Multiple sequence alignment - TraesCS1A01G055200

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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 TraesCS1A01G055200 chr1A 100.000 3412 0 0 1 3412 36281282 36277871 0.000000e+00 6301
1 TraesCS1A01G055200 chr1A 86.614 254 27 5 887 1135 193520209 193519958 1.210000e-69 274
2 TraesCS1A01G055200 chr1A 98.485 66 0 1 712 777 384314897 384314833 7.740000e-22 115
3 TraesCS1A01G055200 chr1D 92.673 1979 84 19 784 2747 36845480 36843548 0.000000e+00 2795
4 TraesCS1A01G055200 chr1D 89.212 723 33 9 17 716 36846180 36845480 0.000000e+00 861
5 TraesCS1A01G055200 chr1D 93.462 413 13 3 3014 3412 36842793 36842381 4.870000e-168 601
6 TraesCS1A01G055200 chr1D 94.253 261 13 1 2748 3008 36843391 36843133 6.860000e-107 398
7 TraesCS1A01G055200 chr1D 85.547 256 32 3 884 1136 308871471 308871218 2.610000e-66 263
8 TraesCS1A01G055200 chr1D 80.252 238 36 5 2453 2687 36842968 36842739 5.860000e-38 169
9 TraesCS1A01G055200 chr1B 91.106 922 55 13 1204 2107 56893237 56892325 0.000000e+00 1223
10 TraesCS1A01G055200 chr1B 96.764 649 21 0 2099 2747 56891488 56890840 0.000000e+00 1083
11 TraesCS1A01G055200 chr1B 90.719 431 28 8 781 1207 56893781 56893359 6.390000e-157 564
12 TraesCS1A01G055200 chr1B 91.827 416 14 7 3014 3412 56889961 56889549 2.300000e-156 562
13 TraesCS1A01G055200 chr1B 83.910 578 45 22 175 716 56894329 56893764 3.040000e-140 508
14 TraesCS1A01G055200 chr1B 84.825 257 32 5 884 1135 596880264 596880010 5.650000e-63 252
15 TraesCS1A01G055200 chr1B 91.824 159 9 3 2845 3003 56890457 56890303 5.730000e-53 219
16 TraesCS1A01G055200 chr1B 98.077 104 2 0 2744 2847 56890718 56890615 7.520000e-42 182
17 TraesCS1A01G055200 chr1B 81.277 235 33 6 2453 2687 56890133 56889910 2.710000e-41 180
18 TraesCS1A01G055200 chr6B 87.712 236 23 4 884 1116 64075644 64075412 1.560000e-68 270
19 TraesCS1A01G055200 chr6B 97.101 69 1 1 712 780 704696046 704696113 7.740000e-22 115
20 TraesCS1A01G055200 chr6B 93.506 77 2 2 712 786 212973464 212973389 1.000000e-20 111
21 TraesCS1A01G055200 chr5A 86.047 258 27 7 884 1135 81351741 81351995 5.610000e-68 268
22 TraesCS1A01G055200 chr5A 98.529 68 0 1 712 779 633983934 633983868 5.980000e-23 119
23 TraesCS1A01G055200 chr3A 85.214 257 29 6 884 1135 618091724 618091472 4.370000e-64 255
24 TraesCS1A01G055200 chr2A 85.098 255 31 6 884 1135 374125454 374125704 1.570000e-63 254
25 TraesCS1A01G055200 chr3B 95.946 74 0 3 711 782 805577447 805577519 2.150000e-22 117
26 TraesCS1A01G055200 chr2B 98.507 67 0 1 711 777 142536929 142536864 2.150000e-22 117
27 TraesCS1A01G055200 chrUn 95.833 72 2 1 712 783 282392584 282392514 7.740000e-22 115
28 TraesCS1A01G055200 chr7B 98.485 66 0 1 712 777 3553239 3553175 7.740000e-22 115
29 TraesCS1A01G055200 chr7B 98.485 66 0 1 712 777 457548598 457548662 7.740000e-22 115


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 TraesCS1A01G055200 chr1A 36277871 36281282 3411 True 6301.000 6301 100.0000 1 3412 1 chr1A.!!$R1 3411
1 TraesCS1A01G055200 chr1D 36842381 36846180 3799 True 964.800 2795 89.9704 17 3412 5 chr1D.!!$R2 3395
