Multiple sequence alignment - TraesCS3B01G071900

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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 TraesCS3B01G071900 chr3B 100.000 3358 0 0 1 3358 43347598 43344241 0.000000e+00 6202.0
1 TraesCS3B01G071900 chr3D 89.362 2839 182 49 149 2967 26119592 26116854 0.000000e+00 3459.0
2 TraesCS3B01G071900 chr3D 93.269 208 14 0 3151 3358 26106036 26105829 1.170000e-79 307.0
3 TraesCS3B01G071900 chr3A 93.017 1432 69 10 1541 2967 35965058 35963653 0.000000e+00 2061.0
4 TraesCS3B01G071900 chr3A 92.934 1387 67 15 3 1379 35966503 35965138 0.000000e+00 1989.0
5 TraesCS3B01G071900 chr3A 91.603 393 29 2 2966 3358 35963682 35963294 1.060000e-149 540.0
6 TraesCS3B01G071900 chr3A 82.222 90 3 4 1427 1516 35965138 35965062 7.780000e-07 65.8
7 TraesCS3B01G071900 chr7D 76.812 207 40 6 531 736 18949823 18949624 3.540000e-20 110.0
8 TraesCS3B01G071900 chr5D 80.952 126 16 5 3164 3283 100940289 100940166 3.570000e-15 93.5
9 TraesCS3B01G071900 chr2B 89.062 64 6 1 3295 3358 750060575 750060513 9.990000e-11 78.7


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 TraesCS3B01G071900 chr3B 43344241 43347598 3357 True 6202.00 6202 100.000 1 3358 1 chr3B.!!$R1 3357
1 TraesCS3B01G071900 chr3D 26116854 26119592 2738 True 3459.00 3459 89.362 149 2967 1 chr3D.!!$R2 2818
2 TraesCS3B01G071900 chr3A 35963294 35966503 3209 True 1163.95 2061 89.944 3 3358 4 chr3A.!!$R1 3355

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
197 203 0.108615 GGTGGAGTCTGTGGTCATCG 60.109 60.0 0.0 0.0 0.0 3.84 F
964 972 0.178301 CCCTCCTCGCTAAAACCTCC 59.822 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1256 0.613853 TCAGGGATTCGGTCTCGGTT 60.614 55.0 0.00 0.00 36.95 4.44 R
2580 2607 0.380733 TACTAGCTGGACATCACGCG 59.619 55.0 3.53 3.53 0.00 6.01 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
23 24 3.660865 GAGATGTTAGAACCACGGTGTT 58.339 45.455 7.45 1.71 0.00 3.32
36 37 1.274447 ACGGTGTTAGGGTGCTAGAAC 59.726 52.381 0.00 0.00 0.00 3.01
42 43 0.815734 TAGGGTGCTAGAACGAGTGC 59.184 55.000 0.00 0.00 0.00 4.40
71 72 0.249996 TTGGAACCGACGAGGAAACC 60.250 55.000 8.56 8.45 45.00 3.27
88 89 4.581409 GGAAACCAAAGCTACAACCAACTA 59.419 41.667 0.00 0.00 0.00 2.24
122 128 1.181098 GGTGTTGGCATGCTGGAACT 61.181 55.000 18.92 0.00 0.00 3.01
125 131 2.277591 TTGGCATGCTGGAACTGGC 61.278 57.895 18.92 0.00 36.12 4.85
162 168 1.298859 CCCAAGCAACCTACGCACTC 61.299 60.000 0.00 0.00 0.00 3.51
164 170 1.374252 AAGCAACCTACGCACTCGG 60.374 57.895 0.00 0.00 40.69 4.63
186 192 0.889186 ATGTTGCAACCGGTGGAGTC 60.889 55.000 26.14 1.78 0.00 3.36
197 203 0.108615 GGTGGAGTCTGTGGTCATCG 60.109 60.000 0.00 0.00 0.00 3.84
225 231 7.015877 CAGTACCTTAACGAAAGCAGATTTTC 58.984 38.462 0.00 0.00 33.49 2.29
226 232 6.935208 AGTACCTTAACGAAAGCAGATTTTCT 59.065 34.615 0.00 0.00 35.42 2.52
227 233 6.635030 ACCTTAACGAAAGCAGATTTTCTT 57.365 33.333 0.00 0.00 35.42 2.52
334 341 6.767524 ATGTTTAACCGATCAATAAAGCCA 57.232 33.333 0.00 0.00 0.00 4.75
389 396 3.215151 TGAGTCCGTCCATCTAGATGAC 58.785 50.000 30.40 23.23 41.20 3.06
410 417 4.148838 ACGCTCTAGATTAGATTCCTGCT 58.851 43.478 0.00 0.00 33.66 4.24
501 508 7.279981 TGTTTCTTGATATCTATTCACGGGTTG 59.720 37.037 3.98 0.00 0.00 3.77
522 529 4.787999 GGTGACGACTAAGGCTCG 57.212 61.111 0.00 0.00 37.17 5.03
668 675 1.134788 GTGGTCATTCGGTGGTCTAGG 60.135 57.143 0.00 0.00 0.00 3.02
