Multiple sequence alignment - TraesCS6D01G151800

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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 TraesCS6D01G151800 chr6D 100.000 2411 0 0 1 2411 125023106 125020696 0.000000e+00 4453
1 TraesCS6D01G151800 chr6D 88.152 211 21 4 1255 1463 95860474 95860266 5.150000e-62 248
2 TraesCS6D01G151800 chr6D 89.571 163 12 5 926 1087 95860844 95860686 4.060000e-48 202
3 TraesCS6D01G151800 chr6D 82.967 182 25 6 1702 1881 315747574 315747397 2.480000e-35 159
4 TraesCS6D01G151800 chr6D 90.526 95 7 2 781 875 95861145 95861053 9.050000e-25 124
5 TraesCS6D01G151800 chr6B 92.110 1204 66 16 939 2136 223259069 223257889 0.000000e+00 1670
6 TraesCS6D01G151800 chr6B 84.653 404 24 10 293 679 223259775 223259393 3.790000e-98 368
7 TraesCS6D01G151800 chr6B 95.000 220 8 2 678 897 223259278 223259062 2.300000e-90 342
8 TraesCS6D01G151800 chr6B 90.868 219 12 6 2191 2405 223257888 223257674 1.090000e-73 287
9 TraesCS6D01G151800 chr6B 91.573 178 7 8 1290 1464 176768575 176768747 3.100000e-59 239
10 TraesCS6D01G151800 chr6B 88.961 154 15 2 934 1087 176767349 176767500 3.160000e-44 189
11 TraesCS6D01G151800 chr6B 91.111 90 6 2 783 872 176767175 176767262 1.170000e-23 121
12 TraesCS6D01G151800 chr6A 92.059 1146 73 15 1278 2411 155795089 155796228 0.000000e+00 1596
13 TraesCS6D01G151800 chr6A 80.691 492 62 22 607 1088 155794438 155794906 3.810000e-93 351
14 TraesCS6D01G151800 chr6A 80.952 378 43 17 1291 1666 112587309 112587659 3.050000e-69 272
15 TraesCS6D01G151800 chr6A 78.198 344 40 24 765 1081 112585937 112586272 1.140000e-43 187
16 TraesCS6D01G151800 chr1B 83.376 776 74 37 1313 2041 413985323 413984556 0.000000e+00 667
17 TraesCS6D01G151800 chr1B 94.495 109 6 0 979 1087 656674726 656674618 4.120000e-38 169
18 TraesCS6D01G151800 chr1B 94.000 100 3 2 2249 2345 656853546 656853645 5.370000e-32 148
19 TraesCS6D01G151800 chr1B 80.465 215 22 11 1942 2156 656853412 656853606 1.930000e-31 147
20 TraesCS6D01G151800 chr1B 87.402 127 11 5 1942 2064 677998042 677998167 8.990000e-30 141
21 TraesCS6D01G151800 chr1D 81.169 770 89 36 1288 2035 486868724 486869459 3.480000e-158 568
22 TraesCS6D01G151800 chr1D 84.381 525 59 19 1291 1799 306636424 306635907 5.990000e-136 494
23 TraesCS6D01G151800 chr1D 82.857 210 24 10 1842 2041 306635900 306635693 6.850000e-41 178
24 TraesCS6D01G151800 chr1D 94.175 103 3 2 2246 2345 486869530 486869632 1.150000e-33 154
25 TraesCS6D01G151800 chr1D 93.204 103 4 2 2246 2345 486865306 486865408 5.370000e-32 148
26 TraesCS6D01G151800 chr1D 81.319 182 25 8 1702 1881 436855524 436855698 3.230000e-29 139
27 TraesCS6D01G151800 chr3A 81.200 750 73 41 1292 2035 77893333 77892646 2.110000e-150 542
28 TraesCS6D01G151800 chr3A 94.000 100 2 3 2249 2345 77892589 77892491 5.370000e-32 148
29 TraesCS6D01G151800 chr3B 80.713 757 84 44 1292 2041 111554724 111554023 1.270000e-147 532
30 TraesCS6D01G151800 chr3B 79.810 738 80 42 1311 2041 119965429 119964754 7.800000e-130 473
31 TraesCS6D01G151800 chr3B 94.792 96 2 2 2252 2345 119964702 119964608 1.930000e-31 147
32 TraesCS6D01G151800 chr3B 93.750 96 3 2 2252 2345 111553968 111553874 8.990000e-30 141
33 TraesCS6D01G151800 chr3D 79.539 738 78 46 1311 2041 66730583 66729912 2.180000e-125 459
34 TraesCS6D01G151800 chr1A 87.918 389 33 13 1290 1670 385276367 385275985 1.700000e-121 446
35 TraesCS6D01G151800 chr1A 84.424 321 25 13 1290 1605 385276716 385276416 2.340000e-75 292
36 TraesCS6D01G151800 chr1A 95.413 109 5 0 979 1087 566414665 566414557 8.860000e-40 174
37 TraesCS6D01G151800 chr1A 84.066 182 23 6 1702 1881 566410768 566410591 1.150000e-38 171
38 TraesCS6D01G151800 chr1A 84.066 182 23 6 1702 1881 566416408 566416231 1.150000e-38 171
39 TraesCS6D01G151800 chr1A 80.841 214 26 13 1702 1912 566413553 566413352 1.150000e-33 154
40 TraesCS6D01G151800 chr1A 93.814 97 5 1 1945 2041 385275863 385275768 6.950000e-31 145
41 TraesCS6D01G151800 chr2A 88.125 160 16 3 1504 1660 540772331 540772490 1.140000e-43 187
42 TraesCS6D01G151800 chr5B 95.413 109 5 0 979 1087 13841501 13841393 8.860000e-40 174
43 TraesCS6D01G151800 chr5B 95.413 109 5 0 979 1087 36191360 36191468 8.860000e-40 174
44 TraesCS6D01G151800 chr4B 91.000 100 7 1 2252 2349 501183800 501183899 1.500000e-27 134


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 TraesCS6D01G151800 chr6D 125020696 125023106 2410 True 4453.000000 4453 100.000000 1 2411 1 chr6D.!!$R1 2410
1 TraesCS6D01G151800 chr6B 223257674 223259775 2101 True 666.750000 1670 90.657750 293 2405 4 chr6B.!!$R1 2112
2 TraesCS6D01G151800 chr6A 155794438 155796228 1790 False 973.500000 1596 86.375000 607 2411 2 chr6A.!!$F2 1804
3 TraesCS6D01G151800 chr6A 112585937 112587659 1722 False 229.500000 272 79.575000 765 1666 2 chr6A.!!$F1 901
4 TraesCS6D01G151800 chr1B 413984556 413985323 767 True 667.000000 667 83.376000 1313 2041 1 chr1B.!!$R1 728
5 TraesCS6D01G151800 chr1D 306635693 306636424 731 True 336.000000 494 83.619000 1291 2041 2 chr1D.!!$R1 750
6 TraesCS6D01G151800 chr1D 486865306 486869632 4326 False 290.000000 568 89.516000 1288 2345 3 chr1D.!!$F2 1057
