Multiple sequence alignment - TraesCS7A01G218300

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 TraesCS7A01G218300 chr7A 100.000 3121 0 0 1 3121 185062927 185066047 0.000000e+00 5764.0
1 TraesCS7A01G218300 chr7A 96.037 2927 111 5 1 2924 185132382 185135306 0.000000e+00 4758.0
2 TraesCS7A01G218300 chr7A 93.283 2799 150 17 350 3121 184971300 184974087 0.000000e+00 4093.0
3 TraesCS7A01G218300 chr7A 85.554 623 77 10 2506 3121 519186783 519186167 9.440000e-180 640.0
4 TraesCS7A01G218300 chr7A 89.510 143 13 2 1 142 184971117 184971258 2.470000e-41 180.0
5 TraesCS7A01G218300 chr7D 96.472 1984 62 5 524 2506 180592596 180594572 0.000000e+00 3269.0
6 TraesCS7A01G218300 chr7D 87.752 1837 186 17 549 2364 585182921 585184739 0.000000e+00 2109.0
7 TraesCS7A01G218300 chr7D 87.534 1837 185 20 549 2364 585191941 585193754 0.000000e+00 2084.0
8 TraesCS7A01G218300 chr7D 88.614 202 18 3 144 340 511154391 511154190 1.120000e-59 241.0
9 TraesCS7A01G218300 chr7D 88.614 202 18 3 144 340 511156806 511156605 1.120000e-59 241.0
10 TraesCS7A01G218300 chr7D 88.614 202 18 3 144 340 511159223 511159022 1.120000e-59 241.0
11 TraesCS7A01G218300 chr7D 88.614 202 18 3 144 340 511161649 511161448 1.120000e-59 241.0
12 TraesCS7A01G218300 chr7D 88.614 202 18 3 144 340 511164071 511163870 1.120000e-59 241.0
13 TraesCS7A01G218300 chr7D 89.944 179 13 4 349 524 180592368 180592544 3.130000e-55 226.0
14 TraesCS7A01G218300 chr7D 90.845 142 13 0 1 142 180592184 180592325 1.140000e-44 191.0
15 TraesCS7A01G218300 chr7B 91.037 1986 165 7 525 2506 146256134 146258110 0.000000e+00 2669.0
16 TraesCS7A01G218300 chr7B 87.266 1445 168 10 885 2326 653800122 653801553 0.000000e+00 1635.0
17 TraesCS7A01G218300 chr7B 93.443 61 4 0 82 142 146251507 146251567 1.190000e-14 91.6
18 TraesCS7A01G218300 chr5B 87.157 1822 195 17 549 2352 684386322 684388122 0.000000e+00 2032.0
19 TraesCS7A01G218300 chr5B 84.135 624 90 6 2503 3121 176244506 176243887 2.070000e-166 595.0
20 TraesCS7A01G218300 chr6D 80.558 1111 198 14 1021 2125 432931413 432930315 0.000000e+00 839.0
21 TraesCS7A01G218300 chr5A 85.256 624 84 6 2502 3121 428709179 428708560 1.220000e-178 636.0
22 TraesCS7A01G218300 chr2D 84.776 624 87 6 2504 3121 552101551 552102172 1.230000e-173 619.0
23 TraesCS7A01G218300 chr4D 84.102 629 88 8 2502 3121 275767452 275766827 5.760000e-167 597.0
24 TraesCS7A01G218300 chr4D 89.109 202 17 3 144 340 36473772 36473571 2.400000e-61 246.0
25 TraesCS7A01G218300 chr4D 88.614 202 18 3 144 340 36474366 36474165 1.120000e-59 241.0
26 TraesCS7A01G218300 chr2A 84.185 626 88 8 2502 3120 539961875 539961254 5.760000e-167 597.0
27 TraesCS7A01G218300 chr2B 84.051 627 91 6 2502 3121 161225909 161225285 2.070000e-166 595.0
28 TraesCS7A01G218300 chr1D 85.437 206 26 4 145 348 42956627 42956830 8.770000e-51 211.0


