Multiple sequence alignment - TraesCS7B01G326600

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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 TraesCS7B01G326600 chr7B 100.000 2553 0 0 1 2553 580187409 580184857 0.000000e+00 4715.0
1 TraesCS7B01G326600 chr7D 89.570 2234 86 57 1 2173 537684877 537682730 0.000000e+00 2699.0
2 TraesCS7B01G326600 chr7D 83.514 370 23 11 2215 2553 537682641 537682279 6.860000e-81 311.0
3 TraesCS7B01G326600 chr7A 87.202 1969 110 63 282 2173 619042950 619041047 0.000000e+00 2109.0
4 TraesCS7B01G326600 chr7A 86.909 275 11 11 2249 2506 619040919 619040653 4.160000e-73 285.0
5 TraesCS7B01G326600 chr3B 97.143 35 1 0 2466 2500 380513192 380513158 2.740000e-05 60.2


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 TraesCS7B01G326600 chr7B 580184857 580187409 2552 True 4715 4715 100.0000 1 2553 1 chr7B.!!$R1 2552
1 TraesCS7B01G326600 chr7D 537682279 537684877 2598 True 1505 2699 86.5420 1 2553 2 chr7D.!!$R1 2552
2 TraesCS7B01G326600 chr7A 619040653 619042950 2297 True 1197 2109 87.0555 282 2506 2 chr7A.!!$R1 2224

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
521 564 0.034756 CCATTCCATGCCATGCCATG 59.965 55.0 9.68 9.68 41.71 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 2761 0.106708 GGATCCTACTCATTGCGCCA 59.893 55.0 4.18 0.0 0.0 5.69 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
25 26 2.719354 GGTCACCAACACCAACGC 59.281 61.111 0.00 0.00 33.63 4.84
62 63 3.551846 TGTTCCGAAAGAGAAGGCTTTT 58.448 40.909 0.00 0.00 38.16 2.27
69 70 4.682860 CGAAAGAGAAGGCTTTTGTACGTA 59.317 41.667 0.00 0.00 38.16 3.57
133 134 3.160047 AGCGAGGGAGGGATGCAG 61.160 66.667 0.00 0.00 0.00 4.41
209 211 2.429930 CGCCTCCCTTGTGGACAA 59.570 61.111 0.00 0.00 38.61 3.18
293 304 4.079154 TCTGCACCCTAGAGAGAGGAATTA 60.079 45.833 0.00 0.00 39.15 1.40
296 307 4.462133 CACCCTAGAGAGAGGAATTACGA 58.538 47.826 0.00 0.00 39.15 3.43
299 310 4.138290 CCTAGAGAGAGGAATTACGAGCA 58.862 47.826 0.00 0.00 39.15 4.26
365 385 0.494095 AGACAAGGGAAGGGAGGAGT 59.506 55.000 0.00 0.00 0.00 3.85
512 555 1.299620 GCGACATGCCATTCCATGC 60.300 57.895 0.00 0.00 44.98 4.06
513 556 1.361271 CGACATGCCATTCCATGCC 59.639 57.895 0.00 0.00 44.98 4.40
514 557 1.385756 CGACATGCCATTCCATGCCA 61.386 55.000 0.00 0.00 44.98 4.92
