Multiple sequence alignment - TraesCS2D01G046900

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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 TraesCS2D01G046900 chr2D 100.000 1820 0 0 822 2641 17184007 17185826 0.000000e+00 3362.0
1 TraesCS2D01G046900 chr2D 96.221 1032 25 2 891 1914 17336729 17337754 0.000000e+00 1677.0
2 TraesCS2D01G046900 chr2D 88.158 1216 104 22 822 2017 17238741 17239936 0.000000e+00 1411.0
3 TraesCS2D01G046900 chr2D 95.317 726 20 2 1197 1914 17347191 17347910 0.000000e+00 1140.0
4 TraesCS2D01G046900 chr2D 95.317 726 20 2 1197 1914 17356409 17357128 0.000000e+00 1140.0
5 TraesCS2D01G046900 chr2D 92.029 690 32 4 1916 2599 17337942 17338614 0.000000e+00 948.0
6 TraesCS2D01G046900 chr2D 92.029 690 32 4 1916 2599 17348293 17348965 0.000000e+00 948.0
7 TraesCS2D01G046900 chr2D 92.029 690 32 4 1916 2599 17357959 17358631 0.000000e+00 948.0
8 TraesCS2D01G046900 chr2D 100.000 454 0 0 1 454 17183186 17183639 0.000000e+00 839.0
9 TraesCS2D01G046900 chr2D 97.577 454 11 0 1 454 17327518 17327971 0.000000e+00 778.0
10 TraesCS2D01G046900 chr2D 90.339 590 34 8 2017 2599 17239970 17240543 0.000000e+00 752.0
11 TraesCS2D01G046900 chr2D 98.361 305 5 0 891 1195 17346382 17346686 1.080000e-148 536.0
12 TraesCS2D01G046900 chr2D 98.361 305 5 0 891 1195 17355689 17355993 1.080000e-148 536.0
13 TraesCS2D01G046900 chr2D 86.747 249 31 2 1 248 17238278 17238525 2.590000e-70 276.0
14 TraesCS2D01G046900 chr2D 100.000 48 0 0 822 869 17327998 17328045 3.620000e-14 89.8
15 TraesCS2D01G046900 chr2A 88.850 1426 98 28 822 2218 18615122 18616515 0.000000e+00 1696.0
16 TraesCS2D01G046900 chr2A 92.573 929 49 6 822 1743 18647779 18648694 0.000000e+00 1315.0
17 TraesCS2D01G046900 chr2A 91.377 777 58 4 870 1638 18676672 18677447 0.000000e+00 1055.0
18 TraesCS2D01G046900 chr2A 96.681 452 15 0 1 452 18647297 18647748 0.000000e+00 752.0
19 TraesCS2D01G046900 chr2A 91.126 462 29 4 2017 2467 18650628 18651088 1.340000e-172 616.0
20 TraesCS2D01G046900 chr2A 87.118 458 47 6 1 452 18614627 18615078 2.350000e-140 508.0
21 TraesCS2D01G046900 chr2A 83.664 453 70 3 1 452 18676139 18676588 8.740000e-115 424.0
22 TraesCS2D01G046900 chr2A 85.359 362 39 7 2250 2598 18616518 18616878 1.930000e-96 363.0
23 TraesCS2D01G046900 chr2A 94.819 193 10 0 2407 2599 18679509 18679701 4.270000e-78 302.0
24 TraesCS2D01G046900 chr2B 90.333 931 70 16 822 1743 28998346 28999265 0.000000e+00 1203.0
25 TraesCS2D01G046900 chr2B 89.400 934 72 16 824 1743 29056213 29057133 0.000000e+00 1151.0
26 TraesCS2D01G046900 chr2B 86.740 822 80 13 1199 2017 29869624 29868829 0.000000e+00 887.0
27 TraesCS2D01G046900 chr2B 92.150 586 37 3 2022 2598 29000955 29001540 0.000000e+00 819.0
28 TraesCS2D01G046900 chr2B 91.341 589 39 9 2019 2600 29868791 29868208 0.000000e+00 795.0
29 TraesCS2D01G046900 chr2B 85.839 459 52 6 1 452 29055715 29056167 2.380000e-130 475.0
30 TraesCS2D01G046900 chr2B 88.089 403 39 4 2017 2412 29058824 29059224 1.110000e-128 470.0
