Multiple sequence alignment - TraesCS2B01G610200

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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 TraesCS2B01G610200 chr2B 100.000 7678 0 0 1 7678 789875925 789868248 0.000000e+00 14179.0
1 TraesCS2B01G610200 chr2B 85.351 1611 161 28 5116 6688 789795350 789793777 0.000000e+00 1598.0
2 TraesCS2B01G610200 chr2B 86.145 729 74 14 3770 4492 789796533 789795826 0.000000e+00 761.0
3 TraesCS2B01G610200 chr2B 90.421 261 19 6 6765 7022 789793727 789793470 9.540000e-89 339.0
4 TraesCS2B01G610200 chr2B 88.755 249 21 6 4536 4779 789795820 789795574 1.620000e-76 298.0
5 TraesCS2B01G610200 chr2B 84.192 291 28 10 930 1218 789799668 789799394 4.570000e-67 267.0
6 TraesCS2B01G610200 chr2B 90.404 198 18 1 3308 3505 789797112 789796916 7.640000e-65 259.0
7 TraesCS2B01G610200 chr2B 92.453 159 12 0 1322 1480 789799403 789799245 2.160000e-55 228.0
8 TraesCS2B01G610200 chr2B 80.513 195 24 8 2005 2191 47107811 47107623 3.740000e-28 137.0
9 TraesCS2B01G610200 chr2B 100.000 31 0 0 3532 3562 789796866 789796836 2.990000e-04 58.4
10 TraesCS2B01G610200 chr2D 89.253 3201 153 66 399 3532 645705361 645708437 0.000000e+00 3829.0
11 TraesCS2B01G610200 chr2D 94.450 1856 86 13 5828 7678 645710971 645712814 0.000000e+00 2841.0
12 TraesCS2B01G610200 chr2D 94.858 1517 48 17 3558 5049 645708542 645710053 0.000000e+00 2342.0
13 TraesCS2B01G610200 chr2D 86.820 1654 155 30 5053 6668 645797942 645796314 0.000000e+00 1788.0
14 TraesCS2B01G610200 chr2D 94.375 800 38 6 5047 5842 645710131 645710927 0.000000e+00 1221.0
15 TraesCS2B01G610200 chr2D 83.395 813 77 39 2006 2781 645806124 645805333 0.000000e+00 701.0
16 TraesCS2B01G610200 chr2D 82.866 642 55 24 3871 4497 645804192 645803591 6.830000e-145 525.0
17 TraesCS2B01G610200 chr2D 82.451 359 58 4 2 360 645704368 645704721 7.480000e-80 309.0
18 TraesCS2B01G610200 chr2D 90.187 214 17 1 3562 3775 645804494 645804285 7.590000e-70 276.0
19 TraesCS2B01G610200 chr2D 82.143 308 33 10 5741 6028 645739119 645739424 2.140000e-60 244.0
20 TraesCS2B01G610200 chr2D 96.479 142 5 0 1322 1463 645806561 645806420 1.290000e-57 235.0
21 TraesCS2B01G610200 chr2D 82.414 290 26 9 930 1218 645806817 645806552 5.990000e-56 230.0
22 TraesCS2B01G610200 chr2D 87.425 167 18 2 3371 3534 645804762 645804596 1.020000e-43 189.0
23 TraesCS2B01G610200 chr2D 86.061 165 13 4 4567 4721 645803599 645803435 1.330000e-37 169.0
24 TraesCS2B01G610200 chr2D 78.926 242 34 7 5668 5894 645712820 645713059 1.730000e-31 148.0
25 TraesCS2B01G610200 chr2D 82.222 180 21 8 1973 2150 566786032 566785862 2.230000e-30 145.0
26 TraesCS2B01G610200 chr2D 92.647 68 4 1 7369 7435 645710752 645710819 6.340000e-16 97.1
27 TraesCS2B01G610200 chr2D 100.000 32 0 0 3532 3563 645708451 645708482 8.320000e-05 60.2
28 TraesCS2B01G610200 chr2A 89.793 3086 163 66 501 3532 771243203 771240216 0.000000e+00 3814.0
29 TraesCS2B01G610200 chr2A 91.820 2665 146 37 5047 7678 771458758 771461383 0.000000e+00 3648.0
30 TraesCS2B01G610200 chr2A 93.437 1859 97 19 5828 7678 771238136 771236295 0.000000e+00 2734.0
31 TraesCS2B01G610200 chr2A 93.529 1499 72 13 3558 5049 771457223 771458703 0.000000e+00 2207.0
32 TraesCS2B01G610200 chr2A 84.349 2019 212 47 5047 7022 771187683 771185726 0.000000e+00 1882.0
33 TraesCS2B01G610200 chr2A 94.803 1116 46 8 3558 4670 771240111 771239005 0.000000e+00 1729.0
34 TraesCS2B01G610200 chr2A 88.672 1386 96 32 2169 3517 771455775 771457136 0.000000e+00 1633.0
35 TraesCS2B01G610200 chr2A 93.009 801 47 8 5047 5842 771238976 771238180 0.000000e+00 1160.0
36 TraesCS2B01G610200 chr2A 88.661 926 72 13 5814 6725 771494236 771495142 0.000000e+00 1098.0
37 TraesCS2B01G610200 chr2A 87.551 972 60 13 3558 4497 771189657 771188715 0.000000e+00 1068.0
38 TraesCS2B01G610200 chr2A 89.041 730 67 6 5047 5764 771493506 771494234 0.000000e+00 893.0
39 TraesCS2B01G610200 chr2A 85.550 609 51 18 3770 4363 771491936 771492522 3.070000e-168 603.0
40 TraesCS2B01G610200 chr2A 80.595 840 93 39 1970 2756 771486755 771487577 1.110000e-162 584.0
41 TraesCS2B01G610200 chr2A 80.595 840 93 39 1970 2756 771488479 771489301 1.110000e-162 584.0
42 TraesCS2B01G610200 chr2A 81.864 590 62 30 2005 2568 771191319 771190749 9.080000e-124 455.0
43 TraesCS2B01G610200 chr2A 81.834 589 53 26 1104 1669 771454337 771454894 5.470000e-121 446.0
44 TraesCS2B01G610200 chr2A 85.976 328 35 9 1 323 771300626 771300305 2.650000e-89 340.0
45 TraesCS2B01G610200 chr2A 84.551 356 36 15 1329 1671 771191802 771191453 1.230000e-87 335.0
46 TraesCS2B01G610200 chr2A 96.447 197 7 0 3336 3532 771189958 771189762 7.430000e-85 326.0
47 TraesCS2B01G610200 chr2A 92.857 210 13 2 4571 4778 771188272 771188063 3.480000e-78 303.0
48 TraesCS2B01G610200 chr2A 89.024 246 19 6 4536 4777 771493176 771493417 1.620000e-76 298.0
49 TraesCS2B01G610200 chr2A 88.430 242 26 2 3293 3532 771490576 771490817 2.710000e-74 291.0
50 TraesCS2B01G610200 chr2A 87.678 211 26 0 3565 3775 771490905 771491115 5.950000e-61 246.0
51 TraesCS2B01G610200 chr2A 77.609 460 54 26 771 1218 771485997 771486419 4.630000e-57 233.0
52 TraesCS2B01G610200 chr2A 81.034 290 29 11 930 1218 771192064 771191800 2.810000e-49 207.0
53 TraesCS2B01G610200 chr2A 92.029 138 10 1 1322 1458 771486410 771486547 7.860000e-45 193.0
54 TraesCS2B01G610200 chr2A 83.838 198 28 1 2568 2765 771190784 771190591 1.320000e-42 185.0
55 TraesCS2B01G610200 chr2A 76.265 257 46 13 7430 7674 771236878 771236625 1.050000e-23 122.0
