Multiple sequence alignment - TraesCS7B01G192900

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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 TraesCS7B01G192900 chr7B 100.000 2450 0 0 1 2450 331659076 331656627 0.000000e+00 4525.0
1 TraesCS7B01G192900 chr7D 91.901 2457 186 9 1 2450 187916394 187913944 0.000000e+00 3422.0
2 TraesCS7B01G192900 chr7A 89.461 2467 222 19 17 2450 196141843 196144304 0.000000e+00 3081.0
3 TraesCS7B01G192900 chr3B 100.000 36 0 0 2144 2179 275390738 275390773 1.570000e-07 67.6
4 TraesCS7B01G192900 chr6B 97.222 36 1 0 2144 2179 502479114 502479079 7.320000e-06 62.1
5 TraesCS7B01G192900 chr4B 97.222 36 1 0 2144 2179 226965937 226965972 7.320000e-06 62.1
6 TraesCS7B01G192900 chr4B 91.489 47 1 3 2144 2187 659673759 659673805 7.320000e-06 62.1
7 TraesCS7B01G192900 chr3D 97.222 36 1 0 2144 2179 244986614 244986579 7.320000e-06 62.1
8 TraesCS7B01G192900 chr3D 97.222 36 1 0 2144 2179 332875137 332875102 7.320000e-06 62.1
9 TraesCS7B01G192900 chr2B 93.023 43 1 2 2144 2184 637855954 637855912 7.320000e-06 62.1


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 TraesCS7B01G192900 chr7B 331656627 331659076 2449 True 4525 4525 100.000 1 2450 1 chr7B.!!$R1 2449
1 TraesCS7B01G192900 chr7D 187913944 187916394 2450 True 3422 3422 91.901 1 2450 1 chr7D.!!$R1 2449
2 TraesCS7B01G192900 chr7A 196141843 196144304 2461 False 3081 3081 89.461 17 2450 1 chr7A.!!$F1 2433

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
27 28 0.035458 CCCATTATCGACCTCCCAGC 59.965 60.0 0.0 0.0 0.00 4.85 F
89 90 0.396556 TGCATCACCCCGAGTAGCTA 60.397 55.0 0.0 0.0 0.00 3.32 F
926 954 0.463654 GCATCCACTTGGCCGATACA 60.464 55.0 0.0 0.0 34.44 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1128 0.951040 CACCACGAGCTTGGAGGTTC 60.951 60.000 15.58 0.0 39.24 3.62 R
1178 1211 3.304057 CGAGAACTCCTTGGACTTTTTGC 60.304 47.826 0.00 0.0 0.00 3.68 R
2335 2370 1.684248 GGAGCAGATTTCCAGCACCAT 60.684 52.381 0.00 0.0 38.62 3.55 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
27 28 0.035458 CCCATTATCGACCTCCCAGC 59.965 60.000 0.00 0.00 0.00 4.85
29 30 0.758734 CATTATCGACCTCCCAGCCA 59.241 55.000 0.00 0.00 0.00 4.75
35 36 4.316823 ACCTCCCAGCCAGGTCGA 62.317 66.667 0.00 0.00 40.54 4.20
84 85 2.045926 GCTTGCATCACCCCGAGT 60.046 61.111 0.00 0.00 0.00 4.18
88 89 1.264749 TTGCATCACCCCGAGTAGCT 61.265 55.000 0.00 0.00 0.00 3.32
89 90 0.396556 TGCATCACCCCGAGTAGCTA 60.397 55.000 0.00 0.00 0.00 3.32
105 106 1.376466 CTACCACAGCAAGCCACCT 59.624 57.895 0.00 0.00 0.00 4.00
