Multiple sequence alignment - TraesCS1B01G111300

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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 TraesCS1B01G111300 chr1B 100.000 3461 0 0 1 3461 129178651 129175191 0.000000e+00 6392.0
1 TraesCS1B01G111300 chr1B 95.791 879 36 1 1 879 629157422 629158299 0.000000e+00 1417.0
2 TraesCS1B01G111300 chr1B 94.582 886 48 0 1 886 605010073 605009188 0.000000e+00 1371.0
3 TraesCS1B01G111300 chr1B 94.401 893 47 3 1 892 537665873 537664983 0.000000e+00 1369.0
4 TraesCS1B01G111300 chr1B 92.833 879 61 2 1 879 601005090 601005966 0.000000e+00 1273.0
5 TraesCS1B01G111300 chr1B 75.300 834 172 28 1421 2237 129513275 129512459 5.460000e-98 368.0
6 TraesCS1B01G111300 chr1B 98.000 50 1 0 3281 3330 129175329 129175280 1.710000e-13 87.9
7 TraesCS1B01G111300 chr1B 98.000 50 1 0 3323 3372 129175371 129175322 1.710000e-13 87.9
8 TraesCS1B01G111300 chr1D 90.730 2287 137 32 890 3138 79051176 79048927 0.000000e+00 2979.0
9 TraesCS1B01G111300 chr1D 74.300 821 183 21 1434 2240 79078194 79077388 4.310000e-84 322.0
10 TraesCS1B01G111300 chr1D 90.580 138 8 3 3329 3461 79048882 79048745 9.870000e-41 178.0
11 TraesCS1B01G111300 chr1D 95.349 43 1 1 3239 3281 139142225 139142184 2.230000e-07 67.6
12 TraesCS1B01G111300 chr1D 95.122 41 2 0 3239 3279 486005994 486006034 8.020000e-07 65.8
13 TraesCS1B01G111300 chr1A 90.594 2020 116 22 890 2869 96453180 96455165 0.000000e+00 2610.0
14 TraesCS1B01G111300 chr1A 75.151 829 176 23 1421 2234 96446158 96446971 2.540000e-96 363.0
15 TraesCS1B01G111300 chr3B 94.198 879 50 1 1 879 587971779 587972656 0.000000e+00 1339.0
16 TraesCS1B01G111300 chr3B 90.909 99 7 1 3145 3241 765314414 765314512 7.790000e-27 132.0
17 TraesCS1B01G111300 chr2B 93.126 902 58 4 1 901 491007586 491008484 0.000000e+00 1319.0
18 TraesCS1B01G111300 chr2B 90.816 98 7 1 3146 3241 556203062 556203159 2.800000e-26 130.0
19 TraesCS1B01G111300 chr6B 93.296 895 54 5 1 892 579044233 579043342 0.000000e+00 1315.0
20 TraesCS1B01G111300 chr6B 93.068 880 59 2 1 879 493326734 493325856 0.000000e+00 1286.0
21 TraesCS1B01G111300 chr4A 92.601 892 65 1 1 891 734248450 734247559 0.000000e+00 1280.0
22 TraesCS1B01G111300 chr3A 92.929 99 5 1 3149 3245 21364618 21364520 3.600000e-30 143.0
23 TraesCS1B01G111300 chr2A 91.837 98 6 1 3149 3244 419206977 419206880 6.030000e-28 135.0
24 TraesCS1B01G111300 chr2D 91.753 97 6 1 3147 3241 157450254 157450350 2.170000e-27 134.0
25 TraesCS1B01G111300 chr2D 90.909 99 7 1 3148 3244 169037731 169037633 7.790000e-27 132.0
26 TraesCS1B01G111300 chr2D 83.942 137 13 7 3147 3278 446941883 446942015 4.690000e-24 122.0
27 TraesCS1B01G111300 chr4D 90.909 99 7 1 3148 3244 64390633 64390535 7.790000e-27 132.0
28 TraesCS1B01G111300 chr4D 97.368 38 1 0 3239 3276 509089248 509089285 8.020000e-07 65.8
29 TraesCS1B01G111300 chr3D 91.667 96 6 1 3148 3241 536881483 536881578 7.790000e-27 132.0
30 TraesCS1B01G111300 chr5A 86.325 117 8 6 3131 3241 19681124 19681238 1.690000e-23 121.0
31 TraesCS1B01G111300 chr7A 100.000 37 0 0 3239 3275 203515179 203515215 6.200000e-08 69.4
32 TraesCS1B01G111300 chr6D 97.297 37 1 0 3239 3275 178003353 178003389 2.880000e-06 63.9
33 TraesCS1B01G111300 chrUn 95.000 40 0 1 3236 3275 34149842 34149879 1.040000e-05 62.1
34 TraesCS1B01G111300 chrUn 95.000 40 0 1 3236 3275 282034148 282034185 1.040000e-05 62.1


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 TraesCS1B01G111300 chr1B 129175191 129178651 3460 True 2189.266667 6392 98.666667 1 3461 3 chr1B.!!$R4 3460
1 TraesCS1B01G111300 chr1B 629157422 629158299 877 False 1417.000000 1417 95.791000 1 879 1 chr1B.!!$F2 878
2 TraesCS1B01G111300 chr1B 605009188 605010073 885 True 1371.000000 1371 94.582000 1 886 1 chr1B.!!$R3 885
3 TraesCS1B01G111300 chr1B 537664983 537665873 890 True 1369.000000 1369 94.401000 1 892 1 chr1B.!!$R2 891
4 TraesCS1B01G111300 chr1B 601005090 601005966 876 False 1273.000000 1273 92.833000 1 879 1 chr1B.!!$F1 878
5 TraesCS1B01G111300 chr1B 129512459 129513275 816 True 368.000000 368 75.300000 1421 2237 1 chr1B.!!$R1 816
6 TraesCS1B01G111300 chr1D 79048745 79051176 2431 True 1578.500000 2979 90.655000 890 3461 2 chr1D.!!$R3 2571
7 TraesCS1B01G111300 chr1D 79077388 79078194 806 True 322.000000 322 74.300000 1434 2240 1 chr1D.!!$R1 806
8 TraesCS1B01G111300 chr1A 96453180 96455165 1985 False 2610.000000 2610 90.594000 890 2869 1 chr1A.!!$F2 1979
9 TraesCS1B01G111300 chr1A 96446158 96446971 813 False 363.000000 363 75.151000 1421 2234 1 chr1A.!!$F1 813
