Multiple sequence alignment - TraesCS3B01G429800

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 TraesCS3B01G429800 chr3B 100.000 2524 0 0 1 2524 669396467 669393944 0.000000e+00 4662
1 TraesCS3B01G429800 chr3B 89.077 1712 143 23 203 1876 246274084 246275789 0.000000e+00 2085
2 TraesCS3B01G429800 chr3B 93.237 207 11 1 5 208 377246255 377246049 4.080000e-78 302
3 TraesCS3B01G429800 chr4B 89.050 2338 209 23 3 2306 136097234 136099558 0.000000e+00 2856
4 TraesCS3B01G429800 chr5D 91.231 2121 150 23 203 2306 361378700 361380801 0.000000e+00 2854
5 TraesCS3B01G429800 chr5D 91.135 1692 125 13 625 2306 125554850 125553174 0.000000e+00 2270
6 TraesCS3B01G429800 chr5D 91.846 650 48 4 1658 2306 530656191 530655546 0.000000e+00 902
7 TraesCS3B01G429800 chr5D 92.823 209 12 1 2 207 125555680 125555472 1.470000e-77 300
8 TraesCS3B01G429800 chr1D 88.865 2371 167 45 203 2524 409935795 409933473 0.000000e+00 2826
9 TraesCS3B01G429800 chr1D 88.691 1910 156 36 2 1876 80778646 80776762 0.000000e+00 2276
10 TraesCS3B01G429800 chr1D 88.649 1762 150 29 2 1736 361507804 361509542 0.000000e+00 2100
11 TraesCS3B01G429800 chr1D 94.224 277 14 1 2248 2524 386743761 386744035 3.000000e-114 422
12 TraesCS3B01G429800 chr1D 94.182 275 14 1 2250 2524 250772194 250772466 3.880000e-113 418
13 TraesCS3B01G429800 chr7D 90.306 2125 150 27 203 2306 29347535 29349624 0.000000e+00 2732
14 TraesCS3B01G429800 chr7D 89.718 1702 141 20 203 1877 461787417 461789111 0.000000e+00 2143
15 TraesCS3B01G429800 chr7D 88.464 1725 128 28 203 1876 165224611 165222907 0.000000e+00 2017
16 TraesCS3B01G429800 chr7D 88.033 1713 152 24 203 1876 584364550 584362852 0.000000e+00 1978
17 TraesCS3B01G429800 chr7D 92.090 885 65 4 1424 2306 281452728 281451847 0.000000e+00 1242
18 TraesCS3B01G429800 chr3D 90.991 1998 140 21 539 2524 327716858 327718827 0.000000e+00 2656
19 TraesCS3B01G429800 chr2A 89.563 2127 176 26 203 2306 363692249 363690146 0.000000e+00 2656
20 TraesCS3B01G429800 chr2A 88.867 1545 147 16 203 1728 514289420 514290958 0.000000e+00 1877
21 TraesCS3B01G429800 chr2A 91.413 920 61 9 1612 2524 435085932 435085024 0.000000e+00 1245
22 TraesCS3B01G429800 chr2D 89.480 1635 137 22 203 1809 511279496 511281123 0.000000e+00 2034
23 TraesCS3B01G429800 chr2D 91.881 973 66 6 1341 2306 504125770 504124804 0.000000e+00 1347
24 TraesCS3B01G429800 chr6D 91.913 1385 89 16 932 2306 56950693 56949322 0.000000e+00 1916
25 TraesCS3B01G429800 chr6D 90.100 697 52 11 1612 2306 139950662 139951343 0.000000e+00 889
26 TraesCS3B01G429800 chr6D 89.894 564 31 8 1984 2524 126948518 126947958 0.000000e+00 702
27 TraesCS3B01G429800 chr6D 89.753 566 33 8 1984 2524 465238166 465238731 0.000000e+00 701
