Multiple sequence alignment - TraesCS3B01G378700

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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 TraesCS3B01G378700 chr3B 100.000 2543 0 0 1 2543 596856058 596858600 0.000000e+00 4697
1 TraesCS3B01G378700 chr3A 90.557 2605 177 32 1 2543 596361358 596363955 0.000000e+00 3384
2 TraesCS3B01G378700 chr3D 90.802 1870 103 29 1 1812 454230078 454231936 0.000000e+00 2436
3 TraesCS3B01G378700 chr3D 88.022 718 63 15 1847 2543 454231995 454232710 0.000000e+00 828
4 TraesCS3B01G378700 chr3D 82.510 263 39 5 5 263 435486036 435485777 9.160000e-55 224
5 TraesCS3B01G378700 chr6D 88.750 320 23 8 2235 2543 373342297 373342614 1.850000e-101 379
6 TraesCS3B01G378700 chr6D 91.760 267 19 3 1977 2240 373341883 373342149 4.000000e-98 368
7 TraesCS3B01G378700 chr7A 83.774 265 33 8 2 261 694329402 694329661 2.530000e-60 243
8 TraesCS3B01G378700 chr5A 83.650 263 35 8 2 257 338390392 338390131 9.090000e-60 241
9 TraesCS3B01G378700 chr4D 83.270 263 32 9 2 258 40220803 40221059 5.470000e-57 231
10 TraesCS3B01G378700 chr7B 83.203 256 38 4 5 257 137557212 137556959 1.970000e-56 230
11 TraesCS3B01G378700 chr4B 82.707 266 32 11 2 257 348949633 348949894 9.160000e-55 224
12 TraesCS3B01G378700 chr4B 82.812 256 32 9 5 253 68089012 68088762 4.260000e-53 219
13 TraesCS3B01G378700 chr5B 82.171 258 34 10 5 256 330004923 330004672 7.130000e-51 211


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 TraesCS3B01G378700 chr3B 596856058 596858600 2542 False 4697.0 4697 100.000 1 2543 1 chr3B.!!$F1 2542
1 TraesCS3B01G378700 chr3A 596361358 596363955 2597 False 3384.0 3384 90.557 1 2543 1 chr3A.!!$F1 2542
2 TraesCS3B01G378700 chr3D 454230078 454232710 2632 False 1632.0 2436 89.412 1 2543 2 chr3D.!!$F1 2542
3 TraesCS3B01G378700 chr6D 373341883 373342614 731 False 373.5 379 90.255 1977 2543 2 chr6D.!!$F1 566

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
558 611 0.945265 CGACCCTTTAAACGTCCGCA 60.945 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1803 0.17902 TCTGGCCCAGTTTGTGTGAG 60.179 55.0 11.27 0.0 32.61 3.51 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
165 170 6.039941 TCTGAAAAACCAAAAGGATTTCGCTA 59.960 34.615 0.00 0.00 37.28 4.26
207 212 6.321181 GTGGCAAAATGGATAGTAATGAGGAA 59.679 38.462 0.00 0.00 0.00 3.36
209 214 6.442112 GCAAAATGGATAGTAATGAGGAAGC 58.558 40.000 0.00 0.00 0.00 3.86
236 241 7.860613 TGAATCATATTACTTTATGCCACACG 58.139 34.615 0.00 0.00 31.02 4.49
253 258 2.742053 ACACGTGTGGCACTTATCATTC 59.258 45.455 22.71 0.00 34.19 2.67
273 278 8.058667 TCATTCGGGCTAATTAATATACGAGA 57.941 34.615 0.00 0.00 0.00 4.04
274 279 8.692710 TCATTCGGGCTAATTAATATACGAGAT 58.307 33.333 0.00 0.00 0.00 2.75
