Multiple sequence alignment - TraesCS6B01G317800

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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 TraesCS6B01G317800 chr6B 100.000 5341 0 0 1 5341 565748243 565753583 0.000000e+00 9864.0
1 TraesCS6B01G317800 chr6B 97.778 180 4 0 1 180 48564920 48565099 1.440000e-80 311.0
2 TraesCS6B01G317800 chr6B 97.253 182 5 0 1 182 143176203 143176384 5.200000e-80 309.0
3 TraesCS6B01G317800 chr6B 97.253 182 5 0 1 182 347118341 347118522 5.200000e-80 309.0
4 TraesCS6B01G317800 chr6B 94.805 77 3 1 1586 1661 278674697 278674621 9.400000e-23 119.0
5 TraesCS6B01G317800 chr3A 96.473 5189 119 23 178 5341 730968971 730974120 0.000000e+00 8510.0
6 TraesCS6B01G317800 chr3A 96.875 192 5 1 1 192 399580668 399580858 2.400000e-83 320.0
7 TraesCS6B01G317800 chr3A 97.802 182 4 0 1 182 388093999 388093818 1.120000e-81 315.0
8 TraesCS6B01G317800 chr4A 97.385 4169 85 4 1143 5288 373805877 373810044 0.000000e+00 7073.0
9 TraesCS6B01G317800 chr4A 89.885 1572 112 9 3796 5339 276800438 276798886 0.000000e+00 1978.0
10 TraesCS6B01G317800 chr4A 95.282 975 32 4 178 1150 373801249 373802211 0.000000e+00 1533.0
11 TraesCS6B01G317800 chr4A 94.094 491 24 3 3293 3783 276800990 276800505 0.000000e+00 741.0
12 TraesCS6B01G317800 chr4A 97.268 183 5 0 1 183 515666265 515666447 1.440000e-80 311.0
13 TraesCS6B01G317800 chr4A 97.268 183 4 1 1 183 16241388 16241207 5.200000e-80 309.0
14 TraesCS6B01G317800 chr7D 94.248 1530 75 4 1679 3206 213066782 213068300 0.000000e+00 2326.0
15 TraesCS6B01G317800 chr7D 90.289 1246 85 9 273 1514 213065544 213066757 0.000000e+00 1598.0
16 TraesCS6B01G317800 chr7D 96.875 64 2 0 3232 3295 213068299 213068362 2.030000e-19 108.0
17 TraesCS6B01G317800 chr6A 93.534 1531 92 6 1508 3037 161780035 161781559 0.000000e+00 2272.0
18 TraesCS6B01G317800 chr6A 93.151 1533 93 7 1511 3037 233958509 233956983 0.000000e+00 2239.0
19 TraesCS6B01G317800 chr6A 92.801 1528 103 6 1511 3037 299985201 299983680 0.000000e+00 2206.0
20 TraesCS6B01G317800 chr6A 93.197 588 37 2 929 1514 233959191 233958605 0.000000e+00 861.0
21 TraesCS6B01G317800 chr6A 93.015 587 38 3 929 1514 161779358 161779942 0.000000e+00 854.0
22 TraesCS6B01G317800 chr6A 92.662 586 40 3 929 1514 299985879 299985297 0.000000e+00 841.0
23 TraesCS6B01G317800 chr6A 87.215 657 50 15 271 924 161778644 161779269 0.000000e+00 717.0
24 TraesCS6B01G317800 chr6A 86.997 646 49 16 291 933 233959884 233959271 0.000000e+00 695.0
25 TraesCS6B01G317800 chr6A 84.932 657 63 13 272 925 299986589 299985966 2.710000e-177 632.0
26 TraesCS6B01G317800 chr6A 94.737 266 12 1 3030 3295 299982917 299982654 3.850000e-111 412.0
27 TraesCS6B01G317800 chr6A 93.985 266 14 1 3030 3295 233956218 233955955 8.330000e-108 401.0
