Multiple sequence alignment - TraesCS2B01G300000

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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 TraesCS2B01G300000 chr2B 100.000 2543 0 0 1 2543 421259908 421257366 0.000000 4697.0
1 TraesCS2B01G300000 chr2D 91.595 2558 73 29 30 2543 354391754 354389295 0.000000 3402.0
2 TraesCS2B01G300000 chr2D 100.000 30 0 0 3 32 354391804 354391775 0.000353 56.5
3 TraesCS2B01G300000 chr2A 89.842 2589 85 63 30 2543 473644938 473642453 0.000000 3160.0
4 TraesCS2B01G300000 chr2A 100.000 30 0 0 3 32 473644988 473644959 0.000353 56.5
5 TraesCS2B01G300000 chr4D 100.000 29 0 0 1135 1163 474441508 474441536 0.001000 54.7
6 TraesCS2B01G300000 chr5B 100.000 28 0 0 1138 1165 567876755 567876782 0.005000 52.8


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 TraesCS2B01G300000 chr2B 421257366 421259908 2542 True 4697.00 4697 100.0000 1 2543 1 chr2B.!!$R1 2542
1 TraesCS2B01G300000 chr2D 354389295 354391804 2509 True 1729.25 3402 95.7975 3 2543 2 chr2D.!!$R1 2540
2 TraesCS2B01G300000 chr2A 473642453 473644988 2535 True 1608.25 3160 94.9210 3 2543 2 chr2A.!!$R1 2540

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
440 464 1.132201 TCCCTTCCCTTCCTTCCTTGA 60.132 52.381 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
1665 1771 0.534203 TCGTCTCAAACAGGGGCAAC 60.534 55.0 0.0 0.0 0.0 4.17 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
141 165 1.810030 AACGAAGAAGCCCGATCGC 60.810 57.895 10.32 0.00 38.80 4.58
142 166 2.962253 CGAAGAAGCCCGATCGCC 60.962 66.667 10.32 2.47 0.00 5.54
430 454 1.839894 GGCATCGATCCCTTCCCTT 59.160 57.895 0.00 0.00 0.00 3.95
439 463 1.372501 TCCCTTCCCTTCCTTCCTTG 58.627 55.000 0.00 0.00 0.00 3.61
440 464 1.132201 TCCCTTCCCTTCCTTCCTTGA 60.132 52.381 0.00 0.00 0.00 3.02
441 465 1.283321 CCCTTCCCTTCCTTCCTTGAG 59.717 57.143 0.00 0.00 0.00 3.02
442 466 1.283321 CCTTCCCTTCCTTCCTTGAGG 59.717 57.143 0.00 0.00 38.20 3.86
483 508 4.338710 CCCCGCGGGTGAAGGAAA 62.339 66.667 40.52 0.00 38.25 3.13
484 509 2.281900 CCCGCGGGTGAAGGAAAA 60.282 61.111 36.64 0.00 0.00 2.29
485 510 1.899534 CCCGCGGGTGAAGGAAAAA 60.900 57.895 36.64 0.00 0.00 1.94
525 550 2.746142 CGTGGTACCCCTACTCGTATCA 60.746 54.545 10.07 0.00 0.00 2.15
660 691 1.544246 GTGGTGGTATTTCCTTGTGGC 59.456 52.381 0.00 0.00 37.07 5.01
