Multiple sequence alignment - TraesCS4A01G089000

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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 TraesCS4A01G089000 chr4A 100.000 3483 0 0 1 3483 94982626 94979144 0.000000e+00 6433.0
1 TraesCS4A01G089000 chr4D 94.526 2868 100 12 1 2858 369667548 369670368 0.000000e+00 4373.0
2 TraesCS4A01G089000 chr4D 89.256 363 38 1 2877 3239 369670432 369670793 1.470000e-123 453.0
3 TraesCS4A01G089000 chr4D 88.889 171 18 1 5 175 391466628 391466797 3.520000e-50 209.0
4 TraesCS4A01G089000 chr4D 86.111 180 24 1 1 180 461423526 461423348 3.550000e-45 193.0
5 TraesCS4A01G089000 chr4D 83.439 157 25 1 169 324 481494215 481494059 1.010000e-30 145.0
6 TraesCS4A01G089000 chr4B 95.384 1993 58 18 695 2672 454922810 454924783 0.000000e+00 3140.0
7 TraesCS4A01G089000 chr4B 88.789 223 23 2 328 550 454922514 454922734 4.430000e-69 272.0
8 TraesCS4A01G089000 chr4B 96.939 98 2 1 583 679 454922725 454922822 2.780000e-36 163.0
9 TraesCS4A01G089000 chr5B 87.778 180 21 1 1 180 357161156 357160978 3.520000e-50 209.0
10 TraesCS4A01G089000 chr5B 81.395 129 22 2 168 295 543878601 543878474 1.710000e-18 104.0
11 TraesCS4A01G089000 chr1D 88.235 170 19 1 6 175 481697982 481697814 5.890000e-48 202.0
12 TraesCS4A01G089000 chr1D 86.111 180 24 1 1 180 447360198 447360020 3.550000e-45 193.0
13 TraesCS4A01G089000 chrUn 86.188 181 22 3 1 180 27664032 27663854 3.550000e-45 193.0
14 TraesCS4A01G089000 chr5D 86.111 180 23 2 1 180 346012491 346012668 3.550000e-45 193.0
15 TraesCS4A01G089000 chr5D 86.111 180 24 1 1 180 501121979 501122157 3.550000e-45 193.0
16 TraesCS4A01G089000 chr1B 87.261 157 17 3 3329 3483 679464981 679464826 3.570000e-40 176.0
17 TraesCS4A01G089000 chr6D 88.406 138 15 1 169 305 42959839 42959702 7.730000e-37 165.0
18 TraesCS4A01G089000 chr7D 87.770 139 16 1 168 305 483278648 483278786 1.000000e-35 161.0
19 TraesCS4A01G089000 chr3D 82.609 138 20 3 169 305 607226918 607227052 6.110000e-23 119.0
20 TraesCS4A01G089000 chr6B 79.882 169 19 9 169 324 34442585 34442419 3.680000e-20 110.0
21 TraesCS4A01G089000 chr7B 86.076 79 11 0 246 324 123743644 123743722 6.190000e-13 86.1


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 TraesCS4A01G089000 chr4A 94979144 94982626 3482 True 6433.000000 6433 100.000 1 3483 1 chr4A.!!$R1 3482
1 TraesCS4A01G089000 chr4D 369667548 369670793 3245 False 2413.000000 4373 91.891 1 3239 2 chr4D.!!$F2 3238
2 TraesCS4A01G089000 chr4B 454922514 454924783 2269 False 1191.666667 3140 93.704 328 2672 3 chr4B.!!$F1 2344

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
754 758 0.388659 AAGCAACGAAGGCATGCAAA 59.611 45.0 21.36 0.0 42.45 3.68 F
977 981 0.665835 TTTTCGTCCGCATGCAAACT 59.334 45.0 19.57 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2073 0.661552 CTAGTGTGCATGCATGAGCC 59.338 55.000 30.64 16.04 41.13 4.70 R
2638 2659 1.067495 GCCTTGTACTTCTCGTGAGCT 60.067 52.381 0.00 0.00 0.00 4.09 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.388460 AGAGATGCTTGAAGAAATAAACCAG 57.612 36.000 0.00 0.00 0.00 4.00
45 46 6.959639 AAACCAGACTTTTCTTAAGCATCA 57.040 33.333 0.00 0.00 0.00 3.07
82 83 2.094390 TGGCAGACGCTTAATTAGACGT 60.094 45.455 12.86 12.86 38.63 4.34
90 91 5.121811 ACGCTTAATTAGACGTCTCTCCTA 58.878 41.667 23.89 6.91 33.43 2.94
105 106 6.144080 CGTCTCTCCTATAAAAATAAGCACCG 59.856 42.308 0.00 0.00 0.00 4.94
186 187 7.739498 TGTACAAGGTCTTGGAGAAATAAAC 57.261 36.000 14.29 0.00 44.45 2.01
206 207 6.835819 AAACCAGGCTTTCTTTAAGTATCC 57.164 37.500 0.00 0.00 36.19 2.59
224 225 7.534723 AGTATCCGTGCTTATTTATACAGGA 57.465 36.000 0.00 0.00 0.00 3.86
240 241 6.710597 ATACAGGACAGACGCTTAATTAGA 57.289 37.500 0.00 0.00 0.00 2.10
244 245 4.082354 AGGACAGACGCTTAATTAGACGTT 60.082 41.667 13.84 1.90 36.96 3.99
265 266 5.755409 TTTCTCCTGTAGAAATAGGCACA 57.245 39.130 0.00 0.00 46.88 4.57
266 267 5.755409 TTCTCCTGTAGAAATAGGCACAA 57.245 39.130 0.00 0.00 41.35 3.33
303 306 8.474006 AAATCCGATTTGTTTTTATAAGCACC 57.526 30.769 5.53 0.00 0.00 5.01
306 309 7.981142 TCCGATTTGTTTTTATAAGCACCTAG 58.019 34.615 0.00 0.00 0.00 3.02
318 321 1.571919 GCACCTAGCATTGTACGAGG 58.428 55.000 0.00 0.00 44.79 4.63
324 327 2.311124 AGCATTGTACGAGGCCTTAC 57.689 50.000 15.94 7.26 0.00 2.34
326 329 1.738030 GCATTGTACGAGGCCTTACGT 60.738 52.381 21.58 21.58 44.72 3.57
333 336 3.323751 ACGAGGCCTTACGTATTTGTT 57.676 42.857 17.20 0.00 40.92 2.83
347 350 5.980715 ACGTATTTGTTGGGTGCTTAAAAAG 59.019 36.000 0.00 0.00 0.00 2.27
348 351 5.404066 CGTATTTGTTGGGTGCTTAAAAAGG 59.596 40.000 0.00 0.00 0.00 3.11
353 356 4.340950 TGTTGGGTGCTTAAAAAGGAAGAG 59.659 41.667 0.00 0.00 0.00 2.85
376 379 8.091449 AGAGAAAGAAAGAAAGAAAGCGATCTA 58.909 33.333 0.00 0.00 0.00 1.98
377 380 8.250538 AGAAAGAAAGAAAGAAAGCGATCTAG 57.749 34.615 0.00 0.00 0.00 2.43
409 412 0.834261 TGAAGGGACCCATGTCGTCA 60.834 55.000 14.60 3.26 42.73 4.35
483 486 5.338789 GCCAATTATCTCTCCCTCTAATCCC 60.339 48.000 0.00 0.00 0.00 3.85
488 491 5.912954 ATCTCTCCCTCTAATCCCCTTAT 57.087 43.478 0.00 0.00 0.00 1.73
553 556 5.520288 ACGAATGATACCGAATTCTTGACTG 59.480 40.000 3.52 0.00 31.83 3.51
