Multiple sequence alignment - TraesCS1B01G100900

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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 TraesCS1B01G100900 chr1B 100.000 2366 0 0 1 2366 110616499 110614134 0.000000e+00 4370.0
1 TraesCS1B01G100900 chr2D 79.880 2341 393 48 2 2312 451325142 451327434 0.000000e+00 1642.0
2 TraesCS1B01G100900 chr2A 78.113 2321 450 46 22 2312 118425571 118423279 0.000000e+00 1419.0
3 TraesCS1B01G100900 chr6A 79.528 2032 365 33 186 2191 214433854 214431848 0.000000e+00 1400.0
4 TraesCS1B01G100900 chr4D 84.962 1330 180 13 2 1323 419456595 419455278 0.000000e+00 1330.0
5 TraesCS1B01G100900 chr5D 88.828 734 77 5 586 1314 477828926 477828193 0.000000e+00 896.0
6 TraesCS1B01G100900 chr4A 72.662 417 104 10 282 694 216144419 216144009 1.910000e-26 130.0
7 TraesCS1B01G100900 chr3B 84.211 57 9 0 273 329 146975707 146975651 3.290000e-04 56.5


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 TraesCS1B01G100900 chr1B 110614134 110616499 2365 True 4370 4370 100.000 1 2366 1 chr1B.!!$R1 2365
1 TraesCS1B01G100900 chr2D 451325142 451327434 2292 False 1642 1642 79.880 2 2312 1 chr2D.!!$F1 2310
2 TraesCS1B01G100900 chr2A 118423279 118425571 2292 True 1419 1419 78.113 22 2312 1 chr2A.!!$R1 2290
3 TraesCS1B01G100900 chr6A 214431848 214433854 2006 True 1400 1400 79.528 186 2191 1 chr6A.!!$R1 2005
4 TraesCS1B01G100900 chr4D 419455278 419456595 1317 True 1330 1330 84.962 2 1323 1 chr4D.!!$R1 1321
5 TraesCS1B01G100900 chr5D 477828193 477828926 733 True 896 896 88.828 586 1314 1 chr5D.!!$R1 728

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
708 718 0.108138 CTTCCGCTGTTCCCGAAGAT 60.108 55.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1764 0.035915 GTCACCCCTCTCTCCTTTGC 60.036 60.0 0.0 0.0 0.0 3.68 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
108 110 3.782443 GCGACCATTCCCCTCCGT 61.782 66.667 0.00 0.00 0.00 4.69
133 135 0.471191 ATGGCATCTGGATCTCGCAA 59.529 50.000 0.00 0.00 0.00 4.85
160 162 2.544694 CCTCTGTCACATACTCGATGCC 60.545 54.545 0.00 0.00 39.39 4.40
182 184 3.134127 GAGCGGCCAATGGTGTCC 61.134 66.667 2.24 0.00 0.00 4.02
209 211 3.535962 CTCTCGGGCTCTCCTGGC 61.536 72.222 0.00 0.00 39.31 4.85
