Multiple sequence alignment - TraesCS4B01G148400

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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 TraesCS4B01G148400 chr4B 100.000 2591 0 0 1 2591 214007629 214010219 0.000000e+00 4785.0
1 TraesCS4B01G148400 chr4B 91.849 822 41 13 1733 2535 231364686 231365500 0.000000e+00 1123.0
2 TraesCS4B01G148400 chr2D 94.435 2246 101 7 369 2591 649859379 649857135 0.000000e+00 3434.0
3 TraesCS4B01G148400 chr2D 88.483 547 54 6 2051 2591 90781183 90780640 0.000000e+00 652.0
4 TraesCS4B01G148400 chr2D 92.509 267 20 0 987 1253 63381319 63381053 1.450000e-102 383.0
5 TraesCS4B01G148400 chr1B 93.675 2245 120 5 369 2591 81013810 81011566 0.000000e+00 3339.0
6 TraesCS4B01G148400 chr1B 86.667 345 37 6 12 354 649052375 649052712 8.760000e-100 374.0
7 TraesCS4B01G148400 chr3B 92.879 2261 122 11 352 2591 734326187 734323945 0.000000e+00 3247.0
8 TraesCS4B01G148400 chr3B 92.045 880 48 7 1733 2591 398623541 398624419 0.000000e+00 1218.0
9 TraesCS4B01G148400 chr3B 97.727 44 1 0 1703 1746 398623488 398623531 2.760000e-10 76.8
10 TraesCS4B01G148400 chr5D 91.685 1383 71 15 1250 2591 235710795 235709416 0.000000e+00 1877.0
11 TraesCS4B01G148400 chr5D 89.180 1220 76 24 1425 2591 12011720 12012936 0.000000e+00 1471.0
12 TraesCS4B01G148400 chr5D 95.122 615 30 0 346 960 12008052 12008666 0.000000e+00 970.0
13 TraesCS4B01G148400 chr5D 92.491 293 22 0 961 1253 235711579 235711287 1.110000e-113 420.0
14 TraesCS4B01G148400 chr5D 92.096 291 23 0 961 1251 12008637 12008927 6.670000e-111 411.0
15 TraesCS4B01G148400 chr5D 95.436 241 11 0 720 960 235711790 235711550 4.040000e-103 385.0
16 TraesCS4B01G148400 chr6A 91.604 1334 85 7 1280 2591 32066986 32068314 0.000000e+00 1818.0
17 TraesCS4B01G148400 chr6A 95.865 919 38 0 369 1287 32066041 32066959 0.000000e+00 1487.0
18 TraesCS4B01G148400 chr6D 87.477 1094 77 24 1250 2303 242422951 242421878 0.000000e+00 1206.0
19 TraesCS4B01G148400 chr6D 95.702 605 26 0 352 956 242424311 242423707 0.000000e+00 974.0
20 TraesCS4B01G148400 chr6D 91.792 597 33 7 1855 2435 367270733 367270137 0.000000e+00 817.0
21 TraesCS4B01G148400 chr6D 92.150 293 20 1 961 1253 242423732 242423443 6.670000e-111 411.0
22 TraesCS4B01G148400 chr7D 91.878 591 38 5 1855 2435 610726179 610726769 0.000000e+00 817.0
23 TraesCS4B01G148400 chr7D 87.143 210 10 4 1733 1926 23482208 23482416 3.360000e-54 222.0
24 TraesCS4B01G148400 chr3A 93.750 352 22 0 577 928 514169334 514169685 1.770000e-146 529.0
25 TraesCS4B01G148400 chr3D 93.277 357 19 4 577 928 394766801 394767157 2.950000e-144 521.0
26 TraesCS4B01G148400 chr3D 87.855 387 32 4 1307 1693 564094550 564094921 8.510000e-120 440.0
27 TraesCS4B01G148400 chr3D 85.788 387 38 9 1307 1693 23499065 23499434 6.720000e-106 394.0
28 TraesCS4B01G148400 chr3D 96.045 177 4 2 419 595 134545227 134545054 4.220000e-73 285.0
29 TraesCS4B01G148400 chr6B 97.544 285 7 0 541 825 59504582 59504298 3.000000e-134 488.0
30 TraesCS4B01G148400 chr1D 89.296 355 21 10 12 352 469217439 469217790 1.840000e-116 429.0
31 TraesCS4B01G148400 chr1D 86.905 168 18 3 1266 1433 392133241 392133078 4.400000e-43 185.0
32 TraesCS4B01G148400 chr4D 87.080 387 35 7 1307 1693 435253699 435254070 8.570000e-115 424.0
33 TraesCS4B01G148400 chr4D 92.884 267 19 0 987 1253 435253047 435253313 3.130000e-104 388.0
34 TraesCS4B01G148400 chr1A 87.080 387 32 6 1307 1693 428884074 428884442 3.080000e-114 422.0
35 TraesCS4B01G148400 chr1A 82.153 353 43 12 12 354 562318640 562318982 4.220000e-73 285.0
36 TraesCS4B01G148400 chr2B 97.059 170 5 0 419 588 141277307 141277138 1.170000e-73 287.0
37 TraesCS4B01G148400 chr5B 96.471 170 6 0 419 588 12741082 12740913 5.460000e-72 281.0
38 TraesCS4B01G148400 chr4A 85.096 208 17 1 1733 1926 722475730 722475523 1.570000e-47 200.0
39 TraesCS4B01G148400 chr4A 97.727 44 1 0 1703 1746 190336678 190336635 2.760000e-10 76.8


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 TraesCS4B01G148400 chr4B 214007629 214010219 2590 False 4785.000000 4785 100.000000 1 2591 1 chr4B.!!$F1 2590
1 TraesCS4B01G148400 chr4B 231364686 231365500 814 False 1123.000000 1123 91.849000 1733 2535 1 chr4B.!!$F2 802
2 TraesCS4B01G148400 chr2D 649857135 649859379 2244 True 3434.000000 3434 94.435000 369 2591 1 chr2D.!!$R3 2222
3 TraesCS4B01G148400 chr2D 90780640 90781183 543 True 652.000000 652 88.483000 2051 2591 1 chr2D.!!$R2 540
4 TraesCS4B01G148400 chr1B 81011566 81013810 2244 True 3339.000000 3339 93.675000 369 2591 1 chr1B.!!$R1 2222
