Multiple sequence alignment - TraesCS2B01G552200

Loading Multiple Alignment...

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 TraesCS2B01G552200 chr2B 100.000 2327 0 0 1 2327 748211315 748213641 0.000000e+00 4298.0
1 TraesCS2B01G552200 chr2B 95.447 1208 45 4 1125 2327 748363416 748364618 0.000000e+00 1917.0
2 TraesCS2B01G552200 chr2B 96.922 1072 29 3 67 1135 748361883 748362953 0.000000e+00 1794.0
3 TraesCS2B01G552200 chr2B 86.139 303 22 6 1671 1955 770676506 770676206 2.250000e-80 309.0
4 TraesCS2B01G552200 chr2B 88.415 164 17 2 1954 2117 366017519 366017680 1.820000e-46 196.0
5 TraesCS2B01G552200 chr2B 80.476 210 32 7 1466 1672 298008743 298008946 4.000000e-33 152.0
6 TraesCS2B01G552200 chr6B 92.226 1608 119 6 67 1671 715763165 715761561 0.000000e+00 2272.0
7 TraesCS2B01G552200 chr6B 86.903 1611 196 12 67 1670 232074004 232075606 0.000000e+00 1792.0
8 TraesCS2B01G552200 chr6B 85.990 1606 206 16 72 1671 79247722 79246130 0.000000e+00 1701.0
9 TraesCS2B01G552200 chr6B 81.750 1611 261 27 69 1670 695921098 695922684 0.000000e+00 1315.0
10 TraesCS2B01G552200 chr6B 91.318 311 26 1 1361 1671 417217028 417216719 7.690000e-115 424.0
11 TraesCS2B01G552200 chr6B 82.805 221 33 5 1452 1670 545330489 545330272 2.360000e-45 193.0
12 TraesCS2B01G552200 chr6B 92.647 68 3 2 1 66 715763265 715763198 1.900000e-16 97.1
13 TraesCS2B01G552200 chr7B 84.286 1610 236 15 69 1669 38632531 38630930 0.000000e+00 1555.0
14 TraesCS2B01G552200 chr7B 91.831 355 27 2 1318 1671 613794948 613794595 5.780000e-136 494.0
15 TraesCS2B01G552200 chr7B 87.952 166 19 1 1954 2119 490208151 490207987 6.560000e-46 195.0
16 TraesCS2B01G552200 chr1B 83.933 1612 242 15 69 1671 613010009 613008406 0.000000e+00 1526.0
17 TraesCS2B01G552200 chr6D 83.662 1622 236 23 67 1670 367879703 367878093 0.000000e+00 1500.0
18 TraesCS2B01G552200 chr6D 86.250 160 21 1 2169 2327 32520715 32520556 3.070000e-39 172.0
19 TraesCS2B01G552200 chr5D 83.539 1622 240 22 67 1671 564670454 564672065 0.000000e+00 1491.0
20 TraesCS2B01G552200 chr2A 83.015 1625 227 35 82 1671 757997239 757995629 0.000000e+00 1426.0
21 TraesCS2B01G552200 chr3A 86.535 1270 155 15 67 1329 466100129 466098869 0.000000e+00 1384.0
22 TraesCS2B01G552200 chr3A 88.095 168 18 2 1954 2120 600923240 600923074 5.070000e-47 198.0
23 TraesCS2B01G552200 chr3A 89.103 156 15 2 1516 1671 691506038 691505885 2.360000e-45 193.0
24 TraesCS2B01G552200 chr3D 85.915 213 27 3 1459 1671 500310922 500310713 8.370000e-55 224.0
25 TraesCS2B01G552200 chr4D 88.554 166 18 1 1953 2118 64390633 64390469 1.410000e-47 200.0
26 TraesCS2B01G552200 chr2D 88.415 164 17 2 1954 2117 296364209 296364048 1.820000e-46 196.0
27 TraesCS2B01G552200 chr5B 87.425 167 20 1 1951 2117 313151793 313151958 8.490000e-45 191.0
28 TraesCS2B01G552200 chr1D 87.879 165 15 2 1954 2118 452344571 452344730 3.050000e-44 189.0
