Multiple sequence alignment - TraesCS6A01G156200

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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 TraesCS6A01G156200 chr6A 100.000 2666 0 0 1 2666 145135454 145132789 0.000000e+00 4924
1 TraesCS6A01G156200 chr6D 91.310 2359 106 42 1 2330 116954155 116951867 0.000000e+00 3129
2 TraesCS6A01G156200 chr6D 92.705 329 13 4 2344 2666 116951882 116951559 5.200000e-127 464
3 TraesCS6A01G156200 chr6B 91.239 2340 103 44 1 2283 207156707 207154413 0.000000e+00 3092
4 TraesCS6A01G156200 chr6B 92.812 320 12 4 2352 2666 207154387 207154074 1.130000e-123 453
5 TraesCS6A01G156200 chr7B 78.521 284 37 19 1098 1370 646210283 646210013 5.900000e-37 165
6 TraesCS6A01G156200 chr7A 81.221 213 26 10 1098 1300 671483724 671483516 2.750000e-35 159
7 TraesCS6A01G156200 chr7D 77.817 284 39 19 1098 1370 579961746 579961476 1.280000e-33 154


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 TraesCS6A01G156200 chr6A 145132789 145135454 2665 True 4924.0 4924 100.0000 1 2666 1 chr6A.!!$R1 2665
1 TraesCS6A01G156200 chr6D 116951559 116954155 2596 True 1796.5 3129 92.0075 1 2666 2 chr6D.!!$R1 2665
2 TraesCS6A01G156200 chr6B 207154074 207156707 2633 True 1772.5 3092 92.0255 1 2666 2 chr6B.!!$R1 2665

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
42 43 0.036388 ATCCGATCAAAGGTGCACGT 60.036 50.0 11.45 8.83 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2100 0.526524 CGAGACAAGCTAAGGCGAGG 60.527 60.0 0.0 0.0 44.37 4.63 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
36 37 1.584724 AGTGGGATCCGATCAAAGGT 58.415 50.000 5.45 0.00 0.00 3.50
40 41 1.017387 GGATCCGATCAAAGGTGCAC 58.983 55.000 8.80 8.80 0.00 4.57
41 42 0.652592 GATCCGATCAAAGGTGCACG 59.347 55.000 11.45 0.00 0.00 5.34
42 43 0.036388 ATCCGATCAAAGGTGCACGT 60.036 50.000 11.45 8.83 0.00 4.49
43 44 0.948623 TCCGATCAAAGGTGCACGTG 60.949 55.000 13.63 12.28 0.00 4.49
102 103 0.544357 ACCCACAGTGGTGCTAGCTA 60.544 55.000 18.82 0.00 43.88 3.32
168 169 2.724977 GCTTTGGCCTTTAGTTGGTC 57.275 50.000 3.32 0.00 0.00 4.02
187 188 2.510238 AAGCTTCGCGGCTAGCTG 60.510 61.111 24.54 19.74 46.53 4.24
235 241 0.939577 CGTGCCACGATATTCCCTCG 60.940 60.000 12.85 0.00 46.05 4.63
252 258 1.200252 CTCGTCTCTTCTTCCTTCGCA 59.800 52.381 0.00 0.00 0.00 5.10
257 263 1.741770 CTTCTTCCTTCGCACCCCG 60.742 63.158 0.00 0.00 38.61 5.73
258 264 3.248446 TTCTTCCTTCGCACCCCGG 62.248 63.158 0.00 0.00 37.59 5.73
321 332 0.515564 GTTGTGTAAAGCGCGGACAT 59.484 50.000 8.83 0.00 0.00 3.06
