Multiple sequence alignment - TraesCS4D01G102600

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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 TraesCS4D01G102600 chr4D 100.000 3266 0 0 1 3266 81667436 81664171 0.000000e+00 6032.0
1 TraesCS4D01G102600 chr4D 87.324 71 7 2 1152 1221 394379251 394379182 2.700000e-11 80.5
2 TraesCS4D01G102600 chr4A 93.307 3242 121 41 97 3266 491454850 491451633 0.000000e+00 4697.0
3 TraesCS4D01G102600 chr4B 94.814 2526 91 18 97 2588 115102370 115099851 0.000000e+00 3903.0
4 TraesCS4D01G102600 chr4B 89.526 401 22 5 2868 3266 115099132 115098750 1.050000e-134 490.0
5 TraesCS4D01G102600 chr4B 99.177 243 2 0 2574 2816 115099376 115099134 3.870000e-119 438.0
6 TraesCS4D01G102600 chr2A 85.315 143 21 0 1073 1215 598642510 598642368 7.300000e-32 148.0
7 TraesCS4D01G102600 chr2D 84.615 143 22 0 1070 1212 450918189 450918331 3.400000e-30 143.0
8 TraesCS4D01G102600 chr2B 83.916 143 23 0 1070 1212 531053096 531053238 1.580000e-28 137.0
9 TraesCS4D01G102600 chr2B 89.474 76 7 1 8 82 635083253 635083328 9.650000e-16 95.3
10 TraesCS4D01G102600 chr7B 91.954 87 7 0 11 97 387424962 387425048 4.430000e-24 122.0
11 TraesCS4D01G102600 chr7B 94.444 72 4 0 11 82 579836605 579836676 9.580000e-21 111.0
12 TraesCS4D01G102600 chr1B 93.421 76 4 1 11 85 364822769 364822694 9.580000e-21 111.0
13 TraesCS4D01G102600 chr1B 89.157 83 6 3 3 82 664313181 664313263 2.070000e-17 100.0
14 TraesCS4D01G102600 chr1B 85.135 74 5 6 1150 1220 596248438 596248368 1.630000e-08 71.3
15 TraesCS4D01G102600 chr7A 93.243 74 3 2 11 82 214783294 214783367 1.240000e-19 108.0
16 TraesCS4D01G102600 chr7A 85.135 74 5 6 1150 1220 152507295 152507365 1.630000e-08 71.3
17 TraesCS4D01G102600 chr7D 85.915 71 6 4 1164 1230 561700269 561700339 4.520000e-09 73.1


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 TraesCS4D01G102600 chr4D 81664171 81667436 3265 True 6032.000000 6032 100.000000 1 3266 1 chr4D.!!$R1 3265
1 TraesCS4D01G102600 chr4A 491451633 491454850 3217 True 4697.000000 4697 93.307000 97 3266 1 chr4A.!!$R1 3169
2 TraesCS4D01G102600 chr4B 115098750 115102370 3620 True 1610.333333 3903 94.505667 97 3266 3 chr4B.!!$R1 3169

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
913 961 0.970640 AAAACCCCATTAACGCCACC 59.029 50.000 0.0 0.0 0.0 4.61 F
