Multiple sequence alignment - TraesCS4B01G265000

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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 TraesCS4B01G265000 chr4B 100.000 2558 0 0 1 2558 535751449 535748892 0.000000e+00 4724
1 TraesCS4B01G265000 chr4B 95.053 1597 74 4 1 1593 643943416 643945011 0.000000e+00 2507
2 TraesCS4B01G265000 chr2B 96.048 1594 57 4 1 1591 43642187 43643777 0.000000e+00 2590
3 TraesCS4B01G265000 chr2B 89.352 432 40 4 1663 2090 24524209 24523780 2.900000e-149 538
4 TraesCS4B01G265000 chr2B 89.327 431 40 4 1664 2090 749082346 749082774 1.040000e-148 536
5 TraesCS4B01G265000 chr7B 96.048 1594 55 6 1 1590 629017121 629015532 0.000000e+00 2588
6 TraesCS4B01G265000 chr7B 92.678 478 27 7 2087 2558 208140394 208139919 0.000000e+00 682
7 TraesCS4B01G265000 chr7B 92.827 474 27 7 2087 2558 133520553 133521021 0.000000e+00 680
8 TraesCS4B01G265000 chr2D 94.448 1585 80 6 1 1582 387938923 387940502 0.000000e+00 2433
9 TraesCS4B01G265000 chr7A 94.099 1593 91 2 1 1590 97852712 97851120 0.000000e+00 2418
10 TraesCS4B01G265000 chr1A 93.155 1607 104 5 1 1604 252736565 252734962 0.000000e+00 2353
11 TraesCS4B01G265000 chr1A 88.844 744 52 19 1843 2558 585906936 585906196 0.000000e+00 885
12 TraesCS4B01G265000 chr4A 93.216 1592 101 5 1 1590 468155544 468153958 0.000000e+00 2335
13 TraesCS4B01G265000 chr4A 89.327 431 40 4 1664 2090 702146474 702146902 1.040000e-148 536
14 TraesCS4B01G265000 chr2A 92.409 1594 110 5 1 1591 654881033 654882618 0.000000e+00 2263
15 TraesCS4B01G265000 chr1D 91.771 1592 127 3 1 1589 113842100 113840510 0.000000e+00 2211
16 TraesCS4B01G265000 chr3B 94.961 893 21 11 1688 2558 7300327 7299437 0.000000e+00 1378
17 TraesCS4B01G265000 chr3B 88.435 441 38 8 1665 2097 667719763 667720198 1.050000e-143 520
18 TraesCS4B01G265000 chr5B 93.723 924 28 12 1663 2558 467161707 467162628 0.000000e+00 1358
19 TraesCS4B01G265000 chr5B 89.352 432 39 5 1664 2090 257331198 257330769 1.040000e-148 536
20 TraesCS4B01G265000 chr5A 89.437 871 67 12 1696 2558 141567880 141567027 0.000000e+00 1075
21 TraesCS4B01G265000 chr3A 87.961 922 80 19 1663 2557 238823915 238822998 0.000000e+00 1059
22 TraesCS4B01G265000 chr6D 86.947 904 71 22 1698 2558 46906945 46907844 0.000000e+00 972
23 TraesCS4B01G265000 chr6B 92.827 474 28 6 2087 2558 577925310 577924841 0.000000e+00 682
