Multiple sequence alignment - TraesCS6A01G263000

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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 TraesCS6A01G263000 chr6A 100.000 2594 0 0 1 2594 486012798 486010205 0.000000e+00 4791.0
1 TraesCS6A01G263000 chr6A 100.000 30 0 0 128 157 539867592 539867563 3.610000e-04 56.5
2 TraesCS6A01G263000 chr6B 94.001 2367 56 28 280 2594 521521014 521518682 0.000000e+00 3506.0
3 TraesCS6A01G263000 chr6B 96.875 32 1 0 123 154 62502241 62502272 1.000000e-03 54.7
4 TraesCS6A01G263000 chr6D 92.599 1824 91 23 2 1804 345396718 345394918 0.000000e+00 2580.0
5 TraesCS6A01G263000 chr6D 93.103 812 29 9 1799 2594 345394745 345393945 0.000000e+00 1164.0
6 TraesCS6A01G263000 chr6D 96.939 98 2 1 1707 1804 345394871 345394775 2.070000e-36 163.0
7 TraesCS6A01G263000 chr6D 96.875 32 1 0 123 154 380704553 380704584 1.000000e-03 54.7
8 TraesCS6A01G263000 chr2A 92.683 41 3 0 118 158 61510080 61510040 2.790000e-05 60.2
9 TraesCS6A01G263000 chr7B 100.000 29 0 0 126 154 577462707 577462679 1.000000e-03 54.7
10 TraesCS6A01G263000 chr5A 100.000 29 0 0 126 154 500975214 500975186 1.000000e-03 54.7
11 TraesCS6A01G263000 chr3A 100.000 29 0 0 126 154 142520471 142520443 1.000000e-03 54.7
12 TraesCS6A01G263000 chr3A 100.000 29 0 0 126 154 536322476 536322448 1.000000e-03 54.7


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 TraesCS6A01G263000 chr6A 486010205 486012798 2593 True 4791.000000 4791 100.000000 1 2594 1 chr6A.!!$R1 2593
1 TraesCS6A01G263000 chr6B 521518682 521521014 2332 True 3506.000000 3506 94.001000 280 2594 1 chr6B.!!$R1 2314
2 TraesCS6A01G263000 chr6D 345393945 345396718 2773 True 1302.333333 2580 94.213667 2 2594 3 chr6D.!!$R1 2592

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
243 247 1.221466 CCGTCGTTGAGCAAAGCAGA 61.221 55.0 0.00 0.00 0.00 4.26 F
1028 1032 0.840288 TCCCATATCACCGGGGATGG 60.840 60.0 29.89 23.65 45.83 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 1054 0.321671 ACATTGTCCACCCAGACTCG 59.678 55.0 0.0 0.0 37.66 4.18 R
2479 2723 0.835941 ATCCCTGTCTGTCTGATGGC 59.164 55.0 0.0 0.0 0.00 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
22 23 3.945346 TGGTTTATATGCACAACGGACT 58.055 40.909 0.00 0.00 0.00 3.85
99 101 4.715523 CGGACACGGCCCCATTGT 62.716 66.667 0.00 0.00 36.18 2.71
106 108 3.991318 GGCCCCATTGTCACCCCA 61.991 66.667 0.00 0.00 0.00 4.96
108 110 1.984026 GCCCCATTGTCACCCCAAG 60.984 63.158 0.00 0.00 0.00 3.61
109 111 1.984026 CCCCATTGTCACCCCAAGC 60.984 63.158 0.00 0.00 0.00 4.01
