Multiple sequence alignment - TraesCS7B01G221800

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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 TraesCS7B01G221800 chr7B 100.000 2834 0 0 1 2834 413972154 413974987 0.000000e+00 5234.0
1 TraesCS7B01G221800 chr7D 96.887 2666 65 9 171 2834 405879178 405881827 0.000000e+00 4447.0
2 TraesCS7B01G221800 chr7D 89.610 77 4 4 2732 2807 383219941 383219868 8.360000e-16 95.3
3 TraesCS7B01G221800 chr7A 96.110 2648 58 21 171 2791 463204202 463206831 0.000000e+00 4277.0
4 TraesCS7B01G221800 chr4A 92.308 78 3 3 2728 2804 595568158 595568233 1.070000e-19 108.0
5 TraesCS7B01G221800 chr4A 90.667 75 4 3 2732 2805 595568233 595568161 2.320000e-16 97.1
6 TraesCS7B01G221800 chr6B 94.286 70 1 3 2737 2804 240042514 240042582 1.390000e-18 104.0
7 TraesCS7B01G221800 chr2D 91.026 78 2 4 2728 2804 324914797 324914870 1.800000e-17 100.0
8 TraesCS7B01G221800 chr2B 89.744 78 3 4 2728 2804 393999895 393999968 8.360000e-16 95.3
9 TraesCS7B01G221800 chr2A 89.744 78 1 6 2728 2804 393196620 393196549 3.010000e-15 93.5


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 TraesCS7B01G221800 chr7B 413972154 413974987 2833 False 5234 5234 100.000 1 2834 1 chr7B.!!$F1 2833
1 TraesCS7B01G221800 chr7D 405879178 405881827 2649 False 4447 4447 96.887 171 2834 1 chr7D.!!$F1 2663
2 TraesCS7B01G221800 chr7A 463204202 463206831 2629 False 4277 4277 96.110 171 2791 1 chr7A.!!$F1 2620

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
366 389 0.098728 AAGAAACGCACTGCACACAC 59.901 50.0 1.11 0.0 0.0 3.82 F
368 391 0.861450 GAAACGCACTGCACACACAC 60.861 55.0 1.11 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1326 1.065928 GACGCTCGGGTCGATGATT 59.934 57.895 6.13 0.0 34.61 2.57 R
2343 2371 2.109834 ACTGGGGACAACAAATCCATGA 59.890 45.455 0.00 0.0 42.06 3.07 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
141 142 4.936081 GGGGAGCGCTAGGGCCTA 62.936 72.222 26.51 13.73 34.44 3.93
142 143 3.307108 GGGAGCGCTAGGGCCTAG 61.307 72.222 32.12 32.12 37.16 3.02
143 144 3.307108 GGAGCGCTAGGGCCTAGG 61.307 72.222 35.37 26.68 34.88 3.02
144 145 2.522193 GAGCGCTAGGGCCTAGGT 60.522 66.667 35.37 21.17 34.88 3.08
145 146 2.840102 AGCGCTAGGGCCTAGGTG 60.840 66.667 35.37 24.42 34.88 4.00
146 147 2.838225 GCGCTAGGGCCTAGGTGA 60.838 66.667 35.37 7.77 34.88 4.02
147 148 2.862223 GCGCTAGGGCCTAGGTGAG 61.862 68.421 35.37 18.11 34.88 3.51