10 TraesCS1B01G111300 chr3B 587971779 587972656 877 False 1339.000000 1339 94.198000 1 879 1 chr3B.!!$F1 878
11 TraesCS1B01G111300 chr2B 491007586 491008484 898 False 1319.000000 1319 93.126000 1 901 1 chr2B.!!$F1 900
12 TraesCS1B01G111300 chr6B 579043342 579044233 891 True 1315.000000 1315 93.296000 1 892 1 chr6B.!!$R2 891
13 TraesCS1B01G111300 chr6B 493325856 493326734 878 True 1286.000000 1286 93.068000 1 879 1 chr6B.!!$R1 878
14 TraesCS1B01G111300 chr4A 734247559 734248450 891 True 1280.000000 1280 92.601000 1 891 1 chr4A.!!$R1 890

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
78 79 0.861837 GTTCACACGCTTGGACAGAG 59.138 55.0 0.00 0.0 0.00 3.35 F
1362 1398 0.393077 CGTGGAAGGTCTTGGACAGT 59.607 55.0 0.14 0.0 33.68 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1782 0.460987 CGCCCTTGAGCTTCCAGTAG 60.461 60.0 0.00 0.0 0.0 2.57 R
3332 3387 0.036010 CCGTCAGAGGGAAAGCATGT 60.036 55.0 2.65 0.0 0.0 3.21 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
78 79 0.861837 GTTCACACGCTTGGACAGAG 59.138 55.000 0.00 0.00 0.00 3.35
288 289 1.738030 GCTGCCATCTGGAAATGTTGC 60.738 52.381 0.00 0.00 37.39 4.17
334 335 1.451207 TGGCTCGCGGTGCAATATT 60.451 52.632 22.05 0.00 0.00 1.28
507 508 1.909986 GGAGTAGACCTTCTTTGCCCT 59.090 52.381 0.00 0.00 0.00 5.19
613 614 7.711772 CGGTGGTTATGTTAATATGTTGGTCTA 59.288 37.037 0.00 0.00 0.00 2.59
680 681 2.182614 GATGTGTTTGGCGTGACGGG 62.183 60.000 7.25 0.00 0.00 5.28
789 790 2.362503 AGTGGAGGCGATGTCCGA 60.363 61.111 0.00 0.00 41.76 4.55
845 846 7.246027 ACCTCTTTTGTACATATTTTTCCCCT 58.754 34.615 0.00 0.00 0.00 4.79
995 1010 2.595754 GATCCCCATTCTGCGCCC 60.596 66.667 4.18 0.00 0.00 6.13
1322 1358 2.685380 CTCCTTCCTGCCCGACCT 60.685 66.667 0.00 0.00 0.00 3.85
1362 1398 0.393077 CGTGGAAGGTCTTGGACAGT 59.607 55.000 0.14 0.00 33.68 3.55
1507 1543 4.770362 TCGCCGATCCCCTGACCA 62.770 66.667 0.00 0.00 0.00 4.02
1719 1755 0.464735 AGCATACTCTCGCGGACTCT 60.465 55.000 6.13 0.00 0.00 3.24
1893 1929 2.838225 GCTGGCGGGCTCTACCTA 60.838 66.667 2.38 0.00 39.10 3.08
1915 1951 1.135046 CACTATGCTCGGATTCTGCG 58.865 55.000 0.00 0.00 0.00 5.18
1983 2019 0.038159 CACTGGTGGAGAAGTCGGTC 60.038 60.000 0.00 0.00 0.00 4.79
2118 2157 3.009363 TGCTCTCCATTGATCTGGAAACA 59.991 43.478 5.30 1.89 44.59 2.83
2131 2170 1.888512 TGGAAACAATGAAGCTCAGGC 59.111 47.619 0.00 0.00 37.44 4.85
2161 2200 1.610624 GGAAAGACAAGTGCCCATCGA 60.611 52.381 0.00 0.00 0.00 3.59
2281 2321 8.995027 TTGGCCAACAATCTGATTATTATACT 57.005 30.769 16.05 0.00 33.18 2.12
2282 2322 8.394971 TGGCCAACAATCTGATTATTATACTG 57.605 34.615 0.61 0.00 0.00 2.74
2283 2323 7.998383 TGGCCAACAATCTGATTATTATACTGT 59.002 33.333 0.61 0.00 0.00 3.55
2284 2324 9.502091 GGCCAACAATCTGATTATTATACTGTA 57.498 33.333 0.00 0.00 0.00 2.74
2374 2418 5.458041 ACATACAAAGAACATGCTGCTTT 57.542 34.783 0.00 0.00 32.46 3.51
2395 2442 6.198403 GCTTTACACTCCAAAACTTACTTTGC 59.802 38.462 0.00 0.00 35.38 3.68
2444 2491 7.083062 TCTGATATGCTGAATACCCTGATTT 57.917 36.000 0.00 0.00 0.00 2.17
2486 2533 6.589523 GGCTCACTACAGCTTATGATGATAAG 59.410 42.308 7.50 7.50 42.84 1.73
2513 2560 2.433868 TGTGCAGAGGTAACGAAGAC 57.566 50.000 0.00 0.00 46.39 3.01
2569 2616 2.509336 CCAGTCTAACCGCGCCTG 60.509 66.667 0.00 0.52 0.00 4.85
2572 2619 1.080025 AGTCTAACCGCGCCTGAAC 60.080 57.895 0.00 0.00 0.00 3.18
2584 2631 0.033504 GCCTGAACGTCTGAACCTCA 59.966 55.000 0.00 0.00 0.00 3.86
2634 2684 3.898741 TCTTGGTATGTGTGTGGTCACTA 59.101 43.478 2.66 0.00 44.14 2.74
2640 2690 7.494211 TGGTATGTGTGTGGTCACTATATAAC 58.506 38.462 2.66 4.07 44.14 1.89
2674 2724 2.705658 TCTGGGGAATGCAGTATGTAGG 59.294 50.000 0.00 0.00 39.31 3.18
2685 2735 4.285862 GCAGTATGTAGGACGCTTCCTTG 61.286 52.174 18.06 9.39 45.02 3.61
2730 2784 5.325239 TCTGTCTGACTGTCTCCTCAAATA 58.675 41.667 9.51 0.00 0.00 1.40
2731 2785 5.954752 TCTGTCTGACTGTCTCCTCAAATAT 59.045 40.000 9.51 0.00 0.00 1.28
2749 2803 6.262944 TCAAATATGTGTGATACAATCCTGGC 59.737 38.462 0.00 0.00 43.77 4.85
2760 2814 2.155197 AATCCTGGCTGGGGTTGGAC 62.155 60.000 10.79 0.00 36.20 4.02
2828 2883 5.601662 TCTCAGTCTAATAAATGGGCTTCG 58.398 41.667 0.00 0.00 0.00 3.79
2845 2900 0.462581 TCGAGAATCATGCACAGGGC 60.463 55.000 0.00 0.00 37.98 5.19
2858 2913 2.819608 GCACAGGGCATAAACTGAAGAA 59.180 45.455 0.00 0.00 43.97 2.52
2859 2914 3.119708 GCACAGGGCATAAACTGAAGAAG 60.120 47.826 0.00 0.00 43.97 2.85
2860 2915 4.326826 CACAGGGCATAAACTGAAGAAGA 58.673 43.478 0.00 0.00 38.09 2.87
2861 2916 4.154918 CACAGGGCATAAACTGAAGAAGAC 59.845 45.833 0.00 0.00 38.09 3.01
