Multiple sequence alignment - TraesCS2A01G315800

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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 TraesCS2A01G315800 chr2A 100.000 3978 0 0 1 3978 541774873 541778850 0.000000e+00 7347.0
1 TraesCS2A01G315800 chr2A 93.103 261 18 0 1980 2240 540849099 540848839 2.240000e-102 383.0
2 TraesCS2A01G315800 chr2A 90.732 205 19 0 1675 1879 540849415 540849211 1.410000e-69 274.0
3 TraesCS2A01G315800 chr2A 84.490 245 30 8 1052 1292 540850074 540849834 6.650000e-58 235.0
4 TraesCS2A01G315800 chr2D 90.501 3095 185 61 1 3029 403477336 403480387 0.000000e+00 3986.0
5 TraesCS2A01G315800 chr2D 92.481 266 19 1 1980 2245 403346825 403346561 2.900000e-101 379.0
6 TraesCS2A01G315800 chr2D 90.732 205 19 0 1675 1879 403347141 403346937 1.410000e-69 274.0
7 TraesCS2A01G315800 chr2D 84.490 245 30 8 1052 1292 403347824 403347584 6.650000e-58 235.0
8 TraesCS2A01G315800 chr2D 78.927 261 35 13 3494 3738 207902402 207902146 4.110000e-35 159.0
9 TraesCS2A01G315800 chr2D 81.000 200 24 4 3461 3648 54126941 54127138 3.200000e-31 147.0
10 TraesCS2A01G315800 chr2B 87.245 2352 162 66 1 2256 477572312 477574621 0.000000e+00 2555.0
11 TraesCS2A01G315800 chr2B 91.568 842 51 13 2278 3110 477574671 477575501 0.000000e+00 1144.0
12 TraesCS2A01G315800 chr2B 84.870 575 68 13 1675 2245 477529207 477528648 2.680000e-156 562.0
13 TraesCS2A01G315800 chr2B 83.919 541 45 12 3449 3977 78092110 78092620 2.780000e-131 479.0
14 TraesCS2A01G315800 chr2B 92.857 182 11 2 3274 3453 594834053 594833872 3.050000e-66 263.0
15 TraesCS2A01G315800 chr2B 85.366 246 26 10 1052 1292 477529845 477529605 3.070000e-61 246.0
16 TraesCS2A01G315800 chr2B 82.781 151 13 7 3494 3632 76900982 76900833 5.400000e-24 122.0
17 TraesCS2A01G315800 chr2B 82.432 148 13 7 3494 3629 47203457 47203603 2.510000e-22 117.0
18 TraesCS2A01G315800 chr2B 92.857 42 3 0 3067 3108 476463612 476463571 1.190000e-05 62.1
19 TraesCS2A01G315800 chr1B 83.239 883 95 21 3112 3977 645897166 645898012 0.000000e+00 761.0
20 TraesCS2A01G315800 chr1B 79.934 608 96 15 3233 3818 129514166 129514769 1.320000e-114 424.0
21 TraesCS2A01G315800 chr4A 88.991 545 44 9 3449 3977 34712096 34711552 0.000000e+00 660.0
22 TraesCS2A01G315800 chr4A 79.125 800 127 32 1106 1888 75215105 75214329 2.120000e-142 516.0
23 TraesCS2A01G315800 chr4A 91.954 261 19 2 1979 2238 75214244 75213985 8.120000e-97 364.0
24 TraesCS2A01G315800 chr4A 90.667 225 19 2 1670 1893 574870428 574870205 8.360000e-77 298.0
25 TraesCS2A01G315800 chr4A 77.736 530 86 21 1385 1893 641451581 641452099 3.010000e-76 296.0
26 TraesCS2A01G315800 chr4A 89.840 187 19 0 1106 1292 574872596 574872410 1.430000e-59 241.0
27 TraesCS2A01G315800 chr4A 88.144 194 23 0 1099 1292 641451293 641451486 8.600000e-57 231.0
28 TraesCS2A01G315800 chr4D 78.947 798 130 31 1106 1884 393635986 393636764 3.550000e-140 508.0
29 TraesCS2A01G315800 chr4D 92.720 261 17 2 1979 2238 393636858 393637117 3.750000e-100 375.0
30 TraesCS2A01G315800 chr4D 91.538 260 20 2 1979 2237 28839749 28840007 1.360000e-94 357.0
31 TraesCS2A01G315800 chr4D 93.401 197 13 0 1673 1869 28839448 28839644 3.890000e-75 292.0
32 TraesCS2A01G315800 chr4D 81.188 404 34 16 3449 3838 483527203 483527578 1.810000e-73 287.0
33 TraesCS2A01G315800 chr4D 93.855 179 10 1 3283 3461 379253482 379253305 6.550000e-68 268.0
34 TraesCS2A01G315800 chr4D 89.305 187 19 1 1106 1292 28560251 28560436 2.390000e-57 233.0
35 TraesCS2A01G315800 chr4D 88.770 187 21 0 1106 1292 28837100 28837286 3.090000e-56 230.0
36 TraesCS2A01G315800 chr4D 89.286 140 15 0 3702 3841 173107452 173107591 4.090000e-40 176.0
37 TraesCS2A01G315800 chr4D 82.564 195 19 5 3449 3629 173095327 173095520 1.480000e-34 158.0
38 TraesCS2A01G315800 chr4D 81.818 77 14 0 3032 3108 287283020 287283096 9.230000e-07 65.8
39 TraesCS2A01G315800 chr5B 83.670 545 42 15 3449 3977 526441294 526441807 1.670000e-128 470.0
40 TraesCS2A01G315800 chr5B 79.840 501 84 13 1385 1883 670067633 670067148 2.270000e-92 350.0
41 TraesCS2A01G315800 chr5B 87.895 190 23 0 1105 1294 670067931 670067742 1.440000e-54 224.0
42 TraesCS2A01G315800 chr5B 85.795 176 22 3 3114 3288 526441122 526441295 2.440000e-42 183.0
43 TraesCS2A01G315800 chr4B 92.337 261 18 2 1979 2238 483334259 483334000 1.750000e-98 370.0
44 TraesCS2A01G315800 chr4B 93.467 199 13 0 1671 1869 41012540 41012738 3.010000e-76 296.0
45 TraesCS2A01G315800 chr4B 89.498 219 23 0 1675 1893 483334557 483334339 1.090000e-70 278.0
