Multiple sequence alignment - TraesCS3D01G333300

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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 TraesCS3D01G333300 chr3D 100.000 4398 0 0 1 4398 445287113 445291510 0.000000e+00 8122.0
1 TraesCS3D01G333300 chr3D 100.000 323 0 0 4836 5158 445291948 445292270 9.560000e-167 597.0
2 TraesCS3D01G333300 chr3A 95.603 2547 60 12 1899 4398 586878885 586881426 0.000000e+00 4036.0
3 TraesCS3D01G333300 chr3A 94.031 1759 63 22 13 1741 586876011 586877757 0.000000e+00 2628.0
4 TraesCS3D01G333300 chr3A 90.556 180 3 1 4836 5015 586881521 586881686 5.200000e-55 226.0
5 TraesCS3D01G333300 chr3A 97.727 88 2 0 5049 5136 586881685 586881772 8.950000e-33 152.0
6 TraesCS3D01G333300 chr3B 96.296 2376 59 8 1903 4251 583844310 583846683 0.000000e+00 3873.0
7 TraesCS3D01G333300 chr3B 95.252 1411 52 5 2979 4380 583849594 583850998 0.000000e+00 2220.0
8 TraesCS3D01G333300 chr3B 93.902 1148 47 8 426 1567 583842637 583843767 0.000000e+00 1711.0
9 TraesCS3D01G333300 chr3B 91.749 303 14 5 1605 1907 583843953 583844244 1.340000e-110 411.0
10 TraesCS3D01G333300 chr3B 85.326 368 39 9 1 362 583842287 583842645 2.930000e-97 366.0
11 TraesCS3D01G333300 chr3B 94.068 236 14 0 4901 5136 583851290 583851525 4.910000e-95 359.0
12 TraesCS3D01G333300 chr3B 95.122 164 6 2 4973 5136 583848444 583848605 1.840000e-64 257.0
13 TraesCS3D01G333300 chr3B 95.035 141 1 2 4262 4398 583846757 583846895 3.130000e-52 217.0
14 TraesCS3D01G333300 chr3B 95.098 102 4 1 4887 4988 583847880 583847980 5.350000e-35 159.0
15 TraesCS3D01G333300 chr3B 100.000 43 0 0 1565 1607 583843788 583843830 4.280000e-11 80.5
16 TraesCS3D01G333300 chr3B 91.525 59 1 1 4836 4894 583846944 583846998 1.540000e-10 78.7


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 TraesCS3D01G333300 chr3D 445287113 445292270 5157 False 4359.500000 8122 100.00000 1 5158 2 chr3D.!!$F1 5157
1 TraesCS3D01G333300 chr3A 586876011 586881772 5761 False 1760.500000 4036 94.47925 13 5136 4 chr3A.!!$F1 5123
2 TraesCS3D01G333300 chr3B 583842287 583851525 9238 False 884.745455 3873 93.94300 1 5136 11 chr3B.!!$F1 5135

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
743 751 1.227823 CTGTCCCACGTCAAGCCAA 60.228 57.895 0.0 0.0 0.0 4.52 F
1837 2906 1.601166 ACAAAGTTGGTTCTACGGGC 58.399 50.000 0.0 0.0 0.0 6.13 F
3062 4229 0.933796 GTAGAGCGGCTGAAGATTGC 59.066 55.000 7.5 0.0 0.0 3.56 F
