Multiple sequence alignment - TraesCS5A01G519900

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 TraesCS5A01G519900 chr5A 100.000 2527 0 0 1 2527 680980467 680977941 0.000000e+00 4667.0
1 TraesCS5A01G519900 chr5A 88.095 84 7 2 982 1065 680971442 680971362 2.070000e-16 97.1
2 TraesCS5A01G519900 chr5A 94.000 50 3 0 1592 1641 680970406 680970357 2.700000e-10 76.8
3 TraesCS5A01G519900 chr5A 100.000 29 0 0 1183 1211 680863999 680863971 1.000000e-03 54.7
4 TraesCS5A01G519900 chr4B 89.089 1668 130 24 1 1648 643628375 643626740 0.000000e+00 2025.0
5 TraesCS5A01G519900 chr4B 92.115 279 17 2 953 1231 643534195 643533922 3.050000e-104 388.0
6 TraesCS5A01G519900 chr4B 85.025 394 29 16 248 633 643534563 643534192 8.540000e-100 374.0
7 TraesCS5A01G519900 chr4B 89.492 295 19 6 1289 1571 643533906 643533612 1.850000e-96 363.0
8 TraesCS5A01G519900 chr4B 88.837 215 19 2 1 215 643534770 643534561 2.490000e-65 259.0
9 TraesCS5A01G519900 chr4B 85.083 181 12 7 1666 1831 643626617 643626437 1.200000e-38 171.0
10 TraesCS5A01G519900 chr4B 100.000 29 0 0 1183 1211 643556365 643556337 1.000000e-03 54.7
11 TraesCS5A01G519900 chr4D 90.462 996 53 23 849 1832 500299389 500298424 0.000000e+00 1275.0
12 TraesCS5A01G519900 chr4D 90.756 476 38 4 369 841 500299968 500299496 4.590000e-177 630.0
13 TraesCS5A01G519900 chr4D 87.683 479 27 13 1837 2308 500298368 500297915 1.720000e-146 529.0
14 TraesCS5A01G519900 chr4D 92.593 216 15 1 1 215 500300230 500300015 2.440000e-80 309.0
15 TraesCS5A01G519900 chr4D 95.960 99 2 2 2298 2395 211031186 211031089 2.600000e-35 159.0
16 TraesCS5A01G519900 chr4D 98.387 62 1 0 2387 2448 500297919 500297858 2.660000e-20 110.0
17 TraesCS5A01G519900 chr4D 88.889 63 4 3 1085 1145 500285829 500285768 9.700000e-10 75.0
18 TraesCS5A01G519900 chr6A 97.917 96 0 2 2298 2391 26976065 26975970 5.590000e-37 165.0
19 TraesCS5A01G519900 chr3D 100.000 89 0 0 2306 2394 419904770 419904858 5.590000e-37 165.0
20 TraesCS5A01G519900 chr7D 98.901 91 1 0 2304 2394 85908473 85908383 2.010000e-36 163.0
21 TraesCS5A01G519900 chr7D 86.250 80 11 0 2448 2527 106315664 106315743 1.250000e-13 87.9
22 TraesCS5A01G519900 chr6B 97.872 94 2 0 2298 2391 716607778 716607871 2.010000e-36 163.0
23 TraesCS5A01G519900 chr5B 96.939 98 2 1 2298 2395 664669404 664669500 2.010000e-36 163.0
24 TraesCS5A01G519900 chr5B 96.907 97 1 2 2305 2400 582585142 582585237 7.230000e-36 161.0
25 TraesCS5A01G519900 chr6D 96.875 96 2 1 2304 2399 316625955 316625861 2.600000e-35 159.0
26 TraesCS5A01G519900 chr4A 94.175 103 4 2 2305 2407 25596248 25596348 3.370000e-34 156.0
27 TraesCS5A01G519900 chrUn 100.000 44 0 0 162 205 277590214 277590257 5.790000e-12 82.4
28 TraesCS5A01G519900 chrUn 100.000 29 0 0 1183 1211 60476945 60476973 1.000000e-03 54.7
29 TraesCS5A01G519900 chr2D 83.951 81 11 2 2448 2527 118818810 118818889 2.700000e-10 76.8


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 TraesCS5A01G519900 chr5A 680977941 680980467 2526 True 4667.0 4667 100.00000 1 2527 1 chr5A.!!$R2 2526
1 TraesCS5A01G519900 chr4B 643626437 643628375 1938 True 1098.0 2025 87.08600 1 1831 2 chr4B.!!$R3 1830
2 TraesCS5A01G519900 chr4B 643533612 643534770 1158 True 346.0 388 88.86725 1 1571 4 chr4B.!!$R2 1570
3 TraesCS5A01G519900 chr4D 500297858 500300230 2372 True 570.6 1275 91.97620 1 2448 5 chr4D.!!$R3 2447

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
400 442 0.174845 CGCAGTCCGGGAAGAACATA 59.825 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2486 0.106967 GGTGGCTTCTCCTCATTCCC 60.107 60.0 0.0 0.0 35.26 3.97 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
43 44 2.032178 GTCCTGACGATTGCTAAATGGC 59.968 50.000 0.00 0.00 0.00 4.40
47 48 1.369209 CGATTGCTAAATGGCCGCG 60.369 57.895 0.00 0.00 0.00 6.46
48 49 1.771073 CGATTGCTAAATGGCCGCGA 61.771 55.000 8.23 0.00 0.00 5.87
114 115 9.515020 GATTCAGACTGAGAAAGTAACAGATAG 57.485 37.037 5.10 0.00 40.07 2.08
215 254 7.707104 AGAAACATAGTTTTTCTGTCAGTTGG 58.293 34.615 0.00 0.00 40.93 3.77
216 255 7.556275 AGAAACATAGTTTTTCTGTCAGTTGGA 59.444 33.333 0.00 0.00 40.93 3.53
217 256 7.823745 AACATAGTTTTTCTGTCAGTTGGAT 57.176 32.000 0.00 0.00 0.00 3.41
218 257 7.206981 ACATAGTTTTTCTGTCAGTTGGATG 57.793 36.000 0.00 0.00 0.00 3.51
219 258 4.574599 AGTTTTTCTGTCAGTTGGATGC 57.425 40.909 0.00 0.00 0.00 3.91
220 259 3.319122 AGTTTTTCTGTCAGTTGGATGCC 59.681 43.478 0.00 0.00 0.00 4.40
221 260 2.957402 TTTCTGTCAGTTGGATGCCT 57.043 45.000 0.00 0.00 0.00 4.75
222 261 4.365514 TTTTCTGTCAGTTGGATGCCTA 57.634 40.909 0.00 0.00 0.00 3.93
223 262 4.365514 TTTCTGTCAGTTGGATGCCTAA 57.634 40.909 0.00 0.00 0.00 2.69
224 263 3.334583 TCTGTCAGTTGGATGCCTAAC 57.665 47.619 0.00 0.00 0.00 2.34
225 264 2.637382 TCTGTCAGTTGGATGCCTAACA 59.363 45.455 0.00 0.00 0.00 2.41
226 265 3.072330 TCTGTCAGTTGGATGCCTAACAA 59.928 43.478 0.00 0.00 0.00 2.83
