Multiple sequence alignment - TraesCS1D01G146200

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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 TraesCS1D01G146200 chr1D 100.000 5556 0 0 1 5556 202148747 202154302 0.000000e+00 10261.0
1 TraesCS1D01G146200 chr1B 93.151 3577 183 36 1 3571 290185236 290188756 0.000000e+00 5192.0
2 TraesCS1D01G146200 chr1B 93.737 1996 116 6 3560 5553 290190173 290192161 0.000000e+00 2985.0
3 TraesCS1D01G146200 chr1A 92.683 2214 129 20 2967 5177 256378500 256380683 0.000000e+00 3160.0
4 TraesCS1D01G146200 chr1A 91.814 2211 145 21 735 2920 256376300 256378499 0.000000e+00 3048.0
5 TraesCS1D01G146200 chr1A 92.618 718 45 4 1 711 256375596 256376312 0.000000e+00 1026.0
6 TraesCS1D01G146200 chr1A 90.107 374 37 0 5180 5553 256381011 256381384 2.330000e-133 486.0
7 TraesCS1D01G146200 chr1A 81.910 199 26 7 1505 1694 569353849 569353652 5.760000e-35 159.0
8 TraesCS1D01G146200 chr4B 82.673 202 23 6 1499 1691 368106063 368106261 9.570000e-38 169.0
9 TraesCS1D01G146200 chr4A 81.407 199 27 7 1505 1694 624755989 624756186 2.680000e-33 154.0
10 TraesCS1D01G146200 chrUn 78.818 203 27 9 1499 1691 93657389 93657585 7.560000e-24 122.0
11 TraesCS1D01G146200 chr5D 84.298 121 12 4 1581 1694 544804935 544805055 1.640000e-20 111.0
12 TraesCS1D01G146200 chr7A 79.545 132 21 2 1549 1674 158288041 158287910 7.670000e-14 89.8


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 TraesCS1D01G146200 chr1D 202148747 202154302 5555 False 10261.0 10261 100.0000 1 5556 1 chr1D.!!$F1 5555
1 TraesCS1D01G146200 chr1B 290185236 290192161 6925 False 4088.5 5192 93.4440 1 5553 2 chr1B.!!$F1 5552
2 TraesCS1D01G146200 chr1A 256375596 256381384 5788 False 1930.0 3160 91.8055 1 5553 4 chr1A.!!$F1 5552

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
607 616 2.082231 TGACACCTAGACTACTGCGTC 58.918 52.381 0.00 0.00 0.00 5.19 F
919 929 2.121948 TCAGGAATGGGTCTGAGGATG 58.878 52.381 0.00 0.00 35.37 3.51 F
2133 2147 1.597663 GGCAGGACGAAATGTATTCCG 59.402 52.381 0.00 0.00 32.97 4.30 F
2634 2651 3.596214 CACGGGGGACATATATAGCAAC 58.404 50.000 0.00 0.00 0.00 4.17 F
4186 5651 2.168521 TGGCTCTTGTTAGGATCCGAAG 59.831 50.000 7.65 8.29 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1766 1.446907 AGAGCTTGGTTTCATCTGCG 58.553 50.000 0.00 0.0 0.0 5.18 R
2614 2631 3.244582 TGTTGCTATATATGTCCCCCGT 58.755 45.455 0.00 0.0 0.0 5.28 R
3674 5137 3.372206 GTCGTTTGGAGGATGATTGACAG 59.628 47.826 0.00 0.0 0.0 3.51 R
4349 5814 1.407979 CTTTCCATTCCCATCAGCTGC 59.592 52.381 9.47 0.0 0.0 5.25 R
5477 7268 2.503869 AGCCCTCCATGATAAGGTCT 57.496 50.000 0.00 0.0 0.0 3.85 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
