Multiple sequence alignment - TraesCS7B01G147900

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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 TraesCS7B01G147900 chr7B 100.000 6778 0 0 1 6778 194120445 194127222 0 12517
1 TraesCS7B01G147900 chr7B 98.615 6788 77 15 1 6778 666533817 666527037 0 11998
2 TraesCS7B01G147900 chr6A 98.896 6791 54 17 1 6778 480630570 480637352 0 12105
3 TraesCS7B01G147900 chr6A 98.660 6792 71 14 1 6778 87933843 87940628 0 12020
4 TraesCS7B01G147900 chr6A 98.431 6630 81 16 164 6778 12700532 12693911 0 11646
5 TraesCS7B01G147900 chr7A 98.513 6790 78 17 1 6778 624766389 624759611 0 11958
6 TraesCS7B01G147900 chr7A 98.088 6800 94 21 1 6778 634123103 634129888 0 11804
7 TraesCS7B01G147900 chr1B 98.321 6789 85 22 1 6778 637607140 637613910 0 11878
8 TraesCS7B01G147900 chr6B 98.172 6783 88 22 1 6778 21371766 21365015 0 11806
9 TraesCS7B01G147900 chr5A 98.079 5415 80 20 1 5407 396395854 396401252 0 9402
10 TraesCS7B01G147900 chr4B 97.843 1947 26 14 1 1942 14719139 14717204 0 3349


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 TraesCS7B01G147900 chr7B 194120445 194127222 6777 False 12517 12517 100.000 1 6778 1 chr7B.!!$F1 6777
1 TraesCS7B01G147900 chr7B 666527037 666533817 6780 True 11998 11998 98.615 1 6778 1 chr7B.!!$R1 6777
2 TraesCS7B01G147900 chr6A 480630570 480637352 6782 False 12105 12105 98.896 1 6778 1 chr6A.!!$F2 6777
3 TraesCS7B01G147900 chr6A 87933843 87940628 6785 False 12020 12020 98.660 1 6778 1 chr6A.!!$F1 6777
4 TraesCS7B01G147900 chr6A 12693911 12700532 6621 True 11646 11646 98.431 164 6778 1 chr6A.!!$R1 6614
5 TraesCS7B01G147900 chr7A 624759611 624766389 6778 True 11958 11958 98.513 1 6778 1 chr7A.!!$R1 6777
6 TraesCS7B01G147900 chr7A 634123103 634129888 6785 False 11804 11804 98.088 1 6778 1 chr7A.!!$F1 6777
7 TraesCS7B01G147900 chr1B 637607140 637613910 6770 False 11878 11878 98.321 1 6778 1 chr1B.!!$F1 6777
8 TraesCS7B01G147900 chr6B 21365015 21371766 6751 True 11806 11806 98.172 1 6778 1 chr6B.!!$R1 6777
9 TraesCS7B01G147900 chr5A 396395854 396401252 5398 False 9402 9402 98.079 1 5407 1 chr5A.!!$F1 5406
10 TraesCS7B01G147900 chr4B 14717204 14719139 1935 True 3349 3349 97.843 1 1942 1 chr4B.!!$R1 1941

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
90 91 0.108186 CTCAGTTGGCTGCGTCCATA 60.108 55.000 0.00 0.00 42.29 2.74 F
118 119 0.179037 TGGCTGTCCATATGCTCTGC 60.179 55.000 14.17 14.17 37.47 4.26 F
634 642 2.158682 TCCTGCTTTTGTGCAACTAGGA 60.159 45.455 0.00 0.00 42.83 2.94 F
2233 2262 1.160137 CACTAAGTTCCTGGTGCAGC 58.840 55.000 9.47 9.47 0.00 5.25 F
3220 3255 0.828762 AGGTGCCATGTGTGTTGCAT 60.829 50.000 0.00 0.00 35.96 3.96 F
4173 4212 0.960861 ACGACGAGGAGACAGATGCA 60.961 55.000 0.00 0.00 0.00 3.96 F
4759 4813 0.670162 GCTCTGCAACTTGAAGCCAA 59.330 50.000 0.00 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1397 1.073722 CAGCTCCCTTGCCAAGTGA 59.926 57.895 3.37 0.0 0.0 3.41 R
1563 1582 6.627953 GCCAACTAATGCCAACTAATGTCAAT 60.628 38.462 0.00 0.0 0.0 2.57 R
