Multiple sequence alignment - TraesCS1A01G240800

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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 TraesCS1A01G240800 chr1A 100.000 2438 0 0 1 2438 428211521 428209084 0.000000e+00 4503.0
1 TraesCS1A01G240800 chr1A 87.097 1488 99 44 398 1833 428236654 428235208 0.000000e+00 1598.0
2 TraesCS1A01G240800 chr1A 84.590 597 78 6 884 1475 300927728 300927141 4.520000e-162 580.0
3 TraesCS1A01G240800 chr1A 82.703 370 32 15 554 919 428237307 428236966 1.420000e-77 300.0
4 TraesCS1A01G240800 chr1A 82.222 225 30 6 167 388 428236957 428236740 4.140000e-43 185.0
5 TraesCS1A01G240800 chr1A 89.744 78 5 2 713 787 300927897 300927820 2.000000e-16 97.1
6 TraesCS1A01G240800 chr1D 92.515 1376 73 19 464 1829 331198276 331196921 0.000000e+00 1943.0
7 TraesCS1A01G240800 chr1D 88.394 1482 82 41 400 1830 331283829 331282387 0.000000e+00 1701.0
8 TraesCS1A01G240800 chr1D 88.843 484 38 10 1 472 331199152 331198673 4.520000e-162 580.0
9 TraesCS1A01G240800 chr1D 84.653 202 27 1 2112 2313 235092414 235092611 5.320000e-47 198.0
10 TraesCS1A01G240800 chr1D 78.027 223 28 12 167 383 331284109 331283902 1.180000e-23 121.0
11 TraesCS1A01G240800 chr1B 92.623 1220 74 11 625 1838 445671301 445670092 0.000000e+00 1740.0
12 TraesCS1A01G240800 chr1B 94.667 75 3 1 554 627 445671629 445671555 5.510000e-22 115.0
13 TraesCS1A01G240800 chr5A 89.414 614 32 5 1852 2438 477815692 477816299 0.000000e+00 743.0
14 TraesCS1A01G240800 chr3B 81.798 923 131 25 636 1546 59045882 59046779 0.000000e+00 739.0
15 TraesCS1A01G240800 chr2A 89.379 612 31 6 1855 2438 766140737 766141342 0.000000e+00 739.0
16 TraesCS1A01G240800 chr7A 88.799 616 34 7 1851 2438 518690717 518691325 0.000000e+00 723.0
17 TraesCS1A01G240800 chr3D 81.382 854 121 26 633 1475 36179834 36180660 0.000000e+00 662.0
18 TraesCS1A01G240800 chr3D 83.358 673 88 14 884 1546 36238251 36238909 3.470000e-168 601.0
19 TraesCS1A01G240800 chr4D 87.215 571 39 8 1896 2438 379693816 379694380 9.580000e-174 619.0
20 TraesCS1A01G240800 chr3A 82.975 605 85 11 885 1478 46841281 46841878 4.620000e-147 531.0
21 TraesCS1A01G240800 chr6B 81.461 178 14 7 2248 2407 159949065 159949241 7.080000e-26 128.0
22 TraesCS1A01G240800 chr7B 87.500 48 6 0 312 359 533846748 533846795 3.390000e-04 56.5


