Multiple sequence alignment - TraesCS3B01G427600

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 TraesCS3B01G427600 chr3B 100.000 3452 0 0 2901 6352 666508426 666511877 0.000000e+00 6375.0
1 TraesCS3B01G427600 chr3B 100.000 2158 0 0 505 2662 666506030 666508187 0.000000e+00 3986.0
2 TraesCS3B01G427600 chr3B 90.722 194 14 2 3779 3972 666509099 666509288 8.170000e-64 255.0
3 TraesCS3B01G427600 chr3B 90.722 194 14 2 3574 3763 666509304 666509497 8.170000e-64 255.0
4 TraesCS3B01G427600 chr3B 84.434 212 28 5 6144 6352 62973134 62973343 3.000000e-48 204.0
5 TraesCS3B01G427600 chr3B 100.000 109 0 0 1 109 666505526 666505634 1.080000e-47 202.0
6 TraesCS3B01G427600 chr3B 81.696 224 25 2 6024 6247 457159124 457158917 8.470000e-39 172.0
7 TraesCS3B01G427600 chr3B 82.547 212 19 6 6011 6220 807748202 807748397 3.050000e-38 171.0
8 TraesCS3B01G427600 chr3B 79.134 254 32 8 6011 6259 685399620 685399383 8.530000e-34 156.0
9 TraesCS3B01G427600 chr3B 78.906 256 33 11 6005 6256 457157478 457157716 3.070000e-33 154.0
10 TraesCS3B01G427600 chr3B 85.915 142 17 3 6164 6303 215901065 215900925 1.430000e-31 148.0
11 TraesCS3B01G427600 chr3A 93.968 2039 93 14 3573 5600 642957239 642959258 0.000000e+00 3057.0
12 TraesCS3B01G427600 chr3A 93.696 1396 76 8 505 1891 642955861 642957253 0.000000e+00 2080.0
13 TraesCS3B01G427600 chr3A 89.202 213 14 5 3764 3970 642957225 642957434 2.270000e-64 257.0
14 TraesCS3B01G427600 chr3A 90.206 194 15 2 3574 3763 642957452 642957645 3.800000e-62 250.0
15 TraesCS3B01G427600 chr3A 97.248 109 3 0 1 109 642955244 642955352 1.090000e-42 185.0
16 TraesCS3B01G427600 chr3D 93.991 1398 71 7 505 1890 504974240 504975636 0.000000e+00 2104.0
17 TraesCS3B01G427600 chr3D 95.806 906 32 5 4895 5797 504976850 504977752 0.000000e+00 1458.0
18 TraesCS3B01G427600 chr3D 93.535 990 32 13 3856 4844 504975877 504976835 0.000000e+00 1445.0
19 TraesCS3B01G427600 chr3D 93.307 254 13 2 3574 3823 504975624 504975877 7.780000e-99 372.0
20 TraesCS3B01G427600 chr3D 90.741 216 20 0 5795 6010 504981590 504981805 8.060000e-74 289.0
21 TraesCS3B01G427600 chr3D 85.561 187 24 3 6166 6352 611021703 611021520 6.500000e-45 193.0
22 TraesCS3B01G427600 chr3D 97.248 109 3 0 1 109 504974099 504974207 1.090000e-42 185.0
23 TraesCS3B01G427600 chr3D 100.000 45 0 0 3574 3618 504975833 504975877 4.080000e-12 84.2
24 TraesCS3B01G427600 chr7B 99.364 786 5 0 1877 2662 237914940 237914155 0.000000e+00 1424.0
25 TraesCS3B01G427600 chr7B 99.554 673 3 0 2901 3573 237913899 237913227 0.000000e+00 1227.0
26 TraesCS3B01G427600 chr7B 98.514 673 10 0 2901 3573 720161331 720162003 0.000000e+00 1188.0
27 TraesCS3B01G427600 chr5B 99.356 777 5 0 1886 2662 631459601 631460377 0.000000e+00 1408.0
28 TraesCS3B01G427600 chr5B 99.114 677 4 1 2901 3577 631460633 631461307 0.000000e+00 1216.0
29 TraesCS3B01G427600 chr5B 86.387 191 21 5 6164 6352 61362889 61362702 3.000000e-48 204.0
30 TraesCS3B01G427600 chr4B 99.735 754 2 0 1909 2662 104565031 104565784 0.000000e+00 1382.0
31 TraesCS3B01G427600 chr4B 99.557 677 2 1 2901 3577 104565929 104566604 0.000000e+00 1232.0
32 TraesCS3B01G427600 chr4B 98.811 673 8 0 2901 3573 416116690 416116018 0.000000e+00 1199.0
33 TraesCS3B01G427600 chr4B 80.252 238 30 3 6011 6247 612327000 612326779 5.100000e-36 163.0
34 TraesCS3B01G427600 chr5A 97.995 798 2 1 1865 2662 626086915 626087698 0.000000e+00 1373.0
35 TraesCS3B01G427600 chr5A 98.257 746 10 1 1917 2662 364682519 364683261 0.000000e+00 1303.0
36 TraesCS3B01G427600 chr5A 99.114 677 5 1 2901 3577 626087954 626088629 0.000000e+00 1216.0
37 TraesCS3B01G427600 chr5A 99.108 673 6 0 2901 3573 364683517 364684189 0.000000e+00 1210.0
38 TraesCS3B01G427600 chr5A 93.324 749 43 5 1918 2662 580518816 580519561 0.000000e+00 1099.0
39 TraesCS3B01G427600 chr5A 84.737 190 24 5 6164 6351 43543562 43543376 1.090000e-42 185.0
40 TraesCS3B01G427600 chr5A 79.394 165 27 7 6144 6303 239404472 239404310 6.730000e-20 110.0
41 TraesCS3B01G427600 chr2A 98.536 683 7 2 2901 3582 133477598 133478278 0.000000e+00 1203.0
42 TraesCS3B01G427600 chr6B 94.555 753 39 2 1910 2662 440553626 440554376 0.000000e+00 1162.0
43 TraesCS3B01G427600 chr6B 95.401 674 30 1 2901 3573 440554633 440555306 0.000000e+00 1072.0
44 TraesCS3B01G427600 chr6B 81.416 226 25 11 6011 6220 240248107 240248331 1.100000e-37 169.0
45 TraesCS3B01G427600 chr6B 80.591 237 28 5 6011 6245 278544780 278544560 3.940000e-37 167.0
46 TraesCS3B01G427600 chr1B 92.967 583 26 5 2080 2662 6468604 6469171 0.000000e+00 835.0
47 TraesCS3B01G427600 chr7A 93.404 379 22 3 1918 2293 26553425 26553047 5.560000e-155 558.0
48 TraesCS3B01G427600 chr7A 85.185 189 21 6 6164 6351 100549397 100549579 3.020000e-43 187.0
