Multiple sequence alignment - TraesCS4B01G349200

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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 TraesCS4B01G349200 chr4B 100.000 2261 0 0 1 2261 642454628 642456888 0.000000e+00 4176
1 TraesCS4B01G349200 chr4D 86.743 2278 109 81 50 2261 499500650 499502800 0.000000e+00 2355
2 TraesCS4B01G349200 chr5A 82.340 1325 112 48 1 1271 680501201 680502457 0.000000e+00 1038
3 TraesCS4B01G349200 chr5A 90.710 183 13 3 2083 2261 680502706 680502888 8.070000e-60 241


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 TraesCS4B01G349200 chr4B 642454628 642456888 2260 False 4176.0 4176 100.000 1 2261 1 chr4B.!!$F1 2260
1 TraesCS4B01G349200 chr4D 499500650 499502800 2150 False 2355.0 2355 86.743 50 2261 1 chr4D.!!$F1 2211
2 TraesCS4B01G349200 chr5A 680501201 680502888 1687 False 639.5 1038 86.525 1 2261 2 chr5A.!!$F1 2260

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
710 754 0.100503 GCACGGCGCCATTAATTTCT 59.899 50.0 28.98 0.0 32.94 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 1773 0.031857 CCAGCATAGAGAGTCAGCCG 59.968 60.0 0.0 0.0 0.0 5.52 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
96 101 7.336427 CAGCATCTAAAGAAATCACTTTCCTCT 59.664 37.037 0.00 0.00 41.46 3.69
131 136 2.027745 AGATGGAAAGAAAGCGAGCTCA 60.028 45.455 15.40 0.00 0.00 4.26
283 288 0.469917 CGGGCACATACCTTCCTCAT 59.530 55.000 0.00 0.00 0.00 2.90
293 298 3.347077 ACCTTCCTCATTCTCTTGCTG 57.653 47.619 0.00 0.00 0.00 4.41
294 299 2.026449 ACCTTCCTCATTCTCTTGCTGG 60.026 50.000 0.00 0.00 0.00 4.85
295 300 2.026449 CCTTCCTCATTCTCTTGCTGGT 60.026 50.000 0.00 0.00 0.00 4.00
296 301 2.775911 TCCTCATTCTCTTGCTGGTG 57.224 50.000 0.00 0.00 0.00 4.17
297 302 1.093159 CCTCATTCTCTTGCTGGTGC 58.907 55.000 0.00 0.00 40.20 5.01
298 303 1.339824 CCTCATTCTCTTGCTGGTGCT 60.340 52.381 0.00 0.00 40.48 4.40
331 336 4.880696 GCCTATGATAAATCTCATGCCTCC 59.119 45.833 0.00 0.00 36.55 4.30
365 375 4.860072 AGAAATGTTTCTCCTGAAAACGC 58.140 39.130 2.25 0.00 43.72 4.84
466 495 3.118629 TGCCAGATCGGATAATATCTGCC 60.119 47.826 4.24 0.00 45.09 4.85
468 497 4.739137 GCCAGATCGGATAATATCTGCCTC 60.739 50.000 4.24 4.32 45.09 4.70
514 543 1.508088 CTTGCCATGACCGCCTTTC 59.492 57.895 0.00 0.00 0.00 2.62
631 675 9.492730 AAAGGAAAAATGATATCCCATTACAGT 57.507 29.630 0.00 0.00 35.86 3.55
633 677 9.574516 AGGAAAAATGATATCCCATTACAGTAC 57.425 33.333 0.00 0.00 35.86 2.73
710 754 0.100503 GCACGGCGCCATTAATTTCT 59.899 50.000 28.98 0.00 32.94 2.52
713 757 3.550030 GCACGGCGCCATTAATTTCTTAT 60.550 43.478 28.98 0.00 32.94 1.73
715 759 3.880490 ACGGCGCCATTAATTTCTTATGA 59.120 39.130 28.98 0.00 0.00 2.15