2 TraesCS1A01G055200 chr1B 56889549 56894329 4780 True 565.125 1223 90.6880 175 3412 8 chr1B.!!$R2 3237

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
971 1041 0.037790 GATGCTGTCTCTATCCCGGC 60.038 60.0 0.0 0.0 0.0 6.13 F
1546 1754 0.112995 TTGCAATGGGAAGCCTGTCT 59.887 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 3267 0.532862 GGCACAGGGTATCCATGTCG 60.533 60.000 3.06 1.92 34.83 4.35 R
2936 4319 1.271102 GATCGGAGGGAGCATACACTC 59.729 57.143 0.00 0.00 39.35 3.51 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
57 58 4.020573 TCCTTTCAGGCGAGATTCAGTTAA 60.021 41.667 0.00 0.00 34.61 2.01
58 59 4.695455 CCTTTCAGGCGAGATTCAGTTAAA 59.305 41.667 0.00 0.00 0.00 1.52
59 60 5.181245 CCTTTCAGGCGAGATTCAGTTAAAA 59.819 40.000 0.00 0.00 0.00 1.52
60 61 6.293955 CCTTTCAGGCGAGATTCAGTTAAAAA 60.294 38.462 0.00 0.00 0.00 1.94
61 62 5.862924 TCAGGCGAGATTCAGTTAAAAAG 57.137 39.130 0.00 0.00 0.00 2.27
62 63 5.547465 TCAGGCGAGATTCAGTTAAAAAGA 58.453 37.500 0.00 0.00 0.00 2.52
63 64 6.173339 TCAGGCGAGATTCAGTTAAAAAGAT 58.827 36.000 0.00 0.00 0.00 2.40
64 65 6.655003 TCAGGCGAGATTCAGTTAAAAAGATT 59.345 34.615 0.00 0.00 0.00 2.40
65 66 6.963805 CAGGCGAGATTCAGTTAAAAAGATTC 59.036 38.462 0.00 0.00 0.00 2.52
66 67 5.960105 GGCGAGATTCAGTTAAAAAGATTCG 59.040 40.000 0.00 0.00 0.00 3.34
67 68 5.960105 GCGAGATTCAGTTAAAAAGATTCGG 59.040 40.000 0.00 0.00 0.00 4.30
68 69 6.402226 GCGAGATTCAGTTAAAAAGATTCGGT 60.402 38.462 0.00 0.00 0.00 4.69
69 70 7.174082 CGAGATTCAGTTAAAAAGATTCGGTC 58.826 38.462 0.00 0.00 0.00 4.79
70 71 7.063544 CGAGATTCAGTTAAAAAGATTCGGTCT 59.936 37.037 0.00 0.00 39.43 3.85
84 85 6.522054 AGATTCGGTCTTCTTTCTGTAACAA 58.478 36.000 0.00 0.00 31.47 2.83
87 88 5.054477 TCGGTCTTCTTTCTGTAACAAAGG 58.946 41.667 0.00 0.00 32.55 3.11
107 108 2.751806 GGCAAAGATTCTCCCTTCTGTG 59.248 50.000 0.00 0.00 31.51 3.66
108 109 3.416156 GCAAAGATTCTCCCTTCTGTGT 58.584 45.455 0.00 0.00 31.09 3.72
137 138 3.370231 CCCGGAAAAGCCCAACCG 61.370 66.667 0.73 0.00 44.16 4.44
140 141 2.338620 GGAAAAGCCCAACCGTGC 59.661 61.111 0.00 0.00 0.00 5.34
259 264 1.488393 CAGACCTTCCTTCCTCCATCC 59.512 57.143 0.00 0.00 0.00 3.51
321 326 5.358160 GGGAGAAGAGAAGAGAAGAGAAGAG 59.642 48.000 0.00 0.00 0.00 2.85
403 446 1.372251 CGGCCCGATCTCGATCTTG 60.372 63.158 0.00 0.00 43.02 3.02
453 496 1.697754 GGGATGGGATGGGAGTGGT 60.698 63.158 0.00 0.00 0.00 4.16
558 609 2.190578 GGAGTGGGAGCCGGAATG 59.809 66.667 5.05 0.00 0.00 2.67
609 669 6.745159 TCGATAGATTGATGCTAGGAGTAC 57.255 41.667 0.00 0.00 42.67 2.73
620 680 5.258456 TGCTAGGAGTACTACCATTTTCG 57.742 43.478 0.00 0.00 0.00 3.46
624 684 5.479124 AGGAGTACTACCATTTTCGTTGT 57.521 39.130 0.00 0.00 0.00 3.32
653 713 2.543848 TGTAATTTCGGATGCGCAGATC 59.456 45.455 18.32 9.68 0.00 2.75
660 720 3.873026 GATGCGCAGATCCCCTCGG 62.873 68.421 18.32 0.00 0.00 4.63
671 731 1.125633 TCCCCTCGGCAACTTATACC 58.874 55.000 0.00 0.00 0.00 2.73
678 738 2.367567 TCGGCAACTTATACCCATCCTC 59.632 50.000 0.00 0.00 0.00 3.71
721 781 5.984233 TGTTATGCTAGTTTATTGAGCCG 57.016 39.130 0.00 0.00 35.24 5.52
722 782 5.424757 TGTTATGCTAGTTTATTGAGCCGT 58.575 37.500 0.00 0.00 35.24 5.68
723 783 6.575267 TGTTATGCTAGTTTATTGAGCCGTA 58.425 36.000 0.00 0.00 35.24 4.02
