Multiple sequence alignment - TraesCS4A01G102500

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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 TraesCS4A01G102500 chr4A 100.000 9659 0 0 1 9659 115291843 115282185 0.000000e+00 17837.0
1 TraesCS4A01G102500 chr4A 99.653 865 2 1 3398 4262 208829786 208830649 0.000000e+00 1580.0
2 TraesCS4A01G102500 chr4A 94.537 897 8 3 3398 4261 314680582 314681470 0.000000e+00 1347.0
3 TraesCS4A01G102500 chr4A 93.130 131 7 1 3162 3292 617925776 617925904 3.560000e-44 191.0
4 TraesCS4A01G102500 chr4A 88.462 52 5 1 6408 6458 146553804 146553753 2.910000e-05 62.1
5 TraesCS4A01G102500 chr4A 85.455 55 7 1 6405 6458 569475752 569475698 1.000000e-03 56.5
6 TraesCS4A01G102500 chr4D 96.156 4448 126 17 4262 8690 349570407 349574828 0.000000e+00 7225.0
7 TraesCS4A01G102500 chr4D 95.129 2443 74 15 727 3161 349567976 349570381 0.000000e+00 3810.0
8 TraesCS4A01G102500 chr4D 95.289 849 28 3 3398 4242 175791145 175790305 0.000000e+00 1336.0
9 TraesCS4A01G102500 chr4D 91.231 707 20 15 8985 9659 349575328 349576024 0.000000e+00 924.0
10 TraesCS4A01G102500 chr4D 87.900 719 85 2 1 717 349567187 349567905 0.000000e+00 845.0
11 TraesCS4A01G102500 chr4D 83.062 307 32 10 8695 8985 349574995 349575297 2.680000e-65 261.0
12 TraesCS4A01G102500 chr4D 88.571 175 8 4 3160 3334 309504531 309504693 1.640000e-47 202.0
13 TraesCS4A01G102500 chr4D 85.556 180 17 5 3160 3338 192738923 192739094 7.710000e-41 180.0
14 TraesCS4A01G102500 chr4D 78.481 158 26 7 6270 6420 479313185 479313341 7.980000e-16 97.1
15 TraesCS4A01G102500 chr4B 96.218 3940 111 15 4494 8414 432817376 432821296 0.000000e+00 6416.0
16 TraesCS4A01G102500 chr4B 96.015 2409 72 17 801 3200 432814303 432816696 0.000000e+00 3895.0
17 TraesCS4A01G102500 chr4B 98.843 864 1 2 3398 4261 563222945 563222091 0.000000e+00 1531.0
18 TraesCS4A01G102500 chr4B 86.920 711 27 20 8985 9659 432823226 432823906 0.000000e+00 737.0
19 TraesCS4A01G102500 chr4B 88.909 559 39 11 8445 8985 432822642 432823195 0.000000e+00 667.0
20 TraesCS4A01G102500 chr4B 89.160 369 13 8 3042 3397 432816716 432817070 1.490000e-117 435.0
21 TraesCS4A01G102500 chr4B 98.283 233 4 0 4262 4494 432817063 432817295 9.030000e-110 409.0
22 TraesCS4A01G102500 chr4B 89.326 178 7 4 3160 3337 386210238 386210403 7.600000e-51 213.0
23 TraesCS4A01G102500 chr4B 85.263 190 11 6 3160 3337 643784548 643784364 7.710000e-41 180.0
24 TraesCS4A01G102500 chr5B 99.057 848 6 2 3398 4245 153897780 153896935 0.000000e+00 1520.0
25 TraesCS4A01G102500 chr5A 98.385 867 9 2 3397 4261 426300057 426300920 0.000000e+00 1519.0
26 TraesCS4A01G102500 chr5A 82.524 103 14 4 6272 6373 337936016 337935917 4.810000e-13 87.9
27 TraesCS4A01G102500 chr1A 97.353 869 14 2 3395 4263 581435601 581434742 0.000000e+00 1469.0
28 TraesCS4A01G102500 chr1A 86.538 52 7 0 6404 6455 324567202 324567253 3.770000e-04 58.4
29 TraesCS4A01G102500 chr2B 96.697 878 9 2 3398 4263 365983973 365983104 0.000000e+00 1443.0
30 TraesCS4A01G102500 chr2B 84.483 174 12 7 3196 3366 57787493 57787654 3.610000e-34 158.0
31 TraesCS4A01G102500 chr2B 85.870 92 12 1 6291 6382 749228006 749227916 7.980000e-16 97.1
32 TraesCS4A01G102500 chr6A 96.767 866 5 2 3398 4261 430939533 430940377 0.000000e+00 1423.0
33 TraesCS4A01G102500 chr6A 91.304 138 11 1 3196 3332 252847242 252847379 4.610000e-43 187.0
34 TraesCS4A01G102500 chr7A 96.331 845 10 3 3398 4242 216730929 216731752 0.000000e+00 1369.0
35 TraesCS4A01G102500 chr7A 89.510 143 11 1 3196 3338 654795130 654795268 2.770000e-40 178.0
36 TraesCS4A01G102500 chr7A 92.857 42 1 2 3308 3347 475962283 475962242 1.050000e-04 60.2
37 TraesCS4A01G102500 chr6D 92.054 881 36 15 3392 4268 78853685 78852835 0.000000e+00 1208.0
38 TraesCS4A01G102500 chr6D 87.701 187 19 2 4080 4263 248582472 248582287 2.110000e-51 215.0
39 TraesCS4A01G102500 chr6D 92.754 138 9 1 3196 3332 199663586 199663723 2.130000e-46 198.0
40 TraesCS4A01G102500 chr6D 95.000 40 1 1 6408 6446 3320394 3320433 2.910000e-05 62.1
41 TraesCS4A01G102500 chr6D 95.000 40 1 1 6408 6446 3326269 3326308 2.910000e-05 62.1
42 TraesCS4A01G102500 chr6D 95.000 40 1 1 6408 6446 3332145 3332184 2.910000e-05 62.1
43 TraesCS4A01G102500 chr6D 95.000 40 1 1 6408 6446 3338025 3338064 2.910000e-05 62.1
44 TraesCS4A01G102500 chr6D 96.875 32 1 0 6405 6436 186804318 186804349 5.000000e-03 54.7
45 TraesCS4A01G102500 chr1D 92.000 850 52 6 3402 4245 481042062 481041223 0.000000e+00 1179.0
46 TraesCS4A01G102500 chr1D 94.521 146 8 0 4116 4261 47850831 47850976 9.760000e-55 226.0
47 TraesCS4A01G102500 chr1D 86.486 185 14 5 4080 4261 314715849 314716025 9.900000e-45 193.0
48 TraesCS4A01G102500 chr1D 77.863 131 20 8 6258 6383 439932025 439931899 1.350000e-08 73.1
49 TraesCS4A01G102500 chr1D 87.273 55 7 0 6404 6458 253017897 253017951 8.100000e-06 63.9
50 TraesCS4A01G102500 chr1D 88.000 50 6 0 6404 6453 400018719 400018670 1.050000e-04 60.2
51 TraesCS4A01G102500 chr7D 91.257 183 9 1 4080 4262 420735616 420735791 9.690000e-60 243.0