227 266 3.820467 CTGTCAGTTGGATGCCTAACAAA 59.180 43.478 0.00 0.00 0.00 2.83
228 267 4.406456 TGTCAGTTGGATGCCTAACAAAT 58.594 39.130 0.00 0.00 0.00 2.32
229 268 4.832266 TGTCAGTTGGATGCCTAACAAATT 59.168 37.500 0.00 0.00 0.00 1.82
230 269 5.304101 TGTCAGTTGGATGCCTAACAAATTT 59.696 36.000 0.00 0.00 0.00 1.82
231 270 5.634859 GTCAGTTGGATGCCTAACAAATTTG 59.365 40.000 16.67 16.67 0.00 2.32
232 271 4.389687 CAGTTGGATGCCTAACAAATTTGC 59.610 41.667 18.12 4.32 0.00 3.68
233 272 4.284234 AGTTGGATGCCTAACAAATTTGCT 59.716 37.500 18.12 8.75 0.00 3.91
234 273 4.888326 TGGATGCCTAACAAATTTGCTT 57.112 36.364 18.12 13.16 0.00 3.91
235 274 5.226194 TGGATGCCTAACAAATTTGCTTT 57.774 34.783 18.12 8.51 0.00 3.51
254 293 6.826893 GCTTTGTATCAAAGCTTTGTTTCA 57.173 33.333 32.46 25.58 46.64 2.69
319 358 2.803155 TAGCCGCTGGACTTGCCTTG 62.803 60.000 2.16 0.00 37.63 3.61
327 366 3.709987 CTGGACTTGCCTTGAAGTTTTG 58.290 45.455 0.00 0.00 36.27 2.44
356 395 1.758440 TAGGGAGACATGATGGCGCC 61.758 60.000 22.73 22.73 45.45 6.53
399 441 1.079127 CGCAGTCCGGGAAGAACAT 60.079 57.895 0.00 0.00 0.00 2.71
400 442 0.174845 CGCAGTCCGGGAAGAACATA 59.825 55.000 0.00 0.00 0.00 2.29
402 444 2.741878 CGCAGTCCGGGAAGAACATATT 60.742 50.000 0.00 0.00 0.00 1.28
403 445 2.614057 GCAGTCCGGGAAGAACATATTG 59.386 50.000 0.00 0.00 0.00 1.90
404 446 3.681594 GCAGTCCGGGAAGAACATATTGA 60.682 47.826 0.00 0.00 0.00 2.57
405 447 4.122776 CAGTCCGGGAAGAACATATTGAG 58.877 47.826 0.00 0.00 0.00 3.02
407 449 2.158813 TCCGGGAAGAACATATTGAGCC 60.159 50.000 0.00 0.00 0.00 4.70
409 451 3.545703 CGGGAAGAACATATTGAGCCTT 58.454 45.455 0.00 0.00 0.00 4.35
410 452 3.313526 CGGGAAGAACATATTGAGCCTTG 59.686 47.826 0.00 0.00 0.00 3.61
411 453 3.633986 GGGAAGAACATATTGAGCCTTGG 59.366 47.826 0.00 0.00 0.00 3.61
421 467 1.211190 GAGCCTTGGCGCAAGAAAG 59.789 57.895 10.83 7.06 43.42 2.62
617 664 6.381801 GCAATAGCTAGCAACTCTTGAAAAA 58.618 36.000 18.83 0.00 37.91 1.94
626 673 4.024048 GCAACTCTTGAAAAAGACATCCGA 60.024 41.667 0.00 0.00 0.00 4.55
688 735 3.417069 ACTGTGCTAGTGCCACAATTA 57.583 42.857 0.00 0.00 38.49 1.40
692 739 5.106157 ACTGTGCTAGTGCCACAATTATTTC 60.106 40.000 0.00 0.00 38.49 2.17
702 749 7.029563 GTGCCACAATTATTTCTACTCTTTGG 58.970 38.462 0.00 0.00 0.00 3.28
704 751 7.094377 TGCCACAATTATTTCTACTCTTTGGTC 60.094 37.037 0.00 0.00 0.00 4.02
705 752 7.628580 GCCACAATTATTTCTACTCTTTGGTCC 60.629 40.741 0.00 0.00 0.00 4.46
721 768 2.046892 CCAAGGGCGTGGTCTGAG 60.047 66.667 0.00 0.00 33.63 3.35
741 788 5.632118 TGAGGTAGTACAGTCTTTGTCTCT 58.368 41.667 2.06 0.00 41.29 3.10
760 807 0.607762 TGCGTGCACATGGTGGTATT 60.608 50.000 18.64 0.00 33.64 1.89
798 845 7.343316 TCCTCTCTTTTTCCCTCTCTAGTTATG 59.657 40.741 0.00 0.00 0.00 1.90
844 893 1.944709 GTTGAAGGCGTGTGGTAGTTT 59.055 47.619 0.00 0.00 0.00 2.66
845 894 3.132925 GTTGAAGGCGTGTGGTAGTTTA 58.867 45.455 0.00 0.00 0.00 2.01
846 895 2.758009 TGAAGGCGTGTGGTAGTTTAC 58.242 47.619 0.00 0.00 0.00 2.01
847 896 2.366266 TGAAGGCGTGTGGTAGTTTACT 59.634 45.455 0.00 0.00 0.00 2.24
933 1081 0.678950 TCATCAGTGACAGAACCGCA 59.321 50.000 0.00 0.00 0.00 5.69
936 1084 3.132824 TCATCAGTGACAGAACCGCATAT 59.867 43.478 0.00 0.00 0.00 1.78
963 1111 4.036380 TGCTCGATCGACTAATTAAGCTGA 59.964 41.667 15.15 0.00 0.00 4.26
969 1117 6.255887 CGATCGACTAATTAAGCTGACCTTTT 59.744 38.462 10.26 0.00 34.95 2.27
977 1125 2.100605 AGCTGACCTTTTCCTAAGCG 57.899 50.000 0.00 0.00 35.82 4.68
993 1141 1.437986 GCGAGGTAGCTGGTAGTGG 59.562 63.158 0.00 0.00 0.00 4.00
1015 1163 3.908081 CAATGGCATCCCCGCTGC 61.908 66.667 0.00 0.00 38.93 5.25
1016 1164 4.133373 AATGGCATCCCCGCTGCT 62.133 61.111 0.00 0.00 39.60 4.24
1017 1165 4.889112 ATGGCATCCCCGCTGCTG 62.889 66.667 0.00 0.00 39.60 4.41
1083 1231 2.665185 GCTCAAGCCGTGGTTCGT 60.665 61.111 0.00 0.00 37.94 3.85
1123 1271 2.362736 CAGGTATGCAGTGCACTCAAT 58.637 47.619 22.44 15.63 43.04 2.57
1147 1295 5.541953 ATCTACTCTCAGCATGCATGTTA 57.458 39.130 26.79 12.20 34.76 2.41
1151 1299 3.055602 ACTCTCAGCATGCATGTTACTCA 60.056 43.478 26.79 2.38 34.76 3.41
1194 1342 1.810031 GCGCTAACATACTCCATGGCA 60.810 52.381 6.96 0.00 39.13 4.92
1466 1626 4.396478 GGGAGCTCAAGAATGTTTCCTAAC 59.604 45.833 17.19 0.00 34.75 2.34
1474 1634 2.781681 ATGTTTCCTAACCACCCGAG 57.218 50.000 0.00 0.00 33.15 4.63
1495 1655 1.065491 TCATGAACCCGGACATCCTTG 60.065 52.381 0.73 0.00 0.00 3.61
1534 1694 3.637229 CCTGTAAGATCCTGATACGGTGT 59.363 47.826 0.00 0.00 34.07 4.16
1567 1727 2.871182 TCTCGGCTGTTGCATAGTAG 57.129 50.000 0.00 0.00 41.91 2.57
1568 1728 2.100197 TCTCGGCTGTTGCATAGTAGT 58.900 47.619 0.00 0.00 41.91 2.73
1569 1729 3.284617 TCTCGGCTGTTGCATAGTAGTA 58.715 45.455 0.00 0.00 41.91 1.82
1573 1733 4.275196 TCGGCTGTTGCATAGTAGTACTAG 59.725 45.833 15.08 8.71 41.91 2.57
1638 1798 4.493350 GTCGAATTGATCAAGAAATGTGCG 59.507 41.667 14.54 6.41 0.00 5.34
1641 1801 0.179192 TGATCAAGAAATGTGCGCGC 60.179 50.000 27.26 27.26 0.00 6.86