784 791 9.503427 AAGAGTAGTTTCATTTTCGAAAACTTG 57.497 29.630 24.68 19.31 36.67 3.16
785 792 8.674607 AGAGTAGTTTCATTTTCGAAAACTTGT 58.325 29.630 24.68 7.05 36.67 3.16
787 794 9.285770 AGTAGTTTCATTTTCGAAAACTTGTTC 57.714 29.630 24.68 13.51 36.67 3.18
788 795 7.520119 AGTTTCATTTTCGAAAACTTGTTCC 57.480 32.000 24.68 11.70 36.67 3.62
789 796 7.093992 AGTTTCATTTTCGAAAACTTGTTCCA 58.906 30.769 24.68 0.30 36.67 3.53
790 797 7.275560 AGTTTCATTTTCGAAAACTTGTTCCAG 59.724 33.333 24.68 7.31 36.67 3.86
791 798 5.587289 TCATTTTCGAAAACTTGTTCCAGG 58.413 37.500 24.68 2.24 0.00 4.45
793 800 4.625972 TTTCGAAAACTTGTTCCAGGAC 57.374 40.909 8.44 0.00 0.00 3.85
794 801 2.206750 TCGAAAACTTGTTCCAGGACG 58.793 47.619 0.00 0.00 0.00 4.79
795 802 1.263217 CGAAAACTTGTTCCAGGACGG 59.737 52.381 0.00 0.00 0.00 4.79
796 803 2.294979 GAAAACTTGTTCCAGGACGGT 58.705 47.619 0.00 0.00 35.57 4.83
797 804 3.469739 GAAAACTTGTTCCAGGACGGTA 58.530 45.455 0.00 0.00 35.57 4.02
798 805 3.782656 AAACTTGTTCCAGGACGGTAT 57.217 42.857 0.00 0.00 35.57 2.73
799 806 4.895668 AAACTTGTTCCAGGACGGTATA 57.104 40.909 0.00 0.00 35.57 1.47
800 807 4.467198 AACTTGTTCCAGGACGGTATAG 57.533 45.455 0.00 0.00 35.57 1.31
801 808 2.764572 ACTTGTTCCAGGACGGTATAGG 59.235 50.000 0.00 0.00 35.57 2.57
803 810 1.288633 TGTTCCAGGACGGTATAGGGA 59.711 52.381 0.00 0.00 35.57 4.20
805 812 2.767960 GTTCCAGGACGGTATAGGGAAA 59.232 50.000 0.00 0.00 36.29 3.13
806 813 3.119009 TCCAGGACGGTATAGGGAAAA 57.881 47.619 0.00 0.00 35.57 2.29
807 814 2.767960 TCCAGGACGGTATAGGGAAAAC 59.232 50.000 0.00 0.00 35.57 2.43
808 815 2.502538 CCAGGACGGTATAGGGAAAACA 59.497 50.000 0.00 0.00 0.00 2.83
809 816 3.135895 CCAGGACGGTATAGGGAAAACAT 59.864 47.826 0.00 0.00 0.00 2.71
810 817 4.377897 CAGGACGGTATAGGGAAAACATC 58.622 47.826 0.00 0.00 0.00 3.06
811 818 4.035112 AGGACGGTATAGGGAAAACATCA 58.965 43.478 0.00 0.00 0.00 3.07
812 819 4.658901 AGGACGGTATAGGGAAAACATCAT 59.341 41.667 0.00 0.00 0.00 2.45
813 820 4.995487 GGACGGTATAGGGAAAACATCATC 59.005 45.833 0.00 0.00 0.00 2.92
814 821 5.454187 GGACGGTATAGGGAAAACATCATCA 60.454 44.000 0.00 0.00 0.00 3.07
815 822 6.187727 ACGGTATAGGGAAAACATCATCAT 57.812 37.500 0.00 0.00 0.00 2.45
816 823 7.311092 ACGGTATAGGGAAAACATCATCATA 57.689 36.000 0.00 0.00 0.00 2.15
817 824 7.918076 ACGGTATAGGGAAAACATCATCATAT 58.082 34.615 0.00 0.00 0.00 1.78
818 825 8.383175 ACGGTATAGGGAAAACATCATCATATT 58.617 33.333 0.00 0.00 0.00 1.28
875 882 9.592720 AAACTTGTTCAAATTCGTTTTCTTTTG 57.407 25.926 0.00 0.00 0.00 2.44
913 920 1.354705 AGGTTTAAGCCCTTCCTGACC 59.645 52.381 4.49 0.00 0.00 4.02
925 932 4.087892 CTGACCGGTGGGCTCCTG 62.088 72.222 14.63 0.00 36.48 3.86
964 972 0.178301 CCCTCCTCGCTAAAACCTCC 59.822 60.000 0.00 0.00 0.00 4.30
996 1004 1.497716 AGAAAAACCCTCTTTCCCGGT 59.502 47.619 0.00 0.00 34.00 5.28
1043 1051 2.446802 GGCCTCCTCCCTACCCAG 60.447 72.222 0.00 0.00 0.00 4.45
1050 1058 3.680196 TCCCTACCCAGCCTCCGT 61.680 66.667 0.00 0.00 0.00 4.69
1128 1136 3.729489 TCCTCCTCCCTCGACGCT 61.729 66.667 0.00 0.00 0.00 5.07
1143 1151 1.294780 CGCTGCAGTCTCCTCCTTT 59.705 57.895 16.64 0.00 0.00 3.11
1234 1242 3.956314 GTACCGTGTTGGGCCCCA 61.956 66.667 22.27 4.90 44.64 4.96
1248 1256 1.912220 CCCCATCCGTGCCTTCTTA 59.088 57.895 0.00 0.00 0.00 2.10
1332 1340 0.165944 CGATCAAGTCCCGCAACAAC 59.834 55.000 0.00 0.00 0.00 3.32
1425 1444 3.508840 CAAATCCACCGAGCGGGC 61.509 66.667 14.07 0.00 40.62 6.13
