Multiple sequence alignment - TraesCS7D01G230000

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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 TraesCS7D01G230000 chr7D 100.000 3605 0 0 1 3605 191057452 191061056 0.000000e+00 6658
1 TraesCS7D01G230000 chr7A 93.103 3668 156 30 1 3602 199670791 199674427 0.000000e+00 5282
2 TraesCS7D01G230000 chr7B 94.553 2809 112 17 400 3179 335620505 335623301 0.000000e+00 4301
3 TraesCS7D01G230000 chr7B 91.549 426 32 4 1 422 335620072 335620497 5.190000e-163 584
4 TraesCS7D01G230000 chr7B 89.016 437 22 4 3166 3602 335623884 335624294 5.340000e-143 518
5 TraesCS7D01G230000 chr3B 77.200 250 43 11 2265 2513 4744304 4744068 2.260000e-27 134
6 TraesCS7D01G230000 chr3B 89.362 94 10 0 2265 2358 3864215 3864122 6.320000e-23 119
7 TraesCS7D01G230000 chr3A 77.049 244 41 9 2265 2505 7297375 7297606 3.780000e-25 126
8 TraesCS7D01G230000 chr3D 76.856 229 41 9 2265 2493 1733647 1733431 6.320000e-23 119
9 TraesCS7D01G230000 chr6D 88.095 84 9 1 33 116 453167541 453167623 8.240000e-17 99


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 TraesCS7D01G230000 chr7D 191057452 191061056 3604 False 6658 6658 100.000 1 3605 1 chr7D.!!$F1 3604
1 TraesCS7D01G230000 chr7A 199670791 199674427 3636 False 5282 5282 93.103 1 3602 1 chr7A.!!$F1 3601
2 TraesCS7D01G230000 chr7B 335620072 335624294 4222 False 1801 4301 91.706 1 3602 3 chr7B.!!$F1 3601

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
845 880 1.072965 CATATGTCAGAGGGGCCTTCC 59.927 57.143 12.67 0.0 0.00 3.46 F
1364 1399 1.093972 CCATGGTGCTTTATGCGTGA 58.906 50.000 2.57 0.0 46.63 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1767 0.984995 AAGGAAGTACTGGGCACTCC 59.015 55.0 0.00 0.0 0.0 3.85 R
2929 3018 0.390209 TACGCTTTACCGGGCTCAAC 60.390 55.0 6.32 0.0 0.0 3.18 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
139 140 4.278669 AGTCAAAGCGAGTACTTCTGAAGA 59.721 41.667 23.36 5.08 0.00 2.87
192 193 7.399191 TCACCTAAGAACCTTCACACACTATAT 59.601 37.037 0.00 0.00 0.00 0.86
199 200 9.823647 AGAACCTTCACACACTATATTATGAAG 57.176 33.333 5.08 5.08 41.65 3.02
231 232 1.735559 GTAAAGCCTCGCGAACCGT 60.736 57.895 11.33 0.00 38.35 4.83
232 233 1.444895 TAAAGCCTCGCGAACCGTC 60.445 57.895 11.33 0.00 38.35 4.79
379 384 8.871686 AAAAGGTCATTCACATTTGTAAACTC 57.128 30.769 0.00 0.00 38.04 3.01
474 509 2.728383 ATATACGACGCACGCGGC 60.728 61.111 16.70 12.42 46.94 6.53
539 574 5.049405 GCAAATAGACCCAAATCATCTACGG 60.049 44.000 0.00 0.00 0.00 4.02
