Multiple sequence alignment - TraesCS7A01G015500

Loading Multiple Alignment...

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 TraesCS7A01G015500 chr7A 100.000 2880 0 0 1 2880 6708789 6711668 0.000000e+00 5319
1 TraesCS7A01G015500 chr7A 92.152 1338 94 5 873 2204 148015683 148014351 0.000000e+00 1879
2 TraesCS7A01G015500 chr7A 97.290 775 18 2 1 772 518745645 518744871 0.000000e+00 1312
3 TraesCS7A01G015500 chr1A 98.549 2205 30 2 1 2204 336239980 336237777 0.000000e+00 3893
4 TraesCS7A01G015500 chr1A 98.160 1141 17 4 1064 2204 320272196 320271060 0.000000e+00 1988
5 TraesCS7A01G015500 chr1A 97.674 1075 22 2 1 1073 320287908 320286835 0.000000e+00 1844
6 TraesCS7A01G015500 chr1A 97.637 677 13 3 2204 2880 50250609 50249936 0.000000e+00 1158
7 TraesCS7A01G015500 chr1A 97.493 678 15 1 2205 2880 514279972 514280649 0.000000e+00 1157
8 TraesCS7A01G015500 chr1A 97.072 683 16 2 2202 2880 422057435 422056753 0.000000e+00 1147
9 TraesCS7A01G015500 chr1A 97.067 682 16 2 2203 2880 567670452 567669771 0.000000e+00 1146
10 TraesCS7A01G015500 chr6A 98.277 2205 24 5 1 2204 10051962 10049771 0.000000e+00 3849
11 TraesCS7A01G015500 chr6A 96.542 1446 45 5 760 2204 90085505 90086946 0.000000e+00 2388
12 TraesCS7A01G015500 chr6A 97.548 775 16 2 1 772 58005942 58005168 0.000000e+00 1323
13 TraesCS7A01G015500 chr1D 95.643 1446 41 10 760 2204 22167874 22169298 0.000000e+00 2302
14 TraesCS7A01G015500 chr4D 94.436 1330 65 4 882 2204 150016590 150017917 0.000000e+00 2037
15 TraesCS7A01G015500 chr5A 93.651 1323 77 2 882 2198 605326660 605325339 0.000000e+00 1971
16 TraesCS7A01G015500 chr5B 92.148 1401 88 12 776 2176 607045110 607046488 0.000000e+00 1958
17 TraesCS7A01G015500 chr5B 91.589 1403 95 13 776 2176 607101945 607103326 0.000000e+00 1916
18 TraesCS7A01G015500 chr5B 95.512 557 21 4 1 554 607044479 607045034 0.000000e+00 887
19 TraesCS7A01G015500 chr5B 95.153 557 23 4 1 554 607101314 607101869 0.000000e+00 876
20 TraesCS7A01G015500 chr5B 96.386 166 6 0 607 772 607045038 607045203 1.020000e-69 274
21 TraesCS7A01G015500 chr4A 97.489 677 14 2 2205 2879 801359 802034 0.000000e+00 1153
22 TraesCS7A01G015500 chr4A 97.063 681 15 3 2205 2880 603009161 603009841 0.000000e+00 1142
23 TraesCS7A01G015500 chr3A 97.050 678 19 1 2204 2880 14422554 14421877 0.000000e+00 1140
24 TraesCS7A01G015500 chr3A 96.788 685 17 4 2201 2880 748545873 748545189 0.000000e+00 1138
25 TraesCS7A01G015500 chr3A 96.784 684 15 1 2204 2880 23400274 23400957 0.000000e+00 1134
26 TraesCS7A01G015500 chr3B 95.048 626 28 2 148 772 802583629 802584252 0.000000e+00 981
27 TraesCS7A01G015500 chr7B 95.153 557 24 3 1 554 664313293 664313849 0.000000e+00 876