679 683 3.282021 TCCTGGATCACTTTATGCTTGC 58.718 45.455 0.00 0.00 0.00 4.01
680 684 3.054139 TCCTGGATCACTTTATGCTTGCT 60.054 43.478 0.00 0.00 0.00 3.91
681 685 3.698040 CCTGGATCACTTTATGCTTGCTT 59.302 43.478 0.00 0.00 0.00 3.91
682 686 4.159135 CCTGGATCACTTTATGCTTGCTTT 59.841 41.667 0.00 0.00 0.00 3.51
683 687 5.337009 CCTGGATCACTTTATGCTTGCTTTT 60.337 40.000 0.00 0.00 0.00 2.27
684 688 6.100404 TGGATCACTTTATGCTTGCTTTTT 57.900 33.333 0.00 0.00 0.00 1.94
754 758 0.388659 AAGCAACGAAGGCATGCAAA 59.611 45.000 21.36 0.00 42.45 3.68
862 866 1.300311 CGTGCGTGCCGGGATAATA 60.300 57.895 2.18 0.00 0.00 0.98
867 871 1.463444 GCGTGCCGGGATAATATTGTC 59.537 52.381 2.18 3.71 0.00 3.18
904 908 2.879233 AACTCCCGTGCATGTCGGT 61.879 57.895 22.58 8.32 45.63 4.69
977 981 0.665835 TTTTCGTCCGCATGCAAACT 59.334 45.000 19.57 0.00 0.00 2.66
1938 1954 2.480555 CCAAACGGCGTGCAGATC 59.519 61.111 15.70 0.00 0.00 2.75
2051 2067 3.914426 AGGAACTGATGACGCCTTTAT 57.086 42.857 0.00 0.00 37.18 1.40
2052 2068 4.222124 AGGAACTGATGACGCCTTTATT 57.778 40.909 0.00 0.00 37.18 1.40
2053 2069 5.353394 AGGAACTGATGACGCCTTTATTA 57.647 39.130 0.00 0.00 37.18 0.98
2054 2070 5.741011 AGGAACTGATGACGCCTTTATTAA 58.259 37.500 0.00 0.00 37.18 1.40
2055 2071 6.357367 AGGAACTGATGACGCCTTTATTAAT 58.643 36.000 0.00 0.00 37.18 1.40
2056 2072 6.483640 AGGAACTGATGACGCCTTTATTAATC 59.516 38.462 0.00 0.00 37.18 1.75
2057 2073 5.907197 ACTGATGACGCCTTTATTAATCG 57.093 39.130 0.00 0.00 0.00 3.34
2353 2369 4.754667 GGCGAGGGGAACGTGGTC 62.755 72.222 0.00 0.00 0.00 4.02
2359 2375 1.978617 GGGGAACGTGGTCGAGGTA 60.979 63.158 0.00 0.00 40.62 3.08
2470 2486 1.048601 ACATCGCCACGATCCCTTAT 58.951 50.000 0.00 0.00 45.19 1.73
2474 2490 1.746517 GCCACGATCCCTTATCCGT 59.253 57.895 0.00 0.00 0.00 4.69
2496 2516 4.368565 TGGACTAGAGTGTGTAGTGTCT 57.631 45.455 0.00 0.00 30.60 3.41
2512 2532 4.147321 AGTGTCTCATTTGATTTGCTGGT 58.853 39.130 0.00 0.00 0.00 4.00
2638 2659 8.932791 GTGACAAGAACTCGGATCTTTATAAAA 58.067 33.333 0.00 0.00 34.99 1.52
2656 2678 6.952935 ATAAAAGCTCACGAGAAGTACAAG 57.047 37.500 0.00 0.00 0.00 3.16
2720 2743 9.926158 TGCAATTGTTTGAGTTTTCATGTATAT 57.074 25.926 7.40 0.00 34.60 0.86
2769 2792 2.516906 TGTACACCACCTCGACATACA 58.483 47.619 0.00 0.00 0.00 2.29
2784 2807 5.421056 TCGACATACAAGGACCAAAGAGTAT 59.579 40.000 0.00 0.00 0.00 2.12
2805 2828 8.915057 AGTATAAGGACTTATAGTTCTACGCA 57.085 34.615 11.08 0.00 38.05 5.24
2830 2853 1.001378 GCTCAACCTCAAACGCATTGT 60.001 47.619 1.98 0.00 40.11 2.71
2878 2946 2.121786 GCAATATTGATGCAAGCACCG 58.878 47.619 19.73 0.00 43.29 4.94
2907 2975 0.324943 GTTGGCCCTCTACAGCTTGA 59.675 55.000 0.00 0.00 0.00 3.02
2935 3003 3.375299 GTCATCATCTACTTGGTTGCCAC 59.625 47.826 0.00 0.00 30.78 5.01
2937 3005 1.346395 TCATCTACTTGGTTGCCACGT 59.654 47.619 2.94 2.94 39.36 4.49
2941 3009 2.300723 TCTACTTGGTTGCCACGTACAT 59.699 45.455 1.12 0.00 37.24 2.29
2943 3011 0.109781 CTTGGTTGCCACGTACATGC 60.110 55.000 0.00 0.00 30.78 4.06
2948 3016 1.067915 GTTGCCACGTACATGCCAATT 60.068 47.619 0.00 0.00 0.00 2.32
2960 3028 7.593644 ACGTACATGCCAATTTAGAAGTTTTTC 59.406 33.333 0.00 0.00 0.00 2.29
3017 3085 3.004734 CCGTTGAGGCCATGGAAATATTC 59.995 47.826 18.40 3.40 0.00 1.75
3025 3093 3.573967 GCCATGGAAATATTCGAATGGGT 59.426 43.478 20.87 5.01 41.38 4.51
3029 3097 4.377021 TGGAAATATTCGAATGGGTCTCG 58.623 43.478 20.87 0.00 37.66 4.04
3030 3098 3.746492 GGAAATATTCGAATGGGTCTCGG 59.254 47.826 20.87 0.00 36.93 4.63
3050 3118 0.394899 CCTGCCCACTCCAAATCTCC 60.395 60.000 0.00 0.00 0.00 3.71
3057 3125 0.909610 ACTCCAAATCTCCCGCTCCA 60.910 55.000 0.00 0.00 0.00 3.86
3060 3128 0.536006 CCAAATCTCCCGCTCCATCC 60.536 60.000 0.00 0.00 0.00 3.51
3068 3136 0.034089 CCCGCTCCATCCCTTTCTTT 60.034 55.000 0.00 0.00 0.00 2.52
3076 3144 5.320277 CTCCATCCCTTTCTTTGTTCTTCT 58.680 41.667 0.00 0.00 0.00 2.85
3086 3154 6.598753 TTCTTTGTTCTTCTAGTCCAAACG 57.401 37.500 0.00 0.00 0.00 3.60
3091 3159 5.617252 TGTTCTTCTAGTCCAAACGGAAAT 58.383 37.500 0.00 0.00 33.16 2.17
3111 3179 7.013846 CGGAAATATGAGAGAAGGTTAGAGTCT 59.986 40.741 0.00 0.00 0.00 3.24
3115 3183 9.432982 AATATGAGAGAAGGTTAGAGTCTTGAT 57.567 33.333 0.00 0.00 0.00 2.57
3123 3191 4.757149 AGGTTAGAGTCTTGATTGTTGTGC 59.243 41.667 0.00 0.00 0.00 4.57
3126 3194 4.623932 AGAGTCTTGATTGTTGTGCCTA 57.376 40.909 0.00 0.00 0.00 3.93
3212 3280 0.666374 CGTGGGTGTTTGGTTCCTTC 59.334 55.000 0.00 0.00 0.00 3.46
3213 3281 1.749286 CGTGGGTGTTTGGTTCCTTCT 60.749 52.381 0.00 0.00 0.00 2.85
3216 3284 3.050089 TGGGTGTTTGGTTCCTTCTCTA 58.950 45.455 0.00 0.00 0.00 2.43
3217 3285 3.072476 TGGGTGTTTGGTTCCTTCTCTAG 59.928 47.826 0.00 0.00 0.00 2.43
3224 3292 2.158219 TGGTTCCTTCTCTAGGTGGTCA 60.158 50.000 0.00 0.00 45.03 4.02
3229 3297 3.578716 TCCTTCTCTAGGTGGTCAGTTTG 59.421 47.826 0.00 0.00 45.03 2.93
3239 3307 3.211045 GTGGTCAGTTTGTCCTTTAGCA 58.789 45.455 0.00 0.00 0.00 3.49
3240 3308 3.003378 GTGGTCAGTTTGTCCTTTAGCAC 59.997 47.826 0.00 0.00 0.00 4.40
3241 3309 3.118038 TGGTCAGTTTGTCCTTTAGCACT 60.118 43.478 0.00 0.00 0.00 4.40
3242 3310 3.883489 GGTCAGTTTGTCCTTTAGCACTT 59.117 43.478 0.00 0.00 0.00 3.16
