Multiple sequence alignment - TraesCS4A01G477600

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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 TraesCS4A01G477600 chr4A 100.000 2999 0 0 1 2999 735366048 735363050 0.000000e+00 5539.0
1 TraesCS4A01G477600 chr4A 95.031 2093 82 8 1 2090 734998622 735000695 0.000000e+00 3269.0
2 TraesCS4A01G477600 chr4A 86.828 2103 246 18 1 2078 735778307 735780403 0.000000e+00 2320.0
3 TraesCS4A01G477600 chr4A 83.262 2103 304 27 1 2078 735560824 735558745 0.000000e+00 1890.0
4 TraesCS4A01G477600 chr4A 82.224 2104 316 34 1 2078 736758188 736760259 0.000000e+00 1760.0
5 TraesCS4A01G477600 chr4A 81.413 2109 335 35 1 2078 735690928 735693010 0.000000e+00 1670.0
6 TraesCS4A01G477600 chr4A 81.304 2102 338 35 1 2075 734387054 734389127 0.000000e+00 1653.0
7 TraesCS4A01G477600 chr4A 81.161 2102 352 29 1 2078 736468820 736466739 0.000000e+00 1648.0
8 TraesCS4A01G477600 chr4A 82.418 1911 308 24 173 2069 736121740 736123636 0.000000e+00 1642.0
9 TraesCS4A01G477600 chr4A 82.464 1899 300 20 195 2069 735005442 735007331 0.000000e+00 1631.0
10 TraesCS4A01G477600 chr4A 82.115 1929 301 26 1 1906 736898640 736900547 0.000000e+00 1611.0
11 TraesCS4A01G477600 chr4A 82.229 1750 271 26 354 2078 734482988 734484722 0.000000e+00 1472.0
12 TraesCS4A01G477600 chr4A 84.254 362 42 12 1 361 734482018 734482365 3.700000e-89 339.0
13 TraesCS4A01G477600 chr4A 93.333 120 7 1 2067 2185 655433722 655433841 3.070000e-40 176.0
14 TraesCS4A01G477600 chr4A 96.154 52 2 0 2170 2221 735000830 735000881 5.330000e-13 86.1
15 TraesCS4A01G477600 chr7D 88.868 2111 209 14 1 2088 5636211 5634104 0.000000e+00 2573.0
16 TraesCS4A01G477600 chr7D 81.150 2069 337 35 1 2041 5647515 5645472 0.000000e+00 1611.0
17 TraesCS4A01G477600 chr7D 80.813 2116 333 44 1 2077 5447241 5445160 0.000000e+00 1591.0
18 TraesCS4A01G477600 chr7D 80.654 2109 343 38 1 2078 5664981 5662907 0.000000e+00 1574.0
19 TraesCS4A01G477600 chr7D 80.180 2109 362 40 1 2078 5485002 5482919 0.000000e+00 1528.0
20 TraesCS4A01G477600 chr7D 79.563 2104 366 48 5 2075 5786272 5784200 0.000000e+00 1445.0
21 TraesCS4A01G477600 chr7D 81.920 1344 206 24 763 2078 5798370 5797036 0.000000e+00 1101.0
22 TraesCS4A01G477600 chr7D 95.536 112 5 0 2074 2185 174803146 174803257 2.380000e-41 180.0
23 TraesCS4A01G477600 chr7D 87.500 128 16 0 9 136 5458288 5458161 6.700000e-32 148.0
24 TraesCS4A01G477600 chr7D 93.478 46 3 0 2182 2227 5634116 5634071 5.360000e-08 69.4
25 TraesCS4A01G477600 chr7A 82.406 2103 322 28 1 2078 6926778 6924699 0.000000e+00 1790.0
26 TraesCS4A01G477600 chr7A 81.247 2085 331 37 1 2052 7320469 7318412 0.000000e+00 1629.0