31 TraesCS2D01G046900 chr2B 86.207 290 28 4 1732 2014 29058501 29058785 1.190000e-78 303.0
32 TraesCS2D01G046900 chr2B 87.864 206 19 4 58 262 28996226 28996426 1.220000e-58 237.0
33 TraesCS2D01G046900 chr2B 92.216 167 10 1 288 454 28998152 28998315 1.580000e-57 233.0
34 TraesCS2D01G046900 chr2B 83.534 249 35 5 1 248 29871342 29871099 7.350000e-56 228.0
35 TraesCS2D01G046900 chrUn 92.029 690 32 4 1916 2599 384030296 384030968 0.000000e+00 948.0


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 TraesCS2D01G046900 chr2D 17183186 17185826 2640 False 2100.500000 3362 100.000000 1 2641 2 chr2D.!!$F1 2640
1 TraesCS2D01G046900 chr2D 17336729 17338614 1885 False 1312.500000 1677 94.125000 891 2599 2 chr2D.!!$F4 1708
2 TraesCS2D01G046900 chr2D 17346382 17348965 2583 False 874.666667 1140 95.235667 891 2599 3 chr2D.!!$F5 1708
3 TraesCS2D01G046900 chr2D 17355689 17358631 2942 False 874.666667 1140 95.235667 891 2599 3 chr2D.!!$F6 1708
4 TraesCS2D01G046900 chr2D 17238278 17240543 2265 False 813.000000 1411 88.414667 1 2599 3 chr2D.!!$F2 2598
5 TraesCS2D01G046900 chr2D 17327518 17328045 527 False 433.900000 778 98.788500 1 869 2 chr2D.!!$F3 868
6 TraesCS2D01G046900 chr2A 18647297 18651088 3791 False 894.333333 1315 93.460000 1 2467 3 chr2A.!!$F2 2466
7 TraesCS2D01G046900 chr2A 18614627 18616878 2251 False 855.666667 1696 87.109000 1 2598 3 chr2A.!!$F1 2597
8 TraesCS2D01G046900 chr2A 18676139 18679701 3562 False 593.666667 1055 89.953333 1 2599 3 chr2A.!!$F3 2598
9 TraesCS2D01G046900 chr2B 29868208 29871342 3134 True 636.666667 887 87.205000 1 2600 3 chr2B.!!$R1 2599
10 TraesCS2D01G046900 chr2B 28996226 29001540 5314 False 623.000000 1203 90.640750 58 2598 4 chr2B.!!$F1 2540
11 TraesCS2D01G046900 chr2B 29055715 29059224 3509 False 599.750000 1151 87.383750 1 2412 4 chr2B.!!$F2 2411
12 TraesCS2D01G046900 chrUn 384030296 384030968 672 False 948.000000 948 92.029000 1916 2599 1 chrUn.!!$F1 683

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
861 2576 4.264253 CCTGCCATCATTTCTCTACACAA 58.736 43.478 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 9248 0.667184 CACGTGCAATGGCCTTTTCC 60.667 55.0 0.82 0.0 40.13 3.13 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
167 169 8.321716 CACTCTTGCACGTAGACTATTTATTTC 58.678 37.037 0.00 0.00 0.00 2.17
861 2576 4.264253 CCTGCCATCATTTCTCTACACAA 58.736 43.478 0.00 0.00 0.00 3.33
862 2577 4.885907 CCTGCCATCATTTCTCTACACAAT 59.114 41.667 0.00 0.00 0.00 2.71
863 2578 5.008415 CCTGCCATCATTTCTCTACACAATC 59.992 44.000 0.00 0.00 0.00 2.67
864 2579 5.748402 TGCCATCATTTCTCTACACAATCT 58.252 37.500 0.00 0.00 0.00 2.40
865 2580 5.819379 TGCCATCATTTCTCTACACAATCTC 59.181 40.000 0.00 0.00 0.00 2.75
866 2581 5.238214 GCCATCATTTCTCTACACAATCTCC 59.762 44.000 0.00 0.00 0.00 3.71
867 2582 6.351711 CCATCATTTCTCTACACAATCTCCA 58.648 40.000 0.00 0.00 0.00 3.86
868 2583 6.482641 CCATCATTTCTCTACACAATCTCCAG 59.517 42.308 0.00 0.00 0.00 3.86
910 2629 4.588899 TCCATTTTCCATGGTAGAGTGTG 58.411 43.478 12.58 3.28 40.06 3.82
