Multiple sequence alignment - TraesCS7A01G131100

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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 TraesCS7A01G131100 chr7A 100.000 5137 0 0 1 5137 84692305 84697441 0.000000e+00 9487.0
1 TraesCS7A01G131100 chr7A 97.846 1532 31 1 3606 5137 47819268 47820797 0.000000e+00 2645.0
2 TraesCS7A01G131100 chr7A 98.326 657 11 0 2952 3608 47816943 47817599 0.000000e+00 1153.0
3 TraesCS7A01G131100 chr7A 97.690 303 6 1 86 388 2538875 2539176 2.120000e-143 520.0
4 TraesCS7A01G131100 chr7A 93.243 74 3 2 4481 4554 32698317 32698246 1.960000e-19 108.0
5 TraesCS7A01G131100 chr7A 100.000 31 0 0 3892 3922 47819618 47819648 2.000000e-04 58.4
6 TraesCS7A01G131100 chr7A 100.000 28 0 0 3959 3986 47819557 47819584 9.000000e-03 52.8
7 TraesCS7A01G131100 chr7A 96.774 31 1 0 3956 3986 84696196 84696226 9.000000e-03 52.8
8 TraesCS7A01G131100 chr7A 96.774 31 1 0 3892 3922 84696260 84696290 9.000000e-03 52.8
9 TraesCS7A01G131100 chr3A 98.587 5095 53 3 43 5137 93564772 93569847 0.000000e+00 8992.0
10 TraesCS7A01G131100 chr3A 91.026 390 30 5 4089 4477 509231 509616 5.890000e-144 521.0
11 TraesCS7A01G131100 chr3A 100.000 31 0 0 3892 3922 93568685 93568715 2.000000e-04 58.4
12 TraesCS7A01G131100 chr3A 96.774 31 1 0 3956 3986 93568621 93568651 9.000000e-03 52.8
13 TraesCS7A01G131100 chr3A 100.000 28 0 0 2 29 717805867 717805840 9.000000e-03 52.8
14 TraesCS7A01G131100 chr4A 98.036 2953 52 2 2186 5137 636118429 636115482 0.000000e+00 5127.0
15 TraesCS7A01G131100 chr4A 98.119 1808 24 5 394 2192 636122629 636120823 0.000000e+00 3142.0
16 TraesCS7A01G131100 chr4A 86.575 581 56 5 396 973 598523287 598522726 5.650000e-174 621.0
17 TraesCS7A01G131100 chr4A 93.720 414 12 4 2 401 636123302 636122889 4.400000e-170 608.0
18 TraesCS7A01G131100 chr4A 94.269 349 19 1 38 386 156782427 156782774 2.720000e-147 532.0
19 TraesCS7A01G131100 chr4A 83.380 361 33 18 977 1313 598522663 598522306 5.000000e-80 309.0
20 TraesCS7A01G131100 chr4A 88.889 99 8 3 3487 3582 673443981 673443883 9.040000e-23 119.0
21 TraesCS7A01G131100 chr4A 95.455 66 2 1 4490 4555 608348671 608348735 2.530000e-18 104.0
22 TraesCS7A01G131100 chr4A 100.000 31 0 0 3892 3922 636116658 636116628 2.000000e-04 58.4
23 TraesCS7A01G131100 chr4A 100.000 28 0 0 3959 3986 636116719 636116692 9.000000e-03 52.8
24 TraesCS7A01G131100 chr1A 97.531 2916 62 2 969 3883 6072055 6069149 0.000000e+00 4977.0
25 TraesCS7A01G131100 chr1A 95.433 1051 33 7 4089 5137 6068103 6067066 0.000000e+00 1661.0
26 TraesCS7A01G131100 chr1A 96.213 581 15 1 393 973 6072686 6072113 0.000000e+00 944.0
