Multiple sequence alignment - TraesCS4A01G123500

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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 TraesCS4A01G123500 chr4A 100.000 2234 0 0 1 2234 155593032 155595265 0.000000e+00 4126.0
1 TraesCS4A01G123500 chr4A 79.487 351 49 12 1901 2234 540963525 540963181 6.210000e-56 228.0
2 TraesCS4A01G123500 chr4A 81.008 258 40 9 1957 2211 676230505 676230756 1.750000e-46 196.0
3 TraesCS4A01G123500 chr4D 91.298 2126 105 44 127 2234 318607301 318605238 0.000000e+00 2828.0
4 TraesCS4A01G123500 chr4D 98.214 56 1 0 61 116 318607529 318607474 5.080000e-17 99.0
5 TraesCS4A01G123500 chr4D 95.082 61 2 1 1 61 318607680 318607621 6.570000e-16 95.3
6 TraesCS4A01G123500 chr4B 89.872 2261 110 58 1 2232 395911562 395909392 0.000000e+00 2796.0
7 TraesCS4A01G123500 chr6A 78.739 555 80 27 1661 2211 50933512 50934032 9.880000e-89 337.0
8 TraesCS4A01G123500 chr7A 79.503 483 57 21 1755 2223 468932146 468932600 2.790000e-79 305.0
9 TraesCS4A01G123500 chr7A 81.481 135 19 4 2094 2226 83700308 83700178 3.030000e-19 106.0
10 TraesCS4A01G123500 chr1A 78.814 472 64 25 1790 2234 521712531 521712069 3.630000e-73 285.0
11 TraesCS4A01G123500 chr7D 78.810 420 50 20 1831 2234 408740486 408740882 1.710000e-61 246.0
12 TraesCS4A01G123500 chr7B 77.660 376 60 14 1865 2234 544439770 544440127 8.090000e-50 207.0
13 TraesCS4A01G123500 chr5D 79.062 320 41 18 1930 2234 513547571 513547263 1.750000e-46 196.0
14 TraesCS4A01G123500 chr2A 76.399 411 64 24 1834 2224 498577018 498577415 8.140000e-45 191.0
15 TraesCS4A01G123500 chr6B 80.784 255 33 11 1985 2234 188700418 188700175 3.790000e-43 185.0


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 TraesCS4A01G123500 chr4A 155593032 155595265 2233 False 4126.000000 4126 100.000000 1 2234 1 chr4A.!!$F1 2233
1 TraesCS4A01G123500 chr4D 318605238 318607680 2442 True 1007.433333 2828 94.864667 1 2234 3 chr4D.!!$R1 2233
2 TraesCS4A01G123500 chr4B 395909392 395911562 2170 True 2796.000000 2796 89.872000 1 2232 1 chr4B.!!$R1 2231
3 TraesCS4A01G123500 chr6A 50933512 50934032 520 False 337.000000 337 78.739000 1661 2211 1 chr6A.!!$F1 550

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