1687 1952 2.475818 TGAACTTTGCTGCTTTGCATG 58.524 42.857 0.00 0.00 42.96 4.06
1750 2029 4.723309 AGGCTGTCAACTCAAGAAAGAAT 58.277 39.130 0.00 0.00 0.00 2.40
1752 2031 6.299141 AGGCTGTCAACTCAAGAAAGAATAA 58.701 36.000 0.00 0.00 0.00 1.40
1753 2032 6.944862 AGGCTGTCAACTCAAGAAAGAATAAT 59.055 34.615 0.00 0.00 0.00 1.28
1755 2034 8.178313 GGCTGTCAACTCAAGAAAGAATAATAC 58.822 37.037 0.00 0.00 0.00 1.89
1756 2035 8.178313 GCTGTCAACTCAAGAAAGAATAATACC 58.822 37.037 0.00 0.00 0.00 2.73
1757 2036 8.561738 TGTCAACTCAAGAAAGAATAATACCC 57.438 34.615 0.00 0.00 0.00 3.69
1758 2037 7.333423 TGTCAACTCAAGAAAGAATAATACCCG 59.667 37.037 0.00 0.00 0.00 5.28
1759 2038 6.315393 TCAACTCAAGAAAGAATAATACCCGC 59.685 38.462 0.00 0.00 0.00 6.13
1832 2113 1.210204 AGTGATGTGGGTGATGGCCT 61.210 55.000 3.32 0.00 0.00 5.19
1833 2114 0.749454 GTGATGTGGGTGATGGCCTC 60.749 60.000 3.32 0.00 0.00 4.70
1834 2115 0.915872 TGATGTGGGTGATGGCCTCT 60.916 55.000 3.32 0.00 0.00 3.69
1835 2116 1.131638 GATGTGGGTGATGGCCTCTA 58.868 55.000 3.32 0.00 0.00 2.43
1876 2210 4.466015 TGAACCCCTTTCCATTAATTGCTC 59.534 41.667 0.00 0.00 32.58 4.26
1885 2219 5.309323 TCCATTAATTGCTCAACGGAAAG 57.691 39.130 0.00 0.00 0.00 2.62
1899 2233 6.626302 TCAACGGAAAGAACATTGTTTTCTT 58.374 32.000 3.08 0.79 43.67 2.52
1904 2238 7.860872 ACGGAAAGAACATTGTTTTCTTACATC 59.139 33.333 3.08 0.00 41.48 3.06
1906 2240 9.185192 GGAAAGAACATTGTTTTCTTACATCAG 57.815 33.333 3.08 0.00 41.48 2.90
1974 2309 4.044191 AGTTGGGGCAATAGAAGTAAACCT 59.956 41.667 0.00 0.00 0.00 3.50
1975 2310 3.963129 TGGGGCAATAGAAGTAAACCTG 58.037 45.455 0.00 0.00 0.00 4.00
2004 2339 2.968156 CGCCGTCAAAACACCCGA 60.968 61.111 0.00 0.00 0.00 5.14
2007 2342 2.549282 CGTCAAAACACCCGAGCG 59.451 61.111 0.00 0.00 0.00 5.03
2075 2413 6.285990 CCACGCAGGGGTATATATATAAACC 58.714 44.000 3.96 9.43 0.00 3.27
2076 2414 6.126997 CCACGCAGGGGTATATATATAAACCA 60.127 42.308 19.08 0.00 33.46 3.67
2077 2415 7.332557 CACGCAGGGGTATATATATAAACCAA 58.667 38.462 19.08 0.00 33.46 3.67
2078 2416 7.825270 CACGCAGGGGTATATATATAAACCAAA 59.175 37.037 19.08 0.00 33.46 3.28
2079 2417 8.044908 ACGCAGGGGTATATATATAAACCAAAG 58.955 37.037 19.08 13.63 33.46 2.77
2080 2418 7.497909 CGCAGGGGTATATATATAAACCAAAGG 59.502 40.741 19.08 10.76 33.46 3.11
2106 2444 7.923878 GCAAAACTCCAAAAGTATAACAAGGAA 59.076 33.333 0.00 0.00 37.17 3.36
2107 2445 9.981114 CAAAACTCCAAAAGTATAACAAGGAAT 57.019 29.630 0.00 0.00 37.17 3.01
2108 2446 9.981114 AAAACTCCAAAAGTATAACAAGGAATG 57.019 29.630 0.00 0.00 37.17 2.67
2109 2447 8.934023 AACTCCAAAAGTATAACAAGGAATGA 57.066 30.769 0.00 0.00 37.17 2.57
2112 2450 6.889722 TCCAAAAGTATAACAAGGAATGAGGG 59.110 38.462 0.00 0.00 0.00 4.30
2113 2451 6.889722 CCAAAAGTATAACAAGGAATGAGGGA 59.110 38.462 0.00 0.00 0.00 4.20
2114 2452 7.396055 CCAAAAGTATAACAAGGAATGAGGGAA 59.604 37.037 0.00 0.00 0.00 3.97
2115 2453 8.802267 CAAAAGTATAACAAGGAATGAGGGAAA 58.198 33.333 0.00 0.00 0.00 3.13
2116 2454 7.939784 AAGTATAACAAGGAATGAGGGAAAC 57.060 36.000 0.00 0.00 0.00 2.78
2117 2455 7.272144 AGTATAACAAGGAATGAGGGAAACT 57.728 36.000 0.00 0.00 0.00 2.66
2118 2456 8.388656 AGTATAACAAGGAATGAGGGAAACTA 57.611 34.615 0.00 0.00 0.00 2.24
2119 2457 8.265764 AGTATAACAAGGAATGAGGGAAACTAC 58.734 37.037 0.00 0.00 0.00 2.73
2120 2458 4.993705 ACAAGGAATGAGGGAAACTACA 57.006 40.909 0.00 0.00 0.00 2.74
2121 2459 5.520748 ACAAGGAATGAGGGAAACTACAT 57.479 39.130 0.00 0.00 0.00 2.29
2122 2460 5.501156 ACAAGGAATGAGGGAAACTACATC 58.499 41.667 0.00 0.00 0.00 3.06
2123 2461 5.014123 ACAAGGAATGAGGGAAACTACATCA 59.986 40.000 0.00 0.00 0.00 3.07
2124 2462 5.365021 AGGAATGAGGGAAACTACATCAG 57.635 43.478 0.00 0.00 0.00 2.90
2125 2463 3.879892 GGAATGAGGGAAACTACATCAGC 59.120 47.826 0.00 0.00 0.00 4.26
2126 2464 3.567478 ATGAGGGAAACTACATCAGCC 57.433 47.619 0.00 0.00 0.00 4.85
2137 2475 1.021390 ACATCAGCCAACTACAGCGC 61.021 55.000 0.00 0.00 0.00 5.92
2171 2509 1.661463 ATGAGGAGAAGCCACCAAGA 58.339 50.000 0.00 0.00 40.02 3.02
2176 2514 2.579860 AGGAGAAGCCACCAAGAATCAT 59.420 45.455 0.00 0.00 40.02 2.45
2186 2525 2.684881 ACCAAGAATCATCATCGGCAAC 59.315 45.455 0.00 0.00 0.00 4.17
2210 2549 1.741770 GAACGCTTCCTCGTGCCAT 60.742 57.895 0.00 0.00 42.46 4.40
2231 2570 1.152694 TCTGGCCAGCAAGCACTTT 60.153 52.632 28.91 0.00 0.00 2.66
2248 2587 0.035317 TTTCGCAGTCTGCATCACCT 59.965 50.000 24.13 0.00 45.36 4.00
2257 2596 4.940046 CAGTCTGCATCACCTTCTGTATTT 59.060 41.667 0.00 0.00 0.00 1.40
2268 2607 6.042781 TCACCTTCTGTATTTCACCTTGTACT 59.957 38.462 0.00 0.00 0.00 2.73
2269 2608 6.369065 CACCTTCTGTATTTCACCTTGTACTC 59.631 42.308 0.00 0.00 0.00 2.59
2278 2617 1.887198 CACCTTGTACTCTCTCACGGT 59.113 52.381 0.00 0.00 36.80 4.83
2303 2642 0.694771 ATCTTCAGCAGCCTTGTCCA 59.305 50.000 0.00 0.00 0.00 4.02
2304 2643 0.035881 TCTTCAGCAGCCTTGTCCAG 59.964 55.000 0.00 0.00 0.00 3.86
2305 2644 0.250640 CTTCAGCAGCCTTGTCCAGT 60.251 55.000 0.00 0.00 0.00 4.00