2862 2917 4.042187 ACAGGGCATAAACTGAAGAAGACT 59.958 41.667 0.00 0.00 38.09 3.24
2864 2919 4.287067 AGGGCATAAACTGAAGAAGACTGA 59.713 41.667 0.00 0.00 0.00 3.41
2869 2924 6.870965 GCATAAACTGAAGAAGACTGAAGAGA 59.129 38.462 0.00 0.00 0.00 3.10
2874 2929 5.127031 ACTGAAGAAGACTGAAGAGATAGCC 59.873 44.000 0.00 0.00 0.00 3.93
2903 2958 3.117171 GCGAGTGCTGTGAGCCTG 61.117 66.667 0.00 0.00 41.51 4.85
2904 2959 2.341543 CGAGTGCTGTGAGCCTGT 59.658 61.111 0.00 0.00 41.51 4.00
2905 2960 2.025969 CGAGTGCTGTGAGCCTGTG 61.026 63.158 0.00 0.00 41.51 3.66
2906 2961 1.368950 GAGTGCTGTGAGCCTGTGA 59.631 57.895 0.00 0.00 41.51 3.58
2912 2967 0.109086 CTGTGAGCCTGTGACTACGG 60.109 60.000 0.00 0.00 0.00 4.02
2914 2969 0.317479 GTGAGCCTGTGACTACGGTT 59.683 55.000 0.00 0.00 0.00 4.44
2915 2970 1.542915 GTGAGCCTGTGACTACGGTTA 59.457 52.381 0.00 0.00 0.00 2.85
2917 2972 2.230508 TGAGCCTGTGACTACGGTTAAG 59.769 50.000 0.00 0.00 0.00 1.85
2933 2988 9.813446 CTACGGTTAAGGTTGATAAATAGTTCT 57.187 33.333 0.00 0.00 0.00 3.01
2935 2990 9.591792 ACGGTTAAGGTTGATAAATAGTTCTAC 57.408 33.333 0.00 0.00 0.00 2.59
2936 2991 9.813446 CGGTTAAGGTTGATAAATAGTTCTACT 57.187 33.333 0.00 0.00 0.00 2.57
2955 3010 5.932303 TCTACTATCAGTTTGTGTTTGAGCC 59.068 40.000 0.00 0.00 0.00 4.70
2956 3011 4.460263 ACTATCAGTTTGTGTTTGAGCCA 58.540 39.130 0.00 0.00 0.00 4.75
2981 3036 9.487790 CATCTTATCTAACCTCTGAAGAATTCC 57.512 37.037 0.65 0.00 46.93 3.01
2982 3037 7.717568 TCTTATCTAACCTCTGAAGAATTCCG 58.282 38.462 0.65 0.00 46.93 4.30
2990 3045 1.863454 CTGAAGAATTCCGGAGATGCG 59.137 52.381 3.34 0.00 46.93 4.73
2995 3050 2.535485 AATTCCGGAGATGCGCCACA 62.535 55.000 3.34 0.00 0.00 4.17
3023 3078 1.407979 CCATCTGCCTCAGAATTTGGC 59.592 52.381 0.27 0.00 44.04 4.52
3028 3083 1.598701 GCCTCAGAATTTGGCGCCTT 61.599 55.000 29.70 14.38 37.11 4.35
3037 3092 0.673437 TTTGGCGCCTTTTTCCTCAG 59.327 50.000 29.70 0.00 0.00 3.35
3039 3094 1.172180 TGGCGCCTTTTTCCTCAGTG 61.172 55.000 29.70 0.00 0.00 3.66
3040 3095 1.172812 GGCGCCTTTTTCCTCAGTGT 61.173 55.000 22.15 0.00 0.00 3.55
3041 3096 1.519408 GCGCCTTTTTCCTCAGTGTA 58.481 50.000 0.00 0.00 0.00 2.90
3045 3100 4.003648 CGCCTTTTTCCTCAGTGTATCTT 58.996 43.478 0.00 0.00 0.00 2.40
3050 3105 3.868757 TTCCTCAGTGTATCTTGGTCG 57.131 47.619 0.00 0.00 0.00 4.79
3051 3106 3.081710 TCCTCAGTGTATCTTGGTCGA 57.918 47.619 0.00 0.00 0.00 4.20
3052 3107 3.017442 TCCTCAGTGTATCTTGGTCGAG 58.983 50.000 0.00 0.00 0.00 4.04
3053 3108 2.099921 CCTCAGTGTATCTTGGTCGAGG 59.900 54.545 0.00 0.00 33.40 4.63
3054 3109 2.755655 CTCAGTGTATCTTGGTCGAGGT 59.244 50.000 0.00 0.00 0.00 3.85
3055 3110 3.162666 TCAGTGTATCTTGGTCGAGGTT 58.837 45.455 0.00 0.00 0.00 3.50
3067 3122 4.634199 TGGTCGAGGTTAAGGTTTTGTAG 58.366 43.478 0.00 0.00 0.00 2.74
3098 3153 0.393077 CTGGTTTCACAGAGACGGGT 59.607 55.000 0.00 0.00 40.97 5.28
3121 3176 6.126449 GGTTATCCCTGTCTTCCTAATTTCCT 60.126 42.308 0.00 0.00 0.00 3.36
3124 3179 6.749036 TCCCTGTCTTCCTAATTTCCTATC 57.251 41.667 0.00 0.00 0.00 2.08
3140 3195 8.743085 ATTTCCTATCATGTATGCATATGGAC 57.257 34.615 10.16 0.00 33.30 4.02
3141 3196 7.500629 TTCCTATCATGTATGCATATGGACT 57.499 36.000 10.16 0.00 33.30 3.85
3142 3197 7.500629 TCCTATCATGTATGCATATGGACTT 57.499 36.000 10.16 0.00 33.30 3.01
3143 3198 7.333323 TCCTATCATGTATGCATATGGACTTG 58.667 38.462 10.16 8.12 33.30 3.16
3151 3206 4.220693 TGCATATGGACTTGCAACTACT 57.779 40.909 4.56 0.00 45.30 2.57
3152 3207 3.940852 TGCATATGGACTTGCAACTACTG 59.059 43.478 4.56 0.00 45.30 2.74
3161 3216 3.460648 GCAACTACTGCCTCCGATT 57.539 52.632 0.00 0.00 46.13 3.34
3163 3218 1.134670 GCAACTACTGCCTCCGATTCT 60.135 52.381 0.00 0.00 46.13 2.40
3165 3220 3.430374 GCAACTACTGCCTCCGATTCTAA 60.430 47.826 0.00 0.00 46.13 2.10
3166 3221 4.755411 CAACTACTGCCTCCGATTCTAAA 58.245 43.478 0.00 0.00 0.00 1.85
3167 3222 5.360591 CAACTACTGCCTCCGATTCTAAAT 58.639 41.667 0.00 0.00 0.00 1.40
3168 3223 6.513180 CAACTACTGCCTCCGATTCTAAATA 58.487 40.000 0.00 0.00 0.00 1.40
3169 3224 6.919775 ACTACTGCCTCCGATTCTAAATAT 57.080 37.500 0.00 0.00 0.00 1.28
3172 3227 8.524487 ACTACTGCCTCCGATTCTAAATATAAG 58.476 37.037 0.00 0.00 0.00 1.73
3174 3229 7.379750 ACTGCCTCCGATTCTAAATATAAGTC 58.620 38.462 0.00 0.00 0.00 3.01
3175 3230 7.233757 ACTGCCTCCGATTCTAAATATAAGTCT 59.766 37.037 0.00 0.00 0.00 3.24
3177 3232 8.429641 TGCCTCCGATTCTAAATATAAGTCTTT 58.570 33.333 0.00 0.00 0.00 2.52
3196 3251 8.602472 AGTCTTTAGAGATTCCAGTATGAACT 57.398 34.615 0.00 0.00 33.55 3.01
3197 3252 9.702253 AGTCTTTAGAGATTCCAGTATGAACTA 57.298 33.333 0.00 0.00 33.55 2.24
