Multiple sequence alignment - TraesCS1A01G067900

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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 TraesCS1A01G067900 chr1A 100.000 2454 0 0 1 2454 49360360 49362813 0.000000e+00 4532
1 TraesCS1A01G067900 chr1A 100.000 1147 0 0 2848 3994 49363207 49364353 0.000000e+00 2119
2 TraesCS1A01G067900 chr1D 93.147 2291 67 28 225 2451 50191870 50194134 0.000000e+00 3278
3 TraesCS1A01G067900 chr1D 92.602 1149 50 10 2848 3994 50194270 50195385 0.000000e+00 1618
4 TraesCS1A01G067900 chr1D 90.789 228 15 4 1 226 50191615 50191838 2.330000e-77 300
5 TraesCS1A01G067900 chr1B 92.169 2158 86 34 348 2454 70706262 70708387 0.000000e+00 2972
6 TraesCS1A01G067900 chr1B 93.062 1153 62 12 2848 3994 70708714 70709854 0.000000e+00 1670
7 TraesCS1A01G067900 chr1B 90.909 231 7 8 1 226 70705770 70705991 8.390000e-77 298
8 TraesCS1A01G067900 chr1B 94.355 124 2 3 225 347 70706023 70706142 6.820000e-43 185


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 TraesCS1A01G067900 chr1A 49360360 49364353 3993 False 3325.50 4532 100.000000 1 3994 2 chr1A.!!$F1 3993
1 TraesCS1A01G067900 chr1D 50191615 50195385 3770 False 1732.00 3278 92.179333 1 3994 3 chr1D.!!$F1 3993
2 TraesCS1A01G067900 chr1B 70705770 70709854 4084 False 1281.25 2972 92.623750 1 3994 4 chr1B.!!$F1 3993

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
422 588 0.535780 TGTGGACTGGCTGAGCTTTG 60.536 55.0 3.72 0.0 0.00 2.77 F
967 1167 0.543883 AGAACAGAGCAGGAGCAGGA 60.544 55.0 0.00 0.0 45.49 3.86 F
2424 2643 0.608130 GATGTTTGGTTTCAGCCCCC 59.392 55.0 0.00 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2202 1.590932 CACCCAGACTGCATGATAGC 58.409 55.000 0.0 0.0 0.00 2.97 R
2947 3166 0.462047 GAACCATCGCCACCTGTAGG 60.462 60.000 0.0 0.0 42.17 3.18 R
3886 4108 1.342174 TCCTTACCAGACAACCACGTC 59.658 52.381 0.0 0.0 36.08 4.34 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
30 33 3.523972 ACCCTCCTTCCATCTTTTCTACC 59.476 47.826 0.00 0.00 0.00 3.18
47 50 4.842574 TCTACCTGCATGCAAAGTGATAA 58.157 39.130 25.69 10.57 0.00 1.75
55 58 4.327898 GCATGCAAAGTGATAATGGTTGTG 59.672 41.667 14.21 0.00 0.00 3.33
60 63 5.106869 GCAAAGTGATAATGGTTGTGTCGTA 60.107 40.000 0.00 0.00 0.00 3.43
