Multiple sequence alignment - TraesCS1A01G300200

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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 TraesCS1A01G300200 chr1A 100.000 3606 0 0 1 3606 495194269 495190664 0.000000e+00 6660.0
1 TraesCS1A01G300200 chr1A 87.975 158 18 1 3426 3582 50834358 50834515 6.150000e-43 185.0
2 TraesCS1A01G300200 chr1B 86.817 3368 199 104 188 3402 533325815 533322540 0.000000e+00 3533.0
3 TraesCS1A01G300200 chr1B 79.266 545 47 26 2845 3331 1452096 1452632 1.620000e-83 320.0
4 TraesCS1A01G300200 chr1B 78.000 550 48 31 2845 3331 56678675 56678136 9.860000e-71 278.0
5 TraesCS1A01G300200 chr1B 94.479 163 4 2 1 163 533326165 533326008 2.780000e-61 246.0
6 TraesCS1A01G300200 chr1B 81.847 314 29 16 3041 3331 355094392 355094084 4.650000e-59 239.0
7 TraesCS1A01G300200 chr1B 81.773 203 21 6 2845 3036 94686849 94687046 4.820000e-34 156.0
8 TraesCS1A01G300200 chr1D 87.937 3150 147 91 412 3402 397974855 397971780 0.000000e+00 3496.0
9 TraesCS1A01G300200 chr1D 92.010 413 23 4 1 412 397981237 397980834 4.040000e-159 571.0
10 TraesCS1A01G300200 chr3B 89.937 318 31 1 1934 2251 593164391 593164707 3.350000e-110 409.0
11 TraesCS1A01G300200 chr3B 89.423 312 33 0 1940 2251 593541860 593542171 9.380000e-106 394.0
12 TraesCS1A01G300200 chr3B 86.728 324 41 2 1337 1659 593163819 593164141 3.420000e-95 359.0
13 TraesCS1A01G300200 chr3B 86.728 324 41 2 1337 1659 593541303 593541625 3.420000e-95 359.0
14 TraesCS1A01G300200 chr3B 83.121 314 25 16 3041 3331 377073550 377073858 9.930000e-66 261.0
15 TraesCS1A01G300200 chr3B 80.122 327 51 9 1339 1655 228690784 228690462 7.790000e-57 231.0
16 TraesCS1A01G300200 chr3B 86.207 174 23 1 3425 3597 409536828 409536655 1.710000e-43 187.0
17 TraesCS1A01G300200 chr3B 84.000 175 20 5 3419 3591 822004379 822004547 1.040000e-35 161.0
18 TraesCS1A01G300200 chr3D 89.286 308 33 0 1944 2251 451886117 451886424 1.570000e-103 387.0
19 TraesCS1A01G300200 chr3D 88.636 308 35 0 1944 2251 451710642 451710949 3.400000e-100 375.0
20 TraesCS1A01G300200 chr3D 86.626 329 41 3 1333 1659 451885572 451885899 9.520000e-96 361.0
21 TraesCS1A01G300200 chr3D 86.111 324 43 2 1337 1659 451710100 451710422 7.410000e-92 348.0
22 TraesCS1A01G300200 chr3D 83.088 272 32 10 1339 1600 157443377 157443110 6.020000e-58 235.0
23 TraesCS1A01G300200 chr3D 86.905 168 21 1 3425 3591 6025228 6025061 1.710000e-43 187.0
24 TraesCS1A01G300200 chr3D 88.288 111 10 2 1139 1249 451709860 451709967 2.920000e-26 130.0
25 TraesCS1A01G300200 chr3D 88.785 107 9 2 1139 1245 451885359 451885462 1.050000e-25 128.0
26 TraesCS1A01G300200 chr3A 88.961 308 34 0 1944 2251 594493031 594493338 7.310000e-102 381.0
27 TraesCS1A01G300200 chr3A 87.037 324 40 2 1337 1659 594492469 594492791 7.360000e-97 364.0
28 TraesCS1A01G300200 chr4B 80.748 535 44 27 2847 3331 620078778 620078253 2.650000e-96 363.0
29 TraesCS1A01G300200 chr4B 78.532 545 51 26 2845 3331 672981618 672982154 7.570000e-77 298.0
30 TraesCS1A01G300200 chr4B 88.889 81 5 3 2845 2925 82678132 82678208 2.960000e-16 97.1
31 TraesCS1A01G300200 chr2B 79.380 548 42 26 2845 3331 355042499 355041962 1.620000e-83 320.0
32 TraesCS1A01G300200 chr2B 80.317 315 32 18 3041 3332 763145285 763144978 1.010000e-50 211.0
33 TraesCS1A01G300200 chr2B 87.500 168 20 1 3425 3591 731334370 731334203 3.670000e-45 193.0
34 TraesCS1A01G300200 chr2B 86.585 82 7 3 2845 2926 155233427 155233504 1.780000e-13 87.9
35 TraesCS1A01G300200 chr4A 78.716 545 50 26 2845 3331 740379637 740380173 1.630000e-78 303.0
36 TraesCS1A01G300200 chr4A 81.847 314 28 17 3041 3331 646064197 646063890 1.670000e-58 237.0
37 TraesCS1A01G300200 chr4A 80.859 256 23 14 3041 3273 717603212 717602960 1.030000e-40 178.0
38 TraesCS1A01G300200 chr6A 83.388 307 45 6 1944 2247 542430361 542430058 2.740000e-71 279.0
39 TraesCS1A01G300200 chr6D 83.387 313 39 10 1944 2248 396010784 396010477 9.860000e-71 278.0
40 TraesCS1A01G300200 chr7B 88.166 169 18 2 3425 3591 715364767 715364935 2.200000e-47 200.0
41 TraesCS1A01G300200 chrUn 85.714 175 22 3 3419 3591 98340198 98340371 7.950000e-42 182.0
42 TraesCS1A01G300200 chr7A 86.667 165 21 1 3419 3582 269965214 269965378 7.950000e-42 182.0
43 TraesCS1A01G300200 chr5A 86.228 167 22 1 3426 3591 471305586 471305752 2.860000e-41 180.0
44 TraesCS1A01G300200 chr6B 96.226 53 2 0 1197 1249 592464857 592464805 1.780000e-13 87.9


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 TraesCS1A01G300200 chr1A 495190664 495194269 3605 True 6660.000000 6660 100.000000 1 3606 1 chr1A.!!$R1 3605
