Multiple sequence alignment - TraesCS7A01G153200

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 TraesCS7A01G153200 chr7A 100.000 2898 0 0 1 2898 106411034 106408137 0.000000e+00 5352
1 TraesCS7A01G153200 chr7A 84.069 408 54 4 477 884 22278852 22278456 1.630000e-102 383
2 TraesCS7A01G153200 chr6A 96.578 1987 59 6 1 1981 563487853 563489836 0.000000e+00 3284
3 TraesCS7A01G153200 chr6A 91.608 1418 102 10 566 1981 591517046 591518448 0.000000e+00 1943
4 TraesCS7A01G153200 chr6A 95.311 917 39 1 1982 2898 563493086 563493998 0.000000e+00 1452
5 TraesCS7A01G153200 chr4B 95.968 1984 73 6 1 1981 168271657 168269678 0.000000e+00 3214
6 TraesCS7A01G153200 chr4B 95.643 918 35 2 1982 2898 168266389 168265476 0.000000e+00 1469
7 TraesCS7A01G153200 chr7D 94.466 1789 85 7 1 1779 199528039 199529823 0.000000e+00 2743
8 TraesCS7A01G153200 chr7D 88.141 1248 128 10 737 1981 136701157 136699927 0.000000e+00 1467
9 TraesCS7A01G153200 chr7D 87.122 893 108 2 1985 2877 136696569 136695684 0.000000e+00 1005
10 TraesCS7A01G153200 chr7D 85.996 914 122 3 1986 2898 99609737 99610645 0.000000e+00 974
11 TraesCS7A01G153200 chr1A 90.973 1418 110 10 566 1981 8361911 8360510 0.000000e+00 1893
12 TraesCS7A01G153200 chr1A 95.747 917 35 1 1982 2898 13163119 13164031 0.000000e+00 1474
13 TraesCS7A01G153200 chr1A 94.382 267 15 0 1 267 13139074 13139340 7.470000e-111 411
14 TraesCS7A01G153200 chr5B 89.843 1398 109 16 1 1396 551738256 551736890 0.000000e+00 1764
15 TraesCS7A01G153200 chr5B 94.875 917 43 1 1982 2898 668596528 668595616 0.000000e+00 1430
16 TraesCS7A01G153200 chr5B 91.257 915 76 1 1984 2898 551702002 551701092 0.000000e+00 1243
17 TraesCS7A01G153200 chr5B 94.491 599 31 2 1 598 668606242 668605645 0.000000e+00 922
18 TraesCS7A01G153200 chr5B 89.134 543 43 8 105 636 487444339 487443802 0.000000e+00 662
19 TraesCS7A01G153200 chr2A 94.318 1144 40 9 1 1140 21993927 21992805 0.000000e+00 1729
20 TraesCS7A01G153200 chr2A 95.420 917 38 1 1982 2898 21937140 21936228 0.000000e+00 1458
21 TraesCS7A01G153200 chr3D 88.452 1247 126 8 737 1981 418712397 418711167 0.000000e+00 1489
22 TraesCS7A01G153200 chr3D 83.911 1125 148 12 2 1107 70237887 70238997 0.000000e+00 1044
23 TraesCS7A01G153200 chr3A 87.927 1259 139 9 727 1981 667164342 667163093 0.000000e+00 1471
24 TraesCS7A01G153200 chr1B 82.457 1294 214 11 648 1939 502774558 502775840 0.000000e+00 1120
25 TraesCS7A01G153200 chr5A 87.075 882 99 7 288 1159 457792314 457793190 0.000000e+00 983
26 TraesCS7A01G153200 chr2D 86.238 901 120 1 1985 2885 646278077 646277181 0.000000e+00 974
27 TraesCS7A01G153200 chr6D 91.837 147 12 0 1835 1981 318068899 318068753 3.790000e-49 206


