Multiple sequence alignment - TraesCS5B01G259300

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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 TraesCS5B01G259300 chr5B 100.000 2609 0 0 1 2609 441645762 441648370 0.000000e+00 4819
1 TraesCS5B01G259300 chr5B 96.721 122 4 0 1107 1228 441646826 441646947 1.220000e-48 204
2 TraesCS5B01G259300 chr5B 96.721 122 4 0 1065 1186 441646868 441646989 1.220000e-48 204
3 TraesCS5B01G259300 chr5B 95.000 80 4 0 1149 1228 441646826 441646905 2.730000e-25 126
4 TraesCS5B01G259300 chr5B 95.000 80 4 0 1065 1144 441646910 441646989 2.730000e-25 126
5 TraesCS5B01G259300 chr5D 94.160 1524 64 13 1107 2609 371797373 371798892 0.000000e+00 2298
6 TraesCS5B01G259300 chr5D 93.489 1198 51 15 5 1186 371796308 371797494 0.000000e+00 1755
7 TraesCS5B01G259300 chr5D 93.204 103 6 1 1 102 345936157 345936259 1.620000e-32 150
8 TraesCS5B01G259300 chr5D 92.405 79 6 0 1066 1144 371797416 371797494 2.120000e-21 113
9 TraesCS5B01G259300 chr5A 93.878 1519 68 12 1107 2608 474828878 474830388 0.000000e+00 2266
10 TraesCS5B01G259300 chr5A 93.927 1202 46 15 1 1186 474827809 474828999 0.000000e+00 1790
11 TraesCS5B01G259300 chr5A 95.181 83 4 0 1149 1231 474828878 474828960 5.860000e-27 132
12 TraesCS5B01G259300 chr5A 92.500 80 6 0 1065 1144 474828920 474828999 5.900000e-22 115
13 TraesCS5B01G259300 chr6A 93.137 102 6 1 1 101 538097723 538097824 5.820000e-32 148
14 TraesCS5B01G259300 chr6A 92.157 102 7 1 1 101 47141636 47141535 2.710000e-30 143
15 TraesCS5B01G259300 chr7D 92.157 102 7 1 1 101 34756974 34756873 2.710000e-30 143
16 TraesCS5B01G259300 chr6D 92.157 102 7 1 1 101 392273118 392273219 2.710000e-30 143
17 TraesCS5B01G259300 chr6D 92.157 102 7 1 1 101 410398387 410398286 2.710000e-30 143
18 TraesCS5B01G259300 chr1A 88.793 116 9 4 1 115 555641215 555641103 3.500000e-29 139
19 TraesCS5B01G259300 chr4D 91.176 102 8 1 1 101 74079396 74079497 1.260000e-28 137
20 TraesCS5B01G259300 chr3B 91.176 102 8 1 1 101 396271923 396272024 1.260000e-28 137


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 TraesCS5B01G259300 chr5B 441645762 441648370 2608 False 1095.800000 4819 96.688400 1 2609 5 chr5B.!!$F1 2608
1 TraesCS5B01G259300 chr5D 371796308 371798892 2584 False 1388.666667 2298 93.351333 5 2609 3 chr5D.!!$F2 2604
2 TraesCS5B01G259300 chr5A 474827809 474830388 2579 False 1075.750000 2266 93.871500 1 2608 4 chr5A.!!$F1 2607

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
650 666 0.5966 TTCGTATTCTCCGCGGATGC 60.597 55.0 31.19 16.94 37.91 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1668 1.253593 GCCCCTTTTCTTCCAGCCTG 61.254 60.0 0.0 0.0 0.0 4.85 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