515 558 1.045407 GACATGCCATTCCATGCCAT 58.955 50.000 0.00 0.00 44.98 4.40
516 559 0.756294 ACATGCCATTCCATGCCATG 59.244 50.000 6.22 6.22 44.98 3.66
517 560 0.602638 CATGCCATTCCATGCCATGC 60.603 55.000 0.00 0.00 36.52 4.06
518 561 1.764571 ATGCCATTCCATGCCATGCC 61.765 55.000 0.00 0.00 0.00 4.40
519 562 2.436544 GCCATTCCATGCCATGCCA 61.437 57.895 0.00 0.00 0.00 4.92
520 563 1.764571 GCCATTCCATGCCATGCCAT 61.765 55.000 0.00 0.00 0.00 4.40
521 564 0.034756 CCATTCCATGCCATGCCATG 59.965 55.000 9.68 9.68 41.71 3.66
522 565 0.602638 CATTCCATGCCATGCCATGC 60.603 55.000 11.13 0.00 40.92 4.06
523 566 1.764571 ATTCCATGCCATGCCATGCC 61.765 55.000 11.13 0.00 40.92 4.40
524 567 4.293648 CCATGCCATGCCATGCCG 62.294 66.667 11.13 0.00 40.92 5.69
525 568 4.293648 CATGCCATGCCATGCCGG 62.294 66.667 3.39 0.00 36.52 6.13
579 622 4.157120 ACGGGAGTACGGGCATGC 62.157 66.667 9.90 9.90 44.60 4.06
581 624 4.910585 GGGAGTACGGGCATGCCG 62.911 72.222 29.90 25.34 36.85 5.69
755 812 0.038526 GCTGTACCTGTACGTGCAGT 60.039 55.000 28.26 19.42 45.20 4.40
796 861 1.002087 CCCTCCGTGTTTAGAAGCTGT 59.998 52.381 0.00 0.00 0.00 4.40
810 875 9.267096 GTTTAGAAGCTGTGAGAAAATAAATCG 57.733 33.333 0.00 0.00 0.00 3.34
811 876 8.547967 TTAGAAGCTGTGAGAAAATAAATCGT 57.452 30.769 0.00 0.00 0.00 3.73
871 936 5.696724 CGCTATTCGGGAACTCATTAGATTT 59.303 40.000 0.00 0.00 33.78 2.17
881 946 5.277857 ACTCATTAGATTTACCCCGTCTG 57.722 43.478 0.00 0.00 0.00 3.51
911 976 4.645921 GCTTGTGGTTGTGGCGCC 62.646 66.667 22.73 22.73 0.00 6.53
1028 1100 3.615811 TGTGCCTCCCTCCCTCCT 61.616 66.667 0.00 0.00 0.00 3.69
1029 1105 2.285743 GTGCCTCCCTCCCTCCTT 60.286 66.667 0.00 0.00 0.00 3.36
1196 1272 4.756458 GTCCTGCTGCAGCTCGCT 62.756 66.667 36.61 0.00 43.06 4.93
1515 1597 3.112075 ACAACAGGTGATCGCGCG 61.112 61.111 26.76 26.76 0.00 6.86
1516 1598 2.809174 CAACAGGTGATCGCGCGA 60.809 61.111 36.65 36.65 0.00 5.87
1517 1599 2.507102 AACAGGTGATCGCGCGAG 60.507 61.111 36.99 24.21 0.00 5.03
1518 1600 2.989881 AACAGGTGATCGCGCGAGA 61.990 57.895 36.99 23.52 0.00 4.04
1519 1601 2.202610 CAGGTGATCGCGCGAGAA 60.203 61.111 36.99 24.64 0.00 2.87
1522 1604 2.580867 GTGATCGCGCGAGAAGCT 60.581 61.111 36.99 21.14 45.59 3.74
1528 1610 2.183046 GCGCGAGAAGCTCTTCCT 59.817 61.111 12.10 0.00 45.59 3.36