52 TraesCS4A01G102500 chr7D 88.757 169 7 3 3160 3328 126649574 126649730 7.650000e-46 196.0
53 TraesCS4A01G102500 chr7D 84.524 168 15 8 3163 3329 463885786 463885629 1.300000e-33 156.0
54 TraesCS4A01G102500 chr3D 88.764 178 8 4 3160 3337 467283654 467283489 3.540000e-49 207.0
55 TraesCS4A01G102500 chr3D 86.822 129 13 2 3196 3324 402804147 402804271 3.640000e-29 141.0
56 TraesCS4A01G102500 chr3D 82.677 127 17 5 6264 6387 103824718 103824842 3.690000e-19 108.0
57 TraesCS4A01G102500 chr3D 80.159 126 18 5 6267 6390 606934896 606934776 4.810000e-13 87.9
58 TraesCS4A01G102500 chr7B 92.958 142 9 1 3196 3337 15031480 15031620 1.270000e-48 206.0
59 TraesCS4A01G102500 chr3B 86.822 129 13 2 3196 3324 528638990 528639114 3.640000e-29 141.0
60 TraesCS4A01G102500 chr2D 78.495 186 27 6 6263 6446 407968043 407967869 1.030000e-19 110.0
61 TraesCS4A01G102500 chr5D 89.583 48 4 1 6402 6448 105095007 105095054 1.050000e-04 60.2
62 TraesCS4A01G102500 chr1B 89.130 46 5 0 6408 6453 536755727 536755682 3.770000e-04 58.4


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 TraesCS4A01G102500 chr4A 115282185 115291843 9658 True 17837.000000 17837 100.000000 1 9659 1 chr4A.!!$R1 9658
1 TraesCS4A01G102500 chr4A 208829786 208830649 863 False 1580.000000 1580 99.653000 3398 4262 1 chr4A.!!$F1 864
2 TraesCS4A01G102500 chr4A 314680582 314681470 888 False 1347.000000 1347 94.537000 3398 4261 1 chr4A.!!$F2 863
3 TraesCS4A01G102500 chr4D 349567187 349576024 8837 False 2613.000000 7225 90.695600 1 9659 5 chr4D.!!$F4 9658
4 TraesCS4A01G102500 chr4D 175790305 175791145 840 True 1336.000000 1336 95.289000 3398 4242 1 chr4D.!!$R1 844
5 TraesCS4A01G102500 chr4B 432814303 432823906 9603 False 2093.166667 6416 92.584167 801 9659 6 chr4B.!!$F2 8858
6 TraesCS4A01G102500 chr4B 563222091 563222945 854 True 1531.000000 1531 98.843000 3398 4261 1 chr4B.!!$R1 863
7 TraesCS4A01G102500 chr5B 153896935 153897780 845 True 1520.000000 1520 99.057000 3398 4245 1 chr5B.!!$R1 847
8 TraesCS4A01G102500 chr5A 426300057 426300920 863 False 1519.000000 1519 98.385000 3397 4261 1 chr5A.!!$F1 864
9 TraesCS4A01G102500 chr1A 581434742 581435601 859 True 1469.000000 1469 97.353000 3395 4263 1 chr1A.!!$R1 868
10 TraesCS4A01G102500 chr2B 365983104 365983973 869 True 1443.000000 1443 96.697000 3398 4263 1 chr2B.!!$R1 865
11 TraesCS4A01G102500 chr6A 430939533 430940377 844 False 1423.000000 1423 96.767000 3398 4261 1 chr6A.!!$F2 863
12 TraesCS4A01G102500 chr7A 216730929 216731752 823 False 1369.000000 1369 96.331000 3398 4242 1 chr7A.!!$F1 844
13 TraesCS4A01G102500 chr6D 78852835 78853685 850 True 1208.000000 1208 92.054000 3392 4268 1 chr6D.!!$R1 876
14 TraesCS4A01G102500 chr1D 481041223 481042062 839 True 1179.000000 1179 92.000000 3402 4245 1 chr1D.!!$R3 843

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
367 368 0.034896 GACGACAACCATCACCCACT 59.965 55.000 0.00 0.00 0.0 4.00 F
819 887 0.035630 GTGGCTCAGGATCTGTGCTT 60.036 55.000 17.55 0.00 46.2 3.91 F
1818 1890 0.248621 GATTACGCCAATGTGCCAGC 60.249 55.000 0.00 0.00 0.0 4.85 F
1830 1902 0.677731 GTGCCAGCTTCTGCCATGTA 60.678 55.000 0.00 0.00 40.8 2.29 F
2068 2140 0.764271 TTGTGGTCTGTGGATGCTCA 59.236 50.000 0.00 0.00 0.0 4.26 F
2893 2972 1.028905 CTGGCCCGTGAAAACAAGAA 58.971 50.000 0.00 0.00 0.0 2.52 F
3297 3563 1.072173 CCTCATGGTCACAAGTGGTCA 59.928 52.381 0.00 0.22 0.0 4.02 F
3302 3568 1.308998 GGTCACAAGTGGTCACAAGG 58.691 55.000 3.82 0.00 0.0 3.61 F
4639 5056 0.249398 AATACACCCTGGCGACTCAC 59.751 55.000 0.00 0.00 0.0 3.51 F
5122 5543 0.742281 CAGAATGCGGGTCCACTGAG 60.742 60.000 0.00 0.00 0.0 3.35 F
6376 6804 1.477553 CCCACCATAACATGCAGCTT 58.522 50.000 0.00 0.00 0.0 3.74 F
7370 7807 0.754957 TGTTGTGCAAGGGTGAAGGG 60.755 55.000 0.00 0.00 0.0 3.95 F
8364 8805 0.543410 TGGGAGAGGAGCCGTTTACA 60.543 55.000 0.00 0.00 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1868 0.304705 GGCACATTGGCGTAATCGAG 59.695 55.000 0.00 0.0 39.71 4.04 R
2763 2842 2.706890 AGCAACATAAGTACAACGGGG 58.293 47.619 0.00 0.0 0.00 5.73 R
3258 3524 0.391597 GTCACGGGTTCAAGTCCTGA 59.608 55.000 0.00 0.0 35.49 3.86 R
3292 3558 0.764890 AAGCTGCTACCTTGTGACCA 59.235 50.000 0.90 0.0 0.00 4.02 R
3293 3559 1.897560 AAAGCTGCTACCTTGTGACC 58.102 50.000 0.90 0.0 0.00 4.02 R
4568 4985 2.363680 CTGGAGCATAGACGAACCTCAT 59.636 50.000 0.00 0.0 0.00 2.90 R
4639 5056 4.904241 ACCTTCTGAAAATGAGTCTCCAG 58.096 43.478 0.00 0.0 0.00 3.86 R
4819 5239 6.316140 TGAATATTGAGACACTAACCATGTGC 59.684 38.462 0.00 0.0 38.86 4.57 R
5930 6351 3.411446 CTTCTGGTGCAATAGGTCAACA 58.589 45.455 0.00 0.0 0.00 3.33 R
6553 6986 4.461081 AGCCTCTACAGAACAGTAAGAGTG 59.539 45.833 0.00 0.0 0.00 3.51 R
8295 8736 0.745845 GCGACCTTCACAGGATGCAT 60.746 55.000 0.00 0.0 44.19 3.96 R
8455 10211 0.669318 CGCAGACGGGTAAAAGAGCA 60.669 55.000 0.00 0.0 34.97 4.26 R
9276 11286 2.350772 GGTGAATTCAACAAGCTGGTCG 60.351 50.000 18.74 0.0 32.77 4.79 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
27 28 1.892209 ACAGGCCAGAAAACTTACCG 58.108 50.000 5.01 0.00 0.00 4.02
35 36 4.214758 GCCAGAAAACTTACCGTGTTATGT 59.785 41.667 0.00 0.00 31.52 2.29
