Multiple sequence alignment - TraesCS7B01G427100

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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 TraesCS7B01G427100 chr7B 100.000 2918 0 0 1 2918 696238507 696241424 0.000000e+00 5389
1 TraesCS7B01G427100 chr7B 95.004 2682 124 6 239 2918 698682699 698685372 0.000000e+00 4202
2 TraesCS7B01G427100 chr7B 94.092 1862 106 4 644 2502 693664476 693666336 0.000000e+00 2826
3 TraesCS7B01G427100 chr7B 91.994 1886 131 5 190 2075 693714342 693716207 0.000000e+00 2628
4 TraesCS7B01G427100 chr7B 92.750 1338 76 9 1591 2918 693698819 693700145 0.000000e+00 1914
5 TraesCS7B01G427100 chr7B 91.069 1254 75 8 1675 2918 694748766 694749992 0.000000e+00 1661
6 TraesCS7B01G427100 chr7B 93.750 1072 56 4 1591 2661 693684866 693685927 0.000000e+00 1598
7 TraesCS7B01G427100 chr7B 90.805 261 14 6 1 260 693663782 693664033 1.000000e-89 340
8 TraesCS7B01G427100 chr7B 93.333 180 9 3 1 178 698682511 698682689 2.230000e-66 263
9 TraesCS7B01G427100 chrUn 92.872 2806 147 15 129 2918 77521196 77523964 0.000000e+00 4024
10 TraesCS7B01G427100 chrUn 93.487 998 54 4 1591 2587 349917742 349916755 0.000000e+00 1472
11 TraesCS7B01G427100 chrUn 91.821 648 42 4 1 647 344773363 344772726 0.000000e+00 893
12 TraesCS7B01G427100 chrUn 83.762 505 61 10 179 678 83474874 83474386 2.650000e-125 459
13 TraesCS7B01G427100 chr7D 92.908 2665 152 19 1 2661 610421840 610419209 0.000000e+00 3840
14 TraesCS7B01G427100 chr7D 90.517 2457 181 19 1 2445 608272553 608274969 0.000000e+00 3199
15 TraesCS7B01G427100 chr7D 89.722 1654 137 13 959 2606 514918648 514920274 0.000000e+00 2082
16 TraesCS7B01G427100 chr7D 91.701 976 54 9 6 963 514912846 514913812 0.000000e+00 1328
17 TraesCS7B01G427100 chr7D 95.667 300 12 1 2620 2918 608275078 608275377 5.660000e-132 481
18 TraesCS7B01G427100 chr7D 92.881 295 15 4 2623 2916 514930675 514930964 9.670000e-115 424
19 TraesCS7B01G427100 chr7D 81.272 566 68 19 178 732 610404849 610404311 9.670000e-115 424
20 TraesCS7B01G427100 chr7D 77.622 715 108 25 145 849 608280142 608280814 1.270000e-103 387
21 TraesCS7B01G427100 chr7A 91.924 2365 148 14 1 2352 700299970 700302304 0.000000e+00 3269
22 TraesCS7B01G427100 chr7A 91.797 2365 151 14 1 2352 700337788 700340122 0.000000e+00 3253
23 TraesCS7B01G427100 chr7A 89.671 668 25 13 2280 2918 700340098 700340750 0.000000e+00 811
24 TraesCS7B01G427100 chr7A 89.521 668 26 13 2280 2918 700302280 700302932 0.000000e+00 806
25 TraesCS7B01G427100 chr7A 86.184 152 21 0 563 714 700387290 700387441 6.470000e-37 165
26 TraesCS7B01G427100 chr4A 85.303 694 87 8 1893 2577 662021098 662020411 0.000000e+00 702
27 TraesCS7B01G427100 chr4A 92.574 404 29 1 2516 2918 735216127 735215724 1.950000e-161 579
28 TraesCS7B01G427100 chr4A 88.338 343 30 2 1 341 662053107 662052773 1.260000e-108 403
29 TraesCS7B01G427100 chr4A 89.686 223 21 2 2273 2493 735216342 735216120 1.710000e-72 283


