Multiple sequence alignment - TraesCS2A01G051800

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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 TraesCS2A01G051800 chr2A 100.000 3566 0 0 1 3566 20364473 20368038 0.000000e+00 6586.0
1 TraesCS2A01G051800 chr2A 91.444 1800 98 18 292 2052 17299399 17301181 0.000000e+00 2420.0
2 TraesCS2A01G051800 chr2A 90.401 1073 63 16 2084 3151 17301299 17302336 0.000000e+00 1375.0
3 TraesCS2A01G051800 chr2A 87.662 154 14 4 1902 2050 20551825 20551978 1.320000e-39 174.0
4 TraesCS2A01G051800 chr2A 100.000 31 0 0 2054 2084 17301256 17301286 1.380000e-04 58.4
5 TraesCS2A01G051800 chr2D 94.885 2659 88 18 886 3538 19849365 19846749 0.000000e+00 4113.0
6 TraesCS2A01G051800 chr2D 86.980 1828 127 51 292 2052 15248827 15250610 0.000000e+00 1954.0
7 TraesCS2A01G051800 chr2D 88.751 1609 103 39 486 2052 15228235 15229807 0.000000e+00 1897.0
8 TraesCS2A01G051800 chr2D 92.233 927 59 7 2084 3005 15229924 15230842 0.000000e+00 1301.0
9 TraesCS2A01G051800 chr2D 92.125 927 60 7 2084 3005 15265635 15266553 0.000000e+00 1295.0
10 TraesCS2A01G051800 chr2D 88.889 900 50 17 1 855 19850254 19849360 0.000000e+00 1062.0
11 TraesCS2A01G051800 chr2D 88.766 543 43 10 1 526 15331267 15331808 0.000000e+00 649.0
12 TraesCS2A01G051800 chr2D 84.644 267 35 2 1 264 615481337 615481074 9.820000e-66 261.0
13 TraesCS2A01G051800 chrUn 90.841 1725 97 23 361 2050 233477867 233476169 0.000000e+00 2254.0
14 TraesCS2A01G051800 chrUn 90.276 1738 96 27 361 2055 16444887 16443180 0.000000e+00 2206.0
15 TraesCS2A01G051800 chrUn 90.276 1738 96 27 361 2055 366814639 366812932 0.000000e+00 2206.0
16 TraesCS2A01G051800 chrUn 94.835 1336 52 7 726 2052 16657276 16658603 0.000000e+00 2069.0
17 TraesCS2A01G051800 chrUn 87.507 1833 122 49 292 2055 266171912 266170118 0.000000e+00 2017.0
18 TraesCS2A01G051800 chrUn 91.814 1466 83 8 2081 3538 272512891 272514327 0.000000e+00 2008.0
19 TraesCS2A01G051800 chrUn 91.814 1466 83 8 2081 3538 288702016 288703452 0.000000e+00 2008.0
20 TraesCS2A01G051800 chrUn 91.423 1469 89 7 2081 3538 16658718 16660160 0.000000e+00 1980.0
21 TraesCS2A01G051800 chrUn 94.063 1297 56 8 772 2052 16612153 16613444 0.000000e+00 1949.0
22 TraesCS2A01G051800 chrUn 91.002 1467 95 9 2081 3538 16613559 16614997 0.000000e+00 1943.0
23 TraesCS2A01G051800 chrUn 93.027 1348 59 10 716 2052 272511452 272512775 0.000000e+00 1936.0
24 TraesCS2A01G051800 chrUn 93.027 1348 59 10 716 2052 288700577 288701900 0.000000e+00 1936.0
25 TraesCS2A01G051800 chrUn 93.510 1094 58 6 2084 3173 16443074 16441990 0.000000e+00 1615.0
26 TraesCS2A01G051800 chrUn 93.163 1097 62 6 2081 3173 344032373 344033460 0.000000e+00 1598.0
27 TraesCS2A01G051800 chrUn 92.082 922 60 7 2089 3005 266169999 266169086 0.000000e+00 1286.0
28 TraesCS2A01G051800 chrUn 92.082 922 60 7 2089 3005 379210521 379209608 0.000000e+00 1286.0
