Multiple sequence alignment - TraesCS7A01G411900

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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 TraesCS7A01G411900 chr7A 100.000 2978 0 0 1 2978 602808721 602811698 0.000000e+00 5500
1 TraesCS7A01G411900 chr7D 94.014 3007 133 15 1 2978 522512579 522515567 0.000000e+00 4512
2 TraesCS7A01G411900 chr7B 95.879 2475 89 9 509 2978 556461609 556464075 0.000000e+00 3993
3 TraesCS7A01G411900 chr7B 90.234 471 19 6 25 469 556460917 556461386 9.190000e-165 590


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 TraesCS7A01G411900 chr7A 602808721 602811698 2977 False 5500.0 5500 100.0000 1 2978 1 chr7A.!!$F1 2977
1 TraesCS7A01G411900 chr7D 522512579 522515567 2988 False 4512.0 4512 94.0140 1 2978 1 chr7D.!!$F1 2977
2 TraesCS7A01G411900 chr7B 556460917 556464075 3158 False 2291.5 3993 93.0565 25 2978 2 chr7B.!!$F1 2953

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
355 370 0.168788 AAATGATGTGTCTTGGCGCG 59.831 50.0 0.0 0.0 0.00 6.86 F
487 513 1.014352 CTAAACGCCCCAGCATGTAC 58.986 55.0 0.0 0.0 39.83 2.90 F
1438 1661 0.965866 CAGGTACTCCTCCGTGCTCA 60.966 60.0 0.0 0.0 43.07 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 1409 0.036765 TAACCGGACATTGCGAGCTT 60.037 50.000 9.46 0.0 30.86 3.74 R
1621 1844 0.528470 CTCGTGACCCTCCTCTTGAC 59.472 60.000 0.00 0.0 0.00 3.18 R
2581 2814 4.626287 GCCACTTCTAACTTCATGGATGGA 60.626 45.833 0.00 0.0 0.00 3.41 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
109 110 6.429385 ACAGAGATTGTCCTCTCATTTTTGTC 59.571 38.462 4.11 0.00 43.44 3.18
123 124 6.918626 TCATTTTTGTCAAGTCACTGTTCAA 58.081 32.000 0.00 0.00 0.00 2.69
130 131 6.686630 TGTCAAGTCACTGTTCAATTTTGTT 58.313 32.000 0.00 0.00 0.00 2.83
134 135 5.343249 AGTCACTGTTCAATTTTGTTCAGC 58.657 37.500 13.08 0.00 35.35 4.26
147 148 4.981806 TTGTTCAGCAGTTTAAGCAAGT 57.018 36.364 0.00 0.00 0.00 3.16
178 193 1.442526 GATCTGGTGGCTTGCATCCG 61.443 60.000 0.00 0.00 0.00 4.18
207 222 7.552687 TGATCTGTTAATATGTTCTGAACACCC 59.447 37.037 24.17 9.80 45.50 4.61
280 295 4.304110 CATGCCCATAATGCACTCAATTC 58.696 43.478 0.00 0.00 42.38 2.17
285 300 6.324512 TGCCCATAATGCACTCAATTCTTTAT 59.675 34.615 0.00 0.00 32.85 1.40
355 370 0.168788 AAATGATGTGTCTTGGCGCG 59.831 50.000 0.00 0.00 0.00 6.86
487 513 1.014352 CTAAACGCCCCAGCATGTAC 58.986 55.000 0.00 0.00 39.83 2.90
528 737 5.006455 CACAGATGATGAAGATGTACACTGC 59.994 44.000 0.00 0.00 0.00 4.40
799 1014 2.648059 GTGCACCAAGATAAGAGGCAT 58.352 47.619 5.22 0.00 31.92 4.40
808 1023 4.946478 AGATAAGAGGCATACAGTGACC 57.054 45.455 0.00 0.00 36.01 4.02
867 1082 1.798223 CCTTGAAGAATCAACGCGTGA 59.202 47.619 14.98 13.43 40.59 4.35
870 1085 4.466828 CTTGAAGAATCAACGCGTGAATT 58.533 39.130 14.98 15.98 40.59 2.17