5 TraesCS4B01G148400 chr3B 734323945 734326187 2242 True 3247.000000 3247 92.879000 352 2591 1 chr3B.!!$R1 2239
6 TraesCS4B01G148400 chr3B 398623488 398624419 931 False 647.400000 1218 94.886000 1703 2591 2 chr3B.!!$F1 888
7 TraesCS4B01G148400 chr5D 12008052 12012936 4884 False 950.666667 1471 92.132667 346 2591 3 chr5D.!!$F1 2245
8 TraesCS4B01G148400 chr5D 235709416 235711790 2374 True 894.000000 1877 93.204000 720 2591 3 chr5D.!!$R1 1871
9 TraesCS4B01G148400 chr6A 32066041 32068314 2273 False 1652.500000 1818 93.734500 369 2591 2 chr6A.!!$F1 2222
10 TraesCS4B01G148400 chr6D 242421878 242424311 2433 True 863.666667 1206 91.776333 352 2303 3 chr6D.!!$R2 1951
11 TraesCS4B01G148400 chr6D 367270137 367270733 596 True 817.000000 817 91.792000 1855 2435 1 chr6D.!!$R1 580
12 TraesCS4B01G148400 chr7D 610726179 610726769 590 False 817.000000 817 91.878000 1855 2435 1 chr7D.!!$F2 580
13 TraesCS4B01G148400 chr4D 435253047 435254070 1023 False 406.000000 424 89.982000 987 1693 2 chr4D.!!$F1 706

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
110 111 0.250467 ATGGAAGTTGTCGCTGTGCT 60.250 50.0 0.0 0.0 0.0 4.40 F
111 112 0.391228 TGGAAGTTGTCGCTGTGCTA 59.609 50.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 4149 0.179234 TGTCGCTGTCTTGGTTTCCA 59.821 50.0 0.00 0.00 0.00 3.53 R
2068 4856 1.308998 AAGCGAAACAGTGGTTCCTG 58.691 50.0 15.26 3.47 35.82 3.86 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
61 62 9.384764 ACTGCAATACTCTTAGAAAAATAGGAC 57.615 33.333 0.00 0.00 0.00 3.85
62 63 8.420374 TGCAATACTCTTAGAAAAATAGGACG 57.580 34.615 0.00 0.00 0.00 4.79
63 64 7.011109 TGCAATACTCTTAGAAAAATAGGACGC 59.989 37.037 0.00 0.00 0.00 5.19
64 65 7.518529 GCAATACTCTTAGAAAAATAGGACGCC 60.519 40.741 0.00 0.00 0.00 5.68
65 66 5.678955 ACTCTTAGAAAAATAGGACGCCT 57.321 39.130 3.87 3.87 37.71 5.52
66 67 6.051179 ACTCTTAGAAAAATAGGACGCCTT 57.949 37.500 3.71 0.00 34.61 4.35
67 68 5.875359 ACTCTTAGAAAAATAGGACGCCTTG 59.125 40.000 3.71 0.00 34.61 3.61
68 69 5.801380 TCTTAGAAAAATAGGACGCCTTGT 58.199 37.500 3.71 0.00 34.61 3.16
69 70 5.642063 TCTTAGAAAAATAGGACGCCTTGTG 59.358 40.000 3.71 0.00 34.61 3.33
70 71 2.488153 AGAAAAATAGGACGCCTTGTGC 59.512 45.455 3.71 0.00 39.61 4.57
75 76 2.980233 GGACGCCTTGTGCTTGCT 60.980 61.111 0.00 0.00 38.05 3.91
76 77 2.555547 GGACGCCTTGTGCTTGCTT 61.556 57.895 0.00 0.00 38.05 3.91
77 78 1.234615 GGACGCCTTGTGCTTGCTTA 61.235 55.000 0.00 0.00 38.05 3.09
78 79 0.591170 GACGCCTTGTGCTTGCTTAA 59.409 50.000 0.00 0.00 38.05 1.85
79 80 0.593128 ACGCCTTGTGCTTGCTTAAG 59.407 50.000 0.00 0.00 38.05 1.85
80 81 0.874390 CGCCTTGTGCTTGCTTAAGA 59.126 50.000 6.67 0.00 38.05 2.10
81 82 1.470098 CGCCTTGTGCTTGCTTAAGAT 59.530 47.619 6.67 0.00 38.05 2.40
82 83 2.476854 CGCCTTGTGCTTGCTTAAGATC 60.477 50.000 6.67 0.00 38.05 2.75
83 84 2.751806 GCCTTGTGCTTGCTTAAGATCT 59.248 45.455 6.67 0.00 36.87 2.75
84 85 3.427233 GCCTTGTGCTTGCTTAAGATCTG 60.427 47.826 6.67 0.00 36.87 2.90
85 86 4.005650 CCTTGTGCTTGCTTAAGATCTGA 58.994 43.478 6.67 0.00 0.00 3.27
86 87 4.639310 CCTTGTGCTTGCTTAAGATCTGAT 59.361 41.667 6.67 0.00 0.00 2.90
87 88 5.819379 CCTTGTGCTTGCTTAAGATCTGATA 59.181 40.000 6.67 0.00 0.00 2.15
88 89 6.485984 CCTTGTGCTTGCTTAAGATCTGATAT 59.514 38.462 6.67 0.00 0.00 1.63
89 90 7.658982 CCTTGTGCTTGCTTAAGATCTGATATA 59.341 37.037 6.67 0.00 0.00 0.86
90 91 9.217278 CTTGTGCTTGCTTAAGATCTGATATAT 57.783 33.333 6.67 0.00 0.00 0.86
94 95 9.828039 TGCTTGCTTAAGATCTGATATATATGG 57.172 33.333 6.67 0.00 0.00 2.74
104 105 8.194104 AGATCTGATATATATGGAAGTTGTCGC 58.806 37.037 0.00 0.00 0.00 5.19
105 106 7.468141 TCTGATATATATGGAAGTTGTCGCT 57.532 36.000 0.00 0.00 0.00 4.93
106 107 7.315890 TCTGATATATATGGAAGTTGTCGCTG 58.684 38.462 0.00 0.00 0.00 5.18
107 108 6.993079 TGATATATATGGAAGTTGTCGCTGT 58.007 36.000 0.00 0.00 0.00 4.40
108 109 6.868339 TGATATATATGGAAGTTGTCGCTGTG 59.132 38.462 0.00 0.00 0.00 3.66
109 110 1.438651 TATGGAAGTTGTCGCTGTGC 58.561 50.000 0.00 0.00 0.00 4.57
110 111 0.250467 ATGGAAGTTGTCGCTGTGCT 60.250 50.000 0.00 0.00 0.00 4.40
111 112 0.391228 TGGAAGTTGTCGCTGTGCTA 59.609 50.000 0.00 0.00 0.00 3.49
112 113 1.071605 GGAAGTTGTCGCTGTGCTAG 58.928 55.000 0.00 0.00 0.00 3.42
113 114 1.336887 GGAAGTTGTCGCTGTGCTAGA 60.337 52.381 0.00 0.00 0.00 2.43
114 115 2.404215 GAAGTTGTCGCTGTGCTAGAA 58.596 47.619 0.00 0.00 0.00 2.10
115 116 1.784525 AGTTGTCGCTGTGCTAGAAC 58.215 50.000 0.00 0.00 29.99 3.01
116 117 1.341531 AGTTGTCGCTGTGCTAGAACT 59.658 47.619 1.64 1.83 34.17 3.01
