Multiple sequence alignment - TraesCS4A01G146800

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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 TraesCS4A01G146800 chr4A 100.000 3239 0 0 1 3239 259692194 259688956 0 5982
1 TraesCS4A01G146800 chr4A 85.352 1816 196 29 1444 3200 704436864 704438668 0 1816
2 TraesCS4A01G146800 chr4D 93.315 3276 175 14 4 3239 326946526 326943255 0 4796
3 TraesCS4A01G146800 chr7D 92.145 3272 217 19 1 3239 53168457 53165193 0 4582
4 TraesCS4A01G146800 chr7D 90.975 3302 229 18 1 3239 147042072 147045367 0 4383
5 TraesCS4A01G146800 chr5D 91.904 3298 204 21 1 3239 318511307 318514600 0 4553
6 TraesCS4A01G146800 chr5D 91.769 2843 169 17 1 2787 534901585 534904418 0 3893
7 TraesCS4A01G146800 chrUn 91.481 2911 182 23 1 2850 91267090 91269995 0 3941
8 TraesCS4A01G146800 chrUn 91.673 1405 98 9 1686 3073 97510898 97512300 0 1929
9 TraesCS4A01G146800 chr6B 87.935 3274 299 40 1 3211 465632182 465628942 0 3770
10 TraesCS4A01G146800 chr2A 89.275 2965 247 27 1 2922 56491116 56488180 0 3648
11 TraesCS4A01G146800 chr2A 90.107 2527 201 18 733 3213 492880829 492878306 0 3236
12 TraesCS4A01G146800 chr1D 92.106 2559 177 12 1 2556 375165080 375162544 0 3583
13 TraesCS4A01G146800 chr1D 93.017 1962 93 12 1319 3239 71595540 71593582 0 2824
14 TraesCS4A01G146800 chr1D 90.324 1850 158 10 710 2556 243249229 243247398 0 2405
15 TraesCS4A01G146800 chr1D 91.892 1406 94 10 1686 3073 290312318 290310915 0 1947
16 TraesCS4A01G146800 chr6D 90.019 2685 210 30 578 3239 417415495 417418144 0 3421
17 TraesCS4A01G146800 chr4B 88.953 2788 229 34 115 2852 79657657 79660415 0 3369
18 TraesCS4A01G146800 chr4B 88.452 2312 218 23 1 2295 649066246 649068525 0 2745
19 TraesCS4A01G146800 chr7A 92.514 1937 128 5 1 1923 451573174 451575107 0 2758
20 TraesCS4A01G146800 chr7A 90.819 1405 111 8 1686 3073 291593748 291592345 0 1864
21 TraesCS4A01G146800 chr3D 91.530 1405 101 8 1686 3073 167490599 167489196 0 1919
22 TraesCS4A01G146800 chr2D 92.130 1258 91 5 1821 3073 491309025 491307771 0 1768
23 TraesCS4A01G146800 chr2D 91.481 1080 85 3 578 1651 491319267 491318189 0 1478


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 TraesCS4A01G146800 chr4A 259688956 259692194 3238 True 5982 5982 100.000 1 3239 1 chr4A.!!$R1 3238
1 TraesCS4A01G146800 chr4A 704436864 704438668 1804 False 1816 1816 85.352 1444 3200 1 chr4A.!!$F1 1756
2 TraesCS4A01G146800 chr4D 326943255 326946526 3271 True 4796 4796 93.315 4 3239 1 chr4D.!!$R1 3235
3 TraesCS4A01G146800 chr7D 53165193 53168457 3264 True 4582 4582 92.145 1 3239 1 chr7D.!!$R1 3238
4 TraesCS4A01G146800 chr7D 147042072 147045367 3295 False 4383 4383 90.975 1 3239 1 chr7D.!!$F1 3238
5 TraesCS4A01G146800 chr5D 318511307 318514600 3293 False 4553 4553 91.904 1 3239 1 chr5D.!!$F1 3238
6 TraesCS4A01G146800 chr5D 534901585 534904418 2833 False 3893 3893 91.769 1 2787 1 chr5D.!!$F2 2786