2527 2556 0.185901 TTTGGGCTGAGCTTCAAGGT 59.814 50.000 3.72 0.0 0.0 3.50 R
4014 4053 1.274167 CCAGTTTGCATTGATGGCTGT 59.726 47.619 0.00 0.0 0.0 4.40 R
4759 4813 1.119684 GGAAAGGTGGTTGGCAAAGT 58.880 50.000 0.00 0.0 0.0 2.66 R
5310 5366 1.380785 CCCCTGCATCAATGGCTGT 60.381 57.895 0.00 0.0 0.0 4.40 R
6261 6330 3.818773 GTGCAACTAAAAGCCCTGTTCTA 59.181 43.478 0.00 0.0 0.0 2.10 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
80 81 3.858503 GCACAAAATTCTCCTCAGTTGGC 60.859 47.826 0.00 0.00 0.00 4.52
81 82 3.571401 CACAAAATTCTCCTCAGTTGGCT 59.429 43.478 0.00 0.00 0.00 4.75
82 83 3.571401 ACAAAATTCTCCTCAGTTGGCTG 59.429 43.478 0.00 0.00 43.87 4.85
83 84 1.831580 AATTCTCCTCAGTTGGCTGC 58.168 50.000 0.00 0.00 42.29 5.25
84 85 0.392193 ATTCTCCTCAGTTGGCTGCG 60.392 55.000 0.00 0.00 42.29 5.18
85 86 1.758440 TTCTCCTCAGTTGGCTGCGT 61.758 55.000 0.00 0.00 42.29 5.24
86 87 1.739562 CTCCTCAGTTGGCTGCGTC 60.740 63.158 0.00 0.00 42.29 5.19
88 89 2.031012 CTCAGTTGGCTGCGTCCA 59.969 61.111 0.00 0.00 42.29 4.02
89 90 1.376424 CTCAGTTGGCTGCGTCCAT 60.376 57.895 0.00 0.00 42.29 3.41
90 91 0.108186 CTCAGTTGGCTGCGTCCATA 60.108 55.000 0.00 0.00 42.29 2.74
91 92 0.541392 TCAGTTGGCTGCGTCCATAT 59.459 50.000 0.00 0.00 42.29 1.78
92 93 1.760029 TCAGTTGGCTGCGTCCATATA 59.240 47.619 0.00 0.00 42.29 0.86
93 94 2.138320 CAGTTGGCTGCGTCCATATAG 58.862 52.381 0.00 0.00 35.77 1.31
94 95 1.762957 AGTTGGCTGCGTCCATATAGT 59.237 47.619 0.00 0.00 35.77 2.12
95 96 2.963101 AGTTGGCTGCGTCCATATAGTA 59.037 45.455 0.00 0.00 35.77 1.82
96 97 3.057734 GTTGGCTGCGTCCATATAGTAC 58.942 50.000 0.00 0.00 35.77 2.73
97 98 2.594131 TGGCTGCGTCCATATAGTACT 58.406 47.619 0.00 0.00 0.00 2.73
118 119 0.179037 TGGCTGTCCATATGCTCTGC 60.179 55.000 14.17 14.17 37.47 4.26
231 232 5.362430 TGGTTAGTTGCACAAAATTCTCCTT 59.638 36.000 0.00 0.00 0.00 3.36
320 321 4.335315 TCAGTTGGCTCACTGTTTTTGTAG 59.665 41.667 14.53 0.00 44.10 2.74
540 547 9.469807 CTTGTTTGTACATTTTTAGCACCAATA 57.530 29.630 0.00 0.00 33.44 1.90
634 642 2.158682 TCCTGCTTTTGTGCAACTAGGA 60.159 45.455 0.00 0.00 42.83 2.94
1049 1059 6.268566 GTGGCAATGAAGGAGATGTATTTTC 58.731 40.000 0.00 0.00 0.00 2.29
1364 1382 4.951254 TGATCAGTTCCGTGTTGTAAAGA 58.049 39.130 0.00 0.00 0.00 2.52
1379 1397 3.762288 TGTAAAGAGGACTAGACGTGCAT 59.238 43.478 0.00 0.00 36.26 3.96
2233 2262 1.160137 CACTAAGTTCCTGGTGCAGC 58.840 55.000 9.47 9.47 0.00 5.25
2527 2556 2.158871 ACTTTTCTAGCACCAACCACGA 60.159 45.455 0.00 0.00 0.00 4.35
3220 3255 0.828762 AGGTGCCATGTGTGTTGCAT 60.829 50.000 0.00 0.00 35.96 3.96
3234 3269 5.455525 GTGTGTTGCATAGTTTTTGTGTCTC 59.544 40.000 0.00 0.00 0.00 3.36
3332 3367 6.091986 GTGTGGTTTCATTCAACACACAAATT 59.908 34.615 18.09 0.00 38.47 1.82
3581 3618 8.911918 TGGACATGTATAACTTTTGTAGTTGT 57.088 30.769 0.00 0.00 46.46 3.32
4008 4047 6.498651 ACGAGGAACCAGATATTGATCCTTAT 59.501 38.462 0.00 0.00 40.72 1.73
4014 4053 9.778741 GAACCAGATATTGATCCTTATGTACAA 57.221 33.333 0.00 0.00 31.81 2.41
4158 4197 1.664629 CGATAGATGCTGACGACGAC 58.335 55.000 0.00 0.00 39.76 4.34
4173 4212 0.960861 ACGACGAGGAGACAGATGCA 60.961 55.000 0.00 0.00 0.00 3.96
