Multiple sequence alignment - TraesCS4A01G263200

Loading Multiple Alignment...

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 TraesCS4A01G263200 chr4A 100.000 4344 0 0 1 4344 575738805 575734462 0.000000e+00 8022.0
1 TraesCS4A01G263200 chr4A 90.050 201 17 1 1770 1970 743708685 743708882 1.550000e-64 257.0
2 TraesCS4A01G263200 chr4A 94.118 102 5 1 2264 2365 38740540 38740440 2.090000e-33 154.0
3 TraesCS4A01G263200 chr4B 88.189 2049 140 52 2340 4344 40235248 40233258 0.000000e+00 2350.0
4 TraesCS4A01G263200 chr4B 88.416 1761 110 39 457 2165 40237166 40235448 0.000000e+00 2036.0
5 TraesCS4A01G263200 chr4B 89.629 1456 97 37 2911 4344 40437502 40438925 0.000000e+00 1803.0
6 TraesCS4A01G263200 chr4B 84.817 764 67 24 3580 4319 40419655 40420393 0.000000e+00 723.0
7 TraesCS4A01G263200 chr4B 98.901 91 1 0 2274 2364 392046697 392046787 3.480000e-36 163.0
8 TraesCS4A01G263200 chr4B 77.985 268 29 17 77 332 40237589 40237340 1.630000e-29 141.0
9 TraesCS4A01G263200 chr4B 98.039 51 1 0 2165 2215 627252280 627252230 5.980000e-14 89.8
10 TraesCS4A01G263200 chr4D 88.871 1905 114 47 2359 4238 27560533 27562364 0.000000e+00 2254.0
11 TraesCS4A01G263200 chr4D 89.122 1572 76 33 537 2051 27558832 27560365 0.000000e+00 1868.0
12 TraesCS4A01G263200 chr4D 84.274 496 33 17 3744 4216 27562944 27563417 3.990000e-120 442.0
13 TraesCS4A01G263200 chr4D 83.333 156 10 10 193 332 27558343 27558498 3.530000e-26 130.0
14 TraesCS4A01G263200 chr4D 83.838 99 16 0 2762 2860 28243934 28243836 1.290000e-15 95.3
15 TraesCS4A01G263200 chr2B 85.113 618 64 17 1302 1912 69350472 69351068 1.340000e-169 606.0
16 TraesCS4A01G263200 chr2B 85.340 191 15 4 1927 2116 69351054 69351232 7.420000e-43 185.0
17 TraesCS4A01G263200 chr2B 90.816 98 8 1 2069 2165 69351232 69351329 3.530000e-26 130.0
18 TraesCS4A01G263200 chr2B 96.296 54 2 0 2162 2215 244591921 244591974 5.980000e-14 89.8
19 TraesCS4A01G263200 chr1B 84.422 398 33 9 1770 2165 2839112 2839482 8.880000e-97 364.0
20 TraesCS4A01G263200 chr1B 89.552 201 18 1 1770 1970 627870725 627870528 7.210000e-63 252.0
21 TraesCS4A01G263200 chr1B 89.552 201 18 1 1770 1970 677582187 677582384 7.210000e-63 252.0
22 TraesCS4A01G263200 chr1B 89.055 201 19 1 1770 1970 609697985 609698182 3.360000e-61 246.0
23 TraesCS4A01G263200 chr1B 95.385 65 3 0 1302 1366 589507688 589507624 2.140000e-18 104.0
24 TraesCS4A01G263200 chr1B 98.077 52 1 0 2164 2215 269461267 269461318 1.660000e-14 91.6
25 TraesCS4A01G263200 chr1B 98.039 51 1 0 2165 2215 221530449 221530399 5.980000e-14 89.8
26 TraesCS4A01G263200 chr7B 90.050 201 17 1 1770 1970 742023416 742023613 1.550000e-64 257.0
27 TraesCS4A01G263200 chr7B 89.552 201 18 1 1770 1970 575512535 575512732 7.210000e-63 252.0
28 TraesCS4A01G263200 chr7B 94.792 96 3 2 2275 2369 361147170 361147076 9.730000e-32 148.0
29 TraesCS4A01G263200 chr6B 89.604 202 16 4 1770 1970 138404267 138404070 7.210000e-63 252.0
30 TraesCS4A01G263200 chr6B 89.552 201 18 2 1770 1970 659283133 659282936 7.210000e-63 252.0
31 TraesCS4A01G263200 chrUn 96.040 101 4 0 2274 2374 279936301 279936201 9.660000e-37 165.0
32 TraesCS4A01G263200 chrUn 96.040 101 4 0 2274 2374 395541688 395541588 9.660000e-37 165.0
33 TraesCS4A01G263200 chr2D 96.809 94 2 1 2267 2360 174430838 174430746 5.820000e-34 156.0
34 TraesCS4A01G263200 chr2A 92.593 108 6 2 2254 2360 98882837 98882731 2.090000e-33 154.0
35 TraesCS4A01G263200 chr3A 93.269 104 3 4 2273 2376 648870444 648870543 2.710000e-32 150.0
36 TraesCS4A01G263200 chr3A 100.000 51 0 0 2165 2215 749456957 749456907 1.290000e-15 95.3
37 TraesCS4A01G263200 chr3A 94.828 58 2 1 2159 2215 722365410 722365467 5.980000e-14 89.8
38 TraesCS4A01G263200 chr5B 90.909 110 8 2 2272 2380 25333685 25333577 3.500000e-31 147.0
39 TraesCS4A01G263200 chr3B 98.039 51 1 0 2165 2215 582414777 582414727 5.980000e-14 89.8
40 TraesCS4A01G263200 chr6D 93.103 58 3 1 2165 2221 144895633 144895690 2.780000e-12 84.2
41 TraesCS4A01G263200 chr3D 96.078 51 2 0 2165 2215 9191189 9191139 2.780000e-12 84.2


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 TraesCS4A01G263200 chr4A 575734462 575738805 4343 True 8022.0 8022 100.000000 1 4344 1 chr4A.!!$R2 4343
1 TraesCS4A01G263200 chr4B 40437502 40438925 1423 False 1803.0 1803 89.629000 2911 4344 1 chr4B.!!$F2 1433
2 TraesCS4A01G263200 chr4B 40233258 40237589 4331 True 1509.0 2350 84.863333 77 4344 3 chr4B.!!$R2 4267
3 TraesCS4A01G263200 chr4B 40419655 40420393 738 False 723.0 723 84.817000 3580 4319 1 chr4B.!!$F1 739
4 TraesCS4A01G263200 chr4D 27558343 27563417 5074 False 1173.5 2254 86.400000 193 4238 4 chr4D.!!$F1 4045
5 TraesCS4A01G263200 chr2B 69350472 69351329 857 False 307.0 606 87.089667 1302 2165 3 chr2B.!!$F2 863

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
133 134 0.111253 CAAGGCCAGTTTCCACTCCT 59.889 55.0 5.01 0.0 30.00 3.69 F
1396 1637 0.108138 CGTCAAGCCCAGGTAGGAAG 60.108 60.0 0.00 0.0 41.22 3.46 F
1398 1639 0.118346 TCAAGCCCAGGTAGGAAGGA 59.882 55.0 0.00 0.0 41.22 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1738 0.884704 GACAAGAACAAGCGCCCTGA 60.885 55.000 13.61 0.0 0.0 3.86 R
3334 3756 0.181350 ACCCGCCTGATCAAATCCTC 59.819 55.000 0.00 0.0 0.0 3.71 R
