Multiple sequence alignment - TraesCS4D01G044500

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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 TraesCS4D01G044500 chr4D 100.000 1628 0 0 1 1628 20110707 20112334 0.000000e+00 3007
1 TraesCS4D01G044500 chr4D 100.000 599 0 0 1729 2327 20112435 20113033 0.000000e+00 1107
2 TraesCS4D01G044500 chr4D 97.329 599 16 0 1729 2327 300796102 300795504 0.000000e+00 1018
3 TraesCS4D01G044500 chr4D 96.863 510 16 0 1018 1527 300797036 300796527 0.000000e+00 854
4 TraesCS4D01G044500 chr4D 89.881 168 3 7 65 218 497644080 497644247 1.090000e-48 204
5 TraesCS4D01G044500 chr4D 93.333 105 2 3 1528 1628 20112149 20112252 1.440000e-32 150
6 TraesCS4D01G044500 chr4D 95.181 83 2 2 1528 1609 461470327 461470408 1.880000e-26 130
7 TraesCS4D01G044500 chr4D 92.771 83 4 2 1528 1609 300796611 300796530 4.060000e-23 119
8 TraesCS4D01G044500 chr4A 95.513 1560 36 7 1 1527 477954659 477953101 0.000000e+00 2462
9 TraesCS4D01G044500 chr4A 97.162 599 17 0 1729 2327 477952676 477952078 0.000000e+00 1013
10 TraesCS4D01G044500 chr4B 95.379 1558 38 7 3 1527 529350059 529351615 0.000000e+00 2447
11 TraesCS4D01G044500 chr4B 97.162 599 17 0 1729 2327 529352040 529352638 0.000000e+00 1013
12 TraesCS4D01G044500 chr4B 94.000 150 6 2 1 148 285018731 285018879 8.370000e-55 224
13 TraesCS4D01G044500 chr3A 94.872 1560 46 14 1 1527 579480453 579478895 0.000000e+00 2407
14 TraesCS4D01G044500 chr3A 95.238 105 5 0 232 336 108911226 108911330 1.430000e-37 167
15 TraesCS4D01G044500 chr5A 94.872 1326 38 15 232 1527 649233408 649234733 0.000000e+00 2045
16 TraesCS4D01G044500 chr5A 97.659 598 14 0 1730 2327 649235159 649235756 0.000000e+00 1027
17 TraesCS4D01G044500 chr5A 96.828 599 19 0 1729 2327 521196145 521195547 0.000000e+00 1002
18 TraesCS4D01G044500 chr5A 95.652 138 5 1 37 174 521197642 521197506 1.080000e-53 220
19 TraesCS4D01G044500 chr5A 95.181 83 2 2 1528 1609 649234649 649234730 1.880000e-26 130
20 TraesCS4D01G044500 chr5A 93.750 80 5 0 1530 1609 598303799 598303878 1.130000e-23 121
21 TraesCS4D01G044500 chr5A 100.000 62 0 0 228 289 677947825 677947886 5.250000e-22 115
22 TraesCS4D01G044500 chr6D 94.479 1268 39 6 290 1527 93883886 93882620 0.000000e+00 1925
23 TraesCS4D01G044500 chr6D 96.833 600 17 2 1729 2327 4288600 4289198 0.000000e+00 1002
24 TraesCS4D01G044500 chr6D 93.976 83 3 2 1528 1609 93882704 93882623 8.730000e-25 124
25 TraesCS4D01G044500 chr6A 94.095 1287 43 4 273 1527 419487795 419486510 0.000000e+00 1925
26 TraesCS4D01G044500 chr7D 95.683 1112 36 3 1 1109 116236999 116238101 0.000000e+00 1777
27 TraesCS4D01G044500 chr7D 97.329 599 16 0 1729 2327 140799538 140800136 0.000000e+00 1018
