Multiple sequence alignment - TraesCS7A01G402700

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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 TraesCS7A01G402700 chr7A 100.000 2752 0 0 1 2752 582406490 582409241 0.000000e+00 5083.0
1 TraesCS7A01G402700 chr7A 79.859 1132 177 30 1008 2109 582406969 582405859 0.000000e+00 780.0
2 TraesCS7A01G402700 chr7A 100.000 38 0 0 3064 3101 582409553 582409590 1.540000e-08 71.3
3 TraesCS7A01G402700 chr7D 95.879 2621 89 7 49 2652 511187610 511190228 0.000000e+00 4224.0
4 TraesCS7A01G402700 chr7D 83.092 692 108 6 1424 2110 511168669 511167982 3.400000e-174 621.0
5 TraesCS7A01G402700 chr7D 94.915 59 1 1 1 59 511168613 511168669 1.180000e-14 91.6
6 TraesCS7A01G402700 chr7B 94.713 2175 77 9 1 2141 539989242 539991412 0.000000e+00 3345.0
7 TraesCS7A01G402700 chr7B 91.143 621 38 8 2134 2752 539995883 539996488 0.000000e+00 826.0
8 TraesCS7A01G402700 chr7B 79.102 646 94 19 1010 1627 539989724 539989092 1.040000e-109 407.0
9 TraesCS7A01G402700 chr5A 89.967 1505 101 27 816 2281 658800349 658798856 0.000000e+00 1897.0
10 TraesCS7A01G402700 chr5A 86.224 392 35 11 102 483 658801049 658800667 1.040000e-109 407.0
11 TraesCS7A01G402700 chr4B 81.638 1111 185 13 1010 2109 673224135 673225237 0.000000e+00 904.0
12 TraesCS7A01G402700 chr4B 87.568 555 36 14 1 542 673224608 673224074 2.040000e-171 612.0
13 TraesCS7A01G402700 chr6B 77.402 1124 218 26 1010 2103 127919387 127918270 1.210000e-178 636.0
14 TraesCS7A01G402700 chr6B 77.402 1124 218 26 1010 2103 129157609 129156492 1.210000e-178 636.0
15 TraesCS7A01G402700 chr3D 85.714 56 8 0 1841 1896 604229069 604229014 3.340000e-05 60.2
16 TraesCS7A01G402700 chrUn 72.195 205 51 5 1841 2042 108923966 108923765 1.200000e-04 58.4
17 TraesCS7A01G402700 chr6D 97.059 34 1 0 3064 3097 127328315 127328348 1.200000e-04 58.4
18 TraesCS7A01G402700 chr1B 100.000 29 0 0 3069 3097 412011163 412011135 2.000000e-03 54.7


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 TraesCS7A01G402700 chr7A 582406490 582409590 3100 False 2577.15 5083 100.0000 1 3101 2 chr7A.!!$F1 3100
1 TraesCS7A01G402700 chr7A 582405859 582406969 1110 True 780.00 780 79.8590 1008 2109 1 chr7A.!!$R1 1101
2 TraesCS7A01G402700 chr7D 511187610 511190228 2618 False 4224.00 4224 95.8790 49 2652 1 chr7D.!!$F2 2603
3 TraesCS7A01G402700 chr7D 511167982 511168669 687 True 621.00 621 83.0920 1424 2110 1 chr7D.!!$R1 686
