Multiple sequence alignment - TraesCS2A01G447300

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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 TraesCS2A01G447300 chr2A 100.000 3091 0 0 1 3091 696218214 696221304 0.000000e+00 5709.0
1 TraesCS2A01G447300 chr2A 90.080 1250 98 10 1609 2839 696307720 696308962 0.000000e+00 1598.0
2 TraesCS2A01G447300 chr2A 83.042 1657 146 65 714 2276 696040132 696041747 0.000000e+00 1378.0
3 TraesCS2A01G447300 chr2A 81.473 1371 146 58 968 2244 695999081 696000437 0.000000e+00 1026.0
4 TraesCS2A01G447300 chr2A 85.731 876 62 24 18 874 696286735 696287566 0.000000e+00 867.0
5 TraesCS2A01G447300 chr2A 88.700 646 39 11 970 1597 696307007 696307636 0.000000e+00 758.0
6 TraesCS2A01G447300 chr2A 81.279 219 33 7 2819 3035 696309130 696309342 1.470000e-38 171.0
7 TraesCS2A01G447300 chr2A 82.178 101 8 7 2145 2235 696826522 696826622 9.190000e-11 78.7
8 TraesCS2A01G447300 chr2D 94.211 2142 87 20 968 3091 556365460 556367582 0.000000e+00 3234.0
9 TraesCS2A01G447300 chr2D 92.514 2164 93 34 968 3091 556619104 556621238 0.000000e+00 3035.0
10 TraesCS2A01G447300 chr2D 91.869 1316 54 24 968 2256 556408004 556409293 0.000000e+00 1788.0
11 TraesCS2A01G447300 chr2D 94.982 1136 49 6 1960 3091 556333871 556335002 0.000000e+00 1775.0
12 TraesCS2A01G447300 chr2D 95.352 753 31 3 223 971 556364668 556365420 0.000000e+00 1194.0
13 TraesCS2A01G447300 chr2D 94.197 741 39 3 2253 2990 556411563 556412302 0.000000e+00 1127.0
14 TraesCS2A01G447300 chr2D 82.288 1355 133 51 968 2237 556267194 556268526 0.000000e+00 1074.0
15 TraesCS2A01G447300 chr2D 82.273 1320 137 43 996 2238 556350544 556351843 0.000000e+00 1051.0
16 TraesCS2A01G447300 chr2D 88.399 862 57 15 129 968 556407134 556407974 0.000000e+00 998.0
17 TraesCS2A01G447300 chr2D 84.551 958 83 30 573 1509 556317994 556318907 0.000000e+00 889.0
18 TraesCS2A01G447300 chr2D 87.053 811 66 26 999 1787 556642397 556643190 0.000000e+00 880.0
19 TraesCS2A01G447300 chr2D 79.381 970 100 55 1365 2237 556339260 556340226 2.650000e-165 592.0
20 TraesCS2A01G447300 chr2D 88.866 476 29 12 1504 1956 556333284 556333758 5.790000e-157 564.0
21 TraesCS2A01G447300 chr2D 75.468 481 50 25 188 623 556349767 556350224 4.100000e-39 172.0
22 TraesCS2A01G447300 chr2D 96.154 104 4 0 2988 3091 556421605 556421708 1.470000e-38 171.0
23 TraesCS2A01G447300 chr2D 80.791 177 26 6 476 649 556265743 556265914 6.950000e-27 132.0
24 TraesCS2A01G447300 chr2D 87.736 106 3 2 1 106 556364138 556364233 7.000000e-22 115.0
25 TraesCS2A01G447300 chr2D 100.000 31 0 0 478 508 556618663 556618693 1.200000e-04 58.4
26 TraesCS2A01G447300 chr2B 90.577 1422 95 17 968 2375 663885996 663887392 0.000000e+00 1847.0
27 TraesCS2A01G447300 chr2B 82.226 1294 140 46 987 2228 663838006 663839261 0.000000e+00 1033.0
28 TraesCS2A01G447300 chr2B 85.802 810 72 31 999 1787 663898756 663899543 0.000000e+00 819.0
