Multiple sequence alignment - TraesCS2B01G150000

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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 TraesCS2B01G150000 chr2B 100.000 2309 0 0 1 2309 116394829 116392521 0.000000e+00 4265
1 TraesCS2B01G150000 chr2A 94.412 1539 76 3 6 1540 75635277 75633745 0.000000e+00 2357
2 TraesCS2B01G150000 chr2A 90.909 231 13 4 1451 1680 75633667 75633444 1.040000e-78 303
3 TraesCS2B01G150000 chr2D 90.277 1697 132 13 3 1696 75754703 75756369 0.000000e+00 2189
4 TraesCS2B01G150000 chr2D 87.872 874 72 16 1451 2309 75559678 75560532 0.000000e+00 996
5 TraesCS2B01G150000 chr2D 93.923 181 9 1 1218 1398 75559491 75559669 2.920000e-69 272
6 TraesCS2B01G150000 chr5D 78.000 700 149 5 267 963 515245733 515245036 3.520000e-118 435
7 TraesCS2B01G150000 chr3D 81.614 533 86 12 1739 2265 436212282 436212808 4.560000e-117 431
8 TraesCS2B01G150000 chr5A 77.383 703 148 10 267 963 643358377 643357680 7.680000e-110 407
9 TraesCS2B01G150000 chr3A 82.287 446 69 8 1863 2301 574926535 574926977 6.020000e-101 377
10 TraesCS2B01G150000 chr3A 80.972 494 67 16 1823 2309 691048541 691049014 1.300000e-97 366
11 TraesCS2B01G150000 chr4B 80.675 326 53 8 1897 2214 606574248 606573925 6.370000e-61 244


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 TraesCS2B01G150000 chr2B 116392521 116394829 2308 True 4265 4265 100.0000 1 2309 1 chr2B.!!$R1 2308
1 TraesCS2B01G150000 chr2A 75633444 75635277 1833 True 1330 2357 92.6605 6 1680 2 chr2A.!!$R1 1674
2 TraesCS2B01G150000 chr2D 75754703 75756369 1666 False 2189 2189 90.2770 3 1696 1 chr2D.!!$F1 1693
3 TraesCS2B01G150000 chr2D 75559491 75560532 1041 False 634 996 90.8975 1218 2309 2 chr2D.!!$F2 1091
4 TraesCS2B01G150000 chr5D 515245036 515245733 697 True 435 435 78.0000 267 963 1 chr5D.!!$R1 696
5 TraesCS2B01G150000 chr3D 436212282 436212808 526 False 431 431 81.6140 1739 2265 1 chr3D.!!$F1 526
6 TraesCS2B01G150000 chr5A 643357680 643358377 697 True 407 407 77.3830 267 963 1 chr5A.!!$R1 696

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
61 62 0.039165 CTTTTGTTGGCTTCTCCGGC 60.039 55.0 0.0 0.0 37.8 6.13 F
62 63 0.467290 TTTTGTTGGCTTCTCCGGCT 60.467 50.0 0.0 0.0 37.8 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1259 0.09820 CGATGCTCGTCGTTAGGTCA 59.902 55.0 3.52 0.0 36.88 4.02 R
1732 1907 0.61782 ATAGGAACTCCTGTGCCGGT 60.618 55.0 8.61 0.0 46.79 5.28 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
31 32 0.742281 CCAACCTCTCCGATGTGCTG 60.742 60.000 0.00 0.00 0.00 4.41
40 41 2.187946 GATGTGCTGGAGGACCCG 59.812 66.667 0.00 0.00 37.93 5.28
58 59 1.266989 CCGTCTTTTGTTGGCTTCTCC 59.733 52.381 0.00 0.00 0.00 3.71
61 62 0.039165 CTTTTGTTGGCTTCTCCGGC 60.039 55.000 0.00 0.00 37.80 6.13
62 63 0.467290 TTTTGTTGGCTTCTCCGGCT 60.467 50.000 0.00 0.00 37.80 5.52
