Multiple sequence alignment - TraesCS7B01G428100

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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 TraesCS7B01G428100 chr7B 100.000 2657 0 0 1 2657 697265827 697263171 0.000000e+00 4907
1 TraesCS7B01G428100 chr7B 91.427 1458 95 11 723 2165 693258367 693256925 0.000000e+00 1973
2 TraesCS7B01G428100 chr7B 99.781 912 2 0 1443 2354 697227756 697226845 0.000000e+00 1674
3 TraesCS7B01G428100 chr7B 99.671 913 3 0 1442 2354 697230266 697229354 0.000000e+00 1670
4 TraesCS7B01G428100 chr7B 97.241 725 18 2 1 724 589946992 589947715 0.000000e+00 1227
5 TraesCS7B01G428100 chr7B 90.670 761 59 6 1411 2165 696906814 696906060 0.000000e+00 1002
6 TraesCS7B01G428100 chr7B 92.909 691 40 1 723 1413 696909228 696908547 0.000000e+00 996
7 TraesCS7B01G428100 chr7B 91.379 638 50 2 1028 1661 700731675 700732311 0.000000e+00 869
8 TraesCS7B01G428100 chr7B 91.481 540 46 0 1028 1567 700679183 700679722 0.000000e+00 743
9 TraesCS7B01G428100 chr7B 91.789 341 18 8 2063 2397 693954667 693954331 1.440000e-127 466
10 TraesCS7B01G428100 chr7B 93.893 262 12 2 2396 2657 693256673 693256416 2.480000e-105 392
11 TraesCS7B01G428100 chr7B 93.511 262 11 3 2396 2657 696905808 696905553 4.150000e-103 385
12 TraesCS7B01G428100 chr7B 90.547 201 13 4 2200 2397 693256924 693256727 7.300000e-66 261
13 TraesCS7B01G428100 chr7B 84.024 169 17 4 2396 2564 693954232 693954074 1.270000e-33 154
14 TraesCS7B01G428100 chr7B 77.451 204 38 7 723 922 685062135 685062334 6.010000e-22 115
15 TraesCS7B01G428100 chr7D 93.210 1679 90 8 986 2657 607622331 607620670 0.000000e+00 2447
16 TraesCS7B01G428100 chr7D 93.258 1587 82 10 1039 2618 610203362 610204930 0.000000e+00 2314
17 TraesCS7B01G428100 chr7D 89.210 1177 110 8 723 1884 608422795 608423969 0.000000e+00 1454
18 TraesCS7B01G428100 chr7D 88.333 240 23 4 2162 2397 608423964 608424202 1.560000e-72 283
19 TraesCS7B01G428100 chr7D 85.380 171 19 4 2396 2565 608424255 608424420 3.520000e-39 172
20 TraesCS7B01G428100 chrUn 87.160 1690 155 35 723 2386 83447505 83445852 0.000000e+00 1862
21 TraesCS7B01G428100 chrUn 91.667 84 7 0 2574 2657 83446494 83446411 1.670000e-22 117
22 TraesCS7B01G428100 chr7A 91.913 1150 76 7 723 1867 699865558 699864421 0.000000e+00 1592
23 TraesCS7B01G428100 chr7A 88.946 1176 100 12 723 1884 700422016 700423175 0.000000e+00 1424
24 TraesCS7B01G428100 chr7A 98.207 725 12 1 1 724 712592187 712591463 0.000000e+00 1266
25 TraesCS7B01G428100 chr7A 86.471 170 17 4 2396 2564 700423425 700423589 5.840000e-42 182
26 TraesCS7B01G428100 chr7A 93.590 78 5 0 2574 2651 700423027 700423104 1.670000e-22 117
27 TraesCS7B01G428100 chr1B 89.478 1169 115 5 723 1884 455356548 455357715 0.000000e+00 1471
28 TraesCS7B01G428100 chr1B 96.966 725 21 1 1 724 296747545 296748269 0.000000e+00 1216
29 TraesCS7B01G428100 chr1B 87.448 239 25 4 2163 2397 455357711 455357948 1.210000e-68 270
30 TraesCS7B01G428100 chr1B 84.795 171 20 4 2396 2565 455358002 455358167 1.640000e-37 167
31 TraesCS7B01G428100 chr4A 97.931 725 13 2 1 724 115553679 115552956 0.000000e+00 1254
32 TraesCS7B01G428100 chr4A 97.793 725 15 1 1 724 181639487 181640211 0.000000e+00 1249
33 TraesCS7B01G428100 chr6B 97.796 726 15 1 1 725 172322960 172323685 0.000000e+00 1251