498 509 3.848301 TTGCAGTGCACCGGCTGAT 62.848 57.895 25.67 0.00 38.71 2.90
512 523 3.350909 CTGATCGGCGGTCGTGGAA 62.351 63.158 16.28 0.00 40.32 3.53
514 525 4.446413 ATCGGCGGTCGTGGAACC 62.446 66.667 7.21 0.00 40.32 3.62
594 617 2.256461 GACGCCACTCCGTAACGT 59.744 61.111 0.00 0.00 42.24 3.99
625 648 0.377203 GGCGACCCGATTCAAACATC 59.623 55.000 0.00 0.00 0.00 3.06
656 679 6.001449 TCCTTTTAGAGAGAGAGAGAGAGG 57.999 45.833 0.00 0.00 0.00 3.69
657 680 5.729229 TCCTTTTAGAGAGAGAGAGAGAGGA 59.271 44.000 0.00 0.00 0.00 3.71
658 681 6.058183 CCTTTTAGAGAGAGAGAGAGAGGAG 58.942 48.000 0.00 0.00 0.00 3.69
659 682 5.630415 TTTAGAGAGAGAGAGAGAGGAGG 57.370 47.826 0.00 0.00 0.00 4.30
661 684 1.421646 GAGAGAGAGAGAGAGGAGGGG 59.578 61.905 0.00 0.00 0.00 4.79
662 685 1.010793 AGAGAGAGAGAGAGGAGGGGA 59.989 57.143 0.00 0.00 0.00 4.81
845 872 3.966543 GACCCCACACCCACCCTG 61.967 72.222 0.00 0.00 0.00 4.45
846 873 4.525028 ACCCCACACCCACCCTGA 62.525 66.667 0.00 0.00 0.00 3.86
933 960 1.199558 CGCGGGTCTCCTATAAGTAGC 59.800 57.143 0.00 0.00 0.00 3.58
967 994 1.026584 GGCTCGAGAACTCTACTCCC 58.973 60.000 18.75 0.00 0.00 4.30
970 997 1.213430 CTCGAGAACTCTACTCCCCCT 59.787 57.143 6.58 0.00 0.00 4.79
1514 1544 2.174349 GCAGCAGCAACAGTACGC 59.826 61.111 0.00 0.00 41.58 4.42
1581 1626 4.710167 TCGTCGGCGGAGGACAGA 62.710 66.667 10.62 0.00 38.89 3.41
1668 1713 2.158957 TGGCTACAACTTCGGATGATCC 60.159 50.000 0.08 0.08 0.00 3.36
1670 1715 2.807108 GCTACAACTTCGGATGATCCCC 60.807 54.545 5.78 0.00 31.13 4.81
1704 1749 3.307480 CCCCTATACCCCGTTGATCAATC 60.307 52.174 12.12 4.81 0.00 2.67
1762 1824 0.167689 CTTTGCTTTCTCCGCTCTGC 59.832 55.000 0.00 0.00 0.00 4.26
1774 1836 2.147133 GCTCTGCGAAGACGACGAC 61.147 63.158 0.00 0.00 42.66 4.34
1775 1837 1.859564 CTCTGCGAAGACGACGACG 60.860 63.158 5.58 5.58 42.66 5.12
1785 1847 3.305623 CGACGACGTTGTTGCTGT 58.694 55.556 10.42 0.00 34.56 4.40
1786 1848 1.634225 CGACGACGTTGTTGCTGTT 59.366 52.632 10.42 0.00 34.56 3.16
1787 1849 0.381428 CGACGACGTTGTTGCTGTTC 60.381 55.000 10.42 0.00 34.56 3.18
1788 1850 0.042448 GACGACGTTGTTGCTGTTCC 60.042 55.000 10.42 0.00 0.00 3.62
1789 1851 0.741574 ACGACGTTGTTGCTGTTCCA 60.742 50.000 1.48 0.00 0.00 3.53
1829 1891 4.874977 GCCGTAGAGAGGGCGTGC 62.875 72.222 0.00 0.00 46.11 5.34
1844 1912 3.277133 TGCGATGAAGCAAAGGCC 58.723 55.556 0.00 0.00 45.06 5.19
1857 1925 2.098770 GCAAAGGCCAGCTGATTAAGAG 59.901 50.000 17.39 0.00 0.00 2.85
1956 2024 5.813080 ACGGAAGGCATGTAAATAGTTTC 57.187 39.130 0.00 0.00 0.00 2.78
