Multiple sequence alignment - TraesCS4B01G242900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G242900 chr4B 100.000 8080 0 0 1 8080 503003759 502995680 0.000000e+00 14922.0
1 TraesCS4B01G242900 chr4B 96.959 592 18 0 1 592 543756809 543756218 0.000000e+00 994.0
2 TraesCS4B01G242900 chr4D 92.586 5274 280 51 668 5878 405065430 405060205 0.000000e+00 7470.0
3 TraesCS4B01G242900 chr4D 94.190 2186 100 14 5916 8080 405060197 405058018 0.000000e+00 3308.0
4 TraesCS4B01G242900 chr4A 89.754 4353 249 86 611 4891 62564588 62560361 0.000000e+00 5385.0
5 TraesCS4B01G242900 chr4A 89.500 2600 176 43 4891 7459 62560060 62557527 0.000000e+00 3199.0
6 TraesCS4B01G242900 chr4A 92.391 460 27 7 7457 7913 62557495 62557041 0.000000e+00 649.0
7 TraesCS4B01G242900 chr4A 95.294 170 7 1 7911 8080 62556961 62556793 1.340000e-67 268.0
8 TraesCS4B01G242900 chr4A 96.226 53 1 1 5869 5921 21349125 21349176 1.440000e-12 86.1
9 TraesCS4B01G242900 chr4A 91.803 61 3 2 5876 5935 597691392 597691333 5.200000e-12 84.2
10 TraesCS4B01G242900 chr7B 93.581 592 38 0 1 592 639234911 639235502 0.000000e+00 883.0
11 TraesCS4B01G242900 chr7B 83.529 85 9 5 5836 5917 81689020 81689102 3.130000e-09 75.0
12 TraesCS4B01G242900 chr2B 92.088 594 45 1 1 592 185774133 185774726 0.000000e+00 835.0
13 TraesCS4B01G242900 chr2B 93.846 65 4 0 608 672 361281974 361282038 1.860000e-16 99.0
14 TraesCS4B01G242900 chr2B 93.220 59 4 0 609 667 93630846 93630904 4.020000e-13 87.9
15 TraesCS4B01G242900 chr1A 89.713 593 58 3 1 592 93771590 93772180 0.000000e+00 754.0
16 TraesCS4B01G242900 chr1A 89.207 593 60 3 1 592 554275101 554274512 0.000000e+00 737.0
17 TraesCS4B01G242900 chr6A 88.364 593 62 3 1 592 597907519 597908105 0.000000e+00 706.0
18 TraesCS4B01G242900 chr3A 87.312 599 64 5 1 592 727660639 727660046 0.000000e+00 675.0
19 TraesCS4B01G242900 chr2D 82.521 595 95 7 1 592 32411726 32412314 1.550000e-141 514.0
20 TraesCS4B01G242900 chr5A 82.047 596 94 11 4 592 644805145 644804556 5.630000e-136 496.0
21 TraesCS4B01G242900 chr5A 89.119 193 21 0 7888 8080 514300971 514301163 2.910000e-59 241.0
22 TraesCS4B01G242900 chr7A 85.052 194 29 0 7887 8080 691269389 691269196 1.780000e-46 198.0
23 TraesCS4B01G242900 chr7D 82.667 225 28 3 1927 2151 571386767 571386980 1.070000e-43 189.0
24 TraesCS4B01G242900 chr7D 98.039 51 0 1 5869 5919 18804066 18804115 4.020000e-13 87.9
25 TraesCS4B01G242900 chr7D 94.545 55 2 1 5865 5919 561960131 561960184 5.200000e-12 84.2
26 TraesCS4B01G242900 chr7D 92.982 57 2 2 5863 5919 264491079 264491025 1.870000e-11 82.4
27 TraesCS4B01G242900 chr1B 96.923 65 2 0 608 672 162083009 162082945 8.570000e-20 110.0
28 TraesCS4B01G242900 chr1B 92.188 64 5 0 609 672 453181422 453181359 3.110000e-14 91.6
29 TraesCS4B01G242900 chr5D 92.308 65 5 0 609 673 511815852 511815916 8.630000e-15 93.5
30 TraesCS4B01G242900 chr5D 92.982 57 2 2 5863 5919 501203737 501203791 1.870000e-11 82.4
31 TraesCS4B01G242900 chr6D 94.828 58 1 2 5870 5926 370847697 370847753 1.120000e-13 89.8
32 TraesCS4B01G242900 chr3B 98.000 50 1 0 5870 5919 730758413 730758364 4.020000e-13 87.9
33 TraesCS4B01G242900 chr3B 94.737 38 1 1 608 644 738500750 738500713 3.150000e-04 58.4


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 TraesCS4B01G242900 chr4B 502995680 503003759 8079 True 14922.00 14922 100.00000 1 8080 1 chr4B.!!$R1 8079
1 TraesCS4B01G242900 chr4B 543756218 543756809 591 True 994.00 994 96.95900 1 592 1 chr4B.!!$R2 591
2 TraesCS4B01G242900 chr4D 405058018 405065430 7412 True 5389.00 7470 93.38800 668 8080 2 chr4D.!!$R1 7412
3 TraesCS4B01G242900 chr4A 62556793 62564588 7795 True 2375.25 5385 91.73475 611 8080 4 chr4A.!!$R2 7469
4 TraesCS4B01G242900 chr7B 639234911 639235502 591 False 883.00 883 93.58100 1 592 1 chr7B.!!$F2 591
5 TraesCS4B01G242900 chr2B 185774133 185774726 593 False 835.00 835 92.08800 1 592 1 chr2B.!!$F2 591
6 TraesCS4B01G242900 chr1A 93771590 93772180 590 False 754.00 754 89.71300 1 592 1 chr1A.!!$F1 591
7 TraesCS4B01G242900 chr1A 554274512 554275101 589 True 737.00 737 89.20700 1 592 1 chr1A.!!$R1 591
8 TraesCS4B01G242900 chr6A 597907519 597908105 586 False 706.00 706 88.36400 1 592 1 chr6A.!!$F1 591
9 TraesCS4B01G242900 chr3A 727660046 727660639 593 True 675.00 675 87.31200 1 592 1 chr3A.!!$R1 591
10 TraesCS4B01G242900 chr2D 32411726 32412314 588 False 514.00 514 82.52100 1 592 1 chr2D.!!$F1 591
11 TraesCS4B01G242900 chr5A 644804556 644805145 589 True 496.00 496 82.04700 4 592 1 chr5A.!!$R1 588

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
978 991 0.179029 CAACTTCCCAACCCTGACGT 60.179 55.0 0.0 0.0 0.00 4.34 F
1535 1559 0.250513 GGCACCAGAGGGAACACTAG 59.749 60.0 0.0 0.0 38.05 2.57 F
