Multiple sequence alignment - TraesCS6B01G225900

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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 TraesCS6B01G225900 chr6B 100.000 2201 0 0 1 2201 347228525 347230725 0.000000e+00 4065.0
1 TraesCS6B01G225900 chr6A 92.853 1553 56 19 690 2201 356972777 356971239 0.000000e+00 2202.0
2 TraesCS6B01G225900 chr6A 91.082 684 34 12 1 663 356973551 356972874 0.000000e+00 900.0
3 TraesCS6B01G225900 chr6D 92.669 1555 62 20 688 2201 262752971 262751428 0.000000e+00 2193.0
4 TraesCS6B01G225900 chr6D 87.946 672 55 19 1 663 262753720 262753066 0.000000e+00 769.0
5 TraesCS6B01G225900 chr3D 80.723 83 16 0 1414 1496 4972508 4972426 5.070000e-07 65.8


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 TraesCS6B01G225900 chr6B 347228525 347230725 2200 False 4065 4065 100.0000 1 2201 1 chr6B.!!$F1 2200
1 TraesCS6B01G225900 chr6A 356971239 356973551 2312 True 1551 2202 91.9675 1 2201 2 chr6A.!!$R1 2200
2 TraesCS6B01G225900 chr6D 262751428 262753720 2292 True 1481 2193 90.3075 1 2201 2 chr6D.!!$R1 2200

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
558 579 0.249953 TGGGTCGCTCGCTTGTAAAA 60.25 50.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1726 0.036952 AGTTGATGACCAGTGGCTCG 60.037 55.0 9.78 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
42 43 7.503566 AGCATCTGCAAATATATGTGGTTTACT 59.496 33.333 5.03 0.00 45.16 2.24
47 51 7.915508 TGCAAATATATGTGGTTTACTTCTCG 58.084 34.615 5.03 0.00 0.00 4.04
53 57 5.668558 ATGTGGTTTACTTCTCGTTTCAC 57.331 39.130 0.00 0.00 0.00 3.18
56 60 5.064198 TGTGGTTTACTTCTCGTTTCACTTG 59.936 40.000 0.00 0.00 0.00 3.16
109 113 9.765795 GGAGCCATATTATTACGCTAAGATAAT 57.234 33.333 0.00 0.00 32.44 1.28
205 221 1.271856 TCCGTTCTAATGCAGGGTCA 58.728 50.000 0.00 0.00 0.00 4.02
218 235 5.033589 TGCAGGGTCATTGATTTGTTTTT 57.966 34.783 0.00 0.00 0.00 1.94
321 338 8.213679 TGAATAAGGAATAGCACATAAAGCTCT 58.786 33.333 0.00 0.00 42.32 4.09
329 346 4.026744 AGCACATAAAGCTCTGGACTCTA 58.973 43.478 0.00 0.00 38.01 2.43
341 358 6.007703 GCTCTGGACTCTACCATACTAGATT 58.992 44.000 0.00 0.00 39.34 2.40
348 365 8.301002 GGACTCTACCATACTAGATTTCATGAC 58.699 40.741 0.00 0.00 0.00 3.06
358 376 9.911788 ATACTAGATTTCATGACCAACAAGATT 57.088 29.630 0.00 0.00 0.00 2.40
365 383 5.624159 TCATGACCAACAAGATTGAGAACT 58.376 37.500 0.00 0.00 0.00 3.01
411 432 6.484643 GCTTGCATTCAATATCTAGAGTCCAA 59.515 38.462 0.00 0.00 0.00 3.53
