Multiple sequence alignment - TraesCS1D01G104500

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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 TraesCS1D01G104500 chr1D 100.000 3414 0 0 1 3414 95934621 95938034 0.000000e+00 6305
1 TraesCS1D01G104500 chr1B 91.013 3494 194 64 16 3414 156839983 156836515 0.000000e+00 4602
2 TraesCS1D01G104500 chr1A 91.537 2446 135 40 306 2699 91173904 91176329 0.000000e+00 3304
3 TraesCS1D01G104500 chr1A 87.295 488 28 18 2945 3414 91176350 91176821 8.390000e-146 527
4 TraesCS1D01G104500 chr1A 87.048 332 38 3 1 331 91173473 91173800 1.500000e-98 370
5 TraesCS1D01G104500 chr6A 88.722 798 72 5 1459 2256 20508943 20509722 0.000000e+00 959
6 TraesCS1D01G104500 chr6A 86.873 259 30 2 973 1231 20508459 20508713 1.550000e-73 287
7 TraesCS1D01G104500 chr6B 89.605 760 67 2 1492 2251 35515358 35516105 0.000000e+00 955
8 TraesCS1D01G104500 chr6B 86.831 243 28 2 982 1224 35514867 35515105 5.620000e-68 268
9 TraesCS1D01G104500 chr6B 88.696 115 11 2 1315 1428 35515148 35515261 4.590000e-29 139
10 TraesCS1D01G104500 chr6D 83.165 1087 118 34 1459 2521 20590306 20591351 0.000000e+00 933
11 TraesCS1D01G104500 chr6D 87.259 259 29 2 973 1231 20589823 20590077 3.330000e-75 292
12 TraesCS1D01G104500 chr6D 77.938 485 79 18 385 852 20588993 20589466 9.330000e-71 278
13 TraesCS1D01G104500 chr6D 88.034 117 12 2 1315 1430 20590116 20590231 1.650000e-28 137


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 TraesCS1D01G104500 chr1D 95934621 95938034 3413 False 6305.000000 6305 100.000000 1 3414 1 chr1D.!!$F1 3413
1 TraesCS1D01G104500 chr1B 156836515 156839983 3468 True 4602.000000 4602 91.013000 16 3414 1 chr1B.!!$R1 3398
2 TraesCS1D01G104500 chr1A 91173473 91176821 3348 False 1400.333333 3304 88.626667 1 3414 3 chr1A.!!$F1 3413
3 TraesCS1D01G104500 chr6A 20508459 20509722 1263 False 623.000000 959 87.797500 973 2256 2 chr6A.!!$F1 1283
4 TraesCS1D01G104500 chr6B 35514867 35516105 1238 False 454.000000 955 88.377333 982 2251 3 chr6B.!!$F1 1269
5 TraesCS1D01G104500 chr6D 20588993 20591351 2358 False 410.000000 933 84.099000 385 2521 4 chr6D.!!$F1 2136

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
161 162 0.313987 CGGAAAACAAAGTGAGGCCC 59.686 55.000 0.0 0.0 0.0 5.80 F
777 946 0.894141 TGAGAGCAAGCCAGAGAGAC 59.106 55.000 0.0 0.0 0.0 3.36 F
780 951 1.001860 AGAGCAAGCCAGAGAGACAAC 59.998 52.381 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 2123 0.528684 CGGCGAAGAGGAAGGTGATC 60.529 60.000 0.00 0.0 0.00 2.92 R
1723 2285 2.121963 TGGTTGAGGGGGCTGAGT 60.122 61.111 0.00 0.0 0.00 3.41 R
2521 3086 2.348666 CGTGCATTTCCTAGTGCTGTAC 59.651 50.000 4.86 0.0 41.78 2.90 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