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 TraesCS7A01G218300 chr7A 185062927 185066047 3120 False 5764.000000 5764 100.000000 1 3121 1 chr7A.!!$F1 3120
1 TraesCS7A01G218300 chr7A 185132382 185135306 2924 False 4758.000000 4758 96.037000 1 2924 1 chr7A.!!$F2 2923
2 TraesCS7A01G218300 chr7A 184971117 184974087 2970 False 2136.500000 4093 91.396500 1 3121 2 chr7A.!!$F3 3120
3 TraesCS7A01G218300 chr7A 519186167 519186783 616 True 640.000000 640 85.554000 2506 3121 1 chr7A.!!$R1 615
4 TraesCS7A01G218300 chr7D 585182921 585184739 1818 False 2109.000000 2109 87.752000 549 2364 1 chr7D.!!$F1 1815
5 TraesCS7A01G218300 chr7D 585191941 585193754 1813 False 2084.000000 2084 87.534000 549 2364 1 chr7D.!!$F2 1815
6 TraesCS7A01G218300 chr7D 180592184 180594572 2388 False 1228.666667 3269 92.420333 1 2506 3 chr7D.!!$F3 2505
7 TraesCS7A01G218300 chr7D 511154190 511164071 9881 True 241.000000 241 88.614000 144 340 5 chr7D.!!$R1 196
8 TraesCS7A01G218300 chr7B 146256134 146258110 1976 False 2669.000000 2669 91.037000 525 2506 1 chr7B.!!$F2 1981
9 TraesCS7A01G218300 chr7B 653800122 653801553 1431 False 1635.000000 1635 87.266000 885 2326 1 chr7B.!!$F3 1441
10 TraesCS7A01G218300 chr5B 684386322 684388122 1800 False 2032.000000 2032 87.157000 549 2352 1 chr5B.!!$F1 1803
11 TraesCS7A01G218300 chr5B 176243887 176244506 619 True 595.000000 595 84.135000 2503 3121 1 chr5B.!!$R1 618
12 TraesCS7A01G218300 chr6D 432930315 432931413 1098 True 839.000000 839 80.558000 1021 2125 1 chr6D.!!$R1 1104
13 TraesCS7A01G218300 chr5A 428708560 428709179 619 True 636.000000 636 85.256000 2502 3121 1 chr5A.!!$R1 619
14 TraesCS7A01G218300 chr2D 552101551 552102172 621 False 619.000000 619 84.776000 2504 3121 1 chr2D.!!$F1 617
15 TraesCS7A01G218300 chr4D 275766827 275767452 625 True 597.000000 597 84.102000 2502 3121 1 chr4D.!!$R1 619
16 TraesCS7A01G218300 chr4D 36473571 36474366 795 True 243.500000 246 88.861500 144 340 2 chr4D.!!$R2 196
17 TraesCS7A01G218300 chr2A 539961254 539961875 621 True 597.000000 597 84.185000 2502 3120 1 chr2A.!!$R1 618
18 TraesCS7A01G218300 chr2B 161225285 161225909 624 True 595.000000 595 84.051000 2502 3121 1 chr2B.!!$R1 619

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
224 226 0.652071 CGCACACACGCACATCATAT 59.348 50.000 0.00 0.0 0.00 1.78 F
865 3373 0.796312 CTTCGTGCAAGCACCGTATT 59.204 50.000 18.54 0.0 43.49 1.89 F
1685 8973 1.227527 CGGGCTTATGGACGATGCA 60.228 57.895 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1112 3624 0.393537 CTGGGCCATCCAACTCTCAC 60.394 60.000 6.72 0.0 46.51 3.51 R
1935 9710 1.005805 TGCAATGCCATGGTCTAGGTT 59.994 47.619 14.67 0.0 0.00 3.50 R
2946 11521 1.107538 CGAAGGCCCTATCCGTCTCA 61.108 60.000 0.00 0.0 33.31 3.27 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
