Multiple sequence alignment - TraesCS3B01G502700

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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 TraesCS3B01G502700 chr3B 100.000 4462 0 0 1 4462 746857492 746853031 0.000000e+00 8240.0
1 TraesCS3B01G502700 chr3B 96.556 4500 83 21 1 4462 744589469 744593934 0.000000e+00 7385.0
2 TraesCS3B01G502700 chr3B 84.170 1434 171 28 1058 2457 745203453 745202042 0.000000e+00 1339.0
3 TraesCS3B01G502700 chr3B 83.982 1361 159 32 1062 2400 745540068 745541391 0.000000e+00 1251.0
4 TraesCS3B01G502700 chr3B 86.861 1134 115 13 1049 2150 745474960 745473829 0.000000e+00 1238.0
5 TraesCS3B01G502700 chr3B 86.593 1089 138 6 1067 2150 747492983 747494068 0.000000e+00 1195.0
6 TraesCS3B01G502700 chr3B 86.501 1089 139 6 1067 2150 744419917 744418832 0.000000e+00 1190.0
7 TraesCS3B01G502700 chr3B 82.208 1422 199 29 1047 2417 744728492 744729910 0.000000e+00 1175.0
8 TraesCS3B01G502700 chr3B 82.194 1404 197 28 1047 2400 744847065 744848465 0.000000e+00 1158.0
9 TraesCS3B01G502700 chr3B 84.643 1120 150 17 1052 2150 744512987 744511869 0.000000e+00 1096.0
10 TraesCS3B01G502700 chr3B 89.024 574 53 5 2914 3481 746792901 746792332 0.000000e+00 702.0
11 TraesCS3B01G502700 chr3B 84.047 514 66 8 2972 3470 746286471 746286983 8.680000e-132 481.0
12 TraesCS3B01G502700 chr3B 85.177 452 62 4 3026 3473 744339123 744338673 4.070000e-125 459.0
13 TraesCS3B01G502700 chr3B 86.239 218 26 4 2216 2432 744511625 744511411 2.680000e-57 233.0
14 TraesCS3B01G502700 chr3B 83.401 247 34 4 2218 2457 745473740 745473494 5.810000e-54 222.0
15 TraesCS3B01G502700 chr3B 79.874 318 23 21 3682 3985 746853465 746853175 1.270000e-45 195.0
16 TraesCS3B01G502700 chr3B 79.874 318 23 21 4028 4318 746853811 746853508 1.270000e-45 195.0
17 TraesCS3B01G502700 chr3B 78.995 219 21 16 3781 3985 744593583 744593790 4.690000e-25 126.0
18 TraesCS3B01G502700 chr3B 77.778 207 28 13 3660 3854 746849093 746849293 1.310000e-20 111.0
19 TraesCS3B01G502700 chr3B 77.295 207 29 14 3660 3854 744597055 744596855 6.100000e-19 106.0
20 TraesCS3B01G502700 chr3B 89.655 58 6 0 3485 3542 744852436 744852379 1.720000e-09 75.0
21 TraesCS3B01G502700 chr3B 89.091 55 6 0 3488 3542 746295396 746295342 8.010000e-08 69.4
22 TraesCS3B01G502700 chr3B 86.441 59 5 2 523 581 744590082 744590137 1.340000e-05 62.1
23 TraesCS3B01G502700 chr3B 86.441 59 5 2 523 581 746856878 746856823 1.340000e-05 62.1
24 TraesCS3B01G502700 chr3B 86.441 59 5 2 615 670 746856970 746856912 1.340000e-05 62.1
25 TraesCS3B01G502700 chr3D 92.929 1584 68 10 1049 2606 560331064 560332629 0.000000e+00 2265.0
26 TraesCS3B01G502700 chr3D 86.101 1439 152 28 976 2392 560477644 560479056 0.000000e+00 1506.0
27 TraesCS3B01G502700 chr3D 84.400 1359 175 25 1061 2400 560826822 560828162 0.000000e+00 1301.0
28 TraesCS3B01G502700 chr3D 84.245 1371 169 25 1072 2400 560235163 560233798 0.000000e+00 1291.0
29 TraesCS3B01G502700 chr3D 93.288 879 33 4 2608 3481 560332722 560333579 0.000000e+00 1273.0