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 TraesCS1A01G240800 chr1A 428209084 428211521 2437 True 4503.000000 4503 100.000000 1 2438 1 chr1A.!!$R1 2437
1 TraesCS1A01G240800 chr1A 428235208 428237307 2099 True 694.333333 1598 84.007333 167 1833 3 chr1A.!!$R3 1666
2 TraesCS1A01G240800 chr1A 300927141 300927897 756 True 338.550000 580 87.167000 713 1475 2 chr1A.!!$R2 762
3 TraesCS1A01G240800 chr1D 331196921 331199152 2231 True 1261.500000 1943 90.679000 1 1829 2 chr1D.!!$R1 1828
4 TraesCS1A01G240800 chr1D 331282387 331284109 1722 True 911.000000 1701 83.210500 167 1830 2 chr1D.!!$R2 1663
5 TraesCS1A01G240800 chr1B 445670092 445671629 1537 True 927.500000 1740 93.645000 554 1838 2 chr1B.!!$R1 1284
6 TraesCS1A01G240800 chr5A 477815692 477816299 607 False 743.000000 743 89.414000 1852 2438 1 chr5A.!!$F1 586
7 TraesCS1A01G240800 chr3B 59045882 59046779 897 False 739.000000 739 81.798000 636 1546 1 chr3B.!!$F1 910
8 TraesCS1A01G240800 chr2A 766140737 766141342 605 False 739.000000 739 89.379000 1855 2438 1 chr2A.!!$F1 583
9 TraesCS1A01G240800 chr7A 518690717 518691325 608 False 723.000000 723 88.799000 1851 2438 1 chr7A.!!$F1 587
10 TraesCS1A01G240800 chr3D 36179834 36180660 826 False 662.000000 662 81.382000 633 1475 1 chr3D.!!$F1 842
11 TraesCS1A01G240800 chr3D 36238251 36238909 658 False 601.000000 601 83.358000 884 1546 1 chr3D.!!$F2 662
12 TraesCS1A01G240800 chr4D 379693816 379694380 564 False 619.000000 619 87.215000 1896 2438 1 chr4D.!!$F1 542
13 TraesCS1A01G240800 chr3A 46841281 46841878 597 False 531.000000 531 82.975000 885 1478 1 chr3A.!!$F1 593

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
74 75 2.095053 GCTCGCATTGTTCCTCTCTTTC 59.905 50.0 0.0 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2844 0.389948 ATGTCCTTGGTCGAACGCTC 60.39 55.0 0.0 0.0 0.0 5.03 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
74 75 2.095053 GCTCGCATTGTTCCTCTCTTTC 59.905 50.000 0.00 0.0 0.00 2.62
288 476 4.019174 CCATAGGCATGTGTTTTCTCCTT 58.981 43.478 0.00 0.0 0.00 3.36
289 477 4.463891 CCATAGGCATGTGTTTTCTCCTTT 59.536 41.667 0.00 0.0 0.00 3.11
341 530 2.288213 GCTGCAGTTTTGAACTAACCCC 60.288 50.000 16.64 0.0 40.46 4.95
353 542 5.139001 TGAACTAACCCCGGTTTAAAACAT 58.861 37.500 4.08 0.0 39.31 2.71
369 558 7.865875 TTAAAACATCGACACATTTTGGATG 57.134 32.000 0.00 0.0 40.15 3.51
370 559 4.439305 AACATCGACACATTTTGGATGG 57.561 40.909 0.00 0.0 38.97 3.51
