Multiple sequence alignment - TraesCS7B01G053600

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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 TraesCS7B01G053600 chr7B 100.000 2393 0 0 1 2393 56682450 56684842 0 4420
1 TraesCS7B01G053600 chr4B 96.381 2404 73 9 1 2393 330839408 330841808 0 3945
2 TraesCS7B01G053600 chr4B 95.875 2400 89 8 1 2393 201314998 201312602 0 3875
3 TraesCS7B01G053600 chr2B 96.200 2395 85 6 1 2393 658519489 658521879 0 3914
4 TraesCS7B01G053600 chr2B 96.127 2401 79 7 1 2393 429566798 429569192 0 3906
5 TraesCS7B01G053600 chr2B 95.795 2402 90 6 1 2393 434812248 434814647 0 3866
6 TraesCS7B01G053600 chr4A 96.080 2398 86 8 1 2393 718383702 718386096 0 3901
7 TraesCS7B01G053600 chr5B 96.038 2398 88 5 1 2393 34802968 34805363 0 3895
8 TraesCS7B01G053600 chr5B 95.710 2401 93 5 1 2393 394922726 394925124 0 3855
9 TraesCS7B01G053600 chr1B 95.955 2398 90 5 1 2393 305508681 305511076 0 3884


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 TraesCS7B01G053600 chr7B 56682450 56684842 2392 False 4420 4420 100.000 1 2393 1 chr7B.!!$F1 2392
1 TraesCS7B01G053600 chr4B 330839408 330841808 2400 False 3945 3945 96.381 1 2393 1 chr4B.!!$F1 2392
2 TraesCS7B01G053600 chr4B 201312602 201314998 2396 True 3875 3875 95.875 1 2393 1 chr4B.!!$R1 2392
3 TraesCS7B01G053600 chr2B 658519489 658521879 2390 False 3914 3914 96.200 1 2393 1 chr2B.!!$F3 2392
4 TraesCS7B01G053600 chr2B 429566798 429569192 2394 False 3906 3906 96.127 1 2393 1 chr2B.!!$F1 2392
5 TraesCS7B01G053600 chr2B 434812248 434814647 2399 False 3866 3866 95.795 1 2393 1 chr2B.!!$F2 2392
6 TraesCS7B01G053600 chr4A 718383702 718386096 2394 False 3901 3901 96.080 1 2393 1 chr4A.!!$F1 2392
7 TraesCS7B01G053600 chr5B 34802968 34805363 2395 False 3895 3895 96.038 1 2393 1 chr5B.!!$F1 2392
8 TraesCS7B01G053600 chr5B 394922726 394925124 2398 False 3855 3855 95.710 1 2393 1 chr5B.!!$F2 2392
9 TraesCS7B01G053600 chr1B 305508681 305511076 2395 False 3884 3884 95.955 1 2393 1 chr1B.!!$F1 2392

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
989 993 0.322816 ATTTGTGGGCGCTGAGATGT 60.323 50.0 7.64 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2176 1.648504 TCAACTGCATGCTCATCTCG 58.351 50.0 20.33 1.1 0.0 4.04 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
41 42 6.855763 TTAATTGGGATTGAGAATGCTGTT 57.144 33.333 0.00 0.00 0.00 3.16
