Multiple sequence alignment - TraesCS1A01G300700

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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 TraesCS1A01G300700 chr1A 100.000 2662 0 0 1 2662 495335733 495333072 0 4916
1 TraesCS1A01G300700 chr1B 87.276 2735 218 50 2 2661 533818660 533815981 0 3003
2 TraesCS1A01G300700 chr1D 90.299 2144 133 30 554 2662 398382564 398380461 0 2737
3 TraesCS1A01G300700 chr1D 89.464 541 49 7 1 537 398383181 398382645 0 676


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 TraesCS1A01G300700 chr1A 495333072 495335733 2661 True 4916.0 4916 100.0000 1 2662 1 chr1A.!!$R1 2661
1 TraesCS1A01G300700 chr1B 533815981 533818660 2679 True 3003.0 3003 87.2760 2 2661 1 chr1B.!!$R1 2659
2 TraesCS1A01G300700 chr1D 398380461 398383181 2720 True 1706.5 2737 89.8815 1 2662 2 chr1D.!!$R1 2661

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
530 543 0.373716 GACCATCGTTGGATCGCAAC 59.626 55.0 19.34 13.86 46.92 4.17 F
866 958 0.383491 GACATTGCGATTCCGATGCG 60.383 55.0 0.00 0.00 38.22 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1654 0.250338 AGAACGGAGGAGCAACAACC 60.250 55.0 0.0 0.0 0.00 3.77 R
1991 2103 0.392461 TTCAACCGCCTGGATGCTAC 60.392 55.0 0.0 0.0 37.92 3.58 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
39 40 3.133464 CGCGGCCATGGTCACAAT 61.133 61.111 18.31 0.00 0.00 2.71
45 46 1.549203 GCCATGGTCACAATGTCCTT 58.451 50.000 14.67 0.00 0.00 3.36
98 99 1.002624 GTGGTTGATGGAGGCGGAA 60.003 57.895 0.00 0.00 0.00 4.30
103 104 1.401905 GTTGATGGAGGCGGAAATGAC 59.598 52.381 0.00 0.00 0.00 3.06
104 105 0.617935 TGATGGAGGCGGAAATGACA 59.382 50.000 0.00 0.00 0.00 3.58
111 112 0.523335 GGCGGAAATGACATTGACGC 60.523 55.000 27.91 27.91 43.16 5.19
113 114 1.663643 GCGGAAATGACATTGACGCTA 59.336 47.619 28.24 0.00 41.72 4.26
123 124 0.973632 ATTGACGCTACCACTCACCA 59.026 50.000 0.00 0.00 0.00 4.17
188 194 4.035675 GCAATTACAGACCTTGTAGATGCC 59.964 45.833 11.89 0.00 43.10 4.40
201 207 1.300620 GATGCCAGGTGCGCGTATA 60.301 57.895 8.43 0.00 45.60 1.47
305 312 1.601171 GTGGCAGCTCTCATCCACT 59.399 57.895 9.90 0.00 44.09 4.00
326 333 4.405358 ACTGGGCATGAGTTTTCTTCAAAA 59.595 37.500 0.00 0.00 0.00 2.44
345 352 4.859629 AAAAAGGACTCGATGCGAATAC 57.140 40.909 0.00 0.00 34.74 1.89
397 404 0.895100 TGTCCAAATGCACAGGCTCC 60.895 55.000 0.00 0.00 41.91 4.70
402 409 1.237285 AAATGCACAGGCTCCGTCAC 61.237 55.000 0.00 0.00 41.91 3.67
484 497 3.895041 AGTTTGATTTCGGTTTGTGGGAT 59.105 39.130 0.00 0.00 0.00 3.85
525 538 4.497473 TTTGTTTGACCATCGTTGGATC 57.503 40.909 19.34 12.47 46.92 3.36
530 543 0.373716 GACCATCGTTGGATCGCAAC 59.626 55.000 19.34 13.86 46.92 4.17