4 TraesCS7A01G402700 chr7B 539989242 539991412 2170 False 3345.00 3345 94.7130 1 2141 1 chr7B.!!$F1 2140
5 TraesCS7A01G402700 chr7B 539995883 539996488 605 False 826.00 826 91.1430 2134 2752 1 chr7B.!!$F2 618
6 TraesCS7A01G402700 chr7B 539989092 539989724 632 True 407.00 407 79.1020 1010 1627 1 chr7B.!!$R1 617
7 TraesCS7A01G402700 chr5A 658798856 658801049 2193 True 1152.00 1897 88.0955 102 2281 2 chr5A.!!$R1 2179
8 TraesCS7A01G402700 chr4B 673224135 673225237 1102 False 904.00 904 81.6380 1010 2109 1 chr4B.!!$F1 1099
9 TraesCS7A01G402700 chr4B 673224074 673224608 534 True 612.00 612 87.5680 1 542 1 chr4B.!!$R1 541
10 TraesCS7A01G402700 chr6B 127918270 127919387 1117 True 636.00 636 77.4020 1010 2103 1 chr6B.!!$R1 1093
11 TraesCS7A01G402700 chr6B 129156492 129157609 1117 True 636.00 636 77.4020 1010 2103 1 chr6B.!!$R2 1093

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
910 1075 0.611618 TGCCCGATGTTTCATGGCTT 60.612 50.0 10.76 0.0 39.2 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 2774 0.233848 GTTCGGTGCAAGTGTAACGG 59.766 55.0 6.99 0.0 45.86 4.44 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
24 25 2.642254 CCACACATGCCCTTGCCTG 61.642 63.158 0.00 0.00 38.85 4.85
45 46 2.620585 GGCTTTAGCAAGATGATGGGAC 59.379 50.000 3.88 0.00 44.36 4.46
71 72 2.679930 GCGGTTGTTGGTCCTTATAGCT 60.680 50.000 0.00 0.00 0.00 3.32
130 131 6.364701 TGTGGATCCTAAATGATTCGGAAAT 58.635 36.000 14.23 0.00 34.40 2.17
144 145 2.026729 TCGGAAATACTGCCAATGACCA 60.027 45.455 0.00 0.00 0.00 4.02
195 196 6.065976 TCCTTGAGAAAGGATTAAGCATCA 57.934 37.500 3.04 0.00 43.68 3.07
393 427 1.910772 AGGAACGGCAGACTGCTCT 60.911 57.895 25.92 11.31 44.28 4.09
426 476 2.041265 AATCGGGTCAGGGAGGCT 59.959 61.111 0.00 0.00 0.00 4.58
432 482 3.474570 GTCAGGGAGGCTGGCGAT 61.475 66.667 0.00 0.00 0.00 4.58
433 483 3.473647 TCAGGGAGGCTGGCGATG 61.474 66.667 0.00 0.00 0.00 3.84
434 484 3.473647 CAGGGAGGCTGGCGATGA 61.474 66.667 0.00 0.00 0.00 2.92
435 485 2.688666 AGGGAGGCTGGCGATGAA 60.689 61.111 0.00 0.00 0.00 2.57
436 486 2.203126 GGGAGGCTGGCGATGAAG 60.203 66.667 0.00 0.00 0.00 3.02
437 487 2.899339 GGAGGCTGGCGATGAAGC 60.899 66.667 0.00 0.00 38.76 3.86
893 1058 6.537453 ACTCCATCCATAGTCTGTATATGC 57.463 41.667 0.00 0.00 30.68 3.14
908 1073 1.317613 TATGCCCGATGTTTCATGGC 58.682 50.000 0.00 0.00 39.02 4.40
