Multiple sequence alignment - TraesCS4B01G316800

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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 TraesCS4B01G316800 chr4B 100.000 2369 0 0 1 2369 606754147 606756515 0.000000e+00 4375
1 TraesCS4B01G316800 chr4D 87.943 2455 144 70 1 2369 479524161 479526549 0.000000e+00 2754
2 TraesCS4B01G316800 chr4D 80.220 182 30 6 1024 1202 739005 739183 5.310000e-27 132
3 TraesCS4B01G316800 chr4A 89.933 1639 89 42 33 1629 685825808 685827412 0.000000e+00 2043
4 TraesCS4B01G316800 chr4A 89.614 337 26 7 1818 2153 685827620 685827948 1.010000e-113 420
5 TraesCS4B01G316800 chr4A 89.041 146 13 2 2217 2360 685829814 685829958 6.730000e-41 178
6 TraesCS4B01G316800 chr4A 80.328 183 28 7 1024 1202 1076598 1076776 5.310000e-27 132
7 TraesCS4B01G316800 chr6B 83.333 186 27 4 1025 1208 506835955 506835772 4.050000e-38 169
8 TraesCS4B01G316800 chr2B 87.903 124 12 3 1030 1153 640765309 640765189 2.450000e-30 143
9 TraesCS4B01G316800 chr3A 82.530 166 22 7 1024 1187 445280406 445280246 3.170000e-29 139
10 TraesCS4B01G316800 chr1D 80.978 184 27 6 1027 1206 421226624 421226803 3.170000e-29 139
11 TraesCS4B01G316800 chr3D 81.928 166 23 7 1024 1187 330062839 330062679 1.480000e-27 134
12 TraesCS4B01G316800 chr2A 77.966 177 30 7 1027 1200 672265663 672265493 4.170000e-18 102


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 TraesCS4B01G316800 chr4B 606754147 606756515 2368 False 4375.000000 4375 100.000000 1 2369 1 chr4B.!!$F1 2368
1 TraesCS4B01G316800 chr4D 479524161 479526549 2388 False 2754.000000 2754 87.943000 1 2369 1 chr4D.!!$F2 2368
2 TraesCS4B01G316800 chr4A 685825808 685829958 4150 False 880.333333 2043 89.529333 33 2360 3 chr4A.!!$F2 2327

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
548 580 0.250467 CCTATCCCATCCCAACTGCG 60.25 60.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2160 0.181114 TGATGATTCTGAAGGCGGGG 59.819 55.0 0.0 0.0 0.0 5.73 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
45 46 0.672342 GATTCCCAGTGCATGCATCC 59.328 55.000 25.64 12.26 0.00 3.51
49 50 2.125326 CCAGTGCATGCATCCCCAG 61.125 63.158 25.64 7.56 0.00 4.45
55 56 1.826921 CATGCATCCCCAGTGCTCC 60.827 63.158 0.00 0.00 42.92 4.70
95 96 0.306840 CCGTGACATGCATGCAGATC 59.693 55.000 26.69 23.67 31.94 2.75
96 97 1.296727 CGTGACATGCATGCAGATCT 58.703 50.000 26.69 6.06 0.00 2.75
97 98 1.003866 CGTGACATGCATGCAGATCTG 60.004 52.381 26.69 20.69 0.00 2.90
99 100 2.879026 GTGACATGCATGCAGATCTGAT 59.121 45.455 27.04 13.48 0.00 2.90