28 29 0.823460 TACATGCATGAGTCGAGCCA 59.177 50.000 32.75 3.58 0.00 4.75
31 32 2.125391 GCATGAGTCGAGCCAGCA 60.125 61.111 0.00 0.00 0.00 4.41
38 39 2.917227 TCGAGCCAGCAGTGGTCA 60.917 61.111 0.00 0.00 46.96 4.02
59 60 2.279851 CGGACAGCACCGTCAACA 60.280 61.111 8.46 0.00 46.70 3.33
63 64 1.606994 GGACAGCACCGTCAACACATA 60.607 52.381 3.75 0.00 37.66 2.29
64 65 2.346803 GACAGCACCGTCAACACATAT 58.653 47.619 0.00 0.00 35.88 1.78
69 70 2.935238 GCACCGTCAACACATATCTGGT 60.935 50.000 0.00 0.00 0.00 4.00
89 90 3.686726 GGTGACTGGATTCTTTACTGCTG 59.313 47.826 0.00 0.00 0.00 4.41
96 97 2.248280 TTCTTTACTGCTGTGCCGAA 57.752 45.000 6.48 3.36 0.00 4.30
136 137 0.452987 CATGGCCACAATGACTTCCG 59.547 55.000 8.16 0.00 0.00 4.30
140 141 0.321653 GCCACAATGACTTCCGGACT 60.322 55.000 1.83 0.00 0.00 3.85
146 147 1.541310 ATGACTTCCGGACTGCGGAA 61.541 55.000 21.61 21.61 42.45 4.30
161 162 0.313987 CGGAAAACAAAGTGAGGCCC 59.686 55.000 0.00 0.00 0.00 5.80
289 291 6.428083 TGTTGACTTTGGTTAGTGGATCTA 57.572 37.500 0.00 0.00 0.00 1.98
301 303 2.769095 AGTGGATCTAGTGGCTTCTTCC 59.231 50.000 0.00 0.00 0.00 3.46
314 316 6.954102 AGTGGCTTCTTCCCAAAATAAAGTAT 59.046 34.615 0.00 0.00 33.39 2.12
408 542 8.767085 CAAAAATGAGTTATTTCAATGTGTGCT 58.233 29.630 0.00 0.00 38.01 4.40
415 549 7.889469 AGTTATTTCAATGTGTGCTTGAAGAT 58.111 30.769 0.00 0.72 41.98 2.40
416 550 8.025445 AGTTATTTCAATGTGTGCTTGAAGATC 58.975 33.333 0.00 0.00 41.98 2.75
418 552 3.084039 TCAATGTGTGCTTGAAGATCCC 58.916 45.455 0.00 0.00 29.96 3.85
438 578 3.606886 ACGTAGTTGCAACAGGAGG 57.393 52.632 30.11 20.75 37.78 4.30
568 709 6.708054 GGTATATTCTCACACTTCCCATCAAG 59.292 42.308 0.00 0.00 0.00 3.02
570 711 4.916041 TTCTCACACTTCCCATCAAGAT 57.084 40.909 0.00 0.00 0.00 2.40
608 749 8.209584 AGATATTTTAGCAGAAGCAAGATGAGA 58.790 33.333 0.00 0.00 45.49 3.27
616 762 3.752222 AGAAGCAAGATGAGAAAGCACTG 59.248 43.478 0.00 0.00 0.00 3.66
634 780 3.618690 CTGGCTAGTTGGCTAGTTTCT 57.381 47.619 0.00 0.00 44.93 2.52
681 832 3.198068 AGTGCTATACAACCGCATCAAG 58.802 45.455 0.00 0.00 35.93 3.02
777 946 0.894141 TGAGAGCAAGCCAGAGAGAC 59.106 55.000 0.00 0.00 0.00 3.36
780 951 1.001860 AGAGCAAGCCAGAGAGACAAC 59.998 52.381 0.00 0.00 0.00 3.32
782 953 1.350351 AGCAAGCCAGAGAGACAACAT 59.650 47.619 0.00 0.00 0.00 2.71
796 967 1.880027 ACAACATTCGCCAGAAGGAAC 59.120 47.619 0.00 0.00 40.28 3.62
1250 1701 7.191551 AGTCATGATTAAGATGCAAACAATCG 58.808 34.615 0.00 0.00 0.00 3.34
1299 1769 9.932207 TTAGTTGATCCATCTTAAGTTCGTAAA 57.068 29.630 1.63 0.00 0.00 2.01
1302 1772 9.704098 GTTGATCCATCTTAAGTTCGTAAATTC 57.296 33.333 1.63 0.00 0.00 2.17
1331 1810 4.047822 GCGAGATCCATGACTGTTAAGAG 58.952 47.826 0.00 0.00 0.00 2.85
