Multiple sequence alignment - TraesCS2A01G449500

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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 TraesCS2A01G449500 chr2A 100.000 5455 0 0 1 5455 699510507 699515961 0.000000e+00 10074.0
1 TraesCS2A01G449500 chr2D 91.200 3159 165 46 1981 5082 558801192 558804294 0.000000e+00 4189.0
2 TraesCS2A01G449500 chr2D 92.550 1490 54 19 524 1986 558799707 558801166 0.000000e+00 2084.0
3 TraesCS2A01G449500 chr2D 81.690 497 57 18 12 503 558799014 558799481 3.080000e-102 383.0
4 TraesCS2A01G449500 chr2D 92.017 238 17 1 2156 2393 194819082 194818847 3.150000e-87 333.0
5 TraesCS2A01G449500 chr2D 91.393 244 19 2 2156 2397 315859014 315859257 3.150000e-87 333.0
6 TraesCS2A01G449500 chr2D 96.269 134 1 1 5163 5292 558804293 558804426 3.310000e-52 217.0
7 TraesCS2A01G449500 chr2B 91.923 1882 103 22 3587 5451 667416468 667418317 0.000000e+00 2588.0
8 TraesCS2A01G449500 chr2B 92.378 1312 47 19 541 1816 667413403 667414697 0.000000e+00 1820.0
9 TraesCS2A01G449500 chr2B 92.674 546 21 9 2389 2919 667415141 667415682 0.000000e+00 769.0
10 TraesCS2A01G449500 chr2B 92.744 317 14 4 2965 3272 667415678 667415994 3.000000e-122 449.0
11 TraesCS2A01G449500 chr2B 93.567 171 11 0 1981 2151 667414970 667415140 7.010000e-64 255.0
12 TraesCS2A01G449500 chr2B 98.246 114 2 0 1873 1986 667414831 667414944 3.330000e-47 200.0
13 TraesCS2A01G449500 chr6B 84.284 1069 85 29 1140 2150 560650359 560651402 0.000000e+00 966.0
14 TraesCS2A01G449500 chr6B 80.505 554 57 25 2388 2936 560651398 560651905 1.430000e-100 377.0
15 TraesCS2A01G449500 chr6D 92.946 241 17 0 2156 2396 410373754 410373514 8.690000e-93 351.0
16 TraesCS2A01G449500 chr5D 92.917 240 17 0 2156 2395 202399581 202399342 3.130000e-92 350.0
17 TraesCS2A01G449500 chr5D 92.373 236 18 0 2156 2391 279293105 279292870 2.430000e-88 337.0
18 TraesCS2A01G449500 chr5B 92.373 236 18 0 2156 2391 317293870 317293635 2.430000e-88 337.0
19 TraesCS2A01G449500 chr7A 90.837 251 20 2 2156 2403 329488514 329488264 3.150000e-87 333.0
20 TraesCS2A01G449500 chr7A 90.984 244 21 1 2156 2398 75247428 75247185 1.470000e-85 327.0
21 TraesCS2A01G449500 chr7A 95.122 41 2 0 1396 1436 448727653 448727693 1.270000e-06 65.8
22 TraesCS2A01G449500 chr7D 97.561 41 1 0 1396 1436 395602825 395602865 2.730000e-08 71.3


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 TraesCS2A01G449500 chr2A 699510507 699515961 5454 False 10074.00 10074 100.000000 1 5455 1 chr2A.!!$F1 5454
1 TraesCS2A01G449500 chr2D 558799014 558804426 5412 False 1718.25 4189 90.427250 12 5292 4 chr2D.!!$F2 5280
2 TraesCS2A01G449500 chr2B 667413403 667418317 4914 False 1013.50 2588 93.588667 541 5451 6 chr2B.!!$F1 4910
3 TraesCS2A01G449500 chr6B 560650359 560651905 1546 False 671.50 966 82.394500 1140 2936 2 chr6B.!!$F1 1796

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
448 450 0.179045 ATGGGTAGAGCGAATGGTGC 60.179 55.000 0.00 0.0 0.00 5.01 F
458 460 0.893270 CGAATGGTGCCCCACAAGAA 60.893 55.000 0.00 0.0 45.65 2.52 F
1781 2065 1.347707 TGGGAAGTACACCTCTGCTTG 59.652 52.381 8.59 0.0 0.00 4.01 F
2432 2935 0.738389 TGATGTCATCGCGTGCTCTA 59.262 50.000 5.77 0.0 0.00 2.43 F
2945 3482 1.285962 ACCAATCCACATCCTCCCTTG 59.714 52.381 0.00 0.0 0.00 3.61 F
3354 3982 1.065926 TCTGCACTCTGTTGGCCTATG 60.066 52.381 3.32 0.0 0.00 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 1878 1.867615 GCTGCTGCTGAGTGAACAG 59.132 57.895 10.92 0.0 40.43 3.16 R
2348 2849 2.428171 AGTCCGCGTATTAGCTTTGGTA 59.572 45.455 4.92 0.0 34.40 3.25 R
3001 3547 0.250727 AGCATAAACGCCCACTGTGT 60.251 50.000 7.08 0.0 40.09 3.72 R
3334 3962 1.065926 CATAGGCCAACAGAGTGCAGA 60.066 52.381 5.01 0.0 0.00 4.26 R
3995 4760 1.148310 CTGCAACACAACCTCCTACG 58.852 55.000 0.00 0.0 0.00 3.51 R
5051 5835 0.029567 CAAACGGCCGCAGTTGTTAA 59.970 50.000 28.58 0.0 31.43 2.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.550437 ACGCTAAGAGCTGAATTGGAT 57.450 42.857 0.00 0.00 39.60 3.41
44 45 3.317149 TGGATTTCTGATTGCTATGCTGC 59.683 43.478 0.00 0.00 0.00 5.25
59 60 6.994496 TGCTATGCTGCAGTATAGAAGAATTT 59.006 34.615 39.78 12.97 41.38 1.82
60 61 7.041576 TGCTATGCTGCAGTATAGAAGAATTTG 60.042 37.037 39.78 20.91 41.38 2.32
61 62 7.041508 GCTATGCTGCAGTATAGAAGAATTTGT 60.042 37.037 39.78 12.33 41.38 2.83
62 63 6.668541 TGCTGCAGTATAGAAGAATTTGTC 57.331 37.500 16.64 0.00 0.00 3.18
63 64 5.291858 TGCTGCAGTATAGAAGAATTTGTCG 59.708 40.000 16.64 0.00 0.00 4.35
80 81 5.940192 TTGTCGTGCTACATGAAGAAATT 57.060 34.783 0.00 0.00 30.77 1.82
81 82 5.940192 TGTCGTGCTACATGAAGAAATTT 57.060 34.783 0.00 0.00 30.77 1.82
82 83 5.688823 TGTCGTGCTACATGAAGAAATTTG 58.311 37.500 0.00 0.00 30.77 2.32
83 84 5.238432 TGTCGTGCTACATGAAGAAATTTGT 59.762 36.000 0.00 0.00 30.77 2.83
84 85 5.565259 GTCGTGCTACATGAAGAAATTTGTG 59.435 40.000 0.00 0.00 30.77 3.33
