Multiple sequence alignment - TraesCS2A01G365200

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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 TraesCS2A01G365200 chr2A 100.000 2870 0 0 1 2870 608937200 608940069 0.000000e+00 5301.0
1 TraesCS2A01G365200 chr2A 89.512 553 52 4 2321 2868 705811152 705811703 0.000000e+00 695.0
2 TraesCS2A01G365200 chr2A 90.164 61 4 1 647 705 81468197 81468257 8.530000e-11 78.7
3 TraesCS2A01G365200 chr2D 93.936 1781 67 12 737 2501 469167939 469169694 0.000000e+00 2652.0
4 TraesCS2A01G365200 chr2B 92.956 1519 64 16 737 2255 547836343 547837818 0.000000e+00 2172.0
5 TraesCS2A01G365200 chr5B 98.310 710 12 0 1 710 239324992 239325701 0.000000e+00 1245.0
6 TraesCS2A01G365200 chr5B 87.477 551 60 7 2323 2868 532534208 532534754 6.750000e-176 627.0
7 TraesCS2A01G365200 chr7B 98.036 713 14 0 1 713 516450819 516450107 0.000000e+00 1240.0
8 TraesCS2A01G365200 chr5A 98.036 713 14 0 1 713 320269823 320269111 0.000000e+00 1240.0
9 TraesCS2A01G365200 chr5A 87.862 552 59 7 2321 2868 622993810 622994357 2.410000e-180 641.0
10 TraesCS2A01G365200 chr4B 98.036 713 14 0 1 713 92550342 92549630 0.000000e+00 1240.0
11 TraesCS2A01G365200 chr6B 98.028 710 14 0 1 710 346416226 346416935 0.000000e+00 1234.0
12 TraesCS2A01G365200 chr3D 88.225 552 56 8 2321 2868 562355628 562355082 0.000000e+00 651.0
13 TraesCS2A01G365200 chr6A 86.874 579 75 1 1 579 106071539 106072116 0.000000e+00 647.0
14 TraesCS2A01G365200 chr6D 87.703 553 61 6 2321 2868 397352675 397352125 3.120000e-179 638.0
15 TraesCS2A01G365200 chr6D 86.140 570 69 7 142 705 88091127 88091692 8.790000e-170 606.0
16 TraesCS2A01G365200 chr1A 87.751 547 62 4 2326 2870 547419400 547418857 4.030000e-178 634.0
17 TraesCS2A01G365200 chr5D 87.636 550 60 6 2321 2868 557652621 557653164 1.450000e-177 632.0
18 TraesCS2A01G365200 chr1D 87.161 553 63 7 2321 2870 203875906 203875359 3.140000e-174 621.0
19 TraesCS2A01G365200 chr7A 86.918 558 64 7 2315 2868 693483715 693484267 4.060000e-173 617.0
20 TraesCS2A01G365200 chr7D 92.492 333 25 0 1 333 580113212 580113544 7.190000e-131 477.0
21 TraesCS2A01G365200 chr3B 77.616 688 131 18 2 678 478095651 478094976 2.070000e-106 396.0


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 TraesCS2A01G365200 chr2A 608937200 608940069 2869 False 5301 5301 100.000 1 2870 1 chr2A.!!$F2 2869
1 TraesCS2A01G365200 chr2A 705811152 705811703 551 False 695 695 89.512 2321 2868 1 chr2A.!!$F3 547
2 TraesCS2A01G365200 chr2D 469167939 469169694 1755 False 2652 2652 93.936 737 2501 1 chr2D.!!$F1 1764
3 TraesCS2A01G365200 chr2B 547836343 547837818 1475 False 2172 2172 92.956 737 2255 1 chr2B.!!$F1 1518
4 TraesCS2A01G365200 chr5B 239324992 239325701 709 False 1245 1245 98.310 1 710 1 chr5B.!!$F1 709
5 TraesCS2A01G365200 chr5B 532534208 532534754 546 False 627 627 87.477 2323 2868 1 chr5B.!!$F2 545
6 TraesCS2A01G365200 chr7B 516450107 516450819 712 True 1240 1240 98.036 1 713 1 chr7B.!!$R1 712
