Multiple sequence alignment - TraesCS1B01G476300

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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 TraesCS1B01G476300 chr1B 100.000 3315 0 0 1 3315 685170908 685167594 0.000000e+00 6122
1 TraesCS1B01G476300 chr1B 88.579 718 76 4 1695 2409 685179537 685178823 0.000000e+00 867
2 TraesCS1B01G476300 chr1A 93.572 3158 115 30 193 3315 590834136 590831032 0.000000e+00 4626
3 TraesCS1B01G476300 chr1A 86.823 979 108 15 1447 2414 590863337 590862369 0.000000e+00 1074
4 TraesCS1B01G476300 chr1A 94.643 168 9 0 1 168 590834377 590834210 9.120000e-66 261
5 TraesCS1B01G476300 chr1D 94.925 2916 108 15 420 3315 492502177 492499282 0.000000e+00 4529
6 TraesCS1B01G476300 chr1D 87.718 977 100 14 1447 2414 492513556 492512591 0.000000e+00 1122
7 TraesCS1B01G476300 chr1D 91.919 198 11 4 197 392 492502369 492502175 4.210000e-69 272
8 TraesCS1B01G476300 chr1D 94.048 168 10 0 1 168 492502619 492502452 4.240000e-64 255


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 TraesCS1B01G476300 chr1B 685167594 685170908 3314 True 6122.000000 6122 100.000000 1 3315 1 chr1B.!!$R1 3314
1 TraesCS1B01G476300 chr1B 685178823 685179537 714 True 867.000000 867 88.579000 1695 2409 1 chr1B.!!$R2 714
2 TraesCS1B01G476300 chr1A 590831032 590834377 3345 True 2443.500000 4626 94.107500 1 3315 2 chr1A.!!$R2 3314
3 TraesCS1B01G476300 chr1A 590862369 590863337 968 True 1074.000000 1074 86.823000 1447 2414 1 chr1A.!!$R1 967
4 TraesCS1B01G476300 chr1D 492499282 492502619 3337 True 1685.333333 4529 93.630667 1 3315 3 chr1D.!!$R2 3314
5 TraesCS1B01G476300 chr1D 492512591 492513556 965 True 1122.000000 1122 87.718000 1447 2414 1 chr1D.!!$R1 967

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
24 25 0.321564 TGTCTTTGGCCTGGTCGATG 60.322 55.0 3.32 0.00 0.0 3.84 F
97 98 0.605589 GTTTCCTTCCCCACCACGAG 60.606 60.0 0.00 0.00 0.0 4.18 F
1117 1185 0.766131 TTCGTCCAAGGGCCTTAACA 59.234 50.0 20.44 2.36 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1185 0.036164 TCATTAGTGCAAGCCGGTGT 59.964 50.0 1.9 0.0 0.00 4.16 R
1120 1188 0.099436 GCTTCATTAGTGCAAGCCGG 59.901 55.0 0.0 0.0 34.89 6.13 R
2730 2831 0.243907 TACACTTCTCACAGCTCCGC 59.756 55.0 0.0 0.0 0.00 5.54 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
24 25 0.321564 TGTCTTTGGCCTGGTCGATG 60.322 55.000 3.32 0.00 0.00 3.84
44 45 9.043079 GTCGATGTATATATCAGACGGAATAGA 57.957 37.037 9.79 0.00 0.00 1.98
97 98 0.605589 GTTTCCTTCCCCACCACGAG 60.606 60.000 0.00 0.00 0.00 4.18