85 86 5.468409 TCGTGCTACATGAAGAAATTTGTGA 59.532 36.000 0.00 0.00 0.00 3.58
86 87 6.017523 TCGTGCTACATGAAGAAATTTGTGAA 60.018 34.615 0.00 0.00 0.00 3.18
87 88 6.636447 CGTGCTACATGAAGAAATTTGTGAAA 59.364 34.615 0.00 0.00 0.00 2.69
88 89 7.326789 CGTGCTACATGAAGAAATTTGTGAAAT 59.673 33.333 0.00 0.00 0.00 2.17
89 90 8.981647 GTGCTACATGAAGAAATTTGTGAAATT 58.018 29.630 0.00 0.00 42.62 1.82
111 112 5.450818 TTGCTTACCTATCCAGGAATTGT 57.549 39.130 0.00 0.00 45.91 2.71
120 121 4.785346 ATCCAGGAATTGTGATGCTAGT 57.215 40.909 0.00 0.00 0.00 2.57
122 123 5.282055 TCCAGGAATTGTGATGCTAGTAG 57.718 43.478 0.00 0.00 0.00 2.57
126 127 6.344500 CAGGAATTGTGATGCTAGTAGAAGT 58.656 40.000 0.00 0.00 0.00 3.01
127 128 6.820656 CAGGAATTGTGATGCTAGTAGAAGTT 59.179 38.462 0.00 0.00 0.00 2.66
134 135 5.814705 GTGATGCTAGTAGAAGTTGATTGCT 59.185 40.000 0.00 0.00 0.00 3.91
139 140 5.988561 GCTAGTAGAAGTTGATTGCTATGCT 59.011 40.000 0.00 0.00 0.00 3.79
145 146 2.810274 AGTTGATTGCTATGCTATGGCG 59.190 45.455 0.00 0.00 39.94 5.69
162 163 2.947448 GCGAAAAGAATTGCCATCCT 57.053 45.000 0.00 0.00 0.00 3.24
164 165 3.695816 GCGAAAAGAATTGCCATCCTAC 58.304 45.455 0.00 0.00 0.00 3.18
165 166 3.128589 GCGAAAAGAATTGCCATCCTACA 59.871 43.478 0.00 0.00 0.00 2.74
166 167 4.662145 CGAAAAGAATTGCCATCCTACAC 58.338 43.478 0.00 0.00 0.00 2.90
167 168 4.438744 CGAAAAGAATTGCCATCCTACACC 60.439 45.833 0.00 0.00 0.00 4.16
168 169 2.332063 AGAATTGCCATCCTACACCG 57.668 50.000 0.00 0.00 0.00 4.94
169 170 1.837439 AGAATTGCCATCCTACACCGA 59.163 47.619 0.00 0.00 0.00 4.69
170 171 2.238646 AGAATTGCCATCCTACACCGAA 59.761 45.455 0.00 0.00 0.00 4.30
171 172 2.332063 ATTGCCATCCTACACCGAAG 57.668 50.000 0.00 0.00 0.00 3.79
172 173 1.271856 TTGCCATCCTACACCGAAGA 58.728 50.000 0.00 0.00 0.00 2.87
173 174 1.271856 TGCCATCCTACACCGAAGAA 58.728 50.000 0.00 0.00 0.00 2.52
174 175 1.626321 TGCCATCCTACACCGAAGAAA 59.374 47.619 0.00 0.00 0.00 2.52
175 176 2.039216 TGCCATCCTACACCGAAGAAAA 59.961 45.455 0.00 0.00 0.00 2.29
176 177 2.678336 GCCATCCTACACCGAAGAAAAG 59.322 50.000 0.00 0.00 0.00 2.27
177 178 3.868754 GCCATCCTACACCGAAGAAAAGT 60.869 47.826 0.00 0.00 0.00 2.66
178 179 4.324267 CCATCCTACACCGAAGAAAAGTT 58.676 43.478 0.00 0.00 0.00 2.66
179 180 4.154195 CCATCCTACACCGAAGAAAAGTTG 59.846 45.833 0.00 0.00 0.00 3.16
180 181 3.135994 TCCTACACCGAAGAAAAGTTGC 58.864 45.455 0.00 0.00 0.00 4.17
181 182 2.225727 CCTACACCGAAGAAAAGTTGCC 59.774 50.000 0.00 0.00 0.00 4.52
241 242 6.301486 ACATTGAGAATTGCCATGCTATAGA 58.699 36.000 3.21 0.00 0.00 1.98
243 244 6.872628 TTGAGAATTGCCATGCTATAGAAG 57.127 37.500 3.21 0.00 0.00 2.85
244 245 6.178607 TGAGAATTGCCATGCTATAGAAGA 57.821 37.500 3.21 0.00 0.00 2.87
245 246 6.228995 TGAGAATTGCCATGCTATAGAAGAG 58.771 40.000 3.21 0.00 0.00 2.85
248 249 7.285566 AGAATTGCCATGCTATAGAAGAGAAA 58.714 34.615 3.21 0.00 0.00 2.52
249 250 7.776969 AGAATTGCCATGCTATAGAAGAGAAAA 59.223 33.333 3.21 0.00 0.00 2.29
250 251 6.683974 TTGCCATGCTATAGAAGAGAAAAC 57.316 37.500 3.21 0.00 0.00 2.43
251 252 5.744171 TGCCATGCTATAGAAGAGAAAACA 58.256 37.500 3.21 0.00 0.00 2.83
252 253 6.359804 TGCCATGCTATAGAAGAGAAAACAT 58.640 36.000 3.21 0.00 0.00 2.71
253 254 6.484643 TGCCATGCTATAGAAGAGAAAACATC 59.515 38.462 3.21 0.00 0.00 3.06
261 263 7.750229 ATAGAAGAGAAAACATCACTGCAAA 57.250 32.000 0.00 0.00 27.08 3.68
262 264 5.825507 AGAAGAGAAAACATCACTGCAAAC 58.174 37.500 0.00 0.00 27.08 2.93
264 266 5.779529 AGAGAAAACATCACTGCAAACAT 57.220 34.783 0.00 0.00 0.00 2.71
273 275 7.458409 ACATCACTGCAAACATAGAGAAAAT 57.542 32.000 0.00 0.00 0.00 1.82
290 292 4.341806 AGAAAATTGCCACACATGTCTCAA 59.658 37.500 0.00 0.00 0.00 3.02
294 296 6.534475 AATTGCCACACATGTCTCAATAAT 57.466 33.333 0.00 0.00 31.27 1.28
295 297 5.981088 TTGCCACACATGTCTCAATAATT 57.019 34.783 0.00 0.00 0.00 1.40
296 298 5.981088 TGCCACACATGTCTCAATAATTT 57.019 34.783 0.00 0.00 0.00 1.82
297 299 5.712004 TGCCACACATGTCTCAATAATTTG 58.288 37.500 0.00 0.00 0.00 2.32
298 300 5.243507 TGCCACACATGTCTCAATAATTTGT 59.756 36.000 0.00 0.00 34.32 2.83
299 301 5.801947 GCCACACATGTCTCAATAATTTGTC 59.198 40.000 0.00 0.00 34.32 3.18
300 302 6.570186 GCCACACATGTCTCAATAATTTGTCA 60.570 38.462 0.00 0.00 34.32 3.58
303 305 8.077991 CACACATGTCTCAATAATTTGTCAAGT 58.922 33.333 0.00 0.00 34.32 3.16
304 306 8.632679 ACACATGTCTCAATAATTTGTCAAGTT 58.367 29.630 0.00 0.00 34.32 2.66
379 381 6.363088 TCATTTGTTCAAGATTTGCATCGTTC 59.637 34.615 0.00 0.00 34.17 3.95
381 383 2.525750 TCAAGATTTGCATCGTTCGC 57.474 45.000 0.00 0.00 34.17 4.70
383 385 2.094258 TCAAGATTTGCATCGTTCGCTC 59.906 45.455 0.00 0.00 34.17 5.03
385 387 2.076100 AGATTTGCATCGTTCGCTCAA 58.924 42.857 0.00 0.00 34.17 3.02
389 391 2.464459 GCATCGTTCGCTCAAGGGG 61.464 63.158 0.00 0.00 0.00 4.79
427 429 2.112380 TGCATCATTCGCTCAGGAAA 57.888 45.000 0.00 0.00 0.00 3.13
