Multiple sequence alignment - TraesCS6B01G198700

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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 TraesCS6B01G198700 chr6B 100.000 2667 0 0 1 2667 237729911 237732577 0.000000e+00 4926
1 TraesCS6B01G198700 chr6D 91.589 1510 62 28 594 2066 138383808 138385289 0.000000e+00 2025
2 TraesCS6B01G198700 chr6D 91.500 600 34 6 1 591 138383053 138383644 0.000000e+00 809
3 TraesCS6B01G198700 chr6D 95.062 324 10 3 2076 2394 138385671 138385993 3.060000e-139 505
4 TraesCS6B01G198700 chr6D 93.750 256 14 2 2395 2648 138386194 138386449 1.500000e-102 383
5 TraesCS6B01G198700 chr6A 90.137 1389 80 25 699 2066 181012745 181014097 0.000000e+00 1753
6 TraesCS6B01G198700 chr6A 94.077 574 30 4 2076 2646 181014452 181015024 0.000000e+00 869
7 TraesCS6B01G198700 chr6A 91.060 604 50 4 1 603 181011862 181012462 0.000000e+00 813
8 TraesCS6B01G198700 chr6A 86.139 101 14 0 589 689 181012499 181012599 2.810000e-20 110
9 TraesCS6B01G198700 chr7B 82.422 256 33 10 1330 1578 530590638 530590388 2.080000e-51 213
10 TraesCS6B01G198700 chr7B 82.101 257 32 12 1330 1578 530434731 530434481 9.680000e-50 207
11 TraesCS6B01G198700 chr7A 83.122 237 28 10 1348 1578 567591240 567591010 3.480000e-49 206
12 TraesCS6B01G198700 chr7D 81.857 237 31 10 1348 1578 501108284 501108054 3.500000e-44 189


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 TraesCS6B01G198700 chr6B 237729911 237732577 2666 False 4926.00 4926 100.00000 1 2667 1 chr6B.!!$F1 2666
1 TraesCS6B01G198700 chr6D 138383053 138386449 3396 False 930.50 2025 92.97525 1 2648 4 chr6D.!!$F1 2647
2 TraesCS6B01G198700 chr6A 181011862 181015024 3162 False 886.25 1753 90.35325 1 2646 4 chr6A.!!$F1 2645

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
683 854 0.041576 GGTCGGACGTTGAACAAAGC 60.042 55.0 1.43 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 2813 0.032403 TCGTTCTGTACCGGTGGTTG 59.968 55.0 19.93 4.81 37.09 3.77 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
33 34 4.526262 ACTGACATAGCCATTAGAGCCTAG 59.474 45.833 0.00 0.00 0.00 3.02
38 39 0.948141 GCCATTAGAGCCTAGCTGCG 60.948 60.000 0.00 0.00 39.88 5.18
45 46 2.027605 GCCTAGCTGCGCGACATA 59.972 61.111 12.10 0.00 0.00 2.29
84 85 6.732154 GCACAAGCTACATCAATGAATATGT 58.268 36.000 0.00 0.00 39.56 2.29
85 86 6.854892 GCACAAGCTACATCAATGAATATGTC 59.145 38.462 0.00 0.00 37.50 3.06