27 TraesCS4A01G477600 chr7A 80.454 2113 342 36 1 2078 7043621 7041545 0.000000e+00 1548.0
28 TraesCS4A01G477600 chr7A 96.734 398 13 0 2602 2999 104653774 104653377 0.000000e+00 664.0
29 TraesCS4A01G477600 chr7A 93.333 120 7 1 2064 2183 675402419 675402301 3.070000e-40 176.0
30 TraesCS4A01G477600 chr7A 91.935 124 9 1 2063 2186 32594505 32594383 3.970000e-39 172.0
31 TraesCS4A01G477600 chr6A 89.058 722 74 5 2268 2987 587729696 587730414 0.000000e+00 891.0
32 TraesCS4A01G477600 chr6A 93.077 390 23 4 2222 2609 74229497 74229884 4.340000e-158 568.0
33 TraesCS4A01G477600 chr6A 95.575 113 5 0 2074 2186 158088026 158087914 6.600000e-42 182.0
34 TraesCS4A01G477600 chr6A 94.643 112 6 0 2072 2183 613616590 613616701 1.110000e-39 174.0
35 TraesCS4A01G477600 chr6A 95.370 108 5 0 2077 2184 408886183 408886076 3.970000e-39 172.0
36 TraesCS4A01G477600 chr6D 85.841 791 95 10 2222 2997 19233605 19232817 0.000000e+00 824.0
37 TraesCS4A01G477600 chr6D 93.860 114 7 0 2073 2186 14121692 14121579 3.970000e-39 172.0
38 TraesCS4A01G477600 chr6D 95.370 108 5 0 2077 2184 382979379 382979486 3.970000e-39 172.0
39 TraesCS4A01G477600 chr6D 94.495 109 6 0 2076 2184 81674637 81674745 5.140000e-38 169.0
40 TraesCS4A01G477600 chr6D 92.982 114 8 0 2073 2186 75829295 75829182 1.850000e-37 167.0
41 TraesCS4A01G477600 chr6D 93.694 111 7 0 2073 2183 98415524 98415634 1.850000e-37 167.0
42 TraesCS4A01G477600 chr6D 94.444 108 6 0 2077 2184 130300957 130301064 1.850000e-37 167.0
43 TraesCS4A01G477600 chr6D 93.694 111 7 0 2073 2183 419759904 419759794 1.850000e-37 167.0
44 TraesCS4A01G477600 chr6D 93.694 111 7 0 2077 2187 455247124 455247234 1.850000e-37 167.0
45 TraesCS4A01G477600 chr6D 94.393 107 6 0 2077 2183 3196382 3196488 6.650000e-37 165.0
46 TraesCS4A01G477600 chr6D 92.105 114 9 0 2073 2186 169843871 169843758 8.600000e-36 161.0
47 TraesCS4A01G477600 chr6D 90.909 121 10 1 2063 2183 303338221 303338102 8.600000e-36 161.0
48 TraesCS4A01G477600 chr6D 89.600 125 11 2 2061 2184 9064269 9064392 1.110000e-34 158.0
49 TraesCS4A01G477600 chr3A 73.330 2006 457 57 22 1987 557417215 557415248 0.000000e+00 669.0
50 TraesCS4A01G477600 chr3A 97.222 108 3 0 2076 2183 255066135 255066028 1.840000e-42 183.0
51 TraesCS4A01G477600 chr3A 93.548 124 5 3 2071 2193 405503660 405503781 6.600000e-42 182.0
52 TraesCS4A01G477600 chr1B 96.977 397 11 1 2603 2999 670858342 670857947 0.000000e+00 665.0
53 TraesCS4A01G477600 chr1B 96.734 398 13 0 2602 2999 313489554 313489951 0.000000e+00 664.0
54 TraesCS4A01G477600 chr1B 96.474 397 13 1 2603 2999 19078319 19078714 0.000000e+00 654.0
