Multiple sequence alignment - TraesCS7D01G049800

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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 TraesCS7D01G049800 chr7D 100.000 3896 0 0 1 3896 25399161 25403056 0.000000e+00 7195
1 TraesCS7D01G049800 chr4A 93.402 3410 166 33 1 3375 709893611 709896996 0.000000e+00 4996
2 TraesCS7D01G049800 chr4A 89.009 555 23 18 3372 3894 709897042 709897590 0.000000e+00 652
3 TraesCS7D01G049800 chr7A 93.206 3415 151 37 1 3383 26415637 26419002 0.000000e+00 4946
4 TraesCS7D01G049800 chr7A 86.393 463 28 15 3372 3801 26419055 26419515 1.270000e-129 473
5 TraesCS7D01G049800 chr7A 88.430 121 7 2 3783 3896 26419679 26419799 5.250000e-29 139


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 TraesCS7D01G049800 chr7D 25399161 25403056 3895 False 7195.000000 7195 100.0000 1 3896 1 chr7D.!!$F1 3895
1 TraesCS7D01G049800 chr4A 709893611 709897590 3979 False 2824.000000 4996 91.2055 1 3894 2 chr4A.!!$F1 3893
2 TraesCS7D01G049800 chr7A 26415637 26419799 4162 False 1852.666667 4946 89.3430 1 3896 3 chr7A.!!$F1 3895

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
520 546 0.035343 GGAGGGAGCTAACCAACCAC 60.035 60.0 9.41 0.0 0.00 4.16 F
1564 1598 0.030773 CATCCGACACCGATGACGAT 59.969 55.0 2.38 0.0 45.16 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1759 0.099968 TCCGGATCAACATCGTCGTC 59.900 55.0 0.0 0.0 0.0 4.20 R
3414 3531 0.539438 CAACCCTGCTTTGCCCAGTA 60.539 55.0 0.0 0.0 0.0 2.74 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
164 165 5.052693 TCATTGATGGGAAATACCAGGAG 57.947 43.478 0.00 0.00 45.20 3.69
181 182 4.588951 CCAGGAGTTCCTAGTGCATATGTA 59.411 45.833 4.29 0.00 46.65 2.29
182 183 5.509840 CCAGGAGTTCCTAGTGCATATGTAC 60.510 48.000 15.38 15.38 46.65 2.90
184 185 5.303078 AGGAGTTCCTAGTGCATATGTACAG 59.697 44.000 23.49 17.46 46.48 2.74
185 186 5.509840 GGAGTTCCTAGTGCATATGTACAGG 60.510 48.000 23.49 23.62 33.68 4.00
186 187 4.962995 AGTTCCTAGTGCATATGTACAGGT 59.037 41.667 26.07 12.90 33.89 4.00
300 312 2.271944 ACAGTTAGTTCAGTTGGGGC 57.728 50.000 0.00 0.00 0.00 5.80
399 423 8.181573 CCCGCGCATATATTTATAATTTGTTCT 58.818 33.333 8.75 0.00 0.00 3.01
416 440 9.863845 AATTTGTTCTTAAATTTGTATACCGGG 57.136 29.630 6.32 0.00 37.02 5.73
520 546 0.035343 GGAGGGAGCTAACCAACCAC 60.035 60.000 9.41 0.00 0.00 4.16
595 623 3.099141 AGCTGGGAGAAGAGAAGAGAAG 58.901 50.000 0.00 0.00 0.00 2.85
597 625 3.131046 GCTGGGAGAAGAGAAGAGAAGAG 59.869 52.174 0.00 0.00 0.00 2.85
753 782 3.631127 GCGCTTCGATTCCGCTCC 61.631 66.667 14.86 0.00 43.95 4.70
1113 1144 3.003378 TCGAGTATGTGATCGGTGATGTC 59.997 47.826 0.00 0.00 39.38 3.06
