Multiple sequence alignment - TraesCS7D01G264200

Loading Multiple Alignment...

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 TraesCS7D01G264200 chr7D 100.000 2825 0 0 1 2825 244950308 244953132 0.000000e+00 5217
1 TraesCS7D01G264200 chr7D 85.413 569 82 1 21 589 211879740 211880307 8.720000e-165 590
2 TraesCS7D01G264200 chr7A 92.286 2113 91 28 757 2825 261220362 261222446 0.000000e+00 2933
3 TraesCS7D01G264200 chr7A 84.495 574 84 5 21 591 223792179 223792750 1.900000e-156 562
4 TraesCS7D01G264200 chr7A 88.554 166 16 1 588 750 261219482 261219647 6.170000e-47 198
5 TraesCS7D01G264200 chr7B 91.325 2098 95 29 771 2825 220865221 220867274 0.000000e+00 2785
6 TraesCS7D01G264200 chr6A 85.866 566 76 4 21 583 144704137 144704701 1.450000e-167 599
7 TraesCS7D01G264200 chr6A 83.101 574 95 2 16 589 180928632 180928061 3.220000e-144 521
8 TraesCS7D01G264200 chr1B 83.888 571 91 1 26 595 289096506 289095936 6.880000e-151 544
9 TraesCS7D01G264200 chr4B 83.048 584 95 3 5 587 415112742 415112162 6.930000e-146 527
10 TraesCS7D01G264200 chr2B 83.275 574 94 2 16 589 183307867 183308438 6.930000e-146 527
11 TraesCS7D01G264200 chr6B 83.045 578 95 3 16 592 382736732 382736157 3.220000e-144 521
12 TraesCS7D01G264200 chr5A 82.957 575 95 3 16 589 122127402 122127974 1.500000e-142 516


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 TraesCS7D01G264200 chr7D 244950308 244953132 2824 False 5217.0 5217 100.000 1 2825 1 chr7D.!!$F2 2824
1 TraesCS7D01G264200 chr7D 211879740 211880307 567 False 590.0 590 85.413 21 589 1 chr7D.!!$F1 568
2 TraesCS7D01G264200 chr7A 261219482 261222446 2964 False 1565.5 2933 90.420 588 2825 2 chr7A.!!$F2 2237
3 TraesCS7D01G264200 chr7A 223792179 223792750 571 False 562.0 562 84.495 21 591 1 chr7A.!!$F1 570
4 TraesCS7D01G264200 chr7B 220865221 220867274 2053 False 2785.0 2785 91.325 771 2825 1 chr7B.!!$F1 2054
5 TraesCS7D01G264200 chr6A 144704137 144704701 564 False 599.0 599 85.866 21 583 1 chr6A.!!$F1 562
6 TraesCS7D01G264200 chr6A 180928061 180928632 571 True 521.0 521 83.101 16 589 1 chr6A.!!$R1 573
7 TraesCS7D01G264200 chr1B 289095936 289096506 570 True 544.0 544 83.888 26 595 1 chr1B.!!$R1 569
8 TraesCS7D01G264200 chr4B 415112162 415112742 580 True 527.0 527 83.048 5 587 1 chr4B.!!$R1 582
9 TraesCS7D01G264200 chr2B 183307867 183308438 571 False 527.0 527 83.275 16 589 1 chr2B.!!$F1 573
10 TraesCS7D01G264200 chr6B 382736157 382736732 575 True 521.0 521 83.045 16 592 1 chr6B.!!$R1 576
11 TraesCS7D01G264200 chr5A 122127402 122127974 572 False 516.0 516 82.957 16 589 1 chr5A.!!$F1 573

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
