Multiple sequence alignment - TraesCS7D01G478400

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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 TraesCS7D01G478400 chr7D 100.000 2671 0 0 1 2671 589288604 589291274 0.000000e+00 4933
1 TraesCS7D01G478400 chr7D 90.546 1629 114 10 4 1631 609917190 609918779 0.000000e+00 2119
2 TraesCS7D01G478400 chr7D 92.920 1017 63 6 1658 2670 609919030 609920041 0.000000e+00 1471
3 TraesCS7D01G478400 chr7B 89.466 2677 260 14 3 2670 583697189 583694526 0.000000e+00 3362
4 TraesCS7D01G478400 chr7B 86.700 1188 152 6 78 1261 688068408 688067223 0.000000e+00 1314
5 TraesCS7D01G478400 chr4B 85.171 2286 285 36 404 2670 672993752 672991502 0.000000e+00 2294
6 TraesCS7D01G478400 chr1A 88.914 1795 181 13 10 1791 253373176 253371387 0.000000e+00 2196
7 TraesCS7D01G478400 chr1A 89.572 374 36 3 2247 2619 253368055 253367684 3.110000e-129 472
8 TraesCS7D01G478400 chr2D 89.847 1635 155 9 3 1629 60048801 60047170 0.000000e+00 2089
9 TraesCS7D01G478400 chr2D 91.019 913 64 8 1723 2619 60046959 60046049 0.000000e+00 1216
10 TraesCS7D01G478400 chr2D 81.100 1291 195 36 1387 2667 278287155 278285904 0.000000e+00 987
11 TraesCS7D01G478400 chr4D 91.886 1479 97 13 4 1479 318517416 318518874 0.000000e+00 2045
12 TraesCS7D01G478400 chr4D 93.443 1159 61 7 1521 2670 318518874 318520026 0.000000e+00 1705
13 TraesCS7D01G478400 chr2B 84.296 1974 261 28 112 2064 575338072 575336127 0.000000e+00 1882
14 TraesCS7D01G478400 chr2B 88.616 1019 96 14 1669 2670 104599070 104598055 0.000000e+00 1221
15 TraesCS7D01G478400 chr2B 88.466 815 83 8 797 1608 104600104 104599298 0.000000e+00 974
16 TraesCS7D01G478400 chr2B 88.594 754 81 5 4 755 104601027 104600277 0.000000e+00 911
17 TraesCS7D01G478400 chr3B 85.489 1585 196 22 148 1718 571321313 571319749 0.000000e+00 1622
18 TraesCS7D01G478400 chr3B 85.611 966 107 18 1714 2666 571315258 571314312 0.000000e+00 985


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 TraesCS7D01G478400 chr7D 589288604 589291274 2670 False 4933.000000 4933 100.000000 1 2671 1 chr7D.!!$F1 2670
1 TraesCS7D01G478400 chr7D 609917190 609920041 2851 False 1795.000000 2119 91.733000 4 2670 2 chr7D.!!$F2 2666
2 TraesCS7D01G478400 chr7B 583694526 583697189 2663 True 3362.000000 3362 89.466000 3 2670 1 chr7B.!!$R1 2667
3 TraesCS7D01G478400 chr7B 688067223 688068408 1185 True 1314.000000 1314 86.700000 78 1261 1 chr7B.!!$R2 1183
4 TraesCS7D01G478400 chr4B 672991502 672993752 2250 True 2294.000000 2294 85.171000 404 2670 1 chr4B.!!$R1 2266
5 TraesCS7D01G478400 chr1A 253367684 253373176 5492 True 1334.000000 2196 89.243000 10 2619 2 chr1A.!!$R1 2609
6 TraesCS7D01G478400 chr2D 60046049 60048801 2752 True 1652.500000 2089 90.433000 3 2619 2 chr2D.!!$R2 2616
7 TraesCS7D01G478400 chr2D 278285904 278287155 1251 True 987.000000 987 81.100000 1387 2667 1 chr2D.!!$R1 1280
8 TraesCS7D01G478400 chr4D 318517416 318520026 2610 False 1875.000000 2045 92.664500 4 2670 2 chr4D.!!$F1 2666
9 TraesCS7D01G478400 chr2B 575336127 575338072 1945 True 1882.000000 1882 84.296000 112 2064 1 chr2B.!!$R1 1952
10 TraesCS7D01G478400 chr2B 104598055 104601027 2972 True 1035.333333 1221 88.558667 4 2670 3 chr2B.!!$R2 2666
11 TraesCS7D01G478400 chr3B 571319749 571321313 1564 True 1622.000000 1622 85.489000 148 1718 1 chr3B.!!$R2 1570
12 TraesCS7D01G478400 chr3B 571314312 571315258 946 True 985.000000 985 85.611000 1714 2666 1 chr3B.!!$R1 952