1 TraesCS1A01G300200 chr1B 533322540 533326165 3625 True 1889.500000 3533 90.648000 1 3402 2 chr1B.!!$R3 3401
2 TraesCS1A01G300200 chr1B 1452096 1452632 536 False 320.000000 320 79.266000 2845 3331 1 chr1B.!!$F1 486
3 TraesCS1A01G300200 chr1B 56678136 56678675 539 True 278.000000 278 78.000000 2845 3331 1 chr1B.!!$R1 486
4 TraesCS1A01G300200 chr1D 397971780 397974855 3075 True 3496.000000 3496 87.937000 412 3402 1 chr1D.!!$R1 2990
5 TraesCS1A01G300200 chr3B 593163819 593164707 888 False 384.000000 409 88.332500 1337 2251 2 chr3B.!!$F3 914
6 TraesCS1A01G300200 chr3B 593541303 593542171 868 False 376.500000 394 88.075500 1337 2251 2 chr3B.!!$F4 914
7 TraesCS1A01G300200 chr3D 451885359 451886424 1065 False 292.000000 387 88.232333 1139 2251 3 chr3D.!!$F2 1112
8 TraesCS1A01G300200 chr3D 451709860 451710949 1089 False 284.333333 375 87.678333 1139 2251 3 chr3D.!!$F1 1112
9 TraesCS1A01G300200 chr3A 594492469 594493338 869 False 372.500000 381 87.999000 1337 2251 2 chr3A.!!$F1 914
10 TraesCS1A01G300200 chr4B 620078253 620078778 525 True 363.000000 363 80.748000 2847 3331 1 chr4B.!!$R1 484
11 TraesCS1A01G300200 chr4B 672981618 672982154 536 False 298.000000 298 78.532000 2845 3331 1 chr4B.!!$F2 486
12 TraesCS1A01G300200 chr2B 355041962 355042499 537 True 320.000000 320 79.380000 2845 3331 1 chr2B.!!$R1 486
13 TraesCS1A01G300200 chr4A 740379637 740380173 536 False 303.000000 303 78.716000 2845 3331 1 chr4A.!!$F1 486

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
415 604 0.027586 GCACCGTGACACAGAAACAC 59.972 55.0 6.37 0.0 0.00 3.32 F
914 1138 0.179001 ATATTAACCTGCACGGCCCC 60.179 55.0 0.00 0.0 35.61 5.80 F
1154 1378 0.325110 TCTCCTCCTTCTGCCTCCTG 60.325 60.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1580 0.179076 TGTCTGTGTCTGTGTGGCAG 60.179 55.0 0.0 0.0 46.34 4.85 R
2515 2979 0.108804 GAGTGCCAAGCTGCTACGTA 60.109 55.0 0.9 0.0 0.00 3.57 R
3038 3563 0.252197 AAATCACACCCCTAGACGGC 59.748 55.0 0.0 0.0 0.00 5.68 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
123 124 0.460311 CCGATGGTCCAGTGTACTCC 59.540 60.000 0.00 0.00 0.00 3.85
130 131 0.904865 TCCAGTGTACTCCCCAGCAG 60.905 60.000 0.00 0.00 0.00 4.24
145 146 3.260884 CCCAGCAGGACTAAGTTAAGTGA 59.739 47.826 0.00 0.00 38.24 3.41
159 160 2.969628 AAGTGACCCGAGATTAGCAG 57.030 50.000 0.00 0.00 0.00 4.24
160 161 1.853963 AGTGACCCGAGATTAGCAGT 58.146 50.000 0.00 0.00 0.00 4.40
162 163 0.824109 TGACCCGAGATTAGCAGTGG 59.176 55.000 0.00 0.00 0.00 4.00
163 164 1.112113 GACCCGAGATTAGCAGTGGA 58.888 55.000 0.00 0.00 0.00 4.02
164 165 1.067821 GACCCGAGATTAGCAGTGGAG 59.932 57.143 0.00 0.00 0.00 3.86
165 166 1.115467 CCCGAGATTAGCAGTGGAGT 58.885 55.000 0.00 0.00 0.00 3.85
166 167 2.307768 CCCGAGATTAGCAGTGGAGTA 58.692 52.381 0.00 0.00 0.00 2.59
167 168 2.034812 CCCGAGATTAGCAGTGGAGTAC 59.965 54.545 0.00 0.00 0.00 2.73
168 169 2.287069 CCGAGATTAGCAGTGGAGTACG 60.287 54.545 0.00 0.00 0.00 3.67
169 170 2.355132 CGAGATTAGCAGTGGAGTACGT 59.645 50.000 0.00 0.00 0.00 3.57
170 171 3.181499 CGAGATTAGCAGTGGAGTACGTT 60.181 47.826 0.00 0.00 0.00 3.99
171 172 4.674623 CGAGATTAGCAGTGGAGTACGTTT 60.675 45.833 0.00 0.00 0.00 3.60
172 173 4.495422 AGATTAGCAGTGGAGTACGTTTG 58.505 43.478 0.00 0.00 0.00 2.93
173 174 2.736144 TAGCAGTGGAGTACGTTTGG 57.264 50.000 0.00 0.00 0.00 3.28
174 175 0.756903 AGCAGTGGAGTACGTTTGGT 59.243 50.000 0.00 0.00 0.00 3.67
175 176 0.865769 GCAGTGGAGTACGTTTGGTG 59.134 55.000 0.00 0.00 0.00 4.17
176 177 1.508632 CAGTGGAGTACGTTTGGTGG 58.491 55.000 0.00 0.00 0.00 4.61
177 178 1.069513 CAGTGGAGTACGTTTGGTGGA 59.930 52.381 0.00 0.00 0.00 4.02
178 179 1.343465 AGTGGAGTACGTTTGGTGGAG 59.657 52.381 0.00 0.00 0.00 3.86
179 180 0.034337 TGGAGTACGTTTGGTGGAGC 59.966 55.000 0.00 0.00 0.00 4.70
180 181 0.320697 GGAGTACGTTTGGTGGAGCT 59.679 55.000 0.00 0.00 0.00 4.09
211 399 2.411031 CCACTGCAACAATACGTTCGTC 60.411 50.000 0.00 0.00 34.86 4.20
216 404 2.719688 GCAACAATACGTTCGTCGAACC 60.720 50.000 27.62 13.29 39.14 3.62
227 415 0.790207 CGTCGAACCATCCAACACAG 59.210 55.000 0.00 0.00 0.00 3.66
233 421 2.693762 CCATCCAACACAGGCAGCG 61.694 63.158 0.00 0.00 0.00 5.18
235 423 1.376424 ATCCAACACAGGCAGCGAG 60.376 57.895 0.00 0.00 0.00 5.03
254 442 0.966875 GTTCCTGGACCATGCATGCA 60.967 55.000 25.04 25.04 0.00 3.96
256 444 2.782222 CCTGGACCATGCATGCAGC 61.782 63.158 26.69 14.37 45.96 5.25
259 447 2.104331 GACCATGCATGCAGCTGC 59.896 61.111 31.89 31.89 45.94 5.25
262 450 1.359117 CCATGCATGCAGCTGCTAC 59.641 57.895 36.61 25.55 45.94 3.58
