Multiple sequence alignment - TraesCS1A01G205800

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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 TraesCS1A01G205800 chr1A 100.000 3970 0 0 1 3970 368364274 368360305 0.000000e+00 7332
1 TraesCS1A01G205800 chr1D 95.818 3252 79 13 2 3223 295186776 295183552 0.000000e+00 5199
2 TraesCS1A01G205800 chr1D 91.818 770 33 11 3222 3967 295147777 295147014 0.000000e+00 1046
3 TraesCS1A01G205800 chr1D 93.333 105 6 1 2111 2215 354518920 354519023 1.910000e-33 154
4 TraesCS1A01G205800 chr1B 92.863 2410 108 29 1602 3967 396595367 396592978 0.000000e+00 3439
5 TraesCS1A01G205800 chr1B 94.409 1574 46 16 2 1571 396596903 396595368 0.000000e+00 2381
6 TraesCS1A01G205800 chr1B 93.069 101 6 1 2109 2208 572529355 572529455 3.200000e-31 147
7 TraesCS1A01G205800 chr4A 92.308 104 8 0 2105 2208 606584345 606584242 8.890000e-32 148
8 TraesCS1A01G205800 chrUn 93.000 100 7 0 2112 2211 71312953 71312854 3.200000e-31 147
9 TraesCS1A01G205800 chr5B 92.308 104 5 3 2111 2212 316712702 316712600 1.150000e-30 145
10 TraesCS1A01G205800 chr3D 91.346 104 9 0 2105 2208 138076233 138076336 4.140000e-30 143
11 TraesCS1A01G205800 chr4D 90.000 110 9 2 2101 2210 47858148 47858041 1.490000e-29 141


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 TraesCS1A01G205800 chr1A 368360305 368364274 3969 True 7332 7332 100.000 1 3970 1 chr1A.!!$R1 3969
1 TraesCS1A01G205800 chr1D 295183552 295186776 3224 True 5199 5199 95.818 2 3223 1 chr1D.!!$R2 3221
2 TraesCS1A01G205800 chr1D 295147014 295147777 763 True 1046 1046 91.818 3222 3967 1 chr1D.!!$R1 745
3 TraesCS1A01G205800 chr1B 396592978 396596903 3925 True 2910 3439 93.636 2 3967 2 chr1B.!!$R1 3965

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
345 347 0.037975 GGTAAGCCTCGGTTTCGTCA 60.038 55.0 0.00 0.0 37.69 4.35 F
678 682 0.519519 TTGTTAGGGCGCGAATTGTG 59.480 50.0 12.10 0.0 0.00 3.33 F
679 683 0.604243 TGTTAGGGCGCGAATTGTGT 60.604 50.0 12.10 0.0 0.00 3.72 F
2432 2450 0.675633 GCAACTGTGGCAAATCAGGT 59.324 50.0 1.37 0.0 36.17 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2243 1.457346 GCTTTCCTGGTCACATGGAG 58.543 55.000 0.0 0.0 0.00 3.86 R
2534 2552 0.183492 AGTTGTTGCAGGCCTTCTCA 59.817 50.000 0.0 0.0 0.00 3.27 R
