Multiple sequence alignment - TraesCS3A01G339000

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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 TraesCS3A01G339000 chr3A 100.000 3903 0 0 1 3903 585603386 585607288 0.000000e+00 7208.0
1 TraesCS3A01G339000 chr3A 92.500 200 12 3 2247 2444 611185135 611185333 2.300000e-72 283.0
2 TraesCS3A01G339000 chr3D 93.941 2162 72 22 143 2255 444794913 444797064 0.000000e+00 3212.0
3 TraesCS3A01G339000 chr3D 97.901 905 16 2 2416 3317 444797062 444797966 0.000000e+00 1563.0
4 TraesCS3A01G339000 chr3D 95.507 601 14 6 3316 3903 444797995 444798595 0.000000e+00 948.0
5 TraesCS3A01G339000 chr3D 88.182 110 10 3 1 107 18787927 18787818 1.140000e-25 128.0
6 TraesCS3A01G339000 chr3B 92.021 2068 91 32 149 2192 582789504 582791521 0.000000e+00 2837.0
7 TraesCS3A01G339000 chr3B 95.066 912 34 5 2416 3318 582791658 582792567 0.000000e+00 1424.0
8 TraesCS3A01G339000 chr3B 89.583 576 39 10 3316 3878 582792595 582793162 0.000000e+00 712.0
9 TraesCS3A01G339000 chr3B 87.862 552 31 15 2753 3292 582793170 582793697 1.990000e-172 616.0
10 TraesCS3A01G339000 chr3B 100.000 34 0 0 108 141 582789488 582789521 3.260000e-06 63.9
11 TraesCS3A01G339000 chr7A 97.714 175 4 0 2246 2420 347249522 347249348 6.340000e-78 302.0
12 TraesCS3A01G339000 chr7A 90.000 110 8 3 1 107 151346613 151346504 5.260000e-29 139.0
13 TraesCS3A01G339000 chr6A 97.175 177 4 1 2250 2425 105041908 105042084 8.200000e-77 298.0
14 TraesCS3A01G339000 chr7D 94.330 194 9 2 2242 2433 50710232 50710425 2.950000e-76 296.0
15 TraesCS3A01G339000 chr1D 97.159 176 3 2 2242 2417 178466297 178466470 2.950000e-76 296.0
16 TraesCS3A01G339000 chr1D 94.709 189 7 3 2236 2423 288702868 288702682 1.370000e-74 291.0
17 TraesCS3A01G339000 chr1D 96.552 174 5 1 2253 2425 39871979 39871806 1.770000e-73 287.0
18 TraesCS3A01G339000 chr1D 87.963 108 12 1 1 107 109761748 109761855 4.090000e-25 126.0
19 TraesCS3A01G339000 chr2D 92.611 203 11 3 2243 2443 34261047 34261247 4.930000e-74 289.0
20 TraesCS3A01G339000 chr6B 97.024 168 5 0 2250 2417 685530958 685531125 2.300000e-72 283.0
21 TraesCS3A01G339000 chr6B 86.239 109 13 2 1 107 573989448 573989340 2.460000e-22 117.0
22 TraesCS3A01G339000 chr5B 88.679 106 9 3 2 106 41252277 41252380 4.090000e-25 126.0
23 TraesCS3A01G339000 chr7B 87.273 110 11 3 1 107 191730993 191731102 5.300000e-24 122.0
24 TraesCS3A01G339000 chr2A 87.156 109 12 2 1 107 710389922 710389814 5.300000e-24 122.0
25 TraesCS3A01G339000 chr2B 86.111 108 13 2 1 107 154935028 154934922 8.860000e-22 115.0
26 TraesCS3A01G339000 chr2B 85.321 109 14 2 1 107 729774857 729774749 1.150000e-20 111.0


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 TraesCS3A01G339000 chr3A 585603386 585607288 3902 False 7208.000000 7208 100.0000 1 3903 1 chr3A.!!$F1 3902
1 TraesCS3A01G339000 chr3D 444794913 444798595 3682 False 1907.666667 3212 95.7830 143 3903 3 chr3D.!!$F1 3760
2 TraesCS3A01G339000 chr3B 582789488 582793697 4209 False 1130.580000 2837 92.9064 108 3878 5 chr3B.!!$F1 3770

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
469 489 0.250510 GCAATCCTCCCCCGATTCTC 60.251 60.0 0.00 0.0 0.00 2.87 F
1289 1328 0.250989 TGGTGGGTGGATTTTCCGTC 60.251 55.0 0.00 0.0 40.17 4.79 F
1560 1619 0.962489 CACCCAATTACAAACGGCCA 59.038 50.0 2.24 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 2543 0.316204 CAAACACGTACTCCCTCCGT 59.684 55.0 0.0 0.0 34.71 4.69 R
2407 2545 2.224113 TGAACAAACACGTACTCCCTCC 60.224 50.0 0.0 0.0 0.00 4.30 R
3447 3657 1.107945 CCAAAACTCCGTGGTTGGTT 58.892 50.0 0.0 0.0 36.55 3.67 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
23 24 3.691342 CCGGCGACTGAGGACCAA 61.691 66.667 9.30 0.00 0.00 3.67
