Multiple sequence alignment - TraesCS6D01G156800

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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 TraesCS6D01G156800 chr6D 100.000 2156 0 0 1 2156 133213051 133210896 0.000000e+00 3982
1 TraesCS6D01G156800 chr6A 92.048 1421 62 19 770 2156 172117229 172115826 0.000000e+00 1951
2 TraesCS6D01G156800 chr6A 92.170 728 39 11 1 715 172118040 172117318 0.000000e+00 1013
3 TraesCS6D01G156800 chr6B 94.000 650 32 5 1 644 231354757 231354109 0.000000e+00 977
4 TraesCS6D01G156800 chr6B 97.250 509 13 1 1648 2156 231352912 231352405 0.000000e+00 861
5 TraesCS6D01G156800 chr6B 96.026 302 9 1 1251 1549 231353541 231353240 2.490000e-134 488
6 TraesCS6D01G156800 chr6B 85.640 383 44 5 778 1156 231353996 231353621 2.010000e-105 392
7 TraesCS6D01G156800 chr6B 84.868 304 36 10 858 1157 166114690 166114987 4.500000e-77 298
8 TraesCS6D01G156800 chr5D 85.437 309 31 14 857 1158 495614817 495615118 2.080000e-80 309
9 TraesCS6D01G156800 chr4B 85.016 307 34 11 857 1158 579103350 579103649 3.480000e-78 302
10 TraesCS6D01G156800 chr4A 85.016 307 35 11 857 1158 21844254 21844554 3.480000e-78 302
11 TraesCS6D01G156800 chr3B 85.113 309 30 14 858 1158 708954584 708954884 3.480000e-78 302
12 TraesCS6D01G156800 chr3B 85.113 309 30 14 858 1158 709075246 709075546 3.480000e-78 302
13 TraesCS6D01G156800 chr3A 84.641 306 35 11 859 1158 645405794 645406093 5.820000e-76 294


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 TraesCS6D01G156800 chr6D 133210896 133213051 2155 True 3982.0 3982 100.000 1 2156 1 chr6D.!!$R1 2155
1 TraesCS6D01G156800 chr6A 172115826 172118040 2214 True 1482.0 1951 92.109 1 2156 2 chr6A.!!$R1 2155
2 TraesCS6D01G156800 chr6B 231352405 231354757 2352 True 679.5 977 93.229 1 2156 4 chr6B.!!$R1 2155

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
278 279 0.590195 ATCTAGCGCCGTAAGTACCG 59.41 55.0 2.29 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1945 0.323178 AGGGTTCTAGGTCTTCGCGA 60.323 55.0 3.71 3.71 0.0 5.87 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
104 105 2.743718 CGAGGTGCCCAGTTCACT 59.256 61.111 0.00 0.00 34.97 3.41
122 123 1.759445 ACTGTGACTGTGACTTCTGCT 59.241 47.619 0.00 0.00 0.00 4.24
278 279 0.590195 ATCTAGCGCCGTAAGTACCG 59.410 55.000 2.29 0.00 0.00 4.02
282 283 1.870901 GCGCCGTAAGTACCGTCAG 60.871 63.158 0.00 0.00 0.00 3.51
318 321 5.661056 ACTTCAGTTCGATAATCTCCACA 57.339 39.130 0.00 0.00 0.00 4.17
325 328 6.019237 CAGTTCGATAATCTCCACATGTCTTG 60.019 42.308 0.00 0.00 0.00 3.02