46 TraesCS2A01G315800 chr4B 90.374 187 18 0 1106 1292 41010060 41010246 3.070000e-61 246.0
47 TraesCS2A01G315800 chr4B 85.075 201 26 4 3287 3484 54367162 54366963 6.740000e-48 202.0
48 TraesCS2A01G315800 chr5D 79.412 544 86 17 3450 3975 174317417 174317952 1.050000e-95 361.0
49 TraesCS2A01G315800 chr5D 81.624 468 48 12 3449 3902 474552879 474552436 1.760000e-93 353.0
50 TraesCS2A01G315800 chr5D 78.702 493 81 17 1105 1594 530826179 530825708 1.390000e-79 307.0
51 TraesCS2A01G315800 chr5D 80.982 163 24 5 3114 3276 439021713 439021868 5.400000e-24 122.0
52 TraesCS2A01G315800 chr3D 80.384 469 51 15 3449 3902 599452947 599452505 6.420000e-83 318.0
53 TraesCS2A01G315800 chr3D 89.062 192 21 0 1101 1292 7590678 7590869 5.140000e-59 239.0
54 TraesCS2A01G315800 chr3D 77.103 214 34 9 3495 3695 591375793 591375582 4.200000e-20 110.0
55 TraesCS2A01G315800 chr3D 77.500 200 28 7 3495 3679 268070932 268071129 1.960000e-18 104.0
56 TraesCS2A01G315800 chr6D 82.108 408 34 14 3449 3841 56563310 56563693 2.980000e-81 313.0
57 TraesCS2A01G315800 chr5A 81.281 406 38 14 3449 3841 617908676 617909056 1.080000e-75 294.0
58 TraesCS2A01G315800 chr5A 93.750 176 9 2 3283 3458 385268911 385268738 3.050000e-66 263.0
59 TraesCS2A01G315800 chr7D 79.325 474 51 21 3449 3902 65662641 65663087 5.030000e-74 289.0
60 TraesCS2A01G315800 chr7D 79.717 424 45 18 3495 3902 36803009 36802611 6.550000e-68 268.0
61 TraesCS2A01G315800 chr3B 94.767 172 7 2 3287 3457 550322776 550322946 2.360000e-67 267.0
62 TraesCS2A01G315800 chr3B 92.857 182 11 2 3270 3450 655849601 655849421 3.050000e-66 263.0
63 TraesCS2A01G315800 chr3B 89.947 189 19 0 1104 1292 9914577 9914765 1.100000e-60 244.0
64 TraesCS2A01G315800 chr3B 80.124 322 43 9 3453 3757 545675001 545674684 1.860000e-53 220.0
65 TraesCS2A01G315800 chr3B 75.882 170 30 10 3287 3450 54082911 54083075 4.260000e-10 76.8
66 TraesCS2A01G315800 chr3B 75.294 170 31 10 3287 3450 54158622 54158786 1.980000e-08 71.3
67 TraesCS2A01G315800 chr6A 94.220 173 10 0 3287 3459 346594860 346594688 8.480000e-67 265.0
68 TraesCS2A01G315800 chr6A 79.567 323 51 5 3449 3757 49736282 49736603 2.410000e-52 217.0
69 TraesCS2A01G315800 chr6A 76.471 255 43 11 3457 3695 8445009 8444756 5.400000e-24 122.0
70 TraesCS2A01G315800 chr7A 94.220 173 9 1 3287 3458 48767349 48767521 3.050000e-66 263.0
71 TraesCS2A01G315800 chr7A 87.245 196 22 3 3287 3481 290741296 290741489 1.860000e-53 220.0
72 TraesCS2A01G315800 chr3A 89.305 187 20 0 1106 1292 12814991 12814805 6.650000e-58 235.0
73 TraesCS2A01G315800 chr3A 82.558 86 11 3 3024 3108 38116452 38116370 5.510000e-09 73.1
74 TraesCS2A01G315800 chr6B 80.741 135 17 6 267 396 638509491 638509361 3.270000e-16 97.1


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 TraesCS2A01G315800 chr2A 541774873 541778850 3977 False 7347.000000 7347 100.000000 1 3978 1 chr2A.!!$F1 3977
1 TraesCS2A01G315800 chr2A 540848839 540850074 1235 True 297.333333 383 89.441667 1052 2240 3 chr2A.!!$R1 1188
2 TraesCS2A01G315800 chr2D 403477336 403480387 3051 False 3986.000000 3986 90.501000 1 3029 1 chr2D.!!$F2 3028
3 TraesCS2A01G315800 chr2D 403346561 403347824 1263 True 296.000000 379 89.234333 1052 2245 3 chr2D.!!$R2 1193
4 TraesCS2A01G315800 chr2B 477572312 477575501 3189 False 1849.500000 2555 89.406500 1 3110 2 chr2B.!!$F3 3109
5 TraesCS2A01G315800 chr2B 78092110 78092620 510 False 479.000000 479 83.919000 3449 3977 1 chr2B.!!$F2 528
6 TraesCS2A01G315800 chr2B 477528648 477529845 1197 True 404.000000 562 85.118000 1052 2245 2 chr2B.!!$R4 1193
7 TraesCS2A01G315800 chr1B 645897166 645898012 846 False 761.000000 761 83.239000 3112 3977 1 chr1B.!!$F2 865
8 TraesCS2A01G315800 chr1B 129514166 129514769 603 False 424.000000 424 79.934000 3233 3818 1 chr1B.!!$F1 585
9 TraesCS2A01G315800 chr4A 34711552 34712096 544 True 660.000000 660 88.991000 3449 3977 1 chr4A.!!$R1 528
10 TraesCS2A01G315800 chr4A 75213985 75215105 1120 True 440.000000 516 85.539500 1106 2238 2 chr4A.!!$R2 1132
11 TraesCS2A01G315800 chr4A 574870205 574872596 2391 True 269.500000 298 90.253500 1106 1893 2 chr4A.!!$R3 787
12 TraesCS2A01G315800 chr4A 641451293 641452099 806 False 263.500000 296 82.940000 1099 1893 2 chr4A.!!$F1 794
13 TraesCS2A01G315800 chr4D 393635986 393637117 1131 False 441.500000 508 85.833500 1106 2238 2 chr4D.!!$F7 1132
14 TraesCS2A01G315800 chr4D 28837100 28840007 2907 False 293.000000 357 91.236333 1106 2237 3 chr4D.!!$F6 1131
15 TraesCS2A01G315800 chr5B 526441122 526441807 685 False 326.500000 470 84.732500 3114 3977 2 chr5B.!!$F1 863
