Multiple sequence alignment - TraesCS4D01G313800

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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 TraesCS4D01G313800 chr4D 100.000 3578 0 0 1 3578 479677446 479673869 0.000000e+00 6608.0
1 TraesCS4D01G313800 chr4D 92.956 2030 84 39 339 2328 479639438 479637428 0.000000e+00 2902.0
2 TraesCS4D01G313800 chr4D 99.430 1579 9 0 972 2550 479637327 479635749 0.000000e+00 2867.0
3 TraesCS4D01G313800 chr4D 80.750 400 49 18 3182 3576 138277017 138276641 1.630000e-73 287.0
4 TraesCS4D01G313800 chr4B 94.751 2515 106 9 276 2777 606909872 606907371 0.000000e+00 3890.0
5 TraesCS4D01G313800 chr4B 93.797 1999 96 21 974 2950 606828487 606826495 0.000000e+00 2979.0
6 TraesCS4D01G313800 chr4B 94.526 1900 66 20 918 2783 606867795 606865900 0.000000e+00 2898.0
7 TraesCS4D01G313800 chr4B 91.178 2097 125 36 496 2550 606818971 606816893 0.000000e+00 2793.0
8 TraesCS4D01G313800 chr4B 97.337 338 9 0 2847 3184 606874399 606874062 3.100000e-160 575.0
9 TraesCS4D01G313800 chr4B 84.454 476 52 16 344 809 606869415 606868952 1.960000e-122 449.0
10 TraesCS4D01G313800 chr4B 97.942 243 4 1 2781 3023 606875389 606875148 1.540000e-113 420.0
11 TraesCS4D01G313800 chr4B 88.514 296 17 8 1 279 606910269 606909974 3.420000e-90 342.0
12 TraesCS4D01G313800 chr4B 93.396 106 7 0 2845 2950 606852266 606852161 1.330000e-34 158.0
13 TraesCS4D01G313800 chr4B 92.537 67 5 0 3014 3080 606874469 606874403 2.940000e-16 97.1
14 TraesCS4D01G313800 chr4A 91.274 2842 160 42 178 2976 686140926 686138130 0.000000e+00 3794.0
15 TraesCS4D01G313800 chr4A 91.567 2087 119 30 504 2550 685941526 685939457 0.000000e+00 2826.0
16 TraesCS4D01G313800 chr4A 92.813 1934 104 21 770 2675 686170408 686168482 0.000000e+00 2769.0
17 TraesCS4D01G313800 chr4A 81.333 525 56 24 209 715 686171217 686170717 4.330000e-104 388.0
18 TraesCS4D01G313800 chrUn 95.765 2007 54 21 972 2950 61732957 61730954 0.000000e+00 3206.0
19 TraesCS4D01G313800 chrUn 92.864 2032 85 41 336 2328 61735068 61733058 0.000000e+00 2894.0
20 TraesCS4D01G313800 chrUn 83.648 318 42 9 3182 3492 29468402 29468088 1.260000e-74 291.0
21 TraesCS4D01G313800 chr3D 82.885 409 51 9 3184 3578 46520803 46521206 2.040000e-92 350.0
22 TraesCS4D01G313800 chr5D 82.178 404 57 14 3184 3578 37894364 37894761 2.060000e-87 333.0
23 TraesCS4D01G313800 chr2D 81.955 399 51 15 3181 3566 145734682 145735072 5.760000e-83 318.0
24 TraesCS4D01G313800 chr2D 84.345 313 45 4 3184 3495 494648101 494647792 1.610000e-78 303.0
25 TraesCS4D01G313800 chr2D 81.301 246 33 10 3338 3575 422066341 422066581 1.700000e-43 187.0
26 TraesCS4D01G313800 chr7D 81.114 413 59 16 3178 3578 17255177 17254772 2.680000e-81 313.0
27 TraesCS4D01G313800 chr3B 82.031 384 53 14 3202 3577 242161279 242160904 2.680000e-81 313.0
28 TraesCS4D01G313800 chr3B 79.649 285 45 9 3218 3492 695507967 695507686 3.650000e-45 193.0
29 TraesCS4D01G313800 chr1B 83.143 350 47 11 3181 3526 45804293 45803952 3.470000e-80 309.0
30 TraesCS4D01G313800 chr7B 82.109 313 53 3 3181 3492 492753358 492753668 7.620000e-67 265.0
31 TraesCS4D01G313800 chr7A 78.261 437 57 21 3177 3578 245827046 245826613 2.760000e-61 246.0
32 TraesCS4D01G313800 chr2B 78.025 405 73 13 3184 3577 170421719 170421320 1.280000e-59 241.0
33 TraesCS4D01G313800 chr6B 77.830 212 31 11 3374 3577 635184126 635184329 2.260000e-22 117.0
34 TraesCS4D01G313800 chr1A 100.000 28 0 0 57 84 9237187 9237160 6.000000e-03 52.8


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 TraesCS4D01G313800 chr4D 479673869 479677446 3577 True 6608.000000 6608 100.000000 1 3578 1 chr4D.!!$R2 3577
1 TraesCS4D01G313800 chr4D 479635749 479639438 3689 True 2884.500000 2902 96.193000 339 2550 2 chr4D.!!$R3 2211
2 TraesCS4D01G313800 chr4B 606826495 606828487 1992 True 2979.000000 2979 93.797000 974 2950 1 chr4B.!!$R2 1976
3 TraesCS4D01G313800 chr4B 606816893 606818971 2078 True 2793.000000 2793 91.178000 496 2550 1 chr4B.!!$R1 2054
4 TraesCS4D01G313800 chr4B 606907371 606910269 2898 True 2116.000000 3890 91.632500 1 2777 2 chr4B.!!$R6 2776
5 TraesCS4D01G313800 chr4B 606865900 606869415 3515 True 1673.500000 2898 89.490000 344 2783 2 chr4B.!!$R4 2439
6 TraesCS4D01G313800 chr4B 606874062 606875389 1327 True 364.033333 575 95.938667 2781 3184 3 chr4B.!!$R5 403
7 TraesCS4D01G313800 chr4A 686138130 686140926 2796 True 3794.000000 3794 91.274000 178 2976 1 chr4A.!!$R2 2798
