Multiple sequence alignment - TraesCS4B01G183300

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 TraesCS4B01G183300 chr4B 100.000 2375 0 0 1 2375 402841799 402844173 0.000000e+00 4386
1 TraesCS4B01G183300 chr4B 97.392 1649 36 2 1 1642 402866638 402868286 0.000000e+00 2800
2 TraesCS4B01G183300 chr4B 95.148 742 34 2 1636 2375 327372171 327371430 0.000000e+00 1170
3 TraesCS4B01G183300 chr4B 91.098 820 60 4 1 807 213134179 213133360 0.000000e+00 1098
4 TraesCS4B01G183300 chr7B 97.522 807 19 1 837 1642 112890845 112891651 0.000000e+00 1378
5 TraesCS4B01G183300 chr7B 94.959 734 37 0 1642 2375 509578536 509579269 0.000000e+00 1151
6 TraesCS4B01G183300 chr7D 97.274 807 17 4 837 1642 150833784 150834586 0.000000e+00 1363
7 TraesCS4B01G183300 chr7D 91.597 833 44 9 1 807 16359378 16360210 0.000000e+00 1127
8 TraesCS4B01G183300 chr6B 95.539 807 36 0 1 807 556779737 556780543 0.000000e+00 1291
9 TraesCS4B01G183300 chr6B 92.874 828 45 6 1 814 191374630 191373803 0.000000e+00 1190
10 TraesCS4B01G183300 chr6B 94.370 746 40 2 1632 2375 524346460 524347205 0.000000e+00 1144
11 TraesCS4B01G183300 chr6B 94.474 742 40 1 1634 2375 668990603 668991343 0.000000e+00 1142
12 TraesCS4B01G183300 chr6B 86.983 822 77 11 1 807 126861648 126862454 0.000000e+00 898
13 TraesCS4B01G183300 chr3B 95.415 807 35 1 1 807 657496400 657497204 0.000000e+00 1284
14 TraesCS4B01G183300 chr3B 96.097 743 25 4 1635 2375 709821667 709820927 0.000000e+00 1208
15 TraesCS4B01G183300 chr3B 95.907 733 29 1 1643 2375 730281743 730281012 0.000000e+00 1186
16 TraesCS4B01G183300 chr4D 93.245 829 41 5 1 814 506289856 506289028 0.000000e+00 1206
17 TraesCS4B01G183300 chr2B 94.624 744 36 3 1632 2375 50392209 50391470 0.000000e+00 1149
18 TraesCS4B01G183300 chr2B 86.842 836 72 18 1 808 542930069 542930894 0.000000e+00 900
19 TraesCS4B01G183300 chr2B 91.667 492 28 3 337 815 207709169 207709660 0.000000e+00 669
20 TraesCS4B01G183300 chr5B 94.595 740 40 0 1636 2375 49306804 49307543 0.000000e+00 1146
21 TraesCS4B01G183300 chr5B 94.687 734 39 0 1642 2375 450555668 450554935 0.000000e+00 1140
22 TraesCS4B01G183300 chr5B 84.054 740 62 32 837 1561 631479712 631480410 0.000000e+00 662
23 TraesCS4B01G183300 chr5B 84.951 206 12 9 837 1036 629771625 629771817 8.660000e-45 191
24 TraesCS4B01G183300 chr5B 84.466 206 12 10 837 1036 626703962 626704153 4.030000e-43 185
25 TraesCS4B01G183300 chr7A 91.542 804 47 8 1 783 126369101 126368298 0.000000e+00 1088
26 TraesCS4B01G183300 chr5D 90.188 744 40 7 97 807 394269147 394268404 0.000000e+00 939
27 TraesCS4B01G183300 chr5D 91.353 451 23 11 1109 1556 502702187 502702624 9.390000e-169 603
28 TraesCS4B01G183300 chr5D 82.833 233 26 9 1192 1421 502698708 502698929 1.860000e-46 196
29 TraesCS4B01G183300 chr6A 89.957 468 32 5 356 808 49153733 49153266 7.310000e-165 590
30 TraesCS4B01G183300 chr5A 86.188 543 33 18 1101 1642 631359813 631360314 1.240000e-152 549
31 TraesCS4B01G183300 chr5A 81.273 267 29 13 1162 1420 631354312 631354565 1.860000e-46 196
32 TraesCS4B01G183300 chr5A 89.157 83 4 4 837 914 631359368 631359450 5.400000e-17 99


