Multiple sequence alignment - TraesCS7A01G510400

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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 TraesCS7A01G510400 chr7A 100.000 3130 0 0 1 3130 697974617 697977746 0.000000e+00 5781.0
1 TraesCS7A01G510400 chr7A 96.843 2914 82 5 217 3130 697877282 697880185 0.000000e+00 4863.0
2 TraesCS7A01G510400 chr7A 95.559 2950 93 15 183 3130 697822605 697825518 0.000000e+00 4687.0
3 TraesCS7A01G510400 chr7A 97.301 667 18 0 1 667 698131081 698131747 0.000000e+00 1133.0
4 TraesCS7A01G510400 chr7A 95.918 49 1 1 506 554 43038349 43038396 9.310000e-11 78.7
5 TraesCS7A01G510400 chr7B 91.321 2051 146 15 1102 3130 690094234 690096274 0.000000e+00 2772.0
6 TraesCS7A01G510400 chr7B 91.887 1590 104 9 1561 3130 690080898 690082482 0.000000e+00 2198.0
7 TraesCS7A01G510400 chr7B 86.653 1993 170 39 1177 3130 690199622 690201557 0.000000e+00 2119.0
8 TraesCS7A01G510400 chr7B 91.105 1484 102 13 1102 2563 690119695 690121170 0.000000e+00 1982.0
9 TraesCS7A01G510400 chr7B 92.774 1121 69 5 1073 2186 690030081 690031196 0.000000e+00 1611.0
10 TraesCS7A01G510400 chr7B 91.056 928 70 6 2211 3130 690031465 690032387 0.000000e+00 1242.0
11 TraesCS7A01G510400 chr7B 77.668 2024 331 74 1154 3113 677961315 677963281 0.000000e+00 1122.0
12 TraesCS7A01G510400 chr7B 89.037 374 18 6 544 895 690029638 690030010 2.860000e-120 442.0
13 TraesCS7A01G510400 chr7B 88.562 306 32 3 506 809 690119162 690119466 4.930000e-98 368.0
14 TraesCS7A01G510400 chr7B 88.235 306 32 4 506 809 690093702 690094005 2.290000e-96 363.0
15 TraesCS7A01G510400 chr7B 84.817 191 24 4 622 809 690915200 690915388 1.480000e-43 187.0
16 TraesCS7A01G510400 chr7B 87.671 146 14 2 931 1075 690094095 690094237 1.930000e-37 167.0
17 TraesCS7A01G510400 chr7B 87.671 146 14 2 931 1075 690119556 690119698 1.930000e-37 167.0
18 TraesCS7A01G510400 chr7B 98.765 81 1 0 848 928 690029984 690030064 9.050000e-31 145.0
19 TraesCS7A01G510400 chr7D 91.090 2065 136 23 1102 3130 606010719 606012771 0.000000e+00 2750.0
20 TraesCS7A01G510400 chr7D 90.739 1760 121 20 1404 3129 606107122 606108873 0.000000e+00 2309.0
21 TraesCS7A01G510400 chr7D 88.494 1886 144 37 506 2340 605946645 605948508 0.000000e+00 2213.0
22 TraesCS7A01G510400 chr7D 87.500 1992 150 38 1177 3130 606301763 606303693 0.000000e+00 2207.0
23 TraesCS7A01G510400 chr7D 93.152 993 52 7 1404 2383 606181448 606182437 0.000000e+00 1443.0
24 TraesCS7A01G510400 chr7D 90.517 812 56 9 2336 3130 605957469 605958276 0.000000e+00 1053.0
25 TraesCS7A01G510400 chr7D 89.548 775 56 11 2371 3128 606182717 606183483 0.000000e+00 959.0
26 TraesCS7A01G510400 chr7D 88.644 590 42 15 818 1397 606106489 606107063 0.000000e+00 695.0
27 TraesCS7A01G510400 chr7D 87.119 590 51 15 818 1397 606180815 606181389 0.000000e+00 645.0
28 TraesCS7A01G510400 chr7D 84.276 566 53 21 506 1069 606301175 606301706 1.290000e-143 520.0
29 TraesCS7A01G510400 chr7D 86.133 375 39 10 506 875 606180330 606180696 2.930000e-105 392.0
30 TraesCS7A01G510400 chr5B 89.197 361 36 2 147 504 313118210 313117850 6.160000e-122 448.0
31 TraesCS7A01G510400 chr3D 88.043 368 42 2 147 512 586370189 586369822 4.790000e-118 435.0
