Multiple sequence alignment - TraesCS7B01G371800

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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 TraesCS7B01G371800 chr7B 100.000 3258 0 0 1 3258 637747216 637743959 0 6017
1 TraesCS7B01G371800 chr7B 93.067 2250 126 18 2 2227 549382664 549384907 0 3264
2 TraesCS7B01G371800 chr1B 92.580 3329 167 41 2 3258 549431834 549435154 0 4706
3 TraesCS7B01G371800 chr1B 92.277 2292 122 21 2 2250 667329459 667331738 0 3201
4 TraesCS7B01G371800 chr1B 91.070 1187 62 11 2115 3258 667331652 667332837 0 1565
5 TraesCS7B01G371800 chr1B 88.755 996 64 21 2302 3258 171630795 171629809 0 1175
6 TraesCS7B01G371800 chr4B 93.237 2351 89 21 2 2307 657448562 657446237 0 3397
7 TraesCS7B01G371800 chr4B 93.175 2271 108 23 2 2227 403116372 403114104 0 3291
8 TraesCS7B01G371800 chr4B 93.165 1624 64 24 2 1579 66832974 66834596 0 2340
9 TraesCS7B01G371800 chr4B 93.718 1162 53 9 2115 3258 403114170 403113011 0 1724
10 TraesCS7B01G371800 chr4B 93.164 1141 73 5 1090 2227 5266033 5267171 0 1670
11 TraesCS7B01G371800 chr4B 92.771 1162 64 7 2115 3258 66834909 66836068 0 1663
12 TraesCS7B01G371800 chr4B 87.514 913 78 28 2372 3258 665834810 665833908 0 1022
13 TraesCS7B01G371800 chr4A 94.042 2249 109 15 2 2227 664493473 664495719 0 3387
14 TraesCS7B01G371800 chr4A 94.892 1155 45 13 2115 3258 664495653 664496804 0 1794
15 TraesCS7B01G371800 chr4A 92.427 1162 67 8 2115 3258 711314533 711315691 0 1639
16 TraesCS7B01G371800 chr2B 93.597 2249 116 18 2 2227 665884231 665886474 0 3330
17 TraesCS7B01G371800 chr2B 92.734 2037 115 18 242 2250 393862085 393864116 0 2911
18 TraesCS7B01G371800 chr2B 93.548 1240 55 14 2 1217 559154495 559153257 0 1823
19 TraesCS7B01G371800 chr2B 92.784 1164 77 5 1090 2250 559153338 559152179 0 1677
20 TraesCS7B01G371800 chr2B 91.652 1162 76 8 2115 3258 393864054 393865212 0 1589
21 TraesCS7B01G371800 chr2B 94.176 1013 53 6 2115 3124 559152241 559151232 0 1539
22 TraesCS7B01G371800 chr2B 92.292 973 55 9 2302 3258 665886291 665887259 0 1363
23 TraesCS7B01G371800 chr3B 91.777 2274 131 27 2 2250 71169476 71167234 0 3112
24 TraesCS7B01G371800 chr3B 94.669 1238 44 10 2 1219 698396142 698397377 0 1901
25 TraesCS7B01G371800 chr3B 94.575 1235 47 9 2 1217 543578097 543576864 0 1892
26 TraesCS7B01G371800 chr3B 93.865 1141 66 4 1090 2227 698397294 698398433 0 1716
27 TraesCS7B01G371800 chr3B 92.150 1070 44 5 2205 3258 543550791 543549746 0 1474
28 TraesCS7B01G371800 chr6B 90.954 1216 98 10 2 1215 169052603 169051398 0 1626
29 TraesCS7B01G371800 chr6B 88.313 907 78 15 2372 3258 177555068 177554170 0 1062
30 TraesCS7B01G371800 chr6B 87.762 907 83 15 2372 3258 704383325 704384223 0 1035