29 TraesCS2B01G552200 chr7D 86.905 168 19 2 1954 2119 465477946 465477780 3.950000e-43 185.0
30 TraesCS2B01G552200 chr7D 86.875 160 20 1 2169 2327 85520936 85521095 6.610000e-41 178.0
31 TraesCS2B01G552200 chr7D 86.792 159 21 0 2169 2327 621937489 621937331 6.610000e-41 178.0
32 TraesCS2B01G552200 chrUn 87.500 160 19 1 2169 2327 31511251 31511092 1.420000e-42 183.0
33 TraesCS2B01G552200 chr4B 84.524 168 17 4 2169 2327 413276931 413277098 8.610000e-35 158.0
34 TraesCS2B01G552200 chr4B 84.524 168 17 4 2169 2327 413307648 413307815 8.610000e-35 158.0
35 TraesCS2B01G552200 chr4B 83.832 167 19 4 2169 2327 413201977 413202143 4.000000e-33 152.0
36 TraesCS2B01G552200 chr4B 83.041 171 17 4 2169 2327 413397177 413397347 6.700000e-31 145.0


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 TraesCS2B01G552200 chr2B 748211315 748213641 2326 False 4298.00 4298 100.0000 1 2327 1 chr2B.!!$F3 2326
1 TraesCS2B01G552200 chr2B 748361883 748364618 2735 False 1855.50 1917 96.1845 67 2327 2 chr2B.!!$F4 2260
2 TraesCS2B01G552200 chr6B 232074004 232075606 1602 False 1792.00 1792 86.9030 67 1670 1 chr6B.!!$F1 1603
3 TraesCS2B01G552200 chr6B 79246130 79247722 1592 True 1701.00 1701 85.9900 72 1671 1 chr6B.!!$R1 1599
4 TraesCS2B01G552200 chr6B 695921098 695922684 1586 False 1315.00 1315 81.7500 69 1670 1 chr6B.!!$F2 1601
5 TraesCS2B01G552200 chr6B 715761561 715763265 1704 True 1184.55 2272 92.4365 1 1671 2 chr6B.!!$R4 1670
6 TraesCS2B01G552200 chr7B 38630930 38632531 1601 True 1555.00 1555 84.2860 69 1669 1 chr7B.!!$R1 1600
7 TraesCS2B01G552200 chr1B 613008406 613010009 1603 True 1526.00 1526 83.9330 69 1671 1 chr1B.!!$R1 1602
8 TraesCS2B01G552200 chr6D 367878093 367879703 1610 True 1500.00 1500 83.6620 67 1670 1 chr6D.!!$R2 1603
9 TraesCS2B01G552200 chr5D 564670454 564672065 1611 False 1491.00 1491 83.5390 67 1671 1 chr5D.!!$F1 1604
10 TraesCS2B01G552200 chr2A 757995629 757997239 1610 True 1426.00 1426 83.0150 82 1671 1 chr2A.!!$R1 1589
11 TraesCS2B01G552200 chr3A 466098869 466100129 1260 True 1384.00 1384 86.5350 67 1329 1 chr3A.!!$R1 1262

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
949 1004 1.534959 AGAGAGACAGCCCAGCACA 60.535 57.895 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2840 0.953727 TGCTGCAAGGTTAAGCACTG 59.046 50.0 7.52 5.03 41.83 3.66 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
33 34 4.141824 GGATTTCTTGGACGAGAGATTCCT 60.142 45.833 0.00 0.0 32.55 3.36
34 35 4.891992 TTTCTTGGACGAGAGATTCCTT 57.108 40.909 0.00 0.0 32.55 3.36
40 43 4.087182 TGGACGAGAGATTCCTTAAGTGT 58.913 43.478 0.97 0.0 32.55 3.55
51 54 7.918076 AGATTCCTTAAGTGTTGTGAATCCTA 58.082 34.615 18.48 0.0 39.08 2.94
130 165 7.857569 TGTCGATGTTTTTACTCTCGAAAAAT 58.142 30.769 0.00 0.0 39.73 1.82
225 260 6.985653 TTTGGTGAAATGGTCCAGAATTTA 57.014 33.333 0.00 0.0 32.63 1.40
