Multiple sequence alignment - TraesCS4A01G058000

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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 TraesCS4A01G058000 chr4A 100.000 5040 0 0 1 5040 48534335 48529296 0.000000e+00 9308.0
1 TraesCS4A01G058000 chr4A 81.499 427 69 7 1 421 362115686 362116108 4.830000e-90 342.0
2 TraesCS4A01G058000 chr4A 82.645 363 54 7 39 397 710661800 710662157 3.790000e-81 313.0
3 TraesCS4A01G058000 chr4A 79.810 421 65 15 1 410 688765636 688766047 6.380000e-74 289.0
4 TraesCS4A01G058000 chr4A 78.676 408 68 12 1 397 688853655 688854054 2.330000e-63 254.0
5 TraesCS4A01G058000 chr4D 90.760 4340 267 61 554 4862 414993389 414997625 0.000000e+00 5670.0
6 TraesCS4A01G058000 chr4D 79.759 415 66 10 9 421 277434990 277435388 8.260000e-73 285.0
7 TraesCS4A01G058000 chr4D 84.615 260 33 5 1 257 487353636 487353381 8.380000e-63 252.0
8 TraesCS4A01G058000 chr4D 94.304 158 3 1 4889 5040 414997620 414997777 2.350000e-58 237.0
9 TraesCS4A01G058000 chr4D 94.048 84 4 1 487 570 414993289 414993371 5.300000e-25 126.0
10 TraesCS4A01G058000 chr4B 91.788 3373 199 27 1168 4480 511158059 511161413 0.000000e+00 4623.0
11 TraesCS4A01G058000 chr4B 94.241 573 21 9 486 1057 511156977 511157538 0.000000e+00 865.0
12 TraesCS4A01G058000 chr4B 86.035 401 42 2 58 457 511155471 511155858 7.800000e-113 418.0
13 TraesCS4A01G058000 chr4B 79.157 427 80 6 16 437 665195643 665195221 2.300000e-73 287.0
14 TraesCS4A01G058000 chr4B 78.923 427 74 10 1 421 242752111 242752527 4.970000e-70 276.0
15 TraesCS4A01G058000 chr4B 79.515 454 34 28 4591 5038 511161445 511161845 8.320000e-68 268.0
16 TraesCS4A01G058000 chr4B 95.833 48 1 1 4513 4559 511161414 511161461 5.410000e-10 76.8
17 TraesCS4A01G058000 chr4B 95.652 46 2 0 1 46 511155366 511155411 1.950000e-09 75.0
18 TraesCS4A01G058000 chr6A 79.412 510 65 24 2495 3000 613792051 613791578 1.750000e-84 324.0
19 TraesCS4A01G058000 chr5B 83.955 268 31 7 112 379 214105820 214106075 3.900000e-61 246.0
20 TraesCS4A01G058000 chr3A 79.740 385 43 14 9 392 445876402 445876052 3.900000e-61 246.0
21 TraesCS4A01G058000 chr2D 85.202 223 30 1 14 236 571203795 571203576 5.080000e-55 226.0
22 TraesCS4A01G058000 chr2B 75.354 495 98 19 1 480 57145876 57145391 3.060000e-52 217.0
23 TraesCS4A01G058000 chr3D 84.974 193 26 3 9 201 330294227 330294038 5.150000e-45 193.0
24 TraesCS4A01G058000 chr6B 85.714 126 12 3 3105 3224 54417521 54417646 1.470000e-25 128.0
25 TraesCS4A01G058000 chr7A 90.361 83 8 0 2934 3016 450089287 450089205 5.330000e-20 110.0
26 TraesCS4A01G058000 chr7B 78.431 153 28 5 298 447 244743521 244743671 1.490000e-15 95.3


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 TraesCS4A01G058000 chr4A 48529296 48534335 5039 True 9308.0 9308 100.000000 1 5040 1 chr4A.!!$R1 5039
1 TraesCS4A01G058000 chr4D 414993289 414997777 4488 False 2011.0 5670 93.037333 487 5040 3 chr4D.!!$F2 4553
2 TraesCS4A01G058000 chr4B 511155366 511161845 6479 False 1054.3 4623 90.510667 1 5038 6 chr4B.!!$F2 5037

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
54 55 0.249868 TGTGAAACCTGGCAGAGACG 60.250 55.0 17.94 0.84 34.36 4.18 F
55 56 0.249911 GTGAAACCTGGCAGAGACGT 60.250 55.0 17.94 1.59 0.00 4.34 F
1240 2836 0.387929 TCGCTCGTTTGGTCTTCAGT 59.612 50.0 0.00 0.00 0.00 3.41 F
2207 3805 0.819582 GGCCACCATGTTCAATGAGG 59.180 55.0 0.00 0.00 0.00 3.86 F
3478 5102 0.034059 ACAAGAAGGTGACTGAGGCG 59.966 55.0 0.00 0.00 42.68 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 2764 0.109504 GCAGATAGATCCGGCGAGAC 60.110 60.0 9.30 0.0 0.0 3.36 R
1248 2845 0.181114 CGGGGCAAATGGAGAGATCA 59.819 55.0 0.00 0.0 0.0 2.92 R
2350 3948 0.625849 TGAAAGATTCCCCCTCAGCC 59.374 55.0 0.00 0.0 0.0 4.85 R
3614 5238 0.468226 AAGAGCCACGGTGAACAAGA 59.532 50.0 10.28 0.0 0.0 3.02 R
4886 6549 0.109342 CTCCCAGCAACCAGTCACTT 59.891 55.0 0.00 0.0 0.0 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.833406 TTATGACAATGTTGGTAGCCATG 57.167 39.130 0.00 0.00 31.53 3.66
41 42 3.894427 ACAATGTTGGTAGCCATGTGAAA 59.106 39.130 0.00 0.00 31.53 2.69
50 51 3.344703 CCATGTGAAACCTGGCAGA 57.655 52.632 17.94 0.00 45.53 4.26
53 54 1.808945 CATGTGAAACCTGGCAGAGAC 59.191 52.381 17.94 5.32 34.36 3.36
54 55 0.249868 TGTGAAACCTGGCAGAGACG 60.250 55.000 17.94 0.84 34.36 4.18
55 56 0.249911 GTGAAACCTGGCAGAGACGT 60.250 55.000 17.94 1.59 0.00 4.34
56 57 1.000506 GTGAAACCTGGCAGAGACGTA 59.999 52.381 17.94 0.00 0.00 3.57
62 111 1.751351 CCTGGCAGAGACGTAGATGAA 59.249 52.381 17.94 0.00 0.00 2.57
