Multiple sequence alignment - TraesCS7D01G183900

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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 TraesCS7D01G183900 chr7D 100.000 7730 0 0 1 7730 137566098 137558369 0.000000e+00 14275.0
1 TraesCS7D01G183900 chr7D 95.413 109 5 0 1016 1124 137565032 137564924 2.870000e-39 174.0
2 TraesCS7D01G183900 chr7D 95.413 109 5 0 1067 1175 137565083 137564975 2.870000e-39 174.0
3 TraesCS7D01G183900 chr7D 98.214 56 1 0 1018 1073 137564979 137564924 1.780000e-16 99.0
4 TraesCS7D01G183900 chr7D 98.214 56 1 0 1120 1175 137565081 137565026 1.780000e-16 99.0
5 TraesCS7D01G183900 chr7A 92.843 2613 98 25 3871 6434 137770402 137767830 0.000000e+00 3707.0
6 TraesCS7D01G183900 chr7A 97.823 1975 43 0 1016 2990 137773284 137771310 0.000000e+00 3410.0
7 TraesCS7D01G183900 chr7A 89.992 1289 56 31 6474 7730 137767828 137766581 0.000000e+00 1598.0
8 TraesCS7D01G183900 chr7A 96.005 776 14 6 3102 3874 137771313 137770552 0.000000e+00 1245.0
9 TraesCS7D01G183900 chr7A 87.937 829 54 14 1 804 137774400 137773593 0.000000e+00 935.0
10 TraesCS7D01G183900 chr7A 96.791 374 11 1 803 1175 137773549 137773176 2.370000e-174 623.0
11 TraesCS7D01G183900 chr7A 91.724 145 12 0 5072 5216 491827845 491827701 1.320000e-47 202.0
12 TraesCS7D01G183900 chr7A 91.724 145 12 0 5072 5216 600552629 600552773 1.320000e-47 202.0
13 TraesCS7D01G183900 chr7A 95.690 116 5 0 1060 1175 137773342 137773227 3.680000e-43 187.0
14 TraesCS7D01G183900 chr7A 95.413 109 5 0 1016 1124 137773233 137773125 2.870000e-39 174.0
15 TraesCS7D01G183900 chr7A 98.214 56 1 0 1120 1175 137773333 137773278 1.780000e-16 99.0
16 TraesCS7D01G183900 chr7A 94.828 58 3 0 1016 1073 137773182 137773125 2.970000e-14 91.6
17 TraesCS7D01G183900 chr7B 97.877 1931 40 1 1060 2990 102237302 102235373 0.000000e+00 3338.0
18 TraesCS7D01G183900 chr7B 91.783 1935 92 28 5824 7730 102231944 102230049 0.000000e+00 2630.0
19 TraesCS7D01G183900 chr7B 96.778 776 13 6 3102 3874 102235376 102234610 0.000000e+00 1284.0
20 TraesCS7D01G183900 chr7B 94.063 758 31 7 5067 5824 102232949 102232206 0.000000e+00 1138.0
21 TraesCS7D01G183900 chr7B 90.292 855 44 11 4232 5067 102233886 102233052 0.000000e+00 1083.0
22 TraesCS7D01G183900 chr7B 88.026 618 45 9 185 802 102238146 102237558 0.000000e+00 704.0
23 TraesCS7D01G183900 chr7B 97.118 347 10 0 3871 4217 102234320 102233974 3.110000e-163 586.0
24 TraesCS7D01G183900 chr7B 94.410 322 18 0 803 1124 102237508 102237187 5.390000e-136 496.0
25 TraesCS7D01G183900 chr7B 90.698 86 3 4 4329 4409 102233972 102233887 8.200000e-20 110.0
26 TraesCS7D01G183900 chr7B 98.276 58 1 0 1016 1073 102237244 102237187 1.370000e-17 102.0
27 TraesCS7D01G183900 chr7B 98.214 56 1 0 1120 1175 102237293 102237238 1.780000e-16 99.0
28 TraesCS7D01G183900 chr3D 84.878 410 39 10 4830 5224 118545159 118545560 7.270000e-105 392.0
29 TraesCS7D01G183900 chr3D 93.496 123 8 0 2985 3107 554066200 554066078 4.760000e-42 183.0
30 TraesCS7D01G183900 chr5A 92.208 154 12 0 5072 5225 47458918 47459071 1.310000e-52 219.0
31 TraesCS7D01G183900 chr5A 90.850 153 14 0 5072 5224 3455630 3455478 1.020000e-48 206.0
32 TraesCS7D01G183900 chr5A 91.724 145 12 0 5072 5216 299777057 299776913 1.320000e-47 202.0
33 TraesCS7D01G183900 chr5D 92.414 145 11 0 5072 5216 549893197 549893053 2.830000e-49 207.0
34 TraesCS7D01G183900 chr5D 93.443 122 8 0 2988 3109 34049894 34049773 1.710000e-41 182.0
35 TraesCS7D01G183900 chr1A 90.850 153 13 1 5072 5224 452758573 452758724 3.660000e-48 204.0
36 TraesCS7D01G183900 chr5B 94.215 121 7 0 2988 3108 680987412 680987292 1.320000e-42 185.0
37 TraesCS7D01G183900 chr4B 93.333 120 8 0 2989 3108 506580658 506580539 2.220000e-40 178.0
38 TraesCS7D01G183900 chr2B 92.742 124 8 1 2985 3108 95798159 95798037 2.220000e-40 178.0
39 TraesCS7D01G183900 chr6D 90.370 135 12 1 2973 3107 379335343 379335476 7.970000e-40 176.0
40 TraesCS7D01G183900 chr2A 92.126 127 7 2 2979 3105 240467225 240467348 7.970000e-40 176.0
41 TraesCS7D01G183900 chr2D 90.840 131 10 2 2975 3105 571079815 571079943 2.870000e-39 174.0
42 TraesCS7D01G183900 chr2D 90.698 129 12 0 2981 3109 441085891 441085763 1.030000e-38 172.0


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 TraesCS7D01G183900 chr7D 137558369 137566098 7729 True 2964.200000 14275 97.450800 1 7730 5 chr7D.!!$R1 7729
1 TraesCS7D01G183900 chr7A 137766581 137774400 7819 True 1206.960000 3707 94.553600 1 7730 10 chr7A.!!$R2 7729
2 TraesCS7D01G183900 chr7B 102230049 102238146 8097 True 1051.818182 3338 94.321364 185 7730 11 chr7B.!!$R1 7545

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