49 TraesCS3B01G427600 chr7A 87.500 144 17 1 6148 6290 724362454 724362597 1.420000e-36 165.0
50 TraesCS3B01G427600 chrUn 89.655 406 37 2 2259 2662 50925013 50925415 4.390000e-141 512.0
51 TraesCS3B01G427600 chr2B 90.268 298 27 2 1922 2217 38430920 38430623 7.720000e-104 388.0
52 TraesCS3B01G427600 chr2B 82.731 249 28 9 6011 6256 672813900 672814136 2.320000e-49 207.0
53 TraesCS3B01G427600 chr2B 84.293 191 25 5 6163 6351 672815408 672815221 1.410000e-41 182.0
54 TraesCS3B01G427600 chr6D 84.434 212 27 6 6144 6352 143661268 143661060 3.000000e-48 204.0
55 TraesCS3B01G427600 chr7D 85.340 191 24 4 6163 6352 265265218 265265405 1.810000e-45 195.0
56 TraesCS3B01G427600 chr4D 83.854 192 26 5 6163 6352 481450040 481450228 1.820000e-40 178.0
57 TraesCS3B01G427600 chr1D 80.876 251 27 7 6011 6256 285110083 285110317 1.820000e-40 178.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G427600 chr3B 666505526 666511877 6351 False 2214.600000 6375 96.288800 1 6352 5 chr3B.!!$F4 6351
1 TraesCS3B01G427600 chr3A 642955244 642959258 4014 False 1165.800000 3057 92.864000 1 5600 5 chr3A.!!$F1 5599
2 TraesCS3B01G427600 chr3D 504974099 504981805 7706 False 848.171429 2104 94.946857 1 6010 7 chr3D.!!$F1 6009
3 TraesCS3B01G427600 chr7B 237913227 237914940 1713 True 1325.500000 1424 99.459000 1877 3573 2 chr7B.!!$R1 1696
4 TraesCS3B01G427600 chr7B 720161331 720162003 672 False 1188.000000 1188 98.514000 2901 3573 1 chr7B.!!$F1 672
5 TraesCS3B01G427600 chr5B 631459601 631461307 1706 False 1312.000000 1408 99.235000 1886 3577 2 chr5B.!!$F1 1691
6 TraesCS3B01G427600 chr4B 104565031 104566604 1573 False 1307.000000 1382 99.646000 1909 3577 2 chr4B.!!$F1 1668
7 TraesCS3B01G427600 chr4B 416116018 416116690 672 True 1199.000000 1199 98.811000 2901 3573 1 chr4B.!!$R1 672
8 TraesCS3B01G427600 chr5A 626086915 626088629 1714 False 1294.500000 1373 98.554500 1865 3577 2 chr5A.!!$F3 1712
9 TraesCS3B01G427600 chr5A 364682519 364684189 1670 False 1256.500000 1303 98.682500 1917 3573 2 chr5A.!!$F2 1656
10 TraesCS3B01G427600 chr5A 580518816 580519561 745 False 1099.000000 1099 93.324000 1918 2662 1 chr5A.!!$F1 744
11 TraesCS3B01G427600 chr2A 133477598 133478278 680 False 1203.000000 1203 98.536000 2901 3582 1 chr2A.!!$F1 681
12 TraesCS3B01G427600 chr6B 440553626 440555306 1680 False 1117.000000 1162 94.978000 1910 3573 2 chr6B.!!$F2 1663
13 TraesCS3B01G427600 chr1B 6468604 6469171 567 False 835.000000 835 92.967000 2080 2662 1 chr1B.!!$F1 582

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
718 832 1.448540 CACGGATCTGCCACCACTC 60.449 63.158 0.00 0.0 35.94 3.51 F
1014 1128 0.697658 TGACCATGTCCATTGCTCCA 59.302 50.000 0.00 0.0 0.00 3.86 F
1676 1801 0.099968 TTTCCGTAGTCCTCGATGCG 59.900 55.000 0.00 0.0 0.00 4.73 F
1750 1878 0.162933 CTTCGCGCGTGTTATTGTGT 59.837 50.000 30.98 0.0 0.00 3.72 F
1754 1882 1.154301 CGCGTGTTATTGTGTGGCC 60.154 57.895 0.00 0.0 0.00 5.36 F
3718 3879 1.677217 GCCGAGCAGGACAGAAAGAAT 60.677 52.381 2.12 0.0 45.00 2.40 F
4107 4268 0.388659 TTGTTGGTGATGTTGCTGGC 59.611 50.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1785 1.359475 GGGTCGCATCGAGGACTAC 59.641 63.158 0.00 0.00 36.23 2.73 R
1874 2002 3.533487 AGGGGCCTCCTGAAAATTTCTAT 59.467 43.478 11.62 0.00 46.07 1.98 R
3639 3789 8.293699 TCTTACTAACTCACTTAGATGCATCA 57.706 34.615 27.81 11.65 36.13 3.07 R
3718 3879 1.202794 TCCAATGACTCAGCAACTGCA 60.203 47.619 4.22 0.00 45.16 4.41 R
3857 4018 8.343366 TGCTGTACTCATATTCTTACTAACTCG 58.657 37.037 0.00 0.00 0.00 4.18 R
5199 5366 0.106708 TCAGCTGCATCCCGGATTAC 59.893 55.000 9.47 0.00 0.00 1.89 R
5902 9911 0.033920 AGTCGTCCGGTTAAACACCC 59.966 55.000 0.00 0.00 43.83 4.61 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
93 94 2.361610 CACCATGAGCACCCCCAC 60.362 66.667 0.00 0.00 0.00 4.61
718 832 1.448540 CACGGATCTGCCACCACTC 60.449 63.158 0.00 0.00 35.94 3.51
724 838 2.172483 ATCTGCCACCACTCACCGTC 62.172 60.000 0.00 0.00 0.00 4.79
898 1012 6.926313 AGTGAGTAACTGGACTAAATCACTC 58.074 40.000 0.00 0.00 37.88 3.51
903 1017 2.897969 ACTGGACTAAATCACTCCGTGT 59.102 45.455 0.00 0.00 34.79 4.49
916 1030 3.679980 CACTCCGTGTTTCCAGTAGATTG 59.320 47.826 0.00 0.00 0.00 2.67
1014 1128 0.697658 TGACCATGTCCATTGCTCCA 59.302 50.000 0.00 0.00 0.00 3.86
1084 1198 1.884464 GCGATGATTGGAGCGCTCA 60.884 57.895 36.27 19.60 46.90 4.26
1137 1251 3.052082 GACATGGTGCACTGCGCT 61.052 61.111 17.98 0.00 43.06 5.92
1192 1306 7.233389 AGGACATGCACTAAATCGATACTAT 57.767 36.000 0.00 0.00 0.00 2.12
1202 1316 8.420945 CACTAAATCGATACTATCTGCGAAAAG 58.579 37.037 0.00 0.00 36.28 2.27
1203 1317 6.771188 AAATCGATACTATCTGCGAAAAGG 57.229 37.500 0.00 0.00 36.28 3.11
