Multiple sequence alignment - TraesCS5A01G290700

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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 TraesCS5A01G290700 chr5A 100.000 2625 0 0 1 2625 500831776 500834400 0.000000e+00 4848
1 TraesCS5A01G290700 chr5A 92.436 2102 141 7 1 2088 497431265 497429168 0.000000e+00 2985
2 TraesCS5A01G290700 chr5A 93.678 1218 56 8 894 2092 603019456 603020671 0.000000e+00 1803
3 TraesCS5A01G290700 chr5A 91.437 981 69 6 1 980 500279164 500278198 0.000000e+00 1332
4 TraesCS5A01G290700 chr5A 96.118 541 18 3 2086 2625 500275980 500275442 0.000000e+00 880
5 TraesCS5A01G290700 chr5A 95.941 542 18 4 2086 2625 603030676 603031215 0.000000e+00 876
6 TraesCS5A01G290700 chr7A 93.105 2103 127 10 1 2088 339969266 339971365 0.000000e+00 3064
7 TraesCS5A01G290700 chr7A 95.203 542 21 5 2086 2625 339972920 339973458 0.000000e+00 852
8 TraesCS5A01G290700 chr3D 92.898 2112 117 17 2 2088 307675003 307677106 0.000000e+00 3038
9 TraesCS5A01G290700 chr3D 91.076 2118 123 16 2 2088 485942487 485940405 0.000000e+00 2804
10 TraesCS5A01G290700 chr3D 96.494 542 16 3 2086 2625 307677228 307677768 0.000000e+00 893
11 TraesCS5A01G290700 chr6B 90.066 2124 129 34 2 2087 687835942 687833863 0.000000e+00 2678
12 TraesCS5A01G290700 chr6B 95.018 542 20 4 2086 2625 687832299 687831763 0.000000e+00 845
13 TraesCS5A01G290700 chr6D 93.430 1659 92 6 445 2088 221068905 221067249 0.000000e+00 2444
14 TraesCS5A01G290700 chr6D 93.932 412 23 2 2 412 221078122 221077712 2.870000e-174 621
15 TraesCS5A01G290700 chr5D 95.735 1102 38 2 993 2088 428545668 428546766 0.000000e+00 1766
16 TraesCS5A01G290700 chr5D 90.400 875 53 9 2 861 428544482 428545340 0.000000e+00 1122
17 TraesCS5A01G290700 chr5B 92.279 1075 74 5 1021 2088 39550379 39549307 0.000000e+00 1517
18 TraesCS5A01G290700 chr5B 88.350 1133 84 33 2 1091 464382710 464383837 0.000000e+00 1317
19 TraesCS5A01G290700 chr5B 92.279 544 35 6 2086 2625 508086026 508085486 0.000000e+00 765
20 TraesCS5A01G290700 chr7B 84.915 1538 117 31 2 1456 227231641 227230136 0.000000e+00 1448
21 TraesCS5A01G290700 chr7B 95.756 542 19 4 2086 2625 24714595 24715134 0.000000e+00 870
22 TraesCS5A01G290700 chr3A 88.820 1127 83 13 2 1091 181042511 181043631 0.000000e+00 1343
23 TraesCS5A01G290700 chr4A 86.349 1260 101 21 238 1456 292379327 292380556 0.000000e+00 1308
24 TraesCS5A01G290700 chr2B 88.499 913 64 11 1 873 414758242 414757331 0.000000e+00 1066
25 TraesCS5A01G290700 chr2B 87.225 955 72 10 2 908 237061389 237060437 0.000000e+00 1042
26 TraesCS5A01G290700 chr2B 95.792 404 14 3 2224 2625 237057758 237057356 0.000000e+00 649
27 TraesCS5A01G290700 chr3B 94.843 543 24 4 2086 2625 620076622 620077163 0.000000e+00 845
28 TraesCS5A01G290700 chr3B 93.606 391 23 2 2 392 620072743 620073131 1.350000e-162 582
