Multiple sequence alignment - TraesCS4A01G048800

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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 TraesCS4A01G048800 chr4A 100.000 3097 0 0 1 3097 39543038 39539942 0 5720
1 TraesCS4A01G048800 chr4D 93.207 3106 161 25 1 3096 425226628 425229693 0 4521
2 TraesCS4A01G048800 chr4B 92.350 1830 100 11 1272 3097 520890772 520892565 0 2567
3 TraesCS4A01G048800 chr4B 93.070 1241 46 15 1 1228 520889556 520890769 0 1779


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 TraesCS4A01G048800 chr4A 39539942 39543038 3096 True 5720 5720 100.000 1 3097 1 chr4A.!!$R1 3096
1 TraesCS4A01G048800 chr4D 425226628 425229693 3065 False 4521 4521 93.207 1 3096 1 chr4D.!!$F1 3095
2 TraesCS4A01G048800 chr4B 520889556 520892565 3009 False 2173 2567 92.710 1 3097 2 chr4B.!!$F1 3096

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
819 833 0.807667 CCATGCTGACACCTACGAGC 60.808 60.0 0.0 0.0 0.0 5.03 F
1219 1233 0.034896 TCCTGTTCCGTTTCCTCTGC 59.965 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2070 0.590195 CAGAATGCGCATCCTTAGGC 59.410 55.0 25.53 7.31 0.00 3.93 R
2344 2366 1.115326 GGGTGCCCCAGAATAATGCC 61.115 60.0 5.45 0.00 44.65 4.40 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
118 119 2.442272 TGCGACCTAGGAGGCTCC 60.442 66.667 26.42 26.42 39.63 4.70
225 226 2.040412 GGCAATACCAGGAGGATAAGGG 59.960 54.545 0.00 0.00 38.86 3.95
239 240 6.296720 GGAGGATAAGGGAAGATAATTCAGGG 60.297 46.154 0.00 0.00 0.00 4.45
334 335 1.000396 GAACCTGCCCCTTGATGCT 60.000 57.895 0.00 0.00 0.00 3.79
370 371 5.854866 CAGTACAGTTTCGACATCTTTACGA 59.145 40.000 0.00 0.00 0.00 3.43
403 413 8.511604 ACATCCTATGATCTGTAAAGGTTTTG 57.488 34.615 0.00 0.00 0.00 2.44
404 414 7.557719 ACATCCTATGATCTGTAAAGGTTTTGG 59.442 37.037 0.00 0.00 0.00 3.28
424 434 3.081804 GGGGGTGAAGTTGTATCAGTTG 58.918 50.000 0.00 0.00 0.00 3.16
490 502 4.575885 TCAACTCCCCTATCTTTCAAACG 58.424 43.478 0.00 0.00 0.00 3.60
512 524 2.633860 CAGGTTTCTGTGCACCCTC 58.366 57.895 15.69 0.31 36.30 4.30
819 833 0.807667 CCATGCTGACACCTACGAGC 60.808 60.000 0.00 0.00 0.00 5.03
940 954 4.704833 GCCGGTGCTGAAGCCTGA 62.705 66.667 1.90 0.00 41.18 3.86
941 955 2.032528 CCGGTGCTGAAGCCTGAA 59.967 61.111 0.00 0.00 41.18 3.02
942 956 2.037136 CCGGTGCTGAAGCCTGAAG 61.037 63.158 0.00 0.00 41.18 3.02
943 957 2.684843 CGGTGCTGAAGCCTGAAGC 61.685 63.158 0.00 0.00 41.18 3.86
960 974 2.157421 GCTCAAGCGTCTCACCTTG 58.843 57.895 0.00 0.00 39.74 3.61
997 1011 1.004560 TTGCAAGCGGTGGAGAGAG 60.005 57.895 0.00 0.00 0.00 3.20
1044 1058 4.135493 GCTTTGCTCGTCGTCGCC 62.135 66.667 0.00 0.00 36.96 5.54
