Multiple sequence alignment - TraesCS3B01G040200

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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 TraesCS3B01G040200 chr3B 100.000 3312 0 0 1 3312 19733451 19736762 0.000000e+00 6117
1 TraesCS3B01G040200 chr3D 95.204 2231 62 13 1097 3312 13553391 13555591 0.000000e+00 3485
2 TraesCS3B01G040200 chr3D 95.095 734 21 10 330 1056 13552671 13553396 0.000000e+00 1142
3 TraesCS3B01G040200 chr3D 94.152 342 6 3 1 342 13552314 13552641 2.950000e-140 508
4 TraesCS3B01G040200 chr3A 91.595 2558 95 42 330 2845 23477113 23474634 0.000000e+00 3422
5 TraesCS3B01G040200 chr3A 90.244 492 15 8 2841 3312 23474586 23474108 2.180000e-171 612
6 TraesCS3B01G040200 chr3A 88.764 356 10 19 1 338 23477784 23477441 3.080000e-110 409


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 TraesCS3B01G040200 chr3B 19733451 19736762 3311 False 6117.000000 6117 100.000 1 3312 1 chr3B.!!$F1 3311
1 TraesCS3B01G040200 chr3D 13552314 13555591 3277 False 1711.666667 3485 94.817 1 3312 3 chr3D.!!$F1 3311
2 TraesCS3B01G040200 chr3A 23474108 23477784 3676 True 1481.000000 3422 90.201 1 3312 3 chr3A.!!$R1 3311

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
836 1229 0.178068 ACACACTCCACACCACTGAC 59.822 55.000 0.0 0.0 0.0 3.51 F
983 1379 0.246086 CTCTCACACCACTGCTCTCC 59.754 60.000 0.0 0.0 0.0 3.71 F
1953 2370 1.153823 CGGCCGTCTCGATTCTTGT 60.154 57.895 19.5 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 2713 0.461163 TGTATCATTGCGTCACCGGG 60.461 55.0 6.32 0.0 33.68 5.73 R
2297 2714 0.930310 CTGTATCATTGCGTCACCGG 59.070 55.0 0.00 0.0 33.68 5.28 R
3120 3611 0.755327 ACCGGCCAGCCCATAATTTC 60.755 55.0 0.00 0.0 0.00 2.17 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
102 103 5.704978 TGTGTTTGCTTGCACAAGATCTATA 59.295 36.000 14.44 0.00 41.89 1.31
116 136 8.786898 CACAAGATCTATAAAGAGAGAGAGAGG 58.213 40.741 0.00 0.00 34.49 3.69
117 137 7.944554 ACAAGATCTATAAAGAGAGAGAGAGGG 59.055 40.741 0.00 0.00 34.49 4.30
118 138 7.032598 AGATCTATAAAGAGAGAGAGAGGGG 57.967 44.000 0.00 0.00 34.49 4.79
119 139 5.592587 TCTATAAAGAGAGAGAGAGGGGG 57.407 47.826 0.00 0.00 0.00 5.40
155 175 6.208204 GGCTTACTCCATTAATGATTCATGCT 59.792 38.462 17.23 0.00 0.00 3.79
178 198 1.225799 GAGTCGTCGTCTCAGCGTC 60.226 63.158 13.56 0.00 32.79 5.19
262 282 1.072331 CTTTCCTGCCTAGTGTGGTGT 59.928 52.381 0.00 0.00 0.00 4.16
342 703 3.650281 ATGCAGACTCTCTCTCTCTCA 57.350 47.619 0.00 0.00 0.00 3.27