142 144 3.128589 TCGGAAGCAATAGCAATTGTTCC 59.871 43.478 7.40 9.16 43.75 3.62
181 183 2.061773 GACGCAAGCGCTCATATACAT 58.938 47.619 12.06 0.00 44.19 2.29
221 223 2.100024 GAACGCACACACGCACATCA 62.100 55.000 0.00 0.00 36.19 3.07
224 226 0.652071 CGCACACACGCACATCATAT 59.348 50.000 0.00 0.00 0.00 1.78
264 2688 1.696336 AGACTGAGCCGGCATATCATT 59.304 47.619 31.54 17.84 0.00 2.57
319 2748 1.078426 GGCTGCGGATACCACAGTT 60.078 57.895 0.00 0.00 39.02 3.16
336 2765 5.338708 CCACAGTTCCTCTAATCATCCAACT 60.339 44.000 0.00 0.00 0.00 3.16
341 2770 6.897966 AGTTCCTCTAATCATCCAACTACAGA 59.102 38.462 0.00 0.00 0.00 3.41
437 2868 7.902032 TCGACTTAATTACGCAGGAAAATAAG 58.098 34.615 0.00 0.00 31.05 1.73
438 2869 7.546667 TCGACTTAATTACGCAGGAAAATAAGT 59.453 33.333 11.30 11.30 36.56 2.24
528 3013 8.314021 ACAATGAAAAAGAAAGAGGAAACAAGT 58.686 29.630 0.00 0.00 0.00 3.16
535 3020 2.256117 AGAGGAAACAAGTCGTTGGG 57.744 50.000 0.00 0.00 38.07 4.12
687 3175 2.787473 TGGACCAGAAGTAATGGCTG 57.213 50.000 0.00 0.00 41.87 4.85
688 3176 1.985159 TGGACCAGAAGTAATGGCTGT 59.015 47.619 0.00 0.00 41.87 4.40
703 3191 5.975693 ATGGCTGTCTCTAGATTAGCTAC 57.024 43.478 17.32 7.30 37.32 3.58
865 3373 0.796312 CTTCGTGCAAGCACCGTATT 59.204 50.000 18.54 0.00 43.49 1.89
937 3447 7.562088 ACCTAGTTCCATTTGTTAAACCAAAGA 59.438 33.333 0.00 0.00 37.71 2.52
1011 3523 2.120909 GGTCAACATGGCCATCCCG 61.121 63.158 17.61 7.75 42.98 5.14
1013 3525 2.440796 CAACATGGCCATCCCGCT 60.441 61.111 17.61 0.00 35.87 5.52
1146 3658 1.514087 CCAGTACGGCCGTGTGTAT 59.486 57.895 40.02 17.99 0.00 2.29
1253 4703 4.568152 AGTTCTTTTTGGGTGTCAATCG 57.432 40.909 0.00 0.00 34.98 3.34
1389 8068 2.301870 ACTTCCGGCAACAGTAGATTGA 59.698 45.455 0.00 0.00 0.00 2.57
1685 8973 1.227527 CGGGCTTATGGACGATGCA 60.228 57.895 0.00 0.00 0.00 3.96
1741 9029 6.153942 TGGTGAGTCTAGCTACCCATATAT 57.846 41.667 0.00 0.00 32.20 0.86
1807 9095 2.402305 CATCAAGAGCTACGAGGATGC 58.598 52.381 0.00 0.00 0.00 3.91
1935 9710 0.320421 GACTGGTTCTTGCGGCACTA 60.320 55.000 0.05 0.00 0.00 2.74
1987 10043 1.740380 CGGAAAGACGAGTGATGGCAT 60.740 52.381 0.00 0.00 35.47 4.40
2187 10588 9.169468 GATTAAATAAACATATGCACCTTGTCG 57.831 33.333 1.58 0.00 0.00 4.35
2448 10987 5.601313 AGTTTACTGTCCTACAAGTTCTCCA 59.399 40.000 0.00 0.00 0.00 3.86
2461 11000 2.624838 AGTTCTCCATGTGGCAAACAAG 59.375 45.455 14.58 0.00 43.61 3.16
2492 11031 4.503910 CATGTTCGTCTTCTCCATGGTAA 58.496 43.478 12.58 6.87 31.49 2.85
2647 11192 3.203040 AGCCTTGCAACCCTCTGTATATT 59.797 43.478 0.00 0.00 0.00 1.28
2751 11296 5.423015 GTCTATGTTCTTCATCCTTGCAGA 58.577 41.667 0.00 0.00 37.91 4.26
2903 11478 5.144359 GTGTAGTCATTAAACGCACAAAGG 58.856 41.667 0.00 0.00 33.35 3.11
2946 11521 4.104102 TCTTAATTATCGAGGCAACCCCAT 59.896 41.667 0.00 0.00 35.39 4.00