1159 1192 4.771590 TTAGCATCTGCACTTTTCAAGG 57.228 40.909 4.79 0.00 45.16 3.61
1168 1201 6.877236 TCTGCACTTTTCAAGGAAAATTCTT 58.123 32.000 4.76 0.00 40.14 2.52
1349 1382 2.534298 ACTTCAGATGAACAGATCGCG 58.466 47.619 0.00 0.00 0.00 5.87
1401 1434 3.237746 GAGATGGAGGATCTGGATGTGA 58.762 50.000 0.00 0.00 41.91 3.58
1416 1449 1.525077 GTGAACACGCCTCCCAACA 60.525 57.895 0.00 0.00 0.00 3.33
1564 1598 0.030773 CATCCGACACCGATGACGAT 59.969 55.000 2.38 0.00 45.16 3.73
1600 1634 5.686397 CGACGAAGAGGAGGTGATTTATTAC 59.314 44.000 0.00 0.00 0.00 1.89
1670 1704 6.146673 GCAGCTTGCATCAAACTAAAAATTCT 59.853 34.615 0.00 0.00 44.26 2.40
1674 1708 7.148689 GCTTGCATCAAACTAAAAATTCTGAGG 60.149 37.037 0.00 0.00 0.00 3.86
1722 1759 0.662077 TGATGACAACGACGACACCG 60.662 55.000 0.00 0.00 42.50 4.94
1867 1904 2.105328 GCCGCGGTTGGTTGTTTT 59.895 55.556 28.70 0.00 0.00 2.43
1876 1913 4.429108 CGGTTGGTTGTTTTGTCAGAAAT 58.571 39.130 0.00 0.00 0.00 2.17
1881 1918 7.095017 GGTTGGTTGTTTTGTCAGAAATTTTGA 60.095 33.333 0.00 0.00 0.00 2.69
1888 1925 7.548427 TGTTTTGTCAGAAATTTTGATTGCTGA 59.452 29.630 5.85 5.85 42.38 4.26
1889 1926 8.553696 GTTTTGTCAGAAATTTTGATTGCTGAT 58.446 29.630 11.80 0.00 45.22 2.90
1890 1927 8.665643 TTTGTCAGAAATTTTGATTGCTGATT 57.334 26.923 11.80 0.00 45.22 2.57
1953 1995 0.405585 AACTGGTGGAATCAGTGGGG 59.594 55.000 0.00 0.00 43.82 4.96
2074 2116 1.341531 AGTGAGTCCACAACCTTCTCG 59.658 52.381 0.00 0.00 45.54 4.04
2184 2226 6.840780 TGTCACTGATGAATCTCTCTGTTA 57.159 37.500 0.00 0.00 36.31 2.41
2185 2227 7.415592 TGTCACTGATGAATCTCTCTGTTAT 57.584 36.000 0.00 0.00 36.31 1.89
2488 2531 1.136305 GCATGTCATCAGCAGCCAATT 59.864 47.619 0.00 0.00 0.00 2.32
2496 2539 0.179171 CAGCAGCCAATTGAAGCTCG 60.179 55.000 7.12 4.73 37.18 5.03
2556 2599 5.045215 ACGTCGACTCATTCAGTACAAAAA 58.955 37.500 14.70 0.00 34.41 1.94
2603 2651 8.062065 ACTTAGTTGGATTTCACTGTCAAAAA 57.938 30.769 0.00 0.00 0.00 1.94
2683 2733 4.536765 AGTTGGATTTCACTGTCAAAGGT 58.463 39.130 0.00 0.00 0.00 3.50
2684 2734 5.690865 AGTTGGATTTCACTGTCAAAGGTA 58.309 37.500 0.00 0.00 0.00 3.08
2685 2735 6.126409 AGTTGGATTTCACTGTCAAAGGTAA 58.874 36.000 0.00 0.00 0.00 2.85
2686 2736 6.605594 AGTTGGATTTCACTGTCAAAGGTAAA 59.394 34.615 0.00 0.00 0.00 2.01
2691 2741 8.194769 GGATTTCACTGTCAAAGGTAAAGAAAA 58.805 33.333 0.00 0.00 0.00 2.29
2692 2742 9.237846 GATTTCACTGTCAAAGGTAAAGAAAAG 57.762 33.333 0.00 0.00 0.00 2.27
2697 2747 8.458843 CACTGTCAAAGGTAAAGAAAAGAAAGA 58.541 33.333 0.00 0.00 0.00 2.52
2921 2972 4.479619 GGCAACTCAAGTCAAACATGATC 58.520 43.478 0.00 0.00 0.00 2.92
2963 3014 9.102757 GAATGTTTCATCAGTCTAAGATAAGCA 57.897 33.333 0.00 0.00 31.06 3.91
