Multiple sequence alignment - TraesCS3B01G595900

Loading Multiple Alignment...

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 TraesCS3B01G595900 chr3B 100.000 3638 0 0 1 3638 818877454 818873817 0.000000e+00 6719.0
1 TraesCS3B01G595900 chr3B 91.093 1089 41 8 937 1978 87430454 87431533 0.000000e+00 1423.0
2 TraesCS3B01G595900 chr3B 90.967 941 77 5 5 939 87429196 87430134 0.000000e+00 1260.0
3 TraesCS3B01G595900 chr3B 90.672 461 28 5 2918 3363 87432093 87432553 1.870000e-167 599.0
4 TraesCS3B01G595900 chr3B 96.575 292 9 1 2088 2379 87431526 87431816 1.960000e-132 483.0
5 TraesCS3B01G595900 chr3B 97.308 260 7 0 2370 2629 87431839 87432098 3.330000e-120 442.0
6 TraesCS3B01G595900 chr3B 98.367 245 3 1 3394 3638 87432552 87432795 2.600000e-116 429.0
7 TraesCS3B01G595900 chr3B 92.857 140 10 0 3499 3638 200086896 200086757 1.710000e-48 204.0
8 TraesCS3B01G595900 chr3B 92.857 140 10 0 3499 3638 200105644 200105505 1.710000e-48 204.0
9 TraesCS3B01G595900 chr1B 94.090 1489 35 15 937 2379 44984142 44982661 0.000000e+00 2213.0
10 TraesCS3B01G595900 chr1B 93.758 1490 33 9 937 2379 51508199 51509675 0.000000e+00 2182.0
11 TraesCS3B01G595900 chr1B 96.267 1286 28 8 2372 3638 51509700 51510984 0.000000e+00 2091.0
12 TraesCS3B01G595900 chr1B 96.184 1284 34 6 2370 3638 44982638 44981355 0.000000e+00 2085.0
13 TraesCS3B01G595900 chr1B 94.793 941 45 3 3 939 44985403 44984463 0.000000e+00 1463.0
14 TraesCS3B01G595900 chr1B 93.891 933 50 4 13 939 51506970 51507901 0.000000e+00 1400.0
15 TraesCS3B01G595900 chr1B 95.946 74 3 0 2716 2789 114007176 114007103 1.770000e-23 121.0
16 TraesCS3B01G595900 chr5B 93.133 932 57 4 13 939 5809074 5810003 0.000000e+00 1360.0
17 TraesCS3B01G595900 chr5B 92.704 932 60 7 13 939 4719292 4720220 0.000000e+00 1338.0
18 TraesCS3B01G595900 chr5B 86.882 526 26 12 3129 3638 667470716 667470218 1.910000e-152 549.0
19 TraesCS3B01G595900 chr7B 93.059 922 57 5 13 930 645439212 645438294 0.000000e+00 1341.0
20 TraesCS3B01G595900 chr7B 87.857 280 25 7 1143 1418 242511357 242511631 1.630000e-83 320.0
21 TraesCS3B01G595900 chr7B 87.636 275 32 1 2894 3168 499386904 499387176 5.860000e-83 318.0
22 TraesCS3B01G595900 chr7B 100.000 28 0 0 1003 1030 743597411 743597438 7.000000e-03 52.8
23 TraesCS3B01G595900 chr4B 91.974 922 70 3 13 930 668733580 668732659 0.000000e+00 1290.0
24 TraesCS3B01G595900 chr4B 84.011 369 37 9 1543 1909 662855656 662856004 5.820000e-88 335.0
25 TraesCS3B01G595900 chr4B 88.390 267 31 0 2894 3160 560547277 560547543 4.530000e-84 322.0
26 TraesCS3B01G595900 chr4B 100.000 28 0 0 1003 1030 127535010 127535037 7.000000e-03 52.8
