Multiple sequence alignment - TraesCS7A01G105800

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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 TraesCS7A01G105800 chr7A 100.000 2240 0 0 1 2240 64293399 64295638 0.000000e+00 4137
1 TraesCS7A01G105800 chr7A 89.394 990 79 11 667 1653 64210171 64209205 0.000000e+00 1223
2 TraesCS7A01G105800 chr7A 98.198 666 12 0 1 666 64270060 64270725 0.000000e+00 1164
3 TraesCS7A01G105800 chr7A 97.898 666 14 0 1 666 504442975 504443640 0.000000e+00 1153
4 TraesCS7A01G105800 chr7A 95.879 461 19 0 1780 2240 26979749 26979289 0.000000e+00 747
5 TraesCS7A01G105800 chr7A 92.308 130 7 3 1650 1779 26979960 26979834 4.910000e-42 182
6 TraesCS7A01G105800 chr7A 90.323 124 8 4 1652 1774 669743575 669743695 2.300000e-35 159
7 TraesCS7A01G105800 chr1A 97.904 668 14 0 1 668 316888445 316889112 0.000000e+00 1157
8 TraesCS7A01G105800 chr1A 97.748 666 15 0 1 666 213141232 213140567 0.000000e+00 1147
9 TraesCS7A01G105800 chr1A 97.748 666 15 0 1 666 355204361 355205026 0.000000e+00 1147
10 TraesCS7A01G105800 chr1A 96.095 461 18 0 1780 2240 61034813 61035273 0.000000e+00 752
11 TraesCS7A01G105800 chr1A 90.977 133 8 3 1650 1779 325030648 325030779 2.290000e-40 176
12 TraesCS7A01G105800 chr6A 97.898 666 14 0 1 666 286523657 286522992 0.000000e+00 1153
13 TraesCS7A01G105800 chr6A 84.945 724 85 12 685 1401 79703147 79702441 0.000000e+00 712
14 TraesCS7A01G105800 chr2A 97.754 668 15 0 1 668 751437990 751438657 0.000000e+00 1151
15 TraesCS7A01G105800 chr2A 97.397 461 12 0 1780 2240 38224264 38223804 0.000000e+00 785
16 TraesCS7A01G105800 chr2A 96.095 461 18 0 1780 2240 752029996 752030456 0.000000e+00 752
17 TraesCS7A01G105800 chr4A 97.470 672 17 0 1 672 120155425 120154754 0.000000e+00 1147
18 TraesCS7A01G105800 chr4A 97.748 666 15 0 1 666 184165991 184165326 0.000000e+00 1147
19 TraesCS7A01G105800 chr4A 89.048 630 61 4 667 1293 677731052 677730428 0.000000e+00 774
20 TraesCS7A01G105800 chr4A 96.746 461 15 0 1780 2240 115303706 115303246 0.000000e+00 769
21 TraesCS7A01G105800 chr4A 96.529 461 16 0 1780 2240 620627328 620626868 0.000000e+00 763
22 TraesCS7A01G105800 chr4A 96.312 461 16 1 1780 2240 626061916 626062375 0.000000e+00 756
23 TraesCS7A01G105800 chr4A 91.603 131 7 3 1652 1779 626061704 626061833 6.360000e-41 178
24 TraesCS7A01G105800 chr4A 89.147 129 10 3 1653 1779 620627539 620627413 8.280000e-35 158
25 TraesCS7A01G105800 chr7B 86.083 1006 90 22 667 1652 2328971 2327996 0.000000e+00 1037
26 TraesCS7A01G105800 chr7B 89.474 627 57 6 667 1290 2334880 2335500 0.000000e+00 784
27 TraesCS7A01G105800 chr5A 97.180 461 12 1 1780 2240 345363402 345362943 0.000000e+00 778
28 TraesCS7A01G105800 chr5A 96.312 461 17 0 1780 2240 40057885 40058345 0.000000e+00 758
