Multiple sequence alignment - TraesCS5B01G506600

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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 TraesCS5B01G506600 chr5B 100.000 2497 0 0 1 2497 671854346 671856842 0 4612
1 TraesCS5B01G506600 chr7B 93.227 2510 147 13 1 2497 54289176 54286677 0 3672
2 TraesCS5B01G506600 chr7B 93.511 2404 133 14 1 2390 330999787 330997393 0 3554
3 TraesCS5B01G506600 chr7B 93.038 2413 150 17 89 2489 655033393 655030987 0 3509
4 TraesCS5B01G506600 chr6B 93.036 2513 153 12 1 2497 169048034 169050540 0 3651
5 TraesCS5B01G506600 chr6B 92.871 2511 152 15 1 2497 593274270 593271773 0 3620
6 TraesCS5B01G506600 chr6B 91.271 2509 192 19 1 2494 689394787 689397283 0 3395
7 TraesCS5B01G506600 chr4B 91.532 2539 165 25 1 2497 546152111 546154641 0 3452
8 TraesCS5B01G506600 chr2B 91.438 2511 184 17 8 2497 675965695 675963195 0 3417
9 TraesCS5B01G506600 chr2B 89.273 2517 227 24 8 2497 67194170 67191670 0 3112
10 TraesCS5B01G506600 chr3B 94.228 2235 119 9 265 2497 725404132 725401906 0 3404
11 TraesCS5B01G506600 chr3B 92.497 2359 163 13 143 2497 661695857 661693509 0 3363
12 TraesCS5B01G506600 chr3B 87.449 2430 254 37 5 2390 706230023 706227601 0 2750
13 TraesCS5B01G506600 chr3B 87.882 982 83 22 1 961 17179549 17178583 0 1122
14 TraesCS5B01G506600 chr4A 89.939 1312 104 17 1 1289 647862435 647863741 0 1666
15 TraesCS5B01G506600 chr7A 89.969 1286 92 19 5 1274 139499824 139498560 0 1626
16 TraesCS5B01G506600 chr7A 90.498 1105 69 13 1 1091 67376119 67375037 0 1426
17 TraesCS5B01G506600 chr7A 90.273 1100 72 12 5 1091 67114078 67113001 0 1406
18 TraesCS5B01G506600 chr7A 90.000 1100 75 12 5 1091 67142232 67141155 0 1389


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 TraesCS5B01G506600 chr5B 671854346 671856842 2496 False 4612 4612 100.000 1 2497 1 chr5B.!!$F1 2496
1 TraesCS5B01G506600 chr7B 54286677 54289176 2499 True 3672 3672 93.227 1 2497 1 chr7B.!!$R1 2496
2 TraesCS5B01G506600 chr7B 330997393 330999787 2394 True 3554 3554 93.511 1 2390 1 chr7B.!!$R2 2389
3 TraesCS5B01G506600 chr7B 655030987 655033393 2406 True 3509 3509 93.038 89 2489 1 chr7B.!!$R3 2400
4 TraesCS5B01G506600 chr6B 169048034 169050540 2506 False 3651 3651 93.036 1 2497 1 chr6B.!!$F1 2496
5 TraesCS5B01G506600 chr6B 593271773 593274270 2497 True 3620 3620 92.871 1 2497 1 chr6B.!!$R1 2496
6 TraesCS5B01G506600 chr6B 689394787 689397283 2496 False 3395 3395 91.271 1 2494 1 chr6B.!!$F2 2493
7 TraesCS5B01G506600 chr4B 546152111 546154641 2530 False 3452 3452 91.532 1 2497 1 chr4B.!!$F1 2496
8 TraesCS5B01G506600 chr2B 675963195 675965695 2500 True 3417 3417 91.438 8 2497 1 chr2B.!!$R2 2489
9 TraesCS5B01G506600 chr2B 67191670 67194170 2500 True 3112 3112 89.273 8 2497 1 chr2B.!!$R1 2489
10 TraesCS5B01G506600 chr3B 725401906 725404132 2226 True 3404 3404 94.228 265 2497 1 chr3B.!!$R4 2232
11 TraesCS5B01G506600 chr3B 661693509 661695857 2348 True 3363 3363 92.497 143 2497 1 chr3B.!!$R2 2354
12 TraesCS5B01G506600 chr3B 706227601 706230023 2422 True 2750 2750 87.449 5 2390 1 chr3B.!!$R3 2385
13 TraesCS5B01G506600 chr3B 17178583 17179549 966 True 1122 1122 87.882 1 961 1 chr3B.!!$R1 960
14 TraesCS5B01G506600 chr4A 647862435 647863741 1306 False 1666 1666 89.939 1 1289 1 chr4A.!!$F1 1288
15 TraesCS5B01G506600 chr7A 139498560 139499824 1264 True 1626 1626 89.969 5 1274 1 chr7A.!!$R4 1269
16 TraesCS5B01G506600 chr7A 67375037 67376119 1082 True 1426 1426 90.498 1 1091 1 chr7A.!!$R3 1090
17 TraesCS5B01G506600 chr7A 67113001 67114078 1077 True 1406 1406 90.273 5 1091 1 chr7A.!!$R1 1086
18 TraesCS5B01G506600 chr7A 67141155 67142232 1077 True 1389 1389 90.000 5 1091 1 chr7A.!!$R2 1086