56 TraesCS2B01G610200 chr2A 82.550 149 17 7 7534 7674 771460906 771461053 1.050000e-23 122.0
57 TraesCS2B01G610200 chr2A 92.647 68 4 1 7369 7435 771238355 771238288 6.340000e-16 97.1
58 TraesCS2B01G610200 chr2A 92.424 66 4 1 7371 7435 771494141 771494206 8.200000e-15 93.5
59 TraesCS2B01G610200 chr2A 100.000 31 0 0 3532 3562 771189748 771189718 2.990000e-04 58.4
60 TraesCS2B01G610200 chr2A 100.000 31 0 0 3532 3562 771240202 771240172 2.990000e-04 58.4
61 TraesCS2B01G610200 chr2A 100.000 31 0 0 3532 3562 771490831 771490861 2.990000e-04 58.4
62 TraesCS2B01G610200 chr6B 89.098 266 23 4 4672 4933 630604738 630605001 7.430000e-85 326.0
63 TraesCS2B01G610200 chr6B 90.698 43 3 1 5367 5409 630604987 630605028 1.000000e-03 56.5
64 TraesCS2B01G610200 chr3D 82.609 230 22 10 1970 2191 112212224 112212005 3.660000e-43 187.0
65 TraesCS2B01G610200 chr3A 81.223 229 26 9 1970 2190 92078617 92078398 1.330000e-37 169.0
66 TraesCS2B01G610200 chr5D 80.513 195 24 7 2005 2191 392946346 392946534 3.740000e-28 137.0
67 TraesCS2B01G610200 chrUn 80.000 195 25 8 2005 2191 49199106 49198918 1.740000e-26 132.0
68 TraesCS2B01G610200 chr1A 86.735 98 13 0 1116 1213 19278170 19278073 8.150000e-20 110.0
69 TraesCS2B01G610200 chr1A 86.735 98 13 0 1116 1213 19392318 19392221 8.150000e-20 110.0
70 TraesCS2B01G610200 chr4B 78.453 181 27 5 2018 2191 544006625 544006450 2.930000e-19 108.0


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 TraesCS2B01G610200 chr2B 789868248 789875925 7677 True 14179.000000 14179 100.000000 1 7678 1 chr2B.!!$R2 7677
1 TraesCS2B01G610200 chr2B 789793470 789799668 6198 True 476.050000 1598 89.715125 930 7022 8 chr2B.!!$R3 6092
2 TraesCS2B01G610200 chr2D 645796314 645797942 1628 True 1788.000000 1788 86.820000 5053 6668 1 chr2D.!!$R2 1615
3 TraesCS2B01G610200 chr2D 645704368 645713059 8691 False 1355.912500 3829 90.870000 2 7678 8 chr2D.!!$F2 7676
4 TraesCS2B01G610200 chr2D 645803435 645806817 3382 True 332.142857 701 86.975286 930 4721 7 chr2D.!!$R3 3791
5 TraesCS2B01G610200 chr2A 771454337 771461383 7046 False 1611.200000 3648 87.681000 1104 7678 5 chr2A.!!$F1 6574
6 TraesCS2B01G610200 chr2A 771236295 771243203 6908 True 1387.785714 3814 91.422000 501 7678 7 chr2A.!!$R3 7177
7 TraesCS2B01G610200 chr2A 771185726 771192064 6338 True 535.488889 1882 88.054556 930 7022 9 chr2A.!!$R2 6092
8 TraesCS2B01G610200 chr2A 771485997 771495142 9145 False 431.241667 1098 87.636333 771 7435 12 chr2A.!!$F2 6664

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
368 369 0.108585 GTGGCTTGAACCAGACCAGA 59.891 55.000 0.0 0.0 41.46 3.86 F
371 372 0.108585 GCTTGAACCAGACCAGACCA 59.891 55.000 0.0 0.0 0.00 4.02 F
373 374 0.108585 TTGAACCAGACCAGACCAGC 59.891 55.000 0.0 0.0 0.00 4.85 F
1260 1911 0.318445 CAAAGCTCACACCTTGCTGC 60.318 55.000 0.0 0.0 37.11 5.25 F
2547 6058 0.179702 TCAGTCCATCTGCCATGAGC 59.820 55.000 0.0 0.0 43.32 4.26 F
3284 7845 0.108585 ACACTTGACAACGGATGCCT 59.891 50.000 0.0 0.0 0.00 4.75 F
4194 9740 1.112113 TTTACGGGGCTTGCACAAAA 58.888 45.000 0.0 0.0 0.00 2.44 F
5698 12703 1.278985 TCATTTGTCCTGTCGCATCCT 59.721 47.619 0.0 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 5285 0.250513 GCAGGGAGACAGTGGGTAAG 59.749 60.000 0.00 0.00 0.00 2.34 R
2046 5402 0.614294 TTTGGGCAAAGCATCCATGG 59.386 50.000 4.97 4.97 0.00 3.66 R
2342 5835 1.003580 ACACCCACTTGCCAGACTATG 59.996 52.381 0.00 0.00 0.00 2.23 R
2765 6296 0.040336 ACGCGTATAGATGTGCTCCG 60.040 55.000 11.67 0.00 0.00 4.63 R
3765 8462 1.694696 AGTGGTGTCTGTCTTTCCTCC 59.305 52.381 0.00 0.00 0.00 4.30 R
5089 11992 1.376942 GCAGCTGATCAGTGCAGGT 60.377 57.895 29.47 10.51 44.17 4.00 R
6082 13174 0.471617 AGCTGCAGAGAACACCAAGT 59.528 50.000 20.43 0.00 0.00 3.16 R
7461 14588 0.521291 TCTTTCAATTTCTGCCGCCG 59.479 50.000 0.00 0.00 0.00 6.46 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
49 50 2.654863 ACATAGCCTGTAAATGCACCC 58.345 47.619 0.00 0.00 35.91 4.61
50 51 2.025416 ACATAGCCTGTAAATGCACCCA 60.025 45.455 0.00 0.00 35.91 4.51
51 52 2.889170 TAGCCTGTAAATGCACCCAA 57.111 45.000 0.00 0.00 0.00 4.12
94 95 6.677913 ACATGAATAAACACCAAACTAGTGC 58.322 36.000 0.00 0.00 38.87 4.40
115 116 1.206849 TCATGTAGCTGCCATCGAACA 59.793 47.619 0.00 0.00 0.00 3.18
118 119 3.535280 TGTAGCTGCCATCGAACATTA 57.465 42.857 0.00 0.00 0.00 1.90
126 127 5.678132 TGCCATCGAACATTATCAATCTG 57.322 39.130 0.00 0.00 0.00 2.90
129 130 5.686834 CCATCGAACATTATCAATCTGCAG 58.313 41.667 7.63 7.63 0.00 4.41
131 132 5.022282 TCGAACATTATCAATCTGCAGGA 57.978 39.130 15.13 3.44 0.00 3.86
138 139 6.664816 ACATTATCAATCTGCAGGAAAAAGGA 59.335 34.615 15.13 2.93 0.00 3.36
140 141 5.656213 ATCAATCTGCAGGAAAAAGGAAG 57.344 39.130 15.13 0.00 0.00 3.46
141 142 4.728772 TCAATCTGCAGGAAAAAGGAAGA 58.271 39.130 15.13 0.00 0.00 2.87
145 146 5.930837 TCTGCAGGAAAAAGGAAGAAAAA 57.069 34.783 15.13 0.00 0.00 1.94
146 147 6.484364 TCTGCAGGAAAAAGGAAGAAAAAT 57.516 33.333 15.13 0.00 0.00 1.82
153 154 9.927668 CAGGAAAAAGGAAGAAAAATATAGCAA 57.072 29.630 0.00 0.00 0.00 3.91
168 169 9.586435 AAAATATAGCAAGCTATTTCACCAAAC 57.414 29.630 18.65 0.00 39.65 2.93
170 171 6.780457 ATAGCAAGCTATTTCACCAAACAT 57.220 33.333 8.71 0.00 35.92 2.71
171 172 4.813027 AGCAAGCTATTTCACCAAACATG 58.187 39.130 0.00 0.00 0.00 3.21
172 173 3.928375 GCAAGCTATTTCACCAAACATGG 59.072 43.478 0.00 0.00 0.00 3.66
174 175 2.164219 AGCTATTTCACCAAACATGGCG 59.836 45.455 0.00 0.00 0.00 5.69
177 178 1.393603 TTTCACCAAACATGGCGTGA 58.606 45.000 14.82 0.00 33.56 4.35
210 211 2.480555 GCCGACAGGAACAATGCG 59.519 61.111 0.00 0.00 41.02 4.73
