Multiple sequence alignment - TraesCS7B01G153300

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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 TraesCS7B01G153300 chr7B 100.000 2381 0 0 1 2381 203886014 203888394 0.000000e+00 4397
1 TraesCS7B01G153300 chr1D 87.195 1515 164 24 889 2381 58565521 58564015 0.000000e+00 1696
2 TraesCS7B01G153300 chr1D 94.941 850 41 2 1 848 388595711 388594862 0.000000e+00 1330
3 TraesCS7B01G153300 chr2A 87.169 1512 149 23 848 2337 190313156 190311668 0.000000e+00 1676
4 TraesCS7B01G153300 chr5A 86.337 1559 171 28 848 2381 584545340 584546881 0.000000e+00 1661
5 TraesCS7B01G153300 chr5A 86.786 1453 163 19 889 2320 241455120 241456564 0.000000e+00 1592
6 TraesCS7B01G153300 chr7A 86.460 1551 160 32 849 2378 292816681 292818202 0.000000e+00 1655
7 TraesCS7B01G153300 chr2D 87.131 1492 152 29 912 2379 177454567 177453092 0.000000e+00 1655
8 TraesCS7B01G153300 chr2D 86.453 1528 175 26 849 2354 338340160 338341677 0.000000e+00 1646
9 TraesCS7B01G153300 chr2D 87.537 1364 150 17 889 2248 531478134 531476787 0.000000e+00 1559
10 TraesCS7B01G153300 chr2D 85.554 1516 166 32 890 2380 630543004 630544491 0.000000e+00 1537
11 TraesCS7B01G153300 chr2D 95.065 851 40 2 1 849 138653207 138654057 0.000000e+00 1338
12 TraesCS7B01G153300 chr2D 94.965 854 40 3 1 851 518048621 518047768 0.000000e+00 1336
13 TraesCS7B01G153300 chr1A 86.091 1553 173 31 847 2381 309397296 309395769 0.000000e+00 1631
14 TraesCS7B01G153300 chr1A 85.554 1516 190 20 889 2380 520576969 520578479 0.000000e+00 1559
15 TraesCS7B01G153300 chr4B 86.694 1473 173 17 849 2307 609587906 609586443 0.000000e+00 1613
16 TraesCS7B01G153300 chr2B 85.772 1490 190 18 901 2381 439421525 439420049 0.000000e+00 1557
17 TraesCS7B01G153300 chr2B 87.417 151 17 2 2231 2381 744191079 744190931 3.150000e-39 172
18 TraesCS7B01G153300 chr7D 95.176 850 39 2 1 848 113234087 113233238 0.000000e+00 1341
19 TraesCS7B01G153300 chr7D 95.277 847 38 2 5 849 510286730 510287576 0.000000e+00 1341
20 TraesCS7B01G153300 chr7D 95.165 848 37 4 5 849 447351673 447352519 0.000000e+00 1336
21 TraesCS7B01G153300 chr7D 87.417 151 15 3 2231 2381 371254040 371253894 1.130000e-38 171
22 TraesCS7B01G153300 chr4D 95.059 850 40 2 1 848 62494155 62493306 0.000000e+00 1336
23 TraesCS7B01G153300 chr4D 94.953 852 41 2 1 850 298233544 298232693 0.000000e+00 1334
24 TraesCS7B01G153300 chr5D 95.053 849 41 1 1 848 343254510 343253662 0.000000e+00 1334
25 TraesCS7B01G153300 chr5D 88.079 151 15 3 2231 2381 222985137 222985284 2.430000e-40 176