117 118 2.557056 AGTTGTCGCTGTGCTAGAACTA 59.443 45.455 1.64 0.00 36.43 2.24
118 119 3.193691 AGTTGTCGCTGTGCTAGAACTAT 59.806 43.478 1.64 0.00 36.43 2.12
119 120 3.868757 TGTCGCTGTGCTAGAACTATT 57.131 42.857 1.64 0.00 0.00 1.73
120 121 4.188247 TGTCGCTGTGCTAGAACTATTT 57.812 40.909 1.64 0.00 0.00 1.40
121 122 4.174009 TGTCGCTGTGCTAGAACTATTTC 58.826 43.478 1.64 0.00 0.00 2.17
122 123 3.240861 GTCGCTGTGCTAGAACTATTTCG 59.759 47.826 1.64 0.00 36.78 3.46
123 124 3.119602 TCGCTGTGCTAGAACTATTTCGT 60.120 43.478 1.64 0.00 36.78 3.85
124 125 3.000674 CGCTGTGCTAGAACTATTTCGTG 60.001 47.826 1.64 0.00 36.78 4.35
125 126 4.174009 GCTGTGCTAGAACTATTTCGTGA 58.826 43.478 1.64 0.00 36.78 4.35
126 127 4.806247 GCTGTGCTAGAACTATTTCGTGAT 59.194 41.667 1.64 0.00 36.78 3.06
127 128 5.276584 GCTGTGCTAGAACTATTTCGTGATG 60.277 44.000 1.64 0.00 36.78 3.07
128 129 5.109210 TGTGCTAGAACTATTTCGTGATGG 58.891 41.667 1.64 0.00 36.78 3.51
129 130 5.105513 TGTGCTAGAACTATTTCGTGATGGA 60.106 40.000 1.64 0.00 36.78 3.41
130 131 5.232414 GTGCTAGAACTATTTCGTGATGGAC 59.768 44.000 0.00 0.00 36.78 4.02
131 132 5.127194 TGCTAGAACTATTTCGTGATGGACT 59.873 40.000 0.00 0.00 36.78 3.85
132 133 5.460419 GCTAGAACTATTTCGTGATGGACTG 59.540 44.000 0.00 0.00 36.78 3.51
133 134 5.661056 AGAACTATTTCGTGATGGACTGA 57.339 39.130 0.00 0.00 36.78 3.41
134 135 6.227298 AGAACTATTTCGTGATGGACTGAT 57.773 37.500 0.00 0.00 36.78 2.90
135 136 6.045318 AGAACTATTTCGTGATGGACTGATG 58.955 40.000 0.00 0.00 36.78 3.07
136 137 4.697514 ACTATTTCGTGATGGACTGATGG 58.302 43.478 0.00 0.00 0.00 3.51
137 138 3.634397 ATTTCGTGATGGACTGATGGT 57.366 42.857 0.00 0.00 0.00 3.55
138 139 3.417069 TTTCGTGATGGACTGATGGTT 57.583 42.857 0.00 0.00 0.00 3.67
139 140 4.545208 TTTCGTGATGGACTGATGGTTA 57.455 40.909 0.00 0.00 0.00 2.85
140 141 4.545208 TTCGTGATGGACTGATGGTTAA 57.455 40.909 0.00 0.00 0.00 2.01
141 142 3.857052 TCGTGATGGACTGATGGTTAAC 58.143 45.455 0.00 0.00 0.00 2.01
142 143 2.603110 CGTGATGGACTGATGGTTAACG 59.397 50.000 0.00 0.00 0.00 3.18
143 144 3.674955 CGTGATGGACTGATGGTTAACGA 60.675 47.826 0.00 0.00 0.00 3.85
144 145 3.617263 GTGATGGACTGATGGTTAACGAC 59.383 47.826 0.00 0.00 0.00 4.34
145 146 3.259625 TGATGGACTGATGGTTAACGACA 59.740 43.478 0.00 0.00 0.00 4.35
146 147 3.034721 TGGACTGATGGTTAACGACAC 57.965 47.619 0.00 0.00 0.00 3.67
147 148 2.365941 TGGACTGATGGTTAACGACACA 59.634 45.455 0.00 0.00 0.00 3.72
148 149 2.735134 GGACTGATGGTTAACGACACAC 59.265 50.000 0.00 0.00 0.00 3.82
149 150 3.386486 GACTGATGGTTAACGACACACA 58.614 45.455 0.00 0.00 0.00 3.72
150 151 3.799366 ACTGATGGTTAACGACACACAA 58.201 40.909 0.00 0.00 0.00 3.33
151 152 4.385825 ACTGATGGTTAACGACACACAAT 58.614 39.130 0.00 0.00 0.00 2.71
152 153 5.543714 ACTGATGGTTAACGACACACAATA 58.456 37.500 0.00 0.00 0.00 1.90
153 154 6.170506 ACTGATGGTTAACGACACACAATAT 58.829 36.000 0.00 0.00 0.00 1.28
154 155 6.653320 ACTGATGGTTAACGACACACAATATT 59.347 34.615 0.00 0.00 0.00 1.28
155 156 7.174253 ACTGATGGTTAACGACACACAATATTT 59.826 33.333 0.00 0.00 0.00 1.40
156 157 8.549338 TGATGGTTAACGACACACAATATTTA 57.451 30.769 0.00 0.00 0.00 1.40
157 158 9.168451 TGATGGTTAACGACACACAATATTTAT 57.832 29.630 0.00 0.00 0.00 1.40
158 159 9.997482 GATGGTTAACGACACACAATATTTATT 57.003 29.630 0.00 0.00 0.00 1.40
203 204 7.837202 ATGATGCATTACATGTTTTTCTTGG 57.163 32.000 2.30 0.00 39.84 3.61
204 205 5.638657 TGATGCATTACATGTTTTTCTTGGC 59.361 36.000 2.30 0.00 39.84 4.52
205 206 5.212532 TGCATTACATGTTTTTCTTGGCT 57.787 34.783 2.30 0.00 0.00 4.75
206 207 6.338214 TGCATTACATGTTTTTCTTGGCTA 57.662 33.333 2.30 0.00 0.00 3.93
207 208 6.155827 TGCATTACATGTTTTTCTTGGCTAC 58.844 36.000 2.30 0.00 0.00 3.58
208 209 6.015519 TGCATTACATGTTTTTCTTGGCTACT 60.016 34.615 2.30 0.00 0.00 2.57
209 210 6.868339 GCATTACATGTTTTTCTTGGCTACTT 59.132 34.615 2.30 0.00 0.00 2.24
210 211 8.026607 GCATTACATGTTTTTCTTGGCTACTTA 58.973 33.333 2.30 0.00 0.00 2.24
211 212 9.906660 CATTACATGTTTTTCTTGGCTACTTAA 57.093 29.630 2.30 0.00 0.00 1.85
213 214 7.582667 ACATGTTTTTCTTGGCTACTTAAGT 57.417 32.000 13.68 13.68 0.00 2.24
214 215 7.425606 ACATGTTTTTCTTGGCTACTTAAGTG 58.574 34.615 18.56 9.20 0.00 3.16
215 216 5.827666 TGTTTTTCTTGGCTACTTAAGTGC 58.172 37.500 18.56 17.53 0.00 4.40
216 217 5.220381 GTTTTTCTTGGCTACTTAAGTGCC 58.780 41.667 28.08 28.08 40.32 5.01
217 218 4.367039 TTTCTTGGCTACTTAAGTGCCT 57.633 40.909 31.33 8.93 40.45 4.75
218 219 5.492855 TTTCTTGGCTACTTAAGTGCCTA 57.507 39.130 31.33 26.61 40.45 3.93
219 220 5.492855 TTCTTGGCTACTTAAGTGCCTAA 57.507 39.130 31.33 25.00 40.45 2.69