647 728 4.227864 AGGAATTTTCTCTGCTGGGTAG 57.772 45.455 0.00 0.00 0.00 3.18
662 743 2.895404 TGGGTAGTTAAAGCGACAGAGT 59.105 45.455 0.00 0.00 0.00 3.24
663 744 3.057033 TGGGTAGTTAAAGCGACAGAGTC 60.057 47.826 0.00 0.00 0.00 3.36
681 762 6.128227 ACAGAGTCAGAATCTCGTACTACAAC 60.128 42.308 0.00 0.00 37.07 3.32
747 828 2.331019 AAGGCAACGTGTTGTTCGGC 62.331 55.000 13.73 1.01 42.31 5.54
766 847 1.333791 GCTGTGTTGTTCCTTGCGTAC 60.334 52.381 0.00 0.00 0.00 3.67
855 944 1.883084 GGAGGCCGTAGACATTGCG 60.883 63.158 0.00 0.00 34.41 4.85
859 951 0.582005 GGCCGTAGACATTGCGATTC 59.418 55.000 0.00 0.00 37.02 2.52
866 958 0.383491 GACATTGCGATTCCGATGCG 60.383 55.000 0.00 0.00 38.22 4.73
903 995 2.104331 CGAGCCGTACGGAGCAAT 59.896 61.111 37.62 16.50 37.50 3.56
908 1000 0.808453 GCCGTACGGAGCAATAAGCA 60.808 55.000 37.62 0.00 40.07 3.91
909 1001 2.139821 GCCGTACGGAGCAATAAGCAT 61.140 52.381 37.62 0.00 40.07 3.79
935 1033 4.814294 ACGATCCTTGCCGTCGCC 62.814 66.667 0.00 0.00 38.85 5.54
964 1062 3.431725 CTCGGGCCAACTTTCGCC 61.432 66.667 4.39 0.00 44.92 5.54
1072 1170 3.408020 GTACGAGCGGCGCAACAA 61.408 61.111 35.02 13.88 46.04 2.83
1085 1183 4.624015 GGCGCAACAATACTGGTATAGTA 58.376 43.478 10.83 0.00 45.50 1.82
1087 1185 4.446719 GCGCAACAATACTGGTATAGTACC 59.553 45.833 0.30 0.00 44.30 3.34
1111 1209 5.518943 CCATGGATGGCTCGTCGATAGAG 62.519 56.522 5.56 14.24 44.09 2.43
1310 1408 3.384532 GGTTCGTAGACCCGGCCA 61.385 66.667 2.24 0.00 34.32 5.36
1537 1635 2.259204 CCACGGGTGCAATTGCTG 59.741 61.111 29.37 18.81 42.66 4.41
1551 1649 4.201950 GCAATTGCTGGACTACCTATGTTG 60.202 45.833 23.21 0.00 38.21 3.33
1556 1654 4.184629 GCTGGACTACCTATGTTGAGTTG 58.815 47.826 0.00 0.00 37.04 3.16
1561 1659 5.512576 GGACTACCTATGTTGAGTTGGTTGT 60.513 44.000 0.00 0.00 38.88 3.32
1563 1661 5.763204 ACTACCTATGTTGAGTTGGTTGTTG 59.237 40.000 0.00 0.00 34.23 3.33
1585 1684 1.000955 TCCTCCGTTCTGCTTCTGAAC 59.999 52.381 6.54 6.54 38.40 3.18
1591 1690 1.193426 GTTCTGCTTCTGAACGTCTGC 59.807 52.381 0.00 0.00 33.95 4.26
1686 1788 3.242870 CGTAAAGAGCTCCATCATTTGCC 60.243 47.826 10.93 0.00 0.00 4.52
1711 1816 2.032675 CCTAACGCGGTAACTCCTAGAC 59.967 54.545 12.47 0.00 0.00 2.59
1723 1828 1.067212 CTCCTAGACGGTGCCACATAC 59.933 57.143 0.00 0.00 0.00 2.39
1776 1881 2.000447 GCTAGACCGTCCAATCAACAC 59.000 52.381 0.00 0.00 0.00 3.32
1777 1882 2.259618 CTAGACCGTCCAATCAACACG 58.740 52.381 0.00 0.00 0.00 4.49
1779 1884 0.788391 GACCGTCCAATCAACACGAC 59.212 55.000 0.00 0.00 35.49 4.34
1810 1915 2.524306 TGATTCATGGTTGGGTGGTTC 58.476 47.619 0.00 0.00 0.00 3.62
1838 1943 1.369091 AATCGAGCCACCAATCACGC 61.369 55.000 0.00 0.00 0.00 5.34
