Multiple sequence alignment - TraesCS2B01G270200

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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 TraesCS2B01G270200 chr2B 100.000 2798 0 0 1 2798 368416487 368413690 0.000000e+00 5168.0
1 TraesCS2B01G270200 chr2B 80.196 409 60 12 255 645 58831555 58831150 1.270000e-73 287.0
2 TraesCS2B01G270200 chr2D 96.168 2114 55 5 689 2798 291994262 291992171 0.000000e+00 3432.0
3 TraesCS2B01G270200 chr2D 95.960 495 19 1 124 617 291996573 291996079 0.000000e+00 802.0
4 TraesCS2B01G270200 chr2D 93.130 131 7 1 1 129 291996742 291996612 1.020000e-44 191.0
5 TraesCS2B01G270200 chr2D 85.039 127 15 2 1 124 586984105 586983980 2.930000e-25 126.0
6 TraesCS2B01G270200 chr2D 94.937 79 4 0 620 698 291995207 291995129 1.050000e-24 124.0
7 TraesCS2B01G270200 chr2A 96.539 1907 47 8 587 2488 342650037 342648145 0.000000e+00 3138.0
8 TraesCS2B01G270200 chr2A 94.979 478 23 1 124 600 342650534 342650057 0.000000e+00 749.0
9 TraesCS2B01G270200 chr2A 96.667 210 7 0 2584 2793 342647895 342647686 1.590000e-92 350.0
10 TraesCS2B01G270200 chr2A 90.909 132 9 2 1 129 342650703 342650572 1.030000e-39 174.0
11 TraesCS2B01G270200 chr4D 84.859 568 71 11 124 685 308469629 308470187 2.430000e-155 558.0
12 TraesCS2B01G270200 chr4D 77.707 157 22 9 2337 2487 117658485 117658336 1.790000e-12 84.2
13 TraesCS2B01G270200 chr4B 84.127 567 76 10 124 685 384336753 384337310 1.140000e-148 536.0
14 TraesCS2B01G270200 chr6B 81.206 564 87 13 123 672 62159351 62158793 1.190000e-118 436.0
15 TraesCS2B01G270200 chr6B 81.013 237 37 7 218 450 647110 646878 6.160000e-42 182.0
16 TraesCS2B01G270200 chr6B 86.486 74 9 1 1 74 10603048 10603120 2.310000e-11 80.5
17 TraesCS2B01G270200 chr7B 82.051 195 24 8 2364 2551 203741573 203741763 3.730000e-34 156.0
18 TraesCS2B01G270200 chr7A 86.957 115 11 2 1 112 16616940 16617053 2.930000e-25 126.0
19 TraesCS2B01G270200 chr7A 94.444 36 2 0 2264 2299 110927131 110927096 3.890000e-04 56.5
20 TraesCS2B01G270200 chr7A 94.444 36 2 0 2264 2299 177697389 177697354 3.890000e-04 56.5
21 TraesCS2B01G270200 chr4A 77.160 162 27 9 2334 2487 457822177 457822336 4.970000e-13 86.1
22 TraesCS2B01G270200 chr6A 92.857 42 3 0 2264 2305 99990337 99990296 8.370000e-06 62.1
23 TraesCS2B01G270200 chr1B 100.000 33 0 0 2264 2296 164949810 164949842 8.370000e-06 62.1
24 TraesCS2B01G270200 chr1B 97.222 36 1 0 2264 2299 487040978 487040943 8.370000e-06 62.1
25 TraesCS2B01G270200 chr6D 94.737 38 2 0 2268 2305 3123562 3123525 3.010000e-05 60.2


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 TraesCS2B01G270200 chr2B 368413690 368416487 2797 True 5168.00 5168 100.00000 1 2798 1 chr2B.!!$R2 2797
1 TraesCS2B01G270200 chr2D 291992171 291996742 4571 True 1137.25 3432 95.04875 1 2798 4 chr2D.!!$R2 2797
2 TraesCS2B01G270200 chr2A 342647686 342650703 3017 True 1102.75 3138 94.77350 1 2793 4 chr2A.!!$R1 2792
3 TraesCS2B01G270200 chr4D 308469629 308470187 558 False 558.00 558 84.85900 124 685 1 chr4D.!!$F1 561
4 TraesCS2B01G270200 chr4B 384336753 384337310 557 False 536.00 536 84.12700 124 685 1 chr4B.!!$F1 561
5 TraesCS2B01G270200 chr6B 62158793 62159351 558 True 436.00 436 81.20600 123 672 1 chr6B.!!$R2 549