16 TraesCS2A01G315800 chr5B 670067148 670067931 783 True 287.000000 350 83.867500 1105 1883 2 chr5B.!!$R1 778
17 TraesCS2A01G315800 chr4B 483334000 483334557 557 True 324.000000 370 90.917500 1675 2238 2 chr4B.!!$R2 563
18 TraesCS2A01G315800 chr4B 41010060 41012738 2678 False 271.000000 296 91.920500 1106 1869 2 chr4B.!!$F1 763
19 TraesCS2A01G315800 chr5D 174317417 174317952 535 False 361.000000 361 79.412000 3450 3975 1 chr5D.!!$F1 525

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
569 635 0.108585 TTTGAGCTCGGGCAGAAACT 59.891 50.0 11.4 0.0 41.70 2.66 F
587 654 0.179000 CTCCCAAGTCCCATTCTCCG 59.821 60.0 0.0 0.0 0.00 4.63 F
1904 4786 0.465460 AACAAGGTCGGCTTGCTCAA 60.465 50.0 0.0 0.0 35.39 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 5043 0.106769 TGTTGCGCCATATCACCCAT 60.107 50.000 4.18 0.0 0.00 4.00 R
2471 5419 1.367665 GCATGCGGCGATACGAAAC 60.368 57.895 12.98 0.0 35.47 2.78 R
3220 6177 0.606401 CTTTCTCCACCACCACGCAT 60.606 55.000 0.00 0.0 0.00 4.73 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
38 40 8.680001 AGTGTTTTTAAATAGTTATTAGCGGGG 58.320 33.333 0.00 0.00 0.00 5.73
39 41 7.916977 GTGTTTTTAAATAGTTATTAGCGGGGG 59.083 37.037 0.00 0.00 0.00 5.40
40 42 6.638096 TTTTAAATAGTTATTAGCGGGGGC 57.362 37.500 0.00 0.00 0.00 5.80
48 50 1.657804 ATTAGCGGGGGCTAGCTATT 58.342 50.000 15.72 0.00 44.29 1.73
51 53 0.685660 AGCGGGGGCTAGCTATTTAC 59.314 55.000 15.72 0.40 42.60 2.01
54 56 2.767505 CGGGGGCTAGCTATTTACTTG 58.232 52.381 15.72 0.00 0.00 3.16
80 82 6.317857 AGAAGATAAATTGAAGACGCAAAGC 58.682 36.000 0.00 0.00 0.00 3.51
86 88 1.953559 TGAAGACGCAAAGCTGAAGT 58.046 45.000 0.00 0.00 0.00 3.01
123 126 7.810766 ATACAAAATTATTTTCCGCACTGTG 57.189 32.000 2.76 2.76 0.00 3.66
135 138 2.548178 CACTGTGTGCTTAGGCCAG 58.452 57.895 5.01 0.00 37.74 4.85
137 140 0.474184 ACTGTGTGCTTAGGCCAGTT 59.526 50.000 5.01 0.00 35.87 3.16
145 148 2.580783 TGCTTAGGCCAGTTTTAGGGAT 59.419 45.455 5.01 0.00 37.74 3.85
147 150 3.381590 GCTTAGGCCAGTTTTAGGGATTG 59.618 47.826 5.01 0.00 0.00 2.67
148 151 1.852633 AGGCCAGTTTTAGGGATTGC 58.147 50.000 5.01 0.00 0.00 3.56
149 152 1.359130 AGGCCAGTTTTAGGGATTGCT 59.641 47.619 5.01 0.00 0.00 3.91
151 154 2.446435 GCCAGTTTTAGGGATTGCTCA 58.554 47.619 0.00 0.00 0.00 4.26
152 155 2.424956 GCCAGTTTTAGGGATTGCTCAG 59.575 50.000 0.00 0.00 0.00 3.35
153 156 3.873801 GCCAGTTTTAGGGATTGCTCAGA 60.874 47.826 0.00 0.00 0.00 3.27
154 157 3.691609 CCAGTTTTAGGGATTGCTCAGAC 59.308 47.826 0.00 0.00 0.00 3.51
156 159 5.338381 CCAGTTTTAGGGATTGCTCAGACTA 60.338 44.000 0.00 0.00 0.00 2.59
163 166 3.561313 GGGATTGCTCAGACTAAACCCAA 60.561 47.826 0.00 0.00 36.66 4.12
170 173 4.734917 CTCAGACTAAACCCAAGTACGAG 58.265 47.826 0.00 0.00 0.00 4.18
178 181 2.595238 ACCCAAGTACGAGAACAGACT 58.405 47.619 0.00 0.00 0.00 3.24
184 187 7.039504 ACCCAAGTACGAGAACAGACTAATAAA 60.040 37.037 0.00 0.00 0.00 1.40
186 189 7.811236 CCAAGTACGAGAACAGACTAATAAACA 59.189 37.037 0.00 0.00 0.00 2.83
187 190 8.636843 CAAGTACGAGAACAGACTAATAAACAC 58.363 37.037 0.00 0.00 0.00 3.32
197 200 5.812642 CAGACTAATAAACACATTCTCCGCT 59.187 40.000 0.00 0.00 0.00 5.52
206 209 4.196971 ACACATTCTCCGCTAAAATACCC 58.803 43.478 0.00 0.00 0.00 3.69
232 241 4.889832 AATTCTAAGCTCAAATGCTCCG 57.110 40.909 0.00 0.00 43.24 4.63
233 242 1.656652 TCTAAGCTCAAATGCTCCGC 58.343 50.000 0.00 0.00 43.24 5.54
298 326 9.986833 AACAATAAACATTGCTTTGTTTTCTTC 57.013 25.926 18.33 0.00 45.14 2.87
299 327 9.160496 ACAATAAACATTGCTTTGTTTTCTTCA 57.840 25.926 18.33 5.37 45.14 3.02
303 331 6.849588 ACATTGCTTTGTTTTCTTCATTCC 57.150 33.333 0.00 0.00 0.00 3.01
304 332 6.585416 ACATTGCTTTGTTTTCTTCATTCCT 58.415 32.000 0.00 0.00 0.00 3.36
305 333 6.480981 ACATTGCTTTGTTTTCTTCATTCCTG 59.519 34.615 0.00 0.00 0.00 3.86
306 334 5.850557 TGCTTTGTTTTCTTCATTCCTGA 57.149 34.783 0.00 0.00 0.00 3.86
307 335 6.219417 TGCTTTGTTTTCTTCATTCCTGAA 57.781 33.333 0.00 0.00 39.07 3.02
308 336 6.638610 TGCTTTGTTTTCTTCATTCCTGAAA 58.361 32.000 0.00 0.00 40.78 2.69
309 337 7.102346 TGCTTTGTTTTCTTCATTCCTGAAAA 58.898 30.769 0.00 0.00 40.78 2.29
310 338 7.769970 TGCTTTGTTTTCTTCATTCCTGAAAAT 59.230 29.630 0.00 0.00 40.78 1.82
311 339 8.615211 GCTTTGTTTTCTTCATTCCTGAAAATT 58.385 29.630 0.00 0.00 40.78 1.82
315 343 8.816144 TGTTTTCTTCATTCCTGAAAATTTTCG 58.184 29.630 22.51 17.19 40.78 3.46
316 344 8.817100 GTTTTCTTCATTCCTGAAAATTTTCGT 58.183 29.630 22.51 6.60 40.78 3.85
327 355 8.306038 TCCTGAAAATTTTCGTGATGAAATCAT 58.694 29.630 22.51 0.00 45.62 2.45
348 376 2.543777 TTCGTGGAGGTCTGGAAAAG 57.456 50.000 0.00 0.00 0.00 2.27