412 433 7.174599 GCTTGCATTCAATATCTAGAGTCCAAT 59.825 37.037 0.00 0.00 0.00 3.16
539 560 5.017431 TGGGATATATGCTAGGGTTACTCCT 59.983 44.000 4.09 0.00 40.79 3.69
552 573 3.764466 CTCCTGGGTCGCTCGCTT 61.764 66.667 0.00 0.00 0.00 4.68
558 579 0.249953 TGGGTCGCTCGCTTGTAAAA 60.250 50.000 0.00 0.00 0.00 1.52
566 587 3.605922 CGCTCGCTTGTAAAACAACATGA 60.606 43.478 0.00 0.00 33.96 3.07
598 620 5.765182 GCTGCTAGTTGTACAAATGGGATAT 59.235 40.000 18.30 0.00 0.00 1.63
641 663 4.047822 GACATCTCTAGCATTTCAGTCGG 58.952 47.826 0.00 0.00 0.00 4.79
669 746 5.163794 CGCTTAAATCATTGTTCTTACCCGT 60.164 40.000 0.00 0.00 0.00 5.28
672 749 7.574217 GCTTAAATCATTGTTCTTACCCGTTGA 60.574 37.037 0.00 0.00 0.00 3.18
686 763 1.379527 CGTTGATTCCTAACCAGCCC 58.620 55.000 0.00 0.00 0.00 5.19
706 798 1.135575 CGTTTCCTTGCATCTTCCAGC 60.136 52.381 0.00 0.00 0.00 4.85
715 807 3.211865 TGCATCTTCCAGCTTGATGATC 58.788 45.455 11.87 8.68 39.72 2.92
750 846 4.985413 ACCAAAATATGCACACTGATTCG 58.015 39.130 0.00 0.00 0.00 3.34
758 854 1.600164 GCACACTGATTCGCAAAGCAA 60.600 47.619 0.00 0.00 28.79 3.91
768 864 7.025485 TGATTCGCAAAGCAATACATTCATA 57.975 32.000 0.00 0.00 0.00 2.15
784 880 3.887621 TCATAGCTTCACTGTGGTACC 57.112 47.619 4.43 4.43 38.03 3.34
794 890 2.158841 CACTGTGGTACCGCACATAAAC 59.841 50.000 24.25 5.92 32.59 2.01
805 901 4.941263 ACCGCACATAAACAGTACATGAAT 59.059 37.500 0.00 0.00 0.00 2.57
870 985 5.116180 TGCATACATTTCTTCCTACTTCCG 58.884 41.667 0.00 0.00 0.00 4.30
876 991 5.936372 ACATTTCTTCCTACTTCCGTTTACC 59.064 40.000 0.00 0.00 0.00 2.85
884 999 6.400568 TCCTACTTCCGTTTACCTACATTTG 58.599 40.000 0.00 0.00 0.00 2.32
900 1015 5.808042 ACATTTGAAGGAATCATCACTCG 57.192 39.130 0.00 0.00 38.03 4.18
915 1030 6.040247 TCATCACTCGTATTTATCGTTTGCT 58.960 36.000 0.00 0.00 0.00 3.91
920 1035 6.252869 CACTCGTATTTATCGTTTGCTGTAGT 59.747 38.462 0.00 0.00 0.00 2.73
921 1036 6.471519 ACTCGTATTTATCGTTTGCTGTAGTC 59.528 38.462 0.00 0.00 0.00 2.59
922 1037 6.324042 TCGTATTTATCGTTTGCTGTAGTCA 58.676 36.000 0.00 0.00 0.00 3.41
923 1038 6.807720 TCGTATTTATCGTTTGCTGTAGTCAA 59.192 34.615 0.00 0.00 0.00 3.18
924 1039 7.008901 TCGTATTTATCGTTTGCTGTAGTCAAG 59.991 37.037 0.00 0.00 0.00 3.02
925 1040 7.201410 CGTATTTATCGTTTGCTGTAGTCAAGT 60.201 37.037 0.00 0.00 0.00 3.16
926 1041 9.079833 GTATTTATCGTTTGCTGTAGTCAAGTA 57.920 33.333 0.00 0.00 0.00 2.24
927 1042 6.939551 TTATCGTTTGCTGTAGTCAAGTAC 57.060 37.500 0.00 0.00 0.00 2.73
