Multiple sequence alignment - TraesCS7D01G007800

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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 TraesCS7D01G007800 chr7D 100.000 4072 0 0 1 4072 3779164 3783235 0.000000e+00 7520.0
1 TraesCS7D01G007800 chr7D 96.789 3083 59 11 993 4072 2350912 2353957 0.000000e+00 5108.0
2 TraesCS7D01G007800 chr7D 93.403 1152 63 8 2673 3819 3622635 3623778 0.000000e+00 1694.0
3 TraesCS7D01G007800 chr7D 89.108 762 57 12 2848 3587 3426084 3426841 0.000000e+00 924.0
4 TraesCS7D01G007800 chr7D 82.675 658 77 21 2566 3201 3766762 3767404 2.140000e-152 549.0
5 TraesCS7D01G007800 chr7D 90.592 287 22 4 993 1279 3765393 3765674 3.840000e-100 375.0
6 TraesCS7D01G007800 chr7D 78.293 668 70 33 2566 3201 3576060 3576684 1.080000e-95 361.0
7 TraesCS7D01G007800 chr7D 94.241 191 11 0 3200 3390 3426984 3427174 3.980000e-75 292.0
8 TraesCS7D01G007800 chr7D 99.379 161 1 0 3912 4072 3629262 3629422 3.980000e-75 292.0
9 TraesCS7D01G007800 chr7D 90.950 221 12 3 3375 3587 3428784 3429004 1.430000e-74 291.0
10 TraesCS7D01G007800 chr7D 83.451 284 37 7 3294 3572 3767451 3767729 5.220000e-64 255.0
11 TraesCS7D01G007800 chr7D 90.055 181 16 2 815 994 3765178 3765357 2.450000e-57 233.0
12 TraesCS7D01G007800 chr7D 84.615 221 22 4 76 284 3759706 3759486 4.120000e-50 209.0
13 TraesCS7D01G007800 chr7D 87.719 171 18 2 2079 2246 3766200 3766370 3.210000e-46 196.0
14 TraesCS7D01G007800 chr7D 98.113 106 1 1 3815 3919 3624185 3624290 2.500000e-42 183.0
15 TraesCS7D01G007800 chr7D 91.346 104 9 0 68 171 3910545 3910442 4.240000e-30 143.0
16 TraesCS7D01G007800 chr7D 83.019 159 22 3 1 155 3570048 3570205 5.490000e-29 139.0
17 TraesCS7D01G007800 chr7D 89.216 102 9 2 2146 2246 3575558 3575658 4.270000e-25 126.0
18 TraesCS7D01G007800 chr7D 76.449 276 36 17 183 445 3570203 3570462 5.530000e-24 122.0
19 TraesCS7D01G007800 chr7D 84.615 104 16 0 1118 1221 2437400 2437297 2.000000e-18 104.0
20 TraesCS7D01G007800 chr4A 94.269 2251 83 22 1419 3639 741477848 741480082 0.000000e+00 3400.0
21 TraesCS7D01G007800 chr4A 82.451 661 76 23 2566 3201 742281527 742280882 3.580000e-150 542.0
22 TraesCS7D01G007800 chr4A 89.234 418 8 12 3684 4070 741480086 741480497 4.730000e-134 488.0
23 TraesCS7D01G007800 chr4A 83.124 557 54 18 1454 2006 742282672 742282152 4.760000e-129 472.0
24 TraesCS7D01G007800 chr4A 94.595 296 16 0 993 1288 741477553 741477848 3.710000e-125 459.0
25 TraesCS7D01G007800 chr4A 91.930 285 20 2 995 1279 742282964 742282683 2.950000e-106 396.0
26 TraesCS7D01G007800 chr4A 85.342 307 31 9 3294 3591 742280730 742280429 5.110000e-79 305.0
27 TraesCS7D01G007800 chr4A 82.736 307 28 15 1454 1760 741879090 741879371 2.430000e-62 250.0
28 TraesCS7D01G007800 chr4A 81.159 345 33 15 1 319 741996347 741996009 8.740000e-62 248.0
29 TraesCS7D01G007800 chr4A 91.160 181 14 2 815 994 741477338 741477517 1.130000e-60 244.0
30 TraesCS7D01G007800 chr4A 89.266 177 18 1 550 725 741995941 741995765 1.910000e-53 220.0
31 TraesCS7D01G007800 chr4A 87.709 179 20 2 817 994 742283179 742283002 1.480000e-49 207.0
32 TraesCS7D01G007800 chr4A 87.500 176 21 1 551 725 742154780 742154955 6.900000e-48 202.0
33 TraesCS7D01G007800 chr4A 87.571 177 19 2 2082 2255 742282133 742281957 6.900000e-48 202.0
34 TraesCS7D01G007800 chr4A 82.096 229 18 10 3796 4021 741785174 741785382 1.500000e-39 174.0
35 TraesCS7D01G007800 chr4A 86.076 158 19 3 3915 4069 740015167 740015324 2.520000e-37 167.0
36 TraesCS7D01G007800 chr4A 85.906 149 20 1 578 725 741871026 741871174 1.520000e-34 158.0
37 TraesCS7D01G007800 chr4A 94.565 92 3 2 3980 4070 740582928 740582838 1.530000e-29 141.0
38 TraesCS7D01G007800 chr4A 88.235 85 9 1 1130 1214 739688793 739688710 2.590000e-17 100.0
39 TraesCS7D01G007800 chr4A 88.235 85 9 1 1130 1214 742082899 742082816 2.590000e-17 100.0
40 TraesCS7D01G007800 chr4A 94.643 56 3 0 1502 1557 739910466 739910521 2.020000e-13 87.9
41 TraesCS7D01G007800 chr4A 82.353 102 7 9 218 309 740371000 740371100 1.210000e-10 78.7
42 TraesCS7D01G007800 chr4A 91.667 48 3 1 1511 1558 740201600 740201646 9.450000e-07 65.8
