Multiple sequence alignment - TraesCS1B01G457000

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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 TraesCS1B01G457000 chr1B 100.000 4953 0 0 1 4953 671297595 671292643 0.000000e+00 9147.0
1 TraesCS1B01G457000 chr1B 100.000 1579 0 0 1039 2617 671339981 671338403 0.000000e+00 2916.0
2 TraesCS1B01G457000 chr1B 100.000 1579 0 0 1039 2617 671368260 671366682 0.000000e+00 2916.0
3 TraesCS1B01G457000 chr1B 99.710 1036 3 0 2 1037 671341706 671340671 0.000000e+00 1897.0
4 TraesCS1B01G457000 chr1B 96.103 1129 29 7 3834 4953 671337177 671336055 0.000000e+00 1827.0
5 TraesCS1B01G457000 chr1B 99.237 918 7 0 120 1037 671391109 671390192 0.000000e+00 1657.0
6 TraesCS1B01G457000 chr1B 96.292 836 20 5 2626 3451 671338284 671337450 0.000000e+00 1362.0
7 TraesCS1B01G457000 chr1B 100.000 596 0 0 442 1037 671368985 671368390 0.000000e+00 1101.0
8 TraesCS1B01G457000 chr1B 81.364 220 14 11 680 878 51027864 51028077 2.390000e-33 154.0
9 TraesCS1B01G457000 chrUn 95.867 2347 60 13 2626 4953 316150550 316148222 0.000000e+00 3762.0
10 TraesCS1B01G457000 chrUn 95.344 902 23 7 3575 4474 461976335 461977219 0.000000e+00 1415.0
11 TraesCS1B01G457000 chrUn 88.382 241 21 4 80 320 184644289 184644522 2.920000e-72 283.0
12 TraesCS1B01G457000 chrUn 96.000 50 0 2 2061 2110 310881871 310881918 4.110000e-11 80.5
13 TraesCS1B01G457000 chrUn 100.000 41 0 0 2071 2111 64149702 64149742 5.320000e-10 76.8
14 TraesCS1B01G457000 chrUn 97.674 43 1 0 2069 2111 11031788 11031746 1.910000e-09 75.0
15 TraesCS1B01G457000 chrUn 97.619 42 1 0 2070 2111 31527793 31527834 6.880000e-09 73.1
16 TraesCS1B01G457000 chrUn 97.619 42 1 0 2070 2111 31527924 31527965 6.880000e-09 73.1
17 TraesCS1B01G457000 chrUn 97.619 42 1 0 2069 2110 64149830 64149789 6.880000e-09 73.1
18 TraesCS1B01G457000 chrUn 97.619 42 1 0 2069 2110 87983129 87983170 6.880000e-09 73.1
19 TraesCS1B01G457000 chrUn 95.556 45 2 0 2067 2111 121530353 121530309 6.880000e-09 73.1
20 TraesCS1B01G457000 chrUn 95.652 46 1 1 2067 2111 297895072 297895117 6.880000e-09 73.1
21 TraesCS1B01G457000 chrUn 95.556 45 2 0 2067 2111 310279895 310279851 6.880000e-09 73.1
22 TraesCS1B01G457000 chrUn 95.556 45 2 0 2067 2111 327435840 327435884 6.880000e-09 73.1
23 TraesCS1B01G457000 chrUn 90.566 53 4 1 2059 2110 128516265 128516317 8.900000e-08 69.4
24 TraesCS1B01G457000 chrUn 97.368 38 1 0 2117 2154 229900316 229900353 1.150000e-06 65.8
25 TraesCS1B01G457000 chr1A 95.238 1428 39 9 1923 3334 579105843 579107257 0.000000e+00 2233.0
26 TraesCS1B01G457000 chr1A 95.326 1027 33 5 3488 4505 579107641 579108661 0.000000e+00 1616.0
27 TraesCS1B01G457000 chr1A 85.032 775 63 31 680 1417 579104215 579104973 0.000000e+00 739.0
28 TraesCS1B01G457000 chr1A 90.962 520 34 8 1408 1922 579105015 579105526 0.000000e+00 688.0
