Multiple sequence alignment - TraesCS3D01G241900

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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 TraesCS3D01G241900 chr3D 100.000 4275 0 0 1 4275 336595096 336590822 0.000000e+00 7895.0
1 TraesCS3D01G241900 chr3A 96.010 3784 116 16 457 4224 453939179 453935415 0.000000e+00 6119.0
2 TraesCS3D01G241900 chr3A 92.510 494 17 15 1 475 453939685 453939193 0.000000e+00 689.0
3 TraesCS3D01G241900 chr3A 96.364 55 1 1 4220 4274 453935172 453935119 5.890000e-14 89.8
4 TraesCS3D01G241900 chr3B 95.903 2221 61 6 155 2355 434427384 434425174 0.000000e+00 3570.0
5 TraesCS3D01G241900 chr3B 94.430 1885 63 17 2351 4224 434425062 434423209 0.000000e+00 2861.0
6 TraesCS3D01G241900 chr3B 98.347 121 1 1 1 120 434427795 434427675 1.200000e-50 211.0


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 TraesCS3D01G241900 chr3D 336590822 336595096 4274 True 7895.000000 7895 100.000000 1 4275 1 chr3D.!!$R1 4274
1 TraesCS3D01G241900 chr3A 453935119 453939685 4566 True 2299.266667 6119 94.961333 1 4274 3 chr3A.!!$R1 4273
2 TraesCS3D01G241900 chr3B 434423209 434427795 4586 True 2214.000000 3570 96.226667 1 4224 3 chr3B.!!$R1 4223

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
402 660 0.031721 GGGCGTCCTATCAAGGTACG 59.968 60.0 0.00 10.21 44.09 3.67 F
1163 1474 0.035458 AGGAAGAACAAGGCCGTGAG 59.965 55.0 26.25 5.42 0.00 3.51 F
2536 2965 0.304705 CCGACGCAAGCCATATCAAC 59.695 55.0 0.00 0.00 45.62 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1307 1618 2.028020 GTCTCTTCCAAGGGTGGTACAG 60.028 54.545 0.0 0.0 46.11 2.74 R
3126 3559 2.158682 TGTGGCAAGAGTAAAAGCTCCA 60.159 45.455 0.0 0.0 36.20 3.86 R
4174 4623 0.033699 AAAGAGATGGGAGCCTTGCC 60.034 55.000 0.0 0.0 34.91 4.52 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
120 122 1.062488 ACACTGCAACCCCTTCTCCT 61.062 55.000 0.00 0.00 0.00 3.69
121 123 0.322008 CACTGCAACCCCTTCTCCTC 60.322 60.000 0.00 0.00 0.00 3.71
122 124 1.301293 CTGCAACCCCTTCTCCTCC 59.699 63.158 0.00 0.00 0.00 4.30
123 125 1.151810 TGCAACCCCTTCTCCTCCT 60.152 57.895 0.00 0.00 0.00 3.69
124 126 1.201429 TGCAACCCCTTCTCCTCCTC 61.201 60.000 0.00 0.00 0.00 3.71
125 127 1.916206 GCAACCCCTTCTCCTCCTCC 61.916 65.000 0.00 0.00 0.00 4.30
135 137 1.550374 TCCTCCTCCTCCTCCCCTT 60.550 63.158 0.00 0.00 0.00 3.95