43 TraesCS7D01G007800 chr4A 100.000 32 0 0 272 303 733907976 733908007 4.400000e-05 60.2
44 TraesCS7D01G007800 chr4A 100.000 29 0 0 958 986 740201320 740201348 2.000000e-03 54.7
45 TraesCS7D01G007800 chr7A 93.925 2255 77 23 1419 3639 1990071 1992299 0.000000e+00 3350.0
46 TraesCS7D01G007800 chr7A 93.944 611 26 7 3186 3790 2112888 2113493 0.000000e+00 913.0
47 TraesCS7D01G007800 chr7A 98.571 280 4 0 3790 4069 2113522 2113801 2.830000e-136 496.0
48 TraesCS7D01G007800 chr7A 88.756 418 8 13 3684 4070 1992303 1992712 3.680000e-130 475.0
49 TraesCS7D01G007800 chr7A 95.270 296 14 0 993 1288 1989776 1990071 1.710000e-128 470.0
50 TraesCS7D01G007800 chr7A 90.712 323 23 2 1456 1774 2760410 2760729 1.350000e-114 424.0
51 TraesCS7D01G007800 chr7A 82.655 467 53 11 1466 1931 3625315 3625754 4.940000e-104 388.0
52 TraesCS7D01G007800 chr7A 93.361 241 12 3 2961 3201 2864768 2864532 1.800000e-93 353.0
53 TraesCS7D01G007800 chr7A 81.007 437 51 16 2735 3164 3012258 3011847 6.570000e-83 318.0
54 TraesCS7D01G007800 chr7A 85.953 299 35 4 549 845 3624882 3625175 3.060000e-81 313.0
55 TraesCS7D01G007800 chr7A 79.744 390 51 21 10 382 3013445 3013067 1.450000e-64 257.0
56 TraesCS7D01G007800 chr7A 87.442 215 21 5 1849 2061 2760751 2760961 4.070000e-60 243.0
57 TraesCS7D01G007800 chr7A 81.973 294 35 10 1 286 2673319 2673036 2.450000e-57 233.0
58 TraesCS7D01G007800 chr7A 89.503 181 17 2 815 994 1989561 1989740 1.140000e-55 228.0
59 TraesCS7D01G007800 chr7A 88.950 181 19 1 549 728 3593782 3593602 5.300000e-54 222.0
60 TraesCS7D01G007800 chr7A 91.772 158 12 1 1 158 2754311 2754467 6.850000e-53 219.0
61 TraesCS7D01G007800 chr7A 87.952 166 19 1 2079 2243 3625805 3625970 1.150000e-45 195.0
62 TraesCS7D01G007800 chr7A 91.176 102 9 0 893 994 2667613 2667512 5.490000e-29 139.0
63 TraesCS7D01G007800 chr7A 81.967 122 10 5 1328 1448 711669303 711669413 4.330000e-15 93.5
64 TraesCS7D01G007800 chr7A 90.164 61 6 0 1388 1448 18992948 18992888 3.370000e-11 80.5
65 TraesCS7D01G007800 chr7A 95.745 47 1 1 405 451 3624699 3624744 1.570000e-09 75.0
66 TraesCS7D01G007800 chr1D 91.964 112 8 1 1338 1448 22436126 22436237 5.450000e-34 156.0
67 TraesCS7D01G007800 chr1D 100.000 28 0 0 1339 1366 408923093 408923120 7.000000e-03 52.8
68 TraesCS7D01G007800 chr6B 86.066 122 15 2 1325 1445 157797912 157798032 3.300000e-26 130.0
69 TraesCS7D01G007800 chr6B 79.365 126 14 7 1328 1452 574463789 574463675 1.210000e-10 78.7
70 TraesCS7D01G007800 chrUn 87.500 104 12 1 1126 1229 462942002 462942104 7.150000e-23 119.0
71 TraesCS7D01G007800 chrUn 100.000 32 0 0 420 451 462941556 462941587 4.400000e-05 60.2
72 TraesCS7D01G007800 chr2B 81.061 132 14 3 1328 1448 734760862 734760993 1.200000e-15 95.3
73 TraesCS7D01G007800 chr2B 97.436 39 1 0 2028 2066 793283509 793283547 2.630000e-07 67.6
74 TraesCS7D01G007800 chr7B 89.831 59 6 0 1390 1448 620359496 620359554 4.360000e-10 76.8
75 TraesCS7D01G007800 chr6D 91.304 46 3 1 1330 1374 384221887 384221842 1.220000e-05 62.1


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 TraesCS7D01G007800 chr7D 3779164 3783235 4071 False 7520.000000 7520 100.00000 1 4072 1 chr7D.!!$F3 4071
1 TraesCS7D01G007800 chr7D 2350912 2353957 3045 False 5108.000000 5108 96.78900 993 4072 1 chr7D.!!$F1 3079
2 TraesCS7D01G007800 chr7D 3622635 3624290 1655 False 938.500000 1694 95.75800 2673 3919 2 chr7D.!!$F7 1246
3 TraesCS7D01G007800 chr7D 3426084 3429004 2920 False 502.333333 924 91.43300 2848 3587 3 chr7D.!!$F4 739
4 TraesCS7D01G007800 chr7D 3765178 3767729 2551 False 321.600000 549 86.89840 815 3572 5 chr7D.!!$F8 2757
5 TraesCS7D01G007800 chr7D 3575558 3576684 1126 False 243.500000 361 83.75450 2146 3201 2 chr7D.!!$F6 1055
6 TraesCS7D01G007800 chr4A 741477338 741480497 3159 False 1147.750000 3400 92.31450 815 4070 4 chr4A.!!$F10 3255
7 TraesCS7D01G007800 chr4A 742280429 742283179 2750 True 354.000000 542 86.35450 817 3591 6 chr4A.!!$R5 2774
8 TraesCS7D01G007800 chr4A 741995765 741996347 582 True 234.000000 248 85.21250 1 725 2 chr4A.!!$R4 724