362 731 4.033709 TCACTAGGAGATGAAGAAAGGGG 58.966 47.826 0.00 0.00 0.00 4.79
385 754 4.740334 GCCAAGAGAGAGAAAGGATAGCAG 60.740 50.000 0.00 0.00 0.00 4.24
492 861 3.584848 AGAGGGATCTAGAGAGAGAGAGC 59.415 52.174 0.00 0.00 34.35 4.09
525 894 7.039313 TGTAGATGTACTAGCATTGTAGGTG 57.961 40.000 1.30 0.00 0.00 4.00
526 895 5.537300 AGATGTACTAGCATTGTAGGTGG 57.463 43.478 0.00 0.00 0.00 4.61
625 998 3.028130 CTCTCTCTCTCCACCTAAACCC 58.972 54.545 0.00 0.00 0.00 4.11
836 1229 0.178068 ACACACTCCACACCACTGAC 59.822 55.000 0.00 0.00 0.00 3.51
922 1316 2.414785 CCGGCCCCTTCCAAAATCG 61.415 63.158 0.00 0.00 0.00 3.34
947 1343 5.007430 CCATTGCATCATAGAGTGTTCAGTC 59.993 44.000 0.00 0.00 0.00 3.51
959 1355 1.668751 TGTTCAGTCGTTGCTGTTTCC 59.331 47.619 0.00 0.00 37.70 3.13
983 1379 0.246086 CTCTCACACCACTGCTCTCC 59.754 60.000 0.00 0.00 0.00 3.71
1060 1456 3.604582 CCTCATCACTTTCCCTTGTCTC 58.395 50.000 0.00 0.00 0.00 3.36
1088 1489 7.835822 TGTTATTGTTCATCCCCATGTTTTAG 58.164 34.615 0.00 0.00 0.00 1.85
1098 1499 6.134535 TCCCCATGTTTTAGTTGTACATCT 57.865 37.500 11.11 11.11 30.45 2.90
1125 1531 3.753272 TGAAACACTATTCTCCTTGCTGC 59.247 43.478 0.00 0.00 0.00 5.25
1194 1600 8.480643 AACTAGTTGCATATCAGTACACTTTC 57.519 34.615 7.48 0.00 0.00 2.62
1395 1805 8.421002 TGTATGAATCTCCATGAACTAATCGAA 58.579 33.333 0.00 0.00 0.00 3.71
1409 1819 8.783093 TGAACTAATCGAATGTTTTCAACTCAT 58.217 29.630 0.00 0.00 0.00 2.90
1486 1896 2.507992 CAAGCCGTGGAGAGCTCG 60.508 66.667 8.37 0.00 38.74 5.03
1604 2014 7.340999 TCTTGCATAGAGGTACTAACATGTACA 59.659 37.037 0.00 0.00 41.55 2.90
1791 2204 6.043411 CACAACCCTAGCTAGATGTTACTTC 58.957 44.000 22.70 0.00 0.00 3.01
1823 2240 6.648879 TGCAAAGCTGGTAATCTTACTTTT 57.351 33.333 0.00 0.00 34.16 2.27
1953 2370 1.153823 CGGCCGTCTCGATTCTTGT 60.154 57.895 19.50 0.00 0.00 3.16
2123 2540 4.003788 CGAGCCACCACCCGTTCT 62.004 66.667 0.00 0.00 0.00 3.01
2699 3119 5.542616 TTTGTGTGCTCATTTTGGTTTTG 57.457 34.783 0.00 0.00 0.00 2.44
2831 3252 9.107177 TCAGTTAAAACAGGTTACACGAAATTA 57.893 29.630 0.00 0.00 0.00 1.40
2943 3422 5.588648 CCATTGTCAACGACTAAACCCATAT 59.411 40.000 0.00 0.00 33.15 1.78
3076 3567 5.010415 TGGCATGTCAATGTCACATTAAACA 59.990 36.000 16.32 16.32 43.45 2.83
3120 3611 3.440173 AGTCAACCAATGTAAAGATGGCG 59.560 43.478 0.00 0.00 37.77 5.69
3129 3620 6.642131 CCAATGTAAAGATGGCGAAATTATGG 59.358 38.462 0.00 0.00 0.00 2.74
3146 3637 2.503382 GGGCTGGCCGGTTCAAAAA 61.503 57.895 14.55 0.00 36.85 1.94
3174 3665 9.979270 CTATGAGAAAAACTATAGTGTTTGCTG 57.021 33.333 23.02 7.22 39.71 4.41