2257 2299 0.247460 TCTCTCAAGACATGGTGCGG 59.753 55.0 0.0 0.0 0.00 5.69 F
2819 2884 0.533308 GTGGTTGGAACACGGTAGCA 60.533 55.0 0.0 0.0 39.29 3.49 F
2829 2894 0.681733 CACGGTAGCATATCCTGGCT 59.318 55.0 0.0 0.0 43.94 4.75 F
4719 4803 0.619832 AGGCTTCCATCTCCAGCTCA 60.620 55.0 0.0 0.0 33.76 4.26 F
6203 6613 0.034186 TATGCAGGCACAAGAAGGGG 60.034 55.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2285 0.391661 AGCTACCGCACCATGTCTTG 60.392 55.000 0.00 0.00 39.10 3.02 R
2797 2862 0.540454 TACCGTGTTCCAACCACACA 59.460 50.000 4.23 0.00 44.14 3.72 R
3747 3821 1.217585 CCACAGACGTCACACTGCAG 61.218 60.000 19.50 13.48 37.61 4.41 R
4699 4783 0.106521 GAGCTGGAGATGGAAGCCTC 59.893 60.000 0.00 0.00 37.68 4.70 R
4771 4855 1.200948 GGCTTGCCAAGAGATGTCAAC 59.799 52.381 9.04 0.00 0.00 3.18 R
6645 7055 0.040067 CTTGGTCGCTTTGGTGCTTC 60.040 55.000 0.00 0.00 0.00 3.86 R
7471 7888 0.037975 AAGCGGCCTTGCATCAAAAG 60.038 50.000 0.00 0.00 37.31 2.27 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
170 171 2.093288 CCACTTCAGCATAGCCTCTCAA 60.093 50.000 0.00 0.00 0.00 3.02
491 501 2.303311 TGTCGTGGGTGATATTGTTCCA 59.697 45.455 0.00 0.00 0.00 3.53
615 627 1.067635 CATGGTGGGCTTTTGTACTGC 60.068 52.381 0.00 0.00 0.00 4.40
643 655 6.036517 CCCTATCTATCAATGCAAAGATACGC 59.963 42.308 7.22 0.00 31.38 4.42
727 740 4.201960 ACTCACTCATACACGAGCATACAG 60.202 45.833 0.00 0.00 36.42 2.74
728 741 2.791560 CACTCATACACGAGCATACAGC 59.208 50.000 0.00 0.00 46.19 4.40
745 758 0.689745 AGCCATACACTCGCCCCTAA 60.690 55.000 0.00 0.00 0.00 2.69
764 777 2.787191 TTGCAAACGTCAGGCAAGA 58.213 47.368 14.89 0.00 42.12 3.02
886 899 1.578926 CGTCCTCGCATTGCCAAAA 59.421 52.632 2.41 0.00 0.00 2.44
892 905 0.321021 TCGCATTGCCAAAATTGCCT 59.679 45.000 2.41 0.00 0.00 4.75
944 957 6.079424 TGACAAAAGATTTCCCCTAAAACG 57.921 37.500 0.00 0.00 0.00 3.60
974 987 0.251341 CTCCCAACTTCCCAACCCTG 60.251 60.000 0.00 0.00 0.00 4.45
975 988 0.699577 TCCCAACTTCCCAACCCTGA 60.700 55.000 0.00 0.00 0.00 3.86
976 989 0.539669 CCCAACTTCCCAACCCTGAC 60.540 60.000 0.00 0.00 0.00 3.51
978 991 0.179029 CAACTTCCCAACCCTGACGT 60.179 55.000 0.00 0.00 0.00 4.34
980 993 1.003718 CTTCCCAACCCTGACGTCC 60.004 63.158 14.12 0.00 0.00 4.79
981 994 2.465055 CTTCCCAACCCTGACGTCCC 62.465 65.000 14.12 0.00 0.00 4.46
984 997 2.928396 CAACCCTGACGTCCCCCT 60.928 66.667 14.12 0.00 0.00 4.79
985 998 2.122099 AACCCTGACGTCCCCCTT 60.122 61.111 14.12 0.00 0.00 3.95
986 999 2.222013 AACCCTGACGTCCCCCTTC 61.222 63.158 14.12 0.00 0.00 3.46
987 1000 3.771160 CCCTGACGTCCCCCTTCG 61.771 72.222 14.12 0.00 0.00 3.79
1066 1079 1.471684 ACTACAACGCCCTCTACTTCG 59.528 52.381 0.00 0.00 0.00 3.79
1182 1195 1.679032 GGTGCCATCTAGGTTCGCTTT 60.679 52.381 0.00 0.00 40.61 3.51
1210 1223 1.146637 GCTTATGCAGATCGAGGCTG 58.853 55.000 12.36 12.36 39.41 4.85
1281 1294 1.073125 TCCCCTTCGAAAATCACTGCA 59.927 47.619 0.00 0.00 0.00 4.41
1290 1303 1.155889 AAATCACTGCACATTCGCGA 58.844 45.000 3.71 3.71 33.35 5.87
1293 1306 2.357396 ACTGCACATTCGCGAGCA 60.357 55.556 18.16 18.16 35.43 4.26
1299 1312 1.845266 CACATTCGCGAGCAGTCTAT 58.155 50.000 9.59 0.00 0.00 1.98
1303 1316 4.089208 CACATTCGCGAGCAGTCTATATTC 59.911 45.833 9.59 0.00 0.00 1.75
1314 1327 7.502120 AGCAGTCTATATTCGATGCATTTTT 57.498 32.000 0.00 0.00 36.15 1.94
1315 1328 7.358066 AGCAGTCTATATTCGATGCATTTTTG 58.642 34.615 0.00 0.00 36.15 2.44
1316 1329 7.227314 AGCAGTCTATATTCGATGCATTTTTGA 59.773 33.333 0.00 0.00 36.15 2.69
1317 1330 8.019669 GCAGTCTATATTCGATGCATTTTTGAT 58.980 33.333 0.00 0.00 33.92 2.57
1402 1424 1.981495 AGAGGTTTAGCAGCCTTGTCT 59.019 47.619 0.00 0.00 34.81 3.41
1403 1425 3.173965 AGAGGTTTAGCAGCCTTGTCTA 58.826 45.455 0.00 0.00 34.81 2.59
1535 1559 0.250513 GGCACCAGAGGGAACACTAG 59.749 60.000 0.00 0.00 38.05 2.57
1544 1568 3.031736 GAGGGAACACTAGTGCTATCCA 58.968 50.000 29.44 0.00 34.65 3.41
1545 1569 3.450904 AGGGAACACTAGTGCTATCCAA 58.549 45.455 29.44 0.00 34.65 3.53
1782 1811 8.642432 CAGTATGTATCTTCCACATCCTTTCTA 58.358 37.037 0.00 0.00 37.74 2.10
1837 1866 5.410355 AATGTTTATGCACTTGCCATCTT 57.590 34.783 0.00 0.00 41.18 2.40
1844 1873 5.864418 ATGCACTTGCCATCTTGATTAAT 57.136 34.783 0.00 0.00 41.18 1.40
2024 2066 4.214332 GGTTGAGATCCGATTATTTGGCTC 59.786 45.833 0.00 0.00 0.00 4.70
2025 2067 4.687901 TGAGATCCGATTATTTGGCTCA 57.312 40.909 0.00 0.00 0.00 4.26
2098 2140 4.489771 CCGGCGGCCATTTCCTCT 62.490 66.667 20.71 0.00 0.00 3.69
2107 2149 2.624636 GCCATTTCCTCTGCCAAAATG 58.375 47.619 0.00 0.00 39.16 2.32
2190 2232 7.307811 GGCCGAAAATCTTCCTATTGTACATAC 60.308 40.741 0.00 0.00 0.00 2.39
2257 2299 0.247460 TCTCTCAAGACATGGTGCGG 59.753 55.000 0.00 0.00 0.00 5.69
2277 2319 4.292784 GCTCTGAGCTCCAACACC 57.707 61.111 21.93 0.00 38.45 4.16
