Multiple sequence alignment - TraesCS2D01G051500

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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 TraesCS2D01G051500 chr2D 100.000 1599 0 0 3587 5185 19561588 19559990 0.000000e+00 2953
1 TraesCS2D01G051500 chr2D 100.000 1204 0 0 1 1204 19565174 19563971 0.000000e+00 2224
2 TraesCS2D01G051500 chr2D 100.000 1004 0 0 1468 2471 19563707 19562704 0.000000e+00 1855
3 TraesCS2D01G051500 chr2D 86.467 835 82 22 324 1143 645162273 645161455 0.000000e+00 887
4 TraesCS2D01G051500 chr2D 83.067 939 122 25 3620 4525 19239850 19238916 0.000000e+00 819
5 TraesCS2D01G051500 chr2D 82.372 936 125 25 3620 4525 19533010 19532085 0.000000e+00 778
6 TraesCS2D01G051500 chr2D 84.987 746 99 8 3692 4431 19529253 19528515 0.000000e+00 745
7 TraesCS2D01G051500 chr2D 86.635 419 53 3 1750 2168 19534174 19533759 1.320000e-125 460
8 TraesCS2D01G051500 chr2D 83.607 427 38 12 1750 2168 19241006 19240604 6.340000e-99 372
9 TraesCS2D01G051500 chr2D 81.159 414 52 17 2079 2471 19529718 19529310 5.040000e-80 309
10 TraesCS2D01G051500 chr2D 88.462 234 21 2 2188 2419 19533658 19533429 1.420000e-70 278
11 TraesCS2D01G051500 chr2D 86.800 250 25 3 2188 2435 19240501 19240258 6.620000e-69 272
12 TraesCS2D01G051500 chr2D 82.918 281 40 4 1755 2034 19530008 19529735 4.010000e-61 246
13 TraesCS2D01G051500 chr2D 84.615 117 14 4 1643 1758 22562170 22562283 4.240000e-21 113
14 TraesCS2D01G051500 chr3D 97.439 1601 35 4 3587 5185 589667407 589669003 0.000000e+00 2724
15 TraesCS2D01G051500 chr3D 98.090 1204 22 1 1 1204 589708442 589709644 0.000000e+00 2095
16 TraesCS2D01G051500 chr3D 97.674 1204 25 3 1 1204 589664778 589665978 0.000000e+00 2065
17 TraesCS2D01G051500 chr3D 98.193 332 4 1 1480 1809 589709914 589710245 3.480000e-161 579
18 TraesCS2D01G051500 chr3D 97.626 337 6 1 1475 1809 589666232 589666568 1.250000e-160 577
19 TraesCS2D01G051500 chr3D 97.727 220 5 0 2243 2462 589666566 589666785 3.790000e-101 379
20 TraesCS2D01G051500 chr3D 97.727 220 5 0 2243 2462 589710243 589710462 3.790000e-101 379
21 TraesCS2D01G051500 chr3A 92.870 1108 72 5 97 1204 452616005 452617105 0.000000e+00 1602
22 TraesCS2D01G051500 chr3A 92.440 291 18 2 1468 1754 452617133 452617423 3.740000e-111 412
23 TraesCS2D01G051500 chr3A 86.408 103 12 2 1662 1764 495020655 495020755 1.530000e-20 111
24 TraesCS2D01G051500 chr4B 89.596 817 69 15 325 1131 110285128 110284318 0.000000e+00 1024
25 TraesCS2D01G051500 chr4B 85.904 830 86 23 326 1143 480918348 480917538 0.000000e+00 856
26 TraesCS2D01G051500 chr2A 87.470 830 93 9 3589 4412 20385345 20384521 0.000000e+00 946
27 TraesCS2D01G051500 chr2A 87.030 825 97 9 3589 4409 20604522 20605340 0.000000e+00 922
28 TraesCS2D01G051500 chr2A 87.035 833 82 21 325 1149 165546700 165547514 0.000000e+00 917
29 TraesCS2D01G051500 chr2A 83.890 838 101 24 3634 4442 20593704 20594536 0.000000e+00 769
30 TraesCS2D01G051500 chr2A 86.946 429 45 3 1750 2170 20592566 20592991 6.080000e-129 472