309 498 1.709147 CTAGGTCGGCATGCACTTGC 61.709 60.000 21.36 3.60 42.01 4.01
310 499 4.465512 GGTCGGCATGCACTTGCG 62.466 66.667 21.36 13.45 45.83 4.85
318 507 3.022401 ATGCACTTGCGCCGTTACG 62.022 57.895 4.18 0.00 45.83 3.18
349 538 6.681777 TCATGAGTGGATTATCATCACGTAG 58.318 40.000 0.00 0.00 33.91 3.51
350 539 6.265422 TCATGAGTGGATTATCATCACGTAGT 59.735 38.462 0.00 0.00 35.75 2.73
351 540 7.447238 TCATGAGTGGATTATCATCACGTAGTA 59.553 37.037 0.00 0.00 33.73 1.82
363 552 6.756221 TCATCACGTAGTATCTAGTAGCAGA 58.244 40.000 0.00 0.00 41.61 4.26
408 597 4.961511 GCCGAGCACCGTGACACA 62.962 66.667 6.37 0.00 36.31 3.72
409 598 2.734723 CCGAGCACCGTGACACAG 60.735 66.667 6.37 0.00 36.31 3.66
415 604 0.027586 GCACCGTGACACAGAAACAC 59.972 55.000 6.37 0.00 0.00 3.32
427 616 0.974383 AGAAACACGACCGGATTCCT 59.026 50.000 9.46 0.00 0.00 3.36
531 737 1.374252 ACGGAGTTAAGGCACGCTG 60.374 57.895 0.00 0.00 37.78 5.18
532 738 1.374252 CGGAGTTAAGGCACGCTGT 60.374 57.895 0.00 0.00 0.00 4.40
533 739 1.626654 CGGAGTTAAGGCACGCTGTG 61.627 60.000 4.61 4.61 36.51 3.66
627 833 2.000701 CCATGTGGGGAGTAGGGCA 61.001 63.158 0.00 0.00 0.00 5.36
677 884 1.887242 CCAGTCCACCACACACACG 60.887 63.158 0.00 0.00 0.00 4.49
837 1061 1.524849 GAGCCGGCCTTCAATCTCC 60.525 63.158 26.15 0.00 0.00 3.71
845 1069 2.432146 GGCCTTCAATCTCCCATTTTCC 59.568 50.000 0.00 0.00 0.00 3.13
846 1070 3.369175 GCCTTCAATCTCCCATTTTCCT 58.631 45.455 0.00 0.00 0.00 3.36
847 1071 3.382865 GCCTTCAATCTCCCATTTTCCTC 59.617 47.826 0.00 0.00 0.00 3.71
848 1072 3.956848 CCTTCAATCTCCCATTTTCCTCC 59.043 47.826 0.00 0.00 0.00 4.30
849 1073 3.669939 TCAATCTCCCATTTTCCTCCC 57.330 47.619 0.00 0.00 0.00 4.30
854 1078 1.492599 CTCCCATTTTCCTCCCTCTCC 59.507 57.143 0.00 0.00 0.00 3.71
860 1084 0.340208 TTTCCTCCCTCTCCCTCTCC 59.660 60.000 0.00 0.00 0.00 3.71
862 1086 2.328589 CCTCCCTCTCCCTCTCCCA 61.329 68.421 0.00 0.00 0.00 4.37
867 1091 0.264359 CCTCTCCCTCTCCCACTCAT 59.736 60.000 0.00 0.00 0.00 2.90
874 1098 2.484417 CCCTCTCCCACTCATCAAATCG 60.484 54.545 0.00 0.00 0.00 3.34
914 1138 0.179001 ATATTAACCTGCACGGCCCC 60.179 55.000 0.00 0.00 35.61 5.80
967 1191 5.057149 CACCGAGCTTTACTTTGGCTATAT 58.943 41.667 0.00 0.00 36.37 0.86
1034 1258 3.210232 TCGAGCCTAGCTAGCTTTAGA 57.790 47.619 24.88 11.21 41.75 2.10
1036 1260 2.350007 CGAGCCTAGCTAGCTTTAGACG 60.350 54.545 24.88 18.56 41.75 4.18
1085 1309 1.759445 TGCTGATACAGGGAAGCTCTC 59.241 52.381 0.00 0.00 36.60 3.20
1086 1310 1.069978 GCTGATACAGGGAAGCTCTCC 59.930 57.143 6.43 6.43 44.54 3.71
1098 1322 1.898863 AGCTCTCCCTCTCTCTCTCT 58.101 55.000 0.00 0.00 0.00 3.10
1133 1357 2.424246 CACCGGTACTCTCTTCTTCCTC 59.576 54.545 6.87 0.00 0.00 3.71
1154 1378 0.325110 TCTCCTCCTTCTGCCTCCTG 60.325 60.000 0.00 0.00 0.00 3.86
1278 1571 2.584143 GGCTGGCGAATGCAATGC 60.584 61.111 0.00 0.00 45.35 3.56
1296 1589 2.248135 CGTAAACGCCTGCCACACA 61.248 57.895 0.00 0.00 0.00 3.72
1660 1970 3.082548 CGTCTCCTACAGAAGGTGAGAA 58.917 50.000 0.00 0.00 46.14 2.87
1661 1971 3.127895 CGTCTCCTACAGAAGGTGAGAAG 59.872 52.174 0.00 0.00 46.14 2.85
1665 2003 5.839063 TCTCCTACAGAAGGTGAGAAGAAAA 59.161 40.000 0.00 0.00 46.62 2.29
1699 2051 1.675310 TGTACCACGACCGACCGAT 60.675 57.895 3.56 0.00 0.00 4.18
1766 2118 2.281276 GAGGACCGCGGTTGGTTT 60.281 61.111 34.65 16.11 44.01 3.27
1780 2132 3.398406 GTTGGTTTGGCCCATAAGTTTG 58.602 45.455 0.00 0.00 33.60 2.93
1803 2155 2.125147 GCCACACCGCTGCAGATA 60.125 61.111 20.43 0.00 0.00 1.98
1804 2156 1.524621 GCCACACCGCTGCAGATAT 60.525 57.895 20.43 0.00 0.00 1.63
1805 2157 1.779025 GCCACACCGCTGCAGATATG 61.779 60.000 20.43 13.67 0.00 1.78
1881 2290 3.173853 GCGCCTTGTAATGTCGCA 58.826 55.556 0.00 0.00 44.50 5.10
1883 2292 1.060937 CGCCTTGTAATGTCGCAGC 59.939 57.895 0.00 0.00 0.00 5.25
1897 2306 4.758692 CAGCTTCACTGTCACCGT 57.241 55.556 0.00 0.00 41.86 4.83
1932 2353 3.688414 GCTAATCCTGCATGTTACCCCTT 60.688 47.826 0.00 0.00 0.00 3.95
1934 2355 1.367346 TCCTGCATGTTACCCCTTGA 58.633 50.000 0.00 0.00 0.00 3.02
1935 2356 1.922447 TCCTGCATGTTACCCCTTGAT 59.078 47.619 0.00 0.00 0.00 2.57
1936 2357 2.092429 TCCTGCATGTTACCCCTTGATC 60.092 50.000 0.00 0.00 0.00 2.92
2030 2483 2.978010 GCTGGTGACCAACGTGGG 60.978 66.667 7.67 7.67 43.37 4.61
2279 2733 3.169099 CCTCCTCTTCTCTTCTCCACAA 58.831 50.000 0.00 0.00 0.00 3.33
2308 2768 0.738389 CTGGAGAGAAGAGACGGAGC 59.262 60.000 0.00 0.00 0.00 4.70
2310 2770 0.454196 GGAGAGAAGAGACGGAGCAC 59.546 60.000 0.00 0.00 0.00 4.40
2312 2772 2.634600 GAGAGAAGAGACGGAGCACTA 58.365 52.381 0.00 0.00 0.00 2.74