725 785 7.170828 TGTTATGCTAGTTTATTGAGCCGTATG 59.829 37.037 0.00 0.00 35.24 2.39
726 786 3.807622 TGCTAGTTTATTGAGCCGTATGC 59.192 43.478 0.00 0.00 41.71 3.14
727 787 3.807622 GCTAGTTTATTGAGCCGTATGCA 59.192 43.478 0.00 0.00 44.83 3.96
728 788 4.452455 GCTAGTTTATTGAGCCGTATGCAT 59.548 41.667 3.79 3.79 44.83 3.96
729 789 5.389935 GCTAGTTTATTGAGCCGTATGCATC 60.390 44.000 0.19 0.00 44.83 3.91
730 790 4.708177 AGTTTATTGAGCCGTATGCATCT 58.292 39.130 0.19 0.00 44.83 2.90
731 791 5.126067 AGTTTATTGAGCCGTATGCATCTT 58.874 37.500 0.19 0.00 44.83 2.40
732 792 6.288294 AGTTTATTGAGCCGTATGCATCTTA 58.712 36.000 0.19 0.00 44.83 2.10
733 793 6.936900 AGTTTATTGAGCCGTATGCATCTTAT 59.063 34.615 0.19 0.00 44.83 1.73
734 794 7.445402 AGTTTATTGAGCCGTATGCATCTTATT 59.555 33.333 0.19 0.00 44.83 1.40
735 795 5.618056 ATTGAGCCGTATGCATCTTATTG 57.382 39.130 0.19 0.00 44.83 1.90
736 796 4.335400 TGAGCCGTATGCATCTTATTGA 57.665 40.909 0.19 0.00 44.83 2.57
737 797 4.898320 TGAGCCGTATGCATCTTATTGAT 58.102 39.130 0.19 0.00 44.83 2.57
747 807 4.750952 CATCTTATTGATGCAGAGGCTG 57.249 45.455 0.00 0.00 44.96 4.85
748 808 3.204306 TCTTATTGATGCAGAGGCTGG 57.796 47.619 0.00 0.00 41.91 4.85
749 809 2.158711 TCTTATTGATGCAGAGGCTGGG 60.159 50.000 0.00 0.00 41.91 4.45
750 810 0.475475 TATTGATGCAGAGGCTGGGG 59.525 55.000 0.00 0.00 41.91 4.96
751 811 1.578215 ATTGATGCAGAGGCTGGGGT 61.578 55.000 0.00 0.00 41.91 4.95
752 812 1.792757 TTGATGCAGAGGCTGGGGTT 61.793 55.000 0.00 0.00 41.91 4.11
753 813 1.751927 GATGCAGAGGCTGGGGTTG 60.752 63.158 0.00 0.00 41.91 3.77
754 814 3.951769 ATGCAGAGGCTGGGGTTGC 62.952 63.158 0.00 0.00 41.91 4.17
755 815 4.666253 GCAGAGGCTGGGGTTGCA 62.666 66.667 0.00 0.00 36.96 4.08
756 816 2.674380 CAGAGGCTGGGGTTGCAC 60.674 66.667 0.00 0.00 0.00 4.57
757 817 3.971702 AGAGGCTGGGGTTGCACC 61.972 66.667 0.00 0.00 37.60 5.01
768 828 2.700722 GGTTGCACCCCTTTTCAAAA 57.299 45.000 0.00 0.00 30.04 2.44
769 829 2.992593 GGTTGCACCCCTTTTCAAAAA 58.007 42.857 0.00 0.00 30.04 1.94
864 924 2.307686 GGAAATGCCGGGGGATATAAGA 59.692 50.000 2.18 0.00 0.00 2.10
865 925 3.610911 GAAATGCCGGGGGATATAAGAG 58.389 50.000 2.18 0.00 0.00 2.85
866 926 1.584724 ATGCCGGGGGATATAAGAGG 58.415 55.000 2.18 0.00 0.00 3.69
867 927 0.192566 TGCCGGGGGATATAAGAGGT 59.807 55.000 2.18 0.00 0.00 3.85
898 965 9.321562 GTTATTACTAGCCTAGTTGCATTTACA 57.678 33.333 10.14 0.00 40.14 2.41
964 1034 6.527423 TGCATTGATATTGATGCTGTCTCTA 58.473 36.000 18.97 1.93 46.68 2.43
970 1040 1.332195 TGATGCTGTCTCTATCCCGG 58.668 55.000 0.00 0.00 0.00 5.73
971 1041 0.037790 GATGCTGTCTCTATCCCGGC 60.038 60.000 0.00 0.00 0.00 6.13
978 1048 1.742268 GTCTCTATCCCGGCGGTATAC 59.258 57.143 26.32 5.74 0.00 1.47
1151 1221 1.597742 TGCACTTTCTTGTGGAGAGC 58.402 50.000 0.00 0.00 38.31 4.09
1157 1231 0.319900 TTCTTGTGGAGAGCGCTGAC 60.320 55.000 18.48 8.47 35.37 3.51
1158 1232 1.181741 TCTTGTGGAGAGCGCTGACT 61.182 55.000 18.48 6.45 0.00 3.41
1159 1233 1.005748 TTGTGGAGAGCGCTGACTG 60.006 57.895 18.48 0.00 0.00 3.51
1160 1234 1.463553 TTGTGGAGAGCGCTGACTGA 61.464 55.000 18.48 0.00 0.00 3.41
1249 1451 4.706962 ACCACCTCCTTTGCAATAAGATTC 59.293 41.667 0.00 0.00 0.00 2.52