86 135 7.617041 AATCACTGCATTTCTTAAGACCTAC 57.383 36.000 4.18 0.00 0.00 3.18
89 138 4.222145 ACTGCATTTCTTAAGACCTACCGA 59.778 41.667 4.18 0.00 0.00 4.69
94 143 6.539103 GCATTTCTTAAGACCTACCGAAAGAT 59.461 38.462 4.18 0.00 0.00 2.40
135 184 5.181811 CACAACCAACTCAAGCATGATCTTA 59.818 40.000 0.00 0.00 34.37 2.10
136 185 5.948162 ACAACCAACTCAAGCATGATCTTAT 59.052 36.000 0.00 0.00 34.37 1.73
137 186 6.094603 ACAACCAACTCAAGCATGATCTTATC 59.905 38.462 0.00 0.00 34.37 1.75
138 187 4.813161 ACCAACTCAAGCATGATCTTATCG 59.187 41.667 0.00 0.00 34.37 2.92
139 188 5.052481 CCAACTCAAGCATGATCTTATCGA 58.948 41.667 0.00 0.00 34.37 3.59
140 189 5.177142 CCAACTCAAGCATGATCTTATCGAG 59.823 44.000 0.00 0.00 34.37 4.04
141 190 4.305769 ACTCAAGCATGATCTTATCGAGC 58.694 43.478 0.00 0.00 34.37 5.03
142 191 4.202192 ACTCAAGCATGATCTTATCGAGCA 60.202 41.667 0.00 0.00 43.06 4.26
144 193 4.928020 TCAAGCATGATCTTATCGAGCATC 59.072 41.667 0.00 0.00 45.08 3.91
145 194 4.532314 AGCATGATCTTATCGAGCATCA 57.468 40.909 0.00 0.00 45.08 3.07
146 195 5.087391 AGCATGATCTTATCGAGCATCAT 57.913 39.130 0.00 0.00 45.08 2.45
147 196 5.489249 AGCATGATCTTATCGAGCATCATT 58.511 37.500 0.00 0.00 45.08 2.57
160 209 4.807834 CGAGCATCATTGACAACTCTATGT 59.192 41.667 9.47 0.00 33.00 2.29
170 219 4.895889 TGACAACTCTATGTGGGGAGATAG 59.104 45.833 0.00 0.00 32.57 2.08
175 224 5.337788 ACTCTATGTGGGGAGATAGATTCC 58.662 45.833 0.00 0.00 32.10 3.01
220 269 6.307776 TGTGTGGGATTTAGACAATTTGGTA 58.692 36.000 0.78 0.00 0.00 3.25
267 316 6.704512 ACATTTATTGCAATGAAAACGGTC 57.295 33.333 22.27 0.00 37.55 4.79
276 325 4.677832 GCAATGAAAACGGTCGTTGTATTT 59.322 37.500 9.57 0.35 43.53 1.40
351 401 5.588648 TCCCATCCGATTTCTATGTTGAAAC 59.411 40.000 0.00 0.00 38.54 2.78
372 422 8.548877 TGAAACCTCTAATTTAGGAAGCTATGT 58.451 33.333 12.26 0.00 37.57 2.29
388 438 6.431198 AGCTATGTAAAATTTGTGGTACCG 57.569 37.500 7.57 0.00 0.00 4.02
397 447 4.078516 GTGGTACCGCGAGCCCTT 62.079 66.667 8.23 0.00 0.00 3.95
410 460 2.356553 CCCTTCGACGCGGAACAA 60.357 61.111 12.47 0.00 0.00 2.83
422 472 1.808343 GCGGAACAAATCCCGTAAACT 59.192 47.619 0.00 0.00 46.39 2.66
423 473 2.227149 GCGGAACAAATCCCGTAAACTT 59.773 45.455 0.00 0.00 46.39 2.66
426 476 4.612033 CGGAACAAATCCCGTAAACTTGTC 60.612 45.833 0.00 0.00 46.39 3.18
440 490 2.820330 ACTTGTCCCGCAAAACATTTG 58.180 42.857 0.00 0.00 36.53 2.32
457 507 3.564027 GCGGGATCTGTTTCGCCG 61.564 66.667 0.00 0.00 42.02 6.46
458 508 2.890474 CGGGATCTGTTTCGCCGG 60.890 66.667 0.00 0.00 0.00 6.13
459 509 2.582436 GGGATCTGTTTCGCCGGA 59.418 61.111 5.05 0.00 0.00 5.14
473 523 4.189188 CGGAGGCTCACGGTACCG 62.189 72.222 32.22 32.22 46.03 4.02
496 1636 0.666374 AAAAAGTGTTTCCGCTCCCG 59.334 50.000 0.00 0.00 0.00 5.14
507 1647 1.134007 TCCGCTCCCGAAGTCAGTATA 60.134 52.381 0.00 0.00 36.29 1.47
525 1665 1.048724 TATCCTCTTCCCACGGCCAG 61.049 60.000 2.24 0.00 0.00 4.85
664 1838 2.997075 TACCACCACACCGCTAGCG 61.997 63.158 29.93 29.93 39.44 4.26
753 1927 1.537990 CCACCAAAACGGAGCCAAAAG 60.538 52.381 0.00 0.00 38.63 2.27
763 1937 3.699538 ACGGAGCCAAAAGAAAGAAAACT 59.300 39.130 0.00 0.00 0.00 2.66
806 1980 1.303317 AGAAACCCGCGGCAATTCT 60.303 52.632 22.85 23.62 0.00 2.40
822 1996 1.544825 TTCTCAGGAGCCTCAACCCG 61.545 60.000 0.00 0.00 0.00 5.28
1149 2324 1.254284 CGTGAGTGCTCTCCCTCCTT 61.254 60.000 13.00 0.00 39.75 3.36
1152 2327 1.641192 TGAGTGCTCTCCCTCCTTCTA 59.359 52.381 13.00 0.00 39.75 2.10
1156 2331 0.601057 GCTCTCCCTCCTTCTATCGC 59.399 60.000 0.00 0.00 0.00 4.58
1161 2336 1.152226 CCTCCTTCTATCGCCCCCT 60.152 63.158 0.00 0.00 0.00 4.79
1162 2337 1.188871 CCTCCTTCTATCGCCCCCTC 61.189 65.000 0.00 0.00 0.00 4.30
1163 2338 1.152312 TCCTTCTATCGCCCCCTCC 60.152 63.158 0.00 0.00 0.00 4.30
1164 2339 2.217745 CCTTCTATCGCCCCCTCCC 61.218 68.421 0.00 0.00 0.00 4.30
1165 2340 2.122547 TTCTATCGCCCCCTCCCC 60.123 66.667 0.00 0.00 0.00 4.81
1166 2341 3.786866 TTCTATCGCCCCCTCCCCC 62.787 68.421 0.00 0.00 0.00 5.40
1210 2795 3.106986 TATCTGCCCCTTCTGCGCC 62.107 63.158 4.18 0.00 0.00 6.53
1240 2836 0.387929 TCGCTCGTTTGGTCTTCAGT 59.612 50.000 0.00 0.00 0.00 3.41
1248 2845 5.607477 TCGTTTGGTCTTCAGTATCTGTTT 58.393 37.500 0.00 0.00 32.61 2.83
1290 2888 1.363744 CGGCACAGATCTGTTCTTCC 58.636 55.000 25.84 20.47 42.83 3.46
1315 2913 1.543429 GCCGATTTCCCCCTGTATGAG 60.543 57.143 0.00 0.00 0.00 2.90
1321 2919 1.806496 TCCCCCTGTATGAGATGTGG 58.194 55.000 0.00 0.00 0.00 4.17
1514 3112 3.528532 GGACAAGTAAGTACAATCCCCG 58.471 50.000 0.00 0.00 0.00 5.73
1563 3161 3.809832 CGTTTCATCCTTCACTGAACACT 59.190 43.478 0.00 0.00 31.41 3.55