254 256 4.783621 GTGCAGGCGGAGATGGCA 62.784 66.667 0.00 0.00 36.77 4.92
255 257 4.032452 TGCAGGCGGAGATGGCAA 62.032 61.111 0.00 0.00 36.77 4.52
258 260 1.377725 CAGGCGGAGATGGCAACTT 60.378 57.895 0.00 0.00 36.77 2.66
263 265 2.115291 GGAGATGGCAACTTCGGGC 61.115 63.158 0.00 0.00 45.04 6.13
264 266 1.078143 GAGATGGCAACTTCGGGCT 60.078 57.895 0.00 0.00 45.04 5.19
277 283 2.600470 GGGCTTGGAGGCGGTTTT 60.600 61.111 0.00 0.00 42.43 2.43
280 286 2.255252 CTTGGAGGCGGTTTTGCG 59.745 61.111 0.00 0.00 35.06 4.85
283 289 3.972276 GGAGGCGGTTTTGCGCAA 61.972 61.111 21.02 21.02 35.06 4.85
377 385 4.698625 AGGTCGGCGTCCCCTTCT 62.699 66.667 19.30 0.00 0.00 2.85
400 408 2.509336 CGAGCGGCGTCAAATCCT 60.509 61.111 9.37 0.00 34.64 3.24
402 410 1.741770 GAGCGGCGTCAAATCCTGT 60.742 57.895 9.37 0.00 0.00 4.00
476 484 1.593006 GATTGTATGAACGACCCGCTG 59.407 52.381 0.00 0.00 0.00 5.18
485 493 2.265739 GACCCGCTGTGCATCAGA 59.734 61.111 17.12 0.00 46.27 3.27
518 527 3.461982 CACGTCTCGTCGCAGTGC 61.462 66.667 4.58 4.58 38.32 4.40
533 542 2.363018 TGCTCGCAGCCTAGGAGT 60.363 61.111 14.75 0.00 41.51 3.85
541 550 1.799933 CAGCCTAGGAGTCCCATCTT 58.200 55.000 14.75 0.00 33.88 2.40
542 551 1.415659 CAGCCTAGGAGTCCCATCTTG 59.584 57.143 14.75 0.00 33.88 3.02
562 571 4.021925 GGAGGAGTTGCGCAGGGT 62.022 66.667 11.31 0.00 0.00 4.34
572 581 4.457496 CGCAGGGTGGTCATCGCT 62.457 66.667 0.00 0.00 0.00 4.93
704 714 1.987855 ATCCTTCCGCTGTTCCCGA 60.988 57.895 0.00 0.00 0.00 5.14
708 718 0.108138 CTTCCGCTGTTCCCGAAGAT 60.108 55.000 0.00 0.00 0.00 2.40
712 722 1.377202 GCTGTTCCCGAAGATGCCA 60.377 57.895 0.00 0.00 0.00 4.92
723 734 1.966901 AAGATGCCATCGCCGTGGTA 61.967 55.000 0.00 3.82 41.47 3.25
746 757 4.809496 CTGCATCCTGCCCCGCTT 62.809 66.667 0.00 0.00 44.23 4.68
749 760 4.431131 CATCCTGCCCCGCTTGGT 62.431 66.667 0.00 0.00 0.00 3.67
751 762 3.645268 ATCCTGCCCCGCTTGGTTC 62.645 63.158 0.00 0.00 0.00 3.62
846 862 1.080434 GATACGGCGGCAGAGATCC 60.080 63.158 13.24 0.00 0.00 3.36
848 864 0.251209 ATACGGCGGCAGAGATCCTA 60.251 55.000 13.24 0.00 0.00 2.94
852 868 1.244697 GGCGGCAGAGATCCTATCGA 61.245 60.000 3.07 0.00 0.00 3.59
853 869 0.109504 GCGGCAGAGATCCTATCGAC 60.110 60.000 0.00 0.00 0.00 4.20
890 906 4.701663 CACAGGTTCTCGGTGCAT 57.298 55.556 0.00 0.00 35.02 3.96