24 TraesCS4B01G265000 chr4D 89.401 434 37 6 1664 2092 31654177 31653748 2.900000e-149 538
25 TraesCS4B01G265000 chr1B 89.327 431 40 4 1664 2090 60529326 60529754 1.040000e-148 536


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 TraesCS4B01G265000 chr4B 535748892 535751449 2557 True 4724 4724 100.000 1 2558 1 chr4B.!!$R1 2557
1 TraesCS4B01G265000 chr4B 643943416 643945011 1595 False 2507 2507 95.053 1 1593 1 chr4B.!!$F1 1592
2 TraesCS4B01G265000 chr2B 43642187 43643777 1590 False 2590 2590 96.048 1 1591 1 chr2B.!!$F1 1590
3 TraesCS4B01G265000 chr7B 629015532 629017121 1589 True 2588 2588 96.048 1 1590 1 chr7B.!!$R2 1589
4 TraesCS4B01G265000 chr2D 387938923 387940502 1579 False 2433 2433 94.448 1 1582 1 chr2D.!!$F1 1581
5 TraesCS4B01G265000 chr7A 97851120 97852712 1592 True 2418 2418 94.099 1 1590 1 chr7A.!!$R1 1589
6 TraesCS4B01G265000 chr1A 252734962 252736565 1603 True 2353 2353 93.155 1 1604 1 chr1A.!!$R1 1603
7 TraesCS4B01G265000 chr1A 585906196 585906936 740 True 885 885 88.844 1843 2558 1 chr1A.!!$R2 715
8 TraesCS4B01G265000 chr4A 468153958 468155544 1586 True 2335 2335 93.216 1 1590 1 chr4A.!!$R1 1589
9 TraesCS4B01G265000 chr2A 654881033 654882618 1585 False 2263 2263 92.409 1 1591 1 chr2A.!!$F1 1590
10 TraesCS4B01G265000 chr1D 113840510 113842100 1590 True 2211 2211 91.771 1 1589 1 chr1D.!!$R1 1588
11 TraesCS4B01G265000 chr3B 7299437 7300327 890 True 1378 1378 94.961 1688 2558 1 chr3B.!!$R1 870
12 TraesCS4B01G265000 chr5B 467161707 467162628 921 False 1358 1358 93.723 1663 2558 1 chr5B.!!$F1 895
13 TraesCS4B01G265000 chr5A 141567027 141567880 853 True 1075 1075 89.437 1696 2558 1 chr5A.!!$R1 862
14 TraesCS4B01G265000 chr3A 238822998 238823915 917 True 1059 1059 87.961 1663 2557 1 chr3A.!!$R1 894
15 TraesCS4B01G265000 chr6D 46906945 46907844 899 False 972 972 86.947 1698 2558 1 chr6D.!!$F1 860

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
996 1003 0.035458 CTCAGGAAGCGTCCCAAACT 59.965 55.0 15.64 0.0 46.3 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1843 0.60864 AGTGGTTAGGCGACTGGAAG 59.391 55.0 0.0 0.0 43.88 3.46 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
24 25 5.491982 AGGAGGAATGTGTTTCTGTGATAC 58.508 41.667 0.00 0.00 34.56 2.24
80 81 4.220724 AGCATGGCATCTTGTGGATAATT 58.779 39.130 0.00 0.00 32.64 1.40
121 123 7.475840 CAACAATCCTAAGAGCCAAGTATTTC 58.524 38.462 0.00 0.00 0.00 2.17
