Multiple sequence alignment - TraesCS7D01G351100

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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 TraesCS7D01G351100 chr7D 100.000 2458 0 0 1 2458 451970785 451973242 0.000000e+00 4540.0
1 TraesCS7D01G351100 chr7B 95.005 1982 59 14 1 1958 474407291 474409256 0.000000e+00 3075.0
2 TraesCS7D01G351100 chr7B 93.333 315 19 2 2144 2458 474411401 474411713 4.790000e-127 464.0
3 TraesCS7D01G351100 chr7B 96.985 199 6 0 1954 2152 474409283 474409481 3.920000e-88 335.0
4 TraesCS7D01G351100 chr7A 86.824 888 80 24 1590 2458 545543281 545542412 0.000000e+00 957.0
5 TraesCS7D01G351100 chr7A 84.790 881 59 36 721 1561 545544120 545543275 0.000000e+00 815.0
6 TraesCS7D01G351100 chr6B 93.023 43 3 0 624 666 13932667 13932625 2.040000e-06 63.9
7 TraesCS7D01G351100 chr6B 90.909 44 3 1 624 667 18765184 18765226 9.490000e-05 58.4
8 TraesCS7D01G351100 chr5A 93.023 43 3 0 624 666 689619263 689619221 2.040000e-06 63.9
9 TraesCS7D01G351100 chr5A 97.222 36 1 0 631 666 293860730 293860695 7.340000e-06 62.1
10 TraesCS7D01G351100 chr2D 91.489 47 2 1 631 677 419045783 419045827 2.040000e-06 63.9
11 TraesCS7D01G351100 chr3D 86.207 58 4 4 616 671 594810519 594810464 2.640000e-05 60.2
12 TraesCS7D01G351100 chr6D 96.970 33 1 0 634 666 33882685 33882717 3.410000e-04 56.5
13 TraesCS7D01G351100 chr1B 94.286 35 2 0 634 668 193790256 193790290 1.000000e-03 54.7


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 TraesCS7D01G351100 chr7D 451970785 451973242 2457 False 4540.000000 4540 100.000000 1 2458 1 chr7D.!!$F1 2457
1 TraesCS7D01G351100 chr7B 474407291 474411713 4422 False 1291.333333 3075 95.107667 1 2458 3 chr7B.!!$F1 2457
2 TraesCS7D01G351100 chr7A 545542412 545544120 1708 True 886.000000 957 85.807000 721 2458 2 chr7A.!!$R1 1737

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
398 411 1.616327 TGGACATCCACCAGGGGAG 60.616 63.158 0.0 0.0 42.01 4.30 F
1095 1124 0.108615 CTCTTGCACCACCTCTACCG 60.109 60.000 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 1260 0.179048 CATGGCGGCACAATCTCCTA 60.179 55.0 16.34 0.0 0.00 2.94 R
1973 2078 0.390998 GCTTCAGGGACAGCTCAGAC 60.391 60.0 0.00 0.0 32.87 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
79 80 5.794894 TCCTCTGAAAACCTTGTGAGTATC 58.205 41.667 0.00 0.00 0.00 2.24
142 143 4.455877 ACACTAGTAGCACAGGCAAAAATC 59.544 41.667 0.00 0.00 44.61 2.17
144 145 5.048782 CACTAGTAGCACAGGCAAAAATCAA 60.049 40.000 0.00 0.00 44.61 2.57
192 195 2.064014 CTTTTAACCGACTCACGACCC 58.936 52.381 0.00 0.00 45.77 4.46
