Multiple sequence alignment - TraesCS7D01G294500

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 TraesCS7D01G294500 chr7D 100.000 5183 0 0 1 5183 368008563 368013745 0.000000e+00 9572.0
1 TraesCS7D01G294500 chr7A 96.780 4254 55 19 990 5183 407296185 407300416 0.000000e+00 7022.0
2 TraesCS7D01G294500 chr7A 90.490 673 58 4 1 672 407257446 407258113 0.000000e+00 883.0
3 TraesCS7D01G294500 chr7A 88.667 300 13 7 667 964 407295909 407296189 3.840000e-91 346.0
4 TraesCS7D01G294500 chr7B 98.066 3465 40 5 815 4276 312812831 312816271 0.000000e+00 6002.0
5 TraesCS7D01G294500 chr7B 94.793 653 12 7 4443 5074 312816805 312817456 0.000000e+00 998.0
6 TraesCS7D01G294500 chr7B 87.820 821 58 21 1 815 312811044 312811828 0.000000e+00 924.0
7 TraesCS7D01G294500 chr7B 96.795 156 1 2 4293 4444 312816544 312816699 1.850000e-64 257.0
8 TraesCS7D01G294500 chr7B 98.611 72 1 0 5112 5183 312817569 312817640 1.510000e-25 128.0
9 TraesCS7D01G294500 chr7B 94.444 54 3 0 5078 5131 312817503 312817556 3.330000e-12 84.2
10 TraesCS7D01G294500 chr2B 85.199 277 26 9 992 1268 143938285 143938024 2.380000e-68 270.0
11 TraesCS7D01G294500 chr2B 92.308 117 6 3 1 115 610007764 610007879 4.150000e-36 163.0
12 TraesCS7D01G294500 chr2D 83.209 268 31 9 992 1255 90824846 90824589 3.120000e-57 233.0
13 TraesCS7D01G294500 chr5B 93.162 117 7 1 1 116 505864705 505864589 2.480000e-38 171.0
14 TraesCS7D01G294500 chr2A 95.370 108 3 2 1 107 233096790 233096684 2.480000e-38 171.0
15 TraesCS7D01G294500 chr2A 93.860 114 5 2 4 116 528983400 528983288 2.480000e-38 171.0
16 TraesCS7D01G294500 chr2A 92.241 116 9 0 1 116 711026873 711026988 1.150000e-36 165.0
17 TraesCS7D01G294500 chr6B 90.476 126 8 4 1 124 356745117 356744994 4.150000e-36 163.0
18 TraesCS7D01G294500 chr1A 90.984 122 8 3 1 121 528632038 528632157 1.490000e-35 161.0


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 TraesCS7D01G294500 chr7D 368008563 368013745 5182 False 9572.000000 9572 100.000000 1 5183 1 chr7D.!!$F1 5182
1 TraesCS7D01G294500 chr7A 407295909 407300416 4507 False 3684.000000 7022 92.723500 667 5183 2 chr7A.!!$F2 4516
2 TraesCS7D01G294500 chr7A 407257446 407258113 667 False 883.000000 883 90.490000 1 672 1 chr7A.!!$F1 671
3 TraesCS7D01G294500 chr7B 312811044 312817640 6596 False 1398.866667 6002 95.088167 1 5183 6 chr7B.!!$F1 5182

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
51 52 1.066908 CTTCTCGTGAGCCTCTGATCC 59.933 57.143 0.00 0.0 0.00 3.36 F
961 1971 1.153628 CGTCTAGGGTTTCCGCCTG 60.154 63.158 0.00 0.0 38.33 4.85 F
1872 2909 0.806868 TCGACGCGTTTATGGACTCT 59.193 50.000 15.53 0.0 0.00 3.24 F