24 25 2.579201 CGGCGACTGAGGACCAAT 59.421 61.111 0.00 0.00 0.00 3.16
25 26 1.079127 CGGCGACTGAGGACCAATT 60.079 57.895 0.00 0.00 0.00 2.32
26 27 1.084370 CGGCGACTGAGGACCAATTC 61.084 60.000 0.00 0.00 0.00 2.17
27 28 1.084370 GGCGACTGAGGACCAATTCG 61.084 60.000 0.00 0.00 34.92 3.34
28 29 1.696832 GCGACTGAGGACCAATTCGC 61.697 60.000 13.56 13.56 44.11 4.70
29 30 1.084370 CGACTGAGGACCAATTCGCC 61.084 60.000 0.00 0.00 0.00 5.54
30 31 0.250513 GACTGAGGACCAATTCGCCT 59.749 55.000 0.00 0.00 33.97 5.52
31 32 0.250513 ACTGAGGACCAATTCGCCTC 59.749 55.000 9.71 9.71 46.60 4.70
33 34 3.071580 GAGGACCAATTCGCCTCAG 57.928 57.895 11.16 0.00 45.89 3.35
34 35 0.462759 GAGGACCAATTCGCCTCAGG 60.463 60.000 11.16 0.00 45.89 3.86
35 36 2.115291 GGACCAATTCGCCTCAGGC 61.115 63.158 5.22 5.22 46.75 4.85
56 57 3.027292 TTTTTGTGCCGGCTCGTC 58.973 55.556 29.70 15.44 0.00 4.20
57 58 2.548295 TTTTTGTGCCGGCTCGTCC 61.548 57.895 29.70 10.65 0.00 4.79
71 72 4.796495 GTCCCCAGGCGGCGATTT 62.796 66.667 12.98 0.00 0.00 2.17
72 73 4.041762 TCCCCAGGCGGCGATTTT 62.042 61.111 12.98 0.00 0.00 1.82
73 74 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
74 75 2.186826 CCCCAGGCGGCGATTTTAG 61.187 63.158 12.98 0.00 0.00 1.85
75 76 2.186826 CCCAGGCGGCGATTTTAGG 61.187 63.158 12.98 2.42 0.00 2.69
76 77 2.715624 CAGGCGGCGATTTTAGGC 59.284 61.111 12.98 0.00 0.00 3.93
82 83 3.023118 GCGATTTTAGGCGCCCTC 58.977 61.111 26.15 11.49 46.93 4.30
83 84 1.523938 GCGATTTTAGGCGCCCTCT 60.524 57.895 26.15 7.52 46.93 3.69
84 85 1.776034 GCGATTTTAGGCGCCCTCTG 61.776 60.000 26.15 8.08 46.93 3.35
85 86 1.160329 CGATTTTAGGCGCCCTCTGG 61.160 60.000 26.15 2.58 34.61 3.86
102 103 2.360191 GGGGGCAATGGCTGAAGA 59.640 61.111 6.78 0.00 40.87 2.87
103 104 1.075748 GGGGGCAATGGCTGAAGAT 60.076 57.895 6.78 0.00 40.87 2.40
104 105 1.397390 GGGGGCAATGGCTGAAGATG 61.397 60.000 6.78 0.00 40.87 2.90
105 106 1.440476 GGGCAATGGCTGAAGATGC 59.560 57.895 6.78 0.00 40.87 3.91
106 107 1.041447 GGGCAATGGCTGAAGATGCT 61.041 55.000 6.78 0.00 40.87 3.79
141 142 4.287067 TCTGGAACAAAAGCAGAGTATCCT 59.713 41.667 0.00 0.00 38.70 3.24
142 143 4.985538 TGGAACAAAAGCAGAGTATCCTT 58.014 39.130 0.00 0.00 29.61 3.36
143 144 5.385198 TGGAACAAAAGCAGAGTATCCTTT 58.615 37.500 0.00 0.00 29.61 3.11
144 145 5.833131 TGGAACAAAAGCAGAGTATCCTTTT 59.167 36.000 0.00 0.00 38.82 2.27
145 146 6.016276 TGGAACAAAAGCAGAGTATCCTTTTC 60.016 38.462 0.00 0.00 36.85 2.29
146 147 5.613358 ACAAAAGCAGAGTATCCTTTTCG 57.387 39.130 0.00 0.00 36.85 3.46
147 148 4.083271 ACAAAAGCAGAGTATCCTTTTCGC 60.083 41.667 0.00 0.00 36.85 4.70
148 149 3.334583 AAGCAGAGTATCCTTTTCGCA 57.665 42.857 0.00 0.00 33.66 5.10
149 150 3.334583 AGCAGAGTATCCTTTTCGCAA 57.665 42.857 0.00 0.00 33.66 4.85
150 151 3.674997 AGCAGAGTATCCTTTTCGCAAA 58.325 40.909 0.00 0.00 33.66 3.68
175 176 7.854166 AAAAGCAGAGTATCCAGAGATAGAT 57.146 36.000 0.00 0.00 35.61 1.98
285 293 4.323751 CAGCGCTAATCTCGTAACAAAAC 58.676 43.478 10.99 0.00 0.00 2.43
469 489 0.250510 GCAATCCTCCCCCGATTCTC 60.251 60.000 0.00 0.00 0.00 2.87
593 618 2.878406 CGCCTTTTCTTTCTCCTTCACA 59.122 45.455 0.00 0.00 0.00 3.58
604 629 1.795286 CTCCTTCACAAACTCGCAGTC 59.205 52.381 0.00 0.00 0.00 3.51
669 694 1.332375 GAATTTAAGTGGCGCCGCATA 59.668 47.619 39.02 29.92 0.00 3.14
713 738 8.446273 AGATGTGACTCTGTTTTTCGATTATTG 58.554 33.333 0.00 0.00 0.00 1.90
819 846 1.745115 CTGCCCGGATTCAAAGCGA 60.745 57.895 0.73 0.00 0.00 4.93
861 891 1.069227 GGATAAATTGCCACCGATCGC 60.069 52.381 10.32 0.00 0.00 4.58
927 957 2.314215 TAGCGAGAGGGGAGGTCCA 61.314 63.158 0.00 0.00 37.91 4.02
1163 1202 7.777095 TGCTTTTACCTATCTGTTTGTTTTGT 58.223 30.769 0.00 0.00 0.00 2.83
