Multiple sequence alignment - TraesCS1D01G200900

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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 TraesCS1D01G200900 chr1D 100.000 3128 0 0 1 3128 283616134 283619261 0.000000e+00 5777.0
1 TraesCS1D01G200900 chr1A 92.430 3025 129 45 142 3128 355342181 355345143 0.000000e+00 4226.0
2 TraesCS1D01G200900 chr1A 91.724 145 8 4 1 145 355341078 355341218 6.840000e-47 198.0
3 TraesCS1D01G200900 chr1B 91.221 3087 168 46 91 3128 385295174 385298206 0.000000e+00 4104.0
4 TraesCS1D01G200900 chr2D 87.582 153 18 1 1711 1863 553729964 553729813 3.210000e-40 176.0
5 TraesCS1D01G200900 chr2B 87.582 153 18 1 1711 1863 659533300 659533149 3.210000e-40 176.0
6 TraesCS1D01G200900 chr3D 91.870 123 10 0 1709 1831 399380486 399380364 4.150000e-39 172.0
7 TraesCS1D01G200900 chr3D 85.075 67 10 0 1645 1711 390041932 390041998 5.600000e-08 69.4
8 TraesCS1D01G200900 chr3A 91.870 123 10 0 1709 1831 518642730 518642608 4.150000e-39 172.0
9 TraesCS1D01G200900 chr7D 81.690 213 32 6 1647 1854 428952595 428952805 1.490000e-38 171.0
10 TraesCS1D01G200900 chr7B 81.690 213 32 6 1647 1854 446665448 446665658 1.490000e-38 171.0
11 TraesCS1D01G200900 chr7A 81.905 210 31 6 1650 1854 503052302 503052095 1.490000e-38 171.0
12 TraesCS1D01G200900 chr3B 100.000 28 0 0 2418 2445 576434094 576434121 6.000000e-03 52.8


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 TraesCS1D01G200900 chr1D 283616134 283619261 3127 False 5777 5777 100.000 1 3128 1 chr1D.!!$F1 3127
1 TraesCS1D01G200900 chr1A 355341078 355345143 4065 False 2212 4226 92.077 1 3128 2 chr1A.!!$F1 3127
2 TraesCS1D01G200900 chr1B 385295174 385298206 3032 False 4104 4104 91.221 91 3128 1 chr1B.!!$F1 3037

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
243 1210 0.242825 TTCAGAAAGCTGCTGCATGC 59.757 50.0 18.42 11.82 42.01 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 3152 0.103755 CAGCGCTAGAGGCAGATGAA 59.896 55.0 10.99 0.0 41.91 2.57 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
87 88 9.923143 TGTATACTTATTGTGGCATACATAGTC 57.077 33.333 4.17 0.00 39.48 2.59
88 89 9.367444 GTATACTTATTGTGGCATACATAGTCC 57.633 37.037 0.00 0.00 39.48 3.85
175 1142 2.770164 AAACCCTGTCGGAGAGAATG 57.230 50.000 3.35 0.00 36.95 2.67
240 1207 3.822735 AGTAAATTCAGAAAGCTGCTGCA 59.177 39.130 18.42 0.88 42.01 4.41