907 1177 0.097674 GAACGATGCATGCGAGCTTT 59.902 50.0 20.36 5.09 34.99 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1989 1.739067 ATGTGTAAAAGCCGGCTCTC 58.261 50.0 32.93 18.16 0.0 3.2 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
42 43 1.272490 TCTGTACTCTCGGTGCAAAGG 59.728 52.381 0.00 0.00 39.86 3.11
96 188 0.107066 TGGACCGCATGCATTCTGAT 60.107 50.000 19.57 0.00 0.00 2.90
117 209 5.655974 TGATCTGGAGGAGTCTGCATATATC 59.344 44.000 0.00 0.00 40.54 1.63
118 210 4.348486 TCTGGAGGAGTCTGCATATATCC 58.652 47.826 0.00 0.00 40.54 2.59
119 211 4.045207 TCTGGAGGAGTCTGCATATATCCT 59.955 45.833 9.05 9.05 43.08 3.24
120 212 5.254032 TCTGGAGGAGTCTGCATATATCCTA 59.746 44.000 9.22 0.00 40.48 2.94
121 213 5.265191 TGGAGGAGTCTGCATATATCCTAC 58.735 45.833 11.05 11.05 40.48 3.18
122 214 5.015710 TGGAGGAGTCTGCATATATCCTACT 59.984 44.000 16.37 0.00 41.00 2.57
123 215 6.217693 TGGAGGAGTCTGCATATATCCTACTA 59.782 42.308 16.37 5.14 41.00 1.82
124 216 6.544564 GGAGGAGTCTGCATATATCCTACTAC 59.455 46.154 10.80 0.00 40.48 2.73
144 398 7.377766 ACTACTTACTTAACGTCGGTGATTA 57.622 36.000 0.00 0.00 0.00 1.75
473 731 8.365060 TGATCTCTCTTCTCTCTGAAAAAGAT 57.635 34.615 0.00 0.00 33.29 2.40
474 732 8.252417 TGATCTCTCTTCTCTCTGAAAAAGATG 58.748 37.037 0.00 0.00 33.29 2.90
475 733 6.934056 TCTCTCTTCTCTCTGAAAAAGATGG 58.066 40.000 0.00 0.00 33.29 3.51
476 734 5.486526 TCTCTTCTCTCTGAAAAAGATGGC 58.513 41.667 0.00 0.00 33.29 4.40
477 735 4.248859 TCTTCTCTCTGAAAAAGATGGCG 58.751 43.478 0.00 0.00 33.29 5.69
478 736 2.350522 TCTCTCTGAAAAAGATGGCGC 58.649 47.619 0.00 0.00 33.29 6.53
479 737 1.399791 CTCTCTGAAAAAGATGGCGCC 59.600 52.381 22.73 22.73 33.29 6.53
480 738 1.003580 TCTCTGAAAAAGATGGCGCCT 59.996 47.619 29.70 13.55 33.29 5.52
481 739 2.236146 TCTCTGAAAAAGATGGCGCCTA 59.764 45.455 29.70 14.84 33.29 3.93
482 740 2.352960 CTCTGAAAAAGATGGCGCCTAC 59.647 50.000 29.70 20.74 33.29 3.18
483 741 1.401905 CTGAAAAAGATGGCGCCTACC 59.598 52.381 29.70 16.22 0.00 3.18
484 742 1.271652 TGAAAAAGATGGCGCCTACCA 60.272 47.619 29.70 7.47 45.82 3.25
491 749 1.760527 TGGCGCCTACCATATGCAT 59.239 52.632 29.70 3.79 33.75 3.96
518 776 1.071299 TGGCGCCTACCATATGCAG 59.929 57.895 29.70 0.00 33.75 4.41
707 976 4.671569 GCCGCGCCCCTATCTCTG 62.672 72.222 0.00 0.00 0.00 3.35
757 1026 1.344953 TTCGCATATGGGGGAGTGCT 61.345 55.000 18.68 0.00 35.52 4.40
834 1104 6.406370 CCGATACATCCCTATCAAAGCATAA 58.594 40.000 0.00 0.00 0.00 1.90