1250 1452 4.706476 CCACCTCCTTTGCAATAAGATTCA 59.294 41.667 0.00 0.00 0.00 2.57
1252 1454 6.460676 CCACCTCCTTTGCAATAAGATTCATC 60.461 42.308 0.00 0.00 0.00 2.92
1258 1460 3.544684 TGCAATAAGATTCATCGCCTGT 58.455 40.909 0.00 0.00 0.00 4.00
1262 1464 5.449041 GCAATAAGATTCATCGCCTGTGAAA 60.449 40.000 0.00 0.00 38.89 2.69
1275 1477 3.707316 CCTGTGAAATTTGGGTCCCATA 58.293 45.455 12.68 7.62 31.53 2.74
1354 1557 5.353678 GGGAGCATGCATAATCAGACTAATC 59.646 44.000 21.98 2.74 0.00 1.75
1363 1566 7.994911 TGCATAATCAGACTAATCATGGAAACT 59.005 33.333 0.00 0.00 0.00 2.66
1373 1576 4.525912 ATCATGGAAACTTCAAACTGCC 57.474 40.909 0.00 0.00 0.00 4.85
1406 1609 7.892609 TCTTAGCTGACTGTAACTTGTTATGA 58.107 34.615 0.00 0.00 0.00 2.15
1442 1650 9.834628 GAATAATTTAACTCGGTGTGAATTTCA 57.165 29.630 0.00 0.00 31.83 2.69
1546 1754 0.112995 TTGCAATGGGAAGCCTGTCT 59.887 50.000 0.00 0.00 0.00 3.41
1561 1769 3.149196 CCTGTCTATTGTGGCACTTGTT 58.851 45.455 19.83 3.48 0.00 2.83
1688 1896 7.455058 TGTTATTGCTGAGTAAGTTCCCTTTA 58.545 34.615 0.00 0.00 31.89 1.85
1706 1914 4.517285 CTTTAGCTCTGTGGCCAAGAATA 58.483 43.478 7.24 6.27 0.00 1.75
1710 1918 2.877168 GCTCTGTGGCCAAGAATATCAG 59.123 50.000 7.24 9.22 0.00 2.90
1741 1953 8.082852 ACTAGATGCAATAGTACCTAATGTTCG 58.917 37.037 12.03 0.00 31.71 3.95
1754 1966 4.640201 CCTAATGTTCGGATGTTGGTTCAT 59.360 41.667 0.00 0.00 0.00 2.57
1755 1967 4.439305 AATGTTCGGATGTTGGTTCATG 57.561 40.909 0.00 0.00 0.00 3.07
1792 2004 6.294342 GCCATTTGATGAAGATTAGCTATGCA 60.294 38.462 0.00 0.00 0.00 3.96
1793 2005 7.577046 GCCATTTGATGAAGATTAGCTATGCAT 60.577 37.037 3.79 3.79 0.00 3.96
1794 2006 8.304596 CCATTTGATGAAGATTAGCTATGCATT 58.695 33.333 3.54 0.00 0.00 3.56
1798 2010 6.993902 TGATGAAGATTAGCTATGCATTGTCA 59.006 34.615 3.54 1.00 0.00 3.58
1799 2011 6.856135 TGAAGATTAGCTATGCATTGTCAG 57.144 37.500 3.54 0.00 0.00 3.51
1800 2012 6.351711 TGAAGATTAGCTATGCATTGTCAGT 58.648 36.000 3.54 0.00 0.00 3.41
1801 2013 6.481313 TGAAGATTAGCTATGCATTGTCAGTC 59.519 38.462 3.54 1.83 0.00 3.51
1802 2014 4.987285 AGATTAGCTATGCATTGTCAGTCG 59.013 41.667 3.54 0.00 0.00 4.18
1803 2015 2.680312 AGCTATGCATTGTCAGTCGT 57.320 45.000 3.54 0.00 0.00 4.34
1806 2018 3.372206 AGCTATGCATTGTCAGTCGTTTC 59.628 43.478 3.54 0.00 0.00 2.78
1829 2041 4.935352 TGGACCCTTGTTTCTTTTGATG 57.065 40.909 0.00 0.00 0.00 3.07
1834 2046 5.205056 ACCCTTGTTTCTTTTGATGGTGTA 58.795 37.500 0.00 0.00 0.00 2.90
1844 2056 7.905604 TCTTTTGATGGTGTACACTTCATAG 57.094 36.000 24.55 22.01 0.00 2.23
1845 2057 7.676004 TCTTTTGATGGTGTACACTTCATAGA 58.324 34.615 24.55 23.35 0.00 1.98
1846 2058 8.321353 TCTTTTGATGGTGTACACTTCATAGAT 58.679 33.333 24.55 6.53 0.00 1.98
1873 2085 2.756829 TGCTGAACATTGCCAACATTG 58.243 42.857 0.00 0.00 34.14 2.82
1876 2088 4.021280 TGCTGAACATTGCCAACATTGTAT 60.021 37.500 0.00 0.00 38.97 2.29
1883 2095 6.757237 ACATTGCCAACATTGTATTTCTTCA 58.243 32.000 0.00 0.00 38.32 3.02
1949 2161 6.700960 TGTTCAAGTGTTTAATTCTGCCATTG 59.299 34.615 0.00 0.00 0.00 2.82
2002 2214 9.929722 TTAATTCTGCAAGCTGTTATATTTACG 57.070 29.630 0.00 0.00 0.00 3.18
2003 2215 6.978343 TTCTGCAAGCTGTTATATTTACGT 57.022 33.333 0.00 0.00 0.00 3.57