258 261 4.797275 GCTCCTTCCAAATGGTTCAAACAG 60.797 45.833 0.00 0.00 36.34 3.16
361 374 7.602517 TGAACTAGCTTCTTTCTATCTTTGC 57.397 36.000 0.00 0.00 0.00 3.68
398 411 1.616327 TGGACATCCACCAGGGGAG 60.616 63.158 0.00 0.00 42.01 4.30
399 412 2.378634 GGACATCCACCAGGGGAGG 61.379 68.421 0.00 0.00 44.12 4.30
400 413 2.286425 ACATCCACCAGGGGAGGG 60.286 66.667 5.47 0.00 42.88 4.30
401 414 3.099170 CATCCACCAGGGGAGGGG 61.099 72.222 0.00 0.00 41.08 4.79
402 415 3.300962 ATCCACCAGGGGAGGGGA 61.301 66.667 0.00 0.00 41.08 4.81
464 485 3.070159 AGTTCTCTGCTTGAGCTACACAA 59.930 43.478 4.44 0.00 42.38 3.33
553 574 4.080863 ACACGATGGGCTTTCTAATCTCTT 60.081 41.667 0.00 0.00 0.00 2.85
1012 1041 1.012841 GCTCAACATGTCTGCTAGCC 58.987 55.000 13.29 0.00 0.00 3.93
1095 1124 0.108615 CTCTTGCACCACCTCTACCG 60.109 60.000 0.00 0.00 0.00 4.02
1155 1184 6.886459 ACATTGTTATCAGTGGTAATCTGCTT 59.114 34.615 0.00 0.00 35.94 3.91
1164 1193 6.014584 TCAGTGGTAATCTGCTTAAACTCTCA 60.015 38.462 0.00 0.00 33.48 3.27
1165 1194 6.650807 CAGTGGTAATCTGCTTAAACTCTCAA 59.349 38.462 0.00 0.00 0.00 3.02
1172 1205 7.846644 ATCTGCTTAAACTCTCAATCTCTTG 57.153 36.000 0.00 0.00 0.00 3.02
1184 1217 5.816258 TCTCAATCTCTTGTCATGATGCTTC 59.184 40.000 0.00 0.00 33.87 3.86
1188 1222 3.516700 TCTCTTGTCATGATGCTTCTCCA 59.483 43.478 0.00 0.00 0.00 3.86
1225 1259 6.044682 GCTTTGACATGCTTTTGGCTATTAT 58.955 36.000 0.00 0.00 42.39 1.28
1226 1260 6.536224 GCTTTGACATGCTTTTGGCTATTATT 59.464 34.615 0.00 0.00 42.39 1.40
1227 1261 7.706179 GCTTTGACATGCTTTTGGCTATTATTA 59.294 33.333 0.00 0.00 42.39 0.98
1270 1306 2.751259 TGCTTTGCATCATCAGTCTTCC 59.249 45.455 0.00 0.00 31.71 3.46
1279 1315 3.002791 TCATCAGTCTTCCAACATTCGC 58.997 45.455 0.00 0.00 0.00 4.70
1315 1351 9.691362 ACATTTGTTACAAAACATACTGGAATC 57.309 29.630 14.70 0.00 44.85 2.52
1341 1377 8.024865 CACTGATTTTCTTGAAATAGATGTGCA 58.975 33.333 0.00 0.00 38.06 4.57
1351 1387 6.589135 TGAAATAGATGTGCAGAGATGACAT 58.411 36.000 0.00 0.00 32.95 3.06
1451 1487 2.825532 ACCTGTTTGTGAAAAGTGCTGT 59.174 40.909 0.00 0.00 0.00 4.40
1460 1496 6.539649 TGTGAAAAGTGCTGTGAGTAATAC 57.460 37.500 0.00 0.00 0.00 1.89
1546 1609 8.341903 CGGCATGATTTTGTAGTAAATACATCA 58.658 33.333 0.00 0.00 43.87 3.07
1751 1823 1.538634 GCCAGAGTATCAGCAGCTCAG 60.539 57.143 0.00 0.00 37.82 3.35
1752 1824 1.538634 CCAGAGTATCAGCAGCTCAGC 60.539 57.143 0.00 0.00 37.82 4.26
1829 1901 6.268387 ACTTCACCACCAAATGATTTGAAGAT 59.732 34.615 18.82 0.00 43.26 2.40
1923 1997 3.318017 AGTGCTACAAGTAGAAGTTGCG 58.682 45.455 11.25 0.00 38.92 4.85
1949 2023 5.020132 TGAAAACTTCTGTTCAAGGGGAAA 58.980 37.500 0.00 0.00 37.23 3.13