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 TraesCS4B01G183300 chr4B 402841799 402844173 2374 False 4386.0 4386 100.0000 1 2375 1 chr4B.!!$F1 2374
1 TraesCS4B01G183300 chr4B 402866638 402868286 1648 False 2800.0 2800 97.3920 1 1642 1 chr4B.!!$F2 1641
2 TraesCS4B01G183300 chr4B 327371430 327372171 741 True 1170.0 1170 95.1480 1636 2375 1 chr4B.!!$R2 739
3 TraesCS4B01G183300 chr4B 213133360 213134179 819 True 1098.0 1098 91.0980 1 807 1 chr4B.!!$R1 806
4 TraesCS4B01G183300 chr7B 112890845 112891651 806 False 1378.0 1378 97.5220 837 1642 1 chr7B.!!$F1 805
5 TraesCS4B01G183300 chr7B 509578536 509579269 733 False 1151.0 1151 94.9590 1642 2375 1 chr7B.!!$F2 733
6 TraesCS4B01G183300 chr7D 150833784 150834586 802 False 1363.0 1363 97.2740 837 1642 1 chr7D.!!$F2 805
7 TraesCS4B01G183300 chr7D 16359378 16360210 832 False 1127.0 1127 91.5970 1 807 1 chr7D.!!$F1 806
8 TraesCS4B01G183300 chr6B 556779737 556780543 806 False 1291.0 1291 95.5390 1 807 1 chr6B.!!$F3 806
9 TraesCS4B01G183300 chr6B 191373803 191374630 827 True 1190.0 1190 92.8740 1 814 1 chr6B.!!$R1 813
10 TraesCS4B01G183300 chr6B 524346460 524347205 745 False 1144.0 1144 94.3700 1632 2375 1 chr6B.!!$F2 743
11 TraesCS4B01G183300 chr6B 668990603 668991343 740 False 1142.0 1142 94.4740 1634 2375 1 chr6B.!!$F4 741
12 TraesCS4B01G183300 chr6B 126861648 126862454 806 False 898.0 898 86.9830 1 807 1 chr6B.!!$F1 806
13 TraesCS4B01G183300 chr3B 657496400 657497204 804 False 1284.0 1284 95.4150 1 807 1 chr3B.!!$F1 806
14 TraesCS4B01G183300 chr3B 709820927 709821667 740 True 1208.0 1208 96.0970 1635 2375 1 chr3B.!!$R1 740
15 TraesCS4B01G183300 chr3B 730281012 730281743 731 True 1186.0 1186 95.9070 1643 2375 1 chr3B.!!$R2 732
16 TraesCS4B01G183300 chr4D 506289028 506289856 828 True 1206.0 1206 93.2450 1 814 1 chr4D.!!$R1 813
17 TraesCS4B01G183300 chr2B 50391470 50392209 739 True 1149.0 1149 94.6240 1632 2375 1 chr2B.!!$R1 743
18 TraesCS4B01G183300 chr2B 542930069 542930894 825 False 900.0 900 86.8420 1 808 1 chr2B.!!$F2 807
19 TraesCS4B01G183300 chr5B 49306804 49307543 739 False 1146.0 1146 94.5950 1636 2375 1 chr5B.!!$F1 739
20 TraesCS4B01G183300 chr5B 450554935 450555668 733 True 1140.0 1140 94.6870 1642 2375 1 chr5B.!!$R1 733
21 TraesCS4B01G183300 chr5B 631479712 631480410 698 False 662.0 662 84.0540 837 1561 1 chr5B.!!$F4 724
22 TraesCS4B01G183300 chr7A 126368298 126369101 803 True 1088.0 1088 91.5420 1 783 1 chr7A.!!$R1 782
23 TraesCS4B01G183300 chr5D 394268404 394269147 743 True 939.0 939 90.1880 97 807 1 chr5D.!!$R1 710
24 TraesCS4B01G183300 chr5D 502698708 502702624 3916 False 399.5 603 87.0930 1109 1556 2 chr5D.!!$F1 447
25 TraesCS4B01G183300 chr5A 631359368 631360314 946 False 324.0 549 87.6725 837 1642 2 chr5A.!!$F2 805

