Multiple sequence alignment - TraesCS7B01G377200

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 TraesCS7B01G377200 chr7B 100.000 2747 0 0 1 2747 642078003 642075257 0.000000e+00 5073.0
1 TraesCS7B01G377200 chr7B 84.509 723 72 14 1382 2078 641554873 641555581 0.000000e+00 678.0
2 TraesCS7B01G377200 chr7B 90.929 463 25 5 893 1345 641460556 641461011 8.410000e-170 606.0
3 TraesCS7B01G377200 chr7B 82.803 692 61 22 185 834 641459870 641460545 1.430000e-157 566.0
4 TraesCS7B01G377200 chr7B 82.662 571 91 6 1080 1646 641368976 641369542 1.470000e-137 499.0
5 TraesCS7B01G377200 chr7B 90.503 179 15 1 1 177 641459650 641459828 4.570000e-58 235.0
6 TraesCS7B01G377200 chr7B 77.089 371 49 19 528 890 641742571 641742229 6.040000e-42 182.0
7 TraesCS7B01G377200 chr7B 80.645 186 25 7 1 175 641367831 641368016 1.720000e-27 134.0
8 TraesCS7B01G377200 chr7B 73.315 371 52 23 528 890 641368438 641368769 2.910000e-15 93.5
9 TraesCS7B01G377200 chr7A 89.495 2275 141 43 1 2194 670343369 670341112 0.000000e+00 2787.0
10 TraesCS7B01G377200 chr7A 84.878 820 82 26 1382 2194 670289845 670289061 0.000000e+00 789.0
11 TraesCS7B01G377200 chr7A 78.659 328 34 20 2357 2666 670340965 670340656 4.670000e-43 185.0
12 TraesCS7B01G377200 chr7A 81.720 186 23 7 1 175 670166303 670166488 7.930000e-31 145.0
13 TraesCS7B01G377200 chr7A 75.202 371 56 17 528 890 670166904 670167246 2.850000e-30 143.0
14 TraesCS7B01G377200 chr7A 76.446 242 31 9 2343 2583 670303180 670302964 1.040000e-19 108.0
15 TraesCS7B01G377200 chr7D 90.192 1091 52 19 893 1949 577963315 577964384 0.000000e+00 1371.0
16 TraesCS7B01G377200 chr7D 92.737 950 44 11 893 1829 578163719 578162782 0.000000e+00 1349.0
17 TraesCS7B01G377200 chr7D 85.697 811 79 11 1383 2164 577989424 577990226 0.000000e+00 821.0
18 TraesCS7B01G377200 chr7D 84.845 805 75 16 1382 2156 577991985 577992772 0.000000e+00 767.0
19 TraesCS7B01G377200 chr7D 84.832 745 64 12 185 890 577962532 577963266 0.000000e+00 704.0
20 TraesCS7B01G377200 chr7D 85.452 598 44 12 331 890 578164352 578163760 1.420000e-162 582.0
21 TraesCS7B01G377200 chr7D 81.754 570 98 4 1080 1646 577922030 577922596 3.200000e-129 472.0
22 TraesCS7B01G377200 chr7D 92.179 179 12 1 4 180 578165014 578164836 4.540000e-63 252.0
23 TraesCS7B01G377200 chr7D 76.596 376 52 20 528 894 577921448 577921796 1.010000e-39 174.0
24 TraesCS7B01G377200 chr7D 81.250 240 19 16 2428 2660 577964417 577964637 1.310000e-38 171.0
25 TraesCS7B01G377200 chr7D 85.616 146 18 1 185 327 578164797 578164652 1.700000e-32 150.0
26 TraesCS7B01G377200 chr7D 77.406 239 24 10 2343 2580 577976538 577976747 6.220000e-22 115.0
27 TraesCS7B01G377200 chr7D 98.077 52 1 0 2184 2235 157235110 157235059 1.050000e-14 91.6
28 TraesCS7B01G377200 chr7D 98.077 52 1 0 2184 2235 285298887 285298938 1.050000e-14 91.6
29 TraesCS7B01G377200 chr7D 93.103 58 4 0 2184 2241 393671259 393671202 4.870000e-13 86.1
30 TraesCS7B01G377200 chr7D 97.619 42 1 0 528 569 577885312 577885353 3.790000e-09 73.1
31 TraesCS7B01G377200 chr3D 82.011 567 96 4 1080 1646 55156543 55157103 6.880000e-131 477.0
32 TraesCS7B01G377200 chr3D 76.984 378 47 21 528 894 55155977 55156325 2.170000e-41 180.0
33 TraesCS7B01G377200 chr3D 98.077 52 1 0 2184 2235 348379033 348379084 1.050000e-14 91.6
34 TraesCS7B01G377200 chr3D 93.103 58 4 0 2184 2241 321575677 321575620 4.870000e-13 86.1
35 TraesCS7B01G377200 chr1D 98.077 52 1 0 2184 2235 76621347 76621296 1.050000e-14 91.6
36 TraesCS7B01G377200 chr1D 89.333 75 5 3 2184 2258 269642765 269642694 1.050000e-14 91.6
37 TraesCS7B01G377200 chr4D 93.103 58 4 0 2184 2241 265262222 265262165 4.870000e-13 86.1
38 TraesCS7B01G377200 chr2B 86.301 73 9 1 2170 2241 695583065 695582993 8.160000e-11 78.7


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 TraesCS7B01G377200 chr7B 642075257 642078003 2746 True 5073.000000 5073 100.000000 1 2747 1 chr7B.!!$R2 2746
1 TraesCS7B01G377200 chr7B 641554873 641555581 708 False 678.000000 678 84.509000 1382 2078 1 chr7B.!!$F1 696
2 TraesCS7B01G377200 chr7B 641459650 641461011 1361 False 469.000000 606 88.078333 1 1345 3 chr7B.!!$F3 1344
3 TraesCS7B01G377200 chr7B 641367831 641369542 1711 False 242.166667 499 78.874000 1 1646 3 chr7B.!!$F2 1645
4 TraesCS7B01G377200 chr7A 670340656 670343369 2713 True 1486.000000 2787 84.077000 1 2666 2 chr7A.!!$R3 2665
5 TraesCS7B01G377200 chr7A 670289061 670289845 784 True 789.000000 789 84.878000 1382 2194 1 chr7A.!!$R1 812
6 TraesCS7B01G377200 chr7D 577989424 577992772 3348 False 794.000000 821 85.271000 1382 2164 2 chr7D.!!$F6 782
7 TraesCS7B01G377200 chr7D 577962532 577964637 2105 False 748.666667 1371 85.424667 185 2660 3 chr7D.!!$F5 2475
8 TraesCS7B01G377200 chr7D 578162782 578165014 2232 True 583.250000 1349 88.996000 4 1829 4 chr7D.!!$R3 1825
9 TraesCS7B01G377200 chr7D 577921448 577922596 1148 False 323.000000 472 79.175000 528 1646 2 chr7D.!!$F4 1118
10 TraesCS7B01G377200 chr3D 55155977 55157103 1126 False 328.500000 477 79.497500 528 1646 2 chr3D.!!$F2 1118

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
350 696 2.214376 TTCCACCATTGTCACCATCC 57.786 50.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 5040 0.306533 GACACCGCGACAACAACAAT 59.693 50.0 8.23 0.0 0.0 2.71 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
