Multiple sequence alignment - TraesCS7A01G006500

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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 TraesCS7A01G006500 chr7A 100.000 5447 0 0 1 5447 3156992 3151546 0.000000e+00 10059.0
1 TraesCS7A01G006500 chr7A 94.615 1207 64 1 2351 3557 2685985 2684780 0.000000e+00 1868.0
2 TraesCS7A01G006500 chr7A 92.511 1135 44 9 4252 5377 2684018 2682916 0.000000e+00 1587.0
3 TraesCS7A01G006500 chr7A 96.493 941 33 0 981 1921 2688417 2687477 0.000000e+00 1555.0
4 TraesCS7A01G006500 chr7A 85.844 883 124 1 981 1862 2805903 2805021 0.000000e+00 937.0
5 TraesCS7A01G006500 chr7A 96.627 504 17 0 3753 4256 2684780 2684277 0.000000e+00 837.0
6 TraesCS7A01G006500 chr7A 80.037 1092 196 15 981 2056 3844171 3843086 0.000000e+00 789.0
7 TraesCS7A01G006500 chr7A 88.743 382 32 6 463 842 2689112 2688740 1.790000e-124 457.0
8 TraesCS7A01G006500 chr7A 85.373 335 26 14 1928 2240 2687422 2687089 5.260000e-85 326.0
9 TraesCS7A01G006500 chr7A 100.000 38 0 0 5364 5401 2682868 2682831 2.720000e-08 71.3
10 TraesCS7A01G006500 chr7D 92.495 3451 197 18 981 4373 3552637 3549191 0.000000e+00 4881.0
11 TraesCS7A01G006500 chr7D 91.327 3482 235 23 983 4403 2904906 2901431 0.000000e+00 4695.0
12 TraesCS7A01G006500 chr7D 84.823 2003 232 28 1812 3761 2687464 2685481 0.000000e+00 1949.0
13 TraesCS7A01G006500 chr7D 83.566 858 139 2 981 1837 3425025 3424169 0.000000e+00 802.0
14 TraesCS7A01G006500 chr7D 83.391 861 135 8 981 1837 2522449 2521593 0.000000e+00 791.0
15 TraesCS7A01G006500 chr7D 91.684 469 24 6 4779 5246 3548323 3547869 2.140000e-178 636.0
16 TraesCS7A01G006500 chr7D 79.545 748 139 12 3707 4448 2672076 2671337 6.250000e-144 521.0
17 TraesCS7A01G006500 chr7D 90.331 362 19 5 99 460 3553443 3553098 1.380000e-125 460.0
18 TraesCS7A01G006500 chr7D 96.899 258 8 0 474 731 3553015 3552758 3.010000e-117 433.0
19 TraesCS7A01G006500 chr7D 89.426 331 21 8 467 791 2905389 2905067 6.570000e-109 405.0
20 TraesCS7A01G006500 chr7D 91.964 224 10 5 472 694 2719937 2719721 1.910000e-79 307.0
21 TraesCS7A01G006500 chr7D 87.562 201 19 5 4591 4790 3548970 3548775 1.530000e-55 228.0
22 TraesCS7A01G006500 chr7D 91.250 160 12 2 680 837 2687735 2687576 3.300000e-52 217.0
23 TraesCS7A01G006500 chr7D 96.800 125 4 0 5323 5447 3547824 3547700 5.530000e-50 209.0
24 TraesCS7A01G006500 chr7D 93.798 129 8 0 4779 4907 2900640 2900512 1.550000e-45 195.0
25 TraesCS7A01G006500 chr7D 83.920 199 25 5 4784 4982 3404000 3404191 3.350000e-42 183.0
26 TraesCS7A01G006500 chr7D 94.898 98 5 0 1 98 601165465 601165562 2.630000e-33 154.0
27 TraesCS7A01G006500 chr7D 93.407 91 6 0 893 983 2905039 2904949 9.520000e-28 135.0
28 TraesCS7A01G006500 chr7D 95.238 84 4 0 900 983 3552761 3552678 3.420000e-27 134.0
29 TraesCS7A01G006500 chr7D 90.123 81 7 1 280 359 3426072 3425992 2.680000e-18 104.0
30 TraesCS7A01G006500 chr4A 81.666 3398 494 84 981 4292 742019792 742023146 0.000000e+00 2704.0
31 TraesCS7A01G006500 chr4A 79.714 3421 523 96 1453 4778 740494221 740497565 0.000000e+00 2314.0
32 TraesCS7A01G006500 chr4A 84.736 2162 275 34 2242 4371 739606904 739609042 0.000000e+00 2113.0
33 TraesCS7A01G006500 chr4A 82.970 2296 333 45 2031 4292 740122964 740120693 0.000000e+00 2021.0
34 TraesCS7A01G006500 chr4A 84.556 2059 296 19 2242 4292 742159785 742157741 0.000000e+00 2021.0