1973 2078 8.954950 AATACTGTCCAATCTACATTTCTCTG 57.045 34.615 0.00 0.00 0.00 3.35
2003 2108 1.202830 TCCCTGAAGCGCCAAAGTAAA 60.203 47.619 2.29 0.00 0.00 2.01
2075 2180 4.142609 TGAGGAAGCTATGGTTGCTAAG 57.857 45.455 3.71 0.00 41.37 2.18
2110 2217 3.473923 AACAAATGTTGCCCTGGAAAG 57.526 42.857 0.00 0.00 36.80 2.62
2183 4218 4.354087 ACTCCCTCAAGATAAAAGGTGGTT 59.646 41.667 0.00 0.00 0.00 3.67
2223 4258 3.006940 CTGCGAACAAATAGCCCTTACA 58.993 45.455 0.00 0.00 0.00 2.41
2224 4259 2.745281 TGCGAACAAATAGCCCTTACAC 59.255 45.455 0.00 0.00 0.00 2.90
2261 4299 5.183331 TCTGCTAGACATGTTCGAAAGTACT 59.817 40.000 0.00 0.00 32.11 2.73
2264 4302 3.990092 AGACATGTTCGAAAGTACTGCA 58.010 40.909 0.00 0.00 32.11 4.41
2267 4305 1.508632 TGTTCGAAAGTACTGCAGGC 58.491 50.000 19.93 10.58 32.11 4.85
2283 4321 1.066143 CAGGCAGAACGGTTACCAGAT 60.066 52.381 1.13 0.00 0.00 2.90
2421 4459 8.560124 AGGAACTCCTGATATCAAAAGTAGAT 57.440 34.615 16.15 5.30 46.55 1.98
2423 4461 9.699703 GGAACTCCTGATATCAAAAGTAGATAC 57.300 37.037 16.15 3.24 31.32 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.754552 GCCACCTGATCATTAAGCACAA 59.245 45.455 0.00 0.00 0.00 3.33
72 73 4.021229 TCTAAAGAACGCAGGGATACTCA 58.979 43.478 0.00 0.00 0.00 3.41
79 80 2.157085 GTCGTTTCTAAAGAACGCAGGG 59.843 50.000 4.66 0.00 33.13 4.45
144 145 8.352942 GGATGCGGATTAGTATTCAGAATTTTT 58.647 33.333 0.00 0.00 0.00 1.94
149 150 4.556233 CGGATGCGGATTAGTATTCAGAA 58.444 43.478 0.00 0.00 0.00 3.02
150 151 3.614150 GCGGATGCGGATTAGTATTCAGA 60.614 47.826 9.20 0.00 0.00 3.27
151 152 2.668457 GCGGATGCGGATTAGTATTCAG 59.332 50.000 9.20 0.00 0.00 3.02
192 195 1.749634 CAAGTACACCCCTCTCCTACG 59.250 57.143 0.00 0.00 0.00 3.51
342 355 5.189736 TCAGGGCAAAGATAGAAAGAAGCTA 59.810 40.000 0.00 0.00 0.00 3.32
361 374 2.035704 CCACGAGAGATGATCTTCAGGG 59.964 54.545 10.90 0.00 38.84 4.45
401 414 0.179134 CGGTTGATCAGGACCTCGTC 60.179 60.000 13.47 0.00 33.69 4.20
402 415 0.611062 TCGGTTGATCAGGACCTCGT 60.611 55.000 13.47 0.00 33.69 4.18
464 485 3.513515 GCCTGCTGATTACCTATAGCTCT 59.486 47.826 0.00 0.00 37.10 4.09
508 529 6.151144 GTGTTTTCTCACTACCTTATTGGCAT 59.849 38.462 0.00 0.00 35.98 4.40
515 536 5.475719 CCATCGTGTTTTCTCACTACCTTA 58.524 41.667 0.00 0.00 36.33 2.69
553 574 8.651389 CCTCATCCTGTAAAAGTCCATAAGATA 58.349 37.037 0.00 0.00 0.00 1.98
683 704 8.599774 GTTTACAAAGTGCAAAAATGCTAGAAA 58.400 29.630 0.00 0.00 35.49 2.52
961 987 0.677731 GCTGATAGCAACACCAGGCA 60.678 55.000 0.00 0.00 41.89 4.75
1012 1041 5.909621 ATCCTCATGAAAATGGTCTTGTG 57.090 39.130 0.00 0.00 0.00 3.33
1074 1103 1.834263 GGTAGAGGTGGTGCAAGAGAT 59.166 52.381 0.00 0.00 0.00 2.75