148 149 1.152735 CGCTAGGGCCTAGGTGAGA 60.153 63.158 35.37 6.22 34.88 3.27
149 150 1.175983 CGCTAGGGCCTAGGTGAGAG 61.176 65.000 35.37 16.69 34.88 3.20
150 151 1.468506 GCTAGGGCCTAGGTGAGAGC 61.469 65.000 35.37 22.15 34.88 4.09
151 152 1.152735 TAGGGCCTAGGTGAGAGCG 60.153 63.158 9.81 0.00 0.00 5.03
152 153 4.228567 GGGCCTAGGTGAGAGCGC 62.229 72.222 11.31 0.00 0.00 5.92
153 154 3.151022 GGCCTAGGTGAGAGCGCT 61.151 66.667 11.27 11.27 0.00 5.92
154 155 1.828660 GGCCTAGGTGAGAGCGCTA 60.829 63.158 11.50 0.00 0.00 4.26
155 156 1.657556 GCCTAGGTGAGAGCGCTAG 59.342 63.158 11.50 1.02 0.00 3.42
156 157 1.104577 GCCTAGGTGAGAGCGCTAGT 61.105 60.000 11.50 0.00 0.00 2.57
157 158 0.948678 CCTAGGTGAGAGCGCTAGTC 59.051 60.000 11.50 11.51 0.00 2.59
158 159 1.669604 CTAGGTGAGAGCGCTAGTCA 58.330 55.000 11.50 14.44 0.00 3.41
159 160 2.226330 CTAGGTGAGAGCGCTAGTCAT 58.774 52.381 21.34 11.48 0.00 3.06
160 161 1.479709 AGGTGAGAGCGCTAGTCATT 58.520 50.000 21.34 12.31 0.00 2.57
161 162 1.407258 AGGTGAGAGCGCTAGTCATTC 59.593 52.381 21.34 16.75 0.00 2.67
162 163 1.407258 GGTGAGAGCGCTAGTCATTCT 59.593 52.381 21.34 8.83 0.00 2.40
163 164 2.159170 GGTGAGAGCGCTAGTCATTCTT 60.159 50.000 21.34 0.00 0.00 2.52
164 165 3.516615 GTGAGAGCGCTAGTCATTCTTT 58.483 45.455 21.34 0.00 0.00 2.52
165 166 3.929610 GTGAGAGCGCTAGTCATTCTTTT 59.070 43.478 21.34 0.00 0.00 2.27
166 167 4.390297 GTGAGAGCGCTAGTCATTCTTTTT 59.610 41.667 21.34 0.00 0.00 1.94
261 284 7.741027 AATTGCATCTCTACATACCATTCTG 57.259 36.000 0.00 0.00 0.00 3.02
330 353 5.007528 GGTAGTAGTAGTAGCTTTGGACGAG 59.992 48.000 6.91 0.00 0.00 4.18
358 381 6.972901 CCTAGAAAAAGAAAAAGAAACGCACT 59.027 34.615 0.00 0.00 0.00 4.40
359 382 6.632171 AGAAAAAGAAAAAGAAACGCACTG 57.368 33.333 0.00 0.00 0.00 3.66
360 383 4.840401 AAAAGAAAAAGAAACGCACTGC 57.160 36.364 0.00 0.00 0.00 4.40
361 384 3.502191 AAGAAAAAGAAACGCACTGCA 57.498 38.095 1.11 0.00 0.00 4.41
362 385 2.797491 AGAAAAAGAAACGCACTGCAC 58.203 42.857 1.11 0.00 0.00 4.57
363 386 2.163412 AGAAAAAGAAACGCACTGCACA 59.837 40.909 1.11 0.00 0.00 4.57
364 387 1.908065 AAAAGAAACGCACTGCACAC 58.092 45.000 1.11 0.00 0.00 3.82
365 388 0.808125 AAAGAAACGCACTGCACACA 59.192 45.000 1.11 0.00 0.00 3.72
366 389 0.098728 AAGAAACGCACTGCACACAC 59.901 50.000 1.11 0.00 0.00 3.82
367 390 1.024046 AGAAACGCACTGCACACACA 61.024 50.000 1.11 0.00 0.00 3.72
