Multiple sequence alignment - TraesCS7D01G214500

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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 TraesCS7D01G214500 chr7D 100.000 2645 0 0 1 2645 174295018 174297662 0.000000e+00 4885
1 TraesCS7D01G214500 chr7B 90.043 1627 116 24 10 1624 138754427 138756019 0.000000e+00 2065
2 TraesCS7D01G214500 chr4D 95.878 1019 42 0 1627 2645 13570686 13571704 0.000000e+00 1650
3 TraesCS7D01G214500 chr6A 94.406 1019 57 0 1627 2645 111396802 111395784 0.000000e+00 1567
4 TraesCS7D01G214500 chr6A 79.121 273 48 6 1145 1417 614967671 614967408 2.090000e-41 180
5 TraesCS7D01G214500 chr3A 93.327 1019 68 0 1627 2645 476090906 476089888 0.000000e+00 1506
6 TraesCS7D01G214500 chr4A 92.934 1019 72 0 1627 2645 599761879 599760861 0.000000e+00 1483
7 TraesCS7D01G214500 chr2A 91.871 1021 64 3 1627 2645 415060584 415061587 0.000000e+00 1408
8 TraesCS7D01G214500 chr2B 90.980 1020 90 2 1627 2645 503639863 503638845 0.000000e+00 1373
9 TraesCS7D01G214500 chr2D 97.727 792 18 0 1854 2645 572344559 572345350 0.000000e+00 1363
10 TraesCS7D01G214500 chr2D 89.009 1019 111 1 1627 2645 370885030 370884013 0.000000e+00 1260
11 TraesCS7D01G214500 chr6B 89.314 1020 107 2 1627 2645 186688199 186687181 0.000000e+00 1279
12 TraesCS7D01G214500 chr7A 93.000 800 52 1 776 1571 176277713 176278512 0.000000e+00 1164
13 TraesCS7D01G214500 chr7A 89.717 778 66 7 3 768 176276242 176277017 0.000000e+00 981
14 TraesCS7D01G214500 chr4B 88.776 294 33 0 1245 1538 602296971 602296678 6.960000e-96 361
15 TraesCS7D01G214500 chr5D 75.000 528 125 6 1000 1525 553910501 553911023 1.220000e-58 237
16 TraesCS7D01G214500 chr6D 75.758 396 78 12 1145 1525 470104399 470104007 1.620000e-42 183


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 TraesCS7D01G214500 chr7D 174295018 174297662 2644 False 4885.0 4885 100.0000 1 2645 1 chr7D.!!$F1 2644
1 TraesCS7D01G214500 chr7B 138754427 138756019 1592 False 2065.0 2065 90.0430 10 1624 1 chr7B.!!$F1 1614
2 TraesCS7D01G214500 chr4D 13570686 13571704 1018 False 1650.0 1650 95.8780 1627 2645 1 chr4D.!!$F1 1018
3 TraesCS7D01G214500 chr6A 111395784 111396802 1018 True 1567.0 1567 94.4060 1627 2645 1 chr6A.!!$R1 1018
4 TraesCS7D01G214500 chr3A 476089888 476090906 1018 True 1506.0 1506 93.3270 1627 2645 1 chr3A.!!$R1 1018
5 TraesCS7D01G214500 chr4A 599760861 599761879 1018 True 1483.0 1483 92.9340 1627 2645 1 chr4A.!!$R1 1018
6 TraesCS7D01G214500 chr2A 415060584 415061587 1003 False 1408.0 1408 91.8710 1627 2645 1 chr2A.!!$F1 1018