3198 3253 9.738832 GTCTTTAGAGATTCCAGTATGAACTAC 57.261 37.037 0.00 0.00 33.55 2.73
3199 3254 9.475620 TCTTTAGAGATTCCAGTATGAACTACA 57.524 33.333 0.00 0.00 39.69 2.74
3213 3268 5.794687 TGAACTACATACGGAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
3214 3269 5.483811 TGAACTACATACGGAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
3215 3270 5.935206 TGAACTACATACGGAGCAAAATGAA 59.065 36.000 0.00 0.00 0.00 2.57
3216 3271 6.597672 TGAACTACATACGGAGCAAAATGAAT 59.402 34.615 0.00 0.00 0.00 2.57
3217 3272 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
3218 3273 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
3219 3274 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
3220 3275 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
3221 3276 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
3222 3277 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
3223 3278 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
3224 3279 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
3225 3280 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
3226 3281 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
3227 3282 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
3228 3283 7.192232 GGAGCAAAATGAATGAATCTACACTC 58.808 38.462 0.00 0.00 0.00 3.51
3229 3284 7.066766 GGAGCAAAATGAATGAATCTACACTCT 59.933 37.037 0.00 0.00 0.00 3.24
3230 3285 9.102757 GAGCAAAATGAATGAATCTACACTCTA 57.897 33.333 0.00 0.00 0.00 2.43
3231 3286 9.453572 AGCAAAATGAATGAATCTACACTCTAA 57.546 29.630 0.00 0.00 0.00 2.10
3266 3321 9.199982 TCTACAAAGACTTATGTTTAGAAACGG 57.800 33.333 7.88 0.00 41.74 4.44
3267 3322 9.199982 CTACAAAGACTTATGTTTAGAAACGGA 57.800 33.333 7.88 0.00 41.74 4.69
3268 3323 8.084590 ACAAAGACTTATGTTTAGAAACGGAG 57.915 34.615 0.97 1.89 41.74 4.63
3269 3324 7.172703 ACAAAGACTTATGTTTAGAAACGGAGG 59.827 37.037 0.97 0.00 41.74 4.30
3270 3325 5.731591 AGACTTATGTTTAGAAACGGAGGG 58.268 41.667 0.97 0.00 41.74 4.30
3271 3326 5.482878 AGACTTATGTTTAGAAACGGAGGGA 59.517 40.000 0.97 0.00 41.74 4.20
3272 3327 5.731591 ACTTATGTTTAGAAACGGAGGGAG 58.268 41.667 0.97 0.00 41.74 4.30
3273 3328 5.247792 ACTTATGTTTAGAAACGGAGGGAGT 59.752 40.000 0.97 0.00 41.74 3.85
3274 3329 6.438425 ACTTATGTTTAGAAACGGAGGGAGTA 59.562 38.462 0.97 0.00 41.74 2.59
3275 3330 4.525912 TGTTTAGAAACGGAGGGAGTAC 57.474 45.455 0.97 0.00 41.74 2.73
3276 3331 3.896888 TGTTTAGAAACGGAGGGAGTACA 59.103 43.478 0.00 0.00 41.74 2.90
3277 3332 4.344679 TGTTTAGAAACGGAGGGAGTACAA 59.655 41.667 0.00 0.00 41.74 2.41
3278 3333 5.012354 TGTTTAGAAACGGAGGGAGTACAAT 59.988 40.000 0.00 0.00 41.74 2.71
3279 3334 3.611766 AGAAACGGAGGGAGTACAATG 57.388 47.619 0.00 0.00 0.00 2.82
3280 3335 2.007608 GAAACGGAGGGAGTACAATGC 58.992 52.381 0.00 0.00 0.00 3.56
3281 3336 0.981183 AACGGAGGGAGTACAATGCA 59.019 50.000 0.00 0.00 0.00 3.96
3282 3337 0.981183 ACGGAGGGAGTACAATGCAA 59.019 50.000 0.00 0.00 0.00 4.08
3283 3338 1.066143 ACGGAGGGAGTACAATGCAAG 60.066 52.381 0.00 0.00 0.00 4.01
3284 3339 1.066143 CGGAGGGAGTACAATGCAAGT 60.066 52.381 0.00 0.00 0.00 3.16
3285 3340 2.359900 GGAGGGAGTACAATGCAAGTG 58.640 52.381 5.51 2.53 38.30 3.16
3299 3354 2.926165 GCAAGTGTCAGACATGCTTTC 58.074 47.619 18.29 5.18 44.32 2.62
3319 3374 0.588252 CCTCTGACGGTGCAGTTTTG 59.412 55.000 0.00 0.00 37.20 2.44
3320 3375 1.299541 CTCTGACGGTGCAGTTTTGT 58.700 50.000 0.00 0.00 37.20 2.83
3321 3376 1.670811 CTCTGACGGTGCAGTTTTGTT 59.329 47.619 0.00 0.00 37.20 2.83
3322 3377 1.668751 TCTGACGGTGCAGTTTTGTTC 59.331 47.619 0.00 0.00 37.20 3.18
3323 3378 1.400142 CTGACGGTGCAGTTTTGTTCA 59.600 47.619 0.00 0.00 0.00 3.18
3324 3379 1.813178 TGACGGTGCAGTTTTGTTCAA 59.187 42.857 0.00 0.00 0.00 2.69
3325 3380 2.159448 TGACGGTGCAGTTTTGTTCAAG 60.159 45.455 0.00 0.00 0.00 3.02
3326 3381 1.816224 ACGGTGCAGTTTTGTTCAAGT 59.184 42.857 0.00 0.00 0.00 3.16
3327 3382 2.184448 CGGTGCAGTTTTGTTCAAGTG 58.816 47.619 0.00 0.00 0.00 3.16
3328 3383 2.415357 CGGTGCAGTTTTGTTCAAGTGT 60.415 45.455 0.00 0.00 30.74 3.55
3329 3384 3.179048 GGTGCAGTTTTGTTCAAGTGTC 58.821 45.455 0.00 0.00 30.74 3.67
3330 3385 3.366883 GGTGCAGTTTTGTTCAAGTGTCA 60.367 43.478 0.00 0.00 30.74 3.58
3331 3386 3.853671 GTGCAGTTTTGTTCAAGTGTCAG 59.146 43.478 0.00 0.00 30.74 3.51
3332 3387 3.755905 TGCAGTTTTGTTCAAGTGTCAGA 59.244 39.130 0.00 0.00 30.74 3.27
3333 3388 4.098416 GCAGTTTTGTTCAAGTGTCAGAC 58.902 43.478 0.00 0.00 30.74 3.51
3334 3389 4.379394 GCAGTTTTGTTCAAGTGTCAGACA 60.379 41.667 0.00 0.00 30.74 3.41
