Multiple sequence alignment - TraesCS2D01G067100

Loading Multiple Alignment...

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 TraesCS2D01G067100 chr2D 100.000 2696 0 0 1 2696 28047691 28050386 0.000000e+00 4979.0
1 TraesCS2D01G067100 chr2D 90.405 740 51 9 775 1506 28407494 28408221 0.000000e+00 955.0
2 TraesCS2D01G067100 chr2D 86.515 749 73 13 1958 2690 28057854 28058590 0.000000e+00 798.0
3 TraesCS2D01G067100 chr2D 87.719 513 37 14 793 1302 28099324 28099813 2.330000e-160 575.0
4 TraesCS2D01G067100 chr2D 88.889 351 29 3 1631 1977 28412345 28412689 8.920000e-115 424.0
5 TraesCS2D01G067100 chr2D 88.596 342 28 6 1631 1967 28057482 28057817 3.230000e-109 405.0
6 TraesCS2D01G067100 chr2D 92.063 63 3 2 701 762 28407302 28407363 1.330000e-13 87.9
7 TraesCS2D01G067100 chr2D 100.000 41 0 0 719 759 28099228 28099268 2.880000e-10 76.8
8 TraesCS2D01G067100 chr2A 89.474 855 56 13 775 1612 30222665 30223502 0.000000e+00 1050.0
9 TraesCS2D01G067100 chr2A 91.600 500 36 5 278 773 30221812 30222309 0.000000e+00 686.0
10 TraesCS2D01G067100 chr2B 90.515 738 55 9 775 1506 44943031 44942303 0.000000e+00 961.0
11 TraesCS2D01G067100 chr2B 89.237 734 60 10 777 1506 45608098 45608816 0.000000e+00 900.0
12 TraesCS2D01G067100 chr2B 90.117 597 48 6 914 1506 45642250 45641661 0.000000e+00 765.0
13 TraesCS2D01G067100 chr2B 81.242 821 110 20 1898 2685 45630605 45629796 8.200000e-175 623.0
14 TraesCS2D01G067100 chr2B 89.970 329 28 4 1631 1955 44932557 44932230 1.150000e-113 420.0
15 TraesCS2D01G067100 chr2B 77.747 719 98 25 1999 2685 44932241 44931553 4.210000e-103 385.0
16 TraesCS2D01G067100 chr2B 90.809 272 22 1 1631 1902 45637506 45637238 7.100000e-96 361.0
17 TraesCS2D01G067100 chr2B 93.519 216 12 1 1 214 734839837 734840052 1.200000e-83 320.0
18 TraesCS2D01G067100 chr2B 90.110 182 15 2 520 701 45647757 45647579 1.610000e-57 233.0
19 TraesCS2D01G067100 chr2B 90.000 180 16 2 293 471 45647934 45647756 5.800000e-57 231.0
20 TraesCS2D01G067100 chr2B 83.471 121 14 5 2022 2138 251374812 251374930 1.020000e-19 108.0
21 TraesCS2D01G067100 chr2B 100.000 41 0 0 719 759 45645119 45645079 2.880000e-10 76.8
22 TraesCS2D01G067100 chr2B 95.122 41 2 0 719 759 44943123 44943083 6.230000e-07 65.8
23 TraesCS2D01G067100 chr3B 93.607 219 12 1 1 217 489694137 489693919 2.590000e-85 326.0
24 TraesCS2D01G067100 chr3B 82.576 132 15 6 2013 2138 647906928 647907057 2.840000e-20 110.0
25 TraesCS2D01G067100 chr7D 93.519 216 12 1 1 214 631022773 631022988 1.200000e-83 320.0
26 TraesCS2D01G067100 chr7D 92.694 219 14 1 1 217 20424156 20423938 5.600000e-82 315.0
27 TraesCS2D01G067100 chr7A 93.056 216 13 1 1 214 287486346 287486561 5.600000e-82 315.0
28 TraesCS2D01G067100 chr1D 92.694 219 14 1 1 217 211805731 211805513 5.600000e-82 315.0
29 TraesCS2D01G067100 chr1D 80.800 125 16 6 2020 2138 246649978 246650100 1.030000e-14 91.6
30 TraesCS2D01G067100 chr5D 92.627 217 14 1 1 215 542299319 542299103 7.250000e-81 311.0
31 TraesCS2D01G067100 chr1B 92.958 213 13 1 1 211 211634209 211634421 2.610000e-80 309.0
32 TraesCS2D01G067100 chr1A 92.593 216 14 1 1 214 23030204 23030419 2.610000e-80 309.0
33 TraesCS2D01G067100 chr1A 80.620 129 18 5 2015 2138 395177608 395177482 2.860000e-15 93.5
34 TraesCS2D01G067100 chr5A 82.787 122 15 5 2022 2138 303399812 303399932 1.320000e-18 104.0
35 TraesCS2D01G067100 chr6B 82.500 120 16 4 2023 2138 183308246 183308364 1.710000e-17 100.0
36 TraesCS2D01G067100 chr6B 81.818 121 16 4 2023 2138 209587388 209587507 2.210000e-16 97.1
37 TraesCS2D01G067100 chr4A 81.818 121 15 7 2023 2138 703266008 703265890 7.950000e-16 95.3
38 TraesCS2D01G067100 chr4B 80.992 121 17 4 2023 2138 438375181 438375300 1.030000e-14 91.6


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 TraesCS2D01G067100 chr2D 28047691 28050386 2695 False 4979.00 4979 100.00000 1 2696 1 chr2D.!!$F1 2695
1 TraesCS2D01G067100 chr2D 28057482 28058590 1108 False 601.50 798 87.55550 1631 2690 2 chr2D.!!$F3 1059
2 TraesCS2D01G067100 chr2D 28407302 28408221 919 False 521.45 955 91.23400 701 1506 2 chr2D.!!$F5 805
3 TraesCS2D01G067100 chr2D 28099228 28099813 585 False 325.90 575 93.85950 719 1302 2 chr2D.!!$F4 583
4 TraesCS2D01G067100 chr2A 30221812 30223502 1690 False 868.00 1050 90.53700 278 1612 2 chr2A.!!$F1 1334
5 TraesCS2D01G067100 chr2B 45608098 45608816 718 False 900.00 900 89.23700 777 1506 1 chr2B.!!$F1 729
6 TraesCS2D01G067100 chr2B 45629796 45630605 809 True 623.00 623 81.24200 1898 2685 1 chr2B.!!$R1 787
7 TraesCS2D01G067100 chr2B 44942303 44943123 820 True 513.40 961 92.81850 719 1506 2 chr2B.!!$R4 787
8 TraesCS2D01G067100 chr2B 44931553 44932557 1004 True 402.50 420 83.85850 1631 2685 2 chr2B.!!$R3 1054
9 TraesCS2D01G067100 chr2B 45641661 45647934 6273 True 326.45 765 92.55675 293 1506 4 chr2B.!!$R5 1213

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
95 96 0.039437 ACTACGAGCACCAACACGAG 60.039 55.0 0.00 0.0 0.0 4.18 F
