Multiple sequence alignment - TraesCS2D01G412700

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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 TraesCS2D01G412700 chr2D 100.000 2198 0 0 1 2198 527392531 527394728 0.000000e+00 4060.0
1 TraesCS2D01G412700 chr2A 87.693 1487 99 39 716 2155 672348492 672349941 0.000000e+00 1655.0
2 TraesCS2D01G412700 chr2A 91.089 101 7 2 123 221 672347888 672347988 3.810000e-28 135.0
3 TraesCS2D01G412700 chr2B 89.272 1333 66 32 501 1802 624540941 624542227 0.000000e+00 1598.0
4 TraesCS2D01G412700 chr2B 87.017 362 31 8 1810 2165 624542308 624542659 5.690000e-106 394.0
5 TraesCS2D01G412700 chr2B 88.150 346 15 7 1 341 624540319 624540643 2.650000e-104 388.0
6 TraesCS2D01G412700 chr2B 93.077 130 9 0 370 499 624540643 624540772 8.010000e-45 191.0
7 TraesCS2D01G412700 chr4B 89.498 219 14 2 992 1201 576745592 576745810 3.600000e-68 268.0
8 TraesCS2D01G412700 chr4D 88.940 217 15 2 994 1201 461465772 461465988 2.160000e-65 259.0
9 TraesCS2D01G412700 chr4A 88.837 215 15 4 994 1199 7177029 7176815 2.800000e-64 255.0
10 TraesCS2D01G412700 chr4A 75.882 170 30 6 1936 2095 118634637 118634469 2.340000e-10 76.8


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 TraesCS2D01G412700 chr2D 527392531 527394728 2197 False 4060.00 4060 100.000 1 2198 1 chr2D.!!$F1 2197
1 TraesCS2D01G412700 chr2A 672347888 672349941 2053 False 895.00 1655 89.391 123 2155 2 chr2A.!!$F1 2032
2 TraesCS2D01G412700 chr2B 624540319 624542659 2340 False 642.75 1598 89.379 1 2165 4 chr2B.!!$F1 2164

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
353 383 0.037326 GTCATGGCAGGTCGACAAGA 60.037 55.0 18.91 0.0 34.96 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 2134 0.179084 CCAACCACAGTGACACGAGT 60.179 55.0 0.62 0.25 0.0 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
28 32 1.678598 CGGCTCCCGGTACCATTGTA 61.679 60.000 13.54 0.00 44.15 2.41
47 51 0.179029 ATGCGTAATGGTACCTGGCC 60.179 55.000 14.36 0.00 0.00 5.36
123 127 3.142393 CCGATCGCCTCCATTCCT 58.858 61.111 10.32 0.00 0.00 3.36
165 169 7.171653 TGGAATAATGGTACTGTTGTTGATGA 58.828 34.615 0.00 0.00 0.00 2.92
222 227 1.203038 ACATGGATCAAACAGGGCACA 60.203 47.619 0.00 0.00 0.00 4.57
223 228 2.104967 CATGGATCAAACAGGGCACAT 58.895 47.619 0.00 0.00 0.00 3.21