106 107 0.613260 CTACCACAGCAAGCCACCTA 59.387 55.000 0.00 0.00 0.00 3.08
144 145 2.119495 CATGGGAGTACTGGCTAGGTT 58.881 52.381 0.00 0.00 0.00 3.50
145 146 3.052414 TCATGGGAGTACTGGCTAGGTTA 60.052 47.826 0.00 0.00 0.00 2.85
146 147 3.478175 TGGGAGTACTGGCTAGGTTAA 57.522 47.619 0.00 0.00 0.00 2.01
216 217 4.041762 GCCCCGGACAATCCACCA 62.042 66.667 0.73 0.00 35.91 4.17
269 270 0.916086 TCCGGGCAGTTCATATGGTT 59.084 50.000 0.00 0.00 0.00 3.67
291 292 4.400961 GCGCTCCCAACTGGCTCT 62.401 66.667 0.00 0.00 0.00 4.09
312 313 2.270257 TGGCAAGGCACTGCATGAC 61.270 57.895 12.79 4.20 40.86 3.06
346 347 1.881903 CTCTCTCCGCCTGTGAGCAA 61.882 60.000 0.00 0.00 35.11 3.91
357 358 3.986054 TGAGCAACACAGGGAGGT 58.014 55.556 0.00 0.00 0.00 3.85
358 359 3.157518 TGAGCAACACAGGGAGGTA 57.842 52.632 0.00 0.00 0.00 3.08
379 380 5.071923 GGTAGCTACTCCACCTTCCATTATT 59.928 44.000 22.74 0.00 0.00 1.40
436 437 1.485066 AGGTGAGAGTCAAAACACGGT 59.515 47.619 0.00 0.00 34.59 4.83
441 442 5.284079 GTGAGAGTCAAAACACGGTAAGTA 58.716 41.667 0.00 0.00 0.00 2.24
471 472 5.360714 AGTGAAACACTTGGATTGTTCACAT 59.639 36.000 14.64 0.66 42.59 3.21
480 481 5.588958 TGGATTGTTCACATGACACAAAA 57.411 34.783 0.00 0.00 32.87 2.44
481 482 5.970592 TGGATTGTTCACATGACACAAAAA 58.029 33.333 0.00 0.00 32.87 1.94
482 483 6.580788 TGGATTGTTCACATGACACAAAAAT 58.419 32.000 0.00 0.00 32.87 1.82
575 576 5.902613 TCAAATGTCCATGAAACCATCTC 57.097 39.130 0.00 0.00 0.00 2.75
654 682 3.879892 GCAAACTCTCTCAAGTTGGACTT 59.120 43.478 2.34 0.00 39.40 3.01
670 698 7.112779 AGTTGGACTTCCTGAATTGGTAATAG 58.887 38.462 0.00 0.00 36.82 1.73
678 706 4.757149 CCTGAATTGGTAATAGCACCTAGC 59.243 45.833 0.00 0.00 46.19 3.42
702 730 6.430000 GCTTTCTTGAACCATTTACTACTCCA 59.570 38.462 0.00 0.00 0.00 3.86
810 838 4.277174 TCGGCTCTTTATCTTTTTGTGCAA 59.723 37.500 0.00 0.00 0.00 4.08
876 904 7.852971 AATTTATTTCGTTCCTCGTATTCCA 57.147 32.000 0.00 0.00 40.80 3.53
921 949 1.173043 TAAAAGCATCCACTTGGCCG 58.827 50.000 0.00 0.00 34.44 6.13
926 954 0.463654 GCATCCACTTGGCCGATACA 60.464 55.000 0.00 0.00 34.44 2.29
942 970 5.734786 GCCGATACATAGCACATAGATCTCC 60.735 48.000 0.00 0.00 0.00 3.71
987 1019 1.947456 GCAAGGGTCTTTCGTTGAAGT 59.053 47.619 0.00 0.00 35.32 3.01
988 1020 2.031944 GCAAGGGTCTTTCGTTGAAGTC 60.032 50.000 0.00 0.00 35.32 3.01
1010 1043 1.811965 CATCAAGTTCATGGCAACCGA 59.188 47.619 0.00 0.00 0.00 4.69
1095 1128 0.970937 TCTGCCCTAGGACCTTCACG 60.971 60.000 11.48 0.00 0.00 4.35
1178 1211 4.970711 AGGAAGCATGAGGAATACATGAG 58.029 43.478 0.00 0.00 45.22 2.90
1306 1339 5.357032 CCAATACAAATGTCCAGGGAGTTAC 59.643 44.000 0.00 0.00 0.00 2.50