61 64 6.403200 GCAAAGTGATAATGGTTGTGTCGTAT 60.403 38.462 0.00 0.00 0.00 3.06
62 65 7.201574 GCAAAGTGATAATGGTTGTGTCGTATA 60.202 37.037 0.00 0.00 0.00 1.47
63 66 8.826710 CAAAGTGATAATGGTTGTGTCGTATAT 58.173 33.333 0.00 0.00 0.00 0.86
114 117 2.736719 CGTGCACTCTGATGTAAGGAGG 60.737 54.545 16.19 0.00 0.00 4.30
127 135 5.746990 TGTAAGGAGGAGAAGAAGAAAGG 57.253 43.478 0.00 0.00 0.00 3.11
244 285 3.383761 GGCCATAATTCCGATGCTTTTG 58.616 45.455 0.00 0.00 0.00 2.44
284 325 3.164268 CCAAACATGGAAATCTGTGGGA 58.836 45.455 0.00 0.00 0.00 4.37
380 543 9.875708 ATCCTTGTTTATTGGTATTATAAGGCA 57.124 29.630 0.00 0.00 33.84 4.75
391 557 6.881065 TGGTATTATAAGGCATGATGCTCTTC 59.119 38.462 17.84 0.00 44.28 2.87
422 588 0.535780 TGTGGACTGGCTGAGCTTTG 60.536 55.000 3.72 0.00 0.00 2.77
426 592 1.339438 GGACTGGCTGAGCTTTGATGA 60.339 52.381 3.72 0.00 0.00 2.92
428 594 3.015327 GACTGGCTGAGCTTTGATGAAT 58.985 45.455 3.72 0.00 0.00 2.57
429 595 2.753452 ACTGGCTGAGCTTTGATGAATG 59.247 45.455 3.72 0.00 0.00 2.67
432 598 2.751259 GGCTGAGCTTTGATGAATGTGA 59.249 45.455 3.72 0.00 0.00 3.58
586 756 4.041723 CGAAAGCTTGAACCGAAACAAAT 58.958 39.130 0.00 0.00 0.00 2.32
591 761 6.822073 AGCTTGAACCGAAACAAATTAAAC 57.178 33.333 0.00 0.00 0.00 2.01
602 772 7.738176 CCGAAACAAATTAAACAAATAAAGGCG 59.262 33.333 0.00 0.00 0.00 5.52
709 902 1.250328 CATTGCAGGGACACACACAT 58.750 50.000 0.00 0.00 0.00 3.21
710 903 2.435422 CATTGCAGGGACACACACATA 58.565 47.619 0.00 0.00 0.00 2.29
743 936 3.191371 CACCAGGATGCAAAAGTAGTTCC 59.809 47.826 0.00 0.00 31.97 3.62
754 947 2.861147 AGTAGTTCCTCCAAGGCAAC 57.139 50.000 0.00 0.00 34.61 4.17
766 959 2.476821 CAAGGCAACAAGAAAGGCAAG 58.523 47.619 0.00 0.00 41.41 4.01
835 1028 6.038603 CCAATCAGTAGAAGAGAGAGTGAGAG 59.961 46.154 0.00 0.00 0.00 3.20
836 1029 5.755409 TCAGTAGAAGAGAGAGTGAGAGT 57.245 43.478 0.00 0.00 0.00 3.24
837 1030 5.487433 TCAGTAGAAGAGAGAGTGAGAGTG 58.513 45.833 0.00 0.00 0.00 3.51
838 1031 5.247337 TCAGTAGAAGAGAGAGTGAGAGTGA 59.753 44.000 0.00 0.00 0.00 3.41
872 1065 5.334802 GCCAAATCAAATTAAGGGCAACAAC 60.335 40.000 0.00 0.00 39.66 3.32
873 1066 5.762218 CCAAATCAAATTAAGGGCAACAACA 59.238 36.000 0.00 0.00 39.74 3.33
874 1067 6.261826 CCAAATCAAATTAAGGGCAACAACAA 59.738 34.615 0.00 0.00 39.74 2.83
898 1091 1.204941 CCAAGAACACCGTAGCTAGCT 59.795 52.381 23.12 23.12 0.00 3.32