28 TraesCS6B01G317800 chr6A 93.609 266 15 1 3030 3295 161782326 161782589 3.880000e-106 396.0
29 TraesCS6B01G317800 chr6A 97.778 180 4 0 1 180 572591223 572591402 1.440000e-80 311.0
30 TraesCS6B01G317800 chr6A 97.222 180 5 0 1 180 38726557 38726378 6.720000e-79 305.0
31 TraesCS6B01G317800 chr6A 97.222 180 5 0 1 180 38757912 38758091 6.720000e-79 305.0
32 TraesCS6B01G317800 chr6A 96.721 183 6 0 1 183 371732574 371732392 6.720000e-79 305.0
33 TraesCS6B01G317800 chr6A 96.721 183 6 0 1 183 602239518 602239336 6.720000e-79 305.0
34 TraesCS6B01G317800 chr6A 96.721 183 4 2 1 183 558982897 558982717 2.420000e-78 303.0
35 TraesCS6B01G317800 chr6A 94.805 77 3 1 1586 1661 209391425 209391349 9.400000e-23 119.0
36 TraesCS6B01G317800 chr3D 92.595 1445 72 6 3919 5341 564547947 564546516 0.000000e+00 2043.0
37 TraesCS6B01G317800 chr3D 91.855 442 17 6 3293 3733 564548581 564548158 2.750000e-167 599.0
38 TraesCS6B01G317800 chr7A 89.530 1595 93 26 3796 5336 713192474 713194048 0.000000e+00 1953.0
39 TraesCS6B01G317800 chr7A 90.515 1107 61 8 4262 5339 699549416 699548325 0.000000e+00 1423.0
40 TraesCS6B01G317800 chr7A 94.297 491 24 2 3293 3783 699550095 699549609 0.000000e+00 749.0
41 TraesCS6B01G317800 chr7A 94.262 488 21 4 3293 3780 713191935 713192415 0.000000e+00 739.0
42 TraesCS6B01G317800 chr7A 98.333 180 3 0 1 180 14291752 14291573 3.100000e-82 316.0
43 TraesCS6B01G317800 chr7A 98.333 180 3 0 1 180 78662765 78662944 3.100000e-82 316.0
44 TraesCS6B01G317800 chr7A 97.297 185 5 0 1 185 603096192 603096376 1.120000e-81 315.0
45 TraesCS6B01G317800 chr2A 91.315 1232 64 16 4133 5336 23543403 23544619 0.000000e+00 1642.0
46 TraesCS6B01G317800 chr2A 94.877 488 21 2 3293 3780 23542530 23543013 0.000000e+00 760.0
47 TraesCS6B01G317800 chrUn 91.676 889 44 8 4470 5341 1288002 1288877 0.000000e+00 1205.0
48 TraesCS6B01G317800 chrUn 91.761 886 43 8 4473 5341 263139132 263138260 0.000000e+00 1205.0
49 TraesCS6B01G317800 chrUn 91.676 889 44 8 4470 5341 311658578 311659453 0.000000e+00 1205.0
50 TraesCS6B01G317800 chrUn 91.676 889 44 8 4470 5341 327805339 327806214 0.000000e+00 1205.0
51 TraesCS6B01G317800 chrUn 91.676 889 44 8 4470 5341 327835198 327836073 0.000000e+00 1205.0
52 TraesCS6B01G317800 chrUn 93.205 677 45 1 3796 4471 1286068 1286744 0.000000e+00 994.0
53 TraesCS6B01G317800 chrUn 93.489 599 38 1 3796 4393 313522250 313522848 0.000000e+00 889.0
54 TraesCS6B01G317800 chrUn 93.489 599 38 1 3796 4393 324875073 324875671 0.000000e+00 889.0
55 TraesCS6B01G317800 chrUn 93.648 551 25 4 4791 5341 1290725 1291265 0.000000e+00 815.0
56 TraesCS6B01G317800 chrUn 93.888 409 24 1 3796 4203 296264210 296264618 2.730000e-172 616.0
57 TraesCS6B01G317800 chrUn 90.745 443 21 6 3293 3733 313521639 313522063 1.670000e-159 573.0
58 TraesCS6B01G317800 chrUn 90.745 443 21 6 3293 3733 324874462 324874886 1.670000e-159 573.0