7 TraesCS4A01G146800 chrUn 91267090 91269995 2905 False 3941 3941 91.481 1 2850 1 chrUn.!!$F1 2849
8 TraesCS4A01G146800 chrUn 97510898 97512300 1402 False 1929 1929 91.673 1686 3073 1 chrUn.!!$F2 1387
9 TraesCS4A01G146800 chr6B 465628942 465632182 3240 True 3770 3770 87.935 1 3211 1 chr6B.!!$R1 3210
10 TraesCS4A01G146800 chr2A 56488180 56491116 2936 True 3648 3648 89.275 1 2922 1 chr2A.!!$R1 2921
11 TraesCS4A01G146800 chr2A 492878306 492880829 2523 True 3236 3236 90.107 733 3213 1 chr2A.!!$R2 2480
12 TraesCS4A01G146800 chr1D 375162544 375165080 2536 True 3583 3583 92.106 1 2556 1 chr1D.!!$R4 2555
13 TraesCS4A01G146800 chr1D 71593582 71595540 1958 True 2824 2824 93.017 1319 3239 1 chr1D.!!$R1 1920
14 TraesCS4A01G146800 chr1D 243247398 243249229 1831 True 2405 2405 90.324 710 2556 1 chr1D.!!$R2 1846
15 TraesCS4A01G146800 chr1D 290310915 290312318 1403 True 1947 1947 91.892 1686 3073 1 chr1D.!!$R3 1387
16 TraesCS4A01G146800 chr6D 417415495 417418144 2649 False 3421 3421 90.019 578 3239 1 chr6D.!!$F1 2661
17 TraesCS4A01G146800 chr4B 79657657 79660415 2758 False 3369 3369 88.953 115 2852 1 chr4B.!!$F1 2737
18 TraesCS4A01G146800 chr4B 649066246 649068525 2279 False 2745 2745 88.452 1 2295 1 chr4B.!!$F2 2294
19 TraesCS4A01G146800 chr7A 451573174 451575107 1933 False 2758 2758 92.514 1 1923 1 chr7A.!!$F1 1922
20 TraesCS4A01G146800 chr7A 291592345 291593748 1403 True 1864 1864 90.819 1686 3073 1 chr7A.!!$R1 1387
21 TraesCS4A01G146800 chr3D 167489196 167490599 1403 True 1919 1919 91.530 1686 3073 1 chr3D.!!$R1 1387
22 TraesCS4A01G146800 chr2D 491307771 491309025 1254 True 1768 1768 92.130 1821 3073 1 chr2D.!!$R1 1252
23 TraesCS4A01G146800 chr2D 491318189 491319267 1078 True 1478 1478 91.481 578 1651 1 chr2D.!!$R2 1073

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
489 501 1.374631 GGCACGTGAGAGTCATGCA 60.375 57.895 22.23 0.0 36.89 3.96 F
1176 1226 1.448540 CAGCAATCCCGACGAAGCT 60.449 57.895 0.00 0.0 36.63 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2129 1.068055 CCTGCAACATCAGCCAAAGAC 60.068 52.381 0.0 0.0 32.87 3.01 R
3064 3345 0.249280 CAACAAAACCCCACTTCCGC 60.249 55.000 0.0 0.0 0.00 5.54 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
17 18 3.894947 GTTGGGCGCACCGTTTGT 61.895 61.111 7.46 0.00 44.64 2.83
34 35 4.025563 CGTTTGTTGGTGTGTATCTCGAAA 60.026 41.667 0.00 0.00 0.00 3.46
102 104 2.572104 ACTCTACTTCGAATTTGGGCCT 59.428 45.455 4.53 0.00 0.00 5.19
184 189 4.013728 GAGAGGAAGCAAGAGAGTAGTGA 58.986 47.826 0.00 0.00 0.00 3.41
256 262 6.595326 TCTGATTTTAGCATCAAGATTCGTGT 59.405 34.615 0.00 0.00 32.63 4.49
268 274 4.662961 TCGTGTCGCCTGGCTGTG 62.663 66.667 17.92 0.88 0.00 3.66
355 366 5.611374 CACCGACATTGGAATTATAGAGGT 58.389 41.667 0.00 0.00 0.00 3.85
453 465 6.756221 ACGGTTGTGAAGTCTTTAGAGTTAT 58.244 36.000 0.00 0.00 37.79 1.89
489 501 1.374631 GGCACGTGAGAGTCATGCA 60.375 57.895 22.23 0.00 36.89 3.96
552 565 6.021030 ACTTAGAGAGTATTGGTTGTGGGTA 58.979 40.000 0.00 0.00 36.65 3.69
