Multiple sequence alignment - TraesCS5B01G407700

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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 TraesCS5B01G407700 chr5B 100.000 2578 0 0 1 2578 583471566 583474143 0.000000e+00 4761
1 TraesCS5B01G407700 chr5A 87.113 1777 115 49 1 1735 595406948 595408652 0.000000e+00 1908
2 TraesCS5B01G407700 chr5A 92.174 690 36 6 1904 2578 595408663 595409349 0.000000e+00 959
3 TraesCS5B01G407700 chr5D 91.398 1302 54 21 1318 2577 476011351 476012636 0.000000e+00 1731
4 TraesCS5B01G407700 chr5D 90.065 463 23 10 821 1260 476010877 476011339 1.720000e-161 579
5 TraesCS5B01G407700 chr5D 91.176 306 22 5 1 303 476009884 476010187 6.640000e-111 411
6 TraesCS5B01G407700 chr5D 86.610 351 16 9 458 797 476010548 476010878 2.440000e-95 359
7 TraesCS5B01G407700 chr3B 89.268 792 41 20 830 1592 689166066 689166842 0.000000e+00 952
8 TraesCS5B01G407700 chr3B 90.368 353 15 11 452 795 689165727 689166069 1.820000e-121 446


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 TraesCS5B01G407700 chr5B 583471566 583474143 2577 False 4761.0 4761 100.00000 1 2578 1 chr5B.!!$F1 2577
1 TraesCS5B01G407700 chr5A 595406948 595409349 2401 False 1433.5 1908 89.64350 1 2578 2 chr5A.!!$F1 2577
2 TraesCS5B01G407700 chr5D 476009884 476012636 2752 False 770.0 1731 89.81225 1 2577 4 chr5D.!!$F1 2576
3 TraesCS5B01G407700 chr3B 689165727 689166842 1115 False 699.0 952 89.81800 452 1592 2 chr3B.!!$F1 1140

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
953 1184 0.032267 GGCGCCTCTGTATGTACTCC 59.968 60.0 22.15 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2290 0.0293 CAAGGTTTATGCCGCCGATG 59.971 55.0 0.0 0.0 0.0 3.84 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
22 23 1.896220 TACTGTGGCCTTCAAAGCAG 58.104 50.000 3.32 3.70 33.97 4.24
27 28 0.038166 TGGCCTTCAAAGCAGGGTAG 59.962 55.000 3.32 0.00 31.20 3.18
71 72 4.154195 CCCCTTTCACTTACTGTTGATTCG 59.846 45.833 0.00 0.00 0.00 3.34
125 126 3.818961 ATCGAATGAACAAGCAGTGTG 57.181 42.857 0.00 0.00 40.60 3.82
180 181 5.067544 TGAGCATTTTCATGTCTTGTTGTCA 59.932 36.000 0.00 0.00 32.28 3.58
216 217 8.917088 ACCATGTATTTTCTCCTTGATAATTGG 58.083 33.333 0.00 0.00 32.58 3.16
226 227 9.730705 TTCTCCTTGATAATTGGCAGATATAAG 57.269 33.333 0.00 0.00 0.00 1.73
227 228 9.104713 TCTCCTTGATAATTGGCAGATATAAGA 57.895 33.333 0.00 0.00 0.00 2.10
228 229 9.902684 CTCCTTGATAATTGGCAGATATAAGAT 57.097 33.333 0.00 0.00 0.00 2.40
252 255 9.196552 GATAATTTTGGGTGTCTTTTTCTCAAG 57.803 33.333 0.00 0.00 0.00 3.02
256 259 3.053245 TGGGTGTCTTTTTCTCAAGGGAA 60.053 43.478 0.00 0.00 0.00 3.97
332 492 2.550830 CCAGCTTGTGGTAAGTCTGT 57.449 50.000 0.00 0.00 42.17 3.41
344 504 3.065095 GGTAAGTCTGTACTAGCAGTCGG 59.935 52.174 0.00 0.00 37.70 4.79
