Multiple sequence alignment - TraesCS7D01G543500

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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 TraesCS7D01G543500 chr7D 100.000 3710 0 0 1 3710 631936669 631932960 0.000000e+00 6852.0
1 TraesCS7D01G543500 chr7D 82.882 2290 315 40 753 3025 631921794 631919565 0.000000e+00 1986.0
2 TraesCS7D01G543500 chr7D 84.727 1100 144 18 767 1857 631968856 631967772 0.000000e+00 1079.0
3 TraesCS7D01G543500 chr7D 82.202 1090 142 35 774 1857 631959879 631958836 0.000000e+00 891.0
4 TraesCS7D01G543500 chr7D 80.977 1146 169 29 1905 3041 631958819 631957714 0.000000e+00 863.0
5 TraesCS7D01G543500 chr7D 83.273 831 127 10 1905 2732 631967755 631966934 0.000000e+00 754.0
6 TraesCS7D01G543500 chr7D 80.231 951 166 12 1905 2853 631962315 631961385 0.000000e+00 695.0
7 TraesCS7D01G543500 chr7D 85.646 627 86 3 1231 1857 631964734 631964112 0.000000e+00 656.0
8 TraesCS7D01G543500 chr7D 98.162 272 5 0 1 272 212549312 212549583 3.350000e-130 475.0
9 TraesCS7D01G543500 chr7D 97.473 277 7 0 1 277 259353878 259354154 1.210000e-129 473.0
10 TraesCS7D01G543500 chr7D 97.464 276 7 0 1 276 103755187 103754912 4.340000e-129 472.0
11 TraesCS7D01G543500 chr7D 86.194 268 28 8 3062 3326 631966780 631966519 7.840000e-72 281.0
12 TraesCS7D01G543500 chr7D 84.074 270 31 8 3060 3326 631957723 631957463 2.210000e-62 250.0
13 TraesCS7D01G543500 chr7D 87.117 163 18 2 3167 3326 631995106 631994944 8.180000e-42 182.0
14 TraesCS7D01G543500 chr7A 97.466 2762 68 2 273 3034 736465000 736467759 0.000000e+00 4711.0
15 TraesCS7D01G543500 chr7A 81.970 2751 375 61 352 3033 736496148 736498846 0.000000e+00 2220.0
16 TraesCS7D01G543500 chr7A 86.963 1396 136 20 273 1652 736444522 736445887 0.000000e+00 1528.0
17 TraesCS7D01G543500 chr7A 96.336 655 23 1 3056 3710 736467749 736468402 0.000000e+00 1075.0
18 TraesCS7D01G543500 chr7B 94.262 2771 144 9 273 3036 743458777 743456015 0.000000e+00 4222.0
19 TraesCS7D01G543500 chr7B 88.141 1366 147 9 1653 3018 743494061 743492711 0.000000e+00 1611.0
20 TraesCS7D01G543500 chr7B 86.477 1161 141 12 753 1900 743448263 743447106 0.000000e+00 1260.0
21 TraesCS7D01G543500 chr7B 80.637 1131 168 22 1915 3033 743433013 743431922 0.000000e+00 828.0
22 TraesCS7D01G543500 chr7B 86.202 732 87 8 430 1158 743502977 743502257 0.000000e+00 780.0
23 TraesCS7D01G543500 chr7B 79.676 802 124 23 2176 2964 743489546 743488771 3.260000e-150 542.0
24 TraesCS7D01G543500 chr7B 88.889 261 22 2 3070 3327 743473430 743473686 7.730000e-82 315.0
25 TraesCS7D01G543500 chr7B 89.655 203 20 1 3126 3327 743489821 743489619 1.320000e-64 257.0
26 TraesCS7D01G543500 chr7B 87.742 155 16 2 3175 3326 743488652 743488498 1.060000e-40 178.0
27 TraesCS7D01G543500 chr7B 86.250 80 6 4 3062 3141 743488738 743488664 8.540000e-12 82.4
28 TraesCS7D01G543500 chr3B 93.473 383 24 1 3328 3710 169367078 169366697 5.380000e-158 568.0
29 TraesCS7D01G543500 chr3B 84.358 358 47 9 3325 3676 34225209 34224855 3.550000e-90 342.0
30 TraesCS7D01G543500 chr1D 98.529 272 4 0 1 272 314342125 314342396 7.210000e-132 481.0
31 TraesCS7D01G543500 chr1D 98.529 272 3 1 1 272 364569244 364569514 2.590000e-131 479.0
32 TraesCS7D01G543500 chr1D 98.162 272 4 1 1 272 414593390 414593660 1.210000e-129 473.0
33 TraesCS7D01G543500 chr1D 85.070 355 45 6 3328 3676 343525589 343525237 4.560000e-94 355.0
34 TraesCS7D01G543500 chr5D 98.529 272 3 1 1 272 83976680 83976410 2.590000e-131 479.0
35 TraesCS7D01G543500 chr5D 98.162 272 3 2 1 272 109561372 109561103 1.210000e-129 473.0
36 TraesCS7D01G543500 chr2D 98.162 272 3 2 1 272 591012395 591012126 1.210000e-129 473.0
37 TraesCS7D01G543500 chr6A 85.070 355 43 9 3328 3676 566156673 566157023 1.640000e-93 353.0
38 TraesCS7D01G543500 chr2A 84.874 357 46 7 3325 3675 605497359 605497713 1.640000e-93 353.0
39 TraesCS7D01G543500 chr1B 84.444 360 47 9 3321 3675 184231982 184231627 2.740000e-91 346.0
40 TraesCS7D01G543500 chr5B 84.463 354 45 7 3329 3676 89065020 89065369 1.280000e-89 340.0
41 TraesCS7D01G543500 chr1A 84.123 359 48 8 3325 3676 446710526 446710170 4.590000e-89 339.0


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 TraesCS7D01G543500 chr7D 631932960 631936669 3709 True 6852.000 6852 100.0000 1 3710 1 chr7D.!!$R3 3709
1 TraesCS7D01G543500 chr7D 631919565 631921794 2229 True 1986.000 1986 82.8820 753 3025 1 chr7D.!!$R2 2272
2 TraesCS7D01G543500 chr7D 631957463 631968856 11393 True 683.625 1079 83.4155 767 3326 8 chr7D.!!$R5 2559
3 TraesCS7D01G543500 chr7A 736465000 736468402 3402 False 2893.000 4711 96.9010 273 3710 2 chr7A.!!$F3 3437
4 TraesCS7D01G543500 chr7A 736496148 736498846 2698 False 2220.000 2220 81.9700 352 3033 1 chr7A.!!$F2 2681