1100 2821 7.494625 CGTCTTCCTGCAGTTATCCTAATTAAA 59.505 37.037 13.81 0.00 0.00 1.52
1396 4508 4.986054 TGGAGGAAACTAAGGCAAACTA 57.014 40.909 0.00 0.00 44.43 2.24
1588 4713 4.566004 TGCTACTGATGTACTGGTTGAAC 58.434 43.478 0.00 0.00 0.00 3.18
1753 7610 6.992715 GGCAGAGATGCTTAGGTTTATTCTTA 59.007 38.462 0.00 0.00 34.73 2.10
1825 7682 6.528321 TCAAGTCTGAACTCATGTTGATCTT 58.472 36.000 0.00 0.00 36.39 2.40
1826 7683 6.426025 TCAAGTCTGAACTCATGTTGATCTTG 59.574 38.462 0.00 0.00 36.39 3.02
1827 7684 6.106648 AGTCTGAACTCATGTTGATCTTGA 57.893 37.500 0.00 0.00 36.39 3.02
1828 7685 6.709281 AGTCTGAACTCATGTTGATCTTGAT 58.291 36.000 0.00 0.00 36.39 2.57
1829 7686 6.817641 AGTCTGAACTCATGTTGATCTTGATC 59.182 38.462 3.82 3.82 36.39 2.92
1830 7687 6.817641 GTCTGAACTCATGTTGATCTTGATCT 59.182 38.462 11.31 0.00 36.39 2.75
1845 7710 3.876274 TGATCTCCAGAAGAAAGTCGG 57.124 47.619 0.00 0.00 37.61 4.79
1936 8630 4.826274 AGCTTAAGATTCAGGCTGTACA 57.174 40.909 15.27 0.00 31.68 2.90
1954 8648 6.259167 GCTGTACATGGAAATATACCAACGAA 59.741 38.462 0.00 0.00 40.93 3.85
2049 9076 0.037326 TTCTTGCAAGAGTCGGCGAT 60.037 50.000 27.02 1.58 36.22 4.58
2104 9136 1.881973 CTAACAGTGTTGCCACATGCT 59.118 47.619 18.90 0.00 44.39 3.79
2132 9164 7.623268 AAGCATCTAATCAACGAACAAAAAC 57.377 32.000 0.00 0.00 0.00 2.43
2196 9240 4.219725 GCCTGAAACCCATAAGTAAGCAAA 59.780 41.667 0.00 0.00 0.00 3.68
2204 9248 6.512297 ACCCATAAGTAAGCAAAAACAGTTG 58.488 36.000 0.00 0.00 0.00 3.16
2220 9264 1.070601 AGTTGGAAAAGGCCATTGCAC 59.929 47.619 13.76 9.87 37.86 4.57
2300 10561 2.939103 ACGATTGAGAAATGCCAGCTAC 59.061 45.455 0.00 0.00 0.00 3.58
2314 10575 3.435671 GCCAGCTACTAAACGTCAAATGT 59.564 43.478 0.00 0.00 0.00 2.71
2315 10576 4.669197 GCCAGCTACTAAACGTCAAATGTG 60.669 45.833 0.00 0.00 0.00 3.21
2336 10605 6.941857 TGTGTATAACTCCATAAGCAACAGA 58.058 36.000 0.00 0.00 0.00 3.41
2486 10853 7.710676 AACTGATAGTTCACTGTCTGATAGT 57.289 36.000 14.72 0.77 31.77 2.12
2487 10854 7.094508 ACTGATAGTTCACTGTCTGATAGTG 57.905 40.000 23.66 23.66 45.30 2.74
2527 10895 7.009357 CCTGTAGAAGCTTCGTACTCAAATTAC 59.991 40.741 20.43 13.08 0.00 1.89
2594 10965 8.916062 TCGGTAAACCATTATATGTCAAGACTA 58.084 33.333 0.00 0.00 35.14 2.59
2618 10989 3.040147 TCGAAAGAAGTCCACATCACC 57.960 47.619 0.00 0.00 37.03 4.02
2619 10990 2.076863 CGAAAGAAGTCCACATCACCC 58.923 52.381 0.00 0.00 0.00 4.61
2620 10991 2.437413 GAAAGAAGTCCACATCACCCC 58.563 52.381 0.00 0.00 0.00 4.95
2621 10992 0.698818 AAGAAGTCCACATCACCCCC 59.301 55.000 0.00 0.00 0.00 5.40
2635 11006 4.854587 CCCCCGGGATTTCACAAA 57.145 55.556 26.32 0.00 37.50 2.83
2636 11007 2.272923 CCCCCGGGATTTCACAAAC 58.727 57.895 26.32 0.00 37.50 2.93
2637 11008 1.254975 CCCCCGGGATTTCACAAACC 61.255 60.000 26.32 0.00 37.50 3.27
2638 11009 1.591504 CCCCGGGATTTCACAAACCG 61.592 60.000 26.32 0.00 43.89 4.44
2640 11011 1.211709 CGGGATTTCACAAACCGGC 59.788 57.895 0.00 0.00 40.79 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
266 291 6.719370 TGTTTAACCTATGGTCATTTGAGCTT 59.281 34.615 10.74 7.23 42.60 3.74
