Multiple sequence alignment - TraesCS5B01G492800

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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 TraesCS5B01G492800 chr5B 100.000 2379 0 0 1 2379 660796576 660798954 0.000000e+00 4394.0
1 TraesCS5B01G492800 chr5B 88.660 97 10 1 1734 1830 459415464 459415559 1.490000e-22 117.0
2 TraesCS5B01G492800 chr6A 90.894 2394 156 22 18 2379 6441430 6443793 0.000000e+00 3157.0
3 TraesCS5B01G492800 chr6A 85.000 500 49 11 855 1353 594975514 594975988 3.560000e-133 484.0
4 TraesCS5B01G492800 chr6A 79.716 493 74 19 855 1342 594953445 594953916 1.360000e-87 333.0
5 TraesCS5B01G492800 chr6A 87.500 120 12 2 1800 1917 114843765 114843647 4.120000e-28 135.0
6 TraesCS5B01G492800 chr6A 95.349 43 1 1 1691 1733 569998878 569998837 1.530000e-07 67.6
7 TraesCS5B01G492800 chr1D 93.949 628 35 2 824 1451 416125277 416125901 0.000000e+00 946.0
8 TraesCS5B01G492800 chr1D 95.175 456 17 2 18 469 416124822 416125276 0.000000e+00 715.0
9 TraesCS5B01G492800 chr1D 95.806 310 10 2 1371 1680 416125900 416126206 4.570000e-137 497.0
10 TraesCS5B01G492800 chr1B 83.333 864 72 35 18 852 565991503 565990683 0.000000e+00 732.0
11 TraesCS5B01G492800 chr1B 97.059 34 1 0 1360 1393 565990591 565990558 9.180000e-05 58.4
12 TraesCS5B01G492800 chr2D 83.121 865 76 34 18 852 44652714 44653538 0.000000e+00 725.0
13 TraesCS5B01G492800 chr2D 93.023 43 3 0 1691 1733 11861762 11861804 1.970000e-06 63.9
14 TraesCS5B01G492800 chr3B 83.727 805 71 26 52 829 17862714 17861943 0.000000e+00 706.0
15 TraesCS5B01G492800 chr3B 95.070 284 14 0 1700 1983 7584965 7585248 4.660000e-122 448.0
16 TraesCS5B01G492800 chr3B 96.377 138 4 1 1978 2115 7589214 7589350 2.380000e-55 226.0
17 TraesCS5B01G492800 chr3B 84.967 153 20 3 1357 1508 17861832 17861682 4.100000e-33 152.0
18 TraesCS5B01G492800 chr7D 82.688 826 66 32 34 829 95107811 95108589 0.000000e+00 662.0
19 TraesCS5B01G492800 chr7D 88.783 526 51 6 1800 2321 595979546 595979025 2.580000e-179 638.0
20 TraesCS5B01G492800 chr7D 92.308 39 3 0 1357 1395 95108746 95108784 3.300000e-04 56.5
21 TraesCS5B01G492800 chr3D 88.994 527 49 8 1800 2321 610732704 610732182 0.000000e+00 643.0
22 TraesCS5B01G492800 chr3D 88.046 527 55 6 1800 2321 29688494 29687971 3.360000e-173 617.0
23 TraesCS5B01G492800 chr3D 92.000 50 4 0 1694 1743 473829209 473829160 1.180000e-08 71.3
24 TraesCS5B01G492800 chr6D 86.939 490 51 6 866 1353 448899143 448899621 2.690000e-149 538.0