100 101 5.049129 TGAATATGTCGTGCACATTTTGTCA 60.049 36.000 18.64 8.61 43.89 3.58
111 112 4.062293 CACATTTTGTCAAGGACGAGGTA 58.938 43.478 0.00 0.00 34.95 3.08
276 279 4.096732 CAAAGCCCTTTGTAGAATTCCG 57.903 45.455 11.60 0.00 43.52 4.30
316 319 9.066892 GCTATCACCACTCATTAATCCAAATTA 57.933 33.333 0.00 0.00 0.00 1.40
365 369 2.257676 GACGTGACACTCGACCCC 59.742 66.667 3.68 0.00 0.00 4.95
378 382 1.205417 TCGACCCCGTGTTTTCCTATC 59.795 52.381 0.00 0.00 37.05 2.08
379 383 1.741394 CGACCCCGTGTTTTCCTATCC 60.741 57.143 0.00 0.00 0.00 2.59
413 417 7.703328 TCATAATCGTTTCAATTAAAGAGGCC 58.297 34.615 0.00 0.00 0.00 5.19
421 425 1.222567 ATTAAAGAGGCCGGATGGGT 58.777 50.000 5.05 0.00 38.44 4.51
466 470 0.600557 ATTGGTCGGAATTTTGCGCA 59.399 45.000 5.66 5.66 41.99 6.09
472 476 1.059942 CGGAATTTTGCGCAAAGACC 58.940 50.000 31.88 29.82 34.72 3.85
533 539 2.605094 CCGTGAGTAATCGGCCATG 58.395 57.895 2.24 0.00 40.28 3.66
566 576 1.640670 ACTTGGTGGTGGCTTCCATAT 59.359 47.619 5.42 0.00 39.81 1.78
622 793 7.852945 GTCTTATGCGTATTCCAGAAAAATCTG 59.147 37.037 0.00 0.00 37.48 2.90
629 800 1.885887 TCCAGAAAAATCTGTTGGGCG 59.114 47.619 5.23 0.00 36.06 6.13
635 806 1.322538 AAATCTGTTGGGCGGCATCC 61.323 55.000 12.47 0.00 0.00 3.51
679 850 1.589461 CACGGTCGGACGTTGAACA 60.589 57.895 1.43 0.00 46.25 3.18
683 854 0.041576 GGTCGGACGTTGAACAAAGC 60.042 55.000 1.43 0.00 0.00 3.51
688 865 1.529438 GGACGTTGAACAAAGCGATCA 59.471 47.619 0.00 0.00 0.00 2.92
724 1031 2.830321 TGTAATGCAATGCCATTCCACA 59.170 40.909 1.53 2.91 36.80 4.17
725 1032 2.389962 AATGCAATGCCATTCCACAC 57.610 45.000 1.53 0.00 29.81 3.82
808 1115 6.073765 GCTGTTACTTTCGACAGAATTTCTCA 60.074 38.462 5.40 0.00 44.65 3.27
823 1130 7.220683 CAGAATTTCTCAACGCAGAAAAGAAAA 59.779 33.333 8.40 0.00 43.88 2.29
825 1132 4.552166 TCTCAACGCAGAAAAGAAAAGG 57.448 40.909 0.00 0.00 0.00 3.11
826 1133 3.045688 CTCAACGCAGAAAAGAAAAGGC 58.954 45.455 0.00 0.00 0.00 4.35
833 1140 3.731216 GCAGAAAAGAAAAGGCGTTCTTC 59.269 43.478 16.30 8.07 45.09 2.87
901 1208 5.108593 CGACAGATTACGAATCAAGACGATG 60.109 44.000 9.31 0.00 40.42 3.84
960 1270 2.030007 CCAAATTTGCTCACGTCACCAT 60.030 45.455 12.92 0.00 0.00 3.55
1010 1320 2.406596 TTTCCCGCGGTTTATAAGCT 57.593 45.000 26.12 0.00 0.00 3.74
1014 1324 1.275657 CGCGGTTTATAAGCTGCGG 59.724 57.895 34.62 21.89 42.99 5.69