29 TraesCS2A01G447300 chr2B 88.225 569 27 10 139 706 663885200 663885729 0.000000e+00 643.0
30 TraesCS2A01G447300 chr2B 85.781 429 44 8 2447 2871 663887609 663888024 3.660000e-119 438.0
31 TraesCS2A01G447300 chr2B 83.946 299 33 6 681 969 663828606 663828899 3.930000e-69 272.0
32 TraesCS2A01G447300 chr2B 87.805 205 25 0 129 333 663827807 663828011 1.110000e-59 241.0
33 TraesCS2A01G447300 chr2B 84.034 238 26 5 746 971 663885723 663885960 5.190000e-53 219.0
34 TraesCS2A01G447300 chr2B 93.548 93 6 0 2999 3091 663892710 663892802 4.160000e-29 139.0
35 TraesCS2A01G447300 chr2B 75.636 275 49 15 214 477 663835089 663835356 1.510000e-23 121.0
36 TraesCS2A01G447300 chr2B 93.220 59 2 1 2394 2450 663887439 663887497 5.490000e-13 86.1
37 TraesCS2A01G447300 chr2B 79.137 139 15 7 2145 2270 663900032 663900169 1.980000e-12 84.2
38 TraesCS2A01G447300 chr2B 86.250 80 6 4 574 653 663837575 663837649 7.100000e-12 82.4


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 TraesCS2A01G447300 chr2A 696218214 696221304 3090 False 5709.000000 5709 100.000000 1 3091 1 chr2A.!!$F3 3090
1 TraesCS2A01G447300 chr2A 696040132 696041747 1615 False 1378.000000 1378 83.042000 714 2276 1 chr2A.!!$F2 1562
2 TraesCS2A01G447300 chr2A 695999081 696000437 1356 False 1026.000000 1026 81.473000 968 2244 1 chr2A.!!$F1 1276
3 TraesCS2A01G447300 chr2A 696286735 696287566 831 False 867.000000 867 85.731000 18 874 1 chr2A.!!$F4 856
4 TraesCS2A01G447300 chr2A 696307007 696309342 2335 False 842.333333 1598 86.686333 970 3035 3 chr2A.!!$F6 2065
5 TraesCS2A01G447300 chr2D 556618663 556621238 2575 False 1546.700000 3035 96.257000 478 3091 2 chr2D.!!$F10 2613
6 TraesCS2A01G447300 chr2D 556364138 556367582 3444 False 1514.333333 3234 92.433000 1 3091 3 chr2D.!!$F8 3090
7 TraesCS2A01G447300 chr2D 556407134 556412302 5168 False 1304.333333 1788 91.488333 129 2990 3 chr2D.!!$F9 2861
8 TraesCS2A01G447300 chr2D 556333284 556335002 1718 False 1169.500000 1775 91.924000 1504 3091 2 chr2D.!!$F6 1587
9 TraesCS2A01G447300 chr2D 556317994 556318907 913 False 889.000000 889 84.551000 573 1509 1 chr2D.!!$F1 936
10 TraesCS2A01G447300 chr2D 556642397 556643190 793 False 880.000000 880 87.053000 999 1787 1 chr2D.!!$F4 788
11 TraesCS2A01G447300 chr2D 556349767 556351843 2076 False 611.500000 1051 78.870500 188 2238 2 chr2D.!!$F7 2050
12 TraesCS2A01G447300 chr2D 556265743 556268526 2783 False 603.000000 1074 81.539500 476 2237 2 chr2D.!!$F5 1761
13 TraesCS2A01G447300 chr2D 556339260 556340226 966 False 592.000000 592 79.381000 1365 2237 1 chr2D.!!$F2 872
14 TraesCS2A01G447300 chr2B 663885200 663888024 2824 False 646.620000 1847 88.367400 139 2871 5 chr2B.!!$F4 2732
15 TraesCS2A01G447300 chr2B 663898756 663900169 1413 False 451.600000 819 82.469500 999 2270 2 chr2B.!!$F5 1271
16 TraesCS2A01G447300 chr2B 663835089 663839261 4172 False 412.133333 1033 81.370667 214 2228 3 chr2B.!!$F3 2014