2306 2645 1.002430 CTTCAGCAGCCTTGTCCAGTA 59.998 52.381 0.00 0.00 0.00 2.74
2307 2646 0.321671 TCAGCAGCCTTGTCCAGTAC 59.678 55.000 0.00 0.00 0.00 2.73
2308 2647 0.322975 CAGCAGCCTTGTCCAGTACT 59.677 55.000 0.00 0.00 0.00 2.73
2309 2648 0.610687 AGCAGCCTTGTCCAGTACTC 59.389 55.000 0.00 0.00 0.00 2.59
2310 2649 0.391793 GCAGCCTTGTCCAGTACTCC 60.392 60.000 0.00 0.00 0.00 3.85
2311 2650 0.250513 CAGCCTTGTCCAGTACTCCC 59.749 60.000 0.00 0.00 0.00 4.30
2312 2651 0.117340 AGCCTTGTCCAGTACTCCCT 59.883 55.000 0.00 0.00 0.00 4.20
2313 2652 0.537653 GCCTTGTCCAGTACTCCCTC 59.462 60.000 0.00 0.00 0.00 4.30
2314 2653 1.897647 GCCTTGTCCAGTACTCCCTCT 60.898 57.143 0.00 0.00 0.00 3.69
2315 2654 1.827969 CCTTGTCCAGTACTCCCTCTG 59.172 57.143 0.00 0.00 0.00 3.35
2316 2655 2.530701 CTTGTCCAGTACTCCCTCTGT 58.469 52.381 0.00 0.00 0.00 3.41
2317 2656 3.563697 CCTTGTCCAGTACTCCCTCTGTA 60.564 52.174 0.00 0.00 0.00 2.74
2318 2657 3.820195 TGTCCAGTACTCCCTCTGTAA 57.180 47.619 0.00 0.00 0.00 2.41
2319 2658 4.122337 TGTCCAGTACTCCCTCTGTAAA 57.878 45.455 0.00 0.00 0.00 2.01
2320 2659 3.830755 TGTCCAGTACTCCCTCTGTAAAC 59.169 47.826 0.00 0.00 0.00 2.01
2321 2660 4.087907 GTCCAGTACTCCCTCTGTAAACT 58.912 47.826 0.00 0.00 0.00 2.66
2322 2661 5.222192 TGTCCAGTACTCCCTCTGTAAACTA 60.222 44.000 0.00 0.00 0.00 2.24
2323 2662 5.713861 GTCCAGTACTCCCTCTGTAAACTAA 59.286 44.000 0.00 0.00 0.00 2.24
2324 2663 6.380560 GTCCAGTACTCCCTCTGTAAACTAAT 59.619 42.308 0.00 0.00 0.00 1.73
2325 2664 7.559170 GTCCAGTACTCCCTCTGTAAACTAATA 59.441 40.741 0.00 0.00 0.00 0.98
2326 2665 8.287350 TCCAGTACTCCCTCTGTAAACTAATAT 58.713 37.037 0.00 0.00 0.00 1.28
2327 2666 9.584008 CCAGTACTCCCTCTGTAAACTAATATA 57.416 37.037 0.00 0.00 0.00 0.86
2332 2671 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2333 2672 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
2334 2673 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
2363 2702 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
2364 2703 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
2365 2704 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
2366 2705 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
2367 2706 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
2381 2720 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2382 2721 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2383 2722 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2384 2723 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2385 2724 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2448 2787 3.000322 CGGAGTTCGAACAATATGAGCAC 60.000 47.826 28.78 0.00 42.43 4.40
2449 2788 3.932710 GGAGTTCGAACAATATGAGCACA 59.067 43.478 28.78 0.00 0.00 4.57
2450 2789 4.033358 GGAGTTCGAACAATATGAGCACAG 59.967 45.833 28.78 0.00 0.00 3.66
2451 2790 4.820897 AGTTCGAACAATATGAGCACAGA 58.179 39.130 28.78 0.00 0.00 3.41
2452 2791 4.867047 AGTTCGAACAATATGAGCACAGAG 59.133 41.667 28.78 0.00 0.00 3.35
2453 2792 3.190079 TCGAACAATATGAGCACAGAGC 58.810 45.455 0.00 0.00 46.19 4.09
2463 2802 3.052082 CACAGAGCCGGGCAACAG 61.052 66.667 23.09 13.66 39.74 3.16
2471 2810 3.646715 CGGGCAACAGGAAGGGGA 61.647 66.667 0.00 0.00 39.74 4.81
2472 2811 2.035783 GGGCAACAGGAAGGGGAC 59.964 66.667 0.00 0.00 39.74 4.46
2473 2812 2.359975 GGCAACAGGAAGGGGACG 60.360 66.667 0.00 0.00 0.00 4.79
2474 2813 3.056328 GCAACAGGAAGGGGACGC 61.056 66.667 0.00 0.00 0.00 5.19
2475 2814 2.750350 CAACAGGAAGGGGACGCT 59.250 61.111 0.00 0.00 0.00 5.07
2476 2815 1.672356 CAACAGGAAGGGGACGCTG 60.672 63.158 0.00 0.00 0.00 5.18
2477 2816 2.147387 AACAGGAAGGGGACGCTGT 61.147 57.895 0.00 0.00 0.00 4.40
2478 2817 1.705997 AACAGGAAGGGGACGCTGTT 61.706 55.000 0.00 0.00 0.00 3.16
2479 2818 0.834687 ACAGGAAGGGGACGCTGTTA 60.835 55.000 0.00 0.00 0.00 2.41
2480 2819 0.391263 CAGGAAGGGGACGCTGTTAC 60.391 60.000 0.00 0.00 0.00 2.50
2481 2820 0.544595 AGGAAGGGGACGCTGTTACT 60.545 55.000 0.00 0.00 0.00 2.24
2482 2821 1.188863 GGAAGGGGACGCTGTTACTA 58.811 55.000 0.00 0.00 0.00 1.82
2483 2822 1.551883 GGAAGGGGACGCTGTTACTAA 59.448 52.381 0.00 0.00 0.00 2.24
2484 2823 2.614779 GAAGGGGACGCTGTTACTAAC 58.385 52.381 0.00 0.00 0.00 2.34
2485 2824 0.529378 AGGGGACGCTGTTACTAACG 59.471 55.000 0.00 0.00 0.00 3.18
2486 2825 0.459063 GGGGACGCTGTTACTAACGG 60.459 60.000 3.65 3.65 40.80 4.44
2495 2834 3.195661 CTGTTACTAACGGCCTTGATCC 58.804 50.000 0.00 0.00 0.00 3.36
2496 2835 2.835764 TGTTACTAACGGCCTTGATCCT 59.164 45.455 0.00 0.00 0.00 3.24
2497 2836 3.195661 GTTACTAACGGCCTTGATCCTG 58.804 50.000 0.00 0.00 0.00 3.86
2498 2837 1.276622 ACTAACGGCCTTGATCCTGT 58.723 50.000 0.00 0.00 0.00 4.00
2499 2838 1.066143 ACTAACGGCCTTGATCCTGTG 60.066 52.381 0.00 0.00 0.00 3.66
2500 2839 0.251916 TAACGGCCTTGATCCTGTGG 59.748 55.000 0.00 0.00 0.00 4.17
2501 2840 2.825836 CGGCCTTGATCCTGTGGC 60.826 66.667 0.00 6.77 44.22 5.01
2502 2841 2.825836 GGCCTTGATCCTGTGGCG 60.826 66.667 0.00 0.00 45.75 5.69