102 103 2.034685 ACATGCATGCAGATCTGATTGC 59.965 45.455 29.27 29.27 39.14 3.56
116 117 4.070009 TCTGATTGCATGCCTAGCTAATG 58.930 43.478 16.68 0.00 0.00 1.90
177 185 3.605743 CTGTAAGGTCGACCGATAGAC 57.394 52.381 28.26 20.90 42.08 2.59
328 346 3.435186 GCTTTCCAGCGCCAGTCC 61.435 66.667 2.29 0.00 35.91 3.85
495 515 6.073276 CGATCACCAGTAAATTCAAACTGACA 60.073 38.462 14.06 2.32 44.79 3.58
499 519 7.023575 CACCAGTAAATTCAAACTGACATAGC 58.976 38.462 14.06 0.00 44.79 2.97
548 580 0.250467 CCTATCCCATCCCAACTGCG 60.250 60.000 0.00 0.00 0.00 5.18
608 644 0.933509 CGTCGCGGTAGTAGAATGGC 60.934 60.000 6.13 0.00 0.00 4.40
663 699 2.434884 CCCGGTAGTGCAGTGCAG 60.435 66.667 20.42 6.15 40.08 4.41
669 705 1.293924 GTAGTGCAGTGCAGCTATGG 58.706 55.000 20.42 0.00 40.08 2.74
671 707 2.438975 TGCAGTGCAGCTATGGCC 60.439 61.111 15.37 0.00 39.73 5.36
845 924 2.994578 CGCAGCTAGCTACGAGTATCTA 59.005 50.000 29.47 0.00 42.61 1.98
984 1080 2.239400 CATATAGACCGACCCTCAGCA 58.761 52.381 0.00 0.00 0.00 4.41
1355 1462 0.100861 GCGGAGGACTACTACAGCAC 59.899 60.000 0.00 0.00 32.24 4.40
1356 1463 1.752683 CGGAGGACTACTACAGCACT 58.247 55.000 0.00 0.00 0.00 4.40
1358 1465 3.276857 CGGAGGACTACTACAGCACTAA 58.723 50.000 0.00 0.00 0.00 2.24
1359 1466 3.312973 CGGAGGACTACTACAGCACTAAG 59.687 52.174 0.00 0.00 0.00 2.18
1395 1502 1.666553 CTAGCACGCACACCCGAAA 60.667 57.895 0.00 0.00 0.00 3.46
1396 1503 1.626654 CTAGCACGCACACCCGAAAG 61.627 60.000 0.00 0.00 0.00 2.62
1397 1504 2.089887 TAGCACGCACACCCGAAAGA 62.090 55.000 0.00 0.00 0.00 2.52
1415 1522 7.435784 CCCGAAAGAAGAAGAATAAGCTACTAC 59.564 40.741 0.00 0.00 0.00 2.73
1416 1523 8.192110 CCGAAAGAAGAAGAATAAGCTACTACT 58.808 37.037 0.00 0.00 0.00 2.57
1441 1553 4.770795 TCCTAATTAAGCTGCTTGGAGTC 58.229 43.478 24.35 0.00 0.00 3.36
1476 1592 0.306533 CTTCGTTGGTTTGGTCGGTG 59.693 55.000 0.00 0.00 0.00 4.94
1593 1718 3.499157 AGCGTGCTTTAATTTGTTACCGA 59.501 39.130 0.00 0.00 0.00 4.69
1594 1719 3.600786 GCGTGCTTTAATTTGTTACCGAC 59.399 43.478 0.00 0.00 0.00 4.79
1701 1854 9.586435 CAATGGTCGCATCAAATCTATAGTATA 57.414 33.333 0.00 0.00 0.00 1.47
1720 1873 6.658849 AGTATACTGCATTTACCCATGTTCA 58.341 36.000 4.10 0.00 0.00 3.18
1721 1874 7.290061 AGTATACTGCATTTACCCATGTTCAT 58.710 34.615 4.10 0.00 0.00 2.57
1780 1943 8.517062 TTTGTCATGGATTTTTCACCAATTTT 57.483 26.923 0.00 0.00 39.69 1.82
1784 1947 8.220434 GTCATGGATTTTTCACCAATTTTTACG 58.780 33.333 0.00 0.00 39.69 3.18
1788 1951 7.650104 TGGATTTTTCACCAATTTTTACGAGTC 59.350 33.333 0.00 0.00 32.93 3.36
1789 1952 7.865889 GGATTTTTCACCAATTTTTACGAGTCT 59.134 33.333 0.00 0.00 0.00 3.24