1460 1483 1.792118 CTGCGATCCCATGCATGGTG 61.792 60.000 37.30 29.04 46.65 4.17
1461 1484 1.526686 GCGATCCCATGCATGGTGA 60.527 57.895 37.30 32.33 46.65 4.02
1462 1485 0.892358 GCGATCCCATGCATGGTGAT 60.892 55.000 37.30 34.66 46.65 3.06
1463 1486 0.879090 CGATCCCATGCATGGTGATG 59.121 55.000 35.18 26.63 46.65 3.07
1464 1487 1.254026 GATCCCATGCATGGTGATGG 58.746 55.000 35.18 25.20 46.65 3.51
1465 1488 0.559205 ATCCCATGCATGGTGATGGT 59.441 50.000 37.30 20.24 46.65 3.55
1469 1492 1.187974 CATGCATGGTGATGGTTGGT 58.812 50.000 19.40 0.00 0.00 3.67
1488 1511 3.461831 TGGTAACTTGGGATAGATTGGGG 59.538 47.826 0.00 0.00 37.61 4.96
1505 1528 2.087646 GGGGCTGTTCTGATCTTTGTC 58.912 52.381 0.00 0.00 0.00 3.18
1516 1539 4.111198 CTGATCTTTGTCACCTCGATCAG 58.889 47.826 11.67 11.67 46.44 2.90
1519 1542 4.808414 TCTTTGTCACCTCGATCAGATT 57.192 40.909 0.00 0.00 0.00 2.40
1520 1543 4.498241 TCTTTGTCACCTCGATCAGATTG 58.502 43.478 0.00 0.00 0.00 2.67
1521 1544 4.220602 TCTTTGTCACCTCGATCAGATTGA 59.779 41.667 0.06 0.06 0.00 2.57
1522 1545 4.743057 TTGTCACCTCGATCAGATTGAT 57.257 40.909 0.34 0.00 40.34 2.57
1535 1558 5.771153 TCAGATTGATCAAGTTTTGTGCA 57.229 34.783 14.54 0.00 0.00 4.57
1536 1559 6.335471 TCAGATTGATCAAGTTTTGTGCAT 57.665 33.333 14.54 0.00 0.00 3.96
1537 1560 6.384224 TCAGATTGATCAAGTTTTGTGCATC 58.616 36.000 14.54 2.49 0.00 3.91
1538 1561 6.016108 TCAGATTGATCAAGTTTTGTGCATCA 60.016 34.615 14.54 0.00 0.00 3.07
1539 1562 6.089016 CAGATTGATCAAGTTTTGTGCATCAC 59.911 38.462 14.54 0.00 34.56 3.06
1558 1581 4.088634 TCACATGCCTTTAATCCTGCTTT 58.911 39.130 0.00 0.00 0.00 3.51
1559 1582 4.527816 TCACATGCCTTTAATCCTGCTTTT 59.472 37.500 0.00 0.00 0.00 2.27
1570 1593 7.621428 TTAATCCTGCTTTTGAGAATCTGAG 57.379 36.000 0.00 0.00 34.92 3.35
1573 1596 5.380043 TCCTGCTTTTGAGAATCTGAGTTT 58.620 37.500 0.00 0.00 34.92 2.66
1574 1597 5.471456 TCCTGCTTTTGAGAATCTGAGTTTC 59.529 40.000 0.00 0.00 34.92 2.78
1577 1600 5.152804 GCTTTTGAGAATCTGAGTTTCTGC 58.847 41.667 10.29 4.12 33.65 4.26
1579 1602 6.551385 TTTTGAGAATCTGAGTTTCTGCTC 57.449 37.500 10.29 0.00 33.65 4.26
1596 1619 2.026641 GCTCATGCCTTTAATCCTGCA 58.973 47.619 0.00 0.00 38.23 4.41
1598 1621 3.069158 GCTCATGCCTTTAATCCTGCATT 59.931 43.478 0.00 0.00 42.22 3.56
1601 1624 5.693961 TCATGCCTTTAATCCTGCATTAGA 58.306 37.500 0.00 0.00 42.22 2.10
1614 1637 4.396166 CCTGCATTAGAATCCGAGTTGTTT 59.604 41.667 0.00 0.00 0.00 2.83
1616 1639 5.938322 TGCATTAGAATCCGAGTTGTTTTC 58.062 37.500 0.00 0.00 0.00 2.29
1617 1640 5.106317 TGCATTAGAATCCGAGTTGTTTTCC 60.106 40.000 0.00 0.00 0.00 3.13
1618 1641 5.676331 GCATTAGAATCCGAGTTGTTTTCCC 60.676 44.000 0.00 0.00 0.00 3.97
1619 1642 3.502123 AGAATCCGAGTTGTTTTCCCA 57.498 42.857 0.00 0.00 0.00 4.37
1631 1654 2.978278 TGTTTTCCCATTTGCCCTCAAT 59.022 40.909 0.00 0.00 31.33 2.57
1839 1862 3.982475 TCACATGAGGATGTAGAATCGC 58.018 45.455 0.00 0.00 41.12 4.58
1901 1924 5.418840 TGGCCAGAAGAACAAATTAAGATCC 59.581 40.000 0.00 0.00 0.00 3.36
1964 1987 1.370900 GCTTGCGTTCACCTGCTTG 60.371 57.895 0.00 0.00 0.00 4.01
1967 1990 3.286751 GCGTTCACCTGCTTGGCA 61.287 61.111 0.00 0.00 40.22 4.92
2017 2040 2.027073 GCATGTTGTCGCGGACAGA 61.027 57.895 6.13 0.97 43.69 3.41
2036 2059 5.128919 ACAGATAAAGATGATGTTCAGGCC 58.871 41.667 0.00 0.00 0.00 5.19
2115 2138 3.616317 GGCAACACTTTTTGGTGTCTTGT 60.616 43.478 0.72 0.00 44.90 3.16
2127 2150 3.279434 GGTGTCTTGTCTTGTTGAAGGT 58.721 45.455 0.00 0.00 0.00 3.50