25 TraesCS5B01G492800 chr5D 85.905 525 44 14 1800 2321 529531677 529531180 1.250000e-147 532.0
26 TraesCS5B01G492800 chr5D 95.455 44 0 2 1691 1733 115410326 115410284 4.240000e-08 69.4
27 TraesCS5B01G492800 chr6B 79.555 494 70 21 866 1353 680704624 680705092 8.200000e-85 324.0
28 TraesCS5B01G492800 chr4B 90.323 62 6 0 182 243 624754134 624754073 5.450000e-12 82.4
29 TraesCS5B01G492800 chr4D 93.617 47 3 0 1690 1736 98936717 98936763 1.180000e-08 71.3
30 TraesCS5B01G492800 chr5A 91.667 48 4 0 182 229 670102048 670102001 1.530000e-07 67.6
31 TraesCS5B01G492800 chr4A 93.182 44 3 0 1691 1734 467543808 467543851 5.490000e-07 65.8
32 TraesCS5B01G492800 chr1A 93.182 44 3 0 1690 1733 304031930 304031887 5.490000e-07 65.8


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 TraesCS5B01G492800 chr5B 660796576 660798954 2378 False 4394.000000 4394 100.000000 1 2379 1 chr5B.!!$F2 2378
1 TraesCS5B01G492800 chr6A 6441430 6443793 2363 False 3157.000000 3157 90.894000 18 2379 1 chr6A.!!$F1 2361
2 TraesCS5B01G492800 chr1D 416124822 416126206 1384 False 719.333333 946 94.976667 18 1680 3 chr1D.!!$F1 1662
3 TraesCS5B01G492800 chr1B 565990558 565991503 945 True 395.200000 732 90.196000 18 1393 2 chr1B.!!$R1 1375
4 TraesCS5B01G492800 chr2D 44652714 44653538 824 False 725.000000 725 83.121000 18 852 1 chr2D.!!$F2 834
5 TraesCS5B01G492800 chr3B 17861682 17862714 1032 True 429.000000 706 84.347000 52 1508 2 chr3B.!!$R1 1456
6 TraesCS5B01G492800 chr3B 7584965 7589350 4385 False 337.000000 448 95.723500 1700 2115 2 chr3B.!!$F1 415
7 TraesCS5B01G492800 chr7D 595979025 595979546 521 True 638.000000 638 88.783000 1800 2321 1 chr7D.!!$R1 521
8 TraesCS5B01G492800 chr7D 95107811 95108784 973 False 359.250000 662 87.498000 34 1395 2 chr7D.!!$F1 1361
9 TraesCS5B01G492800 chr3D 610732182 610732704 522 True 643.000000 643 88.994000 1800 2321 1 chr3D.!!$R3 521
10 TraesCS5B01G492800 chr3D 29687971 29688494 523 True 617.000000 617 88.046000 1800 2321 1 chr3D.!!$R1 521

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
586 605 0.861837 CACGAAGAAGTCAGTGGCAC 59.138 55.0 10.29 10.29 31.34 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1559 0.323816 TGAGACCGACCAGCAGAGAT 60.324 55.0 0.0 0.0 0.0 2.75 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
296 303 7.701539 TTTAGGACATCATAAATTGTGCTGT 57.298 32.000 7.25 0.00 43.27 4.40
