Multiple sequence alignment - TraesCS7B01G230100

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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 TraesCS7B01G230100 chr7B 100.000 4973 0 0 1 4973 432505504 432500532 0.000000e+00 9184.0
1 TraesCS7B01G230100 chr7D 95.500 5022 131 33 1 4973 416633991 416629016 0.000000e+00 7934.0
2 TraesCS7B01G230100 chr7D 88.235 85 10 0 199 283 416633831 416633747 8.810000e-18 102.0
3 TraesCS7B01G230100 chr7A 95.135 4645 145 44 241 4837 481251864 481247253 0.000000e+00 7251.0
4 TraesCS7B01G230100 chr7A 90.148 203 15 2 1 199 481252023 481251822 4.940000e-65 259.0
5 TraesCS7B01G230100 chr3D 89.744 78 8 0 4838 4915 524778788 524778711 3.170000e-17 100.0
6 TraesCS7B01G230100 chr1D 89.744 78 8 0 4839 4916 250256929 250257006 3.170000e-17 100.0
7 TraesCS7B01G230100 chr2B 90.541 74 6 1 4842 4915 215214341 215214269 4.100000e-16 97.1
8 TraesCS7B01G230100 chr3A 87.654 81 9 1 4836 4915 40999127 40999047 5.300000e-15 93.5
9 TraesCS7B01G230100 chr5D 84.615 91 9 4 4830 4915 7006503 7006413 8.870000e-13 86.1
10 TraesCS7B01G230100 chr1A 91.803 61 5 0 4855 4915 135508459 135508399 8.870000e-13 86.1
11 TraesCS7B01G230100 chr1A 95.238 42 1 1 4875 4915 314879217 314879176 1.160000e-06 65.8
12 TraesCS7B01G230100 chr4D 100.000 35 0 0 4883 4917 64709317 64709351 1.160000e-06 65.8
13 TraesCS7B01G230100 chrUn 81.707 82 7 2 4842 4915 65434690 65434609 1.490000e-05 62.1


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 TraesCS7B01G230100 chr7B 432500532 432505504 4972 True 9184 9184 100.0000 1 4973 1 chr7B.!!$R1 4972
1 TraesCS7B01G230100 chr7D 416629016 416633991 4975 True 4018 7934 91.8675 1 4973 2 chr7D.!!$R1 4972
2 TraesCS7B01G230100 chr7A 481247253 481252023 4770 True 3755 7251 92.6415 1 4837 2 chr7A.!!$R1 4836

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
177 182 0.094730 GGCATGAAACACGAGCGTAC 59.905 55.000 0.00 0.00 0.00 3.67 F
1671 1709 0.179034 GACCTGGACCTGATGCATCC 60.179 60.000 23.67 10.33 0.00 3.51 F
1746 1784 0.317160 CGTCTACCAGTGCCTTCACA 59.683 55.000 0.00 0.00 45.49 3.58 F
1895 1933 1.426251 AATCAGGAGCACACCCACCA 61.426 55.000 0.00 0.00 0.00 4.17 F
3799 3839 2.875933 CACACGTACCAACCTGACATTT 59.124 45.455 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1748 1.266718 GACGCACTCCAATCAGCAAAA 59.733 47.619 0.00 0.00 0.00 2.44 R
