Multiple sequence alignment - TraesCS3A01G361000

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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 TraesCS3A01G361000 chr3A 100.000 2246 0 0 1 2246 608737179 608739424 0.000000e+00 4148.0
1 TraesCS3A01G361000 chr3D 90.736 1889 107 35 126 1968 465459789 465461655 0.000000e+00 2457.0
2 TraesCS3A01G361000 chr3D 90.000 300 19 7 1902 2197 465461655 465461947 5.860000e-101 377.0
3 TraesCS3A01G361000 chr3D 92.308 117 8 1 1 116 481929176 481929292 4.960000e-37 165.0
4 TraesCS3A01G361000 chr3D 87.218 133 13 4 1 130 556024054 556024185 5.000000e-32 148.0
5 TraesCS3A01G361000 chr3B 91.197 1738 96 31 227 1925 618860715 618862434 0.000000e+00 2309.0
6 TraesCS3A01G361000 chr3B 89.734 263 18 4 1939 2197 618862707 618862964 5.980000e-86 327.0
7 TraesCS3A01G361000 chr4B 92.742 124 6 3 1 123 161559704 161559825 2.290000e-40 176.0
8 TraesCS3A01G361000 chr4D 90.076 131 11 2 2 130 99207499 99207629 3.840000e-38 169.0
9 TraesCS3A01G361000 chr7A 92.308 117 8 1 1 116 562174544 562174660 4.960000e-37 165.0
10 TraesCS3A01G361000 chr7A 92.241 116 8 1 1 115 432148103 432148218 1.780000e-36 163.0
11 TraesCS3A01G361000 chr7D 91.379 116 8 2 2 116 127762356 127762470 8.300000e-35 158.0
12 TraesCS3A01G361000 chr1B 90.517 116 10 1 2 116 465362504 465362619 3.860000e-33 152.0
13 TraesCS3A01G361000 chr5D 87.500 128 12 3 2 126 457669243 457669369 6.460000e-31 145.0
14 TraesCS3A01G361000 chrUn 100.000 28 0 0 2194 2221 16161842 16161869 4.000000e-03 52.8


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 TraesCS3A01G361000 chr3A 608737179 608739424 2245 False 4148 4148 100.0000 1 2246 1 chr3A.!!$F1 2245
1 TraesCS3A01G361000 chr3D 465459789 465461947 2158 False 1417 2457 90.3680 126 2197 2 chr3D.!!$F3 2071
2 TraesCS3A01G361000 chr3B 618860715 618862964 2249 False 1318 2309 90.4655 227 2197 2 chr3B.!!$F1 1970

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
109 110 0.249911 ATAGATCGGCACTTTCCCGC 60.25 55.0 0.0 0.0 45.19 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1823 0.038526 GATTCGTGGTCACACCGTCT 60.039 55.0 1.9 0.0 44.86 4.18 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
18 19 2.062779 CAGTGCTTGTAGTCGTCGC 58.937 57.895 0.00 0.00 0.00 5.19
19 20 0.387367 CAGTGCTTGTAGTCGTCGCT 60.387 55.000 0.00 0.00 0.00 4.93
20 21 1.135774 CAGTGCTTGTAGTCGTCGCTA 60.136 52.381 0.00 0.00 0.00 4.26
21 22 1.130749 AGTGCTTGTAGTCGTCGCTAG 59.869 52.381 0.00 0.00 0.00 3.42
22 23 1.135746 GTGCTTGTAGTCGTCGCTAGT 60.136 52.381 0.00 0.00 0.00 2.57
23 24 1.135774 TGCTTGTAGTCGTCGCTAGTG 60.136 52.381 0.00 0.00 0.00 2.74
24 25 1.129998 GCTTGTAGTCGTCGCTAGTGA 59.870 52.381 0.70 0.70 0.00 3.41
25 26 2.223294 GCTTGTAGTCGTCGCTAGTGAT 60.223 50.000 9.64 0.00 0.00 3.06
26 27 3.609475 CTTGTAGTCGTCGCTAGTGATC 58.391 50.000 9.64 3.90 0.00 2.92
27 28 2.902523 TGTAGTCGTCGCTAGTGATCT 58.097 47.619 9.64 10.72 0.00 2.75
28 29 4.050852 TGTAGTCGTCGCTAGTGATCTA 57.949 45.455 9.64 9.82 0.00 1.98
29 30 4.629092 TGTAGTCGTCGCTAGTGATCTAT 58.371 43.478 9.64 0.00 0.00 1.98
