Multiple sequence alignment - TraesCS1B01G135000

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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 TraesCS1B01G135000 chr1B 100.000 5018 0 0 1 5018 171616324 171621341 0.000000e+00 9267
1 TraesCS1B01G135000 chr1B 88.406 207 19 4 538 742 171614772 171614569 1.400000e-60 244
2 TraesCS1B01G135000 chr1D 96.719 2530 60 13 1698 4214 112352188 112354707 0.000000e+00 4191
3 TraesCS1B01G135000 chr1D 96.774 961 27 2 750 1706 112351073 112352033 0.000000e+00 1600
4 TraesCS1B01G135000 chr1A 95.580 2534 68 12 750 3256 119493425 119495941 0.000000e+00 4019
5 TraesCS1B01G135000 chr1A 95.747 917 36 2 3300 4214 119495937 119496852 0.000000e+00 1474
6 TraesCS1B01G135000 chr1A 92.173 741 25 4 1 741 440682270 440682977 0.000000e+00 1016
7 TraesCS1B01G135000 chr2A 99.602 754 1 2 1 752 513651698 513652451 0.000000e+00 1375
8 TraesCS1B01G135000 chr2A 86.640 247 28 3 498 742 404907679 404907436 8.280000e-68 268
9 TraesCS1B01G135000 chr2A 86.235 247 29 3 498 742 396204300 396204543 3.850000e-66 263
10 TraesCS1B01G135000 chr5B 100.000 743 0 0 1 743 639133740 639134482 0.000000e+00 1373
11 TraesCS1B01G135000 chr5B 93.587 499 28 3 4215 4710 532532661 532532164 0.000000e+00 741
12 TraesCS1B01G135000 chr5B 88.406 207 19 4 538 742 639129756 639129553 1.400000e-60 244
13 TraesCS1B01G135000 chr5A 99.866 745 1 0 1 745 341141136 341140392 0.000000e+00 1371
14 TraesCS1B01G135000 chr5A 88.406 207 19 4 538 742 341142802 341143005 1.400000e-60 244
15 TraesCS1B01G135000 chr3A 99.866 745 1 0 1 745 363422886 363422142 0.000000e+00 1371
16 TraesCS1B01G135000 chr6A 82.453 1060 121 30 3185 4214 524767280 524768304 0.000000e+00 867
17 TraesCS1B01G135000 chr6A 86.022 744 79 19 986 1719 524764075 524764803 0.000000e+00 774
18 TraesCS1B01G135000 chr6A 90.890 483 36 4 2665 3140 524766377 524766858 4.240000e-180 641
19 TraesCS1B01G135000 chr6A 80.866 439 48 19 2174 2584 524765794 524766224 3.770000e-81 313
20 TraesCS1B01G135000 chr6B 87.821 739 73 11 998 1727 572402086 572402816 0.000000e+00 850
21 TraesCS1B01G135000 chr6B 81.896 1055 131 27 3185 4214 572405022 572406041 0.000000e+00 835
22 TraesCS1B01G135000 chr6B 94.366 497 27 1 4215 4710 459202326 459202822 0.000000e+00 761
23 TraesCS1B01G135000 chr6B 93.173 498 34 0 4213 4710 683181217 683180720 0.000000e+00 732
24 TraesCS1B01G135000 chr6B 92.972 498 35 0 4213 4710 683150758 683150261 0.000000e+00 726
25 TraesCS1B01G135000 chr6B 90.685 365 27 5 2665 3026 572404035 572404395 3.510000e-131 479
