Multiple sequence alignment - TraesCS3B01G276900

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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 TraesCS3B01G276900 chr3B 100.000 3534 0 0 1 3534 447010168 447006635 0.000000e+00 6527.0
1 TraesCS3B01G276900 chr3D 96.889 3471 70 11 92 3534 346980021 346976561 0.000000e+00 5777.0
2 TraesCS3B01G276900 chr3D 95.238 63 3 0 7 69 346980078 346980016 2.240000e-17 100.0
3 TraesCS3B01G276900 chr3A 95.824 3472 106 15 90 3534 466113542 466110083 0.000000e+00 5572.0
4 TraesCS3B01G276900 chr4D 87.554 233 13 4 2842 3066 7831711 7831487 4.530000e-64 255.0
5 TraesCS3B01G276900 chr4A 84.167 240 20 5 2835 3066 595566777 595567006 2.140000e-52 217.0
6 TraesCS3B01G276900 chr4B 84.286 210 15 5 2835 3036 14120969 14121168 4.660000e-44 189.0
7 TraesCS3B01G276900 chr5A 86.239 109 12 3 2961 3066 43689729 43689837 8.020000e-22 115.0
8 TraesCS3B01G276900 chr5A 85.321 109 13 3 2961 3066 43737652 43737760 3.730000e-20 110.0
9 TraesCS3B01G276900 chr5B 82.812 128 18 4 2961 3084 57871848 57871975 1.040000e-20 111.0
10 TraesCS3B01G276900 chr2D 86.364 88 11 1 2933 3019 522750928 522750841 1.040000e-15 95.3
11 TraesCS3B01G276900 chr1D 100.000 28 0 0 2807 2834 176386072 176386099 6.000000e-03 52.8
12 TraesCS3B01G276900 chr1B 100.000 28 0 0 2807 2834 242737823 242737850 6.000000e-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 TraesCS3B01G276900 chr3B 447006635 447010168 3533 True 6527.0 6527 100.0000 1 3534 1 chr3B.!!$R1 3533
1 TraesCS3B01G276900 chr3D 346976561 346980078 3517 True 2938.5 5777 96.0635 7 3534 2 chr3D.!!$R1 3527
2 TraesCS3B01G276900 chr3A 466110083 466113542 3459 True 5572.0 5572 95.8240 90 3534 1 chr3A.!!$R1 3444

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
19 20 0.179045 ACCTCCAGCATATGTTCGGC 60.179 55.0 4.29 0.0 0.00 5.54 F
404 405 0.752009 CCTCCTGCCTCGTAGTAGCA 60.752 60.0 0.00 0.0 35.61 3.49 F
420 421 0.911769 AGCATCGTCATTCTTCCCCA 59.088 50.0 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1929 1.071471 CTCTTCCTGTGCCAACCGT 59.929 57.895 0.0 0.00 0.00 4.83 R
2367 2390 2.222027 CCACATATCTTCCTTTCCCGC 58.778 52.381 0.0 0.00 0.00 6.13 R
2702 2733 8.887036 TCACTACCTGTATGTTTTGCATATAG 57.113 34.615 0.0 4.65 44.17 1.31 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
19 20 0.179045 ACCTCCAGCATATGTTCGGC 60.179 55.000 4.29 0.00 0.00 5.54
69 70 3.376540 CGCAATTCGTTTCCCAAAAAGA 58.623 40.909 0.00 0.00 32.13 2.52