332 335 5.954296 ATCTCCACATGTCTTGTTTTGAG 57.046 39.130 0.00 0.00 36.00 3.02
416 419 2.420058 ATTCAACTGGAATCGTCCCC 57.580 50.000 0.00 0.00 42.62 4.81
460 463 1.815408 GCTCATGTCAAGTGGTGGTGT 60.815 52.381 0.00 0.00 0.00 4.16
499 502 8.862325 TGTTTGTCATATGTAATCCTTCAAGT 57.138 30.769 1.90 0.00 0.00 3.16
500 503 9.952030 TGTTTGTCATATGTAATCCTTCAAGTA 57.048 29.630 1.90 0.00 0.00 2.24
517 525 6.814506 TCAAGTAGTGGTCTGTACTTCTAC 57.185 41.667 0.00 0.00 37.37 2.59
527 535 6.151312 TGGTCTGTACTTCTACTCAGTTGATC 59.849 42.308 0.00 0.00 0.00 2.92
608 617 5.105146 TGGCACTGTGTTGGAAAAAGTATTT 60.105 36.000 9.86 0.00 42.41 1.40
646 655 8.685838 TTTTGTAACTTGTATAAGAGTTGGCT 57.314 30.769 6.19 0.00 36.79 4.75
648 657 6.999950 TGTAACTTGTATAAGAGTTGGCTGA 58.000 36.000 6.19 0.00 36.79 4.26
649 658 7.620880 TGTAACTTGTATAAGAGTTGGCTGAT 58.379 34.615 6.19 0.00 36.79 2.90
650 659 6.992063 AACTTGTATAAGAGTTGGCTGATG 57.008 37.500 6.19 0.00 37.36 3.07
651 660 6.299805 ACTTGTATAAGAGTTGGCTGATGA 57.700 37.500 6.19 0.00 37.36 2.92
652 661 6.893583 ACTTGTATAAGAGTTGGCTGATGAT 58.106 36.000 6.19 0.00 37.36 2.45
654 663 8.486210 ACTTGTATAAGAGTTGGCTGATGATAA 58.514 33.333 6.19 0.00 37.36 1.75
655 664 9.499479 CTTGTATAAGAGTTGGCTGATGATAAT 57.501 33.333 0.00 0.00 35.92 1.28
656 665 8.837788 TGTATAAGAGTTGGCTGATGATAATG 57.162 34.615 0.00 0.00 0.00 1.90
682 692 6.434018 GCATCTCTGCTTAGTTGAAATTCT 57.566 37.500 0.00 0.00 45.32 2.40
683 693 6.485393 GCATCTCTGCTTAGTTGAAATTCTC 58.515 40.000 0.00 0.00 45.32 2.87
684 694 6.315891 GCATCTCTGCTTAGTTGAAATTCTCT 59.684 38.462 0.00 0.00 45.32 3.10
685 695 7.465781 GCATCTCTGCTTAGTTGAAATTCTCTC 60.466 40.741 0.00 0.00 45.32 3.20
686 696 6.096036 TCTCTGCTTAGTTGAAATTCTCTCG 58.904 40.000 0.00 0.00 0.00 4.04
687 697 6.025749 TCTGCTTAGTTGAAATTCTCTCGA 57.974 37.500 0.00 0.00 0.00 4.04
720 734 4.282496 ACATCTCCCCGGCTTATCTATAG 58.718 47.826 0.00 0.00 0.00 1.31
721 735 4.264442 ACATCTCCCCGGCTTATCTATAGT 60.264 45.833 0.00 0.00 0.00 2.12
724 738 6.088541 TCTCCCCGGCTTATCTATAGTATT 57.911 41.667 0.00 0.00 0.00 1.89
726 740 7.645942 TCTCCCCGGCTTATCTATAGTATTAA 58.354 38.462 0.00 0.00 0.00 1.40
729 743 8.921205 TCCCCGGCTTATCTATAGTATTAATTC 58.079 37.037 0.00 0.00 0.00 2.17
730 744 8.701895 CCCCGGCTTATCTATAGTATTAATTCA 58.298 37.037 0.00 0.00 0.00 2.57
731 745 9.530633 CCCGGCTTATCTATAGTATTAATTCAC 57.469 37.037 0.00 0.00 0.00 3.18
748 798 9.877178 ATTAATTCACTTTGTTGTTTGTTACCA 57.123 25.926 0.00 0.00 0.00 3.25