29 TraesCS1B01G457000 chr1A 96.448 366 13 0 4588 4953 579108658 579109023 5.480000e-169 604.0
30 TraesCS1B01G457000 chr1A 91.176 204 14 1 482 681 579103929 579104132 1.760000e-69 274.0
31 TraesCS1B01G457000 chr1D 90.497 1168 58 17 680 1819 483011571 483010429 0.000000e+00 1493.0
32 TraesCS1B01G457000 chr1D 88.627 1020 82 14 2277 3269 483009282 483008270 0.000000e+00 1210.0
33 TraesCS1B01G457000 chr1D 90.667 150 7 3 1923 2072 483009990 483009848 5.060000e-45 193.0
34 TraesCS1B01G457000 chr1D 86.777 121 13 2 364 482 3259672 3259553 1.120000e-26 132.0
35 TraesCS1B01G457000 chr1D 87.719 114 13 1 1809 1922 483010410 483010298 1.120000e-26 132.0
36 TraesCS1B01G457000 chr1D 83.803 142 4 6 13 149 3285957 3285830 3.130000e-22 117.0
37 TraesCS1B01G457000 chr1D 97.778 45 1 0 2067 2111 299925727 299925771 1.480000e-10 78.7
38 TraesCS1B01G457000 chr1D 87.692 65 7 1 2047 2111 290446443 290446506 1.910000e-09 75.0
39 TraesCS1B01G457000 chr1D 93.333 45 2 1 2101 2144 7692157 7692113 1.150000e-06 65.8
40 TraesCS1B01G457000 chr2A 84.091 396 38 10 2285 2663 13021790 13021403 4.710000e-95 359.0
41 TraesCS1B01G457000 chr2A 81.356 236 32 8 189 418 456670762 456670991 1.100000e-41 182.0
42 TraesCS1B01G457000 chr2A 84.158 101 11 4 2071 2170 446667940 446668036 5.280000e-15 93.5
43 TraesCS1B01G457000 chr2A 100.000 30 0 0 2700 2729 13021382 13021353 6.930000e-04 56.5
44 TraesCS1B01G457000 chr7D 89.606 279 28 1 140 418 631544376 631544653 2.190000e-93 353.0
45 TraesCS1B01G457000 chr7D 82.639 144 6 6 13 151 80228358 80228229 5.240000e-20 110.0
46 TraesCS1B01G457000 chr3D 89.494 257 26 1 140 396 556806715 556806460 1.720000e-84 324.0
47 TraesCS1B01G457000 chr3D 86.905 84 5 6 2067 2144 33368769 33368852 6.830000e-14 89.8
48 TraesCS1B01G457000 chr3D 87.013 77 6 3 2069 2144 13259724 13259797 3.180000e-12 84.2
49 TraesCS1B01G457000 chr3A 88.261 230 22 3 93 322 25134362 25134586 2.270000e-68 270.0
50 TraesCS1B01G457000 chr3A 88.261 230 22 3 93 322 37675747 37675971 2.270000e-68 270.0
51 TraesCS1B01G457000 chr3A 87.446 231 18 3 92 322 692476284 692476503 6.360000e-64 255.0
52 TraesCS1B01G457000 chr3A 84.247 146 18 5 3379 3521 528678720 528678577 2.400000e-28 137.0
53 TraesCS1B01G457000 chr7A 87.446 231 22 5 93 322 595474632 595474408 4.920000e-65 259.0
54 TraesCS1B01G457000 chr7A 80.571 175 14 5 13 182 576203897 576204056 3.130000e-22 117.0
55 TraesCS1B01G457000 chr7A 92.208 77 5 1 2068 2144 28406868 28406793 1.890000e-19 108.0
56 TraesCS1B01G457000 chr6A 84.766 256 33 2 2737 2987 292621946 292622200 8.230000e-63 252.0
57 TraesCS1B01G457000 chr6A 81.143 175 13 5 13 182 83161448 83161607 6.730000e-24 122.0
58 TraesCS1B01G457000 chr6A 85.882 85 6 5 2061 2144 605043166 605043087 8.830000e-13 86.1
59 TraesCS1B01G457000 chr6D 84.496 258 33 3 2736 2987 208260190 208259934 1.060000e-61 248.0