220 221 5.693769 TCTTGGCTACTTAAGTGCCTAAT 57.306 39.130 31.33 7.44 40.45 1.73
221 222 5.428253 TCTTGGCTACTTAAGTGCCTAATG 58.572 41.667 31.33 22.83 40.45 1.90
222 223 5.188948 TCTTGGCTACTTAAGTGCCTAATGA 59.811 40.000 31.33 23.92 40.45 2.57
223 224 5.429681 TGGCTACTTAAGTGCCTAATGAA 57.570 39.130 31.33 18.07 40.45 2.57
224 225 5.811190 TGGCTACTTAAGTGCCTAATGAAA 58.189 37.500 31.33 17.59 40.45 2.69
225 226 6.423182 TGGCTACTTAAGTGCCTAATGAAAT 58.577 36.000 31.33 5.09 40.45 2.17
226 227 6.889722 TGGCTACTTAAGTGCCTAATGAAATT 59.110 34.615 31.33 4.74 40.45 1.82
227 228 7.396055 TGGCTACTTAAGTGCCTAATGAAATTT 59.604 33.333 31.33 0.00 40.45 1.82
228 229 7.915923 GGCTACTTAAGTGCCTAATGAAATTTC 59.084 37.037 27.77 11.41 38.39 2.17
229 230 8.458843 GCTACTTAAGTGCCTAATGAAATTTCA 58.541 33.333 22.52 22.52 42.14 2.69
232 233 8.306761 ACTTAAGTGCCTAATGAAATTTCAAGG 58.693 33.333 25.36 25.36 41.13 3.61
233 234 6.670695 AAGTGCCTAATGAAATTTCAAGGT 57.329 33.333 27.95 18.41 41.13 3.50
234 235 6.670695 AGTGCCTAATGAAATTTCAAGGTT 57.329 33.333 27.95 19.71 41.13 3.50
235 236 7.066307 AGTGCCTAATGAAATTTCAAGGTTT 57.934 32.000 27.95 19.43 41.13 3.27
236 237 6.930722 AGTGCCTAATGAAATTTCAAGGTTTG 59.069 34.615 27.95 18.01 41.13 2.93
237 238 6.928492 GTGCCTAATGAAATTTCAAGGTTTGA 59.072 34.615 27.95 14.56 41.13 2.69
249 250 6.693315 TTCAAGGTTTGAACTTAAGAGGTG 57.307 37.500 10.09 0.00 44.21 4.00
250 251 5.751586 TCAAGGTTTGAACTTAAGAGGTGT 58.248 37.500 10.09 0.00 36.59 4.16
251 252 6.184789 TCAAGGTTTGAACTTAAGAGGTGTT 58.815 36.000 10.09 0.00 36.59 3.32
252 253 6.094881 TCAAGGTTTGAACTTAAGAGGTGTTG 59.905 38.462 10.09 2.96 36.59 3.33
253 254 4.338400 AGGTTTGAACTTAAGAGGTGTTGC 59.662 41.667 10.09 0.00 0.00 4.17
254 255 4.499188 GGTTTGAACTTAAGAGGTGTTGCC 60.499 45.833 10.09 0.00 37.58 4.52
288 289 7.360575 TGATTCTAAACTACTTTTCGGAAGC 57.639 36.000 0.00 0.00 31.58 3.86
289 290 7.159372 TGATTCTAAACTACTTTTCGGAAGCT 58.841 34.615 0.00 0.00 31.90 3.74
290 291 6.780706 TTCTAAACTACTTTTCGGAAGCTG 57.219 37.500 0.00 0.00 0.00 4.24
291 292 5.850614 TCTAAACTACTTTTCGGAAGCTGT 58.149 37.500 0.00 0.00 0.00 4.40
292 293 6.285990 TCTAAACTACTTTTCGGAAGCTGTT 58.714 36.000 0.00 3.36 0.00 3.16
293 294 5.830000 AAACTACTTTTCGGAAGCTGTTT 57.170 34.783 0.00 12.63 0.00 2.83
294 295 5.830000 AACTACTTTTCGGAAGCTGTTTT 57.170 34.783 0.00 0.00 0.00 2.43
295 296 5.169836 ACTACTTTTCGGAAGCTGTTTTG 57.830 39.130 0.00 0.00 0.00 2.44
296 297 4.879545 ACTACTTTTCGGAAGCTGTTTTGA 59.120 37.500 0.00 0.00 0.00 2.69
297 298 4.292977 ACTTTTCGGAAGCTGTTTTGAG 57.707 40.909 0.00 0.00 0.00 3.02
298 299 3.694566 ACTTTTCGGAAGCTGTTTTGAGT 59.305 39.130 0.00 0.00 0.00 3.41
299 300 4.879545 ACTTTTCGGAAGCTGTTTTGAGTA 59.120 37.500 0.00 0.00 0.00 2.59
300 301 4.806342 TTTCGGAAGCTGTTTTGAGTAC 57.194 40.909 0.00 0.00 0.00 2.73
301 302 3.746045 TCGGAAGCTGTTTTGAGTACT 57.254 42.857 0.00 0.00 0.00 2.73
302 303 4.859304 TCGGAAGCTGTTTTGAGTACTA 57.141 40.909 0.00 0.00 0.00 1.82
303 304 4.806330 TCGGAAGCTGTTTTGAGTACTAG 58.194 43.478 0.00 0.00 0.00 2.57
304 305 4.280174 TCGGAAGCTGTTTTGAGTACTAGT 59.720 41.667 0.00 0.00 0.00 2.57
305 306 4.989168 CGGAAGCTGTTTTGAGTACTAGTT 59.011 41.667 0.00 0.00 0.00 2.24
306 307 5.118817 CGGAAGCTGTTTTGAGTACTAGTTC 59.881 44.000 0.00 0.00 0.00 3.01
307 308 5.989777 GGAAGCTGTTTTGAGTACTAGTTCA 59.010 40.000 0.00 0.00 0.00 3.18
308 309 6.482308 GGAAGCTGTTTTGAGTACTAGTTCAA 59.518 38.462 0.00 2.97 0.00 2.69
309 310 6.846325 AGCTGTTTTGAGTACTAGTTCAAC 57.154 37.500 9.10 0.00 33.36 3.18
310 311 6.583562 AGCTGTTTTGAGTACTAGTTCAACT 58.416 36.000 9.10 3.19 33.36 3.16
311 312 7.048512 AGCTGTTTTGAGTACTAGTTCAACTT 58.951 34.615 9.10 0.00 33.36 2.66
312 313 7.224949 AGCTGTTTTGAGTACTAGTTCAACTTC 59.775 37.037 9.10 4.78 33.36 3.01
313 314 7.011109 GCTGTTTTGAGTACTAGTTCAACTTCA 59.989 37.037 9.10 8.10 33.36 3.02
314 315 8.958119 TGTTTTGAGTACTAGTTCAACTTCAT 57.042 30.769 9.10 0.00 33.36 2.57
315 316 8.826710 TGTTTTGAGTACTAGTTCAACTTCATG 58.173 33.333 9.10 0.00 33.36 3.07
316 317 8.827677 GTTTTGAGTACTAGTTCAACTTCATGT 58.172 33.333 9.10 0.00 33.36 3.21
345 346 9.833182 TTTTTGTTCTTTGCCTTTTAAAATCAC 57.167 25.926 0.09 0.00 0.00 3.06
346 347 6.820470 TGTTCTTTGCCTTTTAAAATCACG 57.180 33.333 0.09 0.00 0.00 4.35
347 348 6.334202 TGTTCTTTGCCTTTTAAAATCACGT 58.666 32.000 0.09 0.00 0.00 4.49
348 349 7.481642 TGTTCTTTGCCTTTTAAAATCACGTA 58.518 30.769 0.09 0.00 0.00 3.57
349 350 8.138712 TGTTCTTTGCCTTTTAAAATCACGTAT 58.861 29.630 0.09 0.00 0.00 3.06
350 351 8.974408 GTTCTTTGCCTTTTAAAATCACGTATT 58.026 29.630 0.09 0.00 0.00 1.89