61 62 8.081633 TGCTGTTAACCATTCTCAATGTTTAAG 58.918 33.333 2.48 0.00 36.73 1.85
126 128 6.548993 AGGGAAAAATTGGCTTTATGCAAAAA 59.451 30.769 0.00 0.00 45.15 1.94
156 158 0.407139 AGAGCTTTTCCACCAGCCAT 59.593 50.000 0.00 0.00 36.62 4.40
178 180 9.935241 GCCATATATGCATGTAGTATAGCTTAT 57.065 33.333 10.16 0.00 33.61 1.73
259 261 1.535860 GGCTGCAACGTTTCATGTTGT 60.536 47.619 0.00 0.00 44.66 3.32
682 686 3.128242 GGATGCAAGGATCAAGTTCACAG 59.872 47.826 3.99 0.00 0.00 3.66
756 760 4.833390 ACTTGAACATAGGAGTACCAAGC 58.167 43.478 0.00 0.00 36.55 4.01
774 778 0.591659 GCTTCACCGGGACTTTCAAC 59.408 55.000 6.32 0.00 0.00 3.18
846 850 1.462731 GGACATTTGCACCAGCCACA 61.463 55.000 0.00 0.00 41.13 4.17
870 874 6.092807 CAGAGCCAATAGAGTTTACCTTTGAC 59.907 42.308 0.00 0.00 0.00 3.18
885 889 3.399330 CTTTGACGTACCAACATGGAGT 58.601 45.455 2.85 0.41 40.96 3.85
959 963 8.041323 AGTTTACCACAACGATCTCAAGAATAT 58.959 33.333 0.00 0.00 0.00 1.28
989 993 0.322816 ATTTGTGGGCGCTGAGATGT 60.323 50.000 7.64 0.00 0.00 3.06
1064 1068 4.141287 CAGGAGTTAAACCAACACATCCA 58.859 43.478 3.35 0.00 39.81 3.41
1117 1121 1.698532 AGGATCTGCAGAAGGCTATGG 59.301 52.381 22.50 0.00 45.15 2.74
1135 1139 1.210478 TGGCCAAGATCAAGGAGCTAC 59.790 52.381 0.61 0.00 0.00 3.58
1237 1241 6.409695 GGAGAAGATTGGAGTATTCATGGGAA 60.410 42.308 0.00 0.00 37.45 3.97
1310 1314 0.809385 ATCATCGACGACACCGACTT 59.191 50.000 0.00 0.00 38.97 3.01
1357 1361 2.275134 TGTTGATGAAGCTGGAGCAA 57.725 45.000 0.65 0.00 45.16 3.91
1376 1380 6.295123 GGAGCAAATATCATGGAATCTGCATT 60.295 38.462 8.56 0.00 0.00 3.56
1490 1497 2.294791 CCGTTGTATGCCCTTGTTTGAA 59.705 45.455 0.00 0.00 0.00 2.69
1715 1735 0.804156 GCAACAACAACAACCCACCG 60.804 55.000 0.00 0.00 0.00 4.94
1970 1990 2.585330 TGGAATCAGTTTCAGCAAGCA 58.415 42.857 0.00 0.00 35.94 3.91
2123 2144 1.756375 CGTTGCTACGGATGCAGCTC 61.756 60.000 13.04 0.00 43.94 4.09
2155 2176 7.382898 AGAAGTTTCTAGAAGGACTGAATGAC 58.617 38.462 9.98 0.49 35.34 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 8.573035 GTGGTTCTTAAACATTGAGAATGGTTA 58.427 33.333 3.22 3.22 46.46 2.85
126 128 5.246307 GTGGAAAAGCTCTATGGTTACAGT 58.754 41.667 0.00 0.00 35.02 3.55
178 180 9.952030 TGTAACACATAGAGAATAACAATGGAA 57.048 29.630 0.00 0.00 0.00 3.53
190 192 3.432186 GCTGGCCATGTAACACATAGAGA 60.432 47.826 5.51 0.00 36.53 3.10
206 208 0.316204 GCACATGGAATATGCTGGCC 59.684 55.000 0.00 0.00 36.40 5.36