212 213 1.671054 CCGACAGGAACAATGCGGT 60.671 57.895 0.00 0.00 41.02 5.68
235 236 3.723554 GACTGATGTCGAGACCCAC 57.276 57.895 0.34 0.00 33.15 4.61
238 239 1.177401 CTGATGTCGAGACCCACAGA 58.823 55.000 12.41 0.00 31.56 3.41
241 242 3.361786 TGATGTCGAGACCCACAGAATA 58.638 45.455 0.34 0.00 0.00 1.75
245 246 3.513912 TGTCGAGACCCACAGAATAATGT 59.486 43.478 0.34 0.00 0.00 2.71
260 261 0.815213 AATGTCCATGGTGATCCGCG 60.815 55.000 12.58 0.00 36.30 6.46
273 274 1.538167 TCCGCGGGGATTCCTAGTA 59.462 57.895 27.83 0.00 37.43 1.82
279 280 1.125633 GGGGATTCCTAGTAACGGCA 58.874 55.000 2.01 0.00 0.00 5.69
280 281 1.487558 GGGGATTCCTAGTAACGGCAA 59.512 52.381 2.01 0.00 0.00 4.52
289 290 0.249398 AGTAACGGCAAGGAAGCGAT 59.751 50.000 0.00 0.00 34.64 4.58
290 291 0.373716 GTAACGGCAAGGAAGCGATG 59.626 55.000 0.00 0.00 34.64 3.84
291 292 1.366111 TAACGGCAAGGAAGCGATGC 61.366 55.000 0.00 0.00 39.33 3.91
295 296 2.693762 GCAAGGAAGCGATGCTGCA 61.694 57.895 4.13 4.13 39.62 4.41
297 298 0.241749 CAAGGAAGCGATGCTGCAAA 59.758 50.000 6.36 0.00 39.62 3.68
308 309 1.022982 TGCTGCAAAGAGATGCTCGG 61.023 55.000 0.00 0.00 46.54 4.63
315 316 3.532155 GAGATGCTCGGCGGAGGT 61.532 66.667 21.36 0.00 40.80 3.85
327 328 2.717044 CGGAGGTGGCGGTGTATGA 61.717 63.158 0.00 0.00 0.00 2.15
328 329 1.830145 GGAGGTGGCGGTGTATGAT 59.170 57.895 0.00 0.00 0.00 2.45
330 331 1.000955 GGAGGTGGCGGTGTATGATAG 59.999 57.143 0.00 0.00 0.00 2.08
331 332 1.961394 GAGGTGGCGGTGTATGATAGA 59.039 52.381 0.00 0.00 0.00 1.98
333 334 2.769663 AGGTGGCGGTGTATGATAGAAA 59.230 45.455 0.00 0.00 0.00 2.52
336 337 2.169561 TGGCGGTGTATGATAGAAAGCA 59.830 45.455 0.00 0.00 0.00 3.91
343 344 2.717639 ATGATAGAAAGCAAGGCGGT 57.282 45.000 0.00 0.00 0.00 5.68
346 347 0.328258 ATAGAAAGCAAGGCGGTGGT 59.672 50.000 0.00 0.00 0.00 4.16
360 361 1.739667 GTGGTTGGTGGCTTGAACC 59.260 57.895 0.00 0.00 39.77 3.62
364 365 4.898607 TGGTGGCTTGAACCAGAC 57.101 55.556 0.00 0.00 42.82 3.51
365 366 1.150536 TGGTGGCTTGAACCAGACC 59.849 57.895 0.00 0.00 42.82 3.85
367 368 0.890996 GGTGGCTTGAACCAGACCAG 60.891 60.000 0.00 0.00 41.46 4.00
368 369 0.108585 GTGGCTTGAACCAGACCAGA 59.891 55.000 0.00 0.00 41.46 3.86
369 370 0.108585 TGGCTTGAACCAGACCAGAC 59.891 55.000 0.00 0.00 33.75 3.51
370 371 0.606673 GGCTTGAACCAGACCAGACC 60.607 60.000 0.00 0.00 0.00 3.85
371 372 0.108585 GCTTGAACCAGACCAGACCA 59.891 55.000 0.00 0.00 0.00 4.02
372 373 1.879796 GCTTGAACCAGACCAGACCAG 60.880 57.143 0.00 0.00 0.00 4.00
373 374 0.108585 TTGAACCAGACCAGACCAGC 59.891 55.000 0.00 0.00 0.00 4.85
374 375 1.374758 GAACCAGACCAGACCAGCG 60.375 63.158 0.00 0.00 0.00 5.18
389 981 0.745845 CAGCGGATGAGGTCAAAGGG 60.746 60.000 0.00 0.00 0.00 3.95
390 982 2.115291 GCGGATGAGGTCAAAGGGC 61.115 63.158 0.00 0.00 0.00 5.19
391 983 1.452108 CGGATGAGGTCAAAGGGCC 60.452 63.158 0.00 0.00 0.00 5.80
392 984 1.915078 CGGATGAGGTCAAAGGGCCT 61.915 60.000 0.00 0.00 37.91 5.19
394 986 0.394899 GATGAGGTCAAAGGGCCTGG 60.395 60.000 6.92 2.22 34.81 4.45
396 988 1.065410 TGAGGTCAAAGGGCCTGGAA 61.065 55.000 6.92 0.00 34.81 3.53
397 989 0.332972 GAGGTCAAAGGGCCTGGAAT 59.667 55.000 6.92 0.17 34.81 3.01
400 1002 1.683319 GGTCAAAGGGCCTGGAATCTC 60.683 57.143 6.92 0.00 0.00 2.75
416 1018 1.066587 CTCCCACGGAATCTCGAGC 59.933 63.158 7.81 0.00 0.00 5.03
430 1032 0.755698 TCGAGCACCAGTATCTCCCC 60.756 60.000 0.00 0.00 0.00 4.81
431 1033 1.043116 CGAGCACCAGTATCTCCCCA 61.043 60.000 0.00 0.00 0.00 4.96
432 1034 1.428869 GAGCACCAGTATCTCCCCAT 58.571 55.000 0.00 0.00 0.00 4.00
433 1035 1.346068 GAGCACCAGTATCTCCCCATC 59.654 57.143 0.00 0.00 0.00 3.51
435 1037 2.042301 GCACCAGTATCTCCCCATCCT 61.042 57.143 0.00 0.00 0.00 3.24
450 1052 4.101077 CCTCCCCTGCCCCTCTCT 62.101 72.222 0.00 0.00 0.00 3.10
497 1103 1.395826 ATAGCCCAGTCTCGTCTGCC 61.396 60.000 0.00 0.00 34.47 4.85
498 1104 2.781431 TAGCCCAGTCTCGTCTGCCA 62.781 60.000 0.00 0.00 34.47 4.92
499 1105 2.262915 CCCAGTCTCGTCTGCCAC 59.737 66.667 0.00 0.00 34.47 5.01
514 1120 2.010582 GCCACTCTGCCTCCTCTACG 62.011 65.000 0.00 0.00 0.00 3.51
658 1265 0.611896 CTTTTCCGCCATTCCTGGGT 60.612 55.000 0.00 0.00 43.36 4.51
662 1269 2.824041 CGCCATTCCTGGGTTCGG 60.824 66.667 0.00 0.00 43.36 4.30
663 1270 2.674754 GCCATTCCTGGGTTCGGA 59.325 61.111 0.00 0.00 43.36 4.55
665 1272 1.077716 CCATTCCTGGGTTCGGACC 60.078 63.158 3.45 3.45 45.75 4.46
725 1332 1.290324 CGGAGGACAGACACACCAG 59.710 63.158 0.00 0.00 0.00 4.00
726 1333 1.004440 GGAGGACAGACACACCAGC 60.004 63.158 0.00 0.00 0.00 4.85
727 1334 1.748403 GAGGACAGACACACCAGCA 59.252 57.895 0.00 0.00 0.00 4.41
728 1335 0.320247 GAGGACAGACACACCAGCAG 60.320 60.000 0.00 0.00 0.00 4.24
869 1482 4.047125 CCGCCACCCCACCTCAAT 62.047 66.667 0.00 0.00 0.00 2.57
889 1507 1.289694 CAACCCACTGCCGTACGTA 59.710 57.895 15.21 1.73 0.00 3.57
891 1509 2.202703 CCCACTGCCGTACGTAGC 60.203 66.667 15.21 11.94 0.00 3.58
896 1514 3.746409 CTGCCGTACGTAGCCGTCC 62.746 68.421 15.21 0.00 46.28 4.79
897 1515 4.559229 GCCGTACGTAGCCGTCCC 62.559 72.222 15.21 0.00 46.28 4.46
898 1516 3.892581 CCGTACGTAGCCGTCCCC 61.893 72.222 15.21 0.00 46.28 4.81
899 1517 3.133464 CGTACGTAGCCGTCCCCA 61.133 66.667 7.22 0.00 46.28 4.96
900 1518 2.699768 CGTACGTAGCCGTCCCCAA 61.700 63.158 7.22 0.00 46.28 4.12
901 1519 1.153765 GTACGTAGCCGTCCCCAAC 60.154 63.158 0.00 0.00 46.28 3.77
916 1534 1.000896 CAACTCACCATCCACCCCC 60.001 63.158 0.00 0.00 0.00 5.40
940 1574 3.695606 GAGTCGCCAGCTCCCACA 61.696 66.667 0.00 0.00 0.00 4.17
1111 1754 4.357947 TGCAGCTGTCCGACGTCC 62.358 66.667 16.64 0.00 0.00 4.79