128 134 2.237143 CTCTGAAGGGGATACAAGTGCA 59.763 50.000 0.00 0.00 39.74 4.57
183 196 6.947258 TCGATGCACAAAATATGTCTACATG 58.053 36.000 5.85 0.00 41.46 3.21
199 246 7.862648 TGTCTACATGTCAGATATTCGTACTC 58.137 38.462 0.00 0.00 0.00 2.59
207 254 6.377429 TGTCAGATATTCGTACTCCTTTCTGT 59.623 38.462 10.06 0.00 33.00 3.41
241 288 2.563620 TGTCCACTGCTGGTATTCGTAA 59.436 45.455 0.00 0.00 38.90 3.18
242 289 3.196901 TGTCCACTGCTGGTATTCGTAAT 59.803 43.478 0.00 0.00 38.90 1.89
300 350 6.845758 AAATGGCTATGATGTGAATATGGG 57.154 37.500 0.00 0.00 0.00 4.00
305 355 6.610830 TGGCTATGATGTGAATATGGGTTTTT 59.389 34.615 0.00 0.00 0.00 1.94
350 696 2.214376 TTCCACCATTGTCACCATCC 57.786 50.000 0.00 0.00 0.00 3.51
359 709 5.653769 ACCATTGTCACCATCCTATTTTCAG 59.346 40.000 0.00 0.00 0.00 3.02
450 801 3.971702 GAGCACCTGTGGGGCCTT 61.972 66.667 7.27 0.00 39.10 4.35
455 806 3.260100 CCTGTGGGGCCTTCCTGT 61.260 66.667 0.84 0.00 35.33 4.00
506 859 3.259064 TGCTTGTGTAATCTAAGCCGTC 58.741 45.455 0.00 0.00 44.60 4.79
603 1012 8.037758 ACAGGATCTCAAGTTTCTATTACAGTG 58.962 37.037 0.00 0.00 0.00 3.66
656 1065 8.647143 ATTTCTGTCAACCATTTAGTTTGTTG 57.353 30.769 0.00 0.00 39.47 3.33
684 1097 6.995686 TCTTGCCGATGTATATTTGGTTGTAT 59.004 34.615 0.00 0.00 0.00 2.29
825 1241 6.788930 CGTAACAAAGAAATAAACTCGGTGTC 59.211 38.462 0.00 0.00 0.00 3.67
827 1243 6.687081 ACAAAGAAATAAACTCGGTGTCAA 57.313 33.333 0.00 0.00 0.00 3.18
829 1245 6.970613 ACAAAGAAATAAACTCGGTGTCAAAC 59.029 34.615 0.00 0.00 0.00 2.93
830 1246 6.937436 AAGAAATAAACTCGGTGTCAAACT 57.063 33.333 0.00 0.00 0.00 2.66
831 1247 6.937436 AGAAATAAACTCGGTGTCAAACTT 57.063 33.333 0.00 0.00 0.00 2.66
832 1248 8.441312 AAGAAATAAACTCGGTGTCAAACTTA 57.559 30.769 0.00 0.00 0.00 2.24
875 1291 7.062605 CCACAAATGTTCACATTCATCTAAAGC 59.937 37.037 5.64 0.00 45.06 3.51
876 1292 7.595875 CACAAATGTTCACATTCATCTAAAGCA 59.404 33.333 5.64 0.00 45.06 3.91
877 1293 7.596248 ACAAATGTTCACATTCATCTAAAGCAC 59.404 33.333 5.64 0.00 45.06 4.40
878 1294 7.458409 AATGTTCACATTCATCTAAAGCACT 57.542 32.000 0.00 0.00 42.45 4.40
879 1295 6.245115 TGTTCACATTCATCTAAAGCACTG 57.755 37.500 0.00 0.00 0.00 3.66
880 1296 4.952262 TCACATTCATCTAAAGCACTGC 57.048 40.909 0.00 0.00 0.00 4.40
883 1299 5.241285 TCACATTCATCTAAAGCACTGCAAA 59.759 36.000 3.30 0.00 0.00 3.68
1026 1577 4.323417 GTGATGTTGGTGGATCACAAGTA 58.677 43.478 0.00 0.00 45.27 2.24
1047 1598 0.104777 ATCCTGCCTCAGCCTATCCA 60.105 55.000 0.00 0.00 38.69 3.41
1077 1628 4.341783 GTGGCTGCAGCTCCTGGT 62.342 66.667 35.82 0.00 41.70 4.00
1435 1995 1.447838 GAGAACAAGCGCCGGATCA 60.448 57.895 5.05 0.00 0.00 2.92
1457 2017 0.387929 AAGAAGAGTGACGTTGCCGA 59.612 50.000 0.00 0.00 37.88 5.54
1504 2067 2.103263 GACTTCCTGGCGGACATAATCT 59.897 50.000 0.00 0.00 39.60 2.40
1517 2080 3.722147 ACATAATCTGCATGGACGAGAC 58.278 45.455 0.00 0.00 0.00 3.36
1541 2104 3.839432 GGAGGGAGTCGGGCTTCG 61.839 72.222 0.00 0.00 40.90 3.79
1598 4723 3.240203 CGCATACCCGCATTACCG 58.760 61.111 0.00 0.00 0.00 4.02
1699 4824 4.406972 TGTGGATAGATCTTCAGGAACAGG 59.593 45.833 0.00 0.00 0.00 4.00
1756 4893 1.518056 AAGCGGCTGACAACATGTGG 61.518 55.000 1.81 0.00 0.00 4.17
1806 4943 1.915141 AGCCAGGACATCCAAAGTTG 58.085 50.000 0.00 0.00 38.89 3.16
1835 4973 7.982224 ACTAATTTTCAGGTTTCGTAATAGCC 58.018 34.615 0.00 0.00 0.00 3.93
1867 5026 4.277515 TCAGAGATTGACTGGTTCCTTG 57.722 45.455 0.00 0.00 36.22 3.61
1876 5040 3.072330 TGACTGGTTCCTTGATGCAAGTA 59.928 43.478 6.44 0.00 39.58 2.24
1928 5092 4.072131 GGATTATGCTTCGAGGCCAATTA 58.928 43.478 17.65 0.00 0.00 1.40
1930 5094 1.312815 ATGCTTCGAGGCCAATTAGC 58.687 50.000 17.65 9.31 0.00 3.09
1938 5102 5.499139 TCGAGGCCAATTAGCTAAAATTG 57.501 39.130 10.85 12.15 43.45 2.32
1964 5134 2.624636 ACCGTGTCCATTTCCGTAATC 58.375 47.619 0.00 0.00 0.00 1.75
1969 5147 2.207590 GTCCATTTCCGTAATCCCGTC 58.792 52.381 0.00 0.00 0.00 4.79
1973 5151 2.373540 TTTCCGTAATCCCGTCACTG 57.626 50.000 0.00 0.00 0.00 3.66
2012 5190 4.372656 CTCCAGATTCCGGTTATGTCTTC 58.627 47.826 0.00 0.00 0.00 2.87
2027 5205 4.307443 TGTCTTCTCGATATGCAATCGT 57.693 40.909 21.99 0.00 41.77 3.73
2028 5206 4.290969 TGTCTTCTCGATATGCAATCGTC 58.709 43.478 21.99 6.19 41.77 4.20
2029 5207 3.359286 GTCTTCTCGATATGCAATCGTCG 59.641 47.826 21.99 15.27 41.77 5.12
2030 5208 3.250040 TCTTCTCGATATGCAATCGTCGA 59.750 43.478 21.99 17.75 39.98 4.20
2032 5210 1.646238 CTCGATATGCAATCGTCGAGC 59.354 52.381 21.74 0.00 46.82 5.03
2045 5229 2.489040 TCGAGCTCGAGTGCCATAA 58.511 52.632 33.84 9.60 44.22 1.90
2053 5237 3.506455 GCTCGAGTGCCATAATACCTCTA 59.494 47.826 15.13 0.00 0.00 2.43
2107 5293 2.259917 TCTGATCCTGGTGAAGCTGAA 58.740 47.619 0.00 0.00 0.00 3.02
2116 5310 3.565307 TGGTGAAGCTGAATTGGTCTTT 58.435 40.909 0.00 0.00 0.00 2.52
2154 5348 3.682921 GCATTTTGCAAAACCACAGTTG 58.317 40.909 26.05 18.50 44.26 3.16
2156 5350 5.686960 GCATTTTGCAAAACCACAGTTGGA 61.687 41.667 26.05 0.25 44.16 3.53
2194 5391 1.466360 CGAAGCATGGCAAGCAAGTAC 60.466 52.381 17.75 2.55 0.00 2.73
2195 5392 1.815003 GAAGCATGGCAAGCAAGTACT 59.185 47.619 17.75 0.00 0.00 2.73
2196 5393 1.457346 AGCATGGCAAGCAAGTACTC 58.543 50.000 17.75 0.00 0.00 2.59
2197 5394 0.453390 GCATGGCAAGCAAGTACTCC 59.547 55.000 10.23 0.00 0.00 3.85
2198 5395 1.825090 CATGGCAAGCAAGTACTCCA 58.175 50.000 0.00 0.00 0.00 3.86
2199 5396 2.372264 CATGGCAAGCAAGTACTCCAT 58.628 47.619 5.84 5.84 34.90 3.41
2200 5397 2.113860 TGGCAAGCAAGTACTCCATC 57.886 50.000 0.00 0.00 0.00 3.51