117 133 0.165944 CAGTGCGTTCATCCGGTTTC 59.834 55.000 0.00 0.00 0.00 2.78 F
241 261 0.318955 ACCTGCAAATGCGTTTGAGC 60.319 50.000 30.83 18.76 46.03 4.26 F
465 489 0.445436 CGAGCAGAGCATTTGTGGTC 59.555 55.000 0.00 0.00 42.39 4.02 F
2130 2273 1.004862 GCTCCTTTGCCTCCTTTACCT 59.995 52.381 0.00 0.00 0.00 3.08 F
3004 3147 0.702902 AAGTACTCCCTCAGTCCGGA 59.297 55.000 0.00 0.00 36.43 5.14 F
3006 3149 1.076677 AGTACTCCCTCAGTCCGGAAA 59.923 52.381 5.23 0.00 36.43 3.13 F
4398 4917 1.269621 CCTAGGGCGTAATCAGTTCCG 60.270 57.143 0.00 0.00 0.00 4.30 F
4959 5498 1.603634 TTTAGGGATTGGGAGGGGAC 58.396 55.000 0.00 0.00 0.00 4.46 F
5205 5846 2.434702 AGTCTCAACCTTGGAACGACTT 59.565 45.455 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1478 1621 1.959282 ACCCTTGCTGAGCTTTTGAAG 59.041 47.619 5.83 0.00 0.00 3.02 R
2139 2282 0.459899 TCCCACATCCAGATTCGTCG 59.540 55.000 0.00 0.00 0.00 5.12 R
2462 2605 7.466746 TCCTAAATGTGAAATCCTTTCCAAG 57.533 36.000 0.00 0.00 38.90 3.61 R
3974 4414 0.178301 GCCCTTTCTAGGAGGAACCG 59.822 60.000 12.94 0.54 45.05 4.44 R
4576 5098 0.738975 CAATGCAGATCAGCTGGTGG 59.261 55.000 15.13 1.98 45.03 4.61 R
4908 5440 1.071436 GTCGAACGACTCAAAGTGCAC 60.071 52.381 18.12 9.40 41.57 4.57 R
6033 6938 1.670811 CCTAATAGGGCAAAGCACACG 59.329 52.381 0.00 0.00 32.33 4.49 R
6651 7571 1.419387 AGCAACTCCAAGAACTGCTCT 59.581 47.619 0.00 0.00 39.04 4.09 R
7016 7941 2.032636 GGCATCAGCAAACAAAACAAGC 60.033 45.455 0.00 0.00 44.61 4.01 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.869832 GGTTTCTCTAGGGTTTATCGCAC 59.130 47.826 0.00 0.00 0.00 5.34
55 56 2.818132 CTGGGAGTGGGATCTCGC 59.182 66.667 0.00 0.00 44.20 5.03
58 59 3.148279 GGAGTGGGATCTCGCGGT 61.148 66.667 6.13 0.00 35.52 5.68
89 105 4.354162 GCTGGGGCCGGTTGGTTA 62.354 66.667 1.90 0.00 37.67 2.85
103 119 4.055360 GGTTGGTTATTTTGGTTCAGTGC 58.945 43.478 0.00 0.00 0.00 4.40
117 133 0.165944 CAGTGCGTTCATCCGGTTTC 59.834 55.000 0.00 0.00 0.00 2.78
152 168 1.650314 GGTGCGGGTTTATTGTCGGG 61.650 60.000 0.00 0.00 0.00 5.14
168 184 2.126502 GGAATGCAAACACCGCGG 60.127 61.111 26.86 26.86 0.00 6.46
227 247 1.416813 CGCGTGAGATCTCAACCTGC 61.417 60.000 26.70 23.50 41.85 4.85
241 261 0.318955 ACCTGCAAATGCGTTTGAGC 60.319 50.000 30.83 18.76 46.03 4.26
274 294 1.845809 GCACCGTGCATATGGCTAGC 61.846 60.000 18.79 6.04 44.26 3.42
352 376 3.069872 TGGTAACGTTGATGTACTGGTGT 59.930 43.478 11.99 0.00 42.51 4.16
375 399 1.133730 GGCCCCGTGGTTTATTGGATA 60.134 52.381 0.00 0.00 0.00 2.59
396 420 1.178534 AACGTGTCTGCATTTGGGGG 61.179 55.000 0.00 0.00 0.00 5.40
464 488 1.580845 GCGAGCAGAGCATTTGTGGT 61.581 55.000 0.00 0.00 32.89 4.16
465 489 0.445436 CGAGCAGAGCATTTGTGGTC 59.555 55.000 0.00 0.00 42.39 4.02
471 495 2.502510 GCATTTGTGGTCGCTGCG 60.503 61.111 17.25 17.25 0.00 5.18
498 522 1.284982 GCCGATCGCGTGCATATCTT 61.285 55.000 10.32 0.00 34.99 2.40
531 555 1.933181 GCACAACAAAGGCTTTTCACC 59.067 47.619 10.36 0.00 0.00 4.02
591 615 4.814234 GCGGGTGACAAATCTGTATCAATA 59.186 41.667 0.00 0.00 35.30 1.90
715 758 5.061179 GGTACTAACCATACCATGCGATTT 58.939 41.667 0.00 0.00 45.98 2.17
763 806 5.535753 ATGCCCTCTATGCAAATTTAACC 57.464 39.130 0.00 0.00 42.92 2.85
791 834 5.695851 AACAGTTCATTCCATTCTGACAC 57.304 39.130 0.00 0.00 0.00 3.67
838 930 1.089920 GATCACTGTGCCACATGTCC 58.910 55.000 0.00 0.00 0.00 4.02
903 995 6.044682 CCAGCAGAATTTTATTTCCATCCAC 58.955 40.000 0.00 0.00 0.00 4.02
1098 1190 8.064814 GTGATAAAAACTTCTGTCAGTGAAGAC 58.935 37.037 10.00 0.00 42.37 3.01
1371 1514 6.198639 ACCTATAGATTCAGACCAGACTGTT 58.801 40.000 0.00 0.00 38.79 3.16
1478 1621 2.355132 CTGATCAATCTGTGGAGCTTGC 59.645 50.000 0.00 0.00 0.00 4.01
1845 1988 7.978099 ACCAATAGCAAAAGGAAGGATTATT 57.022 32.000 0.00 0.00 0.00 1.40
2130 2273 1.004862 GCTCCTTTGCCTCCTTTACCT 59.995 52.381 0.00 0.00 0.00 3.08
2317 2460 8.261522 AGTATTTGGAGAGAGATGAGGTAAAAC 58.738 37.037 0.00 0.00 0.00 2.43
2401 2544 5.066505 ACAACATGACTCTTGGTTTTGTCTC 59.933 40.000 0.00 0.00 0.00 3.36
2491 2634 6.916360 AAGGATTTCACATTTAGGAAAGCA 57.084 33.333 0.00 0.00 40.23 3.91
2543 2686 6.635030 ACTGTCACCTTCCTTAACATTTTC 57.365 37.500 0.00 0.00 0.00 2.29
2739 2882 5.450592 TGCTTGTATTGCAGTGAAAATGA 57.549 34.783 0.00 0.00 30.28 2.57
2833 2976 2.511659 CCTAGGGGCATCATTGATGTG 58.488 52.381 23.86 5.79 41.60 3.21
2854 2997 1.606313 ACCAAAACCCATGGCGGAG 60.606 57.895 6.09 0.00 41.89 4.63
2986 3129 9.509956 AAAAGGTTAGCACATGTACATACTTAA 57.490 29.630 8.32 3.07 0.00 1.85
2987 3130 8.718102 AAGGTTAGCACATGTACATACTTAAG 57.282 34.615 8.32 0.00 0.00 1.85
2988 3131 7.848128 AGGTTAGCACATGTACATACTTAAGT 58.152 34.615 13.68 13.68 0.00 2.24
2989 3132 8.974238 AGGTTAGCACATGTACATACTTAAGTA 58.026 33.333 17.41 17.41 34.67 2.24
2990 3133 9.028185 GGTTAGCACATGTACATACTTAAGTAC 57.972 37.037 17.45 8.28 40.68 2.73