7 TraesCS7D01G214500 chr2B 503638845 503639863 1018 True 1373.0 1373 90.9800 1627 2645 1 chr2B.!!$R1 1018
8 TraesCS7D01G214500 chr2D 572344559 572345350 791 False 1363.0 1363 97.7270 1854 2645 1 chr2D.!!$F1 791
9 TraesCS7D01G214500 chr2D 370884013 370885030 1017 True 1260.0 1260 89.0090 1627 2645 1 chr2D.!!$R1 1018
10 TraesCS7D01G214500 chr6B 186687181 186688199 1018 True 1279.0 1279 89.3140 1627 2645 1 chr6B.!!$R1 1018
11 TraesCS7D01G214500 chr7A 176276242 176278512 2270 False 1072.5 1164 91.3585 3 1571 2 chr7A.!!$F1 1568
12 TraesCS7D01G214500 chr5D 553910501 553911023 522 False 237.0 237 75.0000 1000 1525 1 chr5D.!!$F1 525

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
695 710 0.105658 AAGTAGCTCCGCCCCTCATA 60.106 55.0 0.0 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2982 1.603456 TTTGCGATGAGGTCAAGCAA 58.397 45.0 17.08 17.08 45.05 3.91 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
178 182 0.677288 ATTGTCCGGAGTTGACGTGA 59.323 50.000 3.06 0.00 35.46 4.35
221 225 6.825721 AGAGGGCAATAAGATTACAGTCAAAG 59.174 38.462 0.00 0.00 0.00 2.77
249 256 4.212214 GGCGATGAATCAGAACAGTTATCC 59.788 45.833 0.00 0.00 0.00 2.59
256 263 4.703645 TCAGAACAGTTATCCTCACTCG 57.296 45.455 0.00 0.00 0.00 4.18
264 271 2.625790 GTTATCCTCACTCGGCTGATCT 59.374 50.000 0.00 0.00 0.00 2.75
340 347 5.305585 AGAAATAACGTCCAGAAAAGCTCA 58.694 37.500 0.00 0.00 0.00 4.26
410 417 5.169295 GTTGGACTTGTGATAGAGGTGTAC 58.831 45.833 0.00 0.00 0.00 2.90
495 502 5.949952 TCTGTACTGGCTGAACTATACTTCA 59.050 40.000 0.00 0.00 0.00 3.02
546 553 6.275335 AGTTTTGGAATGTTGTGAAGACATG 58.725 36.000 0.00 0.00 37.76 3.21
558 565 4.692155 TGTGAAGACATGTGTAGATTGCTG 59.308 41.667 1.15 0.00 0.00 4.41
695 710 0.105658 AAGTAGCTCCGCCCCTCATA 60.106 55.000 0.00 0.00 0.00 2.15
697 712 1.228894 TAGCTCCGCCCCTCATAGG 60.229 63.158 0.00 0.00 34.30 2.57
754 770 3.460857 AGATAACATCTTCGGCTGGTC 57.539 47.619 0.00 0.00 35.76 4.02
768 784 5.525484 TCGGCTGGTCCCTATATGTATATT 58.475 41.667 0.00 0.00 0.00 1.28
769 785 5.962031 TCGGCTGGTCCCTATATGTATATTT 59.038 40.000 0.00 0.00 0.00 1.40
771 787 6.761714 CGGCTGGTCCCTATATGTATATTTTC 59.238 42.308 0.00 0.00 0.00 2.29
801 1505 6.183360 ACAAGATGACAAGTAGCTAGCTAGAC 60.183 42.308 24.78 16.65 0.00 2.59
804 1508 1.331138 ACAAGTAGCTAGCTAGACGCG 59.669 52.381 24.78 14.52 45.59 6.01
859 1567 5.799213 AGCTACTTAACAAAGTGATCAGCT 58.201 37.500 0.00 7.23 36.62 4.24