3205 3696 4.236527 ACCCTTTGGATTATGGACAGTC 57.763 45.455 0.00 0.00 34.81 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 139 4.484872 GTAAGCCACGCCTCCCCC 62.485 72.222 0.00 0.00 0.00 5.40
120 140 3.387225 GAGTAAGCCACGCCTCCCC 62.387 68.421 0.00 0.00 0.00 4.81
121 141 2.187163 GAGTAAGCCACGCCTCCC 59.813 66.667 0.00 0.00 0.00 4.30
122 142 1.972660 ATGGAGTAAGCCACGCCTCC 61.973 60.000 9.69 0.00 46.63 4.30
155 175 2.360852 GAGACGACGACTCCCCCA 60.361 66.667 15.12 0.00 0.00 4.96
285 305 6.162079 GTGAATCTGATCTCTGTGTTTGAGA 58.838 40.000 0.00 0.00 43.59 3.27
327 347 4.649674 TCTCCTAGTGAGAGAGAGAGAGTC 59.350 50.000 6.79 0.00 45.29 3.36
328 348 4.620723 TCTCCTAGTGAGAGAGAGAGAGT 58.379 47.826 6.79 0.00 45.29 3.24
342 703 2.774809 GCCCCTTTCTTCATCTCCTAGT 59.225 50.000 0.00 0.00 0.00 2.57
358 727 1.284313 CTTTCTCTCTCTTGGCCCCT 58.716 55.000 0.00 0.00 0.00 4.79
362 731 3.133721 TGCTATCCTTTCTCTCTCTTGGC 59.866 47.826 0.00 0.00 0.00 4.52
492 861 3.620929 AGTACATCTACATACACCGCG 57.379 47.619 0.00 0.00 0.00 6.46
525 894 1.333619 GTCACACACATTCACACACCC 59.666 52.381 0.00 0.00 0.00 4.61
526 895 2.013400 TGTCACACACATTCACACACC 58.987 47.619 0.00 0.00 0.00 4.16
625 998 6.018262 GTGTGTAGAGATAGAGTGCACTAGAG 60.018 46.154 21.73 0.00 0.00 2.43
772 1157 0.556380 AGAGGGAGGGGGAGAGAGAA 60.556 60.000 0.00 0.00 0.00 2.87
836 1229 2.066262 GGTGGTGTGTTCAGTACATCG 58.934 52.381 0.00 0.00 39.39 3.84
922 1316 3.628942 TGAACACTCTATGATGCAATGGC 59.371 43.478 0.00 0.00 41.68 4.40
947 1343 1.001406 AGAGGAGAGGAAACAGCAACG 59.999 52.381 0.00 0.00 0.00 4.10
959 1355 0.246086 GCAGTGGTGTGAGAGGAGAG 59.754 60.000 0.00 0.00 0.00 3.20
983 1379 2.677289 ATGGTGGAGCAGGAGCAGG 61.677 63.158 0.00 0.00 45.49 4.85
1038 1434 2.307098 AGACAAGGGAAAGTGATGAGGG 59.693 50.000 0.00 0.00 0.00 4.30
1039 1435 3.604582 GAGACAAGGGAAAGTGATGAGG 58.395 50.000 0.00 0.00 0.00 3.86
1060 1456 4.157656 ACATGGGGATGAACAATAACAACG 59.842 41.667 0.00 0.00 0.00 4.10
1088 1489 8.764524 ATAGTGTTTCAGAAGAGATGTACAAC 57.235 34.615 0.00 0.00 0.00 3.32
1098 1499 5.934625 GCAAGGAGAATAGTGTTTCAGAAGA 59.065 40.000 0.00 0.00 0.00 2.87
1125 1531 7.038659 AGAGAAGAGGATGAATAAACAAGACG 58.961 38.462 0.00 0.00 0.00 4.18
1183 1589 7.865385 GGAGCTTATGATAGAGAAAGTGTACTG 59.135 40.741 0.00 0.00 0.00 2.74
1194 1600 4.202295 TGGCAACAGGAGCTTATGATAGAG 60.202 45.833 6.15 0.00 46.17 2.43
1409 1819 1.271926 GCTCCCTTGTTGCCTCCTTTA 60.272 52.381 0.00 0.00 0.00 1.85
1520 1930 0.390124 TTCTTACTGGTTGCGTCGGT 59.610 50.000 0.00 0.00 0.00 4.69