1204 1318 5.707242 ATCGATACTATCTGCGAAAAGGA 57.293 39.130 0.00 0.00 36.28 3.36
1206 1320 5.520632 TCGATACTATCTGCGAAAAGGAAG 58.479 41.667 0.00 0.00 0.00 3.46
1208 1322 5.399892 CGATACTATCTGCGAAAAGGAAGAC 59.600 44.000 0.00 0.00 0.00 3.01
1210 1324 5.091261 ACTATCTGCGAAAAGGAAGACAT 57.909 39.130 0.00 0.00 0.00 3.06
1213 1327 7.275920 ACTATCTGCGAAAAGGAAGACATATT 58.724 34.615 0.00 0.00 0.00 1.28
1215 1329 6.422776 TCTGCGAAAAGGAAGACATATTTC 57.577 37.500 0.00 0.00 0.00 2.17
1218 1332 6.611381 TGCGAAAAGGAAGACATATTTCTTG 58.389 36.000 8.84 0.00 35.90 3.02
1220 1334 7.389330 TGCGAAAAGGAAGACATATTTCTTGTA 59.611 33.333 8.84 0.00 35.90 2.41
1224 1338 8.438676 AAAGGAAGACATATTTCTTGTATCCG 57.561 34.615 8.84 0.00 37.84 4.18
1283 1406 4.285517 CACCTATAGCTGATTCCAGATGGT 59.714 45.833 0.00 0.00 43.02 3.55
1340 1463 3.194620 TGGTGGGTATTGGGTTATGTCT 58.805 45.455 0.00 0.00 0.00 3.41
1420 1543 4.631813 CCTTGATGGTGAACAGTTAGCTAC 59.368 45.833 0.00 0.00 0.00 3.58
1421 1544 4.882842 TGATGGTGAACAGTTAGCTACA 57.117 40.909 0.00 0.00 0.00 2.74
1517 1640 2.359981 ATCATCTCCATTGTGCCCAG 57.640 50.000 0.00 0.00 0.00 4.45
1534 1657 2.224621 CCCAGGAAGCAGAGTTCTTGAA 60.225 50.000 0.00 0.00 35.98 2.69
1601 1724 0.957888 GTTCTCCTTGGCAGCCTGAC 60.958 60.000 14.15 0.00 0.00 3.51
1671 1794 5.636543 ACTGTTTTATTTTCCGTAGTCCTCG 59.363 40.000 0.00 0.00 0.00 4.63
1676 1801 0.099968 TTTCCGTAGTCCTCGATGCG 59.900 55.000 0.00 0.00 0.00 4.73
1698 1823 1.605710 CCCAAGAAGTTGACACTGCAG 59.394 52.381 13.48 13.48 35.46 4.41
1733 1861 9.875708 TTGGCCAGGATTAATGTTTATATACTT 57.124 29.630 5.11 0.00 0.00 2.24
1750 1878 0.162933 CTTCGCGCGTGTTATTGTGT 59.837 50.000 30.98 0.00 0.00 3.72
1754 1882 1.154301 CGCGTGTTATTGTGTGGCC 60.154 57.895 0.00 0.00 0.00 5.36
1769 1897 3.821033 GTGTGGCCAAGAAGAAACATACT 59.179 43.478 7.24 0.00 0.00 2.12
1770 1898 4.072131 TGTGGCCAAGAAGAAACATACTC 58.928 43.478 7.24 0.00 0.00 2.59
1771 1899 3.440522 GTGGCCAAGAAGAAACATACTCC 59.559 47.826 7.24 0.00 0.00 3.85
1772 1900 2.678336 GGCCAAGAAGAAACATACTCCG 59.322 50.000 0.00 0.00 0.00 4.63
1775 1903 4.329256 GCCAAGAAGAAACATACTCCGTAC 59.671 45.833 0.00 0.00 0.00 3.67
1824 1952 3.748660 TACATGACATGCGGGGGCG 62.749 63.158 15.49 0.00 0.00 6.13
1874 2002 4.517453 GGGTTAGTTGAACATAAGTGTGCA 59.483 41.667 0.00 0.00 42.26 4.57
3639 3789 7.039082 ACCCAATACTTGAAGCATGTACAAAAT 60.039 33.333 0.00 0.00 29.23 1.82
3641 3791 8.028354 CCAATACTTGAAGCATGTACAAAATGA 58.972 33.333 0.00 0.00 29.23 2.57
3688 3845 7.122799 AGAGTATGAGTACAGCACAGTGAATAA 59.877 37.037 4.15 0.00 33.09 1.40
3718 3879 1.677217 GCCGAGCAGGACAGAAAGAAT 60.677 52.381 2.12 0.00 45.00 2.40
3857 4018 2.422276 ACAAAAAGGTGCATCGAAGC 57.578 45.000 5.52 5.52 0.00 3.86
3983 4144 0.809385 CCATCTCTTGCTTGCACTGG 59.191 55.000 0.00 0.00 0.00 4.00
3985 4146 2.156917 CATCTCTTGCTTGCACTGGAA 58.843 47.619 0.00 0.00 0.00 3.53
3998 4159 6.094048 GCTTGCACTGGAAGATTACTTTATCA 59.906 38.462 14.08 0.00 37.43 2.15
4083 4244 5.866633 GTGTAGAACTCATCTTCCAAGAGTG 59.133 44.000 0.00 0.00 41.45 3.51
4107 4268 0.388659 TTGTTGGTGATGTTGCTGGC 59.611 50.000 0.00 0.00 0.00 4.85
4108 4269 1.290009 GTTGGTGATGTTGCTGGCC 59.710 57.895 0.00 0.00 0.00 5.36
4380 4541 6.663093 TGGTTCCTGCAAATATAACAGACAAT 59.337 34.615 0.00 0.00 33.10 2.71
4381 4542 7.831690 TGGTTCCTGCAAATATAACAGACAATA 59.168 33.333 0.00 0.00 33.10 1.90
4382 4543 8.682710 GGTTCCTGCAAATATAACAGACAATAA 58.317 33.333 0.00 0.00 33.10 1.40
4442 4606 6.183360 GGAACATACATGGACTGGTAATGTTG 60.183 42.308 0.00 7.58 37.15 3.33
4649 4815 8.327941 TCCTCATAATTCTCTTTGTTCAAGTG 57.672 34.615 0.00 0.00 33.66 3.16
4784 4950 3.007506 CACTACACACCCTATGGTTCACA 59.992 47.826 0.00 0.00 44.75 3.58
4819 4985 3.391296 GGGCATACTCTCCCTGAACATAA 59.609 47.826 0.00 0.00 39.46 1.90
4875 5041 4.324099 GGCCATGGATATCTGCTTACTGAT 60.324 45.833 18.40 0.00 38.03 2.90
4990 5156 9.128107 CAGTATGTGTACAATTTGTCAATTTCC 57.872 33.333 5.07 0.00 33.09 3.13
4991 5157 8.303876 AGTATGTGTACAATTTGTCAATTTCCC 58.696 33.333 5.07 0.00 33.09 3.97
5016 5183 2.094906 CGCAAAAGGGGCCTAAAGTTAC 60.095 50.000 0.84 0.00 0.00 2.50
5101 5268 1.745653 GCAACTCAGGAAGGTATTGCC 59.254 52.381 0.00 0.00 37.14 4.52
5252 5419 1.886777 GAAGGAGGCTGCTGATCGC 60.887 63.158 10.05 3.07 39.77 4.58
5281 5448 2.268076 GCAGCCGGGTTGTCAACAT 61.268 57.895 17.29 0.00 0.00 2.71
5321 5488 2.165234 TCCTCAGAAGCTTCTCATCGTG 59.835 50.000 26.18 14.68 34.74 4.35
5335 5502 0.806102 ATCGTGGACAATTCGCTCCG 60.806 55.000 0.00 0.00 0.00 4.63
5371 5538 3.387397 AGTACAAGAACTACAACGGCAC 58.613 45.455 0.00 0.00 0.00 5.01
5429 5596 1.174783 GAGTACAGACGAAGAGCCCA 58.825 55.000 0.00 0.00 0.00 5.36
5459 5626 3.120199 GGCTACACTTGCAGTTACATGTG 60.120 47.826 9.11 8.48 45.98 3.21
5485 5652 7.308830 GCAGATAAGATAAGCAAATAACCCTGG 60.309 40.741 0.00 0.00 0.00 4.45
