Multiple sequence alignment - TraesCS2D01G471000

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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 TraesCS2D01G471000 chr2D 100.000 3428 0 0 1 3428 575237878 575241305 0.000000e+00 6331.0
1 TraesCS2D01G471000 chr2D 93.150 2613 134 15 824 3420 634407274 634409857 0.000000e+00 3792.0
2 TraesCS2D01G471000 chr2A 95.069 1602 57 7 824 2415 713531023 713532612 0.000000e+00 2501.0
3 TraesCS2D01G471000 chr2A 91.529 1027 74 9 2409 3428 713532776 713533796 0.000000e+00 1402.0
4 TraesCS2D01G471000 chr2A 83.486 109 16 2 3199 3307 12047101 12046995 2.180000e-17 100.0
5 TraesCS2D01G471000 chr2B 89.572 1707 121 20 824 2503 691417668 691415992 0.000000e+00 2113.0
6 TraesCS2D01G471000 chr2B 93.103 1450 60 12 945 2373 691270532 691271962 0.000000e+00 2087.0
7 TraesCS2D01G471000 chr2B 90.720 819 51 11 2369 3182 691282963 691283761 0.000000e+00 1068.0
8 TraesCS2D01G471000 chr2B 97.521 242 5 1 3179 3420 691307428 691307668 2.460000e-111 412.0
9 TraesCS2D01G471000 chr2B 91.971 137 1 2 824 950 691268895 691269031 2.100000e-42 183.0
10 TraesCS2D01G471000 chr5D 93.709 763 31 12 1 761 168658843 168659590 0.000000e+00 1127.0
11 TraesCS2D01G471000 chr5D 93.581 701 39 5 125 823 486198143 486197447 0.000000e+00 1040.0
12 TraesCS2D01G471000 chr5D 90.948 707 52 11 123 824 29020412 29021111 0.000000e+00 941.0
13 TraesCS2D01G471000 chr1D 93.785 708 39 5 118 823 137420321 137419617 0.000000e+00 1059.0
14 TraesCS2D01G471000 chr1D 90.671 686 51 12 144 823 475806245 475806923 0.000000e+00 900.0
15 TraesCS2D01G471000 chr1D 76.722 421 77 16 1007 1412 69197741 69197327 7.450000e-52 215.0
16 TraesCS2D01G471000 chr1D 72.840 567 122 28 1874 2432 69196976 69196434 7.610000e-37 165.0
17 TraesCS2D01G471000 chr6D 92.877 716 38 11 118 826 429953995 429953286 0.000000e+00 1027.0
18 TraesCS2D01G471000 chr6D 84.000 150 22 2 3225 3372 387726749 387726600 3.570000e-30 143.0
19 TraesCS2D01G471000 chr3D 93.010 701 42 6 125 823 564993934 564993239 0.000000e+00 1016.0
20 TraesCS2D01G471000 chr4A 90.105 667 56 9 163 824 652003219 652002558 0.000000e+00 857.0
21 TraesCS2D01G471000 chr4D 88.062 712 67 16 118 823 461817005 461816306 0.000000e+00 828.0
22 TraesCS2D01G471000 chr1B 72.830 887 203 31 1538 2408 111259230 111258366 5.640000e-68 268.0
23 TraesCS2D01G471000 chr1B 80.473 338 57 7 2820 3150 574306297 574305962 2.040000e-62 250.0
24 TraesCS2D01G471000 chr1B 72.663 567 123 26 1874 2432 111051268 111050726 3.540000e-35 159.0
25 TraesCS2D01G471000 chr1A 71.896 886 213 30 1538 2408 69187682 69186818 1.240000e-54 224.0
