Multiple sequence alignment - TraesCS7A01G438700

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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 TraesCS7A01G438700 chr7A 100.000 3014 0 0 1 3014 632912509 632909496 0.000000e+00 5566.0
1 TraesCS7A01G438700 chr7A 99.172 3019 18 5 1 3014 633041251 633038235 0.000000e+00 5430.0
2 TraesCS7A01G438700 chr7A 98.839 3015 23 4 1 3003 632974973 632971959 0.000000e+00 5363.0
3 TraesCS7A01G438700 chr7A 100.000 2190 0 0 3340 5529 632909170 632906981 0.000000e+00 4045.0
4 TraesCS7A01G438700 chr7A 99.272 2199 7 1 3340 5529 632971723 632969525 0.000000e+00 3965.0
5 TraesCS7A01G438700 chr7A 99.315 2190 15 0 3340 5529 633038164 633035975 0.000000e+00 3962.0
6 TraesCS7A01G438700 chr7A 96.954 2134 42 15 898 3014 632590949 632588822 0.000000e+00 3559.0
7 TraesCS7A01G438700 chr7A 93.904 1296 48 12 3831 5119 632588145 632586874 0.000000e+00 1927.0
8 TraesCS7A01G438700 chr7A 97.267 1061 27 2 4469 5529 632712321 632711263 0.000000e+00 1797.0
9 TraesCS7A01G438700 chr7A 97.078 1061 30 1 4469 5529 633096635 633095576 0.000000e+00 1786.0
10 TraesCS7A01G438700 chr7A 90.757 898 68 14 1 891 435002687 435003576 0.000000e+00 1184.0
11 TraesCS7A01G438700 chr7A 87.639 987 107 7 3694 4667 630389933 630390917 0.000000e+00 1133.0
12 TraesCS7A01G438700 chr7A 93.194 764 35 8 1 759 632594041 632593290 0.000000e+00 1107.0
13 TraesCS7A01G438700 chr7A 86.473 998 100 22 2042 3014 631964009 631963022 0.000000e+00 1062.0
14 TraesCS7A01G438700 chr7A 87.174 959 90 22 2039 2974 630388346 630389294 0.000000e+00 1059.0
15 TraesCS7A01G438700 chr7A 87.300 811 88 11 3857 4652 631961123 631960313 0.000000e+00 913.0
16 TraesCS7A01G438700 chr7A 97.107 484 11 1 3340 3823 632588748 632588268 0.000000e+00 813.0
17 TraesCS7A01G438700 chr7A 85.185 810 92 10 3899 4698 630035649 630036440 0.000000e+00 806.0
18 TraesCS7A01G438700 chr7A 87.234 423 44 6 2598 3014 630034536 630034954 1.800000e-129 473.0
19 TraesCS7A01G438700 chr7A 90.617 373 7 2 5157 5529 632586875 632586531 2.330000e-128 470.0
20 TraesCS7A01G438700 chr7A 91.509 318 24 2 3340 3657 630389626 630389940 8.510000e-118 435.0
21 TraesCS7A01G438700 chr7A 86.510 341 37 4 943 1283 630032731 630033062 3.150000e-97 366.0
22 TraesCS7A01G438700 chr7A 87.213 305 17 9 3353 3657 631961642 631961360 1.490000e-85 327.0
23 TraesCS7A01G438700 chr7A 85.099 302 41 1 982 1283 631965199 631965496 6.960000e-79 305.0
24 TraesCS7A01G438700 chr7A 81.793 368 50 12 1595 1956 630033382 630033738 5.420000e-75 292.0
25 TraesCS7A01G438700 chr7A 80.267 375 64 4 1510 1876 630387922 630388294 1.960000e-69 274.0
26 TraesCS7A01G438700 chr7A 91.960 199 11 2 3694 3889 631961367 631961171 1.960000e-69 274.0
27 TraesCS7A01G438700 chr7A 85.795 176 19 5 1337 1510 630033093 630033264 1.220000e-41 182.0
28 TraesCS7A01G438700 chr7A 97.143 35 1 0 1264 1298 630033063 630033097 5.980000e-05 60.2
29 TraesCS7A01G438700 chr7B 95.242 2207 79 8 3340 5529 592362371 592360174 0.000000e+00 3470.0
30 TraesCS7A01G438700 chr7B 94.014 2105 87 20 948 3014 592364549 592362446 0.000000e+00 3153.0
31 TraesCS7A01G438700 chr7B 87.417 151 14 2 5379 5529 592417078 592416933 9.530000e-38 169.0
32 TraesCS7A01G438700 chr7D 94.787 2187 88 8 3345 5529 548805680 548803518 0.000000e+00 3384.0
33 TraesCS7A01G438700 chr7D 96.117 927 22 8 2049 2965 548806668 548805746 0.000000e+00 1500.0
34 TraesCS7A01G438700 chr7D 92.697 1027 47 15 948 1947 548807694 548806669 0.000000e+00 1456.0
35 TraesCS7A01G438700 chr7D 92.531 897 55 11 1 891 15396156 15397046 0.000000e+00 1275.0
36 TraesCS7A01G438700 chr7D 88.417 941 85 18 2087 3014 548132996 548132067 0.000000e+00 1112.0
37 TraesCS7A01G438700 chr7D 88.743 835 59 18 2 803 14255911 14256743 0.000000e+00 989.0
38 TraesCS7A01G438700 chr7D 85.200 750 96 4 3899 4638 546754399 546755143 0.000000e+00 756.0
39 TraesCS7A01G438700 chr7D 91.026 312 18 5 3340 3646 548131983 548131677 3.990000e-111 412.0
40 TraesCS7A01G438700 chr7D 87.539 321 34 3 978 1298 546751694 546752008 3.150000e-97 366.0
41 TraesCS7A01G438700 chr7D 86.275 306 20 5 4417 4715 548129988 548129698 4.160000e-81 313.0
42 TraesCS7A01G438700 chr7D 91.447 152 11 2 5379 5529 548811063 548810913 2.020000e-49 207.0
43 TraesCS7A01G438700 chr3D 91.759 898 62 10 1 891 551894056 551894948 0.000000e+00 1238.0
44 TraesCS7A01G438700 chr3A 91.435 899 65 9 1 891 143227540 143228434 0.000000e+00 1223.0
45 TraesCS7A01G438700 chr5A 90.279 895 69 13 1 891 576737752 576738632 0.000000e+00 1155.0
46 TraesCS7A01G438700 chr2A 86.731 927 86 25 1 907 236540168 236541077 0.000000e+00 996.0
47 TraesCS7A01G438700 chr2A 86.667 930 81 24 1 891 307931900 307932825 0.000000e+00 990.0
48 TraesCS7A01G438700 chr1A 83.889 360 45 8 4798 5155 500838142 500837794 1.150000e-86 331.0
49 TraesCS7A01G438700 chr1D 83.648 318 45 4 4787 5100 445557863 445558177 5.420000e-75 292.0
50 TraesCS7A01G438700 chr5D 80.940 383 40 15 542 896 338103995 338103618 7.060000e-69 272.0
51 TraesCS7A01G438700 chr5B 88.000 100 6 5 3799 3895 13704400 13704496 4.530000e-21 113.0
52 TraesCS7A01G438700 chr4D 88.764 89 6 2 3804 3892 432765544 432765460 7.570000e-19 106.0