120 121 0.108567 GAAGACCGGAGAGAAGTGCC 60.109 60.0 9.46 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 6884 0.105964 TGACTTCCAGTGAACGTGGG 59.894 55.0 0.00 0.0 35.58 4.61 R
1826 7095 0.181824 GGGGCCCGTCAAGCTTATTA 59.818 55.0 17.79 0.0 0.00 0.98 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
19 20 4.760047 CCAACCGGAGCCGACCAG 62.760 72.222 9.46 0.00 42.83 4.00
24 25 4.697756 CGGAGCCGACCAGCCAAA 62.698 66.667 2.00 0.00 42.83 3.28
25 26 3.056328 GGAGCCGACCAGCCAAAC 61.056 66.667 0.00 0.00 0.00 2.93
26 27 3.056328 GAGCCGACCAGCCAAACC 61.056 66.667 0.00 0.00 0.00 3.27
27 28 3.842925 GAGCCGACCAGCCAAACCA 62.843 63.158 0.00 0.00 0.00 3.67
28 29 3.670377 GCCGACCAGCCAAACCAC 61.670 66.667 0.00 0.00 0.00 4.16
29 30 2.983592 CCGACCAGCCAAACCACC 60.984 66.667 0.00 0.00 0.00 4.61
30 31 3.353836 CGACCAGCCAAACCACCG 61.354 66.667 0.00 0.00 0.00 4.94
31 32 3.670377 GACCAGCCAAACCACCGC 61.670 66.667 0.00 0.00 0.00 5.68
35 36 4.531426 AGCCAAACCACCGCCCAA 62.531 61.111 0.00 0.00 0.00 4.12
36 37 4.293648 GCCAAACCACCGCCCAAC 62.294 66.667 0.00 0.00 0.00 3.77
37 38 2.835431 CCAAACCACCGCCCAACA 60.835 61.111 0.00 0.00 0.00 3.33
38 39 2.415426 CAAACCACCGCCCAACAC 59.585 61.111 0.00 0.00 0.00 3.32
39 40 2.835895 AAACCACCGCCCAACACC 60.836 61.111 0.00 0.00 0.00 4.16
40 41 3.663815 AAACCACCGCCCAACACCA 62.664 57.895 0.00 0.00 0.00 4.17
41 42 2.937959 AAACCACCGCCCAACACCAT 62.938 55.000 0.00 0.00 0.00 3.55
42 43 3.372730 CCACCGCCCAACACCATG 61.373 66.667 0.00 0.00 0.00 3.66
43 44 4.054825 CACCGCCCAACACCATGC 62.055 66.667 0.00 0.00 0.00 4.06
48 49 3.069946 CCCAACACCATGCGCCAT 61.070 61.111 4.18 0.00 0.00 4.40
49 50 2.491152 CCAACACCATGCGCCATC 59.509 61.111 4.18 0.00 0.00 3.51
50 51 2.100797 CAACACCATGCGCCATCG 59.899 61.111 4.18 0.00 39.07 3.84
76 77 4.100084 CCGCCACCCATGCTCTCA 62.100 66.667 0.00 0.00 0.00 3.27
77 78 2.821366 CGCCACCCATGCTCTCAC 60.821 66.667 0.00 0.00 0.00 3.51
78 79 2.673523 GCCACCCATGCTCTCACT 59.326 61.111 0.00 0.00 0.00 3.41
79 80 1.907739 GCCACCCATGCTCTCACTA 59.092 57.895 0.00 0.00 0.00 2.74
80 81 0.462759 GCCACCCATGCTCTCACTAC 60.463 60.000 0.00 0.00 0.00 2.73
81 82 0.179100 CCACCCATGCTCTCACTACG 60.179 60.000 0.00 0.00 0.00 3.51
82 83 0.817654 CACCCATGCTCTCACTACGA 59.182 55.000 0.00 0.00 0.00 3.43
83 84 1.107114 ACCCATGCTCTCACTACGAG 58.893 55.000 0.00 0.00 43.80 4.18
90 91 1.983972 CTCTCACTACGAGCACCAAC 58.016 55.000 0.00 0.00 41.98 3.77
91 92 1.269723 CTCTCACTACGAGCACCAACA 59.730 52.381 0.00 0.00 41.98 3.33
92 93 1.000607 TCTCACTACGAGCACCAACAC 60.001 52.381 0.00 0.00 41.98 3.32
93 94 0.318360 TCACTACGAGCACCAACACG 60.318 55.000 0.00 0.00 0.00 4.49
94 95 0.318360 CACTACGAGCACCAACACGA 60.318 55.000 0.00 0.00 0.00 4.35
95 96 0.039437 ACTACGAGCACCAACACGAG 60.039 55.000 0.00 0.00 0.00 4.18
96 97 0.732880 CTACGAGCACCAACACGAGG 60.733 60.000 0.00 0.00 0.00 4.63
97 98 2.758770 TACGAGCACCAACACGAGGC 62.759 60.000 0.00 0.00 0.00 4.70
98 99 3.050275 GAGCACCAACACGAGGCC 61.050 66.667 0.00 0.00 0.00 5.19
99 100 3.825160 GAGCACCAACACGAGGCCA 62.825 63.158 5.01 0.00 0.00 5.36
100 101 2.904866 GCACCAACACGAGGCCAA 60.905 61.111 5.01 0.00 0.00 4.52
101 102 2.908073 GCACCAACACGAGGCCAAG 61.908 63.158 5.01 0.00 0.00 3.61
102 103 1.227823 CACCAACACGAGGCCAAGA 60.228 57.895 5.01 0.00 0.00 3.02
103 104 0.817634 CACCAACACGAGGCCAAGAA 60.818 55.000 5.01 0.00 0.00 2.52
104 105 0.535102 ACCAACACGAGGCCAAGAAG 60.535 55.000 5.01 0.00 0.00 2.85
105 106 0.250295 CCAACACGAGGCCAAGAAGA 60.250 55.000 5.01 0.00 0.00 2.87
106 107 0.868406 CAACACGAGGCCAAGAAGAC 59.132 55.000 5.01 0.00 0.00 3.01
107 108 0.250338 AACACGAGGCCAAGAAGACC 60.250 55.000 5.01 0.00 0.00 3.85
108 109 1.738099 CACGAGGCCAAGAAGACCG 60.738 63.158 5.01 0.00 0.00 4.79
109 110 2.125512 CGAGGCCAAGAAGACCGG 60.126 66.667 5.01 0.00 0.00 5.28
110 111 2.646175 CGAGGCCAAGAAGACCGGA 61.646 63.158 9.46 0.00 0.00 5.14
111 112 1.219393 GAGGCCAAGAAGACCGGAG 59.781 63.158 9.46 0.00 0.00 4.63
112 113 1.229209 AGGCCAAGAAGACCGGAGA 60.229 57.895 9.46 0.00 0.00 3.71
113 114 1.219393 GGCCAAGAAGACCGGAGAG 59.781 63.158 9.46 0.00 0.00 3.20
114 115 1.258445 GGCCAAGAAGACCGGAGAGA 61.258 60.000 9.46 0.00 0.00 3.10
115 116 0.608640 GCCAAGAAGACCGGAGAGAA 59.391 55.000 9.46 0.00 0.00 2.87
116 117 1.404851 GCCAAGAAGACCGGAGAGAAG 60.405 57.143 9.46 0.00 0.00 2.85
117 118 1.896465 CCAAGAAGACCGGAGAGAAGT 59.104 52.381 9.46 0.00 0.00 3.01
118 119 2.353208 CCAAGAAGACCGGAGAGAAGTG 60.353 54.545 9.46 0.00 0.00 3.16
119 120 0.892063 AGAAGACCGGAGAGAAGTGC 59.108 55.000 9.46 0.00 0.00 4.40
120 121 0.108567 GAAGACCGGAGAGAAGTGCC 60.109 60.000 9.46 0.00 0.00 5.01
121 122 0.832135 AAGACCGGAGAGAAGTGCCA 60.832 55.000 9.46 0.00 0.00 4.92
122 123 0.832135 AGACCGGAGAGAAGTGCCAA 60.832 55.000 9.46 0.00 0.00 4.52
123 124 0.390472 GACCGGAGAGAAGTGCCAAG 60.390 60.000 9.46 0.00 0.00 3.61
124 125 1.743252 CCGGAGAGAAGTGCCAAGC 60.743 63.158 0.00 0.00 0.00 4.01
125 126 2.097038 CGGAGAGAAGTGCCAAGCG 61.097 63.158 0.00 0.00 0.00 4.68
126 127 1.293498 GGAGAGAAGTGCCAAGCGA 59.707 57.895 0.00 0.00 0.00 4.93
127 128 1.016653 GGAGAGAAGTGCCAAGCGAC 61.017 60.000 0.00 0.00 0.00 5.19