372 381 1.422531 AAATGTTGGCATGTGGTGGT 58.577 45.000 0.00 0.00 35.15 4.16
406 430 1.064003 ACATGTAAGTGGGTGCCTCA 58.936 50.000 0.00 0.00 0.00 3.86
445 469 1.065199 CCCACTAGCAGCCAATTCTGA 60.065 52.381 0.00 0.00 36.19 3.27
472 496 5.125097 GTCGTAACCCAGTCTCATCTTTCTA 59.875 44.000 0.00 0.00 0.00 2.10
485 509 5.101529 TCATCTTTCTACCCCCTTTCTTCT 58.898 41.667 0.00 0.00 0.00 2.85
496 549 3.570125 CCCCTTTCTTCTGTTGTTTCCTC 59.430 47.826 0.00 0.00 0.00 3.71
532 585 4.862902 GAGCATCTATAGCTGAACCTGA 57.137 45.455 7.77 0.00 43.58 3.86
534 587 3.005261 AGCATCTATAGCTGAACCTGACG 59.995 47.826 7.77 0.00 41.61 4.35
545 598 0.974383 AACCTGACGAATTCGACCCT 59.026 50.000 33.05 11.76 43.02 4.34
558 611 0.945265 CGACCCTTTAAACGTCCGCA 60.945 55.000 0.00 0.00 0.00 5.69
567 620 2.257286 AAACGTCCGCAGATGCATGC 62.257 55.000 11.82 11.82 42.21 4.06
588 641 1.687494 GCGTGATCTTGGACAGCGAC 61.687 60.000 0.00 0.00 0.00 5.19
639 692 4.993705 ATCACACTCCTTAACCCTCAAA 57.006 40.909 0.00 0.00 0.00 2.69
867 925 2.208431 CATCTCATCTGACGGAAAGCC 58.792 52.381 0.00 0.00 0.00 4.35
923 981 4.942852 CTTCACCAGGAAGCTGAGTATAG 58.057 47.826 0.00 0.00 45.99 1.31
924 982 4.251103 TCACCAGGAAGCTGAGTATAGA 57.749 45.455 0.00 0.00 0.00 1.98
946 1004 7.369803 AGATCATTTGCCTATATACAAAGCG 57.630 36.000 0.00 0.00 39.01 4.68
950 1008 3.469008 TGCCTATATACAAAGCGCAGT 57.531 42.857 11.47 7.88 0.00 4.40
953 1011 4.035091 TGCCTATATACAAAGCGCAGTTTG 59.965 41.667 17.65 17.65 42.21 2.93
968 1026 2.354510 CAGTTTGTTTCTCCACTTCGCA 59.645 45.455 0.00 0.00 0.00 5.10
985 1043 1.160137 GCAGCATCCGAAGTTTGTCT 58.840 50.000 0.00 0.00 0.00 3.41
1056 1119 2.125269 ACGCCGGTTACCATCTGC 60.125 61.111 1.90 0.00 0.00 4.26
1068 1131 0.963856 CCATCTGCAGCAGGCTTCAA 60.964 55.000 22.62 1.78 45.15 2.69
1083 1146 0.108585 TTCAAAGAGCCTTCCACGCT 59.891 50.000 0.00 0.00 39.95 5.07
1251 1314 0.460987 CTCCAGTAGGCAAAGCTCCG 60.461 60.000 0.00 0.00 33.74 4.63
1610 1673 2.939103 AGCTGAATTACGCATCTCCAAC 59.061 45.455 0.00 0.00 0.00 3.77
1621 1684 2.636830 CATCTCCAACGCCATTCTCTT 58.363 47.619 0.00 0.00 0.00 2.85
1683 1747 2.869897 CTCTCCGTTCTGCTGTAACTC 58.130 52.381 0.00 0.00 0.00 3.01
1694 1758 6.605471 TCTGCTGTAACTCCAGATTTTCTA 57.395 37.500 0.00 0.00 34.23 2.10
1738 1803 0.256177 GGGATCACCAGGAGGGAAAC 59.744 60.000 0.00 0.00 41.15 2.78
1755 1820 0.033601 AACTCACACAAACTGGGCCA 60.034 50.000 5.85 5.85 0.00 5.36
1767 1832 1.613928 TGGGCCAGATTGTACCGGA 60.614 57.895 9.46 0.00 0.00 5.14
1771 1836 1.676006 GGCCAGATTGTACCGGAAATG 59.324 52.381 9.46 0.00 0.00 2.32
1839 1905 9.921637 ATCTATTTATTTTGCAACTCGGAAAAA 57.078 25.926 0.00 0.00 46.36 1.94
1893 1983 1.021390 ATCCTTCGCCGAACTGCAAG 61.021 55.000 0.00 0.00 42.29 4.01