9 TraesCS7D01G007800 chr7A 1989561 1992712 3151 False 1130.750000 3350 91.86350 815 4070 4 chr7A.!!$F3 3255
10 TraesCS7D01G007800 chr7A 2112888 2113801 913 False 704.500000 913 96.25750 3186 4069 2 chr7A.!!$F4 883
11 TraesCS7D01G007800 chr7A 2760410 2760961 551 False 333.500000 424 89.07700 1456 2061 2 chr7A.!!$F5 605
12 TraesCS7D01G007800 chr7A 3011847 3013445 1598 True 287.500000 318 80.37550 10 3164 2 chr7A.!!$R6 3154
13 TraesCS7D01G007800 chr7A 3624699 3625970 1271 False 242.750000 388 88.07625 405 2243 4 chr7A.!!$F6 1838

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
178 188 0.031616 AGGAGGAAGATTCTCGGGCT 60.032 55.0 0.00 0.00 32.34 5.19 F
404 440 0.036448 AGTCAGAGTCGAGGTCGGAA 59.964 55.0 0.00 0.00 40.29 4.30 F
454 490 0.041535 TTTGCAATCCAGGCCCAGAT 59.958 50.0 0.00 0.00 0.00 2.90 F
497 558 0.179073 CAGGTAAGCCGTCCAGGATG 60.179 60.0 0.93 0.93 45.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1531 0.109735 GGACCAAAGTTGCTTAGCGC 60.110 55.000 0.00 0.0 39.77 5.92 R
1713 1925 0.469892 CCACCAAGGTCAAGGCCTTT 60.470 55.000 17.61 0.0 45.91 3.11 R
2402 2867 3.713288 TCGATTTGCTTCCCACGTATAG 58.287 45.455 0.00 0.0 0.00 1.31 R
3137 3681 9.581099 AATGACCAGTAACAAAAGTACAAAAAG 57.419 29.630 0.00 0.0 0.00 2.27 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 5.169295 GTCGCTAGTTAAGTTTCCTGATGT 58.831 41.667 0.00 0.00 0.00 3.06
30 31 6.472808 CGCTAGTTAAGTTTCCTGATGTAGTC 59.527 42.308 0.00 0.00 0.00 2.59
97 102 6.204882 AGTGTGTATTCTCCTTGCTAACAAAC 59.795 38.462 0.00 0.00 34.74 2.93
144 154 1.865970 GAGAAGGCAGCATCTCAATCG 59.134 52.381 18.11 0.00 41.37 3.34
150 160 3.076104 AGCATCTCAATCGGTGCTG 57.924 52.632 0.00 0.00 45.44 4.41
152 162 0.376152 GCATCTCAATCGGTGCTGTG 59.624 55.000 0.00 0.00 34.85 3.66
170 180 1.555533 GTGGTCGGAAGGAGGAAGATT 59.444 52.381 0.00 0.00 0.00 2.40
171 181 1.831736 TGGTCGGAAGGAGGAAGATTC 59.168 52.381 0.00 0.00 0.00 2.52
174 184 2.025155 TCGGAAGGAGGAAGATTCTCG 58.975 52.381 0.00 0.00 32.34 4.04
175 185 1.067821 CGGAAGGAGGAAGATTCTCGG 59.932 57.143 0.00 0.00 32.34 4.63
177 187 0.833949 AAGGAGGAAGATTCTCGGGC 59.166 55.000 0.00 0.00 32.34 6.13
178 188 0.031616 AGGAGGAAGATTCTCGGGCT 60.032 55.000 0.00 0.00 32.34 5.19
180 190 1.408969 GAGGAAGATTCTCGGGCTCT 58.591 55.000 0.00 0.00 0.00 4.09
181 191 2.588620 GAGGAAGATTCTCGGGCTCTA 58.411 52.381 0.00 0.00 0.00 2.43
182 192 2.556622 GAGGAAGATTCTCGGGCTCTAG 59.443 54.545 0.00 0.00 0.00 2.43
183 193 1.616374 GGAAGATTCTCGGGCTCTAGG 59.384 57.143 0.00 0.00 0.00 3.02
184 194 2.312390 GAAGATTCTCGGGCTCTAGGT 58.688 52.381 0.00 0.00 0.00 3.08
185 195 1.989706 AGATTCTCGGGCTCTAGGTC 58.010 55.000 0.00 0.00 0.00 3.85
186 196 0.594110 GATTCTCGGGCTCTAGGTCG 59.406 60.000 0.00 0.00 0.00 4.79
187 197 0.183014 ATTCTCGGGCTCTAGGTCGA 59.817 55.000 0.00 0.00 0.00 4.20
188 198 0.747283 TTCTCGGGCTCTAGGTCGAC 60.747 60.000 7.13 7.13 0.00 4.20
189 199 2.124403 TCGGGCTCTAGGTCGACC 60.124 66.667 27.67 27.67 0.00 4.79
209 219 2.158755 CCTGACACCTGAAACCTCAAGT 60.159 50.000 0.00 0.00 0.00 3.16
251 273 1.891150 CAAAAGCAGAGGAAGCCACAT 59.109 47.619 0.00 0.00 0.00 3.21
258 284 1.630369 AGAGGAAGCCACATGCAAGTA 59.370 47.619 0.00 0.00 44.83 2.24
261 287 3.434309 AGGAAGCCACATGCAAGTATTT 58.566 40.909 0.00 0.00 44.83 1.40
265 291 4.235079 AGCCACATGCAAGTATTTAGGA 57.765 40.909 0.00 0.00 44.83 2.94
270 296 6.405731 GCCACATGCAAGTATTTAGGATTCAA 60.406 38.462 0.00 0.00 40.77 2.69
288 324 3.023119 TCAAAAAGCAGAGGAAGCACAA 58.977 40.909 0.00 0.00 0.00 3.33
291 327 3.655276 AAAGCAGAGGAAGCACAATTG 57.345 42.857 3.24 3.24 0.00 2.32
314 350 9.761504 ATTGCAGTCTGTATCTATATATGCATC 57.238 33.333 0.19 0.00 40.46 3.91
315 351 8.297470 TGCAGTCTGTATCTATATATGCATCA 57.703 34.615 0.19 0.00 36.33 3.07
316 352 8.411683 TGCAGTCTGTATCTATATATGCATCAG 58.588 37.037 0.19 0.71 36.33 2.90
317 353 8.412456 GCAGTCTGTATCTATATATGCATCAGT 58.588 37.037 0.19 0.00 0.00 3.41
341 377 5.563592 TGATTCAGTTCTGATTGTCCATGT 58.436 37.500 3.28 0.00 0.00 3.21
345 381 4.022935 TCAGTTCTGATTGTCCATGTTTGC 60.023 41.667 0.00 0.00 0.00 3.68
347 383 3.159213 TCTGATTGTCCATGTTTGCCT 57.841 42.857 0.00 0.00 0.00 4.75
