Multiple sequence alignment - TraesCS1D01G290900

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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 TraesCS1D01G290900 chr1D 100.000 3843 0 0 1 3843 389212098 389215940 0.000000e+00 7097.0
1 TraesCS1D01G290900 chr1D 95.157 1590 53 9 773 2348 389603240 389601661 0.000000e+00 2488.0
2 TraesCS1D01G290900 chr1D 94.253 1305 55 14 2546 3843 389600243 389598952 0.000000e+00 1977.0
3 TraesCS1D01G290900 chr1D 83.831 1608 168 47 921 2466 388991039 388992616 0.000000e+00 1445.0
4 TraesCS1D01G290900 chr1D 83.474 1301 163 32 1198 2466 389555751 389554471 0.000000e+00 1164.0
5 TraesCS1D01G290900 chr1D 87.160 514 41 12 296 784 389610366 389609853 9.320000e-156 560.0
6 TraesCS1D01G290900 chr1D 89.524 315 22 4 1 304 389624206 389623892 4.660000e-104 388.0
7 TraesCS1D01G290900 chr1D 86.686 353 27 11 3500 3843 389553859 389553518 1.300000e-99 374.0
8 TraesCS1D01G290900 chr1D 73.695 996 164 64 958 1874 390409579 390408603 8.070000e-77 298.0
9 TraesCS1D01G290900 chr1D 91.549 213 13 4 3616 3823 388993290 388993502 4.860000e-74 289.0
10 TraesCS1D01G290900 chr1D 72.616 1143 184 83 826 1874 390581371 390580264 1.370000e-64 257.0
11 TraesCS1D01G290900 chr1D 95.455 132 6 0 2335 2466 389600371 389600240 1.080000e-50 211.0
12 TraesCS1D01G290900 chr1D 75.938 453 65 19 2544 2955 388992611 388993060 3.920000e-45 193.0
13 TraesCS1D01G290900 chr1D 93.750 96 6 0 2454 2549 457943269 457943174 1.110000e-30 145.0
14 TraesCS1D01G290900 chr1D 81.250 176 18 7 1284 1459 390402018 390401858 1.120000e-25 128.0
15 TraesCS1D01G290900 chr1D 81.290 155 23 3 3063 3216 489715055 489714906 1.880000e-23 121.0
16 TraesCS1D01G290900 chr1D 78.022 182 34 3 3036 3216 49311733 49311909 4.060000e-20 110.0
17 TraesCS1D01G290900 chr1D 75.073 341 28 35 60 358 353645441 353645766 5.250000e-19 106.0
18 TraesCS1D01G290900 chr1D 98.276 58 1 0 1 58 346835685 346835628 6.790000e-18 102.0
19 TraesCS1D01G290900 chr1D 96.610 59 2 0 1 59 159289747 159289689 8.790000e-17 99.0
20 TraesCS1D01G290900 chr1D 96.610 59 2 0 1 59 173049511 173049453 8.790000e-17 99.0
21 TraesCS1D01G290900 chr1D 90.141 71 5 2 826 894 390855213 390855283 1.470000e-14 91.6
22 TraesCS1D01G290900 chr1D 93.333 60 3 1 826 884 389243681 389243740 1.900000e-13 87.9
23 TraesCS1D01G290900 chr1D 94.737 57 2 1 829 884 389525513 389525457 1.900000e-13 87.9
24 TraesCS1D01G290900 chr1D 94.643 56 2 1 829 883 390409679 390409624 6.840000e-13 86.1
25 TraesCS1D01G290900 chr1A 94.670 1726 65 11 755 2466 488112168 488110456 0.000000e+00 2652.0
26 TraesCS1D01G290900 chr1A 90.008 1301 62 35 2546 3843 488110459 488109224 0.000000e+00 1620.0
27 TraesCS1D01G290900 chr1A 83.107 1622 173 52 921 2465 488071446 488073043 0.000000e+00 1384.0
28 TraesCS1D01G290900 chr1A 73.988 642 124 27 1114 1726 488103697 488103070 1.800000e-53 220.0
29 TraesCS1D01G290900 chr1A 83.117 231 20 10 3616 3843 488073688 488073902 3.920000e-45 193.0
30 TraesCS1D01G290900 chr1A 86.957 115 12 2 1281 1395 488244185 488244296 4.030000e-25 126.0
31 TraesCS1D01G290900 chr1A 93.023 43 3 0 826 868 488235668 488235710 3.210000e-06 63.9
32 TraesCS1D01G290900 chr1B 83.769 1608 177 43 921 2466 522362786 522364371 0.000000e+00 1447.0
33 TraesCS1D01G290900 chr1B 82.660 1436 170 39 915 2323 522626433 522627816 0.000000e+00 1199.0