28 TraesCS4D01G044500 chr7D 96.833 600 17 2 1729 2327 116239004 116239602 0.000000e+00 1002
29 TraesCS4D01G044500 chr7D 97.059 510 15 0 1018 1527 140798604 140799113 0.000000e+00 859
30 TraesCS4D01G044500 chr6B 93.588 1154 43 14 290 1413 132427547 132428699 0.000000e+00 1692
31 TraesCS4D01G044500 chr5B 95.488 820 37 0 290 1109 346108672 346109491 0.000000e+00 1310
32 TraesCS4D01G044500 chr5B 97.260 511 13 1 1018 1527 346109430 346109940 0.000000e+00 865
33 TraesCS4D01G044500 chr5B 99.029 103 0 1 1 103 680670165 680670266 1.420000e-42 183
34 TraesCS4D01G044500 chr3D 97.000 600 16 2 1729 2327 40697759 40697161 0.000000e+00 1007
35 TraesCS4D01G044500 chr3D 97.843 510 10 1 1018 1527 40698692 40698184 0.000000e+00 880
36 TraesCS4D01G044500 chr3D 93.976 83 2 3 1528 1609 40698267 40698187 3.140000e-24 122
37 TraesCS4D01G044500 chr1B 97.059 510 15 0 1018 1527 405390372 405390881 0.000000e+00 859
38 TraesCS4D01G044500 chr2A 95.397 478 8 4 1 475 88725622 88725156 0.000000e+00 749
39 TraesCS4D01G044500 chr2A 95.181 83 2 2 1528 1609 88724764 88724683 1.880000e-26 130
40 TraesCS4D01G044500 chr2A 93.976 83 3 2 1528 1609 14743862 14743943 8.730000e-25 124
41 TraesCS4D01G044500 chr7A 98.844 173 1 1 1 173 150415707 150415536 8.080000e-80 307


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 TraesCS4D01G044500 chr4D 20110707 20113033 2326 False 1421.333333 3007 97.777667 1 2327 3 chr4D.!!$F3 2326
1 TraesCS4D01G044500 chr4D 300795504 300797036 1532 True 663.666667 1018 95.654333 1018 2327 3 chr4D.!!$R1 1309
2 TraesCS4D01G044500 chr4A 477952078 477954659 2581 True 1737.500000 2462 96.337500 1 2327 2 chr4A.!!$R1 2326
3 TraesCS4D01G044500 chr4B 529350059 529352638 2579 False 1730.000000 2447 96.270500 3 2327 2 chr4B.!!$F2 2324
4 TraesCS4D01G044500 chr3A 579478895 579480453 1558 True 2407.000000 2407 94.872000 1 1527 1 chr3A.!!$R1 1526
5 TraesCS4D01G044500 chr5A 649233408 649235756 2348 False 1067.333333 2045 95.904000 232 2327 3 chr5A.!!$F3 2095
6 TraesCS4D01G044500 chr5A 521195547 521197642 2095 True 611.000000 1002 96.240000 37 2327 2 chr5A.!!$R1 2290
7 TraesCS4D01G044500 chr6D 93882620 93883886 1266 True 1024.500000 1925 94.227500 290 1609 2 chr6D.!!$R1 1319
8 TraesCS4D01G044500 chr6D 4288600 4289198 598 False 1002.000000 1002 96.833000 1729 2327 1 chr6D.!!$F1 598
9 TraesCS4D01G044500 chr6A 419486510 419487795 1285 True 1925.000000 1925 94.095000 273 1527 1 chr6A.!!$R1 1254
10 TraesCS4D01G044500 chr7D 116236999 116239602 2603 False 1389.500000 1777 96.258000 1 2327 2 chr7D.!!$F1 2326
11 TraesCS4D01G044500 chr7D 140798604 140800136 1532 False 938.500000 1018 97.194000 1018 2327 2 chr7D.!!$F2 1309
