Multiple sequence alignment - TraesCS7A01G436000

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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 TraesCS7A01G436000 chr7A 100.000 3317 0 0 1 3317 630248243 630244927 0.000000e+00 6126
1 TraesCS7A01G436000 chr7A 94.467 2205 100 8 5 2208 305701127 305698944 0.000000e+00 3376
2 TraesCS7A01G436000 chr7A 95.625 1120 37 8 2207 3317 305698846 305697730 0.000000e+00 1786
3 TraesCS7A01G436000 chr7A 88.984 935 61 22 649 1554 675230335 675231256 0.000000e+00 1118
4 TraesCS7A01G436000 chr7A 88.820 161 15 3 3160 3317 181654593 181654753 9.390000e-46 195
5 TraesCS7A01G436000 chr6A 95.477 2211 89 6 1 2208 546622144 546619942 0.000000e+00 3518
6 TraesCS7A01G436000 chr6A 95.532 1119 38 8 2207 3317 546619844 546618730 0.000000e+00 1779
7 TraesCS7A01G436000 chr6A 92.072 946 64 5 2207 3149 409120457 409121394 0.000000e+00 1321
8 TraesCS7A01G436000 chr6A 93.740 623 36 1 1589 2208 409119737 409120359 0.000000e+00 931
9 TraesCS7A01G436000 chr6A 92.264 530 38 3 91 619 409119177 409119704 0.000000e+00 749
10 TraesCS7A01G436000 chr6A 90.168 417 38 3 690 1105 376681342 376680928 1.050000e-149 540
11 TraesCS7A01G436000 chr7B 94.549 1798 91 4 5 1798 660061416 660063210 0.000000e+00 2771
12 TraesCS7A01G436000 chr7B 93.987 948 43 6 2207 3149 660063621 660064559 0.000000e+00 1423
13 TraesCS7A01G436000 chr7B 90.487 904 62 17 650 1536 653019128 653018232 0.000000e+00 1171
14 TraesCS7A01G436000 chr3A 92.194 948 66 5 2207 3149 356688659 356689603 0.000000e+00 1334
15 TraesCS7A01G436000 chr2D 92.300 948 59 7 2207 3149 154508852 154507914 0.000000e+00 1334
16 TraesCS7A01G436000 chr2D 95.016 622 29 2 1589 2208 154509546 154508925 0.000000e+00 976
17 TraesCS7A01G436000 chr2D 93.585 530 32 2 91 619 154510107 154509579 0.000000e+00 789
18 TraesCS7A01G436000 chr2D 91.685 457 26 2 647 1103 87982068 87981624 1.010000e-174 623
19 TraesCS7A01G436000 chrUn 91.658 947 69 4 2207 3149 316628993 316629933 0.000000e+00 1303
20 TraesCS7A01G436000 chrUn 92.742 620 45 0 1589 2208 316628276 316628895 0.000000e+00 896
21 TraesCS7A01G436000 chr3B 91.774 936 72 4 2215 3149 422098055 422097124 0.000000e+00 1297
22 TraesCS7A01G436000 chr3B 93.065 620 43 0 1589 2208 565037379 565037998 0.000000e+00 907
23 TraesCS7A01G436000 chr6B 91.561 948 61 8 2207 3149 553539416 553540349 0.000000e+00 1290
24 TraesCS7A01G436000 chr6B 94.194 620 36 0 1589 2208 553538699 553539318 0.000000e+00 946
25 TraesCS7A01G436000 chr6B 92.453 530 36 3 91 619 553538140 553538666 0.000000e+00 754
26 TraesCS7A01G436000 chr7D 90.939 905 56 13 649 1536 584855246 584854351 0.000000e+00 1194
27 TraesCS7A01G436000 chr7D 90.629 715 43 9 648 1355 92809621 92808924 0.000000e+00 928
