Multiple sequence alignment - TraesCS1D01G173000

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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 TraesCS1D01G173000 chr1D 100.000 2140 0 0 1 2140 246971653 246969514 0.000000e+00 3952.0
1 TraesCS1D01G173000 chr1D 87.446 1163 88 31 572 1711 247123747 247122620 0.000000e+00 1286.0
2 TraesCS1D01G173000 chr1D 90.018 561 48 5 985 1544 246679974 246679421 0.000000e+00 719.0
3 TraesCS1D01G173000 chr1D 100.000 176 0 0 2353 2528 246969301 246969126 2.430000e-85 326.0
4 TraesCS1D01G173000 chr1A 92.905 1494 44 9 272 1711 300671877 300673362 0.000000e+00 2115.0
5 TraesCS1D01G173000 chr1A 88.354 1142 80 24 572 1693 300576597 300577705 0.000000e+00 1323.0
6 TraesCS1D01G173000 chr1A 89.305 561 53 2 985 1545 300944073 300944626 0.000000e+00 697.0
7 TraesCS1D01G173000 chr1A 91.892 296 20 2 1 296 300671283 300671574 6.510000e-111 411.0
8 TraesCS1D01G173000 chr1A 87.273 330 19 10 1832 2140 300673517 300673844 3.090000e-94 355.0
9 TraesCS1D01G173000 chr1A 90.798 163 15 0 573 735 300943813 300943975 4.230000e-53 219.0
10 TraesCS1D01G173000 chr1A 94.574 129 4 2 1727 1852 300673347 300673475 1.980000e-46 196.0
11 TraesCS1D01G173000 chr1A 86.441 177 17 3 2353 2527 300673916 300674087 1.190000e-43 187.0
12 TraesCS1D01G173000 chr1A 85.030 167 8 11 1732 1891 300577708 300577864 1.210000e-33 154.0
13 TraesCS1D01G173000 chr1B 91.456 1463 35 28 327 1716 331083334 331084779 0.000000e+00 1927.0
14 TraesCS1D01G173000 chr1B 87.175 1154 72 36 572 1693 330991079 330992188 0.000000e+00 1242.0
15 TraesCS1D01G173000 chr1B 90.018 561 48 5 985 1544 331363488 331364041 0.000000e+00 719.0
16 TraesCS1D01G173000 chr1B 91.520 342 23 2 1 336 331072171 331072512 1.370000e-127 466.0
17 TraesCS1D01G173000 chr1B 92.025 163 13 0 573 735 331363231 331363393 1.960000e-56 230.0
18 TraesCS1D01G173000 chr1B 88.800 125 8 3 1741 1862 330992203 330992324 5.630000e-32 148.0
19 TraesCS1D01G173000 chr1B 92.135 89 5 1 1886 1974 331084958 331085044 9.500000e-25 124.0
20 TraesCS1D01G173000 chr5A 81.168 685 82 26 887 1547 491301796 491302457 8.070000e-140 507.0
21 TraesCS1D01G173000 chr5A 100.000 29 0 0 18 46 671539981 671540009 1.000000e-03 54.7
22 TraesCS1D01G173000 chr5D 82.007 578 67 18 984 1547 388109777 388110331 8.240000e-125 457.0
23 TraesCS1D01G173000 chr6D 82.895 152 19 4 583 727 46861041 46861192 2.040000e-26 130.0
24 TraesCS1D01G173000 chr6B 82.895 152 19 4 583 727 116106905 116107056 2.040000e-26 130.0


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 TraesCS1D01G173000 chr1D 246969126 246971653 2527 True 2139.0 3952 100.0000 1 2528 2 chr1D.!!$R3 2527
1 TraesCS1D01G173000 chr1D 247122620 247123747 1127 True 1286.0 1286 87.4460 572 1711 1 chr1D.!!$R2 1139
