Multiple sequence alignment - TraesCS4D01G084500

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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 TraesCS4D01G084500 chr4D 100.000 2324 0 0 1 2324 58266318 58268641 0.000000e+00 4292.0
1 TraesCS4D01G084500 chr3A 85.832 1461 162 22 4 1425 743850055 743848601 0.000000e+00 1509.0
2 TraesCS4D01G084500 chr4B 90.861 1127 84 10 1205 2324 87680913 87682027 0.000000e+00 1493.0
3 TraesCS4D01G084500 chr4A 92.580 903 52 12 1424 2324 537547304 537546415 0.000000e+00 1282.0
4 TraesCS4D01G084500 chr7D 76.967 1398 286 23 63 1430 147821337 147819946 0.000000e+00 765.0
5 TraesCS4D01G084500 chr7D 75.730 1405 294 25 63 1425 301323064 301321665 0.000000e+00 662.0
6 TraesCS4D01G084500 chr1B 75.776 1288 275 26 161 1418 101216137 101217417 1.180000e-172 616.0
7 TraesCS4D01G084500 chr3D 78.309 816 165 10 618 1425 452168882 452168071 1.230000e-142 516.0
8 TraesCS4D01G084500 chr3B 71.831 852 198 33 72 895 500323445 500324282 3.030000e-49 206.0
9 TraesCS4D01G084500 chr3B 94.595 37 0 1 1184 1220 173043601 173043567 3.230000e-04 56.5
10 TraesCS4D01G084500 chr5D 91.228 57 1 4 1372 1425 438557360 438557415 8.910000e-10 75.0
11 TraesCS4D01G084500 chr6A 97.368 38 0 1 1389 1425 236989158 236989121 1.930000e-06 63.9
12 TraesCS4D01G084500 chr2D 87.931 58 2 4 1378 1430 68320576 68320519 1.930000e-06 63.9


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 TraesCS4D01G084500 chr4D 58266318 58268641 2323 False 4292 4292 100.000 1 2324 1 chr4D.!!$F1 2323
1 TraesCS4D01G084500 chr3A 743848601 743850055 1454 True 1509 1509 85.832 4 1425 1 chr3A.!!$R1 1421
2 TraesCS4D01G084500 chr4B 87680913 87682027 1114 False 1493 1493 90.861 1205 2324 1 chr4B.!!$F1 1119
3 TraesCS4D01G084500 chr4A 537546415 537547304 889 True 1282 1282 92.580 1424 2324 1 chr4A.!!$R1 900
4 TraesCS4D01G084500 chr7D 147819946 147821337 1391 True 765 765 76.967 63 1430 1 chr7D.!!$R1 1367
5 TraesCS4D01G084500 chr7D 301321665 301323064 1399 True 662 662 75.730 63 1425 1 chr7D.!!$R2 1362
6 TraesCS4D01G084500 chr1B 101216137 101217417 1280 False 616 616 75.776 161 1418 1 chr1B.!!$F1 1257
7 TraesCS4D01G084500 chr3D 452168071 452168882 811 True 516 516 78.309 618 1425 1 chr3D.!!$R1 807
8 TraesCS4D01G084500 chr3B 500323445 500324282 837 False 206 206 71.831 72 895 1 chr3B.!!$F1 823

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
611 643 0.040425 GGTCACACACATTTGCGTCC 60.04 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1727 2.360801 GGTTAGCACTGAAGCACCAAAA 59.639 45.455 0.0 0.0 36.85 2.44 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 3.988976 TGCAATTCTACAGAGCTTCCT 57.011 42.857 0.00 0.00 0.00 3.36
