Multiple sequence alignment - TraesCS2B01G581500

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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 TraesCS2B01G581500 chr2B 100.000 3668 0 0 1 3668 769052457 769048790 0.000000e+00 6774.0
1 TraesCS2B01G581500 chr2B 95.062 405 20 0 2132 2536 768778744 768778340 3.990000e-179 638.0
2 TraesCS2B01G581500 chr2B 93.289 298 13 2 1848 2138 768791142 768790845 2.020000e-117 433.0
3 TraesCS2B01G581500 chr2B 88.539 349 32 6 3287 3633 768778333 768777991 2.040000e-112 416.0
4 TraesCS2B01G581500 chr2B 93.750 272 12 2 1871 2138 768850372 768850102 1.590000e-108 403.0
5 TraesCS2B01G581500 chr2B 93.382 272 14 1 1871 2138 768873662 768873391 2.050000e-107 399.0
6 TraesCS2B01G581500 chr2B 92.308 65 4 1 1871 1935 768906313 768906250 1.400000e-14 91.6
7 TraesCS2B01G581500 chr2B 82.524 103 14 3 3396 3497 768617842 768617743 1.810000e-13 87.9
8 TraesCS2B01G581500 chr2D 95.159 3677 154 9 2 3666 627239118 627235454 0.000000e+00 5782.0
9 TraesCS2B01G581500 chr2D 87.442 645 67 5 1367 2003 630120865 630121503 0.000000e+00 730.0
10 TraesCS2B01G581500 chr2D 88.000 325 27 6 2368 2681 630121551 630121874 1.240000e-99 374.0
11 TraesCS2B01G581500 chr2D 76.144 306 53 15 3211 3497 627171261 627170957 3.820000e-30 143.0
12 TraesCS2B01G581500 chr2A 90.698 3655 249 44 2 3633 757937133 757933547 0.000000e+00 4782.0


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 TraesCS2B01G581500 chr2B 769048790 769052457 3667 True 6774 6774 100.0000 1 3668 1 chr2B.!!$R6 3667
1 TraesCS2B01G581500 chr2B 768777991 768778744 753 True 527 638 91.8005 2132 3633 2 chr2B.!!$R7 1501
2 TraesCS2B01G581500 chr2D 627235454 627239118 3664 True 5782 5782 95.1590 2 3666 1 chr2D.!!$R2 3664
3 TraesCS2B01G581500 chr2D 630120865 630121874 1009 False 552 730 87.7210 1367 2681 2 chr2D.!!$F1 1314
4 TraesCS2B01G581500 chr2A 757933547 757937133 3586 True 4782 4782 90.6980 2 3633 1 chr2A.!!$R1 3631

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
396 400 0.038892 ATGGTTTGCTCTTTGCTGCG 60.039 50.0 0.0 0.0 43.37 5.18 F
1197 1201 0.520827 CGTTCTCGTCGGTACTCAGC 60.521 60.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1253 1.216710 GCTCCTCCGACTTCACCAG 59.783 63.158 0.0 0.0 0.0 4.00 R
2790 2813 0.540597 GCCCTTTCCAACCTTCAGCT 60.541 55.000 0.0 0.0 0.0 4.24 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
22 23 0.317269 GTCGACTTCACCAACGACGA 60.317 55.000 8.70 0.00 43.60 4.20
23 24 0.594602 TCGACTTCACCAACGACGAT 59.405 50.000 0.00 0.00 0.00 3.73
26 27 2.132762 GACTTCACCAACGACGATGTT 58.867 47.619 0.00 0.00 0.00 2.71
34 35 0.942410 AACGACGATGTTGGACACCG 60.942 55.000 0.00 0.00 0.00 4.94
36 37 1.374252 GACGATGTTGGACACCGCT 60.374 57.895 0.00 0.00 0.00 5.52