354 355 8.649973 TTGCCTTTTAAAATCACGTATTTGTT 57.350 26.923 0.09 0.00 37.85 2.83
362 363 7.410800 AAAATCACGTATTTGTTCACGACTA 57.589 32.000 0.62 0.00 40.56 2.59
382 383 9.268268 ACGACTAATTGTTTTCTTGATTCACTA 57.732 29.630 0.00 0.00 0.00 2.74
495 496 8.614469 TGATTGTGTGAACATTATAACACTCA 57.386 30.769 6.38 0.00 42.66 3.41
673 674 7.581213 ACAGAAACAAGTTACATCAAATGGA 57.419 32.000 0.00 0.00 33.60 3.41
826 827 3.614092 AGCATACCCAGATTGTGTGAAG 58.386 45.455 0.00 0.00 0.00 3.02
852 853 2.676176 GCATAACAGCAGCAGTCTCTCA 60.676 50.000 0.00 0.00 0.00 3.27
867 868 1.554160 CTCTCAGACAAGCTGGGTCAT 59.446 52.381 18.00 4.05 45.74 3.06
1010 1041 2.614057 CGACCTTCAGGATGCATTTACC 59.386 50.000 0.00 0.00 38.94 2.85
1023 1054 3.376859 TGCATTTACCTATTGCAACCGAG 59.623 43.478 0.00 0.00 42.95 4.63
1076 1107 3.062763 CAGTCTGCTCACACGAAATCTT 58.937 45.455 0.00 0.00 0.00 2.40
1310 1870 1.421382 CATGCCCTCGCTTTGTTTTG 58.579 50.000 0.00 0.00 35.36 2.44
1362 1922 1.429463 AGTTCGCTCGGAAATGACAC 58.571 50.000 0.00 0.00 36.14 3.67
1462 4162 2.050144 AGCTCTCTGGAAACCAAGACA 58.950 47.619 0.00 0.00 30.80 3.41
1487 4187 2.552819 GCATCGACGGGATCCTCGA 61.553 63.158 23.62 23.62 42.79 4.04
1494 4194 1.153429 CGGGATCCTCGAACAACCC 60.153 63.158 12.58 7.17 0.00 4.11
1529 4243 1.338136 CGTCCTTCCCCTACCATGCT 61.338 60.000 0.00 0.00 0.00 3.79
1530 4244 0.919710 GTCCTTCCCCTACCATGCTT 59.080 55.000 0.00 0.00 0.00 3.91
1548 4262 2.501128 GCGACCTGCATCCAGCTA 59.499 61.111 0.00 0.00 45.94 3.32
1549 4263 1.070445 GCGACCTGCATCCAGCTAT 59.930 57.895 0.00 0.00 45.94 2.97
1561 4275 1.070445 CAGCTATTCCTGCCCCGAG 59.930 63.158 0.00 0.00 0.00 4.63
1607 4321 3.771479 AGCTGATGTAGGTGAGACAATCA 59.229 43.478 0.00 0.00 35.38 2.57
1635 4349 5.622460 CGATCTGTTGCTACTGGTAGAACTT 60.622 44.000 11.44 4.03 35.21 2.66
1817 4577 1.289160 TATTCCTGGCTCACCTGCTT 58.711 50.000 0.00 0.00 36.63 3.91
1953 4736 7.537596 TTTGTTTCATCATGTCCTGGTTTAT 57.462 32.000 0.00 0.00 0.00 1.40
2068 4856 7.118825 TGCTATCTAACTATGATCATTGCAAGC 59.881 37.037 14.65 13.92 0.00 4.01
2083 4871 1.269257 GCAAGCAGGAACCACTGTTTC 60.269 52.381 0.00 0.00 39.44 2.78
2088 4876 1.676006 CAGGAACCACTGTTTCGCTTT 59.324 47.619 0.00 0.00 34.94 3.51
2133 4923 0.329261 ACGGCCCATATGCATGCTAT 59.671 50.000 20.33 12.94 0.00 2.97
2172 4962 1.732809 TGACGTGCACGAAAACTTGAA 59.267 42.857 42.94 15.18 43.02 2.69
2242 5034 7.012232 GCTCTAGCTCTTCTTAATTTTCATGCT 59.988 37.037 0.00 0.00 38.21 3.79
2268 5060 4.467198 TCTTTCCGGACTTGATCTTACC 57.533 45.455 1.83 0.00 0.00 2.85
2300 5104 2.627699 ACCCCATCACATGTTGTTGTTC 59.372 45.455 0.00 0.00 0.00 3.18
2381 5192 6.713903 AGATGAAAGATGTTCAAAGAAGCTCA 59.286 34.615 0.00 0.00 31.55 4.26
2394 5205 7.865707 TCAAAGAAGCTCAAAGACATTCTTAC 58.134 34.615 0.00 0.00 38.82 2.34
2482 5295 7.786030 TCTTCTCTCCGTATCTGAATGAAATT 58.214 34.615 0.00 0.00 40.93 1.82
2577 5390 2.349590 TGGAAACATGACTCATGCGAG 58.650 47.619 17.50 0.00 44.80 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.384764 GTCCTATTTTTCTAAGAGTATTGCAGT 57.615 33.333 0.00 0.00 0.00 4.40
36 37 8.543774 CGTCCTATTTTTCTAAGAGTATTGCAG 58.456 37.037 0.00 0.00 0.00 4.41
37 38 7.011109 GCGTCCTATTTTTCTAAGAGTATTGCA 59.989 37.037 0.00 0.00 0.00 4.08
38 39 7.345943 GCGTCCTATTTTTCTAAGAGTATTGC 58.654 38.462 0.00 0.00 0.00 3.56
39 40 7.711339 AGGCGTCCTATTTTTCTAAGAGTATTG 59.289 37.037 0.00 0.00 28.47 1.90
40 41 7.793036 AGGCGTCCTATTTTTCTAAGAGTATT 58.207 34.615 0.00 0.00 28.47 1.89
41 42 7.362802 AGGCGTCCTATTTTTCTAAGAGTAT 57.637 36.000 0.00 0.00 28.47 2.12
42 43 6.786967 AGGCGTCCTATTTTTCTAAGAGTA 57.213 37.500 0.00 0.00 28.47 2.59
43 44 5.678955 AGGCGTCCTATTTTTCTAAGAGT 57.321 39.130 0.00 0.00 28.47 3.24
44 45 5.875359 ACAAGGCGTCCTATTTTTCTAAGAG 59.125 40.000 0.00 0.00 31.13 2.85
45 46 5.642063 CACAAGGCGTCCTATTTTTCTAAGA 59.358 40.000 0.00 0.00 31.13 2.10
46 47 5.673818 GCACAAGGCGTCCTATTTTTCTAAG 60.674 44.000 0.00 0.00 31.13 2.18
47 48 4.155280 GCACAAGGCGTCCTATTTTTCTAA 59.845 41.667 0.00 0.00 31.13 2.10
48 49 3.687698 GCACAAGGCGTCCTATTTTTCTA 59.312 43.478 0.00 0.00 31.13 2.10
49 50 2.488153 GCACAAGGCGTCCTATTTTTCT 59.512 45.455 0.00 0.00 31.13 2.52
50 51 2.863739 GCACAAGGCGTCCTATTTTTC 58.136 47.619 0.00 0.00 31.13 2.29
62 63 2.751806 AGATCTTAAGCAAGCACAAGGC 59.248 45.455 0.00 0.00 45.30 4.35
63 64 4.005650 TCAGATCTTAAGCAAGCACAAGG 58.994 43.478 0.00 0.00 0.00 3.61
64 65 5.814764 ATCAGATCTTAAGCAAGCACAAG 57.185 39.130 0.00 0.00 0.00 3.16
68 69 9.828039 CCATATATATCAGATCTTAAGCAAGCA 57.172 33.333 0.00 0.00 0.00 3.91