67 68 1.267574 TTGGCTTCTCCGGCTCATCT 61.268 55.000 0.00 0.00 37.80 2.90
195 196 2.032620 GGAGGCTCGATCCAAAGTCTA 58.967 52.381 8.23 0.00 36.79 2.59
238 239 2.385875 CGCAGTGTTCATCGCAGCT 61.386 57.895 0.00 0.00 37.01 4.24
241 242 1.713597 CAGTGTTCATCGCAGCTGTA 58.286 50.000 16.64 4.31 0.00 2.74
383 384 5.574970 AGGATTCAAGAACAAGAACCTCT 57.425 39.130 0.00 0.00 0.00 3.69
409 410 1.889170 GAAGGAGGCTTTGGGAAAGTG 59.111 52.381 0.00 0.00 40.64 3.16
507 508 3.255379 GTTCATCGCCGAGGTCGC 61.255 66.667 0.00 0.00 38.18 5.19
553 554 0.764890 ACCTAGTGCAGTTGCTTGGA 59.235 50.000 0.00 0.00 42.66 3.53
649 650 2.182030 GGAGAGGACAAGCCGACG 59.818 66.667 0.00 0.00 43.43 5.12
736 737 6.183360 ACGAGAAATGGGAAAAAGTTGTCATT 60.183 34.615 0.00 0.00 0.00 2.57
835 836 7.331026 CAAGGTTATATGATCATGGTACCGAT 58.669 38.462 18.72 4.61 0.00 4.18
927 929 4.649674 TCTCCTCTTACGGATGTTTATGCT 59.350 41.667 0.00 0.00 31.43 3.79
966 968 1.137872 GAGGTAGCATGTGGACAGAGG 59.862 57.143 0.00 0.00 0.00 3.69
1029 1031 1.714899 ATTGGGTACGCGAGCATTGC 61.715 55.000 15.93 0.00 43.93 3.56
1066 1068 3.222173 TGCAAACTATGGACACAAGGT 57.778 42.857 0.00 0.00 0.00 3.50
1161 1163 0.744414 GTGCGAGGCCTAGCATGAAA 60.744 55.000 38.03 16.63 42.78 2.69
1182 1184 2.755655 ACAAGTCATGGAGTACCTCGAG 59.244 50.000 5.13 5.13 37.04 4.04
1234 1236 4.140963 CACACATATCAACAACGTCAACG 58.859 43.478 0.12 0.12 46.33 4.10
1287 1289 2.315246 GAGCATCGGCACATTCTCC 58.685 57.895 0.00 0.00 44.61 3.71
1439 1444 4.816126 AGTAGAGTTAGTATGATGCCCCA 58.184 43.478 0.00 0.00 0.00 4.96
1453 1458 3.074538 GATGCCCCAAGGGAATATGTAGT 59.925 47.826 6.74 0.00 42.34 2.73
1570 1731 2.151202 GCCTTTTGCTAGCACAGTGTA 58.849 47.619 19.17 0.00 36.87 2.90
1598 1759 6.090483 TCAAGAGTCAAGACCTACTTTCAG 57.910 41.667 0.00 0.00 36.61 3.02
1607 1768 4.475345 AGACCTACTTTCAGTGTCTCACT 58.525 43.478 0.00 0.00 46.51 3.41
1616 1777 6.042093 ACTTTCAGTGTCTCACTCCAGAAATA 59.958 38.462 11.43 0.00 43.43 1.40
1621 1782 7.038729 TCAGTGTCTCACTCCAGAAATATCTTT 60.039 37.037 0.00 0.00 43.43 2.52
1648 1809 7.878127 GCCTTATTATACTTTCAGCCTGACATA 59.122 37.037 0.00 0.00 0.00 2.29
1649 1810 9.950496 CCTTATTATACTTTCAGCCTGACATAT 57.050 33.333 0.00 0.00 0.00 1.78
1674 1835 1.339535 GCCTAGCCCATATTGCTCTCC 60.340 57.143 0.00 0.00 40.23 3.71
1732 1907 5.193728 AGAATTAAATCTAGTCCAAGGGCCA 59.806 40.000 6.18 0.00 0.00 5.36
1734 1909 0.919710 AATCTAGTCCAAGGGCCACC 59.080 55.000 6.18 0.00 0.00 4.61
1765 1940 2.582226 CTATGCGCCGCTCGTTGA 60.582 61.111 11.67 0.00 41.07 3.18
1841 2016 3.057806 GGGTAACACAGTGAAAAATCCCG 60.058 47.826 7.81 0.00 39.74 5.14
1866 2041 1.002274 AGTGCTCGAGGGAGGGATT 59.998 57.895 15.58 0.00 40.80 3.01
1892 2068 0.320697 GGGACCTCTGTTGCTTACGT 59.679 55.000 0.00 0.00 0.00 3.57
1967 2143 4.778213 AGCTAAAGGCAATGTAGATCCA 57.222 40.909 0.00 0.00 44.79 3.41
