Multiple sequence alignment - TraesCS6D01G294400

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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 TraesCS6D01G294400 chr6D 100.000 2692 0 0 1 2692 405121774 405119083 0.000000e+00 4972.0
1 TraesCS6D01G294400 chr6D 86.842 114 14 1 13 125 229435813 229435700 2.810000e-25 126.0
2 TraesCS6D01G294400 chr6D 100.000 43 0 0 2142 2184 9669751 9669793 2.220000e-11 80.5
3 TraesCS6D01G294400 chr6D 100.000 43 0 0 2142 2184 298384567 298384609 2.220000e-11 80.5
4 TraesCS6D01G294400 chr6D 84.884 86 6 6 2141 2222 382353214 382353296 2.220000e-11 80.5
5 TraesCS6D01G294400 chr6D 100.000 43 0 0 2142 2184 447633853 447633811 2.220000e-11 80.5
6 TraesCS6D01G294400 chr6D 100.000 42 0 0 2143 2184 24554522 24554563 7.990000e-11 78.7
7 TraesCS6D01G294400 chr6D 97.778 45 1 0 2144 2188 24554633 24554589 7.990000e-11 78.7
8 TraesCS6D01G294400 chr6D 100.000 41 0 0 2144 2184 26738821 26738781 2.870000e-10 76.8
9 TraesCS6D01G294400 chr6D 93.878 49 3 0 2136 2184 221219408 221219360 1.030000e-09 75.0
10 TraesCS6D01G294400 chr6D 95.556 45 2 0 2140 2184 44495675 44495719 3.720000e-09 73.1
11 TraesCS6D01G294400 chr6D 92.000 50 4 0 2135 2184 316625962 316625913 1.340000e-08 71.3
12 TraesCS6D01G294400 chr6D 89.091 55 5 1 2131 2184 441898394 441898340 1.730000e-07 67.6
13 TraesCS6D01G294400 chr6A 92.463 1937 128 12 6 1933 551657167 551655240 0.000000e+00 2752.0
14 TraesCS6D01G294400 chr6A 93.241 725 36 8 1971 2692 551655105 551654391 0.000000e+00 1055.0
15 TraesCS6D01G294400 chr6A 89.474 114 11 1 13 125 352670254 352670141 2.790000e-30 143.0
16 TraesCS6D01G294400 chr6A 85.227 88 6 6 2139 2222 524313033 524313117 1.720000e-12 84.2
17 TraesCS6D01G294400 chr6A 94.118 51 3 0 2134 2184 614304659 614304709 7.990000e-11 78.7
18 TraesCS6D01G294400 chr6B 92.968 1223 45 15 938 2136 609076822 609075617 0.000000e+00 1744.0
19 TraesCS6D01G294400 chr6B 94.325 511 18 5 2184 2692 609073999 609073498 0.000000e+00 773.0
20 TraesCS6D01G294400 chr6B 93.011 186 13 0 1 186 609077595 609077410 3.420000e-69 272.0
21 TraesCS6D01G294400 chr1D 86.074 754 96 6 126 871 57063707 57062955 0.000000e+00 802.0
22 TraesCS6D01G294400 chr1D 85.053 756 96 12 126 868 270293435 270294186 0.000000e+00 754.0
23 TraesCS6D01G294400 chr1D 91.071 112 9 1 13 124 273628589 273628699 1.670000e-32 150.0
24 TraesCS6D01G294400 chr1D 100.000 43 0 0 2142 2184 28358597 28358639 2.220000e-11 80.5
25 TraesCS6D01G294400 chr1D 100.000 43 0 0 2142 2184 49707614 49707656 2.220000e-11 80.5
26 TraesCS6D01G294400 chr1A 85.771 752 98 6 126 868 56215666 56216417 0.000000e+00 787.0
27 TraesCS6D01G294400 chr4B 85.733 750 96 8 126 868 460406246 460406991 0.000000e+00 782.0
28 TraesCS6D01G294400 chr1B 85.220 751 98 9 126 867 395940342 395939596 0.000000e+00 760.0