28 TraesCS7A01G015500 chr7B 97.590 166 4 0 607 772 664313853 664314018 4.700000e-73 285
29 TraesCS7A01G015500 chr6B 96.471 255 8 1 519 772 48105843 48105589 1.230000e-113 420
30 TraesCS7A01G015500 chr3D 80.408 245 11 3 798 1042 554336398 554336191 4.970000e-33 152


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 TraesCS7A01G015500 chr7A 6708789 6711668 2879 False 5319.000000 5319 100.0000 1 2880 1 chr7A.!!$F1 2879
1 TraesCS7A01G015500 chr7A 148014351 148015683 1332 True 1879.000000 1879 92.1520 873 2204 1 chr7A.!!$R1 1331
2 TraesCS7A01G015500 chr7A 518744871 518745645 774 True 1312.000000 1312 97.2900 1 772 1 chr7A.!!$R2 771
3 TraesCS7A01G015500 chr1A 336237777 336239980 2203 True 3893.000000 3893 98.5490 1 2204 1 chr1A.!!$R4 2203
4 TraesCS7A01G015500 chr1A 320271060 320272196 1136 True 1988.000000 1988 98.1600 1064 2204 1 chr1A.!!$R2 1140
5 TraesCS7A01G015500 chr1A 320286835 320287908 1073 True 1844.000000 1844 97.6740 1 1073 1 chr1A.!!$R3 1072
6 TraesCS7A01G015500 chr1A 50249936 50250609 673 True 1158.000000 1158 97.6370 2204 2880 1 chr1A.!!$R1 676
7 TraesCS7A01G015500 chr1A 514279972 514280649 677 False 1157.000000 1157 97.4930 2205 2880 1 chr1A.!!$F1 675
8 TraesCS7A01G015500 chr1A 422056753 422057435 682 True 1147.000000 1147 97.0720 2202 2880 1 chr1A.!!$R5 678
9 TraesCS7A01G015500 chr1A 567669771 567670452 681 True 1146.000000 1146 97.0670 2203 2880 1 chr1A.!!$R6 677
10 TraesCS7A01G015500 chr6A 10049771 10051962 2191 True 3849.000000 3849 98.2770 1 2204 1 chr6A.!!$R1 2203
11 TraesCS7A01G015500 chr6A 90085505 90086946 1441 False 2388.000000 2388 96.5420 760 2204 1 chr6A.!!$F1 1444
12 TraesCS7A01G015500 chr6A 58005168 58005942 774 True 1323.000000 1323 97.5480 1 772 1 chr6A.!!$R2 771
13 TraesCS7A01G015500 chr1D 22167874 22169298 1424 False 2302.000000 2302 95.6430 760 2204 1 chr1D.!!$F1 1444
14 TraesCS7A01G015500 chr4D 150016590 150017917 1327 False 2037.000000 2037 94.4360 882 2204 1 chr4D.!!$F1 1322
15 TraesCS7A01G015500 chr5A 605325339 605326660 1321 True 1971.000000 1971 93.6510 882 2198 1 chr5A.!!$R1 1316
16 TraesCS7A01G015500 chr5B 607101314 607103326 2012 False 1396.000000 1916 93.3710 1 2176 2 chr5B.!!$F2 2175
17 TraesCS7A01G015500 chr5B 607044479 607046488 2009 False 1039.666667 1958 94.6820 1 2176 3 chr5B.!!$F1 2175
18 TraesCS7A01G015500 chr4A 801359 802034 675 False 1153.000000 1153 97.4890 2205 2879 1 chr4A.!!$F1 674
19 TraesCS7A01G015500 chr4A 603009161 603009841 680 False 1142.000000 1142 97.0630 2205 2880 1 chr4A.!!$F2 675
20 TraesCS7A01G015500 chr3A 14421877 14422554 677 True 1140.000000 1140 97.0500 2204 2880 1 chr3A.!!$R1 676