881 1595 0.324943 CTCCGGTGGACTCATTTGGT 59.675 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 3350 0.179936 GCTCTTCCCATGACAGAGGG 59.82 60.0 9.06 9.06 46.9 4.3 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
77 78 2.517959 CAAAACAGGAGGATGGAGCAA 58.482 47.619 0.00 0.00 0.00 3.91
114 116 4.678509 TGTTAAGTTGAATGTCGATGCC 57.321 40.909 0.00 0.00 0.00 4.40
127 130 7.714813 TGAATGTCGATGCCTCTTTTAATCATA 59.285 33.333 0.00 0.00 0.00 2.15
174 177 5.509501 GGCTGTCCTCAGAGATGATAAAGAG 60.510 48.000 0.00 0.00 43.76 2.85
194 198 2.076863 GAGGTTCATTGTCGGTGGAAG 58.923 52.381 0.00 0.00 0.00 3.46
203 207 2.266055 CGGTGGAAGCTGGAGGAC 59.734 66.667 0.00 0.00 0.00 3.85
213 217 1.294780 CTGGAGGACTGACTGGTGC 59.705 63.158 0.00 0.00 0.00 5.01
215 219 2.262915 GAGGACTGACTGGTGCGG 59.737 66.667 0.00 0.00 32.80 5.69
217 221 2.048127 GGACTGACTGGTGCGGTC 60.048 66.667 0.00 0.00 39.93 4.79
347 351 5.776716 ACACAATGAAGAATGGAGGACAATT 59.223 36.000 0.00 0.00 0.00 2.32
407 412 7.662604 ATTTCATGGCTTGTGATTTTTCTTC 57.337 32.000 0.00 0.00 0.00 2.87
437 442 5.011635 GGTTTGAACATTGTAATGGGGAAGT 59.988 40.000 9.22 0.00 40.70 3.01
495 500 6.318648 CGAAATTTTCCATCACTAGGGATTGA 59.681 38.462 4.21 4.46 35.00 2.57
502 507 5.667172 TCCATCACTAGGGATTGATTTGAGA 59.333 40.000 4.21 0.00 28.31 3.27
643 653 7.065563 GGAGATATATGAGATGGTTGTCATTGC 59.934 40.741 0.00 0.00 37.13 3.56
653 663 2.159435 GGTTGTCATTGCGGTGGATTAC 60.159 50.000 0.00 0.00 0.00 1.89
655 665 2.997980 TGTCATTGCGGTGGATTACAT 58.002 42.857 0.00 0.00 0.00 2.29
689 699 6.866770 GCTTATTTTAGTGTTTCTTTGACCCC 59.133 38.462 0.00 0.00 0.00 4.95
690 700 7.470841 GCTTATTTTAGTGTTTCTTTGACCCCA 60.471 37.037 0.00 0.00 0.00 4.96
697 707 3.069443 TGTTTCTTTGACCCCATTTGCTC 59.931 43.478 0.00 0.00 0.00 4.26
701 711 1.923356 TTGACCCCATTTGCTCCTTC 58.077 50.000 0.00 0.00 0.00 3.46
703 713 1.272092 TGACCCCATTTGCTCCTTCTG 60.272 52.381 0.00 0.00 0.00 3.02
710 720 3.686726 CCATTTGCTCCTTCTGTGACTAC 59.313 47.826 0.00 0.00 0.00 2.73
723 733 7.339721 CCTTCTGTGACTACTTATGTAGAGGAA 59.660 40.741 19.61 13.69 46.76 3.36
728 738 9.696572 TGTGACTACTTATGTAGAGGAAACTAT 57.303 33.333 19.61 0.00 46.76 2.12
817 1531 4.378774 TGGCATTTGAATTCAGTTTGTGG 58.621 39.130 8.41 0.00 0.00 4.17
819 1533 5.069648 TGGCATTTGAATTCAGTTTGTGGTA 59.930 36.000 8.41 0.00 0.00 3.25
850 1564 5.578005 TGGAGAAGGTACGTAGATTGAAG 57.422 43.478 0.00 0.00 0.00 3.02
881 1595 0.324943 CTCCGGTGGACTCATTTGGT 59.675 55.000 0.00 0.00 0.00 3.67
898 1612 0.806868 GGTTTAGGTTACGGCCAAGC 59.193 55.000 2.24 0.00 0.00 4.01
947 1662 7.429374 TCCTCTGCCCATATATAGATTCAAG 57.571 40.000 0.00 0.00 0.00 3.02
950 1665 6.409704 TCTGCCCATATATAGATTCAAGCAC 58.590 40.000 0.00 0.00 0.00 4.40
973 1688 6.000840 ACAATTCCTCCAAGTCTTCTCTTTC 58.999 40.000 0.00 0.00 0.00 2.62