348 384 2.821378 TCTGATTGTCCATGTTTGCCTG 59.179 45.455 0.00 0.00 0.00 4.85
352 388 0.178995 TGTCCATGTTTGCCTGCTGA 60.179 50.000 0.00 0.00 0.00 4.26
353 389 0.242017 GTCCATGTTTGCCTGCTGAC 59.758 55.000 0.00 0.00 0.00 3.51
357 393 1.884579 CATGTTTGCCTGCTGACTTCT 59.115 47.619 0.00 0.00 0.00 2.85
362 398 1.744741 GCCTGCTGACTTCTGCCTC 60.745 63.158 5.74 0.00 39.65 4.70
369 405 2.787994 CTGACTTCTGCCTCCACAAAT 58.212 47.619 0.00 0.00 0.00 2.32
382 418 4.437239 CTCCACAAATCTCGCTGATAACT 58.563 43.478 0.00 0.00 34.45 2.24
383 419 5.451937 CCTCCACAAATCTCGCTGATAACTA 60.452 44.000 0.00 0.00 34.45 2.24
384 420 6.161855 TCCACAAATCTCGCTGATAACTAT 57.838 37.500 0.00 0.00 34.45 2.12
385 421 7.284919 TCCACAAATCTCGCTGATAACTATA 57.715 36.000 0.00 0.00 34.45 1.31
386 422 7.371159 TCCACAAATCTCGCTGATAACTATAG 58.629 38.462 0.00 0.00 34.45 1.31
387 423 7.014326 TCCACAAATCTCGCTGATAACTATAGT 59.986 37.037 0.00 0.00 34.45 2.12
388 424 7.327275 CCACAAATCTCGCTGATAACTATAGTC 59.673 40.741 5.70 0.00 34.45 2.59
389 425 7.862873 CACAAATCTCGCTGATAACTATAGTCA 59.137 37.037 5.70 0.00 34.45 3.41
390 426 8.079203 ACAAATCTCGCTGATAACTATAGTCAG 58.921 37.037 5.70 10.41 41.69 3.51
391 427 7.987750 AATCTCGCTGATAACTATAGTCAGA 57.012 36.000 19.24 4.81 41.38 3.27
393 429 6.526526 TCTCGCTGATAACTATAGTCAGAGT 58.473 40.000 19.24 2.42 41.38 3.24
394 430 6.647481 TCTCGCTGATAACTATAGTCAGAGTC 59.353 42.308 19.24 9.09 41.38 3.36
395 431 5.405873 TCGCTGATAACTATAGTCAGAGTCG 59.594 44.000 19.24 14.21 41.38 4.18
396 432 5.405873 CGCTGATAACTATAGTCAGAGTCGA 59.594 44.000 19.24 0.00 41.38 4.20
397 433 6.400621 CGCTGATAACTATAGTCAGAGTCGAG 60.401 46.154 19.24 5.31 41.38 4.04
399 435 6.828788 TGATAACTATAGTCAGAGTCGAGGT 58.171 40.000 5.70 0.00 0.00 3.85
400 436 6.930164 TGATAACTATAGTCAGAGTCGAGGTC 59.070 42.308 5.70 0.00 0.00 3.85
401 437 3.719924 ACTATAGTCAGAGTCGAGGTCG 58.280 50.000 0.00 0.00 41.45 4.79
402 438 1.956297 ATAGTCAGAGTCGAGGTCGG 58.044 55.000 0.00 0.00 40.29 4.79
403 439 0.900421 TAGTCAGAGTCGAGGTCGGA 59.100 55.000 0.00 0.00 40.29 4.55
404 440 0.036448 AGTCAGAGTCGAGGTCGGAA 59.964 55.000 0.00 0.00 40.29 4.30
405 441 0.168568 GTCAGAGTCGAGGTCGGAAC 59.831 60.000 0.00 0.00 40.29 3.62
444 480 2.555757 AGCTCAACAGAGTTTGCAATCC 59.444 45.455 0.00 0.00 0.00 3.01
451 487 0.899717 GAGTTTGCAATCCAGGCCCA 60.900 55.000 0.00 0.00 0.00 5.36
453 489 0.899717 GTTTGCAATCCAGGCCCAGA 60.900 55.000 0.00 0.00 0.00 3.86
454 490 0.041535 TTTGCAATCCAGGCCCAGAT 59.958 50.000 0.00 0.00 0.00 2.90
455 491 0.925558 TTGCAATCCAGGCCCAGATA 59.074 50.000 0.00 0.00 0.00 1.98
456 492 0.475475 TGCAATCCAGGCCCAGATAG 59.525 55.000 0.00 0.00 0.00 2.08
457 493 0.767375 GCAATCCAGGCCCAGATAGA 59.233 55.000 0.00 0.00 0.00 1.98
461 522 3.567375 ATCCAGGCCCAGATAGACATA 57.433 47.619 0.00 0.00 0.00 2.29
464 525 3.584406 TCCAGGCCCAGATAGACATAATG 59.416 47.826 0.00 0.00 0.00 1.90
473 534 6.336566 CCAGATAGACATAATGAAGGGATCG 58.663 44.000 0.00 0.00 0.00 3.69
494 555 2.125106 GCAGGTAAGCCGTCCAGG 60.125 66.667 0.00 0.00 44.97 4.45
495 556 2.656069 GCAGGTAAGCCGTCCAGGA 61.656 63.158 0.00 0.00 45.00 3.86
496 557 1.972660 GCAGGTAAGCCGTCCAGGAT 61.973 60.000 0.00 0.00 45.00 3.24
497 558 0.179073 CAGGTAAGCCGTCCAGGATG 60.179 60.000 0.93 0.93 45.00 3.51
498 559 1.523938 GGTAAGCCGTCCAGGATGC 60.524 63.158 2.62 4.48 45.00 3.91
499 560 1.523938 GTAAGCCGTCCAGGATGCC 60.524 63.158 2.62 0.00 45.00 4.40
518 579 1.372623 GGACGGACAGTTCACGGTC 60.373 63.158 1.93 1.93 39.75 4.79
543 604 3.576078 TTCCTGTTGTGGACTGTTCAT 57.424 42.857 0.00 0.00 35.58 2.57
544 605 2.849942 TCCTGTTGTGGACTGTTCATG 58.150 47.619 0.00 0.00 0.00 3.07
545 606 1.881973 CCTGTTGTGGACTGTTCATGG 59.118 52.381 0.00 0.00 0.00 3.66
555 632 3.314080 GGACTGTTCATGGTCGAAACAAA 59.686 43.478 1.65 0.00 33.70 2.83
600 683 3.795041 CAGCCTGGGCCTCCTCTG 61.795 72.222 4.53 3.18 43.17 3.35
634 717 5.762179 TTTCTGCTCAAGGATTCCTTCTA 57.238 39.130 15.24 5.98 42.67 2.10
637 720 4.346418 TCTGCTCAAGGATTCCTTCTATCC 59.654 45.833 15.24 0.00 42.67 2.59
648 731 6.712547 GGATTCCTTCTATCCGATGATTGTTT 59.287 38.462 0.00 0.00 32.82 2.83