428 430 2.011947 TGCATCATTCGCTCAGGAAAG 58.988 47.619 0.00 0.00 0.00 2.62
429 431 2.283298 GCATCATTCGCTCAGGAAAGA 58.717 47.619 0.00 0.00 0.00 2.52
430 432 2.877168 GCATCATTCGCTCAGGAAAGAT 59.123 45.455 0.00 0.00 35.42 2.40
433 435 1.945394 CATTCGCTCAGGAAAGATGGG 59.055 52.381 0.00 0.00 0.00 4.00
434 436 0.984230 TTCGCTCAGGAAAGATGGGT 59.016 50.000 0.00 0.00 0.00 4.51
436 438 1.757118 TCGCTCAGGAAAGATGGGTAG 59.243 52.381 0.00 0.00 0.00 3.18
444 446 3.134458 GGAAAGATGGGTAGAGCGAATG 58.866 50.000 0.00 0.00 0.00 2.67
446 448 1.794714 AGATGGGTAGAGCGAATGGT 58.205 50.000 0.00 0.00 0.00 3.55
447 449 1.414181 AGATGGGTAGAGCGAATGGTG 59.586 52.381 0.00 0.00 0.00 4.17
448 450 0.179045 ATGGGTAGAGCGAATGGTGC 60.179 55.000 0.00 0.00 0.00 5.01
450 452 1.523938 GGTAGAGCGAATGGTGCCC 60.524 63.158 0.00 0.00 0.00 5.36
458 460 0.893270 CGAATGGTGCCCCACAAGAA 60.893 55.000 0.00 0.00 45.65 2.52
475 477 2.076863 AGAATTGCCACTCTTACGTGC 58.923 47.619 0.00 0.00 33.60 5.34
492 494 1.880340 GCTGAGATTCGTGCGAGGG 60.880 63.158 0.00 0.00 0.00 4.30
505 552 2.519780 GAGGGGATCGGACGCTCT 60.520 66.667 7.11 0.00 42.58 4.09
510 557 1.891150 GGGGATCGGACGCTCTATAAA 59.109 52.381 0.00 0.00 0.00 1.40
514 561 4.995487 GGGATCGGACGCTCTATAAAATTT 59.005 41.667 0.00 0.00 0.00 1.82
520 567 5.176958 CGGACGCTCTATAAAATTTCCGATT 59.823 40.000 0.35 0.00 46.12 3.34
521 568 6.292703 CGGACGCTCTATAAAATTTCCGATTT 60.293 38.462 0.35 0.00 46.12 2.17
522 569 7.415229 GGACGCTCTATAAAATTTCCGATTTT 58.585 34.615 0.00 2.74 35.62 1.82
585 793 8.990163 GGAAGGGTCCATATGTAAGAAAAATA 57.010 34.615 1.24 0.00 44.26 1.40
586 794 9.416284 GGAAGGGTCCATATGTAAGAAAAATAA 57.584 33.333 1.24 0.00 44.26 1.40
692 904 3.670991 GCTCGATATTTCGCGATTTCTCT 59.329 43.478 10.88 0.00 45.10 3.10
693 905 4.201447 GCTCGATATTTCGCGATTTCTCTC 60.201 45.833 10.88 1.70 45.10 3.20
792 1018 2.587612 TCGATTTTTCTTTCCACGCG 57.412 45.000 3.53 3.53 0.00 6.01
896 1129 3.502990 TTCACGTACAACCGCCGCT 62.503 57.895 0.00 0.00 0.00 5.52
978 1211 4.778143 GGATTCGTGCGGTGGCCT 62.778 66.667 3.32 0.00 38.85 5.19
979 1212 3.499737 GATTCGTGCGGTGGCCTG 61.500 66.667 3.32 0.00 38.85 4.85
980 1213 3.950794 GATTCGTGCGGTGGCCTGA 62.951 63.158 3.32 0.00 38.85 3.86
1594 1857 3.361977 GCACCCGCGTTGGTTCAT 61.362 61.111 4.92 0.00 36.12 2.57
1684 1961 7.116376 ACTGTATGTCTTTCTACATGTTTGTCG 59.884 37.037 2.30 0.00 40.29 4.35
1690 1967 5.240623 TCTTTCTACATGTTTGTCGCCATTT 59.759 36.000 2.30 0.00 37.28 2.32
1781 2065 1.347707 TGGGAAGTACACCTCTGCTTG 59.652 52.381 8.59 0.00 0.00 4.01
1835 2254 3.449746 AGTAGTGAGCTCAGGTCTTCT 57.550 47.619 18.89 12.04 0.00 2.85
1836 2255 3.088532 AGTAGTGAGCTCAGGTCTTCTG 58.911 50.000 18.89 0.00 44.68 3.02
2021 2503 5.613812 TGTTAATCGCAGTTTATCACGTTG 58.386 37.500 0.00 0.00 0.00 4.10
2176 2677 6.711277 TCACATATTAGAGTTGGCTGAAGTT 58.289 36.000 0.00 0.00 0.00 2.66
2348 2849 8.831550 TGTCAAAGTTTGCAAAACTTAACTTTT 58.168 25.926 14.67 1.68 44.16 2.27
2351 2852 9.536558 CAAAGTTTGCAAAACTTAACTTTTACC 57.463 29.630 14.67 0.00 44.16 2.85
2432 2935 0.738389 TGATGTCATCGCGTGCTCTA 59.262 50.000 5.77 0.00 0.00 2.43
2466 2969 6.952773 AGTTGCTTTTGGACATTAGTTGTA 57.047 33.333 0.00 0.00 39.18 2.41
2642 3145 6.371809 TGGTACAAACAGCAAGAAGTAAAG 57.628 37.500 0.00 0.00 31.92 1.85
2932 3469 5.822519 TGTCATTATTCTGCAGTACCAATCC 59.177 40.000 14.67 0.00 0.00 3.01
2942 3479 2.127708 AGTACCAATCCACATCCTCCC 58.872 52.381 0.00 0.00 0.00 4.30
2945 3482 1.285962 ACCAATCCACATCCTCCCTTG 59.714 52.381 0.00 0.00 0.00 3.61
2962 3499 6.429385 CCTCCCTTGATAGATATTTGCTGAAC 59.571 42.308 0.00 0.00 0.00 3.18
2963 3500 6.299141 TCCCTTGATAGATATTTGCTGAACC 58.701 40.000 0.00 0.00 0.00 3.62
2996 3542 3.791320 TGTCCCTGGAGTTCAGACTATT 58.209 45.455 0.00 0.00 46.18 1.73
3001 3547 4.469945 CCCTGGAGTTCAGACTATTTACCA 59.530 45.833 0.00 0.00 46.18 3.25
3005 3551 5.305902 TGGAGTTCAGACTATTTACCACACA 59.694 40.000 0.00 0.00 35.88 3.72
3025 3571 3.761752 ACAGTGGGCGTTTATGCTTTAAT 59.238 39.130 0.00 0.00 34.52 1.40
3027 3573 5.167845 CAGTGGGCGTTTATGCTTTAATTT 58.832 37.500 0.00 0.00 34.52 1.82
3195 3741 1.662044 GTCAAGGCCCAACTTGCTG 59.338 57.895 0.00 0.00 45.72 4.41
3214 3760 3.538634 TGAGATCTCAGAGGCATTGTG 57.461 47.619 21.67 0.00 34.14 3.33
3215 3761 2.211806 GAGATCTCAGAGGCATTGTGC 58.788 52.381 18.11 0.00 44.08 4.57
3253 3799 6.858993 TCGTTATTTTTGTGAAGTGGTAATGC 59.141 34.615 0.00 0.00 0.00 3.56
3254 3800 6.638873 CGTTATTTTTGTGAAGTGGTAATGCA 59.361 34.615 0.00 0.00 0.00 3.96
3266 3812 3.317993 GTGGTAATGCACAGGTTCAAAGT 59.682 43.478 0.00 0.00 0.00 2.66
3272 3818 2.171659 TGCACAGGTTCAAAGTCCTACA 59.828 45.455 0.00 0.00 32.26 2.74
3273 3819 2.808543 GCACAGGTTCAAAGTCCTACAG 59.191 50.000 0.00 0.00 32.26 2.74
3309 3937 4.007659 GTCAACGGACCTATGATTTGGTT 58.992 43.478 0.08 0.00 38.12 3.67
3345 3973 4.881019 AATTCTGTAGTCTGCACTCTGT 57.119 40.909 0.00 0.00 33.62 3.41