1577 3175 2.113131 AACACTGCGCTTTGTACGGC 62.113 55.000 9.73 0.00 0.00 5.68
1626 3224 2.997897 GAGGTCGTGTCCCAGGCT 60.998 66.667 0.00 0.00 0.00 4.58
1669 3267 3.320541 CGAGGTCAAGATAGAAGAGCCAT 59.679 47.826 0.00 0.00 0.00 4.40
1673 3271 3.068873 GTCAAGATAGAAGAGCCATCGGT 59.931 47.826 0.00 0.00 0.00 4.69
1703 3301 4.479993 CAAGGAGGAGGCTGCGGG 62.480 72.222 0.00 0.00 0.00 6.13
1752 3350 2.483876 GCTACGATTATGCTGAAGCCA 58.516 47.619 0.00 0.00 41.18 4.75
1832 3430 2.040213 CTTGCATAGCCGCGTCCTTG 62.040 60.000 4.92 0.00 33.35 3.61
1835 3433 2.202932 ATAGCCGCGTCCTTGCTG 60.203 61.111 15.68 0.00 36.57 4.41
1838 3436 1.879737 TAGCCGCGTCCTTGCTGTAA 61.880 55.000 15.68 0.00 36.57 2.41
1868 3466 8.145767 TCTGCTGATGAAATTTGTGAAGAATTT 58.854 29.630 0.00 0.00 38.89 1.82
1869 3467 8.301730 TGCTGATGAAATTTGTGAAGAATTTC 57.698 30.769 12.83 12.83 46.31 2.17
1933 3531 3.197790 CGCTTGGCCATGACGAGG 61.198 66.667 22.21 0.00 0.00 4.63
2113 3711 6.602564 GACAAATGTCAAACGCTTTCATAG 57.397 37.500 8.63 0.00 44.18 2.23
2144 3742 2.032030 CCGAACCAAGTTGCAACTGTAG 60.032 50.000 31.73 23.58 39.66 2.74
2150 3748 2.816087 CAAGTTGCAACTGTAGGCTGAT 59.184 45.455 31.73 10.75 39.66 2.90
2207 3805 0.819582 GGCCACCATGTTCAATGAGG 59.180 55.000 0.00 0.00 0.00 3.86
2227 3825 3.265479 AGGCTGCAAAGAAGTTCTATCCT 59.735 43.478 5.65 0.00 0.00 3.24
2237 3835 6.426646 AGAAGTTCTATCCTGTGTTTGAGT 57.573 37.500 2.75 0.00 0.00 3.41
2239 3837 6.708054 AGAAGTTCTATCCTGTGTTTGAGTTG 59.292 38.462 2.75 0.00 0.00 3.16
2266 3864 3.272551 AGGTCTACTACATCTCCAAGGGT 59.727 47.826 0.00 0.00 0.00 4.34
2269 3867 4.710375 GTCTACTACATCTCCAAGGGTTCA 59.290 45.833 0.00 0.00 0.00 3.18
2278 3876 3.261897 TCTCCAAGGGTTCACTCAGAATC 59.738 47.826 0.00 0.00 38.76 2.52
2334 3932 4.686191 ATGAGATGACCCTGAATGAGAC 57.314 45.455 0.00 0.00 0.00 3.36
2350 3948 3.461061 TGAGACTGCTGTTGTTGAAGAG 58.539 45.455 0.00 0.00 0.00 2.85
2359 3957 0.401738 TTGTTGAAGAGGCTGAGGGG 59.598 55.000 0.00 0.00 0.00 4.79
2449 4047 1.121378 GGGAGTTAGTAGGTGAGGCC 58.879 60.000 0.00 0.00 37.58 5.19
2461 4059 2.024414 GGTGAGGCCGAATTGCTTAAT 58.976 47.619 0.00 0.00 0.00 1.40
2498 4096 1.678360 GCAACTTGATGCGTTCAGTG 58.322 50.000 0.00 0.00 36.45 3.66
2524 4122 9.871238 GTGACTAATTTTACTCTGTTCCATCTA 57.129 33.333 0.00 0.00 0.00 1.98
2569 4167 5.169295 GTTGTTCAGAGTGTATCACCTACC 58.831 45.833 0.00 0.00 34.49 3.18
2575 4173 2.362717 GAGTGTATCACCTACCCTGAGC 59.637 54.545 0.00 0.00 34.49 4.26
2648 4246 2.793790 GCAGATGACTCGTAAGCATCAG 59.206 50.000 0.00 0.00 37.95 2.90
2666 4264 6.433766 GCATCAGCTTTACTTGTTGATATCC 58.566 40.000 0.00 0.00 34.46 2.59
2878 4477 3.149981 ACTTTCAAGGTAAGCTCTTGGC 58.850 45.455 12.31 0.00 41.23 4.52
2888 4488 1.973812 GCTCTTGGCACCCTTCCAC 60.974 63.158 0.00 0.00 41.35 4.02
2942 4566 4.811555 TTGTGCTAACAGCTTGTTACTG 57.188 40.909 0.00 0.00 42.97 2.74
3016 4640 0.984230 TAACCCAGAGTTGCCTGAGG 59.016 55.000 0.00 0.00 39.67 3.86
3056 4680 2.298610 GTAAGGCCCTGATGCTAAACC 58.701 52.381 0.00 0.00 0.00 3.27
3092 4716 9.950680 TTGATTAGCTCTTAAGTTTTTCTGTTG 57.049 29.630 1.63 0.00 0.00 3.33
3110 4734 7.181569 TCTGTTGTAGATCATGACCACATTA 57.818 36.000 0.00 0.00 34.15 1.90
3120 4744 6.778834 TCATGACCACATTATTTGCTGAAT 57.221 33.333 0.00 0.00 34.15 2.57
3264 4888 1.303282 CCCTAACTTGGGCCAGGAC 59.697 63.158 23.86 0.00 40.84 3.85
3275 4899 2.124411 GGGCCAGGACAAGGTAAGATA 58.876 52.381 4.39 0.00 0.00 1.98
3281 4905 5.297029 GCCAGGACAAGGTAAGATATTGAAC 59.703 44.000 0.00 0.00 0.00 3.18
3283 4907 6.106673 CAGGACAAGGTAAGATATTGAACGT 58.893 40.000 0.00 0.00 0.00 3.99
3299 4923 9.820229 ATATTGAACGTTTGTTAACAGTACATG 57.180 29.630 8.56 3.16 38.78 3.21
3311 4935 3.338249 ACAGTACATGGTGCATCTGAAC 58.662 45.455 0.00 0.00 0.00 3.18
3326 4950 6.040054 TGCATCTGAACCTGAATAATTCATGG 59.960 38.462 0.00 0.00 39.30 3.66
3327 4951 6.516194 GCATCTGAACCTGAATAATTCATGGG 60.516 42.308 0.00 0.00 39.30 4.00
3330 4954 4.402155 TGAACCTGAATAATTCATGGGTGC 59.598 41.667 0.00 0.00 38.01 5.01
3332 4956 3.701040 ACCTGAATAATTCATGGGTGCAC 59.299 43.478 8.80 8.80 36.99 4.57
3335 4959 4.343231 TGAATAATTCATGGGTGCACACT 58.657 39.130 21.89 2.60 34.08 3.55
3337 4961 4.724074 ATAATTCATGGGTGCACACTTG 57.276 40.909 25.03 25.03 0.00 3.16
3341 4965 1.904865 ATGGGTGCACACTTGGCAG 60.905 57.895 21.89 0.00 42.85 4.85
3342 4966 2.519302 GGGTGCACACTTGGCAGT 60.519 61.111 20.43 0.00 42.85 4.40
3360 4984 3.126000 GCAGTTGCCTGAAGTAATCTGAC 59.874 47.826 0.00 0.00 41.50 3.51
3362 4986 3.584848 AGTTGCCTGAAGTAATCTGACCT 59.415 43.478 0.00 0.00 0.00 3.85