2991 3134 9.798994 GTTAGCACATGTACATACTTAAGTACT 57.201 33.333 17.45 8.43 40.84 2.73
2993 3136 7.490000 AGCACATGTACATACTTAAGTACTCC 58.510 38.462 17.45 6.92 40.84 3.85
2994 3137 6.700520 GCACATGTACATACTTAAGTACTCCC 59.299 42.308 17.45 7.25 40.84 4.30
2995 3138 7.417570 GCACATGTACATACTTAAGTACTCCCT 60.418 40.741 17.45 0.00 40.84 4.20
2996 3139 8.136165 CACATGTACATACTTAAGTACTCCCTC 58.864 40.741 17.45 7.28 40.84 4.30
2997 3140 7.837689 ACATGTACATACTTAAGTACTCCCTCA 59.162 37.037 17.45 11.91 40.84 3.86
2998 3141 7.876936 TGTACATACTTAAGTACTCCCTCAG 57.123 40.000 17.45 3.76 40.84 3.35
2999 3142 7.408543 TGTACATACTTAAGTACTCCCTCAGT 58.591 38.462 17.45 8.61 40.84 3.41
3000 3143 7.555554 TGTACATACTTAAGTACTCCCTCAGTC 59.444 40.741 17.45 2.19 40.84 3.51
3001 3144 5.892686 ACATACTTAAGTACTCCCTCAGTCC 59.107 44.000 17.45 0.00 36.43 3.85
3002 3145 3.354467 ACTTAAGTACTCCCTCAGTCCG 58.646 50.000 6.26 0.00 36.43 4.79
3003 3146 2.431954 TAAGTACTCCCTCAGTCCGG 57.568 55.000 0.00 0.00 36.43 5.14
3004 3147 0.702902 AAGTACTCCCTCAGTCCGGA 59.297 55.000 0.00 0.00 36.43 5.14
3005 3148 0.702902 AGTACTCCCTCAGTCCGGAA 59.297 55.000 5.23 0.00 36.43 4.30
3006 3149 1.076677 AGTACTCCCTCAGTCCGGAAA 59.923 52.381 5.23 0.00 36.43 3.13
3007 3150 2.108970 GTACTCCCTCAGTCCGGAAAT 58.891 52.381 5.23 0.00 36.43 2.17
3008 3151 2.544844 ACTCCCTCAGTCCGGAAATA 57.455 50.000 5.23 0.00 0.00 1.40
3009 3152 2.108970 ACTCCCTCAGTCCGGAAATAC 58.891 52.381 5.23 0.00 0.00 1.89
3010 3153 2.292323 ACTCCCTCAGTCCGGAAATACT 60.292 50.000 5.23 0.00 0.00 2.12
3011 3154 2.766828 CTCCCTCAGTCCGGAAATACTT 59.233 50.000 5.23 0.00 0.00 2.24
3012 3155 2.500098 TCCCTCAGTCCGGAAATACTTG 59.500 50.000 5.23 0.00 0.00 3.16
3013 3156 2.236395 CCCTCAGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
3014 3157 3.522553 CCTCAGTCCGGAAATACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
3015 3158 3.179830 CTCAGTCCGGAAATACTTGTCG 58.820 50.000 5.23 0.00 0.00 4.35
3016 3159 2.094390 TCAGTCCGGAAATACTTGTCGG 60.094 50.000 5.23 0.00 41.80 4.79
3017 3160 2.094390 CAGTCCGGAAATACTTGTCGGA 60.094 50.000 5.23 0.00 46.06 4.55
3018 3161 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
3019 3162 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
3020 3163 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
3021 3164 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
3022 3165 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
3023 3166 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
3024 3167 4.868171 CGGAAATACTTGTCGGAGAAATGA 59.132 41.667 0.00 0.00 39.69 2.57
3025 3168 5.350365 CGGAAATACTTGTCGGAGAAATGAA 59.650 40.000 0.00 0.00 39.69 2.57
3026 3169 6.037172 CGGAAATACTTGTCGGAGAAATGAAT 59.963 38.462 0.00 0.00 39.69 2.57
3027 3170 7.189512 GGAAATACTTGTCGGAGAAATGAATG 58.810 38.462 0.00 0.00 39.69 2.67
3028 3171 7.148239 GGAAATACTTGTCGGAGAAATGAATGT 60.148 37.037 0.00 0.00 39.69 2.71
3029 3172 8.786826 AAATACTTGTCGGAGAAATGAATGTA 57.213 30.769 0.00 0.00 39.69 2.29
3030 3173 8.964476 AATACTTGTCGGAGAAATGAATGTAT 57.036 30.769 0.00 0.00 39.69 2.29
3031 3174 6.910536 ACTTGTCGGAGAAATGAATGTATC 57.089 37.500 0.00 0.00 39.69 2.24
3032 3175 6.644347 ACTTGTCGGAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 39.69 1.98
3033 3176 7.782049 ACTTGTCGGAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 39.69 1.98
3034 3177 7.923344 ACTTGTCGGAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 39.69 2.43
3035 3178 7.582667 TGTCGGAGAAATGAATGTATCTAGA 57.417 36.000 0.00 0.00 39.69 2.43
3036 3179 8.183104 TGTCGGAGAAATGAATGTATCTAGAT 57.817 34.615 10.73 10.73 39.69 1.98
3037 3180 8.084684 TGTCGGAGAAATGAATGTATCTAGATG 58.915 37.037 15.79 0.00 39.69 2.90
3038 3181 8.085296 GTCGGAGAAATGAATGTATCTAGATGT 58.915 37.037 15.79 0.00 39.69 3.06
3039 3182 9.297037 TCGGAGAAATGAATGTATCTAGATGTA 57.703 33.333 15.79 4.44 0.00 2.29
3079 3222 8.292444 ACATTCATTTTTATCCATTTCTCCGA 57.708 30.769 0.00 0.00 0.00 4.55
3080 3223 8.190784 ACATTCATTTTTATCCATTTCTCCGAC 58.809 33.333 0.00 0.00 0.00 4.79
3081 3224 7.695480 TTCATTTTTATCCATTTCTCCGACA 57.305 32.000 0.00 0.00 0.00 4.35
3082 3225 7.695480 TCATTTTTATCCATTTCTCCGACAA 57.305 32.000 0.00 0.00 0.00 3.18
3083 3226 7.761409 TCATTTTTATCCATTTCTCCGACAAG 58.239 34.615 0.00 0.00 0.00 3.16
3084 3227 7.393234 TCATTTTTATCCATTTCTCCGACAAGT 59.607 33.333 0.00 0.00 0.00 3.16
3085 3228 8.673711 CATTTTTATCCATTTCTCCGACAAGTA 58.326 33.333 0.00 0.00 0.00 2.24
3086 3229 8.801882 TTTTTATCCATTTCTCCGACAAGTAT 57.198 30.769 0.00 0.00 0.00 2.12
3087 3230 8.801882 TTTTATCCATTTCTCCGACAAGTATT 57.198 30.769 0.00 0.00 0.00 1.89
3088 3231 8.801882 TTTATCCATTTCTCCGACAAGTATTT 57.198 30.769 0.00 0.00 0.00 1.40