26 TraesCS1B01G135000 chr6B 93.949 314 15 4 4708 5018 149527709 149528021 5.880000e-129 472
27 TraesCS1B01G135000 chr6B 83.066 437 39 17 2170 2584 572403458 572403881 1.030000e-96 364
28 TraesCS1B01G135000 chr6B 91.597 119 7 3 3025 3140 572404477 572404595 1.450000e-35 161
29 TraesCS1B01G135000 chr6D 81.792 1060 125 33 3185 4214 382624705 382625726 0.000000e+00 826
30 TraesCS1B01G135000 chr6D 86.174 745 76 21 986 1719 382621479 382622207 0.000000e+00 780
31 TraesCS1B01G135000 chr6D 90.683 483 37 4 2665 3140 382623802 382624283 1.970000e-178 636
32 TraesCS1B01G135000 chr6D 80.787 432 49 22 2174 2579 382623220 382623643 1.750000e-79 307
33 TraesCS1B01G135000 chr2B 95.181 498 20 4 4215 4710 107113612 107113117 0.000000e+00 784
34 TraesCS1B01G135000 chr2B 92.986 499 33 1 4214 4710 665917738 665917240 0.000000e+00 726
35 TraesCS1B01G135000 chr2B 96.178 314 9 3 4707 5018 107113061 107112749 1.250000e-140 510
36 TraesCS1B01G135000 chr2B 95.527 313 11 3 4708 5018 130640189 130640500 9.700000e-137 497
37 TraesCS1B01G135000 chr3B 93.988 499 28 1 4214 4710 361613330 361612832 0.000000e+00 754
38 TraesCS1B01G135000 chr3B 96.486 313 8 3 4708 5018 361612776 361612465 9.630000e-142 514
39 TraesCS1B01G135000 chr3B 94.569 313 14 3 4708 5018 178551179 178551490 9.770000e-132 481
40 TraesCS1B01G135000 chr3B 94.569 313 14 3 4708 5018 236194695 236194384 9.770000e-132 481
41 TraesCS1B01G135000 chr4B 92.702 507 31 5 4208 4710 568735234 568734730 0.000000e+00 726
42 TraesCS1B01G135000 chr4B 93.651 315 15 5 4708 5018 330773710 330773397 2.740000e-127 466
43 TraesCS1B01G135000 chr7B 92.323 508 36 2 4206 4710 622296556 622296049 0.000000e+00 719
44 TraesCS1B01G135000 chr7B 93.949 314 15 4 4708 5018 622295994 622295682 5.880000e-129 472
45 TraesCS1B01G135000 chr7B 93.930 313 16 3 4708 5018 746798344 746798033 2.110000e-128 470


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 TraesCS1B01G135000 chr1B 171616324 171621341 5017 False 9267.00 9267 100.00000 1 5018 1 chr1B.!!$F1 5017
1 TraesCS1B01G135000 chr1D 112351073 112354707 3634 False 2895.50 4191 96.74650 750 4214 2 chr1D.!!$F1 3464
2 TraesCS1B01G135000 chr1A 119493425 119496852 3427 False 2746.50 4019 95.66350 750 4214 2 chr1A.!!$F2 3464
3 TraesCS1B01G135000 chr1A 440682270 440682977 707 False 1016.00 1016 92.17300 1 741 1 chr1A.!!$F1 740
4 TraesCS1B01G135000 chr2A 513651698 513652451 753 False 1375.00 1375 99.60200 1 752 1 chr2A.!!$F2 751
5 TraesCS1B01G135000 chr5B 639133740 639134482 742 False 1373.00 1373 100.00000 1 743 1 chr5B.!!$F1 742