28 TraesCS7A01G436000 chr4A 94.847 621 31 1 1589 2208 66422151 66421531 0.000000e+00 968
29 TraesCS7A01G436000 chr4A 91.273 550 47 1 91 639 66422717 66422168 0.000000e+00 749
30 TraesCS7A01G436000 chr1D 94.669 619 31 1 1592 2208 412547959 412547341 0.000000e+00 959
31 TraesCS7A01G436000 chr1D 93.396 530 33 2 91 619 412548523 412547995 0.000000e+00 784
32 TraesCS7A01G436000 chr4D 92.922 551 30 5 91 639 165302480 165303023 0.000000e+00 793
33 TraesCS7A01G436000 chr1A 91.250 80 6 1 5 84 222459531 222459453 1.260000e-19 108


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 TraesCS7A01G436000 chr7A 630244927 630248243 3316 True 6126.000000 6126 100.000000 1 3317 1 chr7A.!!$R1 3316
1 TraesCS7A01G436000 chr7A 305697730 305701127 3397 True 2581.000000 3376 95.046000 5 3317 2 chr7A.!!$R2 3312
2 TraesCS7A01G436000 chr7A 675230335 675231256 921 False 1118.000000 1118 88.984000 649 1554 1 chr7A.!!$F2 905
3 TraesCS7A01G436000 chr6A 546618730 546622144 3414 True 2648.500000 3518 95.504500 1 3317 2 chr6A.!!$R2 3316
4 TraesCS7A01G436000 chr6A 409119177 409121394 2217 False 1000.333333 1321 92.692000 91 3149 3 chr6A.!!$F1 3058
5 TraesCS7A01G436000 chr7B 660061416 660064559 3143 False 2097.000000 2771 94.268000 5 3149 2 chr7B.!!$F1 3144
6 TraesCS7A01G436000 chr7B 653018232 653019128 896 True 1171.000000 1171 90.487000 650 1536 1 chr7B.!!$R1 886
7 TraesCS7A01G436000 chr3A 356688659 356689603 944 False 1334.000000 1334 92.194000 2207 3149 1 chr3A.!!$F1 942
8 TraesCS7A01G436000 chr2D 154507914 154510107 2193 True 1033.000000 1334 93.633667 91 3149 3 chr2D.!!$R2 3058
9 TraesCS7A01G436000 chrUn 316628276 316629933 1657 False 1099.500000 1303 92.200000 1589 3149 2 chrUn.!!$F1 1560
10 TraesCS7A01G436000 chr3B 422097124 422098055 931 True 1297.000000 1297 91.774000 2215 3149 1 chr3B.!!$R1 934
11 TraesCS7A01G436000 chr3B 565037379 565037998 619 False 907.000000 907 93.065000 1589 2208 1 chr3B.!!$F1 619
12 TraesCS7A01G436000 chr6B 553538140 553540349 2209 False 996.666667 1290 92.736000 91 3149 3 chr6B.!!$F1 3058
13 TraesCS7A01G436000 chr7D 584854351 584855246 895 True 1194.000000 1194 90.939000 649 1536 1 chr7D.!!$R2 887
14 TraesCS7A01G436000 chr7D 92808924 92809621 697 True 928.000000 928 90.629000 648 1355 1 chr7D.!!$R1 707
15 TraesCS7A01G436000 chr4A 66421531 66422717 1186 True 858.500000 968 93.060000 91 2208 2 chr4A.!!$R1 2117
16 TraesCS7A01G436000 chr1D 412547341 412548523 1182 True 871.500000 959 94.032500 91 2208 2 chr1D.!!$R1 2117
17 TraesCS7A01G436000 chr4D 165302480 165303023 543 False 793.000000 793 92.922000 91 639 1 chr4D.!!$F1 548

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
226 235 0.035152 ACAATCTCATTCCCGCAGCA 60.035 50.000 0.00 0.0 0.0 4.41 F
263 273 1.628846 ACTAGTGGTTGCCGGATTCTT 59.371 47.619 5.05 0.0 0.0 2.52 F