908 924 2.158943 GCATAAGTACCACCTGGAGGAC 60.159 54.545 17.56 10.29 38.94 3.85
941 957 2.268920 GCGGGCCATGAGTTCAGA 59.731 61.111 4.39 0.00 0.00 3.27
949 965 3.569701 GGCCATGAGTTCAGAAACAAAGA 59.430 43.478 0.00 0.00 37.88 2.52
957 973 8.731275 TGAGTTCAGAAACAAAGATCTTGTTA 57.269 30.769 9.17 0.00 41.30 2.41
1043 1060 2.793288 TTGCAAGCTGATGAGGATGA 57.207 45.000 0.00 0.00 0.00 2.92
1123 1141 1.045407 ACTTCTGGGCAGTTCGTGTA 58.955 50.000 0.00 0.00 0.00 2.90
1184 1202 4.870426 GGATCTGTCGCTATTCAAACTCAA 59.130 41.667 0.00 0.00 0.00 3.02
1204 1224 1.675641 GCCTGGTGTGTGGATCCAC 60.676 63.158 33.97 33.97 46.33 4.02
1305 1325 4.708421 ACATTCTGGCAATTGCTTGAGTAT 59.292 37.500 28.42 17.20 41.70 2.12
1311 1331 2.223340 GCAATTGCTTGAGTATCCCACG 60.223 50.000 23.21 0.00 38.21 4.94
1312 1332 3.009723 CAATTGCTTGAGTATCCCACGT 58.990 45.455 0.00 0.00 34.04 4.49
1333 1353 1.352017 TCATCCATGTTGGCAGAGTGT 59.648 47.619 0.00 0.00 37.47 3.55
1338 1358 0.250901 ATGTTGGCAGAGTGTGGGAC 60.251 55.000 0.00 0.00 0.00 4.46
1362 1382 3.646715 CCACCGGAGCTTTGGGGA 61.647 66.667 9.46 0.00 0.00 4.81
1363 1383 2.677228 CACCGGAGCTTTGGGGAT 59.323 61.111 9.46 0.00 0.00 3.85
1368 1388 1.821332 GGAGCTTTGGGGATGAGCG 60.821 63.158 0.00 0.00 41.19 5.03
1370 1390 2.257409 GAGCTTTGGGGATGAGCGGA 62.257 60.000 0.00 0.00 41.19 5.54
1380 1400 0.102120 GATGAGCGGACAGTGAGGAG 59.898 60.000 0.00 0.00 0.00 3.69
1382 1402 1.679305 GAGCGGACAGTGAGGAGGA 60.679 63.158 0.00 0.00 0.00 3.71
1383 1403 1.939769 GAGCGGACAGTGAGGAGGAC 61.940 65.000 0.00 0.00 0.00 3.85
1388 1408 0.959553 GACAGTGAGGAGGACGACAA 59.040 55.000 0.00 0.00 0.00 3.18
1390 1410 0.673985 CAGTGAGGAGGACGACAACA 59.326 55.000 0.00 0.00 0.00 3.33
1392 1412 0.038159 GTGAGGAGGACGACAACAGG 60.038 60.000 0.00 0.00 0.00 4.00
1408 1428 4.704833 GGCAGAGTGGCTTGCCGA 62.705 66.667 7.18 0.00 40.14 5.54
1431 1451 0.253327 GTTCTCGAGATTTGGGGCCT 59.747 55.000 17.44 0.00 0.00 5.19
1446 1466 4.247781 CCTGGTGGCCATTAGCAG 57.752 61.111 9.72 11.56 46.50 4.24
1451 1471 1.302949 GTGGCCATTAGCAGGTCCA 59.697 57.895 9.72 0.00 46.50 4.02
1454 1474 1.077501 GCCATTAGCAGGTCCAGCA 60.078 57.895 9.19 0.00 42.97 4.41
1480 1500 3.559015 CGCAGCGTCTATGATGACT 57.441 52.632 6.65 0.00 35.00 3.41
1481 1501 2.688364 CGCAGCGTCTATGATGACTA 57.312 50.000 6.65 0.00 35.00 2.59