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 TraesCS7A01G153200 chr7A 106408137 106411034 2897 True 5352.0 5352 100.0000 1 2898 1 chr7A.!!$R2 2897
1 TraesCS7A01G153200 chr6A 563487853 563493998 6145 False 2368.0 3284 95.9445 1 2898 2 chr6A.!!$F2 2897
2 TraesCS7A01G153200 chr6A 591517046 591518448 1402 False 1943.0 1943 91.6080 566 1981 1 chr6A.!!$F1 1415
3 TraesCS7A01G153200 chr4B 168265476 168271657 6181 True 2341.5 3214 95.8055 1 2898 2 chr4B.!!$R1 2897
4 TraesCS7A01G153200 chr7D 199528039 199529823 1784 False 2743.0 2743 94.4660 1 1779 1 chr7D.!!$F2 1778
5 TraesCS7A01G153200 chr7D 136695684 136701157 5473 True 1236.0 1467 87.6315 737 2877 2 chr7D.!!$R1 2140
6 TraesCS7A01G153200 chr7D 99609737 99610645 908 False 974.0 974 85.9960 1986 2898 1 chr7D.!!$F1 912
7 TraesCS7A01G153200 chr1A 8360510 8361911 1401 True 1893.0 1893 90.9730 566 1981 1 chr1A.!!$R1 1415
8 TraesCS7A01G153200 chr1A 13163119 13164031 912 False 1474.0 1474 95.7470 1982 2898 1 chr1A.!!$F2 916
9 TraesCS7A01G153200 chr5B 551736890 551738256 1366 True 1764.0 1764 89.8430 1 1396 1 chr5B.!!$R3 1395
10 TraesCS7A01G153200 chr5B 668595616 668596528 912 True 1430.0 1430 94.8750 1982 2898 1 chr5B.!!$R4 916
11 TraesCS7A01G153200 chr5B 551701092 551702002 910 True 1243.0 1243 91.2570 1984 2898 1 chr5B.!!$R2 914
12 TraesCS7A01G153200 chr5B 668605645 668606242 597 True 922.0 922 94.4910 1 598 1 chr5B.!!$R5 597
13 TraesCS7A01G153200 chr5B 487443802 487444339 537 True 662.0 662 89.1340 105 636 1 chr5B.!!$R1 531
14 TraesCS7A01G153200 chr2A 21992805 21993927 1122 True 1729.0 1729 94.3180 1 1140 1 chr2A.!!$R2 1139
15 TraesCS7A01G153200 chr2A 21936228 21937140 912 True 1458.0 1458 95.4200 1982 2898 1 chr2A.!!$R1 916
16 TraesCS7A01G153200 chr3D 418711167 418712397 1230 True 1489.0 1489 88.4520 737 1981 1 chr3D.!!$R1 1244
17 TraesCS7A01G153200 chr3D 70237887 70238997 1110 False 1044.0 1044 83.9110 2 1107 1 chr3D.!!$F1 1105
18 TraesCS7A01G153200 chr3A 667163093 667164342 1249 True 1471.0 1471 87.9270 727 1981 1 chr3A.!!$R1 1254
19 TraesCS7A01G153200 chr1B 502774558 502775840 1282 False 1120.0 1120 82.4570 648 1939 1 chr1B.!!$F1 1291
20 TraesCS7A01G153200 chr5A 457792314 457793190 876 False 983.0 983 87.0750 288 1159 1 chr5A.!!$F1 871
21 TraesCS7A01G153200 chr2D 646277181 646278077 896 True 974.0 974 86.2380 1985 2885 1 chr2D.!!$R1 900

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
93 94 1.151810 ACCTCCTCTGGGCCAAAGA 60.152 57.895 8.88 6.09 0.0 2.52 F
289 311 1.700955 ACAACAGTACTCCGACCACT 58.299 50.000 0.00 0.00 0.0 4.00 F
1416 1466 4.446719 GGCTCCATAGTTTTTACCGATACG 59.553 45.833 0.00 0.00 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1466 0.177604 CTGGCACTCCATCTCCAGAC 59.822 60.000 1.09 0.0 46.80 3.51 R
1724 1775 1.335780 GGACATCAAACGCATGTGCAA 60.336 47.619 6.08 0.0 41.08 4.08 R