5497 5666 2.993264 CCCTGGCAAGGCTTGGTG 60.993 66.667 27.25 4.74 42.96 4.17
5624 5793 7.604164 AGATGTACATGTTTTTGTAGGAGTGAG 59.396 37.037 14.43 0.00 32.92 3.51
5661 5830 0.608035 GACCTGTTTGGATTCCCGCA 60.608 55.000 0.00 0.00 39.71 5.69
5670 5839 1.425428 GATTCCCGCAGTTTGCTCG 59.575 57.895 0.00 0.00 42.25 5.03
5799 5968 7.141100 CCGAGTTGGTTAAATGATGTAAAGT 57.859 36.000 0.00 0.00 0.00 2.66
5809 9818 6.403866 AAATGATGTAAAGTGTGGCTTTGA 57.596 33.333 2.83 0.00 46.07 2.69
5813 9822 2.295909 TGTAAAGTGTGGCTTTGATGGC 59.704 45.455 2.83 0.00 46.07 4.40
5821 9830 1.010419 GGCTTTGATGGCAGCAAACG 61.010 55.000 25.45 20.72 37.81 3.60
5831 9840 1.425428 CAGCAAACGCGGAGGAATC 59.575 57.895 12.47 0.00 0.00 2.52
5839 9848 1.880340 GCGGAGGAATCTCAGTGCG 60.880 63.158 0.00 0.00 41.69 5.34
5841 9850 0.526524 CGGAGGAATCTCAGTGCGTC 60.527 60.000 0.00 0.00 41.69 5.19
5850 9859 0.439985 CTCAGTGCGTCGGTGAAATG 59.560 55.000 0.00 0.00 0.00 2.32
5852 9861 0.163788 CAGTGCGTCGGTGAAATGAC 59.836 55.000 0.00 0.00 0.00 3.06
5879 9888 2.031919 ATTGCGGTCGCTTGGTCA 59.968 55.556 16.36 0.00 42.51 4.02
5885 9894 1.841663 CGGTCGCTTGGTCACTTTGG 61.842 60.000 0.00 0.00 0.00 3.28
5909 9918 4.193240 ACAAAGGAATACTGGGGTGTTT 57.807 40.909 0.00 0.00 0.00 2.83
5954 9963 1.683011 CCCGGGCAACTCAAGAATCAT 60.683 52.381 8.08 0.00 0.00 2.45
5976 9985 7.982252 TCATATTCTAAATGAGCTCAGGGATT 58.018 34.615 22.96 15.55 0.00 3.01
6010 10019 3.497262 GGACTTGGAGTTGGAGTTTTACG 59.503 47.826 0.00 0.00 0.00 3.18
6011 10020 2.876550 ACTTGGAGTTGGAGTTTTACGC 59.123 45.455 0.00 0.00 0.00 4.42
6012 10021 2.922740 TGGAGTTGGAGTTTTACGCT 57.077 45.000 0.00 0.00 0.00 5.07
6013 10022 4.202284 ACTTGGAGTTGGAGTTTTACGCTA 60.202 41.667 0.00 0.00 0.00 4.26
6014 10023 4.339872 TGGAGTTGGAGTTTTACGCTAA 57.660 40.909 0.00 0.00 0.00 3.09
6015 10024 4.901868 TGGAGTTGGAGTTTTACGCTAAT 58.098 39.130 0.00 0.00 0.00 1.73
6016 10025 5.310451 TGGAGTTGGAGTTTTACGCTAATT 58.690 37.500 0.00 0.00 0.00 1.40
6017 10026 5.766174 TGGAGTTGGAGTTTTACGCTAATTT 59.234 36.000 0.00 0.00 0.00 1.82
6018 10027 6.263617 TGGAGTTGGAGTTTTACGCTAATTTT 59.736 34.615 0.00 0.00 0.00 1.82
6019 10028 7.143340 GGAGTTGGAGTTTTACGCTAATTTTT 58.857 34.615 0.00 0.00 0.00 1.94
6020 10029 7.114388 GGAGTTGGAGTTTTACGCTAATTTTTG 59.886 37.037 0.00 0.00 0.00 2.44
6021 10030 7.485810 AGTTGGAGTTTTACGCTAATTTTTGT 58.514 30.769 0.00 0.00 0.00 2.83
6022 10031 7.977293 AGTTGGAGTTTTACGCTAATTTTTGTT 59.023 29.630 0.00 0.00 0.00 2.83
6023 10032 9.235537 GTTGGAGTTTTACGCTAATTTTTGTTA 57.764 29.630 0.00 0.00 0.00 2.41
6024 10033 9.798994 TTGGAGTTTTACGCTAATTTTTGTTAA 57.201 25.926 0.00 0.00 0.00 2.01
6025 10034 9.968870 TGGAGTTTTACGCTAATTTTTGTTAAT 57.031 25.926 0.00 0.00 0.00 1.40
6098 10107 6.453926 TTTTTAAATAATACCCAGTCGGCC 57.546 37.500 0.00 0.00 33.26 6.13
6099 10108 2.651382 AAATAATACCCAGTCGGCCC 57.349 50.000 0.00 0.00 33.26 5.80
6100 10109 1.513858 AATAATACCCAGTCGGCCCA 58.486 50.000 0.00 0.00 33.26 5.36
6101 10110 0.763035 ATAATACCCAGTCGGCCCAC 59.237 55.000 0.00 0.00 33.26 4.61
6102 10111 0.325860 TAATACCCAGTCGGCCCACT 60.326 55.000 0.00 0.00 33.26 4.00
6103 10112 1.910580 AATACCCAGTCGGCCCACTG 61.911 60.000 22.43 22.43 43.13 3.66
6113 10122 2.362120 GCCCACTGCTGGCTGATT 60.362 61.111 6.47 0.00 45.70 2.57
6114 10123 2.707849 GCCCACTGCTGGCTGATTG 61.708 63.158 6.47 0.00 45.70 2.67
6115 10124 2.050350 CCCACTGCTGGCTGATTGG 61.050 63.158 6.47 4.71 36.00 3.16
6116 10125 1.001764 CCACTGCTGGCTGATTGGA 60.002 57.895 6.47 0.00 0.00 3.53
6117 10126 0.395311 CCACTGCTGGCTGATTGGAT 60.395 55.000 6.47 0.00 0.00 3.41
6118 10127 0.738975 CACTGCTGGCTGATTGGATG 59.261 55.000 6.47 0.00 0.00 3.51
6119 10128 1.035932 ACTGCTGGCTGATTGGATGC 61.036 55.000 6.47 0.00 0.00 3.91
6120 10129 1.000646 TGCTGGCTGATTGGATGCA 60.001 52.632 0.00 0.00 0.00 3.96
6121 10130 1.035385 TGCTGGCTGATTGGATGCAG 61.035 55.000 0.00 0.00 35.28 4.41
6122 10131 1.035932 GCTGGCTGATTGGATGCAGT 61.036 55.000 0.00 0.00 34.66 4.40
6123 10132 1.022735 CTGGCTGATTGGATGCAGTC 58.977 55.000 2.59 2.59 37.27 3.51
6124 10133 0.328926 TGGCTGATTGGATGCAGTCA 59.671 50.000 11.80 11.80 43.75 3.41
6125 10134 1.064240 TGGCTGATTGGATGCAGTCAT 60.064 47.619 12.70 0.00 41.38 3.06
6126 10135 1.607628 GGCTGATTGGATGCAGTCATC 59.392 52.381 12.70 8.77 46.46 2.92
6133 10142 3.595691 GATGCAGTCATCCTACCGG 57.404 57.895 0.00 0.00 42.50 5.28
6134 10143 0.753262 GATGCAGTCATCCTACCGGT 59.247 55.000 13.98 13.98 42.50 5.28
6135 10144 0.465705 ATGCAGTCATCCTACCGGTG 59.534 55.000 19.93 7.24 0.00 4.94
6136 10145 1.144057 GCAGTCATCCTACCGGTGG 59.856 63.158 19.93 15.68 0.00 4.61
6137 10146 1.144057 CAGTCATCCTACCGGTGGC 59.856 63.158 19.93 0.20 0.00 5.01