1963 3000 2.288395 GCAGGTGGTTTGAATGACAAGG 60.288 50.000 0.00 0.0 39.77 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1270 2304 0.340208 TCCCTCTCCCTCTCCCTTTC 59.660 60.000 0.0 0.0 0.00 2.62 R
1963 3000 0.883833 CTTGTGGCATCCTTCACACC 59.116 55.000 0.0 0.0 42.67 4.16 R
2916 3953 3.626670 CCATCTGAATCTCAACAGGCTTC 59.373 47.826 0.0 0.0 35.20 3.86 R
4285 5335 4.505313 TCAGTCTACACACAAGCAGTAG 57.495 45.455 0.0 0.0 37.23 2.57 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
42 43 4.266502 GTGTTGTGATATCTTCTCGTGAGC 59.733 45.833 3.98 0.00 0.00 4.26
51 52 1.066908 CTTCTCGTGAGCCTCTGATCC 59.933 57.143 0.00 0.00 0.00 3.36
61 62 1.271102 GCCTCTGATCCTGATCGTACC 59.729 57.143 2.91 0.00 40.63 3.34
117 118 2.603473 CGTCACACCTCCCCTCCA 60.603 66.667 0.00 0.00 0.00 3.86
221 222 2.396157 CCGCGCCTCAACCTAAACC 61.396 63.158 0.00 0.00 0.00 3.27
228 229 2.239907 GCCTCAACCTAAACCAGATCCT 59.760 50.000 0.00 0.00 0.00 3.24
230 231 4.080526 GCCTCAACCTAAACCAGATCCTAA 60.081 45.833 0.00 0.00 0.00 2.69
232 233 5.045869 CCTCAACCTAAACCAGATCCTAACA 60.046 44.000 0.00 0.00 0.00 2.41
236 237 4.536489 ACCTAAACCAGATCCTAACAAGCT 59.464 41.667 0.00 0.00 0.00 3.74
246 247 2.238898 TCCTAACAAGCTAAGCCCCTTC 59.761 50.000 0.00 0.00 0.00 3.46
281 282 4.776322 CGCCGAGCCCAACATCCA 62.776 66.667 0.00 0.00 0.00 3.41
327 330 3.118531 AGATGCTGGGGATTTCTACAGT 58.881 45.455 0.00 0.00 33.62 3.55
384 387 1.537135 GGAACCTGCTCTGTAGATCGC 60.537 57.143 0.00 0.00 0.00 4.58
435 438 1.516603 GCCTTCGTGCGTAGTCCTC 60.517 63.158 0.00 0.00 0.00 3.71
455 458 4.329545 GCAGTCTTCACCGCCCCA 62.330 66.667 0.00 0.00 0.00 4.96
527 531 1.210722 GGGAGGAGGAACCAGAATGTC 59.789 57.143 0.00 0.00 42.04 3.06
533 537 2.352960 GAGGAACCAGAATGTCGCAATC 59.647 50.000 0.00 0.00 0.00 2.67
540 544 3.256558 CAGAATGTCGCAATCACTCTCA 58.743 45.455 0.00 0.00 0.00 3.27
696 700 6.540914 TCAGTCGGTTGAAATAGACACTTTTT 59.459 34.615 0.00 0.00 36.18 1.94
710 714 6.220930 AGACACTTTTTCATACTGCTTCGTA 58.779 36.000 0.00 0.00 0.00 3.43
711 715 6.145696 AGACACTTTTTCATACTGCTTCGTAC 59.854 38.462 0.00 0.00 0.00 3.67
713 717 5.178623 CACTTTTTCATACTGCTTCGTACCA 59.821 40.000 0.00 0.00 0.00 3.25
714 718 5.178809 ACTTTTTCATACTGCTTCGTACCAC 59.821 40.000 0.00 0.00 0.00 4.16
715 719 3.945981 TTCATACTGCTTCGTACCACA 57.054 42.857 0.00 0.00 0.00 4.17
716 720 3.226346 TCATACTGCTTCGTACCACAC 57.774 47.619 0.00 0.00 0.00 3.82
717 721 2.559231 TCATACTGCTTCGTACCACACA 59.441 45.455 0.00 0.00 0.00 3.72
832 1842 3.529634 AATTGAACGCAAAATCGTCGA 57.470 38.095 0.00 0.00 42.46 4.20
878 1888 5.048364 ACGGCATCTAAACAACTTGCAATAA 60.048 36.000 0.00 0.00 35.04 1.40
879 1889 6.035843 CGGCATCTAAACAACTTGCAATAAT 58.964 36.000 0.00 0.00 35.04 1.28
880 1890 7.148154 ACGGCATCTAAACAACTTGCAATAATA 60.148 33.333 0.00 0.00 35.04 0.98