2154 2177 9.764363 TGTCTTTAATTACTAATCGATGATGCT 57.236 29.630 0.00 0.00 0.00 3.79
2241 2264 4.462834 AGTCATTCGTGAAGTATCTGGACA 59.537 41.667 0.00 0.00 0.00 4.02
2366 2389 3.903714 TCAAGAAAGACTGATCCTCACCA 59.096 43.478 0.00 0.00 0.00 4.17
2596 2629 1.153842 CACGCGTGATGTCCAGCTA 60.154 57.895 34.93 0.00 0.00 3.32
2597 2630 1.139734 ACGCGTGATGTCCAGCTAG 59.860 57.895 12.93 0.00 0.00 3.42
2598 2631 1.139734 CGCGTGATGTCCAGCTAGT 59.860 57.895 0.00 0.00 0.00 2.57
2599 2632 0.380733 CGCGTGATGTCCAGCTAGTA 59.619 55.000 0.00 0.00 0.00 1.82
2600 2633 1.001268 CGCGTGATGTCCAGCTAGTAT 60.001 52.381 0.00 0.00 0.00 2.12
2601 2634 2.543861 CGCGTGATGTCCAGCTAGTATT 60.544 50.000 0.00 0.00 0.00 1.89
2652 2685 4.201485 GCATACGGCAGAAAATTTGAAACG 60.201 41.667 0.00 0.00 43.97 3.60
2660 2693 7.306866 CGGCAGAAAATTTGAAACGGAAATTAA 60.307 33.333 0.00 0.00 32.94 1.40
2679 2712 7.913674 AATTAAAGAGATGGCCGATAGAATC 57.086 36.000 0.00 0.00 39.76 2.52
2878 2917 6.480524 TGTGTAGCAATCAGTTGTATGTTC 57.519 37.500 0.00 0.00 37.65 3.18
2902 2941 7.612677 TCTTAGACCTAGAGCTAACCTTTTTG 58.387 38.462 0.00 0.00 0.00 2.44
2909 2948 8.793592 ACCTAGAGCTAACCTTTTTGTAAATTG 58.206 33.333 0.00 0.00 0.00 2.32
2967 3006 1.536907 TACCTTTGCCCCCGACAGA 60.537 57.895 0.00 0.00 0.00 3.41
2968 3007 1.128809 TACCTTTGCCCCCGACAGAA 61.129 55.000 0.00 0.00 0.00 3.02
2969 3008 1.000896 CCTTTGCCCCCGACAGAAT 60.001 57.895 0.00 0.00 0.00 2.40
2970 3009 0.254747 CCTTTGCCCCCGACAGAATA 59.745 55.000 0.00 0.00 0.00 1.75
2971 3010 1.379527 CTTTGCCCCCGACAGAATAC 58.620 55.000 0.00 0.00 0.00 1.89
2972 3011 0.693622 TTTGCCCCCGACAGAATACA 59.306 50.000 0.00 0.00 0.00 2.29
2973 3012 0.693622 TTGCCCCCGACAGAATACAA 59.306 50.000 0.00 0.00 0.00 2.41
2974 3013 0.693622 TGCCCCCGACAGAATACAAA 59.306 50.000 0.00 0.00 0.00 2.83
2975 3014 1.074084 TGCCCCCGACAGAATACAAAA 59.926 47.619 0.00 0.00 0.00 2.44
2976 3015 1.471287 GCCCCCGACAGAATACAAAAC 59.529 52.381 0.00 0.00 0.00 2.43
2977 3016 2.878526 GCCCCCGACAGAATACAAAACT 60.879 50.000 0.00 0.00 0.00 2.66
2978 3017 3.620472 GCCCCCGACAGAATACAAAACTA 60.620 47.826 0.00 0.00 0.00 2.24
2979 3018 3.937079 CCCCCGACAGAATACAAAACTAC 59.063 47.826 0.00 0.00 0.00 2.73
2980 3019 3.937079 CCCCGACAGAATACAAAACTACC 59.063 47.826 0.00 0.00 0.00 3.18
2981 3020 4.323257 CCCCGACAGAATACAAAACTACCT 60.323 45.833 0.00 0.00 0.00 3.08
2982 3021 5.243207 CCCGACAGAATACAAAACTACCTT 58.757 41.667 0.00 0.00 0.00 3.50
2983 3022 5.704053 CCCGACAGAATACAAAACTACCTTT 59.296 40.000 0.00 0.00 0.00 3.11
2984 3023 6.348213 CCCGACAGAATACAAAACTACCTTTG 60.348 42.308 0.00 0.00 41.24 2.77
2985 3024 6.077838 CGACAGAATACAAAACTACCTTTGC 58.922 40.000 0.00 0.00 39.46 3.68
2986 3025 6.327279 ACAGAATACAAAACTACCTTTGCC 57.673 37.500 0.00 0.00 39.46 4.52
2987 3026 5.243060 ACAGAATACAAAACTACCTTTGCCC 59.757 40.000 0.00 0.00 39.46 5.36
2988 3027 4.770531 AGAATACAAAACTACCTTTGCCCC 59.229 41.667 0.00 0.00 39.46 5.80
2989 3028 1.712056 ACAAAACTACCTTTGCCCCC 58.288 50.000 0.00 0.00 39.46 5.40
2990 3029 0.601057 CAAAACTACCTTTGCCCCCG 59.399 55.000 0.00 0.00 30.03 5.73
2991 3030 0.479378 AAAACTACCTTTGCCCCCGA 59.521 50.000 0.00 0.00 0.00 5.14
2992 3031 0.251033 AAACTACCTTTGCCCCCGAC 60.251 55.000 0.00 0.00 0.00 4.79
2993 3032 1.420532 AACTACCTTTGCCCCCGACA 61.421 55.000 0.00 0.00 0.00 4.35
3001 3040 3.851128 GCCCCCGACAGGACTAGC 61.851 72.222 0.00 0.00 41.02 3.42