34 TraesCS1D01G290900 chr1B 85.836 353 30 11 3500 3843 522628737 522629078 1.310000e-94 357.0
35 TraesCS1D01G290900 chr1B 73.929 840 137 49 956 1722 523338242 523339072 2.940000e-66 263.0
36 TraesCS1D01G290900 chr1B 78.222 450 51 22 2544 2955 522364366 522364806 1.070000e-60 244.0
37 TraesCS1D01G290900 chr1B 77.209 430 66 22 1324 1722 523208366 523208794 5.000000e-54 222.0
38 TraesCS1D01G290900 chr1B 76.081 393 46 25 60 423 671195116 671195489 1.100000e-35 161.0
39 TraesCS1D01G290900 chr1B 82.203 118 17 3 1281 1397 523238314 523238428 8.790000e-17 99.0
40 TraesCS1D01G290900 chr1B 91.379 58 3 1 829 884 522841135 522841078 1.140000e-10 78.7
41 TraesCS1D01G290900 chr1B 94.000 50 2 1 826 874 522739502 522739551 1.480000e-09 75.0
42 TraesCS1D01G290900 chr5D 86.990 392 30 9 62 438 520430284 520430669 4.590000e-114 422.0
43 TraesCS1D01G290900 chr5D 76.330 376 37 23 60 398 134914917 134915277 1.850000e-33 154.0
44 TraesCS1D01G290900 chr7D 82.836 402 37 14 60 438 379309728 379310120 7.960000e-87 331.0
45 TraesCS1D01G290900 chr7D 83.684 380 33 11 60 420 379310668 379311037 7.960000e-87 331.0
46 TraesCS1D01G290900 chr7D 81.934 393 32 27 63 438 595398225 595397855 2.900000e-76 296.0
47 TraesCS1D01G290900 chr7D 81.818 187 21 10 60 245 365487326 365487152 1.110000e-30 145.0
48 TraesCS1D01G290900 chr7D 74.757 412 55 28 60 438 424489323 424488928 5.180000e-29 139.0
49 TraesCS1D01G290900 chr3D 90.811 185 14 3 465 648 83501466 83501648 1.070000e-60 244.0
50 TraesCS1D01G290900 chr3D 75.819 397 40 27 63 423 85024029 85023653 2.390000e-32 150.0
51 TraesCS1D01G290900 chr3D 78.191 188 35 3 3030 3216 546170553 546170735 8.720000e-22 115.0
52 TraesCS1D01G290900 chr3D 93.651 63 4 0 4 66 232837120 232837058 1.140000e-15 95.3
53 TraesCS1D01G290900 chr2B 89.894 188 16 2 465 652 235150146 235150330 4.960000e-59 239.0
54 TraesCS1D01G290900 chr2B 78.142 183 32 5 3036 3216 625805938 625806114 4.060000e-20 110.0
55 TraesCS1D01G290900 chr2B 98.333 60 1 0 1 60 441554049 441553990 5.250000e-19 106.0
56 TraesCS1D01G290900 chr2B 92.647 68 5 0 1 68 368417824 368417891 8.790000e-17 99.0
57 TraesCS1D01G290900 chr3B 77.778 405 49 26 60 423 200853782 200854186 1.080000e-50 211.0
58 TraesCS1D01G290900 chr7A 77.041 392 40 26 60 424 670863657 670864025 3.050000e-41 180.0
59 TraesCS1D01G290900 chr7A 85.849 106 7 1 62 159 610714803 610714698 5.250000e-19 106.0
60 TraesCS1D01G290900 chr5B 76.675 403 46 28 60 423 268285986 268285593 3.050000e-41 180.0
61 TraesCS1D01G290900 chr5B 98.333 60 1 0 1 60 503697276 503697217 5.250000e-19 106.0
62 TraesCS1D01G290900 chr5B 100.000 32 0 0 465 496 631789262 631789293 4.150000e-05 60.2
63 TraesCS1D01G290900 chr6A 88.321 137 9 5 113 243 393236944 393237079 1.430000e-34 158.0
64 TraesCS1D01G290900 chr6A 93.617 94 5 1 2460 2553 182320745 182320837 5.180000e-29 139.0
65 TraesCS1D01G290900 chr6A 80.263 152 24 3 3066 3216 126243566 126243420 4.060000e-20 110.0
66 TraesCS1D01G290900 chr6A 98.305 59 1 0 1 59 220454856 220454914 1.890000e-18 104.0
67 TraesCS1D01G290900 chr7B 93.069 101 5 2 2453 2551 742411879 742411979 3.090000e-31 147.0
68 TraesCS1D01G290900 chr7B 92.857 98 6 1 2459 2555 665540440 665540343 1.440000e-29 141.0
69 TraesCS1D01G290900 chr7B 98.305 59 1 0 1 59 431650753 431650695 1.890000e-18 104.0
