Multiple sequence alignment - TraesCS7A01G462200

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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 TraesCS7A01G462200 chr7A 100.000 2369 0 0 1 2369 658830982 658828614 0.000000e+00 4375.0
1 TraesCS7A01G462200 chr7A 96.226 2385 48 11 1 2369 576140630 576142988 0.000000e+00 3868.0
2 TraesCS7A01G462200 chr7A 93.247 1318 51 13 1056 2369 576226049 576227332 0.000000e+00 1906.0
3 TraesCS7A01G462200 chr7A 88.259 758 53 17 1010 1755 658809015 658808282 0.000000e+00 874.0
4 TraesCS7A01G462200 chr7A 87.763 760 55 19 1010 1755 658784146 658783411 0.000000e+00 854.0
5 TraesCS7A01G462200 chr7A 86.166 759 59 23 1010 1755 576168158 576168883 0.000000e+00 778.0
6 TraesCS7A01G462200 chr7A 87.120 691 54 16 1010 1688 576232656 576233323 0.000000e+00 750.0
7 TraesCS7A01G462200 chr7A 83.364 541 49 16 1012 1532 658930153 658930672 1.660000e-126 462.0
8 TraesCS7A01G462200 chr7A 89.431 369 18 12 1399 1755 576148937 576149296 1.670000e-121 446.0
9 TraesCS7A01G462200 chr7A 85.202 446 43 8 1042 1477 575951333 575951765 1.010000e-118 436.0
10 TraesCS7A01G462200 chr7A 85.238 420 45 5 1015 1434 658891237 658890835 1.310000e-112 416.0
11 TraesCS7A01G462200 chr7A 85.000 420 49 4 1015 1434 576118821 576119226 4.710000e-112 414.0
12 TraesCS7A01G462200 chr7A 79.968 629 67 31 1006 1603 575929249 575929849 2.190000e-110 409.0
13 TraesCS7A01G462200 chr7A 80.594 572 60 25 1009 1548 575460375 575459823 6.140000e-106 394.0
14 TraesCS7A01G462200 chr7A 86.798 356 30 7 1010 1364 658910645 658910306 4.780000e-102 381.0
15 TraesCS7A01G462200 chr7A 86.798 356 30 7 1010 1364 658959952 658959613 4.780000e-102 381.0
16 TraesCS7A01G462200 chr7A 92.000 175 14 0 2195 2369 576169227 576169401 1.820000e-61 246.0
17 TraesCS7A01G462200 chr7A 81.470 313 42 12 2060 2369 575443557 575443258 2.350000e-60 243.0
18 TraesCS7A01G462200 chr7A 91.429 175 15 0 2195 2369 658793859 658793685 8.460000e-60 241.0
19 TraesCS7A01G462200 chr7A 90.857 175 16 0 2195 2369 576149640 576149814 3.940000e-58 235.0
20 TraesCS7A01G462200 chr7A 90.857 175 16 0 2195 2369 576233912 576234086 3.940000e-58 235.0
21 TraesCS7A01G462200 chr7A 92.857 154 8 2 777 930 576213642 576213792 1.100000e-53 220.0
22 TraesCS7A01G462200 chr7A 93.662 142 9 0 921 1062 576214324 576214465 1.840000e-51 213.0
23 TraesCS7A01G462200 chr7A 94.521 73 3 1 1774 1846 576233527 576233598 6.920000e-21 111.0
24 TraesCS7A01G462200 chr7A 91.525 59 5 0 1846 1904 575444409 575444351 5.430000e-12 82.4
25 TraesCS7A01G462200 chr7B 92.201 2231 102 8 159 2369 625983362 625981184 0.000000e+00 3090.0
26 TraesCS7A01G462200 chr7B 82.007 1395 137 50 1011 2355 625972146 625970816 0.000000e+00 1081.0
27 TraesCS7A01G462200 chr7B 82.007 1395 137 50 1011 2355 625975319 625973989 0.000000e+00 1081.0
28 TraesCS7A01G462200 chr7B 85.222 406 45 4 1029 1434 626051388 626050998 1.020000e-108 403.0
29 TraesCS7A01G462200 chr7D 88.435 1029 73 12 1 1012 569709054 569708055 0.000000e+00 1199.0
30 TraesCS7A01G462200 chr7D 91.989 699 43 4 159 844 569455631 569454933 0.000000e+00 968.0
31 TraesCS7A01G462200 chr7D 87.844 691 52 15 1010 1688 569403756 569403086 0.000000e+00 782.0
32 TraesCS7A01G462200 chr7D 86.267 517 38 20 1097 1601 569706876 569706381 4.480000e-147 531.0