71 72 4.085107 CGCAATTCGTTTCCCAAAAAGAAG 60.085 41.667 5.71 0.00 43.08 2.85
72 73 4.211164 GCAATTCGTTTCCCAAAAAGAAGG 59.789 41.667 5.71 2.76 43.08 3.46
73 74 5.596845 CAATTCGTTTCCCAAAAAGAAGGA 58.403 37.500 5.71 0.00 43.08 3.36
74 75 4.642445 TTCGTTTCCCAAAAAGAAGGAC 57.358 40.909 0.00 0.00 37.75 3.85
75 76 3.622630 TCGTTTCCCAAAAAGAAGGACA 58.377 40.909 0.00 0.00 31.24 4.02
76 77 4.211920 TCGTTTCCCAAAAAGAAGGACAT 58.788 39.130 0.00 0.00 31.24 3.06
77 78 4.647399 TCGTTTCCCAAAAAGAAGGACATT 59.353 37.500 0.00 0.00 31.24 2.71
78 79 5.828859 TCGTTTCCCAAAAAGAAGGACATTA 59.171 36.000 0.00 0.00 31.24 1.90
79 80 6.492087 TCGTTTCCCAAAAAGAAGGACATTAT 59.508 34.615 0.00 0.00 31.24 1.28
80 81 6.806739 CGTTTCCCAAAAAGAAGGACATTATC 59.193 38.462 0.00 0.00 0.00 1.75
81 82 7.309194 CGTTTCCCAAAAAGAAGGACATTATCT 60.309 37.037 0.00 0.00 0.00 1.98
82 83 8.367911 GTTTCCCAAAAAGAAGGACATTATCTT 58.632 33.333 0.00 0.00 35.00 2.40
83 84 8.491045 TTCCCAAAAAGAAGGACATTATCTTT 57.509 30.769 0.00 0.00 43.32 2.52
84 85 9.594936 TTCCCAAAAAGAAGGACATTATCTTTA 57.405 29.630 0.90 0.00 41.28 1.85
85 86 9.594936 TCCCAAAAAGAAGGACATTATCTTTAA 57.405 29.630 0.90 0.00 41.28 1.52
117 118 5.774690 AGAAGGACATTAATGGCTTTGTTCA 59.225 36.000 22.25 0.00 35.00 3.18
134 135 6.573664 TTGTTCATCCACAACTAGGAAATG 57.426 37.500 0.00 0.00 38.93 2.32
160 161 4.687483 CCAGCATTTTTGGCAAAGAGTTAG 59.313 41.667 13.04 4.00 0.00 2.34
384 385 5.445540 GCCAAGTCGTCGTTTATAAAAGGAG 60.446 44.000 10.64 6.04 0.00 3.69
404 405 0.752009 CCTCCTGCCTCGTAGTAGCA 60.752 60.000 0.00 0.00 35.61 3.49
420 421 0.911769 AGCATCGTCATTCTTCCCCA 59.088 50.000 0.00 0.00 0.00 4.96
449 450 1.333308 CAACCACACAATGCTGAACGA 59.667 47.619 0.00 0.00 0.00 3.85
537 538 2.307363 CGAAGCACGGTTCAACTGT 58.693 52.632 9.43 0.00 38.46 3.55
694 702 1.609072 GTGCTTCCCTTCACCTTCAAC 59.391 52.381 0.00 0.00 0.00 3.18
749 757 5.948758 GTCTCTGATTCATCTTTTCCCCTTT 59.051 40.000 0.00 0.00 0.00 3.11
792 800 3.520569 GTGTTGGATCTCTGCTTCTCTC 58.479 50.000 0.00 0.00 0.00 3.20
824 832 6.385649 TGAAGTTTCGCCATAAAGAAAAGT 57.614 33.333 0.00 0.00 37.98 2.66
855 863 1.478510 CGAGAGACAGCCACCATAGTT 59.521 52.381 0.00 0.00 0.00 2.24
911 919 1.523938 GCAGTACCTGATTCCCGCC 60.524 63.158 0.00 0.00 32.44 6.13
1023 1043 4.168101 TGTTCTCCTTCAAGTCCAGGTAT 58.832 43.478 0.00 0.00 0.00 2.73
1037 1057 9.543783 CAAGTCCAGGTATAGTATTTAGTTTCC 57.456 37.037 0.00 0.00 0.00 3.13
