Multiple sequence alignment - TraesCS1B01G144200

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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 TraesCS1B01G144200 chr1B 100.000 2997 0 0 1 2997 196063312 196060316 0.000000e+00 5535
1 TraesCS1B01G144200 chr1D 96.284 2126 58 10 2 2114 141901075 141898958 0.000000e+00 3469
2 TraesCS1B01G144200 chr1D 85.361 526 30 18 2498 2997 141898855 141898351 4.460000e-138 501
3 TraesCS1B01G144200 chr1D 88.452 407 37 2 2 398 383180345 383180751 1.620000e-132 483
4 TraesCS1B01G144200 chr1D 93.528 309 20 0 2114 2422 469043760 469044068 7.570000e-126 460
5 TraesCS1B01G144200 chr1D 93.706 143 9 0 2855 2997 84806527 84806669 6.510000e-52 215
6 TraesCS1B01G144200 chr1A 94.212 1313 50 4 487 1797 148744316 148745604 0.000000e+00 1980
7 TraesCS1B01G144200 chr1A 89.877 405 29 4 2 394 557890236 557890640 7.410000e-141 510
8 TraesCS1B01G144200 chr1A 93.949 314 18 1 1802 2114 148745692 148746005 9.720000e-130 473
9 TraesCS1B01G144200 chr1A 87.961 407 37 7 2 398 337814834 337815238 1.260000e-128 470
10 TraesCS1B01G144200 chr1A 96.875 64 2 0 2420 2483 148746001 148746064 1.140000e-19 108
11 TraesCS1B01G144200 chr5B 95.223 314 14 1 2111 2424 38580127 38580439 2.080000e-136 496
12 TraesCS1B01G144200 chr5B 88.943 407 35 2 2 398 361013607 361014013 7.460000e-136 494
13 TraesCS1B01G144200 chr5B 85.354 396 33 9 2 390 710966415 710966038 1.300000e-103 387
14 TraesCS1B01G144200 chr7D 88.264 409 35 3 2 398 168500916 168500509 7.520000e-131 477
15 TraesCS1B01G144200 chr7D 89.153 378 28 6 2 369 65387898 65388272 2.720000e-125 459
16 TraesCS1B01G144200 chr7D 92.767 318 22 1 2109 2426 83598593 83598909 2.720000e-125 459
17 TraesCS1B01G144200 chr7D 84.871 271 24 11 2500 2753 58994982 58994712 1.070000e-64 257
18 TraesCS1B01G144200 chr3D 88.642 405 29 4 4 398 467734978 467734581 7.520000e-131 477
19 TraesCS1B01G144200 chr3D 93.930 313 19 0 2112 2424 606080553 606080241 9.720000e-130 473
20 TraesCS1B01G144200 chr3D 87.469 407 35 3 2 398 545795903 545796303 3.520000e-124 455
21 TraesCS1B01G144200 chr6B 94.194 310 16 1 2115 2422 697461705 697461396 3.500000e-129 472
22 TraesCS1B01G144200 chr7B 93.375 317 21 0 2108 2424 677569230 677569546 1.260000e-128 470
23 TraesCS1B01G144200 chr7B 91.045 201 14 4 2798 2997 691041414 691041611 4.920000e-68 268
24 TraesCS1B01G144200 chr7B 80.556 216 24 10 2499 2697 691041205 691041419 1.860000e-32 150
25 TraesCS1B01G144200 chr2A 88.442 398 35 3 2 389 431081808 431082204 1.260000e-128 470
26 TraesCS1B01G144200 chr2A 85.657 251 27 8 2746 2994 74956743 74956986 3.830000e-64 255
27 TraesCS1B01G144200 chr2A 86.036 222 24 6 2494 2709 144615873 144616093 6.460000e-57 231
28 TraesCS1B01G144200 chr5D 93.590 312 20 0 2114 2425 2622034 2621723 1.630000e-127 466
29 TraesCS1B01G144200 chr4B 88.030 401 36 10 2 394 491805125 491804729 5.850000e-127 464
30 TraesCS1B01G144200 chr4D 87.750 400 36 5 2 390 297775837 297776234 3.520000e-124 455
31 TraesCS1B01G144200 chr3B 92.652 313 21 1 2112 2424 603608922 603609232 1.640000e-122 449
32 TraesCS1B01G144200 chr3B 87.137 241 15 3 2746 2986 41348961 41349185 2.960000e-65 259
33 TraesCS1B01G144200 chr3B 86.607 112 12 3 2494 2605 41336212 41336320 1.460000e-23 121
34 TraesCS1B01G144200 chr2B 92.652 313 19 2 2112 2424 161711152 161711460 5.890000e-122 448
35 TraesCS1B01G144200 chr2B 87.500 248 28 3 2747 2994 730558359 730558603 1.760000e-72 283
36 TraesCS1B01G144200 chr4A 88.889 252 25 3 2746 2997 676494598 676494350 1.040000e-79 307
37 TraesCS1B01G144200 chr4A 88.793 116 12 1 280 394 445990281 445990396 1.120000e-29 141
38 TraesCS1B01G144200 chr7A 87.243 243 28 3 2755 2997 38207196 38206957 1.060000e-69 274
39 TraesCS1B01G144200 chr2D 85.263 285 20 13 2494 2760 645179703 645179423 1.060000e-69 274
40 TraesCS1B01G144200 chr2D 84.861 251 22 3 2746 2996 645179526 645179292 3.860000e-59 239
41 TraesCS1B01G144200 chrUn 84.733 262 26 3 2503 2751 93046523 93046263 1.780000e-62 250
42 TraesCS1B01G144200 chrUn 82.721 272 30 9 2499 2757 378497879 378498146 3.010000e-55 226


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 TraesCS1B01G144200 chr1B 196060316 196063312 2996 True 5535.000000 5535 100.0000 1 2997 1 chr1B.!!$R1 2996
1 TraesCS1B01G144200 chr1D 141898351 141901075 2724 True 1985.000000 3469 90.8225 2 2997 2 chr1D.!!$R1 2995
2 TraesCS1B01G144200 chr1A 148744316 148746064 1748 False 853.666667 1980 95.0120 487 2483 3 chr1A.!!$F3 1996

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
767 781 0.178992 ACCAATCCCATATGTGCCCG 60.179 55.0 1.24 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2254 0.037139 TGGTGGCGTGCTATAACGTT 60.037 50.0 5.88 5.88 45.32 3.99 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
28 29 2.289819 TGACTGCTTCTGTGATCATGCA 60.290 45.455 0.00 4.59 0.00 3.96
252 253 9.856488 GCAATCAGTAGATCTATCGGTTTAATA 57.144 33.333 5.57 0.00 31.90 0.98
277 278 3.713858 TCCATGTGCACAAACTTTGAG 57.286 42.857 25.72 10.89 0.00 3.02
