Multiple sequence alignment - TraesCS5D01G150300

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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 TraesCS5D01G150300 chr5D 100.000 2234 0 0 1 2234 238951143 238948910 0.000000e+00 4126.0
1 TraesCS5D01G150300 chr5D 100.000 67 0 0 1488 1554 380078774 380078840 8.380000e-25 124.0
2 TraesCS5D01G150300 chr5D 100.000 65 0 0 1489 1553 76972625 76972561 1.080000e-23 121.0
3 TraesCS5D01G150300 chr5B 94.921 1516 43 12 4 1488 265284345 265285857 0.000000e+00 2342.0
4 TraesCS5D01G150300 chr5B 92.244 361 28 0 1874 2234 265287190 265287550 1.530000e-141 512.0
5 TraesCS5D01G150300 chr5B 100.000 82 0 0 1785 1866 265287062 265287143 3.840000e-33 152.0
6 TraesCS5D01G150300 chr5B 92.233 103 8 0 1683 1785 265286022 265286124 1.790000e-31 147.0
7 TraesCS5D01G150300 chr5A 96.163 860 28 1 551 1410 315175818 315176672 0.000000e+00 1400.0
8 TraesCS5D01G150300 chrUn 92.040 402 13 4 1 402 474336036 474336418 4.190000e-152 547.0
9 TraesCS5D01G150300 chr6B 97.333 75 2 0 1480 1554 413647400 413647474 6.480000e-26 128.0
10 TraesCS5D01G150300 chr4D 100.000 69 0 0 1486 1554 447293815 447293747 6.480000e-26 128.0
11 TraesCS5D01G150300 chr4D 100.000 66 0 0 1489 1554 320600895 320600830 3.010000e-24 122.0
12 TraesCS5D01G150300 chr7D 100.000 67 0 0 1488 1554 1956692 1956758 8.380000e-25 124.0
13 TraesCS5D01G150300 chr7D 100.000 67 0 0 1488 1554 34300830 34300896 8.380000e-25 124.0
14 TraesCS5D01G150300 chr3D 100.000 66 0 0 1489 1554 529127161 529127226 3.010000e-24 122.0
15 TraesCS5D01G150300 chr3D 87.129 101 8 4 2 100 487243139 487243042 2.350000e-20 110.0
16 TraesCS5D01G150300 chr1B 89.655 87 8 1 1469 1554 28297496 28297410 2.350000e-20 110.0
17 TraesCS5D01G150300 chr2D 82.653 98 14 3 3 100 547603565 547603471 1.420000e-12 84.2


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 TraesCS5D01G150300 chr5D 238948910 238951143 2233 True 4126.00 4126 100.0000 1 2234 1 chr5D.!!$R2 2233
1 TraesCS5D01G150300 chr5B 265284345 265287550 3205 False 788.25 2342 94.8495 4 2234 4 chr5B.!!$F1 2230
2 TraesCS5D01G150300 chr5A 315175818 315176672 854 False 1400.00 1400 96.1630 551 1410 1 chr5A.!!$F1 859

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
290 296 0.041833 TCCTCCTCCTCCACCTCTTG 59.958 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 3153 1.009675 CGCAAGCAGTGTGTTCACC 60.01 57.895 0.37 0.0 44.83 4.02 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
197 198 3.791973 AGTAGTGAATTCAGGAGCTCG 57.208 47.619 8.80 0.00 0.00 5.03
268 274 3.968773 GAGAGGCATGGCTCTCCT 58.031 61.111 46.10 30.70 39.96 3.69
269 275 1.747774 GAGAGGCATGGCTCTCCTC 59.252 63.158 46.10 32.87 45.11 3.71
