Multiple sequence alignment - TraesCS3A01G536600

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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 TraesCS3A01G536600 chr3A 100.000 4279 0 0 1 4279 748080306 748076028 0.000000e+00 7902.0
1 TraesCS3A01G536600 chr3A 99.065 4280 24 4 1 4279 746843007 746838743 0.000000e+00 7668.0
2 TraesCS3A01G536600 chr3A 92.507 1695 123 4 1254 2945 424722574 424724267 0.000000e+00 2423.0
3 TraesCS3A01G536600 chr3A 90.820 610 29 9 181 765 341232104 341231497 0.000000e+00 791.0
4 TraesCS3A01G536600 chr7A 91.703 1820 139 8 1128 2945 148536937 148535128 0.000000e+00 2514.0
5 TraesCS3A01G536600 chr7A 91.159 1199 99 1 1129 2327 499734553 499735744 0.000000e+00 1620.0
6 TraesCS3A01G536600 chr7A 91.339 889 45 12 181 1044 698746942 698746061 0.000000e+00 1186.0
7 TraesCS3A01G536600 chr6B 91.635 1817 133 10 1132 2945 132946761 132944961 0.000000e+00 2495.0
8 TraesCS3A01G536600 chr6B 93.034 1694 115 3 1254 2945 56045465 56047157 0.000000e+00 2471.0
9 TraesCS3A01G536600 chr6B 87.362 633 79 1 1129 1760 529894448 529895080 0.000000e+00 725.0
10 TraesCS3A01G536600 chr2A 92.172 1763 135 3 1185 2945 72209922 72211683 0.000000e+00 2488.0
11 TraesCS3A01G536600 chr2A 88.122 362 31 9 742 1097 397554588 397554233 1.840000e-113 420.0
12 TraesCS3A01G536600 chr2A 88.056 360 31 9 744 1097 399702632 399702985 2.380000e-112 416.0
13 TraesCS3A01G536600 chr3B 91.019 1815 160 3 1132 2945 526359224 526357412 0.000000e+00 2446.0
14 TraesCS3A01G536600 chr3B 91.841 1336 106 2 2945 4279 784155516 784154183 0.000000e+00 1860.0
15 TraesCS3A01G536600 chr3B 91.004 1334 116 4 2947 4279 207053481 207054811 0.000000e+00 1796.0
16 TraesCS3A01G536600 chr3B 89.967 608 32 13 178 763 167240297 167240897 0.000000e+00 758.0
17 TraesCS3A01G536600 chr3B 87.066 634 78 4 1129 1760 732832506 732833137 0.000000e+00 713.0
18 TraesCS3A01G536600 chr3B 87.966 349 27 9 762 1099 821829299 821829643 8.620000e-107 398.0
19 TraesCS3A01G536600 chr3B 92.473 93 7 0 1245 1337 192021220 192021312 2.680000e-27 134.0
20 TraesCS3A01G536600 chr1B 91.551 1728 137 3 1220 2945 357433183 357434903 0.000000e+00 2374.0
21 TraesCS3A01G536600 chr1B 91.236 1335 116 1 2946 4279 205498937 205500271 0.000000e+00 1816.0
22 TraesCS3A01G536600 chr1B 83.155 374 43 14 756 1122 637956731 637956371 1.480000e-84 324.0
23 TraesCS3A01G536600 chr1B 92.174 115 9 0 1137 1251 357433044 357433158 3.420000e-36 163.0
24 TraesCS3A01G536600 chr1B 93.023 86 6 0 1248 1333 635346964 635346879 4.490000e-25 126.0
25 TraesCS3A01G536600 chr1B 89.109 101 9 2 1247 1345 207374585 207374485 1.620000e-24 124.0
26 TraesCS3A01G536600 chr1B 91.860 86 7 0 1248 1333 280096566 280096651 2.090000e-23 121.0
27 TraesCS3A01G536600 chr7B 92.122 1612 121 5 1337 2945 44759024 44760632 0.000000e+00 2268.0