29 TraesCS5A01G290700 chr2A 93.401 394 24 2 1 392 479205323 479205716 1.350000e-162 582
30 TraesCS5A01G290700 chr2A 87.681 138 16 1 2091 2228 683449802 683449666 2.700000e-35 159


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 TraesCS5A01G290700 chr5A 500831776 500834400 2624 False 4848.0 4848 100.0000 1 2625 1 chr5A.!!$F1 2624
1 TraesCS5A01G290700 chr5A 497429168 497431265 2097 True 2985.0 2985 92.4360 1 2088 1 chr5A.!!$R1 2087
2 TraesCS5A01G290700 chr5A 603019456 603020671 1215 False 1803.0 1803 93.6780 894 2092 1 chr5A.!!$F2 1198
3 TraesCS5A01G290700 chr5A 500275442 500279164 3722 True 1106.0 1332 93.7775 1 2625 2 chr5A.!!$R2 2624
4 TraesCS5A01G290700 chr5A 603030676 603031215 539 False 876.0 876 95.9410 2086 2625 1 chr5A.!!$F3 539
5 TraesCS5A01G290700 chr7A 339969266 339973458 4192 False 1958.0 3064 94.1540 1 2625 2 chr7A.!!$F1 2624
6 TraesCS5A01G290700 chr3D 485940405 485942487 2082 True 2804.0 2804 91.0760 2 2088 1 chr3D.!!$R1 2086
7 TraesCS5A01G290700 chr3D 307675003 307677768 2765 False 1965.5 3038 94.6960 2 2625 2 chr3D.!!$F1 2623
8 TraesCS5A01G290700 chr6B 687831763 687835942 4179 True 1761.5 2678 92.5420 2 2625 2 chr6B.!!$R1 2623
9 TraesCS5A01G290700 chr6D 221067249 221068905 1656 True 2444.0 2444 93.4300 445 2088 1 chr6D.!!$R1 1643
10 TraesCS5A01G290700 chr5D 428544482 428546766 2284 False 1444.0 1766 93.0675 2 2088 2 chr5D.!!$F1 2086
11 TraesCS5A01G290700 chr5B 39549307 39550379 1072 True 1517.0 1517 92.2790 1021 2088 1 chr5B.!!$R1 1067
12 TraesCS5A01G290700 chr5B 464382710 464383837 1127 False 1317.0 1317 88.3500 2 1091 1 chr5B.!!$F1 1089
13 TraesCS5A01G290700 chr5B 508085486 508086026 540 True 765.0 765 92.2790 2086 2625 1 chr5B.!!$R2 539
14 TraesCS5A01G290700 chr7B 227230136 227231641 1505 True 1448.0 1448 84.9150 2 1456 1 chr7B.!!$R1 1454
15 TraesCS5A01G290700 chr7B 24714595 24715134 539 False 870.0 870 95.7560 2086 2625 1 chr7B.!!$F1 539
16 TraesCS5A01G290700 chr3A 181042511 181043631 1120 False 1343.0 1343 88.8200 2 1091 1 chr3A.!!$F1 1089
17 TraesCS5A01G290700 chr4A 292379327 292380556 1229 False 1308.0 1308 86.3490 238 1456 1 chr4A.!!$F1 1218
18 TraesCS5A01G290700 chr2B 414757331 414758242 911 True 1066.0 1066 88.4990 1 873 1 chr2B.!!$R1 872
19 TraesCS5A01G290700 chr2B 237057356 237061389 4033 True 845.5 1042 91.5085 2 2625 2 chr2B.!!$R2 2623
20 TraesCS5A01G290700 chr3B 620072743 620077163 4420 False 713.5 845 94.2245 2 2625 2 chr3B.!!$F1 2623

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
501 760 0.254178 CTGCCACCTATGCCTCTTGT 59.746 55.0 0.00 0.0 0.00 3.16 F
1120 1681 0.179181 CTCGCGCAAATGAGCAACAT 60.179 50.0 8.75 0.0 41.01 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1958 0.822532 CTTCCCTGGATCCAGCATGC 60.823 60.000 32.97 10.51 42.35 4.06 R
1975 4259 1.066143 CCCAACGACATCCTAACAGCT 60.066 52.381 0.00 0.00 0.00 4.24 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