406 420 5.892119 AGTACTTGACCTTCGGATAAGATGA 59.108 40.000 0.00 0.00 0.00 2.92
421 435 4.569719 AAGATGAAACATAAGTCCGGGT 57.430 40.909 0.00 0.00 0.00 5.28
423 437 3.517901 AGATGAAACATAAGTCCGGGTGA 59.482 43.478 0.00 0.00 0.00 4.02
425 439 3.404899 TGAAACATAAGTCCGGGTGAAC 58.595 45.455 0.00 0.00 0.00 3.18
437 451 1.334599 CGGGTGAACACGGTTTCATTG 60.335 52.381 0.00 0.00 39.49 2.82
438 452 1.601914 GGGTGAACACGGTTTCATTGC 60.602 52.381 4.49 0.00 37.80 3.56
452 466 3.627732 TCATTGCCGCTTTAAAAACGA 57.372 38.095 10.88 0.00 0.00 3.85
455 469 1.744374 TGCCGCTTTAAAAACGAACG 58.256 45.000 10.88 0.00 0.00 3.95
465 479 2.955607 AAAACGAACGAAATCCGGAC 57.044 45.000 6.12 0.00 43.93 4.79
472 486 1.868469 ACGAAATCCGGACAAAACGA 58.132 45.000 6.12 0.00 43.93 3.85
475 489 0.515564 AAATCCGGACAAAACGAGCG 59.484 50.000 6.12 0.00 0.00 5.03
503 517 2.871096 AGCTTATTCGGGACAAACCA 57.129 45.000 0.00 0.00 41.20 3.67
512 526 1.670791 GGGACAAACCAGTTCGTCAA 58.329 50.000 4.17 0.00 41.20 3.18
641 655 1.215647 CTGTCCTCTTCCCCGTTCG 59.784 63.158 0.00 0.00 0.00 3.95
767 781 0.178992 ACCAATCCCATATGTGCCCG 60.179 55.000 1.24 0.00 0.00 6.13
955 969 1.168407 AGAACGGACTCGACGAACCA 61.168 55.000 17.03 0.00 40.11 3.67
1031 1045 0.529119 GACCACGACAACGGTTCTGT 60.529 55.000 0.00 0.00 44.46 3.41
1790 1806 3.109547 CTGCGTGCGCGGTTTCTA 61.110 61.111 22.73 0.00 45.51 2.10
2013 2112 3.052944 TCCTGAATTTGGAATGGGTAGGG 60.053 47.826 0.00 0.00 0.00 3.53
2095 2195 3.704566 ACATAGATTGGTAGGCGTCTTGA 59.295 43.478 0.00 0.00 0.00 3.02
2117 2217 4.289529 CGTGTTCTTACGTTGTAAGAGC 57.710 45.455 20.05 20.05 39.13 4.09
2118 2218 3.732219 CGTGTTCTTACGTTGTAAGAGCA 59.268 43.478 23.52 23.52 40.66 4.26
2119 2219 4.384846 CGTGTTCTTACGTTGTAAGAGCAT 59.615 41.667 27.31 0.00 43.23 3.79
2120 2220 5.442909 CGTGTTCTTACGTTGTAAGAGCATC 60.443 44.000 27.31 21.30 43.23 3.91
2121 2221 7.543238 CGTGTTCTTACGTTGTAAGAGCATCT 61.543 42.308 27.31 0.00 43.23 2.90
2122 2222 9.224313 CGTGTTCTTACGTTGTAAGAGCATCTC 62.224 44.444 27.31 18.42 43.23 2.75
2131 2231 2.892425 GAGCATCTCCAACGGCCG 60.892 66.667 26.86 26.86 0.00 6.13
2134 2234 3.499737 CATCTCCAACGGCCGCAC 61.500 66.667 28.58 0.00 0.00 5.34
2135 2235 4.015406 ATCTCCAACGGCCGCACA 62.015 61.111 28.58 5.68 0.00 4.57
2136 2236 3.545124 ATCTCCAACGGCCGCACAA 62.545 57.895 28.58 7.99 0.00 3.33
2137 2237 3.283684 CTCCAACGGCCGCACAAA 61.284 61.111 28.58 6.34 0.00 2.83
2138 2238 2.829003 TCCAACGGCCGCACAAAA 60.829 55.556 28.58 2.77 0.00 2.44
2139 2239 2.105128 CCAACGGCCGCACAAAAA 59.895 55.556 28.58 0.00 0.00 1.94
2156 2256 2.287393 AAAATCCGCGCCCAATAAAC 57.713 45.000 0.00 0.00 0.00 2.01
2157 2257 0.099791 AAATCCGCGCCCAATAAACG 59.900 50.000 0.00 0.00 0.00 3.60
2158 2258 1.027792 AATCCGCGCCCAATAAACGT 61.028 50.000 0.00 0.00 0.00 3.99
2159 2259 1.027792 ATCCGCGCCCAATAAACGTT 61.028 50.000 0.00 0.00 0.00 3.99
2160 2260 0.390866 TCCGCGCCCAATAAACGTTA 60.391 50.000 0.00 0.00 0.00 3.18
2161 2261 0.658897 CCGCGCCCAATAAACGTTAT 59.341 50.000 0.00 0.00 0.00 1.89
2162 2262 1.865970 CCGCGCCCAATAAACGTTATA 59.134 47.619 0.00 0.00 0.00 0.98
2163 2263 2.096614 CCGCGCCCAATAAACGTTATAG 60.097 50.000 0.00 0.00 0.00 1.31
2164 2264 2.660900 CGCGCCCAATAAACGTTATAGC 60.661 50.000 0.00 0.00 0.00 2.97
2165 2265 2.288458 GCGCCCAATAAACGTTATAGCA 59.712 45.455 0.00 0.00 0.00 3.49
2166 2266 3.847105 GCGCCCAATAAACGTTATAGCAC 60.847 47.826 0.00 0.00 0.00 4.40
2167 2267 3.602946 CGCCCAATAAACGTTATAGCACG 60.603 47.826 0.00 0.00 46.04 5.34
2168 2268 3.847105 GCCCAATAAACGTTATAGCACGC 60.847 47.826 0.00 0.00 44.37 5.34
2169 2269 3.303526 CCCAATAAACGTTATAGCACGCC 60.304 47.826 0.00 0.00 44.37 5.68
2170 2270 3.310227 CCAATAAACGTTATAGCACGCCA 59.690 43.478 0.00 0.00 44.37 5.69
2171 2271 4.268522 CAATAAACGTTATAGCACGCCAC 58.731 43.478 0.00 0.00 44.37 5.01
2172 2272 1.081094 AAACGTTATAGCACGCCACC 58.919 50.000 0.00 0.00 44.37 4.61
2173 2273 0.037139 AACGTTATAGCACGCCACCA 60.037 50.000 0.00 0.00 44.37 4.17
2174 2274 0.177141 ACGTTATAGCACGCCACCAT 59.823 50.000 0.00 0.00 44.37 3.55
2175 2275 1.409790 ACGTTATAGCACGCCACCATA 59.590 47.619 0.00 0.00 44.37 2.74
2176 2276 2.058798 CGTTATAGCACGCCACCATAG 58.941 52.381 0.00 0.00 32.43 2.23
2177 2277 2.545113 CGTTATAGCACGCCACCATAGT 60.545 50.000 0.00 0.00 32.43 2.12
2178 2278 3.304861 CGTTATAGCACGCCACCATAGTA 60.305 47.826 0.00 0.00 32.43 1.82
2179 2279 2.814280 ATAGCACGCCACCATAGTAC 57.186 50.000 0.00 0.00 0.00 2.73
2180 2280 1.771565 TAGCACGCCACCATAGTACT 58.228 50.000 0.00 0.00 0.00 2.73
2181 2281 0.902531 AGCACGCCACCATAGTACTT 59.097 50.000 0.00 0.00 0.00 2.24
2182 2282 1.278127 AGCACGCCACCATAGTACTTT 59.722 47.619 0.00 0.00 0.00 2.66
2183 2283 2.081462 GCACGCCACCATAGTACTTTT 58.919 47.619 0.00 0.00 0.00 2.27
2184 2284 3.055675 AGCACGCCACCATAGTACTTTTA 60.056 43.478 0.00 0.00 0.00 1.52
2185 2285 3.685756 GCACGCCACCATAGTACTTTTAA 59.314 43.478 0.00 0.00 0.00 1.52
2186 2286 4.154556 GCACGCCACCATAGTACTTTTAAA 59.845 41.667 0.00 0.00 0.00 1.52
