Multiple sequence alignment - TraesCS7A01G320900

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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 TraesCS7A01G320900 chr7A 100.000 1846 0 0 509 2354 463066080 463067925 0.000000e+00 3410.0
1 TraesCS7A01G320900 chr7A 100.000 150 0 0 1 150 463065572 463065721 6.410000e-71 278.0
2 TraesCS7A01G320900 chr3A 93.726 1546 87 8 511 2049 312751890 312750348 0.000000e+00 2309.0
3 TraesCS7A01G320900 chr3A 90.425 1671 138 18 693 2354 312760304 312758647 0.000000e+00 2180.0
4 TraesCS7A01G320900 chr3A 89.554 785 71 6 731 1505 82472235 82471452 0.000000e+00 985.0
5 TraesCS7A01G320900 chr3A 89.427 785 72 6 731 1505 82479079 82478296 0.000000e+00 979.0
6 TraesCS7A01G320900 chr3A 91.239 468 31 5 1888 2354 691023314 691023772 1.540000e-176 628.0
7 TraesCS7A01G320900 chr3A 90.517 464 40 4 1893 2354 561385212 561385673 5.560000e-171 610.0
8 TraesCS7A01G320900 chr3A 91.038 212 13 6 559 765 312760500 312760290 4.950000e-72 281.0
9 TraesCS7A01G320900 chr3A 93.269 104 6 1 1 103 312752462 312752359 4.050000e-33 152.0
10 TraesCS7A01G320900 chr3A 97.297 74 2 0 1432 1505 310770225 310770298 2.460000e-25 126.0
11 TraesCS7A01G320900 chr6B 93.661 631 32 8 1486 2113 544575717 544575092 0.000000e+00 937.0
12 TraesCS7A01G320900 chr6B 93.838 568 26 9 1486 2049 544564523 544563961 0.000000e+00 846.0
13 TraesCS7A01G320900 chr7B 92.369 629 39 9 1486 2110 208347589 208346966 0.000000e+00 887.0
14 TraesCS7A01G320900 chr7B 91.373 568 39 10 1486 2049 208340746 208340185 0.000000e+00 769.0
15 TraesCS7A01G320900 chr1B 88.474 642 67 7 1600 2238 135918725 135919362 0.000000e+00 769.0
16 TraesCS7A01G320900 chr5B 84.707 752 97 15 1610 2354 475972447 475973187 0.000000e+00 736.0
17 TraesCS7A01G320900 chr5B 86.984 630 66 13 1482 2107 622253561 622254178 0.000000e+00 695.0
18 TraesCS7A01G320900 chr1A 90.733 464 39 4 1893 2354 117992550 117992089 1.200000e-172 616.0
19 TraesCS7A01G320900 chr1A 87.685 203 21 4 1135 1335 81214022 81213822 1.410000e-57 233.0
20 TraesCS7A01G320900 chr1A 97.297 74 2 0 1432 1505 130482707 130482780 2.460000e-25 126.0
21 TraesCS7A01G320900 chr1A 95.946 74 3 0 1432 1505 130474757 130474830 1.140000e-23 121.0
22 TraesCS7A01G320900 chr4A 89.765 469 43 5 1888 2354 59876925 59876460 1.560000e-166 595.0
23 TraesCS7A01G320900 chr4A 90.086 464 39 7 1888 2349 415700432 415700890 1.560000e-166 595.0
24 TraesCS7A01G320900 chr4A 84.017 463 48 9 731 1184 632330001 632330446 2.800000e-114 422.0
25 TraesCS7A01G320900 chr2D 85.745 463 40 6 731 1184 296645179 296644734 1.270000e-127 466.0
26 TraesCS7A01G320900 chr2D 84.848 264 31 2 731 985 815014 815277 8.350000e-65 257.0
27 TraesCS7A01G320900 chr4B 87.531 401 34 10 789 1173 364933742 364933342 1.280000e-122 449.0
28 TraesCS7A01G320900 chr4B 86.885 305 37 3 1159 1461 315607163 315607466 2.900000e-89 339.0
29 TraesCS7A01G320900 chr4B 85.627 327 42 5 1135 1459 315629723 315630046 2.900000e-89 339.0
30 TraesCS7A01G320900 chr3B 83.468 496 52 8 699 1184 417973758 417974233 3.590000e-118 435.0
31 TraesCS7A01G320900 chr3B 83.468 496 52 8 699 1184 417981222 417981697 3.590000e-118 435.0
32 TraesCS7A01G320900 chr3B 84.267 464 45 9 731 1184 417966324 417966769 6.010000e-116 427.0
33 TraesCS7A01G320900 chr6A 91.500 200 15 1 1159 1356 375055864 375056063 8.290000e-70 274.0
34 TraesCS7A01G320900 chr6A 84.874 238 24 7 1237 1465 375004789 375005023 1.820000e-56 230.0
35 TraesCS7A01G320900 chr7D 84.906 265 30 6 731 985 433994627 433994363 2.320000e-65 259.0
36 TraesCS7A01G320900 chr5D 84.151 265 32 6 731 985 63040412 63040676 5.020000e-62 248.0
37 TraesCS7A01G320900 chr5D 84.151 265 32 6 731 985 63048256 63048520 5.020000e-62 248.0
38 TraesCS7A01G320900 chr3D 84.211 266 30 8 731 985 41541575 41541839 5.020000e-62 248.0
39 TraesCS7A01G320900 chr3D 90.385 52 3 2 610 661 28756344 28756295 1.510000e-07 67.6
40 TraesCS7A01G320900 chr5A 90.066 151 14 1 1 150 219904666 219904516 6.640000e-46 195.0
41 TraesCS7A01G320900 chr4D 87.313 134 17 0 10 143 313710024 313710157 1.130000e-33 154.0
42 TraesCS7A01G320900 chr1D 93.204 103 6 1 509 611 294146502 294146401 1.460000e-32 150.0
43 TraesCS7A01G320900 chr6D 92.391 92 7 0 509 600 295628082 295627991 5.280000e-27 132.0