31 TraesCS2D01G051500 chr2A 82.997 347 55 4 3689 4032 9646898 9646553 1.400000e-80 311
32 TraesCS2D01G051500 chr2A 86.580 231 24 3 2188 2416 20593072 20593297 1.110000e-61 248
33 TraesCS2D01G051500 chr2A 85.776 232 30 1 1939 2170 20603315 20603543 5.190000e-60 243
34 TraesCS2D01G051500 chr2A 82.986 288 27 14 2188 2471 20386121 20385852 1.870000e-59 241
35 TraesCS2D01G051500 chr2A 87.912 182 16 3 2188 2367 20603624 20603801 5.260000e-50 209
36 TraesCS2D01G051500 chr2A 84.940 166 18 4 1784 1948 20602980 20603139 1.490000e-35 161
37 TraesCS2D01G051500 chr2A 92.391 92 5 2 177 266 191916622 191916713 4.210000e-26 130
38 TraesCS2D01G051500 chr1D 88.310 787 78 12 366 1143 368282550 368281769 0.000000e+00 931
39 TraesCS2D01G051500 chr1A 85.145 828 89 26 334 1149 463190488 463189683 0.000000e+00 817
40 TraesCS2D01G051500 chr7A 85.781 647 83 8 4524 5165 169402138 169402780 0.000000e+00 676
41 TraesCS2D01G051500 chr7A 84.520 646 85 9 4524 5165 460311743 460311109 4.410000e-175 625
42 TraesCS2D01G051500 chr7A 92.391 92 5 2 177 266 175349317 175349408 4.210000e-26 130
43 TraesCS2D01G051500 chr5D 85.168 654 78 11 4524 5169 61485456 61484814 0.000000e+00 652
44 TraesCS2D01G051500 chr5D 81.532 222 34 7 1538 1754 548668849 548668630 5.340000e-40 176
45 TraesCS2D01G051500 chr4D 84.862 654 79 12 4524 5169 87960801 87960160 4.380000e-180 641
46 TraesCS2D01G051500 chr4D 92.391 92 5 2 177 266 146092779 146092870 4.210000e-26 130
47 TraesCS2D01G051500 chr2B 84.783 644 83 9 4524 5162 747861437 747860804 2.630000e-177 632
48 TraesCS2D01G051500 chr2B 89.183 416 44 1 1753 2167 32125451 32125036 7.700000e-143 518
49 TraesCS2D01G051500 chr2B 81.575 597 87 12 3620 4205 32124314 32123730 6.080000e-129 472
50 TraesCS2D01G051500 chr2B 88.000 250 22 4 2188 2435 32124931 32124688 6.570000e-74 289
51 TraesCS2D01G051500 chr2B 88.000 100 10 2 1665 1764 706799284 706799187 3.280000e-22 117
52 TraesCS2D01G051500 chr4A 85.120 625 84 5 4524 5145 162419791 162420409 9.470000e-177 630
53 TraesCS2D01G051500 chr4A 84.603 643 85 9 4524 5161 6819432 6818799 1.230000e-175 627
54 TraesCS2D01G051500 chr4A 89.247 93 10 0 1662 1754 654513773 654513865 3.280000e-22 117
55 TraesCS2D01G051500 chr6B 84.341 645 93 5 4522 5165 137414691 137414054 4.410000e-175 625
56 TraesCS2D01G051500 chr5A 88.889 108 10 2 177 282 158353911 158353804 1.170000e-26 132
57 TraesCS2D01G051500 chr5A 89.423 104 9 2 177 278 511882636 511882533 4.210000e-26 130
58 TraesCS2D01G051500 chr5A 89.247 93 10 0 1662 1754 333816473 333816381 3.280000e-22 117
59 TraesCS2D01G051500 chr6A 92.391 92 5 2 177 266 597454388 597454479 4.210000e-26 130


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 TraesCS2D01G051500 chr2D 19559990 19565174 5184 True 2344.000000 2953 100.000000 1 5185 3 chr2D.!!$R4 5184
1 TraesCS2D01G051500 chr2D 645161455 645162273 818 True 887.000000 887 86.467000 324 1143 1 chr2D.!!$R1 819