35 TraesCS7A01G006500 chr4A 82.329 2224 354 34 2242 4448 733805960 733808161 0.000000e+00 1893.0
36 TraesCS7A01G006500 chr4A 83.020 2126 302 30 2293 4385 739886359 739888458 0.000000e+00 1871.0
37 TraesCS7A01G006500 chr4A 83.639 2017 301 21 2289 4292 741421960 741423960 0.000000e+00 1869.0
38 TraesCS7A01G006500 chr4A 81.365 1363 233 17 3100 4448 741505836 741504481 0.000000e+00 1090.0
39 TraesCS7A01G006500 chr4A 83.597 884 137 7 981 1860 741420769 741421648 0.000000e+00 822.0
40 TraesCS7A01G006500 chr4A 80.713 954 180 4 981 1931 742161105 742160153 0.000000e+00 739.0
41 TraesCS7A01G006500 chr4A 85.965 342 38 7 4779 5112 742156805 742156466 1.870000e-94 357.0
42 TraesCS7A01G006500 chr4A 89.247 93 8 2 6 98 59286845 59286755 1.240000e-21 115.0
43 TraesCS7A01G006500 chr4A 92.308 39 3 0 5144 5182 742156463 742156425 7.620000e-04 56.5
44 TraesCS7A01G006500 chr1D 83.792 1962 283 27 2258 4204 464795416 464797357 0.000000e+00 1829.0
45 TraesCS7A01G006500 chr1D 96.825 63 2 0 4779 4841 464798699 464798761 7.460000e-19 106.0
46 TraesCS7A01G006500 chr4D 95.918 98 4 0 1 98 341704167 341704264 5.650000e-35 159.0
47 TraesCS7A01G006500 chr4D 91.919 99 6 1 1 97 461391413 461391315 2.650000e-28 137.0
48 TraesCS7A01G006500 chr4D 89.796 98 9 1 1 98 107740162 107740258 2.060000e-24 124.0
49 TraesCS7A01G006500 chr6D 91.000 100 7 1 1 98 98104201 98104300 3.420000e-27 134.0
50 TraesCS7A01G006500 chr7B 89.362 94 10 0 4 97 238526533 238526626 9.580000e-23 119.0
51 TraesCS7A01G006500 chr5A 89.362 94 10 0 5 98 640717584 640717491 9.580000e-23 119.0
52 TraesCS7A01G006500 chr3B 88.776 98 10 1 1 98 489983601 489983697 9.580000e-23 119.0


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 TraesCS7A01G006500 chr7A 3151546 3156992 5446 True 10059.000000 10059 100.000000 1 5447 1 chr7A.!!$R2 5446
1 TraesCS7A01G006500 chr7A 2682831 2689112 6281 True 957.328571 1868 93.480286 463 5401 7 chr7A.!!$R4 4938
2 TraesCS7A01G006500 chr7A 2805021 2805903 882 True 937.000000 937 85.844000 981 1862 1 chr7A.!!$R1 881
3 TraesCS7A01G006500 chr7A 3843086 3844171 1085 True 789.000000 789 80.037000 981 2056 1 chr7A.!!$R3 1075
4 TraesCS7A01G006500 chr7D 2900512 2905389 4877 True 1357.500000 4695 91.989500 467 4907 4 chr7D.!!$R5 4440
5 TraesCS7A01G006500 chr7D 2685481 2687735 2254 True 1083.000000 1949 88.036500 680 3761 2 chr7D.!!$R4 3081
6 TraesCS7A01G006500 chr7D 3547700 3553443 5743 True 997.285714 4881 93.001286 99 5447 7 chr7D.!!$R7 5348
7 TraesCS7A01G006500 chr7D 2521593 2522449 856 True 791.000000 791 83.391000 981 1837 1 chr7D.!!$R1 856
8 TraesCS7A01G006500 chr7D 2671337 2672076 739 True 521.000000 521 79.545000 3707 4448 1 chr7D.!!$R2 741
9 TraesCS7A01G006500 chr7D 3424169 3426072 1903 True 453.000000 802 86.844500 280 1837 2 chr7D.!!$R6 1557
10 TraesCS7A01G006500 chr4A 742019792 742023146 3354 False 2704.000000 2704 81.666000 981 4292 1 chr4A.!!$F5 3311
11 TraesCS7A01G006500 chr4A 740494221 740497565 3344 False 2314.000000 2314 79.714000 1453 4778 1 chr4A.!!$F4 3325
12 TraesCS7A01G006500 chr4A 739606904 739609042 2138 False 2113.000000 2113 84.736000 2242 4371 1 chr4A.!!$F2 2129
13 TraesCS7A01G006500 chr4A 740120693 740122964 2271 True 2021.000000 2021 82.970000 2031 4292 1 chr4A.!!$R2 2261