874 1144 0.640262 CGGCTATATATGCGTGCACG 59.360 55.000 34.01 34.01 43.27 5.34
907 1177 0.097674 GAACGATGCATGCGAGCTTT 59.902 50.000 20.36 5.09 34.99 3.51
911 1181 0.097674 GATGCATGCGAGCTTTCGTT 59.902 50.000 14.09 0.00 34.99 3.85
923 1193 4.547532 GAGCTTTCGTTGAAGACTAGTCA 58.452 43.478 24.44 1.89 0.00 3.41
945 1215 2.900546 TCTCTTCTTCGGCCTCTTTTCT 59.099 45.455 0.00 0.00 0.00 2.52
959 1229 1.538950 CTTTTCTCTCCTTGCTGTGGC 59.461 52.381 0.00 0.00 39.26 5.01
1025 1299 1.153269 GGAGTAGCAGGAGCAAGGC 60.153 63.158 0.00 0.00 45.49 4.35
1026 1300 1.520342 GAGTAGCAGGAGCAAGGCG 60.520 63.158 0.00 0.00 45.49 5.52
1027 1301 2.512515 GTAGCAGGAGCAAGGCGG 60.513 66.667 0.00 0.00 45.49 6.13
1028 1302 3.003173 TAGCAGGAGCAAGGCGGT 61.003 61.111 0.00 0.00 45.49 5.68
1029 1303 3.315142 TAGCAGGAGCAAGGCGGTG 62.315 63.158 0.00 0.00 45.49 4.94
1031 1305 2.743928 CAGGAGCAAGGCGGTGTC 60.744 66.667 0.00 0.00 0.00 3.67
1032 1306 4.379243 AGGAGCAAGGCGGTGTCG 62.379 66.667 0.00 0.00 39.81 4.35
1283 1557 1.689959 CAAATTTGTGGACGCTCTGC 58.310 50.000 10.15 0.00 0.00 4.26
1299 1573 2.407268 TGCCGATGCATGAATGGAC 58.593 52.632 2.46 0.00 44.23 4.02
1307 1581 0.966875 GCATGAATGGACCCACAGCA 60.967 55.000 0.00 0.00 0.00 4.41
1395 1672 1.560923 CTTCACGTTCGATAGGGCAG 58.439 55.000 0.00 0.00 0.00 4.85
1401 1678 3.001330 CACGTTCGATAGGGCAGATTTTC 59.999 47.826 0.00 0.00 0.00 2.29
1424 1701 8.571461 TTCTTGTTATGCTCTTTGATTCATCT 57.429 30.769 0.00 0.00 0.00 2.90
1425 1702 9.671279 TTCTTGTTATGCTCTTTGATTCATCTA 57.329 29.630 0.00 0.00 0.00 1.98
1450 1727 3.774766 TGCTATCAGGGTGTGTGTATCTT 59.225 43.478 0.00 0.00 0.00 2.40
1577 1854 1.066002 CAGTTATGCAATGAAGGCCCG 59.934 52.381 0.00 0.00 0.00 6.13
1600 1877 8.413229 CCCGATTATTTTGGTGACTTCAATTAT 58.587 33.333 0.00 0.00 0.00 1.28
1616 1893 5.806818 TCAATTATAGGGGTTCAAACGACA 58.193 37.500 0.00 0.00 0.00 4.35
1623 1900 1.563111 GGTTCAAACGACACGAGTGA 58.437 50.000 10.50 0.00 0.00 3.41
1644 1921 0.852777 GTATCATCGTTGCATCGCGT 59.147 50.000 12.30 1.03 0.00 6.01
1659 1936 0.109458 CGCGTCACTGTTAGCCACTA 60.109 55.000 0.00 0.00 0.00 2.74
1698 1975 4.612536 CAATTCATCGGGCGCGGC 62.613 66.667 26.39 26.39 0.00 6.53
1712 1989 0.030908 CGCGGCCTACTAGAAGGAAG 59.969 60.000 0.00 0.00 39.15 3.46
1734 2011 2.488153 AGAGCCGGCTTTTACACATTTC 59.512 45.455 33.34 13.37 0.00 2.17