351 388 2.436542 TCGTGGAGGTCTGGAAAAGAAA 59.563 45.455 0.00 0.00 36.40 2.52
352 389 2.548480 CGTGGAGGTCTGGAAAAGAAAC 59.452 50.000 0.00 0.00 36.40 2.78
353 390 3.744530 CGTGGAGGTCTGGAAAAGAAACT 60.745 47.826 0.00 0.00 36.40 2.66
354 391 4.502604 CGTGGAGGTCTGGAAAAGAAACTA 60.503 45.833 0.00 0.00 36.40 2.24
355 392 5.374071 GTGGAGGTCTGGAAAAGAAACTAA 58.626 41.667 0.00 0.00 36.40 2.24
356 393 5.826208 GTGGAGGTCTGGAAAAGAAACTAAA 59.174 40.000 0.00 0.00 36.40 1.85
357 394 6.490381 GTGGAGGTCTGGAAAAGAAACTAAAT 59.510 38.462 0.00 0.00 36.40 1.40
358 395 6.490040 TGGAGGTCTGGAAAAGAAACTAAATG 59.510 38.462 0.00 0.00 36.40 2.32
365 402 9.621629 TCTGGAAAAGAAACTAAATGAACACTA 57.378 29.630 0.00 0.00 29.54 2.74
378 415 6.991485 AATGAACACTACAAAATGCTTTCG 57.009 33.333 0.00 0.00 0.00 3.46
401 438 6.072948 TCGAAAATAAGTTTTTGAGGCATCGA 60.073 34.615 0.00 0.00 40.91 3.59
404 441 8.831715 AAAATAAGTTTTTGAGGCATCGATTT 57.168 26.923 0.00 0.00 33.89 2.17
405 442 8.466086 AAATAAGTTTTTGAGGCATCGATTTC 57.534 30.769 0.00 0.00 0.00 2.17
406 443 4.440839 AGTTTTTGAGGCATCGATTTCC 57.559 40.909 0.00 0.00 0.00 3.13
414 451 4.082787 TGAGGCATCGATTTCCTTTGTTTC 60.083 41.667 15.09 4.90 0.00 2.78
430 467 2.028112 TGTTTCCGCTCAGAGCATTAGT 60.028 45.455 22.49 0.00 42.58 2.24
432 469 3.717400 TTCCGCTCAGAGCATTAGTAG 57.283 47.619 22.49 3.82 42.58 2.57
434 471 3.816994 TCCGCTCAGAGCATTAGTAGTA 58.183 45.455 22.49 0.00 42.58 1.82
436 473 4.216472 TCCGCTCAGAGCATTAGTAGTATG 59.784 45.833 22.49 1.12 42.58 2.39
476 514 6.435430 TGCATGTATGTAGAACATTCAACC 57.565 37.500 3.90 0.38 38.92 3.77
493 531 3.937706 TCAACCATGTTTGTTGCCAAAAG 59.062 39.130 2.68 0.00 41.99 2.27
496 534 4.583871 ACCATGTTTGTTGCCAAAAGAAA 58.416 34.783 0.00 0.00 41.99 2.52
497 535 5.192176 ACCATGTTTGTTGCCAAAAGAAAT 58.808 33.333 0.00 0.00 41.99 2.17
499 538 6.482973 ACCATGTTTGTTGCCAAAAGAAATAG 59.517 34.615 0.00 0.00 41.99 1.73
505 544 9.272901 GTTTGTTGCCAAAAGAAATAGTTTTTC 57.727 29.630 0.00 0.00 41.99 2.29
548 614 5.811399 TTATTTTGCTATTCACGAGGTGG 57.189 39.130 0.00 0.00 33.87 4.61
549 615 2.851263 TTTGCTATTCACGAGGTGGT 57.149 45.000 0.00 0.00 33.87 4.16
560 626 2.544726 GAGGTGGTTTTGAGCTCGG 58.455 57.895 9.64 0.00 0.00 4.63
562 628 2.626780 GGTGGTTTTGAGCTCGGGC 61.627 63.158 9.64 0.00 39.06 6.13
563 629 1.896660 GTGGTTTTGAGCTCGGGCA 60.897 57.895 11.40 0.00 41.70 5.36
564 630 1.600636 TGGTTTTGAGCTCGGGCAG 60.601 57.895 11.40 0.00 41.70 4.85
566 632 0.889186 GGTTTTGAGCTCGGGCAGAA 60.889 55.000 11.40 0.00 41.70 3.02
568 634 0.951558 TTTTGAGCTCGGGCAGAAAC 59.048 50.000 11.40 0.00 41.70 2.78
569 635 0.108585 TTTGAGCTCGGGCAGAAACT 59.891 50.000 11.40 0.00 41.70 2.66
574 641 1.374947 CTCGGGCAGAAACTCCCAA 59.625 57.895 0.00 0.00 42.75 4.12
587 654 0.179000 CTCCCAAGTCCCATTCTCCG 59.821 60.000 0.00 0.00 0.00 4.63
627 694 0.521735 GTGAATCGTGACAAAGCCCC 59.478 55.000 0.00 0.00 0.00 5.80
657 724 1.064654 GAGGATCGAACAAATGGCAGC 59.935 52.381 0.00 0.00 0.00 5.25
784 854 4.222114 CCACAAAAAGAATCGAAGCTGAC 58.778 43.478 0.00 0.00 0.00 3.51
949 1026 2.215196 TGGTTCGTGTTGCCTAAGAAC 58.785 47.619 0.00 0.00 40.09 3.01
994 1075 2.360726 TCGCCTGACACGGAGCTA 60.361 61.111 0.00 0.00 0.00 3.32
1347 4117 1.136147 CCGTCTGACCCTTCGTACG 59.864 63.158 9.53 9.53 0.00 3.67
1432 4241 2.735478 CTGTTCAACGCGCCGGTA 60.735 61.111 5.73 0.00 0.00 4.02
1621 4484 0.791422 TAACGCGCGTACATTTGCTT 59.209 45.000 37.93 19.64 0.00 3.91
1623 4486 1.131623 CGCGCGTACATTTGCTTCA 59.868 52.632 24.19 0.00 0.00 3.02
1627 4490 2.727607 GCGCGTACATTTGCTTCATCAA 60.728 45.455 8.43 0.00 0.00 2.57
1628 4491 3.093574 CGCGTACATTTGCTTCATCAAG 58.906 45.455 0.00 0.00 0.00 3.02
1629 4492 3.424829 CGCGTACATTTGCTTCATCAAGT 60.425 43.478 0.00 0.00 31.45 3.16
1633 4496 6.402118 GCGTACATTTGCTTCATCAAGTAAGA 60.402 38.462 0.00 0.00 35.84 2.10
1636 4499 6.906659 ACATTTGCTTCATCAAGTAAGACAG 58.093 36.000 0.00 0.00 35.84 3.51
1638 4501 6.791887 TTTGCTTCATCAAGTAAGACAGAG 57.208 37.500 0.00 0.00 35.84 3.35
1647 4518 6.611613 TCAAGTAAGACAGAGTTGGATCAT 57.388 37.500 0.00 0.00 0.00 2.45
1894 4776 1.217882 AGAACAAGCGAACAAGGTCG 58.782 50.000 2.62 2.62 43.98 4.79
1904 4786 0.465460 AACAAGGTCGGCTTGCTCAA 60.465 50.000 0.00 0.00 35.39 3.02
1949 4844 7.981225 CGGAAATTTCATCAATCCCTGTTTTAT 59.019 33.333 19.49 0.00 0.00 1.40
1951 4846 9.874205 GAAATTTCATCAATCCCTGTTTTATGA 57.126 29.630 13.40 0.00 0.00 2.15
1953 4848 9.657419 AATTTCATCAATCCCTGTTTTATGAAC 57.343 29.630 0.00 0.00 33.08 3.18
1954 4849 8.421249 TTTCATCAATCCCTGTTTTATGAACT 57.579 30.769 0.00 0.00 33.08 3.01
1957 4852 9.699410 TCATCAATCCCTGTTTTATGAACTTAT 57.301 29.630 0.00 0.00 0.00 1.73