2753 2792 1.450312 GAAGGGAGCATCACCACCG 60.450 63.158 0.0 0.0 41.89 4.94 R
3790 3850 0.179018 ACGGCAAGAAAGAAGGTGCT 60.179 50.000 0.0 0.0 37.17 4.40 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
95 97 2.269529 GGAGATCGGACGGCTAGGG 61.270 68.421 0.00 0.00 0.00 3.53
96 98 1.528776 GAGATCGGACGGCTAGGGT 60.529 63.158 0.00 0.00 0.00 4.34
97 99 1.797211 GAGATCGGACGGCTAGGGTG 61.797 65.000 0.00 0.00 0.00 4.61
106 108 1.898154 GGCTAGGGTGATCACGTGT 59.102 57.895 19.33 8.86 0.00 4.49
130 132 2.235898 CCTCTTATAGCCTGGATCTGCC 59.764 54.545 0.00 0.00 37.10 4.85
131 133 3.172339 CTCTTATAGCCTGGATCTGCCT 58.828 50.000 0.00 0.00 37.63 4.75
132 134 2.902486 TCTTATAGCCTGGATCTGCCTG 59.098 50.000 0.00 0.00 37.63 4.85
133 135 0.979665 TATAGCCTGGATCTGCCTGC 59.020 55.000 0.00 0.00 37.63 4.85
345 347 0.037975 GGTAAGCCTCGGTTTCGTCA 60.038 55.000 0.00 0.00 37.69 4.35
390 392 1.202371 CGTGTAGGCAGAAATCGGCTA 60.202 52.381 5.56 5.29 40.25 3.93
424 427 6.525629 AGATTTCGTGCCTTTAGCTGTATAT 58.474 36.000 0.00 0.00 44.23 0.86
425 428 7.667557 AGATTTCGTGCCTTTAGCTGTATATA 58.332 34.615 0.00 0.00 44.23 0.86
426 429 7.599245 AGATTTCGTGCCTTTAGCTGTATATAC 59.401 37.037 5.89 5.89 44.23 1.47
427 430 4.790878 TCGTGCCTTTAGCTGTATATACG 58.209 43.478 8.33 1.04 44.23 3.06
428 431 3.364023 CGTGCCTTTAGCTGTATATACGC 59.636 47.826 16.78 16.78 44.23 4.42
429 432 3.364023 GTGCCTTTAGCTGTATATACGCG 59.636 47.826 3.53 3.53 44.23 6.01
430 433 3.005050 TGCCTTTAGCTGTATATACGCGT 59.995 43.478 19.17 19.17 44.23 6.01
431 434 4.216042 TGCCTTTAGCTGTATATACGCGTA 59.784 41.667 22.94 22.94 44.23 4.42
432 435 5.106038 TGCCTTTAGCTGTATATACGCGTAT 60.106 40.000 32.13 32.13 44.23 3.06
433 436 5.454877 GCCTTTAGCTGTATATACGCGTATC 59.545 44.000 33.31 20.26 38.99 2.24
434 437 5.675877 CCTTTAGCTGTATATACGCGTATCG 59.324 44.000 33.31 18.26 45.38 2.92
508 511 0.743345 CGCCCCTAGGGTTTCTTTCG 60.743 60.000 26.66 12.99 46.51 3.46
516 519 1.202818 AGGGTTTCTTTCGCTGAAGCT 60.203 47.619 0.10 0.00 39.32 3.74
570 573 1.966451 CGGTGGAACTGTTGAGGCC 60.966 63.158 0.00 0.00 38.78 5.19
590 593 5.254737 AGGCCCTCATATGTTGATAATCCAT 59.745 40.000 0.00 0.00 32.72 3.41
628 632 1.090052 GGACGGTTCATGGCTGTAGC 61.090 60.000 0.00 0.00 41.14 3.58
677 681 1.459450 ATTGTTAGGGCGCGAATTGT 58.541 45.000 12.10 0.00 0.00 2.71