3396 3822 4.451150 GCTCGGCGATGTGGTCCA 62.451 66.667 11.27 0.0 0.0 4.02 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
18 19 3.834732 TCGCCTGCTTACTTTCTCC 57.165 52.632 0.00 0.00 0.00 3.71
19 20 1.267121 TCGCCTGCTTACTTTCTCCT 58.733 50.000 0.00 0.00 0.00 3.69
20 21 1.623811 TCGCCTGCTTACTTTCTCCTT 59.376 47.619 0.00 0.00 0.00 3.36
21 22 2.038557 TCGCCTGCTTACTTTCTCCTTT 59.961 45.455 0.00 0.00 0.00 3.11
22 23 2.814336 CGCCTGCTTACTTTCTCCTTTT 59.186 45.455 0.00 0.00 0.00 2.27
23 24 3.120165 CGCCTGCTTACTTTCTCCTTTTC 60.120 47.826 0.00 0.00 0.00 2.29
24 25 3.821033 GCCTGCTTACTTTCTCCTTTTCA 59.179 43.478 0.00 0.00 0.00 2.69
25 26 4.320567 GCCTGCTTACTTTCTCCTTTTCAC 60.321 45.833 0.00 0.00 0.00 3.18
26 27 4.821805 CCTGCTTACTTTCTCCTTTTCACA 59.178 41.667 0.00 0.00 0.00 3.58
27 28 5.299279 CCTGCTTACTTTCTCCTTTTCACAA 59.701 40.000 0.00 0.00 0.00 3.33
28 29 6.015940 CCTGCTTACTTTCTCCTTTTCACAAT 60.016 38.462 0.00 0.00 0.00 2.71
29 30 6.738114 TGCTTACTTTCTCCTTTTCACAATG 58.262 36.000 0.00 0.00 0.00 2.82
30 31 6.321181 TGCTTACTTTCTCCTTTTCACAATGT 59.679 34.615 0.00 0.00 0.00 2.71
31 32 6.638468 GCTTACTTTCTCCTTTTCACAATGTG 59.362 38.462 7.12 7.12 34.45 3.21
32 33 7.468631 GCTTACTTTCTCCTTTTCACAATGTGA 60.469 37.037 12.63 12.63 41.09 3.58
47 48 2.684001 TGTGAACCACAGTCTTCGTT 57.316 45.000 0.00 0.00 39.62 3.85
48 49 2.546778 TGTGAACCACAGTCTTCGTTC 58.453 47.619 0.00 0.00 39.62 3.95
49 50 2.093921 TGTGAACCACAGTCTTCGTTCA 60.094 45.455 0.00 0.00 39.62 3.18
50 51 2.540101 GTGAACCACAGTCTTCGTTCAG 59.460 50.000 1.93 0.00 43.74 3.02
51 52 2.429250 TGAACCACAGTCTTCGTTCAGA 59.571 45.455 0.00 0.00 39.61 3.27
52 53 3.118920 TGAACCACAGTCTTCGTTCAGAA 60.119 43.478 0.00 0.00 39.61 3.02
53 54 3.536956 ACCACAGTCTTCGTTCAGAAA 57.463 42.857 0.00 0.00 38.57 2.52
54 55 3.869065 ACCACAGTCTTCGTTCAGAAAA 58.131 40.909 0.00 0.00 38.57 2.29
55 56 4.258543 ACCACAGTCTTCGTTCAGAAAAA 58.741 39.130 0.00 0.00 38.57 1.94
56 57 4.881850 ACCACAGTCTTCGTTCAGAAAAAT 59.118 37.500 0.00 0.00 38.57 1.82
57 58 5.007724 ACCACAGTCTTCGTTCAGAAAAATC 59.992 40.000 0.00 0.00 38.57 2.17
58 59 5.007626 CCACAGTCTTCGTTCAGAAAAATCA 59.992 40.000 0.00 0.00 38.57 2.57
59 60 6.458206 CCACAGTCTTCGTTCAGAAAAATCAA 60.458 38.462 0.00 0.00 38.57 2.57
60 61 6.966632 CACAGTCTTCGTTCAGAAAAATCAAA 59.033 34.615 0.00 0.00 38.57 2.69
61 62 7.484641 CACAGTCTTCGTTCAGAAAAATCAAAA 59.515 33.333 0.00 0.00 38.57 2.44
62 63 8.026607 ACAGTCTTCGTTCAGAAAAATCAAAAA 58.973 29.630 0.00 0.00 38.57 1.94
63 64 9.023967 CAGTCTTCGTTCAGAAAAATCAAAAAT 57.976 29.630 0.00 0.00 38.57 1.82
64 65 9.237846 AGTCTTCGTTCAGAAAAATCAAAAATC 57.762 29.630 0.00 0.00 38.57 2.17
65 66 9.019764 GTCTTCGTTCAGAAAAATCAAAAATCA 57.980 29.630 0.00 0.00 38.57 2.57
66 67 9.579768 TCTTCGTTCAGAAAAATCAAAAATCAA 57.420 25.926 0.00 0.00 38.57 2.57
129 130 2.979814 AAAACAAGGCCAGTTTCCAC 57.020 45.000 21.85 0.00 38.17 4.02
130 131 2.159179 AAACAAGGCCAGTTTCCACT 57.841 45.000 17.60 0.00 34.27 4.00
131 132 1.692411 AACAAGGCCAGTTTCCACTC 58.308 50.000 5.01 0.00 0.00 3.51
132 133 0.178990 ACAAGGCCAGTTTCCACTCC 60.179 55.000 5.01 0.00 0.00 3.85
133 134 0.111253 CAAGGCCAGTTTCCACTCCT 59.889 55.000 5.01 0.00 30.00 3.69
134 135 1.351017 CAAGGCCAGTTTCCACTCCTA 59.649 52.381 5.01 0.00 28.93 2.94
135 136 1.280457 AGGCCAGTTTCCACTCCTAG 58.720 55.000 5.01 0.00 27.50 3.02
136 137 1.203313 AGGCCAGTTTCCACTCCTAGA 60.203 52.381 5.01 0.00 27.50 2.43
137 138 1.208293 GGCCAGTTTCCACTCCTAGAG 59.792 57.143 0.00 0.00 35.52 2.43
139 140 1.902508 CCAGTTTCCACTCCTAGAGCA 59.097 52.381 0.00 0.00 32.04 4.26
140 141 2.303022 CCAGTTTCCACTCCTAGAGCAA 59.697 50.000 0.00 0.00 32.04 3.91
141 142 3.594134 CAGTTTCCACTCCTAGAGCAAG 58.406 50.000 0.00 0.00 32.04 4.01
142 143 3.259374 CAGTTTCCACTCCTAGAGCAAGA 59.741 47.826 0.00 0.00 32.04 3.02
143 144 3.904339 AGTTTCCACTCCTAGAGCAAGAA 59.096 43.478 0.00 0.00 32.04 2.52
144 145 4.348168 AGTTTCCACTCCTAGAGCAAGAAA 59.652 41.667 0.00 0.00 32.04 2.52
145 146 4.974645 TTCCACTCCTAGAGCAAGAAAA 57.025 40.909 0.00 0.00 32.04 2.29
146 147 4.974645 TCCACTCCTAGAGCAAGAAAAA 57.025 40.909 0.00 0.00 32.04 1.94
159 160 3.399330 CAAGAAAAAGACCACGCCTAGA 58.601 45.455 0.00 0.00 0.00 2.43
166 167 0.246635 GACCACGCCTAGAGCAAGAA 59.753 55.000 0.00 0.00 44.04 2.52
167 168 0.685097 ACCACGCCTAGAGCAAGAAA 59.315 50.000 0.00 0.00 44.04 2.52
171 172 3.067106 CACGCCTAGAGCAAGAAAAAGA 58.933 45.455 0.00 0.00 44.04 2.52
172 173 3.498397 CACGCCTAGAGCAAGAAAAAGAA 59.502 43.478 0.00 0.00 44.04 2.52
173 174 3.748568 ACGCCTAGAGCAAGAAAAAGAAG 59.251 43.478 0.00 0.00 44.04 2.85
174 175 3.425492 CGCCTAGAGCAAGAAAAAGAAGC 60.425 47.826 0.00 0.00 44.04 3.86
176 177 3.997021 CCTAGAGCAAGAAAAAGAAGCGA 59.003 43.478 0.00 0.00 0.00 4.93
177 178 4.452455 CCTAGAGCAAGAAAAAGAAGCGAA 59.548 41.667 0.00 0.00 0.00 4.70
191 192 4.810730 CGAAGCAGCAGAGGAGAG 57.189 61.111 0.00 0.00 0.00 3.20
262 269 3.775654 CCCCGAGCTCACCTCCAC 61.776 72.222 15.40 0.00 37.27 4.02
263 270 3.775654 CCCGAGCTCACCTCCACC 61.776 72.222 15.40 0.00 37.27 4.61
265 272 4.135153 CGAGCTCACCTCCACCCG 62.135 72.222 15.40 0.00 37.27 5.28
267 274 2.997897 AGCTCACCTCCACCCGTC 60.998 66.667 0.00 0.00 0.00 4.79
268 275 4.083862 GCTCACCTCCACCCGTCC 62.084 72.222 0.00 0.00 0.00 4.79
269 276 3.760035 CTCACCTCCACCCGTCCG 61.760 72.222 0.00 0.00 0.00 4.79
