Multiple sequence alignment - TraesCS7D01G158600

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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 TraesCS7D01G158600 chr7D 100.000 2636 0 0 1 2636 107242141 107239506 0 4868
1 TraesCS7D01G158600 chr7D 96.494 713 21 2 1 709 509205933 509205221 0 1175
2 TraesCS7D01G158600 chr5D 95.372 2636 90 10 1 2628 437728567 437725956 0 4163
3 TraesCS7D01G158600 chr5D 94.166 2657 89 18 1 2636 92293763 92296374 0 3988
4 TraesCS7D01G158600 chr5D 94.998 2339 85 13 295 2627 51585548 51583236 0 3642
5 TraesCS7D01G158600 chr5A 94.231 2652 106 12 1 2636 40241598 40238978 0 4006
6 TraesCS7D01G158600 chr5A 94.953 2219 77 7 295 2511 687969721 687971906 0 3445
7 TraesCS7D01G158600 chr5A 95.406 1785 64 2 728 2511 562122532 562120765 0 2826
8 TraesCS7D01G158600 chr5A 96.444 703 16 3 1 700 562123228 562122532 0 1151
9 TraesCS7D01G158600 chr3B 93.467 2648 105 18 1 2636 823895990 823893399 0 3869
10 TraesCS7D01G158600 chr1A 94.115 2515 100 7 1 2511 16224753 16227223 0 3781
11 TraesCS7D01G158600 chr1A 94.250 1826 87 2 687 2511 16218818 16220626 0 2774
12 TraesCS7D01G158600 chr1A 94.915 708 26 4 1 705 16218108 16218808 0 1099
13 TraesCS7D01G158600 chr1D 94.728 2352 94 9 295 2636 152626274 152628605 0 3629
14 TraesCS7D01G158600 chr1D 95.601 2114 88 4 1 2110 152476535 152478647 0 3384
15 TraesCS7D01G158600 chr1D 94.030 536 17 5 2106 2636 152482806 152483331 0 798
16 TraesCS7D01G158600 chr6A 93.612 2348 95 14 295 2636 577152219 577154517 0 3454
17 TraesCS7D01G158600 chr6A 95.518 1785 62 3 728 2511 553572080 553570313 0 2837
18 TraesCS7D01G158600 chr2D 93.243 1702 78 10 1 1692 104541979 104540305 0 2471
19 TraesCS7D01G158600 chr2B 93.203 1633 63 13 1013 2636 559330218 559328625 0 2357
20 TraesCS7D01G158600 chr2B 92.157 1632 56 14 1013 2636 152882418 152880851 0 2239
21 TraesCS7D01G158600 chr7A 93.475 1410 56 4 1 1405 626868713 626870091 0 2061


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 TraesCS7D01G158600 chr7D 107239506 107242141 2635 True 4868.0 4868 100.0000 1 2636 1 chr7D.!!$R1 2635
1 TraesCS7D01G158600 chr7D 509205221 509205933 712 True 1175.0 1175 96.4940 1 709 1 chr7D.!!$R2 708
2 TraesCS7D01G158600 chr5D 437725956 437728567 2611 True 4163.0 4163 95.3720 1 2628 1 chr5D.!!$R2 2627
3 TraesCS7D01G158600 chr5D 92293763 92296374 2611 False 3988.0 3988 94.1660 1 2636 1 chr5D.!!$F1 2635
4 TraesCS7D01G158600 chr5D 51583236 51585548 2312 True 3642.0 3642 94.9980 295 2627 1 chr5D.!!$R1 2332
5 TraesCS7D01G158600 chr5A 40238978 40241598 2620 True 4006.0 4006 94.2310 1 2636 1 chr5A.!!$R1 2635
6 TraesCS7D01G158600 chr5A 687969721 687971906 2185 False 3445.0 3445 94.9530 295 2511 1 chr5A.!!$F1 2216