2351 2405 1.638070 TGGGATGATTTGGGCACAGTA 59.362 47.619 0.00 0.00 0.00 2.74
2420 2474 7.458038 AATACGTTTGTTTGAAATCCACAAC 57.542 32.000 0.00 0.00 30.12 3.32
2430 2495 5.344743 TGAAATCCACAACTCTAGGCTAG 57.655 43.478 15.56 15.56 0.00 3.42
2434 2499 1.550524 CCACAACTCTAGGCTAGCACA 59.449 52.381 18.24 1.84 0.00 4.57
2688 2753 6.051074 TGAGTGAAGTGTATAATGCATCCAG 58.949 40.000 0.00 0.00 0.00 3.86
2735 2800 2.524569 AAATTGTGGAACCAAAGCGG 57.475 45.000 0.00 0.00 42.50 5.52
2760 2825 7.975616 GGTCTATGACATTTGTACATTGCAAAT 59.024 33.333 1.71 0.00 44.46 2.32
2816 2881 3.383092 GTGTGGTTGGAACACGGTA 57.617 52.632 0.00 0.00 41.64 4.02
2819 2884 0.533308 GTGGTTGGAACACGGTAGCA 60.533 55.000 0.00 0.00 39.29 3.49
2829 2894 0.681733 CACGGTAGCATATCCTGGCT 59.318 55.000 0.00 0.00 43.94 4.75
2928 2993 2.767496 CAGGGGCTCCTCCTCCTG 60.767 72.222 0.00 0.00 42.67 3.86
3004 3072 9.225682 TCCAGTTAGGAAATAGTTCAGGATTAT 57.774 33.333 5.15 0.00 45.65 1.28
3134 3202 9.772973 TGGTTTATCATCCACATTAGTATGTAC 57.227 33.333 0.00 0.00 43.07 2.90
3187 3255 9.167311 GTATCACCAGAATAACTGTCTTGAAAT 57.833 33.333 0.00 0.00 44.40 2.17
3369 3443 8.882736 TGTGTGCATCAAAGATAATAACACTAG 58.117 33.333 0.00 0.00 37.04 2.57
3401 3475 9.485206 GGTACTTGTTCAATAAGACAAAGACTA 57.515 33.333 0.12 0.00 0.00 2.59
3476 3550 3.081061 TGTGATTGCAGTAACCATGGTC 58.919 45.455 20.07 6.67 0.00 4.02
3549 3623 5.927030 TCGTCATGTAAGTTGAATTCAAGC 58.073 37.500 21.05 15.04 36.39 4.01
3639 3713 6.038271 CCTCTTGGTGGCTACAACATAATTAC 59.962 42.308 1.52 0.00 45.27 1.89
3747 3821 4.569943 TGAGATTGACAGCTAACCACTTC 58.430 43.478 0.00 0.00 0.00 3.01
3842 3916 3.134458 GAGAATGGGTGCTAATTCCTCG 58.866 50.000 0.00 0.00 34.02 4.63
3883 3957 6.183361 TGTCAATGGCATAGGTATTAGCTCTT 60.183 38.462 0.00 0.00 0.00 2.85
3957 4031 5.184864 TGTTTTATTCATGCCACCGATTTCT 59.815 36.000 0.00 0.00 0.00 2.52
3969 4043 3.620374 CACCGATTTCTCTGACTTGATGG 59.380 47.826 0.00 0.00 0.00 3.51
3989 4063 8.375493 TGATGGTATTCCTTACTTGTTCTAGT 57.625 34.615 0.00 0.00 34.23 2.57
3996 4072 6.982160 TCCTTACTTGTTCTAGTTACCACA 57.018 37.500 0.00 0.00 0.00 4.17
3997 4073 7.364149 TCCTTACTTGTTCTAGTTACCACAA 57.636 36.000 0.00 0.00 0.00 3.33
4184 4261 6.829703 TCGACAAAAACGTGTCTTAAAGAAA 58.170 32.000 0.00 0.00 44.79 2.52
4188 4265 6.745907 ACAAAAACGTGTCTTAAAGAAAGCTC 59.254 34.615 0.00 0.00 34.97 4.09
4229 4306 6.384015 TCCAGTTGTGTCCATGTATATCTTCT 59.616 38.462 0.00 0.00 0.00 2.85
4231 4308 7.554118 CCAGTTGTGTCCATGTATATCTTCTTT 59.446 37.037 0.00 0.00 0.00 2.52
4254 4331 3.801114 TTATGTGATGGAGGAGTCACG 57.199 47.619 0.00 0.00 45.88 4.35
4282 4359 9.254421 CATCAATCTTATGATTACGTAATTGCG 57.746 33.333 21.18 14.67 40.61 4.85
4288 4365 8.647226 TCTTATGATTACGTAATTGCGATCATG 58.353 33.333 27.77 18.71 36.85 3.07
4407 4486 2.544694 GCTCTCACGGTCACTATCATGG 60.545 54.545 0.00 0.00 0.00 3.66
4410 4489 1.762370 TCACGGTCACTATCATGGCAT 59.238 47.619 0.00 0.00 0.00 4.40
4434 4513 4.276431 GGTTTTCCATCTTGGTCGTTGTTA 59.724 41.667 0.00 0.00 39.03 2.41
4551 4632 8.975663 AATAATAAGTTGAAAGGTAGTAGGGC 57.024 34.615 0.00 0.00 0.00 5.19
4552 4633 6.638021 AATAAGTTGAAAGGTAGTAGGGCT 57.362 37.500 0.00 0.00 0.00 5.19
4598 4682 9.415544 ACATGCTTAATTGTCTGAAATCTTTTC 57.584 29.630 0.00 0.00 0.00 2.29
4599 4683 9.635520 CATGCTTAATTGTCTGAAATCTTTTCT 57.364 29.630 2.08 0.00 0.00 2.52
4650 4734 1.045407 AACAGCAGTACCAACGAGGA 58.955 50.000 5.70 0.00 41.22 3.71
4652 4736 1.623811 ACAGCAGTACCAACGAGGAAT 59.376 47.619 5.70 0.00 41.22 3.01
4686 4770 4.471078 AGTATCCTGATAGGTGTAGGCA 57.529 45.455 0.00 0.00 36.53 4.75
4699 4783 1.813178 TGTAGGCAGACAGAGAAGACG 59.187 52.381 0.00 0.00 0.00 4.18
4719 4803 0.619832 AGGCTTCCATCTCCAGCTCA 60.620 55.000 0.00 0.00 33.76 4.26
4771 4855 0.952497 ATGCAACACACAGAGCCTCG 60.952 55.000 0.00 0.00 0.00 4.63
4854 4938 7.324178 AGTTACCTAGTGTAGCATGAAAGAAG 58.676 38.462 0.00 0.00 33.43 2.85
4900 4984 9.767684 TCATGTTTTGAAATAATTGTAGCTACG 57.232 29.630 18.74 0.00 0.00 3.51
4901 4985 9.009327 CATGTTTTGAAATAATTGTAGCTACGG 57.991 33.333 18.74 0.00 0.00 4.02
4902 4986 7.024768 TGTTTTGAAATAATTGTAGCTACGGC 58.975 34.615 18.74 0.00 39.06 5.68
5017 5402 3.715628 ATTAAACAATGCGGGCTCATC 57.284 42.857 0.00 0.00 0.00 2.92
5055 5440 5.355071 TGAGCTCACATTGCTTAATTAGGTG 59.645 40.000 13.74 0.00 41.30 4.00
5065 5450 4.814234 TGCTTAATTAGGTGTATTGGAGCG 59.186 41.667 0.00 0.00 32.66 5.03
5070 5455 1.191535 AGGTGTATTGGAGCGCACTA 58.808 50.000 11.47 0.00 32.90 2.74
5074 5459 3.377172 GGTGTATTGGAGCGCACTAAATT 59.623 43.478 11.47 0.00 32.90 1.82
5233 5618 6.317391 GGATAGCAGAGCTTGTTAAGAAATGT 59.683 38.462 0.00 0.00 40.44 2.71
5242 5627 6.549736 AGCTTGTTAAGAAATGTTGGTAAGGT 59.450 34.615 0.00 0.00 0.00 3.50