1164 1203 8.904834 TGCTTTTACCTATCTGTTTGTTTTGTA 58.095 29.630 0.00 0.00 0.00 2.41
1289 1328 0.250989 TGGTGGGTGGATTTTCCGTC 60.251 55.000 0.00 0.00 40.17 4.79
1293 1332 1.271707 TGGGTGGATTTTCCGTCTTCC 60.272 52.381 0.00 0.00 40.17 3.46
1294 1333 1.460504 GGTGGATTTTCCGTCTTCCC 58.539 55.000 0.00 0.00 40.17 3.97
1446 1501 3.713764 AGTAGTTTGCATGGAGCCTATCT 59.286 43.478 0.00 0.00 44.83 1.98
1447 1502 2.928334 AGTTTGCATGGAGCCTATCTG 58.072 47.619 0.00 0.00 44.83 2.90
1478 1533 3.054361 ACCCTGAGACTTGTTTGACAGTT 60.054 43.478 0.00 0.00 0.00 3.16
1479 1534 3.313526 CCCTGAGACTTGTTTGACAGTTG 59.686 47.826 0.00 0.00 0.00 3.16
1484 1543 3.873952 AGACTTGTTTGACAGTTGAGAGC 59.126 43.478 0.00 0.00 0.00 4.09
1506 1565 4.332268 GCTGCTATTCTCAGAAGTTGGAAG 59.668 45.833 0.00 0.00 33.54 3.46
1558 1617 2.804697 AACACCCAATTACAAACGGC 57.195 45.000 0.00 0.00 0.00 5.68
1560 1619 0.962489 CACCCAATTACAAACGGCCA 59.038 50.000 2.24 0.00 0.00 5.36
1686 1745 1.007580 CAGTCAGCTGCTATGCACTG 58.992 55.000 9.47 12.53 38.25 3.66
1897 1956 2.584064 CGCTGGTGGCAGGACATA 59.416 61.111 0.00 0.00 41.91 2.29
2025 2084 2.028020 AGCTGAGTCGGGAGGTAAAAAG 60.028 50.000 0.05 0.00 0.00 2.27
2070 2129 5.427806 TGTTCCTTCTGATTCTGAGGATGAT 59.572 40.000 4.53 0.00 0.00 2.45
2161 2220 3.064545 GCAGCATCTTGTATTTTCGCTCT 59.935 43.478 0.00 0.00 0.00 4.09
2252 2390 9.709495 ACATTATTGTGTCAGTTGCAAAAATAT 57.291 25.926 0.00 0.00 33.85 1.28
2256 2394 8.970691 ATTGTGTCAGTTGCAAAAATATACTC 57.029 30.769 0.00 0.00 0.00 2.59
2257 2395 6.908825 TGTGTCAGTTGCAAAAATATACTCC 58.091 36.000 0.00 0.00 0.00 3.85
2258 2396 6.072175 TGTGTCAGTTGCAAAAATATACTCCC 60.072 38.462 0.00 0.00 0.00 4.30
2259 2397 6.151144 GTGTCAGTTGCAAAAATATACTCCCT 59.849 38.462 0.00 0.00 0.00 4.20
2260 2398 6.374333 TGTCAGTTGCAAAAATATACTCCCTC 59.626 38.462 0.00 0.00 0.00 4.30
2261 2399 5.885912 TCAGTTGCAAAAATATACTCCCTCC 59.114 40.000 0.00 0.00 0.00 4.30
2262 2400 4.881850 AGTTGCAAAAATATACTCCCTCCG 59.118 41.667 0.00 0.00 0.00 4.63
2263 2401 4.497291 TGCAAAAATATACTCCCTCCGT 57.503 40.909 0.00 0.00 0.00 4.69
2264 2402 4.850680 TGCAAAAATATACTCCCTCCGTT 58.149 39.130 0.00 0.00 0.00 4.44
2265 2403 4.879545 TGCAAAAATATACTCCCTCCGTTC 59.120 41.667 0.00 0.00 0.00 3.95
2266 2404 4.275196 GCAAAAATATACTCCCTCCGTTCC 59.725 45.833 0.00 0.00 0.00 3.62
2267 2405 5.681639 CAAAAATATACTCCCTCCGTTCCT 58.318 41.667 0.00 0.00 0.00 3.36
2268 2406 6.687139 GCAAAAATATACTCCCTCCGTTCCTA 60.687 42.308 0.00 0.00 0.00 2.94
2269 2407 7.277396 CAAAAATATACTCCCTCCGTTCCTAA 58.723 38.462 0.00 0.00 0.00 2.69
2270 2408 7.441903 AAAATATACTCCCTCCGTTCCTAAA 57.558 36.000 0.00 0.00 0.00 1.85
2271 2409 7.628501 AAATATACTCCCTCCGTTCCTAAAT 57.371 36.000 0.00 0.00 0.00 1.40
2272 2410 8.731591 AAATATACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
2273 2411 8.912614 AATATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
2274 2412 8.912614 ATATACTCCCTCCGTTCCTAAATATT 57.087 34.615 0.00 0.00 0.00 1.28
2275 2413 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2276 2414 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2277 2415 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2278 2416 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2279 2417 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2280 2418 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2281 2419 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2282 2420 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2283 2421 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2300 2438 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2301 2439 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2322 2460 9.462606 TGGACTACCACATACAGATGTATATAG 57.537 37.037 5.21 7.73 44.82 1.31