2374 2834 4.410400 AGGAAGAAAGGCCGGCCG 62.410 66.667 38.88 21.04 41.95 6.13
2400 2860 5.221087 CCTCTTCGTTATAGTGAAGGAGGAC 60.221 48.000 17.81 0.00 41.48 3.85
2458 2918 3.430931 CTTAGACGCTTTCCTTCTCTCG 58.569 50.000 0.00 0.00 0.00 4.04
2477 2937 7.085116 TCTCTCGATCAAAGTCTCAAGTTTAC 58.915 38.462 0.00 0.00 0.00 2.01
2513 2977 2.433239 ACCATCCATCAAGTACCGTACC 59.567 50.000 5.02 0.00 0.00 3.34
2515 2979 1.838112 TCCATCAAGTACCGTACCGT 58.162 50.000 5.02 0.00 0.00 4.83
2526 2990 1.717937 CGTACCGTACGTAGCAGCT 59.282 57.895 20.61 0.00 46.41 4.24
2596 3097 9.171877 AGAAGAAGAAGAAGTTAATAATGGCAG 57.828 33.333 0.00 0.00 0.00 4.85
2612 3113 9.712305 AATAATGGCAGTAGTTATGATCAGTAC 57.288 33.333 0.09 1.57 0.00 2.73
2613 3114 6.985653 ATGGCAGTAGTTATGATCAGTACT 57.014 37.500 14.69 14.69 31.60 2.73
2614 3115 8.478775 AATGGCAGTAGTTATGATCAGTACTA 57.521 34.615 13.07 13.07 30.54 1.82
2615 3116 7.511959 TGGCAGTAGTTATGATCAGTACTAG 57.488 40.000 16.07 9.48 30.54 2.57
2616 3117 7.287810 TGGCAGTAGTTATGATCAGTACTAGA 58.712 38.462 16.07 0.00 30.54 2.43
2766 3267 0.674534 CACCCGTAGCCTCCATAGAC 59.325 60.000 0.00 0.00 0.00 2.59
2806 3310 0.729116 CTGTTTGCTGGGCTGTATCG 59.271 55.000 0.00 0.00 0.00 2.92
2816 3320 1.406887 GGGCTGTATCGTGTTGATGGT 60.407 52.381 0.00 0.00 37.99 3.55
2817 3321 1.933853 GGCTGTATCGTGTTGATGGTC 59.066 52.381 0.00 0.00 37.99 4.02
2818 3322 2.616960 GCTGTATCGTGTTGATGGTCA 58.383 47.619 0.00 0.00 37.99 4.02
2819 3323 2.348666 GCTGTATCGTGTTGATGGTCAC 59.651 50.000 0.00 0.00 37.99 3.67
2884 3388 4.465446 CCGGAGAGGAGCCAGGGA 62.465 72.222 0.00 0.00 45.00 4.20
2930 3434 3.050619 CGTTTCGTGTAGATGATAGGCC 58.949 50.000 0.00 0.00 0.00 5.19
2948 3453 1.964552 CCTCTGCAATGGGTCTGATC 58.035 55.000 0.00 0.00 0.00 2.92
2961 3466 2.605823 GGTCTGATCATCCATCGTCGAC 60.606 54.545 5.18 5.18 33.61 4.20
3002 3527 0.736325 CGCTCAAGTTGGTCGTAGGG 60.736 60.000 2.34 0.00 0.00 3.53
3024 3549 1.387539 GGCTCTCCTTCTGAAATGGC 58.612 55.000 0.00 0.00 0.00 4.40
3067 3621 0.798776 GGTGTGATTTCGCAGTCCAG 59.201 55.000 0.00 0.00 37.00 3.86
3168 3743 2.278206 CGAGAGCGTCCCATCGTG 60.278 66.667 0.00 0.00 0.00 4.35
3216 3791 5.975693 TTGTTTCCACCATTTAGGATCAC 57.024 39.130 0.00 0.00 41.22 3.06
3232 3807 3.935203 GGATCACTGATGTGGTACTTGTG 59.065 47.826 0.00 0.00 43.94 3.33
3236 3818 3.742882 CACTGATGTGGTACTTGTGACTG 59.257 47.826 0.00 0.00 40.33 3.51
3260 3843 2.151202 GTCATTCCTTCGCTGGACAAA 58.849 47.619 0.00 0.00 35.58 2.83
3261 3844 2.552315 GTCATTCCTTCGCTGGACAAAA 59.448 45.455 0.00 0.00 35.58 2.44
3262 3845 3.191371 GTCATTCCTTCGCTGGACAAAAT 59.809 43.478 0.00 0.00 35.58 1.82
3266 3849 2.747446 TCCTTCGCTGGACAAAATTAGC 59.253 45.455 0.00 0.00 0.00 3.09
3321 3905 3.257393 CCTCTGATATGATAGCAACGGC 58.743 50.000 0.00 0.00 41.61 5.68
3338 3922 1.172812 GGCTGAGGGTTTTTGTCGCT 61.173 55.000 0.00 0.00 0.00 4.93
3339 3923 0.040067 GCTGAGGGTTTTTGTCGCTG 60.040 55.000 0.00 0.00 0.00 5.18
3402 3986 5.014123 TGGAGGTTGATGTTGAAAGGATAGT 59.986 40.000 0.00 0.00 0.00 2.12
3403 3987 5.946377 GGAGGTTGATGTTGAAAGGATAGTT 59.054 40.000 0.00 0.00 0.00 2.24
3404 3988 6.434340 GGAGGTTGATGTTGAAAGGATAGTTT 59.566 38.462 0.00 0.00 0.00 2.66
3405 3989 7.039714 GGAGGTTGATGTTGAAAGGATAGTTTT 60.040 37.037 0.00 0.00 0.00 2.43
3406 3990 8.250143 AGGTTGATGTTGAAAGGATAGTTTTT 57.750 30.769 0.00 0.00 0.00 1.94
3477 4061 9.906660 AATGTATTACAAAAAGTACACATGTGG 57.093 29.630 28.64 11.35 38.05 4.17
3478 4062 8.453238 TGTATTACAAAAAGTACACATGTGGT 57.547 30.769 28.64 16.26 30.91 4.16
3479 4063 8.561212 TGTATTACAAAAAGTACACATGTGGTC 58.439 33.333 28.64 19.83 30.91 4.02
3480 4064 7.575414 ATTACAAAAAGTACACATGTGGTCA 57.425 32.000 28.64 11.48 30.91 4.02
3481 4065 7.575414 TTACAAAAAGTACACATGTGGTCAT 57.425 32.000 28.64 11.13 30.91 3.06
3482 4066 6.072112 ACAAAAAGTACACATGTGGTCATC 57.928 37.500 28.64 13.67 34.19 2.92
3483 4067 5.592282 ACAAAAAGTACACATGTGGTCATCA 59.408 36.000 28.64 4.80 34.19 3.07
3484 4068 5.689383 AAAAGTACACATGTGGTCATCAC 57.311 39.130 28.64 15.39 46.23 3.06
3496 4080 4.820897 GTGGTCATCACAAGAGACATACA 58.179 43.478 0.00 0.00 45.39 2.29
3497 4081 5.423015 GTGGTCATCACAAGAGACATACAT 58.577 41.667 0.00 0.00 45.39 2.29
3498 4082 6.573434 GTGGTCATCACAAGAGACATACATA 58.427 40.000 0.00 0.00 45.39 2.29
3499 4083 6.699204 GTGGTCATCACAAGAGACATACATAG 59.301 42.308 0.00 0.00 45.39 2.23
3500 4084 6.607198 TGGTCATCACAAGAGACATACATAGA 59.393 38.462 0.00 0.00 34.04 1.98
3501 4085 7.288621 TGGTCATCACAAGAGACATACATAGAT 59.711 37.037 0.00 0.00 34.04 1.98
3502 4086 8.797438 GGTCATCACAAGAGACATACATAGATA 58.203 37.037 0.00 0.00 34.04 1.98