69 70 3.215151 TGGTAACATTGAGCAACGGAAA 58.785 40.909 0.00 0.00 46.17 3.13
72 73 1.317613 ACATTGAGCAACGGAAAGCA 58.682 45.000 0.00 0.00 0.00 3.91
80 81 0.249699 CAACGGAAAGCAAAACCCCC 60.250 55.000 0.00 0.00 0.00 5.40
88 89 3.044280 CAAAACCCCCGAAACCCG 58.956 61.111 0.00 0.00 38.18 5.28
114 115 4.378874 GCAAGCTCTTACTTACAAGCAAGG 60.379 45.833 2.83 0.00 37.22 3.61
119 120 5.148651 TCTTACTTACAAGCAAGGGAGAC 57.851 43.478 2.83 0.00 31.66 3.36
127 128 1.739562 GCAAGGGAGACTGTGCTCG 60.740 63.158 0.00 0.00 35.74 5.03
131 132 2.333417 GGGAGACTGTGCTCGTCGA 61.333 63.158 0.00 0.00 36.53 4.20
138 139 1.867919 CTGTGCTCGTCGAAGAGGGT 61.868 60.000 26.24 0.00 43.36 4.34
144 145 2.687805 CGTCGAAGAGGGTCGCAGA 61.688 63.158 0.00 0.00 40.88 4.26
150 151 1.333636 AAGAGGGTCGCAGATGGAGG 61.334 60.000 0.00 0.00 40.67 4.30
166 167 1.555075 GGAGGAGGTGTGAGTATGCAA 59.445 52.381 0.00 0.00 0.00 4.08
170 171 1.555075 GAGGTGTGAGTATGCAAGGGA 59.445 52.381 0.00 0.00 0.00 4.20
185 186 1.911766 GGGACGGTGGAGGAGTCAA 60.912 63.158 0.00 0.00 36.68 3.18
193 194 1.808945 GTGGAGGAGTCAATGTTGCTG 59.191 52.381 0.00 0.00 0.00 4.41
200 201 0.665369 GTCAATGTTGCTGGTGCTGC 60.665 55.000 0.00 0.00 40.48 5.25
209 210 2.044053 TGGTGCTGCTATTGGGGC 60.044 61.111 0.00 0.00 0.00 5.80
215 216 2.124736 TGCTATTGGGGCTCGTGC 60.125 61.111 0.00 0.00 38.76 5.34
217 218 1.748879 GCTATTGGGGCTCGTGCAA 60.749 57.895 12.07 0.00 41.91 4.08
228 229 2.821366 CGTGCAAGGCTAGGGCTG 60.821 66.667 7.17 0.00 38.81 4.85
245 246 2.032681 GGGGCTTCGACTTGTGCT 59.967 61.111 0.00 0.00 0.00 4.40
253 254 0.320683 TCGACTTGTGCTGGTGATGG 60.321 55.000 0.00 0.00 0.00 3.51
254 255 0.603707 CGACTTGTGCTGGTGATGGT 60.604 55.000 0.00 0.00 0.00 3.55
258 259 0.764271 TTGTGCTGGTGATGGTGAGA 59.236 50.000 0.00 0.00 0.00 3.27
262 263 0.392193 GCTGGTGATGGTGAGAGTGG 60.392 60.000 0.00 0.00 0.00 4.00
273 274 2.757917 AGAGTGGCGGAGGAGAGC 60.758 66.667 0.00 0.00 0.00 4.09
281 282 1.515020 CGGAGGAGAGCTTGGTGAG 59.485 63.158 0.00 0.00 0.00 3.51
285 286 2.270527 GAGAGCTTGGTGAGGGGC 59.729 66.667 0.00 0.00 0.00 5.80
336 337 2.763292 AGCAGCTCATCGCCTCCT 60.763 61.111 0.00 0.00 40.39 3.69
341 342 2.835431 CTCATCGCCTCCTCGGGT 60.835 66.667 0.00 0.00 0.00 5.28
344 345 2.042843 ATCGCCTCCTCGGGTTCT 60.043 61.111 0.00 0.00 0.00 3.01
352 353 2.273179 CCTCGGGTTCTGGTGACGA 61.273 63.158 0.00 0.00 0.00 4.20
367 368 0.034896 GACGACAACCATCACCCACT 59.965 55.000 0.00 0.00 0.00 4.00
376 377 2.592993 ATCACCCACTCCACCCACG 61.593 63.158 0.00 0.00 0.00 4.94
385 386 0.944311 CTCCACCCACGTTTGTCTCG 60.944 60.000 0.00 0.00 0.00 4.04
387 388 1.594293 CACCCACGTTTGTCTCGCT 60.594 57.895 0.00 0.00 0.00 4.93
396 397 0.169230 TTTGTCTCGCTCTCTCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
409 410 2.811317 CTCGCCGAAGCACCAGAC 60.811 66.667 0.00 0.00 39.83 3.51
415 416 2.932234 CGAAGCACCAGACGACCCT 61.932 63.158 0.00 0.00 0.00 4.34
416 417 1.079750 GAAGCACCAGACGACCCTC 60.080 63.158 0.00 0.00 0.00 4.30
417 418 2.820767 GAAGCACCAGACGACCCTCG 62.821 65.000 0.00 0.00 46.93 4.63
419 420 3.680786 CACCAGACGACCCTCGCA 61.681 66.667 0.00 0.00 45.12 5.10
430 432 4.410400 CCTCGCAACCCCTCCCAC 62.410 72.222 0.00 0.00 0.00 4.61
456 458 3.873883 GCACAGCTGAGGCATCGC 61.874 66.667 23.35 7.04 41.70 4.58
488 490 2.124736 CGTGATGGGGCGGTCAAT 60.125 61.111 0.00 0.00 0.00 2.57
496 498 0.815615 GGGGCGGTCAATGATCACTC 60.816 60.000 0.00 0.00 0.00 3.51
521 523 2.778679 CAGAGGCGCAACGTTAGC 59.221 61.111 10.83 16.65 0.00 3.09
528 530 3.440415 GCAACGTTAGCCCCAGCC 61.440 66.667 0.00 0.00 41.25 4.85
576 578 3.855853 GCGAGGGGAGGAGGCTTC 61.856 72.222 0.00 0.00 0.00 3.86
603 605 2.881352 GAGTAGGACGCGCAGTGC 60.881 66.667 5.73 12.02 45.12 4.40
613 615 2.360350 CGCAGTGCCACCCTTCAT 60.360 61.111 10.11 0.00 0.00 2.57
655 658 1.064017 TGAACAGACCAACCAAAGCCT 60.064 47.619 0.00 0.00 0.00 4.58
672 675 1.760029 GCCTCCCTTCTAGTTCTCTGG 59.240 57.143 0.00 0.00 0.00 3.86
683 686 1.431243 AGTTCTCTGGTGAGGTCCTCT 59.569 52.381 19.82 0.00 40.58 3.69
687 690 0.112606 TCTGGTGAGGTCCTCTCGTT 59.887 55.000 19.82 0.00 45.32 3.85
717 720 4.505217 GCATTCGCGACGCCACAG 62.505 66.667 9.15 3.41 0.00 3.66
718 721 3.853330 CATTCGCGACGCCACAGG 61.853 66.667 9.15 0.00 0.00 4.00
723 726 4.681978 GCGACGCCACAGGAACCT 62.682 66.667 9.14 0.00 0.00 3.50
748 812 3.006728 TGAGGGGCGGTGGGTAAG 61.007 66.667 0.00 0.00 0.00 2.34
751 815 1.844544 GAGGGGCGGTGGGTAAGAAA 61.845 60.000 0.00 0.00 0.00 2.52
752 816 1.378119 GGGGCGGTGGGTAAGAAAG 60.378 63.158 0.00 0.00 0.00 2.62
753 817 1.377612 GGGCGGTGGGTAAGAAAGT 59.622 57.895 0.00 0.00 0.00 2.66
754 818 0.675837 GGGCGGTGGGTAAGAAAGTC 60.676 60.000 0.00 0.00 0.00 3.01
761 828 1.068895 TGGGTAAGAAAGTCGTTCGCA 59.931 47.619 0.00 0.00 41.52 5.10
766 833 2.949714 AGAAAGTCGTTCGCATTGTG 57.050 45.000 0.00 0.00 41.52 3.33
804 871 2.927004 TCAAGGAACGTGATGTGGC 58.073 52.632 0.00 0.00 42.83 5.01
808 876 0.036952 AGGAACGTGATGTGGCTCAG 60.037 55.000 0.00 0.00 0.00 3.35
819 887 0.035630 GTGGCTCAGGATCTGTGCTT 60.036 55.000 17.55 0.00 46.20 3.91
826 894 0.917533 AGGATCTGTGCTTGCCATCT 59.082 50.000 0.00 0.00 0.00 2.90