25 26 3.866651 TGCAATTCTACAGAGCTTCCTC 58.133 45.455 0.00 0.00 38.42 3.71
96 97 1.342496 TCACAGTCTCAAGAGTGCTGG 59.658 52.381 13.54 5.42 46.64 4.85
174 176 0.615331 ATCAACACAGCTGGTCGGAT 59.385 50.000 19.93 15.09 0.00 4.18
192 195 4.703703 GACCCTGGTCAAGTCAGC 57.296 61.111 11.45 0.00 44.02 4.26
238 241 2.785540 TCACTGTGCTTGATATGCCA 57.214 45.000 2.12 0.00 0.00 4.92
240 243 2.026915 TCACTGTGCTTGATATGCCACT 60.027 45.455 2.12 0.00 0.00 4.00
274 285 5.771469 CAAAGCATCACCAAGATACAACAA 58.229 37.500 0.00 0.00 34.43 2.83
286 297 7.611467 ACCAAGATACAACAAGCATTTCTATGA 59.389 33.333 0.00 0.00 33.37 2.15
336 347 6.081693 GCAAATGCAAGATCAATTGGAAAAC 58.918 36.000 5.42 0.00 41.59 2.43
392 403 2.036387 TCCTTGACCTCGACAAGTTCA 58.964 47.619 11.86 0.00 41.88 3.18
394 405 2.135933 CTTGACCTCGACAAGTTCACC 58.864 52.381 6.18 0.00 39.57 4.02
399 410 0.393077 CTCGACAAGTTCACCCAGGT 59.607 55.000 0.00 0.00 0.00 4.00
460 471 1.068352 AGAGGGTCTGGTTTGGCCTT 61.068 55.000 3.32 0.00 38.35 4.35
480 491 1.073125 TGAAACCCCATGTGATGACGT 59.927 47.619 0.00 0.00 0.00 4.34
560 571 0.907486 CTTCTGGCACTCTCCATGGA 59.093 55.000 15.27 15.27 35.22 3.41
580 592 5.885465 TGGATTAATGGGCAAAACCAAAAT 58.115 33.333 0.00 0.00 45.13 1.82
589 601 3.932089 GGCAAAACCAAAATACATCGCAT 59.068 39.130 0.00 0.00 38.86 4.73
594 606 1.946768 CCAAAATACATCGCATCGGGT 59.053 47.619 0.00 0.00 0.00 5.28
598 630 0.750249 ATACATCGCATCGGGTCACA 59.250 50.000 0.00 0.00 0.00 3.58
599 631 0.179121 TACATCGCATCGGGTCACAC 60.179 55.000 0.00 0.00 0.00 3.82
611 643 0.040425 GGTCACACACATTTGCGTCC 60.040 55.000 0.00 0.00 0.00 4.79
664 696 1.472082 CACATTAACATGCAAGGCGGA 59.528 47.619 0.00 0.00 33.05 5.54
676 708 0.182775 AAGGCGGACTCTTGGTTGTT 59.817 50.000 0.00 0.00 0.00 2.83
706 738 5.163513 CAACAATTCTATGACCTTTGGTGC 58.836 41.667 0.00 0.00 35.25 5.01
786 830 0.390860 GCGGATGGATGCTACTCTGT 59.609 55.000 0.00 0.00 0.00 3.41
825 869 2.223782 TGCAGTTTGCTGGTTTGATCAC 60.224 45.455 0.00 0.00 45.31 3.06
841 885 0.950555 TCACGTCTGCAATGCCTCAC 60.951 55.000 1.53 0.00 0.00 3.51
859 903 4.566278 CCTCACATGGTTTGGAAGATCTGA 60.566 45.833 0.00 0.00 0.00 3.27
951 997 0.968405 TCAGAGGTTGGCCAAATTGC 59.032 50.000 22.47 7.60 37.19 3.56
953 999 0.539438 AGAGGTTGGCCAAATTGCGA 60.539 50.000 22.47 0.00 37.19 5.10
967 1013 5.261661 CAAATTGCGATCTTTCTCAGCTAC 58.738 41.667 0.00 0.00 0.00 3.58
1046 1092 2.030274 GGGTGTGGAACTTCATTTTCGG 60.030 50.000 0.00 0.00 38.04 4.30
1056 1102 0.178975 TCATTTTCGGTTGGCTGGGT 60.179 50.000 0.00 0.00 0.00 4.51
1078 1124 3.873812 AATCGGCGACCCCATCCC 61.874 66.667 13.76 0.00 0.00 3.85
1091 1137 1.447838 CATCCCGGTGTGACCTTCG 60.448 63.158 0.00 0.00 35.66 3.79