3508 4092 9.138062 CACAAGAGACATACATAGATATCTTGC 57.862 37.037 11.25 0.00 43.81 4.01
3509 4093 8.864087 ACAAGAGACATACATAGATATCTTGCA 58.136 33.333 11.25 0.86 43.81 4.08
3510 4094 9.702494 CAAGAGACATACATAGATATCTTGCAA 57.298 33.333 11.25 0.00 36.91 4.08
3548 4132 6.390987 CTTCGCACGAAGTAAACTAGAATT 57.609 37.500 21.53 0.00 41.61 2.17
3549 4133 6.774354 TTCGCACGAAGTAAACTAGAATTT 57.226 33.333 0.49 0.00 41.61 1.82
3550 4134 6.385537 TCGCACGAAGTAAACTAGAATTTC 57.614 37.500 0.00 0.00 41.61 2.17
3551 4135 5.921976 TCGCACGAAGTAAACTAGAATTTCA 59.078 36.000 0.00 0.00 41.61 2.69
3552 4136 6.007677 CGCACGAAGTAAACTAGAATTTCAC 58.992 40.000 0.00 0.00 41.61 3.18
3553 4137 6.128902 CGCACGAAGTAAACTAGAATTTCACT 60.129 38.462 0.00 0.00 41.61 3.41
3554 4138 7.568861 CGCACGAAGTAAACTAGAATTTCACTT 60.569 37.037 0.00 0.00 41.61 3.16
3555 4139 7.740781 GCACGAAGTAAACTAGAATTTCACTTC 59.259 37.037 11.94 11.94 41.61 3.01
3558 4142 6.723131 AGTAAACTAGAATTTCACTTCGGC 57.277 37.500 0.00 0.00 0.00 5.54
3559 4143 6.228258 AGTAAACTAGAATTTCACTTCGGCA 58.772 36.000 0.00 0.00 0.00 5.69
3560 4144 5.613358 AAACTAGAATTTCACTTCGGCAG 57.387 39.130 0.00 0.00 0.00 4.85
3561 4145 4.537135 ACTAGAATTTCACTTCGGCAGA 57.463 40.909 0.00 0.00 0.00 4.26
3562 4146 4.894784 ACTAGAATTTCACTTCGGCAGAA 58.105 39.130 0.00 0.00 34.76 3.02
3563 4147 5.491982 ACTAGAATTTCACTTCGGCAGAAT 58.508 37.500 0.00 0.00 35.56 2.40
3564 4148 4.954092 AGAATTTCACTTCGGCAGAATC 57.046 40.909 0.00 0.00 35.56 2.52
3565 4149 4.583871 AGAATTTCACTTCGGCAGAATCT 58.416 39.130 0.00 0.00 35.56 2.40
3566 4150 5.006386 AGAATTTCACTTCGGCAGAATCTT 58.994 37.500 0.00 0.00 35.56 2.40
3567 4151 4.691860 ATTTCACTTCGGCAGAATCTTG 57.308 40.909 0.00 0.00 35.56 3.02
3568 4152 2.839486 TCACTTCGGCAGAATCTTGT 57.161 45.000 0.00 0.00 35.56 3.16
3569 4153 2.416747 TCACTTCGGCAGAATCTTGTG 58.583 47.619 0.00 5.15 35.56 3.33
3570 4154 1.135859 CACTTCGGCAGAATCTTGTGC 60.136 52.381 0.00 3.61 45.70 4.57
3575 4159 2.247790 GCAGAATCTTGTGCCACGT 58.752 52.632 0.82 0.00 41.15 4.49
3576 4160 0.166814 GCAGAATCTTGTGCCACGTC 59.833 55.000 0.82 0.00 41.15 4.34
3577 4161 1.511850 CAGAATCTTGTGCCACGTCA 58.488 50.000 0.00 0.00 0.00 4.35
3578 4162 1.872952 CAGAATCTTGTGCCACGTCAA 59.127 47.619 0.00 0.00 0.00 3.18
3579 4163 2.290367 CAGAATCTTGTGCCACGTCAAA 59.710 45.455 0.00 0.00 0.00 2.69
3580 4164 2.948979 AGAATCTTGTGCCACGTCAAAA 59.051 40.909 0.00 0.00 0.00 2.44
3581 4165 2.774439 ATCTTGTGCCACGTCAAAAC 57.226 45.000 0.00 0.00 0.00 2.43
3590 4174 4.295381 CGTCAAAACGTTGCCCAC 57.705 55.556 0.00 0.00 43.94 4.61
3591 4175 1.429825 CGTCAAAACGTTGCCCACA 59.570 52.632 0.00 0.00 43.94 4.17
3592 4176 0.179161 CGTCAAAACGTTGCCCACAA 60.179 50.000 0.00 0.00 43.94 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.136123 CACATGAAGCTGCCCCGG 61.136 66.667 0.00 0.00 0.00 5.73
123 124 3.260884 TCACTTAACTTAGTCCTGCTGGG 59.739 47.826 10.07 0.00 0.00 4.45
130 131 3.760684 TCTCGGGTCACTTAACTTAGTCC 59.239 47.826 0.00 0.00 0.00 3.85
145 146 1.115467 CTCCACTGCTAATCTCGGGT 58.885 55.000 0.00 0.00 0.00 5.28
159 160 1.792006 CTCCACCAAACGTACTCCAC 58.208 55.000 0.00 0.00 0.00 4.02
160 161 0.034337 GCTCCACCAAACGTACTCCA 59.966 55.000 0.00 0.00 0.00 3.86
162 163 1.429463 CAGCTCCACCAAACGTACTC 58.571 55.000 0.00 0.00 0.00 2.59
163 164 0.602905 GCAGCTCCACCAAACGTACT 60.603 55.000 0.00 0.00 0.00 2.73
164 165 0.882927 TGCAGCTCCACCAAACGTAC 60.883 55.000 0.00 0.00 0.00 3.67
165 166 0.036164 ATGCAGCTCCACCAAACGTA 59.964 50.000 0.00 0.00 0.00 3.57
166 167 1.228245 ATGCAGCTCCACCAAACGT 60.228 52.632 0.00 0.00 0.00 3.99
167 168 1.210931 CATGCAGCTCCACCAAACG 59.789 57.895 0.00 0.00 0.00 3.60
168 169 1.588082 CCATGCAGCTCCACCAAAC 59.412 57.895 0.00 0.00 0.00 2.93
169 170 2.277591 GCCATGCAGCTCCACCAAA 61.278 57.895 0.00 0.00 0.00 3.28
170 171 2.677524 GCCATGCAGCTCCACCAA 60.678 61.111 0.00 0.00 0.00 3.67
171 172 3.654143 AGCCATGCAGCTCCACCA 61.654 61.111 0.00 0.00 39.48 4.17
178 179 3.138798 CAGTGGGAGCCATGCAGC 61.139 66.667 0.00 0.00 35.28 5.25
179 180 3.138798 GCAGTGGGAGCCATGCAG 61.139 66.667 0.00 0.00 37.69 4.41
180 181 3.510559 TTGCAGTGGGAGCCATGCA 62.511 57.895 8.60 8.60 41.99 3.96
211 399 0.888736 TGCCTGTGTTGGATGGTTCG 60.889 55.000 0.00 0.00 0.00 3.95
216 404 1.642037 CTCGCTGCCTGTGTTGGATG 61.642 60.000 0.00 0.00 0.00 3.51
227 415 2.435059 GTCCAGGAACTCGCTGCC 60.435 66.667 0.00 0.00 34.60 4.85
233 421 1.386533 CATGCATGGTCCAGGAACTC 58.613 55.000 19.40 0.00 34.60 3.01
235 423 0.966875 TGCATGCATGGTCCAGGAAC 60.967 55.000 27.34 8.37 0.00 3.62