1095 1124 2.727544 CTCCTCGAGCTAGCTGCC 59.272 66.667 24.99 7.77 44.23 4.85
1155 1184 7.279536 GCATCATGACAAGAGATTGAGAGTTTA 59.720 37.037 0.00 0.00 0.00 2.01
1164 1193 5.124645 GGAGAAGCATCATGACAAGAGATT 58.875 41.667 0.00 0.00 0.00 2.40
1165 1194 4.163649 TGGAGAAGCATCATGACAAGAGAT 59.836 41.667 0.00 0.00 0.00 2.75
1172 1205 1.669779 GCTGTGGAGAAGCATCATGAC 59.330 52.381 0.00 0.00 40.52 3.06
1225 1259 0.546122 ATGGCGGCACAATCTCCTAA 59.454 50.000 16.34 0.00 0.00 2.69
1226 1260 0.179048 CATGGCGGCACAATCTCCTA 60.179 55.000 16.34 0.00 0.00 2.94
1227 1261 1.452651 CATGGCGGCACAATCTCCT 60.453 57.895 16.34 0.00 0.00 3.69
1270 1306 7.697710 ACAAATGTATGTATTCTGCGAATGTTG 59.302 33.333 12.17 0.00 0.00 3.33
1315 1351 8.024865 TGCACATCTATTTCAAGAAAATCAGTG 58.975 33.333 0.00 6.70 38.53 3.66
1338 1374 5.361857 TCAGTTCATAGATGTCATCTCTGCA 59.638 40.000 18.74 7.48 40.76 4.41
1341 1377 8.795513 CAGTATCAGTTCATAGATGTCATCTCT 58.204 37.037 18.74 6.76 40.76 3.10
1351 1387 8.362464 ACCTGTAAACAGTATCAGTTCATAGA 57.638 34.615 9.17 0.00 42.27 1.98
1546 1609 6.708054 CCATGTAGTTGAAACTCAGACTTTCT 59.292 38.462 0.00 0.00 40.37 2.52
1724 1796 3.487372 TGCTGATACTCTGGCGTATACT 58.513 45.455 0.56 0.00 30.57 2.12
1751 1823 4.096833 TGTCATGTTATCTTCCATGCTTGC 59.903 41.667 0.00 0.00 38.63 4.01
1752 1824 5.124297 TGTGTCATGTTATCTTCCATGCTTG 59.876 40.000 0.00 0.00 38.63 4.01
1829 1901 6.183360 TGCATGTATTATCCGTGGGTAAGTAA 60.183 38.462 0.00 0.00 0.00 2.24
1923 1997 5.301805 TCCCCTTGAACAGAAGTTTTCATTC 59.698 40.000 0.00 0.00 38.30 2.67
1949 2023 8.083828 ACAGAGAAATGTAGATTGGACAGTAT 57.916 34.615 0.00 0.00 0.00 2.12
1973 2078 0.390998 GCTTCAGGGACAGCTCAGAC 60.391 60.000 0.00 0.00 32.87 3.51
2003 2108 9.354673 CACTCCATAAACAATATTATTGGAGGT 57.645 33.333 22.28 12.84 40.39 3.85
2183 4218 4.367450 GCAGTTCTTAAAACATGCCAACA 58.633 39.130 0.00 0.00 0.00 3.33
2235 4273 4.686554 ACTTTCGAACATGTCTAGCAGAAC 59.313 41.667 0.00 0.00 0.00 3.01
2240 4278 4.031878 GCAGTACTTTCGAACATGTCTAGC 59.968 45.833 0.00 0.00 0.00 3.42
2261 4299 1.302192 GGTAACCGTTCTGCCTGCA 60.302 57.895 0.00 0.00 0.00 4.41
2264 4302 1.276622 ATCTGGTAACCGTTCTGCCT 58.723 50.000 0.00 0.00 0.00 4.75
2267 4305 2.422597 TGCAATCTGGTAACCGTTCTG 58.577 47.619 0.00 0.00 0.00 3.02
2283 4321 3.316029 CGGCAGGAGATATTCATTTGCAA 59.684 43.478 0.00 0.00 33.47 4.08
2421 4459 6.671614 TTTTCTTGAGAACAAAGCTTCGTA 57.328 33.333 0.00 0.00 35.49 3.43
2423 4461 8.560576 TTTATTTTCTTGAGAACAAAGCTTCG 57.439 30.769 0.00 0.00 35.49 3.79


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

AutoCloner maintained by Alex Coulton.