Multiple sequence alignment - TraesCS7D01G205700

Loading Multiple Alignment...

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 TraesCS7D01G205700 chr7D 100.000 2759 0 0 1 2759 163216608 163213850 0.000000e+00 5096
1 TraesCS7D01G205700 chr7D 89.390 1263 85 29 574 1814 163251684 163250449 0.000000e+00 1544
2 TraesCS7D01G205700 chr7D 85.958 819 98 12 997 1804 163199879 163199067 0.000000e+00 859
3 TraesCS7D01G205700 chr7D 84.974 579 57 24 1 571 28187866 28187310 6.670000e-156 560
4 TraesCS7D01G205700 chr7D 84.973 366 39 14 1 359 89056834 89057190 9.400000e-95 357
5 TraesCS7D01G205700 chr7A 89.260 1257 97 24 581 1816 164182541 164181302 0.000000e+00 1539
6 TraesCS7D01G205700 chr7A 88.071 1291 87 30 583 1861 164394420 164393185 0.000000e+00 1469
7 TraesCS7D01G205700 chr7A 94.400 875 41 5 1887 2757 164180997 164180127 0.000000e+00 1338
8 TraesCS7D01G205700 chr7A 84.775 578 63 19 1 571 28572403 28571844 8.630000e-155 556
9 TraesCS7D01G205700 chr7A 83.448 580 66 23 1 571 28601264 28600706 1.900000e-141 512
10 TraesCS7D01G205700 chr7A 83.938 193 19 6 869 1053 163991251 163991063 1.020000e-39 174
11 TraesCS7D01G205700 chr7B 88.803 1295 84 30 575 1846 125363632 125362376 0.000000e+00 1531
12 TraesCS7D01G205700 chr7B 91.485 963 54 14 863 1814 125244379 125243434 0.000000e+00 1299
13 TraesCS7D01G205700 chr7B 92.997 871 51 2 954 1814 125356064 125355194 0.000000e+00 1262
14 TraesCS7D01G205700 chr7B 90.921 749 39 12 574 1309 125208206 125207474 0.000000e+00 979
15 TraesCS7D01G205700 chr7B 92.912 649 39 4 1170 1814 125313255 125312610 0.000000e+00 937
16 TraesCS7D01G205700 chr7B 84.607 955 108 23 869 1804 125192027 125191093 0.000000e+00 913
17 TraesCS7D01G205700 chr7B 89.004 482 49 1 1975 2456 125362314 125361837 6.580000e-166 593
18 TraesCS7D01G205700 chr7B 87.835 411 22 9 2347 2757 125203850 125203468 9.010000e-125 457
19 TraesCS7D01G205700 chr7B 90.882 340 25 6 1975 2313 125204183 125203849 4.190000e-123 451
20 TraesCS7D01G205700 chr7B 93.443 305 16 1 574 874 125244795 125244491 1.510000e-122 449
21 TraesCS7D01G205700 chr7B 93.443 305 16 1 574 874 125280850 125280546 1.510000e-122 449
22 TraesCS7D01G205700 chr7B 93.443 305 16 1 574 874 125314731 125314427 1.510000e-122 449
23 TraesCS7D01G205700 chr7B 86.667 390 24 9 574 935 125231010 125230621 9.200000e-110 407
24 TraesCS7D01G205700 chr7B 84.223 431 36 13 574 988 125419889 125419475 9.260000e-105 390
25 TraesCS7D01G205700 chr7B 88.994 318 30 4 2441 2757 125361354 125361041 3.330000e-104 388