1148 1162 2.358898 TGAAAACTGCCTCTGTTTGCTC 59.641 45.455 8.21 3.05 36.08 4.26
1169 1183 0.901124 TCTCTCTCTTGCCCTCTTGC 59.099 55.000 0.00 0.00 0.00 4.01
1171 1185 1.077858 CTCTCTTGCCCTCTTGCCC 60.078 63.158 0.00 0.00 0.00 5.36
1172 1186 1.539869 TCTCTTGCCCTCTTGCCCT 60.540 57.895 0.00 0.00 0.00 5.19
1173 1187 1.077858 CTCTTGCCCTCTTGCCCTC 60.078 63.158 0.00 0.00 0.00 4.30
1175 1189 1.136329 TCTTGCCCTCTTGCCCTCTT 61.136 55.000 0.00 0.00 0.00 2.85
1176 1190 0.964358 CTTGCCCTCTTGCCCTCTTG 60.964 60.000 0.00 0.00 0.00 3.02
1177 1191 1.719063 TTGCCCTCTTGCCCTCTTGT 61.719 55.000 0.00 0.00 0.00 3.16
1178 1192 1.377856 GCCCTCTTGCCCTCTTGTC 60.378 63.158 0.00 0.00 0.00 3.18
1179 1193 2.069776 CCCTCTTGCCCTCTTGTCA 58.930 57.895 0.00 0.00 0.00 3.58
1180 1194 0.322008 CCCTCTTGCCCTCTTGTCAC 60.322 60.000 0.00 0.00 0.00 3.67
1181 1195 0.689623 CCTCTTGCCCTCTTGTCACT 59.310 55.000 0.00 0.00 0.00 3.41
1182 1196 1.072965 CCTCTTGCCCTCTTGTCACTT 59.927 52.381 0.00 0.00 0.00 3.16
1183 1197 2.303022 CCTCTTGCCCTCTTGTCACTTA 59.697 50.000 0.00 0.00 0.00 2.24
1184 1198 3.054802 CCTCTTGCCCTCTTGTCACTTAT 60.055 47.826 0.00 0.00 0.00 1.73
1185 1199 4.162320 CCTCTTGCCCTCTTGTCACTTATA 59.838 45.833 0.00 0.00 0.00 0.98
1188 1202 5.248477 TCTTGCCCTCTTGTCACTTATAGTT 59.752 40.000 0.00 0.00 0.00 2.24
1214 1228 1.810755 GGTGAATCCTGTTCCGTTTCC 59.189 52.381 0.00 0.00 0.00 3.13
1219 1233 0.034896 TCCTGTTCCGTTTCCTCTGC 59.965 55.000 0.00 0.00 0.00 4.26
1243 1257 4.320275 CCCGTTTGGTTTAGAGAGAAAAGC 60.320 45.833 0.00 0.00 35.44 3.51
1270 1284 2.386661 GCTTTAGCAGCTAGTGTCCA 57.613 50.000 1.49 0.00 46.27 4.02
1278 1292 0.035458 AGCTAGTGTCCAGTGTTGGC 59.965 55.000 0.00 0.00 44.63 4.52
1333 1347 0.310854 GGTGGTGAAAGAAACTGCCG 59.689 55.000 0.00 0.00 0.00 5.69
1357 1371 5.504665 GGTCCGACATGATAAAGCAAATCTG 60.505 44.000 0.00 0.00 0.00 2.90
1406 1420 2.997303 GGGTCTTCTTTCGCTCTCTTTC 59.003 50.000 0.00 0.00 0.00 2.62
1413 1427 2.620779 TTCGCTCTCTTTCTGACGAG 57.379 50.000 0.00 0.00 0.00 4.18
1437 1451 0.037882 TCCTCTTCTCTGCAACTGCG 60.038 55.000 0.00 0.00 45.83 5.18
1554 1568 1.398692 GGTTGGTGCTGGTTTCTTCA 58.601 50.000 0.00 0.00 0.00 3.02
1563 1577 2.550180 GCTGGTTTCTTCAGTTCTCACC 59.450 50.000 0.00 0.00 34.89 4.02
1658 1672 1.486211 CAGACCCGGACTATGGAACT 58.514 55.000 0.73 0.00 0.00 3.01
1703 1721 3.430042 AAGGTGTGCATTCTCAGACAT 57.570 42.857 0.00 0.00 32.51 3.06
1717 1735 7.962964 TTCTCAGACATAACCTGTAAAAGTG 57.037 36.000 0.00 0.00 38.54 3.16
1718 1736 7.062749 TCTCAGACATAACCTGTAAAAGTGT 57.937 36.000 0.00 0.00 38.54 3.55
1719 1737 7.506114 TCTCAGACATAACCTGTAAAAGTGTT 58.494 34.615 0.00 0.00 38.54 3.32