78 79 8.194104 GCGACAACTTCCATATATATCAGATCT 58.806 37.037 0.00 0.00 0.00 2.75
79 80 8.194104 AGCGACAACTTCCATATATATCAGATC 58.806 37.037 0.00 0.00 0.00 2.75
80 81 7.978414 CAGCGACAACTTCCATATATATCAGAT 59.022 37.037 0.00 0.00 0.00 2.90
81 82 7.039714 ACAGCGACAACTTCCATATATATCAGA 60.040 37.037 0.00 0.00 0.00 3.27
82 83 7.062722 CACAGCGACAACTTCCATATATATCAG 59.937 40.741 0.00 0.00 0.00 2.90
83 84 6.868339 CACAGCGACAACTTCCATATATATCA 59.132 38.462 0.00 0.00 0.00 2.15
84 85 6.183360 GCACAGCGACAACTTCCATATATATC 60.183 42.308 0.00 0.00 0.00 1.63
85 86 5.639506 GCACAGCGACAACTTCCATATATAT 59.360 40.000 0.00 0.00 0.00 0.86
86 87 4.988540 GCACAGCGACAACTTCCATATATA 59.011 41.667 0.00 0.00 0.00 0.86
87 88 3.809832 GCACAGCGACAACTTCCATATAT 59.190 43.478 0.00 0.00 0.00 0.86
88 89 3.118775 AGCACAGCGACAACTTCCATATA 60.119 43.478 0.00 0.00 0.00 0.86
89 90 2.009774 GCACAGCGACAACTTCCATAT 58.990 47.619 0.00 0.00 0.00 1.78
90 91 1.001974 AGCACAGCGACAACTTCCATA 59.998 47.619 0.00 0.00 0.00 2.74
91 92 0.250467 AGCACAGCGACAACTTCCAT 60.250 50.000 0.00 0.00 0.00 3.41
92 93 0.391228 TAGCACAGCGACAACTTCCA 59.609 50.000 0.00 0.00 0.00 3.53
93 94 1.071605 CTAGCACAGCGACAACTTCC 58.928 55.000 0.00 0.00 0.00 3.46
94 95 2.065993 TCTAGCACAGCGACAACTTC 57.934 50.000 0.00 0.00 0.00 3.01
95 96 2.135933 GTTCTAGCACAGCGACAACTT 58.864 47.619 0.00 0.00 0.00 2.66
96 97 1.341531 AGTTCTAGCACAGCGACAACT 59.658 47.619 0.00 0.00 0.00 3.16
97 98 1.784525 AGTTCTAGCACAGCGACAAC 58.215 50.000 0.00 0.00 0.00 3.32
98 99 3.868757 ATAGTTCTAGCACAGCGACAA 57.131 42.857 0.00 0.00 0.00 3.18
99 100 3.868757 AATAGTTCTAGCACAGCGACA 57.131 42.857 0.00 0.00 0.00 4.35
100 101 3.240861 CGAAATAGTTCTAGCACAGCGAC 59.759 47.826 0.96 0.00 0.00 5.19
101 102 3.119602 ACGAAATAGTTCTAGCACAGCGA 60.120 43.478 0.96 0.00 0.00 4.93
102 103 3.000674 CACGAAATAGTTCTAGCACAGCG 60.001 47.826 0.96 0.00 0.00 5.18
103 104 4.174009 TCACGAAATAGTTCTAGCACAGC 58.826 43.478 0.96 0.00 0.00 4.40
104 105 5.233050 CCATCACGAAATAGTTCTAGCACAG 59.767 44.000 0.96 0.00 0.00 3.66
105 106 5.105513 TCCATCACGAAATAGTTCTAGCACA 60.106 40.000 0.96 0.00 0.00 4.57
106 107 5.232414 GTCCATCACGAAATAGTTCTAGCAC 59.768 44.000 0.96 0.00 0.00 4.40
107 108 5.127194 AGTCCATCACGAAATAGTTCTAGCA 59.873 40.000 0.96 0.00 0.00 3.49
108 109 5.460419 CAGTCCATCACGAAATAGTTCTAGC 59.540 44.000 0.96 0.00 0.00 3.42
109 110 6.796426 TCAGTCCATCACGAAATAGTTCTAG 58.204 40.000 0.96 0.00 0.00 2.43
110 111 6.769134 TCAGTCCATCACGAAATAGTTCTA 57.231 37.500 0.96 0.00 0.00 2.10
111 112 5.661056 TCAGTCCATCACGAAATAGTTCT 57.339 39.130 0.96 0.00 0.00 3.01
112 113 5.235186 CCATCAGTCCATCACGAAATAGTTC 59.765 44.000 0.00 0.00 0.00 3.01
113 114 5.118990 CCATCAGTCCATCACGAAATAGTT 58.881 41.667 0.00 0.00 0.00 2.24
114 115 4.162320 ACCATCAGTCCATCACGAAATAGT 59.838 41.667 0.00 0.00 0.00 2.12
115 116 4.697514 ACCATCAGTCCATCACGAAATAG 58.302 43.478 0.00 0.00 0.00 1.73
116 117 4.753516 ACCATCAGTCCATCACGAAATA 57.246 40.909 0.00 0.00 0.00 1.40
117 118 3.634397 ACCATCAGTCCATCACGAAAT 57.366 42.857 0.00 0.00 0.00 2.17
118 119 3.417069 AACCATCAGTCCATCACGAAA 57.583 42.857 0.00 0.00 0.00 3.46
119 120 4.250464 GTTAACCATCAGTCCATCACGAA 58.750 43.478 0.00 0.00 0.00 3.85
120 121 3.674955 CGTTAACCATCAGTCCATCACGA 60.675 47.826 0.00 0.00 0.00 4.35
121 122 2.603110 CGTTAACCATCAGTCCATCACG 59.397 50.000 0.00 0.00 0.00 4.35
122 123 3.617263 GTCGTTAACCATCAGTCCATCAC 59.383 47.826 0.00 0.00 0.00 3.06
123 124 3.259625 TGTCGTTAACCATCAGTCCATCA 59.740 43.478 0.00 0.00 0.00 3.07
124 125 3.617263 GTGTCGTTAACCATCAGTCCATC 59.383 47.826 0.00 0.00 0.00 3.51
125 126 3.007506 TGTGTCGTTAACCATCAGTCCAT 59.992 43.478 0.00 0.00 0.00 3.41
126 127 2.365941 TGTGTCGTTAACCATCAGTCCA 59.634 45.455 0.00 0.00 0.00 4.02
127 128 2.735134 GTGTGTCGTTAACCATCAGTCC 59.265 50.000 0.00 0.00 0.00 3.85
128 129 3.386486 TGTGTGTCGTTAACCATCAGTC 58.614 45.455 0.00 0.00 0.00 3.51
129 130 3.462483 TGTGTGTCGTTAACCATCAGT 57.538 42.857 0.00 0.00 0.00 3.41
130 131 6.662414 ATATTGTGTGTCGTTAACCATCAG 57.338 37.500 0.00 0.00 0.00 2.90
131 132 7.441890 AAATATTGTGTGTCGTTAACCATCA 57.558 32.000 0.00 0.00 0.00 3.07
132 133 9.997482 AATAAATATTGTGTGTCGTTAACCATC 57.003 29.630 0.00 0.00 0.00 3.51
187 188 9.127277 ACTTAAGTAGCCAAGAAAAACATGTAA 57.873 29.630 6.26 0.00 0.00 2.41
188 189 8.564574 CACTTAAGTAGCCAAGAAAAACATGTA 58.435 33.333 8.04 0.00 0.00 2.29
189 190 7.425606 CACTTAAGTAGCCAAGAAAAACATGT 58.574 34.615 8.04 0.00 0.00 3.21
190 191 6.363357 GCACTTAAGTAGCCAAGAAAAACATG 59.637 38.462 8.04 0.00 0.00 3.21