236 241 4.398988 ACAGGGCACATATACACACAAATG 59.601 41.667 0.00 0.00 0.00 2.32
239 244 4.640201 GGGCACATATACACACAAATGACT 59.360 41.667 0.00 0.00 0.00 3.41
286 311 0.680061 ACCAGTCCTGTTTCTCCGTC 59.320 55.000 0.00 0.00 0.00 4.79
290 315 2.297597 CAGTCCTGTTTCTCCGTCTTCT 59.702 50.000 0.00 0.00 0.00 2.85
291 316 2.559231 AGTCCTGTTTCTCCGTCTTCTC 59.441 50.000 0.00 0.00 0.00 2.87
293 318 3.006003 GTCCTGTTTCTCCGTCTTCTCTT 59.994 47.826 0.00 0.00 0.00 2.85
294 319 3.256136 TCCTGTTTCTCCGTCTTCTCTTC 59.744 47.826 0.00 0.00 0.00 2.87
295 320 3.257127 CCTGTTTCTCCGTCTTCTCTTCT 59.743 47.826 0.00 0.00 0.00 2.85
306 331 3.687212 GTCTTCTCTTCTTTAAGCTGGGC 59.313 47.826 0.00 0.00 32.36 5.36
332 357 2.770699 GACCCTAGTCATCGGTTACG 57.229 55.000 0.00 0.00 42.99 3.18
345 375 1.740296 GTTACGCGTCATGGCAGGT 60.740 57.895 18.63 0.00 0.00 4.00
347 377 3.693382 TACGCGTCATGGCAGGTCG 62.693 63.158 18.63 13.99 0.00 4.79
352 382 1.354337 CGTCATGGCAGGTCGACAAG 61.354 60.000 18.91 10.01 34.96 3.16
353 383 0.037326 GTCATGGCAGGTCGACAAGA 60.037 55.000 18.91 0.00 34.96 3.02
354 384 0.247460 TCATGGCAGGTCGACAAGAG 59.753 55.000 18.91 4.68 34.96 2.85
375 408 1.065418 CCCACCCTGTACCAGTTCATC 60.065 57.143 0.00 0.00 0.00 2.92
465 498 8.303876 GCTATTCCCAAGTTGATCAAGTTTTTA 58.696 33.333 23.08 10.36 32.02 1.52
469 502 9.541143 TTCCCAAGTTGATCAAGTTTTTATTTC 57.459 29.630 23.08 1.91 32.02 2.17
530 787 4.087892 CAGCTCCCCCACGGTCTG 62.088 72.222 0.00 0.00 0.00 3.51
566 834 6.491714 AGATAAAGATTTCTCTAGCTGCCA 57.508 37.500 0.00 0.00 0.00 4.92
624 893 5.861787 AGCAATAATAAGTTCAAAACGCACC 59.138 36.000 0.00 0.00 36.23 5.01
671 943 4.201753 CGCACTGACAACAATCATTAGAGG 60.202 45.833 0.00 0.00 0.00 3.69
686 958 1.681229 AGAGGCCAGGGGATGTAAAA 58.319 50.000 5.01 0.00 0.00 1.52
746 1018 7.036829 GGTAGAGATAAGAGAGCGTTTTCTTT 58.963 38.462 10.24 0.00 35.42 2.52
809 1081 0.318107 CTCCACAAGGCAAAGCAACG 60.318 55.000 0.00 0.00 33.74 4.10
898 1186 0.107945 ATCTTGCTCCGTGGAGAAGC 60.108 55.000 19.98 5.90 44.53 3.86
932 1220 1.300388 CTGCAAAGCCACAGCAACC 60.300 57.895 0.00 0.00 43.56 3.77
934 1222 3.119193 CAAAGCCACAGCAACCGT 58.881 55.556 0.00 0.00 43.56 4.83
973 1262 2.451490 AGAGATTGACAGGCGAGAAGA 58.549 47.619 0.00 0.00 0.00 2.87
976 1265 2.828520 AGATTGACAGGCGAGAAGAGAA 59.171 45.455 0.00 0.00 0.00 2.87
1213 1509 0.036294 GTGAAGGAAGGAGGTTCGGG 60.036 60.000 0.00 0.00 35.80 5.14