28 TraesCS3A01G536600 chr7B 92.147 1337 103 2 2945 4279 749292813 749294149 0.000000e+00 1886.0
29 TraesCS3A01G536600 chr7B 89.452 1242 125 2 1160 2401 406928484 406929719 0.000000e+00 1563.0
30 TraesCS3A01G536600 chr7B 90.288 278 17 5 181 450 680907839 680907564 5.260000e-94 355.0
31 TraesCS3A01G536600 chr1A 97.309 1338 33 2 2945 4279 592541301 592539964 0.000000e+00 2268.0
32 TraesCS3A01G536600 chr1A 90.594 893 48 17 181 1044 292528897 292528012 0.000000e+00 1151.0
33 TraesCS3A01G536600 chr1A 88.384 947 58 27 181 1099 292539061 292538139 0.000000e+00 1092.0
34 TraesCS3A01G536600 chr1A 89.905 634 62 2 1129 1761 474167996 474168628 0.000000e+00 815.0
35 TraesCS3A01G536600 chr1A 86.825 630 82 1 1132 1760 563782847 563782218 0.000000e+00 702.0
36 TraesCS3A01G536600 chr1A 92.473 93 7 0 1245 1337 173779322 173779230 2.680000e-27 134.0
37 TraesCS3A01G536600 chr1A 91.398 93 8 0 1245 1337 6626475 6626567 1.250000e-25 128.0
38 TraesCS3A01G536600 chr4A 97.231 1336 36 1 2945 4279 490151875 490153210 0.000000e+00 2261.0
39 TraesCS3A01G536600 chr4A 90.089 898 55 14 178 1044 533906775 533907669 0.000000e+00 1134.0
40 TraesCS3A01G536600 chr5D 96.493 1340 42 4 2945 4279 510549802 510548463 0.000000e+00 2209.0
41 TraesCS3A01G536600 chr2B 91.401 1477 119 5 1470 2945 103549825 103548356 0.000000e+00 2017.0
42 TraesCS3A01G536600 chr2B 89.524 315 24 6 762 1070 667269287 667269598 1.440000e-104 390.0
43 TraesCS3A01G536600 chr2B 88.272 324 27 7 760 1073 755620690 755620368 1.120000e-100 377.0
44 TraesCS3A01G536600 chr2B 85.286 367 41 11 770 1127 20670320 20669958 2.430000e-97 366.0
45 TraesCS3A01G536600 chr6A 92.366 1323 100 1 2958 4279 38686799 38688121 0.000000e+00 1882.0
46 TraesCS3A01G536600 chr6A 91.573 890 34 23 181 1046 72392074 72391202 0.000000e+00 1190.0
47 TraesCS3A01G536600 chr4D 91.798 890 43 16 181 1044 329141540 329140655 0.000000e+00 1212.0
48 TraesCS3A01G536600 chr3D 88.878 980 63 27 181 1127 10706833 10705867 0.000000e+00 1164.0
49 TraesCS3A01G536600 chr3D 89.415 633 30 12 178 789 107219202 107219818 0.000000e+00 763.0
50 TraesCS3A01G536600 chr3D 88.000 50 6 0 12 61 590357671 590357622 4.620000e-05 60.2
51 TraesCS3A01G536600 chr4B 90.492 894 54 17 178 1044 599368186 599369075 0.000000e+00 1151.0
52 TraesCS3A01G536600 chr4B 91.398 93 8 0 1245 1337 436882146 436882238 1.250000e-25 128.0
53 TraesCS3A01G536600 chr5A 90.509 864 50 14 201 1036 700784210 700785069 0.000000e+00 1112.0
54 TraesCS3A01G536600 chr5A 89.699 631 63 2 1132 1761 367608614 367607985 0.000000e+00 804.0
55 TraesCS3A01G536600 chr5B 90.720 625 36 6 182 785 344933400 344934023 0.000000e+00 813.0
56 TraesCS3A01G536600 chr1D 91.191 613 32 11 181 773 278095076 278094466 0.000000e+00 813.0
57 TraesCS3A01G536600 chr7D 91.584 606 24 12 181 763 18122352 18121751 0.000000e+00 811.0
58 TraesCS3A01G536600 chr6D 85.000 280 38 2 1490 1766 417758476 417758198 9.060000e-72 281.0