14 TraesCS7A01G006500 chr4A 733805960 733808161 2201 False 1893.000000 1893 82.329000 2242 4448 1 chr4A.!!$F1 2206
15 TraesCS7A01G006500 chr4A 739886359 739888458 2099 False 1871.000000 1871 83.020000 2293 4385 1 chr4A.!!$F3 2092
16 TraesCS7A01G006500 chr4A 741420769 741423960 3191 False 1345.500000 1869 83.618000 981 4292 2 chr4A.!!$F6 3311
17 TraesCS7A01G006500 chr4A 741504481 741505836 1355 True 1090.000000 1090 81.365000 3100 4448 1 chr4A.!!$R3 1348
18 TraesCS7A01G006500 chr4A 742156425 742161105 4680 True 793.375000 2021 85.885500 981 5182 4 chr4A.!!$R4 4201
19 TraesCS7A01G006500 chr1D 464795416 464798761 3345 False 967.500000 1829 90.308500 2258 4841 2 chr1D.!!$F1 2583

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
186 187 0.037046 CTCCATTGCTTTTGGGCCAC 60.037 55.000 5.23 0.0 34.85 5.01 F
189 190 0.247185 CATTGCTTTTGGGCCACGAT 59.753 50.000 5.23 0.0 0.00 3.73 F
874 1407 0.515127 TAGCGTGCACACAAATTCCG 59.485 50.000 18.64 0.0 0.00 4.30 F
1008 1748 1.005097 TGAGAGCAAGCAATGGACCAT 59.995 47.619 0.00 0.0 0.00 3.55 F
2260 3252 1.134461 GGTGCATGCATGTCTCTCTCT 60.134 52.381 25.64 0.0 0.00 3.10 F
2497 4555 1.370900 CAAGAGCGCTTTGGTGTGC 60.371 57.895 13.26 0.0 43.09 4.57 F
3478 5568 0.555769 TGGACTTGGCTGGGAAAAGT 59.444 50.000 0.00 0.0 36.87 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 3068 0.107410 TGGGCGAACAGTCAACAGTT 60.107 50.000 0.00 0.0 0.00 3.16 R
2217 3188 6.039941 ACCATCTACGAGAACTCTATTTCTGG 59.960 42.308 0.00 0.0 35.90 3.86 R
2484 4542 1.994916 ATTATTGCACACCAAAGCGC 58.005 45.000 0.00 0.0 36.92 5.92 R
2773 4835 2.549082 TCATGCCCAAAACCCATTGAT 58.451 42.857 0.00 0.0 31.84 2.57 R
3412 5502 1.549203 TTTCCTTTGGGAGCTCATGC 58.451 50.000 17.19 0.0 43.29 4.06 R
3817 5911 2.040412 GAGTTGTGGAGGGAGGATGTTT 59.960 50.000 0.00 0.0 0.00 2.83 R
5362 8761 0.108945 GCTGCATGCTTTGGTCTTCC 60.109 55.000 20.33 0.0 38.95 3.46 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
56 57 9.465985 TCCGAAACTTTAAAATATGGTTTTCAC 57.534 29.630 4.58 0.00 31.51 3.18
57 58 8.421701 CCGAAACTTTAAAATATGGTTTTCACG 58.578 33.333 4.58 4.36 31.51 4.35
58 59 9.171701 CGAAACTTTAAAATATGGTTTTCACGA 57.828 29.630 0.00 0.00 31.51 4.35
66 67 8.934507 AAAATATGGTTTTCACGAAGTTTTCA 57.065 26.923 0.00 0.00 41.61 2.69
67 68 9.541143 AAAATATGGTTTTCACGAAGTTTTCAT 57.459 25.926 0.00 0.00 41.61 2.57
68 69 8.519492 AATATGGTTTTCACGAAGTTTTCATG 57.481 30.769 0.00 0.00 41.61 3.07
69 70 4.677584 TGGTTTTCACGAAGTTTTCATGG 58.322 39.130 0.00 0.00 41.61 3.66
70 71 4.399618 TGGTTTTCACGAAGTTTTCATGGA 59.600 37.500 0.00 0.00 41.61 3.41
71 72 5.105716 TGGTTTTCACGAAGTTTTCATGGAA 60.106 36.000 0.00 0.00 41.61 3.53
72 73 5.983118 GGTTTTCACGAAGTTTTCATGGAAT 59.017 36.000 0.00 0.00 41.61 3.01
73 74 7.142680 GGTTTTCACGAAGTTTTCATGGAATA 58.857 34.615 0.00 0.00 41.61 1.75
74 75 7.812669 GGTTTTCACGAAGTTTTCATGGAATAT 59.187 33.333 0.00 0.00 41.61 1.28
75 76 9.191995 GTTTTCACGAAGTTTTCATGGAATATT 57.808 29.630 0.00 0.00 41.61 1.28
76 77 9.757227 TTTTCACGAAGTTTTCATGGAATATTT 57.243 25.926 0.00 0.00 41.61 1.40
77 78 8.741101 TTCACGAAGTTTTCATGGAATATTTG 57.259 30.769 0.00 0.00 41.61 2.32
78 79 7.881142 TCACGAAGTTTTCATGGAATATTTGT 58.119 30.769 0.00 0.00 41.61 2.83
79 80 8.356657 TCACGAAGTTTTCATGGAATATTTGTT 58.643 29.630 0.00 0.00 41.61 2.83
80 81 8.977505 CACGAAGTTTTCATGGAATATTTGTTT 58.022 29.630 0.00 0.00 41.61 2.83