678 682 0.519519 TTGTTAGGGCGCGAATTGTG 59.480 50.000 12.10 0.00 0.00 3.33
679 683 0.604243 TGTTAGGGCGCGAATTGTGT 60.604 50.000 12.10 0.00 0.00 3.72
783 791 1.002773 GCGGAAAGTAGGGGAAGTTCA 59.997 52.381 5.01 0.00 0.00 3.18
1141 1149 6.512091 GCCGCCTTATTTAATGAAACACGATA 60.512 38.462 0.00 0.00 0.00 2.92
1154 1162 6.219473 TGAAACACGATAAACATTTGCCATT 58.781 32.000 0.00 0.00 0.00 3.16
1170 1178 3.944650 TGCCATTGTATATCAAGCGTTGT 59.055 39.130 0.00 0.00 39.55 3.32
1182 1190 2.246719 AGCGTTGTTGCTTTCTCTCT 57.753 45.000 0.00 0.00 44.46 3.10
1192 1200 9.204570 GTTGTTGCTTTCTCTCTTAACTGTATA 57.795 33.333 0.00 0.00 0.00 1.47
1226 1234 1.831736 GCTACCTGAAGAGGCCTTACA 59.168 52.381 6.77 7.01 44.33 2.41
1258 1266 2.030027 TCTATGATGGTAGCAGGGGG 57.970 55.000 0.00 0.00 0.00 5.40
1270 1278 1.926426 GCAGGGGGCTGTGTATCCTT 61.926 60.000 0.00 0.00 40.25 3.36
1620 1629 5.782047 TGCAGTTATTTGCTTTTGTATGCT 58.218 33.333 0.00 0.00 44.38 3.79
1679 1688 5.774690 ACTATTGCATTTCTTTTCCTGTGGA 59.225 36.000 0.00 0.00 0.00 4.02
1719 1728 5.579564 ATTCTCGGTAGACCTAGTTGTTC 57.420 43.478 0.59 0.00 31.36 3.18
1775 1784 8.867935 TGATTAATGGTTGCAATTATTTGTTCG 58.132 29.630 0.59 0.00 35.17 3.95
2024 2040 2.489971 TCAGAAAGCGGTGGTTAACAG 58.510 47.619 8.10 0.00 0.00 3.16
2121 2137 3.517612 AGCTTAAGTTGTACTCCCTCCA 58.482 45.455 4.02 0.00 0.00 3.86
2227 2243 7.311408 GGAGTACATAGGTCATACGTTATTCC 58.689 42.308 0.00 0.00 0.00 3.01
2271 2289 6.406692 TTGCATAGTACATCCTCTACCTTC 57.593 41.667 0.00 0.00 0.00 3.46
2289 2307 3.005155 CCTTCCTTCTGAGGCAAAAACAG 59.995 47.826 0.00 0.00 43.21 3.16
2302 2320 3.383761 CAAAAACAGTGCCCACTCAATC 58.616 45.455 0.00 0.00 40.20 2.67
2399 2417 4.164258 GCTAATGCCTGCCCGAAT 57.836 55.556 0.00 0.00 0.00 3.34
2432 2450 0.675633 GCAACTGTGGCAAATCAGGT 59.324 50.000 1.37 0.00 36.17 4.00
2534 2552 2.672996 GCCGTGGAGTGCACCAAT 60.673 61.111 14.63 0.00 41.87 3.16
2606 2624 1.972795 ACCAATGAGCCTGTTTGCAAT 59.027 42.857 0.00 0.00 0.00 3.56
2774 2813 1.918293 TGGTGATGCTCCCTTCCGT 60.918 57.895 0.00 0.00 0.00 4.69
2776 2815 2.109126 GTGATGCTCCCTTCCGTGC 61.109 63.158 0.00 0.00 0.00 5.34
2797 2836 3.059982 CGGTGGTGCTCTCTTCCA 58.940 61.111 0.00 0.00 0.00 3.53
2870 2909 2.032528 CGTGACTGCATGGGTGGT 59.967 61.111 0.00 0.00 0.00 4.16
2873 2912 2.034687 GACTGCATGGGTGGTGCT 59.965 61.111 0.00 0.00 42.92 4.40