207 465 0.878961 GCTGTGTTCGTCTTTCCGGT 60.879 55.000 0.00 0.00 0.00 5.28
392 650 2.742116 GGCTGGATTGGGCGTCCTA 61.742 63.158 7.97 0.00 36.68 2.94
402 660 0.031721 GGGCGTCCTATCAAGGTACG 59.968 60.000 0.00 10.21 44.09 3.67
528 818 0.804364 TCTTGCGATTCATGGTGTGC 59.196 50.000 0.00 0.00 0.00 4.57
532 822 1.996786 GCGATTCATGGTGTGCTGGG 61.997 60.000 0.00 0.00 0.00 4.45
608 898 3.544285 TGCGTGTTTCGTTTGATGTTTTC 59.456 39.130 0.00 0.00 42.13 2.29
609 899 3.789224 GCGTGTTTCGTTTGATGTTTTCT 59.211 39.130 0.00 0.00 42.13 2.52
610 900 4.264380 GCGTGTTTCGTTTGATGTTTTCTT 59.736 37.500 0.00 0.00 42.13 2.52
707 1016 0.968405 TGATTGGTTTGCTTGCTCCC 59.032 50.000 0.00 0.00 0.00 4.30
711 1020 1.905354 GGTTTGCTTGCTCCCAGCT 60.905 57.895 0.00 0.00 42.97 4.24
858 1169 2.408565 CTACCTTGGATTCCCCTGCTA 58.591 52.381 0.00 0.00 35.38 3.49
998 1309 1.401670 CGTCAGACCAACCGAAGAGAG 60.402 57.143 0.00 0.00 0.00 3.20
1134 1445 4.758688 TGTTCATCATAGTACTGTGGCTG 58.241 43.478 18.32 15.44 0.00 4.85
1163 1474 0.035458 AGGAAGAACAAGGCCGTGAG 59.965 55.000 26.25 5.42 0.00 3.51
1307 1618 6.785488 TGACAAATACACACAGATGAAGAC 57.215 37.500 0.00 0.00 0.00 3.01
1317 1628 2.567615 ACAGATGAAGACTGTACCACCC 59.432 50.000 0.00 0.00 45.10 4.61
1347 1658 3.070446 AGACTAGATCTCTCGACGTGGAT 59.930 47.826 0.00 0.00 28.16 3.41
1862 2173 7.598869 GGTGACACATTTCTTCCCTTTATTTTC 59.401 37.037 8.08 0.00 0.00 2.29
1874 2186 7.480760 TCCCTTTATTTTCCTTTCATCTTGG 57.519 36.000 0.00 0.00 0.00 3.61
1968 2280 1.134965 CCGCTAGACTTCCTGTTCTGG 60.135 57.143 0.00 0.00 0.00 3.86
2049 2361 4.892655 TCGTTTTGCGATAATGCTAGTTG 58.107 39.130 0.00 0.00 45.68 3.16
2355 2667 5.089411 CACATGAGACTGTTGACTAGTACG 58.911 45.833 0.00 0.00 0.00 3.67
2536 2965 0.304705 CCGACGCAAGCCATATCAAC 59.695 55.000 0.00 0.00 45.62 3.18
2621 3050 1.952990 TGCTTTTGGAAACGCATCTCA 59.047 42.857 0.00 0.00 38.10 3.27
2633 3062 4.264460 ACGCATCTCATAATCTTCCTCC 57.736 45.455 0.00 0.00 0.00 4.30
2786 3219 2.169352 GCAGATGAGGTAGAGGCAAAGA 59.831 50.000 0.00 0.00 0.00 2.52
3093 3526 8.335532 CCAAGAAGTATGTTGGTTTCTTATCA 57.664 34.615 0.00 0.00 43.31 2.15
3094 3527 8.960591 CCAAGAAGTATGTTGGTTTCTTATCAT 58.039 33.333 0.00 0.00 43.31 2.45
3095 3528 9.994432 CAAGAAGTATGTTGGTTTCTTATCATC 57.006 33.333 0.00 0.00 37.68 2.92
