Multiple sequence alignment - TraesCS7B01G215800

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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 TraesCS7B01G215800 chr7B 100.000 2300 0 0 1 2300 396043691 396045990 0.000000e+00 4248.0
1 TraesCS7B01G215800 chr7B 81.043 211 36 3 1048 1258 399260429 399260635 5.080000e-37 165.0
2 TraesCS7B01G215800 chr7A 90.295 1659 85 29 1 1623 449640156 449641774 0.000000e+00 2102.0
3 TraesCS7B01G215800 chr7A 85.082 429 50 12 1653 2075 449642127 449642547 2.110000e-115 425.0
4 TraesCS7B01G215800 chr7A 80.717 223 23 9 2078 2300 449642734 449642936 3.060000e-34 156.0
5 TraesCS7B01G215800 chr7D 91.180 1474 77 26 543 2000 396112970 396114406 0.000000e+00 1953.0
6 TraesCS7B01G215800 chr7D 88.845 502 32 6 1 500 396103755 396104234 1.520000e-166 595.0
7 TraesCS7B01G215800 chr7D 93.774 257 11 2 2049 2300 396114630 396114886 4.640000e-102 381.0
8 TraesCS7B01G215800 chr7D 89.552 67 6 1 490 556 396104794 396104859 1.460000e-12 84.2


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 TraesCS7B01G215800 chr7B 396043691 396045990 2299 False 4248.000000 4248 100.000000 1 2300 1 chr7B.!!$F1 2299
1 TraesCS7B01G215800 chr7A 449640156 449642936 2780 False 894.333333 2102 85.364667 1 2300 3 chr7A.!!$F1 2299
2 TraesCS7B01G215800 chr7D 396112970 396114886 1916 False 1167.000000 1953 92.477000 543 2300 2 chr7D.!!$F2 1757
3 TraesCS7B01G215800 chr7D 396103755 396104859 1104 False 339.600000 595 89.198500 1 556 2 chr7D.!!$F1 555

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
617 1203 0.320771 CACTTGTACTGCCGCCTCTT 60.321 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2953 0.465642 GGATGGAAGGTTAAGGGCCG 60.466 60.0 0.0 0.0 0.0 6.13 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
90 91 2.962421 GTTCCTTGGTCCATTTCCACAA 59.038 45.455 0.00 0.00 34.45 3.33
91 92 2.593026 TCCTTGGTCCATTTCCACAAC 58.407 47.619 0.00 0.00 34.45 3.32
92 93 2.091610 TCCTTGGTCCATTTCCACAACA 60.092 45.455 0.00 0.00 34.45 3.33
93 94 2.697751 CCTTGGTCCATTTCCACAACAA 59.302 45.455 0.00 0.00 34.45 2.83
94 95 3.492482 CCTTGGTCCATTTCCACAACAAC 60.492 47.826 0.00 0.00 34.45 3.32
95 96 2.035632 TGGTCCATTTCCACAACAACC 58.964 47.619 0.00 0.00 0.00 3.77
96 97 2.316108 GGTCCATTTCCACAACAACCT 58.684 47.619 0.00 0.00 0.00 3.50
97 98 3.117474 TGGTCCATTTCCACAACAACCTA 60.117 43.478 0.00 0.00 0.00 3.08
98 99 3.892588 GGTCCATTTCCACAACAACCTAA 59.107 43.478 0.00 0.00 0.00 2.69
99 100 4.342665 GGTCCATTTCCACAACAACCTAAA 59.657 41.667 0.00 0.00 0.00 1.85