103 104 2.485479 CCTTCCCCACCACGAGAATATG 60.485 54.545 0.00 0.00 0.00 1.78
110 111 2.168521 CACCACGAGAATATGTCAGGGT 59.831 50.000 0.00 0.00 0.00 4.34
134 135 4.349342 AGGAAGGGAGCAGATCGAATTATT 59.651 41.667 0.00 0.00 0.00 1.40
168 169 7.197017 TCATAAAACTAGATGTTCTCTCGAGC 58.803 38.462 7.81 0.00 38.03 5.03
170 171 5.590530 AAACTAGATGTTCTCTCGAGCAT 57.409 39.130 7.81 5.18 42.77 3.79
171 172 6.701145 AAACTAGATGTTCTCTCGAGCATA 57.299 37.500 7.81 0.00 40.58 3.14
172 173 6.892658 AACTAGATGTTCTCTCGAGCATAT 57.107 37.500 7.81 5.38 40.58 1.78
173 174 7.987750 AACTAGATGTTCTCTCGAGCATATA 57.012 36.000 7.81 6.28 40.58 0.86
179 193 6.641169 TGTTCTCTCGAGCATATAGAATGT 57.359 37.500 14.43 0.00 0.00 2.71
185 199 9.320352 TCTCTCGAGCATATAGAATGTCTATAC 57.680 37.037 7.81 0.00 42.71 1.47
189 203 9.178758 TCGAGCATATAGAATGTCTATACATGT 57.821 33.333 2.69 2.69 45.79 3.21
190 204 9.794685 CGAGCATATAGAATGTCTATACATGTT 57.205 33.333 2.30 3.15 45.79 2.71
214 269 1.528076 TGCGTGTGGGTGCATCTTT 60.528 52.632 0.00 0.00 35.90 2.52
300 361 4.214993 ACTGAACCCCAGCCTATATAGT 57.785 45.455 8.92 0.00 46.81 2.12
315 376 7.126421 AGCCTATATAGTACCAATTCCATGAGG 59.874 40.741 8.92 0.00 0.00 3.86
430 491 4.373116 GTGTCGGCCGGAGCAAGA 62.373 66.667 27.83 0.00 42.56 3.02
432 493 4.373116 GTCGGCCGGAGCAAGACA 62.373 66.667 27.83 0.00 43.45 3.41
450 511 1.275291 ACAGCTACATGTACGTGCCTT 59.725 47.619 15.12 0.00 0.00 4.35
465 526 2.125512 CTTCGTCTCCCCAAGCCG 60.126 66.667 0.00 0.00 0.00 5.52
470 531 4.082523 TCTCCCCAAGCCGAAGCG 62.083 66.667 0.00 0.00 46.67 4.68
653 717 2.499289 TCTCTAGCCTTCTTCCTTGCAG 59.501 50.000 0.00 0.00 0.00 4.41
700 764 9.559732 CTGATATTATGGTTTTGTGAGTGGATA 57.440 33.333 0.00 0.00 0.00 2.59
725 789 1.611491 ACATTGCCAATTCGTCGGTTT 59.389 42.857 0.00 0.00 0.00 3.27
921 986 3.745799 TCTGTTGATACGGCTTTGGAAA 58.254 40.909 0.00 0.00 0.00 3.13
1003 1071 3.441222 TCACAAGCTGAATGTTGCTATGG 59.559 43.478 0.00 0.00 38.75 2.74
1062 1130 3.131577 GGTGTATCACCGAGAACCATACA 59.868 47.826 3.12 0.00 44.95 2.29
1082 1150 3.891366 ACAGAGAGGGAACATTTTGTTGG 59.109 43.478 0.00 0.00 41.28 3.77
1117 1185 0.766131 TTCGTCCAAGGGCCTTAACA 59.234 50.000 20.44 2.36 0.00 2.41
1120 1188 1.244816 GTCCAAGGGCCTTAACACAC 58.755 55.000 20.44 7.42 0.00 3.82
1121 1189 0.111639 TCCAAGGGCCTTAACACACC 59.888 55.000 20.44 0.00 0.00 4.16
1159 1227 3.056107 AGCAGAGCGTCCAAGTAACATAA 60.056 43.478 0.00 0.00 0.00 1.90
1173 1241 8.915654 CCAAGTAACATAATGTTTTGCTCTTTC 58.084 33.333 0.00 0.00 41.45 2.62
1186 1254 6.942532 TTTGCTCTTTCACAACATAGACTT 57.057 33.333 0.00 0.00 0.00 3.01