3102 3535 5.533154 TGTTGGTTTCTTATCATCCGTGTTT 59.467 36.000 0.00 0.00 0.00 2.83
3120 3553 4.396790 GTGTTTTCTGTGTCTTTACCACCA 59.603 41.667 0.00 0.00 31.71 4.17
3124 3557 6.385649 TTTCTGTGTCTTTACCACCAAATC 57.614 37.500 0.00 0.00 31.71 2.17
3126 3559 5.690865 TCTGTGTCTTTACCACCAAATCTT 58.309 37.500 0.00 0.00 31.71 2.40
3127 3560 5.530915 TCTGTGTCTTTACCACCAAATCTTG 59.469 40.000 0.00 0.00 31.71 3.02
3243 3676 0.525242 CTAGAGTCGCAGCAGTCAGC 60.525 60.000 0.00 0.00 46.19 4.26
3314 3748 4.967084 ACCCAAAACAAATAGGAAACCC 57.033 40.909 0.00 0.00 0.00 4.11
3449 3884 0.599558 GTGCAAGCTGCTCATTTCCA 59.400 50.000 1.00 0.00 45.31 3.53
3497 3937 2.639839 GGATTGCTTCTATGCTCCCCTA 59.360 50.000 0.00 0.00 0.00 3.53
3498 3938 3.307339 GGATTGCTTCTATGCTCCCCTAG 60.307 52.174 0.00 0.00 0.00 3.02
3609 4049 0.037790 AGCAAGCACTCTCTTCGTCC 60.038 55.000 0.00 0.00 0.00 4.79
3796 4244 4.081697 CCTTATTTACTTGTGGCCAAAGGG 60.082 45.833 23.11 12.53 37.18 3.95
3797 4245 2.463047 TTTACTTGTGGCCAAAGGGT 57.537 45.000 23.11 16.58 36.17 4.34
3798 4246 1.698506 TTACTTGTGGCCAAAGGGTG 58.301 50.000 23.11 8.52 36.17 4.61
3811 4259 2.358247 GGGTGGTCACGCGATTGT 60.358 61.111 15.93 0.00 34.59 2.71
3824 4272 1.965930 GATTGTGCGTGCAGGGTGA 60.966 57.895 8.72 0.00 0.00 4.02
3844 4292 2.544844 TATCTTCCACGGGAGAACCT 57.455 50.000 0.00 0.00 36.97 3.50
3869 4317 4.377897 GAACACCTGCAGTACACTTACTT 58.622 43.478 13.81 0.00 36.31 2.24
4174 4623 2.670905 TCACAAATCTACGCACCATTCG 59.329 45.455 0.00 0.00 0.00 3.34
4185 4634 2.830370 CCATTCGGCAAGGCTCCC 60.830 66.667 0.00 0.00 0.00 4.30
4187 4636 1.454479 CATTCGGCAAGGCTCCCAT 60.454 57.895 5.20 0.00 0.00 4.00
4208 4657 6.458210 CCATCTCTTTTTAGGTGCACAAATT 58.542 36.000 20.43 3.39 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 122 2.647949 GGGAAGGGGAGGAGGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
121 123 2.040359 GGGAAGGGGAGGAGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
122 124 0.253394 AAAGGGAAGGGGAGGAGGAG 60.253 60.000 0.00 0.00 0.00 3.69
123 125 0.550147 CAAAGGGAAGGGGAGGAGGA 60.550 60.000 0.00 0.00 0.00 3.71
124 126 2.002625 CAAAGGGAAGGGGAGGAGG 58.997 63.158 0.00 0.00 0.00 4.30
125 127 1.210885 AGCAAAGGGAAGGGGAGGAG 61.211 60.000 0.00 0.00 0.00 3.69
135 137 2.041216 GAGTAAAGGGGAAGCAAAGGGA 59.959 50.000 0.00 0.00 0.00 4.20