1564 1974 6.417258 TCTATGCAAGACCATCTTCAAATCA 58.583 36.000 0.00 0.00 33.78 2.57
1578 1988 6.791867 ACATGTTAGTACCTCTATGCAAGA 57.208 37.500 0.00 0.00 0.00 3.02
1604 2014 3.833650 TCCCTGATGAAACACATTTGCAT 59.166 39.130 0.00 0.00 39.56 3.96
1791 2204 0.815734 CCAGCTTTGCATGGAAGAGG 59.184 55.000 0.00 0.00 39.02 3.69
1823 2240 0.707024 TCTCCCTCTCTGAGCCAAGA 59.293 55.000 0.00 0.00 0.00 3.02
1953 2370 5.445964 GCCATGGAAAAACCCTAATCTCTA 58.554 41.667 18.40 0.00 38.00 2.43
2293 2710 4.402528 CATTGCGTCACCGGGGGA 62.403 66.667 2.42 0.00 33.68 4.81
2294 2711 2.318519 TATCATTGCGTCACCGGGGG 62.319 60.000 2.42 0.00 33.68 5.40
2295 2712 1.145156 TATCATTGCGTCACCGGGG 59.855 57.895 6.32 0.00 33.68 5.73
2296 2713 0.461163 TGTATCATTGCGTCACCGGG 60.461 55.000 6.32 0.00 33.68 5.73
2297 2714 0.930310 CTGTATCATTGCGTCACCGG 59.070 55.000 0.00 0.00 33.68 5.28
2301 2718 1.009078 GCTGCTGTATCATTGCGTCA 58.991 50.000 0.00 0.00 0.00 4.35
2538 2958 6.316390 AGAGATATCCAAAAACTTAACAGCCG 59.684 38.462 0.00 0.00 0.00 5.52
2699 3119 1.205417 CATCAATTGGGGCAAGTCCAC 59.795 52.381 5.42 0.00 39.32 4.02
2802 3223 4.510340 CGTGTAACCTGTTTTAACTGAGCT 59.490 41.667 0.00 0.00 0.00 4.09
3076 3567 2.029623 GCAGAGCCCATGTCAAATCAT 58.970 47.619 0.00 0.00 0.00 2.45
3120 3611 0.755327 ACCGGCCAGCCCATAATTTC 60.755 55.000 0.00 0.00 0.00 2.17
3129 3620 3.133946 TTTTTGAACCGGCCAGCC 58.866 55.556 0.00 0.00 0.00 4.85
3147 3638 9.726438 AGCAAACACTATAGTTTTTCTCATAGT 57.274 29.630 12.96 0.00 39.55 2.12
3148 3639 9.979270 CAGCAAACACTATAGTTTTTCTCATAG 57.021 33.333 12.96 4.15 39.55 2.23
3149 3640 8.450964 GCAGCAAACACTATAGTTTTTCTCATA 58.549 33.333 12.96 0.00 39.55 2.15
3150 3641 7.040478 TGCAGCAAACACTATAGTTTTTCTCAT 60.040 33.333 12.96 0.00 39.55 2.90
3151 3642 6.262049 TGCAGCAAACACTATAGTTTTTCTCA 59.738 34.615 12.96 7.05 39.55 3.27
3152 3643 6.578919 GTGCAGCAAACACTATAGTTTTTCTC 59.421 38.462 12.96 8.83 39.55 2.87
3153 3644 6.263168 AGTGCAGCAAACACTATAGTTTTTCT 59.737 34.615 12.96 10.68 46.32 2.52
3154 3645 6.360681 CAGTGCAGCAAACACTATAGTTTTTC 59.639 38.462 12.96 9.01 46.44 2.29
3155 3646 6.039270 TCAGTGCAGCAAACACTATAGTTTTT 59.961 34.615 10.56 10.56 46.44 1.94
3156 3647 5.530915 TCAGTGCAGCAAACACTATAGTTTT 59.469 36.000 1.56 0.00 46.44 2.43
3157 3648 5.063204 TCAGTGCAGCAAACACTATAGTTT 58.937 37.500 1.56 0.00 46.44 2.66
3174 3665 2.561478 TCCAAAGGGTACTTCAGTGC 57.439 50.000 0.00 0.00 35.41 4.40


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

AutoCloner maintained by Alex Coulton.