Multiple sequence alignment - TraesCS3B01G355500

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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 TraesCS3B01G355500 chr3B 100.000 5285 0 0 1 5285 565729458 565724174 0.000000e+00 9760.0
1 TraesCS3B01G355500 chr3B 83.557 298 42 5 2586 2879 417730690 417730396 6.740000e-69 272.0
2 TraesCS3B01G355500 chr3B 97.826 138 2 1 3051 3188 261863883 261864019 2.460000e-58 237.0
3 TraesCS3B01G355500 chr3B 94.667 150 4 4 3040 3188 532207121 532207267 4.120000e-56 230.0
4 TraesCS3B01G355500 chr3B 100.000 51 0 0 4490 4540 565724921 565724871 1.570000e-15 95.3
5 TraesCS3B01G355500 chr3B 100.000 51 0 0 4538 4588 565724969 565724919 1.570000e-15 95.3
6 TraesCS3B01G355500 chr3D 95.963 3096 88 14 1 3062 433318825 433315733 0.000000e+00 4990.0
7 TraesCS3B01G355500 chr3D 94.595 1406 26 11 3185 4588 433315742 433314385 0.000000e+00 2130.0
8 TraesCS3B01G355500 chr3D 93.649 803 39 3 4490 5280 433314435 433313633 0.000000e+00 1190.0
9 TraesCS3B01G355500 chr3D 78.098 589 86 31 2308 2883 66337365 66337923 3.050000e-87 333.0
10 TraesCS3B01G355500 chr3D 98.039 51 1 0 4538 4588 433314483 433314433 7.290000e-14 89.8
11 TraesCS3B01G355500 chr3A 95.638 3095 89 20 1 3062 571411655 571408574 0.000000e+00 4926.0
12 TraesCS3B01G355500 chr3A 94.317 1830 67 10 3185 5012 571408583 571406789 0.000000e+00 2769.0
13 TraesCS3B01G355500 chr3A 97.163 141 4 0 3048 3188 193870195 193870335 6.840000e-59 239.0
14 TraesCS3B01G355500 chr3A 100.000 127 0 0 3062 3188 35854703 35854577 8.850000e-58 235.0
15 TraesCS3B01G355500 chr3A 88.889 117 13 0 2311 2427 700950342 700950458 1.530000e-30 145.0
16 TraesCS3B01G355500 chrUn 81.304 583 54 26 2312 2885 103533822 103534358 6.330000e-114 422.0
17 TraesCS3B01G355500 chr7B 82.704 503 44 25 1 486 223716521 223716997 1.770000e-109 407.0
18 TraesCS3B01G355500 chr7B 80.727 275 38 8 2612 2881 603945481 603945217 3.230000e-47 200.0
19 TraesCS3B01G355500 chr6B 80.806 521 61 20 2371 2885 54892458 54892945 6.460000e-99 372.0
20 TraesCS3B01G355500 chr6B 100.000 130 0 0 3059 3188 338654721 338654850 1.900000e-59 241.0
21 TraesCS3B01G355500 chr2D 89.157 249 24 2 288 535 118743863 118744109 1.850000e-79 307.0
22 TraesCS3B01G355500 chr2D 80.000 300 51 7 2593 2886 430508512 430508216 4.150000e-51 213.0
23 TraesCS3B01G355500 chr2D 78.317 309 52 11 2577 2882 65637613 65637317 9.040000e-43 185.0
24 TraesCS3B01G355500 chr2D 81.356 236 27 10 2309 2535 430508747 430508520 5.440000e-40 176.0
25 TraesCS3B01G355500 chr1B 86.429 280 34 3 2609 2885 453137629 453137907 2.390000e-78 303.0
26 TraesCS3B01G355500 chr5A 89.333 225 23 1 312 535 340146307 340146531 1.120000e-71 281.0
27 TraesCS3B01G355500 chr5A 97.101 138 4 0 3051 3188 510204041 510203904 3.180000e-57 233.0
28 TraesCS3B01G355500 chr5A 93.151 146 8 2 1 145 340146087 340146231 4.150000e-51 213.0
29 TraesCS3B01G355500 chr5D 77.799 527 62 30 2309 2827 386761230 386760751 1.880000e-69 274.0
30 TraesCS3B01G355500 chr5D 87.892 223 21 2 287 508 526764216 526764433 1.890000e-64 257.0
31 TraesCS3B01G355500 chr5D 91.463 164 12 2 1 163 526764013 526764175 1.920000e-54 224.0
32 TraesCS3B01G355500 chr5D 100.000 38 0 0 493 530 526764450 526764487 2.640000e-08 71.3
33 TraesCS3B01G355500 chr4D 78.571 434 69 11 2311 2738 98446367 98445952 1.130000e-66 265.0
34 TraesCS3B01G355500 chr4D 97.872 47 1 0 2311 2357 446173810 446173856 1.220000e-11 82.4
35 TraesCS3B01G355500 chr4B 97.810 137 3 0 3052 3188 421859137 421859273 2.460000e-58 237.0
36 TraesCS3B01G355500 chr1A 97.826 138 1 2 3053 3188 435379019 435378882 2.460000e-58 237.0
37 TraesCS3B01G355500 chr1A 89.024 164 16 2 1 163 510352371 510352209 8.970000e-48 202.0
38 TraesCS3B01G355500 chr4A 97.101 138 4 0 3051 3188 557109227 557109090 3.180000e-57 233.0
39 TraesCS3B01G355500 chr4A 84.337 166 26 0 3642 3807 610317742 610317907 4.230000e-36 163.0