81 82 9.191995 ACGAAGTTTTCATGGAATATTTGTTTC 57.808 29.630 0.00 0.00 37.78 2.78
82 83 8.647226 CGAAGTTTTCATGGAATATTTGTTTCC 58.353 33.333 0.00 0.00 42.52 3.13
83 84 8.532977 AAGTTTTCATGGAATATTTGTTTCCG 57.467 30.769 0.00 0.00 44.67 4.30
84 85 7.666623 AGTTTTCATGGAATATTTGTTTCCGT 58.333 30.769 0.00 0.00 44.67 4.69
85 86 8.798402 AGTTTTCATGGAATATTTGTTTCCGTA 58.202 29.630 0.00 0.00 44.67 4.02
86 87 9.581099 GTTTTCATGGAATATTTGTTTCCGTAT 57.419 29.630 0.00 0.00 44.67 3.06
110 111 5.648330 ATATTCTCCCCCAAGAGGTAAAC 57.352 43.478 0.00 0.00 34.46 2.01
182 183 2.220653 TCTCCTCCATTGCTTTTGGG 57.779 50.000 1.20 0.00 34.85 4.12
184 185 0.904394 TCCTCCATTGCTTTTGGGCC 60.904 55.000 0.00 0.00 34.85 5.80
185 186 1.193462 CCTCCATTGCTTTTGGGCCA 61.193 55.000 0.00 0.00 34.85 5.36
186 187 0.037046 CTCCATTGCTTTTGGGCCAC 60.037 55.000 5.23 0.00 34.85 5.01
187 188 1.374505 CCATTGCTTTTGGGCCACG 60.375 57.895 5.23 0.00 0.00 4.94
188 189 1.664873 CATTGCTTTTGGGCCACGA 59.335 52.632 5.23 0.00 0.00 4.35
189 190 0.247185 CATTGCTTTTGGGCCACGAT 59.753 50.000 5.23 0.00 0.00 3.73
190 191 0.975887 ATTGCTTTTGGGCCACGATT 59.024 45.000 5.23 0.00 0.00 3.34
191 192 1.621992 TTGCTTTTGGGCCACGATTA 58.378 45.000 5.23 0.00 0.00 1.75
192 193 1.846007 TGCTTTTGGGCCACGATTAT 58.154 45.000 5.23 0.00 0.00 1.28
193 194 2.175202 TGCTTTTGGGCCACGATTATT 58.825 42.857 5.23 0.00 0.00 1.40
194 195 2.165437 TGCTTTTGGGCCACGATTATTC 59.835 45.455 5.23 0.00 0.00 1.75
195 196 2.481276 GCTTTTGGGCCACGATTATTCC 60.481 50.000 5.23 0.00 0.00 3.01
196 197 2.516227 TTTGGGCCACGATTATTCCA 57.484 45.000 5.23 0.00 0.00 3.53
197 198 2.746279 TTGGGCCACGATTATTCCAT 57.254 45.000 5.23 0.00 0.00 3.41
207 208 3.062763 CGATTATTCCATCGCTCTGCTT 58.937 45.455 0.00 0.00 39.69 3.91
214 215 1.016130 CATCGCTCTGCTTTCACCGT 61.016 55.000 0.00 0.00 0.00 4.83
237 238 0.593128 CCCGCAGAAACCTTGTCTTG 59.407 55.000 0.00 0.00 0.00 3.02
244 245 2.092429 AGAAACCTTGTCTTGAGCACCA 60.092 45.455 0.00 0.00 0.00 4.17
250 251 3.306989 CCTTGTCTTGAGCACCATCACTA 60.307 47.826 0.00 0.00 0.00 2.74
251 252 3.599730 TGTCTTGAGCACCATCACTAG 57.400 47.619 0.00 0.00 0.00 2.57
256 257 3.548745 TGAGCACCATCACTAGGATTG 57.451 47.619 0.00 0.00 32.57 2.67
257 258 2.216898 GAGCACCATCACTAGGATTGC 58.783 52.381 0.00 2.75 39.16 3.56
278 279 1.519455 GCGTCCCTCCAGATGAACG 60.519 63.158 0.00 0.00 0.00 3.95
309 310 7.444792 AGTCCATTGAAGATTGATAGATTGAGC 59.555 37.037 0.00 0.00 0.00 4.26
359 361 2.053244 CTAGATTGGGCCTGGTGATCT 58.947 52.381 4.53 8.39 0.00 2.75
513 582 5.560966 ATTACAACCAAAATGAGGCTACG 57.439 39.130 0.00 0.00 0.00 3.51
820 1323 3.558931 TCAATGGTTACATCGCAGGAT 57.441 42.857 0.00 0.00 35.94 3.24
852 1385 4.023792 GCAATTTTTCAAAAGAGGCCCTTG 60.024 41.667 0.00 0.00 34.79 3.61
874 1407 0.515127 TAGCGTGCACACAAATTCCG 59.485 50.000 18.64 0.00 0.00 4.30
1008 1748 1.005097 TGAGAGCAAGCAATGGACCAT 59.995 47.619 0.00 0.00 0.00 3.55
1106 1846 5.613360 GCGTCAAGGATGATATCAAACATCG 60.613 44.000 9.99 9.86 42.34 3.84
1305 2045 1.401530 CGCACATGCTCAAACAACTG 58.598 50.000 1.82 0.00 39.32 3.16
1542 2282 7.649533 TGATTCATTGAATGAGCTAACCAAT 57.350 32.000 16.41 0.00 40.94 3.16
1586 2326 4.756642 TGATGTGTCCAAGCAACTAAAGAG 59.243 41.667 0.00 0.00 0.00 2.85
1818 2670 9.635520 CGAGTATTACTTGAGAAAAAGAGGTAA 57.364 33.333 5.26 0.00 31.05 2.85