7 TraesCS6D01G151800 chr3A 77892491 77893333 842 True 345.000000 542 87.600000 1292 2345 2 chr3A.!!$R1 1053
8 TraesCS6D01G151800 chr3B 111553874 111554724 850 True 336.500000 532 87.231500 1292 2345 2 chr3B.!!$R1 1053
9 TraesCS6D01G151800 chr3B 119964608 119965429 821 True 310.000000 473 87.301000 1311 2345 2 chr3B.!!$R2 1034
10 TraesCS6D01G151800 chr3D 66729912 66730583 671 True 459.000000 459 79.539000 1311 2041 1 chr3D.!!$R1 730
11 TraesCS6D01G151800 chr1A 385275768 385276716 948 True 294.333333 446 88.718667 1290 2041 3 chr1A.!!$R1 751

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
128 129 0.036022 GCCTCACTGGAGTTGCTCTT 59.964 55.0 0.0 0.0 39.64 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 5427 0.679002 GCAGTGGTGGCATCTGTCAT 60.679 55.0 14.96 0.0 29.66 3.06 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
17 18 2.177531 CAGGCGCAACACAGATGC 59.822 61.111 10.83 0.00 40.41 3.91
18 19 3.058160 AGGCGCAACACAGATGCC 61.058 61.111 10.83 0.00 46.07 4.40
19 20 3.364441 GGCGCAACACAGATGCCA 61.364 61.111 10.83 0.00 45.06 4.92
21 22 1.515519 GCGCAACACAGATGCCATG 60.516 57.895 0.30 0.00 40.72 3.66
22 23 1.515519 CGCAACACAGATGCCATGC 60.516 57.895 0.00 0.00 40.72 4.06
23 24 1.587568 GCAACACAGATGCCATGCA 59.412 52.632 0.00 0.00 44.86 3.96
26 27 2.333926 CAACACAGATGCCATGCAAAG 58.666 47.619 0.00 0.00 43.62 2.77
27 28 0.892755 ACACAGATGCCATGCAAAGG 59.107 50.000 4.27 4.27 43.62 3.11
28 29 1.179152 CACAGATGCCATGCAAAGGA 58.821 50.000 12.36 0.00 43.62 3.36
31 32 2.307768 CAGATGCCATGCAAAGGAGAT 58.692 47.619 12.36 3.49 43.62 2.75
33 34 3.132289 CAGATGCCATGCAAAGGAGATTT 59.868 43.478 12.36 0.00 43.62 2.17
44 45 5.077134 CAAAGGAGATTTGGGTTTGGATC 57.923 43.478 0.00 0.00 43.88 3.36
49 50 0.808755 ATTTGGGTTTGGATCGACGC 59.191 50.000 0.00 3.60 0.00 5.19
50 51 1.570347 TTTGGGTTTGGATCGACGCG 61.570 55.000 3.53 3.53 0.00 6.01
52 53 2.030958 GGGTTTGGATCGACGCGTT 61.031 57.895 15.53 0.00 0.00 4.84
53 54 1.131826 GGTTTGGATCGACGCGTTG 59.868 57.895 20.76 20.76 0.00 4.10
55 56 2.030401 TTTGGATCGACGCGTTGGG 61.030 57.895 25.66 12.67 0.00 4.12
58 59 4.814294 GATCGACGCGTTGGGCCT 62.814 66.667 25.66 8.84 38.94 5.19
59 60 4.814294 ATCGACGCGTTGGGCCTC 62.814 66.667 25.66 4.11 38.94 4.70
65 66 4.643387 GCGTTGGGCCTCCACTGT 62.643 66.667 4.53 0.00 43.94 3.55
67 68 2.260869 CGTTGGGCCTCCACTGTTG 61.261 63.158 4.53 0.00 43.94 3.33
68 69 1.152756 GTTGGGCCTCCACTGTTGT 60.153 57.895 4.53 0.00 43.94 3.32
69 70 1.150536 TTGGGCCTCCACTGTTGTC 59.849 57.895 4.53 0.00 43.94 3.18
72 73 1.003233 GGCCTCCACTGTTGTCCTC 60.003 63.158 0.00 0.00 0.00 3.71
73 74 1.374758 GCCTCCACTGTTGTCCTCG 60.375 63.158 0.00 0.00 0.00 4.63
74 75 1.374758 CCTCCACTGTTGTCCTCGC 60.375 63.158 0.00 0.00 0.00 5.03
75 76 1.374758 CTCCACTGTTGTCCTCGCC 60.375 63.158 0.00 0.00 0.00 5.54
76 77 2.738521 CCACTGTTGTCCTCGCCG 60.739 66.667 0.00 0.00 0.00 6.46
77 78 2.338620 CACTGTTGTCCTCGCCGA 59.661 61.111 0.00 0.00 0.00 5.54
79 80 2.338620 CTGTTGTCCTCGCCGACA 59.661 61.111 0.80 0.80 40.98 4.35
80 81 2.022129 CTGTTGTCCTCGCCGACAC 61.022 63.158 4.14 2.11 42.37 3.67
81 82 2.028484 GTTGTCCTCGCCGACACA 59.972 61.111 4.14 0.00 42.37 3.72
82 83 1.593209 GTTGTCCTCGCCGACACAA 60.593 57.895 4.14 3.36 42.37 3.33
83 84 1.144276 TTGTCCTCGCCGACACAAA 59.856 52.632 4.76 0.00 42.37 2.83
84 85 1.155424 TTGTCCTCGCCGACACAAAC 61.155 55.000 4.76 0.00 42.37 2.93
86 87 1.144276 TCCTCGCCGACACAAACAA 59.856 52.632 0.00 0.00 0.00 2.83
87 88 0.462225 TCCTCGCCGACACAAACAAA 60.462 50.000 0.00 0.00 0.00 2.83
88 89 0.316689 CCTCGCCGACACAAACAAAC 60.317 55.000 0.00 0.00 0.00 2.93
89 90 0.375454 CTCGCCGACACAAACAAACA 59.625 50.000 0.00 0.00 0.00 2.83
90 91 0.097325 TCGCCGACACAAACAAACAC 59.903 50.000 0.00 0.00 0.00 3.32
92 93 1.544686 GCCGACACAAACAAACACAG 58.455 50.000 0.00 0.00 0.00 3.66
93 94 1.797348 GCCGACACAAACAAACACAGG 60.797 52.381 0.00 0.00 0.00 4.00
94 95 1.544686 CGACACAAACAAACACAGGC 58.455 50.000 0.00 0.00 0.00 4.85
95 96 1.135546 CGACACAAACAAACACAGGCA 60.136 47.619 0.00 0.00 0.00 4.75
96 97 2.669670 CGACACAAACAAACACAGGCAA 60.670 45.455 0.00 0.00 0.00 4.52
99 100 3.062763 CACAAACAAACACAGGCAAACA 58.937 40.909 0.00 0.00 0.00 2.83
101 102 4.024556 CACAAACAAACACAGGCAAACAAA 60.025 37.500 0.00 0.00 0.00 2.83
102 103 4.576463 ACAAACAAACACAGGCAAACAAAA 59.424 33.333 0.00 0.00 0.00 2.44
103 104 5.240403 ACAAACAAACACAGGCAAACAAAAT 59.760 32.000 0.00 0.00 0.00 1.82
104 105 4.943142 ACAAACACAGGCAAACAAAATG 57.057 36.364 0.00 0.00 0.00 2.32
105 106 4.322567 ACAAACACAGGCAAACAAAATGT 58.677 34.783 0.00 0.00 0.00 2.71
106 107 4.153835 ACAAACACAGGCAAACAAAATGTG 59.846 37.500 2.29 2.29 45.22 3.21
109 110 2.535166 CACAGGCAAACAAAATGTGTCG 59.465 45.455 0.00 0.00 40.60 4.35
110 111 1.522258 CAGGCAAACAAAATGTGTCGC 59.478 47.619 0.00 0.00 40.60 5.19
111 112 0.858583 GGCAAACAAAATGTGTCGCC 59.141 50.000 1.78 1.78 46.02 5.54
112 113 1.851658 GCAAACAAAATGTGTCGCCT 58.148 45.000 0.00 0.00 40.60 5.52
115 116 2.774439 AACAAAATGTGTCGCCTCAC 57.226 45.000 0.00 0.00 40.60 3.51
117 118 1.603802 ACAAAATGTGTCGCCTCACTG 59.396 47.619 7.30 1.13 34.38 3.66
