Multiple sequence alignment - TraesCS2D01G207500

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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 TraesCS2D01G207500 chr2D 100.000 3240 0 0 1 3240 161529977 161526738 0.000000e+00 5984.0
1 TraesCS2D01G207500 chr2D 99.332 2394 15 1 1 2394 160941521 160943913 0.000000e+00 4331.0
2 TraesCS2D01G207500 chr2D 88.235 68 4 2 2392 2457 107911161 107911096 9.640000e-11 78.7
3 TraesCS2D01G207500 chr1D 97.398 807 18 3 2398 3201 486073258 486072452 0.000000e+00 1371.0
4 TraesCS2D01G207500 chr1D 100.000 44 0 0 3197 3240 486072437 486072394 7.450000e-12 82.4
5 TraesCS2D01G207500 chr6B 91.350 948 49 16 1 943 300368715 300367796 0.000000e+00 1266.0
6 TraesCS2D01G207500 chr6B 91.697 819 45 7 1595 2394 300366874 300366060 0.000000e+00 1114.0
7 TraesCS2D01G207500 chr6B 91.158 622 37 6 992 1596 300367813 300367193 0.000000e+00 828.0
8 TraesCS2D01G207500 chr6B 94.074 270 15 1 2923 3191 65080672 65080941 3.010000e-110 409.0
9 TraesCS2D01G207500 chr3B 90.350 943 53 9 6 943 216400759 216401668 0.000000e+00 1203.0
10 TraesCS2D01G207500 chr3B 93.201 809 46 3 1595 2394 216402591 216403399 0.000000e+00 1181.0
11 TraesCS2D01G207500 chr3B 91.827 624 30 9 992 1596 216401651 216402272 0.000000e+00 850.0
12 TraesCS2D01G207500 chr3B 88.767 365 26 9 2392 2747 239256416 239256774 1.790000e-117 433.0
13 TraesCS2D01G207500 chr6D 88.725 949 89 14 1 943 184815475 184814539 0.000000e+00 1144.0
14 TraesCS2D01G207500 chr6D 87.777 949 99 13 1 943 183949625 183950562 0.000000e+00 1094.0
15 TraesCS2D01G207500 chr6D 87.200 875 90 16 1 867 165534116 165533256 0.000000e+00 976.0
16 TraesCS2D01G207500 chr6D 86.971 875 92 16 1 867 165546167 165545307 0.000000e+00 965.0
17 TraesCS2D01G207500 chr6D 86.560 625 63 12 992 1596 184814556 184813933 0.000000e+00 669.0
18 TraesCS2D01G207500 chr6D 85.852 622 69 9 994 1596 165457841 165457220 0.000000e+00 643.0
19 TraesCS2D01G207500 chr6D 81.730 821 98 28 1595 2374 183956315 183957124 3.530000e-179 638.0
20 TraesCS2D01G207500 chr6D 81.553 824 88 34 1595 2377 184813616 184812816 3.550000e-174 621.0
21 TraesCS2D01G207500 chr6D 88.702 416 47 0 993 1408 183950546 183950961 2.880000e-140 508.0
22 TraesCS2D01G207500 chr6D 89.141 396 43 0 994 1389 120840541 120840936 8.080000e-136 494.0
23 TraesCS2D01G207500 chr6D 85.256 468 55 7 1595 2048 165456896 165456429 1.360000e-128 470.0
24 TraesCS2D01G207500 chr6D 80.531 339 45 16 2050 2377 165456382 165456054 1.160000e-59 241.0
25 TraesCS2D01G207500 chr6D 79.724 217 23 12 1400 1596 183955779 183955994 1.570000e-28 137.0
26 TraesCS2D01G207500 chr6D 85.149 101 13 2 3093 3191 414096413 414096313 5.720000e-18 102.0
27 TraesCS2D01G207500 chr4A 91.235 810 58 6 1595 2394 332023790 332024596 0.000000e+00 1090.0
28 TraesCS2D01G207500 chr4A 90.127 628 38 9 992 1596 332022844 332023470 0.000000e+00 795.0
29 TraesCS2D01G207500 chr4A 88.169 355 34 6 2748 3099 654063486 654063137 1.800000e-112 416.0
30 TraesCS2D01G207500 chr4B 87.144 949 107 13 1 943 210361886 210360947 0.000000e+00 1062.0
31 TraesCS2D01G207500 chr6A 86.538 884 101 13 65 938 158482796 158481921 0.000000e+00 957.0
32 TraesCS2D01G207500 chr6A 88.636 396 45 0 994 1389 158481931 158481536 1.750000e-132 483.0
33 TraesCS2D01G207500 chr7D 95.122 451 20 2 2752 3201 535565646 535565197 0.000000e+00 710.0
34 TraesCS2D01G207500 chr7D 89.888 356 28 7 2748 3099 43693478 43693127 4.930000e-123 451.0
35 TraesCS2D01G207500 chr7D 100.000 42 0 0 3197 3238 535565181 535565140 9.640000e-11 78.7
36 TraesCS2D01G207500 chr3A 91.868 455 36 1 2748 3201 80153259 80153713 4.560000e-178 634.0
37 TraesCS2D01G207500 chr3A 100.000 41 0 0 3200 3240 80153730 80153770 3.470000e-10 76.8
38 TraesCS2D01G207500 chr7A 90.351 456 26 4 2748 3201 338623972 338624411 1.680000e-162 582.0
39 TraesCS2D01G207500 chr7A 100.000 44 0 0 3197 3240 338624427 338624470 7.450000e-12 82.4
40 TraesCS2D01G207500 chr7B 87.789 475 34 9 2748 3201 691171907 691171436 4.760000e-148 534.0
41 TraesCS2D01G207500 chr7B 85.149 101 13 2 3093 3191 430842985 430842885 5.720000e-18 102.0
42 TraesCS2D01G207500 chr7B 100.000 41 0 0 3200 3240 691171417 691171377 3.470000e-10 76.8
43 TraesCS2D01G207500 chr5B 85.021 474 51 10 1594 2048 50230210 50230682 6.330000e-127 464.0
44 TraesCS2D01G207500 chr5B 87.500 56 7 0 2393 2448 417883924 417883979 7.500000e-07 65.8
45 TraesCS2D01G207500 chr3D 88.515 357 31 10 2748 3099 608434765 608435116 1.070000e-114 424.0
46 TraesCS2D01G207500 chr3D 86.139 101 12 2 3093 3191 160723956 160723856 1.230000e-19 108.0
47 TraesCS2D01G207500 chr3D 87.879 66 4 2 2394 2457 505023811 505023748 1.250000e-09 75.0
48 TraesCS2D01G207500 chr4D 87.640 356 36 8 2748 3099 175182533 175182884 1.080000e-109 407.0
49 TraesCS2D01G207500 chr4D 87.879 66 4 2 2394 2457 455267137 455267074 1.250000e-09 75.0
50 TraesCS2D01G207500 chr5A 84.106 302 35 7 2394 2692 512840129 512839838 2.460000e-71 279.0
51 TraesCS2D01G207500 chrUn 93.478 46 3 0 2394 2439 329307845 329307800 5.800000e-08 69.4
52 TraesCS2D01G207500 chrUn 89.091 55 6 0 2385 2439 338307323 338307377 5.800000e-08 69.4


