Multiple sequence alignment - TraesCS6D01G229400

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 TraesCS6D01G229400 chr6D 100.000 3570 0 0 624 4193 321776898 321773329 0.000000e+00 6593.0
1 TraesCS6D01G229400 chr6D 100.000 381 0 0 1 381 321777521 321777141 0.000000e+00 704.0
2 TraesCS6D01G229400 chr6D 85.034 147 13 8 4040 4180 56853571 56853428 1.570000e-29 141.0
3 TraesCS6D01G229400 chr6D 85.294 136 14 3 4040 4171 309592477 309592610 7.310000e-28 135.0
4 TraesCS6D01G229400 chr6B 95.806 3624 66 21 624 4193 501770595 501774186 0.000000e+00 5771.0
5 TraesCS6D01G229400 chr6B 89.062 192 13 3 1 186 501770192 501770381 9.070000e-57 231.0
6 TraesCS6D01G229400 chr6B 88.108 185 20 2 3780 3963 487136363 487136180 7.060000e-53 219.0
7 TraesCS6D01G229400 chr6B 88.050 159 7 5 228 381 501770392 501770543 1.200000e-40 178.0
8 TraesCS6D01G229400 chr6B 86.131 137 11 6 4040 4171 477230324 477230457 1.570000e-29 141.0
9 TraesCS6D01G229400 chr6A 95.618 3286 84 22 649 3898 459077453 459074192 0.000000e+00 5216.0
10 TraesCS6D01G229400 chr6A 90.769 260 13 6 1 249 459082033 459081774 1.870000e-88 337.0
11 TraesCS6D01G229400 chr6A 95.652 115 5 0 267 381 459077997 459077883 7.160000e-43 185.0
12 TraesCS6D01G229400 chr6A 90.083 121 10 2 4075 4193 459074155 459074035 5.610000e-34 156.0
13 TraesCS6D01G229400 chr4B 90.286 175 16 1 3789 3963 471307836 471308009 1.170000e-55 228.0
14 TraesCS6D01G229400 chr7A 89.655 174 17 1 3790 3963 230300984 230301156 1.960000e-53 220.0
15 TraesCS6D01G229400 chr5D 89.205 176 17 2 3788 3963 201311966 201312139 7.060000e-53 219.0
16 TraesCS6D01G229400 chr5D 91.667 96 8 0 3962 4057 34800688 34800593 2.630000e-27 134.0
17 TraesCS6D01G229400 chr5D 91.667 96 8 0 3960 4055 128577586 128577681 2.630000e-27 134.0
18 TraesCS6D01G229400 chr4A 89.205 176 16 2 3788 3963 176860123 176859951 2.540000e-52 217.0
19 TraesCS6D01G229400 chr4A 87.368 190 20 4 3775 3963 166729942 166730128 9.130000e-52 215.0
20 TraesCS6D01G229400 chr3B 89.143 175 18 1 3789 3963 254193186 254193013 2.540000e-52 217.0
21 TraesCS6D01G229400 chr3B 95.876 97 4 0 3954 4050 824388922 824389018 1.560000e-34 158.0
22 TraesCS6D01G229400 chr1B 87.943 141 10 5 4040 4175 555630389 555630527 4.340000e-35 159.0
23 TraesCS6D01G229400 chr3A 86.765 136 15 1 4043 4175 102531052 102531187 9.390000e-32 148.0
24 TraesCS6D01G229400 chrUn 97.647 85 2 0 3962 4046 37028911 37028995 3.380000e-31 147.0
25 TraesCS6D01G229400 chr5B 97.647 85 2 0 3962 4046 655891243 655891159 3.380000e-31 147.0
26 TraesCS6D01G229400 chr5B 91.667 96 8 0 3960 4055 140965928 140966023 2.630000e-27 134.0