6138 10147 2.064581 AGTCATCCTACCGGTGGCC 61.065 63.158 19.93 0.00 0.00 5.36
6153 10162 3.818787 GCCGATTGCCACTGCTGG 61.819 66.667 0.00 0.00 41.13 4.85
6161 10170 3.291611 CCACTGCTGGCCAATTCC 58.708 61.111 7.01 0.00 0.00 3.01
6162 10171 2.353610 CCACTGCTGGCCAATTCCC 61.354 63.158 7.01 0.00 0.00 3.97
6163 10172 2.037847 ACTGCTGGCCAATTCCCC 59.962 61.111 7.01 0.00 0.00 4.81
6164 10173 2.761213 CTGCTGGCCAATTCCCCC 60.761 66.667 7.01 0.00 0.00 5.40
6165 10174 3.598887 TGCTGGCCAATTCCCCCA 61.599 61.111 7.01 0.00 0.00 4.96
6166 10175 2.761213 GCTGGCCAATTCCCCCAG 60.761 66.667 7.01 9.98 46.95 4.45
6167 10176 2.772924 CTGGCCAATTCCCCCAGT 59.227 61.111 7.01 0.00 40.92 4.00
6168 10177 1.380380 CTGGCCAATTCCCCCAGTC 60.380 63.158 7.01 0.00 40.92 3.51
6169 10178 2.440247 GGCCAATTCCCCCAGTCG 60.440 66.667 0.00 0.00 0.00 4.18
6170 10179 2.440247 GCCAATTCCCCCAGTCGG 60.440 66.667 0.00 0.00 0.00 4.79
6171 10180 2.440247 CCAATTCCCCCAGTCGGC 60.440 66.667 0.00 0.00 0.00 5.54
6172 10181 2.440247 CAATTCCCCCAGTCGGCC 60.440 66.667 0.00 0.00 0.00 6.13
6173 10182 3.739613 AATTCCCCCAGTCGGCCC 61.740 66.667 0.00 0.00 0.00 5.80
6220 10229 4.776322 CACTGCCGGCGGATTGGA 62.776 66.667 41.14 11.71 0.00 3.53
6221 10230 3.797353 ACTGCCGGCGGATTGGAT 61.797 61.111 41.14 15.71 0.00 3.41
6222 10231 2.974698 CTGCCGGCGGATTGGATC 60.975 66.667 32.31 10.67 0.00 3.36
6223 10232 4.562425 TGCCGGCGGATTGGATCC 62.562 66.667 33.44 9.82 46.22 3.36
6235 10244 3.837355 GATTGGATCCATTTAGCCCACT 58.163 45.455 17.06 0.00 0.00 4.00
6236 10245 2.734755 TGGATCCATTTAGCCCACTG 57.265 50.000 11.44 0.00 0.00 3.66
6237 10246 1.322442 GGATCCATTTAGCCCACTGC 58.678 55.000 6.95 0.00 41.71 4.40
6247 10256 2.361610 CCCACTGCTGGCCGATTT 60.362 61.111 0.00 0.00 36.00 2.17
6248 10257 2.409870 CCCACTGCTGGCCGATTTC 61.410 63.158 0.00 0.00 36.00 2.17
6249 10258 2.409870 CCACTGCTGGCCGATTTCC 61.410 63.158 0.00 0.00 0.00 3.13
6250 10259 2.044946 ACTGCTGGCCGATTTCCC 60.045 61.111 0.00 0.00 0.00 3.97
6251 10260 2.830370 CTGCTGGCCGATTTCCCC 60.830 66.667 0.00 0.00 0.00 4.81
6252 10261 3.643595 CTGCTGGCCGATTTCCCCA 62.644 63.158 0.00 0.00 0.00 4.96
6253 10262 2.830370 GCTGGCCGATTTCCCCAG 60.830 66.667 0.00 1.66 46.95 4.45
6254 10263 2.677228 CTGGCCGATTTCCCCAGT 59.323 61.111 0.00 0.00 40.92 4.00
6255 10264 1.452108 CTGGCCGATTTCCCCAGTC 60.452 63.158 0.00 0.00 40.92 3.51
6256 10265 2.513897 GGCCGATTTCCCCAGTCG 60.514 66.667 0.00 0.00 35.29 4.18
6258 10267 2.513897 CCGATTTCCCCAGTCGGC 60.514 66.667 0.00 0.00 46.90 5.54
6259 10268 2.513897 CGATTTCCCCAGTCGGCC 60.514 66.667 0.00 0.00 0.00 6.13
6260 10269 2.124278 GATTTCCCCAGTCGGCCC 60.124 66.667 0.00 0.00 0.00 5.80
6261 10270 2.938798 ATTTCCCCAGTCGGCCCA 60.939 61.111 0.00 0.00 0.00 5.36
6262 10271 3.282374 ATTTCCCCAGTCGGCCCAC 62.282 63.158 0.00 0.00 0.00 4.61
6263 10272 4.974438 TTCCCCAGTCGGCCCACT 62.974 66.667 0.00 0.00 0.00 4.00
6275 10284 3.136123 CCCACTGCTGGCCGATTG 61.136 66.667 0.00 0.00 36.00 2.67
6276 10285 3.136123 CCACTGCTGGCCGATTGG 61.136 66.667 0.00 0.00 38.77 3.16
6305 10314 3.197790 CTCACCGCTGGCCGATTG 61.198 66.667 0.00 0.00 40.02 2.67
6306 10315 4.776322 TCACCGCTGGCCGATTGG 62.776 66.667 0.00 0.00 40.02 3.16
6325 10334 2.993853 CCCCCAGTCTGCTTCCTC 59.006 66.667 0.00 0.00 0.00 3.71
6326 10335 1.614824 CCCCCAGTCTGCTTCCTCT 60.615 63.158 0.00 0.00 0.00 3.69
6327 10336 0.325671 CCCCCAGTCTGCTTCCTCTA 60.326 60.000 0.00 0.00 0.00 2.43
6328 10337 1.118838 CCCCAGTCTGCTTCCTCTAG 58.881 60.000 0.00 0.00 0.00 2.43
6329 10338 1.118838 CCCAGTCTGCTTCCTCTAGG 58.881 60.000 0.00 0.00 0.00 3.02
6330 10339 0.463620 CCAGTCTGCTTCCTCTAGGC 59.536 60.000 0.00 0.00 34.44 3.93
6331 10340 0.463620 CAGTCTGCTTCCTCTAGGCC 59.536 60.000 0.00 0.00 34.44 5.19
6332 10341 1.040339 AGTCTGCTTCCTCTAGGCCG 61.040 60.000 0.00 0.00 34.44 6.13
6333 10342 1.038130 GTCTGCTTCCTCTAGGCCGA 61.038 60.000 0.00 0.00 34.44 5.54
6334 10343 1.038130 TCTGCTTCCTCTAGGCCGAC 61.038 60.000 0.00 0.00 34.44 4.79
6335 10344 1.304962 TGCTTCCTCTAGGCCGACA 60.305 57.895 0.00 0.00 34.44 4.35
6336 10345 1.323271 TGCTTCCTCTAGGCCGACAG 61.323 60.000 0.00 0.00 34.44 3.51
6337 10346 2.022240 GCTTCCTCTAGGCCGACAGG 62.022 65.000 9.98 9.98 41.62 4.00
6338 10347 0.684805 CTTCCTCTAGGCCGACAGGT 60.685 60.000 14.53 0.00 40.50 4.00
6339 10348 0.970937 TTCCTCTAGGCCGACAGGTG 60.971 60.000 14.53 3.88 40.50 4.00
6340 10349 2.496817 CTCTAGGCCGACAGGTGC 59.503 66.667 0.00 0.00 40.50 5.01
6341 10350 2.283604 TCTAGGCCGACAGGTGCA 60.284 61.111 0.00 0.00 40.50 4.57
6342 10351 1.680522 CTCTAGGCCGACAGGTGCAT 61.681 60.000 0.00 0.00 40.50 3.96
6343 10352 1.522355 CTAGGCCGACAGGTGCATG 60.522 63.158 0.00 0.00 40.50 4.06
6344 10353 3.680620 TAGGCCGACAGGTGCATGC 62.681 63.158 11.82 11.82 40.50 4.06