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
532 559 1.832883 TGTAGTTGCATGCGGGATTT 58.167 45.0 14.09 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1959 0.304705 ACGCACTCGAAACAGCAAAG 59.695 50.0 0.0 0.0 39.41 2.77 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
80 81 2.102420 CCAATGTGCCTACAGATACGGA 59.898 50.000 0.00 0.00 40.79 4.69
283 294 4.908601 TGACCACACCACATAATCTCTT 57.091 40.909 0.00 0.00 0.00 2.85
532 559 1.832883 TGTAGTTGCATGCGGGATTT 58.167 45.000 14.09 0.00 0.00 2.17
812 876 9.862585 GCCATGTAAACTAACTTTTTGATTTTG 57.137 29.630 0.00 0.00 0.00 2.44
1116 1193 0.171903 AGGTGCTTGATTCAATGCGC 59.828 50.000 18.17 18.17 32.05 6.09
1120 1197 0.374758 GCTTGATTCAATGCGCTCGA 59.625 50.000 9.73 0.00 0.00 4.04
1309 1389 1.272480 GCCCTTTACACCAATCCCACT 60.272 52.381 0.00 0.00 0.00 4.00
1313 1393 3.521937 CCTTTACACCAATCCCACTCCTA 59.478 47.826 0.00 0.00 0.00 2.94
1475 1564 1.029408 TTGTCACAGCTGCAACGGTT 61.029 50.000 15.27 0.00 0.00 4.44
1496 1585 5.154222 GTTGTTGAGCTCCGGAAAATTTAG 58.846 41.667 12.15 0.00 0.00 1.85
1620 1709 2.421739 GCGCTCCATACCGGATGT 59.578 61.111 9.46 0.00 45.19 3.06
1623 1712 0.319040 CGCTCCATACCGGATGTCTG 60.319 60.000 9.46 0.00 45.19 3.51
1624 1713 1.040646 GCTCCATACCGGATGTCTGA 58.959 55.000 9.46 0.23 45.19 3.27
1743 1837 1.783071 TGTAGTGGTGGTGTGTGAGA 58.217 50.000 0.00 0.00 0.00 3.27
1801 1897 6.092259 GGTGTGAACCTATTTAGTCATGACAC 59.908 42.308 27.02 12.28 0.00 3.67
1809 1905 7.344612 ACCTATTTAGTCATGACACCAGATACA 59.655 37.037 27.02 3.96 0.00 2.29
1853 1955 1.959985 TGGTTTCATCGTTTGCACCAT 59.040 42.857 0.00 0.00 34.92 3.55
1857 1959 0.804364 TCATCGTTTGCACCATCAGC 59.196 50.000 0.00 0.00 0.00 4.26
2155 2270 7.686438 TGCAGAGTCATTACAAATAACATGT 57.314 32.000 0.00 0.00 34.81 3.21
2188 2304 6.316140 CAGTACAGCTAACATGGCAGATTTAA 59.684 38.462 0.00 0.00 0.00 1.52
2216 2332 1.945387 ACACGGCAGATTCAGCATAG 58.055 50.000 3.34 0.00 0.00 2.23
2298 2437 4.591924 ACCCAGTATACTTACCATGGTAGC 59.408 45.833 23.40 11.30 31.71 3.58