1387 1460 6.742109 ACGTAGAATTGCACGGTTATACTAT 58.258 36.000 11.78 0.00 42.35 2.12
1493 1566 2.435059 GCTGGCGTTGTCTCTCCC 60.435 66.667 0.00 0.00 0.00 4.30
1531 1605 3.937814 AGCATTGTGGTAATTGTCTCGA 58.062 40.909 0.00 0.00 0.00 4.04
1584 1659 9.881414 GCGCTTTAACTTATTTTATTAGCAAAC 57.119 29.630 0.00 0.00 0.00 2.93
1707 1786 3.565482 GGAAGACACTCATTTGTTGCAGA 59.435 43.478 0.00 0.00 0.00 4.26
1744 1823 1.592400 CCACCGTAGCCTCTGTCGAA 61.592 60.000 0.00 0.00 0.00 3.71
1831 1910 3.078594 ACAAAGAACAACGGTTGCATC 57.921 42.857 20.20 17.53 37.36 3.91
1844 1923 0.037447 TTGCATCGGTGGTCATTCCA 59.963 50.000 0.00 0.00 45.01 3.53
2083 2162 7.293073 ACAATTACAAAGGAGGCATCATAGAT 58.707 34.615 0.00 0.00 0.00 1.98
2167 2246 1.216977 CGGTTATGGCACGGACTCA 59.783 57.895 0.00 0.00 0.00 3.41
2302 2382 3.706698 CACATATCCGGCAGTATATCCG 58.293 50.000 0.00 4.63 44.89 4.18
2409 2493 7.601886 CCATGCAACCTCTTCTATATTGTAGAG 59.398 40.741 11.93 11.93 35.11 2.43
2523 2607 6.146347 GCCACGCCAAAATGTTTTTCTTATAA 59.854 34.615 0.00 0.00 0.00 0.98
2526 2610 8.707839 CACGCCAAAATGTTTTTCTTATAATGT 58.292 29.630 0.00 0.00 0.00 2.71
2683 2772 8.783660 TCTAAGGAGTTGTACAATATGATCCT 57.216 34.615 12.26 15.27 37.53 3.24
2712 2813 4.121317 CAAGATTTTTGGCAAGACAAGCA 58.879 39.130 0.00 0.00 0.00 3.91
2730 2831 3.209410 AGCAAAGAGAATATTCCGCTGG 58.791 45.455 11.92 7.42 0.00 4.85
2933 3034 2.670934 CTGGTGTGCTGCCCTGAC 60.671 66.667 0.00 0.00 0.00 3.51
3186 3290 4.876107 GGGTAAACCACACTCACATAGATG 59.124 45.833 0.81 0.00 39.85 2.90
3187 3291 5.338056 GGGTAAACCACACTCACATAGATGA 60.338 44.000 0.81 0.00 39.85 2.92
3188 3292 6.349300 GGTAAACCACACTCACATAGATGAT 58.651 40.000 0.00 0.00 35.64 2.45
3189 3293 7.418597 GGGTAAACCACACTCACATAGATGATA 60.419 40.741 0.81 0.00 39.85 2.15
3190 3294 7.653713 GGTAAACCACACTCACATAGATGATAG 59.346 40.741 0.00 0.00 35.64 2.08
3191 3295 7.423844 AAACCACACTCACATAGATGATAGA 57.576 36.000 0.00 0.00 0.00 1.98
3192 3296 7.609097 AACCACACTCACATAGATGATAGAT 57.391 36.000 0.00 0.00 0.00 1.98
3193 3297 7.225784 ACCACACTCACATAGATGATAGATC 57.774 40.000 0.00 0.00 0.00 2.75
3194 3298 6.779539 ACCACACTCACATAGATGATAGATCA 59.220 38.462 0.00 0.00 41.70 2.92
3230 3334 4.409570 CATGCTTGCAACATCTTGACTAC 58.590 43.478 10.38 0.00 0.00 2.73
3232 3336 2.813754 GCTTGCAACATCTTGACTACCA 59.186 45.455 0.00 0.00 0.00 3.25
3248 3352 5.129650 TGACTACCAATCATCATTACCCGAA 59.870 40.000 0.00 0.00 0.00 4.30
3249 3353 5.996644 ACTACCAATCATCATTACCCGAAA 58.003 37.500 0.00 0.00 0.00 3.46