30 31 4.448060 TGTAGTCGTCGCTAGTGATCTATG 59.552 45.833 9.64 0.00 0.00 2.23
31 32 3.729966 AGTCGTCGCTAGTGATCTATGA 58.270 45.455 9.64 0.70 0.00 2.15
32 33 4.127907 AGTCGTCGCTAGTGATCTATGAA 58.872 43.478 9.64 0.00 0.00 2.57
33 34 4.757657 AGTCGTCGCTAGTGATCTATGAAT 59.242 41.667 9.64 0.16 0.00 2.57
34 35 5.083389 GTCGTCGCTAGTGATCTATGAATC 58.917 45.833 9.64 0.00 0.00 2.52
35 36 4.998033 TCGTCGCTAGTGATCTATGAATCT 59.002 41.667 9.64 0.00 0.00 2.40
36 37 5.085390 CGTCGCTAGTGATCTATGAATCTG 58.915 45.833 9.64 0.00 0.00 2.90
37 38 5.398169 GTCGCTAGTGATCTATGAATCTGG 58.602 45.833 9.64 0.00 0.00 3.86
38 39 5.182190 GTCGCTAGTGATCTATGAATCTGGA 59.818 44.000 9.64 0.00 0.00 3.86
39 40 5.948758 TCGCTAGTGATCTATGAATCTGGAT 59.051 40.000 0.70 0.00 0.00 3.41
40 41 6.035217 CGCTAGTGATCTATGAATCTGGATG 58.965 44.000 0.00 0.00 0.00 3.51
41 42 6.350027 CGCTAGTGATCTATGAATCTGGATGT 60.350 42.308 0.00 0.00 0.00 3.06
42 43 7.148171 CGCTAGTGATCTATGAATCTGGATGTA 60.148 40.741 0.00 0.00 0.00 2.29
43 44 8.526978 GCTAGTGATCTATGAATCTGGATGTAA 58.473 37.037 0.00 0.00 0.00 2.41
59 60 9.513906 TCTGGATGTAATTTTTGTTATGTCTGA 57.486 29.630 0.00 0.00 0.00 3.27
69 70 9.985730 ATTTTTGTTATGTCTGATGTTCATTGT 57.014 25.926 0.00 0.00 0.00 2.71
71 72 9.891828 TTTTGTTATGTCTGATGTTCATTGTAC 57.108 29.630 0.00 0.00 0.00 2.90
72 73 8.846943 TTGTTATGTCTGATGTTCATTGTACT 57.153 30.769 0.00 0.00 0.00 2.73
73 74 9.936759 TTGTTATGTCTGATGTTCATTGTACTA 57.063 29.630 0.00 0.00 0.00 1.82
74 75 9.366216 TGTTATGTCTGATGTTCATTGTACTAC 57.634 33.333 0.00 0.00 0.00 2.73
75 76 8.818057 GTTATGTCTGATGTTCATTGTACTACC 58.182 37.037 0.00 0.00 0.00 3.18
76 77 6.353404 TGTCTGATGTTCATTGTACTACCA 57.647 37.500 0.00 0.00 0.00 3.25
77 78 6.946340 TGTCTGATGTTCATTGTACTACCAT 58.054 36.000 0.00 0.00 0.00 3.55
78 79 6.818142 TGTCTGATGTTCATTGTACTACCATG 59.182 38.462 0.00 0.00 0.00 3.66
79 80 7.041721 GTCTGATGTTCATTGTACTACCATGA 58.958 38.462 0.00 0.00 0.00 3.07
80 81 7.712639 GTCTGATGTTCATTGTACTACCATGAT 59.287 37.037 4.27 0.00 0.00 2.45
81 82 8.267183 TCTGATGTTCATTGTACTACCATGATT 58.733 33.333 4.27 0.00 0.00 2.57
82 83 8.212317 TGATGTTCATTGTACTACCATGATTG 57.788 34.615 4.27 0.00 0.00 2.67
83 84 8.046107 TGATGTTCATTGTACTACCATGATTGA 58.954 33.333 4.27 0.00 0.00 2.57
84 85 8.806429 ATGTTCATTGTACTACCATGATTGAA 57.194 30.769 4.27 0.00 0.00 2.69
85 86 8.267620 TGTTCATTGTACTACCATGATTGAAG 57.732 34.615 4.27 0.00 0.00 3.02
86 87 8.100164 TGTTCATTGTACTACCATGATTGAAGA 58.900 33.333 4.27 0.00 0.00 2.87
87 88 9.113838 GTTCATTGTACTACCATGATTGAAGAT 57.886 33.333 4.27 0.00 0.00 2.40
88 89 8.667076 TCATTGTACTACCATGATTGAAGATG 57.333 34.615 0.00 0.00 0.00 2.90
89 90 8.485392 TCATTGTACTACCATGATTGAAGATGA 58.515 33.333 0.00 0.00 0.00 2.92
90 91 9.112725 CATTGTACTACCATGATTGAAGATGAA 57.887 33.333 0.00 0.00 0.00 2.57
91 92 9.857656 ATTGTACTACCATGATTGAAGATGAAT 57.142 29.630 0.00 0.00 0.00 2.57
93 94 9.987272 TGTACTACCATGATTGAAGATGAATAG 57.013 33.333 0.00 0.00 0.00 1.73
96 97 9.941325 ACTACCATGATTGAAGATGAATAGATC 57.059 33.333 0.00 0.00 0.00 2.75
97 98 7.902387 ACCATGATTGAAGATGAATAGATCG 57.098 36.000 0.00 0.00 0.00 3.69