961 1971 1.153628 CGTCTAGGGTTTCCGCCTG 60.154 63.158 0.00 0.00 38.33 4.85
1030 2040 3.371063 ACGATGACCGCGTCACCT 61.371 61.111 4.92 0.00 45.65 4.00
1053 2063 3.256960 AAGCACCACCACCGGGAT 61.257 61.111 6.32 0.00 38.05 3.85
1145 2155 3.359523 CGACGACAGGGACGGTGA 61.360 66.667 0.00 0.00 36.51 4.02
1146 2156 2.567049 GACGACAGGGACGGTGAG 59.433 66.667 0.00 0.00 36.51 3.51
1147 2157 3.628280 GACGACAGGGACGGTGAGC 62.628 68.421 0.00 0.00 36.51 4.26
1148 2158 4.778415 CGACAGGGACGGTGAGCG 62.778 72.222 1.13 1.13 36.51 5.03
1149 2159 4.436998 GACAGGGACGGTGAGCGG 62.437 72.222 9.43 0.00 36.51 5.52
1268 2302 2.657459 AGAAGGAGGAGAAGAGGGAGAA 59.343 50.000 0.00 0.00 0.00 2.87
1269 2303 2.846665 AGGAGGAGAAGAGGGAGAAG 57.153 55.000 0.00 0.00 0.00 2.85
1270 2304 1.290732 AGGAGGAGAAGAGGGAGAAGG 59.709 57.143 0.00 0.00 0.00 3.46
1271 2305 1.289530 GGAGGAGAAGAGGGAGAAGGA 59.710 57.143 0.00 0.00 0.00 3.36
1272 2306 2.292587 GGAGGAGAAGAGGGAGAAGGAA 60.293 54.545 0.00 0.00 0.00 3.36
1273 2307 3.445987 GAGGAGAAGAGGGAGAAGGAAA 58.554 50.000 0.00 0.00 0.00 3.13
1274 2308 3.449918 AGGAGAAGAGGGAGAAGGAAAG 58.550 50.000 0.00 0.00 0.00 2.62
1275 2309 2.503765 GGAGAAGAGGGAGAAGGAAAGG 59.496 54.545 0.00 0.00 0.00 3.11
1276 2310 2.503765 GAGAAGAGGGAGAAGGAAAGGG 59.496 54.545 0.00 0.00 0.00 3.95
1277 2311 2.114506 AGAAGAGGGAGAAGGAAAGGGA 59.885 50.000 0.00 0.00 0.00 4.20
1278 2312 2.262266 AGAGGGAGAAGGAAAGGGAG 57.738 55.000 0.00 0.00 0.00 4.30
1279 2313 1.725182 AGAGGGAGAAGGAAAGGGAGA 59.275 52.381 0.00 0.00 0.00 3.71
1503 2540 1.074926 GGAGGAGGAGGAGGATGCA 60.075 63.158 0.00 0.00 0.00 3.96
1710 2747 2.370189 CAAGTCTGGGAAGAAGTGGACT 59.630 50.000 0.00 0.00 35.87 3.85
1818 2855 5.116084 ACATGGATAATGGCAGTAACAGT 57.884 39.130 0.00 0.27 40.94 3.55
1872 2909 0.806868 TCGACGCGTTTATGGACTCT 59.193 50.000 15.53 0.00 0.00 3.24
1963 3000 2.288395 GCAGGTGGTTTGAATGACAAGG 60.288 50.000 0.00 0.00 39.77 3.61
2772 3809 2.843701 AGAGTGACTTTCTTGGTGCTG 58.156 47.619 0.00 0.00 0.00 4.41
3267 4304 5.429957 AAGATCTTGAGCTTGTTGTCAAC 57.570 39.130 7.30 8.86 0.00 3.18
3276 4313 5.764686 TGAGCTTGTTGTCAACTATGATGTT 59.235 36.000 16.45 0.00 38.01 2.71
4460 5867 9.713713 TTGACAACTATATTGCAAAGTACTACA 57.286 29.630 1.71 0.00 0.00 2.74
4679 6086 5.897050 AGCTTGGAACGTTTTGACAATTTA 58.103 33.333 0.46 0.00 0.00 1.40
4734 6163 3.817647 GGACATAAGGCTTAGAATGCAGG 59.182 47.826 13.15 0.00 0.00 4.85
4736 6165 4.455606 ACATAAGGCTTAGAATGCAGGTC 58.544 43.478 13.15 0.00 0.00 3.85
4812 6243 7.496263 TGCAGTTTACTGTTGTGAACACTAATA 59.504 33.333 11.23 0.00 45.45 0.98
4951 6383 6.807789 TGTTGGGAATAAAAACTTAAACGCT 58.192 32.000 0.00 0.00 0.00 5.07
4956 6388 8.848182 TGGGAATAAAAACTTAAACGCTAAAGA 58.152 29.630 0.00 0.00 0.00 2.52