241 1208 3.955650 AAATTCAGAAAGCTGCTGCAT 57.044 38.095 18.42 2.35 42.01 3.96
242 1209 2.941453 ATTCAGAAAGCTGCTGCATG 57.059 45.000 18.42 10.42 42.01 4.06
243 1210 0.242825 TTCAGAAAGCTGCTGCATGC 59.757 50.000 18.42 11.82 42.01 4.06
256 1223 1.350019 CTGCATGCCCAGGATAGATCA 59.650 52.381 16.68 0.00 0.00 2.92
275 1242 6.598503 AGATCAATGCATCTCATTTCTACCA 58.401 36.000 0.00 0.00 42.48 3.25
397 1367 8.700973 AGAAAAGATAAAAGCTAGAGGAGGTAG 58.299 37.037 0.00 0.00 33.71 3.18
455 1425 7.834803 ACAGAAAATGAAAAAGGAGATGGATC 58.165 34.615 0.00 0.00 0.00 3.36
610 1582 5.732647 CCGTTCGTTCAAATATTGTGATCAC 59.267 40.000 19.27 19.27 0.00 3.06
637 1609 9.723601 TTGATTAGATATAGTTACATGCATGCA 57.276 29.630 26.53 25.04 0.00 3.96
673 1647 8.594687 GCGAACTAGTTACCGTGAATTTTATTA 58.405 33.333 8.42 0.00 0.00 0.98
761 1738 1.173444 TTTGCCGCCGCTTTTCCTTA 61.173 50.000 0.00 0.00 35.36 2.69
809 1786 6.438763 GTTTCCAGTTTCCACTCATTTGTAG 58.561 40.000 0.00 0.00 0.00 2.74
810 1787 5.304686 TCCAGTTTCCACTCATTTGTAGT 57.695 39.130 0.00 0.00 0.00 2.73
814 1791 7.233962 TCCAGTTTCCACTCATTTGTAGTACTA 59.766 37.037 0.00 0.00 0.00 1.82
815 1792 7.331193 CCAGTTTCCACTCATTTGTAGTACTAC 59.669 40.741 23.58 23.58 36.63 2.73
816 1793 7.870954 CAGTTTCCACTCATTTGTAGTACTACA 59.129 37.037 27.99 27.99 43.61 2.74
817 1794 8.594550 AGTTTCCACTCATTTGTAGTACTACAT 58.405 33.333 31.05 17.89 44.54 2.29
818 1795 8.656849 GTTTCCACTCATTTGTAGTACTACATG 58.343 37.037 31.05 26.38 44.54 3.21
836 1813 0.247460 TGTGTGTAGCTAGCTGGCTG 59.753 55.000 32.45 4.22 43.01 4.85
858 1835 6.596888 GCTGTCCTCATGCACATATATACAAT 59.403 38.462 0.00 0.00 0.00 2.71
887 1864 2.019668 GCTCGGCTGACTCCTCTCTAA 61.020 57.143 0.00 0.00 0.00 2.10
971 1965 0.762418 ACCAGTGAATCAACACCGGA 59.238 50.000 9.46 0.00 39.79 5.14
975 1969 1.691976 AGTGAATCAACACCGGAGTCA 59.308 47.619 9.46 0.00 41.12 3.41
979 1973 1.532604 ATCAACACCGGAGTCAGCGA 61.533 55.000 9.46 1.89 0.00 4.93
1056 2055 2.679355 GAGATCTCTCCGATGTCGTG 57.321 55.000 15.80 0.00 37.02 4.35
1059 2058 2.158885 AGATCTCTCCGATGTCGTGAGA 60.159 50.000 19.66 19.66 44.45 3.27
1224 2229 1.361271 CATGATGATGGGCGGCAAC 59.639 57.895 12.47 1.52 0.00 4.17
1226 2231 0.468585 ATGATGATGGGCGGCAACAT 60.469 50.000 12.47 12.61 0.00 2.71
1392 2403 2.905880 CCGGAGATAGGCGACCGT 60.906 66.667 0.00 0.00 43.22 4.83