1720 1738 8.644216 TCTCAGACATAACCTGTAAAAGTGTTA 58.356 33.333 0.00 0.00 38.54 2.41
1732 1753 9.825972 CCTGTAAAAGTGTTATACATTTCACAG 57.174 33.333 15.28 15.28 38.72 3.66
1883 1905 3.295973 CCTTTTCCAGGAAAGTGGACAA 58.704 45.455 22.37 5.43 46.75 3.18
1908 1930 6.608002 AGATGTTACTAACAGGAAGACTAGGG 59.392 42.308 7.67 0.00 45.95 3.53
2062 2084 1.153369 GTCAGCCTAAGGATGCGCA 60.153 57.895 14.96 14.96 39.19 6.09
2075 2097 0.107800 ATGCGCATTCTGCTCAGTCT 60.108 50.000 19.28 0.00 41.71 3.24
2101 2123 0.527385 GCTCCTGTCGCTTAGCTGAG 60.527 60.000 1.76 0.05 32.18 3.35
2148 2170 7.447545 GGTACTTGAAAAATTAGAGAACCACCT 59.552 37.037 0.00 0.00 0.00 4.00
2184 2206 7.984050 AGTCTTCTCTGATGTTATGTTATGTGG 59.016 37.037 0.00 0.00 0.00 4.17
2315 2337 6.545504 TTAGTCAACTGCTCAAATCTTGAC 57.454 37.500 0.00 0.00 40.61 3.18
2341 2363 7.116948 CGGCATGTTTCTAGATTAGATAAGGTG 59.883 40.741 0.00 0.00 34.22 4.00
2344 2366 6.513180 TGTTTCTAGATTAGATAAGGTGCCG 58.487 40.000 0.00 0.00 34.22 5.69
2461 2483 8.826710 CAGAACTGTTTACTGAATTCTTGTGTA 58.173 33.333 7.05 2.64 34.07 2.90
2467 2489 8.962679 TGTTTACTGAATTCTTGTGTAACCTTT 58.037 29.630 7.05 0.00 34.36 3.11
2544 2566 6.484288 ACCTATTTCCAGTGTGAATCATTGA 58.516 36.000 0.00 0.00 36.12 2.57
2550 2572 3.340928 CAGTGTGAATCATTGAGCAGGA 58.659 45.455 0.00 0.00 36.12 3.86
2553 2575 4.223700 AGTGTGAATCATTGAGCAGGAGTA 59.776 41.667 0.00 0.00 0.00 2.59
2601 2623 0.382515 CCGGTTTGGAACGCAAGAAA 59.617 50.000 0.00 0.00 42.00 2.52
2666 2689 2.439880 GTCCCAAACATTCCCCCAAAAA 59.560 45.455 0.00 0.00 0.00 1.94
2695 2718 0.951040 CCACTTCTTCCGTCAGCCAC 60.951 60.000 0.00 0.00 0.00 5.01
2754 2777 3.254903 GGTATTGTCAAACCAGGTTCCAC 59.745 47.826 4.93 5.99 35.73 4.02
2771 2794 9.927668 CAGGTTCCACAATTAATAAAAGTTGAT 57.072 29.630 0.00 0.00 0.00 2.57
2847 2870 8.871629 TGCAATAAAGGTTTTCTAAGTATGGA 57.128 30.769 0.00 0.00 0.00 3.41
2916 2939 5.241506 TCCATGTCATTTCCAAAGACACTTC 59.758 40.000 0.00 0.00 44.15 3.01
2980 3003 4.151883 ACATTTTGCACAATCACCTACCT 58.848 39.130 0.00 0.00 0.00 3.08
3080 3103 8.425577 AGAAACTAAGGATCATGTGTTAATCG 57.574 34.615 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 1.293924 CATGATGTCGTTGGAGCCTC 58.706 55.000 0.00 0.00 0.00 4.70
118 119 0.096976 GGTTCGGCATGATGTCGTTG 59.903 55.000 19.49 0.00 46.84 4.10
225 226 4.455877 CCGGTATTGCCCTGAATTATCTTC 59.544 45.833 0.00 0.00 0.00 2.87
315 316 2.409870 GCATCAAGGGGCAGGTTCG 61.410 63.158 0.00 0.00 0.00 3.95
334 335 3.039452 TGTACTGTACAGGACCGCA 57.961 52.632 31.01 13.63 41.64 5.69
379 389 7.013655 CCCAAAACCTTTACAGATCATAGGATG 59.986 40.741 0.00 0.00 32.67 3.51