12 TraesCS4D01G044500 chr6B 132427547 132428699 1152 False 1692.000000 1692 93.588000 290 1413 1 chr6B.!!$F1 1123
13 TraesCS4D01G044500 chr5B 346108672 346109940 1268 False 1087.500000 1310 96.374000 290 1527 2 chr5B.!!$F2 1237
14 TraesCS4D01G044500 chr3D 40697161 40698692 1531 True 669.666667 1007 96.273000 1018 2327 3 chr3D.!!$R1 1309
15 TraesCS4D01G044500 chr1B 405390372 405390881 509 False 859.000000 859 97.059000 1018 1527 1 chr1B.!!$F1 509
16 TraesCS4D01G044500 chr2A 88724683 88725622 939 True 439.500000 749 95.289000 1 1609 2 chr2A.!!$R1 1608

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
389 393 2.159435 GGTTCGAGCAAATAACCGCAAT 60.159 45.455 0.53 0.0 33.85 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 1784 0.385029 TCTGCCACAACAACATGCAC 59.615 50.0 0.0 0.0 0.0 4.57 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
95 96 6.155475 ACAGCTTGTTTGCCTATTTACAAA 57.845 33.333 0.00 0.00 33.55 2.83
389 393 2.159435 GGTTCGAGCAAATAACCGCAAT 60.159 45.455 0.53 0.00 33.85 3.56
476 480 3.547054 AACTATTCGACCCGGCAAATA 57.453 42.857 0.00 0.00 0.00 1.40
533 537 4.665451 ACACATGGAAGACATTGATCCAA 58.335 39.130 12.26 0.00 45.75 3.53
559 563 3.401182 CATCTGGCTTAGGAAGAGATGC 58.599 50.000 0.00 0.00 34.86 3.91
565 569 3.594134 GCTTAGGAAGAGATGCGCATAT 58.406 45.455 25.40 22.20 0.00 1.78
784 789 6.128902 GGTTTTCGATACTACTTGTGTCACAG 60.129 42.308 5.67 3.59 36.72 3.66
833 838 4.819610 TCATATCAAGGTGATCCCTCTCA 58.180 43.478 3.53 0.00 45.47 3.27
876 881 2.774234 AGGGTGTGATAGTCATGAAGGG 59.226 50.000 0.00 0.00 0.00 3.95
963 969 5.624159 AGTCCAAAGATGAATGACAAGTGA 58.376 37.500 0.00 0.00 0.00 3.41
1023 1059 2.229792 GTGGACATCTTTGGTGCAAGA 58.770 47.619 0.00 0.00 38.35 3.02
1026 1062 2.485814 GGACATCTTTGGTGCAAGAGAC 59.514 50.000 0.00 0.00 0.00 3.36
1088 1154 0.698818 GAGGAAAGGGCAAGGGAGAA 59.301 55.000 0.00 0.00 0.00 2.87
1280 1346 2.079158 CACGGCTCATGAATCTGTTGT 58.921 47.619 0.00 0.00 0.00 3.32
1529 1749 7.830099 AATCCAGAAAGAAACAAGAAGATGT 57.170 32.000 0.00 0.00 34.24 3.06
1530 1750 7.830099 ATCCAGAAAGAAACAAGAAGATGTT 57.170 32.000 0.00 0.00 45.12 2.71
1534 1754 8.571336 CCAGAAAGAAACAAGAAGATGTTATGT 58.429 33.333 0.00 0.00 42.49 2.29
1536 1756 8.078596 AGAAAGAAACAAGAAGATGTTATGTGC 58.921 33.333 0.00 0.00 42.49 4.57
1538 1758 7.458409 AGAAACAAGAAGATGTTATGTGCAT 57.542 32.000 0.00 0.00 42.49 3.96
1541 1761 6.579666 ACAAGAAGATGTTATGTGCATGTT 57.420 33.333 0.00 0.00 33.40 2.71
1542 1762 6.384224 ACAAGAAGATGTTATGTGCATGTTG 58.616 36.000 0.00 0.00 31.32 3.33
1543 1763 6.016024 ACAAGAAGATGTTATGTGCATGTTGT 60.016 34.615 0.00 0.00 31.32 3.32
1547 1767 6.816134 AGATGTTATGTGCATGTTGTTGTA 57.184 33.333 0.00 0.00 0.00 2.41