1968 2036 3.831715 AATAGTTTCAGCTTTCGGTGC 57.168 42.857 0.00 0.00 38.50 5.01
2030 2098 3.603965 TCTCCTCCTCCTAGATTGGAC 57.396 52.381 0.00 0.00 31.94 4.02
2031 2099 2.158593 TCTCCTCCTCCTAGATTGGACG 60.159 54.545 0.00 0.00 31.94 4.79
2032 2100 0.676736 CCTCCTCCTAGATTGGACGC 59.323 60.000 0.00 0.00 31.94 5.19
2033 2101 0.676736 CTCCTCCTAGATTGGACGCC 59.323 60.000 0.00 0.00 31.94 5.68
2034 2102 0.261991 TCCTCCTAGATTGGACGCCT 59.738 55.000 0.00 0.00 31.94 5.52
2186 2265 8.635765 AATAAATGTGTCTCTTTCTTTAGCCA 57.364 30.769 0.00 0.00 0.00 4.75
2187 2266 5.948992 AATGTGTCTCTTTCTTTAGCCAC 57.051 39.130 0.00 0.00 0.00 5.01
2191 2270 1.087501 CTCTTTCTTTAGCCACGCCC 58.912 55.000 0.00 0.00 0.00 6.13
2261 2340 9.219603 TCCTTAATTTGTTCTCTGACTAACATG 57.780 33.333 0.00 0.00 35.64 3.21
2307 2386 7.334921 TGTTCCTTACCGTGATTAATTAACTGG 59.665 37.037 0.00 3.07 0.00 4.00
2313 2392 5.642063 ACCGTGATTAATTAACTGGTGACTG 59.358 40.000 0.00 0.00 0.00 3.51
2321 2400 1.901591 AACTGGTGACTGCATTCTGG 58.098 50.000 5.59 0.00 0.00 3.86
2322 2401 1.059098 ACTGGTGACTGCATTCTGGA 58.941 50.000 5.59 0.00 0.00 3.86
2324 2403 2.158623 ACTGGTGACTGCATTCTGGAAA 60.159 45.455 5.59 0.00 0.00 3.13
2325 2404 2.886523 CTGGTGACTGCATTCTGGAAAA 59.113 45.455 5.59 0.00 0.00 2.29
2326 2405 3.295093 TGGTGACTGCATTCTGGAAAAA 58.705 40.909 5.59 0.00 0.00 1.94
2474 2555 3.371063 ATGACGACCCGCTGACGT 61.371 61.111 0.00 0.00 42.84 4.34
2475 2556 2.042259 ATGACGACCCGCTGACGTA 61.042 57.895 0.00 0.00 40.29 3.57
2476 2557 2.202401 GACGACCCGCTGACGTAC 60.202 66.667 0.00 0.00 40.29 3.67
2477 2558 3.989566 GACGACCCGCTGACGTACG 62.990 68.421 15.01 15.01 40.29 3.67
2658 2744 2.033299 GGATCGGTAAATGCATGTGTGG 59.967 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.952675 CTGTGGGTGTGTGTGCGC 61.953 66.667 0.00 0.00 0.00 6.09
74 75 2.513666 ACTGTGGGTGTGTGTGCG 60.514 61.111 0.00 0.00 0.00 5.34
75 76 2.480610 CCACTGTGGGTGTGTGTGC 61.481 63.158 19.23 0.00 43.94 4.57
76 77 1.077787 ACCACTGTGGGTGTGTGTG 60.078 57.895 29.05 2.75 43.37 3.82
77 78 3.410541 ACCACTGTGGGTGTGTGT 58.589 55.556 29.05 4.90 43.37 3.72
105 106 2.724708 GACGTGCGCTGAAGCTGAG 61.725 63.158 9.73 0.00 39.32 3.35
182 183 3.755628 GGTCGACCGGTGCAGCTA 61.756 66.667 20.85 0.00 0.00 3.32
235 241 1.673329 GGGTGCGAAGGAAGAAGAGAC 60.673 57.143 0.00 0.00 0.00 3.36
258 264 4.947147 TGTGTGAACCGGCCTGGC 62.947 66.667 11.05 11.05 43.94 4.85
259 265 2.978010 GTGTGTGAACCGGCCTGG 60.978 66.667 0.00 11.48 46.41 4.45