26 TraesCS7D01G205700 chr7B 84.783 138 15 6 1827 1959 125204303 125204167 1.720000e-27 134
27 TraesCS7D01G205700 chr6D 95.406 566 25 1 1 565 414703108 414703673 0.000000e+00 900
28 TraesCS7D01G205700 chr3A 91.373 568 26 11 1 565 367990631 367991178 0.000000e+00 756
29 TraesCS7D01G205700 chr3A 84.561 570 62 23 1 564 741627501 741626952 2.420000e-150 542
30 TraesCS7D01G205700 chr4A 82.759 580 78 17 1 571 733903942 733903376 5.310000e-137 497
31 TraesCS7D01G205700 chrUn 93.443 305 16 1 574 874 332928288 332927984 1.510000e-122 449
32 TraesCS7D01G205700 chr2B 81.102 508 67 25 1 498 568457112 568457600 2.010000e-101 379


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 TraesCS7D01G205700 chr7D 163213850 163216608 2758 True 5096.000000 5096 100.000000 1 2759 1 chr7D.!!$R3 2758
1 TraesCS7D01G205700 chr7D 163250449 163251684 1235 True 1544.000000 1544 89.390000 574 1814 1 chr7D.!!$R4 1240
2 TraesCS7D01G205700 chr7D 163199067 163199879 812 True 859.000000 859 85.958000 997 1804 1 chr7D.!!$R2 807
3 TraesCS7D01G205700 chr7D 28187310 28187866 556 True 560.000000 560 84.974000 1 571 1 chr7D.!!$R1 570
4 TraesCS7D01G205700 chr7A 164393185 164394420 1235 True 1469.000000 1469 88.071000 583 1861 1 chr7A.!!$R4 1278
5 TraesCS7D01G205700 chr7A 164180127 164182541 2414 True 1438.500000 1539 91.830000 581 2757 2 chr7A.!!$R5 2176
6 TraesCS7D01G205700 chr7A 28571844 28572403 559 True 556.000000 556 84.775000 1 571 1 chr7A.!!$R1 570
7 TraesCS7D01G205700 chr7A 28600706 28601264 558 True 512.000000 512 83.448000 1 571 1 chr7A.!!$R2 570
8 TraesCS7D01G205700 chr7B 125355194 125356064 870 True 1262.000000 1262 92.997000 954 1814 1 chr7B.!!$R4 860
9 TraesCS7D01G205700 chr7B 125191093 125192027 934 True 913.000000 913 84.607000 869 1804 1 chr7B.!!$R1 935
10 TraesCS7D01G205700 chr7B 125243434 125244795 1361 True 874.000000 1299 92.464000 574 1814 2 chr7B.!!$R7 1240
11 TraesCS7D01G205700 chr7B 125361041 125363632 2591 True 837.333333 1531 88.933667 575 2757 3 chr7B.!!$R9 2182
12 TraesCS7D01G205700 chr7B 125312610 125314731 2121 True 693.000000 937 93.177500 574 1814 2 chr7B.!!$R8 1240
13 TraesCS7D01G205700 chr7B 125203468 125208206 4738 True 505.250000 979 88.605250 574 2757 4 chr7B.!!$R6 2183
14 TraesCS7D01G205700 chr6D 414703108 414703673 565 False 900.000000 900 95.406000 1 565 1 chr6D.!!$F1 564
15 TraesCS7D01G205700 chr3A 367990631 367991178 547 False 756.000000 756 91.373000 1 565 1 chr3A.!!$F1 564
16 TraesCS7D01G205700 chr3A 741626952 741627501 549 True 542.000000 542 84.561000 1 564 1 chr3A.!!$R1 563