8 TraesCS4D01G313800 chr4A 685939457 685941526 2069 True 2826.000000 2826 91.567000 504 2550 1 chr4A.!!$R1 2046
9 TraesCS4D01G313800 chr4A 686168482 686171217 2735 True 1578.500000 2769 87.073000 209 2675 2 chr4A.!!$R3 2466
10 TraesCS4D01G313800 chrUn 61730954 61735068 4114 True 3050.000000 3206 94.314500 336 2950 2 chrUn.!!$R2 2614

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
970 2486 1.530293 CACAACAAGAGAGCAGCAGAC 59.47 52.381 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2740 5746 1.763545 GGGAGGGAAGACAGGTGATAC 59.236 57.143 0.0 0.0 0.0 2.24 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
27 28 9.926158 TGCTAAATGAAATCAATGTACAATTGT 57.074 25.926 16.68 16.68 0.00 2.71
37 38 8.662781 ATCAATGTACAATTGTTCGCTATAGT 57.337 30.769 17.78 0.00 0.00 2.12
41 42 5.579119 TGTACAATTGTTCGCTATAGTGTGG 59.421 40.000 17.78 0.00 0.00 4.17
53 54 2.579207 TAGTGTGGAGATAGCGTTGC 57.421 50.000 0.00 0.00 0.00 4.17
109 110 3.492102 AGGGTTGCGCTATTATGTCAT 57.508 42.857 9.73 0.00 0.00 3.06
186 203 8.918202 TTGTTCCTACATTTCTAGAACAATGT 57.082 30.769 20.96 20.96 44.18 2.71
194 211 7.651808 ACATTTCTAGAACAATGTGAACCAAG 58.348 34.615 17.98 0.00 41.18 3.61
262 281 5.421693 AGCCCTTGCATATGTATTTTGTTCA 59.578 36.000 4.29 0.00 41.13 3.18
263 282 6.098695 AGCCCTTGCATATGTATTTTGTTCAT 59.901 34.615 4.29 0.00 41.13 2.57
317 441 4.084900 GCAAGCTAGCAACAACAATTGAAC 60.085 41.667 18.83 0.00 0.00 3.18
319 443 6.437928 CAAGCTAGCAACAACAATTGAACTA 58.562 36.000 18.83 3.57 0.00 2.24
346 480 8.916628 TTATATTTGTATGCCTATGTCTGCAA 57.083 30.769 0.00 0.00 41.50 4.08
452 592 3.838244 TCTTCCTGCCATACCATGTAC 57.162 47.619 0.00 0.00 0.00 2.90
454 594 4.552674 TCTTCCTGCCATACCATGTACTA 58.447 43.478 0.00 0.00 0.00 1.82
455 595 4.588951 TCTTCCTGCCATACCATGTACTAG 59.411 45.833 0.00 0.00 0.00 2.57
457 597 4.295201 TCCTGCCATACCATGTACTAGTT 58.705 43.478 0.00 0.00 0.00 2.24
458 598 5.460416 TCCTGCCATACCATGTACTAGTTA 58.540 41.667 0.00 0.00 0.00 2.24
459 599 6.082031 TCCTGCCATACCATGTACTAGTTAT 58.918 40.000 0.00 0.00 0.00 1.89
460 600 7.243091 TCCTGCCATACCATGTACTAGTTATA 58.757 38.462 0.00 0.00 0.00 0.98
768 1203 2.368548 TGTAGCTCTCAAGGCAAGACAA 59.631 45.455 0.00 0.00 0.00 3.18
970 2486 1.530293 CACAACAAGAGAGCAGCAGAC 59.470 52.381 0.00 0.00 0.00 3.51
2730 5722 4.209307 TGGCCGTAACAGTGATTCAATA 57.791 40.909 0.00 0.00 0.00 1.90
2915 6873 6.528321 CAAGGAGCTCTATCATTGTATTCCA 58.472 40.000 14.64 0.00 36.49 3.53
3015 6973 6.069440 TCCTGGAAGATGATAGAAACCACAAT 60.069 38.462 0.00 0.00 34.07 2.71
3019 6977 9.699410 TGGAAGATGATAGAAACCACAATAAAT 57.301 29.630 0.00 0.00 0.00 1.40
3078 7036 8.814038 ATGGATGCCAATAGATTAATTCCTAC 57.186 34.615 0.00 0.00 36.95 3.18
3079 7037 7.754624 TGGATGCCAATAGATTAATTCCTACA 58.245 34.615 0.00 0.00 0.00 2.74
3111 7069 2.288948 TGCAACCATGTGATTTTCCTGC 60.289 45.455 0.00 0.00 0.00 4.85
3133 7091 6.521162 TGCATATATTTCTAAAGTCGGCTCA 58.479 36.000 0.00 0.00 0.00 4.26
3218 7176 4.702274 CCCCCAACAAGCCCCCAG 62.702 72.222 0.00 0.00 0.00 4.45
3219 7177 4.702274 CCCCAACAAGCCCCCAGG 62.702 72.222 0.00 0.00 0.00 4.45
3229 7187 3.927501 CCCCCAGGGCCCTTTTGT 61.928 66.667 26.10 0.00 35.35 2.83
3230 7188 2.553330 CCCCCAGGGCCCTTTTGTA 61.553 63.158 26.10 0.00 35.35 2.41
3231 7189 1.703461 CCCCAGGGCCCTTTTGTAT 59.297 57.895 26.10 0.00 0.00 2.29
3232 7190 0.397114 CCCCAGGGCCCTTTTGTATC 60.397 60.000 26.10 0.00 0.00 2.24
3233 7191 0.751643 CCCAGGGCCCTTTTGTATCG 60.752 60.000 26.10 8.25 0.00 2.92
3234 7192 1.384222 CCAGGGCCCTTTTGTATCGC 61.384 60.000 26.10 0.00 0.00 4.58
3235 7193 1.076995 AGGGCCCTTTTGTATCGCC 60.077 57.895 22.28 0.00 38.96 5.54
3236 7194 2.478033 GGGCCCTTTTGTATCGCCG 61.478 63.158 17.04 0.00 40.67 6.46
3237 7195 2.478033 GGCCCTTTTGTATCGCCGG 61.478 63.158 0.00 0.00 0.00 6.13
3238 7196 3.107447 CCCTTTTGTATCGCCGGC 58.893 61.111 19.07 19.07 0.00 6.13
3239 7197 2.707039 CCTTTTGTATCGCCGGCG 59.293 61.111 42.13 42.13 41.35 6.46
3240 7198 2.022762 CTTTTGTATCGCCGGCGC 59.977 61.111 42.78 29.19 39.59 6.53
3241 7199 2.742760 TTTTGTATCGCCGGCGCA 60.743 55.556 42.78 31.50 39.59 6.09
3242 7200 2.631696 CTTTTGTATCGCCGGCGCAG 62.632 60.000 42.78 23.18 39.59 5.18
3243 7201 3.650907 TTTGTATCGCCGGCGCAGA 62.651 57.895 42.78 27.69 39.59 4.26
3244 7202 3.650907 TTGTATCGCCGGCGCAGAA 62.651 57.895 42.78 31.32 39.59 3.02
3245 7203 2.888534 GTATCGCCGGCGCAGAAA 60.889 61.111 42.78 26.86 39.59 2.52