55 TraesCS4A01G477600 chr1B 72.833 1984 473 51 16 1971 631201876 631199931 4.250000e-173 617.0
56 TraesCS4A01G477600 chr5B 96.717 396 13 0 2602 2997 656783682 656783287 0.000000e+00 660.0
57 TraesCS4A01G477600 chr5B 94.180 378 19 3 2222 2598 530039933 530040308 9.330000e-160 573.0
58 TraesCS4A01G477600 chr5B 92.405 395 25 5 2222 2613 243904294 243904686 2.610000e-155 558.0
59 TraesCS4A01G477600 chr5B 92.152 395 26 5 2222 2613 113021559 113021951 1.210000e-153 553.0
60 TraesCS4A01G477600 chr5B 92.132 394 28 3 2222 2613 465149311 465148919 1.210000e-153 553.0
61 TraesCS4A01G477600 chr4D 93.258 445 23 4 2559 2999 178673845 178673404 0.000000e+00 649.0
62 TraesCS4A01G477600 chr4D 96.262 107 4 0 2077 2183 50987716 50987610 3.070000e-40 176.0
63 TraesCS4A01G477600 chr4D 94.690 113 6 0 2074 2186 128165800 128165688 3.070000e-40 176.0
64 TraesCS4A01G477600 chr4D 92.500 120 7 2 2065 2183 73597637 73597755 1.430000e-38 171.0
65 TraesCS4A01G477600 chr4D 91.736 121 10 0 2066 2186 160742378 160742258 5.140000e-38 169.0
66 TraesCS4A01G477600 chr4D 91.667 120 10 0 2065 2184 60634341 60634460 1.850000e-37 167.0
67 TraesCS4A01G477600 chr3D 90.171 468 40 4 2530 2995 288663832 288663369 3.310000e-169 604.0
68 TraesCS4A01G477600 chr3D 90.551 127 10 2 2062 2187 41211734 41211609 1.850000e-37 167.0
69 TraesCS4A01G477600 chr6B 95.503 378 15 2 2222 2598 483917784 483917408 1.190000e-168 603.0
70 TraesCS4A01G477600 chr6B 92.386 394 25 4 2222 2613 319819572 319819182 9.390000e-155 556.0
71 TraesCS4A01G477600 chr4B 93.622 392 19 6 2222 2609 376153616 376153227 5.570000e-162 580.0
72 TraesCS4A01G477600 chr4B 92.152 395 26 5 2222 2613 380995583 380995191 1.210000e-153 553.0
73 TraesCS4A01G477600 chr4B 96.364 110 4 0 2074 2183 386723511 386723620 6.600000e-42 182.0
74 TraesCS4A01G477600 chr4B 95.536 112 5 0 2075 2186 240145349 240145460 2.380000e-41 180.0
75 TraesCS4A01G477600 chrUn 80.137 438 80 5 1595 2030 476230249 476229817 1.340000e-83 320.0
76 TraesCS4A01G477600 chrUn 96.429 112 4 0 2074 2185 37054867 37054978 5.110000e-43 185.0
77 TraesCS4A01G477600 chrUn 97.196 107 3 0 2077 2183 77508706 77508812 6.600000e-42 182.0
78 TraesCS4A01G477600 chrUn 92.308 117 9 0 2070 2186 50839304 50839420 1.850000e-37 167.0
79 TraesCS4A01G477600 chr7B 97.297 111 3 0 2076 2186 513956141 513956251 3.950000e-44 189.0
80 TraesCS4A01G477600 chr7B 96.396 111 4 0 2074 2184 450588140 450588030 1.840000e-42 183.0
81 TraesCS4A01G477600 chr7B 94.872 117 6 0 2070 2186 629889965 629889849 1.840000e-42 183.0
82 TraesCS4A01G477600 chr7B 92.623 122 6 3 2077 2197 447705604 447705485 3.970000e-39 172.0
