Multiple sequence alignment - TraesCS5A01G364000

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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 TraesCS5A01G364000 chr5A 100.000 2492 0 0 1 2492 564354427 564351936 0.000000e+00 4602.0
1 TraesCS5A01G364000 chr5A 96.071 789 19 4 687 1463 570478843 570479631 0.000000e+00 1275.0
2 TraesCS5A01G364000 chr5A 95.318 598 23 4 1 596 620525665 620525071 0.000000e+00 944.0
3 TraesCS5A01G364000 chr5A 95.142 597 26 3 1 596 480476440 480475846 0.000000e+00 939.0
4 TraesCS5A01G364000 chr5A 94.975 597 26 4 1 596 222944190 222944783 0.000000e+00 933.0
5 TraesCS5A01G364000 chr5A 98.077 52 1 0 594 645 570478501 570478552 9.490000e-15 91.6
6 TraesCS5A01G364000 chr2A 97.141 1819 37 7 687 2492 57824630 57826446 0.000000e+00 3057.0
7 TraesCS5A01G364000 chr2A 84.473 1082 135 25 714 1772 404904069 404905140 0.000000e+00 1037.0
8 TraesCS5A01G364000 chr2A 84.254 1086 137 25 714 1775 396207912 396206837 0.000000e+00 1027.0
9 TraesCS5A01G364000 chr2A 95.142 597 25 3 1 596 644372431 644371838 0.000000e+00 939.0
10 TraesCS5A01G364000 chr2A 100.000 85 0 0 596 680 57824273 57824357 9.230000e-35 158.0
11 TraesCS5A01G364000 chr4D 90.567 1781 138 19 725 2485 459190009 459191779 0.000000e+00 2331.0
12 TraesCS5A01G364000 chrUn 91.836 1678 115 11 827 2486 96551843 96553516 0.000000e+00 2320.0
13 TraesCS5A01G364000 chr2D 91.697 1674 119 8 828 2485 469109167 469107498 0.000000e+00 2303.0
14 TraesCS5A01G364000 chr2D 90.588 680 41 11 711 1377 330881446 330880777 0.000000e+00 880.0
15 TraesCS5A01G364000 chr2D 95.402 87 4 0 594 680 330881881 330881795 3.340000e-29 139.0
16 TraesCS5A01G364000 chr1A 91.452 1673 124 9 827 2485 461968019 461966352 0.000000e+00 2279.0
17 TraesCS5A01G364000 chr1A 91.219 1674 127 10 827 2485 35565235 35563567 0.000000e+00 2259.0
18 TraesCS5A01G364000 chr1A 94.975 597 26 3 1 596 457807628 457807035 0.000000e+00 933.0
19 TraesCS5A01G364000 chr7A 93.795 1515 89 3 972 2485 48780230 48781740 0.000000e+00 2272.0
20 TraesCS5A01G364000 chr7A 83.333 84 14 0 597 680 7966005 7965922 7.390000e-11 78.7
21 TraesCS5A01G364000 chr7A 83.333 84 14 0 597 680 8105223 8105140 7.390000e-11 78.7
22 TraesCS5A01G364000 chr2B 93.245 1510 97 3 978 2486 677290936 677292441 0.000000e+00 2218.0
23 TraesCS5A01G364000 chr2B 93.285 1504 94 4 984 2486 139362533 139361036 0.000000e+00 2211.0
24 TraesCS5A01G364000 chr3A 95.812 597 21 4 1 596 358839797 358840390 0.000000e+00 961.0
25 TraesCS5A01G364000 chr3A 95.142 597 22 4 1 596 184593101 184592511 0.000000e+00 935.0
26 TraesCS5A01G364000 chr4A 95.310 597 24 3 1 596 268168180 268168773 0.000000e+00 944.0
27 TraesCS5A01G364000 chr4A 95.310 597 25 3 1 596 461084622 461085216 0.000000e+00 944.0