44 48 4.070552 GGACACCGCTCGAAGGCT 62.071 66.667 6.51 0.00 0.00 4.58
66 70 2.425592 CTCGAGCACCCACCAACA 59.574 61.111 0.00 0.00 0.00 3.33
76 80 0.396417 CCCACCAACACCTCCACAAA 60.396 55.000 0.00 0.00 0.00 2.83
78 82 2.038659 CCACCAACACCTCCACAAAAT 58.961 47.619 0.00 0.00 0.00 1.82
79 83 3.226777 CCACCAACACCTCCACAAAATA 58.773 45.455 0.00 0.00 0.00 1.40
80 84 3.255642 CCACCAACACCTCCACAAAATAG 59.744 47.826 0.00 0.00 0.00 1.73
81 85 3.255642 CACCAACACCTCCACAAAATAGG 59.744 47.826 0.00 0.00 36.42 2.57
82 86 2.231235 CCAACACCTCCACAAAATAGGC 59.769 50.000 0.00 0.00 33.42 3.93
83 87 2.215942 ACACCTCCACAAAATAGGCC 57.784 50.000 0.00 0.00 33.42 5.19
84 88 1.710809 ACACCTCCACAAAATAGGCCT 59.289 47.619 11.78 11.78 33.42 5.19
85 89 2.290960 ACACCTCCACAAAATAGGCCTC 60.291 50.000 9.68 0.00 33.42 4.70
86 90 1.285078 ACCTCCACAAAATAGGCCTCC 59.715 52.381 9.68 0.00 33.42 4.30
89 93 0.397114 CCACAAAATAGGCCTCCCCC 60.397 60.000 9.68 0.00 0.00 5.40
124 128 3.991051 CCGTCACCTGCTCCACGT 61.991 66.667 0.00 0.00 0.00 4.49
127 131 2.523168 TCACCTGCTCCACGTGGA 60.523 61.111 34.13 34.13 43.08 4.02
137 141 1.227823 CCACGTGGACTTTGCCTGA 60.228 57.895 31.31 0.00 37.39 3.86
142 146 1.877680 CGTGGACTTTGCCTGATGACA 60.878 52.381 0.00 0.00 0.00 3.58
150 154 2.910360 CCTGATGACATGCCCCGA 59.090 61.111 0.00 0.00 0.00 5.14
167 171 3.645268 GATGGCGGTGAAAGGGGCT 62.645 63.158 0.00 0.00 0.00 5.19
168 172 3.944250 ATGGCGGTGAAAGGGGCTG 62.944 63.158 0.00 0.00 0.00 4.85
173 177 1.915078 CGGTGAAAGGGGCTGAGGAT 61.915 60.000 0.00 0.00 0.00 3.24
179 183 3.017581 GGGGCTGAGGATGGGTGT 61.018 66.667 0.00 0.00 0.00 4.16
185 189 0.617413 CTGAGGATGGGTGTCTGCTT 59.383 55.000 0.00 0.00 0.00 3.91
193 197 0.673985 GGGTGTCTGCTTGGGTTTTC 59.326 55.000 0.00 0.00 0.00 2.29
204 208 0.392336 TGGGTTTTCCAGTTGCATGC 59.608 50.000 11.82 11.82 41.46 4.06
205 209 0.392336 GGGTTTTCCAGTTGCATGCA 59.608 50.000 18.46 18.46 42.91 3.96
213 217 2.202650 GTTGCATGCATGGTCGCC 60.203 61.111 27.34 11.23 0.00 5.54
228 232 3.643320 TGGTCGCCTATTCTTCTCATGAT 59.357 43.478 0.00 0.00 0.00 2.45
229 233 4.241681 GGTCGCCTATTCTTCTCATGATC 58.758 47.826 0.00 0.00 0.00 2.92
236 240 6.426328 GCCTATTCTTCTCATGATCACGATTT 59.574 38.462 0.00 0.00 0.00 2.17
289 293 5.170021 TGGTCATGCTTGTATGCAAATTTC 58.830 37.500 0.00 0.00 46.61 2.17
295 299 7.972832 TCATGCTTGTATGCAAATTTCGAATAA 59.027 29.630 0.00 0.00 46.61 1.40
396 400 0.038892 ATGGTTTGCTCTTTGCTGCG 60.039 50.000 0.00 0.00 43.37 5.18
447 451 2.726760 GGTCGCTATGCTACGAAATGAG 59.273 50.000 0.00 0.00 40.47 2.90
1057 1061 1.131826 GTGTTCGACGAAATGGCGG 59.868 57.895 12.67 0.00 35.12 6.13
1161 1165 2.943265 ATGGTGAGGGCTGGGCTT 60.943 61.111 0.00 0.00 0.00 4.35
1162 1166 2.551413 ATGGTGAGGGCTGGGCTTT 61.551 57.895 0.00 0.00 0.00 3.51