899 1092 2.426024 CCAAGAACACCGTAGCTAGCTA 59.574 50.000 20.67 20.67 0.00 3.32
900 1093 3.068307 CCAAGAACACCGTAGCTAGCTAT 59.932 47.826 26.59 10.30 0.00 2.97
901 1094 4.291783 CAAGAACACCGTAGCTAGCTATC 58.708 47.826 26.59 18.15 0.00 2.08
928 1121 5.669164 TCATATAAACCAAACCAAAGGCC 57.331 39.130 0.00 0.00 0.00 5.19
929 1122 5.087323 TCATATAAACCAAACCAAAGGCCA 58.913 37.500 5.01 0.00 0.00 5.36
930 1123 5.544176 TCATATAAACCAAACCAAAGGCCAA 59.456 36.000 5.01 0.00 0.00 4.52
967 1167 0.543883 AGAACAGAGCAGGAGCAGGA 60.544 55.000 0.00 0.00 45.49 3.86
977 1177 0.977108 AGGAGCAGGAGAAGGAGCAG 60.977 60.000 0.00 0.00 0.00 4.24
1449 1664 3.998672 GTCGTCGGGTCCAAGGCA 61.999 66.667 0.00 0.00 0.00 4.75
1548 1763 2.164219 CACCGGTCCATTTTCTTCCATG 59.836 50.000 2.59 0.00 0.00 3.66
1571 1786 3.701205 TGCTCCTCTTGCTATTTGTCA 57.299 42.857 0.00 0.00 0.00 3.58
1603 1818 5.130292 TCAGCACTTGTAGTTGTAGTACC 57.870 43.478 0.00 0.00 0.00 3.34
1615 1830 7.817478 TGTAGTTGTAGTACCACAGAATTGATG 59.183 37.037 7.22 0.00 0.00 3.07
1631 1850 7.876582 CAGAATTGATGATCTGAACTATAGCCA 59.123 37.037 0.00 0.00 44.64 4.75
1646 1865 4.970662 ATAGCCAGCACAAACATAACAG 57.029 40.909 0.00 0.00 0.00 3.16
1822 2041 1.697982 ACCCAGTAAAGAGTGTGACCC 59.302 52.381 0.00 0.00 0.00 4.46
1886 2105 8.354426 CAAACTAGGTCTACTAAATCTCTAGCC 58.646 40.741 0.00 0.00 0.00 3.93
1925 2144 2.497675 TCCTGCACCTCTGCTACTTTAG 59.502 50.000 0.00 0.00 44.57 1.85
1983 2202 8.556194 TGCTAAAATTACTAATGGAACTATGCG 58.444 33.333 0.00 0.00 0.00 4.73
2384 2603 4.362279 TCTGTTTGATTGCTGCTTTTCAC 58.638 39.130 0.00 0.00 0.00 3.18
2424 2643 0.608130 GATGTTTGGTTTCAGCCCCC 59.392 55.000 0.00 0.00 0.00 5.40
2920 3139 2.098117 GTGGCCATCTATTTGCTGTGAC 59.902 50.000 9.72 0.00 0.00 3.67
2932 3151 4.893424 TTGCTGTGACTTTTCTAACACC 57.107 40.909 0.00 0.00 33.08 4.16
2941 3160 5.761234 TGACTTTTCTAACACCGCTTTATGT 59.239 36.000 0.00 0.00 0.00 2.29
2984 3203 0.685131 TCCGCGATAGGAGGGAACAA 60.685 55.000 8.23 0.00 36.06 2.83
2986 3205 1.287425 CGCGATAGGAGGGAACAAAC 58.713 55.000 0.00 0.00 0.00 2.93
3000 3219 3.119209 GGAACAAACGTACTAGGCTAGCT 60.119 47.826 21.26 11.01 0.00 3.32
3003 3222 5.848833 ACAAACGTACTAGGCTAGCTATT 57.151 39.130 21.26 8.09 0.00 1.73
3146 3365 5.304686 AGTACAAGATGGTGAAGTGGAAA 57.695 39.130 0.00 0.00 0.00 3.13
