Multiple sequence alignment - TraesCS7B01G328000

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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 TraesCS7B01G328000 chr7B 100.000 3489 0 0 1 3489 582699232 582695744 0.000000e+00 6444
1 TraesCS7B01G328000 chr3B 97.937 2521 49 2 969 3489 781352794 781350277 0.000000e+00 4364
2 TraesCS7B01G328000 chr3B 96.101 2539 50 21 954 3489 85344826 85342334 0.000000e+00 4095
3 TraesCS7B01G328000 chr3B 97.844 974 17 4 1 973 85345808 85344838 0.000000e+00 1679
4 TraesCS7B01G328000 chr3B 94.456 974 17 6 1 973 781353760 781352823 0.000000e+00 1465
5 TraesCS7B01G328000 chr3B 83.385 325 41 10 2385 2703 781351312 781350995 4.410000e-74 289
6 TraesCS7B01G328000 chr1B 97.461 2521 42 3 969 3489 512628297 512625799 0.000000e+00 4281
7 TraesCS7B01G328000 chr1B 95.688 974 16 4 1 973 512629274 512628326 0.000000e+00 1543
8 TraesCS7B01G328000 chr4A 97.303 2521 40 4 969 3489 726566237 726563745 0.000000e+00 4253
9 TraesCS7B01G328000 chr4A 98.152 974 15 3 1 973 726567237 726566266 0.000000e+00 1696
10 TraesCS7B01G328000 chr4A 87.389 1015 69 27 9 973 2907818 2908823 0.000000e+00 1110
11 TraesCS7B01G328000 chr4A 89.837 797 43 10 203 973 726662157 726662941 0.000000e+00 989
12 TraesCS7B01G328000 chr4A 89.573 796 42 14 203 973 24021176 24020397 0.000000e+00 972
13 TraesCS7B01G328000 chr4A 85.686 503 42 16 2526 3020 24019723 24019243 1.450000e-138 503
14 TraesCS7B01G328000 chr4A 84.335 549 41 17 2476 3020 2909493 2910000 2.420000e-136 496
15 TraesCS7B01G328000 chr6B 96.796 2528 53 13 962 3489 300672647 300675146 0.000000e+00 4194
16 TraesCS7B01G328000 chr6B 87.873 1039 48 19 1 973 720763402 720764428 0.000000e+00 1149
17 TraesCS7B01G328000 chr6B 98.195 554 8 2 420 973 300672072 300672623 0.000000e+00 966
18 TraesCS7B01G328000 chr6B 96.927 423 12 1 1 422 300671527 300671949 0.000000e+00 708
19 TraesCS7B01G328000 chr7A 96.708 2521 58 4 970 3489 317897037 317894541 0.000000e+00 4172
20 TraesCS7B01G328000 chr7A 94.512 984 19 10 1 973 317898025 317897066 0.000000e+00 1485
21 TraesCS7B01G328000 chr7A 91.199 909 65 12 970 1873 554473788 554474686 0.000000e+00 1221
22 TraesCS7B01G328000 chr7A 84.646 254 16 8 3257 3489 195524173 195523922 7.530000e-57 231
23 TraesCS7B01G328000 chr2A 90.377 2120 121 38 203 2272 343417696 343419782 0.000000e+00 2708
24 TraesCS7B01G328000 chr4D 94.065 1112 50 10 970 2073 211757567 211758670 0.000000e+00 1674
25 TraesCS7B01G328000 chr3A 88.439 1038 45 20 1 973 109880181 109881208 0.000000e+00 1182
26 TraesCS7B01G328000 chr3A 86.053 1011 72 32 9 968 572451096 572452088 0.000000e+00 1022
27 TraesCS7B01G328000 chr3A 85.039 254 16 6 3257 3489 422616518 422616266 4.500000e-59 239
28 TraesCS7B01G328000 chr1A 87.783 1015 64 28 9 973 549336479 549337483 0.000000e+00 1133
29 TraesCS7B01G328000 chr1A 91.092 797 35 12 203 973 22856501 22855715 0.000000e+00 1046