894 965 3.120338 TCGCGCTTTAACATTTCCAGAAG 60.120 43.478 5.56 0.00 0.00 2.85
1383 1454 1.424493 GAATCAGCCGCTTCTGGTCG 61.424 60.000 0.00 0.00 34.91 4.79
1565 1636 4.498520 CGCCTCGTCGATGCCTGT 62.499 66.667 15.55 0.00 0.00 4.00
1584 1655 2.452813 CGACGGTCCCAATCAAGCG 61.453 63.158 1.91 0.00 41.80 4.68
1814 1886 0.316196 GCTCGATTACGCCAATGTGC 60.316 55.000 0.00 0.00 39.58 4.57
1818 1890 0.248621 GATTACGCCAATGTGCCAGC 60.249 55.000 0.00 0.00 0.00 4.85
1828 1900 1.320344 ATGTGCCAGCTTCTGCCATG 61.320 55.000 0.00 0.00 40.80 3.66
1829 1901 1.975407 GTGCCAGCTTCTGCCATGT 60.975 57.895 0.00 0.00 40.80 3.21
1830 1902 0.677731 GTGCCAGCTTCTGCCATGTA 60.678 55.000 0.00 0.00 40.80 2.29
1957 2029 0.953471 TCGGGCATGTTCTTCAACCG 60.953 55.000 0.00 0.00 40.56 4.44
2068 2140 0.764271 TTGTGGTCTGTGGATGCTCA 59.236 50.000 0.00 0.00 0.00 4.26
2150 2222 4.213270 TGTGACTTGGCAGACTTATTTTCG 59.787 41.667 0.00 0.00 0.00 3.46
2258 2334 5.148651 AGTAGACCTTACAGTCGCAATTT 57.851 39.130 0.00 0.00 41.83 1.82
2271 2348 5.351465 CAGTCGCAATTTGACATAGTACCTT 59.649 40.000 0.00 0.00 38.83 3.50
2272 2349 5.581085 AGTCGCAATTTGACATAGTACCTTC 59.419 40.000 0.00 0.00 38.83 3.46
2273 2350 5.350365 GTCGCAATTTGACATAGTACCTTCA 59.650 40.000 0.00 0.00 36.37 3.02
2276 2353 7.120579 TCGCAATTTGACATAGTACCTTCATTT 59.879 33.333 0.00 0.00 0.00 2.32
2277 2354 7.429340 CGCAATTTGACATAGTACCTTCATTTC 59.571 37.037 0.00 0.00 0.00 2.17
2763 2842 4.790765 AGGCCTTAATTTTGAGCACTTC 57.209 40.909 0.00 0.00 0.00 3.01
2840 2919 1.537202 GGCTACCTTTCAGTTGTGCTG 59.463 52.381 0.00 0.00 46.34 4.41
2893 2972 1.028905 CTGGCCCGTGAAAACAAGAA 58.971 50.000 0.00 0.00 0.00 2.52
3109 3190 9.829507 TTTTATTATGCCCATTGGTAAATTCAG 57.170 29.630 1.20 0.00 0.00 3.02
3113 3194 2.831526 GCCCATTGGTAAATTCAGGTGT 59.168 45.455 1.20 0.00 0.00 4.16
3131 3212 3.119137 GGTGTGCTTGTTCTTTGGTTTCT 60.119 43.478 0.00 0.00 0.00 2.52
3132 3213 4.097286 GGTGTGCTTGTTCTTTGGTTTCTA 59.903 41.667 0.00 0.00 0.00 2.10
3160 3241 6.824305 AAAACCATCTTTGTGAGAGTATGG 57.176 37.500 0.00 0.00 37.83 2.74
3186 3267 2.203070 GTGCATGTAGCTCCCCCG 60.203 66.667 0.00 0.00 45.94 5.73
3187 3268 4.175337 TGCATGTAGCTCCCCCGC 62.175 66.667 0.00 0.00 45.94 6.13
3188 3269 3.866582 GCATGTAGCTCCCCCGCT 61.867 66.667 0.00 0.00 43.83 5.52
3189 3270 2.911143 CATGTAGCTCCCCCGCTT 59.089 61.111 0.00 0.00 41.30 4.68
3228 3494 3.688694 TTGGGTCTATTGTACGCAGTT 57.311 42.857 0.00 0.00 37.78 3.16
3295 3561 1.140312 ACCTCATGGTCACAAGTGGT 58.860 50.000 0.00 0.00 44.78 4.16
3296 3562 1.072331 ACCTCATGGTCACAAGTGGTC 59.928 52.381 0.00 0.00 44.78 4.02
3297 3563 1.072173 CCTCATGGTCACAAGTGGTCA 59.928 52.381 0.00 0.22 0.00 4.02
3298 3564 2.146342 CTCATGGTCACAAGTGGTCAC 58.854 52.381 0.00 0.00 0.00 3.67
3299 3565 1.488393 TCATGGTCACAAGTGGTCACA 59.512 47.619 3.82 0.00 0.00 3.58
3300 3566 2.092699 TCATGGTCACAAGTGGTCACAA 60.093 45.455 3.82 0.00 0.00 3.33
3301 3567 2.036958 TGGTCACAAGTGGTCACAAG 57.963 50.000 3.82 0.00 0.00 3.16
3302 3568 1.308998 GGTCACAAGTGGTCACAAGG 58.691 55.000 3.82 0.00 0.00 3.61
3303 3569 1.408266 GGTCACAAGTGGTCACAAGGT 60.408 52.381 3.82 0.00 0.00 3.50
3304 3570 2.158871 GGTCACAAGTGGTCACAAGGTA 60.159 50.000 3.82 0.00 0.00 3.08
4361 4697 8.020819 TGCATGTTTACTTAAAGAAGTGCATAC 58.979 33.333 0.00 0.05 45.74 2.39
4568 4985 4.150897 AGGACTACAAAACTGCAGTTGA 57.849 40.909 31.73 16.37 38.44 3.18
4639 5056 0.249398 AATACACCCTGGCGACTCAC 59.751 55.000 0.00 0.00 0.00 3.51
4819 5239 3.321682 TCCTTGTGCTCCTTTTTGAATGG 59.678 43.478 0.00 0.00 0.00 3.16
5115 5536 5.529060 AGAAGATAAATTCAGAATGCGGGTC 59.471 40.000 0.00 0.00 34.76 4.46
5122 5543 0.742281 CAGAATGCGGGTCCACTGAG 60.742 60.000 0.00 0.00 0.00 3.35
5327 5748 4.740334 GCTGCAGAGGGAAGAATCTCTTAG 60.740 50.000 20.43 0.00 36.16 2.18
5569 5990 6.430000 TGCTAAGGATAAACAAAGAAGGACAC 59.570 38.462 0.00 0.00 0.00 3.67
5624 6045 2.779430 TGTTCTGGTCATATGGATGGCT 59.221 45.455 2.13 0.00 37.83 4.75
5878 6299 9.898152 TTTTTGTTTCATTTTGGAGAGGTAAAT 57.102 25.926 0.00 0.00 0.00 1.40
5930 6351 5.715439 TGGGTCTGGAATTGTCTATTCAT 57.285 39.130 8.88 0.00 43.72 2.57
6376 6804 1.477553 CCCACCATAACATGCAGCTT 58.522 50.000 0.00 0.00 0.00 3.74
6535 6968 3.297134 TGAAGGCTCCACAGTTTTTCT 57.703 42.857 0.00 0.00 0.00 2.52
6553 6986 9.967346 AGTTTTTCTTCTTTGCTTATTAGGTTC 57.033 29.630 0.00 0.00 0.00 3.62
6655 7088 8.836268 TTACAGGTAAATACGAAACTGAATGT 57.164 30.769 0.00 0.00 0.00 2.71
6750 7183 3.513515 ACACTTGAAAGCAAAGGTTTGGA 59.486 39.130 4.67 0.00 38.57 3.53
6757 7190 5.411053 TGAAAGCAAAGGTTTGGAAACTTTG 59.589 36.000 21.02 21.02 38.09 2.77
6814 7247 3.305403 GGAAGTAAGGCTTTTCACTTGCC 60.305 47.826 16.43 13.25 46.42 4.52
6941 7374 4.833478 AGATACATGGAAGTTGCAGTCT 57.167 40.909 2.75 1.47 0.00 3.24
7018 7451 7.878644 TGAAAATTCCAATTGATGATTTCTGCA 59.121 29.630 7.12 6.97 0.00 4.41
7321 7756 6.526325 TGACAACTTGAAAATTTTCAGTGACG 59.474 34.615 29.20 21.74 46.68 4.35
7357 7794 9.103048 GTCATTCGTTAATCTAGTTTTGTTGTG 57.897 33.333 0.00 0.00 0.00 3.33
7369 7806 1.110442 TTGTTGTGCAAGGGTGAAGG 58.890 50.000 0.00 0.00 32.52 3.46
7370 7807 0.754957 TGTTGTGCAAGGGTGAAGGG 60.755 55.000 0.00 0.00 0.00 3.95