98 99 6.877855 ACCATGATTGAAGATGAATAGATCGG 59.122 38.462 0.00 0.00 0.00 4.18
99 100 6.183360 CCATGATTGAAGATGAATAGATCGGC 60.183 42.308 0.00 0.00 0.00 5.54
100 101 5.857268 TGATTGAAGATGAATAGATCGGCA 58.143 37.500 0.00 0.00 0.00 5.69
101 102 5.698089 TGATTGAAGATGAATAGATCGGCAC 59.302 40.000 0.00 0.00 0.00 5.01
102 103 4.944619 TGAAGATGAATAGATCGGCACT 57.055 40.909 0.00 0.00 0.00 4.40
103 104 5.282055 TGAAGATGAATAGATCGGCACTT 57.718 39.130 0.00 0.00 0.00 3.16
104 105 5.674525 TGAAGATGAATAGATCGGCACTTT 58.325 37.500 0.00 0.00 0.00 2.66
105 106 5.755375 TGAAGATGAATAGATCGGCACTTTC 59.245 40.000 0.00 0.00 0.00 2.62
106 107 4.636249 AGATGAATAGATCGGCACTTTCC 58.364 43.478 0.00 0.00 0.00 3.13
107 108 3.194005 TGAATAGATCGGCACTTTCCC 57.806 47.619 0.00 0.00 0.00 3.97
108 109 2.135933 GAATAGATCGGCACTTTCCCG 58.864 52.381 0.00 0.00 46.88 5.14
109 110 0.249911 ATAGATCGGCACTTTCCCGC 60.250 55.000 0.00 0.00 45.19 6.13
110 111 1.609635 TAGATCGGCACTTTCCCGCA 61.610 55.000 0.00 0.00 45.19 5.69
111 112 2.033448 ATCGGCACTTTCCCGCAA 59.967 55.556 0.00 0.00 45.19 4.85
112 113 1.582610 GATCGGCACTTTCCCGCAAA 61.583 55.000 0.00 0.00 45.19 3.68
113 114 1.175983 ATCGGCACTTTCCCGCAAAA 61.176 50.000 0.00 0.00 45.19 2.44
114 115 1.066587 CGGCACTTTCCCGCAAAAA 59.933 52.632 0.00 0.00 39.22 1.94
181 195 2.264794 CCGGGCCGTATATGCTCC 59.735 66.667 26.32 0.00 0.00 4.70
182 196 2.264794 CGGGCCGTATATGCTCCC 59.735 66.667 19.97 9.38 0.00 4.30
185 199 2.580601 GGCCGTATATGCTCCCGGT 61.581 63.158 0.00 0.00 42.36 5.28
186 200 1.370064 GCCGTATATGCTCCCGGTT 59.630 57.895 0.00 0.00 42.36 4.44
212 227 0.528249 CAACACAAGCAACACTGGGC 60.528 55.000 0.00 0.00 0.00 5.36
221 236 1.238439 CAACACTGGGCTGTTGTAGG 58.762 55.000 9.29 0.00 44.09 3.18
222 237 1.136828 AACACTGGGCTGTTGTAGGA 58.863 50.000 0.00 0.00 32.95 2.94
238 253 1.761174 GGAAAGGCCTGTGGACAGA 59.239 57.895 5.69 0.00 46.59 3.41
324 341 1.827399 GACCGTCCAAGCTCCTTCCA 61.827 60.000 0.00 0.00 0.00 3.53
325 342 1.376037 CCGTCCAAGCTCCTTCCAC 60.376 63.158 0.00 0.00 0.00 4.02
622 651 2.925724 CGGCATATCCCCACAAACTTA 58.074 47.619 0.00 0.00 0.00 2.24
628 657 0.479378 TCCCCACAAACTTACCCCAC 59.521 55.000 0.00 0.00 0.00 4.61
636 665 1.768265 AACTTACCCCACCATCCCTT 58.232 50.000 0.00 0.00 0.00 3.95
637 666 1.768265 ACTTACCCCACCATCCCTTT 58.232 50.000 0.00 0.00 0.00 3.11
645 674 2.509548 CCCACCATCCCTTTACAGATCA 59.490 50.000 0.00 0.00 0.00 2.92
648 677 5.203528 CCACCATCCCTTTACAGATCATTT 58.796 41.667 0.00 0.00 0.00 2.32
699 728 2.909006 ACCAGGGGCATATATGTGAGAG 59.091 50.000 14.14 2.80 0.00 3.20
716 745 0.325272 GAGTGGAAACCTCAGGTCCC 59.675 60.000 0.00 1.99 33.12 4.46
748 777 4.215613 AGAGTTTTAAATCGAACAGTGGCC 59.784 41.667 0.00 0.00 0.00 5.36
920 949 2.281276 CCGTTATAAGCCGCCCCC 60.281 66.667 0.00 0.00 0.00 5.40
953 982 1.078656 TCCCTCCCAAATTCCCCTTTG 59.921 52.381 0.00 0.00 36.17 2.77
966 995 2.698274 TCCCCTTTGAAAACAAGGAAGC 59.302 45.455 0.00 0.00 43.32 3.86
1022 1058 3.531207 CATGGAGAGCGGCTCGGA 61.531 66.667 23.15 12.03 44.91 4.55
1249 1285 3.902063 CCTCGTGCGCGTGATTCG 61.902 66.667 22.07 6.10 43.12 3.34