1791 1954 8.623310 TTTTTCACCAATTTTTACGAGTCTTC 57.377 30.769 0.00 0.00 0.00 2.87
1856 2038 0.535335 TACCCACCATCGTCAAGCTC 59.465 55.000 0.00 0.00 0.00 4.09
1874 2056 2.097829 GCTCGCTTGATAAATCGTCGAC 60.098 50.000 5.18 5.18 0.00 4.20
1905 2087 1.736645 TTCGGTCGCAGCTAGCAAC 60.737 57.895 18.83 7.24 46.13 4.17
1978 2160 1.377202 TGAATCCTCGGTTGCCAGC 60.377 57.895 0.00 0.00 0.00 4.85
2000 2182 2.103094 CCCGCCTTCAGAATCATCAGTA 59.897 50.000 0.00 0.00 0.00 2.74
2001 2183 3.126831 CCGCCTTCAGAATCATCAGTAC 58.873 50.000 0.00 0.00 0.00 2.73
2002 2184 3.181471 CCGCCTTCAGAATCATCAGTACT 60.181 47.826 0.00 0.00 0.00 2.73
2003 2185 4.437239 CGCCTTCAGAATCATCAGTACTT 58.563 43.478 0.00 0.00 0.00 2.24
2004 2186 4.269603 CGCCTTCAGAATCATCAGTACTTG 59.730 45.833 0.00 0.00 0.00 3.16
2005 2187 5.181748 GCCTTCAGAATCATCAGTACTTGT 58.818 41.667 0.00 0.00 0.00 3.16
2006 2188 5.293079 GCCTTCAGAATCATCAGTACTTGTC 59.707 44.000 0.00 0.00 0.00 3.18
2007 2189 6.401394 CCTTCAGAATCATCAGTACTTGTCA 58.599 40.000 0.00 0.00 0.00 3.58
2008 2190 6.312426 CCTTCAGAATCATCAGTACTTGTCAC 59.688 42.308 0.00 0.00 0.00 3.67
2009 2191 6.345096 TCAGAATCATCAGTACTTGTCACA 57.655 37.500 0.00 0.00 0.00 3.58
2014 2205 4.048504 TCATCAGTACTTGTCACAACACG 58.951 43.478 0.00 0.00 34.35 4.49
2145 2336 5.049267 CGAGGATTGAAACCCTTACGAAAAA 60.049 40.000 0.00 0.00 31.84 1.94
2170 3125 0.318275 TTGCCGGTCGTTTGATTTGC 60.318 50.000 1.90 0.00 0.00 3.68
2175 3130 3.545426 GCCGGTCGTTTGATTTGCTATAC 60.545 47.826 1.90 0.00 0.00 1.47
2342 4335 7.989826 AGAAAAACAGATAGACACCATATTGC 58.010 34.615 0.00 0.00 0.00 3.56
2363 4356 8.697846 ATTGCAATCATGTGTTTCTTCTATTG 57.302 30.769 5.99 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.002134 ACGGAATTGGAGCACTGGG 60.002 57.895 0.00 0.00 0.00 4.45
49 50 1.359459 GACGGACGGAATTGGAGCAC 61.359 60.000 0.00 0.00 0.00 4.40
55 56 1.808390 GGACGGACGGACGGAATTG 60.808 63.158 6.00 0.00 38.39 2.32
95 96 3.190744 CCATTAGCTAGGCATGCAATCAG 59.809 47.826 21.36 11.01 0.00 2.90
96 97 3.151554 CCATTAGCTAGGCATGCAATCA 58.848 45.455 21.36 0.00 0.00 2.57
97 98 3.152341 ACCATTAGCTAGGCATGCAATC 58.848 45.455 21.36 1.57 0.00 2.67
99 100 2.092484 TGACCATTAGCTAGGCATGCAA 60.092 45.455 21.36 5.87 0.00 4.08
102 103 6.882610 TTTATTGACCATTAGCTAGGCATG 57.117 37.500 0.00 0.00 0.00 4.06
103 104 7.233632 TCATTTATTGACCATTAGCTAGGCAT 58.766 34.615 0.00 0.00 0.00 4.40
104 105 6.600388 TCATTTATTGACCATTAGCTAGGCA 58.400 36.000 0.00 0.00 0.00 4.75
172 180 4.657013 TGAGCTCCATCGTCTATGTCTAT 58.343 43.478 12.15 0.00 33.34 1.98
