Multiple sequence alignment - TraesCS2B01G398300

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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 TraesCS2B01G398300 chr2B 100.000 4262 0 0 1 4262 565187991 565192252 0.000000e+00 7871
1 TraesCS2B01G398300 chr2B 91.068 3493 219 43 553 4003 565076034 565079475 0.000000e+00 4636
2 TraesCS2B01G398300 chr2B 89.702 2816 225 31 694 3502 565209751 565212508 0.000000e+00 3533
3 TraesCS2B01G398300 chr2B 91.515 165 9 2 4103 4262 565081063 565081227 5.550000e-54 222
4 TraesCS2B01G398300 chr2B 87.500 152 11 1 503 646 565209603 565209754 7.330000e-38 169
5 TraesCS2B01G398300 chr2D 92.875 4070 212 36 255 4262 481687854 481691907 0.000000e+00 5838
6 TraesCS2B01G398300 chr2D 94.487 2993 157 5 970 3956 481656055 481659045 0.000000e+00 4606
7 TraesCS2B01G398300 chr2D 90.995 2976 221 19 540 3502 481987948 481990889 0.000000e+00 3967
8 TraesCS2B01G398300 chr2D 90.050 2985 255 27 540 3502 481961016 481963980 0.000000e+00 3829
9 TraesCS2B01G398300 chr2D 81.186 489 36 22 417 869 481655513 481655981 4.080000e-90 342
10 TraesCS2B01G398300 chr2D 85.600 250 34 2 1 248 70482328 70482577 1.180000e-65 261
11 TraesCS2B01G398300 chr2D 87.556 225 28 0 3951 4175 481659605 481659829 1.180000e-65 261
12 TraesCS2B01G398300 chr2D 90.845 142 11 2 252 393 481987617 481987756 5.630000e-44 189
13 TraesCS2B01G398300 chr2D 93.617 94 3 2 4172 4262 481661453 481661546 2.070000e-28 137
14 TraesCS2B01G398300 chr2A 91.932 3731 213 36 561 4262 624393902 624397573 0.000000e+00 5142
15 TraesCS2B01G398300 chr2A 94.293 3294 168 5 972 4262 624447125 624450401 0.000000e+00 5024
16 TraesCS2B01G398300 chr2A 91.247 2982 222 20 540 3499 624457818 624460782 0.000000e+00 4024
17 TraesCS2B01G398300 chr2A 87.670 2579 264 32 972 3521 624359539 624362092 0.000000e+00 2952
18 TraesCS2B01G398300 chr2A 78.193 321 33 17 360 648 624446438 624446753 2.040000e-38 171
19 TraesCS2B01G398300 chr2A 93.023 86 6 0 784 869 624446916 624447001 4.470000e-25 126
20 TraesCS2B01G398300 chr4D 88.000 250 28 2 1 248 67272834 67273083 1.160000e-75 294
21 TraesCS2B01G398300 chr5D 88.000 250 27 3 1 248 451956696 451956944 4.170000e-75 292
22 TraesCS2B01G398300 chr6D 87.500 248 29 2 1 246 10715203 10714956 6.980000e-73 285
23 TraesCS2B01G398300 chr6D 85.887 248 33 2 1 246 287031321 287031568 3.270000e-66 263
24 TraesCS2B01G398300 chr1B 87.097 248 29 3 1 246 638761056 638760810 1.170000e-70 278
25 TraesCS2B01G398300 chr7B 86.508 252 31 3 1 249 544409326 544409075 1.510000e-69 274
26 TraesCS2B01G398300 chr7D 87.554 233 28 1 8 239 510586012 510585780 7.020000e-68 268
27 TraesCS2B01G398300 chr5B 86.777 242 31 1 8 248 381380272 381380513 7.020000e-68 268


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 TraesCS2B01G398300 chr2B 565187991 565192252 4261 False 7871.000000 7871 100.0000 1 4262 1 chr2B.!!$F1 4261
1 TraesCS2B01G398300 chr2B 565076034 565081227 5193 False 2429.000000 4636 91.2915 553 4262 2 chr2B.!!$F2 3709
2 TraesCS2B01G398300 chr2B 565209603 565212508 2905 False 1851.000000 3533 88.6010 503 3502 2 chr2B.!!$F3 2999
3 TraesCS2B01G398300 chr2D 481687854 481691907 4053 False 5838.000000 5838 92.8750 255 4262 1 chr2D.!!$F2 4007
4 TraesCS2B01G398300 chr2D 481961016 481963980 2964 False 3829.000000 3829 90.0500 540 3502 1 chr2D.!!$F3 2962
5 TraesCS2B01G398300 chr2D 481987617 481990889 3272 False 2078.000000 3967 90.9200 252 3502 2 chr2D.!!$F5 3250
6 TraesCS2B01G398300 chr2D 481655513 481661546 6033 False 1336.500000 4606 89.2115 417 4262 4 chr2D.!!$F4 3845
7 TraesCS2B01G398300 chr2A 624393902 624397573 3671 False 5142.000000 5142 91.9320 561 4262 1 chr2A.!!$F2 3701
8 TraesCS2B01G398300 chr2A 624457818 624460782 2964 False 4024.000000 4024 91.2470 540 3499 1 chr2A.!!$F3 2959
9 TraesCS2B01G398300 chr2A 624359539 624362092 2553 False 2952.000000 2952 87.6700 972 3521 1 chr2A.!!$F1 2549
10 TraesCS2B01G398300 chr2A 624446438 624450401 3963 False 1773.666667 5024 88.5030 360 4262 3 chr2A.!!$F4 3902

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
205 206 0.036952 ATGCAATAGGGATCGAGCCG 60.037 55.0 14.60 0.00 0.00 5.52 F
224 225 0.039617 GGATCTGCTCGTCATCGGAG 60.040 60.0 0.00 0.00 37.69 4.63 F
1278 1658 0.108424 GCGTCAAGGAGAGCAGTGAT 60.108 55.0 0.00 0.00 0.00 3.06 F
2307 2731 0.255890 AAGCTATCCACGGTGGCAAT 59.744 50.0 22.42 13.78 37.47 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1488 0.034574 ACCGCATCCAAATGGCTACA 60.035 50.0 0.00 0.00 33.19 2.74 R
1728 2152 0.179145 CGATGTACGAAAGCGGGACT 60.179 55.0 0.00 0.00 45.77 3.85 R
2858 3282 0.464452 GAGTGGGTAGTTGGCGCTAT 59.536 55.0 7.64 0.00 0.00 2.97 R