3243 3311 5.061179 GGTCAGTTTGTCCTTTAGCACTTA 58.939 41.667 0.00 0.00 0.00 2.24
3244 3312 5.179555 GGTCAGTTTGTCCTTTAGCACTTAG 59.820 44.000 0.00 0.00 0.00 2.18
3245 3313 5.989777 GTCAGTTTGTCCTTTAGCACTTAGA 59.010 40.000 0.00 0.00 0.00 2.10
3246 3314 6.651225 GTCAGTTTGTCCTTTAGCACTTAGAT 59.349 38.462 0.00 0.00 0.00 1.98
3247 3315 7.817962 GTCAGTTTGTCCTTTAGCACTTAGATA 59.182 37.037 0.00 0.00 0.00 1.98
3248 3316 8.372459 TCAGTTTGTCCTTTAGCACTTAGATAA 58.628 33.333 0.00 0.00 0.00 1.75
3249 3317 8.999431 CAGTTTGTCCTTTAGCACTTAGATAAA 58.001 33.333 0.00 0.00 35.85 1.40
3250 3318 9.740710 AGTTTGTCCTTTAGCACTTAGATAAAT 57.259 29.630 0.00 0.00 37.45 1.40
3261 3329 7.464358 AGCACTTAGATAAATTTTGTACTGCG 58.536 34.615 0.00 0.00 0.00 5.18
3262 3330 6.687105 GCACTTAGATAAATTTTGTACTGCGG 59.313 38.462 0.00 0.00 0.00 5.69
3263 3331 7.186804 CACTTAGATAAATTTTGTACTGCGGG 58.813 38.462 0.00 0.00 0.00 6.13
3264 3332 4.632538 AGATAAATTTTGTACTGCGGGC 57.367 40.909 0.00 0.00 0.00 6.13
3265 3333 3.380320 AGATAAATTTTGTACTGCGGGCC 59.620 43.478 0.00 0.00 0.00 5.80
3266 3334 1.333177 AAATTTTGTACTGCGGGCCA 58.667 45.000 4.39 0.00 0.00 5.36
3267 3335 1.555967 AATTTTGTACTGCGGGCCAT 58.444 45.000 4.39 0.00 0.00 4.40
3268 3336 2.428544 ATTTTGTACTGCGGGCCATA 57.571 45.000 4.39 0.00 0.00 2.74
3269 3337 1.455248 TTTTGTACTGCGGGCCATAC 58.545 50.000 4.39 0.63 0.00 2.39
3270 3338 0.616371 TTTGTACTGCGGGCCATACT 59.384 50.000 4.39 0.00 0.00 2.12
3271 3339 0.107897 TTGTACTGCGGGCCATACTG 60.108 55.000 4.39 0.00 0.00 2.74
3272 3340 1.261938 TGTACTGCGGGCCATACTGT 61.262 55.000 4.39 5.86 0.00 3.55
3273 3341 0.107848 GTACTGCGGGCCATACTGTT 60.108 55.000 4.39 0.00 0.00 3.16
3274 3342 0.616371 TACTGCGGGCCATACTGTTT 59.384 50.000 4.39 0.00 0.00 2.83
3275 3343 0.616371 ACTGCGGGCCATACTGTTTA 59.384 50.000 4.39 0.00 0.00 2.01
3276 3344 1.211949 ACTGCGGGCCATACTGTTTAT 59.788 47.619 4.39 0.00 0.00 1.40
3277 3345 1.603802 CTGCGGGCCATACTGTTTATG 59.396 52.381 4.39 0.00 0.00 1.90
3278 3346 1.210722 TGCGGGCCATACTGTTTATGA 59.789 47.619 4.39 0.00 0.00 2.15
3279 3347 1.602377 GCGGGCCATACTGTTTATGAC 59.398 52.381 4.39 0.00 0.00 3.06
3280 3348 2.745152 GCGGGCCATACTGTTTATGACT 60.745 50.000 4.39 0.00 0.00 3.41
3281 3349 3.131396 CGGGCCATACTGTTTATGACTC 58.869 50.000 4.39 0.00 0.00 3.36
3282 3350 3.131396 GGGCCATACTGTTTATGACTCG 58.869 50.000 4.39 0.00 0.00 4.18
3283 3351 2.544267 GGCCATACTGTTTATGACTCGC 59.456 50.000 0.00 0.00 0.00 5.03
3284 3352 3.458189 GCCATACTGTTTATGACTCGCT 58.542 45.455 0.00 0.00 0.00 4.93
3285 3353 4.500887 GGCCATACTGTTTATGACTCGCTA 60.501 45.833 0.00 0.00 0.00 4.26
3286 3354 5.230942 GCCATACTGTTTATGACTCGCTAT 58.769 41.667 0.00 0.00 0.00 2.97
3287 3355 5.346281 GCCATACTGTTTATGACTCGCTATC 59.654 44.000 0.00 0.00 0.00 2.08
3288 3356 6.447162 CCATACTGTTTATGACTCGCTATCA 58.553 40.000 0.00 0.00 0.00 2.15
3289 3357 6.584184 CCATACTGTTTATGACTCGCTATCAG 59.416 42.308 0.00 0.00 0.00 2.90
3290 3358 4.363999 ACTGTTTATGACTCGCTATCAGC 58.636 43.478 0.00 0.00 38.02 4.26
3318 3386 3.060615 CAGCTGGCCAGGCAGAAC 61.061 66.667 33.46 15.92 0.00 3.01
3319 3387 3.573229 AGCTGGCCAGGCAGAACA 61.573 61.111 33.46 6.86 0.00 3.18
3320 3388 2.598394 GCTGGCCAGGCAGAACAA 60.598 61.111 33.46 0.00 0.00 2.83
3321 3389 2.202395 GCTGGCCAGGCAGAACAAA 61.202 57.895 33.46 0.00 0.00 2.83
3322 3390 1.538687 GCTGGCCAGGCAGAACAAAT 61.539 55.000 33.46 0.00 0.00 2.32
3323 3391 1.838112 CTGGCCAGGCAGAACAAATA 58.162 50.000 26.14 0.00 0.00 1.40
3324 3392 1.747355 CTGGCCAGGCAGAACAAATAG 59.253 52.381 26.14 0.00 0.00 1.73
3325 3393 1.354031 TGGCCAGGCAGAACAAATAGA 59.646 47.619 15.19 0.00 0.00 1.98
3326 3394 2.224992 TGGCCAGGCAGAACAAATAGAA 60.225 45.455 15.19 0.00 0.00 2.10
3327 3395 3.026694 GGCCAGGCAGAACAAATAGAAT 58.973 45.455 15.19 0.00 0.00 2.40
3328 3396 3.181483 GGCCAGGCAGAACAAATAGAATG 60.181 47.826 15.19 0.00 0.00 2.67
3329 3397 3.736126 GCCAGGCAGAACAAATAGAATGC 60.736 47.826 6.55 0.00 0.00 3.56
3333 3401 4.037858 GCAGAACAAATAGAATGCCTGG 57.962 45.455 0.00 0.00 0.00 4.45
3334 3402 3.181483 GCAGAACAAATAGAATGCCTGGG 60.181 47.826 0.00 0.00 0.00 4.45
3335 3403 3.026694 AGAACAAATAGAATGCCTGGGC 58.973 45.455 4.43 4.43 42.35 5.36
3336 3404 1.392589 ACAAATAGAATGCCTGGGCG 58.607 50.000 7.14 0.00 45.51 6.13
3337 3405 1.064758 ACAAATAGAATGCCTGGGCGA 60.065 47.619 7.14 0.00 45.51 5.54
3338 3406 1.605710 CAAATAGAATGCCTGGGCGAG 59.394 52.381 7.14 0.00 45.51 5.03
3339 3407 0.109342 AATAGAATGCCTGGGCGAGG 59.891 55.000 11.72 11.72 46.13 4.63
3346 3414 3.399181 CCTGGGCGAGGCTAACCA 61.399 66.667 1.48 5.96 39.06 3.67
3347 3415 2.187946 CTGGGCGAGGCTAACCAG 59.812 66.667 14.69 14.69 43.87 4.00
3348 3416 3.391665 CTGGGCGAGGCTAACCAGG 62.392 68.421 18.76 3.88 45.21 4.45
3349 3417 3.400054 GGGCGAGGCTAACCAGGT 61.400 66.667 7.51 0.00 39.06 4.00
3350 3418 2.669240 GGCGAGGCTAACCAGGTT 59.331 61.111 10.50 10.50 39.06 3.50
3351 3419 1.745489 GGCGAGGCTAACCAGGTTG 60.745 63.158 15.82 6.27 39.06 3.77
3352 3420 2.399356 GCGAGGCTAACCAGGTTGC 61.399 63.158 15.82 15.29 39.06 4.17
3353 3421 1.745489 CGAGGCTAACCAGGTTGCC 60.745 63.158 26.55 26.55 38.78 4.52
3354 3422 1.685820 GAGGCTAACCAGGTTGCCT 59.314 57.895 32.30 32.30 45.33 4.75