910 1075 0.611618 TGCCCGATGTTTCATGGCTT 60.612 50.000 10.76 0.00 39.20 4.35
937 1103 5.067153 CGCTTTAATTTGTGATCCATGGGTA 59.933 40.000 13.02 0.00 0.00 3.69
1115 1314 2.604686 TTCCTGGCGCTCTGTCCT 60.605 61.111 7.64 0.00 0.00 3.85
1159 1371 1.993653 CTGCTCCCAACAGGATCCA 59.006 57.895 15.82 0.00 46.33 3.41
1524 1777 1.548985 CATCATCGACGTCGCGTTC 59.451 57.895 32.19 0.05 41.37 3.95
1596 1849 0.800012 GCGTCGCCTTTGATACCAAA 59.200 50.000 5.75 0.00 39.74 3.28
1714 1971 5.599715 GCGACTACATAATTAATGACGCTG 58.400 41.667 0.00 1.17 40.33 5.18
1737 1994 4.893601 TTGGCACGCGACCACGAA 62.894 61.111 22.04 8.14 42.66 3.85
1984 2252 5.263968 GGGTGACGAGATTGAAGAAGATA 57.736 43.478 0.00 0.00 0.00 1.98
2043 2311 2.769095 GAGATCCAAGACTACAAGCCCT 59.231 50.000 0.00 0.00 0.00 5.19
2170 2441 8.432805 TGAAGGGAAAAGATAGATCATAGTTCC 58.567 37.037 0.00 0.19 33.92 3.62
2309 2581 3.930848 GTGTGTACATTTTCCCCTAGTCG 59.069 47.826 0.00 0.00 0.00 4.18
2372 2644 5.117592 CGACTTTTGCATTGCTTTTTAGAGG 59.882 40.000 10.49 0.00 0.00 3.69
2384 2656 4.800582 GCTTTTTAGAGGCAAGGCAAACAT 60.801 41.667 0.00 0.00 0.00 2.71
2490 2762 5.991328 TGTCACAACTCTCAGAAAATCAC 57.009 39.130 0.00 0.00 0.00 3.06
2502 2774 7.703328 TCTCAGAAAATCACCACTTTACAAAC 58.297 34.615 0.00 0.00 0.00 2.93
2534 2806 4.617875 CGAACCGGAGATTTGCCT 57.382 55.556 9.46 0.00 0.00 4.75
2601 2873 3.525609 TCACTAATTGGCCAGACCCATTA 59.474 43.478 5.11 6.08 35.46 1.90
2707 2980 0.725133 TCTCTTTCCCCCTCCCTCAT 59.275 55.000 0.00 0.00 0.00 2.90
2711 2984 0.327576 TTTCCCCCTCCCTCATCTCC 60.328 60.000 0.00 0.00 0.00 3.71
3087 3360 6.892658 TTAACCATTGTTGATGCTACTTGT 57.107 33.333 0.00 0.00 35.87 3.16
3088 3361 4.771590 ACCATTGTTGATGCTACTTGTG 57.228 40.909 0.00 0.00 34.25 3.33
3089 3362 3.057315 ACCATTGTTGATGCTACTTGTGC 60.057 43.478 0.00 0.00 34.25 4.57
3090 3363 3.192001 CCATTGTTGATGCTACTTGTGCT 59.808 43.478 0.00 0.00 34.25 4.40
3091 3364 4.321452 CCATTGTTGATGCTACTTGTGCTT 60.321 41.667 0.00 0.00 34.25 3.91
3092 3365 4.488126 TTGTTGATGCTACTTGTGCTTC 57.512 40.909 0.00 0.00 35.85 3.86
3093 3366 3.475575 TGTTGATGCTACTTGTGCTTCA 58.524 40.909 0.00 0.00 40.95 3.02
3094 3367 3.882288 TGTTGATGCTACTTGTGCTTCAA 59.118 39.130 11.24 11.24 45.62 2.69
3096 3369 4.754372 TGATGCTACTTGTGCTTCAAAG 57.246 40.909 0.00 0.00 40.15 2.77
3097 3370 4.136796 TGATGCTACTTGTGCTTCAAAGT 58.863 39.130 0.00 0.00 40.15 2.66