4086 6564 0.103572 ACACTGACGCGTTAGTTGGT 59.896 50.0 31.22 23.89 0.00 3.67 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
26 27 9.513906 TCAAATTATACAAACTCATCAACTCCA 57.486 29.630 0.00 0.00 0.00 3.86
29 30 7.770801 TTATACAAACTCATCAACTCCATCG 57.229 36.000 0.00 0.00 0.00 3.84
30 31 4.271696 ACAAACTCATCAACTCCATCGA 57.728 40.909 0.00 0.00 0.00 3.59
31 32 4.836825 ACAAACTCATCAACTCCATCGAT 58.163 39.130 0.00 0.00 0.00 3.59
32 33 4.633126 ACAAACTCATCAACTCCATCGATG 59.367 41.667 18.76 18.76 38.29 3.84
33 34 2.831333 ACTCATCAACTCCATCGATGC 58.169 47.619 20.25 0.00 37.14 3.91
34 35 2.169144 ACTCATCAACTCCATCGATGCA 59.831 45.455 20.25 3.95 37.14 3.96
35 36 2.543012 CTCATCAACTCCATCGATGCAC 59.457 50.000 20.25 0.00 37.14 4.57
36 37 2.093553 TCATCAACTCCATCGATGCACA 60.094 45.455 20.25 4.92 37.14 4.57
37 38 2.696989 TCAACTCCATCGATGCACAT 57.303 45.000 20.25 3.15 0.00 3.21
38 39 3.817709 TCAACTCCATCGATGCACATA 57.182 42.857 20.25 0.41 0.00 2.29
39 40 3.457234 TCAACTCCATCGATGCACATAC 58.543 45.455 20.25 0.00 0.00 2.39
40 41 3.118811 TCAACTCCATCGATGCACATACA 60.119 43.478 20.25 0.00 0.00 2.29
41 42 3.758755 ACTCCATCGATGCACATACAT 57.241 42.857 20.25 0.00 0.00 2.29
42 43 3.657634 ACTCCATCGATGCACATACATC 58.342 45.455 20.25 0.00 42.52 3.06
43 44 3.070015 ACTCCATCGATGCACATACATCA 59.930 43.478 20.25 0.00 45.56 3.07
44 45 4.251268 CTCCATCGATGCACATACATCAT 58.749 43.478 20.25 0.00 45.56 2.45
45 46 4.248058 TCCATCGATGCACATACATCATC 58.752 43.478 20.25 0.00 45.56 2.92
46 47 3.373130 CCATCGATGCACATACATCATCC 59.627 47.826 20.25 0.00 45.56 3.51
47 48 2.676076 TCGATGCACATACATCATCCG 58.324 47.619 5.46 0.00 45.56 4.18
48 49 2.295909 TCGATGCACATACATCATCCGA 59.704 45.455 5.46 0.00 45.56 4.55
49 50 2.409715 CGATGCACATACATCATCCGAC 59.590 50.000 5.46 0.00 45.56 4.79
50 51 3.657634 GATGCACATACATCATCCGACT 58.342 45.455 0.00 0.00 44.81 4.18
51 52 4.615912 CGATGCACATACATCATCCGACTA 60.616 45.833 5.46 0.00 45.56 2.59
52 53 3.977427 TGCACATACATCATCCGACTAC 58.023 45.455 0.00 0.00 0.00 2.73
53 54 3.636764 TGCACATACATCATCCGACTACT 59.363 43.478 0.00 0.00 0.00 2.57
54 55 4.230657 GCACATACATCATCCGACTACTC 58.769 47.826 0.00 0.00 0.00 2.59
55 56 4.799678 CACATACATCATCCGACTACTCC 58.200 47.826 0.00 0.00 0.00 3.85
56 57 4.278419 CACATACATCATCCGACTACTCCA 59.722 45.833 0.00 0.00 0.00 3.86
57 58 5.047731 CACATACATCATCCGACTACTCCAT 60.048 44.000 0.00 0.00 0.00 3.41
58 59 5.540337 ACATACATCATCCGACTACTCCATT 59.460 40.000 0.00 0.00 0.00 3.16
59 60 6.719829 ACATACATCATCCGACTACTCCATTA 59.280 38.462 0.00 0.00 0.00 1.90
60 61 5.455056 ACATCATCCGACTACTCCATTAC 57.545 43.478 0.00 0.00 0.00 1.89
61 62 5.141182 ACATCATCCGACTACTCCATTACT 58.859 41.667 0.00 0.00 0.00 2.24
62 63 6.304624 ACATCATCCGACTACTCCATTACTA 58.695 40.000 0.00 0.00 0.00 1.82
63 64 6.207025 ACATCATCCGACTACTCCATTACTAC 59.793 42.308 0.00 0.00 0.00 2.73
64 65 5.938279 TCATCCGACTACTCCATTACTACT 58.062 41.667 0.00 0.00 0.00 2.57
65 66 7.071069 TCATCCGACTACTCCATTACTACTA 57.929 40.000 0.00 0.00 0.00 1.82
66 67 7.512130 TCATCCGACTACTCCATTACTACTAA 58.488 38.462 0.00 0.00 0.00 2.24
67 68 7.443575 TCATCCGACTACTCCATTACTACTAAC 59.556 40.741 0.00 0.00 0.00 2.34
68 69 6.893583 TCCGACTACTCCATTACTACTAACT 58.106 40.000 0.00 0.00 0.00 2.24
69 70 8.023021 TCCGACTACTCCATTACTACTAACTA 57.977 38.462 0.00 0.00 0.00 2.24
70 71 8.486210 TCCGACTACTCCATTACTACTAACTAA 58.514 37.037 0.00 0.00 0.00 2.24
71 72 9.113838 CCGACTACTCCATTACTACTAACTAAA 57.886 37.037 0.00 0.00 0.00 1.85
72 73 9.928236 CGACTACTCCATTACTACTAACTAAAC 57.072 37.037 0.00 0.00 0.00 2.01
76 77 8.943909 ACTCCATTACTACTAACTAAACATGC 57.056 34.615 0.00 0.00 0.00 4.06
77 78 7.985752 ACTCCATTACTACTAACTAAACATGCC 59.014 37.037 0.00 0.00 0.00 4.40
78 79 7.853299 TCCATTACTACTAACTAAACATGCCA 58.147 34.615 0.00 0.00 0.00 4.92
79 80 8.491134 TCCATTACTACTAACTAAACATGCCAT 58.509 33.333 0.00 0.00 0.00 4.40
80 81 8.774586 CCATTACTACTAACTAAACATGCCATC 58.225 37.037 0.00 0.00 0.00 3.51
81 82 7.997107 TTACTACTAACTAAACATGCCATCG 57.003 36.000 0.00 0.00 0.00 3.84
82 83 5.357257 ACTACTAACTAAACATGCCATCGG 58.643 41.667 0.00 0.00 0.00 4.18
83 84 4.481368 ACTAACTAAACATGCCATCGGA 57.519 40.909 0.00 0.00 0.00 4.55
84 85 4.189231 ACTAACTAAACATGCCATCGGAC 58.811 43.478 0.00 0.00 0.00 4.79
85 86 3.350219 AACTAAACATGCCATCGGACT 57.650 42.857 0.00 0.00 0.00 3.85
86 87 4.481368 AACTAAACATGCCATCGGACTA 57.519 40.909 0.00 0.00 0.00 2.59
87 88 3.793559 ACTAAACATGCCATCGGACTAC 58.206 45.455 0.00 0.00 0.00 2.73
88 89 2.038387 AAACATGCCATCGGACTACC 57.962 50.000 0.00 0.00 0.00 3.18
89 90 0.908910 AACATGCCATCGGACTACCA 59.091 50.000 0.00 0.00 35.59 3.25
90 91 0.908910 ACATGCCATCGGACTACCAA 59.091 50.000 0.00 0.00 35.59 3.67
91 92 1.280710 ACATGCCATCGGACTACCAAA 59.719 47.619 0.00 0.00 35.59 3.28