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
919 2760 1.043673 CAAACCCCCACGAAAACCCA 61.044 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2533 4375 1.574526 CCCCCTCCCAAATCTGCTCA 61.575 60.0 0.0 0.0 0.0 4.26 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
100 104 3.031736 TGTGCCTTAGAGTATCCAGGTC 58.968 50.000 0.00 0.00 38.16 3.85
209 258 6.781138 TGTATAAAGAAATCGTCAATGCACC 58.219 36.000 0.00 0.00 0.00 5.01
365 419 7.981102 AAGTGTGGACCTTTCTATAAAAGTC 57.019 36.000 0.00 0.00 35.95 3.01
452 506 9.683069 ATTCACTAACACAAATTTTCATCTGTC 57.317 29.630 0.00 0.00 0.00 3.51
573 629 7.756722 GGTTGAACCAGATGATATTTGAACTTG 59.243 37.037 9.98 0.00 38.42 3.16
574 630 7.395190 TGAACCAGATGATATTTGAACTTGG 57.605 36.000 0.00 0.00 0.00 3.61
575 631 5.841957 ACCAGATGATATTTGAACTTGGC 57.158 39.130 0.00 0.00 0.00 4.52
576 632 5.513233 ACCAGATGATATTTGAACTTGGCT 58.487 37.500 0.00 0.00 0.00 4.75
577 633 6.662755 ACCAGATGATATTTGAACTTGGCTA 58.337 36.000 0.00 0.00 0.00 3.93
610 702 6.200854 GGAACAACTTTGGCTGAAACATTTAG 59.799 38.462 0.00 0.00 0.00 1.85
617 709 9.255029 ACTTTGGCTGAAACATTTAGGTTATAT 57.745 29.630 0.00 0.00 0.00 0.86
618 710 9.520204 CTTTGGCTGAAACATTTAGGTTATATG 57.480 33.333 0.00 0.00 0.00 1.78
677 1640 5.650266 TCGTACCTGTCGGTATTTACCTAAA 59.350 40.000 5.29 0.00 46.93 1.85
781 2620 4.736126 AGTTGTTTTTGGGAAGGTTGAG 57.264 40.909 0.00 0.00 0.00 3.02
880 2721 2.573609 CTACCCCGTTCGCTCCCTTG 62.574 65.000 0.00 0.00 0.00 3.61
919 2760 1.043673 CAAACCCCCACGAAAACCCA 61.044 55.000 0.00 0.00 0.00 4.51
1122 2963 0.036388 ATCGCCACATGAACCTCGTT 60.036 50.000 0.00 0.00 0.00 3.85
1599 3440 4.320456 CCTCCGCCTGCGCCATAT 62.320 66.667 4.18 0.00 38.24 1.78
1785 3626 0.322277 CACAGCAGCCTGGACAGAAT 60.322 55.000 0.00 0.00 43.53 2.40
1808 3649 3.005791 CCCCAGCAGTAGAAAAACCTTTG 59.994 47.826 0.00 0.00 0.00 2.77
1945 3786 8.925700 TCGTATCATGATCTGTAATATTTGCAC 58.074 33.333 12.53 0.00 0.00 4.57
2052 3893 2.145397 AGCTGATGAGACCCGTCTTA 57.855 50.000 0.00 0.00 40.61 2.10
2136 3977 3.455910 AGCCTAGAACATGCCATAACTCA 59.544 43.478 0.00 0.00 0.00 3.41
2361 4203 4.469883 AGTGTCCTTGCACTGCAG 57.530 55.556 13.48 13.48 46.72 4.41
2403 4245 8.891671 ACATGTTCACAAGCTTGAAAATAATT 57.108 26.923 32.50 4.68 37.24 1.40
2404 4246 8.767085 ACATGTTCACAAGCTTGAAAATAATTG 58.233 29.630 32.50 17.03 37.24 2.32
2409 4251 5.121142 CACAAGCTTGAAAATAATTGCCCTG 59.879 40.000 32.50 11.12 0.00 4.45
2533 4375 5.164620 CCAAGGGGTTTTCTGCAAATATT 57.835 39.130 0.00 0.00 0.00 1.28
2624 4620 1.605710 GGTCAGAAATGATGGATGGCG 59.394 52.381 0.00 0.00 0.00 5.69
2740 4736 6.780522 AGTTCCATTTCCTCCTCTAGTCTATC 59.219 42.308 0.00 0.00 0.00 2.08
2760 4756 5.820404 ATCATGAGATGGAAGTGCATCTA 57.180 39.130 14.43 1.01 38.18 1.98