3246 7204 2.125472 TATCGCCGGCGCAGAAAA 60.125 55.556 42.78 26.04 39.59 2.29
3247 7205 1.742140 TATCGCCGGCGCAGAAAAA 60.742 52.632 42.78 25.23 39.59 1.94
3248 7206 1.092921 TATCGCCGGCGCAGAAAAAT 61.093 50.000 42.78 29.73 39.59 1.82
3249 7207 2.322999 ATCGCCGGCGCAGAAAAATC 62.323 55.000 42.78 0.00 39.59 2.17
3250 7208 2.576847 GCCGGCGCAGAAAAATCG 60.577 61.111 12.58 0.00 34.03 3.34
3251 7209 2.100216 CCGGCGCAGAAAAATCGG 59.900 61.111 10.83 6.37 0.00 4.18
3252 7210 2.576847 CGGCGCAGAAAAATCGGC 60.577 61.111 10.83 0.00 43.86 5.54
3253 7211 2.202610 GGCGCAGAAAAATCGGCC 60.203 61.111 10.83 0.00 41.93 6.13
3254 7212 2.202610 GCGCAGAAAAATCGGCCC 60.203 61.111 0.30 0.00 0.00 5.80
3255 7213 2.988688 GCGCAGAAAAATCGGCCCA 61.989 57.895 0.30 0.00 0.00 5.36
3256 7214 1.137404 CGCAGAAAAATCGGCCCAG 59.863 57.895 0.00 0.00 0.00 4.45
3257 7215 1.586154 CGCAGAAAAATCGGCCCAGT 61.586 55.000 0.00 0.00 0.00 4.00
3258 7216 0.171231 GCAGAAAAATCGGCCCAGTC 59.829 55.000 0.00 0.00 0.00 3.51
3259 7217 0.447801 CAGAAAAATCGGCCCAGTCG 59.552 55.000 0.00 0.00 0.00 4.18
3260 7218 1.136774 GAAAAATCGGCCCAGTCGC 59.863 57.895 0.00 0.00 0.00 5.19
3261 7219 2.577763 GAAAAATCGGCCCAGTCGCG 62.578 60.000 0.00 0.00 0.00 5.87
3270 7228 3.227276 CCAGTCGCGCCCCTAGAT 61.227 66.667 0.00 0.00 0.00 1.98
3271 7229 2.028190 CAGTCGCGCCCCTAGATG 59.972 66.667 0.00 0.00 0.00 2.90
3272 7230 3.917760 AGTCGCGCCCCTAGATGC 61.918 66.667 0.00 0.00 0.00 3.91
3273 7231 4.971125 GTCGCGCCCCTAGATGCC 62.971 72.222 0.00 0.00 0.00 4.40
3276 7234 3.958860 GCGCCCCTAGATGCCCAT 61.959 66.667 0.00 0.00 0.00 4.00
3277 7235 2.839098 CGCCCCTAGATGCCCATT 59.161 61.111 0.00 0.00 0.00 3.16
3278 7236 1.151450 CGCCCCTAGATGCCCATTT 59.849 57.895 0.00 0.00 0.00 2.32
3279 7237 0.468029 CGCCCCTAGATGCCCATTTT 60.468 55.000 0.00 0.00 0.00 1.82
3280 7238 1.793414 GCCCCTAGATGCCCATTTTT 58.207 50.000 0.00 0.00 0.00 1.94
3281 7239 1.688735 GCCCCTAGATGCCCATTTTTC 59.311 52.381 0.00 0.00 0.00 2.29
3282 7240 1.956477 CCCCTAGATGCCCATTTTTCG 59.044 52.381 0.00 0.00 0.00 3.46
3283 7241 1.338020 CCCTAGATGCCCATTTTTCGC 59.662 52.381 0.00 0.00 0.00 4.70
3284 7242 1.338020 CCTAGATGCCCATTTTTCGCC 59.662 52.381 0.00 0.00 0.00 5.54
3285 7243 1.002468 CTAGATGCCCATTTTTCGCCG 60.002 52.381 0.00 0.00 0.00 6.46
3286 7244 1.226945 GATGCCCATTTTTCGCCGG 60.227 57.895 0.00 0.00 0.00 6.13
3287 7245 1.944234 GATGCCCATTTTTCGCCGGT 61.944 55.000 1.90 0.00 0.00 5.28
3288 7246 1.540435 ATGCCCATTTTTCGCCGGTT 61.540 50.000 1.90 0.00 0.00 4.44
3289 7247 0.894184 TGCCCATTTTTCGCCGGTTA 60.894 50.000 1.90 0.00 0.00 2.85
3290 7248 0.179148 GCCCATTTTTCGCCGGTTAG 60.179 55.000 1.90 0.00 0.00 2.34
3291 7249 0.454196 CCCATTTTTCGCCGGTTAGG 59.546 55.000 1.90 0.00 44.97 2.69
3292 7250 0.454196 CCATTTTTCGCCGGTTAGGG 59.546 55.000 1.90 0.00 41.48 3.53
3302 7260 4.252983 GGTTAGGGCCGGATTTGG 57.747 61.111 5.05 0.00 0.00 3.28
3303 7261 1.305287 GGTTAGGGCCGGATTTGGT 59.695 57.895 5.05 0.00 0.00 3.67
3304 7262 1.035385 GGTTAGGGCCGGATTTGGTG 61.035 60.000 5.05 0.00 0.00 4.17
3305 7263 1.379309 TTAGGGCCGGATTTGGTGC 60.379 57.895 5.05 0.00 0.00 5.01
3306 7264 1.858739 TTAGGGCCGGATTTGGTGCT 61.859 55.000 5.05 0.00 0.00 4.40
3307 7265 2.550699 TAGGGCCGGATTTGGTGCTG 62.551 60.000 5.05 0.00 0.00 4.41
3308 7266 3.451894 GGCCGGATTTGGTGCTGG 61.452 66.667 5.05 0.00 0.00 4.85
3309 7267 4.133796 GCCGGATTTGGTGCTGGC 62.134 66.667 5.05 0.00 32.85 4.85
3310 7268 3.814268 CCGGATTTGGTGCTGGCG 61.814 66.667 0.00 0.00 0.00 5.69
3311 7269 3.814268 CGGATTTGGTGCTGGCGG 61.814 66.667 0.00 0.00 0.00 6.13
3312 7270 2.361104 GGATTTGGTGCTGGCGGA 60.361 61.111 0.00 0.00 0.00 5.54
3313 7271 2.700773 GGATTTGGTGCTGGCGGAC 61.701 63.158 0.00 0.00 0.00 4.79
3355 7313 4.796495 GGGCGCTCGGGGAAATGT 62.796 66.667 7.64 0.00 0.00 2.71
3356 7314 2.750237 GGCGCTCGGGGAAATGTT 60.750 61.111 7.64 0.00 0.00 2.71
3357 7315 2.340328 GGCGCTCGGGGAAATGTTT 61.340 57.895 7.64 0.00 0.00 2.83
3358 7316 1.584495 GCGCTCGGGGAAATGTTTT 59.416 52.632 0.00 0.00 0.00 2.43
3359 7317 0.038618 GCGCTCGGGGAAATGTTTTT 60.039 50.000 0.00 0.00 0.00 1.94
3360 7318 1.696988 CGCTCGGGGAAATGTTTTTG 58.303 50.000 0.00 0.00 0.00 2.44
3361 7319 1.668628 CGCTCGGGGAAATGTTTTTGG 60.669 52.381 0.00 0.00 0.00 3.28
3362 7320 1.939381 GCTCGGGGAAATGTTTTTGGC 60.939 52.381 0.00 0.00 0.00 4.52
3363 7321 0.315568 TCGGGGAAATGTTTTTGGCG 59.684 50.000 0.00 0.00 0.00 5.69