92 93 2.290641 ACATGCCATCGGACTACCAAAA 60.291 45.455 0.00 0.00 35.59 2.44
93 94 2.107950 TGCCATCGGACTACCAAAAG 57.892 50.000 0.00 0.00 35.59 2.27
94 95 0.733150 GCCATCGGACTACCAAAAGC 59.267 55.000 0.00 0.00 35.59 3.51
95 96 1.679032 GCCATCGGACTACCAAAAGCT 60.679 52.381 0.00 0.00 35.59 3.74
96 97 2.009774 CCATCGGACTACCAAAAGCTG 58.990 52.381 0.00 0.00 35.59 4.24
106 107 1.515081 CCAAAAGCTGGCATGTTTGG 58.485 50.000 17.18 17.18 42.85 3.28
115 116 1.473258 GGCATGTTTGGCTATGGTGA 58.527 50.000 0.00 0.00 44.68 4.02
116 117 1.824230 GGCATGTTTGGCTATGGTGAA 59.176 47.619 0.00 0.00 44.68 3.18
117 118 2.159198 GGCATGTTTGGCTATGGTGAAG 60.159 50.000 0.00 0.00 44.68 3.02
118 119 2.754552 GCATGTTTGGCTATGGTGAAGA 59.245 45.455 0.00 0.00 0.00 2.87
119 120 3.428045 GCATGTTTGGCTATGGTGAAGAC 60.428 47.826 0.00 0.00 0.00 3.01
120 121 2.790433 TGTTTGGCTATGGTGAAGACC 58.210 47.619 0.00 0.00 43.48 3.85
128 129 4.617875 GGTGAAGACCATCCACGG 57.382 61.111 0.00 0.00 42.59 4.94
129 130 1.745489 GGTGAAGACCATCCACGGC 60.745 63.158 0.00 0.00 42.59 5.68
130 131 1.296715 GTGAAGACCATCCACGGCT 59.703 57.895 0.00 0.00 0.00 5.52
131 132 1.021390 GTGAAGACCATCCACGGCTG 61.021 60.000 0.00 0.00 0.00 4.85
132 133 2.045926 AAGACCATCCACGGCTGC 60.046 61.111 0.00 0.00 0.00 5.25
133 134 2.527951 GAAGACCATCCACGGCTGCT 62.528 60.000 0.00 0.00 0.00 4.24
134 135 2.512515 GACCATCCACGGCTGCTC 60.513 66.667 0.00 0.00 0.00 4.26
135 136 3.005539 ACCATCCACGGCTGCTCT 61.006 61.111 0.00 0.00 0.00 4.09
136 137 2.270205 CCATCCACGGCTGCTCTT 59.730 61.111 0.00 0.00 0.00 2.85
137 138 2.110967 CCATCCACGGCTGCTCTTG 61.111 63.158 0.00 0.00 0.00 3.02
138 139 2.437359 ATCCACGGCTGCTCTTGC 60.437 61.111 0.00 0.00 40.20 4.01
139 140 3.984193 ATCCACGGCTGCTCTTGCC 62.984 63.158 0.00 0.00 46.42 4.52
144 145 3.130160 GGCTGCTCTTGCCCTTCG 61.130 66.667 0.00 0.00 44.32 3.79
145 146 3.808656 GCTGCTCTTGCCCTTCGC 61.809 66.667 0.00 0.00 38.71 4.70
146 147 3.494336 CTGCTCTTGCCCTTCGCG 61.494 66.667 0.00 0.00 42.08 5.87
164 165 3.056328 GCACCCTTGCCGTCCTTC 61.056 66.667 0.00 0.00 43.66 3.46
165 166 2.750350 CACCCTTGCCGTCCTTCT 59.250 61.111 0.00 0.00 0.00 2.85
166 167 1.376037 CACCCTTGCCGTCCTTCTC 60.376 63.158 0.00 0.00 0.00 2.87
167 168 2.125512 CCCTTGCCGTCCTTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
168 169 2.815647 CCTTGCCGTCCTTCTCGC 60.816 66.667 0.00 0.00 0.00 5.03
169 170 3.181967 CTTGCCGTCCTTCTCGCG 61.182 66.667 0.00 0.00 0.00 5.87
173 174 3.181967 CCGTCCTTCTCGCGCAAG 61.182 66.667 8.75 5.90 43.44 4.01
174 175 2.430921 CGTCCTTCTCGCGCAAGT 60.431 61.111 8.75 0.00 41.68 3.16
175 176 1.154093 CGTCCTTCTCGCGCAAGTA 60.154 57.895 8.75 0.00 41.68 2.24
176 177 1.403972 CGTCCTTCTCGCGCAAGTAC 61.404 60.000 8.75 2.12 41.68 2.73
177 178 1.077089 GTCCTTCTCGCGCAAGTACC 61.077 60.000 8.75 0.00 41.68 3.34
178 179 2.158959 CCTTCTCGCGCAAGTACCG 61.159 63.158 8.75 0.00 41.68 4.02
179 180 2.126228 TTCTCGCGCAAGTACCGG 60.126 61.111 8.75 0.00 41.68 5.28
180 181 2.814183 CTTCTCGCGCAAGTACCGGT 62.814 60.000 13.98 13.98 41.68 5.28
181 182 2.807631 TTCTCGCGCAAGTACCGGTC 62.808 60.000 12.40 2.55 41.68 4.79
182 183 4.764336 TCGCGCAAGTACCGGTCG 62.764 66.667 12.40 9.78 41.68 4.79
183 184 4.764336 CGCGCAAGTACCGGTCGA 62.764 66.667 12.40 0.00 41.68 4.20
184 185 2.431260 GCGCAAGTACCGGTCGAA 60.431 61.111 12.40 0.00 41.68 3.71
185 186 2.442188 GCGCAAGTACCGGTCGAAG 61.442 63.158 12.40 0.67 41.68 3.79
186 187 1.210931 CGCAAGTACCGGTCGAAGA 59.789 57.895 12.40 0.00 0.00 2.87
187 188 0.179145 CGCAAGTACCGGTCGAAGAT 60.179 55.000 12.40 0.00 40.67 2.40
188 189 1.278238 GCAAGTACCGGTCGAAGATG 58.722 55.000 12.40 4.27 40.67 2.90
189 190 1.278238 CAAGTACCGGTCGAAGATGC 58.722 55.000 12.40 0.00 40.67 3.91
190 191 0.892755 AAGTACCGGTCGAAGATGCA 59.107 50.000 12.40 0.00 40.67 3.96
191 192 0.892755 AGTACCGGTCGAAGATGCAA 59.107 50.000 12.40 0.00 40.67 4.08
192 193 1.480954 AGTACCGGTCGAAGATGCAAT 59.519 47.619 12.40 0.00 40.67 3.56
193 194 2.691526 AGTACCGGTCGAAGATGCAATA 59.308 45.455 12.40 0.00 40.67 1.90
194 195 2.225068 ACCGGTCGAAGATGCAATAG 57.775 50.000 0.00 0.00 40.67 1.73
195 196 1.202533 ACCGGTCGAAGATGCAATAGG 60.203 52.381 0.00 0.00 40.67 2.57
196 197 1.502231 CGGTCGAAGATGCAATAGGG 58.498 55.000 0.00 0.00 40.67 3.53
197 198 1.068588 CGGTCGAAGATGCAATAGGGA 59.931 52.381 0.00 0.00 40.67 4.20
198 199 2.289072 CGGTCGAAGATGCAATAGGGAT 60.289 50.000 0.00 0.00 40.67 3.85
199 200 3.330267 GGTCGAAGATGCAATAGGGATC 58.670 50.000 0.00 0.00 44.08 3.36
204 205 1.731720 GATGCAATAGGGATCGAGCC 58.268 55.000 12.38 12.38 34.49 4.70
205 206 0.036952 ATGCAATAGGGATCGAGCCG 60.037 55.000 14.60 0.00 0.00 5.52
206 207 1.374758 GCAATAGGGATCGAGCCGG 60.375 63.158 14.60 0.00 0.00 6.13