83 TraesCS4A01G477600 chr3B 95.614 114 5 0 2074 2187 64500386 64500273 1.840000e-42 183.0
84 TraesCS4A01G477600 chr3B 90.511 137 11 2 2051 2186 650803691 650803826 2.380000e-41 180.0
85 TraesCS4A01G477600 chr1A 96.364 110 4 0 2074 2183 466345456 466345347 6.600000e-42 182.0
86 TraesCS4A01G477600 chr1A 92.562 121 7 2 2066 2184 531866980 531867100 3.970000e-39 172.0
87 TraesCS4A01G477600 chr2A 93.388 121 7 1 2065 2185 183328467 183328348 8.540000e-41 178.0
88 TraesCS4A01G477600 chr5D 93.913 115 7 0 2070 2184 391376994 391376880 1.110000e-39 174.0
89 TraesCS4A01G477600 chr5D 91.200 125 10 1 2062 2185 522142264 522142140 5.140000e-38 169.0
90 TraesCS4A01G477600 chr1D 94.595 111 6 0 2073 2183 335497202 335497312 3.970000e-39 172.0
91 TraesCS4A01G477600 chr1D 95.370 108 5 0 2076 2183 349422924 349423031 3.970000e-39 172.0
92 TraesCS4A01G477600 chr1D 94.545 110 6 0 2077 2186 464736336 464736227 1.430000e-38 171.0
93 TraesCS4A01G477600 chr1D 93.103 116 6 2 2069 2183 48024737 48024623 5.140000e-38 169.0
94 TraesCS4A01G477600 chr1D 92.982 114 8 0 2070 2183 73714851 73714964 1.850000e-37 167.0
95 TraesCS4A01G477600 chr2D 90.152 132 12 1 2053 2183 627971644 627971513 1.430000e-38 171.0


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 TraesCS4A01G477600 chr4A 735363050 735366048 2998 True 5539.00 5539 100.0000 1 2999 1 chr4A.!!$R1 2998
1 TraesCS4A01G477600 chr4A 735778307 735780403 2096 False 2320.00 2320 86.8280 1 2078 1 chr4A.!!$F5 2077
2 TraesCS4A01G477600 chr4A 735558745 735560824 2079 True 1890.00 1890 83.2620 1 2078 1 chr4A.!!$R2 2077
3 TraesCS4A01G477600 chr4A 736758188 736760259 2071 False 1760.00 1760 82.2240 1 2078 1 chr4A.!!$F7 2077
4 TraesCS4A01G477600 chr4A 734998622 735000881 2259 False 1677.55 3269 95.5925 1 2221 2 chr4A.!!$F10 2220
5 TraesCS4A01G477600 chr4A 735690928 735693010 2082 False 1670.00 1670 81.4130 1 2078 1 chr4A.!!$F4 2077
6 TraesCS4A01G477600 chr4A 734387054 734389127 2073 False 1653.00 1653 81.3040 1 2075 1 chr4A.!!$F2 2074
7 TraesCS4A01G477600 chr4A 736466739 736468820 2081 True 1648.00 1648 81.1610 1 2078 1 chr4A.!!$R3 2077
8 TraesCS4A01G477600 chr4A 736121740 736123636 1896 False 1642.00 1642 82.4180 173 2069 1 chr4A.!!$F6 1896
9 TraesCS4A01G477600 chr4A 735005442 735007331 1889 False 1631.00 1631 82.4640 195 2069 1 chr4A.!!$F3 1874
10 TraesCS4A01G477600 chr4A 736898640 736900547 1907 False 1611.00 1611 82.1150 1 1906 1 chr4A.!!$F8 1905
11 TraesCS4A01G477600 chr4A 734482018 734484722 2704 False 905.50 1472 83.2415 1 2078 2 chr4A.!!$F9 2077
12 TraesCS4A01G477600 chr7D 5645472 5647515 2043 True 1611.00 1611 81.1500 1 2041 1 chr7D.!!$R4 2040