5246 5631 4.853924 AAGAAATGTTGGTAAGGTGCTG 57.146 40.909 0.00 0.00 0.00 4.41
5358 5746 5.070981 ACAACTCCATATACCTGTCAGGATG 59.929 44.000 26.18 17.33 37.67 3.51
5383 5771 1.619654 TTTCAAGCCCCACACTGATG 58.380 50.000 0.00 0.00 0.00 3.07
5708 6108 2.689983 GCCATATGACAACTTCCCCTTG 59.310 50.000 3.65 0.00 0.00 3.61
5731 6131 0.304705 GTGTGACTGTTGTTGAGCCG 59.695 55.000 0.00 0.00 0.00 5.52
5759 6159 6.169557 AGTGTTATGAAGTCAGTTACACCA 57.830 37.500 14.60 0.00 36.69 4.17
5765 6169 1.375523 GTCAGTTACACCAGCGGGG 60.376 63.158 8.08 0.95 44.81 5.73
5801 6205 1.145738 ACCCCAAAGCTGATGACTTGT 59.854 47.619 1.45 0.00 0.00 3.16
5810 6214 8.127327 CCAAAGCTGATGACTTGTTGATAATAG 58.873 37.037 1.45 0.00 0.00 1.73
5844 6248 3.056821 TCGAGTGGGTCAGTAATGTCAAG 60.057 47.826 0.00 0.00 0.00 3.02
5879 6283 5.763355 TGGTAGTGAGGCTAACATACTACT 58.237 41.667 4.46 0.00 42.08 2.57
5880 6284 5.826737 TGGTAGTGAGGCTAACATACTACTC 59.173 44.000 4.46 6.10 42.08 2.59
5881 6285 5.241285 GGTAGTGAGGCTAACATACTACTCC 59.759 48.000 4.46 0.00 41.93 3.85
5882 6286 4.216708 AGTGAGGCTAACATACTACTCCC 58.783 47.826 4.46 0.00 0.00 4.30
5883 6287 4.079096 AGTGAGGCTAACATACTACTCCCT 60.079 45.833 4.46 0.00 0.00 4.20
5884 6288 4.278919 GTGAGGCTAACATACTACTCCCTC 59.721 50.000 0.00 0.00 38.43 4.30
5885 6289 3.827876 GAGGCTAACATACTACTCCCTCC 59.172 52.174 0.00 0.00 33.27 4.30
5886 6290 2.557490 GGCTAACATACTACTCCCTCCG 59.443 54.545 0.00 0.00 0.00 4.63
5887 6291 3.220940 GCTAACATACTACTCCCTCCGT 58.779 50.000 0.00 0.00 0.00 4.69
5888 6292 3.252944 GCTAACATACTACTCCCTCCGTC 59.747 52.174 0.00 0.00 0.00 4.79
5889 6293 2.361643 ACATACTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
5890 6294 1.133544 ACATACTACTCCCTCCGTCCC 60.134 57.143 0.00 0.00 0.00 4.46
5891 6295 1.133575 CATACTACTCCCTCCGTCCCA 60.134 57.143 0.00 0.00 0.00 4.37
5892 6296 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
5893 6297 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
5894 6298 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
5895 6299 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
5896 6300 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
5897 6301 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5898 6302 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5899 6303 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5900 6304 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5901 6305 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5902 6306 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5903 6307 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5904 6308 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5905 6309 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
5906 6310 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
5907 6311 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
5908 6312 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5909 6313 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5969 6373 6.387041 TCCGAGTTTCGTTATGTATCTGAT 57.613 37.500 0.00 0.00 38.40 2.90
5971 6375 8.107399 TCCGAGTTTCGTTATGTATCTGATAT 57.893 34.615 0.00 0.00 38.40 1.63
6008 6415 3.586618 AGCCTGACAAAAGAAGGATCTCT 59.413 43.478 0.00 0.00 33.77 3.10
6058 6465 7.450944 TGATGCAATATCTTACCCAAATATGCA 59.549 33.333 0.00 0.00 30.99 3.96
6105 6513 8.902540 TTCATATTAATCTATCGCCAACTTGT 57.097 30.769 0.00 0.00 0.00 3.16
6152 6562 5.280011 CCACCATATACTCTTGGATGTACCC 60.280 48.000 0.00 0.00 36.79 3.69
6201 6611 1.098050 GGTATGCAGGCACAAGAAGG 58.902 55.000 0.00 0.00 0.00 3.46
6203 6613 0.034186 TATGCAGGCACAAGAAGGGG 60.034 55.000 0.00 0.00 0.00 4.79
6239 6649 8.435982 AGCTATTATAGAGTTGGAAAATCAGCT 58.564 33.333 3.04 0.00 44.66 4.24
6473 6883 7.459795 TGCCAAACATACATCAAATAAGTCA 57.540 32.000 0.00 0.00 0.00 3.41
6520 6930 0.321919 GATGCACCAGCTGAGTTCCA 60.322 55.000 17.39 10.85 42.74 3.53
6525 6935 2.719739 CACCAGCTGAGTTCCATCATT 58.280 47.619 17.39 0.00 0.00 2.57
6531 6941 5.069648 CCAGCTGAGTTCCATCATTCTACTA 59.930 44.000 17.39 0.00 0.00 1.82
6629 7039 0.465460 TTCGCTTTGGCAACCTGACT 60.465 50.000 0.00 0.00 38.60 3.41
6645 7055 0.947244 GACTGGCACAACTGTTCAGG 59.053 55.000 10.51 0.00 38.70 3.86
6722 7132 6.398095 CAGACAAAAGAAAAGGAAAACCAGT 58.602 36.000 0.00 0.00 0.00 4.00
6755 7165 9.743057 GATGGATCCTATTCAATAATAGTCGAG 57.257 37.037 14.23 0.00 42.05 4.04
7042 7452 2.810274 CAGACCATGAAACTGTGGACTG 59.190 50.000 8.89 8.89 46.22 3.51
7078 7488 4.649267 TTGTGGACATTTCAGATGGGTA 57.351 40.909 0.00 0.00 0.00 3.69
7084 7494 6.260936 GTGGACATTTCAGATGGGTAACTATG 59.739 42.308 0.00 0.00 38.25 2.23
7166 7576 1.133982 AGACATCTCGCTACACTGCAG 59.866 52.381 13.48 13.48 0.00 4.41