27 TraesCS7A01G131100 chr1A 86.575 581 56 5 396 973 16478964 16478403 5.650000e-174 621.0
28 TraesCS7A01G131100 chr1A 98.000 300 5 1 89 388 502838920 502838622 2.120000e-143 520.0
29 TraesCS7A01G131100 chr1A 83.380 361 33 18 977 1313 16478340 16477983 5.000000e-80 309.0
30 TraesCS7A01G131100 chr1A 96.000 175 7 0 3916 4090 6069148 6068974 8.420000e-73 285.0
31 TraesCS7A01G131100 chr1B 97.259 2919 71 6 969 3883 38593050 38590137 0.000000e+00 4939.0
32 TraesCS7A01G131100 chr1B 95.256 1054 43 3 4089 5137 38589079 38588028 0.000000e+00 1663.0
33 TraesCS7A01G131100 chr1B 95.264 549 24 1 393 941 38593649 38593103 0.000000e+00 869.0
34 TraesCS7A01G131100 chr1B 95.429 175 6 1 3916 4090 38590136 38589964 1.410000e-70 278.0
35 TraesCS7A01G131100 chr1B 100.000 31 0 0 3892 3922 38590098 38590068 2.000000e-04 58.4
36 TraesCS7A01G131100 chr7D 85.151 1751 172 35 1934 3632 111372087 111373801 0.000000e+00 1712.0
37 TraesCS7A01G131100 chr7D 89.932 586 52 5 4557 5137 111396480 111397063 0.000000e+00 749.0
38 TraesCS7A01G131100 chr7D 83.127 403 48 12 969 1354 29884802 29884403 2.940000e-92 350.0
39 TraesCS7A01G131100 chr7D 85.714 329 32 11 3331 3644 111396041 111396369 2.960000e-87 333.0
40 TraesCS7A01G131100 chr7D 87.952 249 28 1 393 641 29885446 29885200 5.030000e-75 292.0
41 TraesCS7A01G131100 chr7D 88.889 99 8 3 3487 3582 56942229 56942131 9.040000e-23 119.0
42 TraesCS7A01G131100 chr5B 93.986 582 34 1 393 973 315245417 315244836 0.000000e+00 880.0
43 TraesCS7A01G131100 chr5B 94.906 530 23 4 969 1495 315244778 315244250 0.000000e+00 826.0
44 TraesCS7A01G131100 chr5B 100.000 29 0 0 1 29 689211239 689211267 3.000000e-03 54.7
45 TraesCS7A01G131100 chr2B 90.274 658 56 5 2428 3081 557344745 557345398 0.000000e+00 854.0
46 TraesCS7A01G131100 chr3D 89.954 657 59 4 2428 3081 462274468 462273816 0.000000e+00 841.0
47 TraesCS7A01G131100 chr3D 87.852 568 44 8 415 973 528127647 528127096 1.210000e-180 643.0
48 TraesCS7A01G131100 chr3D 86.501 563 54 7 415 972 553220808 553220263 2.650000e-167 599.0
49 TraesCS7A01G131100 chr3D 89.293 467 41 6 4676 5137 462273805 462273343 1.240000e-160 577.0
50 TraesCS7A01G131100 chr3D 98.065 310 6 0 77 386 65439936 65439627 1.630000e-149 540.0
51 TraesCS7A01G131100 chr3D 83.029 383 36 15 969 1328 528127038 528126662 2.310000e-83 320.0
52 TraesCS7A01G131100 chr3D 84.046 351 29 12 969 1296 553220204 553219858 3.860000e-81 313.0
53 TraesCS7A01G131100 chr3B 89.818 658 58 6 2428 3081 817429020 817429672 0.000000e+00 835.0
54 TraesCS7A01G131100 chr3B 89.006 473 42 7 4670 5137 817429677 817430144 1.240000e-160 577.0
55 TraesCS7A01G131100 chrUn 85.124 605 65 13 4557 5137 30148296 30147693 3.420000e-166 595.0