1378 1434 1.738099 GACGAACGAGTGCCTGCAT 60.738 57.895 0.14 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 1300 1.001764 CTCACCATGGCTCAGGCAA 60.002 57.895 13.04 0.00 42.43 4.52 R
1398 1454 2.341101 ATGTTCGTCGCCTCGTCCT 61.341 57.895 0.00 0.00 0.00 3.85 R
3056 3335 1.479730 TGGTTTGCATGTTGAACAGCA 59.520 42.857 15.11 15.11 33.01 4.41 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
84 85 1.448540 CGCTGCGTCCTTCTTCCAT 60.449 57.895 14.93 0.00 0.00 3.41
125 126 7.562135 CCATTTTTGGATGAGGAATCAAGATT 58.438 34.615 0.00 0.00 36.98 2.40
131 132 1.063717 TGAGGAATCAAGATTGCCCCC 60.064 52.381 10.18 1.27 39.57 5.40
143 144 1.341913 TTGCCCCCGCTGCTCTATTA 61.342 55.000 0.00 0.00 35.36 0.98
207 212 2.037367 AGCTCCCACTAGCCACGA 59.963 61.111 0.00 0.00 43.86 4.35
226 235 0.035152 ACAATCTCATTCCCGCAGCA 60.035 50.000 0.00 0.00 0.00 4.41
234 243 2.930385 ATTCCCGCAGCAGATGTCGG 62.930 60.000 12.79 12.79 43.72 4.79
261 271 1.653151 GACTAGTGGTTGCCGGATTC 58.347 55.000 5.05 0.00 0.00 2.52
263 273 1.628846 ACTAGTGGTTGCCGGATTCTT 59.371 47.619 5.05 0.00 0.00 2.52
591 601 1.969200 GCTGATGCTGCCCTCTCAGA 61.969 60.000 17.31 0.00 37.85 3.27
1262 1300 4.699522 GGGACCGAGCCGCAAGTT 62.700 66.667 0.00 0.00 0.00 2.66
1378 1434 1.738099 GACGAACGAGTGCCTGCAT 60.738 57.895 0.14 0.00 0.00 3.96
1561 1619 2.762535 GCACTAGGGAAACTGTGCTA 57.237 50.000 0.00 0.00 44.05 3.49
1600 1658 1.746787 CATGTGCTGATGCTTAGCCAA 59.253 47.619 0.29 0.00 40.42 4.52
1674 1733 5.447624 TGCTATTATGCGTGCTAGAACTA 57.552 39.130 0.00 0.00 35.36 2.24
1981 2044 2.494445 CATAGCTGCGGACGGACA 59.506 61.111 0.00 0.00 0.00 4.02
2085 2150 0.671472 CTGCAGCGAAGTGTCCATGA 60.671 55.000 0.00 0.00 0.00 3.07
2091 2156 2.027745 AGCGAAGTGTCCATGACTGATT 60.028 45.455 0.00 0.00 33.15 2.57
2212 2475 3.130516 CGAAAGACCTACCTATCACTGCA 59.869 47.826 0.00 0.00 0.00 4.41
2213 2476 4.434520 GAAAGACCTACCTATCACTGCAC 58.565 47.826 0.00 0.00 0.00 4.57
2383 2647 7.751768 ATTAGAGGTGGTCTCAAAGAAAAAG 57.248 36.000 0.00 0.00 44.81 2.27
2405 2669 1.425066 TGTTCCCTTTGATGGAGCACT 59.575 47.619 0.00 0.00 38.07 4.40
2561 2826 1.891150 AGCTCGGTAATGTATACGGGG 59.109 52.381 0.00 0.00 0.00 5.73
2684 2954 1.610554 GCATGCTCCATGGGTGCTTT 61.611 55.000 23.97 13.34 41.64 3.51
2692 2962 4.159506 GCTCCATGGGTGCTTTTTGTAATA 59.840 41.667 13.02 0.00 38.91 0.98
2694 2964 6.672266 TCCATGGGTGCTTTTTGTAATAAA 57.328 33.333 13.02 0.00 0.00 1.40
2695 2965 7.251321 TCCATGGGTGCTTTTTGTAATAAAT 57.749 32.000 13.02 0.00 0.00 1.40
2802 3075 2.535574 GCGAGTTCTTTGCAAAAACCAG 59.464 45.455 22.41 19.01 36.12 4.00
2852 3126 5.730550 AGGTTCAAGTAATATGAGAACGCA 58.269 37.500 0.00 0.00 39.45 5.24
2883 3157 5.856156 TGTAGAAGAAAAATGTCGGTGGTA 58.144 37.500 0.00 0.00 0.00 3.25
2945 3222 3.434319 CTGGCCAATCGCGCACTT 61.434 61.111 7.01 0.00 38.94 3.16