928 1043 4.310357 TCGTTTGCTGTAGTCAAGTACA 57.690 40.909 0.00 0.00 0.00 2.90
952 1067 9.561069 ACATCCAATATACTCTTATTTCACACC 57.439 33.333 0.00 0.00 0.00 4.16
956 1071 7.307396 CCAATATACTCTTATTTCACACCGCAG 60.307 40.741 0.00 0.00 0.00 5.18
957 1072 3.678056 ACTCTTATTTCACACCGCAGA 57.322 42.857 0.00 0.00 0.00 4.26
965 1080 7.985184 TCTTATTTCACACCGCAGAACTTATAT 59.015 33.333 0.00 0.00 0.00 0.86
971 1086 8.812147 TCACACCGCAGAACTTATATATTTAG 57.188 34.615 0.00 0.00 0.00 1.85
1020 1135 4.450305 AATGAAGGAAGATGGATCAGGG 57.550 45.455 0.00 0.00 0.00 4.45
1034 1149 2.946650 AGGGGGTGTGGGGATTGG 60.947 66.667 0.00 0.00 0.00 3.16
1035 1150 2.944390 GGGGGTGTGGGGATTGGA 60.944 66.667 0.00 0.00 0.00 3.53
1072 1187 1.875514 TCTGTGTCACTTTCAGCATGC 59.124 47.619 10.51 10.51 34.76 4.06
1095 1210 1.377725 CCGCATTGTTGGCTCCTCT 60.378 57.895 0.00 0.00 0.00 3.69
1158 1273 8.055181 ACCTTCTTTATATTGAAGATTGCCTCA 58.945 33.333 13.57 0.00 41.38 3.86
1172 1287 1.065199 TGCCTCATCATCACCCTTGAC 60.065 52.381 0.00 0.00 33.38 3.18
1197 1312 0.689623 AGTCAAGCCTCCCACTTCTG 59.310 55.000 0.00 0.00 0.00 3.02
1252 1367 1.202440 GCTCCTCATCAGCTGTCTCTG 60.202 57.143 14.67 7.70 33.75 3.35
1284 1399 2.138320 CGTCTGCAACACACAATCTCT 58.862 47.619 0.00 0.00 0.00 3.10
1310 1425 6.152831 AGCAAGATCACCCCAAAACTATAAAC 59.847 38.462 0.00 0.00 0.00 2.01
1311 1426 6.071616 GCAAGATCACCCCAAAACTATAAACA 60.072 38.462 0.00 0.00 0.00 2.83
1353 1468 1.394618 TGTTTTTGAACCACTCGGGG 58.605 50.000 0.00 0.00 42.91 5.73
1497 1612 3.706086 GGGGCTTTATGTCACAATGGATT 59.294 43.478 0.00 0.00 0.00 3.01
1581 1696 2.626780 GCGAAGGTTCCAGGTTGGC 61.627 63.158 0.00 0.00 37.47 4.52
1618 1733 1.604278 GGAATCCATTAAGCGAGCCAC 59.396 52.381 0.00 0.00 0.00 5.01
1658 1773 3.080319 CCAGAAGCCTCTCTTTTCCTTG 58.920 50.000 0.00 0.00 34.56 3.61
1661 1776 3.137360 AGAAGCCTCTCTTTTCCTTGTGT 59.863 43.478 0.00 0.00 34.56 3.72
1671 1786 2.136298 TTCCTTGTGTGCAGAAACCA 57.864 45.000 0.00 0.00 0.00 3.67
1802 1917 3.341823 CAGTCCCAAACTCATCTTCCAG 58.658 50.000 0.00 0.00 35.45 3.86
1947 2062 2.034066 TGGGCTGGCTTCTTTCGG 59.966 61.111 0.00 0.00 0.00 4.30
1949 2064 3.443925 GGCTGGCTTCTTTCGGCC 61.444 66.667 0.00 0.00 46.54 6.13
2047 2180 6.765512 CCAATACCTCTTCTCTTTTCTCCATC 59.234 42.308 0.00 0.00 0.00 3.51
2065 2198 3.393800 CATCTATTGGAGTTACTGGCCG 58.606 50.000 0.00 0.00 0.00 6.13
2097 2230 4.014273 AGGAATATCAGTCCTGGGAACT 57.986 45.455 0.00 0.00 44.14 3.01
