Multiple sequence alignment - TraesCS5B01G066300

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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 TraesCS5B01G066300 chr5B 100.000 2495 0 0 1 2495 74507631 74510125 0.000000e+00 4608.0
1 TraesCS5B01G066300 chr5A 90.984 1819 153 10 2 1815 59564141 59565953 0.000000e+00 2440.0
2 TraesCS5B01G066300 chr5D 90.189 1478 122 15 322 1782 68447814 68449285 0.000000e+00 1905.0
3 TraesCS5B01G066300 chr5D 89.888 356 23 8 2141 2495 68458620 68458963 1.760000e-121 446.0
4 TraesCS5B01G066300 chr5D 89.431 246 12 4 1814 2056 68458360 68458594 5.220000e-77 298.0
5 TraesCS5B01G066300 chr5D 79.545 88 17 1 1623 1709 431538693 431538606 7.450000e-06 62.1
6 TraesCS5B01G066300 chr5D 97.059 34 1 0 291 324 68435894 68435927 9.640000e-05 58.4
7 TraesCS5B01G066300 chr2D 91.139 79 7 0 1625 1703 3034788 3034710 9.440000e-20 108.0
8 TraesCS5B01G066300 chr7B 87.912 91 7 4 1623 1711 20241012 20240924 1.220000e-18 104.0
9 TraesCS5B01G066300 chr7A 94.643 56 3 0 1634 1689 200275035 200274980 1.230000e-13 87.9
10 TraesCS5B01G066300 chr7D 90.476 63 6 0 1628 1690 25309425 25309487 1.590000e-12 84.2
11 TraesCS5B01G066300 chr2A 94.444 54 2 1 1628 1681 202037107 202037159 5.720000e-12 82.4
12 TraesCS5B01G066300 chr1B 83.544 79 9 3 1625 1699 566686830 566686908 1.240000e-08 71.3


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 TraesCS5B01G066300 chr5B 74507631 74510125 2494 False 4608 4608 100.0000 1 2495 1 chr5B.!!$F1 2494
1 TraesCS5B01G066300 chr5A 59564141 59565953 1812 False 2440 2440 90.9840 2 1815 1 chr5A.!!$F1 1813
2 TraesCS5B01G066300 chr5D 68447814 68449285 1471 False 1905 1905 90.1890 322 1782 1 chr5D.!!$F2 1460
3 TraesCS5B01G066300 chr5D 68458360 68458963 603 False 372 446 89.6595 1814 2495 2 chr5D.!!$F3 681

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
498 502 0.738762 TCGACGTGAGAGTCTACCGG 60.739 60.0 0.00 0.0 38.9 5.28 F
1317 1324 0.460311 CCGACGAGAAGGCCAACTAT 59.540 55.0 5.01 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1363 0.459899 CTATCTGCGTGTAGTGCCCA 59.540 55.000 0.00 0.0 0.0 5.36 R
2461 2485 2.885113 GTCCGCAAAATGGGCCTC 59.115 61.111 4.53 0.0 0.0 4.70 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
67 68 1.519234 TCGCCGATGACATCACAGC 60.519 57.895 15.58 12.77 0.00 4.40