383 572 6.104691 ACATTTTGGATGGGAGGGAGTATATT 59.895 38.462 0.00 0.0 0.00 1.28
538 1215 2.407090 TCAACTCTGACACGCATTGAG 58.593 47.619 0.00 0.0 0.00 3.02
579 1272 4.096682 ACTGATGCTCGTTCTAGGAGTAAC 59.903 45.833 0.00 0.0 33.01 2.50
664 1615 3.573772 CTCAACTCCGCCACGAGCA 62.574 63.158 0.00 0.0 44.04 4.26
806 1764 5.319453 CCATAATATCAAGCACACCCATCT 58.681 41.667 0.00 0.0 0.00 2.90
833 1791 3.915437 ATCGTGTTTGCCGAAAGAAAT 57.085 38.095 0.00 0.0 37.93 2.17
839 1797 4.150451 GTGTTTGCCGAAAGAAATGGAATG 59.850 41.667 0.00 0.0 0.00 2.67
977 1965 3.909086 AAGGCAGCCGAAGCAGGAC 62.909 63.158 5.55 0.0 43.56 3.85
978 1966 4.704833 GGCAGCCGAAGCAGGACA 62.705 66.667 0.00 0.0 43.56 4.02
979 1967 3.123620 GCAGCCGAAGCAGGACAG 61.124 66.667 0.00 0.0 43.56 3.51
980 1968 2.435586 CAGCCGAAGCAGGACAGG 60.436 66.667 0.00 0.0 43.56 4.00
981 1969 2.604686 AGCCGAAGCAGGACAGGA 60.605 61.111 0.00 0.0 43.56 3.86
998 1990 4.611367 ACAGGAGCTTACTTAGGCTTAGA 58.389 43.478 7.64 0.0 38.86 2.10
1004 1996 6.408206 GGAGCTTACTTAGGCTTAGAAATGGA 60.408 42.308 7.64 0.0 38.86 3.41
1436 2428 2.092323 CGTCACATGGTCAGACTCCTA 58.908 52.381 0.00 0.0 0.00 2.94
1572 2567 2.027751 GTGCGTATCCTCTCGGCC 59.972 66.667 0.00 0.0 0.00 6.13
1592 2587 2.530177 CGATGCTGCCATATACGTAGG 58.470 52.381 0.08 0.0 0.00 3.18
1656 2651 7.894708 AGAACTGTGATCATATCTCCTACATG 58.105 38.462 0.00 0.0 0.00 3.21
1717 2716 4.222588 TCAATTGGGTTATGGAAAAGCTGG 59.777 41.667 5.42 0.0 0.00 4.85
1732 2731 0.321653 GCTGGGTGGAGTGAATCGTT 60.322 55.000 0.00 0.0 0.00 3.85
1740 2739 6.887545 TGGGTGGAGTGAATCGTTTTTAATAT 59.112 34.615 0.00 0.0 0.00 1.28
1775 2774 7.663905 TGGTTATATAAAGCTTCACACAGTTGT 59.336 33.333 0.00 0.0 35.84 3.32
1816 2819 6.647067 AGTTAATGAGAAGTTTTCAGACTCCG 59.353 38.462 2.27 0.0 0.00 4.63
1839 2842 1.475280 TGCTGGAAAGCATCATCAAGC 59.525 47.619 0.00 0.0 40.23 4.01
1840 2843 1.533338 GCTGGAAAGCATCATCAAGCG 60.533 52.381 0.00 0.0 35.48 4.68
1841 2844 1.065102 CTGGAAAGCATCATCAAGCGG 59.935 52.381 0.00 0.0 35.48 5.52
1842 2845 1.339920 TGGAAAGCATCATCAAGCGGA 60.340 47.619 0.00 0.0 35.48 5.54
1843 2846 1.332997 GGAAAGCATCATCAAGCGGAG 59.667 52.381 0.00 0.0 35.48 4.63
1944 2947 3.382803 CTCCGGCCTCCTCTGCTTG 62.383 68.421 0.00 0.0 0.00 4.01
1977 2980 2.366972 CGGGATCCCCTCCACCTT 60.367 66.667 25.73 0.0 46.98 3.50
1982 2985 1.626631 GGATCCCCTCCACCTTCTCTT 60.627 57.143 0.00 0.0 44.26 2.85