128 129 1.347817 GAGAGAAGTGCCAAGCGACG 61.348 60.000 0.00 0.00 0.00 5.12
129 130 2.357517 AGAAGTGCCAAGCGACGG 60.358 61.111 0.00 0.00 0.00 4.79
130 131 3.423154 GAAGTGCCAAGCGACGGG 61.423 66.667 0.00 0.00 0.00 5.28
131 132 3.876589 GAAGTGCCAAGCGACGGGA 62.877 63.158 0.00 0.00 0.00 5.14
132 133 3.883744 AAGTGCCAAGCGACGGGAG 62.884 63.158 0.00 0.00 0.00 4.30
136 137 3.423154 CCAAGCGACGGGAGCAAC 61.423 66.667 0.00 0.00 37.01 4.17
137 138 2.664851 CAAGCGACGGGAGCAACA 60.665 61.111 0.00 0.00 37.01 3.33
138 139 2.110213 AAGCGACGGGAGCAACAA 59.890 55.556 0.00 0.00 37.01 2.83
139 140 2.251642 AAGCGACGGGAGCAACAAC 61.252 57.895 0.00 0.00 37.01 3.32
140 141 2.933878 AAGCGACGGGAGCAACAACA 62.934 55.000 0.00 0.00 37.01 3.33
141 142 2.935955 CGACGGGAGCAACAACAC 59.064 61.111 0.00 0.00 0.00 3.32
142 143 2.604174 CGACGGGAGCAACAACACC 61.604 63.158 0.00 0.00 0.00 4.16
143 144 1.525077 GACGGGAGCAACAACACCA 60.525 57.895 0.00 0.00 0.00 4.17
144 145 1.077357 ACGGGAGCAACAACACCAA 60.077 52.632 0.00 0.00 0.00 3.67
145 146 1.101049 ACGGGAGCAACAACACCAAG 61.101 55.000 0.00 0.00 0.00 3.61
146 147 1.795170 CGGGAGCAACAACACCAAGG 61.795 60.000 0.00 0.00 0.00 3.61
147 148 1.363807 GGAGCAACAACACCAAGGC 59.636 57.895 0.00 0.00 0.00 4.35
148 149 1.363807 GAGCAACAACACCAAGGCC 59.636 57.895 0.00 0.00 0.00 5.19
149 150 2.027460 GCAACAACACCAAGGCCG 59.973 61.111 0.00 0.00 0.00 6.13
150 151 2.485795 GCAACAACACCAAGGCCGA 61.486 57.895 0.00 0.00 0.00 5.54
151 152 1.654220 CAACAACACCAAGGCCGAG 59.346 57.895 0.00 0.00 0.00 4.63
152 153 2.193536 AACAACACCAAGGCCGAGC 61.194 57.895 0.00 0.00 0.00 5.03
153 154 3.726517 CAACACCAAGGCCGAGCG 61.727 66.667 0.00 0.00 0.00 5.03
175 176 2.046604 GGAACCACCTACACCGCC 60.047 66.667 0.00 0.00 35.41 6.13
176 177 2.433664 GAACCACCTACACCGCCG 60.434 66.667 0.00 0.00 0.00 6.46
177 178 3.230522 GAACCACCTACACCGCCGT 62.231 63.158 0.00 0.00 0.00 5.68
178 179 1.876497 GAACCACCTACACCGCCGTA 61.876 60.000 0.00 0.00 0.00 4.02
179 180 1.880819 AACCACCTACACCGCCGTAG 61.881 60.000 3.22 3.22 38.90 3.51
180 181 2.345760 CCACCTACACCGCCGTAGT 61.346 63.158 8.21 0.00 37.72 2.73
181 182 1.153901 CACCTACACCGCCGTAGTG 60.154 63.158 8.21 0.00 37.72 2.74
182 183 2.202703 CCTACACCGCCGTAGTGC 60.203 66.667 8.21 0.00 38.87 4.40
190 191 4.874977 GCCGTAGTGCGAGAGGCC 62.875 72.222 0.81 0.00 44.77 5.19
191 192 4.208686 CCGTAGTGCGAGAGGCCC 62.209 72.222 0.81 0.00 44.77 5.80
192 193 4.554363 CGTAGTGCGAGAGGCCCG 62.554 72.222 0.00 0.00 44.77 6.13
193 194 3.450115 GTAGTGCGAGAGGCCCGT 61.450 66.667 0.00 0.00 42.61 5.28
194 195 3.449227 TAGTGCGAGAGGCCCGTG 61.449 66.667 0.00 0.00 42.61 4.94
221 222 3.784412 CCGTCGCGGTCGCATTTT 61.784 61.111 15.68 0.00 42.73 1.82
222 223 2.570581 CGTCGCGGTCGCATTTTG 60.571 61.111 15.68 0.00 42.06 2.44
223 224 2.554272 GTCGCGGTCGCATTTTGT 59.446 55.556 15.68 0.00 42.06 2.83
224 225 1.082366 GTCGCGGTCGCATTTTGTT 60.082 52.632 15.68 0.00 42.06 2.83
225 226 1.082431 TCGCGGTCGCATTTTGTTG 60.082 52.632 15.68 0.00 42.06 3.33
226 227 1.369930 CGCGGTCGCATTTTGTTGT 60.370 52.632 15.68 0.00 42.06 3.32
227 228 1.595982 CGCGGTCGCATTTTGTTGTG 61.596 55.000 15.68 0.00 42.06 3.33
228 229 1.274798 GCGGTCGCATTTTGTTGTGG 61.275 55.000 10.67 0.00 41.49 4.17
229 230 0.309302 CGGTCGCATTTTGTTGTGGA 59.691 50.000 0.00 0.00 0.00 4.02
230 231 1.068610 CGGTCGCATTTTGTTGTGGAT 60.069 47.619 0.00 0.00 0.00 3.41
231 232 2.595386 GGTCGCATTTTGTTGTGGATC 58.405 47.619 0.00 0.00 0.00 3.36
232 233 2.228822 GGTCGCATTTTGTTGTGGATCT 59.771 45.455 0.00 0.00 0.00 2.75
233 234 3.305335 GGTCGCATTTTGTTGTGGATCTT 60.305 43.478 0.00 0.00 0.00 2.40
234 235 4.298332 GTCGCATTTTGTTGTGGATCTTT 58.702 39.130 0.00 0.00 0.00 2.52
235 236 4.744631 GTCGCATTTTGTTGTGGATCTTTT 59.255 37.500 0.00 0.00 0.00 2.27
236 237 4.981674 TCGCATTTTGTTGTGGATCTTTTC 59.018 37.500 0.00 0.00 0.00 2.29
237 238 4.150451 CGCATTTTGTTGTGGATCTTTTCC 59.850 41.667 0.00 0.00 45.69 3.13
238 239 4.452114 GCATTTTGTTGTGGATCTTTTCCC 59.548 41.667 0.00 0.00 44.77 3.97
239 240 5.609423 CATTTTGTTGTGGATCTTTTCCCA 58.391 37.500 0.00 0.00 44.77 4.37
240 241 5.885449 TTTTGTTGTGGATCTTTTCCCAT 57.115 34.783 0.00 0.00 44.77 4.00
241 242 5.885449 TTTGTTGTGGATCTTTTCCCATT 57.115 34.783 0.00 0.00 44.77 3.16
242 243 5.885449 TTGTTGTGGATCTTTTCCCATTT 57.115 34.783 0.00 0.00 44.77 2.32
243 244 5.212532 TGTTGTGGATCTTTTCCCATTTG 57.787 39.130 0.00 0.00 44.77 2.32
244 245 3.959535 TGTGGATCTTTTCCCATTTGC 57.040 42.857 0.00 0.00 44.77 3.68
245 246 3.237746 TGTGGATCTTTTCCCATTTGCA 58.762 40.909 0.00 0.00 44.77 4.08
246 247 3.839490 TGTGGATCTTTTCCCATTTGCAT 59.161 39.130 0.00 0.00 44.77 3.96
247 248 4.186159 GTGGATCTTTTCCCATTTGCATG 58.814 43.478 0.00 0.00 44.77 4.06
257 258 3.088194 CCATTTGCATGGTAGCATGTC 57.912 47.619 29.91 23.03 44.81 3.06
258 259 2.542205 CCATTTGCATGGTAGCATGTCG 60.542 50.000 29.91 16.49 44.81 4.35
259 260 2.106477 TTTGCATGGTAGCATGTCGA 57.894 45.000 29.91 20.58 45.19 4.20
260 261 1.655484 TTGCATGGTAGCATGTCGAG 58.345 50.000 29.91 10.22 45.19 4.04
261 262 0.179076 TGCATGGTAGCATGTCGAGG 60.179 55.000 29.91 9.56 40.11 4.63