1482 1502 3.208915 CGCAGCGTCTATGATGACTAT 57.791 47.619 6.65 0.00 35.00 2.12
1488 1508 3.237628 CGTCTATGATGACTATGGTGCG 58.762 50.000 0.00 0.00 35.00 5.34
1546 1566 2.550101 GGCGCCGGTAGATCGTACT 61.550 63.158 12.58 0.00 0.00 2.73
1553 1573 1.400737 GGTAGATCGTACTGGCAGGT 58.599 55.000 20.34 7.13 0.00 4.00
1581 1601 4.175337 CGTGTGGGGCCATCGGAT 62.175 66.667 4.39 0.00 0.00 4.18
1584 1604 2.304831 TGTGGGGCCATCGGATTGA 61.305 57.895 4.39 0.00 0.00 2.57
1602 1622 3.824001 TGAAGAATTCCACCAATGGGA 57.176 42.857 3.55 0.00 46.93 4.37
1603 1623 3.700538 TGAAGAATTCCACCAATGGGAG 58.299 45.455 3.55 0.00 46.93 4.30
1621 1641 2.041265 CTGGTGGGGCCCTAGAGT 59.959 66.667 25.93 0.00 36.04 3.24
1650 1670 3.246880 GGGACAAGGGTCGTGGGT 61.247 66.667 0.00 0.00 45.28 4.51
1658 1678 1.052124 AGGGTCGTGGGTCAGTCAAA 61.052 55.000 0.00 0.00 0.00 2.69
1659 1679 0.883370 GGGTCGTGGGTCAGTCAAAC 60.883 60.000 0.00 0.00 0.00 2.93
1669 1689 4.041723 GGGTCAGTCAAACAATTCAAACG 58.958 43.478 0.00 0.00 0.00 3.60
1670 1690 4.439563 GGGTCAGTCAAACAATTCAAACGT 60.440 41.667 0.00 0.00 0.00 3.99
1687 1707 2.726821 ACGTTCCTATCCGGTCTACAA 58.273 47.619 0.00 0.00 0.00 2.41
1688 1708 3.294214 ACGTTCCTATCCGGTCTACAAT 58.706 45.455 0.00 0.00 0.00 2.71
1692 1712 3.497332 TCCTATCCGGTCTACAATGAGG 58.503 50.000 0.00 0.00 0.00 3.86
1699 1719 1.002403 TCTACAATGAGGGGCGGGA 59.998 57.895 0.00 0.00 0.00 5.14
1700 1720 0.399949 TCTACAATGAGGGGCGGGAT 60.400 55.000 0.00 0.00 0.00 3.85
1701 1721 0.474184 CTACAATGAGGGGCGGGATT 59.526 55.000 0.00 0.00 0.00 3.01
1703 1723 1.281925 ACAATGAGGGGCGGGATTCT 61.282 55.000 0.00 0.00 0.00 2.40
1708 1728 3.140814 GGGGCGGGATTCTGTTGC 61.141 66.667 0.00 0.00 0.00 4.17
1709 1729 2.361104 GGGCGGGATTCTGTTGCA 60.361 61.111 0.00 0.00 0.00 4.08
1714 1734 0.798776 CGGGATTCTGTTGCAGACAC 59.201 55.000 0.00 0.00 40.46 3.67
1719 1739 0.836606 TTCTGTTGCAGACACCTGGA 59.163 50.000 0.00 0.00 40.46 3.86
1729 1749 1.462238 ACACCTGGAGGGCTTGTCT 60.462 57.895 0.00 0.00 40.27 3.41
1744 1764 1.006805 GTCTCATCGGATCCGCTGG 60.007 63.158 31.48 23.14 36.40 4.85
1754 1774 0.813210 GATCCGCTGGCAAAGGAGAG 60.813 60.000 14.62 0.00 37.49 3.20
1780 1801 0.323629 GACCAGTCCCCGAACAATGA 59.676 55.000 0.00 0.00 0.00 2.57