2323 2461 9.682465 GGACTACCACATACAGATGTATATAGA 57.318 37.037 5.21 0.00 44.82 1.98
2357 2495 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2358 2496 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2359 2497 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2360 2498 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2361 2499 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2362 2500 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2363 2501 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2364 2502 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2365 2503 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2366 2504 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2367 2505 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2368 2506 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2369 2507 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2370 2508 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2371 2509 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2372 2510 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2373 2511 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2374 2512 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2375 2513 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2376 2514 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2377 2515 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2378 2516 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2379 2517 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2380 2518 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2381 2519 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2382 2520 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2383 2521 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2384 2522 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2385 2523 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2386 2524 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2387 2525 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2388 2526 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2389 2527 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2390 2528 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2391 2529 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2392 2530 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2393 2531 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2394 2532 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2395 2533 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2411 2549 8.947115 AGAAAGACAAATATTTAGAAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
2412 2550 7.625828 AAGACAAATATTTAGAAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
2413 2551 6.954232 AGACAAATATTTAGAAACGGAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
2414 2552 7.048512 AGACAAATATTTAGAAACGGAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
2420 2558 0.886563 AGAAACGGAGGGAGTACGTG 59.113 55.000 0.00 0.00 41.12 4.49
2494 2634 7.831193 AGTTCTCATTGATAGCTGGTTTGTTAT 59.169 33.333 0.00 0.00 0.00 1.89
2601 2745 9.722056 GAATTTATATCCTTGTACTTTGTGCAG 57.278 33.333 0.00 0.00 28.83 4.41
2810 2954 4.162320 CACCTGAGAAGGGAAGCATTAGTA 59.838 45.833 0.00 0.00 0.00 1.82
2973 3118 5.496556 TGCTTAGGTTGTGTACATAGCATT 58.503 37.500 8.61 0.00 33.71 3.56
3027 3172 1.471676 CCTCTAGCGGTGCGAAGATTT 60.472 52.381 0.00 0.00 0.00 2.17
3076 3225 7.795482 TGTTTCTCTTTTCTCCACGAATTTA 57.205 32.000 0.00 0.00 0.00 1.40
3379 3588 5.066593 AGGTTTCTCAGACTTGAAATCACC 58.933 41.667 11.37 6.51 36.18 4.02
3447 3657 0.537143 GGTGACAAGTGGGCATGTGA 60.537 55.000 0.00 0.00 0.00 3.58