271 278 3.622826 CACCTCCACCCGTCCGTT 61.623 66.667 0.00 0.00 0.00 4.44
272 279 3.622826 ACCTCCACCCGTCCGTTG 61.623 66.667 0.00 0.00 0.00 4.10
304 323 1.774639 AAGAAAACGTTCGCTCGCTA 58.225 45.000 0.00 0.00 38.90 4.26
319 338 3.121030 CTAGCATATGCCGCGGCC 61.121 66.667 44.42 29.47 43.38 6.13
343 404 3.509575 TCCCGAATTTTGTTGGATTCCTG 59.490 43.478 3.95 0.00 0.00 3.86
353 414 2.438434 GATTCCTGCCCCACCACG 60.438 66.667 0.00 0.00 0.00 4.94
355 416 2.876368 GATTCCTGCCCCACCACGAG 62.876 65.000 0.00 0.00 0.00 4.18
356 417 4.631740 TCCTGCCCCACCACGAGA 62.632 66.667 0.00 0.00 0.00 4.04
357 418 4.394712 CCTGCCCCACCACGAGAC 62.395 72.222 0.00 0.00 0.00 3.36
358 419 4.742201 CTGCCCCACCACGAGACG 62.742 72.222 0.00 0.00 0.00 4.18
380 445 2.031616 CGATGCGATGCCCTCCAT 59.968 61.111 0.00 0.00 36.70 3.41
417 482 1.631072 CGCGATCGTGATCACCAAC 59.369 57.895 23.89 5.45 37.69 3.77
427 492 2.945668 GTGATCACCAACAGATAAGGGC 59.054 50.000 15.31 0.00 0.00 5.19
429 494 0.623723 TCACCAACAGATAAGGGCCC 59.376 55.000 16.46 16.46 0.00 5.80
430 495 0.395724 CACCAACAGATAAGGGCCCC 60.396 60.000 21.43 1.95 0.00 5.80
431 496 1.152963 CCAACAGATAAGGGCCCCG 60.153 63.158 21.43 2.41 0.00 5.73
432 497 1.823899 CAACAGATAAGGGCCCCGC 60.824 63.158 21.43 5.27 0.00 6.13
433 498 2.001269 AACAGATAAGGGCCCCGCT 61.001 57.895 21.43 7.94 0.00 5.52
435 500 2.143419 CAGATAAGGGCCCCGCTCT 61.143 63.158 21.43 15.14 43.58 4.09
436 501 1.839296 AGATAAGGGCCCCGCTCTC 60.839 63.158 21.43 8.80 39.10 3.20
444 509 3.528370 CCCCGCTCTCCGACGAAT 61.528 66.667 0.00 0.00 40.02 3.34
447 512 1.009449 CCGCTCTCCGACGAATCTC 60.009 63.158 0.00 0.00 40.02 2.75
448 513 1.440938 CCGCTCTCCGACGAATCTCT 61.441 60.000 0.00 0.00 40.02 3.10
449 514 0.378962 CGCTCTCCGACGAATCTCTT 59.621 55.000 0.00 0.00 40.02 2.85
450 515 1.202200 CGCTCTCCGACGAATCTCTTT 60.202 52.381 0.00 0.00 40.02 2.52
451 516 2.189342 GCTCTCCGACGAATCTCTTTG 58.811 52.381 0.00 0.00 0.00 2.77
452 517 2.803451 CTCTCCGACGAATCTCTTTGG 58.197 52.381 0.00 0.00 0.00 3.28
453 518 2.164624 CTCTCCGACGAATCTCTTTGGT 59.835 50.000 0.00 0.00 0.00 3.67
454 519 2.561419 TCTCCGACGAATCTCTTTGGTT 59.439 45.455 0.00 0.00 0.00 3.67
455 520 2.924290 CTCCGACGAATCTCTTTGGTTC 59.076 50.000 0.00 0.00 0.00 3.62
622 781 1.237285 CCCTCTCCAAGCACAAACCG 61.237 60.000 0.00 0.00 0.00 4.44
672 842 1.668151 GACACTCGGGACAGGCAAC 60.668 63.158 0.00 0.00 0.00 4.17
784 972 2.351835 GGCACGATATAGCACAGTCGAT 60.352 50.000 8.26 0.00 37.51 3.59
787 975 4.092120 CACGATATAGCACAGTCGATAGC 58.908 47.826 8.26 0.00 37.51 2.97
788 976 4.004314 ACGATATAGCACAGTCGATAGCT 58.996 43.478 8.26 8.51 40.92 3.32
789 977 4.093703 ACGATATAGCACAGTCGATAGCTC 59.906 45.833 7.05 0.00 38.47 4.09
790 978 2.979401 ATAGCACAGTCGATAGCTCG 57.021 50.000 7.05 0.00 46.41 5.03
830 1030 5.789710 TTTTGTTCCGGAATAGATTCGAC 57.210 39.130 22.04 5.06 37.67 4.20
831 1031 3.447918 TGTTCCGGAATAGATTCGACC 57.552 47.619 22.04 3.54 37.67 4.79
837 1037 2.288886 CGGAATAGATTCGACCCCCTTC 60.289 54.545 0.00 0.00 37.67 3.46
883 1084 1.582680 CGCCCATTTTTAGCGCGAC 60.583 57.895 12.10 0.04 45.41 5.19
891 1092 2.165362 TTTTAGCGCGACCGTTGCTG 62.165 55.000 12.10 4.08 39.73 4.41
987 1191 3.839432 GCGAACCGAGGAGGAGGG 61.839 72.222 0.00 0.00 45.00 4.30
989 1193 3.471806 GAACCGAGGAGGAGGGGC 61.472 72.222 0.00 0.00 45.00 5.80
1315 1538 4.253257 GCCGGGACTACGAGCTCG 62.253 72.222 33.45 33.45 46.33 5.03
1396 1637 0.108138 CGTCAAGCCCAGGTAGGAAG 60.108 60.000 0.00 0.00 41.22 3.46
1397 1638 0.253327 GTCAAGCCCAGGTAGGAAGG 59.747 60.000 0.00 0.00 41.22 3.46
1398 1639 0.118346 TCAAGCCCAGGTAGGAAGGA 59.882 55.000 0.00 0.00 41.22 3.36
1457 1698 3.157680 CCCGGGTGTCCTCTGTTT 58.842 61.111 14.18 0.00 0.00 2.83
1556 1797 1.337823 ACAGGTGAGAATTCGGTTCCG 60.338 52.381 4.74 4.74 37.56 4.30
1673 1922 1.440938 CTGGCCAAACGGTTGAACGA 61.441 55.000 16.49 2.63 36.83 3.85
1729 1978 3.181443 TGGTGAGTTCCTCCTTCCTTTTC 60.181 47.826 0.00 0.00 0.00 2.29
1881 2134 7.414984 CCAAGGATGTTGAATTCTCTTCTAAGC 60.415 40.741 7.05 0.00 0.00 3.09
1929 2182 5.015733 GCGATTTACTTGTGAATCTGAACG 58.984 41.667 13.68 4.99 31.63 3.95
1951 2204 3.217626 CTTAAGGGATTGGATGAGTGGC 58.782 50.000 0.00 0.00 0.00 5.01
2010 2266 9.891828 TTGTAGTACTGTTCAAAGCATAATTTG 57.108 29.630 5.39 0.00 40.75 2.32
2028 2284 8.807581 CATAATTTGAAATAAAAAGGTCGGCTC 58.192 33.333 0.00 0.00 0.00 4.70
2054 2310 0.370273 GCCGTCGACAGTTAAGCATG 59.630 55.000 17.16 0.00 0.00 4.06
2065 2321 5.831997 ACAGTTAAGCATGGTTCTTTGTTC 58.168 37.500 14.50 0.00 0.00 3.18
2158 2463 1.600023 AAAAATTCTGGCGACGTGGA 58.400 45.000 0.11 0.00 0.00 4.02
2159 2464 1.600023 AAAATTCTGGCGACGTGGAA 58.400 45.000 0.11 0.00 0.00 3.53
2160 2465 0.872388 AAATTCTGGCGACGTGGAAC 59.128 50.000 0.11 0.00 0.00 3.62
2161 2466 0.953960 AATTCTGGCGACGTGGAACC 60.954 55.000 0.11 0.00 0.00 3.62
2162 2467 2.107041 ATTCTGGCGACGTGGAACCA 62.107 55.000 0.11 0.00 0.00 3.67
2163 2468 2.280524 CTGGCGACGTGGAACCAA 60.281 61.111 0.11 0.00 0.00 3.67
2164 2469 1.671054 CTGGCGACGTGGAACCAAT 60.671 57.895 0.11 0.00 0.00 3.16
2165 2470 1.228003 TGGCGACGTGGAACCAATT 60.228 52.632 0.11 0.00 0.00 2.32
2166 2471 0.820074 TGGCGACGTGGAACCAATTT 60.820 50.000 0.11 0.00 0.00 1.82
2167 2472 0.312729 GGCGACGTGGAACCAATTTT 59.687 50.000 0.11 0.00 0.00 1.82