2117 2250 7.315890 GGAACTTTGATAAAAACTGATCCCAG 58.684 38.462 0.00 0.00 45.76 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.159372 AGTGAAACGAGAAGTAAACCACATAT 58.841 34.615 0.00 0.00 45.86 1.78
42 43 2.105821 ACATCCCCAAGTGAAACGAGAA 59.894 45.455 0.00 0.00 45.86 2.87
47 51 7.763985 CCAAATATTAACATCCCCAAGTGAAAC 59.236 37.037 0.00 0.00 0.00 2.78
53 57 9.581289 TGTATACCAAATATTAACATCCCCAAG 57.419 33.333 0.00 0.00 0.00 3.61
56 60 8.344446 GGTGTATACCAAATATTAACATCCCC 57.656 38.462 3.35 0.00 46.71 4.81
109 113 9.778741 CCATATTTAGAATTAGTAGGCTGTTGA 57.221 33.333 0.00 0.00 0.00 3.18
232 249 4.268405 GGTGCAACATGCTTACAAATATGC 59.732 41.667 0.00 0.00 45.31 3.14
321 338 8.004801 TCATGAAATCTAGTATGGTAGAGTCCA 58.995 37.037 0.00 0.00 42.01 4.02
329 346 6.957631 TGTTGGTCATGAAATCTAGTATGGT 58.042 36.000 0.00 0.00 0.00 3.55
341 358 6.064060 AGTTCTCAATCTTGTTGGTCATGAA 58.936 36.000 0.00 0.00 34.65 2.57
348 365 6.382869 AACAGAAGTTCTCAATCTTGTTGG 57.617 37.500 1.26 0.00 30.46 3.77
365 383 6.371809 AGCATTACAACGAAAAGAACAGAA 57.628 33.333 0.00 0.00 0.00 3.02
376 397 4.495911 TTGAATGCAAGCATTACAACGA 57.504 36.364 19.21 5.35 45.50 3.85
422 443 9.715121 CTTCTTAGTGTAACAGTGGGTAATAAA 57.285 33.333 0.00 0.00 41.43 1.40
426 447 6.736110 ACTTCTTAGTGTAACAGTGGGTAA 57.264 37.500 0.00 0.00 41.43 2.85
445 466 8.934507 AACTTAGACAACTGCATCTATACTTC 57.065 34.615 0.00 0.00 0.00 3.01
539 560 0.249953 TTTTACAAGCGAGCGACCCA 60.250 50.000 0.00 0.00 0.00 4.51
552 573 4.515191 GCAGGACTCTCATGTTGTTTTACA 59.485 41.667 0.00 0.00 29.72 2.41
558 579 1.610102 GCAGCAGGACTCTCATGTTGT 60.610 52.381 3.30 0.00 40.61 3.32
566 587 1.638529 ACAACTAGCAGCAGGACTCT 58.361 50.000 0.00 0.00 0.00 3.24
641 663 6.745907 GGTAAGAACAATGATTTAAGCGTTCC 59.254 38.462 0.00 0.00 34.65 3.62
669 746 0.988832 ACGGGCTGGTTAGGAATCAA 59.011 50.000 0.00 0.00 0.00 2.57
672 749 1.340697 GGAAACGGGCTGGTTAGGAAT 60.341 52.381 0.00 0.00 0.00 3.01
686 763 1.135575 GCTGGAAGATGCAAGGAAACG 60.136 52.381 0.00 0.00 34.07 3.60
706 798 9.716531 TTGGTATATTGCTTAGAGATCATCAAG 57.283 33.333 0.00 0.00 0.00 3.02
715 807 9.831737 GTGCATATTTTGGTATATTGCTTAGAG 57.168 33.333 0.00 0.00 0.00 2.43
750 846 6.197842 GTGAAGCTATGAATGTATTGCTTTGC 59.802 38.462 10.72 5.67 44.88 3.68
758 854 5.994250 ACCACAGTGAAGCTATGAATGTAT 58.006 37.500 0.62 0.00 0.00 2.29
768 864 1.004918 GCGGTACCACAGTGAAGCT 60.005 57.895 13.54 0.00 0.00 3.74
784 880 9.580916 GTAATATTCATGTACTGTTTATGTGCG 57.419 33.333 0.00 0.00 0.00 5.34