1895 1985 3.314388 CTTCGCCGAACTGCAAGGC 62.314 63.158 10.91 10.91 46.88 4.35
1900 1990 3.121030 CGAACTGCAAGGCCCTCG 61.121 66.667 0.00 0.00 39.30 4.63
1908 1998 0.453390 GCAAGGCCCTCGAAATTGAG 59.547 55.000 0.00 0.00 35.70 3.02
1926 2016 2.045131 GGCAGCTCTTGGAGGCTTG 61.045 63.158 0.00 0.00 36.59 4.01
1931 2021 1.378250 CTCTTGGAGGCTTGCAGGG 60.378 63.158 0.00 0.00 0.00 4.45
1932 2022 1.845627 CTCTTGGAGGCTTGCAGGGA 61.846 60.000 0.00 0.00 0.00 4.20
1933 2023 1.210204 TCTTGGAGGCTTGCAGGGAT 61.210 55.000 0.00 0.00 0.00 3.85
1934 2024 0.548031 CTTGGAGGCTTGCAGGGATA 59.452 55.000 0.00 0.00 0.00 2.59
1935 2025 1.144503 CTTGGAGGCTTGCAGGGATAT 59.855 52.381 0.00 0.00 0.00 1.63
1936 2026 2.116869 TGGAGGCTTGCAGGGATATA 57.883 50.000 0.00 0.00 0.00 0.86
1937 2027 2.636005 TGGAGGCTTGCAGGGATATAT 58.364 47.619 0.00 0.00 0.00 0.86
1938 2028 3.802132 TGGAGGCTTGCAGGGATATATA 58.198 45.455 0.00 0.00 0.00 0.86
1939 2029 3.519510 TGGAGGCTTGCAGGGATATATAC 59.480 47.826 0.00 0.00 0.00 1.47
1940 2030 3.118223 GGAGGCTTGCAGGGATATATACC 60.118 52.174 5.76 5.76 0.00 2.73
1941 2031 2.501723 AGGCTTGCAGGGATATATACCG 59.498 50.000 8.42 5.05 35.28 4.02
1942 2032 2.236395 GGCTTGCAGGGATATATACCGT 59.764 50.000 8.42 0.16 35.28 4.83
1949 2039 3.994392 CAGGGATATATACCGTGTGTTGC 59.006 47.826 8.42 0.00 38.15 4.17
1970 2060 6.317789 TGCTTCTGAACTTTTGATAGGTTG 57.682 37.500 0.00 0.00 0.00 3.77
2046 2162 2.163509 CAGGTCTCTCTCCTCGTCAAA 58.836 52.381 0.00 0.00 32.37 2.69
2144 2262 6.867662 AGTCTAAACTCAAATCAACCACAG 57.132 37.500 0.00 0.00 0.00 3.66
2147 2266 2.363306 ACTCAAATCAACCACAGGCA 57.637 45.000 0.00 0.00 0.00 4.75
2204 2324 0.678048 GCTGGTCTGTGATGGGTTCC 60.678 60.000 0.00 0.00 0.00 3.62
2240 2513 3.563808 CACAGCACTACCTTTACTTGCAA 59.436 43.478 0.00 0.00 35.57 4.08
2241 2514 4.216257 CACAGCACTACCTTTACTTGCAAT 59.784 41.667 0.00 0.00 35.57 3.56
2359 2639 1.337118 GCACAGGGAAATGGACCAAA 58.663 50.000 0.00 0.00 0.00 3.28
2501 2785 3.512724 TGCTGGTTAGTAGTAACACTCCC 59.487 47.826 19.61 5.16 40.46 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.838565 TCTTGGGCCAAAAGTTGTCATA 58.161 40.909 21.28 0.00 0.00 2.15
7 8 3.990959 TTTTCTTGGGCCAAAAGTTGT 57.009 38.095 21.28 0.00 0.00 3.32
155 160 5.741388 AACAGATGACATTAGCGAAATCC 57.259 39.130 0.00 0.00 0.00 3.01
186 191 7.814264 AGCTTCCTCATTACTATCCATTTTG 57.186 36.000 0.00 0.00 0.00 2.44
207 212 8.571336 GTGGCATAAAGTAATATGATTCAAGCT 58.429 33.333 0.00 0.00 35.69 3.74
209 214 9.669353 GTGTGGCATAAAGTAATATGATTCAAG 57.331 33.333 0.00 0.00 35.69 3.02
236 241 1.670811 CCCGAATGATAAGTGCCACAC 59.329 52.381 0.00 0.00 34.10 3.82
337 346 5.409214 CCAACATTTTGTGGGAGCTTAATTG 59.591 40.000 0.00 0.00 44.46 2.32