28 TraesCS5A01G364000 chr5B 93.740 607 25 6 759 1353 92571469 92572074 0.000000e+00 898.0
29 TraesCS5A01G364000 chr5B 97.674 86 1 1 595 680 92570981 92571065 2.000000e-31 147.0
30 TraesCS5A01G364000 chr5B 100.000 29 0 0 711 739 92571441 92571469 1.000000e-03 54.7
31 TraesCS5A01G364000 chr3B 93.176 381 13 5 898 1266 564172336 564172715 4.690000e-152 547.0
32 TraesCS5A01G364000 chr3B 89.888 178 15 3 707 883 564172098 564172273 2.490000e-55 226.0
33 TraesCS5A01G364000 chr3B 94.186 86 5 0 595 680 564171659 564171744 5.590000e-27 132.0


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 TraesCS5A01G364000 chr5A 564351936 564354427 2491 True 4602.000000 4602 100.000000 1 2492 1 chr5A.!!$R2 2491
1 TraesCS5A01G364000 chr5A 620525071 620525665 594 True 944.000000 944 95.318000 1 596 1 chr5A.!!$R3 595
2 TraesCS5A01G364000 chr5A 480475846 480476440 594 True 939.000000 939 95.142000 1 596 1 chr5A.!!$R1 595
3 TraesCS5A01G364000 chr5A 222944190 222944783 593 False 933.000000 933 94.975000 1 596 1 chr5A.!!$F1 595
4 TraesCS5A01G364000 chr5A 570478501 570479631 1130 False 683.300000 1275 97.074000 594 1463 2 chr5A.!!$F2 869
5 TraesCS5A01G364000 chr2A 57824273 57826446 2173 False 1607.500000 3057 98.570500 596 2492 2 chr2A.!!$F2 1896
6 TraesCS5A01G364000 chr2A 404904069 404905140 1071 False 1037.000000 1037 84.473000 714 1772 1 chr2A.!!$F1 1058
7 TraesCS5A01G364000 chr2A 396206837 396207912 1075 True 1027.000000 1027 84.254000 714 1775 1 chr2A.!!$R1 1061
8 TraesCS5A01G364000 chr2A 644371838 644372431 593 True 939.000000 939 95.142000 1 596 1 chr2A.!!$R2 595
9 TraesCS5A01G364000 chr4D 459190009 459191779 1770 False 2331.000000 2331 90.567000 725 2485 1 chr4D.!!$F1 1760
10 TraesCS5A01G364000 chrUn 96551843 96553516 1673 False 2320.000000 2320 91.836000 827 2486 1 chrUn.!!$F1 1659
11 TraesCS5A01G364000 chr2D 469107498 469109167 1669 True 2303.000000 2303 91.697000 828 2485 1 chr2D.!!$R1 1657
12 TraesCS5A01G364000 chr2D 330880777 330881881 1104 True 509.500000 880 92.995000 594 1377 2 chr2D.!!$R2 783
13 TraesCS5A01G364000 chr1A 461966352 461968019 1667 True 2279.000000 2279 91.452000 827 2485 1 chr1A.!!$R3 1658
14 TraesCS5A01G364000 chr1A 35563567 35565235 1668 True 2259.000000 2259 91.219000 827 2485 1 chr1A.!!$R1 1658
15 TraesCS5A01G364000 chr1A 457807035 457807628 593 True 933.000000 933 94.975000 1 596 1 chr1A.!!$R2 595
16 TraesCS5A01G364000 chr7A 48780230 48781740 1510 False 2272.000000 2272 93.795000 972 2485 1 chr7A.!!$F1 1513
17 TraesCS5A01G364000 chr2B 677290936 677292441 1505 False 2218.000000 2218 93.245000 978 2486 1 chr2B.!!$F1 1508
18 TraesCS5A01G364000 chr2B 139361036 139362533 1497 True 2211.000000 2211 93.285000 984 2486 1 chr2B.!!$R1 1502