3354 3982 1.065926 TCTGCACTCTGTTGGCCTATG 60.066 52.381 3.32 0.00 0.00 2.23
3358 3986 2.355716 GCACTCTGTTGGCCTATGGTTA 60.356 50.000 3.32 0.00 0.00 2.85
3419 4172 6.859112 AGCCTATATGGTCGATTTACTGAT 57.141 37.500 0.00 0.00 38.35 2.90
3474 4227 9.435570 TCCATTACTTCTTTAGTATAGCTTCCT 57.564 33.333 0.00 0.00 39.07 3.36
3480 4233 9.794719 ACTTCTTTAGTATAGCTTCCTTGTTTT 57.205 29.630 0.00 0.00 34.56 2.43
3483 4236 9.787435 TCTTTAGTATAGCTTCCTTGTTTTTCA 57.213 29.630 0.00 0.00 0.00 2.69
3486 4239 9.515226 TTAGTATAGCTTCCTTGTTTTTCATGT 57.485 29.630 0.00 0.00 0.00 3.21
3488 4241 9.686683 AGTATAGCTTCCTTGTTTTTCATGTAT 57.313 29.630 0.00 0.00 0.00 2.29
3492 4245 6.925165 AGCTTCCTTGTTTTTCATGTATTGTG 59.075 34.615 0.00 0.00 0.00 3.33
3500 4253 7.711846 TGTTTTTCATGTATTGTGTGCTAACT 58.288 30.769 0.00 0.00 0.00 2.24
3514 4267 1.807142 GCTAACTGTCTTTGTGAGCCC 59.193 52.381 0.00 0.00 36.22 5.19
3530 4283 4.947388 GTGAGCCCAATATGGAGTTTGTTA 59.053 41.667 0.00 0.00 40.96 2.41
3573 4326 7.862648 TGTGAACATATATAGTCTCTGACGAC 58.137 38.462 0.00 0.00 37.67 4.34
3595 4348 8.035394 ACGACAGAACTGAAATGTCTAATATGT 58.965 33.333 8.87 0.00 40.92 2.29
3620 4373 7.573968 AGTTTTCAGTTTACATCTCAGCTTT 57.426 32.000 0.00 0.00 0.00 3.51
3622 4375 8.470002 AGTTTTCAGTTTACATCTCAGCTTTTT 58.530 29.630 0.00 0.00 0.00 1.94
3634 4387 8.507249 ACATCTCAGCTTTTTAAGTTACATGAC 58.493 33.333 0.00 0.00 0.00 3.06
3639 4392 8.128582 TCAGCTTTTTAAGTTACATGACAACAG 58.871 33.333 0.00 0.00 0.00 3.16
3643 4396 6.870971 TTTAAGTTACATGACAACAGGTCC 57.129 37.500 0.00 0.00 46.38 4.46
3659 4412 7.446013 ACAACAGGTCCGAAAATTTAATCTGTA 59.554 33.333 8.33 0.00 33.34 2.74
3660 4413 7.373778 ACAGGTCCGAAAATTTAATCTGTAC 57.626 36.000 6.82 0.00 32.13 2.90
3661 4414 7.166167 ACAGGTCCGAAAATTTAATCTGTACT 58.834 34.615 6.82 0.00 32.13 2.73
3667 4420 8.932791 TCCGAAAATTTAATCTGTACTTCTCAC 58.067 33.333 0.00 0.00 0.00 3.51
3676 4429 4.678256 TCTGTACTTCTCACTCTCCCATT 58.322 43.478 0.00 0.00 0.00 3.16
3729 4493 3.008704 GGCACCAGGTTTTCTAGACCTTA 59.991 47.826 0.00 0.00 45.06 2.69
3786 4550 4.307432 ACAGAGTCACACCGTATTTCTTG 58.693 43.478 0.00 0.00 0.00 3.02
3795 4560 7.696453 GTCACACCGTATTTCTTGATATTTTGG 59.304 37.037 0.00 0.00 0.00 3.28
3800 4565 8.413229 ACCGTATTTCTTGATATTTTGGAATGG 58.587 33.333 0.00 0.00 0.00 3.16
3801 4566 7.867403 CCGTATTTCTTGATATTTTGGAATGGG 59.133 37.037 0.00 0.00 0.00 4.00
3813 4578 6.985653 TTTTGGAATGGGATGTCAGTTTTA 57.014 33.333 0.00 0.00 0.00 1.52
3815 4580 8.657387 TTTTGGAATGGGATGTCAGTTTTATA 57.343 30.769 0.00 0.00 0.00 0.98
4068 4841 6.533367 GGTTTGTTGATGTTCTTTGCACTTTA 59.467 34.615 0.00 0.00 0.00 1.85
4076 4849 7.648908 TGATGTTCTTTGCACTTTATTGTCAAG 59.351 33.333 0.00 0.00 0.00 3.02
4126 4899 1.539827 GGTGACAGGTTACCATGTTGC 59.460 52.381 3.51 2.99 38.90 4.17
4220 4993 1.746615 AACATCTGCGCCGATGCTT 60.747 52.632 33.22 24.45 43.54 3.91
4537 5310 2.126502 CACCGGCGCCAACAATTC 60.127 61.111 28.98 0.00 0.00 2.17
4584 5357 1.006162 AGAGGTAGTCGGAGAGCCTTT 59.994 52.381 0.00 0.00 36.95 3.11
4586 5359 1.183549 GGTAGTCGGAGAGCCTTTCA 58.816 55.000 0.00 0.00 36.95 2.69
4606 5379 1.380302 GGAAGGCCTGAGGAGCAAA 59.620 57.895 5.69 0.00 0.00 3.68
4619 5392 6.096001 CCTGAGGAGCAAAAATAAGTAGCATT 59.904 38.462 0.00 0.00 0.00 3.56
4634 5408 2.875296 AGCATTGTCTTGCCCTGTTAA 58.125 42.857 0.00 0.00 43.83 2.01
4849 5629 1.797320 TACTCCGGGAATTACTGGGG 58.203 55.000 14.58 14.58 43.41 4.96
4850 5630 0.253020 ACTCCGGGAATTACTGGGGT 60.253 55.000 16.17 16.17 45.89 4.95
4851 5631 1.797320 CTCCGGGAATTACTGGGGTA 58.203 55.000 16.00 0.00 37.50 3.69
4852 5632 2.335933 CTCCGGGAATTACTGGGGTAT 58.664 52.381 16.00 0.00 37.50 2.73
4855 5635 3.905591 TCCGGGAATTACTGGGGTATAAG 59.094 47.826 16.00 0.00 37.50 1.73
4878 5658 6.704310 AGAGAAATTCAACATCCATTTTGGG 58.296 36.000 0.00 0.00 38.32 4.12
4903 5683 1.291272 GTTCTTACGACGGGTGGCT 59.709 57.895 0.00 0.00 0.00 4.75
4904 5684 0.320160 GTTCTTACGACGGGTGGCTT 60.320 55.000 0.00 0.00 0.00 4.35
4905 5685 0.393820 TTCTTACGACGGGTGGCTTT 59.606 50.000 0.00 0.00 0.00 3.51
4906 5686 1.255882 TCTTACGACGGGTGGCTTTA 58.744 50.000 0.00 0.00 0.00 1.85
4909 5689 3.446873 TCTTACGACGGGTGGCTTTATTA 59.553 43.478 0.00 0.00 0.00 0.98
4938 5718 6.127168 ACCGTGTTATTCAGATTCCATAGTCA 60.127 38.462 0.00 0.00 0.00 3.41
4939 5719 6.201044 CCGTGTTATTCAGATTCCATAGTCAC 59.799 42.308 0.00 0.00 0.00 3.67
4940 5720 6.980978 CGTGTTATTCAGATTCCATAGTCACT 59.019 38.462 0.00 0.00 0.00 3.41
4941 5721 8.135529 CGTGTTATTCAGATTCCATAGTCACTA 58.864 37.037 0.00 0.00 0.00 2.74
4942 5722 9.469807 GTGTTATTCAGATTCCATAGTCACTAG 57.530 37.037 0.00 0.00 0.00 2.57
4943 5723 9.201989 TGTTATTCAGATTCCATAGTCACTAGT 57.798 33.333 0.00 0.00 0.00 2.57
4960 5740 8.978472 AGTCACTAGTAAGCCATTATTCACTAA 58.022 33.333 0.00 0.00 0.00 2.24
5051 5835 5.762825 CATGATTCCATGGTTCGAATCTT 57.237 39.130 19.31 13.06 44.88 2.40