342 352 9.819267 AGTTTGTATATCTTAGGTTCTAGCAAC 57.181 33.333 0.00 0.00 0.00 4.17
583 602 1.409412 CGACACGAAGAAGTCAGTGG 58.591 55.000 0.00 0.00 36.02 4.00
586 605 0.861837 CACGAAGAAGTCAGTGGCAC 59.138 55.000 10.29 10.29 31.34 5.01
643 684 4.755266 TGGAGCAGGTAAATCCTTCTAC 57.245 45.455 0.00 0.00 45.67 2.59
753 794 9.172060 AGGCTAGATATATACTTTTTCCTGGTT 57.828 33.333 0.00 0.00 0.00 3.67
771 819 5.689961 CCTGGTTGTTTTTATTGAAGTTCGG 59.310 40.000 0.00 0.00 0.00 4.30
834 986 1.878088 AGAGCTTCTGTTGTGCATGTG 59.122 47.619 0.00 0.00 0.00 3.21
890 1042 8.697846 TTTTCTCGATCACGACAATTATTAGT 57.302 30.769 0.00 0.00 43.81 2.24
902 1054 7.866393 ACGACAATTATTAGTGGAGCATAGTAC 59.134 37.037 0.00 0.00 0.00 2.73
962 1114 2.515996 GAATCAAGGGACGGCACCGA 62.516 60.000 17.40 0.00 42.83 4.69
985 1137 1.616187 CGTCTCCTCTCCCTTGTGGTA 60.616 57.143 0.00 0.00 34.77 3.25
1012 1164 1.694169 GGAGGAATGGGAGGAGGCA 60.694 63.158 0.00 0.00 0.00 4.75
1036 1188 1.827399 GCTCTCCCTGTTCGTTCCCA 61.827 60.000 0.00 0.00 0.00 4.37
1063 1215 4.087892 GCGGCCAGAGCTTCCTGA 62.088 66.667 2.24 0.00 39.73 3.86
1143 1295 3.254903 TGTGCTTTCTCGTGCTTCTACTA 59.745 43.478 0.00 0.00 0.00 1.82
1145 1297 4.865365 GTGCTTTCTCGTGCTTCTACTAAT 59.135 41.667 0.00 0.00 0.00 1.73
1172 1324 0.538287 GGCTTGCTCCTTCAACACCT 60.538 55.000 0.00 0.00 0.00 4.00
1183 1335 5.197451 TCCTTCAACACCTGTTACATGTTT 58.803 37.500 2.30 0.00 36.32 2.83
1186 1338 6.239008 CCTTCAACACCTGTTACATGTTTGAT 60.239 38.462 2.30 0.00 36.32 2.57
1223 1375 2.900106 GCAGAGGGTGGCAAGGACT 61.900 63.158 0.00 0.00 0.00 3.85
1239 1391 1.608717 GACTGCCTCGGTGACCTCAT 61.609 60.000 0.00 0.00 0.00 2.90
1259 1411 3.140225 GACGACCTCCTCCGGCATC 62.140 68.421 0.00 0.00 33.27 3.91
1266 1418 0.036010 CTCCTCCGGCATCTGTTGTT 60.036 55.000 0.00 0.00 0.00 2.83
1275 1427 3.149196 GGCATCTGTTGTTCCTTCTTCA 58.851 45.455 0.00 0.00 0.00 3.02
1330 1482 2.511600 AGGTGGCGCGAACTATGC 60.512 61.111 8.73 0.00 0.00 3.14
1398 1550 1.705997 AAGTTCTCCGCCAACCTGGT 61.706 55.000 0.00 0.00 40.46 4.00
1404 1556 3.964875 CGCCAACCTGGTGTGTGC 61.965 66.667 0.00 0.00 42.85 4.57
1405 1557 2.832661 GCCAACCTGGTGTGTGCA 60.833 61.111 0.00 0.00 40.46 4.57
1407 1559 0.893270 GCCAACCTGGTGTGTGCATA 60.893 55.000 0.00 0.00 40.46 3.14
1411 1638 2.679837 CAACCTGGTGTGTGCATATCTC 59.320 50.000 0.00 0.00 0.00 2.75
1430 1657 2.343758 GCTGGTCGGTCTCAAGCA 59.656 61.111 0.00 0.00 0.00 3.91