2201 5398 1.340017 TGGCAAGCAAGTACTCCATCC 60.340 52.381 0.00 0.00 0.00 3.51
2202 5399 1.009829 GCAAGCAAGTACTCCATCCG 58.990 55.000 0.00 0.00 0.00 4.18
2203 5400 1.676014 GCAAGCAAGTACTCCATCCGT 60.676 52.381 0.00 0.00 0.00 4.69
2204 5401 2.699954 CAAGCAAGTACTCCATCCGTT 58.300 47.619 0.00 0.00 0.00 4.44
2205 5402 2.673368 CAAGCAAGTACTCCATCCGTTC 59.327 50.000 0.00 0.00 0.00 3.95
2206 5403 1.207329 AGCAAGTACTCCATCCGTTCC 59.793 52.381 0.00 0.00 0.00 3.62
2207 5404 1.066430 GCAAGTACTCCATCCGTTCCA 60.066 52.381 0.00 0.00 0.00 3.53
2208 5405 2.614481 GCAAGTACTCCATCCGTTCCAA 60.614 50.000 0.00 0.00 0.00 3.53
2209 5406 3.670625 CAAGTACTCCATCCGTTCCAAA 58.329 45.455 0.00 0.00 0.00 3.28
2210 5407 4.069304 CAAGTACTCCATCCGTTCCAAAA 58.931 43.478 0.00 0.00 0.00 2.44
2211 5408 4.569719 AGTACTCCATCCGTTCCAAAAT 57.430 40.909 0.00 0.00 0.00 1.82
2212 5409 5.687166 AGTACTCCATCCGTTCCAAAATA 57.313 39.130 0.00 0.00 0.00 1.40
2213 5410 5.671493 AGTACTCCATCCGTTCCAAAATAG 58.329 41.667 0.00 0.00 0.00 1.73
2214 5411 4.837093 ACTCCATCCGTTCCAAAATAGA 57.163 40.909 0.00 0.00 0.00 1.98
2215 5412 5.373812 ACTCCATCCGTTCCAAAATAGAT 57.626 39.130 0.00 0.00 0.00 1.98
2216 5413 5.126067 ACTCCATCCGTTCCAAAATAGATG 58.874 41.667 0.00 0.00 31.49 2.90
2217 5414 5.104527 ACTCCATCCGTTCCAAAATAGATGA 60.105 40.000 0.00 0.00 32.55 2.92
2218 5415 5.123227 TCCATCCGTTCCAAAATAGATGAC 58.877 41.667 0.00 0.00 32.55 3.06
2219 5416 4.275936 CCATCCGTTCCAAAATAGATGACC 59.724 45.833 0.00 0.00 32.55 4.02
2220 5417 3.881220 TCCGTTCCAAAATAGATGACCC 58.119 45.455 0.00 0.00 0.00 4.46
2221 5418 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2222 5419 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2223 5420 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2224 5421 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2225 5422 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2226 5423 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2227 5424 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2228 5425 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2229 5426 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2230 5427 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2231 5428 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2232 5429 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2233 5430 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2234 5431 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
2235 5432 5.235516 AGATGACCCAACTTTGTACTAACG 58.764 41.667 0.00 0.00 0.00 3.18
2236 5433 4.669206 TGACCCAACTTTGTACTAACGA 57.331 40.909 0.00 0.00 0.00 3.85
2237 5434 5.021033 TGACCCAACTTTGTACTAACGAA 57.979 39.130 0.00 0.00 0.00 3.85
2248 5445 7.919313 TTTGTACTAACGAAGTAACTGAGTG 57.081 36.000 0.00 0.00 45.00 3.51
2250 5447 4.579454 ACTAACGAAGTAACTGAGTGCA 57.421 40.909 0.00 0.00 45.00 4.57
2253 5450 3.173668 ACGAAGTAACTGAGTGCACAA 57.826 42.857 21.04 5.79 41.94 3.33
2256 5453 3.467803 GAAGTAACTGAGTGCACAAGGT 58.532 45.455 21.04 16.90 0.00 3.50
2262 5459 1.331756 CTGAGTGCACAAGGTGTTGTC 59.668 52.381 21.04 4.76 43.88 3.18
2265 5499 0.808125 GTGCACAAGGTGTTGTCACA 59.192 50.000 13.17 2.80 43.88 3.58
2275 5509 3.763897 AGGTGTTGTCACAGAAAAGCTTT 59.236 39.130 5.69 5.69 45.45 3.51
2276 5510 3.859386 GGTGTTGTCACAGAAAAGCTTTG 59.141 43.478 13.54 3.49 45.45 2.77
2277 5511 3.304293 GTGTTGTCACAGAAAAGCTTTGC 59.696 43.478 13.54 11.40 43.37 3.68
2278 5512 2.473530 TGTCACAGAAAAGCTTTGCG 57.526 45.000 13.54 9.75 0.00 4.85
2279 5513 1.123655 GTCACAGAAAAGCTTTGCGC 58.876 50.000 13.54 0.00 39.57 6.09
2291 5526 1.640428 CTTTGCGCTTCCATCGACTA 58.360 50.000 9.73 0.00 0.00 2.59
2295 5530 1.067142 TGCGCTTCCATCGACTAAACT 60.067 47.619 9.73 0.00 0.00 2.66
2297 5532 3.184541 GCGCTTCCATCGACTAAACTAA 58.815 45.455 0.00 0.00 0.00 2.24
2307 5542 7.827236 TCCATCGACTAAACTAATTGGTTGAAT 59.173 33.333 8.06 0.00 43.63 2.57
2319 5554 9.927668 ACTAATTGGTTGAATTTAGTTTCCATG 57.072 29.630 0.00 0.00 35.74 3.66
2320 5555 9.369904 CTAATTGGTTGAATTTAGTTTCCATGG 57.630 33.333 4.97 4.97 35.74 3.66
2321 5556 6.985653 TTGGTTGAATTTAGTTTCCATGGA 57.014 33.333 11.44 11.44 0.00 3.41
2322 5557 6.339587 TGGTTGAATTTAGTTTCCATGGAC 57.660 37.500 15.91 4.41 0.00 4.02
2323 5558 5.835819 TGGTTGAATTTAGTTTCCATGGACA 59.164 36.000 15.91 4.83 0.00 4.02
2324 5559 6.015519 TGGTTGAATTTAGTTTCCATGGACAG 60.016 38.462 15.91 0.00 0.00 3.51
2325 5560 6.208599 GGTTGAATTTAGTTTCCATGGACAGA 59.791 38.462 15.91 0.00 0.00 3.41
2326 5561 7.255801 GGTTGAATTTAGTTTCCATGGACAGAA 60.256 37.037 15.91 3.13 0.00 3.02
2327 5562 7.831691 TGAATTTAGTTTCCATGGACAGAAA 57.168 32.000 15.91 11.72 0.00 2.52
2328 5563 8.243961 TGAATTTAGTTTCCATGGACAGAAAA 57.756 30.769 15.91 13.23 33.98 2.29
2329 5564 8.359642 TGAATTTAGTTTCCATGGACAGAAAAG 58.640 33.333 15.91 0.00 33.98 2.27
2330 5565 7.839680 ATTTAGTTTCCATGGACAGAAAAGT 57.160 32.000 15.91 11.15 33.98 2.66
2331 5566 7.654022 TTTAGTTTCCATGGACAGAAAAGTT 57.346 32.000 15.91 0.00 33.98 2.66
2332 5567 7.654022 TTAGTTTCCATGGACAGAAAAGTTT 57.346 32.000 15.91 0.00 33.98 2.66
2335 5570 5.930837 TTCCATGGACAGAAAAGTTTTGT 57.069 34.783 15.91 0.00 0.00 2.83
2341 5576 4.421058 GGACAGAAAAGTTTTGTGTCCAC 58.579 43.478 43.40 29.97 45.09 4.02
2355 5598 3.576982 TGTGTCCACCAAACTACTAGGAG 59.423 47.826 0.00 0.00 0.00 3.69
2369 5612 3.034635 ACTAGGAGTAGTTGGCATCTGG 58.965 50.000 8.32 0.00 35.88 3.86