270 276 1.757423 GAGAGGCATGGCTCTCCTCC 61.757 65.000 46.10 32.49 45.73 4.30
290 296 0.041833 TCCTCCTCCTCCACCTCTTG 59.958 60.000 0.00 0.00 0.00 3.02
359 365 1.715862 CTGCGATCTTCGTCCTCGGA 61.716 60.000 0.00 0.00 42.81 4.55
371 377 2.716017 CCTCGGAGACTCCACTGCC 61.716 68.421 21.49 0.00 35.91 4.85
407 413 1.003233 GCTGTCCCTCAACCTCACC 60.003 63.158 0.00 0.00 0.00 4.02
437 443 0.915364 CTTTCTCTAGCCCCTGCCTT 59.085 55.000 0.00 0.00 38.69 4.35
600 606 2.187946 CCGCCACTCATCTCCACC 59.812 66.667 0.00 0.00 0.00 4.61
1224 1230 5.850557 TTACGAACCGGGATTATCTGTTA 57.149 39.130 6.32 0.00 0.00 2.41
1329 1342 0.981183 TGCTACCGGGTGTTCAATCT 59.019 50.000 10.66 0.00 0.00 2.40
1412 1431 7.126398 GTGATCGAAGCATCTTAACCAATTAC 58.874 38.462 0.00 0.00 0.00 1.89
1496 1528 7.756395 TCTAGTTATAGTATTTGAGGACGGG 57.244 40.000 0.00 0.00 0.00 5.28
1497 1529 5.803237 AGTTATAGTATTTGAGGACGGGG 57.197 43.478 0.00 0.00 0.00 5.73
1498 1530 4.040095 AGTTATAGTATTTGAGGACGGGGC 59.960 45.833 0.00 0.00 0.00 5.80
1499 1531 0.748450 TAGTATTTGAGGACGGGGCG 59.252 55.000 0.00 0.00 0.00 6.13
1500 1532 1.219935 GTATTTGAGGACGGGGCGT 59.780 57.895 0.00 0.00 45.10 5.68
1529 1561 3.060615 CTGGGCAGCTGAGGTTGC 61.061 66.667 20.43 0.23 46.58 4.17
1530 1562 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
1535 1567 2.033757 AGCTGAGGTTGCTGCCAG 59.966 61.111 0.00 0.00 39.56 4.85
1536 1568 3.745803 GCTGAGGTTGCTGCCAGC 61.746 66.667 10.45 10.45 44.00 4.85
1537 1569 3.060615 CTGAGGTTGCTGCCAGCC 61.061 66.667 15.29 0.00 41.51 4.85
1538 1570 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
1539 1571 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
1540 1572 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
1549 1581 4.760047 CCAGCCCACCCGAGTTCG 62.760 72.222 0.00 0.00 39.44 3.95
1550 1582 3.691342 CAGCCCACCCGAGTTCGA 61.691 66.667 2.59 0.00 43.02 3.71
1551 1583 3.382832 AGCCCACCCGAGTTCGAG 61.383 66.667 2.59 0.00 43.02 4.04
1552 1584 3.692406 GCCCACCCGAGTTCGAGT 61.692 66.667 2.59 0.00 43.02 4.18
1553 1585 2.572284 CCCACCCGAGTTCGAGTC 59.428 66.667 2.59 0.00 43.02 3.36
1554 1586 2.178521 CCACCCGAGTTCGAGTCG 59.821 66.667 6.09 6.09 43.02 4.18
1560 1592 2.160063 CGAGTTCGAGTCGGTCTCA 58.840 57.895 25.19 3.38 42.88 3.27
1561 1593 0.727970 CGAGTTCGAGTCGGTCTCAT 59.272 55.000 25.19 6.16 42.88 2.90
1562 1594 1.130749 CGAGTTCGAGTCGGTCTCATT 59.869 52.381 25.19 5.08 42.88 2.57
1563 1595 2.414293 CGAGTTCGAGTCGGTCTCATTT 60.414 50.000 25.19 3.85 42.88 2.32
1564 1596 3.576648 GAGTTCGAGTCGGTCTCATTTT 58.423 45.455 22.85 0.96 42.88 1.82
1565 1597 3.988517 GAGTTCGAGTCGGTCTCATTTTT 59.011 43.478 22.85 0.42 42.88 1.94
1607 1639 8.617290 TTTCAATAGAAACTAGTTGTTCCCTC 57.383 34.615 9.34 1.60 38.76 4.30
1608 1640 7.311092 TCAATAGAAACTAGTTGTTCCCTCA 57.689 36.000 9.34 0.00 38.03 3.86