29 TraesCS7A01G105800 chr5A 93.130 131 8 1 1644 1774 40057667 40057796 8.170000e-45 191
30 TraesCS7A01G105800 chr5A 90.000 130 9 4 1652 1779 345363614 345363487 4.950000e-37 165
31 TraesCS7A01G105800 chr5A 89.313 131 10 3 1650 1778 435248184 435248312 6.400000e-36 161
32 TraesCS7A01G105800 chr6D 86.130 721 85 9 667 1383 62324789 62324080 0.000000e+00 763
33 TraesCS7A01G105800 chr6D 88.285 589 61 5 685 1266 62424587 62424000 0.000000e+00 699
34 TraesCS7A01G105800 chr6B 86.288 722 76 12 685 1401 135995947 135995244 0.000000e+00 763
35 TraesCS7A01G105800 chr6B 85.714 721 76 12 685 1402 136100679 136099983 0.000000e+00 736
36 TraesCS7A01G105800 chr3A 84.962 133 10 7 1652 1778 720860040 720859912 2.340000e-25 126


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 TraesCS7A01G105800 chr7A 64293399 64295638 2239 False 4137.0 4137 100.0000 1 2240 1 chr7A.!!$F2 2239
1 TraesCS7A01G105800 chr7A 64209205 64210171 966 True 1223.0 1223 89.3940 667 1653 1 chr7A.!!$R1 986
2 TraesCS7A01G105800 chr7A 64270060 64270725 665 False 1164.0 1164 98.1980 1 666 1 chr7A.!!$F1 665
3 TraesCS7A01G105800 chr7A 504442975 504443640 665 False 1153.0 1153 97.8980 1 666 1 chr7A.!!$F3 665
4 TraesCS7A01G105800 chr7A 26979289 26979960 671 True 464.5 747 94.0935 1650 2240 2 chr7A.!!$R2 590
5 TraesCS7A01G105800 chr1A 316888445 316889112 667 False 1157.0 1157 97.9040 1 668 1 chr1A.!!$F2 667
6 TraesCS7A01G105800 chr1A 213140567 213141232 665 True 1147.0 1147 97.7480 1 666 1 chr1A.!!$R1 665
7 TraesCS7A01G105800 chr1A 355204361 355205026 665 False 1147.0 1147 97.7480 1 666 1 chr1A.!!$F4 665
8 TraesCS7A01G105800 chr6A 286522992 286523657 665 True 1153.0 1153 97.8980 1 666 1 chr6A.!!$R2 665
9 TraesCS7A01G105800 chr6A 79702441 79703147 706 True 712.0 712 84.9450 685 1401 1 chr6A.!!$R1 716
10 TraesCS7A01G105800 chr2A 751437990 751438657 667 False 1151.0 1151 97.7540 1 668 1 chr2A.!!$F1 667
11 TraesCS7A01G105800 chr4A 120154754 120155425 671 True 1147.0 1147 97.4700 1 672 1 chr4A.!!$R2 671
12 TraesCS7A01G105800 chr4A 184165326 184165991 665 True 1147.0 1147 97.7480 1 666 1 chr4A.!!$R3 665
13 TraesCS7A01G105800 chr4A 677730428 677731052 624 True 774.0 774 89.0480 667 1293 1 chr4A.!!$R4 626
14 TraesCS7A01G105800 chr4A 626061704 626062375 671 False 467.0 756 93.9575 1652 2240 2 chr4A.!!$F1 588
15 TraesCS7A01G105800 chr4A 620626868 620627539 671 True 460.5 763 92.8380 1653 2240 2 chr4A.!!$R5 587
16 TraesCS7A01G105800 chr7B 2327996 2328971 975 True 1037.0 1037 86.0830 667 1652 1 chr7B.!!$R1 985
17 TraesCS7A01G105800 chr7B 2334880 2335500 620 False 784.0 784 89.4740 667 1290 1 chr7B.!!$F1 623
18 TraesCS7A01G105800 chr5A 40057667 40058345 678 False 474.5 758 94.7210 1644 2240 2 chr5A.!!$F2 596
19 TraesCS7A01G105800 chr5A 345362943 345363614 671 True 471.5 778 93.5900 1652 2240 2 chr5A.!!$R1 588
