAGGAA 59.380 50.000 0.22 0.00 45.31 3.36
1827 4686 1.878734 GGATGCAGCTTGCTAGGAATC 59.121 52.381 0.22 0.00 45.31 2.52
1859 4721 0.607489 GGTGTCAGCTCTGCCATTGT 60.607 55.000 0.00 0.00 0.00 2.71
1886 4748 2.419990 CCCTCGGCATCTGATTTGTGTA 60.420 50.000 0.00 0.00 0.00 2.90
1896 4758 1.393196 TGATTTGTGTACATGCGCTCG 59.607 47.619 9.73 1.22 0.00 5.03
1898 4760 0.510790 TTTGTGTACATGCGCTCGTG 59.489 50.000 9.73 7.74 35.37 4.35
1899 4761 1.896339 TTGTGTACATGCGCTCGTGC 61.896 55.000 9.73 9.95 32.47 5.34
1940 4802 6.902341 TGGTGATTTCTCGAATTTCTTCTTG 58.098 36.000 0.00 0.00 0.00 3.02
1941 4803 6.486657 TGGTGATTTCTCGAATTTCTTCTTGT 59.513 34.615 0.00 0.00 0.00 3.16
1971 4833 0.386838 GCAATAAGCCAGGGATGTGC 59.613 55.000 0.00 0.00 37.23 4.57
1972 4834 2.025863 GCAATAAGCCAGGGATGTGCT 61.026 52.381 0.00 0.00 37.23 4.40
2005 4867 4.404654 GCCGTGGCGCCTTTTCTG 62.405 66.667 29.70 12.44 0.00 3.02
2032 4894 1.379642 GCCTGCTGGTAGGATTGCAC 61.380 60.000 11.69 0.00 40.42 4.57
2037 4899 2.280628 GCTGGTAGGATTGCACTGTAC 58.719 52.381 0.00 0.00 0.00 2.90
2048 4910 1.070134 TGCACTGTACCTTGAGACCAC 59.930 52.381 0.00 0.00 0.00 4.16
2051 4913 2.035449 CACTGTACCTTGAGACCACGAA 59.965 50.000 0.00 0.00 0.00 3.85
2084 4946 7.588143 TTTCGATTTTTCAAGTTTGCTTTGA 57.412 28.000 0.00 0.00 31.49 2.69
2088 4950 8.167985 TCGATTTTTCAAGTTTGCTTTGAAAAG 58.832 29.630 19.10 12.08 39.61 2.27
2108 4972 4.002906 AGCGAAGTGTGGTTTCTATCAA 57.997 40.909 0.00 0.00 0.00 2.57
2109 4973 4.385825 AGCGAAGTGTGGTTTCTATCAAA 58.614 39.130 0.00 0.00 0.00 2.69
2118 4982 3.017442 GGTTTCTATCAAACTGAGCCCC 58.983 50.000 0.00 0.00 0.00 5.80
2127 4991 0.905337 AACTGAGCCCCGCTTAGAGT 60.905 55.000 11.87 1.16 43.59 3.24
2145 5009 0.599060 GTATCTCTAGCAGACCCCGC 59.401 60.000 0.00 0.00 32.26 6.13
2318 5192 1.667830 CCACGGCGCCCTGTATATG 60.668 63.158 23.46 6.49 0.00 1.78
2331 5212 1.338973 TGTATATGACGGGAGCGGTTC 59.661 52.381 0.00 0.00 0.00 3.62
2355 5268 3.508840 GGACATTTCAGCCCGCGG 61.509 66.667 21.04 21.04 0.00 6.46
2401 5317 2.359975 CCCTCGCCCGCTCTTTTT 60.360 61.111 0.00 0.00 0.00 1.94
2404 5320 1.376037 CTCGCCCGCTCTTTTTCCT 60.376 57.895 0.00 0.00 0.00 3.36
2407 5323 1.366854 CGCCCGCTCTTTTTCCTACC 61.367 60.000 0.00 0.00 0.00 3.18
2410 5326 0.618981 CCGCTCTTTTTCCTACCCCT 59.381 55.000 0.00 0.00 0.00 4.79
2504 5442 1.133809 AGCTTGCCCTCCACCACTTA 61.134 55.000 0.00 0.00 0.00 2.24
2509 5447 1.898154 CCCTCCACCACTTACTCCG 59.102 63.158 0.00 0.00 0.00 4.63
2512 5450 1.534476 TCCACCACTTACTCCGGCA 60.534 57.895 0.00 0.00 0.00 5.69
2546 5484 4.081185 TTGCAGATCGGCGGCTGA 62.081 61.111 26.60 14.84 38.60 4.26
2661 5615 4.552365 AGCGCCGCATGCAGGTAT 62.552 61.111 19.57 7.36 41.33 2.73
2777 5750 2.851386 GCTCATACAGTGCGACGACTAG 60.851 54.545 0.00 0.00 0.00 2.57
2849 5822 4.202202 TGGGTGTTCTTCAAATGCGAAAAT 60.202 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.524414 ACGCTGCTACACACACGATA 59.476 50.000 0.00 0.00 0.00 2.92