1421 2432 1.111277 ATGTCGATCGTCCATCACCA 58.889 50.000 15.94 1.14 0.00 4.17
1431 2442 1.206132 GTCCATCACCATCGTGTACCA 59.794 52.381 0.00 0.00 41.09 3.25
1443 2454 1.535028 CGTGTACCAGCTGCAATGAAA 59.465 47.619 8.66 0.00 0.00 2.69
1459 2470 7.675062 TGCAATGAAACCAAGGTTAACATATT 58.325 30.769 18.11 8.24 37.35 1.28
1467 2478 8.511604 AACCAAGGTTAACATATTCTCATCTG 57.488 34.615 8.10 0.00 36.46 2.90
1470 2481 7.227512 CCAAGGTTAACATATTCTCATCTGTCC 59.772 40.741 8.10 0.00 0.00 4.02
1472 2483 7.504403 AGGTTAACATATTCTCATCTGTCCAG 58.496 38.462 8.10 0.00 0.00 3.86
1489 2506 0.737715 CAGTCTAGCTTCCACACGGC 60.738 60.000 0.00 0.00 0.00 5.68
1503 2520 2.348104 ACGGCTCGATGGCACTACA 61.348 57.895 0.00 0.00 41.89 2.74
1526 2543 7.978106 ACACTACTACGTGTTAAAACATGCCG 61.978 42.308 13.63 8.44 45.27 5.69
1540 2557 0.532640 ATGCCGTAATCGATGCTGCA 60.533 50.000 16.96 16.96 39.71 4.41
1544 2561 0.449993 CGTAATCGATGCTGCATGCG 60.450 55.000 21.53 20.96 41.43 4.73
1545 2562 0.583438 GTAATCGATGCTGCATGCGT 59.417 50.000 21.53 10.45 46.63 5.24
1546 2563 0.582960 TAATCGATGCTGCATGCGTG 59.417 50.000 21.53 9.68 46.63 5.34
1547 2564 1.371337 AATCGATGCTGCATGCGTGT 61.371 50.000 21.53 12.67 46.63 4.49
1922 2942 0.984230 TCTTCCTCTTCATTGGCGGT 59.016 50.000 0.00 0.00 0.00 5.68
2132 3152 5.777802 CTTCTGCGACTACATCTAATCCAT 58.222 41.667 0.00 0.00 0.00 3.41
2146 3172 6.602410 TCTAATCCATTCATCTGCCTCTAG 57.398 41.667 0.00 0.00 0.00 2.43
2182 3208 1.805539 TCGAGCAAGCAATCGACGG 60.806 57.895 2.78 0.00 42.61 4.79
2222 3248 5.734855 TGAGACTTTTTACTTGTGTCAGC 57.265 39.130 0.00 0.00 31.80 4.26
2294 3321 7.225538 GCATGTCACTATAGTTAGCAACAAGAT 59.774 37.037 1.56 0.00 31.05 2.40
2356 3383 9.227777 GACAACTTGGTTAATTATACTGAACCT 57.772 33.333 10.04 0.00 41.64 3.50
2433 3461 1.202855 TCTAATACTCCCTCCGTCCCG 60.203 57.143 0.00 0.00 0.00 5.14
2440 3468 1.483415 CTCCCTCCGTCCCGAAATAAA 59.517 52.381 0.00 0.00 0.00 1.40
2445 3473 3.527533 CTCCGTCCCGAAATAAATGTCA 58.472 45.455 0.00 0.00 0.00 3.58
2447 3475 2.353579 CCGTCCCGAAATAAATGTCACC 59.646 50.000 0.00 0.00 0.00 4.02
2454 3482 6.259167 TCCCGAAATAAATGTCACCGATTTAG 59.741 38.462 0.00 0.00 30.69 1.85
2456 3484 7.201661 CCCGAAATAAATGTCACCGATTTAGAA 60.202 37.037 0.00 0.00 30.69 2.10
2457 3485 7.638683 CCGAAATAAATGTCACCGATTTAGAAC 59.361 37.037 0.00 0.00 30.69 3.01
2458 3486 8.172484 CGAAATAAATGTCACCGATTTAGAACA 58.828 33.333 0.00 0.00 30.69 3.18