2 TraesCS2D01G051500 chr2D 19238916 19241006 2090 True 487.666667 819 84.491333 1750 4525 3 chr2D.!!$R2 2775
3 TraesCS2D01G051500 chr2D 19528515 19534174 5659 True 469.333333 778 84.422167 1750 4525 6 chr2D.!!$R3 2775
4 TraesCS2D01G051500 chr3D 589664778 589669003 4225 False 1436.250000 2724 97.616500 1 5185 4 chr3D.!!$F1 5184
5 TraesCS2D01G051500 chr3D 589708442 589710462 2020 False 1017.666667 2095 98.003333 1 2462 3 chr3D.!!$F2 2461
6 TraesCS2D01G051500 chr3A 452616005 452617423 1418 False 1007.000000 1602 92.655000 97 1754 2 chr3A.!!$F2 1657
7 TraesCS2D01G051500 chr4B 110284318 110285128 810 True 1024.000000 1024 89.596000 325 1131 1 chr4B.!!$R1 806
8 TraesCS2D01G051500 chr4B 480917538 480918348 810 True 856.000000 856 85.904000 326 1143 1 chr4B.!!$R2 817
9 TraesCS2D01G051500 chr2A 165546700 165547514 814 False 917.000000 917 87.035000 325 1149 1 chr2A.!!$F1 824
10 TraesCS2D01G051500 chr2A 20384521 20386121 1600 True 593.500000 946 85.228000 2188 4412 2 chr2A.!!$R2 2224
11 TraesCS2D01G051500 chr2A 20592566 20594536 1970 False 496.333333 769 85.805333 1750 4442 3 chr2A.!!$F3 2692
12 TraesCS2D01G051500 chr2A 20602980 20605340 2360 False 383.750000 922 86.414500 1784 4409 4 chr2A.!!$F4 2625
13 TraesCS2D01G051500 chr1D 368281769 368282550 781 True 931.000000 931 88.310000 366 1143 1 chr1D.!!$R1 777
14 TraesCS2D01G051500 chr1A 463189683 463190488 805 True 817.000000 817 85.145000 334 1149 1 chr1A.!!$R1 815
15 TraesCS2D01G051500 chr7A 169402138 169402780 642 False 676.000000 676 85.781000 4524 5165 1 chr7A.!!$F1 641
16 TraesCS2D01G051500 chr7A 460311109 460311743 634 True 625.000000 625 84.520000 4524 5165 1 chr7A.!!$R1 641
17 TraesCS2D01G051500 chr5D 61484814 61485456 642 True 652.000000 652 85.168000 4524 5169 1 chr5D.!!$R1 645
18 TraesCS2D01G051500 chr4D 87960160 87960801 641 True 641.000000 641 84.862000 4524 5169 1 chr4D.!!$R1 645
19 TraesCS2D01G051500 chr2B 747860804 747861437 633 True 632.000000 632 84.783000 4524 5162 1 chr2B.!!$R2 638
20 TraesCS2D01G051500 chr2B 32123730 32125451 1721 True 426.333333 518 86.252667 1753 4205 3 chr2B.!!$R3 2452
21 TraesCS2D01G051500 chr4A 162419791 162420409 618 False 630.000000 630 85.120000 4524 5145 1 chr4A.!!$F1 621
22 TraesCS2D01G051500 chr4A 6818799 6819432 633 True 627.000000 627 84.603000 4524 5161 1 chr4A.!!$R1 637
23 TraesCS2D01G051500 chr6B 137414054 137414691 637 True 625.000000 625 84.341000 4522 5165 1 chr6B.!!$R1 643

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
303 304 1.546029 TCCTCAACTCTGGATGTCACG 59.454 52.381 0.00 0.00 0.00 4.35 F
1896 1937 1.633852 GCAGGAGCTTCTGACGCAAG 61.634 60.000 26.96 0.00 36.93 4.01 F
2271 2585 0.508641 CGTGCAGGAGAAACAACGAG 59.491 55.000 0.00 0.00 0.00 4.18 F
2279 2593 1.527311 GAGAAACAACGAGAAGCGCTT 59.473 47.619 25.35 25.35 46.04 4.68 F
3871 4673 4.082571 GCAATGACAACACTAGAAATGGCT 60.083 41.667 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2220 1.153489 CTGGAGCCTGGACATGACG 60.153 63.158 0.0 0.0 0.00 4.35 R