2 TraesCS1D01G173000 chr1D 246679421 246679974 553 True 719.0 719 90.0180 985 1544 1 chr1D.!!$R1 559
3 TraesCS1D01G173000 chr1A 300576597 300577864 1267 False 738.5 1323 86.6920 572 1891 2 chr1A.!!$F1 1319
4 TraesCS1D01G173000 chr1A 300671283 300674087 2804 False 652.8 2115 90.6170 1 2527 5 chr1A.!!$F2 2526
5 TraesCS1D01G173000 chr1A 300943813 300944626 813 False 458.0 697 90.0515 573 1545 2 chr1A.!!$F3 972
6 TraesCS1D01G173000 chr1B 331083334 331085044 1710 False 1025.5 1927 91.7955 327 1974 2 chr1B.!!$F3 1647
7 TraesCS1D01G173000 chr1B 330991079 330992324 1245 False 695.0 1242 87.9875 572 1862 2 chr1B.!!$F2 1290
8 TraesCS1D01G173000 chr1B 331363231 331364041 810 False 474.5 719 91.0215 573 1544 2 chr1B.!!$F4 971
9 TraesCS1D01G173000 chr5A 491301796 491302457 661 False 507.0 507 81.1680 887 1547 1 chr5A.!!$F1 660
10 TraesCS1D01G173000 chr5D 388109777 388110331 554 False 457.0 457 82.0070 984 1547 1 chr5D.!!$F1 563

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
126 127 1.003442 TGGCCCTCCTAGAGCATGT 59.997 57.895 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2523 0.4087 AGGACGGTGAGGGTACTCTT 59.591 55.0 0.0 0.0 44.29 2.85 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
31 32 5.128335 TGATGCATGCATTATGGTGGTTTTA 59.872 36.000 32.60 2.19 36.70 1.52
33 34 5.358090 TGCATGCATTATGGTGGTTTTATG 58.642 37.500 18.46 0.00 37.26 1.90
46 47 4.698304 GTGGTTTTATGGATTTCACTCGGA 59.302 41.667 0.00 0.00 0.00 4.55
52 53 9.203421 GTTTTATGGATTTCACTCGGAATTTTT 57.797 29.630 0.00 0.00 34.91 1.94
68 69 1.515081 TTTTGGAAGGAGCGTAACCG 58.485 50.000 0.00 0.00 37.07 4.44
126 127 1.003442 TGGCCCTCCTAGAGCATGT 59.997 57.895 0.00 0.00 0.00 3.21
129 130 1.055040 GCCCTCCTAGAGCATGTCAT 58.945 55.000 0.00 0.00 0.00 3.06
131 132 1.622811 CCCTCCTAGAGCATGTCATCC 59.377 57.143 0.00 0.00 0.00 3.51
138 139 1.959985 AGAGCATGTCATCCTAGGTCG 59.040 52.381 9.08 0.94 0.00 4.79
142 143 2.205074 CATGTCATCCTAGGTCGTTGC 58.795 52.381 9.08 0.00 0.00 4.17
152 153 1.962306 GGTCGTTGCGGTTTGGCTA 60.962 57.895 0.00 0.00 0.00 3.93
162 163 4.013728 TGCGGTTTGGCTATGTCTATTTT 58.986 39.130 0.00 0.00 0.00 1.82
228 229 6.328934 TGGTTGGCTATGTCTATTTAGGATGA 59.671 38.462 0.00 0.00 0.00 2.92
229 230 6.876257 GGTTGGCTATGTCTATTTAGGATGAG 59.124 42.308 0.00 0.00 0.00 2.90
230 231 7.445945 GTTGGCTATGTCTATTTAGGATGAGT 58.554 38.462 0.00 0.00 0.00 3.41
231 232 7.618019 TGGCTATGTCTATTTAGGATGAGTT 57.382 36.000 0.00 0.00 0.00 3.01
324 651 3.888323 TGCAAGCTGAGGTTGTTGAATTA 59.112 39.130 23.33 2.05 42.18 1.40
378 707 4.193826 TCTCGTTCTCCCTTTCATGAAG 57.806 45.455 8.41 3.35 35.02 3.02
503 832 5.784177 ACAACTACCATACACTTGACTCTG 58.216 41.667 0.00 0.00 0.00 3.35