59 TraesCS6B01G317800 chrUn 96.154 182 7 0 1 182 13888453 13888272 1.120000e-76 298.0
60 TraesCS6B01G317800 chrUn 96.154 182 6 1 1 182 50069949 50070129 4.040000e-76 296.0
61 TraesCS6B01G317800 chrUn 96.111 180 7 0 1 180 8618818 8618997 1.450000e-75 294.0
62 TraesCS6B01G317800 chrUn 96.111 180 7 0 1 180 267218519 267218698 1.450000e-75 294.0
63 TraesCS6B01G317800 chrUn 95.055 182 9 0 1 182 9632753 9632934 2.430000e-73 287.0
64 TraesCS6B01G317800 chrUn 94.149 188 11 0 1 188 41170476 41170289 2.430000e-73 287.0
65 TraesCS6B01G317800 chrUn 95.000 180 9 0 1 180 42712471 42712650 3.150000e-72 283.0
66 TraesCS6B01G317800 chrUn 95.000 180 9 0 1 180 42713859 42714038 3.150000e-72 283.0
67 TraesCS6B01G317800 chrUn 95.000 180 9 0 1 180 80797746 80797925 3.150000e-72 283.0
68 TraesCS6B01G317800 chrUn 95.000 180 9 0 1 180 329559681 329559860 3.150000e-72 283.0
69 TraesCS6B01G317800 chrUn 90.789 76 6 1 1586 1660 341187359 341187284 3.400000e-17 100.0
70 TraesCS6B01G317800 chrUn 90.196 51 3 2 1580 1628 1925158 1925208 1.240000e-06 65.8
71 TraesCS6B01G317800 chrUn 94.595 37 1 1 1581 1617 47689584 47689619 7.470000e-04 56.5
72 TraesCS6B01G317800 chr5D 91.429 245 17 2 4353 4596 313839109 313838868 3.080000e-87 333.0
73 TraesCS6B01G317800 chr5B 91.393 244 16 3 4354 4596 361539078 361538839 3.990000e-86 329.0
74 TraesCS6B01G317800 chr5B 98.352 182 3 0 1 182 6929404 6929223 2.400000e-83 320.0
75 TraesCS6B01G317800 chr5B 97.802 182 4 0 1 182 610342179 610342360 1.120000e-81 315.0
76 TraesCS6B01G317800 chr3B 98.361 183 3 0 1 183 474033244 474033062 6.670000e-84 322.0
77 TraesCS6B01G317800 chr5A 98.333 180 3 0 1 180 591365362 591365183 3.100000e-82 316.0
78 TraesCS6B01G317800 chr5A 97.802 182 3 1 1 182 353058499 353058319 4.020000e-81 313.0
79 TraesCS6B01G317800 chr5A 97.778 180 4 0 1 180 596081738 596081559 1.440000e-80 311.0
80 TraesCS6B01G317800 chr1A 97.312 186 5 0 1 186 483028592 483028407 3.100000e-82 316.0
81 TraesCS6B01G317800 chr1A 97.802 182 4 0 1 182 304614092 304614273 1.120000e-81 315.0
82 TraesCS6B01G317800 chr1A 97.253 182 5 0 1 182 208913855 208913674 5.200000e-80 309.0
83 TraesCS6B01G317800 chr1A 97.253 182 5 0 1 182 304793556 304793737 5.200000e-80 309.0
84 TraesCS6B01G317800 chr1A 97.222 180 5 0 1 180 497760044 497759865 6.720000e-79 305.0
85 TraesCS6B01G317800 chr1A 96.667 180 6 0 1 180 505687756 505687577 3.130000e-77 300.0
86 TraesCS6B01G317800 chr1A 96.667 180 6 0 1 180 524388301 524388480 3.130000e-77 300.0
87 TraesCS6B01G317800 chr1A 96.667 180 6 0 1 180 531327195 531327374 3.130000e-77 300.0
88 TraesCS6B01G317800 chr7B 96.774 186 6 0 1 186 619611323 619611138 1.440000e-80 311.0
89 TraesCS6B01G317800 chr4B 97.253 182 5 0 1 182 12513470 12513289 5.200000e-80 309.0