2964 3015 8.659925 ATGTTTCATCAGTCTAAGATAAGCAG 57.340 34.615 0.00 0.00 0.00 4.24
2989 3040 3.004734 ACTGTTCCAGCAGCACAAATAAC 59.995 43.478 0.00 0.00 39.96 1.89
3044 3095 7.986085 ATAATATGGTGTTGAACTGCTATCC 57.014 36.000 0.00 0.00 0.00 2.59
3057 3108 2.409948 GCTATCCAAGCCAACTCACT 57.590 50.000 0.00 0.00 46.25 3.41
3063 3114 1.345741 CCAAGCCAACTCACTCTCTCA 59.654 52.381 0.00 0.00 0.00 3.27
3064 3115 2.612471 CCAAGCCAACTCACTCTCTCAG 60.612 54.545 0.00 0.00 0.00 3.35
3065 3116 1.265236 AGCCAACTCACTCTCTCAGG 58.735 55.000 0.00 0.00 0.00 3.86
3066 3117 0.972883 GCCAACTCACTCTCTCAGGT 59.027 55.000 0.00 0.00 0.00 4.00
3099 3153 9.950680 GGTTTCATAAATATACAATCACCACAG 57.049 33.333 0.00 0.00 0.00 3.66
3125 3179 4.433615 TCCAGACAGCGAAACAAGATATC 58.566 43.478 0.00 0.00 0.00 1.63
3211 3265 1.202770 AGTCAAACTTAGGTTGGCGCT 60.203 47.619 9.06 3.30 35.63 5.92
3357 3411 3.061295 CGATAACACAGTCTGTCACATGC 59.939 47.826 1.37 0.00 30.29 4.06
3375 3443 4.529377 ACATGCTCCATGAAAATCCAGTTT 59.471 37.500 11.78 0.00 43.81 2.66
3376 3444 4.524316 TGCTCCATGAAAATCCAGTTTG 57.476 40.909 0.00 0.00 0.00 2.93
3377 3445 4.151121 TGCTCCATGAAAATCCAGTTTGA 58.849 39.130 0.00 0.00 0.00 2.69
3379 3447 4.219288 GCTCCATGAAAATCCAGTTTGACT 59.781 41.667 0.00 0.00 0.00 3.41
3380 3448 5.279156 GCTCCATGAAAATCCAGTTTGACTT 60.279 40.000 0.00 0.00 0.00 3.01
3382 3450 5.010922 TCCATGAAAATCCAGTTTGACTTGG 59.989 40.000 0.00 0.00 35.74 3.61
3384 3452 3.703556 TGAAAATCCAGTTTGACTTGGCA 59.296 39.130 0.00 0.00 0.00 4.92
3385 3453 4.161189 TGAAAATCCAGTTTGACTTGGCAA 59.839 37.500 0.00 0.00 0.00 4.52
3386 3454 4.751767 AAATCCAGTTTGACTTGGCAAA 57.248 36.364 0.00 0.00 35.54 3.68
3520 3640 0.460987 GAGAGATGGGCCACTTGTCG 60.461 60.000 9.28 0.00 0.00 4.35
3538 3658 0.512952 CGGCGAGTGACTTTGAAAGG 59.487 55.000 10.02 0.00 0.00 3.11
3547 3670 3.498777 GTGACTTTGAAAGGAGGTGCTAC 59.501 47.826 10.02 0.00 0.00 3.58
3622 3745 4.512944 GTGTTCTGCATCTGAAGACTGAAA 59.487 41.667 7.08 0.00 34.52 2.69
3662 3804 9.382275 AGCAAATGGATGATAAACAAAATAACC 57.618 29.630 0.00 0.00 0.00 2.85
3727 3878 9.458727 AGGATCAGCAATATATGTAGAAAATGG 57.541 33.333 0.00 0.00 0.00 3.16
3801 3955 5.600696 CAGCCTTTCAACCAAGTGTTAATT 58.399 37.500 0.00 0.00 34.69 1.40
3802 3956 6.737346 GCAGCCTTTCAACCAAGTGTTAATTA 60.737 38.462 0.00 0.00 34.69 1.40
3803 3957 7.206687 CAGCCTTTCAACCAAGTGTTAATTAA 58.793 34.615 0.00 0.00 34.69 1.40
3804 3958 7.708752 CAGCCTTTCAACCAAGTGTTAATTAAA 59.291 33.333 0.00 0.00 34.69 1.52
3805 3959 7.709182 AGCCTTTCAACCAAGTGTTAATTAAAC 59.291 33.333 0.00 1.56 34.69 2.01
3877 4221 8.722480 TGAGAGGTTTCATCAAATATGTACTG 57.278 34.615 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 5.277857 ACCTGTACATATGCACTAGGAAC 57.722 43.478 21.69 4.37 0.00 3.62