403 413 3.081804 CAACTGATACAACTTCACCCCC 58.918 50.000 0.00 0.00 0.00 5.40
404 414 2.488153 GCAACTGATACAACTTCACCCC 59.512 50.000 0.00 0.00 0.00 4.95
424 434 1.929836 CAGAGAGCAGTAAATCGGTGC 59.070 52.381 0.00 0.00 37.48 5.01
483 495 4.437659 GCACAGAAACCTGTAACGTTTGAA 60.438 41.667 5.91 0.00 42.60 2.69
490 502 1.607148 GGGTGCACAGAAACCTGTAAC 59.393 52.381 20.43 0.00 42.60 2.50
508 520 1.838077 AGGGTTTTCGGTGATAGAGGG 59.162 52.381 0.00 0.00 0.00 4.30
512 524 3.343941 TTCCAGGGTTTTCGGTGATAG 57.656 47.619 0.00 0.00 0.00 2.08
819 833 2.108514 AACCTCCGCATGTGCATCG 61.109 57.895 0.00 0.00 42.21 3.84
937 951 1.066914 GTGAGACGCTTGAGCTTCAG 58.933 55.000 11.38 0.00 41.18 3.02
938 952 0.319900 GGTGAGACGCTTGAGCTTCA 60.320 55.000 11.38 5.27 41.18 3.02
939 953 0.037790 AGGTGAGACGCTTGAGCTTC 60.038 55.000 1.59 1.59 39.31 3.86
940 954 0.394565 AAGGTGAGACGCTTGAGCTT 59.605 50.000 1.07 0.00 39.32 3.74
941 955 0.320247 CAAGGTGAGACGCTTGAGCT 60.320 55.000 1.07 0.00 39.32 4.09
942 956 0.601311 ACAAGGTGAGACGCTTGAGC 60.601 55.000 0.00 0.00 33.53 4.26
943 957 1.143305 CACAAGGTGAGACGCTTGAG 58.857 55.000 0.00 0.00 35.23 3.02
960 974 0.907230 AGGTCCCCTGAGAAGCTCAC 60.907 60.000 0.00 0.00 35.39 3.51
1044 1058 1.215647 CAGGTTCCCTCCGACGAAG 59.784 63.158 0.00 0.00 0.00 3.79
1148 1162 2.677613 GCAAGAGGGCAAGAGAGAGAAG 60.678 54.545 0.00 0.00 0.00 2.85
1169 1183 6.464222 TGAACAACTATAAGTGACAAGAGGG 58.536 40.000 0.00 0.00 0.00 4.30
1171 1185 7.116948 CACCTGAACAACTATAAGTGACAAGAG 59.883 40.741 0.00 0.00 0.00 2.85
1172 1186 6.929049 CACCTGAACAACTATAAGTGACAAGA 59.071 38.462 0.00 0.00 0.00 3.02
1173 1187 6.929049 TCACCTGAACAACTATAAGTGACAAG 59.071 38.462 0.00 0.00 0.00 3.16
1175 1189 6.413783 TCACCTGAACAACTATAAGTGACA 57.586 37.500 0.00 0.00 0.00 3.58
1176 1190 7.064728 GGATTCACCTGAACAACTATAAGTGAC 59.935 40.741 0.00 0.00 36.80 3.67
1177 1191 7.103641 GGATTCACCTGAACAACTATAAGTGA 58.896 38.462 0.00 0.00 36.80 3.41
1178 1192 7.308782 GGATTCACCTGAACAACTATAAGTG 57.691 40.000 0.00 0.00 36.80 3.16
1214 1228 1.165270 CTAAACCAAACGGGGCAGAG 58.835 55.000 0.00 0.00 42.91 3.35
1219 1233 3.412237 TTCTCTCTAAACCAAACGGGG 57.588 47.619 0.00 0.00 42.91 5.73
1270 1284 2.542907 CGAACCAAGCGCCAACACT 61.543 57.895 2.29 0.00 0.00 3.55
1278 1292 5.685841 TCTTTTTAAAGATCGAACCAAGCG 58.314 37.500 0.89 0.00 39.95 4.68
1303 1317 1.763546 TTCACCACCTCGCATCCACA 61.764 55.000 0.00 0.00 0.00 4.17
1333 1347 4.576463 AGATTTGCTTTATCATGTCGGACC 59.424 41.667 5.55 0.00 0.00 4.46
1381 1395 2.739379 GAGAGCGAAAGAAGACCCAAAG 59.261 50.000 0.00 0.00 0.00 2.77
1406 1420 0.528470 GAAGAGGACCCACTCGTCAG 59.472 60.000 0.00 0.00 42.89 3.51