1215 1511 2.538512 GAAGGAAGGAGGTTCGGGCC 62.539 65.000 0.00 0.00 35.80 5.80
1237 1542 4.332637 CTTTGCTGTGCGGCGCTT 62.333 61.111 33.26 0.00 34.52 4.68
1249 1554 4.773117 GCGCTTGCTTGCTCTGCC 62.773 66.667 0.00 0.00 35.07 4.85
1326 1631 9.886132 GTTGGAGTTTTCTTATAGGATTACTGA 57.114 33.333 4.70 0.00 0.00 3.41
1356 1661 4.917998 CCAATCATTGTACCTAGATCGTCG 59.082 45.833 0.00 0.00 0.00 5.12
1357 1662 5.507482 CCAATCATTGTACCTAGATCGTCGT 60.507 44.000 0.00 0.00 0.00 4.34
1358 1663 4.808077 TCATTGTACCTAGATCGTCGTC 57.192 45.455 0.00 0.00 0.00 4.20
1389 1694 0.610687 ACCTCTTCTCCTTCTTGCCG 59.389 55.000 0.00 0.00 0.00 5.69
1393 1698 1.160137 CTTCTCCTTCTTGCCGTTGG 58.840 55.000 0.00 0.00 0.00 3.77
1449 1754 1.742831 TGCGAAATGTTCAGGCATACC 59.257 47.619 0.00 0.00 0.00 2.73
1599 1921 9.868277 ACTGTGAAAATTGAATGAAGTGTAAAA 57.132 25.926 0.00 0.00 0.00 1.52
1662 1987 1.614850 GGTTTTGGCTACCGAATCCCA 60.615 52.381 3.20 0.00 32.99 4.37
1663 1988 2.164338 GTTTTGGCTACCGAATCCCAA 58.836 47.619 0.00 0.00 35.68 4.12
1742 2069 8.616076 TGCCGTTCAAAATTTACAATGAATTTT 58.384 25.926 6.36 2.65 43.64 1.82
1813 2216 2.572191 ACGAAAGAACACTCGTGTCA 57.428 45.000 2.81 0.00 46.01 3.58
1892 2295 4.814294 AAGCATCCGGACGCGTCC 62.814 66.667 41.75 41.75 46.18 4.79
1916 2319 1.692519 GATGGTTATACAGGAGCCGGT 59.307 52.381 1.90 0.00 0.00 5.28
1938 2341 4.935808 GTCATCCAATTCTCACCGTAAACT 59.064 41.667 0.00 0.00 0.00 2.66
1978 2382 6.890663 ACAAATTTGGACATAATTCATGCG 57.109 33.333 21.74 0.00 38.29 4.73
2127 2537 2.555325 ACCTTTGTCGTCGTCTATGTCA 59.445 45.455 0.00 0.00 0.00 3.58
2138 2548 2.541794 CGTCTATGTCATCGTGGTCAGG 60.542 54.545 0.00 0.00 0.00 3.86
2195 2605 2.281761 CAGCCGTTGCCTGAAGGT 60.282 61.111 0.00 0.00 38.69 3.50
2196 2606 2.032681 AGCCGTTGCCTGAAGGTC 59.967 61.111 0.00 0.00 38.69 3.85
2197 2607 3.423154 GCCGTTGCCTGAAGGTCG 61.423 66.667 0.00 1.68 37.57 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.742438 CCATTACGCATACAATGGTACC 57.258 45.455 4.43 4.43 44.11 3.34
28 32 0.179029 GGCCAGGTACCATTACGCAT 60.179 55.000 15.94 0.00 0.00 4.73
58 62 2.670148 CCCTCGGAAGTTCAGGGGG 61.670 68.421 24.45 24.45 45.81 5.40
99 103 4.959596 GAGGCGATCGGCAGCTCC 62.960 72.222 38.28 20.07 46.16 4.70
100 104 4.959596 GGAGGCGATCGGCAGCTC 62.960 72.222 38.28 27.59 46.16 4.09
102 106 4.615815 ATGGAGGCGATCGGCAGC 62.616 66.667 38.28 29.12 46.16 5.25