659 742 8.746052 ATCCGATGATTGTTTAGATTTGGTTA 57.254 30.769 0.00 0.00 0.00 2.85
676 759 3.826157 TGGTTAACCAATCTGAGCCTTTG 59.174 43.478 25.19 0.00 44.35 2.77
677 760 3.367395 GGTTAACCAATCTGAGCCTTTGC 60.367 47.826 20.12 0.00 35.64 3.68
702 787 2.429069 GCTGCGCGTCCTTTTTGG 60.429 61.111 8.43 0.00 37.10 3.28
725 810 9.703892 TTGGAAACATGTTTAGTATTTGGATTG 57.296 29.630 23.33 0.00 42.32 2.67
728 813 9.691362 GAAACATGTTTAGTATTTGGATTGTGT 57.309 29.630 23.33 0.00 32.11 3.72
729 814 9.474920 AAACATGTTTAGTATTTGGATTGTGTG 57.525 29.630 22.10 0.00 0.00 3.82
730 815 8.402798 ACATGTTTAGTATTTGGATTGTGTGA 57.597 30.769 0.00 0.00 0.00 3.58
794 879 3.570540 TGATCTGCATGCTAGAGGTAGT 58.429 45.455 20.33 4.77 0.00 2.73
797 882 4.439253 TCTGCATGCTAGAGGTAGTAGA 57.561 45.455 20.33 6.09 0.00 2.59
798 883 4.793201 TCTGCATGCTAGAGGTAGTAGAA 58.207 43.478 20.33 0.00 0.00 2.10
800 885 6.543735 TCTGCATGCTAGAGGTAGTAGAATA 58.456 40.000 20.33 0.00 0.00 1.75
803 888 7.606349 TGCATGCTAGAGGTAGTAGAATATTG 58.394 38.462 20.33 0.00 0.00 1.90
804 889 7.233553 TGCATGCTAGAGGTAGTAGAATATTGT 59.766 37.037 20.33 0.00 0.00 2.71
805 890 8.091449 GCATGCTAGAGGTAGTAGAATATTGTT 58.909 37.037 11.37 0.00 0.00 2.83
836 921 7.386299 ACAGTCTTGTGTTCTGCTTATTCTTAG 59.614 37.037 0.00 0.00 35.83 2.18
849 934 8.383318 TGCTTATTCTTAGTTTATCTGCATCC 57.617 34.615 0.00 0.00 0.00 3.51
857 942 7.833682 TCTTAGTTTATCTGCATCCCATTGAAA 59.166 33.333 0.00 0.00 0.00 2.69
860 945 6.664816 AGTTTATCTGCATCCCATTGAAAAGA 59.335 34.615 0.00 0.00 0.00 2.52
891 977 1.753930 ATGATGCTCGACAAATGGCA 58.246 45.000 0.00 0.00 39.06 4.92
911 997 2.535166 CACGTGCTGAAAATGTTGTTGG 59.465 45.455 0.82 0.00 0.00 3.77
940 1026 3.055385 TGACCCTTGTTCTCGGGATAAAG 60.055 47.826 0.58 0.00 43.44 1.85
1083 1206 2.498644 AGAGGGAAAGTAAAGCTGGC 57.501 50.000 0.00 0.00 0.00 4.85
1124 1328 5.786574 GCAAATTTTCATGTCAAAGATTGCG 59.213 36.000 18.86 0.00 33.13 4.85
1180 1384 3.323403 TCTGGCGATGTTTTCCCAAAAAT 59.677 39.130 0.00 0.00 36.77 1.82
1292 1496 7.328277 ACAAAATGTTGCTATATTCGCCTAA 57.672 32.000 0.00 0.00 38.39 2.69
1312 1516 6.256975 GCCTAAAAATGGTTTTAAATAGCGGG 59.743 38.462 0.00 0.00 38.43 6.13
1313 1517 7.324935 CCTAAAAATGGTTTTAAATAGCGGGT 58.675 34.615 0.00 0.00 38.43 5.28
1314 1518 8.468399 CCTAAAAATGGTTTTAAATAGCGGGTA 58.532 33.333 0.00 0.00 38.43 3.69
1318 1522 6.812879 ATGGTTTTAAATAGCGGGTATAGC 57.187 37.500 0.00 0.00 0.00 2.97
1319 1523 4.751098 TGGTTTTAAATAGCGGGTATAGCG 59.249 41.667 0.00 0.00 40.04 4.26
1320 1524 4.751600 GGTTTTAAATAGCGGGTATAGCGT 59.248 41.667 0.00 0.00 40.04 5.07
1321 1525 5.237127 GGTTTTAAATAGCGGGTATAGCGTT 59.763 40.000 0.00 0.00 40.04 4.84
1322 1526 6.238456 GGTTTTAAATAGCGGGTATAGCGTTT 60.238 38.462 0.00 0.00 40.04 3.60
1323 1527 7.042119 GGTTTTAAATAGCGGGTATAGCGTTTA 60.042 37.037 0.00 0.00 40.04 2.01
1324 1528 7.406799 TTTAAATAGCGGGTATAGCGTTTAC 57.593 36.000 0.00 0.00 40.04 2.01
1325 1529 3.582714 ATAGCGGGTATAGCGTTTACC 57.417 47.619 0.00 4.70 38.73 2.85
1386 1590 3.325870 TCAAATAGCGCGCTATAGCATT 58.674 40.909 43.81 33.15 42.21 3.56
1409 1613 4.888239 TGCTATAGCGTTTAGAAGAGGTCT 59.112 41.667 19.55 0.00 45.83 3.85
1452 1656 9.384764 GCCCACTATTTAGAACTATGATATTCC 57.615 37.037 0.00 0.00 0.00 3.01
1477 1681 5.259632 AGAACCTTGCTTCTGCTAATGATT 58.740 37.500 0.00 0.00 40.48 2.57
1594 1805 5.486332 TCTCTTATGGATTGGTAAGGGGAT 58.514 41.667 0.00 0.00 30.92 3.85
2402 2867 2.007608 GTATTCCAGGCCAGTTCGAAC 58.992 52.381 20.71 20.71 0.00 3.95
3137 3681 1.740025 GTGTCATTAAGCTGGAGCCAC 59.260 52.381 0.00 0.00 43.38 5.01
3281 4370 5.556915 ACGAACCAATAGACAAAATGAGGA 58.443 37.500 0.00 0.00 0.00 3.71
3344 4437 9.225436 TCTGTGTTGTGTTGCTGATATTATTTA 57.775 29.630 0.00 0.00 0.00 1.40
3365 4458 1.003233 GGGTCGTCTTTGATTGGAGGT 59.997 52.381 0.00 0.00 0.00 3.85
3454 6176 3.623060 GCGCTCCTTGATGTTGAGATTTA 59.377 43.478 0.00 0.00 0.00 1.40
3523 6247 4.323562 GCTAGCCTTCCTTCCTTTTGTCTA 60.324 45.833 2.29 0.00 0.00 2.59
3537 6265 5.358160 CCTTTTGTCTATTGGTTCCTGATCC 59.642 44.000 0.00 0.00 0.00 3.36
3556 6284 6.423182 TGATCCCTTTGGTTAATCTTGTAGG 58.577 40.000 0.00 0.00 0.00 3.18
