Multiple sequence alignment - TraesCS7A01G523100

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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 TraesCS7A01G523100 chr7A 100.000 2620 0 0 1 2620 705940335 705937716 0.000000e+00 4839.0
1 TraesCS7A01G523100 chr7A 91.877 714 47 8 1355 2067 706002349 706001646 0.000000e+00 987.0
2 TraesCS7A01G523100 chr7A 90.896 714 54 8 1355 2067 705968080 705967377 0.000000e+00 948.0
3 TraesCS7A01G523100 chr7A 89.193 694 60 7 1 691 705983358 705982677 0.000000e+00 852.0
4 TraesCS7A01G523100 chr7A 89.193 694 60 7 1 691 706008586 706007905 0.000000e+00 852.0
5 TraesCS7A01G523100 chr7A 89.901 604 49 3 722 1315 705968675 705968074 0.000000e+00 767.0
6 TraesCS7A01G523100 chr7A 88.797 607 54 5 722 1316 706002946 706002342 0.000000e+00 732.0
7 TraesCS7A01G523100 chr7A 79.980 979 156 25 255 1214 705703295 705702338 0.000000e+00 686.0
8 TraesCS7A01G523100 chr7A 80.392 255 24 15 2390 2620 706000835 706000583 1.250000e-38 171.0
9 TraesCS7A01G523100 chr7B 92.060 1272 71 11 1351 2603 705465201 705463941 0.000000e+00 1762.0
10 TraesCS7A01G523100 chr7B 90.231 737 55 12 1336 2067 705518771 705518047 0.000000e+00 946.0
11 TraesCS7A01G523100 chr7B 90.210 715 49 10 1 714 705466651 705465957 0.000000e+00 913.0
12 TraesCS7A01G523100 chr7B 89.496 695 68 4 1 691 705537578 705536885 0.000000e+00 874.0
13 TraesCS7A01G523100 chr7B 91.297 609 35 5 719 1316 705465792 705465191 0.000000e+00 815.0
14 TraesCS7A01G523100 chr7B 88.803 518 47 5 723 1229 705519301 705518784 2.210000e-175 625.0
15 TraesCS7A01G523100 chr7B 82.064 591 50 25 2072 2620 705517968 705517392 1.110000e-123 453.0
16 TraesCS7A01G523100 chr7B 97.368 38 1 0 2583 2620 705463199 705463162 6.050000e-07 65.8
17 TraesCS7A01G523100 chrUn 96.487 797 22 5 1351 2146 92847670 92848461 0.000000e+00 1312.0
18 TraesCS7A01G523100 chrUn 94.002 817 29 4 510 1316 92846874 92847680 0.000000e+00 1219.0
19 TraesCS7A01G523100 chrUn 96.063 508 15 2 1 503 92843152 92843659 0.000000e+00 822.0
20 TraesCS7A01G523100 chrUn 94.009 217 6 2 2126 2342 92850538 92850747 3.250000e-84 322.0
21 TraesCS7A01G523100 chrUn 91.304 184 7 1 2332 2506 92851148 92851331 2.610000e-60 243.0
22 TraesCS7A01G523100 chr5D 91.176 714 52 7 1355 2067 19746907 19746204 0.000000e+00 959.0
23 TraesCS7A01G523100 chr5D 88.852 610 53 4 722 1316 19747509 19746900 0.000000e+00 736.0
24 TraesCS7A01G523100 chr7D 80.553 977 151 25 255 1214 613912186 613911232 0.000000e+00 715.0
25 TraesCS7A01G523100 chr7D 79.532 982 151 33 255 1214 614390992 614390039 0.000000e+00 654.0


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 TraesCS7A01G523100 chr7A 705937716 705940335 2619 True 4839.000000 4839 100.000000 1 2620 1 chr7A.!!$R2 2619
1 TraesCS7A01G523100 chr7A 705967377 705968675 1298 True 857.500000 948 90.398500 722 2067 2 chr7A.!!$R5 1345
2 TraesCS7A01G523100 chr7A 705982677 705983358 681 True 852.000000 852 89.193000 1 691 1 chr7A.!!$R3 690