1769 1835 1.001181 CCAAGCAAACCAACCCATCTG 59.999 52.381 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1930 0.379669 GGATGAAGAAGCATGCCGTG 59.620 55.0 15.66 0.0 31.29 4.94 R
3181 3766 0.116342 TCCTGCTCTCCCAACTACCA 59.884 55.0 0.00 0.0 0.00 3.25 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
47 48 9.436957 TCTCTCTCCTTTTTAATTACATGACAC 57.563 33.333 0.00 0.00 0.00 3.67
48 49 9.219603 CTCTCTCCTTTTTAATTACATGACACA 57.780 33.333 0.00 0.00 0.00 3.72
49 50 9.739276 TCTCTCCTTTTTAATTACATGACACAT 57.261 29.630 0.00 0.00 0.00 3.21
81 82 9.461312 TTTTTCTTATGTGGCATCTATGTTACT 57.539 29.630 0.00 0.00 0.00 2.24
82 83 8.662781 TTTCTTATGTGGCATCTATGTTACTC 57.337 34.615 0.00 0.00 0.00 2.59
83 84 6.759272 TCTTATGTGGCATCTATGTTACTCC 58.241 40.000 0.00 0.00 0.00 3.85
84 85 6.554982 TCTTATGTGGCATCTATGTTACTCCT 59.445 38.462 0.00 0.00 0.00 3.69
85 86 7.728532 TCTTATGTGGCATCTATGTTACTCCTA 59.271 37.037 0.00 0.00 0.00 2.94
86 87 5.531122 TGTGGCATCTATGTTACTCCTAC 57.469 43.478 0.00 0.00 0.00 3.18
87 88 5.208890 TGTGGCATCTATGTTACTCCTACT 58.791 41.667 0.00 0.00 0.00 2.57
88 89 6.370453 TGTGGCATCTATGTTACTCCTACTA 58.630 40.000 0.00 0.00 0.00 1.82
89 90 7.010771 TGTGGCATCTATGTTACTCCTACTAT 58.989 38.462 0.00 0.00 0.00 2.12
90 91 7.039714 TGTGGCATCTATGTTACTCCTACTATG 60.040 40.741 0.00 0.00 0.00 2.23
91 92 7.176865 GTGGCATCTATGTTACTCCTACTATGA 59.823 40.741 0.00 0.00 0.00 2.15
92 93 7.176865 TGGCATCTATGTTACTCCTACTATGAC 59.823 40.741 0.00 0.00 0.00 3.06
93 94 7.394923 GGCATCTATGTTACTCCTACTATGACT 59.605 40.741 0.00 0.00 0.00 3.41
94 95 9.451002 GCATCTATGTTACTCCTACTATGACTA 57.549 37.037 0.00 0.00 0.00 2.59
190 191 1.136611 CGCACACTTTCGTAGTTGAGC 60.137 52.381 0.00 0.00 33.85 4.26
489 507 2.342406 TGGGAGATCAACTTCTGGGA 57.658 50.000 0.00 0.00 0.00 4.37
684 706 6.976934 AAATACTGGTCCAGATTGTTGTTT 57.023 33.333 26.18 10.17 35.18 2.83
812 860 6.734137 CAGTTTTGTACCACTAAATGCTTGA 58.266 36.000 0.00 0.00 0.00 3.02
910 958 4.340097 AGCTTATAAAACCCCATTAACGCC 59.660 41.667 0.00 0.00 0.00 5.68
911 959 4.098196 GCTTATAAAACCCCATTAACGCCA 59.902 41.667 0.00 0.00 0.00 5.69
913 961 0.970640 AAAACCCCATTAACGCCACC 59.029 50.000 0.00 0.00 0.00 4.61
969 1019 4.855715 TTCTTTCTCTCTTTCTCTCGCA 57.144 40.909 0.00 0.00 0.00 5.10
1218 1268 1.177256 ACTGCTTCGTCAGGGTACGT 61.177 55.000 0.00 0.00 43.31 3.57