618 632 3.423154 GCGTCGGGAAAGGTGCAG 61.423 66.667 0.00 0.00 0.00 4.41
669 695 2.299013 TGAACGGAGTGCACACTATCTT 59.701 45.455 21.04 1.86 37.76 2.40
754 789 2.097791 ACGCTTTGACGGTTGCTTTTTA 59.902 40.909 0.00 0.00 37.37 1.52
867 917 3.636231 CCAACCGCCTCCTCCACA 61.636 66.667 0.00 0.00 0.00 4.17
1018 1068 4.532834 GGTAATGGCAAAGGAACCATCTA 58.467 43.478 0.00 0.00 46.04 1.98
1150 1200 2.165998 GCAAGGAAAAGCTGGATGTCT 58.834 47.619 0.00 0.00 0.00 3.41
1176 1226 1.448540 CAGCAATCCCGACGAAGCT 60.449 57.895 0.00 0.00 36.63 3.74
1308 1359 3.386543 GCAGTTATGCGTGGAGGAT 57.613 52.632 0.00 0.00 43.87 3.24
1419 1471 9.377312 GCTATGCACCCTAAAATTTGATTAAAA 57.623 29.630 0.00 0.00 0.00 1.52
1507 1559 5.105146 ACCTGACTCACCAGATCAGTTTATC 60.105 44.000 0.00 0.00 38.56 1.75
1808 1944 4.752101 GGATCCACCTTAAATCTGTCATCG 59.248 45.833 6.95 0.00 35.41 3.84
1992 2129 3.073062 TCAAGGGAAGAAAGAGGTTCCAG 59.927 47.826 3.65 0.00 43.65 3.86
2040 2177 5.191727 TGATCCACCCATTCTACAAACAT 57.808 39.130 0.00 0.00 0.00 2.71
2203 2341 1.133823 TGGAGAGTGCAAAAGAGGCAA 60.134 47.619 0.00 0.00 43.91 4.52
2261 2399 7.548196 AGTGATGACGAAAACTTAGAAAACA 57.452 32.000 0.00 0.00 0.00 2.83
2277 2415 0.538287 AACAGGCCTTGGAGTTGCTC 60.538 55.000 0.00 0.00 0.00 4.26
2349 2488 7.606456 TCTGTTAGAACGAAGCCATTTCTAATT 59.394 33.333 6.36 0.00 41.53 1.40
2543 2683 7.605449 TGGACGCTAAGTATAGTTTAGTTGTT 58.395 34.615 0.00 0.00 32.09 2.83
2589 2801 0.679505 ACGCAGTTAGAGAGGCACAA 59.320 50.000 0.00 0.00 37.78 3.33
2686 2904 2.224843 TGAAGACACCACAAGCATCCAT 60.225 45.455 0.00 0.00 0.00 3.41
2702 2920 1.216977 CATAGGCACGTGGACGGAA 59.783 57.895 18.88 0.00 44.95 4.30
2717 2935 1.569548 ACGGAATAGGAGAGGTGAGGA 59.430 52.381 0.00 0.00 0.00 3.71
2733 2951 6.342338 GGTGAGGACCGAATACATAGTTAT 57.658 41.667 0.00 0.00 30.61 1.89
2857 3133 1.076777 CAAGGCACGGGATTGGGAT 60.077 57.895 0.00 0.00 0.00 3.85
2919 3200 2.338015 GGTGGCAGAGGCATGTGTG 61.338 63.158 0.00 0.00 43.71 3.82
2967 3248 3.186909 TGTGACGTTTGTGAAGAGACAG 58.813 45.455 0.00 0.00 0.00 3.51
2980 3261 1.228769 AGACAGAGGCGTGGTACCA 60.229 57.895 11.60 11.60 0.00 3.25
3044 3325 2.360350 CAGGCACGGAAGGCACAT 60.360 61.111 1.61 0.00 36.37 3.21
3164 3446 3.243434 CGAATACGCAGTTAGGGAGTCAT 60.243 47.826 0.00 0.00 37.78 3.06
3165 3447 4.023450 CGAATACGCAGTTAGGGAGTCATA 60.023 45.833 0.00 0.00 37.78 2.15
3196 3478 1.581402 CTAGAGAGTCGCGCGTGTG 60.581 63.158 30.98 2.36 0.00 3.82
3225 3507 2.756400 GCATGGAGTGGTGTGGGA 59.244 61.111 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.503910 CTCCATTTCGAGATACACACCAA 58.496 43.478 0.00 0.00 30.97 3.67
102 104 1.112916 TCTCCTCCGTTCTGCACACA 61.113 55.000 0.00 0.00 0.00 3.72
184 189 2.243221 CCATTTCCATCTCTCCCACCTT 59.757 50.000 0.00 0.00 0.00 3.50
256 262 1.454847 AAAAACCACAGCCAGGCGA 60.455 52.632 5.55 0.00 0.00 5.54
314 325 1.278127 GTGCCTGTAGAGCCTGGTTTA 59.722 52.381 0.00 0.00 0.00 2.01