26 TraesCS7B01G153300 chr6B 88.514 148 12 5 2233 2379 625240569 625240712 8.750000e-40 174


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 TraesCS7B01G153300 chr7B 203886014 203888394 2380 False 4397 4397 100.000 1 2381 1 chr7B.!!$F1 2380
1 TraesCS7B01G153300 chr1D 58564015 58565521 1506 True 1696 1696 87.195 889 2381 1 chr1D.!!$R1 1492
2 TraesCS7B01G153300 chr1D 388594862 388595711 849 True 1330 1330 94.941 1 848 1 chr1D.!!$R2 847
3 TraesCS7B01G153300 chr2A 190311668 190313156 1488 True 1676 1676 87.169 848 2337 1 chr2A.!!$R1 1489
4 TraesCS7B01G153300 chr5A 584545340 584546881 1541 False 1661 1661 86.337 848 2381 1 chr5A.!!$F2 1533
5 TraesCS7B01G153300 chr5A 241455120 241456564 1444 False 1592 1592 86.786 889 2320 1 chr5A.!!$F1 1431
6 TraesCS7B01G153300 chr7A 292816681 292818202 1521 False 1655 1655 86.460 849 2378 1 chr7A.!!$F1 1529
7 TraesCS7B01G153300 chr2D 177453092 177454567 1475 True 1655 1655 87.131 912 2379 1 chr2D.!!$R1 1467
8 TraesCS7B01G153300 chr2D 338340160 338341677 1517 False 1646 1646 86.453 849 2354 1 chr2D.!!$F2 1505
9 TraesCS7B01G153300 chr2D 531476787 531478134 1347 True 1559 1559 87.537 889 2248 1 chr2D.!!$R3 1359
10 TraesCS7B01G153300 chr2D 630543004 630544491 1487 False 1537 1537 85.554 890 2380 1 chr2D.!!$F3 1490
11 TraesCS7B01G153300 chr2D 138653207 138654057 850 False 1338 1338 95.065 1 849 1 chr2D.!!$F1 848
12 TraesCS7B01G153300 chr2D 518047768 518048621 853 True 1336 1336 94.965 1 851 1 chr2D.!!$R2 850
13 TraesCS7B01G153300 chr1A 309395769 309397296 1527 True 1631 1631 86.091 847 2381 1 chr1A.!!$R1 1534
14 TraesCS7B01G153300 chr1A 520576969 520578479 1510 False 1559 1559 85.554 889 2380 1 chr1A.!!$F1 1491
15 TraesCS7B01G153300 chr4B 609586443 609587906 1463 True 1613 1613 86.694 849 2307 1 chr4B.!!$R1 1458
16 TraesCS7B01G153300 chr2B 439420049 439421525 1476 True 1557 1557 85.772 901 2381 1 chr2B.!!$R1 1480
17 TraesCS7B01G153300 chr7D 113233238 113234087 849 True 1341 1341 95.176 1 848 1 chr7D.!!$R1 847
18 TraesCS7B01G153300 chr7D 510286730 510287576 846 False 1341 1341 95.277 5 849 1 chr7D.!!$F2 844
19 TraesCS7B01G153300 chr7D 447351673 447352519 846 False 1336 1336 95.165 5 849 1 chr7D.!!$F1 844
20 TraesCS7B01G153300 chr4D 62493306 62494155 849 True 1336 1336 95.059 1 848 1 chr4D.!!$R1 847
21 TraesCS7B01G153300 chr4D 298232693 298233544 851 True 1334 1334 94.953 1 850 1 chr4D.!!$R2 849
22 TraesCS7B01G153300 chr5D 343253662 343254510 848 True 1334 1334 95.053 1 848 1 chr5D.!!$R1 847

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