2159 5070 0.546122 TATGGCGCAACAAGGAGGAT 59.454 50.000 10.83 0.00 0.00 3.24
2249 5160 3.383185 TCTCCAAAGGCACGAACATTTTT 59.617 39.130 0.00 0.00 0.00 1.94
2297 5241 5.884792 ACAGACAGAATCCCTGATTTGATTC 59.115 40.000 4.48 4.48 45.78 2.52
2369 5313 1.031571 GGTCCAGCCAAATCATCGCA 61.032 55.000 0.00 0.00 37.17 5.10
2416 5360 6.496338 AGGTTTCGAGGTACAAAATTCATC 57.504 37.500 0.00 0.00 0.00 2.92
2421 5365 6.480524 TCGAGGTACAAAATTCATCAACAG 57.519 37.500 0.00 0.00 0.00 3.16
2429 5373 7.294017 ACAAAATTCATCAACAGACCAATCT 57.706 32.000 0.00 0.00 34.57 2.40
2434 5378 4.582869 TCATCAACAGACCAATCTTCAGG 58.417 43.478 0.00 0.00 30.42 3.86
2435 5379 2.783135 TCAACAGACCAATCTTCAGGC 58.217 47.619 0.00 0.00 30.42 4.85
2471 5419 5.405873 CAGAGCACAGAATAGCAGTCATATG 59.594 44.000 0.00 0.00 0.00 1.78
2484 5441 3.119628 CAGTCATATGTTTCGTATCGCCG 59.880 47.826 1.90 0.00 0.00 6.46
2485 5442 2.055838 TCATATGTTTCGTATCGCCGC 58.944 47.619 1.90 0.00 0.00 6.53
2533 5490 3.381333 CTGCATGGAGAGCGCCAGA 62.381 63.158 8.85 0.00 42.15 3.86
2599 5556 3.936203 AAGGAAGACGGCGTGCCA 61.936 61.111 21.19 0.00 35.37 4.92
2866 5823 3.201494 CTCACCATCGAGCTCGGT 58.799 61.111 33.98 27.09 40.29 4.69
2962 5919 1.866925 GCTTGTTTCCGGGAAGACG 59.133 57.895 9.80 0.00 0.00 4.18
2977 5934 1.045407 AGACGAAGGGTGTGTGCTAA 58.955 50.000 0.00 0.00 0.00 3.09
3029 5986 7.228507 TGCCGATTGTGCTACAGAATAAATTAT 59.771 33.333 0.00 0.00 27.44 1.28
3030 5987 8.717821 GCCGATTGTGCTACAGAATAAATTATA 58.282 33.333 0.00 0.00 27.44 0.98
3110 6067 8.814733 TTGCAAAACGTTCTTATATTATGACG 57.185 30.769 0.00 0.00 0.00 4.35
3125 6082 0.032130 TGACGTCAAGGACTGTGCTC 59.968 55.000 17.62 0.00 0.00 4.26
3132 6089 1.071385 CAAGGACTGTGCTCACTTCCT 59.929 52.381 14.21 14.21 42.52 3.36
3136 6093 2.300437 GGACTGTGCTCACTTCCTAACT 59.700 50.000 11.56 0.00 33.84 2.24
3141 6098 1.623811 TGCTCACTTCCTAACTGGTCC 59.376 52.381 0.00 0.00 37.07 4.46
3145 6102 3.170717 TCACTTCCTAACTGGTCCGAAT 58.829 45.455 0.00 0.00 37.07 3.34
3159 6116 7.110155 ACTGGTCCGAATATAAACAACAGATT 58.890 34.615 0.00 0.00 0.00 2.40
3169 6126 6.877611 ATAAACAACAGATTCGAACACCTT 57.122 33.333 0.00 0.00 0.00 3.50
3170 6127 4.813296 AACAACAGATTCGAACACCTTC 57.187 40.909 0.00 0.00 0.00 3.46
3171 6128 3.139077 ACAACAGATTCGAACACCTTCC 58.861 45.455 0.00 0.00 0.00 3.46
3187 6144 4.079787 CACCTTCCCCTTCTTATCCAATCA 60.080 45.833 0.00 0.00 0.00 2.57
3202 6159 1.996898 CAATCACACATGCATGCAACC 59.003 47.619 26.68 0.00 0.00 3.77
3209 6166 3.691118 ACACATGCATGCAACCTTACTAG 59.309 43.478 26.68 9.46 0.00 2.57
3215 6172 4.576053 TGCATGCAACCTTACTAGCTAATG 59.424 41.667 20.30 0.00 0.00 1.90
3216 6173 4.576463 GCATGCAACCTTACTAGCTAATGT 59.424 41.667 14.21 0.00 0.00 2.71
3219 6176 4.469945 TGCAACCTTACTAGCTAATGTCCT 59.530 41.667 0.00 0.00 0.00 3.85
3220 6177 5.659525 TGCAACCTTACTAGCTAATGTCCTA 59.340 40.000 0.00 0.00 0.00 2.94
3223 6180 6.347859 ACCTTACTAGCTAATGTCCTATGC 57.652 41.667 0.00 0.00 0.00 3.14
3227 6184 2.533266 AGCTAATGTCCTATGCGTGG 57.467 50.000 0.00 0.00 0.00 4.94
3236 6193 1.613317 CCTATGCGTGGTGGTGGAGA 61.613 60.000 0.00 0.00 0.00 3.71
3239 6196 0.606401 ATGCGTGGTGGTGGAGAAAG 60.606 55.000 0.00 0.00 0.00 2.62
3293 6251 2.372264 CATGCATGCAAACTACTCCCT 58.628 47.619 26.68 0.00 0.00 4.20
3294 6252 2.584835 TGCATGCAAACTACTCCCTT 57.415 45.000 20.30 0.00 0.00 3.95
3299 6257 3.202829 TGCAAACTACTCCCTTCGTTT 57.797 42.857 0.00 0.00 0.00 3.60
3316 6274 9.556030 CCCTTCGTTTCTAAATATTTGTCTTTC 57.444 33.333 11.05 0.00 0.00 2.62
3333 6291 8.924511 TTGTCTTTCTAGAGATTTCAAATGGT 57.075 30.769 0.00 0.00 0.00 3.55
3357 6316 8.186821 GGTTACCACATACGGATGTATATAGAC 58.813 40.741 14.23 7.65 44.82 2.59
3393 6352 7.549134 AGTGTATATTCACTCATTTTGCTTCGA 59.451 33.333 9.03 0.00 44.07 3.71
3409 6368 8.766000 TTTGCTTCGAATGTAGTCACTTATTA 57.234 30.769 0.00 0.00 0.00 0.98
3413 6372 9.474249 GCTTCGAATGTAGTCACTTATTAAAAC 57.526 33.333 0.00 0.00 0.00 2.43
3542 6503 2.093625 CGTCGCTCCGATTCAAAATTCA 59.906 45.455 0.00 0.00 38.42 2.57
3625 6599 5.622346 TTTTTCAGGCCAAAAGTTACCAT 57.378 34.783 5.01 0.00 0.00 3.55
3651 6625 6.712547 GCCTAGACCAAATAAACTATCATGCT 59.287 38.462 0.00 0.00 0.00 3.79
3695 6673 5.163258 TGGTTTTACACTAAAGTTACCGGGA 60.163 40.000 6.32 0.00 31.70 5.14
3783 6770 2.956333 TCCACCGTCTATGATCGATGTT 59.044 45.455 0.54 0.00 0.00 2.71
3796 6783 1.907807 GATGTTGTGCCTGGGCCAA 60.908 57.895 8.04 9.75 41.09 4.52
3854 6841 9.474920 CTCACTTATAAAAATGGAAACTTGCAA 57.525 29.630 0.00 0.00 30.51 4.08
3866 6853 2.280524 TTGCAAGTCGTGTCGGGG 60.281 61.111 0.00 0.00 0.00 5.73