70 TraesCS1D01G290900 chr7B 94.118 68 4 0 1 68 460971953 460972020 1.890000e-18 104.0
71 TraesCS1D01G290900 chr4A 93.684 95 6 0 2456 2550 142348617 142348523 4.000000e-30 143.0
72 TraesCS1D01G290900 chr4A 96.875 64 1 1 1 63 264221860 264221797 5.250000e-19 106.0
73 TraesCS1D01G290900 chr4A 92.593 54 1 1 60 113 714836507 714836457 1.480000e-09 75.0
74 TraesCS1D01G290900 chr3A 92.857 98 7 0 2453 2550 123651463 123651366 4.000000e-30 143.0
75 TraesCS1D01G290900 chr2D 91.919 99 8 0 2453 2551 567672203 567672301 5.180000e-29 139.0
76 TraesCS1D01G290900 chr6D 91.667 96 8 0 2453 2548 229430653 229430748 2.410000e-27 134.0
77 TraesCS1D01G290900 chr6D 98.305 59 1 0 1 59 116735326 116735268 1.890000e-18 104.0
78 TraesCS1D01G290900 chr6D 98.305 59 1 0 1 59 460607235 460607177 1.890000e-18 104.0
79 TraesCS1D01G290900 chr6D 94.737 57 3 0 3 59 350373878 350373822 5.290000e-14 89.8
80 TraesCS1D01G290900 chr6D 88.136 59 7 0 1 59 129804158 129804216 1.920000e-08 71.3
81 TraesCS1D01G290900 chrUn 88.182 110 13 0 2463 2572 459259778 459259669 8.660000e-27 132.0
82 TraesCS1D01G290900 chrUn 94.915 59 3 0 1 59 250756494 250756552 4.090000e-15 93.5
83 TraesCS1D01G290900 chrUn 94.915 59 3 0 1 59 258525216 258525158 4.090000e-15 93.5
84 TraesCS1D01G290900 chrUn 72.980 396 51 31 60 409 326014730 326015115 1.900000e-13 87.9
85 TraesCS1D01G290900 chrUn 72.980 396 51 31 60 409 355031335 355031720 1.900000e-13 87.9
86 TraesCS1D01G290900 chrUn 86.441 59 8 0 1 59 75904941 75904883 8.910000e-07 65.8
87 TraesCS1D01G290900 chr2A 75.926 324 36 26 60 349 645803606 645803921 1.120000e-25 128.0
88 TraesCS1D01G290900 chr4D 79.894 189 23 11 3030 3211 299317104 299317284 1.450000e-24 124.0
89 TraesCS1D01G290900 chr4D 74.321 405 50 32 57 423 59626689 59626301 5.210000e-24 122.0
90 TraesCS1D01G290900 chr4D 78.010 191 33 5 3030 3216 298476864 298477049 1.130000e-20 111.0
91 TraesCS1D01G290900 chr4D 98.246 57 1 0 1 57 1608654 1608598 2.440000e-17 100.0
92 TraesCS1D01G290900 chr4D 96.429 56 2 0 3 58 96370213 96370268 4.090000e-15 93.5
93 TraesCS1D01G290900 chr4D 79.310 145 18 4 289 423 222967554 222967696 1.470000e-14 91.6
94 TraesCS1D01G290900 chr4D 93.220 59 4 0 1 59 268423665 268423607 1.900000e-13 87.9
95 TraesCS1D01G290900 chr4D 91.525 59 5 0 1 59 94512664 94512722 8.850000e-12 82.4
96 TraesCS1D01G290900 chr6B 98.305 59 1 0 1 59 180001663 180001721 1.890000e-18 104.0
97 TraesCS1D01G290900 chr4B 96.610 59 2 0 1 59 324889397 324889339 8.790000e-17 99.0
98 TraesCS1D01G290900 chr4B 96.610 59 2 0 1 59 388849146 388849088 8.790000e-17 99.0


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 TraesCS1D01G290900 chr1D 389212098 389215940 3842 False 7097.000000 7097 100.000000 1 3843 1 chr1D.!!$F3 3842
1 TraesCS1D01G290900 chr1D 389598952 389603240 4288 True 1558.666667 2488 94.955000 773 3843 3 chr1D.!!$R12 3070
2 TraesCS1D01G290900 chr1D 389553518 389555751 2233 True 769.000000 1164 85.080000 1198 3843 2 chr1D.!!$R11 2645
3 TraesCS1D01G290900 chr1D 388991039 388993502 2463 False 642.333333 1445 83.772667 921 3823 3 chr1D.!!$F6 2902
4 TraesCS1D01G290900 chr1D 389609853 389610366 513 True 560.000000 560 87.160000 296 784 1 chr1D.!!$R5 488
5 TraesCS1D01G290900 chr1D 390580264 390581371 1107 True 257.000000 257 72.616000 826 1874 1 chr1D.!!$R8 1048
6 TraesCS1D01G290900 chr1A 488109224 488112168 2944 True 2136.000000 2652 92.339000 755 3843 2 chr1A.!!$R2 3088