6 TraesCS1B01G135000 chr5A 341140392 341141136 744 True 1371.00 1371 99.86600 1 745 1 chr5A.!!$R1 744
7 TraesCS1B01G135000 chr3A 363422142 363422886 744 True 1371.00 1371 99.86600 1 745 1 chr3A.!!$R1 744
8 TraesCS1B01G135000 chr6A 524764075 524768304 4229 False 648.75 867 85.05775 986 4214 4 chr6A.!!$F1 3228
9 TraesCS1B01G135000 chr6B 572402086 572406041 3955 False 537.80 850 87.01300 998 4214 5 chr6B.!!$F3 3216
10 TraesCS1B01G135000 chr6D 382621479 382625726 4247 False 637.25 826 84.85900 986 4214 4 chr6D.!!$F1 3228
11 TraesCS1B01G135000 chr2B 107112749 107113612 863 True 647.00 784 95.67950 4215 5018 2 chr2B.!!$R2 803
12 TraesCS1B01G135000 chr3B 361612465 361613330 865 True 634.00 754 95.23700 4214 5018 2 chr3B.!!$R2 804
13 TraesCS1B01G135000 chr4B 568734730 568735234 504 True 726.00 726 92.70200 4208 4710 1 chr4B.!!$R2 502
14 TraesCS1B01G135000 chr7B 622295682 622296556 874 True 595.50 719 93.13600 4206 5018 2 chr7B.!!$R2 812

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
842 843 2.089349 GCTTTCTTCGCTCGCTCGT 61.089 57.895 0.00 0.0 0.00 4.18 F
1074 1087 1.449601 CCAGTTCGGCGCAGGTATT 60.450 57.895 10.83 0.0 0.00 1.89 F
1609 1638 2.407562 TGCTATGTAATGCAGGGAGGA 58.592 47.619 0.00 0.0 34.84 3.71 F
2262 3034 2.767960 CCAGGAAAATATGCTTTGCCCT 59.232 45.455 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2823 1.550524 ACGTACAGAGCACACCATCAT 59.449 47.619 0.00 0.0 0.00 2.45 R
2349 3122 2.418976 TCATCCAGACGAGTCTACAACG 59.581 50.000 5.34 0.0 37.98 4.10 R
2641 3520 4.570772 GTCAACAGTCAAACAGTTAGCTCA 59.429 41.667 0.00 0.0 0.00 4.26 R
4025 5422 0.107459 GTAAGCTCCAGGAGGGCAAG 60.107 60.000 18.83 0.0 34.63 4.01 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
842 843 2.089349 GCTTTCTTCGCTCGCTCGT 61.089 57.895 0.00 0.00 0.00 4.18
850 851 4.863925 GCTCGCTCGTCTGCTCCC 62.864 72.222 0.00 0.00 0.00 4.30
946 947 3.792053 CTTATCTTCCGCGCGGCCT 62.792 63.158 42.78 26.96 34.68 5.19
1074 1087 1.449601 CCAGTTCGGCGCAGGTATT 60.450 57.895 10.83 0.00 0.00 1.89
1159 1173 3.971971 GGATAGCTAACTAGGGTTTGGGA 59.028 47.826 0.00 0.00 36.92 4.37
1354 1374 3.072184 GTGCTACCCATCCATTCATCTCT 59.928 47.826 0.00 0.00 0.00 3.10
1390 1410 8.154203 TGAGAAATTGTCACCTCTACAATGTTA 58.846 33.333 0.00 0.00 44.66 2.41
1391 1411 8.918202 AGAAATTGTCACCTCTACAATGTTAA 57.082 30.769 0.00 0.00 44.66 2.01
1410 1430 2.457366 AGTGGAACCAGTAAGAAGCG 57.543 50.000 0.00 0.00 37.80 4.68
1574 1598 2.762535 TGTAGTTCCAAGCTAGTGCC 57.237 50.000 0.00 0.00 40.80 5.01