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 TraesCS2D01G207500 chr2D 161526738 161529977 3239 True 5984.000000 5984 100.000000 1 3240 1 chr2D.!!$R2 3239
1 TraesCS2D01G207500 chr2D 160941521 160943913 2392 False 4331.000000 4331 99.332000 1 2394 1 chr2D.!!$F1 2393
2 TraesCS2D01G207500 chr1D 486072394 486073258 864 True 726.700000 1371 98.699000 2398 3240 2 chr1D.!!$R1 842
3 TraesCS2D01G207500 chr6B 300366060 300368715 2655 True 1069.333333 1266 91.401667 1 2394 3 chr6B.!!$R1 2393
4 TraesCS2D01G207500 chr3B 216400759 216403399 2640 False 1078.000000 1203 91.792667 6 2394 3 chr3B.!!$F2 2388
5 TraesCS2D01G207500 chr6D 165533256 165534116 860 True 976.000000 976 87.200000 1 867 1 chr6D.!!$R1 866
6 TraesCS2D01G207500 chr6D 165545307 165546167 860 True 965.000000 965 86.971000 1 867 1 chr6D.!!$R2 866
7 TraesCS2D01G207500 chr6D 184812816 184815475 2659 True 811.333333 1144 85.612667 1 2377 3 chr6D.!!$R5 2376
8 TraesCS2D01G207500 chr6D 183949625 183950961 1336 False 801.000000 1094 88.239500 1 1408 2 chr6D.!!$F2 1407
9 TraesCS2D01G207500 chr6D 165456054 165457841 1787 True 451.333333 643 83.879667 994 2377 3 chr6D.!!$R4 1383
10 TraesCS2D01G207500 chr6D 183955779 183957124 1345 False 387.500000 638 80.727000 1400 2374 2 chr6D.!!$F3 974
11 TraesCS2D01G207500 chr4A 332022844 332024596 1752 False 942.500000 1090 90.681000 992 2394 2 chr4A.!!$F1 1402
12 TraesCS2D01G207500 chr4B 210360947 210361886 939 True 1062.000000 1062 87.144000 1 943 1 chr4B.!!$R1 942
13 TraesCS2D01G207500 chr6A 158481536 158482796 1260 True 720.000000 957 87.587000 65 1389 2 chr6A.!!$R1 1324
14 TraesCS2D01G207500 chr7D 535565140 535565646 506 True 394.350000 710 97.561000 2752 3238 2 chr7D.!!$R2 486
15 TraesCS2D01G207500 chr3A 80153259 80153770 511 False 355.400000 634 95.934000 2748 3240 2 chr3A.!!$F1 492
16 TraesCS2D01G207500 chr7B 691171377 691171907 530 True 305.400000 534 93.894500 2748 3240 2 chr7B.!!$R2 492