2187 2287 5.672819 GCACGCCACCATAGTACTTTTAAAG 60.673 44.000 0.00 2.81 0.00 1.85
2188 2288 4.393990 ACGCCACCATAGTACTTTTAAAGC 59.606 41.667 0.00 0.00 0.00 3.51
2189 2289 4.493545 CGCCACCATAGTACTTTTAAAGCG 60.494 45.833 0.00 6.65 0.00 4.68
2190 2290 4.393990 GCCACCATAGTACTTTTAAAGCGT 59.606 41.667 0.00 0.00 0.00 5.07
2191 2291 5.446875 GCCACCATAGTACTTTTAAAGCGTC 60.447 44.000 0.00 0.00 0.00 5.19
2192 2292 5.220340 CCACCATAGTACTTTTAAAGCGTCG 60.220 44.000 0.00 0.00 0.00 5.12
2193 2293 4.866486 ACCATAGTACTTTTAAAGCGTCGG 59.134 41.667 0.00 1.44 0.00 4.79
2194 2294 4.269363 CCATAGTACTTTTAAAGCGTCGGG 59.731 45.833 0.00 0.00 0.00 5.14
2195 2295 3.665745 AGTACTTTTAAAGCGTCGGGA 57.334 42.857 4.42 0.00 0.00 5.14
2196 2296 3.320626 AGTACTTTTAAAGCGTCGGGAC 58.679 45.455 4.42 0.00 0.00 4.46
2197 2297 1.516161 ACTTTTAAAGCGTCGGGACC 58.484 50.000 4.42 0.00 0.00 4.46
2198 2298 1.202675 ACTTTTAAAGCGTCGGGACCA 60.203 47.619 4.42 0.00 0.00 4.02
2199 2299 1.874872 CTTTTAAAGCGTCGGGACCAA 59.125 47.619 0.00 0.00 0.00 3.67
2200 2300 1.228533 TTTAAAGCGTCGGGACCAAC 58.771 50.000 0.00 0.00 0.00 3.77
2201 2301 0.393820 TTAAAGCGTCGGGACCAACT 59.606 50.000 0.00 0.00 0.00 3.16
2202 2302 0.393820 TAAAGCGTCGGGACCAACTT 59.606 50.000 0.00 0.00 0.00 2.66
2203 2303 0.464916 AAAGCGTCGGGACCAACTTT 60.465 50.000 0.00 0.00 0.00 2.66
2204 2304 1.164041 AAGCGTCGGGACCAACTTTG 61.164 55.000 0.00 0.00 0.00 2.77
2205 2305 2.943653 CGTCGGGACCAACTTTGC 59.056 61.111 0.00 0.00 0.00 3.68
2206 2306 1.597027 CGTCGGGACCAACTTTGCT 60.597 57.895 0.00 0.00 0.00 3.91
2207 2307 1.164041 CGTCGGGACCAACTTTGCTT 61.164 55.000 0.00 0.00 0.00 3.91
2208 2308 1.029681 GTCGGGACCAACTTTGCTTT 58.970 50.000 0.00 0.00 0.00 3.51
2209 2309 2.223745 GTCGGGACCAACTTTGCTTTA 58.776 47.619 0.00 0.00 0.00 1.85
2210 2310 2.225727 GTCGGGACCAACTTTGCTTTAG 59.774 50.000 0.00 0.00 0.00 1.85
2211 2311 1.068541 CGGGACCAACTTTGCTTTAGC 60.069 52.381 0.00 0.00 42.50 3.09
2221 2321 4.095590 GCTTTAGCAGGTGCCCAA 57.904 55.556 0.00 0.00 43.38 4.12
2222 2322 2.350738 GCTTTAGCAGGTGCCCAAA 58.649 52.632 0.00 0.00 43.38 3.28
2223 2323 0.678950 GCTTTAGCAGGTGCCCAAAA 59.321 50.000 0.00 0.00 43.38 2.44
2224 2324 1.069978 GCTTTAGCAGGTGCCCAAAAA 59.930 47.619 0.00 0.00 43.38 1.94
2225 2325 2.754472 CTTTAGCAGGTGCCCAAAAAC 58.246 47.619 0.00 0.00 43.38 2.43
2226 2326 1.781786 TTAGCAGGTGCCCAAAAACA 58.218 45.000 0.00 0.00 43.38 2.83
2227 2327 1.036707 TAGCAGGTGCCCAAAAACAC 58.963 50.000 0.00 0.00 43.38 3.32
2228 2328 1.591327 GCAGGTGCCCAAAAACACG 60.591 57.895 0.00 0.00 37.68 4.49
2229 2329 1.591327 CAGGTGCCCAAAAACACGC 60.591 57.895 0.00 0.00 37.68 5.34
2230 2330 2.656973 GGTGCCCAAAAACACGCG 60.657 61.111 3.53 3.53 37.68 6.01
2231 2331 3.326981 GTGCCCAAAAACACGCGC 61.327 61.111 5.73 0.00 0.00 6.86
2232 2332 4.577246 TGCCCAAAAACACGCGCC 62.577 61.111 5.73 0.00 0.00 6.53
2234 2334 3.905678 CCCAAAAACACGCGCCCA 61.906 61.111 5.73 0.00 0.00 5.36
2235 2335 2.105128 CCAAAAACACGCGCCCAA 59.895 55.556 5.73 0.00 0.00 4.12
2236 2336 1.519455 CCAAAAACACGCGCCCAAA 60.519 52.632 5.73 0.00 0.00 3.28
2237 2337 1.084370 CCAAAAACACGCGCCCAAAA 61.084 50.000 5.73 0.00 0.00 2.44
2238 2338 0.721718 CAAAAACACGCGCCCAAAAA 59.278 45.000 5.73 0.00 0.00 1.94
2257 2357 5.783100 AAAAACAGACAGTGCAAATTGTG 57.217 34.783 4.67 0.00 0.00 3.33
2258 2358 4.717233 AAACAGACAGTGCAAATTGTGA 57.283 36.364 4.67 0.00 0.00 3.58
2259 2359 4.717233 AACAGACAGTGCAAATTGTGAA 57.283 36.364 4.67 0.00 0.00 3.18
2260 2360 4.297299 ACAGACAGTGCAAATTGTGAAG 57.703 40.909 4.67 0.00 0.00 3.02
2261 2361 3.047796 CAGACAGTGCAAATTGTGAAGC 58.952 45.455 4.67 0.00 0.00 3.86
2262 2362 2.046313 GACAGTGCAAATTGTGAAGCG 58.954 47.619 4.67 0.00 0.00 4.68
2263 2363 0.780002 CAGTGCAAATTGTGAAGCGC 59.220 50.000 0.00 0.00 37.74 5.92
2264 2364 0.661187 AGTGCAAATTGTGAAGCGCG 60.661 50.000 0.00 0.00 41.96 6.86
2265 2365 2.015627 TGCAAATTGTGAAGCGCGC 61.016 52.632 26.66 26.66 0.00 6.86
2266 2366 3.046460 GCAAATTGTGAAGCGCGCG 62.046 57.895 28.44 28.44 0.00 6.86
2267 2367 2.800746 AAATTGTGAAGCGCGCGC 60.801 55.556 45.10 45.10 42.33 6.86
2282 2382 2.202824 CGCAATCCGACGCCCTAA 60.203 61.111 0.00 0.00 40.02 2.69
2283 2383 1.812093 CGCAATCCGACGCCCTAAA 60.812 57.895 0.00 0.00 40.02 1.85
2284 2384 1.157870 CGCAATCCGACGCCCTAAAT 61.158 55.000 0.00 0.00 40.02 1.40
2285 2385 1.870580 CGCAATCCGACGCCCTAAATA 60.871 52.381 0.00 0.00 40.02 1.40
2286 2386 2.423577 GCAATCCGACGCCCTAAATAT 58.576 47.619 0.00 0.00 0.00 1.28
2287 2387 2.159627 GCAATCCGACGCCCTAAATATG 59.840 50.000 0.00 0.00 0.00 1.78
2288 2388 2.094762 ATCCGACGCCCTAAATATGC 57.905 50.000 0.00 0.00 0.00 3.14
2289 2389 1.045407 TCCGACGCCCTAAATATGCT 58.955 50.000 0.00 0.00 0.00 3.79
2290 2390 1.148310 CCGACGCCCTAAATATGCTG 58.852 55.000 0.00 0.00 0.00 4.41
2291 2391 0.512952 CGACGCCCTAAATATGCTGC 59.487 55.000 0.00 0.00 0.00 5.25
2292 2392 0.512952 GACGCCCTAAATATGCTGCG 59.487 55.000 0.00 0.00 46.69 5.18
2293 2393 1.207593 CGCCCTAAATATGCTGCGC 59.792 57.895 0.00 0.00 35.33 6.09