29 TraesCS2A01G051800 chrUn 84.892 834 72 21 292 1088 375770492 375769676 0.000000e+00 793.0
30 TraesCS2A01G051800 chrUn 95.518 357 16 0 3182 3538 16548874 16549230 3.990000e-159 571.0
31 TraesCS2A01G051800 chrUn 95.518 357 16 0 3182 3538 203046954 203047310 3.990000e-159 571.0
32 TraesCS2A01G051800 chrUn 95.251 358 16 1 3182 3538 16441303 16440946 1.860000e-157 566.0
33 TraesCS2A01G051800 chrUn 94.413 358 19 1 3182 3538 233474049 233473692 1.870000e-152 549.0
34 TraesCS2A01G051800 chrUn 90.785 293 22 2 361 648 16611362 16611654 1.550000e-103 387.0
35 TraesCS2A01G051800 chrUn 90.785 293 22 2 361 648 16656976 16657268 1.550000e-103 387.0
36 TraesCS2A01G051800 chrUn 89.209 278 24 3 367 639 272511175 272511451 3.410000e-90 342.0
37 TraesCS2A01G051800 chrUn 89.209 278 24 3 367 639 288700300 288700576 3.410000e-90 342.0
38 TraesCS2A01G051800 chrUn 85.115 262 38 1 1 262 16610833 16611093 2.110000e-67 267.0
39 TraesCS2A01G051800 chrUn 83.969 262 40 2 1 262 16656444 16656703 2.130000e-62 250.0
40 TraesCS2A01G051800 chrUn 80.451 266 42 6 1 258 290877 291140 1.010000e-45 195.0
41 TraesCS2A01G051800 chrUn 96.825 63 2 0 726 788 16611662 16611724 4.870000e-19 106.0
42 TraesCS2A01G051800 chrUn 100.000 29 0 0 2054 2082 16613519 16613547 2.000000e-03 54.7
43 TraesCS2A01G051800 chrUn 100.000 29 0 0 2054 2082 16658678 16658706 2.000000e-03 54.7
44 TraesCS2A01G051800 chr6B 86.811 1524 126 44 2043 3538 548949774 548951250 0.000000e+00 1631.0
45 TraesCS2A01G051800 chr6B 86.584 1528 128 43 2043 3538 549030286 549031768 0.000000e+00 1615.0
46 TraesCS2A01G051800 chr7D 88.433 951 84 17 2089 3028 110891833 110892768 0.000000e+00 1123.0
47 TraesCS2A01G051800 chr7D 78.652 267 39 10 1 251 62272090 62272354 1.020000e-35 161.0
48 TraesCS2A01G051800 chr7B 87.645 259 32 0 6 264 556454925 556455183 5.790000e-78 302.0
49 TraesCS2A01G051800 chr1A 83.893 298 42 5 1 292 520575292 520574995 2.710000e-71 279.0
50 TraesCS2A01G051800 chr1B 80.970 268 43 4 1 261 38116727 38116461 4.670000e-49 206.0
51 TraesCS2A01G051800 chr3B 82.072 251 34 7 17 261 413966717 413966472 1.680000e-48 204.0
52 TraesCS2A01G051800 chr3D 81.746 252 35 8 16 261 28598026 28597780 2.170000e-47 200.0
53 TraesCS2A01G051800 chr3D 80.843 261 33 8 1 261 2339976 2340219 4.700000e-44 189.0
54 TraesCS2A01G051800 chr3D 88.462 156 17 1 1 156 39925930 39926084 1.690000e-43 187.0
55 TraesCS2A01G051800 chr1D 80.224 268 45 4 1 261 21883340 21883074 1.010000e-45 195.0
56 TraesCS2A01G051800 chr1D 84.831 178 23 2 5 182 483694667 483694840 3.660000e-40 176.0
57 TraesCS2A01G051800 chr6D 82.222 225 30 6 43 257 17237754 17237978 6.080000e-43 185.0
58 TraesCS2A01G051800 chr6D 78.022 182 30 4 1 182 47320341 47320512 4.870000e-19 106.0
59 TraesCS2A01G051800 chr4B 79.661 177 35 1 1 177 94943392 94943217 3.740000e-25 126.0