254 442 2.694397 TGGGATGGATAAGTAGCAGCT 58.306 47.619 0.00 0.00 0.00 4.24
256 444 4.696479 ACTTGGGATGGATAAGTAGCAG 57.304 45.455 0.00 0.00 33.22 4.24
262 450 6.240549 ACTTGACTACTTGGGATGGATAAG 57.759 41.667 0.00 0.00 0.00 1.73
291 480 1.745115 GCAAGTGCATGCCGACCTA 60.745 57.895 16.68 0.00 40.49 3.08
318 507 0.882042 AATCCACTCATGATCGGCGC 60.882 55.000 0.00 0.00 0.00 6.53
349 538 2.617308 TGGCGTGTCTGCTACTAGATAC 59.383 50.000 0.00 0.00 36.01 2.24
350 539 2.927028 TGGCGTGTCTGCTACTAGATA 58.073 47.619 0.00 0.00 34.52 1.98
351 540 1.763968 TGGCGTGTCTGCTACTAGAT 58.236 50.000 0.00 0.00 34.52 1.98
392 581 2.693250 TTCTGTGTCACGGTGCTCGG 62.693 60.000 11.59 5.38 44.45 4.63
401 590 0.575390 CGGTCGTGTTTCTGTGTCAC 59.425 55.000 0.00 0.00 0.00 3.67
408 597 0.974383 AGGAATCCGGTCGTGTTTCT 59.026 50.000 0.00 0.00 0.00 2.52
409 598 1.356938 GAGGAATCCGGTCGTGTTTC 58.643 55.000 0.00 0.00 0.00 2.78
415 604 2.499827 GGAGGGAGGAATCCGGTCG 61.500 68.421 0.00 0.00 0.00 4.79
427 616 2.404750 GGAGGGAGCTAGGGAGGGA 61.405 68.421 0.00 0.00 0.00 4.20
478 667 3.958147 AAGGCGTCTCCACCATGCG 62.958 63.158 0.00 0.00 37.29 4.73
819 1043 1.524849 GGAGATTGAAGGCCGGCTC 60.525 63.158 28.56 18.02 0.00 4.70
837 1061 1.492599 GAGGGAGAGGGAGGAAAATGG 59.507 57.143 0.00 0.00 0.00 3.16
845 1069 1.075600 GTGGGAGAGGGAGAGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
846 1070 1.547755 AGTGGGAGAGGGAGAGGGA 60.548 63.158 0.00 0.00 0.00 4.20
847 1071 1.075600 GAGTGGGAGAGGGAGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
848 1072 0.264359 ATGAGTGGGAGAGGGAGAGG 59.736 60.000 0.00 0.00 0.00 3.69
849 1073 1.063341 TGATGAGTGGGAGAGGGAGAG 60.063 57.143 0.00 0.00 0.00 3.20
854 1078 2.169352 ACGATTTGATGAGTGGGAGAGG 59.831 50.000 0.00 0.00 0.00 3.69
860 1084 3.251479 TCCTGACGATTTGATGAGTGG 57.749 47.619 0.00 0.00 0.00 4.00
885 1109 5.812642 CGTGCAGGTTAATATCACTTCTTCT 59.187 40.000 0.00 0.00 0.00 2.85
886 1110 5.006746 CCGTGCAGGTTAATATCACTTCTTC 59.993 44.000 5.57 0.00 34.51 2.87
895 1119 0.179001 GGGGCCGTGCAGGTTAATAT 60.179 55.000 5.57 0.00 43.70 1.28
914 1138 1.009078 TTGGATTGCAAGCTCGATCG 58.991 50.000 15.27 9.36 0.00 3.69
947 1171 8.408743 GGTATATATAGCCAAAGTAAAGCTCG 57.591 38.462 10.31 0.00 38.06 5.03
1034 1258 0.393077 CTTTCGAGGGGATATGGCGT 59.607 55.000 0.00 0.00 0.00 5.68
1036 1260 0.398318 AGCTTTCGAGGGGATATGGC 59.602 55.000 0.00 0.00 0.00 4.40
1085 1309 2.142356 TTGCTGAGAGAGAGAGAGGG 57.858 55.000 0.00 0.00 0.00 4.30
1086 1310 2.363038 CCATTGCTGAGAGAGAGAGAGG 59.637 54.545 0.00 0.00 0.00 3.69
1087 1311 2.223876 GCCATTGCTGAGAGAGAGAGAG 60.224 54.545 0.00 0.00 33.53 3.20
1088 1312 1.755959 GCCATTGCTGAGAGAGAGAGA 59.244 52.381 0.00 0.00 33.53 3.10
1089 1313 1.536496 CGCCATTGCTGAGAGAGAGAG 60.536 57.143 0.00 0.00 34.43 3.20
1090 1314 0.459078 CGCCATTGCTGAGAGAGAGA 59.541 55.000 0.00 0.00 34.43 3.10
1113 1337 2.309458 AGAGGAAGAAGAGAGTACCGGT 59.691 50.000 13.98 13.98 0.00 5.28
1119 1343 4.569865 GGAGGAGAAGAGGAAGAAGAGAGT 60.570 50.000 0.00 0.00 0.00 3.24
1133 1357 0.829990 GGAGGCAGAAGGAGGAGAAG 59.170 60.000 0.00 0.00 0.00 2.85
1278 1571 2.170260 CTGTGTGGCAGGCGTTTACG 62.170 60.000 0.00 0.00 41.42 3.18
1282 1575 2.591715 GTCTGTGTGGCAGGCGTT 60.592 61.111 0.00 0.00 45.08 4.84
1286 1579 0.882042 GTCTGTGTCTGTGTGGCAGG 60.882 60.000 0.00 0.00 45.08 4.85
1287 1580 0.179076 TGTCTGTGTCTGTGTGGCAG 60.179 55.000 0.00 0.00 46.34 4.85
1292 1585 1.202302 CGTGAGTGTCTGTGTCTGTGT 60.202 52.381 0.00 0.00 0.00 3.72
1296 1589 1.008424 CGCGTGAGTGTCTGTGTCT 60.008 57.895 0.00 0.00 36.71 3.41
1318 1628 1.662517 CAAAACCCAACAAACAGCCC 58.337 50.000 0.00 0.00 0.00 5.19
1793 2145 1.988467 CCGTATCACATATCTGCAGCG 59.012 52.381 9.47 2.26 0.00 5.18
1803 2155 1.813753 GGCGTGCACCGTATCACAT 60.814 57.895 12.15 0.00 39.32 3.21
1804 2156 2.433491 GGCGTGCACCGTATCACA 60.433 61.111 12.15 0.00 39.32 3.58
1840 2194 3.242091 GCACATGCGATGTAAGTACTGTG 60.242 47.826 0.00 0.00 42.70 3.66
1846 2200 0.729116 GCAGCACATGCGATGTAAGT 59.271 50.000 0.42 0.00 46.99 2.24
1847 2201 3.521534 GCAGCACATGCGATGTAAG 57.478 52.632 0.42 0.00 46.99 2.34
1871 2225 2.795121 CAGTGAAGCTGCGACATTAC 57.205 50.000 0.00 0.00 38.52 1.89
1881 2290 0.530650 CACACGGTGACAGTGAAGCT 60.531 55.000 22.04 0.00 41.83 3.74
1883 2292 1.209128 GACACACGGTGACAGTGAAG 58.791 55.000 22.04 15.23 41.83 3.02
1896 2305 2.921754 GGATTAGCACTACGTGACACAC 59.078 50.000 6.37 0.00 35.23 3.82
1897 2306 2.823747 AGGATTAGCACTACGTGACACA 59.176 45.455 6.37 0.00 35.23 3.72
1910 2331 2.158608 AGGGGTAACATGCAGGATTAGC 60.159 50.000 4.84 9.53 39.74 3.09