70 71 0.742281 GCCGATGACATCACAGCAGT 60.742 55.000 15.58 0.00 0.00 4.40
75 76 3.061295 CGATGACATCACAGCAGTAACAC 59.939 47.826 15.58 0.00 0.00 3.32
85 86 1.946768 AGCAGTAACACGCAACAACAT 59.053 42.857 0.00 0.00 0.00 2.71
91 92 0.953727 ACACGCAACAACATCAGCAT 59.046 45.000 0.00 0.00 0.00 3.79
94 95 1.074319 CGCAACAACATCAGCATGGC 61.074 55.000 0.00 0.00 36.16 4.40
117 118 1.517257 CCTCGCACATCACCGTCTC 60.517 63.158 0.00 0.00 0.00 3.36
126 127 0.877649 ATCACCGTCTCGCATCATGC 60.878 55.000 0.00 0.00 40.69 4.06
132 133 1.860326 CGTCTCGCATCATGCATACAA 59.140 47.619 11.00 0.00 45.36 2.41
146 148 2.358898 GCATACAACACCCCATGTCATC 59.641 50.000 0.00 0.00 42.31 2.92
154 156 3.156293 CACCCCATGTCATCTTGTTTGA 58.844 45.455 0.00 0.00 0.00 2.69
159 161 5.279607 CCCCATGTCATCTTGTTTGAAACAT 60.280 40.000 11.97 0.00 41.79 2.71
165 167 6.040729 TGTCATCTTGTTTGAAACATGGATGT 59.959 34.615 30.29 13.45 43.86 3.06
166 168 6.364165 GTCATCTTGTTTGAAACATGGATGTG 59.636 38.462 30.29 20.07 43.86 3.21
172 174 5.535783 TGTTTGAAACATGGATGTGATGAGT 59.464 36.000 6.66 0.00 41.61 3.41
189 191 1.734117 GTGGCGCTGGATTTGCAAC 60.734 57.895 7.64 0.00 0.00 4.17
191 193 1.216178 GGCGCTGGATTTGCAACAT 59.784 52.632 7.64 0.00 0.00 2.71
195 197 1.791555 CGCTGGATTTGCAACATCGAC 60.792 52.381 0.00 0.00 0.00 4.20
203 205 2.340328 GCAACATCGACCCCCAACC 61.340 63.158 0.00 0.00 0.00 3.77
219 221 2.180159 AACCTGTAGCATCGCCGGTT 62.180 55.000 1.90 0.00 0.00 4.44
231 233 2.993471 GCCGGTTGCAGTGGGATTG 61.993 63.158 1.90 0.00 40.77 2.67
253 255 2.401766 CCACGAAGCATGGGTGAGC 61.402 63.158 0.00 0.00 33.58 4.26
254 256 2.045926 ACGAAGCATGGGTGAGCC 60.046 61.111 0.00 0.00 0.00 4.70
256 258 2.825836 GAAGCATGGGTGAGCCGG 60.826 66.667 0.00 0.00 34.97 6.13
258 260 3.335356 AAGCATGGGTGAGCCGGAG 62.335 63.158 5.05 0.00 34.97 4.63
350 352 1.276421 CCTCGTCCAGTTCACTTGGAT 59.724 52.381 0.00 0.00 33.91 3.41
372 374 1.199789 GCGATGCCACAACTCAATTGA 59.800 47.619 8.12 8.12 41.23 2.57
424 428 4.935578 AGGAAAAATGTAAGGAAGAGGGG 58.064 43.478 0.00 0.00 0.00 4.79
432 436 2.368878 GGAAGAGGGGGAGGGCAT 60.369 66.667 0.00 0.00 0.00 4.40
437 441 2.204291 AGGGGGAGGGCATGTGAA 60.204 61.111 0.00 0.00 0.00 3.18
463 467 1.151777 CCACTGAACGTGTGTCGCTT 61.152 55.000 4.10 0.00 42.20 4.68
498 502 0.738762 TCGACGTGAGAGTCTACCGG 60.739 60.000 0.00 0.00 38.90 5.28