2370 5613 1.958288 AGGAGTAGTTGGCATCTGGT 58.042 50.000 8.32 0.00 0.00 4.00
2371 5614 3.116096 AGGAGTAGTTGGCATCTGGTA 57.884 47.619 8.32 0.00 0.00 3.25
2380 5623 1.538666 GCATCTGGTAATGGCCCCT 59.461 57.895 0.00 0.00 0.00 4.79
2383 5626 2.034124 CATCTGGTAATGGCCCCTTTG 58.966 52.381 0.00 0.00 0.00 2.77
2385 5628 1.185315 CTGGTAATGGCCCCTTTGTG 58.815 55.000 0.00 0.00 0.00 3.33
2386 5629 0.780637 TGGTAATGGCCCCTTTGTGA 59.219 50.000 0.00 0.00 0.00 3.58
2387 5630 1.272425 TGGTAATGGCCCCTTTGTGAG 60.272 52.381 0.00 0.00 0.00 3.51
2389 5632 2.525368 GTAATGGCCCCTTTGTGAGTT 58.475 47.619 0.00 0.00 0.00 3.01
2390 5633 1.341080 AATGGCCCCTTTGTGAGTTG 58.659 50.000 0.00 0.00 0.00 3.16
2391 5634 1.187567 ATGGCCCCTTTGTGAGTTGC 61.188 55.000 0.00 0.00 0.00 4.17
2392 5635 1.832167 GGCCCCTTTGTGAGTTGCA 60.832 57.895 0.00 0.00 0.00 4.08
2425 5672 0.108945 GTACTACGCACCCCTGTGTC 60.109 60.000 0.00 0.00 44.65 3.67
2426 5673 0.251474 TACTACGCACCCCTGTGTCT 60.251 55.000 0.00 0.00 44.65 3.41
2428 5675 0.456221 CTACGCACCCCTGTGTCTAG 59.544 60.000 0.00 0.00 44.65 2.43
2431 5678 1.532604 CGCACCCCTGTGTCTAGTGA 61.533 60.000 0.00 0.00 44.65 3.41
2432 5679 0.037232 GCACCCCTGTGTCTAGTGAC 60.037 60.000 0.00 0.00 44.65 3.67
2446 5699 1.008538 GTGACCCTGTTTGCTTGCG 60.009 57.895 0.00 0.00 0.00 4.85
2453 5706 0.318107 CTGTTTGCTTGCGGTTCCTG 60.318 55.000 0.00 0.00 0.00 3.86
2454 5707 1.661509 GTTTGCTTGCGGTTCCTGC 60.662 57.895 0.00 0.00 0.00 4.85
2455 5708 1.827789 TTTGCTTGCGGTTCCTGCT 60.828 52.632 0.00 0.00 0.00 4.24
2458 5711 2.970974 GCTTGCGGTTCCTGCTGTC 61.971 63.158 0.00 0.00 0.00 3.51
2459 5712 1.302033 CTTGCGGTTCCTGCTGTCT 60.302 57.895 0.00 0.00 0.00 3.41
2460 5713 1.294659 CTTGCGGTTCCTGCTGTCTC 61.295 60.000 0.00 0.00 0.00 3.36
2461 5714 1.758440 TTGCGGTTCCTGCTGTCTCT 61.758 55.000 0.00 0.00 0.00 3.10
2467 5723 1.540267 GTTCCTGCTGTCTCTCGTACA 59.460 52.381 0.00 0.00 0.00 2.90
2474 5730 5.342806 TGCTGTCTCTCGTACAAAATTTG 57.657 39.130 3.89 3.89 0.00 2.32
2491 5747 1.737838 TTGAGATCATGTTGCGGGTC 58.262 50.000 0.00 0.00 0.00 4.46
2512 5771 3.641436 TCCAGCTGAGTCTGTCTTAAACA 59.359 43.478 17.39 0.00 36.18 2.83
2513 5772 4.100963 TCCAGCTGAGTCTGTCTTAAACAA 59.899 41.667 17.39 0.00 37.45 2.83
2514 5773 4.450419 CCAGCTGAGTCTGTCTTAAACAAG 59.550 45.833 17.39 0.00 37.45 3.16
2515 5774 5.292765 CAGCTGAGTCTGTCTTAAACAAGA 58.707 41.667 8.42 0.00 37.45 3.02
2568 5827 8.612619 GTGAAATTATTACAGTTGATGATCGGT 58.387 33.333 0.00 0.00 0.00 4.69
2569 5828 8.611757 TGAAATTATTACAGTTGATGATCGGTG 58.388 33.333 0.00 0.00 0.00 4.94
2573 5832 6.609237 ATTACAGTTGATGATCGGTGATTG 57.391 37.500 0.00 0.00 0.00 2.67
2576 5835 3.002042 CAGTTGATGATCGGTGATTGAGC 59.998 47.826 0.00 0.00 0.00 4.26
2578 5837 2.830104 TGATGATCGGTGATTGAGCTG 58.170 47.619 0.00 0.00 0.00 4.24
2580 5839 0.462581 TGATCGGTGATTGAGCTGGC 60.463 55.000 0.00 0.00 0.00 4.85
2581 5840 0.179062 GATCGGTGATTGAGCTGGCT 60.179 55.000 0.00 0.00 0.00 4.75
2582 5841 0.463295 ATCGGTGATTGAGCTGGCTG 60.463 55.000 0.00 0.00 0.00 4.85
2583 5842 2.110967 CGGTGATTGAGCTGGCTGG 61.111 63.158 0.00 0.00 0.00 4.85
2584 5843 1.300963 GGTGATTGAGCTGGCTGGA 59.699 57.895 0.00 0.00 0.00 3.86
2585 5844 0.747283 GGTGATTGAGCTGGCTGGAG 60.747 60.000 0.00 0.00 0.00 3.86
2586 5845 0.747283 GTGATTGAGCTGGCTGGAGG 60.747 60.000 0.00 0.00 0.00 4.30
2587 5846 1.823041 GATTGAGCTGGCTGGAGGC 60.823 63.158 0.00 0.00 41.50 4.70
2600 5859 0.753867 TGGAGGCAACACGTCAAGTA 59.246 50.000 0.00 0.00 41.41 2.24
2602 5861 1.798813 GGAGGCAACACGTCAAGTAAG 59.201 52.381 0.00 0.00 41.41 2.34
2603 5862 2.480845 GAGGCAACACGTCAAGTAAGT 58.519 47.619 0.00 0.00 41.41 2.24
2604 5863 3.553508 GGAGGCAACACGTCAAGTAAGTA 60.554 47.826 0.00 0.00 41.41 2.24
2607 5866 3.059393 GGCAACACGTCAAGTAAGTAACC 60.059 47.826 0.00 0.00 0.00 2.85
2608 5867 3.362304 GCAACACGTCAAGTAAGTAACCG 60.362 47.826 0.00 0.00 0.00 4.44
2610 5869 4.305989 ACACGTCAAGTAAGTAACCGAA 57.694 40.909 0.00 0.00 0.00 4.30
2611 5870 4.044426 ACACGTCAAGTAAGTAACCGAAC 58.956 43.478 0.00 0.00 0.00 3.95
2612 5871 4.043750 CACGTCAAGTAAGTAACCGAACA 58.956 43.478 0.00 0.00 0.00 3.18
2613 5872 4.682860 CACGTCAAGTAAGTAACCGAACAT 59.317 41.667 0.00 0.00 0.00 2.71
2622 5881 2.556622 AGTAACCGAACATGGCCAAAAG 59.443 45.455 10.96 5.45 0.00 2.27
2624 5883 1.184970 ACCGAACATGGCCAAAAGGG 61.185 55.000 10.96 10.72 40.85 3.95
2647 5906 2.790433 TGCCGTTTCTAGCCTGAAAAT 58.210 42.857 3.71 0.00 37.63 1.82
2660 5919 2.288395 CCTGAAAATTGGCACTGTCCAC 60.288 50.000 0.00 0.00 35.50 4.02
2662 5921 1.336755 GAAAATTGGCACTGTCCACGT 59.663 47.619 0.00 0.00 35.50 4.49
2667 5926 4.664677 GCACTGTCCACGTCGGCT 62.665 66.667 0.00 0.00 33.14 5.52
2668 5927 2.959372 CACTGTCCACGTCGGCTA 59.041 61.111 0.00 0.00 33.14 3.93
2669 5928 1.511305 CACTGTCCACGTCGGCTAT 59.489 57.895 0.00 0.00 33.14 2.97
2670 5929 0.525668 CACTGTCCACGTCGGCTATC 60.526 60.000 0.00 0.00 33.14 2.08
2671 5930 0.963856 ACTGTCCACGTCGGCTATCA 60.964 55.000 0.00 0.00 33.14 2.15
2672 5931 0.172578 CTGTCCACGTCGGCTATCAA 59.827 55.000 0.00 0.00 33.14 2.57
2673 5932 0.604073 TGTCCACGTCGGCTATCAAA 59.396 50.000 0.00 0.00 33.14 2.69
2674 5933 1.001068 TGTCCACGTCGGCTATCAAAA 59.999 47.619 0.00 0.00 33.14 2.44
2675 5934 1.392510 GTCCACGTCGGCTATCAAAAC 59.607 52.381 0.00 0.00 33.14 2.43
2676 5935 0.725117 CCACGTCGGCTATCAAAACC 59.275 55.000 0.00 0.00 0.00 3.27