6346 10355 4.107051 GCCGACAGGTGCATGCAC 62.107 66.667 37.29 37.29 45.49 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
694 808 2.359850 GGCAGATCCGTGTTGGCA 60.360 61.111 1.18 0.00 37.35 4.92
701 815 1.913262 TGAGTGGTGGCAGATCCGT 60.913 57.895 0.00 0.00 37.80 4.69
898 1012 1.737793 GGCAATCTACTGGAAACACGG 59.262 52.381 0.00 0.00 35.60 4.94
903 1017 6.662755 AGAACATATGGCAATCTACTGGAAA 58.337 36.000 7.80 0.00 0.00 3.13
916 1030 2.759191 TCAGCGATGAGAACATATGGC 58.241 47.619 0.00 0.00 36.82 4.40
1014 1128 1.513158 CGCATCGTGTCTCTCCCTT 59.487 57.895 0.00 0.00 0.00 3.95
1028 1142 2.753966 GCGAACTGGACATGCGCAT 61.754 57.895 19.28 19.28 46.19 4.73
1091 1205 0.179000 CGAAGGATAAGGCAGCCTGT 59.821 55.000 17.05 7.07 44.39 4.00
1137 1251 2.161855 GTCCATGAAACATGGCAGTCA 58.838 47.619 21.51 5.67 39.01 3.41
1192 1306 6.173339 AGAAATATGTCTTCCTTTTCGCAGA 58.827 36.000 0.00 0.00 32.84 4.26
1202 1316 7.210873 AGTCGGATACAAGAAATATGTCTTCC 58.789 38.462 5.08 3.49 35.63 3.46
1203 1317 8.649973 AAGTCGGATACAAGAAATATGTCTTC 57.350 34.615 5.08 0.00 35.63 2.87
1206 1320 9.692749 TCATAAGTCGGATACAAGAAATATGTC 57.307 33.333 0.00 0.00 32.27 3.06
1210 1324 8.988934 GCAATCATAAGTCGGATACAAGAAATA 58.011 33.333 0.00 0.00 0.00 1.40
1213 1327 6.257849 GTGCAATCATAAGTCGGATACAAGAA 59.742 38.462 0.00 0.00 0.00 2.52
1215 1329 5.523552 TGTGCAATCATAAGTCGGATACAAG 59.476 40.000 0.00 0.00 0.00 3.16
1218 1332 7.834068 ATATGTGCAATCATAAGTCGGATAC 57.166 36.000 1.54 0.00 34.58 2.24
1220 1334 7.750229 AAATATGTGCAATCATAAGTCGGAT 57.250 32.000 1.54 0.00 34.58 4.18
1223 1337 8.337532 TCAGAAAATATGTGCAATCATAAGTCG 58.662 33.333 1.54 0.00 34.58 4.18
1283 1406 5.056480 CGGTCAATTTCCAGCATATACAGA 58.944 41.667 0.00 0.00 0.00 3.41
1420 1543 7.533426 ACAAAGCTTATTTGCAGTATCTTCTG 58.467 34.615 0.00 0.00 38.35 3.02
1421 1544 7.693969 ACAAAGCTTATTTGCAGTATCTTCT 57.306 32.000 0.00 0.00 34.99 2.85
1517 1640 4.083057 GGTGATTTCAAGAACTCTGCTTCC 60.083 45.833 2.54 0.00 0.00 3.46
1534 1657 3.239449 TCTGTACAGAGTGGTGGTGATT 58.761 45.455 21.74 0.00 32.82 2.57
1601 1724 5.589855 ACAAAAATTCCCAGAAAAGCAAAGG 59.410 36.000 0.00 0.00 0.00 3.11
1662 1785 1.359475 GGGTCGCATCGAGGACTAC 59.641 63.158 0.00 0.00 36.23 2.73
1671 1794 1.464997 GTCAACTTCTTGGGTCGCATC 59.535 52.381 0.00 0.00 0.00 3.91
1676 1801 1.604278 GCAGTGTCAACTTCTTGGGTC 59.396 52.381 0.00 0.00 32.98 4.46
1698 1823 6.547510 ACATTAATCCTGGCCAAACTATTCTC 59.452 38.462 7.01 0.00 0.00 2.87
1733 1861 1.489390 CACACAATAACACGCGCGA 59.511 52.632 39.36 15.38 0.00 5.87
1750 1878 3.686016 GGAGTATGTTTCTTCTTGGCCA 58.314 45.455 0.00 0.00 0.00 5.36
1769 1897 3.056678 TCAGAAAATAACAGCCGTACGGA 60.057 43.478 37.62 17.07 37.50 4.69
1770 1898 3.255725 TCAGAAAATAACAGCCGTACGG 58.744 45.455 30.06 30.06 38.57 4.02
1771 1899 4.387862 ACTTCAGAAAATAACAGCCGTACG 59.612 41.667 8.69 8.69 0.00 3.67
1772 1900 5.857822 ACTTCAGAAAATAACAGCCGTAC 57.142 39.130 0.00 0.00 0.00 3.67
1775 1903 5.519722 ACAAACTTCAGAAAATAACAGCCG 58.480 37.500 0.00 0.00 0.00 5.52
1824 1952 7.042797 AGAATTAACATTCATGGCCATACAC 57.957 36.000 20.30 0.00 41.37 2.90
1874 2002 3.533487 AGGGGCCTCCTGAAAATTTCTAT 59.467 43.478 11.62 0.00 46.07 1.98
3639 3789 8.293699 TCTTACTAACTCACTTAGATGCATCA 57.706 34.615 27.81 11.65 36.13 3.07
3641 3791 8.299990 ACTCTTACTAACTCACTTAGATGCAT 57.700 34.615 0.00 0.00 36.13 3.96
3718 3879 1.202794 TCCAATGACTCAGCAACTGCA 60.203 47.619 4.22 0.00 45.16 4.41
3857 4018 8.343366 TGCTGTACTCATATTCTTACTAACTCG 58.657 37.037 0.00 0.00 0.00 4.18
4017 4178 6.989169 ACCTGCAAGATAGAAGACATACAATC 59.011 38.462 0.00 0.00 34.07 2.67
4024 4185 5.939764 ACATACCTGCAAGATAGAAGACA 57.060 39.130 0.00 0.00 34.07 3.41
4083 4244 2.362077 AGCAACATCACCAACAAGTTCC 59.638 45.455 0.00 0.00 0.00 3.62
4107 4268 3.864686 CATTTCTCCACGCGGCGG 61.865 66.667 27.37 14.99 0.00 6.13
4108 4269 3.864686 CCATTTCTCCACGCGGCG 61.865 66.667 22.36 22.36 0.00 6.46
4112 4273 0.960364 TTGAGGCCATTTCTCCACGC 60.960 55.000 5.01 0.00 0.00 5.34
4113 4274 1.470098 CTTTGAGGCCATTTCTCCACG 59.530 52.381 5.01 0.00 0.00 4.94
4380 4541 6.239600 GCTCATAGATGATACCAAGGGTGTTA 60.240 42.308 0.00 0.00 36.02 2.41
4381 4542 5.455326 GCTCATAGATGATACCAAGGGTGTT 60.455 44.000 0.00 0.00 36.02 3.32
4382 4543 4.040952 GCTCATAGATGATACCAAGGGTGT 59.959 45.833 0.00 0.00 36.02 4.16
4485 4649 9.482627 GTGAGTTCTTGTCTATATCTTAATGGG 57.517 37.037 0.00 0.00 0.00 4.00
4649 4815 3.728845 TGCCTCAGAACAGAACAAGTAC 58.271 45.455 0.00 0.00 0.00 2.73
4734 4900 9.962783 CACAGTGGGTACTCTATATTTTAGTAC 57.037 37.037 10.98 10.98 43.08 2.73
4819 4985 1.494721 TGGGTGCCTCTTGAAGTCTTT 59.505 47.619 0.00 0.00 0.00 2.52
4853 5019 4.277515 TCAGTAAGCAGATATCCATGGC 57.722 45.455 6.96 0.00 0.00 4.40
4891 5057 5.526111 GGCGGATTTCATGTAAGCTACTTTA 59.474 40.000 0.29 0.00 0.00 1.85
