Multiple sequence alignment - TraesCS7D01G030600

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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 TraesCS7D01G030600 chr7D 100.000 3185 0 0 1 3185 16121329 16118145 0.000000e+00 5882.0
1 TraesCS7D01G030600 chr7D 88.827 179 18 2 1581 1757 582031182 582031004 5.350000e-53 219.0
2 TraesCS7D01G030600 chr7D 93.243 74 4 1 1581 1653 59952311 59952384 1.210000e-19 108.0
3 TraesCS7D01G030600 chr3D 97.341 2896 67 5 293 3185 584758286 584761174 0.000000e+00 4913.0
4 TraesCS7D01G030600 chr3D 97.394 307 4 1 1 303 584732537 584732843 1.310000e-143 520.0
5 TraesCS7D01G030600 chr7A 93.389 2284 93 22 153 2428 14920518 14918285 0.000000e+00 3328.0
6 TraesCS7D01G030600 chr7A 92.857 322 20 3 2866 3185 14917205 14916885 6.220000e-127 464.0
7 TraesCS7D01G030600 chr7A 75.351 783 151 24 1314 2064 618677792 618678564 3.940000e-89 339.0
8 TraesCS7D01G030600 chr7A 88.636 176 17 3 1 175 14920636 14920463 8.950000e-51 211.0
9 TraesCS7D01G030600 chr7A 94.488 127 7 0 2730 2856 14917848 14917722 2.510000e-46 196.0
10 TraesCS7D01G030600 chr7A 92.920 113 8 0 2427 2539 14918123 14918011 7.070000e-37 165.0
11 TraesCS7D01G030600 chr7A 81.122 196 31 4 1314 1506 619022980 619023172 5.500000e-33 152.0
12 TraesCS7D01G030600 chr7A 83.158 95 8 3 3036 3123 9717488 9717395 2.630000e-11 80.5
13 TraesCS7D01G030600 chr4A 88.969 2484 173 39 297 2744 718753814 718751396 0.000000e+00 2976.0
14 TraesCS7D01G030600 chr4A 84.884 172 17 6 3020 3185 718957311 718957479 7.070000e-37 165.0
15 TraesCS7D01G030600 chr4A 93.333 105 5 2 2866 2968 718957279 718957383 1.530000e-33 154.0
16 TraesCS7D01G030600 chr4A 100.000 39 0 0 226 264 718753853 718753815 4.410000e-09 73.1
17 TraesCS7D01G030600 chr7B 91.658 1954 94 20 462 2399 711443148 711441248 0.000000e+00 2641.0
18 TraesCS7D01G030600 chr7B 91.388 418 25 7 2442 2856 711441238 711440829 2.150000e-156 562.0
19 TraesCS7D01G030600 chr7B 95.035 282 11 3 2907 3185 711440624 711440343 1.050000e-119 440.0
20 TraesCS7D01G030600 chr7B 75.258 776 158 19 1314 2060 580133993 580134763 3.940000e-89 339.0
21 TraesCS7D01G030600 chr7B 75.351 783 152 24 1314 2064 580135127 580135900 3.940000e-89 339.0
22 TraesCS7D01G030600 chr7B 92.143 140 7 2 225 360 711443604 711443465 9.010000e-46 195.0
23 TraesCS7D01G030600 chr7B 89.888 89 8 1 60 148 711444619 711444532 2.600000e-21 113.0
24 TraesCS7D01G030600 chr6D 93.243 74 4 1 1581 1653 55766599 55766672 1.210000e-19 108.0
25 TraesCS7D01G030600 chr5A 92.208 77 5 1 1581 1656 633749650 633749574 1.210000e-19 108.0