2168 2473 1.664874 GGCGACGTGGAACCAATTTTC 60.665 52.381 0.11 0.00 0.00 2.29
2169 2474 1.945207 CGACGTGGAACCAATTTTCG 58.055 50.000 0.00 0.00 0.00 3.46
2170 2475 1.527736 CGACGTGGAACCAATTTTCGA 59.472 47.619 0.00 0.00 0.00 3.71
2171 2476 2.660900 CGACGTGGAACCAATTTTCGAC 60.661 50.000 0.00 1.88 32.49 4.20
2172 2477 2.288458 GACGTGGAACCAATTTTCGACA 59.712 45.455 0.00 0.00 34.76 4.35
2173 2478 2.683867 ACGTGGAACCAATTTTCGACAA 59.316 40.909 7.57 0.00 34.76 3.18
2174 2479 3.128938 ACGTGGAACCAATTTTCGACAAA 59.871 39.130 7.57 0.00 34.76 2.83
2175 2480 3.728718 CGTGGAACCAATTTTCGACAAAG 59.271 43.478 0.00 0.00 34.76 2.77
2176 2481 4.048504 GTGGAACCAATTTTCGACAAAGG 58.951 43.478 0.00 5.02 35.08 3.11
2177 2482 3.068873 TGGAACCAATTTTCGACAAAGGG 59.931 43.478 9.93 6.98 0.00 3.95
2178 2483 2.812358 ACCAATTTTCGACAAAGGGC 57.188 45.000 9.93 0.00 0.00 5.19
2179 2484 1.000717 ACCAATTTTCGACAAAGGGCG 60.001 47.619 9.93 0.00 0.00 6.13
2180 2485 1.268352 CCAATTTTCGACAAAGGGCGA 59.732 47.619 0.00 0.00 34.32 5.54
2181 2486 2.315901 CAATTTTCGACAAAGGGCGAC 58.684 47.619 0.00 0.00 36.11 5.19
2182 2487 1.892209 ATTTTCGACAAAGGGCGACT 58.108 45.000 0.00 0.00 36.11 4.18
2183 2488 1.670791 TTTTCGACAAAGGGCGACTT 58.329 45.000 0.00 0.00 42.52 3.01
2197 2502 7.881775 AAGGGCGACTTTATTATCTCAAAAT 57.118 32.000 0.00 0.00 35.35 1.82
2198 2503 7.264373 AGGGCGACTTTATTATCTCAAAATG 57.736 36.000 0.00 0.00 0.00 2.32
2199 2504 6.828785 AGGGCGACTTTATTATCTCAAAATGT 59.171 34.615 0.00 0.00 0.00 2.71
2200 2505 7.990886 AGGGCGACTTTATTATCTCAAAATGTA 59.009 33.333 0.00 0.00 0.00 2.29
2201 2506 8.283291 GGGCGACTTTATTATCTCAAAATGTAG 58.717 37.037 0.00 0.00 0.00 2.74
2202 2507 7.798982 GGCGACTTTATTATCTCAAAATGTAGC 59.201 37.037 0.00 0.00 0.00 3.58
2203 2508 8.335356 GCGACTTTATTATCTCAAAATGTAGCA 58.665 33.333 0.00 0.00 0.00 3.49
2240 2545 6.102615 ACCAATGGTTACCATCATGTATACCT 59.897 38.462 18.03 0.00 44.40 3.08
2248 2576 3.935203 CCATCATGTATACCTTGGCGATC 59.065 47.826 0.00 0.00 0.00 3.69
2267 2595 9.513906 TGGCGATCCATCTTTTATAATGAAATA 57.486 29.630 0.00 0.00 37.47 1.40
2289 2619 1.637553 ACTACTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
2295 2625 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2296 2626 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2299 2629 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2302 2632 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2303 2633 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2304 2634 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2305 2635 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2306 2636 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2307 2637 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2308 2638 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2309 2639 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2310 2640 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2311 2641 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2312 2642 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2334 2664 6.410942 ACTAAAGTTAGTACGAAGTTGGGT 57.589 37.500 9.24 8.43 41.92 4.51
2335 2665 6.450545 ACTAAAGTTAGTACGAAGTTGGGTC 58.549 40.000 9.24 0.00 41.92 4.46
2336 2666 4.942761 AAGTTAGTACGAAGTTGGGTCA 57.057 40.909 7.86 0.00 37.78 4.02
2337 2667 5.479124 AAGTTAGTACGAAGTTGGGTCAT 57.521 39.130 7.86 0.00 37.78 3.06
2338 2668 5.069501 AGTTAGTACGAAGTTGGGTCATC 57.930 43.478 0.00 0.00 37.78 2.92
2344 2753 6.708285 AGTACGAAGTTGGGTCATCTATTTT 58.292 36.000 0.00 0.00 37.78 1.82
2459 2869 1.133976 GGAAGTGATGGTCTCCATGGG 60.134 57.143 13.02 2.57 45.26 4.00
2474 2884 2.224066 CCATGGGTACGTCCAATCTCTC 60.224 54.545 2.85 0.00 40.62 3.20
2486 2896 2.864946 CCAATCTCTCGATCTTGCTGTG 59.135 50.000 0.00 0.00 0.00 3.66
2512 2922 5.591877 AGGACATGGTATGAGCAAAGAAATC 59.408 40.000 0.00 0.00 0.00 2.17
2525 2935 8.035394 TGAGCAAAGAAATCGACTAGTTATTCT 58.965 33.333 0.00 2.47 0.00 2.40
2567 2977 5.927689 TGCACAAATTCTTATTCAAAGGCTG 59.072 36.000 0.00 0.00 0.00 4.85
2570 2980 7.598493 GCACAAATTCTTATTCAAAGGCTGTTA 59.402 33.333 0.00 0.00 0.00 2.41
2737 3151 7.643528 ATTGTGTATGCAACTCGTATATCTG 57.356 36.000 0.00 0.00 0.00 2.90
2746 3160 7.489160 TGCAACTCGTATATCTGATAGTGTTT 58.511 34.615 3.48 0.00 0.00 2.83
2860 3275 1.381928 ATCCTGTCGTCGCGGTATGT 61.382 55.000 6.13 0.00 0.00 2.29
2861 3276 0.744057 TCCTGTCGTCGCGGTATGTA 60.744 55.000 6.13 0.00 0.00 2.29
2862 3277 0.309922 CCTGTCGTCGCGGTATGTAT 59.690 55.000 6.13 0.00 0.00 2.29
2863 3278 1.268896 CCTGTCGTCGCGGTATGTATT 60.269 52.381 6.13 0.00 0.00 1.89
2864 3279 2.041966 CTGTCGTCGCGGTATGTATTC 58.958 52.381 6.13 0.00 0.00 1.75
2865 3280 1.268692 TGTCGTCGCGGTATGTATTCC 60.269 52.381 6.13 0.00 0.00 3.01
2889 3304 4.143263 GCCATTTTGTCGAAAGAAATGCAG 60.143 41.667 17.37 10.22 45.01 4.41
2891 3306 5.344128 CCATTTTGTCGAAAGAAATGCAGAG 59.656 40.000 17.37 6.50 45.01 3.35
2892 3307 4.488126 TTTGTCGAAAGAAATGCAGAGG 57.512 40.909 0.00 0.00 45.01 3.69
2968 3390 2.112815 CCCGGTTTTCGCCCTGATC 61.113 63.158 0.00 0.00 37.59 2.92
3243 3665 2.606519 CTCCACCCCGGACAAGGA 60.607 66.667 0.73 3.64 39.64 3.36
3330 3752 0.798771 GACATCGTCGACTGGCTGAC 60.799 60.000 14.70 2.62 0.00 3.51
3334 3756 4.436998 GTCGACTGGCTGACCCCG 62.437 72.222 8.70 0.00 33.59 5.73