30 TraesCS7B01G328000 chr1A 84.699 549 39 18 2476 3020 549338154 549338661 1.120000e-139 507
31 TraesCS7B01G328000 chr1A 86.408 103 6 4 3166 3260 548997528 548997426 4.760000e-19 106
32 TraesCS7B01G328000 chr5A 86.726 1017 68 27 7 973 577807981 577806982 0.000000e+00 1068
33 TraesCS7B01G328000 chr5A 85.625 480 38 15 2557 3021 577806309 577805846 3.150000e-130 475
34 TraesCS7B01G328000 chr5D 94.863 292 14 1 2097 2388 553776950 553776660 4.110000e-124 455
35 TraesCS7B01G328000 chr1D 85.039 254 16 3 3257 3489 470573177 470572925 4.500000e-59 239
36 TraesCS7B01G328000 chr1D 86.408 103 6 4 3166 3260 455092592 455092490 4.760000e-19 106
37 TraesCS7B01G328000 chr1D 85.437 103 7 4 3166 3260 455092515 455092413 2.220000e-17 100


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 TraesCS7B01G328000 chr7B 582695744 582699232 3488 True 6444.000000 6444 100.0000 1 3489 1 chr7B.!!$R1 3488
1 TraesCS7B01G328000 chr3B 85342334 85345808 3474 True 2887.000000 4095 96.9725 1 3489 2 chr3B.!!$R1 3488
2 TraesCS7B01G328000 chr3B 781350277 781353760 3483 True 2039.333333 4364 91.9260 1 3489 3 chr3B.!!$R2 3488
3 TraesCS7B01G328000 chr1B 512625799 512629274 3475 True 2912.000000 4281 96.5745 1 3489 2 chr1B.!!$R1 3488
4 TraesCS7B01G328000 chr4A 726563745 726567237 3492 True 2974.500000 4253 97.7275 1 3489 2 chr4A.!!$R2 3488
5 TraesCS7B01G328000 chr4A 726662157 726662941 784 False 989.000000 989 89.8370 203 973 1 chr4A.!!$F1 770
6 TraesCS7B01G328000 chr4A 2907818 2910000 2182 False 803.000000 1110 85.8620 9 3020 2 chr4A.!!$F2 3011
7 TraesCS7B01G328000 chr4A 24019243 24021176 1933 True 737.500000 972 87.6295 203 3020 2 chr4A.!!$R1 2817
8 TraesCS7B01G328000 chr6B 300671527 300675146 3619 False 1956.000000 4194 97.3060 1 3489 3 chr6B.!!$F2 3488
9 TraesCS7B01G328000 chr6B 720763402 720764428 1026 False 1149.000000 1149 87.8730 1 973 1 chr6B.!!$F1 972
10 TraesCS7B01G328000 chr7A 317894541 317898025 3484 True 2828.500000 4172 95.6100 1 3489 2 chr7A.!!$R2 3488
11 TraesCS7B01G328000 chr7A 554473788 554474686 898 False 1221.000000 1221 91.1990 970 1873 1 chr7A.!!$F1 903
12 TraesCS7B01G328000 chr2A 343417696 343419782 2086 False 2708.000000 2708 90.3770 203 2272 1 chr2A.!!$F1 2069
13 TraesCS7B01G328000 chr4D 211757567 211758670 1103 False 1674.000000 1674 94.0650 970 2073 1 chr4D.!!$F1 1103
14 TraesCS7B01G328000 chr3A 109880181 109881208 1027 False 1182.000000 1182 88.4390 1 973 1 chr3A.!!$F1 972
15 TraesCS7B01G328000 chr3A 572451096 572452088 992 False 1022.000000 1022 86.0530 9 968 1 chr3A.!!$F2 959
16 TraesCS7B01G328000 chr1A 22855715 22856501 786 True 1046.000000 1046 91.0920 203 973 1 chr1A.!!$R1 770
17 TraesCS7B01G328000 chr1A 549336479 549338661 2182 False 820.000000 1133 86.2410 9 3020 2 chr1A.!!$F1 3011
18 TraesCS7B01G328000 chr5A 577805846 577807981 2135 True 771.500000 1068 86.1755 7 3021 2 chr5A.!!$R1 3014

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
