Multiple sequence alignment - TraesCS2A01G420600

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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 TraesCS2A01G420600 chr2A 100.000 5152 0 0 1 5152 676271608 676266457 0.000000e+00 9515
1 TraesCS2A01G420600 chr2A 94.684 790 42 0 1414 2203 600419889 600420678 0.000000e+00 1227
2 TraesCS2A01G420600 chr2B 94.081 2855 109 20 2333 5141 631443024 631440184 0.000000e+00 4281
3 TraesCS2A01G420600 chr2B 94.354 797 43 2 1411 2206 713943050 713942255 0.000000e+00 1221
4 TraesCS2A01G420600 chr2B 87.620 1042 70 24 395 1414 631444012 631443008 0.000000e+00 1155
5 TraesCS2A01G420600 chr2B 85.047 428 41 8 1 419 631445039 631444626 1.030000e-111 414
6 TraesCS2A01G420600 chr2D 95.352 2668 104 8 2333 4999 531678620 531675972 0.000000e+00 4222
7 TraesCS2A01G420600 chr2D 94.458 794 38 1 1413 2206 12749398 12750185 0.000000e+00 1218
8 TraesCS2A01G420600 chr2D 88.952 706 43 18 715 1414 531679279 531678603 0.000000e+00 839
9 TraesCS2A01G420600 chr2D 87.437 199 16 5 463 656 531679485 531679291 2.410000e-53 220
10 TraesCS2A01G420600 chr2D 91.096 146 4 4 4997 5142 531675859 531675723 6.810000e-44 189
11 TraesCS2A01G420600 chr2D 87.143 70 4 2 396 464 531679834 531679769 1.990000e-09 75
12 TraesCS2A01G420600 chr1D 94.347 796 45 0 1411 2206 62158997 62159792 0.000000e+00 1221
13 TraesCS2A01G420600 chr1D 94.081 794 46 1 1413 2206 66391696 66392488 0.000000e+00 1205
14 TraesCS2A01G420600 chr1D 89.231 130 14 0 2202 2331 1253932 1254061 4.130000e-36 163
15 TraesCS2A01G420600 chr7D 94.550 789 43 0 1418 2206 46986000 46985212 0.000000e+00 1219
16 TraesCS2A01G420600 chr6A 94.221 796 45 1 1410 2204 605145366 605144571 0.000000e+00 1214
17 TraesCS2A01G420600 chr6A 94.199 793 45 1 1414 2206 604528714 604529505 0.000000e+00 1208
18 TraesCS2A01G420600 chr1A 94.207 794 45 1 1413 2206 425686239 425687031 0.000000e+00 1210
19 TraesCS2A01G420600 chr1A 92.913 127 9 0 2205 2331 547508378 547508252 8.810000e-43 185


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 TraesCS2A01G420600 chr2A 676266457 676271608 5151 True 9515 9515 100.000 1 5152 1 chr2A.!!$R1 5151
1 TraesCS2A01G420600 chr2A 600419889 600420678 789 False 1227 1227 94.684 1414 2203 1 chr2A.!!$F1 789
2 TraesCS2A01G420600 chr2B 631440184 631445039 4855 True 1950 4281 88.916 1 5141 3 chr2B.!!$R2 5140
3 TraesCS2A01G420600 chr2B 713942255 713943050 795 True 1221 1221 94.354 1411 2206 1 chr2B.!!$R1 795
4 TraesCS2A01G420600 chr2D 12749398 12750185 787 False 1218 1218 94.458 1413 2206 1 chr2D.!!$F1 793
5 TraesCS2A01G420600 chr2D 531675723 531679834 4111 True 1109 4222 89.996 396 5142 5 chr2D.!!$R1 4746
6 TraesCS2A01G420600 chr1D 62158997 62159792 795 False 1221 1221 94.347 1411 2206 1 chr1D.!!$F2 795
7 TraesCS2A01G420600 chr1D 66391696 66392488 792 False 1205 1205 94.081 1413 2206 1 chr1D.!!$F3 793
8 TraesCS2A01G420600 chr7D 46985212 46986000 788 True 1219 1219 94.550 1418 2206 1 chr7D.!!$R1 788
9 TraesCS2A01G420600 chr6A 605144571 605145366 795 True 1214 1214 94.221 1410 2204 1 chr6A.!!$R1 794
10 TraesCS2A01G420600 chr6A 604528714 604529505 791 False 1208 1208 94.199 1414 2206 1 chr6A.!!$F1 792
11 TraesCS2A01G420600 chr1A 425686239 425687031 792 False 1210 1210 94.207 1413 2206 1 chr1A.!!$F1 793

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
487 1425 0.035439 AGTGTTCCGGCCCAATACAG 60.035 55.0 0.0 0.0 0.0 2.74 F
1946 2905 0.320421 CCACCAAAGATGTCGTCCGT 60.320 55.0 0.0 0.0 0.0 4.69 F
2252 3211 0.038892 CCACTGCTTGATTGTGCCAC 60.039 55.0 0.0 0.0 0.0 5.01 F
2255 3214 0.038892 CTGCTTGATTGTGCCACCAC 60.039 55.0 0.0 0.0 42.4 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 3192 0.038892 GTGGCACAATCAAGCAGTGG 60.039 55.000 13.86 0.0 44.16 4.00 R
3257 4262 0.926155 CTCGCCGAATCATGTCACAG 59.074 55.000 0.00 0.0 0.00 3.66 R
4043 5048 0.807667 CCTGCACACATAGCTCGACC 60.808 60.000 0.00 0.0 0.00 4.79 R
4164 5169 1.004044 CATCTTCAGAAGTGCAGGGGT 59.996 52.381 10.09 0.0 0.00 4.95 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