55 56 4.304110 TGTTCACTCATTTCAGTCCGTAC 58.696 43.478 0.00 0.00 0.00 3.67
68 69 3.316029 CAGTCCGTACGTGGTCCATATTA 59.684 47.826 15.21 0.00 0.00 0.98
74 75 6.922957 TCCGTACGTGGTCCATATTAAAATAC 59.077 38.462 15.21 0.00 0.00 1.89
99 100 9.942850 ACCCAAAACATCTTATATTTTGAAAGG 57.057 29.630 9.61 5.84 43.07 3.11
122 123 9.442047 AAGGAATAGCAAATACTATGATACTGC 57.558 33.333 0.00 0.00 33.12 4.40
123 124 8.820831 AGGAATAGCAAATACTATGATACTGCT 58.179 33.333 0.00 0.00 41.32 4.24
124 125 8.877779 GGAATAGCAAATACTATGATACTGCTG 58.122 37.037 4.01 0.00 38.96 4.41
145 146 5.462068 GCTGAACATAAAACAAAAGGTCCAC 59.538 40.000 0.00 0.00 0.00 4.02
152 153 8.646900 ACATAAAACAAAAGGTCCACATGTATT 58.353 29.630 0.00 0.00 0.00 1.89
186 193 8.627208 ATCATAGTACATGCCAAGGAAATTAG 57.373 34.615 0.00 0.00 0.00 1.73
284 291 3.655486 CATGCAATGCCAAGAACAGAAA 58.345 40.909 1.53 0.00 37.62 2.52
286 293 3.719924 TGCAATGCCAAGAACAGAAAAG 58.280 40.909 1.53 0.00 0.00 2.27
287 294 3.062042 GCAATGCCAAGAACAGAAAAGG 58.938 45.455 0.00 0.00 0.00 3.11
288 295 3.656559 CAATGCCAAGAACAGAAAAGGG 58.343 45.455 0.00 0.00 0.00 3.95
330 345 6.153000 TCAGAGTTGGTACTATGAAGAAGACC 59.847 42.308 0.53 0.00 46.53 3.85
382 397 1.273327 CCACCTTCCAAGCATTTCACC 59.727 52.381 0.00 0.00 0.00 4.02
396 411 6.063404 AGCATTTCACCATCCAACAATTTTT 58.937 32.000 0.00 0.00 0.00 1.94
476 492 6.594547 GTGAAGAAACCTATACTTTGGACTCC 59.405 42.308 0.00 0.00 0.00 3.85
564 580 3.126831 CTCAGTCACAAGAACACAGGTC 58.873 50.000 0.00 0.00 0.00 3.85
584 600 1.952296 CATGACAAGATTGCCTAGCCC 59.048 52.381 0.00 0.00 0.00 5.19
650 666 0.596600 TTCGTATTCTCCGCGGATGC 60.597 55.000 31.19 16.94 37.91 3.91
696 712 8.052141 TGACCAGGATTATTGTGATTTACATCA 58.948 33.333 0.00 0.00 39.48 3.07
748 764 3.621715 CACCAAGGCGAACTATAAGGTTC 59.378 47.826 0.00 0.00 41.31 3.62
1018 1035 3.612247 ATGGGCTCACGGTCACAGC 62.612 63.158 0.00 0.00 0.00 4.40
1056 1073 2.490509 TGTCAAAGCAATCATCAGCAGG 59.509 45.455 0.00 0.00 0.00 4.85
1122 1139 2.825836 GCCAGATGCGTTGGAGGG 60.826 66.667 10.27 0.00 37.96 4.30
1123 1140 2.989639 CCAGATGCGTTGGAGGGA 59.010 61.111 2.05 0.00 37.96 4.20
1124 1141 1.299648 CCAGATGCGTTGGAGGGAA 59.700 57.895 2.05 0.00 37.96 3.97
1125 1142 0.745845 CCAGATGCGTTGGAGGGAAG 60.746 60.000 2.05 0.00 37.96 3.46
1126 1143 1.078143 AGATGCGTTGGAGGGAAGC 60.078 57.895 0.00 0.00 0.00 3.86
1127 1144 2.044946 ATGCGTTGGAGGGAAGCC 60.045 61.111 0.00 0.00 0.00 4.35
1128 1145 3.976701 ATGCGTTGGAGGGAAGCCG 62.977 63.158 0.00 0.00 0.00 5.52
1130 1147 4.697756 CGTTGGAGGGAAGCCGCA 62.698 66.667 0.00 0.00 0.00 5.69
1131 1148 2.747855 GTTGGAGGGAAGCCGCAG 60.748 66.667 0.00 0.00 0.00 5.18
1132 1149 4.722700 TTGGAGGGAAGCCGCAGC 62.723 66.667 0.00 0.00 40.32 5.25