26 TraesCS2D01G471000 chr1A 78.189 243 45 7 2192 2432 68459183 68458947 7.660000e-32 148.0
27 TraesCS2D01G471000 chr7B 79.439 321 54 8 2834 3147 71287486 71287801 2.070000e-52 217.0
28 TraesCS2D01G471000 chr7D 78.806 335 54 10 2820 3146 211763850 211763525 3.470000e-50 209.0
29 TraesCS2D01G471000 chr6A 84.000 150 22 2 3225 3372 532849352 532849203 3.570000e-30 143.0
30 TraesCS2D01G471000 chr7A 78.421 190 34 6 2951 3135 489562803 489562990 2.160000e-22 117.0
31 TraesCS2D01G471000 chr7A 82.301 113 16 4 3196 3307 694298749 694298858 1.010000e-15 95.3
32 TraesCS2D01G471000 chr5B 82.222 135 13 4 3242 3372 690707271 690707398 4.680000e-19 106.0
33 TraesCS2D01G471000 chr4B 79.433 141 23 2 3232 3366 55032342 55032202 1.010000e-15 95.3


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 TraesCS2D01G471000 chr2D 575237878 575241305 3427 False 6331.0 6331 100.000 1 3428 1 chr2D.!!$F1 3427
1 TraesCS2D01G471000 chr2D 634407274 634409857 2583 False 3792.0 3792 93.150 824 3420 1 chr2D.!!$F2 2596
2 TraesCS2D01G471000 chr2A 713531023 713533796 2773 False 1951.5 2501 93.299 824 3428 2 chr2A.!!$F1 2604
3 TraesCS2D01G471000 chr2B 691415992 691417668 1676 True 2113.0 2113 89.572 824 2503 1 chr2B.!!$R1 1679
4 TraesCS2D01G471000 chr2B 691268895 691271962 3067 False 1135.0 2087 92.537 824 2373 2 chr2B.!!$F3 1549
5 TraesCS2D01G471000 chr2B 691282963 691283761 798 False 1068.0 1068 90.720 2369 3182 1 chr2B.!!$F1 813
6 TraesCS2D01G471000 chr5D 168658843 168659590 747 False 1127.0 1127 93.709 1 761 1 chr5D.!!$F2 760
7 TraesCS2D01G471000 chr5D 486197447 486198143 696 True 1040.0 1040 93.581 125 823 1 chr5D.!!$R1 698
8 TraesCS2D01G471000 chr5D 29020412 29021111 699 False 941.0 941 90.948 123 824 1 chr5D.!!$F1 701
9 TraesCS2D01G471000 chr1D 137419617 137420321 704 True 1059.0 1059 93.785 118 823 1 chr1D.!!$R1 705
10 TraesCS2D01G471000 chr1D 475806245 475806923 678 False 900.0 900 90.671 144 823 1 chr1D.!!$F1 679
11 TraesCS2D01G471000 chr6D 429953286 429953995 709 True 1027.0 1027 92.877 118 826 1 chr6D.!!$R2 708
12 TraesCS2D01G471000 chr3D 564993239 564993934 695 True 1016.0 1016 93.010 125 823 1 chr3D.!!$R1 698
13 TraesCS2D01G471000 chr4A 652002558 652003219 661 True 857.0 857 90.105 163 824 1 chr4A.!!$R1 661
14 TraesCS2D01G471000 chr4D 461816306 461817005 699 True 828.0 828 88.062 118 823 1 chr4D.!!$R1 705
15 TraesCS2D01G471000 chr1B 111258366 111259230 864 True 268.0 268 72.830 1538 2408 1 chr1B.!!$R2 870
16 TraesCS2D01G471000 chr1A 69186818 69187682 864 True 224.0 224 71.896 1538 2408 1 chr1A.!!$R2 870

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