118 119 1.069022 CAAAATGTGTCGCCTCACTGG 60.069 52.381 7.30 0.00 38.90 4.00
120 121 0.036952 AATGTGTCGCCTCACTGGAG 60.037 55.000 7.30 0.00 41.02 3.86
123 124 0.946221 GTGTCGCCTCACTGGAGTTG 60.946 60.000 0.00 0.00 39.64 3.16
124 125 2.029844 GTCGCCTCACTGGAGTTGC 61.030 63.158 0.00 0.00 39.64 4.17
125 126 2.210013 TCGCCTCACTGGAGTTGCT 61.210 57.895 0.00 0.00 39.64 3.91
126 127 1.739562 CGCCTCACTGGAGTTGCTC 60.740 63.158 0.00 0.00 39.64 4.26
127 128 1.676384 GCCTCACTGGAGTTGCTCT 59.324 57.895 0.00 0.00 39.64 4.09
128 129 0.036022 GCCTCACTGGAGTTGCTCTT 59.964 55.000 0.00 0.00 39.64 2.85
129 130 1.805869 CCTCACTGGAGTTGCTCTTG 58.194 55.000 0.00 0.00 39.64 3.02
131 132 2.027377 CCTCACTGGAGTTGCTCTTGAT 60.027 50.000 0.00 0.00 39.64 2.57
132 133 3.196469 CCTCACTGGAGTTGCTCTTGATA 59.804 47.826 0.00 0.00 39.64 2.15
134 135 5.426504 CTCACTGGAGTTGCTCTTGATAAT 58.573 41.667 0.00 0.00 36.36 1.28
135 136 5.423015 TCACTGGAGTTGCTCTTGATAATC 58.577 41.667 0.00 0.00 0.00 1.75
138 139 5.163364 ACTGGAGTTGCTCTTGATAATCGAT 60.163 40.000 0.00 0.00 0.00 3.59
139 140 5.674525 TGGAGTTGCTCTTGATAATCGATT 58.325 37.500 16.15 16.15 0.00 3.34
141 142 6.037500 TGGAGTTGCTCTTGATAATCGATTTG 59.962 38.462 17.19 2.63 0.00 2.32
142 143 6.369059 AGTTGCTCTTGATAATCGATTTGG 57.631 37.500 17.19 2.98 0.00 3.28
143 144 6.115446 AGTTGCTCTTGATAATCGATTTGGA 58.885 36.000 17.19 0.00 0.00 3.53
144 145 6.259608 AGTTGCTCTTGATAATCGATTTGGAG 59.740 38.462 17.19 15.69 0.00 3.86
145 146 4.512944 TGCTCTTGATAATCGATTTGGAGC 59.487 41.667 25.48 25.48 42.41 4.70
146 147 4.754114 GCTCTTGATAATCGATTTGGAGCT 59.246 41.667 25.23 0.00 40.01 4.09
148 149 6.593382 GCTCTTGATAATCGATTTGGAGCTAT 59.407 38.462 25.23 12.39 40.01 2.97
149 150 7.118971 GCTCTTGATAATCGATTTGGAGCTATT 59.881 37.037 25.23 5.11 40.01 1.73
151 152 6.486253 TGATAATCGATTTGGAGCTATTGC 57.514 37.500 17.19 0.00 40.05 3.56
152 153 5.997129 TGATAATCGATTTGGAGCTATTGCA 59.003 36.000 17.19 0.00 42.74 4.08
153 154 4.825546 AATCGATTTGGAGCTATTGCAG 57.174 40.909 4.39 0.00 42.74 4.41
155 156 4.077300 TCGATTTGGAGCTATTGCAGAT 57.923 40.909 1.12 0.00 42.74 2.90
156 157 3.811497 TCGATTTGGAGCTATTGCAGATG 59.189 43.478 1.12 0.00 42.74 2.90
158 159 4.319333 CGATTTGGAGCTATTGCAGATGAC 60.319 45.833 1.12 0.00 42.74 3.06
160 161 3.851458 TGGAGCTATTGCAGATGACAT 57.149 42.857 1.12 0.00 42.74 3.06
161 162 3.473625 TGGAGCTATTGCAGATGACATG 58.526 45.455 1.12 0.00 42.74 3.21
162 163 3.135167 TGGAGCTATTGCAGATGACATGA 59.865 43.478 0.00 0.00 42.74 3.07
163 164 4.132336 GGAGCTATTGCAGATGACATGAA 58.868 43.478 0.00 0.00 42.74 2.57
165 166 4.778579 AGCTATTGCAGATGACATGAAGT 58.221 39.130 0.00 0.00 42.74 3.01
166 167 5.922053 AGCTATTGCAGATGACATGAAGTA 58.078 37.500 0.00 0.00 42.74 2.24
167 168 5.757320 AGCTATTGCAGATGACATGAAGTAC 59.243 40.000 0.00 0.00 42.74 2.73
168 169 5.332883 GCTATTGCAGATGACATGAAGTACG 60.333 44.000 0.00 0.00 39.41 3.67
170 171 4.186856 TGCAGATGACATGAAGTACGAA 57.813 40.909 0.00 0.00 0.00 3.85
171 172 4.758688 TGCAGATGACATGAAGTACGAAT 58.241 39.130 0.00 0.00 0.00 3.34
172 173 5.178061 TGCAGATGACATGAAGTACGAATT 58.822 37.500 0.00 0.00 0.00 2.17
175 176 6.402550 GCAGATGACATGAAGTACGAATTTGT 60.403 38.462 0.00 3.29 0.00 2.83
176 177 7.521529 CAGATGACATGAAGTACGAATTTGTT 58.478 34.615 3.03 0.00 0.00 2.83
177 178 7.689812 CAGATGACATGAAGTACGAATTTGTTC 59.310 37.037 3.03 0.00 0.00 3.18
178 179 6.236017 TGACATGAAGTACGAATTTGTTCC 57.764 37.500 3.03 0.00 0.00 3.62
179 180 5.995282 TGACATGAAGTACGAATTTGTTCCT 59.005 36.000 3.03 0.00 0.00 3.36
181 182 5.763204 ACATGAAGTACGAATTTGTTCCTGT 59.237 36.000 3.03 2.81 0.00 4.00
182 183 5.917541 TGAAGTACGAATTTGTTCCTGTC 57.082 39.130 3.03 0.00 0.00 3.51
183 184 4.446385 TGAAGTACGAATTTGTTCCTGTCG 59.554 41.667 3.03 0.00 37.71 4.35
184 185 3.323243 AGTACGAATTTGTTCCTGTCGG 58.677 45.455 3.03 0.00 36.06 4.79
185 186 0.872388 ACGAATTTGTTCCTGTCGGC 59.128 50.000 0.00 0.00 36.06 5.54
186 187 1.156736 CGAATTTGTTCCTGTCGGCT 58.843 50.000 0.00 0.00 0.00 5.52
187 188 2.289195 ACGAATTTGTTCCTGTCGGCTA 60.289 45.455 0.00 0.00 36.06 3.93
188 189 2.739913 CGAATTTGTTCCTGTCGGCTAA 59.260 45.455 0.00 0.00 0.00 3.09
189 190 3.187637 CGAATTTGTTCCTGTCGGCTAAA 59.812 43.478 0.00 0.00 0.00 1.85
190 191 4.319911 CGAATTTGTTCCTGTCGGCTAAAA 60.320 41.667 0.00 0.00 0.00 1.52
191 192 3.974871 TTTGTTCCTGTCGGCTAAAAC 57.025 42.857 0.00 0.00 0.00 2.43
192 193 2.623878 TGTTCCTGTCGGCTAAAACA 57.376 45.000 0.00 0.00 0.00 2.83
194 195 3.482436 TGTTCCTGTCGGCTAAAACAAT 58.518 40.909 0.00 0.00 0.00 2.71
195 196 3.500680 TGTTCCTGTCGGCTAAAACAATC 59.499 43.478 0.00 0.00 0.00 2.67
196 197 3.410631 TCCTGTCGGCTAAAACAATCA 57.589 42.857 0.00 0.00 0.00 2.57
197 198 3.745799 TCCTGTCGGCTAAAACAATCAA 58.254 40.909 0.00 0.00 0.00 2.57
200 201 4.679654 CCTGTCGGCTAAAACAATCAAAAC 59.320 41.667 0.00 0.00 0.00 2.43
201 202 5.507315 CCTGTCGGCTAAAACAATCAAAACT 60.507 40.000 0.00 0.00 0.00 2.66
202 203 6.293735 CCTGTCGGCTAAAACAATCAAAACTA 60.294 38.462 0.00 0.00 0.00 2.24
203 204 6.432107 TGTCGGCTAAAACAATCAAAACTAC 58.568 36.000 0.00 0.00 0.00 2.73
204 205 5.562623 GTCGGCTAAAACAATCAAAACTACG 59.437 40.000 0.00 0.00 0.00 3.51