31 TraesCS7B01G371800 chr7A 88.171 913 78 17 2368 3258 23542175 23543079 0 1061
32 TraesCS7B01G371800 chr5A 86.186 999 87 32 2303 3258 34680042 34681032 0 1033
33 TraesCS7B01G371800 chr3A 87.090 914 87 18 2368 3258 727568954 727569859 0 1005
34 TraesCS7B01G371800 chr5B 88.331 797 65 17 2479 3258 567606469 567607254 0 931


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 TraesCS7B01G371800 chr7B 637743959 637747216 3257 True 6017.000000 6017 100.000000 1 3258 1 chr7B.!!$R1 3257
1 TraesCS7B01G371800 chr7B 549382664 549384907 2243 False 3264.000000 3264 93.067000 2 2227 1 chr7B.!!$F1 2225
2 TraesCS7B01G371800 chr1B 549431834 549435154 3320 False 4706.000000 4706 92.580000 2 3258 1 chr1B.!!$F1 3256
3 TraesCS7B01G371800 chr1B 667329459 667332837 3378 False 2383.000000 3201 91.673500 2 3258 2 chr1B.!!$F2 3256
4 TraesCS7B01G371800 chr1B 171629809 171630795 986 True 1175.000000 1175 88.755000 2302 3258 1 chr1B.!!$R1 956
5 TraesCS7B01G371800 chr4B 657446237 657448562 2325 True 3397.000000 3397 93.237000 2 2307 1 chr4B.!!$R1 2305
6 TraesCS7B01G371800 chr4B 403113011 403116372 3361 True 2507.500000 3291 93.446500 2 3258 2 chr4B.!!$R3 3256
7 TraesCS7B01G371800 chr4B 66832974 66836068 3094 False 2001.500000 2340 92.968000 2 3258 2 chr4B.!!$F2 3256
8 TraesCS7B01G371800 chr4B 5266033 5267171 1138 False 1670.000000 1670 93.164000 1090 2227 1 chr4B.!!$F1 1137
9 TraesCS7B01G371800 chr4B 665833908 665834810 902 True 1022.000000 1022 87.514000 2372 3258 1 chr4B.!!$R2 886
10 TraesCS7B01G371800 chr4A 664493473 664496804 3331 False 2590.500000 3387 94.467000 2 3258 2 chr4A.!!$F2 3256
11 TraesCS7B01G371800 chr4A 711314533 711315691 1158 False 1639.000000 1639 92.427000 2115 3258 1 chr4A.!!$F1 1143
12 TraesCS7B01G371800 chr2B 665884231 665887259 3028 False 2346.500000 3330 92.944500 2 3258 2 chr2B.!!$F2 3256
13 TraesCS7B01G371800 chr2B 393862085 393865212 3127 False 2250.000000 2911 92.193000 242 3258 2 chr2B.!!$F1 3016
14 TraesCS7B01G371800 chr2B 559151232 559154495 3263 True 1679.666667 1823 93.502667 2 3124 3 chr2B.!!$R1 3122
15 TraesCS7B01G371800 chr3B 71167234 71169476 2242 True 3112.000000 3112 91.777000 2 2250 1 chr3B.!!$R1 2248
16 TraesCS7B01G371800 chr3B 543576864 543578097 1233 True 1892.000000 1892 94.575000 2 1217 1 chr3B.!!$R3 1215
17 TraesCS7B01G371800 chr3B 698396142 698398433 2291 False 1808.500000 1901 94.267000 2 2227 2 chr3B.!!$F1 2225
18 TraesCS7B01G371800 chr3B 543549746 543550791 1045 True 1474.000000 1474 92.150000 2205 3258 1 chr3B.!!$R2 1053
19 TraesCS7B01G371800 chr6B 169051398 169052603 1205 True 1626.000000 1626 90.954000 2 1215 1 chr6B.!!$R1 1213
20 TraesCS7B01G371800 chr6B 177554170 177555068 898 True 1062.000000 1062 88.313000 2372 3258 1 chr6B.!!$R2 886
