Multiple sequence alignment - TraesCS3B01G083700

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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 TraesCS3B01G083700 chr3B 100.000 3759 0 0 1 3759 52840466 52836708 0.000000e+00 6942.0
1 TraesCS3B01G083700 chr3B 96.984 2918 74 7 843 3759 52143526 52146430 0.000000e+00 4889.0
2 TraesCS3B01G083700 chr3B 83.715 2837 401 37 956 3757 52777793 52774983 0.000000e+00 2623.0
3 TraesCS3B01G083700 chr3B 83.598 2835 403 36 954 3754 51727000 51729806 0.000000e+00 2603.0
4 TraesCS3B01G083700 chr3B 88.873 2067 221 5 856 2918 52164490 52166551 0.000000e+00 2534.0
5 TraesCS3B01G083700 chr3B 83.057 2839 417 42 952 3750 52853759 52850945 0.000000e+00 2519.0
6 TraesCS3B01G083700 chr3B 82.833 2831 420 41 954 3745 52426286 52429089 0.000000e+00 2475.0
7 TraesCS3B01G083700 chr3B 83.365 2603 391 26 983 3552 51947770 51950363 0.000000e+00 2370.0
8 TraesCS3B01G083700 chr3B 82.992 2634 401 30 952 3552 51228487 51231106 0.000000e+00 2338.0
9 TraesCS3B01G083700 chr3B 96.951 820 23 2 1 818 52130325 52131144 0.000000e+00 1375.0
10 TraesCS3B01G083700 chr3B 87.879 495 55 3 70 560 52789835 52789342 9.050000e-161 577.0
11 TraesCS3B01G083700 chr3B 84.026 313 30 14 326 621 52164060 52164369 2.210000e-72 283.0
12 TraesCS3B01G083700 chr3A 95.608 3757 128 8 6 3759 41116841 41120563 0.000000e+00 5989.0
13 TraesCS3B01G083700 chr3A 82.713 2956 431 47 849 3759 40936231 40939151 0.000000e+00 2555.0
14 TraesCS3B01G083700 chr3D 83.564 2817 397 37 954 3726 30006656 30009450 0.000000e+00 2577.0
15 TraesCS3B01G083700 chr3D 91.509 212 16 2 463 674 29975672 29975881 1.320000e-74 291.0
16 TraesCS3B01G083700 chr5B 81.159 207 37 2 3349 3554 292752949 292753154 8.350000e-37 165.0
17 TraesCS3B01G083700 chr5D 96.491 57 1 1 787 843 551332507 551332562 4.000000e-15 93.5
18 TraesCS3B01G083700 chr5D 94.828 58 2 1 787 844 551334720 551334776 5.170000e-14 89.8
19 TraesCS3B01G083700 chr1A 96.364 55 1 1 787 841 589107268 589107215 5.170000e-14 89.8
20 TraesCS3B01G083700 chr1A 92.982 57 3 1 787 843 589100907 589100852 8.650000e-12 82.4


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 TraesCS3B01G083700 chr3B 52836708 52840466 3758 True 6942.0 6942 100.0000 1 3759 1 chr3B.!!$R3 3758
1 TraesCS3B01G083700 chr3B 52143526 52146430 2904 False 4889.0 4889 96.9840 843 3759 1 chr3B.!!$F5 2916
2 TraesCS3B01G083700 chr3B 52774983 52777793 2810 True 2623.0 2623 83.7150 956 3757 1 chr3B.!!$R1 2801
3 TraesCS3B01G083700 chr3B 51727000 51729806 2806 False 2603.0 2603 83.5980 954 3754 1 chr3B.!!$F2 2800
4 TraesCS3B01G083700 chr3B 52850945 52853759 2814 True 2519.0 2519 83.0570 952 3750 1 chr3B.!!$R4 2798
5 TraesCS3B01G083700 chr3B 52426286 52429089 2803 False 2475.0 2475 82.8330 954 3745 1 chr3B.!!$F6 2791
6 TraesCS3B01G083700 chr3B 51947770 51950363 2593 False 2370.0 2370 83.3650 983 3552 1 chr3B.!!$F3 2569
7 TraesCS3B01G083700 chr3B 51228487 51231106 2619 False 2338.0 2338 82.9920 952 3552 1 chr3B.!!$F1 2600
8 TraesCS3B01G083700 chr3B 52164060 52166551 2491 False 1408.5 2534 86.4495 326 2918 2 chr3B.!!$F7 2592
9 TraesCS3B01G083700 chr3B 52130325 52131144 819 False 1375.0 1375 96.9510 1 818 1 chr3B.!!$F4 817
10 TraesCS3B01G083700 chr3A 41116841 41120563 3722 False 5989.0 5989 95.6080 6 3759 1 chr3A.!!$F2 3753
11 TraesCS3B01G083700 chr3A 40936231 40939151 2920 False 2555.0 2555 82.7130 849 3759 1 chr3A.!!$F1 2910
12 TraesCS3B01G083700 chr3D 30006656 30009450 2794 False 2577.0 2577 83.5640 954 3726 1 chr3D.!!$F2 2772