1415 1894 5.356470 GCTCTACTCGGGTAAGAACTAAGAA 59.644 44.000 0.00 0.00 0.00 2.52
1585 2120 1.746615 CACCAGCAACTCCATCCCG 60.747 63.158 0.00 0.00 0.00 5.14
1588 2123 1.746615 CAGCAACTCCATCCCGGTG 60.747 63.158 0.00 0.00 35.57 4.94
1708 2243 1.300465 CATCCTCGTCATCGCCCTG 60.300 63.158 0.00 0.00 36.96 4.45
2251 2813 0.475632 TCTGGGGGAAGAGCAAGGAA 60.476 55.000 0.00 0.00 0.00 3.36
2258 2820 1.615384 GGAAGAGCAAGGAACAGCCAT 60.615 52.381 0.00 0.00 40.02 4.40
2521 3086 7.280428 ACAGAGACTCTTGAATGAAATGCATAG 59.720 37.037 0.98 0.00 35.78 2.23
2647 3223 4.563580 GCGGCTATTTCTAAGATGGGATGA 60.564 45.833 0.00 0.00 0.00 2.92
2685 3262 5.130292 AGTGGATGATTCAGCTTTGTTTG 57.870 39.130 1.44 0.00 0.00 2.93
2744 3328 8.649973 AATTACGACTCCATTAGAAATCTGAC 57.350 34.615 0.00 0.00 0.00 3.51
2745 3329 5.661056 ACGACTCCATTAGAAATCTGACA 57.339 39.130 0.00 0.00 0.00 3.58
2750 3334 6.590068 ACTCCATTAGAAATCTGACATCAGG 58.410 40.000 8.99 0.00 43.91 3.86
2790 3378 5.814314 TCGAACGTTTTTATGGCAATTTG 57.186 34.783 0.46 0.00 0.00 2.32
2799 3387 8.491152 CGTTTTTATGGCAATTTGTGTTTATCA 58.509 29.630 0.00 0.00 0.00 2.15
2812 3400 5.953183 TGTGTTTATCATTGATGGCAAGTC 58.047 37.500 9.46 0.00 37.45 3.01
2824 3412 1.362406 GGCAAGTCTAGTTGGCGAGC 61.362 60.000 8.16 0.00 42.40 5.03
2835 3423 2.557924 AGTTGGCGAGCATGAAAATTCA 59.442 40.909 0.00 0.00 42.14 2.57
2842 3430 4.378770 GCGAGCATGAAAATTCAGTCTCAA 60.379 41.667 18.86 0.00 41.08 3.02
2880 3468 4.034742 ACAAAATTGTCGTGCTCGTAAACT 59.965 37.500 8.17 0.00 36.50 2.66
2884 3472 4.697300 TTGTCGTGCTCGTAAACTAAAC 57.303 40.909 8.17 0.00 38.33 2.01
2886 3474 4.362279 TGTCGTGCTCGTAAACTAAACTT 58.638 39.130 8.17 0.00 38.33 2.66
2897 3485 5.354234 CGTAAACTAAACTTGGCATCCTCAT 59.646 40.000 0.00 0.00 0.00 2.90
2911 3499 4.928601 CATCCTCATGCCAACTACATTTG 58.071 43.478 0.00 0.00 0.00 2.32
2989 3587 6.984474 TGGCGATTTAGAAATAGTAACTCTGG 59.016 38.462 0.00 0.00 0.00 3.86
2995 3593 9.780186 ATTTAGAAATAGTAACTCTGGTATGGC 57.220 33.333 0.00 0.00 0.00 4.40
3083 3701 1.004277 GTTGGCCCCTACATGTTCAGA 59.996 52.381 2.30 0.00 0.00 3.27
3291 3919 0.762418 TGACTCATTTGACCCACCGT 59.238 50.000 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.773054 GCTGGCTCGACTCATGCATG 61.773 60.000 21.07 21.07 0.00 4.06
12 13 1.523258 GCTGGCTCGACTCATGCAT 60.523 57.895 0.00 0.00 0.00 3.96
13 14 2.125391 GCTGGCTCGACTCATGCA 60.125 61.111 0.00 0.00 0.00 3.96
14 15 2.125391 TGCTGGCTCGACTCATGC 60.125 61.111 0.00 0.00 0.00 4.06
28 29 1.367840 GTCCGAAGTGACCACTGCT 59.632 57.895 3.13 0.00 41.58 4.24
31 32 1.367840 GCTGTCCGAAGTGACCACT 59.632 57.895 0.00 0.00 44.94 4.00
59 60 5.965033 AAGAATCCAGTCACCAGATATGT 57.035 39.130 0.00 0.00 0.00 2.29