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 TraesCS2A01G051800 chr2A 20364473 20368038 3565 False 6586.000000 6586 100.000000 1 3566 1 chr2A.!!$F1 3565
1 TraesCS2A01G051800 chr2A 17299399 17302336 2937 False 1284.466667 2420 93.948333 292 3151 3 chr2A.!!$F3 2859
2 TraesCS2A01G051800 chr2D 19846749 19850254 3505 True 2587.500000 4113 91.887000 1 3538 2 chr2D.!!$R2 3537
3 TraesCS2A01G051800 chr2D 15248827 15250610 1783 False 1954.000000 1954 86.980000 292 2052 1 chr2D.!!$F1 1760
4 TraesCS2A01G051800 chr2D 15228235 15230842 2607 False 1599.000000 1897 90.492000 486 3005 2 chr2D.!!$F4 2519
5 TraesCS2A01G051800 chr2D 15265635 15266553 918 False 1295.000000 1295 92.125000 2084 3005 1 chr2D.!!$F2 921
6 TraesCS2A01G051800 chr2D 15331267 15331808 541 False 649.000000 649 88.766000 1 526 1 chr2D.!!$F3 525
7 TraesCS2A01G051800 chrUn 366812932 366814639 1707 True 2206.000000 2206 90.276000 361 2055 1 chrUn.!!$R1 1694
8 TraesCS2A01G051800 chrUn 266169086 266171912 2826 True 1651.500000 2017 89.794500 292 3005 2 chrUn.!!$R6 2713
9 TraesCS2A01G051800 chrUn 344032373 344033460 1087 False 1598.000000 1598 93.163000 2081 3173 1 chrUn.!!$F4 1092
10 TraesCS2A01G051800 chrUn 16440946 16444887 3941 True 1462.333333 2206 93.012333 361 3538 3 chrUn.!!$R4 3177
11 TraesCS2A01G051800 chrUn 272511175 272514327 3152 False 1428.666667 2008 91.350000 367 3538 3 chrUn.!!$F7 3171
12 TraesCS2A01G051800 chrUn 288700300 288703452 3152 False 1428.666667 2008 91.350000 367 3538 3 chrUn.!!$F8 3171
13 TraesCS2A01G051800 chrUn 233473692 233477867 4175 True 1401.500000 2254 92.627000 361 3538 2 chrUn.!!$R5 3177
14 TraesCS2A01G051800 chrUn 379209608 379210521 913 True 1286.000000 1286 92.082000 2089 3005 1 chrUn.!!$R3 916
15 TraesCS2A01G051800 chrUn 16656444 16660160 3716 False 948.140000 2069 92.202400 1 3538 5 chrUn.!!$F6 3537
16 TraesCS2A01G051800 chrUn 375769676 375770492 816 True 793.000000 793 84.892000 292 1088 1 chrUn.!!$R2 796
17 TraesCS2A01G051800 chrUn 16610833 16614997 4164 False 784.450000 1949 92.965000 1 3538 6 chrUn.!!$F5 3537
18 TraesCS2A01G051800 chr6B 548949774 548951250 1476 False 1631.000000 1631 86.811000 2043 3538 1 chr6B.!!$F1 1495
19 TraesCS2A01G051800 chr6B 549030286 549031768 1482 False 1615.000000 1615 86.584000 2043 3538 1 chr6B.!!$F2 1495
20 TraesCS2A01G051800 chr7D 110891833 110892768 935 False 1123.000000 1123 88.433000 2089 3028 1 chr7D.!!$F2 939

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
460 667 0.107066 TCCCTCCGTCGCATACTGTA 60.107 55.0 0.00 0.0 0.00 2.74 F
629 889 0.107410 TGTTGGTCCGTGACAGCTTT 60.107 50.0 6.41 0.0 33.68 3.51 F
2052 2799 0.588252 CACGCACCCAAGTTCTTCTG 59.412 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 2156 0.250081 GGACGGATGAGGAGGCATTC 60.250 60.000 0.00 0.0 0.00 2.67 R
2484 3321 1.000274 GGCAGTTCGACATTTTTGCCT 60.000 47.619 6.08 0.0 45.73 4.75 R
3024 3888 1.257750 GGAGCCATCCAACCAAACCC 61.258 60.000 0.00 0.0 45.87 4.11 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