3 TraesCS7A01G523100 chr7A 706007905 706008586 681 True 852.000000 852 89.193000 1 691 1 chr7A.!!$R4 690
4 TraesCS7A01G523100 chr7A 705702338 705703295 957 True 686.000000 686 79.980000 255 1214 1 chr7A.!!$R1 959
5 TraesCS7A01G523100 chr7A 706000583 706002946 2363 True 630.000000 987 87.022000 722 2620 3 chr7A.!!$R6 1898
6 TraesCS7A01G523100 chr7B 705463162 705466651 3489 True 888.950000 1762 92.733750 1 2620 4 chr7B.!!$R2 2619
7 TraesCS7A01G523100 chr7B 705536885 705537578 693 True 874.000000 874 89.496000 1 691 1 chr7B.!!$R1 690
8 TraesCS7A01G523100 chr7B 705517392 705519301 1909 True 674.666667 946 87.032667 723 2620 3 chr7B.!!$R3 1897
9 TraesCS7A01G523100 chrUn 92843152 92851331 8179 False 783.600000 1312 94.373000 1 2506 5 chrUn.!!$F1 2505
10 TraesCS7A01G523100 chr5D 19746204 19747509 1305 True 847.500000 959 90.014000 722 2067 2 chr5D.!!$R1 1345
11 TraesCS7A01G523100 chr7D 613911232 613912186 954 True 715.000000 715 80.553000 255 1214 1 chr7D.!!$R1 959
12 TraesCS7A01G523100 chr7D 614390039 614390992 953 True 654.000000 654 79.532000 255 1214 1 chr7D.!!$R2 959

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
743 4126 0.039256 AATGTGCATTTGCGAGCGTT 60.039 45.0 0.0 0.0 45.83 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 5534 0.179018 GGGGGCTTGAGCAATCGTAT 60.179 55.0 5.24 0.0 44.36 3.06 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
174 177 3.509967 ACGTCAGGGCGATTATATCATCA 59.490 43.478 0.00 0.00 35.59 3.07
186 189 1.070821 TATCATCAATAGCAGCGCGC 58.929 50.000 26.66 26.66 42.91 6.86
295 300 4.992951 GCCTCCATTTATTTGCATCAATCC 59.007 41.667 0.00 0.00 0.00 3.01
312 317 8.134895 GCATCAATCCCAAATATTAGAAAACGA 58.865 33.333 0.00 0.00 0.00 3.85
331 337 9.831737 GAAAACGAAAATGGATGGATATATCAG 57.168 33.333 14.60 0.00 0.00 2.90
365 371 7.447374 TGGATATGGTTTATTTTATGGAGCG 57.553 36.000 0.00 0.00 0.00 5.03
422 436 5.446143 ACATACGAAGCAAAAATTGGACA 57.554 34.783 0.00 0.00 0.00 4.02
696 3919 4.510340 CCGTATGGAGCAATGTTAGGTTAC 59.490 45.833 0.00 0.00 37.49 2.50
743 4126 0.039256 AATGTGCATTTGCGAGCGTT 60.039 45.000 0.00 0.00 45.83 4.84
773 4156 4.665833 AGTCTTTTAAACTTTGGGCCAC 57.334 40.909 5.23 0.00 0.00 5.01
793 4176 1.473080 CCAATGCGCCCCAAAATTAGG 60.473 52.381 4.18 0.00 0.00 2.69
807 4190 6.779539 CCCAAAATTAGGAGCCTGAGATTTAT 59.220 38.462 0.00 0.00 0.00 1.40
825 4208 9.132521 GAGATTTATTGTTCATCACCAACTTTG 57.867 33.333 0.00 0.00 0.00 2.77
911 4304 6.973474 ACGCCTCTATATATAAGAATGAACGC 59.027 38.462 0.00 0.00 0.00 4.84
944 4337 3.281727 TCGCCAGCTAATTCTTGGATT 57.718 42.857 6.91 0.00 0.00 3.01
1073 4466 5.617751 CGATACTTCTCCTTGTTTGCTTTGG 60.618 44.000 0.00 0.00 0.00 3.28
1250 4658 9.372369 TCGTTGTTGTTTCATATTTTCCTTTTT 57.628 25.926 0.00 0.00 0.00 1.94
1426 4882 7.496346 AAGACATAGGTAACAGGAAGATCAA 57.504 36.000 0.00 0.00 41.41 2.57
1622 5080 1.328279 CCCTCCCACCAAACTGAAAC 58.672 55.000 0.00 0.00 0.00 2.78
1758 5216 1.356624 GGCACCGCTGCAACATATC 59.643 57.895 4.88 0.00 46.28 1.63
1859 5317 2.640332 AGTCCCTCTCAAAACCCTCTTC 59.360 50.000 0.00 0.00 0.00 2.87