20 TraesCS7A01G105800 chr6D 62324080 62324789 709 True 763.0 763 86.1300 667 1383 1 chr6D.!!$R1 716
21 TraesCS7A01G105800 chr6D 62424000 62424587 587 True 699.0 699 88.2850 685 1266 1 chr6D.!!$R2 581
22 TraesCS7A01G105800 chr6B 135995244 135995947 703 True 763.0 763 86.2880 685 1401 1 chr6B.!!$R1 716
23 TraesCS7A01G105800 chr6B 136099983 136100679 696 True 736.0 736 85.7140 685 1402 1 chr6B.!!$R2 717

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
799 812 0.038166 GGTCATCAAGGCCAAGGACA 59.962 55.0 5.01 0.0 43.39 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1758 0.037697 TGGAGCACGCATAAACGTCT 60.038 50.0 0.0 0.0 46.34 4.18 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
171 172 1.749258 GTCCGAAATGACCCTGGGC 60.749 63.158 14.08 6.42 0.00 5.36
293 294 3.784701 TTCGCTCTCATAGTCTTCACC 57.215 47.619 0.00 0.00 0.00 4.02
410 411 7.039882 ACACAGAAGAAAGAGAACTACGAAAA 58.960 34.615 0.00 0.00 0.00 2.29
451 452 2.664402 AGGCTTCATGTGGTGTCTTT 57.336 45.000 0.00 0.00 0.00 2.52
648 649 2.107552 CTCCAAAACCAACTAGGGGTGA 59.892 50.000 8.90 2.30 43.89 4.02
701 708 0.538287 AAGCAGCCCAGGAACTCAAC 60.538 55.000 0.00 0.00 34.60 3.18
708 715 1.543429 CCCAGGAACTCAACGAGCTTT 60.543 52.381 0.00 0.00 34.60 3.51
719 726 2.665185 GAGCTTTGGCCGTCGTGT 60.665 61.111 0.00 0.00 39.73 4.49
766 779 2.692557 CAGGATCTTGAGGACGAGATGT 59.307 50.000 0.00 0.00 44.54 3.06
799 812 0.038166 GGTCATCAAGGCCAAGGACA 59.962 55.000 5.01 0.00 43.39 4.02
801 814 2.238521 GTCATCAAGGCCAAGGACAAA 58.761 47.619 5.01 0.00 0.00 2.83
1031 1044 1.873270 TTCGAGCTGCTCCGCAACTA 61.873 55.000 22.97 0.77 34.98 2.24
1071 1084 1.760086 CCAGGAGGACATCGAGGCT 60.760 63.158 0.00 0.00 36.89 4.58
1145 1158 4.742201 GGTGGCGCTGAAGCTCGA 62.742 66.667 7.64 0.00 39.32 4.04
1175 1188 0.756294 TCGGACCTGAAGCAGTTCAA 59.244 50.000 0.00 0.00 42.27 2.69
1271 1289 4.484236 CATTCACTGACTCACTCACTCTC 58.516 47.826 0.00 0.00 0.00 3.20
1279 1297 2.353269 ACTCACTCACTCTCGAATAGCG 59.647 50.000 0.00 0.00 42.69 4.26
1419 1442 6.007076 TCCCAATTTGCAAAGTATACACTCA 58.993 36.000 18.19 0.00 32.29 3.41
1440 1463 5.047847 TCACGAGTTTGAAGTTTAGACTGG 58.952 41.667 0.00 0.00 35.91 4.00
1458 1481 6.458210 AGACTGGGATTACAATTTTTGCAAG 58.542 36.000 0.00 0.00 0.00 4.01
1459 1482 6.267471 AGACTGGGATTACAATTTTTGCAAGA 59.733 34.615 0.00 0.00 0.00 3.02
1460 1483 6.825610 ACTGGGATTACAATTTTTGCAAGAA 58.174 32.000 4.71 4.71 0.00 2.52
1461 1484 7.278875 ACTGGGATTACAATTTTTGCAAGAAA 58.721 30.769 6.49 7.71 0.00 2.52
1462 1485 7.938490 ACTGGGATTACAATTTTTGCAAGAAAT 59.062 29.630 6.49 9.53 0.00 2.17
1463 1486 8.097078 TGGGATTACAATTTTTGCAAGAAATG 57.903 30.769 14.42 14.42 0.00 2.32
1471 1494 4.320608 TTTTGCAAGAAATGGTCTGACC 57.679 40.909 19.96 19.96 36.40 4.02