34 TraesCS7B01G428100 chr3A 98.184 716 11 2 1 715 470841502 470842216 0.000000e+00 1249
35 TraesCS7B01G428100 chr1A 97.517 725 17 1 1 724 593269409 593270133 0.000000e+00 1238
36 TraesCS7B01G428100 chr2B 96.974 727 16 2 1 726 650415010 650415731 0.000000e+00 1216


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 TraesCS7B01G428100 chr7B 697263171 697265827 2656 True 4907.000000 4907 100.000000 1 2657 1 chr7B.!!$R1 2656
1 TraesCS7B01G428100 chr7B 697226845 697230266 3421 True 1672.000000 1674 99.726000 1442 2354 2 chr7B.!!$R5 912
2 TraesCS7B01G428100 chr7B 589946992 589947715 723 False 1227.000000 1227 97.241000 1 724 1 chr7B.!!$F1 723
3 TraesCS7B01G428100 chr7B 693256416 693258367 1951 True 875.333333 1973 91.955667 723 2657 3 chr7B.!!$R2 1934
4 TraesCS7B01G428100 chr7B 700731675 700732311 636 False 869.000000 869 91.379000 1028 1661 1 chr7B.!!$F4 633
5 TraesCS7B01G428100 chr7B 696905553 696909228 3675 True 794.333333 1002 92.363333 723 2657 3 chr7B.!!$R4 1934
6 TraesCS7B01G428100 chr7B 700679183 700679722 539 False 743.000000 743 91.481000 1028 1567 1 chr7B.!!$F3 539
7 TraesCS7B01G428100 chr7B 693954074 693954667 593 True 310.000000 466 87.906500 2063 2564 2 chr7B.!!$R3 501
8 TraesCS7B01G428100 chr7D 607620670 607622331 1661 True 2447.000000 2447 93.210000 986 2657 1 chr7D.!!$R1 1671
9 TraesCS7B01G428100 chr7D 610203362 610204930 1568 False 2314.000000 2314 93.258000 1039 2618 1 chr7D.!!$F1 1579
10 TraesCS7B01G428100 chr7D 608422795 608424420 1625 False 636.333333 1454 87.641000 723 2565 3 chr7D.!!$F2 1842
11 TraesCS7B01G428100 chrUn 83445852 83447505 1653 True 989.500000 1862 89.413500 723 2657 2 chrUn.!!$R1 1934
12 TraesCS7B01G428100 chr7A 699864421 699865558 1137 True 1592.000000 1592 91.913000 723 1867 1 chr7A.!!$R1 1144
13 TraesCS7B01G428100 chr7A 712591463 712592187 724 True 1266.000000 1266 98.207000 1 724 1 chr7A.!!$R2 723
14 TraesCS7B01G428100 chr7A 700422016 700423589 1573 False 574.333333 1424 89.669000 723 2651 3 chr7A.!!$F1 1928
15 TraesCS7B01G428100 chr1B 296747545 296748269 724 False 1216.000000 1216 96.966000 1 724 1 chr1B.!!$F1 723
16 TraesCS7B01G428100 chr1B 455356548 455358167 1619 False 636.000000 1471 87.240333 723 2565 3 chr1B.!!$F2 1842
17 TraesCS7B01G428100 chr4A 115552956 115553679 723 True 1254.000000 1254 97.931000 1 724 1 chr4A.!!$R1 723
18 TraesCS7B01G428100 chr4A 181639487 181640211 724 False 1249.000000 1249 97.793000 1 724 1 chr4A.!!$F1 723
19 TraesCS7B01G428100 chr6B 172322960 172323685 725 False 1251.000000 1251 97.796000 1 725 1 chr6B.!!$F1 724
20 TraesCS7B01G428100 chr3A 470841502 470842216 714 False 1249.000000 1249 98.184000 1 715 1 chr3A.!!$F1 714
21 TraesCS7B01G428100 chr1A 593269409 593270133 724 False 1238.000000 1238 97.517000 1 724 1 chr1A.!!$F1 723
22 TraesCS7B01G428100 chr2B 650415010 650415731 721 False 1216.000000 1216 96.974000 1 726 1 chr2B.!!$F1 725

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
711 713 0.865769 GAGCAAGTGTGGTACCAACG 59.134 55.0 18.31 4.56 35.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 6629 3.191371 GGGTTCTAGCCACAATCAACAAG 59.809 47.826 0.0 0.0 35.4 3.16 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
73 74 4.949966 AGGACAGACTAAGAACCTCCTA 57.050 45.455 0.00 0.00 0.00 2.94