27 TraesCS3B01G595900 chr6B 90.909 935 74 6 3 930 546204317 546203387 0.000000e+00 1245.0
28 TraesCS3B01G595900 chr6B 83.908 609 67 14 2553 3130 223656960 223656352 1.480000e-153 553.0
29 TraesCS3B01G595900 chr6B 90.638 235 16 4 3404 3638 223619939 223619711 1.270000e-79 307.0
30 TraesCS3B01G595900 chr6B 91.429 140 12 0 3499 3638 368565962 368565823 3.710000e-45 193.0
31 TraesCS3B01G595900 chr6B 97.297 74 2 0 2716 2789 38550076 38550149 3.810000e-25 126.0
32 TraesCS3B01G595900 chr2B 90.812 936 76 8 3 930 129750475 129749542 0.000000e+00 1243.0
33 TraesCS3B01G595900 chr2B 87.895 380 30 11 1537 1909 23583164 23582794 2.010000e-117 433.0
34 TraesCS3B01G595900 chr2B 86.545 275 35 1 2894 3168 91296075 91296347 5.900000e-78 302.0
35 TraesCS3B01G595900 chr2B 91.156 147 12 1 1269 1414 16376973 16376827 7.970000e-47 198.0
36 TraesCS3B01G595900 chr2B 84.810 158 22 2 938 1094 617124712 617124556 1.350000e-34 158.0
37 TraesCS3B01G595900 chr2B 96.250 80 3 0 1332 1411 785894208 785894129 8.200000e-27 132.0
38 TraesCS3B01G595900 chr2A 89.160 941 65 18 2726 3638 507019579 507018648 0.000000e+00 1138.0
39 TraesCS3B01G595900 chr2A 88.267 929 64 12 2726 3638 347015143 347016042 0.000000e+00 1070.0
40 TraesCS3B01G595900 chr2A 88.860 386 20 9 1537 1909 15004409 15004034 1.540000e-123 453.0
41 TraesCS3B01G595900 chr2A 95.429 175 4 3 2553 2723 507020888 507020714 3.580000e-70 276.0
42 TraesCS3B01G595900 chr2A 93.258 178 8 3 2550 2723 347013870 347014047 3.600000e-65 259.0
43 TraesCS3B01G595900 chr2A 94.253 87 4 1 1332 1418 775012882 775012967 8.200000e-27 132.0
44 TraesCS3B01G595900 chr2A 81.356 118 16 4 2806 2923 613184799 613184688 1.390000e-14 91.6
45 TraesCS3B01G595900 chr2A 100.000 29 0 0 1002 1030 734857438 734857466 2.000000e-03 54.7
46 TraesCS3B01G595900 chr2D 85.140 895 75 25 2553 3400 247463977 247463094 0.000000e+00 863.0
47 TraesCS3B01G595900 chr2D 87.200 375 19 18 1537 1909 12885154 12884807 2.040000e-107 399.0
48 TraesCS3B01G595900 chr2D 83.553 456 31 17 2980 3400 567488920 567488474 1.580000e-103 387.0
49 TraesCS3B01G595900 chr2D 89.686 223 19 3 3416 3638 247462815 247462597 7.690000e-72 281.0
50 TraesCS3B01G595900 chr2D 94.253 87 4 1 1332 1418 649820959 649820874 8.200000e-27 132.0
51 TraesCS3B01G595900 chr5D 86.692 526 28 11 3129 3638 448113974 448114473 2.470000e-151 545.0
52 TraesCS3B01G595900 chr5D 86.312 526 29 18 3129 3638 445141320 445140822 1.920000e-147 532.0
53 TraesCS3B01G595900 chr5D 86.592 179 13 1 938 1105 489746809 489746631 1.720000e-43 187.0
54 TraesCS3B01G595900 chr7D 80.191 419 41 26 1537 1950 457938122 457937741 3.580000e-70 276.0