1790 1811 2.093500 CCCGAACAATGAGATCAGGACA 60.093 50.000 0.00 0.00 0.00 4.02
1791 1812 3.599343 CCGAACAATGAGATCAGGACAA 58.401 45.455 0.00 0.00 0.00 3.18
1793 1814 4.248859 CGAACAATGAGATCAGGACAACT 58.751 43.478 0.00 0.00 0.00 3.16
1814 1835 0.251832 TCCAGGTTCTCGAGCCTTCT 60.252 55.000 7.81 0.00 40.24 2.85
1816 1837 2.035632 CCAGGTTCTCGAGCCTTCTAT 58.964 52.381 7.81 0.00 40.24 1.98
1822 1843 1.035923 CTCGAGCCTTCTATGCCAGA 58.964 55.000 0.00 0.00 0.00 3.86
1823 1844 1.617850 CTCGAGCCTTCTATGCCAGAT 59.382 52.381 0.00 0.00 31.77 2.90
1827 1848 1.493871 AGCCTTCTATGCCAGATGCTT 59.506 47.619 4.90 0.00 38.11 3.91
1829 1850 2.928334 CCTTCTATGCCAGATGCTTGT 58.072 47.619 0.00 0.00 42.00 3.16
1830 1851 2.617308 CCTTCTATGCCAGATGCTTGTG 59.383 50.000 0.00 0.00 42.00 3.33
1843 1864 1.002868 CTTGTGCAGGGGTGGAGAG 60.003 63.158 0.00 0.00 0.00 3.20
1862 1883 4.421365 GGCACCAATCAGGCAGAA 57.579 55.556 0.00 0.00 43.14 3.02
1865 1886 1.246056 GCACCAATCAGGCAGAAGCA 61.246 55.000 0.00 0.00 44.61 3.91
1870 1891 0.403271 AATCAGGCAGAAGCACAGGT 59.597 50.000 0.00 0.00 44.61 4.00
1891 1912 3.499737 GGCCGCGACAATCTGGTG 61.500 66.667 8.23 0.00 0.00 4.17
1892 1913 2.434185 GCCGCGACAATCTGGTGA 60.434 61.111 8.23 0.00 0.00 4.02
1894 1915 1.766143 GCCGCGACAATCTGGTGATC 61.766 60.000 8.23 0.00 31.51 2.92
1895 1916 1.154205 CCGCGACAATCTGGTGATCC 61.154 60.000 8.23 0.00 31.51 3.36
1896 1917 1.154205 CGCGACAATCTGGTGATCCC 61.154 60.000 0.00 0.00 31.51 3.85
1897 1918 0.107703 GCGACAATCTGGTGATCCCA 60.108 55.000 3.30 3.30 42.51 4.37
1901 1922 1.097547 CAATCTGGTGATCCCACGGC 61.098 60.000 0.00 0.00 44.09 5.68
1902 1923 1.561769 AATCTGGTGATCCCACGGCA 61.562 55.000 0.00 0.00 44.09 5.69
1903 1924 1.561769 ATCTGGTGATCCCACGGCAA 61.562 55.000 0.00 0.00 44.09 4.52
1904 1925 1.746615 CTGGTGATCCCACGGCAAG 60.747 63.158 0.00 0.00 44.09 4.01
1905 1926 2.438434 GGTGATCCCACGGCAAGG 60.438 66.667 0.00 0.00 44.09 3.61
1912 1933 4.047125 CCACGGCAAGGGGGACAT 62.047 66.667 0.00 0.00 40.70 3.06
1915 1936 1.921346 ACGGCAAGGGGGACATGTA 60.921 57.895 0.00 0.00 0.00 2.29
1927 1955 1.486726 GGACATGTAGAGGAGTTGGGG 59.513 57.143 0.00 0.00 0.00 4.96
1951 1979 4.394712 CAGGTGGTGGAGCCGACC 62.395 72.222 0.41 0.41 41.21 4.79
1960 1988 4.719369 GAGCCGACCGCGACAACT 62.719 66.667 8.23 0.00 44.76 3.16