989 1206 2.975851 CAAGCTGAAATTCTGCGTGTTC 59.024 45.455 24.13 0.29 44.61 3.18
990 1207 2.498167 AGCTGAAATTCTGCGTGTTCT 58.502 42.857 17.01 0.00 44.61 3.01
991 1208 2.225019 AGCTGAAATTCTGCGTGTTCTG 59.775 45.455 17.01 0.00 44.61 3.02
992 1209 2.578495 CTGAAATTCTGCGTGTTCTGC 58.422 47.619 0.00 0.00 0.00 4.26
993 1210 1.946081 TGAAATTCTGCGTGTTCTGCA 59.054 42.857 0.00 0.00 40.70 4.41
1051 1274 5.011125 GGCCTGAACATAGAGCAAGAGTATA 59.989 44.000 0.00 0.00 0.00 1.47
1146 1369 2.102084 TCAGCAAGATCTCATCCTTCCG 59.898 50.000 0.00 0.00 0.00 4.30
1158 1381 2.559698 TCCTTCCGATGCTTCACAAA 57.440 45.000 0.08 0.00 0.00 2.83
1162 1385 3.504863 CTTCCGATGCTTCACAAAATGG 58.495 45.455 0.08 0.00 0.00 3.16
1166 1389 1.275856 GATGCTTCACAAAATGGGGCA 59.724 47.619 0.00 0.00 39.31 5.36
1169 1392 1.344114 GCTTCACAAAATGGGGCAGAA 59.656 47.619 0.00 0.00 0.00 3.02
1257 1480 1.280133 TGCAAGCAGCTACTGAGGAAT 59.720 47.619 0.00 0.00 45.94 3.01
1438 1661 0.965866 CAGGTACTCCTCCGTGCTCA 60.966 60.000 0.00 0.00 43.07 4.26
1548 1771 3.302344 GGTGGTGCGGTTGCCATT 61.302 61.111 0.00 0.00 41.78 3.16
1621 1844 2.592861 GGCTCTGCCCTATTGCGG 60.593 66.667 0.00 0.00 44.06 5.69
1749 1972 2.022129 CGACACGGTGAGCCAACTC 61.022 63.158 16.29 0.00 43.76 3.01
1767 1990 4.521062 GCCGTGCGCCTCTCTGAT 62.521 66.667 4.18 0.00 0.00 2.90
1773 1996 0.676184 TGCGCCTCTCTGATGGTATC 59.324 55.000 4.18 0.00 0.00 2.24
1846 2069 2.665000 CGGTGCAGGAGATGGTGT 59.335 61.111 0.00 0.00 0.00 4.16
1890 2113 2.902486 CAGCTCTAGGAGATTGGCCATA 59.098 50.000 6.09 0.00 0.00 2.74
1974 2197 2.676176 CGAAGAGATCTCCAAGCAAGCA 60.676 50.000 19.30 0.00 0.00 3.91
2014 2237 8.317891 TGTTTAGTTAGTGTGGACATTATGTG 57.682 34.615 1.24 0.00 0.00 3.21
2023 2246 6.040878 GTGTGGACATTATGTGTAGGAGTAC 58.959 44.000 1.24 0.00 42.36 2.73
2024 2247 5.955959 TGTGGACATTATGTGTAGGAGTACT 59.044 40.000 1.24 0.00 42.36 2.73
2025 2248 7.067859 GTGTGGACATTATGTGTAGGAGTACTA 59.932 40.741 1.24 0.00 42.36 1.82
2089 2314 9.241317 GAATTTGCACTTCAATACATTAGGATG 57.759 33.333 3.82 0.00 35.54 3.51
2114 2339 8.522830 TGGAAAATTAGGACAATTTAGCTTCAG 58.477 33.333 0.00 0.00 30.38 3.02
2123 2348 6.160576 ACAATTTAGCTTCAGCCAAAGAAA 57.839 33.333 0.00 0.00 43.38 2.52
2222 2447 3.322211 TGCAGGGAAATTGATGCTTTG 57.678 42.857 0.00 0.00 39.42 2.77
2581 2814 3.808728 ACCTGATAGCGTGCATTGTATT 58.191 40.909 0.00 0.00 0.00 1.89
2623 2856 4.510038 GGCGAGAATTGGCATCATTATT 57.490 40.909 0.00 0.00 46.01 1.40
2707 2940 7.604164 ACAGAAACTGTGATGATAACTACAAGG 59.396 37.037 3.54 0.00 43.63 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 6.237648 GCTGAACAAAATTGAACAGTGACTTG 60.238 38.462 17.60 0.00 37.28 3.16
123 124 6.340522 ACTTGCTTAAACTGCTGAACAAAAT 58.659 32.000 0.00 0.00 0.00 1.82
130 131 4.981806 AACAACTTGCTTAAACTGCTGA 57.018 36.364 0.00 0.00 0.00 4.26