21 TraesCS7B01G371800 chr6B 704383325 704384223 898 False 1035.000000 1035 87.762000 2372 3258 1 chr6B.!!$F1 886
22 TraesCS7B01G371800 chr7A 23542175 23543079 904 False 1061.000000 1061 88.171000 2368 3258 1 chr7A.!!$F1 890
23 TraesCS7B01G371800 chr5A 34680042 34681032 990 False 1033.000000 1033 86.186000 2303 3258 1 chr5A.!!$F1 955
24 TraesCS7B01G371800 chr3A 727568954 727569859 905 False 1005.000000 1005 87.090000 2368 3258 1 chr3A.!!$F1 890
25 TraesCS7B01G371800 chr5B 567606469 567607254 785 False 931.000000 931 88.331000 2479 3258 1 chr5B.!!$F1 779

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
114 115 1.049402 GGGATAGAGGGGGTCTTTCG 58.951 60.0 0.0 0.0 34.83 3.46 F
1088 1121 0.874390 GCCAGTCGAAAGTGCAATGA 59.126 50.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1577 0.618458 TTCGCCTTGGCCTATTGAGT 59.382 50.0 3.32 0.0 0.00 3.41 R
2703 3525 0.813184 CTTTCCTGCGGTTGATGCAT 59.187 50.0 0.00 0.0 42.32 3.96 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
69 70 6.260050 GGACTTGCTCCGATGAACATAATAAA 59.740 38.462 0.00 0.00 0.00 1.40
114 115 1.049402 GGGATAGAGGGGGTCTTTCG 58.951 60.000 0.00 0.00 34.83 3.46
482 483 3.947910 AGCAATACACAGCTTTGCAAT 57.052 38.095 19.34 3.13 46.28 3.56
515 516 3.194062 GGATCTGAGCTACAGCAAGAAC 58.806 50.000 3.70 5.10 45.38 3.01
625 626 3.805971 ACAAGTAAGTCAGTTGCGTTACC 59.194 43.478 0.00 0.00 40.69 2.85
754 757 4.305769 TCAAATGCAGTTGCCATGTTTAC 58.694 39.130 21.53 0.00 41.18 2.01
755 758 4.056740 CAAATGCAGTTGCCATGTTTACA 58.943 39.130 14.60 0.00 41.18 2.41
764 787 1.804151 GCCATGTTTACAGTTGCTCGA 59.196 47.619 0.00 0.00 0.00 4.04
794 818 2.429610 GGCATCTTCAATGGAATGCAGT 59.570 45.455 9.98 0.00 39.61 4.40
898 925 6.820656 TGCCAAATGAAAATGTTGTGTAGTTT 59.179 30.769 0.00 0.00 0.00 2.66
1018 1051 6.036300 CCATGTTTAATAAATGCAGTTGCCAG 59.964 38.462 10.14 0.00 41.18 4.85
1075 1108 2.170166 TGGAAATGACAATGGCCAGTC 58.830 47.619 13.05 15.05 35.37 3.51
1088 1121 0.874390 GCCAGTCGAAAGTGCAATGA 59.126 50.000 0.00 0.00 0.00 2.57
1286 1480 0.877071 CAGCATGTTCACGGCTTTCT 59.123 50.000 0.00 0.00 35.27 2.52
1346 1540 3.118261 GGGCATGTCAGATTCAGAACCTA 60.118 47.826 0.00 0.00 0.00 3.08
1383 1577 4.587684 AGGAAGGAACTACTTCGTGAAAGA 59.412 41.667 0.00 0.00 46.06 2.52
1487 1681 1.270785 TGGACATGAACGCTGTGACAT 60.271 47.619 0.00 0.00 0.00 3.06
1526 1720 4.467084 GGCGGCGATGGACTTGGA 62.467 66.667 12.98 0.00 0.00 3.53
1561 1755 2.255252 GCGCCGCAGACAACAAAT 59.745 55.556 3.15 0.00 0.00 2.32
1796 1990 0.321653 ATCAAGTGTGCCTTCGTCCC 60.322 55.000 0.00 0.00 0.00 4.46
1797 1991 1.071471 CAAGTGTGCCTTCGTCCCT 59.929 57.895 0.00 0.00 0.00 4.20
1917 2111 4.607239 AGAGAGGTAAGGTACAAATCGGA 58.393 43.478 0.00 0.00 0.00 4.55
1922 2116 6.057321 AGGTAAGGTACAAATCGGAATTGA 57.943 37.500 12.50 0.00 0.00 2.57