3365 3433 2.999063 GTTGCCTGGGCCAAGCAT 60.999 61.111 29.18 0.00 41.09 3.79
3366 3434 2.998480 TTGCCTGGGCCAAGCATG 60.998 61.111 29.18 6.70 41.09 4.06
3367 3435 3.831727 TTGCCTGGGCCAAGCATGT 62.832 57.895 29.18 0.00 41.09 3.21
3368 3436 2.999063 GCCTGGGCCAAGCATGTT 60.999 61.111 22.09 0.00 34.56 2.71
3369 3437 2.586293 GCCTGGGCCAAGCATGTTT 61.586 57.895 22.09 0.00 34.56 2.83
3370 3438 1.593265 CCTGGGCCAAGCATGTTTC 59.407 57.895 8.04 0.00 0.00 2.78
3371 3439 0.901580 CCTGGGCCAAGCATGTTTCT 60.902 55.000 8.04 0.00 0.00 2.52
3372 3440 0.971386 CTGGGCCAAGCATGTTTCTT 59.029 50.000 8.04 0.00 0.00 2.52
3373 3441 1.345415 CTGGGCCAAGCATGTTTCTTT 59.655 47.619 8.04 0.00 0.00 2.52
3374 3442 1.344114 TGGGCCAAGCATGTTTCTTTC 59.656 47.619 2.13 0.00 0.00 2.62
3375 3443 1.620323 GGGCCAAGCATGTTTCTTTCT 59.380 47.619 4.39 0.00 0.00 2.52
3376 3444 2.037641 GGGCCAAGCATGTTTCTTTCTT 59.962 45.455 4.39 0.00 0.00 2.52
3377 3445 3.494924 GGGCCAAGCATGTTTCTTTCTTT 60.495 43.478 4.39 0.00 0.00 2.52
3378 3446 4.129380 GGCCAAGCATGTTTCTTTCTTTT 58.871 39.130 0.00 0.00 0.00 2.27
3379 3447 4.024641 GGCCAAGCATGTTTCTTTCTTTTG 60.025 41.667 0.00 0.00 0.00 2.44
3380 3448 4.571984 GCCAAGCATGTTTCTTTCTTTTGT 59.428 37.500 0.00 0.00 0.00 2.83
3381 3449 5.065090 GCCAAGCATGTTTCTTTCTTTTGTT 59.935 36.000 0.00 0.00 0.00 2.83
3382 3450 6.403527 GCCAAGCATGTTTCTTTCTTTTGTTT 60.404 34.615 0.00 0.00 0.00 2.83
3383 3451 7.529158 CCAAGCATGTTTCTTTCTTTTGTTTT 58.471 30.769 0.00 0.00 0.00 2.43
3384 3452 8.022550 CCAAGCATGTTTCTTTCTTTTGTTTTT 58.977 29.630 0.00 0.00 0.00 1.94
3409 3477 9.715121 TTTAAATCTAGACCAAGTTAATCACGT 57.285 29.630 0.00 0.00 0.00 4.49
3410 3478 9.715121 TTAAATCTAGACCAAGTTAATCACGTT 57.285 29.630 0.00 0.00 0.00 3.99
3411 3479 7.596749 AATCTAGACCAAGTTAATCACGTTG 57.403 36.000 0.00 0.00 0.00 4.10
3412 3480 4.927425 TCTAGACCAAGTTAATCACGTTGC 59.073 41.667 0.00 0.00 0.00 4.17
3413 3481 3.472652 AGACCAAGTTAATCACGTTGCA 58.527 40.909 0.00 0.00 0.00 4.08
3414 3482 4.072131 AGACCAAGTTAATCACGTTGCAT 58.928 39.130 0.00 0.00 0.00 3.96
3415 3483 4.083324 AGACCAAGTTAATCACGTTGCATG 60.083 41.667 0.00 0.00 0.00 4.06
3416 3484 3.057596 ACCAAGTTAATCACGTTGCATGG 60.058 43.478 0.00 0.00 0.00 3.66
3417 3485 3.190327 CCAAGTTAATCACGTTGCATGGA 59.810 43.478 0.00 0.00 0.00 3.41
3418 3486 4.158384 CAAGTTAATCACGTTGCATGGAC 58.842 43.478 0.00 0.00 0.00 4.02
3419 3487 3.674997 AGTTAATCACGTTGCATGGACT 58.325 40.909 0.00 0.00 0.00 3.85
3420 3488 3.684788 AGTTAATCACGTTGCATGGACTC 59.315 43.478 0.00 0.00 0.00 3.36
3421 3489 1.453155 AATCACGTTGCATGGACTCC 58.547 50.000 0.00 0.00 0.00 3.85
3422 3490 0.392998 ATCACGTTGCATGGACTCCC 60.393 55.000 0.00 0.00 0.00 4.30
3431 3499 2.124768 TGGACTCCCATGCCAGGA 59.875 61.111 0.00 0.00 37.58 3.86
3432 3500 1.541118 TGGACTCCCATGCCAGGAA 60.541 57.895 0.00 0.00 37.58 3.36
3433 3501 1.225704 GGACTCCCATGCCAGGAAG 59.774 63.158 0.00 0.00 31.49 3.46
3434 3502 1.274703 GGACTCCCATGCCAGGAAGA 61.275 60.000 0.00 0.00 31.49 2.87
3435 3503 0.842635 GACTCCCATGCCAGGAAGAT 59.157 55.000 0.00 0.00 31.49 2.40
3436 3504 0.549950 ACTCCCATGCCAGGAAGATG 59.450 55.000 0.00 0.00 31.49 2.90
3437 3505 0.549950 CTCCCATGCCAGGAAGATGT 59.450 55.000 0.00 0.00 31.49 3.06
3438 3506 1.002069 TCCCATGCCAGGAAGATGTT 58.998 50.000 0.00 0.00 0.00 2.71
3439 3507 1.358787 TCCCATGCCAGGAAGATGTTT 59.641 47.619 0.00 0.00 0.00 2.83
3440 3508 1.753073 CCCATGCCAGGAAGATGTTTC 59.247 52.381 0.00 0.00 0.00 2.78
3441 3509 2.449464 CCATGCCAGGAAGATGTTTCA 58.551 47.619 0.00 0.00 0.00 2.69
3442 3510 3.028850 CCATGCCAGGAAGATGTTTCAT 58.971 45.455 0.00 0.00 0.00 2.57
3443 3511 3.449737 CCATGCCAGGAAGATGTTTCATT 59.550 43.478 0.00 0.00 0.00 2.57
3444 3512 4.081309 CCATGCCAGGAAGATGTTTCATTT 60.081 41.667 0.00 0.00 0.00 2.32
3445 3513 5.484715 CATGCCAGGAAGATGTTTCATTTT 58.515 37.500 0.00 0.00 0.00 1.82
3446 3514 5.138125 TGCCAGGAAGATGTTTCATTTTC 57.862 39.130 0.00 4.98 0.00 2.29
3447 3515 4.834496 TGCCAGGAAGATGTTTCATTTTCT 59.166 37.500 11.00 0.00 0.00 2.52
3448 3516 6.009589 TGCCAGGAAGATGTTTCATTTTCTA 58.990 36.000 11.00 0.00 0.00 2.10
3449 3517 6.151648 TGCCAGGAAGATGTTTCATTTTCTAG 59.848 38.462 11.00 0.00 0.00 2.43
3450 3518 6.405176 GCCAGGAAGATGTTTCATTTTCTAGG 60.405 42.308 11.00 12.53 0.00 3.02
3451 3519 6.886459 CCAGGAAGATGTTTCATTTTCTAGGA 59.114 38.462 11.00 0.00 0.00 2.94
3452 3520 7.148171 CCAGGAAGATGTTTCATTTTCTAGGAC 60.148 40.741 11.00 0.00 0.00 3.85
3453 3521 7.391554 CAGGAAGATGTTTCATTTTCTAGGACA 59.608 37.037 11.00 0.00 0.00 4.02
3454 3522 7.391833 AGGAAGATGTTTCATTTTCTAGGACAC 59.608 37.037 11.00 0.00 0.00 3.67
3455 3523 7.362142 GGAAGATGTTTCATTTTCTAGGACACC 60.362 40.741 11.00 0.00 0.00 4.16
3456 3524 6.542821 AGATGTTTCATTTTCTAGGACACCA 58.457 36.000 0.00 0.00 0.00 4.17
3457 3525 7.177878 AGATGTTTCATTTTCTAGGACACCAT 58.822 34.615 0.00 0.00 0.00 3.55
3458 3526 6.817765 TGTTTCATTTTCTAGGACACCATC 57.182 37.500 0.00 0.00 0.00 3.51
3473 3541 6.076981 GACACCATCCAAATAAATAGCAGG 57.923 41.667 0.00 0.00 0.00 4.85
3474 3542 4.342092 ACACCATCCAAATAAATAGCAGGC 59.658 41.667 0.00 0.00 0.00 4.85
3475 3543 4.341806 CACCATCCAAATAAATAGCAGGCA 59.658 41.667 0.00 0.00 0.00 4.75