1061 1371 1.098712 GTCCGGGCAAGAAACACACA 61.099 55.000 0.00 0.00 0.00 3.72
1085 1409 6.966435 AAAGAAAATCCACCAATAATTGCG 57.034 33.333 0.00 0.00 0.00 4.85
1087 1411 5.894807 AGAAAATCCACCAATAATTGCGAG 58.105 37.500 0.00 0.00 0.00 5.03
1201 1528 2.544698 GGTCTACGATCCTCGCGCT 61.545 63.158 5.56 0.00 45.12 5.92
1326 1653 2.967397 GGTGGACGATGACGGTCA 59.033 61.111 14.01 14.01 44.46 4.02
1605 1932 2.029666 GGACGAGGCCGATGATGG 59.970 66.667 0.00 0.00 39.50 3.51
1647 1974 3.330275 CGGCAATACGGCTTAGCC 58.670 61.111 14.22 14.22 46.75 3.93
1813 2148 1.736645 CTGTAGACGGCCGGTGTTG 60.737 63.158 31.76 10.97 0.00 3.33
1814 2149 2.433664 GTAGACGGCCGGTGTTGG 60.434 66.667 31.76 0.00 0.00 3.77
1815 2150 2.601067 TAGACGGCCGGTGTTGGA 60.601 61.111 31.76 3.91 0.00 3.53
1824 2159 0.666374 CCGGTGTTGGAAGTTGGAAC 59.334 55.000 0.00 0.00 0.00 3.62
1836 2171 0.037232 GTTGGAACCGGGTGAGAGAG 60.037 60.000 6.32 0.00 0.00 3.20
1844 2179 0.397254 CGGGTGAGAGAGGGGTGTAT 60.397 60.000 0.00 0.00 0.00 2.29
1848 2183 3.492337 GGTGAGAGAGGGGTGTATAGAG 58.508 54.545 0.00 0.00 0.00 2.43
1849 2184 2.888414 GTGAGAGAGGGGTGTATAGAGC 59.112 54.545 0.00 0.00 0.00 4.09
1852 2187 1.616374 GAGAGGGGTGTATAGAGCAGC 59.384 57.143 1.20 0.00 0.00 5.25
1854 2189 1.069358 GAGGGGTGTATAGAGCAGCAC 59.931 57.143 1.20 0.00 37.96 4.40
1903 2248 2.099921 GCCGAGGCATATCGACTATCAT 59.900 50.000 9.58 0.00 45.56 2.45
2109 2877 4.527816 AGGACAGCAAAAGAAAATGGCATA 59.472 37.500 0.00 0.00 0.00 3.14
2187 2956 1.002257 CTGGGCTGCCACATGTACA 60.002 57.895 22.05 6.19 0.00 2.90
2326 3100 4.623932 AGCCACAGAACAATACTGAAGA 57.376 40.909 0.00 0.00 38.55 2.87
2330 3104 5.063204 CCACAGAACAATACTGAAGAACCA 58.937 41.667 0.00 0.00 38.55 3.67
2335 3109 5.940470 AGAACAATACTGAAGAACCACATCC 59.060 40.000 0.00 0.00 0.00 3.51
2419 3393 8.262933 TGTATATTGGAGCATGAAGGATATCAG 58.737 37.037 4.83 0.00 31.76 2.90
2524 3499 0.320771 CATAGGTATGCTCCGGTGCC 60.321 60.000 24.73 10.11 0.00 5.01
2565 3540 5.473066 AAAAGGCTACATGTTTGATTGCT 57.527 34.783 2.30 0.00 0.00 3.91
2623 3598 7.295672 TGGACTCCTATTGATGATAATTTCCCT 59.704 37.037 0.00 0.00 0.00 4.20
2646 3621 9.725019 CCCTTGCAGATATAATTATGTAACAGA 57.275 33.333 8.28 0.00 0.00 3.41
2659 3634 8.986477 ATTATGTAACAGAAATTTGTTCAGGC 57.014 30.769 0.00 0.00 41.31 4.85
2660 3635 5.843673 TGTAACAGAAATTTGTTCAGGCA 57.156 34.783 0.00 0.00 41.31 4.75