7 TraesCS2A01G365200 chr5A 320269111 320269823 712 True 1240 1240 98.036 1 713 1 chr5A.!!$R1 712
8 TraesCS2A01G365200 chr5A 622993810 622994357 547 False 641 641 87.862 2321 2868 1 chr5A.!!$F1 547
9 TraesCS2A01G365200 chr4B 92549630 92550342 712 True 1240 1240 98.036 1 713 1 chr4B.!!$R1 712
10 TraesCS2A01G365200 chr6B 346416226 346416935 709 False 1234 1234 98.028 1 710 1 chr6B.!!$F1 709
11 TraesCS2A01G365200 chr3D 562355082 562355628 546 True 651 651 88.225 2321 2868 1 chr3D.!!$R1 547
12 TraesCS2A01G365200 chr6A 106071539 106072116 577 False 647 647 86.874 1 579 1 chr6A.!!$F1 578
13 TraesCS2A01G365200 chr6D 397352125 397352675 550 True 638 638 87.703 2321 2868 1 chr6D.!!$R1 547
14 TraesCS2A01G365200 chr6D 88091127 88091692 565 False 606 606 86.140 142 705 1 chr6D.!!$F1 563
15 TraesCS2A01G365200 chr1A 547418857 547419400 543 True 634 634 87.751 2326 2870 1 chr1A.!!$R1 544
16 TraesCS2A01G365200 chr5D 557652621 557653164 543 False 632 632 87.636 2321 2868 1 chr5D.!!$F1 547
17 TraesCS2A01G365200 chr1D 203875359 203875906 547 True 621 621 87.161 2321 2870 1 chr1D.!!$R1 549
18 TraesCS2A01G365200 chr7A 693483715 693484267 552 False 617 617 86.918 2315 2868 1 chr7A.!!$F1 553
19 TraesCS2A01G365200 chr3B 478094976 478095651 675 True 396 396 77.616 2 678 1 chr3B.!!$R1 676


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
393 394 0.110056 CCAGCACGACAGCATTCAAC 60.11 55.0 0.0 0.0 36.85 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2306 0.248866 CGGGTGAAATATTTGGCGCC 60.249 55.0 22.73 22.73 0.0 6.53 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
393 394 0.110056 CCAGCACGACAGCATTCAAC 60.110 55.000 0.00 0.00 36.85 3.18
717 727 3.302344 GTGGGTGCGGGCAACATT 61.302 61.111 11.26 0.00 34.85 2.71
718 728 2.522923 TGGGTGCGGGCAACATTT 60.523 55.556 11.26 0.00 34.85 2.32
719 729 2.136878 TGGGTGCGGGCAACATTTT 61.137 52.632 11.26 0.00 34.85 1.82
720 730 1.070615 GGGTGCGGGCAACATTTTT 59.929 52.632 11.26 0.00 34.85 1.94
759 769 9.768662 GGAATTAGGCAATCATATTTGTTGATT 57.231 29.630 0.00 0.00 42.95 2.57
803 813 5.750067 AGCTTTTGTCTGTTTTATGTGCAAG 59.250 36.000 0.00 0.00 0.00 4.01
848 858 7.012515 GTGTGTGTCTGTCTACTAGCACTATAT 59.987 40.741 0.00 0.00 0.00 0.86
916 926 1.615392 ACTTTTCATGGCTTGCCTGTC 59.385 47.619 13.18 0.00 0.00 3.51
994 1005 2.584835 TTCAACAGCATGGTAGGCTT 57.415 45.000 0.00 0.00 43.62 4.35
1128 1139 1.428869 AGTCAGGACCAGAGCAAACT 58.571 50.000 0.00 0.00 0.00 2.66
1175 1186 4.301637 ACCAAAAGTTCACGGAAATGTC 57.698 40.909 0.00 0.00 0.00 3.06
1285 1296 3.260632 TGAAATGTGCCTAGACACTGCTA 59.739 43.478 10.70 0.00 41.30 3.49
1350 1361 3.634397 AGATCGGAGGCTGATCAAAAA 57.366 42.857 16.17 0.00 45.70 1.94
1656 1671 4.244066 GTTTCTTACCTCCTTTCTCGGTC 58.756 47.826 0.00 0.00 32.36 4.79
1665 1680 1.536284 CCTTTCTCGGTCCAGCGTATC 60.536 57.143 0.00 0.00 0.00 2.24
1842 1865 1.881602 GGCTTTCCAGCTGCTCAAG 59.118 57.895 8.66 10.49 46.44 3.02