7 TraesCS1D01G290900 chr1A 488071446 488073902 2456 False 788.500000 1384 83.112000 921 3843 2 chr1A.!!$F3 2922
8 TraesCS1D01G290900 chr1A 488103070 488103697 627 True 220.000000 220 73.988000 1114 1726 1 chr1A.!!$R1 612
9 TraesCS1D01G290900 chr1B 522362786 522364806 2020 False 845.500000 1447 80.995500 921 2955 2 chr1B.!!$F6 2034
10 TraesCS1D01G290900 chr1B 522626433 522629078 2645 False 778.000000 1199 84.248000 915 3843 2 chr1B.!!$F7 2928
11 TraesCS1D01G290900 chr1B 523338242 523339072 830 False 263.000000 263 73.929000 956 1722 1 chr1B.!!$F4 766
12 TraesCS1D01G290900 chr7D 379309728 379311037 1309 False 331.000000 331 83.260000 60 438 2 chr7D.!!$F1 378

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
23 24 0.178903 TGGCTCCACACCTAAGTCCT 60.179 55.000 0.0 0.0 0.00 3.85 F
57 58 0.665835 TGCCATGACAAAACCACGAC 59.334 50.000 0.0 0.0 0.00 4.34 F
58 59 0.665835 GCCATGACAAAACCACGACA 59.334 50.000 0.0 0.0 0.00 4.35 F
610 645 0.740737 CCAAATCCGATGTGAAGGGC 59.259 55.000 0.0 0.0 0.00 5.19 F
654 689 1.405105 CGTTGGTCAATGCCCTAATGG 59.595 52.381 0.0 0.0 37.09 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2840 6.509418 TTCAAGTGCAGTAAACTTCAAAGT 57.491 33.333 0.00 0.0 42.04 2.66 R
2199 2861 2.514803 ACCTGTGCACCCTAACAATTC 58.485 47.619 15.69 0.0 0.00 2.17 R
2302 2996 6.003950 CCCCTTCAGAAACTTCAATACAGAA 58.996 40.000 0.00 0.0 0.00 3.02 R
2765 4954 0.443869 CAATTGGTCGTCTTGCTCGG 59.556 55.000 0.00 0.0 0.00 4.63 R
2929 5189 7.521509 ACACGAGAAAGGAAAATATAAGACG 57.478 36.000 0.00 0.0 0.00 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
17 18 2.900273 GCGATGGCTCCACACCTA 59.100 61.111 0.00 0.00 35.83 3.08
18 19 1.220749 GCGATGGCTCCACACCTAA 59.779 57.895 0.00 0.00 35.83 2.69
19 20 0.811616 GCGATGGCTCCACACCTAAG 60.812 60.000 0.00 0.00 35.83 2.18
20 21 0.537188 CGATGGCTCCACACCTAAGT 59.463 55.000 0.00 0.00 0.00 2.24
21 22 1.471676 CGATGGCTCCACACCTAAGTC 60.472 57.143 0.00 0.00 0.00 3.01
22 23 0.912486 ATGGCTCCACACCTAAGTCC 59.088 55.000 0.00 0.00 0.00 3.85
23 24 0.178903 TGGCTCCACACCTAAGTCCT 60.179 55.000 0.00 0.00 0.00 3.85
24 25 0.984995 GGCTCCACACCTAAGTCCTT 59.015 55.000 0.00 0.00 0.00 3.36
25 26 1.351350 GGCTCCACACCTAAGTCCTTT 59.649 52.381 0.00 0.00 0.00 3.11
26 27 2.224793 GGCTCCACACCTAAGTCCTTTT 60.225 50.000 0.00 0.00 0.00 2.27
27 28 3.008704 GGCTCCACACCTAAGTCCTTTTA 59.991 47.826 0.00 0.00 0.00 1.52
28 29 4.001652 GCTCCACACCTAAGTCCTTTTAC 58.998 47.826 0.00 0.00 0.00 2.01
29 30 4.504340 GCTCCACACCTAAGTCCTTTTACA 60.504 45.833 0.00 0.00 0.00 2.41
30 31 5.617252 CTCCACACCTAAGTCCTTTTACAA 58.383 41.667 0.00 0.00 0.00 2.41
31 32 5.617252 TCCACACCTAAGTCCTTTTACAAG 58.383 41.667 0.00 0.00 0.00 3.16
40 41 2.947448 CCTTTTACAAGGGCATCTGC 57.053 50.000 0.00 0.00 45.63 4.26
52 53 2.000429 GCATCTGCCATGACAAAACC 58.000 50.000 0.00 0.00 34.31 3.27
53 54 1.273048 GCATCTGCCATGACAAAACCA 59.727 47.619 0.00 0.00 34.31 3.67
54 55 2.927871 GCATCTGCCATGACAAAACCAC 60.928 50.000 0.00 0.00 34.31 4.16
55 56 0.950836 TCTGCCATGACAAAACCACG 59.049 50.000 0.00 0.00 0.00 4.94
56 57 0.950836 CTGCCATGACAAAACCACGA 59.049 50.000 0.00 0.00 0.00 4.35
57 58 0.665835 TGCCATGACAAAACCACGAC 59.334 50.000 0.00 0.00 0.00 4.34
58 59 0.665835 GCCATGACAAAACCACGACA 59.334 50.000 0.00 0.00 0.00 4.35
72 73 2.214216 CGACACCTCCCACCTTCCA 61.214 63.158 0.00 0.00 0.00 3.53