1413 1427 0.687354 TTGCAGAGAAGAGGACCCAC 59.313 55.000 0.00 0.00 0.00 4.61
1437 1451 6.569780 ACCAAACATTTCCTTCAAGTTGTAC 58.430 36.000 2.11 0.00 0.00 2.90
1563 1577 3.533606 AGTAGCTGCTGAACCTACATG 57.466 47.619 13.43 0.00 35.15 3.21
1658 1672 1.375908 CCTGCCGTTTAGCTCAGCA 60.376 57.895 0.00 0.00 0.00 4.41
1717 1735 5.801350 TGCTGCTCTGTGAAATGTATAAC 57.199 39.130 0.00 0.00 0.00 1.89
1718 1736 8.681486 ATTATGCTGCTCTGTGAAATGTATAA 57.319 30.769 0.00 0.00 0.00 0.98
1719 1737 9.948964 ATATTATGCTGCTCTGTGAAATGTATA 57.051 29.630 0.00 0.00 0.00 1.47
1720 1738 8.859236 ATATTATGCTGCTCTGTGAAATGTAT 57.141 30.769 0.00 0.00 0.00 2.29
1732 1753 6.038161 TGTGGTGTTTGTATATTATGCTGCTC 59.962 38.462 0.00 0.00 0.00 4.26
1734 1755 6.130298 TGTGGTGTTTGTATATTATGCTGC 57.870 37.500 0.00 0.00 0.00 5.25
1808 1829 8.108551 TCCTTCGGAGTTTATAGAAGCTATAC 57.891 38.462 0.00 0.00 38.87 1.47
1827 1849 6.574350 ACATGACTTAGGTAATCTTCCTTCG 58.426 40.000 0.00 0.00 36.60 3.79
1837 1859 8.480501 GGTATACAAGGAACATGACTTAGGTAA 58.519 37.037 5.01 0.00 0.00 2.85
1848 1870 6.187682 CCTGGAAAAGGTATACAAGGAACAT 58.812 40.000 5.01 0.00 41.74 2.71
1883 1905 6.608002 CCCTAGTCTTCCTGTTAGTAACATCT 59.392 42.308 15.91 9.93 41.26 2.90
1908 1930 6.818644 TCATCAGCCTTTACATCTTGTAAGTC 59.181 38.462 0.91 0.00 42.93 3.01
2048 2070 0.590195 CAGAATGCGCATCCTTAGGC 59.410 55.000 25.53 7.31 0.00 3.93
2101 2123 1.742268 GCCTCTGGAGCATTTCAGTTC 59.258 52.381 0.00 0.00 33.13 3.01
2148 2170 7.009179 ACATCAGAGAAGACTTTGGACATAA 57.991 36.000 0.00 0.00 0.00 1.90
2315 2337 7.116948 CACCTTATCTAATCTAGAAACATGCCG 59.883 40.741 0.00 0.00 38.50 5.69
2341 2363 2.564721 GCCCCAGAATAATGCCGGC 61.565 63.158 22.73 22.73 0.00 6.13
2344 2366 1.115326 GGGTGCCCCAGAATAATGCC 61.115 60.000 5.45 0.00 44.65 4.40
2363 2385 4.759782 ACAATAGTAGTGCAGCTTACCTG 58.240 43.478 0.00 0.00 44.67 4.00
2415 2437 9.148879 AGTTCTGACTAATACCATAGTTATGCT 57.851 33.333 0.00 0.00 36.28 3.79
2461 2483 3.525268 CTTCAACCAAGCACAAAGGTT 57.475 42.857 0.00 0.00 46.03 3.50
2544 2566 7.213678 GCTTAGATTAGTGAATTACTCCTGCT 58.786 38.462 0.00 0.00 40.89 4.24
2666 2689 6.414732 TGACGGAAGAAGTGGATGAATAAAT 58.585 36.000 0.00 0.00 0.00 1.40
2695 2718 5.009631 TGTCAAATCCACCATCTTTACAGG 58.990 41.667 0.00 0.00 0.00 4.00
2771 2794 7.211966 ACGAGAAACACTTAGAGCTTAAGTA 57.788 36.000 16.07 0.00 36.14 2.24
2821 2844 9.474313 TCCATACTTAGAAAACCTTTATTGCAT 57.526 29.630 0.00 0.00 0.00 3.96
2847 2870 2.052468 ACCGACCAAAACTAGAGGGTT 58.948 47.619 0.00 0.00 32.77 4.11
2951 2974 5.288804 GTGATTGTGCAAAATGTAACCAGT 58.711 37.500 6.90 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.