90 TraesCS6B01G317800 chr4B 94.792 192 10 0 1 192 203203458 203203649 3.130000e-77 300.0
91 TraesCS6B01G317800 chr1D 96.703 182 6 0 1 182 27904619 27904438 2.420000e-78 303.0
92 TraesCS6B01G317800 chr1D 92.308 78 5 1 1585 1661 141706061 141705984 5.660000e-20 110.0
93 TraesCS6B01G317800 chr6D 96.111 180 6 1 3 182 452435864 452436042 5.230000e-75 292.0
94 TraesCS6B01G317800 chr6D 95.556 180 8 0 1 180 451075015 451075194 6.770000e-74 289.0
95 TraesCS6B01G317800 chr6D 93.506 77 4 1 1586 1661 155602045 155601969 4.370000e-21 113.0
96 TraesCS6B01G317800 chr6D 89.610 77 7 1 1586 1661 13067041 13067117 4.400000e-16 97.1
97 TraesCS6B01G317800 chr4D 95.604 182 8 0 1 182 440037095 440036914 5.230000e-75 292.0
98 TraesCS6B01G317800 chr4D 96.591 176 6 0 5 180 458109299 458109474 5.230000e-75 292.0
99 TraesCS6B01G317800 chr4D 93.421 76 4 1 1586 1660 482160745 482160670 1.570000e-20 111.0
100 TraesCS6B01G317800 chr4D 90.278 72 2 3 1594 1661 455601569 455601499 7.370000e-14 89.8
101 TraesCS6B01G317800 chr4D 93.333 60 3 1 1603 1661 348306098 348306157 2.650000e-13 87.9


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 TraesCS6B01G317800 chr6B 565748243 565753583 5340 False 9864.000000 9864 100.00000 1 5341 1 chr6B.!!$F4 5340
1 TraesCS6B01G317800 chr3A 730968971 730974120 5149 False 8510.000000 8510 96.47300 178 5341 1 chr3A.!!$F2 5163
2 TraesCS6B01G317800 chr4A 373801249 373810044 8795 False 4303.000000 7073 96.33350 178 5288 2 chr4A.!!$F2 5110
3 TraesCS6B01G317800 chr4A 276798886 276800990 2104 True 1359.500000 1978 91.98950 3293 5339 2 chr4A.!!$R2 2046
4 TraesCS6B01G317800 chr7D 213065544 213068362 2818 False 1344.000000 2326 93.80400 273 3295 3 chr7D.!!$F1 3022
5 TraesCS6B01G317800 chr6A 161778644 161782589 3945 False 1059.750000 2272 91.84325 271 3295 4 chr6A.!!$F3 3024
6 TraesCS6B01G317800 chr6A 233955955 233959884 3929 True 1049.000000 2239 91.83250 291 3295 4 chr6A.!!$R6 3004
7 TraesCS6B01G317800 chr6A 299982654 299986589 3935 True 1022.750000 2206 91.28300 272 3295 4 chr6A.!!$R7 3023
8 TraesCS6B01G317800 chr3D 564546516 564548581 2065 True 1321.000000 2043 92.22500 3293 5341 2 chr3D.!!$R1 2048
9 TraesCS6B01G317800 chr7A 713191935 713194048 2113 False 1346.000000 1953 91.89600 3293 5336 2 chr7A.!!$F3 2043
10 TraesCS6B01G317800 chr7A 699548325 699550095 1770 True 1086.000000 1423 92.40600 3293 5339 2 chr7A.!!$R2 2046
11 TraesCS6B01G317800 chr2A 23542530 23544619 2089 False 1201.000000 1642 93.09600 3293 5336 2 chr2A.!!$F1 2043
12 TraesCS6B01G317800 chrUn 263138260 263139132 872 True 1205.000000 1205 91.76100 4473 5341 1 chrUn.!!$R3 868
13 TraesCS6B01G317800 chrUn 311658578 311659453 875 False 1205.000000 1205 91.67600 4470 5341 1 chrUn.!!$F9 871
14 TraesCS6B01G317800 chrUn 327805339 327806214 875 False 1205.000000 1205 91.67600 4470 5341 1 chrUn.!!$F10 871