262 263 0.179073 GCATGGTAGCATGTCGAGGT 60.179 55.000 29.91 0.00 35.16 3.85
263 264 1.575244 CATGGTAGCATGTCGAGGTG 58.425 55.000 23.73 0.30 0.00 4.00
264 265 1.134699 CATGGTAGCATGTCGAGGTGT 60.135 52.381 23.73 0.00 0.00 4.16
265 266 0.530744 TGGTAGCATGTCGAGGTGTC 59.469 55.000 0.00 0.00 0.00 3.67
266 267 0.179108 GGTAGCATGTCGAGGTGTCC 60.179 60.000 0.00 0.00 0.00 4.02
267 268 0.818296 GTAGCATGTCGAGGTGTCCT 59.182 55.000 0.00 0.00 36.03 3.85
268 269 1.204941 GTAGCATGTCGAGGTGTCCTT 59.795 52.381 0.00 0.00 31.76 3.36
269 270 0.687354 AGCATGTCGAGGTGTCCTTT 59.313 50.000 0.00 0.00 31.76 3.11
270 271 1.072331 AGCATGTCGAGGTGTCCTTTT 59.928 47.619 0.00 0.00 31.76 2.27
271 272 1.464997 GCATGTCGAGGTGTCCTTTTC 59.535 52.381 0.00 0.00 31.76 2.29
272 273 2.076863 CATGTCGAGGTGTCCTTTTCC 58.923 52.381 0.00 0.00 31.76 3.13
273 274 1.124780 TGTCGAGGTGTCCTTTTCCA 58.875 50.000 0.00 0.00 31.76 3.53
274 275 1.697432 TGTCGAGGTGTCCTTTTCCAT 59.303 47.619 0.00 0.00 31.76 3.41
275 276 2.289444 TGTCGAGGTGTCCTTTTCCATC 60.289 50.000 0.00 0.00 31.76 3.51
276 277 1.278127 TCGAGGTGTCCTTTTCCATCC 59.722 52.381 0.00 0.00 31.76 3.51
382 385 8.691661 TCCTTAGAAATTTATTCTATGGTGGC 57.308 34.615 20.56 0.00 42.41 5.01
447 450 6.266103 CCAATAGGACTCATTTGCACCATATT 59.734 38.462 0.00 0.00 36.89 1.28
481 484 8.608844 AGTTTTCTATACACTCAAACCTCTTG 57.391 34.615 0.00 0.00 0.00 3.02
497 500 6.487299 ACCTCTTGGTAGAATTCCTGTATC 57.513 41.667 0.65 0.00 46.43 2.24
504 507 6.889198 TGGTAGAATTCCTGTATCTTTCCTG 58.111 40.000 0.65 0.00 0.00 3.86
518 522 8.590204 TGTATCTTTCCTGTACTATCAAACACA 58.410 33.333 0.00 0.00 0.00 3.72
523 527 5.790593 TCCTGTACTATCAAACACACTTCC 58.209 41.667 0.00 0.00 0.00 3.46
529 533 9.865321 TGTACTATCAAACACACTTCCTATAAC 57.135 33.333 0.00 0.00 0.00 1.89
568 572 2.710471 TCATGCAGGATACAATAGGGCA 59.290 45.455 0.00 0.00 41.41 5.36
581 585 9.372369 GATACAATAGGGCATGTTACTCTATTC 57.628 37.037 2.05 0.00 30.85 1.75
590 594 5.297029 GCATGTTACTCTATTCCTGGGTTTC 59.703 44.000 0.00 0.00 0.00 2.78
648 652 5.238006 ACTAGCAGACGAGTCTTTGTATC 57.762 43.478 2.55 0.00 37.98 2.24
773 3219 0.326238 AGGATCGGGGCAGGAAAGTA 60.326 55.000 0.00 0.00 0.00 2.24
809 5063 5.204409 TCAAAATGTCAAGATTTGCTGCT 57.796 34.783 0.00 0.00 34.77 4.24
810 5064 6.330004 TCAAAATGTCAAGATTTGCTGCTA 57.670 33.333 0.00 0.00 34.77 3.49
830 5084 9.205719 GCTGCTATACATGAGATGGAATATATG 57.794 37.037 0.00 0.00 33.60 1.78
906 5169 6.776094 AGCAGTAGTTTATTCTTTCAATCGC 58.224 36.000 0.00 0.00 0.00 4.58
937 6190 4.696479 ATAGGGCAAGTCCAACATCTAG 57.304 45.455 0.00 0.00 36.21 2.43
960 6221 5.889853 AGTCCTACTTATACCATTCACACGA 59.110 40.000 0.00 0.00 0.00 4.35
1027 6293 1.204941 CTACGGAAACCACTAGCAGCT 59.795 52.381 0.00 0.00 0.00 4.24
1083 6349 2.284625 TCCAGCCACATCGGACCT 60.285 61.111 0.00 0.00 36.56 3.85
1101 6367 3.909258 TTTCACCGAGCTCGCCGTC 62.909 63.158 30.49 0.00 38.18 4.79
1187 6453 3.851845 TTGTCCGGTCGTTGCTCCG 62.852 63.158 0.00 0.00 45.42 4.63
1208 6474 3.794270 GCACGAGAATGCGGCTAA 58.206 55.556 0.00 0.00 35.50 3.09
1224 6493 3.869473 TAACGGCGGCACACCTGTC 62.869 63.158 13.24 0.00 0.00 3.51
1285 6554 1.906824 AAGGGCGTCGAGAACCTCA 60.907 57.895 0.00 0.00 31.69 3.86
1292 6561 4.421479 CGAGAACCTCAGCGCGGT 62.421 66.667 4.23 4.23 35.97 5.68
1296 6565 3.642778 GAACCTCAGCGCGGTAGCA 62.643 63.158 11.92 0.00 45.49 3.49
1519 6788 3.763356 ATCTCACGCTGGCGCTCA 61.763 61.111 15.04 2.39 44.19 4.26
1536 6805 3.588955 GCTCATTTCCAATTCCAACACC 58.411 45.455 0.00 0.00 0.00 4.16
1537 6806 3.006752 GCTCATTTCCAATTCCAACACCA 59.993 43.478 0.00 0.00 0.00 4.17
1538 6807 4.502950 GCTCATTTCCAATTCCAACACCAA 60.503 41.667 0.00 0.00 0.00 3.67
1539 6808 4.954875 TCATTTCCAATTCCAACACCAAC 58.045 39.130 0.00 0.00 0.00 3.77
1540 6809 4.406972 TCATTTCCAATTCCAACACCAACA 59.593 37.500 0.00 0.00 0.00 3.33
1541 6810 5.071519 TCATTTCCAATTCCAACACCAACAT 59.928 36.000 0.00 0.00 0.00 2.71
1549 6818 3.560105 TCCAACACCAACATCAACATCA 58.440 40.909 0.00 0.00 0.00 3.07
1612 6881 0.678684 TGAGATACGAGTGCCCACGA 60.679 55.000 0.00 0.00 36.20 4.35
1613 6882 0.669077 GAGATACGAGTGCCCACGAT 59.331 55.000 0.00 0.00 36.20 3.73
1614 6883 0.385751 AGATACGAGTGCCCACGATG 59.614 55.000 0.00 0.00 36.20 3.84
1615 6884 1.215655 GATACGAGTGCCCACGATGC 61.216 60.000 0.00 0.00 36.20 3.91
1616 6885 2.644555 ATACGAGTGCCCACGATGCC 62.645 60.000 0.00 0.00 36.20 4.40
1618 6887 4.408821 GAGTGCCCACGATGCCCA 62.409 66.667 0.00 0.00 36.20 5.36
1619 6888 4.722700 AGTGCCCACGATGCCCAC 62.723 66.667 0.00 0.00 36.20 4.61
1623 6892 3.124921 CCCACGATGCCCACGTTC 61.125 66.667 0.00 0.00 42.07 3.95
1624 6893 2.358125 CCACGATGCCCACGTTCA 60.358 61.111 0.00 0.00 42.07 3.18
1625 6894 2.677003 CCACGATGCCCACGTTCAC 61.677 63.158 0.00 0.00 42.07 3.18
1626 6895 1.667830 CACGATGCCCACGTTCACT 60.668 57.895 0.00 0.00 42.07 3.41
1627 6896 1.667830 ACGATGCCCACGTTCACTG 60.668 57.895 0.00 0.00 41.18 3.66
1628 6897 2.390599 CGATGCCCACGTTCACTGG 61.391 63.158 0.00 0.00 0.00 4.00
1629 6898 1.003839 GATGCCCACGTTCACTGGA 60.004 57.895 0.00 0.00 0.00 3.86