28 TraesCS3B01G429800 chr6D 96.029 277 9 1 2248 2524 56949338 56949064 1.380000e-122 449
29 TraesCS3B01G429800 chr6D 94.464 289 15 1 2236 2524 214765860 214765573 6.410000e-121 444
30 TraesCS3B01G429800 chr6D 93.502 277 16 1 2248 2524 9801589 9801315 6.500000e-111 411
31 TraesCS3B01G429800 chr6D 92.419 277 18 1 2248 2524 344611318 344611045 2.350000e-105 392
32 TraesCS3B01G429800 chr6D 92.419 277 15 2 2248 2524 11449114 11448844 8.470000e-105 390
33 TraesCS3B01G429800 chr6D 91.336 277 18 3 2248 2524 143365452 143365722 8.530000e-100 374
34 TraesCS3B01G429800 chr2B 90.634 1388 107 16 932 2306 604524682 604523305 0.000000e+00 1821
35 TraesCS3B01G429800 chr2B 90.113 971 75 10 2 954 604525590 604524623 0.000000e+00 1242
36 TraesCS3B01G429800 chr2B 89.397 962 80 11 2 947 504508720 504507765 0.000000e+00 1192
37 TraesCS3B01G429800 chr4D 90.360 1390 117 9 929 2306 394549107 394550491 0.000000e+00 1808
38 TraesCS3B01G429800 chr4D 93.966 348 18 2 2177 2524 450006198 450006542 8.000000e-145 523
39 TraesCS3B01G429800 chr6B 90.248 646 38 14 2 630 120041463 120042100 0.000000e+00 821
40 TraesCS3B01G429800 chr7B 93.301 209 11 1 2 207 117602481 117602273 3.150000e-79 305
41 TraesCS3B01G429800 chr3A 93.269 208 11 2 2 207 51344593 51344799 1.130000e-78 303
42 TraesCS3B01G429800 chr4A 92.308 208 14 1 2 207 33374968 33374761 6.830000e-76 294


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 TraesCS3B01G429800 chr3B 669393944 669396467 2523 True 4662.0 4662 100.0000 1 2524 1 chr3B.!!$R2 2523
1 TraesCS3B01G429800 chr3B 246274084 246275789 1705 False 2085.0 2085 89.0770 203 1876 1 chr3B.!!$F1 1673
2 TraesCS3B01G429800 chr4B 136097234 136099558 2324 False 2856.0 2856 89.0500 3 2306 1 chr4B.!!$F1 2303
3 TraesCS3B01G429800 chr5D 361378700 361380801 2101 False 2854.0 2854 91.2310 203 2306 1 chr5D.!!$F1 2103
4 TraesCS3B01G429800 chr5D 125553174 125555680 2506 True 1285.0 2270 91.9790 2 2306 2 chr5D.!!$R2 2304
5 TraesCS3B01G429800 chr5D 530655546 530656191 645 True 902.0 902 91.8460 1658 2306 1 chr5D.!!$R1 648
6 TraesCS3B01G429800 chr1D 409933473 409935795 2322 True 2826.0 2826 88.8650 203 2524 1 chr1D.!!$R2 2321
7 TraesCS3B01G429800 chr1D 80776762 80778646 1884 True 2276.0 2276 88.6910 2 1876 1 chr1D.!!$R1 1874
8 TraesCS3B01G429800 chr1D 361507804 361509542 1738 False 2100.0 2100 88.6490 2 1736 1 chr1D.!!$F2 1734
9 TraesCS3B01G429800 chr7D 29347535 29349624 2089 False 2732.0 2732 90.3060 203 2306 1 chr7D.!!$F1 2103
10 TraesCS3B01G429800 chr7D 461787417 461789111 1694 False 2143.0 2143 89.7180 203 1877 1 chr7D.!!$F2 1674
11 TraesCS3B01G429800 chr7D 165222907 165224611 1704 True 2017.0 2017 88.4640 203 1876 1 chr7D.!!$R1 1673