2294 2394 1.207593 GCCCTAAATATGCTGCGCG 59.792 57.895 0.00 0.00 0.00 6.86
2295 2395 1.207593 CCCTAAATATGCTGCGCGC 59.792 57.895 27.26 27.26 39.77 6.86
2296 2396 1.207593 CCTAAATATGCTGCGCGCC 59.792 57.895 30.77 15.18 38.05 6.53
2297 2397 1.506309 CCTAAATATGCTGCGCGCCA 61.506 55.000 30.77 21.06 38.05 5.69
2298 2398 0.518636 CTAAATATGCTGCGCGCCAT 59.481 50.000 30.77 26.23 38.05 4.40
2299 2399 0.950836 TAAATATGCTGCGCGCCATT 59.049 45.000 30.77 16.26 38.05 3.16
2300 2400 0.595567 AAATATGCTGCGCGCCATTG 60.596 50.000 30.77 16.81 38.05 2.82
2301 2401 3.547249 ATATGCTGCGCGCCATTGC 62.547 57.895 30.77 25.52 38.05 3.56
2312 2412 1.774727 GCCATTGCGTTTTTCAGCG 59.225 52.632 0.00 0.00 35.87 5.18
2313 2413 0.939106 GCCATTGCGTTTTTCAGCGT 60.939 50.000 0.00 0.00 35.87 5.07
2314 2414 0.777631 CCATTGCGTTTTTCAGCGTG 59.222 50.000 0.00 0.00 35.87 5.34
2315 2415 0.159345 CATTGCGTTTTTCAGCGTGC 59.841 50.000 0.00 0.00 35.87 5.34
2316 2416 1.268113 ATTGCGTTTTTCAGCGTGCG 61.268 50.000 0.00 0.00 35.87 5.34
2317 2417 3.742137 GCGTTTTTCAGCGTGCGC 61.742 61.111 8.67 8.67 42.33 6.09
2318 2418 3.091022 CGTTTTTCAGCGTGCGCC 61.091 61.111 13.21 0.00 43.17 6.53
2319 2419 2.729491 GTTTTTCAGCGTGCGCCC 60.729 61.111 13.21 0.00 43.17 6.13
2320 2420 3.212682 TTTTTCAGCGTGCGCCCA 61.213 55.556 13.21 0.00 43.17 5.36
2321 2421 2.775856 TTTTTCAGCGTGCGCCCAA 61.776 52.632 13.21 3.45 43.17 4.12
2322 2422 2.284798 TTTTTCAGCGTGCGCCCAAA 62.285 50.000 13.21 9.33 43.17 3.28
2323 2423 2.284798 TTTTCAGCGTGCGCCCAAAA 62.285 50.000 13.21 14.28 43.17 2.44
2324 2424 2.284798 TTTCAGCGTGCGCCCAAAAA 62.285 50.000 13.21 6.14 43.17 1.94
2325 2425 2.945398 TTCAGCGTGCGCCCAAAAAC 62.945 55.000 13.21 0.00 43.17 2.43
2326 2426 3.216292 AGCGTGCGCCCAAAAACT 61.216 55.556 13.21 0.00 43.17 2.66
2327 2427 2.279186 GCGTGCGCCCAAAAACTT 60.279 55.556 4.18 0.00 34.56 2.66
2328 2428 1.880796 GCGTGCGCCCAAAAACTTT 60.881 52.632 4.18 0.00 34.56 2.66
2329 2429 1.425267 GCGTGCGCCCAAAAACTTTT 61.425 50.000 4.18 0.00 34.56 2.27
2330 2430 1.841450 CGTGCGCCCAAAAACTTTTA 58.159 45.000 4.18 0.00 0.00 1.52
2331 2431 1.784283 CGTGCGCCCAAAAACTTTTAG 59.216 47.619 4.18 0.00 0.00 1.85
2332 2432 1.525197 GTGCGCCCAAAAACTTTTAGC 59.475 47.619 4.18 0.00 0.00 3.09
2333 2433 0.781787 GCGCCCAAAAACTTTTAGCG 59.218 50.000 19.34 19.34 46.24 4.26
2334 2434 0.781787 CGCCCAAAAACTTTTAGCGC 59.218 50.000 14.61 0.00 41.67 5.92
2335 2435 1.601914 CGCCCAAAAACTTTTAGCGCT 60.602 47.619 17.26 17.26 41.67 5.92
2336 2436 2.350964 CGCCCAAAAACTTTTAGCGCTA 60.351 45.455 14.45 14.45 41.67 4.26
2337 2437 2.984471 GCCCAAAAACTTTTAGCGCTAC 59.016 45.455 18.63 0.00 0.00 3.58
2338 2438 3.551250 GCCCAAAAACTTTTAGCGCTACA 60.551 43.478 18.63 8.18 0.00 2.74
2339 2439 4.226761 CCCAAAAACTTTTAGCGCTACAG 58.773 43.478 18.63 18.01 0.00 2.74
2340 2440 3.668656 CCAAAAACTTTTAGCGCTACAGC 59.331 43.478 18.63 0.00 37.78 4.40
2342 2442 4.830826 AAAACTTTTAGCGCTACAGCTT 57.169 36.364 18.63 10.81 46.80 3.74
2343 2443 4.406001 AAACTTTTAGCGCTACAGCTTC 57.594 40.909 18.63 0.00 46.80 3.86
2344 2444 3.320673 ACTTTTAGCGCTACAGCTTCT 57.679 42.857 18.63 0.00 46.80 2.85
2345 2445 2.996621 ACTTTTAGCGCTACAGCTTCTG 59.003 45.455 18.63 4.43 46.80 3.02
2346 2446 1.359848 TTTAGCGCTACAGCTTCTGC 58.640 50.000 18.63 0.00 46.80 4.26
2356 2456 3.887783 GCTTCTGCTGGAGCTGAC 58.112 61.111 16.22 0.00 46.26 3.51
2357 2457 1.744741 GCTTCTGCTGGAGCTGACC 60.745 63.158 16.22 0.00 46.26 4.02
2358 2458 1.447489 CTTCTGCTGGAGCTGACCG 60.447 63.158 7.65 0.00 46.26 4.79
2359 2459 2.849120 CTTCTGCTGGAGCTGACCGG 62.849 65.000 0.00 0.00 46.26 5.28
2369 2469 3.291383 CTGACCGGCGCCCAAAAA 61.291 61.111 23.46 1.63 0.00 1.94
2388 2488 3.423996 AAAACAAACTTTTAGCGCGGA 57.576 38.095 8.83 0.00 0.00 5.54
2389 2489 2.681152 AACAAACTTTTAGCGCGGAG 57.319 45.000 8.83 0.93 0.00 4.63
2390 2490 1.873698 ACAAACTTTTAGCGCGGAGA 58.126 45.000 8.83 0.00 0.00 3.71
2391 2491 1.798813 ACAAACTTTTAGCGCGGAGAG 59.201 47.619 8.83 1.60 0.00 3.20
2401 2501 1.790387 CGCGGAGAGCTCTTTTTGG 59.210 57.895 19.36 6.86 45.59 3.28
2402 2502 1.639298 CGCGGAGAGCTCTTTTTGGG 61.639 60.000 19.36 12.12 45.59 4.12
2403 2503 1.927608 GCGGAGAGCTCTTTTTGGGC 61.928 60.000 19.36 11.18 44.04 5.36
2404 2504 1.639298 CGGAGAGCTCTTTTTGGGCG 61.639 60.000 19.36 0.00 0.00 6.13
2405 2505 1.503994 GAGAGCTCTTTTTGGGCGC 59.496 57.895 19.36 0.00 0.00 6.53
2406 2506 1.927608 GAGAGCTCTTTTTGGGCGCC 61.928 60.000 21.18 21.18 0.00 6.53
2407 2507 1.973812 GAGCTCTTTTTGGGCGCCT 60.974 57.895 28.56 0.61 0.00 5.52
2408 2508 2.205243 GAGCTCTTTTTGGGCGCCTG 62.205 60.000 28.56 9.84 0.00 4.85
2409 2509 2.564721 GCTCTTTTTGGGCGCCTGT 61.565 57.895 28.56 0.00 0.00 4.00
2410 2510 2.041153 CTCTTTTTGGGCGCCTGTT 58.959 52.632 28.56 0.00 0.00 3.16
2411 2511 0.318955 CTCTTTTTGGGCGCCTGTTG 60.319 55.000 28.56 12.02 0.00 3.33
2412 2512 1.300853 CTTTTTGGGCGCCTGTTGG 60.301 57.895 28.56 8.87 0.00 3.77
2413 2513 1.743321 CTTTTTGGGCGCCTGTTGGA 61.743 55.000 28.56 7.57 34.57 3.53
2414 2514 1.743321 TTTTTGGGCGCCTGTTGGAG 61.743 55.000 28.56 0.00 36.16 3.86