3364 7322 1.288419 CGGGGAAATGTTTTTGGCGC 61.288 55.000 0.00 0.00 0.00 6.53
3365 7323 1.288419 GGGGAAATGTTTTTGGCGCG 61.288 55.000 0.00 0.00 0.00 6.86
3366 7324 0.319125 GGGAAATGTTTTTGGCGCGA 60.319 50.000 12.10 0.00 0.00 5.87
3367 7325 1.492720 GGAAATGTTTTTGGCGCGAA 58.507 45.000 12.10 0.00 0.00 4.70
3368 7326 1.861575 GGAAATGTTTTTGGCGCGAAA 59.138 42.857 13.91 13.91 0.00 3.46
3369 7327 2.285488 GGAAATGTTTTTGGCGCGAAAA 59.715 40.909 23.88 23.88 0.00 2.29
3370 7328 3.276660 GAAATGTTTTTGGCGCGAAAAC 58.723 40.909 28.93 28.93 43.88 2.43
3371 7329 1.213491 ATGTTTTTGGCGCGAAAACC 58.787 45.000 30.72 24.80 43.31 3.27
3372 7330 0.173708 TGTTTTTGGCGCGAAAACCT 59.826 45.000 30.72 0.00 43.31 3.50
3373 7331 0.574922 GTTTTTGGCGCGAAAACCTG 59.425 50.000 26.79 0.00 40.11 4.00
3374 7332 0.528684 TTTTTGGCGCGAAAACCTGG 60.529 50.000 26.79 0.00 0.00 4.45
3375 7333 2.962697 TTTTGGCGCGAAAACCTGGC 62.963 55.000 23.88 0.00 0.00 4.85
3377 7335 4.404654 GGCGCGAAAACCTGGCAG 62.405 66.667 12.10 7.75 0.00 4.85
3378 7336 4.404654 GCGCGAAAACCTGGCAGG 62.405 66.667 31.62 31.62 42.49 4.85
3379 7337 4.404654 CGCGAAAACCTGGCAGGC 62.405 66.667 33.04 16.64 39.63 4.85
3380 7338 4.056125 GCGAAAACCTGGCAGGCC 62.056 66.667 33.04 17.90 39.63 5.19
3381 7339 3.373565 CGAAAACCTGGCAGGCCC 61.374 66.667 33.04 17.55 39.63 5.80
3382 7340 3.373565 GAAAACCTGGCAGGCCCG 61.374 66.667 33.04 10.29 39.63 6.13
3400 7358 4.003788 CCGAGTCAGCAACCGGGT 62.004 66.667 6.32 0.00 37.78 5.28
3401 7359 2.738521 CGAGTCAGCAACCGGGTG 60.739 66.667 17.47 17.47 46.38 4.61
3402 7360 3.050275 GAGTCAGCAACCGGGTGC 61.050 66.667 37.52 37.52 44.65 5.01
3408 7366 4.676586 GCAACCGGGTGCGTTTCG 62.677 66.667 31.79 0.00 34.21 3.46
3409 7367 3.273834 CAACCGGGTGCGTTTCGT 61.274 61.111 6.53 0.00 0.00 3.85
3410 7368 2.968697 AACCGGGTGCGTTTCGTC 60.969 61.111 6.32 0.00 0.00 4.20
3411 7369 3.450043 AACCGGGTGCGTTTCGTCT 62.450 57.895 6.32 0.00 0.00 4.18
3412 7370 2.086251 AACCGGGTGCGTTTCGTCTA 62.086 55.000 6.32 0.00 0.00 2.59
3413 7371 2.090524 CCGGGTGCGTTTCGTCTAC 61.091 63.158 0.00 0.00 0.00 2.59
3414 7372 2.090524 CGGGTGCGTTTCGTCTACC 61.091 63.158 0.00 0.00 0.00 3.18
3415 7373 1.291272 GGGTGCGTTTCGTCTACCT 59.709 57.895 0.00 0.00 0.00 3.08
3416 7374 0.735287 GGGTGCGTTTCGTCTACCTC 60.735 60.000 0.00 0.00 0.00 3.85
3417 7375 0.038892 GGTGCGTTTCGTCTACCTCA 60.039 55.000 0.00 0.00 0.00 3.86
3418 7376 1.403780 GGTGCGTTTCGTCTACCTCAT 60.404 52.381 0.00 0.00 0.00 2.90
3419 7377 1.654105 GTGCGTTTCGTCTACCTCATG 59.346 52.381 0.00 0.00 0.00 3.07
3420 7378 1.278238 GCGTTTCGTCTACCTCATGG 58.722 55.000 0.00 0.00 39.83 3.66
3421 7379 1.278238 CGTTTCGTCTACCTCATGGC 58.722 55.000 0.00 0.00 36.63 4.40
3422 7380 1.653151 GTTTCGTCTACCTCATGGCC 58.347 55.000 0.00 0.00 36.63 5.36
3423 7381 1.207329 GTTTCGTCTACCTCATGGCCT 59.793 52.381 3.32 0.00 36.63 5.19
3424 7382 1.112113 TTCGTCTACCTCATGGCCTC 58.888 55.000 3.32 0.00 36.63 4.70
3425 7383 1.101635 TCGTCTACCTCATGGCCTCG 61.102 60.000 3.32 0.00 36.63 4.63
3426 7384 1.742768 GTCTACCTCATGGCCTCGG 59.257 63.158 3.32 1.07 36.63 4.63
3427 7385 1.043673 GTCTACCTCATGGCCTCGGT 61.044 60.000 3.32 7.67 36.63 4.69
3428 7386 0.325296 TCTACCTCATGGCCTCGGTT 60.325 55.000 3.32 0.00 36.63 4.44
3429 7387 0.541863 CTACCTCATGGCCTCGGTTT 59.458 55.000 3.32 0.00 36.63 3.27
3430 7388 0.539986 TACCTCATGGCCTCGGTTTC 59.460 55.000 3.32 0.00 36.63 2.78
3431 7389 1.452108 CCTCATGGCCTCGGTTTCC 60.452 63.158 3.32 0.00 0.00 3.13
3432 7390 1.604378 CTCATGGCCTCGGTTTCCT 59.396 57.895 3.32 0.00 0.00 3.36
3433 7391 0.745845 CTCATGGCCTCGGTTTCCTG 60.746 60.000 3.32 0.00 0.00 3.86
3434 7392 2.044946 ATGGCCTCGGTTTCCTGC 60.045 61.111 3.32 0.00 0.00 4.85
3435 7393 3.976701 ATGGCCTCGGTTTCCTGCG 62.977 63.158 3.32 0.00 0.00 5.18
3438 7396 4.778143 CCTCGGTTTCCTGCGGGG 62.778 72.222 12.87 0.00 0.00 5.73
3439 7397 3.702048 CTCGGTTTCCTGCGGGGA 61.702 66.667 12.87 0.00 43.41 4.81
3448 7406 0.472471 TCCTGCGGGGAATCAATACC 59.528 55.000 12.87 0.00 41.91 2.73
3449 7407 0.182537 CCTGCGGGGAATCAATACCA 59.817 55.000 2.57 0.00 37.23 3.25
3450 7408 1.409521 CCTGCGGGGAATCAATACCAA 60.410 52.381 2.57 0.00 37.23 3.67
3451 7409 1.949525 CTGCGGGGAATCAATACCAAG 59.050 52.381 0.00 0.00 0.00 3.61
3452 7410 1.318576 GCGGGGAATCAATACCAAGG 58.681 55.000 0.00 0.00 0.00 3.61
3453 7411 1.318576 CGGGGAATCAATACCAAGGC 58.681 55.000 0.00 0.00 0.00 4.35
3454 7412 1.133792 CGGGGAATCAATACCAAGGCT 60.134 52.381 0.00 0.00 0.00 4.58