2950 3228 2.813474 CAATCGCGCACTTCCGGA 60.813 61.111 8.75 0.00 0.00 5.14
3088 3367 6.756299 ACATGCAAACCAATTGAAAAACTT 57.244 29.167 7.12 0.00 41.85 2.66
3240 3519 9.528489 AAACCTAGAAGCTCAATTAAAATACCA 57.472 29.630 0.00 0.00 0.00 3.25
3262 3541 4.330074 CAGAGCGGTTCAGTGTTTATAAGG 59.670 45.833 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.955428 GTGCATGGAAGAAGGACGCA 60.955 55.000 0.00 0.00 0.00 5.24
84 85 0.111061 ATGGCCAAGTTCTGAGTGCA 59.889 50.000 10.96 0.00 0.00 4.57
125 126 1.758440 CTAATAGAGCAGCGGGGGCA 61.758 60.000 0.00 0.00 0.00 5.36
131 132 4.201773 CGAGTAGATCCTAATAGAGCAGCG 60.202 50.000 0.00 0.00 0.00 5.18
143 144 1.115467 CCAGCAACCGAGTAGATCCT 58.885 55.000 0.00 0.00 0.00 3.24
207 212 0.035152 TGCTGCGGGAATGAGATTGT 60.035 50.000 0.00 0.00 0.00 2.71
226 235 2.437895 TCGAGGTCGCCGACATCT 60.438 61.111 26.44 12.58 40.58 2.90
234 243 0.456312 CAACCACTAGTCGAGGTCGC 60.456 60.000 3.97 0.00 35.36 5.19
263 273 8.845227 TGCATCAGTTTTGTATAGAAGAAACAA 58.155 29.630 0.00 0.00 35.13 2.83
444 454 0.815734 GCTGGCTGCATGAGTTGAAT 59.184 50.000 11.80 0.00 42.31 2.57
591 601 4.284490 TGTGCCAAACTGAGATAAGAGAGT 59.716 41.667 0.00 0.00 0.00 3.24
757 773 0.325390 CTTCCCCTCGTACCCCTCTT 60.325 60.000 0.00 0.00 0.00 2.85
758 774 1.310373 CTTCCCCTCGTACCCCTCT 59.690 63.158 0.00 0.00 0.00 3.69
950 966 2.753029 GCCAGCACCTTCTCCAGT 59.247 61.111 0.00 0.00 0.00 4.00
1224 1262 3.434319 CTTGAAGCCGGCGCACAT 61.434 61.111 23.20 6.07 37.52 3.21
1262 1300 1.001764 CTCACCATGGCTCAGGCAA 60.002 57.895 13.04 0.00 42.43 4.52
1378 1434 4.680237 CAGCACCCGCCGTTCTGA 62.680 66.667 0.00 0.00 37.90 3.27
1398 1454 2.341101 ATGTTCGTCGCCTCGTCCT 61.341 57.895 0.00 0.00 0.00 3.85
1561 1619 5.126869 CACATGAGACTATGAGTGAACCTCT 59.873 44.000 0.00 0.00 41.11 3.69
1674 1733 8.667076 AAAAGAGCTAATCACAAAAATGCTTT 57.333 26.923 0.00 0.00 0.00 3.51
1782 1842 6.392354 CACCACATGTTGCATTTCTATCTTT 58.608 36.000 0.00 0.00 0.00 2.52
1981 2044 4.202212 GGGTTGCAGTACAGTTGGAATTTT 60.202 41.667 0.00 0.00 0.00 1.82
2085 2150 7.517614 AAAACAAAACCCAACAAAAATCAGT 57.482 28.000 0.00 0.00 0.00 3.41
2383 2647 2.029918 GTGCTCCATCAAAGGGAACAAC 60.030 50.000 0.00 0.00 32.68 3.32
2852 3126 7.255139 CCGACATTTTTCTTCTACAAACTTCCT 60.255 37.037 0.00 0.00 0.00 3.36
2883 3157 3.565482 CCAATGTAGCTGACAACAACTGT 59.435 43.478 0.00 0.00 42.78 3.55
2950 3228 6.013379 TCTCAACTTCTTAGTGTGGATCCATT 60.013 38.462 19.62 9.56 34.01 3.16
3056 3335 1.479730 TGGTTTGCATGTTGAACAGCA 59.520 42.857 15.11 15.11 33.01 4.41
3240 3519 4.222145 TCCTTATAAACACTGAACCGCTCT 59.778 41.667 0.00 0.00 0.00 4.09
3262 3541 5.629079 ATGAACGAAGAAATCCAGGTTTC 57.371 39.130 0.00 0.00 38.16 2.78
3291 3570 8.950007 TTATCTTAATTTGAACTTCTTGGGGT 57.050 30.769 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.