3089 3232 6.927294 ATCCATTTCTCCGACAAGTATTTC 57.073 37.500 0.00 0.00 0.00 2.17
3090 3233 6.049955 TCCATTTCTCCGACAAGTATTTCT 57.950 37.500 0.00 0.00 0.00 2.52
3091 3234 7.177832 TCCATTTCTCCGACAAGTATTTCTA 57.822 36.000 0.00 0.00 0.00 2.10
3092 3235 7.265673 TCCATTTCTCCGACAAGTATTTCTAG 58.734 38.462 0.00 0.00 0.00 2.43
3093 3236 7.123697 TCCATTTCTCCGACAAGTATTTCTAGA 59.876 37.037 0.00 0.00 0.00 2.43
3094 3237 7.222999 CCATTTCTCCGACAAGTATTTCTAGAC 59.777 40.741 0.00 0.00 0.00 2.59
3095 3238 5.481200 TCTCCGACAAGTATTTCTAGACG 57.519 43.478 0.00 0.00 0.00 4.18
3096 3239 4.334759 TCTCCGACAAGTATTTCTAGACGG 59.665 45.833 6.36 6.36 36.83 4.79
3097 3240 4.264253 TCCGACAAGTATTTCTAGACGGA 58.736 43.478 10.31 10.31 39.50 4.69
3098 3241 4.334759 TCCGACAAGTATTTCTAGACGGAG 59.665 45.833 10.31 0.00 38.21 4.63
3099 3242 4.497674 CCGACAAGTATTTCTAGACGGAGG 60.498 50.000 6.77 0.00 37.25 4.30
3100 3243 4.497674 CGACAAGTATTTCTAGACGGAGGG 60.498 50.000 0.00 0.00 0.00 4.30
3111 3254 2.520069 AGACGGAGGGAGTATATGCAG 58.480 52.381 0.00 0.00 0.00 4.41
3142 3285 7.984422 TGGAACTGCATAATCCATGTATTAG 57.016 36.000 10.30 0.00 38.30 1.73
3143 3286 7.517320 TGGAACTGCATAATCCATGTATTAGT 58.483 34.615 10.30 0.00 38.30 2.24
3814 3960 4.716287 TGATGATACCTGGACTCATGTTCA 59.284 41.667 16.58 9.42 30.00 3.18
3879 4319 9.884465 CAAGTTATGCTTCTTTAAGTATATGCC 57.116 33.333 0.00 0.00 39.22 4.40
3974 4414 5.887035 ACTCTAGGGTATACAATCTATCCGC 59.113 44.000 5.01 0.00 0.00 5.54
3980 4420 2.806608 TACAATCTATCCGCGGTTCC 57.193 50.000 27.15 0.00 0.00 3.62
4037 4477 2.948979 TCTGTGTTGGTGCCTGTAAAAG 59.051 45.455 0.00 0.00 0.00 2.27
4099 4539 6.753180 TGCCTATTGTGTGCAAGAAATAAAA 58.247 32.000 0.00 0.00 38.10 1.52
4144 4584 9.927668 CTATTTCAAACAAATAACATGGGTCTT 57.072 29.630 0.00 0.00 0.00 3.01
4190 4630 2.805671 TGATTTAATATCCGGTGCAGCG 59.194 45.455 30.27 30.27 0.00 5.18
4230 4743 1.271325 TGCAAGGGTACATGTGAGTGG 60.271 52.381 9.11 0.00 0.00 4.00
4286 4799 6.153851 TGGTCGAAGTCCTTTTACATCAGATA 59.846 38.462 0.00 0.00 36.46 1.98
4398 4917 1.269621 CCTAGGGCGTAATCAGTTCCG 60.270 57.143 0.00 0.00 0.00 4.30
4450 4969 4.392138 GCCTACCGTCTTTCCATTATATGC 59.608 45.833 0.00 0.00 0.00 3.14
4724 5246 6.304126 AGTGCGACATTCTATTTAAAACACG 58.696 36.000 0.00 0.00 0.00 4.49
4748 5270 9.511272 ACGGTCATTTTAAACTACTAAATTCCT 57.489 29.630 0.00 0.00 0.00 3.36
4763 5285 8.541899 ACTAAATTCCTTGGTTGGTTCTTAAA 57.458 30.769 0.00 0.00 0.00 1.52
4854 5376 7.414540 GCATTCTGGATGTCGACTAGAAAATTT 60.415 37.037 17.92 4.32 38.09 1.82
4860 5382 6.766467 GGATGTCGACTAGAAAATTTGGGTAT 59.234 38.462 17.92 0.00 0.00 2.73
4959 5498 1.603634 TTTAGGGATTGGGAGGGGAC 58.396 55.000 0.00 0.00 0.00 4.46
5029 5568 9.625747 TTGTATTTATCCACTTCTCATGCATTA 57.374 29.630 0.00 0.00 0.00 1.90
5069 5608 8.155510 ACTGTACTGTGCTACTGCTATATAGTA 58.844 37.037 11.38 6.00 40.48 1.82
5166 5807 6.428295 ACTAGTCCAGCAATAGTCTAGACTT 58.572 40.000 29.57 14.90 42.54 3.01
5205 5846 2.434702 AGTCTCAACCTTGGAACGACTT 59.565 45.455 0.00 0.00 0.00 3.01
5786 6429 4.574828 GCTTTGTCAGTCTTGTAGTTGGAA 59.425 41.667 0.00 0.00 0.00 3.53
5824 6467 5.397899 CCAGTCTGATTTGGGGCTATTCTTA 60.398 44.000 0.00 0.00 0.00 2.10
5825 6468 6.122277 CAGTCTGATTTGGGGCTATTCTTAA 58.878 40.000 0.00 0.00 0.00 1.85
5826 6469 6.038714 CAGTCTGATTTGGGGCTATTCTTAAC 59.961 42.308 0.00 0.00 0.00 2.01
5841 6746 6.582437 ATTCTTAACGTTTGCTTGGTTTTG 57.418 33.333 5.91 0.00 0.00 2.44
5849 6754 4.266739 CGTTTGCTTGGTTTTGGTTACTTC 59.733 41.667 0.00 0.00 0.00 3.01
6181 7086 7.450634 AGTCTGTGGTCACTAGAAATACAACTA 59.549 37.037 0.00 0.00 0.00 2.24
6223 7128 4.718940 AATTAAGGGAATGCGGTTTCAG 57.281 40.909 0.00 0.00 0.00 3.02
6262 7181 4.034626 TGTGACATCGGCCATTTATTAACG 59.965 41.667 2.24 0.00 0.00 3.18
6345 7264 3.514777 TTGCTAGAGTGCAAGTCCG 57.485 52.632 0.00 0.00 46.43 4.79
6358 7277 7.390718 AGAGTGCAAGTCCGAAATATTAACTTT 59.609 33.333 0.00 0.00 36.80 2.66
6541 7461 9.559958 GTACACAGATTTTGGTAAAATGAGATG 57.440 33.333 4.42 2.05 40.97 2.90
6667 7587 1.000283 CGTCAGAGCAGTTCTTGGAGT 60.000 52.381 0.00 0.00 32.41 3.85
6672 7592 2.158696 AGAGCAGTTCTTGGAGTTGCTT 60.159 45.455 0.00 0.00 44.46 3.91
6812 7732 2.507407 TTTGTGGAAGGATGCTACCC 57.493 50.000 0.00 0.00 0.00 3.69
6934 7854 2.208326 CATTTGACTAAATGGGCGCC 57.792 50.000 21.18 21.18 45.99 6.53
6935 7855 1.111277 ATTTGACTAAATGGGCGCCC 58.889 50.000 39.40 39.40 35.26 6.13
6936 7856 0.039035 TTTGACTAAATGGGCGCCCT 59.961 50.000 43.34 27.93 36.94 5.19
6937 7857 0.393808 TTGACTAAATGGGCGCCCTC 60.394 55.000 43.34 31.29 36.94 4.30
7015 7940 5.885912 AGATGTTATGTTGCCTTCGGTATTT 59.114 36.000 0.00 0.00 0.00 1.40
7016 7941 5.303747 TGTTATGTTGCCTTCGGTATTTG 57.696 39.130 0.00 0.00 0.00 2.32