982 1697 2.098443 AGTCTTCTCTTTCTCCGATCGC 59.902 50.000 10.32 0.00 0.00 4.58
999 1734 1.801512 GCTTTTTCATCCGCCGCAC 60.802 57.895 0.00 0.00 0.00 5.34
1235 1980 1.039785 TCTCTCGCCATGCAGCTAGT 61.040 55.000 0.00 0.00 0.00 2.57
1255 2000 1.937546 GCATGCCCCTTCCTTCGTTG 61.938 60.000 6.36 0.00 0.00 4.10
1257 2002 0.625849 ATGCCCCTTCCTTCGTTGAT 59.374 50.000 0.00 0.00 0.00 2.57
1264 2009 3.998341 CCCTTCCTTCGTTGATTCGTTAA 59.002 43.478 0.00 0.00 0.00 2.01
1277 2022 7.059147 CGTTGATTCGTTAATTAGATCGATCGA 59.941 37.037 21.86 21.86 32.54 3.59
1292 2037 2.915775 TCGATCTCGATCTCCCGTC 58.084 57.895 0.00 0.00 44.22 4.79
1481 2229 3.143728 ACGTACGGCAAGAAGGAAAAAT 58.856 40.909 21.06 0.00 0.00 1.82
1485 2233 6.072342 ACGTACGGCAAGAAGGAAAAATAAAT 60.072 34.615 21.06 0.00 0.00 1.40
1512 2262 7.948034 ATCCATCTAAGCTAGTAGACCATAC 57.052 40.000 0.00 0.00 32.97 2.39
1513 2263 5.938710 TCCATCTAAGCTAGTAGACCATACG 59.061 44.000 0.00 0.00 32.97 3.06
1514 2264 5.706369 CCATCTAAGCTAGTAGACCATACGT 59.294 44.000 0.00 0.00 32.97 3.57
1515 2265 6.128227 CCATCTAAGCTAGTAGACCATACGTC 60.128 46.154 0.00 0.00 42.32 4.34
1516 2266 5.303971 TCTAAGCTAGTAGACCATACGTCC 58.696 45.833 0.00 0.00 43.08 4.79
1517 2267 3.572632 AGCTAGTAGACCATACGTCCA 57.427 47.619 0.00 0.00 43.08 4.02
1518 2268 4.101645 AGCTAGTAGACCATACGTCCAT 57.898 45.455 0.00 0.00 43.08 3.41
1519 2269 3.821600 AGCTAGTAGACCATACGTCCATG 59.178 47.826 0.00 0.00 43.08 3.66
1520 2270 3.612004 GCTAGTAGACCATACGTCCATGC 60.612 52.174 0.00 0.00 43.08 4.06
1521 2271 2.667470 AGTAGACCATACGTCCATGCT 58.333 47.619 0.00 0.00 43.08 3.79
1547 2297 0.813210 TGCATCTGTGTTCGTGCACA 60.813 50.000 18.64 12.52 45.85 4.57
1596 2348 1.593006 CGTCGTTCTCTGCTTTGTTGT 59.407 47.619 0.00 0.00 0.00 3.32
1632 2384 2.048597 CTACAGACGGCGGCAACA 60.049 61.111 18.30 0.00 0.00 3.33
1825 2577 2.514592 CGCCGGCCAGACATTGAT 60.515 61.111 23.46 0.00 0.00 2.57
1843 2599 8.954950 ACATTGATCAATCAGTTAGGAGTAAG 57.045 34.615 18.16 4.75 38.19 2.34
1864 2620 2.615912 GAGCAGCACCTTGATATGTTCC 59.384 50.000 0.00 0.00 0.00 3.62
1869 2625 4.701651 CAGCACCTTGATATGTTCCAAAGA 59.298 41.667 0.00 0.00 0.00 2.52
1917 2675 7.929785 AGTTCTTAGGAGTAAATTGTTTGTCGA 59.070 33.333 0.00 0.00 0.00 4.20
1924 2682 7.013846 AGGAGTAAATTGTTTGTCGATTTGGAA 59.986 33.333 0.00 0.00 39.60 3.53
1926 2684 6.921307 AGTAAATTGTTTGTCGATTTGGAACC 59.079 34.615 0.00 0.00 39.60 3.62
2062 2824 4.982241 ATGTGTTCTGAGGAGAAAAGGA 57.018 40.909 0.00 0.00 40.00 3.36
2079 2841 7.574607 AGAAAAGGAGAGGTCTCTTACAAAAA 58.425 34.615 6.94 0.00 42.48 1.94
2136 2898 4.435917 CGATGCTGAAAATGATGACGACAA 60.436 41.667 0.00 0.00 0.00 3.18
2179 2941 1.671979 GCATCATGCTTAGGTGCAGA 58.328 50.000 1.02 0.00 46.71 4.26