1322 1355 4.101585 GGAGTTACCTGATGATGATGGTGA 59.898 45.833 0.00 0.00 34.33 4.02
1454 1487 7.502226 TGATCTTACCTTGAAGTTGTGATTTGT 59.498 33.333 0.00 0.00 0.00 2.83
1508 1541 5.451937 CGAGGCTCTATGTTCCATTTCACTA 60.452 44.000 13.50 0.00 0.00 2.74
1624 1657 8.608317 TGTAAAACACACCATATCATGTTATCG 58.392 33.333 0.00 0.00 34.24 2.92
1643 1676 9.961266 TGTTATCGTTTTTATCATTGTACGAAG 57.039 29.630 0.00 0.00 40.74 3.79
1663 1696 6.260050 ACGAAGTGCTTCTTATCAACTTTCAA 59.740 34.615 9.84 0.00 42.51 2.69
1682 1715 9.030301 ACTTTCAAAGTTTGGTGAATAAATTCG 57.970 29.630 15.47 0.15 39.04 3.34
1701 1734 4.866508 TCGTAGAATGGTGAGTCTGTTT 57.133 40.909 0.00 0.00 0.00 2.83
1703 1736 4.038763 TCGTAGAATGGTGAGTCTGTTTGT 59.961 41.667 0.00 0.00 0.00 2.83
1708 1741 3.111853 TGGTGAGTCTGTTTGTAGCAG 57.888 47.619 0.00 0.00 35.43 4.24
1819 1854 7.080353 TGTAGTAAATCTAGGCCTAGGGAATT 58.920 38.462 34.43 24.65 34.06 2.17
1827 1862 2.919602 AGGCCTAGGGAATTGACTGAAA 59.080 45.455 1.29 0.00 0.00 2.69
1886 1921 9.547753 AGTCACTAATGCAATAATTACCTAGTG 57.452 33.333 0.00 0.00 0.00 2.74
1977 2012 5.336150 TGCATCCTTTCAGTGTTTCAAAA 57.664 34.783 0.00 0.00 0.00 2.44
2017 2052 6.098124 TCAAACACCATCAAATCCTTTCAGTT 59.902 34.615 0.00 0.00 0.00 3.16
2019 2054 6.575162 ACACCATCAAATCCTTTCAGTTAC 57.425 37.500 0.00 0.00 0.00 2.50
2098 2133 2.168728 GTCTTTGAACTATCCCCGCTCT 59.831 50.000 0.00 0.00 0.00 4.09
2179 2214 7.023197 AGGCGTGTAATATACCATTGAAAAC 57.977 36.000 0.00 0.00 0.00 2.43
2232 2267 7.359262 ACATCATTCTTGCAAATTTGTCATG 57.641 32.000 19.03 17.05 0.00 3.07
2242 2277 8.498054 TTGCAAATTTGTCATGGTTTAAAAGA 57.502 26.923 19.03 0.00 0.00 2.52
2251 2286 8.189119 TGTCATGGTTTAAAAGAAGCCTTAAT 57.811 30.769 0.00 0.00 31.15 1.40
2310 2345 8.140677 TGAAATTTTGATCGCATTTTCAAACT 57.859 26.923 9.78 0.00 40.51 2.66
2354 2389 1.760192 ATGGTGCTGGAAATCTGCTC 58.240 50.000 0.00 0.00 40.43 4.26
2370 2405 1.659794 CTCCAAACACGCCCCTTTG 59.340 57.895 0.00 0.00 0.00 2.77
2382 2417 2.037121 CGCCCCTTTGGAAACATTTCTT 59.963 45.455 4.45 0.00 42.32 2.52
2400 2435 7.759433 ACATTTCTTAAATTCCATGCGGTTTAG 59.241 33.333 0.00 0.00 0.00 1.85
2416 2451 5.689961 GCGGTTTAGAGAAATTTGAAAAGCA 59.310 36.000 0.00 0.00 0.00 3.91
2419 2454 8.073768 CGGTTTAGAGAAATTTGAAAAGCAGTA 58.926 33.333 0.00 0.00 0.00 2.74
2431 2469 6.295039 TGAAAAGCAGTAGACTTTTTACCG 57.705 37.500 3.28 0.00 45.02 4.02
2442 2480 9.993454 AGTAGACTTTTTACCGAAAATAGAAGT 57.007 29.630 7.35 0.00 36.68 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.035458 GCTGGGAGGTCGATAATGGG 59.965 60.000 0.00 0.00 0.00 4.00