13 TraesCS4A01G477600 chr7D 5445160 5447241 2081 True 1591.00 1591 80.8130 1 2077 1 chr7D.!!$R1 2076
14 TraesCS4A01G477600 chr7D 5662907 5664981 2074 True 1574.00 1574 80.6540 1 2078 1 chr7D.!!$R5 2077
15 TraesCS4A01G477600 chr7D 5482919 5485002 2083 True 1528.00 1528 80.1800 1 2078 1 chr7D.!!$R3 2077
16 TraesCS4A01G477600 chr7D 5784200 5786272 2072 True 1445.00 1445 79.5630 5 2075 1 chr7D.!!$R6 2070
17 TraesCS4A01G477600 chr7D 5634071 5636211 2140 True 1321.20 2573 91.1730 1 2227 2 chr7D.!!$R8 2226
18 TraesCS4A01G477600 chr7D 5797036 5798370 1334 True 1101.00 1101 81.9200 763 2078 1 chr7D.!!$R7 1315
19 TraesCS4A01G477600 chr7A 6924699 6926778 2079 True 1790.00 1790 82.4060 1 2078 1 chr7A.!!$R1 2077
20 TraesCS4A01G477600 chr7A 7318412 7320469 2057 True 1629.00 1629 81.2470 1 2052 1 chr7A.!!$R3 2051
21 TraesCS4A01G477600 chr7A 7041545 7043621 2076 True 1548.00 1548 80.4540 1 2078 1 chr7A.!!$R2 2077
22 TraesCS4A01G477600 chr6A 587729696 587730414 718 False 891.00 891 89.0580 2268 2987 1 chr6A.!!$F2 719
23 TraesCS4A01G477600 chr6D 19232817 19233605 788 True 824.00 824 85.8410 2222 2997 1 chr6D.!!$R2 775
24 TraesCS4A01G477600 chr3A 557415248 557417215 1967 True 669.00 669 73.3300 22 1987 1 chr3A.!!$R2 1965
25 TraesCS4A01G477600 chr1B 631199931 631201876 1945 True 617.00 617 72.8330 16 1971 1 chr1B.!!$R1 1955

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
828 1470 3.139397 ACAACTTGGGTTAATCTGGGACA 59.861 43.478 0.0 0.0 33.88 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2914 1.47973 ACTCCCTCCGTTCGGAATTAC 59.52 52.381 14.79 0.0 33.41 1.89 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
76 77 4.990543 TGCAGTCACTTCTGTTAAATCG 57.009 40.909 0.00 0.00 37.70 3.34
165 166 8.296713 ACCGTGATTGGCATAATGATTTAATAC 58.703 33.333 0.00 0.00 0.00 1.89
552 1184 4.276678 GCTGGTTGCTTGATGCTTCATATA 59.723 41.667 2.75 0.00 43.37 0.86
728 1361 4.859629 ACGAATAGAAAAATGTCCGCTC 57.140 40.909 0.00 0.00 0.00 5.03
739 1372 6.436843 AAAATGTCCGCTCCTTGTATTTAG 57.563 37.500 0.00 0.00 0.00 1.85
741 1374 4.119442 TGTCCGCTCCTTGTATTTAGTC 57.881 45.455 0.00 0.00 0.00 2.59
773 1415 7.017319 TGAGCTGGAATATGATGATCAGATT 57.983 36.000 14.48 14.48 40.58 2.40
828 1470 3.139397 ACAACTTGGGTTAATCTGGGACA 59.861 43.478 0.00 0.00 33.88 4.02
932 1591 7.933577 TCAAAATCTTGAAAGTGCTCTAGAAGA 59.066 33.333 0.00 6.55 38.65 2.87
1077 1736 8.552034 AGACTTTGTGAACTTTATCTTTCTTCG 58.448 33.333 0.00 0.00 0.00 3.79
1225 1885 4.932200 CAGAACTTGACTACTTGTCCATCC 59.068 45.833 0.00 0.00 44.75 3.51
1487 2158 6.681729 TGGTAGTCTCACCTCTGTTAAATT 57.318 37.500 0.00 0.00 39.50 1.82