1879 5337 7.283354 CCTCTTCCCATCTTAATTAAGGTTGTC 59.717 40.741 22.11 0.00 34.14 3.18
2067 5534 1.900016 CACTGGCCAGAGCAAGCAA 60.900 57.895 39.19 0.00 44.80 3.91
2123 5664 9.366216 TCGCGTTTAGAAGCATATATAATTGAT 57.634 29.630 5.77 0.00 0.00 2.57
2152 7790 6.339730 TGACTGTTGTCTGCATTTGAAAATT 58.660 32.000 0.00 0.00 43.29 1.82
2309 7955 1.901591 AGATTGCAACCACCTGTCTG 58.098 50.000 0.00 0.00 0.00 3.51
2506 8945 5.691305 AGCAACGGACGCGTATATATTAAAA 59.309 36.000 13.97 0.00 0.00 1.52
2507 8946 6.200665 AGCAACGGACGCGTATATATTAAAAA 59.799 34.615 13.97 0.00 0.00 1.94
2526 8965 4.791069 TCCCCCTAGCCGACCCAC 62.791 72.222 0.00 0.00 0.00 4.61
2548 8987 1.897398 CTGGCGTGGTACGTGAAAGC 61.897 60.000 0.00 0.00 44.73 3.51
2558 9011 3.188460 GGTACGTGAAAGCATGACATGTT 59.812 43.478 16.62 8.17 35.73 2.71
2559 9012 3.272439 ACGTGAAAGCATGACATGTTG 57.728 42.857 16.62 0.00 35.02 3.33
2599 9815 5.503031 CGCTAATAGTTTCTGCAATCAGTGG 60.503 44.000 0.00 0.00 41.10 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 189 5.082059 GCACACGATCTTGTAATTTGTGAG 58.918 41.667 4.30 0.00 35.89 3.51
270 275 4.659111 TGATGCAAATAAATGGAGGCAG 57.341 40.909 0.00 0.00 34.43 4.85
307 312 8.924511 ACTGATATATCCATCCATTTTCGTTT 57.075 30.769 10.25 0.00 0.00 3.60
312 317 9.956640 GAGAAGACTGATATATCCATCCATTTT 57.043 33.333 10.25 0.00 0.00 1.82
416 427 5.765182 GGAGAAGATTTTTCTGTCTGTCCAA 59.235 40.000 0.00 0.00 32.48 3.53
422 436 6.131972 TCCATGGAGAAGATTTTTCTGTCT 57.868 37.500 11.44 0.00 0.00 3.41
735 4118 0.669625 ACTACCCAAGAAACGCTCGC 60.670 55.000 0.00 0.00 0.00 5.03
743 4126 7.068962 CCCAAAGTTTAAAAGACTACCCAAGAA 59.931 37.037 0.00 0.00 0.00 2.52
773 4156 1.473080 CCTAATTTTGGGGCGCATTGG 60.473 52.381 10.83 0.57 0.00 3.16
793 4176 6.238593 GGTGATGAACAATAAATCTCAGGCTC 60.239 42.308 0.00 0.00 0.00 4.70
807 4190 8.006298 AGTAAATCAAAGTTGGTGATGAACAA 57.994 30.769 0.00 0.00 35.87 2.83
944 4337 1.563879 AGGCCCAATATGTGTGTGCTA 59.436 47.619 0.00 0.00 0.00 3.49
1031 4424 1.025812 CGAGAGTGGCACTAGTAGGG 58.974 60.000 22.11 0.00 0.00 3.53
1073 4466 6.797033 GTGTTACTTACATTGAACATGAGCAC 59.203 38.462 0.00 0.00 39.39 4.40
1426 4882 3.582647 TCCGCACAATCCATATGGTAGAT 59.417 43.478 21.28 5.12 36.34 1.98
1652 5110 8.642432 TCCAACTGTAGAGAACAAGATATATGG 58.358 37.037 0.00 0.00 37.74 2.74
1668 5126 6.366332 GTCTCAACATGTAACTCCAACTGTAG 59.634 42.308 0.00 0.00 0.00 2.74
1923 5382 4.522971 GCTTTAGCGTGAGAGGGG 57.477 61.111 0.00 0.00 0.00 4.79
2007 5466 1.072331 AGAATCGGTTGTTGGCAGTCT 59.928 47.619 0.00 0.00 0.00 3.24
2067 5534 0.179018 GGGGGCTTGAGCAATCGTAT 60.179 55.000 5.24 0.00 44.36 3.06
2123 5664 5.067544 TCAAATGCAGACAACAGTCATTTCA 59.932 36.000 0.00 0.00 35.81 2.69
2182 7820 1.808945 CTGCATCTTCAAACCTCGCTT 59.191 47.619 0.00 0.00 0.00 4.68
2284 7930 4.944048 ACAGGTGGTTGCAATCTTAAAAC 58.056 39.130 11.73 0.00 0.00 2.43
2506 8945 2.076803 GGGTCGGCTAGGGGGAATT 61.077 63.158 0.00 0.00 0.00 2.17
2507 8946 2.447959 GGGTCGGCTAGGGGGAAT 60.448 66.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.