3618 6353 1.700955 AATCCGGGTCACTAGCGTAT 58.299 50.000 0.00 0.00 0.00 3.06
3635 6372 9.912634 ACTAGCGTATGTAGTTGTTTTAGTAAA 57.087 29.630 0.00 0.00 0.00 2.01
3664 6401 7.065563 CCTTCACATTACAATGGAAGAAGAGAG 59.934 40.741 22.14 11.17 41.28 3.20
3669 6406 7.127032 ACATTACAATGGAAGAAGAGAGATCCT 59.873 37.037 6.87 0.00 40.70 3.24
3813 7023 2.438868 TGTCAGACGGAACATGAGTG 57.561 50.000 0.00 0.00 0.00 3.51
4009 7220 7.383102 AGTAAATACATTTCAGAACAGCTGG 57.617 36.000 19.93 0.00 44.98 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.331061 ACTACATCAGGAAACTTAACTAGCG 58.669 40.000 0.00 0.00 40.21 4.26
26 27 2.554142 TCTACGAAGCCGAATCGACTA 58.446 47.619 3.36 0.00 42.76 2.59
30 31 1.319172 CGATCTACGAAGCCGAATCG 58.681 55.000 0.00 0.00 45.77 3.34
97 102 0.461548 TGGCGGCTGATAACTCTCTG 59.538 55.000 11.43 0.00 0.00 3.35
140 150 2.047274 CCGACCACAGCACCGATT 60.047 61.111 0.00 0.00 0.00 3.34
144 154 2.358737 CCTTCCGACCACAGCACC 60.359 66.667 0.00 0.00 0.00 5.01
150 160 1.196012 ATCTTCCTCCTTCCGACCAC 58.804 55.000 0.00 0.00 0.00 4.16
152 162 2.101750 GAGAATCTTCCTCCTTCCGACC 59.898 54.545 0.00 0.00 0.00 4.79
170 180 1.153208 GTCGACCTAGAGCCCGAGA 60.153 63.158 3.51 0.00 0.00 4.04
171 181 2.188161 GGTCGACCTAGAGCCCGAG 61.188 68.421 27.64 0.00 32.92 4.63
174 184 1.076923 TCAGGTCGACCTAGAGCCC 60.077 63.158 35.80 6.55 46.65 5.19
175 185 0.680280 TGTCAGGTCGACCTAGAGCC 60.680 60.000 35.80 21.78 46.65 4.70
177 187 1.096416 GGTGTCAGGTCGACCTAGAG 58.904 60.000 35.80 23.72 46.65 2.43
178 188 0.697079 AGGTGTCAGGTCGACCTAGA 59.303 55.000 35.80 28.93 46.65 2.43
180 190 0.402887 TCAGGTGTCAGGTCGACCTA 59.597 55.000 35.80 19.18 46.65 3.08
182 192 0.391597 TTTCAGGTGTCAGGTCGACC 59.608 55.000 27.67 27.67 44.71 4.79
183 193 1.499049 GTTTCAGGTGTCAGGTCGAC 58.501 55.000 7.13 7.13 45.61 4.20
184 194 0.391597 GGTTTCAGGTGTCAGGTCGA 59.608 55.000 0.00 0.00 0.00 4.20
185 195 0.393077 AGGTTTCAGGTGTCAGGTCG 59.607 55.000 0.00 0.00 0.00 4.79
186 196 1.416401 TGAGGTTTCAGGTGTCAGGTC 59.584 52.381 0.00 0.00 0.00 3.85
187 197 1.507140 TGAGGTTTCAGGTGTCAGGT 58.493 50.000 0.00 0.00 0.00 4.00
188 198 2.158755 ACTTGAGGTTTCAGGTGTCAGG 60.159 50.000 0.00 0.00 41.54 3.86
189 199 3.199880 ACTTGAGGTTTCAGGTGTCAG 57.800 47.619 0.00 0.00 41.54 3.51
190 200 3.644966 AACTTGAGGTTTCAGGTGTCA 57.355 42.857 0.00 0.00 42.19 3.58
209 219 3.812053 GCTCTGCTTTCTTGAGTCTGAAA 59.188 43.478 10.07 10.07 0.00 2.69
211 221 2.366590 TGCTCTGCTTTCTTGAGTCTGA 59.633 45.455 0.00 0.00 0.00 3.27
215 225 3.243334 GCTTTTGCTCTGCTTTCTTGAGT 60.243 43.478 0.00 0.00 43.35 3.41
217 227 3.360249 GCTTTTGCTCTGCTTTCTTGA 57.640 42.857 0.00 0.00 43.35 3.02
251 273 7.665690 TGCTTTTTGAATCCTAAATACTTGCA 58.334 30.769 0.00 0.00 0.00 4.08
258 284 7.578380 GCTTCCTCTGCTTTTTGAATCCTAAAT 60.578 37.037 0.00 0.00 0.00 1.40
261 287 4.702131 GCTTCCTCTGCTTTTTGAATCCTA 59.298 41.667 0.00 0.00 0.00 2.94
265 291 3.638160 TGTGCTTCCTCTGCTTTTTGAAT 59.362 39.130 0.00 0.00 0.00 2.57
270 296 3.986277 CAATTGTGCTTCCTCTGCTTTT 58.014 40.909 0.00 0.00 0.00 2.27
288 324 9.761504 GATGCATATATAGATACAGACTGCAAT 57.238 33.333 0.00 0.00 40.11 3.56
291 327 8.412456 ACTGATGCATATATAGATACAGACTGC 58.588 37.037 0.00 3.97 0.00 4.40
309 345 4.644498 TCAGAACTGAATCAACTGATGCA 58.356 39.130 1.79 0.41 37.75 3.96
313 349 5.702670 GGACAATCAGAACTGAATCAACTGA 59.297 40.000 8.59 13.56 43.58 3.41
314 350 5.471116 TGGACAATCAGAACTGAATCAACTG 59.529 40.000 8.59 5.74 43.58 3.16
315 351 5.624159 TGGACAATCAGAACTGAATCAACT 58.376 37.500 8.59 0.00 43.58 3.16
316 352 5.947228 TGGACAATCAGAACTGAATCAAC 57.053 39.130 8.59 1.50 43.58 3.18
317 353 6.005823 ACATGGACAATCAGAACTGAATCAA 58.994 36.000 8.59 2.01 43.58 2.57
318 354 5.563592 ACATGGACAATCAGAACTGAATCA 58.436 37.500 8.59 4.18 43.58 2.57
319 355 6.506500 AACATGGACAATCAGAACTGAATC 57.493 37.500 8.59 6.98 43.58 2.52
320 356 6.684686 CAAACATGGACAATCAGAACTGAAT 58.315 36.000 8.59 0.00 43.58 2.57
321 357 5.507817 GCAAACATGGACAATCAGAACTGAA 60.508 40.000 8.59 0.00 43.58 3.02
341 377 1.174712 GGCAGAAGTCAGCAGGCAAA 61.175 55.000 0.00 0.00 0.00 3.68
345 381 1.078567 GGAGGCAGAAGTCAGCAGG 60.079 63.158 0.00 0.00 0.00 4.85