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 TraesCS7A01G438700 chr7A 632906981 632912509 5528 True 4805.500000 5566 100.000000 1 5529 2 chr7A.!!$R5 5528
1 TraesCS7A01G438700 chr7A 633035975 633041251 5276 True 4696.000000 5430 99.243500 1 5529 2 chr7A.!!$R7 5528
2 TraesCS7A01G438700 chr7A 632969525 632974973 5448 True 4664.000000 5363 99.055500 1 5529 2 chr7A.!!$R6 5528
3 TraesCS7A01G438700 chr7A 632711263 632712321 1058 True 1797.000000 1797 97.267000 4469 5529 1 chr7A.!!$R1 1060
4 TraesCS7A01G438700 chr7A 633095576 633096635 1059 True 1786.000000 1786 97.078000 4469 5529 1 chr7A.!!$R2 1060
5 TraesCS7A01G438700 chr7A 632586531 632594041 7510 True 1575.200000 3559 94.355200 1 5529 5 chr7A.!!$R4 5528
6 TraesCS7A01G438700 chr7A 435002687 435003576 889 False 1184.000000 1184 90.757000 1 891 1 chr7A.!!$F1 890
7 TraesCS7A01G438700 chr7A 630387922 630390917 2995 False 725.250000 1133 86.647250 1510 4667 4 chr7A.!!$F4 3157
8 TraesCS7A01G438700 chr7A 631960313 631964009 3696 True 644.000000 1062 88.236500 2042 4652 4 chr7A.!!$R3 2610
9 TraesCS7A01G438700 chr7A 630032731 630036440 3709 False 363.200000 806 87.276667 943 4698 6 chr7A.!!$F3 3755
10 TraesCS7A01G438700 chr7B 592360174 592364549 4375 True 3311.500000 3470 94.628000 948 5529 2 chr7B.!!$R2 4581
11 TraesCS7A01G438700 chr7D 548803518 548811063 7545 True 1636.750000 3384 93.762000 948 5529 4 chr7D.!!$R2 4581
12 TraesCS7A01G438700 chr7D 15396156 15397046 890 False 1275.000000 1275 92.531000 1 891 1 chr7D.!!$F2 890
13 TraesCS7A01G438700 chr7D 14255911 14256743 832 False 989.000000 989 88.743000 2 803 1 chr7D.!!$F1 801
14 TraesCS7A01G438700 chr7D 548129698 548132996 3298 True 612.333333 1112 88.572667 2087 4715 3 chr7D.!!$R1 2628
15 TraesCS7A01G438700 chr7D 546751694 546755143 3449 False 561.000000 756 86.369500 978 4638 2 chr7D.!!$F3 3660
16 TraesCS7A01G438700 chr3D 551894056 551894948 892 False 1238.000000 1238 91.759000 1 891 1 chr3D.!!$F1 890
17 TraesCS7A01G438700 chr3A 143227540 143228434 894 False 1223.000000 1223 91.435000 1 891 1 chr3A.!!$F1 890
18 TraesCS7A01G438700 chr5A 576737752 576738632 880 False 1155.000000 1155 90.279000 1 891 1 chr5A.!!$F1 890
19 TraesCS7A01G438700 chr2A 236540168 236541077 909 False 996.000000 996 86.731000 1 907 1 chr2A.!!$F1 906
20 TraesCS7A01G438700 chr2A 307931900 307932825 925 False 990.000000 990 86.667000 1 891 1 chr2A.!!$F2 890