1137 1780 4.570663 ATCTACGACCGCCTGCGC 62.571 66.667 5.91 0.00 38.24 6.09
1246 1897 2.480555 CGCCGTCCACATCAAAGC 59.519 61.111 0.00 0.00 0.00 3.51
1250 1901 0.798776 CCGTCCACATCAAAGCTCAC 59.201 55.000 0.00 0.00 0.00 3.51
1257 1908 1.610522 ACATCAAAGCTCACACCTTGC 59.389 47.619 0.00 0.00 0.00 4.01
1258 1909 1.884579 CATCAAAGCTCACACCTTGCT 59.115 47.619 0.00 0.00 38.87 3.91
1259 1910 1.311859 TCAAAGCTCACACCTTGCTG 58.688 50.000 0.00 0.00 37.11 4.41
1260 1911 0.318445 CAAAGCTCACACCTTGCTGC 60.318 55.000 0.00 0.00 37.11 5.25
1483 2175 2.039746 TCCTTCCATCCATTCAACACGT 59.960 45.455 0.00 0.00 0.00 4.49
1537 2244 5.759506 GCAGTCTCACTTACTCTGCTATA 57.240 43.478 7.98 0.00 45.14 1.31
1538 2245 6.325919 GCAGTCTCACTTACTCTGCTATAT 57.674 41.667 7.98 0.00 45.14 0.86
1539 2246 7.441890 GCAGTCTCACTTACTCTGCTATATA 57.558 40.000 7.98 0.00 45.14 0.86
1541 2248 7.041030 GCAGTCTCACTTACTCTGCTATATACA 60.041 40.741 7.98 0.00 45.14 2.29
1542 2249 9.008965 CAGTCTCACTTACTCTGCTATATACAT 57.991 37.037 0.00 0.00 0.00 2.29
1543 2250 9.008965 AGTCTCACTTACTCTGCTATATACATG 57.991 37.037 0.00 0.00 0.00 3.21
1545 2252 7.667635 TCTCACTTACTCTGCTATATACATGCT 59.332 37.037 0.00 0.00 0.00 3.79
1546 2253 7.821652 TCACTTACTCTGCTATATACATGCTC 58.178 38.462 0.00 0.00 0.00 4.26
1547 2254 7.667635 TCACTTACTCTGCTATATACATGCTCT 59.332 37.037 0.00 0.00 0.00 4.09
1548 2255 7.754475 CACTTACTCTGCTATATACATGCTCTG 59.246 40.741 0.00 0.00 0.00 3.35
1549 2256 7.450014 ACTTACTCTGCTATATACATGCTCTGT 59.550 37.037 0.00 0.00 42.13 3.41
1550 2257 6.266168 ACTCTGCTATATACATGCTCTGTC 57.734 41.667 0.00 0.00 39.39 3.51
1551 2258 6.009589 ACTCTGCTATATACATGCTCTGTCT 58.990 40.000 0.00 0.00 39.39 3.41
1552 2259 6.150976 ACTCTGCTATATACATGCTCTGTCTC 59.849 42.308 0.00 0.00 39.39 3.36
1553 2260 5.417266 TCTGCTATATACATGCTCTGTCTCC 59.583 44.000 0.00 0.00 39.39 3.71
1554 2261 5.079643 TGCTATATACATGCTCTGTCTCCA 58.920 41.667 0.00 0.00 39.39 3.86
1555 2262 5.718607 TGCTATATACATGCTCTGTCTCCAT 59.281 40.000 0.00 0.00 39.39 3.41
1556 2263 6.041511 GCTATATACATGCTCTGTCTCCATG 58.958 44.000 0.00 0.00 41.49 3.66
1672 2512 5.618284 TCTGAGGTATAGGTTATCCCCACTA 59.382 44.000 0.00 0.00 0.00 2.74
1699 2552 1.648467 CCCTGCCTTACGCTTGCTTC 61.648 60.000 0.00 0.00 38.78 3.86
1722 2962 7.854557 TCATCATCATTTCAAGTTACAGGAG 57.145 36.000 0.00 0.00 0.00 3.69
1723 2963 6.825213 TCATCATCATTTCAAGTTACAGGAGG 59.175 38.462 0.00 0.00 0.00 4.30
1724 2964 6.373005 TCATCATTTCAAGTTACAGGAGGA 57.627 37.500 0.00 0.00 0.00 3.71
1820 5116 4.568760 GCTTGCTAAGACAAGGTCTGTATC 59.431 45.833 6.42 0.00 45.83 2.24
1821 5117 4.371855 TGCTAAGACAAGGTCTGTATCG 57.628 45.455 0.00 0.00 42.59 2.92
1822 5118 3.762288 TGCTAAGACAAGGTCTGTATCGT 59.238 43.478 0.00 0.00 42.59 3.73
1824 5120 4.563184 GCTAAGACAAGGTCTGTATCGTTG 59.437 45.833 0.00 0.00 42.59 4.10
1825 5121 4.866508 AAGACAAGGTCTGTATCGTTGA 57.133 40.909 0.00 0.00 42.59 3.18
1912 5211 1.152652 TTGGGGCGAAGAAAAGGCA 60.153 52.632 0.00 0.00 34.32 4.75
1914 5213 0.965363 TGGGGCGAAGAAAAGGCATC 60.965 55.000 0.00 0.00 34.32 3.91
1932 5231 4.403976 GACGACTTCGAGGCCATC 57.596 61.111 5.01 0.00 43.02 3.51
1985 5285 5.693104 TCTGAAATTCAGTTGAAATGCTTGC 59.307 36.000 20.91 0.00 44.58 4.01
2109 5475 1.738099 GCTCGTGGTGTCGCTGAAT 60.738 57.895 0.00 0.00 0.00 2.57
2266 5739 1.317613 ATCTTCGTGCAGTTTGGCAA 58.682 45.000 0.00 0.00 46.93 4.52
2317 5799 2.818130 TTTCTCCATGCTTTTGTGCC 57.182 45.000 0.00 0.00 0.00 5.01
2331 5819 7.617225 TGCTTTTGTGCCTACTACTTATCTAA 58.383 34.615 0.00 0.00 0.00 2.10
2357 5850 4.397481 TCTCATCATAGTCTGGCAAGTG 57.603 45.455 0.00 0.00 0.00 3.16
2416 5910 3.442977 AGCAATGAACTTTGATCCTCAGC 59.557 43.478 4.94 0.00 0.00 4.26
2474 5984 9.755804 GAAATTCCCCTTCTTCATGAAATTATC 57.244 33.333 9.88 2.06 33.79 1.75
2547 6058 0.179702 TCAGTCCATCTGCCATGAGC 59.820 55.000 0.00 0.00 43.32 4.26
2558 6069 6.293845 CCATCTGCCATGAGCTTTCTATTTAC 60.294 42.308 0.00 0.00 44.23 2.01
2593 6106 7.010771 TCTGCCATGTCATACTACTTATACCT 58.989 38.462 0.00 0.00 0.00 3.08
2765 6296 5.298527 GGTAAACTTGGAGCATGGTTATACC 59.701 44.000 0.00 0.00 39.22 2.73
2847 6744 4.397382 CTTTACATCATGTCGCTTGTGTG 58.603 43.478 0.00 0.00 0.00 3.82
2875 6772 0.958091 AGCCAAGGAGATCTCGATCG 59.042 55.000 16.46 9.36 42.48 3.69
2908 6805 6.947733 TCCTCACAAATTCTTGGTGATAACAT 59.052 34.615 0.00 0.00 36.82 2.71
2909 6806 7.451255 TCCTCACAAATTCTTGGTGATAACATT 59.549 33.333 0.00 0.00 36.82 2.71
2910 6807 7.756722 CCTCACAAATTCTTGGTGATAACATTC 59.243 37.037 0.00 0.00 36.82 2.67
2911 6808 8.175925 TCACAAATTCTTGGTGATAACATTCA 57.824 30.769 0.00 0.00 36.82 2.57
2912 6809 8.805175 TCACAAATTCTTGGTGATAACATTCAT 58.195 29.630 0.00 0.00 36.82 2.57
2918 6815 7.263100 TCTTGGTGATAACATTCATATGTGC 57.737 36.000 1.90 0.00 44.14 4.57
2919 6816 6.827762 TCTTGGTGATAACATTCATATGTGCA 59.172 34.615 1.90 0.00 44.14 4.57
2927 6836 9.740239 GATAACATTCATATGTGCAGTCATTTT 57.260 29.630 1.90 0.00 44.14 1.82
3027 7573 5.732633 AGAGAAGATCCTGAAAGACACATG 58.267 41.667 0.00 0.00 34.07 3.21
3086 7635 4.577834 AAACCAGTTTATGTGTTTCCCG 57.422 40.909 0.00 0.00 30.94 5.14
3139 7692 6.069673 ACCATGGACACCATCTTAGTTGATAA 60.070 38.462 21.47 0.00 43.15 1.75
3147 7700 9.396022 ACACCATCTTAGTTGATAAAAGTATGG 57.604 33.333 0.00 0.00 35.86 2.74
3229 7786 4.250464 CATGAATTTGGAGTGCATGCTTT 58.750 39.130 20.33 6.74 31.24 3.51
3274 7835 7.247728 GTCATTTTGACTTTACACACTTGACA 58.752 34.615 0.45 0.00 43.73 3.58
3277 7838 4.850859 TGACTTTACACACTTGACAACG 57.149 40.909 0.00 0.00 0.00 4.10
3281 7842 4.272504 ACTTTACACACTTGACAACGGATG 59.727 41.667 0.00 0.00 0.00 3.51