1267 1317 5.627503 GCCAGGGTAAAGGAAGTAATTCGTA 60.628 44.000 0.00 0.00 0.00 3.43
1405 1458 4.873129 CTCCGCGGGATGGACGTG 62.873 72.222 27.83 0.00 41.15 4.49
1520 1575 6.270815 GCATTCGTAAGTAGTAACATCCTCA 58.729 40.000 0.00 0.00 39.48 3.86
1524 1579 5.358725 TCGTAAGTAGTAACATCCTCATGCA 59.641 40.000 0.00 0.00 39.48 3.96
1766 1832 1.506025 AACCAAGCAAACCAACCCAT 58.494 45.000 0.00 0.00 0.00 4.00
1769 1835 1.001181 CCAAGCAAACCAACCCATCTG 59.999 52.381 0.00 0.00 0.00 2.90
1793 1859 1.140407 CTTGCGTTCCCTCGATCGAC 61.140 60.000 15.15 3.56 33.86 4.20
1796 1862 1.226603 CGTTCCCTCGATCGACCAC 60.227 63.158 15.15 7.37 33.86 4.16
1801 1867 2.113433 CCTCGATCGACCACGGACT 61.113 63.158 15.15 0.00 40.21 3.85
1803 1869 1.366854 CTCGATCGACCACGGACTCA 61.367 60.000 15.15 0.00 40.21 3.41
1893 1966 0.543410 TCCAGGACCGGCTCTACAAA 60.543 55.000 0.00 0.00 0.00 2.83
1938 2011 2.050350 GTCAGACCCGTCGATCCCA 61.050 63.158 0.00 0.00 34.09 4.37
2273 2346 3.960755 TCCAAGTTCAACTGAGAGAGACA 59.039 43.478 0.00 0.00 0.00 3.41
2279 2352 2.489722 TCAACTGAGAGAGACACATCCG 59.510 50.000 0.00 0.00 0.00 4.18
2345 2423 3.939740 TGGCTAGCTGGAGATGAAAAT 57.060 42.857 15.72 0.00 0.00 1.82
2413 2491 3.434319 CGTGGCGCTTTCATGGCT 61.434 61.111 7.64 0.00 0.00 4.75
2832 3404 4.996758 TCGTTGCACCATGATATTGATAGG 59.003 41.667 0.00 0.00 0.00 2.57
2840 3412 7.310052 GCACCATGATATTGATAGGTCTAGACA 60.310 40.741 23.91 5.26 0.00 3.41
2845 3417 6.264518 TGATATTGATAGGTCTAGACAACGCA 59.735 38.462 23.91 13.20 0.00 5.24
2847 3419 3.086282 TGATAGGTCTAGACAACGCACA 58.914 45.455 23.91 12.49 0.00 4.57
2930 3508 4.538089 AGAGCTCCCAAGGAAATCTTTACT 59.462 41.667 10.93 0.00 32.41 2.24
3024 3602 2.509336 CCTGCTAAGTCACCGCGG 60.509 66.667 26.86 26.86 0.00 6.46
3025 3603 2.261671 CTGCTAAGTCACCGCGGT 59.738 61.111 28.70 28.70 0.00 5.68
3071 3649 1.350684 TGTGGTAGAATCCAAGCTGCA 59.649 47.619 1.02 0.00 39.34 4.41
3103 3681 0.622136 TGTCAGCTGGAGGATGCAAT 59.378 50.000 15.13 0.00 34.45 3.56
3115 3693 1.952296 GGATGCAATTGGGTAGCTGAG 59.048 52.381 7.72 0.00 0.00 3.35
3153 3738 0.804989 GTGTACTGCCCTGTTGATGC 59.195 55.000 0.00 0.00 0.00 3.91
3169 3754 4.604114 GCAATGGCCTTTGCTTCC 57.396 55.556 36.53 16.96 46.66 3.46
3175 3760 0.832983 TGGCCTTTGCTTCCATGCTT 60.833 50.000 3.32 0.00 37.74 3.91
3180 3765 3.469739 CCTTTGCTTCCATGCTTTGTTT 58.530 40.909 0.00 0.00 0.00 2.83