7445 7882 1.734465 GGAGGTCTGTCAAAGCAATCG 59.266 52.381 0.00 0.00 0.00 3.34
7558 7995 5.329399 ACAGAGGACAACAAGATCTCTAGT 58.671 41.667 0.00 0.00 33.95 2.57
7559 7996 6.486056 ACAGAGGACAACAAGATCTCTAGTA 58.514 40.000 0.00 0.00 33.95 1.82
7560 7997 6.948886 ACAGAGGACAACAAGATCTCTAGTAA 59.051 38.462 0.00 0.00 33.95 2.24
7561 7998 7.094118 ACAGAGGACAACAAGATCTCTAGTAAC 60.094 40.741 0.00 0.00 33.95 2.50
7637 8074 3.764434 TGTGCTTTTGTTTCAGGTGGTAA 59.236 39.130 0.00 0.00 0.00 2.85
7739 8179 9.690913 TCATCAAGAATCAAGATAATGACCTTT 57.309 29.630 0.00 0.00 30.82 3.11
7740 8180 9.947669 CATCAAGAATCAAGATAATGACCTTTC 57.052 33.333 0.00 0.00 30.82 2.62
7746 8186 8.430801 AATCAAGATAATGACCTTTCTTCTCG 57.569 34.615 0.00 0.00 30.82 4.04
7793 8234 5.559035 CGAAACATGTCTTCAACTTCACTCC 60.559 44.000 0.00 0.00 0.00 3.85
7796 8237 0.784778 GTCTTCAACTTCACTCCGCG 59.215 55.000 0.00 0.00 0.00 6.46
7800 8241 2.049433 AACTTCACTCCGCGACCG 60.049 61.111 8.23 0.00 0.00 4.79
7805 8246 4.111016 CACTCCGCGACCGCACTA 62.111 66.667 8.23 0.00 42.06 2.74
7844 8285 4.000331 ACATGTATGCAGGCTAGATGAC 58.000 45.455 9.28 0.00 0.00 3.06
8190 8631 2.832672 GCAAAGGCTCGAATAGTTGG 57.167 50.000 0.00 0.00 36.96 3.77
8228 8669 3.006967 ACTGAAGATCGGGGTATGTATGC 59.993 47.826 0.00 0.00 0.00 3.14
8265 8706 7.715249 ACATAGTTGTGGTGTACATTATGATCC 59.285 37.037 0.00 0.00 38.34 3.36
8274 8715 6.347725 GGTGTACATTATGATCCGCTTCATTC 60.348 42.308 0.00 0.00 37.51 2.67
8295 8736 2.558795 CTCTCCTCGAAGACTTGTTGGA 59.441 50.000 0.00 0.00 0.00 3.53
8352 8793 2.941064 CACTGCACATATGTTGGGAGAG 59.059 50.000 17.88 8.98 0.00 3.20
8364 8805 0.543410 TGGGAGAGGAGCCGTTTACA 60.543 55.000 0.00 0.00 0.00 2.41
8414 8855 7.544566 AGTGAAATTGACCATACTTGTAGTACG 59.455 37.037 0.00 0.00 32.84 3.67
8415 8856 7.330208 GTGAAATTGACCATACTTGTAGTACGT 59.670 37.037 0.00 0.00 32.84 3.57
8416 8857 8.522003 TGAAATTGACCATACTTGTAGTACGTA 58.478 33.333 0.00 0.00 32.84 3.57
8417 8858 8.693542 AAATTGACCATACTTGTAGTACGTAC 57.306 34.615 18.10 18.10 32.84 3.67
8419 8860 6.668541 TGACCATACTTGTAGTACGTACTC 57.331 41.667 30.53 21.12 37.73 2.59
8420 8861 5.291858 TGACCATACTTGTAGTACGTACTCG 59.708 44.000 30.53 18.88 43.34 4.18
8455 10211 2.777692 TCCAGTGAAAAGTCAACCTCCT 59.222 45.455 0.00 0.00 34.87 3.69
8456 10212 2.880890 CCAGTGAAAAGTCAACCTCCTG 59.119 50.000 0.00 0.00 34.87 3.86
8725 10649 2.168496 TCGTCTCCTCAGTTTACTGGG 58.832 52.381 9.82 6.42 44.00 4.45
8744 10668 1.377536 GGCTTCATCCTGAGTTGAGC 58.622 55.000 0.00 0.00 0.00 4.26
8839 10763 6.066032 GCTCAAATCTCTCTACCCTACTACT 58.934 44.000 0.00 0.00 0.00 2.57
8841 10765 7.255346 GCTCAAATCTCTCTACCCTACTACTTC 60.255 44.444 0.00 0.00 0.00 3.01
8843 10767 9.000978 TCAAATCTCTCTACCCTACTACTTCTA 57.999 37.037 0.00 0.00 0.00 2.10
8845 10769 8.571460 AATCTCTCTACCCTACTACTTCTAGT 57.429 38.462 0.00 0.00 37.04 2.57
8846 10770 7.993349 TCTCTCTACCCTACTACTTCTAGTT 57.007 40.000 0.00 0.00 34.79 2.24
8848 10772 8.923270 TCTCTCTACCCTACTACTTCTAGTTAC 58.077 40.741 0.00 0.00 34.79 2.50
8849 10773 8.852671 TCTCTACCCTACTACTTCTAGTTACT 57.147 38.462 0.00 0.00 34.79 2.24
8850 10774 9.278011 TCTCTACCCTACTACTTCTAGTTACTT 57.722 37.037 0.00 0.00 34.79 2.24
8851 10775 9.904198 CTCTACCCTACTACTTCTAGTTACTTT 57.096 37.037 0.00 0.00 34.79 2.66
8888 10812 4.286707 ACACAGGCAGGAGTACATACATA 58.713 43.478 0.00 0.00 0.00 2.29
8889 10813 4.099573 ACACAGGCAGGAGTACATACATAC 59.900 45.833 0.00 0.00 0.00 2.39
8891 10815 4.714802 ACAGGCAGGAGTACATACATACAA 59.285 41.667 0.00 0.00 0.00 2.41
8892 10816 5.163405 ACAGGCAGGAGTACATACATACAAG 60.163 44.000 0.00 0.00 0.00 3.16
8893 10817 5.069119 CAGGCAGGAGTACATACATACAAGA 59.931 44.000 0.00 0.00 0.00 3.02
8898 10838 8.141909 GCAGGAGTACATACATACAAGATACAA 58.858 37.037 0.00 0.00 0.00 2.41
8978 10930 4.617762 GGAGTACCAGCAAGTGTACTACAC 60.618 50.000 10.90 10.90 45.69 2.90
9018 11001 5.067273 CGAAGGTCATCTGATCTACTAGGT 58.933 45.833 0.00 0.00 33.65 3.08
9024 11020 3.885976 TCTGATCTACTAGGTGGGAGG 57.114 52.381 0.00 0.00 0.00 4.30
9082 11089 0.473694 TCAGCCTCCAAGACAAGGGA 60.474 55.000 0.00 0.00 32.98 4.20
9083 11090 0.401738 CAGCCTCCAAGACAAGGGAA 59.598 55.000 0.00 0.00 32.98 3.97
9084 11091 0.695347 AGCCTCCAAGACAAGGGAAG 59.305 55.000 0.00 0.00 32.98 3.46
9085 11092 0.322906 GCCTCCAAGACAAGGGAAGG 60.323 60.000 0.00 0.00 32.98 3.46
9185 11192 6.293900 CCTTGCCCATAATTTTTGTTCAAACC 60.294 38.462 0.00 0.00 0.00 3.27
9231 11241 3.632645 CCCTCTATTAACTCACTCCCCCA 60.633 52.174 0.00 0.00 0.00 4.96
9261 11271 4.717629 TTGCGACCGTCGGAGCAG 62.718 66.667 27.66 14.39 42.14 4.24
9294 11304 2.413371 GCTCGACCAGCTTGTTGAATTC 60.413 50.000 9.08 0.00 45.83 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.744795 ATGTTACCAGGTTGTTTTGCAA 57.255 36.364 0.00 0.00 34.16 4.08
48 49 2.552599 TCCGTTGCTCAATGTTACCA 57.447 45.000 1.71 0.00 0.00 3.25
69 70 1.835267 GGGTTTCGGGGGTTTTGCT 60.835 57.895 0.00 0.00 0.00 3.91
72 73 0.250858 CTACGGGTTTCGGGGGTTTT 60.251 55.000 0.00 0.00 44.45 2.43
80 81 0.389948 AGAGCTTGCTACGGGTTTCG 60.390 55.000 0.00 0.00 45.88 3.46