63 64 5.738909 CAGTAAAGAATCCAGTCACCAGAT 58.261 41.667 0.00 0.00 0.00 2.90
64 65 4.563580 GCAGTAAAGAATCCAGTCACCAGA 60.564 45.833 0.00 0.00 0.00 3.86
69 70 4.318332 CACAGCAGTAAAGAATCCAGTCA 58.682 43.478 0.00 0.00 0.00 3.41
118 119 0.680921 CCGGAAGTCATTGTGGCCAT 60.681 55.000 9.72 0.00 0.00 4.40
136 137 1.673920 TCACTTTGTTTTCCGCAGTCC 59.326 47.619 0.00 0.00 0.00 3.85
140 141 0.383949 GCCTCACTTTGTTTTCCGCA 59.616 50.000 0.00 0.00 0.00 5.69
146 147 1.152756 AGCGGGCCTCACTTTGTTT 60.153 52.632 0.84 0.00 0.00 2.83
176 177 2.355756 CCAAATGAGCCACTATTGTCGG 59.644 50.000 0.00 0.00 0.00 4.79
289 291 5.147767 ACTTTATTTTGGGAAGAAGCCACT 58.852 37.500 0.00 0.00 0.00 4.00
345 347 9.825109 CAAAAACTATTTTTCAGGAAAAGGGTA 57.175 29.630 7.21 3.05 40.65 3.69
346 348 7.773224 CCAAAAACTATTTTTCAGGAAAAGGGT 59.227 33.333 7.21 5.63 40.65 4.34
347 349 7.773224 ACCAAAAACTATTTTTCAGGAAAAGGG 59.227 33.333 13.31 5.13 40.65 3.95
354 484 8.387354 GTGTTGAACCAAAAACTATTTTTCAGG 58.613 33.333 0.00 7.68 40.65 3.86
365 495 7.355778 TCATTTTTGTGTGTTGAACCAAAAAC 58.644 30.769 18.82 1.91 43.60 2.43
408 542 3.071479 GCAACTACGTTGGGATCTTCAA 58.929 45.455 8.60 0.00 42.99 2.69
415 549 1.588674 CTGTTGCAACTACGTTGGGA 58.411 50.000 28.61 5.75 42.99 4.37
416 550 0.591170 CCTGTTGCAACTACGTTGGG 59.409 55.000 28.61 14.92 42.99 4.12
418 552 1.531149 CCTCCTGTTGCAACTACGTTG 59.469 52.381 28.61 14.03 45.24 4.10
438 578 2.221169 TCTCAACCATGTGAACAGTGC 58.779 47.619 0.00 0.00 0.00 4.40
522 662 2.671351 CGGCTAGTGTGTGTCTTGTAGG 60.671 54.545 0.00 0.00 0.00 3.18
570 711 6.805713 TGCTAAAATATCTGTGATCACTCGA 58.194 36.000 25.55 20.72 0.00 4.04
583 724 8.375608 TCTCATCTTGCTTCTGCTAAAATATC 57.624 34.615 0.00 0.00 40.48 1.63
591 732 2.748532 GCTTTCTCATCTTGCTTCTGCT 59.251 45.455 0.00 0.00 40.48 4.24
634 780 7.213216 TGTTCAGTGCTTATTGCTCATTTTA 57.787 32.000 0.00 0.00 43.37 1.52
656 802 2.773487 TGCGGTTGTATAGCACTTTGT 58.227 42.857 0.00 0.00 35.81 2.83
668 819 1.880027 GGAAAGACTTGATGCGGTTGT 59.120 47.619 0.00 0.00 0.00 3.32
731 896 7.222872 TCACACATTTTATTTCTTTGGGCAAT 58.777 30.769 0.00 0.00 0.00 3.56
777 946 2.154462 AGTTCCTTCTGGCGAATGTTG 58.846 47.619 0.00 0.00 0.00 3.33
780 951 3.131223 TCTCTAGTTCCTTCTGGCGAATG 59.869 47.826 0.00 0.00 0.00 2.67
782 953 2.803956 TCTCTAGTTCCTTCTGGCGAA 58.196 47.619 0.00 0.00 0.00 4.70
796 967 6.146347 GGCGATAATGTTAGCCTTTTCTCTAG 59.854 42.308 0.00 0.00 45.67 2.43
1250 1701 0.824595 TCCATGCATGCATAGCCACC 60.825 55.000 31.73 0.00 34.91 4.61
1295 1765 7.547019 TCATGGATCTCGCTCATATGAATTTAC 59.453 37.037 6.90 0.00 0.00 2.01
1299 1769 5.187381 AGTCATGGATCTCGCTCATATGAAT 59.813 40.000 6.90 0.00 0.00 2.57