7017 7942 2.939460 ATGTTGCCTTCGGTATTTGC 57.061 45.000 0.00 0.00 0.00 3.68
7018 7943 1.904287 TGTTGCCTTCGGTATTTGCT 58.096 45.000 0.00 0.00 0.00 3.91
7028 7975 5.522097 CCTTCGGTATTTGCTTGTTTTGTTT 59.478 36.000 0.00 0.00 0.00 2.83
7039 7986 3.096489 TGTTTTGTTTGCTGATGCCTC 57.904 42.857 0.00 0.00 38.71 4.70
7078 8026 8.984764 GCGGTGTTTATTATTTTCCTTCTTTTT 58.015 29.630 0.00 0.00 0.00 1.94
7240 8191 2.808906 ATAGGTCCTTTGGAGGTTGC 57.191 50.000 0.00 0.00 43.97 4.17
7255 8206 2.314647 TTGCGGAAAAGCGACGAGG 61.315 57.895 0.00 0.00 40.67 4.63
7257 8208 1.444895 GCGGAAAAGCGACGAGGTA 60.445 57.895 0.00 0.00 0.00 3.08
7261 8212 2.613691 GGAAAAGCGACGAGGTATCAA 58.386 47.619 0.00 0.00 0.00 2.57
7279 8230 7.393515 AGGTATCAATTCCAGTTCCTTGTTTAC 59.606 37.037 0.00 0.00 0.00 2.01
7323 8274 6.633500 TTGTCTTAACCAAATGAGTTGAGG 57.367 37.500 0.00 0.00 39.87 3.86
7353 8304 5.008019 CGAACTTCCATGGACTGAATATTGG 59.992 44.000 15.91 0.00 0.00 3.16
7354 8305 4.796606 ACTTCCATGGACTGAATATTGGG 58.203 43.478 15.91 0.00 0.00 4.12
7355 8306 4.230502 ACTTCCATGGACTGAATATTGGGT 59.769 41.667 15.91 0.00 0.00 4.51
7356 8307 5.431731 ACTTCCATGGACTGAATATTGGGTA 59.568 40.000 15.91 0.00 0.00 3.69
7357 8308 6.103205 ACTTCCATGGACTGAATATTGGGTAT 59.897 38.462 15.91 0.00 0.00 2.73
7358 8309 7.294720 ACTTCCATGGACTGAATATTGGGTATA 59.705 37.037 15.91 0.00 0.00 1.47
7359 8310 7.829224 TCCATGGACTGAATATTGGGTATAT 57.171 36.000 11.44 0.00 0.00 0.86
7360 8311 8.230848 TCCATGGACTGAATATTGGGTATATT 57.769 34.615 11.44 0.00 41.16 1.28
7361 8312 8.108999 TCCATGGACTGAATATTGGGTATATTG 58.891 37.037 11.44 0.00 39.09 1.90
7362 8313 7.340232 CCATGGACTGAATATTGGGTATATTGG 59.660 40.741 5.56 0.00 39.09 3.16
7367 8318 5.016173 TGAATATTGGGTATATTGGGCAGC 58.984 41.667 0.00 0.00 39.09 5.25
7403 8354 2.427245 CCAGACGGGCCTCCAGTAG 61.427 68.421 0.84 0.00 0.00 2.57
7526 8488 0.877071 CATGTTATCATCCCTGGCGC 59.123 55.000 0.00 0.00 31.15 6.53
7527 8489 0.767375 ATGTTATCATCCCTGGCGCT 59.233 50.000 7.64 0.00 0.00 5.92
7647 8609 4.830765 GGCGCGGTCCAGCACATA 62.831 66.667 8.83 0.00 36.85 2.29
7706 8668 1.946768 ACTGCAAAGCAAAGCTACGAA 59.053 42.857 0.00 0.00 38.25 3.85
7725 8688 4.398044 ACGAACAGAAGAACCAAAACACAT 59.602 37.500 0.00 0.00 0.00 3.21
7727 8690 5.907391 CGAACAGAAGAACCAAAACACATAC 59.093 40.000 0.00 0.00 0.00 2.39
7729 8692 6.767524 ACAGAAGAACCAAAACACATACAA 57.232 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.510012 CAGCTCGCGGATGAAGCA 60.510 61.111 17.57 0.00 32.28 3.91
82 98 3.733727 CGCACTGAACCAAAATAACCAAC 59.266 43.478 0.00 0.00 0.00 3.77
89 105 3.305335 GGATGAACGCACTGAACCAAAAT 60.305 43.478 0.00 0.00 0.00 1.82
103 119 1.644786 GCCCAGAAACCGGATGAACG 61.645 60.000 9.46 0.00 0.00 3.95
117 133 4.087892 CCTCACCTCACCGCCCAG 62.088 72.222 0.00 0.00 0.00 4.45
152 168 2.804931 GCCGCGGTGTTTGCATTC 60.805 61.111 28.70 0.93 0.00 2.67
180 196 1.885388 CCCGGATTAATCGCACGCA 60.885 57.895 0.73 0.00 0.00 5.24
241 261 4.228097 GTGCTAGGCATGTGCGCG 62.228 66.667 0.00 0.00 41.91 6.86
274 294 2.501650 CGCGCAATCACCAAACCG 60.502 61.111 8.75 0.00 0.00 4.44
352 376 0.969894 CAATAAACCACGGGGCCAAA 59.030 50.000 1.73 0.00 37.90 3.28
375 399 0.667993 CCCAAATGCAGACACGTTGT 59.332 50.000 0.00 0.00 0.00 3.32
396 420 6.260271 GGCAAATAGTACCTGACTGATTAACC 59.740 42.308 0.00 0.00 39.39 2.85
448 472 1.580845 GCGACCACAAATGCTCTGCT 61.581 55.000 0.00 0.00 0.00 4.24
464 488 2.815211 GGCAATCAGACGCAGCGA 60.815 61.111 24.65 0.00 0.00 4.93
465 489 4.214383 CGGCAATCAGACGCAGCG 62.214 66.667 14.82 14.82 45.03 5.18
471 495 1.878522 ACGCGATCGGCAATCAGAC 60.879 57.895 15.93 0.00 43.84 3.51
498 522 0.307453 GTTGTGCGTGATGAACTGCA 59.693 50.000 0.00 0.00 36.44 4.41
510 534 1.587946 GTGAAAAGCCTTTGTTGTGCG 59.412 47.619 0.00 0.00 0.00 5.34
531 555 2.279582 ACGGAATAGAAGAGTGCACG 57.720 50.000 12.01 0.00 0.00 5.34
692 735 3.738830 TCGCATGGTATGGTTAGTACC 57.261 47.619 0.00 0.00 45.26 3.34
693 736 6.613755 AAAATCGCATGGTATGGTTAGTAC 57.386 37.500 0.00 0.00 0.00 2.73
763 806 6.094464 TCAGAATGGAATGAACTGTTATGCAG 59.906 38.462 0.00 0.00 43.79 4.41
791 834 6.215121 ACCATATGACAAAACACAACACATG 58.785 36.000 3.65 0.00 0.00 3.21
903 995 7.378181 ACTTGTAAACTAAAAATGGCATGGAG 58.622 34.615 0.00 0.00 0.00 3.86
1008 1100 3.275617 TTTATCACATCCTTGTCCCCG 57.724 47.619 0.00 0.00 32.34 5.73
1118 1210 6.998074 ACTGACAGAAGTTTTTATCACATCCA 59.002 34.615 10.08 0.00 0.00 3.41
1444 1587 3.401033 TTGATCAGAAGAACGCCTCAA 57.599 42.857 0.00 0.00 0.00 3.02
1478 1621 1.959282 ACCCTTGCTGAGCTTTTGAAG 59.041 47.619 5.83 0.00 0.00 3.02
1695 1838 6.531021 TCTTTCCTCGGATTTCTTTTGTACT 58.469 36.000 0.00 0.00 0.00 2.73
1701 1844 4.216472 GTGCTTCTTTCCTCGGATTTCTTT 59.784 41.667 0.00 0.00 0.00 2.52