761 811 3.195698 GAGCGGTTCGTGATGCCC 61.196 66.667 0.00 0.00 0.00 5.36
855 924 3.292492 AAAAACCTTCCCGTTCTGTCT 57.708 42.857 0.00 0.00 0.00 3.41
857 926 2.256117 AACCTTCCCGTTCTGTCTTG 57.744 50.000 0.00 0.00 0.00 3.02
890 964 0.404040 GGGTTGGATCCAAGTGTCCA 59.596 55.000 27.73 0.98 42.55 4.02
922 996 2.645802 ACGGCTACGAGAAATCTCTCT 58.354 47.619 8.67 0.00 45.26 3.10
923 997 2.614983 ACGGCTACGAGAAATCTCTCTC 59.385 50.000 8.67 0.00 45.26 3.20
924 998 2.875933 CGGCTACGAGAAATCTCTCTCT 59.124 50.000 8.67 0.00 45.26 3.10
925 999 3.059188 CGGCTACGAGAAATCTCTCTCTC 60.059 52.174 8.67 0.00 45.26 3.20
926 1000 4.134563 GGCTACGAGAAATCTCTCTCTCT 58.865 47.826 8.67 0.00 45.26 3.10
927 1001 4.213482 GGCTACGAGAAATCTCTCTCTCTC 59.787 50.000 8.67 0.00 45.26 3.20
928 1002 5.057149 GCTACGAGAAATCTCTCTCTCTCT 58.943 45.833 8.67 0.00 45.26 3.10
929 1003 5.177696 GCTACGAGAAATCTCTCTCTCTCTC 59.822 48.000 8.67 0.00 45.26 3.20
930 1004 5.359194 ACGAGAAATCTCTCTCTCTCTCT 57.641 43.478 8.67 0.00 45.26 3.10
931 1005 5.360591 ACGAGAAATCTCTCTCTCTCTCTC 58.639 45.833 8.67 0.00 45.26 3.20
932 1006 5.129485 ACGAGAAATCTCTCTCTCTCTCTCT 59.871 44.000 8.67 0.00 45.26 3.10
1066 1164 4.899239 GGCACTGGATCGAGCGGG 62.899 72.222 4.41 0.00 0.00 6.13
1067 1165 4.148825 GCACTGGATCGAGCGGGT 62.149 66.667 4.41 0.00 0.00 5.28
1068 1166 2.202797 CACTGGATCGAGCGGGTG 60.203 66.667 4.41 9.50 0.00 4.61
1069 1167 3.461773 ACTGGATCGAGCGGGTGG 61.462 66.667 4.41 0.00 0.00 4.61
1070 1168 4.899239 CTGGATCGAGCGGGTGGC 62.899 72.222 0.00 0.00 44.05 5.01
1308 1434 1.949133 CATGCATGCATCTTGCCGC 60.949 57.895 30.07 3.04 44.23 6.53
1330 1456 5.157067 GCCTCTGCTCTGTTGTTAATTTTC 58.843 41.667 0.00 0.00 33.53 2.29
1331 1457 5.703876 CCTCTGCTCTGTTGTTAATTTTCC 58.296 41.667 0.00 0.00 0.00 3.13
1332 1458 5.474876 CCTCTGCTCTGTTGTTAATTTTCCT 59.525 40.000 0.00 0.00 0.00 3.36
1336 1462 8.257306 TCTGCTCTGTTGTTAATTTTCCTTTTT 58.743 29.630 0.00 0.00 0.00 1.94
1337 1463 8.419076 TGCTCTGTTGTTAATTTTCCTTTTTC 57.581 30.769 0.00 0.00 0.00 2.29
1339 1465 9.098355 GCTCTGTTGTTAATTTTCCTTTTTCTT 57.902 29.630 0.00 0.00 0.00 2.52
1350 1476 5.548706 TTCCTTTTTCTTTTTCGTCGTCA 57.451 34.783 0.00 0.00 0.00 4.35
1447 1596 2.490270 ATTCAAAGGAGGCAGCCGCT 62.490 55.000 15.60 0.00 38.60 5.52
1449 1598 4.729918 AAAGGAGGCAGCCGCTGG 62.730 66.667 21.77 4.12 38.60 4.85
1466 1615 6.260271 AGCCGCTGGTTCTAATAAGAAATAAC 59.740 38.462 0.00 0.00 43.30 1.89
1485 1671 3.845781 ACACTGTATTAGGCCAGATGG 57.154 47.619 5.01 0.00 38.53 3.51
1565 1752 3.679824 AAGGTGTGCTAACTCACTACC 57.320 47.619 0.00 0.00 39.65 3.18
1567 1754 1.403780 GGTGTGCTAACTCACTACCGG 60.404 57.143 0.00 0.00 39.65 5.28
1568 1755 1.542915 GTGTGCTAACTCACTACCGGA 59.457 52.381 9.46 0.00 37.33 5.14
