Multiple sequence alignment - TraesCS7B01G313900

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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 TraesCS7B01G313900 chr7B 100.000 4708 0 0 1 4708 560800076 560795369 0 8695
1 TraesCS7B01G313900 chr7B 95.290 4735 182 21 9 4708 112904709 112899981 0 7470
2 TraesCS7B01G313900 chr7B 94.710 4726 224 18 1 4708 142416428 142421145 0 7319
3 TraesCS7B01G313900 chr2B 96.057 4742 153 6 1 4708 87797822 87793081 0 7690
4 TraesCS7B01G313900 chr5B 95.994 4743 154 7 1 4708 541969148 541964407 0 7673
5 TraesCS7B01G313900 chr5B 95.274 4719 182 14 1 4708 688581315 688576627 0 7441
6 TraesCS7B01G313900 chr5B 94.719 4715 220 11 9 4708 695860915 695856215 0 7300
7 TraesCS7B01G313900 chr5B 95.720 3995 158 6 725 4708 246859565 246863557 0 6418
8 TraesCS7B01G313900 chr5B 95.033 4087 185 10 1 4071 130897268 130901352 0 6407
9 TraesCS7B01G313900 chr6B 94.821 4731 215 20 1 4708 392460654 392465377 0 7352
10 TraesCS7B01G313900 chr6B 94.543 4728 226 17 1 4708 114885936 114890651 0 7273
11 TraesCS7B01G313900 chr6B 95.041 1956 88 3 2762 4708 633499150 633497195 0 3066
12 TraesCS7B01G313900 chr3B 94.540 4725 228 19 9 4708 706223695 706228414 0 7269
13 TraesCS7B01G313900 chr6A 94.367 4740 232 26 1 4708 60187219 60182483 0 7241
14 TraesCS7B01G313900 chr5A 94.361 4735 234 22 1 4708 538776903 538781631 0 7234
15 TraesCS7B01G313900 chr3A 94.129 4735 246 24 1 4708 597889686 597894415 0 7175
16 TraesCS7B01G313900 chr1B 94.479 1956 97 5 2762 4708 534839430 534837477 0 3003
17 TraesCS7B01G313900 chr1B 95.550 1191 42 5 3528 4708 661031111 661029922 0 1895
18 TraesCS7B01G313900 chr4B 95.779 1682 60 5 3038 4708 646939781 646938100 0 2702


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 TraesCS7B01G313900 chr7B 560795369 560800076 4707 True 8695 8695 100.000 1 4708 1 chr7B.!!$R2 4707
1 TraesCS7B01G313900 chr7B 112899981 112904709 4728 True 7470 7470 95.290 9 4708 1 chr7B.!!$R1 4699
2 TraesCS7B01G313900 chr7B 142416428 142421145 4717 False 7319 7319 94.710 1 4708 1 chr7B.!!$F1 4707
3 TraesCS7B01G313900 chr2B 87793081 87797822 4741 True 7690 7690 96.057 1 4708 1 chr2B.!!$R1 4707
4 TraesCS7B01G313900 chr5B 541964407 541969148 4741 True 7673 7673 95.994 1 4708 1 chr5B.!!$R1 4707
5 TraesCS7B01G313900 chr5B 688576627 688581315 4688 True 7441 7441 95.274 1 4708 1 chr5B.!!$R2 4707
6 TraesCS7B01G313900 chr5B 695856215 695860915 4700 True 7300 7300 94.719 9 4708 1 chr5B.!!$R3 4699
7 TraesCS7B01G313900 chr5B 246859565 246863557 3992 False 6418 6418 95.720 725 4708 1 chr5B.!!$F2 3983