2980 3019 2.034305 GCCGATACTGAACGACTACCAT 59.966 50.000 0.00 0.00 0.00 3.55
3004 3051 3.999663 AGCTCTTTCAGTCCTTTTGATCG 59.000 43.478 0.00 0.00 0.00 3.69
3053 3100 2.353269 TGCGTCGTGTTTTTGAATGTCT 59.647 40.909 0.00 0.00 0.00 3.41
3062 3109 7.662258 TCGTGTTTTTGAATGTCTAAGGGATTA 59.338 33.333 0.00 0.00 0.00 1.75
3096 3143 6.322491 GTTGTTTCTGCAACTTGTTAGTCTT 58.678 36.000 0.00 0.00 43.74 3.01
3122 3169 5.430417 TGGTTATTGAATGGCTTCTAGGGTA 59.570 40.000 0.00 0.00 32.29 3.69
3213 3260 8.232913 ACCAAGTGTTTATCTGTAAATTGTGT 57.767 30.769 0.00 0.00 32.76 3.72
3271 3321 3.118629 TGGATCTATATGAATGGAGCGCC 60.119 47.826 2.29 0.00 30.33 6.53
3290 3340 7.133891 AGCGCCTTATATTAATGCTTACAAG 57.866 36.000 2.29 0.00 0.00 3.16
3342 3395 9.638239 GTATTATTTCACATTTTCTTGAGGCAA 57.362 29.630 0.00 0.00 0.00 4.52
3370 3425 9.747898 TGTCAAATTTGGTAGTATGTCCTATTT 57.252 29.630 17.90 0.00 0.00 1.40
3588 3648 4.576330 AGCTGCTTAAAGGTTATCTGGT 57.424 40.909 0.00 0.00 0.00 4.00
3622 3682 3.437049 GTCAGCATAACAAGTTCAGGGAC 59.563 47.826 0.00 0.00 0.00 4.46
3676 3736 8.621532 AATCACATAACAAGAACTACACATGT 57.378 30.769 0.00 0.00 0.00 3.21
3709 3769 6.523840 ACACAACTATTTTCACAATGCCATT 58.476 32.000 0.00 0.00 0.00 3.16
3775 3835 4.922206 AGACCATCTAATCCAACTTTGCA 58.078 39.130 0.00 0.00 0.00 4.08
3790 3850 2.017138 TTGCATAAGCGAATCCGTCA 57.983 45.000 0.00 0.00 46.23 4.35
3804 3864 1.416401 TCCGTCAGCACCTTCTTTCTT 59.584 47.619 0.00 0.00 0.00 2.52
3817 3877 1.507141 CTTTCTTGCCGTCGCTTGGT 61.507 55.000 0.00 0.00 35.36 3.67
3903 3966 4.098914 AGTCACCTTAACAGCCAATTCA 57.901 40.909 0.00 0.00 0.00 2.57
3967 4044 9.793252 GGTAAAGTATATGTAACGACAGAAGAA 57.207 33.333 0.00 0.00 39.50 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 97 2.457366 AAGAGGGAACACGTGATCAC 57.543 50.000 25.01 21.98 0.00 3.06
96 98 4.202121 GCTATAAGAGGGAACACGTGATCA 60.202 45.833 25.01 2.91 0.00 2.92
97 99 4.299978 GCTATAAGAGGGAACACGTGATC 58.700 47.826 25.01 20.50 0.00 2.92
106 108 4.163427 CAGATCCAGGCTATAAGAGGGAA 58.837 47.826 0.00 0.00 0.00 3.97
179 181 3.686978 CGATGTTGGATTGGGATTGGGTA 60.687 47.826 0.00 0.00 0.00 3.69
345 347 3.005791 GCAAATTAGGTGCAGGTGAAGTT 59.994 43.478 0.00 0.00 41.80 2.66
427 430 1.200839 GCAACATACGCCGATACGC 59.799 57.895 0.00 0.00 36.19 4.42