1569 1756 1.542915 TGTGCTAACTCACTACCGGAC 59.457 52.381 9.46 0.00 37.81 4.79
1570 1757 1.817447 GTGCTAACTCACTACCGGACT 59.183 52.381 9.46 0.00 34.29 3.85
1571 1758 2.089980 TGCTAACTCACTACCGGACTC 58.910 52.381 9.46 0.00 0.00 3.36
1572 1759 1.063764 GCTAACTCACTACCGGACTCG 59.936 57.143 9.46 0.00 0.00 4.18
1573 1760 1.063764 CTAACTCACTACCGGACTCGC 59.936 57.143 9.46 0.00 34.56 5.03
1574 1761 1.593296 AACTCACTACCGGACTCGCC 61.593 60.000 9.46 0.00 34.56 5.54
1583 1770 4.971125 GGACTCGCCGCCTATGCC 62.971 72.222 0.00 0.00 0.00 4.40
1673 1860 0.185901 TTTGCCTGAGCCCAGTTTCT 59.814 50.000 0.00 0.00 38.74 2.52
1674 1861 0.538057 TTGCCTGAGCCCAGTTTCTG 60.538 55.000 0.00 0.00 38.74 3.02
1676 1863 0.324943 GCCTGAGCCCAGTTTCTGTA 59.675 55.000 0.00 0.00 38.74 2.74
1677 1864 1.677217 GCCTGAGCCCAGTTTCTGTAG 60.677 57.143 0.00 0.00 38.74 2.74
1678 1865 1.065854 CCTGAGCCCAGTTTCTGTAGG 60.066 57.143 0.00 0.00 38.74 3.18
1679 1866 0.324943 TGAGCCCAGTTTCTGTAGGC 59.675 55.000 8.32 8.32 38.49 3.93
1680 1867 0.393132 GAGCCCAGTTTCTGTAGGCC 60.393 60.000 0.00 0.00 38.82 5.19
1681 1868 1.745489 GCCCAGTTTCTGTAGGCCG 60.745 63.158 0.00 0.00 34.33 6.13
1682 1869 1.745489 CCCAGTTTCTGTAGGCCGC 60.745 63.158 0.00 0.00 0.00 6.53
1684 1871 0.321653 CCAGTTTCTGTAGGCCGCTT 60.322 55.000 0.00 0.00 0.00 4.68
1685 1872 1.079503 CAGTTTCTGTAGGCCGCTTC 58.920 55.000 0.00 0.00 0.00 3.86
1686 1873 0.685097 AGTTTCTGTAGGCCGCTTCA 59.315 50.000 0.00 0.00 0.00 3.02
1687 1874 1.071699 AGTTTCTGTAGGCCGCTTCAA 59.928 47.619 0.00 0.00 0.00 2.69
1688 1875 2.084546 GTTTCTGTAGGCCGCTTCAAT 58.915 47.619 0.00 0.00 0.00 2.57
1689 1876 2.488153 GTTTCTGTAGGCCGCTTCAATT 59.512 45.455 0.00 0.00 0.00 2.32
1734 1921 1.362224 TTCTGCCTTTGCTAGTCCCT 58.638 50.000 0.00 0.00 38.71 4.20
1760 1947 8.600449 TTTTTGTCTTCGCAAATTGGATTAAT 57.400 26.923 0.00 0.00 38.05 1.40
1867 2054 1.621317 TCTTACTGACCAACATGCCGA 59.379 47.619 0.00 0.00 0.00 5.54
1868 2055 2.236146 TCTTACTGACCAACATGCCGAT 59.764 45.455 0.00 0.00 0.00 4.18
2048 2239 2.695666 ACAGACAGAACACACTGCTACT 59.304 45.455 0.00 0.00 41.06 2.57
2072 2263 1.072331 ACCAGGCACCAGAACTTACTG 59.928 52.381 0.00 0.00 37.61 2.74
2100 2291 1.673760 CAAAACGATTGCACGACCAG 58.326 50.000 3.48 0.00 37.03 4.00
2138 2333 4.401714 GTCGTAGTCTTCCTAGTCGTTTG 58.598 47.826 0.00 0.00 0.00 2.93
2139 2334 4.153117 GTCGTAGTCTTCCTAGTCGTTTGA 59.847 45.833 0.00 0.00 0.00 2.69
2142 2337 5.738225 CGTAGTCTTCCTAGTCGTTTGATTC 59.262 44.000 0.00 0.00 0.00 2.52
2157 2352 2.006888 TGATTCACGAAATTCGAGGGC 58.993 47.619 22.92 7.76 43.74 5.19
2224 2419 6.435904 ACGAATCCTCCAAAATTTTGATACCA 59.564 34.615 28.44 11.09 40.55 3.25