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
769 787 3.819368 TCTGTTCACATCTTTTGAGCCA 58.181 40.909 0.00 0.0 0.00 4.75 F
1041 1090 1.354506 GCTTCGATCATGTGCCAGC 59.645 57.895 0.00 0.0 0.00 4.85 F
2138 2200 1.238439 GCTAGTGTTCTGGCAAGCAA 58.762 50.000 0.44 0.0 45.49 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 2200 4.895889 TCCACTCATTATCTGTTCGATCCT 59.104 41.667 0.00 0.00 33.48 3.24 R
2386 2448 5.897851 AGCTCATAGTAGTACTCCTCTGA 57.102 43.478 5.96 0.55 0.00 3.27 R
3669 3761 4.827284 AGCTTTAAGCAGCCTTCAAGTTTA 59.173 37.500 19.63 0.00 45.56 2.01 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
407 419 4.106197 CCATCGTTTCTAGTCTAGCACAC 58.894 47.826 1.60 0.00 0.00 3.82
408 420 4.142359 CCATCGTTTCTAGTCTAGCACACT 60.142 45.833 1.60 0.00 0.00 3.55
753 771 9.998106 AACAACAACTAAGTAGTGATATCTGTT 57.002 29.630 3.98 0.00 36.50 3.16
754 772 9.640963 ACAACAACTAAGTAGTGATATCTGTTC 57.359 33.333 3.98 0.00 36.50 3.18
755 773 9.639601 CAACAACTAAGTAGTGATATCTGTTCA 57.360 33.333 3.98 0.00 36.50 3.18
756 774 9.640963 AACAACTAAGTAGTGATATCTGTTCAC 57.359 33.333 3.98 0.00 43.05 3.18
757 775 8.803235 ACAACTAAGTAGTGATATCTGTTCACA 58.197 33.333 3.98 0.00 44.73 3.58
758 776 9.809096 CAACTAAGTAGTGATATCTGTTCACAT 57.191 33.333 3.98 0.00 44.73 3.21
760 778 9.415008 ACTAAGTAGTGATATCTGTTCACATCT 57.585 33.333 3.98 1.97 44.73 2.90
763 781 9.950496 AAGTAGTGATATCTGTTCACATCTTTT 57.050 29.630 3.98 0.00 44.73 2.27
764 782 9.376075 AGTAGTGATATCTGTTCACATCTTTTG 57.624 33.333 3.98 0.00 44.73 2.44
765 783 9.371136 GTAGTGATATCTGTTCACATCTTTTGA 57.629 33.333 3.98 0.00 44.73 2.69
766 784 8.489990 AGTGATATCTGTTCACATCTTTTGAG 57.510 34.615 3.98 0.00 44.73 3.02
767 785 7.065563 AGTGATATCTGTTCACATCTTTTGAGC 59.934 37.037 3.98 0.00 44.73 4.26
768 786 6.317140 TGATATCTGTTCACATCTTTTGAGCC 59.683 38.462 3.98 0.00 0.00 4.70
769 787 3.819368 TCTGTTCACATCTTTTGAGCCA 58.181 40.909 0.00 0.00 0.00 4.75
770 788 4.206375 TCTGTTCACATCTTTTGAGCCAA 58.794 39.130 0.00 0.00 0.00 4.52
771 789 4.828939 TCTGTTCACATCTTTTGAGCCAAT 59.171 37.500 0.00 0.00 0.00 3.16
892 936 8.800370 TCAGTTCAAAGCATGTTAATATACCA 57.200 30.769 0.00 0.00 0.00 3.25
1041 1090 1.354506 GCTTCGATCATGTGCCAGC 59.645 57.895 0.00 0.00 0.00 4.85
2138 2200 1.238439 GCTAGTGTTCTGGCAAGCAA 58.762 50.000 0.44 0.00 45.49 3.91
2386 2448 3.584848 AGGCCAACTTCTAGAAGACACAT 59.415 43.478 33.94 17.04 40.79 3.21
3328 3414 0.746204 TTTGTCTTCGCTGGCACACA 60.746 50.000 0.00 0.00 0.00 3.72
3479 3568 2.808543 GTGATCCCCTATGCAACGAATC 59.191 50.000 0.00 0.00 0.00 2.52
3669 3761 5.717654 TCTGTTTCCTTGTTTGGTAAGGTTT 59.282 36.000 0.00 0.00 44.06 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.336993 ACGCACACTGATTAACTGGAAAAA 59.663 37.500 0.00 0.00 0.00 1.94
168 170 8.766476 AGGAAAACAGAGAATAGAAGATCATCA 58.234 33.333 0.10 0.00 0.00 3.07