3335 3390 5.677091 GCAGTTTTGTTCAAGTGTCAGACAT 60.677 40.000 6.51 0.00 30.74 3.06
3336 3391 5.740569 CAGTTTTGTTCAAGTGTCAGACATG 59.259 40.000 6.51 1.90 0.00 3.21
3337 3392 3.969117 TTGTTCAAGTGTCAGACATGC 57.031 42.857 6.51 0.00 0.00 4.06
3338 3393 3.198409 TGTTCAAGTGTCAGACATGCT 57.802 42.857 6.51 0.00 0.00 3.79
3339 3394 3.544684 TGTTCAAGTGTCAGACATGCTT 58.455 40.909 6.51 3.52 0.00 3.91
3340 3395 3.947196 TGTTCAAGTGTCAGACATGCTTT 59.053 39.130 6.51 0.00 0.00 3.51
3341 3396 4.035558 TGTTCAAGTGTCAGACATGCTTTC 59.964 41.667 6.51 0.00 0.00 2.62
3342 3397 3.141398 TCAAGTGTCAGACATGCTTTCC 58.859 45.455 6.51 0.00 0.00 3.13
3343 3398 2.191128 AGTGTCAGACATGCTTTCCC 57.809 50.000 6.51 0.00 0.00 3.97
3344 3399 1.701847 AGTGTCAGACATGCTTTCCCT 59.298 47.619 6.51 0.00 0.00 4.20
3345 3400 2.079925 GTGTCAGACATGCTTTCCCTC 58.920 52.381 6.51 0.00 0.00 4.30
3346 3401 1.980765 TGTCAGACATGCTTTCCCTCT 59.019 47.619 0.00 0.00 0.00 3.69
3347 3402 2.289882 TGTCAGACATGCTTTCCCTCTG 60.290 50.000 0.00 0.00 0.00 3.35
3348 3403 2.027745 GTCAGACATGCTTTCCCTCTGA 60.028 50.000 5.98 5.98 35.98 3.27
3349 3404 2.027745 TCAGACATGCTTTCCCTCTGAC 60.028 50.000 5.98 0.00 33.92 3.51
3350 3405 1.066573 AGACATGCTTTCCCTCTGACG 60.067 52.381 0.00 0.00 0.00 4.35
3351 3406 0.036010 ACATGCTTTCCCTCTGACGG 60.036 55.000 0.00 0.00 0.00 4.79
3352 3407 0.036010 CATGCTTTCCCTCTGACGGT 60.036 55.000 0.00 0.00 0.00 4.83
3353 3408 0.036010 ATGCTTTCCCTCTGACGGTG 60.036 55.000 0.00 0.00 0.00 4.94
3354 3409 2.035442 GCTTTCCCTCTGACGGTGC 61.035 63.158 0.00 0.00 0.00 5.01
3355 3410 1.371183 CTTTCCCTCTGACGGTGCA 59.629 57.895 0.00 0.00 0.00 4.57
3356 3411 0.671781 CTTTCCCTCTGACGGTGCAG 60.672 60.000 0.00 0.00 37.24 4.41
3357 3412 1.407656 TTTCCCTCTGACGGTGCAGT 61.408 55.000 0.00 0.00 37.20 4.40
3358 3413 1.407656 TTCCCTCTGACGGTGCAGTT 61.408 55.000 0.00 0.00 37.20 3.16
3359 3414 1.071471 CCCTCTGACGGTGCAGTTT 59.929 57.895 0.00 0.00 37.20 2.66
3369 3424 1.199624 GGTGCAGTTTTGTTCAAGCG 58.800 50.000 0.00 0.00 0.00 4.68
3380 3437 1.600636 TTCAAGCGTCTGGGCCTTG 60.601 57.895 4.53 0.00 0.00 3.61
3391 3448 3.055385 GTCTGGGCCTTGACATGTTACTA 60.055 47.826 19.97 0.00 33.75 1.82
3393 3450 3.879295 CTGGGCCTTGACATGTTACTATG 59.121 47.826 4.53 0.00 0.00 2.23
3409 3466 8.948631 TGTTACTATGAAAGTGATCATCCTTC 57.051 34.615 0.00 3.20 40.44 3.46
3413 3470 3.955471 TGAAAGTGATCATCCTTCCACC 58.045 45.455 0.00 0.00 0.00 4.61
3445 3502 4.763793 ACATTCAGAAAAGACACAGGGATG 59.236 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 0.107361 CAAGGGTCCCGGTAATGTCC 60.107 60.000 0.99 0.00 0.00 4.02
210 211 2.288213 CCTATAAGTCGATGCTGCGGAA 60.288 50.000 0.00 0.00 0.00 4.30
334 335 0.250295 CTGTCCGAAGTCCAAAGGCA 60.250 55.000 0.00 0.00 0.00 4.75
382 383 2.298661 AAAGGTAGCACGGGGAGGG 61.299 63.158 0.00 0.00 0.00 4.30
439 440 1.107945 TGCCTAGCATACACGCACTA 58.892 50.000 0.00 0.00 31.71 2.74
507 508 1.561769 CCAGGTGGGACTGCACCATA 61.562 60.000 0.00 0.00 43.61 2.74
613 614 1.203052 CGCATTCCTTTGCTTCCACAT 59.797 47.619 0.00 0.00 40.54 3.21
789 790 0.248907 CACGTGGTCACAAGTCGACT 60.249 55.000 13.58 13.58 37.20 4.18
840 841 7.310237 GCGTACCATAGATTTATAGAAAGGGGA 60.310 40.741 0.00 0.00 0.00 4.81
845 846 9.268268 CAAAGGCGTACCATAGATTTATAGAAA 57.732 33.333 0.00 0.00 39.06 2.52
855 856 3.772619 GCCAAAGGCGTACCATAGA 57.227 52.632 0.00 0.00 39.62 1.98
909 910 4.012895 GCGTGGGACGTGTTGCTG 62.013 66.667 0.00 0.00 44.73 4.41
1107 1128 4.729918 AAGGGCTTGCAGGCGAGG 62.730 66.667 15.24 0.00 42.43 4.63
1349 1385 1.668294 CTGCGACTGTCCAAGACCT 59.332 57.895 1.55 0.00 0.00 3.85
1507 1543 2.757917 GAGAGAGACCCAGCGCCT 60.758 66.667 2.29 0.00 0.00 5.52
1578 1614 4.287781 TGGAACGCCGACGAGCAA 62.288 61.111 0.00 0.00 43.93 3.91
1606 1642 2.861006 GCCGCCGTCTTCTGAAAC 59.139 61.111 0.00 0.00 0.00 2.78
1646 1682 3.073735 CGCTGGAGGAGAGCACCT 61.074 66.667 0.00 0.00 43.64 4.00
1706 1742 3.578272 CCCGAGAGTCCGCGAGAG 61.578 72.222 8.23 0.00 37.82 3.20
1719 1755 2.032634 GTTCGCTTGCATCACCCGA 61.033 57.895 0.00 0.00 0.00 5.14
1746 1782 0.460987 CGCCCTTGAGCTTCCAGTAG 60.461 60.000 0.00 0.00 0.00 2.57
1782 1818 1.733041 CATCGTCGCCGTGTTGAGT 60.733 57.895 0.00 0.00 35.01 3.41
1893 1929 2.223923 GCAGAATCCGAGCATAGTGAGT 60.224 50.000 0.00 0.00 0.00 3.41
1983 2019 1.077212 CATGGCCCTCTGGAACCTG 60.077 63.158 0.00 0.00 0.00 4.00
2020 2056 0.958091 CCATGCCGGAAAAACTGTGA 59.042 50.000 5.05 0.00 36.56 3.58
2030 2066 0.535335 GACAACTAGTCCATGCCGGA 59.465 55.000 5.05 0.00 43.61 5.14
2043 2079 1.703411 CAACCACCCCAATGACAACT 58.297 50.000 0.00 0.00 0.00 3.16