1130 1176 2.185310 ATTTCGAGCGAGGGCCAACT 62.185 55.000 6.18 0.00 41.24 3.16
1148 1194 3.735720 ACTAGGTTACTCTCGGAAGGT 57.264 47.619 0.00 0.00 0.00 3.50
1153 1199 2.101082 GGTTACTCTCGGAAGGTGATCC 59.899 54.545 0.00 0.00 36.05 3.36
1175 1221 4.397103 CCACTCTTTGCAAATGCTCATCTA 59.603 41.667 13.23 0.00 42.66 1.98
1222 1268 2.623416 GCTAGGGTCTTTTGCAACAAGT 59.377 45.455 0.00 0.00 0.00 3.16
1223 1269 3.818773 GCTAGGGTCTTTTGCAACAAGTA 59.181 43.478 0.00 0.00 0.00 2.24
1229 1275 4.556233 GTCTTTTGCAACAAGTATTCCCC 58.444 43.478 0.00 0.00 0.00 4.81
1290 1336 1.925285 CTTGGGTGATAGCAGGGGCA 61.925 60.000 0.00 0.00 44.61 5.36
1304 1350 3.117926 GCAGGGGCAATATTTTTGGGAAT 60.118 43.478 0.00 0.00 40.72 3.01
1309 1355 7.779326 CAGGGGCAATATTTTTGGGAATTATTT 59.221 33.333 0.00 0.00 0.00 1.40
1340 1386 6.183360 GGAGAGTAATCCCTTTATTTCGGACT 60.183 42.308 0.00 0.00 32.79 3.85
1360 1406 3.135712 ACTTGTGTGGTCCTGTAATGACA 59.864 43.478 0.00 0.00 32.70 3.58
1395 1445 9.103861 GTTCTTTCTCCTTATTTAGTGAGATGG 57.896 37.037 0.00 0.00 33.22 3.51
1649 1701 5.414765 TCGACAAGACTTATTGTAGCAGAGA 59.585 40.000 0.00 0.00 43.32 3.10
1663 1715 7.750229 TGTAGCAGAGAGAAAACATTCAATT 57.250 32.000 0.00 0.00 0.00 2.32
1674 1727 8.154649 AGAAAACATTCAATTGACGTAGAGTT 57.845 30.769 7.89 4.38 0.00 3.01
1756 1809 9.327529 CAAGATATTCCTACTAATCGTCGTAAC 57.672 37.037 0.00 0.00 0.00 2.50
1844 1897 6.200854 GTCACAATGGTTGAAAAATGACTTCC 59.799 38.462 0.00 0.00 32.26 3.46
2009 2066 5.817816 AGTAATTCTTAATGCTCTTCCACCG 59.182 40.000 0.00 0.00 0.00 4.94
2058 2115 1.136565 CAACATAGGGTTTGCGGCG 59.863 57.895 0.51 0.51 37.72 6.46
2065 2122 3.660111 GGTTTGCGGCGCTTCACT 61.660 61.111 33.26 0.00 0.00 3.41
2085 2142 4.094887 CACTGCCATCATTTACACCACTAC 59.905 45.833 0.00 0.00 0.00 2.73
2151 2208 2.441750 ACTTAGGGTTTGTGGCTCTTCA 59.558 45.455 0.00 0.00 0.00 3.02
2222 2279 6.932960 ACACTCTTAGTAACCACCATAACAAC 59.067 38.462 0.00 0.00 0.00 3.32
2235 2292 4.214758 ACCATAACAACGTAAAGCTTGTCC 59.785 41.667 0.00 0.00 30.11 4.02
2269 2326 9.898152 TTCCCTAAGAAATTTGTCAATGTTTTT 57.102 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.808466 AGCTCTGTAGAATTGCATCGA 57.192 42.857 0.00 0.00 0.00 3.59
1 2 3.247173 GGAAGCTCTGTAGAATTGCATCG 59.753 47.826 0.00 0.00 0.00 3.84
2 3 4.450053 AGGAAGCTCTGTAGAATTGCATC 58.550 43.478 0.00 0.00 0.00 3.91
11 12 2.542824 GCTTAGCGAGGAAGCTCTGTAG 60.543 54.545 8.59 0.00 45.67 2.74
12 13 1.405821 GCTTAGCGAGGAAGCTCTGTA 59.594 52.381 8.59 0.00 45.67 2.74
43 44 3.646637 GGAGGCTTAAGTATCTTAGGGCA 59.353 47.826 20.42 0.00 0.00 5.36
44 45 3.008157 GGGAGGCTTAAGTATCTTAGGGC 59.992 52.174 14.06 14.06 0.00 5.19
48 49 5.778542 AGAGTGGGAGGCTTAAGTATCTTA 58.221 41.667 4.02 0.00 0.00 2.10