205 206 4.849383 CGGCTAAAACAATCAAAACTACGG 59.151 41.667 0.00 0.00 0.00 4.02
209 210 7.908601 GGCTAAAACAATCAAAACTACGGATAG 59.091 37.037 0.00 0.00 34.25 2.08
210 211 8.448615 GCTAAAACAATCAAAACTACGGATAGT 58.551 33.333 0.00 0.00 43.91 2.12
223 224 7.105241 ACTACGGATAGTTTAGGTAAACAGG 57.895 40.000 13.68 2.58 45.97 4.00
224 225 6.665248 ACTACGGATAGTTTAGGTAAACAGGT 59.335 38.462 13.68 7.11 45.97 4.00
226 227 6.772605 ACGGATAGTTTAGGTAAACAGGTTT 58.227 36.000 13.68 2.66 45.97 3.27
227 228 7.226441 ACGGATAGTTTAGGTAAACAGGTTTT 58.774 34.615 13.68 0.00 45.97 2.43
255 256 9.268268 TGTACTGTGTAAGAATTTCTAGTTTGG 57.732 33.333 0.00 0.00 0.00 3.28
260 261 9.436957 TGTGTAAGAATTTCTAGTTTGGATCTC 57.563 33.333 0.00 0.00 0.00 2.75
261 262 8.884726 GTGTAAGAATTTCTAGTTTGGATCTCC 58.115 37.037 0.00 0.00 0.00 3.71
263 264 9.674068 GTAAGAATTTCTAGTTTGGATCTCCTT 57.326 33.333 0.00 0.00 36.82 3.36
264 265 8.572855 AAGAATTTCTAGTTTGGATCTCCTTG 57.427 34.615 0.00 0.00 36.82 3.61
265 266 7.694093 AGAATTTCTAGTTTGGATCTCCTTGT 58.306 34.615 0.00 0.00 36.82 3.16
266 267 7.826744 AGAATTTCTAGTTTGGATCTCCTTGTC 59.173 37.037 0.00 0.00 36.82 3.18
267 268 6.433847 TTTCTAGTTTGGATCTCCTTGTCA 57.566 37.500 0.00 0.00 36.82 3.58
270 271 4.647564 AGTTTGGATCTCCTTGTCACAT 57.352 40.909 0.00 0.00 36.82 3.21
271 272 4.330250 AGTTTGGATCTCCTTGTCACATG 58.670 43.478 0.00 0.00 36.82 3.21
272 273 4.042062 AGTTTGGATCTCCTTGTCACATGA 59.958 41.667 0.00 0.00 36.82 3.07
273 274 4.849813 TTGGATCTCCTTGTCACATGAT 57.150 40.909 0.00 0.00 36.82 2.45
274 275 4.849813 TGGATCTCCTTGTCACATGATT 57.150 40.909 0.00 0.00 36.82 2.57
275 276 5.183530 TGGATCTCCTTGTCACATGATTT 57.816 39.130 0.00 0.00 36.82 2.17
276 277 6.312141 TGGATCTCCTTGTCACATGATTTA 57.688 37.500 0.00 0.00 36.82 1.40
277 278 6.903516 TGGATCTCCTTGTCACATGATTTAT 58.096 36.000 0.00 0.00 36.82 1.40
278 279 6.769341 TGGATCTCCTTGTCACATGATTTATG 59.231 38.462 0.00 0.00 38.68 1.90
280 281 6.065976 TCTCCTTGTCACATGATTTATGGT 57.934 37.500 0.00 0.00 41.25 3.55
281 282 6.484288 TCTCCTTGTCACATGATTTATGGTT 58.516 36.000 0.00 0.00 41.25 3.67
282 283 6.599244 TCTCCTTGTCACATGATTTATGGTTC 59.401 38.462 0.00 0.00 41.25 3.62
283 284 6.244654 TCCTTGTCACATGATTTATGGTTCA 58.755 36.000 0.00 0.00 41.25 3.18
284 285 6.718912 TCCTTGTCACATGATTTATGGTTCAA 59.281 34.615 0.00 0.00 41.25 2.69
285 286 7.031372 CCTTGTCACATGATTTATGGTTCAAG 58.969 38.462 0.00 3.87 41.25 3.02
286 287 5.953183 TGTCACATGATTTATGGTTCAAGC 58.047 37.500 0.00 0.00 41.25 4.01
287 288 5.105797 TGTCACATGATTTATGGTTCAAGCC 60.106 40.000 0.00 0.00 41.25 4.35
288 289 5.015515 TCACATGATTTATGGTTCAAGCCA 58.984 37.500 0.00 0.00 41.25 4.75
290 291 6.832900 TCACATGATTTATGGTTCAAGCCATA 59.167 34.615 0.00 1.83 46.58 2.74
320 321 6.811665 GGCAGGAAAATCAAATGTTACTAACC 59.188 38.462 0.00 0.00 0.00 2.85
337 338 5.083821 ACTAACCAACCAAACAGGCATTAT 58.916 37.500 0.00 0.00 43.14 1.28
340 341 3.900601 ACCAACCAAACAGGCATTATGAA 59.099 39.130 0.00 0.00 43.14 2.57
346 347 5.990996 ACCAAACAGGCATTATGAAACAAAG 59.009 36.000 0.00 0.00 43.14 2.77
395 396 9.567848 CAACAAAAACTACAGCTCTTAAAAGAA 57.432 29.630 0.00 0.00 34.03 2.52
402 403 5.048846 ACAGCTCTTAAAAGAACCCTTCA 57.951 39.130 0.00 0.00 34.03 3.02
404 405 6.779860 ACAGCTCTTAAAAGAACCCTTCATA 58.220 36.000 0.00 0.00 34.03 2.15
417 434 6.605594 AGAACCCTTCATAACAAAGTGTTCAA 59.394 34.615 11.78 0.00 41.02 2.69
427 444 3.181487 ACAAAGTGTTCAACCAGATGTGC 60.181 43.478 0.00 0.00 0.00 4.57
451 468 2.437359 AAGATCGCCCTGCAGCAC 60.437 61.111 8.66 0.54 0.00 4.40
453 470 3.200593 GATCGCCCTGCAGCACAG 61.201 66.667 8.66 0.00 46.77 3.66
491 508 2.525368 GGTAACAATGCCTTCCTTGGT 58.475 47.619 0.00 0.00 0.00 3.67
502 519 2.619849 CCTTCCTTGGTGACATGCAGAT 60.620 50.000 0.00 0.00 42.32 2.90
503 520 2.408271 TCCTTGGTGACATGCAGATC 57.592 50.000 0.00 0.00 42.32 2.75
504 521 1.629861 TCCTTGGTGACATGCAGATCA 59.370 47.619 0.00 0.00 42.32 2.92
505 522 2.040145 TCCTTGGTGACATGCAGATCAA 59.960 45.455 4.34 0.00 42.32 2.57
506 523 2.821378 CCTTGGTGACATGCAGATCAAA 59.179 45.455 4.34 0.00 42.32 2.69
507 524 3.119602 CCTTGGTGACATGCAGATCAAAG 60.120 47.826 4.34 6.01 42.32 2.77
508 525 3.144657 TGGTGACATGCAGATCAAAGT 57.855 42.857 4.34 0.00 33.40 2.66
509 526 3.076621 TGGTGACATGCAGATCAAAGTC 58.923 45.455 4.34 0.00 35.58 3.01
510 527 3.076621 GGTGACATGCAGATCAAAGTCA 58.923 45.455 4.34 0.00 39.71 3.41
511 528 3.126514 GGTGACATGCAGATCAAAGTCAG 59.873 47.826 4.34 0.00 41.36 3.51
512 529 3.126514 GTGACATGCAGATCAAAGTCAGG 59.873 47.826 4.34 0.00 41.36 3.86
513 530 2.681848 GACATGCAGATCAAAGTCAGGG 59.318 50.000 0.00 0.00 35.30 4.45
514 531 2.022195 CATGCAGATCAAAGTCAGGGG 58.978 52.381 0.00 0.00 0.00 4.79
515 532 0.329261 TGCAGATCAAAGTCAGGGGG 59.671 55.000 0.00 0.00 0.00 5.40
516 533 1.034292 GCAGATCAAAGTCAGGGGGC 61.034 60.000 0.00 0.00 0.00 5.80
517 534 0.394899 CAGATCAAAGTCAGGGGGCC 60.395 60.000 0.00 0.00 0.00 5.80
518 535 0.551131 AGATCAAAGTCAGGGGGCCT 60.551 55.000 0.84 0.00 0.00 5.19
519 536 1.213296 GATCAAAGTCAGGGGGCCTA 58.787 55.000 0.84 0.00 29.64 3.93
520 537 1.564348 GATCAAAGTCAGGGGGCCTAA 59.436 52.381 0.84 0.00 29.64 2.69