5 TraesCS7D01G543500 chr7A 736444522 736445887 1365 False 1528.000 1528 86.9630 273 1652 1 chr7A.!!$F1 1379
6 TraesCS7D01G543500 chr7B 743456015 743458777 2762 True 4222.000 4222 94.2620 273 3036 1 chr7B.!!$R3 2763
7 TraesCS7D01G543500 chr7B 743447106 743448263 1157 True 1260.000 1260 86.4770 753 1900 1 chr7B.!!$R2 1147
8 TraesCS7D01G543500 chr7B 743431922 743433013 1091 True 828.000 828 80.6370 1915 3033 1 chr7B.!!$R1 1118
9 TraesCS7D01G543500 chr7B 743502257 743502977 720 True 780.000 780 86.2020 430 1158 1 chr7B.!!$R4 728
10 TraesCS7D01G543500 chr7B 743488498 743494061 5563 True 534.080 1611 86.2928 1653 3327 5 chr7B.!!$R5 1674

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
196 197 0.108945 CGTCAGTCCGGGTTAGTTCC 60.109 60.0 0.0 0.0 0.00 3.62 F
466 480 0.615331 CTGACACCTGTAGGCACCAT 59.385 55.0 0.0 0.0 39.32 3.55 F
1755 1840 0.036732 AGGTTGCACCGATGTGTGAT 59.963 50.0 0.0 0.0 44.90 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 1305 1.730451 TACATCCTCAATCGCCGCGA 61.730 55.000 19.34 19.34 41.13 5.87 R
2009 2096 2.114625 GGGTATTTAGGCGCCCCC 59.885 66.667 26.15 21.92 35.18 5.40 R
3361 16369 0.318441 CTAGCGCCTAAGCATGCCTA 59.682 55.000 15.66 4.68 39.83 3.93 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
36 37 3.391382 CCCCTCACCCTCGTGGAC 61.391 72.222 4.76 0.00 40.65 4.02
37 38 2.603473 CCCTCACCCTCGTGGACA 60.603 66.667 4.76 0.00 40.65 4.02
38 39 2.650116 CCCTCACCCTCGTGGACAG 61.650 68.421 4.76 0.00 40.65 3.51
39 40 2.650116 CCTCACCCTCGTGGACAGG 61.650 68.421 4.76 3.22 40.65 4.00
43 44 2.923035 CCCTCGTGGACAGGGTGT 60.923 66.667 4.76 0.00 45.35 4.16
44 45 2.343758 CCTCGTGGACAGGGTGTG 59.656 66.667 0.00 0.00 34.57 3.82
45 46 2.343758 CTCGTGGACAGGGTGTGG 59.656 66.667 0.00 0.00 0.00 4.17
46 47 3.238497 TCGTGGACAGGGTGTGGG 61.238 66.667 0.00 0.00 0.00 4.61
48 49 4.660938 GTGGACAGGGTGTGGGCC 62.661 72.222 0.00 0.00 0.00 5.80
62 63 3.728373 GGCCCCCTGACGTGGATT 61.728 66.667 0.00 0.00 0.00 3.01
63 64 2.355115 GCCCCCTGACGTGGATTT 59.645 61.111 0.00 0.00 0.00 2.17
64 65 1.304134 GCCCCCTGACGTGGATTTT 60.304 57.895 0.00 0.00 0.00 1.82
65 66 0.898326 GCCCCCTGACGTGGATTTTT 60.898 55.000 0.00 0.00 0.00 1.94
66 67 1.173913 CCCCCTGACGTGGATTTTTC 58.826 55.000 0.00 0.00 0.00 2.29
67 68 1.271926 CCCCCTGACGTGGATTTTTCT 60.272 52.381 0.00 0.00 0.00 2.52
68 69 2.514803 CCCCTGACGTGGATTTTTCTT 58.485 47.619 0.00 0.00 0.00 2.52
69 70 2.488153 CCCCTGACGTGGATTTTTCTTC 59.512 50.000 0.00 0.00 0.00 2.87
70 71 2.488153 CCCTGACGTGGATTTTTCTTCC 59.512 50.000 0.00 0.00 0.00 3.46
71 72 3.146066 CCTGACGTGGATTTTTCTTCCA 58.854 45.455 0.00 0.00 40.96 3.53
72 73 3.189287 CCTGACGTGGATTTTTCTTCCAG 59.811 47.826 0.00 0.00 43.78 3.86
73 74 3.815401 CTGACGTGGATTTTTCTTCCAGT 59.185 43.478 0.00 0.00 43.78 4.00
74 75 4.963373 TGACGTGGATTTTTCTTCCAGTA 58.037 39.130 0.00 0.00 43.78 2.74
75 76 5.556915 TGACGTGGATTTTTCTTCCAGTAT 58.443 37.500 0.00 0.00 43.78 2.12
76 77 6.001460 TGACGTGGATTTTTCTTCCAGTATT 58.999 36.000 0.00 0.00 43.78 1.89
77 78 6.488683 TGACGTGGATTTTTCTTCCAGTATTT 59.511 34.615 0.00 0.00 43.78 1.40
78 79 7.013846 TGACGTGGATTTTTCTTCCAGTATTTT 59.986 33.333 0.00 0.00 43.78 1.82
79 80 7.722363 ACGTGGATTTTTCTTCCAGTATTTTT 58.278 30.769 0.00 0.00 43.78 1.94
80 81 7.865889 ACGTGGATTTTTCTTCCAGTATTTTTC 59.134 33.333 0.00 0.00 43.78 2.29
81 82 8.082242 CGTGGATTTTTCTTCCAGTATTTTTCT 58.918 33.333 0.00 0.00 43.78 2.52
82 83 9.764363 GTGGATTTTTCTTCCAGTATTTTTCTT 57.236 29.630 0.00 0.00 43.78 2.52
105 106 8.682710 TCTTATTTTTCAAATAGATGTTCCGGG 58.317 33.333 0.00 0.00 0.00 5.73
106 107 5.652994 TTTTTCAAATAGATGTTCCGGGG 57.347 39.130 0.00 0.00 0.00 5.73
107 108 4.577988 TTTCAAATAGATGTTCCGGGGA 57.422 40.909 0.00 0.00 0.00 4.81
108 109 3.838244 TCAAATAGATGTTCCGGGGAG 57.162 47.619 0.00 0.00 0.00 4.30
109 110 3.112263 TCAAATAGATGTTCCGGGGAGT 58.888 45.455 0.00 0.00 0.00 3.85
110 111 3.521937 TCAAATAGATGTTCCGGGGAGTT 59.478 43.478 0.00 0.00 0.00 3.01
111 112 4.018779 TCAAATAGATGTTCCGGGGAGTTT 60.019 41.667 0.00 0.00 0.00 2.66
112 113 3.840124 ATAGATGTTCCGGGGAGTTTC 57.160 47.619 0.00 0.00 0.00 2.78
113 114 1.358152 AGATGTTCCGGGGAGTTTCA 58.642 50.000 0.00 0.00 0.00 2.69
114 115 1.279271 AGATGTTCCGGGGAGTTTCAG 59.721 52.381 0.00 0.00 0.00 3.02
115 116 0.328258 ATGTTCCGGGGAGTTTCAGG 59.672 55.000 0.00 0.00 0.00 3.86
116 117 1.057851 TGTTCCGGGGAGTTTCAGGT 61.058 55.000 0.00 0.00 0.00 4.00
117 118 0.321387 GTTCCGGGGAGTTTCAGGTC 60.321 60.000 0.00 0.00 0.00 3.85
118 119 0.765135 TTCCGGGGAGTTTCAGGTCA 60.765 55.000 0.00 0.00 0.00 4.02
119 120 0.546747 TCCGGGGAGTTTCAGGTCAT 60.547 55.000 0.00 0.00 0.00 3.06
120 121 0.328258 CCGGGGAGTTTCAGGTCATT 59.672 55.000 0.00 0.00 0.00 2.57