173 181 4.068599 CTGAGCTCCATCGTCTATGTCTA 58.931 47.826 12.15 0.00 33.34 2.59
174 182 2.884012 CTGAGCTCCATCGTCTATGTCT 59.116 50.000 12.15 0.00 33.34 3.41
175 183 2.606795 GCTGAGCTCCATCGTCTATGTC 60.607 54.545 12.15 0.00 33.34 3.06
176 184 1.339610 GCTGAGCTCCATCGTCTATGT 59.660 52.381 12.15 0.00 33.34 2.29
177 185 1.612950 AGCTGAGCTCCATCGTCTATG 59.387 52.381 12.15 0.00 30.62 2.23
215 229 0.320073 ACGGACGGAGAATTTTCGCA 60.320 50.000 0.00 0.00 0.00 5.10
240 256 1.131315 CTAAGCCGAGAAAAGCAAGCC 59.869 52.381 0.00 0.00 0.00 4.35
241 257 1.807142 ACTAAGCCGAGAAAAGCAAGC 59.193 47.619 0.00 0.00 0.00 4.01
282 300 1.743995 GAATCCCGGTTCACGTGGG 60.744 63.158 17.00 8.81 44.75 4.61
283 301 1.743995 GGAATCCCGGTTCACGTGG 60.744 63.158 17.00 0.00 42.24 4.94
377 395 2.283298 CGTGAGTTCCATTCCATCCTG 58.717 52.381 0.00 0.00 0.00 3.86
486 506 5.276114 CGATCGAGAAAGCTATGTCAGTTTG 60.276 44.000 10.26 0.00 0.00 2.93
548 580 2.287915 ACGAATAATCAGCCGCAATCAC 59.712 45.455 0.00 0.00 0.00 3.06
622 658 2.125753 CTGCTGACCAGTCTCGGC 60.126 66.667 0.00 2.39 42.18 5.54
646 682 2.434884 CTGCACTGCACTACCGGG 60.435 66.667 6.32 0.00 33.79 5.73
647 683 2.225791 TAGCTGCACTGCACTACCGG 62.226 60.000 0.00 0.00 33.79 5.28
648 684 0.179100 ATAGCTGCACTGCACTACCG 60.179 55.000 0.00 0.00 33.79 4.02
650 686 1.293924 CCATAGCTGCACTGCACTAC 58.706 55.000 0.00 0.00 33.79 2.73
651 687 0.462581 GCCATAGCTGCACTGCACTA 60.463 55.000 0.00 7.57 33.79 2.74
652 688 1.748122 GCCATAGCTGCACTGCACT 60.748 57.895 0.00 5.58 33.79 4.40
653 689 2.768492 GGCCATAGCTGCACTGCAC 61.768 63.158 0.00 0.00 39.73 4.57
654 690 2.438975 GGCCATAGCTGCACTGCA 60.439 61.111 3.11 3.11 39.73 4.41
655 691 2.124403 AGGCCATAGCTGCACTGC 60.124 61.111 5.01 0.00 39.73 4.40
656 692 2.478890 GCAGGCCATAGCTGCACTG 61.479 63.158 5.01 2.76 40.60 3.66
663 699 1.379044 ACACAAGGCAGGCCATAGC 60.379 57.895 13.63 5.81 38.92 2.97
669 705 1.604593 ATCACCACACAAGGCAGGC 60.605 57.895 0.00 0.00 0.00 4.85
671 707 0.594602 CACATCACCACACAAGGCAG 59.405 55.000 0.00 0.00 0.00 4.85
968 1059 1.605058 GCTTGCTGAGGGTCGGTCTA 61.605 60.000 0.00 0.00 0.00 2.59
1395 1502 9.346005 GGAGTAGTAGTAGCTTATTCTTCTTCT 57.654 37.037 0.00 0.00 0.00 2.85
1396 1503 9.346005 AGGAGTAGTAGTAGCTTATTCTTCTTC 57.654 37.037 0.00 0.00 0.00 2.87
1415 1522 5.918608 TCCAAGCAGCTTAATTAGGAGTAG 58.081 41.667 7.52 0.00 0.00 2.57
1416 1523 5.918608 CTCCAAGCAGCTTAATTAGGAGTA 58.081 41.667 22.35 0.95 37.28 2.59
1417 1524 4.775236 CTCCAAGCAGCTTAATTAGGAGT 58.225 43.478 22.35 0.00 37.28 3.85
1418 1525 4.775236 ACTCCAAGCAGCTTAATTAGGAG 58.225 43.478 26.30 26.30 45.24 3.69