3476 3544 4.586001 ACCATCCAAATAAATAGCAGGCAG 59.414 41.667 0.00 0.00 0.00 4.85
3477 3545 4.021719 CCATCCAAATAAATAGCAGGCAGG 60.022 45.833 0.00 0.00 0.00 4.85
3478 3546 3.565307 TCCAAATAAATAGCAGGCAGGG 58.435 45.455 0.00 0.00 0.00 4.45
3479 3547 3.052944 TCCAAATAAATAGCAGGCAGGGT 60.053 43.478 0.00 0.00 0.00 4.34
3480 3548 3.319122 CCAAATAAATAGCAGGCAGGGTC 59.681 47.826 0.00 0.00 0.00 4.46
3481 3549 2.959465 ATAAATAGCAGGCAGGGTCC 57.041 50.000 0.00 0.00 0.00 4.46
3482 3550 1.590591 TAAATAGCAGGCAGGGTCCA 58.409 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.967346 GCTTAAGAAAAGTCTGGTTTATTTCTT 57.033 29.630 6.67 14.07 46.39 2.52
45 46 5.466728 CGTCTGCCATGTATAAATAAGCACT 59.533 40.000 0.00 0.00 0.00 4.40
82 83 6.099269 ACCGGTGCTTATTTTTATAGGAGAGA 59.901 38.462 6.12 0.00 0.00 3.10
105 106 1.886542 ACCGGATTTTTCTCAAGCACC 59.113 47.619 9.46 0.00 0.00 5.01
171 172 4.657814 AGCCTGGTTTATTTCTCCAAGA 57.342 40.909 0.00 0.00 0.00 3.02
186 187 4.332819 CACGGATACTTAAAGAAAGCCTGG 59.667 45.833 0.00 0.00 38.93 4.45
206 207 5.173312 CGTCTGTCCTGTATAAATAAGCACG 59.827 44.000 0.00 0.00 0.00 5.34
217 218 6.505272 GTCTAATTAAGCGTCTGTCCTGTAT 58.495 40.000 0.00 0.00 0.00 2.29
224 225 5.467705 AGAAACGTCTAATTAAGCGTCTGT 58.532 37.500 12.40 4.25 37.10 3.41
244 245 5.755409 TTGTGCCTATTTCTACAGGAGAA 57.245 39.130 0.00 0.00 42.69 2.87
281 282 6.827586 AGGTGCTTATAAAAACAAATCGGA 57.172 33.333 0.00 0.00 0.00 4.55
285 288 9.369904 CAATGCTAGGTGCTTATAAAAACAAAT 57.630 29.630 0.00 0.00 43.37 2.32
287 290 7.891561 ACAATGCTAGGTGCTTATAAAAACAA 58.108 30.769 0.00 0.00 43.37 2.83
289 292 7.638683 CGTACAATGCTAGGTGCTTATAAAAAC 59.361 37.037 0.00 0.00 43.37 2.43
295 298 4.501571 CCTCGTACAATGCTAGGTGCTTAT 60.502 45.833 0.00 0.00 43.37 1.73
303 306 2.604046 AAGGCCTCGTACAATGCTAG 57.396 50.000 5.23 0.00 0.00 3.42
306 309 0.928229 CGTAAGGCCTCGTACAATGC 59.072 55.000 5.23 0.00 0.00 3.56
315 318 2.681344 CCCAACAAATACGTAAGGCCTC 59.319 50.000 5.23 0.00 46.39 4.70
318 321 2.414957 GCACCCAACAAATACGTAAGGC 60.415 50.000 0.00 0.00 46.39 4.35
324 327 5.404066 CCTTTTTAAGCACCCAACAAATACG 59.596 40.000 0.00 0.00 0.00 3.06
326 329 6.732896 TCCTTTTTAAGCACCCAACAAATA 57.267 33.333 0.00 0.00 0.00 1.40
333 336 4.447138 TCTCTTCCTTTTTAAGCACCCA 57.553 40.909 0.00 0.00 0.00 4.51
347 350 6.017852 TCGCTTTCTTTCTTTCTTTCTCTTCC 60.018 38.462 0.00 0.00 0.00 3.46
348 351 6.949449 TCGCTTTCTTTCTTTCTTTCTCTTC 58.051 36.000 0.00 0.00 0.00 2.87
353 356 8.245701 TCTAGATCGCTTTCTTTCTTTCTTTC 57.754 34.615 0.00 0.00 0.00 2.62
376 379 5.538813 GGGTCCCTTCAGTGTTTAAATTTCT 59.461 40.000 0.00 0.00 0.00 2.52
377 380 5.303333 TGGGTCCCTTCAGTGTTTAAATTTC 59.697 40.000 10.00 0.00 0.00 2.17
409 412 1.229723 TTTCGGAAGGCCCTAGGGT 60.230 57.895 28.96 9.67 37.65 4.34
537 540 2.093658 GGGAGCAGTCAAGAATTCGGTA 60.094 50.000 0.00 0.00 0.00 4.02
553 556 0.322366 AAGCAGAAGAGCAAGGGAGC 60.322 55.000 0.00 0.00 36.85 4.70
682 686 7.725251 ACAAGCATAAAGTGGATTCTCAAAAA 58.275 30.769 0.00 0.00 0.00 1.94
683 687 7.288810 ACAAGCATAAAGTGGATTCTCAAAA 57.711 32.000 0.00 0.00 0.00 2.44
684 688 6.899393 ACAAGCATAAAGTGGATTCTCAAA 57.101 33.333 0.00 0.00 0.00 2.69
685 689 6.489700 TCAACAAGCATAAAGTGGATTCTCAA 59.510 34.615 0.00 0.00 0.00 3.02
686 690 6.003326 TCAACAAGCATAAAGTGGATTCTCA 58.997 36.000 0.00 0.00 0.00 3.27
687 691 6.317857 GTCAACAAGCATAAAGTGGATTCTC 58.682 40.000 0.00 0.00 0.00 2.87
688 692 5.183904 GGTCAACAAGCATAAAGTGGATTCT 59.816 40.000 0.00 0.00 0.00 2.40
689 693 5.183904 AGGTCAACAAGCATAAAGTGGATTC 59.816 40.000 0.00 0.00 0.00 2.52
690 694 5.047802 CAGGTCAACAAGCATAAAGTGGATT 60.048 40.000 0.00 0.00 0.00 3.01
691 695 4.460382 CAGGTCAACAAGCATAAAGTGGAT 59.540 41.667 0.00 0.00 0.00 3.41
692 696 3.820467 CAGGTCAACAAGCATAAAGTGGA 59.180 43.478 0.00 0.00 0.00 4.02
693 697 3.569701 ACAGGTCAACAAGCATAAAGTGG 59.430 43.478 0.00 0.00 0.00 4.00
694 698 4.836125 ACAGGTCAACAAGCATAAAGTG 57.164 40.909 0.00 0.00 0.00 3.16
695 699 5.373222 TGTACAGGTCAACAAGCATAAAGT 58.627 37.500 0.00 0.00 0.00 2.66
696 700 5.940192 TGTACAGGTCAACAAGCATAAAG 57.060 39.130 0.00 0.00 0.00 1.85
697 701 6.237901 AGATGTACAGGTCAACAAGCATAAA 58.762 36.000 0.33 0.00 0.00 1.40
698 702 5.804639 AGATGTACAGGTCAACAAGCATAA 58.195 37.500 0.33 0.00 0.00 1.90
699 703 5.420725 AGATGTACAGGTCAACAAGCATA 57.579 39.130 0.33 0.00 0.00 3.14
700 704 4.292186 AGATGTACAGGTCAACAAGCAT 57.708 40.909 0.33 0.00 0.00 3.79
701 705 3.769739 AGATGTACAGGTCAACAAGCA 57.230 42.857 0.33 0.00 0.00 3.91
702 706 3.365364 GCAAGATGTACAGGTCAACAAGC 60.365 47.826 0.33 0.00 0.00 4.01
703 707 3.814842 TGCAAGATGTACAGGTCAACAAG 59.185 43.478 0.33 0.00 0.00 3.16
704 708 3.814625 TGCAAGATGTACAGGTCAACAA 58.185 40.909 0.33 0.00 0.00 2.83
705 709 3.483808 TGCAAGATGTACAGGTCAACA 57.516 42.857 0.33 0.00 0.00 3.33
706 710 4.002982 TGATGCAAGATGTACAGGTCAAC 58.997 43.478 0.33 0.00 0.00 3.18
754 758 1.066215 GGCGCTTTTGGAATTTGGGAT 60.066 47.619 7.64 0.00 0.00 3.85
852 856 3.040147 AGCGTGACAATATTATCCCGG 57.960 47.619 0.91 0.00 0.00 5.73
862 866 1.546029 TGAGTCAGCTAGCGTGACAAT 59.454 47.619 31.16 20.45 45.76 2.71