80 81 3.841078 CCACCTTCCAGGGACCAT 58.159 61.111 0.00 0.00 40.58 3.55
81 82 2.087248 CCACCTTCCAGGGACCATT 58.913 57.895 0.00 0.00 40.58 3.16
131 140 2.181021 GGCGACGAGGACGACAAT 59.819 61.111 0.00 0.00 42.66 2.71
136 145 2.180769 CGAGGACGACAATGGCGA 59.819 61.111 18.23 0.00 42.66 5.54
140 149 3.109547 GACGACAATGGCGACGCA 61.110 61.111 18.23 8.33 0.00 5.24
148 157 4.794439 TGGCGACGCATGAGACGG 62.794 66.667 23.09 5.22 34.00 4.79
225 234 7.534085 TCTGTTAATTATGTTCTAAGCACCG 57.466 36.000 0.00 0.00 0.00 4.94
341 351 5.576563 ATTTTATATCATGTCCACCCCGA 57.423 39.130 0.00 0.00 0.00 5.14
356 366 2.017049 CCCCGAACATGATTTGAGGTC 58.983 52.381 0.00 0.00 0.00 3.85
362 381 2.436417 ACATGATTTGAGGTCGTTGGG 58.564 47.619 0.00 0.00 0.00 4.12
431 455 1.228124 CCCAAACGGAAGCAGACCA 60.228 57.895 0.00 0.00 0.00 4.02
438 462 2.335712 GGAAGCAGACCAAAGCGGG 61.336 63.158 0.00 0.00 40.22 6.13
439 463 2.282462 AAGCAGACCAAAGCGGGG 60.282 61.111 0.00 0.00 40.22 5.73
504 539 1.414181 GCATTGGCTAGGTGAGAGCTA 59.586 52.381 0.00 0.00 39.98 3.32
526 561 5.394224 AAAACGACTTTTTGTCAGGGAAA 57.606 34.783 0.00 0.00 45.60 3.13
528 563 4.632538 ACGACTTTTTGTCAGGGAAAAG 57.367 40.909 6.66 6.66 45.60 2.27
538 573 2.751837 GGGAAAAGGCAGCCTCCG 60.752 66.667 16.53 0.00 30.89 4.63
573 608 1.416030 TCCACTCTGCAAGCAACACTA 59.584 47.619 0.00 0.00 0.00 2.74
604 639 1.714899 GGACCGCCAAATCCGATGTG 61.715 60.000 0.00 0.00 0.00 3.21
605 640 0.742990 GACCGCCAAATCCGATGTGA 60.743 55.000 0.00 0.00 0.00 3.58
610 645 0.740737 CCAAATCCGATGTGAAGGGC 59.259 55.000 0.00 0.00 0.00 5.19
621 656 2.747855 GAAGGGCTGGAGCAACCG 60.748 66.667 0.20 0.00 44.36 4.44
654 689 1.405105 CGTTGGTCAATGCCCTAATGG 59.595 52.381 0.00 0.00 37.09 3.16
684 719 1.439679 GAACTGGCGGTTACCTGAAG 58.560 55.000 12.53 0.00 38.41 3.02
710 746 3.940852 GGCCCTTATCATTTGGCAAAAAG 59.059 43.478 17.70 14.82 45.83 2.27
713 749 5.704978 GCCCTTATCATTTGGCAAAAAGAAA 59.295 36.000 17.70 12.56 43.46 2.52
787 823 4.143094 CGAAATTCGAACTCACCTTTCTCC 60.143 45.833 10.18 0.00 43.74 3.71
1095 1145 2.039405 CCCTGGGCCCTCACCTAT 60.039 66.667 25.70 0.00 0.00 2.57
2466 4626 4.091509 CGCAGGCGGAATTATGTATTACTC 59.908 45.833 5.63 0.00 35.56 2.59
2467 4627 5.238583 GCAGGCGGAATTATGTATTACTCT 58.761 41.667 0.00 0.00 0.00 3.24
2468 4628 5.348997 GCAGGCGGAATTATGTATTACTCTC 59.651 44.000 0.00 0.00 0.00 3.20
2469 4629 6.692486 CAGGCGGAATTATGTATTACTCTCT 58.308 40.000 0.00 0.00 0.00 3.10
2470 4630 7.155328 CAGGCGGAATTATGTATTACTCTCTT 58.845 38.462 0.00 0.00 0.00 2.85
2471 4631 7.657761 CAGGCGGAATTATGTATTACTCTCTTT 59.342 37.037 0.00 0.00 0.00 2.52
2472 4632 7.657761 AGGCGGAATTATGTATTACTCTCTTTG 59.342 37.037 0.00 0.00 0.00 2.77
2473 4633 7.441458 GGCGGAATTATGTATTACTCTCTTTGT 59.559 37.037 0.00 0.00 0.00 2.83
2474 4634 9.472361 GCGGAATTATGTATTACTCTCTTTGTA 57.528 33.333 0.00 0.00 0.00 2.41
2541 4701 9.977762 AAACGCTTTTATATTAGTTTACGGAAG 57.022 29.630 0.00 0.00 31.14 3.46
2542 4702 8.134905 ACGCTTTTATATTAGTTTACGGAAGG 57.865 34.615 0.00 0.00 0.00 3.46
2543 4703 7.981225 ACGCTTTTATATTAGTTTACGGAAGGA 59.019 33.333 0.00 0.00 0.00 3.36
2544 4704 8.485591 CGCTTTTATATTAGTTTACGGAAGGAG 58.514 37.037 0.00 0.00 0.00 3.69
2545 4705 9.322773 GCTTTTATATTAGTTTACGGAAGGAGT 57.677 33.333 0.00 0.00 0.00 3.85
2596 4759 4.898320 TGCACTGGACATGTGATATATCC 58.102 43.478 1.15 0.00 37.60 2.59