2460 3488 9.620660 AAATAAATGTCACCGATTTAGAACAAC 57.379 29.630 0.00 0.00 30.69 3.32
2462 3490 7.972832 AAATGTCACCGATTTAGAACAACTA 57.027 32.000 0.00 0.00 0.00 2.24
2465 3493 6.460781 TGTCACCGATTTAGAACAACTATGT 58.539 36.000 0.00 0.00 43.14 2.29
2466 3494 7.604549 TGTCACCGATTTAGAACAACTATGTA 58.395 34.615 0.00 0.00 39.40 2.29
2467 3495 7.543172 TGTCACCGATTTAGAACAACTATGTAC 59.457 37.037 0.00 0.00 39.40 2.90
2468 3496 7.758528 GTCACCGATTTAGAACAACTATGTACT 59.241 37.037 0.00 0.00 39.40 2.73
2469 3497 8.959548 TCACCGATTTAGAACAACTATGTACTA 58.040 33.333 0.00 0.00 39.40 1.82
2470 3498 9.577110 CACCGATTTAGAACAACTATGTACTAA 57.423 33.333 0.00 0.00 39.40 2.24
2479 3507 9.640963 AGAACAACTATGTACTAAATCAGACAC 57.359 33.333 0.00 0.00 39.40 3.67
2480 3508 9.640963 GAACAACTATGTACTAAATCAGACACT 57.359 33.333 0.00 0.00 39.40 3.55
2524 3552 6.622462 GCAACTGTTTCTGAATCTCTTGATCC 60.622 42.308 0.00 0.00 31.51 3.36
2548 3576 5.560722 TCACTTCAAGTTCCACCAATCTA 57.439 39.130 0.00 0.00 0.00 1.98
2796 3824 8.814038 AGTTTCATGCATAATTTTCTAGACCT 57.186 30.769 0.00 0.00 0.00 3.85
2805 3833 7.040823 GCATAATTTTCTAGACCTATTGCAGCT 60.041 37.037 0.00 0.00 0.00 4.24
2864 3892 4.576463 GCTCTTTATCCTTGGGTACACATG 59.424 45.833 0.00 0.25 0.00 3.21
3008 4036 5.097742 TCTCCGAATCACAACCACAATAT 57.902 39.130 0.00 0.00 0.00 1.28
3016 4044 9.186323 CGAATCACAACCACAATATAAACAAAA 57.814 29.630 0.00 0.00 0.00 2.44
3112 4147 3.756933 AAACATTGGCATGTGAAGCTT 57.243 38.095 0.00 0.00 43.34 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 8.305441 TGTATGCCACAATAAGTATACAATCG 57.695 34.615 5.50 0.00 38.22 3.34
61 62 9.923143 GACTATGTATGCCACAATAAGTATACA 57.077 33.333 5.50 3.92 42.92 2.29
110 111 7.984050 TCAAGATCTATTTTGACCATGAGAGTC 59.016 37.037 0.00 0.00 34.72 3.36
240 1207 2.377531 TGCATTGATCTATCCTGGGCAT 59.622 45.455 0.00 0.00 0.00 4.40
241 1208 1.776063 TGCATTGATCTATCCTGGGCA 59.224 47.619 0.00 0.00 0.00 5.36
242 1209 2.574006 TGCATTGATCTATCCTGGGC 57.426 50.000 0.00 0.00 0.00 5.36
243 1210 4.019591 TGAGATGCATTGATCTATCCTGGG 60.020 45.833 0.00 0.00 32.57 4.45
292 1259 2.346847 CGAGCACTAGCAGCTTGTTAAG 59.653 50.000 6.78 0.00 43.58 1.85
397 1367 3.202706 GCCGGCCCTCGATTTCAC 61.203 66.667 18.11 0.00 42.43 3.18
455 1425 4.051554 TCGTTTCAGCGACGATCG 57.948 55.556 14.88 14.88 43.79 3.69
637 1609 0.978146 ACTAGTTCGCCAGGGAGCAT 60.978 55.000 0.00 0.00 0.00 3.79