3797 4968 1.069978 TCCATGTTCAACTCGCTGTCA 59.930 47.619 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 3311 1.143073 AGAACGGAAAGGAAAGCACCT 59.857 47.619 0.0 0.0 42.69 4.00 R
3797 4968 2.431057 GAGGACCGTGGTGATTATCAGT 59.569 50.000 0.0 0.0 0.00 3.41 R
4007 5200 0.332632 CTTTCCCCCAGAGGAATGCA 59.667 55.000 0.0 0.0 45.30 3.96 R
5040 7667 0.732880 CCAGGTAGCGTGTTCAGTCG 60.733 60.000 0.0 0.0 0.00 4.18 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
144 145 9.515020 GACAAGATTGAAATTAAATTATCCGCA 57.485 29.630 0.00 0.00 0.00 5.69
234 235 1.954927 GAGGATAAGTTTGGCCTCGG 58.045 55.000 3.32 0.00 37.75 4.63
370 377 4.567159 GGCAGTCTGGTAGTATTTCTTTCG 59.433 45.833 1.14 0.00 0.00 3.46
401 408 1.949525 CCCTCCGCATCACCAATTAAG 59.050 52.381 0.00 0.00 0.00 1.85
402 409 2.643551 CCTCCGCATCACCAATTAAGT 58.356 47.619 0.00 0.00 0.00 2.24
403 410 3.433031 CCCTCCGCATCACCAATTAAGTA 60.433 47.826 0.00 0.00 0.00 2.24
408 415 5.105269 TCCGCATCACCAATTAAGTAGTACA 60.105 40.000 2.52 0.00 0.00 2.90
553 561 2.027625 GCGACCAACCAGAACCTCG 61.028 63.158 0.00 0.00 0.00 4.63
571 579 2.861935 CTCGGCATTTTGAAATGATGGC 59.138 45.455 18.03 9.88 46.72 4.40
688 696 2.956987 GCACTGGTGTGGATGTGC 59.043 61.111 0.00 0.00 46.66 4.57
743 751 1.227823 CTGTCCCACGTCAAGCCAA 60.228 57.895 0.00 0.00 0.00 4.52
797 806 4.248058 GGGTTTCTTGCATTGAGATTTGG 58.752 43.478 0.00 0.00 0.00 3.28
832 841 2.816672 GCAGAAAGCAAGAGCCTTAAGT 59.183 45.455 0.97 0.00 44.79 2.24
833 842 4.003648 GCAGAAAGCAAGAGCCTTAAGTA 58.996 43.478 0.97 0.00 44.79 2.24
884 893 1.891150 GCATCCCCATTTGGATAGCTG 59.109 52.381 0.00 0.00 43.39 4.24
943 953 2.357009 CAGTTTGCTCACTTTCTGCTGT 59.643 45.455 0.00 0.00 0.00 4.40
962 972 3.817084 CTGTGAAAGCATCTTCAACCTCA 59.183 43.478 0.00 0.00 37.08 3.86
1323 1341 9.617523 GTCTTATAGACTGTAGGATAGTATCCC 57.382 40.741 23.23 11.25 44.86 3.85
1347 1365 4.698304 ACTCTGTTTTGTTTGACCGAGAAA 59.302 37.500 0.00 0.00 33.19 2.52
1741 2727 5.069648 TGTTTTCCCACATGCTATGAACAAA 59.930 36.000 0.00 0.00 0.00 2.83
1743 2729 3.760738 TCCCACATGCTATGAACAAACA 58.239 40.909 0.00 0.00 0.00 2.83
1837 2906 1.601166 ACAAAGTTGGTTCTACGGGC 58.399 50.000 0.00 0.00 0.00 6.13
1892 2961 8.157476 ACATACTGATGGTCAAGTAGAAAGTTT 58.843 33.333 0.00 0.00 37.39 2.66
1964 3104 8.010540 GTCTTACATTTCGAGGAAAGAAAACTC 58.989 37.037 0.00 0.00 40.44 3.01
1967 3107 4.789095 TTTCGAGGAAAGAAAACTCACG 57.211 40.909 0.00 0.00 35.00 4.35