55 TraesCS3B01G595900 chr7D 95.783 166 7 0 3473 3638 590894586 590894751 5.990000e-68 268.0
56 TraesCS3B01G595900 chr7D 90.449 178 13 2 2550 2723 81910417 81910594 7.860000e-57 231.0
57 TraesCS3B01G595900 chr7D 97.479 119 3 0 3311 3429 590894467 590894585 1.710000e-48 204.0
58 TraesCS3B01G595900 chr6A 96.296 162 6 0 2550 2711 158666619 158666780 2.150000e-67 267.0
59 TraesCS3B01G595900 chr6A 92.593 162 9 1 2726 2887 158667892 158668050 2.830000e-56 230.0
60 TraesCS3B01G595900 chr6A 100.000 28 0 0 1003 1030 120277012 120276985 7.000000e-03 52.8
61 TraesCS3B01G595900 chr6D 84.672 274 26 11 1534 1807 21352809 21353066 3.600000e-65 259.0
62 TraesCS3B01G595900 chr4D 77.949 390 57 24 1538 1922 201935495 201935860 2.200000e-52 217.0
63 TraesCS3B01G595900 chr4D 84.358 179 17 1 938 1105 200717419 200717241 8.080000e-37 165.0
64 TraesCS3B01G595900 chr1A 93.007 143 9 1 1269 1410 315062102 315061960 1.320000e-49 207.0
65 TraesCS3B01G595900 chr1A 94.595 37 2 0 2436 2472 524120977 524121013 1.410000e-04 58.4
66 TraesCS3B01G595900 chr1A 100.000 28 0 0 1003 1030 33805730 33805757 7.000000e-03 52.8
67 TraesCS3B01G595900 chr3D 86.592 179 13 3 938 1105 172532212 172532034 1.720000e-43 187.0
68 TraesCS3B01G595900 chr3D 86.034 179 14 1 938 1105 497286764 497286942 8.020000e-42 182.0
69 TraesCS3B01G595900 chr3A 83.051 118 14 4 2806 2923 106301101 106301212 6.430000e-18 102.0
70 TraesCS3B01G595900 chr3A 100.000 28 0 0 1003 1030 59552848 59552821 7.000000e-03 52.8


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 TraesCS3B01G595900 chr3B 818873817 818877454 3637 True 6719.000000 6719 100.000000 1 3638 1 chr3B.!!$R3 3637
1 TraesCS3B01G595900 chr3B 87429196 87432795 3599 False 772.666667 1423 94.163667 5 3638 6 chr3B.!!$F1 3633
2 TraesCS3B01G595900 chr1B 44981355 44985403 4048 True 1920.333333 2213 95.022333 3 3638 3 chr1B.!!$R2 3635
3 TraesCS3B01G595900 chr1B 51506970 51510984 4014 False 1891.000000 2182 94.638667 13 3638 3 chr1B.!!$F1 3625
4 TraesCS3B01G595900 chr5B 5809074 5810003 929 False 1360.000000 1360 93.133000 13 939 1 chr5B.!!$F2 926
5 TraesCS3B01G595900 chr5B 4719292 4720220 928 False 1338.000000 1338 92.704000 13 939 1 chr5B.!!$F1 926
6 TraesCS3B01G595900 chr7B 645438294 645439212 918 True 1341.000000 1341 93.059000 13 930 1 chr7B.!!$R1 917
7 TraesCS3B01G595900 chr4B 668732659 668733580 921 True 1290.000000 1290 91.974000 13 930 1 chr4B.!!$R1 917
8 TraesCS3B01G595900 chr6B 546203387 546204317 930 True 1245.000000 1245 90.909000 3 930 1 chr6B.!!$R4 927
9 TraesCS3B01G595900 chr6B 223656352 223656960 608 True 553.000000 553 83.908000 2553 3130 1 chr6B.!!$R2 577