8 TraesCS7B01G313900 chr5B 130897268 130901352 4084 False 6407 6407 95.033 1 4071 1 chr5B.!!$F1 4070
9 TraesCS7B01G313900 chr6B 392460654 392465377 4723 False 7352 7352 94.821 1 4708 1 chr6B.!!$F2 4707
10 TraesCS7B01G313900 chr6B 114885936 114890651 4715 False 7273 7273 94.543 1 4708 1 chr6B.!!$F1 4707
11 TraesCS7B01G313900 chr6B 633497195 633499150 1955 True 3066 3066 95.041 2762 4708 1 chr6B.!!$R1 1946
12 TraesCS7B01G313900 chr3B 706223695 706228414 4719 False 7269 7269 94.540 9 4708 1 chr3B.!!$F1 4699
13 TraesCS7B01G313900 chr6A 60182483 60187219 4736 True 7241 7241 94.367 1 4708 1 chr6A.!!$R1 4707
14 TraesCS7B01G313900 chr5A 538776903 538781631 4728 False 7234 7234 94.361 1 4708 1 chr5A.!!$F1 4707
15 TraesCS7B01G313900 chr3A 597889686 597894415 4729 False 7175 7175 94.129 1 4708 1 chr3A.!!$F1 4707
16 TraesCS7B01G313900 chr1B 534837477 534839430 1953 True 3003 3003 94.479 2762 4708 1 chr1B.!!$R1 1946
17 TraesCS7B01G313900 chr1B 661029922 661031111 1189 True 1895 1895 95.550 3528 4708 1 chr1B.!!$R2 1180
18 TraesCS7B01G313900 chr4B 646938100 646939781 1681 True 2702 2702 95.779 3038 4708 1 chr4B.!!$R1 1670

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
422 427 1.002868 GCTGCCATGACTGGACAGT 60.003 57.895 4.35 4.35 46.37 3.55 F
1690 1700 0.320946 CACGGATGGGTACGTTTGGT 60.321 55.000 0.00 0.00 44.02 3.67 F
1918 1928 0.528901 CGTGGACCACAACTTGACGA 60.529 55.000 24.18 0.00 33.40 4.20 F
3170 3241 0.754472 ACTGCCAATGCTGCAAGTTT 59.246 45.000 6.36 0.00 39.83 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1888 0.250467 ACAGCTCGAATGCCTTGTGT 60.250 50.000 0.0 0.0 0.00 3.72 R
3490 3561 0.323629 CCGGTGTAAGGCTTCCTCAA 59.676 55.000 1.3 0.0 30.89 3.02 R
3599 3670 2.063015 TTGTGATGGAACGGGGTGCT 62.063 55.000 0.0 0.0 0.00 4.40 R
4167 4288 3.181524 CCGTGTCGTATTGTCATGGAAAC 60.182 47.826 0.0 0.0 43.13 2.78 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
149 151 1.657594 CAGATGTCGTGCTAGCACAAG 59.342 52.381 38.95 27.05 46.47 3.16
177 179 2.323599 TGCCATGAATTGACCAACCAA 58.676 42.857 0.00 0.00 0.00 3.67
422 427 1.002868 GCTGCCATGACTGGACAGT 60.003 57.895 4.35 4.35 46.37 3.55
441 446 3.691118 CAGTTACAGCTGCCATACATGTT 59.309 43.478 15.27 0.00 0.00 2.71
444 449 2.362736 ACAGCTGCCATACATGTTCAG 58.637 47.619 15.27 8.07 32.88 3.02
487 493 4.989797 TGTTTGAAATGATGTCATGCCAAC 59.010 37.500 0.00 2.34 36.56 3.77
525 531 2.935849 TGATCCGTTGTGATACACATGC 59.064 45.455 5.43 2.13 44.16 4.06
781 787 2.514592 ATGGAACTGCCGCCGATG 60.515 61.111 0.00 0.00 40.66 3.84
868 874 1.138247 GTACCTCAGCCACCGTACG 59.862 63.158 8.69 8.69 0.00 3.67
908 914 3.813166 TCGTTCGAAGAAGCAAAGGAATT 59.187 39.130 0.00 0.00 45.90 2.17