110 112 2.342650 CCCATTGTCACCCCAAGCG 61.343 63.158 0.00 0.00 0.00 4.68
111 113 2.342650 CCATTGTCACCCCAAGCGG 61.343 63.158 0.00 0.00 0.00 5.52
112 114 1.303236 CATTGTCACCCCAAGCGGA 60.303 57.895 0.00 0.00 0.00 5.54
113 115 1.303317 ATTGTCACCCCAAGCGGAC 60.303 57.895 0.00 0.00 0.00 4.79
114 116 3.818121 TTGTCACCCCAAGCGGACG 62.818 63.158 0.00 0.00 33.04 4.79
117 121 2.281208 CACCCCAAGCGGACGAAA 60.281 61.111 0.00 0.00 0.00 3.46
137 141 4.510038 AAGTATGTACGTTTGGAGTCGT 57.490 40.909 0.00 0.00 42.82 4.34
158 162 1.948611 GCGTTGGAGTTGGCCTAATGA 60.949 52.381 3.32 0.00 0.00 2.57
175 179 6.982724 GCCTAATGAGCTTATTGCAGAAAAAT 59.017 34.615 13.66 0.00 45.94 1.82
176 180 7.168804 GCCTAATGAGCTTATTGCAGAAAAATC 59.831 37.037 13.66 0.00 45.94 2.17
177 181 7.650903 CCTAATGAGCTTATTGCAGAAAAATCC 59.349 37.037 13.66 0.00 45.94 3.01
178 182 5.329035 TGAGCTTATTGCAGAAAAATCCC 57.671 39.130 0.00 0.00 45.94 3.85
180 184 4.356436 AGCTTATTGCAGAAAAATCCCCT 58.644 39.130 0.00 0.00 45.94 4.79
209 213 6.476706 TGAATACATGATAACAGTGAAGAGCG 59.523 38.462 0.00 0.00 0.00 5.03
218 222 1.532437 CAGTGAAGAGCGTGCAAATGA 59.468 47.619 0.00 0.00 0.00 2.57
219 223 2.031769 CAGTGAAGAGCGTGCAAATGAA 60.032 45.455 0.00 0.00 0.00 2.57
220 224 2.816087 AGTGAAGAGCGTGCAAATGAAT 59.184 40.909 0.00 0.00 0.00 2.57
221 225 2.912967 GTGAAGAGCGTGCAAATGAATG 59.087 45.455 0.00 0.00 0.00 2.67
240 244 2.556287 CCCGTCGTTGAGCAAAGC 59.444 61.111 0.00 0.00 0.00 3.51
243 247 1.221466 CCGTCGTTGAGCAAAGCAGA 61.221 55.000 0.00 0.00 0.00 4.26
278 282 2.035704 AGAAGGCATATGAGCTCACTCG 59.964 50.000 20.97 11.10 46.69 4.18
464 468 1.835121 TGCTATTGCTACGTACGCAG 58.165 50.000 16.72 13.80 38.80 5.18
567 571 3.012518 CACAGTTGGAAGGATAAGCTGG 58.987 50.000 0.00 0.00 0.00 4.85
740 744 5.412904 AGGTATTCAAAGAGCTAGCACAAAC 59.587 40.000 18.83 2.79 0.00 2.93
745 749 5.065914 TCAAAGAGCTAGCACAAACAAGAT 58.934 37.500 18.83 0.00 0.00 2.40
746 750 6.230472 TCAAAGAGCTAGCACAAACAAGATA 58.770 36.000 18.83 0.00 0.00 1.98
747 751 6.147821 TCAAAGAGCTAGCACAAACAAGATAC 59.852 38.462 18.83 0.00 0.00 2.24
787 791 1.805943 CGGTGTTGCATTGATGAGTGA 59.194 47.619 0.00 0.00 0.00 3.41
901 905 3.536570 GTCTGTTCCCTTGGCTATCTTC 58.463 50.000 0.00 0.00 0.00 2.87
1028 1032 0.840288 TCCCATATCACCGGGGATGG 60.840 60.000 29.89 23.65 45.83 3.51
1093 1097 2.054453 GTCTCCCCCATGCAAAGCC 61.054 63.158 0.00 0.00 0.00 4.35
1158 1162 2.292267 GGAAGCAATGTCGATGATGGT 58.708 47.619 0.00 0.00 0.00 3.55
1212 1222 1.134068 GGAGGCAAGGAATACCAGGAC 60.134 57.143 0.00 0.00 38.94 3.85