56 57 2.567615 GAGTTGAGAGTGGGAGGCTTAA 59.432 50.000 0.00 0.00 0.00 1.85
59 60 0.178921 TGAGTTGAGAGTGGGAGGCT 60.179 55.000 0.00 0.00 0.00 4.58
139 140 3.509575 TGTTGATGTTATTCCCTTGCCAC 59.490 43.478 0.00 0.00 0.00 5.01
192 195 7.040478 TGTGGAAAATCACAAGAGATGTTAAGG 60.040 37.037 0.00 0.00 43.70 2.69
225 228 0.625316 ACCCAGTGGCATATCAAGCA 59.375 50.000 2.61 0.00 33.59 3.91
238 241 2.584835 TGCTTTGCTTGATACCCAGT 57.415 45.000 0.00 0.00 0.00 4.00
240 243 2.754552 GTGATGCTTTGCTTGATACCCA 59.245 45.455 0.00 0.00 0.00 4.51
274 285 2.565841 GTTCCCGCTCATAGAAATGCT 58.434 47.619 0.00 0.00 32.76 3.79
286 297 1.546476 GATATCTGATCCGTTCCCGCT 59.454 52.381 0.00 0.00 0.00 5.52
304 315 1.026182 TCTTGCATTTGCCGCTCGAT 61.026 50.000 0.00 0.00 41.18 3.59
308 319 0.889994 TTGATCTTGCATTTGCCGCT 59.110 45.000 0.00 0.00 41.18 5.52
336 347 1.808411 ATTTGTAGGGCGACACACAG 58.192 50.000 0.00 0.00 0.00 3.66
392 403 4.656112 CCATCTAAGTCTAATCACCTGGGT 59.344 45.833 0.00 0.00 0.00 4.51
394 405 4.346418 AGCCATCTAAGTCTAATCACCTGG 59.654 45.833 0.00 0.00 0.00 4.45
399 410 7.618019 AACCATAGCCATCTAAGTCTAATCA 57.382 36.000 0.00 0.00 0.00 2.57
401 412 6.712547 GCAAACCATAGCCATCTAAGTCTAAT 59.287 38.462 0.00 0.00 0.00 1.73
452 463 1.055040 CATGGGGTTTCAAGGCCAAA 58.945 50.000 5.01 0.00 0.00 3.28
460 471 1.073125 ACGTCATCACATGGGGTTTCA 59.927 47.619 0.00 0.00 0.00 2.69
480 491 3.751175 CGCATAGAAAAGGTTCTTGTCCA 59.249 43.478 0.00 0.00 41.55 4.02
530 541 2.507992 CCAGAAGCTCGCCGACAG 60.508 66.667 0.00 0.00 0.00 3.51
560 571 7.279758 CGATGTATTTTGGTTTTGCCCATTAAT 59.720 33.333 0.00 0.00 33.60 1.40
580 592 0.179121 GTGTGACCCGATGCGATGTA 60.179 55.000 0.00 0.00 0.00 2.29
589 601 1.502990 CGCAAATGTGTGTGACCCGA 61.503 55.000 0.00 0.00 0.00 5.14
598 630 1.178534 CCTTGGGGACGCAAATGTGT 61.179 55.000 0.00 0.00 42.13 3.72
599 631 1.586028 CCTTGGGGACGCAAATGTG 59.414 57.895 3.41 0.00 33.58 3.21
633 665 4.797471 CATGTTAATGTGTGTGACCCAAG 58.203 43.478 0.00 0.00 0.00 3.61
664 696 4.137543 GTTGGATCAGAACAACCAAGAGT 58.862 43.478 9.24 0.00 41.97 3.24
676 708 6.566079 AGGTCATAGAATTGTTGGATCAGA 57.434 37.500 0.00 0.00 0.00 3.27
706 738 1.926511 GATGCACCGCCTGAGTTTGG 61.927 60.000 0.00 0.00 0.00 3.28
825 869 0.098200 CATGTGAGGCATTGCAGACG 59.902 55.000 11.39 0.00 35.19 4.18
841 885 3.128242 GTGCTCAGATCTTCCAAACCATG 59.872 47.826 0.00 0.00 0.00 3.66
859 903 3.933861 ATTTAATCTTCGGGAGGTGCT 57.066 42.857 0.00 0.00 0.00 4.40
932 978 0.968405 GCAATTTGGCCAACCTCTGA 59.032 50.000 20.35 1.87 36.63 3.27
951 997 5.163913 CCTTTTGTGTAGCTGAGAAAGATCG 60.164 44.000 0.00 0.00 0.00 3.69
953 999 5.006386 CCCTTTTGTGTAGCTGAGAAAGAT 58.994 41.667 0.00 0.00 0.00 2.40
967 1013 4.048504 GTCGATTTTGGTTCCCTTTTGTG 58.951 43.478 0.00 0.00 0.00 3.33
