Multiple sequence alignment - TraesCS2A01G212400

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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 TraesCS2A01G212400 chr2A 100.000 2348 0 0 1 2348 197225640 197227987 0.000000e+00 4337
1 TraesCS2A01G212400 chr2D 94.529 1718 46 17 379 2081 181485285 181486969 0.000000e+00 2608
2 TraesCS2A01G212400 chr2D 96.715 274 9 0 2075 2348 181487127 181487400 7.650000e-125 457
3 TraesCS2A01G212400 chr2D 92.332 313 23 1 67 379 181484465 181484776 5.950000e-121 444
4 TraesCS2A01G212400 chr2B 92.044 1634 58 20 158 1758 238263916 238265510 0.000000e+00 2231
5 TraesCS2A01G212400 chr2B 95.150 433 17 2 1757 2189 238265614 238266042 0.000000e+00 680
6 TraesCS2A01G212400 chr2B 96.212 132 5 0 2217 2348 238272176 238272307 1.410000e-52 217
7 TraesCS2A01G212400 chr2B 89.922 129 13 0 113 241 748586009 748585881 1.440000e-37 167
8 TraesCS2A01G212400 chr3D 85.185 216 19 9 76 280 56310513 56310726 2.360000e-50 209
9 TraesCS2A01G212400 chr3D 85.294 170 15 2 121 280 515958510 515958679 1.440000e-37 167
10 TraesCS2A01G212400 chr5B 87.500 168 19 2 67 233 13266277 13266443 2.380000e-45 193
11 TraesCS2A01G212400 chr6A 86.264 182 15 4 109 280 55887324 55887505 3.080000e-44 189
12 TraesCS2A01G212400 chr6A 84.884 172 13 7 120 280 55885969 55886138 6.720000e-36 161
13 TraesCS2A01G212400 chr7D 87.143 140 16 2 108 246 561701278 561701140 8.690000e-35 158
14 TraesCS2A01G212400 chr1B 88.372 129 11 4 118 244 649425859 649425985 4.040000e-33 152


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 TraesCS2A01G212400 chr2A 197225640 197227987 2347 False 4337.000000 4337 100.000000 1 2348 1 chr2A.!!$F1 2347
1 TraesCS2A01G212400 chr2D 181484465 181487400 2935 False 1169.666667 2608 94.525333 67 2348 3 chr2D.!!$F1 2281
2 TraesCS2A01G212400 chr2B 238263916 238266042 2126 False 1455.500000 2231 93.597000 158 2189 2 chr2B.!!$F2 2031

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
911 1437 0.760189 ACCAACACCAAGGCAAGCAT 60.76 50.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 3139 0.732571 ACGTGCAGTTCAACAACCAG 59.267 50.0 0.0 0.0 32.22 4.0 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
17 18 2.923035 CCACTCCCCACTGTCGGT 60.923 66.667 0.00 0.00 0.00 4.69
18 19 2.657237 CACTCCCCACTGTCGGTC 59.343 66.667 0.00 0.00 0.00 4.79
19 20 2.603776 ACTCCCCACTGTCGGTCC 60.604 66.667 0.00 0.00 0.00 4.46
20 21 2.283966 CTCCCCACTGTCGGTCCT 60.284 66.667 0.00 0.00 0.00 3.85
21 22 2.283676 TCCCCACTGTCGGTCCTC 60.284 66.667 0.00 0.00 0.00 3.71
22 23 2.283966 CCCCACTGTCGGTCCTCT 60.284 66.667 0.00 0.00 0.00 3.69
23 24 2.650116 CCCCACTGTCGGTCCTCTG 61.650 68.421 0.00 0.00 0.00 3.35