3010 3049 1.153549 CAGGACTAGCGAGGTTGCC 60.154 63.158 0.00 0.00 34.65 4.52
3020 3059 0.888619 CGAGGTTGCCAGTCTCACTA 59.111 55.000 0.00 0.00 0.00 2.74
3067 3106 5.964958 ACACAAGTGTATGGAAGATTTGG 57.035 39.130 3.64 0.00 42.90 3.28
3075 3114 4.586421 TGTATGGAAGATTTGGTTGCAACA 59.414 37.500 29.55 13.95 0.00 3.33
3076 3115 4.686191 ATGGAAGATTTGGTTGCAACAA 57.314 36.364 29.55 17.93 0.00 2.83
3077 3116 4.478206 TGGAAGATTTGGTTGCAACAAA 57.522 36.364 29.55 23.02 41.50 2.83
3078 3117 4.836825 TGGAAGATTTGGTTGCAACAAAA 58.163 34.783 29.42 29.42 40.74 2.44
3109 3148 6.830114 AAAAGTAAGGAATCGATAAGAGCG 57.170 37.500 0.00 0.00 0.00 5.03
3113 3152 5.749109 AGTAAGGAATCGATAAGAGCGTTTG 59.251 40.000 0.00 0.00 0.00 2.93
3131 3170 7.103641 AGCGTTTGATCTAGGTTGAAAGAATA 58.896 34.615 0.00 0.00 0.00 1.75
3175 3214 2.230025 CCATGGTGCGGTGAACAAATTA 59.770 45.455 2.57 0.00 0.00 1.40
3177 3216 1.264557 TGGTGCGGTGAACAAATTACG 59.735 47.619 0.00 0.00 0.00 3.18
3181 3220 3.059051 GTGCGGTGAACAAATTACGGTTA 60.059 43.478 0.00 0.00 0.00 2.85
3182 3221 3.059051 TGCGGTGAACAAATTACGGTTAC 60.059 43.478 0.00 0.00 0.00 2.50
3188 3227 4.451435 TGAACAAATTACGGTTACGCATCA 59.549 37.500 0.00 0.00 46.04 3.07
3260 3299 4.025040 TGAGCATCATGTCCCAATATCC 57.975 45.455 0.00 0.00 42.56 2.59
3275 3314 5.380043 CCAATATCCTGTTATCCAACTGCT 58.620 41.667 0.00 0.00 35.56 4.24
3283 3322 6.611642 TCCTGTTATCCAACTGCTTCTATAGT 59.388 38.462 0.00 0.00 35.56 2.12
3334 3373 9.474920 GCTAATGCTCCATACAAGATAGATATC 57.525 37.037 0.00 0.00 36.03 1.63
3337 3376 7.415592 TGCTCCATACAAGATAGATATCCAG 57.584 40.000 0.00 0.00 33.17 3.86
3341 3380 7.789026 TCCATACAAGATAGATATCCAGCATG 58.211 38.462 0.00 0.00 33.17 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.278238 CCGTGGTTCTAACATCTCGC 58.722 55.000 0.00 0.00 0.00 5.03
1 2 2.259618 CACCGTGGTTCTAACATCTCG 58.740 52.381 0.00 0.00 0.00 4.04
23 24 0.815734 GCACTCGTTCTAGCACCCTA 59.184 55.000 0.00 0.00 0.00 3.53
36 37 1.143305 CCAACTTCTCTGTGCACTCG 58.857 55.000 19.41 9.36 0.00 4.18
42 43 2.135933 GTCGGTTCCAACTTCTCTGTG 58.864 52.381 0.00 0.00 0.00 3.66
45 46 1.269998 CTCGTCGGTTCCAACTTCTCT 59.730 52.381 0.00 0.00 0.00 3.10
88 89 2.286365 ACACCATGGTTCCAAACGAT 57.714 45.000 16.84 0.00 0.00 3.73
122 128 3.366883 GGTTGTAGCAATCAAATTCGCCA 60.367 43.478 0.00 0.00 0.00 5.69
125 131 4.433186 TGGGTTGTAGCAATCAAATTCG 57.567 40.909 0.00 0.00 0.00 3.34
162 168 3.439540 CCGGTTGCAACATCCCCG 61.440 66.667 29.55 22.53 38.39 5.73
164 170 2.635443 CCACCGGTTGCAACATCCC 61.635 63.158 29.55 12.57 0.00 3.85
186 192 1.135083 GGTACTGACCGATGACCACAG 60.135 57.143 0.00 0.00 35.52 3.66
227 233 8.744652 TGGAAGTTACATCAGTCTTTTGAAAAA 58.255 29.630 0.00 0.00 0.00 1.94
260 267 5.887035 TGATGATGAACACCAAATATCTGCA 59.113 36.000 0.00 0.00 0.00 4.41
298 305 9.915629 GATCGGTTAAACATAGTAGATCAGATT 57.084 33.333 0.00 0.00 34.91 2.40
389 396 4.022416 ACAGCAGGAATCTAATCTAGAGCG 60.022 45.833 0.00 0.00 38.38 5.03
501 508 0.739561 AGCCTTAGTCGTCACCGATC 59.260 55.000 0.00 0.00 46.30 3.69
522 529 1.272554 CCCTAAGGACCACCACCCTC 61.273 65.000 0.00 0.00 38.94 4.30
639 646 2.125269 AATGACCACTACCGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
758 765 9.503427 CAAGTTTTCGAAAATGAAACTACTCTT 57.497 29.630 24.93 15.79 37.57 2.85
769 776 5.458779 GTCCTGGAACAAGTTTTCGAAAATG 59.541 40.000 24.93 21.20 38.70 2.32
779 786 3.197116 CCTATACCGTCCTGGAACAAGTT 59.803 47.826 0.00 0.00 42.00 2.66