2131 2170 1.532868 CTTGTCTTTCCGAGCCAACAG 59.467 52.381 0.00 0.00 0.00 3.16
2161 2200 3.638860 TCGTGTAAGGATACATCAGGGT 58.361 45.455 0.00 0.00 43.60 4.34
2193 2232 1.282157 GTAGGGTTCAGGCATGAAGGT 59.718 52.381 15.13 4.59 45.96 3.50
2357 2401 4.863491 AGTGTAAAGCAGCATGTTCTTTG 58.137 39.130 14.75 1.04 39.31 2.77
2374 2418 5.235616 CGAGCAAAGTAAGTTTTGGAGTGTA 59.764 40.000 1.28 0.00 38.25 2.90
2395 2442 0.321564 TCACCCAACCAAGATGCGAG 60.322 55.000 0.00 0.00 0.00 5.03
2444 2491 1.246056 GCCTCACATTCCTGCAGCAA 61.246 55.000 8.66 0.00 0.00 3.91
2486 2533 3.303791 CGTTACCTCTGCACAAAACCTTC 60.304 47.826 0.00 0.00 0.00 3.46
2513 2560 5.696270 TCGTATGGATGATTGAATTCCTTCG 59.304 40.000 2.27 1.43 33.86 3.79
2569 2616 5.352284 ACATCATATGAGGTTCAGACGTTC 58.648 41.667 16.96 0.00 35.29 3.95
2572 2619 7.953158 AATTACATCATATGAGGTTCAGACG 57.047 36.000 26.29 2.20 39.91 4.18
2606 2653 3.250744 CACACACATACCAAGACCGTAG 58.749 50.000 0.00 0.00 0.00 3.51
2634 2684 6.465321 CCCCAGATTACAAAGTCGGGTTATAT 60.465 42.308 0.00 0.00 30.95 0.86
2640 2690 1.557832 TCCCCAGATTACAAAGTCGGG 59.442 52.381 0.00 0.00 0.00 5.14
2674 2724 1.160137 ACAATCAGCAAGGAAGCGTC 58.840 50.000 0.00 0.00 40.15 5.19
2685 2735 4.829064 TGAACTGGTACAAACAATCAGC 57.171 40.909 0.00 0.00 38.70 4.26
2730 2784 3.548770 CAGCCAGGATTGTATCACACAT 58.451 45.455 0.00 0.00 36.90 3.21
2731 2785 2.356022 CCAGCCAGGATTGTATCACACA 60.356 50.000 0.00 0.00 41.22 3.72
2749 2803 3.967326 TGATAGATACAGTCCAACCCCAG 59.033 47.826 0.00 0.00 0.00 4.45
2760 2814 6.652900 TCGAAGGAGACAGATGATAGATACAG 59.347 42.308 0.00 0.00 0.00 2.74
2858 2913 2.038659 GCCAGGCTATCTCTTCAGTCT 58.961 52.381 3.29 0.00 0.00 3.24
2859 2914 2.038659 AGCCAGGCTATCTCTTCAGTC 58.961 52.381 14.18 0.00 36.99 3.51
2860 2915 2.173126 AGCCAGGCTATCTCTTCAGT 57.827 50.000 14.18 0.00 36.99 3.41
2899 2954 1.274447 ACCTTAACCGTAGTCACAGGC 59.726 52.381 0.00 0.00 0.00 4.85
2900 2955 3.006110 TCAACCTTAACCGTAGTCACAGG 59.994 47.826 0.00 0.00 0.00 4.00
2901 2956 4.247267 TCAACCTTAACCGTAGTCACAG 57.753 45.455 0.00 0.00 0.00 3.66
2902 2957 4.877378 ATCAACCTTAACCGTAGTCACA 57.123 40.909 0.00 0.00 0.00 3.58
2903 2958 7.838771 ATTTATCAACCTTAACCGTAGTCAC 57.161 36.000 0.00 0.00 0.00 3.67
2904 2959 8.752187 ACTATTTATCAACCTTAACCGTAGTCA 58.248 33.333 0.00 0.00 0.00 3.41
2905 2960 9.591792 AACTATTTATCAACCTTAACCGTAGTC 57.408 33.333 0.00 0.00 0.00 2.59
2906 2961 9.591792 GAACTATTTATCAACCTTAACCGTAGT 57.408 33.333 0.00 0.00 0.00 2.73
2933 2988 5.616270 TGGCTCAAACACAAACTGATAGTA 58.384 37.500 0.00 0.00 0.00 1.82
2934 2989 4.460263 TGGCTCAAACACAAACTGATAGT 58.540 39.130 0.00 0.00 0.00 2.12
2935 2990 5.413833 AGATGGCTCAAACACAAACTGATAG 59.586 40.000 0.00 0.00 0.00 2.08
2936 2991 5.316167 AGATGGCTCAAACACAAACTGATA 58.684 37.500 0.00 0.00 0.00 2.15
2943 2998 6.374333 GGTTAGATAAGATGGCTCAAACACAA 59.626 38.462 0.00 0.00 0.00 3.33
2955 3010 9.487790 GGAATTCTTCAGAGGTTAGATAAGATG 57.512 37.037 5.23 0.00 0.00 2.90
2956 3011 8.364142 CGGAATTCTTCAGAGGTTAGATAAGAT 58.636 37.037 5.23 0.00 0.00 2.40
2980 3035 3.451556 ATCTGTGGCGCATCTCCGG 62.452 63.158 10.83 0.00 0.00 5.14
2981 3036 2.107750 ATCTGTGGCGCATCTCCG 59.892 61.111 10.83 0.00 0.00 4.63
2982 3037 1.890979 CCATCTGTGGCGCATCTCC 60.891 63.158 10.83 0.00 39.01 3.71
2990 3045 2.520260 GATGGCCCCATCTGTGGC 60.520 66.667 17.90 0.00 46.67 5.01
3016 3071 1.691434 TGAGGAAAAAGGCGCCAAATT 59.309 42.857 31.54 19.63 0.00 1.82
3017 3072 1.273327 CTGAGGAAAAAGGCGCCAAAT 59.727 47.619 31.54 11.91 0.00 2.32
3023 3078 3.600388 AGATACACTGAGGAAAAAGGCG 58.400 45.455 0.00 0.00 0.00 5.52
3028 3083 4.282449 TCGACCAAGATACACTGAGGAAAA 59.718 41.667 0.00 0.00 0.00 2.29
3037 3092 4.081807 ACCTTAACCTCGACCAAGATACAC 60.082 45.833 0.00 0.00 0.00 2.90
3039 3094 4.732672 ACCTTAACCTCGACCAAGATAC 57.267 45.455 0.00 0.00 0.00 2.24
3040 3095 5.750352 AAACCTTAACCTCGACCAAGATA 57.250 39.130 0.00 0.00 0.00 1.98
3041 3096 4.635699 AAACCTTAACCTCGACCAAGAT 57.364 40.909 0.00 0.00 0.00 2.40
3045 3100 3.564053 ACAAAACCTTAACCTCGACCA 57.436 42.857 0.00 0.00 0.00 4.02
3050 3105 4.825634 ACTTGCCTACAAAACCTTAACCTC 59.174 41.667 0.00 0.00 34.74 3.85
3051 3106 4.800023 ACTTGCCTACAAAACCTTAACCT 58.200 39.130 0.00 0.00 34.74 3.50
3052 3107 6.638096 TTACTTGCCTACAAAACCTTAACC 57.362 37.500 0.00 0.00 34.74 2.85
3053 3108 7.709947 AGTTTACTTGCCTACAAAACCTTAAC 58.290 34.615 0.00 0.00 34.74 2.01
3054 3109 7.776500 AGAGTTTACTTGCCTACAAAACCTTAA 59.224 33.333 0.00 0.00 34.74 1.85
3055 3110 7.227910 CAGAGTTTACTTGCCTACAAAACCTTA 59.772 37.037 0.00 0.00 34.74 2.69