34 35 8.868916 TCTGTATTTCTGAAAAACAAAACAAGC 58.131 29.630 6.95 0.00 0.00 4.01
44 45 3.427161 ACAAAACAAGCTGTGCTTCTC 57.573 42.857 1.45 0.00 46.77 2.87
95 103 5.500771 GCTTCTGCCTTTGTTTTTCTTTTCG 60.501 40.000 0.00 0.00 0.00 3.46
226 234 0.879090 AAAAATCTTGACGCGGGTCC 59.121 50.000 27.39 11.82 42.73 4.46
239 247 1.401800 GCGGGTCCAATGGTAAAAACG 60.402 52.381 0.00 0.00 0.00 3.60
241 249 2.241160 GGGTCCAATGGTAAAAACGGT 58.759 47.619 0.00 0.00 0.00 4.83
244 252 3.557508 GTCCAATGGTAAAAACGGTTCG 58.442 45.455 0.00 0.00 0.00 3.95
248 256 1.881591 TGGTAAAAACGGTTCGGGAG 58.118 50.000 0.00 0.00 0.00 4.30
255 263 2.431942 CGGTTCGGGAGTTGGACG 60.432 66.667 0.00 0.00 0.00 4.79
259 267 3.524648 TTCGGGAGTTGGACGCACC 62.525 63.158 0.00 0.00 39.54 5.01
262 270 2.280592 GGAGTTGGACGCACCGTT 60.281 61.111 0.00 0.00 41.37 4.44
268 276 1.144276 TGGACGCACCGTTCAAGAA 59.856 52.632 0.00 0.00 42.74 2.52
269 277 0.250124 TGGACGCACCGTTCAAGAAT 60.250 50.000 0.00 0.00 42.74 2.40
270 278 0.872388 GGACGCACCGTTCAAGAATT 59.128 50.000 0.00 0.00 41.37 2.17
271 279 1.136057 GGACGCACCGTTCAAGAATTC 60.136 52.381 0.00 0.00 41.37 2.17
336 346 8.631676 TTAACATTACGATAAGCGATGTACAA 57.368 30.769 0.00 0.00 44.57 2.41
364 374 0.315251 TCACTTGTGAGCGTCTGGAG 59.685 55.000 0.00 0.00 0.00 3.86
414 1062 3.197766 ACAAGTGATCTCGGGCAAATAGA 59.802 43.478 0.00 0.00 0.00 1.98
453 1107 4.342427 TGGAACAGCCATCCATGC 57.658 55.556 0.00 0.00 43.33 4.06
457 1111 1.684248 GGAACAGCCATCCATGCTCTT 60.684 52.381 0.00 0.00 36.81 2.85
458 1112 2.097825 GAACAGCCATCCATGCTCTTT 58.902 47.619 0.00 0.00 36.81 2.52
459 1113 1.760192 ACAGCCATCCATGCTCTTTC 58.240 50.000 0.00 0.00 36.81 2.62
487 1425 0.035439 AGTGTTCCGGCCCAATACAG 60.035 55.000 0.00 0.00 0.00 2.74
499 1437 1.382522 CAATACAGGCGGATGCACTT 58.617 50.000 0.00 0.00 45.35 3.16
502 1440 0.739462 TACAGGCGGATGCACTTTCG 60.739 55.000 0.00 0.00 45.35 3.46
504 1442 0.739462 CAGGCGGATGCACTTTCGTA 60.739 55.000 0.00 0.00 45.35 3.43
528 1466 2.230130 TTACAGCCCATTTCCCCAAG 57.770 50.000 0.00 0.00 0.00 3.61
529 1467 0.334676 TACAGCCCATTTCCCCAAGG 59.665 55.000 0.00 0.00 0.00 3.61
573 1516 4.202223 ACCTACGGGCTATGTGTGAATAAG 60.202 45.833 0.00 0.00 35.63 1.73
593 1536 9.922305 GAATAAGAAACGGAGATATTTTCACTG 57.078 33.333 0.00 0.00 0.00 3.66
619 1562 3.300388 TGTTCTTATCTCTCTCCGCCAT 58.700 45.455 0.00 0.00 0.00 4.40
685 1636 3.791586 GCAGAGCTCCACCCTCCC 61.792 72.222 10.93 0.00 0.00 4.30
686 1637 2.040278 CAGAGCTCCACCCTCCCT 59.960 66.667 10.93 0.00 0.00 4.20
688 1639 2.766229 GAGCTCCACCCTCCCTCC 60.766 72.222 0.87 0.00 0.00 4.30
689 1640 3.288381 AGCTCCACCCTCCCTCCT 61.288 66.667 0.00 0.00 0.00 3.69
690 1641 2.766229 GCTCCACCCTCCCTCCTC 60.766 72.222 0.00 0.00 0.00 3.71
691 1642 2.041405 CTCCACCCTCCCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
692 1643 4.075793 TCCACCCTCCCTCCTCCG 62.076 72.222 0.00 0.00 0.00 4.63
817 1768 3.151022 GGCTCGGTCTCTCCCTGG 61.151 72.222 0.00 0.00 0.00 4.45
844 1795 3.798511 CCCCGGCCCTTCTCTTCC 61.799 72.222 0.00 0.00 0.00 3.46
906 1857 2.766400 CGTCTGCTCCTCCTCCGTC 61.766 68.421 0.00 0.00 0.00 4.79
910 1861 2.277404 GCTCCTCCTCCGTCTCCT 59.723 66.667 0.00 0.00 0.00 3.69
949 1900 3.157087 CTGAACCCACATTAAGTTGCCT 58.843 45.455 0.00 0.00 0.00 4.75
969 1920 4.024809 GCCTTCCGTATCTGCTGAATTTAC 60.025 45.833 0.00 0.00 0.00 2.01
970 1921 5.116180 CCTTCCGTATCTGCTGAATTTACA 58.884 41.667 0.00 0.00 0.00 2.41
1079 2036 3.553508 CCACAGTTCCATTGCCTTTTCAG 60.554 47.826 0.00 0.00 0.00 3.02
1088 2045 6.672593 TCCATTGCCTTTTCAGTATCCTAAT 58.327 36.000 0.00 0.00 0.00 1.73
1238 2195 3.438297 TCCTTGCTCTCGCTATACAAC 57.562 47.619 0.00 0.00 36.97 3.32
1268 2225 2.158623 AGTCAATCACAGGACAGCCAAA 60.159 45.455 0.00 0.00 36.50 3.28
1311 2268 5.023533 TGTCATCTGTAGGTTAGCCAATC 57.976 43.478 0.00 0.00 37.19 2.67
1319 2276 6.206243 TCTGTAGGTTAGCCAATCGAGTATAC 59.794 42.308 0.00 0.00 37.19 1.47
1323 2281 6.827727 AGGTTAGCCAATCGAGTATACAAAT 58.172 36.000 5.50 0.00 37.19 2.32
1340 2298 2.302445 CAAATTGCCCTCCAACCATTCA 59.698 45.455 0.00 0.00 35.99 2.57