3882 6870 1.405121 CGGGGCAGACCTGTTTAGTAC 60.405 57.143 0.00 0.00 41.03 2.73
3891 6879 1.134907 CCTGTTTAGTACGTGCCGGAT 60.135 52.381 5.05 0.00 0.00 4.18
3914 6902 1.517361 CAGTGCATGAGCCGACCTA 59.483 57.895 0.00 0.00 41.13 3.08
3940 6928 4.219944 GGCCACGTATGATTAGGTCTATGA 59.780 45.833 0.00 0.00 0.00 2.15
3977 6965 7.551262 ACCATGACATTTACGCTGAAGTTATTA 59.449 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 28 0.685660 AGCTAGCCCCCGCTAATAAC 59.314 55.000 12.13 0.00 46.89 1.89
30 32 1.430992 AAATAGCTAGCCCCCGCTAA 58.569 50.000 12.13 0.00 46.89 3.09
51 53 7.963981 TGCGTCTTCAATTTATCTTCTACAAG 58.036 34.615 0.00 0.00 0.00 3.16
54 56 7.426743 GCTTTGCGTCTTCAATTTATCTTCTAC 59.573 37.037 0.00 0.00 0.00 2.59
73 75 6.363088 TGAAAATTAATCACTTCAGCTTTGCG 59.637 34.615 0.00 0.00 0.00 4.85
102 104 5.903703 CACACAGTGCGGAAAATAATTTTG 58.096 37.500 0.00 0.00 31.94 2.44
123 126 2.092323 CCCTAAAACTGGCCTAAGCAC 58.908 52.381 3.32 0.00 42.56 4.40
135 138 6.127980 GGTTTAGTCTGAGCAATCCCTAAAAC 60.128 42.308 0.00 0.00 0.00 2.43
137 140 5.497474 GGTTTAGTCTGAGCAATCCCTAAA 58.503 41.667 0.00 0.00 0.00 1.85
145 148 3.857157 ACTTGGGTTTAGTCTGAGCAA 57.143 42.857 0.00 0.00 0.00 3.91
147 150 3.057033 TCGTACTTGGGTTTAGTCTGAGC 60.057 47.826 0.00 0.00 0.00 4.26
148 151 4.458295 TCTCGTACTTGGGTTTAGTCTGAG 59.542 45.833 0.00 0.00 32.53 3.35
149 152 4.401022 TCTCGTACTTGGGTTTAGTCTGA 58.599 43.478 0.00 0.00 0.00 3.27
151 154 4.586001 TGTTCTCGTACTTGGGTTTAGTCT 59.414 41.667 0.00 0.00 0.00 3.24
152 155 4.874970 TGTTCTCGTACTTGGGTTTAGTC 58.125 43.478 0.00 0.00 0.00 2.59
153 156 4.586001 TCTGTTCTCGTACTTGGGTTTAGT 59.414 41.667 0.00 0.00 0.00 2.24
154 157 4.922103 GTCTGTTCTCGTACTTGGGTTTAG 59.078 45.833 0.00 0.00 0.00 1.85
156 159 3.387050 AGTCTGTTCTCGTACTTGGGTTT 59.613 43.478 0.00 0.00 0.00 3.27
163 166 7.879070 TGTGTTTATTAGTCTGTTCTCGTACT 58.121 34.615 0.00 0.00 0.00 2.73
170 173 7.674240 GCGGAGAATGTGTTTATTAGTCTGTTC 60.674 40.741 0.00 0.00 0.00 3.18
184 187 4.080526 AGGGTATTTTAGCGGAGAATGTGT 60.081 41.667 0.00 0.00 0.00 3.72
186 189 4.772886 AGGGTATTTTAGCGGAGAATGT 57.227 40.909 0.00 0.00 0.00 2.71
187 190 5.368989 AGAAGGGTATTTTAGCGGAGAATG 58.631 41.667 0.00 0.00 0.00 2.67
203 206 6.319911 GCATTTGAGCTTAGAATTAGAAGGGT 59.680 38.462 0.00 0.00 0.00 4.34
206 209 7.518052 CGGAGCATTTGAGCTTAGAATTAGAAG 60.518 40.741 0.00 0.00 46.75 2.85
289 317 8.816144 CGAAAATTTTCAGGAATGAAGAAAACA 58.184 29.630 26.20 0.00 42.09 2.83
296 324 7.656412 TCATCACGAAAATTTTCAGGAATGAA 58.344 30.769 26.20 12.60 37.01 2.57
297 325 7.213216 TCATCACGAAAATTTTCAGGAATGA 57.787 32.000 26.20 22.72 37.01 2.57
298 326 7.872163 TTCATCACGAAAATTTTCAGGAATG 57.128 32.000 26.20 21.32 37.01 2.67
299 327 9.143631 GATTTCATCACGAAAATTTTCAGGAAT 57.856 29.630 26.20 16.58 46.48 3.01
300 328 8.140628 TGATTTCATCACGAAAATTTTCAGGAA 58.859 29.630 26.20 18.06 46.48 3.36
301 329 7.656412 TGATTTCATCACGAAAATTTTCAGGA 58.344 30.769 26.20 22.01 46.48 3.86
302 330 7.872163 TGATTTCATCACGAAAATTTTCAGG 57.128 32.000 26.20 18.30 46.48 3.86
307 335 9.787532 ACGAATATGATTTCATCACGAAAATTT 57.212 25.926 15.38 0.00 46.48 1.82
308 336 9.225201 CACGAATATGATTTCATCACGAAAATT 57.775 29.630 15.38 3.01 46.48 1.82
309 337 7.857389 CCACGAATATGATTTCATCACGAAAAT 59.143 33.333 15.38 0.00 46.48 1.82
310 338 7.065204 TCCACGAATATGATTTCATCACGAAAA 59.935 33.333 15.38 0.00 46.48 2.29
312 340 6.045955 TCCACGAATATGATTTCATCACGAA 58.954 36.000 15.38 0.00 43.01 3.85
313 341 5.596845 TCCACGAATATGATTTCATCACGA 58.403 37.500 15.38 0.00 43.01 4.35
314 342 5.107337 CCTCCACGAATATGATTTCATCACG 60.107 44.000 0.00 4.77 43.01 4.35
315 343 5.760253 ACCTCCACGAATATGATTTCATCAC 59.240 40.000 0.00 0.00 43.01 3.06
316 344 5.928976 ACCTCCACGAATATGATTTCATCA 58.071 37.500 0.00 0.00 44.55 3.07
327 355 3.835978 TCTTTTCCAGACCTCCACGAATA 59.164 43.478 0.00 0.00 0.00 1.75
348 376 9.463443 AGCATTTTGTAGTGTTCATTTAGTTTC 57.537 29.630 0.00 0.00 0.00 2.78
351 388 9.463443 GAAAGCATTTTGTAGTGTTCATTTAGT 57.537 29.630 0.00 0.00 39.27 2.24
352 389 8.629986 CGAAAGCATTTTGTAGTGTTCATTTAG 58.370 33.333 0.00 0.00 39.27 1.85
353 390 8.346300 TCGAAAGCATTTTGTAGTGTTCATTTA 58.654 29.630 0.00 0.00 39.27 1.40
354 391 7.199766 TCGAAAGCATTTTGTAGTGTTCATTT 58.800 30.769 0.00 0.00 39.27 2.32
355 392 6.734137 TCGAAAGCATTTTGTAGTGTTCATT 58.266 32.000 0.00 0.00 39.27 2.57
356 393 6.312399 TCGAAAGCATTTTGTAGTGTTCAT 57.688 33.333 0.00 0.00 39.27 2.57
357 394 5.743026 TCGAAAGCATTTTGTAGTGTTCA 57.257 34.783 0.00 0.00 39.27 3.18
358 395 7.444558 TTTTCGAAAGCATTTTGTAGTGTTC 57.555 32.000 10.98 0.00 39.27 3.18
378 415 8.466086 AATCGATGCCTCAAAAACTTATTTTC 57.534 30.769 0.00 0.00 37.01 2.29