17 TraesCS2A01G447300 chr2B 663827807 663828899 1092 False 256.500000 272 85.875500 129 969 2 chr2B.!!$F2 840


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
225 307 0.313987 AACGCAGGCCTAACTTTTGC 59.686 50.000 3.98 2.09 0.00 3.68 F
1197 5097 1.637553 TGGACTAACTACCTCCGTCCT 59.362 52.381 8.08 0.00 43.45 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 5221 0.107703 CTGTGTGTGTGTGGTGGACT 60.108 55.000 0.0 0.0 0.00 3.85 R
2920 9878 1.003112 TATTTCGCCGTGTGCCCTT 60.003 52.632 0.0 0.0 36.24 3.95 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
61 62 4.809426 CCTCTGTAACCGGATTTGACATAC 59.191 45.833 9.46 0.00 0.00 2.39
147 224 4.640771 AAATTCAGAGGTAGCACAGGAA 57.359 40.909 0.00 0.00 0.00 3.36
168 245 3.818787 CAAGAGCCATGGTGCCGC 61.819 66.667 14.67 0.00 0.00 6.53
225 307 0.313987 AACGCAGGCCTAACTTTTGC 59.686 50.000 3.98 2.09 0.00 3.68
272 604 3.932822 TCCGATTCTTCACCGAATTCAA 58.067 40.909 6.22 0.00 33.96 2.69
284 616 3.506067 ACCGAATTCAAGACCCAAATCAC 59.494 43.478 6.22 0.00 0.00 3.06
285 617 3.426159 CCGAATTCAAGACCCAAATCACG 60.426 47.826 6.22 0.00 0.00 4.35
424 1025 7.598278 ACGTAATTTGGAACATTATTCAGCAA 58.402 30.769 0.00 0.00 39.30 3.91
583 3373 6.017605 GTGACCTCATAGCACATTTTCTATGG 60.018 42.308 8.76 0.00 41.34 2.74
616 3406 4.450419 CCACTTGTTGAGAGTGATCACTTC 59.550 45.833 28.46 24.19 45.72 3.01
679 3475 3.419915 GAAGCATTATGTGTGAACTGCG 58.580 45.455 0.00 0.00 34.89 5.18
792 4540 8.008513 AGAGTATATCCGACATACACAAACTT 57.991 34.615 0.00 0.00 32.35 2.66
1197 5097 1.637553 TGGACTAACTACCTCCGTCCT 59.362 52.381 8.08 0.00 43.45 3.85
1203 5103 3.377253 AACTACCTCCGTCCTGACATA 57.623 47.619 0.00 0.00 0.00 2.29
1304 5214 4.214971 TCACGTCAAGTCTAACTACTCCAC 59.785 45.833 0.00 0.00 0.00 4.02
1305 5215 4.023450 CACGTCAAGTCTAACTACTCCACA 60.023 45.833 0.00 0.00 0.00 4.17
1306 5216 4.765856 ACGTCAAGTCTAACTACTCCACAT 59.234 41.667 0.00 0.00 0.00 3.21
1307 5217 5.106237 ACGTCAAGTCTAACTACTCCACATC 60.106 44.000 0.00 0.00 0.00 3.06
1308 5218 5.652518 GTCAAGTCTAACTACTCCACATCC 58.347 45.833 0.00 0.00 0.00 3.51
1309 5219 4.398358 TCAAGTCTAACTACTCCACATCCG 59.602 45.833 0.00 0.00 0.00 4.18
1310 5220 2.688958 AGTCTAACTACTCCACATCCGC 59.311 50.000 0.00 0.00 0.00 5.54
1311 5221 2.426024 GTCTAACTACTCCACATCCGCA 59.574 50.000 0.00 0.00 0.00 5.69
1312 5222 2.688446 TCTAACTACTCCACATCCGCAG 59.312 50.000 0.00 0.00 0.00 5.18
1313 5223 1.267121 AACTACTCCACATCCGCAGT 58.733 50.000 0.00 0.00 0.00 4.40
1314 5224 0.818296 ACTACTCCACATCCGCAGTC 59.182 55.000 0.00 0.00 0.00 3.51
1315 5225 0.103208 CTACTCCACATCCGCAGTCC 59.897 60.000 0.00 0.00 0.00 3.85
1316 5226 0.613572 TACTCCACATCCGCAGTCCA 60.614 55.000 0.00 0.00 0.00 4.02
1317 5227 1.448540 CTCCACATCCGCAGTCCAC 60.449 63.158 0.00 0.00 0.00 4.02
1318 5228 2.436646 CCACATCCGCAGTCCACC 60.437 66.667 0.00 0.00 0.00 4.61
1319 5229 2.347114 CACATCCGCAGTCCACCA 59.653 61.111 0.00 0.00 0.00 4.17