3365 4989 3.776969 TGCCTGAAGTAATCTGACCTGAT 59.223 43.478 0.00 0.00 0.00 2.90
3415 5039 5.394443 CCTGTATGCCAACATAAGCAACATT 60.394 40.000 0.00 0.00 43.36 2.71
3478 5102 0.034059 ACAAGAAGGTGACTGAGGCG 59.966 55.000 0.00 0.00 42.68 5.52
3525 5149 1.929836 GTGCCAGAAGAACTATGAGCG 59.070 52.381 0.00 0.00 0.00 5.03
3591 5215 3.202906 GCTACTGCCATTTAACGATCCA 58.797 45.455 0.00 0.00 0.00 3.41
3597 5221 4.992688 TGCCATTTAACGATCCATGAAAC 58.007 39.130 0.00 0.00 0.00 2.78
3609 5233 5.392919 CGATCCATGAAACACCAATGCTAAA 60.393 40.000 0.00 0.00 0.00 1.85
3614 5238 3.378742 TGAAACACCAATGCTAAACGTGT 59.621 39.130 0.00 0.00 39.27 4.49
3642 5266 0.389948 CCGTGGCTCTTCAGGTACAC 60.390 60.000 0.00 0.00 0.00 2.90
3673 5297 0.980231 AGGTCTCTGATCCCACTGGC 60.980 60.000 0.00 0.00 0.00 4.85
3715 5339 4.914983 TCAATGACCAAGCAGAGAGAATT 58.085 39.130 0.00 0.00 0.00 2.17
3768 5392 5.351740 GGATCAGGAAAGAGGTAAAAACTCG 59.648 44.000 0.00 0.00 39.90 4.18
3781 5405 1.039856 AAACTCGTGCCTTGCCATTT 58.960 45.000 0.00 0.00 0.00 2.32
3782 5406 0.314935 AACTCGTGCCTTGCCATTTG 59.685 50.000 0.00 0.00 0.00 2.32
3792 5416 2.169769 CCTTGCCATTTGGAATGCAGAT 59.830 45.455 0.00 0.00 37.39 2.90
3850 5476 2.629617 CAAATTCTGTTTGCAGGAGGGT 59.370 45.455 0.00 0.00 42.78 4.34
3916 5542 2.310233 CCTGTTCCGTGTCAGCGTG 61.310 63.158 0.00 0.00 0.00 5.34
3937 5563 0.973632 TGCAGAACGAGTACATGGGT 59.026 50.000 0.00 0.00 0.00 4.51
3988 5614 2.267006 TCGCCGGTCGACTACTCT 59.733 61.111 16.46 0.00 43.16 3.24
4018 5644 2.839228 AGGTACCAGCTTGAGGAGATT 58.161 47.619 15.94 0.00 0.00 2.40
4052 5678 3.866651 TCCAGCTAGAAGAAGATGCAAC 58.133 45.455 0.00 0.00 31.47 4.17
4094 5720 2.093764 CGAGGAGATTTCCAAGCTCACT 60.094 50.000 4.89 0.00 45.44 3.41
4155 5789 5.077864 TCCCCTTGAGGAGATAGATATCCAA 59.922 44.000 5.99 0.00 40.59 3.53
4238 5872 1.221466 TTCAGCCGTGTCTTTCTGCG 61.221 55.000 0.00 0.00 0.00 5.18
4239 5873 1.664649 CAGCCGTGTCTTTCTGCGA 60.665 57.895 0.00 0.00 0.00 5.10
4369 6018 6.183360 GCAAATTCCTTCTGCATATACAAGGT 60.183 38.462 0.00 0.00 37.32 3.50
4406 6057 4.095483 ACTGCTAGCTGATGTTAAACATGC 59.905 41.667 26.29 0.00 39.27 4.06
4462 6113 6.963805 GCAAGAATCACTGCACTATTCTTTAC 59.036 38.462 17.41 11.98 43.85 2.01
4485 6136 1.810755 GTGTCCCGGGAATGTTTTCTC 59.189 52.381 28.84 10.19 32.16 2.87
4497 6148 5.748630 GGAATGTTTTCTCCTGTGTTTTGAC 59.251 40.000 0.00 0.00 32.16 3.18
4498 6149 6.405842 GGAATGTTTTCTCCTGTGTTTTGACT 60.406 38.462 0.00 0.00 32.16 3.41
4499 6150 5.309323 TGTTTTCTCCTGTGTTTTGACTG 57.691 39.130 0.00 0.00 0.00 3.51
4500 6151 5.007034 TGTTTTCTCCTGTGTTTTGACTGA 58.993 37.500 0.00 0.00 0.00 3.41
4542 6194 6.982141 TGTATAACGTTGTGAATCCACCTATC 59.018 38.462 11.99 0.00 42.53 2.08
4543 6195 4.553330 AACGTTGTGAATCCACCTATCT 57.447 40.909 0.00 0.00 42.53 1.98
4544 6196 5.670792 AACGTTGTGAATCCACCTATCTA 57.329 39.130 0.00 0.00 42.53 1.98
4545 6197 5.263968 ACGTTGTGAATCCACCTATCTAG 57.736 43.478 0.00 0.00 42.53 2.43
4586 6238 4.081198 ACCAAATCTGTTGGCTGACAAAAA 60.081 37.500 0.00 0.00 43.23 1.94
4603 6255 6.260050 TGACAAAAAGTACTAGGTTTGAGCAG 59.740 38.462 23.24 6.52 35.44 4.24
4605 6257 2.656560 AGTACTAGGTTTGAGCAGCG 57.343 50.000 0.00 0.00 0.00 5.18
4633 6285 2.033141 TCAGTCTTGCCCTGCTGC 59.967 61.111 0.00 0.00 0.00 5.25
4634 6286 3.060615 CAGTCTTGCCCTGCTGCC 61.061 66.667 0.00 0.00 0.00 4.85
4635 6287 3.255397 AGTCTTGCCCTGCTGCCT 61.255 61.111 0.00 0.00 0.00 4.75
4636 6288 3.060615 GTCTTGCCCTGCTGCCTG 61.061 66.667 0.00 0.00 0.00 4.85
4758 6411 3.443099 AAACTGAACAAGCCTTGAAGC 57.557 42.857 12.25 0.42 0.00 3.86
4759 6412 1.322442 ACTGAACAAGCCTTGAAGCC 58.678 50.000 12.25 0.00 0.00 4.35
4760 6413 1.321474 CTGAACAAGCCTTGAAGCCA 58.679 50.000 12.25 2.54 0.00 4.75
4761 6414 1.682854 CTGAACAAGCCTTGAAGCCAA 59.317 47.619 12.25 0.00 0.00 4.52
4762 6415 1.408702 TGAACAAGCCTTGAAGCCAAC 59.591 47.619 12.25 0.00 0.00 3.77
4764 6417 1.322442 ACAAGCCTTGAAGCCAACTC 58.678 50.000 12.25 0.00 0.00 3.01
4765 6418 1.321474 CAAGCCTTGAAGCCAACTCA 58.679 50.000 0.00 0.00 0.00 3.41
4766 6419 1.268899 CAAGCCTTGAAGCCAACTCAG 59.731 52.381 0.00 0.00 0.00 3.35
4779 6436 5.621193 AGCCAACTCAGTAACAATGTACTT 58.379 37.500 0.00 0.00 31.78 2.24
4783 6443 8.512138 GCCAACTCAGTAACAATGTACTTTATT 58.488 33.333 0.00 0.00 31.78 1.40
4855 6518 5.045505 TGGGTGTCATGTAAATGGTAAGCTA 60.046 40.000 0.00 0.00 0.00 3.32
4856 6519 5.296035 GGGTGTCATGTAAATGGTAAGCTAC 59.704 44.000 0.00 0.00 0.00 3.58
4857 6520 6.113411 GGTGTCATGTAAATGGTAAGCTACT 58.887 40.000 0.00 0.00 0.00 2.57
4858 6521 6.037172 GGTGTCATGTAAATGGTAAGCTACTG 59.963 42.308 0.00 0.00 0.00 2.74