88 89 4.929808 TGCTTGTAAGTAAGAGCTTGCTAC 59.070 41.667 1.28 2.42 34.44 3.58
114 115 0.455295 CTTCGACGAGCACAGTCTCC 60.455 60.000 0.00 0.00 36.53 3.71
119 120 1.153939 CCCTCTTCGACGAGCACAG 60.154 63.158 13.21 0.16 0.00 3.66
127 128 0.526524 CATCTGCGACCCTCTTCGAC 60.527 60.000 0.00 0.00 41.78 4.20
131 132 1.333636 CCTCCATCTGCGACCCTCTT 61.334 60.000 0.00 0.00 0.00 2.85
138 139 1.305297 ACACCTCCTCCATCTGCGA 60.305 57.895 0.00 0.00 0.00 5.10
144 145 1.765314 GCATACTCACACCTCCTCCAT 59.235 52.381 0.00 0.00 0.00 3.41
150 151 1.555075 TCCCTTGCATACTCACACCTC 59.445 52.381 0.00 0.00 0.00 3.85
166 167 2.037527 GACTCCTCCACCGTCCCT 59.962 66.667 0.00 0.00 0.00 4.20
170 171 1.056660 AACATTGACTCCTCCACCGT 58.943 50.000 0.00 0.00 0.00 4.83
185 186 1.475280 CAATAGCAGCACCAGCAACAT 59.525 47.619 0.00 0.00 45.49 2.71
193 194 1.825622 GAGCCCCAATAGCAGCACC 60.826 63.158 0.00 0.00 0.00 5.01
200 201 1.097547 CCTTGCACGAGCCCCAATAG 61.098 60.000 1.39 0.00 41.13 1.73
209 210 2.512515 GCCCTAGCCTTGCACGAG 60.513 66.667 0.00 0.00 0.00 4.18
215 216 4.512914 GCCCCAGCCCTAGCCTTG 62.513 72.222 0.00 0.00 41.25 3.61
217 218 4.767892 AAGCCCCAGCCCTAGCCT 62.768 66.667 0.00 0.00 41.25 4.58
228 229 2.032681 AGCACAAGTCGAAGCCCC 59.967 61.111 0.00 0.00 0.00 5.80
245 246 1.679311 GCCACTCTCACCATCACCA 59.321 57.895 0.00 0.00 0.00 4.17
253 254 1.662438 CTCTCCTCCGCCACTCTCAC 61.662 65.000 0.00 0.00 0.00 3.51
254 255 1.379176 CTCTCCTCCGCCACTCTCA 60.379 63.158 0.00 0.00 0.00 3.27
258 259 2.284258 AAGCTCTCCTCCGCCACT 60.284 61.111 0.00 0.00 0.00 4.00
262 263 2.125350 CACCAAGCTCTCCTCCGC 60.125 66.667 0.00 0.00 0.00 5.54
327 328 2.042843 AGAACCCGAGGAGGCGAT 60.043 61.111 0.00 0.00 39.21 4.58
336 337 1.393487 TTGTCGTCACCAGAACCCGA 61.393 55.000 0.00 0.00 0.00 5.14
341 342 1.414550 TGATGGTTGTCGTCACCAGAA 59.585 47.619 8.66 0.00 36.54 3.02
352 353 0.110486 GTGGAGTGGGTGATGGTTGT 59.890 55.000 0.00 0.00 0.00 3.32
367 368 1.068417 CGAGACAAACGTGGGTGGA 59.932 57.895 0.00 0.00 0.00 4.02
376 377 1.889891 CGAGAGAGAGCGAGACAAAC 58.110 55.000 0.00 0.00 0.00 2.93
385 386 2.278531 GCTTCGGCGAGAGAGAGC 60.279 66.667 13.90 13.90 0.00 4.09
387 388 2.701780 GGTGCTTCGGCGAGAGAGA 61.702 63.158 10.46 0.00 45.37 3.10
396 397 2.432628 GGTCGTCTGGTGCTTCGG 60.433 66.667 0.00 0.00 0.00 4.30
409 410 4.452733 GAGGGGTTGCGAGGGTCG 62.453 72.222 0.00 0.00 43.89 4.79
417 418 3.728373 ATCCGTGGGAGGGGTTGC 61.728 66.667 0.00 0.00 34.05 4.17
418 419 2.272146 CATCCGTGGGAGGGGTTG 59.728 66.667 0.00 0.00 34.05 3.77
432 434 3.200593 CTCAGCTGTGCGCCCATC 61.201 66.667 14.67 0.00 40.39 3.51
439 441 3.873883 GCGATGCCTCAGCTGTGC 61.874 66.667 14.67 17.66 40.80 4.57
471 473 2.124736 ATTGACCGCCCCATCACG 60.125 61.111 0.00 0.00 0.00 4.35
488 490 0.395724 TCTGCGGGCTAGAGTGATCA 60.396 55.000 0.00 0.00 0.00 2.92
514 516 2.465055 GAACAGGCTGGGGCTAACGT 62.465 60.000 20.34 0.00 36.44 3.99
516 518 1.378646 GGAACAGGCTGGGGCTAAC 60.379 63.158 20.34 1.81 36.44 2.34
517 519 2.612493 GGGAACAGGCTGGGGCTAA 61.612 63.158 20.34 0.00 36.44 3.09
518 520 3.015145 GGGAACAGGCTGGGGCTA 61.015 66.667 20.34 0.00 36.44 3.93
528 530 4.410400 GGAGGCACGGGGGAACAG 62.410 72.222 0.00 0.00 0.00 3.16
560 562 3.532155 CGAAGCCTCCTCCCCTCG 61.532 72.222 0.00 0.00 0.00 4.63
597 599 1.588082 CAATGAAGGGTGGCACTGC 59.412 57.895 18.45 0.93 0.00 4.40
601 603 1.243342 CGAAGCAATGAAGGGTGGCA 61.243 55.000 0.00 0.00 0.00 4.92
655 658 3.564571 CCTCACCAGAGAACTAGAAGGGA 60.565 52.174 0.00 0.00 44.98 4.20
672 675 1.079750 GGCAACGAGAGGACCTCAC 60.080 63.158 23.60 16.19 42.06 3.51
683 686 2.350895 CAGGGGATGTGGCAACGA 59.649 61.111 0.00 0.00 42.51 3.85
687 690 1.380246 GAATGCAGGGGATGTGGCA 60.380 57.895 0.00 0.00 41.00 4.92
717 720 2.663196 CTCACCCACCGAGGTTCC 59.337 66.667 0.00 0.00 38.39 3.62
718 721 2.663196 CCTCACCCACCGAGGTTC 59.337 66.667 0.00 0.00 44.35 3.62
746 810 2.602217 GCACAATGCGAACGACTTTCTT 60.602 45.455 0.00 0.00 31.71 2.52
748 812 1.318251 GCACAATGCGAACGACTTTC 58.682 50.000 0.00 0.00 31.71 2.62
761 828 2.519302 GCCCCCTATGCGCACAAT 60.519 61.111 14.90 0.00 0.00 2.71
799 866 1.196766 AGCACAGATCCTGAGCCACA 61.197 55.000 11.64 0.00 46.32 4.17
801 868 0.035725 CAAGCACAGATCCTGAGCCA 60.036 55.000 11.64 0.00 46.32 4.75
804 871 0.035725 TGGCAAGCACAGATCCTGAG 60.036 55.000 0.45 0.00 35.18 3.35
808 876 1.022735 CAGATGGCAAGCACAGATCC 58.977 55.000 0.00 0.00 0.00 3.36
826 894 2.829043 AAATGCGTCGCTAGCCGTCA 62.829 55.000 19.50 10.40 38.35 4.35
901 972 2.223947 GCTTCCCAAAACGAATGGTGTT 60.224 45.455 0.00 0.00 36.14 3.32
902 973 1.339929 GCTTCCCAAAACGAATGGTGT 59.660 47.619 0.00 0.00 36.14 4.16
903 974 1.665735 CGCTTCCCAAAACGAATGGTG 60.666 52.381 0.00 0.00 36.14 4.17
904 975 0.596082 CGCTTCCCAAAACGAATGGT 59.404 50.000 0.00 0.00 36.14 3.55
905 976 0.596082 ACGCTTCCCAAAACGAATGG 59.404 50.000 0.00 0.00 37.71 3.16
1151 1222 4.150454 CCCTCCGCCTCCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
1383 1454 7.252865 GCAAACACGACAATAAATAATCACGAC 60.253 37.037 0.00 0.00 0.00 4.34
1565 1636 1.079405 GCTTGATTGGGACCGTCGA 60.079 57.895 0.00 0.00 0.00 4.20
1796 1868 0.304705 GGCACATTGGCGTAATCGAG 59.695 55.000 0.00 0.00 39.71 4.04