1962 1990 3.343421 GCCGACCGCGACAACTTT 61.343 61.111 8.23 0.00 40.82 2.66
1969 1997 0.165944 CCGCGACAACTTTGGTGATC 59.834 55.000 8.23 0.00 0.00 2.92
1974 2002 2.582052 GACAACTTTGGTGATCCCACA 58.418 47.619 2.70 0.00 45.19 4.17
1975 2003 3.157087 GACAACTTTGGTGATCCCACAT 58.843 45.455 2.70 0.00 45.19 3.21
1978 2006 3.077484 ACTTTGGTGATCCCACATCAG 57.923 47.619 2.70 1.22 45.19 2.90
2012 2040 2.178580 GTGGAATTGGGAATGGAGCAA 58.821 47.619 0.00 0.00 0.00 3.91
2013 2041 2.094026 GTGGAATTGGGAATGGAGCAAC 60.094 50.000 0.00 0.00 0.00 4.17
2014 2042 1.482182 GGAATTGGGAATGGAGCAACC 59.518 52.381 0.00 0.00 39.54 3.77
2019 2047 2.115291 GGAATGGAGCAACCCTCGC 61.115 63.158 0.00 0.00 41.71 5.03
2021 2049 0.678048 GAATGGAGCAACCCTCGCTT 60.678 55.000 0.00 0.00 40.63 4.68
2023 2051 2.032681 GGAGCAACCCTCGCTTGT 59.967 61.111 0.00 0.00 40.63 3.16
2031 2059 1.299648 CCCTCGCTTGTGGATCCAA 59.700 57.895 18.20 0.00 0.00 3.53
2044 2072 3.409384 TCCAATGCGGGTGGATGA 58.591 55.556 0.00 0.00 40.33 2.92
2047 2075 0.680921 CCAATGCGGGTGGATGACTT 60.681 55.000 0.00 0.00 38.54 3.01
2052 2080 1.377202 CGGGTGGATGACTTGGTGG 60.377 63.158 0.00 0.00 0.00 4.61
2054 2082 1.678970 GGTGGATGACTTGGTGGCC 60.679 63.158 0.00 0.00 0.00 5.36
2107 2135 0.394488 ACGCAGAAGATCTCCTCGGA 60.394 55.000 0.00 0.00 0.00 4.55
2115 2143 2.648613 GATCTCCTCGGAGCCAGGGA 62.649 65.000 8.11 0.00 41.71 4.20
2119 2147 2.439701 CTCGGAGCCAGGGACGTA 60.440 66.667 0.00 0.00 0.00 3.57
2126 2154 0.757188 AGCCAGGGACGTATGGAGAG 60.757 60.000 16.00 0.00 39.02 3.20
2131 2159 1.041437 GGGACGTATGGAGAGAAGGG 58.959 60.000 0.00 0.00 0.00 3.95
2135 2163 1.342076 ACGTATGGAGAGAAGGGAGCA 60.342 52.381 0.00 0.00 0.00 4.26
2139 2167 1.786937 TGGAGAGAAGGGAGCAGATC 58.213 55.000 0.00 0.00 0.00 2.75
2141 2169 1.688197 GGAGAGAAGGGAGCAGATCAG 59.312 57.143 0.00 0.00 0.00 2.90
2166 2194 2.349100 GACTGATGGATGGGCCCCAG 62.349 65.000 22.27 20.14 40.27 4.45
2177 2205 0.178873 GGGCCCCAGTGGAGGATATA 60.179 60.000 12.23 0.00 35.39 0.86
2180 2208 2.225547 GGCCCCAGTGGAGGATATACTA 60.226 54.545 11.95 0.00 35.39 1.82
2194 2222 4.581824 GGATATACTACGGTCCAACACAGA 59.418 45.833 0.00 0.00 0.00 3.41
2195 2223 5.243283 GGATATACTACGGTCCAACACAGAT 59.757 44.000 0.00 0.00 0.00 2.90