391 553 4.093408 GTCATCAGCTTGCTTGATAAACGA 59.907 41.667 0.00 0.00 33.67 3.85
467 684 3.430098 GCTTGGAACATGAAAACACCACA 60.430 43.478 0.00 0.00 39.30 4.17
634 855 2.113243 GAAGTGCAGAACGGTCCCCT 62.113 60.000 0.00 0.00 0.00 4.79
667 888 1.466167 GTAGTTGTCGCCGTCAGACTA 59.534 52.381 0.00 0.00 39.24 2.59
946 1177 2.111878 GCCATGGCGCCTCTGTAT 59.888 61.111 29.70 9.53 0.00 2.29
947 1178 2.256591 GCCATGGCGCCTCTGTATG 61.257 63.158 29.70 21.40 0.00 2.39
948 1179 1.146930 CCATGGCGCCTCTGTATGT 59.853 57.895 29.70 0.07 0.00 2.29
949 1180 0.392706 CCATGGCGCCTCTGTATGTA 59.607 55.000 29.70 3.35 0.00 2.29
950 1181 1.502231 CATGGCGCCTCTGTATGTAC 58.498 55.000 29.70 0.00 0.00 2.90
951 1182 1.069204 CATGGCGCCTCTGTATGTACT 59.931 52.381 29.70 0.00 0.00 2.73
953 1184 0.032267 GGCGCCTCTGTATGTACTCC 59.968 60.000 22.15 0.00 0.00 3.85
1034 1289 2.830923 CACTCACACTGAAGATCTCCCT 59.169 50.000 0.00 0.00 0.00 4.20
1056 1311 0.031314 TCGATCCTCGCATTCAGCTC 59.969 55.000 0.00 0.00 40.21 4.09
1060 1315 2.226896 CCTCGCATTCAGCTCGTCG 61.227 63.158 0.00 0.00 42.61 5.12
1077 1332 0.808125 TCGCTCTCTGTCTCTCTTGC 59.192 55.000 0.00 0.00 0.00 4.01
1106 1361 0.588252 CAGTTGTTCTGTTCCCTGCG 59.412 55.000 0.00 0.00 39.17 5.18
1166 1421 1.553690 CGGTGGAGGTGGACAGGATT 61.554 60.000 0.00 0.00 0.00 3.01
1174 1429 2.124695 GGACAGGATTCGGGCCAC 60.125 66.667 4.39 0.00 36.19 5.01
1476 1755 3.602390 TGCAACTAAAGTGTCTTTCGC 57.398 42.857 0.00 0.19 0.00 4.70
1553 1832 7.551262 TGTTACAATACAAATCAACGCCTATCT 59.449 33.333 0.00 0.00 0.00 1.98
1554 1833 6.604735 ACAATACAAATCAACGCCTATCTC 57.395 37.500 0.00 0.00 0.00 2.75
1555 1834 6.349300 ACAATACAAATCAACGCCTATCTCT 58.651 36.000 0.00 0.00 0.00 3.10
1556 1835 6.823689 ACAATACAAATCAACGCCTATCTCTT 59.176 34.615 0.00 0.00 0.00 2.85
1557 1836 7.011482 ACAATACAAATCAACGCCTATCTCTTC 59.989 37.037 0.00 0.00 0.00 2.87
1566 1845 2.690497 CGCCTATCTCTTCTCCAGTCAA 59.310 50.000 0.00 0.00 0.00 3.18
1592 1871 4.122776 CGTTTTCATGATGGTCCCTAGAG 58.877 47.826 0.00 0.00 0.00 2.43
1631 1912 1.728425 CATGGGCATGTACGATCGATG 59.272 52.381 24.34 16.05 34.23 3.84
1642 1923 1.658717 GATCGATGGAGACGGTGCG 60.659 63.158 0.54 0.00 0.00 5.34
1660 1941 4.432741 GCCAAGTGGGAGGGGAGC 62.433 72.222 0.00 0.00 40.01 4.70
1662 1943 1.306997 CCAAGTGGGAGGGGAGCTA 60.307 63.158 0.00 0.00 40.01 3.32
1717 1998 7.867752 AGTAGTAGCGAAATATCTCTCTTCAC 58.132 38.462 0.00 0.00 0.00 3.18
1741 2022 9.855361 CACTGAGATATTTTTGCTTCTTATACG 57.145 33.333 0.00 0.00 0.00 3.06
1757 2056 1.216122 TACGTTTTTGGAACGGACGG 58.784 50.000 14.68 0.00 46.86 4.79
1767 2066 1.145803 GAACGGACGGGAAACTCAAG 58.854 55.000 0.00 0.00 0.00 3.02
1789 2088 9.671279 TCAAGCTTGACATAAAGAAATATCTCA 57.329 29.630 25.16 0.00 30.57 3.27
1829 2128 6.560253 TGCTTCAATTCTTACCAGAAACTC 57.440 37.500 0.00 0.00 42.53 3.01