3173 3392 7.713507 GCATGTGTAGTTTATCCAGTATTGGTA 59.286 37.037 3.93 0.00 45.26 3.25
3174 3393 9.261180 CATGTGTAGTTTATCCAGTATTGGTAG 57.739 37.037 3.93 0.00 45.26 3.18
3175 3394 8.598202 TGTGTAGTTTATCCAGTATTGGTAGA 57.402 34.615 3.93 0.00 45.26 2.59
3329 3548 3.838795 CCATGTTTTGGTCATGCCC 57.161 52.632 4.07 0.00 40.99 5.36
3397 3616 5.958380 TCTAAGACAGGCTCTCCATCTTTAA 59.042 40.000 6.29 0.00 39.42 1.52
3403 3622 3.118956 AGGCTCTCCATCTTTAACACTCG 60.119 47.826 0.00 0.00 33.74 4.18
3418 3637 2.994995 TCGTGGCATGGACCGTCT 60.995 61.111 6.90 0.00 0.00 4.18
3428 3647 4.097892 GGCATGGACCGTCTTATTTTGAAT 59.902 41.667 0.00 0.00 0.00 2.57
3584 3806 6.674694 AAAGTGCAGTGATCATCTACAATC 57.325 37.500 0.00 0.00 0.00 2.67
3646 3868 4.098155 TCCACTATGGTAGCCAAAGTGTA 58.902 43.478 13.83 0.62 39.03 2.90
3709 3931 7.763071 TGAAAGAGAAGTGATGTCATGTCTATG 59.237 37.037 0.00 0.00 35.57 2.23
3805 4027 2.582052 TGTTTTGGCCTGTCTACCTTG 58.418 47.619 3.32 0.00 0.00 3.61
3817 4039 6.647067 GCCTGTCTACCTTGTGATATGATTAC 59.353 42.308 0.00 0.00 0.00 1.89
3831 4053 3.926058 TGATTACCCCTAAACTGAGGC 57.074 47.619 0.00 0.00 35.00 4.70
3832 4054 3.460825 TGATTACCCCTAAACTGAGGCT 58.539 45.455 0.00 0.00 35.00 4.58
3863 4085 1.620819 GACAGGCTCTCCAACTTCAGA 59.379 52.381 0.00 0.00 33.74 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 33 4.380841 ACCATTATCACTTTGCATGCAG 57.619 40.909 21.50 13.01 0.00 4.41
47 50 5.865085 AGCCATAATATACGACACAACCAT 58.135 37.500 0.00 0.00 0.00 3.55
114 117 2.040412 TGGCCCTTCCTTTCTTCTTCTC 59.960 50.000 0.00 0.00 35.26 2.87
127 135 2.124695 GGACGACCATGGCCCTTC 60.125 66.667 13.04 7.16 35.97 3.46
168 176 5.104900 ACACATAAACACAGGAGATAGGTCC 60.105 44.000 0.00 0.00 36.79 4.46
244 285 0.595095 GCATCGATTCTCCATTGCCC 59.405 55.000 0.00 0.00 0.00 5.36
375 538 4.279145 AGAATTGAAGAGCATCATGCCTT 58.721 39.130 5.84 9.50 46.52 4.35
377 540 4.650754 AAGAATTGAAGAGCATCATGCC 57.349 40.909 5.84 0.00 46.52 4.40
379 542 7.228906 ACAGGATAAGAATTGAAGAGCATCATG 59.771 37.037 0.00 0.00 37.82 3.07
380 543 7.228906 CACAGGATAAGAATTGAAGAGCATCAT 59.771 37.037 0.00 0.00 37.82 2.45
391 557 3.629398 GCCAGTCCACAGGATAAGAATTG 59.371 47.826 0.00 0.00 32.73 2.32
437 603 2.901839 AGGAAGCACTGCCATTTTCATT 59.098 40.909 0.00 0.00 0.00 2.57