5054 5838 7.706159 CATGATTCCATGGTTCGAATCTTTAA 58.294 34.615 19.31 1.14 44.88 1.52
5129 5913 0.318762 ACTTCTCAGACGGAAGGCAC 59.681 55.000 8.08 0.00 46.78 5.01
5146 5930 4.910195 AGGCACTGTTGTTCATTCAGATA 58.090 39.130 10.54 0.00 37.18 1.98
5147 5931 5.316167 AGGCACTGTTGTTCATTCAGATAA 58.684 37.500 10.54 0.00 37.18 1.75
5283 6072 3.330720 CCCTCGCCTTTCCCTGGT 61.331 66.667 0.00 0.00 0.00 4.00
5306 6095 0.840722 ACCCCATGGTCGGAACTCTT 60.841 55.000 11.73 0.00 43.06 2.85
5326 6115 2.361483 ACGCATGCTTGGATGGCA 60.361 55.556 17.13 0.00 44.05 4.92
5335 6124 4.657408 TGGATGGCAACTGCGGCA 62.657 61.111 1.29 1.29 46.50 5.69
5336 6125 3.818787 GGATGGCAACTGCGGCAG 61.819 66.667 27.43 27.43 45.56 4.85
5338 6127 3.332493 GATGGCAACTGCGGCAGTG 62.332 63.158 33.94 26.26 44.62 3.66
5362 6152 1.068417 ACGACGGTGTAAGCTGCAA 59.932 52.632 1.02 0.00 0.00 4.08
5375 6165 3.011949 AGCTGCAAAATTACCAACGTG 57.988 42.857 1.02 0.00 0.00 4.49
5385 6175 2.093306 TACCAACGTGCCAGATTCAG 57.907 50.000 0.00 0.00 0.00 3.02
5420 6212 5.614668 GCGCATTATAGCAAAAAGATAGCGA 60.615 40.000 0.30 0.00 42.47 4.93
5423 6215 6.575201 GCATTATAGCAAAAAGATAGCGACAC 59.425 38.462 0.00 0.00 0.00 3.67
5426 6218 3.138304 AGCAAAAAGATAGCGACACACA 58.862 40.909 0.00 0.00 0.00 3.72
5430 6222 5.734498 GCAAAAAGATAGCGACACACATAAG 59.266 40.000 0.00 0.00 0.00 1.73
5434 6226 7.849804 AAAGATAGCGACACACATAAGATTT 57.150 32.000 0.00 0.00 0.00 2.17
5442 6234 7.042456 AGCGACACACATAAGATTTGCTATTAG 60.042 37.037 0.00 0.00 0.00 1.73
5443 6235 7.065894 CGACACACATAAGATTTGCTATTAGC 58.934 38.462 8.80 8.80 42.82 3.09
5451 6243 4.744570 AGATTTGCTATTAGCGCGCTATA 58.255 39.130 38.51 28.09 46.26 1.31
5452 6244 4.800993 AGATTTGCTATTAGCGCGCTATAG 59.199 41.667 38.51 34.05 46.26 1.31
5453 6245 1.909376 TGCTATTAGCGCGCTATAGC 58.091 50.000 39.66 39.66 46.26 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.804843 ATCAGAAATCCAATTCAGCTCTTAG 57.195 36.000 0.00 0.00 0.00 2.18
10 11 7.415989 GCAATCAGAAATCCAATTCAGCTCTTA 60.416 37.037 0.00 0.00 0.00 2.10
11 12 6.627508 GCAATCAGAAATCCAATTCAGCTCTT 60.628 38.462 0.00 0.00 0.00 2.85
12 13 5.163540 GCAATCAGAAATCCAATTCAGCTCT 60.164 40.000 0.00 0.00 0.00 4.09
13 14 5.041940 GCAATCAGAAATCCAATTCAGCTC 58.958 41.667 0.00 0.00 0.00 4.09
14 15 4.710375 AGCAATCAGAAATCCAATTCAGCT 59.290 37.500 0.00 0.00 0.00 4.24
15 16 5.007385 AGCAATCAGAAATCCAATTCAGC 57.993 39.130 0.00 0.00 0.00 4.26
16 17 6.641314 GCATAGCAATCAGAAATCCAATTCAG 59.359 38.462 0.00 0.00 0.00 3.02
17 18 6.322969 AGCATAGCAATCAGAAATCCAATTCA 59.677 34.615 0.00 0.00 0.00 2.57
26 27 3.349927 ACTGCAGCATAGCAATCAGAAA 58.650 40.909 15.27 0.00 45.13 2.52
44 45 6.893958 AGCACGACAAATTCTTCTATACTG 57.106 37.500 0.00 0.00 0.00 2.74
59 60 5.238432 ACAAATTTCTTCATGTAGCACGACA 59.762 36.000 0.00 0.00 0.00 4.35
60 61 5.565259 CACAAATTTCTTCATGTAGCACGAC 59.435 40.000 0.00 0.00 0.00 4.34
61 62 5.468409 TCACAAATTTCTTCATGTAGCACGA 59.532 36.000 0.00 0.00 0.00 4.35
62 63 5.688823 TCACAAATTTCTTCATGTAGCACG 58.311 37.500 0.00 0.00 0.00 5.34
63 64 7.928908 TTTCACAAATTTCTTCATGTAGCAC 57.071 32.000 0.00 0.00 0.00 4.40
80 81 6.152661 CCTGGATAGGTAAGCAAATTTCACAA 59.847 38.462 0.00 0.00 39.39 3.33
81 82 5.652014 CCTGGATAGGTAAGCAAATTTCACA 59.348 40.000 0.00 0.00 39.39 3.58
82 83 5.885912 TCCTGGATAGGTAAGCAAATTTCAC 59.114 40.000 0.00 0.00 44.88 3.18
83 84 6.073447 TCCTGGATAGGTAAGCAAATTTCA 57.927 37.500 0.00 0.00 44.88 2.69
84 85 7.588497 ATTCCTGGATAGGTAAGCAAATTTC 57.412 36.000 0.00 0.00 44.88 2.17
85 86 7.400052 ACAATTCCTGGATAGGTAAGCAAATTT 59.600 33.333 0.00 0.00 44.88 1.82
86 87 6.897413 ACAATTCCTGGATAGGTAAGCAAATT 59.103 34.615 0.00 0.00 44.88 1.82
87 88 6.322201 CACAATTCCTGGATAGGTAAGCAAAT 59.678 38.462 0.00 0.00 44.88 2.32
88 89 5.652014 CACAATTCCTGGATAGGTAAGCAAA 59.348 40.000 0.00 0.00 44.88 3.68
89 90 5.045213 TCACAATTCCTGGATAGGTAAGCAA 60.045 40.000 0.00 0.00 44.88 3.91
111 112 5.982356 AGCAATCAACTTCTACTAGCATCA 58.018 37.500 0.00 0.00 0.00 3.07
120 121 5.702670 GCCATAGCATAGCAATCAACTTCTA 59.297 40.000 0.00 0.00 39.53 2.10
122 123 4.612259 CGCCATAGCATAGCAATCAACTTC 60.612 45.833 0.00 0.00 39.83 3.01
126 127 3.124578 TCGCCATAGCATAGCAATCAA 57.875 42.857 0.00 0.00 39.83 2.57
127 128 2.837532 TCGCCATAGCATAGCAATCA 57.162 45.000 0.00 0.00 39.83 2.57
134 135 4.261572 GGCAATTCTTTTCGCCATAGCATA 60.262 41.667 0.00 0.00 44.25 3.14
145 146 4.438744 CGGTGTAGGATGGCAATTCTTTTC 60.439 45.833 0.00 0.00 0.00 2.29
162 163 2.875933 CTGGCAACTTTTCTTCGGTGTA 59.124 45.455 0.00 0.00 37.61 2.90
163 164 1.676006 CTGGCAACTTTTCTTCGGTGT 59.324 47.619 0.00 0.00 37.61 4.16
164 165 1.676006 ACTGGCAACTTTTCTTCGGTG 59.324 47.619 0.00 0.00 37.61 4.94
165 166 2.052782 ACTGGCAACTTTTCTTCGGT 57.947 45.000 0.00 0.00 37.61 4.69
166 167 2.731217 CAACTGGCAACTTTTCTTCGG 58.269 47.619 0.00 0.00 37.61 4.30