56 TraesCS7A01G131100 chrUn 79.714 350 36 14 3427 3766 30148633 30148309 2.410000e-53 220.0
57 TraesCS7A01G131100 chr4B 84.838 554 73 9 4557 5101 666928098 666928649 9.720000e-152 547.0
58 TraesCS7A01G131100 chr4B 93.410 349 20 3 39 386 144349387 144349041 9.860000e-142 514.0
59 TraesCS7A01G131100 chr2D 95.349 344 15 1 38 381 6461398 6461740 3.500000e-151 545.0
60 TraesCS7A01G131100 chr2D 91.282 390 32 2 4089 4478 467999535 467999922 9.790000e-147 531.0
61 TraesCS7A01G131100 chr5D 91.969 386 29 2 4094 4479 500227094 500226711 1.630000e-149 540.0
62 TraesCS7A01G131100 chr5D 97.444 313 8 0 74 386 80205583 80205895 7.570000e-148 534.0
63 TraesCS7A01G131100 chr5D 92.000 75 4 2 4481 4555 112924550 112924622 2.530000e-18 104.0
64 TraesCS7A01G131100 chr1D 90.513 390 35 1 4089 4478 221083063 221082676 9.860000e-142 514.0
65 TraesCS7A01G131100 chr1D 83.500 400 49 12 969 1354 115569583 115569187 1.760000e-94 357.0
66 TraesCS7A01G131100 chr6D 83.292 401 49 13 969 1354 454644456 454644059 2.280000e-93 353.0
67 TraesCS7A01G131100 chr6D 88.400 250 26 2 393 641 454645099 454644852 1.080000e-76 298.0
68 TraesCS7A01G131100 chr6B 83.246 191 26 6 1170 1355 712293793 712293982 2.460000e-38 171.0
69 TraesCS7A01G131100 chr2A 92.000 75 4 2 4481 4555 370218792 370218864 2.530000e-18 104.0


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 TraesCS7A01G131100 chr7A 84692305 84697441 5136 False 3197.533333 9487 97.849333 1 5137 3 chr7A.!!$F3 5136
1 TraesCS7A01G131100 chr7A 47816943 47820797 3854 False 977.300000 2645 99.043000 2952 5137 4 chr7A.!!$F2 2185
2 TraesCS7A01G131100 chr3A 93564772 93569847 5075 False 3034.400000 8992 98.453667 43 5137 3 chr3A.!!$F2 5094
3 TraesCS7A01G131100 chr4A 636120823 636123302 2479 True 1875.000000 3142 95.919500 2 2192 2 chr4A.!!$R4 2190
4 TraesCS7A01G131100 chr4A 636115482 636118429 2947 True 1746.066667 5127 99.345333 2186 5137 3 chr4A.!!$R3 2951
5 TraesCS7A01G131100 chr4A 598522306 598523287 981 True 465.000000 621 84.977500 396 1313 2 chr4A.!!$R2 917
6 TraesCS7A01G131100 chr1A 6067066 6072686 5620 True 1966.750000 4977 96.294250 393 5137 4 chr1A.!!$R2 4744
7 TraesCS7A01G131100 chr1A 16477983 16478964 981 True 465.000000 621 84.977500 396 1313 2 chr1A.!!$R3 917
8 TraesCS7A01G131100 chr1B 38588028 38593649 5621 True 1561.480000 4939 96.641600 393 5137 5 chr1B.!!$R1 4744
9 TraesCS7A01G131100 chr7D 111372087 111373801 1714 False 1712.000000 1712 85.151000 1934 3632 1 chr7D.!!$F1 1698
10 TraesCS7A01G131100 chr7D 111396041 111397063 1022 False 541.000000 749 87.823000 3331 5137 2 chr7D.!!$F2 1806