1648 6917 3.450817 TGGAAGTCAGTGTCTCACTTTGA 59.549 43.478 0.00 0.00 42.59 2.69
1776 7045 3.469863 GACCCGTCCAACTGCCACA 62.470 63.158 0.00 0.00 0.00 4.17
1826 7095 1.199097 GGGCGACGTGACATTTTGAAT 59.801 47.619 0.00 0.00 0.00 2.57
1834 7103 7.180079 CGACGTGACATTTTGAATAATAAGCT 58.820 34.615 0.00 0.00 0.00 3.74
1969 7289 7.170393 TGTTATCATAGGAACATAGGATCGG 57.830 40.000 0.00 0.00 30.72 4.18
1972 7292 4.087182 TCATAGGAACATAGGATCGGTCC 58.913 47.826 6.61 6.61 45.45 4.46
2011 7331 7.046033 GTGCATGAGATATATGTGATCATCCA 58.954 38.462 0.00 0.00 35.70 3.41
2012 7332 7.715686 GTGCATGAGATATATGTGATCATCCAT 59.284 37.037 0.00 0.94 35.70 3.41
2013 7333 7.715249 TGCATGAGATATATGTGATCATCCATG 59.285 37.037 0.00 8.33 35.70 3.66
2035 7355 0.822164 CCGACGTACTCCCTCCATTT 59.178 55.000 0.00 0.00 0.00 2.32
2109 7437 4.370364 AGTGTGTTTGTTCGCTCATTTT 57.630 36.364 0.00 0.00 0.00 1.82
2113 7441 5.741982 GTGTGTTTGTTCGCTCATTTTAGTT 59.258 36.000 0.00 0.00 0.00 2.24
2114 7442 5.741510 TGTGTTTGTTCGCTCATTTTAGTTG 59.258 36.000 0.00 0.00 0.00 3.16
2207 7545 1.066587 GCCAGCTAGCTACAGTCCG 59.933 63.158 18.86 2.66 0.00 4.79
2302 7640 1.815003 CGCAGGAATGGATGACGCA 60.815 57.895 0.00 0.00 0.00 5.24
2315 7653 2.579201 ACGCAGTGATAGCCGCTT 59.421 55.556 0.00 0.00 42.51 4.68
2330 7668 0.025001 CGCTTCACTTAACGCATCGG 59.975 55.000 0.00 0.00 0.00 4.18
2346 7684 1.002134 CGGTTCACCTTGGAGGCAT 60.002 57.895 0.00 0.00 39.63 4.40
2348 7686 0.329596 GGTTCACCTTGGAGGCATCT 59.670 55.000 0.00 0.00 39.63 2.90
2458 7813 2.409651 CTAGCGTCCACGAGCTCC 59.590 66.667 8.47 0.00 43.44 4.70
2490 7845 6.270096 GGTAACTCTACATAAACATGACGC 57.730 41.667 0.00 0.00 0.00 5.19
2491 7846 5.051907 GGTAACTCTACATAAACATGACGCG 60.052 44.000 3.53 3.53 0.00 6.01
2492 7847 3.444916 ACTCTACATAAACATGACGCGG 58.555 45.455 12.47 0.00 0.00 6.46
2496 7851 3.241067 ACATAAACATGACGCGGTAGT 57.759 42.857 12.47 0.00 0.00 2.73
2497 7852 2.927477 ACATAAACATGACGCGGTAGTG 59.073 45.455 12.47 6.27 0.00 2.74
2500 7855 0.034337 AACATGACGCGGTAGTGGTT 59.966 50.000 12.47 4.12 0.00 3.67
2501 7856 0.889994 ACATGACGCGGTAGTGGTTA 59.110 50.000 12.47 0.00 0.00 2.85
2510 7865 3.740115 GCGGTAGTGGTTATTCATCCAT 58.260 45.455 0.00 0.00 36.09 3.41
2526 7881 0.180171 CCATGGGCGATCAAGGTACA 59.820 55.000 2.85 0.00 0.00 2.90
2528 7883 2.575532 CATGGGCGATCAAGGTACATT 58.424 47.619 0.00 0.00 0.00 2.71
2558 7913 1.154263 GAGGTCCTCGTTGTCGTCG 60.154 63.158 2.28 0.00 38.33 5.12
2563 7918 2.050351 CTCGTTGTCGTCGTGCCT 60.050 61.111 0.00 0.00 38.33 4.75
2587 7942 1.464687 CGCTGCAATTTTGGACGAGAG 60.465 52.381 0.00 0.00 0.00 3.20
2603 7958 1.373497 GAGGCCAGTGTCACAGTCG 60.373 63.158 5.01 0.00 0.00 4.18
2613 7968 0.104304 GTCACAGTCGGGTCAGTTGT 59.896 55.000 0.00 0.00 0.00 3.32
2682 8039 2.214376 TAAAATGTGACAGCCCTGGG 57.786 50.000 8.86 8.86 34.19 4.45
2686 8043 0.706433 ATGTGACAGCCCTGGGAAAT 59.294 50.000 19.27 0.00 34.19 2.17
2690 8047 1.707989 TGACAGCCCTGGGAAATAACA 59.292 47.619 19.27 5.33 34.19 2.41
2691 8048 2.092323 GACAGCCCTGGGAAATAACAC 58.908 52.381 19.27 0.00 34.19 3.32
2692 8049 1.710809 ACAGCCCTGGGAAATAACACT 59.289 47.619 19.27 0.00 34.19 3.55
2693 8050 2.916934 ACAGCCCTGGGAAATAACACTA 59.083 45.455 19.27 0.00 34.19 2.74
2694 8051 3.054361 ACAGCCCTGGGAAATAACACTAG 60.054 47.826 19.27 0.00 34.19 2.57
2695 8052 3.054361 CAGCCCTGGGAAATAACACTAGT 60.054 47.826 19.27 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.760047 CTGGTCGGCTCCGGTTGG 62.760 72.222 8.59 0.00 40.25 3.77
7 8 4.697756 TTTGGCTGGTCGGCTCCG 62.698 66.667 1.14 1.14 39.32 4.63
8 9 3.056328 GTTTGGCTGGTCGGCTCC 61.056 66.667 1.58 0.00 39.32 4.70
9 10 3.056328 GGTTTGGCTGGTCGGCTC 61.056 66.667 1.58 0.00 39.32 4.70
11 12 3.670377 GTGGTTTGGCTGGTCGGC 61.670 66.667 0.00 0.00 38.97 5.54
12 13 2.983592 GGTGGTTTGGCTGGTCGG 60.984 66.667 0.00 0.00 0.00 4.79
13 14 3.353836 CGGTGGTTTGGCTGGTCG 61.354 66.667 0.00 0.00 0.00 4.79
14 15 3.670377 GCGGTGGTTTGGCTGGTC 61.670 66.667 0.00 0.00 0.00 4.02
18 19 4.531426 TTGGGCGGTGGTTTGGCT 62.531 61.111 0.00 0.00 0.00 4.75
19 20 4.293648 GTTGGGCGGTGGTTTGGC 62.294 66.667 0.00 0.00 0.00 4.52
20 21 2.835431 TGTTGGGCGGTGGTTTGG 60.835 61.111 0.00 0.00 0.00 3.28
21 22 2.415426 GTGTTGGGCGGTGGTTTG 59.585 61.111 0.00 0.00 0.00 2.93
22 23 2.835895 GGTGTTGGGCGGTGGTTT 60.836 61.111 0.00 0.00 0.00 3.27
23 24 3.444818 ATGGTGTTGGGCGGTGGTT 62.445 57.895 0.00 0.00 0.00 3.67
24 25 3.897122 ATGGTGTTGGGCGGTGGT 61.897 61.111 0.00 0.00 0.00 4.16
25 26 3.372730 CATGGTGTTGGGCGGTGG 61.373 66.667 0.00 0.00 0.00 4.61
26 27 4.054825 GCATGGTGTTGGGCGGTG 62.055 66.667 0.00 0.00 0.00 4.94
31 32 3.067480 GATGGCGCATGGTGTTGGG 62.067 63.158 10.83 0.00 0.00 4.12
32 33 2.491152 GATGGCGCATGGTGTTGG 59.509 61.111 10.83 0.00 0.00 3.77
33 34 2.100797 CGATGGCGCATGGTGTTG 59.899 61.111 10.83 0.00 0.00 3.33
59 60 4.100084 TGAGAGCATGGGTGGCGG 62.100 66.667 0.00 0.00 36.08 6.13
60 61 1.960040 TAGTGAGAGCATGGGTGGCG 61.960 60.000 0.00 0.00 36.08 5.69
61 62 0.462759 GTAGTGAGAGCATGGGTGGC 60.463 60.000 0.00 0.00 0.00 5.01
62 63 0.179100 CGTAGTGAGAGCATGGGTGG 60.179 60.000 0.00 0.00 0.00 4.61