17 TraesCS7D01G205700 chr4A 733903376 733903942 566 True 497.000000 497 82.759000 1 571 1 chr4A.!!$R1 570

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
540 562 0.601558 TAAGTCCTGGCGTCTGTGAC 59.398 55.0 7.21 7.21 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 6352 0.991146 TAGGACTCAAGGCCATGCAA 59.009 50.0 5.01 0.0 0.0 4.08 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
228 230 4.414846 ACTTGGAGGCTCCTAATGATCAAT 59.585 41.667 32.28 0.00 37.46 2.57
401 419 5.125367 AGTTTGTTCTGGGTTTCCTTAGT 57.875 39.130 0.00 0.00 0.00 2.24
501 520 8.357796 TCTTCAACATATCATCGTCAGAATTC 57.642 34.615 0.00 0.00 0.00 2.17
508 529 0.824109 ATCGTCAGAATTCGCTCCCA 59.176 50.000 0.00 0.00 0.00 4.37
540 562 0.601558 TAAGTCCTGGCGTCTGTGAC 59.398 55.000 7.21 7.21 0.00 3.67
752 809 9.685005 CGTATGTACTAGTAAAAAGAAACATGC 57.315 33.333 3.61 6.66 31.43 4.06
825 887 5.063438 TGCGTGTAAAATCAAGAGCACTATC 59.937 40.000 0.00 0.00 0.00 2.08
925 1118 4.569865 GGAACTTGATTACTCCCACCCATT 60.570 45.833 0.00 0.00 0.00 3.16
951 1148 3.313803 TCATCAGTAGTCTCTGCATCGAC 59.686 47.826 7.28 7.28 35.63 4.20
952 1149 2.992593 TCAGTAGTCTCTGCATCGACT 58.007 47.619 18.41 18.41 42.67 4.18
962 1159 2.680339 TCTGCATCGACTGAGAGTACAG 59.320 50.000 0.00 0.00 42.78 2.74
1013 1222 2.348104 TACACATGGCTCCTCGCGT 61.348 57.895 5.77 0.00 40.44 6.01
1278 2339 2.290896 CCATACCAGCCCAAGAACTGAA 60.291 50.000 0.00 0.00 35.90 3.02
1337 5036 6.773976 ATGTACTCCATTTGGGTGTAATTG 57.226 37.500 0.00 0.00 44.77 2.32
1392 5099 1.096386 AGGGCTACGACTACAGCTCG 61.096 60.000 0.00 0.00 43.33 5.03
1497 5204 2.125147 GCCACCACGCTCATGCTA 60.125 61.111 0.00 0.00 36.97 3.49
1601 5308 2.126071 CCACGATGTCGAGGCGTT 60.126 61.111 9.67 0.00 42.60 4.84
1638 5345 2.437343 CGACGGCGAGCAGAAACTC 61.437 63.158 16.62 0.00 40.82 3.01
1760 5468 5.105554 TCAGGATCTTCAAGAAGCACTAGAC 60.106 44.000 4.95 0.00 38.28 2.59
1764 5472 6.091986 GGATCTTCAAGAAGCACTAGACTTTG 59.908 42.308 4.95 0.00 38.28 2.77
2033 6038 4.273318 ACAAGCTAGATTGGATTGAACCC 58.727 43.478 23.65 0.00 34.65 4.11
2159 6164 5.150342 TCACGTGACAATGTTTAGTTGTG 57.850 39.130 15.76 0.00 39.72 3.33
2182 6187 8.799367 TGTGCCATCGTACTAATGTACTATATT 58.201 33.333 0.00 0.00 44.97 1.28
2333 6340 3.615224 GGTACCACCCATTTTACTCGA 57.385 47.619 7.15 0.00 30.04 4.04
2345 6352 5.355596 CATTTTACTCGAGAATCCTGCTCT 58.644 41.667 21.68 0.00 0.00 4.09
2534 7039 0.171231 GAGTTGCTTCCCAATTCGCC 59.829 55.000 0.00 0.00 35.55 5.54
2537 7042 4.193334 GCTTCCCAATTCGCCGGC 62.193 66.667 19.07 19.07 0.00 6.13
2543 7048 2.120909 CCAATTCGCCGGCTCCATT 61.121 57.895 26.68 16.21 0.00 3.16