401 438 3.486383 TCTGAGCGGAAACAAAGGAAAT 58.514 40.909 0.00 0.00 0.00 2.17
404 441 1.878102 GCTCTGAGCGGAAACAAAGGA 60.878 52.381 14.68 0.00 0.00 3.36
405 442 0.519077 GCTCTGAGCGGAAACAAAGG 59.481 55.000 14.68 0.00 0.00 3.11
406 443 1.229428 TGCTCTGAGCGGAAACAAAG 58.771 50.000 23.35 0.00 46.26 2.77
414 451 4.022762 ACATACTACTAATGCTCTGAGCGG 60.023 45.833 23.35 15.36 46.26 5.52
442 479 7.878547 TCTACATACATGCAAATTTCCATGA 57.121 32.000 25.38 11.59 40.92 3.07
447 485 9.571810 TGAATGTTCTACATACATGCAAATTTC 57.428 29.630 0.00 0.00 38.34 2.17
528 594 3.686016 ACCACCTCGTGAATAGCAAAAT 58.314 40.909 0.00 0.00 35.23 1.82
533 599 3.071479 TCAAAACCACCTCGTGAATAGC 58.929 45.455 0.00 0.00 35.23 2.97
534 600 3.125316 GCTCAAAACCACCTCGTGAATAG 59.875 47.826 0.00 0.00 35.23 1.73
543 609 1.073199 CCCGAGCTCAAAACCACCT 59.927 57.895 15.40 0.00 0.00 4.00
548 614 0.951558 TTTCTGCCCGAGCTCAAAAC 59.048 50.000 15.40 0.07 40.80 2.43
549 615 0.951558 GTTTCTGCCCGAGCTCAAAA 59.048 50.000 15.40 1.36 40.80 2.44
560 626 0.609406 GGGACTTGGGAGTTTCTGCC 60.609 60.000 0.38 0.38 42.53 4.85
562 628 2.887151 ATGGGACTTGGGAGTTTCTG 57.113 50.000 0.00 0.00 35.88 3.02
563 629 2.989571 AGAATGGGACTTGGGAGTTTCT 59.010 45.455 0.00 0.00 35.88 2.52
564 630 3.348119 GAGAATGGGACTTGGGAGTTTC 58.652 50.000 0.00 0.00 35.88 2.78
566 632 1.636003 GGAGAATGGGACTTGGGAGTT 59.364 52.381 0.00 0.00 35.88 3.01
568 634 0.179000 CGGAGAATGGGACTTGGGAG 59.821 60.000 0.00 0.00 0.00 4.30
569 635 1.271840 CCGGAGAATGGGACTTGGGA 61.272 60.000 0.00 0.00 0.00 4.37
627 694 2.094026 TGTTCGATCCTCCAGTGATGTG 60.094 50.000 0.00 0.00 0.00 3.21
657 724 6.701340 TCAAAGATGACCGAGAATATATGGG 58.299 40.000 0.00 0.00 0.00 4.00
784 854 0.804364 TGCGGCTGCTTTACTTGATG 59.196 50.000 20.27 0.00 43.34 3.07
868 938 0.863144 GCTTTGCTTGCCACATGTTG 59.137 50.000 0.00 0.00 0.00 3.33
949 1026 6.150140 CCTTTCTTATTTCCCTCTGAACACAG 59.850 42.308 0.00 0.00 31.05 3.66
994 1075 1.672356 GCGTCAGAACCATGCCTGT 60.672 57.895 7.53 0.00 0.00 4.00
1100 1181 0.382515 GTCCTTGGAGATCGACCTCG 59.617 60.000 0.00 0.00 41.45 4.63
1103 1184 1.227002 GCGTCCTTGGAGATCGACC 60.227 63.158 0.00 5.27 0.00 4.79
1621 4484 6.211384 TGATCCAACTCTGTCTTACTTGATGA 59.789 38.462 0.00 0.00 0.00 2.92
1623 4486 6.611613 TGATCCAACTCTGTCTTACTTGAT 57.388 37.500 0.00 0.00 0.00 2.57
1627 4490 7.726033 ACTTATGATCCAACTCTGTCTTACT 57.274 36.000 0.00 0.00 0.00 2.24
1628 4491 9.303537 GTTACTTATGATCCAACTCTGTCTTAC 57.696 37.037 0.00 0.00 0.00 2.34
1629 4492 9.031537 TGTTACTTATGATCCAACTCTGTCTTA 57.968 33.333 0.00 0.00 0.00 2.10
1633 4496 7.624549 ACATGTTACTTATGATCCAACTCTGT 58.375 34.615 0.00 0.00 0.00 3.41
1636 4499 8.607459 CAGAACATGTTACTTATGATCCAACTC 58.393 37.037 11.95 0.00 30.33 3.01
1638 4501 7.066284 AGCAGAACATGTTACTTATGATCCAAC 59.934 37.037 11.95 0.00 30.33 3.77
1647 4518 6.096673 TCACAGAGCAGAACATGTTACTTA 57.903 37.500 11.95 0.00 0.00 2.24
1894 4776 3.429960 GGATTTGAGGATTTGAGCAAGCC 60.430 47.826 0.00 0.00 0.00 4.35
1904 4786 1.942657 CGATGCACGGATTTGAGGATT 59.057 47.619 0.00 0.00 38.46 3.01
1949 4844 9.366216 GCCACGTCATAATCATATATAAGTTCA 57.634 33.333 0.00 0.00 0.00 3.18
1951 4846 9.371136 CAGCCACGTCATAATCATATATAAGTT 57.629 33.333 0.00 0.00 0.00 2.66
1952 4847 7.981789 CCAGCCACGTCATAATCATATATAAGT 59.018 37.037 0.00 0.00 0.00 2.24
1953 4848 7.042456 GCCAGCCACGTCATAATCATATATAAG 60.042 40.741 0.00 0.00 0.00 1.73
1954 4849 6.761242 GCCAGCCACGTCATAATCATATATAA 59.239 38.462 0.00 0.00 0.00 0.98
1957 4852 4.020662 TGCCAGCCACGTCATAATCATATA 60.021 41.667 0.00 0.00 0.00 0.86
1960 4855 1.134128 TGCCAGCCACGTCATAATCAT 60.134 47.619 0.00 0.00 0.00 2.45
2045 4956 1.216710 GAAGTCCCACTCCAGCTCG 59.783 63.158 0.00 0.00 0.00 5.03
2132 5043 0.106769 TGTTGCGCCATATCACCCAT 60.107 50.000 4.18 0.00 0.00 4.00
2159 5070 1.824329 GATGAGCTCGTCGGGGAGA 60.824 63.158 19.79 0.00 36.08 3.71
2249 5160 7.662258 TGTTGATCGGTTAATTTCTTGGACTAA 59.338 33.333 0.00 0.00 0.00 2.24
2251 5162 6.001460 TGTTGATCGGTTAATTTCTTGGACT 58.999 36.000 0.00 0.00 0.00 3.85
2252 5163 6.148811 TCTGTTGATCGGTTAATTTCTTGGAC 59.851 38.462 0.00 0.00 0.00 4.02
2253 5164 6.148811 GTCTGTTGATCGGTTAATTTCTTGGA 59.851 38.462 0.00 0.00 0.00 3.53
2254 5165 6.072728 TGTCTGTTGATCGGTTAATTTCTTGG 60.073 38.462 0.00 0.00 0.00 3.61
2256 5167 6.934645 TCTGTCTGTTGATCGGTTAATTTCTT 59.065 34.615 0.00 0.00 0.00 2.52
2257 5168 6.464222 TCTGTCTGTTGATCGGTTAATTTCT 58.536 36.000 0.00 0.00 0.00 2.52
2258 5169 6.721571 TCTGTCTGTTGATCGGTTAATTTC 57.278 37.500 0.00 0.00 0.00 2.17
2259 5170 7.148239 GGATTCTGTCTGTTGATCGGTTAATTT 60.148 37.037 0.00 0.00 0.00 1.82