1186 1203 4.126390 CGCAGCGTTGTGAGAGCG 62.126 66.667 7.04 0.00 36.95 5.03
1299 1316 2.186384 CAGCAGAGCTTCGAGGGG 59.814 66.667 0.00 0.00 36.40 4.79
1371 1388 2.688446 GCTTAACCTGGATTGCCCTTAC 59.312 50.000 0.00 0.00 35.38 2.34
1557 1574 6.436027 TGAGGAATCCACAGAGAGTATAAGT 58.564 40.000 0.61 0.00 0.00 2.24
1586 1603 0.613012 ATTGGTGCAAAGAGGCCTCC 60.613 55.000 29.54 14.36 0.00 4.30
1649 1668 5.207033 GCAACATCAAAAATCAAAACAGGC 58.793 37.500 0.00 0.00 0.00 4.85
1668 1687 1.077445 AGGCTGGAAGAAAAGGGGC 59.923 57.895 0.00 0.00 34.07 5.80
1676 1695 2.306847 GAAGAAAAGGGGCTCACAACA 58.693 47.619 0.00 0.00 0.00 3.33
1686 1705 1.597937 GGCTCACAACAAACAAGCTCG 60.598 52.381 0.00 0.00 33.50 5.03
1705 1724 3.674997 TCGTTGCTCAGGCTATTTCTTT 58.325 40.909 0.00 0.00 39.59 2.52
1741 1760 9.988815 ACTTATATGGTACTGAAGCAATAGAAG 57.011 33.333 0.00 0.00 39.48 2.85
1742 1761 9.988815 CTTATATGGTACTGAAGCAATAGAAGT 57.011 33.333 0.00 0.00 39.48 3.01
1745 1764 9.935241 ATATGGTACTGAAGCAATAGAAGTATG 57.065 33.333 0.00 0.00 39.48 2.39
1746 1765 7.182817 TGGTACTGAAGCAATAGAAGTATGT 57.817 36.000 0.00 0.00 31.13 2.29
1747 1766 7.041721 TGGTACTGAAGCAATAGAAGTATGTG 58.958 38.462 0.00 0.00 31.13 3.21
1748 1767 7.042335 GGTACTGAAGCAATAGAAGTATGTGT 58.958 38.462 0.00 0.00 0.00 3.72
1749 1768 7.222999 GGTACTGAAGCAATAGAAGTATGTGTC 59.777 40.741 0.00 0.00 0.00 3.67
1750 1769 6.940739 ACTGAAGCAATAGAAGTATGTGTCT 58.059 36.000 0.00 0.00 0.00 3.41
1751 1770 7.390027 ACTGAAGCAATAGAAGTATGTGTCTT 58.610 34.615 0.00 0.00 0.00 3.01
1752 1771 7.332926 ACTGAAGCAATAGAAGTATGTGTCTTG 59.667 37.037 0.00 0.00 0.00 3.02
1753 1772 7.386059 TGAAGCAATAGAAGTATGTGTCTTGA 58.614 34.615 0.00 0.00 0.00 3.02
1757 1776 8.700051 AGCAATAGAAGTATGTGTCTTGATAGT 58.300 33.333 0.00 0.00 0.00 2.12
1792 1811 8.859090 CCAGGAATATGATATTTGCCACTTTAA 58.141 33.333 0.00 0.00 0.00 1.52
1793 1812 9.683069 CAGGAATATGATATTTGCCACTTTAAC 57.317 33.333 0.00 0.00 0.00 2.01
1804 1851 6.607735 TTGCCACTTTAACGCCTAATATAC 57.392 37.500 0.00 0.00 0.00 1.47
1851 1899 3.513515 TGTGTTTCTTGCCCTTCACTTTT 59.486 39.130 0.00 0.00 0.00 2.27
1856 1904 5.612725 TTCTTGCCCTTCACTTTTTCAAT 57.387 34.783 0.00 0.00 0.00 2.57
1857 1905 4.947645 TCTTGCCCTTCACTTTTTCAATG 58.052 39.130 0.00 0.00 0.00 2.82
2027 2075 5.908247 AGACTAGGGGCAAAAGATAAGAGAT 59.092 40.000 0.00 0.00 0.00 2.75
2141 2189 2.154462 GGATGAGAAACACCAGGTGTG 58.846 52.381 26.61 5.31 46.79 3.82
2373 2423 8.903820 AGTATAATTGCCTCATTTCTAAACCAC 58.096 33.333 0.00 0.00 0.00 4.16
2500 2550 2.452937 GGATGGCTAGGGGGTGTCC 61.453 68.421 0.00 0.00 0.00 4.02
2547 2597 2.184830 CATGTGGCCATGCTCTCGG 61.185 63.158 9.72 0.00 41.88 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 6.945938 TTGGGTATTTTAATATGGACCACG 57.054 37.500 0.00 0.00 0.00 4.94