3181 3766 3.878699 CCTTTGCTTCCATGCTTTGTTTT 59.121 39.130 0.00 0.00 0.00 2.43
3191 3776 3.810310 TGCTTTGTTTTGGTAGTTGGG 57.190 42.857 0.00 0.00 0.00 4.12
3192 3777 3.366396 TGCTTTGTTTTGGTAGTTGGGA 58.634 40.909 0.00 0.00 0.00 4.37
3196 3781 2.858745 TGTTTTGGTAGTTGGGAGAGC 58.141 47.619 0.00 0.00 0.00 4.09
3204 3789 1.439543 AGTTGGGAGAGCAGGAAGTT 58.560 50.000 0.00 0.00 0.00 2.66
3210 3795 1.303155 AGAGCAGGAAGTTGGCAGC 60.303 57.895 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.436957 GTGTCATGTAATTAAAAAGGAGAGAGA 57.563 33.333 0.00 0.00 0.00 3.10
22 23 9.219603 TGTGTCATGTAATTAAAAAGGAGAGAG 57.780 33.333 0.00 0.00 0.00 3.20
23 24 9.739276 ATGTGTCATGTAATTAAAAAGGAGAGA 57.261 29.630 0.00 0.00 0.00 3.10
55 56 9.461312 AGTAACATAGATGCCACATAAGAAAAA 57.539 29.630 0.00 0.00 0.00 1.94
56 57 9.109393 GAGTAACATAGATGCCACATAAGAAAA 57.891 33.333 0.00 0.00 0.00 2.29
57 58 7.715249 GGAGTAACATAGATGCCACATAAGAAA 59.285 37.037 0.00 0.00 0.00 2.52
58 59 7.071196 AGGAGTAACATAGATGCCACATAAGAA 59.929 37.037 0.00 0.00 0.00 2.52
59 60 6.554982 AGGAGTAACATAGATGCCACATAAGA 59.445 38.462 0.00 0.00 0.00 2.10
60 61 6.763355 AGGAGTAACATAGATGCCACATAAG 58.237 40.000 0.00 0.00 0.00 1.73
61 62 6.747414 AGGAGTAACATAGATGCCACATAA 57.253 37.500 0.00 0.00 0.00 1.90
62 63 7.010771 AGTAGGAGTAACATAGATGCCACATA 58.989 38.462 0.00 0.00 0.00 2.29
63 64 5.841237 AGTAGGAGTAACATAGATGCCACAT 59.159 40.000 0.00 0.00 0.00 3.21
64 65 5.208890 AGTAGGAGTAACATAGATGCCACA 58.791 41.667 0.00 0.00 0.00 4.17
65 66 5.793030 AGTAGGAGTAACATAGATGCCAC 57.207 43.478 0.00 0.00 0.00 5.01
66 67 7.176865 GTCATAGTAGGAGTAACATAGATGCCA 59.823 40.741 0.00 0.00 0.00 4.92
67 68 7.394923 AGTCATAGTAGGAGTAACATAGATGCC 59.605 40.741 0.00 0.00 0.00 4.40
68 69 8.343168 AGTCATAGTAGGAGTAACATAGATGC 57.657 38.462 0.00 0.00 0.00 3.91
70 71 9.675464 GCTAGTCATAGTAGGAGTAACATAGAT 57.325 37.037 1.35 0.00 0.00 1.98
71 72 8.657712 TGCTAGTCATAGTAGGAGTAACATAGA 58.342 37.037 1.35 0.00 0.00 1.98
72 73 8.850007 TGCTAGTCATAGTAGGAGTAACATAG 57.150 38.462 1.35 0.00 0.00 2.23
73 74 9.232473 CATGCTAGTCATAGTAGGAGTAACATA 57.768 37.037 12.76 0.00 30.06 2.29
74 75 7.945109 TCATGCTAGTCATAGTAGGAGTAACAT 59.055 37.037 8.92 8.92 30.86 2.71
75 76 7.287810 TCATGCTAGTCATAGTAGGAGTAACA 58.712 38.462 5.49 5.49 30.86 2.41
76 77 7.747155 TCATGCTAGTCATAGTAGGAGTAAC 57.253 40.000 1.35 0.00 30.86 2.50