570 605 7.710475 CCAATTTTCACTTTAGTCACCAACATT 59.290 33.333 0.00 0.00 0.00 2.71
578 613 8.017373 CACTTTAGTCACCAACATTTGTATCTG 58.983 37.037 0.00 0.00 0.00 2.90
646 681 1.844003 GTGCCATATACGACGCACG 59.156 57.895 0.00 1.21 41.86 5.34
704 739 9.935682 CACGCAAAATAGACTAAAATCATGTAT 57.064 29.630 0.00 0.00 0.00 2.29
737 772 9.757227 TCAATTTTAATTTTAGTCACCAACCTG 57.243 29.630 0.00 0.00 0.00 4.00
791 826 4.099419 ACATATGATCACGTCAGTAAGCCA 59.901 41.667 10.38 0.00 40.92 4.75
845 880 1.072965 CATATGTCAGAGGGGCCTTCC 59.927 57.143 12.67 0.00 0.00 3.46
943 978 3.255725 CACCAAAATGTCCATGTCATGC 58.744 45.455 7.35 0.00 0.00 4.06
1006 1041 4.382470 CCTCACACTTTCTCCTCCATACAG 60.382 50.000 0.00 0.00 0.00 2.74
1244 1279 2.202610 TGCGAGATCAAGCCGTCG 60.203 61.111 9.46 3.10 35.51 5.12
1364 1399 1.093972 CCATGGTGCTTTATGCGTGA 58.906 50.000 2.57 0.00 46.63 4.35
1400 1435 2.072298 GCGCTCTGATTCAGTTGAAGT 58.928 47.619 13.23 0.00 37.48 3.01
1411 1446 8.149973 TGATTCAGTTGAAGTTACTGTAAACC 57.850 34.615 1.10 0.00 42.77 3.27
1434 1469 1.202076 GCGTGCTCTAATTTGCAGGTC 60.202 52.381 16.11 9.04 44.02 3.85
1741 1777 2.158534 ACTGTATGTTTTGGAGTGCCCA 60.159 45.455 0.00 0.00 44.93 5.36
1938 1975 4.078516 GGACACGTAGCGGGCCTT 62.079 66.667 0.84 0.00 31.12 4.35
2022 2059 2.892914 CGCCACAACGGACACACA 60.893 61.111 0.00 0.00 36.56 3.72
2185 2237 2.358267 GCTACACTCCAGCACGTACTAT 59.642 50.000 0.00 0.00 38.93 2.12
2595 2667 1.000394 GCGCCGGCCCAATAAATTAAT 60.000 47.619 23.46 0.00 0.00 1.40
2701 2781 7.867921 ACTCTTTGGACCATGTATATTTACCA 58.132 34.615 0.00 0.00 0.00 3.25
2753 2833 2.976903 GAGATCCATGGCAGCGGC 60.977 66.667 6.96 0.00 40.13 6.53
2771 2851 0.109412 GCCGCGTAGTGTGAAGTACT 60.109 55.000 4.92 0.00 35.45 2.73
2786 2866 0.169672 GTACTTGTGGCTGCATGCAG 59.830 55.000 37.81 37.81 45.15 4.41
2863 2952 4.448732 TGCATGATATTGTGTGATAGACGC 59.551 41.667 0.00 0.00 35.45 5.19
2974 3067 2.109609 CACCGCATGCATGATGTAAC 57.890 50.000 30.64 10.15 34.14 2.50
3094 3187 4.373156 AAGTGTCAATGAAAGTAGGGCT 57.627 40.909 0.00 0.00 0.00 5.19
3146 3239 1.871039 TGCGACCAAAGTTAGCAAGTC 59.129 47.619 0.00 0.00 37.11 3.01
3151 3244 2.618709 ACCAAAGTTAGCAAGTCAGTGC 59.381 45.455 0.00 0.00 45.28 4.40
3169 3262 0.392461 GCGCAACCCTATCCTGAACA 60.392 55.000 0.30 0.00 0.00 3.18
3174 3267 2.947652 CAACCCTATCCTGAACATGCTG 59.052 50.000 0.00 0.00 0.00 4.41
3273 3987 5.358160 GCCAGTGTAGAATCAAATAAAGCCT 59.642 40.000 0.00 0.00 0.00 4.58
3360 4074 1.227350 CTCCGATTCCAGCGCATCA 60.227 57.895 11.47 0.00 0.00 3.07