1942 2136 6.890663 TTGAAGATTCAAGCAAAACACAAG 57.109 33.333 3.91 0.00 41.88 3.16
1943 2137 6.206395 TGAAGATTCAAGCAAAACACAAGA 57.794 33.333 0.00 0.00 33.55 3.02
1944 2138 6.629128 TGAAGATTCAAGCAAAACACAAGAA 58.371 32.000 0.00 0.00 33.55 2.52
1945 2139 7.095910 TGAAGATTCAAGCAAAACACAAGAAA 58.904 30.769 0.00 0.00 33.55 2.52
2089 2295 1.339151 GGGCGTCAGAAGTTGAAGGAT 60.339 52.381 0.00 0.00 37.61 3.24
2377 2704 9.970395 ATTGAATGTATAAATGTAGTTGCCATG 57.030 29.630 0.00 0.00 0.00 3.66
2378 2705 8.518430 TGAATGTATAAATGTAGTTGCCATGT 57.482 30.769 0.00 0.00 0.00 3.21
2407 2783 8.359642 TGGATACTAAATTTGCCATGCTATTTC 58.640 33.333 0.00 0.00 37.61 2.17
2431 2807 9.748708 TTCATACTAAATTTGCCATGCTATTTC 57.251 29.630 0.00 0.00 30.77 2.17
2585 3404 6.967199 GCCATGTTAGCTGTACTGAAAAATAC 59.033 38.462 3.61 0.00 0.00 1.89
2592 3411 4.094294 GCTGTACTGAAAAATACGCCATGA 59.906 41.667 3.61 0.00 0.00 3.07
2615 3434 8.913487 TGATATTTGTAATGACTCTGCATCAT 57.087 30.769 0.00 0.00 38.47 2.45
2789 3613 4.978580 AGCGATGAAAAAGAAGAAGCAAAC 59.021 37.500 0.00 0.00 0.00 2.93
2878 3705 1.556564 AACATCGTAGACGCATTCGG 58.443 50.000 0.00 0.00 42.51 4.30
2979 3810 6.855763 AAATGGTTCACATCCACACATATT 57.144 33.333 0.00 0.00 39.40 1.28
3060 3892 4.097741 GGTTGCCATCATAACATAGCACAA 59.902 41.667 0.00 0.00 0.00 3.33
3142 3974 0.457035 TAAGGTATGCGTCCGGTGTC 59.543 55.000 0.00 0.00 0.00 3.67
3162 3994 6.351033 GGTGTCTAACTCCATGTGATCACTTA 60.351 42.308 25.55 13.61 32.30 2.24
3251 4098 4.399303 CCAGTTCCATGTGTAGATTTTCCC 59.601 45.833 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.097825 GCATGCTGAAATCCTGGTCTT 58.902 47.619 11.37 0.00 0.00 3.01
97 98 1.790818 ACCGAAAGACCCCCTCTATC 58.209 55.000 0.00 0.00 0.00 2.08
114 115 3.982241 GCCTGTGCACTGCCAACC 61.982 66.667 19.41 0.27 37.47 3.77
219 220 1.968017 AAGCTGTGGTCCATGCACG 60.968 57.895 18.15 0.00 0.00 5.34
515 516 2.388232 GCTTTAGTGCGGTGGTCGG 61.388 63.158 0.00 0.00 39.69 4.79
625 626 6.250819 CCTTCATACTTGTGCAAATAAGACG 58.749 40.000 12.07 0.00 0.00 4.18
689 691 5.895534 AGTTCATTAAACATGGCATCCTCAT 59.104 36.000 0.00 0.00 40.56 2.90
755 758 0.882042 CCAACTGCAGTCGAGCAACT 60.882 55.000 21.95 0.00 45.13 3.16
794 818 4.386711 TGCATTTCATTGAACATGGCAAA 58.613 34.783 16.37 0.00 0.00 3.68
898 925 5.771469 CAAATGCAGTTCAGTAAACATGGA 58.229 37.500 0.00 0.00 40.56 3.41
989 1022 8.594687 GCAACTGCATTTATTAAACATGGTAAG 58.405 33.333 0.00 0.00 41.59 2.34
1044 1077 7.549839 CCATTGTCATTTCCATACAAACATCT 58.450 34.615 0.00 0.00 36.75 2.90
1088 1121 4.396166 GCAGTACATTAGACATGGCAACTT 59.604 41.667 0.00 0.00 37.61 2.66
1229 1423 7.735480 TTCTTCCTAGAATCTGCAAGTTTTTGC 60.735 37.037 5.36 5.36 45.55 3.68
1231 1425 7.823745 TTCTTCCTAGAATCTGCAAGTTTTT 57.176 32.000 0.00 0.00 35.49 1.94