24 25 2.262915 CCACTGTCGGTCCTCTGC 59.737 66.667 0.00 0.00 0.00 4.26
25 26 2.262915 CACTGTCGGTCCTCTGCC 59.737 66.667 0.00 0.00 0.00 4.85
43 44 2.448542 GCCCCAGCCATCCCTCTA 60.449 66.667 0.00 0.00 0.00 2.43
44 45 2.524204 GCCCCAGCCATCCCTCTAG 61.524 68.421 0.00 0.00 0.00 2.43
45 46 2.524204 CCCCAGCCATCCCTCTAGC 61.524 68.421 0.00 0.00 0.00 3.42
46 47 2.524204 CCCAGCCATCCCTCTAGCC 61.524 68.421 0.00 0.00 0.00 3.93
47 48 2.524204 CCAGCCATCCCTCTAGCCC 61.524 68.421 0.00 0.00 0.00 5.19
48 49 2.122189 AGCCATCCCTCTAGCCCC 60.122 66.667 0.00 0.00 0.00 5.80
49 50 3.253061 GCCATCCCTCTAGCCCCC 61.253 72.222 0.00 0.00 0.00 5.40
86 87 1.959282 CCCTGTGCTGAGCTTTTTCTT 59.041 47.619 5.83 0.00 0.00 2.52
90 91 1.604278 GTGCTGAGCTTTTTCTTCGGT 59.396 47.619 5.83 0.00 0.00 4.69
91 92 1.603802 TGCTGAGCTTTTTCTTCGGTG 59.396 47.619 5.83 0.00 0.00 4.94
93 94 2.096019 GCTGAGCTTTTTCTTCGGTGAG 60.096 50.000 0.00 0.00 0.00 3.51
95 96 3.131396 TGAGCTTTTTCTTCGGTGAGTC 58.869 45.455 0.00 0.00 0.00 3.36
151 152 4.954118 TCCACCACCGCCCTCACT 62.954 66.667 0.00 0.00 0.00 3.41
170 171 6.553100 CCTCACTCTGAACCCTAAGATAGATT 59.447 42.308 0.00 0.00 0.00 2.40
173 174 7.841729 TCACTCTGAACCCTAAGATAGATTCTT 59.158 37.037 0.00 0.00 46.53 2.52
244 255 7.039504 CCTTCTCCTTCCTTCATTCAAAAATCA 60.040 37.037 0.00 0.00 0.00 2.57
249 260 9.850198 TCCTTCCTTCATTCAAAAATCAAATTT 57.150 25.926 0.00 0.00 0.00 1.82
292 303 2.860735 GCTAAACTGCTCGGAGTACATG 59.139 50.000 6.90 0.00 0.00 3.21
316 327 5.449304 GGTAAGCAACACATTGTACACTTC 58.551 41.667 0.00 0.00 38.17 3.01
358 369 3.125316 CGTCATGCTCCCTTTGAGTTTAC 59.875 47.826 0.00 0.00 43.48 2.01
385 905 8.485578 TTTGTACCCAATCAAGAAATACCTTT 57.514 30.769 0.00 0.00 0.00 3.11
397 917 7.596995 TCAAGAAATACCTTTAAACGGCATTTG 59.403 33.333 14.51 6.57 29.77 2.32
540 1066 1.079543 CTGCTCCGTCCAAGACCTG 60.080 63.158 0.00 0.00 0.00 4.00
685 1211 2.614057 CGCCCAATGATTCCTAGAACAC 59.386 50.000 0.00 0.00 0.00 3.32
767 1293 2.094675 CCCAGCAAATCAAGATCCGTT 58.905 47.619 0.00 0.00 0.00 4.44
809 1335 1.185121 CGCGAGTCGTCACAAATATCG 59.815 52.381 15.08 0.85 0.00 2.92
810 1336 2.447250 GCGAGTCGTCACAAATATCGA 58.553 47.619 15.08 0.00 0.00 3.59
811 1337 2.850060 GCGAGTCGTCACAAATATCGAA 59.150 45.455 15.08 0.00 34.23 3.71
812 1338 3.301007 GCGAGTCGTCACAAATATCGAAC 60.301 47.826 15.08 0.00 34.23 3.95
813 1339 4.096311 CGAGTCGTCACAAATATCGAACT 58.904 43.478 3.82 0.00 34.23 3.01
814 1340 4.028429 CGAGTCGTCACAAATATCGAACTG 60.028 45.833 3.82 0.00 34.23 3.16
824 1350 7.441157 TCACAAATATCGAACTGAACTGAACTT 59.559 33.333 0.00 0.00 0.00 2.66
875 1401 3.668115 TCCTATATAAGAGCCCCTCCTGT 59.332 47.826 0.00 0.00 0.00 4.00