7 TraesCS7D01G158600 chr5A 562120765 562123228 2463 True 1988.5 2826 95.9250 1 2511 2 chr5A.!!$R2 2510
8 TraesCS7D01G158600 chr3B 823893399 823895990 2591 True 3869.0 3869 93.4670 1 2636 1 chr3B.!!$R1 2635
9 TraesCS7D01G158600 chr1A 16224753 16227223 2470 False 3781.0 3781 94.1150 1 2511 1 chr1A.!!$F1 2510
10 TraesCS7D01G158600 chr1A 16218108 16220626 2518 False 1936.5 2774 94.5825 1 2511 2 chr1A.!!$F2 2510
11 TraesCS7D01G158600 chr1D 152626274 152628605 2331 False 3629.0 3629 94.7280 295 2636 1 chr1D.!!$F3 2341
12 TraesCS7D01G158600 chr1D 152476535 152478647 2112 False 3384.0 3384 95.6010 1 2110 1 chr1D.!!$F1 2109
13 TraesCS7D01G158600 chr1D 152482806 152483331 525 False 798.0 798 94.0300 2106 2636 1 chr1D.!!$F2 530
14 TraesCS7D01G158600 chr6A 577152219 577154517 2298 False 3454.0 3454 93.6120 295 2636 1 chr6A.!!$F1 2341
15 TraesCS7D01G158600 chr6A 553570313 553572080 1767 True 2837.0 2837 95.5180 728 2511 1 chr6A.!!$R1 1783
16 TraesCS7D01G158600 chr2D 104540305 104541979 1674 True 2471.0 2471 93.2430 1 1692 1 chr2D.!!$R1 1691
17 TraesCS7D01G158600 chr2B 559328625 559330218 1593 True 2357.0 2357 93.2030 1013 2636 1 chr2B.!!$R2 1623
18 TraesCS7D01G158600 chr2B 152880851 152882418 1567 True 2239.0 2239 92.1570 1013 2636 1 chr2B.!!$R1 1623
19 TraesCS7D01G158600 chr7A 626868713 626870091 1378 False 2061.0 2061 93.4750 1 1405 1 chr7A.!!$F1 1404

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
218 219 2.201921 ATCATCCATCTGCCTCATGC 57.798 50.0 0.0 0.0 41.77 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1851 1.071019 AATACTCGTCAGCACACGCG 61.071 55.0 3.53 3.53 45.49 6.01 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
182 183 8.537728 TTTATATGATGTTCATTTCTTGGCCT 57.462 30.769 3.32 0.00 38.26 5.19
218 219 2.201921 ATCATCCATCTGCCTCATGC 57.798 50.000 0.00 0.00 41.77 4.06
461 486 4.161942 TGGGTTCAATTCTTGGGCAATATG 59.838 41.667 0.00 0.00 0.00 1.78
484 510 3.319972 TGGTACTTTACACTCTTCACGCT 59.680 43.478 0.00 0.00 0.00 5.07
488 514 4.632153 ACTTTACACTCTTCACGCTCAAT 58.368 39.130 0.00 0.00 0.00 2.57
515 541 2.668120 GCTGCAGCTCTCCCTCCTT 61.668 63.158 31.33 0.00 38.21 3.36
719 747 5.861222 ATATGTATGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
720 748 2.979240 TGTATGTGTGTGTGTGTGTGT 58.021 42.857 0.00 0.00 0.00 3.72
855 939 3.007290 TGCTCTGCTCATGTTGTTAGACT 59.993 43.478 0.00 0.00 0.00 3.24
856 940 3.616379 GCTCTGCTCATGTTGTTAGACTC 59.384 47.826 0.00 0.00 0.00 3.36
871 955 7.223260 TGTTAGACTCGATTTTCACTTCCTA 57.777 36.000 0.00 0.00 0.00 2.94
916 1000 5.685511 GCTTACAAGATTTTTCTTTGCACGA 59.314 36.000 0.00 0.00 0.00 4.35