1609 1638 2.407562 TGCTATGTAATGCAGGGAGGA 58.592 47.619 0.00 0.00 34.84 3.71
2214 2974 8.644216 ACATATCCATGCATTTTGTCATTATGT 58.356 29.630 0.00 0.39 35.39 2.29
2262 3034 2.767960 CCAGGAAAATATGCTTTGCCCT 59.232 45.455 0.00 0.00 0.00 5.19
2349 3122 5.522456 TCACAATGCTTCTGTTTTCATGTC 58.478 37.500 0.00 0.00 0.00 3.06
2491 3281 8.511604 AGTTCAACCATCTATTACTTCCAATG 57.488 34.615 0.00 0.00 0.00 2.82
2743 3631 2.378945 AAGCACGTGCAAGACAAGCG 62.379 55.000 39.21 0.00 45.16 4.68
3110 4093 6.379386 GCCTTTTGGTATCAAGTACAAGTTC 58.621 40.000 0.00 0.00 42.99 3.01
3249 4623 6.113411 TGTGCCTAGCTTCCTATTTTTACTC 58.887 40.000 0.00 0.00 0.00 2.59
3404 4792 7.308782 GCAACTAATCTATTGCTTAGTGTGT 57.691 36.000 4.55 0.00 46.21 3.72
3436 4824 8.482128 TGACCTGTGTTTTTATTTCCTCATTTT 58.518 29.630 0.00 0.00 0.00 1.82
3527 4918 6.942532 TTTACAAGTTTGCTCTGACAGATT 57.057 33.333 5.42 0.00 0.00 2.40
3678 5069 1.021390 GTGCTCTTGGTGATGGACGG 61.021 60.000 0.00 0.00 0.00 4.79
3742 5133 5.120674 TCTCAGTAAATGTCACTTCATTGCG 59.879 40.000 0.00 0.00 37.96 4.85
3831 5222 4.588278 GCATTTGTTCTGCGTAAGGTATC 58.412 43.478 0.00 0.00 38.28 2.24
3858 5249 6.534793 ACAAACACAATTTCACCATTTCTCAC 59.465 34.615 0.00 0.00 0.00 3.51
3891 5282 0.798776 GAAACCTCATGCAGTCACGG 59.201 55.000 0.00 0.00 0.00 4.94
3975 5372 3.826157 CCAACAATGCTAACAGAGGGAAA 59.174 43.478 0.00 0.00 0.00 3.13
4025 5422 8.058915 CGAGTTTCTTAGCATATAAAGCAGAAC 58.941 37.037 3.73 0.00 0.00 3.01
4055 5452 6.127026 CCTCCTGGAGCTTACTAACAAGTTAT 60.127 42.308 18.51 0.00 34.57 1.89
4087 5484 3.117346 GCGTCACATTGCGTAAAAGAAAC 59.883 43.478 0.00 0.00 0.00 2.78
4145 5545 6.359087 CGAGGCGTATCTGTTATGTAACTTAC 59.641 42.308 4.71 0.00 37.12 2.34
4204 5605 7.015226 TCGTTATGTAATTTTGCAGAGATGG 57.985 36.000 0.00 0.00 0.00 3.51
4262 5663 1.404181 CGTTCACCATCTCGACCACAT 60.404 52.381 0.00 0.00 0.00 3.21
4408 5809 1.893808 CGGTCAGCAGTTGCCACTT 60.894 57.895 0.00 0.00 43.38 3.16
4409 5810 1.845809 CGGTCAGCAGTTGCCACTTC 61.846 60.000 0.00 0.00 43.38 3.01
4519 5923 2.635915 TCACGGTTCCATTTACTCACCT 59.364 45.455 0.00 0.00 0.00 4.00
4520 5924 3.071892 TCACGGTTCCATTTACTCACCTT 59.928 43.478 0.00 0.00 0.00 3.50
4924 6388 7.169140 GGTTTGAATTGGTGTTTGTAATCAGTC 59.831 37.037 0.00 0.00 0.00 3.51
4934 6399 2.759355 TGTAATCAGTCCGGGGAGAAT 58.241 47.619 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1074 1087 1.064979 GGTGAAGAAGGCGGGGAATAA 60.065 52.381 0.00 0.00 0.00 1.40
1159 1173 3.131478 GCCACCGCCTACGCAAAT 61.131 61.111 0.00 0.00 38.22 2.32
1354 1374 6.603201 AGGTGACAATTTCTCAAGAGTTTGAA 59.397 34.615 13.12 0.00 42.48 2.69