893 1419 1.071605 GTCCGTCATCTTCTGCACAC 58.928 55.000 0.00 0.00 0.00 3.82
911 1437 0.760189 ACCAACACCAAGGCAAGCAT 60.760 50.000 0.00 0.00 0.00 3.79
934 1460 1.203187 AGTCCACTCCTCCACAGCTAA 60.203 52.381 0.00 0.00 0.00 3.09
942 1468 2.024846 TCCTCCACAGCTAAGCTCTAGT 60.025 50.000 0.00 0.00 36.40 2.57
1088 1614 3.823330 CCCCGTCTTCCTCGTCGG 61.823 72.222 0.00 0.00 42.22 4.79
1089 1615 3.060615 CCCGTCTTCCTCGTCGGT 61.061 66.667 0.00 0.00 41.17 4.69
1130 1656 0.897401 GCCCCTTCTGCTTCTGCTTT 60.897 55.000 0.00 0.00 40.48 3.51
1181 1707 1.538047 TTGGAGTCCAGATTTGCAGC 58.462 50.000 12.67 0.00 33.81 5.25
1182 1708 0.401356 TGGAGTCCAGATTTGCAGCA 59.599 50.000 8.12 0.00 0.00 4.41
1354 1880 4.989168 TCGAGCCAAAAACTTAGACTTCTC 59.011 41.667 0.00 0.00 0.00 2.87
1419 1945 3.429207 GTCTTTCTTTGTAGCGAGGACAC 59.571 47.826 0.00 0.00 0.00 3.67
1544 2076 1.002430 CAGGTCCAGTGTGCTGTGTAT 59.998 52.381 0.00 0.00 41.02 2.29
1555 2088 0.731417 GCTGTGTATGCCTTGCTGAG 59.269 55.000 0.00 0.00 0.00 3.35
1590 2123 7.568199 TTTCATACGTATCTCTGATGTCTGA 57.432 36.000 4.74 0.00 0.00 3.27
1646 2179 6.744537 GTGAATGATGCATGTCAAGTTCTTAC 59.255 38.462 2.46 0.00 0.00 2.34
1844 2497 4.717279 ACCCTAAACTTCAGCTAAACCA 57.283 40.909 0.00 0.00 0.00 3.67
1970 2623 6.500589 TCTAACTTTGCTCCATTATAGGCT 57.499 37.500 0.00 0.00 0.00 4.58
2015 2668 0.895559 GGAAAAGGTGGCACCAGAGG 60.896 60.000 36.28 0.00 41.95 3.69
2050 2703 2.688446 TGGAGTACCACACATCGATCTC 59.312 50.000 0.00 0.00 41.77 2.75
2073 2726 5.352293 TCTTCAGCTACAACATGTGCAATAG 59.648 40.000 0.00 0.41 30.52 1.73
2081 2734 6.974932 ACAACATGTGCAATAGTTCTAGAG 57.025 37.500 0.00 0.00 0.00 2.43
2117 2934 5.428184 AGCTAGTTCTGCTTTCTGGTAAT 57.572 39.130 0.00 0.00 37.52 1.89
2130 2947 6.631314 GCTTTCTGGTAATGAGGAGAAGATGA 60.631 42.308 0.00 0.00 0.00 2.92
2209 3026 7.975616 TCATTAATTCAACATTAGCCTTTCTGC 59.024 33.333 0.00 0.00 0.00 4.26
2217 3034 0.324943 TAGCCTTTCTGCTGGGTCAC 59.675 55.000 0.00 0.00 42.77 3.67
2289 3106 5.220854 GCAGTGATATTCCAACGTGCTTTAT 60.221 40.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.603776 GGACCGACAGTGGGGAGT 60.604 66.667 6.55 0.00 0.00 3.85
3 4 2.283966 AGGACCGACAGTGGGGAG 60.284 66.667 6.55 0.00 0.00 4.30
5 6 2.283966 AGAGGACCGACAGTGGGG 60.284 66.667 6.55 0.00 0.00 4.96
6 7 2.973899 CAGAGGACCGACAGTGGG 59.026 66.667 0.00 0.00 0.00 4.61
7 8 2.262915 GCAGAGGACCGACAGTGG 59.737 66.667 0.00 0.00 0.00 4.00
8 9 2.262915 GGCAGAGGACCGACAGTG 59.737 66.667 0.00 0.00 0.00 3.66
26 27 2.448542 TAGAGGGATGGCTGGGGC 60.449 66.667 0.00 0.00 37.82 5.80
27 28 2.524204 GCTAGAGGGATGGCTGGGG 61.524 68.421 0.00 0.00 0.00 4.96
28 29 2.524204 GGCTAGAGGGATGGCTGGG 61.524 68.421 0.00 0.00 0.00 4.45