11 TraesCS7A01G131100 chr7D 29884403 29885446 1043 True 321.000000 350 85.539500 393 1354 2 chr7D.!!$R2 961
12 TraesCS7A01G131100 chr5B 315244250 315245417 1167 True 853.000000 880 94.446000 393 1495 2 chr5B.!!$R1 1102
13 TraesCS7A01G131100 chr2B 557344745 557345398 653 False 854.000000 854 90.274000 2428 3081 1 chr2B.!!$F1 653
14 TraesCS7A01G131100 chr3D 462273343 462274468 1125 True 709.000000 841 89.623500 2428 5137 2 chr3D.!!$R2 2709
15 TraesCS7A01G131100 chr3D 528126662 528127647 985 True 481.500000 643 85.440500 415 1328 2 chr3D.!!$R3 913
16 TraesCS7A01G131100 chr3D 553219858 553220808 950 True 456.000000 599 85.273500 415 1296 2 chr3D.!!$R4 881
17 TraesCS7A01G131100 chr3B 817429020 817430144 1124 False 706.000000 835 89.412000 2428 5137 2 chr3B.!!$F1 2709
18 TraesCS7A01G131100 chrUn 30147693 30148633 940 True 407.500000 595 82.419000 3427 5137 2 chrUn.!!$R1 1710
19 TraesCS7A01G131100 chr4B 666928098 666928649 551 False 547.000000 547 84.838000 4557 5101 1 chr4B.!!$F1 544
20 TraesCS7A01G131100 chr6D 454644059 454645099 1040 True 325.500000 353 85.846000 393 1354 2 chr6D.!!$R1 961

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
81 96 0.963962 ACGAAGAAAGACCTACGCCA 59.036 50.000 0.0 0.0 0.0 5.69 F
632 990 1.546923 CAATTGGTGAATCTGGCTGCA 59.453 47.619 0.5 0.0 0.0 4.41 F
842 1264 4.689345 GCGTGTTTCAGGTAGTTAGATGTT 59.311 41.667 0.0 0.0 0.0 2.71 F
2543 3183 3.194755 TCTGCGTTTCCTCTGCTATTGTA 59.805 43.478 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 2001 6.237901 TGTGCTCAGTTATGAACCAACTATT 58.762 36.000 0.0 0.0 34.5 1.73 R
2543 3183 5.075493 AGGAGCAGAAAGTGATGAAACAAT 58.925 37.500 0.0 0.0 0.0 2.71 R
2690 3330 2.398588 TGATCAGGGGCGTAATCTTCT 58.601 47.619 0.0 0.0 0.0 2.85 R
4380 7625 1.732917 CACAAGCACGCCCAAAAGA 59.267 52.632 0.0 0.0 0.0 2.52 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
81 96 0.963962 ACGAAGAAAGACCTACGCCA 59.036 50.000 0.00 0.00 0.00 5.69
257 272 2.679716 GGAAGCCATGGCCTGAGT 59.320 61.111 33.14 11.80 43.17 3.41
632 990 1.546923 CAATTGGTGAATCTGGCTGCA 59.453 47.619 0.50 0.00 0.00 4.41
806 1225 6.664816 AGTTAATTTGAAATCATGGGAGCAGA 59.335 34.615 0.00 0.00 0.00 4.26
842 1264 4.689345 GCGTGTTTCAGGTAGTTAGATGTT 59.311 41.667 0.00 0.00 0.00 2.71
1348 1959 5.095145 AGAATAGCCGATCATGCATGTAT 57.905 39.130 25.43 17.09 0.00 2.29
2543 3183 3.194755 TCTGCGTTTCCTCTGCTATTGTA 59.805 43.478 0.00 0.00 0.00 2.41
2690 3330 4.202121 GGATCTCAGGTAATCGTTGCAGTA 60.202 45.833 0.00 0.00 0.00 2.74
2839 3479 2.693591 CGAGGACTTCTACAATGGGCTA 59.306 50.000 0.00 0.00 0.00 3.93
2911 3551 4.400961 AGCAAGGACCTGCCGAGC 62.401 66.667 11.03 4.26 43.73 5.03