259 261 5.698089 TCTTACTCGTCGTCTGAAAAGTCTA 59.302 40.000 0.00 0.00 0.00 2.59
421 423 8.040727 AGTAGCAATCACACACTTATTACATCA 58.959 33.333 0.00 0.00 0.00 3.07
565 568 1.245732 GGTCGTGTCCTACAGTCAGT 58.754 55.000 0.00 0.00 0.00 3.41
682 686 3.971245 AGGTGAGTTCTCATCTGGTTC 57.029 47.619 13.87 0.00 28.49 3.62
756 760 0.865769 CGTTGAAAGTCCCGGTGAAG 59.134 55.000 0.00 0.00 0.00 3.02
774 778 1.743995 CCCTTCGGGTAAAGTGGCG 60.744 63.158 0.00 0.00 38.25 5.69
791 795 2.110006 GAATCCTCCAGCGCTCCC 59.890 66.667 7.13 0.00 0.00 4.30
846 850 6.174049 GTCAAAGGTAAACTCTATTGGCTCT 58.826 40.000 0.00 0.00 0.00 4.09
870 874 3.021695 TCCTAGACTCCATGTTGGTACG 58.978 50.000 0.00 0.00 39.03 3.67
885 889 1.134280 GCTGCCATGCTCTTTCCTAGA 60.134 52.381 0.00 0.00 0.00 2.43
959 963 3.129638 GCGCCCACAAATTTGGTAGATAA 59.870 43.478 21.74 0.00 34.44 1.75
969 973 0.813184 CATCTCAGCGCCCACAAATT 59.187 50.000 2.29 0.00 0.00 1.82
989 993 1.565288 TGGTGATCATCTCCCAATGCA 59.435 47.619 7.64 0.00 0.00 3.96
1064 1068 1.556911 ACATCTGATTCTCCTGGCGTT 59.443 47.619 0.00 0.00 0.00 4.84
1117 1121 2.698855 TGTAGCTCCTTGATCTTGGC 57.301 50.000 0.00 0.00 0.00 4.52
1135 1139 3.430218 CGTGTAGCCTTGAGTTCTTCTTG 59.570 47.826 0.00 0.00 0.00 3.02
1237 1241 0.337773 TCTCCTCTGGGTGCTGATCT 59.662 55.000 0.00 0.00 0.00 2.75
1310 1314 3.822192 CGCTGTCGTCGGGATCCA 61.822 66.667 15.23 0.00 0.00 3.41
1328 1332 5.007430 CCAGCTTCATCAACATAGTCATCAC 59.993 44.000 0.00 0.00 0.00 3.06
1357 1361 5.185249 GCTCCAATGCAGATTCCATGATATT 59.815 40.000 0.00 0.00 0.00 1.28
1376 1380 4.134563 GGTCAACTAGAAAAACTGCTCCA 58.865 43.478 0.00 0.00 0.00 3.86
1490 1497 7.356089 AGCACACAATATCATTCCAATCAAT 57.644 32.000 0.00 0.00 0.00 2.57
1572 1580 1.728701 AGGGTTTAGAGGGGAGAGGAA 59.271 52.381 0.00 0.00 0.00 3.36
1575 1583 2.023888 TCTGAGGGTTTAGAGGGGAGAG 60.024 54.545 0.00 0.00 0.00 3.20
1715 1735 2.193536 GTCAACAGGTGGTGGTGGC 61.194 63.158 0.00 0.00 44.94 5.01
1849 1869 5.563671 GCAAACTTCACCTTTTCTCCATCTC 60.564 44.000 0.00 0.00 0.00 2.75
1970 1990 3.417101 TGAAACATGGGCAGTACGAAAT 58.583 40.909 0.00 0.00 0.00 2.17
2123 2144 4.221703 TCCTTCTAGAAACTTCTCCTGCTG 59.778 45.833 6.63 0.00 38.70 4.41
2155 2176 1.648504 TCAACTGCATGCTCATCTCG 58.351 50.000 20.33 1.10 0.00 4.04
2263 2284 7.707467 ATTGTACTTCCCCTATCCATACTTT 57.293 36.000 0.00 0.00 0.00 2.66
2273 2294 3.454812 GCTCCAGAATTGTACTTCCCCTA 59.545 47.826 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.