2415 2515 2.632602 TTTTGGGCGCCTGTTGGAGA 62.633 55.000 28.56 1.45 34.95 3.71
2416 2516 2.424842 TTTGGGCGCCTGTTGGAGAT 62.425 55.000 28.56 0.00 34.95 2.75
2417 2517 2.825836 GGGCGCCTGTTGGAGATG 60.826 66.667 28.56 0.00 34.95 2.90
2418 2518 3.512516 GGCGCCTGTTGGAGATGC 61.513 66.667 22.15 0.00 34.95 3.91
2419 2519 2.437359 GCGCCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 34.95 3.79
2476 2579 4.810491 ACAAAACACAAATGCTGCCTAAAG 59.190 37.500 0.00 0.00 0.00 1.85
2494 2597 1.529244 GGCAAATGGGCGAGGCTAT 60.529 57.895 0.00 0.00 33.57 2.97
2495 2598 1.518903 GGCAAATGGGCGAGGCTATC 61.519 60.000 0.00 0.00 33.57 2.08
2518 2647 3.002965 GGGTCAGTCGATTTTTCAAACGT 59.997 43.478 0.00 0.00 30.57 3.99
2531 2660 6.456447 TTTTCAAACGTACGATCGAAATCT 57.544 33.333 24.34 0.39 34.70 2.40
2538 2667 2.572191 ACGATCGAAATCTAACGGCA 57.428 45.000 24.34 0.00 0.00 5.69
2559 2688 0.178301 CCGGCCTTTCTTCTACCTCC 59.822 60.000 0.00 0.00 0.00 4.30
2576 2705 4.946646 ACCTCCATCTCTTCTTCTTCTCT 58.053 43.478 0.00 0.00 0.00 3.10
2578 2707 6.129179 ACCTCCATCTCTTCTTCTTCTCTAG 58.871 44.000 0.00 0.00 0.00 2.43
2579 2708 5.010012 CCTCCATCTCTTCTTCTTCTCTAGC 59.990 48.000 0.00 0.00 0.00 3.42
2580 2709 4.892934 TCCATCTCTTCTTCTTCTCTAGCC 59.107 45.833 0.00 0.00 0.00 3.93
2581 2710 4.261572 CCATCTCTTCTTCTTCTCTAGCCG 60.262 50.000 0.00 0.00 0.00 5.52
2582 2711 2.685897 TCTCTTCTTCTTCTCTAGCCGC 59.314 50.000 0.00 0.00 0.00 6.53
2583 2712 1.751924 TCTTCTTCTTCTCTAGCCGCC 59.248 52.381 0.00 0.00 0.00 6.13
2584 2713 0.456221 TTCTTCTTCTCTAGCCGCCG 59.544 55.000 0.00 0.00 0.00 6.46
2585 2714 1.590259 CTTCTTCTCTAGCCGCCGC 60.590 63.158 0.00 0.00 0.00 6.53
2586 2715 2.962697 CTTCTTCTCTAGCCGCCGCC 62.963 65.000 0.00 0.00 34.57 6.13
2587 2716 4.593864 CTTCTCTAGCCGCCGCCC 62.594 72.222 0.00 0.00 34.57 6.13
2616 2745 1.285641 CCAAACCACATGCGACCAC 59.714 57.895 0.00 0.00 0.00 4.16
2693 2822 4.435970 TCTAGTCGCTGCCCCCGA 62.436 66.667 0.00 0.00 0.00 5.14
2709 2838 2.565645 CGACCATCCCTCTAGGCCG 61.566 68.421 0.00 0.00 34.51 6.13
2727 2856 1.068816 CCGGCCCTCGTTTAAGTTTTG 60.069 52.381 0.00 0.00 37.11 2.44
2733 2863 2.803956 CCTCGTTTAAGTTTTGCTCCGA 59.196 45.455 0.00 0.00 0.00 4.55
2779 2933 3.851128 GGTCTAGCCGCTGTCCCC 61.851 72.222 2.16 0.00 0.00 4.81
2780 2934 4.208686 GTCTAGCCGCTGTCCCCG 62.209 72.222 2.16 0.00 0.00 5.73
2901 3055 4.527427 CCCTAAGTTAGATACTGGGGTAGC 59.473 50.000 11.66 0.00 41.80 3.58
2907 3061 1.152312 ATACTGGGGTAGCCCTCCG 60.152 63.158 29.64 19.54 44.66 4.63
2938 3092 4.421574 TTCCTTCTCCTTCCTTACCTCT 57.578 45.455 0.00 0.00 0.00 3.69
2949 3103 1.561643 CTTACCTCTGGCTCACTCCA 58.438 55.000 0.00 0.00 34.42 3.86
2959 3113 0.104671 GCTCACTCCAGCCATCTCTC 59.895 60.000 0.00 0.00 32.76 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.369860 TCACAGAAGCAGTCATCACCTT 59.630 45.455 0.00 0.00 0.00 3.50
28 29 5.237996 CGCTCATCCTTAATGATCATGTTGT 59.762 40.000 9.46 0.00 43.44 3.32
38 39 3.814842 TGCCATTACGCTCATCCTTAATG 59.185 43.478 0.00 0.00 36.65 1.90
39 40 4.067896 CTGCCATTACGCTCATCCTTAAT 58.932 43.478 0.00 0.00 0.00 1.40
42 43 1.959042 CTGCCATTACGCTCATCCTT 58.041 50.000 0.00 0.00 0.00 3.36
45 46 1.196354 GATGCTGCCATTACGCTCATC 59.804 52.381 0.00 0.00 34.68 2.92
252 253 4.942761 AAGTTTGTGCACATGGAAAGAT 57.057 36.364 22.39 0.67 0.00 2.40
258 259 3.441496 ACTCAAAGTTTGTGCACATGG 57.559 42.857 22.39 11.48 0.00 3.66
406 420 3.143728 GTGTTCACCCGGACTTATGTTT 58.856 45.455 0.73 0.00 0.00 2.83
421 435 0.309302 CGGCAATGAAACCGTGTTCA 59.691 50.000 1.00 1.00 44.46 3.18
433 447 3.419908 CGTTCGTTTTTAAAGCGGCAATG 60.420 43.478 13.38 4.16 0.00 2.82
437 451 2.021443 TCGTTCGTTTTTAAAGCGGC 57.979 45.000 13.38 6.70 0.00 6.53
438 452 4.087507 GGATTTCGTTCGTTTTTAAAGCGG 59.912 41.667 13.38 0.00 0.00 5.52
442 456 5.204101 GTCCGGATTTCGTTCGTTTTTAAA 58.796 37.500 7.81 0.00 37.11 1.52
445 459 2.613133 TGTCCGGATTTCGTTCGTTTTT 59.387 40.909 7.81 0.00 37.11 1.94
452 466 2.211806 TCGTTTTGTCCGGATTTCGTT 58.788 42.857 7.81 0.00 37.11 3.85
455 469 1.463528 CGCTCGTTTTGTCCGGATTTC 60.464 52.381 7.81 0.00 0.00 2.17
472 486 2.601763 CGAATAAGCTTAAACGGACGCT 59.398 45.455 20.36 0.00 0.00 5.07
475 489 3.308053 GTCCCGAATAAGCTTAAACGGAC 59.692 47.826 34.86 27.88 42.40 4.79
483 497 3.081804 CTGGTTTGTCCCGAATAAGCTT 58.918 45.455 3.48 3.48 34.77 3.74
484 498 2.039879 ACTGGTTTGTCCCGAATAAGCT 59.960 45.455 0.00 0.00 34.77 3.74
503 517 0.828022 TCCGGCCATATTGACGAACT 59.172 50.000 3.09 0.00 0.00 3.01
512 526 3.432186 CGATCCACATATTCCGGCCATAT 60.432 47.826 2.24 0.00 0.00 1.78
641 655 0.744771 GCTTGGGAGTTGGGATCGAC 60.745 60.000 0.00 0.00 0.00 4.20
739 753 0.546598 ATGGGATTGGTCGGAACTCC 59.453 55.000 0.00 0.00 0.00 3.85
767 781 2.772287 ACCTGCTGTGAAGAGCTAAAC 58.228 47.619 0.86 0.00 39.90 2.01
955 969 4.665833 TCGTGACTCGGGATGATTAATT 57.334 40.909 0.00 0.00 40.32 1.40
2013 2112 3.751175 TGGATTCGACATGTCCAAACTTC 59.249 43.478 20.03 8.29 38.99 3.01
2110 2210 1.291132 GCCGTTGGAGATGCTCTTAC 58.709 55.000 0.00 0.00 0.00 2.34
