Multiple sequence alignment - TraesCS4B01G312500

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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 TraesCS4B01G312500 chr4B 100.000 2609 0 0 1 2609 602293337 602290729 0.000000e+00 4819
1 TraesCS4B01G312500 chr4B 90.177 1812 123 30 840 2608 194219979 194221778 0.000000e+00 2309
2 TraesCS4B01G312500 chr4B 87.630 865 55 30 1 850 194219098 194219925 0.000000e+00 957
3 TraesCS4B01G312500 chr6D 91.682 2633 154 33 1 2608 14045561 14048153 0.000000e+00 3589
4 TraesCS4B01G312500 chr5D 90.964 2634 154 39 1 2608 373747708 373750283 0.000000e+00 3469
5 TraesCS4B01G312500 chr6A 86.556 2648 258 54 1 2608 74674998 74677587 0.000000e+00 2828
6 TraesCS4B01G312500 chr5B 91.553 2060 135 19 558 2608 445131422 445133451 0.000000e+00 2804
7 TraesCS4B01G312500 chr5B 90.929 1797 118 24 854 2608 420718032 420719825 0.000000e+00 2374
8 TraesCS4B01G312500 chr5B 90.221 1810 124 29 840 2608 179227840 179229637 0.000000e+00 2313
9 TraesCS4B01G312500 chr5B 88.051 862 54 22 1 850 179226962 179227786 0.000000e+00 976
10 TraesCS4B01G312500 chr5B 87.963 864 54 26 1 850 406870655 406869828 0.000000e+00 974
11 TraesCS4B01G312500 chr5B 87.826 575 51 10 1 562 445111491 445112059 0.000000e+00 656
12 TraesCS4B01G312500 chr2D 93.764 1764 99 9 849 2608 617164184 617162428 0.000000e+00 2638
13 TraesCS4B01G312500 chr2D 93.140 860 39 12 1 850 617165088 617164239 0.000000e+00 1243
14 TraesCS4B01G312500 chr1D 93.718 1767 97 12 848 2608 485158460 485160218 0.000000e+00 2636
15 TraesCS4B01G312500 chr1D 94.416 591 27 5 263 850 485157818 485158405 0.000000e+00 904
16 TraesCS4B01G312500 chr2A 92.325 1772 104 18 848 2608 17676655 17674905 0.000000e+00 2490
17 TraesCS4B01G312500 chr2A 87.935 862 54 23 1 850 719453738 719454561 0.000000e+00 970
18 TraesCS4B01G312500 chr2A 87.703 862 58 23 1 850 43380232 43381057 0.000000e+00 961
19 TraesCS4B01G312500 chr2A 94.247 591 29 4 263 850 17677299 17676711 0.000000e+00 898
20 TraesCS4B01G312500 chr7B 90.558 1811 122 26 840 2608 68098241 68100044 0.000000e+00 2351
21 TraesCS4B01G312500 chr7B 88.079 864 52 24 1 850 528879444 528880270 0.000000e+00 977
22 TraesCS4B01G312500 chr3B 90.492 1809 123 23 840 2608 552478977 552480776 0.000000e+00 2342
23 TraesCS4B01G312500 chr3B 88.208 865 52 23 1 851 552478097 552478925 0.000000e+00 987
24 TraesCS4B01G312500 chr7A 90.387 1810 121 29 840 2608 171419456 171421253 0.000000e+00 2329
25 TraesCS4B01G312500 chr7A 85.681 866 53 35 1 850 171418592 171419402 0.000000e+00 846