150 154 9.764363 AATTTTCCTGAAAACTTATTCACCTTC 57.236 29.630 7.18 0.00 42.32 3.46
377 381 4.218686 GCCCACCACACCAACCCT 62.219 66.667 0.00 0.00 0.00 4.34
469 728 1.619363 CCTCACAATCCCTCCCCCA 60.619 63.158 0.00 0.00 0.00 4.96
474 733 1.167033 ACAATCCCTCCCCCAAAACT 58.833 50.000 0.00 0.00 0.00 2.66
483 742 1.903404 CCCCAAAACTCTTGCCGCT 60.903 57.895 0.00 0.00 0.00 5.52
499 758 1.225704 GCTGCCACCTATGCCTCTT 59.774 57.895 0.00 0.00 0.00 2.85
500 759 1.099879 GCTGCCACCTATGCCTCTTG 61.100 60.000 0.00 0.00 0.00 3.02
501 760 0.254178 CTGCCACCTATGCCTCTTGT 59.746 55.000 0.00 0.00 0.00 3.16
502 761 0.698238 TGCCACCTATGCCTCTTGTT 59.302 50.000 0.00 0.00 0.00 2.83
503 762 1.340017 TGCCACCTATGCCTCTTGTTC 60.340 52.381 0.00 0.00 0.00 3.18
504 763 2.019156 GCCACCTATGCCTCTTGTTCC 61.019 57.143 0.00 0.00 0.00 3.62
505 764 1.656652 CACCTATGCCTCTTGTTCCG 58.343 55.000 0.00 0.00 0.00 4.30
506 765 0.541863 ACCTATGCCTCTTGTTCCGG 59.458 55.000 0.00 0.00 0.00 5.14
507 766 0.815615 CCTATGCCTCTTGTTCCGGC 60.816 60.000 0.00 0.00 44.02 6.13
508 767 1.153449 TATGCCTCTTGTTCCGGCG 60.153 57.895 0.00 0.00 46.67 6.46
599 889 2.043852 AGATCCACCTCTCGCGGT 60.044 61.111 6.13 0.00 37.93 5.68
627 917 1.151474 TCATCCCCAACCCCTTCCA 60.151 57.895 0.00 0.00 0.00 3.53
740 1034 1.078497 TGGCACGACCATGGACATC 60.078 57.895 21.47 4.53 46.36 3.06
741 1035 1.078497 GGCACGACCATGGACATCA 60.078 57.895 21.47 0.00 38.86 3.07
743 1037 0.673333 GCACGACCATGGACATCACA 60.673 55.000 21.47 0.00 0.00 3.58
831 1125 3.636231 CCGCCACCACCTCCTTCA 61.636 66.667 0.00 0.00 0.00 3.02
885 1186 1.528824 CAGATGCCGTCCCCAATCT 59.471 57.895 0.00 0.00 0.00 2.40
908 1209 2.754254 GCGTTCCCCAATCCCCAC 60.754 66.667 0.00 0.00 0.00 4.61
916 1218 2.362375 CAATCCCCACCCCCAACG 60.362 66.667 0.00 0.00 0.00 4.10
958 1266 1.194781 GCCAGTTCTCCTCCTGTCCA 61.195 60.000 0.00 0.00 0.00 4.02
1093 1654 2.124403 GCTGGGTGGGAGCATCTG 60.124 66.667 0.00 0.00 36.40 2.90
1120 1681 0.179181 CTCGCGCAAATGAGCAACAT 60.179 50.000 8.75 0.00 41.01 2.71
1171 1732 0.614697 TGCCTCAACGAGATCTCCCA 60.615 55.000 17.13 0.89 0.00 4.37
1229 1790 3.386237 GAGACCCTCGCTGCTGGT 61.386 66.667 5.25 5.25 34.33 4.00
1253 1814 1.024046 ACAAGCGGCGCATCATACAA 61.024 50.000 35.02 0.00 0.00 2.41
1390 1953 2.665603 GCCGTCTTCAGGGAGCTT 59.334 61.111 0.00 0.00 0.00 3.74
1395 1958 1.163554 GTCTTCAGGGAGCTTTGCAG 58.836 55.000 0.00 0.00 0.00 4.41
1572 3856 6.204882 ACTCTGTGTGTAGCATTTTTCTAACC 59.795 38.462 0.00 0.00 0.00 2.85
1574 3858 6.204688 TCTGTGTGTAGCATTTTTCTAACCAG 59.795 38.462 0.00 0.00 0.00 4.00
1738 4022 5.425217 TCCCTGCTGATCTACATCTTTTACA 59.575 40.000 0.00 0.00 0.00 2.41
1768 4052 5.106396 ACATGCTTGACTGAATTTGCTACTC 60.106 40.000 6.60 0.00 0.00 2.59
1906 4190 6.989659 AGATGAACTTGACATTGATTTGCTT 58.010 32.000 0.00 0.00 0.00 3.91
2159 6015 3.434319 GTCACAGTGCGCCCATGG 61.434 66.667 4.18 4.14 0.00 3.66