1419 1526 4.225042 TGACTCCAAGCAGCTTAATTAGGA 59.775 41.667 7.52 9.09 0.00 2.94
1420 1527 4.517285 TGACTCCAAGCAGCTTAATTAGG 58.483 43.478 7.52 4.64 0.00 2.69
1424 1536 3.009473 TCCTTGACTCCAAGCAGCTTAAT 59.991 43.478 7.52 0.00 46.42 1.40
1426 1538 1.977854 TCCTTGACTCCAAGCAGCTTA 59.022 47.619 7.52 0.00 46.42 3.09
1441 1553 2.234908 ACGAAGACCATTCTCCTCCTTG 59.765 50.000 0.00 0.00 0.00 3.61
1476 1592 1.153086 CTAGTCCTGCCATGCACCC 60.153 63.158 0.00 0.00 33.79 4.61
1593 1718 7.067008 CCCATTAATTACTTCGTTCCATCTTGT 59.933 37.037 0.00 0.00 0.00 3.16
1594 1719 7.067008 ACCCATTAATTACTTCGTTCCATCTTG 59.933 37.037 0.00 0.00 0.00 3.02
1651 1804 2.198406 GTACACACACGTCTTTGCAGA 58.802 47.619 0.00 0.00 0.00 4.26
1675 1828 6.791887 ACTATAGATTTGATGCGACCATTG 57.208 37.500 6.78 0.00 0.00 2.82
1701 1854 5.743636 AAATGAACATGGGTAAATGCAGT 57.256 34.783 0.00 0.00 0.00 4.40
1780 1943 4.030314 TCCCAGAAGAGAAGACTCGTAA 57.970 45.455 0.00 0.00 46.64 3.18
1784 1947 3.436243 TCCTTCCCAGAAGAGAAGACTC 58.564 50.000 5.92 0.00 41.69 3.36
1788 1951 3.177228 TCCTTCCTTCCCAGAAGAGAAG 58.823 50.000 18.67 18.67 42.80 2.85
1789 1952 3.275848 TCCTTCCTTCCCAGAAGAGAA 57.724 47.619 5.92 6.91 42.80 2.87
1791 1954 4.471386 TGTTATCCTTCCTTCCCAGAAGAG 59.529 45.833 5.92 0.00 42.80 2.85
1874 2056 1.635663 GACCGAACATTGACCAGCGG 61.636 60.000 0.00 0.00 43.95 5.52
1905 2087 1.089920 CTGTCGGGGAATCAGCTTTG 58.910 55.000 0.00 0.00 0.00 2.77
1978 2160 0.181114 TGATGATTCTGAAGGCGGGG 59.819 55.000 0.00 0.00 0.00 5.73
2001 2183 1.084290 CGCGACGTGTTGTGACAAG 60.084 57.895 0.00 0.00 40.50 3.16
2002 2184 2.518312 CCGCGACGTGTTGTGACAA 61.518 57.895 8.23 0.00 37.57 3.18
2003 2185 2.957489 CCGCGACGTGTTGTGACA 60.957 61.111 8.23 0.00 0.00 3.58
2004 2186 2.924285 GACCGCGACGTGTTGTGAC 61.924 63.158 8.23 0.00 0.00 3.67
2005 2187 2.656007 GACCGCGACGTGTTGTGA 60.656 61.111 8.23 0.00 0.00 3.58
2006 2188 3.698463 GGACCGCGACGTGTTGTG 61.698 66.667 8.23 0.00 0.00 3.33
2007 2189 3.908081 AGGACCGCGACGTGTTGT 61.908 61.111 8.23 0.00 0.00 3.32
2008 2190 3.403057 CAGGACCGCGACGTGTTG 61.403 66.667 8.23 0.00 0.00 3.33
2029 2220 4.740695 GTCGATCAATAGAGTGCTGTTACC 59.259 45.833 0.00 0.00 0.00 2.85
2145 2336 1.950909 TCAAACGACCGGCAAAGAAAT 59.049 42.857 0.00 0.00 0.00 2.17
2295 4288 4.487714 TGGTCATGTCTATCCAACTTCC 57.512 45.455 0.00 0.00 0.00 3.46
2299 4292 6.817765 TTTTCTTGGTCATGTCTATCCAAC 57.182 37.500 0.00 0.00 36.23 3.77
2342 4335 6.317088 ACGCAATAGAAGAAACACATGATTG 58.683 36.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.