32 TraesCS7A01G510400 chr6D 88.022 359 38 3 148 506 292078159 292078512 1.340000e-113 420.0
33 TraesCS7A01G510400 chr1A 87.097 372 42 4 147 512 32742901 32742530 1.740000e-112 416.0
34 TraesCS7A01G510400 chr5D 86.667 375 37 5 147 512 276266283 276265913 1.350000e-108 403.0
35 TraesCS7A01G510400 chr5D 91.096 146 13 0 1 146 424079751 424079896 6.850000e-47 198.0
36 TraesCS7A01G510400 chr2D 86.777 363 42 6 149 506 629575120 629575481 1.750000e-107 399.0
37 TraesCS7A01G510400 chr1D 92.754 138 10 0 9 146 399164888 399164751 1.900000e-47 200.0
38 TraesCS7A01G510400 chr1D 89.726 146 15 0 1 146 50190250 50190105 1.480000e-43 187.0
39 TraesCS7A01G510400 chr1D 90.000 140 14 0 7 146 261091473 261091334 6.900000e-42 182.0
40 TraesCS7A01G510400 chr1D 88.571 140 16 0 7 146 376789438 376789299 1.490000e-38 171.0
41 TraesCS7A01G510400 chrUn 89.726 146 15 0 1 146 407847596 407847451 1.480000e-43 187.0
42 TraesCS7A01G510400 chrUn 89.726 146 15 0 1 146 428313335 428313480 1.480000e-43 187.0
43 TraesCS7A01G510400 chrUn 89.041 146 16 0 1 146 407861518 407861663 6.900000e-42 182.0
44 TraesCS7A01G510400 chrUn 87.671 146 14 2 931 1075 477661877 477662019 1.930000e-37 167.0


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 TraesCS7A01G510400 chr7A 697974617 697977746 3129 False 5781.000000 5781 100.000000 1 3130 1 chr7A.!!$F4 3129
1 TraesCS7A01G510400 chr7A 697877282 697880185 2903 False 4863.000000 4863 96.843000 217 3130 1 chr7A.!!$F3 2913
2 TraesCS7A01G510400 chr7A 697822605 697825518 2913 False 4687.000000 4687 95.559000 183 3130 1 chr7A.!!$F2 2947
3 TraesCS7A01G510400 chr7A 698131081 698131747 666 False 1133.000000 1133 97.301000 1 667 1 chr7A.!!$F5 666
4 TraesCS7A01G510400 chr7B 690080898 690082482 1584 False 2198.000000 2198 91.887000 1561 3130 1 chr7B.!!$F2 1569
5 TraesCS7A01G510400 chr7B 690199622 690201557 1935 False 2119.000000 2119 86.653000 1177 3130 1 chr7B.!!$F3 1953
6 TraesCS7A01G510400 chr7B 677961315 677963281 1966 False 1122.000000 1122 77.668000 1154 3113 1 chr7B.!!$F1 1959
7 TraesCS7A01G510400 chr7B 690093702 690096274 2572 False 1100.666667 2772 89.075667 506 3130 3 chr7B.!!$F6 2624
8 TraesCS7A01G510400 chr7B 690029638 690032387 2749 False 860.000000 1611 92.908000 544 3130 4 chr7B.!!$F5 2586
9 TraesCS7A01G510400 chr7B 690119162 690121170 2008 False 839.000000 1982 89.112667 506 2563 3 chr7B.!!$F7 2057
10 TraesCS7A01G510400 chr7D 606010719 606012771 2052 False 2750.000000 2750 91.090000 1102 3130 1 chr7D.!!$F3 2028
11 TraesCS7A01G510400 chr7D 605946645 605948508 1863 False 2213.000000 2213 88.494000 506 2340 1 chr7D.!!$F1 1834
12 TraesCS7A01G510400 chr7D 606106489 606108873 2384 False 1502.000000 2309 89.691500 818 3129 2 chr7D.!!$F4 2311
13 TraesCS7A01G510400 chr7D 606301175 606303693 2518 False 1363.500000 2207 85.888000 506 3130 2 chr7D.!!$F6 2624
14 TraesCS7A01G510400 chr7D 605957469 605958276 807 False 1053.000000 1053 90.517000 2336 3130 1 chr7D.!!$F2 794
15 TraesCS7A01G510400 chr7D 606180330 606183483 3153 False 859.750000 1443 88.988000 506 3128 4 chr7D.!!$F5 2622

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
303 305 0.749818 CTCTAGGACTCCAGCGCTCA 60.750 60.0 7.13 0.0 0.00 4.26 F