40 TraesCS3B01G355500 chr7A 75.641 234 51 3 2308 2535 38660382 38660615 1.560000e-20 111.0
41 TraesCS3B01G355500 chr2A 100.000 30 0 0 2308 2337 61509696 61509667 7.390000e-04 56.5


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 TraesCS3B01G355500 chr3B 565724174 565729458 5284 True 9760.00 9760 100.0000 1 5285 1 chr3B.!!$R2 5284
1 TraesCS3B01G355500 chr3D 433313633 433318825 5192 True 2099.95 4990 95.5615 1 5280 4 chr3D.!!$R1 5279
2 TraesCS3B01G355500 chr3D 66337365 66337923 558 False 333.00 333 78.0980 2308 2883 1 chr3D.!!$F1 575
3 TraesCS3B01G355500 chr3A 571406789 571411655 4866 True 3847.50 4926 94.9775 1 5012 2 chr3A.!!$R2 5011
4 TraesCS3B01G355500 chrUn 103533822 103534358 536 False 422.00 422 81.3040 2312 2885 1 chrUn.!!$F1 573

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
405 411 1.079543 GCTCGATGTGGTGCAGACT 60.080 57.895 0.00 0.00 0.0 3.24 F
831 858 1.165907 TTCTGCGAACAACCCAGCTG 61.166 55.000 6.78 6.78 0.0 4.24 F
1013 1040 1.281899 GTTGCTATGGAGTCGTCAGC 58.718 55.000 2.46 2.46 0.0 4.26 F
2469 2501 0.608640 TTCTCCTCACGCTTCTTCCC 59.391 55.000 0.00 0.00 0.0 3.97 F
3154 3197 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1621 1.690633 CTTCTAGGCCAGGGCTCCA 60.691 63.158 21.26 3.99 39.70 3.86 R
2176 2206 1.894466 CACCCAAATCATTGAGCACCA 59.106 47.619 0.00 0.00 38.94 4.17 R
2863 2905 2.395336 AGAGCATCCTAGCAGATCCA 57.605 50.000 0.00 0.00 36.85 3.41 R
4271 4324 0.397254 ACCCCCTCAGTAGTCATCCG 60.397 60.000 0.00 0.00 0.00 4.18 R
5111 5215 0.438830 CCTGACTTTGCTTCGTACGC 59.561 55.000 11.24 0.00 0.00 4.42 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
55 58 1.937191 TCTGGACAGTGGATAGCACA 58.063 50.000 0.00 0.00 0.00 4.57
69 72 5.359576 TGGATAGCACAACAAAGAACAAACT 59.640 36.000 0.00 0.00 0.00 2.66
88 92 6.014584 ACAAACTCTAAATCAATTGGGGGTTC 60.015 38.462 5.42 0.00 25.08 3.62
405 411 1.079543 GCTCGATGTGGTGCAGACT 60.080 57.895 0.00 0.00 0.00 3.24
453 459 4.404073 TGCTTGTTGGGTCAAGTGTTATTT 59.596 37.500 7.98 0.00 44.41 1.40
476 482 3.364068 GGCTTTTCTTTTTCTCTCCGACG 60.364 47.826 0.00 0.00 0.00 5.12
741 768 1.281925 AATACACAGGGGAGGCTGGG 61.282 60.000 0.00 0.00 0.00 4.45
814 841 2.531522 ACCAAACCTGCATTGCTTTC 57.468 45.000 10.49 0.00 0.00 2.62
831 858 1.165907 TTCTGCGAACAACCCAGCTG 61.166 55.000 6.78 6.78 0.00 4.24
1013 1040 1.281899 GTTGCTATGGAGTCGTCAGC 58.718 55.000 2.46 2.46 0.00 4.26
1101 1128 3.848975 ACATCCTCCAGAAAATCCTGTCT 59.151 43.478 0.00 0.00 32.43 3.41
1125 1152 3.250040 GCGTGTGGATTAGAACTGTTGTT 59.750 43.478 0.00 0.00 39.42 2.83
1278 1305 2.400399 CGTCGGAAAGTAGACTTGCAA 58.600 47.619 0.00 0.00 36.12 4.08
1594 1621 4.564782 TCTCTGAACAGATTCATTGCCT 57.435 40.909 4.96 0.00 43.92 4.75
1640 1667 3.525268 TTTGATAGACTCTGCGATGCA 57.475 42.857 0.00 0.00 36.92 3.96
1697 1724 2.270434 ACCCTTGATGGCTTCCTAGA 57.730 50.000 0.00 0.00 0.00 2.43
2176 2206 7.438160 GCAACAAAAAGGTAAAATCTAAGTGCT 59.562 33.333 0.00 0.00 0.00 4.40
2178 2208 7.433680 ACAAAAAGGTAAAATCTAAGTGCTGG 58.566 34.615 0.00 0.00 0.00 4.85
2208 2238 8.642432 TCAATGATTTGGGTGTACATTTTGTTA 58.358 29.630 0.00 0.00 33.44 2.41
2266 2296 7.715657 TGAATGCAAAACCTAATATCCATGAC 58.284 34.615 0.00 0.00 0.00 3.06
2393 2424 0.801836 ACGAATTTACGGTACCGCGG 60.802 55.000 33.62 26.86 44.19 6.46
2428 2459 3.109151 ACAGATCCCATAAACCCGTACA 58.891 45.455 0.00 0.00 0.00 2.90
2468 2500 2.457366 TTTCTCCTCACGCTTCTTCC 57.543 50.000 0.00 0.00 0.00 3.46
2469 2501 0.608640 TTCTCCTCACGCTTCTTCCC 59.391 55.000 0.00 0.00 0.00 3.97
2580 2617 2.048127 GCTCCAGCGACTTTCCGT 60.048 61.111 0.00 0.00 0.00 4.69
2743 2780 5.356751 CGGTTTGAATCCTCCAAATATGACA 59.643 40.000 0.00 0.00 36.14 3.58
2863 2905 5.187687 TCTGAAGGTTTGACCGTTTTTACT 58.812 37.500 0.00 0.00 44.90 2.24
2973 3016 9.325198 GTTCCACAATTTGATTTTCTTACCTTT 57.675 29.630 2.79 0.00 0.00 3.11
2984 3027 9.308000 TGATTTTCTTACCTTTGTTATGTCCAT 57.692 29.630 0.00 0.00 0.00 3.41
3062 3105 5.560722 TTCAGAGTGTGAAACCTGGATAA 57.439 39.130 0.00 0.00 42.49 1.75