1985 3125 7.513190 ACTCACGAGAAATAGAAAGAAATCG 57.487 36.000 0.00 0.00 35.21 3.34
2001 3141 8.506168 AAAGAAATCGTATATCCATGTGTGTT 57.494 30.769 0.00 0.00 0.00 3.32
2058 3201 6.252015 CGAATCATGACATTTCCATGTGTTTC 59.748 38.462 0.00 0.00 44.22 2.78
2059 3202 5.045668 TCATGACATTTCCATGTGTTTCG 57.954 39.130 0.00 0.00 44.22 3.46
2060 3203 4.759183 TCATGACATTTCCATGTGTTTCGA 59.241 37.500 0.00 0.00 44.22 3.71
2143 3291 4.696877 TCGTCTCGGTTTAGTAAGACATGA 59.303 41.667 0.00 0.00 38.41 3.07
2163 3311 6.493115 ACATGAGGTGGACAAACATGAAAATA 59.507 34.615 0.00 0.00 40.13 1.40
2193 3341 9.485206 GCTTTCCTTTCCGTTCTATATATGTAA 57.515 33.333 0.00 0.00 0.00 2.41
2232 3380 4.394920 CGGCCTTGTTGTTGATGTATAACT 59.605 41.667 0.00 0.00 0.00 2.24
2279 3443 5.368230 TCACCCATACAGGAAATAGTATGCA 59.632 40.000 6.97 0.00 43.81 3.96
2511 3675 5.873179 TTGACATACGGAATTTTCTCCAC 57.127 39.130 0.00 0.00 34.91 4.02
2777 3941 5.656416 TGTCAATTTCCTTAATGTGATCCCC 59.344 40.000 0.00 0.00 0.00 4.81
2853 4017 8.870116 TCTATTAATCTGCATTGCCTAACTCTA 58.130 33.333 6.12 0.00 0.00 2.43
3062 4229 0.933796 GTAGAGCGGCTGAAGATTGC 59.066 55.000 7.50 0.00 0.00 3.56
3300 4467 5.497464 TCTGGTTCATCATACAGGTTCAA 57.503 39.130 0.00 0.00 0.00 2.69
3630 4801 3.705051 AGCAATTTGATGTGACCATCCT 58.295 40.909 0.00 0.00 45.78 3.24
3797 4968 1.069978 TCCATGTTCAACTCGCTGTCA 59.930 47.619 0.00 0.00 0.00 3.58
3845 5016 1.239296 TGCTGCTTGGCACAGATGTC 61.239 55.000 9.12 0.00 42.39 3.06
3891 5062 3.593096 TCTGTCATGTGCATCTTCAGAC 58.407 45.455 0.00 0.00 0.00 3.51
3902 5073 3.894759 CATCTTCAGACATGGGATGGTT 58.105 45.455 0.00 0.00 35.45 3.67
4007 5200 2.354503 GCTGATCATCATCGGGCTGTAT 60.355 50.000 0.00 0.00 36.06 2.29
4037 5230 0.485543 GGGGGAAAGGGAAGGAAACA 59.514 55.000 0.00 0.00 0.00 2.83
4989 7616 3.873952 GAGCTATGCCCTAGTTTTGTCTG 59.126 47.826 0.00 0.00 0.00 3.51
5030 7657 0.733150 GCCAGGCGTAGAAAATGGAC 59.267 55.000 0.00 0.00 32.55 4.02
5039 7666 2.185004 AGAAAATGGACACCTGGACG 57.815 50.000 0.00 0.00 0.00 4.79
5040 7667 0.521735 GAAAATGGACACCTGGACGC 59.478 55.000 0.00 0.00 0.00 5.19
5136 10683 3.882131 GCCAGGCCAGACAATCTAA 57.118 52.632 5.01 0.00 0.00 2.10
5137 10684 1.383523 GCCAGGCCAGACAATCTAAC 58.616 55.000 5.01 0.00 0.00 2.34
5138 10685 1.340017 GCCAGGCCAGACAATCTAACA 60.340 52.381 5.01 0.00 0.00 2.41
5139 10686 2.879756 GCCAGGCCAGACAATCTAACAA 60.880 50.000 5.01 0.00 0.00 2.83
5140 10687 3.420893 CCAGGCCAGACAATCTAACAAA 58.579 45.455 5.01 0.00 0.00 2.83