500 504 1.991099 GACGTGAGAGTCTACCGGCC 61.991 65.000 0.00 0.00 38.09 6.13
502 506 2.439701 TGAGAGTCTACCGGCCGG 60.440 66.667 42.17 42.17 42.03 6.13
512 516 2.045340 CCGGCCGGTGAAAGGAAT 60.045 61.111 36.64 0.00 0.00 3.01
600 604 6.330004 TGTGTGTGCAAACATATTCTTCAT 57.670 33.333 14.04 0.00 31.49 2.57
607 611 9.171877 TGTGCAAACATATTCTTCATACATACA 57.828 29.630 0.00 0.00 0.00 2.29
608 612 9.655769 GTGCAAACATATTCTTCATACATACAG 57.344 33.333 0.00 0.00 0.00 2.74
625 630 9.903682 ATACATACAGAGATTGCATTATTTTGC 57.096 29.630 0.00 0.00 43.07 3.68
635 640 9.059260 AGATTGCATTATTTTGCTGTTCTTTTT 57.941 25.926 0.00 0.00 43.18 1.94
723 730 8.903820 ACTTAGGTGATCTTTTAATGGTAATGC 58.096 33.333 0.00 0.00 0.00 3.56
760 767 9.579932 GATCTCCATTCCCTCATTAATACTTTT 57.420 33.333 0.00 0.00 0.00 2.27
886 893 9.219497 GCCATAGTTACGTATACTCGATAATTC 57.781 37.037 11.88 0.00 34.70 2.17
903 910 1.083489 TTCCGGCTTATGCTTCAACG 58.917 50.000 0.00 0.00 39.59 4.10
919 926 7.748847 TGCTTCAACGAAATTCCTCTATAAAC 58.251 34.615 0.00 0.00 0.00 2.01
926 933 7.383687 ACGAAATTCCTCTATAAACACACTGA 58.616 34.615 0.00 0.00 0.00 3.41
934 941 8.429641 TCCTCTATAAACACACTGAGAAAGTTT 58.570 33.333 0.00 0.00 36.83 2.66
951 958 4.595762 AGTTTACGCTACCTCACAAGAA 57.404 40.909 0.00 0.00 0.00 2.52
966 973 6.856426 CCTCACAAGAATACGAAAGAAAAACC 59.144 38.462 0.00 0.00 0.00 3.27
967 974 6.423862 TCACAAGAATACGAAAGAAAAACCG 58.576 36.000 0.00 0.00 0.00 4.44
976 983 5.449304 ACGAAAGAAAAACCGAAGCAATAG 58.551 37.500 0.00 0.00 0.00 1.73
979 986 7.118680 ACGAAAGAAAAACCGAAGCAATAGATA 59.881 33.333 0.00 0.00 0.00 1.98
987 994 5.126067 ACCGAAGCAATAGATAGCACATTT 58.874 37.500 0.00 0.00 0.00 2.32
1020 1027 1.045350 TGGAGGCATCTAAGCTCGCT 61.045 55.000 0.00 0.00 34.17 4.93
1317 1324 0.460311 CCGACGAGAAGGCCAACTAT 59.540 55.000 5.01 0.00 0.00 2.12
1320 1327 3.243771 CCGACGAGAAGGCCAACTATAAT 60.244 47.826 5.01 0.00 0.00 1.28
1323 1330 6.157211 CGACGAGAAGGCCAACTATAATTAT 58.843 40.000 5.01 2.97 0.00 1.28
1338 1345 2.814805 ATTATGCCTCCAACAGCTGT 57.185 45.000 15.25 15.25 0.00 4.40
1425 1432 2.182791 CGTCTGCTCTGCGACCAT 59.817 61.111 0.00 0.00 32.00 3.55
1426 1433 2.163390 CGTCTGCTCTGCGACCATG 61.163 63.158 0.00 0.00 32.00 3.66
1456 1463 3.840209 CGTGTTCATCACTTGCAATTACG 59.160 43.478 0.00 0.00 44.16 3.18