3063 3106 5.560722 TCAGAGTGTGAAACCTGGATAAA 57.439 39.130 0.00 0.00 34.36 1.40
3064 3107 5.935945 TCAGAGTGTGAAACCTGGATAAAA 58.064 37.500 0.00 0.00 34.36 1.52
3065 3108 5.997746 TCAGAGTGTGAAACCTGGATAAAAG 59.002 40.000 0.00 0.00 34.36 2.27
3066 3109 5.182001 CAGAGTGTGAAACCTGGATAAAAGG 59.818 44.000 0.00 0.00 40.93 3.11
3067 3110 4.407365 AGTGTGAAACCTGGATAAAAGGG 58.593 43.478 0.00 0.00 39.30 3.95
3068 3111 3.056821 GTGTGAAACCTGGATAAAAGGGC 60.057 47.826 0.00 0.00 39.30 5.19
3069 3112 3.161866 GTGAAACCTGGATAAAAGGGCA 58.838 45.455 0.00 0.00 39.30 5.36
3070 3113 3.576550 GTGAAACCTGGATAAAAGGGCAA 59.423 43.478 0.00 0.00 39.30 4.52
3071 3114 3.576550 TGAAACCTGGATAAAAGGGCAAC 59.423 43.478 0.00 0.00 39.30 4.17
3083 3126 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
3084 3127 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
3085 3128 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
3086 3129 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
3087 3130 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
3093 3136 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3094 3137 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3095 3138 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3096 3139 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3099 3142 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3111 3154 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
3112 3155 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
3113 3156 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
3114 3157 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3115 3158 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3116 3159 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3117 3160 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3118 3161 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3119 3162 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3120 3163 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3121 3164 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
3122 3165 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
3123 3166 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3124 3167 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3125 3168 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3126 3169 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3127 3170 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3128 3171 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3129 3172 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3139 3182 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
3140 3183 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
3141 3184 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
3142 3185 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
3143 3186 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
3144 3187 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
3145 3188 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
3146 3189 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
3147 3190 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
3148 3191 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
3149 3192 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
3150 3193 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
3151 3194 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
3152 3195 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
3153 3196 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
3154 3197 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3155 3198 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3156 3199 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3157 3200 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3158 3201 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3159 3202 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3160 3203 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3161 3204 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