100 101 5.163395 GGTCCATTTCCACAACAACCTAAAA 60.163 40.000 0.00 0.00 0.00 1.52
101 102 6.342111 GTCCATTTCCACAACAACCTAAAAA 58.658 36.000 0.00 0.00 0.00 1.94
102 103 6.256975 GTCCATTTCCACAACAACCTAAAAAC 59.743 38.462 0.00 0.00 0.00 2.43
103 104 6.070767 TCCATTTCCACAACAACCTAAAAACA 60.071 34.615 0.00 0.00 0.00 2.83
104 105 6.595716 CCATTTCCACAACAACCTAAAAACAA 59.404 34.615 0.00 0.00 0.00 2.83
143 144 2.613977 CGACCTTCAATTCTCTGGTGCT 60.614 50.000 0.00 0.00 0.00 4.40
194 195 1.355916 CGTCCTTCGGTCTCGATCC 59.644 63.158 0.00 0.00 45.51 3.36
240 241 2.388232 CGGCCGCAACTCAACTACC 61.388 63.158 14.67 0.00 0.00 3.18
269 270 8.955388 GCCATTCCCAAAACACAAAATTATAAT 58.045 29.630 0.00 0.00 0.00 1.28
342 348 6.607004 TTTTACAGAAACTGGAAACCCAAA 57.393 33.333 8.42 0.00 43.06 3.28
345 351 4.197503 ACAGAAACTGGAAACCCAAAGGG 61.198 47.826 0.00 0.00 41.67 3.95
359 365 2.358898 CCAAAGGGCAATCGAATCGAAT 59.641 45.455 10.12 0.00 39.99 3.34
375 381 6.198216 CGAATCGAATCCAAAACACAAAAACT 59.802 34.615 0.00 0.00 0.00 2.66
389 397 8.986477 AACACAAAAACTGGAGCATATAAATC 57.014 30.769 0.00 0.00 0.00 2.17
390 398 7.547227 ACACAAAAACTGGAGCATATAAATCC 58.453 34.615 0.00 0.00 0.00 3.01
414 422 8.310382 TCCAATTATTTGTTGAAAATCGTGGAT 58.690 29.630 0.00 0.00 0.00 3.41
539 1120 4.608774 ATGGCCGGGGATGCATGG 62.609 66.667 2.46 0.00 0.00 3.66
554 1135 3.700109 TGGCTCTCCAAGTCTCGG 58.300 61.111 0.00 0.00 39.99 4.63
617 1203 0.320771 CACTTGTACTGCCGCCTCTT 60.321 55.000 0.00 0.00 0.00 2.85
664 1250 0.883814 CTGCAGCCAGCTATAGCACC 60.884 60.000 26.07 13.30 45.94 5.01
669 1255 1.367840 CCAGCTATAGCACCGGGAC 59.632 63.158 26.07 0.00 45.16 4.46
672 1258 1.115930 AGCTATAGCACCGGGACTGG 61.116 60.000 26.07 0.00 45.16 4.00
697 1283 8.492748 GGTTTGATTAAATATCAATGCATGCAG 58.507 33.333 26.69 13.62 37.79 4.41
698 1284 9.251792 GTTTGATTAAATATCAATGCATGCAGA 57.748 29.630 26.69 18.75 37.79 4.26
699 1285 9.990360 TTTGATTAAATATCAATGCATGCAGAT 57.010 25.926 26.69 23.85 37.79 2.90
733 1324 4.827036 ATATAGGGACAGTACACTCCCA 57.173 45.455 23.40 13.35 44.63 4.37
734 1325 2.526888 TAGGGACAGTACACTCCCAG 57.473 55.000 23.40 0.00 44.63 4.45
735 1326 0.487772 AGGGACAGTACACTCCCAGT 59.512 55.000 23.40 7.08 44.63 4.00
736 1327 0.896226 GGGACAGTACACTCCCAGTC 59.104 60.000 18.78 5.11 41.89 3.51
737 1328 1.550409 GGGACAGTACACTCCCAGTCT 60.550 57.143 18.78 0.00 41.89 3.24
762 1353 1.176527 GCCATGTCCAGCTTAGCAAA 58.823 50.000 7.07 0.00 0.00 3.68
795 1386 2.195567 ACAACCAGTTGCAGCGCAT 61.196 52.632 11.47 0.00 44.03 4.73