2503 2842 3.512516 GCCTTGATCCTGTGGCGC 61.513 66.667 0.00 0.00 35.79 6.53
2504 2843 2.046023 CCTTGATCCTGTGGCGCA 60.046 61.111 10.83 0.00 0.00 6.09
2505 2844 1.452651 CCTTGATCCTGTGGCGCAT 60.453 57.895 10.83 0.00 0.00 4.73
2506 2845 0.179048 CCTTGATCCTGTGGCGCATA 60.179 55.000 10.83 0.00 0.00 3.14
2507 2846 1.544093 CCTTGATCCTGTGGCGCATAT 60.544 52.381 10.83 0.00 0.00 1.78
2508 2847 1.534163 CTTGATCCTGTGGCGCATATG 59.466 52.381 10.83 0.00 0.00 1.78
2509 2848 0.250424 TGATCCTGTGGCGCATATGG 60.250 55.000 10.83 6.03 0.00 2.74
2510 2849 1.580845 GATCCTGTGGCGCATATGGC 61.581 60.000 10.83 6.25 39.90 4.40
2511 2850 2.060567 ATCCTGTGGCGCATATGGCT 62.061 55.000 10.83 0.00 41.67 4.75
2512 2851 2.549198 CCTGTGGCGCATATGGCTG 61.549 63.158 10.83 0.00 41.67 4.85
2513 2852 2.516695 TGTGGCGCATATGGCTGG 60.517 61.111 10.83 0.00 41.67 4.85
2514 2853 2.203195 GTGGCGCATATGGCTGGA 60.203 61.111 10.83 0.00 41.67 3.86
2515 2854 1.823470 GTGGCGCATATGGCTGGAA 60.823 57.895 10.83 0.00 41.67 3.53
2516 2855 1.823470 TGGCGCATATGGCTGGAAC 60.823 57.895 10.83 0.00 41.67 3.62
2517 2856 2.633657 GCGCATATGGCTGGAACG 59.366 61.111 0.30 0.00 41.67 3.95
2518 2857 1.887242 GCGCATATGGCTGGAACGA 60.887 57.895 0.30 0.00 41.67 3.85
2519 2858 1.436195 GCGCATATGGCTGGAACGAA 61.436 55.000 0.30 0.00 41.67 3.85
2520 2859 1.013596 CGCATATGGCTGGAACGAAA 58.986 50.000 4.56 0.00 41.67 3.46
2521 2860 1.268032 CGCATATGGCTGGAACGAAAC 60.268 52.381 4.56 0.00 41.67 2.78
2522 2861 2.017049 GCATATGGCTGGAACGAAACT 58.983 47.619 4.56 0.00 40.25 2.66
2523 2862 2.223340 GCATATGGCTGGAACGAAACTG 60.223 50.000 4.56 0.00 40.25 3.16
2524 2863 1.448985 TATGGCTGGAACGAAACTGC 58.551 50.000 0.00 0.00 0.00 4.40
2525 2864 0.250901 ATGGCTGGAACGAAACTGCT 60.251 50.000 0.00 0.00 0.00 4.24
2526 2865 1.165907 TGGCTGGAACGAAACTGCTG 61.166 55.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 0.527817 GGTCTACAAGGATGTCGCGG 60.528 60.000 6.13 0.00 41.05 6.46
47 48 3.056749 AGTCAACGGTCTACAAGGATGTC 60.057 47.826 0.00 0.00 41.05 3.06
48 49 2.897969 AGTCAACGGTCTACAAGGATGT 59.102 45.455 0.00 0.00 43.74 3.06
156 157 2.831526 GGTATCCCCAGCAAAACATGTT 59.168 45.455 4.92 4.92 0.00 2.71
232 271 8.655092 TGTTTGAAACAAAGCTTTGATACAAAG 58.345 29.630 38.78 15.51 40.55 2.77
233 272 8.539770 TGTTTGAAACAAAGCTTTGATACAAA 57.460 26.923 38.78 34.13 40.55 2.83
234 273 8.715191 ATGTTTGAAACAAAGCTTTGATACAA 57.285 26.923 38.78 31.76 45.86 2.41
235 274 8.715191 AATGTTTGAAACAAAGCTTTGATACA 57.285 26.923 38.78 27.91 45.86 2.29
236 275 8.275632 GGAATGTTTGAAACAAAGCTTTGATAC 58.724 33.333 38.78 27.35 45.86 2.24
237 276 7.984050 TGGAATGTTTGAAACAAAGCTTTGATA 59.016 29.630 38.78 21.09 45.86 2.15
238 277 6.822676 TGGAATGTTTGAAACAAAGCTTTGAT 59.177 30.769 38.78 27.97 45.86 2.57
239 278 6.169094 TGGAATGTTTGAAACAAAGCTTTGA 58.831 32.000 38.78 18.64 45.86 2.69
240 279 6.419980 TGGAATGTTTGAAACAAAGCTTTG 57.580 33.333 32.53 32.53 45.86 2.77
241 280 7.390162 TCTTTGGAATGTTTGAAACAAAGCTTT 59.610 29.630 15.31 5.69 45.86 3.51
242 281 6.878389 TCTTTGGAATGTTTGAAACAAAGCTT 59.122 30.769 15.31 4.59 45.86 3.74
243 282 6.405538 TCTTTGGAATGTTTGAAACAAAGCT 58.594 32.000 15.31 0.16 45.86 3.74
244 283 6.660887 TCTTTGGAATGTTTGAAACAAAGC 57.339 33.333 15.31 7.16 45.86 3.51
245 284 6.238184 GGCTCTTTGGAATGTTTGAAACAAAG 60.238 38.462 15.31 12.94 45.86 2.77
246 285 5.584251 GGCTCTTTGGAATGTTTGAAACAAA 59.416 36.000 15.31 1.79 45.86 2.83
247 286 5.115480 GGCTCTTTGGAATGTTTGAAACAA 58.885 37.500 15.31 0.00 45.86 2.83
248 287 4.442753 GGGCTCTTTGGAATGTTTGAAACA 60.443 41.667 13.66 13.66 46.94 2.83
249 288 4.058124 GGGCTCTTTGGAATGTTTGAAAC 58.942 43.478 0.14 0.14 0.00 2.78
254 293 2.037641 GCTTGGGCTCTTTGGAATGTTT 59.962 45.455 0.00 0.00 35.22 2.83
276 315 3.084536 TGGATGGAATTTGCTGCTACA 57.915 42.857 0.00 0.00 0.00 2.74
289 328 1.679139 CAGCGGCTAATTTGGATGGA 58.321 50.000 0.26 0.00 0.00 3.41
319 358 4.526650 TCCCTAATTTCTGGGCAAAACTTC 59.473 41.667 6.12 0.00 43.04 3.01
327 366 3.117888 TCATGTCTCCCTAATTTCTGGGC 60.118 47.826 6.12 0.00 43.04 5.36
356 395 1.402968 GACATGCTTAGGTGCACATGG 59.597 52.381 20.43 10.37 46.33 3.66
359 398 2.153645 CAAGACATGCTTAGGTGCACA 58.846 47.619 20.43 0.00 46.33 4.57
367 406 2.337583 GACTGCGTCAAGACATGCTTA 58.662 47.619 0.00 0.00 34.31 3.09
389 431 3.633986 CCAAGGCTCAATATGTTCTTCCC 59.366 47.826 0.00 0.00 0.00 3.97
390 432 3.067320 GCCAAGGCTCAATATGTTCTTCC 59.933 47.826 3.29 0.00 38.26 3.46
399 441 0.035534 TCTTGCGCCAAGGCTCAATA 60.036 50.000 15.98 7.30 43.48 1.90
400 442 0.895100 TTCTTGCGCCAAGGCTCAAT 60.895 50.000 15.98 0.00 43.48 2.57
402 444 1.518056 CTTTCTTGCGCCAAGGCTCA 61.518 55.000 4.18 4.36 41.33 4.26
403 445 1.211190 CTTTCTTGCGCCAAGGCTC 59.789 57.895 4.18 1.20 41.33 4.70
404 446 2.270986 CCTTTCTTGCGCCAAGGCT 61.271 57.895 4.18 0.00 41.33 4.58
405 447 1.805428 TTCCTTTCTTGCGCCAAGGC 61.805 55.000 16.16 0.00 41.33 4.35
