Multiple sequence alignment - TraesCS7D01G032400

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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 TraesCS7D01G032400 chr7D 100.000 3092 0 0 1 3092 16769627 16772718 0.000000e+00 5710.0
1 TraesCS7D01G032400 chr7D 84.695 1065 137 13 908 1947 16717983 16719046 0.000000e+00 1040.0
2 TraesCS7D01G032400 chr7D 83.147 1074 139 25 889 1950 16751503 16752546 0.000000e+00 942.0
3 TraesCS7D01G032400 chr7D 76.074 489 81 25 1949 2409 16757389 16757869 4.010000e-54 222.0
4 TraesCS7D01G032400 chr7D 83.186 226 22 9 522 735 16717447 16717668 3.150000e-45 193.0
5 TraesCS7D01G032400 chr7A 93.259 1528 79 11 408 1913 15995917 15997442 0.000000e+00 2230.0
6 TraesCS7D01G032400 chr7A 93.990 1148 54 5 1949 3092 15997555 15998691 0.000000e+00 1724.0
7 TraesCS7D01G032400 chr7A 86.251 1331 156 14 642 1948 16398350 16397023 0.000000e+00 1419.0
8 TraesCS7D01G032400 chr7A 83.364 1076 138 24 889 1950 15787503 15788551 0.000000e+00 957.0
9 TraesCS7D01G032400 chr7A 88.393 672 78 0 1277 1948 15843058 15843729 0.000000e+00 809.0
10 TraesCS7D01G032400 chr7A 84.927 617 69 12 646 1244 15842445 15843055 1.230000e-168 603.0
11 TraesCS7D01G032400 chr7A 87.966 349 26 7 4 350 15995428 15995762 6.210000e-107 398.0
12 TraesCS7D01G032400 chr7A 79.201 601 85 28 1949 2548 16396964 16396403 6.260000e-102 381.0
13 TraesCS7D01G032400 chr7A 83.000 200 15 9 2867 3066 15845261 15845441 2.470000e-36 163.0
14 TraesCS7D01G032400 chr7A 88.750 80 7 2 2384 2462 15844454 15844532 2.540000e-16 97.1
15 TraesCS7D01G032400 chr7A 96.552 58 1 1 2862 2918 15844813 15844870 9.130000e-16 95.3
16 TraesCS7D01G032400 chr4A 94.978 1334 50 7 632 1950 717760318 717758987 0.000000e+00 2076.0
17 TraesCS7D01G032400 chr4A 93.429 1324 70 13 632 1950 717296391 717297702 0.000000e+00 1947.0
18 TraesCS7D01G032400 chr4A 91.210 1149 63 18 1949 3092 717297759 717298874 0.000000e+00 1528.0
19 TraesCS7D01G032400 chr4A 79.343 1583 212 67 437 1950 717923124 717921588 0.000000e+00 1005.0
20 TraesCS7D01G032400 chr4A 91.907 729 28 13 1949 2676 717758930 717758232 0.000000e+00 990.0
21 TraesCS7D01G032400 chr4A 82.762 1079 143 24 889 1950 717823465 717822413 0.000000e+00 922.0
22 TraesCS7D01G032400 chr4A 95.956 272 11 0 2736 3007 717758230 717757959 2.830000e-120 442.0
23 TraesCS7D01G032400 chr4A 91.509 318 15 11 39 350 717295752 717296063 7.920000e-116 427.0
24 TraesCS7D01G032400 chr4A 93.532 201 11 2 353 551 717296188 717296388 6.480000e-77 298.0
25 TraesCS7D01G032400 chr4A 93.258 178 9 1 380 554 717760495 717760318 3.060000e-65 259.0
26 TraesCS7D01G032400 chr4A 79.322 295 51 5 1949 2243 717257208 717257492 6.760000e-47 198.0
27 TraesCS7D01G032400 chr4A 78.983 295 52 5 1949 2243 717222031 717222315 3.150000e-45 193.0
28 TraesCS7D01G032400 chr7B 83.411 1073 142 16 888 1950 655819728 655818682 0.000000e+00 963.0