1975 2151 5.969423 AGGCAATGTAGATCCAAACATTTG 58.031 37.500 13.27 10.87 42.22 2.32
1989 2165 6.595772 CAAACATTTGGTCAAATTCCGAAA 57.404 33.333 6.23 0.00 38.84 3.46
1995 2171 2.619177 TGGTCAAATTCCGAAAGCGAAA 59.381 40.909 0.00 0.00 40.82 3.46
2001 2177 7.383361 GTCAAATTCCGAAAGCGAAAATTATG 58.617 34.615 0.00 0.00 40.82 1.90
2013 2189 8.419076 AAGCGAAAATTATGTTGAAAAAGTGT 57.581 26.923 0.00 0.00 0.00 3.55
2070 2246 9.502091 GGGAAGAAAAATTAAAAGCTAAACCAT 57.498 29.630 0.00 0.00 0.00 3.55
2149 2327 8.751335 ACGAACATTTTTGAATATGTGAACAAC 58.249 29.630 0.00 0.00 35.29 3.32
2172 2351 9.767684 CAACTTTTTGTTAAAGGGAACATTTTC 57.232 29.630 0.00 0.00 39.04 2.29
2184 2363 8.712228 AAGGGAACATTTTCTAAAACTCTGAT 57.288 30.769 0.00 0.00 31.71 2.90
2185 2364 8.712228 AGGGAACATTTTCTAAAACTCTGATT 57.288 30.769 0.00 0.00 31.71 2.57
2186 2365 9.147732 AGGGAACATTTTCTAAAACTCTGATTT 57.852 29.630 0.00 0.00 31.71 2.17
2187 2366 9.764363 GGGAACATTTTCTAAAACTCTGATTTT 57.236 29.630 0.00 0.00 35.89 1.82
2214 2395 7.938563 TTGGAAACACGAATATTTTTGGAAG 57.061 32.000 0.00 0.00 42.67 3.46
2225 2406 7.148918 CGAATATTTTTGGAAGCTGTGAACAAG 60.149 37.037 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.033448 GGTTGGTGATGGCGGTGA 59.967 61.111 0.00 0.00 0.00 4.02
2 3 2.185310 GAGAGGTTGGTGATGGCGGT 62.185 60.000 0.00 0.00 0.00 5.68
3 4 1.450312 GAGAGGTTGGTGATGGCGG 60.450 63.158 0.00 0.00 0.00 6.13
4 5 1.450312 GGAGAGGTTGGTGATGGCG 60.450 63.158 0.00 0.00 0.00 5.69
31 32 1.235724 CAACAAAAGACGGGTCCTCC 58.764 55.000 0.00 0.00 0.00 4.30
40 41 1.266989 CCGGAGAAGCCAACAAAAGAC 59.733 52.381 0.00 0.00 35.94 3.01
58 59 1.227205 GAGTGAGCCAGATGAGCCG 60.227 63.158 0.00 0.00 0.00 5.52
61 62 3.365976 GCTGAGTGAGCCAGATGAG 57.634 57.895 0.00 0.00 42.54 2.90
84 85 0.034896 CCAACCAAGCACGGAGTAGT 59.965 55.000 0.00 0.00 41.61 2.73
195 196 4.338815 TCGGAAGGACGATCTGCT 57.661 55.556 0.00 0.00 38.06 4.24
238 239 1.600107 GGTGATGGCGGTTCCTACA 59.400 57.895 0.00 0.00 35.26 2.74
241 242 2.198304 GAAGGGTGATGGCGGTTCCT 62.198 60.000 0.00 0.00 35.26 3.36
383 384 1.603455 CAAAGCCTCCTTCGCCCAA 60.603 57.895 0.00 0.00 0.00 4.12
385 386 2.751837 CCAAAGCCTCCTTCGCCC 60.752 66.667 0.00 0.00 0.00 6.13
507 508 0.742990 TCGAAGGCGGCCAATACTTG 60.743 55.000 23.09 3.51 38.28 3.16
553 554 0.662619 CATGTTCACGCCGGCAATAT 59.337 50.000 28.98 14.17 0.00 1.28
649 650 1.298014 CCTCTGGGTCCAGTCAAGC 59.702 63.158 15.77 0.00 43.96 4.01
673 674 4.157840 CCACATGCTATCCCATTGATGATG 59.842 45.833 0.00 0.00 34.76 3.07
736 737 7.337689 ACATTGCTTGCTTTTATGTCTCTATGA 59.662 33.333 0.00 0.00 0.00 2.15
927 929 2.813754 CTCAAGAAGGAATGTGCCGAAA 59.186 45.455 0.00 0.00 0.00 3.46
966 968 2.128771 TGGAGTCTTGCTTAATGGGC 57.871 50.000 0.00 0.00 0.00 5.36
1029 1031 0.890683 GCAAGAGGGTTCCATTGTGG 59.109 55.000 0.00 0.00 39.43 4.17