781 788 2.102588 CCCTATACCGTCCTGGAACAAG 59.897 54.545 0.00 0.00 42.00 3.16
782 789 2.112998 CCCTATACCGTCCTGGAACAA 58.887 52.381 0.00 0.00 42.00 2.83
783 790 1.288633 TCCCTATACCGTCCTGGAACA 59.711 52.381 0.00 0.00 42.00 3.18
784 791 2.077687 TCCCTATACCGTCCTGGAAC 57.922 55.000 0.00 0.00 42.00 3.62
785 792 2.852714 TTCCCTATACCGTCCTGGAA 57.147 50.000 0.00 0.00 42.00 3.53
787 794 2.502538 TGTTTTCCCTATACCGTCCTGG 59.497 50.000 0.00 0.00 46.41 4.45
788 795 3.899052 TGTTTTCCCTATACCGTCCTG 57.101 47.619 0.00 0.00 0.00 3.86
789 796 4.035112 TGATGTTTTCCCTATACCGTCCT 58.965 43.478 0.00 0.00 0.00 3.85
790 797 4.411256 TGATGTTTTCCCTATACCGTCC 57.589 45.455 0.00 0.00 0.00 4.79
791 798 5.607477 TGATGATGTTTTCCCTATACCGTC 58.393 41.667 0.00 0.00 0.00 4.79
793 800 8.792830 AATATGATGATGTTTTCCCTATACCG 57.207 34.615 0.00 0.00 0.00 4.02
798 805 9.066892 GCAGTTAATATGATGATGTTTTCCCTA 57.933 33.333 0.00 0.00 0.00 3.53
799 806 7.560991 TGCAGTTAATATGATGATGTTTTCCCT 59.439 33.333 0.00 0.00 0.00 4.20
800 807 7.715657 TGCAGTTAATATGATGATGTTTTCCC 58.284 34.615 0.00 0.00 0.00 3.97
801 808 9.241317 CTTGCAGTTAATATGATGATGTTTTCC 57.759 33.333 0.00 0.00 0.00 3.13
805 812 7.255381 GGCTCTTGCAGTTAATATGATGATGTT 60.255 37.037 0.00 0.00 41.91 2.71
806 813 6.206243 GGCTCTTGCAGTTAATATGATGATGT 59.794 38.462 0.00 0.00 41.91 3.06
807 814 6.430308 AGGCTCTTGCAGTTAATATGATGATG 59.570 38.462 0.00 0.00 41.91 3.07
808 815 6.430308 CAGGCTCTTGCAGTTAATATGATGAT 59.570 38.462 0.00 0.00 41.91 2.45
809 816 5.761726 CAGGCTCTTGCAGTTAATATGATGA 59.238 40.000 0.00 0.00 41.91 2.92
810 817 5.562307 GCAGGCTCTTGCAGTTAATATGATG 60.562 44.000 0.00 0.00 43.53 3.07
811 818 4.518211 GCAGGCTCTTGCAGTTAATATGAT 59.482 41.667 0.00 0.00 43.53 2.45
812 819 3.879295 GCAGGCTCTTGCAGTTAATATGA 59.121 43.478 0.00 0.00 43.53 2.15
813 820 3.303593 CGCAGGCTCTTGCAGTTAATATG 60.304 47.826 4.89 0.00 44.28 1.78
814 821 2.874701 CGCAGGCTCTTGCAGTTAATAT 59.125 45.455 4.89 0.00 44.28 1.28
815 822 2.093711 TCGCAGGCTCTTGCAGTTAATA 60.094 45.455 4.89 0.00 44.28 0.98
816 823 1.089920 CGCAGGCTCTTGCAGTTAAT 58.910 50.000 4.89 0.00 44.28 1.40
817 824 0.034756 TCGCAGGCTCTTGCAGTTAA 59.965 50.000 4.89 0.00 44.28 2.01
818 825 0.034756 TTCGCAGGCTCTTGCAGTTA 59.965 50.000 4.89 0.00 44.28 2.24
875 882 2.249557 CTGGACGATGTGCTTGCTGC 62.250 60.000 0.00 0.00 43.25 5.25
891 898 1.354368 TCAGGAAGGGCTTAAACCTGG 59.646 52.381 0.00 0.00 45.41 4.45
913 920 0.955919 GAGAAAACAGGAGCCCACCG 60.956 60.000 0.00 0.00 34.73 4.94
925 932 4.159693 AGGGTTTTGGTTGTCTGAGAAAAC 59.840 41.667 6.97 6.97 36.31 2.43
964 972 7.767250 AGAGGGTTTTTCTTCCAGAATTTAG 57.233 36.000 0.00 0.00 33.67 1.85
1234 1242 0.899720 TCGGTTAAGAAGGCACGGAT 59.100 50.000 0.00 0.00 0.00 4.18
1248 1256 0.613853 TCAGGGATTCGGTCTCGGTT 60.614 55.000 0.00 0.00 36.95 4.44
1425 1444 1.023513 GCAGTTAGCACAGGCAGAGG 61.024 60.000 0.00 0.00 44.61 3.69
1460 1483 5.367945 TCTATCCCAAGTTACCAACCATC 57.632 43.478 0.00 0.00 0.00 3.51
1461 1484 5.994416 ATCTATCCCAAGTTACCAACCAT 57.006 39.130 0.00 0.00 0.00 3.55
1462 1485 5.505780 CAATCTATCCCAAGTTACCAACCA 58.494 41.667 0.00 0.00 0.00 3.67
1463 1486 4.887655 CCAATCTATCCCAAGTTACCAACC 59.112 45.833 0.00 0.00 0.00 3.77
1464 1487 4.887655 CCCAATCTATCCCAAGTTACCAAC 59.112 45.833 0.00 0.00 0.00 3.77
1465 1488 4.079443 CCCCAATCTATCCCAAGTTACCAA 60.079 45.833 0.00 0.00 0.00 3.67
1469 1492 3.138283 CAGCCCCAATCTATCCCAAGTTA 59.862 47.826 0.00 0.00 0.00 2.24