28 29 1.082756 GCAACGCTGCTACACACAC 60.083 57.895 2.93 0.00 45.74 3.82
520 2546 4.402155 TGTGTGTGATCCTTTTGAGCTTTT 59.598 37.500 0.00 0.00 0.00 2.27
952 3793 4.018960 ACCTGGTCAGATGCAACTTCTAAT 60.019 41.667 0.00 0.00 0.00 1.73
979 3820 4.341502 CGCCGGTGCTTGGGTTTG 62.342 66.667 0.00 0.00 34.43 2.93
1318 4159 1.153529 ACGTGTTCACGGTGCTCAA 60.154 52.632 25.14 0.00 37.45 3.02
1645 4489 2.464459 GCTGTGCTACACCGGCATC 61.464 63.158 0.00 0.00 41.86 3.91
1693 4552 3.931247 CCCAACGACACCACCGGA 61.931 66.667 9.46 0.00 0.00 5.14
1716 4575 4.640690 ACGTCCTCCAGGGCCTGT 62.641 66.667 30.68 8.83 36.14 4.00
1723 4582 4.087892 CTGCCCCACGTCCTCCAG 62.088 72.222 0.00 0.00 0.00 3.86
1872 4734 3.064408 AGCGCATGTACACAAATCAGATG 59.936 43.478 11.47 0.00 0.00 2.90
1873 4735 3.273434 AGCGCATGTACACAAATCAGAT 58.727 40.909 11.47 0.00 0.00 2.90
1898 4760 3.615536 AAAGCAATCACGCCGCTGC 62.616 57.895 0.00 0.00 35.79 5.25
1899 4761 1.798725 CAAAGCAATCACGCCGCTG 60.799 57.895 0.00 0.00 35.79 5.18
1900 4762 2.562912 CAAAGCAATCACGCCGCT 59.437 55.556 0.00 0.00 37.68 5.52
1903 4765 0.527565 ATCACCAAAGCAATCACGCC 59.472 50.000 0.00 0.00 0.00 5.68
1911 4773 5.241506 AGAAATTCGAGAAATCACCAAAGCA 59.758 36.000 0.00 0.00 0.00 3.91
1914 4776 7.510549 AGAAGAAATTCGAGAAATCACCAAA 57.489 32.000 0.00 0.00 0.00 3.28
1940 4802 3.372060 GGCTTATTGCGCCAGAAATAAC 58.628 45.455 4.18 3.96 46.77 1.89
1941 4803 3.708563 GGCTTATTGCGCCAGAAATAA 57.291 42.857 4.18 7.69 46.77 1.40
1971 4833 0.321122 GGCTGGTCAGGAGTTCACAG 60.321 60.000 0.00 0.00 0.00 3.66
1972 4834 1.754745 GGCTGGTCAGGAGTTCACA 59.245 57.895 0.00 0.00 0.00 3.58
2032 4894 2.296471 ACTTCGTGGTCTCAAGGTACAG 59.704 50.000 0.00 0.00 0.00 2.74
2037 4899 3.380479 TTACACTTCGTGGTCTCAAGG 57.620 47.619 0.00 0.00 37.94 3.61
2048 4910 9.763979 CTTGAAAAATCGAAAAATTACACTTCG 57.236 29.630 0.00 0.00 42.49 3.79
2084 4946 4.819630 TGATAGAAACCACACTTCGCTTTT 59.180 37.500 0.00 0.00 0.00 2.27
2088 4950 4.213482 AGTTTGATAGAAACCACACTTCGC 59.787 41.667 0.00 0.00 0.00 4.70
2108 4972 0.905337 ACTCTAAGCGGGGCTCAGTT 60.905 55.000 0.00 0.00 38.25 3.16
2109 4973 0.033405 TACTCTAAGCGGGGCTCAGT 60.033 55.000 0.00 0.00 38.25 3.41
2118 4982 4.153475 GGTCTGCTAGAGATACTCTAAGCG 59.847 50.000 9.31 10.32 41.74 4.68
2127 4991 0.185175 TGCGGGGTCTGCTAGAGATA 59.815 55.000 0.00 0.00 31.63 1.98
2155 5019 1.138036 GCGGTTATTTTGCGGGTCC 59.862 57.895 0.00 0.00 0.00 4.46
2301 5175 0.944311 GTCATATACAGGGCGCCGTG 60.944 60.000 39.63 39.63 37.77 4.94
2302 5176 1.366366 GTCATATACAGGGCGCCGT 59.634 57.895 22.54 20.09 0.00 5.68
2355 5268 1.835267 GGTGGTGGGTGGGGAAAAC 60.835 63.158 0.00 0.00 0.00 2.43
2395 5311 0.616891 GGCGAGGGGTAGGAAAAAGA 59.383 55.000 0.00 0.00 0.00 2.52
2661 5615 3.384348 GGCTACAGGACGAACCCA 58.616 61.111 0.00 0.00 40.05 4.51
2849 5822 2.496111 GAAACAACACATACCCCGTCA 58.504 47.619 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.