695 706 0.035152 AATGATGGCTCCTCGTTGCA 60.035 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2671 4422 1.544246 GTGTTTGTTCCCTGTATGGCC 59.456 52.381 0.0 0.0 0.0 5.36 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
161 164 1.005630 CTCGGGATGCGGATCTTCC 60.006 63.158 16.91 9.33 38.07 3.46
192 195 2.813908 GAACTCCGACGGCGCATT 60.814 61.111 4.27 0.00 35.83 3.56
272 276 4.471386 ACTCCCTATAGTGCAGTCAACAAT 59.529 41.667 0.00 0.00 0.00 2.71
348 352 1.284785 TCTTGGGAGGAAAATCCGCAT 59.715 47.619 2.60 0.00 42.75 4.73
695 706 0.035152 AATGATGGCTCCTCGTTGCA 60.035 50.000 0.00 0.00 0.00 4.08
728 741 5.404395 GACTAGGGGTCAAGGGATAAGTAT 58.596 45.833 0.00 0.00 43.94 2.12
764 779 2.076803 GGGAAACGGGAGGGGCTAT 61.077 63.158 0.00 0.00 0.00 2.97
778 793 1.587054 GCTATCCCTAGCGATGCGT 59.413 57.895 0.00 0.00 40.95 5.24
995 2551 4.208746 ACCGAACAAAATTAGAACACCCA 58.791 39.130 0.00 0.00 0.00 4.51
1019 2575 0.251354 ATGTCCACGCTCAGCTTCAT 59.749 50.000 0.00 0.00 0.00 2.57
1023 2579 0.179137 CCACGCTCAGCTTCATCGTA 60.179 55.000 0.00 0.00 0.00 3.43
1140 2696 2.764314 GCACATCCGCGGCATCTTT 61.764 57.895 23.51 0.00 0.00 2.52
1401 2957 0.975040 AGCTCTGCTTCGAGGTGGAT 60.975 55.000 0.00 0.00 40.02 3.41
1455 3011 5.357878 GGTGATCATTCAGGTAAGCATTTCA 59.642 40.000 0.00 0.00 30.85 2.69
1456 3012 6.459298 GGTGATCATTCAGGTAAGCATTTCAG 60.459 42.308 0.00 0.00 30.85 3.02
1463 3019 6.500684 TCAGGTAAGCATTTCAGATTTCAC 57.499 37.500 0.00 0.00 0.00 3.18
1486 3042 1.082561 GCACGTGAGCACACACATG 60.083 57.895 22.23 9.86 46.20 3.21
1487 3043 1.498043 GCACGTGAGCACACACATGA 61.498 55.000 22.23 0.00 46.20 3.07
1488 3044 0.233074 CACGTGAGCACACACATGAC 59.767 55.000 10.90 0.00 46.20 3.06
1489 3045 0.179086 ACGTGAGCACACACATGACA 60.179 50.000 14.75 0.00 46.20 3.58
1490 3046 0.233074 CGTGAGCACACACATGACAC 59.767 55.000 14.75 0.00 46.20 3.67
1491 3047 1.298602 GTGAGCACACACATGACACA 58.701 50.000 9.58 0.00 45.32 3.72
1492 3048 1.875514 GTGAGCACACACATGACACAT 59.124 47.619 9.58 0.00 45.32 3.21
1499 3055 4.096833 GCACACACATGACACATTATCCAT 59.903 41.667 0.00 0.00 0.00 3.41
1557 3113 4.664677 GTGACGCGGCTCCTGTGT 62.665 66.667 15.80 0.00 0.00 3.72
1617 3173 4.517815 GACGCCGCGGGGTTCATA 62.518 66.667 42.69 0.00 41.41 2.15
1625 3181 1.087771 GCGGGGTTCATACAGTTCCG 61.088 60.000 0.00 0.00 39.07 4.30
1772 3349 1.300620 CTCGGACGCAGACACCAAA 60.301 57.895 0.00 0.00 0.00 3.28
2152 3732 4.699522 GCTCCACGGCGGACCTTT 62.700 66.667 13.24 0.00 39.64 3.11
2488 4239 4.384098 CCTCCTTTTCCAAACAAAAAGCCT 60.384 41.667 3.41 0.00 40.68 4.58
2614 4365 7.159372 AGAGTCTTAACGGTGTTAAATGACAT 58.841 34.615 17.03 8.11 0.00 3.06
2615 4366 8.308931 AGAGTCTTAACGGTGTTAAATGACATA 58.691 33.333 17.03 0.00 0.00 2.29