30 TraesCS3B01G502700 chr3D 84.472 1230 157 18 1220 2417 560640212 560641439 0.000000e+00 1182.0
31 TraesCS3B01G502700 chr3D 88.014 584 52 8 2907 3481 560479168 560479742 0.000000e+00 675.0
32 TraesCS3B01G502700 chr3D 84.047 514 66 8 2972 3470 560553062 560553574 8.680000e-132 481.0
33 TraesCS3B01G502700 chr3D 85.523 449 59 4 3026 3470 560197550 560197104 8.740000e-127 464.0
34 TraesCS3B01G502700 chr3D 92.788 208 14 1 3485 3692 560333632 560333838 2.610000e-77 300.0
35 TraesCS3B01G502700 chr3D 93.229 192 11 2 3728 3919 560333839 560334028 9.450000e-72 281.0
36 TraesCS3B01G502700 chr3D 84.270 267 34 5 2208 2467 560784653 560784388 2.060000e-63 254.0
37 TraesCS3B01G502700 chr3D 86.190 210 16 7 3663 3867 560334178 560334379 9.720000e-52 215.0
38 TraesCS3B01G502700 chr3D 84.259 216 17 6 2637 2836 437486160 437486374 1.270000e-45 195.0
39 TraesCS3B01G502700 chr3D 81.641 256 25 12 3668 3918 560754904 560755142 4.550000e-45 193.0
40 TraesCS3B01G502700 chr3D 85.792 183 14 6 4028 4198 560334197 560334379 2.740000e-42 183.0
41 TraesCS3B01G502700 chr3D 94.737 114 6 0 3916 4029 560334054 560334167 1.280000e-40 178.0
42 TraesCS3B01G502700 chr3D 97.938 97 2 0 963 1059 560330951 560331047 7.680000e-38 169.0
43 TraesCS3B01G502700 chr3D 84.076 157 11 6 4089 4237 560333866 560334016 6.020000e-29 139.0
44 TraesCS3B01G502700 chr3D 82.895 152 19 4 4089 4234 560480025 560480175 3.620000e-26 130.0
45 TraesCS3B01G502700 chr3D 91.566 83 7 0 2068 2150 560268617 560268535 1.010000e-21 115.0
46 TraesCS3B01G502700 chr3D 89.091 55 6 0 3488 3542 560556237 560556183 8.010000e-08 69.4
47 TraesCS3B01G502700 chr6B 96.344 930 32 2 5 933 720199040 720199968 0.000000e+00 1528.0
48 TraesCS3B01G502700 chr6B 94.640 541 28 1 407 946 688883150 688882610 0.000000e+00 837.0
49 TraesCS3B01G502700 chr6B 95.135 370 18 0 1 370 688883723 688883354 6.430000e-163 584.0
50 TraesCS3B01G502700 chr6B 86.441 59 5 2 523 581 688882942 688882887 1.340000e-05 62.1
51 TraesCS3B01G502700 chr6B 86.441 59 5 2 523 581 720199650 720199705 1.340000e-05 62.1
52 TraesCS3B01G502700 chr5B 95.284 933 43 1 4 936 56826921 56825990 0.000000e+00 1478.0
53 TraesCS3B01G502700 chr5B 88.136 59 4 2 615 670 56826403 56826345 2.880000e-07 67.6
54 TraesCS3B01G502700 chr4B 94.612 928 38 6 4 931 619785548 619786463 0.000000e+00 1426.0
55 TraesCS3B01G502700 chr4B 76.309 363 77 8 1 360 101774467 101774111 7.620000e-43 185.0
56 TraesCS3B01G502700 chr3A 86.410 1089 140 6 1067 2150 629086951 629088036 0.000000e+00 1184.0
57 TraesCS3B01G502700 chr3A 86.318 1089 141 6 1067 2150 696333014 696331929 0.000000e+00 1179.0
58 TraesCS3B01G502700 chr3A 81.979 1132 144 32 1043 2150 696344907 696343812 0.000000e+00 905.0
59 TraesCS3B01G502700 chr3A 81.026 838 117 21 1635 2432 629019536 629018701 2.930000e-176 628.0
60 TraesCS3B01G502700 chr3A 80.499 841 117 23 1635 2432 696270292 696269456 6.390000e-168 601.0
61 TraesCS3B01G502700 chr3A 85.969 449 58 4 3026 3470 696288811 696288364 4.040000e-130 475.0