207 208 1.816863 GCAATAGGGATCGAGCCGGA 61.817 60.000 14.60 3.86 0.00 5.14
208 209 0.898320 CAATAGGGATCGAGCCGGAT 59.102 55.000 14.60 0.00 0.00 4.18
209 210 1.134965 CAATAGGGATCGAGCCGGATC 60.135 57.143 14.60 10.41 41.67 3.36
210 211 0.333312 ATAGGGATCGAGCCGGATCT 59.667 55.000 19.08 7.55 41.99 2.75
211 212 0.609406 TAGGGATCGAGCCGGATCTG 60.609 60.000 19.08 11.53 41.99 2.90
212 213 2.048690 GGATCGAGCCGGATCTGC 60.049 66.667 19.08 6.46 41.99 4.26
213 214 2.569354 GGATCGAGCCGGATCTGCT 61.569 63.158 19.08 9.58 41.99 4.24
217 218 2.026879 GAGCCGGATCTGCTCGTC 59.973 66.667 13.71 2.21 45.05 4.20
218 219 2.755876 AGCCGGATCTGCTCGTCA 60.756 61.111 5.05 0.00 32.41 4.35
219 220 2.081425 GAGCCGGATCTGCTCGTCAT 62.081 60.000 13.71 0.00 45.05 3.06
220 221 1.663074 GCCGGATCTGCTCGTCATC 60.663 63.158 5.05 0.00 0.00 2.92
221 222 1.371022 CCGGATCTGCTCGTCATCG 60.371 63.158 0.00 0.00 38.55 3.84
222 223 1.371022 CGGATCTGCTCGTCATCGG 60.371 63.158 0.00 0.00 37.69 4.18
223 224 1.786049 CGGATCTGCTCGTCATCGGA 61.786 60.000 0.00 0.00 37.69 4.55
224 225 0.039617 GGATCTGCTCGTCATCGGAG 60.040 60.000 0.00 0.00 37.69 4.63
225 226 0.665835 GATCTGCTCGTCATCGGAGT 59.334 55.000 0.00 0.00 37.69 3.85
226 227 1.066303 GATCTGCTCGTCATCGGAGTT 59.934 52.381 0.00 0.00 37.69 3.01
227 228 0.171231 TCTGCTCGTCATCGGAGTTG 59.829 55.000 0.00 0.00 37.69 3.16
228 229 0.109086 CTGCTCGTCATCGGAGTTGT 60.109 55.000 0.00 0.00 37.69 3.32
229 230 0.109272 TGCTCGTCATCGGAGTTGTC 60.109 55.000 0.00 0.00 37.69 3.18
230 231 0.802607 GCTCGTCATCGGAGTTGTCC 60.803 60.000 0.00 0.00 39.88 4.02
231 232 0.811915 CTCGTCATCGGAGTTGTCCT 59.188 55.000 0.00 0.00 41.34 3.85
232 233 0.526211 TCGTCATCGGAGTTGTCCTG 59.474 55.000 0.00 0.00 41.34 3.86
233 234 0.458543 CGTCATCGGAGTTGTCCTGG 60.459 60.000 0.00 0.00 41.34 4.45
234 235 0.741221 GTCATCGGAGTTGTCCTGGC 60.741 60.000 0.00 0.00 41.34 4.85
235 236 0.904865 TCATCGGAGTTGTCCTGGCT 60.905 55.000 0.00 0.00 41.34 4.75
236 237 0.742281 CATCGGAGTTGTCCTGGCTG 60.742 60.000 0.00 0.00 41.34 4.85
237 238 1.194781 ATCGGAGTTGTCCTGGCTGT 61.195 55.000 0.00 0.00 41.34 4.40
238 239 1.374758 CGGAGTTGTCCTGGCTGTC 60.375 63.158 0.00 0.00 41.34 3.51
239 240 1.374758 GGAGTTGTCCTGGCTGTCG 60.375 63.158 0.00 0.00 40.17 4.35
240 241 2.029844 GAGTTGTCCTGGCTGTCGC 61.030 63.158 0.00 0.00 0.00 5.19
241 242 2.031163 GTTGTCCTGGCTGTCGCT 59.969 61.111 0.00 0.00 36.09 4.93
242 243 2.031012 TTGTCCTGGCTGTCGCTG 59.969 61.111 0.00 0.00 36.09 5.18
243 244 2.807107 TTGTCCTGGCTGTCGCTGT 61.807 57.895 0.00 0.00 36.09 4.40
244 245 2.433318 GTCCTGGCTGTCGCTGTC 60.433 66.667 0.00 0.00 36.09 3.51
245 246 3.695606 TCCTGGCTGTCGCTGTCC 61.696 66.667 0.00 0.00 36.09 4.02
246 247 3.699894 CCTGGCTGTCGCTGTCCT 61.700 66.667 0.00 0.00 36.09 3.85
247 248 2.125753 CTGGCTGTCGCTGTCCTC 60.126 66.667 0.00 0.00 36.09 3.71
248 249 2.601666 TGGCTGTCGCTGTCCTCT 60.602 61.111 0.00 0.00 36.09 3.69
249 250 2.125753 GGCTGTCGCTGTCCTCTG 60.126 66.667 0.00 0.00 36.09 3.35
250 251 2.813042 GCTGTCGCTGTCCTCTGC 60.813 66.667 0.00 0.00 35.62 4.26
338 340 1.946768 CATACCAACGTTGCCCATAGG 59.053 52.381 22.93 9.83 0.00 2.57
368 370 4.702131 AGATTCCTCGGAAACAAAGATTGG 59.298 41.667 2.00 0.00 37.69 3.16
432 578 6.058183 AGATTAAGTGAAGAAACACAGCAGT 58.942 36.000 0.00 0.00 42.45 4.40
433 579 6.543831 AGATTAAGTGAAGAAACACAGCAGTT 59.456 34.615 0.00 0.00 42.45 3.16
434 580 4.622701 AAGTGAAGAAACACAGCAGTTC 57.377 40.909 0.00 0.00 42.45 3.01
437 588 4.127171 GTGAAGAAACACAGCAGTTCCTA 58.873 43.478 0.00 0.00 40.11 2.94
472 635 4.681978 GCACCTGGCGTTCGACCT 62.682 66.667 0.00 0.00 0.00 3.85
473 636 2.738521 CACCTGGCGTTCGACCTG 60.739 66.667 0.00 1.45 0.00 4.00
909 1249 6.364435 CACAGATCAATCCAGATACACATACG 59.636 42.308 0.00 0.00 0.00 3.06
912 1252 2.724977 ATCCAGATACACATACGCCG 57.275 50.000 0.00 0.00 0.00 6.46
942 1289 2.701780 CCGACGTCTAGCTGCCAGT 61.702 63.158 14.70 0.00 0.00 4.00
1275 1655 2.259818 CGCGTCAAGGAGAGCAGT 59.740 61.111 0.00 0.00 0.00 4.40
1278 1658 0.108424 GCGTCAAGGAGAGCAGTGAT 60.108 55.000 0.00 0.00 0.00 3.06
1466 1861 8.900781 TCTGTTAGTTATGTGTACCAGACTATC 58.099 37.037 0.00 2.50 30.36 2.08
1477 1896 8.033038 TGTGTACCAGACTATCAATTGAGTTAC 58.967 37.037 14.54 7.22 0.00 2.50
1527 1951 3.496884 GTGTGTTCAGATTCCTTAACGCA 59.503 43.478 0.00 0.00 41.78 5.24
1728 2152 0.613572 TCACAGCATCCGGTGACCTA 60.614 55.000 0.00 0.00 43.56 3.08
1748 2172 0.457337 GTCCCGCTTTCGTACATCGT 60.457 55.000 0.00 0.00 40.80 3.73
1839 2263 1.001378 GCATTTAAGATCGCCGGCATT 60.001 47.619 28.98 17.06 0.00 3.56
1948 2372 4.022068 TGCTTTTTGAGGCTAACATCCTTG 60.022 41.667 0.00 0.00 33.24 3.61
1980 2404 1.122019 AGGTCCTGTCAGCCGTCTTT 61.122 55.000 0.00 0.00 0.00 2.52