1814 1886 2.831333 CTACTACATGGCAGAAGCTGG 58.169 52.381 0.00 0.00 41.70 4.85
1818 1890 5.011090 TGTAAGCTACTACATGGCAGAAG 57.989 43.478 0.00 0.00 37.23 2.85
1828 1900 7.067981 ACTGTACTAACCCATGTAAGCTACTAC 59.932 40.741 0.00 0.00 0.00 2.73
1829 1901 7.121382 ACTGTACTAACCCATGTAAGCTACTA 58.879 38.462 0.00 0.00 0.00 1.82
1830 1902 5.956563 ACTGTACTAACCCATGTAAGCTACT 59.043 40.000 0.00 0.00 0.00 2.57
1882 1954 5.583854 AGTTGGAACTTCATGAATCTGATCG 59.416 40.000 8.96 0.00 35.21 3.69
1957 2029 9.865321 TGTATAACAAGTAACTAGTCATCCAAC 57.135 33.333 0.00 0.00 0.00 3.77
2008 2080 3.122480 TCCAGATTATCCTTCAAGCCCA 58.878 45.455 0.00 0.00 0.00 5.36
2068 2140 3.067106 CCGTTAAGACACATTCTGCAGT 58.933 45.455 14.67 0.00 33.46 4.40
2150 2222 6.620733 GCACCAATACTTCATCACTGTAACAC 60.621 42.308 0.00 0.00 0.00 3.32
2526 2605 6.839657 TCCCCAAACAAATTAGTTAACCTTGA 59.160 34.615 0.88 0.00 0.00 3.02
2763 2842 2.706890 AGCAACATAAGTACAACGGGG 58.293 47.619 0.00 0.00 0.00 5.73
2840 2919 5.215160 CACACACACTAAAAAGAATCAGCC 58.785 41.667 0.00 0.00 0.00 4.85
3109 3190 2.959507 AACCAAAGAACAAGCACACC 57.040 45.000 0.00 0.00 0.00 4.16
3113 3194 8.911918 TTAGTATAGAAACCAAAGAACAAGCA 57.088 30.769 0.00 0.00 0.00 3.91
3160 3241 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
3187 3268 3.365265 GGTTGGACCCAGCGCAAG 61.365 66.667 11.47 0.38 33.53 4.01
3188 3269 4.196778 TGGTTGGACCCAGCGCAA 62.197 61.111 11.47 0.00 37.50 4.85
3189 3270 4.947147 GTGGTTGGACCCAGCGCA 62.947 66.667 11.47 0.00 37.50 6.09
3192 3273 2.041153 CAAAGTGGTTGGACCCAGC 58.959 57.895 0.00 0.00 37.50 4.85
3201 3467 4.320870 CGTACAATAGACCCAAAGTGGTT 58.679 43.478 0.00 0.00 39.24 3.67
3227 3493 5.243730 CCTCTTGCAGAAATGTAGGGAAAAA 59.756 40.000 0.00 0.00 0.00 1.94
3228 3494 4.766891 CCTCTTGCAGAAATGTAGGGAAAA 59.233 41.667 0.00 0.00 0.00 2.29
3258 3524 0.391597 GTCACGGGTTCAAGTCCTGA 59.608 55.000 0.00 0.00 35.49 3.86
3292 3558 0.764890 AAGCTGCTACCTTGTGACCA 59.235 50.000 0.90 0.00 0.00 4.02
3293 3559 1.897560 AAAGCTGCTACCTTGTGACC 58.102 50.000 0.90 0.00 0.00 4.02
3294 3560 2.742589 GGTAAAGCTGCTACCTTGTGAC 59.257 50.000 13.20 0.00 36.62 3.67
3295 3561 2.370519 TGGTAAAGCTGCTACCTTGTGA 59.629 45.455 19.42 0.00 39.73 3.58
3296 3562 2.484264 GTGGTAAAGCTGCTACCTTGTG 59.516 50.000 19.42 0.00 39.73 3.33
3297 3563 2.372172 AGTGGTAAAGCTGCTACCTTGT 59.628 45.455 19.42 4.68 39.73 3.16
3298 3564 2.744202 CAGTGGTAAAGCTGCTACCTTG 59.256 50.000 19.42 14.39 39.73 3.61
3299 3565 3.059352 CAGTGGTAAAGCTGCTACCTT 57.941 47.619 19.42 6.71 39.73 3.50
3300 3566 2.770164 CAGTGGTAAAGCTGCTACCT 57.230 50.000 19.42 4.02 39.73 3.08
3331 3597 9.231297 TCTCATAAACTGTTTTCAATAGAAGGG 57.769 33.333 11.48 0.00 34.71 3.95
3388 3654 4.517285 ACTCGTAATCACTGCATCCAATT 58.483 39.130 0.00 0.00 0.00 2.32
3392 3658 2.120232 CGACTCGTAATCACTGCATCC 58.880 52.381 0.00 0.00 0.00 3.51
3393 3659 3.066369 TCGACTCGTAATCACTGCATC 57.934 47.619 0.00 0.00 0.00 3.91
3394 3660 3.179830 GTTCGACTCGTAATCACTGCAT 58.820 45.455 0.00 0.00 0.00 3.96
3395 3661 2.592194 GTTCGACTCGTAATCACTGCA 58.408 47.619 0.00 0.00 0.00 4.41
4361 4697 6.603237 TCGGAATATATGCACAAAAGACTG 57.397 37.500 0.00 0.00 0.00 3.51
4553 4970 3.290710 ACCTCATCAACTGCAGTTTTGT 58.709 40.909 29.23 14.94 35.83 2.83
4568 4985 2.363680 CTGGAGCATAGACGAACCTCAT 59.636 50.000 0.00 0.00 0.00 2.90
4639 5056 4.904241 ACCTTCTGAAAATGAGTCTCCAG 58.096 43.478 0.00 0.00 0.00 3.86
4744 5164 9.899226 AAAAAGCTCAAATATTCTACTGTGTTC 57.101 29.630 0.00 0.00 0.00 3.18
4819 5239 6.316140 TGAATATTGAGACACTAACCATGTGC 59.684 38.462 0.00 0.00 38.86 4.57
5115 5536 8.579863 AGATTTTTCCAAATAACTTCTCAGTGG 58.420 33.333 0.00 0.00 32.35 4.00
5327 5748 9.356929 CTTCATTTGTTTTCGTAATTTTGAAGC 57.643 29.630 0.00 0.00 32.68 3.86
5540 5961 7.607991 TCCTTCTTTGTTTATCCTTAGCAAGAG 59.392 37.037 0.00 0.00 0.00 2.85
5569 5990 7.550551 TGAAGACAAATATTAGAGCTTGTGAGG 59.449 37.037 0.00 0.00 32.31 3.86
5649 6070 8.617290 TCTCACCTTCTAATTCCTTTTACAAC 57.383 34.615 0.00 0.00 0.00 3.32
5878 6299 6.000246 TCTGCCAGGTGAATTACATATTCA 58.000 37.500 0.00 0.00 35.86 2.57
5930 6351 3.411446 CTTCTGGTGCAATAGGTCAACA 58.589 45.455 0.00 0.00 0.00 3.33
6289 6717 9.559732 CATGTTGAGATAAATATGTTAGTGGGA 57.440 33.333 0.00 0.00 0.00 4.37
6535 6968 9.216117 GTAAGAGTGAACCTAATAAGCAAAGAA 57.784 33.333 0.00 0.00 0.00 2.52
6553 6986 4.461081 AGCCTCTACAGAACAGTAAGAGTG 59.539 45.833 0.00 0.00 0.00 3.51
7208 7641 7.149569 ACCAGTTGAGACACAATATGAAATG 57.850 36.000 0.00 0.00 40.76 2.32
7321 7756 9.408069 CTAGATTAACGAATGACAACTATACCC 57.592 37.037 0.00 0.00 0.00 3.69
7357 7794 1.303643 CAGGTCCCTTCACCCTTGC 60.304 63.158 0.00 0.00 37.09 4.01
7369 7806 5.582689 AATAGCATAAGCAAAACAGGTCC 57.417 39.130 0.00 0.00 45.49 4.46
7370 7807 7.321745 ACTAATAGCATAAGCAAAACAGGTC 57.678 36.000 0.00 0.00 45.49 3.85
7445 7882 3.442100 CTCGAGGTATTTACGTGGGTTC 58.558 50.000 3.91 0.00 0.00 3.62
7499 7936 5.030147 TCTCAGGAAGCAGGGTAAAGAATA 58.970 41.667 0.00 0.00 0.00 1.75
7558 7995 5.011635 TGTTCTGGATGTCAGCTGTAAGTTA 59.988 40.000 14.67 0.00 43.06 2.24
7559 7996 4.202357 TGTTCTGGATGTCAGCTGTAAGTT 60.202 41.667 14.67 0.00 43.06 2.66