873 1581 4.934602 GTGATCAGCTTAAGAAACTCAGCT 59.065 41.667 6.67 0.00 43.59 4.24
896 1604 0.647410 CAGCATAAGAGAACACCGCG 59.353 55.000 0.00 0.00 0.00 6.46
925 1633 5.643348 TGCTAACCATGTGCATATATACTGC 59.357 40.000 0.00 9.09 40.10 4.40
945 1656 2.868899 CCCATTGAGAGATTAAGGGGC 58.131 52.381 0.00 0.00 40.54 5.80
953 1664 4.468510 TGAGAGATTAAGGGGCGAGTTTTA 59.531 41.667 0.00 0.00 0.00 1.52
981 1692 1.552337 TGACCATTGAGTGAGAGGCTC 59.448 52.381 6.34 6.34 0.00 4.70
1040 1751 2.558380 GATTGGTGGGAGGAGTGGCC 62.558 65.000 0.00 0.00 0.00 5.36
1068 1779 2.299993 TTCTCGTTATCTGCAGCCAG 57.700 50.000 9.47 0.00 40.54 4.85
1095 1806 5.960811 TGTTCAATGGATCCTCTACTTCTCT 59.039 40.000 14.23 0.00 0.00 3.10
1117 1828 2.345991 GCCGGTGTAAGTCTGCCA 59.654 61.111 1.90 0.00 0.00 4.92
1550 2261 2.586079 CACTACGGCGCAGATGGG 60.586 66.667 16.26 3.31 0.00 4.00
1573 2284 1.141019 GAGGAATACAGCCGCGACA 59.859 57.895 8.23 0.00 0.00 4.35
1612 2323 7.765307 AGAATATGTGGAAAAAGTATGTGCTG 58.235 34.615 0.00 0.00 0.00 4.41
1624 2335 5.072040 AGTATGTGCTGTTTTTAATGCCC 57.928 39.130 0.00 0.00 0.00 5.36
1625 2336 4.526262 AGTATGTGCTGTTTTTAATGCCCA 59.474 37.500 0.00 0.00 0.00 5.36
1740 2451 0.178938 TTGCTTCCCATGGCCAAAGA 60.179 50.000 10.96 3.63 0.00 2.52
1892 2603 3.640498 TCAGGGATCTATCAGCTCACAAG 59.360 47.826 0.00 0.00 0.00 3.16
2039 2750 3.386768 TTCTGGAGAGGTCTCAAAACG 57.613 47.619 9.20 0.00 44.60 3.60
2067 2778 2.289444 CCGCTGGTCTTGTTTTCCTCTA 60.289 50.000 0.00 0.00 0.00 2.43
2271 2982 1.539065 CGACACAAGAGTTGCAGGTCT 60.539 52.381 0.00 0.00 31.44 3.85
2360 3073 0.107459 GGAAGGAGCTTGCTACAGGG 60.107 60.000 7.65 0.00 0.00 4.45
2423 3136 2.205022 TTGAGCAGTGGATTTGGGAG 57.795 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.442625 GCCGCTAACTTAAAATTGAGGGT 59.557 43.478 0.00 0.00 0.00 4.34
1 2 3.486875 CGCCGCTAACTTAAAATTGAGGG 60.487 47.826 0.00 0.00 0.00 4.30
119 123 7.992033 AGAACTCTGGATAATTCTGAATGAAGG 59.008 37.037 3.22 0.00 38.18 3.46
178 182 5.942826 GCCCTCTATTTATTCTAGCAGCAAT 59.057 40.000 0.00 0.00 0.00 3.56
221 225 3.002791 TGTTCTGATTCATCGCCAGTTC 58.997 45.455 0.00 0.00 0.00 3.01
228 232 6.199908 GTGAGGATAACTGTTCTGATTCATCG 59.800 42.308 0.00 0.00 0.00 3.84
249 256 2.228582 CCAGATAGATCAGCCGAGTGAG 59.771 54.545 0.00 0.00 0.00 3.51
256 263 1.622811 CTGGGACCAGATAGATCAGCC 59.377 57.143 13.06 0.00 46.30 4.85
410 417 7.305474 AGATTGTTTTGCATAGGTTTACTTCG 58.695 34.615 0.00 0.00 0.00 3.79
495 502 9.424319 CTACAGAATTACTTGTTGATACACTGT 57.576 33.333 0.00 0.00 36.35 3.55