2307 2731 0.255890 AAGCTATCCACGGTGGCAAT 59.744 50.000 22.42 13.78 37.47 3.56
2544 2968 4.519610 GGCAACCCTGTGACCAAT 57.480 55.556 0.00 0.00 0.00 3.16
2841 3265 2.712539 CGTGAAGCCGTGTTTGCA 59.287 55.556 0.00 0.00 0.00 4.08
2858 3282 1.679153 TGCATACGCAGACGATCCTTA 59.321 47.619 0.00 0.00 45.36 2.69
2908 3332 0.880278 GCGTGCAGTTCTTGTGGAGA 60.880 55.000 0.00 0.00 0.00 3.71
2981 3405 4.430423 GCTTGCCACGTTCGAGCG 62.430 66.667 20.50 20.50 31.98 5.03
3087 3511 2.202974 GAATGCCGGTCGTACCCC 60.203 66.667 1.90 0.00 33.75 4.95
3385 3832 5.620738 ATGTTCTTCTAGAGCTGCCAATA 57.379 39.130 0.00 0.00 0.00 1.90
3529 3978 3.502123 TTTTGAGATCAACCGGTCCTT 57.498 42.857 8.04 0.00 35.28 3.36
3549 3998 5.071788 TCCTTGTGACAATAGTCCAAGAACT 59.928 40.000 19.26 0.00 45.62 3.01
3609 4058 3.122445 CGGAAAGTAAAACTCGTGCCTAC 59.878 47.826 0.00 0.00 0.00 3.18
3610 4059 3.434641 GGAAAGTAAAACTCGTGCCTACC 59.565 47.826 0.00 0.00 0.00 3.18
3738 4189 7.604545 GCTTACTAGTTTCAGTCTGGATTTCTT 59.395 37.037 0.00 0.00 0.00 2.52
3741 4192 5.444663 AGTTTCAGTCTGGATTTCTTTGC 57.555 39.130 0.00 0.00 0.00 3.68
3765 4216 5.984926 CAGGCACACAATGATGTTTAACTTT 59.015 36.000 0.00 0.00 37.82 2.66
3795 4246 1.696063 ACTACCGTACCACCGCATAT 58.304 50.000 0.00 0.00 0.00 1.78
3807 4283 4.225942 ACCACCGCATATCTATGAATCCAT 59.774 41.667 1.37 0.00 35.75 3.41
3876 4355 7.399191 AGGGTACATACACATGAAGTTTCTCTA 59.601 37.037 0.00 0.00 35.96 2.43
4086 6564 4.380945 ACCGGCCACCGTACCCTA 62.381 66.667 0.00 0.00 46.80 3.53
4153 6686 6.536582 CAGTTGTGTCCTAATCTCGAATTCAT 59.463 38.462 6.22 0.00 0.00 2.57
4163 6696 9.717942 CCTAATCTCGAATTCATTAGGAGAAAT 57.282 33.333 25.33 15.15 46.81 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.513906 TGGAGTTGATGAGTTTGTATAATTTGA 57.486 29.630 0.00 0.00 0.00 2.69
3 4 8.830580 CGATGGAGTTGATGAGTTTGTATAATT 58.169 33.333 0.00 0.00 0.00 1.40
4 5 8.204160 TCGATGGAGTTGATGAGTTTGTATAAT 58.796 33.333 0.00 0.00 0.00 1.28
5 6 7.552459 TCGATGGAGTTGATGAGTTTGTATAA 58.448 34.615 0.00 0.00 0.00 0.98
6 7 7.107639 TCGATGGAGTTGATGAGTTTGTATA 57.892 36.000 0.00 0.00 0.00 1.47
7 8 5.977635 TCGATGGAGTTGATGAGTTTGTAT 58.022 37.500 0.00 0.00 0.00 2.29
8 9 5.400066 TCGATGGAGTTGATGAGTTTGTA 57.600 39.130 0.00 0.00 0.00 2.41
9 10 4.271696 TCGATGGAGTTGATGAGTTTGT 57.728 40.909 0.00 0.00 0.00 2.83
17 18 2.696989 TGTGCATCGATGGAGTTGAT 57.303 45.000 26.00 0.00 0.00 2.57
18 19 2.696989 ATGTGCATCGATGGAGTTGA 57.303 45.000 26.00 8.68 0.00 3.18
19 20 3.197265 TGTATGTGCATCGATGGAGTTG 58.803 45.455 26.00 2.01 0.00 3.16
20 21 3.541996 TGTATGTGCATCGATGGAGTT 57.458 42.857 26.00 15.61 0.00 3.01
21 22 3.070015 TGATGTATGTGCATCGATGGAGT 59.930 43.478 26.00 16.89 45.98 3.85
22 23 3.656559 TGATGTATGTGCATCGATGGAG 58.343 45.455 26.00 1.96 45.98 3.86
23 24 3.749665 TGATGTATGTGCATCGATGGA 57.250 42.857 26.00 21.56 45.98 3.41
24 25 3.373130 GGATGATGTATGTGCATCGATGG 59.627 47.826 26.00 8.82 45.98 3.51
25 26 3.061697 CGGATGATGTATGTGCATCGATG 59.938 47.826 21.27 21.27 45.98 3.84
26 27 3.056607 TCGGATGATGTATGTGCATCGAT 60.057 43.478 0.00 0.00 45.98 3.59
27 28 2.295909 TCGGATGATGTATGTGCATCGA 59.704 45.455 6.60 0.00 45.98 3.59
28 29 2.409715 GTCGGATGATGTATGTGCATCG 59.590 50.000 6.60 0.00 45.98 3.84
29 30 3.657634 AGTCGGATGATGTATGTGCATC 58.342 45.455 4.40 4.40 43.97 3.91
30 31 3.758755 AGTCGGATGATGTATGTGCAT 57.241 42.857 0.00 0.00 0.00 3.96
31 32 3.636764 AGTAGTCGGATGATGTATGTGCA 59.363 43.478 0.00 0.00 0.00 4.57
32 33 4.230657 GAGTAGTCGGATGATGTATGTGC 58.769 47.826 0.00 0.00 0.00 4.57
33 34 4.278419 TGGAGTAGTCGGATGATGTATGTG 59.722 45.833 0.00 0.00 0.00 3.21
34 35 4.470602 TGGAGTAGTCGGATGATGTATGT 58.529 43.478 0.00 0.00 0.00 2.29
35 36 5.651387 ATGGAGTAGTCGGATGATGTATG 57.349 43.478 0.00 0.00 0.00 2.39
36 37 6.948886 AGTAATGGAGTAGTCGGATGATGTAT 59.051 38.462 0.00 0.00 0.00 2.29
37 38 6.304624 AGTAATGGAGTAGTCGGATGATGTA 58.695 40.000 0.00 0.00 0.00 2.29
38 39 5.141182 AGTAATGGAGTAGTCGGATGATGT 58.859 41.667 0.00 0.00 0.00 3.06
39 40 5.713792 AGTAATGGAGTAGTCGGATGATG 57.286 43.478 0.00 0.00 0.00 3.07
40 41 6.544650 AGTAGTAATGGAGTAGTCGGATGAT 58.455 40.000 0.00 0.00 0.00 2.45
41 42 5.938279 AGTAGTAATGGAGTAGTCGGATGA 58.062 41.667 0.00 0.00 0.00 2.92
42 43 7.444792 AGTTAGTAGTAATGGAGTAGTCGGATG 59.555 40.741 0.00 0.00 0.00 3.51
43 44 7.516452 AGTTAGTAGTAATGGAGTAGTCGGAT 58.484 38.462 0.00 0.00 0.00 4.18
44 45 6.893583 AGTTAGTAGTAATGGAGTAGTCGGA 58.106 40.000 0.00 0.00 0.00 4.55
45 46 8.668510 TTAGTTAGTAGTAATGGAGTAGTCGG 57.331 38.462 0.00 0.00 0.00 4.79
46 47 9.928236 GTTTAGTTAGTAGTAATGGAGTAGTCG 57.072 37.037 0.00 0.00 0.00 4.18
51 52 7.985752 GGCATGTTTAGTTAGTAGTAATGGAGT 59.014 37.037 0.00 0.00 0.00 3.85
52 53 7.985184 TGGCATGTTTAGTTAGTAGTAATGGAG 59.015 37.037 0.00 0.00 0.00 3.86