521 538 0.696501 TCAAAGTCAGGGGGCCTAAC 59.303 55.000 0.84 0.00 29.64 2.34
522 539 0.698818 CAAAGTCAGGGGGCCTAACT 59.301 55.000 0.84 0.00 29.64 2.24
523 540 0.698818 AAAGTCAGGGGGCCTAACTG 59.301 55.000 0.84 10.21 29.64 3.16
539 556 3.423539 AACTGAAGGTGCTGCAGAATA 57.576 42.857 20.43 0.00 39.42 1.75
555 572 7.601886 GCTGCAGAATACAGATACTATGTCAAT 59.398 37.037 20.43 0.00 37.32 2.57
566 583 9.599866 CAGATACTATGTCAATTTTGTCAGGTA 57.400 33.333 0.00 3.73 30.34 3.08
567 584 9.823647 AGATACTATGTCAATTTTGTCAGGTAG 57.176 33.333 9.72 5.32 30.34 3.18
568 585 6.743575 ACTATGTCAATTTTGTCAGGTAGC 57.256 37.500 0.00 0.00 30.34 3.58
622 639 5.793817 TCAACATAGCAGAGCAAAAGTAGA 58.206 37.500 0.00 0.00 0.00 2.59
729 863 9.806203 CCAGCATCATAAGAACAAAATGAAATA 57.194 29.630 0.00 0.00 33.60 1.40
798 932 7.443302 TTGGTCTTCTTATTCATCCTCAGAT 57.557 36.000 0.00 0.00 0.00 2.90
953 1119 9.001542 ACCAAACATCAAACAAAATGAATATGG 57.998 29.630 0.00 0.00 0.00 2.74
954 1120 9.001542 CCAAACATCAAACAAAATGAATATGGT 57.998 29.630 0.00 0.00 0.00 3.55
958 1124 9.426837 ACATCAAACAAAATGAATATGGTTCAG 57.573 29.630 2.49 0.00 0.00 3.02
1118 1285 7.767198 TCTTAACATCCACGAGGGTAAAAATAG 59.233 37.037 0.00 0.00 38.11 1.73
1147 1338 3.669557 CGTTGTGTATAAAACCCTGCAGC 60.670 47.826 8.66 0.00 0.00 5.25
1192 1432 5.236282 ACCATTCATTCATATCTCTCTGCG 58.764 41.667 0.00 0.00 0.00 5.18
1213 1453 3.742433 GCACTATGCACACCTCTATCT 57.258 47.619 0.00 0.00 44.26 1.98
1214 1454 3.648009 GCACTATGCACACCTCTATCTC 58.352 50.000 0.00 0.00 44.26 2.75
1215 1455 3.068732 GCACTATGCACACCTCTATCTCA 59.931 47.826 0.00 0.00 44.26 3.27
1216 1456 4.795635 GCACTATGCACACCTCTATCTCAG 60.796 50.000 0.00 0.00 44.26 3.35
1463 4822 9.265901 CACCATTGATTTACACCAATTACAAAA 57.734 29.630 0.00 0.00 31.25 2.44
1611 4991 0.578683 CTCGGCACAATGTAGCATCG 59.421 55.000 9.30 5.56 0.00 3.84
1757 5161 2.669364 CTGAATCAAGCTGGTGCAAAC 58.331 47.619 0.00 0.00 42.74 2.93
1832 5238 2.359230 AGCGGCAGAGAAACAGCC 60.359 61.111 1.45 0.00 45.81 4.85
1914 5323 3.307339 TCCAAGAAACGAACGAAAACG 57.693 42.857 0.14 0.00 0.00 3.60
1922 5331 1.203313 GAACGAAAACGTGCGAGGG 59.797 57.895 11.85 0.00 0.00 4.30
1924 5333 0.601841 AACGAAAACGTGCGAGGGAT 60.602 50.000 11.85 0.00 0.00 3.85
1988 5427 4.170256 GTTTTTGGTTTGAAAGCTCACGA 58.830 39.130 8.67 0.00 0.00 4.35
2075 5514 4.083590 CCAAGAAGAAAAGAGAAAGCGAGG 60.084 45.833 0.00 0.00 0.00 4.63
2156 5595 0.532862 GATGAATCCGCCACACCGAT 60.533 55.000 0.00 0.00 0.00 4.18
2179 5618 5.808042 ATTTTGAGATGAACCATCACGAG 57.192 39.130 9.30 0.00 42.72 4.18
2227 5666 0.979665 TCACCAGAGAAGGCAAGGAG 59.020 55.000 0.00 0.00 0.00 3.69
2352 5814 2.077687 ATCATCACAAGCAATCCCCC 57.922 50.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.177531 GCATCTGTGTTGCGCCTG 59.822 61.111 4.18 0.00 0.00 4.85
1 2 3.058160 GGCATCTGTGTTGCGCCT 61.058 61.111 4.18 0.00 41.07 5.52
2 3 2.703798 ATGGCATCTGTGTTGCGCC 61.704 57.895 4.18 0.00 41.07 6.53
3 4 1.515519 CATGGCATCTGTGTTGCGC 60.516 57.895 0.00 0.00 41.07 6.09
4 5 1.515519 GCATGGCATCTGTGTTGCG 60.516 57.895 0.00 0.00 41.07 4.85
5 6 0.038067 TTGCATGGCATCTGTGTTGC 60.038 50.000 0.00 0.00 38.76 4.17
6 7 2.333926 CTTTGCATGGCATCTGTGTTG 58.666 47.619 0.00 0.00 38.76 3.33
7 8 1.274167 CCTTTGCATGGCATCTGTGTT 59.726 47.619 0.00 0.00 38.76 3.32
8 9 0.892755 CCTTTGCATGGCATCTGTGT 59.107 50.000 0.00 0.00 38.76 3.72
9 10 1.134367 CTCCTTTGCATGGCATCTGTG 59.866 52.381 0.00 0.00 38.76 3.66
10 11 1.005097 TCTCCTTTGCATGGCATCTGT 59.995 47.619 0.00 0.00 38.76 3.41
11 12 1.758936 TCTCCTTTGCATGGCATCTG 58.241 50.000 0.00 0.00 38.76 2.90
14 15 2.169769 CCAAATCTCCTTTGCATGGCAT 59.830 45.455 0.00 0.00 42.46 4.40
15 16 1.551430 CCAAATCTCCTTTGCATGGCA 59.449 47.619 0.00 0.00 42.46 4.92
16 17 1.134610 CCCAAATCTCCTTTGCATGGC 60.135 52.381 0.00 0.00 42.46 4.40
17 18 2.181975 ACCCAAATCTCCTTTGCATGG 58.818 47.619 0.00 0.00 42.46 3.66
18 19 3.967332 AACCCAAATCTCCTTTGCATG 57.033 42.857 0.00 0.00 42.46 4.06
19 20 3.008266 CCAAACCCAAATCTCCTTTGCAT 59.992 43.478 0.00 0.00 42.46 3.96
21 22 2.632512 TCCAAACCCAAATCTCCTTTGC 59.367 45.455 0.00 0.00 42.46 3.68
22 23 4.380867 CGATCCAAACCCAAATCTCCTTTG 60.381 45.833 0.00 0.00 43.27 2.77
23 24 3.763897 CGATCCAAACCCAAATCTCCTTT 59.236 43.478 0.00 0.00 0.00 3.11
26 27 2.683362 GTCGATCCAAACCCAAATCTCC 59.317 50.000 0.00 0.00 0.00 3.71
27 28 2.351726 CGTCGATCCAAACCCAAATCTC 59.648 50.000 0.00 0.00 0.00 2.75
28 29 2.356135 CGTCGATCCAAACCCAAATCT 58.644 47.619 0.00 0.00 0.00 2.40
31 32 1.570347 CGCGTCGATCCAAACCCAAA 61.570 55.000 0.00 0.00 0.00 3.28
33 34 2.433491 CGCGTCGATCCAAACCCA 60.433 61.111 0.00 0.00 0.00 4.51
35 36 1.131826 CAACGCGTCGATCCAAACC 59.868 57.895 14.44 0.00 0.00 3.27
36 37 1.131826 CCAACGCGTCGATCCAAAC 59.868 57.895 14.44 0.00 0.00 2.93
37 38 2.030401 CCCAACGCGTCGATCCAAA 61.030 57.895 14.44 0.00 0.00 3.28
38 39 2.433491 CCCAACGCGTCGATCCAA 60.433 61.111 14.44 0.00 0.00 3.53
42 43 4.814294 GAGGCCCAACGCGTCGAT 62.814 66.667 14.44 0.00 42.10 3.59
49 50 2.113139 AACAGTGGAGGCCCAACG 59.887 61.111 0.00 0.00 45.59 4.10
50 51 1.152756 ACAACAGTGGAGGCCCAAC 60.153 57.895 0.00 0.00 45.59 3.77
52 53 2.829384 GGACAACAGTGGAGGCCCA 61.829 63.158 0.00 0.00 40.95 5.36