1848 2147 6.656632 AACTCAGACATGAAGTACAGAAGA 57.343 37.500 0.00 0.00 34.23 2.87
1883 2183 1.597937 GCCAGTGCAACGTTTTCTCTG 60.598 52.381 16.42 16.42 45.86 3.35
1885 2185 2.354510 CCAGTGCAACGTTTTCTCTGAA 59.645 45.455 21.43 0.00 45.86 3.02
1973 2273 1.871039 CACCTCACAAAACGTTCCGAT 59.129 47.619 0.00 0.00 0.00 4.18
2175 2490 2.032681 GGGCAGTCAGTGGTCACC 59.967 66.667 0.00 0.00 0.00 4.02
2176 2491 2.357517 GGCAGTCAGTGGTCACCG 60.358 66.667 0.00 0.00 0.00 4.94
2548 2878 0.034059 CTTCCTTCACACCTGCGAGT 59.966 55.000 0.00 0.00 0.00 4.18
2566 2896 3.640592 GAGTTGTATAAGTAGAGCCGGC 58.359 50.000 21.89 21.89 0.00 6.13
2567 2897 3.028850 AGTTGTATAAGTAGAGCCGGCA 58.971 45.455 31.54 4.59 0.00 5.69
2570 2900 3.028850 TGTATAAGTAGAGCCGGCAACT 58.971 45.455 31.54 27.52 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 5.518848 TGACAACAAGACATGAAAATGCT 57.481 34.783 0.00 0.00 0.00 3.79
165 166 7.041635 ACAATGAAATGACAACAAGACATGA 57.958 32.000 0.00 0.00 32.96 3.07
216 217 9.289782 AGACACCCAAAATTATCTTATATCTGC 57.710 33.333 0.00 0.00 0.00 4.26
226 227 9.196552 CTTGAGAAAAAGACACCCAAAATTATC 57.803 33.333 0.00 0.00 0.00 1.75
227 228 8.150296 CCTTGAGAAAAAGACACCCAAAATTAT 58.850 33.333 0.00 0.00 0.00 1.28
228 229 7.418483 CCCTTGAGAAAAAGACACCCAAAATTA 60.418 37.037 0.00 0.00 0.00 1.40
229 230 6.348498 CCTTGAGAAAAAGACACCCAAAATT 58.652 36.000 0.00 0.00 0.00 1.82
268 271 5.415701 TGTCTGAGATTTTTATGGTCCAAGC 59.584 40.000 0.00 0.00 0.00 4.01
303 309 1.068055 CCACAAGCTGGCAATGTTCTC 60.068 52.381 0.00 0.00 31.36 2.87
304 310 0.963962 CCACAAGCTGGCAATGTTCT 59.036 50.000 0.00 0.00 31.36 3.01
305 311 0.675633 ACCACAAGCTGGCAATGTTC 59.324 50.000 0.00 0.00 45.32 3.18
306 312 1.993956 TACCACAAGCTGGCAATGTT 58.006 45.000 0.00 0.00 45.32 2.71
307 313 1.888512 CTTACCACAAGCTGGCAATGT 59.111 47.619 0.00 0.00 45.32 2.71
308 314 1.888512 ACTTACCACAAGCTGGCAATG 59.111 47.619 0.00 0.00 45.32 2.82
309 315 2.162681 GACTTACCACAAGCTGGCAAT 58.837 47.619 0.00 0.00 45.32 3.56
329 489 3.784701 ATTGACCGACTGCTAGTACAG 57.215 47.619 0.00 0.00 43.59 2.74
332 492 5.648178 TTTGTATTGACCGACTGCTAGTA 57.352 39.130 0.00 0.00 0.00 1.82
344 504 7.145323 ACTGCTTTTGTGGTATTTGTATTGAC 58.855 34.615 0.00 0.00 0.00 3.18
378 540 3.056107 ACTGGTAGCTCGTTTATCAAGCA 60.056 43.478 0.00 0.00 38.51 3.91
391 553 1.203137 TGGTGTGGTAGACTGGTAGCT 60.203 52.381 0.00 0.00 0.00 3.32
483 700 6.480524 TGTAACTGTGTGAATTATGCTGTC 57.519 37.500 0.00 0.00 0.00 3.51
529 748 4.438336 CGAACGCCAACTCTGTCTAGAATA 60.438 45.833 0.00 0.00 31.21 1.75
634 855 4.261322 GCGACAACTACGGAGGTATATCAA 60.261 45.833 0.00 0.00 0.00 2.57
667 888 1.043673 GGTACCGTGGGCTCTCTGAT 61.044 60.000 0.00 0.00 0.00 2.90
765 996 4.889427 TCGTGCTCCGAATGACAG 57.111 55.556 0.00 0.00 44.03 3.51