3455 7413 2.310538 GGGGAATCAATACCAAGGCTG 58.689 52.381 0.00 0.00 0.00 4.85
3456 7414 1.683385 GGGAATCAATACCAAGGCTGC 59.317 52.381 0.00 0.00 0.00 5.25
3457 7415 1.334869 GGAATCAATACCAAGGCTGCG 59.665 52.381 0.00 0.00 0.00 5.18
3458 7416 0.740737 AATCAATACCAAGGCTGCGC 59.259 50.000 0.00 0.00 0.00 6.09
3470 7428 3.123620 CTGCGCCAGTCAGCCTTC 61.124 66.667 4.18 0.00 0.00 3.46
3471 7429 4.704833 TGCGCCAGTCAGCCTTCC 62.705 66.667 4.18 0.00 0.00 3.46
3472 7430 4.704833 GCGCCAGTCAGCCTTCCA 62.705 66.667 0.00 0.00 0.00 3.53
3473 7431 2.270205 CGCCAGTCAGCCTTCCAT 59.730 61.111 0.00 0.00 0.00 3.41
3474 7432 1.377725 CGCCAGTCAGCCTTCCATT 60.378 57.895 0.00 0.00 0.00 3.16
3475 7433 1.651240 CGCCAGTCAGCCTTCCATTG 61.651 60.000 0.00 0.00 0.00 2.82
3476 7434 0.322816 GCCAGTCAGCCTTCCATTGA 60.323 55.000 0.00 0.00 0.00 2.57
3477 7435 1.684248 GCCAGTCAGCCTTCCATTGAT 60.684 52.381 0.00 0.00 0.00 2.57
3478 7436 2.731572 CCAGTCAGCCTTCCATTGATT 58.268 47.619 0.00 0.00 0.00 2.57
3479 7437 2.686915 CCAGTCAGCCTTCCATTGATTC 59.313 50.000 0.00 0.00 0.00 2.52
3480 7438 2.686915 CAGTCAGCCTTCCATTGATTCC 59.313 50.000 0.00 0.00 0.00 3.01
3481 7439 2.579860 AGTCAGCCTTCCATTGATTCCT 59.420 45.455 0.00 0.00 0.00 3.36
3482 7440 2.948315 GTCAGCCTTCCATTGATTCCTC 59.052 50.000 0.00 0.00 0.00 3.71
3483 7441 2.577563 TCAGCCTTCCATTGATTCCTCA 59.422 45.455 0.00 0.00 0.00 3.86
3484 7442 2.686915 CAGCCTTCCATTGATTCCTCAC 59.313 50.000 0.00 0.00 0.00 3.51
3485 7443 1.672881 GCCTTCCATTGATTCCTCACG 59.327 52.381 0.00 0.00 0.00 4.35
3486 7444 2.292267 CCTTCCATTGATTCCTCACGG 58.708 52.381 0.00 0.00 0.00 4.94
3487 7445 2.292267 CTTCCATTGATTCCTCACGGG 58.708 52.381 0.00 0.00 0.00 5.28
3488 7446 0.107214 TCCATTGATTCCTCACGGGC 60.107 55.000 0.00 0.00 34.39 6.13
3489 7447 1.439353 CCATTGATTCCTCACGGGCG 61.439 60.000 0.00 0.00 34.39 6.13
3490 7448 1.153168 ATTGATTCCTCACGGGCGG 60.153 57.895 0.00 0.00 34.39 6.13
3491 7449 3.969250 TTGATTCCTCACGGGCGGC 62.969 63.158 0.00 0.00 34.39 6.53
3492 7450 4.467084 GATTCCTCACGGGCGGCA 62.467 66.667 12.47 0.00 34.39 5.69
3493 7451 4.778143 ATTCCTCACGGGCGGCAC 62.778 66.667 12.47 0.00 34.39 5.01
3506 7464 4.373116 GGCACAACGGAGAGGCGA 62.373 66.667 0.00 0.00 0.00 5.54
3507 7465 3.112709 GCACAACGGAGAGGCGAC 61.113 66.667 0.00 0.00 0.00 5.19
3508 7466 2.805353 CACAACGGAGAGGCGACG 60.805 66.667 0.00 0.00 0.00 5.12
3509 7467 4.719369 ACAACGGAGAGGCGACGC 62.719 66.667 12.43 12.43 0.00 5.19
3535 7493 3.467119 CGTACACACGTCTGCCGC 61.467 66.667 0.00 0.00 43.31 6.53
3536 7494 2.049433 GTACACACGTCTGCCGCT 60.049 61.111 0.00 0.00 41.42 5.52
3537 7495 2.087009 GTACACACGTCTGCCGCTC 61.087 63.158 0.00 0.00 41.42 5.03
3538 7496 3.277211 TACACACGTCTGCCGCTCC 62.277 63.158 0.00 0.00 41.42 4.70
3551 7509 3.622826 GCTCCCCCGCCGCTATAA 61.623 66.667 0.00 0.00 0.00 0.98
3552 7510 3.144285 CTCCCCCGCCGCTATAAA 58.856 61.111 0.00 0.00 0.00 1.40
3553 7511 1.448497 CTCCCCCGCCGCTATAAAA 59.552 57.895 0.00 0.00 0.00 1.52
3554 7512 0.602905 CTCCCCCGCCGCTATAAAAG 60.603 60.000 0.00 0.00 0.00 2.27
3562 7520 4.900815 GCTATAAAAGCCGCCCCT 57.099 55.556 0.00 0.00 46.25 4.79
3563 7521 2.630214 GCTATAAAAGCCGCCCCTC 58.370 57.895 0.00 0.00 46.25 4.30
3564 7522 0.889638 GCTATAAAAGCCGCCCCTCC 60.890 60.000 0.00 0.00 46.25 4.30
3565 7523 0.250770 CTATAAAAGCCGCCCCTCCC 60.251 60.000 0.00 0.00 0.00 4.30
3566 7524 0.696485 TATAAAAGCCGCCCCTCCCT 60.696 55.000 0.00 0.00 0.00 4.20
3567 7525 1.996070 ATAAAAGCCGCCCCTCCCTC 61.996 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.768130 GCTATCTCCACACTATAGCGAA 57.232 45.455 0.00 0.00 38.89 4.70
37 38 0.613260 AAGGCAACGCTATCTCCACA 59.387 50.000 0.00 0.00 46.39 4.17
41 42 1.132588 CGCTAAGGCAACGCTATCTC 58.867 55.000 0.00 0.00 46.39 2.75
53 54 2.177977 CGAAGCTATATCGCGCTAAGG 58.822 52.381 5.56 0.00 34.96 2.69
159 176 7.979444 TTGTTCTAGAAATGTAGGAACAAGG 57.021 36.000 6.78 0.00 45.60 3.61
163 180 8.547967 TCACATTGTTCTAGAAATGTAGGAAC 57.452 34.615 18.17 1.35 43.41 3.62
186 203 1.422531 AAAAGGCCATGCTTGGTTCA 58.577 45.000 19.05 0.00 45.57 3.18
194 211 5.323371 TCTGTTACATAAAAAGGCCATGC 57.677 39.130 5.01 0.00 0.00 4.06
199 216 6.509418 TGGTCATCTGTTACATAAAAAGGC 57.491 37.500 0.00 0.00 0.00 4.35
298 422 7.873739 AATTAGTTCAATTGTTGTTGCTAGC 57.126 32.000 8.10 8.10 35.46 3.42
319 443 9.519191 TGCAGACATAGGCATACAAATATAATT 57.481 29.630 0.00 0.00 34.58 1.40
346 480 3.589951 AATGGATGCAATGCTAGGTCT 57.410 42.857 6.82 0.00 34.76 3.85