12 TraesCS3B01G429800 chr7D 584362852 584364550 1698 True 1978.0 1978 88.0330 203 1876 1 chr7D.!!$R3 1673
13 TraesCS3B01G429800 chr7D 281451847 281452728 881 True 1242.0 1242 92.0900 1424 2306 1 chr7D.!!$R2 882
14 TraesCS3B01G429800 chr3D 327716858 327718827 1969 False 2656.0 2656 90.9910 539 2524 1 chr3D.!!$F1 1985
15 TraesCS3B01G429800 chr2A 363690146 363692249 2103 True 2656.0 2656 89.5630 203 2306 1 chr2A.!!$R1 2103
16 TraesCS3B01G429800 chr2A 514289420 514290958 1538 False 1877.0 1877 88.8670 203 1728 1 chr2A.!!$F1 1525
17 TraesCS3B01G429800 chr2A 435085024 435085932 908 True 1245.0 1245 91.4130 1612 2524 1 chr2A.!!$R2 912
18 TraesCS3B01G429800 chr2D 511279496 511281123 1627 False 2034.0 2034 89.4800 203 1809 1 chr2D.!!$F1 1606
19 TraesCS3B01G429800 chr2D 504124804 504125770 966 True 1347.0 1347 91.8810 1341 2306 1 chr2D.!!$R1 965
20 TraesCS3B01G429800 chr6D 56949064 56950693 1629 True 1182.5 1916 93.9710 932 2524 2 chr6D.!!$R6 1592
21 TraesCS3B01G429800 chr6D 139950662 139951343 681 False 889.0 889 90.1000 1612 2306 1 chr6D.!!$F1 694
22 TraesCS3B01G429800 chr6D 126947958 126948518 560 True 702.0 702 89.8940 1984 2524 1 chr6D.!!$R3 540
23 TraesCS3B01G429800 chr6D 465238166 465238731 565 False 701.0 701 89.7530 1984 2524 1 chr6D.!!$F3 540
24 TraesCS3B01G429800 chr2B 604523305 604525590 2285 True 1531.5 1821 90.3735 2 2306 2 chr2B.!!$R2 2304
25 TraesCS3B01G429800 chr2B 504507765 504508720 955 True 1192.0 1192 89.3970 2 947 1 chr2B.!!$R1 945
26 TraesCS3B01G429800 chr4D 394549107 394550491 1384 False 1808.0 1808 90.3600 929 2306 1 chr4D.!!$F1 1377
27 TraesCS3B01G429800 chr6B 120041463 120042100 637 False 821.0 821 90.2480 2 630 1 chr6B.!!$F1 628

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
823 1096 0.528466 GCTCTGCATCGTTGGATCGA 60.528 55.0 0.0 0.0 43.86 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2675 0.320247 GCCGAGCCATAGACATCCTG 60.32 60.0 0.0 0.0 0.0 3.86 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
37 38 4.709397 TGAACCAACACTTGAAGTCCATTT 59.291 37.500 0.00 0.00 0.00 2.32
51 52 3.591527 AGTCCATTTCCCTATGGTGTGAA 59.408 43.478 0.00 0.00 44.48 3.18
171 174 3.434940 CCCAAGCTAGGGTAAACAACT 57.565 47.619 3.86 0.00 44.24 3.16
173 176 3.009143 CCCAAGCTAGGGTAAACAACTCT 59.991 47.826 3.86 0.00 44.24 3.24
305 501 2.246849 GGAACCCTACCTCCTCTCCTTA 59.753 54.545 0.00 0.00 0.00 2.69
579 793 2.056577 ACGAACGACGAAGGTTTCATC 58.943 47.619 0.00 0.00 45.77 2.92
592 813 7.969508 ACGAAGGTTTCATCTTTTTCGTTTTTA 59.030 29.630 4.46 0.00 45.52 1.52
635 908 1.132881 AGCCTTGGAAACCCCATTGAA 60.133 47.619 0.00 0.00 46.10 2.69
694 967 1.568504 ACCCTAGCTCCGAATGTCAA 58.431 50.000 0.00 0.00 0.00 3.18