4901 5067 1.525077 GCCGGGCGGATTTCATGTA 60.525 57.895 1.81 0.00 37.50 2.29
4990 5156 2.493273 TAGGCCCCTTTTGCGGAAGG 62.493 60.000 0.00 10.20 44.74 3.46
4991 5157 0.610785 TTAGGCCCCTTTTGCGGAAG 60.611 55.000 0.00 0.00 0.00 3.46
5016 5183 3.059634 TGCGTTGAAAAAGGAGAAACG 57.940 42.857 2.13 2.13 44.72 3.60
5199 5366 0.106708 TCAGCTGCATCCCGGATTAC 59.893 55.000 9.47 0.00 0.00 1.89
5207 5374 2.089980 AGAACAACATCAGCTGCATCC 58.910 47.619 9.47 0.00 0.00 3.51
5281 5448 2.275715 ATCTGGGCCCTCATCCTCCA 62.276 60.000 25.70 0.00 0.00 3.86
5321 5488 1.696832 GCAGTCGGAGCGAATTGTCC 61.697 60.000 0.00 0.00 37.72 4.02
5335 5502 0.747852 GTACTAGCTCCCTGGCAGTC 59.252 60.000 14.43 0.00 34.17 3.51
5371 5538 2.168521 AGATCATGGTACTGTCAACGGG 59.831 50.000 0.00 0.00 0.00 5.28
5429 5596 0.955919 GCAAGTGTAGCCTCGCCTTT 60.956 55.000 0.00 0.00 0.00 3.11
5459 5626 7.308830 CCAGGGTTATTTGCTTATCTTATCTGC 60.309 40.741 0.00 0.00 0.00 4.26
5485 5652 4.272100 CAATGCACCAAGCCTTGC 57.728 55.556 0.00 0.00 40.96 4.01
5624 5793 1.048601 TCTGACCAGTGACCAACTCC 58.951 55.000 0.00 0.00 36.83 3.85
5670 5839 4.458989 TCCAGAAACCATACATTGCTTCAC 59.541 41.667 0.00 0.00 0.00 3.18
5751 5920 1.024579 ATTTGGACGCCGTTAGCCAG 61.025 55.000 0.00 0.00 38.78 4.85
5797 5966 1.530013 GCTGCCATCAAAGCCACACT 61.530 55.000 0.00 0.00 33.12 3.55
5799 5968 1.114119 TTGCTGCCATCAAAGCCACA 61.114 50.000 0.00 0.00 38.71 4.17
5809 9818 3.434319 CTCCGCGTTTGCTGCCAT 61.434 61.111 4.92 0.00 39.65 4.40
5813 9822 1.021390 AGATTCCTCCGCGTTTGCTG 61.021 55.000 4.92 0.00 39.65 4.41
5821 9830 1.880340 CGCACTGAGATTCCTCCGC 60.880 63.158 0.00 0.00 38.66 5.54
5831 9840 0.439985 CATTTCACCGACGCACTGAG 59.560 55.000 0.00 0.00 0.00 3.35
5839 9848 2.031191 ACAAACGTGTCATTTCACCGAC 59.969 45.455 0.00 0.00 35.18 4.79
5841 9850 2.748461 ACAAACGTGTCATTTCACCG 57.252 45.000 0.00 0.00 35.18 4.94
5852 9861 0.721155 CGACCGCAATGACAAACGTG 60.721 55.000 0.00 0.00 0.00 4.49
5885 9894 4.149598 ACACCCCAGTATTCCTTTGTTTC 58.850 43.478 0.00 0.00 0.00 2.78
5894 9903 3.011818 CCGGTTAAACACCCCAGTATTC 58.988 50.000 0.00 0.00 43.83 1.75
5898 9907 0.109153 GTCCGGTTAAACACCCCAGT 59.891 55.000 0.00 0.00 43.83 4.00
5901 9910 0.950555 GTCGTCCGGTTAAACACCCC 60.951 60.000 0.00 0.00 43.83 4.95
5902 9911 0.033920 AGTCGTCCGGTTAAACACCC 59.966 55.000 0.00 0.00 43.83 4.61
5909 9918 3.663995 TTGAATTCAGTCGTCCGGTTA 57.336 42.857 8.41 0.00 0.00 2.85
5917 9926 2.095853 CCGGGTGATTTGAATTCAGTCG 59.904 50.000 8.41 6.27 0.00 4.18
5954 9963 6.329986 TCCAATCCCTGAGCTCATTTAGAATA 59.670 38.462 18.63 0.00 0.00 1.75
5976 9985 0.401738 CCAAGTCCTGCCTCTTTCCA 59.598 55.000 0.00 0.00 0.00 3.53
6075 10084 5.360429 GGGCCGACTGGGTATTATTTAAAAA 59.640 40.000 0.00 0.00 38.44 1.94
6076 10085 4.888823 GGGCCGACTGGGTATTATTTAAAA 59.111 41.667 0.00 0.00 38.44 1.52
6077 10086 4.079901 TGGGCCGACTGGGTATTATTTAAA 60.080 41.667 0.00 0.00 38.44 1.52
6078 10087 3.458857 TGGGCCGACTGGGTATTATTTAA 59.541 43.478 0.00 0.00 38.44 1.52
6079 10088 3.047115 TGGGCCGACTGGGTATTATTTA 58.953 45.455 0.00 0.00 38.44 1.40
6080 10089 1.847737 TGGGCCGACTGGGTATTATTT 59.152 47.619 0.00 0.00 38.44 1.40
6081 10090 1.142262 GTGGGCCGACTGGGTATTATT 59.858 52.381 11.17 0.00 38.44 1.40
6082 10091 0.763035 GTGGGCCGACTGGGTATTAT 59.237 55.000 11.17 0.00 38.44 1.28
6083 10092 0.325860 AGTGGGCCGACTGGGTATTA 60.326 55.000 20.84 0.00 38.44 0.98
6084 10093 1.615424 AGTGGGCCGACTGGGTATT 60.615 57.895 20.84 0.00 38.44 1.89
6085 10094 2.040606 AGTGGGCCGACTGGGTAT 59.959 61.111 20.84 0.00 38.44 2.73
6086 10095 3.000819 CAGTGGGCCGACTGGGTA 61.001 66.667 33.66 0.00 39.85 3.69
6097 10106 2.050350 CCAATCAGCCAGCAGTGGG 61.050 63.158 0.00 0.00 45.17 4.61
6099 10108 0.738975 CATCCAATCAGCCAGCAGTG 59.261 55.000 0.00 0.00 0.00 3.66
6100 10109 1.035932 GCATCCAATCAGCCAGCAGT 61.036 55.000 0.00 0.00 0.00 4.40
6101 10110 1.035385 TGCATCCAATCAGCCAGCAG 61.035 55.000 0.00 0.00 0.00 4.24
6102 10111 1.000646 TGCATCCAATCAGCCAGCA 60.001 52.632 0.00 0.00 0.00 4.41
6103 10112 1.035932 ACTGCATCCAATCAGCCAGC 61.036 55.000 0.00 0.00 33.80 4.85
6104 10113 1.022735 GACTGCATCCAATCAGCCAG 58.977 55.000 0.00 0.00 33.80 4.85
6105 10114 0.328926 TGACTGCATCCAATCAGCCA 59.671 50.000 0.00 0.00 33.80 4.75
6106 10115 1.607628 GATGACTGCATCCAATCAGCC 59.392 52.381 0.00 0.00 44.12 4.85
6116 10125 0.465705 CACCGGTAGGATGACTGCAT 59.534 55.000 6.87 0.00 41.02 3.96
6117 10126 1.613317 CCACCGGTAGGATGACTGCA 61.613 60.000 6.87 0.00 41.02 4.41
6118 10127 1.144057 CCACCGGTAGGATGACTGC 59.856 63.158 6.87 0.00 41.02 4.40
6119 10128 1.144057 GCCACCGGTAGGATGACTG 59.856 63.158 22.51 1.90 41.02 3.51
6120 10129 2.064581 GGCCACCGGTAGGATGACT 61.065 63.158 22.51 0.00 41.02 3.41
6121 10130 2.504519 GGCCACCGGTAGGATGAC 59.495 66.667 22.51 8.09 41.02 3.06