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 TraesCS7B01G427100 chr7B 696238507 696241424 2917 False 5389.0 5389 100.0000 1 2918 1 chr7B.!!$F5 2917
1 TraesCS7B01G427100 chr7B 693714342 693716207 1865 False 2628.0 2628 91.9940 190 2075 1 chr7B.!!$F3 1885
2 TraesCS7B01G427100 chr7B 698682511 698685372 2861 False 2232.5 4202 94.1685 1 2918 2 chr7B.!!$F7 2917
3 TraesCS7B01G427100 chr7B 693698819 693700145 1326 False 1914.0 1914 92.7500 1591 2918 1 chr7B.!!$F2 1327
4 TraesCS7B01G427100 chr7B 694748766 694749992 1226 False 1661.0 1661 91.0690 1675 2918 1 chr7B.!!$F4 1243
5 TraesCS7B01G427100 chr7B 693684866 693685927 1061 False 1598.0 1598 93.7500 1591 2661 1 chr7B.!!$F1 1070
6 TraesCS7B01G427100 chr7B 693663782 693666336 2554 False 1583.0 2826 92.4485 1 2502 2 chr7B.!!$F6 2501
7 TraesCS7B01G427100 chrUn 77521196 77523964 2768 False 4024.0 4024 92.8720 129 2918 1 chrUn.!!$F1 2789
8 TraesCS7B01G427100 chrUn 349916755 349917742 987 True 1472.0 1472 93.4870 1591 2587 1 chrUn.!!$R3 996
9 TraesCS7B01G427100 chrUn 344772726 344773363 637 True 893.0 893 91.8210 1 647 1 chrUn.!!$R2 646
10 TraesCS7B01G427100 chr7D 610419209 610421840 2631 True 3840.0 3840 92.9080 1 2661 1 chr7D.!!$R2 2660
11 TraesCS7B01G427100 chr7D 514918648 514920274 1626 False 2082.0 2082 89.7220 959 2606 1 chr7D.!!$F2 1647
12 TraesCS7B01G427100 chr7D 608272553 608275377 2824 False 1840.0 3199 93.0920 1 2918 2 chr7D.!!$F5 2917
13 TraesCS7B01G427100 chr7D 514912846 514913812 966 False 1328.0 1328 91.7010 6 963 1 chr7D.!!$F1 957
14 TraesCS7B01G427100 chr7D 610404311 610404849 538 True 424.0 424 81.2720 178 732 1 chr7D.!!$R1 554
15 TraesCS7B01G427100 chr7D 608280142 608280814 672 False 387.0 387 77.6220 145 849 1 chr7D.!!$F4 704
16 TraesCS7B01G427100 chr7A 700299970 700302932 2962 False 2037.5 3269 90.7225 1 2918 2 chr7A.!!$F2 2917
17 TraesCS7B01G427100 chr7A 700337788 700340750 2962 False 2032.0 3253 90.7340 1 2918 2 chr7A.!!$F3 2917
18 TraesCS7B01G427100 chr4A 662020411 662021098 687 True 702.0 702 85.3030 1893 2577 1 chr4A.!!$R1 684
19 TraesCS7B01G427100 chr4A 735215724 735216342 618 True 431.0 579 91.1300 2273 2918 2 chr4A.!!$R3 645

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
217 231 0.161658 CGACAACACGTGCTTAGCTG 59.838 55.0 17.22 6.16 0.0 4.24 F
1190 1525 0.308376 GACGTCTATGACCTCGAGCC 59.692 60.0 8.70 1.18 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1576 0.107703 GACGATGATGGACTTGCCCA 60.108 55.000 0.0 0.0 41.05 5.36 R
2887 3349 1.931172 ACGGTTCGACTTGTTTGTCTG 59.069 47.619 0.0 0.0 35.00 3.51 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
69 77 0.615331 ATCCTGACGCATCTGGTTGT 59.385 50.000 5.57 0.00 42.99 3.32
76 88 3.262420 GACGCATCTGGTTGTCTACAAT 58.738 45.455 0.00 0.00 38.24 2.71
78 90 5.023533 ACGCATCTGGTTGTCTACAATAT 57.976 39.130 0.00 0.00 38.24 1.28