1180 1184 1.399744 TTCACCCACTGAGAGCACGT 61.400 55.000 0.00 0.00 0.00 4.49
1197 1201 0.520827 CGTTCTCGTCGGTACTCAGC 60.521 60.000 0.00 0.00 0.00 4.26
1203 1207 3.755628 TCGGTACTCAGCGGGTGC 61.756 66.667 1.51 0.00 45.57 5.01
1249 1253 3.880846 GCGTGCTACATGGCTGGC 61.881 66.667 0.00 0.00 0.00 4.85
1315 1319 1.517361 CTGCTCGGCATGTACTCCA 59.483 57.895 0.00 0.00 38.13 3.86
1364 1368 4.379186 GCATGTGTTTGACAGGATTGAGAG 60.379 45.833 0.00 0.00 38.73 3.20
1372 1376 2.614001 AGGATTGAGAGGCCTGACC 58.386 57.895 12.00 4.06 39.61 4.02
1417 1421 1.152830 GGGTTTTCTGGTGCTGGGA 59.847 57.895 0.00 0.00 0.00 4.37
1488 1492 1.666872 CGAACCGGTTGTCCCTGAC 60.667 63.158 27.87 6.43 0.00 3.51
1908 1920 3.387962 TGAAGGGAATATCTGTGCCTCT 58.612 45.455 0.00 0.00 35.45 3.69
1947 1959 5.565592 TGTATGCTAAAAATGGTGCTCTG 57.434 39.130 0.00 0.00 0.00 3.35
1961 1973 1.941999 GCTCTGCAAGGTGCCCATTC 61.942 60.000 0.00 0.00 44.23 2.67
2230 2242 5.235186 CACTATACTAGCATGGTGAGTTTGC 59.765 44.000 12.87 0.00 39.12 3.68
2385 2397 2.666190 GCTGAACAGGCACTCGCA 60.666 61.111 3.99 0.00 41.24 5.10
2477 2489 6.899114 ACGTTGTAGCTGAAATTAGGAAAAG 58.101 36.000 0.00 0.00 0.00 2.27
2511 2523 1.518367 TGGTTGAGAAGGAACCTGGT 58.482 50.000 0.00 0.00 43.00 4.00
2725 2747 3.665745 TTGCTTTCCTTTGAGGATTGC 57.334 42.857 12.03 12.03 45.34 3.56
2790 2813 1.270518 GGTGCTTGTCTTCTCTGCAGA 60.271 52.381 17.19 17.19 34.15 4.26
3035 3062 7.391148 TCAATTTAAGGTTCCAATAGCACTC 57.609 36.000 0.00 0.00 0.00 3.51
3143 3172 3.326880 AGTCCGACTTATGTTTGGTTCCT 59.673 43.478 0.00 0.00 0.00 3.36
3206 3235 3.466836 ACAAACAATTGCTCGAGTCTGA 58.533 40.909 15.13 0.00 40.34 3.27
3207 3236 3.876914 ACAAACAATTGCTCGAGTCTGAA 59.123 39.130 15.13 2.68 40.34 3.02
3228 3264 2.614259 TGGGAGAGAGAAGTTTGAGCT 58.386 47.619 0.00 0.00 0.00 4.09
3247 3283 2.095364 GCTGATGCTTTGGTGTCTCTTG 60.095 50.000 0.00 0.00 36.03 3.02
3250 3286 1.985473 TGCTTTGGTGTCTCTTGCAT 58.015 45.000 0.00 0.00 0.00 3.96
3302 3339 3.257469 TCTGTGATCACCAGCAGAATC 57.743 47.619 22.85 0.00 33.31 2.52
3448 3486 6.094719 CACATTAATCATTTGTCAGGTGTGG 58.905 40.000 0.00 0.00 32.03 4.17
3554 3592 9.651718 GTTCTAACAGAAGACAAAAATGTACAG 57.348 33.333 0.33 0.00 34.42 2.74
3614 3654 1.693640 CCAGTCAAGCCCTTCCCAT 59.306 57.895 0.00 0.00 0.00 4.00
3666 3706 1.669265 GTTACCGGGCATTTAGACTGC 59.331 52.381 6.32 0.00 38.93 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.008194 CGTTGGTGAAGTCGACGGA 60.008 57.895 10.46 0.00 38.10 4.69
4 5 0.594602 ATCGTCGTTGGTGAAGTCGA 59.405 50.000 0.00 0.00 0.00 4.20
22 23 0.670546 CTTCGAGCGGTGTCCAACAT 60.671 55.000 0.00 0.00 0.00 2.71
23 24 1.300620 CTTCGAGCGGTGTCCAACA 60.301 57.895 0.00 0.00 0.00 3.33
26 27 4.373116 GCCTTCGAGCGGTGTCCA 62.373 66.667 0.00 0.00 0.00 4.02