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
911 936 2.327343 TGCAGTTGAGTCGCATGCC 61.327 57.895 13.15 0.0 36.04 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2663 3113 1.003262 CGGCGTTGCTGGAATTTGTG 61.003 55.0 0.0 0.0 0.0 3.33 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
63 65 3.992943 AAATGGAACGGATGGAGTACA 57.007 42.857 0.00 0.00 0.00 2.90
911 936 2.327343 TGCAGTTGAGTCGCATGCC 61.327 57.895 13.15 0.00 36.04 4.40
956 981 6.881065 TGAATGTCCCTCTCTTTTCAATACAG 59.119 38.462 0.00 0.00 0.00 2.74
2395 2845 9.639601 GAGAGGTTGGTTATATTTTGAAAAAGG 57.360 33.333 0.00 0.00 0.00 3.11
2396 2846 8.593679 AGAGGTTGGTTATATTTTGAAAAAGGG 58.406 33.333 0.00 0.00 0.00 3.95
2413 2863 8.192110 TGAAAAAGGGAAATGTTTATATACGGC 58.808 33.333 0.00 0.00 0.00 5.68
2414 2864 5.934935 AAGGGAAATGTTTATATACGGCG 57.065 39.130 4.80 4.80 0.00 6.46
2561 3011 0.952280 TATCTCCTTACCAGCGCTCG 59.048 55.000 7.13 2.49 0.00 5.03
2663 3113 1.445582 CCCGACGACTACTGTTGCC 60.446 63.158 0.00 0.00 0.00 4.52
2948 3418 2.351706 TAGTTTTTGCTGGAACCGGT 57.648 45.000 0.00 0.00 0.00 5.28
3026 3497 6.631763 TTATGCTACATCCATCTCCATGAT 57.368 37.500 0.00 0.00 35.40 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 4.849813 TGAGGATGATGTGGTCAAGAAT 57.150 40.909 0.00 0.00 40.97 2.40
956 981 3.292423 GCAAGAAGACTTTGCGTTTCTC 58.708 45.455 0.00 0.00 33.70 2.87
1939 2328 2.212812 TGCAATTCTATGGTGGCACA 57.787 45.000 20.82 6.09 0.00 4.57
2394 2844 4.152938 GTCCGCCGTATATAAACATTTCCC 59.847 45.833 0.00 0.00 0.00 3.97
2395 2845 4.152938 GGTCCGCCGTATATAAACATTTCC 59.847 45.833 0.00 0.00 0.00 3.13
2396 2846 5.273523 GGTCCGCCGTATATAAACATTTC 57.726 43.478 0.00 0.00 0.00 2.17
2561 3011 4.811557 CGAGGAAACTGAATGGATAAGGTC 59.188 45.833 0.00 0.00 44.43 3.85
2639 3089 1.203994 ACAGTAGTCGTCGGGATTTGG 59.796 52.381 0.00 0.00 0.00 3.28
2663 3113 1.003262 CGGCGTTGCTGGAATTTGTG 61.003 55.000 0.00 0.00 0.00 3.33
2948 3418 2.952978 ACGGTTGTAGCAAAATGGTTCA 59.047 40.909 0.00 0.00 0.00 3.18
3026 3497 3.034721 ACGACTGGAAAAACAGCGATA 57.965 42.857 13.73 0.00 42.21 2.92
3177 3650 8.940768 ACAAACAACATAGTTGTAGCAAAATT 57.059 26.923 15.04 2.68 34.06 1.82


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

AutoCloner maintained by Alex Coulton.