53 54 7.853299 TGGCATGTTTAGTTAGTAGTAATGGA 58.147 34.615 0.00 0.00 0.00 3.41
54 55 8.677148 ATGGCATGTTTAGTTAGTAGTAATGG 57.323 34.615 0.00 0.00 0.00 3.16
55 56 8.487970 CGATGGCATGTTTAGTTAGTAGTAATG 58.512 37.037 3.81 0.00 0.00 1.90
56 57 7.656137 CCGATGGCATGTTTAGTTAGTAGTAAT 59.344 37.037 3.81 0.00 0.00 1.89
57 58 6.982141 CCGATGGCATGTTTAGTTAGTAGTAA 59.018 38.462 3.81 0.00 0.00 2.24
58 59 6.321945 TCCGATGGCATGTTTAGTTAGTAGTA 59.678 38.462 3.81 0.00 0.00 1.82
59 60 5.128171 TCCGATGGCATGTTTAGTTAGTAGT 59.872 40.000 3.81 0.00 0.00 2.73
60 61 5.462398 GTCCGATGGCATGTTTAGTTAGTAG 59.538 44.000 3.81 0.00 0.00 2.57
61 62 5.128171 AGTCCGATGGCATGTTTAGTTAGTA 59.872 40.000 3.81 0.00 0.00 1.82
62 63 4.081087 AGTCCGATGGCATGTTTAGTTAGT 60.081 41.667 3.81 0.00 0.00 2.24
63 64 4.442706 AGTCCGATGGCATGTTTAGTTAG 58.557 43.478 3.81 0.00 0.00 2.34
64 65 4.481368 AGTCCGATGGCATGTTTAGTTA 57.519 40.909 3.81 0.00 0.00 2.24
65 66 3.350219 AGTCCGATGGCATGTTTAGTT 57.650 42.857 3.81 0.00 0.00 2.24
66 67 3.431766 GGTAGTCCGATGGCATGTTTAGT 60.432 47.826 3.81 0.00 0.00 2.24
67 68 3.131396 GGTAGTCCGATGGCATGTTTAG 58.869 50.000 3.81 0.00 0.00 1.85
68 69 2.502130 TGGTAGTCCGATGGCATGTTTA 59.498 45.455 3.81 0.00 36.30 2.01
69 70 1.280710 TGGTAGTCCGATGGCATGTTT 59.719 47.619 3.81 0.00 36.30 2.83
70 71 0.908910 TGGTAGTCCGATGGCATGTT 59.091 50.000 3.81 0.00 36.30 2.71
71 72 0.908910 TTGGTAGTCCGATGGCATGT 59.091 50.000 3.81 0.00 36.30 3.21
72 73 2.036958 TTTGGTAGTCCGATGGCATG 57.963 50.000 3.81 0.00 36.30 4.06
73 74 2.643551 CTTTTGGTAGTCCGATGGCAT 58.356 47.619 0.00 0.00 36.30 4.40
74 75 1.948611 GCTTTTGGTAGTCCGATGGCA 60.949 52.381 0.00 0.00 36.30 4.92
75 76 0.733150 GCTTTTGGTAGTCCGATGGC 59.267 55.000 0.00 0.00 36.30 4.40
76 77 2.009774 CAGCTTTTGGTAGTCCGATGG 58.990 52.381 0.00 0.00 36.30 3.51
77 78 2.009774 CCAGCTTTTGGTAGTCCGATG 58.990 52.381 0.00 0.00 42.41 3.84
78 79 2.403252 CCAGCTTTTGGTAGTCCGAT 57.597 50.000 0.00 0.00 42.41 4.18
79 80 3.927555 CCAGCTTTTGGTAGTCCGA 57.072 52.632 0.00 0.00 42.41 4.55
88 89 0.869730 GCCAAACATGCCAGCTTTTG 59.130 50.000 0.00 0.24 0.00 2.44
89 90 0.760572 AGCCAAACATGCCAGCTTTT 59.239 45.000 0.00 0.00 0.00 2.27
90 91 1.631405 TAGCCAAACATGCCAGCTTT 58.369 45.000 5.57 0.00 35.03 3.51
91 92 1.479323 CATAGCCAAACATGCCAGCTT 59.521 47.619 5.57 0.00 35.03 3.74
92 93 1.108776 CATAGCCAAACATGCCAGCT 58.891 50.000 0.00 0.00 37.58 4.24
93 94 0.103572 CCATAGCCAAACATGCCAGC 59.896 55.000 0.00 0.00 0.00 4.85
94 95 1.135527 CACCATAGCCAAACATGCCAG 59.864 52.381 0.00 0.00 0.00 4.85
95 96 1.184431 CACCATAGCCAAACATGCCA 58.816 50.000 0.00 0.00 0.00 4.92
96 97 1.473258 TCACCATAGCCAAACATGCC 58.527 50.000 0.00 0.00 0.00 4.40
97 98 2.754552 TCTTCACCATAGCCAAACATGC 59.245 45.455 0.00 0.00 0.00 4.06
98 99 3.129287 GGTCTTCACCATAGCCAAACATG 59.871 47.826 0.00 0.00 43.17 3.21
99 100 3.356290 GGTCTTCACCATAGCCAAACAT 58.644 45.455 0.00 0.00 43.17 2.71
100 101 2.790433 GGTCTTCACCATAGCCAAACA 58.210 47.619 0.00 0.00 43.17 2.83
111 112 1.745489 GCCGTGGATGGTCTTCACC 60.745 63.158 0.00 0.00 44.10 4.02
112 113 1.021390 CAGCCGTGGATGGTCTTCAC 61.021 60.000 0.00 0.00 0.00 3.18
113 114 1.296392 CAGCCGTGGATGGTCTTCA 59.704 57.895 0.00 0.00 0.00 3.02
114 115 2.109126 GCAGCCGTGGATGGTCTTC 61.109 63.158 6.25 0.00 31.39 2.87
115 116 2.045926 GCAGCCGTGGATGGTCTT 60.046 61.111 6.25 0.00 31.39 3.01
116 117 3.005539 AGCAGCCGTGGATGGTCT 61.006 61.111 2.51 0.00 37.75 3.85
118 119 2.596851 AAGAGCAGCCGTGGATGGT 61.597 57.895 8.81 8.81 45.16 3.55
119 120 2.110967 CAAGAGCAGCCGTGGATGG 61.111 63.158 6.25 0.00 31.39 3.51
120 121 2.758089 GCAAGAGCAGCCGTGGATG 61.758 63.158 0.00 0.00 41.58 3.51
121 122 2.437359 GCAAGAGCAGCCGTGGAT 60.437 61.111 0.00 0.00 41.58 3.41
122 123 4.704833 GGCAAGAGCAGCCGTGGA 62.705 66.667 0.00 0.00 43.15 4.02
128 129 3.808656 GCGAAGGGCAAGAGCAGC 61.809 66.667 0.00 0.00 44.61 5.25
129 130 3.494336 CGCGAAGGGCAAGAGCAG 61.494 66.667 0.00 0.00 44.61 4.24
148 149 1.376037 GAGAAGGACGGCAAGGGTG 60.376 63.158 0.00 0.00 0.00 4.61
149 150 2.943978 CGAGAAGGACGGCAAGGGT 61.944 63.158 0.00 0.00 0.00 4.34
150 151 2.125512 CGAGAAGGACGGCAAGGG 60.126 66.667 0.00 0.00 0.00 3.95
151 152 2.815647 GCGAGAAGGACGGCAAGG 60.816 66.667 0.00 0.00 0.00 3.61
152 153 3.181967 CGCGAGAAGGACGGCAAG 61.182 66.667 0.00 0.00 0.00 4.01
156 157 2.537792 TACTTGCGCGAGAAGGACGG 62.538 60.000 31.19 2.96 0.00 4.79
157 158 1.154093 TACTTGCGCGAGAAGGACG 60.154 57.895 31.19 3.77 0.00 4.79
158 159 1.077089 GGTACTTGCGCGAGAAGGAC 61.077 60.000 31.19 20.82 33.85 3.85
159 160 1.214589 GGTACTTGCGCGAGAAGGA 59.785 57.895 31.19 9.43 0.00 3.36
160 161 2.158959 CGGTACTTGCGCGAGAAGG 61.159 63.158 31.19 12.69 0.00 3.46