2006 2218 5.328691 TGCAAGCTGTTATATTTACGTTGC 58.671 37.500 0.00 0.00 38.56 4.17
2129 3192 7.907389 ACTGTTCTTATGAAATCAGACTGGTA 58.093 34.615 12.96 0.00 33.30 3.25
2171 3234 2.456119 GCTCTGGGCAACGATCACG 61.456 63.158 0.00 0.00 42.25 4.35
2196 3259 0.389296 TCACCATCGCACCAGTAACG 60.389 55.000 0.00 0.00 0.00 3.18
2204 3267 0.584876 GCACCAGTAACGTTCACCAC 59.415 55.000 2.82 0.00 0.00 4.16
2385 3448 3.058016 CGAATATGGCCAGGTTTATGCTG 60.058 47.826 13.05 0.00 0.00 4.41
2415 3478 1.112916 TGGCACGAAGGTCTGAGTCA 61.113 55.000 0.00 0.00 0.00 3.41
2437 3500 6.978080 GTCAGTTAACTGCAGGATTTCAAAAA 59.022 34.615 27.49 5.38 43.46 1.94
2546 3609 4.276678 CCATTCCCGTAGTCGTACATAAGA 59.723 45.833 0.00 0.00 35.01 2.10
2690 3753 4.219033 GTTCCGTTGTTCTGCTATTTGTG 58.781 43.478 0.00 0.00 0.00 3.33
2809 4032 8.051535 AGAATCAAAGAACAGATACATGGACAT 58.948 33.333 0.00 0.00 0.00 3.06
2810 4033 6.990341 TCAAAGAACAGATACATGGACATG 57.010 37.500 10.57 10.57 44.15 3.21
2864 4247 8.891985 ATGATGTAGATACCATCATGTCTAGT 57.108 34.615 13.45 0.00 42.42 2.57
2895 4278 7.113544 GCTAAATGTTCTGCTTTAACAACTCAC 59.886 37.037 3.76 0.00 40.05 3.51
2896 4279 6.449635 AATGTTCTGCTTTAACAACTCACA 57.550 33.333 3.76 0.00 40.05 3.58
2921 4304 5.104735 ACAATGGCAAAAAGGGTTCTAAACA 60.105 36.000 0.00 0.00 0.00 2.83
2923 4306 5.017294 TGGCAAAAAGGGTTCTAAACAAG 57.983 39.130 0.00 0.00 0.00 3.16
2936 4319 8.727910 GGGTTCTAAACAAGAAGTATTACAAGG 58.272 37.037 0.00 0.00 44.94 3.61
2985 4368 1.618837 GTCTGAGTCAGTTACCTGCCA 59.381 52.381 19.53 0.00 38.66 4.92
2994 4377 6.245408 AGTCAGTTACCTGCCATATTTCAAA 58.755 36.000 0.00 0.00 38.66 2.69
3008 4391 9.341899 GCCATATTTCAAAGTTAGTACAGTTTG 57.658 33.333 7.03 7.03 0.00 2.93
3040 4757 8.121305 TGTTATCTGTGAATGTTTTATGGCTT 57.879 30.769 0.00 0.00 0.00 4.35
3084 4802 9.777297 TGTGCTATTATGCTATTGTAATTCTGA 57.223 29.630 0.00 0.00 0.00 3.27
3356 5090 3.287312 ACATCCATGACAAAAACTGCG 57.713 42.857 0.00 0.00 0.00 5.18
3359 5093 1.262950 TCCATGACAAAAACTGCGTCG 59.737 47.619 0.00 0.00 32.17 5.12
3400 5134 1.077663 AGCATCACCTGTCCCCAAAAT 59.922 47.619 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.586258 ACTGATCTCGTTCCATTCGG 57.414 50.000 0.00 0.00 0.00 4.30
1 2 4.921547 TCTAACTGATCTCGTTCCATTCG 58.078 43.478 4.58 0.00 0.00 3.34
2 3 6.334202 AGTTCTAACTGATCTCGTTCCATTC 58.666 40.000 4.58 0.00 37.98 2.67
3 4 6.287589 AGTTCTAACTGATCTCGTTCCATT 57.712 37.500 4.58 0.00 37.98 3.16
4 5 5.923733 AGTTCTAACTGATCTCGTTCCAT 57.076 39.130 4.58 0.00 37.98 3.41
5 6 7.406031 AATAGTTCTAACTGATCTCGTTCCA 57.594 36.000 5.62 0.00 40.07 3.53
6 7 8.705048 AAAATAGTTCTAACTGATCTCGTTCC 57.295 34.615 5.62 0.00 40.07 3.62
7 8 9.355215 TGAAAATAGTTCTAACTGATCTCGTTC 57.645 33.333 5.62 1.60 40.07 3.95
8 9 9.877178 ATGAAAATAGTTCTAACTGATCTCGTT 57.123 29.630 5.62 0.23 40.07 3.85
9 10 9.522804 GATGAAAATAGTTCTAACTGATCTCGT 57.477 33.333 5.62 0.00 40.07 4.18
10 11 8.973378 GGATGAAAATAGTTCTAACTGATCTCG 58.027 37.037 5.62 0.00 40.07 4.04
60 61 6.097915 TGTTACAGAAAGAAGACCGAATCT 57.902 37.500 0.00 0.00 40.46 2.40
61 62 6.780706 TTGTTACAGAAAGAAGACCGAATC 57.219 37.500 0.00 0.00 0.00 2.52
62 63 6.204882 CCTTTGTTACAGAAAGAAGACCGAAT 59.795 38.462 0.00 0.00 33.01 3.34