2299 5243 9.277565 CAATTCAAGAACGTGAAATCGAATTAT 57.722 29.630 7.18 0.00 40.76 1.28
2341 5285 2.036256 GGCTGGACCCTGCACAAT 59.964 61.111 17.63 0.00 41.69 2.71
2369 5313 7.228706 CCTAGCCGAAGAAATTGGTAATATTGT 59.771 37.037 0.00 0.00 34.66 2.71
2416 5360 2.787994 AGCCTGAAGATTGGTCTGTTG 58.212 47.619 0.00 0.00 34.13 3.33
2421 5365 7.631717 AAATTAGTTAGCCTGAAGATTGGTC 57.368 36.000 0.00 0.00 0.00 4.02
2429 5373 6.594159 GTGCTCTGTAAATTAGTTAGCCTGAA 59.406 38.462 0.00 0.00 0.00 3.02
2434 5378 7.596749 TTCTGTGCTCTGTAAATTAGTTAGC 57.403 36.000 0.00 0.00 0.00 3.09
2471 5419 1.367665 GCATGCGGCGATACGAAAC 60.368 57.895 12.98 0.00 35.47 2.78
2484 5441 1.406539 CATTCTTGTACCCCTGCATGC 59.593 52.381 11.82 11.82 0.00 4.06
2485 5442 2.424601 CACATTCTTGTACCCCTGCATG 59.575 50.000 0.00 0.00 33.76 4.06
2882 5839 3.069318 GACGGACGCCTCCTCCTT 61.069 66.667 0.07 0.00 33.79 3.36
2962 5919 1.740025 GCAGATTAGCACACACCCTTC 59.260 52.381 0.00 0.00 0.00 3.46
2977 5934 1.145598 CAGTCATCTGGCGGCAGAT 59.854 57.895 39.87 39.87 42.18 2.90
2997 5954 4.166011 GCACAATCGGCAGGCGTC 62.166 66.667 17.01 0.00 0.00 5.19
3062 6019 9.980780 GCAAGCTAAAACAACTTGAAAAATAAA 57.019 25.926 6.18 0.00 42.71 1.40
3064 6021 8.709386 TGCAAGCTAAAACAACTTGAAAAATA 57.291 26.923 6.18 0.00 42.71 1.40
3069 6026 6.400515 CGTTTTGCAAGCTAAAACAACTTGAA 60.401 34.615 18.63 0.00 44.28 2.69
3070 6027 5.061560 CGTTTTGCAAGCTAAAACAACTTGA 59.938 36.000 18.63 0.00 44.28 3.02
3086 6043 7.966111 ACGTCATAATATAAGAACGTTTTGCA 58.034 30.769 0.46 0.00 0.00 4.08
3110 6067 2.139118 GAAGTGAGCACAGTCCTTGAC 58.861 52.381 3.19 0.00 0.00 3.18
3125 6082 3.611766 ATTCGGACCAGTTAGGAAGTG 57.388 47.619 0.00 0.00 41.22 3.16
3132 6089 7.613585 TCTGTTGTTTATATTCGGACCAGTTA 58.386 34.615 0.00 0.00 0.00 2.24
3136 6093 6.256975 CGAATCTGTTGTTTATATTCGGACCA 59.743 38.462 0.00 0.00 43.05 4.02
3141 6098 7.634817 GGTGTTCGAATCTGTTGTTTATATTCG 59.365 37.037 0.00 8.93 46.25 3.34
3145 6102 7.118680 GGAAGGTGTTCGAATCTGTTGTTTATA 59.881 37.037 0.00 0.00 32.92 0.98
3159 6116 1.430992 AAGAAGGGGAAGGTGTTCGA 58.569 50.000 0.00 0.00 32.92 3.71
3169 6126 3.849574 TGTGTGATTGGATAAGAAGGGGA 59.150 43.478 0.00 0.00 0.00 4.81
3170 6127 4.235079 TGTGTGATTGGATAAGAAGGGG 57.765 45.455 0.00 0.00 0.00 4.79
3171 6128 4.037208 GCATGTGTGATTGGATAAGAAGGG 59.963 45.833 0.00 0.00 0.00 3.95
3187 6144 2.517959 AGTAAGGTTGCATGCATGTGT 58.482 42.857 26.79 10.29 0.00 3.72
3202 6159 5.859114 CACGCATAGGACATTAGCTAGTAAG 59.141 44.000 0.00 0.00 0.00 2.34
3209 6166 1.867233 CACCACGCATAGGACATTAGC 59.133 52.381 0.00 0.00 0.00 3.09
3215 6172 1.449601 CCACCACCACGCATAGGAC 60.450 63.158 0.00 0.00 0.00 3.85
3216 6173 1.610967 TCCACCACCACGCATAGGA 60.611 57.895 0.00 0.00 0.00 2.94
3219 6176 0.687920 TTTCTCCACCACCACGCATA 59.312 50.000 0.00 0.00 0.00 3.14
3220 6177 0.606401 CTTTCTCCACCACCACGCAT 60.606 55.000 0.00 0.00 0.00 4.73
3223 6180 2.317609 CGCTTTCTCCACCACCACG 61.318 63.158 0.00 0.00 0.00 4.94
3227 6184 1.503542 CATGCGCTTTCTCCACCAC 59.496 57.895 9.73 0.00 0.00 4.16
3236 6193 1.300853 GGTTGGTTGCATGCGCTTT 60.301 52.632 14.09 0.00 39.64 3.51
3239 6196 2.023223 CAAGGTTGGTTGCATGCGC 61.023 57.895 14.09 0.00 39.24 6.09
3316 6274 7.921786 TGTGGTAACCATTTGAAATCTCTAG 57.078 36.000 0.00 0.00 35.28 2.43
3333 6291 8.866970 TGTCTATATACATCCGTATGTGGTAA 57.133 34.615 3.56 0.00 45.99 2.85
3373 6332 7.144722 ACATTCGAAGCAAAATGAGTGAATA 57.855 32.000 3.35 0.00 36.57 1.75
3387 6346 9.474249 GTTTTAATAAGTGACTACATTCGAAGC 57.526 33.333 3.35 0.00 0.00 3.86
3560 6522 3.777465 TGGGATCTAGTTTCGAAGACG 57.223 47.619 0.00 0.00 34.32 4.18
3561 6523 5.012328 ACATGGGATCTAGTTTCGAAGAC 57.988 43.478 0.00 0.18 34.32 3.01
3625 6599 6.486657 GCATGATAGTTTATTTGGTCTAGGCA 59.513 38.462 0.00 0.00 0.00 4.75
3669 6643 6.878389 CCCGGTAACTTTAGTGTAAAACCATA 59.122 38.462 0.00 0.00 29.52 2.74
3756 6737 4.157840 TCGATCATAGACGGTGGATATTGG 59.842 45.833 0.00 0.00 0.00 3.16
3783 6770 3.970410 CCTCTTGGCCCAGGCACA 61.970 66.667 11.50 3.36 44.11 4.57
3796 6783 1.557269 GGCATGTGGACCTCACCTCT 61.557 60.000 0.00 0.00 45.48 3.69
3854 6841 3.681835 GTCTGCCCCGACACGACT 61.682 66.667 0.00 0.00 34.11 4.18
3866 6853 1.725164 GCACGTACTAAACAGGTCTGC 59.275 52.381 0.00 0.00 0.00 4.26
3891 6879 2.743538 GGCTCATGCACTGCACGA 60.744 61.111 5.67 2.11 43.04 4.35
3914 6902 3.391296 AGACCTAATCATACGTGGCCAAT 59.609 43.478 7.24 0.12 0.00 3.16
3940 6928 7.594758 GCGTAAATGTCATGGTATTTTATGCAT 59.405 33.333 19.31 3.79 0.00 3.96


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

AutoCloner maintained by Alex Coulton.