3044 11621 4.261801 CATCCCCACTTCGTTTCATAACT 58.738 43.478 0.00 0.00 31.89 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.180492 CGGCCTCTCATGTTTTAACTTGTAA 59.820 40.000 0.00 0.00 36.02 2.41
154 156 2.202518 GCGCTTGCGTCCGTACTA 60.203 61.111 16.38 0.00 0.00 1.82
181 183 2.003937 TAGGGGTGAGTATATGCGCA 57.996 50.000 14.96 14.96 0.00 6.09
189 191 1.479323 GTGCGTTCATAGGGGTGAGTA 59.521 52.381 0.00 0.00 0.00 2.59
221 223 3.779444 TCGAAGGTGCTCATAGGGATAT 58.221 45.455 0.00 0.00 0.00 1.63
224 226 1.860641 TTCGAAGGTGCTCATAGGGA 58.139 50.000 0.00 0.00 0.00 4.20
264 2688 4.198530 TCCTGATGCTCGCATTTATCAAA 58.801 39.130 5.79 0.00 36.70 2.69
319 2748 7.730084 CAATCTGTAGTTGGATGATTAGAGGA 58.270 38.462 0.00 0.00 0.00 3.71
336 2765 7.120579 AGCGAAAATGTTATCAACCAATCTGTA 59.879 33.333 0.00 0.00 0.00 2.74
341 2770 7.033185 GGTTAGCGAAAATGTTATCAACCAAT 58.967 34.615 0.00 0.00 34.42 3.16
410 2839 9.531942 TTATTTTCCTGCGTAATTAAGTCGATA 57.468 29.630 0.35 0.00 0.00 2.92
528 3013 3.059982 CTCTGACTGCCCCAACGA 58.940 61.111 0.00 0.00 0.00 3.85
535 3020 2.999355 CAACTTCTTAGCTCTGACTGCC 59.001 50.000 0.00 0.00 0.00 4.85
582 3068 9.274065 GCCTTTAACGATTATTACAACTTCTTG 57.726 33.333 0.00 0.00 0.00 3.02
865 3373 8.707449 ACGTAATTAAGTATTGGGGATAGTGAA 58.293 33.333 1.92 0.00 0.00 3.18
937 3447 5.070001 AGTATGCAGTATGTGTGTGGTTTT 58.930 37.500 0.00 0.00 39.31 2.43
1011 3523 2.677199 GCAAGGAGCAAAACCTTTAGC 58.323 47.619 0.00 0.00 44.13 3.09
1112 3624 0.393537 CTGGGCCATCCAACTCTCAC 60.394 60.000 6.72 0.00 46.51 3.51
1389 8068 3.236003 GACCGCACCCTTCGTCCTT 62.236 63.158 0.00 0.00 0.00 3.36
1673 8797 4.512484 TGAACTTGAATGCATCGTCCATA 58.488 39.130 0.00 0.00 0.00 2.74
1685 8973 6.642131 CACCGTTTGAAATGATGAACTTGAAT 59.358 34.615 0.00 0.00 0.00 2.57
1741 9029 1.202915 TGCACTTTCCATCTTCTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
1807 9095 2.179018 CTTCATTGTTGGCCGGCG 59.821 61.111 22.54 4.34 0.00 6.46
1935 9710 1.005805 TGCAATGCCATGGTCTAGGTT 59.994 47.619 14.67 0.00 0.00 3.50
2187 10588 8.128322 TGAAGACATATAAGAGAATCCCTAGC 57.872 38.462 0.00 0.00 33.66 3.42
2448 10987 3.555586 GCTGAATTCCTTGTTTGCCACAT 60.556 43.478 2.27 0.00 34.43 3.21
2461 11000 3.686726 AGAAGACGAACATGCTGAATTCC 59.313 43.478 2.27 0.00 0.00 3.01
2540 11079 7.268586 GTCATAGAACACATCATGAAGGTAGT 58.731 38.462 0.00 0.49 31.71 2.73
2647 11192 3.164268 CACTTCCATTGATCCCCACAAA 58.836 45.455 0.00 0.00 0.00 2.83
2751 11296 3.116590 TCACTCTCCATGATCCTGGGTAT 60.117 47.826 16.09 0.00 36.89 2.73
2800 11345 1.295792 TCAGAACAACACTTCACGGC 58.704 50.000 0.00 0.00 0.00 5.68
2867 11442 6.380079 AATGACTACACCTCTTGAATCCTT 57.620 37.500 0.00 0.00 0.00 3.36
2946 11521 1.107538 CGAAGGCCCTATCCGTCTCA 61.108 60.000 0.00 0.00 33.31 3.27
3044 11621 1.204704 GTCACCCATCGAGATGTGACA 59.795 52.381 26.33 0.00 41.05 3.58


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

AutoCloner maintained by Alex Coulton.