33 TraesCS7A01G462200 chr7D 86.939 490 31 18 1131 1604 569454495 569454023 9.700000e-144 520.0
34 TraesCS7A01G462200 chr7D 85.203 419 46 2 1020 1434 569497822 569497416 1.310000e-112 416.0
35 TraesCS7A01G462200 chr7D 85.273 421 40 14 1020 1434 569577282 569576878 4.710000e-112 414.0
36 TraesCS7A01G462200 chr7D 96.040 202 7 1 942 1143 569454885 569454685 6.310000e-86 327.0
37 TraesCS7A01G462200 chr7D 90.960 177 14 2 2195 2369 569402489 569402313 1.090000e-58 237.0
38 TraesCS7A01G462200 chr7D 86.452 155 17 3 1601 1755 570235864 570235714 1.460000e-37 167.0
39 TraesCS7A01G462200 chr7D 86.400 125 16 1 1769 1892 570233818 570233694 4.110000e-28 135.0
40 TraesCS7A01G462200 chr7D 98.485 66 0 1 849 914 569454948 569454884 5.350000e-22 115.0
41 TraesCS7A01G462200 chr7D 91.803 61 5 0 1844 1904 570235606 570235546 4.200000e-13 86.1
42 TraesCS7A01G462200 chr7D 95.556 45 1 1 1842 1886 569706021 569705978 1.170000e-08 71.3
43 TraesCS7A01G462200 chr2D 83.824 68 9 2 203 269 122701109 122701043 1.970000e-06 63.9


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 TraesCS7A01G462200 chr7A 658828614 658830982 2368 True 4375.000000 4375 100.000000 1 2369 1 chr7A.!!$R5 2368
1 TraesCS7A01G462200 chr7A 576140630 576142988 2358 False 3868.000000 3868 96.226000 1 2369 1 chr7A.!!$F4 2368
2 TraesCS7A01G462200 chr7A 576226049 576227332 1283 False 1906.000000 1906 93.247000 1056 2369 1 chr7A.!!$F5 1313
3 TraesCS7A01G462200 chr7A 658808282 658809015 733 True 874.000000 874 88.259000 1010 1755 1 chr7A.!!$R4 745
4 TraesCS7A01G462200 chr7A 658783411 658784146 735 True 854.000000 854 87.763000 1010 1755 1 chr7A.!!$R2 745
5 TraesCS7A01G462200 chr7A 576168158 576169401 1243 False 512.000000 778 89.083000 1010 2369 2 chr7A.!!$F8 1359
6 TraesCS7A01G462200 chr7A 658930153 658930672 519 False 462.000000 462 83.364000 1012 1532 1 chr7A.!!$F6 520
7 TraesCS7A01G462200 chr7A 575929249 575929849 600 False 409.000000 409 79.968000 1006 1603 1 chr7A.!!$F1 597
8 TraesCS7A01G462200 chr7A 575459823 575460375 552 True 394.000000 394 80.594000 1009 1548 1 chr7A.!!$R1 539
9 TraesCS7A01G462200 chr7A 576232656 576234086 1430 False 365.333333 750 90.832667 1010 2369 3 chr7A.!!$F10 1359
10 TraesCS7A01G462200 chr7A 576148937 576149814 877 False 340.500000 446 90.144000 1399 2369 2 chr7A.!!$F7 970
11 TraesCS7A01G462200 chr7A 576213642 576214465 823 False 216.500000 220 93.259500 777 1062 2 chr7A.!!$F9 285
12 TraesCS7A01G462200 chr7B 625981184 625983362 2178 True 3090.000000 3090 92.201000 159 2369 1 chr7B.!!$R1 2210
13 TraesCS7A01G462200 chr7B 625970816 625975319 4503 True 1081.000000 1081 82.007000 1011 2355 2 chr7B.!!$R3 1344
14 TraesCS7A01G462200 chr7D 569705978 569709054 3076 True 600.433333 1199 90.086000 1 1886 3 chr7D.!!$R5 1885
15 TraesCS7A01G462200 chr7D 569402313 569403756 1443 True 509.500000 782 89.402000 1010 2369 2 chr7D.!!$R3 1359
16 TraesCS7A01G462200 chr7D 569454023 569455631 1608 True 482.500000 968 93.363250 159 1604 4 chr7D.!!$R4 1445

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
396 402 2.048127 GTTCGAGGAGCTTGCGGT 60.048 61.111 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 7837 0.108329 ATTACAGGTCCTTGCGGTCG 60.108 55.0 0.0 0.0 0.0 4.79 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
27 28 2.373224 GCATTAAAGCAGGAGAGCCTT 58.627 47.619 0.00 0.0 43.90 4.35