62 TraesCS3B01G502700 chr3A 87.054 224 28 1 2234 2457 696476928 696476706 7.410000e-63 252.0
63 TraesCS3B01G502700 chr1A 82.202 545 83 11 12 551 381817146 381816611 1.460000e-124 457.0
64 TraesCS3B01G502700 chr1A 80.473 169 23 7 765 926 381319455 381319290 2.180000e-23 121.0
65 TraesCS3B01G502700 chr1A 94.545 55 3 0 2582 2636 547376775 547376829 7.950000e-13 86.1
66 TraesCS3B01G502700 chr1D 81.647 425 70 6 3 423 489445013 489444593 3.300000e-91 346.0
67 TraesCS3B01G502700 chr4D 82.073 357 59 2 5 360 503366643 503366291 2.610000e-77 300.0
68 TraesCS3B01G502700 chr2B 75.770 487 99 17 5 484 53910539 53910065 1.250000e-55 228.0
69 TraesCS3B01G502700 chr1B 91.429 70 6 0 2515 2584 622620270 622620339 3.670000e-16 97.1
70 TraesCS3B01G502700 chr1B 97.222 36 1 0 4355 4390 638893351 638893316 1.340000e-05 62.1


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 TraesCS3B01G502700 chr3B 746853031 746857492 4461 True 8240.000000 8240 100.000000 1 4462 1 chr3B.!!$R8 4461
1 TraesCS3B01G502700 chr3B 744589469 744593934 4465 False 2524.366667 7385 87.330667 1 4462 3 chr3B.!!$F7 4461
2 TraesCS3B01G502700 chr3B 745202042 745203453 1411 True 1339.000000 1339 84.170000 1058 2457 1 chr3B.!!$R5 1399
3 TraesCS3B01G502700 chr3B 745540068 745541391 1323 False 1251.000000 1251 83.982000 1062 2400 1 chr3B.!!$F3 1338
4 TraesCS3B01G502700 chr3B 747492983 747494068 1085 False 1195.000000 1195 86.593000 1067 2150 1 chr3B.!!$F6 1083
5 TraesCS3B01G502700 chr3B 744418832 744419917 1085 True 1190.000000 1190 86.501000 1067 2150 1 chr3B.!!$R2 1083
6 TraesCS3B01G502700 chr3B 744728492 744729910 1418 False 1175.000000 1175 82.208000 1047 2417 1 chr3B.!!$F1 1370
7 TraesCS3B01G502700 chr3B 744847065 744848465 1400 False 1158.000000 1158 82.194000 1047 2400 1 chr3B.!!$F2 1353
8 TraesCS3B01G502700 chr3B 745473494 745474960 1466 True 730.000000 1238 85.131000 1049 2457 2 chr3B.!!$R10 1408
9 TraesCS3B01G502700 chr3B 746792332 746792901 569 True 702.000000 702 89.024000 2914 3481 1 chr3B.!!$R7 567
10 TraesCS3B01G502700 chr3B 744511411 744512987 1576 True 664.500000 1096 85.441000 1052 2432 2 chr3B.!!$R9 1380
11 TraesCS3B01G502700 chr3B 746286471 746286983 512 False 481.000000 481 84.047000 2972 3470 1 chr3B.!!$F4 498
12 TraesCS3B01G502700 chr3D 560826822 560828162 1340 False 1301.000000 1301 84.400000 1061 2400 1 chr3D.!!$F5 1339
13 TraesCS3B01G502700 chr3D 560233798 560235163 1365 True 1291.000000 1291 84.245000 1072 2400 1 chr3D.!!$R2 1328
14 TraesCS3B01G502700 chr3D 560640212 560641439 1227 False 1182.000000 1182 84.472000 1220 2417 1 chr3D.!!$F3 1197
15 TraesCS3B01G502700 chr3D 560477644 560480175 2531 False 770.333333 1506 85.670000 976 4234 3 chr3D.!!$F7 3258
16 TraesCS3B01G502700 chr3D 560330951 560334379 3428 False 555.888889 2265 91.218556 963 4237 9 chr3D.!!$F6 3274
17 TraesCS3B01G502700 chr3D 560553062 560553574 512 False 481.000000 481 84.047000 2972 3470 1 chr3D.!!$F2 498