2249 2444 5.308825 AGAACAATTCATGACGAAGACCTT 58.691 37.500 0.00 0.00 36.95 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.605083 TGGCTATCAGCTATGAGCCG 59.395 55.000 20.91 0.00 45.44 5.52
31 36 8.627208 TCTCTCAGTTTTCTTGCAATCTATTT 57.373 30.769 0.00 0.00 0.00 1.40
80 85 4.633565 GCGATTCAGAGGAAAGTGATTTCT 59.366 41.667 0.00 0.00 36.43 2.52
131 136 2.356313 CAAGCCTGTCGTGCTCGT 60.356 61.111 8.17 0.00 38.34 4.18
283 288 0.535780 CACCAGCACCAGCAAGAGAA 60.536 55.000 0.00 0.00 45.49 2.87
294 299 2.826777 ATAGGCACCAGCACCAGCAC 62.827 60.000 0.00 0.00 45.49 4.40
295 300 2.605607 ATAGGCACCAGCACCAGCA 61.606 57.895 0.00 0.00 45.49 4.41
296 301 2.117156 CATAGGCACCAGCACCAGC 61.117 63.158 0.00 0.00 44.61 4.85
297 302 0.182061 ATCATAGGCACCAGCACCAG 59.818 55.000 0.00 0.00 44.61 4.00
298 303 1.506025 TATCATAGGCACCAGCACCA 58.494 50.000 0.00 0.00 44.61 4.17
331 336 6.073548 GGAGAAACATTTCTACCATATGCTCG 60.074 42.308 6.85 0.00 46.84 5.03
365 375 4.432712 GCCAGTAGCATTTTTACAATGGG 58.567 43.478 0.00 0.00 42.97 4.00
466 495 5.641777 TTCGCGATGTAAATGATGAAGAG 57.358 39.130 10.88 0.00 0.00 2.85
468 497 8.766493 TTTAATTCGCGATGTAAATGATGAAG 57.234 30.769 10.88 0.00 0.00 3.02
514 543 5.763444 ATATAATGTCGATTTTCCTCGCG 57.237 39.130 0.00 0.00 38.52 5.87
547 582 9.594936 TCCTTCTTAATTAAAACTGGATTTCCA 57.405 29.630 0.00 0.00 45.30 3.53
713 757 8.972662 TTCCACCATTATTATCTAGATCCTCA 57.027 34.615 8.95 0.00 0.00 3.86
841 910 2.135933 GACACAAGACAGAACGGGAAG 58.864 52.381 0.00 0.00 0.00 3.46
874 943 6.381498 TTTATACTGGACACTTGGATCCAA 57.619 37.500 25.53 25.53 44.42 3.53
878 947 8.889717 CGTTTTATTTATACTGGACACTTGGAT 58.110 33.333 0.00 0.00 0.00 3.41
879 948 7.334921 CCGTTTTATTTATACTGGACACTTGGA 59.665 37.037 0.00 0.00 0.00 3.53
881 950 6.964934 GCCGTTTTATTTATACTGGACACTTG 59.035 38.462 0.00 0.00 0.00 3.16
890 964 8.931385 TTTCTCGTAGCCGTTTTATTTATACT 57.069 30.769 0.00 0.00 35.01 2.12
922 996 4.096681 AGACAGAGTCAGAGAGAGAGAGA 58.903 47.826 0.00 0.00 34.60 3.10
923 997 4.161189 AGAGACAGAGTCAGAGAGAGAGAG 59.839 50.000 0.00 0.00 34.60 3.20
924 998 4.096681 AGAGACAGAGTCAGAGAGAGAGA 58.903 47.826 0.00 0.00 34.60 3.10
925 999 4.161189 AGAGAGACAGAGTCAGAGAGAGAG 59.839 50.000 0.00 0.00 34.60 3.20
926 1000 4.096681 AGAGAGACAGAGTCAGAGAGAGA 58.903 47.826 0.00 0.00 34.60 3.10
927 1001 4.437239 GAGAGAGACAGAGTCAGAGAGAG 58.563 52.174 0.00 0.00 34.60 3.20
928 1002 3.119137 CGAGAGAGACAGAGTCAGAGAGA 60.119 52.174 0.00 0.00 34.60 3.10
929 1003 3.190079 CGAGAGAGACAGAGTCAGAGAG 58.810 54.545 0.00 0.00 34.60 3.20
930 1004 2.676750 GCGAGAGAGACAGAGTCAGAGA 60.677 54.545 0.00 0.00 34.60 3.10
931 1005 1.665679 GCGAGAGAGACAGAGTCAGAG 59.334 57.143 0.00 0.00 34.60 3.35
932 1006 1.677518 GGCGAGAGAGACAGAGTCAGA 60.678 57.143 0.00 0.00 34.60 3.27