1276 1325 4.838152 GAAGGCATGCGGCGGAGA 62.838 66.667 12.44 0.00 46.16 3.71
1361 1411 3.057337 CGGTAGCGGATTAGGGGG 58.943 66.667 6.39 0.00 0.00 5.40
1372 1422 2.055579 GATTAGGGGGTGTTCTAGGGG 58.944 57.143 0.00 0.00 0.00 4.79
1491 1541 4.942761 ATTTGTTTCTTGGCACTGATGT 57.057 36.364 0.00 0.00 0.00 3.06
1492 1542 3.988379 TTGTTTCTTGGCACTGATGTC 57.012 42.857 0.00 0.00 0.00 3.06
1524 1574 3.303395 GCTTATTGCGCACTTCTGTATCC 60.303 47.826 11.12 0.00 0.00 2.59
1555 1610 3.364764 GCTGATGTTGCTGAAGTTCTGAC 60.365 47.826 13.44 4.62 0.00 3.51
1576 1631 3.127548 ACGTTGTTCTTCATGATGCCATC 59.872 43.478 0.00 0.00 0.00 3.51
1577 1632 3.127376 CGTTGTTCTTCATGATGCCATCA 59.873 43.478 10.29 10.29 44.55 3.07
1609 1664 8.114290 TCGATTGTTGAGCTACGATTAATTTTC 58.886 33.333 0.00 0.00 0.00 2.29
1767 1834 0.737715 GAGGCATCAGACGGTGTGAC 60.738 60.000 10.40 0.00 0.00 3.67
1771 1838 1.008875 CATCAGACGGTGTGACCACG 61.009 60.000 10.40 0.00 42.80 4.94
1814 1881 0.322816 TGAAATGCCTCCTGTCCAGC 60.323 55.000 0.00 0.00 0.00 4.85
1872 1939 2.823628 GTGCCTCCACTGTTCGTAC 58.176 57.895 0.00 0.00 38.93 3.67
1873 1940 0.317479 GTGCCTCCACTGTTCGTACT 59.683 55.000 0.00 0.00 38.93 2.73
1895 1962 3.840890 TGTTCGTTTGCTTCAGTGTTT 57.159 38.095 0.00 0.00 0.00 2.83
1896 1963 4.167554 TGTTCGTTTGCTTCAGTGTTTT 57.832 36.364 0.00 0.00 0.00 2.43
1897 1964 3.917380 TGTTCGTTTGCTTCAGTGTTTTG 59.083 39.130 0.00 0.00 0.00 2.44
1898 1965 3.143807 TCGTTTGCTTCAGTGTTTTGG 57.856 42.857 0.00 0.00 0.00 3.28
1899 1966 1.587946 CGTTTGCTTCAGTGTTTTGGC 59.412 47.619 0.00 0.00 0.00 4.52
1900 1967 1.933181 GTTTGCTTCAGTGTTTTGGCC 59.067 47.619 0.00 0.00 0.00 5.36
1922 2308 5.491982 CCTTATGGGCCATCTGATTAGTAC 58.508 45.833 25.07 0.00 0.00 2.73
1923 2309 5.249393 CCTTATGGGCCATCTGATTAGTACT 59.751 44.000 25.07 0.00 0.00 2.73
1926 2312 3.578716 TGGGCCATCTGATTAGTACTAGC 59.421 47.826 0.00 0.59 0.00 3.42
1928 2314 4.223923 GGGCCATCTGATTAGTACTAGCAT 59.776 45.833 4.39 0.00 0.00 3.79
1946 2335 4.430908 AGCATTAGGAGTTACACTAACGC 58.569 43.478 8.90 8.90 43.29 4.84
1950 2339 2.685100 AGGAGTTACACTAACGCTTGC 58.315 47.619 0.00 0.00 43.29 4.01
2036 2426 2.097160 CGACATGAAGCAGTGCGC 59.903 61.111 10.00 0.00 42.91 6.09
2048 2438 1.664965 AGTGCGCGGTCTTGAAGAC 60.665 57.895 16.70 16.70 44.32 3.01
2065 2455 2.253513 ACGCAGTTAATGTGGGTGC 58.746 52.632 8.98 0.00 37.78 5.01
2067 2457 1.506262 GCAGTTAATGTGGGTGCGG 59.494 57.895 0.00 0.00 0.00 5.69
2116 2508 4.838152 TCTTCGCCTCGCATGCCC 62.838 66.667 13.15 0.00 0.00 5.36
2135 2527 4.421515 CCTGCCTGCCTCCTGGTG 62.422 72.222 0.00 0.00 35.27 4.17
2136 2528 3.324930 CTGCCTGCCTCCTGGTGA 61.325 66.667 0.00 0.00 35.27 4.02
2137 2529 2.853542 TGCCTGCCTCCTGGTGAA 60.854 61.111 0.00 0.00 35.27 3.18
2197 2589 1.815003 GGTGTCAAGGCTTCATTCAGG 59.185 52.381 0.00 0.00 0.00 3.86
2198 2590 1.200948 GTGTCAAGGCTTCATTCAGGC 59.799 52.381 0.00 0.00 39.69 4.85
2202 2594 3.204418 GGCTTCATTCAGGCTGGC 58.796 61.111 15.73 8.66 36.41 4.85
2203 2595 2.421399 GGCTTCATTCAGGCTGGCC 61.421 63.158 15.73 14.30 36.41 5.36
2204 2596 1.679977 GCTTCATTCAGGCTGGCCA 60.680 57.895 15.73 4.71 38.92 5.36