2966 3004 1.683025 CTGAATGCCCCCATGCACA 60.683 57.895 0.00 0.00 45.48 4.57 R
3418 3458 9.383519 CATGACTAACTATCATTAACCAACACT 57.616 33.333 0.00 0.00 34.49 3.55 R
3889 3930 2.223900 GGAGGAGCATAAATTTGGCAGC 60.224 50.000 16.02 8.16 0.00 5.25 R
4664 4746 2.093447 CGAGGCAAACTAGTTGATCCCT 60.093 50.000 9.34 11.89 39.87 4.20 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
56 57 5.590663 TCGCTACATCTCTTTCTCTACACAT 59.409 40.000 0.00 0.00 0.00 3.21
68 69 7.966753 TCTTTCTCTACACATATCAACGTGTAC 59.033 37.037 0.00 0.00 44.32 2.90
115 116 2.092429 ACAACTGCTCCCTTCAACTTCA 60.092 45.455 0.00 0.00 0.00 3.02
142 143 7.448469 ACAACAACATGAAAGCCTTAATCTAGT 59.552 33.333 0.00 0.00 0.00 2.57
169 174 2.235898 AGAGAGAGGAGGCATGAAACAC 59.764 50.000 0.00 0.00 0.00 3.32
177 182 0.094730 GGCATGAAACACGAGCGTAC 59.905 55.000 0.00 0.00 0.00 3.67
179 184 1.393539 GCATGAAACACGAGCGTACAT 59.606 47.619 0.00 0.00 0.00 2.29
182 187 1.717113 TGAAACACGAGCGTACATTCG 59.283 47.619 12.80 12.80 42.26 3.34
194 199 0.319083 TACATTCGTCGCAAGGTGGT 59.681 50.000 5.42 0.00 38.47 4.16
203 208 2.358737 CAAGGTGGTGACGAGGCC 60.359 66.667 0.00 0.00 0.00 5.19
268 273 2.360794 GCAAGAGCGTACCTTCGTC 58.639 57.895 0.00 0.00 0.00 4.20
269 274 1.403972 GCAAGAGCGTACCTTCGTCG 61.404 60.000 0.00 0.00 0.00 5.12
278 283 3.423154 CCTTCGTCGCAAGGTGGC 61.423 66.667 12.59 0.00 38.58 5.01
320 325 2.379972 AGGAGAAGTATGACACTCGGG 58.620 52.381 0.00 0.00 36.04 5.14
383 388 8.757982 AAGGCTATGTTTCATACAAGATCATT 57.242 30.769 0.00 0.00 40.89 2.57
429 434 1.949525 ACTGCAGCACGAAGAAAATGT 59.050 42.857 15.27 0.00 0.00 2.71
464 469 9.161629 CATGTCATACTTTTCATGGTACTTGTA 57.838 33.333 0.00 0.00 35.47 2.41
547 553 2.027192 ACGGAGTTATGTGCATCCTTGT 60.027 45.455 0.00 0.00 37.78 3.16
559 565 5.092781 GTGCATCCTTGTGGTAAATTTACG 58.907 41.667 19.48 7.53 34.50 3.18
572 578 6.654582 TGGTAAATTTACGGGGAGTTTTAGAC 59.345 38.462 19.48 4.04 34.50 2.59
573 579 6.881065 GGTAAATTTACGGGGAGTTTTAGACT 59.119 38.462 19.48 0.00 36.52 3.24
574 580 6.812879 AAATTTACGGGGAGTTTTAGACTG 57.187 37.500 0.00 0.00 39.19 3.51
622 628 6.072893 CCCAAGAAATTGCATTTTCTCTTTGG 60.073 38.462 27.64 27.64 43.42 3.28
714 726 0.533032 GAAAGGGTGGGAGAGAGTCG 59.467 60.000 0.00 0.00 0.00 4.18
722 734 1.637724 GGGAGAGAGTCGGAGAGGGA 61.638 65.000 0.00 0.00 36.95 4.20
1166 1188 0.543749 CCCCTCAATGGTCAGTCCTC 59.456 60.000 0.00 0.00 37.07 3.71