718 1067 5.122239 CAGCCATTTTTGTTCTGTATCGAGA 59.878 40.000 0.00 0.00 0.00 4.04
884 1257 2.666190 GCAGCTGGTTCTCGTGCA 60.666 61.111 17.12 0.00 34.18 4.57
999 1385 1.450312 CCAGGCAGGAGGTTTAGCG 60.450 63.158 0.00 0.00 41.22 4.26
1374 1796 1.913778 TCAACATCACCAGCAAGCAT 58.086 45.000 0.00 0.00 0.00 3.79
1440 1862 1.973281 CCACGGCTGCAAGACCAAT 60.973 57.895 0.50 0.00 40.92 3.16
1715 2163 9.826574 TCGTATAATAACAGAATAAAACAGCCT 57.173 29.630 0.00 0.00 0.00 4.58
1716 2164 9.864034 CGTATAATAACAGAATAAAACAGCCTG 57.136 33.333 0.00 0.00 0.00 4.85
1717 2165 9.665264 GTATAATAACAGAATAAAACAGCCTGC 57.335 33.333 0.00 0.00 0.00 4.85
1718 2166 6.588719 AATAACAGAATAAAACAGCCTGCA 57.411 33.333 0.00 0.00 0.00 4.41
1719 2167 4.935352 AACAGAATAAAACAGCCTGCAA 57.065 36.364 0.00 0.00 0.00 4.08
1720 2168 4.935352 ACAGAATAAAACAGCCTGCAAA 57.065 36.364 0.00 0.00 0.00 3.68
1721 2169 5.275067 ACAGAATAAAACAGCCTGCAAAA 57.725 34.783 0.00 0.00 0.00 2.44
1722 2170 5.669477 ACAGAATAAAACAGCCTGCAAAAA 58.331 33.333 0.00 0.00 0.00 1.94
1772 2222 4.270325 GTGGATGGTAGTGCGTTTATCTTC 59.730 45.833 0.00 0.00 0.00 2.87
1810 2261 4.307258 CGTGTGTACGTGTCGGTT 57.693 55.556 0.00 0.00 44.99 4.44
1962 2523 1.568504 ACCTGTCTTATTCGAGGGCA 58.431 50.000 0.00 0.00 0.00 5.36
1977 2538 1.218316 GGCAAGAGTACCCTCACCG 59.782 63.158 0.00 0.00 40.40 4.94
1980 2541 0.531200 CAAGAGTACCCTCACCGTCC 59.469 60.000 0.00 0.00 40.40 4.79
2010 2584 0.539518 GAGGTCTTTCAGGGGCTCTC 59.460 60.000 0.00 0.00 0.00 3.20
2023 2597 1.445095 GCTCTCTGTGCCATCCGAT 59.555 57.895 0.00 0.00 0.00 4.18
2120 2696 4.047125 CCATGGGCCGGTTCTGGT 62.047 66.667 2.85 0.00 0.00 4.00
2374 2950 1.079405 ATGTTTGATCGCGACGGGT 60.079 52.632 12.93 0.00 0.00 5.28
2391 2968 2.124653 TGGGTCGCGGTGTGTTTT 60.125 55.556 6.13 0.00 0.00 2.43
2421 2998 1.635663 GCCAGGACCAAATGTCGACG 61.636 60.000 11.62 0.00 45.46 5.12
2448 3025 0.530744 TTGCGCCGATCTAGTTCAGT 59.469 50.000 4.18 0.00 0.00 3.41
2452 3029 0.930742 GCCGATCTAGTTCAGTCGCG 60.931 60.000 0.00 0.00 33.06 5.87
2463 3041 2.203509 AGTCGCGATAGGAGGGGG 60.204 66.667 14.06 0.00 0.00 5.40
2494 3072 2.729862 CTACGCCGGCTCGCATAC 60.730 66.667 26.68 0.00 0.00 2.39
2495 3073 3.478724 CTACGCCGGCTCGCATACA 62.479 63.158 26.68 0.00 0.00 2.29
2497 3075 4.569023 CGCCGGCTCGCATACAGA 62.569 66.667 26.68 0.00 0.00 3.41
2500 3078 2.786495 CCGGCTCGCATACAGAGGT 61.786 63.158 0.00 0.00 36.31 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.977134 AAAACCACCATAATGCATGCA 57.023 38.095 25.04 25.04 32.84 3.96
31 32 5.480073 TCCAAAAATTCCGAGTGAAATCCAT 59.520 36.000 0.00 0.00 36.33 3.41
33 34 5.385509 TCCAAAAATTCCGAGTGAAATCC 57.614 39.130 0.00 0.00 36.33 3.01
46 47 3.057806 CGGTTACGCTCCTTCCAAAAATT 60.058 43.478 0.00 0.00 0.00 1.82