1842 1947 2.202650 GCCACCAATCACGCATGC 60.203 61.111 7.91 7.91 0.00 4.06
1867 1972 1.093972 TGCATATGTTTGCCACGGAG 58.906 50.000 4.29 0.00 42.06 4.63
1888 1993 2.163509 GTGGCCTCTTTTTCCTCCTTC 58.836 52.381 3.32 0.00 0.00 3.46
1989 2101 1.149361 TTATTCAGCTAACCCGCGCG 61.149 55.000 25.67 25.67 34.40 6.86
2065 2179 3.646715 GCCACCCCCACTAGTGCA 61.647 66.667 17.86 0.00 32.48 4.57
2192 2307 4.085204 TTATCCCGGCGGTTGCGT 62.085 61.111 26.32 8.04 44.10 5.24
2458 2577 6.138088 GCAAATTGATCCAGCAAAACTTTTC 58.862 36.000 0.00 0.00 0.00 2.29
2463 2582 3.691049 TCCAGCAAAACTTTTCACTCG 57.309 42.857 0.00 0.00 0.00 4.18
2468 2587 2.851824 GCAAAACTTTTCACTCGTGGTG 59.148 45.455 0.00 5.25 46.60 4.17
2473 2592 1.257936 CTTTTCACTCGTGGTGTGTCG 59.742 52.381 10.04 0.00 45.50 4.35
2502 2621 1.802337 TACAGTGTTCTGCGCCGTCT 61.802 55.000 4.18 0.00 44.77 4.18
2518 2637 4.663140 CGCCGTCTAATATTTACATGTGCG 60.663 45.833 9.11 6.28 0.00 5.34
2523 2642 6.427150 GTCTAATATTTACATGTGCGGTTGG 58.573 40.000 9.11 0.00 0.00 3.77
2527 2646 1.240641 TTACATGTGCGGTTGGGCAG 61.241 55.000 9.11 0.00 44.93 4.85
2609 2734 1.337118 GGAAAATGGTGCCACAAGGA 58.663 50.000 0.00 0.00 36.89 3.36
2611 2736 1.000843 GAAAATGGTGCCACAAGGACC 59.999 52.381 0.00 0.00 36.89 4.46
2639 2764 0.797542 CAGAGCTGTGCTGCTTTCTC 59.202 55.000 0.00 2.74 44.17 2.87
2643 2768 1.502163 GCTGTGCTGCTTTCTCGTGT 61.502 55.000 0.00 0.00 0.00 4.49
2646 2771 0.658536 GTGCTGCTTTCTCGTGTTGC 60.659 55.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.489329 GACCAAGGACATTGTGACCATG 59.511 50.000 0.00 0.00 37.17 3.66
39 40 2.224843 TGTACTACGAGGACCAAGGACA 60.225 50.000 0.00 0.00 30.32 4.02
45 46 2.494471 CACCATTGTACTACGAGGACCA 59.506 50.000 0.00 0.00 0.00 4.02
98 99 3.262420 GAGTGGTAGCGTCAATGTCATT 58.738 45.455 0.00 0.00 0.00 2.57
103 104 1.337728 TGGTGAGTGGTAGCGTCAATG 60.338 52.381 0.00 0.00 0.00 2.82
104 105 0.973632 TGGTGAGTGGTAGCGTCAAT 59.026 50.000 0.00 0.00 0.00 2.57
111 112 0.179100 CTGGCGATGGTGAGTGGTAG 60.179 60.000 0.00 0.00 0.00 3.18
113 114 1.480212 TTCTGGCGATGGTGAGTGGT 61.480 55.000 0.00 0.00 0.00 4.16
123 124 3.181454 CCATACTAAGGGTTTCTGGCGAT 60.181 47.826 0.00 0.00 0.00 4.58
188 194 1.065701 ACTTCTCTATACGCGCACCTG 59.934 52.381 5.73 0.00 0.00 4.00
201 207 3.394836 GGCCGCTGGGACTTCTCT 61.395 66.667 0.00 0.00 38.83 3.10
284 290 1.227205 GGATGAGAGCTGCCACGAG 60.227 63.158 0.00 0.00 0.00 4.18
292 299 0.987081 ATGCCCAGTGGATGAGAGCT 60.987 55.000 11.95 0.00 0.00 4.09
305 312 5.350504 TTTTTGAAGAAAACTCATGCCCA 57.649 34.783 0.00 0.00 30.56 5.36
326 333 3.802948 AGTATTCGCATCGAGTCCTTT 57.197 42.857 0.00 0.00 37.14 3.11