28 29 2.048127 AAGCCTTCGAGCGGTGTC 60.048 61.111 0.00 0.00 38.01 3.67
34 35 2.164026 CGAGCAGAAGCCTTCGAGC 61.164 63.158 14.49 14.49 39.85 5.03
36 37 1.508545 CTCGAGCAGAAGCCTTCGA 59.491 57.895 0.00 0.00 42.70 3.71
60 64 3.496331 CCTATTTTGTGGAGGTGTTGGT 58.504 45.455 0.00 0.00 0.00 3.67
64 68 1.710809 AGGCCTATTTTGTGGAGGTGT 59.289 47.619 1.29 0.00 32.53 4.16
66 70 1.285078 GGAGGCCTATTTTGTGGAGGT 59.715 52.381 4.42 0.00 32.53 3.85
86 90 2.444256 GGGAGGTCAAGATCGGGGG 61.444 68.421 0.00 0.00 0.00 5.40
89 93 2.815308 CGGGGAGGTCAAGATCGG 59.185 66.667 0.00 0.00 0.00 4.18
112 116 1.696097 AAAGTCCACGTGGAGCAGGT 61.696 55.000 37.04 17.71 46.49 4.00
114 118 1.845809 GCAAAGTCCACGTGGAGCAG 61.846 60.000 37.04 25.55 46.49 4.24
115 119 1.891919 GCAAAGTCCACGTGGAGCA 60.892 57.895 37.04 14.53 46.49 4.26
124 128 2.439409 CATGTCATCAGGCAAAGTCCA 58.561 47.619 0.00 0.00 0.00 4.02
150 154 3.661648 AGCCCCTTTCACCGCCAT 61.662 61.111 0.00 0.00 0.00 4.40
157 161 1.574526 CCCATCCTCAGCCCCTTTCA 61.575 60.000 0.00 0.00 0.00 2.69
160 164 2.128226 ACCCATCCTCAGCCCCTT 59.872 61.111 0.00 0.00 0.00 3.95
167 171 0.325933 CAAGCAGACACCCATCCTCA 59.674 55.000 0.00 0.00 0.00 3.86
168 172 0.393537 CCAAGCAGACACCCATCCTC 60.394 60.000 0.00 0.00 0.00 3.71
173 177 0.032615 AAAACCCAAGCAGACACCCA 60.033 50.000 0.00 0.00 0.00 4.51
179 183 2.031120 CAACTGGAAAACCCAAGCAGA 58.969 47.619 0.00 0.00 46.07 4.26
185 189 0.392336 GCATGCAACTGGAAAACCCA 59.608 50.000 14.21 0.00 44.25 4.51
193 197 1.138036 CGACCATGCATGCAACTGG 59.862 57.895 30.26 30.26 33.56 4.00
196 200 1.375853 TAGGCGACCATGCATGCAAC 61.376 55.000 26.68 14.89 36.28 4.17
201 205 2.105477 AGAAGAATAGGCGACCATGCAT 59.895 45.455 0.00 0.00 36.28 3.96
204 208 3.459232 TGAGAAGAATAGGCGACCATG 57.541 47.619 0.00 0.00 0.00 3.66
205 209 3.643320 TCATGAGAAGAATAGGCGACCAT 59.357 43.478 0.00 0.00 0.00 3.55
213 217 8.585189 TCAAATCGTGATCATGAGAAGAATAG 57.415 34.615 21.61 7.03 0.00 1.73
236 240 6.034161 AGCATATTCACATGAGATCGATCA 57.966 37.500 26.47 9.77 0.00 2.92
241 245 8.710551 CAAGTTCTAGCATATTCACATGAGATC 58.289 37.037 0.00 0.00 0.00 2.75
242 246 7.660617 CCAAGTTCTAGCATATTCACATGAGAT 59.339 37.037 0.00 0.00 0.00 2.75
243 247 6.988580 CCAAGTTCTAGCATATTCACATGAGA 59.011 38.462 0.00 0.00 0.00 3.27
245 249 6.653020 ACCAAGTTCTAGCATATTCACATGA 58.347 36.000 0.00 0.00 0.00 3.07
246 250 6.539826 TGACCAAGTTCTAGCATATTCACATG 59.460 38.462 0.00 0.00 0.00 3.21
247 251 6.653020 TGACCAAGTTCTAGCATATTCACAT 58.347 36.000 0.00 0.00 0.00 3.21
248 252 6.048732 TGACCAAGTTCTAGCATATTCACA 57.951 37.500 0.00 0.00 0.00 3.58
319 323 8.519799 AATTAATAACATGGTGTGGTTCCTAG 57.480 34.615 0.00 0.00 0.00 3.02
660 664 0.605319 GGTTGACGATGAAGGTGCCA 60.605 55.000 0.00 0.00 0.00 4.92