26 TraesCS4B01G312500 chr1A 90.306 1795 126 29 854 2608 567477295 567475509 0.000000e+00 2307
27 TraesCS4B01G312500 chr1A 85.658 509 36 21 2131 2608 567471887 567471385 3.880000e-138 501
28 TraesCS4B01G312500 chr6B 87.963 864 53 26 1 850 704850743 704849917 0.000000e+00 972


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 TraesCS4B01G312500 chr4B 602290729 602293337 2608 True 4819.0 4819 100.0000 1 2609 1 chr4B.!!$R1 2608
1 TraesCS4B01G312500 chr4B 194219098 194221778 2680 False 1633.0 2309 88.9035 1 2608 2 chr4B.!!$F1 2607
2 TraesCS4B01G312500 chr6D 14045561 14048153 2592 False 3589.0 3589 91.6820 1 2608 1 chr6D.!!$F1 2607
3 TraesCS4B01G312500 chr5D 373747708 373750283 2575 False 3469.0 3469 90.9640 1 2608 1 chr5D.!!$F1 2607
4 TraesCS4B01G312500 chr6A 74674998 74677587 2589 False 2828.0 2828 86.5560 1 2608 1 chr6A.!!$F1 2607
5 TraesCS4B01G312500 chr5B 445131422 445133451 2029 False 2804.0 2804 91.5530 558 2608 1 chr5B.!!$F3 2050
6 TraesCS4B01G312500 chr5B 420718032 420719825 1793 False 2374.0 2374 90.9290 854 2608 1 chr5B.!!$F1 1754
7 TraesCS4B01G312500 chr5B 179226962 179229637 2675 False 1644.5 2313 89.1360 1 2608 2 chr5B.!!$F4 2607
8 TraesCS4B01G312500 chr5B 406869828 406870655 827 True 974.0 974 87.9630 1 850 1 chr5B.!!$R1 849
9 TraesCS4B01G312500 chr5B 445111491 445112059 568 False 656.0 656 87.8260 1 562 1 chr5B.!!$F2 561
10 TraesCS4B01G312500 chr2D 617162428 617165088 2660 True 1940.5 2638 93.4520 1 2608 2 chr2D.!!$R1 2607
11 TraesCS4B01G312500 chr1D 485157818 485160218 2400 False 1770.0 2636 94.0670 263 2608 2 chr1D.!!$F1 2345
12 TraesCS4B01G312500 chr2A 17674905 17677299 2394 True 1694.0 2490 93.2860 263 2608 2 chr2A.!!$R1 2345
13 TraesCS4B01G312500 chr2A 719453738 719454561 823 False 970.0 970 87.9350 1 850 1 chr2A.!!$F2 849
14 TraesCS4B01G312500 chr2A 43380232 43381057 825 False 961.0 961 87.7030 1 850 1 chr2A.!!$F1 849
15 TraesCS4B01G312500 chr7B 68098241 68100044 1803 False 2351.0 2351 90.5580 840 2608 1 chr7B.!!$F1 1768
16 TraesCS4B01G312500 chr7B 528879444 528880270 826 False 977.0 977 88.0790 1 850 1 chr7B.!!$F2 849
17 TraesCS4B01G312500 chr3B 552478097 552480776 2679 False 1664.5 2342 89.3500 1 2608 2 chr3B.!!$F1 2607
18 TraesCS4B01G312500 chr7A 171418592 171421253 2661 False 1587.5 2329 88.0340 1 2608 2 chr7A.!!$F1 2607
19 TraesCS4B01G312500 chr1A 567471385 567477295 5910 True 1404.0 2307 87.9820 854 2608 2 chr1A.!!$R1 1754
20 TraesCS4B01G312500 chr6B 704849917 704850743 826 True 972.0 972 87.9630 1 850 1 chr6B.!!$R1 849