864 979 6.464749 TCCTTCAAATGTAGGTAAACGGAAGT 60.465 38.462 6.05 0.00 38.77 3.01
870 985 8.956426 TGATGATTCCTTCAAATGTAGGTAAAC 58.044 33.333 6.05 0.96 38.03 2.01
876 991 6.536582 ACGAGTGATGATTCCTTCAAATGTAG 59.463 38.462 0.00 0.00 38.03 2.74
884 999 7.595502 ACGATAAATACGAGTGATGATTCCTTC 59.404 37.037 0.00 0.00 34.70 3.46
900 1015 7.960793 ACTTGACTACAGCAAACGATAAATAC 58.039 34.615 0.00 0.00 0.00 1.89
915 1030 9.642343 AGAGTATATTGGATGTACTTGACTACA 57.358 33.333 0.00 0.00 37.33 2.74
926 1041 9.561069 GGTGTGAAATAAGAGTATATTGGATGT 57.439 33.333 0.00 0.00 0.00 3.06
927 1042 8.712363 CGGTGTGAAATAAGAGTATATTGGATG 58.288 37.037 0.00 0.00 0.00 3.51
928 1043 7.387948 GCGGTGTGAAATAAGAGTATATTGGAT 59.612 37.037 0.00 0.00 0.00 3.41
999 1114 3.139770 CCCCTGATCCATCTTCCTTCATT 59.860 47.826 0.00 0.00 0.00 2.57
1020 1135 1.677633 CGTTCCAATCCCCACACCC 60.678 63.158 0.00 0.00 0.00 4.61
1034 1149 2.547211 CAGATGCTTGATGGATCCGTTC 59.453 50.000 8.18 7.73 43.44 3.95
1035 1150 2.092753 ACAGATGCTTGATGGATCCGTT 60.093 45.455 8.18 0.00 43.44 4.44
1072 1187 2.432972 GCCAACAATGCGGCCAAG 60.433 61.111 2.24 0.00 42.82 3.61
1172 1287 2.039084 AGTGGGAGGCTTGACTTGTTAG 59.961 50.000 0.00 0.00 0.00 2.34
1197 1312 4.339247 ACATATTGGGCAAATGACTGCTAC 59.661 41.667 0.00 0.00 42.25 3.58
1252 1367 2.109126 GCAGACGGAATGTGGAGCC 61.109 63.158 0.00 0.00 0.00 4.70
1284 1399 3.806949 AGTTTTGGGGTGATCTTGCTA 57.193 42.857 0.00 0.00 0.00 3.49
1497 1612 5.711506 ACATGAGGAATGCAACACTCAAATA 59.288 36.000 17.68 0.16 42.55 1.40
1611 1726 0.036952 AGTTGATGACCAGTGGCTCG 60.037 55.000 9.78 0.00 0.00 5.03
1618 1733 2.029380 TGGTGTACGAGTTGATGACCAG 60.029 50.000 0.00 0.00 0.00 4.00
1658 1773 1.559831 GTTGCTTGGTTTCTGCACAC 58.440 50.000 0.00 0.00 36.37 3.82
1661 1776 1.034838 ACGGTTGCTTGGTTTCTGCA 61.035 50.000 0.00 0.00 34.69 4.41
1671 1786 2.616842 CAGAAACTTGGTACGGTTGCTT 59.383 45.455 3.65 0.00 31.96 3.91
1802 1917 2.612221 GGTATCGTATACAAGGGCCAGC 60.612 54.545 6.18 0.00 0.00 4.85
1947 2062 1.940613 GGATCTTACCGTGTCATTGGC 59.059 52.381 0.00 0.00 0.00 4.52
1949 2064 5.621197 TTTTGGATCTTACCGTGTCATTG 57.379 39.130 0.00 0.00 0.00 2.82
2047 2180 2.431057 AGTCGGCCAGTAACTCCAATAG 59.569 50.000 2.24 0.00 0.00 1.73
2081 2214 6.884472 TTATCAAAGTTCCCAGGACTGATA 57.116 37.500 0.00 0.00 0.00 2.15
2084 2217 6.265422 AGTTTTTATCAAAGTTCCCAGGACTG 59.735 38.462 0.00 0.00 0.00 3.51
2117 2250 3.261981 ACGGAATGGAAGGTGACATAC 57.738 47.619 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.