339 348 4.563374 GCCAACATTTTGTGGGAGCTTAAT 60.563 41.667 5.21 0.00 44.46 1.40
406 430 1.379527 GCCTAAAACGCTGCACCTAT 58.620 50.000 0.00 0.00 0.00 2.57
472 496 3.296854 GAAACAACAGAAGAAAGGGGGT 58.703 45.455 0.00 0.00 0.00 4.95
485 509 3.149196 GCAGATTGAGGAGGAAACAACA 58.851 45.455 0.00 0.00 0.00 3.33
524 577 1.337447 GGGTCGAATTCGTCAGGTTCA 60.337 52.381 25.93 2.59 40.80 3.18
532 585 3.392882 ACGTTTAAAGGGTCGAATTCGT 58.607 40.909 25.93 9.49 40.80 3.85
534 587 3.181527 CGGACGTTTAAAGGGTCGAATTC 60.182 47.826 12.21 0.00 0.00 2.17
545 598 1.514003 TGCATCTGCGGACGTTTAAA 58.486 45.000 0.00 0.00 45.83 1.52
558 611 2.203112 ATCACGCCGCATGCATCT 60.203 55.556 19.57 0.00 41.33 2.90
567 620 2.456119 GCTGTCCAAGATCACGCCG 61.456 63.158 0.00 0.00 0.00 6.46
569 622 1.446099 TCGCTGTCCAAGATCACGC 60.446 57.895 0.00 0.00 0.00 5.34
588 641 2.824041 CATTTGAGGGGCCGTCCG 60.824 66.667 22.54 5.81 36.01 4.79
867 925 2.285834 GGACGCATTTCGCTACATCTTG 60.286 50.000 0.00 0.00 43.23 3.02
923 981 6.024049 GCGCTTTGTATATAGGCAAATGATC 58.976 40.000 0.00 0.00 34.60 2.92
924 982 5.473162 TGCGCTTTGTATATAGGCAAATGAT 59.527 36.000 9.73 0.00 34.60 2.45
940 998 2.119457 GGAGAAACAAACTGCGCTTTG 58.881 47.619 17.65 17.65 37.20 2.77
941 999 1.748493 TGGAGAAACAAACTGCGCTTT 59.252 42.857 9.73 0.00 0.00 3.51
946 1004 2.854805 GCGAAGTGGAGAAACAAACTGC 60.855 50.000 0.00 0.00 0.00 4.40
950 1008 1.333619 GCTGCGAAGTGGAGAAACAAA 59.666 47.619 0.00 0.00 38.54 2.83
953 1011 1.129437 GATGCTGCGAAGTGGAGAAAC 59.871 52.381 0.00 0.00 38.54 2.78
968 1026 2.480419 CGAAAGACAAACTTCGGATGCT 59.520 45.455 0.00 0.00 37.93 3.79
1039 1102 2.125269 GCAGATGGTAACCGGCGT 60.125 61.111 6.01 0.00 0.00 5.68
1045 1108 0.393537 AGCCTGCTGCAGATGGTAAC 60.394 55.000 30.10 10.29 44.83 2.50
1046 1109 0.329261 AAGCCTGCTGCAGATGGTAA 59.671 50.000 30.10 0.00 44.83 2.85
1201 1264 2.032634 CACGTGCCGGCAATACAGT 61.033 57.895 34.66 22.23 0.00 3.55
1202 1265 2.784596 CACGTGCCGGCAATACAG 59.215 61.111 34.66 21.56 0.00 2.74
1281 1344 4.025401 GGTTTCTGTGGCACCGCG 62.025 66.667 16.26 0.00 0.00 6.46
1290 1353 2.980233 GCAGCAGCCGGTTTCTGT 60.980 61.111 18.22 0.00 34.21 3.41
1546 1609 2.289820 CCTGGCGATTCAGTTGATCATG 59.710 50.000 0.00 0.00 33.14 3.07
1610 1673 3.074412 ACACTGGTAAAAGAGAATGGCG 58.926 45.455 0.00 0.00 0.00 5.69
1683 1747 7.870509 TCCATCAACAAGATAGAAAATCTGG 57.129 36.000 0.00 0.00 34.43 3.86
1694 1758 6.548622 CCCAAGTGATAATCCATCAACAAGAT 59.451 38.462 0.00 0.00 45.28 2.40
1738 1803 0.179020 TCTGGCCCAGTTTGTGTGAG 60.179 55.000 11.27 0.00 32.61 3.51
1744 1809 1.818674 GGTACAATCTGGCCCAGTTTG 59.181 52.381 25.94 25.94 43.04 2.93
1755 1820 7.445402 CCAAGAATATCATTTCCGGTACAATCT 59.555 37.037 0.00 0.00 0.00 2.40