4859 6522 6.816640 GTGTCATGTAAATGGTAAGCTACTGA 59.183 38.462 0.00 0.00 0.00 3.41
4860 6523 6.816640 TGTCATGTAAATGGTAAGCTACTGAC 59.183 38.462 0.00 0.00 0.00 3.51
4861 6524 7.042335 GTCATGTAAATGGTAAGCTACTGACT 58.958 38.462 0.00 0.00 0.00 3.41
4862 6525 7.549488 GTCATGTAAATGGTAAGCTACTGACTT 59.451 37.037 0.00 0.00 0.00 3.01
4863 6526 7.549134 TCATGTAAATGGTAAGCTACTGACTTG 59.451 37.037 0.00 0.00 0.00 3.16
4864 6527 6.999950 TGTAAATGGTAAGCTACTGACTTGA 58.000 36.000 0.00 0.00 0.00 3.02
4865 6528 7.446769 TGTAAATGGTAAGCTACTGACTTGAA 58.553 34.615 0.00 0.00 0.00 2.69
4866 6529 7.602644 TGTAAATGGTAAGCTACTGACTTGAAG 59.397 37.037 0.00 0.00 0.00 3.02
4867 6530 6.360370 AATGGTAAGCTACTGACTTGAAGA 57.640 37.500 0.00 0.00 0.00 2.87
4868 6531 6.552445 ATGGTAAGCTACTGACTTGAAGAT 57.448 37.500 0.00 0.00 0.00 2.40
4886 6549 5.832595 TGAAGATGAAACAGGTTCCATCAAA 59.167 36.000 12.85 0.00 35.12 2.69
4906 6569 0.764369 AGTGACTGGTTGCTGGGAGA 60.764 55.000 0.00 0.00 0.00 3.71
4973 6636 5.541101 TGACCAGGCTAACAAAGTACTCTAA 59.459 40.000 0.00 0.00 0.00 2.10
4974 6637 6.042322 TGACCAGGCTAACAAAGTACTCTAAA 59.958 38.462 0.00 0.00 0.00 1.85
4975 6638 6.465084 ACCAGGCTAACAAAGTACTCTAAAG 58.535 40.000 0.00 0.00 0.00 1.85
4976 6639 5.351740 CCAGGCTAACAAAGTACTCTAAAGC 59.648 44.000 0.00 2.35 0.00 3.51
4977 6640 5.351740 CAGGCTAACAAAGTACTCTAAAGCC 59.648 44.000 20.35 20.35 45.80 4.35
4978 6641 5.243207 GGCTAACAAAGTACTCTAAAGCCA 58.757 41.667 21.88 0.00 45.00 4.75
4979 6642 5.121925 GGCTAACAAAGTACTCTAAAGCCAC 59.878 44.000 21.88 5.22 45.00 5.01
4980 6643 5.121925 GCTAACAAAGTACTCTAAAGCCACC 59.878 44.000 0.00 0.00 0.00 4.61
4981 6644 3.660865 ACAAAGTACTCTAAAGCCACCG 58.339 45.455 0.00 0.00 0.00 4.94
4982 6645 3.322828 ACAAAGTACTCTAAAGCCACCGA 59.677 43.478 0.00 0.00 0.00 4.69
4983 6646 3.589495 AAGTACTCTAAAGCCACCGAC 57.411 47.619 0.00 0.00 0.00 4.79
4984 6647 2.805194 AGTACTCTAAAGCCACCGACT 58.195 47.619 0.00 0.00 0.00 4.18
4985 6648 2.754002 AGTACTCTAAAGCCACCGACTC 59.246 50.000 0.00 0.00 0.00 3.36
4986 6649 1.926108 ACTCTAAAGCCACCGACTCT 58.074 50.000 0.00 0.00 0.00 3.24
4987 6650 1.546476 ACTCTAAAGCCACCGACTCTG 59.454 52.381 0.00 0.00 0.00 3.35
4988 6651 1.819288 CTCTAAAGCCACCGACTCTGA 59.181 52.381 0.00 0.00 0.00 3.27
5016 6700 5.106436 TGTGATGAAGATGTTGCATCAGTTC 60.106 40.000 13.95 12.59 46.24 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.249911 ACGTCTCTGCCAGGTTTCAC 60.250 55.000 0.00 0.00 0.00 3.18
41 42 1.107114 CATCTACGTCTCTGCCAGGT 58.893 55.000 0.00 0.00 0.00 4.00
46 47 4.502282 CAGTGATTTCATCTACGTCTCTGC 59.498 45.833 0.00 0.00 0.00 4.26
49 50 4.424626 TGCAGTGATTTCATCTACGTCTC 58.575 43.478 0.00 0.00 0.00 3.36
50 51 4.456280 TGCAGTGATTTCATCTACGTCT 57.544 40.909 0.00 0.00 0.00 4.18
53 54 6.355397 AGAAATGCAGTGATTTCATCTACG 57.645 37.500 20.47 0.00 42.50 3.51
54 55 9.713740 CTTAAGAAATGCAGTGATTTCATCTAC 57.286 33.333 20.47 4.00 42.50 2.59
55 56 9.671279 TCTTAAGAAATGCAGTGATTTCATCTA 57.329 29.630 20.47 11.56 42.50 1.98
56 57 8.457261 GTCTTAAGAAATGCAGTGATTTCATCT 58.543 33.333 20.47 12.17 42.50 2.90
62 111 6.599638 GGTAGGTCTTAAGAAATGCAGTGATT 59.400 38.462 6.78 0.00 0.00 2.57
89 138 3.871594 GTGAATCACGATTCCCGATCTTT 59.128 43.478 15.39 0.00 44.93 2.52
94 143 2.004583 GTGTGAATCACGATTCCCGA 57.995 50.000 15.39 0.00 44.93 5.14
103 152 4.601019 CTTGAGTTGGTTGTGTGAATCAC 58.399 43.478 6.41 6.41 46.31 3.06
135 184 4.134379 AGAGTTGTCAATGATGCTCGAT 57.866 40.909 0.00 0.00 0.00 3.59
136 185 3.599730 AGAGTTGTCAATGATGCTCGA 57.400 42.857 0.00 0.00 0.00 4.04
137 186 4.807834 ACATAGAGTTGTCAATGATGCTCG 59.192 41.667 0.00 0.00 0.00 5.03
138 187 5.007430 CCACATAGAGTTGTCAATGATGCTC 59.993 44.000 0.00 0.00 0.00 4.26
139 188 4.880120 CCACATAGAGTTGTCAATGATGCT 59.120 41.667 0.00 0.00 0.00 3.79
140 189 4.036027 CCCACATAGAGTTGTCAATGATGC 59.964 45.833 0.00 0.00 0.00 3.91
141 190 4.577693 CCCCACATAGAGTTGTCAATGATG 59.422 45.833 0.00 0.00 0.00 3.07
142 191 4.474651 TCCCCACATAGAGTTGTCAATGAT 59.525 41.667 0.00 0.00 0.00 2.45
143 192 3.843619 TCCCCACATAGAGTTGTCAATGA 59.156 43.478 0.00 0.00 0.00 2.57
144 193 4.080919 TCTCCCCACATAGAGTTGTCAATG 60.081 45.833 0.00 0.00 0.00 2.82
145 194 4.104086 TCTCCCCACATAGAGTTGTCAAT 58.896 43.478 0.00 0.00 0.00 2.57
146 195 3.516586 TCTCCCCACATAGAGTTGTCAA 58.483 45.455 0.00 0.00 0.00 3.18
147 196 3.184382 TCTCCCCACATAGAGTTGTCA 57.816 47.619 0.00 0.00 0.00 3.58
195 244 5.600484 ACCAAATTGTCTAAATCCCACACAA 59.400 36.000 0.00 0.00 0.00 3.33
199 248 7.836842 ACAATACCAAATTGTCTAAATCCCAC 58.163 34.615 0.00 0.00 37.69 4.61