2677 5936 0.725117 CACGTCGGCTATCAAAACCC 59.275 55.000 0.00 0.00 0.00 4.11
2678 5937 0.738412 ACGTCGGCTATCAAAACCCG 60.738 55.000 0.00 0.00 41.97 5.28
2679 5938 1.426041 CGTCGGCTATCAAAACCCGG 61.426 60.000 0.00 0.00 41.02 5.73
2680 5939 0.392060 GTCGGCTATCAAAACCCGGT 60.392 55.000 0.00 0.00 41.02 5.28
2681 5940 0.391927 TCGGCTATCAAAACCCGGTG 60.392 55.000 0.00 0.00 41.02 4.94
2682 5941 1.373590 CGGCTATCAAAACCCGGTGG 61.374 60.000 0.00 0.00 37.21 4.61
2695 5954 2.299993 CCGGTGGGATGATCGATATG 57.700 55.000 0.00 0.00 34.06 1.78
2696 5955 1.824852 CCGGTGGGATGATCGATATGA 59.175 52.381 0.00 0.00 34.06 2.15
2697 5956 2.417379 CCGGTGGGATGATCGATATGAC 60.417 54.545 0.00 0.00 34.06 3.06
2698 5957 2.231235 CGGTGGGATGATCGATATGACA 59.769 50.000 0.00 0.00 0.00 3.58
2699 5958 3.674410 CGGTGGGATGATCGATATGACAG 60.674 52.174 0.00 0.00 0.00 3.51
2700 5959 3.257393 GTGGGATGATCGATATGACAGC 58.743 50.000 0.00 0.00 0.00 4.40
2701 5960 2.234661 TGGGATGATCGATATGACAGCC 59.765 50.000 9.91 9.91 35.07 4.85
2702 5961 2.534298 GGATGATCGATATGACAGCCG 58.466 52.381 0.00 0.00 29.16 5.52
2703 5962 1.923204 GATGATCGATATGACAGCCGC 59.077 52.381 0.00 0.00 0.00 6.53
2704 5963 0.038251 TGATCGATATGACAGCCGCC 60.038 55.000 0.00 0.00 0.00 6.13
2705 5964 1.073216 GATCGATATGACAGCCGCCG 61.073 60.000 0.00 0.00 0.00 6.46
2706 5965 3.406361 CGATATGACAGCCGCCGC 61.406 66.667 0.00 0.00 0.00 6.53
2726 5985 4.415150 CTGGCCGGCCATGTGTCT 62.415 66.667 46.65 0.00 46.15 3.41
2727 5986 4.408821 TGGCCGGCCATGTGTCTC 62.409 66.667 44.23 15.73 41.89 3.36
2728 5987 4.101448 GGCCGGCCATGTGTCTCT 62.101 66.667 40.73 0.00 35.81 3.10
2729 5988 2.821366 GCCGGCCATGTGTCTCTG 60.821 66.667 18.11 0.00 0.00 3.35
2730 5989 2.821366 CCGGCCATGTGTCTCTGC 60.821 66.667 2.24 0.00 0.00 4.26
2731 5990 2.046988 CGGCCATGTGTCTCTGCA 60.047 61.111 2.24 0.00 0.00 4.41
2732 5991 2.104859 CGGCCATGTGTCTCTGCAG 61.105 63.158 7.63 7.63 0.00 4.41
2733 5992 2.404995 GGCCATGTGTCTCTGCAGC 61.405 63.158 9.47 0.00 0.00 5.25
2734 5993 2.404995 GCCATGTGTCTCTGCAGCC 61.405 63.158 9.47 0.00 0.00 4.85
2735 5994 2.104859 CCATGTGTCTCTGCAGCCG 61.105 63.158 9.47 2.34 0.00 5.52
2736 5995 1.079612 CATGTGTCTCTGCAGCCGA 60.080 57.895 9.47 5.05 0.00 5.54
2737 5996 0.671472 CATGTGTCTCTGCAGCCGAA 60.671 55.000 9.47 0.00 0.00 4.30
2738 5997 0.671781 ATGTGTCTCTGCAGCCGAAC 60.672 55.000 9.47 5.69 0.00 3.95
2739 5998 1.300931 GTGTCTCTGCAGCCGAACA 60.301 57.895 9.47 7.48 0.00 3.18
2740 5999 0.880278 GTGTCTCTGCAGCCGAACAA 60.880 55.000 9.47 0.00 0.00 2.83
2741 6000 0.035317 TGTCTCTGCAGCCGAACAAT 59.965 50.000 9.47 0.00 0.00 2.71
2742 6001 0.723981 GTCTCTGCAGCCGAACAATC 59.276 55.000 9.47 0.00 0.00 2.67
2743 6002 0.391661 TCTCTGCAGCCGAACAATCC 60.392 55.000 9.47 0.00 0.00 3.01
2744 6003 1.372087 CTCTGCAGCCGAACAATCCC 61.372 60.000 9.47 0.00 0.00 3.85
2745 6004 2.745884 TGCAGCCGAACAATCCCG 60.746 61.111 0.00 0.00 0.00 5.14
2746 6005 2.435938 GCAGCCGAACAATCCCGA 60.436 61.111 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.998672 GTGGGACCGCTTCGACCA 61.999 66.667 0.00 0.00 0.00 4.02
128 134 4.218635 ACGCGTATTCTGATATCACCATCT 59.781 41.667 11.67 0.00 0.00 2.90
180 192 7.380870 CAGAAAGGAGTACGAATATCTGACATG 59.619 40.741 12.68 0.00 36.11 3.21
183 196 6.797454 ACAGAAAGGAGTACGAATATCTGAC 58.203 40.000 20.37 0.00 37.18 3.51
199 246 7.770433 TGGACATGAATATACAGAACAGAAAGG 59.230 37.037 0.00 0.00 0.00 3.11
207 254 6.051074 CAGCAGTGGACATGAATATACAGAA 58.949 40.000 0.00 0.00 0.00 3.02
305 355 4.082463 GGATCAAACACGGCTGGAAAATAA 60.082 41.667 0.00 0.00 0.00 1.40
310 360 0.953471 CGGATCAAACACGGCTGGAA 60.953 55.000 0.00 0.00 0.00 3.53
319 369 2.350057 TGGTGGAAACGGATCAAACA 57.650 45.000 0.00 0.00 0.00 2.83
359 709 6.020678 CACAGATGGTTTCGAACAAAGAAAAC 60.021 38.462 0.00 0.29 43.49 2.43
450 801 7.675195 TGGTAATAGTGGTTTCTAACTACAGGA 59.325 37.037 8.44 0.00 44.36 3.86
506 859 7.201767 GCCCAAGCATCTAAAGGCATATAATAG 60.202 40.741 0.00 0.00 40.20 1.73
603 1012 6.109359 TAGAAGAAATCTGGCTACAAAGCTC 58.891 40.000 0.00 0.00 42.97 4.09
656 1065 4.578928 ACCAAATATACATCGGCAAGAACC 59.421 41.667 0.00 0.00 0.00 3.62
719 1135 2.158827 TGAGTAACAGCACCAGAGCAAA 60.159 45.455 0.00 0.00 36.85 3.68
720 1136 1.416030 TGAGTAACAGCACCAGAGCAA 59.584 47.619 0.00 0.00 36.85 3.91
801 1217 7.632721 TGACACCGAGTTTATTTCTTTGTTAC 58.367 34.615 0.00 0.00 0.00 2.50
827 1243 9.905713 TGTGGCTATCTTTCAAGATAATAAGTT 57.094 29.630 9.94 0.00 44.82 2.66
832 1248 9.193806 ACATTTGTGGCTATCTTTCAAGATAAT 57.806 29.630 9.94 0.00 44.82 1.28
846 1262 5.711506 AGATGAATGTGAACATTTGTGGCTA 59.288 36.000 9.90 0.00 45.72 3.93
1026 1577 2.225727 TGGATAGGCTGAGGCAGGATAT 60.226 50.000 9.23 0.00 40.87 1.63
1047 1598 2.113986 GCCACTGTTGCTCCAGGT 59.886 61.111 7.87 0.00 36.75 4.00
1077 1628 0.535335 GTGAACCGGCAGGAGTGATA 59.465 55.000 10.86 0.00 41.02 2.15
1101 1657 3.134127 GCAGGGAATGGTGGCGTC 61.134 66.667 0.00 0.00 0.00 5.19
1141 1701 3.117046 GCTCGTACATAAGCTGGTTCTC 58.883 50.000 0.00 0.00 35.60 2.87
1368 1928 3.834231 TCATCTCCAGTGTCAACATCTCA 59.166 43.478 0.00 0.00 0.00 3.27
1435 1995 2.417719 GGCAACGTCACTCTTCTTCAT 58.582 47.619 0.00 0.00 0.00 2.57
1457 2017 1.625315 TGTCAGTCCTAGCAACAGCAT 59.375 47.619 0.00 0.00 0.00 3.79
1504 2067 2.710902 CCTCCGTCTCGTCCATGCA 61.711 63.158 0.00 0.00 0.00 3.96
1517 2080 2.517402 CGACTCCCTCCTCCTCCG 60.517 72.222 0.00 0.00 0.00 4.63
1699 4824 1.673168 GCATGATGTCCCTTCTGTCC 58.327 55.000 0.00 0.00 0.00 4.02