213 214 6.275692 TCCTCCTTCCTTTCTTTTTACCTT 57.724 37.500 0.00 0.00 0.00 3.50
300 312 2.074576 CCTGTCTCTGTTCACTGCATG 58.925 52.381 0.00 0.00 0.00 4.06
399 423 3.212685 CCCGCCCGGTATACAAATTTAA 58.787 45.455 5.01 0.00 0.00 1.52
416 440 3.541713 CTGTAGAGGAGGCCCCGC 61.542 72.222 0.00 1.87 40.87 6.13
520 546 2.231235 GTGCTTTGTTAATGAGGGTGGG 59.769 50.000 0.00 0.00 0.00 4.61
595 623 2.168313 CCTTTCCTGCTCTTCTCCTCTC 59.832 54.545 0.00 0.00 0.00 3.20
597 625 1.209261 CCCTTTCCTGCTCTTCTCCTC 59.791 57.143 0.00 0.00 0.00 3.71
753 782 1.345176 GAAGATCGACAAAGGCGCG 59.655 57.895 0.00 0.00 0.00 6.86
783 812 7.304497 AGCAGTAATAATTTACGAGGAGGAT 57.696 36.000 0.00 0.00 42.14 3.24
784 813 6.726490 AGCAGTAATAATTTACGAGGAGGA 57.274 37.500 0.00 0.00 42.14 3.71
1065 1096 1.872234 ATCGTGGTTCGCATCGTCG 60.872 57.895 0.00 0.00 39.67 5.12
1113 1144 0.034896 AGCGTACCTGGTGTTGAAGG 59.965 55.000 10.23 0.00 39.65 3.46
1159 1192 7.041721 AGGTTTCAGTTGACCAAAGAATTTTC 58.958 34.615 0.00 0.00 35.03 2.29
1208 1241 4.044698 AGGCCCTCCTAAGAAAACAAATCT 59.955 41.667 0.00 0.00 42.06 2.40
1286 1319 1.112950 CTCTGCTGCTCTCTCCATGA 58.887 55.000 0.00 0.00 0.00 3.07
1292 1325 1.890625 CTGTGCCTCTGCTGCTCTCT 61.891 60.000 0.00 0.00 38.71 3.10
1349 1382 2.178235 GGCGTATTTGAGGTCGGCC 61.178 63.158 0.00 0.00 41.64 6.13
1401 1434 2.184167 CGTTGTTGGGAGGCGTGTT 61.184 57.895 0.00 0.00 0.00 3.32
1416 1449 1.758783 GTACCGTCTTGTTCGTCGTT 58.241 50.000 0.00 0.00 0.00 3.85
1564 1598 3.404141 TTCGTCGCCGCGATCATCA 62.404 57.895 20.03 0.00 40.76 3.07
1600 1634 4.328983 AGCAACTACAAATATCGGTTCGTG 59.671 41.667 0.00 0.00 0.00 4.35
1722 1759 0.099968 TCCGGATCAACATCGTCGTC 59.900 55.000 0.00 0.00 0.00 4.20
1867 1904 9.932207 AATAATCAGCAATCAAAATTTCTGACA 57.068 25.926 7.05 1.01 44.35 3.58
1876 1913 6.127366 GGGACTGGAATAATCAGCAATCAAAA 60.127 38.462 0.00 0.00 35.78 2.44
1881 1918 4.803329 AGGGACTGGAATAATCAGCAAT 57.197 40.909 0.00 0.00 37.18 3.56
1916 1953 2.919602 AGTTCCTGCCTTTCCTGGATTA 59.080 45.455 0.00 0.00 33.57 1.75
1953 1995 5.911752 TCAGATAAACCTCTGCTCTCATTC 58.088 41.667 0.00 0.00 42.00 2.67
2137 2179 7.449704 ACAAAGAGAGATTTACTGCCAAAAGAT 59.550 33.333 0.00 0.00 0.00 2.40
2184 2226 2.568062 TGCTGCATCCATTGGTTGAAAT 59.432 40.909 16.36 0.00 0.00 2.17
2185 2227 1.969208 TGCTGCATCCATTGGTTGAAA 59.031 42.857 16.36 4.23 0.00 2.69
2297 2339 1.425066 ACCCTGTTGATCTTGAGCCAA 59.575 47.619 0.00 0.00 0.00 4.52
2496 2539 3.712881 GACGTGTCACCGCCTTGC 61.713 66.667 0.00 0.00 0.00 4.01
2532 2575 3.197434 TGTACTGAATGAGTCGACGTG 57.803 47.619 10.46 0.00 35.96 4.49
