Multiple sequence alignment - TraesCS1B01G311500

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 TraesCS1B01G311500 chr1B 100.000 2601 0 0 1 2601 534835883 534838483 0.000000e+00 4804
1 TraesCS1B01G311500 chr1B 95.657 2602 86 4 1 2598 83652244 83654822 0.000000e+00 4154
2 TraesCS1B01G311500 chr1B 95.467 2603 113 5 1 2601 661028330 661030929 0.000000e+00 4148
3 TraesCS1B01G311500 chr7B 96.849 2602 79 3 1 2601 112898388 112900987 0.000000e+00 4348
4 TraesCS1B01G311500 chr7B 95.665 2630 80 6 1 2601 610536335 610538959 0.000000e+00 4194
5 TraesCS1B01G311500 chr5B 96.775 2605 77 5 1 2601 695854620 695857221 0.000000e+00 4338
6 TraesCS1B01G311500 chr5B 95.083 2603 117 8 1 2601 246865143 246862550 0.000000e+00 4087
7 TraesCS1B01G311500 chr2B 96.046 2605 76 5 1 2601 499577059 499574478 0.000000e+00 4215
8 TraesCS1B01G311500 chr2B 95.813 2603 102 4 1 2601 87791491 87794088 0.000000e+00 4196
9 TraesCS1B01G311500 chr2B 86.458 288 32 7 2318 2601 676180376 676180092 2.510000e-80 309
10 TraesCS1B01G311500 chr4B 95.238 2604 116 7 1 2601 646936511 646939109 0.000000e+00 4115


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 TraesCS1B01G311500 chr1B 534835883 534838483 2600 False 4804 4804 100.000 1 2601 1 chr1B.!!$F2 2600
1 TraesCS1B01G311500 chr1B 83652244 83654822 2578 False 4154 4154 95.657 1 2598 1 chr1B.!!$F1 2597
2 TraesCS1B01G311500 chr1B 661028330 661030929 2599 False 4148 4148 95.467 1 2601 1 chr1B.!!$F3 2600
3 TraesCS1B01G311500 chr7B 112898388 112900987 2599 False 4348 4348 96.849 1 2601 1 chr7B.!!$F1 2600
4 TraesCS1B01G311500 chr7B 610536335 610538959 2624 False 4194 4194 95.665 1 2601 1 chr7B.!!$F2 2600
5 TraesCS1B01G311500 chr5B 695854620 695857221 2601 False 4338 4338 96.775 1 2601 1 chr5B.!!$F1 2600
6 TraesCS1B01G311500 chr5B 246862550 246865143 2593 True 4087 4087 95.083 1 2601 1 chr5B.!!$R1 2600
7 TraesCS1B01G311500 chr2B 499574478 499577059 2581 True 4215 4215 96.046 1 2601 1 chr2B.!!$R1 2600
8 TraesCS1B01G311500 chr2B 87791491 87794088 2597 False 4196 4196 95.813 1 2601 1 chr2B.!!$F1 2600
9 TraesCS1B01G311500 chr4B 646936511 646939109 2598 False 4115 4115 95.238 1 2601 1 chr4B.!!$F1 2600