819 867 1.302752 AGGGGCGTTCCGGTAAAAC 60.303 57.895 0.00 0.00 36.01 2.43
934 987 5.595257 AACACCTAACTAAGCTAGGCTAC 57.405 43.478 0.00 0.00 38.25 3.58
935 988 4.869451 ACACCTAACTAAGCTAGGCTACT 58.131 43.478 0.00 0.00 38.25 2.57
988 1049 2.297597 GAGATATACCTCGCTGCTTGGT 59.702 50.000 15.58 15.58 37.83 3.67
1005 1066 2.682594 TGGTCTCGATCTTCCATGGAT 58.317 47.619 17.06 0.00 0.00 3.41
1209 1279 1.886585 GAACGAGAGCAGGAGAGCA 59.113 57.895 0.00 0.00 36.85 4.26
1551 1633 4.065789 GCTTCCATCCTTAATTAGGTCGG 58.934 47.826 0.00 0.00 45.03 4.79
1552 1634 3.764237 TCCATCCTTAATTAGGTCGGC 57.236 47.619 0.00 0.00 45.03 5.54
1553 1635 2.370849 TCCATCCTTAATTAGGTCGGCC 59.629 50.000 0.00 0.00 45.03 6.13
1554 1636 2.413837 CATCCTTAATTAGGTCGGCCG 58.586 52.381 22.12 22.12 45.03 6.13
1555 1637 0.754472 TCCTTAATTAGGTCGGCCGG 59.246 55.000 27.83 6.80 45.03 6.13
1556 1638 0.883370 CCTTAATTAGGTCGGCCGGC 60.883 60.000 27.83 26.31 39.39 6.13
1557 1639 0.883370 CTTAATTAGGTCGGCCGGCC 60.883 60.000 41.56 41.56 40.91 6.13
1558 1640 1.624479 TTAATTAGGTCGGCCGGCCA 61.624 55.000 46.94 30.97 43.56 5.36
1559 1641 1.624479 TAATTAGGTCGGCCGGCCAA 61.624 55.000 46.94 36.26 43.56 4.52
1560 1642 3.692370 ATTAGGTCGGCCGGCCAAC 62.692 63.158 46.94 36.48 43.56 3.77
1615 1697 1.144716 CCTGCTCGCCATTGCTAGA 59.855 57.895 0.00 0.00 32.21 2.43
1671 1777 3.660111 GTGCCAGTCACGTTGCCC 61.660 66.667 0.00 0.00 35.76 5.36
1797 1909 1.113788 ATGTGGGCGCATGCTTAATT 58.886 45.000 17.13 0.00 42.25 1.40
1955 2072 1.405821 GACGGATCCCTCTGTACTGTG 59.594 57.143 6.06 0.00 41.19 3.66
1979 2101 0.242825 TAGTGCGGTGACAGCAGTAC 59.757 55.000 18.87 5.08 45.40 2.73
2035 2160 3.010472 TGGATGATTTCAGCTCCTTTGGA 59.990 43.478 0.00 0.00 31.98 3.53
2228 2360 4.652881 AGATGATGCCATACACTGAGAGAA 59.347 41.667 0.00 0.00 32.09 2.87
2312 2444 9.383519 CCGAGCTTTTGACACCAATATATATAT 57.616 33.333 0.00 0.00 31.46 0.86
2515 2651 2.272447 TGACCACGACGGATGAGCA 61.272 57.895 0.00 0.00 38.63 4.26
2522 2658 1.522092 GACGGATGAGCACCATGGA 59.478 57.895 21.47 0.00 35.17 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.944376 AAAAGATCAACTAGCTACAAGACAATA 57.056 29.630 0.00 0.00 0.00 1.90
1 2 8.854614 AAAAGATCAACTAGCTACAAGACAAT 57.145 30.769 0.00 0.00 0.00 2.71
46 70 5.179368 CGTATTGGGATCGTTAATCAATGCT 59.821 40.000 0.00 0.00 35.96 3.79