1767 1832 5.235186 CGAACTCGAGCCAAGAATATCATTT 59.765 40.000 13.61 0.00 43.02 2.32
1771 1836 3.707793 ACGAACTCGAGCCAAGAATATC 58.292 45.455 13.61 0.00 43.02 1.63
1839 1905 7.573968 AAGCGCAATAAATAGATCCTCTTTT 57.426 32.000 11.47 0.00 0.00 2.27
1841 1907 7.573968 AAAAGCGCAATAAATAGATCCTCTT 57.426 32.000 11.47 0.00 0.00 2.85
1859 1949 6.237490 CGGCGAAGGATAGTATAATAAAAGCG 60.237 42.308 0.00 0.00 0.00 4.68
1861 1951 8.645487 GTTCGGCGAAGGATAGTATAATAAAAG 58.355 37.037 24.41 0.00 0.00 2.27
1862 1952 8.362639 AGTTCGGCGAAGGATAGTATAATAAAA 58.637 33.333 24.41 0.00 0.00 1.52
1873 1963 0.248012 TTGCAGTTCGGCGAAGGATA 59.752 50.000 24.41 7.52 36.28 2.59
1900 1990 2.422832 CTCCAAGAGCTGCCTCAATTTC 59.577 50.000 0.00 0.00 40.68 2.17
1908 1998 2.045131 CAAGCCTCCAAGAGCTGCC 61.045 63.158 0.00 0.00 39.87 4.85
1926 2016 3.955650 ACACACGGTATATATCCCTGC 57.044 47.619 0.00 0.00 0.00 4.85
1931 2021 6.213677 TCAGAAGCAACACACGGTATATATC 58.786 40.000 0.00 0.00 0.00 1.63
1932 2022 6.156748 TCAGAAGCAACACACGGTATATAT 57.843 37.500 0.00 0.00 0.00 0.86
1933 2023 5.585820 TCAGAAGCAACACACGGTATATA 57.414 39.130 0.00 0.00 0.00 0.86
1934 2024 4.465632 TCAGAAGCAACACACGGTATAT 57.534 40.909 0.00 0.00 0.00 0.86
1935 2025 3.945981 TCAGAAGCAACACACGGTATA 57.054 42.857 0.00 0.00 0.00 1.47
1936 2026 2.806244 GTTCAGAAGCAACACACGGTAT 59.194 45.455 0.00 0.00 0.00 2.73
1937 2027 2.159014 AGTTCAGAAGCAACACACGGTA 60.159 45.455 0.00 0.00 0.00 4.02
1938 2028 1.014352 GTTCAGAAGCAACACACGGT 58.986 50.000 0.00 0.00 0.00 4.83
1939 2029 1.299541 AGTTCAGAAGCAACACACGG 58.700 50.000 0.00 0.00 0.00 4.94
1940 2030 3.405170 AAAGTTCAGAAGCAACACACG 57.595 42.857 0.00 0.00 0.00 4.49
1941 2031 4.732784 TCAAAAGTTCAGAAGCAACACAC 58.267 39.130 0.00 0.00 0.00 3.82
1942 2032 5.581126 ATCAAAAGTTCAGAAGCAACACA 57.419 34.783 0.00 0.00 0.00 3.72
1949 2039 6.884280 ACCAACCTATCAAAAGTTCAGAAG 57.116 37.500 0.00 0.00 0.00 2.85
1970 2060 5.407407 TCACCTATCAGAAGTTCAGAACC 57.593 43.478 9.85 0.00 0.00 3.62
2046 2162 5.192927 TCCATTTTACAGGCGAAGATGAAT 58.807 37.500 0.00 0.00 0.00 2.57
2078 2195 6.458478 CCACCACAAAAACTCGTGTATGTAAA 60.458 38.462 0.00 0.00 0.00 2.01
2147 2266 7.741554 AGAATGATAAGTAGTCAGGAAACCT 57.258 36.000 0.00 0.00 0.00 3.50
2204 2324 2.227388 GTGCTGTGAAGTTCCCATCTTG 59.773 50.000 0.00 0.00 0.00 3.02
2240 2513 8.918202 TTGTTGAAACTACTCCACAATCTTAT 57.082 30.769 0.00 0.00 28.86 1.73
2241 2514 8.918202 ATTGTTGAAACTACTCCACAATCTTA 57.082 30.769 0.00 0.00 37.18 2.10
2364 2644 6.975772 CCGTCAAACAAATTCCTTCTAACAAA 59.024 34.615 0.00 0.00 0.00 2.83
2482 2766 4.482030 TGTGGGAGTGTTACTACTAACCA 58.518 43.478 0.00 0.00 36.21 3.67


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

AutoCloner maintained by Alex Coulton.