7224 7634 3.128259 CGCATATCGCAGCTATGGT 57.872 52.632 4.32 0.00 42.60 3.55
7235 7645 0.763652 AGCTATGGTGAGGATGCTGG 59.236 55.000 0.00 0.00 0.00 4.85
7251 7661 1.442769 CTGGGTCGTCCTGTGAAATG 58.557 55.000 0.00 0.00 36.20 2.32
7255 7665 1.798813 GGTCGTCCTGTGAAATGTGTC 59.201 52.381 0.00 0.00 0.00 3.67
7256 7666 1.798813 GTCGTCCTGTGAAATGTGTCC 59.201 52.381 0.00 0.00 0.00 4.02
7257 7667 1.691976 TCGTCCTGTGAAATGTGTCCT 59.308 47.619 0.00 0.00 0.00 3.85
7258 7668 1.800586 CGTCCTGTGAAATGTGTCCTG 59.199 52.381 0.00 0.00 0.00 3.86
7361 7778 1.901833 TGTATGCTCTCACTTCAGGCA 59.098 47.619 0.00 0.00 37.32 4.75
7369 7786 2.094182 TCTCACTTCAGGCAACCGTATC 60.094 50.000 0.00 0.00 37.17 2.24
7387 7804 6.535508 ACCGTATCTCACTTTTCTATTTCTGC 59.464 38.462 0.00 0.00 0.00 4.26
7410 7827 0.792640 GACGACAGTGGCAAGTCATG 59.207 55.000 17.94 7.93 34.48 3.07
7411 7828 0.603707 ACGACAGTGGCAAGTCATGG 60.604 55.000 17.94 7.38 34.48 3.66
7431 7848 2.162809 GGAATTGCGGACGTATGGTTTT 59.837 45.455 0.00 0.00 0.00 2.43
7434 7851 0.322322 TGCGGACGTATGGTTTTCCT 59.678 50.000 0.00 0.00 41.38 3.36
7487 7937 0.314935 ACACTTTTGATGCAAGGCCG 59.685 50.000 0.00 0.00 0.00 6.13
7496 7946 0.243636 ATGCAAGGCCGCTTTGTAAC 59.756 50.000 15.80 1.41 0.00 2.50
7504 7954 1.607148 GCCGCTTTGTAACTTGGTTCT 59.393 47.619 0.00 0.00 0.00 3.01
7514 7964 5.741011 TGTAACTTGGTTCTGACTTTGACT 58.259 37.500 0.00 0.00 0.00 3.41
7562 8015 7.148490 TGTCACATGTCACAAAAGGTATTATCG 60.148 37.037 0.00 0.00 0.00 2.92
7591 8044 6.767524 TTTGTATGCGGAATAAGTTTCCAT 57.232 33.333 5.32 0.00 38.49 3.41
7593 8046 6.767524 TGTATGCGGAATAAGTTTCCATTT 57.232 33.333 5.32 0.00 38.49 2.32
7595 8048 7.254852 TGTATGCGGAATAAGTTTCCATTTTC 58.745 34.615 5.32 0.00 38.49 2.29
7598 8051 5.102313 GCGGAATAAGTTTCCATTTTCAGG 58.898 41.667 5.32 0.00 38.49 3.86
7622 8075 9.586732 AGGTTTGTTATGGCATGTAACATATAT 57.413 29.630 14.69 3.40 40.55 0.86
7767 8220 9.737427 AGACTTTTCGTAATCTATATGTCACTG 57.263 33.333 0.00 0.00 0.00 3.66
7768 8221 8.354011 ACTTTTCGTAATCTATATGTCACTGC 57.646 34.615 0.00 0.00 0.00 4.40
7769 8222 8.198109 ACTTTTCGTAATCTATATGTCACTGCT 58.802 33.333 0.00 0.00 0.00 4.24
7770 8223 9.678941 CTTTTCGTAATCTATATGTCACTGCTA 57.321 33.333 0.00 0.00 0.00 3.49
7883 8339 9.132521 GAAACCACATCAAAGAATGTTAGATTG 57.867 33.333 0.00 0.00 37.78 2.67
8075 8613 6.384015 TCTGAATAACAGGAAAGATGAGGCTA 59.616 38.462 0.00 0.00 45.76 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 1.375523 GGTGTCATCTTCGCCCGTT 60.376 57.895 0.00 0.00 0.00 4.44
491 501 1.697432 TGTGGACGATTTGGACCTCTT 59.303 47.619 0.00 0.00 0.00 2.85
594 606 1.545582 CAGTACAAAAGCCCACCATGG 59.454 52.381 11.19 11.19 37.25 3.66
595 607 1.067635 GCAGTACAAAAGCCCACCATG 60.068 52.381 0.00 0.00 0.00 3.66
596 608 1.256812 GCAGTACAAAAGCCCACCAT 58.743 50.000 0.00 0.00 0.00 3.55
597 609 0.825840 GGCAGTACAAAAGCCCACCA 60.826 55.000 7.24 0.00 42.58 4.17
598 610 1.964448 GGCAGTACAAAAGCCCACC 59.036 57.895 7.24 0.00 42.58 4.61
603 615 2.194201 TAGGGTGGCAGTACAAAAGC 57.806 50.000 0.00 0.00 0.00 3.51
604 616 4.222124 AGATAGGGTGGCAGTACAAAAG 57.778 45.455 0.00 0.00 0.00 2.27
605 617 5.427157 TGATAGATAGGGTGGCAGTACAAAA 59.573 40.000 0.00 0.00 0.00 2.44
606 618 4.966168 TGATAGATAGGGTGGCAGTACAAA 59.034 41.667 0.00 0.00 0.00 2.83
607 619 4.552674 TGATAGATAGGGTGGCAGTACAA 58.447 43.478 0.00 0.00 0.00 2.41
608 620 4.193240 TGATAGATAGGGTGGCAGTACA 57.807 45.455 0.00 0.00 0.00 2.90
609 621 5.482908 CATTGATAGATAGGGTGGCAGTAC 58.517 45.833 0.00 0.00 0.00 2.73
615 627 5.624159 TCTTTGCATTGATAGATAGGGTGG 58.376 41.667 0.00 0.00 0.00 4.61
618 630 6.036517 GCGTATCTTTGCATTGATAGATAGGG 59.963 42.308 8.77 4.42 36.62 3.53
643 655 3.550561 TCACGAATACGCAAAAGCTTTG 58.449 40.909 13.54 8.26 43.96 2.77
671 684 9.435688 GATTGTATTGGGTTAAAAGAAAGCATT 57.564 29.630 0.00 0.00 0.00 3.56
727 740 0.396811 ATTAGGGGCGAGTGTATGGC 59.603 55.000 0.00 0.00 0.00 4.40
728 741 2.494059 CAATTAGGGGCGAGTGTATGG 58.506 52.381 0.00 0.00 0.00 2.74
730 743 1.488812 TGCAATTAGGGGCGAGTGTAT 59.511 47.619 0.00 0.00 0.00 2.29
731 744 0.906066 TGCAATTAGGGGCGAGTGTA 59.094 50.000 0.00 0.00 0.00 2.90
732 745 0.037590 TTGCAATTAGGGGCGAGTGT 59.962 50.000 0.00 0.00 0.00 3.55
734 747 1.173913 GTTTGCAATTAGGGGCGAGT 58.826 50.000 0.00 0.00 0.00 4.18
736 749 0.606944 ACGTTTGCAATTAGGGGCGA 60.607 50.000 0.00 0.00 0.00 5.54
738 751 0.885196 TGACGTTTGCAATTAGGGGC 59.115 50.000 0.00 0.00 0.00 5.80
745 758 1.317613 TCTTGCCTGACGTTTGCAAT 58.682 45.000 17.00 0.00 43.38 3.56
763 776 1.370051 GTTCGCTTGCCGGTGTTTC 60.370 57.895 1.90 0.00 37.59 2.78
764 777 2.719354 GTTCGCTTGCCGGTGTTT 59.281 55.556 1.90 0.00 37.59 2.83
845 858 3.366679 CCGCCGGTCGTCATATATTTACT 60.367 47.826 15.38 0.00 36.19 2.24
886 899 1.613437 GTAATGGGCGCATAAGGCAAT 59.387 47.619 17.51 1.78 45.17 3.56