141 165 3.181500 GCAAAAACTATTCGCCTACAGGG 60.181 47.826 0.00 0.00 35.18 4.45
142 166 3.438781 TGCAAAAACTATTCGCCTACAGG 59.561 43.478 0.00 0.00 38.53 4.00
250 274 3.864686 CTTTCATGGGGCGCGTCG 61.865 66.667 8.43 0.00 0.00 5.12
430 454 1.362224 CCTCAACCCTCAAGGAAGGA 58.638 55.000 0.00 0.00 38.87 3.36
439 463 1.152830 TTTGGTGGCCTCAACCCTC 59.847 57.895 3.32 0.00 0.00 4.30
440 464 1.152546 GTTTGGTGGCCTCAACCCT 60.153 57.895 3.32 0.00 0.00 4.34
441 465 2.207229 GGTTTGGTGGCCTCAACCC 61.207 63.158 13.56 11.51 33.95 4.11
442 466 1.045911 TTGGTTTGGTGGCCTCAACC 61.046 55.000 16.42 16.42 37.76 3.77
443 467 0.827368 TTTGGTTTGGTGGCCTCAAC 59.173 50.000 3.32 1.58 0.00 3.18
482 507 1.826487 AAGACGCCACCCGCTTTTT 60.826 52.632 0.00 0.00 41.76 1.94
483 508 2.203294 AAGACGCCACCCGCTTTT 60.203 55.556 0.00 0.00 41.76 2.27
484 509 2.386064 TACAAGACGCCACCCGCTTT 62.386 55.000 0.00 0.00 41.76 3.51
485 510 2.874664 TACAAGACGCCACCCGCTT 61.875 57.895 0.00 0.00 41.76 4.68
486 511 3.307906 TACAAGACGCCACCCGCT 61.308 61.111 0.00 0.00 41.76 5.52
487 512 3.116531 GTACAAGACGCCACCCGC 61.117 66.667 0.00 0.00 41.76 6.13
488 513 2.807895 CGTACAAGACGCCACCCG 60.808 66.667 0.00 0.00 46.27 5.28
525 550 3.118454 GCACTGCATGCGTACGGT 61.118 61.111 18.39 1.73 46.55 4.83
561 587 5.691754 GTGGACGCAATTCAGATTTTTCTTT 59.308 36.000 0.00 0.00 0.00 2.52
660 691 4.332637 GCAGCTGCGTTGTGTGGG 62.333 66.667 25.23 0.00 0.00 4.61
819 867 2.018866 GCATCTAGCTAGCGTGCGG 61.019 63.158 25.14 10.37 41.15 5.69
828 876 1.745141 CGAAAGCAAGGGCATCTAGCT 60.745 52.381 0.00 0.00 44.61 3.32
829 877 0.659957 CGAAAGCAAGGGCATCTAGC 59.340 55.000 0.00 0.00 44.61 3.42
934 987 2.288395 CCCTTGTTGTGCTTTGGCTTAG 60.288 50.000 0.00 0.00 39.59 2.18
935 988 1.686052 CCCTTGTTGTGCTTTGGCTTA 59.314 47.619 0.00 0.00 39.59 3.09
988 1049 2.298446 GCTCATCCATGGAAGATCGAGA 59.702 50.000 20.67 7.36 0.00 4.04
1005 1066 2.285668 CCCCTCTCCCCTTGCTCA 60.286 66.667 0.00 0.00 0.00 4.26
1255 1325 3.738246 CACCTGCTGCTGCTGCTG 61.738 66.667 27.67 25.97 40.48 4.41
1256 1326 3.949980 TCACCTGCTGCTGCTGCT 61.950 61.111 27.67 9.19 40.48 4.24
1554 1636 4.980805 TCGTCGGTGCAGTTGGCC 62.981 66.667 0.00 0.00 43.89 5.36
1555 1637 3.712881 GTCGTCGGTGCAGTTGGC 61.713 66.667 0.00 0.00 45.13 4.52
1556 1638 1.667830 ATGTCGTCGGTGCAGTTGG 60.668 57.895 0.00 0.00 0.00 3.77
1557 1639 1.492873 CATGTCGTCGGTGCAGTTG 59.507 57.895 0.00 0.00 0.00 3.16
