Multiple sequence alignment - TraesCS7D01G169900

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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 TraesCS7D01G169900 chr7D 100.000 2339 0 0 1 2339 122681612 122683950 0.000000e+00 4320
1 TraesCS7D01G169900 chr7D 98.864 88 1 0 76 163 94261224 94261311 8.650000e-35 158
2 TraesCS7D01G169900 chr7B 87.979 1539 58 42 855 2338 83922204 83920738 0.000000e+00 1700
3 TraesCS7D01G169900 chr7A 87.628 978 47 27 792 1718 125676597 125677551 0.000000e+00 1068
4 TraesCS7D01G169900 chr7A 97.959 392 5 1 1948 2339 125677923 125678311 0.000000e+00 676
5 TraesCS7D01G169900 chr7A 92.375 459 31 3 346 800 299294908 299294450 0.000000e+00 651
6 TraesCS7D01G169900 chr7A 94.798 173 6 2 165 337 299295366 299295197 1.380000e-67 267
7 TraesCS7D01G169900 chr7A 81.439 264 18 8 792 1038 125915462 125915213 1.100000e-43 187
8 TraesCS7D01G169900 chr7A 83.673 196 11 2 1124 1319 125913744 125913570 5.170000e-37 165
9 TraesCS7D01G169900 chr7A 98.750 80 1 0 1 80 299295447 299295368 2.420000e-30 143
10 TraesCS7D01G169900 chr4D 94.311 457 24 1 338 792 325887479 325887935 0.000000e+00 699
11 TraesCS7D01G169900 chr4D 96.591 176 3 2 162 337 325887045 325887217 2.940000e-74 289
12 TraesCS7D01G169900 chr4D 93.750 80 2 1 1 80 325886970 325887046 1.470000e-22 117
13 TraesCS7D01G169900 chr2A 92.688 465 26 7 341 800 28335053 28334592 0.000000e+00 664
14 TraesCS7D01G169900 chr5A 92.544 456 30 2 339 792 564710568 564710115 0.000000e+00 651
15 TraesCS7D01G169900 chr5A 92.634 448 29 2 346 791 396369159 396369604 1.960000e-180 641
16 TraesCS7D01G169900 chr5A 94.886 176 6 2 162 337 396368698 396368870 2.960000e-69 272
17 TraesCS7D01G169900 chr5A 97.163 141 4 0 165 305 564710775 564710635 3.000000e-59 239
18 TraesCS7D01G169900 chr5A 93.333 105 3 4 75 176 428189442 428189339 4.030000e-33 152
19 TraesCS7D01G169900 chr5A 98.750 80 1 0 1 80 396368620 396368699 2.420000e-30 143
20 TraesCS7D01G169900 chr1A 91.775 462 33 4 339 797 66702738 66703197 2.530000e-179 638
21 TraesCS7D01G169900 chr1A 92.878 337 21 2 460 793 100365057 100364721 9.720000e-134 486
22 TraesCS7D01G169900 chr1A 94.798 173 6 2 165 337 100365469 100365300 1.380000e-67 267
23 TraesCS7D01G169900 chr1A 93.750 176 4 4 162 337 66702307 66702475 8.290000e-65 257
24 TraesCS7D01G169900 chr1A 96.739 92 3 0 72 163 575557264 575557355 1.120000e-33 154
25 TraesCS7D01G169900 chr1A 98.750 80 1 0 1 80 100365550 100365471 2.420000e-30 143
26 TraesCS7D01G169900 chr4B 89.869 306 23 3 495 792 157954524 157954829 1.010000e-103 387
27 TraesCS7D01G169900 chr4B 94.318 176 8 1 162 337 157953904 157954077 3.830000e-68 268
28 TraesCS7D01G169900 chr4B 90.683 161 13 2 338 498 157954337 157954495 1.820000e-51 213
29 TraesCS7D01G169900 chr4B 96.250 80 3 0 1 80 157953826 157953905 5.240000e-27 132