26 TraesCS7D01G030600 chr2D 93.243 74 4 1 1581 1653 7330102 7330175 1.210000e-19 108.0
27 TraesCS7D01G030600 chr4B 86.000 100 9 5 2992 3088 7841666 7841763 5.620000e-18 102.0
28 TraesCS7D01G030600 chr5D 88.732 71 7 1 2995 3064 556375219 556375149 5.660000e-13 86.1
29 TraesCS7D01G030600 chr3B 88.000 75 5 3 3016 3086 760141356 760141430 5.660000e-13 86.1
30 TraesCS7D01G030600 chr3B 82.292 96 12 5 2996 3086 140396343 140396248 9.470000e-11 78.7


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 TraesCS7D01G030600 chr7D 16118145 16121329 3184 True 5882.00 5882 100.0000 1 3185 1 chr7D.!!$R1 3184
1 TraesCS7D01G030600 chr3D 584758286 584761174 2888 False 4913.00 4913 97.3410 293 3185 1 chr3D.!!$F2 2892
2 TraesCS7D01G030600 chr7A 14916885 14920636 3751 True 872.80 3328 92.4580 1 3185 5 chr7A.!!$R2 3184
3 TraesCS7D01G030600 chr7A 618677792 618678564 772 False 339.00 339 75.3510 1314 2064 1 chr7A.!!$F1 750
4 TraesCS7D01G030600 chr4A 718751396 718753853 2457 True 1524.55 2976 94.4845 226 2744 2 chr4A.!!$R1 2518
5 TraesCS7D01G030600 chr7B 711440343 711444619 4276 True 790.20 2641 92.0224 60 3185 5 chr7B.!!$R1 3125
6 TraesCS7D01G030600 chr7B 580133993 580135900 1907 False 339.00 339 75.3045 1314 2064 2 chr7B.!!$F1 750

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
313 1204 0.820482 AACAACCCGTTTCCCTTCCG 60.82 55.0 0.00 0.00 32.35 4.30 F
1107 2269 0.109597 GCCCGCTTCACTCAATTGTG 60.11 55.0 5.13 5.59 39.15 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 3982 0.604073 TGGCGATGAACTGACCGTTA 59.396 50.0 0.00 0.00 35.56 3.18 R
2319 4662 1.012841 GTTGCTGATGCTCTGCCTAC 58.987 55.0 10.77 6.93 40.10 3.18 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
73 75 4.702131 GCTGATTGTCCCATGAGTACTTTT 59.298 41.667 0.00 0.00 0.00 2.27
74 76 5.392380 GCTGATTGTCCCATGAGTACTTTTG 60.392 44.000 0.00 0.00 0.00 2.44
108 110 1.266989 CTCAAAGTTCCCCGCAAAGAC 59.733 52.381 0.00 0.00 0.00 3.01
115 117 1.172180 TCCCCGCAAAGACAAAGCAG 61.172 55.000 0.00 0.00 0.00 4.24
128 130 5.611374 AGACAAAGCAGAAACTAGCAGTTA 58.389 37.500 2.60 0.00 37.47 2.24
131 133 5.467063 ACAAAGCAGAAACTAGCAGTTAGTC 59.533 40.000 0.00 0.00 41.80 2.59
133 135 5.476091 AGCAGAAACTAGCAGTTAGTCTT 57.524 39.130 0.00 0.00 41.80 3.01
158 160 5.462530 TTTTTAGGGAAAAGCCAACTAGC 57.537 39.130 0.00 0.00 35.96 3.42
159 161 3.799432 TTAGGGAAAAGCCAACTAGCA 57.201 42.857 0.00 0.00 38.95 3.49
160 162 2.206576 AGGGAAAAGCCAACTAGCAG 57.793 50.000 0.00 0.00 38.95 4.24
161 163 1.425448 AGGGAAAAGCCAACTAGCAGT 59.575 47.619 0.00 0.00 38.95 4.40
162 164 2.158460 AGGGAAAAGCCAACTAGCAGTT 60.158 45.455 0.00 0.00 39.39 3.16