3374 4020 0.659427 CTATGATGTGCACCGCTTGG 59.341 55.000 15.69 2.86 39.35 3.61
3383 4029 2.032681 ACCGCTTGGAACCAGAGC 59.967 61.111 13.73 13.73 36.26 4.09
3820 6176 4.460263 CAAGCAGGGCATAATGTTAGGTA 58.540 43.478 0.00 0.00 0.00 3.08
3957 6315 5.462068 TCTTTAGTGACATTTCATATCGGCG 59.538 40.000 0.00 0.00 33.11 6.46
3993 6351 7.930217 TGCTATACTGGCTAAGCTTAATTTTG 58.070 34.615 7.74 0.00 35.95 2.44
4444 7689 2.625790 TGGTTGTATTGGGTTGTTGCTC 59.374 45.455 0.00 0.00 0.00 4.26
4586 7832 6.430000 TCTGAAGGGCAAAAACTTAGTACATC 59.570 38.462 0.00 0.00 0.00 3.06
4664 7920 9.619316 CGAGTTATTCTTCTCATATCTGTAAGG 57.381 37.037 0.00 0.00 0.00 2.69
4674 7930 8.078060 TCTCATATCTGTAAGGACACATTTCA 57.922 34.615 0.00 0.00 0.00 2.69
4852 8112 2.434702 ACCAACTAGCCCACTACTATGC 59.565 50.000 0.00 0.00 0.00 3.14
4954 8216 6.097270 ACATCCAATGGAACCTGACATTAATG 59.903 38.462 14.01 14.01 35.67 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 54 4.595986 AGGTTAACCGTGGCAGATTTATT 58.404 39.130 18.91 0.00 42.08 1.40
42 57 2.579410 AGGTTAACCGTGGCAGATTT 57.421 45.000 18.91 0.00 42.08 2.17
43 58 2.675889 CGTAGGTTAACCGTGGCAGATT 60.676 50.000 18.91 0.77 42.08 2.40
45 60 0.244450 CGTAGGTTAACCGTGGCAGA 59.756 55.000 18.91 0.00 42.08 4.26
46 61 0.244450 TCGTAGGTTAACCGTGGCAG 59.756 55.000 18.91 8.74 42.08 4.85
47 62 0.678395 TTCGTAGGTTAACCGTGGCA 59.322 50.000 18.91 2.03 42.08 4.92
48 63 1.067635 TCTTCGTAGGTTAACCGTGGC 60.068 52.381 18.91 9.37 42.08 5.01
49 64 3.302365 TTCTTCGTAGGTTAACCGTGG 57.698 47.619 18.91 11.59 42.08 4.94
50 65 4.383948 GTCTTTCTTCGTAGGTTAACCGTG 59.616 45.833 18.91 12.46 42.08 4.94
806 1225 2.588027 AACACGCCGAAACCAAATTT 57.412 40.000 0.00 0.00 0.00 1.82
1389 2001 6.237901 TGTGCTCAGTTATGAACCAACTATT 58.762 36.000 0.00 0.00 34.50 1.73
2543 3183 5.075493 AGGAGCAGAAAGTGATGAAACAAT 58.925 37.500 0.00 0.00 0.00 2.71
2690 3330 2.398588 TGATCAGGGGCGTAATCTTCT 58.601 47.619 0.00 0.00 0.00 2.85
2911 3551 1.073008 TCCCCATGGTATCCCCCTG 60.073 63.158 11.73 0.00 0.00 4.45
3374 4020 3.784701 TCATTAGACTCGCTCTGGTTC 57.215 47.619 0.00 0.00 0.00 3.62
3383 4029 2.194271 GCCCGTCTTTCATTAGACTCG 58.806 52.381 0.00 0.00 41.89 4.18
3820 6176 2.161855 TCAGCAATTCCGCAAACAGAT 58.838 42.857 0.00 0.00 0.00 2.90
3993 6351 7.819900 ACTTATCTACATGTTCACAGGAAGAAC 59.180 37.037 2.30 0.00 44.26 3.01
4380 7625 1.732917 CACAAGCACGCCCAAAAGA 59.267 52.632 0.00 0.00 0.00 2.52
4444 7689 4.793353 GCTTTCGCCCCGCTATATAGATAG 60.793 50.000 14.16 0.00 38.51 2.08
4674 7930 6.384305 AGTCGCCCTAATAGAAGCCATATATT 59.616 38.462 0.00 0.00 0.00 1.28
4954 8216 7.679638 GCACACTGTCATTGTAGGGAATTTATC 60.680 40.741 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.