1451 5407 1.195442 TGGGCATTAGGTGGTCGACA 61.195 55.000 18.91 0.27 0.00 4.35
1838 5917 4.572985 TCTCTGCAACAACTCCAATTTG 57.427 40.909 0.00 0.00 0.00 2.32
1839 5918 3.953612 TCTCTGCAACAACTCCAATTTGT 59.046 39.130 0.00 0.00 38.88 2.83
2131 6434 8.812972 ACAGTTTTGTACAGAGTTAGATCCATA 58.187 33.333 0.00 0.00 35.25 2.74
2330 8940 8.503458 AATGAGATTCCAGATAACTGAAACAG 57.497 34.615 0.79 0.00 46.03 3.16
2534 9292 7.799784 ACAAGAGCATTGCATTTTCATAAAAC 58.200 30.769 11.91 0.00 32.37 2.43
2645 9406 6.293698 AGAAAACCATACGGAAAACTGTAGT 58.706 36.000 0.00 0.00 35.59 2.73
2685 9448 2.543777 TTCCTCGGTCACCTTGAAAG 57.456 50.000 0.00 0.00 0.00 2.62
2821 9592 5.376854 GCAACTTTGAAGCCAGATTTAGA 57.623 39.130 0.00 0.00 0.00 2.10
2860 9818 8.650143 AATAGAACCACACTTAACAATTGGAT 57.350 30.769 10.83 0.61 0.00 3.41
2912 9870 0.930310 ATGACGCAATCGATTGGACG 59.070 50.000 33.05 29.36 38.21 4.79
2919 9877 3.520555 CAATCGATTGGACGTGTCGCG 62.521 57.143 27.09 0.00 39.15 5.87
2920 9878 2.261172 ATCGATTGGACGTGTCGCGA 62.261 55.000 13.68 3.71 44.77 5.87
2940 9898 2.403586 GGCACACGGCGAAATAGC 59.596 61.111 16.62 9.93 46.16 2.97
2965 9923 4.037446 GCCTGTTTTTGTAGGACACATTCA 59.963 41.667 0.00 0.00 36.90 2.57
2994 9952 2.291540 TGGTTTGAGGGGATAAAGCCAG 60.292 50.000 0.00 0.00 34.37 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 4.749245 AAGAATGGAGCAACGTTTACAG 57.251 40.909 0.00 0.00 0.00 2.74
127 204 3.584848 AGTTCCTGTGCTACCTCTGAATT 59.415 43.478 0.00 0.00 0.00 2.17
135 212 3.851098 CTCTTGTAGTTCCTGTGCTACC 58.149 50.000 0.00 0.00 37.39 3.18
137 214 2.233922 GGCTCTTGTAGTTCCTGTGCTA 59.766 50.000 0.00 0.00 0.00 3.49
147 224 0.035056 GGCACCATGGCTCTTGTAGT 60.035 55.000 13.04 0.00 40.14 2.73
168 245 6.029607 CGGATGTTTTTGGAGTATGAACATG 58.970 40.000 4.91 0.00 40.05 3.21
205 282 1.269569 GCAAAAGTTAGGCCTGCGTTT 60.270 47.619 17.99 15.43 0.00 3.60
225 307 0.033781 TACTCGTGGAAAACCGGTGG 59.966 55.000 8.52 0.00 0.00 4.61
272 604 1.671054 CGCCACGTGATTTGGGTCT 60.671 57.895 19.30 0.00 34.35 3.85
374 945 2.293122 CGTTTTGGTCTCTCCATGCAAA 59.707 45.455 0.00 0.00 46.60 3.68
424 1025 3.490590 GCTGATCGACACAGTGATCTCAT 60.491 47.826 7.81 0.00 41.24 2.90
514 1187 7.214381 TGTAATTATCTGGTTAAGCACGCTAT 58.786 34.615 2.54 0.00 0.00 2.97
569 3359 2.533266 GCTGCACCATAGAAAATGTGC 58.467 47.619 6.53 6.53 38.20 4.57
616 3406 1.379527 GCCGGTAACAAGGAGGAATG 58.620 55.000 1.90 0.00 0.00 2.67
700 3501 1.444836 CGGAGATTTGGCCACGTAAA 58.555 50.000 3.88 0.00 0.00 2.01
792 4540 5.130311 TGCTCTATGGCCACTAGTATTGAAA 59.870 40.000 8.16 0.00 0.00 2.69
1086 4986 4.585526 CCGCCGCGCTTCTGGATA 62.586 66.667 7.42 0.00 0.00 2.59
1182 5082 2.885135 TGTCAGGACGGAGGTAGTTA 57.115 50.000 0.00 0.00 0.00 2.24
1197 5097 0.953471 AGTTGCCGCGCTTTATGTCA 60.953 50.000 5.56 0.00 0.00 3.58
1203 5103 2.617274 GGAGAAGTTGCCGCGCTTT 61.617 57.895 5.56 0.00 0.00 3.51
1293 5203 2.426024 GACTGCGGATGTGGAGTAGTTA 59.574 50.000 0.00 0.00 40.92 2.24