1845 1988 5.870706 TCACATCCCAGTTTTGTGTATACA 58.129 37.500 0.08 0.08 41.14 2.29
2130 2273 1.472878 CCAGATTCGTCGTCTTCTCCA 59.527 52.381 0.00 0.00 0.00 3.86
2139 2282 0.459899 TCCCACATCCAGATTCGTCG 59.540 55.000 0.00 0.00 0.00 5.12
2462 2605 7.466746 TCCTAAATGTGAAATCCTTTCCAAG 57.533 36.000 0.00 0.00 38.90 3.61
2491 2634 5.385198 AGGGAACATACAAAACAGATGTGT 58.615 37.500 0.00 0.00 39.19 3.72
2663 2806 5.644636 TCCAACCAACGGAGACATAAATAAC 59.355 40.000 0.00 0.00 0.00 1.89
2739 2882 4.670765 AGGCTGATTTCCATCTTCAAAGT 58.329 39.130 0.00 0.00 0.00 2.66
2833 2976 2.347114 GCCATGGGTTTTGGTGCC 59.653 61.111 15.13 0.00 36.57 5.01
2854 2997 3.686726 ACTTTCTCAACCTTGATGCGATC 59.313 43.478 0.00 0.00 36.46 3.69
2986 3129 0.702902 TTCCGGACTGAGGGAGTACT 59.297 55.000 1.83 0.00 32.49 2.73
2987 3130 1.553706 TTTCCGGACTGAGGGAGTAC 58.446 55.000 1.83 0.00 33.83 2.73
2988 3131 2.544844 ATTTCCGGACTGAGGGAGTA 57.455 50.000 1.83 0.00 33.83 2.59
2989 3132 2.108970 GTATTTCCGGACTGAGGGAGT 58.891 52.381 1.83 0.00 37.76 3.85
2990 3133 2.389715 AGTATTTCCGGACTGAGGGAG 58.610 52.381 1.83 0.00 33.01 4.30
2991 3134 2.500098 CAAGTATTTCCGGACTGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
2992 3135 2.236395 ACAAGTATTTCCGGACTGAGGG 59.764 50.000 1.83 0.00 0.00 4.30
2993 3136 3.522553 GACAAGTATTTCCGGACTGAGG 58.477 50.000 1.83 0.00 0.00 3.86
2994 3137 3.179830 CGACAAGTATTTCCGGACTGAG 58.820 50.000 1.83 0.00 0.00 3.35
2995 3138 2.094390 CCGACAAGTATTTCCGGACTGA 60.094 50.000 1.83 0.00 42.49 3.41
2996 3139 2.094390 TCCGACAAGTATTTCCGGACTG 60.094 50.000 1.83 0.00 43.47 3.51
2997 3140 2.165845 CTCCGACAAGTATTTCCGGACT 59.834 50.000 1.83 0.00 43.47 3.85
2998 3141 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
2999 3142 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
3000 3143 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
3001 3144 4.868171 TCATTTCTCCGACAAGTATTTCCG 59.132 41.667 0.00 0.00 0.00 4.30
3002 3145 6.737254 TTCATTTCTCCGACAAGTATTTCC 57.263 37.500 0.00 0.00 0.00 3.13
3003 3146 7.752695 ACATTCATTTCTCCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
3004 3147 7.687941 ACATTCATTTCTCCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
3005 3148 8.964476 ATACATTCATTTCTCCGACAAGTATT 57.036 30.769 0.00 0.00 0.00 1.89
3006 3149 8.424918 AGATACATTCATTTCTCCGACAAGTAT 58.575 33.333 0.00 0.00 0.00 2.12
3007 3150 7.782049 AGATACATTCATTTCTCCGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
3008 3151 6.644347 AGATACATTCATTTCTCCGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
3009 3152 8.138074 TCTAGATACATTCATTTCTCCGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
3010 3153 8.007405 TCTAGATACATTCATTTCTCCGACAA 57.993 34.615 0.00 0.00 0.00 3.18
3011 3154 7.582667 TCTAGATACATTCATTTCTCCGACA 57.417 36.000 0.00 0.00 0.00 4.35
3012 3155 8.085296 ACATCTAGATACATTCATTTCTCCGAC 58.915 37.037 4.54 0.00 0.00 4.79
3013 3156 8.183104 ACATCTAGATACATTCATTTCTCCGA 57.817 34.615 4.54 0.00 0.00 4.55
3053 3196 9.402320 TCGGAGAAATGGATAAAAATGAATGTA 57.598 29.630 0.00 0.00 0.00 2.29
3054 3197 8.190784 GTCGGAGAAATGGATAAAAATGAATGT 58.809 33.333 0.00 0.00 39.69 2.71
3055 3198 8.190122 TGTCGGAGAAATGGATAAAAATGAATG 58.810 33.333 0.00 0.00 39.69 2.67
3056 3199 8.292444 TGTCGGAGAAATGGATAAAAATGAAT 57.708 30.769 0.00 0.00 39.69 2.57
3057 3200 7.695480 TGTCGGAGAAATGGATAAAAATGAA 57.305 32.000 0.00 0.00 39.69 2.57
3058 3201 7.393234 ACTTGTCGGAGAAATGGATAAAAATGA 59.607 33.333 0.00 0.00 39.69 2.57
3059 3202 7.538575 ACTTGTCGGAGAAATGGATAAAAATG 58.461 34.615 0.00 0.00 39.69 2.32
3060 3203 7.703058 ACTTGTCGGAGAAATGGATAAAAAT 57.297 32.000 0.00 0.00 39.69 1.82
3061 3204 8.801882 ATACTTGTCGGAGAAATGGATAAAAA 57.198 30.769 0.00 0.00 39.69 1.94
3062 3205 8.801882 AATACTTGTCGGAGAAATGGATAAAA 57.198 30.769 0.00 0.00 39.69 1.52
3063 3206 8.801882 AAATACTTGTCGGAGAAATGGATAAA 57.198 30.769 0.00 0.00 39.69 1.40
3064 3207 8.265055 AGAAATACTTGTCGGAGAAATGGATAA 58.735 33.333 0.00 0.00 39.69 1.75
3065 3208 7.792032 AGAAATACTTGTCGGAGAAATGGATA 58.208 34.615 0.00 0.00 39.69 2.59
3066 3209 6.653989 AGAAATACTTGTCGGAGAAATGGAT 58.346 36.000 0.00 0.00 39.69 3.41
3067 3210 6.049955 AGAAATACTTGTCGGAGAAATGGA 57.950 37.500 0.00 0.00 39.69 3.41
3068 3211 7.222999 GTCTAGAAATACTTGTCGGAGAAATGG 59.777 40.741 0.00 0.00 39.69 3.16
3069 3212 7.043986 CGTCTAGAAATACTTGTCGGAGAAATG 60.044 40.741 0.00 0.00 39.69 2.32
3070 3213 6.973474 CGTCTAGAAATACTTGTCGGAGAAAT 59.027 38.462 0.00 0.00 39.69 2.17
3071 3214 6.320171 CGTCTAGAAATACTTGTCGGAGAAA 58.680 40.000 0.00 0.00 39.69 2.52
3072 3215 5.877031 CGTCTAGAAATACTTGTCGGAGAA 58.123 41.667 0.00 0.00 39.69 2.87
3073 3216 5.481200 CGTCTAGAAATACTTGTCGGAGA 57.519 43.478 0.00 0.00 32.33 3.71