1558 1640 1.667830 CCATGTCGTCGGTGCAGTT 60.668 57.895 0.00 0.00 0.00 3.16
1559 1641 2.048222 CCATGTCGTCGGTGCAGT 60.048 61.111 0.00 0.00 0.00 4.40
1560 1642 2.048222 ACCATGTCGTCGGTGCAG 60.048 61.111 0.00 0.00 33.05 4.41
1561 1643 2.048597 GACCATGTCGTCGGTGCA 60.049 61.111 0.00 0.00 34.99 4.57
1570 1652 1.400371 CGATCTCCGATCGACCATGTC 60.400 57.143 18.66 5.96 43.59 3.06
1615 1697 6.872020 GCTACGAGAGATAGAGAGAGTTACAT 59.128 42.308 0.00 0.00 0.00 2.29
1665 1771 0.534203 TCGTCTCAAACAGGGGCAAC 60.534 55.000 0.00 0.00 0.00 4.17
1668 1774 2.396590 TTATCGTCTCAAACAGGGGC 57.603 50.000 0.00 0.00 0.00 5.80
1669 1775 4.137116 TGATTATCGTCTCAAACAGGGG 57.863 45.455 0.00 0.00 0.00 4.79
1670 1776 5.464722 CAGATGATTATCGTCTCAAACAGGG 59.535 44.000 13.49 0.00 40.56 4.45
1671 1777 5.464722 CCAGATGATTATCGTCTCAAACAGG 59.535 44.000 13.49 7.69 40.56 4.00
1781 1893 1.141449 GCAATTAAGCATGCGCCCA 59.859 52.632 13.01 0.00 39.83 5.36
1837 1954 5.828299 TTAGTTTGGTTTCTCAACTGGTG 57.172 39.130 0.00 0.00 32.90 4.17
1839 1956 6.805713 ACAATTAGTTTGGTTTCTCAACTGG 58.194 36.000 0.00 0.00 39.80 4.00
1955 2072 1.153745 CTGTCACCGCACTAGCTCC 60.154 63.158 0.00 0.00 39.10 4.70
2035 2160 2.015588 GCAGTCCACTAGCATGCATGT 61.016 52.381 26.79 14.90 36.88 3.21
2061 2192 5.045651 TGCCTGATCTTCCTTGTTCATCTAA 60.046 40.000 0.00 0.00 0.00 2.10
2228 2360 1.830477 ACCCAACAAACACAACTGCAT 59.170 42.857 0.00 0.00 0.00 3.96
2312 2444 4.039124 AGACATCATGTGTGTGTGTGTCTA 59.961 41.667 0.00 0.00 42.36 2.59
2313 2445 3.133691 GACATCATGTGTGTGTGTGTCT 58.866 45.455 0.00 0.00 42.36 3.41
2314 2446 3.133691 AGACATCATGTGTGTGTGTGTC 58.866 45.455 0.00 0.00 42.36 3.67
2315 2447 3.198409 AGACATCATGTGTGTGTGTGT 57.802 42.857 0.00 0.00 42.36 3.72
2316 2448 5.868801 TGTATAGACATCATGTGTGTGTGTG 59.131 40.000 0.00 0.00 42.36 3.82
2317 2449 6.036577 TGTATAGACATCATGTGTGTGTGT 57.963 37.500 0.00 7.97 42.36 3.72
2318 2450 6.536224 ACATGTATAGACATCATGTGTGTGTG 59.464 38.462 0.00 0.00 44.82 3.82
2319 2451 6.643388 ACATGTATAGACATCATGTGTGTGT 58.357 36.000 0.00 9.27 44.82 3.72
2344 2476 9.579768 GCAAACCTGTATCTGATCTGTATATAG 57.420 37.037 0.00 2.54 0.00 1.31
2515 2651 8.112183 ACTTTTATTTCTCTCTGAATCCATGGT 58.888 33.333 12.58 0.00 34.24 3.55


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

AutoCloner maintained by Alex Coulton.