3162 3205 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
3163 3206 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
3164 3207 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
3165 3208 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
3177 3220 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
3178 3221 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
3179 3222 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
3180 3223 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
3181 3224 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
3182 3225 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3183 3226 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3184 3227 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3185 3228 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3186 3229 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3187 3230 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3188 3231 2.749800 GCTGTTTCCAGGACTTGAACCT 60.750 50.000 0.00 0.00 39.22 3.50
3200 3243 6.735556 AGGACTTGAACCTGGATATGAAATT 58.264 36.000 0.00 0.00 36.30 1.82
3257 3300 2.131972 CACTTAGTTACGTGCTGTGCA 58.868 47.619 0.00 0.00 35.60 4.57
3314 3358 7.443879 TGAGACATTGTGTTTGATAAGCTTACA 59.556 33.333 8.70 6.50 0.00 2.41
3315 3359 8.340618 AGACATTGTGTTTGATAAGCTTACAT 57.659 30.769 8.70 0.00 0.00 2.29
3316 3360 9.448438 AGACATTGTGTTTGATAAGCTTACATA 57.552 29.630 8.70 0.00 0.00 2.29
3348 3392 6.902224 ACTGTAACAAAATTGGCAGTTTTC 57.098 33.333 16.60 7.52 36.86 2.29
3380 3424 7.865706 ATGAGCTTACACTTAGTTATTTGGG 57.134 36.000 0.00 0.00 0.00 4.12
3456 3500 3.909732 AGTGGGAAATTTGGTCTGTTGA 58.090 40.909 0.00 0.00 0.00 3.18
3535 3579 7.281040 ACATTTTCATGATGTCTTGTCTTGT 57.719 32.000 0.00 0.00 32.48 3.16
3537 3581 9.017509 ACATTTTCATGATGTCTTGTCTTGTAT 57.982 29.630 0.00 0.00 32.48 2.29
3543 3587 6.968131 TGATGTCTTGTCTTGTATTGCTAC 57.032 37.500 0.00 0.00 0.00 3.58
3544 3588 6.463360 TGATGTCTTGTCTTGTATTGCTACA 58.537 36.000 0.00 0.00 36.06 2.74
3545 3589 7.105588 TGATGTCTTGTCTTGTATTGCTACAT 58.894 34.615 0.00 0.00 37.68 2.29
3546 3590 7.607607 TGATGTCTTGTCTTGTATTGCTACATT 59.392 33.333 0.00 0.00 37.68 2.71
3547 3591 7.744087 TGTCTTGTCTTGTATTGCTACATTT 57.256 32.000 0.00 0.00 37.68 2.32
3548 3592 8.165239 TGTCTTGTCTTGTATTGCTACATTTT 57.835 30.769 0.00 0.00 37.68 1.82
3549 3593 8.289618 TGTCTTGTCTTGTATTGCTACATTTTC 58.710 33.333 0.00 0.00 37.68 2.29
3550 3594 8.289618 GTCTTGTCTTGTATTGCTACATTTTCA 58.710 33.333 0.00 0.00 37.68 2.69
3551 3595 9.013229 TCTTGTCTTGTATTGCTACATTTTCAT 57.987 29.630 0.00 0.00 37.68 2.57
3552 3596 8.969121 TTGTCTTGTATTGCTACATTTTCATG 57.031 30.769 0.00 0.00 37.68 3.07
3553 3597 8.334263 TGTCTTGTATTGCTACATTTTCATGA 57.666 30.769 0.00 0.00 37.68 3.07
3554 3598 8.959548 TGTCTTGTATTGCTACATTTTCATGAT 58.040 29.630 0.00 0.00 37.68 2.45
3555 3599 9.229784 GTCTTGTATTGCTACATTTTCATGATG 57.770 33.333 0.00 0.00 37.68 3.07
3556 3600 7.916977 TCTTGTATTGCTACATTTTCATGATGC 59.083 33.333 0.00 0.00 37.68 3.91
3557 3601 7.098074 TGTATTGCTACATTTTCATGATGCA 57.902 32.000 0.00 0.00 38.97 3.96
3558 3602 7.545489 TGTATTGCTACATTTTCATGATGCAA 58.455 30.769 15.82 15.82 45.90 4.08
3559 3603 6.897259 ATTGCTACATTTTCATGATGCAAC 57.103 33.333 15.81 0.00 45.34 4.17
3560 3604 5.388408 TGCTACATTTTCATGATGCAACA 57.612 34.783 0.00 0.00 38.34 3.33
3561 3605 5.780984 TGCTACATTTTCATGATGCAACAA 58.219 33.333 0.00 0.00 38.34 2.83
3562 3606 6.399743 TGCTACATTTTCATGATGCAACAAT 58.600 32.000 0.00 0.00 38.34 2.71
3895 3939 9.920946 TTGCTAAAATATATCCTCTCCTTTTGT 57.079 29.630 0.00 0.00 0.00 2.83
3965 4009 1.285280 ATTGACGGGATGACCTTCCA 58.715 50.000 4.63 0.00 36.71 3.53
4161 4205 1.364626 CGAAGGAGCTGCGCATCTTT 61.365 55.000 15.89 11.62 0.00 2.52