18 TraesCS3B01G502700 chr6B 720199040 720199968 928 False 795.050000 1528 91.392500 5 933 2 chr6B.!!$F1 928
19 TraesCS3B01G502700 chr6B 688882610 688883723 1113 True 494.366667 837 92.072000 1 946 3 chr6B.!!$R1 945
20 TraesCS3B01G502700 chr5B 56825990 56826921 931 True 772.800000 1478 91.710000 4 936 2 chr5B.!!$R1 932
21 TraesCS3B01G502700 chr4B 619785548 619786463 915 False 1426.000000 1426 94.612000 4 931 1 chr4B.!!$F1 927
22 TraesCS3B01G502700 chr3A 629086951 629088036 1085 False 1184.000000 1184 86.410000 1067 2150 1 chr3A.!!$F1 1083
23 TraesCS3B01G502700 chr3A 696331929 696333014 1085 True 1179.000000 1179 86.318000 1067 2150 1 chr3A.!!$R4 1083
24 TraesCS3B01G502700 chr3A 696343812 696344907 1095 True 905.000000 905 81.979000 1043 2150 1 chr3A.!!$R5 1107
25 TraesCS3B01G502700 chr3A 629018701 629019536 835 True 628.000000 628 81.026000 1635 2432 1 chr3A.!!$R1 797
26 TraesCS3B01G502700 chr3A 696269456 696270292 836 True 601.000000 601 80.499000 1635 2432 1 chr3A.!!$R2 797
27 TraesCS3B01G502700 chr1A 381816611 381817146 535 True 457.000000 457 82.202000 12 551 1 chr1A.!!$R2 539

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
903 1073 0.110509 GCGGACGCATGAGCATTATG 60.111 55.0 12.31 0.0 42.27 1.90 F
2752 3369 0.035915 TTACCATAGCAGCCACGCAA 60.036 50.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2836 3458 1.131303 TTGAACCCTCCACCGGATGT 61.131 55.0 9.46 0.0 0.0 3.06 R
4402 5175 0.102481 CAACGACGCCTACCTAGCAT 59.898 55.0 0.00 0.0 0.0 3.79 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
174 176 4.929479 ACAAATAACACTCTTGCCCCATA 58.071 39.130 0.00 0.00 0.00 2.74
256 258 1.517242 CGGCATCCTGGAGCTAAATC 58.483 55.000 14.77 1.64 0.00 2.17
431 600 5.843019 TTCCTCTTAGTTCACAATCCCTT 57.157 39.130 0.00 0.00 0.00 3.95
751 921 0.249489 GCCACACGAGTCAACTGAGT 60.249 55.000 0.00 0.00 0.00 3.41
757 927 1.286260 GAGTCAACTGAGTCGCGGT 59.714 57.895 6.13 0.00 35.12 5.68
903 1073 0.110509 GCGGACGCATGAGCATTATG 60.111 55.000 12.31 0.00 42.27 1.90
1479 1717 2.202932 CATCTGCTTCCGGACGGG 60.203 66.667 1.83 0.00 35.59 5.28
2111 2412 2.358737 GCGTGCACCTAACCTGCT 60.359 61.111 12.15 0.00 35.53 4.24
2539 3062 6.226787 AGTGATAGAAACAGAGTTTGACTGG 58.773 40.000 0.00 0.00 39.38 4.00
2728 3345 4.530710 TGGTTCTAAATACACGTCTGCT 57.469 40.909 0.00 0.00 0.00 4.24
2752 3369 0.035915 TTACCATAGCAGCCACGCAA 60.036 50.000 0.00 0.00 0.00 4.85
2757 3379 2.184020 ATAGCAGCCACGCAACAGGA 62.184 55.000 0.00 0.00 0.00 3.86
2790 3412 4.008074 TGGATAGCCTATTAGCAAGTGC 57.992 45.455 0.00 0.00 36.77 4.40
2836 3458 7.812690 TTACCGTCTTAGCAGAATCATAGTA 57.187 36.000 0.00 0.00 0.00 1.82
2884 3506 4.760204 GTGTAGCCTGTCTGGTAATTTTGT 59.240 41.667 0.00 0.00 38.35 2.83
2910 3532 4.883083 ACCAGTGTCCATGTTATATAGCG 58.117 43.478 0.00 0.00 0.00 4.26
2970 3592 1.136305 CTTGGCATGCTGCTGCTATTT 59.864 47.619 18.92 0.00 44.28 1.40
3173 3806 0.251253 AGTTCCGAGGGTCGAGAAGT 60.251 55.000 0.00 0.83 43.74 3.01
3398 4038 2.349886 CCACGAACTAGCTGCTGATTTC 59.650 50.000 13.43 10.50 0.00 2.17