1357 2315 6.074648 ACCATTCAAGGTAGTCAAAATGGAA 58.925 36.000 16.50 0.00 43.70 3.53
1360 2318 6.877611 TTCAAGGTAGTCAAAATGGAAGTC 57.122 37.500 0.00 0.00 0.00 3.01
1380 2338 1.004185 CTATGATGCTGTGTTGCTCGC 60.004 52.381 0.00 0.00 0.00 5.03
1390 2348 1.068333 GTGTTGCTCGCATGAATGGTT 60.068 47.619 0.00 0.00 0.00 3.67
1396 2354 4.640364 TGCTCGCATGAATGGTTATCATA 58.360 39.130 0.00 0.00 35.80 2.15
1404 2362 7.254898 CGCATGAATGGTTATCATAAGAAGTGT 60.255 37.037 0.00 0.00 35.80 3.55
1408 2366 7.336679 TGAATGGTTATCATAAGAAGTGTGGTG 59.663 37.037 0.00 0.00 34.44 4.17
1409 2367 4.941263 TGGTTATCATAAGAAGTGTGGTGC 59.059 41.667 0.00 0.00 0.00 5.01
1485 2443 9.153479 TGCATAGGGCCACTTTATTAATTATTT 57.847 29.630 6.18 0.00 43.89 1.40
1531 2489 4.141574 ACAACAGTAAGACTAAAGCCACCA 60.142 41.667 0.00 0.00 0.00 4.17
1585 2543 0.394565 GATGAAGGGGCGCTGATAGT 59.605 55.000 7.64 0.00 0.00 2.12
1588 2546 1.329256 GAAGGGGCGCTGATAGTCTA 58.671 55.000 7.64 0.00 0.00 2.59
1692 2650 4.814294 CTACCAGTCCGGCGCACC 62.814 72.222 10.83 0.00 39.03 5.01
1773 2731 2.691927 TCAGAGCTGTACTGTTGCATG 58.308 47.619 0.00 0.00 36.81 4.06
1854 2812 2.278206 CGAGTCCATCCTCGCACG 60.278 66.667 0.00 0.00 46.64 5.34
1946 2905 0.320421 CCACCAAAGATGTCGTCCGT 60.320 55.000 0.00 0.00 0.00 4.69
2030 2989 2.413351 CGCCGACATCCGATCAGT 59.587 61.111 0.00 0.00 41.76 3.41
2081 3040 1.850345 TGGAGTTGGGAGTTTCACCTT 59.150 47.619 0.00 0.00 0.00 3.50
2206 3165 2.881266 CGACAACCTGTGCACCGTG 61.881 63.158 15.69 9.33 0.00 4.94
2207 3166 3.181169 GACAACCTGTGCACCGTGC 62.181 63.158 16.93 16.93 45.29 5.34
2208 3167 3.964875 CAACCTGTGCACCGTGCC 61.965 66.667 20.67 12.27 44.23 5.01
2209 3168 4.497984 AACCTGTGCACCGTGCCA 62.498 61.111 20.67 15.89 44.23 4.92
2214 3173 4.973055 GTGCACCGTGCCACCGTA 62.973 66.667 20.67 0.00 44.23 4.02
2215 3174 4.673298 TGCACCGTGCCACCGTAG 62.673 66.667 20.67 0.00 44.23 3.51
2228 3187 2.805546 CGTAGGAGCCTTAGCGCA 59.194 61.111 11.47 0.00 46.67 6.09
2229 3188 1.589196 CGTAGGAGCCTTAGCGCAC 60.589 63.158 11.47 0.00 46.67 5.34
2230 3189 1.227292 GTAGGAGCCTTAGCGCACC 60.227 63.158 11.47 0.91 46.67 5.01
2231 3190 2.782222 TAGGAGCCTTAGCGCACCG 61.782 63.158 11.47 0.00 46.67 4.94
2237 3196 4.760047 CTTAGCGCACCGGCCACT 62.760 66.667 11.47 0.00 36.38 4.00
2244 3203 2.360350 CACCGGCCACTGCTTGAT 60.360 61.111 0.00 0.00 37.74 2.57
2245 3204 1.973281 CACCGGCCACTGCTTGATT 60.973 57.895 0.00 0.00 37.74 2.57
2246 3205 1.973281 ACCGGCCACTGCTTGATTG 60.973 57.895 0.00 0.00 37.74 2.67
2247 3206 1.973281 CCGGCCACTGCTTGATTGT 60.973 57.895 2.24 0.00 37.74 2.71
2248 3207 1.210931 CGGCCACTGCTTGATTGTG 59.789 57.895 2.24 0.00 37.74 3.33
2249 3208 1.080298 GGCCACTGCTTGATTGTGC 60.080 57.895 0.00 0.00 37.74 4.57
2250 3209 1.080298 GCCACTGCTTGATTGTGCC 60.080 57.895 0.00 0.00 33.53 5.01
2251 3210 1.808531 GCCACTGCTTGATTGTGCCA 61.809 55.000 0.00 0.00 33.53 4.92
2252 3211 0.038892 CCACTGCTTGATTGTGCCAC 60.039 55.000 0.00 0.00 0.00 5.01
2253 3212 0.038892 CACTGCTTGATTGTGCCACC 60.039 55.000 0.00 0.00 0.00 4.61
2254 3213 0.467844 ACTGCTTGATTGTGCCACCA 60.468 50.000 0.00 0.00 0.00 4.17
2255 3214 0.038892 CTGCTTGATTGTGCCACCAC 60.039 55.000 0.00 0.00 42.40 4.16
2256 3215 0.467844 TGCTTGATTGTGCCACCACT 60.468 50.000 0.00 0.00 42.54 4.00
2257 3216 0.038892 GCTTGATTGTGCCACCACTG 60.039 55.000 0.00 0.00 42.54 3.66
2258 3217 0.599558 CTTGATTGTGCCACCACTGG 59.400 55.000 0.00 0.00 42.54 4.00
2259 3218 0.184692 TTGATTGTGCCACCACTGGA 59.815 50.000 0.71 0.00 40.55 3.86
2260 3219 0.250858 TGATTGTGCCACCACTGGAG 60.251 55.000 0.71 0.00 40.55 3.86
2261 3220 1.589716 GATTGTGCCACCACTGGAGC 61.590 60.000 0.71 5.01 40.55 4.70
2262 3221 3.790416 TTGTGCCACCACTGGAGCC 62.790 63.158 0.71 0.23 40.55 4.70
2263 3222 3.958860 GTGCCACCACTGGAGCCT 61.959 66.667 0.71 0.00 40.55 4.58
2264 3223 2.203922 TGCCACCACTGGAGCCTA 60.204 61.111 0.71 0.00 40.55 3.93
2265 3224 2.293318 TGCCACCACTGGAGCCTAG 61.293 63.158 0.71 0.00 40.55 3.02
2266 3225 3.036429 GCCACCACTGGAGCCTAGG 62.036 68.421 3.67 3.67 40.55 3.02