7560 7997 3.324846 TGTTCTGGATGTCAGCTGTAAGT 59.675 43.478 14.67 0.00 43.06 2.24
7561 7998 3.930336 TGTTCTGGATGTCAGCTGTAAG 58.070 45.455 14.67 3.94 43.06 2.34
7678 8115 3.751175 TGGTTTTACGCTCTGGATTTGAG 59.249 43.478 0.00 0.00 34.87 3.02
7770 8210 5.559035 CGGAGTGAAGTTGAAGACATGTTTC 60.559 44.000 0.00 6.80 0.00 2.78
7844 8285 4.797275 GCAAACAGATTTTTCACCTCAGGG 60.797 45.833 0.00 0.00 38.88 4.45
7991 8432 4.114997 GAATGGGTTGGCGTGCCG 62.115 66.667 6.37 0.00 39.42 5.69
7992 8433 2.490993 CTTGAATGGGTTGGCGTGCC 62.491 60.000 3.30 3.30 0.00 5.01
7993 8434 1.080569 CTTGAATGGGTTGGCGTGC 60.081 57.895 0.00 0.00 0.00 5.34
8126 8567 4.397417 CCTTCAAGATCATCAAACTCCCAC 59.603 45.833 0.00 0.00 0.00 4.61
8190 8631 6.968131 TCTTCAGTGCTAATGATTGTACAC 57.032 37.500 0.00 0.00 0.00 2.90
8249 8690 4.377021 TGAAGCGGATCATAATGTACACC 58.623 43.478 0.00 0.00 0.00 4.16
8265 8706 2.098280 TCTTCGAGGAGAGAATGAAGCG 59.902 50.000 0.00 0.00 36.77 4.68
8274 8715 2.558795 TCCAACAAGTCTTCGAGGAGAG 59.441 50.000 0.00 0.00 0.00 3.20
8295 8736 0.745845 GCGACCTTCACAGGATGCAT 60.746 55.000 0.00 0.00 44.19 3.96
8352 8793 3.907894 TCAAACATTGTAAACGGCTCC 57.092 42.857 0.00 0.00 0.00 4.70
8364 8805 3.084039 AGATGTGGACGCATCAAACATT 58.916 40.909 23.17 3.56 45.58 2.71
8414 8855 3.001736 GGAGATGTACCACGTACGAGTAC 59.998 52.174 29.50 29.50 41.41 2.73
8415 8856 3.198068 GGAGATGTACCACGTACGAGTA 58.802 50.000 24.41 19.01 41.41 2.59
8416 8857 2.012673 GGAGATGTACCACGTACGAGT 58.987 52.381 24.41 20.05 41.41 4.18
8417 8858 2.011947 TGGAGATGTACCACGTACGAG 58.988 52.381 24.41 14.76 41.41 4.18
8419 8860 1.741706 ACTGGAGATGTACCACGTACG 59.258 52.381 15.01 15.01 41.41 3.67
8420 8861 2.751259 TCACTGGAGATGTACCACGTAC 59.249 50.000 0.00 0.00 39.24 3.67
8422 8863 1.919240 TCACTGGAGATGTACCACGT 58.081 50.000 0.00 0.00 33.57 4.49
8423 8864 3.313012 TTTCACTGGAGATGTACCACG 57.687 47.619 0.00 0.00 33.57 4.94
8424 8865 4.642429 ACTTTTCACTGGAGATGTACCAC 58.358 43.478 0.00 0.00 33.57 4.16
8425 8866 4.346709 TGACTTTTCACTGGAGATGTACCA 59.653 41.667 0.00 0.00 35.96 3.25
8426 8867 4.894784 TGACTTTTCACTGGAGATGTACC 58.105 43.478 0.00 0.00 0.00 3.34
8455 10211 0.669318 CGCAGACGGGTAAAAGAGCA 60.669 55.000 0.00 0.00 34.97 4.26
8456 10212 0.669625 ACGCAGACGGGTAAAAGAGC 60.670 55.000 0.00 0.00 46.04 4.09
8649 10411 4.872691 AGAAAAAGAGCACGTATGGATCAG 59.127 41.667 0.00 0.00 0.00 2.90
8690 10452 8.473358 TGAGGAGACGAATTATTACCTATGAA 57.527 34.615 0.00 0.00 0.00 2.57
8693 10455 8.480133 AACTGAGGAGACGAATTATTACCTAT 57.520 34.615 0.00 0.00 0.00 2.57
8744 10668 3.244105 CGCAAACGGTGTCAGGAG 58.756 61.111 0.00 0.00 34.97 3.69
8776 10700 4.843220 ATGCATGAATAAAGCTACCAGC 57.157 40.909 0.00 0.00 42.84 4.85
8848 10772 8.136800 TGCCTGTGTATTATTGCATGAATAAAG 58.863 33.333 0.00 0.00 39.46 1.85
8849 10773 8.005192 TGCCTGTGTATTATTGCATGAATAAA 57.995 30.769 0.00 0.00 39.46 1.40
8850 10774 7.255555 CCTGCCTGTGTATTATTGCATGAATAA 60.256 37.037 0.00 4.96 40.15 1.40
8851 10775 6.207221 CCTGCCTGTGTATTATTGCATGAATA 59.793 38.462 0.00 0.00 0.00 1.75
8852 10776 5.010314 CCTGCCTGTGTATTATTGCATGAAT 59.990 40.000 0.00 0.00 0.00 2.57
8853 10777 4.338964 CCTGCCTGTGTATTATTGCATGAA 59.661 41.667 0.00 0.00 0.00 2.57
8854 10778 3.884693 CCTGCCTGTGTATTATTGCATGA 59.115 43.478 0.00 0.00 0.00 3.07
8855 10779 3.884693 TCCTGCCTGTGTATTATTGCATG 59.115 43.478 0.00 0.00 0.00 4.06
8856 10780 4.139786 CTCCTGCCTGTGTATTATTGCAT 58.860 43.478 0.00 0.00 0.00 3.96
8857 10781 3.054434 ACTCCTGCCTGTGTATTATTGCA 60.054 43.478 0.00 0.00 0.00 4.08
8858 10782 3.545703 ACTCCTGCCTGTGTATTATTGC 58.454 45.455 0.00 0.00 0.00 3.56
8859 10783 5.670485 TGTACTCCTGCCTGTGTATTATTG 58.330 41.667 0.00 0.00 0.00 1.90
8860 10784 5.950544 TGTACTCCTGCCTGTGTATTATT 57.049 39.130 0.00 0.00 0.00 1.40
8861 10785 6.553476 TGTATGTACTCCTGCCTGTGTATTAT 59.447 38.462 0.00 0.00 0.00 1.28
8862 10786 5.894964 TGTATGTACTCCTGCCTGTGTATTA 59.105 40.000 0.00 0.00 0.00 0.98
8863 10787 4.714802 TGTATGTACTCCTGCCTGTGTATT 59.285 41.667 0.00 0.00 0.00 1.89
8888 10812 7.931948 AGCAAACAGTAACTAGTTGTATCTTGT 59.068 33.333 18.56 9.74 0.00 3.16
8889 10813 8.311650 AGCAAACAGTAACTAGTTGTATCTTG 57.688 34.615 18.56 15.21 0.00 3.02
8891 10815 7.815068 CAGAGCAAACAGTAACTAGTTGTATCT 59.185 37.037 18.56 8.21 0.00 1.98
8892 10816 7.599245 ACAGAGCAAACAGTAACTAGTTGTATC 59.401 37.037 18.56 6.17 0.00 2.24
8893 10817 7.385205 CACAGAGCAAACAGTAACTAGTTGTAT 59.615 37.037 18.56 0.89 0.00 2.29
8898 10838 5.050490 CACACAGAGCAAACAGTAACTAGT 58.950 41.667 0.00 0.00 0.00 2.57
8978 10930 3.746492 CCTTCGTTCCTAGTTGTTGAAGG 59.254 47.826 11.32 11.32 43.35 3.46
8991 10974 3.810310 AGATCAGATGACCTTCGTTCC 57.190 47.619 0.00 0.00 0.00 3.62
9018 11001 1.461268 TTGTGCTCACTCCCTCCCA 60.461 57.895 1.47 0.00 0.00 4.37
9276 11286 2.350772 GGTGAATTCAACAAGCTGGTCG 60.351 50.000 18.74 0.00 32.77 4.79
9496 11512 4.043200 GCGCCACCTTGTCCTTGC 62.043 66.667 0.00 0.00 0.00 4.01
9497 11513 3.365265 GGCGCCACCTTGTCCTTG 61.365 66.667 24.80 0.00 34.51 3.61


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

AutoCloner maintained by Alex Coulton.