1550 1770 6.816134 TGTTATGTGCATGTTGTTGTATCT 57.184 33.333 0.00 0.00 0.00 1.98
1574 1794 9.830975 TCTAATATTACACTATGTGCATGTTGT 57.169 29.630 0.00 1.24 36.98 3.32
1577 1797 6.573664 ATTACACTATGTGCATGTTGTTGT 57.426 33.333 0.00 0.00 36.98 3.32
1579 1799 3.004629 ACACTATGTGCATGTTGTTGTGG 59.995 43.478 0.00 0.00 36.98 4.17
1580 1800 2.030007 ACTATGTGCATGTTGTTGTGGC 60.030 45.455 0.00 0.00 0.00 5.01
1581 1801 0.751452 ATGTGCATGTTGTTGTGGCA 59.249 45.000 0.00 0.00 0.00 4.92
1583 1803 0.385029 GTGCATGTTGTTGTGGCAGA 59.615 50.000 0.00 0.00 34.78 4.26
1585 1805 1.000052 TGCATGTTGTTGTGGCAGATG 60.000 47.619 0.00 0.00 0.00 2.90
1586 1806 1.670674 GCATGTTGTTGTGGCAGATGG 60.671 52.381 0.00 0.00 0.00 3.51
1587 1807 1.887854 CATGTTGTTGTGGCAGATGGA 59.112 47.619 0.00 0.00 0.00 3.41
1588 1808 2.291209 TGTTGTTGTGGCAGATGGAT 57.709 45.000 0.00 0.00 0.00 3.41
1590 1810 3.760738 TGTTGTTGTGGCAGATGGATAA 58.239 40.909 0.00 0.00 0.00 1.75
1591 1811 4.148079 TGTTGTTGTGGCAGATGGATAAA 58.852 39.130 0.00 0.00 0.00 1.40
1592 1812 4.771577 TGTTGTTGTGGCAGATGGATAAAT 59.228 37.500 0.00 0.00 0.00 1.40
1593 1813 5.105797 TGTTGTTGTGGCAGATGGATAAATC 60.106 40.000 0.00 0.00 0.00 2.17
1611 1831 8.743714 GGATAAATCCAGAAAGAAACAAGATGT 58.256 33.333 4.04 0.00 46.38 3.06
1616 1836 8.641498 ATCCAGAAAGAAACAAGATGTTATGT 57.359 30.769 0.00 0.00 40.14 2.29
1617 1837 7.874940 TCCAGAAAGAAACAAGATGTTATGTG 58.125 34.615 0.00 0.00 40.14 3.21
1618 1838 6.583806 CCAGAAAGAAACAAGATGTTATGTGC 59.416 38.462 0.00 0.00 40.14 4.57
1619 1839 7.140705 CAGAAAGAAACAAGATGTTATGTGCA 58.859 34.615 0.00 0.00 40.14 4.57
1620 1840 7.811236 CAGAAAGAAACAAGATGTTATGTGCAT 59.189 33.333 0.00 0.00 40.14 3.96
1621 1841 7.811236 AGAAAGAAACAAGATGTTATGTGCATG 59.189 33.333 0.00 0.00 40.14 4.06
1623 1843 6.985117 AGAAACAAGATGTTATGTGCATGTT 58.015 32.000 0.00 0.00 40.14 2.71
1627 1847 6.384178 CAAGATGTTATGTGCATGTTGTTG 57.616 37.500 0.00 0.00 40.49 3.33
1760 2051 6.435430 AAAACAAAGTTTTGGCCTCATTTC 57.565 33.333 3.32 0.00 42.34 2.17
1919 2211 2.034999 GTTGTTCCCGGATGGCCA 59.965 61.111 8.56 8.56 0.00 5.36
1983 2276 6.655003 AGTTCGTTATGATCACTTTCCACAAT 59.345 34.615 0.00 0.00 0.00 2.71
2180 2473 2.958355 CAGATTTCCAACAACACCCACT 59.042 45.455 0.00 0.00 0.00 4.00
2251 2544 7.447374 AATGTCATCGAAAGAACATTTGGTA 57.553 32.000 10.46 0.00 44.70 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
389 393 2.932855 TGTCCGACAAATAACCACCA 57.067 45.000 0.00 0.00 0.00 4.17
559 563 3.742882 AGCTGCAATAGTGTGTATATGCG 59.257 43.478 1.02 0.00 0.00 4.73
565 569 6.169800 TCATTTGTAGCTGCAATAGTGTGTA 58.830 36.000 18.31 0.81 0.00 2.90
784 789 2.541120 GCACCCTCGCATGCTCATC 61.541 63.158 17.13 0.00 38.84 2.92