4270 4323 1.227089 AGCGACGCATCTGATGACC 60.227 57.895 23.70 7.84 0.00 4.02
4271 4324 2.240500 GCGACGCATCTGATGACCC 61.241 63.158 21.30 7.52 0.00 4.46
4272 4325 1.946156 CGACGCATCTGATGACCCG 60.946 63.158 21.30 16.32 0.00 5.28
4273 4326 1.592669 GACGCATCTGATGACCCGG 60.593 63.158 21.30 0.00 0.00 5.73
4274 4327 2.016393 GACGCATCTGATGACCCGGA 62.016 60.000 21.30 0.00 0.00 5.14
4275 4328 1.368950 CGCATCTGATGACCCGGAT 59.631 57.895 21.30 0.00 32.64 4.18
4319 4372 4.959596 TCAGAGCAATGAATTTGAGAGC 57.040 40.909 0.00 0.00 37.53 4.09
4374 4427 7.451566 ACTGCTTTTATACCCATCCAATATTCC 59.548 37.037 0.00 0.00 0.00 3.01
4415 4469 2.697751 AGACCTTCATCTCTTGGATCCG 59.302 50.000 7.39 0.00 31.27 4.18
4483 4537 2.380084 TCTTATGCTCCGAGCGTTTT 57.620 45.000 20.03 5.44 46.26 2.43
4762 4864 1.274728 CTTGGATCATCGGGGCTAGAG 59.725 57.143 0.00 0.00 0.00 2.43
4784 4886 4.280174 AGTGATCAAAGCACAAAATGAGCT 59.720 37.500 0.00 0.00 45.98 4.09
4854 4957 5.595542 TCAGGCATCCTTCATATTTTGGAAG 59.404 40.000 0.00 0.00 40.11 3.46
4856 4959 4.099881 GGCATCCTTCATATTTTGGAAGCA 59.900 41.667 13.36 0.00 42.80 3.91
4891 4994 8.663911 TGGTTGTTCAAAAGAATTGAATTTCAC 58.336 29.630 6.86 2.89 40.12 3.18
4897 5000 9.520204 TTCAAAAGAATTGAATTTCACTCTCAC 57.480 29.630 0.00 0.00 33.90 3.51
4898 5001 8.685427 TCAAAAGAATTGAATTTCACTCTCACA 58.315 29.630 0.00 0.00 0.00 3.58
4969 5072 5.418310 TTTAACTTTGCCTTCTGTTCGAG 57.582 39.130 0.00 0.00 0.00 4.04
4974 5078 0.984230 TGCCTTCTGTTCGAGGGATT 59.016 50.000 0.00 0.00 41.25 3.01
4992 5096 3.629398 GGATTACTCGGTCCTACGAAAGA 59.371 47.826 0.00 0.00 42.98 2.52
5013 5117 1.273606 AGCTCGCTAAACTCAAGCTCA 59.726 47.619 0.00 0.00 38.96 4.26
5018 5122 3.699538 TCGCTAAACTCAAGCTCATCCTA 59.300 43.478 0.00 0.00 37.85 2.94
5022 5126 6.051717 GCTAAACTCAAGCTCATCCTATTCA 58.948 40.000 0.00 0.00 37.01 2.57
5044 5148 3.358775 TCGACATTCTTTGTGCGTTTTG 58.641 40.909 0.00 0.00 39.18 2.44
5052 5156 1.025812 TTGTGCGTTTTGTTCGGGAT 58.974 45.000 0.00 0.00 0.00 3.85
5053 5157 0.309302 TGTGCGTTTTGTTCGGGATG 59.691 50.000 0.00 0.00 0.00 3.51
5068 5172 1.070289 GGGATGTAGGTTCGGATGGTC 59.930 57.143 0.00 0.00 0.00 4.02
5108 5212 6.518032 CGTGTATTCATCAGATCCAGATCCTT 60.518 42.308 4.01 0.00 38.58 3.36
5111 5215 4.701651 TCATCAGATCCAGATCCTTTGG 57.298 45.455 4.01 0.00 38.58 3.28
5141 5245 2.616510 GCAAAGTCAGGTGGAGCTACAT 60.617 50.000 0.00 0.00 0.00 2.29
5146 5250 1.559682 TCAGGTGGAGCTACATTTCCC 59.440 52.381 0.00 0.00 32.29 3.97
5147 5251 1.561542 CAGGTGGAGCTACATTTCCCT 59.438 52.381 0.00 0.00 32.29 4.20
5258 5374 0.390998 GCACCTCTCTGACTTGCCTC 60.391 60.000 0.00 0.00 0.00 4.70
5274 5390 8.372459 TGACTTGCCTCTACTATTTTACAGAAA 58.628 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.747565 ACACGAATCAACAAACACATAGTG 58.252 37.500 0.00 0.00 39.75 2.74
69 72 3.626930 CCGAACCCCCAATTGATTTAGA 58.373 45.455 7.12 0.00 0.00 2.10
88 92 4.680237 TTGAGGTCGCCACTGCCG 62.680 66.667 0.00 0.00 0.00 5.69
231 237 4.357279 GCAGCCAGCCTCACCCTT 62.357 66.667 0.00 0.00 37.23 3.95
256 262 3.036429 GCTTCTCCGCCATCCACCT 62.036 63.158 0.00 0.00 0.00 4.00
405 411 0.889994 GCATGCATCCACCACTTCAA 59.110 50.000 14.21 0.00 0.00 2.69
453 459 3.564225 GTCGGAGAGAAAAAGAAAAGCCA 59.436 43.478 0.00 0.00 36.95 4.75
476 482 7.547370 CCTTTATACCTATGCAGTTAGAGATGC 59.453 40.741 0.00 0.00 42.86 3.91
605 632 7.467811 CGAGCATTTTCTAGCCAAGTAATGAAT 60.468 37.037 13.38 5.87 33.74 2.57
741 768 5.346522 CAAATTAGGGAAGCAGAGCAATTC 58.653 41.667 0.00 0.00 0.00 2.17
1013 1040 1.153309 TCCATGGCATGCTCGTCAG 60.153 57.895 22.02 6.63 0.00 3.51
1101 1128 3.120321 ACAGTTCTAATCCACACGCAA 57.880 42.857 0.00 0.00 0.00 4.85
1278 1305 1.927487 TCCAATGCAGCTGGAATGTT 58.073 45.000 20.26 4.68 40.08 2.71
1594 1621 1.690633 CTTCTAGGCCAGGGCTCCA 60.691 63.158 21.26 3.99 39.70 3.86
1640 1667 5.764192 GCTTTTGAGGCTATGAGATCAAGAT 59.236 40.000 0.00 0.00 33.53 2.40
1697 1724 2.696989 TGTGAATCCATCGCACTCAT 57.303 45.000 0.00 0.00 43.46 2.90