53 54 2.034221 GGACAACAGTGGAGGCCC 59.966 66.667 0.00 0.00 0.00 5.80
55 56 1.374758 CGAGGACAACAGTGGAGGC 60.375 63.158 0.00 0.00 0.00 4.70
57 58 1.374758 GGCGAGGACAACAGTGGAG 60.375 63.158 0.00 0.00 0.00 3.86
58 59 2.741092 GGCGAGGACAACAGTGGA 59.259 61.111 0.00 0.00 0.00 4.02
59 60 2.738521 CGGCGAGGACAACAGTGG 60.739 66.667 0.00 0.00 0.00 4.00
61 62 2.338984 GTCGGCGAGGACAACAGT 59.661 61.111 11.20 0.00 36.91 3.55
62 63 2.338620 TGTCGGCGAGGACAACAG 59.661 61.111 11.20 0.00 43.55 3.16
67 68 1.155424 TTGTTTGTGTCGGCGAGGAC 61.155 55.000 11.20 11.16 37.45 3.85
68 69 0.462225 TTTGTTTGTGTCGGCGAGGA 60.462 50.000 11.20 0.00 0.00 3.71
69 70 0.316689 GTTTGTTTGTGTCGGCGAGG 60.317 55.000 11.20 0.00 0.00 4.63
72 73 0.179187 TGTGTTTGTTTGTGTCGGCG 60.179 50.000 0.00 0.00 0.00 6.46
73 74 1.544686 CTGTGTTTGTTTGTGTCGGC 58.455 50.000 0.00 0.00 0.00 5.54
74 75 1.797348 GCCTGTGTTTGTTTGTGTCGG 60.797 52.381 0.00 0.00 0.00 4.79
75 76 1.135546 TGCCTGTGTTTGTTTGTGTCG 60.136 47.619 0.00 0.00 0.00 4.35
76 77 2.645730 TGCCTGTGTTTGTTTGTGTC 57.354 45.000 0.00 0.00 0.00 3.67
77 78 3.063485 GTTTGCCTGTGTTTGTTTGTGT 58.937 40.909 0.00 0.00 0.00 3.72
79 80 3.393089 TGTTTGCCTGTGTTTGTTTGT 57.607 38.095 0.00 0.00 0.00 2.83
80 81 4.739046 TTTGTTTGCCTGTGTTTGTTTG 57.261 36.364 0.00 0.00 0.00 2.93
81 82 5.240403 ACATTTTGTTTGCCTGTGTTTGTTT 59.760 32.000 0.00 0.00 0.00 2.83
82 83 4.759183 ACATTTTGTTTGCCTGTGTTTGTT 59.241 33.333 0.00 0.00 0.00 2.83
83 84 4.153835 CACATTTTGTTTGCCTGTGTTTGT 59.846 37.500 0.00 0.00 34.07 2.83
84 85 4.153835 ACACATTTTGTTTGCCTGTGTTTG 59.846 37.500 1.05 0.00 45.94 2.93
86 87 3.936564 ACACATTTTGTTTGCCTGTGTT 58.063 36.364 1.05 0.00 45.94 3.32
87 88 3.608316 ACACATTTTGTTTGCCTGTGT 57.392 38.095 1.05 1.05 44.01 3.72
88 89 2.535166 CGACACATTTTGTTTGCCTGTG 59.465 45.455 0.00 0.00 39.17 3.66
89 90 2.808244 CGACACATTTTGTTTGCCTGT 58.192 42.857 0.00 0.00 39.17 4.00
90 91 1.522258 GCGACACATTTTGTTTGCCTG 59.478 47.619 0.00 0.00 39.17 4.85
92 93 0.858583 GGCGACACATTTTGTTTGCC 59.141 50.000 4.92 4.92 46.60 4.52
93 94 1.786579 GAGGCGACACATTTTGTTTGC 59.213 47.619 0.00 0.00 39.17 3.68
94 95 2.788786 GTGAGGCGACACATTTTGTTTG 59.211 45.455 11.63 0.00 39.17 2.93
95 96 2.687935 AGTGAGGCGACACATTTTGTTT 59.312 40.909 16.96 0.00 39.17 2.83
96 97 2.033299 CAGTGAGGCGACACATTTTGTT 59.967 45.455 16.96 0.00 39.17 2.83
99 100 1.202758 TCCAGTGAGGCGACACATTTT 60.203 47.619 16.96 0.00 42.45 1.82
101 102 0.036952 CTCCAGTGAGGCGACACATT 60.037 55.000 16.96 0.00 42.45 2.71
102 103 1.188219 ACTCCAGTGAGGCGACACAT 61.188 55.000 16.96 3.46 43.29 3.21
103 104 1.399744 AACTCCAGTGAGGCGACACA 61.400 55.000 16.96 0.00 43.29 3.72
104 105 0.946221 CAACTCCAGTGAGGCGACAC 60.946 60.000 9.20 9.20 43.29 3.67
105 106 1.367471 CAACTCCAGTGAGGCGACA 59.633 57.895 0.00 0.00 43.29 4.35
106 107 2.029844 GCAACTCCAGTGAGGCGAC 61.030 63.158 0.00 0.00 43.29 5.19
107 108 2.159819 GAGCAACTCCAGTGAGGCGA 62.160 60.000 0.00 0.00 43.29 5.54
108 109 1.739562 GAGCAACTCCAGTGAGGCG 60.740 63.158 0.00 0.00 43.29 5.52
109 110 0.036022 AAGAGCAACTCCAGTGAGGC 59.964 55.000 0.00 0.00 43.29 4.70
110 111 1.345741 TCAAGAGCAACTCCAGTGAGG 59.654 52.381 0.00 0.00 43.29 3.86
111 112 2.827800 TCAAGAGCAACTCCAGTGAG 57.172 50.000 0.00 0.00 44.62 3.51
112 113 4.890158 TTATCAAGAGCAACTCCAGTGA 57.110 40.909 0.00 0.00 0.00 3.41
115 116 4.686972 TCGATTATCAAGAGCAACTCCAG 58.313 43.478 0.00 0.00 0.00 3.86
117 118 6.425504 CAAATCGATTATCAAGAGCAACTCC 58.574 40.000 11.83 0.00 0.00 3.85
118 119 6.258727 TCCAAATCGATTATCAAGAGCAACTC 59.741 38.462 11.83 0.00 0.00 3.01
120 121 6.363577 TCCAAATCGATTATCAAGAGCAAC 57.636 37.500 11.83 0.00 0.00 4.17
123 124 4.754114 AGCTCCAAATCGATTATCAAGAGC 59.246 41.667 25.03 25.03 43.46 4.09
124 125 8.441608 CAATAGCTCCAAATCGATTATCAAGAG 58.558 37.037 11.83 13.20 0.00 2.85
125 126 7.095060 GCAATAGCTCCAAATCGATTATCAAGA 60.095 37.037 11.83 3.54 37.91 3.02
126 127 7.020010 GCAATAGCTCCAAATCGATTATCAAG 58.980 38.462 11.83 8.04 37.91 3.02
127 128 6.486320 TGCAATAGCTCCAAATCGATTATCAA 59.514 34.615 11.83 0.00 42.74 2.57
128 129 5.997129 TGCAATAGCTCCAAATCGATTATCA 59.003 36.000 11.83 0.00 42.74 2.15
129 130 6.369890 TCTGCAATAGCTCCAAATCGATTATC 59.630 38.462 11.83 0.00 42.74 1.75
131 132 5.610398 TCTGCAATAGCTCCAAATCGATTA 58.390 37.500 11.83 0.00 42.74 1.75
132 133 4.454678 TCTGCAATAGCTCCAAATCGATT 58.545 39.130 4.39 4.39 42.74 3.34
134 135 3.541996 TCTGCAATAGCTCCAAATCGA 57.458 42.857 0.00 0.00 42.74 3.59
135 136 3.811497 TCATCTGCAATAGCTCCAAATCG 59.189 43.478 0.00 0.00 42.74 3.34
138 139 3.954200 TGTCATCTGCAATAGCTCCAAA 58.046 40.909 0.00 0.00 42.74 3.28
139 140 3.632643 TGTCATCTGCAATAGCTCCAA 57.367 42.857 0.00 0.00 42.74 3.53
141 142 3.736720 TCATGTCATCTGCAATAGCTCC 58.263 45.455 0.00 0.00 42.74 4.70
142 143 4.815308 ACTTCATGTCATCTGCAATAGCTC 59.185 41.667 0.00 0.00 42.74 4.09
143 144 4.778579 ACTTCATGTCATCTGCAATAGCT 58.221 39.130 0.00 0.00 42.74 3.32
144 145 5.332883 CGTACTTCATGTCATCTGCAATAGC 60.333 44.000 0.00 0.00 42.57 2.97
145 146 5.979517 TCGTACTTCATGTCATCTGCAATAG 59.020 40.000 0.00 0.00 0.00 1.73
146 147 5.901552 TCGTACTTCATGTCATCTGCAATA 58.098 37.500 0.00 0.00 0.00 1.90