748 752 3.998672 GGAGACGACGTTGGGGCA 61.999 66.667 7.90 0.00 0.00 5.36
1061 1065 3.834447 TTCCACGCGACCACGTCAG 62.834 63.158 15.93 0.00 46.34 3.51
1062 1066 3.902086 TTCCACGCGACCACGTCA 61.902 61.111 15.93 0.00 46.34 4.35
1161 1165 1.367471 CGTGCTCTCAGTGGGTGAA 59.633 57.895 0.00 0.00 33.60 3.18
1162 1166 1.399744 AACGTGCTCTCAGTGGGTGA 61.400 55.000 0.00 0.00 0.00 4.02
1180 1184 1.642037 CCGCTGAGTACCGACGAGAA 61.642 60.000 0.00 0.00 0.00 2.87
1227 1231 4.838152 CCATGTAGCACGCGCCCT 62.838 66.667 5.73 4.97 39.83 5.19
1239 1243 1.303888 CTTCACCAGCCAGCCATGT 60.304 57.895 0.00 0.00 0.00 3.21
1249 1253 1.216710 GCTCCTCCGACTTCACCAG 59.783 63.158 0.00 0.00 0.00 4.00
1315 1319 2.285773 TGTCCAGATCACCGCAGCT 61.286 57.895 0.00 0.00 0.00 4.24
1372 1376 4.743057 TCAGAGTATTCCATGACACCAG 57.257 45.455 0.00 0.00 0.00 4.00
1417 1421 3.813240 GCATCCATAGCACTCCATCCATT 60.813 47.826 0.00 0.00 0.00 3.16
1488 1492 3.001634 CCACAGCTGCAAATGTATACTCG 59.998 47.826 15.27 0.00 0.00 4.18
1908 1920 4.392047 CATACATATCAAGCAGGCTTCCA 58.608 43.478 3.02 0.00 33.42 3.53
1978 1990 4.498009 CCAACACTTCAAATCTCGCTTTGT 60.498 41.667 5.31 0.00 37.39 2.83
2230 2242 2.654863 CAATAAACCTGCCCTACCCAG 58.345 52.381 0.00 0.00 0.00 4.45
2385 2397 3.960755 TCGACATATCATCTGGGTCTTGT 59.039 43.478 0.00 0.00 0.00 3.16
2477 2489 4.102210 TCTCAACCATCATTCCTCTGATCC 59.898 45.833 0.00 0.00 33.59 3.36
2511 2523 5.598416 TTTTTATCTCGATCCAGCTCAGA 57.402 39.130 0.00 0.00 0.00 3.27
2725 2747 4.273148 CCCGAGGGTCCTTATCAATAAG 57.727 50.000 0.00 3.25 39.50 1.73
2790 2813 0.540597 GCCCTTTCCAACCTTCAGCT 60.541 55.000 0.00 0.00 0.00 4.24
2899 2922 3.217626 CAGAGGAAAGCAGTCAAAACCT 58.782 45.455 0.00 0.00 0.00 3.50
3049 3076 6.967199 CAGTTTGACTGTAAACCTTCTTTGAC 59.033 38.462 0.00 0.00 41.19 3.18
3076 3103 5.105567 TCCACCTCAGTAACTTGTTTGAA 57.894 39.130 0.00 0.00 0.00 2.69
3143 3172 6.126565 TGCTTAGTATGTACCTAGTCTCTGGA 60.127 42.308 0.00 0.00 0.00 3.86
3206 3235 3.586618 AGCTCAAACTTCTCTCTCCCATT 59.413 43.478 0.00 0.00 0.00 3.16
3207 3236 3.055240 CAGCTCAAACTTCTCTCTCCCAT 60.055 47.826 0.00 0.00 0.00 4.00
3228 3264 1.881973 GCAAGAGACACCAAAGCATCA 59.118 47.619 0.00 0.00 0.00 3.07
3247 3283 7.538575 ACAGAACCAAACAGACATATTAATGC 58.461 34.615 0.00 0.00 36.50 3.56
3250 3286 9.126151 TGAAACAGAACCAAACAGACATATTAA 57.874 29.630 0.00 0.00 0.00 1.40
3448 3486 2.289694 TGTCTTTCCTAGAAGCAGCCAC 60.290 50.000 0.00 0.00 33.81 5.01
3554 3592 1.387295 GGCCATGCCCTCAGTTAAGC 61.387 60.000 0.00 0.00 44.06 3.09
3614 3654 6.530120 TGTAAACTCAGGAAGCTTACATGAA 58.470 36.000 12.25 0.00 40.12 2.57
3639 3679 6.485648 AGTCTAAATGCCCGGTAACATTAATC 59.514 38.462 13.18 6.67 35.49 1.75


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

AutoCloner maintained by Alex Coulton.