1092 1098 6.894654 AGAGAGGTATCATTCTCAAGACTGAA 59.105 38.462 4.44 0.00 41.78 3.02
1125 1131 4.676196 CGGTGTAAGCTAAACGTAGATGGT 60.676 45.833 0.00 0.00 0.00 3.55
1126 1132 5.449041 CGGTGTAAGCTAAACGTAGATGGTA 60.449 44.000 0.00 0.00 0.00 3.25
1690 1700 0.320946 CACGGATGGGTACGTTTGGT 60.321 55.000 0.00 0.00 44.02 3.67
1878 1888 0.898326 TTGCTGACCGTCCAGAGCTA 60.898 55.000 9.90 1.34 36.29 3.32
1918 1928 0.528901 CGTGGACCACAACTTGACGA 60.529 55.000 24.18 0.00 33.40 4.20
2094 2104 2.817258 CGAGGGGTTCAATGCTGTTTTA 59.183 45.455 0.00 0.00 0.00 1.52
2312 2323 5.178623 TCAGTTGCGTTACAGTCTTATTTGG 59.821 40.000 0.00 0.00 0.00 3.28
2390 2402 3.911868 TGCAGTTGCCATGTTTAATGAC 58.088 40.909 1.06 0.00 41.18 3.06
2452 2466 5.903764 TCAATGAAAATTCTGTTTTGCCG 57.096 34.783 0.00 0.00 0.00 5.69
2557 2571 2.580962 TGCAAGTGCCAATGTCAACTA 58.419 42.857 0.00 0.00 41.18 2.24
2794 2861 1.649664 CATGTCTAGTGTGCTCCAGC 58.350 55.000 0.00 0.00 42.50 4.85
2803 2870 1.975407 GTGCTCCAGCTGCCATGTT 60.975 57.895 8.66 0.00 42.66 2.71
2819 2886 5.010516 TGCCATGTTTAGTGTACTGCATTTT 59.989 36.000 0.00 0.00 0.00 1.82
3170 3241 0.754472 ACTGCCAATGCTGCAAGTTT 59.246 45.000 6.36 0.00 39.83 2.66
3314 3385 3.062639 CACAGACAACACACACAGTTCTC 59.937 47.826 0.00 0.00 0.00 2.87
3490 3561 6.617782 TGATGAGATCAAGAAGAGGAAAGT 57.382 37.500 0.00 0.00 36.11 2.66
3599 3670 1.453015 AACAAGCACGCAGACCCAA 60.453 52.632 0.00 0.00 0.00 4.12
3642 3722 3.244387 GGGTCATCCAAGAGAGATAAGGC 60.244 52.174 0.00 0.00 35.00 4.35
4010 4131 8.647796 ACTAAATATGCCATGCTAGTTGTACTA 58.352 33.333 0.00 0.00 0.00 1.82
4167 4288 4.758165 TGTAATGACTCTGCATGGCATATG 59.242 41.667 8.37 0.00 38.13 1.78
4186 4307 6.238347 GCATATGTTTCCATGACAATACGACA 60.238 38.462 4.29 0.00 32.29 4.35
4404 4528 6.645827 TGATGAACTACATTTGCCATGTTTTG 59.354 34.615 4.09 0.00 39.56 2.44
4457 4584 4.007659 GGGTGATACAAACGATGAAACCT 58.992 43.478 0.00 0.00 0.00 3.50
4524 4653 3.942829 AGTAGGTTCACATCCACACATG 58.057 45.455 0.00 0.00 0.00 3.21
4624 4754 4.334203 AGCACACGAACATAGTTTTTGACA 59.666 37.500 0.00 0.00 0.00 3.58
4663 4795 4.098914 ACCTTACATTCCTCAGCAACAA 57.901 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.450578 CATGGCATGGCAAATGTAGTTC 58.549 45.455 27.04 0.00 0.00 3.01
149 151 4.114794 GGTCAATTCATGGCAAATACAGC 58.885 43.478 0.00 0.00 34.42 4.40
153 155 4.529769 TGGTTGGTCAATTCATGGCAAATA 59.470 37.500 0.00 0.00 34.42 1.40
177 179 7.813148 CAGCGTAATAACCTGTAAGCATAGTAT 59.187 37.037 0.00 0.00 0.00 2.12
422 427 3.940852 CTGAACATGTATGGCAGCTGTAA 59.059 43.478 16.64 4.07 31.18 2.41
487 493 3.443037 GATCACACCATCTTCGAGTGAG 58.557 50.000 8.56 1.41 41.85 3.51