982 1028 1.460743 CATGATATGCGCCGTCGATTT 59.539 47.619 4.18 0.00 38.10 2.17
989 1035 1.599071 ACTTGAACATGATATGCGCCG 59.401 47.619 4.18 0.00 0.00 6.46
1046 1092 1.293179 GATTGCCAACCCAGCCAAC 59.707 57.895 0.00 0.00 0.00 3.77
1091 1137 1.241315 CCACCATTGGTTCACCGTCC 61.241 60.000 5.34 0.00 38.23 4.79
1130 1176 3.726557 TCACCTTCCGAGAGTAACCTA 57.273 47.619 0.00 0.00 0.00 3.08
1148 1194 3.159472 AGCATTTGCAAAGAGTGGATCA 58.841 40.909 18.19 0.00 45.16 2.92
1153 1199 4.436242 AGATGAGCATTTGCAAAGAGTG 57.564 40.909 18.19 12.06 45.16 3.51
1175 1221 3.326747 CTTTCGTTCCAAATCTCCGAGT 58.673 45.455 0.00 0.00 0.00 4.18
1260 1306 1.140312 TCACCCAAGTCTTTGCCTCT 58.860 50.000 0.00 0.00 32.79 3.69
1290 1336 9.839817 CCCGGTAAAATAATTCCCAAAAATATT 57.160 29.630 0.00 0.00 0.00 1.28
1304 1350 6.178607 GGGATTACTCTCCCGGTAAAATAA 57.821 41.667 0.00 0.00 45.41 1.40
1340 1386 3.847671 TGTCATTACAGGACCACACAA 57.152 42.857 0.00 0.00 34.36 3.33
1378 1428 4.437682 TGCCCCATCTCACTAAATAAGG 57.562 45.455 0.00 0.00 0.00 2.69
1568 1620 9.259832 AGAATCAAATCCTAATGTTAGCCTTTT 57.740 29.630 0.00 0.00 0.00 2.27
1649 1701 7.730364 ACTCTACGTCAATTGAATGTTTTCT 57.270 32.000 10.35 0.00 32.78 2.52
1663 1715 3.188159 AGCACCAAAAACTCTACGTCA 57.812 42.857 0.00 0.00 0.00 4.35
1674 1727 2.360801 GGTTAGCACTGAAGCACCAAAA 59.639 45.455 0.00 0.00 36.85 2.44
1756 1809 8.278482 CTTGACAAGACAAGAGCTTTAATTTG 57.722 34.615 9.76 0.00 46.85 2.32
1806 1859 3.980775 CCATTGTGACGGAAAACATTGAC 59.019 43.478 0.00 0.00 32.15 3.18
1917 1970 8.980596 AGGATGGATGAGCAAATTATGTAAAAA 58.019 29.630 0.00 0.00 0.00 1.94
1918 1971 8.537728 AGGATGGATGAGCAAATTATGTAAAA 57.462 30.769 0.00 0.00 0.00 1.52
1919 1972 8.537728 AAGGATGGATGAGCAAATTATGTAAA 57.462 30.769 0.00 0.00 0.00 2.01
1920 1973 9.812347 ATAAGGATGGATGAGCAAATTATGTAA 57.188 29.630 0.00 0.00 0.00 2.41
1925 1979 9.071276 GAGAAATAAGGATGGATGAGCAAATTA 57.929 33.333 0.00 0.00 0.00 1.40
1987 2044 5.741011 ACGGTGGAAGAGCATTAAGAATTA 58.259 37.500 0.00 0.00 0.00 1.40
2058 2115 3.428045 GGTGTAAATGATGGCAGTGAAGC 60.428 47.826 0.00 0.00 0.00 3.86
2065 2122 4.568072 AGTAGTGGTGTAAATGATGGCA 57.432 40.909 0.00 0.00 0.00 4.92
2085 2142 4.699735 TGTATGTATTTGTGCTGACCCAAG 59.300 41.667 0.00 0.00 0.00 3.61
2151 2208 5.761234 TCAGACATTGTTTAAGTTTAGCGGT 59.239 36.000 0.00 0.00 0.00 5.68
2213 2270 4.454504 AGGACAAGCTTTACGTTGTTATGG 59.545 41.667 0.00 0.00 37.02 2.74
2222 2279 5.333875 GGAACTTTACAGGACAAGCTTTACG 60.334 44.000 0.00 0.00 0.00 3.18
2235 2292 8.846211 TGACAAATTTCTTAGGGAACTTTACAG 58.154 33.333 0.00 0.00 43.67 2.74
2269 2326 6.739331 AGGGTATTTTGACAATTTTGGTGA 57.261 33.333 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.