1548 1582 8.314751 AGATATAATACCACATGTCTTACTGCC 58.685 37.037 0.00 0.00 0.00 4.85
1550 1584 5.950544 AATACCACATGTCTTACTGCCTA 57.049 39.130 0.00 0.00 0.00 3.93
1551 1585 5.950544 ATACCACATGTCTTACTGCCTAA 57.049 39.130 0.00 0.00 0.00 2.69
1553 1587 4.770795 ACCACATGTCTTACTGCCTAATC 58.229 43.478 0.00 0.00 0.00 1.75
1554 1588 4.471386 ACCACATGTCTTACTGCCTAATCT 59.529 41.667 0.00 0.00 0.00 2.40
1555 1589 5.661312 ACCACATGTCTTACTGCCTAATCTA 59.339 40.000 0.00 0.00 0.00 1.98
1581 1619 6.651975 ACTAGTAGTACATTATGGCTCACC 57.348 41.667 0.00 0.00 0.00 4.02
1591 1629 2.610438 ATGGCTCACCCTGTCATTTT 57.390 45.000 0.00 0.00 33.59 1.82
1603 1641 6.930722 CACCCTGTCATTTTGCTTTTCTTATT 59.069 34.615 0.00 0.00 0.00 1.40
1620 1658 0.323725 ATTGCTGATCGGTGGCCTTT 60.324 50.000 3.32 0.00 0.00 3.11
1671 1709 0.179034 GACCTGGACCTGATGCATCC 60.179 60.000 23.67 10.33 0.00 3.51
1746 1784 0.317160 CGTCTACCAGTGCCTTCACA 59.683 55.000 0.00 0.00 45.49 3.58
1774 1812 2.659016 TGCAGAGCACTCCTTCCG 59.341 61.111 0.00 0.00 31.71 4.30
1895 1933 1.426251 AATCAGGAGCACACCCACCA 61.426 55.000 0.00 0.00 0.00 4.17
1936 1974 3.432326 CCAGGCTAAAGATCCAGGTACAC 60.432 52.174 0.00 0.00 0.00 2.90
1959 1997 9.185680 ACACTTTAATTTTACTCACCTCAACTT 57.814 29.630 0.00 0.00 0.00 2.66
2158 2196 7.492669 TCTTCCTACTAGAAATTCAATTGAGCG 59.507 37.037 8.41 0.00 0.00 5.03
2213 2251 6.071616 TGACCTTCAAGCAAGTTAGTTTTTGT 60.072 34.615 0.00 0.00 0.00 2.83
2881 2919 6.971527 AATGACGGATTGTAAAATCGTACA 57.028 33.333 0.00 0.75 38.31 2.90
2923 2961 6.291377 TCAGGAGTCTGATACATTAAATGGC 58.709 40.000 0.00 0.00 44.39 4.40
3333 3371 5.852827 ACATGGAAGTGGTTACAATTTTGG 58.147 37.500 0.00 0.00 34.65 3.28
3334 3372 5.600484 ACATGGAAGTGGTTACAATTTTGGA 59.400 36.000 0.00 0.00 34.65 3.53
3418 3458 4.151883 CAAAATCTTGGGGAAGAACTGGA 58.848 43.478 0.00 0.00 31.77 3.86
3753 3793 6.323482 TGTGCCTGGCAAATATGTATGTAAAT 59.677 34.615 25.23 0.00 41.47 1.40
3799 3839 2.875933 CACACGTACCAACCTGACATTT 59.124 45.455 0.00 0.00 0.00 2.32
4020 4061 3.141398 GTCAGTGAGGACATTTCAAGCA 58.859 45.455 0.00 0.00 37.73 3.91
4393 4443 3.375299 GTGCTGTGGCCTTGTTAAGATAG 59.625 47.826 3.32 0.00 37.74 2.08
4394 4444 3.263170 TGCTGTGGCCTTGTTAAGATAGA 59.737 43.478 3.32 0.00 37.74 1.98
4593 4675 2.785562 CCATTGGTCCGTCAAACCTTA 58.214 47.619 0.00 0.00 37.69 2.69