1738 2015 4.521256 AGCCGGCTTTTACACATTTCTTTA 59.479 37.500 27.08 0.00 0.00 1.85
1741 2018 6.201234 GCCGGCTTTTACACATTTCTTTAAAA 59.799 34.615 22.15 0.00 0.00 1.52
1742 2019 7.254488 GCCGGCTTTTACACATTTCTTTAAAAA 60.254 33.333 22.15 0.00 0.00 1.94
1835 2125 2.608640 CGGTTTCCGTCGGTTTCTT 58.391 52.632 11.88 0.00 42.73 2.52
1836 2126 0.939419 CGGTTTCCGTCGGTTTCTTT 59.061 50.000 11.88 0.00 42.73 2.52
1837 2127 1.331447 CGGTTTCCGTCGGTTTCTTTT 59.669 47.619 11.88 0.00 42.73 2.27
1838 2128 2.223317 CGGTTTCCGTCGGTTTCTTTTT 60.223 45.455 11.88 0.00 42.73 1.94
1839 2129 3.365832 GGTTTCCGTCGGTTTCTTTTTC 58.634 45.455 11.88 0.00 0.00 2.29
1840 2130 3.065786 GGTTTCCGTCGGTTTCTTTTTCT 59.934 43.478 11.88 0.00 0.00 2.52
1841 2131 4.439153 GGTTTCCGTCGGTTTCTTTTTCTT 60.439 41.667 11.88 0.00 0.00 2.52
1842 2132 4.968812 TTCCGTCGGTTTCTTTTTCTTT 57.031 36.364 11.88 0.00 0.00 2.52
1843 2133 4.968812 TCCGTCGGTTTCTTTTTCTTTT 57.031 36.364 11.88 0.00 0.00 2.27
1844 2134 4.664188 TCCGTCGGTTTCTTTTTCTTTTG 58.336 39.130 11.88 0.00 0.00 2.44
1845 2135 4.156373 TCCGTCGGTTTCTTTTTCTTTTGT 59.844 37.500 11.88 0.00 0.00 2.83
1846 2136 4.860352 CCGTCGGTTTCTTTTTCTTTTGTT 59.140 37.500 2.08 0.00 0.00 2.83
1847 2137 5.346551 CCGTCGGTTTCTTTTTCTTTTGTTT 59.653 36.000 2.08 0.00 0.00 2.83
1848 2138 6.453265 CCGTCGGTTTCTTTTTCTTTTGTTTC 60.453 38.462 2.08 0.00 0.00 2.78
1987 2286 7.491048 TGCTTTTCTATGTGTCTTTTGGTTTTC 59.509 33.333 0.00 0.00 0.00 2.29
1998 2297 9.959749 GTGTCTTTTGGTTTTCATTCTACATTA 57.040 29.630 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.541863 TAGCTAGCTTGCAGGTTCCC 59.458 55.000 24.88 0.00 34.99 3.97
96 188 4.045207 AGGATATATGCAGACTCCTCCAGA 59.955 45.833 8.19 0.00 30.45 3.86
117 209 5.351465 TCACCGACGTTAAGTAAGTAGTAGG 59.649 44.000 0.00 0.00 0.00 3.18
118 210 6.408858 TCACCGACGTTAAGTAAGTAGTAG 57.591 41.667 0.00 0.00 0.00 2.57
119 211 6.985188 ATCACCGACGTTAAGTAAGTAGTA 57.015 37.500 0.00 0.00 0.00 1.82
120 212 5.886960 ATCACCGACGTTAAGTAAGTAGT 57.113 39.130 0.00 0.00 0.00 2.73
121 213 6.909357 CCTAATCACCGACGTTAAGTAAGTAG 59.091 42.308 0.00 0.00 0.00 2.57
122 214 6.597672 TCCTAATCACCGACGTTAAGTAAGTA 59.402 38.462 0.00 0.00 0.00 2.24
123 215 5.415701 TCCTAATCACCGACGTTAAGTAAGT 59.584 40.000 0.00 0.00 0.00 2.24
124 216 5.883661 TCCTAATCACCGACGTTAAGTAAG 58.116 41.667 0.00 0.00 0.00 2.34