407 449 0.387750 GCTTCCTTTCTTGCGCCAAG 60.388 55.000 4.18 9.13 42.25 3.61
409 451 0.895100 ATGCTTCCTTTCTTGCGCCA 60.895 50.000 4.18 0.00 0.00 5.69
410 452 1.094785 TATGCTTCCTTTCTTGCGCC 58.905 50.000 4.18 0.00 0.00 6.53
411 453 3.058639 CCTATATGCTTCCTTTCTTGCGC 60.059 47.826 0.00 0.00 0.00 6.09
482 529 2.125350 GGACGGAGGCAGAGCAAG 60.125 66.667 0.00 0.00 0.00 4.01
543 590 5.010112 TCTCAATCATCCGAGCTTAACCTAG 59.990 44.000 0.00 0.00 0.00 3.02
611 658 6.128282 GCAGATTAAGTCGGATGTCTTTTTCA 60.128 38.462 0.00 0.00 0.00 2.69
617 664 3.735208 CGTGCAGATTAAGTCGGATGTCT 60.735 47.826 0.00 0.00 0.00 3.41
626 673 1.338769 GGGTGACCGTGCAGATTAAGT 60.339 52.381 0.00 0.00 43.64 2.24
688 735 4.811063 GCCCTTGGACCAAAGAGTAGAAAT 60.811 45.833 8.59 0.00 0.00 2.17
692 739 1.676014 CGCCCTTGGACCAAAGAGTAG 60.676 57.143 8.59 0.00 0.00 2.57
702 749 2.358737 CAGACCACGCCCTTGGAC 60.359 66.667 0.00 0.00 39.24 4.02
704 751 2.046892 CTCAGACCACGCCCTTGG 60.047 66.667 0.00 0.00 43.04 3.61
705 752 1.541310 TACCTCAGACCACGCCCTTG 61.541 60.000 0.00 0.00 0.00 3.61
721 768 4.487019 GCAGAGACAAAGACTGTACTACC 58.513 47.826 0.00 0.00 38.84 3.18
741 788 0.607762 AATACCACCATGTGCACGCA 60.608 50.000 13.13 0.00 31.34 5.24
844 893 3.517612 ACCCAGCTTAGTTTCCTCAGTA 58.482 45.455 0.00 0.00 0.00 2.74
845 894 2.339769 ACCCAGCTTAGTTTCCTCAGT 58.660 47.619 0.00 0.00 0.00 3.41
846 895 3.339141 GAACCCAGCTTAGTTTCCTCAG 58.661 50.000 0.00 0.00 0.00 3.35
847 896 2.039879 GGAACCCAGCTTAGTTTCCTCA 59.960 50.000 3.27 0.00 0.00 3.86
931 1079 3.827625 AGTCGATCGAGCAGTAATATGC 58.172 45.455 20.09 1.68 46.88 3.14
933 1081 9.776158 CTTAATTAGTCGATCGAGCAGTAATAT 57.224 33.333 20.09 11.53 0.00 1.28
936 1084 5.913514 GCTTAATTAGTCGATCGAGCAGTAA 59.086 40.000 20.09 13.76 0.00 2.24
977 1125 1.861982 TTCCCACTACCAGCTACCTC 58.138 55.000 0.00 0.00 0.00 3.85
993 1141 1.809567 GCGGGGATGCCATTGATTCC 61.810 60.000 5.30 0.00 0.00 3.01
1123 1271 5.541953 ACATGCATGCTGAGAGTAGATAA 57.458 39.130 26.53 0.00 0.00 1.75
1147 1295 6.592994 CACGGATATGATCAATAGCAATGAGT 59.407 38.462 0.00 0.00 0.00 3.41
1151 1299 5.583854 GCTCACGGATATGATCAATAGCAAT 59.416 40.000 0.00 0.00 0.00 3.56
1194 1342 2.230508 CAGCACCATCTGAAACTGCAAT 59.769 45.455 0.00 0.00 36.19 3.56
1295 1443 0.466372 TTCCGCCAACCATGTTGTCA 60.466 50.000 6.25 0.00 0.00 3.58
1389 1537 4.899239 GAGGGAGCGTCGCATGGG 62.899 72.222 21.09 2.76 0.00 4.00
1430 1590 2.501723 TGAGCTCCCAAGATAGTTCCAC 59.498 50.000 12.15 0.00 0.00 4.02
1466 1626 1.078426 GGGTTCATGACTCGGGTGG 60.078 63.158 0.00 0.00 0.00 4.61
1474 1634 0.541863 AGGATGTCCGGGTTCATGAC 59.458 55.000 0.00 0.00 42.08 3.06
1495 1655 2.402572 GGCTGCGCCTTTCTTCTCC 61.403 63.158 4.18 0.00 46.69 3.71
1516 1676 3.068165 CAGCACACCGTATCAGGATCTTA 59.932 47.826 0.00 0.00 34.73 2.10
1534 1694 1.473965 GCCGAGATCTTGATTCCAGCA 60.474 52.381 11.89 0.00 0.00 4.41
1567 1727 6.041751 ACCCCTATTTATGACAGTGCTAGTAC 59.958 42.308 2.24 2.24 0.00 2.73
1568 1728 6.141083 ACCCCTATTTATGACAGTGCTAGTA 58.859 40.000 0.00 0.00 0.00 1.82
1569 1729 4.969359 ACCCCTATTTATGACAGTGCTAGT 59.031 41.667 0.00 0.00 0.00 2.57
1573 1733 6.296026 TGAATACCCCTATTTATGACAGTGC 58.704 40.000 0.00 0.00 0.00 4.40
1638 1798 1.199624 CACACCTTTGTTTTGAGCGC 58.800 50.000 0.00 0.00 31.66 5.92
1641 1801 1.134175 ACCGCACACCTTTGTTTTGAG 59.866 47.619 0.00 0.00 31.66 3.02
1687 1952 3.939592 GGCAACAAACATCTAGGAGTACC 59.060 47.826 0.00 0.00 0.00 3.34
1733 2012 7.676572 GCGGGTATTATTCTTTCTTGAGTTGAC 60.677 40.741 0.00 0.00 0.00 3.18
1755 2034 2.980568 TGTGAGTTATAACCTTGCGGG 58.019 47.619 12.05 0.00 41.89 6.13
1756 2035 5.106317 ACAAATGTGAGTTATAACCTTGCGG 60.106 40.000 12.05 0.00 0.00 5.69
1757 2036 5.938322 ACAAATGTGAGTTATAACCTTGCG 58.062 37.500 12.05 0.00 0.00 4.85
1758 2037 7.593825 AGAACAAATGTGAGTTATAACCTTGC 58.406 34.615 12.05 1.73 0.00 4.01
1759 2038 9.003658 AGAGAACAAATGTGAGTTATAACCTTG 57.996 33.333 12.05 8.66 0.00 3.61
1845 2177 1.544246 GGAAAGGGGTTCATCGGTTTG 59.456 52.381 0.00 0.00 38.06 2.93
1876 2210 6.885735 AAGAAAACAATGTTCTTTCCGTTG 57.114 33.333 0.00 0.00 41.47 4.10
1885 2219 5.863935 GGCCTGATGTAAGAAAACAATGTTC 59.136 40.000 0.00 0.00 32.02 3.18
1904 2238 1.000938 GTTTGCTTCTCAGTTGGCCTG 60.001 52.381 3.32 0.00 42.97 4.85
1906 2240 1.322442 AGTTTGCTTCTCAGTTGGCC 58.678 50.000 0.00 0.00 0.00 5.36
1991 2326 0.658897 TTTCGCTCGGGTGTTTTGAC 59.341 50.000 0.00 0.00 0.00 3.18
2004 2339 3.171528 ACTAGGGTAGAAGGTTTTCGCT 58.828 45.455 0.00 0.00 38.38 4.93
2007 2342 9.565090 TTTTTAGAACTAGGGTAGAAGGTTTTC 57.435 33.333 0.00 0.00 0.00 2.29
2038 2376 0.541392 TGCGTGGGTTCTGCTATGAT 59.459 50.000 0.00 0.00 0.00 2.45
2066 2404 8.423906 TTGGAGTTTTGCCTTTGGTTTATATA 57.576 30.769 0.00 0.00 0.00 0.86
2068 2406 6.732896 TTGGAGTTTTGCCTTTGGTTTATA 57.267 33.333 0.00 0.00 0.00 0.98
2070 2408 5.422214 TTTGGAGTTTTGCCTTTGGTTTA 57.578 34.783 0.00 0.00 0.00 2.01
2071 2409 3.990959 TTGGAGTTTTGCCTTTGGTTT 57.009 38.095 0.00 0.00 0.00 3.27