1497 2168 9.442047 CTCACCTCTGTTAAATTATTCTCACTT 57.558 33.333 0.00 0.00 0.00 3.16
1755 2429 7.807977 AGAATTCACAAACTGTACATCTGTT 57.192 32.000 8.44 0.00 39.31 3.16
2055 2751 5.338463 GGAAAGGTAAATAGCTCCTGTCAGT 60.338 44.000 10.05 0.00 37.34 3.41
2070 2766 2.288666 GTCAGTCACCTTTGCACTCAA 58.711 47.619 0.00 0.00 0.00 3.02
2090 2788 4.277672 TCAAAGATATACTCCCTCCGTTCG 59.722 45.833 0.00 0.00 0.00 3.95
2091 2789 2.792878 AGATATACTCCCTCCGTTCGG 58.207 52.381 4.74 4.74 0.00 4.30
2094 2792 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2096 2794 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2097 2795 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2098 2796 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2099 2797 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2103 2801 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2106 2804 3.422603 CCGTTCGGAATTACTTGTCGTTG 60.423 47.826 5.19 0.00 0.00 4.10
2107 2805 3.426191 CGTTCGGAATTACTTGTCGTTGA 59.574 43.478 0.00 0.00 0.00 3.18
2109 2807 5.556758 CGTTCGGAATTACTTGTCGTTGAAA 60.557 40.000 0.00 0.00 0.00 2.69
2110 2808 6.368213 GTTCGGAATTACTTGTCGTTGAAAT 58.632 36.000 0.00 0.00 0.00 2.17
2113 2811 6.203145 TCGGAATTACTTGTCGTTGAAATGAA 59.797 34.615 0.00 0.00 0.00 2.57
2115 2813 7.007367 CGGAATTACTTGTCGTTGAAATGAATG 59.993 37.037 0.00 0.00 0.00 2.67
2116 2814 7.807907 GGAATTACTTGTCGTTGAAATGAATGT 59.192 33.333 0.00 0.00 0.00 2.71
2119 2817 9.988350 ATTACTTGTCGTTGAAATGAATGTATC 57.012 29.630 0.00 0.00 0.00 2.24
2120 2818 7.672983 ACTTGTCGTTGAAATGAATGTATCT 57.327 32.000 0.00 0.00 0.00 1.98
2121 2819 8.771920 ACTTGTCGTTGAAATGAATGTATCTA 57.228 30.769 0.00 0.00 0.00 1.98
2123 2821 8.996024 TTGTCGTTGAAATGAATGTATCTAGA 57.004 30.769 0.00 0.00 0.00 2.43
2124 2822 9.599866 TTGTCGTTGAAATGAATGTATCTAGAT 57.400 29.630 10.73 10.73 0.00 1.98
2125 2823 9.034544 TGTCGTTGAAATGAATGTATCTAGATG 57.965 33.333 15.79 0.00 0.00 2.90
2159 2912 8.879759 GTTTTAGATACATCCATTTTCGAGACA 58.120 33.333 0.00 0.00 0.00 3.41
2160 2913 9.443323 TTTTAGATACATCCATTTTCGAGACAA 57.557 29.630 0.00 0.00 0.00 3.18
2161 2914 8.648557 TTAGATACATCCATTTTCGAGACAAG 57.351 34.615 0.00 0.00 0.00 3.16
2164 2917 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2167 2920 7.752695 ACATCCATTTTCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2168 2921 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2173 2926 3.495193 TCGAGACAAGTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
2174 2927 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2260 3013 2.785743 ACCCAGGGTGCAGAATACA 58.214 52.632 11.70 0.00 32.98 2.29
2282 3035 6.659824 ACATTATTCTTCACCCGAGGTAATT 58.340 36.000 0.00 0.00 32.11 1.40