15 TraesCS6B01G317800 chrUn 327835198 327836073 875 False 1205.000000 1205 91.67600 4470 5341 1 chrUn.!!$F11 871
16 TraesCS6B01G317800 chrUn 1286068 1291265 5197 False 1004.666667 1205 92.84300 3796 5341 3 chrUn.!!$F13 1545
17 TraesCS6B01G317800 chrUn 313521639 313522848 1209 False 731.000000 889 92.11700 3293 4393 2 chrUn.!!$F15 1100
18 TraesCS6B01G317800 chrUn 324874462 324875671 1209 False 731.000000 889 92.11700 3293 4393 2 chrUn.!!$F16 1100
19 TraesCS6B01G317800 chrUn 42712471 42714038 1567 False 283.000000 283 95.00000 1 180 2 chrUn.!!$F14 179

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
362 365 0.248843 GCGCCCCCAAATCAAAATCA 59.751 50.000 0.00 0.0 0.00 2.57 F
715 1273 0.252881 ATCTGGCTCTCCTCCACCAA 60.253 55.000 0.00 0.0 0.00 3.67 F
1497 5938 0.754957 CCACTTCCACAAGCCACCAA 60.755 55.000 0.00 0.0 32.09 3.67 F
1985 6527 2.029828 CCTAGCGCAAGTATAGGGTCTG 60.030 54.545 11.47 0.0 42.01 3.51 F
3280 8610 1.904287 TTTTGTTGTAGCTCGGCCAT 58.096 45.000 2.24 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 6495 2.359981 TGCGCTAGGTACCAGTCTAT 57.640 50.000 15.94 0.00 0.00 1.98 R
2439 6981 2.639751 CGCACACTTTAGTTGCTGAAC 58.360 47.619 12.07 0.00 33.25 3.18 R
3057 8387 0.108424 GCTCTCTCGTGCATTCAGGT 60.108 55.000 0.00 0.00 0.00 4.00 R
3638 8970 2.538512 AATCATGCAGCTGCTCGATA 57.461 45.000 36.61 18.93 42.66 2.92 R
4958 11819 2.106566 TGCCTTCTTTGTTTGCCTTGA 58.893 42.857 0.00 0.00 0.00 3.02 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
26 27 8.965819 TGTCATGCAACAATGTATTTATTAGGT 58.034 29.630 0.00 0.00 28.42 3.08
72 73 4.933400 GTGTGTGATGTTCCGGTAACTTAT 59.067 41.667 0.00 0.00 38.99 1.73
112 113 7.712639 GCACCTCTCTCTTCATTAAATATGTGA 59.287 37.037 0.00 0.00 0.00 3.58
113 114 9.775854 CACCTCTCTCTTCATTAAATATGTGAT 57.224 33.333 0.00 0.00 0.00 3.06
162 163 6.100668 GTGTGATGTTACTCCTAAGTTCCTC 58.899 44.000 0.00 0.00 36.92 3.71
165 166 4.415224 TGTTACTCCTAAGTTCCTCCCT 57.585 45.455 0.00 0.00 36.92 4.20
222 223 2.477825 CCGACTCATTATCTGCCTGTG 58.522 52.381 0.00 0.00 0.00 3.66
262 263 4.441913 CCGAAAATAATTGGCTCATTGGCT 60.442 41.667 0.00 0.00 42.34 4.75
284 285 1.676014 GGGACACCGAGACATTTCAGG 60.676 57.143 0.00 0.00 0.00 3.86
357 360 3.059386 GTCGCGCCCCCAAATCAA 61.059 61.111 0.00 0.00 0.00 2.57
358 361 2.282532 TCGCGCCCCCAAATCAAA 60.283 55.556 0.00 0.00 0.00 2.69
359 362 1.903890 TCGCGCCCCCAAATCAAAA 60.904 52.632 0.00 0.00 0.00 2.44
360 363 1.217779 CGCGCCCCCAAATCAAAAT 59.782 52.632 0.00 0.00 0.00 1.82
361 364 0.805711 CGCGCCCCCAAATCAAAATC 60.806 55.000 0.00 0.00 0.00 2.17
362 365 0.248843 GCGCCCCCAAATCAAAATCA 59.751 50.000 0.00 0.00 0.00 2.57
383 386 1.604378 CAGCCTTCCACCCTCGATT 59.396 57.895 0.00 0.00 0.00 3.34
444 447 1.153429 GCGACAGCCGATAACCCTT 60.153 57.895 0.00 0.00 41.76 3.95