144 398 7.603024 CGTTAGGAAAACTTTTCATAGACTCCT 59.397 37.037 14.76 4.89 0.00 3.69
187 445 1.421485 CTTGCACCGATCGAGCAAC 59.579 57.895 30.62 13.01 42.71 4.17
473 731 0.980423 TATGCATATGGTAGGCGCCA 59.020 50.000 31.54 12.31 43.48 5.69
474 732 1.338674 TGTATGCATATGGTAGGCGCC 60.339 52.381 21.89 21.89 38.52 6.53
475 733 2.093306 TGTATGCATATGGTAGGCGC 57.907 50.000 10.16 0.00 38.52 6.53
476 734 5.660460 TCTATTGTATGCATATGGTAGGCG 58.340 41.667 10.16 0.00 38.52 5.52
477 735 6.484643 CCATCTATTGTATGCATATGGTAGGC 59.515 42.308 10.16 0.00 35.76 3.93
478 736 6.484643 GCCATCTATTGTATGCATATGGTAGG 59.515 42.308 18.95 11.42 35.81 3.18
479 737 6.201615 CGCCATCTATTGTATGCATATGGTAG 59.798 42.308 18.95 15.51 35.81 3.18
480 738 6.048509 CGCCATCTATTGTATGCATATGGTA 58.951 40.000 18.95 8.67 35.81 3.25
481 739 4.877823 CGCCATCTATTGTATGCATATGGT 59.122 41.667 18.95 8.09 35.81 3.55
482 740 4.260907 GCGCCATCTATTGTATGCATATGG 60.261 45.833 10.16 13.24 36.35 2.74
483 741 4.260907 GGCGCCATCTATTGTATGCATATG 60.261 45.833 24.80 3.04 0.00 1.78
484 742 3.879295 GGCGCCATCTATTGTATGCATAT 59.121 43.478 24.80 0.00 0.00 1.78
486 744 2.086869 GGCGCCATCTATTGTATGCAT 58.913 47.619 24.80 3.79 0.00 3.96
491 749 2.321719 TGGTAGGCGCCATCTATTGTA 58.678 47.619 31.54 6.42 32.81 2.41
518 776 4.201532 GCAGATGTTCGTATCGTATGCATC 60.202 45.833 0.19 0.00 38.43 3.91
705 974 0.949105 GCCACGAACCACCTACACAG 60.949 60.000 0.00 0.00 0.00 3.66
707 976 2.025418 CGCCACGAACCACCTACAC 61.025 63.158 0.00 0.00 0.00 2.90
757 1026 0.040246 CATGTGTGTGTTCATGCGCA 60.040 50.000 14.96 14.96 35.72 6.09
834 1104 3.115554 GCAATCTTTGTTGTTTCTGCGT 58.884 40.909 0.00 0.00 0.00 5.24
907 1177 5.941058 AGAAGAGATGACTAGTCTTCAACGA 59.059 40.000 30.01 9.79 45.83 3.85
911 1181 5.355630 CCGAAGAAGAGATGACTAGTCTTCA 59.644 44.000 30.01 12.30 45.83 3.02
923 1193 3.517500 AGAAAAGAGGCCGAAGAAGAGAT 59.482 43.478 0.00 0.00 0.00 2.75
945 1215 2.922503 TCGGCCACAGCAAGGAGA 60.923 61.111 2.24 0.00 42.56 3.71
978 1252 3.708220 CTTCTCGGCCCAGCTCGAC 62.708 68.421 0.00 0.00 30.88 4.20
980 1254 3.423162 CTCTTCTCGGCCCAGCTCG 62.423 68.421 0.00 0.00 0.00 5.03
1033 1307 4.537433 ATGCTTCTCGCCCGCCTC 62.537 66.667 0.00 0.00 38.05 4.70
1053 1327 6.045955 CAGTACCCTAGAATCTTCTTCAAGC 58.954 44.000 0.00 0.00 38.70 4.01