3361 4075 0.602106 CTCCGATTCCAGCGCATCAT 60.602 55.000 11.47 0.00 0.00 2.45
3362 4076 0.179048 TCCGATTCCAGCGCATCATT 60.179 50.000 11.47 0.00 0.00 2.57
3363 4077 1.069978 TCCGATTCCAGCGCATCATTA 59.930 47.619 11.47 0.00 0.00 1.90
3364 4078 1.195448 CCGATTCCAGCGCATCATTAC 59.805 52.381 11.47 0.00 0.00 1.89
3365 4079 1.866601 CGATTCCAGCGCATCATTACA 59.133 47.619 11.47 0.00 0.00 2.41
3366 4080 2.287644 CGATTCCAGCGCATCATTACAA 59.712 45.455 11.47 0.00 0.00 2.41
3367 4081 3.058708 CGATTCCAGCGCATCATTACAAT 60.059 43.478 11.47 0.00 0.00 2.71
3368 4082 3.969117 TTCCAGCGCATCATTACAATC 57.031 42.857 11.47 0.00 0.00 2.67
3369 4083 2.916640 TCCAGCGCATCATTACAATCA 58.083 42.857 11.47 0.00 0.00 2.57
3370 4084 2.874086 TCCAGCGCATCATTACAATCAG 59.126 45.455 11.47 0.00 0.00 2.90
3371 4085 2.603892 CCAGCGCATCATTACAATCAGC 60.604 50.000 11.47 0.00 0.00 4.26
3372 4086 1.262417 AGCGCATCATTACAATCAGCG 59.738 47.619 11.47 0.00 45.68 5.18
3373 4087 1.666904 CGCATCATTACAATCAGCGC 58.333 50.000 0.00 0.00 37.20 5.92
3374 4088 1.003652 CGCATCATTACAATCAGCGCA 60.004 47.619 11.47 0.00 37.20 6.09
3375 4089 2.350102 CGCATCATTACAATCAGCGCAT 60.350 45.455 11.47 0.00 37.20 4.73
3376 4090 3.231965 GCATCATTACAATCAGCGCATC 58.768 45.455 11.47 0.00 0.00 3.91
3508 4222 2.582052 TGAAAGAGCCACCAATTCGTT 58.418 42.857 0.00 0.00 0.00 3.85
3602 4316 3.903090 TCTTCCCCTTGTTAACCTCGTTA 59.097 43.478 2.48 0.00 0.00 3.18
3603 4317 4.347583 TCTTCCCCTTGTTAACCTCGTTAA 59.652 41.667 2.48 0.00 35.92 2.01
3604 4318 4.914177 TCCCCTTGTTAACCTCGTTAAT 57.086 40.909 2.48 0.00 39.64 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.841957 AGCAAAGTCACACTCAAAAGATT 57.158 34.783 0.00 0.00 0.00 2.40
121 122 3.570550 ACACTCTTCAGAAGTACTCGCTT 59.429 43.478 10.09 0.00 0.00 4.68
124 125 4.149046 GCAAACACTCTTCAGAAGTACTCG 59.851 45.833 10.09 0.00 0.00 4.18
139 140 2.269940 ACCATCTAGGAGGCAAACACT 58.730 47.619 1.79 0.00 41.22 3.55
199 200 5.390991 CGAGGCTTTACAAACTCTTGATTCC 60.391 44.000 0.00 0.00 36.33 3.01
232 233 9.311916 CCTCACTATGAGTAGATTTTTGAGAAG 57.688 37.037 5.18 0.00 42.80 2.85
325 326 8.806146 AGAACAGCCACTAAATTGTATTCAAAT 58.194 29.630 0.00 0.00 37.11 2.32
326 327 8.177119 AGAACAGCCACTAAATTGTATTCAAA 57.823 30.769 0.00 0.00 37.11 2.69
329 330 8.718102 TCTAGAACAGCCACTAAATTGTATTC 57.282 34.615 0.00 0.00 0.00 1.75
330 331 9.515226 TTTCTAGAACAGCCACTAAATTGTATT 57.485 29.630 4.18 0.00 0.00 1.89
334 335 7.040409 ACCTTTTCTAGAACAGCCACTAAATTG 60.040 37.037 12.37 0.00 0.00 2.32