3284 7845 0.108585 ACACTTGACAACGGATGCCT 59.891 50.000 0.00 0.00 0.00 4.75
3611 8308 2.102420 TGGTACACAGCCCTCATTATCG 59.898 50.000 0.00 0.00 0.00 2.92
3752 8449 7.544915 GGAGACTTGTAAGAACTACATAACACC 59.455 40.741 0.00 0.00 40.27 4.16
3765 8462 8.718102 ACTACATAACACCTGCTTAGTAAATG 57.282 34.615 0.00 0.00 0.00 2.32
3878 9409 3.559171 GGGACACTGCCAAGAAACATAGA 60.559 47.826 0.00 0.00 0.00 1.98
3889 9420 5.877012 CCAAGAAACATAGAGAAAGCAGCTA 59.123 40.000 0.00 0.00 0.00 3.32
3991 9526 6.164876 CCTTGATGTGGATGTTGCAATAAAA 58.835 36.000 0.59 0.00 0.00 1.52
4112 9650 6.898041 TCGACTTCACTGAACCATTTAATTG 58.102 36.000 0.00 0.00 0.00 2.32
4185 9731 2.030958 CGTTCGCTTTTACGGGGCT 61.031 57.895 0.00 0.00 34.30 5.19
4194 9740 1.112113 TTTACGGGGCTTGCACAAAA 58.888 45.000 0.00 0.00 0.00 2.44
4218 9764 5.288712 ACAGCGAAAGTATCTCATTGTAACG 59.711 40.000 0.00 0.00 0.00 3.18
4233 9779 6.814644 TCATTGTAACGGGTAAGACACTAATG 59.185 38.462 0.00 0.00 0.00 1.90
4329 9879 7.946381 TGGGCACATTTACACTATGATTAAA 57.054 32.000 0.00 0.00 0.00 1.52
4474 10571 6.064717 GTCTTCTATGCATTTTGGTAGGGAT 58.935 40.000 3.54 0.00 0.00 3.85
4911 11427 5.385198 TCTTGTTTCTATCCCAAAAGCACT 58.615 37.500 0.00 0.00 0.00 4.40
5089 11992 4.202357 GCATGTAGATCACTGTTGGGGATA 60.202 45.833 0.00 0.00 0.00 2.59
5169 12143 5.745227 TCAGGTTTCTCATAGTGGAAATCC 58.255 41.667 0.00 0.00 34.26 3.01
5271 12257 9.109393 TGTTAACTGATATTTGGCTCTTGTATC 57.891 33.333 7.22 0.00 0.00 2.24
5362 12349 5.711976 CCTTGGAGCTTTCCTTGATTCTTAA 59.288 40.000 0.00 0.00 0.00 1.85
5689 12694 3.066064 TGTCGGTTTGTTCATTTGTCCTG 59.934 43.478 0.00 0.00 0.00 3.86
5691 12696 3.314080 TCGGTTTGTTCATTTGTCCTGTC 59.686 43.478 0.00 0.00 0.00 3.51
5698 12703 1.278985 TCATTTGTCCTGTCGCATCCT 59.721 47.619 0.00 0.00 0.00 3.24
5782 12793 5.579511 GCAACACACGTATACCAAGACTAAT 59.420 40.000 0.00 0.00 0.00 1.73
5795 12806 4.019321 CCAAGACTAATTCCCTGAACCTCA 60.019 45.833 0.00 0.00 0.00 3.86
5871 12960 5.045213 TCCACATCTTCCCAGCAAGTTTATA 60.045 40.000 0.00 0.00 0.00 0.98
5878 12967 7.007723 TCTTCCCAGCAAGTTTATAAGGAAAA 58.992 34.615 0.00 0.00 32.08 2.29
5976 13068 2.155155 GCCTACGCGATGTGCTTATTAC 59.845 50.000 15.93 0.00 43.27 1.89
6082 13174 6.127563 GGAGTTGGTCACTTCAAAGGTAAAAA 60.128 38.462 0.00 0.00 35.01 1.94
6270 13373 7.686438 TTACAGTTTCAGTATTGTGCATCAT 57.314 32.000 0.00 0.00 0.00 2.45
6281 13384 7.226128 CAGTATTGTGCATCATCTGTCAATAGT 59.774 37.037 0.00 0.00 37.60 2.12
6284 13387 4.080975 TGTGCATCATCTGTCAATAGTGGA 60.081 41.667 0.00 0.00 0.00 4.02
6285 13388 4.272018 GTGCATCATCTGTCAATAGTGGAC 59.728 45.833 0.00 0.00 35.83 4.02
6294 13397 1.471287 TCAATAGTGGACGACTGGACG 59.529 52.381 0.00 0.00 35.96 4.79
6305 13408 1.860676 GACTGGACGTGTGCAAGTAA 58.139 50.000 0.00 0.00 0.00 2.24
6487 13591 1.940613 GCCTATTCAGGTTAGGTTGCG 59.059 52.381 0.00 0.00 44.68 4.85
6528 13632 4.354893 AGGCTCATGAGAAGATGGAATC 57.645 45.455 27.04 4.07 46.04 2.52
6587 13693 0.252057 TGGGTTCCTCCGACTGATGA 60.252 55.000 0.00 0.00 37.00 2.92
6709 13815 2.989639 CTCATGAAGCCGGACCCA 59.010 61.111 5.05 0.00 0.00 4.51
6710 13816 1.450312 CTCATGAAGCCGGACCCAC 60.450 63.158 5.05 0.00 0.00 4.61
6882 13999 9.765795 GCTACATAACCTGAGTGATATAGTTTT 57.234 33.333 0.00 0.00 0.00 2.43
6995 14114 4.159135 AGGAACATGAGATGAAAATGCCAC 59.841 41.667 0.00 0.00 0.00 5.01
7063 14182 6.741358 GTCTGGAACACGATAAATTAACAAGC 59.259 38.462 0.00 0.00 0.00 4.01
7082 14201 1.535860 GCTTTTGCAGCTTCGTTTGGA 60.536 47.619 0.00 0.00 46.27 3.53
7224 14351 2.487986 GGTAATGGATCTCTTGGCCCAG 60.488 54.545 0.00 0.00 31.48 4.45
7320 14447 4.521130 TTGCTAGTATGCTCCTATTCCG 57.479 45.455 0.00 0.00 0.00 4.30
7324 14451 2.679082 AGTATGCTCCTATTCCGGTGT 58.321 47.619 0.00 0.00 0.00 4.16
7335 14462 5.424252 TCCTATTCCGGTGTTTTCTAGATGT 59.576 40.000 0.00 0.00 0.00 3.06
7344 14471 3.519510 TGTTTTCTAGATGTCAGGGAGGG 59.480 47.826 0.00 0.00 0.00 4.30
7364 14491 0.607489 GCACAGAGGAGCATGGTGTT 60.607 55.000 0.00 0.00 0.00 3.32
7365 14492 1.446907 CACAGAGGAGCATGGTGTTC 58.553 55.000 0.00 0.00 0.00 3.18
7380 14507 2.162809 GGTGTTCTGTGTCGGTTTGTTT 59.837 45.455 0.00 0.00 0.00 2.83
7390 14517 5.209977 GTGTCGGTTTGTTTATTGTCCTTC 58.790 41.667 0.00 0.00 0.00 3.46
7461 14588 5.693814 CAGGAAACAATAACAACTCTCAGC 58.306 41.667 0.00 0.00 0.00 4.26
7474 14601 2.359850 TCAGCGGCGGCAGAAATT 60.360 55.556 19.21 0.00 43.41 1.82
7475 14602 2.202518 CAGCGGCGGCAGAAATTG 60.203 61.111 19.21 2.75 43.41 2.32
7480 14607 0.521291 CGGCGGCAGAAATTGAAAGA 59.479 50.000 10.53 0.00 0.00 2.52
7545 14673 4.287552 ACATACTTCATCTCGGGTAAGGT 58.712 43.478 0.00 0.00 0.00 3.50
7595 14725 8.719645 TTTATTTCCATTCCAAGAGAAAAGGA 57.280 30.769 0.00 0.00 39.59 3.36
7668 14798 1.020437 GTGCTTTCTAGATGCAGGGC 58.980 55.000 17.68 6.44 38.88 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.961634 TGCATTTACAGGCTATGTTGTATTTTA 58.038 29.630 0.48 0.00 39.96 1.52
34 35 2.829741 TTTTGGGTGCATTTACAGGC 57.170 45.000 0.00 0.00 0.00 4.85
59 60 9.311916 TGGTGTTTATTCATGTTTTCTTTTGAG 57.688 29.630 0.00 0.00 0.00 3.02
94 95 1.863454 GTTCGATGGCAGCTACATGAG 59.137 52.381 7.72 2.99 0.00 2.90
115 116 7.616935 TCTTCCTTTTTCCTGCAGATTGATAAT 59.383 33.333 17.39 0.00 0.00 1.28
118 119 5.327732 TCTTCCTTTTTCCTGCAGATTGAT 58.672 37.500 17.39 0.00 0.00 2.57
126 127 8.034804 TGCTATATTTTTCTTCCTTTTTCCTGC 58.965 33.333 0.00 0.00 0.00 4.85
129 130 8.873830 GCTTGCTATATTTTTCTTCCTTTTTCC 58.126 33.333 0.00 0.00 0.00 3.13
140 141 9.801873 TTGGTGAAATAGCTTGCTATATTTTTC 57.198 29.630 14.55 14.53 32.98 2.29