2761 4757 5.820404 TCATGAGATGGAAGTGCATCTAT 57.180 39.130 14.43 7.00 38.18 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.106857 TCCTGCGGAAAAAGGTTCCTAA 59.893 45.455 0.00 0.00 36.45 2.69
114 118 6.597672 AGAAATGGTACGCATGATTCTTACAA 59.402 34.615 0.00 0.00 0.00 2.41
209 258 6.920569 AAAGATAGTACCTTTGGCATTACG 57.079 37.500 0.00 0.00 33.07 3.18
257 306 8.227119 ACAAATTTTAGTTCACAAAACAGCAAC 58.773 29.630 0.00 0.00 0.00 4.17
423 477 9.903682 AGATGAAAATTTGTGTTAGTGAATGAG 57.096 29.630 0.00 0.00 0.00 2.90
512 566 1.459975 GAAGCTTCCTTCGAACCGAAC 59.540 52.381 15.97 0.00 41.05 3.95
559 615 9.276590 CTATCATGTAGCCAAGTTCAAATATCA 57.723 33.333 0.00 0.00 0.00 2.15
563 619 6.662755 TCCTATCATGTAGCCAAGTTCAAAT 58.337 36.000 0.00 0.00 0.00 2.32
573 629 5.066505 CCAAAGTTGTTCCTATCATGTAGCC 59.933 44.000 0.00 0.00 0.00 3.93
574 630 5.449177 GCCAAAGTTGTTCCTATCATGTAGC 60.449 44.000 0.00 0.00 0.00 3.58
575 631 5.882557 AGCCAAAGTTGTTCCTATCATGTAG 59.117 40.000 0.00 0.00 0.00 2.74
576 632 5.647658 CAGCCAAAGTTGTTCCTATCATGTA 59.352 40.000 0.00 0.00 0.00 2.29
577 633 4.460382 CAGCCAAAGTTGTTCCTATCATGT 59.540 41.667 0.00 0.00 0.00 3.21
610 702 9.398538 TGGTTACAAACACTTATCCATATAACC 57.601 33.333 0.00 0.00 38.75 2.85
617 709 5.013547 CCCATGGTTACAAACACTTATCCA 58.986 41.667 11.73 0.00 0.00 3.41
618 710 5.014202 ACCCATGGTTACAAACACTTATCC 58.986 41.667 11.73 0.00 27.29 2.59
781 2620 4.891037 GATGGGCCTGGGCAGAGC 62.891 72.222 22.68 6.80 44.11 4.09
880 2721 2.224917 TGAGTTTGTATGGGTTGGGTCC 60.225 50.000 0.00 0.00 0.00 4.46
919 2760 1.478654 GGAGAAGCGGAGAGGAGAGAT 60.479 57.143 0.00 0.00 0.00 2.75
995 2836 3.910914 TTGGGGTTCGACATGGCGG 62.911 63.158 23.19 2.05 0.00 6.13
1785 3626 2.062636 AGGTTTTTCTACTGCTGGGGA 58.937 47.619 0.00 0.00 0.00 4.81
1972 3813 4.261825 GCAAGCCACCACAACACTAATTTA 60.262 41.667 0.00 0.00 0.00 1.40
2136 3977 3.139957 TGTCTAGATCTGAGGAGAGCCAT 59.860 47.826 5.18 0.00 34.98 4.40
2361 4203 6.204688 TGAACATGTATCTATTTTGGATCCGC 59.795 38.462 7.39 0.00 0.00 5.54
2403 4245 4.663120 AGTGATATATACCAAACCAGGGCA 59.337 41.667 0.00 0.00 0.00 5.36
2404 4246 5.242795 AGTGATATATACCAAACCAGGGC 57.757 43.478 0.00 0.00 0.00 5.19
2533 4375 1.574526 CCCCCTCCCAAATCTGCTCA 61.575 60.000 0.00 0.00 0.00 4.26
2624 4620 2.503331 TGGTGATGATGGTGTGTGTTC 58.497 47.619 0.00 0.00 0.00 3.18
2655 4651 7.507616 AGGTAGAACAAATCTCCACTCCTATAG 59.492 40.741 0.00 0.00 39.71 1.31
2740 4736 4.695928 CCATAGATGCACTTCCATCTCATG 59.304 45.833 7.84 9.78 46.75 3.07
2760 4756 7.337938 TCATGACTACATAACATGTGAACCAT 58.662 34.615 0.00 0.00 44.60 3.55
2761 4757 6.706295 TCATGACTACATAACATGTGAACCA 58.294 36.000 0.00 0.00 44.60 3.67


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

AutoCloner maintained by Alex Coulton.