2267 3226 1.306141 CCACCACTGGAGCCTAGGA 60.306 63.158 14.75 0.00 40.55 2.94
2268 3227 1.333636 CCACCACTGGAGCCTAGGAG 61.334 65.000 14.75 2.88 40.55 3.69
2269 3228 1.002274 ACCACTGGAGCCTAGGAGG 59.998 63.158 14.75 4.32 38.80 4.30
2270 3229 1.002274 CCACTGGAGCCTAGGAGGT 59.998 63.158 14.75 0.00 37.80 3.85
2271 3230 1.333636 CCACTGGAGCCTAGGAGGTG 61.334 65.000 14.75 12.13 37.80 4.00
2272 3231 1.002274 ACTGGAGCCTAGGAGGTGG 59.998 63.158 14.75 1.30 37.80 4.61
2273 3232 1.764054 CTGGAGCCTAGGAGGTGGG 60.764 68.421 14.75 0.00 37.80 4.61
2278 3237 2.446802 CCTAGGAGGTGGGCTCCC 60.447 72.222 1.05 0.00 41.76 4.30
2279 3238 2.368594 CTAGGAGGTGGGCTCCCA 59.631 66.667 2.93 2.93 45.02 4.37
2314 3273 4.637489 CCGAGAGCCGCCGAGATG 62.637 72.222 0.00 0.00 36.84 2.90
2315 3274 4.637489 CGAGAGCCGCCGAGATGG 62.637 72.222 0.00 0.00 42.50 3.51
2316 3275 3.219928 GAGAGCCGCCGAGATGGA 61.220 66.667 0.00 0.00 42.00 3.41
2317 3276 2.522923 AGAGCCGCCGAGATGGAT 60.523 61.111 0.00 0.00 42.00 3.41
2318 3277 2.048690 GAGCCGCCGAGATGGATC 60.049 66.667 0.00 0.00 42.00 3.36
2319 3278 3.581687 GAGCCGCCGAGATGGATCC 62.582 68.421 4.20 4.20 42.00 3.36
2320 3279 4.688966 GCCGCCGAGATGGATCCC 62.689 72.222 9.90 0.00 42.00 3.85
2321 3280 3.233980 CCGCCGAGATGGATCCCA 61.234 66.667 9.90 0.00 42.00 4.37
2322 3281 2.029666 CGCCGAGATGGATCCCAC 59.970 66.667 9.90 3.04 42.00 4.61
2323 3282 2.029666 GCCGAGATGGATCCCACG 59.970 66.667 9.90 9.38 42.00 4.94
2324 3283 2.029666 CCGAGATGGATCCCACGC 59.970 66.667 9.90 4.16 42.00 5.34
2325 3284 2.355126 CGAGATGGATCCCACGCG 60.355 66.667 9.90 12.63 35.80 6.01
2326 3285 2.663188 GAGATGGATCCCACGCGC 60.663 66.667 9.90 0.00 35.80 6.86
2327 3286 3.157217 GAGATGGATCCCACGCGCT 62.157 63.158 9.90 0.00 35.80 5.92
2328 3287 2.663188 GATGGATCCCACGCGCTC 60.663 66.667 9.90 0.00 35.80 5.03
2329 3288 4.592192 ATGGATCCCACGCGCTCG 62.592 66.667 9.90 0.00 35.80 5.03
2418 3378 6.179756 TGCCTTTGTCTAGCTTATTGATTGA 58.820 36.000 0.00 0.00 0.00 2.57
2430 3403 6.588756 AGCTTATTGATTGACAAATTGCTGTG 59.411 34.615 0.00 0.00 42.03 3.66
2475 3448 6.788598 ATATCATCTCTATACACCCAGCTG 57.211 41.667 6.78 6.78 0.00 4.24
2511 3484 6.708885 ATTCAGATTCATAGGGCCTATCAA 57.291 37.500 23.27 17.98 0.00 2.57
2521 3494 7.811282 TCATAGGGCCTATCAATTTTCAGTTA 58.189 34.615 23.27 0.00 0.00 2.24
2540 3513 6.268617 TCAGTTAGTGGATATCTTATGCAGCT 59.731 38.462 2.05 0.00 0.00 4.24
2593 3566 5.622770 TTTTGCTTTACGAGATTCCCTTC 57.377 39.130 0.00 0.00 0.00 3.46
2670 3644 0.938713 CGTTGGTCCGTTTTGCTGTA 59.061 50.000 0.00 0.00 0.00 2.74
2671 3645 1.070175 CGTTGGTCCGTTTTGCTGTAG 60.070 52.381 0.00 0.00 0.00 2.74
2746 3720 3.119792 GTCGAAGAGTTTTACGCTCACTG 59.880 47.826 0.00 0.00 36.95 3.66
2763 3737 1.402968 ACTGTCTGTTTGCAAGCACTG 59.597 47.619 12.36 9.99 0.00 3.66
2764 3738 1.402968 CTGTCTGTTTGCAAGCACTGT 59.597 47.619 12.36 0.00 0.00 3.55
2765 3739 1.132834 TGTCTGTTTGCAAGCACTGTG 59.867 47.619 12.36 2.76 0.00 3.66
2766 3740 1.401552 GTCTGTTTGCAAGCACTGTGA 59.598 47.619 12.36 5.41 0.00 3.58
2767 3741 2.033801 GTCTGTTTGCAAGCACTGTGAT 59.966 45.455 12.36 1.09 0.00 3.06
2768 3742 2.291465 TCTGTTTGCAAGCACTGTGATC 59.709 45.455 12.36 0.00 0.00 2.92
2769 3743 1.002576 TGTTTGCAAGCACTGTGATCG 60.003 47.619 12.36 0.00 0.00 3.69
2959 3964 2.360801 CCCGAAGAACAAAAAGAAGCCA 59.639 45.455 0.00 0.00 0.00 4.75
3058 4063 3.062466 GAGCCCCCAAAGAACGGC 61.062 66.667 0.00 0.00 41.96 5.68
3103 4108 2.288825 TGTTGCCTACGAAGTCCTTGAG 60.289 50.000 0.00 0.00 43.93 3.02
3173 4178 6.205853 TGTTACAGTTTATGGTTGCAGGTAAG 59.794 38.462 0.00 0.00 0.00 2.34
3241 4246 5.772393 TGTTTCATGACCCTTGTATAGGT 57.228 39.130 0.00 0.00 43.07 3.08
3248 4253 2.945668 GACCCTTGTATAGGTACGTCGT 59.054 50.000 2.21 2.21 43.07 4.34
3257 4262 5.466728 TGTATAGGTACGTCGTTCACTATCC 59.533 44.000 1.78 1.81 33.36 2.59
3274 4279 0.460109 TCCTGTGACATGATTCGGCG 60.460 55.000 0.00 0.00 0.00 6.46
3275 4280 0.460109 CCTGTGACATGATTCGGCGA 60.460 55.000 4.99 4.99 0.00 5.54
3276 4281 0.926155 CTGTGACATGATTCGGCGAG 59.074 55.000 10.46 0.00 0.00 5.03