1487 1714 2.984562 TGCCGCAGATTACTTCAATCA 58.015 42.857 0.00 0.00 44.81 2.57
1491 1718 4.094887 GCCGCAGATTACTTCAATCAGAAA 59.905 41.667 0.31 0.00 44.81 2.52
1674 1902 1.066143 AGGGTGTTCGCTCTTATGGTG 60.066 52.381 0.00 0.00 31.01 4.17
1698 1927 6.043474 TGACACCTAACACCCTATTAAACTGT 59.957 38.462 0.00 0.00 0.00 3.55
1761 1990 3.456277 AGATTAATCTTCTCCCCGCTGTT 59.544 43.478 12.37 0.00 31.97 3.16
1944 2175 6.267471 TCCTGAAGGTGCACTCATTAAAATTT 59.733 34.615 17.98 0.00 36.34 1.82
1985 6187 6.584185 TTGTTAGGATTTAGAAAGTTGGCC 57.416 37.500 0.00 0.00 0.00 5.36
2123 6326 9.905713 TTAATGTCTGAACTTAAAGCTGGATAT 57.094 29.630 0.00 0.00 0.00 1.63
2125 6328 7.615582 TGTCTGAACTTAAAGCTGGATATTG 57.384 36.000 0.00 0.00 0.00 1.90
2141 6344 6.759272 TGGATATTGCTATCTGGAAGTGTAC 58.241 40.000 0.00 0.00 35.14 2.90
2150 6353 2.696707 TCTGGAAGTGTACCGAGTTTGT 59.303 45.455 0.00 0.00 33.76 2.83
2227 6434 0.901827 TGAGCTGAGCCGTTGGATTA 59.098 50.000 0.00 0.00 0.00 1.75
2291 6499 8.396272 AGACACTTATTTCATAGTTTGCACTT 57.604 30.769 0.00 0.00 34.06 3.16
2294 6502 8.076178 ACACTTATTTCATAGTTTGCACTTGAC 58.924 33.333 0.00 0.00 34.06 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 111 2.403259 GCTTGGGGAAAATTGTTCACG 58.597 47.619 0.00 0.00 0.00 4.35
195 202 9.308318 TCAATCACTTTGATCATATTTTGCATG 57.692 29.630 0.00 0.00 39.44 4.06
342 352 6.808212 ACAAAATTCATACAATCGGAAAGCTG 59.192 34.615 0.00 0.00 0.00 4.24
372 382 3.873805 GCCTGTCTCTTTGGCAAAC 57.126 52.632 8.93 0.17 45.46 2.93
605 624 8.669571 ACCTGCTCCAATAAGTAAATATGGTAT 58.330 33.333 0.00 0.00 0.00 2.73
643 684 5.836347 AGTTAGCTTTGCTTCTCCAAAAAG 58.164 37.500 0.00 0.00 40.44 2.27
753 794 4.339814 AGCACCCGAACTTCAATAAAAACA 59.660 37.500 0.00 0.00 0.00 2.83
771 819 5.348164 ACAAATTGTAAGTTGTGAAGCACC 58.652 37.500 9.33 0.00 44.42 5.01
805 853 4.328440 CACAACAGAAGCTCTTCGAATAGG 59.672 45.833 11.97 0.99 43.97 2.57
808 856 2.481952 GCACAACAGAAGCTCTTCGAAT 59.518 45.455 0.00 0.00 43.97 3.34
816 864 0.956633 CCACATGCACAACAGAAGCT 59.043 50.000 0.00 0.00 0.00 3.74
834 986 1.141053 ACGTGATATGGCTTCTTCCCC 59.859 52.381 0.00 0.00 0.00 4.81
890 1042 5.972935 TCTTTGAAATCGTACTATGCTCCA 58.027 37.500 0.00 0.00 0.00 3.86
902 1054 5.289434 TGTCGTGATCATCTCTTTGAAATCG 59.711 40.000 0.00 0.00 0.00 3.34
962 1114 1.827969 CACAAGGGAGAGGAGACGATT 59.172 52.381 0.00 0.00 0.00 3.34
985 1137 3.587506 CCTCCCATTCCTCCGGTATTTAT 59.412 47.826 0.00 0.00 0.00 1.40
1012 1164 1.270907 ACGAACAGGGAGAGCAAGAT 58.729 50.000 0.00 0.00 0.00 2.40