2618 4369 8.120465 GTCTTAACGGTGTTAAATGACATATGG 58.880 37.037 7.80 0.00 0.00 2.74
2622 4373 7.639113 ACGGTGTTAAATGACATATGGAAAT 57.361 32.000 7.80 0.00 0.00 2.17
2653 4404 3.264193 GCCCCTCATGTGATATATGACCA 59.736 47.826 0.00 0.00 31.66 4.02
2671 4422 5.918082 TGACCACAATTTTACGTGTATTCG 58.082 37.500 0.00 0.00 0.00 3.34
2695 4446 4.795962 GCCATACAGGGAACAAACACTTTG 60.796 45.833 0.00 0.00 41.41 2.77
2774 4525 0.105778 TGCAGTCGACCACATTGACA 59.894 50.000 13.01 3.67 43.52 3.58
2784 4535 1.028905 CACATTGACAAACACCGGGT 58.971 50.000 6.32 0.00 0.00 5.28
2831 4582 1.678728 CCCGTTGGATGCATGTACTGT 60.679 52.381 2.46 0.00 0.00 3.55
2848 4599 0.541764 TGTGGCATGTTTCCTTCCCC 60.542 55.000 0.00 0.00 0.00 4.81
2857 4608 6.012745 GCATGTTTCCTTCCCCATATATTCT 58.987 40.000 0.00 0.00 0.00 2.40
2870 4621 7.231317 TCCCCATATATTCTGCATTCAAGAAAC 59.769 37.037 0.00 0.00 0.00 2.78
2919 4670 3.884169 ACAAAATTGTGTCGAACATCCG 58.116 40.909 0.00 0.00 40.49 4.18
2920 4671 2.611974 AAATTGTGTCGAACATCCGC 57.388 45.000 0.00 0.00 38.99 5.54
2922 4673 0.321210 ATTGTGTCGAACATCCGCCA 60.321 50.000 0.00 0.00 38.99 5.69
2923 4674 0.948623 TTGTGTCGAACATCCGCCAG 60.949 55.000 0.00 0.00 38.99 4.85
2924 4675 1.080093 GTGTCGAACATCCGCCAGA 60.080 57.895 0.00 0.00 0.00 3.86
2925 4676 0.460284 GTGTCGAACATCCGCCAGAT 60.460 55.000 0.00 0.00 34.66 2.90
2983 4737 2.144078 TCACAAACCAGCGAGGGGA 61.144 57.895 3.26 0.00 43.89 4.81
3036 4790 1.459450 TAAGGCTCAAAATGGACGGC 58.541 50.000 0.00 0.00 0.00 5.68
3047 4801 0.468226 ATGGACGGCCGTGTCATAAT 59.532 50.000 39.65 15.64 40.72 1.28
3110 4867 5.461032 TTTGCGGTGTCAAATAAGGAAAT 57.539 34.783 0.00 0.00 31.64 2.17
3162 4919 6.836577 TTTTCTCAAAAATAAAAGGGTGCG 57.163 33.333 0.00 0.00 29.44 5.34
3296 5053 6.053005 ACATCGGTGTAAACTTTTCTTCTCA 58.947 36.000 0.00 0.00 36.63 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 1.518572 CCAGATGACGCCGTACCAC 60.519 63.158 0.00 0.00 0.00 4.16
272 276 2.600790 TGTTCTTGGACTACGAGGGAA 58.399 47.619 0.00 0.00 0.00 3.97
484 491 2.612972 GCTCCATCAACTCTCCGTCAAA 60.613 50.000 0.00 0.00 0.00 2.69
608 616 3.293262 TGTGTCATTTTACTTTTCGCGC 58.707 40.909 0.00 0.00 0.00 6.86
695 706 6.513033 CCTTGACCCCTAGTCCCTATATAAT 58.487 44.000 0.00 0.00 45.68 1.28
728 741 3.509442 TCCCCTCTTTACGTTAAGTGGA 58.491 45.455 27.94 20.82 39.86 4.02
764 779 3.028130 CGTACGCATCGCTAGGGA 58.972 61.111 12.40 12.40 0.00 4.20
995 2551 1.080501 CTGAGCGTGGACATGACGT 60.081 57.895 0.00 0.00 39.08 4.34
1455 3011 3.610114 GCTCACGTGCAAATGTGAAATCT 60.610 43.478 11.67 0.00 43.91 2.40
1456 3012 2.658325 GCTCACGTGCAAATGTGAAATC 59.342 45.455 11.67 7.20 43.91 2.17
1463 3019 0.029167 TGTGTGCTCACGTGCAAATG 59.971 50.000 11.67 0.00 46.49 2.32