1302 1772 4.174762 CAGTCATGGATCTCGCTCATATG 58.825 47.826 0.00 0.00 0.00 1.78
1310 1780 5.255710 ACTCTTAACAGTCATGGATCTCG 57.744 43.478 0.00 0.00 0.00 4.04
1331 1810 1.725973 GCGCGTTTCTCCTGCAAAC 60.726 57.895 8.43 0.00 0.00 2.93
1415 1894 1.066143 GGGAGATCAATGGTGTCGTGT 60.066 52.381 0.00 0.00 0.00 4.49
1469 1999 3.061322 ACGTACGTGCAACACATGTTAT 58.939 40.909 22.14 0.00 46.67 1.89
1570 2105 1.746615 CACCGGGATGGAGTTGCTG 60.747 63.158 6.32 0.00 42.00 4.41
1588 2123 0.528684 CGGCGAAGAGGAAGGTGATC 60.529 60.000 0.00 0.00 0.00 2.92
1723 2285 2.121963 TGGTTGAGGGGGCTGAGT 60.122 61.111 0.00 0.00 0.00 3.41
2521 3086 2.348666 CGTGCATTTCCTAGTGCTGTAC 59.651 50.000 4.86 0.00 41.78 2.90
2598 3171 4.051922 CGTTACATACCAGCAATCCTCTC 58.948 47.826 0.00 0.00 0.00 3.20
2735 3319 7.078011 GGTAGAAAACCTGATGTCAGATTTC 57.922 40.000 21.08 21.08 46.59 2.17
2750 3334 5.788531 CGTTCGATTTGTCATGGTAGAAAAC 59.211 40.000 0.00 0.00 0.00 2.43
2755 3339 4.921470 AACGTTCGATTTGTCATGGTAG 57.079 40.909 0.00 0.00 0.00 3.18
2757 3341 4.561735 AAAACGTTCGATTTGTCATGGT 57.438 36.364 0.00 0.00 0.00 3.55
2790 3378 6.199937 AGACTTGCCATCAATGATAAACAC 57.800 37.500 0.00 0.00 0.00 3.32
2799 3387 3.019564 GCCAACTAGACTTGCCATCAAT 58.980 45.455 0.00 0.00 0.00 2.57
2800 3388 2.436417 GCCAACTAGACTTGCCATCAA 58.564 47.619 0.00 0.00 0.00 2.57
2801 3389 1.675714 CGCCAACTAGACTTGCCATCA 60.676 52.381 0.00 0.00 0.00 3.07
2812 3400 4.142622 TGAATTTTCATGCTCGCCAACTAG 60.143 41.667 0.00 0.00 31.01 2.57
2821 3409 7.310664 TGAATTGAGACTGAATTTTCATGCTC 58.689 34.615 1.24 12.18 37.57 4.26
2851 3439 1.804372 GCACGACAATTTTGTGGCCAA 60.804 47.619 7.24 0.00 42.43 4.52
2858 3446 4.523813 AGTTTACGAGCACGACAATTTTG 58.476 39.130 11.40 0.00 42.66 2.44
2942 3530 8.531530 CGCCAAAAGTTAATTTATCAGTAATGC 58.468 33.333 0.00 0.00 0.00 3.56
2943 3531 9.781834 TCGCCAAAAGTTAATTTATCAGTAATG 57.218 29.630 0.00 0.00 0.00 1.90
2989 3587 7.642586 GTCTACGGAATTTTAACATTGCCATAC 59.357 37.037 0.88 0.00 0.00 2.39
2994 3592 9.006215 GTTATGTCTACGGAATTTTAACATTGC 57.994 33.333 0.00 0.00 0.00 3.56
3036 3642 5.163982 GCCAAGACAGATCAAAAGTACGTAC 60.164 44.000 18.10 18.10 0.00 3.67
3042 3648 2.154462 CGGCCAAGACAGATCAAAAGT 58.846 47.619 2.24 0.00 0.00 2.66
3083 3701 7.170965 ACAACATGAGAAGAGACCAATATGTT 58.829 34.615 0.00 0.00 37.83 2.71
3088 3706 4.999950 GTGACAACATGAGAAGAGACCAAT 59.000 41.667 0.00 0.00 0.00 3.16
3211 3837 6.381707 GGGGTATTAAAGGCTCCATTTTGTTA 59.618 38.462 0.00 0.00 0.00 2.41
3291 3919 8.219178 TGGGTTAACTAGACCATAACTTTTCAA 58.781 33.333 5.42 0.00 38.98 2.69
3365 3994 5.440610 AGTGCCCTCGAAAGATATGAATTT 58.559 37.500 0.00 0.00 40.84 1.82


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

AutoCloner maintained by Alex Coulton.