1922 2785 7.433719 GCGATAAAGAGGTATGCATCTACTATG 59.566 40.741 0.19 0.00 34.31 2.23
1926 2789 8.713708 AAAGAGGTATGCATCTACTATGTAGT 57.286 34.615 0.19 0.00 34.31 2.73
2002 2939 9.855361 GTGATAAATTATGTTTGAGACATCTCG 57.145 33.333 4.49 0.00 45.88 4.04
2024 2963 4.320348 CGTATAGAAGAGTTCGGATGGACC 60.320 50.000 0.00 0.00 34.02 4.46
2098 3060 9.178758 CAAGTTTTCCTACCTTCTTTGCTATAT 57.821 33.333 0.00 0.00 0.00 0.86
2105 3067 9.747898 TCCTACCTTCTTTGCTATATTTTCAAA 57.252 29.630 0.00 0.00 0.00 2.69
2127 3096 1.831389 CTGTTGACTGTTCGCCCACG 61.831 60.000 0.00 0.00 42.01 4.94
2140 3109 4.061357 TCGCCCACGATTCATATGTTTA 57.939 40.909 1.90 0.00 45.12 2.01
2217 3188 7.581011 ATCTGGATTGCGAAATTTTGTTAAC 57.419 32.000 7.27 0.00 0.00 2.01
2260 3252 1.134461 GGTGCATGCATGTCTCTCTCT 60.134 52.381 25.64 0.00 0.00 3.10
2276 3284 4.955335 TCTCTCTTGTACCCCTCCATTTA 58.045 43.478 0.00 0.00 0.00 1.40
2446 4503 6.097356 TGACAGGTACTTAATCGTCATTGAC 58.903 40.000 6.73 6.73 34.60 3.18
2484 4542 6.944234 AAAAACTTGGGAACTAGTCAAGAG 57.056 37.500 22.78 9.67 45.84 2.85
2497 4555 1.370900 CAAGAGCGCTTTGGTGTGC 60.371 57.895 13.26 0.00 43.09 4.57
2666 4724 5.306114 TCCTAATCATCTACCGTCAGAGA 57.694 43.478 0.00 0.00 0.00 3.10
2773 4835 5.105064 GGAGCTTTGGTCTAAGGTATACACA 60.105 44.000 5.01 0.00 36.09 3.72
3159 5246 6.256539 ACTGTATTCGATAGTGACAAGCAATG 59.743 38.462 0.00 0.00 37.40 2.82
3256 5343 3.221771 ACAAGCAAGGTCACTTAATGCA 58.778 40.909 0.00 0.00 34.49 3.96
3265 5352 6.498309 AAGGTCACTTAATGCAATGTGCAGA 61.498 40.000 9.06 0.00 45.94 4.26
3266 5353 7.750934 AAGGTCACTTAATGCAATGTGCAGAT 61.751 38.462 9.06 0.00 45.94 2.90
3412 5502 3.814842 TCAAATTAGCGAGCATGGGTATG 59.185 43.478 0.00 0.00 37.36 2.39
3472 5562 3.136443 TGATAGTATTGGACTTGGCTGGG 59.864 47.826 0.00 0.00 39.81 4.45
3478 5568 0.555769 TGGACTTGGCTGGGAAAAGT 59.444 50.000 0.00 0.00 36.87 2.66
3558 5648 3.316308 AGCGAAACAAAGATTGAAGTGCT 59.684 39.130 0.00 0.00 0.00 4.40
3559 5649 3.423206 GCGAAACAAAGATTGAAGTGCTG 59.577 43.478 0.00 0.00 0.00 4.41
3606 5696 2.247358 AGAAGAGCTATGCCTAGGAGC 58.753 52.381 14.75 13.16 36.42 4.70
3629 5719 6.770785 AGCAGTTGGTATTCACTCAAACTTTA 59.229 34.615 0.00 0.00 0.00 1.85
3741 5834 3.243907 GCGGAGTCTATAGCCAAACTGAT 60.244 47.826 0.00 0.00 0.00 2.90
3791 5885 3.759527 TTCTCGTGTACAGATTCTCCG 57.240 47.619 0.00 0.00 0.00 4.63
3798 5892 3.096852 TGTACAGATTCTCCGGTCATGT 58.903 45.455 0.00 2.13 0.00 3.21
3817 5911 2.874664 CGACAACCCCTGGGAACGA 61.875 63.158 16.20 0.00 38.96 3.85
4109 6206 1.149288 AGGGAGATATGCCGGTCCTTA 59.851 52.381 1.90 0.00 0.00 2.69
4391 6838 0.462581 GCGCTGATCTCCATGGACAA 60.463 55.000 11.44 1.92 0.00 3.18
4397 6844 4.746089 GCTGATCTCCATGGACAATTAGCT 60.746 45.833 26.61 7.05 0.00 3.32
4902 8277 8.276252 TGTCTTATTTATTTGTAGGTCTTGCC 57.724 34.615 0.00 0.00 37.58 4.52
5036 8428 4.911514 TCAAGTTTGGCTAAGTTGGAAC 57.088 40.909 22.83 0.00 44.07 3.62
5038 8430 4.578928 TCAAGTTTGGCTAAGTTGGAACTC 59.421 41.667 22.83 0.00 44.07 3.01
5121 8520 2.409055 CCGGCACCACCATGATGTG 61.409 63.158 0.00 0.00 39.03 3.21
5213 8612 5.247337 AGGTAGAGGAAGAGCTTAATATGCC 59.753 44.000 0.00 0.00 0.00 4.40
5236 8635 4.378874 CGAGCCTTGAATCTCTGGAAAAAC 60.379 45.833 0.00 0.00 0.00 2.43
5241 8640 6.088824 CCTTGAATCTCTGGAAAAACGAATG 58.911 40.000 0.00 0.00 0.00 2.67
5253 8652 5.452302 GGAAAAACGAATGCTTGTATCATCG 59.548 40.000 0.00 0.00 0.00 3.84