671 934 3.884693 TGTGACTGTTCTTGTGATGCATT 59.115 39.13 0.00 0.00 0.00 3.56 F
1474 1903 0.178767 ATGCTGGAGCTCGCAATGTA 59.821 50.00 18.37 3.31 42.66 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2250 4.998672 CCAATAACGGTGGAGAACAACTTA 59.001 41.667 0.0 0.0 38.54 2.24 R
2950 3421 6.605194 ACCCAACATTACAAGGCAAAAATTTT 59.395 30.769 0.0 0.0 0.00 1.82 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
51 63 5.011738 TGGCTTGCTTAGTTGTAGTAGTCTT 59.988 40.000 0.00 0.00 0.00 3.01
429 635 4.038162 GTGGGGTTGCACTGTATTTGTTAA 59.962 41.667 0.00 0.00 0.00 2.01
516 722 4.276642 TGCCATGGATTTGCACTGTATTA 58.723 39.130 18.40 0.00 0.00 0.98
671 934 3.884693 TGTGACTGTTCTTGTGATGCATT 59.115 39.130 0.00 0.00 0.00 3.56
841 1106 6.126409 TGTAATTCTCAGTTGGTTTCCACTT 58.874 36.000 0.00 0.00 30.78 3.16
1048 1379 0.606401 GGGCACTTCTGCTGCTTGTA 60.606 55.000 0.00 0.00 43.66 2.41
1474 1903 0.178767 ATGCTGGAGCTCGCAATGTA 59.821 50.000 18.37 3.31 42.66 2.29
1583 2047 9.803507 TCCTTTTGCAATCTTCATCATATCTAT 57.196 29.630 0.00 0.00 0.00 1.98
1641 2105 7.953752 ACCTAGTTCCATATAGTTCTAGTTGC 58.046 38.462 0.00 0.00 0.00 4.17
1783 2250 6.547880 CCACTACATTCACTAGATACTCTGGT 59.452 42.308 0.00 0.00 38.84 4.00
1909 2377 5.106277 GCCTCTTAGGTTTGTCAAATGGTAC 60.106 44.000 0.40 0.00 37.80 3.34
2138 2609 4.698780 TGAAGAATTGCCTGATGAAGACAG 59.301 41.667 0.00 0.00 35.43 3.51
2497 2968 9.148104 GTCGATTTTACAGTGTAATTCTAGGTT 57.852 33.333 16.26 0.00 0.00 3.50
2787 3258 7.185318 TGTAATTCCTACCGGATTTTCAGTA 57.815 36.000 9.46 0.00 39.58 2.74
2950 3421 9.042450 TGTGGTTAGTTTTAGATTAGAGATGGA 57.958 33.333 0.00 0.00 0.00 3.41
3156 3627 6.723282 GCTATTCTTGTAGCAAAGAGATTGG 58.277 40.000 1.32 0.00 45.03 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 63 6.566141 TCCGTTCGAATTGACTGAATACATA 58.434 36.000 0.00 0.00 0.00 2.29
429 635 7.173218 CACTGACAAATACACTGTAATTCCACT 59.827 37.037 0.00 0.00 0.00 4.00
516 722 9.601217 GTGAATTACACTGTAATTCCACTAGAT 57.399 33.333 32.87 12.08 45.13 1.98
623 885 5.020795 TCCTCTGCTACCAATAACAGTGTA 58.979 41.667 0.00 0.00 0.00 2.90
671 934 6.293407 GCATCACAAGAACTTACAAACTAGCA 60.293 38.462 0.00 0.00 0.00 3.49
841 1106 4.879545 GTGTAGAAATCCCCTGCGAATTAA 59.120 41.667 0.00 0.00 0.00 1.40
950 1215 2.433436 ACGGCAGAAGGGATAAAACAC 58.567 47.619 0.00 0.00 0.00 3.32
1048 1379 7.014326 CCCATCTGAATCATCACAATCTTCAAT 59.986 37.037 0.00 0.00 0.00 2.57
1641 2105 6.963796 ACAAAAGAAAGACATCTAGCAACAG 58.036 36.000 0.00 0.00 0.00 3.16
1700 2166 5.461737 ACAACACAACAAGAAACACAAACAG 59.538 36.000 0.00 0.00 0.00 3.16
1783 2250 4.998672 CCAATAACGGTGGAGAACAACTTA 59.001 41.667 0.00 0.00 38.54 2.24
1909 2377 5.775686 TGAAGCAAGATCAAATTTGGACAG 58.224 37.500 17.90 9.82 0.00 3.51
2138 2609 5.514204 GCAATACACATGAAGCAGATGAAAC 59.486 40.000 0.00 0.00 0.00 2.78
2625 3096 8.836268 ACACTGTAAAATCGACCTACAATTAA 57.164 30.769 0.00 0.00 0.00 1.40
2950 3421 6.605194 ACCCAACATTACAAGGCAAAAATTTT 59.395 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.