63 64 0.817654 TCGTAGTGAGAGCATGGGTG 59.182 55.000 0.00 0.00 0.00 4.61
64 65 3.283020 TCGTAGTGAGAGCATGGGT 57.717 52.632 0.00 0.00 0.00 4.51
74 75 0.318360 CGTGTTGGTGCTCGTAGTGA 60.318 55.000 0.00 0.00 0.00 3.41
75 76 0.318360 TCGTGTTGGTGCTCGTAGTG 60.318 55.000 0.00 0.00 0.00 2.74
76 77 0.039437 CTCGTGTTGGTGCTCGTAGT 60.039 55.000 0.00 0.00 0.00 2.73
77 78 0.732880 CCTCGTGTTGGTGCTCGTAG 60.733 60.000 0.00 0.00 0.00 3.51
78 79 1.287815 CCTCGTGTTGGTGCTCGTA 59.712 57.895 0.00 0.00 0.00 3.43
79 80 2.029073 CCTCGTGTTGGTGCTCGT 59.971 61.111 0.00 0.00 0.00 4.18
80 81 3.414700 GCCTCGTGTTGGTGCTCG 61.415 66.667 0.00 0.00 0.00 5.03
81 82 3.050275 GGCCTCGTGTTGGTGCTC 61.050 66.667 0.00 0.00 0.00 4.26
82 83 3.414136 TTGGCCTCGTGTTGGTGCT 62.414 57.895 3.32 0.00 0.00 4.40
83 84 2.904866 TTGGCCTCGTGTTGGTGC 60.905 61.111 3.32 0.00 0.00 5.01
84 85 0.817634 TTCTTGGCCTCGTGTTGGTG 60.818 55.000 3.32 0.00 0.00 4.17
85 86 0.535102 CTTCTTGGCCTCGTGTTGGT 60.535 55.000 3.32 0.00 0.00 3.67
86 87 0.250295 TCTTCTTGGCCTCGTGTTGG 60.250 55.000 3.32 0.00 0.00 3.77
87 88 0.868406 GTCTTCTTGGCCTCGTGTTG 59.132 55.000 3.32 0.00 0.00 3.33
88 89 0.250338 GGTCTTCTTGGCCTCGTGTT 60.250 55.000 3.32 0.00 37.49 3.32
89 90 1.371558 GGTCTTCTTGGCCTCGTGT 59.628 57.895 3.32 0.00 37.49 4.49
90 91 1.738099 CGGTCTTCTTGGCCTCGTG 60.738 63.158 3.32 0.00 38.58 4.35
91 92 2.657237 CGGTCTTCTTGGCCTCGT 59.343 61.111 3.32 0.00 38.58 4.18
92 93 2.125512 CCGGTCTTCTTGGCCTCG 60.126 66.667 3.32 0.00 38.58 4.63
93 94 1.219393 CTCCGGTCTTCTTGGCCTC 59.781 63.158 3.32 0.00 38.58 4.70
94 95 1.229209 TCTCCGGTCTTCTTGGCCT 60.229 57.895 3.32 0.00 38.58 5.19
95 96 1.219393 CTCTCCGGTCTTCTTGGCC 59.781 63.158 0.00 0.00 37.00 5.36
96 97 0.608640 TTCTCTCCGGTCTTCTTGGC 59.391 55.000 0.00 0.00 0.00 4.52
97 98 1.896465 ACTTCTCTCCGGTCTTCTTGG 59.104 52.381 0.00 0.00 0.00 3.61
98 99 2.928731 GCACTTCTCTCCGGTCTTCTTG 60.929 54.545 0.00 0.00 0.00 3.02
99 100 1.273886 GCACTTCTCTCCGGTCTTCTT 59.726 52.381 0.00 0.00 0.00 2.52
100 101 0.892063 GCACTTCTCTCCGGTCTTCT 59.108 55.000 0.00 0.00 0.00 2.85
101 102 0.108567 GGCACTTCTCTCCGGTCTTC 60.109 60.000 0.00 0.00 0.00 2.87
102 103 0.832135 TGGCACTTCTCTCCGGTCTT 60.832 55.000 0.00 0.00 0.00 3.01
103 104 0.832135 TTGGCACTTCTCTCCGGTCT 60.832 55.000 0.00 0.00 0.00 3.85
104 105 0.390472 CTTGGCACTTCTCTCCGGTC 60.390 60.000 0.00 0.00 0.00 4.79
105 106 1.674057 CTTGGCACTTCTCTCCGGT 59.326 57.895 0.00 0.00 0.00 5.28
106 107 1.743252 GCTTGGCACTTCTCTCCGG 60.743 63.158 0.00 0.00 0.00 5.14
107 108 2.097038 CGCTTGGCACTTCTCTCCG 61.097 63.158 0.00 0.00 0.00 4.63
108 109 1.016653 GTCGCTTGGCACTTCTCTCC 61.017 60.000 0.00 0.00 0.00 3.71
109 110 1.347817 CGTCGCTTGGCACTTCTCTC 61.348 60.000 0.00 0.00 0.00 3.20
110 111 1.373497 CGTCGCTTGGCACTTCTCT 60.373 57.895 0.00 0.00 0.00 3.10
111 112 2.383527 CCGTCGCTTGGCACTTCTC 61.384 63.158 0.00 0.00 0.00 2.87
112 113 2.357517 CCGTCGCTTGGCACTTCT 60.358 61.111 0.00 0.00 0.00 2.85
113 114 3.423154 CCCGTCGCTTGGCACTTC 61.423 66.667 0.00 0.00 0.00 3.01
114 115 3.883744 CTCCCGTCGCTTGGCACTT 62.884 63.158 0.00 0.00 0.00 3.16
115 116 4.379243 CTCCCGTCGCTTGGCACT 62.379 66.667 0.00 0.00 0.00 4.40
119 120 3.423154 GTTGCTCCCGTCGCTTGG 61.423 66.667 0.00 0.00 0.00 3.61
120 121 2.250939 TTGTTGCTCCCGTCGCTTG 61.251 57.895 0.00 0.00 0.00 4.01
121 122 2.110213 TTGTTGCTCCCGTCGCTT 59.890 55.556 0.00 0.00 0.00 4.68
122 123 2.665185 GTTGTTGCTCCCGTCGCT 60.665 61.111 0.00 0.00 0.00 4.93
123 124 2.970324 TGTTGTTGCTCCCGTCGC 60.970 61.111 0.00 0.00 0.00 5.19
124 125 2.604174 GGTGTTGTTGCTCCCGTCG 61.604 63.158 0.00 0.00 0.00 5.12
125 126 1.098712 TTGGTGTTGTTGCTCCCGTC 61.099 55.000 0.00 0.00 0.00 4.79
126 127 1.077357 TTGGTGTTGTTGCTCCCGT 60.077 52.632 0.00 0.00 0.00 5.28
127 128 1.654220 CTTGGTGTTGTTGCTCCCG 59.346 57.895 0.00 0.00 0.00 5.14
128 129 2.041153 CCTTGGTGTTGTTGCTCCC 58.959 57.895 0.00 0.00 0.00 4.30
129 130 1.363807 GCCTTGGTGTTGTTGCTCC 59.636 57.895 0.00 0.00 0.00 4.70
130 131 1.363807 GGCCTTGGTGTTGTTGCTC 59.636 57.895 0.00 0.00 0.00 4.26
131 132 2.489275 CGGCCTTGGTGTTGTTGCT 61.489 57.895 0.00 0.00 0.00 3.91
132 133 2.027460 CGGCCTTGGTGTTGTTGC 59.973 61.111 0.00 0.00 0.00 4.17
133 134 1.654220 CTCGGCCTTGGTGTTGTTG 59.346 57.895 0.00 0.00 0.00 3.33
134 135 2.193536 GCTCGGCCTTGGTGTTGTT 61.194 57.895 0.00 0.00 0.00 2.83
135 136 2.594592 GCTCGGCCTTGGTGTTGT 60.595 61.111 0.00 0.00 0.00 3.32
136 137 3.726517 CGCTCGGCCTTGGTGTTG 61.727 66.667 0.00 0.00 0.00 3.33
148 149 4.452733 GTGGTTCCCTCCCGCTCG 62.453 72.222 0.00 0.00 0.00 5.03
149 150 4.097361 GGTGGTTCCCTCCCGCTC 62.097 72.222 0.00 0.00 31.54 5.03
150 151 3.248248 TAGGTGGTTCCCTCCCGCT 62.248 63.158 0.00 0.00 37.86 5.52
151 152 2.686106 TAGGTGGTTCCCTCCCGC 60.686 66.667 0.00 0.00 37.86 6.13
152 153 1.611261 TGTAGGTGGTTCCCTCCCG 60.611 63.158 0.00 0.00 37.86 5.14
153 154 1.559965 GGTGTAGGTGGTTCCCTCCC 61.560 65.000 0.00 0.00 37.86 4.30
154 155 1.896122 CGGTGTAGGTGGTTCCCTCC 61.896 65.000 0.00 0.00 37.43 4.30
155 156 1.595357 CGGTGTAGGTGGTTCCCTC 59.405 63.158 0.00 0.00 35.97 4.30