528 535 4.836125 ACACATGTCTTCACAACATTCC 57.164 40.909 0.00 0.00 35.19 3.01
546 553 4.701765 ACATCCTCATCAGCAATCTACAC 58.298 43.478 0.00 0.00 0.00 2.90
558 565 4.400251 TGGAAAGCAATGAACATCCTCATC 59.600 41.667 0.00 0.00 34.90 2.92
745 761 2.984435 TACATATAGGGACCAGCCGA 57.016 50.000 0.00 0.00 37.63 5.54
768 784 8.621532 AGCTACTTGTCATCTTGTTTATGAAA 57.378 30.769 0.00 0.00 35.23 2.69
769 785 9.371136 CTAGCTACTTGTCATCTTGTTTATGAA 57.629 33.333 0.00 0.00 35.23 2.57
771 787 7.493971 AGCTAGCTACTTGTCATCTTGTTTATG 59.506 37.037 17.69 0.00 0.00 1.90
786 1490 0.945813 CCGCGTCTAGCTAGCTACTT 59.054 55.000 20.67 0.00 45.59 2.24
801 1505 3.840209 CGTGCATTTAATTATCATCCGCG 59.160 43.478 0.00 0.00 0.00 6.46
804 1508 5.119931 TGCCGTGCATTTAATTATCATCC 57.880 39.130 0.00 0.00 31.71 3.51
873 1581 2.353704 CGGTGTTCTCTTATGCTGTCCA 60.354 50.000 0.00 0.00 0.00 4.02
884 1592 0.666577 GCAGTAACGCGGTGTTCTCT 60.667 55.000 7.07 8.03 42.09 3.10
886 1594 0.599558 TAGCAGTAACGCGGTGTTCT 59.400 50.000 7.07 0.00 42.09 3.01
896 1604 7.672983 ATATATGCACATGGTTAGCAGTAAC 57.327 36.000 0.00 0.00 42.14 2.50
925 1633 2.811873 CGCCCCTTAATCTCTCAATGGG 60.812 54.545 0.00 0.00 33.88 4.00
945 1656 3.325870 TGGTCAGTCTGCATAAAACTCG 58.674 45.455 0.00 0.00 0.00 4.18
953 1664 2.303890 TCACTCAATGGTCAGTCTGCAT 59.696 45.455 0.00 0.00 0.00 3.96
981 1692 2.034104 TCTGCAATTGGCTAGCTCTG 57.966 50.000 15.72 7.96 45.15 3.35
1068 1779 5.091261 AGTAGAGGATCCATTGAACACAC 57.909 43.478 15.82 0.00 33.66 3.82
1095 1806 4.382320 GACTTACACCGGCGGGCA 62.382 66.667 31.78 11.85 36.48 5.36
1105 1816 1.208052 GGCAGAGATGGCAGACTTACA 59.792 52.381 0.00 0.00 0.00 2.41
1117 1828 0.032615 AGTCGGAAGGAGGCAGAGAT 60.033 55.000 0.00 0.00 0.00 2.75
1164 1875 2.027837 AGCATATATCGCCACAGCATCA 60.028 45.455 4.24 0.00 39.83 3.07
1363 2074 5.479724 AGATTGACACTGTGATCTGAGAGAA 59.520 40.000 15.86 0.00 0.00 2.87
1550 2261 1.944676 CGGCTGTATTCCTCGTCGC 60.945 63.158 0.00 0.00 0.00 5.19
1554 2265 1.944676 GTCGCGGCTGTATTCCTCG 60.945 63.158 1.90 0.00 33.50 4.63
1573 2284 7.114754 TCCACATATTCTTCAAGCTTGATCTT 58.885 34.615 28.89 16.24 37.00 2.40
1892 2603 6.254157 CCACAAATTTACACATCATAGCTTGC 59.746 38.462 0.00 0.00 0.00 4.01
2039 2750 2.094762 ACAAGACCAGCGGAATGTAC 57.905 50.000 1.50 0.00 0.00 2.90
2271 2982 1.603456 TTTGCGATGAGGTCAAGCAA 58.397 45.000 17.08 17.08 45.05 3.91
2360 3073 6.258947 GGAAGGTGAGCATCTTGTAGAAATAC 59.741 42.308 0.00 0.00 30.64 1.89
2423 3136 6.404074 CCTTGTGCTTGTTAGGAATGATCTTC 60.404 42.308 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.