95 107 6.485830 ACAATATTGAGCTAGCCAAGTCTA 57.514 37.500 22.16 5.79 0.00 2.59
96 108 6.520272 ACAATATTGAGCTAGCCAAGTCTAG 58.480 40.000 22.16 8.36 39.17 2.43
175 189 1.216710 GGTTCTCCTCACCTGCTCG 59.783 63.158 0.00 0.00 0.00 5.03
176 190 1.216710 GTTCTCCTCACCTGCTCGG 59.783 63.158 0.00 0.00 39.35 4.63
217 231 0.161658 CGACAACACGTGCTTAGCTG 59.838 55.000 17.22 6.16 0.00 4.24
219 233 1.192534 GACAACACGTGCTTAGCTGAC 59.807 52.381 17.22 0.00 0.00 3.51
453 763 1.302949 GCAGAACTATGTGCCCCCA 59.697 57.895 0.00 0.00 39.82 4.96
539 874 1.948145 GATCACCATCTCGGAGTACGT 59.052 52.381 4.69 0.00 44.69 3.57
544 879 1.450848 ATCTCGGAGTACGTCGCCA 60.451 57.895 4.69 0.00 44.69 5.69
666 1001 1.545706 GCAAGAACCTCCGGGTCTCT 61.546 60.000 0.00 0.00 46.67 3.10
700 1035 3.796667 GAGGTCACTGACGACTTCC 57.203 57.895 3.04 0.00 36.33 3.46
792 1127 1.098712 AGGACGAGAGGCGCTTCTAG 61.099 60.000 23.14 23.86 46.04 2.43
829 1164 4.980805 GGCACCGCGACCTTGTCA 62.981 66.667 8.23 0.00 32.09 3.58
837 1172 1.670087 CGCGACCTTGTCATTGACTCT 60.670 52.381 17.26 0.00 33.15 3.24
906 1241 1.227823 CCAACACCGCCTCTTCACA 60.228 57.895 0.00 0.00 0.00 3.58
920 1255 4.470462 CTCTTCACAAACAATGCTAGTGC 58.530 43.478 0.00 0.00 40.20 4.40
969 1304 0.846427 TCTGGAGCCATGTCCCCTTT 60.846 55.000 0.15 0.00 35.49 3.11
1007 1342 3.367743 CACGCTTGCCATGCACCT 61.368 61.111 3.34 0.00 38.71 4.00
1148 1483 1.112113 AAGTCTACCATGATCGCCGT 58.888 50.000 0.00 0.00 0.00 5.68
1164 1499 0.609131 CCGTCATGGCCAACTTCCTT 60.609 55.000 10.96 0.00 0.00 3.36
1179 1514 6.405953 CCAACTTCCTTGACTATGACGTCTAT 60.406 42.308 17.92 10.96 35.00 1.98
1190 1525 0.308376 GACGTCTATGACCTCGAGCC 59.692 60.000 8.70 1.18 0.00 4.70
1241 1576 3.736433 CGGAAGCTCTTCATCGAGACAAT 60.736 47.826 11.27 0.00 41.20 2.71
1280 1615 3.067461 GTCATAGAGGACATCGACTGCTT 59.933 47.826 0.00 0.00 37.73 3.91
1301 1636 5.614923 TTTGTCGACTTCACAAGAAAACA 57.385 34.783 17.92 0.00 35.22 2.83
1341 1676 0.108615 CAAGCGACAAGGACTCCGAT 60.109 55.000 0.00 0.00 0.00 4.18
1447 1782 2.595463 GGCTGTGGTCTGCTTGCA 60.595 61.111 0.00 0.00 38.34 4.08
1510 1845 3.000819 TGGACCCGGCGTTGATCT 61.001 61.111 6.01 0.00 0.00 2.75
1553 1888 3.724508 CATCGAGATGTCTTACTGCCT 57.275 47.619 4.99 0.00 34.23 4.75
1579 1914 3.793144 GCTTCAAGGTGCTCGCCG 61.793 66.667 0.00 0.00 0.00 6.46
1610 1945 1.066645 AGATGTCATTGAGCACGAGCA 60.067 47.619 7.77 0.00 45.49 4.26
1650 1985 3.109044 CTACTCGAGGAGACCGACATA 57.891 52.381 20.78 0.00 33.32 2.29
1653 1988 2.105134 ACTCGAGGAGACCGACATATCT 59.895 50.000 18.41 0.00 33.32 1.98
1707 2042 5.228945 TGTCGAAGAAGAAAAAGAGGGAT 57.771 39.130 0.00 0.00 39.69 3.85
1769 2104 4.394712 CAAGGAGGAAGCGGCGGT 62.395 66.667 5.44 5.44 0.00 5.68
1995 2340 7.113658 TCCCTTACAAAACAAAAATGCAGTA 57.886 32.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 77 6.325028 AGACTTGGCTAGCTCAATATTGTAGA 59.675 38.462 15.72 0.00 0.00 2.59