990 1068 1.079543 CTCCATCATCCCGATCGGC 60.080 63.158 29.12 0.00 29.21 5.54
1185 1295 1.687297 GCTGGAGGTAGTAGGGGTGC 61.687 65.000 0.00 0.00 0.00 5.01
1308 1434 5.474876 AGGAAAATTAACAACAGAGCAGAGG 59.525 40.000 0.00 0.00 0.00 3.69
1330 1456 4.654015 TGTGACGACGAAAAAGAAAAAGG 58.346 39.130 0.00 0.00 0.00 3.11
1331 1457 5.963004 TGATGTGACGACGAAAAAGAAAAAG 59.037 36.000 0.00 0.00 0.00 2.27
1332 1458 5.735427 GTGATGTGACGACGAAAAAGAAAAA 59.265 36.000 0.00 0.00 0.00 1.94
1336 1462 3.449632 TGTGATGTGACGACGAAAAAGA 58.550 40.909 0.00 0.00 0.00 2.52
1337 1463 3.852471 TGTGATGTGACGACGAAAAAG 57.148 42.857 0.00 0.00 0.00 2.27
1339 1465 4.804608 AAATGTGATGTGACGACGAAAA 57.195 36.364 0.00 0.00 0.00 2.29
1408 1540 0.803768 CCTCAGCCGATCTCACAACG 60.804 60.000 0.00 0.00 0.00 4.10
1466 1615 3.845781 ACCATCTGGCCTAATACAGTG 57.154 47.619 3.32 0.00 39.32 3.66
1548 1735 1.542915 TCCGGTAGTGAGTTAGCACAC 59.457 52.381 0.00 0.00 41.19 3.82
1584 1771 1.028905 AGCATAGAGAGTCAGCCGAC 58.971 55.000 0.00 0.00 42.95 4.79
1585 1772 1.028130 CAGCATAGAGAGTCAGCCGA 58.972 55.000 0.00 0.00 0.00 5.54
1586 1773 0.031857 CCAGCATAGAGAGTCAGCCG 59.968 60.000 0.00 0.00 0.00 5.52
1587 1774 0.392336 CCCAGCATAGAGAGTCAGCC 59.608 60.000 0.00 0.00 0.00 4.85
1588 1775 1.407936 TCCCAGCATAGAGAGTCAGC 58.592 55.000 0.00 0.00 0.00 4.26
1589 1776 3.181467 CCTTTCCCAGCATAGAGAGTCAG 60.181 52.174 0.00 0.00 0.00 3.51
1590 1777 2.768527 CCTTTCCCAGCATAGAGAGTCA 59.231 50.000 0.00 0.00 0.00 3.41
1591 1778 2.484594 GCCTTTCCCAGCATAGAGAGTC 60.485 54.545 0.00 0.00 0.00 3.36
1592 1779 1.488393 GCCTTTCCCAGCATAGAGAGT 59.512 52.381 0.00 0.00 0.00 3.24
1881 2068 3.659089 ATGGAAGACGGAACCGCGG 62.659 63.158 26.86 26.86 44.19 6.46
1884 2071 1.518572 CGGATGGAAGACGGAACCG 60.519 63.158 11.83 11.83 46.03 4.44
1885 2072 0.248289 TTCGGATGGAAGACGGAACC 59.752 55.000 0.00 0.00 0.00 3.62
1949 2136 4.462483 TCCAGTCTGCTTGAAAAACTTGTT 59.538 37.500 0.00 0.00 0.00 2.83
1951 2138 4.142403 TGTCCAGTCTGCTTGAAAAACTTG 60.142 41.667 0.00 0.00 0.00 3.16
2048 2239 0.766674 AGTTCTGGTGCCTGGTGGTA 60.767 55.000 0.00 0.00 35.27 3.25
2072 2263 1.052287 CAATCGTTTTGCCGCTGTTC 58.948 50.000 0.00 0.00 0.00 3.18
2138 2333 1.004927 CGCCCTCGAATTTCGTGAATC 60.005 52.381 19.31 8.79 41.35 2.52
2139 2334 1.006832 CGCCCTCGAATTTCGTGAAT 58.993 50.000 19.31 0.00 41.35 2.57
2142 2337 4.178861 TCGCCCTCGAATTTCGTG 57.821 55.556 17.61 14.99 42.44 4.35
2157 2352 3.371898 TCTTGTCAGCAAATGTAGCATCG 59.628 43.478 0.00 0.00 33.73 3.84
2224 2419 6.644347 AGGTCTTCGTCATGAATTGTTCTAT 58.356 36.000 0.00 0.00 35.63 1.98


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

AutoCloner maintained by Alex Coulton.