107 111 1.668419 AAAAGGAATGGAGGCGATCG 58.332 50.000 11.69 11.69 0.00 3.69
123 127 1.063867 TCCAGTTGTTCCCCGGAAAAA 60.064 47.619 0.73 0.00 35.75 1.94
165 169 1.133419 GGGACCTCTCTCCGGATAAGT 60.133 57.143 3.57 0.00 0.00 2.24
222 227 6.038603 GGCATGTCAGTCATTTGTGTGTATAT 59.961 38.462 0.00 0.00 34.09 0.86
223 228 5.353956 GGCATGTCAGTCATTTGTGTGTATA 59.646 40.000 0.00 0.00 34.09 1.47
236 241 4.309933 TCATATTGATCGGCATGTCAGTC 58.690 43.478 0.00 0.00 0.00 3.51
239 244 3.494251 CGTTCATATTGATCGGCATGTCA 59.506 43.478 0.00 0.00 36.32 3.58
286 311 2.675348 CGCCCAGCTTAAAGAAGAGAAG 59.325 50.000 0.00 0.00 34.25 2.85
290 315 1.066143 CCTCGCCCAGCTTAAAGAAGA 60.066 52.381 0.00 0.00 34.25 2.87
291 316 1.066143 TCCTCGCCCAGCTTAAAGAAG 60.066 52.381 0.00 0.00 35.60 2.85
293 318 1.134401 CATCCTCGCCCAGCTTAAAGA 60.134 52.381 0.00 0.00 0.00 2.52
294 319 1.134401 TCATCCTCGCCCAGCTTAAAG 60.134 52.381 0.00 0.00 0.00 1.85
295 320 0.908910 TCATCCTCGCCCAGCTTAAA 59.091 50.000 0.00 0.00 0.00 1.52
332 357 3.188786 GTCGACCTGCCATGACGC 61.189 66.667 3.51 0.00 0.00 5.19
345 375 2.203788 AGGGTGGGCTCTTGTCGA 60.204 61.111 0.00 0.00 0.00 4.20
347 377 0.036294 GTACAGGGTGGGCTCTTGTC 60.036 60.000 0.00 0.00 0.00 3.18
375 408 3.540211 AAGTCCACTTGATGCCTCG 57.460 52.632 0.00 0.00 34.38 4.63
410 443 6.939132 TCCCAAACGACTTGTTAAATGTAA 57.061 33.333 0.00 0.00 40.84 2.41
414 447 7.597369 GCTATTTTCCCAAACGACTTGTTAAAT 59.403 33.333 0.00 1.52 40.84 1.40
431 464 7.285401 TGATCAACTTGGGAATAGCTATTTTCC 59.715 37.037 19.77 21.52 40.60 3.13
451 484 9.814899 TCTGCAAAGAAATAAAAACTTGATCAA 57.185 25.926 8.12 8.12 0.00 2.57
499 532 3.181439 GGGGAGCTGTCAGGCTATTAATT 60.181 47.826 1.14 0.00 43.20 1.40
671 943 2.293399 CGCTTATTTTACATCCCCTGGC 59.707 50.000 0.00 0.00 0.00 4.85
686 958 2.042104 GTACGTACGATGGCGCTTAT 57.958 50.000 24.41 1.68 42.48 1.73
809 1081 0.887387 TCGTTGCTTGGGTAAGTGCC 60.887 55.000 0.00 0.00 36.27 5.01
898 1186 1.078143 CAGGCTTCCCTCCCTTTCG 60.078 63.158 0.00 0.00 40.33 3.46
934 1222 3.452786 CTCGCCCAGGCTTCTCGA 61.453 66.667 7.17 0.00 39.32 4.04
973 1262 0.247736 CAAGTAGCTCCACGCCTTCT 59.752 55.000 0.00 0.00 40.39 2.85
976 1265 1.893786 CTCAAGTAGCTCCACGCCT 59.106 57.895 0.00 0.00 40.39 5.52
1233 1538 4.456253 CGGCAGAGCAAGCAAGCG 62.456 66.667 0.00 0.00 40.15 4.68