675 1649 9.661954 AGAAAGGAGACAACTTATATAGATCCA 57.338 33.333 0.00 0.00 0.00 3.41
761 1738 2.583143 GGGCTGACTTTTAACACTGGT 58.417 47.619 0.00 0.00 0.00 4.00
814 1791 1.406069 GCCAGCTAGCTACACACATGT 60.406 52.381 18.86 0.00 43.30 3.21
815 1792 1.134580 AGCCAGCTAGCTACACACATG 60.135 52.381 18.86 2.89 42.70 3.21
816 1793 1.134580 CAGCCAGCTAGCTACACACAT 60.135 52.381 18.86 0.00 42.61 3.21
817 1794 0.247460 CAGCCAGCTAGCTACACACA 59.753 55.000 18.86 0.00 42.61 3.72
818 1795 0.247736 ACAGCCAGCTAGCTACACAC 59.752 55.000 18.86 5.25 42.61 3.82
836 1813 8.607459 GCTTATTGTATATATGTGCATGAGGAC 58.393 37.037 0.00 0.00 36.51 3.85
887 1864 1.073444 CCATGCATGCATACTCCCTCT 59.927 52.381 31.73 5.79 34.91 3.69
930 1920 2.289320 GCAGGTTATGATCGATCAGCCT 60.289 50.000 30.11 29.19 40.64 4.58
1026 2025 1.299773 GAGATCTCCTTGCTCGCCG 60.300 63.158 12.00 0.00 0.00 6.46
1107 2106 0.547075 TGTACTCCTCCTCCTCCTCG 59.453 60.000 0.00 0.00 0.00 4.63
1197 2202 1.254026 CCATCATCATGGCCACCATC 58.746 55.000 8.16 0.00 43.15 3.51
1224 2229 1.227556 CGAAGGAGGCCGGGTAATG 60.228 63.158 2.18 0.00 0.00 1.90
1226 2231 2.284112 ACGAAGGAGGCCGGGTAA 60.284 61.111 2.18 0.00 0.00 2.85
1392 2403 0.803380 CGATCGACATGTGCTGCAGA 60.803 55.000 20.43 0.69 0.00 4.26
1421 2432 1.066215 TCATTGCAGCTGGTACACGAT 60.066 47.619 17.12 0.23 0.00 3.73
1431 2442 1.708341 ACCTTGGTTTCATTGCAGCT 58.292 45.000 0.00 0.00 0.00 4.24
1443 2454 7.633789 ACAGATGAGAATATGTTAACCTTGGT 58.366 34.615 2.48 0.00 0.00 3.67
1459 2470 3.660970 AGCTAGACTGGACAGATGAGA 57.339 47.619 6.29 0.00 0.00 3.27
1467 2478 1.402984 CGTGTGGAAGCTAGACTGGAC 60.403 57.143 0.00 0.00 0.00 4.02
1470 2481 0.737715 GCCGTGTGGAAGCTAGACTG 60.738 60.000 0.00 0.00 37.49 3.51
1472 2483 0.458716 GAGCCGTGTGGAAGCTAGAC 60.459 60.000 0.00 0.00 36.87 2.59
1489 2506 3.303197 CGTAGTAGTGTAGTGCCATCGAG 60.303 52.174 0.00 0.00 0.00 4.04
1503 2520 4.386652 CGGCATGTTTTAACACGTAGTAGT 59.613 41.667 0.00 0.00 41.61 2.73
1526 2543 0.583438 ACGCATGCAGCATCGATTAC 59.417 50.000 24.76 0.00 46.13 1.89
1540 2557 0.952497 CTCTTCCTGCACACACGCAT 60.952 55.000 0.00 0.00 42.06 4.73
1544 2561 1.227943 TGGCTCTTCCTGCACACAC 60.228 57.895 0.00 0.00 35.26 3.82
1545 2562 1.071987 CTGGCTCTTCCTGCACACA 59.928 57.895 0.00 0.00 35.26 3.72
1546 2563 0.952984 GACTGGCTCTTCCTGCACAC 60.953 60.000 0.00 0.00 37.30 3.82