19 TraesCS5A01G364000 chr3A 358839797 358840390 593 False 961.000000 961 95.812000 1 596 1 chr3A.!!$F1 595
20 TraesCS5A01G364000 chr3A 184592511 184593101 590 True 935.000000 935 95.142000 1 596 1 chr3A.!!$R1 595
21 TraesCS5A01G364000 chr4A 268168180 268168773 593 False 944.000000 944 95.310000 1 596 1 chr4A.!!$F1 595
22 TraesCS5A01G364000 chr4A 461084622 461085216 594 False 944.000000 944 95.310000 1 596 1 chr4A.!!$F2 595
23 TraesCS5A01G364000 chr5B 92570981 92572074 1093 False 366.566667 898 97.138000 595 1353 3 chr5B.!!$F1 758
24 TraesCS5A01G364000 chr3B 564171659 564172715 1056 False 301.666667 547 92.416667 595 1266 3 chr3B.!!$F1 671

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
278 282 0.818938 TTTACGATACGGAGCTGCCA 59.181 50.0 0.0 0.0 35.94 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2704 1.745489 GGTCCATGTCACTTCCGGC 60.745 63.158 0.0 0.0 0.0 6.13 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
122 123 3.646715 GCCCACACCCTAGCCACA 61.647 66.667 0.00 0.00 0.00 4.17
274 278 1.553308 GCGTTTTACGATACGGAGCT 58.447 50.000 3.04 0.00 46.05 4.09
278 282 0.818938 TTTACGATACGGAGCTGCCA 59.181 50.000 0.00 0.00 35.94 4.92
513 517 7.996788 TGATCCCTAGTATCCACTATGTTCTA 58.003 38.462 0.00 0.00 36.66 2.10
526 530 8.539544 TCCACTATGTTCTAAGATTGATGTTGA 58.460 33.333 0.00 0.00 0.00 3.18
680 684 1.674817 CCCGTGTTCAGTTAGCCGAAT 60.675 52.381 0.00 0.00 0.00 3.34
682 686 2.066262 CGTGTTCAGTTAGCCGAATGT 58.934 47.619 0.00 0.00 0.00 2.71
684 688 3.064207 GTGTTCAGTTAGCCGAATGTCA 58.936 45.455 0.00 0.00 0.00 3.58
685 689 3.684788 GTGTTCAGTTAGCCGAATGTCAT 59.315 43.478 0.00 0.00 0.00 3.06
709 1082 2.037367 AGACCTACCTGGCAGCGA 59.963 61.111 9.56 0.00 40.22 4.93
801 1229 7.847848 AGGTATGGTTCCTACTCCTTTGTATAA 59.152 37.037 0.00 0.00 33.04 0.98
974 1471 7.821359 CCAGATCCATGGTTACAAGTCATATAG 59.179 40.741 12.58 0.00 35.47 1.31
1036 1533 5.600696 TGAACAAAAGAAAAAGGATGGCTC 58.399 37.500 0.00 0.00 0.00 4.70
1087 1584 2.198827 AATGGCAGTCATTGTTCGGA 57.801 45.000 0.00 0.00 43.85 4.55
1273 1770 2.027192 AGGGATCGCAACTTGCTAGAAA 60.027 45.455 12.83 0.00 42.25 2.52
1274 1771 2.945668 GGGATCGCAACTTGCTAGAAAT 59.054 45.455 11.93 0.00 42.25 2.17
1334 1836 6.413052 TGTTTTTGCATACAATTGGGCATAT 58.587 32.000 18.29 2.29 35.98 1.78
1339 1841 4.900652 TGCATACAATTGGGCATATCCTTT 59.099 37.500 10.83 0.00 34.39 3.11
1445 1948 8.198109 AGGCGAGCTTCGTAATGATTATATAAT 58.802 33.333 7.72 7.72 42.81 1.28
1943 2450 1.203001 CCAAGCCTGGGTTCTTACCAA 60.203 52.381 8.43 0.00 46.96 3.67
1949 2456 3.386726 GCCTGGGTTCTTACCAACTTTTT 59.613 43.478 0.00 0.00 46.96 1.94
2170 2677 8.575589 TGTTGTGTTCTTCATAATTATGCACTT 58.424 29.630 22.61 0.00 33.76 3.16
2197 2704 7.173735 TCACAAGGGATCGATGAATTCATTATG 59.826 37.037 21.57 14.38 36.57 1.90