29 30 2.524204 GGGCTAGAGGGATGGCTGG 61.524 68.421 0.00 0.00 0.00 4.85
30 31 2.524204 GGGGCTAGAGGGATGGCTG 61.524 68.421 0.00 0.00 0.00 4.85
31 32 2.122189 GGGGCTAGAGGGATGGCT 60.122 66.667 0.00 0.00 0.00 4.75
32 33 3.253061 GGGGGCTAGAGGGATGGC 61.253 72.222 0.00 0.00 0.00 4.40
60 61 4.463879 CTCAGCACAGGGAGCGGG 62.464 72.222 0.00 0.00 37.01 6.13
64 65 1.538950 GAAAAAGCTCAGCACAGGGAG 59.461 52.381 0.00 0.00 0.00 4.30
65 66 1.143684 AGAAAAAGCTCAGCACAGGGA 59.856 47.619 0.00 0.00 0.00 4.20
66 67 1.613836 AGAAAAAGCTCAGCACAGGG 58.386 50.000 0.00 0.00 0.00 4.45
67 68 2.350197 CGAAGAAAAAGCTCAGCACAGG 60.350 50.000 0.00 0.00 0.00 4.00
68 69 2.350197 CCGAAGAAAAAGCTCAGCACAG 60.350 50.000 0.00 0.00 0.00 3.66
69 70 1.603802 CCGAAGAAAAAGCTCAGCACA 59.396 47.619 0.00 0.00 0.00 4.57
70 71 1.604278 ACCGAAGAAAAAGCTCAGCAC 59.396 47.619 0.00 0.00 0.00 4.40
71 72 1.603802 CACCGAAGAAAAAGCTCAGCA 59.396 47.619 0.00 0.00 0.00 4.41
90 91 3.238497 CGGTGGTGTGGGGACTCA 61.238 66.667 0.00 0.00 0.00 3.41
91 92 4.699522 GCGGTGGTGTGGGGACTC 62.700 72.222 0.00 0.00 0.00 3.36
146 147 7.505585 AGAATCTATCTTAGGGTTCAGAGTGAG 59.494 40.741 0.00 0.00 33.39 3.51
147 148 7.358263 AGAATCTATCTTAGGGTTCAGAGTGA 58.642 38.462 0.00 0.00 33.39 3.41
151 152 6.327626 CCCAAGAATCTATCTTAGGGTTCAGA 59.672 42.308 13.23 0.00 46.80 3.27
170 171 4.308458 CGCCGTCACCACCCAAGA 62.308 66.667 0.00 0.00 0.00 3.02
244 255 4.460382 ACATCAGTCAGCCGATTCAAATTT 59.540 37.500 0.00 0.00 0.00 1.82
249 260 1.276138 ACACATCAGTCAGCCGATTCA 59.724 47.619 0.00 0.00 0.00 2.57
292 303 3.818773 AGTGTACAATGTGTTGCTTACCC 59.181 43.478 0.00 0.00 38.96 3.69
316 327 2.588314 GCTGCTGCATCTCCGAGG 60.588 66.667 11.11 0.00 39.41 4.63
358 369 8.122472 AGGTATTTCTTGATTGGGTACAAAAG 57.878 34.615 0.00 0.00 40.55 2.27
397 917 0.113190 ATGGCTGCTAAATAGGGGGC 59.887 55.000 0.00 0.00 0.00 5.80
540 1066 1.491668 GGAGAAGAGAAGGGGAGTCC 58.508 60.000 0.00 0.00 0.00 3.85
541 1067 1.007842 AGGGAGAAGAGAAGGGGAGTC 59.992 57.143 0.00 0.00 0.00 3.36
542 1068 1.097722 AGGGAGAAGAGAAGGGGAGT 58.902 55.000 0.00 0.00 0.00 3.85
543 1069 1.494960 CAGGGAGAAGAGAAGGGGAG 58.505 60.000 0.00 0.00 0.00 4.30
544 1070 0.043334 CCAGGGAGAAGAGAAGGGGA 59.957 60.000 0.00 0.00 0.00 4.81
685 1211 1.127567 TGGAGGGTGGTGAGTTCTGG 61.128 60.000 0.00 0.00 0.00 3.86
797 1323 6.706055 TCAGTTCAGTTCGATATTTGTGAC 57.294 37.500 0.00 0.00 0.00 3.67
798 1324 6.929049 AGTTCAGTTCAGTTCGATATTTGTGA 59.071 34.615 0.00 0.00 0.00 3.58
799 1325 7.121974 AGTTCAGTTCAGTTCGATATTTGTG 57.878 36.000 0.00 0.00 0.00 3.33
809 1335 4.374399 TCCGGTTAAGTTCAGTTCAGTTC 58.626 43.478 0.00 0.00 0.00 3.01
810 1336 4.100498 TCTCCGGTTAAGTTCAGTTCAGTT 59.900 41.667 0.00 0.00 0.00 3.16