781 787 5.388944 GTCAGTTTCATCATTCACTTCAGC 58.611 41.667 0.00 0.00 0.00 4.26
868 874 2.749621 ACGATTCAAATCTCTGCCCAAC 59.250 45.455 0.00 0.00 33.24 3.77
908 914 5.045942 TGGAACTTTGCATATGTCTGGTAGA 60.046 40.000 4.29 0.00 0.00 2.59
989 995 0.901124 GCACCTCATCTCACCTCTGT 59.099 55.000 0.00 0.00 0.00 3.41
1092 1098 1.602237 CTTACACCGGACAGGGCAT 59.398 57.895 9.46 0.00 46.96 4.40
1125 1131 3.233953 AGTGACCACCCACTGTGTA 57.766 52.632 7.08 0.00 44.93 2.90
1126 1132 4.066614 AGTGACCACCCACTGTGT 57.933 55.556 7.08 0.00 44.93 3.72
1142 1148 5.088739 GGTTGTGCTCGTCAAAATATTCAG 58.911 41.667 0.00 0.00 0.00 3.02
1878 1888 0.250467 ACAGCTCGAATGCCTTGTGT 60.250 50.000 0.00 0.00 0.00 3.72
1918 1928 2.646798 AGCTCCTTTCAAACTCCTCCAT 59.353 45.455 0.00 0.00 0.00 3.41
2071 2081 2.044946 AGCATTGAACCCCTCGCC 60.045 61.111 0.00 0.00 0.00 5.54
2094 2104 2.047560 GGGCTGACGTACCGCTTT 60.048 61.111 0.00 0.00 0.00 3.51
2129 2139 1.001378 CTGTGTACTGCTTGGCAAACC 60.001 52.381 0.00 0.00 38.41 3.27
2226 2236 7.068702 TCATTTGCCTCTCCATTGGTAAATAT 58.931 34.615 1.86 0.00 43.36 1.28
2312 2323 4.333926 CCTACTGCCTATGTGCTTTTTCTC 59.666 45.833 0.00 0.00 0.00 2.87
2390 2402 6.866010 TGAGTAAGCATGGCAAATAGTATG 57.134 37.500 0.00 0.00 0.00 2.39
2557 2571 7.151999 TGTGTCGCCAATATAACATTTTTCT 57.848 32.000 0.00 0.00 0.00 2.52
2794 2861 3.073678 TGCAGTACACTAAACATGGCAG 58.926 45.455 0.00 0.00 0.00 4.85
2803 2870 6.237901 AGACATGGAAAATGCAGTACACTAA 58.762 36.000 0.00 0.00 0.00 2.24
2819 2886 5.178061 CAAATGCAGTACACTAGACATGGA 58.822 41.667 0.00 0.00 0.00 3.41
2964 3035 9.677567 GAATCTGCAAGTTTTATGTGTTTTCTA 57.322 29.630 0.00 0.00 33.76 2.10
2975 3046 5.630121 TCTTCCTGGAATCTGCAAGTTTTA 58.370 37.500 10.03 0.00 33.76 1.52
3144 3215 2.290260 TGCAGCATTGGCAGTAGTACTT 60.290 45.455 0.00 0.00 44.61 2.24
3170 3241 1.963855 CACAATGCCGTCCCGTTCA 60.964 57.895 0.00 0.00 0.00 3.18
3314 3385 1.403493 GTCTCTCGTCATGCATAGCG 58.597 55.000 13.74 13.74 0.00 4.26
3490 3561 0.323629 CCGGTGTAAGGCTTCCTCAA 59.676 55.000 1.30 0.00 30.89 3.02
3599 3670 2.063015 TTGTGATGGAACGGGGTGCT 62.063 55.000 0.00 0.00 0.00 4.40
3642 3722 6.036953 GCTTGAATCTCTAATCCTGACTTGTG 59.963 42.308 0.00 0.00 0.00 3.33
4167 4288 3.181524 CCGTGTCGTATTGTCATGGAAAC 60.182 47.826 0.00 0.00 43.13 2.78
4186 4307 6.770746 ATACACTATGTGTCTCTAAACCGT 57.229 37.500 6.62 0.00 43.92 4.83
4404 4528 4.383774 TTCGAATGTGTCACGATGTTTC 57.616 40.909 0.00 0.00 36.02 2.78
4524 4653 9.422196 GCGACATTTGAATAGTTTCTGTAATAC 57.578 33.333 0.00 0.00 32.78 1.89
4663 4795 3.882888 CACCGGATGCATACCTTACATTT 59.117 43.478 9.46 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.