122 123 8.956426 GTGGATTGTCATTGGAAGAGTAATTTA 58.044 33.333 0.00 0.00 0.00 1.40
126 127 8.934023 TTGTCATTGGAAGAGTAATTTACCTT 57.066 30.769 2.92 6.50 0.00 3.50
127 128 8.335532 TGTCATTGGAAGAGTAATTTACCTTG 57.664 34.615 12.24 3.08 0.00 3.61
238 244 9.770097 CAAGGAGCATCACTTTTATCTCTATTA 57.230 33.333 0.00 0.00 36.25 0.98
403 410 5.357596 CCATGTGTCATGACCACATATGAAA 59.642 40.000 28.06 7.09 42.81 2.69
404 411 6.040054 CCATGTGTCATGACCACATATGAAAT 59.960 38.462 28.06 13.77 42.81 2.17
408 415 9.187996 TGTGTCATGACCACATATGAAATAAAT 57.812 29.630 22.85 0.00 35.29 1.40
523 532 5.022282 TCATATTGATGTGTCACGACCAT 57.978 39.130 0.00 0.00 33.11 3.55
525 534 2.542020 TTGATGTGTCACGACCATGT 57.458 45.000 0.00 0.00 33.11 3.21
549 558 6.017275 GTGAGAAAAGATGGCTAGAATGGATG 60.017 42.308 0.00 0.00 0.00 3.51
607 616 2.082231 TGACACCTAGACTACTGCGTC 58.918 52.381 0.00 0.00 0.00 5.19
671 680 2.798976 TACACGTGTTGAGTACCCAC 57.201 50.000 28.55 0.00 0.00 4.61
919 929 2.121948 TCAGGAATGGGTCTGAGGATG 58.878 52.381 0.00 0.00 35.37 3.51
1294 1304 2.766263 ACCAACTCTTCATCATCCGCTA 59.234 45.455 0.00 0.00 0.00 4.26
1410 1420 7.142021 GTCCTTTCAACCATCTTCTTCTTTTC 58.858 38.462 0.00 0.00 0.00 2.29
1457 1467 8.851960 TCATATTACATGTCGAGTGAAGTTAC 57.148 34.615 0.00 0.00 0.00 2.50
1458 1468 7.919091 TCATATTACATGTCGAGTGAAGTTACC 59.081 37.037 0.00 0.00 0.00 2.85
1464 1474 2.155155 GTCGAGTGAAGTTACCGCAAAG 59.845 50.000 0.00 0.00 0.00 2.77
1536 1547 7.329588 TCCACTTCCTTTTTAGTCAAACTTC 57.670 36.000 0.00 0.00 0.00 3.01
1539 1550 7.126398 CACTTCCTTTTTAGTCAAACTTCGAG 58.874 38.462 0.00 0.00 0.00 4.04
1618 1630 6.866010 AAAGTTCTTTCAAATTTGCATCCC 57.134 33.333 13.54 0.15 0.00 3.85
1622 1634 5.486735 TCTTTCAAATTTGCATCCCATGT 57.513 34.783 13.54 0.00 0.00 3.21
1676 1688 9.308000 TGGTAAAATCAATGGTCAAAGTTAGAT 57.692 29.630 0.00 0.00 0.00 1.98
1754 1766 8.770438 TTTTGACATTTGTATATTTCCTTGCC 57.230 30.769 0.00 0.00 0.00 4.52
1776 1788 3.624861 CGCAGATGAAACCAAGCTCTTAT 59.375 43.478 0.00 0.00 0.00 1.73
1792 1804 4.522789 GCTCTTATCCAAAAGGTTTCCACA 59.477 41.667 0.00 0.00 0.00 4.17
1828 1840 2.299013 TCAGCTAACACAACGGAGTCAT 59.701 45.455 0.00 0.00 45.00 3.06
2059 2072 8.902806 CCACATAAAGGCTTGAACAATTAGATA 58.097 33.333 0.00 0.00 0.00 1.98
2068 2081 7.719633 GGCTTGAACAATTAGATATTCCCACTA 59.280 37.037 0.00 0.00 0.00 2.74
2120 2134 2.722094 TCATTTACCATGTGGCAGGAC 58.278 47.619 0.00 0.00 39.32 3.85
2133 2147 1.597663 GGCAGGACGAAATGTATTCCG 59.402 52.381 0.00 0.00 32.97 4.30
2227 2241 5.537300 AGACCGATGGTGATATATATGGC 57.463 43.478 0.00 0.00 35.25 4.40
2268 2282 5.769662 ACATTTATGAGCCACAAGTGAAAGA 59.230 36.000 0.94 0.00 0.00 2.52
2378 2392 6.957150 TGCATGATGAAACAAAATGGAAAAC 58.043 32.000 0.00 0.00 0.00 2.43