428 431 1.850640 GGCAACATACGCCGATACG 59.149 57.895 0.00 0.00 40.35 3.06
516 519 3.262405 AGTCCTATCGTACAAAGCCCAAA 59.738 43.478 0.00 0.00 0.00 3.28
570 573 6.183360 GCACGATGGATTATCAACATATGAGG 60.183 42.308 10.38 0.70 42.53 3.86
590 593 0.317160 CTACAACCACCTCAGCACGA 59.683 55.000 0.00 0.00 0.00 4.35
629 633 3.071892 TGTTTTACCACCTGACCCTACAG 59.928 47.826 0.00 0.00 37.61 2.74
630 634 3.047115 TGTTTTACCACCTGACCCTACA 58.953 45.455 0.00 0.00 0.00 2.74
631 635 3.775261 TGTTTTACCACCTGACCCTAC 57.225 47.619 0.00 0.00 0.00 3.18
632 636 4.792513 TTTGTTTTACCACCTGACCCTA 57.207 40.909 0.00 0.00 0.00 3.53
633 637 3.673543 TTTGTTTTACCACCTGACCCT 57.326 42.857 0.00 0.00 0.00 4.34
634 638 4.948341 ATTTTGTTTTACCACCTGACCC 57.052 40.909 0.00 0.00 0.00 4.46
677 681 1.225983 CCCAGACAACACCACCACA 59.774 57.895 0.00 0.00 0.00 4.17
678 682 0.106918 TTCCCAGACAACACCACCAC 60.107 55.000 0.00 0.00 0.00 4.16
679 683 0.182537 CTTCCCAGACAACACCACCA 59.817 55.000 0.00 0.00 0.00 4.17
744 752 1.745087 GCCATGACCATTCACGACATT 59.255 47.619 0.00 0.00 33.38 2.71
1141 1149 6.476380 CGCTTGATATACAATGGCAAATGTTT 59.524 34.615 13.49 9.13 37.88 2.83
1170 1178 9.944376 AACATATACAGTTAAGAGAGAAAGCAA 57.056 29.630 0.00 0.00 0.00 3.91
1182 1190 7.723616 AGCATTATGGCCAACATATACAGTTAA 59.276 33.333 10.96 0.00 41.49 2.01
1192 1200 3.117550 TCAGGTAGCATTATGGCCAACAT 60.118 43.478 10.96 0.78 43.68 2.71
1226 1234 3.392616 CCATCATAGAAACCAGGGCTAGT 59.607 47.826 0.00 0.00 0.00 2.57
1620 1629 8.768501 ATGGACAGAGTTCTAGATACAATACA 57.231 34.615 0.00 0.00 0.00 2.29
1679 1688 8.739972 ACCGAGAATATTAAAAGCATGAAAACT 58.260 29.630 0.00 0.00 0.00 2.66
1702 1711 3.087031 TGGAGAACAACTAGGTCTACCG 58.913 50.000 0.00 0.00 46.72 4.02
1719 1728 5.360714 ACCCAATGTAAAATATGCACTGGAG 59.639 40.000 0.00 0.00 42.82 3.86
1772 1781 3.305064 GCCTCAAAATGGTTAAGCACGAA 60.305 43.478 9.99 0.00 0.00 3.85
1775 1784 3.317150 GTGCCTCAAAATGGTTAAGCAC 58.683 45.455 9.99 1.42 42.06 4.40
2010 2026 4.481368 TCATTATCTGTTAACCACCGCT 57.519 40.909 2.48 0.00 0.00 5.52
2024 2040 7.011482 ACGGTTCAAGCTTCAAGTATCATTATC 59.989 37.037 0.00 0.00 0.00 1.75
2184 2200 3.198872 CTCCCTCCGTCTCAAAATAAGC 58.801 50.000 0.00 0.00 0.00 3.09
2227 2243 1.457346 GCTTTCCTGGTCACATGGAG 58.543 55.000 0.00 0.00 0.00 3.86
2248 2266 5.304614 GGAAGGTAGAGGATGTACTATGCAA 59.695 44.000 0.00 0.00 34.84 4.08