156 157 2.590114 GCGGTGTAGGTGGTTCCCT 61.590 63.158 0.00 0.00 38.70 4.20
157 158 2.046604 GCGGTGTAGGTGGTTCCC 60.047 66.667 0.00 0.00 36.75 3.97
158 159 2.046604 GGCGGTGTAGGTGGTTCC 60.047 66.667 0.00 0.00 0.00 3.62
159 160 1.876497 TACGGCGGTGTAGGTGGTTC 61.876 60.000 13.24 0.00 0.00 3.62
160 161 1.880819 CTACGGCGGTGTAGGTGGTT 61.881 60.000 13.24 0.00 38.51 3.67
161 162 2.283101 TACGGCGGTGTAGGTGGT 60.283 61.111 13.24 0.00 0.00 4.16
162 163 2.345760 ACTACGGCGGTGTAGGTGG 61.346 63.158 13.24 0.00 44.89 4.61
163 164 1.153901 CACTACGGCGGTGTAGGTG 60.154 63.158 13.24 6.79 44.89 4.00
164 165 2.998279 GCACTACGGCGGTGTAGGT 61.998 63.158 13.24 0.00 44.89 3.08
165 166 2.202703 GCACTACGGCGGTGTAGG 60.203 66.667 13.24 0.00 44.89 3.18
173 174 4.874977 GGCCTCTCGCACTACGGC 62.875 72.222 0.00 0.00 43.89 5.68
174 175 4.208686 GGGCCTCTCGCACTACGG 62.209 72.222 0.84 0.00 43.89 4.02
175 176 4.554363 CGGGCCTCTCGCACTACG 62.554 72.222 0.84 0.00 39.53 3.51
176 177 3.450115 ACGGGCCTCTCGCACTAC 61.450 66.667 0.84 0.00 39.53 2.73
177 178 3.449227 CACGGGCCTCTCGCACTA 61.449 66.667 0.84 0.00 39.53 2.74
205 206 2.570581 CAAAATGCGACCGCGACG 60.571 61.111 8.23 14.72 45.51 5.12
206 207 1.082366 AACAAAATGCGACCGCGAC 60.082 52.632 8.23 0.00 45.51 5.19
207 208 1.082431 CAACAAAATGCGACCGCGA 60.082 52.632 8.23 0.00 45.51 5.87
208 209 1.369930 ACAACAAAATGCGACCGCG 60.370 52.632 9.91 0.00 45.51 6.46
209 210 1.274798 CCACAACAAAATGCGACCGC 61.275 55.000 7.53 7.53 42.35 5.68
210 211 0.309302 TCCACAACAAAATGCGACCG 59.691 50.000 0.00 0.00 0.00 4.79
211 212 2.228822 AGATCCACAACAAAATGCGACC 59.771 45.455 0.00 0.00 0.00 4.79
212 213 3.559238 AGATCCACAACAAAATGCGAC 57.441 42.857 0.00 0.00 0.00 5.19
213 214 4.582701 AAAGATCCACAACAAAATGCGA 57.417 36.364 0.00 0.00 0.00 5.10
214 215 5.254669 GAAAAGATCCACAACAAAATGCG 57.745 39.130 0.00 0.00 0.00 4.73
228 229 4.476628 ACCATGCAAATGGGAAAAGATC 57.523 40.909 11.02 0.00 45.84 2.75
229 230 4.141869 GCTACCATGCAAATGGGAAAAGAT 60.142 41.667 11.02 0.00 45.84 2.40
230 231 3.195396 GCTACCATGCAAATGGGAAAAGA 59.805 43.478 11.02 0.00 45.84 2.52
231 232 3.055963 TGCTACCATGCAAATGGGAAAAG 60.056 43.478 11.02 4.17 45.84 2.27
232 233 2.902486 TGCTACCATGCAAATGGGAAAA 59.098 40.909 11.02 0.00 45.84 2.29
233 234 2.533916 TGCTACCATGCAAATGGGAAA 58.466 42.857 11.02 0.00 45.84 3.13
234 235 2.228545 TGCTACCATGCAAATGGGAA 57.771 45.000 11.02 0.00 45.84 3.97
235 236 2.033372 CATGCTACCATGCAAATGGGA 58.967 47.619 11.02 0.93 46.61 4.37
236 237 2.519377 CATGCTACCATGCAAATGGG 57.481 50.000 11.02 3.63 46.61 4.00
245 246 1.137086 GACACCTCGACATGCTACCAT 59.863 52.381 0.00 0.00 0.00 3.55
246 247 0.530744 GACACCTCGACATGCTACCA 59.469 55.000 0.00 0.00 0.00 3.25
247 248 0.179108 GGACACCTCGACATGCTACC 60.179 60.000 0.00 0.00 0.00 3.18
248 249 0.818296 AGGACACCTCGACATGCTAC 59.182 55.000 0.00 0.00 0.00 3.58
249 250 1.557099 AAGGACACCTCGACATGCTA 58.443 50.000 0.00 0.00 30.89 3.49
250 251 0.687354 AAAGGACACCTCGACATGCT 59.313 50.000 0.00 0.00 30.89 3.79
251 252 1.464997 GAAAAGGACACCTCGACATGC 59.535 52.381 0.00 0.00 30.89 4.06
252 253 2.076863 GGAAAAGGACACCTCGACATG 58.923 52.381 0.00 0.00 30.89 3.21
253 254 1.697432 TGGAAAAGGACACCTCGACAT 59.303 47.619 0.00 0.00 30.89 3.06
254 255 1.124780 TGGAAAAGGACACCTCGACA 58.875 50.000 0.00 0.00 30.89 4.35
255 256 2.347731 GATGGAAAAGGACACCTCGAC 58.652 52.381 0.00 0.00 30.89 4.20
256 257 1.278127 GGATGGAAAAGGACACCTCGA 59.722 52.381 0.00 0.00 30.89 4.04
257 258 1.003118 TGGATGGAAAAGGACACCTCG 59.997 52.381 0.00 0.00 30.89 4.63
258 259 2.879103 TGGATGGAAAAGGACACCTC 57.121 50.000 0.00 0.00 30.89 3.85
259 260 2.649312 TCATGGATGGAAAAGGACACCT 59.351 45.455 0.00 0.00 33.87 4.00
260 261 3.085952 TCATGGATGGAAAAGGACACC 57.914 47.619 0.00 0.00 0.00 4.16
261 262 4.644103 CATCATGGATGGAAAAGGACAC 57.356 45.455 0.00 0.00 36.51 3.67
276 277 6.335471 ACATACCATGTAAATGCCATCATG 57.665 37.500 0.00 0.00 42.78 3.07
382 385 1.396996 CCAGTCCCGCGAATTAAACAG 59.603 52.381 8.23 0.00 0.00 3.16
481 484 6.890293 ACAGGAAAGATACAGGAATTCTACC 58.110 40.000 5.23 0.00 0.00 3.18
497 500 7.095187 GGAAGTGTGTTTGATAGTACAGGAAAG 60.095 40.741 0.00 0.00 0.00 2.62
518 522 9.987272 ACAAAACTACGTAAAGTTATAGGAAGT 57.013 29.630 4.21 0.00 38.76 3.01
529 533 7.692291 CCTGCATGATTACAAAACTACGTAAAG 59.308 37.037 0.00 0.00 31.74 1.85
532 536 6.399743 TCCTGCATGATTACAAAACTACGTA 58.600 36.000 0.00 0.00 0.00 3.57
568 572 6.636454 TGAAACCCAGGAATAGAGTAACAT 57.364 37.500 0.00 0.00 0.00 2.71
581 585 5.076873 TGAGTAGGATTTTTGAAACCCAGG 58.923 41.667 0.00 0.00 0.00 4.45
590 594 5.221621 TGGGCCTTTTTGAGTAGGATTTTTG 60.222 40.000 4.53 0.00 33.13 2.44
635 639 5.236478 ACAAACCACTTGATACAAAGACTCG 59.764 40.000 0.00 0.00 38.50 4.18
648 652 4.635765 TCTCAAGTCTCAACAAACCACTTG 59.364 41.667 4.12 4.12 43.52 3.16
906 5169 1.340405 ACTTGCCCTATTGCTCAGTGG 60.340 52.381 0.00 0.00 0.00 4.00
937 6190 6.140303 TCGTGTGAATGGTATAAGTAGGAC 57.860 41.667 0.00 0.00 0.00 3.85
1083 6349 3.909258 GACGGCGAGCTCGGTGAAA 62.909 63.158 35.10 0.00 40.23 2.69
1128 6394 2.109181 GCGATGGTGGCCTCTACC 59.891 66.667 3.32 3.55 38.71 3.18