148 149 4.186856 TCGTACTTCATGTCATCTGCAA 57.813 40.909 0.00 0.00 0.00 4.08
149 150 3.866883 TCGTACTTCATGTCATCTGCA 57.133 42.857 0.00 0.00 0.00 4.41
151 152 7.065216 ACAAATTCGTACTTCATGTCATCTG 57.935 36.000 0.00 0.00 0.00 2.90
152 153 7.148407 GGAACAAATTCGTACTTCATGTCATCT 60.148 37.037 0.00 0.00 35.48 2.90
153 154 6.961554 GGAACAAATTCGTACTTCATGTCATC 59.038 38.462 0.00 0.00 35.48 2.92
155 156 5.995282 AGGAACAAATTCGTACTTCATGTCA 59.005 36.000 0.00 0.00 35.48 3.58
156 157 6.073222 ACAGGAACAAATTCGTACTTCATGTC 60.073 38.462 3.98 0.00 32.04 3.06
158 159 6.241207 ACAGGAACAAATTCGTACTTCATG 57.759 37.500 2.93 2.93 35.48 3.07
160 161 4.446385 CGACAGGAACAAATTCGTACTTCA 59.554 41.667 0.00 0.00 35.48 3.02
161 162 4.143179 CCGACAGGAACAAATTCGTACTTC 60.143 45.833 0.00 0.00 41.02 3.01
162 163 3.744426 CCGACAGGAACAAATTCGTACTT 59.256 43.478 0.00 0.00 41.02 2.24
163 164 3.323243 CCGACAGGAACAAATTCGTACT 58.677 45.455 0.00 0.00 41.02 2.73
165 166 2.070783 GCCGACAGGAACAAATTCGTA 58.929 47.619 0.00 0.00 41.02 3.43
166 167 0.872388 GCCGACAGGAACAAATTCGT 59.128 50.000 0.00 0.00 41.02 3.85
167 168 1.156736 AGCCGACAGGAACAAATTCG 58.843 50.000 0.00 0.00 41.02 3.34
168 169 4.759516 TTTAGCCGACAGGAACAAATTC 57.240 40.909 0.00 0.00 41.02 2.17
170 171 3.886505 TGTTTTAGCCGACAGGAACAAAT 59.113 39.130 0.00 0.00 41.02 2.32
171 172 3.280295 TGTTTTAGCCGACAGGAACAAA 58.720 40.909 0.00 0.00 41.02 2.83
172 173 2.920524 TGTTTTAGCCGACAGGAACAA 58.079 42.857 0.00 0.00 41.02 2.83
175 176 3.745799 TGATTGTTTTAGCCGACAGGAA 58.254 40.909 0.00 0.00 41.02 3.36
176 177 3.410631 TGATTGTTTTAGCCGACAGGA 57.589 42.857 0.00 0.00 41.02 3.86
177 178 4.497473 TTTGATTGTTTTAGCCGACAGG 57.503 40.909 0.00 0.00 41.62 4.00
178 179 5.519722 AGTTTTGATTGTTTTAGCCGACAG 58.480 37.500 0.00 0.00 0.00 3.51
179 180 5.508200 AGTTTTGATTGTTTTAGCCGACA 57.492 34.783 0.00 0.00 0.00 4.35
181 182 5.334260 CCGTAGTTTTGATTGTTTTAGCCGA 60.334 40.000 0.00 0.00 0.00 5.54
182 183 4.849383 CCGTAGTTTTGATTGTTTTAGCCG 59.151 41.667 0.00 0.00 0.00 5.52
183 184 6.004408 TCCGTAGTTTTGATTGTTTTAGCC 57.996 37.500 0.00 0.00 0.00 3.93
184 185 8.448615 ACTATCCGTAGTTTTGATTGTTTTAGC 58.551 33.333 0.00 0.00 37.94 3.09
200 201 7.105241 ACCTGTTTACCTAAACTATCCGTAG 57.895 40.000 8.92 0.00 44.36 3.51
201 202 7.480760 AACCTGTTTACCTAAACTATCCGTA 57.519 36.000 8.92 0.00 44.36 4.02
202 203 6.364568 AACCTGTTTACCTAAACTATCCGT 57.635 37.500 8.92 0.00 44.36 4.69
203 204 7.677454 AAAACCTGTTTACCTAAACTATCCG 57.323 36.000 8.92 0.00 44.36 4.18
229 230 9.268268 CCAAACTAGAAATTCTTACACAGTACA 57.732 33.333 0.00 0.00 0.00 2.90
230 231 9.485206 TCCAAACTAGAAATTCTTACACAGTAC 57.515 33.333 0.00 0.00 0.00 2.73
232 233 9.220767 GATCCAAACTAGAAATTCTTACACAGT 57.779 33.333 0.00 0.00 0.00 3.55
234 235 9.436957 GAGATCCAAACTAGAAATTCTTACACA 57.563 33.333 0.00 0.00 0.00 3.72
235 236 8.884726 GGAGATCCAAACTAGAAATTCTTACAC 58.115 37.037 0.00 0.00 35.64 2.90
236 237 8.826765 AGGAGATCCAAACTAGAAATTCTTACA 58.173 33.333 0.00 0.00 38.89 2.41
238 239 9.672673 CAAGGAGATCCAAACTAGAAATTCTTA 57.327 33.333 0.00 0.00 38.89 2.10
241 242 7.607991 TGACAAGGAGATCCAAACTAGAAATTC 59.392 37.037 0.00 0.00 38.89 2.17
242 243 7.391833 GTGACAAGGAGATCCAAACTAGAAATT 59.608 37.037 0.00 0.00 38.89 1.82
243 244 6.881602 GTGACAAGGAGATCCAAACTAGAAAT 59.118 38.462 0.00 0.00 38.89 2.17
244 245 6.183361 TGTGACAAGGAGATCCAAACTAGAAA 60.183 38.462 0.00 0.00 38.89 2.52
245 246 5.306937 TGTGACAAGGAGATCCAAACTAGAA 59.693 40.000 0.00 0.00 38.89 2.10
246 247 4.838423 TGTGACAAGGAGATCCAAACTAGA 59.162 41.667 0.00 0.00 38.89 2.43
248 249 5.248248 TCATGTGACAAGGAGATCCAAACTA 59.752 40.000 0.92 0.00 38.89 2.24
250 251 4.326826 TCATGTGACAAGGAGATCCAAAC 58.673 43.478 0.92 0.00 38.89 2.93
251 252 4.639078 TCATGTGACAAGGAGATCCAAA 57.361 40.909 0.92 0.00 38.89 3.28
252 253 4.849813 ATCATGTGACAAGGAGATCCAA 57.150 40.909 0.92 0.00 38.89 3.53
253 254 4.849813 AATCATGTGACAAGGAGATCCA 57.150 40.909 0.92 0.00 38.89 3.41
254 255 6.206243 CCATAAATCATGTGACAAGGAGATCC 59.794 42.308 0.00 0.00 32.21 3.36
255 256 6.769822 ACCATAAATCATGTGACAAGGAGATC 59.230 38.462 0.00 0.00 32.21 2.75
260 261 6.513806 TGAACCATAAATCATGTGACAAGG 57.486 37.500 0.00 0.00 32.21 3.61
261 262 6.529125 GCTTGAACCATAAATCATGTGACAAG 59.471 38.462 0.00 0.00 33.38 3.16
263 264 5.105797 GGCTTGAACCATAAATCATGTGACA 60.106 40.000 0.00 0.00 32.21 3.58
264 265 5.105797 TGGCTTGAACCATAAATCATGTGAC 60.106 40.000 0.00 0.00 33.75 3.67
265 266 5.015515 TGGCTTGAACCATAAATCATGTGA 58.984 37.500 0.00 0.00 33.75 3.58
266 267 5.327616 TGGCTTGAACCATAAATCATGTG 57.672 39.130 0.00 0.00 33.75 3.21
277 278 2.999331 GCCTTAGTATGGCTTGAACCA 58.001 47.619 17.69 0.00 46.38 3.67
286 287 6.773976 TTTGATTTTCCTGCCTTAGTATGG 57.226 37.500 0.00 0.00 0.00 2.74
287 288 7.775120 ACATTTGATTTTCCTGCCTTAGTATG 58.225 34.615 0.00 0.00 0.00 2.39
288 289 7.961326 ACATTTGATTTTCCTGCCTTAGTAT 57.039 32.000 0.00 0.00 0.00 2.12
289 290 7.775053 AACATTTGATTTTCCTGCCTTAGTA 57.225 32.000 0.00 0.00 0.00 1.82
290 291 6.670695 AACATTTGATTTTCCTGCCTTAGT 57.329 33.333 0.00 0.00 0.00 2.24
291 292 7.830739 AGTAACATTTGATTTTCCTGCCTTAG 58.169 34.615 0.00 0.00 0.00 2.18