3250 3354 6.419791 ACTACCAATCATCATTACCCGAAAA 58.580 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.737427 CACCATTCTATTCCGTCTGATATATAC 57.263 37.037 0.00 0.00 0.00 1.47
44 45 0.908198 GGAGGACTCTGAGCACCATT 59.092 55.000 18.85 4.34 0.00 3.16
97 98 4.232091 TCCCTTCCTACCCTGACATATTC 58.768 47.826 0.00 0.00 0.00 1.75
103 104 0.617820 TGCTCCCTTCCTACCCTGAC 60.618 60.000 0.00 0.00 0.00 3.51
110 111 2.454336 TTCGATCTGCTCCCTTCCTA 57.546 50.000 0.00 0.00 0.00 2.94
158 159 8.800370 ATAGACATTCTATATGCTCGAGAGAA 57.200 34.615 18.75 15.78 37.88 2.87
172 173 9.027129 GCACGTAAAACATGTATAGACATTCTA 57.973 33.333 0.00 0.00 44.18 2.10
173 174 7.253983 CGCACGTAAAACATGTATAGACATTCT 60.254 37.037 0.00 0.00 44.18 2.40
179 193 5.061187 CACACGCACGTAAAACATGTATAGA 59.939 40.000 0.00 0.00 0.00 1.98
185 199 1.661743 CCCACACGCACGTAAAACATG 60.662 52.381 0.00 0.00 0.00 3.21
189 203 2.015382 CACCCACACGCACGTAAAA 58.985 52.632 0.00 0.00 0.00 1.52
190 204 2.535788 GCACCCACACGCACGTAAA 61.536 57.895 0.00 0.00 0.00 2.01
191 205 2.968156 GCACCCACACGCACGTAA 60.968 61.111 0.00 0.00 0.00 3.18
257 318 4.542906 TCATATTGGAGGAGACAGGAGA 57.457 45.455 0.00 0.00 0.00 3.71
258 319 4.653341 AGTTCATATTGGAGGAGACAGGAG 59.347 45.833 0.00 0.00 0.00 3.69
259 320 4.406972 CAGTTCATATTGGAGGAGACAGGA 59.593 45.833 0.00 0.00 0.00 3.86
260 321 4.406972 TCAGTTCATATTGGAGGAGACAGG 59.593 45.833 0.00 0.00 0.00 4.00
261 322 5.604758 TCAGTTCATATTGGAGGAGACAG 57.395 43.478 0.00 0.00 0.00 3.51
262 323 5.338381 GGTTCAGTTCATATTGGAGGAGACA 60.338 44.000 0.00 0.00 0.00 3.41
263 324 5.119694 GGTTCAGTTCATATTGGAGGAGAC 58.880 45.833 0.00 0.00 0.00 3.36
300 361 1.408127 CCGCACCTCATGGAATTGGTA 60.408 52.381 0.00 0.00 37.04 3.25
416 477 4.069232 CTGTCTTGCTCCGGCCGA 62.069 66.667 30.73 12.25 37.74 5.54
430 491 0.895530 AGGCACGTACATGTAGCTGT 59.104 50.000 5.62 2.67 0.00 4.40
432 493 1.469251 CGAAGGCACGTACATGTAGCT 60.469 52.381 5.62 0.00 0.00 3.32
465 526 4.093408 TGCAAGATGAAATAGTGACGCTTC 59.907 41.667 0.00 0.00 0.00 3.86
470 531 6.690194 AGGATTGCAAGATGAAATAGTGAC 57.310 37.500 4.94 0.00 0.00 3.67
560 621 2.895404 CCAGCCCCATGAATATTCCTTG 59.105 50.000 12.90 10.09 0.00 3.61
653 717 2.923605 GCACATGGCACTTGAACATCAC 60.924 50.000 0.00 0.00 43.97 3.06
700 764 3.312421 CCGACGAATTGGCAATGTTAGAT 59.688 43.478 14.47 0.00 0.00 1.98
802 866 2.816087 GGGCGTGATCAATGAGCAATAT 59.184 45.455 1.60 0.00 26.97 1.28
803 867 2.158769 AGGGCGTGATCAATGAGCAATA 60.159 45.455 1.60 0.00 26.97 1.90
804 868 1.027357 GGGCGTGATCAATGAGCAAT 58.973 50.000 1.60 0.00 26.97 3.56