80 81 5.248020 AGAGTAGAATGCCATAATGGAGGAG 59.752 44.000 0.00 0.0 40.96 3.69
81 82 3.803186 AGAATGCCATAATGGAGGAGG 57.197 47.619 0.00 0.0 40.96 4.30
82 83 3.330198 AGAATGCCATAATGGAGGAGGA 58.670 45.455 0.00 0.0 40.96 3.71
396 402 2.048127 GTTCGAGGAGCTTGCGGT 60.048 61.111 0.00 0.0 0.00 5.68
532 538 2.233305 ACATCGACCTAACCTCCACT 57.767 50.000 0.00 0.0 0.00 4.00
625 631 3.181469 GGCAAAGAGTATATGACGTGGGA 60.181 47.826 0.00 0.0 0.00 4.37
1106 2782 2.151202 GAAGATGGACCAGCGAAACAA 58.849 47.619 3.62 0.0 0.00 2.83
1214 3097 1.224315 CCATGGACGCCATCAAGGA 59.776 57.895 5.56 0.0 43.15 3.36
1215 3098 0.179009 CCATGGACGCCATCAAGGAT 60.179 55.000 5.56 0.0 43.15 3.24
1319 3202 0.771755 GACCCAAGGACCAAACTCCT 59.228 55.000 0.00 0.0 43.08 3.69
1353 3236 2.093106 GACGTCCTCCACTATGACAGT 58.907 52.381 3.51 0.0 38.32 3.55
1480 3454 7.657336 TGCAAGTGATGATGTTATATCGTAGA 58.343 34.615 0.00 0.0 45.75 2.59
1482 3456 9.144747 GCAAGTGATGATGTTATATCGTAGATT 57.855 33.333 0.00 0.0 45.12 2.40
1484 3458 9.561270 AAGTGATGATGTTATATCGTAGATTCG 57.439 33.333 0.00 0.0 45.12 3.34
1485 3459 8.731605 AGTGATGATGTTATATCGTAGATTCGT 58.268 33.333 0.00 0.0 45.12 3.85
1486 3460 9.983804 GTGATGATGTTATATCGTAGATTCGTA 57.016 33.333 0.00 0.0 45.12 3.43
1965 7495 4.028131 ACTTTGGTACTATGTGGGATCGA 58.972 43.478 0.00 0.0 0.00 3.59
1982 7512 4.508662 GATCGAACACAGGGAAAGATTCT 58.491 43.478 0.00 0.0 0.00 2.40
1985 7515 4.065088 CGAACACAGGGAAAGATTCTTGA 58.935 43.478 0.00 0.0 0.00 3.02
2297 7837 5.457140 TGCACTTTCACGATGGTTTATTTC 58.543 37.500 0.00 0.0 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 3.160748 GCCTGCTCCTCCTCCTCC 61.161 72.222 0.00 0.00 0.00 4.30
81 82 2.364842 TGCCTGCTCCTCCTCCTC 60.365 66.667 0.00 0.00 0.00 3.71
82 83 2.686835 GTGCCTGCTCCTCCTCCT 60.687 66.667 0.00 0.00 0.00 3.69
140 145 3.058016 GTCTCCACCATGACAATGTTGTG 60.058 47.826 2.65 0.00 42.43 3.33
625 631 4.158025 AGTCTATTCTTCGTCGAACATGGT 59.842 41.667 2.90 0.00 0.00 3.55
1106 2782 1.404717 CGAGCAGCCACTTGATGTAGT 60.405 52.381 0.00 0.00 0.00 2.73
1187 3064 2.751436 CGTCCATGGCCTTGTGGG 60.751 66.667 16.81 2.70 36.15 4.61
1319 3202 1.617755 GACGTCGTACTGGTCGTCGA 61.618 60.000 0.00 0.00 41.89 4.20
1353 3236 4.459337 TCAGTAGATCAAGCTTCTTCGTCA 59.541 41.667 0.00 0.00 0.00 4.35
1480 3454 3.447586 AGGACACACTACATGCTACGAAT 59.552 43.478 0.00 0.00 0.00 3.34
1482 3456 2.422479 GAGGACACACTACATGCTACGA 59.578 50.000 0.00 0.00 0.00 3.43
1483 3457 2.163613 TGAGGACACACTACATGCTACG 59.836 50.000 0.00 0.00 0.00 3.51
1484 3458 3.429547 CCTGAGGACACACTACATGCTAC 60.430 52.174 0.00 0.00 0.00 3.58
1485 3459 2.760650 CCTGAGGACACACTACATGCTA 59.239 50.000 0.00 0.00 0.00 3.49
1486 3460 1.552337 CCTGAGGACACACTACATGCT 59.448 52.381 0.00 0.00 0.00 3.79
1487 3461 2.009042 GCCTGAGGACACACTACATGC 61.009 57.143 0.65 0.00 0.00 4.06
1769 7055 5.479375 AGAAGGTAAGTGGACTTATTCGTGA 59.521 40.000 2.65 0.00 40.20 4.35
1965 7495 5.053978 AGTCAAGAATCTTTCCCTGTGTT 57.946 39.130 0.00 0.00 0.00 3.32
2297 7837 0.108329 ATTACAGGTCCTTGCGGTCG 60.108 55.000 0.00 0.00 0.00 4.79
2338 7878 2.642427 TGGATTTACAGATGCATGCGT 58.358 42.857 13.43 13.43 0.00 5.24
2340 7880 4.374843 TGTTGGATTTACAGATGCATGC 57.625 40.909 11.82 11.82 0.00 4.06
2342 7882 5.711506 TCAGTTGTTGGATTTACAGATGCAT 59.288 36.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.