77 78 7.094162 GCATCATGCTAGTCATAGTAGGAGTAA 60.094 40.741 1.02 0.00 37.74 2.24
78 79 6.375736 GCATCATGCTAGTCATAGTAGGAGTA 59.624 42.308 1.02 0.00 37.74 2.59
79 80 5.184864 GCATCATGCTAGTCATAGTAGGAGT 59.815 44.000 1.02 0.00 37.74 3.85
80 81 5.184671 TGCATCATGCTAGTCATAGTAGGAG 59.815 44.000 11.84 0.00 45.31 3.69
81 82 5.079643 TGCATCATGCTAGTCATAGTAGGA 58.920 41.667 11.84 0.00 45.31 2.94
82 83 5.397142 TGCATCATGCTAGTCATAGTAGG 57.603 43.478 11.84 0.00 45.31 3.18
83 84 6.128607 GCTTTGCATCATGCTAGTCATAGTAG 60.129 42.308 11.84 0.00 45.31 2.57
84 85 5.698089 GCTTTGCATCATGCTAGTCATAGTA 59.302 40.000 11.84 0.00 45.31 1.82
85 86 4.514441 GCTTTGCATCATGCTAGTCATAGT 59.486 41.667 11.84 0.00 45.31 2.12
86 87 4.377124 CGCTTTGCATCATGCTAGTCATAG 60.377 45.833 11.84 0.00 45.31 2.23
87 88 3.495753 CGCTTTGCATCATGCTAGTCATA 59.504 43.478 11.84 0.00 45.31 2.15
88 89 2.289820 CGCTTTGCATCATGCTAGTCAT 59.710 45.455 11.84 0.00 45.31 3.06
89 90 1.667212 CGCTTTGCATCATGCTAGTCA 59.333 47.619 11.84 0.00 45.31 3.41
90 91 1.667724 ACGCTTTGCATCATGCTAGTC 59.332 47.619 11.84 4.41 45.31 2.59
91 92 1.667724 GACGCTTTGCATCATGCTAGT 59.332 47.619 11.84 3.58 45.31 2.57
92 93 1.938577 AGACGCTTTGCATCATGCTAG 59.061 47.619 11.84 9.40 45.31 3.42
93 94 1.935873 GAGACGCTTTGCATCATGCTA 59.064 47.619 11.84 0.00 45.31 3.49
94 95 0.731417 GAGACGCTTTGCATCATGCT 59.269 50.000 11.84 0.00 45.31 3.79
95 96 0.248377 GGAGACGCTTTGCATCATGC 60.248 55.000 1.35 1.35 45.29 4.06
240 258 3.181516 CGAGTGAGTAAAGATTTGCTGCC 60.182 47.826 0.40 0.00 33.17 4.85
489 507 4.551671 AGCTGATGAATCTACCACCTAGT 58.448 43.478 0.00 0.00 0.00 2.57
586 605 0.470080 TCTGGTGGGAGATCGGATCC 60.470 60.000 14.19 0.00 35.99 3.36
684 706 5.106869 GGTGTCAGCAATACGTAATTTCACA 60.107 40.000 0.00 0.00 0.00 3.58
812 860 3.606886 CACCGCAAAGAGTAGGTGT 57.393 52.632 5.40 0.00 46.52 4.16
865 913 0.733729 CGTCCGGTGGAGAAGTAGAG 59.266 60.000 0.00 0.00 29.39 2.43
910 958 0.543749 GGATCAAGGTCCTCTGGGTG 59.456 60.000 0.00 0.00 35.32 4.61
911 959 0.419459 AGGATCAAGGTCCTCTGGGT 59.581 55.000 0.00 0.00 45.51 4.51
913 961 1.691434 GCTAGGATCAAGGTCCTCTGG 59.309 57.143 4.89 0.00 45.51 3.86
1050 1100 4.749310 CTGGAGCTGGCGACGCTT 62.749 66.667 20.77 3.04 39.63 4.68
1185 1235 1.374758 GCAGTCGTGGAACTGGAGG 60.375 63.158 6.21 0.00 45.52 4.30