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
172 187 1.681229 TGAAAGAGGGGGTAGGCAAT 58.319 50.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1862 1.627329 TCCCATCTGCCATCTATCAGC 59.373 52.381 0.0 0.0 0.0 4.26 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
95 106 8.830201 TTATCAGCTTGCAAAAATGTAAACAT 57.170 26.923 0.00 0.00 38.41 2.71
106 117 8.223100 GCAAAAATGTAAACATTAGGCAAGAAG 58.777 33.333 8.67 0.00 45.06 2.85
119 130 5.757850 AGGCAAGAAGTACTGTGAAAAAG 57.242 39.130 0.00 0.00 0.00 2.27
161 174 4.861102 AAAGCAACTTGGATGAAAGAGG 57.139 40.909 0.00 0.00 0.00 3.69
162 175 2.800250 AGCAACTTGGATGAAAGAGGG 58.200 47.619 0.00 0.00 0.00 4.30
172 187 1.681229 TGAAAGAGGGGGTAGGCAAT 58.319 50.000 0.00 0.00 0.00 3.56
366 408 6.567959 TGTTGTTGTTGTGATCTTGCAATTA 58.432 32.000 0.00 0.00 0.00 1.40
381 424 2.418609 GCAATTAGTGGGGAACAATGCC 60.419 50.000 0.00 0.00 36.03 4.40
487 541 4.168922 CATCAGTTGCAGCATGAAAAGA 57.831 40.909 2.55 0.00 33.62 2.52
492 546 6.050432 TCAGTTGCAGCATGAAAAGAAAAAT 58.950 32.000 2.55 0.00 33.62 1.82
517 579 2.439507 ACTCATGACCTGGACAAACAGT 59.560 45.455 0.00 1.56 36.75 3.55
562 624 6.912591 CACAAAGACAGTGATAACCAAAGTTC 59.087 38.462 0.00 0.00 39.30 3.01
599 661 9.865321 AAACTTTAGGAGAAAAACAAAAGTACC 57.135 29.630 0.00 0.00 36.45 3.34
796 861 8.065473 TGAAAACCATGCATATGTATGAGTTT 57.935 30.769 28.94 28.10 39.94 2.66
807 872 7.707893 GCATATGTATGAGTTTCCTGCATTTTT 59.292 33.333 4.29 0.00 35.75 1.94
868 1045 6.510960 GCAAAAACCCATGTTGTATGTTGAAC 60.511 38.462 0.00 0.00 34.13 3.18
941 1120 7.024171 GCCTGAATTTAGTTTCTTACTTGCTC 58.976 38.462 0.00 0.00 38.33 4.26
1067 1265 4.588951 TCCAGTGAACTCTACACAACAGAT 59.411 41.667 0.00 0.00 40.25 2.90
1069 1267 5.406780 CCAGTGAACTCTACACAACAGATTC 59.593 44.000 0.00 0.00 40.25 2.52
1077 1275 6.483640 ACTCTACACAACAGATTCCTCAAAAC 59.516 38.462 0.00 0.00 0.00 2.43
1080 1278 3.005791 CACAACAGATTCCTCAAAACCCC 59.994 47.826 0.00 0.00 0.00 4.95
1188 1386 2.156917 CCTGCAGCACAAGAATCTGAA 58.843 47.619 8.66 0.00 0.00 3.02
1390 1588 3.062042 GCCTTGCAGATTGGTTTTTCAG 58.938 45.455 0.00 0.00 0.00 3.02
1397 1595 6.169094 TGCAGATTGGTTTTTCAGTCAAAAA 58.831 32.000 0.00 0.00 40.93 1.94
1606 1809 9.783081 ATAAAACCAAAAAGATGAGCAAGAAAT 57.217 25.926 0.00 0.00 0.00 2.17
1635 1838 6.825721 AGAGAGATAAAATAGTGCAAACTGGG 59.174 38.462 0.00 0.00 0.00 4.45
1659 1862 4.022935 TGCAAAGCTAAGATGGTTGTCAAG 60.023 41.667 0.00 0.00 0.00 3.02
1726 1929 5.241506 CACAACCATCCACTAGTTGACAAAT 59.758 40.000 8.94 0.00 42.76 2.32
1805 2008 5.901276 CCTTCCTTACCCACCTACATAACTA 59.099 44.000 0.00 0.00 0.00 2.24