856 1087 2.295349 CACACAGGATTGAAGCTTTGCT 59.705 45.455 0.00 0.00 42.56 3.91
857 1088 2.669364 CACACAGGATTGAAGCTTTGC 58.331 47.619 0.00 0.00 0.00 3.68
865 1096 1.527034 GCTTCAGCACACAGGATTGA 58.473 50.000 0.00 0.00 41.59 2.57
944 1175 7.819415 GCATGTGCAGATAAATAGGAGTACATA 59.181 37.037 0.00 0.00 41.59 2.29
946 1177 5.991606 GCATGTGCAGATAAATAGGAGTACA 59.008 40.000 0.00 0.00 41.59 2.90
947 1178 6.473397 GCATGTGCAGATAAATAGGAGTAC 57.527 41.667 0.00 0.00 41.59 2.73
1056 1311 1.083489 AAGAGAGACAGAGAGCGACG 58.917 55.000 0.00 0.00 0.00 5.12
1060 1315 1.736696 GCTGCAAGAGAGACAGAGAGC 60.737 57.143 0.00 0.00 34.07 4.09
1077 1332 0.320247 AGAACAACTGAGCCGAGCTG 60.320 55.000 2.98 0.00 39.88 4.24
1106 1361 4.286320 ATGGATCGGTCGCGGCTC 62.286 66.667 11.94 0.00 0.00 4.70
1275 1545 0.454600 CAAGCCATGACACCATCAGC 59.545 55.000 0.00 0.00 41.91 4.26
1476 1755 0.460811 TCAGCAGGCTACAGCAATCG 60.461 55.000 3.24 0.00 44.36 3.34
1553 1832 1.996798 ACGGACTTGACTGGAGAAGA 58.003 50.000 0.00 0.00 0.00 2.87
1554 1833 2.821991 AACGGACTTGACTGGAGAAG 57.178 50.000 0.00 0.00 0.00 2.85
1555 1834 3.118555 TGAAAACGGACTTGACTGGAGAA 60.119 43.478 0.00 0.00 0.00 2.87
1556 1835 2.432874 TGAAAACGGACTTGACTGGAGA 59.567 45.455 0.00 0.00 0.00 3.71
1557 1836 2.833794 TGAAAACGGACTTGACTGGAG 58.166 47.619 0.00 0.00 0.00 3.86
1566 1845 2.618045 GGGACCATCATGAAAACGGACT 60.618 50.000 0.00 0.00 0.00 3.85
1617 1896 2.575363 CGTCTCCATCGATCGTACATG 58.425 52.381 15.94 11.39 0.00 3.21
1642 1923 3.732849 CTCCCCTCCCACTTGGCC 61.733 72.222 0.00 0.00 0.00 5.36
1660 1941 5.932303 CCCGAGTGGTGGTAATGAATTATAG 59.068 44.000 0.00 0.00 0.00 1.31
1662 1943 4.714632 CCCGAGTGGTGGTAATGAATTAT 58.285 43.478 0.00 0.00 0.00 1.28
1741 2022 1.023502 TTCCCGTCCGTTCCAAAAAC 58.976 50.000 0.00 0.00 0.00 2.43
1757 2056 6.560253 TCTTTATGTCAAGCTTGAGTTTCC 57.440 37.500 29.13 17.08 37.98 3.13
1767 2066 9.928236 GAAGTGAGATATTTCTTTATGTCAAGC 57.072 33.333 0.00 0.00 34.70 4.01
1789 2088 4.937620 TGAAGCAAAATATCTCAGCGAAGT 59.062 37.500 0.00 0.00 0.00 3.01
1829 2128 5.173664 TGCATCTTCTGTACTTCATGTCTG 58.826 41.667 0.00 0.00 0.00 3.51
1848 2147 1.339055 ACTGGCTAACACACGATGCAT 60.339 47.619 0.00 0.00 0.00 3.96
1885 2185 0.398318 GGGCAGGTGAAGTTCAGACT 59.602 55.000 5.62 4.99 37.87 3.24
1917 2217 4.138487 ACGTTGAGGTTCAGAGAAAACT 57.862 40.909 0.00 0.00 0.00 2.66
1990 2290 0.029300 CAAGGTTTATGCCGCCGATG 59.971 55.000 0.00 0.00 0.00 3.84
1994 2294 1.312371 TGAGCAAGGTTTATGCCGCC 61.312 55.000 0.00 0.00 44.91 6.13
2070 2384 2.594013 TGCTCGCATGGTTGTGCA 60.594 55.556 0.00 0.00 45.30 4.57
2523 2850 4.898607 GTGTGAAGGAAGGCACCA 57.101 55.556 3.78 0.00 34.19 4.17
2548 2878 3.449737 AGTTGCCGGCTCTACTTATACAA 59.550 43.478 29.70 5.56 0.00 2.41


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

AutoCloner maintained by Alex Coulton.