2605 4768 7.730332 TGGACATGTGATATATCCTGTAGAGTT 59.270 37.037 1.15 0.00 0.00 3.01
2606 4769 8.589338 GGACATGTGATATATCCTGTAGAGTTT 58.411 37.037 1.15 0.00 0.00 2.66
2657 4821 4.053983 AGCATATATCTGTGCAACTGTCG 58.946 43.478 2.76 0.00 41.58 4.35
2669 4833 2.570169 CAACTGTCGTGTTAAATGCCG 58.430 47.619 0.00 0.00 0.00 5.69
2677 4842 3.062909 TCGTGTTAAATGCCGAGCAATAC 59.937 43.478 2.68 1.02 43.62 1.89
2709 4874 5.048504 TCCAAATCTTGCTGTGATGAAGAAC 60.049 40.000 0.00 0.00 29.78 3.01
2719 4904 6.484308 TGCTGTGATGAAGAACCATATACATG 59.516 38.462 0.00 0.00 0.00 3.21
3094 5364 7.665561 TTTTTGTCATAGCTAAAATTTGGCC 57.334 32.000 10.44 0.00 37.96 5.36
3116 5386 4.080413 CCCTTGGTTGGATTATTGCCAATT 60.080 41.667 0.00 0.00 46.21 2.32
3209 5480 1.414550 GGCAACCAAAACCTTAGCCAA 59.585 47.619 0.00 0.00 40.29 4.52
3557 5828 2.688446 CGGGAGTATTGTCTGAGCTACA 59.312 50.000 0.00 0.00 0.00 2.74
3762 6046 2.162408 GGCTGAACTGAAGTATGTTGCC 59.838 50.000 0.00 0.00 31.40 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.811616 CTTAGGTGTGGAGCCATCGC 60.812 60.000 0.00 0.00 0.00 4.58
2 3 1.134371 GGACTTAGGTGTGGAGCCATC 60.134 57.143 0.00 0.00 0.00 3.51
3 4 0.912486 GGACTTAGGTGTGGAGCCAT 59.088 55.000 0.00 0.00 0.00 4.40
4 5 0.178903 AGGACTTAGGTGTGGAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
5 6 0.984995 AAGGACTTAGGTGTGGAGCC 59.015 55.000 0.00 0.00 0.00 4.70
6 7 2.861147 AAAGGACTTAGGTGTGGAGC 57.139 50.000 0.00 0.00 0.00 4.70
7 8 5.223449 TGTAAAAGGACTTAGGTGTGGAG 57.777 43.478 0.00 0.00 0.00 3.86
8 9 5.455612 CCTTGTAAAAGGACTTAGGTGTGGA 60.456 44.000 5.67 0.00 42.62 4.02
9 10 4.760204 CCTTGTAAAAGGACTTAGGTGTGG 59.240 45.833 5.67 0.00 42.62 4.17
10 11 4.760204 CCCTTGTAAAAGGACTTAGGTGTG 59.240 45.833 13.80 0.00 42.62 3.82
11 12 4.748857 GCCCTTGTAAAAGGACTTAGGTGT 60.749 45.833 13.80 0.00 42.62 4.16
12 13 3.756963 GCCCTTGTAAAAGGACTTAGGTG 59.243 47.826 13.80 0.00 42.62 4.00
13 14 3.396611 TGCCCTTGTAAAAGGACTTAGGT 59.603 43.478 13.80 0.00 42.62 3.08
14 15 4.028993 TGCCCTTGTAAAAGGACTTAGG 57.971 45.455 13.80 0.00 42.62 2.69
15 16 5.355350 CAGATGCCCTTGTAAAAGGACTTAG 59.645 44.000 13.80 0.00 42.62 2.18
16 17 5.253330 CAGATGCCCTTGTAAAAGGACTTA 58.747 41.667 13.80 0.00 42.62 2.24
17 18 4.082125 CAGATGCCCTTGTAAAAGGACTT 58.918 43.478 13.80 0.00 42.62 3.01
18 19 3.690460 CAGATGCCCTTGTAAAAGGACT 58.310 45.455 13.80 4.36 42.62 3.85
19 20 2.164422 GCAGATGCCCTTGTAAAAGGAC 59.836 50.000 13.80 1.50 42.62 3.85
20 21 2.446435 GCAGATGCCCTTGTAAAAGGA 58.554 47.619 13.80 0.00 42.62 3.36
21 22 2.947448 GCAGATGCCCTTGTAAAAGG 57.053 50.000 4.48 4.48 39.68 3.11
33 34 1.273048 TGGTTTTGTCATGGCAGATGC 59.727 47.619 0.00 0.00 41.14 3.91
34 35 2.669113 CGTGGTTTTGTCATGGCAGATG 60.669 50.000 0.00 0.00 0.00 2.90
35 36 1.541147 CGTGGTTTTGTCATGGCAGAT 59.459 47.619 0.00 0.00 0.00 2.90
36 37 0.950836 CGTGGTTTTGTCATGGCAGA 59.049 50.000 0.00 0.00 0.00 4.26
37 38 0.950836 TCGTGGTTTTGTCATGGCAG 59.049 50.000 0.00 0.00 0.00 4.85
38 39 0.665835 GTCGTGGTTTTGTCATGGCA 59.334 50.000 0.00 0.00 0.00 4.92
39 40 0.665835 TGTCGTGGTTTTGTCATGGC 59.334 50.000 0.00 0.00 0.00 4.40
40 41 1.001815 GGTGTCGTGGTTTTGTCATGG 60.002 52.381 0.00 0.00 0.00 3.66
41 42 1.946768 AGGTGTCGTGGTTTTGTCATG 59.053 47.619 0.00 0.00 0.00 3.07
42 43 2.218603 GAGGTGTCGTGGTTTTGTCAT 58.781 47.619 0.00 0.00 0.00 3.06
43 44 1.658994 GAGGTGTCGTGGTTTTGTCA 58.341 50.000 0.00 0.00 0.00 3.58