1488 1511 3.406764 AGGTGACAAAGATCAGAACAGC 58.593 45.455 0.00 0.00 0.00 4.40
1516 1539 5.921976 TGTGATGCACAAAACTTGATCAATC 59.078 36.000 8.96 0.06 41.69 2.67
1519 1542 4.915158 TGTGATGCACAAAACTTGATCA 57.085 36.364 0.00 0.00 41.69 2.92
1534 1557 3.635373 AGCAGGATTAAAGGCATGTGATG 59.365 43.478 0.00 0.00 0.00 3.07
1535 1558 3.907221 AGCAGGATTAAAGGCATGTGAT 58.093 40.909 0.00 0.00 0.00 3.06
1536 1559 3.370840 AGCAGGATTAAAGGCATGTGA 57.629 42.857 0.00 0.00 0.00 3.58
1537 1560 4.460948 AAAGCAGGATTAAAGGCATGTG 57.539 40.909 0.00 0.00 0.00 3.21
1538 1561 4.527816 TCAAAAGCAGGATTAAAGGCATGT 59.472 37.500 0.00 0.00 0.00 3.21
1539 1562 5.075858 TCAAAAGCAGGATTAAAGGCATG 57.924 39.130 0.00 0.00 0.00 4.06
1558 1581 5.219343 TGAGCAGAAACTCAGATTCTCAA 57.781 39.130 0.00 0.00 41.72 3.02
1559 1582 4.879197 TGAGCAGAAACTCAGATTCTCA 57.121 40.909 0.00 0.00 41.72 3.27
1570 1593 4.400567 AGGATTAAAGGCATGAGCAGAAAC 59.599 41.667 0.00 0.00 44.61 2.78
1573 1596 3.548770 CAGGATTAAAGGCATGAGCAGA 58.451 45.455 0.00 0.00 44.61 4.26
1574 1597 2.034305 GCAGGATTAAAGGCATGAGCAG 59.966 50.000 0.00 0.00 44.61 4.24
1577 1600 4.931661 AATGCAGGATTAAAGGCATGAG 57.068 40.909 0.00 0.00 45.52 2.90
1579 1602 6.395426 TTCTAATGCAGGATTAAAGGCATG 57.605 37.500 0.00 0.00 45.52 4.06
1596 1619 5.566469 TGGGAAAACAACTCGGATTCTAAT 58.434 37.500 0.00 0.00 0.00 1.73
1598 1621 4.627284 TGGGAAAACAACTCGGATTCTA 57.373 40.909 0.00 0.00 0.00 2.10
1601 1624 4.799255 GCAAATGGGAAAACAACTCGGATT 60.799 41.667 0.00 0.00 0.00 3.01
1614 1637 4.720775 AAAAATTGAGGGCAAATGGGAA 57.279 36.364 0.00 0.00 37.59 3.97
1646 1669 9.308000 CCAGTCTCCTCTATCTGTTTAAGATAT 57.692 37.037 0.00 0.00 45.02 1.63
1653 1676 3.012959 TCCCCAGTCTCCTCTATCTGTTT 59.987 47.826 0.00 0.00 0.00 2.83
1694 1717 5.122396 GCTGGAACGACACTTATTTTCAGAT 59.878 40.000 0.00 0.00 0.00 2.90
1713 1736 5.865085 AGTTCTTGTAAGTGTAATGCTGGA 58.135 37.500 0.00 0.00 0.00 3.86
1714 1737 6.560253 AAGTTCTTGTAAGTGTAATGCTGG 57.440 37.500 0.00 0.00 0.00 4.85
1964 1987 3.270877 GGTGATATTGTCGGGATATGCC 58.729 50.000 2.51 2.51 0.00 4.40
1967 1990 4.782691 TGGATGGTGATATTGTCGGGATAT 59.217 41.667 0.00 0.00 0.00 1.63
2017 2040 4.858850 TGTGGCCTGAACATCATCTTTAT 58.141 39.130 3.32 0.00 0.00 1.40
2115 2138 9.403583 AGTAATTAAAGACAACCTTCAACAAGA 57.596 29.630 0.00 0.00 33.02 3.02
2151 2174 8.910944 ACGGAGAGTAGTTAATTAATAAGAGCA 58.089 33.333 0.31 0.00 0.00 4.26
2182 2205 2.689983 TCGAGCTTACTGCATGAGATCA 59.310 45.455 0.00 0.00 45.94 2.92
2366 2389 9.358406 TGCCTTTCTCATGAACATTATATGAAT 57.642 29.630 0.00 0.00 31.11 2.57
2580 2607 0.380733 TACTAGCTGGACATCACGCG 59.619 55.000 3.53 3.53 0.00 6.01
2582 2609 4.799678 CCTAATACTAGCTGGACATCACG 58.200 47.826 3.17 0.00 0.00 4.35
2652 2685 6.231211 TCTATCGGCCATCTCTTTAATTTCC 58.769 40.000 2.24 0.00 0.00 3.13
2660 2693 4.963318 TTGATTCTATCGGCCATCTCTT 57.037 40.909 2.24 0.00 0.00 2.85
2665 2698 8.299570 GTTCATTTTATTGATTCTATCGGCCAT 58.700 33.333 2.24 0.00 0.00 4.40
2667 2700 7.875971 AGTTCATTTTATTGATTCTATCGGCC 58.124 34.615 0.00 0.00 0.00 6.13
2865 2904 7.148052 GCTCTAGGTCTAAGAACATACAACTGA 60.148 40.741 0.00 0.00 0.00 3.41
2878 2917 7.387643 ACAAAAAGGTTAGCTCTAGGTCTAAG 58.612 38.462 0.00 0.00 0.00 2.18
2902 2941 9.503427 GTACTGATCATTGGCTAAACAATTTAC 57.497 33.333 0.00 0.00 38.94 2.01
2967 3006 3.835978 GGGGGCAAAGGTAGTTTTGTATT 59.164 43.478 1.12 0.00 39.62 1.89
2968 3007 3.437213 GGGGGCAAAGGTAGTTTTGTAT 58.563 45.455 1.12 0.00 39.62 2.29