3277 4282 0.246360 TGTGACATGATTCGGCGAGT 59.754 50.000 10.46 7.31 0.00 4.18
3389 4394 1.841302 ATGGTTCAGGAAGCCAGCGA 61.841 55.000 8.57 0.00 37.97 4.93
3661 4666 0.107654 GAGCCTAAGCCACACCGATT 60.108 55.000 0.00 0.00 41.25 3.34
3776 4781 3.580458 AGAGGACACTGAAAGCATACTGT 59.420 43.478 0.00 0.00 37.60 3.55
3787 4792 1.490693 GCATACTGTGATGTCCGGCG 61.491 60.000 0.00 0.00 0.00 6.46
3795 4800 3.004354 ATGTCCGGCGGGGTGTTA 61.004 61.111 27.98 1.38 37.00 2.41
4137 5142 1.604378 CCAGACCCCGATGAAGCTT 59.396 57.895 0.00 0.00 0.00 3.74
4164 5169 4.280425 TGGCTGCATGAAAACAATGTTCTA 59.720 37.500 0.00 0.00 0.00 2.10
4230 5241 0.323360 TGCTTGTTACCTGGATGCCC 60.323 55.000 0.00 0.00 0.00 5.36
4255 5266 0.751277 TTGGGCCCTGTCATATTGCG 60.751 55.000 25.70 0.00 0.00 4.85
4426 5437 8.026607 GTCTTCCTAGTGATACTATGCATCTTC 58.973 40.741 0.19 0.00 29.08 2.87
4427 5438 7.725844 TCTTCCTAGTGATACTATGCATCTTCA 59.274 37.037 0.19 0.00 29.08 3.02
4440 5451 3.624410 TGCATCTTCAGACCATTTGATCG 59.376 43.478 0.00 0.00 0.00 3.69
4488 5499 4.887655 TGAAGAAAGGAAGTGGAAAAGGAC 59.112 41.667 0.00 0.00 0.00 3.85
4525 5536 9.930158 ATGGTGTATATAACCTTGTTTAATGGT 57.070 29.630 12.44 0.00 38.60 3.55
4616 5627 1.351017 CCTTTCCTCTGCTGGTACCAA 59.649 52.381 17.11 0.32 0.00 3.67
4656 5667 9.401058 CTGATTCTTGGGATTAAACTAATCACT 57.599 33.333 9.45 0.00 46.33 3.41
4772 5783 1.221466 CCGGTGCGGCTACATGTATG 61.221 60.000 5.91 2.21 41.17 2.39
4840 5851 5.050490 GTGCTGTATACTCTGTAACATGGG 58.950 45.833 4.17 0.00 0.00 4.00
4869 5880 6.699575 AAGCTGTATCAAATGGATGGTTAC 57.300 37.500 0.00 0.00 36.72 2.50
4904 5915 9.485206 GAAGTGGACTTAGTGTATTTGTTTCTA 57.515 33.333 0.00 0.00 36.11 2.10
4922 5933 5.692115 TTCTAAAGGATGTATGACAGGCA 57.308 39.130 0.00 0.00 0.00 4.75
5006 6132 4.119136 ACCATTTGCAGTTACAACTTTGC 58.881 39.130 0.00 0.00 37.08 3.68
5148 6275 9.458727 TGAAGTAATATTATAGTACTCCCTCCG 57.541 37.037 11.93 0.00 38.48 4.63
5149 6276 9.460019 GAAGTAATATTATAGTACTCCCTCCGT 57.540 37.037 11.93 0.00 38.48 4.69
5150 6277 9.460019 AAGTAATATTATAGTACTCCCTCCGTC 57.540 37.037 11.93 0.00 38.48 4.79
5151 6278 8.052141 AGTAATATTATAGTACTCCCTCCGTCC 58.948 40.741 6.54 0.00 34.84 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.655092 CAGCTTGTTTTGTTTTTCAGAAATACA 58.345 29.630 13.43 13.43 0.00 2.29
14 15 6.565623 GCACAGCTTGTTTTGTTTTTCAGAAA 60.566 34.615 0.00 0.00 0.00 2.52
67 75 0.385390 AAACAAAGGCAGAAGCACGG 59.615 50.000 0.00 0.00 44.61 4.94
72 80 5.576774 ACGAAAAGAAAAACAAAGGCAGAAG 59.423 36.000 0.00 0.00 0.00 2.85
210 218 0.035439 ATTGGACCCGCGTCAAGATT 60.035 50.000 4.92 0.00 41.13 2.40
222 230 3.609879 CGAACCGTTTTTACCATTGGACC 60.610 47.826 10.37 0.00 0.00 4.46
226 234 2.553172 TCCCGAACCGTTTTTACCATTG 59.447 45.455 0.00 0.00 0.00 2.82
239 247 2.741211 GCGTCCAACTCCCGAACC 60.741 66.667 0.00 0.00 0.00 3.62
241 249 2.029964 GTGCGTCCAACTCCCGAA 59.970 61.111 0.00 0.00 0.00 4.30
244 252 3.819877 AACGGTGCGTCCAACTCCC 62.820 63.158 0.00 0.00 39.99 4.30
248 256 1.155424 TCTTGAACGGTGCGTCCAAC 61.155 55.000 0.00 0.00 39.99 3.77
255 263 8.736751 TTATTAAAAGAATTCTTGAACGGTGC 57.263 30.769 21.15 0.00 36.12 5.01
315 325 6.749216 ACTTGTACATCGCTTATCGTAATG 57.251 37.500 0.00 0.00 39.67 1.90
320 330 5.599715 GCATTACTTGTACATCGCTTATCG 58.400 41.667 0.00 0.00 40.15 2.92
326 336 2.601314 TGACGCATTACTTGTACATCGC 59.399 45.455 0.00 0.00 0.00 4.58
327 337 3.857665 AGTGACGCATTACTTGTACATCG 59.142 43.478 0.00 0.00 0.00 3.84
329 339 5.530519 CAAGTGACGCATTACTTGTACAT 57.469 39.130 9.07 0.00 45.33 2.29
330 340 4.983215 CAAGTGACGCATTACTTGTACA 57.017 40.909 9.07 0.00 45.33 2.90
336 346 2.069273 GCTCACAAGTGACGCATTACT 58.931 47.619 15.09 0.00 35.40 2.24
364 374 7.793036 AGGGTTATTACTGGTAAAGATCACTC 58.207 38.462 0.00 0.00 0.00 3.51
414 1062 5.243060 CCACTCGGTTAAAGAAAGGGAATTT 59.757 40.000 0.00 0.00 0.00 1.82
448 1102 4.003648 ACTCGGTTAAAGAAAGAGCATGG 58.996 43.478 0.00 0.00 32.60 3.66
450 1104 4.642429 ACACTCGGTTAAAGAAAGAGCAT 58.358 39.130 0.00 0.00 32.60 3.79
451 1105 4.067972 ACACTCGGTTAAAGAAAGAGCA 57.932 40.909 0.00 0.00 32.60 4.26