30 TraesCS7D01G169900 chr1B 94.891 137 5 1 201 337 631793726 631793860 1.820000e-51 213
31 TraesCS7D01G169900 chr1B 88.462 130 12 2 665 791 631805847 631805976 1.120000e-33 154
32 TraesCS7D01G169900 chr1B 96.250 80 3 0 3 82 631776362 631776441 5.240000e-27 132
33 TraesCS7D01G169900 chr2B 98.864 88 1 0 76 163 546125979 546125892 8.650000e-35 158
34 TraesCS7D01G169900 chr2B 93.939 99 5 1 66 163 554296026 554296124 5.210000e-32 148
35 TraesCS7D01G169900 chr6D 95.789 95 3 1 79 173 58042761 58042854 4.030000e-33 152
36 TraesCS7D01G169900 chr6D 94.845 97 5 0 79 175 417354786 417354690 4.030000e-33 152
37 TraesCS7D01G169900 chr3A 90.991 111 7 3 56 163 330699692 330699582 1.870000e-31 147
38 TraesCS7D01G169900 chr2D 89.565 115 8 3 52 163 572049239 572049126 2.420000e-30 143


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 TraesCS7D01G169900 chr7D 122681612 122683950 2338 False 4320.000000 4320 100.000000 1 2339 1 chr7D.!!$F2 2338
1 TraesCS7D01G169900 chr7B 83920738 83922204 1466 True 1700.000000 1700 87.979000 855 2338 1 chr7B.!!$R1 1483
2 TraesCS7D01G169900 chr7A 125676597 125678311 1714 False 872.000000 1068 92.793500 792 2339 2 chr7A.!!$F1 1547
3 TraesCS7D01G169900 chr7A 299294450 299295447 997 True 353.666667 651 95.307667 1 800 3 chr7A.!!$R2 799
4 TraesCS7D01G169900 chr4D 325886970 325887935 965 False 368.333333 699 94.884000 1 792 3 chr4D.!!$F1 791
5 TraesCS7D01G169900 chr5A 564710115 564710775 660 True 445.000000 651 94.853500 165 792 2 chr5A.!!$R2 627
6 TraesCS7D01G169900 chr5A 396368620 396369604 984 False 352.000000 641 95.423333 1 791 3 chr5A.!!$F1 790
7 TraesCS7D01G169900 chr1A 66702307 66703197 890 False 447.500000 638 92.762500 162 797 2 chr1A.!!$F2 635
8 TraesCS7D01G169900 chr1A 100364721 100365550 829 True 298.666667 486 95.475333 1 793 3 chr1A.!!$R1 792
9 TraesCS7D01G169900 chr4B 157953826 157954829 1003 False 250.000000 387 92.780000 1 792 4 chr4B.!!$F1 791


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
908 1282 0.868406 CTCCCGCAAGAACAGAACAC 59.132 55.0 0.0 0.0 43.02 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 2189 3.798511 GAAGCGGAAGGGGAGGGG 61.799 72.222 0.0 0.0 0.0 4.79 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
64 65 3.067180 CCACATGGCTCCAATCACATTAC 59.933 47.826 0.00 0.00 0.00 1.89
88 89 7.498443 ACTTTCACTAATTTATACTCCCTCCG 58.502 38.462 0.00 0.00 0.00 4.63
89 90 7.125356 ACTTTCACTAATTTATACTCCCTCCGT 59.875 37.037 0.00 0.00 0.00 4.69
90 91 8.537728 TTTCACTAATTTATACTCCCTCCGTA 57.462 34.615 0.00 0.00 0.00 4.02
91 92 8.537728 TTCACTAATTTATACTCCCTCCGTAA 57.462 34.615 0.00 0.00 0.00 3.18
92 93 8.537728 TCACTAATTTATACTCCCTCCGTAAA 57.462 34.615 0.00 0.00 0.00 2.01
93 94 8.416329 TCACTAATTTATACTCCCTCCGTAAAC 58.584 37.037 0.00 0.00 0.00 2.01