2237 2744 2.819608 ACCCAACCAATTCGAACATCAG 59.180 45.455 0.00 0.00 0.00 2.90
2293 2801 2.806945 TAGGCTACAAATTGCTGCCT 57.193 45.000 26.65 26.65 46.17 4.75
2475 2986 3.747854 TTGCAACATTTTGATGGCTGA 57.252 38.095 0.00 0.00 34.24 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 164 2.039405 AGGGGCCCATGAGGTAGG 60.039 66.667 27.72 0.00 38.26 3.18
162 165 2.455565 CCAGGGGCCCATGAGGTAG 61.456 68.421 37.56 16.70 38.26 3.18
231 235 6.257193 GCGACGAATCCTTCTCCTTTATTTTA 59.743 38.462 0.00 0.00 0.00 1.52
252 256 1.510338 CTCCGTATCGTAAAACGCGAC 59.490 52.381 15.93 0.00 42.21 5.19
274 278 0.830023 GGTTTTAGGGCTTGGTGGCA 60.830 55.000 0.00 0.00 43.83 4.92
278 282 1.003233 CGAGAGGTTTTAGGGCTTGGT 59.997 52.381 0.00 0.00 0.00 3.67
513 517 8.289939 AGCAAAGTCATATCAACATCAATCTT 57.710 30.769 0.00 0.00 0.00 2.40
680 684 1.568504 GTAGGTCTCCACCCATGACA 58.431 55.000 0.00 0.00 45.12 3.58
682 686 0.716591 AGGTAGGTCTCCACCCATGA 59.283 55.000 0.00 0.00 45.12 3.07
684 688 0.326618 CCAGGTAGGTCTCCACCCAT 60.327 60.000 0.00 0.00 45.12 4.00
685 689 1.080354 CCAGGTAGGTCTCCACCCA 59.920 63.158 0.00 0.00 45.12 4.51
709 1082 1.684049 CCGCTCCTTCCTCTCCTGT 60.684 63.158 0.00 0.00 0.00 4.00
801 1229 3.956199 CAATCCATTGTACCCATCAAGCT 59.044 43.478 0.00 0.00 33.22 3.74
974 1471 5.762045 ACAAGTGATGCATACAGTCAAAAC 58.238 37.500 0.00 0.00 0.00 2.43
1036 1533 1.286880 CAAAAACAGCTGCTCCCCG 59.713 57.895 15.27 0.00 0.00 5.73
1087 1584 7.127955 ACATGGTCTCCTCTTCCTTATAATTGT 59.872 37.037 0.00 0.00 0.00 2.71
1300 1797 6.630444 TGTATGCAAAAACATTGCCAATTT 57.370 29.167 10.34 0.00 44.32 1.82
1334 1836 5.076873 CAGAAACAACCCTATTCCAAAGGA 58.923 41.667 0.00 0.00 36.08 3.36
1339 1841 2.109128 TGGCAGAAACAACCCTATTCCA 59.891 45.455 0.00 0.00 0.00 3.53
1379 1881 6.757897 TTCTAAAATAGATGCTGGTTGTGG 57.242 37.500 0.00 0.00 34.22 4.17
1592 2095 4.216687 TCGCACATGTGTACCATCGATATA 59.783 41.667 26.01 2.53 0.00 0.86
1593 2096 3.005367 TCGCACATGTGTACCATCGATAT 59.995 43.478 26.01 0.00 0.00 1.63
1846 2350 7.790782 ATTGGTTACAATGGTTTCATAAGGT 57.209 32.000 0.00 0.00 45.27 3.50
1889 2396 5.163540 CGGCATCAACTAGGTAGTACTTTCT 60.164 44.000 0.00 1.63 34.99 2.52
1943 2450 2.335316 TACCTCACGCCACAAAAAGT 57.665 45.000 0.00 0.00 0.00 2.66
1949 2456 2.027653 TCAAATGATACCTCACGCCACA 60.028 45.455 0.00 0.00 33.22 4.17
2170 2677 4.842574 TGAATTCATCGATCCCTTGTGAA 58.157 39.130 3.38 0.00 33.82 3.18
2197 2704 1.745489 GGTCCATGTCACTTCCGGC 60.745 63.158 0.00 0.00 0.00 6.13
2237 2744 5.394115 CCCTATTGTCACTTAATTGTTGCCC 60.394 44.000 0.00 0.00 0.00 5.36
2293 2801 5.450818 AGTTGCCTATCTTCCCACATTTA 57.549 39.130 0.00 0.00 0.00 1.40
2373 2881 4.500127 CAGCCATCAAATGAATGCAAAGA 58.500 39.130 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.