63 64 5.526111 CCTTTGTTACAGAAAGAAGACCGAA 59.474 40.000 0.00 0.00 33.01 4.30
64 65 5.054477 CCTTTGTTACAGAAAGAAGACCGA 58.946 41.667 0.00 0.00 33.01 4.69
65 66 4.319549 GCCTTTGTTACAGAAAGAAGACCG 60.320 45.833 0.00 0.00 33.01 4.79
66 67 4.578928 TGCCTTTGTTACAGAAAGAAGACC 59.421 41.667 0.00 0.00 33.01 3.85
67 68 5.751243 TGCCTTTGTTACAGAAAGAAGAC 57.249 39.130 0.00 0.00 33.01 3.01
68 69 6.601613 TCTTTGCCTTTGTTACAGAAAGAAGA 59.398 34.615 0.00 0.00 33.01 2.87
69 70 6.795399 TCTTTGCCTTTGTTACAGAAAGAAG 58.205 36.000 0.00 0.00 33.01 2.85
70 71 6.767524 TCTTTGCCTTTGTTACAGAAAGAA 57.232 33.333 0.00 0.00 33.01 2.52
87 88 3.416156 ACACAGAAGGGAGAATCTTTGC 58.584 45.455 0.00 0.00 33.73 3.68
259 264 2.046314 AATTCACGGCGGTGGGAG 60.046 61.111 22.51 0.00 44.50 4.30
295 300 2.687935 CTCTTCTCTTCTCTTCTCCCCG 59.312 54.545 0.00 0.00 0.00 5.73
321 326 1.475441 CCGCGCGTGAATCTCTCTTC 61.475 60.000 29.95 0.00 0.00 2.87
403 446 0.241481 AACGCGAAGAGACTGGAGAC 59.759 55.000 15.93 0.00 0.00 3.36
462 505 1.694150 GGAGAACCGATGGATGGATCA 59.306 52.381 0.00 0.00 31.17 2.92
604 664 4.628766 GGGACAACGAAAATGGTAGTACTC 59.371 45.833 0.00 0.00 0.00 2.59
606 666 3.686241 GGGGACAACGAAAATGGTAGTAC 59.314 47.826 0.00 0.00 0.00 2.73
609 669 2.089201 GGGGGACAACGAAAATGGTAG 58.911 52.381 0.00 0.00 0.00 3.18
620 680 3.119280 CCGAAATTACATTGGGGGACAAC 60.119 47.826 0.00 0.00 42.94 3.32
624 684 3.561143 CATCCGAAATTACATTGGGGGA 58.439 45.455 0.00 0.00 0.00 4.81
653 713 0.108019 GGGTATAAGTTGCCGAGGGG 59.892 60.000 0.00 0.00 0.00 4.79
660 720 7.224297 TCTAAATGAGGATGGGTATAAGTTGC 58.776 38.462 0.00 0.00 0.00 4.17
671 731 6.935771 CCTTCTCAGATTCTAAATGAGGATGG 59.064 42.308 1.93 0.00 40.68 3.51
678 738 6.939132 ACATGCCTTCTCAGATTCTAAATG 57.061 37.500 0.00 0.00 0.00 2.32
716 776 5.213913 CATCAATAAGATGCATACGGCTC 57.786 43.478 0.00 0.00 46.90 4.70
727 787 3.498121 CCCAGCCTCTGCATCAATAAGAT 60.498 47.826 0.00 0.00 41.13 2.40
728 788 2.158711 CCCAGCCTCTGCATCAATAAGA 60.159 50.000 0.00 0.00 41.13 2.10
729 789 2.228059 CCCAGCCTCTGCATCAATAAG 58.772 52.381 0.00 0.00 41.13 1.73
730 790 1.133699 CCCCAGCCTCTGCATCAATAA 60.134 52.381 0.00 0.00 41.13 1.40
731 791 0.475475 CCCCAGCCTCTGCATCAATA 59.525 55.000 0.00 0.00 41.13 1.90
732 792 1.229359 CCCCAGCCTCTGCATCAAT 59.771 57.895 0.00 0.00 41.13 2.57
733 793 1.792757 AACCCCAGCCTCTGCATCAA 61.793 55.000 0.00 0.00 41.13 2.57
734 794 2.233566 AACCCCAGCCTCTGCATCA 61.234 57.895 0.00 0.00 41.13 3.07
735 795 1.751927 CAACCCCAGCCTCTGCATC 60.752 63.158 0.00 0.00 41.13 3.91
736 796 2.357836 CAACCCCAGCCTCTGCAT 59.642 61.111 0.00 0.00 41.13 3.96
737 797 4.666253 GCAACCCCAGCCTCTGCA 62.666 66.667 0.00 0.00 41.13 4.41
738 798 4.666253 TGCAACCCCAGCCTCTGC 62.666 66.667 0.00 0.00 37.95 4.26
739 799 2.674380 GTGCAACCCCAGCCTCTG 60.674 66.667 0.00 0.00 0.00 3.35
780 840 9.677567 CGCCAAATAAATAAACTAGCATAACAT 57.322 29.630 0.00 0.00 0.00 2.71
781 841 7.646130 GCGCCAAATAAATAAACTAGCATAACA 59.354 33.333 0.00 0.00 0.00 2.41
782 842 7.114388 GGCGCCAAATAAATAAACTAGCATAAC 59.886 37.037 24.80 0.00 0.00 1.89
783 843 7.142680 GGCGCCAAATAAATAAACTAGCATAA 58.857 34.615 24.80 0.00 0.00 1.90
784 844 6.263392 TGGCGCCAAATAAATAAACTAGCATA 59.737 34.615 30.74 0.00 0.00 3.14