260 266 2.702751 TACGTGTGTGAACCGGCCTG 62.703 60.000 0.00 0.00 0.00 4.85
261 267 2.030490 TTACGTGTGTGAACCGGCCT 62.030 55.000 0.00 0.00 0.00 5.19
321 332 3.822192 CACGCTCCGTCGATGGGA 61.822 66.667 23.40 15.08 38.32 4.37
435 446 4.308458 CACGTCCACTTGGGCCGA 62.308 66.667 13.10 0.00 36.14 5.54
479 490 3.594775 CAGCCGGTGCACTGCAAA 61.595 61.111 26.08 0.00 41.47 3.68
510 521 2.167861 CGCGAGCAAGCTAGGGTTC 61.168 63.158 0.00 0.00 34.40 3.62
656 679 0.568697 ATTCCTACCTCCCTCCCCTC 59.431 60.000 0.00 0.00 0.00 4.30
657 680 0.568697 GATTCCTACCTCCCTCCCCT 59.431 60.000 0.00 0.00 0.00 4.79
658 681 0.832559 CGATTCCTACCTCCCTCCCC 60.833 65.000 0.00 0.00 0.00 4.81
659 682 0.832559 CCGATTCCTACCTCCCTCCC 60.833 65.000 0.00 0.00 0.00 4.30
661 684 0.470268 AGCCGATTCCTACCTCCCTC 60.470 60.000 0.00 0.00 0.00 4.30
662 685 0.470268 GAGCCGATTCCTACCTCCCT 60.470 60.000 0.00 0.00 0.00 4.20
795 822 4.389576 GCTGACCCGCGCAGTTTG 62.390 66.667 8.75 2.51 35.81 2.93
840 867 2.036731 TGATCGGACGGTCAGGGT 59.963 61.111 10.76 0.00 0.00 4.34
842 869 2.494918 GGTGATCGGACGGTCAGG 59.505 66.667 8.06 1.25 0.00 3.86
844 871 3.445687 CGGGTGATCGGACGGTCA 61.446 66.667 10.76 3.17 0.00 4.02
845 872 3.407046 GACGGGTGATCGGACGGTC 62.407 68.421 0.00 0.00 0.00 4.79
846 873 3.446570 GACGGGTGATCGGACGGT 61.447 66.667 7.49 1.83 0.00 4.83
967 994 1.517832 CTGACCGCAGTAGGAAGGG 59.482 63.158 0.00 0.00 37.37 3.95
1668 1713 2.471084 TAGGGGTGGAGTGGTGAGGG 62.471 65.000 0.00 0.00 0.00 4.30
1670 1715 2.040178 GTATAGGGGTGGAGTGGTGAG 58.960 57.143 0.00 0.00 0.00 3.51
1704 1749 5.112686 GGCTCTCTGATTAAGTGTACCTTG 58.887 45.833 6.81 0.00 34.46 3.61
1774 1836 1.134175 ACCTTTGGAACAGCAACAACG 59.866 47.619 0.00 0.00 42.39 4.10
1775 1837 2.959507 ACCTTTGGAACAGCAACAAC 57.040 45.000 0.00 0.00 42.39 3.32
1776 1838 5.606348 ATTAACCTTTGGAACAGCAACAA 57.394 34.783 0.00 0.00 42.39 2.83
1777 1839 5.606348 AATTAACCTTTGGAACAGCAACA 57.394 34.783 0.00 0.00 42.39 3.33
1778 1840 6.918892 AAAATTAACCTTTGGAACAGCAAC 57.081 33.333 0.00 0.00 42.39 4.17
1779 1841 6.183360 GCAAAAATTAACCTTTGGAACAGCAA 60.183 34.615 11.23 0.00 42.39 3.91
1781 1843 5.527214 AGCAAAAATTAACCTTTGGAACAGC 59.473 36.000 11.23 0.00 42.39 4.40
1782 1844 6.018016 CCAGCAAAAATTAACCTTTGGAACAG 60.018 38.462 11.23 0.00 42.39 3.16
1783 1845 5.819901 CCAGCAAAAATTAACCTTTGGAACA 59.180 36.000 11.23 0.00 33.91 3.18
1785 1847 4.819088 GCCAGCAAAAATTAACCTTTGGAA 59.181 37.500 11.23 0.00 33.91 3.53
1786 1848 4.384940 GCCAGCAAAAATTAACCTTTGGA 58.615 39.130 11.23 0.00 33.91 3.53