418 558 1.079658 AGGAAGAAGGTAGGCACTCCT 59.920 52.381 0.00 0.00 46.57 3.69
459 599 9.261035 AGAGATGGAGTTAATTTGTTCTCTCTA 57.739 33.333 0.00 0.00 35.05 2.43
460 600 8.040132 CAGAGATGGAGTTAATTTGTTCTCTCT 58.960 37.037 0.00 0.00 37.25 3.10
768 1203 7.493320 TCTTACAAAAATATACGCGGAGTCAAT 59.507 33.333 12.47 0.00 0.00 2.57
970 2486 3.548268 GGCGATCTCTCAACTAAACTTCG 59.452 47.826 0.00 0.00 0.00 3.79
2740 5746 1.763545 GGGAGGGAAGACAGGTGATAC 59.236 57.143 0.00 0.00 0.00 2.24
2751 5757 2.603075 TGGAAACAATGGGAGGGAAG 57.397 50.000 0.00 0.00 37.44 3.46
2777 5783 8.532186 TGGTATGTATTAAAGCCATCAATTGT 57.468 30.769 5.13 0.00 0.00 2.71
3078 7036 3.568430 ACATGGTTGCATCATAGATGCTG 59.432 43.478 26.44 19.57 44.79 4.41
3079 7037 3.568430 CACATGGTTGCATCATAGATGCT 59.432 43.478 26.44 8.72 44.79 3.79
3111 7069 8.594881 AACTGAGCCGACTTTAGAAATATATG 57.405 34.615 0.00 0.00 0.00 1.78
3180 7138 0.878086 GCGGCTGGAGATGCTCTTAC 60.878 60.000 0.00 0.00 0.00 2.34
3201 7159 4.702274 CTGGGGGCTTGTTGGGGG 62.702 72.222 0.00 0.00 0.00 5.40
3202 7160 4.702274 CCTGGGGGCTTGTTGGGG 62.702 72.222 0.00 0.00 0.00 4.96
3203 7161 4.702274 CCCTGGGGGCTTGTTGGG 62.702 72.222 4.27 0.00 35.35 4.12
3213 7171 0.397114 GATACAAAAGGGCCCTGGGG 60.397 60.000 29.50 20.02 38.57 4.96
3214 7172 0.751643 CGATACAAAAGGGCCCTGGG 60.752 60.000 29.50 20.42 0.00 4.45
3215 7173 1.384222 GCGATACAAAAGGGCCCTGG 61.384 60.000 29.50 20.82 0.00 4.45
3216 7174 1.384222 GGCGATACAAAAGGGCCCTG 61.384 60.000 29.50 17.53 37.82 4.45
3217 7175 1.076995 GGCGATACAAAAGGGCCCT 60.077 57.895 22.28 22.28 37.82 5.19
3218 7176 2.478033 CGGCGATACAAAAGGGCCC 61.478 63.158 16.46 16.46 40.67 5.80
3219 7177 2.478033 CCGGCGATACAAAAGGGCC 61.478 63.158 9.30 0.00 40.36 5.80
3220 7178 3.107447 CCGGCGATACAAAAGGGC 58.893 61.111 9.30 0.00 0.00 5.19
3221 7179 2.819552 CGCCGGCGATACAAAAGGG 61.820 63.158 44.86 9.41 42.83 3.95
3222 7180 2.707039 CGCCGGCGATACAAAAGG 59.293 61.111 44.86 10.04 42.83 3.11
3232 7190 2.576847 GATTTTTCTGCGCCGGCG 60.577 61.111 43.13 43.13 44.10 6.46
3233 7191 2.576847 CGATTTTTCTGCGCCGGC 60.577 61.111 19.07 19.07 40.52 6.13
3234 7192 2.100216 CCGATTTTTCTGCGCCGG 59.900 61.111 4.18 3.58 0.00 6.13
3235 7193 2.576847 GCCGATTTTTCTGCGCCG 60.577 61.111 4.18 0.00 0.00 6.46
3236 7194 2.202610 GGCCGATTTTTCTGCGCC 60.203 61.111 4.18 0.00 0.00 6.53
3237 7195 2.202610 GGGCCGATTTTTCTGCGC 60.203 61.111 0.00 0.00 0.00 6.09
3238 7196 1.137404 CTGGGCCGATTTTTCTGCG 59.863 57.895 0.00 0.00 0.00 5.18
3239 7197 0.171231 GACTGGGCCGATTTTTCTGC 59.829 55.000 0.00 0.00 0.00 4.26
3240 7198 0.447801 CGACTGGGCCGATTTTTCTG 59.552 55.000 0.00 0.00 0.00 3.02
3241 7199 1.305930 GCGACTGGGCCGATTTTTCT 61.306 55.000 0.00 0.00 0.00 2.52
3242 7200 1.136774 GCGACTGGGCCGATTTTTC 59.863 57.895 0.00 0.00 0.00 2.29
3243 7201 2.686816 CGCGACTGGGCCGATTTTT 61.687 57.895 0.00 0.00 0.00 1.94
3244 7202 3.124921 CGCGACTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
3253 7211 3.227276 ATCTAGGGGCGCGACTGG 61.227 66.667 13.91 7.45 0.00 4.00
3254 7212 2.028190 CATCTAGGGGCGCGACTG 59.972 66.667 13.91 0.00 0.00 3.51
3255 7213 3.917760 GCATCTAGGGGCGCGACT 61.918 66.667 13.91 7.87 0.00 4.18
3256 7214 4.971125 GGCATCTAGGGGCGCGAC 62.971 72.222 12.10 6.99 0.00 5.19
3259 7217 2.983725 AAATGGGCATCTAGGGGCGC 62.984 60.000 0.00 0.00 42.61 6.53
3260 7218 0.468029 AAAATGGGCATCTAGGGGCG 60.468 55.000 0.00 0.00 0.00 6.13
3261 7219 1.688735 GAAAAATGGGCATCTAGGGGC 59.311 52.381 0.00 0.00 0.00 5.80
3262 7220 1.956477 CGAAAAATGGGCATCTAGGGG 59.044 52.381 0.00 0.00 0.00 4.79
3263 7221 1.338020 GCGAAAAATGGGCATCTAGGG 59.662 52.381 0.00 0.00 0.00 3.53
3264 7222 1.338020 GGCGAAAAATGGGCATCTAGG 59.662 52.381 0.00 0.00 0.00 3.02
3265 7223 1.002468 CGGCGAAAAATGGGCATCTAG 60.002 52.381 0.00 0.00 0.00 2.43
3266 7224 1.021202 CGGCGAAAAATGGGCATCTA 58.979 50.000 0.00 0.00 0.00 1.98
3267 7225 1.666209 CCGGCGAAAAATGGGCATCT 61.666 55.000 9.30 0.00 0.00 2.90
3268 7226 1.226945 CCGGCGAAAAATGGGCATC 60.227 57.895 9.30 0.00 0.00 3.91
3269 7227 1.540435 AACCGGCGAAAAATGGGCAT 61.540 50.000 9.30 0.00 0.00 4.40
3270 7228 0.894184 TAACCGGCGAAAAATGGGCA 60.894 50.000 9.30 0.00 0.00 5.36
3271 7229 0.179148 CTAACCGGCGAAAAATGGGC 60.179 55.000 9.30 0.00 0.00 5.36
3272 7230 0.454196 CCTAACCGGCGAAAAATGGG 59.546 55.000 9.30 0.00 0.00 4.00
3273 7231 0.454196 CCCTAACCGGCGAAAAATGG 59.546 55.000 9.30 2.42 0.00 3.16