3067 3122 3.630312 TGTGAAACCAGAGTTTACTTGCC 59.370 43.478 0.00 0.00 46.25 4.52
3098 3153 8.814448 ATAGGAAATTAGGAAGACAGGGATAA 57.186 34.615 0.00 0.00 0.00 1.75
3119 3174 6.037940 GCAAGTCCATATGCATACATGATAGG 59.962 42.308 8.99 3.19 42.12 2.57
3121 3176 6.474630 TGCAAGTCCATATGCATACATGATA 58.525 36.000 8.99 0.00 46.87 2.15
3145 3200 5.615925 ATTTAGAATCGGAGGCAGTAGTT 57.384 39.130 0.00 0.00 0.00 2.24
3146 3201 6.919775 ATATTTAGAATCGGAGGCAGTAGT 57.080 37.500 0.00 0.00 0.00 2.73
3147 3202 8.524487 ACTTATATTTAGAATCGGAGGCAGTAG 58.476 37.037 0.00 0.00 0.00 2.57
3149 3204 7.233757 AGACTTATATTTAGAATCGGAGGCAGT 59.766 37.037 0.00 0.00 0.00 4.40
3151 3206 7.540474 AGACTTATATTTAGAATCGGAGGCA 57.460 36.000 0.00 0.00 0.00 4.75
3152 3207 8.834749 AAAGACTTATATTTAGAATCGGAGGC 57.165 34.615 0.00 0.00 0.00 4.70
3172 3227 9.738832 GTAGTTCATACTGGAATCTCTAAAGAC 57.261 37.037 0.00 0.00 35.78 3.01
3189 3244 7.269316 TCATTTTGCTCCGTATGTAGTTCATA 58.731 34.615 0.00 0.00 37.91 2.15
3190 3245 6.112734 TCATTTTGCTCCGTATGTAGTTCAT 58.887 36.000 0.00 0.00 40.25 2.57
3191 3246 5.483811 TCATTTTGCTCCGTATGTAGTTCA 58.516 37.500 0.00 0.00 0.00 3.18
3192 3247 6.417191 TTCATTTTGCTCCGTATGTAGTTC 57.583 37.500 0.00 0.00 0.00 3.01
3193 3248 6.597672 TCATTCATTTTGCTCCGTATGTAGTT 59.402 34.615 0.00 0.00 0.00 2.24
3194 3249 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
3195 3250 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
3196 3251 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
3197 3252 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
3198 3253 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
3199 3254 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
3200 3255 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
3201 3256 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
3202 3257 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
3203 3258 7.066766 AGAGTGTAGATTCATTCATTTTGCTCC 59.933 37.037 0.00 0.00 0.00 4.70
3204 3259 7.983307 AGAGTGTAGATTCATTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
3205 3260 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
3240 3295 9.199982 CCGTTTCTAAACATAAGTCTTTGTAGA 57.800 33.333 6.41 0.00 38.81 2.59
3241 3296 9.199982 TCCGTTTCTAAACATAAGTCTTTGTAG 57.800 33.333 6.41 0.00 38.81 2.74
3242 3297 9.199982 CTCCGTTTCTAAACATAAGTCTTTGTA 57.800 33.333 6.41 0.00 38.81 2.41
3243 3298 7.172703 CCTCCGTTTCTAAACATAAGTCTTTGT 59.827 37.037 6.41 0.00 38.81 2.83
3244 3299 7.360946 CCCTCCGTTTCTAAACATAAGTCTTTG 60.361 40.741 6.41 0.00 38.81 2.77
3245 3300 6.653740 CCCTCCGTTTCTAAACATAAGTCTTT 59.346 38.462 6.41 0.00 38.81 2.52
3246 3301 6.013984 TCCCTCCGTTTCTAAACATAAGTCTT 60.014 38.462 6.41 0.00 38.81 3.01
3247 3302 5.482878 TCCCTCCGTTTCTAAACATAAGTCT 59.517 40.000 6.41 0.00 38.81 3.24
3248 3303 5.727434 TCCCTCCGTTTCTAAACATAAGTC 58.273 41.667 6.41 0.00 38.81 3.01
3249 3304 5.247792 ACTCCCTCCGTTTCTAAACATAAGT 59.752 40.000 6.41 0.00 38.81 2.24
3250 3305 5.731591 ACTCCCTCCGTTTCTAAACATAAG 58.268 41.667 6.41 0.62 38.81 1.73
3251 3306 5.750352 ACTCCCTCCGTTTCTAAACATAA 57.250 39.130 6.41 0.00 38.81 1.90
3252 3307 5.716228 TGTACTCCCTCCGTTTCTAAACATA 59.284 40.000 6.41 0.00 38.81 2.29
3253 3308 4.529377 TGTACTCCCTCCGTTTCTAAACAT 59.471 41.667 6.41 0.00 38.81 2.71
3254 3309 3.896888 TGTACTCCCTCCGTTTCTAAACA 59.103 43.478 6.41 0.00 38.81 2.83
3255 3310 4.525912 TGTACTCCCTCCGTTTCTAAAC 57.474 45.455 0.00 0.00 35.59 2.01
3256 3311 5.484715 CATTGTACTCCCTCCGTTTCTAAA 58.515 41.667 0.00 0.00 0.00 1.85
3257 3312 4.622220 GCATTGTACTCCCTCCGTTTCTAA 60.622 45.833 0.00 0.00 0.00 2.10
3258 3313 3.118884 GCATTGTACTCCCTCCGTTTCTA 60.119 47.826 0.00 0.00 0.00 2.10
3259 3314 2.354805 GCATTGTACTCCCTCCGTTTCT 60.355 50.000 0.00 0.00 0.00 2.52
3260 3315 2.007608 GCATTGTACTCCCTCCGTTTC 58.992 52.381 0.00 0.00 0.00 2.78
3261 3316 1.349688 TGCATTGTACTCCCTCCGTTT 59.650 47.619 0.00 0.00 0.00 3.60
3262 3317 0.981183 TGCATTGTACTCCCTCCGTT 59.019 50.000 0.00 0.00 0.00 4.44
3263 3318 0.981183 TTGCATTGTACTCCCTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
3264 3319 1.066143 ACTTGCATTGTACTCCCTCCG 60.066 52.381 0.00 0.00 0.00 4.63
3265 3320 2.290323 ACACTTGCATTGTACTCCCTCC 60.290 50.000 0.00 0.00 0.00 4.30
3266 3321 3.003480 GACACTTGCATTGTACTCCCTC 58.997 50.000 1.59 0.00 0.00 4.30
3267 3322 2.371841 TGACACTTGCATTGTACTCCCT 59.628 45.455 1.59 0.00 0.00 4.20
3268 3323 2.744202 CTGACACTTGCATTGTACTCCC 59.256 50.000 1.59 0.00 0.00 4.30
3269 3324 3.433615 GTCTGACACTTGCATTGTACTCC 59.566 47.826 2.24 0.00 0.00 3.85