2205 2597 1.041447 GCTTCATTCAGGCTGGCCAT 61.041 55.000 15.73 1.71 38.92 4.40
2206 2598 1.751733 GCTTCATTCAGGCTGGCCATA 60.752 52.381 15.73 0.00 38.92 2.74
2207 2599 2.658285 CTTCATTCAGGCTGGCCATAA 58.342 47.619 15.73 7.64 38.92 1.90
2208 2600 3.228453 CTTCATTCAGGCTGGCCATAAT 58.772 45.455 15.73 9.52 38.92 1.28
2209 2601 2.589720 TCATTCAGGCTGGCCATAATG 58.410 47.619 22.04 22.04 39.62 1.90
2210 2602 1.616865 CATTCAGGCTGGCCATAATGG 59.383 52.381 15.73 0.00 41.55 3.16
2211 2603 0.106066 TTCAGGCTGGCCATAATGGG 60.106 55.000 15.73 0.00 38.19 4.00
2212 2604 1.532316 CAGGCTGGCCATAATGGGG 60.532 63.158 5.51 0.00 38.19 4.96
2213 2605 2.014550 AGGCTGGCCATAATGGGGT 61.015 57.895 5.51 0.00 38.19 4.95
2214 2606 0.700963 AGGCTGGCCATAATGGGGTA 60.701 55.000 5.51 0.00 38.19 3.69
2215 2607 0.187361 GGCTGGCCATAATGGGGTAA 59.813 55.000 5.51 0.00 38.19 2.85
2216 2608 1.328279 GCTGGCCATAATGGGGTAAC 58.672 55.000 5.51 0.00 38.19 2.50
2217 2609 1.410932 GCTGGCCATAATGGGGTAACA 60.411 52.381 5.51 0.00 38.19 2.41
2218 2610 2.756233 GCTGGCCATAATGGGGTAACAT 60.756 50.000 5.51 0.00 38.19 2.71
2219 2611 3.499563 GCTGGCCATAATGGGGTAACATA 60.500 47.826 5.51 0.00 38.19 2.29
2220 2612 4.735369 CTGGCCATAATGGGGTAACATAA 58.265 43.478 5.51 0.00 38.19 1.90
2221 2613 4.475345 TGGCCATAATGGGGTAACATAAC 58.525 43.478 0.00 0.00 38.19 1.89
2222 2614 3.830178 GGCCATAATGGGGTAACATAACC 59.170 47.826 0.00 0.00 38.19 2.85
2223 2615 4.448640 GGCCATAATGGGGTAACATAACCT 60.449 45.833 0.00 0.00 38.19 3.50
2224 2616 5.144832 GCCATAATGGGGTAACATAACCTT 58.855 41.667 0.00 0.00 38.19 3.50
2225 2617 6.308566 GCCATAATGGGGTAACATAACCTTA 58.691 40.000 0.00 0.00 38.19 2.69
2226 2618 6.778559 GCCATAATGGGGTAACATAACCTTAA 59.221 38.462 0.00 0.00 38.19 1.85
2227 2619 7.255695 GCCATAATGGGGTAACATAACCTTAAC 60.256 40.741 0.00 0.00 38.19 2.01
2228 2620 7.780745 CCATAATGGGGTAACATAACCTTAACA 59.219 37.037 0.00 0.00 39.65 2.41
2229 2621 9.362151 CATAATGGGGTAACATAACCTTAACAT 57.638 33.333 0.00 0.00 39.65 2.71
2232 2624 9.945633 AATGGGGTAACATAACCTTAACATAAT 57.054 29.630 0.00 0.00 39.65 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.387367 AGCGACGACTACAAGCACTG 60.387 55.000 0.00 0.00 0.00 3.66
1 2 1.130749 CTAGCGACGACTACAAGCACT 59.869 52.381 0.00 0.00 0.00 4.40
2 3 1.135746 ACTAGCGACGACTACAAGCAC 60.136 52.381 0.00 0.00 0.00 4.40
3 4 1.135774 CACTAGCGACGACTACAAGCA 60.136 52.381 0.00 0.00 0.00 3.91
4 5 1.129998 TCACTAGCGACGACTACAAGC 59.870 52.381 0.00 0.00 0.00 4.01
5 6 3.310227 AGATCACTAGCGACGACTACAAG 59.690 47.826 0.00 0.00 0.00 3.16
6 7 3.268330 AGATCACTAGCGACGACTACAA 58.732 45.455 0.00 0.00 0.00 2.41
7 8 2.902523 AGATCACTAGCGACGACTACA 58.097 47.619 0.00 0.00 0.00 2.74
8 9 4.685165 TCATAGATCACTAGCGACGACTAC 59.315 45.833 0.00 0.00 31.78 2.73
9 10 4.879598 TCATAGATCACTAGCGACGACTA 58.120 43.478 0.00 0.00 31.78 2.59
10 11 3.729966 TCATAGATCACTAGCGACGACT 58.270 45.455 0.00 0.00 31.78 4.18
11 12 4.469625 TTCATAGATCACTAGCGACGAC 57.530 45.455 0.00 0.00 31.78 4.34
12 13 4.998033 AGATTCATAGATCACTAGCGACGA 59.002 41.667 0.00 0.00 31.78 4.20