145 146 7.880160 TGTTTGGTGAAATAGCTTGCTATAT 57.120 32.000 14.55 4.15 0.00 0.86
146 147 7.201812 CCATGTTTGGTGAAATAGCTTGCTATA 60.202 37.037 14.55 0.00 38.30 1.31
153 154 3.874392 GCCATGTTTGGTGAAATAGCT 57.126 42.857 0.00 0.00 45.57 3.32
197 198 2.268076 GCCACCGCATTGTTCCTGT 61.268 57.895 0.00 0.00 34.03 4.00
198 199 2.568090 GCCACCGCATTGTTCCTG 59.432 61.111 0.00 0.00 34.03 3.86
222 223 4.162320 ACATTATTCTGTGGGTCTCGACAT 59.838 41.667 0.00 0.00 31.38 3.06
223 224 3.513912 ACATTATTCTGTGGGTCTCGACA 59.486 43.478 0.00 0.00 0.00 4.35
224 225 4.113354 GACATTATTCTGTGGGTCTCGAC 58.887 47.826 0.00 0.00 0.00 4.20
229 230 3.885297 CCATGGACATTATTCTGTGGGTC 59.115 47.826 5.56 0.00 0.00 4.46
230 231 3.269381 ACCATGGACATTATTCTGTGGGT 59.731 43.478 21.47 0.00 0.00 4.51
233 234 5.240183 GGATCACCATGGACATTATTCTGTG 59.760 44.000 21.47 0.97 35.97 3.66
234 235 5.380043 GGATCACCATGGACATTATTCTGT 58.620 41.667 21.47 0.00 35.97 3.41
235 236 4.453478 CGGATCACCATGGACATTATTCTG 59.547 45.833 21.47 2.40 35.59 3.02
238 239 3.149196 GCGGATCACCATGGACATTATT 58.851 45.455 21.47 0.00 35.59 1.40
241 242 0.815213 CGCGGATCACCATGGACATT 60.815 55.000 21.47 0.00 35.59 2.71
245 246 3.860605 CCCGCGGATCACCATGGA 61.861 66.667 30.73 0.00 33.52 3.41
260 261 1.125633 TGCCGTTACTAGGAATCCCC 58.874 55.000 0.00 0.00 0.00 4.81
273 274 2.690778 GCATCGCTTCCTTGCCGTT 61.691 57.895 0.00 0.00 0.00 4.44
279 280 0.524862 CTTTGCAGCATCGCTTCCTT 59.475 50.000 0.00 0.00 36.40 3.36
280 281 0.321919 TCTTTGCAGCATCGCTTCCT 60.322 50.000 0.00 0.00 36.40 3.36
289 290 1.022982 CCGAGCATCTCTTTGCAGCA 61.023 55.000 0.00 0.00 45.23 4.41
290 291 1.720301 CCGAGCATCTCTTTGCAGC 59.280 57.895 0.00 0.00 45.23 5.25
291 292 1.720301 GCCGAGCATCTCTTTGCAG 59.280 57.895 0.00 0.00 45.23 4.41
295 296 1.142748 CTCCGCCGAGCATCTCTTT 59.857 57.895 0.00 0.00 0.00 2.52
297 298 3.222855 CCTCCGCCGAGCATCTCT 61.223 66.667 0.00 0.00 34.49 3.10
308 309 4.157120 ATACACCGCCACCTCCGC 62.157 66.667 0.00 0.00 0.00 5.54
315 316 2.169561 TGCTTTCTATCATACACCGCCA 59.830 45.455 0.00 0.00 0.00 5.69
327 328 0.328258 ACCACCGCCTTGCTTTCTAT 59.672 50.000 0.00 0.00 0.00 1.98
328 329 0.109723 AACCACCGCCTTGCTTTCTA 59.890 50.000 0.00 0.00 0.00 2.10
330 331 1.007387 CAACCACCGCCTTGCTTTC 60.007 57.895 0.00 0.00 0.00 2.62
331 332 2.498056 CCAACCACCGCCTTGCTTT 61.498 57.895 0.00 0.00 0.00 3.51
333 334 4.204028 ACCAACCACCGCCTTGCT 62.204 61.111 0.00 0.00 0.00 3.91
343 344 0.754957 CTGGTTCAAGCCACCAACCA 60.755 55.000 2.90 2.90 45.92 3.67
346 347 0.467290 GGTCTGGTTCAAGCCACCAA 60.467 55.000 0.78 0.00 43.96 3.67
360 361 1.153489 CATCCGCTGGTCTGGTCTG 60.153 63.158 0.00 0.00 0.00 3.51
363 364 2.362369 CCTCATCCGCTGGTCTGGT 61.362 63.158 0.00 0.00 0.00 4.00
364 365 2.303549 GACCTCATCCGCTGGTCTGG 62.304 65.000 0.00 0.00 44.84 3.86
365 366 1.142748 GACCTCATCCGCTGGTCTG 59.857 63.158 0.00 0.00 44.84 3.51
368 369 0.036010 CTTTGACCTCATCCGCTGGT 60.036 55.000 0.00 0.00 36.70 4.00
369 370 0.745845 CCTTTGACCTCATCCGCTGG 60.746 60.000 0.00 0.00 0.00 4.85
370 371 0.745845 CCCTTTGACCTCATCCGCTG 60.746 60.000 0.00 0.00 0.00 5.18
371 372 1.604378 CCCTTTGACCTCATCCGCT 59.396 57.895 0.00 0.00 0.00 5.52
372 373 2.115291 GCCCTTTGACCTCATCCGC 61.115 63.158 0.00 0.00 0.00 5.54
373 374 1.452108 GGCCCTTTGACCTCATCCG 60.452 63.158 0.00 0.00 0.00 4.18
374 375 0.394899 CAGGCCCTTTGACCTCATCC 60.395 60.000 0.00 0.00 32.56 3.51
389 981 1.910580 TTCCGTGGGAGATTCCAGGC 61.911 60.000 0.00 0.00 40.31 4.85
390 982 0.839946 ATTCCGTGGGAGATTCCAGG 59.160 55.000 0.00 0.00 38.64 4.45
391 983 1.765314 AGATTCCGTGGGAGATTCCAG 59.235 52.381 0.00 0.00 38.64 3.86
392 984 1.762957 GAGATTCCGTGGGAGATTCCA 59.237 52.381 0.00 0.00 38.64 3.53
394 986 1.681793 TCGAGATTCCGTGGGAGATTC 59.318 52.381 0.00 0.00 31.21 2.52
396 988 1.323412 CTCGAGATTCCGTGGGAGAT 58.677 55.000 6.58 0.00 31.21 2.75
397 989 1.384989 GCTCGAGATTCCGTGGGAGA 61.385 60.000 18.75 0.00 31.21 3.71
400 1002 1.519455 GTGCTCGAGATTCCGTGGG 60.519 63.158 18.75 0.00 0.00 4.61
416 1018 1.974236 GAGGATGGGGAGATACTGGTG 59.026 57.143 0.00 0.00 0.00 4.17
430 1032 3.174265 GAGGGGCAGGGGAGGATG 61.174 72.222 0.00 0.00 0.00 3.51
431 1033 3.381049 AGAGGGGCAGGGGAGGAT 61.381 66.667 0.00 0.00 0.00 3.24
432 1034 4.095400 GAGAGGGGCAGGGGAGGA 62.095 72.222 0.00 0.00 0.00 3.71
433 1035 4.101077 AGAGAGGGGCAGGGGAGG 62.101 72.222 0.00 0.00 0.00 4.30
435 1037 3.284251 TGAGAGAGGGGCAGGGGA 61.284 66.667 0.00 0.00 0.00 4.81
497 1103 1.435515 GCGTAGAGGAGGCAGAGTG 59.564 63.158 0.00 0.00 38.85 3.51
498 1104 1.755008 GGCGTAGAGGAGGCAGAGT 60.755 63.158 0.00 0.00 40.88 3.24
499 1105 2.494530 GGGCGTAGAGGAGGCAGAG 61.495 68.421 0.00 0.00 40.88 3.35
536 1142 3.068590 GTCCTTATCCGGTTCGAATACCA 59.931 47.826 0.00 0.00 38.12 3.25
612 1219 4.271816 CGGACGGATCCTCTGCGG 62.272 72.222 10.75 0.00 43.91 5.69
714 1321 2.033141 CCCCTGCTGGTGTGTCTG 59.967 66.667 9.00 0.00 0.00 3.51
725 1332 2.750237 CCCGTACTTTGCCCCTGC 60.750 66.667 0.00 0.00 38.26 4.85
726 1333 1.376812 GTCCCGTACTTTGCCCCTG 60.377 63.158 0.00 0.00 0.00 4.45
727 1334 1.538135 AGTCCCGTACTTTGCCCCT 60.538 57.895 0.00 0.00 33.35 4.79
728 1335 1.376812 CAGTCCCGTACTTTGCCCC 60.377 63.158 0.00 0.00 35.76 5.80
811 1424 3.883744 CTCTCTTGGCGGTTGCGGT 62.884 63.158 0.00 0.00 44.10 5.68
812 1425 3.121030 CTCTCTTGGCGGTTGCGG 61.121 66.667 0.00 0.00 44.10 5.69
813 1426 3.793144 GCTCTCTTGGCGGTTGCG 61.793 66.667 0.00 0.00 44.10 4.85
814 1427 3.435186 GGCTCTCTTGGCGGTTGC 61.435 66.667 0.00 0.00 41.71 4.17
865 1478 1.303236 CGGCAGTGGGTTGGATTGA 60.303 57.895 0.00 0.00 0.00 2.57