452 1106 4.083961 GGAACACTCGGTTAAAGAAAGAGC 60.084 45.833 0.00 0.00 40.63 4.09
453 1107 4.150098 CGGAACACTCGGTTAAAGAAAGAG 59.850 45.833 0.00 0.00 40.63 2.85
457 1111 2.758009 CCGGAACACTCGGTTAAAGAA 58.242 47.619 0.00 0.00 40.63 2.52
458 1112 2.443887 CCGGAACACTCGGTTAAAGA 57.556 50.000 0.00 0.00 40.63 2.52
499 1437 3.620427 ATGGGCTGTAATGTGTACGAA 57.380 42.857 0.00 0.00 0.00 3.85
502 1440 3.380320 GGGAAATGGGCTGTAATGTGTAC 59.620 47.826 0.00 0.00 0.00 2.90
504 1442 2.456577 GGGAAATGGGCTGTAATGTGT 58.543 47.619 0.00 0.00 0.00 3.72
573 1516 5.795441 GCAACAGTGAAAATATCTCCGTTTC 59.205 40.000 0.00 0.00 32.92 2.78
593 1536 4.109050 CGGAGAGAGATAAGAACAGCAAC 58.891 47.826 0.00 0.00 0.00 4.17
619 1562 3.391631 CGACGAGCGTTGCACGAA 61.392 61.111 15.06 0.00 46.05 3.85
656 1599 0.322008 AGCTCTGCTTAGGCACCAAC 60.322 55.000 0.00 0.00 44.28 3.77
657 1600 0.036010 GAGCTCTGCTTAGGCACCAA 60.036 55.000 6.43 0.00 44.28 3.67
660 1603 0.742635 GTGGAGCTCTGCTTAGGCAC 60.743 60.000 14.64 6.70 44.28 5.01
662 1605 1.153269 GGTGGAGCTCTGCTTAGGC 60.153 63.158 14.64 0.00 39.88 3.93
671 1622 2.766229 GGAGGGAGGGTGGAGCTC 60.766 72.222 4.71 4.71 0.00 4.09
673 1624 2.766229 GAGGAGGGAGGGTGGAGC 60.766 72.222 0.00 0.00 0.00 4.70
688 1639 2.776913 GGAGAAGAGGACGCCGGAG 61.777 68.421 5.05 3.72 0.00 4.63
689 1640 2.754658 GGAGAAGAGGACGCCGGA 60.755 66.667 5.05 0.00 0.00 5.14
690 1641 3.068691 TGGAGAAGAGGACGCCGG 61.069 66.667 0.00 0.00 0.00 6.13
691 1642 2.344203 ACTGGAGAAGAGGACGCCG 61.344 63.158 0.00 0.00 0.00 6.46
692 1643 1.216710 CACTGGAGAAGAGGACGCC 59.783 63.158 0.00 0.00 0.00 5.68
736 1687 0.466124 AGCCCAGCGGAGAAACTATC 59.534 55.000 0.00 0.00 0.00 2.08
906 1857 2.032528 TGCTTCGGTTGCCAGGAG 59.967 61.111 0.00 0.00 0.00 3.69
910 1861 2.518112 TTGCTGCTTCGGTTGCCA 60.518 55.556 0.00 0.00 0.00 4.92
992 1946 5.647658 CAGTTAAGTATCTCCATGCCACAAA 59.352 40.000 0.00 0.00 0.00 2.83
998 1952 5.992217 CCCTTACAGTTAAGTATCTCCATGC 59.008 44.000 0.00 0.00 33.92 4.06
1101 2058 5.819379 AGACGCAATCATACACAATTCTGAT 59.181 36.000 0.00 0.00 0.00 2.90
1238 2195 2.430465 CTGTGATTGACTGGGAACTGG 58.570 52.381 0.00 0.00 0.00 4.00
1268 2225 6.011122 ACATAAGAATCCATTCAAGCCTCT 57.989 37.500 2.21 0.00 39.23 3.69
1311 2268 3.804036 TGGAGGGCAATTTGTATACTCG 58.196 45.455 4.17 0.00 0.00 4.18
1319 2276 2.302445 TGAATGGTTGGAGGGCAATTTG 59.698 45.455 0.00 0.00 0.00 2.32
1323 2281 1.631405 CTTGAATGGTTGGAGGGCAA 58.369 50.000 0.00 0.00 0.00 4.52
1340 2298 7.918076 TCATAGACTTCCATTTTGACTACCTT 58.082 34.615 0.00 0.00 0.00 3.50
1357 2315 3.529533 GAGCAACACAGCATCATAGACT 58.470 45.455 0.00 0.00 36.85 3.24
1360 2318 1.004185 GCGAGCAACACAGCATCATAG 60.004 52.381 0.00 0.00 36.85 2.23
1380 2338 8.347771 CCACACTTCTTATGATAACCATTCATG 58.652 37.037 0.00 0.00 36.71 3.07
1390 2348 7.759489 AAAAAGCACCACACTTCTTATGATA 57.241 32.000 0.00 0.00 0.00 2.15
1465 2423 9.660180 TTGTGAAAATAATTAATAAAGTGGCCC 57.340 29.630 0.00 0.00 0.00 5.80
1485 2443 7.276658 TGTATGACTTTGTAAGGTCTTGTGAA 58.723 34.615 8.11 0.00 34.01 3.18
1585 2543 5.027460 TGTCTGTTTGGTATTAGGCCTAGA 58.973 41.667 13.36 1.10 0.00 2.43
1588 2546 4.683400 CGATGTCTGTTTGGTATTAGGCCT 60.683 45.833 11.78 11.78 0.00 5.19
1692 2650 1.293498 CAGACGTCCTGGTTGAGGG 59.707 63.158 13.01 0.00 43.06 4.30
1773 2731 0.966370 AGAGAGACCTGGCACGGTAC 60.966 60.000 8.34 6.64 35.59 3.34
2206 3165 1.442148 CTAAGGCTCCTACGGTGGC 59.558 63.158 0.00 0.83 41.16 5.01
2207 3166 1.442148 GCTAAGGCTCCTACGGTGG 59.558 63.158 0.00 0.00 35.22 4.61
2208 3167 1.065928 CGCTAAGGCTCCTACGGTG 59.934 63.158 0.00 0.00 36.09 4.94
2209 3168 2.783288 GCGCTAAGGCTCCTACGGT 61.783 63.158 0.00 0.00 36.09 4.83
2210 3169 2.027751 GCGCTAAGGCTCCTACGG 59.972 66.667 0.00 0.00 36.09 4.02
2211 3170 1.589196 GTGCGCTAAGGCTCCTACG 60.589 63.158 9.73 0.00 36.09 3.51
2212 3171 1.227292 GGTGCGCTAAGGCTCCTAC 60.227 63.158 9.73 0.00 41.99 3.18
2213 3172 2.782222 CGGTGCGCTAAGGCTCCTA 61.782 63.158 9.73 0.00 42.83 2.94
2214 3173 4.148825 CGGTGCGCTAAGGCTCCT 62.149 66.667 9.73 0.00 42.83 3.69