163 165 3.073946 AGGGAAAAGCCAACTAGCAGTTA 59.926 43.478 0.00 0.00 36.03 2.24
164 166 3.440522 GGGAAAAGCCAACTAGCAGTTAG 59.559 47.826 0.00 0.00 36.03 2.34
165 167 4.072839 GGAAAAGCCAACTAGCAGTTAGT 58.927 43.478 0.00 0.00 44.55 2.24
313 1204 0.820482 AACAACCCGTTTCCCTTCCG 60.820 55.000 0.00 0.00 32.35 4.30
494 1632 6.432162 CCTTGTTTCATCTATATGGGGTCATG 59.568 42.308 0.00 0.00 34.96 3.07
495 1633 5.316167 TGTTTCATCTATATGGGGTCATGC 58.684 41.667 0.00 0.00 34.96 4.06
496 1634 5.163109 TGTTTCATCTATATGGGGTCATGCA 60.163 40.000 0.00 0.00 34.96 3.96
497 1635 5.784398 TTCATCTATATGGGGTCATGCAT 57.216 39.130 0.00 0.00 34.96 3.96
742 1889 5.912892 TGTCTACTGTTGTGAGACATTTGA 58.087 37.500 6.97 0.00 43.52 2.69
915 2069 5.996669 TGTTCTTGCATGCTATATGTCTG 57.003 39.130 20.33 0.00 0.00 3.51
1101 2263 2.268920 GATGGCCCGCTTCACTCA 59.731 61.111 0.00 0.00 0.00 3.41
1107 2269 0.109597 GCCCGCTTCACTCAATTGTG 60.110 55.000 5.13 5.59 39.15 3.33
1161 2323 3.368571 GCTGCAACCTGCCACTCC 61.369 66.667 0.00 0.00 44.23 3.85
1324 2486 2.032414 TTCTCGATACATGCTACGCG 57.968 50.000 3.53 3.53 0.00 6.01
1360 2522 5.022282 TGATGTAGCTAGCAACAATAGCA 57.978 39.130 18.83 3.88 46.57 3.49
1490 3786 3.381136 CACCGGGGCCATGGTTTG 61.381 66.667 16.29 3.90 35.96 2.93
1647 3958 2.619074 GGAACTCCAACTTCCTCATGGG 60.619 54.545 0.00 0.00 35.23 4.00
1656 3967 5.308825 CAACTTCCTCATGGGTGGATATAC 58.691 45.833 0.00 0.00 36.62 1.47
1671 3982 4.100963 TGGATATACCAGATCGTGCAGTTT 59.899 41.667 0.00 0.00 44.64 2.66
1862 4173 0.319083 TTTGTGCACCTATCGTCCGT 59.681 50.000 15.69 0.00 0.00 4.69
2022 4342 1.594331 GAGGGACGAGCAACAACTTT 58.406 50.000 0.00 0.00 0.00 2.66
2154 4474 0.179020 CGATGGCCATGTGGGTGTAT 60.179 55.000 26.56 0.00 39.65 2.29
2157 4477 1.210885 TGGCCATGTGGGTGTATCCA 61.211 55.000 0.00 0.00 39.65 3.41
2288 4631 1.379916 TGCTAGGCAGTGGCAATGT 59.620 52.632 20.04 0.00 40.22 2.71
2519 5029 4.260985 TCAGAGTTCTCTGTGCTCTCTAG 58.739 47.826 23.46 1.26 37.48 2.43
2739 5388 7.223339 GCGATTTTAATCTGTGAGTATCATCG 58.777 38.462 0.00 0.00 39.42 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 7.201875 GGGAACTTTGAGACCTTTATTCAAACA 60.202 37.037 0.00 0.00 36.28 2.83
74 76 7.145985 GGGAACTTTGAGACCTTTATTCAAAC 58.854 38.462 0.00 0.00 36.28 2.93
108 110 5.698545 AGACTAACTGCTAGTTTCTGCTTTG 59.301 40.000 6.82 0.00 41.17 2.77
140 142 2.642807 ACTGCTAGTTGGCTTTTCCCTA 59.357 45.455 0.00 0.00 0.00 3.53
144 146 5.690997 AACTAACTGCTAGTTGGCTTTTC 57.309 39.130 2.84 0.00 46.96 2.29
205 542 4.568760 GGTCTAACTACTGATTGCTTGCTC 59.431 45.833 0.00 0.00 0.00 4.26
207 544 3.623510 GGGTCTAACTACTGATTGCTTGC 59.376 47.826 0.00 0.00 0.00 4.01