3712 4512 4.645136 TCTGTGTAGGCAATCTGTAGTAGG 59.355 45.833 0.0 0.0 0.00 3.18 R
3871 4673 6.126409 GGTCCATACCAGGTTCATTATTTGA 58.874 40.000 0.0 0.0 45.98 2.69 R
3970 4772 7.054751 GGGTTATCAAGCACCTTTATTAGAGT 58.945 38.462 0.0 0.0 33.09 3.24 R
4691 9217 5.006358 ACTGTCTACTACAACAAGTTTTGCG 59.994 40.000 0.0 0.0 37.74 4.85 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
303 304 1.546029 TCCTCAACTCTGGATGTCACG 59.454 52.381 0.00 0.00 0.00 4.35
322 323 1.732732 CGGATGTCGTTGGTGAGAGAC 60.733 57.143 0.00 0.00 0.00 3.36
1096 1123 4.164988 CCATCTAAAGGTCCAGAATCCACT 59.835 45.833 0.00 0.00 0.00 4.00
1819 1858 6.182627 TGGATAACAAGATGAAGAGCAACAT 58.817 36.000 0.00 0.00 0.00 2.71
1896 1937 1.633852 GCAGGAGCTTCTGACGCAAG 61.634 60.000 26.96 0.00 36.93 4.01
2021 2247 2.771762 AGGCTCCAGGGGATCAGC 60.772 66.667 0.00 0.00 0.00 4.26
2032 2258 1.300963 GGATCAGCACCCAAGCAGA 59.699 57.895 0.00 0.00 36.85 4.26
2043 2269 2.110967 CAAGCAGACGGCCATGGAG 61.111 63.158 18.40 11.25 46.50 3.86
2051 2277 4.408821 GGCCATGGAGCGGTGACA 62.409 66.667 18.40 0.00 0.00 3.58
2063 2289 2.357034 GTGACAGCGCCCTTCGAA 60.357 61.111 2.29 0.00 41.67 3.71
2076 2302 1.662845 CTTCGAACTCGCCGACGTTC 61.663 60.000 15.05 15.05 41.18 3.95
2077 2303 2.121564 TTCGAACTCGCCGACGTTCT 62.122 55.000 19.59 0.00 41.18 3.01
2163 2389 9.057089 GTCAGAAGAGAAGGTTAGAATTTTTCA 57.943 33.333 0.00 0.00 0.00 2.69
2184 2462 8.669946 TTTCAAATAAAGTTCAAATTGGACCC 57.330 30.769 0.00 0.00 0.00 4.46
2201 2515 5.376625 TGGACCCTCTATATGTTTGCATTC 58.623 41.667 0.00 0.00 36.58 2.67
2206 2520 5.380043 CCTCTATATGTTTGCATTCCAGGT 58.620 41.667 0.00 0.00 36.58 4.00
2207 2521 6.465751 CCCTCTATATGTTTGCATTCCAGGTA 60.466 42.308 0.00 0.00 36.58 3.08
2208 2522 7.170965 CCTCTATATGTTTGCATTCCAGGTAT 58.829 38.462 0.00 0.00 36.58 2.73
2209 2523 8.321353 CCTCTATATGTTTGCATTCCAGGTATA 58.679 37.037 0.00 0.00 36.58 1.47
2216 2530 6.873605 TGTTTGCATTCCAGGTATATATCTCG 59.126 38.462 0.00 0.00 0.00 4.04
2222 2536 5.854010 TCCAGGTATATATCTCGCCAATC 57.146 43.478 0.00 0.00 0.00 2.67
2271 2585 0.508641 CGTGCAGGAGAAACAACGAG 59.491 55.000 0.00 0.00 0.00 4.18
2279 2593 1.527311 GAGAAACAACGAGAAGCGCTT 59.473 47.619 25.35 25.35 46.04 4.68
2398 2998 5.857822 ACTACAACTAAGCAATTCGTTCC 57.142 39.130 0.00 0.00 0.00 3.62
3712 4512 9.289303 CATAACAAACTTGTAATTATGCAGGAC 57.711 33.333 0.00 0.00 41.31 3.85
3771 4573 4.624015 CAACCAAGACAATTCAGCAACAT 58.376 39.130 0.00 0.00 0.00 2.71
3780 4582 6.827251 AGACAATTCAGCAACATGATCAGTAT 59.173 34.615 0.00 0.00 0.00 2.12
3810 4612 6.611381 TCTTAATTGTGAAGAGGAAATTGCG 58.389 36.000 0.00 0.00 0.00 4.85
3871 4673 4.082571 GCAATGACAACACTAGAAATGGCT 60.083 41.667 0.00 0.00 0.00 4.75
3970 4772 2.571757 GAGATGTGGACGTGCCGA 59.428 61.111 4.04 0.00 40.66 5.54
4030 4832 5.874810 TGGAACATCATTTGCTAGAGTACAC 59.125 40.000 0.00 0.00 0.00 2.90
4454 8962 3.181448 TGTCCGCTCCCTTTTAGTCTTTT 60.181 43.478 0.00 0.00 0.00 2.27