867 871 0.459063 TGCATGAGTCAGCTAGCGTG 60.459 55.000 9.55 8.38 0.00 5.34
904 908 9.535170 TTAATGGATTTGCCCCGAAAATATATA 57.465 29.630 0.00 0.00 34.97 0.86
966 970 0.097674 GTGGCTCTAGTTTGCATGCG 59.902 55.000 14.09 0.00 0.00 4.73
1938 1954 2.746362 GAGAAATTGCTGGTCCTGTGAG 59.254 50.000 0.00 0.00 0.00 3.51
2045 2061 5.396484 CATGCATGAGCCGATTAATAAAGG 58.604 41.667 22.59 0.00 41.13 3.11
2046 2062 4.855388 GCATGCATGAGCCGATTAATAAAG 59.145 41.667 30.64 0.00 41.13 1.85
2047 2063 4.277921 TGCATGCATGAGCCGATTAATAAA 59.722 37.500 30.64 0.00 41.13 1.40
2048 2064 3.819902 TGCATGCATGAGCCGATTAATAA 59.180 39.130 30.64 0.00 41.13 1.40
2049 2065 3.189080 GTGCATGCATGAGCCGATTAATA 59.811 43.478 30.64 0.00 41.13 0.98
2050 2066 2.030540 GTGCATGCATGAGCCGATTAAT 60.031 45.455 30.64 0.00 41.13 1.40
2051 2067 1.334556 GTGCATGCATGAGCCGATTAA 59.665 47.619 30.64 0.00 41.13 1.40
2052 2068 0.946528 GTGCATGCATGAGCCGATTA 59.053 50.000 30.64 2.45 41.13 1.75
2053 2069 1.033202 TGTGCATGCATGAGCCGATT 61.033 50.000 30.64 0.00 41.13 3.34
2054 2070 1.452470 TGTGCATGCATGAGCCGAT 60.452 52.632 30.64 0.00 41.13 4.18
2055 2071 2.046120 TGTGCATGCATGAGCCGA 60.046 55.556 30.64 5.59 41.13 5.54
2056 2072 1.091197 TAGTGTGCATGCATGAGCCG 61.091 55.000 30.64 3.47 41.13 5.52
2057 2073 0.661552 CTAGTGTGCATGCATGAGCC 59.338 55.000 30.64 16.04 41.13 4.70
2162 2178 4.179361 CTGCCCCTTGCTGTTCAA 57.821 55.556 0.00 0.00 42.00 2.69
2470 2486 1.991121 ACACACTCTAGTCCAACGGA 58.009 50.000 0.00 0.00 0.00 4.69
2474 2490 4.726583 AGACACTACACACTCTAGTCCAA 58.273 43.478 0.00 0.00 0.00 3.53
2512 2532 9.778741 CTGATACACCTCCTTGCTAATATAAAA 57.221 33.333 0.00 0.00 0.00 1.52
2638 2659 1.067495 GCCTTGTACTTCTCGTGAGCT 60.067 52.381 0.00 0.00 0.00 4.09
2672 2694 8.429493 TGCATTACAGTTCTAGAATCTCAATG 57.571 34.615 8.75 15.52 0.00 2.82
2673 2695 9.624373 ATTGCATTACAGTTCTAGAATCTCAAT 57.376 29.630 8.75 9.10 0.00 2.57
2674 2696 9.453572 AATTGCATTACAGTTCTAGAATCTCAA 57.546 29.630 8.75 7.49 0.00 3.02
2676 2698 8.887717 ACAATTGCATTACAGTTCTAGAATCTC 58.112 33.333 8.75 0.00 0.00 2.75
2678 2700 9.846248 AAACAATTGCATTACAGTTCTAGAATC 57.154 29.630 8.75 2.88 0.00 2.52
2679 2701 9.630098 CAAACAATTGCATTACAGTTCTAGAAT 57.370 29.630 8.75 0.00 0.00 2.40
2744 2767 2.093606 TGTCGAGGTGGTGTACAAACAA 60.094 45.455 0.00 0.00 37.36 2.83
2746 2769 2.228138 TGTCGAGGTGGTGTACAAAC 57.772 50.000 0.00 0.00 0.00 2.93
2769 2792 6.954352 AAGTCCTTATACTCTTTGGTCCTT 57.046 37.500 0.00 0.00 0.00 3.36
2784 2807 6.316140 TCGTTGCGTAGAACTATAAGTCCTTA 59.684 38.462 0.00 0.00 0.00 2.69
2805 2828 1.217882 CGTTTGAGGTTGAGCTCGTT 58.782 50.000 9.64 0.00 0.00 3.85
2830 2853 6.891306 TTATTTCAAGGAGAGAAGGGATGA 57.109 37.500 0.00 0.00 0.00 2.92
2858 2910 2.121786 CGGTGCTTGCATCAATATTGC 58.878 47.619 10.76 0.45 40.55 3.56
2907 2975 5.426689 ACCAAGTAGATGATGACACATGT 57.573 39.130 0.00 0.00 0.00 3.21
2916 2984 2.027192 ACGTGGCAACCAAGTAGATGAT 60.027 45.455 3.25 0.00 43.80 2.45
2935 3003 7.807907 AGAAAAACTTCTAAATTGGCATGTACG 59.192 33.333 0.00 0.00 0.00 3.67
3000 3068 4.082571 CCATTCGAATATTTCCATGGCCTC 60.083 45.833 10.97 0.00 32.96 4.70
3017 3085 2.202932 CAGGCCGAGACCCATTCG 60.203 66.667 0.00 0.00 37.78 3.34
3029 3097 2.037847 ATTTGGAGTGGGCAGGCC 59.962 61.111 5.91 5.91 0.00 5.19
3030 3098 1.000396 AGATTTGGAGTGGGCAGGC 60.000 57.895 0.00 0.00 0.00 4.85
3043 3111 0.695803 AGGGATGGAGCGGGAGATTT 60.696 55.000 0.00 0.00 0.00 2.17
3050 3118 1.098050 CAAAGAAAGGGATGGAGCGG 58.902 55.000 0.00 0.00 0.00 5.52
3057 3125 6.044404 TGGACTAGAAGAACAAAGAAAGGGAT 59.956 38.462 0.00 0.00 0.00 3.85
3060 3128 7.418408 GTTTGGACTAGAAGAACAAAGAAAGG 58.582 38.462 0.00 0.00 32.39 3.11
3068 3136 4.675976 TTCCGTTTGGACTAGAAGAACA 57.324 40.909 0.00 0.00 46.45 3.18
3076 3144 6.785337 TCTCTCATATTTCCGTTTGGACTA 57.215 37.500 0.00 0.00 46.45 2.59
3086 3154 8.245195 AGACTCTAACCTTCTCTCATATTTCC 57.755 38.462 0.00 0.00 0.00 3.13
3091 3159 8.690884 CAATCAAGACTCTAACCTTCTCTCATA 58.309 37.037 0.00 0.00 0.00 2.15
3135 3203 2.202987 GGCTCCACTCAGGCATCG 60.203 66.667 0.00 0.00 38.83 3.84
3141 3209 1.595882 CCACTCAGGCTCCACTCAG 59.404 63.158 0.00 0.00 0.00 3.35
3193 3261 0.666374 GAAGGAACCAAACACCCACG 59.334 55.000 0.00 0.00 0.00 4.94
3196 3264 2.658807 AGAGAAGGAACCAAACACCC 57.341 50.000 0.00 0.00 0.00 4.61
3212 3280 2.900546 AGGACAAACTGACCACCTAGAG 59.099 50.000 0.00 0.00 34.63 2.43
3213 3281 2.972348 AGGACAAACTGACCACCTAGA 58.028 47.619 0.00 0.00 34.63 2.43
3216 3284 3.747708 GCTAAAGGACAAACTGACCACCT 60.748 47.826 0.00 0.00 34.63 4.00
3217 3285 2.552743 GCTAAAGGACAAACTGACCACC 59.447 50.000 0.00 0.00 34.63 4.61
3224 3292 9.740710 ATTTATCTAAGTGCTAAAGGACAAACT 57.259 29.630 4.39 0.00 38.96 2.66
3239 3307 6.183360 GCCCGCAGTACAAAATTTATCTAAGT 60.183 38.462 0.00 0.00 0.00 2.24
3240 3308 6.199393 GCCCGCAGTACAAAATTTATCTAAG 58.801 40.000 0.00 0.00 0.00 2.18
3241 3309 5.066764 GGCCCGCAGTACAAAATTTATCTAA 59.933 40.000 0.00 0.00 0.00 2.10
3242 3310 4.577283 GGCCCGCAGTACAAAATTTATCTA 59.423 41.667 0.00 0.00 0.00 1.98
3243 3311 3.380320 GGCCCGCAGTACAAAATTTATCT 59.620 43.478 0.00 0.00 0.00 1.98
3244 3312 3.129638 TGGCCCGCAGTACAAAATTTATC 59.870 43.478 0.00 0.00 0.00 1.75