4626 4708 2.936498 AGGCACCGTCGAAATTAATCTG 59.064 45.455 0.00 0.00 0.00 2.90
4674 4756 1.522569 GTGGCGCTAGGGATCAACT 59.477 57.895 11.61 0.00 0.00 3.16
4716 4799 2.764572 CCCACCCATTTCTACGAGTAGT 59.235 50.000 9.75 0.00 34.84 2.73
4851 4936 1.826720 TGTACTCCCGTCCCACAATAC 59.173 52.381 0.00 0.00 0.00 1.89
4860 4945 2.803956 CGTCCCACAATACAAGACGTTT 59.196 45.455 2.88 0.00 43.89 3.60
4861 4946 3.249080 CGTCCCACAATACAAGACGTTTT 59.751 43.478 2.88 0.00 43.89 2.43
4862 4947 4.260866 CGTCCCACAATACAAGACGTTTTT 60.261 41.667 2.88 0.00 43.89 1.94
4945 5030 8.655651 TGTTTGATAATAGAATATGCACGTCA 57.344 30.769 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.942657 TCCTTCGGACCGTATAACGAG 59.057 52.381 14.79 2.21 46.05 4.18
73 74 5.132502 TGTATTTCTCCTTCGGACCGTATA 58.867 41.667 14.79 0.00 0.00 1.47
115 116 7.054491 AGATTAAGGCTTTCATGTTGTTGTT 57.946 32.000 4.45 0.00 0.00 2.83
142 143 1.294041 TGCCTCCTCTCTCTCTCTCA 58.706 55.000 0.00 0.00 0.00 3.27
177 182 0.948623 TCACCACCTTGCGACGAATG 60.949 55.000 0.00 0.00 0.00 2.67
179 184 1.593209 GTCACCACCTTGCGACGAA 60.593 57.895 0.00 0.00 0.00 3.85
182 187 2.022129 CTCGTCACCACCTTGCGAC 61.022 63.158 0.00 0.00 0.00 5.19
194 199 1.004560 CTTGCTTGAGGCCTCGTCA 60.005 57.895 27.43 20.51 40.92 4.35
203 208 0.520404 AATGCACGCTCTTGCTTGAG 59.480 50.000 0.00 2.82 43.41 3.02
320 325 4.530857 CTCACCGGCGGATCCACC 62.531 72.222 35.78 11.12 34.01 4.61
383 388 9.157104 TGATAAAACTTCGCTACACATTATCAA 57.843 29.630 0.00 0.00 36.27 2.57
429 434 7.936496 TGAAAAGTATGACATGGCTTGATTA 57.064 32.000 7.45 0.00 0.00 1.75
459 464 2.026822 AGTGCAAGAGGGGTGATACAAG 60.027 50.000 0.00 0.00 0.00 3.16
464 469 2.254152 TCTAGTGCAAGAGGGGTGAT 57.746 50.000 0.00 0.00 0.00 3.06
523 529 1.933853 GGATGCACATAACTCCGTCAC 59.066 52.381 0.00 0.00 0.00 3.67
532 538 6.849085 AATTTACCACAAGGATGCACATAA 57.151 33.333 0.00 0.00 38.69 1.90
547 553 6.654582 GTCTAAAACTCCCCGTAAATTTACCA 59.345 38.462 20.08 3.92 0.00 3.25
559 565 4.981812 TCTTTTCCAGTCTAAAACTCCCC 58.018 43.478 0.00 0.00 35.45 4.81
658 666 6.483687 ACACACGTGAGTTAATTTCTTTGTC 58.516 36.000 25.01 0.00 46.40 3.18
714 726 1.817740 CGTCCATCTCTCTCCCTCTCC 60.818 61.905 0.00 0.00 0.00 3.71
722 734 1.379977 TTCGCCCGTCCATCTCTCT 60.380 57.895 0.00 0.00 0.00 3.10
1166 1188 4.728021 GCGCGATTAAAGAAAGAAGAAGGG 60.728 45.833 12.10 0.00 0.00 3.95
1523 1555 8.314751 AGGCAGTAAGACATGTGGTATTATATC 58.685 37.037 1.15 0.00 35.78 1.63