50 51 2.204034 TCAGGCTGACCACCTCCA 59.796 61.111 14.43 0.00 39.06 3.86
275 291 1.374252 CCGCAGCGTAAAGTGGACT 60.374 57.895 15.05 0.00 37.61 3.85
400 605 2.849473 CCAAACGAAACAAAACGACCTG 59.151 45.455 0.00 0.00 0.00 4.00
456 663 2.806608 TTAATCCCTCCGTCGCATAC 57.193 50.000 0.00 0.00 0.00 2.39
460 667 0.107066 TCCCTCCGTCGCATACTGTA 60.107 55.000 0.00 0.00 0.00 2.74
626 886 2.251642 GGTGTTGGTCCGTGACAGC 61.252 63.158 6.41 6.36 33.68 4.40
629 889 0.107410 TGTTGGTCCGTGACAGCTTT 60.107 50.000 6.41 0.00 33.68 3.51
670 1301 3.839823 TTGTTTTGCGTACGACTGTAC 57.160 42.857 21.65 9.93 46.09 2.90
672 1303 2.126467 GTTTTGCGTACGACTGTACCA 58.874 47.619 21.65 1.96 46.71 3.25
673 1304 1.769733 TTTGCGTACGACTGTACCAC 58.230 50.000 21.65 0.00 46.71 4.16
675 1306 1.227342 TGCGTACGACTGTACCACGA 61.227 55.000 21.65 0.00 46.71 4.35
676 1307 0.790866 GCGTACGACTGTACCACGAC 60.791 60.000 21.65 0.00 46.71 4.34
696 1348 1.139095 GTTACGTGGGAGAGGAGCG 59.861 63.158 0.00 0.00 0.00 5.03
697 1349 1.303888 TTACGTGGGAGAGGAGCGT 60.304 57.895 0.00 0.00 39.23 5.07
699 1351 2.473891 TACGTGGGAGAGGAGCGTGA 62.474 60.000 0.00 0.00 37.05 4.35
792 1456 2.593956 GGCCGGAGAAGGAGTTGGT 61.594 63.158 5.05 0.00 0.00 3.67
945 1617 1.594331 ACCTTCCTCAAGTCGTTTGC 58.406 50.000 0.00 0.00 36.70 3.68
1012 1692 1.728490 GAGCATCATGGTTTCCGCCC 61.728 60.000 0.00 0.00 33.17 6.13
1104 1802 2.124693 CCACTCCTCCTCCTCTCGC 61.125 68.421 0.00 0.00 0.00 5.03
1183 1902 3.922910 AGGCTCGTTTTCTACTTGTACC 58.077 45.455 0.00 0.00 0.00 3.34
1432 2156 2.198906 TACGTACGTGCAACCCTCCG 62.199 60.000 30.25 0.00 0.00 4.63
1508 2245 2.680370 CCTCCAGCCCCTAACCCAC 61.680 68.421 0.00 0.00 0.00 4.61
1833 2575 4.697828 TGTGGTAATTATGCGCTTTCAAGA 59.302 37.500 9.73 0.00 0.00 3.02
2052 2799 0.588252 CACGCACCCAAGTTCTTCTG 59.412 55.000 0.00 0.00 0.00 3.02
2341 3178 1.526575 CGCAAACCCAGCCAGACATT 61.527 55.000 0.00 0.00 0.00 2.71
2344 3181 1.270550 CAAACCCAGCCAGACATTCAC 59.729 52.381 0.00 0.00 0.00 3.18
2484 3321 3.655777 ACTACAGATTGACCCCCAAGAAA 59.344 43.478 0.00 0.00 38.31 2.52
2567 3404 5.350365 TCTCCGTCACCATCGAAAAATAAAG 59.650 40.000 0.00 0.00 0.00 1.85
2690 3534 4.220821 AGTCTGAGATCGCCTTTAGTTTCA 59.779 41.667 0.00 0.00 0.00 2.69
2790 3641 6.994496 CCAGAGATGTATTATGACACCATGTT 59.006 38.462 0.00 0.00 34.31 2.71
2821 3672 5.049405 CCTGTTTTCAATCTGCTCTTACGTT 60.049 40.000 0.00 0.00 0.00 3.99
2822 3673 6.371809 TGTTTTCAATCTGCTCTTACGTTT 57.628 33.333 0.00 0.00 0.00 3.60
2829 3680 6.312918 TCAATCTGCTCTTACGTTTTGATACC 59.687 38.462 0.00 0.00 0.00 2.73
2923 3774 4.223556 TGTATTATGTTTCGGGCAAGGA 57.776 40.909 0.00 0.00 0.00 3.36
3024 3888 7.098074 AGGAGACAGACTTAACCTAATTACG 57.902 40.000 0.00 0.00 0.00 3.18
3333 5525 5.771165 GGCTATAACTAGTAAGACTCCAGCT 59.229 44.000 0.00 0.00 0.00 4.24