3480 3699 4.082463 GGAGTTTTGGTGTGTTTTCTCACA 60.082 41.667 0.00 0.00 43.49 3.58
3581 3811 1.009903 TCGTACCGCGTGTCCAAATG 61.010 55.000 4.92 0.00 42.13 2.32
3632 3862 2.095919 CGCCTAGGTTTTCAAAACTCGG 60.096 50.000 12.74 11.03 40.49 4.63
3642 3872 2.294074 TCAAAACTCGGTCCACTTTGG 58.706 47.619 0.00 0.00 39.43 3.28
3650 3880 2.173143 TCGGTCCACTTTGGTAGGTTTT 59.827 45.455 0.00 0.00 39.03 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.521958 AATTGGTCCTCAGTCGCCGG 62.522 60.000 0.00 0.00 0.00 6.13
7 8 1.079127 AATTGGTCCTCAGTCGCCG 60.079 57.895 0.00 0.00 0.00 6.46
8 9 1.084370 CGAATTGGTCCTCAGTCGCC 61.084 60.000 0.00 0.00 31.35 5.54
10 11 1.084370 GGCGAATTGGTCCTCAGTCG 61.084 60.000 7.01 7.01 37.61 4.18
11 12 0.250513 AGGCGAATTGGTCCTCAGTC 59.749 55.000 0.00 0.00 0.00 3.51
12 13 0.250513 GAGGCGAATTGGTCCTCAGT 59.749 55.000 18.93 0.00 44.38 3.41
13 14 3.071580 GAGGCGAATTGGTCCTCAG 57.928 57.895 18.93 0.00 44.38 3.35
15 16 0.462759 CCTGAGGCGAATTGGTCCTC 60.463 60.000 17.78 17.78 45.02 3.71
16 17 1.604378 CCTGAGGCGAATTGGTCCT 59.396 57.895 3.72 3.72 0.00 3.85
17 18 2.115291 GCCTGAGGCGAATTGGTCC 61.115 63.158 8.16 0.00 39.62 4.46
18 19 3.502572 GCCTGAGGCGAATTGGTC 58.497 61.111 8.16 0.00 39.62 4.02
39 40 2.548295 GGACGAGCCGGCACAAAAA 61.548 57.895 31.54 0.00 36.10 1.94
40 41 2.975799 GGACGAGCCGGCACAAAA 60.976 61.111 31.54 0.00 36.10 2.44
57 58 2.186826 CCTAAAATCGCCGCCTGGG 61.187 63.158 0.00 0.00 39.58 4.45
58 59 2.834618 GCCTAAAATCGCCGCCTGG 61.835 63.158 0.00 0.00 38.77 4.45
59 60 2.715624 GCCTAAAATCGCCGCCTG 59.284 61.111 0.00 0.00 0.00 4.85
60 61 2.895372 CGCCTAAAATCGCCGCCT 60.895 61.111 0.00 0.00 0.00 5.52
61 62 4.607606 GCGCCTAAAATCGCCGCC 62.608 66.667 0.00 0.00 45.01 6.13
66 67 1.160329 CCAGAGGGCGCCTAAAATCG 61.160 60.000 28.56 8.50 31.76 3.34
67 68 0.819666 CCCAGAGGGCGCCTAAAATC 60.820 60.000 28.56 16.13 35.35 2.17
68 69 1.227383 CCCAGAGGGCGCCTAAAAT 59.773 57.895 28.56 7.41 35.35 1.82
69 70 2.674754 CCCAGAGGGCGCCTAAAA 59.325 61.111 28.56 0.00 35.35 1.52
85 86 1.075748 ATCTTCAGCCATTGCCCCC 60.076 57.895 0.00 0.00 38.69 5.40
86 87 2.024590 GCATCTTCAGCCATTGCCCC 62.025 60.000 0.00 0.00 38.69 5.80
87 88 1.041447 AGCATCTTCAGCCATTGCCC 61.041 55.000 0.00 0.00 38.69 5.36
88 89 0.102481 CAGCATCTTCAGCCATTGCC 59.898 55.000 0.00 0.00 38.69 4.52
89 90 0.102481 CCAGCATCTTCAGCCATTGC 59.898 55.000 0.00 0.00 37.95 3.56
90 91 0.744874 CCCAGCATCTTCAGCCATTG 59.255 55.000 0.00 0.00 0.00 2.82
91 92 1.041447 GCCCAGCATCTTCAGCCATT 61.041 55.000 0.00 0.00 0.00 3.16
92 93 1.455217 GCCCAGCATCTTCAGCCAT 60.455 57.895 0.00 0.00 0.00 4.40
93 94 2.044650 GCCCAGCATCTTCAGCCA 60.045 61.111 0.00 0.00 0.00 4.75
94 95 2.832201 GGCCCAGCATCTTCAGCC 60.832 66.667 0.00 0.00 0.00 4.85
95 96 3.207669 CGGCCCAGCATCTTCAGC 61.208 66.667 0.00 0.00 0.00 4.26
96 97 0.677731 TTTCGGCCCAGCATCTTCAG 60.678 55.000 0.00 0.00 0.00 3.02
97 98 0.034186 ATTTCGGCCCAGCATCTTCA 60.034 50.000 0.00 0.00 0.00 3.02
98 99 0.665298 GATTTCGGCCCAGCATCTTC 59.335 55.000 0.00 0.00 0.00 2.87
99 100 0.257039 AGATTTCGGCCCAGCATCTT 59.743 50.000 0.00 0.00 0.00 2.40
100 101 0.179034 GAGATTTCGGCCCAGCATCT 60.179 55.000 0.00 0.00 0.00 2.90
101 102 0.179034 AGAGATTTCGGCCCAGCATC 60.179 55.000 0.00 0.00 0.00 3.91
102 103 0.465097 CAGAGATTTCGGCCCAGCAT 60.465 55.000 0.00 0.00 0.00 3.79
103 104 1.078214 CAGAGATTTCGGCCCAGCA 60.078 57.895 0.00 0.00 0.00 4.41
104 105 1.821332 CCAGAGATTTCGGCCCAGC 60.821 63.158 0.00 0.00 0.00 4.85
105 106 0.253044 TTCCAGAGATTTCGGCCCAG 59.747 55.000 0.00 0.00 0.00 4.45
106 107 0.035439 GTTCCAGAGATTTCGGCCCA 60.035 55.000 0.00 0.00 0.00 5.36
150 151 7.667575 TCTATCTCTGGATACTCTGCTTTTT 57.332 36.000 0.00 0.00 33.71 1.94