121 122 1.679032 CCGGGGAGTTTCAGGTCATTC 60.679 57.143 0.00 0.00 0.00 2.67
122 123 1.679032 CGGGGAGTTTCAGGTCATTCC 60.679 57.143 0.00 0.00 0.00 3.01
123 124 1.679032 GGGGAGTTTCAGGTCATTCCG 60.679 57.143 0.00 0.00 41.99 4.30
124 125 1.278127 GGGAGTTTCAGGTCATTCCGA 59.722 52.381 0.00 0.00 41.99 4.55
125 126 2.622436 GGAGTTTCAGGTCATTCCGAG 58.378 52.381 0.00 0.00 41.99 4.63
126 127 2.233922 GGAGTTTCAGGTCATTCCGAGA 59.766 50.000 0.00 0.00 41.99 4.04
127 128 3.306780 GGAGTTTCAGGTCATTCCGAGAA 60.307 47.826 0.00 0.00 41.99 2.87
128 129 3.665190 AGTTTCAGGTCATTCCGAGAAC 58.335 45.455 0.00 0.00 41.99 3.01
129 130 3.325135 AGTTTCAGGTCATTCCGAGAACT 59.675 43.478 0.00 0.00 41.99 3.01
130 131 4.065789 GTTTCAGGTCATTCCGAGAACTT 58.934 43.478 0.00 0.00 41.99 2.66
131 132 4.351874 TTCAGGTCATTCCGAGAACTTT 57.648 40.909 0.00 0.00 41.99 2.66
132 133 4.351874 TCAGGTCATTCCGAGAACTTTT 57.648 40.909 0.00 0.00 41.99 2.27
133 134 4.065088 TCAGGTCATTCCGAGAACTTTTG 58.935 43.478 0.00 0.00 41.99 2.44
134 135 3.815401 CAGGTCATTCCGAGAACTTTTGT 59.185 43.478 0.00 0.00 41.99 2.83
135 136 4.275936 CAGGTCATTCCGAGAACTTTTGTT 59.724 41.667 0.00 0.00 42.83 2.83
136 137 4.887655 AGGTCATTCCGAGAACTTTTGTTT 59.112 37.500 0.00 0.00 41.30 2.83
137 138 5.008712 AGGTCATTCCGAGAACTTTTGTTTC 59.991 40.000 0.00 0.00 41.30 2.78
138 139 5.008712 GGTCATTCCGAGAACTTTTGTTTCT 59.991 40.000 0.00 0.00 43.66 2.52
139 140 5.909610 GTCATTCCGAGAACTTTTGTTTCTG 59.090 40.000 0.00 0.00 43.66 3.02
140 141 3.963383 TCCGAGAACTTTTGTTTCTGC 57.037 42.857 0.00 0.00 43.66 4.26
141 142 3.275143 TCCGAGAACTTTTGTTTCTGCA 58.725 40.909 0.00 0.00 43.66 4.41
142 143 3.064820 TCCGAGAACTTTTGTTTCTGCAC 59.935 43.478 0.00 0.00 43.66 4.57
143 144 3.181501 CCGAGAACTTTTGTTTCTGCACA 60.182 43.478 0.00 0.00 43.66 4.57
144 145 4.498009 CCGAGAACTTTTGTTTCTGCACAT 60.498 41.667 0.00 0.00 43.66 3.21
145 146 5.277779 CCGAGAACTTTTGTTTCTGCACATA 60.278 40.000 0.00 0.00 43.66 2.29
146 147 6.198687 CGAGAACTTTTGTTTCTGCACATAA 58.801 36.000 0.00 0.00 43.66 1.90
147 148 6.690957 CGAGAACTTTTGTTTCTGCACATAAA 59.309 34.615 0.00 0.00 43.66 1.40
148 149 7.379529 CGAGAACTTTTGTTTCTGCACATAAAT 59.620 33.333 0.00 0.00 43.66 1.40
149 150 9.677567 GAGAACTTTTGTTTCTGCACATAAATA 57.322 29.630 0.00 0.00 43.66 1.40
152 153 9.593134 AACTTTTGTTTCTGCACATAAATAACA 57.407 25.926 0.00 0.00 40.17 2.41
153 154 9.030301 ACTTTTGTTTCTGCACATAAATAACAC 57.970 29.630 0.00 0.00 0.00 3.32
154 155 7.938563 TTTGTTTCTGCACATAAATAACACC 57.061 32.000 0.00 0.00 0.00 4.16
155 156 6.641169 TGTTTCTGCACATAAATAACACCA 57.359 33.333 0.00 0.00 0.00 4.17
156 157 7.225784 TGTTTCTGCACATAAATAACACCAT 57.774 32.000 0.00 0.00 0.00 3.55
157 158 7.089538 TGTTTCTGCACATAAATAACACCATG 58.910 34.615 0.00 0.00 0.00 3.66
158 159 5.833406 TCTGCACATAAATAACACCATGG 57.167 39.130 11.19 11.19 0.00 3.66
159 160 5.504853 TCTGCACATAAATAACACCATGGA 58.495 37.500 21.47 0.00 0.00 3.41
160 161 5.948758 TCTGCACATAAATAACACCATGGAA 59.051 36.000 21.47 0.56 0.00 3.53
161 162 6.435591 TCTGCACATAAATAACACCATGGAAA 59.564 34.615 21.47 0.16 0.00 3.13
162 163 6.629128 TGCACATAAATAACACCATGGAAAG 58.371 36.000 21.47 10.40 0.00 2.62
163 164 6.210385 TGCACATAAATAACACCATGGAAAGT 59.790 34.615 21.47 11.10 0.00 2.66
164 165 6.751888 GCACATAAATAACACCATGGAAAGTC 59.248 38.462 21.47 0.00 0.00 3.01
165 166 7.362920 GCACATAAATAACACCATGGAAAGTCT 60.363 37.037 21.47 7.50 0.00 3.24
166 167 7.970061 CACATAAATAACACCATGGAAAGTCTG 59.030 37.037 21.47 7.57 0.00 3.51
167 168 5.391312 AAATAACACCATGGAAAGTCTGC 57.609 39.130 21.47 0.00 0.00 4.26
168 169 2.664402 AACACCATGGAAAGTCTGCT 57.336 45.000 21.47 0.00 0.00 4.24
169 170 1.901591 ACACCATGGAAAGTCTGCTG 58.098 50.000 21.47 5.09 0.00 4.41
170 171 1.421268 ACACCATGGAAAGTCTGCTGA 59.579 47.619 21.47 0.00 0.00 4.26
171 172 2.158623 ACACCATGGAAAGTCTGCTGAA 60.159 45.455 21.47 0.00 0.00 3.02
172 173 2.886523 CACCATGGAAAGTCTGCTGAAA 59.113 45.455 21.47 0.00 0.00 2.69
173 174 3.318839 CACCATGGAAAGTCTGCTGAAAA 59.681 43.478 21.47 0.00 0.00 2.29
174 175 3.319122 ACCATGGAAAGTCTGCTGAAAAC 59.681 43.478 21.47 0.00 0.00 2.43
175 176 3.318839 CCATGGAAAGTCTGCTGAAAACA 59.681 43.478 5.56 0.00 0.00 2.83
176 177 4.543692 CATGGAAAGTCTGCTGAAAACAG 58.456 43.478 0.00 0.00 36.44 3.16
184 185 3.736581 GCTGAAAACAGCGTCAGTC 57.263 52.632 6.46 0.00 42.72 3.51
185 186 0.235926 GCTGAAAACAGCGTCAGTCC 59.764 55.000 6.46 0.00 42.72 3.85
186 187 0.508641 CTGAAAACAGCGTCAGTCCG 59.491 55.000 0.00 0.00 37.16 4.79
187 188 0.878523 TGAAAACAGCGTCAGTCCGG 60.879 55.000 0.00 0.00 0.00 5.14
188 189 1.566018 GAAAACAGCGTCAGTCCGGG 61.566 60.000 0.00 0.00 0.00 5.73
189 190 2.319890 AAAACAGCGTCAGTCCGGGT 62.320 55.000 0.00 0.00 0.00 5.28
190 191 2.319890 AAACAGCGTCAGTCCGGGTT 62.320 55.000 0.00 0.00 0.00 4.11