305 309 5.186992 ACAAAACCACTATTCCAATAAGGGC 59.813 40.000 0.00 0.00 38.24 5.19
390 402 6.479001 TGTTTTGAGTGTGCTAGACTAGAAAC 59.521 38.462 13.91 11.61 33.33 2.78
407 419 7.039784 TCCATTCTACCCTTGATTTGTTTTGAG 60.040 37.037 0.00 0.00 0.00 3.02
408 420 6.780031 TCCATTCTACCCTTGATTTGTTTTGA 59.220 34.615 0.00 0.00 0.00 2.69
681 698 4.661993 TGAAGCTATGCAACGTACAAAG 57.338 40.909 0.00 0.00 0.00 2.77
683 700 6.714492 CATAATGAAGCTATGCAACGTACAA 58.286 36.000 0.00 0.00 0.00 2.41
747 765 4.401022 TGGCTCAAAAGATGTGAACAGAT 58.599 39.130 0.00 0.00 0.00 2.90
748 766 3.819368 TGGCTCAAAAGATGTGAACAGA 58.181 40.909 0.00 0.00 0.00 3.41
749 767 4.572985 TTGGCTCAAAAGATGTGAACAG 57.427 40.909 0.00 0.00 0.00 3.16
750 768 6.839124 ATATTGGCTCAAAAGATGTGAACA 57.161 33.333 0.00 0.00 0.00 3.18
751 769 7.062605 CACAATATTGGCTCAAAAGATGTGAAC 59.937 37.037 19.37 0.00 33.70 3.18
752 770 7.039853 TCACAATATTGGCTCAAAAGATGTGAA 60.040 33.333 19.37 0.00 35.74 3.18
753 771 6.433716 TCACAATATTGGCTCAAAAGATGTGA 59.566 34.615 19.37 7.10 36.00 3.58
754 772 6.623486 TCACAATATTGGCTCAAAAGATGTG 58.377 36.000 19.37 4.89 33.44 3.21
755 773 6.660521 TCTCACAATATTGGCTCAAAAGATGT 59.339 34.615 19.37 0.00 0.00 3.06
756 774 7.092137 TCTCACAATATTGGCTCAAAAGATG 57.908 36.000 19.37 4.95 0.00 2.90
757 775 7.707624 TTCTCACAATATTGGCTCAAAAGAT 57.292 32.000 19.37 0.00 0.00 2.40
758 776 7.231317 ACTTTCTCACAATATTGGCTCAAAAGA 59.769 33.333 24.03 13.38 0.00 2.52
759 777 7.373493 ACTTTCTCACAATATTGGCTCAAAAG 58.627 34.615 19.37 19.61 0.00 2.27
760 778 7.288810 ACTTTCTCACAATATTGGCTCAAAA 57.711 32.000 19.37 11.22 0.00 2.44
761 779 6.899393 ACTTTCTCACAATATTGGCTCAAA 57.101 33.333 19.37 11.18 0.00 2.69
762 780 6.899393 AACTTTCTCACAATATTGGCTCAA 57.101 33.333 19.37 4.54 0.00 3.02
763 781 7.168219 AGTAACTTTCTCACAATATTGGCTCA 58.832 34.615 19.37 0.00 0.00 4.26
764 782 7.617041 AGTAACTTTCTCACAATATTGGCTC 57.383 36.000 19.37 0.00 0.00 4.70
765 783 9.686683 ATTAGTAACTTTCTCACAATATTGGCT 57.313 29.630 19.37 0.00 0.00 4.75
863 906 3.885484 AACATGCTTTGAACTGAGACG 57.115 42.857 0.00 0.00 0.00 4.18
892 936 7.906327 ACCAAAGGCTGAAAATTAATACACAT 58.094 30.769 0.00 0.00 0.00 3.21
1041 1090 8.407832 TCATTGGTAATGATATCTTGCAACTTG 58.592 33.333 3.98 0.00 42.69 3.16
2138 2200 4.895889 TCCACTCATTATCTGTTCGATCCT 59.104 41.667 0.00 0.00 33.48 3.24
2386 2448 5.897851 AGCTCATAGTAGTACTCCTCTGA 57.102 43.478 5.96 0.55 0.00 3.27
3328 3414 6.098409 ACACATCGTAGATTTCTAAGGGTCAT 59.902 38.462 1.56 0.00 45.12 3.06
3479 3568 6.421801 CCATTCAAGTTTAGGAAAAGCAACTG 59.578 38.462 0.00 0.00 29.78 3.16
3669 3761 4.827284 AGCTTTAAGCAGCCTTCAAGTTTA 59.173 37.500 19.63 0.00 45.56 2.01


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

AutoCloner maintained by Alex Coulton.