749 799 7.826260 AATTCACTTTGTTGTTTGTTACCAG 57.174 32.000 0.00 0.00 0.00 4.00
755 805 7.595502 CACTTTGTTGTTTGTTACCAGTTTACA 59.404 33.333 0.00 0.00 0.00 2.41
756 806 8.142551 ACTTTGTTGTTTGTTACCAGTTTACAA 58.857 29.630 0.00 0.00 0.00 2.41
757 807 8.522178 TTTGTTGTTTGTTACCAGTTTACAAG 57.478 30.769 0.00 0.00 33.74 3.16
758 808 7.450124 TGTTGTTTGTTACCAGTTTACAAGA 57.550 32.000 0.00 0.00 33.74 3.02
759 809 7.883217 TGTTGTTTGTTACCAGTTTACAAGAA 58.117 30.769 0.00 0.00 33.74 2.52
760 810 8.358148 TGTTGTTTGTTACCAGTTTACAAGAAA 58.642 29.630 0.00 0.00 33.74 2.52
832 894 4.853924 TCATTGAAAGGAAAGAACAGGC 57.146 40.909 0.00 0.00 0.00 4.85
835 897 1.956477 TGAAAGGAAAGAACAGGCTGC 59.044 47.619 15.89 0.00 0.00 5.25
836 898 1.270826 GAAAGGAAAGAACAGGCTGCC 59.729 52.381 15.89 11.65 0.00 4.85
865 928 7.220875 GTCTGTTTTCCTGACTGACAAATTTTC 59.779 37.037 8.70 0.00 42.22 2.29
1080 1143 0.466124 AGGCCGAGAAAGGTATGAGC 59.534 55.000 0.00 0.00 0.00 4.26
1085 1148 3.712187 CCGAGAAAGGTATGAGCTCTTC 58.288 50.000 16.19 9.05 0.00 2.87
1111 1174 2.807108 GCCCTGCCTCTCCTTTTATACG 60.807 54.545 0.00 0.00 0.00 3.06
1118 1181 3.304794 CCTCTCCTTTTATACGCCTCTCG 60.305 52.174 0.00 0.00 45.38 4.04
1135 1198 4.459089 GCGGCTCCCTCCACTCAC 62.459 72.222 0.00 0.00 0.00 3.51
1167 1230 2.159627 GTGGGACTAAACTTGCATCACG 59.840 50.000 0.00 0.00 0.00 4.35
1169 1232 1.201921 GGACTAAACTTGCATCACGCG 60.202 52.381 3.53 3.53 46.97 6.01
1170 1233 0.165944 ACTAAACTTGCATCACGCGC 59.834 50.000 5.73 0.00 46.97 6.86
1171 1234 0.853224 CTAAACTTGCATCACGCGCG 60.853 55.000 30.96 30.96 46.97 6.86
1173 1236 2.498761 AAACTTGCATCACGCGCGAG 62.499 55.000 39.36 30.24 46.97 5.03
1200 1263 1.520342 GAGCGCTCTGTGTGGGATC 60.520 63.158 29.88 0.00 0.00 3.36
1201 1264 1.954362 GAGCGCTCTGTGTGGGATCT 61.954 60.000 29.88 0.00 31.55 2.75
1208 1271 0.532573 CTGTGTGGGATCTGCGTAGT 59.467 55.000 0.00 0.00 0.00 2.73
1215 1278 0.750850 GGATCTGCGTAGTTGGGCTA 59.249 55.000 0.00 0.00 0.00 3.93
1227 1291 6.626402 GCGTAGTTGGGCTATTTTAACCAAAT 60.626 38.462 0.00 0.00 43.88 2.32
1571 1641 0.524604 CATCGCACGTCATCACCGTA 60.525 55.000 0.00 0.00 36.65 4.02
1581 1651 3.212685 GTCATCACCGTACCTAGCTACT 58.787 50.000 0.00 0.00 0.00 2.57
1589 1659 2.613133 CGTACCTAGCTACTCAGGTGAC 59.387 54.545 15.01 8.77 44.93 3.67
1590 1660 2.146920 ACCTAGCTACTCAGGTGACC 57.853 55.000 5.06 0.00 43.64 4.02
1591 1661 1.641714 ACCTAGCTACTCAGGTGACCT 59.358 52.381 5.06 0.00 43.64 3.85
1598 1668 1.080638 ACTCAGGTGACCTCCTCTCT 58.919 55.000 0.00 0.00 35.37 3.10