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
530 533 0.249447 TTGCATGCGGGATCGACTAG 60.249 55.0 14.09 0.0 39.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 1873 1.064803 ACGCATTCGAAACAGCAAACA 59.935 42.857 17.09 0.0 39.41 2.83 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
106 107 0.535780 CTGGTTCTGTGAGGCAGCAA 60.536 55.000 0.00 0.00 44.66 3.91
176 177 0.895530 CGCTAAGGAACAGACCCAGA 59.104 55.000 0.00 0.00 0.00 3.86
262 263 1.448985 CGTAAATGACCACACCCCAG 58.551 55.000 0.00 0.00 0.00 4.45
264 265 2.711542 GTAAATGACCACACCCCAGAG 58.288 52.381 0.00 0.00 0.00 3.35
292 294 7.271511 TCTCATTTTTGCTTTGCTCCTTTTTA 58.728 30.769 0.00 0.00 0.00 1.52
382 385 4.561752 ACTTAGTAGGCATGATCCTTCCT 58.438 43.478 0.00 0.00 37.66 3.36
418 421 4.650734 TCATACAGCTCATGTTTGGACAA 58.349 39.130 5.05 0.00 39.96 3.18
462 465 1.290203 GACGTACGTCGATCTGGGTA 58.710 55.000 30.48 0.00 42.86 3.69
530 533 0.249447 TTGCATGCGGGATCGACTAG 60.249 55.000 14.09 0.00 39.00 2.57
656 659 2.772568 TTGCTCAACACGGTGATTTG 57.227 45.000 16.29 9.98 0.00 2.32
699 702 3.335786 TGTGAGTACTCCTCCCCTTTCTA 59.664 47.826 20.11 0.00 39.65 2.10
779 782 4.370049 CAGATGTTTTCATGTGGCAACAA 58.630 39.130 0.00 0.00 45.44 2.83
785 788 8.517861 ATGTTTTCATGTGGCAACAACTGTCA 62.518 38.462 0.00 0.00 41.20 3.58
1021 1028 0.991920 GTTCCCCATGTTCCAGGAGA 59.008 55.000 0.00 0.00 0.00 3.71
1099 1106 3.363178 CTGAAGAACCAACGTTTTGAGC 58.637 45.455 0.00 0.00 34.24 4.26
1187 1194 2.711009 ACCTCAAAGAGACATGGAACCA 59.289 45.455 0.00 0.00 0.00 3.67
1356 1363 7.817478 TGAATTGAAGTCTATCTTTTGCTACGA 59.183 33.333 0.00 0.00 36.40 3.43
1368 1375 2.843401 TGCTACGACTGCCCTTTTTA 57.157 45.000 0.00 0.00 0.00 1.52
1519 1526 2.296792 CACACATGGAACTGGTTGACA 58.703 47.619 0.00 0.00 0.00 3.58
1612 1619 2.809601 AAGTGATCACGCGGCGAC 60.810 61.111 30.94 16.16 36.20 5.19
1866 1873 1.263217 GTTTCGTCGTTTGCATCACCT 59.737 47.619 0.00 0.00 0.00 4.00
1938 1945 4.406648 TCATCAGACATGGTTAGCGAAT 57.593 40.909 0.00 0.00 0.00 3.34
1941 1948 3.261580 TCAGACATGGTTAGCGAATGTG 58.738 45.455 0.00 0.00 34.74 3.21
2213 2220 4.513692 TGGCAGATACAGTACAAACAACAC 59.486 41.667 0.00 0.00 0.00 3.32
2224 2231 3.023119 ACAAACAACACTGCAGATCCAA 58.977 40.909 23.35 0.00 0.00 3.53
2471 2527 5.413499 GCAACTGCATTTATCCACTCAATT 58.587 37.500 0.00 0.00 41.59 2.32
2576 2636 0.400213 TCCACAAGGACCATGTCACC 59.600 55.000 0.00 0.00 39.61 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 2.237392 ACATCTGGGTCTGTTCCTTAGC 59.763 50.000 0.00 0.00 0.00 3.09
262 263 5.118642 AGCAAAGCAAAAATGAGAGACTC 57.881 39.130 0.00 0.00 0.00 3.36
264 265 4.022503 AGGAGCAAAGCAAAAATGAGAGAC 60.023 41.667 0.00 0.00 0.00 3.36
292 294 4.618920 AGTACGAAGAAGGTGAATGGTT 57.381 40.909 0.00 0.00 0.00 3.67
382 385 8.710835 TGAGCTGTATGAAAACGATATAACAA 57.289 30.769 0.00 0.00 0.00 2.83
418 421 2.034558 CCGCACTGAATGACTTTGGTTT 59.965 45.455 0.00 0.00 0.00 3.27
455 458 1.480954 GACTCGGCAAGATTACCCAGA 59.519 52.381 0.00 0.00 0.00 3.86
462 465 0.108615 CTCACGGACTCGGCAAGATT 60.109 55.000 0.00 0.00 41.39 2.40
530 533 7.136772 CACACACATCCATATGATTGTTGATC 58.863 38.462 3.65 0.00 36.54 2.92
656 659 6.369890 TCACATATTTCTTCAGTGTGAGCTTC 59.630 38.462 2.68 0.00 42.82 3.86
699 702 3.088532 ACACCATGTGACAAAACAGTGT 58.911 40.909 0.49 0.00 35.68 3.55
779 782 2.038164 AGATGACAGTGTGCATGACAGT 59.962 45.455 0.00 0.00 38.93 3.55
785 788 5.717078 AAAATCAAGATGACAGTGTGCAT 57.283 34.783 0.00 4.12 0.00 3.96
941 947 4.890158 TCACATAAAGAACAGCAGAGGA 57.110 40.909 0.00 0.00 0.00 3.71
953 960 6.981762 ATGAGAAGCAGAGTTCACATAAAG 57.018 37.500 0.00 0.00 36.39 1.85
1021 1028 0.405198 TCCTGGTCATGTGGTGCAAT 59.595 50.000 0.00 0.00 0.00 3.56
1099 1106 2.223112 CCGAACGGATTGAATCAAGCAG 60.223 50.000 13.45 11.50 37.50 4.24
1187 1194 5.995282 TGGACTTTTGAATGTTCGTAGTGAT 59.005 36.000 0.00 0.00 0.00 3.06
1356 1363 3.320826 GGTGAACACATAAAAAGGGCAGT 59.679 43.478 7.25 0.00 0.00 4.40
1368 1375 5.440610 AGAAAAAGAGTCAGGTGAACACAT 58.559 37.500 7.25 0.00 0.00 3.21
1444 1451 2.265467 TAGCGGGGACAATTCTGCCC 62.265 60.000 0.00 0.00 37.87 5.36
1519 1526 5.200368 ACCGCTTGTTGAAATCTTCATTT 57.800 34.783 0.00 0.00 39.84 2.32
1612 1619 3.636043 GTGTGCGTCCGGTGTGTG 61.636 66.667 0.00 0.00 0.00 3.82
1866 1873 1.064803 ACGCATTCGAAACAGCAAACA 59.935 42.857 17.09 0.00 39.41 2.83
1938 1945 4.336713 TCCAAATGAACAACGACAATCACA 59.663 37.500 0.00 0.00 0.00 3.58
1941 1948 3.906008 CGTCCAAATGAACAACGACAATC 59.094 43.478 0.00 0.00 35.45 2.67
2213 2220 6.194463 CGTGTTAATTATGTTGGATCTGCAG 58.806 40.000 7.63 7.63 0.00 4.41
2224 2231 6.346096 ACTGTATCTGCCGTGTTAATTATGT 58.654 36.000 0.00 0.00 0.00 2.29
2471 2527 6.117488 GGTATCGGAAGTGGAAGGAAAATTA 58.883 40.000 0.00 0.00 0.00 1.40
2576 2636 0.602562 TGAGCAAAAATTGGGGCGAG 59.397 50.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.