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
727 748 0.182299 TGTGCATGGTCAGGACACAA 59.818 50.0 1.41 0.0 38.24 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 5814 0.663688 CGACTCGTCATCTCCCGAAT 59.336 55.0 0.0 0.0 31.92 3.34 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
84 91 4.143115 CGACTTTCATGCACGACAACTTAT 60.143 41.667 0.00 0.00 0.00 1.73
96 103 6.074249 GCACGACAACTTATAGCCTTTCTATC 60.074 42.308 0.00 0.00 38.81 2.08
97 104 7.203910 CACGACAACTTATAGCCTTTCTATCT 58.796 38.462 0.00 0.00 38.81 1.98
121 130 8.809066 TCTTTACTACTTTACTTACATGCAGGA 58.191 33.333 4.84 0.00 0.00 3.86
126 135 9.953565 ACTACTTTACTTACATGCAGGATAAAA 57.046 29.630 4.84 0.00 0.00 1.52
296 308 2.712539 CGTTGCTGCCGTGTTGAA 59.287 55.556 0.00 0.00 0.00 2.69
319 331 1.404391 GCAATGAAGGTGCAGGATCAG 59.596 52.381 0.00 0.00 41.80 2.90
320 332 2.022195 CAATGAAGGTGCAGGATCAGG 58.978 52.381 0.00 0.00 0.00 3.86
390 403 1.891933 TTGGTATCCATGAGGCAGGA 58.108 50.000 0.00 0.00 38.50 3.86
437 456 2.480610 CCTGCGCACCAAACACACT 61.481 57.895 5.66 0.00 0.00 3.55
498 517 3.082548 CTGAGAAACCTCGGTCAGTAGA 58.917 50.000 0.00 0.00 33.20 2.59
518 537 5.470845 AGATAAAGATTGCACAAGTACGC 57.529 39.130 0.00 0.00 0.00 4.42
583 602 1.782201 AAGCACATCAGGCTGGACCA 61.782 55.000 15.73 0.00 41.66 4.02
602 621 0.462581 ACATGATCGCACCGCTCATT 60.463 50.000 0.00 0.00 39.18 2.57
620 640 2.553079 TTCGCACACTGTTTCCAAAC 57.447 45.000 0.00 0.00 39.33 2.93
656 677 5.036737 AGTTGACAAGAAATCAGCAAAACG 58.963 37.500 0.00 0.00 30.31 3.60
665 686 3.660111 AGCAAAACGGGCAGTCGC 61.660 61.111 0.00 0.00 37.44 5.19
727 748 0.182299 TGTGCATGGTCAGGACACAA 59.818 50.000 1.41 0.00 38.24 3.33
837 989 2.376109 GTCCAGGAACCGATAGTCTCA 58.624 52.381 0.00 0.00 0.00 3.27
859 1011 9.610705 TCTCATAGAAAGAAAAGATTCATCCAG 57.389 33.333 0.00 0.00 38.06 3.86
920 1072 1.623811 TGTCCCTTACACTCCAAGAGC 59.376 52.381 0.00 0.00 31.43 4.09
932 1084 1.704628 TCCAAGAGCTGACCATCCAAA 59.295 47.619 0.00 0.00 0.00 3.28
1001 1153 0.474184 CGCCCCACTTCCAATCCTAT 59.526 55.000 0.00 0.00 0.00 2.57
1038 1190 2.034001 CGACAAGGACGTCTTTGTTGAC 60.034 50.000 38.40 27.47 45.08 3.18
1117 1269 1.376609 GCACCCTATGGCTTTCACGG 61.377 60.000 0.00 0.00 33.59 4.94
1125 1277 2.904866 GCTTTCACGGCACCACCA 60.905 61.111 0.00 0.00 39.03 4.17
1152 1306 2.098117 CCTCGGAATTGATTTGAGCCAC 59.902 50.000 0.00 0.00 0.00 5.01
1446 1611 4.439563 CCTGACAAGTTTGTTTACCACACC 60.440 45.833 0.00 0.00 42.43 4.16
1618 1786 4.335647 CCCAGGTTCTGTGCGGCT 62.336 66.667 0.00 0.00 0.00 5.52
1691 2083 1.277557 AGGCCACAAAGCAACAACAAA 59.722 42.857 5.01 0.00 0.00 2.83
1800 5140 0.895559 CCACTTCTTGCCCCAACCTC 60.896 60.000 0.00 0.00 0.00 3.85
2179 5537 6.123651 TGAAACCTTTTTCCACTACTGCTTA 58.876 36.000 0.00 0.00 40.55 3.09
2242 5600 1.538047 CCCTTCACCCATTGTCACAG 58.462 55.000 0.00 0.00 0.00 3.66
2311 5670 8.410141 CCTTATGGTTCTTTTACTTTTGACACA 58.590 33.333 0.00 0.00 0.00 3.72
2388 5751 0.814010 GACCCACACGACAAAGCTGT 60.814 55.000 0.00 0.00 38.98 4.40