2111 2211 0.178068 GGCCGTTGGAGATGCTCTTA 59.822 55.000 0.00 0.00 0.00 2.10
2112 2212 1.078143 GGCCGTTGGAGATGCTCTT 60.078 57.895 0.00 0.00 0.00 2.85
2113 2213 2.586792 GGCCGTTGGAGATGCTCT 59.413 61.111 0.00 0.00 0.00 4.09
2114 2214 2.892425 CGGCCGTTGGAGATGCTC 60.892 66.667 19.50 0.00 0.00 4.26
2117 2217 3.499737 GTGCGGCCGTTGGAGATG 61.500 66.667 28.70 0.00 0.00 2.90
2118 2218 3.545124 TTGTGCGGCCGTTGGAGAT 62.545 57.895 28.70 0.00 0.00 2.75
2119 2219 3.758973 TTTGTGCGGCCGTTGGAGA 62.759 57.895 28.70 6.06 0.00 3.71
2120 2220 2.343163 TTTTTGTGCGGCCGTTGGAG 62.343 55.000 28.70 0.00 0.00 3.86
2121 2221 2.415608 TTTTTGTGCGGCCGTTGGA 61.416 52.632 28.70 8.23 0.00 3.53
2122 2222 2.105128 TTTTTGTGCGGCCGTTGG 59.895 55.556 28.70 0.00 0.00 3.77
2136 2236 2.612604 GTTTATTGGGCGCGGATTTTT 58.387 42.857 8.83 0.00 0.00 1.94
2137 2237 1.468395 CGTTTATTGGGCGCGGATTTT 60.468 47.619 8.83 0.00 0.00 1.82
2138 2238 0.099791 CGTTTATTGGGCGCGGATTT 59.900 50.000 8.83 0.00 0.00 2.17
2139 2239 1.027792 ACGTTTATTGGGCGCGGATT 61.028 50.000 8.83 0.00 0.00 3.01
2140 2240 1.027792 AACGTTTATTGGGCGCGGAT 61.028 50.000 8.83 0.00 0.00 4.18
2141 2241 0.390866 TAACGTTTATTGGGCGCGGA 60.391 50.000 5.91 0.00 0.00 5.54
2142 2242 0.658897 ATAACGTTTATTGGGCGCGG 59.341 50.000 5.91 0.00 0.00 6.46
2143 2243 2.660900 GCTATAACGTTTATTGGGCGCG 60.661 50.000 5.91 0.00 0.00 6.86
2144 2244 2.288458 TGCTATAACGTTTATTGGGCGC 59.712 45.455 5.91 0.00 0.00 6.53
2145 2245 3.602946 CGTGCTATAACGTTTATTGGGCG 60.603 47.826 5.91 0.23 38.74 6.13
2146 2246 3.847105 GCGTGCTATAACGTTTATTGGGC 60.847 47.826 5.91 3.92 45.32 5.36
2147 2247 3.303526 GGCGTGCTATAACGTTTATTGGG 60.304 47.826 5.91 0.00 45.32 4.12
2148 2248 3.310227 TGGCGTGCTATAACGTTTATTGG 59.690 43.478 5.91 0.00 45.32 3.16
2149 2249 4.268522 GTGGCGTGCTATAACGTTTATTG 58.731 43.478 5.91 0.86 45.32 1.90
2150 2250 3.310501 GGTGGCGTGCTATAACGTTTATT 59.689 43.478 5.91 0.00 45.32 1.40
2151 2251 2.867975 GGTGGCGTGCTATAACGTTTAT 59.132 45.455 5.91 0.73 45.32 1.40
2152 2252 2.270047 GGTGGCGTGCTATAACGTTTA 58.730 47.619 5.91 0.00 45.32 2.01
2153 2253 1.081094 GGTGGCGTGCTATAACGTTT 58.919 50.000 5.91 0.00 45.32 3.60
2154 2254 0.037139 TGGTGGCGTGCTATAACGTT 60.037 50.000 5.88 5.88 45.32 3.99
2155 2255 0.177141 ATGGTGGCGTGCTATAACGT 59.823 50.000 0.00 0.00 45.32 3.99
2156 2256 2.058798 CTATGGTGGCGTGCTATAACG 58.941 52.381 0.00 0.00 46.30 3.18
2157 2257 3.107642 ACTATGGTGGCGTGCTATAAC 57.892 47.619 0.00 0.00 0.00 1.89
2158 2258 3.893200 AGTACTATGGTGGCGTGCTATAA 59.107 43.478 0.00 0.00 0.00 0.98
2159 2259 3.493334 AGTACTATGGTGGCGTGCTATA 58.507 45.455 0.00 0.00 0.00 1.31
2160 2260 2.317040 AGTACTATGGTGGCGTGCTAT 58.683 47.619 0.00 0.00 0.00 2.97
2161 2261 1.771565 AGTACTATGGTGGCGTGCTA 58.228 50.000 0.00 0.00 0.00 3.49
2162 2262 0.902531 AAGTACTATGGTGGCGTGCT 59.097 50.000 0.00 0.00 0.00 4.40
2163 2263 1.734163 AAAGTACTATGGTGGCGTGC 58.266 50.000 0.00 0.00 0.00 5.34
2164 2264 5.672819 GCTTTAAAAGTACTATGGTGGCGTG 60.673 44.000 0.00 0.00 0.00 5.34
2165 2265 4.393990 GCTTTAAAAGTACTATGGTGGCGT 59.606 41.667 0.00 0.00 0.00 5.68
2166 2266 4.493545 CGCTTTAAAAGTACTATGGTGGCG 60.494 45.833 12.89 12.89 0.00 5.69
2167 2267 4.393990 ACGCTTTAAAAGTACTATGGTGGC 59.606 41.667 0.00 0.00 0.00 5.01
2168 2268 5.220340 CGACGCTTTAAAAGTACTATGGTGG 60.220 44.000 0.00 0.00 0.00 4.61
2169 2269 5.220340 CCGACGCTTTAAAAGTACTATGGTG 60.220 44.000 0.00 0.00 0.00 4.17
2170 2270 4.866486 CCGACGCTTTAAAAGTACTATGGT 59.134 41.667 0.00 0.00 0.00 3.55
2171 2271 4.269363 CCCGACGCTTTAAAAGTACTATGG 59.731 45.833 0.00 0.00 0.00 2.74
2172 2272 5.005107 GTCCCGACGCTTTAAAAGTACTATG 59.995 44.000 0.00 0.00 0.00 2.23
2173 2273 5.105063 GTCCCGACGCTTTAAAAGTACTAT 58.895 41.667 0.00 0.00 0.00 2.12
2174 2274 4.485163 GTCCCGACGCTTTAAAAGTACTA 58.515 43.478 0.00 0.00 0.00 1.82
2175 2275 3.320626 GTCCCGACGCTTTAAAAGTACT 58.679 45.455 0.00 0.00 0.00 2.73
2176 2276 2.413112 GGTCCCGACGCTTTAAAAGTAC 59.587 50.000 0.00 0.00 0.00 2.73
2177 2277 2.036992 TGGTCCCGACGCTTTAAAAGTA 59.963 45.455 0.00 0.00 0.00 2.24
2178 2278 1.202675 TGGTCCCGACGCTTTAAAAGT 60.203 47.619 0.00 0.00 0.00 2.66
2179 2279 1.515081 TGGTCCCGACGCTTTAAAAG 58.485 50.000 0.00 0.00 0.00 2.27
2180 2280 1.603326 GTTGGTCCCGACGCTTTAAAA 59.397 47.619 0.00 0.00 0.00 1.52
2181 2281 1.202675 AGTTGGTCCCGACGCTTTAAA 60.203 47.619 0.00 0.00 35.57 1.52
2182 2282 0.393820 AGTTGGTCCCGACGCTTTAA 59.606 50.000 0.00 0.00 35.57 1.52
2183 2283 0.393820 AAGTTGGTCCCGACGCTTTA 59.606 50.000 0.00 0.00 35.57 1.85
2184 2284 0.464916 AAAGTTGGTCCCGACGCTTT 60.465 50.000 0.00 5.45 35.57 3.51
2185 2285 1.147600 AAAGTTGGTCCCGACGCTT 59.852 52.632 0.00 0.00 35.57 4.68
2186 2286 1.597027 CAAAGTTGGTCCCGACGCT 60.597 57.895 0.00 0.00 35.57 5.07
2187 2287 2.943653 CAAAGTTGGTCCCGACGC 59.056 61.111 0.00 0.00 35.57 5.19
2188 2288 1.164041 AAGCAAAGTTGGTCCCGACG 61.164 55.000 0.00 0.00 38.04 5.12
2189 2289 1.029681 AAAGCAAAGTTGGTCCCGAC 58.970 50.000 0.00 0.00 38.04 4.79