1605 1613 2.518949 GCTGTCGTGCATGTATTTTGG 58.481 47.619 5.68 0.00 0.00 3.28
1637 1645 7.540183 AGAACCATAGATATGTACTCCCTCTT 58.460 38.462 0.00 0.00 31.82 2.85
1642 1650 9.930693 CCATAGATATGTACTCCCTCTTTAAAC 57.069 37.037 0.00 0.00 31.82 2.01
1711 1730 9.209175 GTCTTATATTACTTTGCATAGGGAGTG 57.791 37.037 9.08 0.00 0.00 3.51
1801 1821 8.571461 AGTACTACTACTAGTTATTGTGCACA 57.429 34.615 17.42 17.42 34.79 4.57
2084 2107 7.790823 AATTTCAAAGAAGTTTTCATGGGTG 57.209 32.000 0.00 0.00 0.00 4.61
2195 2218 5.945191 TGTTCATGAGTTTGAAGATATGGCA 59.055 36.000 0.00 0.00 36.34 4.92
2461 2485 6.422776 AGAATGCAGAAAATACTAACGGTG 57.577 37.500 0.00 0.00 0.00 4.94
2472 2496 1.074889 ACTAACGGTGAGGCCCATTTT 59.925 47.619 0.00 0.00 0.00 1.82
2483 2507 1.969064 CCCATTTTGCGGACGGTGA 60.969 57.895 0.00 0.00 0.00 4.02
2484 2508 1.209127 CCATTTTGCGGACGGTGAC 59.791 57.895 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.962995 AGTAGTGTGAGGTGCCTACATTAT 59.037 41.667 0.00 0.00 33.77 1.28
3 4 4.159693 CAGTAGTGTGAGGTGCCTACATTA 59.840 45.833 0.00 0.00 33.77 1.90
4 5 3.055819 CAGTAGTGTGAGGTGCCTACATT 60.056 47.826 0.00 0.00 33.77 2.71
5 6 2.497675 CAGTAGTGTGAGGTGCCTACAT 59.502 50.000 0.00 0.00 33.77 2.29
6 7 1.893137 CAGTAGTGTGAGGTGCCTACA 59.107 52.381 0.00 0.00 33.77 2.74
7 8 1.404315 GCAGTAGTGTGAGGTGCCTAC 60.404 57.143 0.00 0.00 0.00 3.18
67 68 3.544651 CTGATGTTGTTGCGTGTTACTG 58.455 45.455 0.00 0.00 0.00 2.74
70 71 1.943340 TGCTGATGTTGTTGCGTGTTA 59.057 42.857 0.00 0.00 0.00 2.41
75 76 1.074319 GCCATGCTGATGTTGTTGCG 61.074 55.000 0.00 0.00 0.00 4.85
102 103 3.545481 GCGAGACGGTGATGTGCG 61.545 66.667 0.00 0.00 0.00 5.34
126 127 3.889815 AGATGACATGGGGTGTTGTATG 58.110 45.455 0.00 0.00 42.36 2.39
132 133 2.892852 CAAACAAGATGACATGGGGTGT 59.107 45.455 0.00 0.00 45.83 4.16
146 148 6.448852 TCATCACATCCATGTTTCAAACAAG 58.551 36.000 7.14 2.35 45.86 3.16
154 156 2.756760 GCCACTCATCACATCCATGTTT 59.243 45.455 0.00 0.00 39.39 2.83
159 161 1.450134 GCGCCACTCATCACATCCA 60.450 57.895 0.00 0.00 0.00 3.41
165 167 0.035152 AAATCCAGCGCCACTCATCA 60.035 50.000 2.29 0.00 0.00 3.07
166 168 0.379669 CAAATCCAGCGCCACTCATC 59.620 55.000 2.29 0.00 0.00 2.92
172 174 1.534336 ATGTTGCAAATCCAGCGCCA 61.534 50.000 2.29 0.00 33.85 5.69
189 191 0.178068 CTACAGGTTGGGGGTCGATG 59.822 60.000 0.00 0.00 0.00 3.84