161 162 2.158959 CCGGTACTTGCGCGAGAAG 61.159 63.158 31.19 17.59 0.00 2.85
162 163 2.126228 CCGGTACTTGCGCGAGAA 60.126 61.111 31.19 4.90 0.00 2.87
163 164 3.332493 GACCGGTACTTGCGCGAGA 62.332 63.158 31.19 11.90 0.00 4.04
164 165 2.879462 GACCGGTACTTGCGCGAG 60.879 66.667 23.34 23.34 0.00 5.03
165 166 4.764336 CGACCGGTACTTGCGCGA 62.764 66.667 12.10 0.00 0.00 5.87
166 167 4.764336 TCGACCGGTACTTGCGCG 62.764 66.667 7.34 4.90 0.00 6.86
167 168 2.431260 TTCGACCGGTACTTGCGC 60.431 61.111 7.34 0.00 0.00 6.09
168 169 0.179145 ATCTTCGACCGGTACTTGCG 60.179 55.000 7.34 6.70 0.00 4.85
169 170 1.278238 CATCTTCGACCGGTACTTGC 58.722 55.000 7.34 0.00 0.00 4.01
170 171 1.278238 GCATCTTCGACCGGTACTTG 58.722 55.000 7.34 0.74 0.00 3.16
171 172 0.892755 TGCATCTTCGACCGGTACTT 59.107 50.000 7.34 0.00 0.00 2.24
172 173 0.892755 TTGCATCTTCGACCGGTACT 59.107 50.000 7.34 0.00 0.00 2.73
173 174 1.935933 ATTGCATCTTCGACCGGTAC 58.064 50.000 7.34 0.00 0.00 3.34
174 175 2.035449 CCTATTGCATCTTCGACCGGTA 59.965 50.000 7.34 0.00 0.00 4.02
175 176 1.202533 CCTATTGCATCTTCGACCGGT 60.203 52.381 6.92 6.92 0.00 5.28
176 177 1.502231 CCTATTGCATCTTCGACCGG 58.498 55.000 0.00 0.00 0.00 5.28
177 178 1.068588 TCCCTATTGCATCTTCGACCG 59.931 52.381 0.00 0.00 0.00 4.79
178 179 2.910688 TCCCTATTGCATCTTCGACC 57.089 50.000 0.00 0.00 0.00 4.79
179 180 2.989840 CGATCCCTATTGCATCTTCGAC 59.010 50.000 0.00 0.00 0.00 4.20
180 181 2.890945 TCGATCCCTATTGCATCTTCGA 59.109 45.455 0.00 0.00 32.57 3.71
181 182 3.249091 CTCGATCCCTATTGCATCTTCG 58.751 50.000 0.00 0.00 0.00 3.79
182 183 2.999355 GCTCGATCCCTATTGCATCTTC 59.001 50.000 0.00 0.00 0.00 2.87
183 184 2.289945 GGCTCGATCCCTATTGCATCTT 60.290 50.000 0.00 0.00 0.00 2.40
184 185 1.277557 GGCTCGATCCCTATTGCATCT 59.722 52.381 0.00 0.00 0.00 2.90
185 186 1.731720 GGCTCGATCCCTATTGCATC 58.268 55.000 0.00 0.00 0.00 3.91
186 187 0.036952 CGGCTCGATCCCTATTGCAT 60.037 55.000 0.00 0.00 0.00 3.96
187 188 1.367471 CGGCTCGATCCCTATTGCA 59.633 57.895 0.00 0.00 0.00 4.08
188 189 1.374758 CCGGCTCGATCCCTATTGC 60.375 63.158 0.00 0.00 0.00 3.56
189 190 0.898320 ATCCGGCTCGATCCCTATTG 59.102 55.000 0.00 0.00 0.00 1.90
190 191 1.187087 GATCCGGCTCGATCCCTATT 58.813 55.000 0.00 0.00 33.83 1.73
191 192 0.333312 AGATCCGGCTCGATCCCTAT 59.667 55.000 0.00 0.00 39.67 2.57
192 193 0.609406 CAGATCCGGCTCGATCCCTA 60.609 60.000 0.00 0.00 39.67 3.53
193 194 1.905843 CAGATCCGGCTCGATCCCT 60.906 63.158 0.00 0.00 39.67 4.20
194 195 2.653702 CAGATCCGGCTCGATCCC 59.346 66.667 0.00 0.00 39.67 3.85
195 196 2.048690 GCAGATCCGGCTCGATCC 60.049 66.667 0.00 0.00 39.67 3.36
196 197 3.046870 AGCAGATCCGGCTCGATC 58.953 61.111 0.00 0.00 36.81 3.69
201 202 2.081425 GATGACGAGCAGATCCGGCT 62.081 60.000 9.08 9.08 46.07 5.52
202 203 1.663074 GATGACGAGCAGATCCGGC 60.663 63.158 0.00 0.00 0.00 6.13
203 204 1.371022 CGATGACGAGCAGATCCGG 60.371 63.158 0.00 0.00 42.66 5.14
204 205 1.371022 CCGATGACGAGCAGATCCG 60.371 63.158 0.00 0.00 42.66 4.18
205 206 0.039617 CTCCGATGACGAGCAGATCC 60.040 60.000 0.00 0.00 42.66 3.36
206 207 0.665835 ACTCCGATGACGAGCAGATC 59.334 55.000 0.00 0.00 42.66 2.75
207 208 1.107114 AACTCCGATGACGAGCAGAT 58.893 50.000 0.00 0.00 42.66 2.90
208 209 0.171231 CAACTCCGATGACGAGCAGA 59.829 55.000 0.00 0.00 42.66 4.26
209 210 0.109086 ACAACTCCGATGACGAGCAG 60.109 55.000 0.00 0.00 42.66 4.24
210 211 0.109272 GACAACTCCGATGACGAGCA 60.109 55.000 0.00 0.00 42.66 4.26
211 212 0.802607 GGACAACTCCGATGACGAGC 60.803 60.000 0.00 0.00 42.66 5.03
212 213 0.811915 AGGACAACTCCGATGACGAG 59.188 55.000 0.00 0.00 42.22 4.18
213 214 0.526211 CAGGACAACTCCGATGACGA 59.474 55.000 0.00 0.00 42.22 4.20
214 215 0.458543 CCAGGACAACTCCGATGACG 60.459 60.000 0.00 0.00 42.22 4.35
215 216 0.741221 GCCAGGACAACTCCGATGAC 60.741 60.000 0.00 0.00 42.22 3.06
216 217 0.904865 AGCCAGGACAACTCCGATGA 60.905 55.000 0.00 0.00 42.22 2.92
217 218 0.742281 CAGCCAGGACAACTCCGATG 60.742 60.000 0.00 0.00 42.22 3.84
218 219 1.194781 ACAGCCAGGACAACTCCGAT 61.195 55.000 0.00 0.00 42.22 4.18
219 220 1.816863 GACAGCCAGGACAACTCCGA 61.817 60.000 0.00 0.00 42.22 4.55
220 221 1.374758 GACAGCCAGGACAACTCCG 60.375 63.158 0.00 0.00 42.22 4.63
221 222 1.374758 CGACAGCCAGGACAACTCC 60.375 63.158 0.00 0.00 36.71 3.85
222 223 2.029844 GCGACAGCCAGGACAACTC 61.030 63.158 0.00 0.00 37.42 3.01
223 224 2.031163 GCGACAGCCAGGACAACT 59.969 61.111 0.00 0.00 37.42 3.16
224 225 2.031163 AGCGACAGCCAGGACAAC 59.969 61.111 0.00 0.00 46.67 3.32
225 226 2.031012 CAGCGACAGCCAGGACAA 59.969 61.111 0.00 0.00 46.67 3.18
226 227 3.226429 GACAGCGACAGCCAGGACA 62.226 63.158 0.00 0.00 46.67 4.02
227 228 2.433318 GACAGCGACAGCCAGGAC 60.433 66.667 0.00 0.00 46.67 3.85
228 229 3.695606 GGACAGCGACAGCCAGGA 61.696 66.667 0.00 0.00 46.67 3.86