1601 1671 1.034838 CAGGTGACCTCCTCTCTCCG 61.035 65.000 0.00 0.00 35.37 4.63
1602 1672 2.419739 GGTGACCTCCTCTCTCCGC 61.420 68.421 0.00 0.00 0.00 5.54
1605 1675 4.467107 ACCTCCTCTCTCCGCCCC 62.467 72.222 0.00 0.00 0.00 5.80
1638 1937 0.813821 GCTCACCAGCAATTTCTCCC 59.186 55.000 0.00 0.00 46.06 4.30
1641 1940 1.428912 TCACCAGCAATTTCTCCCCTT 59.571 47.619 0.00 0.00 0.00 3.95
1646 1945 4.026052 CCAGCAATTTCTCCCCTTGTAAT 58.974 43.478 0.00 0.00 0.00 1.89
1673 1972 4.883021 AGACCTAGAACCCTATCTGACA 57.117 45.455 0.00 0.00 0.00 3.58
2013 2324 1.153997 GGCGACGACTTCTCAGTCC 60.154 63.158 0.00 0.00 46.19 3.85
2125 2436 5.697633 GTGAGTGATTTGCCATTGTTTTGAT 59.302 36.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 3.132111 TGTTAGCAGAAGTCACAGTCACA 59.868 43.478 0.00 0.00 0.00 3.58
122 123 3.153369 TGGAGCTTTGGCATCTTGTTA 57.847 42.857 0.00 0.00 41.70 2.41
278 279 6.500684 TGAAGTATCAAAATTCAGGCTGAC 57.499 37.500 18.55 2.65 30.99 3.51
318 321 6.706270 AGTGACGATTACTCAAAACAAGACAT 59.294 34.615 0.00 0.00 0.00 3.06
353 356 1.277495 GCCTGCAACAATGTTCGTGC 61.277 55.000 0.00 0.00 0.00 5.34
497 500 6.124316 TGAGTAGAAGTACAGACCACTACT 57.876 41.667 0.00 0.00 42.49 2.57
499 502 6.124316 ACTGAGTAGAAGTACAGACCACTA 57.876 41.667 0.00 0.00 34.88 2.74
500 503 4.988029 ACTGAGTAGAAGTACAGACCACT 58.012 43.478 0.00 0.00 34.88 4.00
517 525 5.813080 TTCATGCATTCTGATCAACTGAG 57.187 39.130 0.00 0.00 0.00 3.35
581 589 0.453793 TTTCCAACACAGTGCCAACG 59.546 50.000 0.00 0.00 0.00 4.10
608 617 5.652994 AGTTACAAAAACTCAGTGCCAAA 57.347 34.783 0.00 0.00 0.00 3.28
644 653 4.632251 CAGAGATGCCTCATTATCATCAGC 59.368 45.833 0.00 0.00 41.87 4.26
646 655 4.286291 AGCAGAGATGCCTCATTATCATCA 59.714 41.667 0.00 0.00 41.87 3.07
648 657 4.912317 AGCAGAGATGCCTCATTATCAT 57.088 40.909 0.00 0.00 41.87 2.45
649 658 4.701651 AAGCAGAGATGCCTCATTATCA 57.298 40.909 0.00 0.00 41.87 2.15
650 659 5.792741 ACTAAGCAGAGATGCCTCATTATC 58.207 41.667 0.00 0.00 41.87 1.75
651 660 5.822132 ACTAAGCAGAGATGCCTCATTAT 57.178 39.130 0.00 0.00 41.87 1.28
652 661 5.129320 TCAACTAAGCAGAGATGCCTCATTA 59.871 40.000 0.00 0.00 41.87 1.90
654 663 3.453717 TCAACTAAGCAGAGATGCCTCAT 59.546 43.478 0.00 0.00 41.87 2.90
655 664 2.833943 TCAACTAAGCAGAGATGCCTCA 59.166 45.455 0.00 0.00 41.87 3.86
656 665 3.533606 TCAACTAAGCAGAGATGCCTC 57.466 47.619 0.00 0.00 39.72 4.70
676 686 6.683110 ATGTACCGCATACTTCGAGAGAATTT 60.683 38.462 0.00 0.00 42.15 1.82
679 689 3.630769 ATGTACCGCATACTTCGAGAGAA 59.369 43.478 0.00 0.00 41.35 2.87
681 691 3.251245 AGATGTACCGCATACTTCGAGAG 59.749 47.826 0.00 0.00 40.99 3.20