60 TraesCS1B01G457000 chr6D 88.312 77 3 1 2067 2143 105826053 105825983 2.460000e-13 87.9
61 TraesCS1B01G457000 chr6D 93.617 47 2 1 2108 2154 62556994 62556949 8.900000e-08 69.4
62 TraesCS1B01G457000 chr6B 84.436 257 33 3 2737 2987 370129691 370129436 3.830000e-61 246.0
63 TraesCS1B01G457000 chr6B 91.026 78 3 4 2071 2144 583626499 583626422 8.770000e-18 102.0
64 TraesCS1B01G457000 chr5D 83.058 242 41 0 1154 1395 557827149 557826908 2.320000e-53 220.0
65 TraesCS1B01G457000 chr5D 84.828 145 18 4 3379 3521 557825018 557824876 5.170000e-30 143.0
66 TraesCS1B01G457000 chr5D 85.882 85 5 7 2066 2144 190474024 190473941 3.180000e-12 84.2
67 TraesCS1B01G457000 chr5B 75.413 484 100 14 1154 1620 704995374 704994893 3.000000e-52 217.0
68 TraesCS1B01G457000 chr5B 83.140 172 9 5 16 182 128781453 128781297 6.690000e-29 139.0
69 TraesCS1B01G457000 chr5B 84.138 145 17 6 3379 3521 704993203 704993063 8.650000e-28 135.0
70 TraesCS1B01G457000 chr5B 93.506 77 2 1 2070 2143 705275880 705275956 1.460000e-20 111.0
71 TraesCS1B01G457000 chr5B 90.000 80 5 2 2071 2147 705275956 705275877 3.150000e-17 100.0
72 TraesCS1B01G457000 chr4B 87.432 183 22 1 236 418 510566116 510565935 5.020000e-50 209.0
73 TraesCS1B01G457000 chr4B 83.448 145 17 6 3379 3521 653272756 653272617 1.450000e-25 128.0
74 TraesCS1B01G457000 chr5A 87.500 184 16 4 236 418 1397481 1397658 6.500000e-49 206.0
75 TraesCS1B01G457000 chr2B 86.957 184 17 4 236 418 47406957 47406780 3.020000e-47 200.0
76 TraesCS1B01G457000 chr2B 76.645 304 55 10 2708 2999 543553009 543553308 2.390000e-33 154.0
77 TraesCS1B01G457000 chr2D 79.094 287 43 10 2708 2984 461384875 461385154 1.100000e-41 182.0
78 TraesCS1B01G457000 chr2D 85.616 146 16 5 3379 3521 1689832 1689689 1.110000e-31 148.0
79 TraesCS1B01G457000 chr2D 82.659 173 10 5 13 180 346165383 346165540 8.650000e-28 135.0
80 TraesCS1B01G457000 chr3B 83.516 182 26 3 237 418 803455547 803455370 3.070000e-37 167.0
81 TraesCS1B01G457000 chr3B 91.250 80 2 1 13 87 706562956 706563035 2.440000e-18 104.0
82 TraesCS1B01G457000 chr3B 91.250 80 2 1 13 87 706605961 706606040 2.440000e-18 104.0
83 TraesCS1B01G457000 chr4D 79.832 238 34 10 3302 3535 462385 462612 1.430000e-35 161.0
84 TraesCS1B01G457000 chr4D 90.789 76 3 2 2070 2145 37513948 37514019 1.130000e-16 99.0
85 TraesCS1B01G457000 chr4D 90.667 75 6 1 2070 2144 100365010 100365083 1.130000e-16 99.0
86 TraesCS1B01G457000 chr4D 90.541 74 5 2 2071 2143 439780317 439780389 4.080000e-16 97.1
87 TraesCS1B01G457000 chr4D 88.158 76 4 5 2070 2140 388098997 388099072 8.830000e-13 86.1
88 TraesCS1B01G457000 chr4D 89.231 65 3 4 2048 2110 323575207 323575269 1.480000e-10 78.7
89 TraesCS1B01G457000 chr4D 97.727 44 1 0 2069 2112 94608138 94608181 5.320000e-10 76.8