499 543 4.065281 CGACCACCCTCCACCGTC 62.065 72.222 0.00 0.00 0.00 4.79
532 576 3.009115 CTCCCGGCTTCCTTCCCA 61.009 66.667 0.00 0.00 0.00 4.37
712 1270 1.743321 CGGATCTGGCTCTCCTCCAC 61.743 65.000 0.00 0.00 0.00 4.02
713 1271 1.406860 GGATCTGGCTCTCCTCCACC 61.407 65.000 0.00 0.00 0.00 4.61
715 1273 0.252881 ATCTGGCTCTCCTCCACCAA 60.253 55.000 0.00 0.00 0.00 3.67
862 1541 4.039004 GCTCTGCTTCTGAATGGAGATCTA 59.961 45.833 14.27 0.00 30.65 1.98
919 1598 2.935481 CCCAACTGGCCCCAGAGA 60.935 66.667 20.59 0.00 46.30 3.10
1497 5938 0.754957 CCACTTCCACAAGCCACCAA 60.755 55.000 0.00 0.00 32.09 3.67
1659 6199 7.390996 TGCCAAAACGTCTTATATTTAGGAACA 59.609 33.333 0.00 0.00 0.00 3.18
1985 6527 2.029828 CCTAGCGCAAGTATAGGGTCTG 60.030 54.545 11.47 0.00 42.01 3.51
2003 6545 4.321824 GGTCTGGTAGACTGGTACAAGAAC 60.322 50.000 3.64 0.00 44.46 3.01
2288 6830 8.990163 ATAACTTAGGTCTTGAAAGGTTTGAA 57.010 30.769 0.00 0.00 0.00 2.69
2466 7008 2.256117 ACTAAAGTGTGCGCCTTTCT 57.744 45.000 12.50 0.10 34.20 2.52
2628 7170 7.280205 GCTAGCTATACTTAAAGCAAGGAACAA 59.720 37.037 7.70 0.00 41.32 2.83
3057 8387 6.721318 AGATACTTTTATTCTTGTCAGCCCA 58.279 36.000 0.00 0.00 0.00 5.36
3280 8610 1.904287 TTTTGTTGTAGCTCGGCCAT 58.096 45.000 2.24 0.00 0.00 4.40
3343 8673 6.879400 ACAAGATATCTCTGGGTCAACTTAC 58.121 40.000 5.51 0.00 0.00 2.34
3693 9094 1.265095 CCTAGCTGTGTTTGTGCACTG 59.735 52.381 19.41 0.00 39.89 3.66
4159 9740 7.333174 CCCCATAACCATTTTGATTTGTACAAC 59.667 37.037 8.07 0.00 0.00 3.32
4324 9905 6.959361 TGTCACTGATTGCTTCTTACTTTTC 58.041 36.000 0.00 0.00 0.00 2.29
4563 11403 1.211457 CCAGAGGGAGAAGGAACCATG 59.789 57.143 0.00 0.00 35.59 3.66
4651 11512 0.387565 GGTGACCGTGGCAAACATTT 59.612 50.000 0.00 0.00 0.00 2.32
4958 11819 1.909700 CTACAGCCAACACCCAACAT 58.090 50.000 0.00 0.00 0.00 2.71
5104 14363 5.541484 AGAGCTCCATTTTGAGTTTCCATTT 59.459 36.000 10.93 0.00 34.74 2.32
5190 14449 2.555325 TGCTGAAGGTTTGCAAGATCTG 59.445 45.455 0.00 2.83 33.48 2.90
5224 14483 3.809832 GTGGAGTGATAATGTAATGCGCT 59.190 43.478 9.73 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.375506 ACACTCCAAGAAACAATGAGTCTATAA 58.624 33.333 0.00 0.00 34.21 0.98
72 73 3.507411 AGAGGTGCTTGTGGTAACTAGA 58.493 45.455 0.00 0.00 31.59 2.43
112 113 8.677300 CACTCCAATACAACTTTGCTTATGTAT 58.323 33.333 0.00 0.00 39.88 2.29
113 114 7.663905 ACACTCCAATACAACTTTGCTTATGTA 59.336 33.333 0.00 0.00 33.24 2.29
125 126 5.689383 AACATCACACACTCCAATACAAC 57.311 39.130 0.00 0.00 0.00 3.32
162 163 3.392616 AGATAAGGCTGGTCACAATAGGG 59.607 47.826 0.00 0.00 0.00 3.53
165 166 3.433598 GGCAGATAAGGCTGGTCACAATA 60.434 47.826 0.00 0.00 36.41 1.90
222 223 4.077188 GTTCGCGCCACAGACAGC 62.077 66.667 0.00 0.00 0.00 4.40
242 243 4.441913 CCGAGCCAATGAGCCAATTATTTT 60.442 41.667 0.00 0.00 0.00 1.82
293 295 1.011333 GTGCGGCGCCTATTTCTTTA 58.989 50.000 30.82 2.71 0.00 1.85