5290 8689 6.718454 ACTTCACGATCTTTTCTCAATCTG 57.282 37.500 0.00 0.00 0.00 2.90
5295 8694 4.932200 ACGATCTTTTCTCAATCTGACCAC 59.068 41.667 0.00 0.00 0.00 4.16
5298 8697 6.073058 CGATCTTTTCTCAATCTGACCACAAA 60.073 38.462 0.00 0.00 0.00 2.83
5302 8701 3.149196 TCTCAATCTGACCACAAAAGGC 58.851 45.455 0.00 0.00 0.00 4.35
5303 8702 3.152341 CTCAATCTGACCACAAAAGGCT 58.848 45.455 0.00 0.00 0.00 4.58
5314 8713 4.040339 ACCACAAAAGGCTTTTTATGAGGG 59.960 41.667 25.00 20.56 33.53 4.30
5362 8761 4.695455 TGGTAATTGCTTCCTTTCTTCTCG 59.305 41.667 0.00 0.00 0.00 4.04
5407 8867 6.473758 GGTTTTTGGATAGGACACTACTTCT 58.526 40.000 0.00 0.00 30.59 2.85
5408 8868 6.594547 GGTTTTTGGATAGGACACTACTTCTC 59.405 42.308 0.00 0.00 30.59 2.87
5424 8884 2.630889 TCTCTGGAAGTGGAGTGGAT 57.369 50.000 0.00 0.00 33.76 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.465985 GTGAAAACCATATTTTAAAGTTTCGGA 57.534 29.630 0.00 0.00 30.66 4.55
31 32 8.421701 CGTGAAAACCATATTTTAAAGTTTCGG 58.578 33.333 0.00 0.00 30.66 4.30
32 33 9.171701 TCGTGAAAACCATATTTTAAAGTTTCG 57.828 29.630 0.00 4.21 30.66 3.46
41 42 8.934507 TGAAAACTTCGTGAAAACCATATTTT 57.065 26.923 0.00 0.00 0.00 1.82
54 55 8.519492 AACAAATATTCCATGAAAACTTCGTG 57.481 30.769 0.00 2.24 44.41 4.35
55 56 9.191995 GAAACAAATATTCCATGAAAACTTCGT 57.808 29.630 0.00 0.00 0.00 3.85
56 57 8.647226 GGAAACAAATATTCCATGAAAACTTCG 58.353 33.333 0.00 0.00 44.70 3.79
57 58 8.647226 CGGAAACAAATATTCCATGAAAACTTC 58.353 33.333 0.00 0.00 45.44 3.01
58 59 8.147704 ACGGAAACAAATATTCCATGAAAACTT 58.852 29.630 0.00 0.00 45.44 2.66
59 60 7.666623 ACGGAAACAAATATTCCATGAAAACT 58.333 30.769 0.00 0.00 45.44 2.66
60 61 7.883229 ACGGAAACAAATATTCCATGAAAAC 57.117 32.000 0.00 0.00 45.44 2.43
72 73 9.729281 GGGGAGAATATTATACGGAAACAAATA 57.271 33.333 0.00 0.00 0.00 1.40
73 74 7.668469 GGGGGAGAATATTATACGGAAACAAAT 59.332 37.037 0.00 0.00 0.00 2.32
74 75 6.999871 GGGGGAGAATATTATACGGAAACAAA 59.000 38.462 0.00 0.00 0.00 2.83
75 76 6.101442 TGGGGGAGAATATTATACGGAAACAA 59.899 38.462 0.00 0.00 0.00 2.83
76 77 5.607592 TGGGGGAGAATATTATACGGAAACA 59.392 40.000 0.00 0.00 0.00 2.83
77 78 6.117975 TGGGGGAGAATATTATACGGAAAC 57.882 41.667 0.00 0.00 0.00 2.78
78 79 6.559539 TCTTGGGGGAGAATATTATACGGAAA 59.440 38.462 0.00 0.00 0.00 3.13
79 80 6.086095 TCTTGGGGGAGAATATTATACGGAA 58.914 40.000 0.00 0.00 0.00 4.30
80 81 5.657446 TCTTGGGGGAGAATATTATACGGA 58.343 41.667 0.00 0.00 0.00 4.69
81 82 5.104900 CCTCTTGGGGGAGAATATTATACGG 60.105 48.000 0.00 0.00 35.52 4.02
82 83 5.484290 ACCTCTTGGGGGAGAATATTATACG 59.516 44.000 0.00 0.00 40.03 3.06
83 84 6.954352 ACCTCTTGGGGGAGAATATTATAC 57.046 41.667 0.00 0.00 40.03 1.47
84 85 8.887393 GTTTACCTCTTGGGGGAGAATATTATA 58.113 37.037 0.00 0.00 40.03 0.98
85 86 7.576649 AGTTTACCTCTTGGGGGAGAATATTAT 59.423 37.037 0.00 0.00 40.03 1.28
86 87 6.912561 AGTTTACCTCTTGGGGGAGAATATTA 59.087 38.462 0.00 0.00 40.03 0.98
87 88 5.736616 AGTTTACCTCTTGGGGGAGAATATT 59.263 40.000 0.00 0.00 40.03 1.28
88 89 5.132816 CAGTTTACCTCTTGGGGGAGAATAT 59.867 44.000 0.00 0.00 40.03 1.28
89 90 4.473559 CAGTTTACCTCTTGGGGGAGAATA 59.526 45.833 0.00 0.00 40.03 1.75
90 91 3.267031 CAGTTTACCTCTTGGGGGAGAAT 59.733 47.826 0.00 0.00 40.03 2.40
91 92 2.642807 CAGTTTACCTCTTGGGGGAGAA 59.357 50.000 0.00 0.00 40.03 2.87
92 93 2.266279 CAGTTTACCTCTTGGGGGAGA 58.734 52.381 0.00 0.00 40.03 3.71