785 845 5.068460 TGGCGCCAAATAAATAAACTAGCAT 59.932 36.000 30.74 0.00 0.00 3.79
786 846 4.399618 TGGCGCCAAATAAATAAACTAGCA 59.600 37.500 30.74 0.00 0.00 3.49
787 847 4.927422 TGGCGCCAAATAAATAAACTAGC 58.073 39.130 30.74 0.00 0.00 3.42
788 848 6.131544 ACTGGCGCCAAATAAATAAACTAG 57.868 37.500 32.09 15.62 0.00 2.57
789 849 6.518208 AACTGGCGCCAAATAAATAAACTA 57.482 33.333 32.09 1.19 0.00 2.24
844 904 3.610911 CTCTTATATCCCCCGGCATTTC 58.389 50.000 0.00 0.00 0.00 2.17
845 905 2.308866 CCTCTTATATCCCCCGGCATTT 59.691 50.000 0.00 0.00 0.00 2.32
864 924 7.492077 ACTAGGCTAGTAATAACAACAACCT 57.508 36.000 25.19 0.00 37.23 3.50
865 925 7.413767 GCAACTAGGCTAGTAATAACAACAACC 60.414 40.741 26.47 1.18 38.26 3.77
866 926 7.118680 TGCAACTAGGCTAGTAATAACAACAAC 59.881 37.037 26.47 6.81 38.26 3.32
867 927 7.162761 TGCAACTAGGCTAGTAATAACAACAA 58.837 34.615 26.47 2.53 38.26 2.83
898 965 0.734889 GACGGCATAGCAACAGCAAT 59.265 50.000 0.00 0.00 0.00 3.56
899 966 1.634757 CGACGGCATAGCAACAGCAA 61.635 55.000 0.00 0.00 0.00 3.91
964 1034 3.045142 CACGTATACCGCCGGGAT 58.955 61.111 5.94 5.94 41.42 3.85
970 1040 2.346924 CGTAACAATGCACGTATACCGC 60.347 50.000 0.00 5.22 41.42 5.68
971 1041 2.346924 GCGTAACAATGCACGTATACCG 60.347 50.000 9.23 0.00 40.25 4.02
978 1048 0.095245 CTCCTGCGTAACAATGCACG 59.905 55.000 0.00 3.95 41.04 5.34
1123 1193 6.413892 TCCACAAGAAAGTGCATGTATGATA 58.586 36.000 0.00 0.00 38.18 2.15
1129 1199 3.144506 CTCTCCACAAGAAAGTGCATGT 58.855 45.455 0.00 0.00 38.18 3.21
1158 1232 4.545208 TCGGGAACATGTACTGAATTCA 57.455 40.909 8.12 8.12 0.00 2.57
1159 1233 7.226720 ACATATTCGGGAACATGTACTGAATTC 59.773 37.037 28.27 11.41 39.94 2.17
1160 1234 7.054124 ACATATTCGGGAACATGTACTGAATT 58.946 34.615 28.27 18.80 39.94 2.17
1249 1451 1.545582 ACCCAAATTTCACAGGCGATG 59.454 47.619 0.00 0.00 0.00 3.84
1250 1452 1.818674 GACCCAAATTTCACAGGCGAT 59.181 47.619 0.00 0.00 0.00 4.58
1252 1454 0.243636 GGACCCAAATTTCACAGGCG 59.756 55.000 0.00 0.00 0.00 5.52
1258 1460 4.231658 TCCTGATATGGGACCCAAATTTCA 59.768 41.667 19.58 15.99 36.95 2.69
1262 1464 3.884037 GTCCTGATATGGGACCCAAAT 57.116 47.619 19.58 4.25 45.31 2.32
1354 1557 5.649782 ATAGGCAGTTTGAAGTTTCCATG 57.350 39.130 0.00 0.00 0.00 3.66
1363 1566 5.648092 GCTAAGAGGAAATAGGCAGTTTGAA 59.352 40.000 0.00 0.00 0.00 2.69
1373 1576 7.777095 AGTTACAGTCAGCTAAGAGGAAATAG 58.223 38.462 0.00 0.00 0.00 1.73
1406 1609 9.892130 ACCGAGTTAAATTATTCAGAAGAGATT 57.108 29.630 0.00 0.00 0.00 2.40
1442 1650 4.718276 AGGAGGCTGCATTAATGGAAAAAT 59.282 37.500 17.02 0.97 0.00 1.82
1546 1754 4.558496 GCAGCTAAAACAAGTGCCACAATA 60.558 41.667 0.00 0.00 0.00 1.90
1561 1769 2.029110 GTGCCCAATGAAAGCAGCTAAA 60.029 45.455 0.00 0.00 37.15 1.85
1688 1896 2.507058 TGATATTCTTGGCCACAGAGCT 59.493 45.455 3.88 6.19 0.00 4.09
1706 1914 6.931790 ACTATTGCATCTAGTCCATCTGAT 57.068 37.500 4.14 0.00 0.00 2.90
1710 1918 6.597832 AGGTACTATTGCATCTAGTCCATC 57.402 41.667 11.55 0.00 36.02 3.51
1741 1953 3.119708 GCTCAAGACATGAACCAACATCC 60.120 47.826 0.00 0.00 37.67 3.51
1754 1966 0.112995 AAATGGCAGGGCTCAAGACA 59.887 50.000 0.00 0.00 0.00 3.41
1755 1967 0.529378 CAAATGGCAGGGCTCAAGAC 59.471 55.000 0.00 0.00 0.00 3.01