59 TraesCS3A01G536600 chrUn 91.398 93 8 0 1245 1337 37060959 37061051 1.250000e-25 128.0


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 TraesCS3A01G536600 chr3A 748076028 748080306 4278 True 7902.0 7902 100.0000 1 4279 1 chr3A.!!$R3 4278
1 TraesCS3A01G536600 chr3A 746838743 746843007 4264 True 7668.0 7668 99.0650 1 4279 1 chr3A.!!$R2 4278
2 TraesCS3A01G536600 chr3A 424722574 424724267 1693 False 2423.0 2423 92.5070 1254 2945 1 chr3A.!!$F1 1691
3 TraesCS3A01G536600 chr3A 341231497 341232104 607 True 791.0 791 90.8200 181 765 1 chr3A.!!$R1 584
4 TraesCS3A01G536600 chr7A 148535128 148536937 1809 True 2514.0 2514 91.7030 1128 2945 1 chr7A.!!$R1 1817
5 TraesCS3A01G536600 chr7A 499734553 499735744 1191 False 1620.0 1620 91.1590 1129 2327 1 chr7A.!!$F1 1198
6 TraesCS3A01G536600 chr7A 698746061 698746942 881 True 1186.0 1186 91.3390 181 1044 1 chr7A.!!$R2 863
7 TraesCS3A01G536600 chr6B 132944961 132946761 1800 True 2495.0 2495 91.6350 1132 2945 1 chr6B.!!$R1 1813
8 TraesCS3A01G536600 chr6B 56045465 56047157 1692 False 2471.0 2471 93.0340 1254 2945 1 chr6B.!!$F1 1691
9 TraesCS3A01G536600 chr6B 529894448 529895080 632 False 725.0 725 87.3620 1129 1760 1 chr6B.!!$F2 631
10 TraesCS3A01G536600 chr2A 72209922 72211683 1761 False 2488.0 2488 92.1720 1185 2945 1 chr2A.!!$F1 1760
11 TraesCS3A01G536600 chr3B 526357412 526359224 1812 True 2446.0 2446 91.0190 1132 2945 1 chr3B.!!$R1 1813
12 TraesCS3A01G536600 chr3B 784154183 784155516 1333 True 1860.0 1860 91.8410 2945 4279 1 chr3B.!!$R2 1334
13 TraesCS3A01G536600 chr3B 207053481 207054811 1330 False 1796.0 1796 91.0040 2947 4279 1 chr3B.!!$F3 1332
14 TraesCS3A01G536600 chr3B 167240297 167240897 600 False 758.0 758 89.9670 178 763 1 chr3B.!!$F1 585
15 TraesCS3A01G536600 chr3B 732832506 732833137 631 False 713.0 713 87.0660 1129 1760 1 chr3B.!!$F4 631
16 TraesCS3A01G536600 chr1B 205498937 205500271 1334 False 1816.0 1816 91.2360 2946 4279 1 chr1B.!!$F1 1333
17 TraesCS3A01G536600 chr1B 357433044 357434903 1859 False 1268.5 2374 91.8625 1137 2945 2 chr1B.!!$F3 1808
18 TraesCS3A01G536600 chr7B 44759024 44760632 1608 False 2268.0 2268 92.1220 1337 2945 1 chr7B.!!$F1 1608
19 TraesCS3A01G536600 chr7B 749292813 749294149 1336 False 1886.0 1886 92.1470 2945 4279 1 chr7B.!!$F3 1334
20 TraesCS3A01G536600 chr7B 406928484 406929719 1235 False 1563.0 1563 89.4520 1160 2401 1 chr7B.!!$F2 1241
21 TraesCS3A01G536600 chr1A 592539964 592541301 1337 True 2268.0 2268 97.3090 2945 4279 1 chr1A.!!$R5 1334
22 TraesCS3A01G536600 chr1A 292528012 292528897 885 True 1151.0 1151 90.5940 181 1044 1 chr1A.!!$R2 863
23 TraesCS3A01G536600 chr1A 292538139 292539061 922 True 1092.0 1092 88.3840 181 1099 1 chr1A.!!$R3 918
24 TraesCS3A01G536600 chr1A 474167996 474168628 632 False 815.0 815 89.9050 1129 1761 1 chr1A.!!$F2 632