3245 3313 3.093057 TGGCCCGCAGTACAAAATTTAT 58.907 40.909 0.00 0.00 0.00 1.40
3246 3314 2.515854 TGGCCCGCAGTACAAAATTTA 58.484 42.857 0.00 0.00 0.00 1.40
3247 3315 1.333177 TGGCCCGCAGTACAAAATTT 58.667 45.000 0.00 0.00 0.00 1.82
3248 3316 1.555967 ATGGCCCGCAGTACAAAATT 58.444 45.000 0.00 0.00 0.00 1.82
3249 3317 2.021457 GTATGGCCCGCAGTACAAAAT 58.979 47.619 0.00 0.00 0.00 1.82
3250 3318 1.003812 AGTATGGCCCGCAGTACAAAA 59.996 47.619 0.00 0.00 0.00 2.44
3251 3319 0.616371 AGTATGGCCCGCAGTACAAA 59.384 50.000 0.00 0.00 0.00 2.83
3252 3320 0.107897 CAGTATGGCCCGCAGTACAA 60.108 55.000 0.00 0.00 0.00 2.41
3253 3321 1.261938 ACAGTATGGCCCGCAGTACA 61.262 55.000 0.00 0.00 43.62 2.90
3254 3322 0.107848 AACAGTATGGCCCGCAGTAC 60.108 55.000 0.00 0.00 43.62 2.73
3255 3323 0.616371 AAACAGTATGGCCCGCAGTA 59.384 50.000 0.00 0.00 43.62 2.74
3256 3324 0.616371 TAAACAGTATGGCCCGCAGT 59.384 50.000 0.00 0.00 43.62 4.40
3257 3325 1.603802 CATAAACAGTATGGCCCGCAG 59.396 52.381 0.00 0.00 43.62 5.18
3258 3326 1.210722 TCATAAACAGTATGGCCCGCA 59.789 47.619 0.00 0.00 43.62 5.69
3259 3327 1.602377 GTCATAAACAGTATGGCCCGC 59.398 52.381 0.00 0.00 43.62 6.13
3260 3328 3.131396 GAGTCATAAACAGTATGGCCCG 58.869 50.000 0.00 0.00 43.62 6.13
3261 3329 3.131396 CGAGTCATAAACAGTATGGCCC 58.869 50.000 0.00 0.00 43.62 5.80
3262 3330 2.544267 GCGAGTCATAAACAGTATGGCC 59.456 50.000 0.00 0.00 43.62 5.36
3263 3331 3.458189 AGCGAGTCATAAACAGTATGGC 58.542 45.455 0.00 0.00 43.62 4.40
3264 3332 6.447162 TGATAGCGAGTCATAAACAGTATGG 58.553 40.000 0.00 0.00 43.62 2.74
3265 3333 6.088749 GCTGATAGCGAGTCATAAACAGTATG 59.911 42.308 0.00 0.00 46.00 2.39
3266 3334 6.153067 GCTGATAGCGAGTCATAAACAGTAT 58.847 40.000 0.00 0.00 0.00 2.12
3267 3335 5.520632 GCTGATAGCGAGTCATAAACAGTA 58.479 41.667 0.00 0.00 0.00 2.74
3268 3336 4.363999 GCTGATAGCGAGTCATAAACAGT 58.636 43.478 0.00 0.00 0.00 3.55
3269 3337 4.963237 GCTGATAGCGAGTCATAAACAG 57.037 45.455 0.00 0.00 0.00 3.16
3282 3350 1.373999 CCTGCCTAGCGCTGATAGC 60.374 63.158 22.90 17.28 38.65 2.97
3283 3351 1.373999 GCCTGCCTAGCGCTGATAG 60.374 63.158 22.90 9.77 38.65 2.08
3284 3352 2.092319 CTGCCTGCCTAGCGCTGATA 62.092 60.000 22.90 0.00 38.65 2.15
3285 3353 3.457625 CTGCCTGCCTAGCGCTGAT 62.458 63.158 22.90 0.00 38.65 2.90
3286 3354 4.152964 CTGCCTGCCTAGCGCTGA 62.153 66.667 22.90 3.06 38.65 4.26
3301 3369 3.060615 GTTCTGCCTGGCCAGCTG 61.061 66.667 28.39 23.48 32.87 4.24
3302 3370 2.645394 TTTGTTCTGCCTGGCCAGCT 62.645 55.000 28.39 0.00 32.87 4.24
3303 3371 1.538687 ATTTGTTCTGCCTGGCCAGC 61.539 55.000 28.39 22.00 32.87 4.85
3304 3372 1.747355 CTATTTGTTCTGCCTGGCCAG 59.253 52.381 26.87 26.87 0.00 4.85
3305 3373 1.354031 TCTATTTGTTCTGCCTGGCCA 59.646 47.619 17.53 4.71 0.00 5.36
3306 3374 2.128771 TCTATTTGTTCTGCCTGGCC 57.871 50.000 17.53 0.00 0.00 5.36
3307 3375 3.736126 GCATTCTATTTGTTCTGCCTGGC 60.736 47.826 12.87 12.87 0.00 4.85
3308 3376 3.181483 GGCATTCTATTTGTTCTGCCTGG 60.181 47.826 4.19 0.00 44.47 4.45
3309 3377 4.037858 GGCATTCTATTTGTTCTGCCTG 57.962 45.455 4.19 0.00 44.47 4.85
3312 3380 3.181483 CCCAGGCATTCTATTTGTTCTGC 60.181 47.826 0.00 0.00 0.00 4.26
3313 3381 3.181483 GCCCAGGCATTCTATTTGTTCTG 60.181 47.826 3.12 0.00 41.49 3.02
3314 3382 3.026694 GCCCAGGCATTCTATTTGTTCT 58.973 45.455 3.12 0.00 41.49 3.01
3315 3383 2.223572 CGCCCAGGCATTCTATTTGTTC 60.224 50.000 9.78 0.00 42.06 3.18
3316 3384 1.750778 CGCCCAGGCATTCTATTTGTT 59.249 47.619 9.78 0.00 42.06 2.83
3317 3385 1.064758 TCGCCCAGGCATTCTATTTGT 60.065 47.619 9.78 0.00 42.06 2.83
3318 3386 1.605710 CTCGCCCAGGCATTCTATTTG 59.394 52.381 9.78 0.00 42.06 2.32
3319 3387 1.477558 CCTCGCCCAGGCATTCTATTT 60.478 52.381 9.78 0.00 42.06 1.40
3320 3388 0.109342 CCTCGCCCAGGCATTCTATT 59.891 55.000 9.78 0.00 42.06 1.73
3321 3389 1.757306 CCTCGCCCAGGCATTCTAT 59.243 57.895 9.78 0.00 42.06 1.98
3322 3390 3.230284 CCTCGCCCAGGCATTCTA 58.770 61.111 9.78 0.00 42.06 2.10
3329 3397 3.391665 CTGGTTAGCCTCGCCCAGG 62.392 68.421 0.00 0.00 46.82 4.45
3330 3398 2.187946 CTGGTTAGCCTCGCCCAG 59.812 66.667 0.00 0.00 38.63 4.45
3331 3399 3.399181 CCTGGTTAGCCTCGCCCA 61.399 66.667 0.00 0.00 35.27 5.36
3332 3400 2.967946 AACCTGGTTAGCCTCGCCC 61.968 63.158 11.07 0.00 35.27 6.13
3333 3401 1.745489 CAACCTGGTTAGCCTCGCC 60.745 63.158 12.53 0.00 35.27 5.54
3334 3402 2.399356 GCAACCTGGTTAGCCTCGC 61.399 63.158 12.53 6.66 35.27 5.03
3335 3403 1.745489 GGCAACCTGGTTAGCCTCG 60.745 63.158 29.67 14.11 37.04 4.63
3336 3404 1.685820 AGGCAACCTGGTTAGCCTC 59.314 57.895 32.02 18.45 42.04 4.70
3337 3405 3.922366 AGGCAACCTGGTTAGCCT 58.078 55.556 32.02 32.02 41.47 4.58
3351 3419 2.511545 GAAACATGCTTGGCCCAGGC 62.512 60.000 11.52 11.52 36.98 4.85
3352 3420 0.901580 AGAAACATGCTTGGCCCAGG 60.902 55.000 5.89 0.00 0.00 4.45
3353 3421 0.971386 AAGAAACATGCTTGGCCCAG 59.029 50.000 0.00 0.00 0.00 4.45
3354 3422 1.344114 GAAAGAAACATGCTTGGCCCA 59.656 47.619 0.00 0.00 0.00 5.36
3355 3423 1.620323 AGAAAGAAACATGCTTGGCCC 59.380 47.619 0.00 0.00 0.00 5.80
3356 3424 3.391506 AAGAAAGAAACATGCTTGGCC 57.608 42.857 0.00 0.00 0.00 5.36
3357 3425 4.571984 ACAAAAGAAAGAAACATGCTTGGC 59.428 37.500 4.44 0.00 0.00 4.52