93 94 1.985895 ACAGTTTACCTCTTGGGGGAG 59.014 52.381 0.00 0.00 40.03 4.30
94 95 2.127651 ACAGTTTACCTCTTGGGGGA 57.872 50.000 0.00 0.00 40.03 4.81
95 96 4.444449 GCTATACAGTTTACCTCTTGGGGG 60.444 50.000 0.00 0.00 40.03 5.40
96 97 4.163458 TGCTATACAGTTTACCTCTTGGGG 59.837 45.833 0.00 0.00 40.03 4.96
97 98 5.353394 TGCTATACAGTTTACCTCTTGGG 57.647 43.478 0.00 0.00 41.89 4.12
187 188 4.512944 TGAAAGCAGAGCGATGGAATAATC 59.487 41.667 0.00 0.00 0.00 1.75
188 189 4.274459 GTGAAAGCAGAGCGATGGAATAAT 59.726 41.667 0.00 0.00 0.00 1.28
189 190 3.623060 GTGAAAGCAGAGCGATGGAATAA 59.377 43.478 0.00 0.00 0.00 1.40
190 191 3.198068 GTGAAAGCAGAGCGATGGAATA 58.802 45.455 0.00 0.00 0.00 1.75
191 192 2.012673 GTGAAAGCAGAGCGATGGAAT 58.987 47.619 0.00 0.00 0.00 3.01
192 193 1.442769 GTGAAAGCAGAGCGATGGAA 58.557 50.000 0.00 0.00 0.00 3.53
193 194 0.391661 GGTGAAAGCAGAGCGATGGA 60.392 55.000 0.00 0.00 0.00 3.41
194 195 1.699656 CGGTGAAAGCAGAGCGATGG 61.700 60.000 0.00 0.00 35.10 3.51
195 196 1.016130 ACGGTGAAAGCAGAGCGATG 61.016 55.000 0.00 0.00 36.89 3.84
196 197 1.016130 CACGGTGAAAGCAGAGCGAT 61.016 55.000 0.74 0.00 36.89 4.58
197 198 1.664649 CACGGTGAAAGCAGAGCGA 60.665 57.895 0.74 0.00 36.89 4.93
207 208 1.746322 TTCTGCGGGTACACGGTGAA 61.746 55.000 20.88 6.56 0.00 3.18
214 215 0.470766 ACAAGGTTTCTGCGGGTACA 59.529 50.000 0.00 0.00 0.00 2.90
237 238 2.216898 GCAATCCTAGTGATGGTGCTC 58.783 52.381 9.10 0.00 35.31 4.26
244 245 1.069765 CGCGGGCAATCCTAGTGAT 59.930 57.895 0.00 0.00 34.22 3.06
257 258 4.227134 CATCTGGAGGGACGCGGG 62.227 72.222 12.47 0.00 0.00 6.13
278 279 1.098050 AATCTTCAATGGACTGCGCC 58.902 50.000 4.18 0.00 0.00 6.53
341 342 0.549950 CAGATCACCAGGCCCAATCT 59.450 55.000 0.00 0.00 0.00 2.40
342 343 0.257039 ACAGATCACCAGGCCCAATC 59.743 55.000 0.00 0.00 0.00 2.67
343 344 0.257039 GACAGATCACCAGGCCCAAT 59.743 55.000 0.00 0.00 0.00 3.16
359 361 3.106827 TGGACATGGAAGAGCTATGACA 58.893 45.455 0.00 0.00 37.65 3.58
461 463 0.741221 GGAGACTTGCACGGATGGTC 60.741 60.000 0.00 0.00 0.00 4.02
465 515 1.202758 TGTTTGGAGACTTGCACGGAT 60.203 47.619 0.00 0.00 0.00 4.18
513 582 1.228245 TCTCCTTGTTGCTGTGGCC 60.228 57.895 0.00 0.00 37.74 5.36
759 852 1.804372 CGACCTATCAAGTCAGCAGCC 60.804 57.143 0.00 0.00 33.70 4.85
768 861 6.576662 ATCACTACCATACGACCTATCAAG 57.423 41.667 0.00 0.00 0.00 3.02
820 1323 7.041235 CCTCTTTTGAAAAATTGCCTGCATTTA 60.041 33.333 0.00 0.00 0.00 1.40
852 1385 3.171277 GGAATTTGTGTGCACGCTATTC 58.829 45.455 30.03 30.03 32.57 1.75
874 1407 1.745653 GGAAGGTTCATGCTAGTTGCC 59.254 52.381 0.00 0.00 42.00 4.52
966 1554 0.612174 AGCTGGAACGAGTGGCTAGA 60.612 55.000 0.00 0.00 0.00 2.43
1106 1846 1.312815 GCTCTCCAGCTCTCTCTCTC 58.687 60.000 0.00 0.00 43.09 3.20
1305 2045 0.179034 AGCCGCCCATCTTCTTCATC 60.179 55.000 0.00 0.00 0.00 2.92
1441 2181 1.135603 CGTGGTTGCAACATCTGGATG 60.136 52.381 29.55 8.81 44.15 3.51
1542 2282 0.752658 CATCCCCGTCACTCAGCATA 59.247 55.000 0.00 0.00 0.00 3.14
1586 2326 5.755861 CCTCCGAATCCAAAAATAGAGAGTC 59.244 44.000 0.00 0.00 0.00 3.36
1697 2437 1.732809 GAAGTTTCTTCACGCTAGGGC 59.267 52.381 6.73 0.00 0.00 5.19
1839 2692 8.702819 ACTCCCCATTTACTACTTGAACTATAC 58.297 37.037 0.00 0.00 0.00 1.47
1922 2785 6.823497 TGCCCCATTTACTACTTGATACTAC 58.177 40.000 0.00 0.00 0.00 2.73
1924 2787 5.968676 TGCCCCATTTACTACTTGATACT 57.031 39.130 0.00 0.00 0.00 2.12