2559 5922 4.272489 TCCATGGTCCAGATCAAACATTC 58.728 43.478 12.58 0.00 0.00 2.67
2623 5987 3.961849 AGATTCTGCCCTTCTTTCCTTC 58.038 45.455 0.00 0.00 0.00 3.46
2670 6034 6.264292 ACACAGGTTTACATGTCATTTTGCTA 59.736 34.615 0.00 0.00 39.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 103 8.997621 TCCTGCATGTAAGTAAAGTAGTAAAG 57.002 34.615 0.00 0.00 0.00 1.85
126 135 4.202398 TGACCAGACTGATTGCTTCTCTTT 60.202 41.667 3.32 0.00 0.00 2.52
174 185 2.281692 TGCATGCGCTCCAACAGT 60.282 55.556 14.09 0.00 39.64 3.55
296 308 1.973281 CCTGCACCTTCATTGCCGT 60.973 57.895 0.00 0.00 39.39 5.68
320 332 2.107901 AGATCAATTCATCAGAGCCCCC 59.892 50.000 0.00 0.00 0.00 5.40
390 403 2.726351 GCTGGGCTACCTTCGAGCT 61.726 63.158 0.00 0.00 39.98 4.09
437 456 3.476740 GCACATGCACCTTAGGCTA 57.523 52.632 0.00 0.00 41.59 3.93
498 517 3.377172 GGGCGTACTTGTGCAATCTTTAT 59.623 43.478 0.00 0.00 0.00 1.40
602 621 0.736053 GGTTTGGAAACAGTGTGCGA 59.264 50.000 0.00 0.00 44.54 5.10
620 640 1.779569 GTCAACTACGTGTGGACAGG 58.220 55.000 16.15 0.00 46.36 4.00
635 656 4.358851 CCGTTTTGCTGATTTCTTGTCAA 58.641 39.130 0.00 0.00 0.00 3.18
656 677 2.579684 CTTCCTGGTAGCGACTGCCC 62.580 65.000 10.45 2.32 44.31 5.36
665 686 1.395826 CCGAGGGCTCTTCCTGGTAG 61.396 65.000 0.00 0.00 37.25 3.18
727 748 2.094675 GGTTGAAGCATGCACATACCT 58.905 47.619 21.98 0.00 0.00 3.08
837 989 9.571816 GGATCTGGATGAATCTTTTCTTTCTAT 57.428 33.333 0.00 0.00 32.78 1.98
859 1011 0.166814 GTGTGCTTGAGCGTTGGATC 59.833 55.000 0.00 0.00 45.83 3.36
932 1084 2.319844 CCTTCTTGGCTGTCCCTTTTT 58.680 47.619 0.00 0.00 0.00 1.94
1001 1153 1.756561 TCGACTGATCCGGCATCCA 60.757 57.895 0.00 0.00 0.00 3.41
1038 1190 2.743928 GCTGCCAACGGAGACAGG 60.744 66.667 0.00 0.00 0.00 4.00
1117 1269 2.401766 CGAGGCTGAATGGTGGTGC 61.402 63.158 0.00 0.00 0.00 5.01
1125 1277 4.272489 TCAAATCAATTCCGAGGCTGAAT 58.728 39.130 0.00 0.00 33.97 2.57
1152 1306 1.019673 CATCAACTGGCTCGATTGGG 58.980 55.000 0.00 0.00 0.00 4.12
1527 1694 1.039856 GAAGGGGCTTTTGTCTGCAA 58.960 50.000 0.00 0.00 0.00 4.08
1618 1786 3.215245 GTTGCACAACCCTTGCCA 58.785 55.556 1.97 0.00 39.39 4.92
1800 5140 7.227512 ACACATGAAGAAAGGTCTGAACTAAAG 59.772 37.037 0.00 0.00 33.05 1.85
2104 5460 7.765360 ACAAATTTCTTCAATGTGAGCTTGAAA 59.235 29.630 0.00 0.00 40.89 2.69
2242 5600 7.280428 GGGAGGTAATACTAAAAAGAACAGCTC 59.720 40.741 0.00 0.00 0.00 4.09
2311 5670 1.967066 TGCACATTCCCCGTGAAAAAT 59.033 42.857 0.00 0.00 36.33 1.82
2318 5678 1.852157 ATCACCTGCACATTCCCCGT 61.852 55.000 0.00 0.00 0.00 5.28
2388 5751 7.228507 AGTTGATGCAAATTGTGTAGTAGTGAA 59.771 33.333 0.00 0.00 0.00 3.18
2451 5814 0.663688 CGACTCGTCATCTCCCGAAT 59.336 55.000 0.00 0.00 31.92 3.34
2541 5904 2.291540 GGGGAATGTTTGATCTGGACCA 60.292 50.000 0.00 0.00 0.00 4.02
2559 5922 3.256136 GGACTTCACATACTCGATAGGGG 59.744 52.174 0.00 0.00 45.13 4.79
2623 5987 4.034048 GTGAATTAGCCGTACACATGGAAG 59.966 45.833 0.00 0.00 31.77 3.46


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

AutoCloner maintained by Alex Coulton.