3076 3219 4.497674 CCTCCGTCTAGAAATACTTGTCGG 60.498 50.000 0.00 0.00 46.52 4.79
3077 3220 4.497674 CCCTCCGTCTAGAAATACTTGTCG 60.498 50.000 0.00 0.00 34.45 4.35
3078 3221 4.643784 TCCCTCCGTCTAGAAATACTTGTC 59.356 45.833 0.00 0.00 0.00 3.18
3079 3222 4.607239 TCCCTCCGTCTAGAAATACTTGT 58.393 43.478 0.00 0.00 0.00 3.16
3080 3223 4.645588 ACTCCCTCCGTCTAGAAATACTTG 59.354 45.833 0.00 0.00 0.00 3.16
3081 3224 4.869451 ACTCCCTCCGTCTAGAAATACTT 58.131 43.478 0.00 0.00 0.00 2.24
3082 3225 4.523168 ACTCCCTCCGTCTAGAAATACT 57.477 45.455 0.00 0.00 0.00 2.12
3083 3226 7.415429 GCATATACTCCCTCCGTCTAGAAATAC 60.415 44.444 0.00 0.00 0.00 1.89
3084 3227 6.602406 GCATATACTCCCTCCGTCTAGAAATA 59.398 42.308 0.00 0.00 0.00 1.40
3085 3228 5.419471 GCATATACTCCCTCCGTCTAGAAAT 59.581 44.000 0.00 0.00 0.00 2.17
3086 3229 4.765856 GCATATACTCCCTCCGTCTAGAAA 59.234 45.833 0.00 0.00 0.00 2.52
3087 3230 4.202535 TGCATATACTCCCTCCGTCTAGAA 60.203 45.833 0.00 0.00 0.00 2.10
3088 3231 3.329814 TGCATATACTCCCTCCGTCTAGA 59.670 47.826 0.00 0.00 0.00 2.43
3089 3232 3.687125 TGCATATACTCCCTCCGTCTAG 58.313 50.000 0.00 0.00 0.00 2.43
3090 3233 3.329814 TCTGCATATACTCCCTCCGTCTA 59.670 47.826 0.00 0.00 0.00 2.59
3091 3234 2.108425 TCTGCATATACTCCCTCCGTCT 59.892 50.000 0.00 0.00 0.00 4.18
3092 3235 2.515854 TCTGCATATACTCCCTCCGTC 58.484 52.381 0.00 0.00 0.00 4.79
3093 3236 2.677542 TCTGCATATACTCCCTCCGT 57.322 50.000 0.00 0.00 0.00 4.69
3094 3237 3.057174 GTCTTCTGCATATACTCCCTCCG 60.057 52.174 0.00 0.00 0.00 4.63
3095 3238 3.898123 TGTCTTCTGCATATACTCCCTCC 59.102 47.826 0.00 0.00 0.00 4.30
3096 3239 5.477510 CATGTCTTCTGCATATACTCCCTC 58.522 45.833 0.00 0.00 0.00 4.30
3097 3240 4.285517 CCATGTCTTCTGCATATACTCCCT 59.714 45.833 0.00 0.00 0.00 4.20
3098 3241 4.284490 TCCATGTCTTCTGCATATACTCCC 59.716 45.833 0.00 0.00 0.00 4.30
3099 3242 5.474578 TCCATGTCTTCTGCATATACTCC 57.525 43.478 0.00 0.00 0.00 3.85
3100 3243 6.423302 CAGTTCCATGTCTTCTGCATATACTC 59.577 42.308 0.00 0.00 0.00 2.59
3111 3254 4.883585 TGGATTATGCAGTTCCATGTCTTC 59.116 41.667 10.18 0.00 34.65 2.87
3814 3960 4.900635 AACACGAAAGCTTCAAGACAAT 57.099 36.364 0.00 0.00 0.00 2.71
3879 4319 5.808042 ACTGAATATGTGCTTTGCTGTAG 57.192 39.130 0.00 0.00 0.00 2.74
3881 4321 5.939883 TCTTACTGAATATGTGCTTTGCTGT 59.060 36.000 0.00 0.00 0.00 4.40
3974 4414 0.178301 GCCCTTTCTAGGAGGAACCG 59.822 60.000 12.94 0.54 45.05 4.44
3980 4420 3.914426 TTAAGCTGCCCTTTCTAGGAG 57.086 47.619 0.00 0.00 45.05 3.69
4037 4477 3.380142 CACCACACTAATGTTTGGCAAC 58.620 45.455 0.00 0.00 45.34 4.17
4170 4610 2.806244 ACGCTGCACCGGATATTAAATC 59.194 45.455 9.46 0.00 0.00 2.17
4230 4743 3.978687 ACACACTGCGCTAGATAATACC 58.021 45.455 9.73 0.00 0.00 2.73
4286 4799 6.669591 TGCCTTCTATATGACTGGTATATGCT 59.330 38.462 0.00 0.00 0.00 3.79
4341 4854 8.115490 AGGTAAGTTTCAATCATTTCTTCCAG 57.885 34.615 0.00 0.00 0.00 3.86
4342 4855 9.231297 CTAGGTAAGTTTCAATCATTTCTTCCA 57.769 33.333 0.00 0.00 0.00 3.53
4398 4917 6.174049 CCTTCTATATTCCTTCGGATTTCCC 58.826 44.000 0.00 0.00 0.00 3.97
4433 4952 6.706270 ACAGGTAAGCATATAATGGAAAGACG 59.294 38.462 0.00 0.00 0.00 4.18
4463 4985 9.658799 CAATCTGACTTTCTAGAACCATAGAAA 57.341 33.333 4.18 8.25 45.19 2.52
4464 4986 9.035890 TCAATCTGACTTTCTAGAACCATAGAA 57.964 33.333 4.18 0.00 39.45 2.10
4556 5078 6.785466 TGGTGGCCAGTTTCTATATATAGTCA 59.215 38.462 5.11 5.27 0.00 3.41
4576 5098 0.738975 CAATGCAGATCAGCTGGTGG 59.261 55.000 15.13 1.98 45.03 4.61
4578 5100 2.636830 GTACAATGCAGATCAGCTGGT 58.363 47.619 15.13 6.50 45.03 4.00
4748 5270 5.606348 ATGCTTGTTTAAGAACCAACCAA 57.394 34.783 0.00 0.00 35.92 3.67
4749 5271 5.606348 AATGCTTGTTTAAGAACCAACCA 57.394 34.783 0.00 0.00 35.92 3.67
4750 5272 5.627780 CGTAATGCTTGTTTAAGAACCAACC 59.372 40.000 0.00 0.00 35.92 3.77
4751 5273 6.432107 TCGTAATGCTTGTTTAAGAACCAAC 58.568 36.000 0.00 0.00 35.92 3.77
4763 5285 1.630148 GCTCGACTCGTAATGCTTGT 58.370 50.000 0.00 0.00 0.00 3.16
4827 5349 3.023832 TCTAGTCGACATCCAGAATGCA 58.976 45.455 19.50 0.00 39.12 3.96
4854 5376 3.368248 ACTCGGCAAACTAGTATACCCA 58.632 45.455 0.00 0.00 0.00 4.51
4860 5382 1.131883 GCTCGACTCGGCAAACTAGTA 59.868 52.381 0.00 0.00 0.00 1.82
4868 5390 4.103103 CGACTGCTCGACTCGGCA 62.103 66.667 12.22 12.22 43.06 5.69
4908 5440 1.071436 GTCGAACGACTCAAAGTGCAC 60.071 52.381 18.12 9.40 41.57 4.57
4987 5526 2.375014 ACAAATTTTCCCTCCCACGT 57.625 45.000 0.00 0.00 0.00 4.49
5029 5568 9.720769 AGCACAGTACAGTATAAATACAAACTT 57.279 29.630 0.00 0.00 35.74 2.66
5166 5807 6.113411 TGAGACTCATAGACTAATCGTGACA 58.887 40.000 0.00 0.00 0.00 3.58
5205 5846 3.067180 AGAACAAGGTTTACGAGTCGACA 59.933 43.478 21.50 3.26 0.00 4.35
5302 5945 3.983044 ACAAGAGGTTCAGGGTATGAC 57.017 47.619 0.00 0.00 37.77 3.06