320 321 5.295950 TGTTTCATAATGCCTGTTTGGTTG 58.704 37.500 0.00 0.00 38.35 3.77
360 361 8.319143 AGCTGTAGTTTTTGTTGTAATACGAT 57.681 30.769 0.00 0.00 0.00 3.73
362 363 7.793902 AGAGCTGTAGTTTTTGTTGTAATACG 58.206 34.615 0.00 0.00 0.00 3.06
378 379 6.231211 TGAAGGGTTCTTTTAAGAGCTGTAG 58.769 40.000 0.00 0.00 36.61 2.74
395 396 5.068591 GGTTGAACACTTTGTTATGAAGGGT 59.931 40.000 0.00 0.00 41.28 4.34
402 403 6.735694 GCACATCTGGTTGAACACTTTGTTAT 60.736 38.462 0.00 0.00 41.28 1.89
404 405 4.677779 GCACATCTGGTTGAACACTTTGTT 60.678 41.667 0.00 0.00 44.37 2.83
417 434 0.896940 CTTGGCCTTGCACATCTGGT 60.897 55.000 3.32 0.00 0.00 4.00
451 468 2.159338 CCGAACTTGCCCAATTGATCTG 60.159 50.000 7.12 0.00 0.00 2.90
453 470 1.818674 ACCGAACTTGCCCAATTGATC 59.181 47.619 7.12 0.00 0.00 2.92
460 477 1.883275 CATTGTTACCGAACTTGCCCA 59.117 47.619 0.00 0.00 36.45 5.36
491 508 3.340928 CCTGACTTTGATCTGCATGTCA 58.659 45.455 0.00 0.00 37.72 3.58
502 519 0.696501 GTTAGGCCCCCTGACTTTGA 59.303 55.000 0.00 0.00 37.20 2.69
503 520 0.698818 AGTTAGGCCCCCTGACTTTG 59.301 55.000 0.00 0.00 46.23 2.77
504 521 0.698818 CAGTTAGGCCCCCTGACTTT 59.301 55.000 0.00 0.00 46.23 2.66
505 522 0.178873 TCAGTTAGGCCCCCTGACTT 60.179 55.000 11.47 0.00 46.23 3.01
507 524 0.253327 CTTCAGTTAGGCCCCCTGAC 59.747 60.000 14.34 0.00 39.96 3.51
508 525 0.914417 CCTTCAGTTAGGCCCCCTGA 60.914 60.000 11.47 11.47 34.61 3.86
509 526 1.208165 ACCTTCAGTTAGGCCCCCTG 61.208 60.000 0.00 2.94 38.99 4.45
510 527 1.163555 ACCTTCAGTTAGGCCCCCT 59.836 57.895 0.00 0.00 38.99 4.79
511 528 1.303282 CACCTTCAGTTAGGCCCCC 59.697 63.158 0.00 0.00 38.99 5.40
512 529 1.378646 GCACCTTCAGTTAGGCCCC 60.379 63.158 0.00 0.00 38.99 5.80
513 530 0.678048 CAGCACCTTCAGTTAGGCCC 60.678 60.000 0.00 0.00 38.99 5.80
514 531 1.308783 GCAGCACCTTCAGTTAGGCC 61.309 60.000 0.00 0.00 38.99 5.19
515 532 0.606401 TGCAGCACCTTCAGTTAGGC 60.606 55.000 0.00 0.00 38.99 3.93
516 533 1.002430 TCTGCAGCACCTTCAGTTAGG 59.998 52.381 9.47 0.00 41.31 2.69
517 534 2.462456 TCTGCAGCACCTTCAGTTAG 57.538 50.000 9.47 0.00 0.00 2.34
518 535 2.928801 TTCTGCAGCACCTTCAGTTA 57.071 45.000 9.47 0.00 0.00 2.24
519 536 2.283145 ATTCTGCAGCACCTTCAGTT 57.717 45.000 9.47 0.00 0.00 3.16
520 537 2.038952 TGTATTCTGCAGCACCTTCAGT 59.961 45.455 9.47 0.00 0.00 3.41
521 538 2.676839 CTGTATTCTGCAGCACCTTCAG 59.323 50.000 9.47 8.67 0.00 3.02
522 539 2.302733 TCTGTATTCTGCAGCACCTTCA 59.697 45.455 9.47 2.69 34.21 3.02
523 540 2.977914 TCTGTATTCTGCAGCACCTTC 58.022 47.619 9.47 0.00 34.21 3.46
539 556 8.103305 ACCTGACAAAATTGACATAGTATCTGT 58.897 33.333 0.00 0.00 32.85 3.41
555 572 5.876357 ACTTATCCAAGCTACCTGACAAAA 58.124 37.500 0.00 0.00 34.94 2.44
566 583 9.905713 TCATAACTGAATTAACTTATCCAAGCT 57.094 29.630 0.00 0.00 34.94 3.74
595 612 6.846350 ACTTTTGCTCTGCTATGTTGATTAC 58.154 36.000 0.00 0.00 0.00 1.89
643 660 2.817258 TGAACAAATAGTCTTTGGCCCG 59.183 45.455 0.00 0.00 33.92 6.13
647 664 9.612620 GTGATTACTTGAACAAATAGTCTTTGG 57.387 33.333 6.02 0.00 33.92 3.28
912 1046 5.413309 TGTTTGGTGGATGTCTTGTTTTT 57.587 34.783 0.00 0.00 0.00 1.94
913 1047 5.128499 TGATGTTTGGTGGATGTCTTGTTTT 59.872 36.000 0.00 0.00 0.00 2.43
914 1048 4.648762 TGATGTTTGGTGGATGTCTTGTTT 59.351 37.500 0.00 0.00 0.00 2.83
917 1051 4.852134 TTGATGTTTGGTGGATGTCTTG 57.148 40.909 0.00 0.00 0.00 3.02
918 1052 4.648762 TGTTTGATGTTTGGTGGATGTCTT 59.351 37.500 0.00 0.00 0.00 3.01
920 1054 4.582701 TGTTTGATGTTTGGTGGATGTC 57.417 40.909 0.00 0.00 0.00 3.06
924 1075 5.982356 TCATTTTGTTTGATGTTTGGTGGA 58.018 33.333 0.00 0.00 0.00 4.02
1118 1285 6.799925 CAGGGTTTTATACACAACGAATGAAC 59.200 38.462 0.00 0.00 30.22 3.18
1147 1338 1.753073 GAACCATGAAATCCCAGCTGG 59.247 52.381 26.87 26.87 0.00 4.85
1192 1432 2.366916 AGATAGAGGTGTGCATAGTGCC 59.633 50.000 0.00 0.00 44.23 5.01
1250 1490 9.574516 GGATCTTGGTTTTAATCTGGTATATGT 57.425 33.333 0.00 0.00 0.00 2.29
1251 1491 9.799106 AGGATCTTGGTTTTAATCTGGTATATG 57.201 33.333 0.00 0.00 0.00 1.78
1391 4740 2.948979 TCTCAAAACATTCGCAGTTGGT 59.051 40.909 0.00 0.00 0.00 3.67
1392 4741 3.624326 TCTCAAAACATTCGCAGTTGG 57.376 42.857 0.00 0.00 0.00 3.77
1463 4822 8.763984 AATATAGTACTAGTTGCTGTAGGTGT 57.236 34.615 8.85 0.00 0.00 4.16
1697 5100 1.471676 CGGTTCTCTGAGGGATTTCGG 60.472 57.143 4.59 0.00 0.00 4.30
1757 5161 1.202770 GGTCTGGGATGGAAATACCCG 60.203 57.143 0.00 0.00 45.91 5.28
1832 5238 3.723835 GCCGTATGACACTGTAAAAAGCG 60.724 47.826 0.00 0.00 0.00 4.68
1914 5323 1.453155 ACATTGTTCATCCCTCGCAC 58.547 50.000 0.00 0.00 0.00 5.34
1922 5331 5.054390 TCGCCCTTTTTACATTGTTCATC 57.946 39.130 0.00 0.00 0.00 2.92
1924 5333 4.804108 CATCGCCCTTTTTACATTGTTCA 58.196 39.130 0.00 0.00 0.00 3.18
1988 5427 0.679002 GCAGTGGTGGCATCTGTCAT 60.679 55.000 14.96 0.00 29.66 3.06
2075 5514 5.329493 CCTTTTTATTCCGATGTTTCCGTC 58.671 41.667 0.00 0.00 0.00 4.79
2156 5595 5.294306 GCTCGTGATGGTTCATCTCAAAATA 59.706 40.000 9.00 0.00 41.06 1.40
2179 5618 3.514645 TCGTTTATCGAAGTAGGTTGGC 58.485 45.455 0.00 0.00 45.98 4.52
2352 5814 9.529325 TCTTCGTATTTTCTTGGTGTATGATAG 57.471 33.333 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.