167 168 2.119457 GCAACTGGCAACTTTTCTTCG 58.881 47.619 0.00 0.00 43.97 3.79
179 180 3.209097 ACGTGTGTGGCAACTGGC 61.209 61.111 0.00 0.00 43.74 4.85
180 181 2.715005 CACGTGTGTGGCAACTGG 59.285 61.111 7.58 0.00 42.59 4.00
181 182 2.024588 GCACGTGTGTGGCAACTG 59.975 61.111 18.38 0.00 46.51 3.16
214 215 2.350498 GCATGGCAATTCTCAATGTTGC 59.650 45.455 0.00 0.97 45.54 4.17
219 220 7.229308 TCTTCTATAGCATGGCAATTCTCAAT 58.771 34.615 0.00 0.00 0.00 2.57
220 221 6.594744 TCTTCTATAGCATGGCAATTCTCAA 58.405 36.000 0.00 0.00 0.00 3.02
241 242 5.581126 TGTTTGCAGTGATGTTTTCTCTT 57.419 34.783 0.00 0.00 0.00 2.85
243 244 6.902341 TCTATGTTTGCAGTGATGTTTTCTC 58.098 36.000 0.00 0.00 0.00 2.87
244 245 6.712095 TCTCTATGTTTGCAGTGATGTTTTCT 59.288 34.615 0.00 0.00 0.00 2.52
245 246 6.902341 TCTCTATGTTTGCAGTGATGTTTTC 58.098 36.000 0.00 0.00 0.00 2.29
248 249 6.882610 TTTCTCTATGTTTGCAGTGATGTT 57.117 33.333 0.00 0.00 0.00 2.71
249 250 6.882610 TTTTCTCTATGTTTGCAGTGATGT 57.117 33.333 0.00 0.00 0.00 3.06
250 251 7.201410 GCAATTTTCTCTATGTTTGCAGTGATG 60.201 37.037 0.00 0.00 39.30 3.07
251 252 6.810182 GCAATTTTCTCTATGTTTGCAGTGAT 59.190 34.615 0.00 0.00 39.30 3.06
252 253 6.151691 GCAATTTTCTCTATGTTTGCAGTGA 58.848 36.000 0.00 0.00 39.30 3.41
253 254 5.346822 GGCAATTTTCTCTATGTTTGCAGTG 59.653 40.000 7.62 0.00 40.81 3.66
261 263 5.477984 ACATGTGTGGCAATTTTCTCTATGT 59.522 36.000 0.00 0.00 0.00 2.29
262 264 5.957798 ACATGTGTGGCAATTTTCTCTATG 58.042 37.500 0.00 0.00 0.00 2.23
264 266 5.316167 AGACATGTGTGGCAATTTTCTCTA 58.684 37.500 1.15 0.00 35.06 2.43
273 275 5.981088 AATTATTGAGACATGTGTGGCAA 57.019 34.783 1.15 0.70 35.06 4.52
354 356 5.771469 ACGATGCAAATCTTGAACAAATGA 58.229 33.333 0.00 0.00 0.00 2.57
355 357 6.456447 AACGATGCAAATCTTGAACAAATG 57.544 33.333 0.00 0.00 0.00 2.32
357 359 4.674662 CGAACGATGCAAATCTTGAACAAA 59.325 37.500 0.00 0.00 0.00 2.83
379 381 2.672996 CCAACCACCCCTTGAGCG 60.673 66.667 0.00 0.00 0.00 5.03
381 383 1.303643 GCTCCAACCACCCCTTGAG 60.304 63.158 0.00 0.00 0.00 3.02
383 385 0.758685 TTTGCTCCAACCACCCCTTG 60.759 55.000 0.00 0.00 0.00 3.61
385 387 1.152546 GTTTGCTCCAACCACCCCT 60.153 57.895 0.00 0.00 0.00 4.79
389 391 1.923864 CAAAACGTTTGCTCCAACCAC 59.076 47.619 15.46 0.00 0.00 4.16
412 414 2.420547 CCCATCTTTCCTGAGCGAATGA 60.421 50.000 0.00 3.20 32.42 2.57
427 429 1.414181 CACCATTCGCTCTACCCATCT 59.586 52.381 0.00 0.00 0.00 2.90
428 430 1.871080 CACCATTCGCTCTACCCATC 58.129 55.000 0.00 0.00 0.00 3.51
429 431 0.179045 GCACCATTCGCTCTACCCAT 60.179 55.000 0.00 0.00 0.00 4.00
430 432 1.220749 GCACCATTCGCTCTACCCA 59.779 57.895 0.00 0.00 0.00 4.51
446 448 1.152376 TGGCAATTCTTGTGGGGCA 60.152 52.632 0.00 0.00 0.00 5.36
447 449 1.187567 AGTGGCAATTCTTGTGGGGC 61.188 55.000 0.00 0.00 0.00 5.80
448 450 0.890683 GAGTGGCAATTCTTGTGGGG 59.109 55.000 0.00 0.00 0.00 4.96
450 452 3.120199 CGTAAGAGTGGCAATTCTTGTGG 60.120 47.826 19.95 9.23 43.02 4.17
458 460 1.001974 TCAGCACGTAAGAGTGGCAAT 59.998 47.619 0.00 0.00 42.09 3.56
466 468 2.863739 CACGAATCTCAGCACGTAAGA 58.136 47.619 0.00 0.00 43.62 2.10
469 471 0.796870 CGCACGAATCTCAGCACGTA 60.797 55.000 0.00 0.00 37.22 3.57
471 473 1.737196 CTCGCACGAATCTCAGCACG 61.737 60.000 0.00 0.00 0.00 5.34
475 477 1.227089 CCCCTCGCACGAATCTCAG 60.227 63.158 0.00 0.00 0.00 3.35
492 494 5.120363 GGAAATTTTATAGAGCGTCCGATCC 59.880 44.000 0.78 0.00 0.00 3.36
581 789 9.964303 GTTTCCTTTTTCATTGGCAAATTATTT 57.036 25.926 3.01 0.00 0.00 1.40
585 793 5.008514 CGGTTTCCTTTTTCATTGGCAAATT 59.991 36.000 3.01 0.00 0.00 1.82
586 794 4.514816 CGGTTTCCTTTTTCATTGGCAAAT 59.485 37.500 3.01 0.00 0.00 2.32
587 795 3.873952 CGGTTTCCTTTTTCATTGGCAAA 59.126 39.130 3.01 0.00 0.00 3.68
588 796 3.133003 TCGGTTTCCTTTTTCATTGGCAA 59.867 39.130 0.68 0.68 0.00 4.52
589 797 2.695666 TCGGTTTCCTTTTTCATTGGCA 59.304 40.909 0.00 0.00 0.00 4.92
590 798 3.317150 CTCGGTTTCCTTTTTCATTGGC 58.683 45.455 0.00 0.00 0.00 4.52
792 1018 2.598619 GAAAGCGGAGGCGGATTTGC 62.599 60.000 0.00 0.00 46.35 3.68
867 1094 0.032952 GTACGTGAACCACCTCTGCA 59.967 55.000 0.00 0.00 0.00 4.41
970 1203 3.470888 CCCTAGGTCAGGCCACCG 61.471 72.222 5.01 0.00 43.98 4.94
975 1208 1.449778 GCGAAACCCTAGGTCAGGC 60.450 63.158 8.29 0.61 43.98 4.85
976 1209 1.221021 GGCGAAACCCTAGGTCAGG 59.779 63.158 8.29 0.00 45.07 3.86
977 1210 1.153628 CGGCGAAACCCTAGGTCAG 60.154 63.158 8.29 0.00 33.12 3.51
978 1211 2.975536 CGGCGAAACCCTAGGTCA 59.024 61.111 8.29 0.00 33.12 4.02
979 1212 2.510918 GCGGCGAAACCCTAGGTC 60.511 66.667 12.98 0.00 33.12 3.85
980 1213 4.446413 CGCGGCGAAACCCTAGGT 62.446 66.667 19.16 0.00 37.65 3.08
1255 1515 2.745884 CATGTCCGCGGGCTTCAA 60.746 61.111 32.34 11.30 0.00 2.69
1615 1878 1.867615 GCTGCTGCTGAGTGAACAG 59.132 57.895 10.92 0.00 40.43 3.16
1656 1922 9.204570 ACAAACATGTAGAAAGACATACAGTAC 57.795 33.333 0.00 0.00 37.99 2.73