347 383 1.372683 GTGGAGGCAGAAGTCAGCA 59.627 57.895 0.00 0.00 0.00 4.41
348 384 0.250467 TTGTGGAGGCAGAAGTCAGC 60.250 55.000 0.00 0.00 0.00 4.26
352 388 2.613977 CGAGATTTGTGGAGGCAGAAGT 60.614 50.000 0.00 0.00 0.00 3.01
353 389 2.005451 CGAGATTTGTGGAGGCAGAAG 58.995 52.381 0.00 0.00 0.00 2.85
357 393 0.674581 CAGCGAGATTTGTGGAGGCA 60.675 55.000 0.00 0.00 0.00 4.75
362 398 7.148641 ACTATAGTTATCAGCGAGATTTGTGG 58.851 38.462 0.00 0.00 38.19 4.17
369 405 6.526526 ACTCTGACTATAGTTATCAGCGAGA 58.473 40.000 6.88 0.00 39.80 4.04
382 418 2.697229 TCCGACCTCGACTCTGACTATA 59.303 50.000 0.00 0.00 43.02 1.31
383 419 1.485480 TCCGACCTCGACTCTGACTAT 59.515 52.381 0.00 0.00 43.02 2.12
384 420 0.900421 TCCGACCTCGACTCTGACTA 59.100 55.000 0.00 0.00 43.02 2.59
385 421 0.036448 TTCCGACCTCGACTCTGACT 59.964 55.000 0.00 0.00 43.02 3.41
386 422 0.168568 GTTCCGACCTCGACTCTGAC 59.831 60.000 0.00 0.00 43.02 3.51
387 423 1.296755 CGTTCCGACCTCGACTCTGA 61.297 60.000 0.00 0.00 43.02 3.27
388 424 1.134901 CGTTCCGACCTCGACTCTG 59.865 63.158 0.00 0.00 43.02 3.35
389 425 0.604780 TTCGTTCCGACCTCGACTCT 60.605 55.000 0.00 0.00 43.02 3.24
390 426 0.179194 CTTCGTTCCGACCTCGACTC 60.179 60.000 0.00 0.00 43.02 3.36
391 427 0.604780 TCTTCGTTCCGACCTCGACT 60.605 55.000 0.00 0.00 43.02 4.18
393 429 0.450583 CATCTTCGTTCCGACCTCGA 59.549 55.000 0.00 0.00 43.02 4.04
394 430 0.450583 TCATCTTCGTTCCGACCTCG 59.549 55.000 0.00 0.00 34.89 4.63
395 431 2.094649 ACTTCATCTTCGTTCCGACCTC 60.095 50.000 0.00 0.00 34.89 3.85
396 432 1.893801 ACTTCATCTTCGTTCCGACCT 59.106 47.619 0.00 0.00 34.89 3.85
397 433 2.260481 GACTTCATCTTCGTTCCGACC 58.740 52.381 0.00 0.00 34.89 4.79
399 435 1.731424 GCGACTTCATCTTCGTTCCGA 60.731 52.381 0.00 0.00 37.56 4.55
400 436 0.640768 GCGACTTCATCTTCGTTCCG 59.359 55.000 0.00 0.00 37.56 4.30
401 437 1.656095 CAGCGACTTCATCTTCGTTCC 59.344 52.381 0.00 0.00 37.56 3.62
402 438 1.656095 CCAGCGACTTCATCTTCGTTC 59.344 52.381 0.00 0.00 37.56 3.95
403 439 1.272490 TCCAGCGACTTCATCTTCGTT 59.728 47.619 0.00 0.00 37.56 3.85
404 440 0.888619 TCCAGCGACTTCATCTTCGT 59.111 50.000 0.00 0.00 37.56 3.85
405 441 1.554392 CTCCAGCGACTTCATCTTCG 58.446 55.000 0.00 0.00 38.31 3.79
406 442 1.285578 GCTCCAGCGACTTCATCTTC 58.714 55.000 0.00 0.00 0.00 2.87
407 443 3.450028 GCTCCAGCGACTTCATCTT 57.550 52.632 0.00 0.00 0.00 2.40
444 480 4.897509 TCATTATGTCTATCTGGGCCTG 57.102 45.455 4.53 4.06 0.00 4.85
451 487 5.105146 GGCGATCCCTTCATTATGTCTATCT 60.105 44.000 0.00 0.00 0.00 1.98
453 489 5.091261 GGCGATCCCTTCATTATGTCTAT 57.909 43.478 0.00 0.00 0.00 1.98
454 490 4.537135 GGCGATCCCTTCATTATGTCTA 57.463 45.455 0.00 0.00 0.00 2.59
455 491 3.409026 GGCGATCCCTTCATTATGTCT 57.591 47.619 0.00 0.00 0.00 3.41
478 539 0.179073 CATCCTGGACGGCTTACCTG 60.179 60.000 0.00 0.00 0.00 4.00
489 550 4.770362 TCCGTCCGGCATCCTGGA 62.770 66.667 0.00 0.00 34.68 3.86
494 555 1.810030 GAACTGTCCGTCCGGCATC 60.810 63.158 0.00 0.00 34.68 3.91
495 556 2.264794 GAACTGTCCGTCCGGCAT 59.735 61.111 0.00 0.00 34.68 4.40
496 557 3.228017 TGAACTGTCCGTCCGGCA 61.228 61.111 0.00 1.99 34.68 5.69
497 558 2.737376 GTGAACTGTCCGTCCGGC 60.737 66.667 0.00 0.00 34.68 6.13
498 559 2.430244 CGTGAACTGTCCGTCCGG 60.430 66.667 0.00 0.00 0.00 5.14
499 560 2.430244 CCGTGAACTGTCCGTCCG 60.430 66.667 0.00 0.00 0.00 4.79
501 562 1.728426 CGACCGTGAACTGTCCGTC 60.728 63.158 0.21 0.00 0.00 4.79
503 564 1.728426 GTCGACCGTGAACTGTCCG 60.728 63.158 3.51 0.00 0.00 4.79
504 565 0.038526 ATGTCGACCGTGAACTGTCC 60.039 55.000 14.12 0.00 0.00 4.02
518 579 1.800586 CAGTCCACAACAGGAATGTCG 59.199 52.381 2.53 0.00 45.92 4.35
543 604 1.661617 CGAGTGTGTTTGTTTCGACCA 59.338 47.619 0.00 0.00 33.38 4.02
544 605 1.004292 CCGAGTGTGTTTGTTTCGACC 60.004 52.381 0.00 0.00 33.38 4.79
545 606 1.662122 ACCGAGTGTGTTTGTTTCGAC 59.338 47.619 0.00 0.00 33.38 4.20
555 632 2.224426 TGATAAGCCAAACCGAGTGTGT 60.224 45.455 0.00 0.00 0.00 3.72
600 683 5.335504 CCTTGAGCAGAAAATTCAGACTTCC 60.336 44.000 0.00 0.00 0.00 3.46
634 717 7.645058 AACCAAATCTAAACAATCATCGGAT 57.355 32.000 0.00 0.00 34.43 4.18