3270 3325 4.058124 TGTCTGACACTTGCATTGTACTC 58.942 43.478 6.36 0.00 0.00 2.59
3271 3326 4.071961 TGTCTGACACTTGCATTGTACT 57.928 40.909 6.36 0.00 0.00 2.73
3272 3327 4.715896 CATGTCTGACACTTGCATTGTAC 58.284 43.478 13.50 0.00 0.00 2.90
3274 3329 3.909776 CATGTCTGACACTTGCATTGT 57.090 42.857 13.50 1.18 0.00 2.71
3280 3335 2.227388 GGGAAAGCATGTCTGACACTTG 59.773 50.000 13.50 9.74 34.01 3.16
3281 3336 2.107204 AGGGAAAGCATGTCTGACACTT 59.893 45.455 13.50 10.03 0.00 3.16
3282 3337 1.701847 AGGGAAAGCATGTCTGACACT 59.298 47.619 13.50 3.77 0.00 3.55
3283 3338 2.079925 GAGGGAAAGCATGTCTGACAC 58.920 52.381 13.50 1.16 0.00 3.67
3284 3339 1.980765 AGAGGGAAAGCATGTCTGACA 59.019 47.619 13.60 13.60 0.00 3.58
3285 3340 2.027745 TCAGAGGGAAAGCATGTCTGAC 60.028 50.000 0.00 0.00 38.94 3.51
3299 3354 0.535102 AAAACTGCACCGTCAGAGGG 60.535 55.000 7.67 7.67 37.51 4.30
3319 3374 4.531332 GAAAGCATGTCTGACACTTGAAC 58.469 43.478 13.50 5.40 32.87 3.18
3320 3375 3.565482 GGAAAGCATGTCTGACACTTGAA 59.435 43.478 13.50 0.00 32.87 2.69
3321 3376 3.141398 GGAAAGCATGTCTGACACTTGA 58.859 45.455 13.50 0.00 32.87 3.02
3322 3377 2.227388 GGGAAAGCATGTCTGACACTTG 59.773 50.000 13.50 9.74 34.01 3.16
3323 3378 2.107204 AGGGAAAGCATGTCTGACACTT 59.893 45.455 13.50 10.03 0.00 3.16
3324 3379 1.701847 AGGGAAAGCATGTCTGACACT 59.298 47.619 13.50 3.77 0.00 3.55
3325 3380 2.079925 GAGGGAAAGCATGTCTGACAC 58.920 52.381 13.50 1.16 0.00 3.67
3326 3381 1.980765 AGAGGGAAAGCATGTCTGACA 59.019 47.619 13.60 13.60 0.00 3.58
3327 3382 2.027745 TCAGAGGGAAAGCATGTCTGAC 60.028 50.000 0.00 0.00 38.94 3.51
3328 3383 2.027745 GTCAGAGGGAAAGCATGTCTGA 60.028 50.000 5.98 5.98 41.01 3.27
3329 3384 2.354259 GTCAGAGGGAAAGCATGTCTG 58.646 52.381 0.00 0.00 36.73 3.51
3330 3385 1.066573 CGTCAGAGGGAAAGCATGTCT 60.067 52.381 0.00 0.00 0.00 3.41
3331 3386 1.363744 CGTCAGAGGGAAAGCATGTC 58.636 55.000 0.00 0.00 0.00 3.06
3332 3387 0.036010 CCGTCAGAGGGAAAGCATGT 60.036 55.000 2.65 0.00 0.00 3.21
3333 3388 0.036010 ACCGTCAGAGGGAAAGCATG 60.036 55.000 16.38 0.00 35.02 4.06
3334 3389 0.036010 CACCGTCAGAGGGAAAGCAT 60.036 55.000 16.38 0.00 35.02 3.79
3335 3390 1.371183 CACCGTCAGAGGGAAAGCA 59.629 57.895 16.38 0.00 35.02 3.91
3336 3391 2.035442 GCACCGTCAGAGGGAAAGC 61.035 63.158 16.38 12.12 35.02 3.51
3337 3392 0.671781 CTGCACCGTCAGAGGGAAAG 60.672 60.000 16.38 6.20 36.19 2.62
3338 3393 1.371183 CTGCACCGTCAGAGGGAAA 59.629 57.895 16.38 0.20 36.19 3.13
3339 3394 1.407656 AACTGCACCGTCAGAGGGAA 61.408 55.000 16.38 0.54 37.51 3.97
3340 3395 1.407656 AAACTGCACCGTCAGAGGGA 61.408 55.000 16.38 0.00 37.51 4.20
3341 3396 0.535102 AAAACTGCACCGTCAGAGGG 60.535 55.000 7.67 7.67 37.51 4.30
3342 3397 0.588252 CAAAACTGCACCGTCAGAGG 59.412 55.000 3.99 0.00 37.51 3.69
3343 3398 1.299541 ACAAAACTGCACCGTCAGAG 58.700 50.000 3.99 0.00 37.51 3.35
3344 3399 1.668751 GAACAAAACTGCACCGTCAGA 59.331 47.619 3.99 0.00 37.51 3.27
3345 3400 1.400142 TGAACAAAACTGCACCGTCAG 59.600 47.619 0.00 0.00 39.86 3.51
3346 3401 1.454201 TGAACAAAACTGCACCGTCA 58.546 45.000 0.00 0.00 0.00 4.35
3347 3402 2.450160 CTTGAACAAAACTGCACCGTC 58.550 47.619 0.00 0.00 0.00 4.79
3348 3403 1.469079 GCTTGAACAAAACTGCACCGT 60.469 47.619 0.00 0.00 0.00 4.83
3349 3404 1.199624 GCTTGAACAAAACTGCACCG 58.800 50.000 0.00 0.00 0.00 4.94
3350 3405 1.199624 CGCTTGAACAAAACTGCACC 58.800 50.000 0.00 0.00 0.00 5.01
3351 3406 1.846175 GACGCTTGAACAAAACTGCAC 59.154 47.619 0.00 0.00 0.00 4.57
3352 3407 1.742831 AGACGCTTGAACAAAACTGCA 59.257 42.857 0.00 0.00 0.00 4.41
3353 3408 2.111756 CAGACGCTTGAACAAAACTGC 58.888 47.619 0.00 0.00 0.00 4.40
3354 3409 2.541588 CCCAGACGCTTGAACAAAACTG 60.542 50.000 0.00 0.00 0.00 3.16
3355 3410 1.676006 CCCAGACGCTTGAACAAAACT 59.324 47.619 0.00 0.00 0.00 2.66
3356 3411 1.864029 GCCCAGACGCTTGAACAAAAC 60.864 52.381 0.00 0.00 0.00 2.43
3357 3412 0.383949 GCCCAGACGCTTGAACAAAA 59.616 50.000 0.00 0.00 0.00 2.44
3358 3413 1.452145 GGCCCAGACGCTTGAACAAA 61.452 55.000 0.00 0.00 0.00 2.83
3359 3414 1.896660 GGCCCAGACGCTTGAACAA 60.897 57.895 0.00 0.00 0.00 2.83
3369 3424 2.084546 GTAACATGTCAAGGCCCAGAC 58.915 52.381 16.21 16.21 35.37 3.51
3380 3437 8.768955 GGATGATCACTTTCATAGTAACATGTC 58.231 37.037 0.00 0.00 36.48 3.06
3391 3448 4.530875 GGTGGAAGGATGATCACTTTCAT 58.469 43.478 9.60 0.00 39.04 2.57
3393 3450 2.939103 CGGTGGAAGGATGATCACTTTC 59.061 50.000 0.00 4.71 0.00 2.62
3409 3466 0.393673 TGAATGTATGGGCACGGTGG 60.394 55.000 10.60 0.00 0.00 4.61
3413 3470 3.689161 TCTTTTCTGAATGTATGGGCACG 59.311 43.478 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.