1042 1126 4.933563 TTGTGGCGCTGCTGCTCA 62.934 61.111 14.03 8.93 36.97 4.26
1071 1155 3.009473 ACATGTCTTGGAGTGCCATTAGT 59.991 43.478 0.00 0.00 45.46 2.24
1176 1261 5.708230 CAGTTAACTAAGTTGTGCCCCATTA 59.292 40.000 8.04 0.00 0.00 1.90
1259 1344 5.705441 TGTGCCTTAATTCTAAGTTCTGGTG 59.295 40.000 0.00 0.00 33.85 4.17
1324 1409 4.836125 ACTTGGTACTGCATGAGTTTTG 57.164 40.909 0.00 0.00 35.96 2.44
1396 1481 1.215244 CATGCTACCTGATGAGTGCG 58.785 55.000 0.00 0.00 0.00 5.34
1449 1535 8.617809 GCATAGGTTTATTCGGTTTGAATTCTA 58.382 33.333 7.05 0.00 45.06 2.10
1452 1538 8.398878 AGGTTTATTCGGTTTGAATTCTACAA 57.601 30.769 7.05 0.00 45.06 2.41
1506 1592 6.206634 TCTCAACTTGTTTTCACTGTCACTTT 59.793 34.615 0.00 0.00 0.00 2.66
1559 1646 5.420409 GGTTAATGTTGGTGGTTTTGTTCA 58.580 37.500 0.00 0.00 0.00 3.18
1571 1658 3.555547 GGTTTTGTTCAACTTGGATGCAC 59.444 43.478 0.00 0.00 0.00 4.57
1638 1728 2.566833 TGGCTGTGTGCATCTAAAGT 57.433 45.000 0.00 0.00 45.15 2.66
1697 1787 3.004210 ACTCAATCCAGATCATCGTCGAG 59.996 47.826 0.00 0.00 0.00 4.04
1723 1813 5.559148 ATCATCCACAGGTATCTTCCTTC 57.441 43.478 0.00 0.00 35.37 3.46
1761 1851 4.575885 TCCTGCCTTTGTGATGTTAGTAC 58.424 43.478 0.00 0.00 0.00 2.73
1789 1879 5.105917 TGTGCTGACGAGTATTGTTAGATCA 60.106 40.000 0.00 0.00 38.30 2.92
1856 1950 0.109781 GGCGCAATGTGTTGTAGTGG 60.110 55.000 10.83 0.00 37.65 4.00
1899 1993 6.861572 GCATATGTGCCATGCATATTCATATC 59.138 38.462 2.47 11.00 46.47 1.63
2019 2116 4.144297 TGTCCTTTTCTTGAATGGTCTGG 58.856 43.478 0.00 0.00 34.85 3.86
2366 2509 7.112122 TGTATTATGTGATCTGGTTGCTCTTT 58.888 34.615 0.00 0.00 0.00 2.52
2460 2608 3.385115 AGATGGGACCCACTTACCTAAG 58.615 50.000 17.78 0.00 35.80 2.18
2472 2620 6.007703 CCACTTACCTAAGAAATGGAAACCA 58.992 40.000 0.00 0.00 36.10 3.67
2589 2742 2.252535 AAAAGGCTGCCATATTGGGT 57.747 45.000 22.65 0.00 38.19 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.454600 CCATGTGCAGGCTTCATCAC 59.545 55.000 0.00 0.00 0.00 3.06
44 45 1.227556 ACACCGAGGCACTGTTGTC 60.228 57.895 0.00 0.00 41.55 3.18
165 166 2.225343 TGGGAGGCCAAGAAATGAACAT 60.225 45.455 5.01 0.00 0.00 2.71
182 183 3.084536 TGATTAGCAAACATGCTGGGA 57.915 42.857 13.27 0.48 45.81 4.37
218 219 9.976776 TGAAGTTACTAGGTAGGGATCATATAG 57.023 37.037 0.00 0.00 0.00 1.31
334 359 9.539825 CACTTATTGATGAAGCTACTAATCAGT 57.460 33.333 0.00 0.00 38.91 3.41
461 486 3.427863 GCGTGAAGAGTGTAAAGTACCAC 59.572 47.826 0.00 0.00 0.00 4.16
484 510 6.106648 AGAGCTGCAGCATACTAATATTGA 57.893 37.500 38.24 0.00 45.16 2.57
488 514 3.259374 GGGAGAGCTGCAGCATACTAATA 59.741 47.826 38.24 0.00 45.16 0.98
515 541 6.526056 ACTAGTACCTGGATGTATGGAGTA 57.474 41.667 0.00 0.00 0.00 2.59
701 729 2.538737 GCACACACACACACACACATAC 60.539 50.000 0.00 0.00 0.00 2.39