368 391 0.861450 GAAACGCACTGCACACACAC 60.861 55.000 1.11 0.00 0.00 3.82
369 392 1.581727 AAACGCACTGCACACACACA 61.582 50.000 1.11 0.00 0.00 3.72
370 393 2.023181 CGCACTGCACACACACAC 59.977 61.111 1.11 0.00 0.00 3.82
371 394 2.023181 GCACTGCACACACACACG 59.977 61.111 0.00 0.00 0.00 4.49
372 395 2.708865 CACTGCACACACACACGG 59.291 61.111 0.00 0.00 0.00 4.94
373 396 3.202001 ACTGCACACACACACGGC 61.202 61.111 0.00 0.00 0.00 5.68
374 397 3.201297 CTGCACACACACACGGCA 61.201 61.111 0.00 0.00 0.00 5.69
375 398 3.172099 CTGCACACACACACGGCAG 62.172 63.158 0.00 0.00 44.91 4.85
376 399 2.894879 GCACACACACACGGCAGA 60.895 61.111 0.00 0.00 0.00 4.26
377 400 2.885676 GCACACACACACGGCAGAG 61.886 63.158 0.00 0.00 0.00 3.35
569 592 5.129485 GTCTCATTCTCTCCCTGTCCAAATA 59.871 44.000 0.00 0.00 0.00 1.40
646 669 5.748152 CACGCCATTTTTATCCAGGTATTTG 59.252 40.000 0.00 0.00 0.00 2.32
736 759 1.508185 TCTAGGCTAGTAATGGGGGCT 59.492 52.381 20.45 0.00 38.17 5.19
917 941 1.040339 GCTGGATCCTGTCGGAGAGT 61.040 60.000 18.82 0.00 44.06 3.24
948 972 3.505184 CGGTTCGGAATTGGGGCG 61.505 66.667 0.00 0.00 0.00 6.13
949 973 2.045731 GGTTCGGAATTGGGGCGA 60.046 61.111 0.00 0.00 0.00 5.54
1299 1326 2.840066 CGGGCACACCTTTTTCGCA 61.840 57.895 0.00 0.00 36.97 5.10
1659 1686 1.751927 GCAGCCAGAGGATGTTGGG 60.752 63.158 3.04 0.00 41.69 4.12
1952 1979 3.296854 GGTAATGGAGGGGATTTGAACC 58.703 50.000 0.00 0.00 0.00 3.62
2047 2074 7.516470 GCTTCATCTCTTGTACATGAGATTTCG 60.516 40.741 34.75 27.28 44.79 3.46
2148 2175 5.149273 GTTGATACTTGTGCAGATGTTGTG 58.851 41.667 7.71 0.00 0.00 3.33
2187 2214 3.627237 GCCCTCCATTCCATGACCTTTTA 60.627 47.826 0.00 0.00 0.00 1.52
2208 2235 8.458573 TTTTAGTGGATTTCTGCTCTTACAAA 57.541 30.769 0.00 0.00 0.00 2.83
2343 2371 2.644798 AGGTTAATTCTGCAGGACTGGT 59.355 45.455 15.13 0.00 0.00 4.00
2488 2516 7.255035 CCATGCAGGTAAGATCTGAAGTTAATG 60.255 40.741 0.00 0.00 34.36 1.90
2509 2537 2.159057 GCAATATTGTCTTGGCTTGGGG 60.159 50.000 16.61 0.00 0.00 4.96
2551 2579 7.736447 ATAGCTGCAACTAAATAATCAGTCC 57.264 36.000 0.04 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.227134 CACCTCCTCCGGCGATGG 62.227 72.222 9.30 10.38 0.00 3.51
11 12 4.227134 CCACCTCCTCCGGCGATG 62.227 72.222 9.30 0.00 0.00 3.84
124 125 4.936081 TAGGCCCTAGCGCTCCCC 62.936 72.222 16.34 10.49 41.24 4.81
125 126 3.307108 CTAGGCCCTAGCGCTCCC 61.307 72.222 16.34 10.90 41.24 4.30