1547 2564 1.372683 GACTGGCTCTTCCTGCACA 59.627 57.895 0.00 0.00 37.30 4.57
1893 2913 0.912006 AAGAGGAAGAGGAGGTGGCC 60.912 60.000 0.00 0.00 0.00 5.36
1897 2917 2.843113 CCAATGAAGAGGAAGAGGAGGT 59.157 50.000 0.00 0.00 0.00 3.85
1922 2942 3.964221 CTGTTACGAGCTGCCGCGA 62.964 63.158 8.23 0.00 42.32 5.87
2132 3152 0.103755 CAGCGCTAGAGGCAGATGAA 59.896 55.000 10.99 0.00 41.91 2.57
2146 3172 2.583685 GATTTCGTGGCCTTCAGCGC 62.584 60.000 3.32 0.00 45.17 5.92
2182 3208 5.105554 AGTCTCATCATCAGGACTGTGTAAC 60.106 44.000 0.00 0.00 37.60 2.50
2294 3321 2.016318 CGAATCTGGCCTTGCATGTTA 58.984 47.619 3.32 0.00 0.00 2.41
2433 3461 9.834628 TTGTTCTAAATCGGTGACATTTATTTC 57.165 29.630 0.00 0.00 0.00 2.17
2440 3468 7.103641 ACATAGTTGTTCTAAATCGGTGACAT 58.896 34.615 0.00 0.00 29.55 3.06
2454 3482 9.640963 AGTGTCTGATTTAGTACATAGTTGTTC 57.359 33.333 0.00 0.00 37.28 3.18
2473 3501 8.007716 CCGTGTTAGTAAACAAATAAGTGTCTG 58.992 37.037 0.00 0.00 46.84 3.51
2474 3502 7.307573 GCCGTGTTAGTAAACAAATAAGTGTCT 60.308 37.037 0.00 0.00 46.84 3.41
2475 3503 6.793680 GCCGTGTTAGTAAACAAATAAGTGTC 59.206 38.462 0.00 0.00 46.84 3.67
2476 3504 6.260493 TGCCGTGTTAGTAAACAAATAAGTGT 59.740 34.615 0.00 0.00 46.84 3.55
2477 3505 6.660722 TGCCGTGTTAGTAAACAAATAAGTG 58.339 36.000 0.00 0.00 46.84 3.16
2478 3506 6.864360 TGCCGTGTTAGTAAACAAATAAGT 57.136 33.333 0.00 0.00 46.84 2.24
2479 3507 7.322699 CAGTTGCCGTGTTAGTAAACAAATAAG 59.677 37.037 0.00 0.00 46.84 1.73
2480 3508 7.133513 CAGTTGCCGTGTTAGTAAACAAATAA 58.866 34.615 0.00 0.00 46.84 1.40
2483 3511 4.395542 ACAGTTGCCGTGTTAGTAAACAAA 59.604 37.500 0.00 0.00 46.84 2.83
2485 3513 3.533547 ACAGTTGCCGTGTTAGTAAACA 58.466 40.909 0.00 0.00 43.32 2.83
2524 3552 4.763793 AGATTGGTGGAACTTGAAGTGATG 59.236 41.667 0.00 0.00 36.74 3.07
2796 3824 6.639632 AAGTTCTCTTTTTGAGCTGCAATA 57.360 33.333 1.02 0.00 42.38 1.90
2805 3833 7.773224 TGTCCATACAGAAAGTTCTCTTTTTGA 59.227 33.333 14.83 3.52 43.77 2.69
2823 3851 6.604735 AAGAGCATCGTTTATTGTCCATAC 57.395 37.500 0.00 0.00 42.67 2.39
2829 3857 7.201732 CCAAGGATAAAGAGCATCGTTTATTGT 60.202 37.037 0.00 0.00 42.67 2.71
2890 3918 2.915349 ACTCTGTGCCATGATAAGCTG 58.085 47.619 0.00 0.00 0.00 4.24
3008 4036 6.922247 TCACATAGTTCACCGTTTTGTTTA 57.078 33.333 0.00 0.00 0.00 2.01
3016 4044 3.442625 TCTCGAATCACATAGTTCACCGT 59.557 43.478 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.