1242 1252 1.376037 CAACGACTCCCTTGCCTCC 60.376 63.158 0.00 0.00 0.00 4.30
1440 1465 4.491409 GAGAAAGGGGGCGAGGGC 62.491 72.222 0.00 0.00 38.90 5.19
1572 1601 3.676049 GCCTTATGCATCATCGGTCGATA 60.676 47.826 0.19 0.00 40.77 2.92
1602 1632 3.940209 TGTTGTTGAAGATGGGAATGC 57.060 42.857 0.00 0.00 0.00 3.56
1672 1702 0.875059 GTCCTCAGTTTTGCCTTCCG 59.125 55.000 0.00 0.00 0.00 4.30
1795 1978 1.247567 TGCCTTCCTGCTTTTACTGC 58.752 50.000 0.00 0.00 0.00 4.40
1827 2048 4.145807 TCTCCTGCTATGTTCCTAGCTAC 58.854 47.826 4.88 0.00 43.68 3.58
1841 2062 3.639094 CCTAGCTACTAATGGAGCACTGT 59.361 47.826 2.96 0.00 41.36 3.55
1870 2091 2.493675 CACAAGCTACACTCTAGCCAGA 59.506 50.000 0.00 0.00 41.25 3.86
1988 2212 2.420687 CCCATTGCCCAGACTCTAGAAC 60.421 54.545 0.00 0.00 0.00 3.01
2016 2246 5.444586 CAGTGTGCAATGCATATGTTTTC 57.555 39.130 12.38 0.00 41.91 2.29
2019 2249 6.146510 CAGTGTGCAATGCATATGTTTTCTTT 59.853 34.615 12.38 0.00 41.91 2.52
2021 2251 7.871973 AGTGTGCAATGCATATGTTTTCTTTAA 59.128 29.630 12.38 0.00 41.91 1.52
2022 2252 7.951565 GTGTGCAATGCATATGTTTTCTTTAAC 59.048 33.333 12.38 0.00 41.91 2.01
2023 2253 7.654923 TGTGCAATGCATATGTTTTCTTTAACA 59.345 29.630 12.38 0.00 41.91 2.41
2024 2254 8.658609 GTGCAATGCATATGTTTTCTTTAACAT 58.341 29.630 12.38 7.12 41.91 2.71
2130 2361 5.359756 ACCAAATCACTTCTTTGCCTTTTC 58.640 37.500 0.00 0.00 33.27 2.29
2143 2374 1.298859 CCTTTTCCTCCAACGGCTCG 61.299 60.000 0.00 0.00 0.00 5.03
2303 2547 2.270986 GCAGGTGACCTTGGCTTGG 61.271 63.158 0.00 0.00 0.00 3.61
2304 2548 2.116125 AGGTGACCTTGGCTTGGC 59.884 61.111 0.00 0.00 0.00 4.52
2305 2549 2.116125 GGTGACCTTGGCTTGGCT 59.884 61.111 0.00 0.00 0.00 4.75
2306 2550 1.531602 GGTGACCTTGGCTTGGCTT 60.532 57.895 0.00 0.00 0.00 4.35
2307 2551 1.662044 GTGACCTTGGCTTGGCTTG 59.338 57.895 0.00 0.00 0.00 4.01
2356 2600 6.597262 TGTGGCAAGTATATAACAATCACG 57.403 37.500 0.00 0.00 0.00 4.35
2479 2723 3.324556 ACAGGGTGGAAACAATGATTTGG 59.675 43.478 0.00 0.00 46.06 3.28
2510 2754 4.660303 ACAGACAGGGATAATCAATAGCCA 59.340 41.667 0.00 0.00 42.13 4.75
2511 2755 5.311649 ACAGACAGGGATAATCAATAGCCAT 59.688 40.000 0.00 0.00 42.13 4.40
2512 2756 6.501805 ACAGACAGGGATAATCAATAGCCATA 59.498 38.462 0.00 0.00 42.13 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.900892 CGGCCGCATCTAGTCCGT 61.901 66.667 14.67 0.00 35.75 4.69
22 23 2.243957 CGCATTTCGGCCGCATCTA 61.244 57.895 23.51 0.00 33.78 1.98
46 47 2.736995 CGGTCGTGCGTCCAACAT 60.737 61.111 8.38 0.00 0.00 2.71
47 48 4.953868 CCGGTCGTGCGTCCAACA 62.954 66.667 8.38 0.00 0.00 3.33