126 127 3.307108 CCTAGGCCCTAGCGCTCC 61.307 72.222 16.34 9.46 41.24 4.70
127 128 2.522193 ACCTAGGCCCTAGCGCTC 60.522 66.667 16.34 0.00 41.24 5.03
128 129 2.840102 CACCTAGGCCCTAGCGCT 60.840 66.667 17.26 17.26 41.24 5.92
129 130 2.838225 TCACCTAGGCCCTAGCGC 60.838 66.667 12.62 0.00 41.24 5.92
130 131 1.152735 TCTCACCTAGGCCCTAGCG 60.153 63.158 12.62 8.32 41.24 4.26
131 132 1.468506 GCTCTCACCTAGGCCCTAGC 61.469 65.000 12.62 9.78 33.12 3.42
132 133 1.175983 CGCTCTCACCTAGGCCCTAG 61.176 65.000 11.08 11.08 34.16 3.02
133 134 1.152735 CGCTCTCACCTAGGCCCTA 60.153 63.158 9.30 0.00 0.00 3.53
134 135 2.443016 CGCTCTCACCTAGGCCCT 60.443 66.667 9.30 0.00 0.00 5.19
135 136 4.228567 GCGCTCTCACCTAGGCCC 62.229 72.222 9.30 0.00 0.00 5.80
136 137 1.801309 CTAGCGCTCTCACCTAGGCC 61.801 65.000 16.34 0.00 0.00 5.19
137 138 1.104577 ACTAGCGCTCTCACCTAGGC 61.105 60.000 16.34 0.00 34.32 3.93
138 139 0.948678 GACTAGCGCTCTCACCTAGG 59.051 60.000 16.34 7.41 34.32 3.02
139 140 1.669604 TGACTAGCGCTCTCACCTAG 58.330 55.000 16.34 6.33 35.75 3.02
140 141 2.350057 ATGACTAGCGCTCTCACCTA 57.650 50.000 16.34 0.00 0.00 3.08
141 142 1.407258 GAATGACTAGCGCTCTCACCT 59.593 52.381 16.34 7.16 0.00 4.00
142 143 1.407258 AGAATGACTAGCGCTCTCACC 59.593 52.381 16.34 11.54 0.00 4.02
143 144 2.861462 AGAATGACTAGCGCTCTCAC 57.139 50.000 16.34 5.37 0.00 3.51
144 145 3.876274 AAAGAATGACTAGCGCTCTCA 57.124 42.857 16.34 17.08 0.00 3.27
163 164 9.352784 CAAATAGAGTTGAGTTTGTGTGAAAAA 57.647 29.630 0.00 0.00 0.00 1.94
164 165 8.519526 ACAAATAGAGTTGAGTTTGTGTGAAAA 58.480 29.630 1.97 0.00 41.64 2.29
165 166 8.050778 ACAAATAGAGTTGAGTTTGTGTGAAA 57.949 30.769 1.97 0.00 41.64 2.69
166 167 7.624360 ACAAATAGAGTTGAGTTTGTGTGAA 57.376 32.000 1.97 0.00 41.64 3.18
261 284 5.849858 TGAGTCGTACGAAAATGCATTAAC 58.150 37.500 21.39 8.86 0.00 2.01
330 353 7.486870 TGCGTTTCTTTTTCTTTTTCTAGGAAC 59.513 33.333 0.00 0.00 0.00 3.62
358 381 3.201297 CTGCCGTGTGTGTGTGCA 61.201 61.111 0.00 0.00 0.00 4.57
359 382 2.885676 CTCTGCCGTGTGTGTGTGC 61.886 63.158 0.00 0.00 0.00 4.57
360 383 1.521457 ACTCTGCCGTGTGTGTGTG 60.521 57.895 0.00 0.00 0.00 3.82
361 384 1.521457 CACTCTGCCGTGTGTGTGT 60.521 57.895 2.55 0.00 31.71 3.72
362 385 2.885676 GCACTCTGCCGTGTGTGTG 61.886 63.158 11.21 0.00 37.42 3.82
363 386 2.588877 GCACTCTGCCGTGTGTGT 60.589 61.111 11.21 0.00 37.42 3.72
364 387 2.588596 TGCACTCTGCCGTGTGTG 60.589 61.111 11.21 5.93 44.23 3.82