1066 1068 5.249622 TGTCCTTGTCATAGTTACCATGGAA 59.750 40.000 21.47 5.58 34.23 3.53
1182 1184 3.902086 GGTAGCGCGGTCTCTCCC 61.902 72.222 16.92 4.52 0.00 4.30
1204 1206 3.872696 TGTTGATATGTGTGGGTGCTAG 58.127 45.455 0.00 0.00 0.00 3.42
1206 1208 2.819608 GTTGTTGATATGTGTGGGTGCT 59.180 45.455 0.00 0.00 0.00 4.40
1234 1236 3.119352 GGAAATCCTCTGGTTTGCATCAC 60.119 47.826 0.00 0.00 0.00 3.06
1257 1259 0.098200 CGATGCTCGTCGTTAGGTCA 59.902 55.000 3.52 0.00 36.88 4.02
1412 1417 9.032624 GGGGCATCATACTAACTCTACTAATTA 57.967 37.037 0.00 0.00 0.00 1.40
1423 1428 2.441750 TCCCTTGGGGCATCATACTAAC 59.558 50.000 5.78 0.00 43.94 2.34
1439 1444 7.255871 GGTCACTCGATTACTACATATTCCCTT 60.256 40.741 0.00 0.00 0.00 3.95
1453 1458 2.927028 TCTGATCGGGTCACTCGATTA 58.073 47.619 15.28 9.47 45.81 1.75
1458 1463 5.704888 CTTATACATCTGATCGGGTCACTC 58.295 45.833 0.62 0.00 32.22 3.51
1570 1731 6.426646 AGTAGGTCTTGACTCTTGAATGTT 57.573 37.500 0.61 0.00 0.00 2.71
1598 1759 6.183360 GCAAAGATATTTCTGGAGTGAGACAC 60.183 42.308 0.00 0.00 30.72 3.67
1616 1777 8.001292 AGGCTGAAAGTATAATAAGGCAAAGAT 58.999 33.333 0.00 0.00 35.30 2.40
1621 1782 6.055588 GTCAGGCTGAAAGTATAATAAGGCA 58.944 40.000 20.62 0.00 35.30 4.75
1712 1882 3.053917 GGTGGCCCTTGGACTAGATTTAA 60.054 47.826 0.00 0.00 0.00 1.52
1732 1907 0.617820 ATAGGAACTCCTGTGCCGGT 60.618 55.000 8.61 0.00 46.79 5.28
1734 1909 3.369381 CATAGGAACTCCTGTGCCG 57.631 57.895 9.29 0.00 46.79 5.69
1790 1965 4.007644 CCCAGCTGGAGTCGCACA 62.008 66.667 34.91 0.00 37.39 4.57
1818 1993 3.257375 GGGATTTTTCACTGTGTTACCCC 59.743 47.826 7.79 8.45 0.00 4.95
1824 1999 4.204012 TCTTTCGGGATTTTTCACTGTGT 58.796 39.130 7.79 0.00 0.00 3.72
1841 2016 1.134175 CTCCCTCGAGCACTCTCTTTC 59.866 57.143 6.99 0.00 37.19 2.62
1866 2041 1.476833 GCAACAGAGGTCCCTTGTTCA 60.477 52.381 5.79 0.00 0.00 3.18
1892 2068 2.499205 CCGTTGGATAGGCTCGCA 59.501 61.111 0.00 0.00 0.00 5.10
1967 2143 5.236263 GCTTTCGGAATTTGACCAAATGTTT 59.764 36.000 8.55 0.00 40.57 2.83
1975 2151 2.981400 TTCGCTTTCGGAATTTGACC 57.019 45.000 0.00 0.00 36.13 4.02
1989 2165 8.419076 AACACTTTTTCAACATAATTTTCGCT 57.581 26.923 0.00 0.00 0.00 4.93
2021 2197 8.100164 TCCCAAATTTGAAAAGTGTTCTCTTTT 58.900 29.630 19.86 10.86 46.14 2.27
2026 2202 7.181569 TCTTCCCAAATTTGAAAAGTGTTCT 57.818 32.000 19.86 0.00 0.00 3.01
2105 2282 9.581099 AATGTTCGTGATTTTAAAGAAGTGTTT 57.419 25.926 0.00 0.00 0.00 2.83
2187 2366 8.718102 TCCAAAAATATTCGTGTTTCCAAAAA 57.282 26.923 0.00 0.00 0.00 1.94
2197 2378 5.698832 TCACAGCTTCCAAAAATATTCGTG 58.301 37.500 0.00 0.00 0.00 4.35
2198 2379 5.957842 TCACAGCTTCCAAAAATATTCGT 57.042 34.783 0.00 0.00 0.00 3.85
2214 2395 5.633182 TCTTGTTTCAAAACTTGTTCACAGC 59.367 36.000 7.12 0.00 39.59 4.40


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

AutoCloner maintained by Alex Coulton.