191 193 2.288025 GCTACAGGTTGGGGGTCGA 61.288 63.158 0.00 0.00 0.00 4.20
195 197 1.153168 CGATGCTACAGGTTGGGGG 60.153 63.158 0.00 0.00 0.00 5.40
203 205 2.813179 GCAACCGGCGATGCTACAG 61.813 63.158 23.94 2.54 39.46 2.74
231 233 1.134521 TCACCCATGCTTCGTGGATAC 60.135 52.381 6.64 0.00 42.73 2.24
239 241 2.825836 CCGGCTCACCCATGCTTC 60.826 66.667 0.00 0.00 0.00 3.86
256 258 2.435586 ACATGGTGCTGCGAGCTC 60.436 61.111 2.73 2.73 42.97 4.09
276 278 0.953727 GTCACAACATCAGCAAGGCA 59.046 50.000 0.00 0.00 0.00 4.75
372 374 3.118445 GGAATGCTTTCAGCTACCTCTCT 60.118 47.826 13.72 0.00 42.97 3.10
400 402 5.516591 CCCCTCTTCCTTACATTTTTCCTCA 60.517 44.000 0.00 0.00 0.00 3.86
424 428 0.538287 GCCCTATTCACATGCCCTCC 60.538 60.000 0.00 0.00 0.00 4.30
432 436 1.004277 GTTCAGTGGGCCCTATTCACA 59.996 52.381 25.70 0.00 34.17 3.58
437 441 1.602237 CACGTTCAGTGGGCCCTAT 59.398 57.895 25.70 8.68 46.77 2.57
470 474 4.986587 TCACGTCGACAACCGCCG 62.987 66.667 17.16 1.70 45.84 6.46
480 484 1.714414 CCGGTAGACTCTCACGTCG 59.286 63.158 0.00 0.00 38.90 5.12
485 489 2.439701 CCGGCCGGTAGACTCTCA 60.440 66.667 36.64 0.00 0.00 3.27
498 502 4.918810 AATTGATATTCCTTTCACCGGC 57.081 40.909 0.00 0.00 0.00 6.13
560 564 6.505732 GCACACACAAGATTACAACGAAAAAC 60.506 38.462 0.00 0.00 0.00 2.43
805 812 4.504858 CACTGGGAATTAGTGTCTACCAC 58.495 47.826 0.00 0.00 44.89 4.16
824 831 9.574516 GTAATGAAAGGATATTGGATAACCACT 57.425 33.333 0.00 0.00 46.80 4.00
886 893 1.083489 TTCGTTGAAGCATAAGCCGG 58.917 50.000 0.00 0.00 43.56 6.13
903 910 9.436957 TTCTCAGTGTGTTTATAGAGGAATTTC 57.563 33.333 0.00 0.00 0.00 2.17
919 926 4.150098 GGTAGCGTAAACTTTCTCAGTGTG 59.850 45.833 0.00 0.00 35.12 3.82
926 933 4.595762 TGTGAGGTAGCGTAAACTTTCT 57.404 40.909 0.00 0.00 0.00 2.52
934 941 3.940852 TCGTATTCTTGTGAGGTAGCGTA 59.059 43.478 0.00 0.00 0.00 4.42
951 958 5.427036 TTGCTTCGGTTTTTCTTTCGTAT 57.573 34.783 0.00 0.00 0.00 3.06
966 973 7.148672 CCTCTAAATGTGCTATCTATTGCTTCG 60.149 40.741 0.00 0.00 0.00 3.79
967 974 7.360776 GCCTCTAAATGTGCTATCTATTGCTTC 60.361 40.741 0.00 0.00 0.00 3.86
976 983 4.444720 GTGTACGCCTCTAAATGTGCTATC 59.555 45.833 0.00 0.00 0.00 2.08
979 986 2.028476 TGTGTACGCCTCTAAATGTGCT 60.028 45.455 3.51 0.00 0.00 4.40
987 994 1.399714 CCTCCATGTGTACGCCTCTA 58.600 55.000 3.51 0.00 0.00 2.43