3347 3773 1.486310 TGACCCCGAGGATTTGATCAG 59.514 52.381 0.00 0.00 36.73 2.90
3581 4015 6.366332 CGGGAAGCTGCATTATTAGTAACTAG 59.634 42.308 1.02 0.00 0.00 2.57
3656 4096 2.745492 GCTCTGCTCCCAGTGTGC 60.745 66.667 0.00 0.00 40.09 4.57
3702 4142 3.219281 CCATATTTTTGTCCGGTAGGGG 58.781 50.000 0.00 0.00 38.33 4.79
3703 4143 3.372241 CCATATTTTTGTCCGGTAGGGGT 60.372 47.826 0.00 0.00 38.33 4.95
3721 4161 2.613595 GGGTAAACAAACGTTCGTTCCT 59.386 45.455 4.86 0.00 0.00 3.36
3773 4217 0.618968 AGACGCATTCCTCCCCTCTT 60.619 55.000 0.00 0.00 0.00 2.85
3774 4218 0.253327 GACGCATTCCTCCCCTCTTT 59.747 55.000 0.00 0.00 0.00 2.52
3826 4271 1.483827 TCTCAATCAGAATCTGCGGCT 59.516 47.619 5.18 0.00 0.00 5.52
3840 4287 3.113322 CTGCGGCTGAATTGATTTGATG 58.887 45.455 0.00 0.00 0.00 3.07
3841 4288 2.159212 TGCGGCTGAATTGATTTGATGG 60.159 45.455 0.00 0.00 0.00 3.51
3842 4289 2.099592 GCGGCTGAATTGATTTGATGGA 59.900 45.455 0.00 0.00 0.00 3.41
3843 4290 3.699067 CGGCTGAATTGATTTGATGGAC 58.301 45.455 0.00 0.00 0.00 4.02
4007 4499 2.464459 GCACGATTTCTCTGGCCGG 61.464 63.158 4.71 4.71 0.00 6.13
4066 4574 1.891811 TGAGAGCTGAGAGTGGACAAG 59.108 52.381 0.00 0.00 0.00 3.16
4220 4743 1.756367 GGCTAACTCTATCGTGACGC 58.244 55.000 0.00 0.00 0.00 5.19
4222 4745 1.920705 GCTAACTCTATCGTGACGCGG 60.921 57.143 12.47 0.00 41.72 6.46
4249 5020 1.402984 GGCTATCGGGTGATTAGCTCG 60.403 57.143 0.00 0.00 35.99 5.03
4253 5024 1.300233 CGGGTGATTAGCTCGGCTC 60.300 63.158 1.46 0.00 40.44 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.267121 AGGAGAAAGTAAGCAGGCGA 58.733 50.000 0.00 0.00 0.00 5.54
1 2 2.100605 AAGGAGAAAGTAAGCAGGCG 57.899 50.000 0.00 0.00 0.00 5.52
3 4 4.821805 TGTGAAAAGGAGAAAGTAAGCAGG 59.178 41.667 0.00 0.00 0.00 4.85
4 5 6.377327 TTGTGAAAAGGAGAAAGTAAGCAG 57.623 37.500 0.00 0.00 0.00 4.24
5 6 6.321181 ACATTGTGAAAAGGAGAAAGTAAGCA 59.679 34.615 0.00 0.00 0.00 3.91
6 7 6.638468 CACATTGTGAAAAGGAGAAAGTAAGC 59.362 38.462 11.45 0.00 35.23 3.09
7 8 7.930217 TCACATTGTGAAAAGGAGAAAGTAAG 58.070 34.615 16.95 0.00 39.78 2.34
8 9 7.873719 TCACATTGTGAAAAGGAGAAAGTAA 57.126 32.000 16.95 0.00 39.78 2.24
22 23 3.558931 AGACTGTGGTTCACATTGTGA 57.441 42.857 15.41 15.41 43.71 3.58
23 24 3.303329 CGAAGACTGTGGTTCACATTGTG 60.303 47.826 10.64 10.64 43.71 3.33
24 25 2.872245 CGAAGACTGTGGTTCACATTGT 59.128 45.455 0.98 0.00 43.71 2.71
25 26 2.872245 ACGAAGACTGTGGTTCACATTG 59.128 45.455 0.98 0.00 43.71 2.82
26 27 3.194005 ACGAAGACTGTGGTTCACATT 57.806 42.857 0.98 0.00 43.71 2.71
27 28 2.910688 ACGAAGACTGTGGTTCACAT 57.089 45.000 0.98 0.00 43.71 3.21
28 29 2.093921 TGAACGAAGACTGTGGTTCACA 60.094 45.455 10.50 0.67 42.56 3.58
29 30 2.540101 CTGAACGAAGACTGTGGTTCAC 59.460 50.000 10.50 0.00 42.56 3.18
30 31 2.429250 TCTGAACGAAGACTGTGGTTCA 59.571 45.455 12.78 12.78 44.49 3.18
31 32 3.093717 TCTGAACGAAGACTGTGGTTC 57.906 47.619 0.00 6.60 39.29 3.62
32 33 3.536956 TTCTGAACGAAGACTGTGGTT 57.463 42.857 0.00 0.00 0.00 3.67
33 34 3.536956 TTTCTGAACGAAGACTGTGGT 57.463 42.857 0.00 0.00 32.21 4.16
34 35 4.875544 TTTTTCTGAACGAAGACTGTGG 57.124 40.909 0.00 0.00 32.21 4.17
35 36 6.048073 TGATTTTTCTGAACGAAGACTGTG 57.952 37.500 0.00 0.00 32.21 3.66
36 37 6.677781 TTGATTTTTCTGAACGAAGACTGT 57.322 33.333 0.00 0.00 32.21 3.55
37 38 7.969387 TTTTGATTTTTCTGAACGAAGACTG 57.031 32.000 0.00 0.00 32.21 3.51
38 39 9.237846 GATTTTTGATTTTTCTGAACGAAGACT 57.762 29.630 0.00 0.00 32.21 3.24
39 40 9.019764 TGATTTTTGATTTTTCTGAACGAAGAC 57.980 29.630 0.00 0.00 32.21 3.01
40 41 9.579768 TTGATTTTTGATTTTTCTGAACGAAGA 57.420 25.926 0.00 0.00 32.21 2.87
77 78 3.547746 TGGTAAGCAAATTCGGGTATCC 58.452 45.455 0.00 0.00 0.00 2.59
78 79 5.278315 GGATTGGTAAGCAAATTCGGGTATC 60.278 44.000 0.00 0.00 0.00 2.24
79 80 4.583073 GGATTGGTAAGCAAATTCGGGTAT 59.417 41.667 0.00 0.00 0.00 2.73
80 81 3.949113 GGATTGGTAAGCAAATTCGGGTA 59.051 43.478 0.00 0.00 0.00 3.69
81 82 2.758423 GGATTGGTAAGCAAATTCGGGT 59.242 45.455 0.00 0.00 0.00 5.28
86 87 5.543507 TGTGTTGGATTGGTAAGCAAATT 57.456 34.783 0.00 0.00 0.00 1.82
121 122 3.511477 TCTTGCTCTAGGAGTGGAAACT 58.489 45.455 0.00 0.00 31.39 2.66
125 126 4.593206 TCTTTTTCTTGCTCTAGGAGTGGA 59.407 41.667 0.00 0.00 31.39 4.02
126 127 4.693095 GTCTTTTTCTTGCTCTAGGAGTGG 59.307 45.833 0.00 0.00 31.39 4.00
127 128 4.693095 GGTCTTTTTCTTGCTCTAGGAGTG 59.307 45.833 0.00 0.00 31.39 3.51
129 130 4.693095 GTGGTCTTTTTCTTGCTCTAGGAG 59.307 45.833 0.00 0.00 0.00 3.69
130 131 4.642429 GTGGTCTTTTTCTTGCTCTAGGA 58.358 43.478 0.00 0.00 0.00 2.94
131 132 3.433615 CGTGGTCTTTTTCTTGCTCTAGG 59.566 47.826 0.00 0.00 0.00 3.02
132 133 3.120511 GCGTGGTCTTTTTCTTGCTCTAG 60.121 47.826 0.00 0.00 0.00 2.43
133 134 2.806244 GCGTGGTCTTTTTCTTGCTCTA 59.194 45.455 0.00 0.00 0.00 2.43
134 135 1.604278 GCGTGGTCTTTTTCTTGCTCT 59.396 47.619 0.00 0.00 0.00 4.09
135 136 1.335051 GGCGTGGTCTTTTTCTTGCTC 60.335 52.381 0.00 0.00 0.00 4.26
136 137 0.668535 GGCGTGGTCTTTTTCTTGCT 59.331 50.000 0.00 0.00 0.00 3.91
137 138 0.668535 AGGCGTGGTCTTTTTCTTGC 59.331 50.000 0.00 0.00 0.00 4.01
139 140 3.665190 CTCTAGGCGTGGTCTTTTTCTT 58.335 45.455 0.00 0.00 0.00 2.52
140 141 2.613223 GCTCTAGGCGTGGTCTTTTTCT 60.613 50.000 0.00 0.00 0.00 2.52
141 142 1.732809 GCTCTAGGCGTGGTCTTTTTC 59.267 52.381 0.00 0.00 0.00 2.29