2019 2042 0.242017 GTCCACCACATCAGCTTTGC 59.758 55.000 0.00 0.00 0.00 3.68
2142 2166 9.651913 ATGGTATAATGTTTGACCAATTTTGTC 57.348 29.630 0.00 0.00 44.83 3.18
2226 2250 7.821652 TCATGAAATAAACAACTTATTGCCGA 58.178 30.769 0.00 0.00 38.94 5.54
2282 2306 4.027065 CACGTATAGTTTTCTCGGTCGAG 58.973 47.826 13.56 13.56 43.21 4.04
2312 2336 4.649705 TCACCCGGAGCCCCTCAA 62.650 66.667 0.73 0.00 31.08 3.02
2465 2495 1.282248 CTCGACAAAGCGCGGAAGAA 61.282 55.000 8.83 0.00 0.00 2.52
2467 2497 1.557443 CGACAAAGCGCGGAAGAACT 61.557 55.000 8.83 0.00 0.00 3.01
2469 2499 1.207593 CAAAGCGCGGAAGAACTGG 59.792 57.895 8.83 0.00 0.00 4.00
2474 2504 2.943978 CGCGGAAGAACTGGGACCT 61.944 63.158 0.00 0.00 39.73 3.85
2501 2531 1.202927 CCTCTGGAAACACACCACCAT 60.203 52.381 0.00 0.00 35.60 3.55
2505 2535 1.423541 TGGAAACACACCACCATAGCT 59.576 47.619 0.00 0.00 33.40 3.32
2508 2538 0.036388 AACACACCACCATAGCTCGG 60.036 55.000 0.00 0.00 0.00 4.63
2560 2590 1.347707 TCCAAGAAGGAATGTGACGCT 59.652 47.619 0.00 0.00 45.65 5.07
2576 2606 4.731612 CTGACGACGCTGCTGCCT 62.732 66.667 10.24 0.00 35.36 4.75
2577 2607 4.299547 TGACGACGCTGCTGCCTT 62.300 61.111 10.24 0.00 35.36 4.35
2713 2743 1.302949 CCGGCAAGGATTTCTCCCA 59.697 57.895 0.00 0.00 43.21 4.37
2777 2807 4.424566 GCCCAACACCATGCGCAG 62.425 66.667 18.32 5.51 0.00 5.18
2815 2845 0.739462 CCATGCCGTCTTACTGCGAA 60.739 55.000 0.00 0.00 30.52 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
393 394 2.796617 CGCTCGGTTTGCTTTGCG 60.797 61.111 0.00 0.00 37.57 4.85
717 727 5.885912 CCTAATTCCCTCTTCATCGGAAAAA 59.114 40.000 0.00 0.00 39.07 1.94
718 728 5.437060 CCTAATTCCCTCTTCATCGGAAAA 58.563 41.667 0.00 0.00 39.07 2.29
719 729 4.686122 GCCTAATTCCCTCTTCATCGGAAA 60.686 45.833 0.00 0.00 39.07 3.13
720 730 3.181454 GCCTAATTCCCTCTTCATCGGAA 60.181 47.826 0.00 0.00 39.89 4.30
721 731 2.368875 GCCTAATTCCCTCTTCATCGGA 59.631 50.000 0.00 0.00 0.00 4.55
722 732 2.104792 TGCCTAATTCCCTCTTCATCGG 59.895 50.000 0.00 0.00 0.00 4.18
723 733 3.475566 TGCCTAATTCCCTCTTCATCG 57.524 47.619 0.00 0.00 0.00 3.84
724 734 5.380043 TGATTGCCTAATTCCCTCTTCATC 58.620 41.667 0.00 0.00 0.00 2.92
725 735 5.393068 TGATTGCCTAATTCCCTCTTCAT 57.607 39.130 0.00 0.00 0.00 2.57
726 736 4.860802 TGATTGCCTAATTCCCTCTTCA 57.139 40.909 0.00 0.00 0.00 3.02
727 737 8.302438 CAAATATGATTGCCTAATTCCCTCTTC 58.698 37.037 0.00 0.00 0.00 2.87
728 738 7.786464 ACAAATATGATTGCCTAATTCCCTCTT 59.214 33.333 0.00 0.00 33.52 2.85
729 739 7.300658 ACAAATATGATTGCCTAATTCCCTCT 58.699 34.615 0.00 0.00 33.52 3.69
730 740 7.530426 ACAAATATGATTGCCTAATTCCCTC 57.470 36.000 0.00 0.00 33.52 4.30
731 741 7.564660 TCAACAAATATGATTGCCTAATTCCCT 59.435 33.333 0.00 0.00 33.52 4.20
732 742 7.725251 TCAACAAATATGATTGCCTAATTCCC 58.275 34.615 0.00 0.00 33.52 3.97
733 743 9.768662 AATCAACAAATATGATTGCCTAATTCC 57.231 29.630 1.26 0.00 43.85 3.01
766 776 6.600822 ACAGACAAAAGCTTCTATACATGCAT 59.399 34.615 0.00 0.00 0.00 3.96