2581 7086 2.672961 TCGTGTTCATGTGATCCCTC 57.327 50.000 0.00 0.00 0.00 4.30
2582 7087 1.207089 TCGTGTTCATGTGATCCCTCC 59.793 52.381 0.00 0.00 0.00 4.30
2583 7088 1.208052 CGTGTTCATGTGATCCCTCCT 59.792 52.381 0.00 0.00 0.00 3.69
2690 7197 8.643324 AGTAATTCTAAGGATAAATGCGAGAGT 58.357 33.333 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 0.943673 TCTGCAACACACACCATTCG 59.056 50.000 0.00 0.00 0.00 3.34
401 419 2.322658 AGACCCTAACGAAAGACCACA 58.677 47.619 0.00 0.00 0.00 4.17
501 520 1.156736 CAAAGTAACAGGTGGGAGCG 58.843 55.000 0.00 0.00 0.00 5.03
508 529 4.745783 GCCAGGACTTACAAAGTAACAGGT 60.746 45.833 0.00 0.00 43.03 4.00
566 588 2.345244 CGTGTCCTGGCAGCTCTT 59.655 61.111 9.56 0.00 0.00 2.85
572 594 1.257750 ATCTACTGCGTGTCCTGGCA 61.258 55.000 0.00 0.00 37.63 4.92
752 809 6.578020 TTGAGTTGTTCAACGTAGTGTAAG 57.422 37.500 9.54 0.00 45.00 2.34
825 887 8.273780 AGTTGGAGAATTGACAGCTTTATTAG 57.726 34.615 0.00 0.00 0.00 1.73
830 892 4.023707 CGAAGTTGGAGAATTGACAGCTTT 60.024 41.667 0.00 0.00 36.11 3.51
925 1118 3.635591 TGCAGAGACTACTGATGATGGA 58.364 45.455 0.00 0.00 39.94 3.41
951 1148 3.667497 TGCCTTGAACTGTACTCTCAG 57.333 47.619 0.00 0.00 40.80 3.35
952 1149 4.380531 CTTTGCCTTGAACTGTACTCTCA 58.619 43.478 0.00 0.00 0.00 3.27
962 1159 1.603931 GGCTTCTGCTTTGCCTTGAAC 60.604 52.381 0.00 0.00 43.05 3.18
1013 1222 6.320926 CAGAGAGACACTAATCCATGAGAGAA 59.679 42.308 0.00 0.00 0.00 2.87
1278 2339 7.573710 TGTAATTACTTACTGCCATCCTGATT 58.426 34.615 16.33 0.00 38.44 2.57
1392 5099 4.980805 TCGAACTGCCACACGCCC 62.981 66.667 0.00 0.00 36.24 6.13
1497 5204 2.202570 GCGCCATCGTAGACGTGT 60.203 61.111 0.00 0.00 42.51 4.49
1601 5308 1.466192 CGATGTACACGGTAAGCGTCA 60.466 52.381 0.00 0.00 0.00 4.35
2033 6038 8.471457 CAAATCTAGTGTGTTTTCATTGAAACG 58.529 33.333 11.30 0.00 41.32 3.60
2236 6241 1.815421 CCAATCAGGCTAGCGCGTT 60.815 57.895 8.43 3.54 36.88 4.84
2283 6290 3.395639 CTTTGCTAAGTAACCCACGTGA 58.604 45.455 19.30 0.00 0.00 4.35
2345 6352 0.991146 TAGGACTCAAGGCCATGCAA 59.009 50.000 5.01 0.00 0.00 4.08
2534 7039 4.275936 CCTAGGTTAAAATGAATGGAGCCG 59.724 45.833 0.00 0.00 0.00 5.52
2543 7048 8.851541 AACACGATTTACCTAGGTTAAAATGA 57.148 30.769 22.11 0.00 0.00 2.57
2581 7086 2.981859 GGTACCCACATGTGAGTAGG 57.018 55.000 27.46 20.50 0.00 3.18
2672 7178 3.964688 TGGGACTCTCGCATTTATCCTTA 59.035 43.478 0.00 0.00 34.23 2.69
2683 7189 1.377202 TGCCAAATGGGACTCTCGC 60.377 57.895 0.90 0.00 40.01 5.03
2690 7197 1.207570 GCATGAATGTGCCAAATGGGA 59.792 47.619 0.00 0.00 40.01 4.37


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

AutoCloner maintained by Alex Coulton.