94 95 8.419442 CACTAATTTATACTCCCTCCGTAAACT 58.581 37.037 0.00 0.00 0.00 2.66
95 96 9.646522 ACTAATTTATACTCCCTCCGTAAACTA 57.353 33.333 0.00 0.00 0.00 2.24
104 105 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
105 106 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
106 107 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
107 108 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
108 109 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
109 110 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
138 139 9.733219 ATAACTACTTTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
139 140 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
140 141 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
141 142 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
142 143 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
157 158 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
158 159 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
159 160 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
160 161 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
161 162 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
206 207 6.303839 TGGTGTGAGCTAATTAAAAGGACTT 58.696 36.000 0.00 0.00 0.00 3.01
309 310 3.002038 TGTGGCTCATATGTGATGCAA 57.998 42.857 8.94 2.78 33.17 4.08
310 311 2.946990 TGTGGCTCATATGTGATGCAAG 59.053 45.455 8.94 0.00 33.17 4.01
375 666 5.047377 ACACCGGCTTGATACATGAAATTTT 60.047 36.000 0.00 0.00 0.00 1.82
379 670 8.908903 ACCGGCTTGATACATGAAATTTTTATA 58.091 29.630 0.00 0.00 0.00 0.98
473 804 1.555075 GCAACTCCCTGTCACCAGATA 59.445 52.381 0.00 0.00 41.50 1.98
691 1061 2.379634 CGCCTGATTCGTCGCAACA 61.380 57.895 0.00 0.00 0.00 3.33
796 1168 4.002316 ACGGGCGTTTTGCTAGTAAAATA 58.998 39.130 19.65 0.00 45.43 1.40
908 1282 0.868406 CTCCCGCAAGAACAGAACAC 59.132 55.000 0.00 0.00 43.02 3.32
939 1333 3.299977 TCGACCACCTCCCGTGTG 61.300 66.667 0.00 0.00 41.26 3.82
940 1334 3.612681 CGACCACCTCCCGTGTGT 61.613 66.667 0.00 0.00 41.26 3.72
941 1335 2.270257 CGACCACCTCCCGTGTGTA 61.270 63.158 0.00 0.00 41.26 2.90
942 1336 1.601419 CGACCACCTCCCGTGTGTAT 61.601 60.000 0.00 0.00 41.26 2.29
943 1337 1.477553 GACCACCTCCCGTGTGTATA 58.522 55.000 0.00 0.00 41.26 1.47
944 1338 2.037144 GACCACCTCCCGTGTGTATAT 58.963 52.381 0.00 0.00 41.26 0.86
960 1354 9.894783 CGTGTGTATATATATATAACTCCAGCC 57.105 37.037 13.00 1.28 0.00 4.85
977 1371 2.551912 CCCGACCAAGGTGCACAAC 61.552 63.158 20.43 1.46 0.00 3.32
1245 1639 4.752879 GGCAAGTACCGCGGCTCA 62.753 66.667 28.58 8.04 0.00 4.26
1246 1640 3.188786 GCAAGTACCGCGGCTCAG 61.189 66.667 28.58 13.11 0.00 3.35
1292 1686 2.034879 CCATGGCGGCGATGGATAC 61.035 63.158 32.67 0.00 41.30 2.24
1319 1713 4.612412 GGCAACGTCCGGGACACA 62.612 66.667 25.80 0.00 32.09 3.72