173 174 4.644685 TGCAAGGTCCCTGCTTTTTATATC 59.355 41.667 13.65 0.00 0.00 1.63
175 176 4.040936 TGCAAGGTCCCTGCTTTTTATA 57.959 40.909 13.65 0.00 0.00 0.98
285 293 4.713792 AGCTTAGAATCCTATTGGTGGG 57.286 45.455 0.00 0.00 34.23 4.61
438 458 0.749454 AGGATTGCGGTTGGAGATGC 60.749 55.000 0.00 0.00 0.00 3.91
579 604 3.131396 GCGAGTTTGTGAAGGAGAAAGA 58.869 45.455 0.00 0.00 0.00 2.52
580 605 2.872245 TGCGAGTTTGTGAAGGAGAAAG 59.128 45.455 0.00 0.00 0.00 2.62
581 606 2.872245 CTGCGAGTTTGTGAAGGAGAAA 59.128 45.455 0.00 0.00 0.00 2.52
582 607 2.158957 ACTGCGAGTTTGTGAAGGAGAA 60.159 45.455 0.00 0.00 0.00 2.87
593 618 4.918810 ATTTCCTTTTGACTGCGAGTTT 57.081 36.364 0.00 0.00 0.00 2.66
604 629 4.702131 AGATGGAGTCGGAATTTCCTTTTG 59.298 41.667 13.45 0.00 33.30 2.44
713 738 1.212616 CCGCCGATGAGAGAATCAAC 58.787 55.000 0.00 0.00 42.53 3.18
927 957 4.299485 CCTTCTAGTTCCCACCTATCCTT 58.701 47.826 0.00 0.00 0.00 3.36
1103 1139 6.255453 GTGATTGCTGTTGTTGTTGTTGTTAT 59.745 34.615 0.00 0.00 0.00 1.89
1104 1140 5.574830 GTGATTGCTGTTGTTGTTGTTGTTA 59.425 36.000 0.00 0.00 0.00 2.41
1105 1141 4.388469 GTGATTGCTGTTGTTGTTGTTGTT 59.612 37.500 0.00 0.00 0.00 2.83
1106 1142 3.925913 GTGATTGCTGTTGTTGTTGTTGT 59.074 39.130 0.00 0.00 0.00 3.32
1107 1143 3.925299 TGTGATTGCTGTTGTTGTTGTTG 59.075 39.130 0.00 0.00 0.00 3.33
1108 1144 4.185467 TGTGATTGCTGTTGTTGTTGTT 57.815 36.364 0.00 0.00 0.00 2.83
1163 1202 5.421056 ACCAAATATCTCCAGACAAGACGTA 59.579 40.000 0.00 0.00 0.00 3.57
1164 1203 4.223032 ACCAAATATCTCCAGACAAGACGT 59.777 41.667 0.00 0.00 0.00 4.34
1260 1299 1.561769 CCACCCACCATCTGCCACTA 61.562 60.000 0.00 0.00 0.00 2.74
1392 1431 9.760077 CCGTTCATGGTTTATCTACTACTAATT 57.240 33.333 0.00 0.00 0.00 1.40
1393 1432 9.139734 TCCGTTCATGGTTTATCTACTACTAAT 57.860 33.333 0.00 0.00 0.00 1.73
1394 1433 8.523915 TCCGTTCATGGTTTATCTACTACTAA 57.476 34.615 0.00 0.00 0.00 2.24
1446 1501 6.195600 ACAAGTCTCAGGGTAATAAAACCA 57.804 37.500 0.00 0.00 41.67 3.67
1447 1502 7.229907 TCAAACAAGTCTCAGGGTAATAAAACC 59.770 37.037 0.00 0.00 38.94 3.27
1478 1533 4.022603 ACTTCTGAGAATAGCAGCTCTCA 58.977 43.478 11.34 11.34 44.49 3.27
1479 1534 4.654091 ACTTCTGAGAATAGCAGCTCTC 57.346 45.455 0.00 0.00 38.87 3.20
1484 1543 5.350914 CACTTCCAACTTCTGAGAATAGCAG 59.649 44.000 0.00 0.00 34.71 4.24
1506 1565 2.806608 TTCAGTACCGAGTTGTCCAC 57.193 50.000 0.00 0.00 0.00 4.02
1558 1617 2.163818 TTTCAAGCTACACGGACTGG 57.836 50.000 0.00 0.00 0.00 4.00
1560 1619 7.604927 TGTAATAATTTTCAAGCTACACGGACT 59.395 33.333 0.00 0.00 0.00 3.85
1611 1670 3.234353 TGGACAAATGTGGCACCATTAA 58.766 40.909 16.26 0.00 34.01 1.40
1612 1671 2.824936 CTGGACAAATGTGGCACCATTA 59.175 45.455 16.26 0.00 34.01 1.90
1613 1672 1.619827 CTGGACAAATGTGGCACCATT 59.380 47.619 16.26 11.77 36.62 3.16
1686 1745 8.803235 GGGGGAATAAAACATTTAGATGATACC 58.197 37.037 0.00 0.00 36.73 2.73
1740 1799 1.302993 AGGCGCAACCCGTGTATTT 60.303 52.632 10.83 0.00 40.58 1.40
1897 1956 1.000274 GGATTGCGTTGAAGCCTTGTT 60.000 47.619 0.00 0.00 36.02 2.83
2025 2084 1.045911 AGACTTGAGCTCCCCCGATC 61.046 60.000 12.15 0.47 0.00 3.69
2070 2129 4.473196 TGACCTTCTAGGCATATTGGACAA 59.527 41.667 0.00 0.00 39.63 3.18
2161 2220 5.416326 CGAAGTGTAAATTGTAAATCCCCCA 59.584 40.000 0.00 0.00 0.00 4.96
2231 2369 8.028938 GGAGTATATTTTTGCAACTGACACAAT 58.971 33.333 0.00 0.00 0.00 2.71
2252 2390 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2253 2391 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2254 2392 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2255 2393 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2256 2394 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2257 2395 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2274 2412 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