5074 6506 6.814146 TCTGTGTTAAATTTGTGGTTTGGTTC 59.186 34.615 0.00 0.00 0.00 3.62
5075 6507 6.702329 TGTGTTAAATTTGTGGTTTGGTTCT 58.298 32.000 0.00 0.00 0.00 3.01
5077 6509 6.592220 GTGTTAAATTTGTGGTTTGGTTCTGT 59.408 34.615 0.00 0.00 0.00 3.41
5078 6510 7.760340 GTGTTAAATTTGTGGTTTGGTTCTGTA 59.240 33.333 0.00 0.00 0.00 2.74
5079 6511 7.976734 TGTTAAATTTGTGGTTTGGTTCTGTAG 59.023 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.889829 GGGTACGATCAGGATCAGAGG 59.110 57.143 9.72 0.00 37.69 3.69
51 52 2.945008 ACATGCAAATGGGTACGATCAG 59.055 45.455 0.00 0.00 0.00 2.90
61 62 8.785946 TCATACACTAATCATACATGCAAATGG 58.214 33.333 0.00 0.00 0.00 3.16
117 118 2.214216 TGTGCTAGGGTTCAGCGGT 61.214 57.895 0.00 0.00 42.13 5.68
172 173 5.433526 CCCTTCGAGGTTGTATTTTGGATA 58.566 41.667 0.00 0.00 31.93 2.59
212 213 5.014228 AGCTTGTTAGGATCTGGTTTAGGTT 59.986 40.000 0.00 0.00 0.00 3.50
221 222 3.471680 GGGCTTAGCTTGTTAGGATCTG 58.528 50.000 3.59 0.00 0.00 2.90
228 229 1.677820 GCGAAGGGGCTTAGCTTGTTA 60.678 52.381 3.59 0.00 38.65 2.41
230 231 1.377333 GCGAAGGGGCTTAGCTTGT 60.377 57.895 3.59 0.00 38.65 3.16
232 233 0.178301 GTAGCGAAGGGGCTTAGCTT 59.822 55.000 3.59 0.00 46.94 3.74
236 237 1.514087 CGTGTAGCGAAGGGGCTTA 59.486 57.895 0.00 0.00 41.39 3.09
246 247 0.921347 CGGAGGATTTTCGTGTAGCG 59.079 55.000 0.00 0.00 43.01 4.26
281 282 2.704065 CCGATATGTGTTTAGGGGAGGT 59.296 50.000 0.00 0.00 0.00 3.85
327 330 2.497792 ATCACCCCCTGAAATGCGCA 62.498 55.000 14.96 14.96 30.60 6.09
455 458 2.362503 TCGTGGCGTCCATCTCCT 60.363 61.111 1.90 0.00 35.28 3.69
527 531 0.036010 ACCCCTTGAGAGTGATTGCG 60.036 55.000 0.00 0.00 0.00 4.85
533 537 2.046892 CCGCACCCCTTGAGAGTG 60.047 66.667 0.00 0.00 34.58 3.51
540 544 3.637273 GTCTGACCCGCACCCCTT 61.637 66.667 0.00 0.00 0.00 3.95
696 700 2.559231 TGTGTGGTACGAAGCAGTATGA 59.441 45.455 0.00 0.00 39.69 2.15
710 714 7.446931 TCAAATAATAAGTGTCACATGTGTGGT 59.553 33.333 24.63 9.95 45.65 4.16
711 715 7.815641 TCAAATAATAAGTGTCACATGTGTGG 58.184 34.615 24.63 0.02 45.65 4.17
757 762 6.830912 AGAATTGTCACATGGCTATTAGCTA 58.169 36.000 15.02 9.88 41.99 3.32
758 763 5.688807 AGAATTGTCACATGGCTATTAGCT 58.311 37.500 15.02 0.00 41.99 3.32
759 764 6.204359 CAAGAATTGTCACATGGCTATTAGC 58.796 40.000 7.16 7.16 42.34 3.09
805 811 5.118510 ACGATTTTGCGTTCAATTTGGATTC 59.881 36.000 0.00 0.00 42.71 2.52
820 1830 1.978782 CAAGCCTTTCGACGATTTTGC 59.021 47.619 0.00 0.00 0.00 3.68
878 1888 9.582431 TTTCTCGTTTTCTCGACTTGATATTAT 57.418 29.630 0.00 0.00 35.91 1.28
879 1889 8.975410 TTTCTCGTTTTCTCGACTTGATATTA 57.025 30.769 0.00 0.00 35.91 0.98
880 1890 7.412020 GCTTTCTCGTTTTCTCGACTTGATATT 60.412 37.037 0.00 0.00 35.91 1.28