2354 3383 2.233654 CGACAGTGCATAGCTCGGC 61.234 63.158 0.00 0.0 0.00 5.54
2355 3384 1.884926 GACAGTGCATAGCTCGGCC 60.885 63.158 7.03 0.0 0.00 6.13
2398 3430 2.743928 CTGCCGCTTGGGTGTCTC 60.744 66.667 0.00 0.0 38.44 3.36
2399 3431 4.329545 TGCCGCTTGGGTGTCTCC 62.330 66.667 0.00 0.0 38.44 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.839474 CCGCTTCGATTCACTTTTCAC 58.161 47.619 0.00 0.00 0.00 3.18
74 75 8.304596 TGTTCTACTACTTCTTGTAACATGAGG 58.695 37.037 0.00 0.00 0.00 3.86
265 453 2.689983 GGAGAAAACACATGCCTATGGG 59.310 50.000 0.00 0.00 43.55 4.00
318 507 3.550842 GGGTTAGTTCAAAACTGCAGCAG 60.551 47.826 21.54 21.54 42.84 4.24
321 510 2.031157 CGGGGTTAGTTCAAAACTGCAG 60.031 50.000 13.48 13.48 42.84 4.41
322 511 1.950909 CGGGGTTAGTTCAAAACTGCA 59.049 47.619 2.65 0.00 42.84 4.41
341 530 6.345408 CCAAAATGTGTCGATGTTTTAAACCG 60.345 38.462 5.32 3.02 0.00 4.44
353 542 2.617788 CCTCCCATCCAAAATGTGTCGA 60.618 50.000 0.00 0.00 0.00 4.20
433 698 2.451273 TGGTTCCCAGGGGTCAAAATTA 59.549 45.455 5.33 0.00 36.47 1.40
436 701 0.637195 TTGGTTCCCAGGGGTCAAAA 59.363 50.000 5.33 0.00 33.81 2.44
493 1170 9.341899 GATTGCGATTCTAACTTTGTGTAAAAT 57.658 29.630 0.00 0.00 0.00 1.82
579 1272 6.952743 AGCTAATTGATTACGCATCTGAAAG 58.047 36.000 0.00 0.00 32.34 2.62
744 1697 1.391157 TTGGGGACACTTGTGCTTGC 61.391 55.000 0.63 0.00 42.67 4.01
806 1764 0.390603 CGGCAAACACGATACCCTCA 60.391 55.000 0.00 0.00 0.00 3.86
833 1791 3.055458 TCACTGCTTATTCGGTCATTCCA 60.055 43.478 0.00 0.00 35.57 3.53
839 1797 0.645868 GCGTCACTGCTTATTCGGTC 59.354 55.000 0.00 0.00 0.00 4.79
871 1830 5.803020 ATCGCTGTCTCTTATTTTGTTCC 57.197 39.130 0.00 0.00 0.00 3.62
977 1965 5.599999 TTCTAAGCCTAAGTAAGCTCCTG 57.400 43.478 0.00 0.00 38.74 3.86
978 1966 6.408662 CCATTTCTAAGCCTAAGTAAGCTCCT 60.409 42.308 0.00 0.00 38.74 3.69
979 1967 5.760743 CCATTTCTAAGCCTAAGTAAGCTCC 59.239 44.000 0.00 0.00 38.74 4.70
980 1968 6.583562 TCCATTTCTAAGCCTAAGTAAGCTC 58.416 40.000 0.00 0.00 38.74 4.09
981 1969 6.561519 TCCATTTCTAAGCCTAAGTAAGCT 57.438 37.500 0.00 0.00 42.40 3.74
998 1990 0.462759 GAGGCTAGCGTGCTCCATTT 60.463 55.000 15.88 0.00 0.00 2.32
1004 1996 4.504916 CTGCGAGGCTAGCGTGCT 62.505 66.667 15.88 2.71 37.44 4.40
1093 2085 1.359459 CCAAAGACCTTAGACGCCGC 61.359 60.000 0.00 0.00 0.00 6.53
1410 2402 2.347490 GACCATGTGACGGCCACT 59.653 61.111 2.24 0.00 45.86 4.00