682 692 3.211865 AGATGTACCGCATACTTCGAGA 58.788 45.455 0.00 0.00 40.99 4.04
683 693 3.556513 GAGATGTACCGCATACTTCGAG 58.443 50.000 0.00 0.00 40.99 4.04
684 694 2.292569 GGAGATGTACCGCATACTTCGA 59.707 50.000 0.00 0.00 40.99 3.71
685 695 2.607282 GGGAGATGTACCGCATACTTCG 60.607 54.545 0.00 0.00 40.99 3.79
686 696 2.288886 GGGGAGATGTACCGCATACTTC 60.289 54.545 0.00 3.88 38.06 3.01
687 697 1.692519 GGGGAGATGTACCGCATACTT 59.307 52.381 0.00 0.00 38.06 2.24
768 818 9.357161 TCCACCTTTTGCTAATCTTAAACTAAA 57.643 29.630 0.00 0.00 0.00 1.85
776 826 4.460731 GCTTCTCCACCTTTTGCTAATCTT 59.539 41.667 0.00 0.00 0.00 2.40
780 830 2.158534 TGGCTTCTCCACCTTTTGCTAA 60.159 45.455 0.00 0.00 40.72 3.09
809 865 5.010415 AGCCTGTTCTTTCCTTTCAATGAAG 59.990 40.000 0.00 0.00 0.00 3.02
832 894 1.202806 TCAGGAAAACAGACAGGGCAG 60.203 52.381 0.00 0.00 0.00 4.85
835 897 2.104792 TCAGTCAGGAAAACAGACAGGG 59.895 50.000 0.00 0.00 38.01 4.45
836 898 3.134458 GTCAGTCAGGAAAACAGACAGG 58.866 50.000 0.00 0.00 38.01 4.00
865 928 1.881591 CACCCCAACCAAAGCAAATG 58.118 50.000 0.00 0.00 0.00 2.32
923 986 3.204467 TTGCTACTGGGGCCCACAC 62.204 63.158 24.76 11.83 0.00 3.82
953 1016 2.332312 TTTGTGAGGGTGGTGGGTCG 62.332 60.000 0.00 0.00 0.00 4.79
1118 1181 4.459089 GTGAGTGGAGGGAGCCGC 62.459 72.222 0.00 0.00 38.73 6.53
1200 1263 4.201881 GGTTAAAATAGCCCAACTACGCAG 60.202 45.833 0.00 0.00 32.32 5.18
1201 1264 3.690628 GGTTAAAATAGCCCAACTACGCA 59.309 43.478 0.00 0.00 32.32 5.24
1208 1271 5.126384 CGGAGATTTGGTTAAAATAGCCCAA 59.874 40.000 0.00 0.00 38.64 4.12
1215 1278 4.159693 GGCCTTCGGAGATTTGGTTAAAAT 59.840 41.667 0.00 0.00 41.33 1.82
1227 1291 1.497309 ATGGTTTGGGCCTTCGGAGA 61.497 55.000 4.53 0.00 0.00 3.71
1283 1347 2.683968 CTGCTAAGCGTGTAGTTTGGA 58.316 47.619 0.00 0.00 0.00 3.53
1413 1483 2.551270 CTTGAACGGTGACTGCGC 59.449 61.111 0.00 0.00 0.00 6.09
1581 1651 0.333312 GGAGAGAGGAGGTCACCTGA 59.667 60.000 0.00 0.00 40.73 3.86
1630 1707 2.169769 TCGCGATTACAAGGGGAGAAAT 59.830 45.455 3.71 0.00 0.00 2.17
1635 1712 1.134907 GTCTTCGCGATTACAAGGGGA 60.135 52.381 10.88 0.00 0.00 4.81
1638 1937 2.295253 AGGTCTTCGCGATTACAAGG 57.705 50.000 10.88 0.00 0.00 3.61
1641 1940 3.181493 GGTTCTAGGTCTTCGCGATTACA 60.181 47.826 10.88 0.00 0.00 2.41
1646 1945 0.323178 AGGGTTCTAGGTCTTCGCGA 60.323 55.000 3.71 3.71 0.00 5.87
2013 2324 0.609957 TTGGTCCAGCAGGCAATGAG 60.610 55.000 0.00 0.00 33.74 2.90


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

AutoCloner maintained by Alex Coulton.