1878 2081 2.039084 ACTGCCCAGACTTTCCTAAGTG 59.961 50.000 1.69 0.00 44.51 3.16
1883 2086 3.815401 CCCAGACTTTCCTAAGTGTTGTG 59.185 47.826 0.00 0.00 44.51 3.33
1885 2088 5.454187 CCCAGACTTTCCTAAGTGTTGTGTA 60.454 44.000 0.00 0.00 44.51 2.90
1900 2103 4.037803 TGTTGTGTACATCTTGCTTGCAAT 59.962 37.500 8.55 0.00 0.00 3.56
2003 2209 9.731819 GCCTTATTTTTAAGTAGTATTTGCCTC 57.268 33.333 0.00 0.00 0.00 4.70
2034 2244 1.470051 AAACAAAGCAAGGGTCGTGT 58.530 45.000 0.00 0.00 0.00 4.49
2060 2270 7.439356 TCTCTGTTGTCTTGTCTTTGTTATGAG 59.561 37.037 0.00 0.00 0.00 2.90
2070 2280 6.406370 TGTCTTTGTTATGAGATGTGGTAGG 58.594 40.000 0.00 0.00 0.00 3.18
2073 2283 5.755409 TTGTTATGAGATGTGGTAGGTGT 57.245 39.130 0.00 0.00 0.00 4.16
2093 2303 6.666546 AGGTGTACTTGCCTAGTATTTGTCTA 59.333 38.462 0.00 0.00 41.26 2.59
2101 2311 9.817809 CTTGCCTAGTATTTGTCTATTAGTTGA 57.182 33.333 0.00 0.00 0.00 3.18
2164 2374 8.243426 CACAAATGCATATTAGTACAAACCACT 58.757 33.333 0.00 0.00 0.00 4.00
2182 2393 3.552684 CCACTGCCCAACATAAGTTTGTG 60.553 47.826 0.00 0.00 35.28 3.33
2184 2395 3.317993 ACTGCCCAACATAAGTTTGTGTC 59.682 43.478 0.00 0.00 35.28 3.67
2255 2466 2.854777 GCATGCGTGTTTGTTGTGTTAA 59.145 40.909 0.00 0.00 0.00 2.01
2307 6663 0.690192 TCTCCATTTGAGTTGCCCGA 59.310 50.000 0.00 0.00 42.12 5.14
2363 6722 7.563724 TCTTAGGTAACAAGGATTAACCACT 57.436 36.000 0.00 0.00 39.69 4.00
2365 6724 7.456902 TCTTAGGTAACAAGGATTAACCACTCT 59.543 37.037 0.00 0.00 39.69 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.710513 ATGCAAGTTGCTTCAGACAATTA 57.289 34.783 27.17 4.04 45.31 1.40
21 22 4.595762 ATGCAAGTTGCTTCAGACAATT 57.404 36.364 27.17 0.00 45.31 2.32
95 106 6.262273 CCTTTTTCACAGTACTTCTTGCCTAA 59.738 38.462 0.00 0.00 0.00 2.69
106 117 3.630312 TGAGTTGCCCTTTTTCACAGTAC 59.370 43.478 0.00 0.00 0.00 2.73
119 130 0.458669 CAATCAGCCATGAGTTGCCC 59.541 55.000 0.00 0.00 39.29 5.36
161 174 5.889289 TCACAATAGTTTTATTGCCTACCCC 59.111 40.000 7.09 0.00 46.60 4.95
162 175 7.338449 TCTTCACAATAGTTTTATTGCCTACCC 59.662 37.037 7.09 0.00 46.60 3.69
172 187 8.445275 TCACTTGCTTCTTCACAATAGTTTTA 57.555 30.769 0.00 0.00 0.00 1.52
332 368 4.023450 TCACAACAACAACAACCGTTTGTA 60.023 37.500 0.00 0.00 45.69 2.41
334 370 3.309388 TCACAACAACAACAACCGTTTG 58.691 40.909 0.00 0.00 38.83 2.93
336 372 3.442273 AGATCACAACAACAACAACCGTT 59.558 39.130 0.00 0.00 35.01 4.44
338 374 3.691049 AGATCACAACAACAACAACCG 57.309 42.857 0.00 0.00 0.00 4.44
366 408 1.603455 CACGGCATTGTTCCCCACT 60.603 57.895 0.00 0.00 0.00 4.00