2661 3636 6.403866 TGTAACAGAAATTTGTTCAGGCAT 57.596 33.333 0.00 0.00 41.31 4.40
2662 3637 7.517614 TGTAACAGAAATTTGTTCAGGCATA 57.482 32.000 0.00 0.00 41.31 3.14
2663 3638 7.946207 TGTAACAGAAATTTGTTCAGGCATAA 58.054 30.769 0.00 0.00 41.31 1.90
2664 3639 7.865385 TGTAACAGAAATTTGTTCAGGCATAAC 59.135 33.333 0.00 0.00 41.31 1.89
2665 3640 5.783111 ACAGAAATTTGTTCAGGCATAACC 58.217 37.500 0.00 0.00 39.61 2.85
2666 3641 5.304101 ACAGAAATTTGTTCAGGCATAACCA 59.696 36.000 0.00 0.00 43.14 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.948141 CGCAGCTAGGCTCTAATGGC 60.948 60.000 0.00 0.00 36.40 4.40
82 83 2.223456 CCTTGACAAAATGTGCACGACA 60.223 45.455 13.13 0.96 39.53 4.35
84 85 2.032799 GTCCTTGACAAAATGTGCACGA 59.967 45.455 13.13 1.58 32.09 4.35
85 86 2.384382 GTCCTTGACAAAATGTGCACG 58.616 47.619 13.13 0.00 32.09 5.34
218 219 8.690203 TTTTTCTCCAATATTGAGTGAGAACA 57.310 30.769 23.88 18.66 0.00 3.18
276 279 4.941263 TGGTGATAGCACATGAAAAGTACC 59.059 41.667 13.97 0.33 46.96 3.34
336 339 3.381908 AGTGTCACGTCCTATGAATCCTC 59.618 47.826 0.00 0.00 0.00 3.71
365 369 7.143340 TGAAGATATACGGATAGGAAAACACG 58.857 38.462 0.00 0.00 0.00 4.49
421 425 9.639563 TTGCCCAATAGATAAATTCAAGATGTA 57.360 29.630 0.00 0.00 0.00 2.29
478 484 2.058057 CATACAACTTTGCCGCAAACC 58.942 47.619 14.60 0.00 0.00 3.27
533 539 5.508320 CCACCACCAAGTACATTGTTTTACC 60.508 44.000 0.00 0.00 37.17 2.85
611 782 1.669795 GCCGCCCAACAGATTTTTCTG 60.670 52.381 1.55 1.55 43.03 3.02
679 850 3.630769 AGTTGCATGATCATGATCGCTTT 59.369 39.130 34.65 12.73 41.20 3.51
683 854 3.808174 ACAGAGTTGCATGATCATGATCG 59.192 43.478 34.65 21.54 41.20 3.69
688 865 4.885325 TGCATTACAGAGTTGCATGATCAT 59.115 37.500 1.18 1.18 41.18 2.45
724 1031 6.774354 ACAAAATACTCGTTCGTTACATGT 57.226 33.333 2.69 2.69 0.00 3.21
725 1032 9.033262 GTAAACAAAATACTCGTTCGTTACATG 57.967 33.333 0.00 0.00 0.00 3.21
781 1088 1.415374 TCTGTCGAAAGTAACAGCGC 58.585 50.000 0.00 0.00 42.10 5.92
808 1115 2.119671 CGCCTTTTCTTTTCTGCGTT 57.880 45.000 0.00 0.00 37.44 4.84
823 1130 3.695830 TTGTTGATAGGAAGAACGCCT 57.304 42.857 0.00 0.00 39.56 5.52
825 1132 3.426292 GGCTTTGTTGATAGGAAGAACGC 60.426 47.826 0.00 0.00 0.00 4.84
826 1133 3.127030 GGGCTTTGTTGATAGGAAGAACG 59.873 47.826 0.00 0.00 0.00 3.95
827 1134 3.127030 CGGGCTTTGTTGATAGGAAGAAC 59.873 47.826 0.00 0.00 0.00 3.01
833 1140 0.394352 AGGCGGGCTTTGTTGATAGG 60.394 55.000 0.00 0.00 0.00 2.57