6122 10131 3.151710 CGGCCACCGGTAGGATGA 61.152 66.667 22.51 0.00 44.15 2.92
6136 10145 3.818787 CCAGCAGTGGCAATCGGC 61.819 66.667 0.00 0.00 44.61 5.54
6145 10154 2.353610 GGGGAATTGGCCAGCAGTG 61.354 63.158 5.11 0.00 0.00 3.66
6146 10155 2.037847 GGGGAATTGGCCAGCAGT 59.962 61.111 5.11 0.00 0.00 4.40
6147 10156 2.761213 GGGGGAATTGGCCAGCAG 60.761 66.667 5.11 0.00 0.00 4.24
6148 10157 3.598887 TGGGGGAATTGGCCAGCA 61.599 61.111 5.11 0.00 0.00 4.41
6149 10158 2.761213 CTGGGGGAATTGGCCAGC 60.761 66.667 5.11 0.00 0.00 4.85
6150 10159 1.380380 GACTGGGGGAATTGGCCAG 60.380 63.158 5.11 0.00 35.00 4.85
6151 10160 2.770130 GACTGGGGGAATTGGCCA 59.230 61.111 0.00 0.00 0.00 5.36
6152 10161 2.440247 CGACTGGGGGAATTGGCC 60.440 66.667 0.00 0.00 0.00 5.36
6153 10162 2.440247 CCGACTGGGGGAATTGGC 60.440 66.667 0.00 0.00 0.00 4.52
6154 10163 2.440247 GCCGACTGGGGGAATTGG 60.440 66.667 0.00 0.00 35.78 3.16
6155 10164 2.440247 GGCCGACTGGGGGAATTG 60.440 66.667 0.00 0.00 35.78 2.32
6156 10165 3.739613 GGGCCGACTGGGGGAATT 61.740 66.667 0.00 0.00 35.78 2.17
6203 10212 4.776322 TCCAATCCGCCGGCAGTG 62.776 66.667 28.98 17.35 0.00 3.66
6204 10213 3.757248 GATCCAATCCGCCGGCAGT 62.757 63.158 28.98 8.51 0.00 4.40
6205 10214 2.974698 GATCCAATCCGCCGGCAG 60.975 66.667 28.98 16.96 0.00 4.85
6206 10215 4.562425 GGATCCAATCCGCCGGCA 62.562 66.667 28.98 8.41 40.13 5.69
6214 10223 3.571401 CAGTGGGCTAAATGGATCCAATC 59.429 47.826 20.67 6.06 0.00 2.67
6215 10224 3.569491 CAGTGGGCTAAATGGATCCAAT 58.431 45.455 20.67 7.74 0.00 3.16
6216 10225 2.949963 GCAGTGGGCTAAATGGATCCAA 60.950 50.000 20.67 0.60 40.25 3.53
6217 10226 1.410083 GCAGTGGGCTAAATGGATCCA 60.410 52.381 18.88 18.88 40.25 3.41
6218 10227 1.322442 GCAGTGGGCTAAATGGATCC 58.678 55.000 4.20 4.20 40.25 3.36
6230 10239 2.361610 AAATCGGCCAGCAGTGGG 60.362 61.111 2.24 0.00 45.17 4.61
6232 10241 2.409870 GGGAAATCGGCCAGCAGTG 61.410 63.158 2.24 0.00 0.00 3.66
6233 10242 2.044946 GGGAAATCGGCCAGCAGT 60.045 61.111 2.24 0.00 0.00 4.40
6234 10243 2.830370 GGGGAAATCGGCCAGCAG 60.830 66.667 2.24 0.00 0.00 4.24
6235 10244 3.643595 CTGGGGAAATCGGCCAGCA 62.644 63.158 2.24 0.00 0.00 4.41
6236 10245 2.830370 CTGGGGAAATCGGCCAGC 60.830 66.667 2.24 0.00 0.00 4.85
6237 10246 1.452108 GACTGGGGAAATCGGCCAG 60.452 63.158 2.24 0.00 32.95 4.85
6238 10247 2.674754 GACTGGGGAAATCGGCCA 59.325 61.111 2.24 0.00 0.00 5.36
6239 10248 2.513897 CGACTGGGGAAATCGGCC 60.514 66.667 0.00 0.00 32.22 6.13
6242 10251 2.513897 GGCCGACTGGGGAAATCG 60.514 66.667 0.00 0.00 35.78 3.34
6243 10252 2.124278 GGGCCGACTGGGGAAATC 60.124 66.667 0.00 0.00 35.78 2.17
6244 10253 2.938798 TGGGCCGACTGGGGAAAT 60.939 61.111 0.00 0.00 35.78 2.17
6245 10254 3.961414 GTGGGCCGACTGGGGAAA 61.961 66.667 11.17 0.00 35.78 3.13
6246 10255 4.974438 AGTGGGCCGACTGGGGAA 62.974 66.667 20.84 0.00 35.78 3.97
6258 10267 3.136123 CAATCGGCCAGCAGTGGG 61.136 66.667 2.24 0.00 45.17 4.61
6288 10297 3.197790 CAATCGGCCAGCGGTGAG 61.198 66.667 17.83 7.47 0.00 3.51
6289 10298 4.776322 CCAATCGGCCAGCGGTGA 62.776 66.667 17.83 0.00 0.00 4.02
6308 10317 0.325671 TAGAGGAAGCAGACTGGGGG 60.326 60.000 4.26 0.00 0.00 5.40
6309 10318 1.118838 CTAGAGGAAGCAGACTGGGG 58.881 60.000 4.26 0.00 0.00 4.96
6310 10319 1.118838 CCTAGAGGAAGCAGACTGGG 58.881 60.000 4.26 0.00 37.39 4.45
6311 10320 0.463620 GCCTAGAGGAAGCAGACTGG 59.536 60.000 4.26 0.00 37.39 4.00
6312 10321 0.463620 GGCCTAGAGGAAGCAGACTG 59.536 60.000 0.00 0.00 37.39 3.51
6313 10322 1.040339 CGGCCTAGAGGAAGCAGACT 61.040 60.000 0.00 0.00 37.39 3.24
6314 10323 1.038130 TCGGCCTAGAGGAAGCAGAC 61.038 60.000 0.00 0.00 37.39 3.51
6315 10324 1.038130 GTCGGCCTAGAGGAAGCAGA 61.038 60.000 0.00 0.00 37.39 4.26
6316 10325 1.323271 TGTCGGCCTAGAGGAAGCAG 61.323 60.000 0.00 0.00 37.39 4.24
6317 10326 1.304962 TGTCGGCCTAGAGGAAGCA 60.305 57.895 0.00 0.00 37.39 3.91
6318 10327 1.439644 CTGTCGGCCTAGAGGAAGC 59.560 63.158 0.00 0.00 37.39 3.86
6319 10328 0.684805 ACCTGTCGGCCTAGAGGAAG 60.685 60.000 25.56 1.27 37.39 3.46
6320 10329 0.970937 CACCTGTCGGCCTAGAGGAA 60.971 60.000 25.56 0.00 37.39 3.36
6321 10330 1.379977 CACCTGTCGGCCTAGAGGA 60.380 63.158 25.56 0.00 37.39 3.71
6322 10331 3.082579 GCACCTGTCGGCCTAGAGG 62.083 68.421 18.14 18.14 36.01 3.69
6323 10332 1.680522 ATGCACCTGTCGGCCTAGAG 61.681 60.000 0.00 0.00 0.00 2.43
6324 10333 1.685765 ATGCACCTGTCGGCCTAGA 60.686 57.895 0.00 0.00 0.00 2.43
6325 10334 1.522355 CATGCACCTGTCGGCCTAG 60.522 63.158 0.00 0.00 0.00 3.02
6326 10335 2.584064 CATGCACCTGTCGGCCTA 59.416 61.111 0.00 0.00 0.00 3.93
6329 10338 4.107051 GTGCATGCACCTGTCGGC 62.107 66.667 35.69 12.07 40.79 5.54


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

AutoCloner maintained by Alex Coulton.