21 TraesCS7A01G015500 chr3A 748545189 748545873 684 True 1138.000000 1138 96.7880 2201 2880 1 chr3A.!!$R2 679
22 TraesCS7A01G015500 chr3A 23400274 23400957 683 False 1134.000000 1134 96.7840 2204 2880 1 chr3A.!!$F1 676
23 TraesCS7A01G015500 chr3B 802583629 802584252 623 False 981.000000 981 95.0480 148 772 1 chr3B.!!$F1 624
24 TraesCS7A01G015500 chr7B 664313293 664314018 725 False 580.500000 876 96.3715 1 772 2 chr7B.!!$F1 771

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
438 441 7.764141 TTCATTCAGACAATTCAGATTCCAA 57.236 32.0 0.0 0.0 0.0 3.53 F
1254 1270 6.880484 TGATGAAAAATGGGATGAATTGAGG 58.120 36.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1270 3.463944 TCTCCACTTCCGTTGTTCTTTC 58.536 45.455 0.0 0.0 0.0 2.62 R
2682 2722 0.997363 TCGGAGAAGGAGAGGTGGTA 59.003 55.000 0.0 0.0 0.0 3.25 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
351 354 9.080097 AGTGTAAATAGACTGTCTAAGACAAGT 57.920 33.333 20.40 12.10 42.26 3.16
438 441 7.764141 TTCATTCAGACAATTCAGATTCCAA 57.236 32.000 0.00 0.00 0.00 3.53
1254 1270 6.880484 TGATGAAAAATGGGATGAATTGAGG 58.120 36.000 0.00 0.00 0.00 3.86
1265 1281 5.393962 GGATGAATTGAGGAAAGAACAACG 58.606 41.667 0.00 0.00 0.00 4.10
1612 1628 5.252397 AGGCATATATGGTGAGGATGTTGAT 59.748 40.000 14.51 0.00 0.00 2.57
1697 1713 1.774254 TGAACACACTTCCTGACCCAT 59.226 47.619 0.00 0.00 0.00 4.00
1848 1864 9.899226 AAAGACAAAACAAATTGAGAGCTATAC 57.101 29.630 0.00 0.00 34.38 1.47
2682 2722 7.779754 ATGCATACAGAGAGAAGTGATATCT 57.220 36.000 0.00 0.00 30.54 1.98
2753 2793 4.368565 TCTATCTGACACTACCGGCTAT 57.631 45.455 0.00 0.00 0.00 2.97
2764 2804 7.228108 TGACACTACCGGCTATATATATACAGC 59.772 40.741 13.63 13.63 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 114 5.106197 ACACATATTTCTGAAAATCGCAGCA 60.106 36.000 6.95 0.00 36.49 4.41
351 354 2.693591 CAGCGAGATTGGGGTTCTACTA 59.306 50.000 0.00 0.00 0.00 1.82
438 441 8.651589 TGAGAATCAGGTTCGAATAGGTATAT 57.348 34.615 0.00 0.00 42.56 0.86
599 603 5.046304 AGCTAGGCAAAAATCTGTAGTGAGA 60.046 40.000 0.00 0.00 0.00 3.27
1254 1270 3.463944 TCTCCACTTCCGTTGTTCTTTC 58.536 45.455 0.00 0.00 0.00 2.62
1265 1281 4.396478 GGAAAGCTTTGTATCTCCACTTCC 59.604 45.833 18.30 2.58 0.00 3.46
1612 1628 5.931294 TCTGTGTTGTTACCAGGAAATACA 58.069 37.500 0.00 0.00 0.00 2.29
1697 1713 4.783227 AGTCCTAGCCTTTTTCATAGGTGA 59.217 41.667 0.00 0.00 36.86 4.02
1848 1864 4.482386 CATCTGTGCCATTTTCACTTCTG 58.518 43.478 0.00 0.00 35.58 3.02
1877 1893 7.716998 GCAATAAGGATCTTTGTCAGGATCTTA 59.283 37.037 0.00 11.30 38.56 2.10
1919 1939 6.428083 TCTGGTATGGTCTTAAGTTTGACA 57.572 37.500 1.63 0.00 35.11 3.58
2682 2722 0.997363 TCGGAGAAGGAGAGGTGGTA 59.003 55.000 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.