52 53 1.909781 ACCGGTTACGCTCCTTCCA 60.910 57.895 0.00 0.00 39.22 3.53
68 69 1.549203 ACATGTTGGGAAGATGCACC 58.451 50.000 0.00 0.00 35.71 5.01
126 127 0.968901 ACCGCAACGACCTAGGATGA 60.969 55.000 17.98 0.00 0.00 2.92
129 130 0.320073 CAAACCGCAACGACCTAGGA 60.320 55.000 17.98 0.00 0.00 2.94
131 132 1.908066 GCCAAACCGCAACGACCTAG 61.908 60.000 0.00 0.00 0.00 3.02
138 139 1.165270 AGACATAGCCAAACCGCAAC 58.835 50.000 0.00 0.00 0.00 4.17
178 179 9.181061 CATTTGGCATGAATGGTCATCTATATA 57.819 33.333 0.00 0.00 42.88 0.86
182 183 4.585581 CCATTTGGCATGAATGGTCATCTA 59.414 41.667 18.71 0.00 45.43 1.98
185 186 3.830744 CCATTTGGCATGAATGGTCAT 57.169 42.857 18.71 0.00 45.43 3.06
324 651 7.965718 TGTCAGAATGGGATTTTCAAAGAAAT 58.034 30.769 0.00 0.00 36.16 2.17
359 688 3.664107 CACTTCATGAAAGGGAGAACGA 58.336 45.455 9.88 0.00 41.26 3.85
790 1149 0.036294 GTGTGGCTCCTAACCTGTCC 60.036 60.000 0.00 0.00 0.00 4.02
864 1237 1.301244 CACGAGAACCAGCTGCAGT 60.301 57.895 16.64 0.00 0.00 4.40
884 1257 3.762288 TCGAGGAGTTTATATAGGCGCAT 59.238 43.478 10.83 3.98 0.00 4.73
967 1342 3.318557 CCTGCCTGGTAAGTACTAGTAGC 59.681 52.174 1.87 1.23 33.49 3.58
981 1356 1.450312 CGCTAAACCTCCTGCCTGG 60.450 63.158 0.00 0.00 37.10 4.45
1440 1862 1.100510 CTTCGGAGGTGTCCACGATA 58.899 55.000 0.00 0.16 44.18 2.92
1630 2066 2.930040 ACAACGACACTCACACTTCAAG 59.070 45.455 0.00 0.00 0.00 3.02
1726 2174 9.449719 CCACAGAGGTAGTTTTATTCTGTTATT 57.550 33.333 2.92 0.00 44.30 1.40
1727 2175 8.822805 TCCACAGAGGTAGTTTTATTCTGTTAT 58.177 33.333 2.92 0.00 44.30 1.89
1772 2222 4.694509 ACGCGTGGATATTAGTAGGAGTAG 59.305 45.833 12.93 0.00 0.00 2.57
1810 2261 5.183331 ACAGCGATAGTAAACTGAGACTCAA 59.817 40.000 6.61 0.00 39.35 3.02
1962 2523 0.408700 AGGACGGTGAGGGTACTCTT 59.591 55.000 0.00 0.00 44.29 2.85
1980 2541 4.731612 AGACCTCGCAGCACGCAG 62.732 66.667 0.00 0.00 42.60 5.18
2056 2630 2.721167 CCCGTCATGGAGCTCCGAA 61.721 63.158 27.43 12.01 42.00 4.30
2103 2679 3.995506 GACCAGAACCGGCCCATGG 62.996 68.421 4.14 4.14 37.07 3.66
2357 2933 2.024868 CACCCGTCGCGATCAAACA 61.025 57.895 14.06 0.00 0.00 2.83
2374 2950 2.124653 AAAACACACCGCGACCCA 60.125 55.556 8.23 0.00 0.00 4.51
2483 3061 1.589993 CACCTCTGTATGCGAGCCG 60.590 63.158 0.00 0.00 0.00 5.52
2484 3062 0.807667 CACACCTCTGTATGCGAGCC 60.808 60.000 0.00 0.00 0.00 4.70
2485 3063 1.424493 GCACACCTCTGTATGCGAGC 61.424 60.000 0.00 0.00 0.00 5.03
2486 3064 0.108662 TGCACACCTCTGTATGCGAG 60.109 55.000 0.00 0.00 0.00 5.03
2487 3065 0.536724 ATGCACACCTCTGTATGCGA 59.463 50.000 0.00 0.00 0.00 5.10
2494 3072 3.171987 GCGTGATGCACACCTCTG 58.828 61.111 11.99 2.33 45.73 3.35


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

AutoCloner maintained by Alex Coulton.