1304 5214 2.034879 GTGTGGTGGACTGCGGATG 61.035 63.158 0.00 0.00 0.00 3.51
1305 5215 2.347490 GTGTGGTGGACTGCGGAT 59.653 61.111 0.00 0.00 0.00 4.18
1306 5216 3.157949 TGTGTGGTGGACTGCGGA 61.158 61.111 0.00 0.00 0.00 5.54
1307 5217 2.972505 GTGTGTGGTGGACTGCGG 60.973 66.667 0.00 0.00 0.00 5.69
1308 5218 2.203001 TGTGTGTGGTGGACTGCG 60.203 61.111 0.00 0.00 0.00 5.18
1309 5219 1.451207 TGTGTGTGTGGTGGACTGC 60.451 57.895 0.00 0.00 0.00 4.40
1310 5220 0.392327 TGTGTGTGTGTGGTGGACTG 60.392 55.000 0.00 0.00 0.00 3.51
1311 5221 0.107703 CTGTGTGTGTGTGGTGGACT 60.108 55.000 0.00 0.00 0.00 3.85
1312 5222 1.714899 GCTGTGTGTGTGTGGTGGAC 61.715 60.000 0.00 0.00 0.00 4.02
1313 5223 1.451207 GCTGTGTGTGTGTGGTGGA 60.451 57.895 0.00 0.00 0.00 4.02
1314 5224 1.031571 AAGCTGTGTGTGTGTGGTGG 61.032 55.000 0.00 0.00 0.00 4.61
1315 5225 1.599071 CTAAGCTGTGTGTGTGTGGTG 59.401 52.381 0.00 0.00 0.00 4.17
1316 5226 1.953559 CTAAGCTGTGTGTGTGTGGT 58.046 50.000 0.00 0.00 0.00 4.16
1317 5227 0.588252 GCTAAGCTGTGTGTGTGTGG 59.412 55.000 0.00 0.00 0.00 4.17
1318 5228 0.588252 GGCTAAGCTGTGTGTGTGTG 59.412 55.000 0.00 0.00 0.00 3.82
1319 5229 0.880278 CGGCTAAGCTGTGTGTGTGT 60.880 55.000 0.00 0.00 0.00 3.72
1451 5407 3.989698 CTCCAGGTGCGTCGCGATT 62.990 63.158 14.06 0.00 0.00 3.34
1576 5532 1.227321 TTGACGTCGTGGTTGGTCC 60.227 57.895 11.62 0.00 0.00 4.46
1838 5917 2.029666 ACCACGTGCTGCTCTGAC 59.970 61.111 10.91 0.00 0.00 3.51
1839 5918 2.029518 CACCACGTGCTGCTCTGA 59.970 61.111 10.91 0.00 0.00 3.27
1978 6177 4.717629 CGCCGAACTCCTGCGTCA 62.718 66.667 0.00 0.00 43.12 4.35
2131 6434 8.447833 CAATGAATGTTGTAGTACACCGTTATT 58.552 33.333 1.43 2.99 0.00 1.40
2240 6577 8.470040 TGTTAACTTATAAGGAAAGTGTAGCG 57.530 34.615 16.73 0.00 37.26 4.26
2330 8940 1.462869 CCACCGTTATTGCGACGAAAC 60.463 52.381 0.00 0.00 42.82 2.78
2417 9057 8.607441 TTAGGTTCGTTCGTATTAGCTAGATA 57.393 34.615 0.00 0.00 0.00 1.98
2485 9242 7.703197 TGTTGGTTCCTCGAAATAAAAGTTTTC 59.297 33.333 3.60 0.00 0.00 2.29
2609 9369 8.041919 TCCGTATGGTTTTCTTGTGAATATGTA 58.958 33.333 0.00 0.00 36.30 2.29
2709 9472 7.797121 AACCATCCTGAACCAATTTTAATCT 57.203 32.000 0.00 0.00 0.00 2.40
2821 9592 6.098982 TGTGGTTCTATTCAAAATGGTTTGGT 59.901 34.615 0.00 0.00 43.70 3.67
2860 9818 6.714356 TGAATGTGACCATCATGTGAAAACTA 59.286 34.615 0.00 0.00 0.00 2.24
2912 9870 3.712881 GTGTGCCCTTCGCGACAC 61.713 66.667 9.15 14.77 42.08 3.67
2919 9877 1.022451 TATTTCGCCGTGTGCCCTTC 61.022 55.000 0.00 0.00 36.24 3.46
2920 9878 1.003112 TATTTCGCCGTGTGCCCTT 60.003 52.632 0.00 0.00 36.24 3.95
2940 9898 2.948979 TGTGTCCTACAAAAACAGGCTG 59.051 45.455 14.16 14.16 36.06 4.85
2965 9923 1.151450 CCCTCAAACCAGCCACACT 59.849 57.895 0.00 0.00 0.00 3.55
2994 9952 1.008767 CGGCGAGGGTTAGACGATC 60.009 63.158 0.00 0.00 42.33 3.69



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

AutoCloner maintained by Alex Coulton.