406 411 3.589951 ACTCTATGGCCAATTGATGCT 57.410 42.857 10.96 0.00 0.00 3.79
649 654 4.630894 TTTTATTTCGCGGATGCTTCAT 57.369 36.364 6.13 0.00 39.65 2.57
730 736 4.114997 GCATGTTTGGACGGGCCG 62.115 66.667 27.06 27.06 40.66 6.13
732 738 4.733542 ATGTTTGGACGGGCCGGG 62.734 66.667 31.78 3.37 40.66 5.73
858 865 2.026449 AGAGGCAGTCCTTGAATTCCTG 60.026 50.000 2.27 3.76 44.46 3.86
907 914 3.430471 TGGGCTCCCAGAATGCAT 58.570 55.556 2.93 0.00 41.89 3.96
923 930 7.211573 CAGAATGCATGGGAATTTATTGCTAA 58.788 34.615 0.00 0.00 34.47 3.09
996 1003 0.035458 CTCAGGAAGCGTCCCAAACT 59.965 55.000 15.64 0.00 46.30 2.66
1349 1356 2.738846 CAATGAAGAACGGAGGACAGTG 59.261 50.000 0.00 0.00 0.00 3.66
1613 1622 7.722949 AAAAATTCCTAAGATGGCTCATTGA 57.277 32.000 0.00 0.00 0.00 2.57
1614 1623 7.909485 AAAATTCCTAAGATGGCTCATTGAT 57.091 32.000 0.00 0.00 0.00 2.57
1615 1624 9.425248 AAAAATTCCTAAGATGGCTCATTGATA 57.575 29.630 0.00 0.00 0.00 2.15
1616 1625 7.992754 AATTCCTAAGATGGCTCATTGATAC 57.007 36.000 0.00 0.00 0.00 2.24
1617 1626 6.499106 TTCCTAAGATGGCTCATTGATACA 57.501 37.500 0.00 0.00 0.00 2.29
1618 1627 6.499106 TCCTAAGATGGCTCATTGATACAA 57.501 37.500 0.00 0.00 0.00 2.41
1619 1628 6.291377 TCCTAAGATGGCTCATTGATACAAC 58.709 40.000 0.00 0.00 0.00 3.32
1620 1629 6.057533 CCTAAGATGGCTCATTGATACAACA 58.942 40.000 0.00 0.00 0.00 3.33
1621 1630 6.204301 CCTAAGATGGCTCATTGATACAACAG 59.796 42.308 0.00 0.00 0.00 3.16
1622 1631 5.363562 AGATGGCTCATTGATACAACAGA 57.636 39.130 0.00 0.00 0.00 3.41
1623 1632 5.748402 AGATGGCTCATTGATACAACAGAA 58.252 37.500 0.00 0.00 0.00 3.02
1624 1633 5.821470 AGATGGCTCATTGATACAACAGAAG 59.179 40.000 0.00 0.00 0.00 2.85
1625 1634 4.910195 TGGCTCATTGATACAACAGAAGT 58.090 39.130 0.00 0.00 0.00 3.01
1626 1635 5.316167 TGGCTCATTGATACAACAGAAGTT 58.684 37.500 0.00 0.00 38.88 2.66
1627 1636 6.472016 TGGCTCATTGATACAACAGAAGTTA 58.528 36.000 0.00 0.00 35.85 2.24
1628 1637 6.939730 TGGCTCATTGATACAACAGAAGTTAA 59.060 34.615 0.00 0.00 35.85 2.01
1629 1638 7.446931 TGGCTCATTGATACAACAGAAGTTAAA 59.553 33.333 0.00 0.00 35.85 1.52
1630 1639 8.296713 GGCTCATTGATACAACAGAAGTTAAAA 58.703 33.333 0.00 0.00 35.85 1.52
1631 1640 9.118236 GCTCATTGATACAACAGAAGTTAAAAC 57.882 33.333 0.00 0.00 35.85 2.43
1820 1843 2.099831 CGCGACGTCCAGTACCTC 59.900 66.667 10.58 0.00 0.00 3.85
1868 1891 6.978080 GCAACCAATCGTACATGGATATTTTT 59.022 34.615 14.38 0.00 39.12 1.94