1609 1641 7.741785 TCAATAGAAACTAGTTGTTCCCTCAA 58.258 34.615 9.34 0.00 38.03 3.02
1610 1642 8.215050 TCAATAGAAACTAGTTGTTCCCTCAAA 58.785 33.333 9.34 0.00 38.03 2.69
1611 1643 8.507249 CAATAGAAACTAGTTGTTCCCTCAAAG 58.493 37.037 9.34 0.00 38.03 2.77
1612 1644 6.248569 AGAAACTAGTTGTTCCCTCAAAGA 57.751 37.500 9.34 0.00 38.03 2.52
1613 1645 6.659824 AGAAACTAGTTGTTCCCTCAAAGAA 58.340 36.000 9.34 0.00 38.03 2.52
1614 1646 7.116736 AGAAACTAGTTGTTCCCTCAAAGAAA 58.883 34.615 9.34 0.00 38.03 2.52
1615 1647 7.614192 AGAAACTAGTTGTTCCCTCAAAGAAAA 59.386 33.333 9.34 0.00 38.03 2.29
1616 1648 7.712204 AACTAGTTGTTCCCTCAAAGAAAAA 57.288 32.000 7.48 0.00 32.63 1.94
1654 1686 7.397221 TGTCATGACAAGAGAAATAGATGGTT 58.603 34.615 26.02 0.00 38.56 3.67
1678 1710 8.826710 GTTACATTCTTTTCCTTTCTTTTTGGG 58.173 33.333 0.00 0.00 0.00 4.12
1679 1711 6.957631 ACATTCTTTTCCTTTCTTTTTGGGT 58.042 32.000 0.00 0.00 0.00 4.51
1680 1712 7.047891 ACATTCTTTTCCTTTCTTTTTGGGTC 58.952 34.615 0.00 0.00 0.00 4.46
1681 1713 6.613153 TTCTTTTCCTTTCTTTTTGGGTCA 57.387 33.333 0.00 0.00 0.00 4.02
1700 1785 4.443394 GGTCAATACAGTAATTAGCCGTCG 59.557 45.833 0.00 0.00 0.00 5.12
1718 1803 2.030457 GTCGCTGTTATTGGATTCGTGG 59.970 50.000 0.00 0.00 0.00 4.94
1728 1813 7.066525 TGTTATTGGATTCGTGGTCCTTTTATC 59.933 37.037 0.00 0.00 36.68 1.75
1751 1836 6.266323 TCTGTAGATTGACGCTCATTAAGAC 58.734 40.000 0.00 0.00 0.00 3.01
1753 1838 3.448686 AGATTGACGCTCATTAAGACGG 58.551 45.455 0.00 0.00 0.00 4.79
1755 1840 2.273370 TGACGCTCATTAAGACGGAC 57.727 50.000 0.00 0.00 0.00 4.79
1866 2889 4.780275 ACGACAAGGTTAGGAAGTACTC 57.220 45.455 0.00 0.00 0.00 2.59
1877 2939 1.136500 GGAAGTACTCCATCCGTGTCC 59.864 57.143 0.00 0.00 44.67 4.02
1884 2946 2.100631 CCATCCGTGTCCTTGCGAC 61.101 63.158 0.00 0.00 42.33 5.19
1885 2947 2.100631 CATCCGTGTCCTTGCGACC 61.101 63.158 0.00 0.00 41.18 4.79
1888 2950 1.597027 CCGTGTCCTTGCGACCTTT 60.597 57.895 0.00 0.00 41.18 3.11
1905 2967 6.664515 CGACCTTTTGCTTGTTATTAGTTGA 58.335 36.000 0.00 0.00 0.00 3.18
2079 3141 0.190069 TCTGGTGGGACCTGTACAGT 59.810 55.000 21.18 9.64 39.58 3.55
2085 3147 0.038526 GGGACCTGTACAGTGTCACG 60.039 60.000 29.56 15.96 33.30 4.35
2106 3168 0.178068 AGACGGTGAACACACTGCTT 59.822 50.000 8.78 0.00 42.61 3.91
2159 3221 0.524392 GACTCCGACACGAGCATCTG 60.524 60.000 0.00 0.00 32.79 2.90
2185 3247 1.180029 CATTACCCTGCAGCAGCTTT 58.820 50.000 17.81 5.42 42.74 3.51
2190 3252 3.437795 CTGCAGCAGCTTTCCGGG 61.438 66.667 10.14 0.00 42.74 5.73
2229 3291 2.288025 ACCGGCGATGGTGTAGGTT 61.288 57.895 9.30 0.00 41.85 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.031537 ACCCCTAAAAATCAAATCTAAATTCGT 57.968 29.630 0.00 0.00 0.00 3.85