229 230 3.655810 GAGGACAGCGACAGCCAGG 62.656 68.421 0.00 0.00 46.67 4.45
230 231 2.125753 GAGGACAGCGACAGCCAG 60.126 66.667 0.00 0.00 46.67 4.85
231 232 2.601666 AGAGGACAGCGACAGCCA 60.602 61.111 0.00 0.00 46.67 4.75
232 233 2.125753 CAGAGGACAGCGACAGCC 60.126 66.667 0.00 0.00 46.67 4.85
233 234 2.813042 GCAGAGGACAGCGACAGC 60.813 66.667 0.00 0.00 45.58 4.40
246 247 1.202557 TGCATGCATCATACTCGCAGA 60.203 47.619 18.46 0.00 39.39 4.26
247 248 1.070108 GTGCATGCATCATACTCGCAG 60.070 52.381 25.64 0.00 39.39 5.18
248 249 0.939419 GTGCATGCATCATACTCGCA 59.061 50.000 25.64 0.00 40.50 5.10
249 250 0.110956 CGTGCATGCATCATACTCGC 60.111 55.000 25.64 6.36 0.00 5.03
250 251 1.211743 ACGTGCATGCATCATACTCG 58.788 50.000 25.64 21.84 32.60 4.18
338 340 6.796705 TTGTTTCCGAGGAATCTAACTTTC 57.203 37.500 5.29 0.00 33.79 2.62
368 370 5.306532 AGATGCAATGATGTGTGTTTCTC 57.693 39.130 0.00 0.00 0.00 2.87
415 561 2.945668 AGGAACTGCTGTGTTTCTTCAC 59.054 45.455 0.00 0.00 37.18 3.18
432 578 2.978824 GGCTCACGCAGGTAGGAA 59.021 61.111 0.00 0.00 38.10 3.36
433 579 3.449227 CGGCTCACGCAGGTAGGA 61.449 66.667 0.00 0.00 38.10 2.94
434 580 3.449227 TCGGCTCACGCAGGTAGG 61.449 66.667 0.00 0.00 43.86 3.18
463 626 1.359848 CTCCATTTCCAGGTCGAACG 58.640 55.000 0.00 0.00 0.00 3.95
464 627 1.278127 TCCTCCATTTCCAGGTCGAAC 59.722 52.381 0.00 0.00 0.00 3.95
465 628 1.278127 GTCCTCCATTTCCAGGTCGAA 59.722 52.381 0.00 0.00 0.00 3.71
466 629 0.902531 GTCCTCCATTTCCAGGTCGA 59.097 55.000 0.00 0.00 0.00 4.20
467 630 0.613260 TGTCCTCCATTTCCAGGTCG 59.387 55.000 0.00 0.00 0.00 4.79
468 631 2.437413 GTTGTCCTCCATTTCCAGGTC 58.563 52.381 0.00 0.00 0.00 3.85
469 632 1.271379 CGTTGTCCTCCATTTCCAGGT 60.271 52.381 0.00 0.00 0.00 4.00
470 633 1.003118 TCGTTGTCCTCCATTTCCAGG 59.997 52.381 0.00 0.00 0.00 4.45
471 634 2.472695 TCGTTGTCCTCCATTTCCAG 57.527 50.000 0.00 0.00 0.00 3.86
472 635 2.105821 ACTTCGTTGTCCTCCATTTCCA 59.894 45.455 0.00 0.00 0.00 3.53
473 636 2.742589 GACTTCGTTGTCCTCCATTTCC 59.257 50.000 0.38 0.00 0.00 3.13
474 637 3.399330 TGACTTCGTTGTCCTCCATTTC 58.601 45.455 7.76 0.00 36.21 2.17
527 717 3.044305 GCTATCGGGCATGGACGC 61.044 66.667 0.00 0.00 0.00 5.19
538 734 3.536917 TGGCACGGAGGGCTATCG 61.537 66.667 0.00 0.00 0.00 2.92
786 1092 3.610260 GGAGGGGAGGGATTAAATAGGT 58.390 50.000 0.00 0.00 0.00 3.08
942 1289 6.003326 TGTGTATCTGGATTCTGAAAGCAAA 58.997 36.000 0.00 0.00 0.00 3.68
1108 1488 0.034574 ACCGCATCCAAATGGCTACA 60.035 50.000 0.00 0.00 33.19 2.74
1275 1655 2.583024 TGCTGTTCATGACCCAATCA 57.417 45.000 0.00 0.00 43.13 2.57
1386 1766 4.980434 CGATTTAATTCGTACCGGATGAGT 59.020 41.667 9.46 0.00 34.46 3.41
1466 1861 7.730364 ATATAAGGCTTCCGTAACTCAATTG 57.270 36.000 1.30 0.00 0.00 2.32
1477 1896 5.924475 ATCACGAAAATATAAGGCTTCCG 57.076 39.130 1.30 0.20 0.00 4.30
1713 2137 1.043673 GGACTAGGTCACCGGATGCT 61.044 60.000 9.46 0.00 33.68 3.79
1728 2152 0.179145 CGATGTACGAAAGCGGGACT 60.179 55.000 0.00 0.00 45.77 3.85
1839 2263 0.742281 GCTCGAAGAAGCCATGCTGA 60.742 55.000 0.00 0.00 39.62 4.26
1980 2404 2.032634 GCCGTTCATCACCTCGCAA 61.033 57.895 0.00 0.00 0.00 4.85
2197 2621 3.492656 GCAGCACGGATAACCTCAATCTA 60.493 47.826 0.00 0.00 0.00 1.98
2354 2778 2.182284 TGCCAATCGCAGCAATGC 59.818 55.556 0.00 0.00 44.64 3.56
2544 2968 1.153765 CTCCGCGCTCTGAACATGA 60.154 57.895 5.56 0.00 0.00 3.07
2676 3100 1.079127 AAGGTGGCGAAGGTCGATG 60.079 57.895 1.05 0.00 43.74 3.84
2841 3265 3.181509 CGCTATAAGGATCGTCTGCGTAT 60.182 47.826 12.63 0.96 39.49 3.06
2858 3282 0.464452 GAGTGGGTAGTTGGCGCTAT 59.536 55.000 7.64 0.00 0.00 2.97
3087 3511 1.944676 GCGCACGAATCGGTAGAGG 60.945 63.158 7.80 0.00 0.00 3.69
3529 3978 7.062749 AGTTAGTTCTTGGACTATTGTCACA 57.937 36.000 9.51 2.55 44.61 3.58
3549 3998 9.747898 ACACACCATAAGAATTTCCAATAGTTA 57.252 29.630 0.00 0.00 0.00 2.24
3561 4010 3.267483 GCCGTACACACACCATAAGAAT 58.733 45.455 0.00 0.00 0.00 2.40
3638 4087 2.853705 TCGTCCCCGTTCAAAGAATTT 58.146 42.857 0.00 0.00 35.02 1.82
3659 4109 5.047802 GGAGATTGTGAATTCAAAGAAGCCA 60.048 40.000 10.35 0.00 0.00 4.75
3667 4117 6.962182 ACTAGATGGGAGATTGTGAATTCAA 58.038 36.000 10.35 0.00 0.00 2.69
3738 4189 1.330234 ACATCATTGTGTGCCTGCAA 58.670 45.000 0.00 0.00 33.85 4.08
3741 4192 5.125100 AGTTAAACATCATTGTGTGCCTG 57.875 39.130 0.00 0.00 35.83 4.85
3765 4216 5.229423 GTGGTACGGTAGTTGAATAACACA 58.771 41.667 0.00 0.00 39.30 3.72
3876 4355 5.909621 AATAGTGCAATGTTCAGAAGCAT 57.090 34.783 0.00 0.00 37.56 3.79
4086 6564 0.103572 ACACTGACGCGTTAGTTGGT 59.896 50.000 31.22 23.89 0.00 3.67
4163 6696 9.078990 TGAAGATGACTACTTGACTTCTTTCTA 57.921 33.333 0.00 0.00 35.96 2.10
4170 8330 5.696724 CGGTTTGAAGATGACTACTTGACTT 59.303 40.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.