3274 7232 0.179148 GCCCTAACCGGCGAAAAATG 60.179 55.000 9.30 0.00 39.64 2.32
3275 7233 2.186155 GCCCTAACCGGCGAAAAAT 58.814 52.632 9.30 0.00 39.64 1.82
3276 7234 3.670989 GCCCTAACCGGCGAAAAA 58.329 55.556 9.30 0.00 39.64 1.94
3285 7243 1.035385 CACCAAATCCGGCCCTAACC 61.035 60.000 0.00 0.00 0.00 2.85
3286 7244 1.663379 GCACCAAATCCGGCCCTAAC 61.663 60.000 0.00 0.00 0.00 2.34
3287 7245 1.379309 GCACCAAATCCGGCCCTAA 60.379 57.895 0.00 0.00 0.00 2.69
3288 7246 2.274104 GCACCAAATCCGGCCCTA 59.726 61.111 0.00 0.00 0.00 3.53
3289 7247 3.661648 AGCACCAAATCCGGCCCT 61.662 61.111 0.00 0.00 0.00 5.19
3290 7248 3.451894 CAGCACCAAATCCGGCCC 61.452 66.667 0.00 0.00 0.00 5.80
3291 7249 3.451894 CCAGCACCAAATCCGGCC 61.452 66.667 0.00 0.00 0.00 6.13
3292 7250 4.133796 GCCAGCACCAAATCCGGC 62.134 66.667 0.00 0.00 0.00 6.13
3293 7251 3.814268 CGCCAGCACCAAATCCGG 61.814 66.667 0.00 0.00 0.00 5.14
3294 7252 3.814268 CCGCCAGCACCAAATCCG 61.814 66.667 0.00 0.00 0.00 4.18
3295 7253 2.361104 TCCGCCAGCACCAAATCC 60.361 61.111 0.00 0.00 0.00 3.01
3296 7254 2.700773 GGTCCGCCAGCACCAAATC 61.701 63.158 0.00 0.00 32.33 2.17
3297 7255 2.676471 GGTCCGCCAGCACCAAAT 60.676 61.111 0.00 0.00 32.33 2.32
3298 7256 4.966787 GGGTCCGCCAGCACCAAA 62.967 66.667 2.03 0.00 33.91 3.28
3338 7296 4.796495 ACATTTCCCCGAGCGCCC 62.796 66.667 2.29 0.00 0.00 6.13
3339 7297 1.873270 AAAACATTTCCCCGAGCGCC 61.873 55.000 2.29 0.00 0.00 6.53
3340 7298 0.038618 AAAAACATTTCCCCGAGCGC 60.039 50.000 0.00 0.00 0.00 5.92
3341 7299 1.668628 CCAAAAACATTTCCCCGAGCG 60.669 52.381 0.00 0.00 0.00 5.03
3342 7300 1.939381 GCCAAAAACATTTCCCCGAGC 60.939 52.381 0.00 0.00 0.00 5.03
3343 7301 1.668628 CGCCAAAAACATTTCCCCGAG 60.669 52.381 0.00 0.00 0.00 4.63
3344 7302 0.315568 CGCCAAAAACATTTCCCCGA 59.684 50.000 0.00 0.00 0.00 5.14
3345 7303 1.288419 GCGCCAAAAACATTTCCCCG 61.288 55.000 0.00 0.00 0.00 5.73
3346 7304 1.288419 CGCGCCAAAAACATTTCCCC 61.288 55.000 0.00 0.00 0.00 4.81
3347 7305 0.319125 TCGCGCCAAAAACATTTCCC 60.319 50.000 0.00 0.00 0.00 3.97
3348 7306 1.492720 TTCGCGCCAAAAACATTTCC 58.507 45.000 0.00 0.00 0.00 3.13
3349 7307 3.276660 GTTTTCGCGCCAAAAACATTTC 58.723 40.909 27.68 9.66 43.08 2.17
3350 7308 2.031068 GGTTTTCGCGCCAAAAACATTT 59.969 40.909 30.74 0.00 44.58 2.32
3351 7309 1.595328 GGTTTTCGCGCCAAAAACATT 59.405 42.857 30.74 0.00 44.58 2.71
3352 7310 1.202475 AGGTTTTCGCGCCAAAAACAT 60.202 42.857 30.74 26.03 44.58 2.71
3353 7311 0.173708 AGGTTTTCGCGCCAAAAACA 59.826 45.000 30.74 7.08 44.58 2.83
3354 7312 0.574922 CAGGTTTTCGCGCCAAAAAC 59.425 50.000 25.99 25.99 42.93 2.43
3355 7313 0.528684 CCAGGTTTTCGCGCCAAAAA 60.529 50.000 14.53 12.23 0.00 1.94
3356 7314 1.066587 CCAGGTTTTCGCGCCAAAA 59.933 52.632 8.92 8.92 0.00 2.44
3357 7315 2.725008 CCAGGTTTTCGCGCCAAA 59.275 55.556 0.00 0.00 0.00 3.28
3358 7316 3.972276 GCCAGGTTTTCGCGCCAA 61.972 61.111 0.00 0.00 0.00 4.52
3360 7318 4.404654 CTGCCAGGTTTTCGCGCC 62.405 66.667 0.00 0.00 0.00 6.53
3361 7319 4.404654 CCTGCCAGGTTTTCGCGC 62.405 66.667 1.39 0.00 0.00 6.86
3362 7320 4.404654 GCCTGCCAGGTTTTCGCG 62.405 66.667 13.35 0.00 37.80 5.87
3363 7321 4.056125 GGCCTGCCAGGTTTTCGC 62.056 66.667 13.35 0.00 37.80 4.70
3364 7322 3.373565 GGGCCTGCCAGGTTTTCG 61.374 66.667 13.35 0.00 37.80 3.46
3365 7323 3.373565 CGGGCCTGCCAGGTTTTC 61.374 66.667 13.35 0.00 37.80 2.29
3383 7341 4.003788 ACCCGGTTGCTGACTCGG 62.004 66.667 0.00 11.04 39.97 4.63
3384 7342 2.738521 CACCCGGTTGCTGACTCG 60.739 66.667 0.00 0.00 0.00 4.18
3385 7343 3.050275 GCACCCGGTTGCTGACTC 61.050 66.667 17.89 0.00 39.59 3.36
3386 7344 4.988598 CGCACCCGGTTGCTGACT 62.989 66.667 22.45 0.00 40.62 3.41
3388 7346 4.555709 AACGCACCCGGTTGCTGA 62.556 61.111 22.45 0.00 40.62 4.26
3389 7347 3.536498 GAAACGCACCCGGTTGCTG 62.536 63.158 22.45 17.01 45.89 4.41
3390 7348 3.284449 GAAACGCACCCGGTTGCT 61.284 61.111 22.45 2.68 45.89 3.91
3391 7349 4.676586 CGAAACGCACCCGGTTGC 62.677 66.667 14.99 14.99 45.89 4.17
3392 7350 3.231324 GACGAAACGCACCCGGTTG 62.231 63.158 0.00 0.00 45.89 3.77
3394 7352 2.563798 TAGACGAAACGCACCCGGT 61.564 57.895 0.00 0.00 39.22 5.28
3395 7353 2.090524 GTAGACGAAACGCACCCGG 61.091 63.158 0.00 0.00 39.22 5.73
3396 7354 2.090524 GGTAGACGAAACGCACCCG 61.091 63.158 0.00 0.00 41.14 5.28
3397 7355 0.735287 GAGGTAGACGAAACGCACCC 60.735 60.000 0.00 0.00 0.00 4.61
3398 7356 0.038892 TGAGGTAGACGAAACGCACC 60.039 55.000 0.00 0.00 0.00 5.01
3399 7357 1.654105 CATGAGGTAGACGAAACGCAC 59.346 52.381 0.00 0.00 0.00 5.34