4461 8969 5.467735 GCTCCCTTTTAGTCTTTTACGAACA 59.532 40.000 0.00 0.00 0.00 3.18
4479 9002 5.126384 ACGAACATCTTTTCTTGAAACCCAA 59.874 36.000 0.00 0.00 0.00 4.12
4656 9182 1.080501 CTGAAGCGAGCCGAAGACA 60.081 57.895 0.00 0.00 0.00 3.41
5178 9710 1.949525 GGCGACTATAGGGACGTAACA 59.050 52.381 4.43 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.592942 TCTTCTCAGCAGCCATTAACAAT 58.407 39.130 0.00 0.00 0.00 2.71
189 190 9.224267 GTATTCATAAGATGTGTAGGCATGAAT 57.776 33.333 0.00 10.63 41.78 2.57
303 304 1.732732 CGTCTCTCACCAACGACATCC 60.733 57.143 0.00 0.00 38.65 3.51
322 323 2.101415 TGCACCTGATATGTTCTCTCCG 59.899 50.000 0.00 0.00 0.00 4.63
400 401 4.230502 ACCAACCTGATCATATCCCTTTGT 59.769 41.667 0.00 0.00 0.00 2.83
657 663 4.505313 AGTTCGAAAAGGCAAGAAATCC 57.495 40.909 0.00 0.00 0.00 3.01
658 664 7.139392 AGTTAAGTTCGAAAAGGCAAGAAATC 58.861 34.615 0.00 0.00 0.00 2.17
1489 1516 2.774439 TCTTGGCGCTCTTTTTGTTC 57.226 45.000 7.64 0.00 0.00 3.18
1816 1855 2.749076 CCATTGACGACCATTGTGATGT 59.251 45.455 0.00 0.00 0.00 3.06
1819 1858 1.164411 GCCATTGACGACCATTGTGA 58.836 50.000 0.00 0.00 0.00 3.58
1994 2220 1.153489 CTGGAGCCTGGACATGACG 60.153 63.158 0.00 0.00 0.00 4.35
2021 2247 3.925630 ATGGCCGTCTGCTTGGGTG 62.926 63.158 0.00 0.00 40.92 4.61
2036 2262 2.821366 GCTGTCACCGCTCCATGG 60.821 66.667 4.97 4.97 0.00 3.66
2047 2273 2.357034 GTTCGAAGGGCGCTGTCA 60.357 61.111 7.64 0.00 40.61 3.58
2076 2302 2.222508 CGGCGTTGTGAGAAATTACGAG 60.223 50.000 0.00 0.00 34.36 4.18
2077 2303 1.722464 CGGCGTTGTGAGAAATTACGA 59.278 47.619 0.00 0.00 34.36 3.43
2163 2389 7.855784 AGAGGGTCCAATTTGAACTTTATTT 57.144 32.000 0.00 0.00 0.00 1.40
2182 2460 4.763793 CCTGGAATGCAAACATATAGAGGG 59.236 45.833 0.00 0.00 34.62 4.30
2184 2462 9.896645 ATATACCTGGAATGCAAACATATAGAG 57.103 33.333 0.00 0.00 34.62 2.43
2201 2515 5.598416 TGATTGGCGAGATATATACCTGG 57.402 43.478 0.00 0.00 0.00 4.45
2271 2585 5.808030 ACTTACAAGAGATCTTAAGCGCTTC 59.192 40.000 28.82 12.46 34.28 3.86
2398 2998 8.639428 GTGTATTACTAATGTGACGATATGCTG 58.361 37.037 0.00 0.00 0.00 4.41
3712 4512 4.645136 TCTGTGTAGGCAATCTGTAGTAGG 59.355 45.833 0.00 0.00 0.00 3.18
3771 4573 8.539544 TCACAATTAAGAGTTCCATACTGATCA 58.460 33.333 0.00 0.00 37.17 2.92
3780 4582 6.433847 TCCTCTTCACAATTAAGAGTTCCA 57.566 37.500 13.08 0.00 45.61 3.53
3871 4673 6.126409 GGTCCATACCAGGTTCATTATTTGA 58.874 40.000 0.00 0.00 45.98 2.69
3909 4711 8.814038 ATTCTGTTAGTGATCCTGCTATTTTT 57.186 30.769 0.00 0.00 0.00 1.94
3970 4772 7.054751 GGGTTATCAAGCACCTTTATTAGAGT 58.945 38.462 0.00 0.00 33.09 3.24
4437 8945 5.467735 TGTTCGTAAAAGACTAAAAGGGAGC 59.532 40.000 0.00 0.00 0.00 4.70
4454 8962 5.823570 TGGGTTTCAAGAAAAGATGTTCGTA 59.176 36.000 0.00 0.00 32.50 3.43
4479 9002 7.094205 ACTGAAATGAAACTGAGAAAACACACT 60.094 33.333 0.00 0.00 0.00 3.55
4691 9217 5.006358 ACTGTCTACTACAACAAGTTTTGCG 59.994 40.000 0.00 0.00 37.74 4.85


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

AutoCloner maintained by Alex Coulton.