1771 1872 5.007921 GCAAGCACTTGATTTTTGGTTTGAT 59.992 36.000 14.44 0.00 42.93 2.57
1777 1878 6.642131 CACTTGATTTTTGGTTTGATGTCGAT 59.358 34.615 0.00 0.00 0.00 3.59
1793 1894 1.202417 TCGATGATCTTGTCCGCTTCC 60.202 52.381 0.00 0.00 0.00 3.46
1794 1895 1.202463 CGATGATCTTGTCCGCTTCCT 60.202 52.381 0.00 0.00 0.00 3.36
1797 1898 1.078143 ATCTTGTCCGCTTCCTGCC 60.078 57.895 0.00 0.00 38.78 4.85
1844 1946 2.605257 TGGTGTATATTCCGCCTAGCT 58.395 47.619 0.00 0.00 33.54 3.32
1846 1948 2.561419 GGTGTATATTCCGCCTAGCTGA 59.439 50.000 0.00 0.00 0.00 4.26
1860 1962 4.583871 CCTAGCTGATGTCCTTTTGTTCT 58.416 43.478 0.00 0.00 0.00 3.01
1911 2019 4.096003 GTAGCTCCCGCTTGGCCA 62.096 66.667 0.00 0.00 46.47 5.36
2039 2155 2.426522 TGTGGAGCCTGAAAGATTTCG 58.573 47.619 1.18 0.00 40.01 3.46
2093 2213 0.027586 CGCAGGCCTTTTACATACGC 59.972 55.000 0.00 0.00 0.00 4.42
2097 2217 1.081094 GGCCTTTTACATACGCGTGT 58.919 50.000 24.59 13.76 36.13 4.49
2099 2219 1.201987 GCCTTTTACATACGCGTGTGG 60.202 52.381 34.22 19.67 33.62 4.17
2173 2320 7.907214 ATAGTTTTGTGACCACATCTTACTC 57.093 36.000 3.47 0.00 41.52 2.59
2175 2322 3.695830 TTGTGACCACATCTTACTCCC 57.304 47.619 3.47 0.00 41.52 4.30
2176 2323 2.615391 TGTGACCACATCTTACTCCCA 58.385 47.619 0.00 0.00 36.21 4.37
2177 2324 3.181329 TGTGACCACATCTTACTCCCAT 58.819 45.455 0.00 0.00 36.21 4.00
2178 2325 3.055167 TGTGACCACATCTTACTCCCATG 60.055 47.826 0.00 0.00 36.21 3.66
2179 2326 3.197766 GTGACCACATCTTACTCCCATGA 59.802 47.826 0.00 0.00 0.00 3.07
2180 2327 4.040047 TGACCACATCTTACTCCCATGAT 58.960 43.478 0.00 0.00 0.00 2.45
2185 2362 6.183361 ACCACATCTTACTCCCATGATTACTC 60.183 42.308 0.00 0.00 0.00 2.59
2199 2379 6.260271 CCATGATTACTCGTACTAGTCACTCA 59.740 42.308 2.87 6.26 0.00 3.41
2207 2387 2.863132 ACTAGTCACTCAGAGACGGT 57.137 50.000 3.79 0.00 40.84 4.83
2221 2416 1.272769 AGACGGTACTGTTCCAAGCTC 59.727 52.381 9.15 0.00 0.00 4.09
2230 2425 3.007398 ACTGTTCCAAGCTCTCTTCGAAT 59.993 43.478 0.00 0.00 33.25 3.34
2231 2426 3.329386 TGTTCCAAGCTCTCTTCGAATG 58.671 45.455 0.00 0.00 33.25 2.67
2241 2436 2.297315 TCTCTTCGAATGTGAGCAGTGT 59.703 45.455 0.00 0.00 0.00 3.55
2247 2442 2.409715 CGAATGTGAGCAGTGTGTAGTG 59.590 50.000 0.00 0.00 0.00 2.74
2269 2473 6.051717 GTGTCATTATCAATGCTCCTGTACT 58.948 40.000 0.00 0.00 38.77 2.73