705 733 0.451383 ATGCACACACACACACACAC 59.549 50.000 0.00 0.00 0.00 3.82
707 735 0.731994 TCATGCACACACACACACAC 59.268 50.000 0.00 0.00 0.00 3.82
709 737 2.159393 AGTTTCATGCACACACACACAC 60.159 45.455 0.00 0.00 0.00 3.82
711 739 2.097304 TCAGTTTCATGCACACACACAC 59.903 45.455 0.00 0.00 0.00 3.82
712 740 2.355444 CTCAGTTTCATGCACACACACA 59.645 45.455 0.00 0.00 0.00 3.72
713 741 2.613595 TCTCAGTTTCATGCACACACAC 59.386 45.455 0.00 0.00 0.00 3.82
714 742 2.916640 TCTCAGTTTCATGCACACACA 58.083 42.857 0.00 0.00 0.00 3.72
715 743 4.224433 CAATCTCAGTTTCATGCACACAC 58.776 43.478 0.00 0.00 0.00 3.82
716 744 3.304861 GCAATCTCAGTTTCATGCACACA 60.305 43.478 0.00 0.00 34.10 3.72
717 745 3.057736 AGCAATCTCAGTTTCATGCACAC 60.058 43.478 0.00 0.00 36.30 3.82
718 746 3.151554 AGCAATCTCAGTTTCATGCACA 58.848 40.909 0.00 0.00 36.30 4.57
719 747 3.844577 AGCAATCTCAGTTTCATGCAC 57.155 42.857 0.00 0.00 36.30 4.57
720 748 3.376234 GCTAGCAATCTCAGTTTCATGCA 59.624 43.478 10.63 0.00 36.30 3.96
855 939 4.383770 GGGATGGTAGGAAGTGAAAATCGA 60.384 45.833 0.00 0.00 0.00 3.59
856 940 3.877508 GGGATGGTAGGAAGTGAAAATCG 59.122 47.826 0.00 0.00 0.00 3.34
871 955 2.196742 TGATAGAAGGCTGGGATGGT 57.803 50.000 0.00 0.00 0.00 3.55
916 1000 1.002087 GCAAGGTACTGGTGCTACTGT 59.998 52.381 8.20 0.00 38.97 3.55
1042 1126 1.701847 ACTCCAAGACATGTTGAGGCT 59.298 47.619 0.00 0.00 0.00 4.58
1071 1155 3.315142 GATGAGCGTGAGGGTGGCA 62.315 63.158 0.00 0.00 0.00 4.92
1324 1409 9.615295 GTAAATACTCTCTATGTTAGCAGTAGC 57.385 37.037 0.00 0.00 42.56 3.58
1355 1440 4.277174 TGCATACAAAATCTTTGTGTCGGT 59.723 37.500 13.64 0.00 34.11 4.69
1358 1443 5.865552 AGCATGCATACAAAATCTTTGTGTC 59.134 36.000 21.98 4.79 34.11 3.67
1559 1646 2.200373 GGTACCAGTGCATCCAAGTT 57.800 50.000 7.15 0.00 0.00 2.66
1697 1787 5.777732 AGGAAGATACCTGTGGATGATAGTC 59.222 44.000 0.00 0.00 39.01 2.59
1723 1813 3.198872 GCAGGAGAGAATAAAGGGAACG 58.801 50.000 0.00 0.00 0.00 3.95
1761 1851 1.071019 AATACTCGTCAGCACACGCG 61.071 55.000 3.53 3.53 45.49 6.01
1789 1879 2.945008 CGACCATACATTCAACTGGCAT 59.055 45.455 0.00 0.00 31.72 4.40
1899 1993 9.011407 GTAGTTCATATAAGAAACAGAGACACG 57.989 37.037 0.00 0.00 0.00 4.49
2019 2116 8.860088 AGAAAAACTGGGGCAAATATATATGAC 58.140 33.333 0.00 0.00 0.00 3.06
2384 2531 8.680903 CAGTATTTAGATTGGCAGAGACAAAAT 58.319 33.333 0.00 0.00 32.77 1.82
2460 2608 5.278808 GGTTCTGGTAACTGGTTTCCATTTC 60.279 44.000 11.21 5.96 38.92 2.17
2472 2620 5.073965 TCCCAATTGTTAGGTTCTGGTAACT 59.926 40.000 4.43 0.00 31.54 2.24
2589 2742 1.077068 GTCGGGATCATGGGCCAAA 60.077 57.895 11.89 1.38 0.00 3.28


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

AutoCloner maintained by Alex Coulton.