142 143 1.071699 TGCTCTAGGCGTGGTCTTTTT 59.928 47.619 0.00 0.00 45.43 1.94
143 144 0.685097 TGCTCTAGGCGTGGTCTTTT 59.315 50.000 0.00 0.00 45.43 2.27
144 145 0.685097 TTGCTCTAGGCGTGGTCTTT 59.315 50.000 0.00 0.00 45.43 2.52
145 146 0.247736 CTTGCTCTAGGCGTGGTCTT 59.752 55.000 0.00 0.00 45.43 3.01
146 147 0.612174 TCTTGCTCTAGGCGTGGTCT 60.612 55.000 0.00 0.00 45.43 3.85
159 160 2.358898 TGCTTCGCTTCTTTTTCTTGCT 59.641 40.909 0.00 0.00 0.00 3.91
166 167 1.534595 CTCTGCTGCTTCGCTTCTTTT 59.465 47.619 0.00 0.00 0.00 2.27
167 168 1.155042 CTCTGCTGCTTCGCTTCTTT 58.845 50.000 0.00 0.00 0.00 2.52
171 172 1.079266 CTCCTCTGCTGCTTCGCTT 60.079 57.895 0.00 0.00 0.00 4.68
172 173 1.947597 CTCTCCTCTGCTGCTTCGCT 61.948 60.000 0.00 0.00 0.00 4.93
173 174 1.519013 CTCTCCTCTGCTGCTTCGC 60.519 63.158 0.00 0.00 0.00 4.70
174 175 0.529833 TTCTCTCCTCTGCTGCTTCG 59.470 55.000 0.00 0.00 0.00 3.79
176 177 1.338960 GCTTTCTCTCCTCTGCTGCTT 60.339 52.381 0.00 0.00 0.00 3.91
177 178 0.249955 GCTTTCTCTCCTCTGCTGCT 59.750 55.000 0.00 0.00 0.00 4.24
179 180 2.075338 GTTGCTTTCTCTCCTCTGCTG 58.925 52.381 0.00 0.00 0.00 4.41
180 181 1.696336 TGTTGCTTTCTCTCCTCTGCT 59.304 47.619 0.00 0.00 0.00 4.24
181 182 2.175878 TGTTGCTTTCTCTCCTCTGC 57.824 50.000 0.00 0.00 0.00 4.26
182 183 3.059325 CGTTTGTTGCTTTCTCTCCTCTG 60.059 47.826 0.00 0.00 0.00 3.35
183 184 3.134458 CGTTTGTTGCTTTCTCTCCTCT 58.866 45.455 0.00 0.00 0.00 3.69
184 185 2.349912 GCGTTTGTTGCTTTCTCTCCTC 60.350 50.000 0.00 0.00 0.00 3.71
185 186 1.604278 GCGTTTGTTGCTTTCTCTCCT 59.396 47.619 0.00 0.00 0.00 3.69
186 187 1.335051 GGCGTTTGTTGCTTTCTCTCC 60.335 52.381 0.00 0.00 0.00 3.71
187 188 1.660333 CGGCGTTTGTTGCTTTCTCTC 60.660 52.381 0.00 0.00 0.00 3.20
188 189 0.307760 CGGCGTTTGTTGCTTTCTCT 59.692 50.000 0.00 0.00 0.00 3.10
189 190 1.268778 GCGGCGTTTGTTGCTTTCTC 61.269 55.000 9.37 0.00 0.00 2.87
190 191 1.299089 GCGGCGTTTGTTGCTTTCT 60.299 52.632 9.37 0.00 0.00 2.52
191 192 1.587613 TGCGGCGTTTGTTGCTTTC 60.588 52.632 9.37 0.00 0.00 2.62
252 259 3.760035 CGGACGGGTGGAGGTGAG 61.760 72.222 0.00 0.00 0.00 3.51
258 265 2.888464 TTTTGCAACGGACGGGTGGA 62.888 55.000 0.00 0.00 0.00 4.02
259 266 2.005960 TTTTTGCAACGGACGGGTGG 62.006 55.000 0.00 0.00 0.00 4.61
261 268 3.921521 TTTTTGCAACGGACGGGT 58.078 50.000 0.00 0.00 0.00 5.28
281 295 2.098542 GCGAGCGAACGTTTTCTTTTTG 60.099 45.455 0.46 0.00 35.59 2.44
316 335 0.246360 CAACAAAATTCGGGAGGGCC 59.754 55.000 0.00 0.00 0.00 5.80
319 338 3.119137 GGAATCCAACAAAATTCGGGAGG 60.119 47.826 0.00 0.00 33.57 4.30
359 420 4.592192 AGGGCATCGCATCGTCGG 62.592 66.667 0.00 0.00 0.00 4.79
361 422 2.663188 GGAGGGCATCGCATCGTC 60.663 66.667 0.00 0.00 0.00 4.20
380 445 3.978491 GGCTCGCATCGGATCGGA 61.978 66.667 5.34 5.34 0.00 4.55
406 471 2.945668 GCCCTTATCTGTTGGTGATCAC 59.054 50.000 17.91 17.91 0.00 3.06
407 472 2.092429 GGCCCTTATCTGTTGGTGATCA 60.092 50.000 0.00 0.00 0.00 2.92
417 482 2.105806 GAGAGCGGGGCCCTTATCTG 62.106 65.000 24.38 4.53 0.00 2.90
427 492 3.486252 GATTCGTCGGAGAGCGGGG 62.486 68.421 0.00 0.00 36.95 5.73
429 494 1.009449 GAGATTCGTCGGAGAGCGG 60.009 63.158 0.00 0.00 36.95 5.52
430 495 0.378962 AAGAGATTCGTCGGAGAGCG 59.621 55.000 0.00 0.00 36.95 5.03
431 496 2.189342 CAAAGAGATTCGTCGGAGAGC 58.811 52.381 0.00 0.00 36.95 4.09
432 497 2.164624 ACCAAAGAGATTCGTCGGAGAG 59.835 50.000 0.00 0.00 36.95 3.20
433 498 2.168496 ACCAAAGAGATTCGTCGGAGA 58.832 47.619 0.00 0.00 0.00 3.71
435 500 2.353406 GGAACCAAAGAGATTCGTCGGA 60.353 50.000 0.00 0.00 0.00 4.55
436 501 2.000447 GGAACCAAAGAGATTCGTCGG 59.000 52.381 0.00 0.00 0.00 4.79
438 503 4.177783 GAGAGGAACCAAAGAGATTCGTC 58.822 47.826 0.00 0.00 37.46 4.20
441 506 3.371059 GGGGAGAGGAACCAAAGAGATTC 60.371 52.174 0.00 0.00 0.00 2.52
442 507 2.578480 GGGGAGAGGAACCAAAGAGATT 59.422 50.000 0.00 0.00 0.00 2.40
443 508 2.200955 GGGGAGAGGAACCAAAGAGAT 58.799 52.381 0.00 0.00 0.00 2.75
444 509 1.152271 AGGGGAGAGGAACCAAAGAGA 59.848 52.381 0.00 0.00 0.00 3.10
447 512 0.329596 CCAGGGGAGAGGAACCAAAG 59.670 60.000 0.00 0.00 0.00 2.77
448 513 1.789576 GCCAGGGGAGAGGAACCAAA 61.790 60.000 0.00 0.00 0.00 3.28
449 514 2.231380 GCCAGGGGAGAGGAACCAA 61.231 63.158 0.00 0.00 0.00 3.67
450 515 2.610859 GCCAGGGGAGAGGAACCA 60.611 66.667 0.00 0.00 0.00 3.67
451 516 3.787001 CGCCAGGGGAGAGGAACC 61.787 72.222 0.00 0.00 0.00 3.62
452 517 4.475135 GCGCCAGGGGAGAGGAAC 62.475 72.222 7.95 0.00 0.00 3.62
622 781 2.718563 AGAGGAGAAGAAGTCGAGTCC 58.281 52.381 0.00 0.00 0.00 3.85
672 842 1.152368 GAGCTGGGGATGGATTGGG 59.848 63.158 0.00 0.00 0.00 4.12
744 928 4.033776 TCTTTCGGCTGGGCTGGG 62.034 66.667 0.00 0.00 35.34 4.45
767 951 4.583426 GAGCTATCGACTGTGCTATATCG 58.417 47.826 0.00 0.00 35.76 2.92
830 1030 1.754234 CGCAAGAATGGGAAGGGGG 60.754 63.158 0.00 0.00 41.79 5.40
831 1031 1.754234 CCGCAAGAATGGGAAGGGG 60.754 63.158 0.00 0.00 41.79 4.79
837 1037 2.046314 ACCGACCGCAAGAATGGG 60.046 61.111 0.00 0.00 43.02 4.00
891 1092 1.581447 CAACAAAAGCTCTCGGGCC 59.419 57.895 0.00 0.00 0.00 5.80
941 1142 3.103911 GACGCACAAGGACCGTCG 61.104 66.667 0.00 0.00 41.32 5.12
943 1144 2.029073 CAGACGCACAAGGACCGT 59.971 61.111 0.00 0.00 37.99 4.83
1396 1637 3.181487 CGTGGATTTGTTGGATGGATTCC 60.181 47.826 0.00 0.00 45.69 3.01
1397 1638 3.734902 GCGTGGATTTGTTGGATGGATTC 60.735 47.826 0.00 0.00 0.00 2.52