191 192 6.447162 GCACTTAAGTAGCCAAGAAAAACAT 58.553 36.000 8.04 0.00 0.00 2.71
192 193 5.827666 GCACTTAAGTAGCCAAGAAAAACA 58.172 37.500 8.04 0.00 0.00 2.83
203 204 8.458843 TGAAATTTCATTAGGCACTTAAGTAGC 58.541 33.333 16.91 13.63 33.65 3.58
206 207 8.306761 CCTTGAAATTTCATTAGGCACTTAAGT 58.693 33.333 21.10 1.12 37.11 2.24
207 208 8.306761 ACCTTGAAATTTCATTAGGCACTTAAG 58.693 33.333 27.84 15.94 38.28 1.85
208 209 8.189119 ACCTTGAAATTTCATTAGGCACTTAA 57.811 30.769 27.84 8.98 38.28 1.85
209 210 7.775053 ACCTTGAAATTTCATTAGGCACTTA 57.225 32.000 27.84 9.40 38.28 2.24
210 211 6.670695 ACCTTGAAATTTCATTAGGCACTT 57.329 33.333 27.84 13.43 38.28 3.16
211 212 6.670695 AACCTTGAAATTTCATTAGGCACT 57.329 33.333 27.84 15.99 38.28 4.40
212 213 6.928492 TCAAACCTTGAAATTTCATTAGGCAC 59.072 34.615 27.84 0.81 38.28 5.01
213 214 7.060383 TCAAACCTTGAAATTTCATTAGGCA 57.940 32.000 27.84 13.83 38.28 4.75
214 215 7.961325 TTCAAACCTTGAAATTTCATTAGGC 57.039 32.000 27.84 2.09 45.94 3.93
226 227 6.184789 ACACCTCTTAAGTTCAAACCTTGAA 58.815 36.000 1.63 0.00 46.68 2.69
227 228 5.751586 ACACCTCTTAAGTTCAAACCTTGA 58.248 37.500 1.63 0.00 38.04 3.02
228 229 6.265577 CAACACCTCTTAAGTTCAAACCTTG 58.734 40.000 1.63 0.00 0.00 3.61
229 230 5.163550 GCAACACCTCTTAAGTTCAAACCTT 60.164 40.000 1.63 0.00 0.00 3.50
230 231 4.338400 GCAACACCTCTTAAGTTCAAACCT 59.662 41.667 1.63 0.00 0.00 3.50
231 232 4.499188 GGCAACACCTCTTAAGTTCAAACC 60.499 45.833 1.63 0.00 34.51 3.27
232 233 4.607955 GGCAACACCTCTTAAGTTCAAAC 58.392 43.478 1.63 0.00 34.51 2.93
233 234 4.911514 GGCAACACCTCTTAAGTTCAAA 57.088 40.909 1.63 0.00 34.51 2.69
262 263 8.451748 GCTTCCGAAAAGTAGTTTAGAATCAAT 58.548 33.333 0.00 0.00 0.00 2.57
263 264 7.660208 AGCTTCCGAAAAGTAGTTTAGAATCAA 59.340 33.333 0.00 0.00 0.00 2.57
264 265 7.117812 CAGCTTCCGAAAAGTAGTTTAGAATCA 59.882 37.037 0.00 0.00 0.00 2.57
265 266 7.117956 ACAGCTTCCGAAAAGTAGTTTAGAATC 59.882 37.037 0.00 0.00 0.00 2.52
266 267 6.935208 ACAGCTTCCGAAAAGTAGTTTAGAAT 59.065 34.615 0.00 0.00 0.00 2.40
267 268 6.285990 ACAGCTTCCGAAAAGTAGTTTAGAA 58.714 36.000 0.00 0.39 0.00 2.10
268 269 5.850614 ACAGCTTCCGAAAAGTAGTTTAGA 58.149 37.500 0.00 0.00 0.00 2.10
269 270 6.541111 AACAGCTTCCGAAAAGTAGTTTAG 57.459 37.500 0.00 0.00 0.00 1.85
270 271 6.930667 AAACAGCTTCCGAAAAGTAGTTTA 57.069 33.333 14.37 0.00 30.57 2.01
271 272 5.830000 AAACAGCTTCCGAAAAGTAGTTT 57.170 34.783 12.16 12.16 0.00 2.66
272 273 5.355910 TCAAAACAGCTTCCGAAAAGTAGTT 59.644 36.000 0.00 0.00 0.00 2.24
273 274 4.879545 TCAAAACAGCTTCCGAAAAGTAGT 59.120 37.500 0.00 0.00 0.00 2.73
274 275 5.007724 ACTCAAAACAGCTTCCGAAAAGTAG 59.992 40.000 0.00 0.00 0.00 2.57
275 276 4.879545 ACTCAAAACAGCTTCCGAAAAGTA 59.120 37.500 0.00 0.00 0.00 2.24
276 277 3.694566 ACTCAAAACAGCTTCCGAAAAGT 59.305 39.130 0.00 0.00 0.00 2.66
277 278 4.292977 ACTCAAAACAGCTTCCGAAAAG 57.707 40.909 0.00 0.00 0.00 2.27
278 279 4.879545 AGTACTCAAAACAGCTTCCGAAAA 59.120 37.500 0.00 0.00 0.00 2.29
279 280 4.448210 AGTACTCAAAACAGCTTCCGAAA 58.552 39.130 0.00 0.00 0.00 3.46
280 281 4.067972 AGTACTCAAAACAGCTTCCGAA 57.932 40.909 0.00 0.00 0.00 4.30
281 282 3.746045 AGTACTCAAAACAGCTTCCGA 57.254 42.857 0.00 0.00 0.00 4.55
282 283 4.557205 ACTAGTACTCAAAACAGCTTCCG 58.443 43.478 0.00 0.00 0.00 4.30
283 284 5.989777 TGAACTAGTACTCAAAACAGCTTCC 59.010 40.000 0.00 0.00 0.00 3.46
284 285 7.224949 AGTTGAACTAGTACTCAAAACAGCTTC 59.775 37.037 10.81 0.00 33.52 3.86
285 286 7.048512 AGTTGAACTAGTACTCAAAACAGCTT 58.951 34.615 10.81 0.00 33.52 3.74
286 287 6.583562 AGTTGAACTAGTACTCAAAACAGCT 58.416 36.000 10.81 2.64 33.52 4.24
287 288 6.846325 AGTTGAACTAGTACTCAAAACAGC 57.154 37.500 10.81 0.66 33.52 4.40
288 289 8.420374 TGAAGTTGAACTAGTACTCAAAACAG 57.580 34.615 10.81 0.00 33.52 3.16
289 290 8.826710 CATGAAGTTGAACTAGTACTCAAAACA 58.173 33.333 10.81 11.08 33.52 2.83
290 291 8.827677 ACATGAAGTTGAACTAGTACTCAAAAC 58.172 33.333 10.81 2.36 33.52 2.43
291 292 8.958119 ACATGAAGTTGAACTAGTACTCAAAA 57.042 30.769 10.81 0.51 33.52 2.44
319 320 9.833182 GTGATTTTAAAAGGCAAAGAACAAAAA 57.167 25.926 6.79 0.00 0.00 1.94
320 321 8.171840 CGTGATTTTAAAAGGCAAAGAACAAAA 58.828 29.630 6.79 0.00 0.00 2.44
321 322 7.332182 ACGTGATTTTAAAAGGCAAAGAACAAA 59.668 29.630 6.79 0.00 0.00 2.83
322 323 6.814146 ACGTGATTTTAAAAGGCAAAGAACAA 59.186 30.769 6.79 0.00 0.00 2.83
323 324 6.334202 ACGTGATTTTAAAAGGCAAAGAACA 58.666 32.000 6.79 0.00 0.00 3.18
324 325 6.822073 ACGTGATTTTAAAAGGCAAAGAAC 57.178 33.333 6.79 0.00 0.00 3.01
325 326 9.535878 AAATACGTGATTTTAAAAGGCAAAGAA 57.464 25.926 6.79 0.00 33.77 2.52