44 45 0.942252 GGAGGTGTCGTGGTTTTGTC 59.058 55.000 0.00 0.00 0.00 3.18
45 46 0.464916 GGGAGGTGTCGTGGTTTTGT 60.465 55.000 0.00 0.00 0.00 2.83
46 47 0.464735 TGGGAGGTGTCGTGGTTTTG 60.465 55.000 0.00 0.00 0.00 2.44
47 48 0.464916 GTGGGAGGTGTCGTGGTTTT 60.465 55.000 0.00 0.00 0.00 2.43
48 49 1.147600 GTGGGAGGTGTCGTGGTTT 59.852 57.895 0.00 0.00 0.00 3.27
49 50 2.814835 GGTGGGAGGTGTCGTGGTT 61.815 63.158 0.00 0.00 0.00 3.67
50 51 3.239253 GGTGGGAGGTGTCGTGGT 61.239 66.667 0.00 0.00 0.00 4.16
51 52 2.450479 GAAGGTGGGAGGTGTCGTGG 62.450 65.000 0.00 0.00 0.00 4.94
52 53 1.004918 GAAGGTGGGAGGTGTCGTG 60.005 63.158 0.00 0.00 0.00 4.35
53 54 2.214920 GGAAGGTGGGAGGTGTCGT 61.215 63.158 0.00 0.00 0.00 4.34
54 55 2.172483 CTGGAAGGTGGGAGGTGTCG 62.172 65.000 0.00 0.00 0.00 4.35
55 56 1.679898 CTGGAAGGTGGGAGGTGTC 59.320 63.158 0.00 0.00 0.00 3.67
56 57 3.906980 CTGGAAGGTGGGAGGTGT 58.093 61.111 0.00 0.00 0.00 4.16
76 77 2.765969 CAGAGGTGGGCCAATGGT 59.234 61.111 8.40 0.00 37.19 3.55
80 81 3.636231 CGTCCAGAGGTGGGCCAA 61.636 66.667 8.40 0.00 46.96 4.52
131 140 4.794439 CCGTCTCATGCGTCGCCA 62.794 66.667 15.88 3.10 0.00 5.69
172 181 3.207547 AAAAAGACAAGCGCCGCCC 62.208 57.895 4.98 0.00 0.00 6.13
202 211 7.180079 CACGGTGCTTAGAACATAATTAACAG 58.820 38.462 0.00 0.00 0.00 3.16
225 234 0.824759 ATAGTCTTCACGGCCTCCAC 59.175 55.000 0.00 0.00 0.00 4.02
341 351 2.819608 CCCAACGACCTCAAATCATGTT 59.180 45.455 0.00 0.00 0.00 2.71
410 430 2.597217 CTGCTTCCGTTTGGGGCA 60.597 61.111 0.00 0.00 40.29 5.36
450 484 1.651240 CTTGCTCCATGCCAACTCCG 61.651 60.000 0.00 0.00 42.00 4.63
462 497 2.338785 GGCAACCTCAGCTTGCTCC 61.339 63.158 4.68 0.00 43.08 4.70
463 498 0.964358 ATGGCAACCTCAGCTTGCTC 60.964 55.000 4.68 0.00 43.08 4.26
496 531 6.044512 GACAAAAAGTCGTTTTAGCTCTCA 57.955 37.500 0.00 0.00 37.32 3.27
538 573 4.451652 GGAACGAGCGCTTGCAGC 62.452 66.667 24.80 13.34 42.66 5.25
550 585 0.040958 GTTGCTTGCAGAGTGGAACG 60.041 55.000 0.00 0.00 45.86 3.95
604 639 2.747855 CGGTTGCTCCAGCCCTTC 60.748 66.667 0.00 0.00 41.18 3.46
605 640 3.553095 GACGGTTGCTCCAGCCCTT 62.553 63.158 0.00 0.00 41.18 3.95
621 656 1.374758 CCAACGCTCCACTCTGGAC 60.375 63.158 0.00 0.00 42.67 4.02
646 681 2.592861 GCCAGAGCGCCATTAGGG 60.593 66.667 2.29 0.00 40.85 3.53
671 706 1.632948 GCCGAACTTCAGGTAACCGC 61.633 60.000 0.00 0.00 37.17 5.68
684 719 1.067060 GCCAAATGATAAGGGCCGAAC 59.933 52.381 0.00 0.00 40.55 3.95
738 774 9.617523 GAAATCCAAATTCATTACCATCCATTT 57.382 29.630 0.00 0.00 0.00 2.32
739 775 7.927629 CGAAATCCAAATTCATTACCATCCATT 59.072 33.333 0.00 0.00 0.00 3.16
741 777 6.605194 TCGAAATCCAAATTCATTACCATCCA 59.395 34.615 0.00 0.00 0.00 3.41
744 780 9.889128 AATTTCGAAATCCAAATTCATTACCAT 57.111 25.926 22.93 0.00 27.97 3.55
745 781 9.364989 GAATTTCGAAATCCAAATTCATTACCA 57.635 29.630 22.93 0.00 43.80 3.25
787 823 1.876664 TCGCAGAGAAGACGACAGG 59.123 57.895 0.00 0.00 0.00 4.00
2178 2840 6.509418 TTCAAGTGCAGTAAACTTCAAAGT 57.491 33.333 0.00 0.00 42.04 2.66
2199 2861 2.514803 ACCTGTGCACCCTAACAATTC 58.485 47.619 15.69 0.00 0.00 2.17
2302 2996 6.003950 CCCCTTCAGAAACTTCAATACAGAA 58.996 40.000 0.00 0.00 0.00 3.02
2515 4675 9.977762 CTTCCGTAAACTAATATAAAAGCGTTT 57.022 29.630 2.53 2.53 0.00 3.60
2516 4676 8.606602 CCTTCCGTAAACTAATATAAAAGCGTT 58.393 33.333 0.00 0.00 0.00 4.84
2517 4677 7.981225 TCCTTCCGTAAACTAATATAAAAGCGT 59.019 33.333 0.00 0.00 0.00 5.07