1877 1900 6.948228 CGTACATGGATATTTTTATCGCGAAG 59.052 38.462 15.24 0.00 0.00 3.79
1902 1925 7.763071 AGGAGTTAAGAATAATTAAAGTCGCGT 59.237 33.333 5.77 0.00 0.00 6.01
1925 1948 4.717233 ATTTATTGCGCACAGATTTGGA 57.283 36.364 11.12 0.00 0.00 3.53
1933 1956 2.467305 CGCACAGATTTGGAAAAACGTG 59.533 45.455 0.00 0.00 0.00 4.49
1934 1957 3.443976 GCACAGATTTGGAAAAACGTGT 58.556 40.909 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.071961 AGCAGTGTGTATCACAGAAACA 57.928 40.909 2.71 0.00 45.43 2.83
24 25 2.297701 ACACCAGGTTAAAGCAGTGTG 58.702 47.619 0.00 0.00 35.19 3.82
80 81 6.604396 AGGATTGTTGCACATAATGATTCAGA 59.396 34.615 0.00 0.00 0.00 3.27
121 123 2.418368 TCATCAAATCACCTTCGGGG 57.582 50.000 0.00 0.00 40.03 5.73
406 411 2.607526 CGAGATCGCTAGGACTCTACGA 60.608 54.545 0.00 0.00 35.36 3.43
425 430 5.221244 CCGACATATTATGCATAGGGATCGA 60.221 44.000 21.24 0.00 0.00 3.59
636 641 1.091771 AGTTCCATGAAGCATCCGCG 61.092 55.000 0.00 0.00 45.49 6.46
649 654 2.244695 ACACGACATGGTAGAGTTCCA 58.755 47.619 0.00 0.00 39.41 3.53
730 736 7.664318 AGAAATAATATATGTTTCGTGTCCCCC 59.336 37.037 13.79 0.00 37.04 5.40
732 738 9.052759 ACAGAAATAATATATGTTTCGTGTCCC 57.947 33.333 13.79 0.00 37.04 4.46
771 777 1.202114 CCCAAATGTTCCCACACATCG 59.798 52.381 0.00 0.00 36.30 3.84
858 865 3.413846 TCATGATCAGGCATAAGGAGC 57.586 47.619 1.57 0.00 0.00 4.70
899 906 5.881923 AGCAATAAATTCCCATGCATTCT 57.118 34.783 0.00 0.00 39.42 2.40
907 914 4.711355 AGCAGCTTTAGCAATAAATTCCCA 59.289 37.500 4.33 0.00 45.16 4.37
913 920 6.773976 ATACCAAGCAGCTTTAGCAATAAA 57.226 33.333 4.38 0.00 45.16 1.40
923 930 3.701040 CCACCATAAATACCAAGCAGCTT 59.299 43.478 0.21 0.21 0.00 3.74
996 1003 4.562425 GCCCGAATCCCCATCGCA 62.562 66.667 0.00 0.00 38.93 5.10
1164 1171 8.391106 CCTACTATGAAGTTTCCTTTTTCATCG 58.609 37.037 2.55 0.47 40.78 3.84
1593 1602 7.083062 TGTATCAATGAGCCATCTTAGGAAT 57.917 36.000 0.00 0.00 0.00 3.01
1594 1603 6.499106 TGTATCAATGAGCCATCTTAGGAA 57.501 37.500 0.00 0.00 0.00 3.36
1595 1604 6.126796 TGTTGTATCAATGAGCCATCTTAGGA 60.127 38.462 0.00 0.00 0.00 2.94
1596 1605 6.057533 TGTTGTATCAATGAGCCATCTTAGG 58.942 40.000 0.00 0.00 0.00 2.69
1598 1607 6.888105 TCTGTTGTATCAATGAGCCATCTTA 58.112 36.000 0.00 0.00 0.00 2.10
1599 1608 5.748402 TCTGTTGTATCAATGAGCCATCTT 58.252 37.500 0.00 0.00 0.00 2.40
1601 1610 5.587844 ACTTCTGTTGTATCAATGAGCCATC 59.412 40.000 0.00 0.00 0.00 3.51
1602 1611 5.503927 ACTTCTGTTGTATCAATGAGCCAT 58.496 37.500 0.00 0.00 0.00 4.40