1057 1331 5.657302 TCACCAGTACCCTAGAATCTTCTTC 59.343 44.000 0.00 0.00 38.70 2.87
1058 1332 5.590818 TCACCAGTACCCTAGAATCTTCTT 58.409 41.667 0.00 0.00 38.70 2.52
1059 1333 5.208294 TCACCAGTACCCTAGAATCTTCT 57.792 43.478 0.00 0.00 41.24 2.85
1283 1557 0.466007 TGGGTCCATTCATGCATCGG 60.466 55.000 0.00 0.00 0.00 4.18
1299 1573 5.643379 AATAGTATGTTTGTTGCTGTGGG 57.357 39.130 0.00 0.00 0.00 4.61
1373 1650 1.068741 GCCCTATCGAACGTGAAGGAT 59.931 52.381 0.00 0.00 0.00 3.24
1379 1656 2.225068 AATCTGCCCTATCGAACGTG 57.775 50.000 0.00 0.00 0.00 4.49
1395 1672 9.630098 TGAATCAAAGAGCATAACAAGAAAATC 57.370 29.630 0.00 0.00 0.00 2.17
1424 1701 6.954102 AGATACACACACCCTGATAGCATATA 59.046 38.462 0.00 0.00 0.00 0.86
1425 1702 5.782331 AGATACACACACCCTGATAGCATAT 59.218 40.000 0.00 0.00 0.00 1.78
1450 1727 1.270094 ACTCACTGGAAATCGCAACGA 60.270 47.619 0.00 0.00 41.13 3.85
1600 1877 1.000060 CTCGTGTCGTTTGAACCCCTA 60.000 52.381 0.00 0.00 0.00 3.53
1616 1893 3.116300 GCAACGATGATACATCACTCGT 58.884 45.455 16.74 16.74 44.60 4.18
1623 1900 1.456923 CGCGATGCAACGATGATACAT 59.543 47.619 21.39 0.00 35.09 2.29
1644 1921 1.067846 CAGCGTAGTGGCTAACAGTGA 60.068 52.381 0.00 0.00 42.53 3.41
1659 1936 1.081376 CGGAACTCGAAGTCAGCGT 60.081 57.895 0.00 0.00 42.43 5.07
1698 1975 2.882137 CGGCTCTCTTCCTTCTAGTAGG 59.118 54.545 9.09 9.09 36.59 3.18
1712 1989 1.739067 ATGTGTAAAAGCCGGCTCTC 58.261 50.000 32.93 18.16 0.00 3.20
1744 2021 6.238925 CCAAGAAAGATACAAAAACCGAGGTT 60.239 38.462 0.93 0.93 40.45 3.50
1745 2022 5.240844 CCAAGAAAGATACAAAAACCGAGGT 59.759 40.000 0.00 0.00 0.00 3.85
1746 2023 5.240844 ACCAAGAAAGATACAAAAACCGAGG 59.759 40.000 0.00 0.00 0.00 4.63
1747 2024 6.313744 ACCAAGAAAGATACAAAAACCGAG 57.686 37.500 0.00 0.00 0.00 4.63
1786 2066 5.772169 ACAGAAGAAATGGAGAAAGAAAGGG 59.228 40.000 0.00 0.00 0.00 3.95
1787 2067 6.890979 ACAGAAGAAATGGAGAAAGAAAGG 57.109 37.500 0.00 0.00 0.00 3.11
1825 2107 7.576750 AGAAACAAAAGAAAAAGAAACCGAC 57.423 32.000 0.00 0.00 0.00 4.79
1872 2162 6.622833 AGAAACAAATGCAAAAAGAATGGG 57.377 33.333 0.00 0.00 0.00 4.00
1873 2163 6.847289 CGAAGAAACAAATGCAAAAAGAATGG 59.153 34.615 0.00 0.00 0.00 3.16
1970 2265 8.006298 TGTAGAATGAAAACCAAAAGACACAT 57.994 30.769 0.00 0.00 0.00 3.21
2112 2416 8.667987 TTAATCTTGCGCTTAAACAATGTTAG 57.332 30.769 9.73 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.