2284 2488 1.911269 TACTGCTCTGCCCGTCCAA 60.911 57.895 0.00 0.00 0.00 3.53
2295 2499 1.734163 CCCGTCCAACGCTCTTAATT 58.266 50.000 0.00 0.00 40.91 1.40
2351 2555 0.729140 CCATGCCGACTCAAAAACGC 60.729 55.000 0.00 0.00 0.00 4.84
2362 2566 2.796031 CTCAAAAACGCACCGTAGTGTA 59.204 45.455 0.00 0.00 46.35 2.90
2372 2599 4.089780 CGCACCGTAGTGTAAAATTTCGTA 59.910 41.667 0.00 0.00 46.35 3.43
2376 2603 7.657364 CACCGTAGTGTAAAATTTCGTAGTAC 58.343 38.462 0.00 0.00 39.30 2.73
2378 2605 7.750903 ACCGTAGTGTAAAATTTCGTAGTACTC 59.249 37.037 0.00 0.00 0.00 2.59
2506 2750 2.884685 CTCGGCTTGCTCTGCTCG 60.885 66.667 0.00 0.00 0.00 5.03
2509 2753 3.194308 GGCTTGCTCTGCTCGCTC 61.194 66.667 0.00 0.00 0.00 5.03
2510 2754 3.194308 GCTTGCTCTGCTCGCTCC 61.194 66.667 0.00 0.00 0.00 4.70
2511 2755 2.884685 CTTGCTCTGCTCGCTCCG 60.885 66.667 0.00 0.00 0.00 4.63
2515 2759 4.567385 CTCTGCTCGCTCCGCTCC 62.567 72.222 0.00 0.00 0.00 4.70
2517 2761 4.218578 CTGCTCGCTCCGCTCCAT 62.219 66.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.830847 GTTGGTGTTGGTGACCCCC 60.831 63.158 0.00 0.00 31.84 5.40
23 24 0.795735 CAAGACCTGTACCGTACGCG 60.796 60.000 10.49 3.53 37.95 6.01
25 26 2.589014 GAACAAGACCTGTACCGTACG 58.411 52.381 8.69 8.69 37.23 3.67
252 254 0.873743 GATAGGAGTGTGCTGCTCGC 60.874 60.000 7.14 7.14 42.60 5.03
293 304 2.108157 TCAGTGCCGTTTGCTCGT 59.892 55.556 0.00 0.00 42.00 4.18
296 307 1.956170 CTCGTCAGTGCCGTTTGCT 60.956 57.895 0.00 0.00 42.00 3.91
299 310 1.660575 CGTCTCGTCAGTGCCGTTT 60.661 57.895 0.00 0.00 0.00 3.60
550 593 4.386951 TCCCGTCCCGTGCATGTG 62.387 66.667 4.96 0.00 0.00 3.21
551 594 4.082523 CTCCCGTCCCGTGCATGT 62.083 66.667 4.96 0.00 0.00 3.21
552 595 2.717044 TACTCCCGTCCCGTGCATG 61.717 63.158 0.00 0.00 0.00 4.06
562 605 4.157120 GCATGCCCGTACTCCCGT 62.157 66.667 6.36 0.00 0.00 5.28
598 654 0.451783 AGCTACGTACGTTAACCGGG 59.548 55.000 27.92 9.16 42.24 5.73
599 655 1.398390 AGAGCTACGTACGTTAACCGG 59.602 52.381 27.92 0.00 42.24 5.28
604 660 2.158900 AGGGCTAGAGCTACGTACGTTA 60.159 50.000 27.92 11.32 41.70 3.18
782 847 9.899226 ATTTATTTTCTCACAGCTTCTAAACAC 57.101 29.630 0.00 0.00 0.00 3.32
796 861 9.321562 GGTCCTACAATACGATTTATTTTCTCA 57.678 33.333 0.00 0.00 0.00 3.27
810 875 1.602377 GCGGCAATGGTCCTACAATAC 59.398 52.381 0.00 0.00 0.00 1.89