2190 2290 2.500229 CTAAAGCAAAGTTGGTCCCGA 58.500 47.619 0.00 0.00 38.04 5.14
2191 2291 1.068541 GCTAAAGCAAAGTTGGTCCCG 60.069 52.381 0.00 0.00 41.59 5.14
2192 2292 2.724977 GCTAAAGCAAAGTTGGTCCC 57.275 50.000 0.00 0.00 41.59 4.46
2214 2314 3.326981 GCGCGTGTTTTTGGGCAC 61.327 61.111 8.43 0.00 42.89 5.01
2215 2315 4.577246 GGCGCGTGTTTTTGGGCA 62.577 61.111 8.43 0.00 44.91 5.36
2217 2317 2.907897 TTTGGGCGCGTGTTTTTGGG 62.908 55.000 8.43 0.00 0.00 4.12
2218 2318 1.084370 TTTTGGGCGCGTGTTTTTGG 61.084 50.000 8.43 0.00 0.00 3.28
2219 2319 0.721718 TTTTTGGGCGCGTGTTTTTG 59.278 45.000 8.43 0.00 0.00 2.44
2220 2320 3.139029 TTTTTGGGCGCGTGTTTTT 57.861 42.105 8.43 0.00 0.00 1.94
2221 2321 4.913126 TTTTTGGGCGCGTGTTTT 57.087 44.444 8.43 0.00 0.00 2.43
2235 2335 5.477510 TCACAATTTGCACTGTCTGTTTTT 58.522 33.333 0.00 0.00 0.00 1.94
2236 2336 5.070770 TCACAATTTGCACTGTCTGTTTT 57.929 34.783 0.00 0.00 0.00 2.43
2237 2337 4.717233 TCACAATTTGCACTGTCTGTTT 57.283 36.364 0.00 0.00 0.00 2.83
2238 2338 4.675510 CTTCACAATTTGCACTGTCTGTT 58.324 39.130 0.00 0.00 0.00 3.16
2239 2339 3.489738 GCTTCACAATTTGCACTGTCTGT 60.490 43.478 0.00 0.00 0.00 3.41
2240 2340 3.047796 GCTTCACAATTTGCACTGTCTG 58.952 45.455 0.00 0.00 0.00 3.51
2241 2341 2.287188 CGCTTCACAATTTGCACTGTCT 60.287 45.455 0.00 0.00 0.00 3.41
2242 2342 2.046313 CGCTTCACAATTTGCACTGTC 58.954 47.619 0.00 0.00 0.00 3.51
2243 2343 1.865248 GCGCTTCACAATTTGCACTGT 60.865 47.619 0.00 0.00 0.00 3.55
2244 2344 0.780002 GCGCTTCACAATTTGCACTG 59.220 50.000 0.00 0.00 0.00 3.66
2245 2345 0.661187 CGCGCTTCACAATTTGCACT 60.661 50.000 5.56 0.00 0.00 4.40
2246 2346 1.768603 CGCGCTTCACAATTTGCAC 59.231 52.632 5.56 0.00 0.00 4.57
2247 2347 2.015627 GCGCGCTTCACAATTTGCA 61.016 52.632 26.67 0.00 0.00 4.08
2248 2348 2.765150 GCGCGCTTCACAATTTGC 59.235 55.556 26.67 0.00 0.00 3.68
2249 2349 3.046460 GCGCGCGCTTCACAATTTG 62.046 57.895 44.38 10.35 38.26 2.32
2250 2350 2.800746 GCGCGCGCTTCACAATTT 60.801 55.556 44.38 0.00 38.26 1.82
2265 2365 1.157870 ATTTAGGGCGTCGGATTGCG 61.158 55.000 0.00 0.00 0.00 4.85
2266 2366 1.873698 TATTTAGGGCGTCGGATTGC 58.126 50.000 0.00 0.00 0.00 3.56
2267 2367 2.159627 GCATATTTAGGGCGTCGGATTG 59.840 50.000 0.00 0.00 0.00 2.67
2268 2368 2.038557 AGCATATTTAGGGCGTCGGATT 59.961 45.455 0.00 0.00 0.00 3.01
2269 2369 1.623811 AGCATATTTAGGGCGTCGGAT 59.376 47.619 0.00 0.00 0.00 4.18
2270 2370 1.045407 AGCATATTTAGGGCGTCGGA 58.955 50.000 0.00 0.00 0.00 4.55
2271 2371 1.148310 CAGCATATTTAGGGCGTCGG 58.852 55.000 0.00 0.00 0.00 4.79
2272 2372 0.512952 GCAGCATATTTAGGGCGTCG 59.487 55.000 0.00 0.00 0.00 5.12
2273 2373 0.512952 CGCAGCATATTTAGGGCGTC 59.487 55.000 0.00 0.00 39.65 5.19
2274 2374 2.616969 CGCAGCATATTTAGGGCGT 58.383 52.632 0.00 0.00 39.65 5.68
2294 2394 0.939106 ACGCTGAAAAACGCAATGGC 60.939 50.000 0.00 0.00 0.00 4.40
2295 2395 0.777631 CACGCTGAAAAACGCAATGG 59.222 50.000 0.00 0.00 0.00 3.16
2296 2396 0.159345 GCACGCTGAAAAACGCAATG 59.841 50.000 0.00 0.00 0.00 2.82
2297 2397 1.268113 CGCACGCTGAAAAACGCAAT 61.268 50.000 0.00 0.00 0.00 3.56
2298 2398 1.936880 CGCACGCTGAAAAACGCAA 60.937 52.632 0.00 0.00 0.00 4.85
2299 2399 2.351774 CGCACGCTGAAAAACGCA 60.352 55.556 0.00 0.00 0.00 5.24
2300 2400 3.742137 GCGCACGCTGAAAAACGC 61.742 61.111 7.96 0.00 39.49 4.84
2301 2401 3.091022 GGCGCACGCTGAAAAACG 61.091 61.111 15.36 0.00 41.60 3.60
2302 2402 2.729491 GGGCGCACGCTGAAAAAC 60.729 61.111 15.36 0.00 41.60 2.43
2303 2403 2.284798 TTTGGGCGCACGCTGAAAAA 62.285 50.000 15.36 0.00 41.60 1.94
2304 2404 2.284798 TTTTGGGCGCACGCTGAAAA 62.285 50.000 15.36 15.56 41.60 2.29
2305 2405 2.284798 TTTTTGGGCGCACGCTGAAA 62.285 50.000 15.36 10.80 41.60 2.69
2306 2406 2.775856 TTTTTGGGCGCACGCTGAA 61.776 52.632 15.36 5.16 41.60 3.02
2307 2407 3.212682 TTTTTGGGCGCACGCTGA 61.213 55.556 15.36 0.00 41.60 4.26
2308 2408 2.952291 AAGTTTTTGGGCGCACGCTG 62.952 55.000 15.36 0.00 41.60 5.18
2309 2409 2.291457 AAAGTTTTTGGGCGCACGCT 62.291 50.000 15.36 0.00 41.60 5.07
2310 2410 1.425267 AAAAGTTTTTGGGCGCACGC 61.425 50.000 10.83 6.46 41.06 5.34
2311 2411 1.784283 CTAAAAGTTTTTGGGCGCACG 59.216 47.619 10.83 0.00 0.00 5.34
2312 2412 1.525197 GCTAAAAGTTTTTGGGCGCAC 59.475 47.619 10.83 6.04 0.00 5.34
2313 2413 1.859383 GCTAAAAGTTTTTGGGCGCA 58.141 45.000 10.83 0.00 0.00 6.09
2314 2414 0.781787 CGCTAAAAGTTTTTGGGCGC 59.218 50.000 20.89 0.00 42.00 6.53
2315 2415 0.781787 GCGCTAAAAGTTTTTGGGCG 59.218 50.000 26.58 25.61 46.09 6.13
2316 2416 2.148916 AGCGCTAAAAGTTTTTGGGC 57.851 45.000 30.39 30.39 37.38 5.36
2317 2417 4.226761 CTGTAGCGCTAAAAGTTTTTGGG 58.773 43.478 20.73 18.10 0.00 4.12
2318 2418 3.668656 GCTGTAGCGCTAAAAGTTTTTGG 59.331 43.478 20.73 0.00 0.00 3.28
2319 2419 4.868581 GCTGTAGCGCTAAAAGTTTTTG 57.131 40.909 20.73 5.79 0.00 2.44
2339 2439 1.744741 GGTCAGCTCCAGCAGAAGC 60.745 63.158 0.48 0.00 45.16 3.86
2340 2440 1.447489 CGGTCAGCTCCAGCAGAAG 60.447 63.158 0.48 0.00 45.16 2.85
2341 2441 2.659016 CGGTCAGCTCCAGCAGAA 59.341 61.111 0.48 0.00 45.16 3.02