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 TraesCS7A01G320900 chr7A 463065572 463067925 2353 False 1844.0 3410 100.0000 1 2354 2 chr7A.!!$F1 2353
1 TraesCS7A01G320900 chr3A 312750348 312752462 2114 True 1230.5 2309 93.4975 1 2049 2 chr3A.!!$R3 2048
2 TraesCS7A01G320900 chr3A 312758647 312760500 1853 True 1230.5 2180 90.7315 559 2354 2 chr3A.!!$R4 1795
3 TraesCS7A01G320900 chr3A 82471452 82472235 783 True 985.0 985 89.5540 731 1505 1 chr3A.!!$R1 774
4 TraesCS7A01G320900 chr3A 82478296 82479079 783 True 979.0 979 89.4270 731 1505 1 chr3A.!!$R2 774
5 TraesCS7A01G320900 chr6B 544575092 544575717 625 True 937.0 937 93.6610 1486 2113 1 chr6B.!!$R2 627
6 TraesCS7A01G320900 chr6B 544563961 544564523 562 True 846.0 846 93.8380 1486 2049 1 chr6B.!!$R1 563
7 TraesCS7A01G320900 chr7B 208346966 208347589 623 True 887.0 887 92.3690 1486 2110 1 chr7B.!!$R2 624
8 TraesCS7A01G320900 chr7B 208340185 208340746 561 True 769.0 769 91.3730 1486 2049 1 chr7B.!!$R1 563
9 TraesCS7A01G320900 chr1B 135918725 135919362 637 False 769.0 769 88.4740 1600 2238 1 chr1B.!!$F1 638
10 TraesCS7A01G320900 chr5B 475972447 475973187 740 False 736.0 736 84.7070 1610 2354 1 chr5B.!!$F1 744
11 TraesCS7A01G320900 chr5B 622253561 622254178 617 False 695.0 695 86.9840 1482 2107 1 chr5B.!!$F2 625