1603 1612 4.910195 ACTTCTGTTGTATCAATGAGCCA 58.090 39.130 0.00 0.00 0.00 4.75
1604 1613 5.886960 AACTTCTGTTGTATCAATGAGCC 57.113 39.130 0.00 0.00 34.71 4.70
1605 1614 9.118236 GTTTTAACTTCTGTTGTATCAATGAGC 57.882 33.333 0.00 0.00 37.59 4.26
1642 1651 9.015367 GCTCCCCTTCTTAAATATAATTCTTCC 57.985 37.037 0.00 0.00 0.00 3.46
1643 1652 9.800572 AGCTCCCCTTCTTAAATATAATTCTTC 57.199 33.333 0.00 0.00 0.00 2.87
1644 1653 9.800572 GAGCTCCCCTTCTTAAATATAATTCTT 57.199 33.333 0.87 0.00 0.00 2.52
1645 1654 8.387039 GGAGCTCCCCTTCTTAAATATAATTCT 58.613 37.037 23.19 0.00 0.00 2.40
1646 1655 8.387039 AGGAGCTCCCCTTCTTAAATATAATTC 58.613 37.037 29.54 0.00 36.42 2.17
1647 1656 8.294311 AGGAGCTCCCCTTCTTAAATATAATT 57.706 34.615 29.54 0.40 36.42 1.40
1648 1657 7.896806 AGGAGCTCCCCTTCTTAAATATAAT 57.103 36.000 29.54 0.79 36.42 1.28
1649 1658 8.657712 GTTAGGAGCTCCCCTTCTTAAATATAA 58.342 37.037 29.54 12.98 37.74 0.98
1650 1659 7.237055 GGTTAGGAGCTCCCCTTCTTAAATATA 59.763 40.741 29.54 7.28 37.74 0.86
1651 1660 6.044520 GGTTAGGAGCTCCCCTTCTTAAATAT 59.955 42.308 29.54 8.34 37.74 1.28
1652 1661 5.368816 GGTTAGGAGCTCCCCTTCTTAAATA 59.631 44.000 29.54 8.03 37.74 1.40
1653 1662 4.166337 GGTTAGGAGCTCCCCTTCTTAAAT 59.834 45.833 29.54 9.11 37.74 1.40
1654 1663 3.522343 GGTTAGGAGCTCCCCTTCTTAAA 59.478 47.826 29.54 8.04 37.74 1.52
1655 1664 3.113043 GGTTAGGAGCTCCCCTTCTTAA 58.887 50.000 29.54 16.56 37.74 1.85
1656 1665 2.760581 GGTTAGGAGCTCCCCTTCTTA 58.239 52.381 29.54 11.12 37.74 2.10
1657 1666 1.585895 GGTTAGGAGCTCCCCTTCTT 58.414 55.000 29.54 12.24 37.74 2.52
1658 1667 0.688087 CGGTTAGGAGCTCCCCTTCT 60.688 60.000 29.54 13.02 37.74 2.85
1659 1668 1.687297 CCGGTTAGGAGCTCCCCTTC 61.687 65.000 29.54 16.35 45.00 3.46
1660 1669 1.689582 CCGGTTAGGAGCTCCCCTT 60.690 63.158 29.54 13.83 45.00 3.95
1661 1670 2.041819 CCGGTTAGGAGCTCCCCT 60.042 66.667 29.54 14.62 45.00 4.79
1820 1843 0.608640 AGTGGTTAGGCGACTGGAAG 59.391 55.000 0.00 0.00 43.88 3.46
1868 1891 9.970395 TTAATTATTCTTAACTCCTTCGCGATA 57.030 29.630 10.88 0.00 0.00 2.92
1877 1900 7.903062 ACGCGACTTTAATTATTCTTAACTCC 58.097 34.615 15.93 0.00 0.00 3.85
1902 1925 6.201226 TCCAAATCTGTGCGCAATAAATAA 57.799 33.333 14.00 0.00 0.00 1.40
2142 2251 7.118101 ACAATTTTGTGATATGCGCTGAAAATT 59.882 29.630 9.73 11.08 40.49 1.82


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

AutoCloner maintained by Alex Coulton.