823 1096 0.528466 GCTCTGCATCGTTGGATCGA 60.528 55.000 0.00 0.00 43.86 3.59
848 1121 3.147595 CCCGTGAGAGGCGATCCA 61.148 66.667 0.00 0.00 33.74 3.41
852 1125 1.511305 GTGAGAGGCGATCCACGAA 59.489 57.895 0.00 0.00 45.77 3.85
911 1205 2.233676 TCTTCTGCTGCTTATTCCACGA 59.766 45.455 0.00 0.00 0.00 4.35
930 1224 2.041115 CGACGAGAGGAGCCACTCA 61.041 63.158 13.20 0.00 39.97 3.41
947 1247 5.792741 CCACTCATCTGTTTCTTCTTCTCT 58.207 41.667 0.00 0.00 0.00 3.10
968 1268 1.670949 GCGATGAGAGGAGCCACTCA 61.671 60.000 17.01 17.01 44.94 3.41
1025 1333 2.596851 GCTCCACTTCAGCCTCCCA 61.597 63.158 0.00 0.00 0.00 4.37
1147 1455 0.739462 CAACTATGGGCGCGAGTTCA 60.739 55.000 12.10 1.32 31.04 3.18
1335 1650 2.767394 CAGATTCAATTCAATGGGGCCA 59.233 45.455 4.39 0.00 0.00 5.36
1357 1672 2.739996 CCCGGGAGCTCAATCTGCT 61.740 63.158 18.48 0.00 44.24 4.24
1398 1713 0.954449 CTGTGGAAGTGCTGCTCTGG 60.954 60.000 4.83 0.00 0.00 3.86
1487 1802 5.243507 TCAATTGAACAAGCAGGCAAATCTA 59.756 36.000 5.45 0.00 0.00 1.98
1584 1902 7.648112 TCGTTAGAGATGTTATTAGTGTGATGC 59.352 37.037 0.00 0.00 0.00 3.91
1629 1947 8.408601 GTTAAATTTGTGGATCATGTGCTCTAT 58.591 33.333 0.00 0.00 0.00 1.98
1728 2046 7.392953 TCTGTGTTGCTTAATTTGTGGATCATA 59.607 33.333 0.00 0.00 0.00 2.15
1730 2048 8.530311 TGTGTTGCTTAATTTGTGGATCATATT 58.470 29.630 0.00 0.00 33.59 1.28
1773 2128 7.253422 ACACTTTCAGTTTCTTCAGTTTCATG 58.747 34.615 0.00 0.00 0.00 3.07
1824 2184 5.206905 ACATAGTTCTAGGGCCCAAATTT 57.793 39.130 27.56 4.81 0.00 1.82
1911 2271 2.351726 CCTAGAAAATAGTGCACACGCC 59.648 50.000 21.04 2.79 37.32 5.68
1974 2339 1.576356 TTGCCATGCCGAACAAAAAC 58.424 45.000 0.00 0.00 0.00 2.43
1976 2341 1.134699 TGCCATGCCGAACAAAAACAA 60.135 42.857 0.00 0.00 0.00 2.83
2070 2439 6.570672 TCCTTCTGTATATAGCCTACAACG 57.429 41.667 0.00 0.00 0.00 4.10
2248 2657 0.620556 AGTCCAGTGGCACCATTAGG 59.379 55.000 15.27 9.02 42.21 2.69
2266 2675 6.344500 CATTAGGCACCATATCCATCTAGAC 58.656 44.000 0.00 0.00 0.00 2.59
2269 2678 3.055530 GGCACCATATCCATCTAGACAGG 60.056 52.174 0.00 0.00 0.00 4.00
2317 2768 7.068716 CACCATATCCATCTACCGATATCTCAA 59.931 40.741 0.34 0.00 30.85 3.02
2427 2884 9.869757 ATAGGCCACAAACTATTCAAAAATTAC 57.130 29.630 5.01 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.934083 AGTGTTGGTTCAAATTCAAAGTTTGT 59.066 30.769 15.08 0.00 37.70 2.83
37 38 3.448093 TTGCAATTCACACCATAGGGA 57.552 42.857 0.00 0.00 38.05 4.20
66 67 9.661563 TTGATCACCTAACGTTCATAATAGTTT 57.338 29.630 2.82 0.00 0.00 2.66
76 77 3.777478 TCGGATTGATCACCTAACGTTC 58.223 45.455 2.82 0.00 0.00 3.95
197 375 8.848474 TCTGAACTTAGTTTTCCATTTAGAGG 57.152 34.615 0.00 0.00 0.00 3.69
283 479 0.338814 GGAGAGGAGGTAGGGTTCCA 59.661 60.000 0.00 0.00 35.88 3.53
385 585 4.646945 TGTGTGACATGTTACCAACCAAAT 59.353 37.500 17.24 0.00 0.00 2.32