1932 2353 1.825341 CACCCTGCTCCATCGATCA 59.175 57.895 0.00 0.00 0.00 2.92
1934 2355 2.507944 GCACCCTGCTCCATCGAT 59.492 61.111 0.00 0.00 40.96 3.59
1935 2356 3.785859 GGCACCCTGCTCCATCGA 61.786 66.667 0.00 0.00 44.28 3.59
2288 2742 0.738389 CTCCGTCTCTTCTCTCCAGC 59.262 60.000 0.00 0.00 0.00 4.85
2289 2743 0.738389 GCTCCGTCTCTTCTCTCCAG 59.262 60.000 0.00 0.00 0.00 3.86
2312 2772 8.981647 GCGAATGCCAAAATAATTCTTGAATAT 58.018 29.630 0.00 0.00 33.98 1.28
2374 2834 3.383825 TCCTTCACTATAACGAAGAGGCC 59.616 47.826 10.88 0.00 40.94 5.19
2375 2835 4.500035 CCTCCTTCACTATAACGAAGAGGC 60.500 50.000 10.88 0.00 40.94 4.70
2376 2836 4.888239 TCCTCCTTCACTATAACGAAGAGG 59.112 45.833 10.88 13.28 40.94 3.69
2377 2837 5.504337 CGTCCTCCTTCACTATAACGAAGAG 60.504 48.000 10.88 7.38 40.94 2.85
2458 2918 8.491950 GTCTTCAGTAAACTTGAGACTTTGATC 58.508 37.037 12.24 0.00 34.77 2.92
2477 2937 2.996621 GGATGGTTGTTCGAGTCTTCAG 59.003 50.000 0.00 0.00 0.00 3.02
2513 2977 1.445410 TGCCAAGCTGCTACGTACG 60.445 57.895 15.01 15.01 0.00 3.67
2515 2979 0.108804 GAGTGCCAAGCTGCTACGTA 60.109 55.000 0.90 0.00 0.00 3.57
2522 2986 0.879765 CTTCAAGGAGTGCCAAGCTG 59.120 55.000 0.00 0.00 36.29 4.24
2526 2990 3.136443 TCTTCTTCTTCAAGGAGTGCCAA 59.864 43.478 0.00 0.00 36.66 4.52
2592 3090 7.747155 TCTAGTACTGATCATAACTACTGCC 57.253 40.000 5.39 0.00 0.00 4.85
2712 3213 4.493547 GCTAGCTAGCTAGAACATGGATG 58.506 47.826 42.59 21.54 46.56 3.51
2736 3237 3.612115 TACGGGTGGCCAGCTAGGT 62.612 63.158 32.43 26.99 40.61 3.08
2737 3238 2.762459 TACGGGTGGCCAGCTAGG 60.762 66.667 32.43 23.30 41.84 3.02
2738 3239 2.815308 CTACGGGTGGCCAGCTAG 59.185 66.667 32.43 26.99 0.00 3.42
2739 3240 3.467226 GCTACGGGTGGCCAGCTA 61.467 66.667 32.43 17.98 0.00 3.32
2757 3258 1.405821 GTCCACACTCGGTCTATGGAG 59.594 57.143 0.00 0.00 40.09 3.86
2766 3267 0.944311 CAAAGTCCGTCCACACTCGG 60.944 60.000 0.00 0.00 46.93 4.63
2806 3310 2.485426 CCATGTGAGTGACCATCAACAC 59.515 50.000 9.17 9.17 36.88 3.32
2816 3320 3.716195 CCCCGCCCATGTGAGTGA 61.716 66.667 0.00 0.00 0.00 3.41
2817 3321 4.802051 CCCCCGCCCATGTGAGTG 62.802 72.222 0.00 0.00 0.00 3.51
2819 3323 4.489771 GTCCCCCGCCCATGTGAG 62.490 72.222 0.00 0.00 0.00 3.51
2906 3410 4.537965 CCTATCATCTACACGAAACGGAG 58.462 47.826 0.00 0.00 0.00 4.63
2907 3411 3.243301 GCCTATCATCTACACGAAACGGA 60.243 47.826 0.00 0.00 0.00 4.69
2930 3434 2.704464 TGATCAGACCCATTGCAGAG 57.296 50.000 0.00 0.00 0.00 3.35
2948 3453 1.752501 GCAACCGTCGACGATGGATG 61.753 60.000 36.52 33.70 42.14 3.51
2980 3485 0.942410 TACGACCAACTTGAGCGTGC 60.942 55.000 14.98 0.00 36.51 5.34
3002 3527 2.275318 CATTTCAGAAGGAGAGCCGAC 58.725 52.381 0.00 0.00 39.96 4.79
3036 3561 4.814294 CACACCCCTAGACGGCGC 62.814 72.222 6.90 0.00 0.00 6.53
3037 3562 1.956629 AATCACACCCCTAGACGGCG 61.957 60.000 4.80 4.80 0.00 6.46
3038 3563 0.252197 AAATCACACCCCTAGACGGC 59.748 55.000 0.00 0.00 0.00 5.68
3040 3565 1.922570 CGAAATCACACCCCTAGACG 58.077 55.000 0.00 0.00 0.00 4.18
3041 3566 1.066430 TGCGAAATCACACCCCTAGAC 60.066 52.381 0.00 0.00 0.00 2.59
3043 3568 1.066143 ACTGCGAAATCACACCCCTAG 60.066 52.381 0.00 0.00 0.00 3.02
3046 3571 1.305930 GGACTGCGAAATCACACCCC 61.306 60.000 0.00 0.00 0.00 4.95
3067 3621 2.264480 GGTTTGCCCGCCCAATTC 59.736 61.111 0.00 0.00 0.00 2.17
3185 3760 2.147958 TGGTGGAAACAATAGTCACGC 58.852 47.619 0.00 0.00 46.06 5.34
3216 3791 2.738846 GCAGTCACAAGTACCACATCAG 59.261 50.000 0.00 0.00 0.00 2.90
3236 3818 1.424493 CCAGCGAAGGAATGACGAGC 61.424 60.000 0.00 0.00 0.00 5.03
3260 3843 1.019673 TCTACGGTCGAGCGCTAATT 58.980 50.000 34.40 18.52 0.00 1.40
3261 3844 1.019673 TTCTACGGTCGAGCGCTAAT 58.980 50.000 34.40 18.89 0.00 1.73
3262 3845 1.019673 ATTCTACGGTCGAGCGCTAA 58.980 50.000 34.40 24.99 0.00 3.09
3266 3849 0.914551 CACAATTCTACGGTCGAGCG 59.085 55.000 33.08 33.08 0.00 5.03
3321 3905 1.002468 CACAGCGACAAAAACCCTCAG 60.002 52.381 0.00 0.00 0.00 3.35
3374 3958 4.301628 CTTTCAACATCAACCTCCAAAGC 58.698 43.478 0.00 0.00 0.00 3.51
3451 4035 9.906660 CCACATGTGTACTTTTTGTAATACATT 57.093 29.630 23.79 0.00 38.25 2.71
3452 4036 9.073475 ACCACATGTGTACTTTTTGTAATACAT 57.927 29.630 23.79 0.00 39.58 2.29
3453 4037 8.453238 ACCACATGTGTACTTTTTGTAATACA 57.547 30.769 23.79 0.00 36.01 2.29
3454 4038 8.561212 TGACCACATGTGTACTTTTTGTAATAC 58.439 33.333 23.79 1.99 32.25 1.89
3455 4039 8.678593 TGACCACATGTGTACTTTTTGTAATA 57.321 30.769 23.79 1.04 32.25 0.98
3456 4040 7.575414 TGACCACATGTGTACTTTTTGTAAT 57.425 32.000 23.79 0.00 32.25 1.89
3457 4041 7.283354 TGATGACCACATGTGTACTTTTTGTAA 59.717 33.333 23.79 6.15 36.82 2.41