29 TraesCS6D01G294400 chr2B 85.027 748 103 7 126 868 359603410 359602667 0.000000e+00 752.0
30 TraesCS6D01G294400 chr2B 88.710 62 5 1 2123 2184 554296143 554296084 1.030000e-09 75.0
31 TraesCS6D01G294400 chr4D 84.483 754 108 6 126 871 407772983 407772231 0.000000e+00 736.0
32 TraesCS6D01G294400 chr4D 96.000 50 2 0 2135 2184 20437782 20437831 6.180000e-12 82.4
33 TraesCS6D01G294400 chr4D 94.000 50 3 0 2135 2184 80976635 80976586 2.870000e-10 76.8
34 TraesCS6D01G294400 chr4D 92.157 51 4 0 2134 2184 198482936 198482986 3.720000e-09 73.1
35 TraesCS6D01G294400 chr2A 84.395 769 94 21 114 871 705483156 705482403 0.000000e+00 732.0
36 TraesCS6D01G294400 chr7B 84.252 127 17 3 1 125 369075185 369075310 1.310000e-23 121.0
37 TraesCS6D01G294400 chr7B 84.615 104 15 1 20 123 646617572 646617470 4.740000e-18 102.0
38 TraesCS6D01G294400 chr2D 85.088 114 16 1 13 125 414290005 414290118 6.090000e-22 115.0
39 TraesCS6D01G294400 chr2D 97.872 47 1 0 2140 2186 378756782 378756828 6.180000e-12 82.4
40 TraesCS6D01G294400 chr2D 100.000 44 0 0 2141 2184 484046247 484046290 6.180000e-12 82.4
41 TraesCS6D01G294400 chr4A 85.849 106 13 2 21 125 415853557 415853453 7.880000e-21 111.0
42 TraesCS6D01G294400 chr3B 97.917 48 1 0 2137 2184 669921184 669921231 1.720000e-12 84.2
43 TraesCS6D01G294400 chr3A 97.917 48 1 0 2137 2184 53027991 53028038 1.720000e-12 84.2
44 TraesCS6D01G294400 chr7D 100.000 43 0 0 2142 2184 204247187 204247229 2.220000e-11 80.5
45 TraesCS6D01G294400 chr3D 97.778 45 1 0 2140 2184 360634105 360634061 7.990000e-11 78.7
46 TraesCS6D01G294400 chrUn 97.619 42 1 0 2143 2184 53798773 53798814 3.720000e-09 73.1
47 TraesCS6D01G294400 chrUn 93.478 46 3 0 2139 2184 132121143 132121188 4.810000e-08 69.4
48 TraesCS6D01G294400 chrUn 95.349 43 2 0 2142 2184 208673219 208673177 4.810000e-08 69.4
49 TraesCS6D01G294400 chrUn 95.349 43 2 0 2142 2184 256172882 256172840 4.810000e-08 69.4
50 TraesCS6D01G294400 chrUn 95.349 43 2 0 2142 2184 277636989 277637031 4.810000e-08 69.4
51 TraesCS6D01G294400 chrUn 95.349 43 2 0 2142 2184 336088369 336088327 4.810000e-08 69.4
52 TraesCS6D01G294400 chrUn 95.349 43 2 0 2142 2184 362373506 362373548 4.810000e-08 69.4
53 TraesCS6D01G294400 chrUn 95.349 43 2 0 2142 2184 371558047 371558089 4.810000e-08 69.4
54 TraesCS6D01G294400 chrUn 95.349 43 2 0 2142 2184 371616854 371616896 4.810000e-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 TraesCS6D01G294400 chr6D 405119083 405121774 2691 True 4972.000000 4972 100.000000 1 2692 1 chr6D.!!$R6 2691
1 TraesCS6D01G294400 chr6A 551654391 551657167 2776 True 1903.500000 2752 92.852000 6 2692 2 chr6A.!!$R2 2686
2 TraesCS6D01G294400 chr6B 609073498 609077595 4097 True 929.666667 1744 93.434667 1 2692 3 chr6B.!!$R1 2691
3 TraesCS6D01G294400 chr1D 57062955 57063707 752 True 802.000000 802 86.074000 126 871 1 chr1D.!!$R1 745