235 284 9.808808 TTTCATTGCAATAAATGTTCAAATTCG 57.191 25.926 12.53 0.00 38.46 3.34
254 303 6.415280 TCAAAATACAACGACCGTTTTCATTG 59.585 34.615 4.93 7.80 36.00 2.82
267 316 8.932963 GTTCAAAAAGCAATTCAAAATACAACG 58.067 29.630 0.00 0.00 0.00 4.10
328 377 5.221048 GGTTTCAACATAGAAATCGGATGGG 60.221 44.000 0.00 0.00 39.46 4.00
343 393 7.231467 AGCTTCCTAAATTAGAGGTTTCAACA 58.769 34.615 0.83 0.00 35.40 3.33
362 412 7.255569 GGTACCACAAATTTTACATAGCTTCC 58.744 38.462 7.15 0.00 0.00 3.46
372 422 2.160022 GCTCGCGGTACCACAAATTTTA 59.840 45.455 13.54 0.00 0.00 1.52
380 430 4.078516 AAGGGCTCGCGGTACCAC 62.079 66.667 13.54 0.07 0.00 4.16
381 431 3.766691 GAAGGGCTCGCGGTACCA 61.767 66.667 13.54 0.00 0.00 3.25
397 447 1.738830 GGGATTTGTTCCGCGTCGA 60.739 57.895 4.92 0.00 46.52 4.20
399 449 2.782615 CGGGATTTGTTCCGCGTC 59.217 61.111 4.92 0.00 46.52 5.19
403 453 3.251487 ACAAGTTTACGGGATTTGTTCCG 59.749 43.478 0.00 0.00 46.52 4.30
410 460 1.947212 GCGGGACAAGTTTACGGGATT 60.947 52.381 0.00 0.00 0.00 3.01
422 472 1.576356 GCAAATGTTTTGCGGGACAA 58.424 45.000 8.98 0.00 35.58 3.18
423 473 3.280920 GCAAATGTTTTGCGGGACA 57.719 47.368 8.98 0.00 35.58 4.02
440 490 3.564027 CGGCGAAACAGATCCCGC 61.564 66.667 0.00 0.00 46.04 6.13
479 529 0.179040 TTCGGGAGCGGAAACACTTT 60.179 50.000 0.00 0.00 0.00 2.66
480 530 0.602905 CTTCGGGAGCGGAAACACTT 60.603 55.000 0.00 0.00 0.00 3.16
481 531 1.004918 CTTCGGGAGCGGAAACACT 60.005 57.895 0.00 0.00 0.00 3.55
484 534 1.005394 TGACTTCGGGAGCGGAAAC 60.005 57.895 0.00 0.00 0.00 2.78
496 1636 5.278561 CGTGGGAAGAGGATATACTGACTTC 60.279 48.000 7.57 7.57 34.80 3.01
507 1647 2.285368 TGGCCGTGGGAAGAGGAT 60.285 61.111 0.00 0.00 0.00 3.24
525 1665 1.173913 GGGGAAATACTGTGTGCACC 58.826 55.000 15.69 6.37 0.00 5.01
558 1698 3.347958 TTTGAATTCGGAAGTGTGTGC 57.652 42.857 0.00 0.00 0.00 4.57
609 1783 2.835895 GGGTCGAGAGGAGGGCTC 60.836 72.222 0.00 0.00 0.00 4.70
679 1853 4.845705 AGAAGCGAGCGAGCGAGC 62.846 66.667 9.12 9.12 43.00 5.03
680 1854 2.948648 CAGAAGCGAGCGAGCGAG 60.949 66.667 1.41 0.00 43.00 5.03
681 1855 4.482684 CCAGAAGCGAGCGAGCGA 62.483 66.667 1.41 0.00 43.00 4.93
753 1927 2.475685 GGCGCGTGGATAGTTTTCTTTC 60.476 50.000 8.43 0.00 0.00 2.62
806 1980 3.003173 CCGGGTTGAGGCTCCTGA 61.003 66.667 12.86 0.00 32.26 3.86
928 2103 4.699522 GTGGAGGTGGTGGGCGTC 62.700 72.222 0.00 0.00 0.00 5.19
1149 2324 4.250170 GGGGGAGGGGGCGATAGA 62.250 72.222 0.00 0.00 39.76 1.98
1179 2764 0.109504 GCAGATAGATCCGGCGAGAC 60.110 60.000 9.30 0.00 0.00 3.36
1232 2828 6.978080 GGAGAGATCAAACAGATACTGAAGAC 59.022 42.308 5.76 0.00 37.00 3.01
1240 2836 5.824624 GGCAAATGGAGAGATCAAACAGATA 59.175 40.000 0.00 0.00 37.00 1.98
1248 2845 0.181114 CGGGGCAAATGGAGAGATCA 59.819 55.000 0.00 0.00 0.00 2.92
1290 2888 3.518068 GGGGGAAATCGGCGCAAG 61.518 66.667 10.83 1.95 43.44 4.01
1315 2913 2.125106 GTCCGTCAGGGCCACATC 60.125 66.667 6.18 0.00 35.69 3.06
1321 2919 0.951040 CAAGAACAGTCCGTCAGGGC 60.951 60.000 0.00 0.00 44.17 5.19
1577 3175 0.597637 GATCACCATCCTGCCGTACG 60.598 60.000 8.69 8.69 0.00 3.67
1578 3176 0.464036 TGATCACCATCCTGCCGTAC 59.536 55.000 0.00 0.00 0.00 3.67
1579 3177 1.344438 GATGATCACCATCCTGCCGTA 59.656 52.381 0.00 0.00 44.59 4.02
1669 3267 0.690192 TTGGGCTTCATGAGAACCGA 59.310 50.000 0.00 0.00 0.00 4.69
1673 3271 1.283029 CCTCCTTGGGCTTCATGAGAA 59.717 52.381 0.00 0.00 30.58 2.87
1735 3333 2.292267 CCTTGGCTTCAGCATAATCGT 58.708 47.619 0.30 0.00 44.36 3.73
1752 3350 1.300697 GGACTTCACGTCGTGCCTT 60.301 57.895 20.56 6.33 43.79 4.35
1832 3430 4.952262 TTCATCAGCAGAACATTACAGC 57.048 40.909 0.00 0.00 0.00 4.40
1835 3433 7.809331 TCACAAATTTCATCAGCAGAACATTAC 59.191 33.333 0.00 0.00 0.00 1.89
1838 3436 6.335471 TCACAAATTTCATCAGCAGAACAT 57.665 33.333 0.00 0.00 0.00 2.71
1868 3466 2.961741 AGAAGTGACAGAAGTGAGCAGA 59.038 45.455 0.00 0.00 0.00 4.26
1869 3467 3.058450 CAGAAGTGACAGAAGTGAGCAG 58.942 50.000 0.00 0.00 0.00 4.24
1933 3531 1.596477 GATCAGAGGATGCACCCGC 60.596 63.158 0.00 0.00 40.05 6.13
2113 3711 4.165779 CAACTTGGTTCGGCAAATACATC 58.834 43.478 0.00 0.00 0.00 3.06
2144 3742 3.057033 ACACAGATCAAGCAAAATCAGCC 60.057 43.478 0.00 0.00 0.00 4.85
2207 3805 4.006319 ACAGGATAGAACTTCTTTGCAGC 58.994 43.478 0.00 0.00 0.00 5.25
2227 3825 1.286553 ACCTTCCCCAACTCAAACACA 59.713 47.619 0.00 0.00 0.00 3.72
2237 3835 4.287552 GAGATGTAGTAGACCTTCCCCAA 58.712 47.826 0.00 0.00 0.00 4.12
2239 3837 3.232662 GGAGATGTAGTAGACCTTCCCC 58.767 54.545 0.00 0.00 0.00 4.81
2266 3864 2.432206 TGTTCGCGATTCTGAGTGAA 57.568 45.000 10.88 0.00 39.24 3.18