329 336 3.617263 ACAAAAGTATTCGCATCGAGTCC 59.383 43.478 0.00 0.00 37.14 3.85
334 341 4.201391 GCAACAACAAAAGTATTCGCATCG 60.201 41.667 0.00 0.00 0.00 3.84
337 344 4.033990 TGCAACAACAAAAGTATTCGCA 57.966 36.364 0.00 0.00 0.00 5.10
341 348 3.067461 TCCGCTGCAACAACAAAAGTATT 59.933 39.130 0.00 0.00 0.00 1.89
345 352 1.919918 TTCCGCTGCAACAACAAAAG 58.080 45.000 0.00 0.00 0.00 2.27
397 404 1.296056 GACCCATCCAAACCGTGACG 61.296 60.000 0.00 0.00 0.00 4.35
402 409 3.131478 GCGGACCCATCCAAACCG 61.131 66.667 0.00 0.00 46.67 4.44
537 550 3.120854 GCTCGATCAAACAGTCAACAGTC 60.121 47.826 0.00 0.00 0.00 3.51
539 552 2.802247 TGCTCGATCAAACAGTCAACAG 59.198 45.455 0.00 0.00 0.00 3.16
540 553 2.802247 CTGCTCGATCAAACAGTCAACA 59.198 45.455 0.00 0.00 0.00 3.33
541 554 3.059884 TCTGCTCGATCAAACAGTCAAC 58.940 45.455 0.00 0.00 0.00 3.18
542 555 3.385193 TCTGCTCGATCAAACAGTCAA 57.615 42.857 0.00 0.00 0.00 3.18
543 556 3.599730 ATCTGCTCGATCAAACAGTCA 57.400 42.857 0.00 0.00 0.00 3.41
546 559 3.048942 GCAATCTGCTCGATCAAACAG 57.951 47.619 0.00 0.00 40.96 3.16
585 662 2.179589 CGCATCATGTAAAGTTGCAGC 58.820 47.619 0.00 0.00 32.63 5.25
640 721 3.056749 ACTCTGTCGCTTTAACTACCCAG 60.057 47.826 0.00 0.00 0.00 4.45
647 728 5.164954 AGATTCTGACTCTGTCGCTTTAAC 58.835 41.667 0.00 0.00 34.95 2.01
662 743 3.437741 TGCGTTGTAGTACGAGATTCTGA 59.562 43.478 0.00 0.00 43.99 3.27
663 744 3.754955 TGCGTTGTAGTACGAGATTCTG 58.245 45.455 0.00 0.00 43.99 3.02
681 762 0.030504 TGTGCTTCACCACAATTGCG 59.969 50.000 5.05 0.00 42.33 4.85
747 828 1.937223 TGTACGCAAGGAACAACACAG 59.063 47.619 0.00 0.00 46.39 3.66
855 944 1.095228 TCAAAGGGCGCATCGGAATC 61.095 55.000 10.83 0.00 0.00 2.52
859 951 0.526096 CAAATCAAAGGGCGCATCGG 60.526 55.000 10.83 0.00 0.00 4.18
866 958 2.923020 CGTGTAATGCAAATCAAAGGGC 59.077 45.455 0.00 0.00 0.00 5.19
903 995 0.179094 ATCGTCGCCGGAAATGCTTA 60.179 50.000 5.05 0.00 33.95 3.09
908 1000 0.810031 CAAGGATCGTCGCCGGAAAT 60.810 55.000 5.05 0.00 33.95 2.17
909 1001 1.447140 CAAGGATCGTCGCCGGAAA 60.447 57.895 5.05 0.00 33.95 3.13
1014 1112 4.752879 TTAGGGAGGCACGCACGC 62.753 66.667 1.41 0.00 35.94 5.34
1025 1123 1.138266 GCCACTCGCTGTATTTAGGGA 59.862 52.381 0.00 0.00 37.92 4.20
1026 1124 1.134521 TGCCACTCGCTGTATTTAGGG 60.135 52.381 0.00 0.00 38.78 3.53
1027 1125 2.309528 TGCCACTCGCTGTATTTAGG 57.690 50.000 0.00 0.00 38.78 2.69
1102 1200 1.082627 GCCGACGAGCTCTATCGAC 60.083 63.158 28.77 19.05 45.56 4.20
1103 1201 2.595878 CGCCGACGAGCTCTATCGA 61.596 63.158 28.77 0.00 45.56 3.59
1104 1202 2.595878 TCGCCGACGAGCTCTATCG 61.596 63.158 23.27 23.27 45.12 2.92
1105 1203 3.331319 TCGCCGACGAGCTCTATC 58.669 61.111 12.85 8.41 45.12 2.08