2220 3179 4.760047 AGTGGCCGGTGCGCTAAG 62.760 66.667 9.73 0.00 38.85 2.18
2227 3186 1.973281 AATCAAGCAGTGGCCGGTG 60.973 57.895 1.90 0.00 42.56 4.94
2228 3187 1.973281 CAATCAAGCAGTGGCCGGT 60.973 57.895 1.90 0.00 42.56 5.28
2229 3188 1.973281 ACAATCAAGCAGTGGCCGG 60.973 57.895 0.00 0.00 42.56 6.13
2230 3189 1.210931 CACAATCAAGCAGTGGCCG 59.789 57.895 0.00 0.00 42.56 6.13
2231 3190 1.080298 GCACAATCAAGCAGTGGCC 60.080 57.895 0.00 0.00 42.56 5.36
2232 3191 4.565531 GCACAATCAAGCAGTGGC 57.434 55.556 0.00 0.00 41.61 5.01
2233 3192 0.038892 GTGGCACAATCAAGCAGTGG 60.039 55.000 13.86 0.00 44.16 4.00
2234 3193 0.038892 GGTGGCACAATCAAGCAGTG 60.039 55.000 20.82 0.00 44.16 3.66
2235 3194 0.467844 TGGTGGCACAATCAAGCAGT 60.468 50.000 20.82 0.00 44.16 4.40
2236 3195 0.038892 GTGGTGGCACAATCAAGCAG 60.039 55.000 20.82 0.00 44.16 4.24
2237 3196 0.467844 AGTGGTGGCACAATCAAGCA 60.468 50.000 20.82 2.98 44.16 3.91
2238 3197 0.038892 CAGTGGTGGCACAATCAAGC 60.039 55.000 20.82 0.00 44.16 4.01
2239 3198 0.599558 CCAGTGGTGGCACAATCAAG 59.400 55.000 20.82 3.63 44.16 3.02
2240 3199 0.184692 TCCAGTGGTGGCACAATCAA 59.815 50.000 20.82 0.00 44.16 2.57
2241 3200 0.250858 CTCCAGTGGTGGCACAATCA 60.251 55.000 20.82 5.39 44.16 2.57
2242 3201 1.589716 GCTCCAGTGGTGGCACAATC 61.590 60.000 20.82 8.77 44.16 2.67
2243 3202 1.604593 GCTCCAGTGGTGGCACAAT 60.605 57.895 20.82 1.95 44.16 2.71
2244 3203 2.203337 GCTCCAGTGGTGGCACAA 60.203 61.111 20.82 4.91 44.16 3.33
2245 3204 4.269523 GGCTCCAGTGGTGGCACA 62.270 66.667 27.54 2.61 44.60 4.57
2246 3205 2.527951 CTAGGCTCCAGTGGTGGCAC 62.528 65.000 31.92 9.70 44.60 5.01
2247 3206 2.203922 TAGGCTCCAGTGGTGGCA 60.204 61.111 31.92 18.86 44.60 4.92
2248 3207 2.586792 CTAGGCTCCAGTGGTGGC 59.413 66.667 25.81 25.81 44.60 5.01
2249 3208 1.306141 TCCTAGGCTCCAGTGGTGG 60.306 63.158 9.54 4.82 46.63 4.61
2250 3209 1.333636 CCTCCTAGGCTCCAGTGGTG 61.334 65.000 9.54 8.11 0.00 4.17
2251 3210 1.002274 CCTCCTAGGCTCCAGTGGT 59.998 63.158 9.54 0.00 0.00 4.16
2252 3211 1.002274 ACCTCCTAGGCTCCAGTGG 59.998 63.158 2.96 1.40 39.63 4.00
2253 3212 1.333636 CCACCTCCTAGGCTCCAGTG 61.334 65.000 2.96 6.69 39.63 3.66
2254 3213 1.002274 CCACCTCCTAGGCTCCAGT 59.998 63.158 2.96 0.00 39.63 4.00
2255 3214 1.764054 CCCACCTCCTAGGCTCCAG 60.764 68.421 2.96 0.00 39.63 3.86
2256 3215 2.368594 CCCACCTCCTAGGCTCCA 59.631 66.667 2.96 0.00 39.63 3.86
2257 3216 3.164977 GCCCACCTCCTAGGCTCC 61.165 72.222 2.96 0.00 43.62 4.70
2286 3245 4.521062 CTCTCGGGGCTTGGCGAG 62.521 72.222 0.00 0.00 0.00 5.03
2297 3256 4.637489 CATCTCGGCGGCTCTCGG 62.637 72.222 7.21 0.00 39.69 4.63
2298 3257 4.637489 CCATCTCGGCGGCTCTCG 62.637 72.222 7.21 0.00 42.76 4.04
2299 3258 2.485188 GATCCATCTCGGCGGCTCTC 62.485 65.000 7.21 0.00 33.14 3.20
2300 3259 2.522923 ATCCATCTCGGCGGCTCT 60.523 61.111 7.21 0.00 33.14 4.09
2301 3260 2.048690 GATCCATCTCGGCGGCTC 60.049 66.667 7.21 0.00 33.14 4.70
2302 3261 3.620785 GGATCCATCTCGGCGGCT 61.621 66.667 6.95 0.00 33.14 5.52
2303 3262 4.688966 GGGATCCATCTCGGCGGC 62.689 72.222 15.23 0.00 33.14 6.53
2304 3263 3.233980 TGGGATCCATCTCGGCGG 61.234 66.667 15.23 0.00 33.14 6.13
2305 3264 2.029666 GTGGGATCCATCTCGGCG 59.970 66.667 15.23 0.00 35.28 6.46
2306 3265 2.029666 CGTGGGATCCATCTCGGC 59.970 66.667 15.23 0.00 35.28 5.54
2307 3266 2.029666 GCGTGGGATCCATCTCGG 59.970 66.667 15.23 0.00 35.28 4.63
2308 3267 2.355126 CGCGTGGGATCCATCTCG 60.355 66.667 15.23 10.78 35.28 4.04
2309 3268 2.663188 GCGCGTGGGATCCATCTC 60.663 66.667 15.23 0.00 35.28 2.75
2310 3269 3.157217 GAGCGCGTGGGATCCATCT 62.157 63.158 15.23 0.24 35.28 2.90
2311 3270 2.663188 GAGCGCGTGGGATCCATC 60.663 66.667 15.23 4.68 35.28 3.51
2312 3271 4.592192 CGAGCGCGTGGGATCCAT 62.592 66.667 15.23 0.00 35.28 3.41
2322 3281 1.674611 CCACACTTCTTACGAGCGCG 61.675 60.000 8.75 8.75 44.79 6.86
2323 3282 0.666577 ACCACACTTCTTACGAGCGC 60.667 55.000 0.00 0.00 0.00 5.92
2324 3283 1.060713 CACCACACTTCTTACGAGCG 58.939 55.000 0.00 0.00 0.00 5.03
2325 3284 0.790814 GCACCACACTTCTTACGAGC 59.209 55.000 0.00 0.00 0.00 5.03