2176 2206 1.894466 CACCCAAATCATTGAGCACCA 59.106 47.619 0.00 0.00 38.94 4.17
2178 2208 3.505680 TGTACACCCAAATCATTGAGCAC 59.494 43.478 0.00 0.00 38.94 4.40
2208 2238 6.485984 CAGATCCACTTTAGCAGCAAGAATAT 59.514 38.462 0.00 0.00 0.00 1.28
2266 2296 9.459640 CAAAGTTAATGGAGCAATATGATGAAG 57.540 33.333 0.00 0.00 0.00 3.02
2688 2725 2.953284 TCCCATAAAACCGGTCAACA 57.047 45.000 8.04 0.00 0.00 3.33
2743 2780 5.084519 TCCCGTATATTAGAGCAACCATCT 58.915 41.667 0.00 0.00 0.00 2.90
2863 2905 2.395336 AGAGCATCCTAGCAGATCCA 57.605 50.000 0.00 0.00 36.85 3.41
2947 2990 8.887036 AAGGTAAGAAAATCAAATTGTGGAAC 57.113 30.769 0.00 0.00 37.35 3.62
2973 3016 6.883756 TGTGCTCTATTTTGATGGACATAACA 59.116 34.615 0.00 0.00 0.00 2.41
3062 3105 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
3063 3106 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
3064 3107 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
3065 3108 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
3066 3109 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
3067 3110 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
3068 3111 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
3069 3112 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
3094 3137 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3095 3138 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3096 3139 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3097 3140 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3098 3141 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3099 3142 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3100 3143 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
3101 3144 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
3102 3145 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
3103 3146 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
3104 3147 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
3105 3148 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
3106 3149 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3107 3150 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3108 3151 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3109 3152 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3110 3153 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3111 3154 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3112 3155 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3113 3156 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3118 3161 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
3119 3162 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
3120 3163 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
3121 3164 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
3122 3165 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
3123 3166 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
3124 3167 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
3125 3168 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
3126 3169 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
3127 3170 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
3128 3171 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
3129 3172 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
3130 3173 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
3131 3174 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
3132 3175 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
3133 3176 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
3134 3177 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
3135 3178 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3136 3179 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3137 3180 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3138 3181 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3139 3182 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3140 3183 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