1756 4893 6.319141 GGATACTGAATTTTAGTGATGGCC 57.681 41.667 0.00 0.00 0.00 5.36
1806 4943 7.917720 TTACGAAACCTGAAAATTAGTTTGC 57.082 32.000 0.00 0.00 32.80 3.68
1841 4979 6.310149 AGGAACCAGTCAATCTCTGAAAATT 58.690 36.000 0.00 0.00 35.22 1.82
1844 4982 4.982241 AGGAACCAGTCAATCTCTGAAA 57.018 40.909 0.00 0.00 35.22 2.69
1845 4983 4.347876 TCAAGGAACCAGTCAATCTCTGAA 59.652 41.667 0.00 0.00 35.22 3.02
1847 4985 4.277515 TCAAGGAACCAGTCAATCTCTG 57.722 45.455 0.00 0.00 0.00 3.35
1867 5026 3.603770 GCGACAACAACAATACTTGCATC 59.396 43.478 0.00 0.00 0.00 3.91
1876 5040 0.306533 GACACCGCGACAACAACAAT 59.693 50.000 8.23 0.00 0.00 2.71
1921 5085 4.993905 ACGGTCAATTTTAGCTAATTGGC 58.006 39.130 17.79 16.57 45.08 4.52
1964 5134 1.002468 CTTTCAGTTTGCAGTGACGGG 60.002 52.381 0.00 0.00 31.59 5.28
1969 5147 3.129287 AGGTCAACTTTCAGTTTGCAGTG 59.871 43.478 0.00 0.00 36.03 3.66
1973 5151 2.687935 TGGAGGTCAACTTTCAGTTTGC 59.312 45.455 0.00 0.00 36.03 3.68
1988 5166 2.434702 GACATAACCGGAATCTGGAGGT 59.565 50.000 16.23 0.38 38.88 3.85
1993 5171 4.045104 CGAGAAGACATAACCGGAATCTG 58.955 47.826 9.46 1.84 0.00 2.90
1994 5172 3.952323 TCGAGAAGACATAACCGGAATCT 59.048 43.478 9.46 0.00 0.00 2.40
2028 5206 2.320367 GTATTATGGCACTCGAGCTCG 58.680 52.381 30.03 30.03 41.45 5.03
2029 5207 2.297597 AGGTATTATGGCACTCGAGCTC 59.702 50.000 13.61 2.73 34.17 4.09
2030 5208 2.297597 GAGGTATTATGGCACTCGAGCT 59.702 50.000 13.61 0.00 34.17 4.09
2031 5209 2.297597 AGAGGTATTATGGCACTCGAGC 59.702 50.000 13.61 0.00 33.58 5.03
2032 5210 5.906113 ATAGAGGTATTATGGCACTCGAG 57.094 43.478 11.84 11.84 33.58 4.04
2045 5229 9.520515 AAAAACACATCACAGAAATAGAGGTAT 57.479 29.630 0.00 0.00 0.00 2.73
2078 5263 4.389374 TCACCAGGATCAGAAAACTTCAC 58.611 43.478 0.00 0.00 0.00 3.18
2134 5328 3.937706 TCCAACTGTGGTTTTGCAAAATG 59.062 39.130 26.24 17.72 46.11 2.32
2135 5329 4.213564 TCCAACTGTGGTTTTGCAAAAT 57.786 36.364 26.24 7.72 46.11 1.82
2142 5336 3.255642 CCGATCATTCCAACTGTGGTTTT 59.744 43.478 0.00 0.00 46.11 2.43
2153 5347 2.343101 GTTGAACGACCGATCATTCCA 58.657 47.619 3.35 0.00 0.00 3.53
2154 5348 1.664151 GGTTGAACGACCGATCATTCC 59.336 52.381 3.35 6.09 0.00 3.01
2172 5369 1.870055 CTTGCTTGCCATGCTTCGGT 61.870 55.000 4.10 0.00 0.00 4.69
2194 5391 5.237344 GTCATCTATTTTGGAACGGATGGAG 59.763 44.000 0.00 0.00 32.58 3.86
2195 5392 5.123227 GTCATCTATTTTGGAACGGATGGA 58.877 41.667 0.00 0.00 32.58 3.41
2196 5393 4.275936 GGTCATCTATTTTGGAACGGATGG 59.724 45.833 0.00 0.00 32.58 3.51
2197 5394 4.275936 GGGTCATCTATTTTGGAACGGATG 59.724 45.833 0.00 0.00 32.78 3.51
2198 5395 4.080015 TGGGTCATCTATTTTGGAACGGAT 60.080 41.667 0.00 0.00 0.00 4.18
2199 5396 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2200 5397 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2201 5398 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2202 5399 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2203 5400 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2204 5401 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2205 5402 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2206 5403 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2207 5404 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
2208 5405 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
2209 5406 7.548075 CGTTAGTACAAAGTTGGGTCATCTATT 59.452 37.037 0.00 0.00 0.00 1.73
2210 5407 7.039882 CGTTAGTACAAAGTTGGGTCATCTAT 58.960 38.462 0.00 0.00 0.00 1.98
2211 5408 6.209192 TCGTTAGTACAAAGTTGGGTCATCTA 59.791 38.462 0.00 0.00 0.00 1.98
2212 5409 5.011329 TCGTTAGTACAAAGTTGGGTCATCT 59.989 40.000 0.00 0.00 0.00 2.90
2213 5410 5.232463 TCGTTAGTACAAAGTTGGGTCATC 58.768 41.667 0.00 0.00 0.00 2.92
2214 5411 5.217978 TCGTTAGTACAAAGTTGGGTCAT 57.782 39.130 0.00 0.00 0.00 3.06
2215 5412 4.669206 TCGTTAGTACAAAGTTGGGTCA 57.331 40.909 0.00 0.00 0.00 4.02
2216 5413 5.052481 ACTTCGTTAGTACAAAGTTGGGTC 58.948 41.667 0.00 0.00 34.56 4.46
2217 5414 5.027293 ACTTCGTTAGTACAAAGTTGGGT 57.973 39.130 0.00 0.00 34.56 4.51
2218 5415 6.703165 AGTTACTTCGTTAGTACAAAGTTGGG 59.297 38.462 0.00 0.00 39.05 4.12
2219 5416 7.436080 TCAGTTACTTCGTTAGTACAAAGTTGG 59.564 37.037 0.00 0.00 39.05 3.77
2220 5417 8.343974 TCAGTTACTTCGTTAGTACAAAGTTG 57.656 34.615 0.00 0.00 39.05 3.16
2221 5418 8.193438 ACTCAGTTACTTCGTTAGTACAAAGTT 58.807 33.333 0.00 0.00 39.05 2.66
2222 5419 7.646922 CACTCAGTTACTTCGTTAGTACAAAGT 59.353 37.037 0.00 0.00 39.05 2.66
2223 5420 7.358187 GCACTCAGTTACTTCGTTAGTACAAAG 60.358 40.741 0.00 0.00 39.05 2.77
2224 5421 6.418819 GCACTCAGTTACTTCGTTAGTACAAA 59.581 38.462 0.00 0.00 39.05 2.83
2225 5422 5.916883 GCACTCAGTTACTTCGTTAGTACAA 59.083 40.000 0.00 0.00 39.05 2.41
2226 5423 5.008911 TGCACTCAGTTACTTCGTTAGTACA 59.991 40.000 0.00 0.00 39.05 2.90
2227 5424 5.341727 GTGCACTCAGTTACTTCGTTAGTAC 59.658 44.000 10.32 0.00 39.05 2.73
2228 5425 5.008911 TGTGCACTCAGTTACTTCGTTAGTA 59.991 40.000 19.41 0.00 38.33 1.82
2229 5426 4.202080 TGTGCACTCAGTTACTTCGTTAGT 60.202 41.667 19.41 0.00 41.04 2.24
2230 5427 4.295870 TGTGCACTCAGTTACTTCGTTAG 58.704 43.478 19.41 0.00 0.00 2.34
2231 5428 4.310357 TGTGCACTCAGTTACTTCGTTA 57.690 40.909 19.41 0.00 0.00 3.18
2232 5429 3.173668 TGTGCACTCAGTTACTTCGTT 57.826 42.857 19.41 0.00 0.00 3.85
2233 5430 2.882927 TGTGCACTCAGTTACTTCGT 57.117 45.000 19.41 0.00 0.00 3.85
2234 5431 2.476619 CCTTGTGCACTCAGTTACTTCG 59.523 50.000 19.41 0.00 0.00 3.79