25 TraesCS3A01G536600 chr1A 563782218 563782847 629 True 702.0 702 86.8250 1132 1760 1 chr1A.!!$R4 628
26 TraesCS3A01G536600 chr4A 490151875 490153210 1335 False 2261.0 2261 97.2310 2945 4279 1 chr4A.!!$F1 1334
27 TraesCS3A01G536600 chr4A 533906775 533907669 894 False 1134.0 1134 90.0890 178 1044 1 chr4A.!!$F2 866
28 TraesCS3A01G536600 chr5D 510548463 510549802 1339 True 2209.0 2209 96.4930 2945 4279 1 chr5D.!!$R1 1334
29 TraesCS3A01G536600 chr2B 103548356 103549825 1469 True 2017.0 2017 91.4010 1470 2945 1 chr2B.!!$R2 1475
30 TraesCS3A01G536600 chr6A 38686799 38688121 1322 False 1882.0 1882 92.3660 2958 4279 1 chr6A.!!$F1 1321
31 TraesCS3A01G536600 chr6A 72391202 72392074 872 True 1190.0 1190 91.5730 181 1046 1 chr6A.!!$R1 865
32 TraesCS3A01G536600 chr4D 329140655 329141540 885 True 1212.0 1212 91.7980 181 1044 1 chr4D.!!$R1 863
33 TraesCS3A01G536600 chr3D 10705867 10706833 966 True 1164.0 1164 88.8780 181 1127 1 chr3D.!!$R1 946
34 TraesCS3A01G536600 chr3D 107219202 107219818 616 False 763.0 763 89.4150 178 789 1 chr3D.!!$F1 611
35 TraesCS3A01G536600 chr4B 599368186 599369075 889 False 1151.0 1151 90.4920 178 1044 1 chr4B.!!$F2 866
36 TraesCS3A01G536600 chr5A 700784210 700785069 859 False 1112.0 1112 90.5090 201 1036 1 chr5A.!!$F1 835
37 TraesCS3A01G536600 chr5A 367607985 367608614 629 True 804.0 804 89.6990 1132 1761 1 chr5A.!!$R1 629
38 TraesCS3A01G536600 chr5B 344933400 344934023 623 False 813.0 813 90.7200 182 785 1 chr5B.!!$F1 603
39 TraesCS3A01G536600 chr1D 278094466 278095076 610 True 813.0 813 91.1910 181 773 1 chr1D.!!$R1 592
40 TraesCS3A01G536600 chr7D 18121751 18122352 601 True 811.0 811 91.5840 181 763 1 chr7D.!!$R1 582

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
1411 1587 2.601868 GAGGAGGCGAGGTAGGGA 59.398 66.667 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3875 4060 2.154462 CTCTGGAGGTTCGCACAAAAT 58.846 47.619 0.0 0.0 0.0 1.82 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
1411 1587 2.601868 GAGGAGGCGAGGTAGGGA 59.398 66.667 0.00 0.00 0.00 4.20
1502 1679 4.120755 CTCCAGCAGGGCCCCTTC 62.121 72.222 21.43 7.93 36.21 3.46
1892 2072 0.755698 GGCGATCCTCCCTGTAGACA 60.756 60.000 0.00 0.00 0.00 3.41
2656 2837 7.816945 AAGCTGTTGCAACATATGTTTATTC 57.183 32.000 31.17 10.17 42.74 1.75
3711 3896 2.833794 TCGTTGAGTGGAAGTTCTTGG 58.166 47.619 2.25 0.00 0.00 3.61
4215 4404 8.671921 CATGAGAGAACACACTTTAGCATATTT 58.328 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1411 1587 0.613853 TCTCCGGAACAGGATTCGGT 60.614 55.000 5.23 0.0 42.71 4.69
1892 2072 2.310538 CTTTCCAGGGACTTTGTTGCT 58.689 47.619 0.00 0.0 34.60 3.91
3875 4060 2.154462 CTCTGGAGGTTCGCACAAAAT 58.846 47.619 0.00 0.0 0.00 1.82
4215 4404 6.662865 TGCAAACTCTATTTCCAATTCCAA 57.337 33.333 0.00 0.0 0.00 3.53


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

AutoCloner maintained by Alex Coulton.