2585 6017 1.002792 GTCGGTGCTCAAAACAACCTC 60.003 52.381 0.00 0.0 0.00 3.85 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
93 94 1.151810 ACCTCCTCTGGGCCAAAGA 60.152 57.895 8.88 6.09 0.00 2.52
176 180 5.467738 TCTCCCTTATCTCCATTGCTTCTA 58.532 41.667 0.00 0.00 0.00 2.10
184 188 3.384789 TCTCCATTGCTTCTATGTACGCT 59.615 43.478 0.00 0.00 0.00 5.07
221 233 1.771255 GATCTTCCCAGGGTGCTACAT 59.229 52.381 5.01 0.00 0.00 2.29
289 311 1.700955 ACAACAGTACTCCGACCACT 58.299 50.000 0.00 0.00 0.00 4.00
482 519 9.841880 GTTCCTTGTCTTTCATAAAAGGTATTC 57.158 33.333 0.00 0.00 41.88 1.75
622 661 5.711976 ACTGTAGGCATAGCTGAAAACATTT 59.288 36.000 0.00 0.00 0.00 2.32
803 851 4.586421 TCACAGCCAACACAAAATATCCAA 59.414 37.500 0.00 0.00 0.00 3.53
979 1029 7.476540 TGTACATCAGCTTTAGAGAACCTTA 57.523 36.000 0.00 0.00 0.00 2.69
1404 1454 7.200434 TCTAGAAATTCTTGGCTCCATAGTT 57.800 36.000 0.00 0.00 0.00 2.24
1410 1460 6.775594 ATTCTTGGCTCCATAGTTTTTACC 57.224 37.500 0.00 0.00 0.00 2.85
1416 1466 4.446719 GGCTCCATAGTTTTTACCGATACG 59.553 45.833 0.00 0.00 0.00 3.06
1618 1669 4.641645 TGCCACTTGGTCGCCCTG 62.642 66.667 0.00 0.00 37.57 4.45
1724 1775 1.846007 TTTGGAGCAAAGTGGTGTGT 58.154 45.000 0.00 0.00 0.00 3.72
1751 1802 2.905075 TGCGTTTGATGTCCCTCATAG 58.095 47.619 0.00 0.00 36.83 2.23
1762 1813 3.780294 TGTCCCTCATAGTGCTGGTATTT 59.220 43.478 0.00 0.00 0.00 1.40
1880 1934 6.035005 TCGAAATCAGATTGACTTGATTCGAC 59.965 38.462 7.80 4.62 31.76 4.20
1897 1951 1.872952 CGACAAGGTGCAGTTGATTGA 59.127 47.619 14.29 0.00 0.00 2.57
2034 5465 6.403866 AGATATGTCACTAAAGGCTCTCAG 57.596 41.667 0.00 0.00 0.00 3.35
2043 5474 5.127845 CACTAAAGGCTCTCAGACCATTCTA 59.872 44.000 0.00 0.00 0.00 2.10
2051 5482 5.244851 GCTCTCAGACCATTCTATCCACATA 59.755 44.000 0.00 0.00 0.00 2.29
2082 5513 6.264832 TGAACGGAAATGCATTAACATGATC 58.735 36.000 13.39 4.40 31.07 2.92
2097 5528 2.270352 TGATCCGCAACTCTTGGTTT 57.730 45.000 0.00 0.00 35.74 3.27
2263 5694 2.940514 TACCCTGAGTGGAAGATGGA 57.059 50.000 0.00 0.00 38.35 3.41
2264 5695 1.577736 ACCCTGAGTGGAAGATGGAG 58.422 55.000 0.00 0.00 38.35 3.86
2265 5696 0.179936 CCCTGAGTGGAAGATGGAGC 59.820 60.000 0.00 0.00 38.35 4.70
2266 5697 1.202330 CCTGAGTGGAAGATGGAGCT 58.798 55.000 0.00 0.00 38.35 4.09
2524 5955 5.366768 TGTTCCACCCTCTTTCCTCATATAG 59.633 44.000 0.00 0.00 0.00 1.31
2585 6017 8.393366 CCAATATCATAACGAGCTTGGATATTG 58.607 37.037 25.68 25.68 45.85 1.90
2684 6116 3.374988 TCTCGCATGCTGGAAATGTTAAG 59.625 43.478 17.13 0.00 0.00 1.85
2688 6120 4.615682 CGCATGCTGGAAATGTTAAGTTCA 60.616 41.667 17.13 0.00 31.96 3.18
2741 6173 5.003160 CCATGTTTCACTTCACCATCTACA 58.997 41.667 0.00 0.00 0.00 2.74
2785 6217 8.656849 CATGTTCTTATACTCACCTACAAACAC 58.343 37.037 0.00 0.00 0.00 3.32