2235 5432 3.248602 CACCTTGTGCACTCAGTTACTTC 59.751 47.826 19.41 0.00 0.00 3.01
2236 5433 3.206150 CACCTTGTGCACTCAGTTACTT 58.794 45.455 19.41 0.00 0.00 2.24
2237 5434 2.170607 ACACCTTGTGCACTCAGTTACT 59.829 45.455 19.41 0.00 36.98 2.24
2238 5435 2.561569 ACACCTTGTGCACTCAGTTAC 58.438 47.619 19.41 0.00 36.98 2.50
2239 5436 2.942376 CAACACCTTGTGCACTCAGTTA 59.058 45.455 19.41 0.00 36.98 2.24
2240 5437 1.745087 CAACACCTTGTGCACTCAGTT 59.255 47.619 19.41 12.26 36.98 3.16
2246 5443 0.808125 TGTGACAACACCTTGTGCAC 59.192 50.000 10.75 10.75 45.40 4.57
2248 5445 1.378531 TCTGTGACAACACCTTGTGC 58.621 50.000 0.00 0.00 45.40 4.57
2250 5447 3.119495 GCTTTTCTGTGACAACACCTTGT 60.119 43.478 0.00 0.00 45.40 3.16
2253 5450 3.004752 AGCTTTTCTGTGACAACACCT 57.995 42.857 0.00 0.00 45.40 4.00
2256 5453 3.510719 GCAAAGCTTTTCTGTGACAACA 58.489 40.909 9.53 0.00 31.35 3.33
2278 5512 5.585047 ACCAATTAGTTTAGTCGATGGAAGC 59.415 40.000 1.60 0.00 0.00 3.86
2279 5513 7.333423 TCAACCAATTAGTTTAGTCGATGGAAG 59.667 37.037 1.60 0.00 0.00 3.46
2295 5530 9.094578 TCCATGGAAACTAAATTCAACCAATTA 57.905 29.630 13.46 0.00 33.16 1.40
2297 5532 7.016072 TGTCCATGGAAACTAAATTCAACCAAT 59.984 33.333 18.20 0.00 0.00 3.16
2307 5542 7.654022 AACTTTTCTGTCCATGGAAACTAAA 57.346 32.000 18.20 13.46 32.20 1.85
2310 5545 6.070824 ACAAAACTTTTCTGTCCATGGAAACT 60.071 34.615 18.20 0.00 32.20 2.66
2311 5546 6.035975 CACAAAACTTTTCTGTCCATGGAAAC 59.964 38.462 18.20 6.29 32.20 2.78
2312 5547 6.105333 CACAAAACTTTTCTGTCCATGGAAA 58.895 36.000 18.20 10.98 0.00 3.13
2313 5548 5.186797 ACACAAAACTTTTCTGTCCATGGAA 59.813 36.000 18.20 6.23 0.00 3.53
2314 5549 4.709397 ACACAAAACTTTTCTGTCCATGGA 59.291 37.500 11.44 11.44 0.00 3.41
2315 5550 5.009854 ACACAAAACTTTTCTGTCCATGG 57.990 39.130 4.97 4.97 0.00 3.66
2316 5551 5.043248 GGACACAAAACTTTTCTGTCCATG 58.957 41.667 25.44 1.75 42.21 3.66
2317 5552 4.709397 TGGACACAAAACTTTTCTGTCCAT 59.291 37.500 27.61 0.00 44.58 3.41
2318 5553 4.082463 GTGGACACAAAACTTTTCTGTCCA 60.082 41.667 27.61 27.61 45.81 4.02
2319 5554 4.421058 GTGGACACAAAACTTTTCTGTCC 58.579 43.478 24.40 24.40 42.57 4.02
2320 5555 4.082463 TGGTGGACACAAAACTTTTCTGTC 60.082 41.667 12.03 12.03 31.72 3.51
2321 5556 3.829601 TGGTGGACACAAAACTTTTCTGT 59.170 39.130 4.69 0.00 0.00 3.41
2322 5557 4.448537 TGGTGGACACAAAACTTTTCTG 57.551 40.909 4.69 0.00 0.00 3.02
2323 5558 5.234752 GTTTGGTGGACACAAAACTTTTCT 58.765 37.500 22.12 0.00 46.55 2.52
2324 5559 5.524511 GTTTGGTGGACACAAAACTTTTC 57.475 39.130 22.12 2.24 46.55 2.29
2330 5565 5.104444 TCCTAGTAGTTTGGTGGACACAAAA 60.104 40.000 4.69 2.77 39.29 2.44
2331 5566 4.409574 TCCTAGTAGTTTGGTGGACACAAA 59.590 41.667 4.69 0.00 35.62 2.83
2332 5567 3.968649 TCCTAGTAGTTTGGTGGACACAA 59.031 43.478 4.69 0.00 0.00 3.33
2335 5570 3.853207 ACTCCTAGTAGTTTGGTGGACA 58.147 45.455 0.00 0.00 0.00 4.02
2355 5598 2.618709 GCCATTACCAGATGCCAACTAC 59.381 50.000 0.00 0.00 0.00 2.73
2366 5609 1.185315 CACAAAGGGGCCATTACCAG 58.815 55.000 2.80 0.00 0.00 4.00
2369 5612 2.215942 ACTCACAAAGGGGCCATTAC 57.784 50.000 2.80 0.00 0.00 1.89
2370 5613 2.524306 CAACTCACAAAGGGGCCATTA 58.476 47.619 2.80 0.00 0.00 1.90
2371 5614 1.341080 CAACTCACAAAGGGGCCATT 58.659 50.000 4.39 0.00 0.00 3.16
2380 5623 3.497118 CTCAACGTTTGCAACTCACAAA 58.503 40.909 0.00 0.00 34.74 2.83
2383 5626 1.466855 GCTCAACGTTTGCAACTCAC 58.533 50.000 15.56 0.00 0.00 3.51
2385 5628 0.657368 CCGCTCAACGTTTGCAACTC 60.657 55.000 18.99 0.00 41.42 3.01
2386 5629 1.355210 CCGCTCAACGTTTGCAACT 59.645 52.632 18.99 0.00 41.42 3.16
2387 5630 2.292916 GCCGCTCAACGTTTGCAAC 61.293 57.895 18.99 9.21 41.42 4.17
2389 5632 4.306471 CGCCGCTCAACGTTTGCA 62.306 61.111 18.99 0.00 41.42 4.08
2390 5633 2.945615 TACGCCGCTCAACGTTTGC 61.946 57.895 0.00 5.45 43.35 3.68
2391 5634 1.154727 GTACGCCGCTCAACGTTTG 60.155 57.895 0.00 0.00 43.35 2.93
2392 5635 0.039256 TAGTACGCCGCTCAACGTTT 60.039 50.000 0.00 0.00 43.35 3.60
2425 5672 1.537202 GCAAGCAAACAGGGTCACTAG 59.463 52.381 0.00 0.00 0.00 2.57
2426 5673 1.604604 GCAAGCAAACAGGGTCACTA 58.395 50.000 0.00 0.00 0.00 2.74
2428 5675 1.008538 CGCAAGCAAACAGGGTCAC 60.009 57.895 0.00 0.00 0.00 3.67
2431 5678 1.734388 GAACCGCAAGCAAACAGGGT 61.734 55.000 0.00 0.00 0.00 4.34
2432 5679 1.007387 GAACCGCAAGCAAACAGGG 60.007 57.895 0.00 0.00 0.00 4.45
2446 5699 1.135344 GTACGAGAGACAGCAGGAACC 60.135 57.143 0.00 0.00 0.00 3.62
2453 5706 5.405571 TCTCAAATTTTGTACGAGAGACAGC 59.594 40.000 8.89 0.00 0.00 4.40
2454 5707 7.329471 TGATCTCAAATTTTGTACGAGAGACAG 59.671 37.037 8.89 0.00 36.26 3.51
2455 5708 7.151976 TGATCTCAAATTTTGTACGAGAGACA 58.848 34.615 8.89 9.54 36.26 3.41
2458 5711 7.968246 ACATGATCTCAAATTTTGTACGAGAG 58.032 34.615 8.89 3.16 36.26 3.20
2459 5712 7.905604 ACATGATCTCAAATTTTGTACGAGA 57.094 32.000 8.89 7.42 37.16 4.04
2460 5713 7.007725 GCAACATGATCTCAAATTTTGTACGAG 59.992 37.037 8.89 0.00 0.00 4.18
2461 5714 6.801377 GCAACATGATCTCAAATTTTGTACGA 59.199 34.615 8.89 5.33 0.00 3.43
2467 5723 4.021192 ACCCGCAACATGATCTCAAATTTT 60.021 37.500 0.00 0.00 0.00 1.82
2474 5730 0.107703 TGGACCCGCAACATGATCTC 60.108 55.000 0.00 0.00 0.00 2.75
2491 5747 3.995199 TGTTTAAGACAGACTCAGCTGG 58.005 45.455 15.13 7.28 40.20 4.85
2512 5771 2.559668 CCACCATTGCACATTCTGTCTT 59.440 45.455 0.00 0.00 0.00 3.01
2513 5772 2.165167 CCACCATTGCACATTCTGTCT 58.835 47.619 0.00 0.00 0.00 3.41