1267 1317 2.341846 ATTCCCACGTCAAACACACT 57.658 45.000 0.00 0.00 0.00 3.55
1405 1458 2.517450 CGCCTTGGCGTTCTCGATC 61.517 63.158 24.03 0.00 39.71 3.69
1531 1586 1.426215 TCCATCCATGCAGGCATATGT 59.574 47.619 6.42 0.00 37.29 2.29
1766 1832 0.472471 AGGGAACGCAAGGAAACAGA 59.528 50.000 0.00 0.00 46.39 3.41
1769 1835 0.601841 TCGAGGGAACGCAAGGAAAC 60.602 55.000 0.00 0.00 46.39 2.78
1801 1867 2.168458 TCGATGGGTTAGGGACATGA 57.832 50.000 0.00 0.00 0.00 3.07
1803 1869 1.699634 CCATCGATGGGTTAGGGACAT 59.300 52.381 32.99 0.00 44.31 3.06
1816 1889 2.281970 ATGCATGCCGCCATCGAT 60.282 55.556 16.68 0.00 41.33 3.59
1857 1930 0.379669 GGATGAAGAAGCATGCCGTG 59.620 55.000 15.66 0.00 31.29 4.94
1863 1936 1.134280 CGGTCCTGGATGAAGAAGCAT 60.134 52.381 0.00 0.00 0.00 3.79
1938 2011 2.282958 TCCGACAGGAAGCCGTCT 60.283 61.111 0.00 0.00 45.12 4.18
2273 2346 1.417890 GGAATCTGGATCCACGGATGT 59.582 52.381 11.44 4.62 36.61 3.06
2345 2423 1.742146 CGCATGGGCTAGCTAGTGA 59.258 57.895 21.62 6.77 38.10 3.41
2832 3404 3.575630 TGATCTTGTGCGTTGTCTAGAC 58.424 45.455 16.32 16.32 0.00 2.59
2860 3432 1.152030 AGGTCCCTGAGTGGCTGAA 60.152 57.895 0.00 0.00 0.00 3.02
2930 3508 1.606668 GTTCCATGCACCTCGTGAAAA 59.393 47.619 0.00 0.00 35.23 2.29
3024 3602 4.574599 ATGCACAGGAGTTTTCTTTCAC 57.425 40.909 0.00 0.00 0.00 3.18
3025 3603 6.489700 TGAATATGCACAGGAGTTTTCTTTCA 59.510 34.615 0.00 0.00 0.00 2.69
3071 3649 3.134401 CTGACACATTCAGCGCTCT 57.866 52.632 7.13 0.00 45.51 4.09
3103 3681 2.256306 TGATGTGTCTCAGCTACCCAA 58.744 47.619 0.00 0.00 33.14 4.12
3115 3693 8.223769 CAGTACACTTTTACTCAATGATGTGTC 58.776 37.037 0.00 0.00 38.23 3.67
3153 3738 2.010043 GCATGGAAGCAAAGGCCATTG 61.010 52.381 16.39 16.39 40.29 2.82
3169 3754 4.057432 CCCAACTACCAAAACAAAGCATG 58.943 43.478 0.00 0.00 0.00 4.06
3175 3760 3.219281 GCTCTCCCAACTACCAAAACAA 58.781 45.455 0.00 0.00 0.00 2.83
3180 3765 0.984230 CCTGCTCTCCCAACTACCAA 59.016 55.000 0.00 0.00 0.00 3.67
3181 3766 0.116342 TCCTGCTCTCCCAACTACCA 59.884 55.000 0.00 0.00 0.00 3.25
3191 3776 1.304509 GCTGCCAACTTCCTGCTCTC 61.305 60.000 0.00 0.00 0.00 3.20
3192 3777 1.303155 GCTGCCAACTTCCTGCTCT 60.303 57.895 0.00 0.00 0.00 4.09
3196 3781 0.798776 CTAACGCTGCCAACTTCCTG 59.201 55.000 0.00 0.00 0.00 3.86
3210 3795 5.390613 CAATAAAGACAAACCCAGCTAACG 58.609 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.