248 283 2.292828 CTCCAAGGAAAAAGGAGGCA 57.707 50.000 0.00 0.0 44.10 4.75
251 286 2.109834 TCCAAGGAAAAAGGAGGCATGA 59.890 45.455 0.00 0.0 0.00 3.07
544 585 2.916640 TGTGATCAATTCCATGCGCTA 58.083 42.857 9.73 0.0 0.00 4.26
549 590 5.049474 GTGATCAATTCCATGCGCTATACAA 60.049 40.000 9.73 0.0 0.00 2.41
796 849 4.451900 CCTGGCTGGTTGTAGTTATAAGG 58.548 47.826 1.62 0.0 0.00 2.69
832 886 7.349598 AGCCAGAATTCCACTTAAGATACAAT 58.650 34.615 10.09 0.0 0.00 2.71
949 1004 1.534959 AGAGAGACAGCCCAGCACA 60.535 57.895 0.00 0.0 0.00 4.57
1038 1093 3.874543 TGTGTCCGAACAATATATGGCAC 59.125 43.478 0.00 0.0 37.08 5.01
1217 1746 7.522542 TGTGGTTATATTACATATTGGGCAGT 58.477 34.615 0.00 0.0 0.00 4.40
1258 1787 1.152881 GAAGCAATGGAGCGGGGAT 60.153 57.895 0.00 0.0 40.15 3.85
1441 1982 1.133809 AGTGGGTTTAGGCTCCTGCA 61.134 55.000 0.00 0.0 41.91 4.41
1547 2117 2.679639 GCCCGATGACAGGTGTTTATCA 60.680 50.000 8.25 0.0 0.00 2.15
1627 2199 5.451242 GGTTTGCTGAACTGTTGTATTTCCA 60.451 40.000 0.00 0.0 38.35 3.53
1696 2268 4.565564 GTCTGACAGTGTAAACGTGAACTT 59.434 41.667 2.24 0.0 0.00 2.66
1756 2328 4.030913 CAGGTGTAAGGTGAGAATAGGGA 58.969 47.826 0.00 0.0 0.00 4.20
1758 2330 5.131142 CAGGTGTAAGGTGAGAATAGGGATT 59.869 44.000 0.00 0.0 0.00 3.01
1763 2335 1.425448 GGTGAGAATAGGGATTGGGGG 59.575 57.143 0.00 0.0 0.00 5.40
1824 2400 3.137360 GGATAGCTCCCAGTTTTCCTCAT 59.863 47.826 0.00 0.0 35.28 2.90
1827 2403 2.912956 AGCTCCCAGTTTTCCTCATGTA 59.087 45.455 0.00 0.0 0.00 2.29
1843 2419 7.720442 TCCTCATGTATCACTTGTAGATTGAG 58.280 38.462 0.00 0.0 31.98 3.02
1881 2457 6.997655 TCATGATACTGCATCCTTAGTTAGG 58.002 40.000 0.00 0.0 46.27 2.69
1936 2512 0.813610 CTGTCAGAAACCGTGTGCCA 60.814 55.000 0.00 0.0 0.00 4.92
1958 2534 5.481472 CAATAGCTTTGCGTTAACTACTCG 58.519 41.667 3.71 0.0 0.00 4.18
1998 2574 5.184892 AGCAGTTTTAGAGATCCCAATGT 57.815 39.130 0.00 0.0 0.00 2.71
2022 2598 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.0 0.00 2.57
2070 2646 2.696989 TACATCCGTCTGTAGTCCGA 57.303 50.000 0.00 0.0 0.00 4.55
2084 2660 7.646130 GTCTGTAGTCCGAATTGAAATCTCTAG 59.354 40.741 0.00 0.0 0.00 2.43
2088 2664 9.367444 GTAGTCCGAATTGAAATCTCTAGAAAA 57.633 33.333 0.00 0.0 0.00 2.29
2110 2686 6.619801 AAGGCTTATATTTAGAAACGCAGG 57.380 37.500 0.00 0.0 0.00 4.85
2111 2687 5.063880 AGGCTTATATTTAGAAACGCAGGG 58.936 41.667 0.00 0.0 0.00 4.45
2112 2688 5.061179 GGCTTATATTTAGAAACGCAGGGA 58.939 41.667 0.00 0.0 0.00 4.20
2113 2689 5.529800 GGCTTATATTTAGAAACGCAGGGAA 59.470 40.000 0.00 0.0 0.00 3.97
2212 2788 3.451526 TGATCATGAGTCGATGACTTGC 58.548 45.455 0.09 0.0 43.53 4.01
2264 2840 3.139077 ACTAAAGGCAGTACACAGTTGC 58.861 45.455 0.00 0.0 37.11 4.17
2300 2876 2.610859 ACAAGGGGCACGAGGGAT 60.611 61.111 0.00 0.0 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.884295 CCCAATCTAGGATTCACAACACTTAA 59.116 38.462 0.00 0.00 0.00 1.85
34 35 6.214615 TCCCAATCTAGGATTCACAACACTTA 59.785 38.462 0.00 0.00 0.00 2.24