2269 3867 1.071605 GCTTGTTCGCGATTCTGAGT 58.928 50.000 10.88 0.00 0.00 3.41
2334 3932 1.266175 CAGCCTCTTCAACAACAGCAG 59.734 52.381 0.00 0.00 0.00 4.24
2350 3948 0.625849 TGAAAGATTCCCCCTCAGCC 59.374 55.000 0.00 0.00 0.00 4.85
2359 3957 3.119352 GCACTGGTGGAATGAAAGATTCC 60.119 47.826 6.50 6.50 45.89 3.01
2449 4047 5.634896 AGCTCACTGAAATTAAGCAATTCG 58.365 37.500 0.00 0.00 33.09 3.34
2480 4078 2.287644 TCACACTGAACGCATCAAGTTG 59.712 45.455 0.00 0.00 37.67 3.16
2487 4085 5.689383 AAAATTAGTCACACTGAACGCAT 57.311 34.783 0.00 0.00 0.00 4.73
2491 4089 8.366671 ACAGAGTAAAATTAGTCACACTGAAC 57.633 34.615 9.92 0.00 35.92 3.18
2569 4167 5.064962 GTCAATCTTTCTTCTGATGCTCAGG 59.935 44.000 11.63 0.31 44.39 3.86
2575 4173 8.041829 ACTCATTGTCAATCTTTCTTCTGATG 57.958 34.615 0.00 0.00 0.00 3.07
2648 4246 8.893727 ACATGTTAGGATATCAACAAGTAAAGC 58.106 33.333 12.50 0.00 35.49 3.51
2652 4250 7.768582 CACCACATGTTAGGATATCAACAAGTA 59.231 37.037 13.32 0.00 35.16 2.24
2666 4264 8.661352 TCAATATCACATACACCACATGTTAG 57.339 34.615 0.00 0.00 43.19 2.34
2869 4468 2.156098 TGGAAGGGTGCCAAGAGCT 61.156 57.895 0.00 0.00 44.23 4.09
2878 4477 5.291971 CAGAAAAGAATTTGTGGAAGGGTG 58.708 41.667 0.00 0.00 39.02 4.61
2942 4566 4.932200 CAGACACACCTGGTAGAGAAATTC 59.068 45.833 0.00 0.00 0.00 2.17
3056 4680 8.457261 ACTTAAGAGCTAATCAAAAGAAGCATG 58.543 33.333 10.09 0.00 37.44 4.06
3092 4716 7.227314 TCAGCAAATAATGTGGTCATGATCTAC 59.773 37.037 7.64 6.23 34.19 2.59
3110 4734 8.985315 TTCAGATTCATACCTATTCAGCAAAT 57.015 30.769 0.00 0.00 0.00 2.32
3120 4744 4.103153 CCCTTGCCTTCAGATTCATACCTA 59.897 45.833 0.00 0.00 0.00 3.08
3275 4899 7.136119 CCATGTACTGTTAACAAACGTTCAAT 58.864 34.615 10.03 0.00 0.00 2.57
3281 4905 4.215965 GCACCATGTACTGTTAACAAACG 58.784 43.478 10.03 0.63 0.00 3.60
3283 4907 5.767665 AGATGCACCATGTACTGTTAACAAA 59.232 36.000 10.03 0.00 0.00 2.83
3290 4914 3.338249 GTTCAGATGCACCATGTACTGT 58.662 45.455 0.00 0.00 0.00 3.55
3298 4922 2.885135 ATTCAGGTTCAGATGCACCA 57.115 45.000 4.48 0.00 33.63 4.17
3299 4923 5.357878 TGAATTATTCAGGTTCAGATGCACC 59.642 40.000 3.20 0.00 34.08 5.01
3311 4935 3.700539 TGTGCACCCATGAATTATTCAGG 59.299 43.478 15.69 12.65 43.98 3.86
3326 4950 1.066257 CAACTGCCAAGTGTGCACC 59.934 57.895 15.69 5.76 36.51 5.01
3327 4951 1.589727 GCAACTGCCAAGTGTGCAC 60.590 57.895 10.75 10.75 38.85 4.57
3341 4965 3.686726 CAGGTCAGATTACTTCAGGCAAC 59.313 47.826 0.00 0.00 0.00 4.17
3342 4966 3.582647 TCAGGTCAGATTACTTCAGGCAA 59.417 43.478 0.00 0.00 0.00 4.52
3349 4973 7.147976 GCAAAACAAATCAGGTCAGATTACTT 58.852 34.615 0.00 0.00 37.24 2.24
3355 4979 3.243501 GCTGCAAAACAAATCAGGTCAGA 60.244 43.478 0.00 0.00 0.00 3.27
3360 4984 2.224113 ACAGGCTGCAAAACAAATCAGG 60.224 45.455 15.89 0.00 0.00 3.86
3362 4986 3.540314 AACAGGCTGCAAAACAAATCA 57.460 38.095 15.89 0.00 0.00 2.57
3365 4989 3.936564 AGAAAACAGGCTGCAAAACAAA 58.063 36.364 15.89 0.00 0.00 2.83
3415 5039 1.278985 CACATGGTCTGGTCAGGCTTA 59.721 52.381 0.00 0.00 32.63 3.09
3478 5102 0.755686 ACCAGAATCCTGATCCGAGC 59.244 55.000 0.00 0.00 43.02 5.03
3525 5149 3.003480 GACTGTTACCTCAATGAGCACC 58.997 50.000 4.40 0.00 0.00 5.01
3591 5215 4.037446 ACACGTTTAGCATTGGTGTTTCAT 59.963 37.500 0.00 0.00 38.59 2.57
3597 5221 3.003275 ACAAGACACGTTTAGCATTGGTG 59.997 43.478 0.00 0.00 34.87 4.17
3609 5233 0.808453 CCACGGTGAACAAGACACGT 60.808 55.000 10.28 0.00 38.90 4.49
3614 5238 0.468226 AAGAGCCACGGTGAACAAGA 59.532 50.000 10.28 0.00 0.00 3.02
3642 5266 2.502947 TCAGAGACCTTGATCACCATGG 59.497 50.000 11.19 11.19 43.61 3.66
3673 5297 2.177594 AAAGAGACAGCCAGGCCTCG 62.178 60.000 8.22 0.00 0.00 4.63
3768 5392 1.729284 CATTCCAAATGGCAAGGCAC 58.271 50.000 0.00 0.00 34.44 5.01
3781 5405 3.181484 GCAAGCAACATATCTGCATTCCA 60.181 43.478 8.62 0.00 42.48 3.53
3782 5406 3.067742 AGCAAGCAACATATCTGCATTCC 59.932 43.478 8.62 0.00 42.48 3.01
3792 5416 3.937079 CAGATCACAGAGCAAGCAACATA 59.063 43.478 0.00 0.00 0.00 2.29
3850 5476 3.340928 CTTGAGCTGGAACATGTCATCA 58.659 45.455 0.00 0.00 38.20 3.07
3916 5542 1.359848 CCATGTACTCGTTCTGCACC 58.640 55.000 0.00 0.00 0.00 5.01
3937 5563 2.106566 GTGATCCTCTGCCTCTTCTCA 58.893 52.381 0.00 0.00 0.00 3.27
3997 5623 2.327325 TCTCCTCAAGCTGGTACCTT 57.673 50.000 14.36 0.00 0.00 3.50
4009 5635 0.986527 TGAGCTTGGCAATCTCCTCA 59.013 50.000 23.88 17.88 0.00 3.86
4018 5644 2.752358 CTGGAGGTGAGCTTGGCA 59.248 61.111 0.00 0.00 0.00 4.92
4083 5709 4.704833 GGCGGCAGTGAGCTTGGA 62.705 66.667 3.07 0.00 44.79 3.53
4167 5801 4.427312 CAAAACATGGCTTCATCCTTAGC 58.573 43.478 0.00 0.00 36.66 3.09