187 445 1.487231 CGGAAAGACGAACACAGCG 59.513 57.895 0.00 0.00 35.47 5.18
207 465 2.675371 TCGGCGAGAGAGAGGGAA 59.325 61.111 4.99 0.00 0.00 3.97
304 562 1.603739 AGAACCAGAAAAGCCCGGC 60.604 57.895 0.00 0.00 0.00 6.13
346 604 1.026718 CAGGGATTCCGTCAACAGGC 61.027 60.000 0.00 0.00 38.33 4.85
402 660 4.265893 GGGGAGAAGGAAGAATCAAGAAC 58.734 47.826 0.00 0.00 0.00 3.01
528 818 1.032114 GGATTTCAGTTCCGGCCCAG 61.032 60.000 0.00 0.00 0.00 4.45
532 822 2.369394 AGAATGGATTTCAGTTCCGGC 58.631 47.619 0.00 0.00 36.75 6.13
610 900 4.240175 ACCGCGCATAAAAAGGTAAAAA 57.760 36.364 8.75 0.00 32.76 1.94
858 1169 3.897505 ACCAAGAAAAAGGTGCATTAGCT 59.102 39.130 0.00 0.00 42.74 3.32
917 1228 2.230266 GCCGTTTGCTGGAGGAATTTAA 59.770 45.455 0.00 0.00 36.87 1.52
918 1229 1.816224 GCCGTTTGCTGGAGGAATTTA 59.184 47.619 0.00 0.00 36.87 1.40
919 1230 0.603065 GCCGTTTGCTGGAGGAATTT 59.397 50.000 0.00 0.00 36.87 1.82
920 1231 0.539438 TGCCGTTTGCTGGAGGAATT 60.539 50.000 0.00 0.00 42.00 2.17
921 1232 1.074775 TGCCGTTTGCTGGAGGAAT 59.925 52.632 0.00 0.00 42.00 3.01
922 1233 1.896660 GTGCCGTTTGCTGGAGGAA 60.897 57.895 0.00 0.00 42.00 3.36
929 1240 1.598130 GAGTCCTGTGCCGTTTGCT 60.598 57.895 0.00 0.00 42.00 3.91
1134 1445 2.762535 TGTTCTTCCTTCGGATGGAC 57.237 50.000 11.82 2.91 36.32 4.02
1158 1469 0.098200 TAGTGTCGAATCCGCTCACG 59.902 55.000 0.00 0.00 41.36 4.35
1163 1474 1.121240 CGATGTAGTGTCGAATCCGC 58.879 55.000 0.00 0.00 41.40 5.54
1307 1618 2.028020 GTCTCTTCCAAGGGTGGTACAG 60.028 54.545 0.00 0.00 46.11 2.74
1909 2221 3.895998 TGCACAAGGTGGATGCATTATA 58.104 40.909 0.00 0.00 44.17 0.98
2047 2359 4.873746 TGACAGGAAAAACACAAACCAA 57.126 36.364 0.00 0.00 0.00 3.67
2049 2361 5.043248 CAGATGACAGGAAAAACACAAACC 58.957 41.667 0.00 0.00 0.00 3.27
2089 2401 3.490419 CGGAGTCGTTTATCTGGTAAGGG 60.490 52.174 0.00 0.00 0.00 3.95
2536 2965 4.577693 CCATATGTTCCCATCACTCTTGTG 59.422 45.833 1.24 0.00 45.07 3.33
2614 3043 4.285517 TCAGGGAGGAAGATTATGAGATGC 59.714 45.833 0.00 0.00 0.00 3.91
2621 3050 6.579214 ACCTATCATCAGGGAGGAAGATTAT 58.421 40.000 0.00 0.00 40.29 1.28
2633 3062 2.868662 CGCGACATACCTATCATCAGG 58.131 52.381 0.00 0.00 41.87 3.86
3093 3526 4.514066 GGTAAAGACACAGAAAACACGGAT 59.486 41.667 0.00 0.00 0.00 4.18
3094 3527 3.872771 GGTAAAGACACAGAAAACACGGA 59.127 43.478 0.00 0.00 0.00 4.69