868 1481 1.298667 GTACGGCAGTGGGTTGGAT 59.701 57.895 0.00 0.00 0.00 3.41
869 1482 2.745037 GTACGGCAGTGGGTTGGA 59.255 61.111 0.00 0.00 0.00 3.53
889 1507 3.637273 GGTGAGTTGGGGACGGCT 61.637 66.667 0.00 0.00 0.00 5.52
891 1509 1.078426 GATGGTGAGTTGGGGACGG 60.078 63.158 0.00 0.00 0.00 4.79
896 1514 1.000896 GGGTGGATGGTGAGTTGGG 60.001 63.158 0.00 0.00 0.00 4.12
897 1515 1.000896 GGGGTGGATGGTGAGTTGG 60.001 63.158 0.00 0.00 0.00 3.77
898 1516 1.000896 GGGGGTGGATGGTGAGTTG 60.001 63.158 0.00 0.00 0.00 3.16
899 1517 3.508048 GGGGGTGGATGGTGAGTT 58.492 61.111 0.00 0.00 0.00 3.01
923 1541 3.695606 TGTGGGAGCTGGCGACTC 61.696 66.667 0.00 0.00 0.00 3.36
924 1542 4.008933 GTGTGGGAGCTGGCGACT 62.009 66.667 0.00 0.00 0.00 4.18
928 1546 2.210144 TTATGGGTGTGGGAGCTGGC 62.210 60.000 0.00 0.00 0.00 4.85
931 1549 0.625849 CCTTTATGGGTGTGGGAGCT 59.374 55.000 0.00 0.00 0.00 4.09
932 1550 3.191182 CCTTTATGGGTGTGGGAGC 57.809 57.895 0.00 0.00 0.00 4.70
1111 1754 2.638154 GTCGTAGATCTCCCGCCG 59.362 66.667 0.00 0.00 40.67 6.46
1114 1757 2.638154 GCGGTCGTAGATCTCCCG 59.362 66.667 15.04 15.04 40.67 5.14
1246 1897 2.623915 GCAGGCAGCAAGGTGTGAG 61.624 63.158 0.00 0.00 44.79 3.51
1483 2175 3.358111 TTCAGAAACACACAGGGACAA 57.642 42.857 0.00 0.00 0.00 3.18
1553 2260 0.548031 AGGTACTGCCCATGGACATG 59.452 55.000 15.22 4.61 37.18 3.21
1554 2261 1.212935 GAAGGTACTGCCCATGGACAT 59.787 52.381 15.22 0.00 40.86 3.06
1555 2262 0.618458 GAAGGTACTGCCCATGGACA 59.382 55.000 15.22 7.03 40.86 4.02
1556 2263 0.618458 TGAAGGTACTGCCCATGGAC 59.382 55.000 15.22 0.55 40.86 4.02
1600 2307 2.795121 CGTTTTGATTCGGAGCAGAG 57.205 50.000 0.00 0.00 0.00 3.35
1672 2512 0.466189 CGTAAGGCAGGGCATTGGAT 60.466 55.000 0.00 0.00 33.64 3.41
1699 2552 6.825213 TCCTCCTGTAACTTGAAATGATGATG 59.175 38.462 0.00 0.00 0.00 3.07
1722 2962 5.006746 ACAAGAGATGATCGCGTATTTTTCC 59.993 40.000 5.77 0.00 0.00 3.13
1723 2963 5.898606 CACAAGAGATGATCGCGTATTTTTC 59.101 40.000 5.77 0.00 0.00 2.29
1724 2964 5.351465 ACACAAGAGATGATCGCGTATTTTT 59.649 36.000 5.77 0.00 0.00 1.94
1771 5067 8.711457 CAAGATTGTTTAAATTAAGCCCAACTG 58.289 33.333 0.00 0.00 0.00 3.16
1820 5116 1.002576 TGCTGTTGCTGTTCATCAACG 60.003 47.619 12.58 9.47 43.91 4.10
1821 5117 2.780065 TGCTGTTGCTGTTCATCAAC 57.220 45.000 11.12 11.12 41.99 3.18
1822 5118 2.426381 TGTTGCTGTTGCTGTTCATCAA 59.574 40.909 0.00 0.00 40.48 2.57
1824 5120 2.658285 CTGTTGCTGTTGCTGTTCATC 58.342 47.619 0.00 0.00 40.48 2.92
1825 5121 1.269413 GCTGTTGCTGTTGCTGTTCAT 60.269 47.619 0.00 0.00 40.48 2.57
1854 5150 3.743886 CCGCTCGTCAAATCCTTTTAAC 58.256 45.455 0.00 0.00 0.00 2.01
1932 5231 0.321671 TGGAGAAAGACCTTGCGGAG 59.678 55.000 0.00 0.00 0.00 4.63
1985 5285 0.250513 GCAGGGAGACAGTGGGTAAG 59.749 60.000 0.00 0.00 0.00 2.34
2046 5402 0.614294 TTTGGGCAAAGCATCCATGG 59.386 50.000 4.97 4.97 0.00 3.66
2048 5404 2.259012 TCTTTTGGGCAAAGCATCCAT 58.741 42.857 0.00 0.00 41.72 3.41
2055 5411 2.409975 CACTGCATCTTTTGGGCAAAG 58.590 47.619 0.00 0.00 43.15 2.77
2205 5666 7.942341 ACTCTCCTAGATAGTCTTATGGTTCAG 59.058 40.741 0.00 0.00 0.00 3.02
2331 5819 6.725369 ACTTGCCAGACTATGATGAGATATCT 59.275 38.462 4.47 4.47 0.00 1.98
2342 5835 1.003580 ACACCCACTTGCCAGACTATG 59.996 52.381 0.00 0.00 0.00 2.23
2348 5841 2.627699 ACAAAATACACCCACTTGCCAG 59.372 45.455 0.00 0.00 0.00 4.85
2357 5850 4.600692 AAAGGAAGCACAAAATACACCC 57.399 40.909 0.00 0.00 0.00 4.61
2474 5984 4.589216 TGGCTTGTCATTGGAAGAAAAG 57.411 40.909 0.00 0.00 34.20 2.27
2547 6058 8.778358 GGCAGATATGGAAGTGTAAATAGAAAG 58.222 37.037 0.00 0.00 0.00 2.62
2558 6069 3.812262 TGACATGGCAGATATGGAAGTG 58.188 45.455 0.00 0.00 0.00 3.16
2693 6207 3.511146 ACACATCCAAACACAATCCATCC 59.489 43.478 0.00 0.00 0.00 3.51
2750 6264 1.608283 GCTCCGGTATAACCATGCTCC 60.608 57.143 0.00 0.00 38.47 4.70
2765 6296 0.040336 ACGCGTATAGATGTGCTCCG 60.040 55.000 11.67 0.00 0.00 4.63
2847 6744 2.610859 TCCTTGGCTCTGACCCCC 60.611 66.667 0.00 0.00 0.00 5.40
2875 6772 3.936564 AGAATTTGTGAGGAGCTCTGTC 58.063 45.455 14.64 11.37 0.00 3.51
2912 6809 9.299963 GCAATATAAACAAAATGACTGCACATA 57.700 29.630 0.00 0.00 0.00 2.29
2913 6810 8.036575 AGCAATATAAACAAAATGACTGCACAT 58.963 29.630 0.00 0.00 0.00 3.21
2914 6811 7.377398 AGCAATATAAACAAAATGACTGCACA 58.623 30.769 0.00 0.00 0.00 4.57
2915 6812 7.816945 AGCAATATAAACAAAATGACTGCAC 57.183 32.000 0.00 0.00 0.00 4.57
2916 6813 8.739039 ACTAGCAATATAAACAAAATGACTGCA 58.261 29.630 0.00 0.00 0.00 4.41
2917 6814 9.226345 GACTAGCAATATAAACAAAATGACTGC 57.774 33.333 0.00 0.00 0.00 4.40
2927 6836 8.840833 TGACAAACAGACTAGCAATATAAACA 57.159 30.769 0.00 0.00 0.00 2.83
2985 6894 7.931948 TCTTCTCTTACAAGAATCGGAAGTTTT 59.068 33.333 13.83 0.00 36.14 2.43
3112 7665 5.428457 TCAACTAAGATGGTGTCCATGGTAT 59.572 40.000 12.58 0.00 45.26 2.73
3121 7674 9.396022 CCATACTTTTATCAACTAAGATGGTGT 57.604 33.333 0.00 0.00 30.51 4.16
3167 7720 4.814771 CAGCCCTAGGTTTTATAACTTCGG 59.185 45.833 8.29 0.00 34.59 4.30
3229 7786 6.335471 TGACTTCGGTTACTTCATCTTACA 57.665 37.500 0.00 0.00 0.00 2.41
3274 7835 2.159014 TGTAGCGATTAAGGCATCCGTT 60.159 45.455 4.36 0.00 0.00 4.44
3277 7838 3.113260 AGTGTAGCGATTAAGGCATCC 57.887 47.619 4.36 0.00 0.00 3.51
3281 7842 6.787085 ATTGATAAGTGTAGCGATTAAGGC 57.213 37.500 0.00 0.00 0.00 4.35
3447 8046 5.302360 ACATTACGTTTTGCTGTCTCCTTA 58.698 37.500 0.00 0.00 0.00 2.69
3490 8091 6.982336 GAAGCATTCACGTACGTAATGTAACG 60.982 42.308 29.62 16.82 46.62 3.18
3611 8308 3.619038 CCGAGGCTGAACTTGTTAGATTC 59.381 47.826 0.00 0.00 0.00 2.52
3700 8397 3.132289 AGATCCGGACGCAATCTTTTCTA 59.868 43.478 6.12 0.00 0.00 2.10