2271 2289 2.544486 GCACTGTTTTTGCCTCAGAAGG 60.544 50.000 0.00 0.00 46.44 3.46
2289 2307 6.587608 CAGAAATTTAAAGATTGAGTGGGCAC 59.412 38.462 0.00 0.00 0.00 5.01
2302 2320 5.390145 GCAATGTGCCTGCAGAAATTTAAAG 60.390 40.000 17.39 0.00 39.69 1.85
2399 2417 0.546122 AGTTGCGGCATATCCCTTCA 59.454 50.000 2.28 0.00 0.00 3.02
2534 2552 0.183492 AGTTGTTGCAGGCCTTCTCA 59.817 50.000 0.00 0.00 0.00 3.27
2753 2792 1.450312 GAAGGGAGCATCACCACCG 60.450 63.158 0.00 0.00 41.89 4.94
2776 2815 3.245668 AAGAGAGCACCACCGCCAG 62.246 63.158 0.00 0.00 0.00 4.85
2797 2836 0.037326 CACGTCACTGTAGCCACCAT 60.037 55.000 0.00 0.00 0.00 3.55
2870 2909 3.570975 AGTTGTTGCAGATCATGAAAGCA 59.429 39.130 13.88 13.88 0.00 3.91
2909 2948 3.068165 CAGATGGACACTCGTAAGCCATA 59.932 47.826 0.00 0.00 39.32 2.74
2980 3019 4.422073 TCAAAAGGACTGAAAGAGCTCA 57.578 40.909 17.77 0.00 37.43 4.26
3004 3051 7.007725 GTCAAAATGATGATTCACAACACGATC 59.992 37.037 0.00 0.00 34.32 3.69
3053 3100 9.457436 GAAACAACTGGAATACTTAATCCCTTA 57.543 33.333 0.00 0.00 34.68 2.69
3062 3109 5.831997 GTTGCAGAAACAACTGGAATACTT 58.168 37.500 0.00 0.00 46.27 2.24
3096 3143 5.192927 CCTAGAAGCCATTCAATAACCACA 58.807 41.667 0.00 0.00 37.94 4.17
3122 3169 4.018597 AGCAAGGGAGTCTGATCTGAAAAT 60.019 41.667 3.59 0.00 0.00 1.82
3290 3340 7.254852 TGAAAACACAGTTTAGACCATGAAAC 58.745 34.615 0.00 0.00 36.08 2.78
3336 3389 5.783111 ACTACCAAATTTGACAATTGCCTC 58.217 37.500 19.86 0.00 32.57 4.70
3342 3395 9.920946 ATAGGACATACTACCAAATTTGACAAT 57.079 29.630 19.86 5.16 0.00 2.71
3370 3425 6.294286 CGTTTTAAACTTTGGGAGGATAGCAA 60.294 38.462 6.27 0.00 0.00 3.91
3505 3563 7.452880 AGAAAAGTATGATTAAGCTTGTGCA 57.547 32.000 9.86 4.29 42.74 4.57
3606 3666 4.062991 GTGAACGTCCCTGAACTTGTTAT 58.937 43.478 0.00 0.00 0.00 1.89
3622 3682 1.013596 TCTTGCAAGTGTGGTGAACG 58.986 50.000 25.19 0.00 0.00 3.95
3676 3736 5.008613 GTGAAAATAGTTGTGTTGAGCTGGA 59.991 40.000 0.00 0.00 0.00 3.86
3709 3769 4.406972 CCTCCCTGATGATCTTGTTCAGTA 59.593 45.833 11.75 3.28 36.06 2.74
3775 3835 1.571919 GTGCTGACGGATTCGCTTAT 58.428 50.000 0.00 0.00 40.63 1.73
3790 3850 0.179018 ACGGCAAGAAAGAAGGTGCT 60.179 50.000 0.00 0.00 37.17 4.40
3817 3877 5.178096 TGAAATAGTTGAAGGATCTGGCA 57.822 39.130 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.