365 388 2.280389 CTGCACTCTGCCGTGTGT 60.280 61.111 11.21 0.00 44.23 3.72
366 389 2.029518 TCTGCACTCTGCCGTGTG 59.970 61.111 6.02 6.02 44.23 3.82
367 390 2.029666 GTCTGCACTCTGCCGTGT 59.970 61.111 0.00 0.00 44.23 4.49
368 391 3.108289 CGTCTGCACTCTGCCGTG 61.108 66.667 0.00 0.00 44.23 4.94
369 392 3.295273 TCGTCTGCACTCTGCCGT 61.295 61.111 0.00 0.00 44.23 5.68
370 393 2.807045 GTCGTCTGCACTCTGCCG 60.807 66.667 0.00 0.00 44.23 5.69
371 394 2.024319 GTGTCGTCTGCACTCTGCC 61.024 63.158 0.00 0.00 44.23 4.85
372 395 2.368105 CGTGTCGTCTGCACTCTGC 61.368 63.158 0.00 0.00 45.29 4.26
373 396 0.109551 ATCGTGTCGTCTGCACTCTG 60.110 55.000 0.00 0.00 34.91 3.35
374 397 0.109551 CATCGTGTCGTCTGCACTCT 60.110 55.000 0.00 0.00 34.91 3.24
375 398 1.678269 GCATCGTGTCGTCTGCACTC 61.678 60.000 11.79 0.00 36.91 3.51
376 399 1.734477 GCATCGTGTCGTCTGCACT 60.734 57.895 11.79 0.00 36.91 4.40
377 400 1.678269 GAGCATCGTGTCGTCTGCAC 61.678 60.000 16.22 9.83 38.35 4.57
472 495 3.702048 CGAAGACTTGGCCGGGGA 61.702 66.667 2.18 0.00 0.00 4.81
646 669 7.468141 AAATAAAGAAAGTGATCTGGGGAAC 57.532 36.000 0.00 0.00 0.00 3.62
787 810 4.065088 TCACGGATCAAGAACTGGAAAAG 58.935 43.478 0.00 0.00 0.00 2.27
948 972 0.600057 ACCCTTCGTACGGACAACTC 59.400 55.000 16.52 0.00 0.00 3.01
949 973 0.316204 CACCCTTCGTACGGACAACT 59.684 55.000 16.52 0.00 0.00 3.16
1299 1326 1.065928 GACGCTCGGGTCGATGATT 59.934 57.895 6.13 0.00 34.61 2.57
1659 1686 3.113745 CGCTCCAATGACATGCCC 58.886 61.111 0.00 0.00 0.00 5.36
1952 1979 2.545526 CCTGAACATATTGCTAGGCGTG 59.454 50.000 0.00 0.00 0.00 5.34
2148 2175 4.183865 GAGGGCAATGAAACAAATTAGGC 58.816 43.478 0.00 0.00 0.00 3.93
2187 2214 5.869579 TCTTTGTAAGAGCAGAAATCCACT 58.130 37.500 0.00 0.00 32.71 4.00
2208 2235 6.152661 CCTATCAGAACTCAGAACTGAACTCT 59.847 42.308 6.01 7.50 42.55 3.24
2214 2241 5.636965 CACAACCTATCAGAACTCAGAACTG 59.363 44.000 0.00 0.00 0.00 3.16
2343 2371 2.109834 ACTGGGGACAACAAATCCATGA 59.890 45.455 0.00 0.00 42.06 3.07
2488 2516 2.159057 CCCCAAGCCAAGACAATATTGC 60.159 50.000 15.48 8.36 0.00 3.56
2539 2567 4.124851 ACGAGCTTCGGACTGATTATTT 57.875 40.909 9.75 0.00 45.59 1.40
2551 2579 2.858344 CCATACCAAAGTACGAGCTTCG 59.142 50.000 0.00 0.00 46.93 3.79
2791 2819 2.382649 ACAGGTAGGTACTCCCTCTGTT 59.617 50.000 0.00 0.00 43.09 3.16
2804 2832 7.065324 TCGTGCTTCAATAAATTTACAGGTAGG 59.935 37.037 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.