29 TraesCS7D01G032400 chr7B 84.959 246 36 1 1949 2193 655653825 655653580 6.620000e-62 248.0
30 TraesCS7D01G032400 chr7B 81.293 294 51 2 1950 2243 655814274 655813985 5.150000e-58 235.0
31 TraesCS7D01G032400 chr7B 78.317 309 58 7 1949 2252 655818625 655818321 1.130000e-44 191.0
32 TraesCS7D01G032400 chr7B 85.714 140 16 3 1111 1248 655654664 655654527 8.940000e-31 145.0
33 TraesCS7D01G032400 chr7B 82.836 134 21 2 1114 1246 655738829 655738697 5.420000e-23 119.0


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 TraesCS7D01G032400 chr7D 16769627 16772718 3091 False 5710.000000 5710 100.000000 1 3092 1 chr7D.!!$F3 3091
1 TraesCS7D01G032400 chr7D 16751503 16752546 1043 False 942.000000 942 83.147000 889 1950 1 chr7D.!!$F1 1061
2 TraesCS7D01G032400 chr7D 16717447 16719046 1599 False 616.500000 1040 83.940500 522 1947 2 chr7D.!!$F4 1425
3 TraesCS7D01G032400 chr7A 15995428 15998691 3263 False 1450.666667 2230 91.738333 4 3092 3 chr7A.!!$F3 3088
4 TraesCS7D01G032400 chr7A 15787503 15788551 1048 False 957.000000 957 83.364000 889 1950 1 chr7A.!!$F1 1061
5 TraesCS7D01G032400 chr7A 16396403 16398350 1947 True 900.000000 1419 82.726000 642 2548 2 chr7A.!!$R1 1906
6 TraesCS7D01G032400 chr7A 15842445 15845441 2996 False 353.480000 809 88.324400 646 3066 5 chr7A.!!$F2 2420
7 TraesCS7D01G032400 chr4A 717295752 717298874 3122 False 1050.000000 1947 92.420000 39 3092 4 chr4A.!!$F3 3053
8 TraesCS7D01G032400 chr4A 717921588 717923124 1536 True 1005.000000 1005 79.343000 437 1950 1 chr4A.!!$R2 1513
9 TraesCS7D01G032400 chr4A 717757959 717760495 2536 True 941.750000 2076 94.024750 380 3007 4 chr4A.!!$R3 2627
10 TraesCS7D01G032400 chr4A 717822413 717823465 1052 True 922.000000 922 82.762000 889 1950 1 chr4A.!!$R1 1061
11 TraesCS7D01G032400 chr7B 655818321 655819728 1407 True 577.000000 963 80.864000 888 2252 2 chr7B.!!$R4 1364

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
806 980 0.844503 CGCGCATAACTTCTCCGTAC 59.155 55.0 8.75 0.0 0.0 3.67 F
1908 2303 0.469892 CCAAGAAGGCAAGGTGGGTT 60.470 55.0 0.00 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2479 0.111089 GAGCTGCGAACGTGTTGAAG 60.111 55.00 0.00 0.0 0.00 3.02 R
2734 3501 4.984295 TCCACATGGAAAAAGAGATGTGA 58.016 39.13 11.58 0.0 45.66 3.58 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
118 121 5.932883 GGGTTAATTTTTGCGTTAAATGGGA 59.067 36.000 0.00 0.00 0.00 4.37
198 201 4.506654 CCGTCATTATAACCGGAAGAGTTG 59.493 45.833 9.46 0.00 43.01 3.16
265 268 4.173924 GGCTCCTCTGCTCAGCCC 62.174 72.222 0.00 0.00 46.20 5.19
291 296 1.048601 ACCGAGAGCTGGAAGAAACA 58.951 50.000 0.00 0.00 34.07 2.83
337 342 1.227380 GAGATGGACGCGCATCCTT 60.227 57.895 24.60 18.00 39.75 3.36
350 355 2.359169 ATCCTTCTTCCTCGGCGCA 61.359 57.895 10.83 0.00 0.00 6.09
351 356 1.690219 ATCCTTCTTCCTCGGCGCAT 61.690 55.000 10.83 0.00 0.00 4.73
377 510 1.905839 TTCTGCATCCCATCCCCTTA 58.094 50.000 0.00 0.00 0.00 2.69