13 14 5.085390 CAGATTCATAGATCACTAGCGACG 58.915 45.833 0.00 0.00 31.78 5.12
14 15 5.182190 TCCAGATTCATAGATCACTAGCGAC 59.818 44.000 0.00 0.00 31.78 5.19
15 16 5.316987 TCCAGATTCATAGATCACTAGCGA 58.683 41.667 0.00 0.00 31.78 4.93
16 17 5.635417 TCCAGATTCATAGATCACTAGCG 57.365 43.478 0.00 0.00 31.78 4.26
17 18 6.934056 ACATCCAGATTCATAGATCACTAGC 58.066 40.000 0.00 0.00 31.78 3.42
33 34 9.513906 TCAGACATAACAAAAATTACATCCAGA 57.486 29.630 0.00 0.00 0.00 3.86
43 44 9.985730 ACAATGAACATCAGACATAACAAAAAT 57.014 25.926 0.00 0.00 0.00 1.82
45 46 9.891828 GTACAATGAACATCAGACATAACAAAA 57.108 29.630 0.00 0.00 0.00 2.44
46 47 9.283768 AGTACAATGAACATCAGACATAACAAA 57.716 29.630 0.00 0.00 0.00 2.83
47 48 8.846943 AGTACAATGAACATCAGACATAACAA 57.153 30.769 0.00 0.00 0.00 2.83
48 49 9.366216 GTAGTACAATGAACATCAGACATAACA 57.634 33.333 0.00 0.00 0.00 2.41
49 50 8.818057 GGTAGTACAATGAACATCAGACATAAC 58.182 37.037 2.06 0.00 0.00 1.89
50 51 8.536175 TGGTAGTACAATGAACATCAGACATAA 58.464 33.333 2.06 0.00 0.00 1.90
51 52 8.073467 TGGTAGTACAATGAACATCAGACATA 57.927 34.615 2.06 0.00 0.00 2.29
52 53 6.946340 TGGTAGTACAATGAACATCAGACAT 58.054 36.000 2.06 0.00 0.00 3.06
53 54 6.353404 TGGTAGTACAATGAACATCAGACA 57.647 37.500 2.06 0.00 0.00 3.41
54 55 7.041721 TCATGGTAGTACAATGAACATCAGAC 58.958 38.462 16.63 0.00 0.00 3.51
55 56 7.181569 TCATGGTAGTACAATGAACATCAGA 57.818 36.000 16.63 0.00 0.00 3.27
56 57 8.340443 CAATCATGGTAGTACAATGAACATCAG 58.660 37.037 21.60 7.06 0.00 2.90
57 58 8.046107 TCAATCATGGTAGTACAATGAACATCA 58.954 33.333 21.60 1.28 0.00 3.07
58 59 8.437360 TCAATCATGGTAGTACAATGAACATC 57.563 34.615 21.60 0.00 0.00 3.06
59 60 8.806429 TTCAATCATGGTAGTACAATGAACAT 57.194 30.769 21.60 10.28 0.00 2.71
60 61 8.100164 TCTTCAATCATGGTAGTACAATGAACA 58.900 33.333 21.60 8.08 0.00 3.18
61 62 8.492673 TCTTCAATCATGGTAGTACAATGAAC 57.507 34.615 21.60 0.00 0.00 3.18
62 63 9.112725 CATCTTCAATCATGGTAGTACAATGAA 57.887 33.333 21.60 7.10 0.00 2.57
63 64 8.485392 TCATCTTCAATCATGGTAGTACAATGA 58.515 33.333 20.34 20.34 0.00 2.57
64 65 8.667076 TCATCTTCAATCATGGTAGTACAATG 57.333 34.615 11.00 11.00 0.00 2.82
65 66 9.857656 ATTCATCTTCAATCATGGTAGTACAAT 57.142 29.630 2.06 0.00 0.00 2.71
67 68 9.987272 CTATTCATCTTCAATCATGGTAGTACA 57.013 33.333 2.06 0.00 0.00 2.90
70 71 9.941325 GATCTATTCATCTTCAATCATGGTAGT 57.059 33.333 0.00 0.00 0.00 2.73
71 72 9.085250 CGATCTATTCATCTTCAATCATGGTAG 57.915 37.037 0.00 0.00 0.00 3.18
72 73 8.037166 CCGATCTATTCATCTTCAATCATGGTA 58.963 37.037 0.00 0.00 0.00 3.25
73 74 6.877855 CCGATCTATTCATCTTCAATCATGGT 59.122 38.462 0.00 0.00 0.00 3.55
74 75 6.183360 GCCGATCTATTCATCTTCAATCATGG 60.183 42.308 0.00 0.00 0.00 3.66
75 76 6.370718 TGCCGATCTATTCATCTTCAATCATG 59.629 38.462 0.00 0.00 0.00 3.07
76 77 6.370994 GTGCCGATCTATTCATCTTCAATCAT 59.629 38.462 0.00 0.00 0.00 2.45
77 78 5.698089 GTGCCGATCTATTCATCTTCAATCA 59.302 40.000 0.00 0.00 0.00 2.57
78 79 5.931146 AGTGCCGATCTATTCATCTTCAATC 59.069 40.000 0.00 0.00 0.00 2.67
79 80 5.862845 AGTGCCGATCTATTCATCTTCAAT 58.137 37.500 0.00 0.00 0.00 2.57
80 81 5.282055 AGTGCCGATCTATTCATCTTCAA 57.718 39.130 0.00 0.00 0.00 2.69