335 336 7.004691 ACCTTTTCTAGAACAGCCACTAAATT 58.995 34.615 12.37 0.00 0.00 1.82
336 337 6.543735 ACCTTTTCTAGAACAGCCACTAAAT 58.456 36.000 12.37 0.00 0.00 1.40
342 347 4.640771 ATGACCTTTTCTAGAACAGCCA 57.359 40.909 12.37 11.98 0.00 4.75
379 384 2.888594 TCTTTCTGATTCCGGCGTTAG 58.111 47.619 6.01 0.00 0.00 2.34
474 509 5.702865 CTTTGATTATATGGGCGTGGAATG 58.297 41.667 0.00 0.00 0.00 2.67
539 574 3.638484 ACTAAAGTGAAAATTGGCGTGC 58.362 40.909 0.00 0.00 0.00 5.34
570 605 6.818233 TGTGGTGTACAACTAACAGATACAA 58.182 36.000 13.07 0.00 36.06 2.41
646 681 0.390735 ACGTGGGTGAGAAATACCGC 60.391 55.000 0.00 0.00 39.14 5.68
791 826 1.376466 GTCACTGACATGTGGGCCT 59.624 57.895 1.15 0.00 38.40 5.19
845 880 1.952193 TGTGTGTGATGTCAGTGTGG 58.048 50.000 0.00 0.00 0.00 4.17
852 887 6.128445 CCAAGTTAGAGATTGTGTGTGATGTC 60.128 42.308 0.00 0.00 0.00 3.06
943 978 1.538876 TGGAGGGAGGTGGTGGAAG 60.539 63.158 0.00 0.00 0.00 3.46
1006 1041 3.430218 GTCTGTGTTGTATGAGCAGTGTC 59.570 47.826 0.00 0.00 0.00 3.67
1259 1294 0.896019 CGGCTATCTGGATCGAGGGT 60.896 60.000 4.78 0.00 0.00 4.34
1364 1399 4.687948 CAGAGCGCATATGCAAGTACTAAT 59.312 41.667 26.52 5.96 42.21 1.73
1400 1435 0.950071 GCACGCCCGGTTTACAGTAA 60.950 55.000 0.00 0.00 0.00 2.24
1411 1446 1.062525 GCAAATTAGAGCACGCCCG 59.937 57.895 0.00 0.00 0.00 6.13
1434 1469 2.509336 GCGTCCGGGTCAGTCATG 60.509 66.667 0.00 0.00 0.00 3.07
1732 1767 0.984995 AAGGAAGTACTGGGCACTCC 59.015 55.000 0.00 0.00 0.00 3.85
1765 1802 5.888161 GGGATCAGAAAATACTGGACAATGT 59.112 40.000 0.00 0.00 38.31 2.71
1917 1954 3.687102 CCCGCTACGTGTCCACCA 61.687 66.667 0.00 0.00 0.00 4.17
2174 2226 2.823747 TCTTCACCACATAGTACGTGCT 59.176 45.455 11.87 11.87 32.85 4.40
2185 2237 7.611467 AGCAAACAAATAGATATCTTCACCACA 59.389 33.333 11.25 0.00 0.00 4.17
2247 2299 5.648960 TGCACGCATGGATCATCATTATTAT 59.351 36.000 0.00 0.00 0.00 1.28
2248 2300 5.002516 TGCACGCATGGATCATCATTATTA 58.997 37.500 0.00 0.00 0.00 0.98
2249 2301 3.822167 TGCACGCATGGATCATCATTATT 59.178 39.130 0.00 0.00 0.00 1.40
2595 2667 3.676291 TGACAACGACAAGATGGATGA 57.324 42.857 0.00 0.00 0.00 2.92
2701 2781 8.936864 CCAATAAATACAACGAAGAGAGAAAGT 58.063 33.333 0.00 0.00 0.00 2.66
2753 2833 1.983605 CAAGTACTTCACACTACGCGG 59.016 52.381 12.47 0.00 0.00 6.46
2771 2851 2.992689 CCCTGCATGCAGCCACAA 60.993 61.111 37.11 6.82 44.83 3.33
2847 2936 3.133901 ACATGGGCGTCTATCACACAATA 59.866 43.478 0.00 0.00 0.00 1.90
2924 3013 3.599285 TTACCGGGCTCAACCTGCG 62.599 63.158 6.32 0.00 44.44 5.18