811 1337 3.640029 TCTCCGGTTAAGTTCAGTTCAGT 59.360 43.478 0.00 0.00 0.00 3.41
812 1338 4.252971 TCTCCGGTTAAGTTCAGTTCAG 57.747 45.455 0.00 0.00 0.00 3.02
813 1339 4.374399 GTTCTCCGGTTAAGTTCAGTTCA 58.626 43.478 0.00 0.00 0.00 3.18
814 1340 3.427863 CGTTCTCCGGTTAAGTTCAGTTC 59.572 47.826 0.00 0.00 0.00 3.01
875 1401 0.037326 GGTGTGCAGAAGATGACGGA 60.037 55.000 0.00 0.00 0.00 4.69
893 1419 0.037975 GATGCTTGCCTTGGTGTTGG 60.038 55.000 0.00 0.00 0.00 3.77
911 1437 1.342074 CTGTGGAGGAGTGGACTTGA 58.658 55.000 0.00 0.00 0.00 3.02
942 1468 3.088789 AGGAGACGGAAGAAGCTAGAA 57.911 47.619 0.00 0.00 0.00 2.10
1107 1633 2.436824 GAAGCAGAAGGGGCGTCC 60.437 66.667 0.00 0.00 34.34 4.79
1116 1642 1.466167 GCATCGAAAGCAGAAGCAGAA 59.534 47.619 8.19 0.00 45.49 3.02
1354 1880 7.456269 AGGTATGATATTAACCAGGGAAGAGAG 59.544 40.741 0.00 0.00 35.64 3.20
1503 2035 3.067106 GCAAGAAAGGAGACGAATCACA 58.933 45.455 0.00 0.00 0.00 3.58
1544 2076 0.700564 AGGATTTCCTCAGCAAGGCA 59.299 50.000 0.33 0.00 44.77 4.75
1555 2088 9.930693 AGAGATACGTATGAAAATAGGATTTCC 57.069 33.333 13.97 0.00 38.30 3.13
1564 2097 8.633561 TCAGACATCAGAGATACGTATGAAAAT 58.366 33.333 13.97 0.00 0.00 1.82
1574 2107 7.171167 CACCATGATTTCAGACATCAGAGATAC 59.829 40.741 5.50 0.00 34.12 2.24
1575 2108 7.147602 ACACCATGATTTCAGACATCAGAGATA 60.148 37.037 5.50 0.00 34.12 1.98
1576 2109 6.056236 CACCATGATTTCAGACATCAGAGAT 58.944 40.000 5.50 0.00 34.12 2.75
1590 2123 5.999205 TTAATCCAAGCACACCATGATTT 57.001 34.783 0.00 0.00 33.63 2.17
1821 2474 5.067954 TGGTTTAGCTGAAGTTTAGGGTTC 58.932 41.667 0.00 0.00 0.00 3.62
1944 2597 8.830741 AGCCTATAATGGAGCAAAGTTAGATAT 58.169 33.333 0.00 0.00 0.00 1.63
1945 2598 8.097038 CAGCCTATAATGGAGCAAAGTTAGATA 58.903 37.037 0.00 0.00 0.00 1.98
1970 2623 9.764363 CTTACTGATAATTAAGTGGTGCTATCA 57.236 33.333 0.85 0.00 0.00 2.15
2015 2668 0.835941 ACTCCATCCAGATCCTGCAC 59.164 55.000 0.00 0.00 0.00 4.57
2050 2703 3.902261 TTGCACATGTTGTAGCTGAAG 57.098 42.857 0.00 0.00 0.00 3.02
2073 2726 8.210265 TAGCTAGGTAGGTTAGTTCTCTAGAAC 58.790 40.741 13.79 13.79 42.88 3.01
2081 2734 6.459985 GCAGAACTAGCTAGGTAGGTTAGTTC 60.460 46.154 27.89 23.52 40.19 3.01
2117 2934 3.441922 CGAGTCAGTTCATCTTCTCCTCA 59.558 47.826 0.00 0.00 0.00 3.86
2130 2947 4.331168 GCTAGCATTTTGATCGAGTCAGTT 59.669 41.667 10.63 0.00 38.29 3.16
2207 3024 1.076014 TCGACCTAGTGACCCAGCA 59.924 57.895 0.00 0.00 0.00 4.41
2289 3106 1.203994 GCCTAACTCTCTAACACGGCA 59.796 52.381 0.00 0.00 36.37 5.69
2322 3139 0.732571 ACGTGCAGTTCAACAACCAG 59.267 50.000 0.00 0.00 32.22 4.00


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

AutoCloner maintained by Alex Coulton.