438 604 2.532843 AGGAAGCACTGCCATTTTCAT 58.467 42.857 0.00 0.00 0.00 2.57
586 756 6.479331 GGTGGTTTTCGCCTTTATTTGTTTAA 59.521 34.615 0.00 0.00 42.62 1.52
591 761 3.738791 GTGGTGGTTTTCGCCTTTATTTG 59.261 43.478 0.00 0.00 46.01 2.32
602 772 3.586100 AATAATGCCGTGGTGGTTTTC 57.414 42.857 0.00 0.00 41.21 2.29
644 837 0.179051 TGGCTTTGGCTTTGGCTTTG 60.179 50.000 0.00 0.00 38.73 2.77
645 838 0.107268 CTGGCTTTGGCTTTGGCTTT 59.893 50.000 0.00 0.00 38.73 3.51
646 839 1.750297 CTGGCTTTGGCTTTGGCTT 59.250 52.632 0.00 0.00 38.73 4.35
647 840 2.875804 GCTGGCTTTGGCTTTGGCT 61.876 57.895 0.00 0.00 38.73 4.75
648 841 2.357881 GCTGGCTTTGGCTTTGGC 60.358 61.111 0.00 0.00 38.73 4.52
649 842 0.035739 AATGCTGGCTTTGGCTTTGG 59.964 50.000 0.00 0.00 38.73 3.28
709 902 1.110518 TCCTGGTGACTGTGCGTGTA 61.111 55.000 0.00 0.00 0.00 2.90
710 903 1.758440 ATCCTGGTGACTGTGCGTGT 61.758 55.000 0.00 0.00 0.00 4.49
743 936 1.000171 GCCTTTCTTGTTGCCTTGGAG 60.000 52.381 0.00 0.00 0.00 3.86
766 959 2.341176 CCTGGTGCAAAGCAAGCC 59.659 61.111 0.00 0.00 41.47 4.35
835 1028 3.141398 TGATTTGGCTTGTCTCACTCAC 58.859 45.455 0.00 0.00 0.00 3.51
836 1029 3.490439 TGATTTGGCTTGTCTCACTCA 57.510 42.857 0.00 0.00 0.00 3.41
837 1030 4.836125 TTTGATTTGGCTTGTCTCACTC 57.164 40.909 0.00 0.00 0.00 3.51
838 1031 5.796424 AATTTGATTTGGCTTGTCTCACT 57.204 34.783 0.00 0.00 0.00 3.41
872 1065 2.069273 CTACGGTGTTCTTGGCTCTTG 58.931 52.381 0.00 0.00 0.00 3.02
873 1066 1.608283 GCTACGGTGTTCTTGGCTCTT 60.608 52.381 0.00 0.00 0.00 2.85
874 1067 0.037232 GCTACGGTGTTCTTGGCTCT 60.037 55.000 0.00 0.00 0.00 4.09
900 1093 9.142014 CCTTTGGTTTGGTTTATATGATATGGA 57.858 33.333 0.00 0.00 0.00 3.41
901 1094 7.872483 GCCTTTGGTTTGGTTTATATGATATGG 59.128 37.037 0.00 0.00 0.00 2.74
928 1121 0.876399 TATGTGCACTGCTGCTGTTG 59.124 50.000 19.41 7.02 44.57 3.33
929 1122 1.538512 CTTATGTGCACTGCTGCTGTT 59.461 47.619 19.41 0.00 44.57 3.16
930 1123 1.162698 CTTATGTGCACTGCTGCTGT 58.837 50.000 19.41 6.33 44.57 4.40
967 1167 2.037385 AGGTTCTTCCTGCTCCTTCT 57.963 50.000 0.00 0.00 46.19 2.85
1224 1439 3.083349 TAGAGCCACAGCGCCCAT 61.083 61.111 2.29 0.00 46.67 4.00
1338 1553 1.814527 GTACTCCCTGTACGGCCTG 59.185 63.158 0.00 0.00 41.58 4.85
1449 1664 1.754234 GTTGGCGATCTTGGGGCAT 60.754 57.895 0.00 0.00 38.59 4.40