2929 3018 0.390209 TACGCTTTACCGGGCTCAAC 60.390 55.000 6.32 0.00 0.00 3.18
2940 3029 1.072391 CGGTGCATGTGTACGCTTTA 58.928 50.000 8.10 0.00 0.00 1.85
2963 3056 5.368145 TCTTCATGTAGGGTTACATCATGC 58.632 41.667 0.00 0.00 45.19 4.06
2974 3067 6.749036 AGGGTTTAGTATCTTCATGTAGGG 57.251 41.667 0.00 0.00 0.00 3.53
3038 3131 7.526192 GCACACTGTAATCCTATCACTATGGAT 60.526 40.741 0.00 0.00 41.85 3.41
3094 3187 4.256110 CATGACTTGTTGGCTACATCAGA 58.744 43.478 1.93 0.00 36.44 3.27
3146 3239 1.091771 CAGGATAGGGTTGCGCACTG 61.092 60.000 11.12 7.92 30.42 3.66
3151 3244 1.942657 CATGTTCAGGATAGGGTTGCG 59.057 52.381 0.00 0.00 0.00 4.85
3169 3262 5.663456 AGTTTGTTCATGTCAAAACAGCAT 58.337 33.333 15.86 0.00 39.20 3.79
3174 3267 4.041723 CGGGAGTTTGTTCATGTCAAAAC 58.958 43.478 15.86 12.98 36.71 2.43
3273 3987 9.042450 TCAGACCTCCTAAGTCATTGTTTTATA 57.958 33.333 0.00 0.00 36.68 0.98
3277 3991 5.513267 GGTCAGACCTCCTAAGTCATTGTTT 60.513 44.000 12.94 0.00 36.68 2.83
3360 4074 6.375945 TTGTAATGATGCGCTGATTGTAAT 57.624 33.333 9.73 0.00 0.00 1.89
3361 4075 5.809719 TTGTAATGATGCGCTGATTGTAA 57.190 34.783 9.73 1.91 0.00 2.41
3362 4076 5.526846 TCATTGTAATGATGCGCTGATTGTA 59.473 36.000 9.73 0.00 40.32 2.41
3363 4077 4.336153 TCATTGTAATGATGCGCTGATTGT 59.664 37.500 9.73 0.00 40.32 2.71
3364 4078 4.851010 TCATTGTAATGATGCGCTGATTG 58.149 39.130 9.73 0.00 40.32 2.67
3365 4079 5.503662 TTCATTGTAATGATGCGCTGATT 57.496 34.783 9.73 6.65 44.27 2.57
3366 4080 5.503662 TTTCATTGTAATGATGCGCTGAT 57.496 34.783 9.73 0.00 44.27 2.90
3367 4081 4.961435 TTTCATTGTAATGATGCGCTGA 57.039 36.364 9.73 0.00 44.27 4.26
3368 4082 5.005012 CCTTTTTCATTGTAATGATGCGCTG 59.995 40.000 9.73 0.00 44.27 5.18
3369 4083 5.104374 CCTTTTTCATTGTAATGATGCGCT 58.896 37.500 9.73 0.00 44.27 5.92
3370 4084 4.864247 ACCTTTTTCATTGTAATGATGCGC 59.136 37.500 0.00 0.00 44.27 6.09
3371 4085 5.863397 ACACCTTTTTCATTGTAATGATGCG 59.137 36.000 8.02 0.00 44.27 4.73
3372 4086 6.033831 CGACACCTTTTTCATTGTAATGATGC 59.966 38.462 8.02 0.42 44.27 3.91
3373 4087 7.271223 GTCGACACCTTTTTCATTGTAATGATG 59.729 37.037 11.55 5.40 44.27 3.07
3374 4088 7.305474 GTCGACACCTTTTTCATTGTAATGAT 58.695 34.615 11.55 0.00 44.27 2.45
3375 4089 6.565060 CGTCGACACCTTTTTCATTGTAATGA 60.565 38.462 17.16 3.28 43.28 2.57
3376 4090 5.563751 CGTCGACACCTTTTTCATTGTAATG 59.436 40.000 17.16 0.00 37.75 1.90
3455 4169 2.596338 TCTGAGGCCGACGACACA 60.596 61.111 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.