3358 3426 6.667007 AACAAAAGAAAGAAACATGCTTGG 57.333 33.333 4.44 0.00 0.00 3.61
3359 3427 8.953507 AAAAACAAAAGAAAGAAACATGCTTG 57.046 26.923 0.00 0.00 0.00 4.01
3383 3451 9.715121 ACGTGATTAACTTGGTCTAGATTTAAA 57.285 29.630 0.00 0.00 0.00 1.52
3384 3452 9.715121 AACGTGATTAACTTGGTCTAGATTTAA 57.285 29.630 0.00 0.00 0.00 1.52
3385 3453 9.146984 CAACGTGATTAACTTGGTCTAGATTTA 57.853 33.333 0.00 0.00 0.00 1.40
3386 3454 7.360946 GCAACGTGATTAACTTGGTCTAGATTT 60.361 37.037 0.00 0.00 0.00 2.17
3387 3455 6.092259 GCAACGTGATTAACTTGGTCTAGATT 59.908 38.462 0.00 0.00 0.00 2.40
3388 3456 5.581085 GCAACGTGATTAACTTGGTCTAGAT 59.419 40.000 0.00 0.00 0.00 1.98
3389 3457 4.927425 GCAACGTGATTAACTTGGTCTAGA 59.073 41.667 0.00 0.00 0.00 2.43
3390 3458 4.688879 TGCAACGTGATTAACTTGGTCTAG 59.311 41.667 0.00 0.00 0.00 2.43
3391 3459 4.633175 TGCAACGTGATTAACTTGGTCTA 58.367 39.130 0.00 0.00 0.00 2.59
3392 3460 3.472652 TGCAACGTGATTAACTTGGTCT 58.527 40.909 0.00 0.00 0.00 3.85
3393 3461 3.889196 TGCAACGTGATTAACTTGGTC 57.111 42.857 0.00 0.00 0.00 4.02
3394 3462 3.057596 CCATGCAACGTGATTAACTTGGT 60.058 43.478 0.00 0.00 0.00 3.67
3395 3463 3.190327 TCCATGCAACGTGATTAACTTGG 59.810 43.478 0.00 0.00 0.00 3.61
3396 3464 4.083324 AGTCCATGCAACGTGATTAACTTG 60.083 41.667 0.00 0.00 0.00 3.16
3397 3465 4.072131 AGTCCATGCAACGTGATTAACTT 58.928 39.130 0.00 0.00 0.00 2.66
3398 3466 3.674997 AGTCCATGCAACGTGATTAACT 58.325 40.909 0.00 0.00 0.00 2.24
3399 3467 3.181510 GGAGTCCATGCAACGTGATTAAC 60.182 47.826 3.60 0.00 0.00 2.01
3400 3468 3.006940 GGAGTCCATGCAACGTGATTAA 58.993 45.455 3.60 0.00 0.00 1.40
3401 3469 2.627945 GGAGTCCATGCAACGTGATTA 58.372 47.619 3.60 0.00 0.00 1.75
3402 3470 1.453155 GGAGTCCATGCAACGTGATT 58.547 50.000 3.60 0.00 0.00 2.57
3403 3471 0.392998 GGGAGTCCATGCAACGTGAT 60.393 55.000 12.30 0.00 0.00 3.06
3404 3472 1.003839 GGGAGTCCATGCAACGTGA 60.004 57.895 12.30 0.00 0.00 4.35
3405 3473 1.302431 TGGGAGTCCATGCAACGTG 60.302 57.895 12.30 0.00 38.32 4.49
3406 3474 3.156714 TGGGAGTCCATGCAACGT 58.843 55.556 12.30 0.00 38.32 3.99
3415 3483 1.225704 CTTCCTGGCATGGGAGTCC 59.774 63.158 0.00 0.00 34.06 3.85
3416 3484 0.842635 ATCTTCCTGGCATGGGAGTC 59.157 55.000 10.05 0.00 34.33 3.36
3417 3485 0.549950 CATCTTCCTGGCATGGGAGT 59.450 55.000 10.05 0.00 34.33 3.85
3418 3486 0.549950 ACATCTTCCTGGCATGGGAG 59.450 55.000 5.24 5.24 34.06 4.30
3419 3487 1.002069 AACATCTTCCTGGCATGGGA 58.998 50.000 0.00 0.00 0.00 4.37
3420 3488 1.753073 GAAACATCTTCCTGGCATGGG 59.247 52.381 0.00 0.00 0.00 4.00
3421 3489 2.449464 TGAAACATCTTCCTGGCATGG 58.551 47.619 0.00 0.00 0.00 3.66
3422 3490 4.730949 AATGAAACATCTTCCTGGCATG 57.269 40.909 0.00 0.00 0.00 4.06
3423 3491 5.482878 AGAAAATGAAACATCTTCCTGGCAT 59.517 36.000 0.00 0.00 0.00 4.40
3424 3492 4.834496 AGAAAATGAAACATCTTCCTGGCA 59.166 37.500 0.00 0.00 0.00 4.92
3425 3493 5.397142 AGAAAATGAAACATCTTCCTGGC 57.603 39.130 0.00 0.00 0.00 4.85
3426 3494 6.886459 TCCTAGAAAATGAAACATCTTCCTGG 59.114 38.462 0.00 0.00 0.00 4.45
3427 3495 7.391554 TGTCCTAGAAAATGAAACATCTTCCTG 59.608 37.037 0.00 0.00 0.00 3.86
3428 3496 7.391833 GTGTCCTAGAAAATGAAACATCTTCCT 59.608 37.037 0.00 0.00 0.00 3.36
3429 3497 7.362142 GGTGTCCTAGAAAATGAAACATCTTCC 60.362 40.741 0.00 0.00 0.00 3.46
3430 3498 7.174946 TGGTGTCCTAGAAAATGAAACATCTTC 59.825 37.037 0.00 0.00 0.00 2.87
3431 3499 7.004086 TGGTGTCCTAGAAAATGAAACATCTT 58.996 34.615 0.00 0.00 0.00 2.40
3432 3500 6.542821 TGGTGTCCTAGAAAATGAAACATCT 58.457 36.000 0.00 0.00 0.00 2.90
3433 3501 6.817765 TGGTGTCCTAGAAAATGAAACATC 57.182 37.500 0.00 0.00 0.00 3.06
3434 3502 6.378280 GGATGGTGTCCTAGAAAATGAAACAT 59.622 38.462 0.00 0.00 44.16 2.71
3435 3503 5.710099 GGATGGTGTCCTAGAAAATGAAACA 59.290 40.000 0.00 0.00 44.16 2.83
3436 3504 6.196079 GGATGGTGTCCTAGAAAATGAAAC 57.804 41.667 0.00 0.00 44.16 2.78
3450 3518 5.507985 GCCTGCTATTTATTTGGATGGTGTC 60.508 44.000 0.00 0.00 0.00 3.67
3451 3519 4.342092 GCCTGCTATTTATTTGGATGGTGT 59.658 41.667 0.00 0.00 0.00 4.16
3452 3520 4.341806 TGCCTGCTATTTATTTGGATGGTG 59.658 41.667 0.00 0.00 0.00 4.17
3453 3521 4.545678 TGCCTGCTATTTATTTGGATGGT 58.454 39.130 0.00 0.00 0.00 3.55
3454 3522 4.021719 CCTGCCTGCTATTTATTTGGATGG 60.022 45.833 0.00 0.00 0.00 3.51
3455 3523 4.021719 CCCTGCCTGCTATTTATTTGGATG 60.022 45.833 0.00 0.00 0.00 3.51
3456 3524 4.154942 CCCTGCCTGCTATTTATTTGGAT 58.845 43.478 0.00 0.00 0.00 3.41
3457 3525 3.052944 ACCCTGCCTGCTATTTATTTGGA 60.053 43.478 0.00 0.00 0.00 3.53
3458 3526 3.299503 ACCCTGCCTGCTATTTATTTGG 58.700 45.455 0.00 0.00 0.00 3.28
3459 3527 3.319122 GGACCCTGCCTGCTATTTATTTG 59.681 47.826 0.00 0.00 0.00 2.32
3460 3528 3.052944 TGGACCCTGCCTGCTATTTATTT 60.053 43.478 0.00 0.00 0.00 1.40
3461 3529 2.513738 TGGACCCTGCCTGCTATTTATT 59.486 45.455 0.00 0.00 0.00 1.40
3462 3530 2.135189 TGGACCCTGCCTGCTATTTAT 58.865 47.619 0.00 0.00 0.00 1.40
3463 3531 1.590591 TGGACCCTGCCTGCTATTTA 58.409 50.000 0.00 0.00 0.00 1.40
3464 3532 2.397815 TGGACCCTGCCTGCTATTT 58.602 52.632 0.00 0.00 0.00 1.40
3465 3533 4.169452 TGGACCCTGCCTGCTATT 57.831 55.556 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.