357 360 0.613012 GGTGGAAGGCTGGCTGATTT 60.613 55.000 3.84 0.00 0.00 2.17
358 361 1.000396 GGTGGAAGGCTGGCTGATT 60.000 57.895 3.84 0.00 0.00 2.57
359 362 2.679716 GGTGGAAGGCTGGCTGAT 59.320 61.111 3.84 0.00 0.00 2.90
360 363 3.650950 GGGTGGAAGGCTGGCTGA 61.651 66.667 3.84 0.00 0.00 4.26
361 364 3.635268 GAGGGTGGAAGGCTGGCTG 62.635 68.421 3.84 0.00 0.00 4.85
362 365 3.334054 GAGGGTGGAAGGCTGGCT 61.334 66.667 0.00 0.00 0.00 4.75
499 543 3.335729 AGCGGTAGGGGTTTGGGG 61.336 66.667 0.00 0.00 0.00 4.96
712 1270 3.136123 CATCCCAGCTGCCGTTGG 61.136 66.667 8.66 3.93 40.84 3.77
713 1271 3.136123 CCATCCCAGCTGCCGTTG 61.136 66.667 8.66 5.72 0.00 4.10
851 1530 4.507691 CGGGTACTCCTCTAGATCTCCATT 60.508 50.000 0.00 0.00 0.00 3.16
853 1532 2.372504 CGGGTACTCCTCTAGATCTCCA 59.627 54.545 0.00 0.00 0.00 3.86
862 1541 4.444081 AGCGGCGGGTACTCCTCT 62.444 66.667 9.78 0.00 0.00 3.69
919 1598 1.673920 CTTGCACCCTTAACGTTGTGT 59.326 47.619 11.99 0.00 0.00 3.72
1722 6264 5.503634 TCCTTGTGGAGATGATTCAAAGA 57.496 39.130 0.00 0.00 37.46 2.52
1953 6495 2.359981 TGCGCTAGGTACCAGTCTAT 57.640 50.000 15.94 0.00 0.00 1.98
1985 6527 8.611654 TTAATTTGTTCTTGTACCAGTCTACC 57.388 34.615 0.00 0.00 0.00 3.18
2003 6545 6.293900 GGCCTGTTTGGAATGGTTTTAATTTG 60.294 38.462 0.00 0.00 38.35 2.32
2288 6830 3.307059 CCTCCGACACCTTCAAGATCTTT 60.307 47.826 4.86 0.00 0.00 2.52
2425 6967 6.573434 AGTTGCTGAACATCATCGTCTATAA 58.427 36.000 0.00 0.00 34.17 0.98
2439 6981 2.639751 CGCACACTTTAGTTGCTGAAC 58.360 47.619 12.07 0.00 33.25 3.18
2466 7008 6.463995 AGCATGTAACTGAAAACTGGAAAA 57.536 33.333 0.00 0.00 0.00 2.29
2628 7170 3.262420 CCAAATCGTTCAGAATCCTCGT 58.738 45.455 0.00 0.00 0.00 4.18
3057 8387 0.108424 GCTCTCTCGTGCATTCAGGT 60.108 55.000 0.00 0.00 0.00 4.00
3280 8610 9.638239 GCAGAATATTGTTTTACTTTGGATCAA 57.362 29.630 0.00 0.00 0.00 2.57
3343 8673 8.122330 TCTGCATGCAAAGATTACTTTATTACG 58.878 33.333 22.88 3.17 43.41 3.18
3638 8970 2.538512 AATCATGCAGCTGCTCGATA 57.461 45.000 36.61 18.93 42.66 2.92
4159 9740 8.006298 TGCATATTGGAAGGTTAAATTACCAG 57.994 34.615 0.31 0.00 40.82 4.00
4221 9802 2.200373 TCAAGGGCTTGCTTAAGGAC 57.800 50.000 4.29 0.00 40.24 3.85
4441 10022 9.997482 GTTTACACTCACATTTTCTTCACTAAA 57.003 29.630 0.00 0.00 0.00 1.85
4563 11403 2.288666 TGATTTGATGCGCCTTAGACC 58.711 47.619 4.18 0.00 0.00 3.85
4651 11512 8.834465 CAACAATAAACACCATTTCATCCAAAA 58.166 29.630 0.00 0.00 0.00 2.44
4708 11569 3.334691 TGACATACCCTGAAGAAAAGCG 58.665 45.455 0.00 0.00 0.00 4.68
4958 11819 2.106566 TGCCTTCTTTGTTTGCCTTGA 58.893 42.857 0.00 0.00 0.00 3.02
5190 14449 7.499232 ACATTATCACTCCACCAACTTAATAGC 59.501 37.037 0.00 0.00 0.00 2.97
5224 14483 4.082845 TGTCTCCAGGTTCAACAAACAAA 58.917 39.130 0.00 0.00 39.81 2.83


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

AutoCloner maintained by Alex Coulton.