1056 1077 2.429610 TCCTCCCGAGTTTTCTTATCCG 59.570 50.000 0.00 0.00 0.00 4.18
1061 1082 4.160814 TCCCGAGTTTTCTTATCCGAATCA 59.839 41.667 0.00 0.00 0.00 2.57
1062 1083 5.057149 CCCGAGTTTTCTTATCCGAATCAT 58.943 41.667 0.00 0.00 0.00 2.45
1063 1084 5.527582 CCCGAGTTTTCTTATCCGAATCATT 59.472 40.000 0.00 0.00 0.00 2.57
1064 1085 6.422223 CCGAGTTTTCTTATCCGAATCATTG 58.578 40.000 0.00 0.00 0.00 2.82
1065 1086 6.257849 CCGAGTTTTCTTATCCGAATCATTGA 59.742 38.462 0.00 0.00 0.00 2.57
1066 1087 7.201609 CCGAGTTTTCTTATCCGAATCATTGAA 60.202 37.037 0.00 0.00 0.00 2.69
1067 1088 8.338259 CGAGTTTTCTTATCCGAATCATTGAAT 58.662 33.333 0.00 0.00 0.00 2.57
1068 1089 9.657121 GAGTTTTCTTATCCGAATCATTGAATC 57.343 33.333 0.00 0.00 0.00 2.52
1149 1170 6.554334 TTAGGTTTCTGTCGAATTTCTTGG 57.446 37.500 0.00 0.00 0.00 3.61
1352 1375 1.066858 AGAAGGTACGTGCACTGGATG 60.067 52.381 16.19 0.68 0.00 3.51
1573 1596 3.457380 AGGCCAAGCTTGAGATAGATTCA 59.543 43.478 28.05 0.00 0.00 2.57
1906 1929 6.484288 TCTGGAAATCATGGAAGAAAAGCTA 58.516 36.000 0.00 0.00 0.00 3.32
2440 2463 4.038642 AGCTCTCCTCGTTCAAAGGATATC 59.961 45.833 0.00 0.00 42.01 1.63
3253 3291 8.296713 GTCTGCAGAACCTGTTTATGAATTTAA 58.703 33.333 20.19 0.00 33.43 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179045 GCCGAACATATGCTGGAGGT 60.179 55.000 11.52 0.00 0.00 3.85
1 2 0.107456 AGCCGAACATATGCTGGAGG 59.893 55.000 11.52 5.96 33.23 4.30
2 3 1.600957 CAAGCCGAACATATGCTGGAG 59.399 52.381 11.52 0.00 35.08 3.86
3 4 1.667236 CAAGCCGAACATATGCTGGA 58.333 50.000 11.52 0.00 35.08 3.86
4 5 0.029834 GCAAGCCGAACATATGCTGG 59.970 55.000 1.58 3.35 35.08 4.85
5 6 1.003116 GAGCAAGCCGAACATATGCTG 60.003 52.381 1.58 0.00 46.58 4.41
19 20 2.515523 CGGATGGGCTGGAGCAAG 60.516 66.667 0.20 0.00 44.36 4.01
30 31 2.903855 GCATGCAGACCCGGATGG 60.904 66.667 14.21 0.00 35.44 3.51
110 111 6.516527 GCATTTCCTAGTTGTGGATGAACAAA 60.517 38.462 0.00 0.00 41.52 2.83
117 118 3.266772 TGGAGCATTTCCTAGTTGTGGAT 59.733 43.478 0.00 0.00 46.92 3.41
134 135 1.802365 CTTTGCCAAAAATGCTGGAGC 59.198 47.619 0.00 0.00 42.50 4.70
140 141 4.151157 CAGCTAACTCTTTGCCAAAAATGC 59.849 41.667 0.00 0.00 0.00 3.56
143 144 3.957497 TCCAGCTAACTCTTTGCCAAAAA 59.043 39.130 0.00 0.00 0.00 1.94
148 149 1.279271 TCCTCCAGCTAACTCTTTGCC 59.721 52.381 0.00 0.00 0.00 4.52
204 205 8.298854 GCTGGATTAATGTGCATTTCATACATA 58.701 33.333 2.56 0.00 34.18 2.29
206 207 6.096564 TGCTGGATTAATGTGCATTTCATACA 59.903 34.615 2.56 3.00 32.50 2.29