1278 1583 4.570930 CCTTACAGAGGGTGAAGAAGAAC 58.429 47.826 0.00 0.00 42.26 3.01
1356 1661 5.067283 GGAGAAGAGGTATTCACAGAGAGAC 59.933 48.000 0.00 0.00 0.00 3.36
1357 1662 5.044476 AGGAGAAGAGGTATTCACAGAGAGA 60.044 44.000 0.00 0.00 0.00 3.10
1358 1663 5.200483 AGGAGAAGAGGTATTCACAGAGAG 58.800 45.833 0.00 0.00 0.00 3.20
1389 1694 0.798776 CCTGAACAGACGATGCCAAC 59.201 55.000 3.19 0.00 0.00 3.77
1393 1698 1.594862 GTATGCCTGAACAGACGATGC 59.405 52.381 3.19 0.00 0.00 3.91
1397 1702 2.386661 AAGGTATGCCTGAACAGACG 57.613 50.000 1.89 0.00 46.33 4.18
1423 1728 3.181482 TGCCTGAACATTTCGCAAAAAGA 60.181 39.130 0.00 0.00 0.00 2.52
1424 1729 3.122297 TGCCTGAACATTTCGCAAAAAG 58.878 40.909 0.00 0.00 0.00 2.27
1449 1754 5.824429 TGTTTCTTTTCTGACAGCAAGATG 58.176 37.500 14.36 0.00 0.00 2.90
1599 1921 6.721318 ACACATACATCTGGTAGTGGAAAAT 58.279 36.000 0.00 0.00 36.38 1.82
1674 1999 3.391382 CGTTTCTCGCCTCCCCCT 61.391 66.667 0.00 0.00 0.00 4.79
1796 2126 3.000322 CACAGTGACACGAGTGTTCTTTC 60.000 47.826 19.71 0.00 45.05 2.62
1804 2134 0.179084 CCAACCACAGTGACACGAGT 60.179 55.000 0.62 0.25 0.00 4.18
1813 2216 1.072331 GATGACCTGACCAACCACAGT 59.928 52.381 0.00 0.00 32.93 3.55
1892 2295 1.935300 GCTCCTGTATAACCATCCGCG 60.935 57.143 0.00 0.00 0.00 6.46
1902 2305 1.133294 TGGATGACCGGCTCCTGTATA 60.133 52.381 16.68 0.00 39.42 1.47
1916 2319 5.160607 AGTTTACGGTGAGAATTGGATGA 57.839 39.130 0.00 0.00 0.00 2.92
1938 2341 0.889638 TGTTTGTATTGCGGGCCGAA 60.890 50.000 33.44 19.61 0.00 4.30
1945 2349 5.896922 TGTCCAAATTTGTTTGTATTGCG 57.103 34.783 16.73 0.00 0.00 4.85
1978 2382 3.435671 AGTCCGTTTGAATGAATTCCGTC 59.564 43.478 2.27 0.78 35.97 4.79
2026 2436 4.140518 TGAACAAACGAAACATCATCCG 57.859 40.909 0.00 0.00 0.00 4.18
2034 2444 9.292846 AGGTTTTATTAGTTGAACAAACGAAAC 57.707 29.630 0.00 3.54 44.04 2.78
2084 2494 2.916052 GCCGACCAGTCACTGTCGA 61.916 63.158 23.19 0.00 37.27 4.20
2085 2495 2.430921 GCCGACCAGTCACTGTCG 60.431 66.667 17.71 17.71 36.02 4.35
2111 2521 2.004733 ACGATGACATAGACGACGACA 58.995 47.619 0.00 0.00 0.00 4.35
2127 2537 2.291043 GGACCACCCTGACCACGAT 61.291 63.158 0.00 0.00 0.00 3.73
2179 2589 2.032681 GACCTTCAGGCAACGGCT 59.967 61.111 0.00 0.00 46.39 5.52
2180 2590 3.423154 CGACCTTCAGGCAACGGC 61.423 66.667 0.00 0.00 46.39 5.68


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

AutoCloner maintained by Alex Coulton.