1 2 9.869757 AACCCCTAAAAATCAAATCTAAATTCG 57.130 29.630 0.00 0.00 0.00 3.34
8 9 7.947890 TGACTACAACCCCTAAAAATCAAATCT 59.052 33.333 0.00 0.00 0.00 2.40
12 13 6.366340 TGTGACTACAACCCCTAAAAATCAA 58.634 36.000 0.00 0.00 32.88 2.57
107 108 8.005662 TGAAAATTTTGAAACATACTCGCATG 57.994 30.769 8.47 0.00 0.00 4.06
146 147 6.754193 TCAGGTATTTGAAAATTTGGTGTCC 58.246 36.000 0.00 0.00 0.00 4.02
156 157 9.787435 ACTACTTGTGTATCAGGTATTTGAAAA 57.213 29.630 0.00 0.00 37.83 2.29
218 219 3.074412 CCAACACAAGTACTAGGCTTGG 58.926 50.000 23.86 17.60 45.38 3.61
220 221 2.779506 GCCAACACAAGTACTAGGCTT 58.220 47.619 0.00 0.00 37.67 4.35
221 222 1.337823 CGCCAACACAAGTACTAGGCT 60.338 52.381 0.00 0.00 38.48 4.58
223 224 1.076332 GCGCCAACACAAGTACTAGG 58.924 55.000 0.00 0.00 0.00 3.02
224 225 1.076332 GGCGCCAACACAAGTACTAG 58.924 55.000 24.80 0.00 0.00 2.57
225 226 0.668096 CGGCGCCAACACAAGTACTA 60.668 55.000 28.98 0.00 0.00 1.82
226 227 1.959226 CGGCGCCAACACAAGTACT 60.959 57.895 28.98 0.00 0.00 2.73
227 228 2.554272 CGGCGCCAACACAAGTAC 59.446 61.111 28.98 0.00 0.00 2.73
268 274 1.547755 AGGTGGAGGAGGAGGAGGA 60.548 63.158 0.00 0.00 0.00 3.71
269 275 1.075600 GAGGTGGAGGAGGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
270 276 0.338120 AAGAGGTGGAGGAGGAGGAG 59.662 60.000 0.00 0.00 0.00 3.69
290 296 1.664321 TAACGAGGCGGAGGAAGAGC 61.664 60.000 0.00 0.00 0.00 4.09
359 365 1.840650 ACAGCTGGCAGTGGAGTCT 60.841 57.895 19.93 0.00 0.00 3.24
552 558 2.831742 ATCTTGGCGGCTGCATGG 60.832 61.111 21.31 8.16 45.35 3.66
588 594 0.898320 CGTTGAGGGTGGAGATGAGT 59.102 55.000 0.00 0.00 0.00 3.41
1224 1230 3.893521 TCAGATTGGTGATCATGCACAT 58.106 40.909 0.00 0.00 40.52 3.21
1284 1290 5.008911 CAGGTGTTCATGTTTCTGAATGTGA 59.991 40.000 0.00 0.00 37.47 3.58
1512 1544 3.060615 GCAACCTCAGCTGCCCAG 61.061 66.667 9.47 0.70 32.18 4.45
1513 1545 3.573229 AGCAACCTCAGCTGCCCA 61.573 61.111 9.47 0.00 41.61 5.36
1518 1550 2.033757 CTGGCAGCAACCTCAGCT 59.966 61.111 0.00 0.00 44.62 4.24
1519 1551 3.745803 GCTGGCAGCAACCTCAGC 61.746 66.667 33.33 4.00 44.34 4.26
1520 1552 3.060615 GGCTGGCAGCAACCTCAG 61.061 66.667 37.49 0.50 44.75 3.35
1521 1553 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
1522 1554 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
1523 1555 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
1532 1564 4.760047 CGAACTCGGGTGGGCTGG 62.760 72.222 0.00 0.00 35.37 4.85
1533 1565 3.649277 CTCGAACTCGGGTGGGCTG 62.649 68.421 0.00 0.00 40.29 4.85
1534 1566 3.382832 CTCGAACTCGGGTGGGCT 61.383 66.667 0.00 0.00 40.29 5.19
1588 1620 7.369551 TCTTTGAGGGAACAACTAGTTTCTA 57.630 36.000 5.07 0.00 41.51 2.10
1590 1622 6.937436 TTCTTTGAGGGAACAACTAGTTTC 57.063 37.500 5.07 1.81 41.51 2.78