2969 3008 2.814842 CGGGGGCAAAGGTAGTTTTGTA 60.815 50.000 1.12 0.00 39.62 2.41
2970 3009 1.712056 GGGGGCAAAGGTAGTTTTGT 58.288 50.000 1.12 0.00 39.62 2.83
2971 3010 0.601057 CGGGGGCAAAGGTAGTTTTG 59.399 55.000 0.00 0.00 40.25 2.44
2972 3011 0.479378 TCGGGGGCAAAGGTAGTTTT 59.521 50.000 0.00 0.00 0.00 2.43
2973 3012 0.251033 GTCGGGGGCAAAGGTAGTTT 60.251 55.000 0.00 0.00 0.00 2.66
2974 3013 1.377612 GTCGGGGGCAAAGGTAGTT 59.622 57.895 0.00 0.00 0.00 2.24
2975 3014 1.838073 CTGTCGGGGGCAAAGGTAGT 61.838 60.000 0.00 0.00 0.00 2.73
2976 3015 1.078426 CTGTCGGGGGCAAAGGTAG 60.078 63.158 0.00 0.00 0.00 3.18
2977 3016 2.598787 CCTGTCGGGGGCAAAGGTA 61.599 63.158 0.00 0.00 0.00 3.08
2978 3017 3.966543 CCTGTCGGGGGCAAAGGT 61.967 66.667 0.00 0.00 0.00 3.50
2979 3018 3.646715 TCCTGTCGGGGGCAAAGG 61.647 66.667 0.00 0.00 35.33 3.11
2980 3019 1.550130 TAGTCCTGTCGGGGGCAAAG 61.550 60.000 0.00 0.00 32.56 2.77
2981 3020 1.536907 TAGTCCTGTCGGGGGCAAA 60.537 57.895 0.00 0.00 32.56 3.68
2982 3021 1.987855 CTAGTCCTGTCGGGGGCAA 60.988 63.158 0.00 0.00 32.56 4.52
2983 3022 2.363795 CTAGTCCTGTCGGGGGCA 60.364 66.667 0.00 0.00 32.56 5.36
2984 3023 3.851128 GCTAGTCCTGTCGGGGGC 61.851 72.222 0.00 0.00 35.33 5.80
2985 3024 3.528370 CGCTAGTCCTGTCGGGGG 61.528 72.222 0.00 0.00 35.33 5.40
2986 3025 2.439701 TCGCTAGTCCTGTCGGGG 60.440 66.667 0.00 0.00 35.33 5.73
2987 3026 2.482333 CCTCGCTAGTCCTGTCGGG 61.482 68.421 0.00 0.00 0.00 5.14
2988 3027 1.313812 AACCTCGCTAGTCCTGTCGG 61.314 60.000 0.00 0.00 0.00 4.79
2989 3028 0.179161 CAACCTCGCTAGTCCTGTCG 60.179 60.000 0.00 0.00 0.00 4.35
2990 3029 0.458716 GCAACCTCGCTAGTCCTGTC 60.459 60.000 0.00 0.00 0.00 3.51
2991 3030 1.592223 GCAACCTCGCTAGTCCTGT 59.408 57.895 0.00 0.00 0.00 4.00
2992 3031 1.153549 GGCAACCTCGCTAGTCCTG 60.154 63.158 0.00 0.00 0.00 3.86
2993 3032 1.608717 CTGGCAACCTCGCTAGTCCT 61.609 60.000 0.00 0.00 35.88 3.85
3001 3040 0.888619 TAGTGAGACTGGCAACCTCG 59.111 55.000 10.09 0.00 0.00 4.63
3010 3049 6.333416 TGTAATTAGCAAGCTAGTGAGACTG 58.667 40.000 1.68 0.00 0.00 3.51
3020 3059 7.466746 TTTCAATCCTTGTAATTAGCAAGCT 57.533 32.000 16.20 0.00 41.27 3.74
3041 3080 7.382218 CCAAATCTTCCATACACTTGTGTTTTC 59.618 37.037 11.80 0.00 0.00 2.29
3099 3138 4.861210 ACCTAGATCAAACGCTCTTATCG 58.139 43.478 0.00 0.00 0.00 2.92
3102 3141 5.654603 TCAACCTAGATCAAACGCTCTTA 57.345 39.130 0.00 0.00 0.00 2.10
3131 3170 4.286813 TCCTGGTCCATCTTCCTCTTAT 57.713 45.455 0.00 0.00 0.00 1.73
3162 3201 3.724277 CGTAACCGTAATTTGTTCACCG 58.276 45.455 0.00 0.00 0.00 4.94
3175 3214 7.074507 TGTAATTTAAATGATGCGTAACCGT 57.925 32.000 0.39 0.00 36.15 4.83
3177 3216 8.905103 AACTGTAATTTAAATGATGCGTAACC 57.095 30.769 0.39 0.00 0.00 2.85
3209 3248 7.645058 TGATTATGCTATGGATAGTCATCGA 57.355 36.000 0.00 0.00 32.95 3.59
3224 3263 7.393515 ACATGATGCTCATATGTTGATTATGCT 59.606 33.333 0.00 0.00 34.28 3.79
3226 3265 8.182227 GGACATGATGCTCATATGTTGATTATG 58.818 37.037 0.00 7.85 34.28 1.90
3254 3293 6.904626 AGAAGCAGTTGGATAACAGGATATT 58.095 36.000 0.00 0.00 39.30 1.28
3260 3299 8.723942 AAACTATAGAAGCAGTTGGATAACAG 57.276 34.615 6.78 0.00 39.30 3.16
3316 3355 7.634429 GCATGCTGGATATCTATCTTGTATGGA 60.634 40.741 11.37 0.00 33.61 3.41
3328 3367 6.540995 ACTTTAAGATGCATGCTGGATATCT 58.459 36.000 20.33 14.90 0.00 1.98


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

AutoCloner maintained by Alex Coulton.