3098 3371 4.214119 TGATGCTACTTGTGCTTCAAAGTC 59.786 41.667 0.00 0.00 40.15 3.01
3099 3372 3.540617 TGCTACTTGTGCTTCAAAGTCA 58.459 40.909 0.00 0.00 35.48 3.41
3100 3373 3.944650 TGCTACTTGTGCTTCAAAGTCAA 59.055 39.130 0.00 0.00 35.48 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.967397 CAGGCAAGGGCATGTGTG 59.033 61.111 0.00 0.00 46.20 3.82
24 25 2.620585 GTCCCATCATCTTGCTAAAGCC 59.379 50.000 0.00 0.00 41.18 4.35
45 46 1.209127 GGACCAACAACCGCAATCG 59.791 57.895 0.00 0.00 0.00 3.34
88 89 1.074405 ACAAGGTGGTCATGCACTCAT 59.926 47.619 0.00 0.00 0.00 2.90
130 131 1.552792 TCGACATGGTCATTGGCAGTA 59.447 47.619 0.00 0.00 32.09 2.74
193 194 1.414919 GGAACCGGCATACCTACATGA 59.585 52.381 0.00 0.00 0.00 3.07
195 196 0.391597 CGGAACCGGCATACCTACAT 59.608 55.000 0.00 0.00 35.56 2.29
393 427 2.190161 CGATTCACCACGCTCGATTTA 58.810 47.619 0.00 0.00 33.07 1.40
429 479 2.595977 CGTATCATCATCGGCTTCATCG 59.404 50.000 0.00 0.00 0.00 3.84
430 480 3.579709 ACGTATCATCATCGGCTTCATC 58.420 45.455 0.00 0.00 0.00 2.92
431 481 3.667497 ACGTATCATCATCGGCTTCAT 57.333 42.857 0.00 0.00 0.00 2.57
432 482 3.818773 TCTACGTATCATCATCGGCTTCA 59.181 43.478 0.00 0.00 0.00 3.02
433 483 4.421033 TCTACGTATCATCATCGGCTTC 57.579 45.455 0.00 0.00 0.00 3.86
434 484 4.799678 CTTCTACGTATCATCATCGGCTT 58.200 43.478 0.00 0.00 0.00 4.35
435 485 3.366476 GCTTCTACGTATCATCATCGGCT 60.366 47.826 0.00 0.00 0.00 5.52
436 486 2.917971 GCTTCTACGTATCATCATCGGC 59.082 50.000 0.00 0.00 0.00 5.54
437 487 4.155099 AGAGCTTCTACGTATCATCATCGG 59.845 45.833 0.00 0.00 0.00 4.18
893 1058 2.223249 CGTAAAGCCATGAAACATCGGG 60.223 50.000 0.00 0.00 0.00 5.14
908 1073 7.220683 CCATGGATCACAAATTAAAGCGTAAAG 59.779 37.037 5.56 0.00 0.00 1.85
910 1075 6.405286 CCCATGGATCACAAATTAAAGCGTAA 60.405 38.462 15.22 0.00 0.00 3.18
1038 1220 1.739562 GAGGGCGGCGATGATGATC 60.740 63.158 12.98 0.00 0.00 2.92
1115 1314 2.126071 GTAGCTTGCGCGGAGACA 60.126 61.111 8.83 0.00 42.32 3.41
1159 1371 1.915141 CTGTCAAAGGGGAGCAACAT 58.085 50.000 0.00 0.00 0.00 2.71
1284 1511 4.890158 TGAGAAAGGATTAGTGAGCACA 57.110 40.909 3.19 0.00 0.00 4.57
1524 1777 3.265791 GGCATAGAGTGTGTCTTTGAGG 58.734 50.000 0.00 0.00 36.59 3.86
1596 1849 2.666098 GGTCACCGTGGGTATGCCT 61.666 63.158 0.00 0.00 32.11 4.75
1737 1994 5.163258 GGTCAGGATATCAACATGAGGTCTT 60.163 44.000 4.83 0.00 0.00 3.01
2043 2311 6.804770 TCGAAACCGAAATCTTTATTTGGA 57.195 33.333 0.00 0.00 35.41 3.53