2518 4678 8.356533 TCCTTCCGTAAACTAATATAAAAGCG 57.643 34.615 0.00 0.00 0.00 4.68
2519 4679 9.322773 ACTCCTTCCGTAAACTAATATAAAAGC 57.677 33.333 0.00 0.00 0.00 3.51
2526 4686 9.553064 CTCTAGTACTCCTTCCGTAAACTAATA 57.447 37.037 0.00 0.00 0.00 0.98
2527 4687 8.270744 TCTCTAGTACTCCTTCCGTAAACTAAT 58.729 37.037 0.00 0.00 0.00 1.73
2528 4688 7.624549 TCTCTAGTACTCCTTCCGTAAACTAA 58.375 38.462 0.00 0.00 0.00 2.24
2529 4689 7.187824 TCTCTAGTACTCCTTCCGTAAACTA 57.812 40.000 0.00 0.00 0.00 2.24
2530 4690 6.059787 TCTCTAGTACTCCTTCCGTAAACT 57.940 41.667 0.00 0.00 0.00 2.66
2531 4691 6.749923 TTCTCTAGTACTCCTTCCGTAAAC 57.250 41.667 0.00 0.00 0.00 2.01
2532 4692 7.282675 CAGATTCTCTAGTACTCCTTCCGTAAA 59.717 40.741 0.00 0.00 0.00 2.01
2533 4693 6.766944 CAGATTCTCTAGTACTCCTTCCGTAA 59.233 42.308 0.00 0.00 0.00 3.18
2534 4694 6.289834 CAGATTCTCTAGTACTCCTTCCGTA 58.710 44.000 0.00 0.00 0.00 4.02
2535 4695 5.127491 CAGATTCTCTAGTACTCCTTCCGT 58.873 45.833 0.00 0.00 0.00 4.69
2536 4696 4.517453 CCAGATTCTCTAGTACTCCTTCCG 59.483 50.000 0.00 0.00 0.00 4.30
2537 4697 5.300792 CACCAGATTCTCTAGTACTCCTTCC 59.699 48.000 0.00 0.00 0.00 3.46
2538 4698 5.889289 ACACCAGATTCTCTAGTACTCCTTC 59.111 44.000 0.00 0.00 0.00 3.46
2539 4699 5.833340 ACACCAGATTCTCTAGTACTCCTT 58.167 41.667 0.00 0.00 0.00 3.36
2540 4700 5.192923 AGACACCAGATTCTCTAGTACTCCT 59.807 44.000 0.00 0.00 0.00 3.69
2541 4701 5.442391 AGACACCAGATTCTCTAGTACTCC 58.558 45.833 0.00 0.00 0.00 3.85
2542 4702 7.399245 AAAGACACCAGATTCTCTAGTACTC 57.601 40.000 0.00 0.00 0.00 2.59
2543 4703 7.233757 ACAAAAGACACCAGATTCTCTAGTACT 59.766 37.037 0.00 0.00 0.00 2.73
2544 4704 7.379750 ACAAAAGACACCAGATTCTCTAGTAC 58.620 38.462 0.00 0.00 0.00 2.73
2545 4705 7.540474 ACAAAAGACACCAGATTCTCTAGTA 57.460 36.000 0.00 0.00 0.00 1.82
2546 4706 6.426646 ACAAAAGACACCAGATTCTCTAGT 57.573 37.500 0.00 0.00 0.00 2.57
2547 4707 6.931281 TCAACAAAAGACACCAGATTCTCTAG 59.069 38.462 0.00 0.00 0.00 2.43
2548 4708 6.826668 TCAACAAAAGACACCAGATTCTCTA 58.173 36.000 0.00 0.00 0.00 2.43
2563 4723 4.044336 TGTCCAGTGCAATCAACAAAAG 57.956 40.909 0.00 0.00 0.00 2.27
2636 4799 3.804325 ACGACAGTTGCACAGATATATGC 59.196 43.478 0.00 0.00 0.00 3.14
2657 4821 4.616181 AGTATTGCTCGGCATTTAACAC 57.384 40.909 0.00 0.00 38.76 3.32
2669 4833 7.565323 AGATTTGGATCAGAAAGTATTGCTC 57.435 36.000 0.00 0.00 34.60 4.26
2677 4842 5.182570 TCACAGCAAGATTTGGATCAGAAAG 59.817 40.000 0.00 0.00 34.60 2.62
2709 4874 9.773328 CAAGAACTTAAACACACATGTATATGG 57.227 33.333 0.00 0.00 38.45 2.74
2719 4904 9.431887 TCCATAGATACAAGAACTTAAACACAC 57.568 33.333 0.00 0.00 0.00 3.82
2765 4954 0.443869 CAATTGGTCGTCTTGCTCGG 59.556 55.000 0.00 0.00 0.00 4.63
2929 5189 7.521509 ACACGAGAAAGGAAAATATAAGACG 57.478 36.000 0.00 0.00 0.00 4.18
3094 5364 4.758773 ATTGGCAATAATCCAACCAAGG 57.241 40.909 11.81 0.00 45.35 3.61
3116 5386 7.990314 TGCTAGAGTGTATATGCATACCAAAAA 59.010 33.333 8.99 0.00 36.90 1.94
3236 5507 1.764134 ACTTGGGGTGTGTTTCGTCTA 59.236 47.619 0.00 0.00 0.00 2.59
3334 5605 5.678132 TGTGACTGAACATGATTCAACAG 57.322 39.130 0.00 0.00 0.00 3.16
3557 5828 5.586877 TGGGTCAAGTTGGTACTAGAGTAT 58.413 41.667 2.34 0.00 33.17 2.12
3610 5891 0.696501 TTGGGTTAAGTCAGAGGCCC 59.303 55.000 0.00 0.00 36.73 5.80


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

AutoCloner maintained by Alex Coulton.