848 1439 2.295885 CCTCTTGATGATTGCCTCCAC 58.704 52.381 0.00 0.00 0.00 4.02
920 1511 3.948719 GCCTCGGTTCCCACCACA 61.949 66.667 0.00 0.00 44.53 4.17
926 1517 0.884704 CGGTTCCCACCACACTTCAG 60.885 60.000 0.00 0.00 44.53 3.02
930 1535 1.507140 TCCCACCACACTTCAGTCTT 58.493 50.000 0.00 0.00 0.00 3.01
952 1557 4.127907 TGTGCAACCGAAACAACATACTA 58.872 39.130 0.00 0.00 34.36 1.82
963 1571 1.665679 CAACATACTACAAGCAGCCCG 59.334 52.381 0.00 0.00 0.00 6.13
1314 1925 3.504134 ACCACTAGATATGTAGCAGCTCG 59.496 47.826 0.00 0.00 0.00 5.03
1420 2035 9.120538 GGATACATTTTGTTATTAGCTGAGGAA 57.879 33.333 0.00 0.00 0.00 3.36
1561 2176 4.142315 ACATTGCAATTTTCTCCAGATCGG 60.142 41.667 9.83 0.00 0.00 4.18
1681 2619 1.889105 CAGTGCCACTGTGTTCGCT 60.889 57.895 16.78 7.22 41.19 4.93
1736 2674 3.689872 TTCCTCTGCCTATCAGTACCT 57.310 47.619 0.00 0.00 43.32 3.08
1737 2675 3.689872 TCCTCTGCCTATCAGTACCTT 57.310 47.619 0.00 0.00 43.32 3.50
1744 2682 5.010719 TCTGCCTATCAGTACCTTTATTCCG 59.989 44.000 0.00 0.00 43.32 4.30
1794 2732 7.465781 GCAGTAGATCATTCTCTCAGCTTTTTC 60.466 40.741 0.00 0.00 33.17 2.29
1820 2758 6.459670 AACGTGGATGGTTTTCTTAACTTT 57.540 33.333 0.00 0.00 0.00 2.66
1821 2759 5.827666 ACGTGGATGGTTTTCTTAACTTTG 58.172 37.500 0.00 0.00 0.00 2.77
1873 2812 1.327690 TACCCGGACCTCTGCATCAC 61.328 60.000 0.73 0.00 0.00 3.06
1889 2828 4.233123 CATCACTTTGATGCACACAACT 57.767 40.909 7.52 0.00 46.37 3.16
1952 2893 6.548321 TCCAATATCACACACTTAAGGGTTT 58.452 36.000 7.90 0.00 0.00 3.27
2002 2944 1.237285 GCGTTGTCAGGTGGCAATCT 61.237 55.000 0.00 0.00 42.06 2.40
2007 2949 0.242017 GTCAGGTGGCAATCTGCAAC 59.758 55.000 12.56 0.00 46.40 4.17
2031 2973 0.106167 GGCCCTTAACCTTCCATCCC 60.106 60.000 0.00 0.00 0.00 3.85
2089 3388 1.593209 GCAACGTCTGGAACCGTCA 60.593 57.895 0.00 0.00 36.04 4.35
2163 3466 3.316573 GAGGAGGCTCCGTTGTGGG 62.317 68.421 27.11 0.00 42.75 4.61
2211 3514 2.285368 TCCATCGCAGGAGGGGTT 60.285 61.111 0.00 0.00 44.27 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.179215 CATGAGCGTTTTGGAGCGAC 60.179 55.000 0.00 0.00 38.61 5.19
61 62 0.404040 GGACCAAGGAACACATGGGA 59.596 55.000 0.00 0.00 38.58 4.37
90 91 3.964031 TGCCTGGATTGTTTTTAGGTTGT 59.036 39.130 0.00 0.00 0.00 3.32
91 92 4.599047 TGCCTGGATTGTTTTTAGGTTG 57.401 40.909 0.00 0.00 0.00 3.77
92 93 5.823861 ATTGCCTGGATTGTTTTTAGGTT 57.176 34.783 0.00 0.00 0.00 3.50
93 94 5.823861 AATTGCCTGGATTGTTTTTAGGT 57.176 34.783 0.00 0.00 0.00 3.08
94 95 5.106594 GCAAATTGCCTGGATTGTTTTTAGG 60.107 40.000 6.72 0.00 37.42 2.69