961 1971 2.563427 GGAACGCAAAGCTCAGGC 59.437 61.111 0.00 0.00 39.06 4.85
1030 2040 1.150536 GGTGGTGGTGCTTGGAGAA 59.849 57.895 0.00 0.00 0.00 2.87
1053 2063 1.588082 GTCGCGGTCCTTGTCCTTA 59.412 57.895 6.13 0.00 0.00 2.69
1268 2302 0.341609 CCTCTCCCTCTCCCTTTCCT 59.658 60.000 0.00 0.00 0.00 3.36
1269 2303 0.692756 CCCTCTCCCTCTCCCTTTCC 60.693 65.000 0.00 0.00 0.00 3.13
1270 2304 0.340208 TCCCTCTCCCTCTCCCTTTC 59.660 60.000 0.00 0.00 0.00 2.62
1271 2305 0.341609 CTCCCTCTCCCTCTCCCTTT 59.658 60.000 0.00 0.00 0.00 3.11
1272 2306 1.598856 CCTCCCTCTCCCTCTCCCTT 61.599 65.000 0.00 0.00 0.00 3.95
1273 2307 2.018086 CCTCCCTCTCCCTCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
1274 2308 2.015726 TCCTCCCTCTCCCTCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1275 2309 0.996762 TCTCCTCCCTCTCCCTCTCC 60.997 65.000 0.00 0.00 0.00 3.71
1276 2310 0.478507 CTCTCCTCCCTCTCCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1277 2311 0.998945 CCTCTCCTCCCTCTCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1278 2312 1.541672 CCTCTCCTCCCTCTCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
1279 2313 2.018086 CCCTCTCCTCCCTCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
1480 2517 0.855855 TCCTCCTCCTCCTCCCTTGA 60.856 60.000 0.00 0.00 0.00 3.02
1503 2540 1.304952 CCGTCTCTCCACCTCCTCT 59.695 63.158 0.00 0.00 0.00 3.69
1710 2747 0.613260 CCGACTCCTCACCATCCAAA 59.387 55.000 0.00 0.00 0.00 3.28
1818 2855 1.460255 CTCTTCCAAACCAGCCCCA 59.540 57.895 0.00 0.00 0.00 4.96
1963 3000 0.883833 CTTGTGGCATCCTTCACACC 59.116 55.000 0.00 0.00 42.67 4.16
2772 3809 5.371526 TCAAACATCCTATCAGCTTCATCC 58.628 41.667 0.00 0.00 0.00 3.51
2916 3953 3.626670 CCATCTGAATCTCAACAGGCTTC 59.373 47.826 0.00 0.00 35.20 3.86
4285 5335 4.505313 TCAGTCTACACACAAGCAGTAG 57.495 45.455 0.00 0.00 37.23 2.57
4286 5336 6.564328 CATATCAGTCTACACACAAGCAGTA 58.436 40.000 0.00 0.00 0.00 2.74
4734 6163 5.295787 TCCATTTAGTGTTCACAACAGTGAC 59.704 40.000 0.00 0.00 44.42 3.67
4736 6165 5.527214 TCTCCATTTAGTGTTCACAACAGTG 59.473 40.000 6.93 0.00 44.42 3.66
4812 6243 1.617536 TGGGAGGCAGCATTCTCCT 60.618 57.895 14.01 1.50 46.51 3.69
4951 6383 3.067106 CAGAAAACTCAGCGCCTCTTTA 58.933 45.455 2.29 0.00 0.00 1.85
4956 6388 0.886490 CACCAGAAAACTCAGCGCCT 60.886 55.000 2.29 0.00 0.00 5.52
5074 6506 3.433615 GGCTACAAGTTCACAAGCTACAG 59.566 47.826 0.00 0.00 33.67 2.74
5075 6507 3.181459 TGGCTACAAGTTCACAAGCTACA 60.181 43.478 0.00 0.00 33.67 2.74
5077 6509 3.762407 TGGCTACAAGTTCACAAGCTA 57.238 42.857 0.00 0.00 33.67 3.32
5078 6510 2.638480 TGGCTACAAGTTCACAAGCT 57.362 45.000 0.00 0.00 33.67 3.74
5079 6511 2.813754 TCATGGCTACAAGTTCACAAGC 59.186 45.455 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.