81 82 4.944619 AGTGCCGATCTATTCATCTTCA 57.055 40.909 0.00 0.00 0.00 3.02
82 83 5.178438 GGAAAGTGCCGATCTATTCATCTTC 59.822 44.000 0.00 0.00 0.00 2.87
83 84 5.059833 GGAAAGTGCCGATCTATTCATCTT 58.940 41.667 0.00 0.00 0.00 2.40
84 85 4.503991 GGGAAAGTGCCGATCTATTCATCT 60.504 45.833 0.00 0.00 0.00 2.90
85 86 3.748568 GGGAAAGTGCCGATCTATTCATC 59.251 47.826 0.00 0.00 0.00 2.92
86 87 3.744660 GGGAAAGTGCCGATCTATTCAT 58.255 45.455 0.00 0.00 0.00 2.57
87 88 3.194005 GGGAAAGTGCCGATCTATTCA 57.806 47.619 0.00 0.00 0.00 2.57
119 120 9.799106 TCTCTCAGGAAAGATGTTTATTTCTTT 57.201 29.630 0.00 0.00 43.12 2.52
120 121 9.799106 TTCTCTCAGGAAAGATGTTTATTTCTT 57.201 29.630 0.00 0.00 36.03 2.52
121 122 9.799106 TTTCTCTCAGGAAAGATGTTTATTTCT 57.201 29.630 0.00 0.00 36.03 2.52
137 138 3.578716 TGTAGGTGTTCCTTTCTCTCAGG 59.421 47.826 0.00 0.00 42.12 3.86
144 145 3.621715 CGGCTAATGTAGGTGTTCCTTTC 59.378 47.826 0.00 0.00 42.12 2.62
151 152 1.525442 GCCCGGCTAATGTAGGTGT 59.475 57.895 0.71 0.00 0.00 4.16
154 155 1.466025 TACGGCCCGGCTAATGTAGG 61.466 60.000 8.57 0.00 0.00 3.18
185 199 4.037803 AGTGTTGCTTGTGTTGATATGCAA 59.962 37.500 0.00 0.00 37.96 4.08
186 200 3.569277 AGTGTTGCTTGTGTTGATATGCA 59.431 39.130 0.00 0.00 0.00 3.96
212 227 2.154462 CACAGGCCTTTCCTACAACAG 58.846 52.381 0.00 0.00 45.52 3.16
221 236 0.957888 GCTCTGTCCACAGGCCTTTC 60.958 60.000 0.00 0.00 43.91 2.62
222 237 1.073897 GCTCTGTCCACAGGCCTTT 59.926 57.895 0.00 0.00 43.91 3.11
622 651 0.999712 CTGTAAAGGGATGGTGGGGT 59.000 55.000 0.00 0.00 0.00 4.95
648 677 7.225538 CCACAATGTTAGGTATTTTGTGCAAAA 59.774 33.333 11.77 11.77 43.52 2.44
687 716 6.042552 CCTGAGGTTTCCACTCTCACATATAT 59.957 42.308 0.00 0.00 35.98 0.86
699 728 0.036875 CAGGGACCTGAGGTTTCCAC 59.963 60.000 21.48 5.48 46.30 4.02
716 745 5.488341 TCGATTTAAAACTCTTCCTCCCAG 58.512 41.667 0.00 0.00 0.00 4.45
902 931 2.281276 GGGGCGGCTTATAACGGG 60.281 66.667 9.56 0.00 0.00 5.28
905 934 2.976350 GCGGGGGCGGCTTATAAC 60.976 66.667 9.56 0.00 0.00 1.89
953 982 5.822519 AGAAATTTTGGGCTTCCTTGTTTTC 59.177 36.000 0.00 0.00 0.00 2.29
989 1019 1.210967 CCATGGCCATTGGATGCTTTT 59.789 47.619 17.92 0.00 0.00 2.27
1233 1269 3.902063 CCGAATCACGCGCACGAG 61.902 66.667 5.73 0.00 43.93 4.18
1260 1296 4.845580 CTCTCCGCCGCATGCCTT 62.846 66.667 13.15 0.00 36.24 4.35
1276 1325 5.058490 CCAAAATCAATCCAAAACACAGCT 58.942 37.500 0.00 0.00 0.00 4.24
1280 1329 6.018016 CACTTCCCAAAATCAATCCAAAACAC 60.018 38.462 0.00 0.00 0.00 3.32
1361 1411 5.453158 ACATACTACTACCCCCTAGAACAC 58.547 45.833 0.00 0.00 0.00 3.32
1372 1422 5.879777 GCCTACCTAGCTACATACTACTACC 59.120 48.000 0.00 0.00 0.00 3.18
1416 1466 2.203181 GCTCATCAGCTCCCAGCC 60.203 66.667 0.00 0.00 43.77 4.85
1491 1541 1.733912 CGCAATAAGCAAGCAGAGTGA 59.266 47.619 0.00 0.00 46.13 3.41
1492 1542 1.792993 GCGCAATAAGCAAGCAGAGTG 60.793 52.381 0.30 0.00 46.13 3.51
1524 1574 0.453950 GCAACATCAGCACTTGAGCG 60.454 55.000 0.00 0.00 39.68 5.03
1555 1610 3.127376 TGATGGCATCATGAAGAACAACG 59.873 43.478 25.63 0.00 33.59 4.10
1576 1631 0.091344 GCTCAACAATCGACGTCGTG 59.909 55.000 34.40 28.01 40.80 4.35