3570 4264 3.770765 CGCATAACGCATCGAATTAGT 57.229 42.857 0.00 0.00 42.60 2.24
3573 4267 4.317769 CGCATAACGCATCGAATTAGTTCA 60.318 41.667 0.00 0.00 42.60 3.18
3771 4465 4.640771 TTAGGTTGGTCTCAGCTCAAAT 57.359 40.909 0.00 0.00 0.00 2.32
3777 4471 4.890158 TGGTCTCAGCTCAAATGAGTAA 57.110 40.909 11.77 0.00 43.79 2.24
3831 4525 9.139174 TCTTCAGTTTTGATTTTCACAAACTTC 57.861 29.630 11.57 0.00 36.52 3.01
3836 4530 9.573133 AGTTTTGATTTTCACAAACTTCTACTG 57.427 29.630 0.00 0.00 35.88 2.74
3996 4726 3.058293 TCATTCACGCTGGAAATGTCAAC 60.058 43.478 0.00 0.00 0.00 3.18
4222 4995 3.609853 CAATTTCACGGAGATCAGGGAA 58.390 45.455 0.00 0.00 31.81 3.97
4224 4997 2.762535 TTCACGGAGATCAGGGAAAC 57.237 50.000 0.00 0.00 30.78 2.78
4248 5021 6.645003 ACCTTCACAAAACAAGAAAAGTTGTC 59.355 34.615 0.00 0.00 39.82 3.18
4402 5175 2.847234 AGGCCAACTCGGTGGTGA 60.847 61.111 5.01 0.00 41.12 4.02
4451 5224 2.037902 TGTATGAAGGAAGTGGCGTCAA 59.962 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.816640 AGACGACGGATAAAATCAGAAAATCA 59.183 34.615 0.00 0.00 0.00 2.57
218 220 2.100991 CGGCGAGCTGATTTTGCC 59.899 61.111 0.00 0.00 40.99 4.52
256 258 3.667960 GCCATAGTGTTGCAGAAACTTCG 60.668 47.826 3.70 0.00 39.70 3.79
751 921 0.457166 CAACTGGATAACGACCGCGA 60.457 55.000 8.23 0.00 41.64 5.87
757 927 2.442212 TTCGTGCAACTGGATAACGA 57.558 45.000 0.00 0.00 41.12 3.85
898 1068 5.104900 AGCTTACCTTCAACCGACTCATAAT 60.105 40.000 0.00 0.00 0.00 1.28
903 1073 2.745515 AGCTTACCTTCAACCGACTC 57.254 50.000 0.00 0.00 0.00 3.36
938 1108 5.450412 GCTGGATCTTTGTTGTCTCAAACAA 60.450 40.000 0.00 0.00 45.77 2.83
2111 2412 3.201930 TGGCTTAAGATATCCCAGCACAA 59.798 43.478 6.67 3.50 31.71 3.33
2539 3062 7.441458 ACACTAAGGAAATCACAACTACAGTTC 59.559 37.037 0.00 0.00 35.83 3.01
2728 3345 1.209504 GTGGCTGCTATGGTAAGTGGA 59.790 52.381 0.00 0.00 0.00 4.02
2752 3369 3.576078 TCCAAGTGTGACAAATCCTGT 57.424 42.857 0.00 0.00 42.61 4.00
2757 3379 4.307032 AGGCTATCCAAGTGTGACAAAT 57.693 40.909 0.00 0.00 33.74 2.32
2790 3412 2.987149 AGACGCGATACAAAACAGAGTG 59.013 45.455 15.93 0.00 0.00 3.51
2836 3458 1.131303 TTGAACCCTCCACCGGATGT 61.131 55.000 9.46 0.00 0.00 3.06
2884 3506 8.248253 CGCTATATAACATGGACACTGGTATTA 58.752 37.037 0.00 0.00 29.57 0.98
2910 3532 5.053145 AGTCTGATTCACAGTTCTGACAAC 58.947 41.667 6.83 0.00 45.86 3.32
2970 3592 3.899980 AGGACATATCATGCAGCAGTAGA 59.100 43.478 0.00 0.00 0.00 2.59
3899 4600 7.559590 ACTTGTGATATTGATCCTGTTTAGC 57.440 36.000 0.00 0.00 0.00 3.09
3996 4726 0.602638 TTCGTAGTGCACTTGCTGGG 60.603 55.000 27.06 8.28 42.66 4.45
4081 4842 4.193826 TGAGCTGAGACCAACAGATTAC 57.806 45.455 0.00 0.00 37.54 1.89
4222 4995 6.989759 ACAACTTTTCTTGTTTTGTGAAGGTT 59.010 30.769 0.00 0.00 29.66 3.50
4224 4997 6.090763 GGACAACTTTTCTTGTTTTGTGAAGG 59.909 38.462 0.00 0.00 34.40 3.46
4248 5021 4.262377 CCATGCTCAACCTCTGATACTAGG 60.262 50.000 0.00 0.00 38.93 3.02
4390 5163 0.537188 CCTAGCATCACCACCGAGTT 59.463 55.000 0.00 0.00 0.00 3.01
4402 5175 0.102481 CAACGACGCCTACCTAGCAT 59.898 55.000 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.