328 329 8.726870 TTTCCCCTTCTAATCAATACTTTACG 57.273 34.615 0.00 0.00 0.00 3.18
384 385 2.034607 CTACTACGAGGCAGGAGGC 58.965 63.158 0.00 0.00 43.74 4.70
395 396 3.975670 GGAAGAATGACGATGCTACTACG 59.024 47.826 0.00 0.00 0.00 3.51
404 405 2.039746 TGTTGTGGGGAAGAATGACGAT 59.960 45.455 0.00 0.00 0.00 3.73
420 421 3.870419 GCATTGTGTGGTTGAATTGTTGT 59.130 39.130 0.00 0.00 0.00 3.32
449 450 2.029073 CACACCACTCGTCGGCTT 59.971 61.111 0.00 0.00 0.00 4.35
694 702 3.181967 CGAACTCCAAGAGCCGCG 61.182 66.667 0.00 0.00 32.04 6.46
749 757 2.941891 CGTCTTCTGCGCTGTTAAAA 57.058 45.000 9.73 0.00 0.00 1.52
762 770 0.389948 AGATCCAACACCGCGTCTTC 60.390 55.000 4.92 0.00 0.00 2.87
773 781 2.158971 GGGAGAGAAGCAGAGATCCAAC 60.159 54.545 0.00 0.00 0.00 3.77
792 800 1.269569 GGCGAAACTTCAAAACAGGGG 60.270 52.381 0.00 0.00 0.00 4.79
824 832 2.352225 GCTGTCTCTCGAAGCAAAGAGA 60.352 50.000 1.19 0.00 44.37 3.10
1023 1043 7.486407 AAACTCGGGAGGAAACTAAATACTA 57.514 36.000 0.00 0.00 44.43 1.82
1037 1057 3.795623 TCGGATAAGAAAACTCGGGAG 57.204 47.619 0.00 0.00 0.00 4.30
1056 1077 9.459640 ACAAATGATTCGATGATTCAATGATTC 57.540 29.630 11.46 0.00 0.00 2.52
1062 1083 9.940166 CAGATAACAAATGATTCGATGATTCAA 57.060 29.630 0.00 0.00 0.00 2.69
1063 1084 9.112725 ACAGATAACAAATGATTCGATGATTCA 57.887 29.630 0.00 0.00 0.00 2.57
1064 1085 9.941664 AACAGATAACAAATGATTCGATGATTC 57.058 29.630 0.00 0.00 0.00 2.52
1065 1086 9.726232 CAACAGATAACAAATGATTCGATGATT 57.274 29.630 0.00 0.00 0.00 2.57
1066 1087 8.347771 CCAACAGATAACAAATGATTCGATGAT 58.652 33.333 0.00 0.00 0.00 2.45
1067 1088 7.679400 GCCAACAGATAACAAATGATTCGATGA 60.679 37.037 0.00 0.00 0.00 2.92
1068 1089 6.415867 GCCAACAGATAACAAATGATTCGATG 59.584 38.462 0.00 0.00 0.00 3.84
1149 1170 9.673454 AGTAATCGAAACAAAGAAATAACAACC 57.327 29.630 0.00 0.00 0.00 3.77
1352 1375 6.463995 TTTCTTCTTGAGCTCCTCTATCTC 57.536 41.667 12.15 0.00 0.00 2.75
1573 1596 4.589908 AGGTCTTGTTGTTGTCTTGAAGT 58.410 39.130 0.00 0.00 0.00 3.01
1906 1929 1.071471 CTCTTCCTGTGCCAACCGT 59.929 57.895 0.00 0.00 0.00 4.83
2367 2390 2.222027 CCACATATCTTCCTTTCCCGC 58.778 52.381 0.00 0.00 0.00 6.13
2702 2733 8.887036 TCACTACCTGTATGTTTTGCATATAG 57.113 34.615 0.00 4.65 44.17 1.31
3036 3073 6.410540 GGATAAGCATCCCTAGTTATCCTTG 58.589 44.000 15.45 0.00 44.55 3.61
3169 3207 5.932619 TGCTAGGTTTCTGCATTAGTCTA 57.067 39.130 0.00 0.00 0.00 2.59
3341 3379 5.325239 AGGAGGTTTAGAACTGGGAAATTG 58.675 41.667 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.