1792 2004 3.074412 GGTCCATGAAACGACTGACAAT 58.926 45.455 0.00 0.00 0.00 2.71
1793 2005 2.489971 GGTCCATGAAACGACTGACAA 58.510 47.619 0.00 0.00 0.00 3.18
1794 2006 1.270625 GGGTCCATGAAACGACTGACA 60.271 52.381 0.00 0.00 0.00 3.58
1798 2010 1.420138 ACAAGGGTCCATGAAACGACT 59.580 47.619 0.00 0.00 0.00 4.18
1799 2011 1.892209 ACAAGGGTCCATGAAACGAC 58.108 50.000 0.00 0.00 0.00 4.34
1800 2012 2.649531 AACAAGGGTCCATGAAACGA 57.350 45.000 0.00 0.00 0.00 3.85
1801 2013 2.884639 AGAAACAAGGGTCCATGAAACG 59.115 45.455 0.00 0.00 0.00 3.60
1802 2014 4.937201 AAGAAACAAGGGTCCATGAAAC 57.063 40.909 0.00 0.00 0.00 2.78
1803 2015 5.423610 TCAAAAGAAACAAGGGTCCATGAAA 59.576 36.000 0.00 0.00 0.00 2.69
1806 2018 4.935352 TCAAAAGAAACAAGGGTCCATG 57.065 40.909 0.00 0.00 0.00 3.66
1844 2056 7.492020 TGTTGGCAATGTTCAGCATTTATTATC 59.508 33.333 1.92 0.00 44.82 1.75
1845 2057 7.329499 TGTTGGCAATGTTCAGCATTTATTAT 58.671 30.769 1.92 0.00 44.82 1.28
1846 2058 6.695429 TGTTGGCAATGTTCAGCATTTATTA 58.305 32.000 1.92 0.00 44.82 0.98
1883 2095 8.814448 TTCCCTAGAGGATAATCCATTTAACT 57.186 34.615 0.00 0.00 46.94 2.24
1949 2161 3.084039 TGAACATCAAGCCTCAACCATC 58.916 45.455 0.00 0.00 0.00 3.51
2000 2212 5.878332 TGATTCAATTAGTCATGCAACGT 57.122 34.783 0.00 0.00 0.00 3.99
2002 2214 9.740239 ATGTAATGATTCAATTAGTCATGCAAC 57.260 29.630 0.00 0.00 33.19 4.17
2171 3234 2.125106 GTGCGATGGTGACCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
2204 3267 0.532862 GGCACAGGGTATCCATGTCG 60.533 60.000 3.06 1.92 34.83 4.35
2415 3478 7.814587 GCTATTTTTGAAATCCTGCAGTTAACT 59.185 33.333 13.81 1.12 0.00 2.24
2546 3609 6.376581 GTCTGAAACTGGAATGAGGAAATGAT 59.623 38.462 0.00 0.00 0.00 2.45
2690 3753 4.751767 ATCTGAAGACACCTCCAGATTC 57.248 45.455 0.00 0.00 41.93 2.52
2864 4247 8.160521 TGTTAAAGCAGAACATTTAGCTTGTA 57.839 30.769 0.00 0.00 45.73 2.41
2895 4278 3.807553 AGAACCCTTTTTGCCATTGTTG 58.192 40.909 0.00 0.00 0.00 3.33
2896 4279 5.622346 TTAGAACCCTTTTTGCCATTGTT 57.378 34.783 0.00 0.00 0.00 2.83
2921 4304 7.852263 AGCATACACTCCTTGTAATACTTCTT 58.148 34.615 0.00 0.00 44.11 2.52
2923 4306 7.701809 GAGCATACACTCCTTGTAATACTTC 57.298 40.000 0.00 0.00 44.11 3.01
2936 4319 1.271102 GATCGGAGGGAGCATACACTC 59.729 57.143 0.00 0.00 39.35 3.51
2994 4377 5.925509 ACATGGTGTCAAACTGTACTAACT 58.074 37.500 0.00 0.00 0.00 2.24
3008 4391 6.500684 AACATTCACAGATAACATGGTGTC 57.499 37.500 0.00 0.00 33.17 3.67
3009 4392 6.899393 AAACATTCACAGATAACATGGTGT 57.101 33.333 0.00 0.00 33.17 4.16
3010 4393 9.292846 CATAAAACATTCACAGATAACATGGTG 57.707 33.333 0.00 0.00 0.00 4.17
3011 4394 8.469200 CCATAAAACATTCACAGATAACATGGT 58.531 33.333 0.00 0.00 0.00 3.55
3012 4395 7.436080 GCCATAAAACATTCACAGATAACATGG 59.564 37.037 0.00 0.00 0.00 3.66
3040 4757 5.900425 AGCACAACAACACAACATAAATCA 58.100 33.333 0.00 0.00 0.00 2.57
3084 4802 5.582269 CGTAGATTCAGAATCACACACCATT 59.418 40.000 22.70 3.92 40.42 3.16
3133 4851 7.603963 TTACATTCTGTACAATGCAACGTAT 57.396 32.000 7.34 0.00 37.28 3.06
3140 4858 5.276270 CAGCCATTACATTCTGTACAATGC 58.724 41.667 7.34 0.00 37.28 3.56
3375 5109 1.282157 GGGGACAGGTGATGCTAAGTT 59.718 52.381 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.