2375 2563 6.127925 ACACACATAACATGGCAGATTAAGTG 60.128 38.462 19.23 19.23 34.99 3.16
2397 2585 1.826921 ATAGCATGGCACCTGCAGC 60.827 57.895 14.90 0.00 44.36 5.25
2410 2598 2.509548 ACCTGCAGCTACCCATTCAATA 59.490 45.455 8.66 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.994463 GGTGGCACTCCCTCAGATT 59.006 57.895 18.45 0.00 35.69 2.40
532 559 9.657419 CATATCCATATGCTTGTTGATGTAGTA 57.343 33.333 0.00 0.00 34.37 1.82
812 876 1.102978 ATAGTTTTGCACGGGGATGC 58.897 50.000 0.00 0.00 46.32 3.91
824 889 6.220726 ACTTTGAAGTTGCCACATAGTTTT 57.779 33.333 0.00 0.00 35.21 2.43
1116 1193 0.805322 GGTCTGCATCAGCTGTCGAG 60.805 60.000 14.67 6.07 42.74 4.04
1120 1197 1.905215 AGTAAGGTCTGCATCAGCTGT 59.095 47.619 14.67 0.00 42.74 4.40
1475 1564 4.454504 GTCTAAATTTTCCGGAGCTCAACA 59.545 41.667 17.19 0.00 0.00 3.33
1496 1585 4.278170 TCATTTGTCAACCAGTTCCATGTC 59.722 41.667 0.00 0.00 0.00 3.06
1620 1709 5.451937 CCTCGGCAATAGAATGTAAGTCAGA 60.452 44.000 0.00 0.00 30.01 3.27
1623 1712 4.945246 TCCTCGGCAATAGAATGTAAGTC 58.055 43.478 0.00 0.00 0.00 3.01
1624 1713 5.353394 TTCCTCGGCAATAGAATGTAAGT 57.647 39.130 0.00 0.00 0.00 2.24
1827 1929 5.971202 GGTGCAAACGATGAAACCATAATAG 59.029 40.000 0.00 0.00 37.30 1.73
1857 1959 0.304705 ACGCACTCGAAACAGCAAAG 59.695 50.000 0.00 0.00 39.41 2.77
1904 2009 7.905604 TTTACTAACCATGTCTGATGAACTG 57.094 36.000 0.00 0.00 0.00 3.16
2155 2270 6.483307 GCCATGTTAGCTGTACTGAAATATGA 59.517 38.462 17.78 0.00 0.00 2.15
2188 2304 4.323417 TGAATCTGCCGTGTTCTTTGTAT 58.677 39.130 0.00 0.00 0.00 2.29
2262 2378 2.200373 ACTGGGTCTGCCATGTTAAC 57.800 50.000 0.00 0.00 36.17 2.01
2375 2563 1.731700 CAGGTGCCATGCTATGTGC 59.268 57.895 0.00 0.00 43.25 4.57
2390 2578 2.062971 ATTGAATGGGTAGCTGCAGG 57.937 50.000 17.12 0.00 0.00 4.85
2397 2585 8.292444 TGAAGGAAAATGTATTGAATGGGTAG 57.708 34.615 0.00 0.00 0.00 3.18
2410 2598 5.279156 GGCATCAGAAGTTGAAGGAAAATGT 60.279 40.000 0.00 0.00 39.77 2.71


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

AutoCloner maintained by Alex Coulton.