4 TraesCS6D01G294400 chr1D 270293435 270294186 751 False 754.000000 754 85.053000 126 868 1 chr1D.!!$F3 742
5 TraesCS6D01G294400 chr1A 56215666 56216417 751 False 787.000000 787 85.771000 126 868 1 chr1A.!!$F1 742
6 TraesCS6D01G294400 chr4B 460406246 460406991 745 False 782.000000 782 85.733000 126 868 1 chr4B.!!$F1 742
7 TraesCS6D01G294400 chr1B 395939596 395940342 746 True 760.000000 760 85.220000 126 867 1 chr1B.!!$R1 741
8 TraesCS6D01G294400 chr2B 359602667 359603410 743 True 752.000000 752 85.027000 126 868 1 chr2B.!!$R1 742
9 TraesCS6D01G294400 chr4D 407772231 407772983 752 True 736.000000 736 84.483000 126 871 1 chr4D.!!$R2 745
10 TraesCS6D01G294400 chr2A 705482403 705483156 753 True 732.000000 732 84.395000 114 871 1 chr2A.!!$R1 757

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
38 39 2.093783 GTCTCCACTTGCGGTTATTTCG 59.906 50.000 0.0 0.0 0.0 3.46 F
138 139 2.296752 TGTCCACCGATACGTCTTCAAA 59.703 45.455 0.0 0.0 0.0 2.69 F
947 1034 2.691526 AGTCTTACGTGTCTGTCAACCA 59.308 45.455 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
1259 1366 0.173481 TTCATCGTCCCTGCTTCGAG 59.827 55.000 0.0 0.0 37.04 4.04 R
1260 1367 0.173481 CTTCATCGTCCCTGCTTCGA 59.827 55.000 0.0 0.0 37.96 3.71 R
2568 4352 1.339151 GGCTGGTGAGTTTACTGGAGG 60.339 57.143 0.0 0.0 0.00 4.30 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
38 39 2.093783 GTCTCCACTTGCGGTTATTTCG 59.906 50.000 0.00 0.00 0.00 3.46
138 139 2.296752 TGTCCACCGATACGTCTTCAAA 59.703 45.455 0.00 0.00 0.00 2.69
414 486 2.866156 CGAAAGAGTCACAAGCTCACAA 59.134 45.455 0.00 0.00 35.55 3.33
549 624 4.081697 CCACCACAAGTTTTTGTTCTTCCT 60.082 41.667 0.00 0.00 45.01 3.36
805 891 6.001460 GGATCCGATGAATTGTGGGTTTATA 58.999 40.000 0.00 0.00 0.00 0.98
932 1019 9.162764 GGCATGAAAACTATCTAAACAGTCTTA 57.837 33.333 0.00 0.00 0.00 2.10
933 1020 9.974750 GCATGAAAACTATCTAAACAGTCTTAC 57.025 33.333 0.00 0.00 0.00 2.34
939 1026 7.684937 ACTATCTAAACAGTCTTACGTGTCT 57.315 36.000 0.00 0.00 0.00 3.41
947 1034 2.691526 AGTCTTACGTGTCTGTCAACCA 59.308 45.455 0.00 0.00 0.00 3.67
1033 1120 3.133721 CCTCCACAAAACCCAATCACAAA 59.866 43.478 0.00 0.00 0.00 2.83
1039 1126 4.020662 ACAAAACCCAATCACAAACACACT 60.021 37.500 0.00 0.00 0.00 3.55
1182 1269 6.506500 ACAGCAGAACAAATTATTGAGAGG 57.493 37.500 0.00 0.00 38.94 3.69
1259 1366 4.332637 CCACACTGCAAGCGCCAC 62.333 66.667 2.29 0.00 37.60 5.01
1260 1367 3.282157 CACACTGCAAGCGCCACT 61.282 61.111 2.29 0.00 37.60 4.00
1261 1368 2.974698 ACACTGCAAGCGCCACTC 60.975 61.111 2.29 0.00 37.60 3.51
1262 1369 4.081030 CACTGCAAGCGCCACTCG 62.081 66.667 2.29 0.00 37.60 4.18
1263 1370 4.299547 ACTGCAAGCGCCACTCGA 62.300 61.111 2.29 0.00 37.73 4.04
1264 1371 3.043713 CTGCAAGCGCCACTCGAA 61.044 61.111 2.29 0.00 41.67 3.71
1265 1372 3.020026 CTGCAAGCGCCACTCGAAG 62.020 63.158 2.29 0.00 41.67 3.79