2405 3171 3.340814 TGAGGAGTGATGAAGAAAGGC 57.659 47.619 0.00 0.00 0.00 4.35
2491 3257 1.671054 GCTGTCCCTGTTTAGCGCA 60.671 57.895 11.47 0.00 0.00 6.09
2512 3278 1.010574 CGTCTCGCTGTCGATCCTC 60.011 63.158 0.00 0.00 44.56 3.71
2626 3392 3.721706 AAGGCCCCTCCTGAAGCG 61.722 66.667 0.00 0.00 46.94 4.68
2720 3486 0.523072 CGCTGTGCTAACCTGCAAAT 59.477 50.000 0.00 0.00 45.12 2.32
2801 3572 6.654161 CAGAAAATTTCACTGATGGAGACTCT 59.346 38.462 15.69 0.00 34.07 3.24
2802 3573 6.654161 AGAAAATTTCACTGATGGAGACTCTG 59.346 38.462 8.55 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.349627 CGTTGCATCACGAGCATCC 59.650 57.895 4.95 0.00 43.15 3.51
1 2 1.349627 CCGTTGCATCACGAGCATC 59.650 57.895 12.38 0.00 43.15 3.91
2 3 2.753966 GCCGTTGCATCACGAGCAT 61.754 57.895 12.38 0.00 43.15 3.79
3 4 3.422303 GCCGTTGCATCACGAGCA 61.422 61.111 12.38 0.00 43.15 4.26
13 14 4.328440 TGCATTAACATAATTTGCCGTTGC 59.672 37.500 0.00 0.00 38.26 4.17
14 15 5.347093 TGTGCATTAACATAATTTGCCGTTG 59.653 36.000 0.00 0.00 32.39 4.10
127 130 3.306919 CCAACTGTGCCCATAAGCAAATT 60.307 43.478 0.00 0.00 46.19 1.82
174 177 2.076863 CTTCCACCGACAATGAACCTC 58.923 52.381 0.00 0.00 0.00 3.85
194 198 1.294780 CACCAGTCAGTCCTCCAGC 59.705 63.158 0.00 0.00 0.00 4.85
203 207 0.246360 TACATGACCGCACCAGTCAG 59.754 55.000 0.00 0.00 46.76 3.51
213 217 3.097877 TCTGCTGCTAATACATGACCG 57.902 47.619 0.00 0.00 0.00 4.79
215 219 7.307632 CCAATACTTCTGCTGCTAATACATGAC 60.308 40.741 0.00 0.00 0.00 3.06
217 221 6.567321 GCCAATACTTCTGCTGCTAATACATG 60.567 42.308 0.00 0.00 0.00 3.21
259 263 0.597377 CCCGCCTTTTGTGCAAGAAC 60.597 55.000 0.00 0.00 0.00 3.01
314 318 6.149973 TCCATTCTTCATTGTGTCAATCACTC 59.850 38.462 0.00 0.00 46.27 3.51
347 351 1.549243 TATTGTCGCTGCTCCCACCA 61.549 55.000 0.00 0.00 0.00 4.17
407 412 7.090173 CCCATTACAATGTTCAAACCTAACAG 58.910 38.462 0.00 0.00 40.00 3.16
437 442 6.434028 AGCAAGTTCATGAGCCACTTTATTTA 59.566 34.615 8.28 0.00 0.00 1.40
495 500 9.872684 ACAATATCATTCATAGGGTTCTCAAAT 57.127 29.630 0.00 0.00 0.00 2.32
629 636 0.171007 CCACCGCAATGACAACCATC 59.829 55.000 0.00 0.00 33.53 3.51
689 699 4.573900 AGTAGTCACAGAAGGAGCAAATG 58.426 43.478 0.00 0.00 0.00 2.32
690 700 4.899352 AGTAGTCACAGAAGGAGCAAAT 57.101 40.909 0.00 0.00 0.00 2.32
697 707 6.829298 TCCTCTACATAAGTAGTCACAGAAGG 59.171 42.308 5.12 3.42 46.30 3.46
701 711 8.057536 AGTTTCCTCTACATAAGTAGTCACAG 57.942 38.462 5.12 0.00 46.30 3.66
755 770 7.010923 TCCTGAATTTTTGTTTGTTCGGAATTG 59.989 33.333 0.00 0.00 0.00 2.32
765 780 8.991026 TGCAAATATCTCCTGAATTTTTGTTTG 58.009 29.630 0.00 0.00 0.00 2.93
769 784 9.595823 AAGATGCAAATATCTCCTGAATTTTTG 57.404 29.630 0.00 0.00 36.42 2.44
817 1531 4.567159 CGTACCTTCTCCAGCTTCATTTAC 59.433 45.833 0.00 0.00 0.00 2.01