1346 1540 2.783510 TCCTTCCTTTGTCCAGGTCTTT 59.216 45.455 0.00 0.00 35.15 2.52
1383 1577 0.618458 TTCGCCTTGGCCTATTGAGT 59.382 50.000 3.32 0.00 0.00 3.41
1487 1681 2.441901 GAAATGGCGGGGCATCCA 60.442 61.111 8.25 0.00 36.70 3.41
1561 1755 1.228337 ATGCACAGCCAGAACTGCA 60.228 52.632 0.00 0.00 43.50 4.41
1796 1990 3.633986 GAGTTTTTAGATGATGGCCCCAG 59.366 47.826 0.00 0.00 0.00 4.45
1797 1991 3.631250 GAGTTTTTAGATGATGGCCCCA 58.369 45.455 0.00 0.00 0.00 4.96
1917 2111 7.765360 TCTTGTGTTTTGCTTGAATCTTCAATT 59.235 29.630 5.86 0.00 45.26 2.32
1922 2116 7.411804 CGTTTTCTTGTGTTTTGCTTGAATCTT 60.412 33.333 0.00 0.00 0.00 2.40
1938 2132 3.311596 CGTCCCTTTCTTCGTTTTCTTGT 59.688 43.478 0.00 0.00 0.00 3.16
1939 2133 3.303791 CCGTCCCTTTCTTCGTTTTCTTG 60.304 47.826 0.00 0.00 0.00 3.02
1940 2134 2.876550 CCGTCCCTTTCTTCGTTTTCTT 59.123 45.455 0.00 0.00 0.00 2.52
1941 2135 2.490991 CCGTCCCTTTCTTCGTTTTCT 58.509 47.619 0.00 0.00 0.00 2.52
1942 2136 1.534163 CCCGTCCCTTTCTTCGTTTTC 59.466 52.381 0.00 0.00 0.00 2.29
1943 2137 1.601166 CCCGTCCCTTTCTTCGTTTT 58.399 50.000 0.00 0.00 0.00 2.43
1944 2138 0.887836 GCCCGTCCCTTTCTTCGTTT 60.888 55.000 0.00 0.00 0.00 3.60
1945 2139 1.302271 GCCCGTCCCTTTCTTCGTT 60.302 57.895 0.00 0.00 0.00 3.85
2016 2218 5.772393 TCACAACATCTAGGGGTACAAAT 57.228 39.130 0.00 0.00 0.00 2.32
2064 2270 0.951040 CAACTTCTGACGCCCCTCAC 60.951 60.000 0.00 0.00 0.00 3.51
2377 2704 7.661040 AGCATGGCAAATTTAGTATCCATAAC 58.339 34.615 0.00 0.00 33.42 1.89
2378 2705 7.838079 AGCATGGCAAATTTAGTATCCATAA 57.162 32.000 0.00 0.00 33.42 1.90
2382 2709 8.359642 TGAAATAGCATGGCAAATTTAGTATCC 58.640 33.333 0.00 0.00 30.51 2.59
2383 2710 9.918630 ATGAAATAGCATGGCAAATTTAGTATC 57.081 29.630 0.00 0.00 30.51 2.24
2407 2783 9.701098 ATGAAATAGCATGGCAAATTTAGTATG 57.299 29.630 0.00 0.00 30.51 2.39
2585 3404 6.596703 CAGAGTCATTACAAATATCATGGCG 58.403 40.000 0.00 0.00 0.00 5.69
2703 3525 0.813184 CTTTCCTGCGGTTGATGCAT 59.187 50.000 0.00 0.00 42.32 3.96
2805 3630 4.699637 TGGTTAGTGAAAGTCATCGTTGT 58.300 39.130 0.00 0.00 0.00 3.32
2806 3631 5.179368 ACATGGTTAGTGAAAGTCATCGTTG 59.821 40.000 0.00 0.00 0.00 4.10
2807 3632 5.305585 ACATGGTTAGTGAAAGTCATCGTT 58.694 37.500 0.00 0.00 0.00 3.85
2924 3751 9.490663 GTGACAGCAGATATGTTTTATGTTTAC 57.509 33.333 0.00 0.00 0.00 2.01
2979 3810 6.653320 AGCGACATTTGAATAGGTTCTGTAAA 59.347 34.615 0.00 0.00 35.33 2.01
3060 3892 9.921637 TTGTTTCTTTGTCAAAAACTATGTTCT 57.078 25.926 12.05 0.00 34.69 3.01
3103 3935 2.795329 ACATTCTGTTGCCGAGGAATT 58.205 42.857 0.00 0.00 0.00 2.17
3142 3974 9.254133 CAAGTATAAGTGATCACATGGAGTTAG 57.746 37.037 27.02 6.74 0.00 2.34
3162 3994 6.328672 AGTTCATGGAGGAAGCTATCAAGTAT 59.671 38.462 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.