191 192 1.466025 AACAGCGTCAGTCCGGGTTA 61.466 55.000 0.00 0.00 0.00 2.85
192 193 1.153823 CAGCGTCAGTCCGGGTTAG 60.154 63.158 0.00 0.00 0.00 2.34
193 194 1.605738 AGCGTCAGTCCGGGTTAGT 60.606 57.895 0.00 0.00 0.00 2.24
194 195 1.183676 AGCGTCAGTCCGGGTTAGTT 61.184 55.000 0.00 0.00 0.00 2.24
195 196 0.735287 GCGTCAGTCCGGGTTAGTTC 60.735 60.000 0.00 0.00 0.00 3.01
196 197 0.108945 CGTCAGTCCGGGTTAGTTCC 60.109 60.000 0.00 0.00 0.00 3.62
197 198 0.971386 GTCAGTCCGGGTTAGTTCCA 59.029 55.000 0.00 0.00 0.00 3.53
198 199 1.553704 GTCAGTCCGGGTTAGTTCCAT 59.446 52.381 0.00 0.00 0.00 3.41
199 200 2.027469 GTCAGTCCGGGTTAGTTCCATT 60.027 50.000 0.00 0.00 0.00 3.16
200 201 2.235402 TCAGTCCGGGTTAGTTCCATTC 59.765 50.000 0.00 0.00 0.00 2.67
201 202 2.027561 CAGTCCGGGTTAGTTCCATTCA 60.028 50.000 0.00 0.00 0.00 2.57
202 203 2.640826 AGTCCGGGTTAGTTCCATTCAA 59.359 45.455 0.00 0.00 0.00 2.69
203 204 3.073356 AGTCCGGGTTAGTTCCATTCAAA 59.927 43.478 0.00 0.00 0.00 2.69
204 205 4.014406 GTCCGGGTTAGTTCCATTCAAAT 58.986 43.478 0.00 0.00 0.00 2.32
205 206 4.095932 GTCCGGGTTAGTTCCATTCAAATC 59.904 45.833 0.00 0.00 0.00 2.17
206 207 4.013728 CCGGGTTAGTTCCATTCAAATCA 58.986 43.478 0.00 0.00 0.00 2.57
207 208 4.644685 CCGGGTTAGTTCCATTCAAATCAT 59.355 41.667 0.00 0.00 0.00 2.45
208 209 5.450412 CCGGGTTAGTTCCATTCAAATCATG 60.450 44.000 0.00 0.00 0.00 3.07
209 210 5.351458 GGGTTAGTTCCATTCAAATCATGC 58.649 41.667 0.00 0.00 0.00 4.06
210 211 5.105392 GGGTTAGTTCCATTCAAATCATGCA 60.105 40.000 0.00 0.00 0.00 3.96
211 212 6.397272 GGTTAGTTCCATTCAAATCATGCAA 58.603 36.000 0.00 0.00 0.00 4.08
212 213 6.532657 GGTTAGTTCCATTCAAATCATGCAAG 59.467 38.462 0.00 0.00 0.00 4.01
213 214 5.733620 AGTTCCATTCAAATCATGCAAGT 57.266 34.783 0.00 0.00 0.00 3.16
214 215 6.105397 AGTTCCATTCAAATCATGCAAGTT 57.895 33.333 0.00 0.00 0.00 2.66
215 216 7.230849 AGTTCCATTCAAATCATGCAAGTTA 57.769 32.000 0.00 0.00 0.00 2.24
216 217 7.318141 AGTTCCATTCAAATCATGCAAGTTAG 58.682 34.615 0.00 0.00 0.00 2.34
217 218 7.177216 AGTTCCATTCAAATCATGCAAGTTAGA 59.823 33.333 0.00 0.00 0.00 2.10
218 219 7.092137 TCCATTCAAATCATGCAAGTTAGAG 57.908 36.000 0.00 0.00 0.00 2.43
219 220 6.660521 TCCATTCAAATCATGCAAGTTAGAGT 59.339 34.615 0.00 0.00 0.00 3.24
220 221 6.971184 CCATTCAAATCATGCAAGTTAGAGTC 59.029 38.462 0.00 0.00 0.00 3.36
221 222 6.500684 TTCAAATCATGCAAGTTAGAGTCC 57.499 37.500 0.00 0.00 0.00 3.85
222 223 5.559770 TCAAATCATGCAAGTTAGAGTCCA 58.440 37.500 0.00 0.00 0.00 4.02
223 224 6.003326 TCAAATCATGCAAGTTAGAGTCCAA 58.997 36.000 0.00 0.00 0.00 3.53
224 225 6.489700 TCAAATCATGCAAGTTAGAGTCCAAA 59.510 34.615 0.00 0.00 0.00 3.28
225 226 6.899393 AATCATGCAAGTTAGAGTCCAAAA 57.101 33.333 0.00 0.00 0.00 2.44
226 227 5.689383 TCATGCAAGTTAGAGTCCAAAAC 57.311 39.130 0.00 0.00 0.00 2.43
227 228 5.129634 TCATGCAAGTTAGAGTCCAAAACA 58.870 37.500 0.00 0.00 0.00 2.83
228 229 5.592282 TCATGCAAGTTAGAGTCCAAAACAA 59.408 36.000 0.00 0.00 0.00 2.83
229 230 5.499139 TGCAAGTTAGAGTCCAAAACAAG 57.501 39.130 0.00 0.00 0.00 3.16
230 231 4.338118 TGCAAGTTAGAGTCCAAAACAAGG 59.662 41.667 0.00 0.00 0.00 3.61
231 232 4.261614 GCAAGTTAGAGTCCAAAACAAGGG 60.262 45.833 4.12 0.00 0.00 3.95
232 233 3.487372 AGTTAGAGTCCAAAACAAGGGC 58.513 45.455 4.12 0.00 0.00 5.19
233 234 3.117663 AGTTAGAGTCCAAAACAAGGGCA 60.118 43.478 0.00 0.00 31.65 5.36
234 235 2.452600 AGAGTCCAAAACAAGGGCAA 57.547 45.000 0.00 0.00 31.65 4.52
235 236 2.745968 AGAGTCCAAAACAAGGGCAAA 58.254 42.857 0.00 0.00 31.65 3.68
236 237 3.103742 AGAGTCCAAAACAAGGGCAAAA 58.896 40.909 0.00 0.00 31.65 2.44
237 238 3.132824 AGAGTCCAAAACAAGGGCAAAAG 59.867 43.478 0.00 0.00 31.65 2.27
238 239 2.837591 AGTCCAAAACAAGGGCAAAAGT 59.162 40.909 0.00 0.00 31.65 2.66
239 240 2.935849 GTCCAAAACAAGGGCAAAAGTG 59.064 45.455 0.00 0.00 0.00 3.16
240 241 2.569404 TCCAAAACAAGGGCAAAAGTGT 59.431 40.909 0.00 0.00 0.00 3.55
241 242 3.008485 TCCAAAACAAGGGCAAAAGTGTT 59.992 39.130 0.00 0.00 35.77 3.32
242 243 3.755905 CCAAAACAAGGGCAAAAGTGTTT 59.244 39.130 0.00 0.00 44.01 2.83
243 244 4.379290 CCAAAACAAGGGCAAAAGTGTTTG 60.379 41.667 1.73 0.00 41.94 2.93
244 245 2.689553 ACAAGGGCAAAAGTGTTTGG 57.310 45.000 1.72 0.00 43.73 3.28
245 246 2.183679 ACAAGGGCAAAAGTGTTTGGA 58.816 42.857 1.72 0.00 43.73 3.53
246 247 2.569404 ACAAGGGCAAAAGTGTTTGGAA 59.431 40.909 1.72 0.00 43.73 3.53
247 248 3.008485 ACAAGGGCAAAAGTGTTTGGAAA 59.992 39.130 1.72 0.00 43.73 3.13
248 249 3.990959 AGGGCAAAAGTGTTTGGAAAA 57.009 38.095 1.72 0.00 43.73 2.29
249 250 3.872696 AGGGCAAAAGTGTTTGGAAAAG 58.127 40.909 1.72 0.00 43.73 2.27
250 251 3.263170 AGGGCAAAAGTGTTTGGAAAAGT 59.737 39.130 1.72 0.00 43.73 2.66
251 252 4.468153 AGGGCAAAAGTGTTTGGAAAAGTA 59.532 37.500 1.72 0.00 43.73 2.24