498 639 5.233689 GGCAAAGATTGATTCTGCTTATTGC 59.766 40.000 0.00 0.00 40.26 3.56
508 649 5.743636 TTCTGCTTATTGCCAAAGGAAAT 57.256 34.783 0.00 0.00 42.00 2.17
551 692 5.428457 TCCCTGCTTTAGATCTCCAACATTA 59.572 40.000 0.00 0.00 0.00 1.90
555 696 6.946340 TGCTTTAGATCTCCAACATTACAGA 58.054 36.000 0.00 0.00 0.00 3.41
557 698 8.704668 TGCTTTAGATCTCCAACATTACAGATA 58.295 33.333 0.00 0.00 0.00 1.98
563 704 9.829507 AGATCTCCAACATTACAGATAAAGAAG 57.170 33.333 0.00 0.00 0.00 2.85
580 726 3.096092 AGAAGAGAGGGTGTCACTGATC 58.904 50.000 2.35 0.00 0.00 2.92
602 748 2.300433 GCCATGCCTGTATCAATGTGA 58.700 47.619 0.00 0.00 0.00 3.58
630 776 2.380064 TCACATTTCCCTTGCCTGTT 57.620 45.000 0.00 0.00 0.00 3.16
763 935 7.939588 AGTTCAGTAGGCCCAAAGATTTATATC 59.060 37.037 0.00 0.00 0.00 1.63
770 942 7.785033 AGGCCCAAAGATTTATATCAAACTTG 58.215 34.615 0.00 0.00 32.95 3.16
791 965 1.488261 GCAACCTGTATCTACCGCGC 61.488 60.000 0.00 0.00 0.00 6.86
806 980 0.844503 CGCGCATAACTTCTCCGTAC 59.155 55.000 8.75 0.00 0.00 3.67
853 1050 1.345741 TGAGCTTCTCAGGGTCAACAG 59.654 52.381 0.00 0.00 38.09 3.16
1198 1538 0.867753 CTCGGTATGCACGTGCTCTC 60.868 60.000 37.59 25.83 42.66 3.20
1295 1641 1.672356 GCACGTGGAGATTGGCTGT 60.672 57.895 18.88 0.00 0.00 4.40
1363 1727 3.439476 CCTCAGAGGCATGTTCTTTCTTG 59.561 47.826 2.60 0.00 0.00 3.02
1678 2042 1.014564 GTCTTTCGGGTCCTTCTGCG 61.015 60.000 0.00 0.00 0.00 5.18
1746 2110 2.826725 ACTTGAGGAAGGTAGAACCGAG 59.173 50.000 0.00 0.00 44.90 4.63
1908 2303 0.469892 CCAAGAAGGCAAGGTGGGTT 60.470 55.000 0.00 0.00 0.00 4.11
1982 2435 5.365021 ACTTCCCAAGTTATCATCCTGAG 57.635 43.478 0.00 0.00 39.04 3.35
2026 2479 3.531262 ATGGCAAAAACGTAACGACTC 57.469 42.857 0.00 0.00 0.00 3.36
2138 2591 1.747355 CAGTGATGATCTTTGGGGCAC 59.253 52.381 0.00 0.00 0.00 5.01
2219 2714 2.511659 ACAGTTGCAGGACGAGTAGTA 58.488 47.619 0.00 0.00 0.00 1.82
2269 2764 7.872993 TCCAAAGTTACTGATGTTGAACTCTAG 59.127 37.037 0.00 0.00 30.98 2.43
2296 2795 2.577606 TGTGTGGTGATTACAAGGGG 57.422 50.000 0.00 0.00 0.00 4.79
2599 3365 3.380479 TTTCTATCCTAATCCGCCGTG 57.620 47.619 0.00 0.00 0.00 4.94
2689 3456 8.483758 GGACAGATTTCCAAAGGTATTACTAGA 58.516 37.037 0.00 0.00 35.49 2.43
2694 3461 9.983804 GATTTCCAAAGGTATTACTAGAAAACG 57.016 33.333 0.00 0.00 0.00 3.60
2716 3483 7.284919 ACGACCCAAAATTTCTCAAAGTAAT 57.715 32.000 0.00 0.00 0.00 1.89
2760 3527 3.765381 TCTCTTTTTCCATGTGGATGCA 58.235 40.909 1.98 0.00 44.98 3.96
3016 4231 3.433615 GGAGAGAAAAAGACACACATCCG 59.566 47.826 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.359243 AGCCCTCTAAAAGGTCCCTTT 58.641 47.619 5.47 5.47 46.90 3.11
1 2 2.061264 AGCCCTCTAAAAGGTCCCTT 57.939 50.000 0.00 0.00 44.56 3.95
3 4 1.064611 GGAAGCCCTCTAAAAGGTCCC 60.065 57.143 0.00 0.00 44.56 4.46
4 5 1.064611 GGGAAGCCCTCTAAAAGGTCC 60.065 57.143 0.00 0.00 44.56 4.46
5 6 1.407025 CGGGAAGCCCTCTAAAAGGTC 60.407 57.143 0.38 0.00 44.56 3.85
18 19 2.264124 GGTTTCCTTTCCGGGAAGC 58.736 57.895 17.91 6.72 44.85 3.86