27 TraesCS6D01G229400 chr5A 85.315 143 16 2 4039 4177 616351690 616351831 4.370000e-30 143.0
28 TraesCS6D01G229400 chr5A 90.816 98 7 2 3960 4056 679658528 679658432 3.400000e-26 130.0
29 TraesCS6D01G229400 chr1D 84.615 143 18 2 4040 4178 461273178 461273320 5.650000e-29 139.0
30 TraesCS6D01G229400 chr1D 87.736 106 13 0 3953 4058 209139268 209139373 1.580000e-24 124.0
31 TraesCS6D01G229400 chr2D 91.579 95 8 0 3959 4053 643235821 643235915 9.460000e-27 132.0
32 TraesCS6D01G229400 chr1A 95.556 45 1 1 2091 2135 569372540 569372497 2.090000e-08 71.3
33 TraesCS6D01G229400 chr3D 100.000 28 0 0 1751 1778 6340602 6340575 8.000000e-03 52.8


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 TraesCS6D01G229400 chr6D 321773329 321777521 4192 True 3648.5 6593 100.000000 1 4193 2 chr6D.!!$R2 4192
1 TraesCS6D01G229400 chr6B 501770192 501774186 3994 False 2060.0 5771 90.972667 1 4193 3 chr6B.!!$F2 4192
2 TraesCS6D01G229400 chr6A 459074035 459082033 7998 True 1473.5 5216 93.030500 1 4193 4 chr6A.!!$R1 4192

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
217 228 0.461961 ATTGACGACTAGCCTCAGCC 59.538 55.000 0.00 0.0 41.25 4.85 F
1011 5015 0.540830 CTAGGTAGATGAGGGCGGCT 60.541 60.000 9.56 0.0 0.00 5.52 F
2368 6378 1.227943 GCCGCTTCCTGCATCCATA 60.228 57.895 0.00 0.0 43.06 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 5062 1.144936 CACAGATCCTTCCCTCCGC 59.855 63.158 0.00 0.00 0.00 5.54 R
2413 6423 0.814410 CGATGAGCAAGCTCCTGCAT 60.814 55.000 18.54 6.64 45.18 3.96 R
3804 7823 2.293122 CCAACGTTTTCAGAATCCTGCA 59.707 45.455 0.00 0.00 40.20 4.41 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
60 65 2.027469 TCTCAGTCTACGGCAGTACTGA 60.027 50.000 27.08 17.86 35.15 3.41
81 92 2.297880 ACACTGTAGCATTACGACACCA 59.702 45.455 0.00 0.00 32.21 4.17
156 167 0.535102 AACAGCCGTCAAAGTCCCAG 60.535 55.000 0.00 0.00 0.00 4.45
210 221 0.855349 CCGCATGATTGACGACTAGC 59.145 55.000 0.00 0.00 0.00 3.42
217 228 0.461961 ATTGACGACTAGCCTCAGCC 59.538 55.000 0.00 0.00 41.25 4.85
218 229 0.612174 TTGACGACTAGCCTCAGCCT 60.612 55.000 0.00 0.00 41.25 4.58
219 230 1.032657 TGACGACTAGCCTCAGCCTC 61.033 60.000 0.00 0.00 41.25 4.70
220 231 1.000771 ACGACTAGCCTCAGCCTCA 60.001 57.895 0.00 0.00 41.25 3.86
238 256 2.804167 GCTCAGCTCAGCTCGCTA 59.196 61.111 0.67 0.00 36.40 4.26
259 277 8.689061 TCGCTACAATAATTTTGGTCTCTACTA 58.311 33.333 0.00 0.00 0.00 1.82
261 279 9.819267 GCTACAATAATTTTGGTCTCTACTACT 57.181 33.333 0.00 0.00 0.00 2.57
265 4042 9.110502 CAATAATTTTGGTCTCTACTACTTCCC 57.889 37.037 0.00 0.00 0.00 3.97
271 4048 3.625313 GGTCTCTACTACTTCCCACGTAC 59.375 52.174 0.00 0.00 0.00 3.67