73 74 2.332654 GCCGTGTCCGCCAGATTTT 61.333 57.895 0.00 0.00 0.00 1.82
91 93 1.984026 GCTTGGGGTGACAATGGGG 60.984 63.158 0.00 0.00 0.00 4.96
93 95 2.342650 CCGCTTGGGGTGACAATGG 61.343 63.158 0.00 0.00 0.00 3.16
99 101 2.725203 CTTTCGTCCGCTTGGGGTGA 62.725 60.000 3.67 1.33 36.01 4.02
106 108 2.095059 ACGTACATACTTTCGTCCGCTT 60.095 45.455 0.00 0.00 30.71 4.68
108 110 1.900237 ACGTACATACTTTCGTCCGC 58.100 50.000 0.00 0.00 30.71 5.54
109 111 3.059834 CCAAACGTACATACTTTCGTCCG 59.940 47.826 0.00 0.00 35.49 4.79
110 112 4.236935 TCCAAACGTACATACTTTCGTCC 58.763 43.478 0.00 0.00 35.49 4.79
111 113 4.919754 ACTCCAAACGTACATACTTTCGTC 59.080 41.667 0.00 0.00 35.49 4.20
112 114 4.874970 ACTCCAAACGTACATACTTTCGT 58.125 39.130 0.00 0.00 38.15 3.85
113 115 4.029861 CGACTCCAAACGTACATACTTTCG 59.970 45.833 0.00 0.00 0.00 3.46
114 116 4.919754 ACGACTCCAAACGTACATACTTTC 59.080 41.667 0.00 0.00 40.92 2.62
117 121 3.829948 CACGACTCCAAACGTACATACT 58.170 45.455 0.00 0.00 40.76 2.12
119 123 2.598589 GCACGACTCCAAACGTACATA 58.401 47.619 0.00 0.00 40.76 2.29
121 125 0.935831 CGCACGACTCCAAACGTACA 60.936 55.000 0.00 0.00 40.76 2.90
124 128 1.519898 AACGCACGACTCCAAACGT 60.520 52.632 0.00 0.00 43.50 3.99
132 136 1.594293 CCAACTCCAACGCACGACT 60.594 57.895 0.00 0.00 0.00 4.18
137 141 0.037590 ATTAGGCCAACTCCAACGCA 59.962 50.000 5.01 0.00 0.00 5.24
158 162 4.356436 AGGGGATTTTTCTGCAATAAGCT 58.644 39.130 0.00 0.00 45.94 3.74
175 179 7.292356 ACTGTTATCATGTATTCACATAGGGGA 59.708 37.037 0.00 0.00 43.73 4.81
176 180 7.388776 CACTGTTATCATGTATTCACATAGGGG 59.611 40.741 0.00 0.00 43.73 4.79
177 181 8.150296 TCACTGTTATCATGTATTCACATAGGG 58.850 37.037 0.00 0.00 43.73 3.53
178 182 9.546428 TTCACTGTTATCATGTATTCACATAGG 57.454 33.333 0.00 0.00 43.73 2.57
197 201 1.265095 CATTTGCACGCTCTTCACTGT 59.735 47.619 0.00 0.00 0.00 3.55
209 213 0.458370 GACGGGCCATTCATTTGCAC 60.458 55.000 4.39 0.00 0.00 4.57
218 222 2.746277 GCTCAACGACGGGCCATT 60.746 61.111 4.39 0.00 0.00 3.16
219 223 3.545124 TTGCTCAACGACGGGCCAT 62.545 57.895 4.39 0.00 0.00 4.40
220 224 3.758973 TTTGCTCAACGACGGGCCA 62.759 57.895 4.39 0.00 0.00 5.36
221 225 2.966309 CTTTGCTCAACGACGGGCC 61.966 63.158 0.00 0.00 0.00 5.80
240 244 1.226802 CTCTCGTGGTCGCCATCTG 60.227 63.158 1.90 0.00 35.28 2.90
243 247 1.513158 CTTCTCTCGTGGTCGCCAT 59.487 57.895 1.90 0.00 35.28 4.40
294 298 1.661341 GACATGTCTGTCCATGGCTC 58.339 55.000 18.83 3.18 45.63 4.70
423 427 2.229792 TGTCACAGGGTTTTCATCTGC 58.770 47.619 0.00 0.00 32.19 4.26
464 468 1.518903 GCCTGTTTCCTCCTGTGCAC 61.519 60.000 10.75 10.75 0.00 4.57