13 14 1.457643 CCTGGCTGGGAGGTCGATA 60.458 63.158 1.84 0.00 0.00 2.92
29 30 2.989824 CACGGACCTGGTCGACCT 60.990 66.667 33.39 15.57 36.82 3.85
62 63 2.048603 GGGGTGATGCAAGCAGTCC 61.049 63.158 0.00 3.00 24.12 3.85
70 71 0.396556 TAGCTACTCGGGGTGATGCA 60.397 55.000 0.00 0.00 0.00 3.96
88 89 0.613260 CTAGGTGGCTTGCTGTGGTA 59.387 55.000 0.00 0.00 0.00 3.25
89 90 1.376466 CTAGGTGGCTTGCTGTGGT 59.624 57.895 0.00 0.00 0.00 4.16
130 131 3.022406 CTCGGTTAACCTAGCCAGTACT 58.978 50.000 22.12 0.00 0.00 2.73
175 176 3.887868 CATTGGGCGGCGTTAGGC 61.888 66.667 9.37 0.00 42.51 3.93
181 182 4.459331 CAACGTCATTGGGCGGCG 62.459 66.667 0.51 0.51 34.34 6.46
244 245 2.045926 GAACTGCCCGGACAGCAT 60.046 61.111 18.72 7.05 41.60 3.79
249 250 0.180406 ACCATATGAACTGCCCGGAC 59.820 55.000 0.73 0.00 0.00 4.79
253 254 1.134220 TCCGAACCATATGAACTGCCC 60.134 52.381 3.65 0.00 0.00 5.36
291 292 3.848301 ATGCAGTGCCTTGCCACGA 62.848 57.895 13.72 0.00 43.43 4.35
312 313 0.108233 GAGAGCCTCCAAGCTGTCTG 60.108 60.000 3.65 0.00 46.70 3.51
346 347 1.342175 GGAGTAGCTACCTCCCTGTGT 60.342 57.143 20.31 0.00 0.00 3.72
357 358 6.174720 CAATAATGGAAGGTGGAGTAGCTA 57.825 41.667 0.00 0.00 35.72 3.32
358 359 5.041191 CAATAATGGAAGGTGGAGTAGCT 57.959 43.478 0.00 0.00 39.21 3.32
428 429 9.720667 GTTTCACTTAAAATACTTACCGTGTTT 57.279 29.630 0.00 0.00 38.40 2.83
453 454 4.036734 GTGTCATGTGAACAATCCAAGTGT 59.963 41.667 0.00 0.00 0.00 3.55
575 576 9.121517 CTCTAAACATTGCTTCTTGTTTGTATG 57.878 33.333 10.40 0.00 43.76 2.39
597 598 4.910195 ACATTCAAAGTGGCATGACTCTA 58.090 39.130 2.99 0.00 0.00 2.43
654 682 5.454755 GCTAGGTGCTATTACCAATTCAGGA 60.455 44.000 0.00 0.00 43.37 3.86
670 698 2.504367 TGGTTCAAGAAAGCTAGGTGC 58.496 47.619 0.00 0.00 43.29 5.01
678 706 7.979444 TGGAGTAGTAAATGGTTCAAGAAAG 57.021 36.000 0.00 0.00 0.00 2.62
771 799 2.434702 AGCCGAGGGAATAGACGAAATT 59.565 45.455 0.00 0.00 0.00 1.82
786 814 4.083324 TGCACAAAAAGATAAAGAGCCGAG 60.083 41.667 0.00 0.00 0.00 4.63
876 904 4.578128 AGGTTCCTGGTAGCCCTAAATAT 58.422 43.478 0.00 0.00 0.00 1.28
921 949 7.038659 GGTTGGAGATCTATGTGCTATGTATC 58.961 42.308 0.00 0.00 0.00 2.24
926 954 5.367937 AGTTGGTTGGAGATCTATGTGCTAT 59.632 40.000 0.00 0.00 0.00 2.97
987 1019 2.170166 GTTGCCATGAACTTGATGGGA 58.830 47.619 9.09 3.50 40.80 4.37
988 1020 1.205417 GGTTGCCATGAACTTGATGGG 59.795 52.381 9.09 0.00 40.80 4.00
1029 1062 3.533606 ATCATTGGTCTCTCGTTGGAG 57.466 47.619 0.00 0.00 41.89 3.86
1040 1073 2.024414 GTGGGCTTGGTATCATTGGTC 58.976 52.381 0.00 0.00 0.00 4.02
1095 1128 0.951040 CACCACGAGCTTGGAGGTTC 60.951 60.000 15.58 0.00 39.24 3.62