2072 2410 3.990959 TTTGGAGTTTTGCCTTTGGTT 57.009 38.095 0.00 0.00 0.00 3.67
2073 2411 3.263170 ACTTTTGGAGTTTTGCCTTTGGT 59.737 39.130 0.00 0.00 33.92 3.67
2074 2412 3.872696 ACTTTTGGAGTTTTGCCTTTGG 58.127 40.909 0.00 0.00 33.92 3.28
2075 2413 7.708752 TGTTATACTTTTGGAGTTTTGCCTTTG 59.291 33.333 0.00 0.00 39.86 2.77
2076 2414 7.787028 TGTTATACTTTTGGAGTTTTGCCTTT 58.213 30.769 0.00 0.00 39.86 3.11
2077 2415 7.354751 TGTTATACTTTTGGAGTTTTGCCTT 57.645 32.000 0.00 0.00 39.86 4.35
2078 2416 6.969993 TGTTATACTTTTGGAGTTTTGCCT 57.030 33.333 0.00 0.00 39.86 4.75
2079 2417 6.645003 CCTTGTTATACTTTTGGAGTTTTGCC 59.355 38.462 0.00 0.00 39.86 4.52
2080 2418 7.430441 TCCTTGTTATACTTTTGGAGTTTTGC 58.570 34.615 0.00 0.00 39.86 3.68
2106 2444 2.846206 TGGCTGATGTAGTTTCCCTCAT 59.154 45.455 0.00 0.00 0.00 2.90
2107 2445 2.265367 TGGCTGATGTAGTTTCCCTCA 58.735 47.619 0.00 0.00 0.00 3.86
2108 2446 3.010420 GTTGGCTGATGTAGTTTCCCTC 58.990 50.000 0.00 0.00 0.00 4.30
2109 2447 2.644798 AGTTGGCTGATGTAGTTTCCCT 59.355 45.455 0.00 0.00 0.00 4.20
2112 2450 4.093556 GCTGTAGTTGGCTGATGTAGTTTC 59.906 45.833 0.00 0.00 0.00 2.78
2113 2451 4.003648 GCTGTAGTTGGCTGATGTAGTTT 58.996 43.478 0.00 0.00 0.00 2.66
2114 2452 3.600388 GCTGTAGTTGGCTGATGTAGTT 58.400 45.455 0.00 0.00 0.00 2.24
2115 2453 2.417379 CGCTGTAGTTGGCTGATGTAGT 60.417 50.000 0.00 0.00 0.00 2.73
2116 2454 2.196749 CGCTGTAGTTGGCTGATGTAG 58.803 52.381 0.00 0.00 0.00 2.74
2117 2455 1.739035 GCGCTGTAGTTGGCTGATGTA 60.739 52.381 0.00 0.00 0.00 2.29
2118 2456 1.021390 GCGCTGTAGTTGGCTGATGT 61.021 55.000 0.00 0.00 0.00 3.06
2119 2457 1.717937 GCGCTGTAGTTGGCTGATG 59.282 57.895 0.00 0.00 0.00 3.07
2120 2458 1.811266 CGCGCTGTAGTTGGCTGAT 60.811 57.895 5.56 0.00 0.00 2.90
2121 2459 2.432456 CGCGCTGTAGTTGGCTGA 60.432 61.111 5.56 0.00 0.00 4.26
2122 2460 4.152625 GCGCGCTGTAGTTGGCTG 62.153 66.667 26.67 0.00 0.00 4.85
2123 2461 4.680237 TGCGCGCTGTAGTTGGCT 62.680 61.111 33.29 0.00 0.00 4.75
2124 2462 3.651480 CTTGCGCGCTGTAGTTGGC 62.651 63.158 33.29 0.00 0.00 4.52
2125 2463 2.476051 CTTGCGCGCTGTAGTTGG 59.524 61.111 33.29 8.99 0.00 3.77
2126 2464 1.841663 AACCTTGCGCGCTGTAGTTG 61.842 55.000 33.29 15.79 0.00 3.16
2137 2475 1.369091 CTCATTCCCGGAACCTTGCG 61.369 60.000 0.73 0.00 41.91 4.85
2148 2486 0.106967 GGTGGCTTCTCCTCATTCCC 60.107 60.000 0.00 0.00 35.26 3.97
2152 2490 1.661463 TCTTGGTGGCTTCTCCTCAT 58.339 50.000 0.00 0.00 35.26 2.90
2171 2509 0.809636 TCGCGTTGCCGATGATGATT 60.810 50.000 5.77 0.00 35.63 2.57
2176 2514 1.373622 TTCTTCGCGTTGCCGATGA 60.374 52.632 5.77 0.00 38.91 2.92
2248 2587 7.232737 TGAGAGAGTACAAGGTGAAATACAGAA 59.767 37.037 0.00 0.00 0.00 3.02
2257 2596 2.160205 CCGTGAGAGAGTACAAGGTGA 58.840 52.381 0.00 0.00 32.63 4.02
2268 2607 2.404923 AGATCGAAGACCGTGAGAGA 57.595 50.000 0.00 0.00 42.51 3.10
2269 2608 2.420372 TGAAGATCGAAGACCGTGAGAG 59.580 50.000 0.00 0.00 42.51 3.20
2278 2617 1.189752 AGGCTGCTGAAGATCGAAGA 58.810 50.000 0.00 0.00 45.75 2.87
2306 2645 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2307 2646 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
2308 2647 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
2337 2676 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
2338 2677 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
2339 2678 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2340 2679 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2341 2680 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2355 2694 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2356 2695 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2357 2696 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2358 2697 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2359 2698 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2360 2699 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2361 2700 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2362 2701 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2363 2702 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2364 2703 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2365 2704 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2366 2705 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2368 2707 9.592196 TTATGTACTCCCTCCGTAAACTAATAT 57.408 33.333 0.00 0.00 0.00 1.28
2369 2708 8.995027 TTATGTACTCCCTCCGTAAACTAATA 57.005 34.615 0.00 0.00 0.00 0.98
2370 2709 7.781693 TCTTATGTACTCCCTCCGTAAACTAAT 59.218 37.037 0.00 0.00 0.00 1.73
2371 2710 7.118723 TCTTATGTACTCCCTCCGTAAACTAA 58.881 38.462 0.00 0.00 0.00 2.24
2372 2711 6.662755 TCTTATGTACTCCCTCCGTAAACTA 58.337 40.000 0.00 0.00 0.00 2.24
2373 2712 5.513233 TCTTATGTACTCCCTCCGTAAACT 58.487 41.667 0.00 0.00 0.00 2.66
2374 2713 5.841957 TCTTATGTACTCCCTCCGTAAAC 57.158 43.478 0.00 0.00 0.00 2.01
2375 2714 6.855763 TTTCTTATGTACTCCCTCCGTAAA 57.144 37.500 0.00 0.00 0.00 2.01