811 876 1.808512 CGCGGCAATGGTCCTACAATA 60.809 52.381 0.00 0.00 0.00 1.90
871 936 2.439701 CTCGAGGCAGACGGGGTA 60.440 66.667 3.91 0.00 0.00 3.69
881 946 1.398390 CCACAAGCAATAACTCGAGGC 59.602 52.381 18.41 9.98 0.00 4.70
911 976 2.598394 CCACTGGCACCCACAAGG 60.598 66.667 0.00 0.00 43.78 3.61
1028 1100 1.768275 TCTGTTGTTGGAGGCAGAGAA 59.232 47.619 0.00 0.00 33.62 2.87
1029 1105 1.423584 TCTGTTGTTGGAGGCAGAGA 58.576 50.000 0.00 0.00 33.62 3.10
1117 1193 2.685017 TCCTCATGGGCGCTGAGT 60.685 61.111 19.95 0.00 38.77 3.41
1382 1464 0.390340 CGCTGGTCTTGCTCTTGCTA 60.390 55.000 0.00 0.00 40.48 3.49
1511 1593 1.876263 GAGGAAGAGCTTCTCGCGC 60.876 63.158 0.00 0.00 45.59 6.86
1512 1594 1.226831 GGAGGAAGAGCTTCTCGCG 60.227 63.158 0.00 0.00 45.59 5.87
1513 1595 1.226831 CGGAGGAAGAGCTTCTCGC 60.227 63.158 9.82 2.97 39.45 5.03
1514 1596 1.380524 TACGGAGGAAGAGCTTCTCG 58.619 55.000 9.82 12.53 39.45 4.04
1515 1597 4.394439 AATTACGGAGGAAGAGCTTCTC 57.606 45.455 9.82 5.88 39.45 2.87
1516 1598 5.422650 ACTTAATTACGGAGGAAGAGCTTCT 59.577 40.000 9.82 0.00 39.45 2.85
1517 1599 5.662456 ACTTAATTACGGAGGAAGAGCTTC 58.338 41.667 1.62 1.62 38.80 3.86
1518 1600 5.678955 ACTTAATTACGGAGGAAGAGCTT 57.321 39.130 0.00 0.00 0.00 3.74
1519 1601 5.221283 GCTACTTAATTACGGAGGAAGAGCT 60.221 44.000 3.55 0.00 0.00 4.09
1522 1604 4.037208 CCGCTACTTAATTACGGAGGAAGA 59.963 45.833 5.73 0.00 46.71 2.87
1528 1610 1.755959 TGGCCGCTACTTAATTACGGA 59.244 47.619 13.86 0.00 46.71 4.69
1732 1833 3.938963 GTGCTTGCTAACTATGGCTAACA 59.061 43.478 0.00 0.00 33.52 2.41
1771 1872 0.817654 AGCGGACAAGATCATCGACA 59.182 50.000 0.00 0.00 0.00 4.35
1777 1878 0.391661 GCAGGAAGCGGACAAGATCA 60.392 55.000 0.00 0.00 0.00 2.92
1793 1894 1.081641 CAAGAGCGCAAACAGGCAG 60.082 57.895 11.47 0.00 0.00 4.85
1794 1895 1.785041 GACAAGAGCGCAAACAGGCA 61.785 55.000 11.47 0.00 0.00 4.75
1797 1898 1.205064 CGGACAAGAGCGCAAACAG 59.795 57.895 11.47 0.00 0.00 3.16
1844 1946 5.875224 TGATGGTAGAACAAAAGGACATCA 58.125 37.500 0.00 0.00 40.54 3.07
1846 1948 6.126863 TCTGATGGTAGAACAAAAGGACAT 57.873 37.500 0.00 0.00 0.00 3.06
1911 2019 4.741239 AGACCCCCTGCGGATGGT 62.741 66.667 5.71 5.71 31.92 3.55
2039 2155 1.833860 GTACAGAGAGAGATGCGCAC 58.166 55.000 14.90 7.11 0.00 5.34
2099 2219 0.464554 GTGATTCTGCAGGGCCTACC 60.465 60.000 15.13 0.08 40.67 3.18