892 905 1.518325 CGGATGTAATGGGCGCATAA 58.482 50.000 17.51 6.43 0.00 1.90
944 957 4.373116 TTGGGAGTGACGGCGAGC 62.373 66.667 16.62 5.63 0.00 5.03
974 987 2.125633 GAAGCGAAGGGGGACGTC 60.126 66.667 7.13 7.13 0.00 4.34
975 988 4.065281 CGAAGCGAAGGGGGACGT 62.065 66.667 0.00 0.00 0.00 4.34
976 989 4.065281 ACGAAGCGAAGGGGGACG 62.065 66.667 0.00 0.00 0.00 4.79
978 991 4.388499 GCACGAAGCGAAGGGGGA 62.388 66.667 0.00 0.00 0.00 4.81
1129 1142 0.042731 AACTCGAGGATTGGGAGGGA 59.957 55.000 18.41 0.00 32.11 4.20
1182 1195 3.405093 CTGCATAAGCCCGGCCAGA 62.405 63.158 5.55 0.00 41.13 3.86
1281 1294 3.924918 ATATAGACTGCTCGCGAATGT 57.075 42.857 11.33 9.22 0.00 2.71
1290 1303 7.227314 TCAAAAATGCATCGAATATAGACTGCT 59.773 33.333 0.00 0.00 0.00 4.24
1303 1316 7.677309 TGCAAGAAATTATCAAAAATGCATCG 58.323 30.769 0.00 0.00 36.46 3.84
1314 1327 6.065976 TCTTCTCCCTGCAAGAAATTATCA 57.934 37.500 1.25 0.00 34.07 2.15
1315 1328 6.183360 GGTTCTTCTCCCTGCAAGAAATTATC 60.183 42.308 1.25 0.00 39.71 1.75
1316 1329 5.654209 GGTTCTTCTCCCTGCAAGAAATTAT 59.346 40.000 1.25 0.00 39.71 1.28
1317 1330 5.010282 GGTTCTTCTCCCTGCAAGAAATTA 58.990 41.667 1.25 0.00 39.71 1.40
1319 1332 3.425659 GGTTCTTCTCCCTGCAAGAAAT 58.574 45.455 1.25 0.00 39.71 2.17
1402 1424 0.729116 CGAACGGCCGTCTAGACTTA 59.271 55.000 34.29 0.00 0.00 2.24
1403 1425 1.239968 ACGAACGGCCGTCTAGACTT 61.240 55.000 34.29 14.80 38.56 3.01
1535 1559 6.511767 CGGAATACTGAACAATTGGATAGCAC 60.512 42.308 10.83 0.00 0.00 4.40
1544 1568 6.264518 ACTTTTGACCGGAATACTGAACAATT 59.735 34.615 9.46 0.00 0.00 2.32
1545 1569 5.768164 ACTTTTGACCGGAATACTGAACAAT 59.232 36.000 9.46 0.00 0.00 2.71
1782 1811 5.953571 ACACTGTTTTCCTATTTCCTTCCT 58.046 37.500 0.00 0.00 0.00 3.36
1837 1866 8.892723 CACTACTTAATTGAGTGGCATTAATCA 58.107 33.333 12.85 0.00 37.52 2.57
2038 2080 2.908916 CGTAATAAAAGGGAAGGGCGA 58.091 47.619 0.00 0.00 0.00 5.54
2090 2132 4.276058 CCAACATTTTGGCAGAGGAAAT 57.724 40.909 0.00 0.00 46.09 2.17
2138 2180 0.614812 GGCCATTTGGATTGTGCCTT 59.385 50.000 0.00 0.00 37.39 4.35
2243 2285 0.391661 AGCTACCGCACCATGTCTTG 60.392 55.000 0.00 0.00 39.10 3.02
2311 2353 4.639755 CCCACCAAAAGTTTTGCTTTCATT 59.360 37.500 20.74 0.00 45.91 2.57
2351 2405 9.831253 GGGTTATTCCTTGAGTGCAAAATTGCT 62.831 40.741 18.05 0.00 44.36 3.91
2420 2474 3.620821 GCTTCTTTTGTGCTAGCCTAGAG 59.379 47.826 13.29 5.68 0.00 2.43
2430 2495 1.269778 GGGTTGAGGCTTCTTTTGTGC 60.270 52.381 0.00 0.00 0.00 4.57
2434 2499 3.117512 TCTTGAGGGTTGAGGCTTCTTTT 60.118 43.478 0.00 0.00 0.00 2.27
2625 2690 8.561738 TGATAAGTCTCACGCATACTATGATA 57.438 34.615 0.00 0.00 0.00 2.15
2626 2691 7.454260 TGATAAGTCTCACGCATACTATGAT 57.546 36.000 0.00 0.00 0.00 2.45
2627 2692 6.877611 TGATAAGTCTCACGCATACTATGA 57.122 37.500 0.00 0.00 0.00 2.15
2628 2693 9.626045 TTAATGATAAGTCTCACGCATACTATG 57.374 33.333 0.00 0.00 0.00 2.23
2688 2753 5.907391 CGTCACTTTTCATGACTGGTTAAAC 59.093 40.000 0.00 0.00 43.60 2.01
2735 2800 8.915871 ATTTGCAATGTACAAATGTCATAGAC 57.084 30.769 0.00 0.00 44.05 2.59
2747 2812 8.604640 AAATTGATTGACATTTGCAATGTACA 57.395 26.923 0.00 0.00 36.19 2.90
2790 2855 3.749609 GTGTTCCAACCACACAGTATACC 59.250 47.826 0.00 0.00 43.52 2.73
2797 2862 0.540454 TACCGTGTTCCAACCACACA 59.460 50.000 4.23 0.00 44.14 3.72
2816 2881 1.070445 GCGTCAGCCAGGATATGCT 59.930 57.895 0.00 0.00 38.67 3.79
2819 2884 1.050988 ACCTGCGTCAGCCAGGATAT 61.051 55.000 13.88 0.00 44.33 1.63
2846 2911 4.580167 CCACGGAATTAATCATGTCCACAT 59.420 41.667 5.06 0.00 36.96 3.21
3004 3072 8.390354 CACTCAAATGAATCGAACTATTAGCAA 58.610 33.333 0.00 0.00 0.00 3.91
3063 3131 3.569701 GCATTGGTTGGACTTCAGAAAGA 59.430 43.478 0.00 0.00 36.30 2.52
3134 3202 8.798153 CGTAACGGTAACTAATAACTACTTTGG 58.202 37.037 0.00 0.00 0.00 3.28
3369 3443 6.821665 TGTCTTATTGAACAAGTACCTATGGC 59.178 38.462 0.00 0.00 0.00 4.40
3401 3475 6.916360 TTTGGAGGCATGTTAGAAAATTCT 57.084 33.333 0.77 0.77 41.24 2.40
3413 3487 6.881570 AGGAAATTAGAAATTTGGAGGCATG 58.118 36.000 0.00 0.00 0.00 4.06
3559 3633 9.702253 AGGAATCTCTTAAGTACAGACTGATTA 57.298 33.333 10.08 2.74 35.52 1.75
3639 3713 6.204301 ACATTTCTTTCTGATATCATGGAGCG 59.796 38.462 5.72 0.00 0.00 5.03
3747 3821 1.217585 CCACAGACGTCACACTGCAG 61.218 60.000 19.50 13.48 37.61 4.41
3758 3832 5.869344 TGATCTAACAAAATCTCCACAGACG 59.131 40.000 0.00 0.00 0.00 4.18
3760 3834 6.655003 GGTTGATCTAACAAAATCTCCACAGA 59.345 38.462 9.31 0.00 41.18 3.41
3842 3916 1.340889 TGACAAGCTGAATTTGGGCAC 59.659 47.619 0.00 0.00 0.00 5.01
3943 4017 1.556911 AGTCAGAGAAATCGGTGGCAT 59.443 47.619 0.00 0.00 0.00 4.40
3957 4031 7.038302 ACAAGTAAGGAATACCATCAAGTCAGA 60.038 37.037 0.00 0.00 38.94 3.27
3969 4043 9.363763 GTGGTAACTAGAACAAGTAAGGAATAC 57.636 37.037 0.00 0.00 37.61 1.89