2514 5773 1.888512 ACCACCATTGCACATTCTGTC 59.111 47.619 0.00 0.00 0.00 3.51
2515 5774 1.999648 ACCACCATTGCACATTCTGT 58.000 45.000 0.00 0.00 0.00 3.41
2516 5775 3.319755 GAAACCACCATTGCACATTCTG 58.680 45.455 0.00 0.00 0.00 3.02
2517 5776 2.299867 GGAAACCACCATTGCACATTCT 59.700 45.455 0.00 0.00 0.00 2.40
2568 5827 1.605992 CCTCCAGCCAGCTCAATCA 59.394 57.895 0.00 0.00 0.00 2.57
2569 5828 1.823041 GCCTCCAGCCAGCTCAATC 60.823 63.158 0.00 0.00 34.35 2.67
2573 5832 2.749441 GTTGCCTCCAGCCAGCTC 60.749 66.667 0.00 0.00 42.71 4.09
2576 5835 3.052082 CGTGTTGCCTCCAGCCAG 61.052 66.667 0.00 0.00 42.71 4.85
2578 5837 3.050275 GACGTGTTGCCTCCAGCC 61.050 66.667 0.00 0.00 42.71 4.85
2580 5839 0.532862 ACTTGACGTGTTGCCTCCAG 60.533 55.000 0.00 0.00 0.00 3.86
2581 5840 0.753867 TACTTGACGTGTTGCCTCCA 59.246 50.000 0.00 0.00 0.00 3.86
2582 5841 1.798813 CTTACTTGACGTGTTGCCTCC 59.201 52.381 0.00 0.00 0.00 4.30
2583 5842 2.480845 ACTTACTTGACGTGTTGCCTC 58.519 47.619 0.00 0.00 0.00 4.70
2584 5843 2.614829 ACTTACTTGACGTGTTGCCT 57.385 45.000 0.00 0.00 0.00 4.75
2585 5844 3.059393 GGTTACTTACTTGACGTGTTGCC 60.059 47.826 0.00 0.00 0.00 4.52
2586 5845 3.362304 CGGTTACTTACTTGACGTGTTGC 60.362 47.826 0.00 0.00 0.00 4.17
2587 5846 4.043750 TCGGTTACTTACTTGACGTGTTG 58.956 43.478 0.00 0.00 0.00 3.33
2588 5847 4.305989 TCGGTTACTTACTTGACGTGTT 57.694 40.909 0.00 0.00 0.00 3.32
2589 5848 3.988379 TCGGTTACTTACTTGACGTGT 57.012 42.857 0.00 0.00 0.00 4.49
2600 5859 2.279935 TTGGCCATGTTCGGTTACTT 57.720 45.000 6.09 0.00 0.00 2.24
2602 5861 2.352323 CCTTTTGGCCATGTTCGGTTAC 60.352 50.000 6.09 0.00 0.00 2.50
2603 5862 1.889829 CCTTTTGGCCATGTTCGGTTA 59.110 47.619 6.09 0.00 0.00 2.85
2604 5863 0.678950 CCTTTTGGCCATGTTCGGTT 59.321 50.000 6.09 0.00 0.00 4.44
2622 5881 2.481471 GGCTAGAAACGGCATGCCC 61.481 63.158 30.79 16.65 34.81 5.36
2624 5883 0.744414 TCAGGCTAGAAACGGCATGC 60.744 55.000 9.90 9.90 39.61 4.06
2647 5906 2.279851 CGACGTGGACAGTGCCAA 60.280 61.111 7.71 0.00 40.20 4.52
2655 5914 1.392510 GTTTTGATAGCCGACGTGGAC 59.607 52.381 0.00 0.00 42.00 4.02
2666 5925 2.092646 TCATCCCACCGGGTTTTGATAG 60.093 50.000 6.32 0.00 44.74 2.08
2667 5926 1.916874 TCATCCCACCGGGTTTTGATA 59.083 47.619 6.32 0.00 44.74 2.15
2668 5927 0.701731 TCATCCCACCGGGTTTTGAT 59.298 50.000 6.32 0.00 44.74 2.57
2669 5928 0.701731 ATCATCCCACCGGGTTTTGA 59.298 50.000 6.32 2.35 44.74 2.69
2670 5929 1.102978 GATCATCCCACCGGGTTTTG 58.897 55.000 6.32 0.00 44.74 2.44
2671 5930 0.393808 CGATCATCCCACCGGGTTTT 60.394 55.000 6.32 0.00 44.74 2.43
2672 5931 1.223487 CGATCATCCCACCGGGTTT 59.777 57.895 6.32 0.00 44.74 3.27
2673 5932 1.054406 ATCGATCATCCCACCGGGTT 61.054 55.000 6.32 0.00 44.74 4.11
2674 5933 0.178944 TATCGATCATCCCACCGGGT 60.179 55.000 6.32 0.00 44.74 5.28
2675 5934 1.134699 CATATCGATCATCCCACCGGG 60.135 57.143 6.32 0.00 46.11 5.73
2676 5935 1.824852 TCATATCGATCATCCCACCGG 59.175 52.381 0.00 0.00 0.00 5.28
2677 5936 2.231235 TGTCATATCGATCATCCCACCG 59.769 50.000 0.00 0.00 0.00 4.94
2678 5937 3.854666 CTGTCATATCGATCATCCCACC 58.145 50.000 0.00 0.00 0.00 4.61
2679 5938 3.257393 GCTGTCATATCGATCATCCCAC 58.743 50.000 0.00 0.00 0.00 4.61
2680 5939 2.234661 GGCTGTCATATCGATCATCCCA 59.765 50.000 0.00 0.00 0.00 4.37
2681 5940 2.736719 CGGCTGTCATATCGATCATCCC 60.737 54.545 0.00 0.00 0.00 3.85
2682 5941 2.534298 CGGCTGTCATATCGATCATCC 58.466 52.381 0.00 0.00 0.00 3.51
2683 5942 1.923204 GCGGCTGTCATATCGATCATC 59.077 52.381 0.00 0.00 0.00 2.92
2684 5943 1.404717 GGCGGCTGTCATATCGATCAT 60.405 52.381 0.00 0.00 0.00 2.45
2685 5944 0.038251 GGCGGCTGTCATATCGATCA 60.038 55.000 0.00 0.00 0.00 2.92
2686 5945 1.073216 CGGCGGCTGTCATATCGATC 61.073 60.000 7.61 0.00 0.00 3.69
2687 5946 1.080501 CGGCGGCTGTCATATCGAT 60.081 57.895 7.61 2.16 0.00 3.59
2688 5947 2.335011 CGGCGGCTGTCATATCGA 59.665 61.111 7.61 0.00 0.00 3.59
2689 5948 3.406361 GCGGCGGCTGTCATATCG 61.406 66.667 9.78 0.00 35.83 2.92
2711 5970 4.101448 AGAGACACATGGCCGGCC 62.101 66.667 39.40 39.40 0.00 6.13
2712 5971 2.821366 CAGAGACACATGGCCGGC 60.821 66.667 21.18 21.18 0.00 6.13
2713 5972 2.821366 GCAGAGACACATGGCCGG 60.821 66.667 0.00 0.00 0.00 6.13
2714 5973 2.046988 TGCAGAGACACATGGCCG 60.047 61.111 0.00 0.00 0.00 6.13
2715 5974 2.404995 GCTGCAGAGACACATGGCC 61.405 63.158 20.43 0.00 0.00 5.36
2716 5975 2.404995 GGCTGCAGAGACACATGGC 61.405 63.158 20.43 0.00 0.00 4.40
2717 5976 2.104859 CGGCTGCAGAGACACATGG 61.105 63.158 20.43 0.00 0.00 3.66
2718 5977 0.671472 TTCGGCTGCAGAGACACATG 60.671 55.000 20.43 0.00 0.00 3.21
2719 5978 0.671781 GTTCGGCTGCAGAGACACAT 60.672 55.000 20.43 0.00 0.00 3.21
2720 5979 1.300931 GTTCGGCTGCAGAGACACA 60.301 57.895 20.43 0.00 0.00 3.72
2721 5980 0.880278 TTGTTCGGCTGCAGAGACAC 60.880 55.000 20.43 15.27 0.00 3.67
2722 5981 0.035317 ATTGTTCGGCTGCAGAGACA 59.965 50.000 20.43 12.45 0.00 3.41
2723 5982 0.723981 GATTGTTCGGCTGCAGAGAC 59.276 55.000 20.43 9.89 0.00 3.36
2724 5983 0.391661 GGATTGTTCGGCTGCAGAGA 60.392 55.000 20.43 13.25 0.00 3.10
2725 5984 1.372087 GGGATTGTTCGGCTGCAGAG 61.372 60.000 20.43 10.80 0.00 3.35
2726 5985 1.377202 GGGATTGTTCGGCTGCAGA 60.377 57.895 20.43 0.00 0.00 4.26
2727 5986 2.753966 CGGGATTGTTCGGCTGCAG 61.754 63.158 10.11 10.11 0.00 4.41
2728 5987 2.745884 CGGGATTGTTCGGCTGCA 60.746 61.111 0.50 0.00 0.00 4.41
2729 5988 2.435938 TCGGGATTGTTCGGCTGC 60.436 61.111 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.