10 TraesCS3B01G595900 chr2B 129749542 129750475 933 True 1243.000000 1243 90.812000 3 930 1 chr2B.!!$R3 927
11 TraesCS3B01G595900 chr2A 507018648 507020888 2240 True 707.000000 1138 92.294500 2553 3638 2 chr2A.!!$R3 1085
12 TraesCS3B01G595900 chr2A 347013870 347016042 2172 False 664.500000 1070 90.762500 2550 3638 2 chr2A.!!$F3 1088
13 TraesCS3B01G595900 chr2D 247462597 247463977 1380 True 572.000000 863 87.413000 2553 3638 2 chr2D.!!$R4 1085
14 TraesCS3B01G595900 chr6A 158666619 158668050 1431 False 248.500000 267 94.444500 2550 2887 2 chr6A.!!$F1 337

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
934 951 1.136828 TTGTGTGGTGCCCTTCTAGT 58.863 50.0 0.00 0.0 0.00 2.57 F
1753 2147 1.078201 CACACGCGAATGCTGCTCTA 61.078 55.0 15.93 0.0 39.65 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 2244 0.796927 GAGCGTCTTGTTGGGCTTAC 59.203 55.000 0.00 0.0 35.54 2.34 R
2769 4337 1.405463 GGATCCAAACTCGAAATGCCC 59.595 52.381 6.95 0.0 0.00 5.36 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
126 127 7.527568 AATTGATTTGGTCCATTTTTGCAAT 57.472 28.000 0.00 0.0 0.00 3.56
178 180 3.251004 CCTCTTTTTGGACACTCGGAAAG 59.749 47.826 0.00 0.0 0.00 2.62
344 347 5.623824 GCTTGAAAGCCATGAATCTTCACAT 60.624 40.000 3.56 0.0 46.20 3.21
357 360 7.264947 TGAATCTTCACATTTGATAGCTCGTA 58.735 34.615 0.00 0.0 31.01 3.43
710 723 5.334105 CGAGTGGTGGATAAAAACTGTTGAG 60.334 44.000 0.00 0.0 0.00 3.02
884 901 7.986889 GGAAATGCATACAAATTGGTCCTTATT 59.013 33.333 0.00 0.0 0.00 1.40
902 919 8.134895 GTCCTTATTCATAAAATGCGATCCAAA 58.865 33.333 0.00 0.0 0.00 3.28
934 951 1.136828 TTGTGTGGTGCCCTTCTAGT 58.863 50.000 0.00 0.0 0.00 2.57
1087 1446 2.743718 CACAACCTCGGCTCCTGT 59.256 61.111 0.00 0.0 0.00 4.00
1201 1560 3.787001 CGTCCCCTTCCTCCCTGC 61.787 72.222 0.00 0.0 0.00 4.85
1622 2016 3.537580 ACTCGTCAGATGTACTCCTCTC 58.462 50.000 0.00 0.0 0.00 3.20
1623 2017 3.199071 ACTCGTCAGATGTACTCCTCTCT 59.801 47.826 0.00 0.0 0.00 3.10
1624 2018 4.196193 CTCGTCAGATGTACTCCTCTCTT 58.804 47.826 0.00 0.0 0.00 2.85
1625 2019 4.193090 TCGTCAGATGTACTCCTCTCTTC 58.807 47.826 0.00 0.0 0.00 2.87
1753 2147 1.078201 CACACGCGAATGCTGCTCTA 61.078 55.000 15.93 0.0 39.65 2.43
1850 2244 4.320456 CATCCGCCTCATCCCCGG 62.320 72.222 0.00 0.0 43.21 5.73
1949 2344 3.373830 CTTCCTCCTCTCCACTCTCAAT 58.626 50.000 0.00 0.0 0.00 2.57
2021 2416 9.323985 GAATGTCTGCATTTCTAGAGAACTAAT 57.676 33.333 0.00 0.0 44.61 1.73
2536 2962 6.062749 TCTATCAAGTCATCTTACTAGCGGT 58.937 40.000 0.00 0.0 32.07 5.68
2769 4337 1.456705 CCCTCTCTTCCTCCCTCCG 60.457 68.421 0.00 0.0 0.00 4.63