2173 2320 5.531659 AGTGACTAGTACGAGTAATCATGGG 59.468 44.000 8.75 0.00 0.00 4.00
2175 2322 7.224949 TCTGAGTGACTAGTACGAGTAATCATG 59.775 40.741 8.75 7.73 0.00 3.07
2176 2323 7.273712 TCTGAGTGACTAGTACGAGTAATCAT 58.726 38.462 8.75 0.00 0.00 2.45
2177 2324 6.637657 TCTGAGTGACTAGTACGAGTAATCA 58.362 40.000 8.75 11.56 0.00 2.57
2178 2325 6.979817 TCTCTGAGTGACTAGTACGAGTAATC 59.020 42.308 8.75 7.92 0.00 1.75
2179 2326 6.757947 GTCTCTGAGTGACTAGTACGAGTAAT 59.242 42.308 8.75 0.00 0.00 1.89
2180 2327 6.098679 GTCTCTGAGTGACTAGTACGAGTAA 58.901 44.000 8.75 0.00 0.00 2.24
2185 2362 2.604011 CCGTCTCTGAGTGACTAGTACG 59.396 54.545 12.20 4.61 32.70 3.67
2199 2379 1.272769 GCTTGGAACAGTACCGTCTCT 59.727 52.381 0.00 0.00 42.39 3.10
2207 2387 3.154710 TCGAAGAGAGCTTGGAACAGTA 58.845 45.455 0.00 0.00 42.39 2.74
2221 2416 2.411069 CACACTGCTCACATTCGAAGAG 59.589 50.000 3.35 6.27 38.43 2.85
2230 2425 1.754226 TGACACTACACACTGCTCACA 59.246 47.619 0.00 0.00 0.00 3.58
2231 2426 2.509052 TGACACTACACACTGCTCAC 57.491 50.000 0.00 0.00 0.00 3.51
2241 2436 6.051074 CAGGAGCATTGATAATGACACTACA 58.949 40.000 5.77 0.00 41.46 2.74
2247 2442 5.049818 GCAGTACAGGAGCATTGATAATGAC 60.050 44.000 5.77 0.00 41.46 3.06
2269 2473 4.680237 CGTTGGACGGGCAGAGCA 62.680 66.667 0.00 0.00 38.08 4.26
2284 2488 2.280628 GCCTGTGCTAATTAAGAGCGT 58.719 47.619 7.45 0.00 43.19 5.07
2362 2566 8.976986 ATCTTGTACGAGTACTACGAAATTTT 57.023 30.769 17.67 1.81 37.00 1.82
2372 2599 6.421485 TCCCTCTTTATCTTGTACGAGTACT 58.579 40.000 10.00 0.00 37.00 2.73
2376 2603 4.038162 CCCTCCCTCTTTATCTTGTACGAG 59.962 50.000 3.44 3.44 0.00 4.18
2378 2605 3.492829 GCCCTCCCTCTTTATCTTGTACG 60.493 52.174 0.00 0.00 0.00 3.67
2511 2755 0.815213 TACTCATTGCGCCATGGAGC 60.815 55.000 31.20 31.20 41.27 4.70
2512 2756 1.224075 CTACTCATTGCGCCATGGAG 58.776 55.000 18.40 14.87 0.00 3.86
2513 2757 0.179048 CCTACTCATTGCGCCATGGA 60.179 55.000 18.40 7.38 0.00 3.41
2514 2758 0.179048 TCCTACTCATTGCGCCATGG 60.179 55.000 20.14 7.63 0.00 3.66
2515 2759 1.802960 GATCCTACTCATTGCGCCATG 59.197 52.381 15.01 15.01 0.00 3.66
2516 2760 1.271054 GGATCCTACTCATTGCGCCAT 60.271 52.381 4.18 0.00 0.00 4.40
2517 2761 0.106708 GGATCCTACTCATTGCGCCA 59.893 55.000 4.18 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.