2193 6049 6.161381 GCAATTCTGAGGACAAATTGAACAT 58.839 36.000 0.00 0.00 40.97 2.71
2204 6060 7.667219 AGGACAAATTGAACATCTTGACTGTAT 59.333 33.333 0.00 0.00 0.00 2.29
2236 6093 9.661563 TTAATACTTCCGAACTTACATGTCATT 57.338 29.630 0.00 0.00 0.00 2.57
2288 6149 9.601217 GTTTACTATGTATAGAATATGGCTGGG 57.399 37.037 5.93 0.00 34.50 4.45
2456 6319 2.821969 GGTCTGAACTGATGCCATGTTT 59.178 45.455 0.00 0.00 0.00 2.83
2458 6321 4.095483 GGTCTGAACTGATGCCATGTTTAG 59.905 45.833 0.00 0.00 0.00 1.85
2529 6393 7.671495 AAAAATTGTGCACTTTGTTCTTCTT 57.329 28.000 19.41 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.223387 CCAAAATGAGTTCTTTTTGTGAAGGAG 59.777 37.037 21.61 9.08 43.54 3.69
21 22 2.151202 TCGAGTGCCCAAAATGAGTTC 58.849 47.619 0.00 0.00 0.00 3.01
147 151 2.224079 CCTTGTCATTGTGTCACCGAAG 59.776 50.000 0.00 0.00 0.00 3.79
150 154 1.593196 ACCTTGTCATTGTGTCACCG 58.407 50.000 0.00 0.00 0.00 4.94
469 728 1.827789 TGGCAGCGGCAAGAGTTTT 60.828 52.632 11.88 0.00 43.71 2.43
474 733 2.669133 ATAGGTGGCAGCGGCAAGA 61.669 57.895 11.88 0.00 43.71 3.02
599 889 2.122989 GGGGATGAGCTACCGGGA 60.123 66.667 6.32 0.00 0.00 5.14
627 917 0.546598 CCCTCGAAACCCTAGCCATT 59.453 55.000 0.00 0.00 0.00 3.16
736 1030 1.153289 GATCTGGCCGCTGTGATGT 60.153 57.895 0.00 0.00 0.00 3.06
740 1034 2.821366 GTGGATCTGGCCGCTGTG 60.821 66.667 0.00 0.00 35.56 3.66
741 1035 4.101448 GGTGGATCTGGCCGCTGT 62.101 66.667 0.00 0.00 38.49 4.40
861 1155 4.467084 GGACGGCATCTGCGGGAA 62.467 66.667 13.35 0.00 44.37 3.97
908 1209 1.182667 GGGAAGATTTTCGTTGGGGG 58.817 55.000 0.00 0.00 33.98 5.40
916 1218 2.424957 GGGGGAGATGGGGAAGATTTTC 60.425 54.545 0.00 0.00 0.00 2.29
1109 1670 2.183478 TCACCGTGATGTTGCTCATT 57.817 45.000 0.00 0.00 36.83 2.57
1120 1681 0.446616 CTTCTCGTCGATCACCGTGA 59.553 55.000 3.10 3.10 39.75 4.35
1171 1732 4.731612 CAGACTGCAGGAGCGCGT 62.732 66.667 19.93 0.00 46.23 6.01
1226 1787 2.666862 CGCCGCTTGTTGGTACCA 60.667 61.111 11.60 11.60 0.00 3.25
1229 1790 2.359354 ATGCGCCGCTTGTTGGTA 60.359 55.556 11.67 0.00 0.00 3.25
1253 1814 2.930562 GGAGTGGGCAGGACCTGT 60.931 66.667 22.58 1.99 39.10 4.00
1395 1958 0.822532 CTTCCCTGGATCCAGCATGC 60.823 60.000 32.97 10.51 42.35 4.06
1572 3856 3.446873 AGAGGAGTGAGTGCTATTGTCTG 59.553 47.826 0.00 0.00 0.00 3.51
1574 3858 4.642885 AGTAGAGGAGTGAGTGCTATTGTC 59.357 45.833 0.00 0.00 0.00 3.18
1738 4022 6.624423 GCAAATTCAGTCAAGCATGTGAGTAT 60.624 38.462 0.00 0.00 29.82 2.12
1768 4052 5.419155 TCTCATTCACCACTAGAGTAACAGG 59.581 44.000 0.00 0.00 0.00 4.00
1906 4190 6.605471 AAGTCTATCCATACTTGACACACA 57.395 37.500 0.00 0.00 34.70 3.72
1975 4259 1.066143 CCCAACGACATCCTAACAGCT 60.066 52.381 0.00 0.00 0.00 4.24
2159 6015 4.005650 TCCTCAGAATTGCAGAATGACAC 58.994 43.478 0.00 0.00 39.69 3.67
2288 6149 7.226772 GTGTTTTATTCGGTTTTCATCATTGC 58.773 34.615 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.