3169 4785 1.908793 AGCTGTACACAGAGCCGGT 60.909 57.895 13.50 0.0 46.59 5.28
3208 4824 5.529060 GGACCAGATTGCTAATTTCTACCTG 59.471 44.000 0.00 0.0 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.358851 TCTGGTGAAAAAGACAAATTGCG 58.641 39.130 0.00 0.00 0.00 4.85
167 169 7.763985 AAAATTCATTTTTCACTTTCCGAGTGT 59.236 29.630 6.12 0.00 42.29 3.55
344 347 5.753438 GTGTTCATGGATACGAGCTATCAAA 59.247 40.000 0.00 0.00 42.51 2.69
710 723 4.931002 CACAATTGATCAAATGGTTGGGTC 59.069 41.667 23.86 0.00 29.16 4.46
814 831 4.954875 TCATTTTTCGAGTGCCCAAAATT 58.045 34.783 1.45 0.00 28.44 1.82
884 901 7.714813 TCACTAGATTTGGATCGCATTTTATGA 59.285 33.333 0.00 0.00 37.37 2.15
902 919 5.278957 GGCACCACACAAATTTTCACTAGAT 60.279 40.000 0.00 0.00 0.00 1.98
934 951 1.474320 CGGTGGGATCGGCTGAATTTA 60.474 52.381 0.00 0.00 0.00 1.40
968 1316 2.930562 GGAGGAGTGGGTGCTGGT 60.931 66.667 0.00 0.00 0.00 4.00
972 1320 4.459089 GCGAGGAGGAGTGGGTGC 62.459 72.222 0.00 0.00 0.00 5.01
978 1326 1.684049 CTGGAAGGCGAGGAGGAGT 60.684 63.158 0.00 0.00 0.00 3.85
1087 1446 2.721167 CGGGGTCGATGGAGAGCAA 61.721 63.158 0.00 0.00 40.14 3.91
1201 1560 4.170723 GTCGCAAGGAGAAGACGG 57.829 61.111 0.00 0.00 38.47 4.79
1506 1900 3.411351 GCACGTTCGTCGCCATGT 61.411 61.111 0.00 0.00 44.19 3.21
1622 2016 2.916269 AGGAAGGAAGGAAGGAAGGAAG 59.084 50.000 0.00 0.00 0.00 3.46
1623 2017 3.005529 AGGAAGGAAGGAAGGAAGGAA 57.994 47.619 0.00 0.00 0.00 3.36
1624 2018 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
1625 2019 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
1753 2147 2.492773 AAGCGCCTGCAAGCAAAGT 61.493 52.632 8.26 0.00 46.23 2.66
1850 2244 0.796927 GAGCGTCTTGTTGGGCTTAC 59.203 55.000 0.00 0.00 35.54 2.34
2536 2962 5.010820 TGCATGATCAAGGTCAATTGAACAA 59.989 36.000 24.89 10.58 42.77 2.83
2769 4337 1.405463 GGATCCAAACTCGAAATGCCC 59.595 52.381 6.95 0.00 0.00 5.36
2883 4499 3.616219 TGAACTGCTGGTTGTTGTTAGT 58.384 40.909 0.73 0.00 38.41 2.24
3169 4785 2.571653 CTGGTCCACCTCAATCTTACCA 59.428 50.000 0.00 0.00 36.82 3.25
3208 4824 4.907582 GCAAACAACGAAATGTACTGTACC 59.092 41.667 14.91 0.00 32.02 3.34
3301 4918 3.623060 GCAGACAACTGAAGACAACTGAA 59.377 43.478 0.00 0.00 46.03 3.02
3302 4919 3.118629 AGCAGACAACTGAAGACAACTGA 60.119 43.478 0.00 0.00 46.03 3.41
3303 4920 3.201290 AGCAGACAACTGAAGACAACTG 58.799 45.455 0.00 0.00 46.03 3.16
3304 4921 3.550437 AGCAGACAACTGAAGACAACT 57.450 42.857 0.00 0.00 46.03 3.16
3305 4922 5.931441 ATTAGCAGACAACTGAAGACAAC 57.069 39.130 0.00 0.00 46.03 3.32
3306 4923 5.277974 GCAATTAGCAGACAACTGAAGACAA 60.278 40.000 0.00 0.00 46.03 3.18


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

AutoCloner maintained by Alex Coulton.