3458 4042 6.768381 TGATGACCACATGTGTACTTTTTGTA 59.232 34.615 23.79 1.41 36.82 2.41
3459 4043 5.592282 TGATGACCACATGTGTACTTTTTGT 59.408 36.000 23.79 11.93 36.82 2.83
3460 4044 5.914635 GTGATGACCACATGTGTACTTTTTG 59.085 40.000 23.79 8.80 45.03 2.44
3461 4045 6.072112 GTGATGACCACATGTGTACTTTTT 57.928 37.500 23.79 2.67 45.03 1.94
3462 4046 5.689383 GTGATGACCACATGTGTACTTTT 57.311 39.130 23.79 4.22 45.03 2.27
3474 4058 4.820897 TGTATGTCTCTTGTGATGACCAC 58.179 43.478 0.00 0.00 45.88 4.16
3475 4059 5.682234 ATGTATGTCTCTTGTGATGACCA 57.318 39.130 0.00 0.00 0.00 4.02
3476 4060 7.043961 TCTATGTATGTCTCTTGTGATGACC 57.956 40.000 0.00 0.00 0.00 4.02
3482 4066 9.138062 GCAAGATATCTATGTATGTCTCTTGTG 57.862 37.037 5.46 0.00 40.12 3.33
3483 4067 8.864087 TGCAAGATATCTATGTATGTCTCTTGT 58.136 33.333 5.46 0.00 40.12 3.16
3484 4068 9.702494 TTGCAAGATATCTATGTATGTCTCTTG 57.298 33.333 5.46 0.00 40.64 3.02
3526 4110 6.421501 TGAAATTCTAGTTTACTTCGTGCGAA 59.578 34.615 6.84 6.84 0.00 4.70
3527 4111 5.921976 TGAAATTCTAGTTTACTTCGTGCGA 59.078 36.000 0.00 0.00 0.00 5.10
3528 4112 6.007677 GTGAAATTCTAGTTTACTTCGTGCG 58.992 40.000 0.00 0.00 0.00 5.34
3529 4113 7.118422 AGTGAAATTCTAGTTTACTTCGTGC 57.882 36.000 0.00 0.00 0.00 5.34
3533 4117 7.095355 TGCCGAAGTGAAATTCTAGTTTACTTC 60.095 37.037 14.40 14.40 39.21 3.01
3534 4118 6.708949 TGCCGAAGTGAAATTCTAGTTTACTT 59.291 34.615 2.55 2.55 0.00 2.24
3535 4119 6.228258 TGCCGAAGTGAAATTCTAGTTTACT 58.772 36.000 0.00 0.00 0.00 2.24
3536 4120 6.367969 TCTGCCGAAGTGAAATTCTAGTTTAC 59.632 38.462 0.00 0.00 0.00 2.01
3537 4121 6.460781 TCTGCCGAAGTGAAATTCTAGTTTA 58.539 36.000 0.00 0.00 0.00 2.01
3538 4122 5.305585 TCTGCCGAAGTGAAATTCTAGTTT 58.694 37.500 0.00 0.00 0.00 2.66
3539 4123 4.894784 TCTGCCGAAGTGAAATTCTAGTT 58.105 39.130 0.00 0.00 0.00 2.24
3540 4124 4.537135 TCTGCCGAAGTGAAATTCTAGT 57.463 40.909 0.00 0.00 0.00 2.57
3541 4125 5.814705 AGATTCTGCCGAAGTGAAATTCTAG 59.185 40.000 0.00 0.00 31.60 2.43
3542 4126 5.734720 AGATTCTGCCGAAGTGAAATTCTA 58.265 37.500 0.00 0.00 31.60 2.10
3543 4127 4.583871 AGATTCTGCCGAAGTGAAATTCT 58.416 39.130 0.00 0.00 31.60 2.40
3544 4128 4.954092 AGATTCTGCCGAAGTGAAATTC 57.046 40.909 0.00 0.00 31.60 2.17
3545 4129 4.520492 ACAAGATTCTGCCGAAGTGAAATT 59.480 37.500 0.00 0.00 31.60 1.82
3546 4130 4.074970 ACAAGATTCTGCCGAAGTGAAAT 58.925 39.130 0.00 0.00 31.60 2.17
3547 4131 3.250762 CACAAGATTCTGCCGAAGTGAAA 59.749 43.478 2.96 0.00 31.60 2.69
3548 4132 2.807967 CACAAGATTCTGCCGAAGTGAA 59.192 45.455 2.96 0.00 31.60 3.18
3549 4133 2.416747 CACAAGATTCTGCCGAAGTGA 58.583 47.619 2.96 0.00 31.60 3.41
3550 4134 1.135859 GCACAAGATTCTGCCGAAGTG 60.136 52.381 0.00 0.74 31.60 3.16
3551 4135 1.160137 GCACAAGATTCTGCCGAAGT 58.840 50.000 0.00 0.00 31.60 3.01
3552 4136 0.449388 GGCACAAGATTCTGCCGAAG 59.551 55.000 0.00 0.00 43.56 3.79
3553 4137 2.555123 GGCACAAGATTCTGCCGAA 58.445 52.632 0.00 0.00 43.56 4.30
3554 4138 4.301505 GGCACAAGATTCTGCCGA 57.698 55.556 0.00 0.00 43.56 5.54
3557 4141 0.166814 GACGTGGCACAAGATTCTGC 59.833 55.000 19.09 0.00 44.16 4.26
3558 4142 1.511850 TGACGTGGCACAAGATTCTG 58.488 50.000 19.09 0.63 44.16 3.02
3559 4143 2.254546 TTGACGTGGCACAAGATTCT 57.745 45.000 19.09 0.00 44.16 2.40
3560 4144 3.042887 GTTTTGACGTGGCACAAGATTC 58.957 45.455 19.09 5.91 44.16 2.52
3561 4145 2.540769 CGTTTTGACGTGGCACAAGATT 60.541 45.455 19.09 0.00 44.16 2.40
3562 4146 1.002900 CGTTTTGACGTGGCACAAGAT 60.003 47.619 19.09 0.00 44.16 2.40
3563 4147 0.375454 CGTTTTGACGTGGCACAAGA 59.625 50.000 19.09 0.00 44.16 3.02
3564 4148 0.098025 ACGTTTTGACGTGGCACAAG 59.902 50.000 19.09 4.60 45.30 3.16
3565 4149 0.522180 AACGTTTTGACGTGGCACAA 59.478 45.000 19.09 1.21 46.41 3.33
3566 4150 0.179187 CAACGTTTTGACGTGGCACA 60.179 50.000 19.09 0.00 46.41 4.57
3567 4151 2.561366 CAACGTTTTGACGTGGCAC 58.439 52.632 7.79 7.79 46.41 5.01
3570 4154 1.298788 GGGCAACGTTTTGACGTGG 60.299 57.895 0.00 3.71 46.41 4.94
3571 4155 0.863957 GTGGGCAACGTTTTGACGTG 60.864 55.000 0.00 2.01 46.41 4.49
3573 4157 0.179161 TTGTGGGCAACGTTTTGACG 60.179 50.000 0.00 0.00 42.43 4.35
3574 4158 1.273688 GTTGTGGGCAACGTTTTGAC 58.726 50.000 0.00 0.00 44.40 3.18
3575 4159 3.723554 GTTGTGGGCAACGTTTTGA 57.276 47.368 0.00 0.00 44.40 2.69
3583 4167 0.178975 ATCCTTTCGGTTGTGGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
3584 4168 0.693622 TATCCTTTCGGTTGTGGGCA 59.306 50.000 0.00 0.00 0.00 5.36
3585 4169 1.379527 CTATCCTTTCGGTTGTGGGC 58.620 55.000 0.00 0.00 0.00 5.36
3586 4170 1.379527 GCTATCCTTTCGGTTGTGGG 58.620 55.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.