4168 5802 5.002464 CCAAAACATGGCTTCATCCTTAG 57.998 43.478 0.00 0.00 43.80 2.18
4238 5872 3.553511 CACTACATTTGAGGAGCGACATC 59.446 47.826 0.00 0.00 0.00 3.06
4239 5873 3.525537 CACTACATTTGAGGAGCGACAT 58.474 45.455 0.00 0.00 0.00 3.06
4380 6029 2.988010 TAACATCAGCTAGCAGTGGG 57.012 50.000 18.83 4.71 0.00 4.61
4462 6113 0.251165 AAACATTCCCGGGACACAGG 60.251 55.000 26.87 13.99 0.00 4.00
4485 6136 2.355756 CACCACTCAGTCAAAACACAGG 59.644 50.000 0.00 0.00 0.00 4.00
4497 6148 3.055819 ACACCTATGCTTACACCACTCAG 60.056 47.826 0.00 0.00 0.00 3.35
4498 6149 2.903784 ACACCTATGCTTACACCACTCA 59.096 45.455 0.00 0.00 0.00 3.41
4499 6150 3.611766 ACACCTATGCTTACACCACTC 57.388 47.619 0.00 0.00 0.00 3.51
4500 6151 6.579865 GTTATACACCTATGCTTACACCACT 58.420 40.000 0.00 0.00 0.00 4.00
4542 6194 4.154918 GGTGAAAGTGATGCTCAAACCTAG 59.845 45.833 0.00 0.00 0.00 3.02
4543 6195 4.072131 GGTGAAAGTGATGCTCAAACCTA 58.928 43.478 0.00 0.00 0.00 3.08
4544 6196 2.887152 GGTGAAAGTGATGCTCAAACCT 59.113 45.455 0.00 0.00 0.00 3.50
4545 6197 2.622942 TGGTGAAAGTGATGCTCAAACC 59.377 45.455 0.00 0.00 0.00 3.27
4546 6198 3.988379 TGGTGAAAGTGATGCTCAAAC 57.012 42.857 0.00 0.00 0.00 2.93
4547 6199 4.998671 TTTGGTGAAAGTGATGCTCAAA 57.001 36.364 0.00 0.00 0.00 2.69
4586 6238 1.404315 GCGCTGCTCAAACCTAGTACT 60.404 52.381 0.00 0.00 0.00 2.73
4603 6255 0.528470 AGACTGAGACTACCTTGCGC 59.472 55.000 0.00 0.00 0.00 6.09
4634 6286 3.850098 AACCCGACAAGCCCAGCAG 62.850 63.158 0.00 0.00 0.00 4.24
4635 6287 3.884774 AACCCGACAAGCCCAGCA 61.885 61.111 0.00 0.00 0.00 4.41
4636 6288 3.365265 CAACCCGACAAGCCCAGC 61.365 66.667 0.00 0.00 0.00 4.85
4637 6289 0.821711 TTTCAACCCGACAAGCCCAG 60.822 55.000 0.00 0.00 0.00 4.45
4638 6290 0.821711 CTTTCAACCCGACAAGCCCA 60.822 55.000 0.00 0.00 0.00 5.36
4639 6291 0.822121 ACTTTCAACCCGACAAGCCC 60.822 55.000 0.00 0.00 0.00 5.19
4647 6299 2.504367 ACTCAATCCACTTTCAACCCG 58.496 47.619 0.00 0.00 0.00 5.28
4758 6411 9.825972 CAATAAAGTACATTGTTACTGAGTTGG 57.174 33.333 0.00 0.00 0.00 3.77
4779 6436 6.655003 CCTTCTGAGTTGGTAGCTTTCAATAA 59.345 38.462 0.00 0.00 0.00 1.40
4783 6443 3.391296 ACCTTCTGAGTTGGTAGCTTTCA 59.609 43.478 0.00 0.00 31.50 2.69
4855 6518 5.041191 ACCTGTTTCATCTTCAAGTCAGT 57.959 39.130 0.00 0.00 0.00 3.41
4856 6519 5.049129 GGAACCTGTTTCATCTTCAAGTCAG 60.049 44.000 0.00 0.00 35.70 3.51
4857 6520 4.821805 GGAACCTGTTTCATCTTCAAGTCA 59.178 41.667 0.00 0.00 35.70 3.41
4858 6521 4.821805 TGGAACCTGTTTCATCTTCAAGTC 59.178 41.667 0.00 0.00 35.70 3.01
4859 6522 4.792068 TGGAACCTGTTTCATCTTCAAGT 58.208 39.130 0.00 0.00 35.70 3.16
4860 6523 5.947443 GATGGAACCTGTTTCATCTTCAAG 58.053 41.667 19.56 0.00 46.89 3.02
4861 6524 5.964958 GATGGAACCTGTTTCATCTTCAA 57.035 39.130 19.56 0.00 46.89 2.69
4867 6530 5.598005 TCACTTTTGATGGAACCTGTTTCAT 59.402 36.000 3.45 3.45 41.29 2.57
4868 6531 4.952957 TCACTTTTGATGGAACCTGTTTCA 59.047 37.500 0.00 0.00 35.70 2.69
4886 6549 0.109342 CTCCCAGCAACCAGTCACTT 59.891 55.000 0.00 0.00 0.00 3.16
4906 6569 1.279496 TAGTGGCTGGCTTCTCACAT 58.721 50.000 2.00 0.00 33.01 3.21
4973 6636 1.066573 CATCTTCAGAGTCGGTGGCTT 60.067 52.381 0.00 0.00 0.00 4.35
4974 6637 0.534412 CATCTTCAGAGTCGGTGGCT 59.466 55.000 0.00 0.00 0.00 4.75
4975 6638 0.247736 ACATCTTCAGAGTCGGTGGC 59.752 55.000 0.00 0.00 0.00 5.01
4976 6639 1.546029 TCACATCTTCAGAGTCGGTGG 59.454 52.381 0.00 0.00 0.00 4.61
4977 6640 3.119352 TCATCACATCTTCAGAGTCGGTG 60.119 47.826 0.00 0.00 0.00 4.94
4978 6641 3.092301 TCATCACATCTTCAGAGTCGGT 58.908 45.455 0.00 0.00 0.00 4.69
4979 6642 3.790152 TCATCACATCTTCAGAGTCGG 57.210 47.619 0.00 0.00 0.00 4.79
4980 6643 4.991472 TCTTCATCACATCTTCAGAGTCG 58.009 43.478 0.00 0.00 0.00 4.18
4981 6644 6.339730 ACATCTTCATCACATCTTCAGAGTC 58.660 40.000 0.00 0.00 0.00 3.36
4982 6645 6.297080 ACATCTTCATCACATCTTCAGAGT 57.703 37.500 0.00 0.00 0.00 3.24
4983 6646 6.457122 GCAACATCTTCATCACATCTTCAGAG 60.457 42.308 0.00 0.00 0.00 3.35
4984 6647 5.353400 GCAACATCTTCATCACATCTTCAGA 59.647 40.000 0.00 0.00 0.00 3.27
4985 6648 5.123344 TGCAACATCTTCATCACATCTTCAG 59.877 40.000 0.00 0.00 0.00 3.02
4986 6649 5.005094 TGCAACATCTTCATCACATCTTCA 58.995 37.500 0.00 0.00 0.00 3.02
4987 6650 5.556355 TGCAACATCTTCATCACATCTTC 57.444 39.130 0.00 0.00 0.00 2.87
4988 6651 5.650703 TGATGCAACATCTTCATCACATCTT 59.349 36.000 8.87 0.00 40.91 2.40
5016 6700 2.467880 ACCATGTACCTGACACCCTAG 58.532 52.381 0.00 0.00 42.17 3.02


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

AutoCloner maintained by Alex Coulton.