1398 1639 2.166254 GCGTGGATTTGTTGGATGGATT 59.834 45.455 0.00 0.00 0.00 3.01
1405 1646 4.034975 ACAAATTTTGCGTGGATTTGTTGG 59.965 37.500 9.04 0.00 46.24 3.77
1457 1698 1.164411 AAATGATCAGCACGGCGAAA 58.836 45.000 16.62 0.00 0.00 3.46
1497 1738 0.884704 GACAAGAACAAGCGCCCTGA 60.885 55.000 13.61 0.00 0.00 3.86
1673 1922 3.701040 GCCATAAACCTTGACATCCATGT 59.299 43.478 0.00 0.00 45.16 3.21
1763 2012 7.684670 GCACTAACACATACTCCTAGTAAGCAT 60.685 40.741 0.00 0.00 33.89 3.79
1764 2013 6.405508 GCACTAACACATACTCCTAGTAAGCA 60.406 42.308 0.00 0.00 33.89 3.91
1765 2014 5.978322 GCACTAACACATACTCCTAGTAAGC 59.022 44.000 0.00 0.00 33.89 3.09
1835 2085 6.929049 CCTTGGTATCTTCTATACGCAATTCA 59.071 38.462 0.00 0.00 0.00 2.57
1836 2086 7.152645 TCCTTGGTATCTTCTATACGCAATTC 58.847 38.462 0.00 0.00 0.00 2.17
1837 2087 7.062749 TCCTTGGTATCTTCTATACGCAATT 57.937 36.000 0.00 0.00 0.00 2.32
1848 2098 7.772757 AGAGAATTCAACATCCTTGGTATCTTC 59.227 37.037 8.44 0.00 0.00 2.87
1853 2103 7.020827 AGAAGAGAATTCAACATCCTTGGTA 57.979 36.000 8.44 0.00 0.00 3.25
1881 2134 6.995091 CCTTAATTCATTCAGTCTAGGGGAAG 59.005 42.308 0.00 0.00 0.00 3.46
1929 2182 3.217626 CCACTCATCCAATCCCTTAAGC 58.782 50.000 0.00 0.00 0.00 3.09
1976 2230 8.947115 GCTTTGAACAGTACTACAATTCCTTAT 58.053 33.333 0.00 0.00 0.00 1.73
2010 2266 7.509797 CAAAAATGAGCCGACCTTTTTATTTC 58.490 34.615 0.00 0.00 31.53 2.17
2028 2284 2.399396 AACTGTCGACGGCAAAAATG 57.601 45.000 24.25 0.00 0.00 2.32
2054 2310 2.165437 TGCCAACACAGAACAAAGAACC 59.835 45.455 0.00 0.00 0.00 3.62
2065 2321 1.338973 ACAGCTTGATTGCCAACACAG 59.661 47.619 0.00 0.00 0.00 3.66
2143 2448 1.375523 GGTTCCACGTCGCCAGAAT 60.376 57.895 0.00 0.00 0.00 2.40
2150 2455 1.527736 TCGAAAATTGGTTCCACGTCG 59.472 47.619 0.00 0.00 0.00 5.12
2157 2462 3.057019 GCCCTTTGTCGAAAATTGGTTC 58.943 45.455 5.75 0.00 0.00 3.62
2158 2463 2.544903 CGCCCTTTGTCGAAAATTGGTT 60.545 45.455 5.75 0.00 0.00 3.67
2159 2464 1.000717 CGCCCTTTGTCGAAAATTGGT 60.001 47.619 5.75 0.00 0.00 3.67
2160 2465 1.268352 TCGCCCTTTGTCGAAAATTGG 59.732 47.619 0.00 0.00 0.00 3.16
2161 2466 2.031157 AGTCGCCCTTTGTCGAAAATTG 60.031 45.455 0.00 0.00 36.41 2.32
2162 2467 2.227194 AGTCGCCCTTTGTCGAAAATT 58.773 42.857 0.00 0.00 36.41 1.82
2163 2468 1.892209 AGTCGCCCTTTGTCGAAAAT 58.108 45.000 0.00 0.00 36.41 1.82
2164 2469 1.670791 AAGTCGCCCTTTGTCGAAAA 58.329 45.000 0.00 0.00 36.41 2.29
2165 2470 1.670791 AAAGTCGCCCTTTGTCGAAA 58.329 45.000 0.00 0.00 41.86 3.46
2166 2471 2.529780 TAAAGTCGCCCTTTGTCGAA 57.470 45.000 9.37 0.00 43.27 3.71
2167 2472 2.754946 ATAAAGTCGCCCTTTGTCGA 57.245 45.000 9.37 0.00 43.27 4.20
2168 2473 4.809426 AGATAATAAAGTCGCCCTTTGTCG 59.191 41.667 9.37 0.00 43.27 4.35
2169 2474 5.815740 TGAGATAATAAAGTCGCCCTTTGTC 59.184 40.000 9.37 4.21 43.27 3.18
2170 2475 5.741011 TGAGATAATAAAGTCGCCCTTTGT 58.259 37.500 9.37 1.66 43.27 2.83
2171 2476 6.677781 TTGAGATAATAAAGTCGCCCTTTG 57.322 37.500 9.37 0.00 43.27 2.77
2172 2477 7.696992 TTTTGAGATAATAAAGTCGCCCTTT 57.303 32.000 5.44 5.44 45.36 3.11
2173 2478 7.339466 ACATTTTGAGATAATAAAGTCGCCCTT 59.661 33.333 0.00 0.00 33.79 3.95
2174 2479 6.828785 ACATTTTGAGATAATAAAGTCGCCCT 59.171 34.615 0.00 0.00 0.00 5.19
2175 2480 7.027778 ACATTTTGAGATAATAAAGTCGCCC 57.972 36.000 0.00 0.00 0.00 6.13
2176 2481 7.798982 GCTACATTTTGAGATAATAAAGTCGCC 59.201 37.037 0.00 0.00 0.00 5.54
2177 2482 8.335356 TGCTACATTTTGAGATAATAAAGTCGC 58.665 33.333 0.00 0.00 0.00 5.19
2184 2489 8.498358 CGCTTGATGCTACATTTTGAGATAATA 58.502 33.333 0.00 0.00 40.11 0.98
2185 2490 7.358066 CGCTTGATGCTACATTTTGAGATAAT 58.642 34.615 0.00 0.00 40.11 1.28
2186 2491 6.238456 CCGCTTGATGCTACATTTTGAGATAA 60.238 38.462 0.00 0.00 40.11 1.75
2187 2492 5.237127 CCGCTTGATGCTACATTTTGAGATA 59.763 40.000 0.00 0.00 40.11 1.98
2188 2493 4.036027 CCGCTTGATGCTACATTTTGAGAT 59.964 41.667 0.00 0.00 40.11 2.75
2189 2494 3.374988 CCGCTTGATGCTACATTTTGAGA 59.625 43.478 0.00 0.00 40.11 3.27
2190 2495 3.374988 TCCGCTTGATGCTACATTTTGAG 59.625 43.478 0.00 0.00 40.11 3.02
2191 2496 3.342719 TCCGCTTGATGCTACATTTTGA 58.657 40.909 0.00 0.00 40.11 2.69
2192 2497 3.763097 TCCGCTTGATGCTACATTTTG 57.237 42.857 0.00 0.00 40.11 2.44
2193 2498 5.221048 GGTTATCCGCTTGATGCTACATTTT 60.221 40.000 0.00 0.00 40.11 1.82
2194 2499 4.275936 GGTTATCCGCTTGATGCTACATTT 59.724 41.667 0.00 0.00 40.11 2.32
2195 2500 3.815401 GGTTATCCGCTTGATGCTACATT 59.185 43.478 0.00 0.00 40.11 2.71
2196 2501 3.181455 TGGTTATCCGCTTGATGCTACAT 60.181 43.478 0.00 0.00 40.11 2.29
2197 2502 2.169561 TGGTTATCCGCTTGATGCTACA 59.830 45.455 0.00 0.00 40.11 2.74
2198 2503 2.833794 TGGTTATCCGCTTGATGCTAC 58.166 47.619 0.00 0.00 40.11 3.58
2199 2504 3.552132 TTGGTTATCCGCTTGATGCTA 57.448 42.857 0.00 0.00 40.11 3.49
2200 2505 2.418368 TTGGTTATCCGCTTGATGCT 57.582 45.000 0.00 0.00 40.11 3.79
2201 2506 2.287788 CCATTGGTTATCCGCTTGATGC 60.288 50.000 0.00 0.00 34.76 3.91
2202 2507 2.951642 ACCATTGGTTATCCGCTTGATG 59.048 45.455 1.37 0.00 34.76 3.07
2203 2508 3.297134 ACCATTGGTTATCCGCTTGAT 57.703 42.857 1.37 0.00 37.49 2.57
2204 2509 2.799126 ACCATTGGTTATCCGCTTGA 57.201 45.000 1.37 0.00 36.30 3.02
2213 2518 7.940137 GGTATACATGATGGTAACCATTGGTTA 59.060 37.037 21.76 21.76 45.26 2.85
2267 2595 3.095332 GGAACGGAGGGAGTAGTAGTTT 58.905 50.000 0.00 0.00 0.00 2.66