1657 1923 9.419297 GACAAACATGTAGAAAGACATACAGTA 57.581 33.333 0.00 0.00 37.99 2.74
1658 1924 7.116376 CGACAAACATGTAGAAAGACATACAGT 59.884 37.037 0.00 0.00 37.99 3.55
1684 1961 7.093945 TGGAGAAATCCTTACAAAGTAAATGGC 60.094 37.037 0.00 0.00 0.00 4.40
1690 1967 7.942341 ACAATGTGGAGAAATCCTTACAAAGTA 59.058 33.333 0.00 0.00 0.00 2.24
1817 2217 3.441500 TCAGAAGACCTGAGCTCACTA 57.558 47.619 13.74 0.00 46.38 2.74
1902 2321 8.642020 GTGACATGATAGAAAAATGAGCAAAAC 58.358 33.333 0.00 0.00 0.00 2.43
2021 2503 3.279434 AGAAGGCCATCGAATTACAACC 58.721 45.455 5.01 0.00 0.00 3.77
2152 2636 6.299805 ACTTCAGCCAACTCTAATATGTGA 57.700 37.500 0.00 0.00 0.00 3.58
2153 2637 6.992063 AACTTCAGCCAACTCTAATATGTG 57.008 37.500 0.00 0.00 0.00 3.21
2154 2638 8.947115 GTTTAACTTCAGCCAACTCTAATATGT 58.053 33.333 0.00 0.00 0.00 2.29
2333 2834 7.534085 AGCTTTGGTAAAAGTTAAGTTTTGC 57.466 32.000 24.83 23.18 44.02 3.68
2338 2839 8.232513 GCGTATTAGCTTTGGTAAAAGTTAAGT 58.767 33.333 11.42 5.18 46.00 2.24
2342 2843 5.391203 CCGCGTATTAGCTTTGGTAAAAGTT 60.391 40.000 4.92 0.00 44.02 2.66
2348 2849 2.428171 AGTCCGCGTATTAGCTTTGGTA 59.572 45.455 4.92 0.00 34.40 3.25
2351 2852 5.652744 ATTTAGTCCGCGTATTAGCTTTG 57.347 39.130 4.92 0.00 34.40 2.77
2432 2935 4.953579 TCCAAAAGCAACTTAGGAACAACT 59.046 37.500 0.00 0.00 29.17 3.16
2466 2969 2.619177 CAATCTACTCGATCCTGACCGT 59.381 50.000 0.00 0.00 0.00 4.83
2642 3145 0.462759 GGGTCCACTCAGTGCTATGC 60.463 60.000 0.00 0.00 31.34 3.14
2932 3469 6.373774 GCAAATATCTATCAAGGGAGGATGTG 59.626 42.308 0.00 0.00 0.00 3.21
2945 3482 9.732130 AAGGAATAGGTTCAGCAAATATCTATC 57.268 33.333 0.00 0.00 36.01 2.08
2962 3499 2.648059 CAGGGACAAGCAAGGAATAGG 58.352 52.381 0.00 0.00 0.00 2.57
2963 3500 2.239654 TCCAGGGACAAGCAAGGAATAG 59.760 50.000 0.00 0.00 0.00 1.73
3001 3547 0.250727 AGCATAAACGCCCACTGTGT 60.251 50.000 7.08 0.00 40.09 3.72
3005 3551 5.400066 AAATTAAAGCATAAACGCCCACT 57.600 34.783 0.00 0.00 0.00 4.00
3025 3571 5.010922 AGCAACATCCTGCAAACAAGATAAA 59.989 36.000 0.00 0.00 45.18 1.40
3027 3573 4.081406 AGCAACATCCTGCAAACAAGATA 58.919 39.130 0.00 0.00 45.18 1.98
3195 3741 2.211806 GCACAATGCCTCTGAGATCTC 58.788 52.381 16.21 16.21 37.42 2.75
3215 3761 6.302313 ACAAAAATAACGAGAAGCGAAAATCG 59.698 34.615 0.00 0.00 44.57 3.34
3253 3799 4.073293 ACTGTAGGACTTTGAACCTGTG 57.927 45.455 0.00 0.00 37.68 3.66
3254 3800 4.262506 GCTACTGTAGGACTTTGAACCTGT 60.263 45.833 16.09 0.00 37.68 4.00
3266 3812 2.428530 CAGCTGTGATGCTACTGTAGGA 59.571 50.000 16.09 13.91 41.98 2.94
3272 3818 2.693069 GTTGACAGCTGTGATGCTACT 58.307 47.619 27.27 0.00 41.98 2.57
3273 3819 1.391485 CGTTGACAGCTGTGATGCTAC 59.609 52.381 27.27 15.13 41.98 3.58
3309 3937 9.967346 GACTACAGAATTATATGCTAGAACACA 57.033 33.333 0.00 0.00 0.00 3.72
3334 3962 1.065926 CATAGGCCAACAGAGTGCAGA 60.066 52.381 5.01 0.00 0.00 4.26
3345 3973 4.929479 ACATTCAGTTAACCATAGGCCAA 58.071 39.130 5.01 0.00 0.00 4.52
3404 4157 8.731275 AATATGAACAATCAGTAAATCGACCA 57.269 30.769 0.00 0.00 39.39 4.02
3462 4215 9.686683 ATACATGAAAAACAAGGAAGCTATACT 57.313 29.630 0.00 0.00 0.00 2.12
3465 4218 8.806146 ACAATACATGAAAAACAAGGAAGCTAT 58.194 29.630 0.00 0.00 0.00 2.97
3467 4220 6.925165 CACAATACATGAAAAACAAGGAAGCT 59.075 34.615 0.00 0.00 0.00 3.74
3468 4221 6.701400 ACACAATACATGAAAAACAAGGAAGC 59.299 34.615 0.00 0.00 0.00 3.86
3469 4222 7.306749 GCACACAATACATGAAAAACAAGGAAG 60.307 37.037 0.00 0.00 0.00 3.46
3470 4223 6.478344 GCACACAATACATGAAAAACAAGGAA 59.522 34.615 0.00 0.00 0.00 3.36
3471 4224 5.982516 GCACACAATACATGAAAAACAAGGA 59.017 36.000 0.00 0.00 0.00 3.36
3472 4225 5.984926 AGCACACAATACATGAAAAACAAGG 59.015 36.000 0.00 0.00 0.00 3.61
3473 4226 8.479280 GTTAGCACACAATACATGAAAAACAAG 58.521 33.333 0.00 0.00 0.00 3.16
3474 4227 8.194104 AGTTAGCACACAATACATGAAAAACAA 58.806 29.630 0.00 0.00 0.00 2.83
3475 4228 7.647318 CAGTTAGCACACAATACATGAAAAACA 59.353 33.333 0.00 0.00 0.00 2.83
3476 4229 7.647715 ACAGTTAGCACACAATACATGAAAAAC 59.352 33.333 0.00 0.00 0.00 2.43
3477 4230 7.711846 ACAGTTAGCACACAATACATGAAAAA 58.288 30.769 0.00 0.00 0.00 1.94
3478 4231 7.228507 AGACAGTTAGCACACAATACATGAAAA 59.771 33.333 0.00 0.00 0.00 2.29
3479 4232 6.710295 AGACAGTTAGCACACAATACATGAAA 59.290 34.615 0.00 0.00 0.00 2.69
3480 4233 6.230472 AGACAGTTAGCACACAATACATGAA 58.770 36.000 0.00 0.00 0.00 2.57
3481 4234 5.793817 AGACAGTTAGCACACAATACATGA 58.206 37.500 0.00 0.00 0.00 3.07
3482 4235 6.486253 AAGACAGTTAGCACACAATACATG 57.514 37.500 0.00 0.00 0.00 3.21
3483 4236 6.486657 ACAAAGACAGTTAGCACACAATACAT 59.513 34.615 0.00 0.00 0.00 2.29
3484 4237 5.820423 ACAAAGACAGTTAGCACACAATACA 59.180 36.000 0.00 0.00 0.00 2.29
3485 4238 6.018262 TCACAAAGACAGTTAGCACACAATAC 60.018 38.462 0.00 0.00 0.00 1.89
3486 4239 6.052360 TCACAAAGACAGTTAGCACACAATA 58.948 36.000 0.00 0.00 0.00 1.90
3487 4240 4.881273 TCACAAAGACAGTTAGCACACAAT 59.119 37.500 0.00 0.00 0.00 2.71