2275 2413 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2279 2417 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2280 2418 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2281 2419 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2282 2420 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2283 2421 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2284 2422 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2285 2423 7.552687 TGTATGTGGTAGTCCATTTGAAATCTC 59.447 37.037 0.00 0.00 46.20 2.75
2286 2424 7.402054 TGTATGTGGTAGTCCATTTGAAATCT 58.598 34.615 0.00 0.00 46.20 2.40
2287 2425 7.552687 TCTGTATGTGGTAGTCCATTTGAAATC 59.447 37.037 0.00 0.00 46.20 2.17
2288 2426 7.402054 TCTGTATGTGGTAGTCCATTTGAAAT 58.598 34.615 0.00 0.00 46.20 2.17
2289 2427 6.774673 TCTGTATGTGGTAGTCCATTTGAAA 58.225 36.000 0.00 0.00 46.20 2.69
2290 2428 6.367374 TCTGTATGTGGTAGTCCATTTGAA 57.633 37.500 0.00 0.00 46.20 2.69
2291 2429 6.070251 ACATCTGTATGTGGTAGTCCATTTGA 60.070 38.462 0.00 0.00 44.79 2.69
2292 2430 6.115446 ACATCTGTATGTGGTAGTCCATTTG 58.885 40.000 0.00 0.00 44.79 2.32
2293 2431 6.313519 ACATCTGTATGTGGTAGTCCATTT 57.686 37.500 0.00 0.00 44.79 2.32
2294 2432 5.957771 ACATCTGTATGTGGTAGTCCATT 57.042 39.130 0.00 0.00 44.79 3.16
2295 2433 8.901472 ATATACATCTGTATGTGGTAGTCCAT 57.099 34.615 12.10 0.00 45.99 3.41
2296 2434 9.462606 CTATATACATCTGTATGTGGTAGTCCA 57.537 37.037 12.10 0.00 45.99 4.02
2297 2435 9.682465 TCTATATACATCTGTATGTGGTAGTCC 57.318 37.037 12.10 0.00 45.99 3.85
2335 2473 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2336 2474 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2337 2475 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2338 2476 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2339 2477 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2340 2478 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2341 2479 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2342 2480 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2343 2481 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2344 2482 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2345 2483 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2346 2484 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2347 2485 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2348 2486 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2349 2487 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2350 2488 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2351 2489 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2352 2490 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2353 2491 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2354 2492 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2355 2493 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2356 2494 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2357 2495 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2358 2496 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2359 2497 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2361 2499 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2362 2500 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2363 2501 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2364 2502 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2365 2503 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2366 2504 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2367 2505 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2368 2506 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2369 2507 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2385 2523 8.947115 CCTCCGTTTCTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