1320 1714 2.358247 GCAACGTCCGGGACACAT 60.358 61.111 25.80 8.73 32.09 3.21
1331 1725 1.517832 GGACACATCCCTCCTCACG 59.482 63.158 0.00 0.00 39.39 4.35
1332 1726 1.153549 GACACATCCCTCCTCACGC 60.154 63.158 0.00 0.00 0.00 5.34
1333 1727 2.187946 CACATCCCTCCTCACGCC 59.812 66.667 0.00 0.00 0.00 5.68
1390 1784 0.939577 CCGCAAGACCGGTCGATATG 60.940 60.000 28.26 23.94 43.24 1.78
1468 1875 6.940298 TGACTATGATGATGTACTCGTATGGA 59.060 38.462 0.00 0.00 0.00 3.41
1469 1876 7.447238 TGACTATGATGATGTACTCGTATGGAA 59.553 37.037 0.00 0.00 0.00 3.53
1470 1877 8.178313 ACTATGATGATGTACTCGTATGGAAA 57.822 34.615 0.00 0.00 0.00 3.13
1471 1878 8.082852 ACTATGATGATGTACTCGTATGGAAAC 58.917 37.037 0.00 0.00 0.00 2.78
1501 1930 2.418628 CTGTGTTTGTTGACCTCGTGTT 59.581 45.455 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 7.498443 ACGGAGGGAGTATAAATTAGTGAAAG 58.502 38.462 0.00 0.00 0.00 2.62
80 81 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
81 82 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
82 83 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
83 84 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
112 113 9.733219 GAGCGTTTAGATCACTAAAGTAGTTAT 57.267 33.333 0.00 0.00 45.42 1.89
113 114 8.954350 AGAGCGTTTAGATCACTAAAGTAGTTA 58.046 33.333 0.00 0.00 45.42 2.24
114 115 7.828712 AGAGCGTTTAGATCACTAAAGTAGTT 58.171 34.615 0.00 0.00 45.42 2.24
115 116 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
116 117 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
131 132 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
132 133 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
133 134 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
134 135 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
135 136 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
141 142 9.884814 ACATCTACTCCCTCTGTAAACTAATAT 57.115 33.333 0.00 0.00 0.00 1.28
142 143 9.710818 AACATCTACTCCCTCTGTAAACTAATA 57.289 33.333 0.00 0.00 0.00 0.98
143 144 8.611051 AACATCTACTCCCTCTGTAAACTAAT 57.389 34.615 0.00 0.00 0.00 1.73
144 145 8.431910 AAACATCTACTCCCTCTGTAAACTAA 57.568 34.615 0.00 0.00 0.00 2.24
145 146 9.537852 TTAAACATCTACTCCCTCTGTAAACTA 57.462 33.333 0.00 0.00 0.00 2.24
146 147 6.936968 AAACATCTACTCCCTCTGTAAACT 57.063 37.500 0.00 0.00 0.00 2.66
147 148 8.092687 TGTTAAACATCTACTCCCTCTGTAAAC 58.907 37.037 0.00 0.00 0.00 2.01
148 149 8.197592 TGTTAAACATCTACTCCCTCTGTAAA 57.802 34.615 0.00 0.00 0.00 2.01
149 150 7.786046 TGTTAAACATCTACTCCCTCTGTAA 57.214 36.000 0.00 0.00 0.00 2.41
150 151 7.233962 TGTTGTTAAACATCTACTCCCTCTGTA 59.766 37.037 0.00 0.00 41.41 2.74
151 152 6.042781 TGTTGTTAAACATCTACTCCCTCTGT 59.957 38.462 0.00 0.00 41.41 3.41
152 153 6.464222 TGTTGTTAAACATCTACTCCCTCTG 58.536 40.000 0.00 0.00 41.41 3.35