1554 1588 9.499479 GTGAGCCATAATGTACTACTAGTAGTA 57.501 37.037 30.50 30.50 43.98 1.82
1555 1589 7.447853 GGTGAGCCATAATGTACTACTAGTAGT 59.552 40.741 32.39 32.39 40.91 2.73
1581 1619 6.647895 AGCAATAAGAAAAGCAAAATGACAGG 59.352 34.615 0.00 0.00 0.00 4.00
1591 1629 4.009675 ACCGATCAGCAATAAGAAAAGCA 58.990 39.130 0.00 0.00 0.00 3.91
1603 1641 1.377202 GAAAGGCCACCGATCAGCA 60.377 57.895 5.01 0.00 0.00 4.41
1620 1658 5.945191 TGAGATGCACATTACATTTCCTTGA 59.055 36.000 0.00 0.00 29.81 3.02
1671 1709 4.832767 CGAGCAGCATTGTGTGTG 57.167 55.556 0.00 0.00 0.00 3.82
1704 1742 1.547372 CTCCAATCAGCAAAACCCCTG 59.453 52.381 0.00 0.00 0.00 4.45
1710 1748 1.266718 GACGCACTCCAATCAGCAAAA 59.733 47.619 0.00 0.00 0.00 2.44
1746 1784 1.378250 GCTCTGCACAGCAAGGGAT 60.378 57.895 9.30 0.00 38.41 3.85
1895 1933 4.463891 CCTGGTTGTTATCAAGGCTGAAAT 59.536 41.667 0.00 0.00 34.49 2.17
1959 1997 9.432982 AATAAAAGAAATGGGGCACATAATAGA 57.567 29.630 0.84 0.00 39.40 1.98
1963 2001 9.829507 CATTAATAAAAGAAATGGGGCACATAA 57.170 29.630 0.84 0.00 39.40 1.90
1965 2003 8.088463 TCATTAATAAAAGAAATGGGGCACAT 57.912 30.769 0.00 0.00 43.07 3.21
2089 2127 5.888724 TGACTCTTAACTCTCTAGGTGATGG 59.111 44.000 0.00 0.00 0.00 3.51
2158 2196 9.935682 CTACATAAATGACACCACATGAAATAC 57.064 33.333 0.00 0.00 0.00 1.89
2881 2919 8.353423 ACTCCTGATTGTGCATTTTAACTATT 57.647 30.769 0.00 0.00 0.00 1.73
2966 3004 1.683025 CTGAATGCCCCCATGCACA 60.683 57.895 0.00 0.00 45.48 4.57
3418 3458 9.383519 CATGACTAACTATCATTAACCAACACT 57.616 33.333 0.00 0.00 34.49 3.55
3753 3793 7.340743 TGAACAGAACAATTAGGACAAGGAAAA 59.659 33.333 0.00 0.00 0.00 2.29
3889 3930 2.223900 GGAGGAGCATAAATTTGGCAGC 60.224 50.000 16.02 8.16 0.00 5.25
3951 3992 4.592942 TCTAATTTGTCTGCTGAATGGCT 58.407 39.130 0.00 0.00 0.00 4.75
4020 4061 1.818674 GATTGCGAACCCACATTCCTT 59.181 47.619 0.00 0.00 0.00 3.36
4567 4649 1.296715 GACGGACCAATGGCAGAGT 59.703 57.895 0.00 0.00 0.00 3.24
4593 4675 3.007635 GACGGTGCCTTAACTAGCATTT 58.992 45.455 0.00 0.00 41.86 2.32
4626 4708 3.812053 GACCTGAATGCACATCTACCATC 59.188 47.826 0.00 0.00 0.00 3.51
4664 4746 2.093447 CGAGGCAAACTAGTTGATCCCT 60.093 50.000 9.34 11.89 39.87 4.20
4851 4936 4.317348 GCTTTAGCTTGCAAAAACGTCTTG 60.317 41.667 0.00 6.08 38.21 3.02


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

AutoCloner maintained by Alex Coulton.