2393 3156 9.588096 AAGGTTAGAAGACCAGAAAAATTACAT 57.412 29.630 0.00 0.00 42.35 2.29
2460 3224 8.182881 TGCGTAACATAAAATATTTTTACGGCT 58.817 29.630 27.52 11.84 35.42 5.52
2494 3258 8.897872 TTTTCTTACGTTCTCCTTTTATGTCT 57.102 30.769 0.00 0.00 0.00 3.41
2536 3301 7.948513 ACGAAACTAAAATTACGATGCATTC 57.051 32.000 0.00 0.00 0.00 2.67
2555 3321 7.555087 TGCATTCATGTTAAAATAGAAAGGGG 58.445 34.615 0.00 0.00 0.00 4.79
2557 3323 7.147742 GCATTCATGTTAAAATAGAAAGGGGGA 60.148 37.037 0.00 0.00 0.00 4.81
2598 3364 1.299926 GGGTGACGAATAGCGCGAT 60.300 57.895 12.10 5.99 46.04 4.58
2672 3438 7.212976 CCCACATATCTCATATACTACCATGC 58.787 42.308 0.00 0.00 0.00 4.06
2673 3439 7.147672 CCCACATATCTCATATACTACCATGCA 60.148 40.741 0.00 0.00 0.00 3.96
2980 3748 4.004196 ACTACCACTGCTTGTAGGAAAC 57.996 45.455 0.00 0.00 38.98 2.78
2988 3756 4.278419 ACTGCTTGTAGGAAACATTTGTCC 59.722 41.667 0.00 0.00 38.10 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 5.368989 TCTCAGGAAAACTCTCAACTTTCC 58.631 41.667 4.93 4.93 45.66 3.13
165 166 3.181493 GGTGCATCTTTGTATGGCTTGAG 60.181 47.826 0.00 0.00 0.00 3.02
552 1184 8.667076 AAGCTTAAAGAATGCAAAAACTCAAT 57.333 26.923 0.00 0.00 0.00 2.57
728 1361 5.424757 TCATCGTTGGGACTAAATACAAGG 58.575 41.667 0.00 0.00 0.00 3.61
739 1372 0.036388 TTCCAGCTCATCGTTGGGAC 60.036 55.000 0.00 0.00 43.59 4.46
741 1374 2.620251 TATTCCAGCTCATCGTTGGG 57.380 50.000 0.00 0.00 43.59 4.12
773 1415 6.312141 TGGTTTGTCCTCATGATATTCTCA 57.688 37.500 0.00 0.00 36.21 3.27
828 1470 7.579940 ACCTAATATGTGATCCTGAATCCAT 57.420 36.000 0.00 0.00 33.01 3.41
965 1624 2.882761 CAGTATGTCCATGCCTTGATGG 59.117 50.000 0.00 0.00 43.96 3.51
990 1649 2.902486 TGTGAGTCTCATCCTTTGCTCT 59.098 45.455 5.68 0.00 0.00 4.09
1077 1736 4.065321 AGCTCCATCTGTAATACTGCAC 57.935 45.455 0.00 0.00 0.00 4.57
1225 1885 3.614092 ACCAGAGACACCAGCAATTATG 58.386 45.455 0.00 0.00 0.00 1.90
1487 2158 6.946340 TCTGGCAAGTGATAAAGTGAGAATA 58.054 36.000 0.00 0.00 0.00 1.75
1497 2168 8.049117 AGAGAACATAAATCTGGCAAGTGATAA 58.951 33.333 0.00 0.00 0.00 1.75
1539 2210 2.489971 TGTAGGTTGTACAGTTGCAGC 58.510 47.619 0.00 0.00 0.00 5.25
2070 2766 3.155501 CCGAACGGAGGGAGTATATCTT 58.844 50.000 7.53 0.00 37.50 2.40
2072 2768 2.787994 TCCGAACGGAGGGAGTATATC 58.212 52.381 12.04 0.00 39.76 1.63
2090 2788 7.807907 ACATTCATTTCAACGACAAGTAATTCC 59.192 33.333 0.00 0.00 0.00 3.01
2091 2789 8.728088 ACATTCATTTCAACGACAAGTAATTC 57.272 30.769 0.00 0.00 0.00 2.17
2094 2792 9.214957 AGATACATTCATTTCAACGACAAGTAA 57.785 29.630 0.00 0.00 0.00 2.24
2096 2794 7.672983 AGATACATTCATTTCAACGACAAGT 57.327 32.000 0.00 0.00 0.00 3.16