2376 2715 6.664816 TCTTTTCTTATGTACTCCCTCCGTAA 59.335 38.462 0.00 0.00 0.00 3.18
2377 2716 6.189859 TCTTTTCTTATGTACTCCCTCCGTA 58.810 40.000 0.00 0.00 0.00 4.02
2378 2717 5.021458 TCTTTTCTTATGTACTCCCTCCGT 58.979 41.667 0.00 0.00 0.00 4.69
2379 2718 5.593679 TCTTTTCTTATGTACTCCCTCCG 57.406 43.478 0.00 0.00 0.00 4.63
2380 2719 6.594547 GTGTTCTTTTCTTATGTACTCCCTCC 59.405 42.308 0.00 0.00 0.00 4.30
2381 2720 7.117956 GTGTGTTCTTTTCTTATGTACTCCCTC 59.882 40.741 0.00 0.00 0.00 4.30
2382 2721 6.935208 GTGTGTTCTTTTCTTATGTACTCCCT 59.065 38.462 0.00 0.00 0.00 4.20
2383 2722 6.708949 TGTGTGTTCTTTTCTTATGTACTCCC 59.291 38.462 0.00 0.00 0.00 4.30
2384 2723 7.441458 ACTGTGTGTTCTTTTCTTATGTACTCC 59.559 37.037 0.00 0.00 0.00 3.85
2385 2724 8.276325 CACTGTGTGTTCTTTTCTTATGTACTC 58.724 37.037 0.00 0.00 0.00 2.59
2437 2776 1.224075 CCGGCTCTGTGCTCATATTG 58.776 55.000 1.44 0.00 42.39 1.90
2448 2787 3.551496 TTCCTGTTGCCCGGCTCTG 62.551 63.158 11.61 7.84 0.00 3.35
2449 2788 3.249189 TTCCTGTTGCCCGGCTCT 61.249 61.111 11.61 0.00 0.00 4.09
2450 2789 2.747855 CTTCCTGTTGCCCGGCTC 60.748 66.667 11.61 4.64 0.00 4.70
2451 2790 4.351054 CCTTCCTGTTGCCCGGCT 62.351 66.667 11.61 0.00 0.00 5.52
2453 2792 4.740822 CCCCTTCCTGTTGCCCGG 62.741 72.222 0.00 0.00 0.00 5.73
2454 2793 3.646715 TCCCCTTCCTGTTGCCCG 61.647 66.667 0.00 0.00 0.00 6.13
2455 2794 2.035783 GTCCCCTTCCTGTTGCCC 59.964 66.667 0.00 0.00 0.00 5.36
2456 2795 2.359975 CGTCCCCTTCCTGTTGCC 60.360 66.667 0.00 0.00 0.00 4.52
2457 2796 3.056328 GCGTCCCCTTCCTGTTGC 61.056 66.667 0.00 0.00 0.00 4.17
2458 2797 1.672356 CAGCGTCCCCTTCCTGTTG 60.672 63.158 0.00 0.00 0.00 3.33
2459 2798 1.705997 AACAGCGTCCCCTTCCTGTT 61.706 55.000 0.00 0.00 42.03 3.16
2460 2799 0.834687 TAACAGCGTCCCCTTCCTGT 60.835 55.000 0.00 0.00 40.02 4.00
2461 2800 0.391263 GTAACAGCGTCCCCTTCCTG 60.391 60.000 0.00 0.00 0.00 3.86
2462 2801 0.544595 AGTAACAGCGTCCCCTTCCT 60.545 55.000 0.00 0.00 0.00 3.36
2463 2802 1.188863 TAGTAACAGCGTCCCCTTCC 58.811 55.000 0.00 0.00 0.00 3.46
2464 2803 2.614779 GTTAGTAACAGCGTCCCCTTC 58.385 52.381 8.20 0.00 0.00 3.46
2465 2804 1.067354 CGTTAGTAACAGCGTCCCCTT 60.067 52.381 13.33 0.00 0.00 3.95
2466 2805 0.529378 CGTTAGTAACAGCGTCCCCT 59.471 55.000 13.33 0.00 0.00 4.79
2467 2806 0.459063 CCGTTAGTAACAGCGTCCCC 60.459 60.000 13.33 0.00 0.00 4.81
2468 2807 1.080435 GCCGTTAGTAACAGCGTCCC 61.080 60.000 13.33 0.00 0.00 4.46
2469 2808 1.080435 GGCCGTTAGTAACAGCGTCC 61.080 60.000 13.68 3.54 35.66 4.79
2470 2809 0.108945 AGGCCGTTAGTAACAGCGTC 60.109 55.000 13.68 3.00 35.66 5.19
2471 2810 0.319405 AAGGCCGTTAGTAACAGCGT 59.681 50.000 13.68 11.86 35.66 5.07
2472 2811 0.719465 CAAGGCCGTTAGTAACAGCG 59.281 55.000 13.68 0.47 35.66 5.18
2473 2812 2.088950 TCAAGGCCGTTAGTAACAGC 57.911 50.000 12.04 12.04 34.08 4.40
2474 2813 3.118738 AGGATCAAGGCCGTTAGTAACAG 60.119 47.826 13.33 2.89 0.00 3.16
2475 2814 2.835764 AGGATCAAGGCCGTTAGTAACA 59.164 45.455 13.33 0.00 0.00 2.41
2476 2815 3.195661 CAGGATCAAGGCCGTTAGTAAC 58.804 50.000 2.72 2.72 0.00 2.50
2477 2816 2.835764 ACAGGATCAAGGCCGTTAGTAA 59.164 45.455 0.00 0.00 0.00 2.24
2478 2817 2.167693 CACAGGATCAAGGCCGTTAGTA 59.832 50.000 0.00 0.00 0.00 1.82
2479 2818 1.066143 CACAGGATCAAGGCCGTTAGT 60.066 52.381 0.00 0.00 0.00 2.24
2480 2819 1.656652 CACAGGATCAAGGCCGTTAG 58.343 55.000 0.00 0.00 0.00 2.34
2481 2820 0.251916 CCACAGGATCAAGGCCGTTA 59.748 55.000 0.00 0.00 0.00 3.18
2482 2821 1.002134 CCACAGGATCAAGGCCGTT 60.002 57.895 0.00 0.00 0.00 4.44
2483 2822 2.671070 CCACAGGATCAAGGCCGT 59.329 61.111 0.00 0.00 0.00 5.68
2484 2823 2.825836 GCCACAGGATCAAGGCCG 60.826 66.667 0.00 0.00 41.25 6.13
2485 2824 2.825836 CGCCACAGGATCAAGGCC 60.826 66.667 0.00 0.00 44.18 5.19
2486 2825 3.512516 GCGCCACAGGATCAAGGC 61.513 66.667 0.00 0.83 43.61 4.35
2487 2826 0.179048 TATGCGCCACAGGATCAAGG 60.179 55.000 4.18 0.00 0.00 3.61
2488 2827 1.534163 CATATGCGCCACAGGATCAAG 59.466 52.381 4.18 0.00 0.00 3.02
2489 2828 1.596603 CATATGCGCCACAGGATCAA 58.403 50.000 4.18 0.00 0.00 2.57
2490 2829 0.250424 CCATATGCGCCACAGGATCA 60.250 55.000 4.18 0.00 0.00 2.92
2491 2830 1.580845 GCCATATGCGCCACAGGATC 61.581 60.000 4.18 0.00 0.00 3.36
2492 2831 1.601759 GCCATATGCGCCACAGGAT 60.602 57.895 4.18 0.00 0.00 3.24
2493 2832 2.203195 GCCATATGCGCCACAGGA 60.203 61.111 4.18 0.00 0.00 3.86
2502 2841 2.017049 AGTTTCGTTCCAGCCATATGC 58.983 47.619 0.00 0.00 41.71 3.14
2503 2842 2.223340 GCAGTTTCGTTCCAGCCATATG 60.223 50.000 0.00 0.00 0.00 1.78
2504 2843 2.017049 GCAGTTTCGTTCCAGCCATAT 58.983 47.619 0.00 0.00 0.00 1.78
2505 2844 1.003118 AGCAGTTTCGTTCCAGCCATA 59.997 47.619 0.00 0.00 0.00 2.74
2506 2845 0.250901 AGCAGTTTCGTTCCAGCCAT 60.251 50.000 0.00 0.00 0.00 4.40
2507 2846 1.148273 AGCAGTTTCGTTCCAGCCA 59.852 52.632 0.00 0.00 0.00 4.75
2508 2847 1.576421 CAGCAGTTTCGTTCCAGCC 59.424 57.895 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.