2634 2651 3.596214 CACGGGGGACATATATAGCAAC 58.404 50.000 0.00 0.00 0.00 4.17
2761 2779 8.395633 CAACCCTTAAAAACATAGGTTATCTCG 58.604 37.037 0.00 0.00 35.88 4.04
2862 2897 9.797556 CAATTAGTGTAGTGTACTATAGTGCAA 57.202 33.333 23.05 8.10 42.05 4.08
2867 2902 4.657436 AGTGTACTATAGTGCAAGAGGC 57.343 45.455 23.05 11.77 42.05 4.70
2885 2920 7.500992 CAAGAGGCACCTGAGTTAAGATAATA 58.499 38.462 0.00 0.00 0.00 0.98
2887 2922 6.841755 AGAGGCACCTGAGTTAAGATAATACT 59.158 38.462 0.00 0.00 0.00 2.12
3001 3036 5.354842 AGCTTAACATTACCCTCAGTACC 57.645 43.478 0.00 0.00 0.00 3.34
3016 3051 9.102453 ACCCTCAGTACCTATTTTCTTATATCC 57.898 37.037 0.00 0.00 0.00 2.59
3061 3096 9.618890 ACCAATATATGTATGATATTGCCTCAC 57.381 33.333 9.04 0.00 42.30 3.51
3259 3294 4.202441 ACAGCTTTGCTAGGTTCCATATG 58.798 43.478 0.00 0.00 36.40 1.78
3674 5137 6.042143 TCATTTTCTCAACTTCCAAAGCAAC 58.958 36.000 0.00 0.00 0.00 4.17
3692 5155 3.507233 GCAACTGTCAATCATCCTCCAAA 59.493 43.478 0.00 0.00 0.00 3.28
3706 5169 3.328343 TCCTCCAAACGACCCTATTTCAA 59.672 43.478 0.00 0.00 0.00 2.69
4007 5471 9.541143 AAAAACCATGTGTTAGGTTCTTATTTG 57.459 29.630 0.00 0.00 46.92 2.32
4095 5559 7.208225 TGGCTATTATTTTACGCATAATGCA 57.792 32.000 0.00 0.00 45.36 3.96
4173 5638 7.025963 GTCTATTTGAATTCACTTGGCTCTTG 58.974 38.462 7.89 0.00 0.00 3.02
4186 5651 2.168521 TGGCTCTTGTTAGGATCCGAAG 59.831 50.000 7.65 8.29 0.00 3.79
4195 5660 2.682155 AGGATCCGAAGAAGAAGCAC 57.318 50.000 5.98 0.00 0.00 4.40
4220 5685 6.186957 TGGTGGCTATTCTATGACACAAAAT 58.813 36.000 0.00 0.00 0.00 1.82
4349 5814 2.679837 CAGATGGGAAGTGGACATTTCG 59.320 50.000 2.18 0.00 0.00 3.46
4357 5822 1.089920 GTGGACATTTCGCAGCTGAT 58.910 50.000 20.43 0.00 0.00 2.90
4382 5847 1.453928 GGAAAGGCCGCCTATGCTT 60.454 57.895 13.73 2.54 31.13 3.91
4487 5952 4.678509 TGCTACACGGTTGATTCATTTC 57.321 40.909 0.00 0.00 0.00 2.17
4621 6086 6.234177 AGTATGGACAAAGGAAGAAGACAAG 58.766 40.000 0.00 0.00 0.00 3.16
4628 6093 3.133141 AGGAAGAAGACAAGCCAAGTC 57.867 47.619 0.00 0.00 36.26 3.01
4806 6272 3.838244 TCAGTTACCATGGGCAGATAC 57.162 47.619 18.09 4.52 0.00 2.24
4930 6396 5.419542 TCACTCTCTATTCCCGACATTTTG 58.580 41.667 0.00 0.00 0.00 2.44
4963 6429 3.244770 TGGAAGTTGTGGGTTCCTATCAC 60.245 47.826 2.96 0.00 42.51 3.06
5087 6553 4.917415 TCGCTAAGTACGAGTTTGGTTTAC 59.083 41.667 0.00 0.00 33.96 2.01
5131 6597 3.005554 CAGTCTAAAGTCCCACATGCAG 58.994 50.000 0.00 0.00 0.00 4.41
5207 6998 2.536761 TACTCCCAAAAGTGGTGTCG 57.463 50.000 0.00 0.00 44.30 4.35
5260 7051 8.045507 CAGAACCCAATGCATAGATGATACTAT 58.954 37.037 0.00 0.00 33.95 2.12
5332 7123 2.105134 ACACCCGTTACACATTGAGGAA 59.895 45.455 0.00 0.00 0.00 3.36
5340 7131 6.183360 CCGTTACACATTGAGGAATTAGACAC 60.183 42.308 0.00 0.00 0.00 3.67