1577 1632 0.039437 AGCTCAACAATCGACGTCGT 60.039 50.000 34.40 20.51 40.80 4.34
1609 1664 2.886523 TGACCTTGGATTCTTTGCAGTG 59.113 45.455 0.00 0.00 0.00 3.66
1690 1757 1.673808 ATACAGCGACGGTTCCCTCC 61.674 60.000 0.00 0.00 0.00 4.30
1756 1823 0.038526 GATTCGTGGTCACACCGTCT 60.039 55.000 1.90 0.00 44.86 4.18
1814 1881 2.030540 CACTGTGGTTTCTGATTGCAGG 60.031 50.000 0.00 0.00 42.53 4.85
1872 1939 3.758300 ACACTGAAGCAAACGAACAAAG 58.242 40.909 0.00 0.00 0.00 2.77
1873 1940 3.840890 ACACTGAAGCAAACGAACAAA 57.159 38.095 0.00 0.00 0.00 2.83
1899 1966 4.647564 ACTAATCAGATGGCCCATAAGG 57.352 45.455 0.00 0.00 39.47 2.69
1900 1967 6.365970 AGTACTAATCAGATGGCCCATAAG 57.634 41.667 0.00 0.00 0.00 1.73
1946 2335 2.164219 ACAGTCAACCACACTTTGCAAG 59.836 45.455 0.00 0.00 0.00 4.01
1950 2339 1.330521 CCGACAGTCAACCACACTTTG 59.669 52.381 0.41 0.00 0.00 2.77
2036 2426 2.060326 TAACTGCGTCTTCAAGACCG 57.940 50.000 12.12 8.29 42.12 4.79
2048 2438 1.134487 CGCACCCACATTAACTGCG 59.866 57.895 0.00 0.00 44.06 5.18
2065 2455 3.849951 CCGGATCTCCCACACCCG 61.850 72.222 0.00 0.00 39.85 5.28
2066 2456 4.176752 GCCGGATCTCCCACACCC 62.177 72.222 5.05 0.00 34.14 4.61
2067 2457 3.391665 CTGCCGGATCTCCCACACC 62.392 68.421 5.05 0.00 34.14 4.16
2121 2513 2.045536 CTTCACCAGGAGGCAGGC 60.046 66.667 0.00 0.00 39.06 4.85
2127 2519 1.009829 GCAATACGCTTCACCAGGAG 58.990 55.000 0.00 0.00 37.77 3.69
2128 2520 0.323302 TGCAATACGCTTCACCAGGA 59.677 50.000 0.00 0.00 43.06 3.86
2130 2522 2.789208 CATTGCAATACGCTTCACCAG 58.211 47.619 12.53 0.00 43.06 4.00
2131 2523 1.135431 GCATTGCAATACGCTTCACCA 60.135 47.619 12.53 0.00 43.06 4.17
2132 2524 1.548986 GCATTGCAATACGCTTCACC 58.451 50.000 12.53 0.00 43.06 4.02
2133 2525 1.182673 CGCATTGCAATACGCTTCAC 58.817 50.000 18.40 0.00 43.06 3.18
2134 2526 1.062440 CTCGCATTGCAATACGCTTCA 59.938 47.619 24.13 8.75 43.06 3.02
2135 2527 1.595489 CCTCGCATTGCAATACGCTTC 60.595 52.381 24.13 4.53 43.06 3.86
2136 2528 0.378257 CCTCGCATTGCAATACGCTT 59.622 50.000 24.13 0.00 43.06 4.68
2137 2529 0.744414 ACCTCGCATTGCAATACGCT 60.744 50.000 24.13 8.62 43.06 5.07
2176 2568 1.466167 CTGAATGAAGCCTTGACACCG 59.534 52.381 0.00 0.00 0.00 4.94
2177 2569 1.815003 CCTGAATGAAGCCTTGACACC 59.185 52.381 0.00 0.00 0.00 4.16
2184 2576 1.379576 GCCAGCCTGAATGAAGCCT 60.380 57.895 0.00 0.00 0.00 4.58
2197 2589 1.328279 GTTACCCCATTATGGCCAGC 58.672 55.000 13.05 0.00 35.79 4.85
2198 2590 2.746279 TGTTACCCCATTATGGCCAG 57.254 50.000 13.05 0.00 35.79 4.85
2199 2591 4.475345 GTTATGTTACCCCATTATGGCCA 58.525 43.478 8.56 8.56 35.79 5.36
2200 2592 3.830178 GGTTATGTTACCCCATTATGGCC 59.170 47.826 5.57 0.00 35.79 5.36
2201 2593 4.736473 AGGTTATGTTACCCCATTATGGC 58.264 43.478 5.57 0.00 39.08 4.40
2202 2594 7.780745 TGTTAAGGTTATGTTACCCCATTATGG 59.219 37.037 3.85 3.85 39.08 2.74
2203 2595 8.754991 TGTTAAGGTTATGTTACCCCATTATG 57.245 34.615 0.00 0.00 39.08 1.90
2206 2598 9.945633 ATTATGTTAAGGTTATGTTACCCCATT 57.054 29.630 0.00 0.00 39.08 3.16


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

AutoCloner maintained by Alex Coulton.