810 820 0.179056 ACACACACATATAGGCGCCC 60.179 55.000 26.15 5.07 0.00 6.13
814 824 4.392921 AGACAGACACACACATATAGGC 57.607 45.455 0.00 0.00 0.00 3.93
848 858 4.250464 CAGGCAAACCATAAGAAGTCGTA 58.750 43.478 0.00 0.00 39.06 3.43
916 926 4.017126 GGTTCAGTTCCCCCTCTAATTTG 58.983 47.826 0.00 0.00 0.00 2.32
994 1005 7.094549 GGCTACAACCACACAGAACATAAAATA 60.095 37.037 0.00 0.00 0.00 1.40
1128 1139 3.577415 CCTGTGATCCTAGCATCTCATCA 59.423 47.826 0.00 0.00 0.00 3.07
1175 1186 2.103143 CAGCAGCGTCGTCTAGGG 59.897 66.667 0.00 0.00 0.00 3.53
1207 1218 6.491062 TCTGGATCATCTTGCTTTTCTTGAAA 59.509 34.615 0.00 0.00 0.00 2.69
1285 1296 8.893563 TTTTCTTGGTTAATATCAGTTCCCAT 57.106 30.769 0.00 0.00 0.00 4.00
1387 1398 3.244875 TGCTCTTCTGGCTTAACATTGGA 60.245 43.478 0.00 0.00 0.00 3.53
1656 1671 3.763097 TGCATCAAAAAGATACGCTGG 57.237 42.857 0.00 0.00 34.43 4.85
1842 1865 0.306533 GAGACTCGTCGATCCTGCTC 59.693 60.000 0.00 0.00 34.09 4.26
1901 1924 0.804933 CGCTAACCACTAACTCGCCC 60.805 60.000 0.00 0.00 0.00 6.13
2019 2042 3.666902 CGTTAATCAAAACAGACGCTGGG 60.667 47.826 10.80 0.00 35.51 4.45
2121 2145 8.879342 TTTCGACAAAATTGGTCAAACATTAT 57.121 26.923 1.05 0.00 34.97 1.28
2149 2173 9.534565 TTGATAAATTTTCGACAAAATTGGTCA 57.465 25.926 8.24 11.34 46.93 4.02
2150 2174 9.791838 GTTGATAAATTTTCGACAAAATTGGTC 57.208 29.630 8.24 9.51 46.93 4.02
2151 2175 9.319143 TGTTGATAAATTTTCGACAAAATTGGT 57.681 25.926 15.34 1.92 46.93 3.67
2158 2182 9.619316 CCATAGTTGTTGATAAATTTTCGACAA 57.381 29.630 20.53 20.53 42.46 3.18
2159 2183 8.788806 ACCATAGTTGTTGATAAATTTTCGACA 58.211 29.630 14.39 14.39 36.04 4.35
2226 2250 1.696884 GCCCTGCTAGAGGCTCTAATT 59.303 52.381 23.62 2.37 46.14 1.40
2249 2273 2.639065 ACTATACGTGGGCCATGTTTG 58.361 47.619 34.48 24.68 35.12 2.93
2282 2306 0.248866 CGGGTGAAATATTTGGCGCC 60.249 55.000 22.73 22.73 0.00 6.53
2312 2336 5.648178 AAACCTTTTTCGGTACACTTGTT 57.352 34.783 0.00 0.00 35.89 2.83
2469 2499 4.154347 CAGAGGGCGCAGAGGTCC 62.154 72.222 10.83 0.00 0.00 4.46
2474 2504 2.347490 GTTTCCAGAGGGCGCAGA 59.653 61.111 10.83 0.00 0.00 4.26
2505 2535 1.138883 CGGTTGATCGAAGCTCCGA 59.861 57.895 0.00 0.00 43.16 4.55
2508 2538 0.524816 TACGCGGTTGATCGAAGCTC 60.525 55.000 12.47 0.00 0.00 4.09
2519 2549 1.012486 GTGCTGCTTAGTACGCGGTT 61.012 55.000 12.47 0.00 36.17 4.44
2560 2590 4.299547 AAGGCAGCAGCGTCGTCA 62.300 61.111 0.00 0.00 43.41 4.35
2602 2632 2.838225 CCACCTCCCTCCGCGTAT 60.838 66.667 4.92 0.00 0.00 3.06
2713 2743 0.463116 GACGGTGGAGTTTGGTGTGT 60.463 55.000 0.00 0.00 0.00 3.72
2794 2824 2.472909 GCAGTAAGACGGCATGGGC 61.473 63.158 0.00 0.00 39.14 5.36
2799 2829 0.942410 GTGTTCGCAGTAAGACGGCA 60.942 55.000 0.00 0.00 39.28 5.69
2807 2837 0.102663 TCGTGTTGGTGTTCGCAGTA 59.897 50.000 0.00 0.00 0.00 2.74
2815 2845 1.525995 CTTGGCCTCGTGTTGGTGT 60.526 57.895 3.32 0.00 0.00 4.16
2851 2883 4.742201 TTGCTGCTCCCGTCGCTC 62.742 66.667 0.00 0.00 0.00 5.03



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

AutoCloner maintained by Alex Coulton.