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
609 645 8.598202 TTAGTAATCCATCTGGTTACACTGTA 57.402 34.615 16.76 0.0 35.78 2.74 F
1139 3563 2.345991 GCCTTACTGGTCGCCACA 59.654 61.111 0.00 0.0 38.35 4.17 F
3794 8142 6.689178 ATTAATGTTGCAAGTAAAACAGCG 57.311 33.333 0.00 0.0 39.50 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3485 7819 9.800433 CATGATATACTCACTCAGTTCCATATC 57.200 37.037 0.00 0.0 36.48 1.63 R
3535 7869 2.565834 AGCAACTAAGAGCCCGAACTAA 59.434 45.455 0.00 0.0 0.00 2.24 R
5405 11273 6.013379 TGCTTGGTTTTCTTGAACCCATATA 58.987 36.000 4.49 0.0 46.85 0.86 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
609 645 8.598202 TTAGTAATCCATCTGGTTACACTGTA 57.402 34.615 16.76 0.0 35.78 2.74
1139 3563 2.345991 GCCTTACTGGTCGCCACA 59.654 61.111 0.00 0.0 38.35 4.17
3794 8142 6.689178 ATTAATGTTGCAAGTAAAACAGCG 57.311 33.333 0.00 0.0 39.50 5.18
4256 10091 0.454285 GCGCTTGCGCTGTTTTATCA 60.454 50.000 29.13 0.0 0.00 2.15
5391 11259 0.250945 TGCGGCACATTAGAACCCAA 60.251 50.000 0.00 0.0 0.00 4.12
5405 11273 3.334881 AGAACCCAATTCCTTCCACTGAT 59.665 43.478 0.00 0.0 38.16 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
504 540 6.911250 ACGAAGGTTTATTCCCTTTGATTT 57.089 33.333 12.30 0.00 43.51 2.17
577 613 6.006275 ACCAGATGGATTACTAATTGCAGT 57.994 37.500 5.72 0.00 38.94 4.40
609 645 1.271982 TGCTTCGACCACTCTCCTACT 60.272 52.381 0.00 0.00 0.00 2.57
3485 7819 9.800433 CATGATATACTCACTCAGTTCCATATC 57.200 37.037 0.00 0.00 36.48 1.63
3535 7869 2.565834 AGCAACTAAGAGCCCGAACTAA 59.434 45.455 0.00 0.00 0.00 2.24
3794 8142 4.158209 GGAACAGAGGGTGTACTTCTCTAC 59.842 50.000 11.03 7.47 39.03 2.59
5391 11259 6.332635 TGAACCCATATATCAGTGGAAGGAAT 59.667 38.462 3.87 0.00 37.72 3.01
5405 11273 6.013379 TGCTTGGTTTTCTTGAACCCATATA 58.987 36.000 4.49 0.00 46.85 0.86


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

AutoCloner maintained by Alex Coulton.