95 96 5.469421 TGCAAATTGCCTGGATTGTTTTTAG 59.531 36.000 15.98 0.00 44.23 1.85
96 97 5.238214 GTGCAAATTGCCTGGATTGTTTTTA 59.762 36.000 15.98 0.00 44.23 1.52
97 98 4.036616 GTGCAAATTGCCTGGATTGTTTTT 59.963 37.500 15.98 0.00 44.23 1.94
98 99 3.565063 GTGCAAATTGCCTGGATTGTTTT 59.435 39.130 15.98 0.00 44.23 2.43
99 100 3.140623 GTGCAAATTGCCTGGATTGTTT 58.859 40.909 15.98 0.00 44.23 2.83
100 101 2.769893 GTGCAAATTGCCTGGATTGTT 58.230 42.857 15.98 0.00 44.23 2.83
101 102 1.337074 CGTGCAAATTGCCTGGATTGT 60.337 47.619 15.98 0.00 44.23 2.71
102 103 1.352114 CGTGCAAATTGCCTGGATTG 58.648 50.000 15.98 0.00 44.23 2.67
103 104 0.390209 GCGTGCAAATTGCCTGGATT 60.390 50.000 15.98 0.00 44.23 3.01
104 105 1.216178 GCGTGCAAATTGCCTGGAT 59.784 52.632 15.98 0.00 44.23 3.41
121 122 1.734465 CACCAGAGAATTGAAGGTCGC 59.266 52.381 0.00 0.00 0.00 5.19
240 241 1.047002 TGTGTTTTGGGAATGGCAGG 58.953 50.000 0.00 0.00 0.00 4.85
269 270 9.521503 TTTTTGTAAAATTCGAATGTCATGACA 57.478 25.926 29.67 29.67 46.44 3.58
302 303 5.150683 TGTAAAATTCGAATGCGTTTCCAG 58.849 37.500 12.25 0.00 38.98 3.86
342 348 1.140852 TGGATTCGATTCGATTGCCCT 59.859 47.619 9.96 0.00 35.23 5.19
345 351 4.262976 GTGTTTTGGATTCGATTCGATTGC 59.737 41.667 9.96 12.01 35.23 3.56
346 352 5.389778 TGTGTTTTGGATTCGATTCGATTG 58.610 37.500 9.96 0.00 35.23 2.67
347 353 5.621197 TGTGTTTTGGATTCGATTCGATT 57.379 34.783 9.96 6.37 35.23 3.34
348 354 5.621197 TTGTGTTTTGGATTCGATTCGAT 57.379 34.783 9.96 0.25 35.23 3.59
349 355 5.425577 TTTGTGTTTTGGATTCGATTCGA 57.574 34.783 4.29 4.29 0.00 3.71
350 356 6.198216 AGTTTTTGTGTTTTGGATTCGATTCG 59.802 34.615 0.00 0.00 0.00 3.34
351 357 7.336975 CAGTTTTTGTGTTTTGGATTCGATTC 58.663 34.615 0.00 0.00 0.00 2.52
359 365 3.259374 TGCTCCAGTTTTTGTGTTTTGGA 59.741 39.130 0.00 0.00 33.90 3.53
389 397 7.881643 TCCACGATTTTCAACAAATAATTGG 57.118 32.000 0.00 0.00 41.01 3.16
395 403 7.921786 TCTCTATCCACGATTTTCAACAAAT 57.078 32.000 0.00 0.00 0.00 2.32
409 417 2.102252 CCTGTGGCTCTTCTCTATCCAC 59.898 54.545 2.99 2.99 45.43 4.02
411 419 2.364002 GACCTGTGGCTCTTCTCTATCC 59.636 54.545 0.00 0.00 0.00 2.59
414 422 2.909504 AGACCTGTGGCTCTTCTCTA 57.090 50.000 0.00 0.00 0.00 2.43
530 1111 0.106819 ACTTGGAGAGCCATGCATCC 60.107 55.000 0.00 0.00 45.46 3.51
532 1113 0.917533 AGACTTGGAGAGCCATGCAT 59.082 50.000 0.00 0.00 45.46 3.96
539 1120 2.185608 GGCCGAGACTTGGAGAGC 59.814 66.667 13.45 0.00 0.00 4.09
549 1130 2.525629 TGGTGAACCAGGCCGAGA 60.526 61.111 0.00 0.00 42.01 4.04