1170 6436 4.351938 CGGAGCAACGACCGGACA 62.352 66.667 9.46 0.00 44.59 4.02
1205 6471 3.118454 CAGGTGTGCCGCCGTTAG 61.118 66.667 0.00 0.00 39.30 2.34
1206 6472 3.869473 GACAGGTGTGCCGCCGTTA 62.869 63.158 0.00 0.00 39.30 3.18
1224 6493 2.433664 GGGTACGTCGCCACCTTG 60.434 66.667 14.34 0.00 35.04 3.61
1292 6561 3.770040 ATGCGTCGGCCTGTGCTA 61.770 61.111 0.00 0.00 38.85 3.49
1519 6788 5.071519 TGATGTTGGTGTTGGAATTGGAAAT 59.928 36.000 0.00 0.00 0.00 2.17
1536 6805 1.811965 TCCGGCTTGATGTTGATGTTG 59.188 47.619 0.00 0.00 0.00 3.33
1537 6806 2.086869 CTCCGGCTTGATGTTGATGTT 58.913 47.619 0.00 0.00 0.00 2.71
1538 6807 1.742761 CTCCGGCTTGATGTTGATGT 58.257 50.000 0.00 0.00 0.00 3.06
1539 6808 0.379669 GCTCCGGCTTGATGTTGATG 59.620 55.000 0.00 0.00 35.22 3.07
1540 6809 0.749454 GGCTCCGGCTTGATGTTGAT 60.749 55.000 0.00 0.00 38.73 2.57
1541 6810 1.377202 GGCTCCGGCTTGATGTTGA 60.377 57.895 0.00 0.00 38.73 3.18
1612 6881 0.606401 CTTCCAGTGAACGTGGGCAT 60.606 55.000 0.00 0.00 35.58 4.40
1613 6882 1.227823 CTTCCAGTGAACGTGGGCA 60.228 57.895 0.00 0.00 35.58 5.36
1614 6883 1.227853 ACTTCCAGTGAACGTGGGC 60.228 57.895 0.00 0.00 35.58 5.36
1615 6884 0.105964 TGACTTCCAGTGAACGTGGG 59.894 55.000 0.00 0.00 35.58 4.61
1616 6885 1.502231 CTGACTTCCAGTGAACGTGG 58.498 55.000 0.00 0.00 38.10 4.94
1625 6894 3.742433 AAGTGAGACACTGACTTCCAG 57.258 47.619 5.17 0.00 44.62 3.86
1626 6895 3.450817 TCAAAGTGAGACACTGACTTCCA 59.549 43.478 5.17 0.00 44.62 3.53
1627 6896 4.060038 TCAAAGTGAGACACTGACTTCC 57.940 45.455 5.17 0.00 44.62 3.46
1628 6897 5.176590 GTGATCAAAGTGAGACACTGACTTC 59.823 44.000 0.00 2.77 44.62 3.01
1629 6898 5.053145 GTGATCAAAGTGAGACACTGACTT 58.947 41.667 0.00 0.00 44.62 3.01
1648 6917 9.975218 ATTTAGGGTATTTTGAAGTACAGTGAT 57.025 29.630 0.00 0.00 0.00 3.06
1689 6958 2.627945 CCGTATTGAGGCACTTAAGCA 58.372 47.619 1.29 0.00 41.55 3.91
1710 6979 5.183014 TGTATGTCAAGTCATACTAGCGG 57.817 43.478 15.05 0.00 45.82 5.52
1739 7008 4.081087 GGGTCAACTCTATGCCAACTAAGA 60.081 45.833 0.00 0.00 0.00 2.10
1776 7045 2.224992 TGTCCACATAGTTGTTGCCCAT 60.225 45.455 0.00 0.00 32.34 4.00
1805 7074 0.533085 TCAAAATGTCACGTCGCCCA 60.533 50.000 0.00 0.00 0.00 5.36
1826 7095 0.181824 GGGGCCCGTCAAGCTTATTA 59.818 55.000 17.79 0.00 0.00 0.98
1834 7103 2.285818 ATAGGTGGGGCCCGTCAA 60.286 61.111 19.83 3.73 38.26 3.18
1860 7130 8.416329 ACTTAAGTTCTGCATTTTGTTTCTCAT 58.584 29.630 1.12 0.00 0.00 2.90
1919 7189 2.939103 GACTATGTGGACATGAACAGGC 59.061 50.000 0.00 0.00 37.15 4.85
1923 7193 6.274001 CATAACGACTATGTGGACATGAAC 57.726 41.667 0.00 0.00 37.15 3.18
1959 7233 3.055891 TGCATGTATGGACCGATCCTATG 60.056 47.826 0.00 0.00 46.43 2.23
1967 7241 2.802247 CACTACATGCATGTATGGACCG 59.198 50.000 33.66 24.18 41.92 4.79
2146 7484 7.939784 AGTGACTAGTACATCACATGTTCTA 57.060 36.000 20.48 0.00 46.34 2.10
2147 7485 6.842437 AGTGACTAGTACATCACATGTTCT 57.158 37.500 20.48 0.00 46.34 3.01
2207 7545 1.608283 CGTCAGGTCTTCTTCAACCCC 60.608 57.143 0.00 0.00 36.11 4.95
2287 7625 0.904649 TCACTGCGTCATCCATTCCT 59.095 50.000 0.00 0.00 0.00 3.36
2288 7626 1.959042 ATCACTGCGTCATCCATTCC 58.041 50.000 0.00 0.00 0.00 3.01
2315 7653 2.063266 GTGAACCGATGCGTTAAGTGA 58.937 47.619 0.00 0.00 0.00 3.41
2321 7659 1.234615 CCAAGGTGAACCGATGCGTT 61.235 55.000 0.00 0.00 42.08 4.84
2330 7668 1.743996 GAGATGCCTCCAAGGTGAAC 58.256 55.000 0.00 0.00 37.80 3.18
2346 7684 1.075226 AAGAGCTATGGCCCCGAGA 60.075 57.895 0.00 0.00 39.73 4.04
2348 7686 0.397957 TACAAGAGCTATGGCCCCGA 60.398 55.000 0.00 0.00 39.73 5.14
2396 7734 1.215382 CGATCAGGTGAAGTCGGCA 59.785 57.895 0.00 0.00 0.00 5.69
2458 7813 0.745468 GTAGAGTTACCTCGGCAGGG 59.255 60.000 7.70 0.10 45.53 4.45
2460 7815 4.913335 TTATGTAGAGTTACCTCGGCAG 57.087 45.455 0.00 0.00 42.86 4.85
2461 7816 4.463539 TGTTTATGTAGAGTTACCTCGGCA 59.536 41.667 0.00 0.00 42.86 5.69
2490 7845 4.065088 CCATGGATGAATAACCACTACCG 58.935 47.826 5.56 0.00 39.06 4.02
2491 7846 4.398319 CCCATGGATGAATAACCACTACC 58.602 47.826 15.22 0.00 39.06 3.18
2492 7847 3.821033 GCCCATGGATGAATAACCACTAC 59.179 47.826 15.22 0.00 39.06 2.73
2496 7851 1.492599 TCGCCCATGGATGAATAACCA 59.507 47.619 15.22 0.00 40.57 3.67
2497 7852 2.270352 TCGCCCATGGATGAATAACC 57.730 50.000 15.22 0.00 0.00 2.85
2500 7855 3.559811 CCTTGATCGCCCATGGATGAATA 60.560 47.826 15.22 1.27 34.35 1.75
2501 7856 2.511659 CTTGATCGCCCATGGATGAAT 58.488 47.619 15.22 0.54 0.00 2.57
2510 7865 2.026729 TGAAATGTACCTTGATCGCCCA 60.027 45.455 0.00 0.00 0.00 5.36
2526 7881 4.216257 CGAGGACCTCAACAATGTTGAAAT 59.784 41.667 26.23 18.14 0.00 2.17
2528 7883 3.138304 CGAGGACCTCAACAATGTTGAA 58.862 45.455 26.23 12.64 0.00 2.69
2558 7913 0.318955 AAATTGCAGCGTCAAGGCAC 60.319 50.000 0.00 0.00 37.26 5.01
2563 7918 1.599171 CGTCCAAAATTGCAGCGTCAA 60.599 47.619 0.00 0.00 0.00 3.18
2587 7942 2.357517 CCGACTGTGACACTGGCC 60.358 66.667 15.85 0.00 0.00 5.36
2603 7958 0.831307 CCTAGGGCTACAACTGACCC 59.169 60.000 0.00 0.00 43.17 4.46
2662 8019 2.109128 TCCCAGGGCTGTCACATTTTAA 59.891 45.455 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.