21 22 0.848053 ACAAGGTTTCCTTTCCGGGA 59.152 50.000 0.00 0.00 41.69 5.14
86 87 7.485418 AACGCAAAAATTAACCCCTAAAAAG 57.515 32.000 0.00 0.00 0.00 2.27
178 181 8.624367 TTTTTCAACTCTTCCGGTTATAATGA 57.376 30.769 0.00 0.00 0.00 2.57
272 277 1.001406 CTGTTTCTTCCAGCTCTCGGT 59.999 52.381 0.00 0.00 0.00 4.69
280 285 2.863153 CGCCGCTGTTTCTTCCAG 59.137 61.111 0.00 0.00 0.00 3.86
337 342 0.102481 GAACTATGCGCCGAGGAAGA 59.898 55.000 4.18 0.00 0.00 2.87
350 355 4.446889 GGGATGGGATGCAGAAAGAACTAT 60.447 45.833 0.00 0.00 0.00 2.12
351 356 3.117888 GGGATGGGATGCAGAAAGAACTA 60.118 47.826 0.00 0.00 0.00 2.24
377 510 0.472471 AACATCCACAGGTGAACGGT 59.528 50.000 0.00 0.00 0.00 4.83
551 692 5.046950 GTGACACCCTCTCTTCTTTATCTGT 60.047 44.000 0.00 0.00 0.00 3.41
555 696 5.087323 TCAGTGACACCCTCTCTTCTTTAT 58.913 41.667 0.84 0.00 0.00 1.40
557 698 3.309296 TCAGTGACACCCTCTCTTCTTT 58.691 45.455 0.84 0.00 0.00 2.52
563 704 1.134848 GCAGATCAGTGACACCCTCTC 60.135 57.143 0.84 0.00 0.00 3.20
580 726 2.034179 CACATTGATACAGGCATGGCAG 59.966 50.000 22.64 16.46 0.00 4.85
602 748 5.136105 GCAAGGGAAATGTGATTCTCCTAT 58.864 41.667 0.00 0.00 32.84 2.57
702 865 7.964604 ATCACCTGTTTCTCAAACTAGTAAC 57.035 36.000 0.00 0.00 41.90 2.50
706 869 6.293626 CCACAATCACCTGTTTCTCAAACTAG 60.294 42.308 1.11 0.00 41.90 2.57
763 935 5.122396 GGTAGATACAGGTTGCTCAAGTTTG 59.878 44.000 0.00 0.00 0.00 2.93
770 942 1.854227 GCGGTAGATACAGGTTGCTC 58.146 55.000 0.00 0.00 0.00 4.26
791 965 7.596749 ATTTCAGTTGTACGGAGAAGTTATG 57.403 36.000 0.00 0.00 0.00 1.90
853 1050 8.845413 AAAGAAGGATACAGATGATATTGAGC 57.155 34.615 0.00 0.00 41.41 4.26
1198 1538 0.685785 TGTAGGAGGAGAGGCTGCAG 60.686 60.000 10.11 10.11 0.00 4.41
1238 1578 1.065418 AGCGGTTAAACTGGGGAGATG 60.065 52.381 0.00 0.00 0.00 2.90
1295 1641 1.300963 GATGAGGTGCCAGCAGGAA 59.699 57.895 0.00 0.00 36.89 3.36
1645 2009 2.784347 GAAAGACCCTAGGGCATATGC 58.216 52.381 28.88 19.79 39.32 3.14
1678 2042 6.465084 AGAGACTGGGTAAGAATTGTACAAC 58.535 40.000 11.22 0.00 0.00 3.32
1908 2303 4.019681 CAGTTATCCAACCTGTCCACCTTA 60.020 45.833 0.00 0.00 35.05 2.69
2026 2479 0.111089 GAGCTGCGAACGTGTTGAAG 60.111 55.000 0.00 0.00 0.00 3.02
2138 2591 3.792047 CACCAGACGCATGCACGG 61.792 66.667 19.57 13.76 37.37 4.94
2199 2693 1.329256 ACTACTCGTCCTGCAACTGT 58.671 50.000 0.00 0.00 0.00 3.55
2219 2714 7.396540 AAAACAAGTCAAGAACATTCAGTCT 57.603 32.000 0.00 0.00 0.00 3.24
2583 3349 0.178955 TCCCACGGCGGATTAGGATA 60.179 55.000 13.24 0.00 36.56 2.59
2599 3365 4.137543 AGTTGTTCAACAGTTGATCTCCC 58.862 43.478 16.89 8.15 39.84 4.30
2689 3456 6.403049 ACTTTGAGAAATTTTGGGTCGTTTT 58.597 32.000 0.00 0.00 0.00 2.43
2734 3501 4.984295 TCCACATGGAAAAAGAGATGTGA 58.016 39.130 11.58 0.00 45.66 3.58
2760 3527 5.952347 GGATAAAGGGGTCTTCAAAGTGATT 59.048 40.000 0.00 0.00 31.82 2.57


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

AutoCloner maintained by Alex Coulton.