272 4049 4.256920 GTCTCTACTACTTCCCACGTACA 58.743 47.826 0.00 0.00 0.00 2.90
689 4634 2.634940 GCATCCAGGGAAGATAGCAGTA 59.365 50.000 0.00 0.00 0.00 2.74
690 4635 3.306641 GCATCCAGGGAAGATAGCAGTAG 60.307 52.174 0.00 0.00 0.00 2.57
1011 5015 0.540830 CTAGGTAGATGAGGGCGGCT 60.541 60.000 9.56 0.00 0.00 5.52
1308 5318 2.517166 GAGCTTCCGCCCATTCCC 60.517 66.667 0.00 0.00 36.60 3.97
1498 5508 2.202756 GCGGCTTCGGATTCTCGT 60.203 61.111 0.00 0.00 0.00 4.18
1761 5771 2.417719 CTCTTCAACCAGTACCAGCAC 58.582 52.381 0.00 0.00 0.00 4.40
1766 5776 1.705002 AACCAGTACCAGCACCAGCA 61.705 55.000 0.00 0.00 45.49 4.41
1767 5777 1.672356 CCAGTACCAGCACCAGCAC 60.672 63.158 0.00 0.00 45.49 4.40
1768 5778 1.672356 CAGTACCAGCACCAGCACC 60.672 63.158 0.00 0.00 45.49 5.01
1769 5779 2.146724 AGTACCAGCACCAGCACCA 61.147 57.895 0.00 0.00 45.49 4.17
1770 5780 1.672356 GTACCAGCACCAGCACCAG 60.672 63.158 0.00 0.00 45.49 4.00
1771 5781 3.551496 TACCAGCACCAGCACCAGC 62.551 63.158 0.00 0.00 45.49 4.85
1857 5867 1.669115 CTCACAACTCCACCAGCCG 60.669 63.158 0.00 0.00 0.00 5.52
2313 6323 1.461127 CTGCAGTTCGCTAACTTCACC 59.539 52.381 5.25 0.00 43.60 4.02
2368 6378 1.227943 GCCGCTTCCTGCATCCATA 60.228 57.895 0.00 0.00 43.06 2.74
2413 6423 2.436109 GGCAGTGGGCTTCCTTCA 59.564 61.111 0.00 0.00 44.01 3.02
2439 6449 3.869272 CTTGCTCATCGCCGTGGC 61.869 66.667 0.00 0.00 38.05 5.01
3460 7471 9.914131 GTACAGTATTGATATCTGCTCATGTTA 57.086 33.333 3.98 0.00 33.12 2.41
3667 7682 7.978975 AGAGACAACAGAGCAGAATCTTTATAC 59.021 37.037 0.00 0.00 0.00 1.47
3668 7683 7.615403 AGACAACAGAGCAGAATCTTTATACA 58.385 34.615 0.00 0.00 0.00 2.29
3672 7687 8.602328 CAACAGAGCAGAATCTTTATACAAGAG 58.398 37.037 0.00 0.00 0.00 2.85
3804 7823 7.310983 GCTATAGAATAGGGCCTCTTTTGATCT 60.311 40.741 10.74 1.96 0.00 2.75
3869 7888 8.515695 TTGAAATGTCATGCTCATCTAAATCT 57.484 30.769 4.24 0.00 32.48 2.40
3989 8008 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
4081 8103 6.817184 TCCTTAGGAATTCTTGTAGGATTCG 58.183 40.000 15.10 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.926511 CTGACGATGGGCAGGCAAAC 61.927 60.000 1.90 0.00 0.00 2.93
60 65 2.297880 TGGTGTCGTAATGCTACAGTGT 59.702 45.455 0.00 0.00 0.00 3.55
235 253 9.819267 AGTAGTAGAGACCAAAATTATTGTAGC 57.181 33.333 0.00 0.00 0.00 3.58
238 256 9.668497 GGAAGTAGTAGAGACCAAAATTATTGT 57.332 33.333 0.00 0.00 0.00 2.71
259 277 2.895404 ACTGTATGTGTACGTGGGAAGT 59.105 45.455 0.00 0.00 33.36 3.01
261 279 2.231964 GGACTGTATGTGTACGTGGGAA 59.768 50.000 0.00 0.00 33.36 3.97
262 280 1.820519 GGACTGTATGTGTACGTGGGA 59.179 52.381 0.00 0.00 33.36 4.37