95 107 2.170012 ATGGATCCAATGGCAAAGCT 57.830 45.000 20.67 0.00 0.00 3.74
96 108 2.994186 AATGGATCCAATGGCAAAGC 57.006 45.000 20.67 0.00 0.00 3.51
97 109 5.603170 ACTTAATGGATCCAATGGCAAAG 57.397 39.130 20.67 13.02 0.00 2.77
217 231 3.569701 TGATTTTGCTGAGGTTGAAGGTC 59.430 43.478 0.00 0.00 0.00 3.85
219 233 4.219070 TGATGATTTTGCTGAGGTTGAAGG 59.781 41.667 0.00 0.00 0.00 3.46
369 677 4.394712 GCCCACCTCTCCACCACG 62.395 72.222 0.00 0.00 0.00 4.94
389 698 2.499205 CCACCGCTAATCCGAGCA 59.501 61.111 0.00 0.00 42.99 4.26
453 763 0.252103 TGAGGTAGAGGCGGAAGGTT 60.252 55.000 0.00 0.00 0.00 3.50
700 1035 4.838152 CCAGATGGTGGTCCCGCG 62.838 72.222 0.00 0.00 42.17 6.46
792 1127 2.582498 CGATGGAAGACGACCCGC 60.582 66.667 0.00 0.00 0.00 6.13
829 1164 5.485209 ACGAAAGGAAGGTAAGAGTCAAT 57.515 39.130 0.00 0.00 0.00 2.57
837 1172 3.057315 CACCGAGTACGAAAGGAAGGTAA 60.057 47.826 0.00 0.00 42.66 2.85
920 1255 0.035056 CTGGTAGGGGTTCCAGCTTG 60.035 60.000 0.00 0.00 43.45 4.01
921 1256 1.208165 CCTGGTAGGGGTTCCAGCTT 61.208 60.000 5.77 0.00 46.83 3.74
1007 1342 2.171003 TGACAGCTTCCTTCTCATCGA 58.829 47.619 0.00 0.00 0.00 3.59
1148 1483 1.425066 AGTCAAGGAAGTTGGCCATGA 59.575 47.619 6.09 1.64 42.23 3.07
1164 1499 3.808174 CGAGGTCATAGACGTCATAGTCA 59.192 47.826 19.50 0.00 44.50 3.41
1179 1514 3.785859 GCCATGGGCTCGAGGTCA 61.786 66.667 15.13 0.00 46.69 4.02
1190 1525 0.240945 GTTGTTCTTGACCGCCATGG 59.759 55.000 7.63 7.63 46.41 3.66
1241 1576 0.107703 GACGATGATGGACTTGCCCA 60.108 55.000 0.00 0.00 41.05 5.36
1280 1615 4.142773 GGTGTTTTCTTGTGAAGTCGACAA 60.143 41.667 19.50 2.12 33.28 3.18
1301 1636 3.307379 GACTTCTTGTCCTTGCGGT 57.693 52.632 0.00 0.00 39.69 5.68
1318 1653 0.603569 GAGTCCTTGTCGCTTGAGGA 59.396 55.000 0.00 0.00 37.24 3.71
1341 1676 1.448985 GCTTGGGCTTGTCATCGTTA 58.551 50.000 0.00 0.00 35.22 3.18
1401 1736 0.905337 AGTTAAGCAGGCCCGAGAGT 60.905 55.000 0.00 0.00 0.00 3.24
1447 1782 1.617850 GATGATGATCCGCTCACCTCT 59.382 52.381 0.00 0.00 36.48 3.69
1553 1888 1.819305 GCACCTTGAAGCCCTCAAAGA 60.819 52.381 2.58 0.00 43.54 2.52
1579 1914 6.183360 TGCTCAATGACATCTAGGTAGTTCTC 60.183 42.308 0.00 0.00 0.00 2.87
1610 1945 1.172812 GCGCTGAACTTCCCCAAACT 61.173 55.000 0.00 0.00 0.00 2.66
1650 1985 2.125512 GCAACGTCAGCGGGAGAT 60.126 61.111 0.00 0.00 43.45 2.75
1653 1988 3.573772 CTCTGCAACGTCAGCGGGA 62.574 63.158 18.27 12.56 43.45 5.14
1707 2042 1.138859 CCTATCAAGCACACATCCGGA 59.861 52.381 6.61 6.61 0.00 5.14
1769 2104 3.170362 CCTCCTTCACCTTGGCCA 58.830 61.111 0.00 0.00 0.00 5.36
1931 2275 4.901250 TCATTCTTTTTCCTTGGCTTCCTT 59.099 37.500 0.00 0.00 0.00 3.36
1995 2340 7.038799 AGGTGCATTATTTTTCTCTCACCAAAT 60.039 33.333 10.21 0.00 43.66 2.32
2336 2747 4.158394 GCTGAAAGAATGCAGAATTGGGTA 59.842 41.667 0.00 0.00 34.07 3.69
2887 3349 1.931172 ACGGTTCGACTTGTTTGTCTG 59.069 47.619 0.00 0.00 35.00 3.51


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

AutoCloner maintained by Alex Coulton.