3141 3184 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
3142 3185 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
3143 3186 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3144 3187 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
3145 3188 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3146 3189 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
3147 3190 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
3148 3191 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3149 3192 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3150 3193 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
3151 3194 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
3152 3195 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
3153 3196 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3154 3197 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3155 3198 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
3169 3212 2.930950 CAGGTTCAAGTCCTGGAAACA 58.069 47.619 0.00 0.00 46.03 2.83
3176 3219 5.779241 TTTCATATCCAGGTTCAAGTCCT 57.221 39.130 0.00 0.00 35.45 3.85
3177 3220 7.410120 AAATTTCATATCCAGGTTCAAGTCC 57.590 36.000 0.00 0.00 0.00 3.85
3247 3290 1.012086 ATCTGCTTATGCACAGCACG 58.988 50.000 16.70 13.09 45.31 5.34
3282 3325 4.198530 TCAAACACAATGTCTCAAGCTCA 58.801 39.130 0.00 0.00 0.00 4.26
3283 3326 4.818534 TCAAACACAATGTCTCAAGCTC 57.181 40.909 0.00 0.00 0.00 4.09
3284 3327 6.569226 GCTTATCAAACACAATGTCTCAAGCT 60.569 38.462 0.00 0.00 32.75 3.74
3315 3359 9.255304 GCCAATTTTGTTACAGTTGAGAAAATA 57.745 29.630 8.17 0.00 0.00 1.40
3316 3360 7.768120 TGCCAATTTTGTTACAGTTGAGAAAAT 59.232 29.630 8.17 0.00 0.00 1.82
3317 3361 7.099764 TGCCAATTTTGTTACAGTTGAGAAAA 58.900 30.769 8.17 0.00 0.00 2.29
3318 3362 6.634805 TGCCAATTTTGTTACAGTTGAGAAA 58.365 32.000 8.17 0.00 0.00 2.52
3319 3363 6.127479 ACTGCCAATTTTGTTACAGTTGAGAA 60.127 34.615 8.17 0.00 33.78 2.87
3320 3364 5.359576 ACTGCCAATTTTGTTACAGTTGAGA 59.640 36.000 8.17 0.00 33.78 3.27
3321 3365 5.591099 ACTGCCAATTTTGTTACAGTTGAG 58.409 37.500 8.17 3.25 33.78 3.02
3322 3366 5.590530 ACTGCCAATTTTGTTACAGTTGA 57.409 34.783 8.17 0.00 33.78 3.18
3323 3367 6.660887 AAACTGCCAATTTTGTTACAGTTG 57.339 33.333 17.15 0.00 40.67 3.16
3324 3368 6.035542 CGAAAACTGCCAATTTTGTTACAGTT 59.964 34.615 13.44 13.44 41.99 3.16
3325 3369 5.518487 CGAAAACTGCCAATTTTGTTACAGT 59.482 36.000 0.00 0.00 36.87 3.55
3326 3370 5.518487 ACGAAAACTGCCAATTTTGTTACAG 59.482 36.000 0.00 0.00 30.74 2.74
3327 3371 5.411781 ACGAAAACTGCCAATTTTGTTACA 58.588 33.333 0.00 0.00 30.74 2.41
3328 3372 5.959652 ACGAAAACTGCCAATTTTGTTAC 57.040 34.783 0.00 0.00 30.74 2.50
3355 3399 8.764558 TCCCAAATAACTAAGTGTAAGCTCATA 58.235 33.333 0.00 0.00 0.00 2.15
3380 3424 2.558359 ACATGCAAGTGGTTAAAGCCTC 59.442 45.455 0.00 0.00 0.00 4.70
3535 3579 7.545489 TGTTGCATCATGAAAATGTAGCAATA 58.455 30.769 16.92 13.72 40.88 1.90
3537 3581 5.780984 TGTTGCATCATGAAAATGTAGCAA 58.219 33.333 0.00 12.80 38.73 3.91
3543 3587 9.060547 CATCAAAATTGTTGCATCATGAAAATG 57.939 29.630 0.00 0.00 0.00 2.32
3544 3588 8.788806 ACATCAAAATTGTTGCATCATGAAAAT 58.211 25.926 0.00 0.00 32.51 1.82
3545 3589 8.155821 ACATCAAAATTGTTGCATCATGAAAA 57.844 26.923 0.00 0.00 32.51 2.29
3546 3590 7.731882 ACATCAAAATTGTTGCATCATGAAA 57.268 28.000 0.00 0.00 32.51 2.69
3547 3591 7.731882 AACATCAAAATTGTTGCATCATGAA 57.268 28.000 0.00 0.00 36.02 2.57
3548 3592 7.577107 CAAACATCAAAATTGTTGCATCATGA 58.423 30.769 0.00 0.00 37.38 3.07
3549 3593 6.304445 GCAAACATCAAAATTGTTGCATCATG 59.696 34.615 11.87 0.00 37.38 3.07
3550 3594 6.017026 TGCAAACATCAAAATTGTTGCATCAT 60.017 30.769 14.24 0.00 37.38 2.45
3551 3595 5.296035 TGCAAACATCAAAATTGTTGCATCA 59.704 32.000 14.24 0.00 37.38 3.07
3552 3596 5.622041 GTGCAAACATCAAAATTGTTGCATC 59.378 36.000 18.62 11.94 40.12 3.91