1486 3042 4.970662 AACTGTGCATGGATAATGTGTC 57.029 40.909 0.00 0.00 38.65 3.67
1487 3043 4.766373 TCAAACTGTGCATGGATAATGTGT 59.234 37.500 0.00 0.00 38.65 3.72
1488 3044 5.313520 TCAAACTGTGCATGGATAATGTG 57.686 39.130 0.00 0.00 38.65 3.21
1489 3045 4.400251 CCTCAAACTGTGCATGGATAATGT 59.600 41.667 0.00 0.00 38.65 2.71
1490 3046 4.735578 GCCTCAAACTGTGCATGGATAATG 60.736 45.833 0.00 0.00 39.49 1.90
1491 3047 3.382546 GCCTCAAACTGTGCATGGATAAT 59.617 43.478 0.00 0.00 0.00 1.28
1492 3048 2.754552 GCCTCAAACTGTGCATGGATAA 59.245 45.455 0.00 0.00 0.00 1.75
1499 3055 2.340210 TGTTAGCCTCAAACTGTGCA 57.660 45.000 0.00 0.00 0.00 4.57
1743 3320 2.710902 CGTCCGAGGCACTGGATCA 61.711 63.158 0.00 0.00 41.55 2.92
1772 3349 2.158900 CGCCTTACAATGTCATCCTCCT 60.159 50.000 0.00 0.00 0.00 3.69
2517 4268 8.460831 ACAACAAATTTCAAGACAGTGTTAAC 57.539 30.769 0.00 0.00 0.00 2.01
2574 4325 8.596380 CGTTAAGACTCTAAATGGATGAAAGTC 58.404 37.037 0.00 0.00 33.53 3.01
2593 4344 8.041919 TCCATATGTCATTTAACACCGTTAAGA 58.958 33.333 1.24 0.00 30.55 2.10
2614 4365 7.881912 TGAGGGGCTAATAGTTATTTCCATA 57.118 36.000 0.00 0.00 0.00 2.74
2615 4366 6.780198 TGAGGGGCTAATAGTTATTTCCAT 57.220 37.500 0.00 0.00 0.00 3.41
2618 4369 7.224297 TCACATGAGGGGCTAATAGTTATTTC 58.776 38.462 0.00 0.00 0.00 2.17
2622 4373 9.729550 ATATATCACATGAGGGGCTAATAGTTA 57.270 33.333 0.00 0.00 0.00 2.24
2653 4404 3.752222 TGGCCGAATACACGTAAAATTGT 59.248 39.130 0.00 0.00 0.00 2.71
2671 4422 1.544246 GTGTTTGTTCCCTGTATGGCC 59.456 52.381 0.00 0.00 0.00 5.36
2695 4446 2.386660 GCTCCGCACAAGCTGTCTC 61.387 63.158 0.00 0.00 39.10 3.36
2774 4525 0.816421 CAACCTCGAACCCGGTGTTT 60.816 55.000 0.00 0.00 37.29 2.83
2811 4562 1.016627 CAGTACATGCATCCAACGGG 58.983 55.000 0.00 0.00 0.00 5.28
2831 4582 0.413037 ATGGGGAAGGAAACATGCCA 59.587 50.000 0.00 0.00 41.90 4.92
2857 4608 9.545105 AATTACTGAAATTGTTTCTTGAATGCA 57.455 25.926 0.00 0.00 40.32 3.96
2916 4667 0.104855 GCATGTGACTATCTGGCGGA 59.895 55.000 0.00 0.00 0.00 5.54
2919 4670 3.249559 GCTTTAGCATGTGACTATCTGGC 59.750 47.826 0.00 0.00 41.59 4.85
2920 4671 4.701765 AGCTTTAGCATGTGACTATCTGG 58.298 43.478 4.33 0.00 45.16 3.86
2922 4673 7.560368 AGTTTAGCTTTAGCATGTGACTATCT 58.440 34.615 4.33 0.00 45.16 1.98
2923 4674 7.778470 AGTTTAGCTTTAGCATGTGACTATC 57.222 36.000 4.33 0.00 45.16 2.08
2924 4675 7.711339 GGTAGTTTAGCTTTAGCATGTGACTAT 59.289 37.037 4.33 0.00 45.16 2.12
2925 4676 7.039882 GGTAGTTTAGCTTTAGCATGTGACTA 58.960 38.462 4.33 2.81 45.16 2.59
3136 4893 9.150348 CGCACCCTTTTATTTTTGAGAAAATAT 57.850 29.630 5.47 0.00 43.53 1.28


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

AutoCloner maintained by Alex Coulton.