637 720 8.240682 TGGTTAACCAAATCTAAACAATCATCG 58.759 33.333 25.19 0.00 44.35 3.84
702 787 9.691362 ACACAATCCAAATACTAAACATGTTTC 57.309 29.630 26.46 0.00 34.23 2.78
725 810 7.658179 TCAATAGATGAAGAGTGTTTCACAC 57.342 36.000 0.00 0.00 41.39 3.82
754 839 7.609960 CAGATCAGCACACCTTGATATATACT 58.390 38.462 0.00 0.00 0.00 2.12
755 840 6.312426 GCAGATCAGCACACCTTGATATATAC 59.688 42.308 5.05 0.00 0.00 1.47
762 847 0.397564 TGCAGATCAGCACACCTTGA 59.602 50.000 8.95 0.00 40.11 3.02
798 883 9.998106 AGAACACAAGACTGTACTTAACAATAT 57.002 29.630 0.00 0.00 37.74 1.28
800 885 7.254795 GCAGAACACAAGACTGTACTTAACAAT 60.255 37.037 0.00 0.00 37.74 2.71
803 888 5.753921 AGCAGAACACAAGACTGTACTTAAC 59.246 40.000 0.00 0.00 33.22 2.01
804 889 5.914033 AGCAGAACACAAGACTGTACTTAA 58.086 37.500 0.00 0.00 33.22 1.85
805 890 5.531122 AGCAGAACACAAGACTGTACTTA 57.469 39.130 0.00 0.00 33.22 2.24
806 891 4.408182 AGCAGAACACAAGACTGTACTT 57.592 40.909 0.00 0.00 33.22 2.24
811 896 6.551385 AAGAATAAGCAGAACACAAGACTG 57.449 37.500 0.00 0.00 35.14 3.51
813 898 7.659652 ACTAAGAATAAGCAGAACACAAGAC 57.340 36.000 0.00 0.00 0.00 3.01
836 921 6.866480 TCTTTTCAATGGGATGCAGATAAAC 58.134 36.000 0.00 0.00 0.00 2.01
873 958 0.804364 GTGCCATTTGTCGAGCATCA 59.196 50.000 0.00 0.00 37.60 3.07
874 959 0.247814 CGTGCCATTTGTCGAGCATC 60.248 55.000 0.00 0.00 37.60 3.91
891 977 2.425312 TCCAACAACATTTTCAGCACGT 59.575 40.909 0.00 0.00 0.00 4.49
911 997 0.980423 AGAACAAGGGTCAGCCTCTC 59.020 55.000 0.00 0.00 34.45 3.20
1011 1134 5.134339 TGGAAGACCATCCCTTAAAGCATAT 59.866 40.000 0.00 0.00 41.77 1.78
1124 1328 4.757149 AGTGTTATCTCAAACAGTGCTTCC 59.243 41.667 0.00 0.00 40.62 3.46
1180 1384 3.255888 CGCAAGGACTATACCAGCATCTA 59.744 47.826 0.00 0.00 34.51 1.98
1269 1473 8.627487 TTTTAGGCGAATATAGCAACATTTTG 57.373 30.769 5.61 0.00 36.08 2.44
1292 1496 8.139350 GCTATACCCGCTATTTAAAACCATTTT 58.861 33.333 0.00 0.00 36.67 1.82
1318 1522 1.628447 TTGCTTAGCGCGGGTAAACG 61.628 55.000 8.83 0.00 43.27 3.60
1319 1523 0.179207 GTTGCTTAGCGCGGGTAAAC 60.179 55.000 8.83 1.92 43.27 2.01
1320 1524 0.320946 AGTTGCTTAGCGCGGGTAAA 60.321 50.000 8.83 0.00 43.27 2.01
1321 1525 0.320946 AAGTTGCTTAGCGCGGGTAA 60.321 50.000 8.83 4.15 43.27 2.85
1322 1526 0.320946 AAAGTTGCTTAGCGCGGGTA 60.321 50.000 8.83 0.00 43.27 3.69
1323 1527 1.599797 AAAGTTGCTTAGCGCGGGT 60.600 52.632 8.83 0.00 43.27 5.28
1324 1528 1.154225 CAAAGTTGCTTAGCGCGGG 60.154 57.895 8.83 0.00 43.27 6.13
1325 1529 1.154225 CCAAAGTTGCTTAGCGCGG 60.154 57.895 8.83 0.00 43.27 6.46
1326 1530 0.452784 GACCAAAGTTGCTTAGCGCG 60.453 55.000 0.00 0.00 43.27 6.86
1327 1531 0.109735 GGACCAAAGTTGCTTAGCGC 60.110 55.000 0.00 0.00 39.77 5.92
1328 1532 1.234821 TGGACCAAAGTTGCTTAGCG 58.765 50.000 0.00 0.00 0.00 4.26
1332 1536 2.564947 TGTGTTTGGACCAAAGTTGCTT 59.435 40.909 20.14 0.00 33.82 3.91
1336 1540 4.221703 TGTTCATGTGTTTGGACCAAAGTT 59.778 37.500 20.14 2.78 33.82 2.66
1386 1590 4.888239 AGACCTCTTCTAAACGCTATAGCA 59.112 41.667 23.99 3.96 34.73 3.49
1452 1656 2.370281 TAGCAGAAGCAAGGTTCTCG 57.630 50.000 11.25 8.69 45.49 4.04
1713 1925 0.469892 CCACCAAGGTCAAGGCCTTT 60.470 55.000 17.61 0.00 45.91 3.11
1797 2010 8.926715 TCATATGAACATAGTAACACAGTGAC 57.073 34.615 7.81 0.00 0.00 3.67
2402 2867 3.713288 TCGATTTGCTTCCCACGTATAG 58.287 45.455 0.00 0.00 0.00 1.31
3137 3681 9.581099 AATGACCAGTAACAAAAGTACAAAAAG 57.419 29.630 0.00 0.00 0.00 2.27
3281 4370 9.573133 GCATTTAATCAACTAGCATAAACAACT 57.427 29.630 0.00 0.00 0.00 3.16
3344 4437 1.279271 CCTCCAATCAAAGACGACCCT 59.721 52.381 0.00 0.00 0.00 4.34
3454 6176 8.330466 TCAAACAAAGTTATACATCGACCAAT 57.670 30.769 0.00 0.00 0.00 3.16
3523 6247 2.383338 ACCAAAGGGATCAGGAACCAAT 59.617 45.455 0.00 0.00 38.05 3.16
3618 6353 7.012610 GTGAAGGCCTTTACTAAAACAACTACA 59.987 37.037 28.32 10.22 0.00 2.74
3635 6372 3.737559 TCCATTGTAATGTGAAGGCCT 57.262 42.857 0.00 0.00 34.60 5.19
3664 6401 1.428869 ACATAGGTGCCCTCAGGATC 58.571 55.000 0.00 0.00 34.61 3.36
3669 6406 4.231273 ACATACATACATAGGTGCCCTCA 58.769 43.478 0.00 0.00 34.61 3.86
4009 7220 0.387929 TGGACCCGACGATATTCAGC 59.612 55.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.