1020 1027 0.749818 TTGCCAGCACGACCAAAAGA 60.750 50.000 0.00 0.00 0.00 2.52
1226 1233 0.974383 CAGGTTCTCCCCGTACTGTT 59.026 55.000 0.00 0.00 0.00 3.16
1278 1285 0.469917 CCCATATCTTCACGGCCTGT 59.530 55.000 0.00 0.00 0.00 4.00
1317 1324 3.947196 CACAGCTGTTGGAGGCATAATTA 59.053 43.478 18.94 0.00 0.00 1.40
1320 1327 1.825090 CACAGCTGTTGGAGGCATAA 58.175 50.000 18.94 0.00 0.00 1.90
1323 1330 2.595463 GCACAGCTGTTGGAGGCA 60.595 61.111 18.94 0.00 0.00 4.75
1356 1363 0.459899 CTATCTGCGTGTAGTGCCCA 59.540 55.000 0.00 0.00 0.00 5.36
1605 1613 9.796120 GAGTACATATCTATGGTTCTTAGCATC 57.204 37.037 0.00 0.00 41.37 3.91
1700 1719 7.817418 TTTTCATAAATACCACTCCCTATGC 57.183 36.000 0.00 0.00 0.00 3.14
1800 1820 2.228822 GCACCTGGGACTGTTTATTGTG 59.771 50.000 0.00 0.00 0.00 3.33
1801 1821 2.158534 TGCACCTGGGACTGTTTATTGT 60.159 45.455 0.00 0.00 0.00 2.71
1810 1830 4.335647 CGCCTTGCACCTGGGACT 62.336 66.667 0.00 0.00 0.00 3.85
1893 1913 5.112686 TGCAAAGTTTCGCAAAGGTAATTT 58.887 33.333 9.38 0.00 34.59 1.82
1894 1914 4.688021 TGCAAAGTTTCGCAAAGGTAATT 58.312 34.783 9.38 0.00 34.59 1.40
1896 1916 3.784701 TGCAAAGTTTCGCAAAGGTAA 57.215 38.095 9.38 0.00 34.59 2.85
2056 2079 8.676401 CCCATGAAAACTTCTTTGAAATTTGTT 58.324 29.630 0.00 0.00 0.00 2.83
2057 2080 7.828717 ACCCATGAAAACTTCTTTGAAATTTGT 59.171 29.630 0.00 0.00 0.00 2.83
2058 2081 8.124199 CACCCATGAAAACTTCTTTGAAATTTG 58.876 33.333 0.00 0.00 0.00 2.32
2059 2082 7.828717 ACACCCATGAAAACTTCTTTGAAATTT 59.171 29.630 0.00 0.00 0.00 1.82
2060 2083 7.280652 CACACCCATGAAAACTTCTTTGAAATT 59.719 33.333 0.00 0.00 0.00 1.82
2061 2084 6.762661 CACACCCATGAAAACTTCTTTGAAAT 59.237 34.615 0.00 0.00 0.00 2.17
2062 2085 6.071108 TCACACCCATGAAAACTTCTTTGAAA 60.071 34.615 0.00 0.00 0.00 2.69
2063 2086 5.420421 TCACACCCATGAAAACTTCTTTGAA 59.580 36.000 0.00 0.00 0.00 2.69
2064 2087 4.952957 TCACACCCATGAAAACTTCTTTGA 59.047 37.500 0.00 0.00 0.00 2.69
2065 2088 5.261209 TCACACCCATGAAAACTTCTTTG 57.739 39.130 0.00 0.00 0.00 2.77
2066 2089 5.930837 TTCACACCCATGAAAACTTCTTT 57.069 34.783 0.00 0.00 35.65 2.52
2067 2090 5.930837 TTTCACACCCATGAAAACTTCTT 57.069 34.783 0.00 0.00 43.81 2.52
2175 2198 9.806203 TTAAATTGCCATATCTTCAAACTCATG 57.194 29.630 0.00 0.00 0.00 3.07
2461 2485 2.885113 GTCCGCAAAATGGGCCTC 59.115 61.111 4.53 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.