2386 2524 8.182227 CCCTCCGTTTCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
2387 2525 7.886446 TCCCTCCGTTTCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
2388 2526 7.399634 TCCCTCCGTTTCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
2389 2527 6.954232 TCCCTCCGTTTCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
2390 2528 6.822170 ACTCCCTCCGTTTCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
2391 2529 6.718294 ACTCCCTCCGTTTCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
2392 2530 7.042925 CGTACTCCCTCCGTTTCTAAATATTTG 60.043 40.741 11.05 1.65 0.00 2.32
2393 2531 6.982724 CGTACTCCCTCCGTTTCTAAATATTT 59.017 38.462 5.89 5.89 0.00 1.40
2394 2532 6.097412 ACGTACTCCCTCCGTTTCTAAATATT 59.903 38.462 0.00 0.00 0.00 1.28
2395 2533 5.595952 ACGTACTCCCTCCGTTTCTAAATAT 59.404 40.000 0.00 0.00 0.00 1.28
2396 2534 4.949856 ACGTACTCCCTCCGTTTCTAAATA 59.050 41.667 0.00 0.00 0.00 1.40
2397 2535 3.766051 ACGTACTCCCTCCGTTTCTAAAT 59.234 43.478 0.00 0.00 0.00 1.40
2398 2536 3.057315 CACGTACTCCCTCCGTTTCTAAA 60.057 47.826 0.00 0.00 31.46 1.85
2399 2537 2.489329 CACGTACTCCCTCCGTTTCTAA 59.511 50.000 0.00 0.00 31.46 2.10
2400 2538 2.086869 CACGTACTCCCTCCGTTTCTA 58.913 52.381 0.00 0.00 31.46 2.10
2401 2539 0.886563 CACGTACTCCCTCCGTTTCT 59.113 55.000 0.00 0.00 31.46 2.52
2402 2540 0.600057 ACACGTACTCCCTCCGTTTC 59.400 55.000 0.00 0.00 31.46 2.78
2403 2541 1.043022 AACACGTACTCCCTCCGTTT 58.957 50.000 0.00 0.00 31.46 3.60
2404 2542 1.043022 AAACACGTACTCCCTCCGTT 58.957 50.000 0.00 0.00 31.46 4.44
2405 2543 0.316204 CAAACACGTACTCCCTCCGT 59.684 55.000 0.00 0.00 34.71 4.69
2406 2544 0.316204 ACAAACACGTACTCCCTCCG 59.684 55.000 0.00 0.00 0.00 4.63
2407 2545 2.224113 TGAACAAACACGTACTCCCTCC 60.224 50.000 0.00 0.00 0.00 4.30
2408 2546 3.102052 TGAACAAACACGTACTCCCTC 57.898 47.619 0.00 0.00 0.00 4.30
2409 2547 3.764237 ATGAACAAACACGTACTCCCT 57.236 42.857 0.00 0.00 0.00 4.20
2410 2548 4.823790 AAATGAACAAACACGTACTCCC 57.176 40.909 0.00 0.00 0.00 4.30
2411 2549 8.071368 TGATTAAAATGAACAAACACGTACTCC 58.929 33.333 0.00 0.00 0.00 3.85
2412 2550 8.996988 TGATTAAAATGAACAAACACGTACTC 57.003 30.769 0.00 0.00 0.00 2.59
2413 2551 9.959749 AATGATTAAAATGAACAAACACGTACT 57.040 25.926 0.00 0.00 0.00 2.73
2494 2634 4.863689 CGTGGCAGCAATTTGATAAAATGA 59.136 37.500 0.00 0.00 0.00 2.57
2601 2745 5.295540 AGAAGACAAGAAGAGCAAACAACTC 59.704 40.000 0.00 0.00 0.00 3.01
2810 2954 8.593945 TTTTTGCCAGATTAGATCAAATACCT 57.406 30.769 0.00 0.00 0.00 3.08
2973 3118 3.885724 TCTAGCGACATGATTTCACCA 57.114 42.857 0.00 0.00 0.00 4.17
3027 3172 2.639839 ACTGCTCTAGAAGGAAAAGCCA 59.360 45.455 0.00 0.00 40.02 4.75
3286 3435 8.938801 TCAATAATAACGATACACTAGGGGTA 57.061 34.615 0.00 0.00 0.00 3.69
3447 3657 1.107945 CCAAAACTCCGTGGTTGGTT 58.892 50.000 0.00 0.00 36.55 3.67
3480 3699 1.446907 CTCACATCCTCAAGCGCTTT 58.553 50.000 22.51 1.84 0.00 3.51
3521 3751 9.104965 TGAAACAAACGAATCTAAGAAGAAGAA 57.895 29.630 0.00 0.00 34.73 2.52
3522 3752 8.657074 TGAAACAAACGAATCTAAGAAGAAGA 57.343 30.769 0.00 0.00 34.73 2.87
3523 3753 9.716507 TTTGAAACAAACGAATCTAAGAAGAAG 57.283 29.630 0.00 0.00 34.73 2.85
3632 3862 4.825085 TCATCAAAACCTACCAAAGTGGAC 59.175 41.667 0.18 0.00 40.96 4.02
3642 3872 6.417930 GCAGAAAACTGTTCATCAAAACCTAC 59.582 38.462 0.00 0.00 0.00 3.18
3650 3880 6.808829 AGATTTTGCAGAAAACTGTTCATCA 58.191 32.000 0.00 0.00 33.86 3.07


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

AutoCloner maintained by Alex Coulton.