487 541 7.595819 TGTCCAGGTCATGAGTTTTATTTTT 57.404 32.000 0.00 0.00 0.00 1.94
492 546 5.441500 TGTTTGTCCAGGTCATGAGTTTTA 58.558 37.500 0.00 0.00 0.00 1.52
517 579 6.665474 TGTGTAGTCGCTTTTTCAAGTAAA 57.335 33.333 0.00 0.00 31.86 2.01
562 624 6.282199 TCTCCTAAAGTTTGTACTAGCAGG 57.718 41.667 0.00 0.00 33.17 4.85
599 661 8.964420 ACATATGTTTGTCCTTTTTATGTTCG 57.036 30.769 1.41 0.00 0.00 3.95
834 901 4.881920 ACATGGGTTTTTGCTTGTATCAC 58.118 39.130 0.00 0.00 0.00 3.06
914 1093 6.582672 GCAAGTAAGAAACTAAATTCAGGCAC 59.417 38.462 0.00 0.00 37.50 5.01
1031 1229 3.751479 TCACTGGATCACCAATATCGG 57.249 47.619 0.00 0.00 46.32 4.18
1032 1230 4.697514 AGTTCACTGGATCACCAATATCG 58.302 43.478 0.00 0.00 46.32 2.92
1067 1265 2.740506 AAACTCGGGGTTTTGAGGAA 57.259 45.000 0.00 0.00 44.77 3.36
1069 1267 2.156917 GGTAAACTCGGGGTTTTGAGG 58.843 52.381 11.82 0.00 44.77 3.86
1080 1278 2.165845 AGGAGAATCACCGGTAAACTCG 59.834 50.000 6.87 0.00 36.25 4.18
1188 1386 4.385643 CCATCAAGGGTATGACCATCAGTT 60.386 45.833 0.00 0.00 41.02 3.16
1595 1798 8.853077 TTTATCTCTCTTTCATTTCTTGCTCA 57.147 30.769 0.00 0.00 0.00 4.26
1606 1809 9.507329 AGTTTGCACTATTTTATCTCTCTTTCA 57.493 29.630 0.00 0.00 0.00 2.69
1635 1838 3.253188 TGACAACCATCTTAGCTTTGCAC 59.747 43.478 0.00 0.00 0.00 4.57
1659 1862 1.627329 TCCCATCTGCCATCTATCAGC 59.373 52.381 0.00 0.00 0.00 4.26
1824 2027 4.220163 CGGAGAGGAGGGTAATATGGTTAC 59.780 50.000 0.00 0.00 0.00 2.50
1878 2081 3.624326 TGCAAGCAAGATGTACACAAC 57.376 42.857 0.00 0.00 0.00 3.32
1900 2103 4.019792 AGTCTGGCAAATCACACACATA 57.980 40.909 0.00 0.00 0.00 2.29
2003 2209 5.464389 CCTTGCTTTGTTTTCTGATCAAAGG 59.536 40.000 20.71 0.00 44.37 3.11
2034 2244 7.272244 TCATAACAAAGACAAGACAACAGAGA 58.728 34.615 0.00 0.00 0.00 3.10
2060 2270 2.236395 AGGCAAGTACACCTACCACATC 59.764 50.000 0.00 0.00 33.38 3.06
2070 2280 8.943909 AATAGACAAATACTAGGCAAGTACAC 57.056 34.615 0.00 0.00 43.47 2.90
2164 2374 3.561143 AGACACAAACTTATGTTGGGCA 58.439 40.909 1.32 0.00 36.39 5.36
2182 2393 3.503748 ACAAGCTGCATAAAACCAGAGAC 59.496 43.478 1.02 0.00 0.00 3.36
2184 2395 4.217118 AGAACAAGCTGCATAAAACCAGAG 59.783 41.667 1.02 0.00 0.00 3.35
2255 2466 4.574674 TTCATCCTCCTGTACAAGCAAT 57.425 40.909 0.00 0.00 0.00 3.56
2363 6722 6.541278 CCTGCATTCAATGAAGTCAGAATAGA 59.459 38.462 21.04 0.00 33.84 1.98
2365 6724 5.591472 CCCTGCATTCAATGAAGTCAGAATA 59.409 40.000 21.04 0.00 33.84 1.75
2537 6907 7.823745 AAAAGTCTGGATCTTCTTTTTGCTA 57.176 32.000 0.00 0.00 36.96 3.49


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

AutoCloner maintained by Alex Coulton.