1436 2428 1.812507 GGATCGGCGCGGTTAACTT 60.813 57.895 15.06 0.00 0.00 2.66
1572 2567 2.530177 CCTACGTATATGGCAGCATCG 58.470 52.381 0.00 0.00 0.00 3.84
1592 2587 7.085052 AGGAAGAAAACATCGTTTAATAGGC 57.915 36.000 0.00 0.00 0.00 3.93
1594 2589 9.760660 CTTGAGGAAGAAAACATCGTTTAATAG 57.239 33.333 0.00 0.00 0.00 1.73
1595 2590 9.496873 TCTTGAGGAAGAAAACATCGTTTAATA 57.503 29.630 0.00 0.00 35.14 0.98
1597 2592 7.795482 TCTTGAGGAAGAAAACATCGTTTAA 57.205 32.000 0.00 0.00 35.14 1.52
1656 2651 4.153117 GCATGCATACATTGTAGGAGTAGC 59.847 45.833 14.21 6.33 32.87 3.58
1775 2774 6.237154 TCATTAACTGAACCACATCACATCA 58.763 36.000 0.00 0.00 0.00 3.07
1830 2833 1.148157 CGAACGCTCCGCTTGATGAT 61.148 55.000 0.00 0.00 0.00 2.45
1831 2834 1.805539 CGAACGCTCCGCTTGATGA 60.806 57.895 0.00 0.00 0.00 2.92
1832 2835 1.805539 TCGAACGCTCCGCTTGATG 60.806 57.895 0.00 0.00 0.00 3.07
1833 2836 1.805945 GTCGAACGCTCCGCTTGAT 60.806 57.895 0.00 0.00 0.00 2.57
1834 2837 2.430244 GTCGAACGCTCCGCTTGA 60.430 61.111 0.00 0.00 0.00 3.02
1835 2838 3.479269 GGTCGAACGCTCCGCTTG 61.479 66.667 0.00 0.00 0.00 4.01
1836 2839 3.509137 TTGGTCGAACGCTCCGCTT 62.509 57.895 0.00 0.00 0.00 4.68
1838 2841 3.479269 CTTGGTCGAACGCTCCGC 61.479 66.667 0.00 0.00 0.00 5.54
1839 2842 2.809601 CCTTGGTCGAACGCTCCG 60.810 66.667 0.00 0.00 0.00 4.63
1840 2843 1.737008 GTCCTTGGTCGAACGCTCC 60.737 63.158 0.00 0.00 0.00 4.70
1841 2844 0.389948 ATGTCCTTGGTCGAACGCTC 60.390 55.000 0.00 0.00 0.00 5.03
1842 2845 0.670546 CATGTCCTTGGTCGAACGCT 60.671 55.000 0.00 0.00 0.00 5.07
1843 2846 0.669318 TCATGTCCTTGGTCGAACGC 60.669 55.000 0.00 0.00 0.00 4.84
1844 2847 1.067846 TCTCATGTCCTTGGTCGAACG 60.068 52.381 0.00 0.00 0.00 3.95
1845 2848 2.611518 CTCTCATGTCCTTGGTCGAAC 58.388 52.381 0.00 0.00 0.00 3.95
1846 2849 1.550524 CCTCTCATGTCCTTGGTCGAA 59.449 52.381 0.00 0.00 0.00 3.71
1847 2850 1.186200 CCTCTCATGTCCTTGGTCGA 58.814 55.000 0.00 0.00 0.00 4.20
1848 2851 0.460987 GCCTCTCATGTCCTTGGTCG 60.461 60.000 0.00 0.00 0.00 4.79
1849 2852 0.908198 AGCCTCTCATGTCCTTGGTC 59.092 55.000 0.00 0.00 0.00 4.02
1937 2940 0.459078 CCGATCTCAGCTCAAGCAGA 59.541 55.000 4.59 0.60 45.16 4.26
1944 2947 1.583986 CCGGATCCGATCTCAGCTC 59.416 63.158 35.42 0.00 42.83 4.09
1977 2980 0.898320 CTTCGCAGGGGAGAAAGAGA 59.102 55.000 0.00 0.00 32.28 3.10
1982 2985 1.296715 GAAGCTTCGCAGGGGAGAA 59.703 57.895 11.40 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.