3488 4241 4.257731 TCACAAAGACAGTTAGCACACAA 58.742 39.130 0.00 0.00 0.00 3.33
3492 4245 2.224314 GGCTCACAAAGACAGTTAGCAC 59.776 50.000 0.00 0.00 37.82 4.40
3500 4253 3.010027 TCCATATTGGGCTCACAAAGACA 59.990 43.478 0.00 0.00 38.32 3.41
3570 4323 8.412608 ACATATTAGACATTTCAGTTCTGTCG 57.587 34.615 0.00 0.00 43.15 4.35
3595 4348 8.677148 AAAGCTGAGATGTAAACTGAAAACTA 57.323 30.769 0.00 0.00 0.00 2.24
3599 4352 9.950680 CTTAAAAAGCTGAGATGTAAACTGAAA 57.049 29.630 0.00 0.00 0.00 2.69
3613 4366 7.990917 TGTTGTCATGTAACTTAAAAAGCTGA 58.009 30.769 13.80 0.00 0.00 4.26
3620 4373 5.467399 CGGACCTGTTGTCATGTAACTTAAA 59.533 40.000 13.80 0.00 46.38 1.52
3622 4375 4.281435 TCGGACCTGTTGTCATGTAACTTA 59.719 41.667 13.80 0.00 46.38 2.24
3634 4387 6.677913 ACAGATTAAATTTTCGGACCTGTTG 58.322 36.000 0.00 0.00 0.00 3.33
3639 4392 8.265165 AGAAGTACAGATTAAATTTTCGGACC 57.735 34.615 0.00 0.00 0.00 4.46
3643 4396 9.959775 GAGTGAGAAGTACAGATTAAATTTTCG 57.040 33.333 0.00 0.00 0.00 3.46
3659 4412 4.323104 GCACTTAATGGGAGAGTGAGAAGT 60.323 45.833 6.89 0.00 42.54 3.01
3660 4413 4.187694 GCACTTAATGGGAGAGTGAGAAG 58.812 47.826 6.89 0.00 42.54 2.85
3661 4414 3.582647 TGCACTTAATGGGAGAGTGAGAA 59.417 43.478 6.89 0.00 42.54 2.87
3667 4420 5.240713 GTGATTTGCACTTAATGGGAGAG 57.759 43.478 0.00 0.00 44.27 3.20
3695 4459 1.474077 CCTGGTGCCTTTAACATGCTC 59.526 52.381 0.00 0.00 0.00 4.26
3696 4460 1.203050 ACCTGGTGCCTTTAACATGCT 60.203 47.619 0.00 0.00 0.00 3.79
3697 4461 1.256812 ACCTGGTGCCTTTAACATGC 58.743 50.000 0.00 0.00 0.00 4.06
3727 4491 9.613428 CATGAAGGAACCAGTAAACTATCATAA 57.387 33.333 0.00 0.00 0.00 1.90
3729 4493 7.554118 CACATGAAGGAACCAGTAAACTATCAT 59.446 37.037 0.00 0.00 0.00 2.45
3740 4504 2.038952 TCTGACCACATGAAGGAACCAG 59.961 50.000 14.40 15.31 0.00 4.00
3782 4546 7.124721 TGACATCCCATTCCAAAATATCAAGA 58.875 34.615 0.00 0.00 0.00 3.02
3786 4550 6.966534 ACTGACATCCCATTCCAAAATATC 57.033 37.500 0.00 0.00 0.00 1.63
3995 4760 1.148310 CTGCAACACAACCTCCTACG 58.852 55.000 0.00 0.00 0.00 3.51
4053 4826 6.751425 CACTTGACAATAAAGTGCAAAGAACA 59.249 34.615 3.60 0.00 45.68 3.18
4068 4841 2.089980 GCAGAGATGCCACTTGACAAT 58.910 47.619 0.00 0.00 0.00 2.71
4076 4849 1.466856 TTTGGATGCAGAGATGCCAC 58.533 50.000 0.00 0.00 0.00 5.01
4126 4899 2.029743 CCCACCACAACCTGAAACG 58.970 57.895 0.00 0.00 0.00 3.60
4298 5071 1.561076 CCTGGGTCATCAGAATGGTCA 59.439 52.381 0.00 0.00 36.93 4.02
4304 5077 1.274703 GGCTCCCTGGGTCATCAGAA 61.275 60.000 13.56 0.00 36.93 3.02
4337 5110 1.724654 GCATTGTTGAACGTGCTACCG 60.725 52.381 15.34 0.00 32.08 4.02
4584 5357 1.630126 GCTCCTCAGGCCTTCCATGA 61.630 60.000 0.00 0.00 33.74 3.07
4586 5359 1.210204 TTGCTCCTCAGGCCTTCCAT 61.210 55.000 0.00 0.00 33.74 3.41
4606 5379 5.126061 CAGGGCAAGACAATGCTACTTATTT 59.874 40.000 0.00 0.00 45.68 1.40
4619 5392 2.295909 GCAACATTAACAGGGCAAGACA 59.704 45.455 0.00 0.00 0.00 3.41
4796 5575 6.101150 TCCAGCCCTCTGAATAAATAAGCTAA 59.899 38.462 0.00 0.00 42.95 3.09
4851 5631 9.880157 CCAAAATGGATGTTGAATTTCTCTTAT 57.120 29.630 0.00 0.00 40.96 1.73
4852 5632 8.313292 CCCAAAATGGATGTTGAATTTCTCTTA 58.687 33.333 0.00 0.00 40.96 2.10
4855 5635 5.352293 GCCCAAAATGGATGTTGAATTTCTC 59.648 40.000 0.00 0.00 40.96 2.87
4898 5678 9.442033 GAATAACACGGTAATTAATAAAGCCAC 57.558 33.333 0.00 0.00 0.00 5.01
4906 5686 9.621629 TGGAATCTGAATAACACGGTAATTAAT 57.378 29.630 0.00 0.00 0.00 1.40
4909 5689 9.273016 CTATGGAATCTGAATAACACGGTAATT 57.727 33.333 0.00 0.00 0.00 1.40
5045 5829 2.727916 CGGCCGCAGTTGTTAAAGATTC 60.728 50.000 14.67 0.00 0.00 2.52
5051 5835 0.029567 CAAACGGCCGCAGTTGTTAA 59.970 50.000 28.58 0.00 31.43 2.01
5054 5838 2.331019 GAACAAACGGCCGCAGTTGT 62.331 55.000 27.45 27.45 31.43 3.32
5104 5888 4.628074 CCTTCCGTCTGAGAAGTTACAAA 58.372 43.478 6.08 0.00 39.29 2.83
5129 5913 5.707298 ACCCACTTATCTGAATGAACAACAG 59.293 40.000 0.00 0.00 0.00 3.16
5146 5930 2.025416 TGCTATGGCATGTTACCCACTT 60.025 45.455 10.98 0.00 44.28 3.16
5147 5931 1.563879 TGCTATGGCATGTTACCCACT 59.436 47.619 10.98 0.00 44.28 4.00
5306 6095 1.936436 GCCATCCAAGCATGCGTGAA 61.936 55.000 31.43 15.62 0.00 3.18
5348 6138 3.057876 TGGTAATTTTGCAGCTTACACCG 60.058 43.478 13.67 0.00 0.00 4.94
5362 6152 3.823873 TGAATCTGGCACGTTGGTAATTT 59.176 39.130 0.00 0.00 0.00 1.82
5413 6205 5.235186 AGCAAATCTTATGTGTGTCGCTATC 59.765 40.000 0.00 0.00 0.00 2.08
5420 6212 6.511767 GCGCTAATAGCAAATCTTATGTGTGT 60.512 38.462 13.15 0.00 42.58 3.72
5423 6215 5.075448 CGCGCTAATAGCAAATCTTATGTG 58.925 41.667 13.15 0.00 42.58 3.21
5426 6218 3.997021 AGCGCGCTAATAGCAAATCTTAT 59.003 39.130 35.79 0.63 42.58 1.73
5430 6222 3.999229 ATAGCGCGCTAATAGCAAATC 57.001 42.857 40.90 3.96 42.58 2.17
5434 6226 1.909376 GCTATAGCGCGCTAATAGCA 58.091 50.000 40.28 28.46 42.58 3.49


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

AutoCloner maintained by Alex Coulton.