3989 4063 3.569194 TGTTGAGAAGCCTTGTGGTAA 57.431 42.857 0.00 0.00 35.27 2.85
3996 4072 2.945668 GTGACAGTTGTTGAGAAGCCTT 59.054 45.455 0.00 0.00 0.00 4.35
3997 4073 2.092968 TGTGACAGTTGTTGAGAAGCCT 60.093 45.455 0.00 0.00 0.00 4.58
4170 4247 8.067784 TGTAAATTGAGCTTTCTTTAAGACACG 58.932 33.333 0.00 0.00 35.80 4.49
4184 4261 6.888632 ACTGGATCTGAAATGTAAATTGAGCT 59.111 34.615 0.00 0.00 0.00 4.09
4188 4265 8.084073 ACACAACTGGATCTGAAATGTAAATTG 58.916 33.333 0.00 0.00 0.00 2.32
4231 4308 4.935205 CGTGACTCCTCCATCACATAAAAA 59.065 41.667 5.33 0.00 44.54 1.94
4407 4486 2.415893 CGACCAAGATGGAAAACCATGC 60.416 50.000 6.48 0.00 40.96 4.06
4410 4489 2.621055 CAACGACCAAGATGGAAAACCA 59.379 45.455 2.85 0.00 40.96 3.67
4427 4506 6.018832 TGTGATGTCATAGATGCATAACAACG 60.019 38.462 0.00 0.00 35.10 4.10
4434 4513 5.926663 AGAGTTGTGATGTCATAGATGCAT 58.073 37.500 0.00 0.00 0.00 3.96
4535 4616 9.984590 ATTATTTTTAGCCCTACTACCTTTCAA 57.015 29.630 0.00 0.00 0.00 2.69
4686 4770 1.816224 GAAGCCTCGTCTTCTCTGTCT 59.184 52.381 7.30 0.00 39.39 3.41
4699 4783 0.106521 GAGCTGGAGATGGAAGCCTC 59.893 60.000 0.00 0.00 37.68 4.70
4719 4803 3.387962 TCCCATGTGCCTTCTAGATCTT 58.612 45.455 0.00 0.00 0.00 2.40
4771 4855 1.200948 GGCTTGCCAAGAGATGTCAAC 59.799 52.381 9.04 0.00 0.00 3.18
4874 4958 9.767684 CGTAGCTACAATTATTTCAAAACATGA 57.232 29.630 23.21 0.00 35.85 3.07
4895 4979 4.268884 CAGTCTAGAAAATCAAGCCGTAGC 59.731 45.833 0.00 0.00 40.32 3.58
4896 4980 5.411781 ACAGTCTAGAAAATCAAGCCGTAG 58.588 41.667 0.00 0.00 0.00 3.51
4897 4981 5.047590 TGACAGTCTAGAAAATCAAGCCGTA 60.048 40.000 1.31 0.00 0.00 4.02
4898 4982 4.246458 GACAGTCTAGAAAATCAAGCCGT 58.754 43.478 0.00 0.00 0.00 5.68
4899 4983 4.245660 TGACAGTCTAGAAAATCAAGCCG 58.754 43.478 1.31 0.00 0.00 5.52
4900 4984 6.560253 TTTGACAGTCTAGAAAATCAAGCC 57.440 37.500 1.31 0.00 0.00 4.35
5017 5402 4.811024 TGTGAGCTCAGACTGTTACAAAAG 59.189 41.667 18.89 0.00 0.00 2.27
5055 5440 3.377172 ACCAATTTAGTGCGCTCCAATAC 59.623 43.478 9.73 0.00 0.00 1.89
5065 5450 3.928375 CAGGCAATCAACCAATTTAGTGC 59.072 43.478 0.00 0.00 0.00 4.40
5074 5459 7.894753 TGATAATTTATCAGGCAATCAACCA 57.105 32.000 13.83 0.00 40.09 3.67
5233 5618 1.228429 GCCCACAGCACCTTACCAA 60.228 57.895 0.00 0.00 42.97 3.67
5242 5627 3.364441 GATGCAACGCCCACAGCA 61.364 61.111 0.00 0.00 44.04 4.41
5246 5631 2.672996 ACAGGATGCAACGCCCAC 60.673 61.111 0.00 0.00 42.53 4.61
5280 5665 1.487976 CTCCAGCTTAAGATCCAGGCA 59.512 52.381 6.67 0.00 0.00 4.75
5383 5771 2.359230 AGGTCTTGCAGAAGCCGC 60.359 61.111 0.00 0.00 41.13 6.53
5536 5926 1.666700 TCGTTGGTTTCTTGTGGTTCG 59.333 47.619 0.00 0.00 0.00 3.95
5708 6108 3.171277 GCTCAACAACAGTCACACAAAC 58.829 45.455 0.00 0.00 0.00 2.93
5731 6131 7.116519 GTGTAACTGACTTCATAACACTCCTTC 59.883 40.741 9.79 0.00 33.57 3.46
5785 6189 8.886719 TCTATTATCAACAAGTCATCAGCTTTG 58.113 33.333 0.00 0.00 0.00 2.77
5823 6227 3.056821 TCTTGACATTACTGACCCACTCG 60.057 47.826 0.00 0.00 0.00 4.18
5844 6248 6.525629 AGCCTCACTACCATTACATAACATC 58.474 40.000 0.00 0.00 0.00 3.06
5875 6279 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
5878 6282 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
5879 6283 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
5880 6284 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
5881 6285 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
5882 6286 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
5883 6287 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
5884 6288 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
5885 6289 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5906 6310 7.335924 AGCAGACAGTGAAAACTAGTGTAAAAA 59.664 33.333 0.00 0.00 32.14 1.94
5907 6311 6.821665 AGCAGACAGTGAAAACTAGTGTAAAA 59.178 34.615 0.00 0.00 32.14 1.52
5908 6312 6.346096 AGCAGACAGTGAAAACTAGTGTAAA 58.654 36.000 0.00 0.00 32.14 2.01
5909 6313 5.914033 AGCAGACAGTGAAAACTAGTGTAA 58.086 37.500 0.00 0.00 32.14 2.41
5910 6314 5.531122 AGCAGACAGTGAAAACTAGTGTA 57.469 39.130 0.00 0.00 32.14 2.90
5911 6315 4.408182 AGCAGACAGTGAAAACTAGTGT 57.592 40.909 0.00 0.00 34.56 3.55
5912 6316 7.426929 AATTAGCAGACAGTGAAAACTAGTG 57.573 36.000 0.00 0.00 0.00 2.74
5913 6317 9.155975 CATAATTAGCAGACAGTGAAAACTAGT 57.844 33.333 0.00 0.00 0.00 2.57
5914 6318 8.119226 GCATAATTAGCAGACAGTGAAAACTAG 58.881 37.037 0.00 0.00 0.00 2.57
5915 6319 7.606073 TGCATAATTAGCAGACAGTGAAAACTA 59.394 33.333 0.00 0.00 37.02 2.24
5916 6320 6.430925 TGCATAATTAGCAGACAGTGAAAACT 59.569 34.615 0.00 0.00 37.02 2.66
5917 6321 6.611381 TGCATAATTAGCAGACAGTGAAAAC 58.389 36.000 0.00 0.00 37.02 2.43
5918 6322 6.816134 TGCATAATTAGCAGACAGTGAAAA 57.184 33.333 0.00 0.00 37.02 2.29