3400 7358 1.403647 CCATGAGGTAGACGAAACGCA 60.404 52.381 0.00 0.00 0.00 5.24
3401 7359 1.278238 CCATGAGGTAGACGAAACGC 58.722 55.000 0.00 0.00 0.00 4.84
3402 7360 1.278238 GCCATGAGGTAGACGAAACG 58.722 55.000 0.00 0.00 37.19 3.60
3403 7361 1.207329 AGGCCATGAGGTAGACGAAAC 59.793 52.381 5.01 0.00 37.19 2.78
3404 7362 1.480954 GAGGCCATGAGGTAGACGAAA 59.519 52.381 5.01 0.00 37.19 3.46
3405 7363 1.112113 GAGGCCATGAGGTAGACGAA 58.888 55.000 5.01 0.00 37.19 3.85
3406 7364 1.101635 CGAGGCCATGAGGTAGACGA 61.102 60.000 5.01 0.00 37.19 4.20
3407 7365 1.360551 CGAGGCCATGAGGTAGACG 59.639 63.158 5.01 0.00 37.19 4.18
3408 7366 1.043673 ACCGAGGCCATGAGGTAGAC 61.044 60.000 5.01 0.00 34.83 2.59
3409 7367 0.325296 AACCGAGGCCATGAGGTAGA 60.325 55.000 5.01 0.00 35.68 2.59
3410 7368 0.541863 AAACCGAGGCCATGAGGTAG 59.458 55.000 5.01 0.00 35.68 3.18
3411 7369 0.539986 GAAACCGAGGCCATGAGGTA 59.460 55.000 5.01 0.00 35.68 3.08
3412 7370 1.299976 GAAACCGAGGCCATGAGGT 59.700 57.895 5.01 5.47 38.88 3.85
3413 7371 1.452108 GGAAACCGAGGCCATGAGG 60.452 63.158 5.01 4.72 38.23 3.86
3414 7372 0.745845 CAGGAAACCGAGGCCATGAG 60.746 60.000 5.01 0.00 0.00 2.90
3415 7373 1.299648 CAGGAAACCGAGGCCATGA 59.700 57.895 5.01 0.00 0.00 3.07
3416 7374 2.409870 GCAGGAAACCGAGGCCATG 61.410 63.158 5.01 0.00 0.00 3.66
3417 7375 2.044946 GCAGGAAACCGAGGCCAT 60.045 61.111 5.01 0.00 0.00 4.40
3418 7376 4.697756 CGCAGGAAACCGAGGCCA 62.698 66.667 5.01 0.00 0.00 5.36
3431 7389 1.949525 CTTGGTATTGATTCCCCGCAG 59.050 52.381 0.00 0.00 0.00 5.18
3432 7390 1.409521 CCTTGGTATTGATTCCCCGCA 60.410 52.381 0.00 0.00 0.00 5.69
3433 7391 1.318576 CCTTGGTATTGATTCCCCGC 58.681 55.000 0.00 0.00 0.00 6.13
3434 7392 1.133792 AGCCTTGGTATTGATTCCCCG 60.134 52.381 0.00 0.00 0.00 5.73
3435 7393 2.310538 CAGCCTTGGTATTGATTCCCC 58.689 52.381 0.00 0.00 0.00 4.81
3436 7394 1.683385 GCAGCCTTGGTATTGATTCCC 59.317 52.381 0.00 0.00 0.00 3.97
3437 7395 1.334869 CGCAGCCTTGGTATTGATTCC 59.665 52.381 0.00 0.00 0.00 3.01
3438 7396 2.763249 CGCAGCCTTGGTATTGATTC 57.237 50.000 0.00 0.00 0.00 2.52
3453 7411 3.123620 GAAGGCTGACTGGCGCAG 61.124 66.667 10.83 7.58 46.88 5.18
3454 7412 4.704833 GGAAGGCTGACTGGCGCA 62.705 66.667 10.83 0.00 46.88 6.09
3455 7413 3.984193 ATGGAAGGCTGACTGGCGC 62.984 63.158 0.00 0.00 46.88 6.53
3456 7414 1.377725 AATGGAAGGCTGACTGGCG 60.378 57.895 0.00 0.00 46.88 5.69
3457 7415 0.322816 TCAATGGAAGGCTGACTGGC 60.323 55.000 0.00 0.00 42.15 4.85
3458 7416 2.431954 ATCAATGGAAGGCTGACTGG 57.568 50.000 0.00 0.00 0.00 4.00
3459 7417 2.686915 GGAATCAATGGAAGGCTGACTG 59.313 50.000 0.00 0.00 0.00 3.51
3460 7418 2.579860 AGGAATCAATGGAAGGCTGACT 59.420 45.455 0.00 0.00 0.00 3.41
3461 7419 2.948315 GAGGAATCAATGGAAGGCTGAC 59.052 50.000 0.00 0.00 0.00 3.51
3462 7420 2.577563 TGAGGAATCAATGGAAGGCTGA 59.422 45.455 0.00 0.00 0.00 4.26
3463 7421 2.686915 GTGAGGAATCAATGGAAGGCTG 59.313 50.000 0.00 0.00 0.00 4.85
3464 7422 2.681976 CGTGAGGAATCAATGGAAGGCT 60.682 50.000 0.00 0.00 0.00 4.58
3465 7423 1.672881 CGTGAGGAATCAATGGAAGGC 59.327 52.381 0.00 0.00 0.00 4.35
3489 7447 4.373116 TCGCCTCTCCGTTGTGCC 62.373 66.667 0.00 0.00 0.00 5.01
3490 7448 3.112709 GTCGCCTCTCCGTTGTGC 61.113 66.667 0.00 0.00 0.00 4.57
3491 7449 2.805353 CGTCGCCTCTCCGTTGTG 60.805 66.667 0.00 0.00 0.00 3.33
3492 7450 4.719369 GCGTCGCCTCTCCGTTGT 62.719 66.667 5.75 0.00 0.00 3.32
3519 7477 2.049433 AGCGGCAGACGTGTGTAC 60.049 61.111 14.77 6.98 46.52 2.90
3520 7478 2.257371 GAGCGGCAGACGTGTGTA 59.743 61.111 14.77 0.00 46.52 2.90
3521 7479 4.664677 GGAGCGGCAGACGTGTGT 62.665 66.667 14.77 0.00 46.52 3.72
3534 7492 2.669777 TTTTATAGCGGCGGGGGAGC 62.670 60.000 9.78 0.00 0.00 4.70
3535 7493 0.602905 CTTTTATAGCGGCGGGGGAG 60.603 60.000 9.78 0.00 0.00 4.30
3536 7494 1.448497 CTTTTATAGCGGCGGGGGA 59.552 57.895 9.78 0.00 0.00 4.81
3537 7495 2.258726 GCTTTTATAGCGGCGGGGG 61.259 63.158 9.78 0.00 40.71 5.40
3538 7496 3.340789 GCTTTTATAGCGGCGGGG 58.659 61.111 9.78 0.00 40.71 5.73
3546 7504 0.250770 GGGAGGGGCGGCTTTTATAG 60.251 60.000 9.56 0.00 0.00 1.31
3547 7505 0.696485 AGGGAGGGGCGGCTTTTATA 60.696 55.000 9.56 0.00 0.00 0.98
3548 7506 1.996070 GAGGGAGGGGCGGCTTTTAT 61.996 60.000 9.56 0.00 0.00 1.40
3549 7507 2.612746 AGGGAGGGGCGGCTTTTA 60.613 61.111 9.56 0.00 0.00 1.52
3550 7508 4.048470 GAGGGAGGGGCGGCTTTT 62.048 66.667 9.56 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.