3348 5540 3.157087 TCCAGCTCTTTCCCACAAATTC 58.843 45.455 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.463204 ACGCTGGATGGTCAGATCTG 59.537 55.000 17.07 17.07 36.93 2.90
50 51 0.842030 TGGTGGCCATCTCCTCTGTT 60.842 55.000 18.94 0.00 0.00 3.16
265 281 2.349755 GGCCGCCAGTCCACTTTA 59.650 61.111 3.91 0.00 0.00 1.85
294 310 3.662759 AAACCCAACTCTTGTTCTCCA 57.337 42.857 0.00 0.00 33.52 3.86
353 557 1.488812 TCGTTCCCCCATCGATCAAAT 59.511 47.619 0.00 0.00 0.00 2.32
400 605 8.186821 TCTTTCTACTATTAAAGTGGAGTACGC 58.813 37.037 0.00 0.00 45.35 4.42
440 645 0.755698 ACAGTATGCGACGGAGGGAT 60.756 55.000 0.00 0.00 42.53 3.85
626 886 1.576421 GACAACCCTGAGCGCAAAG 59.424 57.895 11.47 6.23 0.00 2.77
629 889 3.241530 AGGACAACCCTGAGCGCA 61.242 61.111 11.47 0.00 45.61 6.09
672 1303 0.879765 CTCTCCCACGTAACAGTCGT 59.120 55.000 0.00 0.00 42.33 4.34
673 1304 0.170561 CCTCTCCCACGTAACAGTCG 59.829 60.000 0.00 0.00 0.00 4.18
675 1306 1.546961 CTCCTCTCCCACGTAACAGT 58.453 55.000 0.00 0.00 0.00 3.55
676 1307 0.173708 GCTCCTCTCCCACGTAACAG 59.826 60.000 0.00 0.00 0.00 3.16
696 1348 3.437049 CCAGACGAAGGAAAAAGGATCAC 59.563 47.826 0.00 0.00 0.00 3.06
697 1349 3.326588 TCCAGACGAAGGAAAAAGGATCA 59.673 43.478 0.00 0.00 30.71 2.92
699 1351 4.367039 TTCCAGACGAAGGAAAAAGGAT 57.633 40.909 5.71 0.00 41.94 3.24
706 1358 3.473625 GTCCTTTTTCCAGACGAAGGAA 58.526 45.455 10.82 2.31 46.58 3.36
792 1456 3.490439 TGATTTGAGTGCAGTCCTCAA 57.510 42.857 18.82 15.52 44.83 3.02
945 1617 2.419198 CTCGATTGCTCGGGGGAG 59.581 66.667 0.00 0.00 45.10 4.30
1012 1692 2.568090 GATGTTGCGGGCCACTTG 59.432 61.111 4.39 0.00 0.00 3.16
1183 1902 2.277756 GTCGGCCTGCGTACGTAG 60.278 66.667 24.32 24.32 0.00 3.51
1432 2156 0.250081 GGACGGATGAGGAGGCATTC 60.250 60.000 0.00 0.00 0.00 2.67
1742 2479 5.458015 ACAAGTTAAAGCGGTTATCAAAGC 58.542 37.500 0.00 0.00 0.00 3.51
1871 2614 5.947228 TTAAGGTCTGTCAAAAGCATCTG 57.053 39.130 0.00 0.00 0.00 2.90
2052 2799 3.462021 CTGAGCTAGTAATTCACCCTGC 58.538 50.000 0.00 0.00 0.00 4.85
2341 3178 1.270826 CGCTGAGGAGTTCTTGAGTGA 59.729 52.381 0.00 0.00 0.00 3.41
2344 3181 1.671261 CCACGCTGAGGAGTTCTTGAG 60.671 57.143 0.00 0.00 0.00 3.02
2397 3234 1.397390 GGGCATTGGGGATCTGCAAG 61.397 60.000 6.27 0.00 37.64 4.01
2398 3235 1.381599 GGGCATTGGGGATCTGCAA 60.382 57.895 6.27 0.00 37.64 4.08
2484 3321 1.000274 GGCAGTTCGACATTTTTGCCT 60.000 47.619 6.08 0.00 45.73 4.75
2652 3496 8.015087 CGATCTCAGACTCTAATAGCTAACAAG 58.985 40.741 0.00 0.00 0.00 3.16
2690 3534 2.699954 GGACAGACGACAATGGTTCAT 58.300 47.619 0.00 0.00 0.00 2.57
2790 3641 4.099881 AGCAGATTGAAAACAGGAAAGCAA 59.900 37.500 0.00 0.00 0.00 3.91
2923 3774 6.746745 TTTTGTACAGAAAACGAAAGAGGT 57.253 33.333 0.00 0.00 0.00 3.85
3024 3888 1.257750 GGAGCCATCCAACCAAACCC 61.258 60.000 0.00 0.00 45.87 4.11
3333 5525 6.895204 CCCTTAATAGGAATTTGTGGGAAAGA 59.105 38.462 0.00 0.00 45.05 2.52
3366 5558 6.012658 TGTTGCTTCAAGTTGGATGTTATC 57.987 37.500 2.34 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.