90 TraesCS1B01G457000 chr4D 94.000 50 1 2 2063 2110 226974471 226974520 1.910000e-09 75.0
91 TraesCS1B01G457000 chr4D 100.000 35 0 0 2110 2144 52048668 52048634 1.150000e-06 65.8
92 TraesCS1B01G457000 chr4D 100.000 34 0 0 2110 2143 115245796 115245829 4.140000e-06 63.9
93 TraesCS1B01G457000 chr4A 83.333 144 19 5 3380 3521 610252309 610252449 1.450000e-25 128.0
94 TraesCS1B01G457000 chr4A 82.759 145 6 4 13 152 732328391 732328521 1.460000e-20 111.0


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 TraesCS1B01G457000 chr1B 671292643 671297595 4952 True 9147.000000 9147 100.000000 1 4953 1 chr1B.!!$R1 4952
1 TraesCS1B01G457000 chr1B 671366682 671368985 2303 True 2008.500000 2916 100.000000 442 2617 2 chr1B.!!$R4 2175
2 TraesCS1B01G457000 chr1B 671336055 671341706 5651 True 2000.500000 2916 98.026250 2 4953 4 chr1B.!!$R3 4951
3 TraesCS1B01G457000 chr1B 671390192 671391109 917 True 1657.000000 1657 99.237000 120 1037 1 chr1B.!!$R2 917
4 TraesCS1B01G457000 chrUn 316148222 316150550 2328 True 3762.000000 3762 95.867000 2626 4953 1 chrUn.!!$R5 2327
5 TraesCS1B01G457000 chrUn 461976335 461977219 884 False 1415.000000 1415 95.344000 3575 4474 1 chrUn.!!$F9 899
6 TraesCS1B01G457000 chr1A 579103929 579109023 5094 False 1025.666667 2233 92.363667 482 4953 6 chr1A.!!$F1 4471
7 TraesCS1B01G457000 chr1D 483008270 483011571 3301 True 757.000000 1493 89.377500 680 3269 4 chr1D.!!$R4 2589

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
152 153 1.134098 CATCGCACCCTTTAGTCCCAT 60.134 52.381 0.00 0.00 0.00 4.00 F
2697 4498 2.035626 ACCCTGAAACCCATGCGG 59.964 61.111 0.00 0.00 37.81 5.69 F
3756 5809 1.099295 ATGGACACTGATGCATGCGG 61.099 55.000 14.09 3.56 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2836 4643 1.148273 TGTCGCAAAGCCTGGAAGT 59.852 52.632 0.00 0.0 0.00 3.01 R
3820 5874 0.323178 CAGGCTGGGACTGAGCAATT 60.323 55.000 6.61 0.0 42.14 2.32 R
4618 6682 2.318908 AGCACAATTGTCACACCCAAT 58.681 42.857 8.48 0.0 34.07 3.16 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
60 61 4.283722 ACCCTTTAGTCTCGTGTCTCAAAT 59.716 41.667 0.00 0.00 0.00 2.32
152 153 1.134098 CATCGCACCCTTTAGTCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
2697 4498 2.035626 ACCCTGAAACCCATGCGG 59.964 61.111 0.00 0.00 37.81 5.69
2808 4615 3.942130 GCAACCTTGTTGCTAAAGGAT 57.058 42.857 21.26 5.01 46.08 3.24
2829 4636 3.195698 GCGACGCTTTGGGCTAGG 61.196 66.667 13.73 0.00 39.13 3.02
2836 4643 3.264052 TTTGGGCTAGGGCTGGCA 61.264 61.111 2.88 0.00 38.96 4.92
2984 4791 4.271049 CAGAAGTCTCTTTGCGTTTTCTCA 59.729 41.667 0.00 0.00 0.00 3.27
3347 5170 1.697432 TGTACCCCCTCTTGTCTTGTG 59.303 52.381 0.00 0.00 0.00 3.33
3407 5230 5.426504 TGCTTGTTGTTTTTCAATGTGGAT 58.573 33.333 0.00 0.00 38.38 3.41
3756 5809 1.099295 ATGGACACTGATGCATGCGG 61.099 55.000 14.09 3.56 0.00 5.69
3838 5892 1.289160 TAATTGCTCAGTCCCAGCCT 58.711 50.000 0.00 0.00 35.89 4.58