306 307 0.598419 GTCACTTTGCTTGCAAGGCC 60.598 55.0 27.1 12.47 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1859 0.610687 CGCTTCTCCTCCCTTGAGTT 59.389 55.0 0.0 0.0 36.86 3.01 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
138 139 8.112016 TCTATGAAGATCTTTATCGGTCGAAT 57.888 34.615 15.42 0.00 37.19 3.34
237 238 3.129988 CCTAGTTCAATCTCGTTACCGGT 59.870 47.826 13.98 13.98 33.95 5.28
306 307 0.598419 GTCACTTTGCTTGCAAGGCC 60.598 55.000 27.10 12.47 0.00 5.19
582 583 8.607441 ATGATCATAATGCTAAGCTAACGAAA 57.393 30.769 6.36 0.00 0.00 3.46
636 638 4.525996 TGTGATCCCGTTCATCAAATGAT 58.474 39.130 0.00 0.00 39.39 2.45
754 756 4.000988 ACACATGTATCAAGTTTCCGGTC 58.999 43.478 0.00 0.00 0.00 4.79
853 857 2.625314 GGGCATATTTCCTTCAAGAGCC 59.375 50.000 0.00 0.00 38.84 4.70
861 865 4.647564 TTCCTTCAAGAGCCTCATCTTT 57.352 40.909 0.00 0.00 37.43 2.52
924 937 2.792947 GGCTGGCTACGATCCCGAA 61.793 63.158 0.00 0.00 39.50 4.30
986 999 2.216898 GACCTATGATCAAGCTGCCAC 58.783 52.381 0.00 0.00 0.00 5.01
1012 1025 1.065926 ACGCCTTCATGCAAGATCAGA 60.066 47.619 0.00 0.00 33.29 3.27
1137 1150 1.205064 CGAGCTCGCAAACCAAGTG 59.795 57.895 25.07 0.00 0.00 3.16
1225 1239 0.105964 TTGTGAGTGTTGGAGGGACG 59.894 55.000 0.00 0.00 0.00 4.79
1257 1271 2.978010 AAGGTTGGCGCCGAACAG 60.978 61.111 33.05 0.00 0.00 3.16
1401 1415 3.848726 ACAAGAGTGCAACAAGTTTTGG 58.151 40.909 0.00 0.00 41.43 3.28
1502 1531 0.029300 CCATTCCCGTTATGCTTGCG 59.971 55.000 0.00 0.00 0.00 4.85
1521 1550 2.541588 GCGTGTCCATTTGCATATCCAC 60.542 50.000 0.00 0.00 0.00 4.02
1552 1581 3.729966 TGCTTGCATGCTTTTCATTTGA 58.270 36.364 23.31 0.00 31.79 2.69
1653 1684 1.430992 ACGGGGAGGAGAAGTTCAAA 58.569 50.000 5.50 0.00 0.00 2.69
1655 1686 1.339151 CGGGGAGGAGAAGTTCAAAGG 60.339 57.143 5.50 0.00 0.00 3.11
1656 1687 1.705745 GGGGAGGAGAAGTTCAAAGGT 59.294 52.381 5.50 0.00 0.00 3.50
1668 1699 4.270008 AGTTCAAAGGTTAATATGCCGCT 58.730 39.130 0.00 0.00 0.00 5.52
1707 1742 0.622665 AGAAAGCCATGGAGGAGGTG 59.377 55.000 18.40 0.00 41.22 4.00
1776 1812 2.185310 GAGGACAAGTGGGATGCGGT 62.185 60.000 0.00 0.00 0.00 5.68
1812 1848 2.040544 CAACCGTGGAGGGCATGAC 61.041 63.158 0.00 0.00 46.96 3.06
1823 1859 0.391661 GGGCATGACGAGCAAGAAGA 60.392 55.000 0.00 0.00 0.00 2.87
1867 1904 4.377841 CGACAAGACAAGGAAGAGCAAATC 60.378 45.833 0.00 0.00 0.00 2.17
2100 2139 3.201290 GTCATGGTTCGAGAAGATGCAT 58.799 45.455 0.00 0.00 0.00 3.96
2102 2141 2.768253 TGGTTCGAGAAGATGCATGT 57.232 45.000 2.46 0.00 0.00 3.21
2104 2143 1.936547 GGTTCGAGAAGATGCATGTCC 59.063 52.381 2.46 0.00 0.00 4.02