2255 2527 9.899226 TGTAGATAGATAGATCAAAACACATCG 57.101 33.333 0.00 0.00 0.00 3.84
2309 2581 3.078594 ACATTGCGTGTTTGGACTTTC 57.921 42.857 0.00 0.00 38.01 2.62
2372 2644 5.929992 TCCGTACTATATATGTTTGCCTTGC 59.070 40.000 0.00 0.00 0.00 4.01
2417 2689 3.080300 ACAACAAAGGAGACCAACACA 57.920 42.857 0.00 0.00 0.00 3.72
2467 2739 5.471456 GGTGATTTTCTGAGAGTTGTGACAT 59.529 40.000 0.00 0.00 0.00 3.06
2490 2762 5.267776 CAAGTGTAACGGTTTGTAAAGTGG 58.732 41.667 0.00 0.00 45.86 4.00
2502 2774 0.233848 GTTCGGTGCAAGTGTAACGG 59.766 55.000 6.99 0.00 45.86 4.44
2534 2806 1.713937 CGTCAGTGTGCTTTGCCACA 61.714 55.000 11.50 0.00 42.99 4.17
2568 2840 5.479724 TGGCCAATTAGTGACATCATCAAAA 59.520 36.000 0.61 0.00 39.72 2.44
2577 2849 1.004277 GGGTCTGGCCAATTAGTGACA 59.996 52.381 18.94 0.00 39.65 3.58
2601 2873 3.241530 TGCCAACTCAGCCCGACT 61.242 61.111 0.00 0.00 0.00 4.18
2707 2980 2.690881 CGGGTGGGAATGGGGAGA 60.691 66.667 0.00 0.00 0.00 3.71
2729 3002 1.217511 AGCAGCGAGATCACTGGTG 59.782 57.895 12.51 9.61 42.67 4.17
3063 3336 7.315142 CACAAGTAGCATCAACAATGGTTAAT 58.685 34.615 0.00 0.00 43.52 1.40
3064 3337 6.676950 CACAAGTAGCATCAACAATGGTTAA 58.323 36.000 0.00 0.00 43.52 2.01
3065 3338 5.335583 GCACAAGTAGCATCAACAATGGTTA 60.336 40.000 0.00 0.00 43.52 2.85
3066 3339 4.559300 GCACAAGTAGCATCAACAATGGTT 60.559 41.667 0.00 0.00 43.52 3.67
3068 3341 3.192001 AGCACAAGTAGCATCAACAATGG 59.808 43.478 0.00 0.00 35.77 3.16
3069 3342 4.430137 AGCACAAGTAGCATCAACAATG 57.570 40.909 0.00 0.00 38.50 2.82
3070 3343 4.520111 TGAAGCACAAGTAGCATCAACAAT 59.480 37.500 0.00 0.00 36.85 2.71
3071 3344 3.882288 TGAAGCACAAGTAGCATCAACAA 59.118 39.130 0.00 0.00 36.85 2.83
3072 3345 3.475575 TGAAGCACAAGTAGCATCAACA 58.524 40.909 0.00 0.00 36.85 3.33
3073 3346 4.488126 TTGAAGCACAAGTAGCATCAAC 57.512 40.909 2.22 0.00 42.54 3.18
3074 3347 4.580167 ACTTTGAAGCACAAGTAGCATCAA 59.420 37.500 2.22 2.22 44.75 2.57
3075 3348 4.136796 ACTTTGAAGCACAAGTAGCATCA 58.863 39.130 0.00 0.00 39.77 3.07
3076 3349 4.214119 TGACTTTGAAGCACAAGTAGCATC 59.786 41.667 0.00 0.00 39.77 3.91
3077 3350 4.136796 TGACTTTGAAGCACAAGTAGCAT 58.863 39.130 0.00 0.00 39.77 3.79
3078 3351 3.540617 TGACTTTGAAGCACAAGTAGCA 58.459 40.909 0.00 0.00 39.77 3.49
3079 3352 4.552166 TTGACTTTGAAGCACAAGTAGC 57.448 40.909 0.00 0.00 39.77 3.58


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

AutoCloner maintained by Alex Coulton.