4292 4346 4.640647 GGACAAACAAGAAGAGGACAAAGT 59.359 41.667 0.00 0.00 0.00 2.66
4465 4519 4.340617 AGAAGACGAGGATGAAGAAGACT 58.659 43.478 0.00 0.00 0.00 3.24
4759 4813 0.670162 GCTCTGCAACTTGAAGCCAA 59.330 50.000 0.00 0.00 0.00 4.52
5183 5238 5.305386 TCAGAGAAGTTCAACAGATCAAGGA 59.695 40.000 5.50 0.00 0.00 3.36
5310 5366 2.362247 AGAGAGAGCTGCGAGCCA 60.362 61.111 0.00 0.00 43.77 4.75
5441 5497 1.063469 GTCACAGTCAAAACCACCACG 59.937 52.381 0.00 0.00 0.00 4.94
6261 6330 5.449588 GCACAGAAAGCATAGTATGTTGCAT 60.450 40.000 11.73 0.00 41.35 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 3.741344 GCCAAAGTACTATATGGACGCAG 59.259 47.826 20.66 0.65 34.82 5.18
81 82 3.386726 AGCCAAAGTACTATATGGACGCA 59.613 43.478 20.66 0.00 34.82 5.24
82 83 3.741344 CAGCCAAAGTACTATATGGACGC 59.259 47.826 20.66 9.41 34.82 5.19
83 84 4.945246 ACAGCCAAAGTACTATATGGACG 58.055 43.478 20.66 14.13 34.82 4.79
84 85 5.163343 TGGACAGCCAAAGTACTATATGGAC 60.163 44.000 20.66 13.70 42.49 4.02
85 86 4.966168 TGGACAGCCAAAGTACTATATGGA 59.034 41.667 20.66 2.19 42.49 3.41
86 87 5.290493 TGGACAGCCAAAGTACTATATGG 57.710 43.478 14.80 14.80 42.49 2.74
97 98 5.769333 TGCAGAGCATATGGACAGCCAAA 62.769 47.826 4.56 0.00 40.05 3.28
118 119 1.928503 CCAAAACAACTGCTGCAACTG 59.071 47.619 3.02 6.44 0.00 3.16
231 232 2.963101 ACTATATGGACGCAGCCAACTA 59.037 45.455 0.00 0.00 42.16 2.24
320 321 5.656213 ACACAGTATAGACAACCACCTAC 57.344 43.478 0.00 0.00 0.00 3.18
634 642 4.436113 AATTTGCACAAATCAAGGGGTT 57.564 36.364 8.94 0.00 39.88 4.11
1364 1382 1.840737 AGTGATGCACGTCTAGTCCT 58.159 50.000 0.00 0.00 39.64 3.85
1379 1397 1.073722 CAGCTCCCTTGCCAAGTGA 59.926 57.895 3.37 0.00 0.00 3.41
1563 1582 6.627953 GCCAACTAATGCCAACTAATGTCAAT 60.628 38.462 0.00 0.00 0.00 2.57
2233 2262 1.613630 AGGTCTGTGGCTGGTAGGG 60.614 63.158 0.00 0.00 0.00 3.53
2527 2556 0.185901 TTTGGGCTGAGCTTCAAGGT 59.814 50.000 3.72 0.00 0.00 3.50
3220 3255 6.403200 GCAACTGAACAGAGACACAAAAACTA 60.403 38.462 8.87 0.00 0.00 2.24
3581 3618 7.652909 CACAGCCAACTAAATTCTGAATTTTCA 59.347 33.333 27.59 13.83 41.16 2.69
4008 4047 2.512705 TGCATTGATGGCTGTTGTACA 58.487 42.857 0.00 0.00 0.00 2.90
4014 4053 1.274167 CCAGTTTGCATTGATGGCTGT 59.726 47.619 0.00 0.00 0.00 4.40
4158 4197 1.680207 TCATCTGCATCTGTCTCCTCG 59.320 52.381 0.00 0.00 0.00 4.63
4173 4212 3.052262 TGTCCTCCTCCTCTGATTCATCT 60.052 47.826 0.00 0.00 0.00 2.90
4292 4346 4.676799 TCTTCCTTGTTCTCCTCCTCTA 57.323 45.455 0.00 0.00 0.00 2.43
4465 4519 8.551440 CCCTTTATCATCACCATAATCATCCTA 58.449 37.037 0.00 0.00 0.00 2.94
4578 4632 1.185618 TGGCGTGAGTGCTAGTCCTT 61.186 55.000 0.00 0.00 34.52 3.36
4759 4813 1.119684 GGAAAGGTGGTTGGCAAAGT 58.880 50.000 0.00 0.00 0.00 2.66
5183 5238 3.049344 ACTGTTGAAAGGGGAGTCTTCT 58.951 45.455 0.00 0.00 0.00 2.85
5310 5366 1.380785 CCCCTGCATCAATGGCTGT 60.381 57.895 0.00 0.00 0.00 4.40
5441 5497 2.360475 GTGCCTTCCTGACCAGCC 60.360 66.667 0.00 0.00 0.00 4.85
6261 6330 3.818773 GTGCAACTAAAAGCCCTGTTCTA 59.181 43.478 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.