1614 1646 9.573133 CTTGTCATGACAACTTAGTTTCTTTTT 57.427 29.630 32.36 0.00 45.42 1.94
1615 1647 8.956426 TCTTGTCATGACAACTTAGTTTCTTTT 58.044 29.630 32.36 0.00 45.42 2.27
1616 1648 8.506168 TCTTGTCATGACAACTTAGTTTCTTT 57.494 30.769 32.36 0.00 45.42 2.52
1617 1649 7.987458 TCTCTTGTCATGACAACTTAGTTTCTT 59.013 33.333 32.36 0.00 45.42 2.52
1618 1650 7.500992 TCTCTTGTCATGACAACTTAGTTTCT 58.499 34.615 32.36 0.00 45.42 2.52
1619 1651 7.715265 TCTCTTGTCATGACAACTTAGTTTC 57.285 36.000 32.36 0.97 45.42 2.78
1620 1652 8.506168 TTTCTCTTGTCATGACAACTTAGTTT 57.494 30.769 32.36 0.00 45.42 2.66
1621 1653 8.682936 ATTTCTCTTGTCATGACAACTTAGTT 57.317 30.769 32.36 16.07 45.42 2.24
1622 1654 9.429359 CTATTTCTCTTGTCATGACAACTTAGT 57.571 33.333 32.36 19.86 45.42 2.24
1623 1655 9.645059 TCTATTTCTCTTGTCATGACAACTTAG 57.355 33.333 32.36 26.86 45.42 2.18
1625 1657 8.944029 CATCTATTTCTCTTGTCATGACAACTT 58.056 33.333 32.36 17.20 45.42 2.66
1654 1686 8.084985 ACCCAAAAAGAAAGGAAAAGAATGTA 57.915 30.769 0.00 0.00 0.00 2.29
1666 1698 9.981114 AATTACTGTATTGACCCAAAAAGAAAG 57.019 29.630 0.00 0.00 0.00 2.62
1678 1710 4.085210 GCGACGGCTAATTACTGTATTGAC 60.085 45.833 0.00 0.00 35.83 3.18
1679 1711 4.046462 GCGACGGCTAATTACTGTATTGA 58.954 43.478 0.00 0.00 35.83 2.57
1680 1712 4.370620 GCGACGGCTAATTACTGTATTG 57.629 45.455 0.00 0.00 35.83 1.90
1700 1785 2.354821 GGACCACGAATCCAATAACAGC 59.645 50.000 0.00 0.00 36.15 4.40
1703 1788 5.638596 AAAAGGACCACGAATCCAATAAC 57.361 39.130 0.00 0.00 38.86 1.89
1708 1793 4.019681 ACAGATAAAAGGACCACGAATCCA 60.020 41.667 0.00 0.00 38.86 3.41
1718 1803 6.043411 AGCGTCAATCTACAGATAAAAGGAC 58.957 40.000 0.00 0.00 33.73 3.85
1728 1813 5.172232 CGTCTTAATGAGCGTCAATCTACAG 59.828 44.000 0.00 0.00 0.00 2.74
1751 1836 2.094258 CCGATGAACATGACTTTGTCCG 59.906 50.000 0.00 0.00 0.00 4.79
1753 1838 3.667960 GCACCGATGAACATGACTTTGTC 60.668 47.826 0.00 0.00 0.00 3.18
1755 1840 2.226200 TGCACCGATGAACATGACTTTG 59.774 45.455 0.00 0.00 0.00 2.77
1866 2889 2.100631 GTCGCAAGGACACGGATGG 61.101 63.158 0.00 0.00 45.36 3.51
1877 2939 2.208326 AACAAGCAAAAGGTCGCAAG 57.792 45.000 0.00 0.00 0.00 4.01
1943 3005 1.719063 AAACCCTGCAGGCTCCAAGA 61.719 55.000 28.39 0.00 40.58 3.02
1998 3060 2.819595 CCGATGGTGCCACCGAAG 60.820 66.667 9.78 2.32 42.58 3.79
2059 3121 1.203313 ACTGTACAGGTCCCACCAGAT 60.203 52.381 26.12 0.00 41.95 2.90
2079 3141 1.361271 GTTCACCGTCTCCGTGACA 59.639 57.895 6.61 0.00 45.60 3.58
2085 3147 1.222115 GCAGTGTGTTCACCGTCTCC 61.222 60.000 0.37 0.00 44.83 3.71
2091 3153 1.009675 CGCAAGCAGTGTGTTCACC 60.010 57.895 0.37 0.00 44.83 4.02
2146 3208 3.558411 GCGGCAGATGCTCGTGTC 61.558 66.667 14.22 0.00 41.70 3.67
2155 3217 2.515901 GGTAATGGGGCGGCAGAT 59.484 61.111 12.47 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.