1178 1211 3.304057 CGAGAACTCCTTGGACTTTTTGC 60.304 47.826 0.00 0.00 0.00 3.68
1306 1339 4.277672 GGTTGATTCACCATCATCATCAGG 59.722 45.833 0.00 0.00 41.82 3.86
1311 1344 5.018149 ACATTGGTTGATTCACCATCATCA 58.982 37.500 8.25 0.00 46.60 3.07
1426 1459 6.861065 TCACAACTTCAAGGTAAGATCAAC 57.139 37.500 0.00 0.00 0.00 3.18
1454 1487 8.969260 ATATCAGCAAACTCATAGTGATGAAA 57.031 30.769 0.00 0.00 40.68 2.69
1508 1541 8.070034 TCATACATCAAATTCTTCCAGCAAAT 57.930 30.769 0.00 0.00 0.00 2.32
1624 1657 8.015658 AGAAGCACTTCGTACAATGATAAAAAC 58.984 33.333 4.81 0.00 43.97 2.43
1633 1666 6.874134 AGTTGATAAGAAGCACTTCGTACAAT 59.126 34.615 7.98 0.00 43.97 2.71
1663 1696 9.840427 CATTCTACGAATTTATTCACCAAACTT 57.160 29.630 0.00 0.00 36.61 2.66
1671 1704 8.258007 AGACTCACCATTCTACGAATTTATTCA 58.742 33.333 0.00 0.00 36.61 2.57
1682 1715 5.348997 GCTACAAACAGACTCACCATTCTAC 59.651 44.000 0.00 0.00 0.00 2.59
1819 1854 7.679783 TGATTAGTTTCTCATCCTTTCAGTCA 58.320 34.615 0.00 0.00 0.00 3.41
1827 1862 6.151817 GCAAGGTTTGATTAGTTTCTCATCCT 59.848 38.462 0.00 0.00 31.76 3.24
1913 1948 9.161629 TCGAATTTGAAGAGAGTAATTATGCAA 57.838 29.630 0.00 0.00 0.00 4.08
1977 2012 9.260002 GATGGTGTTTGAAAGTATTTGATGTTT 57.740 29.630 0.00 0.00 39.27 2.83
1979 2014 7.950512 TGATGGTGTTTGAAAGTATTTGATGT 58.049 30.769 0.00 0.00 39.27 3.06
2070 2105 5.240121 GGGGATAGTTCAAAGACGTTAACA 58.760 41.667 6.39 0.00 0.00 2.41
2111 2146 9.277783 GCTTGACCTAGACATTTTATCATATGT 57.722 33.333 1.90 0.00 37.68 2.29
2153 2188 5.538849 TCAATGGTATATTACACGCCTCA 57.461 39.130 0.00 0.00 0.00 3.86
2202 2237 9.537192 ACAAATTTGCAAGAATGATGTATATGG 57.463 29.630 18.12 0.00 0.00 2.74
2281 2316 9.947669 TTGAAAATGCGATCAAAATTTCATTTT 57.052 22.222 18.48 18.48 42.91 1.82
2325 2360 7.013559 CAGATTTCCAGCACCATATCATTTGTA 59.986 37.037 0.00 0.00 0.00 2.41
2335 2370 1.684248 GGAGCAGATTTCCAGCACCAT 60.684 52.381 0.00 0.00 38.62 3.55
2354 2389 2.733945 CCAAAGGGGCGTGTTTGG 59.266 61.111 8.83 8.83 45.08 3.28
2370 2405 6.035975 CCGCATGGAATTTAAGAAATGTTTCC 59.964 38.462 0.00 0.00 36.06 3.13
2382 2417 7.639113 ATTTCTCTAAACCGCATGGAATTTA 57.361 32.000 0.00 0.00 39.21 1.40
2392 2427 5.689961 TGCTTTTCAAATTTCTCTAAACCGC 59.310 36.000 0.00 0.00 0.00 5.68
2400 2435 9.521503 AAAAGTCTACTGCTTTTCAAATTTCTC 57.478 29.630 0.00 0.00 40.81 2.87
2416 2451 9.993454 ACTTCTATTTTCGGTAAAAAGTCTACT 57.007 29.630 0.00 0.00 40.09 2.57
2419 2454 9.993454 AGTACTTCTATTTTCGGTAAAAAGTCT 57.007 29.630 0.00 0.00 40.09 3.24


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

AutoCloner maintained by Alex Coulton.