1787 1849 3.501828 GGCCAGCAAAAATTAACCTTTGG 59.498 43.478 0.00 0.00 33.91 3.28
1788 1850 4.388485 AGGCCAGCAAAAATTAACCTTTG 58.612 39.130 5.01 6.70 35.95 2.77
1789 1851 4.705110 AGGCCAGCAAAAATTAACCTTT 57.295 36.364 5.01 0.00 0.00 3.11
1814 1876 2.835705 ATCGCACGCCCTCTCTACG 61.836 63.158 0.00 0.00 0.00 3.51
1825 1887 1.512734 GCCTTTGCTTCATCGCACG 60.513 57.895 0.00 0.00 40.09 5.34
1826 1888 1.153958 GGCCTTTGCTTCATCGCAC 60.154 57.895 0.00 0.00 40.09 5.34
1829 1891 1.138247 GCTGGCCTTTGCTTCATCG 59.862 57.895 3.32 0.00 37.74 3.84
1886 1954 1.607148 GAACCTGTAAAGTGGTGTGGC 59.393 52.381 0.00 0.00 36.57 5.01
1956 2024 0.944311 ACACTACGCACCGAAAGCTG 60.944 55.000 0.00 0.00 0.00 4.24
1968 2036 2.158959 GCCGCTGCACTACACTACG 61.159 63.158 0.00 0.00 37.47 3.51
1990 2058 5.195001 AGAAGATTCCTCGCTATCAACTC 57.805 43.478 0.00 0.00 0.00 3.01
1992 2060 4.038642 AGGAGAAGATTCCTCGCTATCAAC 59.961 45.833 0.00 0.00 44.33 3.18
2019 2087 1.300233 GCGAGGCGTCCAATCTAGG 60.300 63.158 0.00 0.00 0.00 3.02
2030 2098 2.125512 ACAAGCTAAGGCGAGGCG 60.126 61.111 0.00 0.00 44.37 5.52
2031 2099 0.808060 GAGACAAGCTAAGGCGAGGC 60.808 60.000 0.00 0.00 44.37 4.70
2032 2100 0.526524 CGAGACAAGCTAAGGCGAGG 60.527 60.000 0.00 0.00 44.37 4.63
2033 2101 0.526524 CCGAGACAAGCTAAGGCGAG 60.527 60.000 0.00 0.00 44.37 5.03
2034 2102 0.963856 TCCGAGACAAGCTAAGGCGA 60.964 55.000 0.00 0.00 44.37 5.54
2115 2188 3.414700 GCGGCGACTTGACCAGTG 61.415 66.667 12.98 0.00 35.01 3.66
2191 2270 0.519519 TGAACAAATTACAGGCGGCG 59.480 50.000 0.51 0.51 0.00 6.46
2227 2306 7.766278 TCAGAGAACAAATTAAGGAGCTGATAC 59.234 37.037 0.00 0.00 0.00 2.24
2261 2340 0.713883 CGGTACATGTGCACTCGAAC 59.286 55.000 19.41 10.94 0.00 3.95
2400 2481 6.752351 CCCACATATCTACATTCTATACACGC 59.248 42.308 0.00 0.00 0.00 5.34
2402 2483 7.042335 GCCCCACATATCTACATTCTATACAC 58.958 42.308 0.00 0.00 0.00 2.90
2407 2488 3.844211 GGGCCCCACATATCTACATTCTA 59.156 47.826 12.23 0.00 0.00 2.10
2474 2555 0.753867 TGTGACTTTGACCTGCCGTA 59.246 50.000 0.00 0.00 0.00 4.02
2475 2556 0.107410 TTGTGACTTTGACCTGCCGT 60.107 50.000 0.00 0.00 0.00 5.68
2476 2557 0.307760 GTTGTGACTTTGACCTGCCG 59.692 55.000 0.00 0.00 0.00 5.69
2477 2558 1.334869 CAGTTGTGACTTTGACCTGCC 59.665 52.381 0.00 0.00 32.54 4.85
2561 2647 5.723295 AGGCAAAACATTAAGCATGGTTAG 58.277 37.500 16.29 9.41 42.48 2.34
2610 2696 0.249531 TACGCGTGAAAGCTTGACCA 60.250 50.000 24.59 0.00 34.40 4.02


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

AutoCloner maintained by Alex Coulton.