252 253 4.808895 GGGCAAAAGTGTTTGGAAAAGTAG 59.191 41.667 1.72 0.00 43.73 2.57
253 254 5.394773 GGGCAAAAGTGTTTGGAAAAGTAGA 60.395 40.000 1.72 0.00 43.73 2.59
254 255 6.280643 GGCAAAAGTGTTTGGAAAAGTAGAT 58.719 36.000 1.72 0.00 43.73 1.98
255 256 7.430441 GGCAAAAGTGTTTGGAAAAGTAGATA 58.570 34.615 1.72 0.00 43.73 1.98
256 257 7.381408 GGCAAAAGTGTTTGGAAAAGTAGATAC 59.619 37.037 1.72 0.00 43.73 2.24
257 258 7.112984 GCAAAAGTGTTTGGAAAAGTAGATACG 59.887 37.037 1.72 0.00 43.73 3.06
258 259 8.339714 CAAAAGTGTTTGGAAAAGTAGATACGA 58.660 33.333 0.00 0.00 40.47 3.43
259 260 7.417496 AAGTGTTTGGAAAAGTAGATACGAC 57.583 36.000 0.00 0.00 0.00 4.34
260 261 5.632347 AGTGTTTGGAAAAGTAGATACGACG 59.368 40.000 0.00 0.00 0.00 5.12
261 262 4.925054 TGTTTGGAAAAGTAGATACGACGG 59.075 41.667 0.00 0.00 0.00 4.79
262 263 5.163513 GTTTGGAAAAGTAGATACGACGGA 58.836 41.667 0.00 0.00 0.00 4.69
263 264 4.627611 TGGAAAAGTAGATACGACGGAG 57.372 45.455 0.00 0.00 0.00 4.63
264 265 4.264253 TGGAAAAGTAGATACGACGGAGA 58.736 43.478 0.00 0.00 0.00 3.71
265 266 4.095483 TGGAAAAGTAGATACGACGGAGAC 59.905 45.833 0.00 0.00 0.00 3.36
412 413 1.040646 GTAGAGATCGGTCATGGCCA 58.959 55.000 18.31 8.56 0.00 5.36
466 480 0.615331 CTGACACCTGTAGGCACCAT 59.385 55.000 0.00 0.00 39.32 3.55
549 583 2.880890 GAGACTTCCACAAAGCACACAT 59.119 45.455 0.00 0.00 38.67 3.21
636 670 0.667993 CACGAAACAGTGGGCAATGT 59.332 50.000 0.00 0.00 41.83 2.71
751 789 1.600663 CGAGTAGGGCTAGCACGAATG 60.601 57.143 18.24 0.73 0.00 2.67
871 931 4.638421 CGCATAGTTGTAAAGATGGGGAAA 59.362 41.667 0.00 0.00 32.73 3.13
1226 1305 1.714794 CTCGATGAAGCCTTCGTTGT 58.285 50.000 12.58 0.00 39.86 3.32
1245 1324 1.299850 CGCGGCGATTGAGGATGTA 60.300 57.895 19.16 0.00 0.00 2.29
1302 1381 0.914417 AGGCGAAGATGGGGGAGAAA 60.914 55.000 0.00 0.00 0.00 2.52
1721 1806 7.865889 TGAATATTACTCACAGTAGCCAATACG 59.134 37.037 0.00 0.00 39.55 3.06
1755 1840 0.036732 AGGTTGCACCGATGTGTGAT 59.963 50.000 0.00 0.00 44.90 3.06
2009 2096 4.527944 TCCTGAGATGGACACTAGTACAG 58.472 47.826 0.00 0.00 43.16 2.74
2267 2356 1.375098 GGAGCAGAACATCAGCAGGC 61.375 60.000 0.00 0.00 30.69 4.85
2605 2694 0.610174 GATGCTGTCACAGGAGGACA 59.390 55.000 7.00 0.00 42.62 4.02
2729 11733 4.948847 TGATGATCAGATAACCCAAGACG 58.051 43.478 0.09 0.00 0.00 4.18
2994 16001 5.299582 TGTGTGTACATCATGCATCTTTG 57.700 39.130 0.00 0.00 0.00 2.77
3131 16138 6.379133 ATGTGTGCATTGTATCTGGAAAAGAT 59.621 34.615 0.00 0.00 39.58 2.40
3336 16344 5.029807 TGTTTCACACATACTCTGTTGGA 57.970 39.130 0.00 0.00 35.29 3.53
3434 16442 0.746204 GAAGTCTAGGCAGGCCAAGC 60.746 60.000 13.63 8.90 38.92 4.01
3438 16446 1.200760 TCTAGGCAGGCCAAGCAAGA 61.201 55.000 20.05 17.64 38.92 3.02
3478 16486 4.379813 GGGAAATCATGCTATATTGCACCG 60.380 45.833 14.10 8.73 46.33 4.94
3485 16493 4.206477 TGCTATATTGCACCGATATGCT 57.794 40.909 7.80 0.00 46.28 3.79
3582 16590 9.730705 ATAATAATCACAGATACACCCTGATTG 57.269 33.333 0.00 0.00 34.28 2.67
3611 16619 0.395312 TATTACCGCCTAGGCTTGCC 59.605 55.000 30.55 2.97 46.52 4.52
3655 16663 0.736325 CACTAGGCGAAGGTCAACCG 60.736 60.000 0.00 0.00 42.08 4.44
3665 16673 2.098831 GGTCAACCGCCTCGCTTAC 61.099 63.158 0.00 0.00 0.00 2.34
3689 16697 5.503683 CGCCTACCGCTCACATATATAGTAC 60.504 48.000 0.00 0.00 34.21 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.343758 CACACCCTGTCCACGAGG 59.656 66.667 0.00 0.00 0.00 4.63
28 29 2.343758 CCACACCCTGTCCACGAG 59.656 66.667 0.00 0.00 0.00 4.18
29 30 3.238497 CCCACACCCTGTCCACGA 61.238 66.667 0.00 0.00 0.00 4.35
31 32 4.660938 GGCCCACACCCTGTCCAC 62.661 72.222 0.00 0.00 0.00 4.02
45 46 2.781431 AAAATCCACGTCAGGGGGCC 62.781 60.000 0.00 0.00 42.67 5.80
46 47 0.898326 AAAAATCCACGTCAGGGGGC 60.898 55.000 0.00 0.00 42.67 5.80
47 48 1.173913 GAAAAATCCACGTCAGGGGG 58.826 55.000 0.00 0.00 42.67 5.40
48 49 2.200373 AGAAAAATCCACGTCAGGGG 57.800 50.000 0.00 0.00 44.22 4.79
49 50 2.488153 GGAAGAAAAATCCACGTCAGGG 59.512 50.000 0.00 0.00 36.92 4.45
50 51 3.146066 TGGAAGAAAAATCCACGTCAGG 58.854 45.455 0.00 0.00 41.98 3.86
51 52 3.815401 ACTGGAAGAAAAATCCACGTCAG 59.185 43.478 0.00 0.00 41.98 3.51
52 53 3.815809 ACTGGAAGAAAAATCCACGTCA 58.184 40.909 0.00 0.00 41.98 4.35
53 54 6.496338 AATACTGGAAGAAAAATCCACGTC 57.504 37.500 0.00 0.00 41.98 4.34
54 55 6.894339 AAATACTGGAAGAAAAATCCACGT 57.106 33.333 0.00 0.00 41.98 4.49
55 56 8.082242 AGAAAAATACTGGAAGAAAAATCCACG 58.918 33.333 0.00 0.00 41.98 4.94
56 57 9.764363 AAGAAAAATACTGGAAGAAAAATCCAC 57.236 29.630 0.00 0.00 41.98 4.02
79 80 8.682710 CCCGGAACATCTATTTGAAAAATAAGA 58.317 33.333 0.73 0.00 0.00 2.10
80 81 7.920682 CCCCGGAACATCTATTTGAAAAATAAG 59.079 37.037 0.73 0.00 0.00 1.73
81 82 7.616150 TCCCCGGAACATCTATTTGAAAAATAA 59.384 33.333 0.73 0.00 0.00 1.40