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
728 1169 1.070445 AGCAACAGAAGCAGCTCGT 59.93 52.632 0.0 0.0 30.05 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2506 0.250513 GGAGGAGAATTGTGACGCCT 59.749 55.0 0.0 0.0 38.88 5.52 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
683 1062 1.667191 CAGCAAGTCAGCAGCGAGT 60.667 57.895 0.00 0.00 36.85 4.18
695 1074 2.517875 GCGAGTAGGGACGGGCTA 60.518 66.667 0.00 0.00 0.00 3.93
728 1169 1.070445 AGCAACAGAAGCAGCTCGT 59.930 52.632 0.00 0.00 30.05 4.18
744 1185 2.595463 GTGGCAGCAGGTGAGCAA 60.595 61.111 3.02 0.00 36.85 3.91
941 1391 4.498520 ATGCGTGGACGAGGCGAG 62.499 66.667 2.73 0.00 43.02 5.03
1065 1516 3.023832 GGAATCGAATGGGAAACATGGT 58.976 45.455 0.00 0.00 40.44 3.55
1253 1704 2.267961 GACAACGGGGAAGCGGAT 59.732 61.111 0.00 0.00 0.00 4.18
1892 2354 7.119553 GTGAATATTTGCAACCCATCAAACATT 59.880 33.333 0.00 0.00 33.55 2.71
2023 2490 5.123502 GTGGCATCATTAGCAGAGGATTATG 59.876 44.000 0.00 0.00 0.00 1.90
2027 2494 7.772292 GGCATCATTAGCAGAGGATTATGATAA 59.228 37.037 0.00 0.00 32.95 1.75
2153 2620 5.105106 TGAATCTTATCGGTCTTGGTTGCTA 60.105 40.000 0.00 0.00 0.00 3.49
2159 2626 2.565391 TCGGTCTTGGTTGCTATTCTCA 59.435 45.455 0.00 0.00 0.00 3.27
2161 2628 3.125316 CGGTCTTGGTTGCTATTCTCAAC 59.875 47.826 0.00 0.00 42.13 3.18
2164 2631 4.631813 GTCTTGGTTGCTATTCTCAACGAT 59.368 41.667 0.00 0.00 43.37 3.73
2183 2650 4.745125 ACGATGTCGATCCATTACATTGAC 59.255 41.667 9.67 3.18 43.02 3.18
2194 2661 6.841119 TCCATTACATTGACGTCTTCATTTG 58.159 36.000 17.92 7.60 32.84 2.32
2222 2689 2.905736 TCAGGTCACCATGATGAAGTCA 59.094 45.455 0.00 0.00 42.06 3.41
2240 2708 6.881065 TGAAGTCATCATCTTTTCTTCGGAAT 59.119 34.615 0.00 0.00 35.51 3.01
2242 2710 7.693969 AGTCATCATCTTTTCTTCGGAATTT 57.306 32.000 0.00 0.00 33.58 1.82
2245 2713 7.483059 GTCATCATCTTTTCTTCGGAATTTCAC 59.517 37.037 0.00 0.00 33.58 3.18
2289 2757 1.602237 GGCATTCCGGGAGAACAGA 59.398 57.895 0.00 0.00 37.29 3.41
2336 2804 0.533491 TAACATCGGGGAAGGTGTCG 59.467 55.000 0.00 0.00 0.00 4.35
2337 2805 2.511600 CATCGGGGAAGGTGTCGC 60.512 66.667 0.00 0.00 38.47 5.19
2338 2806 3.000819 ATCGGGGAAGGTGTCGCA 61.001 61.111 0.00 0.00 40.96 5.10
2350 2818 2.364324 AGGTGTCGCAAAGTAACTCTCA 59.636 45.455 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
728 1169 2.595463 GTTGCTCACCTGCTGCCA 60.595 61.111 0.00 0.00 0.00 4.92
744 1185 4.767255 GCTGCGCTACTGCCCTGT 62.767 66.667 9.73 0.00 37.26 4.00
935 1385 1.190833 CCATAGATGGGAGCTCGCCT 61.191 60.000 26.18 17.79 44.31 5.52
1065 1516 1.337703 GTGAGCACCACATCAAAAGCA 59.662 47.619 4.63 0.00 45.03 3.91
1095 1546 1.672356 GTCCACAAGCCGTCTGCAT 60.672 57.895 0.00 0.00 44.83 3.96
1099 1550 4.681978 GGCGTCCACAAGCCGTCT 62.682 66.667 0.00 0.00 44.22 4.18
1131 1582 0.389948 GTTCTCCGTCAATCCGCTGT 60.390 55.000 0.00 0.00 0.00 4.40
1239 1690 2.584608 CTCATCCGCTTCCCCGTT 59.415 61.111 0.00 0.00 0.00 4.44
1253 1704 1.596934 CGCCCTAGGAACTTGCTCA 59.403 57.895 11.48 0.00 41.75 4.26
1288 1739 0.684535 TGGTTCTCATCGTCCTTGCA 59.315 50.000 0.00 0.00 0.00 4.08
1613 2068 7.402862 AGTGGCTAACTGAAATACATAAAGGT 58.597 34.615 0.00 0.00 37.88 3.50
2023 2490 6.704493 TGTGACGCCTGGATAATTAAGTTATC 59.296 38.462 0.00 8.17 45.24 1.75
2027 2494 4.481368 TGTGACGCCTGGATAATTAAGT 57.519 40.909 0.00 0.00 0.00 2.24
2039 2506 0.250513 GGAGGAGAATTGTGACGCCT 59.749 55.000 0.00 0.00 38.88 5.52
2137 2604 3.197766 TGAGAATAGCAACCAAGACCGAT 59.802 43.478 0.00 0.00 0.00 4.18
2153 2620 3.801114 TGGATCGACATCGTTGAGAAT 57.199 42.857 0.00 0.00 40.80 2.40
2159 2626 5.234329 GTCAATGTAATGGATCGACATCGTT 59.766 40.000 0.54 0.00 40.80 3.85
2161 2628 4.143535 CGTCAATGTAATGGATCGACATCG 60.144 45.833 0.00 0.00 41.45 3.84
2164 2631 4.109766 GACGTCAATGTAATGGATCGACA 58.890 43.478 11.55 0.00 29.47 4.35
2183 2650 3.120408 CCTGAAGCAGACAAATGAAGACG 60.120 47.826 0.00 0.00 32.44 4.18
2194 2661 1.002430 TCATGGTGACCTGAAGCAGAC 59.998 52.381 2.11 0.00 32.44 3.51
2222 2689 6.856895 GGTGAAATTCCGAAGAAAAGATGAT 58.143 36.000 0.00 0.00 35.09 2.45
2242 2710 7.388500 CCCTTTATTCTTTTGTAAGTACGGTGA 59.612 37.037 0.00 0.00 32.98 4.02
2245 2713 7.361457 CCACCCTTTATTCTTTTGTAAGTACGG 60.361 40.741 0.00 0.00 32.98 4.02
2255 2723 4.225042 GGAATGCCCACCCTTTATTCTTTT 59.775 41.667 0.00 0.00 34.14 2.27


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

AutoCloner maintained by Alex Coulton.