1548 1763 4.216257 TGACAAATAGCAAGAGGAGCAAAC 59.784 41.667 0.00 0.00 0.00 2.93
1603 1818 8.710551 GCTATAGTTCAGATCATCAATTCTGTG 58.289 37.037 0.84 0.00 40.22 3.66
1615 1830 4.327982 TGTGCTGGCTATAGTTCAGATC 57.672 45.455 21.40 15.18 0.00 2.75
1631 1850 6.389830 TTGACAATCTGTTATGTTTGTGCT 57.610 33.333 0.00 0.00 32.17 4.40
1822 2041 2.383855 TGGGTTCAAACTTTGTCCTGG 58.616 47.619 13.76 0.00 0.00 4.45
1983 2202 1.590932 CACCCAGACTGCATGATAGC 58.409 55.000 0.00 0.00 0.00 2.97
2384 2603 5.443185 TCTGAAGAGAAAACAAATGCCAG 57.557 39.130 0.00 0.00 0.00 4.85
2424 2643 4.873817 TGAGACTGTGGAAATGCATTTTG 58.126 39.130 24.81 14.70 0.00 2.44
2920 3139 7.924103 AAAACATAAAGCGGTGTTAGAAAAG 57.076 32.000 0.00 0.00 37.56 2.27
2947 3166 0.462047 GAACCATCGCCACCTGTAGG 60.462 60.000 0.00 0.00 42.17 3.18
2984 3203 4.467769 TCCAATAGCTAGCCTAGTACGTT 58.532 43.478 12.13 0.00 0.00 3.99
2986 3205 4.519730 AGTTCCAATAGCTAGCCTAGTACG 59.480 45.833 12.13 0.00 0.00 3.67
3110 3329 7.126421 ACCATCTTGTACTTTCCTCATACTGAT 59.874 37.037 0.00 0.00 0.00 2.90
3146 3365 6.767902 CCAATACTGGATAAACTACACATGCT 59.232 38.462 0.00 0.00 46.92 3.79
3329 3548 8.465999 GGTCTACTGATATCATATCAGAAGGTG 58.534 40.741 32.82 19.35 46.25 4.00
3397 3616 2.347490 GGTCCATGCCACGAGTGT 59.653 61.111 2.36 0.00 0.00 3.55
3403 3622 2.038387 AATAAGACGGTCCATGCCAC 57.962 50.000 4.14 0.00 0.00 5.01
3428 3647 8.514594 CCACTATCTAAAGTGCTTTCAAATCAA 58.485 33.333 0.00 0.00 44.56 2.57
3557 3779 5.764686 TGTAGATGATCACTGCACTTTTTGT 59.235 36.000 0.00 0.00 0.00 2.83
3558 3780 6.245115 TGTAGATGATCACTGCACTTTTTG 57.755 37.500 0.00 0.00 0.00 2.44
3683 3905 6.106648 AGACATGACATCACTTCTCTTTCA 57.893 37.500 0.00 0.00 0.00 2.69
3709 3931 5.407407 TGACTCTCTGTGGATTTTACTCC 57.593 43.478 0.00 0.00 35.74 3.85
3805 4027 7.162082 CCTCAGTTTAGGGGTAATCATATCAC 58.838 42.308 0.00 0.00 32.55 3.06
3817 4039 3.370633 GGTTTAGAGCCTCAGTTTAGGGG 60.371 52.174 0.00 0.00 37.11 4.79
3886 4108 1.342174 TCCTTACCAGACAACCACGTC 59.658 52.381 0.00 0.00 36.08 4.34
3887 4109 1.416243 TCCTTACCAGACAACCACGT 58.584 50.000 0.00 0.00 0.00 4.49
3888 4110 2.536761 TTCCTTACCAGACAACCACG 57.463 50.000 0.00 0.00 0.00 4.94
3947 4172 6.417191 TCGTTACATTATTCTGCCTTGAAC 57.583 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.