1063 1215 2.172930 AGAGAATGCAGCATCACCTGAT 59.827 45.455 8.77 0.00 34.77 2.90
1164 1316 7.220740 TCTATCAAACATGTAACAGGTGTTGA 58.779 34.615 0.00 3.11 38.90 3.18
1172 1324 8.075574 CACAAGCTTTCTATCAAACATGTAACA 58.924 33.333 0.00 0.00 0.00 2.41
1183 1335 3.282021 GGCCATCACAAGCTTTCTATCA 58.718 45.455 0.00 0.00 0.00 2.15
1186 1338 1.737838 CGGCCATCACAAGCTTTCTA 58.262 50.000 2.24 0.00 0.00 2.10
1223 1375 1.191489 TCAATGAGGTCACCGAGGCA 61.191 55.000 0.00 0.00 0.00 4.75
1259 1411 1.882623 GGGCTGAAGAAGGAACAACAG 59.117 52.381 0.00 0.00 0.00 3.16
1284 1436 1.227853 ACACAAGTCTTCGGGGCAC 60.228 57.895 0.00 0.00 0.00 5.01
1290 1442 3.013276 TGTCTAGCACACAAGTCTTCG 57.987 47.619 0.00 0.00 0.00 3.79
1404 1556 1.959985 AGACCGACCAGCAGAGATATG 59.040 52.381 0.00 0.00 0.00 1.78
1405 1557 2.235016 GAGACCGACCAGCAGAGATAT 58.765 52.381 0.00 0.00 0.00 1.63
1407 1559 0.323816 TGAGACCGACCAGCAGAGAT 60.324 55.000 0.00 0.00 0.00 2.75
1411 1638 1.739562 GCTTGAGACCGACCAGCAG 60.740 63.158 0.00 0.00 0.00 4.24
1430 1657 4.202461 TGGCAGAGAACTTCTACAACCAAT 60.202 41.667 0.00 0.00 33.83 3.16
1487 1714 3.313526 GCAATACCATCATGACGCTTTCT 59.686 43.478 0.00 0.00 0.00 2.52
1491 1718 2.627515 AGCAATACCATCATGACGCT 57.372 45.000 0.00 0.00 0.00 5.07
1674 1902 6.470278 ACAGTTTAATAGGGTGTTAGGTGTC 58.530 40.000 0.00 0.00 0.00 3.67
1680 1908 8.000127 ACTTTTGGACAGTTTAATAGGGTGTTA 59.000 33.333 0.00 0.00 0.00 2.41
1810 2039 9.710900 AAAAAGAATTAATAAAGAAGGGCACAG 57.289 29.630 0.00 0.00 0.00 3.66
1967 2198 6.582929 AGATAGGCCAACTTTCTAAATCCT 57.417 37.500 5.01 0.00 35.99 3.24
2031 6233 9.416794 CATACGCTATTCTAAAGATCATTCTGT 57.583 33.333 0.00 0.00 30.72 3.41
2123 6326 3.093814 TCGGTACACTTCCAGATAGCAA 58.906 45.455 0.00 0.00 0.00 3.91
2125 6328 2.688958 ACTCGGTACACTTCCAGATAGC 59.311 50.000 0.00 0.00 0.00 2.97
2197 6404 2.022754 GCTCAGCTCAGGCCATCAATT 61.023 52.381 5.01 0.00 39.73 2.32
2227 6434 6.822667 TGTTCATAGTTTGCACTTCATCAT 57.177 33.333 0.00 0.00 34.06 2.45
2267 6474 8.289618 TCAAGTGCAAACTATGAAATAAGTGTC 58.710 33.333 0.00 0.00 0.00 3.67
2291 6499 2.689553 ATGTGTGCATCCATACGTCA 57.310 45.000 0.00 0.00 36.02 4.35
2321 6529 4.648651 TGACCAGTAAAGCTAAAAGGACC 58.351 43.478 0.00 0.00 0.00 4.46
2334 6542 3.139397 ACCTCCCACAATTTGACCAGTAA 59.861 43.478 2.79 0.00 0.00 2.24
2335 6543 2.714250 ACCTCCCACAATTTGACCAGTA 59.286 45.455 2.79 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.