2572 2620 6.595716 ACAGTGAAATCCAACTAAGTATCTGC 59.404 38.462 0.00 0.00 0.00 4.26
2707 2757 9.665264 GGACAGTGAACTTAAACTAAAAATCTG 57.335 33.333 0.00 0.00 0.00 2.90
2804 2854 4.993705 AGGACAGGAAAAGGTTGATGTA 57.006 40.909 0.00 0.00 0.00 2.29
2805 2855 3.884037 AGGACAGGAAAAGGTTGATGT 57.116 42.857 0.00 0.00 0.00 3.06
2813 2863 5.163519 ACAAACATGACAAGGACAGGAAAAG 60.164 40.000 0.00 0.00 0.00 2.27
2989 3040 3.119743 CCTACAATGACATGCTGTGGTTG 60.120 47.826 3.47 2.49 31.55 3.77
3023 3074 5.372343 TGGATAGCAGTTCAACACCATAT 57.628 39.130 0.00 0.00 0.00 1.78
3026 3077 3.411446 CTTGGATAGCAGTTCAACACCA 58.589 45.455 0.00 0.00 0.00 4.17
3044 3095 2.612471 CCTGAGAGAGTGAGTTGGCTTG 60.612 54.545 0.00 0.00 0.00 4.01
3057 3108 2.599408 AACCTTCGGTACCTGAGAGA 57.401 50.000 10.90 0.00 33.12 3.10
3063 3114 8.707449 TGTATATTTATGAAACCTTCGGTACCT 58.293 33.333 10.90 0.00 33.12 3.08
3064 3115 8.891671 TGTATATTTATGAAACCTTCGGTACC 57.108 34.615 0.16 0.16 33.12 3.34
3081 3135 6.945435 TGGAACACTGTGGTGATTGTATATTT 59.055 34.615 13.09 0.00 45.61 1.40
3082 3136 6.480763 TGGAACACTGTGGTGATTGTATATT 58.519 36.000 13.09 0.00 45.61 1.28
3089 3143 2.172505 TGTCTGGAACACTGTGGTGATT 59.827 45.455 13.09 0.00 45.61 2.57
3097 3151 1.261619 GTTTCGCTGTCTGGAACACTG 59.738 52.381 0.00 0.00 33.24 3.66
3099 3153 1.295792 TGTTTCGCTGTCTGGAACAC 58.704 50.000 0.00 0.00 33.24 3.32
3357 3411 5.972107 AGTCAAACTGGATTTTCATGGAG 57.028 39.130 0.00 0.00 0.00 3.86
3375 3443 7.158021 CCTTTGGTTAATATTTTGCCAAGTCA 58.842 34.615 13.83 4.40 39.89 3.41
3376 3444 7.158697 ACCTTTGGTTAATATTTTGCCAAGTC 58.841 34.615 13.83 0.00 39.89 3.01
3377 3445 7.073457 ACCTTTGGTTAATATTTTGCCAAGT 57.927 32.000 13.83 9.44 39.89 3.16
3414 3531 0.539438 CAACCCTGCTTTGCCCAGTA 60.539 55.000 0.00 0.00 0.00 2.74
3466 3584 4.095782 CCGTCTTTCTTTTTCTGTGGTTCA 59.904 41.667 0.00 0.00 0.00 3.18
3481 3600 1.668419 CATGATCCCCACCGTCTTTC 58.332 55.000 0.00 0.00 0.00 2.62
3520 3640 1.801178 CTCCTTTCAAAGTCACTCGCC 59.199 52.381 0.00 0.00 0.00 5.54
3523 3643 2.550180 GCACCTCCTTTCAAAGTCACTC 59.450 50.000 0.00 0.00 0.00 3.51
3547 3670 1.236616 TGCAGTCCTCATGTTTGCCG 61.237 55.000 0.00 0.00 33.98 5.69
3727 3878 0.524862 CAGTGTGCTTGGATTCCTGC 59.475 55.000 3.95 9.00 0.00 4.85
3813 4153 3.825908 TGGAAGGAGCAATTACCCTTT 57.174 42.857 0.00 0.00 40.14 3.11
3815 4155 4.665009 TCATATGGAAGGAGCAATTACCCT 59.335 41.667 2.13 0.00 0.00 4.34
3831 4171 9.731819 CTCTCATCTCATTTGTTTTTCATATGG 57.268 33.333 2.13 0.00 36.57 2.74
3832 4172 9.731819 CCTCTCATCTCATTTGTTTTTCATATG 57.268 33.333 0.00 0.00 37.02 1.78


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

AutoCloner maintained by Alex Coulton.