3752 8449 6.173339 TGTCTTTCCTCCATTTACTAAGCAG 58.827 40.000 0.00 0.00 0.00 4.24
3765 8462 1.694696 AGTGGTGTCTGTCTTTCCTCC 59.305 52.381 0.00 0.00 0.00 4.30
3878 9409 8.790718 CCACAAATCATAATATAGCTGCTTTCT 58.209 33.333 7.79 0.00 0.00 2.52
3991 9526 7.876068 TCGTTAACATGTTCAGTTCTAAGGAAT 59.124 33.333 15.85 0.00 33.71 3.01
4065 9600 8.600625 TCGATTATGTTTCACGGAAATAAGAAG 58.399 33.333 3.00 0.00 33.97 2.85
4137 9683 5.670485 TCATGATTAACGCTCCTGTACATT 58.330 37.500 0.00 0.00 0.00 2.71
4185 9731 2.645730 ACTTTCGCTGTTTTGTGCAA 57.354 40.000 0.00 0.00 0.00 4.08
4194 9740 5.288712 CGTTACAATGAGATACTTTCGCTGT 59.711 40.000 0.00 0.00 0.00 4.40
4218 9764 4.760204 ACAAGCAACATTAGTGTCTTACCC 59.240 41.667 0.00 0.00 37.67 3.69
4233 9779 5.584649 TGCTATCCATACTACAACAAGCAAC 59.415 40.000 0.00 0.00 34.75 4.17
4329 9879 6.074648 TGACCTCCAATTTTAGTCACCAATT 58.925 36.000 0.00 0.00 32.75 2.32
4474 10571 6.097554 CCCTCTAGACTTATCTGCTCTTGAAA 59.902 42.308 0.00 0.00 36.29 2.69
4562 10659 7.473366 TCTCTTGTATTCTGTCGACTTACATC 58.527 38.462 17.92 4.46 0.00 3.06
4563 10660 7.392494 TCTCTTGTATTCTGTCGACTTACAT 57.608 36.000 17.92 6.26 0.00 2.29
4565 10662 7.251994 ACATCTCTTGTATTCTGTCGACTTAC 58.748 38.462 17.92 12.93 36.57 2.34
4911 11427 2.409055 GCGGCCAATGCATGTCAGA 61.409 57.895 2.24 0.00 40.13 3.27
5026 11543 4.271049 CGTATCAAACTACTGGATGCCTTG 59.729 45.833 0.00 0.00 0.00 3.61
5089 11992 1.376942 GCAGCTGATCAGTGCAGGT 60.377 57.895 29.47 10.51 44.17 4.00
5169 12143 2.363018 TGGGAGACAGAGGCCTCG 60.363 66.667 26.95 22.44 34.09 4.63
5260 12242 2.806244 ACAAACACACGATACAAGAGCC 59.194 45.455 0.00 0.00 0.00 4.70
5271 12257 4.850859 TGTACTCTGAAACAAACACACG 57.149 40.909 0.00 0.00 0.00 4.49
5506 12493 5.063180 TGAATTGACAAGTGCATGGATTC 57.937 39.130 0.00 0.00 0.00 2.52
5550 12543 5.588648 TCTTCACGACCTGTTTCAAAAGAAT 59.411 36.000 0.00 0.00 0.00 2.40
5610 12615 4.125703 GTTTCAGCAGTCATATCTCCCTG 58.874 47.826 0.00 0.00 0.00 4.45
5689 12694 1.472878 GAAAGGGGAAAAGGATGCGAC 59.527 52.381 0.00 0.00 0.00 5.19
5691 12696 1.839424 AGAAAGGGGAAAAGGATGCG 58.161 50.000 0.00 0.00 0.00 4.73
5698 12703 9.782900 ATTGGATATTTTCTAGAAAGGGGAAAA 57.217 29.630 17.05 10.33 41.21 2.29
5739 12750 2.822561 TGCAACAACAAAAGAGTGGTCA 59.177 40.909 0.00 0.00 0.00 4.02
5782 12793 1.361204 TCTGCATGAGGTTCAGGGAA 58.639 50.000 0.00 0.00 26.05 3.97
5795 12806 6.595682 AGGTTATAGCACATAGTTTCTGCAT 58.404 36.000 0.00 0.00 33.06 3.96
5905 12994 4.462483 CCTCTGAGCTCTGACTAAAGTTCT 59.538 45.833 18.39 0.00 0.00 3.01
5976 13068 0.670162 CCTGGCAGGACAACAACTTG 59.330 55.000 29.96 0.00 37.67 3.16
6082 13174 0.471617 AGCTGCAGAGAACACCAAGT 59.528 50.000 20.43 0.00 0.00 3.16
6210 13313 2.380084 TCAAATGTCGTACCTGCCTC 57.620 50.000 0.00 0.00 0.00 4.70
6256 13359 7.226128 CACTATTGACAGATGATGCACAATACT 59.774 37.037 0.00 0.00 38.88 2.12
6270 13373 2.492088 CCAGTCGTCCACTATTGACAGA 59.508 50.000 0.00 0.00 32.21 3.41
6281 13384 2.725641 CACACGTCCAGTCGTCCA 59.274 61.111 0.00 0.00 42.27 4.02
6284 13387 1.591594 CTTGCACACGTCCAGTCGT 60.592 57.895 0.00 0.00 45.10 4.34
6285 13388 0.318360 TACTTGCACACGTCCAGTCG 60.318 55.000 0.00 0.00 0.00 4.18
6294 13397 3.185391 GCTCACTTCTCTTACTTGCACAC 59.815 47.826 0.00 0.00 0.00 3.82
6295 13398 3.181466 TGCTCACTTCTCTTACTTGCACA 60.181 43.478 0.00 0.00 0.00 4.57
6487 13591 3.307762 CCTTAAGGCCTACATATCCAGCC 60.308 52.174 5.16 0.00 44.20 4.85
6709 13815 2.028130 TGGGCGACAATGTGAAAAAGT 58.972 42.857 0.00 0.00 0.00 2.66
6710 13816 2.034558 AGTGGGCGACAATGTGAAAAAG 59.965 45.455 1.61 0.00 0.00 2.27
6817 13932 1.067776 CCCAGTTCGTCCTGTGAGTAC 60.068 57.143 3.98 0.00 0.00 2.73
6819 13935 0.759436 ACCCAGTTCGTCCTGTGAGT 60.759 55.000 3.98 0.00 0.00 3.41
6882 13999 8.768955 GCAAAACAAATAACCACATCAAACATA 58.231 29.630 0.00 0.00 0.00 2.29
6889 14006 5.116983 CACTCGCAAAACAAATAACCACATC 59.883 40.000 0.00 0.00 0.00 3.06
7063 14182 2.490328 TCCAAACGAAGCTGCAAAAG 57.510 45.000 1.02 0.00 0.00 2.27
7108 14228 0.693622 TTCCTGTGGCCACCGAATTA 59.306 50.000 32.62 12.36 0.00 1.40
7304 14431 2.679082 ACACCGGAATAGGAGCATACT 58.321 47.619 9.46 0.00 34.73 2.12
7320 14447 4.508662 CTCCCTGACATCTAGAAAACACC 58.491 47.826 0.00 0.00 0.00 4.16
7324 14451 3.115390 CCCCTCCCTGACATCTAGAAAA 58.885 50.000 0.00 0.00 0.00 2.29
7335 14462 2.284921 CTCTGTGCCCCTCCCTGA 60.285 66.667 0.00 0.00 0.00 3.86
7344 14471 1.748122 CACCATGCTCCTCTGTGCC 60.748 63.158 0.00 0.00 0.00 5.01
7364 14491 4.273969 GGACAATAAACAAACCGACACAGA 59.726 41.667 0.00 0.00 0.00 3.41
7365 14492 4.274950 AGGACAATAAACAAACCGACACAG 59.725 41.667 0.00 0.00 0.00 3.66
7380 14507 4.526970 GGAAAGGATGCTGAAGGACAATA 58.473 43.478 0.00 0.00 0.00 1.90
7390 14517 2.521547 AGAAAGGGGAAAGGATGCTG 57.478 50.000 0.00 0.00 0.00 4.41
7461 14588 0.521291 TCTTTCAATTTCTGCCGCCG 59.479 50.000 0.00 0.00 0.00 6.46
7489 14616 1.056660 CTAGCCCAATCCCATACGGT 58.943 55.000 0.00 0.00 0.00 4.83
7499 14626 2.834638 ACAAATGAGCCTAGCCCAAT 57.165 45.000 0.00 0.00 0.00 3.16
7570 14698 8.719645 TCCTTTTCTCTTGGAATGGAAATAAA 57.280 30.769 0.00 0.00 35.54 1.40
7608 14738 7.468084 GCCAGCGAGACCATTTTTACATTATTA 60.468 37.037 0.00 0.00 0.00 0.98
7609 14739 6.680378 GCCAGCGAGACCATTTTTACATTATT 60.680 38.462 0.00 0.00 0.00 1.40
7612 14742 3.119495 GCCAGCGAGACCATTTTTACATT 60.119 43.478 0.00 0.00 0.00 2.71
7615 14745 1.810151 TGCCAGCGAGACCATTTTTAC 59.190 47.619 0.00 0.00 0.00 2.01
7622 14752 3.670637 GAGCATGCCAGCGAGACCA 62.671 63.158 15.66 0.00 40.15 4.02


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

AutoCloner maintained by Alex Coulton.