98 99 8.877779 CAGCAGTATCATAGTATTTGCTATTCC 58.122 37.037 0.00 0.00 38.26 3.01
99 100 9.645059 TCAGCAGTATCATAGTATTTGCTATTC 57.355 33.333 0.00 0.00 38.26 1.75
101 102 9.429359 GTTCAGCAGTATCATAGTATTTGCTAT 57.571 33.333 0.00 0.00 38.26 2.97
122 123 6.568869 TGTGGACCTTTTGTTTTATGTTCAG 58.431 36.000 0.00 0.00 0.00 3.02
123 124 6.531503 TGTGGACCTTTTGTTTTATGTTCA 57.468 33.333 0.00 0.00 0.00 3.18
124 125 6.983890 ACATGTGGACCTTTTGTTTTATGTTC 59.016 34.615 0.00 0.00 0.00 3.18
186 193 4.077300 TCTGATATGCCCTGATGACAAC 57.923 45.455 0.00 0.00 0.00 3.32
279 286 1.407258 TCGTTGTTTGCCCCTTTTCTG 59.593 47.619 0.00 0.00 0.00 3.02
280 287 1.770294 TCGTTGTTTGCCCCTTTTCT 58.230 45.000 0.00 0.00 0.00 2.52
281 288 2.035321 TCATCGTTGTTTGCCCCTTTTC 59.965 45.455 0.00 0.00 0.00 2.29
284 291 1.545582 CATCATCGTTGTTTGCCCCTT 59.454 47.619 0.00 0.00 0.00 3.95
286 293 0.887933 ACATCATCGTTGTTTGCCCC 59.112 50.000 0.00 0.00 0.00 5.80
287 294 1.539388 TGACATCATCGTTGTTTGCCC 59.461 47.619 0.00 0.00 0.00 5.36
288 295 2.483877 TCTGACATCATCGTTGTTTGCC 59.516 45.455 0.00 0.00 0.00 4.52
346 361 3.584733 GGTGGAAAGCCTCCTGAATAT 57.415 47.619 4.20 0.00 45.64 1.28
421 437 3.442977 ACGCCGTTGTTATCTAGTCTTCT 59.557 43.478 0.00 0.00 0.00 2.85
476 492 6.203338 ACTTGTACAGGGTGTATACAAAAACG 59.797 38.462 7.25 0.00 35.05 3.60
564 580 1.952296 GGGCTAGGCAATCTTGTCATG 59.048 52.381 19.14 0.00 34.61 3.07
584 600 0.251742 ATTGTGGATGGTGGGGTGTG 60.252 55.000 0.00 0.00 0.00 3.82
650 666 6.828273 TGGTCACATTTGGAGTTCAATATAGG 59.172 38.462 0.00 0.00 34.98 2.57
700 716 0.804364 TTGTTGTCATCGCATCCAGC 59.196 50.000 0.00 0.00 40.87 4.85
865 881 0.249447 GTTGGGCTTGGCTTTGTCAC 60.249 55.000 0.00 0.00 0.00 3.67
1018 1035 1.258982 GACATAGCAAGAACCGCATCG 59.741 52.381 0.00 0.00 0.00 3.84
1105 1122 2.819984 TTCCCTCCAACGCATCTGGC 62.820 60.000 0.00 0.00 39.90 4.85
1106 1123 0.745845 CTTCCCTCCAACGCATCTGG 60.746 60.000 0.00 0.00 35.05 3.86
1107 1124 1.372087 GCTTCCCTCCAACGCATCTG 61.372 60.000 0.00 0.00 0.00 2.90
1108 1125 1.078143 GCTTCCCTCCAACGCATCT 60.078 57.895 0.00 0.00 0.00 2.90
1109 1126 2.115291 GGCTTCCCTCCAACGCATC 61.115 63.158 0.00 0.00 0.00 3.91
1110 1127 2.044946 GGCTTCCCTCCAACGCAT 60.045 61.111 0.00 0.00 0.00 4.73
1111 1128 4.697756 CGGCTTCCCTCCAACGCA 62.698 66.667 0.00 0.00 0.00 5.24
1113 1130 4.697756 TGCGGCTTCCCTCCAACG 62.698 66.667 0.00 0.00 0.00 4.10
1114 1131 2.747855 CTGCGGCTTCCCTCCAAC 60.748 66.667 0.00 0.00 0.00 3.77
1115 1132 4.722700 GCTGCGGCTTCCCTCCAA 62.723 66.667 11.21 0.00 35.22 3.53
1121 1138 4.389576 CACAACGCTGCGGCTTCC 62.390 66.667 26.95 0.00 36.09 3.46
1122 1139 3.300667 CTCACAACGCTGCGGCTTC 62.301 63.158 26.95 0.00 36.09 3.86
1123 1140 3.349006 CTCACAACGCTGCGGCTT 61.349 61.111 26.95 9.65 36.09 4.35