153 154 6.681729 TGTTGTTAAACATCTACTCCCTCT 57.318 37.500 0.00 0.00 41.41 3.69
309 310 0.111253 CCCAACCAAAGCACCTCTCT 59.889 55.000 0.00 0.00 0.00 3.10
310 311 1.527433 GCCCAACCAAAGCACCTCTC 61.527 60.000 0.00 0.00 0.00 3.20
481 812 1.328680 CATGAACAGTGTAGCATCCGC 59.671 52.381 0.00 0.00 38.99 5.54
691 1061 4.323417 TGTTTATGATCGGAGCAAACACT 58.677 39.130 8.88 0.00 34.97 3.55
801 1173 2.890945 CCCTCGTTGACTTTTCCCAAAT 59.109 45.455 0.00 0.00 0.00 2.32
802 1174 2.303175 CCCTCGTTGACTTTTCCCAAA 58.697 47.619 0.00 0.00 0.00 3.28
805 1177 1.574702 CGCCCTCGTTGACTTTTCCC 61.575 60.000 0.00 0.00 0.00 3.97
817 1189 1.355066 GAGAAAGCTTCACGCCCTCG 61.355 60.000 0.00 0.00 40.39 4.63
829 1201 1.743252 CGGTGAGCAGGGAGAAAGC 60.743 63.158 0.00 0.00 0.00 3.51
830 1202 0.321671 TTCGGTGAGCAGGGAGAAAG 59.678 55.000 0.00 0.00 0.00 2.62
831 1203 0.762418 TTTCGGTGAGCAGGGAGAAA 59.238 50.000 0.00 0.00 0.00 2.52
838 1210 3.793144 GCGCCTTTCGGTGAGCAG 61.793 66.667 0.00 0.00 43.70 4.24
908 1282 2.579518 TCGACTGCGCTGCGTATG 60.580 61.111 24.04 15.39 37.46 2.39
939 1333 8.738106 GGTCGGGCTGGAGTTATATATATATAC 58.262 40.741 11.30 7.70 0.00 1.47
940 1334 8.450434 TGGTCGGGCTGGAGTTATATATATATA 58.550 37.037 8.16 8.16 0.00 0.86
941 1335 7.302948 TGGTCGGGCTGGAGTTATATATATAT 58.697 38.462 10.10 10.10 0.00 0.86
942 1336 6.675565 TGGTCGGGCTGGAGTTATATATATA 58.324 40.000 0.00 0.00 0.00 0.86
943 1337 5.525484 TGGTCGGGCTGGAGTTATATATAT 58.475 41.667 0.00 0.00 0.00 0.86
944 1338 4.938028 TGGTCGGGCTGGAGTTATATATA 58.062 43.478 0.00 0.00 0.00 0.86
960 1354 1.821759 TGTTGTGCACCTTGGTCGG 60.822 57.895 15.69 0.00 0.00 4.79
977 1371 2.064014 GGTACCGTTTCTTTCTCCGTG 58.936 52.381 0.00 0.00 0.00 4.94
983 1377 3.187842 GTCCATGTGGTACCGTTTCTTTC 59.812 47.826 7.57 0.00 36.34 2.62
1277 1671 4.293648 CCGTATCCATCGCCGCCA 62.294 66.667 0.00 0.00 0.00 5.69
1305 1699 2.660802 GGATGTGTCCCGGACGTT 59.339 61.111 13.02 0.00 38.69 3.99
1319 1713 4.779733 ACGGGCGTGAGGAGGGAT 62.780 66.667 0.00 0.00 0.00 3.85
1328 1722 2.278206 CTCGATCTCACGGGCGTG 60.278 66.667 0.00 0.00 46.64 5.34
1333 1727 2.279502 TTTCCCGCTCGATCTCACGG 62.280 60.000 9.46 9.46 45.21 4.94
1379 1773 0.603065 TCATGGAGCATATCGACCGG 59.397 55.000 0.00 0.00 0.00 5.28
1406 1805 2.436469 TGCAGCCAGGCACATACG 60.436 61.111 15.80 0.00 39.25 3.06
1664 2106 2.282180 GCCGGAAACTGGCAAGGA 60.282 61.111 5.05 0.00 45.41 3.36
1740 2188 4.348495 AAGCGGAAGGGGAGGGGA 62.348 66.667 0.00 0.00 0.00 4.81
1741 2189 3.798511 GAAGCGGAAGGGGAGGGG 61.799 72.222 0.00 0.00 0.00 4.79
1742 2190 3.798511 GGAAGCGGAAGGGGAGGG 61.799 72.222 0.00 0.00 0.00 4.30
1743 2191 3.798511 GGGAAGCGGAAGGGGAGG 61.799 72.222 0.00 0.00 0.00 4.30
1744 2192 3.798511 GGGGAAGCGGAAGGGGAG 61.799 72.222 0.00 0.00 0.00 4.30



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

AutoCloner maintained by Alex Coulton.