861 2576 4.078922 TCCACTAACTGGAGATCTGGAGAT 60.079 45.833 0.00 0.00 44.99 2.75
862 2577 3.269643 TCCACTAACTGGAGATCTGGAGA 59.730 47.826 0.00 0.00 44.99 3.71
863 2578 3.636679 TCCACTAACTGGAGATCTGGAG 58.363 50.000 0.00 0.00 44.99 3.86
864 2579 3.757947 TCCACTAACTGGAGATCTGGA 57.242 47.619 0.00 0.00 44.99 3.86
1396 4508 5.630415 TTCATTCCGTCTCATAATCCCTT 57.370 39.130 0.00 0.00 0.00 3.95
1631 4756 6.253727 CACACTTTACTGTATCTTAGCTTCGG 59.746 42.308 0.00 0.00 0.00 4.30
1753 7610 7.495606 GGTGTGTTCTTTCTTTTGAAATGGAAT 59.504 33.333 0.00 0.00 46.05 3.01
1766 7623 4.600062 AGTTCCAAAGGTGTGTTCTTTCT 58.400 39.130 0.00 0.00 32.72 2.52
1825 7682 3.056536 CACCGACTTTCTTCTGGAGATCA 60.057 47.826 0.00 0.00 33.49 2.92
1826 7683 3.516615 CACCGACTTTCTTCTGGAGATC 58.483 50.000 0.00 0.00 33.49 2.75
1827 7684 2.354203 GCACCGACTTTCTTCTGGAGAT 60.354 50.000 0.00 0.00 33.49 2.75
1828 7685 1.000955 GCACCGACTTTCTTCTGGAGA 59.999 52.381 0.00 0.00 0.00 3.71
1829 7686 1.001406 AGCACCGACTTTCTTCTGGAG 59.999 52.381 0.00 0.00 0.00 3.86
1830 7687 1.048601 AGCACCGACTTTCTTCTGGA 58.951 50.000 0.00 0.00 0.00 3.86
1845 7710 3.568007 TGTGTTCACCCTGAAATAAGCAC 59.432 43.478 0.37 0.00 38.22 4.40
1972 8667 3.446310 TGCTTGTTTCAGTCTACGACA 57.554 42.857 0.00 0.00 34.60 4.35
2078 9105 3.006112 TGGCAACACTGTTAGGACAAA 57.994 42.857 0.00 0.00 46.17 2.83
2104 9136 6.552859 TGTTCGTTGATTAGATGCTTTGAA 57.447 33.333 0.00 0.00 0.00 2.69
2196 9240 3.807553 CAATGGCCTTTTCCAACTGTTT 58.192 40.909 3.32 0.00 39.96 2.83
2204 9248 0.667184 CACGTGCAATGGCCTTTTCC 60.667 55.000 0.82 0.00 40.13 3.13
2220 9264 0.792640 GGATTCTGCAGTGTGACACG 59.207 55.000 14.67 6.63 39.64 4.49
2300 10561 8.246908 TGGAGTTATACACATTTGACGTTTAG 57.753 34.615 0.00 0.00 0.00 1.85
2336 10605 8.983702 TGTTAACCAAAGGTAGTTGAGTATTT 57.016 30.769 2.48 0.00 33.12 1.40
2473 10840 4.489810 GTGTCCTTCACTATCAGACAGTG 58.510 47.826 2.01 2.01 43.92 3.66
2481 10848 3.444388 AGGTTCTCGTGTCCTTCACTATC 59.556 47.826 0.00 0.00 44.16 2.08
2486 10853 1.410004 ACAGGTTCTCGTGTCCTTCA 58.590 50.000 2.41 0.00 38.07 3.02
2487 10854 2.818432 TCTACAGGTTCTCGTGTCCTTC 59.182 50.000 0.00 0.00 41.81 3.46
2527 10895 7.424803 TCACAAACATTGTTTTACCTGATCTG 58.575 34.615 12.02 1.10 43.23 2.90
2594 10965 5.048713 GGTGATGTGGACTTCTTTCGATTTT 60.049 40.000 0.00 0.00 0.00 1.82
2600 10971 2.437413 GGGGTGATGTGGACTTCTTTC 58.563 52.381 0.00 0.00 0.00 2.62
2601 10972 1.075536 GGGGGTGATGTGGACTTCTTT 59.924 52.381 0.00 0.00 0.00 2.52
2602 10973 0.698818 GGGGGTGATGTGGACTTCTT 59.301 55.000 0.00 0.00 0.00 2.52
2603 10974 2.387952 GGGGGTGATGTGGACTTCT 58.612 57.895 0.00 0.00 0.00 2.85
2618 10989 1.254975 GGTTTGTGAAATCCCGGGGG 61.255 60.000 23.50 0.00 0.00 5.40
2619 10990 1.591504 CGGTTTGTGAAATCCCGGGG 61.592 60.000 23.50 6.77 35.11 5.73
2620 10991 1.880186 CGGTTTGTGAAATCCCGGG 59.120 57.895 16.85 16.85 35.11 5.73
2622 10993 1.211709 GCCGGTTTGTGAAATCCCG 59.788 57.895 1.90 0.00 38.39 5.14


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

AutoCloner maintained by Alex Coulton.