1266 1373 4.451652 GCAAGCGCCACTCGAAGC 62.452 66.667 2.29 0.00 41.67 3.86
1396 1503 2.562912 GTGCGTACCGTCGAGGAA 59.437 61.111 6.70 0.00 45.00 3.36
1468 1575 1.603455 GGTGCTTGCTTACAGCCCA 60.603 57.895 0.00 0.00 41.51 5.36
1667 1775 1.002011 GGGCCCTTCTTCCACTGAC 60.002 63.158 17.04 0.00 0.00 3.51
1694 1802 4.767409 AGAAAGCTGTGGGGAGATAAAAAC 59.233 41.667 0.00 0.00 0.00 2.43
1697 1805 4.677182 AGCTGTGGGGAGATAAAAACAAT 58.323 39.130 0.00 0.00 0.00 2.71
1849 1957 3.823873 TGGTTTGCGTTATCAGTTTCCAT 59.176 39.130 0.00 0.00 0.00 3.41
1870 1979 5.338365 CATGAAGAAAGGATAAACAGCTGC 58.662 41.667 15.27 0.00 0.00 5.25
1888 1997 5.292589 CAGCTGCAACAAGAGAAAAATGTTT 59.707 36.000 0.00 0.00 35.22 2.83
1894 2003 6.978080 GCAACAAGAGAAAAATGTTTAGTGGA 59.022 34.615 0.00 0.00 35.22 4.02
1917 2027 8.597167 TGGAATATGATCGATTAGTCAAAGGAT 58.403 33.333 0.00 0.00 0.00 3.24
1921 2031 5.769367 TGATCGATTAGTCAAAGGATACGG 58.231 41.667 0.00 0.00 46.39 4.02
1965 2157 6.282199 TCTAAAACTGACTCATCCTGTACC 57.718 41.667 0.00 0.00 0.00 3.34
2003 2210 4.545610 CCATGTGCGTGAGTTTATGTTTT 58.454 39.130 0.00 0.00 0.00 2.43
2038 2245 8.237267 AGAAATTCCGTGAGTTCATGTTATTTC 58.763 33.333 18.69 18.69 38.83 2.17
2141 2352 3.258372 AGTGAGCTGACCACGATTAGAAA 59.742 43.478 0.00 0.00 39.38 2.52
2159 2370 8.667592 ATTAGAAAGTACTCCCTCTGTAAACT 57.332 34.615 0.00 0.00 0.00 2.66
2370 4151 5.564550 AGGTCAGTTTAATGCATGAAGACT 58.435 37.500 0.00 3.00 0.00 3.24
2429 4211 1.396996 ACGTATTGCGGCAATCTCAAC 59.603 47.619 29.70 20.75 46.52 3.18
2442 4224 5.689961 GGCAATCTCAACGTTACAACAATTT 59.310 36.000 0.00 0.00 0.00 1.82
2487 4269 3.751479 AGGATGTTTTTGCAGGAAACC 57.249 42.857 19.06 8.92 36.43 3.27
2568 4352 3.896648 TGACCGATGTTTTTGCTCTTC 57.103 42.857 0.00 0.00 0.00 2.87
2604 4388 2.119457 CAGCCTTTTGTTTGCTTCGTC 58.881 47.619 0.00 0.00 31.77 4.20
2678 4462 2.318908 TGCAAGAAACTTCAGGCCATT 58.681 42.857 5.01 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.162666 AGTGGAGACGAGGATGTGTTTA 58.837 45.455 0.00 0.00 0.00 2.01
70 71 7.661040 AGTAACAAGTGCAAGCAAGATTAAAT 58.339 30.769 0.00 0.00 0.00 1.40
232 299 1.286849 GGGCACTGGGTTAATAGGGTT 59.713 52.381 0.00 0.00 0.00 4.11
234 301 0.923358 TGGGCACTGGGTTAATAGGG 59.077 55.000 0.00 0.00 0.00 3.53
348 420 1.691434 GCATCTAGGGTCTCTTCCAGG 59.309 57.143 0.00 0.00 0.00 4.45
350 422 2.856760 AGCATCTAGGGTCTCTTCCA 57.143 50.000 0.00 0.00 0.00 3.53
351 423 2.035321 CGAAGCATCTAGGGTCTCTTCC 59.965 54.545 0.00 0.00 0.00 3.46
356 428 0.261991 TCCCGAAGCATCTAGGGTCT 59.738 55.000 2.40 0.00 44.13 3.85
488 561 1.272092 TGGCTCTCTGTTGATTTGGGG 60.272 52.381 0.00 0.00 0.00 4.96
896 983 8.045176 AGATAGTTTTCATGCCTTGTTACTTC 57.955 34.615 0.00 0.00 0.00 3.01
899 986 9.556030 GTTTAGATAGTTTTCATGCCTTGTTAC 57.444 33.333 0.00 0.00 0.00 2.50
932 1019 2.325583 AATGTGGTTGACAGACACGT 57.674 45.000 6.98 4.43 38.23 4.49