3095 3528 3.623960 TGGTAAAGACACAGAAAACACGG 59.376 43.478 0.00 0.00 0.00 4.94
3102 3535 5.690865 AGATTTGGTGGTAAAGACACAGAA 58.309 37.500 0.00 0.00 40.54 3.02
3120 3553 5.047731 GGCAAGAGTAAAAGCTCCAAGATTT 60.048 40.000 0.00 0.00 35.00 2.17
3124 3557 3.057946 GTGGCAAGAGTAAAAGCTCCAAG 60.058 47.826 0.00 0.00 36.20 3.61
3126 3559 2.158682 TGTGGCAAGAGTAAAAGCTCCA 60.159 45.455 0.00 0.00 36.20 3.86
3127 3560 2.504367 TGTGGCAAGAGTAAAAGCTCC 58.496 47.619 0.00 0.00 36.20 4.70
3243 3676 2.935201 GCACTGTTTGATAGCTCCTCTG 59.065 50.000 0.00 0.00 0.00 3.35
3314 3748 8.932945 TCAGCTGTCACTATCAAATAACTTAG 57.067 34.615 14.67 0.00 0.00 2.18
3408 3842 5.048713 CACCTAACTGAATTCAACAACCTCC 60.049 44.000 9.88 0.00 0.00 4.30
3549 3989 8.664211 AAGAAGACTAGACAAAACACTAAAGG 57.336 34.615 0.00 0.00 0.00 3.11
3609 4049 5.105752 GGTAGCTCACTGACAATAACTCAG 58.894 45.833 0.00 0.00 40.97 3.35
3748 4196 3.131396 CTCACAAGGTACACCAACAGAC 58.869 50.000 0.38 0.00 38.89 3.51
3796 4244 2.173382 GCACAATCGCGTGACCAC 59.827 61.111 5.77 0.00 39.34 4.16
3811 4259 0.541392 AAGATATCACCCTGCACGCA 59.459 50.000 5.32 0.00 0.00 5.24
3824 4272 3.047695 AGGTTCTCCCGTGGAAGATAT 57.952 47.619 0.00 0.00 38.74 1.63
3844 4292 2.605257 AGTGTACTGCAGGTGTTCCTA 58.395 47.619 19.93 0.00 43.07 2.94
3869 4317 1.619654 CAGCTCATTCCCCACAACAA 58.380 50.000 0.00 0.00 0.00 2.83
3936 4384 1.533625 TTCGCAATCAAAGGTGGGAG 58.466 50.000 0.00 0.00 37.89 4.30
3940 4389 3.963665 TCAGTTTTCGCAATCAAAGGTG 58.036 40.909 0.00 0.00 0.00 4.00
4069 4518 5.124617 GTCCATTAGAAAAAGGAGGAAGCTG 59.875 44.000 0.00 0.00 33.26 4.24
4070 4519 5.257262 GTCCATTAGAAAAAGGAGGAAGCT 58.743 41.667 0.00 0.00 33.26 3.74
4071 4520 4.399618 GGTCCATTAGAAAAAGGAGGAAGC 59.600 45.833 0.00 0.00 33.26 3.86
4072 4521 5.570320 TGGTCCATTAGAAAAAGGAGGAAG 58.430 41.667 0.00 0.00 33.26 3.46
4073 4522 5.592587 TGGTCCATTAGAAAAAGGAGGAA 57.407 39.130 0.00 0.00 33.26 3.36
4074 4523 5.796502 ATGGTCCATTAGAAAAAGGAGGA 57.203 39.130 0.00 0.00 33.26 3.71
4174 4623 0.033699 AAAGAGATGGGAGCCTTGCC 60.034 55.000 0.00 0.00 34.91 4.52
4185 4634 7.951530 AAATTTGTGCACCTAAAAAGAGATG 57.048 32.000 15.69 0.00 0.00 2.90
4187 4636 9.474920 CATAAAATTTGTGCACCTAAAAAGAGA 57.525 29.630 15.69 0.00 0.00 3.10
4208 4657 9.941664 GTACTAGCAACTACTTATCGACATAAA 57.058 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.