326 327 8.973378 CAAATACGTGATTTTAAAAGGCAAAGA 58.027 29.630 6.79 0.00 35.45 2.52
327 328 8.760569 ACAAATACGTGATTTTAAAAGGCAAAG 58.239 29.630 6.79 7.48 35.45 2.77
328 329 8.649973 ACAAATACGTGATTTTAAAAGGCAAA 57.350 26.923 6.79 0.00 35.45 3.68
329 330 8.649973 AACAAATACGTGATTTTAAAAGGCAA 57.350 26.923 6.79 0.00 35.45 4.52
330 331 7.921214 TGAACAAATACGTGATTTTAAAAGGCA 59.079 29.630 6.79 4.68 35.45 4.75
331 332 8.211838 GTGAACAAATACGTGATTTTAAAAGGC 58.788 33.333 6.79 2.12 35.45 4.35
332 333 8.414173 CGTGAACAAATACGTGATTTTAAAAGG 58.586 33.333 6.79 0.00 35.45 3.11
333 334 9.160576 TCGTGAACAAATACGTGATTTTAAAAG 57.839 29.630 6.79 0.00 40.87 2.27
334 335 8.945930 GTCGTGAACAAATACGTGATTTTAAAA 58.054 29.630 2.51 2.51 40.87 1.52
335 336 8.336806 AGTCGTGAACAAATACGTGATTTTAAA 58.663 29.630 0.00 0.00 40.87 1.52
336 337 7.853524 AGTCGTGAACAAATACGTGATTTTAA 58.146 30.769 0.00 0.00 40.87 1.52
337 338 7.410800 AGTCGTGAACAAATACGTGATTTTA 57.589 32.000 0.00 0.00 40.87 1.52
338 339 6.295039 AGTCGTGAACAAATACGTGATTTT 57.705 33.333 0.00 0.00 40.87 1.82
339 340 5.917541 AGTCGTGAACAAATACGTGATTT 57.082 34.783 0.00 0.00 40.87 2.17
340 341 7.591006 ATTAGTCGTGAACAAATACGTGATT 57.409 32.000 0.00 0.00 40.87 2.57
341 342 7.117236 ACAATTAGTCGTGAACAAATACGTGAT 59.883 33.333 0.00 0.00 40.87 3.06
342 343 6.421501 ACAATTAGTCGTGAACAAATACGTGA 59.578 34.615 0.00 0.00 40.87 4.35
343 344 6.586751 ACAATTAGTCGTGAACAAATACGTG 58.413 36.000 0.00 0.00 40.87 4.49
344 345 6.774354 ACAATTAGTCGTGAACAAATACGT 57.226 33.333 0.00 0.00 40.87 3.57
345 346 8.483743 AAAACAATTAGTCGTGAACAAATACG 57.516 30.769 0.00 0.00 41.38 3.06
346 347 9.659830 AGAAAACAATTAGTCGTGAACAAATAC 57.340 29.630 0.00 0.00 0.00 1.89
348 349 9.019764 CAAGAAAACAATTAGTCGTGAACAAAT 57.980 29.630 0.00 0.00 0.00 2.32
349 350 8.237949 TCAAGAAAACAATTAGTCGTGAACAAA 58.762 29.630 0.00 0.00 0.00 2.83
350 351 7.753659 TCAAGAAAACAATTAGTCGTGAACAA 58.246 30.769 0.00 0.00 0.00 2.83
354 355 8.067784 GTGAATCAAGAAAACAATTAGTCGTGA 58.932 33.333 0.00 0.00 33.95 4.35
382 383 3.424703 CAACATCCTCCATCCAACTTGT 58.575 45.455 0.00 0.00 0.00 3.16
495 496 7.094805 ACGAGTGTCACAGCAACATTAATTTAT 60.095 33.333 5.62 0.00 0.00 1.40
498 499 4.515191 ACGAGTGTCACAGCAACATTAATT 59.485 37.500 5.62 0.00 0.00 1.40
551 552 8.806429 TCATTTAGGTAATTGCAGAGAATCAA 57.194 30.769 0.00 0.00 37.82 2.57
673 674 5.977129 CAGTTTTACCGAAAGCTTCACAATT 59.023 36.000 0.00 0.00 34.21 2.32
852 853 1.599047 CCGATGACCCAGCTTGTCT 59.401 57.895 12.94 1.26 33.83 3.41
1010 1041 3.185246 AGGATGACTCGGTTGCAATAG 57.815 47.619 0.59 3.57 0.00 1.73
1019 1050 9.526713 CAATGAGAATAATATAGGATGACTCGG 57.473 37.037 0.00 0.00 0.00 4.63
1046 1077 4.617959 GTGTGAGCAGACTGTGTAAACTA 58.382 43.478 3.99 0.00 0.00 2.24
1050 1081 1.679153 TCGTGTGAGCAGACTGTGTAA 59.321 47.619 3.99 0.00 0.00 2.41
1089 1120 7.124901 AGCTGGATGATAGTTCTTGACTTCTTA 59.875 37.037 0.00 0.00 39.86 2.10
1229 1260 2.080062 CGCGGGTTTTGCATCAACG 61.080 57.895 0.00 0.00 0.00 4.10
1440 4140 1.163554 CTTGGTTTCCAGAGAGCTGC 58.836 55.000 0.00 0.00 40.91 5.25
1449 4149 0.179234 TGTCGCTGTCTTGGTTTCCA 59.821 50.000 0.00 0.00 0.00 3.53
1487 4187 1.597027 CAGAAGGACGCGGGTTGTT 60.597 57.895 12.47 3.16 0.00 2.83
1548 4262 3.483869 GAGGCTCGGGGCAGGAAT 61.484 66.667 13.05 0.00 44.01 3.01
1590 4304 4.462834 TCGAGTTGATTGTCTCACCTACAT 59.537 41.667 0.00 0.00 32.17 2.29
1607 4321 2.563179 ACCAGTAGCAACAGATCGAGTT 59.437 45.455 0.00 1.37 0.00 3.01
1635 4349 2.758979 GCTACACCCTAACTACAGCAGA 59.241 50.000 0.00 0.00 0.00 4.26
1953 4736 5.930837 AACCAAAAACAATCTGACTTGGA 57.069 34.783 5.69 0.00 0.00 3.53
2009 4794 8.361592 ACTACAGTTCATGTTACAAACACTAC 57.638 34.615 3.25 0.00 45.50 2.73
2068 4856 1.308998 AAGCGAAACAGTGGTTCCTG 58.691 50.000 15.26 3.47 35.82 3.86
2083 4871 2.044123 AATGAGGAAGGGCTAAAGCG 57.956 50.000 0.00 0.00 43.26 4.68
2088 4876 5.393068 AATGATCAAATGAGGAAGGGCTA 57.607 39.130 0.00 0.00 0.00 3.93
2133 4923 1.408340 CATGCCAAGTCAACCAACACA 59.592 47.619 0.00 0.00 0.00 3.72
2172 4962 6.330250 AGAAGTGGTATTTAGTATGGATGCCT 59.670 38.462 0.00 0.00 0.00 4.75
2242 5034 4.714632 AGATCAAGTCCGGAAAGAAACAA 58.285 39.130 5.23 0.00 0.00 2.83
2268 5060 3.884895 TGTGATGGGGTGCTATTTAGTG 58.115 45.455 0.00 0.00 0.00 2.74
2300 5104 3.441572 CAGAACAGCAAGGATGGGTTAAG 59.558 47.826 0.00 0.00 0.00 1.85
2394 5205 9.144747 CCAGCTATTACTACATAACTTGCTATG 57.855 37.037 0.00 0.00 35.71 2.23
2410 5223 3.072476 TGCCCAGATAACCCAGCTATTAC 59.928 47.826 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.