933 1020 3.312421 AGAAAATGTGGTTGACAGACACG 59.688 43.478 6.98 0.00 38.23 4.49
939 1026 3.286353 TCAGCAGAAAATGTGGTTGACA 58.714 40.909 0.00 0.00 39.53 3.58
947 1034 9.598517 TTCAAACTTAATTTCAGCAGAAAATGT 57.401 25.926 8.45 3.03 46.06 2.71
994 1081 4.527157 GCGAACGATGCTGGCTGC 62.527 66.667 9.67 9.67 43.25 5.25
1033 1120 0.832135 ATGTCCGGTCTCCAGTGTGT 60.832 55.000 0.00 0.00 0.00 3.72
1039 1126 2.348104 CGTCCATGTCCGGTCTCCA 61.348 63.158 0.00 0.00 0.00 3.86
1182 1269 4.778143 CCTGTGGGGCGTGCCTAC 62.778 72.222 11.25 10.80 36.10 3.18
1257 1364 0.803768 CATCGTCCCTGCTTCGAGTG 60.804 60.000 0.00 0.00 37.04 3.51
1258 1365 0.965866 TCATCGTCCCTGCTTCGAGT 60.966 55.000 0.00 0.00 37.04 4.18
1259 1366 0.173481 TTCATCGTCCCTGCTTCGAG 59.827 55.000 0.00 0.00 37.04 4.04
1260 1367 0.173481 CTTCATCGTCCCTGCTTCGA 59.827 55.000 0.00 0.00 37.96 3.71
1261 1368 1.424493 GCTTCATCGTCCCTGCTTCG 61.424 60.000 0.00 0.00 0.00 3.79
1262 1369 1.092345 GGCTTCATCGTCCCTGCTTC 61.092 60.000 0.00 0.00 0.00 3.86
1263 1370 1.078143 GGCTTCATCGTCCCTGCTT 60.078 57.895 0.00 0.00 0.00 3.91
1264 1371 2.586792 GGCTTCATCGTCCCTGCT 59.413 61.111 0.00 0.00 0.00 4.24
1265 1372 2.892425 CGGCTTCATCGTCCCTGC 60.892 66.667 0.00 0.00 0.00 4.85
1266 1373 2.892425 GCGGCTTCATCGTCCCTG 60.892 66.667 0.00 0.00 0.00 4.45
1468 1575 0.460311 CTCCGTAGCCGATGGAAGTT 59.540 55.000 0.00 0.00 43.04 2.66
1694 1802 5.238432 TGAGCTTACACAGTAACCACAATTG 59.762 40.000 3.24 3.24 0.00 2.32
1697 1805 4.409718 TGAGCTTACACAGTAACCACAA 57.590 40.909 0.00 0.00 0.00 3.33
1849 1957 4.397420 TGCAGCTGTTTATCCTTTCTTCA 58.603 39.130 16.64 0.00 0.00 3.02
1870 1979 8.925161 TTCCACTAAACATTTTTCTCTTGTTG 57.075 30.769 0.00 0.00 34.04 3.33
1888 1997 9.914131 CTTTGACTAATCGATCATATTCCACTA 57.086 33.333 0.00 0.00 0.00 2.74
1894 2003 9.574458 CGTATCCTTTGACTAATCGATCATATT 57.426 33.333 0.00 0.00 0.00 1.28
1902 2011 5.828747 TCTTCCGTATCCTTTGACTAATCG 58.171 41.667 0.00 0.00 0.00 3.34
1917 2027 3.004419 CCGAGCAGATTACATCTTCCGTA 59.996 47.826 0.00 0.00 37.58 4.02
1921 2031 3.104843 AGCCGAGCAGATTACATCTTC 57.895 47.619 0.00 0.00 37.58 2.87
1965 2157 6.201556 GCACATGGCGTTTGAATAATATTG 57.798 37.500 0.00 0.00 0.00 1.90
2012 2219 7.687941 AATAACATGAACTCACGGAATTTCT 57.312 32.000 0.00 0.00 0.00 2.52
2370 4151 7.402054 TCTGCTTCTTACCCTGATGATTTAAA 58.598 34.615 0.00 0.00 0.00 1.52
2429 4211 7.027161 CCCATCCTAAGAAAATTGTTGTAACG 58.973 38.462 0.00 0.00 0.00 3.18
2442 4224 3.521531 TGTGTGTATGCCCATCCTAAGAA 59.478 43.478 0.00 0.00 0.00 2.52
2487 4269 6.751425 TGCTTCCAAAATATTGCAATTCTACG 59.249 34.615 18.75 4.18 35.10 3.51
2568 4352 1.339151 GGCTGGTGAGTTTACTGGAGG 60.339 57.143 0.00 0.00 0.00 4.30
2604 4388 3.924918 TCAAGGAGAACAGAACTCTCG 57.075 47.619 0.00 0.00 40.29 4.04


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

AutoCloner maintained by Alex Coulton.