5141 10688 3.191371 CCAGGCCAGACAATCTAACAAAC 59.809 47.826 5.01 0.00 0.00 2.93
5142 10689 3.820467 CAGGCCAGACAATCTAACAAACA 59.180 43.478 5.01 0.00 0.00 2.83
5143 10690 4.074970 AGGCCAGACAATCTAACAAACAG 58.925 43.478 5.01 0.00 0.00 3.16
5144 10691 3.821033 GGCCAGACAATCTAACAAACAGT 59.179 43.478 0.00 0.00 0.00 3.55
5145 10692 4.278419 GGCCAGACAATCTAACAAACAGTT 59.722 41.667 0.00 0.00 44.27 3.16
5146 10693 5.472137 GGCCAGACAATCTAACAAACAGTTA 59.528 40.000 0.00 0.00 41.64 2.24
5147 10694 6.151144 GGCCAGACAATCTAACAAACAGTTAT 59.849 38.462 0.00 0.00 41.62 1.89
5148 10695 7.244192 GCCAGACAATCTAACAAACAGTTATC 58.756 38.462 0.00 0.00 41.62 1.75
5149 10696 7.094805 GCCAGACAATCTAACAAACAGTTATCA 60.095 37.037 0.00 0.00 41.62 2.15
5150 10697 8.446273 CCAGACAATCTAACAAACAGTTATCAG 58.554 37.037 0.00 0.00 41.62 2.90
5151 10698 8.446273 CAGACAATCTAACAAACAGTTATCAGG 58.554 37.037 0.00 0.00 41.62 3.86
5152 10699 7.119846 AGACAATCTAACAAACAGTTATCAGGC 59.880 37.037 0.00 0.00 41.62 4.85
5153 10700 6.714810 ACAATCTAACAAACAGTTATCAGGCA 59.285 34.615 0.00 0.00 41.62 4.75
5154 10701 6.743575 ATCTAACAAACAGTTATCAGGCAC 57.256 37.500 0.00 0.00 41.62 5.01
5155 10702 5.616270 TCTAACAAACAGTTATCAGGCACA 58.384 37.500 0.00 0.00 41.62 4.57
5156 10703 6.237901 TCTAACAAACAGTTATCAGGCACAT 58.762 36.000 0.00 0.00 41.62 3.21
5157 10704 4.771590 ACAAACAGTTATCAGGCACATG 57.228 40.909 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.031245 TCAAATTTGTAGGTGCGCACAG 60.031 45.455 38.60 15.78 0.00 3.66
38 39 1.218316 GGTCCTGGTCCTGTTAGCG 59.782 63.158 2.47 0.00 0.00 4.26
101 102 6.798427 TCTTGTCTAGCAGAGATTATTGGT 57.202 37.500 0.00 0.00 36.29 3.67
233 234 5.007724 CCGCTTAACTAAAACCTGATGATCC 59.992 44.000 0.00 0.00 0.00 3.36
234 235 5.504173 GCCGCTTAACTAAAACCTGATGATC 60.504 44.000 0.00 0.00 0.00 2.92
370 377 2.710902 GCGGAGGGAACAATTGGGC 61.711 63.158 10.83 0.66 0.00 5.36
401 408 9.668497 AGAGGTTTATGGAAATTCTTGTACTAC 57.332 33.333 0.00 0.00 0.00 2.73
402 409 9.667107 CAGAGGTTTATGGAAATTCTTGTACTA 57.333 33.333 0.00 0.00 0.00 1.82
403 410 7.611855 CCAGAGGTTTATGGAAATTCTTGTACT 59.388 37.037 0.00 0.00 37.94 2.73
408 415 6.794534 ACTCCAGAGGTTTATGGAAATTCTT 58.205 36.000 0.00 0.00 43.77 2.52
416 423 4.762289 AGCTTACTCCAGAGGTTTATGG 57.238 45.455 0.00 0.00 37.01 2.74
553 561 2.940410 CTGGCCATCATTTCAAAATGCC 59.060 45.455 5.51 8.55 44.15 4.40
582 590 3.834610 CGTCTTGACGGTCTTCTATGTT 58.165 45.455 14.53 0.00 0.00 2.71