819 1533 3.008049 ACGTACCTTCTCCAGCTTCATTT 59.992 43.478 0.00 0.00 0.00 2.32
881 1595 3.252979 GGCTTGGCCGTAACCTAAA 57.747 52.632 0.00 0.00 39.62 1.85
930 1645 8.680903 GGAATTGTGCTTGAATCTATATATGGG 58.319 37.037 0.00 0.00 0.00 4.00
947 1662 3.416156 AGAAGACTTGGAGGAATTGTGC 58.584 45.455 0.00 0.00 0.00 4.57
950 1665 6.237154 AGAAAGAGAAGACTTGGAGGAATTG 58.763 40.000 0.00 0.00 0.00 2.32
973 1688 1.258982 CGGATGAAAAAGCGATCGGAG 59.741 52.381 18.30 0.00 0.00 4.63
982 1697 0.171007 ATGTGCGGCGGATGAAAAAG 59.829 50.000 9.78 0.00 0.00 2.27
999 1734 2.951745 GAGGCGCGACGAGTCATG 60.952 66.667 12.10 0.00 0.00 3.07
1176 1911 2.169832 ACATGGTGAAGTTGACCTCG 57.830 50.000 12.98 6.17 34.26 4.63
1235 1980 2.045045 CGAAGGAAGGGGCATGCA 60.045 61.111 21.36 0.00 0.00 3.96
1242 1987 2.094762 ACGAATCAACGAAGGAAGGG 57.905 50.000 0.00 0.00 37.03 3.95
1277 2022 0.179004 AGCAGACGGGAGATCGAGAT 60.179 55.000 0.00 0.00 0.00 2.75
1512 2262 2.528743 GCATGGACGAGCATGGACG 61.529 63.158 0.00 0.00 0.00 4.79
1513 2263 1.450134 TGCATGGACGAGCATGGAC 60.450 57.895 0.00 0.00 35.51 4.02
1514 2264 2.988800 TGCATGGACGAGCATGGA 59.011 55.556 0.00 0.00 35.51 3.41
1518 2268 0.741927 CACAGATGCATGGACGAGCA 60.742 55.000 2.46 0.00 45.92 4.26
1519 2269 0.742281 ACACAGATGCATGGACGAGC 60.742 55.000 2.46 0.00 0.00 5.03
1520 2270 1.662629 GAACACAGATGCATGGACGAG 59.337 52.381 2.46 0.00 0.00 4.18
1521 2271 1.725641 GAACACAGATGCATGGACGA 58.274 50.000 2.46 0.00 0.00 4.20
1547 2297 2.416027 CCGTCAGTCGAGATCAATGTGT 60.416 50.000 0.00 0.00 42.86 3.72
1549 2299 2.092323 TCCGTCAGTCGAGATCAATGT 58.908 47.619 0.00 0.00 42.86 2.71
1553 2303 1.366854 CCGTCCGTCAGTCGAGATCA 61.367 60.000 0.00 0.00 42.86 2.92
1596 2348 1.823470 GTTCACCACCAGCTGCACA 60.823 57.895 8.66 0.00 0.00 4.57
1821 2573 7.093333 TGCTCTTACTCCTAACTGATTGATCAA 60.093 37.037 11.26 11.26 36.18 2.57
1825 2577 5.394663 GCTGCTCTTACTCCTAACTGATTGA 60.395 44.000 0.00 0.00 0.00 2.57
1843 2599 2.615912 GGAACATATCAAGGTGCTGCTC 59.384 50.000 0.00 0.00 0.00 4.26
1905 2663 4.100189 TGGGTTCCAAATCGACAAACAATT 59.900 37.500 0.00 0.00 0.00 2.32
2079 2841 5.354234 GGATCATATTCACGGTGTGTTCTTT 59.646 40.000 8.17 0.00 34.79 2.52
2082 2844 4.442706 AGGATCATATTCACGGTGTGTTC 58.557 43.478 8.17 3.91 34.79 3.18
2083 2845 4.162320 AGAGGATCATATTCACGGTGTGTT 59.838 41.667 8.17 0.00 37.82 3.32
2179 2941 0.463204 CACGGAGATGACATCCTGCT 59.537 55.000 11.92 0.00 34.45 4.24
2256 3022 1.596220 GGCCGTTTTGTCAAGTCGAAC 60.596 52.381 11.29 1.63 0.00 3.95
2405 3171 8.084684 TGAATGAACCGATGAACAGATAGATAG 58.915 37.037 0.00 0.00 0.00 2.08
2584 3350 0.179936 GCTCTTCCCATGACAGAGGG 59.820 60.000 9.06 9.06 46.90 4.30
2782 3553 5.719085 AGTACAGAGTCTCCATCAGTGAAAT 59.281 40.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.