2813 6245 5.293569 CGTGTAGGAAGTGAATAACCCAATC 59.706 44.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 131 2.113139 CACCTCCGGCCAACTTGT 59.887 61.111 2.24 0.00 0.00 3.16
176 180 3.388024 ACAATGATAGGGACAGCGTACAT 59.612 43.478 0.00 0.00 0.00 2.29
184 188 5.397899 GGAAGATCCAACAATGATAGGGACA 60.398 44.000 0.00 0.00 36.28 4.02
221 233 7.274033 CGTACCTTCTATGACGACAAATTACAA 59.726 37.037 0.00 0.00 37.50 2.41
289 311 7.302948 TCACTAATTAGGGGCTAGTAGAATGA 58.697 38.462 14.77 2.68 0.00 2.57
803 851 6.993079 GGATACTCACATTTTCCCAAGTTTT 58.007 36.000 0.00 0.00 0.00 2.43
979 1029 9.118300 CCTCATCTTAGCAATCTGATAAAAACT 57.882 33.333 0.00 0.00 26.95 2.66
1404 1454 4.202080 CCATCTCCAGACGTATCGGTAAAA 60.202 45.833 0.00 0.00 0.00 1.52
1410 1460 2.031595 CACTCCATCTCCAGACGTATCG 60.032 54.545 0.00 0.00 0.00 2.92
1416 1466 0.177604 CTGGCACTCCATCTCCAGAC 59.822 60.000 1.09 0.00 46.80 3.51
1494 1544 2.775911 ACAATAGAGCAAGAGCAGCA 57.224 45.000 0.00 0.00 45.49 4.41
1618 1669 7.433680 TCTTTGGGCTTCTCAAAAATAACTTC 58.566 34.615 0.00 0.00 34.26 3.01
1724 1775 1.335780 GGACATCAAACGCATGTGCAA 60.336 47.619 6.08 0.00 41.08 4.08
1751 1802 5.297029 GGTGAGGAGAATAAAATACCAGCAC 59.703 44.000 0.00 0.00 0.00 4.40
1762 1813 7.432869 CAACACAAATTTGGTGAGGAGAATAA 58.567 34.615 21.74 0.00 36.14 1.40
1880 1934 3.713858 TTGTCAATCAACTGCACCTTG 57.286 42.857 0.00 0.00 0.00 3.61
1897 1951 7.015974 TGCTCTAGAAGATCATCATATGGTTGT 59.984 37.037 2.13 0.00 0.00 3.32
2043 5474 9.166173 CATTTCCGTTCATGTATATATGTGGAT 57.834 33.333 15.69 5.65 30.87 3.41
2051 5482 8.845227 TGTTAATGCATTTCCGTTCATGTATAT 58.155 29.630 18.75 0.00 0.00 0.86
2082 5513 2.861462 TTCAAAACCAAGAGTTGCGG 57.139 45.000 0.00 0.00 39.19 5.69
2097 5528 4.560128 CCAGAGTTCAGACGAAGATTCAA 58.440 43.478 0.00 0.00 0.00 2.69
2132 5563 6.034161 TGATGACGATGAGCATGATTCTAT 57.966 37.500 0.00 0.00 0.00 1.98
2133 5564 5.458041 TGATGACGATGAGCATGATTCTA 57.542 39.130 0.00 0.00 0.00 2.10
2263 5694 6.437162 TGATTTTTACAGGGAAAATGCTAGCT 59.563 34.615 17.23 0.00 36.96 3.32
2264 5695 6.630071 TGATTTTTACAGGGAAAATGCTAGC 58.370 36.000 8.10 8.10 36.96 3.42
2355 5786 4.415596 AGGCAATCACAAAGGTATGGAAA 58.584 39.130 0.00 0.00 0.00 3.13
2585 6017 1.002792 GTCGGTGCTCAAAACAACCTC 60.003 52.381 0.00 0.00 0.00 3.85
2688 6120 4.024670 GGTGTGGAGTATAGTGTTCCTCT 58.975 47.826 0.00 0.00 32.12 3.69
2725 6157 6.212589 TCTGGTTTATGTAGATGGTGAAGTGA 59.787 38.462 0.00 0.00 0.00 3.41
2741 6173 8.561738 AGAACATGTTAATCGTTCTGGTTTAT 57.438 30.769 11.95 0.00 45.73 1.40
2785 6217 4.325472 GGTTATTCACTTCCTACACGTTCG 59.675 45.833 0.00 0.00 0.00 3.95
2830 6262 9.815936 GAAGCCAAATTTTCAATCATTAGTTTG 57.184 29.630 0.00 0.00 0.00 2.93
2836 6268 7.335924 CCATGAGAAGCCAAATTTTCAATCATT 59.664 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.