487 513 2.818274 GTCCTTTACCAGCCGCCG 60.818 66.667 0.00 0.00 0.00 6.46
528 737 2.614779 CACATCACTGTAGCAGTCCAG 58.385 52.381 0.00 0.00 43.43 3.86
787 1002 3.319405 CGGTCACTGTATGCCTCTTATCT 59.681 47.826 0.00 0.00 0.00 1.98
799 1014 2.160205 CCTTCTGAGACGGTCACTGTA 58.840 52.381 11.27 1.66 0.00 2.74
808 1023 4.448537 AGTTCTTGATCCTTCTGAGACG 57.551 45.455 0.00 0.00 0.00 4.18
867 1082 4.744795 AGCTCGATCTTACCTGTGAATT 57.255 40.909 0.00 0.00 0.00 2.17
870 1085 3.357203 AGAAGCTCGATCTTACCTGTGA 58.643 45.455 0.67 0.00 0.00 3.58
989 1206 1.880271 CATCTCCATACCTGCTGCAG 58.120 55.000 22.44 22.44 0.00 4.41
990 1207 0.179037 GCATCTCCATACCTGCTGCA 60.179 55.000 0.88 0.88 0.00 4.41
991 1208 0.108207 AGCATCTCCATACCTGCTGC 59.892 55.000 0.00 0.00 43.02 5.25
993 1210 0.763652 CCAGCATCTCCATACCTGCT 59.236 55.000 0.00 0.00 45.41 4.24
994 1211 0.888285 GCCAGCATCTCCATACCTGC 60.888 60.000 0.00 0.00 34.85 4.85
1026 1249 1.908619 TCTTGCTCTATGTTCAGGCCA 59.091 47.619 5.01 0.00 0.00 5.36
1078 1301 3.188460 TCCTTGTTTGATAAGAAGCGCAC 59.812 43.478 11.47 2.78 34.27 5.34
1146 1369 1.275856 TGCCCCATTTTGTGAAGCATC 59.724 47.619 0.00 0.00 32.83 3.91
1169 1392 5.159209 CGAGCTTGATTTCAGCAGATTTTT 58.841 37.500 0.00 0.00 0.00 1.94
1185 1408 1.577328 AACCGGACATTGCGAGCTTG 61.577 55.000 9.46 0.00 30.86 4.01
1186 1409 0.036765 TAACCGGACATTGCGAGCTT 60.037 50.000 9.46 0.00 30.86 3.74
1257 1480 4.385825 AGTTGCTTTCGGTGTTCTTGATA 58.614 39.130 0.00 0.00 0.00 2.15
1327 1550 2.694109 GTGCAAGGGAGGTACTACTAGG 59.306 54.545 0.00 0.00 40.83 3.02
1438 1661 4.763793 CCTGTGACTTGATTTGATGGTCTT 59.236 41.667 0.00 0.00 0.00 3.01
1521 1744 2.983030 GCACCACCGGCAATGACA 60.983 61.111 0.00 0.00 0.00 3.58
1548 1771 1.604308 CAGGTGTGCTGCAATCCCA 60.604 57.895 16.94 4.00 0.00 4.37
1621 1844 0.528470 CTCGTGACCCTCCTCTTGAC 59.472 60.000 0.00 0.00 0.00 3.18
1767 1990 0.673985 CATTCTCCCGCTCGATACCA 59.326 55.000 0.00 0.00 0.00 3.25
1773 1996 1.645455 CATTGCATTCTCCCGCTCG 59.355 57.895 0.00 0.00 0.00 5.03
1846 2069 0.979665 CAACTCCTCCTCAGCTCCAA 59.020 55.000 0.00 0.00 0.00 3.53
1869 2092 1.126488 TGGCCAATCTCCTAGAGCTG 58.874 55.000 0.61 0.00 0.00 4.24
2038 2261 7.936847 TCCCTGCACGATCTAACAAAAATATAT 59.063 33.333 0.00 0.00 0.00 0.86
2054 2279 4.490696 TGCAAATTCCCTGCACGA 57.509 50.000 0.00 0.00 44.67 4.35
2089 2314 7.489435 GCTGAAGCTAAATTGTCCTAATTTTCC 59.511 37.037 3.32 0.00 38.21 3.13
2114 2339 7.609760 TTTTTCTTCCTTTTCTTTCTTTGGC 57.390 32.000 0.00 0.00 0.00 4.52
2154 2379 1.939934 TGCTCAAACTCTCACAAACCG 59.060 47.619 0.00 0.00 0.00 4.44
2368 2593 7.867909 CGAATAGTAGCCATCAGATTGAACTTA 59.132 37.037 0.00 0.00 0.00 2.24
2581 2814 4.626287 GCCACTTCTAACTTCATGGATGGA 60.626 45.833 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.