5969 6373 7.059788 TGTCAGGCTTAAATTTAGATGCCATA 58.940 34.615 26.24 17.25 42.46 2.74
5971 6375 5.260424 TGTCAGGCTTAAATTTAGATGCCA 58.740 37.500 26.24 13.66 42.46 4.92
6083 6491 7.822822 GGGTACAAGTTGGCGATAGATTAATAT 59.177 37.037 7.96 0.00 39.76 1.28
6105 6513 6.275144 TGGAAAGGAGGTACAAAAATAGGGTA 59.725 38.462 0.00 0.00 0.00 3.69
6239 6649 0.610174 CTAGTTCTGCACAGCCTGGA 59.390 55.000 0.00 0.00 0.00 3.86
6473 6883 3.370840 TCATGCTTATTGCTTGTCCCT 57.629 42.857 0.00 0.00 44.28 4.20
6520 6930 6.865726 GTCGACTGCATCATTAGTAGAATGAT 59.134 38.462 8.70 6.90 45.40 2.45
6525 6935 5.576447 TTGTCGACTGCATCATTAGTAGA 57.424 39.130 17.92 0.00 0.00 2.59
6531 6941 3.376234 CCTGATTTGTCGACTGCATCATT 59.624 43.478 17.92 0.00 0.00 2.57
6540 6950 1.726853 CCCAGTCCTGATTTGTCGAC 58.273 55.000 9.11 9.11 0.00 4.20
6609 7019 0.598065 GTCAGGTTGCCAAAGCGAAT 59.402 50.000 0.00 0.00 44.31 3.34
6629 7039 1.679139 CTTCCTGAACAGTTGTGCCA 58.321 50.000 0.00 0.00 0.00 4.92
6645 7055 0.040067 CTTGGTCGCTTTGGTGCTTC 60.040 55.000 0.00 0.00 0.00 3.86
6755 7165 5.860641 TCGAAACAGTAATAATTCAACCGC 58.139 37.500 0.00 0.00 0.00 5.68
7078 7488 8.763601 AGGAGCTAATTAAACTCTGTCATAGTT 58.236 33.333 12.53 0.00 38.82 2.24
7084 7494 9.471084 GATAAGAGGAGCTAATTAAACTCTGTC 57.529 37.037 12.53 10.31 35.65 3.51
7166 7576 5.529800 TCCAAGTTTACAACCTTAGCACTTC 59.470 40.000 0.00 0.00 0.00 3.01
7173 7583 5.058490 CCGAGTTCCAAGTTTACAACCTTA 58.942 41.667 0.00 0.00 0.00 2.69
7193 7603 1.131504 GATATGCGCAAACCAAACCGA 59.868 47.619 17.11 0.00 0.00 4.69
7216 7626 0.763652 CCAGCATCCTCACCATAGCT 59.236 55.000 0.00 0.00 0.00 3.32
7224 7634 2.359169 GGACGACCCAGCATCCTCA 61.359 63.158 0.00 0.00 34.14 3.86
7235 7645 1.798813 GACACATTTCACAGGACGACC 59.201 52.381 0.00 0.00 0.00 4.79
7251 7661 1.376037 GTACAGCAGCCCAGGACAC 60.376 63.158 0.00 0.00 0.00 3.67
7255 7665 0.833287 ACTATGTACAGCAGCCCAGG 59.167 55.000 0.33 0.00 0.00 4.45
7256 7666 1.759445 AGACTATGTACAGCAGCCCAG 59.241 52.381 0.33 0.00 0.00 4.45
7257 7667 1.866015 AGACTATGTACAGCAGCCCA 58.134 50.000 0.33 0.00 0.00 5.36
7258 7668 2.093447 ACAAGACTATGTACAGCAGCCC 60.093 50.000 0.33 0.00 0.00 5.19
7361 7778 7.064728 GCAGAAATAGAAAAGTGAGATACGGTT 59.935 37.037 0.00 0.00 0.00 4.44
7369 7786 6.597614 GTCAGTGCAGAAATAGAAAAGTGAG 58.402 40.000 0.00 0.00 0.00 3.51
7399 7816 0.527113 CGCAATTCCATGACTTGCCA 59.473 50.000 16.21 0.00 42.53 4.92
7410 7827 1.375551 AACCATACGTCCGCAATTCC 58.624 50.000 0.00 0.00 0.00 3.01
7411 7828 3.422655 GAAAACCATACGTCCGCAATTC 58.577 45.455 0.00 0.00 0.00 2.17
7417 7834 2.165845 AGAGAGGAAAACCATACGTCCG 59.834 50.000 0.00 0.00 35.19 4.79
7420 7837 4.755123 CACAAAGAGAGGAAAACCATACGT 59.245 41.667 0.00 0.00 0.00 3.57
7460 7877 6.507023 CCTTGCATCAAAAGTGTAGAAACTT 58.493 36.000 0.00 0.00 42.21 2.66
7461 7878 5.507985 GCCTTGCATCAAAAGTGTAGAAACT 60.508 40.000 0.00 0.00 0.00 2.66
7463 7880 4.261994 GGCCTTGCATCAAAAGTGTAGAAA 60.262 41.667 0.00 0.00 0.00 2.52
7464 7881 3.255642 GGCCTTGCATCAAAAGTGTAGAA 59.744 43.478 0.00 0.00 0.00 2.10
7465 7882 2.819608 GGCCTTGCATCAAAAGTGTAGA 59.180 45.455 0.00 0.00 0.00 2.59
7466 7883 2.414559 CGGCCTTGCATCAAAAGTGTAG 60.415 50.000 0.00 0.00 0.00 2.74
7467 7884 1.539388 CGGCCTTGCATCAAAAGTGTA 59.461 47.619 0.00 0.00 0.00 2.90
7469 7886 1.010419 GCGGCCTTGCATCAAAAGTG 61.010 55.000 0.00 0.00 34.15 3.16
7470 7887 1.181098 AGCGGCCTTGCATCAAAAGT 61.181 50.000 0.00 0.00 37.31 2.66
7471 7888 0.037975 AAGCGGCCTTGCATCAAAAG 60.038 50.000 0.00 0.00 37.31 2.27
7487 7937 5.500645 AAGTCAGAACCAAGTTACAAAGC 57.499 39.130 0.00 0.00 0.00 3.51
7496 7946 5.601662 TCAGTAGTCAAAGTCAGAACCAAG 58.398 41.667 0.00 0.00 0.00 3.61
7504 7954 5.924356 TGGTCAAATCAGTAGTCAAAGTCA 58.076 37.500 0.00 0.00 0.00 3.41
7532 7983 5.976458 ACCTTTTGTGACATGTGACATTTT 58.024 33.333 19.03 0.00 0.00 1.82
7533 7984 5.596836 ACCTTTTGTGACATGTGACATTT 57.403 34.783 19.03 0.00 0.00 2.32
7539 7990 5.965334 GCGATAATACCTTTTGTGACATGTG 59.035 40.000 1.15 0.00 0.00 3.21
7562 8015 5.762045 ACTTATTCCGCATACAAATCATGC 58.238 37.500 0.00 0.00 44.31 4.06
7591 8044 5.543507 ACATGCCATAACAAACCTGAAAA 57.456 34.783 0.00 0.00 0.00 2.29
7593 8046 5.536538 TGTTACATGCCATAACAAACCTGAA 59.463 36.000 5.23 0.00 39.10 3.02
7595 8048 5.384063 TGTTACATGCCATAACAAACCTG 57.616 39.130 5.23 0.00 39.10 4.00
7773 8226 7.232118 AGCACAGTGAGGCTTATAAATTTTT 57.768 32.000 4.15 0.00 36.92 1.94
7775 8228 9.799106 ATATAGCACAGTGAGGCTTATAAATTT 57.201 29.630 16.82 0.00 41.41 1.82
7777 8230 7.335422 GCATATAGCACAGTGAGGCTTATAAAT 59.665 37.037 16.82 8.48 44.79 1.40
8049 8587 5.295540 GCCTCATCTTTCCTGTTATTCAGAC 59.704 44.000 0.00 0.00 46.27 3.51


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

AutoCloner maintained by Alex Coulton.