4033 6094 4.584743 GGATGGTTTTTGAGTCTGGAAGTT 59.415 41.667 0.00 0.00 33.76 2.66
4149 6211 4.041567 ACATGTAGAAGACATCCCAACACA 59.958 41.667 0.00 0.00 46.33 3.72
4575 6639 2.874694 CTCGGCCGATGCGACATTG 61.875 63.158 31.19 9.85 38.85 2.82
4843 6907 1.812571 CACCAACGCCTGCTTATCTTT 59.187 47.619 0.00 0.00 0.00 2.52
4874 6944 8.350852 TCGTATGTTTGTAATGGGGTTTTATT 57.649 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.511146 TCCCGGTTCGTTATTTAGACACT 59.489 43.478 0.00 0.00 0.00 3.55
60 61 4.313020 AAGACTAGACCTTTAGTCCCGA 57.687 45.455 0.00 0.00 46.95 5.14
100 101 1.648504 GGTTCGTATCTCAAACCGGG 58.351 55.000 6.32 0.00 33.68 5.73
152 153 0.032952 CCCGGTTCGTGTCTCAAAGA 59.967 55.000 0.00 0.00 0.00 2.52
2836 4643 1.148273 TGTCGCAAAGCCTGGAAGT 59.852 52.632 0.00 0.00 0.00 3.01
3187 5010 1.075374 TGCTAAAATGCAGGGGTGACT 59.925 47.619 0.00 0.00 38.12 3.41
3317 5140 5.014755 ACAAGAGGGGGTACAATCACAATAA 59.985 40.000 0.00 0.00 0.00 1.40
3347 5170 5.159209 CCAAGATGCAACACTTTCAGATTC 58.841 41.667 0.00 0.00 0.00 2.52
3407 5230 2.176045 TCGCTTCACCTTCACCTGATA 58.824 47.619 0.00 0.00 0.00 2.15
3531 5584 4.764823 TGACGGTAAAAATCCTGCTTCATT 59.235 37.500 0.00 0.00 0.00 2.57
3547 5600 1.068055 GCGAGAGGAAAAGTGACGGTA 60.068 52.381 0.00 0.00 0.00 4.02
3721 5774 6.372381 CAGTGTCCATCATGTTTATCAGACAA 59.628 38.462 0.00 0.00 35.02 3.18
3756 5809 6.374578 GTCTTCATCTACAGTTTGAAAAGCC 58.625 40.000 0.00 0.00 0.00 4.35
3820 5874 0.323178 CAGGCTGGGACTGAGCAATT 60.323 55.000 6.61 0.00 42.14 2.32
3838 5892 1.032014 GGTCTTCTGGCAAAACTGCA 58.968 50.000 0.00 0.00 36.33 4.41
4033 6094 7.415095 CCATCAGCACGTAAAATGGAAATCTTA 60.415 37.037 11.12 0.00 39.39 2.10
4149 6211 0.524862 ACGACGAGCGGTTGATACTT 59.475 50.000 9.28 0.00 46.49 2.24
4200 6262 5.470777 CCGTTTAAACTTGTGTCATCCCTTA 59.529 40.000 16.01 0.00 0.00 2.69
4201 6263 4.277423 CCGTTTAAACTTGTGTCATCCCTT 59.723 41.667 16.01 0.00 0.00 3.95
4254 6316 8.593679 TCAGATATATCAGGCCGAAAAGAATTA 58.406 33.333 15.08 0.00 0.00 1.40
4396 6458 7.922811 GGTTCTGAGAATTGTCAGTTCAATTTT 59.077 33.333 26.60 1.55 44.62 1.82
4397 6459 7.428826 GGTTCTGAGAATTGTCAGTTCAATTT 58.571 34.615 26.60 0.00 44.62 1.82
4398 6460 6.293626 CGGTTCTGAGAATTGTCAGTTCAATT 60.294 38.462 26.60 4.66 46.41 2.32
4399 6461 5.180117 CGGTTCTGAGAATTGTCAGTTCAAT 59.820 40.000 26.60 0.00 43.89 2.57
4406 6469 2.839486 AGCGGTTCTGAGAATTGTCA 57.161 45.000 5.05 5.05 0.00 3.58
4500 6564 2.289631 TGTGAGCACATACTCCCAACAG 60.290 50.000 0.00 0.00 36.21 3.16
4575 6639 4.110036 AGAACAAACACTGCACTTTTCC 57.890 40.909 0.00 0.00 0.00 3.13
4618 6682 2.318908 AGCACAATTGTCACACCCAAT 58.681 42.857 8.48 0.00 34.07 3.16
4792 6856 4.382254 CCTTACCCGCAGAACAGTAATACA 60.382 45.833 0.00 0.00 0.00 2.29
4843 6907 5.336055 CCCCATTACAAACATACGAAAAGCA 60.336 40.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.