592 813 7.814587 GGCTTTGAGTGAGCATAACTAATTTTT 59.185 33.333 0.00 0.00 41.89 1.94
610 831 0.969149 GGGGTTTCCAAGGCTTTGAG 59.031 55.000 10.61 0.41 36.36 3.02
635 908 2.956333 GTTTACAGGGGTTTTGAGCTGT 59.044 45.455 0.00 0.00 0.00 4.40
694 967 1.906990 CTAGGGTATGATCGGACGGT 58.093 55.000 0.00 0.00 0.00 4.83
848 1121 2.365582 AGCACAACCAAGAACTTTCGT 58.634 42.857 0.00 0.00 0.00 3.85
852 1125 2.430694 GGGAAAGCACAACCAAGAACTT 59.569 45.455 0.00 0.00 0.00 2.66
911 1205 2.034376 AGTGGCTCCTCTCGTCGT 59.966 61.111 0.00 0.00 0.00 4.34
930 1224 3.259374 TCGCCAGAGAAGAAGAAACAGAT 59.741 43.478 0.00 0.00 0.00 2.90
968 1268 1.021390 CGCCGGAAGAAGAAGCACAT 61.021 55.000 5.05 0.00 0.00 3.21
970 1270 0.741221 ATCGCCGGAAGAAGAAGCAC 60.741 55.000 5.05 0.00 0.00 4.40
1025 1333 2.177529 ATACTGGGTCCACGAGGGGT 62.178 60.000 0.00 0.00 37.22 4.95
1051 1359 0.107214 GGACATCGCTCCATGGGAAA 60.107 55.000 13.02 0.00 41.04 3.13
1228 1536 5.536951 TGAACCATAAATCCATCCCCAATT 58.463 37.500 0.00 0.00 0.00 2.32
1229 1537 5.155035 TGAACCATAAATCCATCCCCAAT 57.845 39.130 0.00 0.00 0.00 3.16
1232 1540 4.482990 ACATGAACCATAAATCCATCCCC 58.517 43.478 0.00 0.00 0.00 4.81
1233 1541 6.484364 AAACATGAACCATAAATCCATCCC 57.516 37.500 0.00 0.00 0.00 3.85
1234 1542 6.697019 CGAAAACATGAACCATAAATCCATCC 59.303 38.462 0.00 0.00 0.00 3.51
1235 1543 7.257722 ACGAAAACATGAACCATAAATCCATC 58.742 34.615 0.00 0.00 0.00 3.51
1236 1544 7.169158 ACGAAAACATGAACCATAAATCCAT 57.831 32.000 0.00 0.00 0.00 3.41
1245 1560 5.559991 CGATCTGAAACGAAAACATGAACCA 60.560 40.000 0.00 0.00 0.00 3.67
1335 1650 1.201429 AGATTGAGCTCCCGGGTTGT 61.201 55.000 22.86 5.54 0.00 3.32
1381 1696 2.331132 GCCAGAGCAGCACTTCCAC 61.331 63.158 0.00 0.00 39.53 4.02
1398 1713 0.106819 AGATCTGCATCCCCAACTGC 60.107 55.000 0.00 0.00 38.87 4.40
1527 1845 4.943705 CCAGCAAGTAAGCAAATCCTAGAA 59.056 41.667 0.00 0.00 36.85 2.10
1584 1902 3.287867 ACCAAATCCTAGAGCACATGG 57.712 47.619 0.00 0.00 0.00 3.66
1773 2128 2.022129 CTGCGGTCGGTGTTGTCTC 61.022 63.158 0.00 0.00 0.00 3.36
1824 2184 2.290705 GGCCCAACCAGAGCTTAGTTTA 60.291 50.000 0.00 0.00 38.86 2.01
1974 2339 8.975410 ATAAATCGATTTACCATCATGCATTG 57.025 30.769 28.12 0.00 35.31 2.82
1976 2341 8.579006 ACAATAAATCGATTTACCATCATGCAT 58.421 29.630 28.12 10.43 35.31 3.96
2248 2657 3.834813 TCCTGTCTAGATGGATATGGTGC 59.165 47.826 11.87 0.00 0.00 5.01
2266 2675 0.320247 GCCGAGCCATAGACATCCTG 60.320 60.000 0.00 0.00 0.00 3.86
2269 2678 1.401670 CGTAGCCGAGCCATAGACATC 60.402 57.143 0.00 0.00 35.63 3.06
2317 2768 5.928976 TGTTATGGATGTATGCTTGCTACT 58.071 37.500 0.00 0.00 0.00 2.57
2451 2908 2.685106 TTGTTGGTGGCCCTATTTCA 57.315 45.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.