82 83 7.120051 TCCCCGGAACATCTATTTGAAAAATA 58.880 34.615 0.73 0.00 0.00 1.40
83 84 5.955355 TCCCCGGAACATCTATTTGAAAAAT 59.045 36.000 0.73 0.00 0.00 1.82
84 85 5.326069 TCCCCGGAACATCTATTTGAAAAA 58.674 37.500 0.73 0.00 0.00 1.94
85 86 4.924625 TCCCCGGAACATCTATTTGAAAA 58.075 39.130 0.73 0.00 0.00 2.29
86 87 4.018779 ACTCCCCGGAACATCTATTTGAAA 60.019 41.667 0.73 0.00 0.00 2.69
87 88 3.521937 ACTCCCCGGAACATCTATTTGAA 59.478 43.478 0.73 0.00 0.00 2.69
88 89 3.112263 ACTCCCCGGAACATCTATTTGA 58.888 45.455 0.73 0.00 0.00 2.69
89 90 3.560636 ACTCCCCGGAACATCTATTTG 57.439 47.619 0.73 0.00 0.00 2.32
90 91 4.018779 TGAAACTCCCCGGAACATCTATTT 60.019 41.667 0.73 0.00 0.00 1.40
91 92 3.521937 TGAAACTCCCCGGAACATCTATT 59.478 43.478 0.73 0.00 0.00 1.73
92 93 3.112263 TGAAACTCCCCGGAACATCTAT 58.888 45.455 0.73 0.00 0.00 1.98
93 94 2.500098 CTGAAACTCCCCGGAACATCTA 59.500 50.000 0.73 0.00 0.00 1.98
94 95 1.279271 CTGAAACTCCCCGGAACATCT 59.721 52.381 0.73 0.00 0.00 2.90
95 96 1.679032 CCTGAAACTCCCCGGAACATC 60.679 57.143 0.73 0.00 0.00 3.06
96 97 0.328258 CCTGAAACTCCCCGGAACAT 59.672 55.000 0.73 0.00 0.00 2.71
97 98 1.057851 ACCTGAAACTCCCCGGAACA 61.058 55.000 0.73 0.00 0.00 3.18
98 99 0.321387 GACCTGAAACTCCCCGGAAC 60.321 60.000 0.73 0.00 0.00 3.62
99 100 0.765135 TGACCTGAAACTCCCCGGAA 60.765 55.000 0.73 0.00 0.00 4.30
100 101 0.546747 ATGACCTGAAACTCCCCGGA 60.547 55.000 0.73 0.00 0.00 5.14
101 102 0.328258 AATGACCTGAAACTCCCCGG 59.672 55.000 0.00 0.00 0.00 5.73
102 103 1.679032 GGAATGACCTGAAACTCCCCG 60.679 57.143 0.00 0.00 35.41 5.73
103 104 1.679032 CGGAATGACCTGAAACTCCCC 60.679 57.143 0.00 0.00 36.31 4.81
104 105 1.278127 TCGGAATGACCTGAAACTCCC 59.722 52.381 0.00 0.00 36.31 4.30
105 106 2.233922 TCTCGGAATGACCTGAAACTCC 59.766 50.000 0.00 0.00 36.31 3.85
106 107 3.594603 TCTCGGAATGACCTGAAACTC 57.405 47.619 0.00 0.00 36.31 3.01
107 108 3.325135 AGTTCTCGGAATGACCTGAAACT 59.675 43.478 0.00 0.00 36.31 2.66
108 109 3.665190 AGTTCTCGGAATGACCTGAAAC 58.335 45.455 0.00 0.00 36.31 2.78
109 110 4.351874 AAGTTCTCGGAATGACCTGAAA 57.648 40.909 0.00 0.00 36.31 2.69
110 111 4.351874 AAAGTTCTCGGAATGACCTGAA 57.648 40.909 0.00 0.00 36.31 3.02
111 112 4.065088 CAAAAGTTCTCGGAATGACCTGA 58.935 43.478 0.00 0.00 36.31 3.86
112 113 3.815401 ACAAAAGTTCTCGGAATGACCTG 59.185 43.478 0.00 0.00 36.31 4.00
113 114 4.086706 ACAAAAGTTCTCGGAATGACCT 57.913 40.909 0.00 0.00 36.31 3.85
114 115 4.830826 AACAAAAGTTCTCGGAATGACC 57.169 40.909 0.00 0.00 0.00 4.02
115 116 5.909610 CAGAAACAAAAGTTCTCGGAATGAC 59.090 40.000 0.00 0.00 32.96 3.06
116 117 5.505654 GCAGAAACAAAAGTTCTCGGAATGA 60.506 40.000 0.00 0.00 32.96 2.57
117 118 4.676924 GCAGAAACAAAAGTTCTCGGAATG 59.323 41.667 0.00 0.00 32.96 2.67
118 119 4.338118 TGCAGAAACAAAAGTTCTCGGAAT 59.662 37.500 0.00 0.00 32.96 3.01
119 120 3.692101 TGCAGAAACAAAAGTTCTCGGAA 59.308 39.130 0.00 0.00 32.96 4.30
120 121 3.064820 GTGCAGAAACAAAAGTTCTCGGA 59.935 43.478 0.00 0.00 32.96 4.55
121 122 3.181501 TGTGCAGAAACAAAAGTTCTCGG 60.182 43.478 0.00 0.00 32.96 4.63
122 123 4.014847 TGTGCAGAAACAAAAGTTCTCG 57.985 40.909 0.00 0.00 32.96 4.04
123 124 7.985634 TTTATGTGCAGAAACAAAAGTTCTC 57.014 32.000 0.00 0.00 32.96 2.87
126 127 9.593134 TGTTATTTATGTGCAGAAACAAAAGTT 57.407 25.926 0.00 0.00 32.81 2.66
127 128 9.030301 GTGTTATTTATGTGCAGAAACAAAAGT 57.970 29.630 0.15 0.00 32.81 2.66
128 129 8.487176 GGTGTTATTTATGTGCAGAAACAAAAG 58.513 33.333 0.15 0.00 32.81 2.27
129 130 7.981789 TGGTGTTATTTATGTGCAGAAACAAAA 59.018 29.630 0.15 0.00 32.81 2.44
130 131 7.492524 TGGTGTTATTTATGTGCAGAAACAAA 58.507 30.769 0.15 0.00 32.81 2.83
131 132 7.043961 TGGTGTTATTTATGTGCAGAAACAA 57.956 32.000 0.15 0.00 32.81 2.83
132 133 6.641169 TGGTGTTATTTATGTGCAGAAACA 57.359 33.333 0.00 0.00 0.00 2.83
133 134 6.531240 CCATGGTGTTATTTATGTGCAGAAAC 59.469 38.462 2.57 0.00 0.00 2.78
134 135 6.435591 TCCATGGTGTTATTTATGTGCAGAAA 59.564 34.615 12.58 0.00 0.00 2.52
135 136 5.948758 TCCATGGTGTTATTTATGTGCAGAA 59.051 36.000 12.58 0.00 0.00 3.02
136 137 5.504853 TCCATGGTGTTATTTATGTGCAGA 58.495 37.500 12.58 0.00 0.00 4.26
137 138 5.833406 TCCATGGTGTTATTTATGTGCAG 57.167 39.130 12.58 0.00 0.00 4.41
138 139 6.210385 ACTTTCCATGGTGTTATTTATGTGCA 59.790 34.615 12.58 0.00 0.00 4.57
139 140 6.630071 ACTTTCCATGGTGTTATTTATGTGC 58.370 36.000 12.58 0.00 0.00 4.57
140 141 7.970061 CAGACTTTCCATGGTGTTATTTATGTG 59.030 37.037 12.58 0.00 0.00 3.21
141 142 7.362920 GCAGACTTTCCATGGTGTTATTTATGT 60.363 37.037 12.58 0.00 0.00 2.29
142 143 6.974622 GCAGACTTTCCATGGTGTTATTTATG 59.025 38.462 12.58 2.79 0.00 1.90
143 144 6.891908 AGCAGACTTTCCATGGTGTTATTTAT 59.108 34.615 12.58 0.00 0.00 1.40
144 145 6.150976 CAGCAGACTTTCCATGGTGTTATTTA 59.849 38.462 12.58 0.00 37.59 1.40