960 1270 2.611971 CGCTCTAAAGTTGTGGCTGGTA 60.612 50.000 0.00 0.00 0.00 3.25
1014 1324 2.557372 GGGAGATCGAGCGGAGACC 61.557 68.421 0.00 0.00 0.00 3.85
1061 1371 7.158021 TCGCAATTATTGGTGGATTTTCTTTT 58.842 30.769 7.08 0.00 0.00 2.27
1102 1426 1.226773 GCGTTGCATGCTTGGGATC 60.227 57.895 20.33 0.00 0.00 3.36
1160 1487 4.465512 CAGCATGAACACGCCGGC 62.466 66.667 19.07 19.07 39.69 6.13
1201 1528 1.140161 GTCGTACTGCCCATGCGTA 59.860 57.895 0.00 0.00 41.78 4.42
1684 2012 2.971997 GCTACGTGCCATGAATCGA 58.028 52.632 0.00 0.00 35.15 3.59
1813 2148 0.605589 CTCACCCGGTTCCAACTTCC 60.606 60.000 0.00 0.00 0.00 3.46
1814 2149 0.395312 TCTCACCCGGTTCCAACTTC 59.605 55.000 0.00 0.00 0.00 3.01
1815 2150 0.396811 CTCTCACCCGGTTCCAACTT 59.603 55.000 0.00 0.00 0.00 2.66
1824 2159 2.509931 TACACCCCTCTCTCACCCGG 62.510 65.000 0.00 0.00 0.00 5.73
1836 2171 0.249489 CGTGCTGCTCTATACACCCC 60.249 60.000 0.00 0.00 0.00 4.95
1844 2179 1.587043 AAGTCGCTCGTGCTGCTCTA 61.587 55.000 7.97 0.00 36.97 2.43
1848 2183 2.724708 CTGAAGTCGCTCGTGCTGC 61.725 63.158 7.97 0.00 36.97 5.25
1849 2184 2.724708 GCTGAAGTCGCTCGTGCTG 61.725 63.158 7.97 1.69 36.97 4.41
1852 2187 1.016130 AATGGCTGAAGTCGCTCGTG 61.016 55.000 0.00 0.00 0.00 4.35
1854 2189 0.737367 TCAATGGCTGAAGTCGCTCG 60.737 55.000 0.00 0.00 0.00 5.03
1861 2196 2.031807 CGCAGATTCTCAATGGCTGAAG 59.968 50.000 0.00 0.00 32.17 3.02
1903 2248 5.699097 ACCGCTCTTGCTTATTTTGTTTA 57.301 34.783 0.00 0.00 36.97 2.01
2064 2813 0.032403 TCGTTCTGTACCGGTGGTTG 59.968 55.000 19.93 4.81 37.09 3.77
2109 2877 6.142817 CCGAAGATGTTTCAGAACGAAATTT 58.857 36.000 0.00 0.00 45.21 1.82
2187 2956 8.306761 CACATTTTCAGGAAGGCTTAATAGTTT 58.693 33.333 0.00 0.00 0.00 2.66
2242 3015 1.704641 TCCATCTACCATCCACTCCG 58.295 55.000 0.00 0.00 0.00 4.63
2326 3100 1.679153 GTTTGTGTTCGGGATGTGGTT 59.321 47.619 0.00 0.00 0.00 3.67
2330 3104 1.946768 CTGTGTTTGTGTTCGGGATGT 59.053 47.619 0.00 0.00 0.00 3.06
2335 3109 4.545823 ATTGTACTGTGTTTGTGTTCGG 57.454 40.909 0.00 0.00 0.00 4.30
2408 3382 8.887717 CCCGATTCATTAATTCTGATATCCTTC 58.112 37.037 0.00 0.00 0.00 3.46
2432 3406 9.628500 AACCAGTAACATCTATTTATCTTTCCC 57.372 33.333 0.00 0.00 0.00 3.97
2524 3499 6.146184 GCCTTTTTAGCCTTTAGCAAAAGAAG 59.854 38.462 10.21 4.78 42.71 2.85
2565 3540 6.581171 TTGCACATCACATTTTGGTATACA 57.419 33.333 5.01 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.