1537 1635 4.820894 ACCAACTCAACATAGGTAGTCC 57.179 45.455 0.00 0.00 0.00 3.85
1551 1649 1.239347 GGAGGAGCAACAACCAACTC 58.761 55.000 0.00 0.00 0.00 3.01
1556 1654 0.250338 AGAACGGAGGAGCAACAACC 60.250 55.000 0.00 0.00 0.00 3.77
1561 1659 0.320771 GAAGCAGAACGGAGGAGCAA 60.321 55.000 0.00 0.00 0.00 3.91
1563 1661 0.739112 CAGAAGCAGAACGGAGGAGC 60.739 60.000 0.00 0.00 0.00 4.70
1585 1684 4.394941 CACACGCGAACGCAGACG 62.395 66.667 15.93 5.28 45.53 4.18
1601 1700 5.060662 TCCAACAACAACGACAAAAATCA 57.939 34.783 0.00 0.00 0.00 2.57
1651 1753 4.392138 AGCTCTTTACGGTTTACATGCTTC 59.608 41.667 0.00 0.00 0.00 3.86
1657 1759 4.020928 TGATGGAGCTCTTTACGGTTTACA 60.021 41.667 14.64 0.00 0.00 2.41
1658 1760 4.501071 TGATGGAGCTCTTTACGGTTTAC 58.499 43.478 14.64 0.00 0.00 2.01
1660 1762 3.695830 TGATGGAGCTCTTTACGGTTT 57.304 42.857 14.64 0.00 0.00 3.27
1663 1765 3.242870 GCAAATGATGGAGCTCTTTACGG 60.243 47.826 14.64 0.00 0.00 4.02
1686 1788 1.468736 GGAGTTACCGCGTTAGGACAG 60.469 57.143 4.92 0.00 34.73 3.51
1711 1816 3.254654 CGAGCGTATGTGGCACCG 61.255 66.667 16.26 12.67 0.00 4.94
1731 1836 4.201832 CGATCGGGTAAGATAAGATCCTCG 60.202 50.000 7.38 0.00 35.56 4.63
1779 1884 5.107491 CCAACCATGAATCATCACGTATACG 60.107 44.000 23.24 23.24 46.33 3.06
1810 1915 2.552743 TGGTGGCTCGATTACTCTATCG 59.447 50.000 0.00 0.00 46.63 2.92
1867 1972 0.405973 AGGAGGAAAAAGAGGCCACC 59.594 55.000 5.01 0.00 33.25 4.61
1910 2022 4.267928 CCTTTGCCGACTAAAACTATCTCG 59.732 45.833 0.00 0.00 0.00 4.04
1989 2101 4.530857 ACCGCCTGGATGCTACGC 62.531 66.667 0.00 0.00 39.21 4.42
1990 2102 2.173669 CAACCGCCTGGATGCTACG 61.174 63.158 0.00 0.00 39.21 3.51
1991 2103 0.392461 TTCAACCGCCTGGATGCTAC 60.392 55.000 0.00 0.00 37.92 3.58
1992 2104 0.392461 GTTCAACCGCCTGGATGCTA 60.392 55.000 0.00 0.00 37.92 3.49
2063 2177 4.819761 TCAGGCATCCTCGCGTGC 62.820 66.667 5.77 8.67 45.16 5.34
2065 2179 1.227380 GATTCAGGCATCCTCGCGT 60.227 57.895 5.77 0.00 0.00 6.01
2463 2582 1.577328 CTGGCAATCCGACACACCAC 61.577 60.000 0.00 0.00 34.14 4.16
2468 2587 1.337823 ACTGTACTGGCAATCCGACAC 60.338 52.381 4.66 0.00 34.14 3.67
2473 2592 2.744202 CAGAACACTGTACTGGCAATCC 59.256 50.000 4.66 0.00 0.00 3.01
2502 2621 4.036971 GCCCAACCGCACATGTAAATATTA 59.963 41.667 0.00 0.00 0.00 0.98
2518 2637 1.940613 GTATGATCGAACTGCCCAACC 59.059 52.381 0.00 0.00 0.00 3.77
2523 2642 2.536365 TCAACGTATGATCGAACTGCC 58.464 47.619 0.00 0.00 31.50 4.85
2609 2734 3.336568 AGCTCTGCATGCCCAGGT 61.337 61.111 16.68 13.34 33.64 4.00
2611 2736 2.045242 ACAGCTCTGCATGCCCAG 60.045 61.111 16.68 11.88 0.00 4.45


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

AutoCloner maintained by Alex Coulton.