145 146 5.047802 CAGCAGACTTTCCATGGTGTTATTT 60.048 40.000 12.58 0.00 37.59 1.40
146 147 4.460382 CAGCAGACTTTCCATGGTGTTATT 59.540 41.667 12.58 0.00 37.59 1.40
147 148 4.012374 CAGCAGACTTTCCATGGTGTTAT 58.988 43.478 12.58 0.00 37.59 1.89
148 149 3.072330 TCAGCAGACTTTCCATGGTGTTA 59.928 43.478 12.58 0.00 41.82 2.41
149 150 2.158623 TCAGCAGACTTTCCATGGTGTT 60.159 45.455 12.58 0.00 41.82 3.32
150 151 1.421268 TCAGCAGACTTTCCATGGTGT 59.579 47.619 12.58 9.46 41.82 4.16
151 152 2.189594 TCAGCAGACTTTCCATGGTG 57.810 50.000 12.58 2.17 42.34 4.17
152 153 2.957402 TTCAGCAGACTTTCCATGGT 57.043 45.000 12.58 0.00 0.00 3.55
153 154 3.318839 TGTTTTCAGCAGACTTTCCATGG 59.681 43.478 4.97 4.97 0.00 3.66
154 155 4.543692 CTGTTTTCAGCAGACTTTCCATG 58.456 43.478 0.00 0.00 41.24 3.66
155 156 4.843220 CTGTTTTCAGCAGACTTTCCAT 57.157 40.909 0.00 0.00 41.24 3.41
168 169 0.878523 CCGGACTGACGCTGTTTTCA 60.879 55.000 0.00 0.00 0.00 2.69
169 170 1.566018 CCCGGACTGACGCTGTTTTC 61.566 60.000 0.73 0.00 0.00 2.29
170 171 1.597027 CCCGGACTGACGCTGTTTT 60.597 57.895 0.73 0.00 0.00 2.43
171 172 2.030562 CCCGGACTGACGCTGTTT 59.969 61.111 0.73 0.00 0.00 2.83
172 173 1.466025 TAACCCGGACTGACGCTGTT 61.466 55.000 0.73 0.00 33.80 3.16
173 174 1.874345 CTAACCCGGACTGACGCTGT 61.874 60.000 0.73 0.00 0.00 4.40
174 175 1.153823 CTAACCCGGACTGACGCTG 60.154 63.158 0.73 0.00 0.00 5.18
175 176 1.183676 AACTAACCCGGACTGACGCT 61.184 55.000 0.73 0.00 0.00 5.07
176 177 0.735287 GAACTAACCCGGACTGACGC 60.735 60.000 0.73 0.00 0.00 5.19
177 178 0.108945 GGAACTAACCCGGACTGACG 60.109 60.000 0.73 0.00 0.00 4.35
178 179 0.971386 TGGAACTAACCCGGACTGAC 59.029 55.000 0.73 0.00 0.00 3.51
179 180 1.946984 ATGGAACTAACCCGGACTGA 58.053 50.000 0.73 0.00 0.00 3.41
180 181 2.027561 TGAATGGAACTAACCCGGACTG 60.028 50.000 0.73 0.00 0.00 3.51
181 182 2.262637 TGAATGGAACTAACCCGGACT 58.737 47.619 0.73 0.00 0.00 3.85
182 183 2.773993 TGAATGGAACTAACCCGGAC 57.226 50.000 0.73 0.00 0.00 4.79
183 184 3.791953 TTTGAATGGAACTAACCCGGA 57.208 42.857 0.73 0.00 0.00 5.14
184 185 4.013728 TGATTTGAATGGAACTAACCCGG 58.986 43.478 0.00 0.00 0.00 5.73
185 186 5.581605 CATGATTTGAATGGAACTAACCCG 58.418 41.667 0.00 0.00 0.00 5.28
186 187 5.105392 TGCATGATTTGAATGGAACTAACCC 60.105 40.000 0.00 0.00 0.00 4.11
187 188 5.964758 TGCATGATTTGAATGGAACTAACC 58.035 37.500 0.00 0.00 0.00 2.85
188 189 7.092716 ACTTGCATGATTTGAATGGAACTAAC 58.907 34.615 6.60 0.00 32.71 2.34
189 190 7.230849 ACTTGCATGATTTGAATGGAACTAA 57.769 32.000 6.60 0.00 32.71 2.24
190 191 6.839124 ACTTGCATGATTTGAATGGAACTA 57.161 33.333 6.60 0.00 32.71 2.24
191 192 5.733620 ACTTGCATGATTTGAATGGAACT 57.266 34.783 6.60 0.00 32.71 3.01
192 193 7.315142 TCTAACTTGCATGATTTGAATGGAAC 58.685 34.615 6.60 0.00 32.71 3.62
193 194 7.177216 ACTCTAACTTGCATGATTTGAATGGAA 59.823 33.333 6.60 0.00 34.65 3.53
194 195 6.660521 ACTCTAACTTGCATGATTTGAATGGA 59.339 34.615 6.60 0.00 0.00 3.41
195 196 6.860080 ACTCTAACTTGCATGATTTGAATGG 58.140 36.000 6.60 0.00 0.00 3.16
196 197 6.971184 GGACTCTAACTTGCATGATTTGAATG 59.029 38.462 6.60 0.00 0.00 2.67
197 198 6.660521 TGGACTCTAACTTGCATGATTTGAAT 59.339 34.615 6.60 0.00 0.00 2.57
198 199 6.003326 TGGACTCTAACTTGCATGATTTGAA 58.997 36.000 6.60 0.00 0.00 2.69
199 200 5.559770 TGGACTCTAACTTGCATGATTTGA 58.440 37.500 6.60 3.51 0.00 2.69
200 201 5.885230 TGGACTCTAACTTGCATGATTTG 57.115 39.130 6.60 0.00 0.00 2.32
201 202 6.899393 TTTGGACTCTAACTTGCATGATTT 57.101 33.333 6.60 0.00 0.00 2.17
202 203 6.265196 TGTTTTGGACTCTAACTTGCATGATT 59.735 34.615 6.60 0.30 0.00 2.57
203 204 5.769662 TGTTTTGGACTCTAACTTGCATGAT 59.230 36.000 6.60 0.00 0.00 2.45
204 205 5.129634 TGTTTTGGACTCTAACTTGCATGA 58.870 37.500 6.60 0.00 0.00 3.07
205 206 5.437289 TGTTTTGGACTCTAACTTGCATG 57.563 39.130 0.00 0.00 0.00 4.06
206 207 5.010012 CCTTGTTTTGGACTCTAACTTGCAT 59.990 40.000 0.00 0.00 0.00 3.96
207 208 4.338118 CCTTGTTTTGGACTCTAACTTGCA 59.662 41.667 0.00 0.00 0.00 4.08
208 209 4.261614 CCCTTGTTTTGGACTCTAACTTGC 60.262 45.833 0.00 0.00 0.00 4.01
209 210 4.261614 GCCCTTGTTTTGGACTCTAACTTG 60.262 45.833 0.00 0.00 0.00 3.16
210 211 3.889538 GCCCTTGTTTTGGACTCTAACTT 59.110 43.478 0.00 0.00 0.00 2.66
211 212 3.117663 TGCCCTTGTTTTGGACTCTAACT 60.118 43.478 0.00 0.00 0.00 2.24
212 213 3.219281 TGCCCTTGTTTTGGACTCTAAC 58.781 45.455 0.00 0.00 0.00 2.34
213 214 3.586470 TGCCCTTGTTTTGGACTCTAA 57.414 42.857 0.00 0.00 0.00 2.10
214 215 3.586470 TTGCCCTTGTTTTGGACTCTA 57.414 42.857 0.00 0.00 0.00 2.43
215 216 2.452600 TTGCCCTTGTTTTGGACTCT 57.547 45.000 0.00 0.00 0.00 3.24
216 217 3.118775 ACTTTTGCCCTTGTTTTGGACTC 60.119 43.478 0.00 0.00 0.00 3.36
217 218 2.837591 ACTTTTGCCCTTGTTTTGGACT 59.162 40.909 0.00 0.00 0.00 3.85
218 219 2.935849 CACTTTTGCCCTTGTTTTGGAC 59.064 45.455 0.00 0.00 0.00 4.02