2283 2613 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2310 2640 7.230510 TGACCCAACTTCGTACTAACTTTAGTA 59.769 37.037 4.98 4.98 43.36 1.82
2311 2641 6.040842 TGACCCAACTTCGTACTAACTTTAGT 59.959 38.462 6.85 6.85 45.39 2.24
2312 2642 6.449698 TGACCCAACTTCGTACTAACTTTAG 58.550 40.000 0.00 0.00 36.82 1.85
2314 2644 5.280654 TGACCCAACTTCGTACTAACTTT 57.719 39.130 0.00 0.00 0.00 2.66
2317 2647 5.069501 AGATGACCCAACTTCGTACTAAC 57.930 43.478 0.00 0.00 0.00 2.34
2318 2648 7.414222 AATAGATGACCCAACTTCGTACTAA 57.586 36.000 0.00 0.00 0.00 2.24
2319 2649 7.414222 AAATAGATGACCCAACTTCGTACTA 57.586 36.000 0.00 0.00 0.00 1.82
2320 2650 5.934402 AATAGATGACCCAACTTCGTACT 57.066 39.130 0.00 0.00 0.00 2.73
2321 2651 6.183360 CCAAAATAGATGACCCAACTTCGTAC 60.183 42.308 0.00 0.00 0.00 3.67
2322 2652 5.878116 CCAAAATAGATGACCCAACTTCGTA 59.122 40.000 0.00 0.00 0.00 3.43
2325 2655 6.621613 GTTCCAAAATAGATGACCCAACTTC 58.378 40.000 0.00 0.00 0.00 3.01
2327 2657 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2328 2658 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2330 2660 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2331 2661 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2334 2664 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2335 2665 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2336 2666 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2337 2667 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2338 2668 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2344 2753 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2377 2786 7.821652 ACAGTAGATACGTATCATCATGGAAG 58.178 38.462 31.52 15.84 35.17 3.46
2398 2807 3.074412 CAAAATCGCCAGGTTAGACAGT 58.926 45.455 0.00 0.00 0.00 3.55
2474 2884 0.671472 TGTCCTGCACAGCAAGATCG 60.671 55.000 0.00 0.00 38.41 3.69
2486 2896 2.042686 TTGCTCATACCATGTCCTGC 57.957 50.000 0.00 0.00 0.00 4.85
2525 2935 6.048732 TGTGCAGATGGTCTTAGATAACAA 57.951 37.500 0.00 0.00 0.00 2.83
2534 2944 7.177216 TGAATAAGAATTTGTGCAGATGGTCTT 59.823 33.333 8.04 8.04 0.00 3.01
2579 2989 8.206325 TCTTCTTCAGATACATTTTCTGCATC 57.794 34.615 0.00 0.00 40.35 3.91
2737 3151 7.488150 GCCTATAGCCAAAACAAAAACACTATC 59.512 37.037 0.00 0.00 34.35 2.08
2746 3160 3.056891 GCACAGCCTATAGCCAAAACAAA 60.057 43.478 0.00 0.00 45.47 2.83
2830 3245 4.329545 ACAGGATGCGCGGGTTGT 62.330 61.111 8.83 1.89 42.53 3.32
2860 3275 4.004314 TCTTTCGACAAAATGGCGGAATA 58.996 39.130 5.68 0.00 46.70 1.75
2861 3276 2.817258 TCTTTCGACAAAATGGCGGAAT 59.183 40.909 5.68 0.00 46.70 3.01
2866 3281 3.740321 TGCATTTCTTTCGACAAAATGGC 59.260 39.130 19.75 14.79 39.59 4.40
2867 3282 5.221880 TCTGCATTTCTTTCGACAAAATGG 58.778 37.500 19.75 10.10 39.59 3.16
2868 3283 5.344128 CCTCTGCATTTCTTTCGACAAAATG 59.656 40.000 16.40 16.40 41.26 2.32
2869 3284 5.241506 TCCTCTGCATTTCTTTCGACAAAAT 59.758 36.000 0.00 0.00 0.00 1.82
2889 3304 7.592903 GTCAATTTGTTTCTGAAGATGTTCCTC 59.407 37.037 0.00 0.00 0.00 3.71
2891 3306 7.380602 CAGTCAATTTGTTTCTGAAGATGTTCC 59.619 37.037 0.00 0.00 0.00 3.62
2892 3307 8.131100 TCAGTCAATTTGTTTCTGAAGATGTTC 58.869 33.333 14.17 0.00 33.18 3.18
2968 3390 4.430765 AACTGGTACCGAGGCGCG 62.431 66.667 7.57 0.00 40.47 6.86
3243 3665 3.108343 CGTCGTAGAGCCGGATGT 58.892 61.111 5.05 0.00 36.95 3.06
3330 3752 0.536006 GCCTGATCAAATCCTCGGGG 60.536 60.000 0.00 0.00 38.21 5.73
3334 3756 0.181350 ACCCGCCTGATCAAATCCTC 59.819 55.000 0.00 0.00 0.00 3.71
3396 3822 4.451150 GCTCGGCGATGTGGTCCA 62.451 66.667 11.27 0.00 0.00 4.02
3440 3872 2.125106 GTCATCACCGGCAGGGAC 60.125 66.667 8.08 0.51 43.47 4.46
3581 4015 3.240069 CCACACGTACTAGTTGTAGTGC 58.760 50.000 0.00 0.00 39.96 4.40
3656 4096 0.108329 AAACATAGCTCGGGGACACG 60.108 55.000 0.00 0.00 0.00 4.49
3702 4142 4.496539 CCAAAGGAACGAACGTTTGTTTAC 59.503 41.667 29.65 24.62 41.18 2.01
3703 4143 4.394300 TCCAAAGGAACGAACGTTTGTTTA 59.606 37.500 29.65 10.91 41.18 2.01
3721 4161 3.552384 ACACCGGGCGACTCCAAA 61.552 61.111 6.32 0.00 36.21 3.28
3773 4217 1.028905 CAGAAAAACGACCCCTGCAA 58.971 50.000 0.00 0.00 0.00 4.08
3774 4218 1.452145 GCAGAAAAACGACCCCTGCA 61.452 55.000 0.00 0.00 46.68 4.41
3826 4271 6.720748 TCAAGGAAGTCCATCAAATCAATTCA 59.279 34.615 0.00 0.00 38.89 2.57
3857 4304 8.579850 ACAAATACACATTGTGACAAGGATAT 57.420 30.769 23.12 10.60 39.43 1.63
3859 4306 6.899393 ACAAATACACATTGTGACAAGGAT 57.101 33.333 23.12 6.84 39.43 3.24
3989 4481 2.464459 CCGGCCAGAGAAATCGTGC 61.464 63.158 2.24 0.00 0.00 5.34
3992 4484 0.528684 GAGTCCGGCCAGAGAAATCG 60.529 60.000 2.24 0.00 0.00 3.34
4007 4499 1.733399 GTGGACAGAACCGCGAGTC 60.733 63.158 8.23 3.90 0.00 3.36
4052 4560 1.202687 TGCCAACTTGTCCACTCTCAG 60.203 52.381 0.00 0.00 0.00 3.35
4054 4562 1.604278 GTTGCCAACTTGTCCACTCTC 59.396 52.381 0.00 0.00 0.00 3.20
4055 4563 1.064758 TGTTGCCAACTTGTCCACTCT 60.065 47.619 9.30 0.00 0.00 3.24
4056 4564 1.065551 GTGTTGCCAACTTGTCCACTC 59.934 52.381 9.30 0.00 0.00 3.51
4066 4574 1.687494 TTTTTGCGCGTGTTGCCAAC 61.687 50.000 8.43 0.00 42.08 3.77
4220 4743 3.671411 CCGATAGCCGACCTCCCG 61.671 72.222 0.00 0.00 41.76 5.14
4222 4745 2.521224 ACCCGATAGCCGACCTCC 60.521 66.667 0.00 0.00 41.76 4.30


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

AutoCloner maintained by Alex Coulton.