567 571 3.367395 GCAGTGTCCTTAAATGGGAAAGC 60.367 47.826 0.00 0.00 34.35 3.51
768 772 2.095059 GGTCACTCATCAATGCAACACC 60.095 50.000 0.00 0.00 0.00 4.16
787 791 4.654262 TCTCTATTTATGCTTTCTCCGGGT 59.346 41.667 0.00 0.00 0.00 5.28
901 905 0.695347 AGGGAAAACCAGAGAGGCTG 59.305 55.000 0.00 0.00 43.89 4.85
990 994 2.496291 GGATTCCATGGCAGGCAGC 61.496 63.158 6.96 0.00 44.65 5.25
1050 1054 0.321671 ACATTGTCCACCCAGACTCG 59.678 55.000 0.00 0.00 37.66 4.18
1093 1097 4.806481 ACCATCGTCGTCGTCGCG 62.806 66.667 0.00 0.00 38.33 5.87
1158 1162 3.382546 GGACGAGGTAAGTGTAGCCATAA 59.617 47.826 0.00 0.00 0.00 1.90
1212 1222 0.802222 AGTCGTTGTCATCGCCATCG 60.802 55.000 0.00 0.00 0.00 3.84
1302 1312 0.967380 CCTTTCGATGGCCTTGGCTT 60.967 55.000 11.71 0.00 0.00 4.35
1305 1315 1.369091 CGTCCTTTCGATGGCCTTGG 61.369 60.000 3.32 0.00 0.00 3.61
1440 1465 4.292186 TCCCTTCTTCTTGGATGACTTG 57.708 45.455 0.00 0.00 0.00 3.16
1572 1601 6.711645 CCCATCTTCAACAACAAATGGAAAAT 59.288 34.615 0.00 0.00 36.58 1.82
1602 1632 2.181954 GCTCCTAGCAATGAGGGATG 57.818 55.000 0.00 0.00 41.89 3.51
1614 1644 2.368221 CCCTCTTCTCCAATGCTCCTAG 59.632 54.545 0.00 0.00 0.00 3.02
1672 1702 3.335579 GTCAACCATGGGAGAACACTAC 58.664 50.000 18.09 0.00 0.00 2.73
1795 1978 2.034104 TAGCAGGAGATTGCAAGCAG 57.966 50.000 18.24 4.85 46.47 4.24
1827 2048 5.578727 GTGAGTTAGAACAGTGCTCCATTAG 59.421 44.000 0.00 0.00 0.00 1.73
1841 2062 6.349445 GCTAGAGTGTAGCTTGTGAGTTAGAA 60.349 42.308 11.91 0.00 37.56 2.10
1870 2091 4.764679 TGTTTTGCTCGCAAATATCTGT 57.235 36.364 16.75 0.00 44.14 3.41
1962 2186 1.213926 GAGTCTGGGCAATGGGAAGAT 59.786 52.381 0.00 0.00 0.00 2.40
1988 2212 1.441515 GCATTGCACACTGCTGACG 60.442 57.895 3.15 0.00 45.31 4.35
2130 2361 2.432628 GTGACGAGCCGTTGGAGG 60.433 66.667 1.80 0.00 41.37 4.30
2143 2374 1.975660 TTGGGCTGTGTTTAGGTGAC 58.024 50.000 0.00 0.00 0.00 3.67
2303 2547 4.211164 GCACCCAACAAAATTACTTCAAGC 59.789 41.667 0.00 0.00 0.00 4.01
2304 2548 4.749598 GGCACCCAACAAAATTACTTCAAG 59.250 41.667 0.00 0.00 0.00 3.02
2305 2549 4.698575 GGCACCCAACAAAATTACTTCAA 58.301 39.130 0.00 0.00 0.00 2.69
2306 2550 4.329462 GGCACCCAACAAAATTACTTCA 57.671 40.909 0.00 0.00 0.00 3.02
2356 2600 2.659428 AGGCCACATAATTCTTCTGGC 58.341 47.619 5.01 7.50 45.73 4.85
2479 2723 0.835941 ATCCCTGTCTGTCTGATGGC 59.164 55.000 0.00 0.00 0.00 4.40
2512 2756 9.855021 GCTTACATGATTGTTGGTTAGTTTATT 57.145 29.630 0.00 0.00 37.28 1.40


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

AutoCloner maintained by Alex Coulton.