324 326 4.036027 GTCGTCGGAGAGGTTCATGTATTA 59.964 45.833 0.00 0.00 43.64 0.98
363 365 3.473647 CTCCTCCTCCATGGCGCA 61.474 66.667 10.83 0.00 35.26 6.09
603 605 7.123847 GGATACCCGGTCAATACTCACTTATAT 59.876 40.741 0.00 0.00 0.00 0.86
648 650 1.568504 TAGGCCCTGAGTTGGTACTG 58.431 55.000 0.00 0.00 33.84 2.74
688 690 3.577649 AGTGGTACTGATTCGTGAGTG 57.422 47.619 0.00 0.00 0.00 3.51
711 713 0.865769 GAGCAAGTGTGGTACCAACG 59.134 55.000 18.31 4.56 35.00 4.10
879 881 1.683365 GTACGTCCTGCTACCCCCA 60.683 63.158 0.00 0.00 0.00 4.96
888 890 2.768344 CTACCCCCAGTGCCCGAT 60.768 66.667 0.00 0.00 0.00 4.18
895 897 4.100084 CAGTGCCCGATGCCCTCA 62.100 66.667 0.00 0.00 40.16 3.86
897 899 2.124151 GTGCCCGATGCCCTCATT 60.124 61.111 0.00 0.00 40.16 2.57
975 977 4.493747 CCCCTCGGCGAGAACGAC 62.494 72.222 36.47 0.00 45.02 4.34
1001 1018 1.153168 CGGAAGGGACGGCATTCAT 60.153 57.895 7.65 0.00 0.00 2.57
1008 1025 0.664761 GGACGGCATTCATGGTGATG 59.335 55.000 0.00 0.00 0.00 3.07
1041 1059 2.359169 CGAGACTAAGCTGGCCCCA 61.359 63.158 0.00 0.00 0.00 4.96
1043 1061 0.548510 GAGACTAAGCTGGCCCCATT 59.451 55.000 0.00 0.00 0.00 3.16
1214 1237 0.592637 TTGCTTGTGCTCAACATCCG 59.407 50.000 0.00 0.00 38.99 4.18
2369 6702 8.986929 AGCTAGGCAATAAAATATCTGAACTT 57.013 30.769 0.00 0.00 0.00 2.66
2380 6713 7.516198 AAATATCTGAACTTCTGCAAACACT 57.484 32.000 0.00 0.00 0.00 3.55
2381 6714 8.621532 AAATATCTGAACTTCTGCAAACACTA 57.378 30.769 0.00 0.00 0.00 2.74
2382 6715 7.840342 ATATCTGAACTTCTGCAAACACTAG 57.160 36.000 0.00 0.00 0.00 2.57
2410 6847 5.929992 GCTACCAGTTTGTTATGTGTACTCA 59.070 40.000 0.00 0.00 0.00 3.41
2454 6891 2.159393 GCTGAAGCTGAACACACAACAA 60.159 45.455 0.00 0.00 38.21 2.83
2511 6950 6.260936 CCTTACTGATGGAACGAATGCTATTT 59.739 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 2.172851 TCGAAGCATTTAACACGGGT 57.827 45.000 0.00 0.00 0.00 5.28
324 326 2.125512 GCCAGGACTCAATCGCGT 60.126 61.111 5.77 0.00 0.00 6.01
583 585 4.929808 GCCATATAAGTGAGTATTGACCGG 59.070 45.833 0.00 0.00 0.00 5.28
614 616 1.873591 GGCCTAAGTGATGCATAACGG 59.126 52.381 8.61 5.47 0.00 4.44
688 690 0.605589 GGTACCACACTTGCTCACCC 60.606 60.000 7.15 0.00 0.00 4.61
711 713 3.942115 GGAGGAAGGAGAGTTAATTGCAC 59.058 47.826 0.00 0.00 0.00 4.57
888 890 4.802051 GCCGAGGCAATGAGGGCA 62.802 66.667 9.58 0.00 43.23 5.36
1001 1018 3.281158 CAATGCACCATAGACATCACCA 58.719 45.455 0.00 0.00 0.00 4.17
1008 1025 1.594862 GTCTCGCAATGCACCATAGAC 59.405 52.381 5.91 6.04 0.00 2.59
2299 6629 3.191371 GGGTTCTAGCCACAATCAACAAG 59.809 47.826 0.00 0.00 35.40 3.16
2367 6700 5.348997 GGTAGCTTACTAGTGTTTGCAGAAG 59.651 44.000 5.39 0.00 0.00 2.85
2369 6702 4.282449 TGGTAGCTTACTAGTGTTTGCAGA 59.718 41.667 5.39 0.00 0.00 4.26
2380 6713 7.673180 ACACATAACAAACTGGTAGCTTACTA 58.327 34.615 0.00 0.00 0.00 1.82
2381 6714 6.531021 ACACATAACAAACTGGTAGCTTACT 58.469 36.000 0.00 0.00 0.00 2.24
2382 6715 6.796705 ACACATAACAAACTGGTAGCTTAC 57.203 37.500 0.00 0.00 0.00 2.34
2410 6847 4.751098 CACTGTAATTTGCAATGCAGGTTT 59.249 37.500 18.48 6.34 40.61 3.27
2454 6891 6.209192 TCAACCTGATTTGAAATATGCAGTGT 59.791 34.615 0.00 0.00 32.42 3.55
2536 6975 8.413229 GCTTGAAGGAACAAATTATAGGCATTA 58.587 33.333 0.00 0.00 0.00 1.90
2619 7058 5.301551 TGACTGAGCACAAAAACATAACCAT 59.698 36.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.