1124 1141 4.299547 TCTCACAACGCTGCGGCT 62.300 61.111 26.95 10.15 36.09 5.52
1125 1142 3.782244 CTCTCACAACGCTGCGGC 61.782 66.667 26.95 7.70 0.00 6.53
1126 1143 3.782244 GCTCTCACAACGCTGCGG 61.782 66.667 26.95 11.89 0.00 5.69
1127 1144 4.126390 CGCTCTCACAACGCTGCG 62.126 66.667 21.91 21.91 37.57 5.18
1128 1145 3.782244 CCGCTCTCACAACGCTGC 61.782 66.667 0.00 0.00 0.00 5.25
1129 1146 3.782244 GCCGCTCTCACAACGCTG 61.782 66.667 0.00 0.00 0.00 5.18
1136 1153 4.521062 ATCTGGCGCCGCTCTCAC 62.521 66.667 23.90 0.00 0.00 3.51
1179 1196 4.519437 CATCTGGCGCCGCTCTCA 62.519 66.667 23.90 0.87 0.00 3.27
1299 1316 0.186873 ATGGTGCCCCAATCTCATCC 59.813 55.000 0.00 0.00 46.04 3.51
1479 1496 4.067896 GTGCGGGAATGATGAATATGTCT 58.932 43.478 0.00 0.00 0.00 3.41
1530 1547 3.717576 ACTCTCTGTGGATTCCTCATCA 58.282 45.455 7.86 0.00 32.79 3.07
1536 1553 6.716934 TCACTTATACTCTCTGTGGATTCC 57.283 41.667 0.00 0.00 0.00 3.01
1649 1668 1.253593 GCCCCTTTTCTTCCAGCCTG 61.254 60.000 0.00 0.00 0.00 4.85
1668 1687 3.100817 CAACGAGCTTGTTTGTTGTGAG 58.899 45.455 17.05 0.00 37.57 3.51
1686 1705 5.643777 TCTGTAAAGAAATAGCCTGAGCAAC 59.356 40.000 0.00 0.00 43.56 4.17
1720 1739 8.924303 ACATACTTCTATTGCTTCAGTACCATA 58.076 33.333 0.00 0.00 0.00 2.74
1740 1759 7.822822 GGTAAACCAACTATCAAGACACATACT 59.177 37.037 0.00 0.00 35.64 2.12
1741 1760 7.065443 GGGTAAACCAACTATCAAGACACATAC 59.935 40.741 0.81 0.00 39.85 2.39
1742 1761 7.107542 GGGTAAACCAACTATCAAGACACATA 58.892 38.462 0.81 0.00 39.85 2.29
1743 1762 5.944007 GGGTAAACCAACTATCAAGACACAT 59.056 40.000 0.81 0.00 39.85 3.21
1744 1763 5.310451 GGGTAAACCAACTATCAAGACACA 58.690 41.667 0.81 0.00 39.85 3.72
1745 1764 5.874895 GGGTAAACCAACTATCAAGACAC 57.125 43.478 0.81 0.00 39.85 3.67
1792 1811 5.215252 ACTGCATGAAGTATATTAGGCGT 57.785 39.130 3.85 0.00 0.00 5.68
1793 1812 6.390721 ACTACTGCATGAAGTATATTAGGCG 58.609 40.000 14.20 2.77 32.32 5.52
1874 1922 3.624861 CACTTCAGTTCAGAACAGCAAGT 59.375 43.478 15.85 15.03 0.00 3.16
1881 1929 9.477484 TTTCTTAGATACACTTCAGTTCAGAAC 57.523 33.333 5.00 5.00 0.00 3.01
2027 2075 3.467374 TTATGAGGTCATATGTGCGCA 57.533 42.857 5.66 5.66 38.49 6.09
2141 2189 9.615295 GAATATAGCTAAGTGTACAGAAGTAGC 57.385 37.037 14.67 14.67 0.00 3.58
2334 2384 5.049405 GGCAATTATACTCACCCATTTCTCG 60.049 44.000 0.00 0.00 0.00 4.04
2373 2423 4.533707 TCCTAGATAATGGAGCATTCCCAG 59.466 45.833 0.00 0.00 43.33 4.45
2434 2484 8.545472 TGATGATGAGGAGATATTTGCATATGA 58.455 33.333 6.97 0.00 0.00 2.15
2500 2550 3.386726 TCTGAGGTAATGGTTCCCATACG 59.613 47.826 0.00 0.00 44.40 3.06
2547 2597 3.194116 ACCAAGTTGATGTTGATCATGCC 59.806 43.478 3.87 0.00 38.43 4.40


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

AutoCloner maintained by Alex Coulton.