208 545 4.832248 TGGGTCTAACTACTGATTGCTTG 58.168 43.478 0.00 0.00 0.00 4.01
209 546 5.431765 CATGGGTCTAACTACTGATTGCTT 58.568 41.667 0.00 0.00 0.00 3.91
210 547 4.684485 GCATGGGTCTAACTACTGATTGCT 60.684 45.833 0.00 0.00 0.00 3.91
212 549 4.769688 TGCATGGGTCTAACTACTGATTG 58.230 43.478 0.00 0.00 0.00 2.67
213 550 5.435686 TTGCATGGGTCTAACTACTGATT 57.564 39.130 0.00 0.00 0.00 2.57
214 551 5.186198 GTTTGCATGGGTCTAACTACTGAT 58.814 41.667 0.00 0.00 0.00 2.90
215 552 4.564821 GGTTTGCATGGGTCTAACTACTGA 60.565 45.833 0.00 0.00 0.00 3.41
216 553 3.689649 GGTTTGCATGGGTCTAACTACTG 59.310 47.826 0.00 0.00 0.00 2.74
217 554 3.308188 GGGTTTGCATGGGTCTAACTACT 60.308 47.826 0.00 0.00 0.00 2.57
218 555 3.014623 GGGTTTGCATGGGTCTAACTAC 58.985 50.000 0.00 0.00 0.00 2.73
220 557 1.427368 TGGGTTTGCATGGGTCTAACT 59.573 47.619 0.00 0.00 0.00 2.24
221 558 1.917872 TGGGTTTGCATGGGTCTAAC 58.082 50.000 0.00 0.00 0.00 2.34
222 559 2.158385 ACTTGGGTTTGCATGGGTCTAA 60.158 45.455 0.00 0.00 0.00 2.10
494 1632 5.579904 AGATGATTCGTAGACATATGCATGC 59.420 40.000 11.82 11.82 34.32 4.06
495 1633 8.186821 TCTAGATGATTCGTAGACATATGCATG 58.813 37.037 10.16 0.00 34.32 4.06
496 1634 8.286191 TCTAGATGATTCGTAGACATATGCAT 57.714 34.615 3.79 3.79 34.32 3.96
497 1635 7.687941 TCTAGATGATTCGTAGACATATGCA 57.312 36.000 1.58 0.00 34.32 3.96
1101 2263 2.450476 GATCCCAACAGAGCCACAATT 58.550 47.619 0.00 0.00 0.00 2.32
1161 2323 1.303799 AAGAGAATGCTGCACGCCAG 61.304 55.000 3.57 0.00 44.67 4.85
1324 2486 7.096558 GCTAGCTACATCAATGACTTTACGTAC 60.097 40.741 7.70 0.00 0.00 3.67
1360 2522 1.078143 GAATCTGGCAGCGAAGGGT 60.078 57.895 10.34 0.00 0.00 4.34
1490 3786 2.523453 GAAAGGGAGACGTGGAGGCC 62.523 65.000 0.00 0.00 0.00 5.19
1647 3958 3.005897 ACTGCACGATCTGGTATATCCAC 59.994 47.826 0.00 0.00 41.93 4.02
1656 3967 1.393539 CCGTTAAACTGCACGATCTGG 59.606 52.381 0.00 0.00 38.76 3.86
1671 3982 0.604073 TGGCGATGAACTGACCGTTA 59.396 50.000 0.00 0.00 35.56 3.18
2022 4342 2.688446 CTGAGAGTGATGGGCGTAGTAA 59.312 50.000 0.00 0.00 0.00 2.24
2067 4387 3.070576 GCAAGGTCCACATGGCCC 61.071 66.667 0.00 0.00 33.61 5.80
2154 4474 2.176045 TCGGAGTAGAACATGCTTGGA 58.824 47.619 4.44 0.00 0.00 3.53
2157 4477 2.743183 GCCATCGGAGTAGAACATGCTT 60.743 50.000 0.00 0.00 0.00 3.91
2314 4657 2.823984 CTGATGCTCTGCCTACAAGAG 58.176 52.381 0.00 0.00 0.00 2.85
2319 4662 1.012841 GTTGCTGATGCTCTGCCTAC 58.987 55.000 10.77 6.93 40.10 3.18
2739 5388 6.264832 TGATGAACACACACTTGTTTTGATC 58.735 36.000 0.00 0.00 39.88 2.92


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

AutoCloner maintained by Alex Coulton.