3553 3597 5.297278 AGTGCAAACATCAAAATTGTTGCAT 59.703 32.000 18.62 9.72 40.12 3.96
3554 3598 4.634883 AGTGCAAACATCAAAATTGTTGCA 59.365 33.333 14.24 14.24 37.38 4.08
3555 3599 5.006941 AGAGTGCAAACATCAAAATTGTTGC 59.993 36.000 10.52 10.52 37.38 4.17
3556 3600 6.592798 AGAGTGCAAACATCAAAATTGTTG 57.407 33.333 0.00 3.32 37.38 3.33
3557 3601 7.464444 CGAAAGAGTGCAAACATCAAAATTGTT 60.464 33.333 0.00 0.00 38.91 2.83
3558 3602 6.019640 CGAAAGAGTGCAAACATCAAAATTGT 60.020 34.615 0.00 0.00 0.00 2.71
3559 3603 6.019640 ACGAAAGAGTGCAAACATCAAAATTG 60.020 34.615 0.00 0.00 0.00 2.32
3560 3604 6.042143 ACGAAAGAGTGCAAACATCAAAATT 58.958 32.000 0.00 0.00 0.00 1.82
3561 3605 5.591099 ACGAAAGAGTGCAAACATCAAAAT 58.409 33.333 0.00 0.00 0.00 1.82
3562 3606 4.992688 ACGAAAGAGTGCAAACATCAAAA 58.007 34.783 0.00 0.00 0.00 2.44
3895 3939 9.725019 TTCATCAAGCTAGAGATAAACAGAAAA 57.275 29.630 0.00 0.00 0.00 2.29
3965 4009 2.505819 ACACTTTCAAGGAGTGGACACT 59.494 45.455 4.35 4.35 46.77 3.55
4161 4205 4.223923 GGATTTCTCTTCACCCTCTTCTCA 59.776 45.833 0.00 0.00 0.00 3.27
4270 4323 1.115930 CCCCCTCAGTAGTCATCCGG 61.116 65.000 0.00 0.00 0.00 5.14
4271 4324 0.397254 ACCCCCTCAGTAGTCATCCG 60.397 60.000 0.00 0.00 0.00 4.18
4272 4325 2.769602 TACCCCCTCAGTAGTCATCC 57.230 55.000 0.00 0.00 0.00 3.51
4273 4326 2.900546 CCATACCCCCTCAGTAGTCATC 59.099 54.545 0.00 0.00 0.00 2.92
4274 4327 2.977808 CCATACCCCCTCAGTAGTCAT 58.022 52.381 0.00 0.00 0.00 3.06
4275 4328 1.691482 GCCATACCCCCTCAGTAGTCA 60.691 57.143 0.00 0.00 0.00 3.41
4276 4329 1.049402 GCCATACCCCCTCAGTAGTC 58.951 60.000 0.00 0.00 0.00 2.59
4277 4330 0.642710 AGCCATACCCCCTCAGTAGT 59.357 55.000 0.00 0.00 0.00 2.73
4278 4331 1.807814 AAGCCATACCCCCTCAGTAG 58.192 55.000 0.00 0.00 0.00 2.57
4319 4372 1.520342 GCAGGGCTCTAGCGTCAAG 60.520 63.158 0.00 0.00 43.26 3.02
4374 4427 5.336744 GTCTCATCTAGAACAGAAGGAACG 58.663 45.833 0.00 0.00 36.67 3.95
4415 4469 5.467063 CACCAAGTTTCAGAAGTAAGAGGAC 59.533 44.000 0.00 0.00 0.00 3.85
4483 4537 8.503196 CATTACACAACTATGCTCAAACAGTAA 58.497 33.333 0.00 0.00 0.00 2.24
4762 4864 4.553323 AGCTCATTTTGTGCTTTGATCAC 58.447 39.130 0.00 0.00 43.76 3.06
4854 4957 5.627499 TTTGAACAACCATCTCTGTATGC 57.373 39.130 0.00 0.00 0.00 3.14
4856 4959 8.641498 ATTCTTTTGAACAACCATCTCTGTAT 57.359 30.769 0.00 0.00 41.77 2.29
4897 5000 8.970859 ATCTCTCATTTATTAAACACCTCCTG 57.029 34.615 0.00 0.00 0.00 3.86
4911 5014 7.733773 TCCTCCACAAACTATCTCTCATTTA 57.266 36.000 0.00 0.00 0.00 1.40
4956 5059 2.168728 AGTAATCCCTCGAACAGAAGGC 59.831 50.000 0.00 0.00 30.35 4.35
4969 5072 1.972872 TCGTAGGACCGAGTAATCCC 58.027 55.000 0.00 0.00 35.38 3.85
4974 5078 2.421424 GCTTCTTTCGTAGGACCGAGTA 59.579 50.000 0.00 0.00 38.23 2.59
4986 5090 2.987149 TGAGTTTAGCGAGCTTCTTTCG 59.013 45.455 1.86 0.00 40.85 3.46
4992 5096 2.289072 TGAGCTTGAGTTTAGCGAGCTT 60.289 45.455 1.86 0.00 43.22 3.74
5013 5117 6.017605 GCACAAAGAATGTCGATGAATAGGAT 60.018 38.462 0.00 0.00 41.46 3.24
5018 5122 3.436704 ACGCACAAAGAATGTCGATGAAT 59.563 39.130 0.00 0.00 41.46 2.57
5022 5126 3.896648 AAACGCACAAAGAATGTCGAT 57.103 38.095 0.00 0.00 41.46 3.59
5044 5148 0.819582 TCCGAACCTACATCCCGAAC 59.180 55.000 0.00 0.00 0.00 3.95
5052 5156 1.100510 CTCGACCATCCGAACCTACA 58.899 55.000 0.00 0.00 38.17 2.74
5053 5157 1.065251 GTCTCGACCATCCGAACCTAC 59.935 57.143 0.00 0.00 38.17 3.18
5068 5172 1.225881 CACGTGCTCTCGAGTCTCG 60.226 63.158 16.33 16.33 42.10 4.04
5108 5212 0.863144 GACTTTGCTTCGTACGCCAA 59.137 50.000 11.24 10.70 0.00 4.52
5111 5215 0.438830 CCTGACTTTGCTTCGTACGC 59.561 55.000 11.24 0.00 0.00 4.42
5141 5245 0.762418 TCGAAGGCAAGTCAGGGAAA 59.238 50.000 0.00 0.00 0.00 3.13
5146 5250 2.483876 TCACTTTCGAAGGCAAGTCAG 58.516 47.619 7.26 0.00 30.78 3.51
5147 5251 2.612212 GTTCACTTTCGAAGGCAAGTCA 59.388 45.455 7.26 0.00 30.78 3.41
5236 5352 0.034616 GCAAGTCAGAGAGGTGCAGT 59.965 55.000 0.00 0.00 35.28 4.40


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

AutoCloner maintained by Alex Coulton.