265 4042 2.984471 GTGTGGACTGTATGTGTACGTG 59.016 50.000 0.00 0.00 33.36 4.49
271 4048 4.891627 TTGTTTGTGTGGACTGTATGTG 57.108 40.909 0.00 0.00 0.00 3.21
272 4049 7.575414 TTATTTGTTTGTGTGGACTGTATGT 57.425 32.000 0.00 0.00 0.00 2.29
689 4634 2.022035 TCTCTCCCCTCTCTCTCTCTCT 60.022 54.545 0.00 0.00 0.00 3.10
690 4635 2.104963 GTCTCTCCCCTCTCTCTCTCTC 59.895 59.091 0.00 0.00 0.00 3.20
1055 5059 4.610714 GATCCTTCCCTCCGCCGC 62.611 72.222 0.00 0.00 0.00 6.53
1056 5060 2.840102 AGATCCTTCCCTCCGCCG 60.840 66.667 0.00 0.00 0.00 6.46
1057 5061 2.066999 ACAGATCCTTCCCTCCGCC 61.067 63.158 0.00 0.00 0.00 6.13
1058 5062 1.144936 CACAGATCCTTCCCTCCGC 59.855 63.158 0.00 0.00 0.00 5.54
1059 5063 1.144936 GCACAGATCCTTCCCTCCG 59.855 63.158 0.00 0.00 0.00 4.63
1060 5064 1.414550 GTAGCACAGATCCTTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
1061 5065 2.102252 CAGTAGCACAGATCCTTCCCTC 59.898 54.545 0.00 0.00 0.00 4.30
1062 5066 2.114616 CAGTAGCACAGATCCTTCCCT 58.885 52.381 0.00 0.00 0.00 4.20
1503 5513 4.516195 GAGAAGCCGAGCGGGTCC 62.516 72.222 14.44 0.81 46.38 4.46
1707 5717 3.157949 CCGAGGAGAGGGGGCTTC 61.158 72.222 0.00 0.00 0.00 3.86
1938 5948 2.377810 TGAGCCATGTAGCAGGGGG 61.378 63.158 1.98 0.00 35.67 5.40
2368 6378 4.836825 ACACCAAGATCGAAGTCAATGAT 58.163 39.130 0.00 0.00 0.00 2.45
2413 6423 0.814410 CGATGAGCAAGCTCCTGCAT 60.814 55.000 18.54 6.64 45.18 3.96
3460 7471 5.631119 AGTTGCACCAGGAATAACTAAAGT 58.369 37.500 0.00 0.00 30.45 2.66
3804 7823 2.293122 CCAACGTTTTCAGAATCCTGCA 59.707 45.455 0.00 0.00 40.20 4.41
3846 7865 9.875675 GTAAGATTTAGATGAGCATGACATTTC 57.124 33.333 0.00 0.00 0.00 2.17
3869 7888 8.394121 GCAATCAAACAACCAAAAATCTTGTAA 58.606 29.630 0.00 0.00 0.00 2.41
3922 7941 7.004555 TCTAGCATCCACTCAAACTTCTTTA 57.995 36.000 0.00 0.00 0.00 1.85
3926 7945 5.106515 GGTTTCTAGCATCCACTCAAACTTC 60.107 44.000 0.00 0.00 0.00 3.01
3996 8015 8.648693 AGGGCGTTAAGATCACTAAATTAGTAT 58.351 33.333 5.23 0.86 37.23 2.12
4005 8024 8.867097 AGAAATATAAGGGCGTTAAGATCACTA 58.133 33.333 3.51 0.00 0.00 2.74
4006 8025 7.736893 AGAAATATAAGGGCGTTAAGATCACT 58.263 34.615 3.51 2.46 0.00 3.41
4007 8026 7.964604 AGAAATATAAGGGCGTTAAGATCAC 57.035 36.000 3.51 0.59 0.00 3.06
4008 8027 8.974060 AAAGAAATATAAGGGCGTTAAGATCA 57.026 30.769 3.51 0.00 0.00 2.92
4010 8029 9.841295 TGTAAAGAAATATAAGGGCGTTAAGAT 57.159 29.630 3.51 0.00 0.00 2.40
4011 8030 9.321562 CTGTAAAGAAATATAAGGGCGTTAAGA 57.678 33.333 3.51 0.00 0.00 2.10
4014 8033 7.929785 CCTCTGTAAAGAAATATAAGGGCGTTA 59.070 37.037 1.70 1.70 0.00 3.18
4081 8103 7.156876 TGTTGGTTGTTTGATTCATAGGATC 57.843 36.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.