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
980 1106 1.047002 CCACAAATCCCCACTTTGCA 58.953 50.0 0.0 0.0 37.15 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 4850 0.631753 TTGGGGTGTGGTTTTGAGGA 59.368 50.0 0.0 0.0 0.0 3.71 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
102 117 7.707624 TCTATTTTTGTCAGATGGCTTGAAT 57.292 32.000 0.00 0.00 0.00 2.57
477 512 4.681942 GCATAACTAACACGCTAGATCCTG 59.318 45.833 0.00 0.00 0.00 3.86
681 733 1.440618 TACCAAGGAAACCTGCAGGA 58.559 50.000 39.19 9.77 38.94 3.86
873 938 3.648545 GGGATCATAGCTCCTAGGTTTGT 59.351 47.826 9.08 0.00 33.05 2.83
980 1106 1.047002 CCACAAATCCCCACTTTGCA 58.953 50.000 0.00 0.00 37.15 4.08
1748 4638 3.174682 ATGTTCGCGCGCACAAACA 62.175 52.632 36.21 32.19 36.19 2.83
1760 4650 3.669344 CAAACACACGGCCCGCAT 61.669 61.111 1.23 0.00 0.00 4.73
1838 4728 1.568612 CGCACGACCAAGCAGTTCAT 61.569 55.000 0.00 0.00 0.00 2.57
1897 4787 2.606519 CCCACCTCTCGAACCCCA 60.607 66.667 0.00 0.00 0.00 4.96
1994 4885 3.661648 CAACCCTCCCCACCCCAG 61.662 72.222 0.00 0.00 0.00 4.45
2065 4956 1.195900 GAGAATCTCCCGATCTCGACG 59.804 57.143 0.00 0.00 43.02 5.12
2105 4996 4.081142 TGAAAATCTCCCGATCTTGTGCTA 60.081 41.667 0.00 0.00 0.00 3.49
2255 5146 8.531146 CAAGTAGTTGGGTATGAAAAATGGATT 58.469 33.333 2.05 0.00 0.00 3.01
2338 5230 8.268850 AGAAATTAGTTGCCACTTGTGTATAG 57.731 34.615 0.00 0.00 34.06 1.31
2342 5234 2.936498 GTTGCCACTTGTGTATAGCGAT 59.064 45.455 0.00 0.00 0.00 4.58
2363 5255 0.673985 GTTGCCACCTTTCCTTGTCC 59.326 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
477 512 2.094417 GGTTATGCAAGCAGTCGAAGTC 59.906 50.000 0.00 0.00 32.26 3.01
681 733 1.106351 TGATTATTGCGGCGGCCATT 61.106 50.000 20.71 2.51 38.85 3.16
741 794 8.970859 ATGAAATAGAGAGAAAATTGGATCGT 57.029 30.769 0.00 0.00 0.00 3.73
905 970 1.302667 GGGGTAGGGACTAGGGAGGT 61.303 65.000 0.00 0.00 44.14 3.85
980 1106 1.745489 GCCAAGAAGATTCGCCGGT 60.745 57.895 1.90 0.00 0.00 5.28
1100 1226 1.635663 GCACGAAGGAACCATCACCG 61.636 60.000 0.00 0.00 0.00 4.94
1101 1227 0.605319 TGCACGAAGGAACCATCACC 60.605 55.000 0.00 0.00 0.00 4.02
1102 1228 1.197721 CTTGCACGAAGGAACCATCAC 59.802 52.381 0.00 0.00 0.00 3.06
1104 1230 1.523758 ACTTGCACGAAGGAACCATC 58.476 50.000 0.00 0.00 35.78 3.51
1105 1231 2.423577 GTACTTGCACGAAGGAACCAT 58.576 47.619 0.00 0.00 35.78 3.55
1106 1232 1.541670 GGTACTTGCACGAAGGAACCA 60.542 52.381 0.00 0.00 39.76 3.67
1107 1233 1.154197 GGTACTTGCACGAAGGAACC 58.846 55.000 0.00 0.00 35.71 3.62
1108 1234 1.529865 GTGGTACTTGCACGAAGGAAC 59.470 52.381 0.00 0.00 35.78 3.62
1110 1236 0.034337 GGTGGTACTTGCACGAAGGA 59.966 55.000 0.00 0.00 35.78 3.36
1112 1238 1.148310 CAGGTGGTACTTGCACGAAG 58.852 55.000 0.00 0.00 37.73 3.79
1140 4022 0.325296 TTAGGACCGCCTGGACAGAT 60.325 55.000 0.00 0.00 46.45 2.90
1549 4439 4.910195 TGATAAATGACAAGAGTGCCAGT 58.090 39.130 0.00 0.00 0.00 4.00
1731 4621 3.865830 TGTTTGTGCGCGCGAACA 61.866 55.556 39.62 39.62 39.62 3.18
1760 4650 3.578272 GTTGGCACGCAACGGACA 61.578 61.111 0.00 0.00 0.00 4.02
1838 4728 2.452064 GGGGATTGATCGGAGGCCA 61.452 63.158 5.01 0.00 0.00 5.36
1960 4850 0.631753 TTGGGGTGTGGTTTTGAGGA 59.368 50.000 0.00 0.00 0.00 3.71
1993 4884 1.360393 TGGGTTGGAGTTTGGAGCCT 61.360 55.000 0.00 0.00 0.00 4.58
1994 4885 0.895559 CTGGGTTGGAGTTTGGAGCC 60.896 60.000 0.00 0.00 0.00 4.70
2105 4996 6.893005 GTGTTCTACCCCTATAGCATAGATCT 59.107 42.308 0.00 0.00 0.00 2.75
2255 5146 7.894364 ACTGTCCTTCTTTAGTGATTCCTACTA 59.106 37.037 0.00 0.00 0.00 1.82
2338 5230 0.733150 GGAAAGGTGGCAACTATCGC 59.267 55.000 4.97 0.00 37.61 4.58
2342 5234 2.488347 GGACAAGGAAAGGTGGCAACTA 60.488 50.000 4.97 0.00 37.61 2.24


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

AutoCloner maintained by Alex Coulton.