833 838 5.246981 TGAGTCATCCTCCAAACTGATTT 57.753 39.130 0.00 0.00 39.65 2.17
876 881 4.556233 GATTTTGAACAGGGGTAACTTGC 58.444 43.478 0.00 0.00 0.00 4.01
1023 1059 1.202330 CCTCTGCATCCCTCTTGTCT 58.798 55.000 0.00 0.00 0.00 3.41
1026 1062 1.413445 CTCTCCTCTGCATCCCTCTTG 59.587 57.143 0.00 0.00 0.00 3.02
1088 1154 1.692121 CCCTCTTCTCTGCATCCCTCT 60.692 57.143 0.00 0.00 0.00 3.69
1220 1286 9.740239 CATCACGATATTTCTTTTCCATGAAAT 57.260 29.630 0.00 0.00 42.98 2.17
1280 1346 4.975147 TCCTCTTTATCCATCCAAGCCTTA 59.025 41.667 0.00 0.00 0.00 2.69
1557 1777 3.004629 CCACAACAACATGCACATAGTGT 59.995 43.478 0.00 0.00 35.75 3.55
1560 1780 2.030096 TGCCACAACAACATGCACATAG 60.030 45.455 0.00 0.00 0.00 2.23
1561 1781 1.959282 TGCCACAACAACATGCACATA 59.041 42.857 0.00 0.00 0.00 2.29
1564 1784 0.385029 TCTGCCACAACAACATGCAC 59.615 50.000 0.00 0.00 0.00 4.57
1567 1787 1.887854 TCCATCTGCCACAACAACATG 59.112 47.619 0.00 0.00 0.00 3.21
1568 1788 2.291209 TCCATCTGCCACAACAACAT 57.709 45.000 0.00 0.00 0.00 2.71
1569 1789 2.291209 ATCCATCTGCCACAACAACA 57.709 45.000 0.00 0.00 0.00 3.33
1573 1793 4.574599 GGATTTATCCATCTGCCACAAC 57.425 45.455 3.87 0.00 46.38 3.32
1590 1810 9.082313 ACATAACATCTTGTTTCTTTCTGGATT 57.918 29.630 0.00 0.00 41.45 3.01
1591 1811 8.517878 CACATAACATCTTGTTTCTTTCTGGAT 58.482 33.333 0.00 0.00 41.45 3.41
1592 1812 7.522073 GCACATAACATCTTGTTTCTTTCTGGA 60.522 37.037 0.00 0.00 41.45 3.86
1593 1813 6.583806 GCACATAACATCTTGTTTCTTTCTGG 59.416 38.462 0.00 0.00 41.45 3.86
1594 1814 7.140705 TGCACATAACATCTTGTTTCTTTCTG 58.859 34.615 0.00 0.00 41.45 3.02
1595 1815 7.275888 TGCACATAACATCTTGTTTCTTTCT 57.724 32.000 0.00 0.00 41.45 2.52
1597 1817 7.436118 ACATGCACATAACATCTTGTTTCTTT 58.564 30.769 0.00 0.00 41.45 2.52
1598 1818 6.985117 ACATGCACATAACATCTTGTTTCTT 58.015 32.000 0.00 0.00 41.45 2.52
1599 1819 6.579666 ACATGCACATAACATCTTGTTTCT 57.420 33.333 0.00 0.00 41.45 2.52
1600 1820 6.642131 ACAACATGCACATAACATCTTGTTTC 59.358 34.615 0.00 0.00 41.45 2.78
1602 1822 6.088016 ACAACATGCACATAACATCTTGTT 57.912 33.333 0.00 0.00 43.88 2.83
1604 1824 6.384178 CAACAACATGCACATAACATCTTG 57.616 37.500 0.00 0.00 31.91 3.02
1919 2211 2.300152 ACGTGTGTCATGAACAGATCCT 59.700 45.455 0.00 0.00 38.97 3.24
1983 2276 1.580059 GAGATGTTACCTGTGGGGGA 58.420 55.000 0.00 0.00 40.03 4.81
2092 2385 0.679505 TTTGGATATCCGGAGCCGAG 59.320 55.000 17.04 0.73 42.83 4.63
2096 2389 1.543429 CCCTGTTTGGATATCCGGAGC 60.543 57.143 17.04 10.44 39.43 4.70
2180 2473 7.419057 GGTTGAATGTCTCATATCTCCCAACTA 60.419 40.741 0.00 0.00 32.78 2.24
2251 2544 6.320672 AGAATTCGCCATTTCATCTTGAGAAT 59.679 34.615 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.