2258 2330 2.314647 GCGCCAGCGTTGAACTGTA 61.315 57.895 14.22 0.00 42.09 2.74
2259 2331 1.635663 GCGCCAGCGTTGAACTGTAT 61.636 55.000 14.22 0.00 42.09 2.29
2260 2332 0.095245 CGCCAGCGTTGAACTGTATG 59.905 55.000 0.00 0.00 33.09 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 6.476380 GGGAATAACGTATGTTGTCATTACGA 59.524 38.462 10.68 0.00 39.12 3.43
306 307 7.309177 CCTCTCGGTAATACACATCATAAGAG 58.691 42.308 0.00 0.00 0.00 2.85
441 442 5.120053 TGTGCTATCAAACGTCACAACATAG 59.880 40.000 1.90 0.00 35.08 2.23
582 583 0.994247 TGATGTGATGGCAAGACCCT 59.006 50.000 0.00 0.00 37.83 4.34
636 638 7.913789 AGTTTCCTAACCATAGACATGTGTTA 58.086 34.615 1.15 4.28 34.71 2.41
829 832 5.133221 GCTCTTGAAGGAAATATGCCCTAA 58.867 41.667 0.00 0.00 31.36 2.69
924 937 0.035458 CGTCTTGGCTTTGGGTCTCT 59.965 55.000 0.00 0.00 0.00 3.10
951 964 2.604174 GGTCGTTGGCGTGAACTGG 61.604 63.158 0.00 0.00 39.49 4.00
953 966 0.606604 ATAGGTCGTTGGCGTGAACT 59.393 50.000 0.00 0.00 39.49 3.01
986 999 1.840630 TTGCATGAAGGCGTCGTGTG 61.841 55.000 20.95 9.51 44.08 3.82
1012 1025 3.083997 GTCCAGGTCCAGGCCGAT 61.084 66.667 0.00 0.00 0.00 4.18
1128 1141 1.528309 CACCTCGGCCACTTGGTTT 60.528 57.895 2.24 0.00 37.57 3.27
1137 1150 4.388499 TTCGGCTTCACCTCGGCC 62.388 66.667 0.00 0.00 42.18 6.13
1194 1208 2.092968 ACACTCACAAAGGAGCTTGTCA 60.093 45.455 0.00 0.00 37.43 3.58
1289 1303 3.057969 TCTTGCGTTCATGGAACTCAT 57.942 42.857 7.43 0.00 37.17 2.90
1348 1362 4.081142 TCTCCATCGCTTAGAAATGGACAA 60.081 41.667 10.62 2.41 43.06 3.18
1371 1385 6.936900 ACTTGTTGCACTCTTGTTATATCACT 59.063 34.615 0.00 0.00 0.00 3.41
1401 1415 1.452833 GATGCTCTCAAGGGTGGCC 60.453 63.158 0.00 0.00 0.00 5.36
1502 1531 4.675510 CAAGTGGATATGCAAATGGACAC 58.324 43.478 0.00 0.00 0.00 3.67
1521 1550 1.872237 GCATGCAAGCATATGGGCAAG 60.872 52.381 14.21 0.00 40.02 4.01
1552 1581 2.301009 CCTCCAAAGCTTGAAATGCCTT 59.699 45.455 0.00 0.00 37.80 4.35
1653 1684 3.557898 CCATGAGAGCGGCATATTAACCT 60.558 47.826 1.45 0.00 0.00 3.50
1812 1848 2.072298 CCCTTGAGTTCTTCTTGCTCG 58.928 52.381 0.00 0.00 32.32 5.03
1823 1859 0.610687 CGCTTCTCCTCCCTTGAGTT 59.389 55.000 0.00 0.00 36.86 3.01
1867 1904 2.940158 TGGATCTCCATGAAGGCATTG 58.060 47.619 0.00 0.00 42.01 2.82
1990 2028 0.889186 GCCACTTCTTTCGCCTTGGA 60.889 55.000 0.00 0.00 0.00 3.53
2100 2139 1.069978 TCGAACTTGAGCATGTGGACA 59.930 47.619 0.00 0.00 0.00 4.02
2102 2141 1.795768 GTCGAACTTGAGCATGTGGA 58.204 50.000 0.00 0.00 0.00 4.02
2104 2143 1.125021 GTCGTCGAACTTGAGCATGTG 59.875 52.381 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.