2097 2795 9.087424 TCTAGATACATTCATTTCAACGACAAG 57.913 33.333 0.00 0.00 0.00 3.16
2098 2796 8.996024 TCTAGATACATTCATTTCAACGACAA 57.004 30.769 0.00 0.00 0.00 3.18
2099 2797 9.034544 CATCTAGATACATTCATTTCAACGACA 57.965 33.333 4.54 0.00 0.00 4.35
2134 2832 9.443323 TTGTCTCGAAAATGGATGTATCTAAAA 57.557 29.630 0.00 0.00 0.00 1.52
2135 2833 9.098355 CTTGTCTCGAAAATGGATGTATCTAAA 57.902 33.333 0.00 0.00 0.00 1.85
2136 2834 8.258007 ACTTGTCTCGAAAATGGATGTATCTAA 58.742 33.333 0.00 0.00 0.00 2.10
2137 2835 7.782049 ACTTGTCTCGAAAATGGATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
2139 2837 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2140 2838 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2141 2839 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2142 2840 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
2143 2841 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
2145 2843 5.350365 CGGAATTACTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
2146 2844 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
2147 2845 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
2149 2847 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
2153 2851 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2154 2852 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2159 2912 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2160 2913 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2161 2914 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2164 2917 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2167 2920 1.817447 GGATATACTCCCTCCGTTCGG 59.183 57.143 4.74 4.74 38.19 4.30
2227 2980 4.080526 ACCCTGGGTGATGAATAGTAACAC 60.081 45.833 19.82 0.00 32.98 3.32
2259 3012 7.568199 AAATTACCTCGGGTGAAGAATAATG 57.432 36.000 5.90 0.00 36.19 1.90
2260 3013 9.117183 GTAAAATTACCTCGGGTGAAGAATAAT 57.883 33.333 5.90 0.00 36.19 1.28
2435 3198 8.551122 AGCCGTAAAAATATTTTATGTTACGC 57.449 30.769 24.38 20.80 34.42 4.42
2515 3279 9.638239 AACATGAATGCATCGTAATTTTAGTTT 57.362 25.926 0.00 0.00 30.68 2.66
2529 3294 8.206189 CCCCTTTCTATTTTAACATGAATGCAT 58.794 33.333 0.00 0.00 34.29 3.96
2536 3301 8.361169 TCTTTCCCCCTTTCTATTTTAACATG 57.639 34.615 0.00 0.00 0.00 3.21
2550 3316 6.027025 GGGAATAGTTATTCTTTCCCCCTT 57.973 41.667 8.14 0.00 41.80 3.95
2551 3317 5.664815 GGGAATAGTTATTCTTTCCCCCT 57.335 43.478 8.14 0.00 41.80 4.79
2555 3321 5.138276 GGGTGGGGAATAGTTATTCTTTCC 58.862 45.833 10.71 10.28 41.33 3.13
2557 3323 5.340863 CCTGGGTGGGGAATAGTTATTCTTT 60.341 44.000 10.71 0.00 41.33 2.52


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

AutoCloner maintained by Alex Coulton.