2342 2442 3.385384 CCGGTCAGCTCCAGCAGA 61.385 66.667 0.48 0.00 45.16 4.26
2352 2452 3.291383 TTTTTGGGCGCCGGTCAG 61.291 61.111 22.54 0.00 0.00 3.51
2367 2467 3.771798 TCCGCGCTAAAAGTTTGTTTTT 58.228 36.364 5.56 0.00 34.78 1.94
2368 2468 3.065648 TCTCCGCGCTAAAAGTTTGTTTT 59.934 39.130 5.56 0.00 0.00 2.43
2369 2469 2.614983 TCTCCGCGCTAAAAGTTTGTTT 59.385 40.909 5.56 0.00 0.00 2.83
2370 2470 2.215196 TCTCCGCGCTAAAAGTTTGTT 58.785 42.857 5.56 0.00 0.00 2.83
2371 2471 1.798813 CTCTCCGCGCTAAAAGTTTGT 59.201 47.619 5.56 0.00 0.00 2.83
2372 2472 1.464189 GCTCTCCGCGCTAAAAGTTTG 60.464 52.381 5.56 0.00 0.00 2.93
2373 2473 0.796927 GCTCTCCGCGCTAAAAGTTT 59.203 50.000 5.56 0.00 0.00 2.66
2374 2474 0.037232 AGCTCTCCGCGCTAAAAGTT 60.037 50.000 5.56 0.00 45.59 2.66
2375 2475 0.458716 GAGCTCTCCGCGCTAAAAGT 60.459 55.000 6.43 0.00 45.59 2.66
2376 2476 2.292803 GAGCTCTCCGCGCTAAAAG 58.707 57.895 6.43 0.00 45.59 2.27
2377 2477 4.496670 GAGCTCTCCGCGCTAAAA 57.503 55.556 6.43 0.00 45.59 1.52
2382 2482 1.133458 CAAAAAGAGCTCTCCGCGC 59.867 57.895 18.55 0.00 45.59 6.86
2383 2483 1.639298 CCCAAAAAGAGCTCTCCGCG 61.639 60.000 18.55 0.00 45.59 6.46
2384 2484 1.927608 GCCCAAAAAGAGCTCTCCGC 61.928 60.000 18.55 8.62 39.57 5.54
2385 2485 1.639298 CGCCCAAAAAGAGCTCTCCG 61.639 60.000 18.55 5.71 0.00 4.63
2386 2486 1.927608 GCGCCCAAAAAGAGCTCTCC 61.928 60.000 18.55 0.00 0.00 3.71
2387 2487 1.503994 GCGCCCAAAAAGAGCTCTC 59.496 57.895 18.55 1.03 0.00 3.20
2388 2488 1.973812 GGCGCCCAAAAAGAGCTCT 60.974 57.895 18.11 11.45 0.00 4.09
2389 2489 1.973812 AGGCGCCCAAAAAGAGCTC 60.974 57.895 26.15 5.27 0.00 4.09
2390 2490 2.116125 AGGCGCCCAAAAAGAGCT 59.884 55.556 26.15 0.00 0.00 4.09
2391 2491 2.087462 AACAGGCGCCCAAAAAGAGC 62.087 55.000 26.15 0.00 0.00 4.09
2392 2492 0.318955 CAACAGGCGCCCAAAAAGAG 60.319 55.000 26.15 5.50 0.00 2.85
2393 2493 1.739049 CAACAGGCGCCCAAAAAGA 59.261 52.632 26.15 0.00 0.00 2.52
2394 2494 1.300853 CCAACAGGCGCCCAAAAAG 60.301 57.895 26.15 8.61 0.00 2.27
2395 2495 1.743321 CTCCAACAGGCGCCCAAAAA 61.743 55.000 26.15 3.57 0.00 1.94
2396 2496 2.123683 TCCAACAGGCGCCCAAAA 60.124 55.556 26.15 0.41 0.00 2.44
2397 2497 2.424842 ATCTCCAACAGGCGCCCAAA 62.425 55.000 26.15 1.70 0.00 3.28
2398 2498 2.905996 ATCTCCAACAGGCGCCCAA 61.906 57.895 26.15 0.88 0.00 4.12
2399 2499 3.329889 ATCTCCAACAGGCGCCCA 61.330 61.111 26.15 0.00 0.00 5.36
2400 2500 2.825836 CATCTCCAACAGGCGCCC 60.826 66.667 26.15 5.07 0.00 6.13
2401 2501 3.512516 GCATCTCCAACAGGCGCC 61.513 66.667 21.89 21.89 0.00 6.53
2402 2502 2.437359 AGCATCTCCAACAGGCGC 60.437 61.111 0.00 0.00 0.00 6.53
2403 2503 3.805267 GAGCATCTCCAACAGGCG 58.195 61.111 0.00 0.00 0.00 5.52
2414 2514 8.125448 ACTCGCAAATTCTTTTATTAGAGCATC 58.875 33.333 0.00 0.00 0.00 3.91
2415 2515 7.989826 ACTCGCAAATTCTTTTATTAGAGCAT 58.010 30.769 0.00 0.00 0.00 3.79
2416 2516 7.377766 ACTCGCAAATTCTTTTATTAGAGCA 57.622 32.000 0.00 0.00 0.00 4.26
2417 2517 7.253453 GCAACTCGCAAATTCTTTTATTAGAGC 60.253 37.037 0.00 0.00 41.79 4.09
2418 2518 7.045354 CGCAACTCGCAAATTCTTTTATTAGAG 60.045 37.037 0.00 0.00 42.60 2.43
2419 2519 6.740905 CGCAACTCGCAAATTCTTTTATTAGA 59.259 34.615 0.00 0.00 42.60 2.10
2476 2579 1.518903 GATAGCCTCGCCCATTTGCC 61.519 60.000 0.00 0.00 0.00 4.52
2494 2597 2.823924 TGAAAAATCGACTGACCCGA 57.176 45.000 0.00 0.00 40.53 5.14
2495 2598 3.551551 GTTTGAAAAATCGACTGACCCG 58.448 45.455 0.00 0.00 0.00 5.28
2496 2599 3.002965 ACGTTTGAAAAATCGACTGACCC 59.997 43.478 0.00 0.00 0.00 4.46
2518 2647 3.365832 GTGCCGTTAGATTTCGATCGTA 58.634 45.455 15.94 1.77 0.00 3.43
2538 2667 0.546988 AGGTAGAAGAAAGGCCGGGT 60.547 55.000 2.18 0.00 0.00 5.28
2543 2672 3.709141 AGAGATGGAGGTAGAAGAAAGGC 59.291 47.826 0.00 0.00 0.00 4.35
2559 2688 4.792704 GCGGCTAGAGAAGAAGAAGAGATG 60.793 50.000 0.00 0.00 0.00 2.90
2600 2729 1.152860 TGGTGGTCGCATGTGGTTT 60.153 52.632 6.39 0.00 0.00 3.27
2605 2734 4.697756 CGGGTGGTGGTCGCATGT 62.698 66.667 0.00 0.00 0.00 3.21
2642 2771 4.043100 GTTTCGGGGAGGGTGGGG 62.043 72.222 0.00 0.00 0.00 4.96
2693 2822 2.122813 CCGGCCTAGAGGGATGGT 60.123 66.667 0.00 0.00 37.23 3.55
2709 2838 1.611977 AGCAAAACTTAAACGAGGGCC 59.388 47.619 0.00 0.00 0.00 5.80
2727 2856 3.112709 GGTGCACTTCGTCGGAGC 61.113 66.667 17.98 0.00 0.00 4.70
2753 2907 4.509737 GGCTAGACCGTCGGTGGC 62.510 72.222 24.45 21.13 35.25 5.01
2775 2929 1.153989 CTAGAGAGATGGCCGGGGA 59.846 63.158 2.18 0.00 0.00 4.81
2781 2935 1.288752 GCGAGCCTAGAGAGATGGC 59.711 63.158 0.00 0.00 46.42 4.40
2866 3020 0.195096 ACTTAGGGTTCAGGGTGGGA 59.805 55.000 0.00 0.00 0.00 4.37
2873 3027 5.070580 CCCCAGTATCTAACTTAGGGTTCAG 59.929 48.000 0.00 0.00 41.56 3.02
2907 3061 1.524849 GAGAAGGAATGGGCTCGCC 60.525 63.158 0.00 0.00 0.00 5.54
2916 3070 4.719273 CAGAGGTAAGGAAGGAGAAGGAAT 59.281 45.833 0.00 0.00 0.00 3.01
2949 3103 0.895530 TCGGTTTTCGAGAGATGGCT 59.104 50.000 0.00 0.00 43.74 4.75
2959 3113 2.667473 ATAGGGTCAGTCGGTTTTCG 57.333 50.000 0.00 0.00 40.90 3.46


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

AutoCloner maintained by Alex Coulton.