664 1250 6.935741 TGATATTTAATCAAACCAGTCCCG 57.064 37.500 0.00 0.00 0.00 5.14
669 1255 8.492748 GCATGCATTGATATTTAATCAAACCAG 58.507 33.333 14.21 0.00 40.84 4.00
672 1258 9.251792 TCTGCATGCATTGATATTTAATCAAAC 57.748 29.630 22.97 1.97 40.84 2.93
700 1286 9.463902 GTACTGTCCCTATATATCTATGTGTGT 57.536 37.037 0.00 0.00 0.00 3.72
701 1287 9.462606 TGTACTGTCCCTATATATCTATGTGTG 57.537 37.037 0.00 0.00 0.00 3.82
762 1353 1.134936 GGTTGTGTGGCGGTTTCTTTT 60.135 47.619 0.00 0.00 0.00 2.27
848 1439 3.753272 GGAGATACTCTGCTCTGCTCTAG 59.247 52.174 0.00 0.00 31.63 2.43
920 1511 1.134521 TCGGTTGCACAAGACTGAAGT 60.135 47.619 0.00 0.00 0.00 3.01
926 1517 2.182014 GTTGTTTCGGTTGCACAAGAC 58.818 47.619 0.00 0.00 31.10 3.01
930 1535 2.946329 AGTATGTTGTTTCGGTTGCACA 59.054 40.909 0.00 0.00 0.00 4.57
952 1557 2.281761 CAAGACCGGGCTGCTTGT 60.282 61.111 12.91 0.00 35.49 3.16
963 1571 1.268079 GAGCTTCCAGCAAACAAGACC 59.732 52.381 0.00 0.00 45.56 3.85
986 1594 1.072159 GCCATTGATCTCCTCCCCG 59.928 63.158 0.00 0.00 0.00 5.73
990 1598 1.072159 CCCCGCCATTGATCTCCTC 59.928 63.158 0.00 0.00 0.00 3.71
1349 1960 4.103627 AGTGATCATATCAATGGCTGGACA 59.896 41.667 0.00 0.00 41.69 4.02
1360 1971 6.356186 AGCAATCTAGCAGTGATCATATCA 57.644 37.500 0.00 0.00 36.85 2.15
1420 2035 4.839121 TGCCACGTTCCAAGAATAACTAT 58.161 39.130 0.00 0.00 0.00 2.12
1423 2038 4.434713 AATGCCACGTTCCAAGAATAAC 57.565 40.909 0.00 0.00 0.00 1.89
1426 2041 3.686016 ACTAATGCCACGTTCCAAGAAT 58.314 40.909 0.00 0.00 0.00 2.40
1561 2176 2.774439 AAGCAACCAACATCGAACAC 57.226 45.000 0.00 0.00 0.00 3.32
1736 2674 5.873712 TCGTGTAATAAAGTGGCGGAATAAA 59.126 36.000 0.00 0.00 0.00 1.40
1737 2675 5.417811 TCGTGTAATAAAGTGGCGGAATAA 58.582 37.500 0.00 0.00 0.00 1.40
1744 2682 7.762615 TGCCTATATATCGTGTAATAAAGTGGC 59.237 37.037 0.00 0.00 0.00 5.01
1794 2732 7.198306 AGTTAAGAAAACCATCCACGTTAAG 57.802 36.000 0.00 0.00 0.00 1.85
1873 2812 7.191551 CCTATCAATAGTTGTGTGCATCAAAG 58.808 38.462 8.46 1.97 0.00 2.77
1928 2867 5.772393 ACCCTTAAGTGTGTGATATTGGA 57.228 39.130 0.97 0.00 0.00 3.53
2005 2947 4.728110 GGTTAAGGGCCGGCGGTT 62.728 66.667 28.82 18.44 0.00 4.44
2007 2949 4.419921 AAGGTTAAGGGCCGGCGG 62.420 66.667 24.35 24.35 0.00 6.13
2011 2953 0.465642 GGATGGAAGGTTAAGGGCCG 60.466 60.000 0.00 0.00 0.00 6.13
2031 2973 2.639327 CGGCAGCAAGGAAAAGGGG 61.639 63.158 0.00 0.00 0.00 4.79
2211 3514 2.506231 AGAGAGACTCATCGGTGGACTA 59.494 50.000 5.02 0.00 32.06 2.59


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

AutoCloner maintained by Alex Coulton.