40 43 4.889409 GCATTCCCAATCTAGGATTCACAA 59.111 41.667 0.00 0.00 32.10 3.33
51 54 4.591321 TTAAGGACTGCATTCCCAATCT 57.409 40.909 18.82 0.00 36.12 2.40
130 165 3.068024 GCTTGTCAAGTTTCCCAATCACA 59.932 43.478 14.03 0.00 0.00 3.58
225 260 0.476771 TCCTTTTTCCTTGGAGCGGT 59.523 50.000 0.00 0.00 0.00 5.68
544 585 6.154877 TCCCTTGATCATTGCAAATGTTGTAT 59.845 34.615 1.71 0.00 0.00 2.29
549 590 5.272283 GATCCCTTGATCATTGCAAATGT 57.728 39.130 1.71 0.00 45.63 2.71
796 849 0.106318 ATTCTGGCTTGCCAGATCCC 60.106 55.000 35.59 0.90 44.85 3.85
832 886 3.261897 TGGAAAAGTTGCCACAGGAAAAA 59.738 39.130 0.00 0.00 0.00 1.94
1038 1093 7.775561 AGGAAACTATAGCACCAGGAAAAATAG 59.224 37.037 0.00 0.00 40.61 1.73
1217 1746 2.432146 CGGTCTTCTCCCATCATCAGAA 59.568 50.000 0.00 0.00 0.00 3.02
1258 1787 5.926663 AGCATTGATTCTCAGCATCTTAGA 58.073 37.500 0.00 0.00 0.00 2.10
1441 1982 4.154195 CAGGCTAAACAAAGTTACGCTCAT 59.846 41.667 0.00 0.00 0.00 2.90
1627 2199 4.731929 ACCCCTTCCCATTACTCACATAAT 59.268 41.667 0.00 0.00 0.00 1.28
1696 2268 2.203470 TCACATGCCAAGCTCATCAA 57.797 45.000 0.00 0.00 0.00 2.57
1745 2317 2.605825 ACCCCCAATCCCTATTCTCA 57.394 50.000 0.00 0.00 0.00 3.27
1824 2400 5.658634 AGGAGCTCAATCTACAAGTGATACA 59.341 40.000 17.19 0.00 30.34 2.29
1827 2403 5.690464 AAGGAGCTCAATCTACAAGTGAT 57.310 39.130 17.19 0.00 30.34 3.06
1843 2419 3.863142 ATCATGAACAAGCAAAGGAGC 57.137 42.857 0.00 0.00 0.00 4.70
1881 2457 9.730420 GTCCAATTCATAAACAATACACCATAC 57.270 33.333 0.00 0.00 0.00 2.39
1936 2512 5.697848 CGAGTAGTTAACGCAAAGCTATT 57.302 39.130 0.00 0.00 0.00 1.73
1958 2534 5.298347 ACTGCTTATATTTAGGAACGGAGC 58.702 41.667 0.00 0.00 0.00 4.70
1959 2535 7.787725 AAACTGCTTATATTTAGGAACGGAG 57.212 36.000 0.00 0.00 0.00 4.63
1998 2574 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2045 2621 6.592994 TCGGACTACAGACGGATGTATATAAG 59.407 42.308 2.89 0.00 35.21 1.73
2046 2622 6.466812 TCGGACTACAGACGGATGTATATAA 58.533 40.000 2.89 0.00 35.21 0.98
2084 2660 7.644157 CCTGCGTTTCTAAATATAAGCCTTTTC 59.356 37.037 0.00 0.00 0.00 2.29
2088 2664 5.063880 CCCTGCGTTTCTAAATATAAGCCT 58.936 41.667 0.00 0.00 0.00 4.58
2110 2686 4.226620 TCCCCAACCTCAACTTACTATTCC 59.773 45.833 0.00 0.00 0.00 3.01
2111 2687 5.431179 TCCCCAACCTCAACTTACTATTC 57.569 43.478 0.00 0.00 0.00 1.75
2112 2688 5.853572 TTCCCCAACCTCAACTTACTATT 57.146 39.130 0.00 0.00 0.00 1.73
2113 2689 5.806734 GCTTTCCCCAACCTCAACTTACTAT 60.807 44.000 0.00 0.00 0.00 2.12
2212 2788 3.306019 GGTAACCACAGCCCTCAATTTTG 60.306 47.826 0.00 0.00 0.00 2.44
2246 2822 1.949525 CTGCAACTGTGTACTGCCTTT 59.050 47.619 2.01 0.00 35.13 3.11
2264 2840 0.953727 TGCTGCAAGGTTAAGCACTG 59.046 50.000 7.52 5.03 41.83 3.66
2294 2870 4.411540 ACCAGCCATATGATGATATCCCTC 59.588 45.833 3.65 0.00 0.00 4.30
2300 2876 8.629158 GTTGTTTTTACCAGCCATATGATGATA 58.371 33.333 3.65 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.