1390 1410 2.550208 CCGCTTCTTACTGGTTCCACTT 60.550 50.000 0.00 0.00 0.00 3.16
1391 1411 1.002087 CCGCTTCTTACTGGTTCCACT 59.998 52.381 0.00 0.00 0.00 4.00
1410 1430 2.545946 GTGAGATTTGAGGATTAGCGCC 59.454 50.000 2.29 0.00 0.00 6.53
1476 1496 2.303175 AGATCTAGAACGCAGTCTCCC 58.697 52.381 0.00 0.00 45.00 4.30
1609 1638 6.071320 GGCCTTATCCCACTTTATCAAATCT 58.929 40.000 0.00 0.00 0.00 2.40
1811 2482 9.052759 TCTTTTATCAAGGACACTGAGTTAAAC 57.947 33.333 0.00 0.00 0.00 2.01
1815 2486 7.054124 TGTTCTTTTATCAAGGACACTGAGTT 58.946 34.615 0.00 0.00 31.14 3.01
2115 2823 1.550524 ACGTACAGAGCACACCATCAT 59.449 47.619 0.00 0.00 0.00 2.45
2349 3122 2.418976 TCATCCAGACGAGTCTACAACG 59.581 50.000 5.34 0.00 37.98 4.10
2431 3204 5.668558 ACAACGAACTTCCTTGAACATAC 57.331 39.130 7.32 0.00 0.00 2.39
2641 3520 4.570772 GTCAACAGTCAAACAGTTAGCTCA 59.429 41.667 0.00 0.00 0.00 4.26
2743 3631 6.192234 AGCAATGCAGATATATTAGCAAGC 57.808 37.500 20.70 20.70 40.76 4.01
3110 4093 4.826274 TCCTGTTCTCACCTCTAAATGG 57.174 45.455 0.00 0.00 0.00 3.16
3273 4654 9.550811 AAGAATTTGTTACCGAATCGTAATTTC 57.449 29.630 0.82 2.36 31.19 2.17
3401 4789 4.911514 AAAACACAGGTCACCATAACAC 57.088 40.909 0.00 0.00 0.00 3.32
3404 4792 7.507616 AGGAAATAAAAACACAGGTCACCATAA 59.492 33.333 0.00 0.00 0.00 1.90
3678 5069 6.038985 GGTAATCTACTTACTTTGGACCGAC 58.961 44.000 0.00 0.00 39.78 4.79
3742 5133 5.445540 GCCTGCGTAACTCAACTATGTTAAC 60.446 44.000 0.00 0.00 31.56 2.01
3831 5222 7.064371 TGAGAAATGGTGAAATTGTGTTTGTTG 59.936 33.333 0.00 0.00 0.00 3.33
3858 5249 4.204012 TGAGGTTTCAGTTGTTAACAGGG 58.796 43.478 8.56 2.91 0.00 4.45
3891 5282 6.027749 CGGAACATTTTAGCAAACATAGGTC 58.972 40.000 0.00 0.00 0.00 3.85
4025 5422 0.107459 GTAAGCTCCAGGAGGGCAAG 60.107 60.000 18.83 0.00 34.63 4.01
4055 5452 2.267426 CAATGTGACGCGTAGAATCCA 58.733 47.619 13.97 0.64 0.00 3.41
4087 5484 4.872691 CAGGTGAGCCACTAAAGATACAAG 59.127 45.833 5.48 0.00 37.19 3.16
4145 5545 7.195646 CCATGCTGTTTATACATTACACTTGG 58.804 38.462 0.00 0.00 32.86 3.61
4204 5605 7.536281 GGGCGTTAACATTTCCGAATATTTATC 59.464 37.037 6.39 0.00 0.00 1.75
4262 5663 0.405198 ACCCAACAGTGATGGATGCA 59.595 50.000 20.38 0.00 40.56 3.96
4519 5923 0.941542 GTTGTGCCAGTAACTGCGAA 59.058 50.000 0.00 0.00 0.00 4.70
4520 5924 0.882927 GGTTGTGCCAGTAACTGCGA 60.883 55.000 0.00 0.00 37.17 5.10
4924 6388 2.215942 ACCTCAAAAATTCTCCCCGG 57.784 50.000 0.00 0.00 0.00 5.73
4934 6399 8.881743 CAATGACTTCAAATTCAACCTCAAAAA 58.118 29.630 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.