5341 7132 6.367695 CGTTACACATTGAGGAATTAGACACA 59.632 38.462 0.00 0.00 0.00 3.72
5359 7150 5.011533 AGACACAGCTAACTCAAGATCAAGT 59.988 40.000 0.00 0.00 0.00 3.16
5377 7168 5.023452 TCAAGTAGCTAGGAATCAGAACCA 58.977 41.667 0.00 0.00 0.00 3.67
5410 7201 3.331478 TCGGGCAATGCAAATTCAAAT 57.669 38.095 7.79 0.00 0.00 2.32
5428 7219 4.819630 TCAAATTGACTTGCGTAAGGACTT 59.180 37.500 17.79 2.97 38.26 3.01
5429 7220 5.992829 TCAAATTGACTTGCGTAAGGACTTA 59.007 36.000 17.79 4.86 38.26 2.24
5440 7231 5.046878 TGCGTAAGGACTTAGAATTGAGGAA 60.047 40.000 0.00 0.00 38.28 3.36
5480 7271 2.047179 GGGAACTCGTGCCCAGAC 60.047 66.667 8.31 0.00 44.07 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.941325 TCAAACCAGCATTTATAATGAATTGTT 57.059 25.926 3.70 0.00 0.00 2.83
9 10 9.806203 TCTCAAACCAGCATTTATAATGAATTG 57.194 29.630 3.70 1.87 0.00 2.32
25 26 5.181009 TGCTTCTATGTCATCTCAAACCAG 58.819 41.667 0.00 0.00 0.00 4.00
122 123 6.894339 AAAACATTAGTCGAAATCCAAGGT 57.106 33.333 0.00 0.00 0.00 3.50
201 207 4.272991 GTGATGCTCCTTGCTTTCTAGATG 59.727 45.833 0.00 0.00 43.37 2.90
202 208 4.163839 AGTGATGCTCCTTGCTTTCTAGAT 59.836 41.667 0.00 0.00 43.37 1.98
245 251 8.615878 TTTAGTTGCACAATACATCTAGTTGT 57.384 30.769 11.11 11.11 36.57 3.32
517 526 2.096496 GCCATCTTTTCTCACATGGTCG 59.904 50.000 0.00 0.00 38.49 4.79
523 532 5.045651 TCCATTCTAGCCATCTTTTCTCACA 60.046 40.000 0.00 0.00 0.00 3.58
525 534 5.698741 TCCATTCTAGCCATCTTTTCTCA 57.301 39.130 0.00 0.00 0.00 3.27
620 629 3.391965 TGCATTTGAGGTGCATTCAAAC 58.608 40.909 23.32 15.69 46.76 2.93
671 680 6.796426 TCATTAGTGTCTTCCTCGTATTCTG 58.204 40.000 0.00 0.00 0.00 3.02
811 820 9.646427 GTGGGCATATCAAAAAGTTATTGTTAA 57.354 29.630 0.00 0.00 0.00 2.01
919 929 2.380084 TATGCGGTTGTCTTCCTCAC 57.620 50.000 0.00 0.00 0.00 3.51
1294 1304 4.020485 ACCTGTAGCGAATGGTTCTTTAGT 60.020 41.667 0.00 0.00 0.00 2.24
1433 1443 7.096599 CGGTAACTTCACTCGACATGTAATATG 60.097 40.741 0.00 0.00 0.00 1.78
1457 1467 6.793492 TTTTGGGATAAAATTTCTTTGCGG 57.207 33.333 0.00 0.00 0.00 5.69
1458 1468 7.745594 CACATTTTGGGATAAAATTTCTTTGCG 59.254 33.333 0.00 0.00 0.00 4.85
1526 1536 8.021396 GCCAAAATTATAACTCGAAGTTTGACT 58.979 33.333 6.94 0.00 41.00 3.41
1536 1547 8.594687 CATTTTCTTGGCCAAAATTATAACTCG 58.405 33.333 20.91 2.98 32.25 4.18
1539 1550 8.450180 CCACATTTTCTTGGCCAAAATTATAAC 58.550 33.333 20.91 0.00 32.25 1.89
1593 1605 7.134163 GGGATGCAAATTTGAAAGAACTTTTG 58.866 34.615 22.31 0.00 32.11 2.44
1618 1630 6.147656 TGCGAGTTATATGCCATAAAGACATG 59.852 38.462 0.00 0.00 0.00 3.21
1622 1634 7.744087 AAATGCGAGTTATATGCCATAAAGA 57.256 32.000 0.00 0.00 0.00 2.52
1754 1766 1.446907 AGAGCTTGGTTTCATCTGCG 58.553 50.000 0.00 0.00 0.00 5.18