1567 1605 4.274950 CCTTGAGGTCGTATTGTTGTTGTT 59.725 41.667 0.00 0.00 0.00 2.83
1568 1606 5.467399 CCTTGAGGTCGTATTGTTGTTGTTA 59.533 40.000 0.00 0.00 0.00 2.41
1569 1607 6.148811 CCTTGAGGTCGTATTGTTGTTGTTAT 59.851 38.462 0.00 0.00 0.00 1.89
1939 2065 0.460311 CACCTACTCCGCCGAGATTT 59.540 55.000 9.16 0.00 38.52 2.17
1983 2109 1.050767 GTCTCGGAACTTTCGACACG 58.949 55.000 0.00 0.00 32.86 4.49
2167 2293 2.685017 ATCGTCTCAGGCTGGCCA 60.685 61.111 15.73 4.71 38.92 5.36
2206 2332 2.887568 CGCTGTGGAGTCATCGCC 60.888 66.667 0.00 0.00 0.00 5.54
2227 2353 1.663739 CCGGAAGACACCAACGAGA 59.336 57.895 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 2.223971 ACACGTGTCAGTTCCTTAGTGG 60.224 50.000 17.22 0.00 33.18 4.00
410 411 5.242838 CCTATGGAGCTCGAAGACTTAGATT 59.757 44.000 7.83 0.00 0.00 2.40
451 452 8.853077 ATTCACATTGAAGACTATGACAAGAA 57.147 30.769 0.00 0.00 40.05 2.52
648 649 2.881074 CGCTGTAAGTGCATCTAGTGT 58.119 47.619 0.00 0.00 37.80 3.55
701 708 3.777925 CACGACGGCCAAAGCTCG 61.778 66.667 2.24 2.78 41.16 5.03
766 779 0.326904 ATGACCCTCAGGATGCCTCA 60.327 55.000 0.00 0.00 36.73 3.86
973 986 2.742372 GTGCTCCACCGCGTTCAT 60.742 61.111 4.92 0.00 0.00 2.57
1155 1168 0.318441 TGAACTGCTTCAGGTCCGAG 59.682 55.000 9.14 0.00 46.60 4.63
1271 1289 4.051237 TGAATTCATCTGTCCGCTATTCG 58.949 43.478 3.38 0.00 38.08 3.34
1279 1297 6.860080 ACACATTTCATGAATTCATCTGTCC 58.140 36.000 18.16 0.00 33.61 4.02
1407 1428 6.746120 ACTTCAAACTCGTGAGTGTATACTT 58.254 36.000 2.78 0.00 41.58 2.24
1419 1442 4.100498 TCCCAGTCTAAACTTCAAACTCGT 59.900 41.667 0.00 0.00 31.71 4.18
1440 1463 8.098220 ACCATTTCTTGCAAAAATTGTAATCC 57.902 30.769 15.54 0.00 34.77 3.01
1458 1481 1.200020 CTTTGCCGGTCAGACCATTTC 59.800 52.381 20.13 5.54 38.47 2.17
1459 1482 1.202879 TCTTTGCCGGTCAGACCATTT 60.203 47.619 20.13 0.00 38.47 2.32
1460 1483 0.400213 TCTTTGCCGGTCAGACCATT 59.600 50.000 20.13 0.00 38.47 3.16
1461 1484 0.620556 ATCTTTGCCGGTCAGACCAT 59.379 50.000 20.13 0.35 38.47 3.55
1462 1485 0.321564 CATCTTTGCCGGTCAGACCA 60.322 55.000 20.13 0.00 38.47 4.02
1463 1486 1.648467 GCATCTTTGCCGGTCAGACC 61.648 60.000 9.92 9.92 43.38 3.85
1483 1506 1.443802 TGTTCTTGTGCGTGTTGACA 58.556 45.000 0.00 0.00 0.00 3.58
1584 1623 4.201990 GGCTCAGCTCAGATAAAAACATGG 60.202 45.833 0.00 0.00 0.00 3.66
1586 1625 4.592942 TGGCTCAGCTCAGATAAAAACAT 58.407 39.130 0.00 0.00 0.00 2.71
1613 1652 4.913924 CAGAAACAAGCTAGTGTGAAATGC 59.086 41.667 0.00 0.00 0.00 3.56
1660 1699 3.483235 CTTTTGGCGCGGCTGTTGT 62.483 57.895 33.23 0.00 0.00 3.32
1715 1758 0.037697 TGGAGCACGCATAAACGTCT 60.038 50.000 0.00 0.00 46.34 4.18
2167 2293 0.254178 ATGGCTTGCTCGTCCATCTT 59.746 50.000 0.00 0.00 35.85 2.40
2206 2332 1.374252 CGTTGGTGTCTTCCGGGAG 60.374 63.158 2.10 2.10 0.00 4.30


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

AutoCloner maintained by Alex Coulton.