717 725 2.821366 CGTGGGACAGATGCCTGC 60.821 66.667 0.00 0.00 44.16 4.85
743 751 6.490040 TGGAAAGAAACAAAAGCTAGCTATGT 59.510 34.615 23.44 23.44 0.00 2.29
900 910 8.243961 ACTGATCTATGTAGAGTAAATGCACT 57.756 34.615 0.00 0.00 35.50 4.40
914 924 6.370994 CAGAAAGTGAGCAAACTGATCTATGT 59.629 38.462 0.00 0.00 33.24 2.29
943 953 4.090761 ACTGAGGTTGAAGATGCTTTCA 57.909 40.909 0.00 0.00 35.38 2.69
962 972 3.193263 CTGCAGCTTGATCAATCGTACT 58.807 45.455 8.96 0.00 0.00 2.73
1323 1341 3.621268 TCTCGGTCAAACAAAACAGAGTG 59.379 43.478 0.00 0.00 38.40 3.51
1477 1496 6.515272 ACTTCAGTGAACATGAACAAAACT 57.485 33.333 0.08 0.00 33.28 2.66
1478 1497 8.856490 AATACTTCAGTGAACATGAACAAAAC 57.144 30.769 0.08 0.00 33.28 2.43
1837 2906 3.355378 TGCCTATGTGGGTGAAATGAAG 58.645 45.455 0.00 0.00 36.00 3.02
1892 2961 4.998671 TTGGTGCTTCTTTTCACAATCA 57.001 36.364 0.00 0.00 35.04 2.57
1985 3125 9.811995 TCTAACACTTAACACACATGGATATAC 57.188 33.333 0.00 0.00 0.00 1.47
1994 3134 8.902540 ATCATTCTTCTAACACTTAACACACA 57.097 30.769 0.00 0.00 0.00 3.72
2143 3291 5.243730 CACCTATTTTCATGTTTGTCCACCT 59.756 40.000 0.00 0.00 0.00 4.00
2163 3311 1.143073 AGAACGGAAAGGAAAGCACCT 59.857 47.619 0.00 0.00 42.69 4.00
2193 3341 5.163301 ACAAGGCCGATTGATGTATCTAACT 60.163 40.000 11.47 0.00 34.20 2.24
2232 3380 3.138304 AGATCAGCAGCAACGTTTTACA 58.862 40.909 0.00 0.00 0.00 2.41
2279 3443 3.815401 CCAACAAGAAAGTTCGACCTGAT 59.185 43.478 0.00 0.00 0.00 2.90
2511 3675 7.359262 TCAGTCATGGTAAGTGTAAAATTCG 57.641 36.000 0.00 0.00 0.00 3.34
2777 3941 4.685169 AGCAATGATAAAGGTGACAACG 57.315 40.909 0.00 0.00 0.00 4.10
2853 4017 8.575649 AATAACTACTCCATCCGTTTTGAAAT 57.424 30.769 0.00 0.00 0.00 2.17
3797 4968 2.431057 GAGGACCGTGGTGATTATCAGT 59.569 50.000 0.00 0.00 0.00 3.41
3839 5010 0.415429 ACCTCCCCACAGAGACATCT 59.585 55.000 0.00 0.00 35.82 2.90
3845 5016 1.209019 CATTCTCACCTCCCCACAGAG 59.791 57.143 0.00 0.00 0.00 3.35
3891 5062 3.800949 GCATTGCATACAACCATCCCATG 60.801 47.826 3.15 0.00 38.99 3.66
4007 5200 0.332632 CTTTCCCCCAGAGGAATGCA 59.667 55.000 0.00 0.00 45.30 3.96
4037 5230 1.727511 TTTGCTTGCGCTGCTCTTGT 61.728 50.000 22.08 0.00 36.97 3.16
5030 7657 2.022129 GTTCAGTCGCGTCCAGGTG 61.022 63.158 5.77 0.00 0.00 4.00
5040 7667 0.732880 CCAGGTAGCGTGTTCAGTCG 60.733 60.000 0.00 0.00 0.00 4.18
5136 10683 4.771590 CATGTGCCTGATAACTGTTTGT 57.228 40.909 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.