1216 1496 0.555769 TGCCAGGTGGGAAGAAGTTT 59.444 50.0 0.00 0.0 40.01 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1847 0.036952 CTTGGCATCCGTCACAGTCT 60.037 55.0 0.0 0.0 0.0 3.24 R
3067 4050 5.268387 TGCCTAAACCATCATAACACCATT 58.732 37.5 0.0 0.0 0.0 3.16 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
20 21 4.597032 CTCTCGGAGGAGGAGCAT 57.403 61.111 4.96 0.00 40.85 3.79
82 83 1.807981 CATACTTCGAACGCCGGCA 60.808 57.895 28.98 2.40 39.14 5.69
104 105 2.507324 GAGCTGTTCGCCTCCGTC 60.507 66.667 0.00 0.00 40.39 4.79
140 141 1.455587 CAGGGGGTGCAACAACAGT 60.456 57.895 3.06 0.00 39.98 3.55
141 142 1.455587 AGGGGGTGCAACAACAGTG 60.456 57.895 3.06 0.00 39.98 3.66
167 168 3.001902 TACCTCGAGGGCAGCAACG 62.002 63.158 34.04 7.20 40.27 4.10
262 264 1.392534 GGTCTTCCTCCTCCTCCCA 59.607 63.158 0.00 0.00 0.00 4.37
293 295 2.781174 CTCCTACCACTCCTCTAGGACT 59.219 54.545 0.00 0.00 39.78 3.85
303 305 0.749818 CTCTAGGACTCCAGCGCTCA 60.750 60.000 7.13 0.00 0.00 4.26
545 547 5.107760 GCGACTTCGATTGTACTGTGTTAAA 60.108 40.000 2.02 0.00 43.02 1.52
756 767 6.254589 CGTGCTCCAACATTTGTTAAGAAAAA 59.745 34.615 1.47 0.00 36.32 1.94
839 1045 4.463539 TGGCACAAGCAGACATCAAAATAT 59.536 37.500 0.00 0.00 44.61 1.28
1216 1496 0.555769 TGCCAGGTGGGAAGAAGTTT 59.444 50.000 0.00 0.00 40.01 2.66
1227 1508 4.959210 TGGGAAGAAGTTTGGAAAACATGA 59.041 37.500 0.00 0.00 0.00 3.07
1229 1510 4.976116 GGAAGAAGTTTGGAAAACATGACG 59.024 41.667 0.00 0.00 0.00 4.35
2230 2872 7.038231 CCCCTATAGGAATCGGTTCTATTTTCT 60.038 40.741 21.07 0.00 38.24 2.52
2329 2972 4.345257 AGTGCCTGAAGTCTAGAGTTCAAA 59.655 41.667 32.52 22.30 46.52 2.69
2334 2977 6.351456 GCCTGAAGTCTAGAGTTCAAATACCT 60.351 42.308 32.52 5.57 46.52 3.08
2627 3576 4.464008 AGGGTGGCATGAGTAATACAATG 58.536 43.478 0.00 0.00 0.00 2.82
2686 3635 7.856415 AGGATTACCCATCTATAATCTGCTTC 58.144 38.462 0.00 0.00 37.74 3.86
2736 3699 8.423906 TCCTGAGAATACCATATAAAGGAGTC 57.576 38.462 1.89 0.00 0.00 3.36
3042 4025 7.305813 TCAGGTTCACCAGTACTTAAATGTA 57.694 36.000 0.00 0.00 38.89 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 1.144276 TTGTTGACGGAGGCGAACA 59.856 52.632 0.00 0.00 0.00 3.18
104 105 3.521308 GACCACCAGCGCGTTGTTG 62.521 63.158 21.64 17.58 0.00 3.33
167 168 1.007618 GGTACTGTAGCGGCGGATC 60.008 63.158 9.78 0.00 0.00 3.36
202 204 3.000819 ATGGGCCGACACTCCGAA 61.001 61.111 0.00 0.00 0.00 4.30
262 264 0.106116 GTGGTAGGAGGATCGGGAGT 60.106 60.000 0.00 0.00 34.37 3.85
303 305 0.036732 TTCTTGGGCTTGACGCTGAT 59.963 50.000 0.00 0.00 39.13 2.90
488 490 2.439960 ATCCCGCGCCCACTTCATA 61.440 57.895 0.00 0.00 0.00 2.15
545 547 8.470002 GTGAGGCCTAAACTCATATTCATTTTT 58.530 33.333 4.42 0.00 45.72 1.94
674 680 2.144833 CTTTGTTCGGCTGCATGGCA 62.145 55.000 0.50 0.00 41.89 4.92
1216 1496 0.801872 CATCGCCGTCATGTTTTCCA 59.198 50.000 0.00 0.00 0.00 3.53
1288 1571 2.796651 CGAGGACTCGTAACCCGG 59.203 66.667 13.23 0.00 46.99 5.73
1479 1847 0.036952 CTTGGCATCCGTCACAGTCT 60.037 55.000 0.00 0.00 0.00 3.24
1505 1873 1.555075 CCCCGACCTGAGAATCTTCAA 59.445 52.381 0.00 0.00 34.92 2.69
2627 3576 8.526681 CGTAAATACAACATACGTAGTTTCCTC 58.473 37.037 0.08 0.00 37.78 3.71
2736 3699 6.375455 ACTCAATGTATCTGCTTAAAAGTGGG 59.625 38.462 0.00 0.00 0.00 4.61
3067 4050 5.268387 TGCCTAAACCATCATAACACCATT 58.732 37.500 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.