1925 2788 6.826741 TCTTTGCCCCATTTACTACTTGATAC 59.173 38.462 0.00 0.00 0.00 2.24
1926 2789 6.964464 TCTTTGCCCCATTTACTACTTGATA 58.036 36.000 0.00 0.00 0.00 2.15
1940 2858 0.392461 GTGACGCTATCTTTGCCCCA 60.392 55.000 0.00 0.00 0.00 4.96
2002 2939 4.583489 TGGTCCATCCGAACTCTTCTATAC 59.417 45.833 0.00 0.00 39.52 1.47
2098 3060 5.117897 GCGAACAGTCAACAGTTTTTGAAAA 59.882 36.000 0.00 0.00 37.24 2.29
2102 3064 2.851824 GGCGAACAGTCAACAGTTTTTG 59.148 45.455 0.00 0.00 0.00 2.44
2105 3067 1.021968 GGGCGAACAGTCAACAGTTT 58.978 50.000 0.00 0.00 0.00 2.66
2106 3068 0.107410 TGGGCGAACAGTCAACAGTT 60.107 50.000 0.00 0.00 0.00 3.16
2217 3188 6.039941 ACCATCTACGAGAACTCTATTTCTGG 59.960 42.308 0.00 0.00 35.90 3.86
2484 4542 1.994916 ATTATTGCACACCAAAGCGC 58.005 45.000 0.00 0.00 36.92 5.92
2497 4555 7.434307 GTGATGATTCTGCTTCCACAATTATTG 59.566 37.037 3.07 3.07 0.00 1.90
2644 4702 5.306114 TCTCTGACGGTAGATGATTAGGA 57.694 43.478 0.00 0.00 0.00 2.94
2773 4835 2.549082 TCATGCCCAAAACCCATTGAT 58.451 42.857 0.00 0.00 31.84 2.57
3007 5070 3.068024 TCATGCTTTTGTTCACCAACTCC 59.932 43.478 0.00 0.00 33.17 3.85
3142 5229 5.348724 AGTTGTACATTGCTTGTCACTATCG 59.651 40.000 0.00 0.00 39.87 2.92
3159 5246 5.424121 AGAGTTGCAATGTGAAGTTGTAC 57.576 39.130 0.59 0.00 0.00 2.90
3256 5343 4.277672 GGCAACATCTCATATCTGCACATT 59.722 41.667 0.00 0.00 0.00 2.71
3412 5502 1.549203 TTTCCTTTGGGAGCTCATGC 58.451 50.000 17.19 0.00 43.29 4.06
3558 5648 5.351948 TGTCAAATCTCCGATCCAATACA 57.648 39.130 0.00 0.00 0.00 2.29
3559 5649 5.760253 ACATGTCAAATCTCCGATCCAATAC 59.240 40.000 0.00 0.00 0.00 1.89
3606 5696 8.783093 TCATAAAGTTTGAGTGAATACCAACTG 58.217 33.333 0.00 0.00 0.00 3.16
3629 5719 4.263462 TGTCAGCTTACCCAATTCTGTCAT 60.263 41.667 0.00 0.00 0.00 3.06
3741 5834 7.186570 TCAATGTCTATGACTTGGATCTTGA 57.813 36.000 0.00 0.00 33.15 3.02
3798 5892 2.874664 CGTTCCCAGGGGTTGTCGA 61.875 63.158 5.33 0.00 36.47 4.20
3817 5911 2.040412 GAGTTGTGGAGGGAGGATGTTT 59.960 50.000 0.00 0.00 0.00 2.83
4537 7071 4.274978 AGGAGAGAACTAGGTAAGCTGAC 58.725 47.826 0.00 0.00 0.00 3.51
4897 8272 8.453320 AGAAAATGAAGAAAAACAAAAGGCAAG 58.547 29.630 0.00 0.00 0.00 4.01
5121 8520 3.567478 AATACACCTTCAGCTCCCATC 57.433 47.619 0.00 0.00 0.00 3.51
5213 8612 2.680312 TTCCAGAGATTCAAGGCTCG 57.320 50.000 0.00 0.00 36.29 5.03
5236 8635 3.183172 CCAGACGATGATACAAGCATTCG 59.817 47.826 0.00 0.00 0.00 3.34
5241 8640 5.545658 TTTTTCCAGACGATGATACAAGC 57.454 39.130 0.00 0.00 0.00 4.01
5253 8652 7.807680 AGATCGTGAAGTTAATTTTTCCAGAC 58.192 34.615 0.00 0.00 0.00 3.51
5290 8689 5.230182 CCTCATAAAAAGCCTTTTGTGGTC 58.770 41.667 14.86 0.00 41.48 4.02
5295 8694 7.416817 CAAAAACCCTCATAAAAAGCCTTTTG 58.583 34.615 2.64 0.00 35.50 2.44
5298 8697 5.063204 GCAAAAACCCTCATAAAAAGCCTT 58.937 37.500 0.00 0.00 0.00 4.35
5302 8701 5.759763 AGCTTGCAAAAACCCTCATAAAAAG 59.240 36.000 0.00 0.00 0.00 2.27
5303 8702 5.679601 AGCTTGCAAAAACCCTCATAAAAA 58.320 33.333 0.00 0.00 0.00 1.94
5314 8713 6.587608 AGAGCAAATATGTAGCTTGCAAAAAC 59.412 34.615 10.77 0.00 46.26 2.43
5362 8761 0.108945 GCTGCATGCTTTGGTCTTCC 60.109 55.000 20.33 0.00 38.95 3.46
5407 8867 9.256228 GTATATATAATCCACTCCACTTCCAGA 57.744 37.037 0.00 0.00 0.00 3.86
5408 8868 9.035890 TGTATATATAATCCACTCCACTTCCAG 57.964 37.037 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.