2326 3285 2.440539 AGCACCACACTTCTTACGAG 57.559 50.000 0.00 0.00 0.00 4.18
2327 3286 4.491676 GAATAGCACCACACTTCTTACGA 58.508 43.478 0.00 0.00 0.00 3.43
2328 3287 3.617263 GGAATAGCACCACACTTCTTACG 59.383 47.826 0.00 0.00 0.00 3.18
2329 3288 4.575885 TGGAATAGCACCACACTTCTTAC 58.424 43.478 0.00 0.00 32.03 2.34
2330 3289 4.901197 TGGAATAGCACCACACTTCTTA 57.099 40.909 0.00 0.00 32.03 2.10
2331 3290 3.788227 TGGAATAGCACCACACTTCTT 57.212 42.857 0.00 0.00 32.03 2.52
2332 3291 5.028549 CTATGGAATAGCACCACACTTCT 57.971 43.478 0.00 0.00 40.54 2.85
2418 3378 6.183360 TGGTCTTTAATGTCACAGCAATTTGT 60.183 34.615 0.00 0.00 0.00 2.83
2511 3484 9.851686 TGCATAAGATATCCACTAACTGAAAAT 57.148 29.630 0.00 0.00 0.00 1.82
2521 3494 4.081198 GCCTAGCTGCATAAGATATCCACT 60.081 45.833 1.02 0.00 0.00 4.00
2540 3513 4.415150 GGCACTGCAGCAGGCCTA 62.415 66.667 32.15 0.00 41.35 3.93
2593 3566 4.012374 ACAAAGATAATGGTGCAGACTGG 58.988 43.478 4.26 0.00 0.00 4.00
2670 3644 4.142038 AGCATTCTACCGAAACCAAAACT 58.858 39.130 0.00 0.00 31.91 2.66
2671 3645 4.473199 GAGCATTCTACCGAAACCAAAAC 58.527 43.478 0.00 0.00 31.91 2.43
2698 3672 2.730090 GCAGCACTCCATCACAAATTCG 60.730 50.000 0.00 0.00 0.00 3.34
2746 3720 1.401552 TCACAGTGCTTGCAAACAGAC 59.598 47.619 2.00 0.00 0.00 3.51
2763 3737 8.557029 CAAAAGGGATAAGTATAAACCGATCAC 58.443 37.037 0.00 0.00 0.00 3.06
2764 3738 8.269317 ACAAAAGGGATAAGTATAAACCGATCA 58.731 33.333 0.00 0.00 0.00 2.92
2765 3739 8.672823 ACAAAAGGGATAAGTATAAACCGATC 57.327 34.615 0.00 0.00 0.00 3.69
2766 3740 9.470399 AAACAAAAGGGATAAGTATAAACCGAT 57.530 29.630 0.00 0.00 0.00 4.18
2767 3741 8.866970 AAACAAAAGGGATAAGTATAAACCGA 57.133 30.769 0.00 0.00 0.00 4.69
2768 3742 9.992910 GTAAACAAAAGGGATAAGTATAAACCG 57.007 33.333 0.00 0.00 0.00 4.44
2959 3964 7.038088 AGCATCTTTTTAATTGGGACAGGAAAT 60.038 33.333 0.00 0.00 42.39 2.17
3058 4063 3.057946 GGACAAGCTCTGGTAAAAGCAAG 60.058 47.826 0.00 0.00 41.06 4.01
3103 4108 3.668447 TCTGATGAGCACTTTCCAGTTC 58.332 45.455 0.00 0.00 0.00 3.01
3173 4178 6.674694 ATGACACAGATCAGAATTTAGTGC 57.325 37.500 0.00 0.00 30.46 4.40
3241 4246 3.337358 TCACAGGATAGTGAACGACGTA 58.663 45.455 0.00 0.00 44.92 3.57
3257 4262 0.926155 CTCGCCGAATCATGTCACAG 59.074 55.000 0.00 0.00 0.00 3.66
3389 4394 3.306780 CCCAAGAGTGGTGACTATTTCGT 60.307 47.826 0.00 0.00 44.30 3.85
3661 4666 5.303078 GCAAGAAGAGATATACAGTCCTCCA 59.697 44.000 0.00 0.00 0.00 3.86
3727 4732 2.179018 CTTTCACATTGGCCGGCG 59.821 61.111 22.54 9.21 0.00 6.46
3731 4736 1.738030 GCATGCTCTTTCACATTGGCC 60.738 52.381 11.37 0.00 0.00 5.36
3787 4792 1.078426 ATCAGCTGCGTAACACCCC 60.078 57.895 9.47 0.00 0.00 4.95
3902 4907 4.393155 TGCTTGCCGTCTCGCCAT 62.393 61.111 0.00 0.00 0.00 4.40
4043 5048 0.807667 CCTGCACACATAGCTCGACC 60.808 60.000 0.00 0.00 0.00 4.79
4137 5142 1.630223 TGTTTTCATGCAGCCATCCA 58.370 45.000 0.00 0.00 0.00 3.41
4164 5169 1.004044 CATCTTCAGAAGTGCAGGGGT 59.996 52.381 10.09 0.00 0.00 4.95
4255 5266 4.883026 CATTTGCTGCTGCCTCAC 57.117 55.556 13.47 0.00 38.71 3.51
4301 5312 0.320683 TGTCTGGTCATGGTTCAGCG 60.321 55.000 0.00 0.00 0.00 5.18
4346 5357 7.526608 TCACCTTTTGATGAATACTTTTAGCG 58.473 34.615 0.00 0.00 0.00 4.26
4426 5437 1.376543 AGCAGCGATCAAATGGTCTG 58.623 50.000 0.00 0.00 0.00 3.51
4427 5438 2.119801 AAGCAGCGATCAAATGGTCT 57.880 45.000 0.00 0.00 0.00 3.85
4488 5499 6.323266 GTTATATACACCATAGCAGAGGACG 58.677 44.000 0.00 0.00 0.00 4.79
4525 5536 4.715751 AGGGAAGCATAAGGCATCTCACA 61.716 47.826 0.00 0.00 43.15 3.58
4656 5667 4.083003 GCACAAATACCCGAACAAATCTCA 60.083 41.667 0.00 0.00 0.00 3.27
4772 5783 7.849804 ACATTATACCGATAAATCTGATGGC 57.150 36.000 0.00 0.00 31.28 4.40
4840 5851 5.290158 CATCCATTTGATACAGCTTTTGCAC 59.710 40.000 0.00 0.00 39.10 4.57
4904 5915 5.263599 TGAATTGCCTGTCATACATCCTTT 58.736 37.500 0.00 0.00 0.00 3.11
4922 5933 2.519771 TTGATCAGGCTGGCTGAATT 57.480 45.000 33.27 20.67 34.26 2.17
5006 6132 3.091545 ACTTGCTGGGACATGGTTTATG 58.908 45.455 0.00 0.00 42.68 1.90


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

AutoCloner maintained by Alex Coulton.