1003 1071 6.201806 CCAACAGCAGAGAATGTAGCTATAAC 59.798 42.308 0.00 0.00 35.19 1.89
1062 1130 3.891366 CACCAACAAAATGTTCCCTCTCT 59.109 43.478 0.00 0.00 38.77 3.10
1082 1150 3.254892 GACGAAGACTTGGGAATCTCAC 58.745 50.000 2.09 0.00 0.00 3.51
1117 1185 0.036164 TCATTAGTGCAAGCCGGTGT 59.964 50.000 1.90 0.00 0.00 4.16
1120 1188 0.099436 GCTTCATTAGTGCAAGCCGG 59.901 55.000 0.00 0.00 34.89 6.13
1121 1189 0.804364 TGCTTCATTAGTGCAAGCCG 59.196 50.000 14.90 0.00 37.53 5.52
1387 1460 4.030913 AGCAGCCCTATACTCTTTGTACA 58.969 43.478 0.00 0.00 33.45 2.90
1493 1566 3.143807 TGCTTTTGTTTCCTCACAACG 57.856 42.857 0.00 0.00 36.36 4.10
1584 1659 2.355197 TGCACGTGGAATCAACTATGG 58.645 47.619 18.88 0.00 0.00 2.74
1707 1786 1.678724 GCCATGGCCCAACAACAAT 59.321 52.632 27.24 0.00 34.56 2.71
1744 1823 8.046708 TGTTTGGTCTTCATATAGTGTAATGCT 58.953 33.333 0.00 0.00 0.00 3.79
1844 1923 6.555812 TCGTATATACTCGAGAGCAACATT 57.444 37.500 21.68 0.00 0.00 2.71
2083 2162 5.997746 CAGAGTTGTTGGAAGGTCTTCATAA 59.002 40.000 12.13 4.77 41.20 1.90
2095 2174 1.271543 CCATCAGGCAGAGTTGTTGGA 60.272 52.381 0.00 0.00 36.65 3.53
2167 2246 8.057536 TGAAACGCCAATACTTAATACCATTT 57.942 30.769 0.00 0.00 0.00 2.32
2302 2382 2.359848 GGTACAACTTCACCAAACCACC 59.640 50.000 0.00 0.00 34.77 4.61
2409 2493 6.376978 CACAACTGAGAGAATGGATGAAAAC 58.623 40.000 0.00 0.00 0.00 2.43
2549 2633 4.340666 TGAAAAGGTTGCTGCACAATAGAA 59.659 37.500 0.00 0.00 41.27 2.10
2683 2772 3.815856 TGCCAAAAATCTTGTGCTTGA 57.184 38.095 0.00 0.00 0.00 3.02
2712 2813 2.213499 CGCCAGCGGAATATTCTCTTT 58.787 47.619 14.95 0.00 35.56 2.52
2730 2831 0.243907 TACACTTCTCACAGCTCCGC 59.756 55.000 0.00 0.00 0.00 5.54
2773 2874 5.803967 CAGGCGTATTCGGTATAAACCTATC 59.196 44.000 0.00 0.00 44.35 2.08
2933 3034 5.627367 CGAGGAGAGCAGACTTAAAATATCG 59.373 44.000 0.00 0.00 0.00 2.92
3081 3185 6.492007 TTTTGCACTGCTTTTCATCAAAAA 57.508 29.167 1.98 0.00 35.56 1.94
3186 3290 4.241681 GGAAGGCATCGACTTGATCTATC 58.758 47.826 0.00 0.00 34.13 2.08
3187 3291 3.643320 TGGAAGGCATCGACTTGATCTAT 59.357 43.478 0.00 0.00 34.13 1.98
3188 3292 3.031013 TGGAAGGCATCGACTTGATCTA 58.969 45.455 0.00 0.00 34.13 1.98
3189 3293 1.833630 TGGAAGGCATCGACTTGATCT 59.166 47.619 0.00 0.00 34.13 2.75
3190 3294 2.315925 TGGAAGGCATCGACTTGATC 57.684 50.000 0.00 0.00 34.13 2.92
3191 3295 2.569059 CATGGAAGGCATCGACTTGAT 58.431 47.619 0.00 0.00 38.01 2.57
3192 3296 2.028420 CATGGAAGGCATCGACTTGA 57.972 50.000 0.00 0.00 26.99 3.02


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

AutoCloner maintained by Alex Coulton.