5548 6191 3.057019 CGCACACTACTAAGCAAGAACA 58.943 45.455 0.00 0.00 0.00 3.18
5689 6332 7.880623 AGGGTTGTAACTTATACCTAGAGAGA 58.119 38.462 0.00 0.00 0.00 3.10
5690 6333 9.287373 CTAGGGTTGTAACTTATACCTAGAGAG 57.713 40.741 14.01 0.00 45.56 3.20
5691 6334 9.007494 TCTAGGGTTGTAACTTATACCTAGAGA 57.993 37.037 16.23 4.94 45.98 3.10
5768 6411 6.093633 ACTTTGTTTCCAACTACAAGACTGAC 59.906 38.462 0.00 0.00 35.83 3.51
5786 6429 9.003658 CAAATCAGACTGGTATTCTACTTTGTT 57.996 33.333 1.81 0.00 0.00 2.83
5824 6467 2.753055 ACCAAAACCAAGCAAACGTT 57.247 40.000 0.00 0.00 0.00 3.99
5825 6468 2.753055 AACCAAAACCAAGCAAACGT 57.247 40.000 0.00 0.00 0.00 3.99
5826 6469 3.776340 AGTAACCAAAACCAAGCAAACG 58.224 40.909 0.00 0.00 0.00 3.60
5841 6746 2.163613 CCAAGGGCGAATTGAAGTAACC 59.836 50.000 0.00 0.00 0.00 2.85
5849 6754 3.574614 CAACTTAACCAAGGGCGAATTG 58.425 45.455 0.00 0.00 35.97 2.32
5894 6799 2.741612 TGACCGCTTTTTGAAGCATTG 58.258 42.857 11.22 2.34 45.75 2.82
5932 6837 2.616376 TGAGTGTTAATGCACCACACAC 59.384 45.455 21.02 16.76 42.81 3.82
6033 6938 1.670811 CCTAATAGGGCAAAGCACACG 59.329 52.381 0.00 0.00 32.33 4.49
6082 6987 7.643569 TGGATAAAGCAATCTCAATAAGCAA 57.356 32.000 0.00 0.00 0.00 3.91
6096 7001 6.155910 TGGCCTTCAAATTATTGGATAAAGCA 59.844 34.615 3.32 0.00 37.15 3.91
6223 7128 5.868043 TGTCACATCATCAATGAACTCAC 57.132 39.130 0.00 0.00 40.69 3.51
6262 7181 6.311935 TCAAGTAGTAACACGGTAATGCATTC 59.688 38.462 16.86 7.72 0.00 2.67
6358 7277 8.458052 CACAGTGCATATCAGGTAAAATTAACA 58.542 33.333 0.00 0.00 0.00 2.41
6434 7353 2.158534 ACATACCAAAGTGCAGGTCCAA 60.159 45.455 0.00 0.00 39.31 3.53
6541 7461 4.040376 CAGAACAAGAGTTTTTGAGCTGC 58.960 43.478 0.00 0.00 38.30 5.25
6651 7571 1.419387 AGCAACTCCAAGAACTGCTCT 59.581 47.619 0.00 0.00 39.04 4.09
6657 7577 2.860136 GTTTGCAAGCAACTCCAAGAAC 59.140 45.455 8.58 0.00 35.46 3.01
6667 7587 2.491298 TCAGTTGAGTGTTTGCAAGCAA 59.509 40.909 18.08 2.89 0.00 3.91
6672 7592 2.682856 GACCTTCAGTTGAGTGTTTGCA 59.317 45.455 0.00 0.00 0.00 4.08
6874 7794 2.401766 GCCATCCAGTTCGCCACAG 61.402 63.158 0.00 0.00 0.00 3.66
6933 7853 6.042638 AGATACGATAATCAACATGGAGGG 57.957 41.667 0.00 0.00 0.00 4.30
6934 7854 6.810676 CAGAGATACGATAATCAACATGGAGG 59.189 42.308 0.00 0.00 0.00 4.30
6935 7855 7.374272 ACAGAGATACGATAATCAACATGGAG 58.626 38.462 0.00 0.00 0.00 3.86
6936 7856 7.290110 ACAGAGATACGATAATCAACATGGA 57.710 36.000 0.00 0.00 0.00 3.41
6937 7857 7.116948 GGAACAGAGATACGATAATCAACATGG 59.883 40.741 0.00 0.00 0.00 3.66
7015 7940 2.608546 GCATCAGCAAACAAAACAAGCA 59.391 40.909 0.00 0.00 41.58 3.91
7016 7941 2.032636 GGCATCAGCAAACAAAACAAGC 60.033 45.455 0.00 0.00 44.61 4.01
7017 7942 3.460103 AGGCATCAGCAAACAAAACAAG 58.540 40.909 0.00 0.00 44.61 3.16
7018 7943 3.456280 GAGGCATCAGCAAACAAAACAA 58.544 40.909 0.00 0.00 44.61 2.83
7050 7997 6.852664 AGAAGGAAAATAATAAACACCGCAG 58.147 36.000 0.00 0.00 0.00 5.18
7178 8129 8.543862 TCATATATGACAGCTAAATTGCTCAG 57.456 34.615 11.49 0.00 41.98 3.35
7187 8138 8.777413 GCAGAAATGTTCATATATGACAGCTAA 58.223 33.333 15.10 0.00 36.36 3.09
7240 8191 1.197910 GATACCTCGTCGCTTTTCCG 58.802 55.000 0.00 0.00 0.00 4.30
7255 8206 8.336801 AGTAAACAAGGAACTGGAATTGATAC 57.663 34.615 0.00 0.00 40.86 2.24
7257 8208 8.934023 TTAGTAAACAAGGAACTGGAATTGAT 57.066 30.769 0.00 0.00 40.86 2.57
7261 8212 9.588096 AAAGATTAGTAAACAAGGAACTGGAAT 57.412 29.630 0.00 0.00 40.86 3.01
7279 8230 7.816031 AGACAAAATGCAACATCCAAAGATTAG 59.184 33.333 0.00 0.00 0.00 1.73
7323 8274 0.323629 TCCATGGAAGTTCGGTGGAC 59.676 55.000 13.46 0.00 34.23 4.02
7353 8304 4.367039 TTTCCTAGCTGCCCAATATACC 57.633 45.455 0.00 0.00 0.00 2.73
7354 8305 5.416013 GGAATTTCCTAGCTGCCCAATATAC 59.584 44.000 8.25 0.00 32.53 1.47
7355 8306 5.570320 GGAATTTCCTAGCTGCCCAATATA 58.430 41.667 8.25 0.00 32.53 0.86
7356 8307 4.411013 GGAATTTCCTAGCTGCCCAATAT 58.589 43.478 8.25 0.00 32.53 1.28
7357 8308 3.832527 GGAATTTCCTAGCTGCCCAATA 58.167 45.455 8.25 0.00 32.53 1.90
7358 8309 2.670939 GGAATTTCCTAGCTGCCCAAT 58.329 47.619 8.25 0.00 32.53 3.16
7359 8310 2.143876 GGAATTTCCTAGCTGCCCAA 57.856 50.000 8.25 0.00 32.53 4.12
7360 8311 3.903208 GGAATTTCCTAGCTGCCCA 57.097 52.632 8.25 0.00 32.53 5.36
7367 8318 8.880410 CCGTCTGGATCGAAGGAATTTCCTAG 62.880 50.000 18.24 14.78 41.93 3.02
7403 8354 0.249911 AGTCTTCAACCACTCCGCAC 60.250 55.000 0.00 0.00 0.00 5.34
7526 8488 1.302033 GTGACAGGGTGGCTGACAG 60.302 63.158 0.00 0.00 0.00 3.51
7527 8489 1.631071 TTGTGACAGGGTGGCTGACA 61.631 55.000 0.00 0.00 0.00 3.58
7646 8608 1.270839 GGAGCAGTTGCCTTGTCAGTA 60.271 52.381 0.00 0.00 43.38 2.74
7647 8609 0.536006 GGAGCAGTTGCCTTGTCAGT 60.536 55.000 0.00 0.00 43.38 3.41
7706 8668 6.767524 TTGTATGTGTTTTGGTTCTTCTGT 57.232 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.