316 327 1.679898 GTGCCTGTAGAGCCTGGTT 59.320 57.895 0.00 0.00 0.00 3.67
355 366 5.838521 TGCATCCATAGAGTTGATACCAGTA 59.161 40.000 0.00 0.00 0.00 2.74
428 440 5.779529 ACTCTAAAGACTTCACAACCGTA 57.220 39.130 0.00 0.00 0.00 4.02
489 501 3.288964 CTCTACTACCACACTTCCCGAT 58.711 50.000 0.00 0.00 0.00 4.18
552 565 6.578944 TGTTGTAGAGACTTTACACATGTGT 58.421 36.000 32.47 32.47 46.87 3.72
562 575 4.750098 CACGACCAATGTTGTAGAGACTTT 59.250 41.667 0.00 0.00 36.96 2.66
618 632 2.540101 GCACGTACTATGATGAACTGCC 59.460 50.000 0.00 0.00 0.00 4.85
867 917 1.280457 TTTGTGGCAAGGTTTGGGTT 58.720 45.000 0.00 0.00 0.00 4.11
900 950 1.517242 GGAATTGAGCGGCTATGGAG 58.483 55.000 0.60 0.00 0.00 3.86
1018 1068 3.256960 ACCACGGGGATGCTTGGT 61.257 61.111 12.96 0.00 37.53 3.67
1122 1172 0.603065 GCTTTTCCTTGCCGTGGATT 59.397 50.000 0.00 0.00 33.09 3.01
1167 1217 1.982612 TCATCTTGTCAGCTTCGTCG 58.017 50.000 0.00 0.00 0.00 5.12
1193 1243 0.615331 GCAGACCCACTTCAGGATCA 59.385 55.000 0.00 0.00 0.00 2.92
1204 1254 2.345991 GTACAAGCCGCAGACCCA 59.654 61.111 0.00 0.00 0.00 4.51
1419 1471 9.857656 ACTGATACATCAAGTCCATAAATGAAT 57.142 29.630 0.00 0.00 36.18 2.57
1422 1474 8.667076 TCACTGATACATCAAGTCCATAAATG 57.333 34.615 0.00 0.00 36.18 2.32
1992 2129 1.068055 CCTGCAACATCAGCCAAAGAC 60.068 52.381 0.00 0.00 32.87 3.01
2040 2177 8.548025 TCAACCCTGTCAATCTTATTCTTCATA 58.452 33.333 0.00 0.00 0.00 2.15
2203 2341 7.604657 AGTAGGGATCGTCATAATTCTTCTT 57.395 36.000 0.00 0.00 0.00 2.52
2261 2399 2.348998 CGAGCAACTCCAAGGCCT 59.651 61.111 0.00 0.00 0.00 5.19
2277 2415 2.614057 AGAAAGGACAAGCAGAAACACG 59.386 45.455 0.00 0.00 0.00 4.49
2369 2508 9.116067 ACTACAAACTTGACATAAGCAAACTTA 57.884 29.630 0.00 0.00 42.47 2.24
2543 2683 2.316867 CCATGTCGCGCTTGTGTGA 61.317 57.895 5.56 0.00 0.00 3.58
2589 2801 2.028567 GTGGCTCTAGAGACTGCAAACT 60.029 50.000 25.95 0.00 37.35 2.66
2660 2873 4.734398 TGCTTGTGGTGTCTTCATTTTT 57.266 36.364 0.00 0.00 0.00 1.94
2686 2904 0.742505 CTATTCCGTCCACGTGCCTA 59.257 55.000 10.91 0.00 37.74 3.93
2702 2920 1.223501 TCGGTCCTCACCTCTCCTAT 58.776 55.000 0.00 0.00 41.17 2.57
2717 2935 6.072286 CGTGACCCTATAACTATGTATTCGGT 60.072 42.308 0.00 0.00 0.00 4.69
2733 2951 1.071071 CACTTCCAAACCGTGACCCTA 59.929 52.381 0.00 0.00 0.00 3.53
2857 3133 1.478916 TGATACCCGTGCATCGAGAAA 59.521 47.619 9.75 0.00 42.86 2.52
2882 3158 0.877071 CACACTCTTGTGCATCCACC 59.123 55.000 0.00 0.00 46.60 4.61
2919 3200 2.760374 CATCTCTAACCGAGCATTCCC 58.240 52.381 0.00 0.00 39.70 3.97
3044 3325 1.596934 CCTCTTGCGGCTTCACCTA 59.403 57.895 0.00 0.00 35.61 3.08
3064 3345 0.249280 CAACAAAACCCCACTTCCGC 60.249 55.000 0.00 0.00 0.00 5.54
3164 3446 4.924625 ACTCTCTAGAGGCTTCACAACTA 58.075 43.478 19.67 0.00 46.13 2.24
3165 3447 3.761752 GACTCTCTAGAGGCTTCACAACT 59.238 47.826 19.67 0.00 46.61 3.16
3196 3478 2.163010 CACTCCATGCCTGTGATGAAAC 59.837 50.000 5.41 0.00 33.95 2.78


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

AutoCloner maintained by Alex Coulton.