219 220 2.569404 ACACTTTTGCCCTTGTTTTGGA 59.431 40.909 0.00 0.00 0.00 3.53
220 221 2.984562 ACACTTTTGCCCTTGTTTTGG 58.015 42.857 0.00 0.00 0.00 3.28
221 222 4.379290 CCAAACACTTTTGCCCTTGTTTTG 60.379 41.667 0.00 0.00 39.56 2.44
222 223 3.755905 CCAAACACTTTTGCCCTTGTTTT 59.244 39.130 0.00 0.00 39.56 2.43
223 224 3.008485 TCCAAACACTTTTGCCCTTGTTT 59.992 39.130 0.00 0.00 41.69 2.83
224 225 2.569404 TCCAAACACTTTTGCCCTTGTT 59.431 40.909 0.00 0.00 40.84 2.83
225 226 2.183679 TCCAAACACTTTTGCCCTTGT 58.816 42.857 0.00 0.00 40.84 3.16
226 227 2.977772 TCCAAACACTTTTGCCCTTG 57.022 45.000 0.00 0.00 40.84 3.61
227 228 3.990959 TTTCCAAACACTTTTGCCCTT 57.009 38.095 0.00 0.00 40.84 3.95
228 229 3.263170 ACTTTTCCAAACACTTTTGCCCT 59.737 39.130 0.00 0.00 40.84 5.19
229 230 3.605634 ACTTTTCCAAACACTTTTGCCC 58.394 40.909 0.00 0.00 40.84 5.36
230 231 5.656480 TCTACTTTTCCAAACACTTTTGCC 58.344 37.500 0.00 0.00 40.84 4.52
231 232 7.112984 CGTATCTACTTTTCCAAACACTTTTGC 59.887 37.037 0.00 0.00 40.84 3.68
232 233 8.339714 TCGTATCTACTTTTCCAAACACTTTTG 58.660 33.333 0.00 0.00 41.71 2.44
233 234 8.340443 GTCGTATCTACTTTTCCAAACACTTTT 58.660 33.333 0.00 0.00 0.00 2.27
234 235 7.306983 CGTCGTATCTACTTTTCCAAACACTTT 60.307 37.037 0.00 0.00 0.00 2.66
235 236 6.145048 CGTCGTATCTACTTTTCCAAACACTT 59.855 38.462 0.00 0.00 0.00 3.16
236 237 5.632347 CGTCGTATCTACTTTTCCAAACACT 59.368 40.000 0.00 0.00 0.00 3.55
237 238 5.164022 CCGTCGTATCTACTTTTCCAAACAC 60.164 44.000 0.00 0.00 0.00 3.32
238 239 4.925054 CCGTCGTATCTACTTTTCCAAACA 59.075 41.667 0.00 0.00 0.00 2.83
239 240 5.163513 TCCGTCGTATCTACTTTTCCAAAC 58.836 41.667 0.00 0.00 0.00 2.93
240 241 5.183713 TCTCCGTCGTATCTACTTTTCCAAA 59.816 40.000 0.00 0.00 0.00 3.28
241 242 4.701651 TCTCCGTCGTATCTACTTTTCCAA 59.298 41.667 0.00 0.00 0.00 3.53
242 243 4.095483 GTCTCCGTCGTATCTACTTTTCCA 59.905 45.833 0.00 0.00 0.00 3.53
243 244 4.596097 GTCTCCGTCGTATCTACTTTTCC 58.404 47.826 0.00 0.00 0.00 3.13
244 245 4.201763 ACGTCTCCGTCGTATCTACTTTTC 60.202 45.833 0.00 0.00 46.28 2.29
245 246 3.686726 ACGTCTCCGTCGTATCTACTTTT 59.313 43.478 0.00 0.00 46.28 2.27
246 247 3.265791 ACGTCTCCGTCGTATCTACTTT 58.734 45.455 0.00 0.00 46.28 2.66
247 248 2.898705 ACGTCTCCGTCGTATCTACTT 58.101 47.619 0.00 0.00 46.28 2.24
248 249 2.593346 ACGTCTCCGTCGTATCTACT 57.407 50.000 0.00 0.00 46.28 2.57
254 255 0.933097 GCTGATACGTCTCCGTCGTA 59.067 55.000 0.00 0.00 46.28 3.43
255 256 1.022982 TGCTGATACGTCTCCGTCGT 61.023 55.000 0.00 0.00 46.28 4.34
256 257 0.308068 ATGCTGATACGTCTCCGTCG 59.692 55.000 0.00 0.00 46.28 5.12
257 258 1.065701 ACATGCTGATACGTCTCCGTC 59.934 52.381 0.00 0.00 46.28 4.79
259 260 3.349488 TTACATGCTGATACGTCTCCG 57.651 47.619 0.00 0.00 40.83 4.63
260 261 3.491267 GCTTTACATGCTGATACGTCTCC 59.509 47.826 0.00 0.00 0.00 3.71
261 262 4.112634 TGCTTTACATGCTGATACGTCTC 58.887 43.478 0.00 0.00 0.00 3.36
262 263 4.123497 TGCTTTACATGCTGATACGTCT 57.877 40.909 0.00 0.00 0.00 4.18
298 299 5.419542 TGAATTCCCGCATGTATAGATAGC 58.580 41.667 2.27 0.00 0.00 2.97
466 480 7.460910 TGCTTAATTGATAATCCTCCATGCTA 58.539 34.615 0.00 0.00 0.00 3.49
549 583 6.005198 CCCTACCACAGGTTTACACAAAATA 58.995 40.000 0.00 0.00 43.80 1.40
619 653 3.848272 ATAACATTGCCCACTGTTTCG 57.152 42.857 8.90 0.00 36.02 3.46
1117 1196 4.718961 AGTACCAACTGTTTCTGCTGAAT 58.281 39.130 6.88 0.00 33.57 2.57
1226 1305 1.730451 TACATCCTCAATCGCCGCGA 61.730 55.000 19.34 19.34 41.13 5.87
1245 1324 2.158871 TGGCTCGTACTTGTTGAGGTTT 60.159 45.455 0.00 0.00 0.00 3.27
1302 1381 3.771216 TCGGGAGTAAAAGTACCACTCT 58.229 45.455 11.86 0.00 38.95 3.24
1721 1806 4.982295 GTGCAACCTTGTAATTCTTTCCAC 59.018 41.667 0.00 0.00 0.00 4.02
1755 1840 2.705658 GTCATGGTGGATGTATCTCCCA 59.294 50.000 0.00 5.82 34.12 4.37
1845 1932 3.117587 ACTCACCTCGGCCTACTAGTATT 60.118 47.826 2.33 0.00 0.00 1.89
2009 2096 2.114625 GGGTATTTAGGCGCCCCC 59.885 66.667 26.15 21.92 35.18 5.40
2230 2319 3.084039 CTCCTGTGTACATTGGCATGTT 58.916 45.455 0.00 0.00 41.16 2.71
2267 2356 5.006746 GGCAATGTATCTAAGTCGACAAAGG 59.993 44.000 19.50 4.98 0.00 3.11
2729 11733 6.484818 TGCATGCACACACATATATATGTC 57.515 37.500 22.81 13.25 44.57 3.06
3147 16154 3.056832 GGATGGAAATCCCCTCTAGGTT 58.943 50.000 0.00 0.00 34.66 3.50
3361 16369 0.318441 CTAGCGCCTAAGCATGCCTA 59.682 55.000 15.66 4.68 39.83 3.93
3434 16442 5.235305 CCGATTGGGTAGACAATTTCTTG 57.765 43.478 0.00 0.00 40.92 3.02
3568 16576 3.763897 AGTTTTGGCAATCAGGGTGTATC 59.236 43.478 0.00 0.00 0.00 2.24
3582 16590 4.694037 CCTAGGCGGTAATATAGTTTTGGC 59.306 45.833 0.00 0.00 0.00 4.52
3611 16619 1.090052 GCGGTGCTTAAGTGCCCTAG 61.090 60.000 4.02 0.00 0.00 3.02
3689 16697 2.810650 GTAGACCAAGCCTATGTCACG 58.189 52.381 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.