2010 2023 6.262049 TGGACGTAATAAGTTATGCATGCAAT 59.738 34.615 26.68 15.44 31.32 3.56
2120 2134 9.406828 TGAATAAGATCTACGGAATACATTTCG 57.593 33.333 0.00 1.06 44.16 3.46
2227 2241 4.640805 AATGTTAAGTGTTACTCGTGCG 57.359 40.909 0.00 0.00 0.00 5.34
2268 2282 7.823745 ACTTGTGAACTAAAATCTCCATGTT 57.176 32.000 0.00 0.00 0.00 2.71
2608 2625 4.223477 GCTATATATGTCCCCCGTGGTTTA 59.777 45.833 0.00 0.00 34.77 2.01
2614 2631 3.244582 TGTTGCTATATATGTCCCCCGT 58.755 45.455 0.00 0.00 0.00 5.28
2800 2818 5.423290 TCTCTCACCTTTGCTATGATTCAGA 59.577 40.000 0.00 0.00 0.00 3.27
2862 2897 6.841755 AGTATTATCTTAACTCAGGTGCCTCT 59.158 38.462 0.00 0.00 0.00 3.69
3016 3051 9.959749 ATATTGGTAAACCTATTTTTGTATGCG 57.040 29.630 1.43 0.00 36.82 4.73
3674 5137 3.372206 GTCGTTTGGAGGATGATTGACAG 59.628 47.826 0.00 0.00 0.00 3.51
4007 5471 4.305989 TGGCAACATGTCTCTTGTTTTC 57.694 40.909 0.00 0.00 46.17 2.29
4173 5638 3.866327 GTGCTTCTTCTTCGGATCCTAAC 59.134 47.826 10.75 0.00 0.00 2.34
4186 5651 2.409948 ATAGCCACCAGTGCTTCTTC 57.590 50.000 0.00 0.00 40.23 2.87
4195 5660 4.406648 TGTGTCATAGAATAGCCACCAG 57.593 45.455 0.00 0.00 0.00 4.00
4258 5723 7.584122 TTCTACTATATTCGCCTTGACTCTT 57.416 36.000 0.00 0.00 0.00 2.85
4349 5814 1.407979 CTTTCCATTCCCATCAGCTGC 59.592 52.381 9.47 0.00 0.00 5.25
4357 5822 2.362375 GCGGCCTTTCCATTCCCA 60.362 61.111 0.00 0.00 34.01 4.37
4382 5847 8.934697 ACTGCTATCTACTATTTTAACATCCCA 58.065 33.333 0.00 0.00 0.00 4.37
4621 6086 4.632153 ACCATGAATCGTATAGACTTGGC 58.368 43.478 0.00 0.00 0.00 4.52
4628 6093 6.398095 TCAATGGCTACCATGAATCGTATAG 58.602 40.000 0.00 0.00 44.40 1.31
4695 6160 1.703411 ACATGGCCCCATTAATTCGG 58.297 50.000 0.00 0.00 33.90 4.30
4806 6272 9.255304 GACTTAATTCTAGATAGTTTGCTCCAG 57.745 37.037 0.00 0.00 0.00 3.86
4930 6396 2.291741 CACAACTTCCAAGACAAGAGGC 59.708 50.000 0.00 0.00 0.00 4.70
4963 6429 9.513906 TGGATCATCTAGTAATAGAGAGTGAAG 57.486 37.037 6.05 0.00 0.00 3.02
5065 6531 4.201428 CGTAAACCAAACTCGTACTTAGCG 60.201 45.833 0.00 0.00 0.00 4.26
5122 6588 7.592938 TCTTTGTAAATACTTTCTGCATGTGG 58.407 34.615 0.00 0.00 0.00 4.17
5207 6998 4.381411 AGGCTATTCCTGCTCGTTATTTC 58.619 43.478 0.00 0.00 45.54 2.17
5332 7123 7.175347 TGATCTTGAGTTAGCTGTGTCTAAT 57.825 36.000 0.00 0.00 31.92 1.73
5340 7131 5.659463 AGCTACTTGATCTTGAGTTAGCTG 58.341 41.667 16.95 0.00 34.55 4.24
5341 7132 5.930837 AGCTACTTGATCTTGAGTTAGCT 57.069 39.130 14.60 14.60 32.80 3.32
5359 7150 2.700897 GGCTGGTTCTGATTCCTAGCTA 59.299 50.000 0.00 0.00 32.61 3.32
5450 7241 4.099573 CACGAGTTCCCCATGACTTAGTAT 59.900 45.833 0.00 0.00 0.00 2.12
5477 7268 2.503869 AGCCCTCCATGATAAGGTCT 57.496 50.000 0.00 0.00 0.00 3.85
5480 7271 5.053978 AGTTTTAGCCCTCCATGATAAGG 57.946 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.