2198 2226 0.611200 TACGGTCCAACACAGATGGG 59.389 55.000 0.00 0.00 38.54 4.00
2200 2228 1.678970 GGTCCAACACAGATGGGGC 60.679 63.158 0.00 0.00 38.54 5.80
2202 2230 2.220586 TCCAACACAGATGGGGCGA 61.221 57.895 0.00 0.00 38.54 5.54
2204 2232 2.045926 AACACAGATGGGGCGAGC 60.046 61.111 0.00 0.00 0.00 5.03
2236 2264 3.785859 GGAGGCAGCCACATCGGA 61.786 66.667 15.80 0.00 36.56 4.55
2237 2265 2.507944 GAGGCAGCCACATCGGAT 59.492 61.111 15.80 0.00 36.56 4.18
2238 2266 1.748403 GAGGCAGCCACATCGGATA 59.252 57.895 15.80 0.00 36.56 2.59
2239 2267 0.601311 GAGGCAGCCACATCGGATAC 60.601 60.000 15.80 0.00 36.56 2.24
2240 2268 1.598130 GGCAGCCACATCGGATACC 60.598 63.158 6.55 0.00 36.56 2.73
2252 2280 1.227853 GGATACCGTGCCCATCCAC 60.228 63.158 0.00 0.00 38.50 4.02
2273 2301 1.256812 CAATGGTGGGTTTGGAGACC 58.743 55.000 0.00 0.00 39.04 3.85
2279 2307 1.809133 TGGGTTTGGAGACCACTGTA 58.191 50.000 0.00 0.00 41.65 2.74
2282 2310 2.039879 GGGTTTGGAGACCACTGTACAT 59.960 50.000 0.00 0.00 41.65 2.29
2312 2340 0.873312 CGTCGATCCCATGCAGTGAG 60.873 60.000 0.00 0.00 0.00 3.51
2313 2341 1.144716 TCGATCCCATGCAGTGAGC 59.855 57.895 0.00 0.00 45.96 4.26
2314 2342 1.890979 CGATCCCATGCAGTGAGCC 60.891 63.158 0.00 0.00 44.83 4.70
2315 2343 1.225426 GATCCCATGCAGTGAGCCA 59.775 57.895 0.00 0.00 44.83 4.75
2316 2344 0.394762 GATCCCATGCAGTGAGCCAA 60.395 55.000 0.00 0.00 44.83 4.52
2317 2345 0.395311 ATCCCATGCAGTGAGCCAAG 60.395 55.000 0.00 0.00 44.83 3.61
2318 2346 2.050350 CCCATGCAGTGAGCCAAGG 61.050 63.158 0.00 0.00 44.83 3.61
2319 2347 1.001764 CCATGCAGTGAGCCAAGGA 60.002 57.895 0.00 0.00 44.83 3.36
2320 2348 0.609957 CCATGCAGTGAGCCAAGGAA 60.610 55.000 0.00 0.00 44.83 3.36
2321 2349 1.471119 CATGCAGTGAGCCAAGGAAT 58.529 50.000 0.00 0.00 44.83 3.01
2322 2350 1.134367 CATGCAGTGAGCCAAGGAATG 59.866 52.381 0.00 0.00 44.83 2.67
2323 2351 0.111061 TGCAGTGAGCCAAGGAATGT 59.889 50.000 0.00 0.00 44.83 2.71
2324 2352 0.524862 GCAGTGAGCCAAGGAATGTG 59.475 55.000 0.00 0.00 37.23 3.21
2325 2353 1.883638 GCAGTGAGCCAAGGAATGTGA 60.884 52.381 0.00 0.00 37.23 3.58
2326 2354 2.507484 CAGTGAGCCAAGGAATGTGAA 58.493 47.619 0.00 0.00 0.00 3.18
2327 2355 3.087031 CAGTGAGCCAAGGAATGTGAAT 58.913 45.455 0.00 0.00 0.00 2.57
2328 2356 3.508793 CAGTGAGCCAAGGAATGTGAATT 59.491 43.478 0.00 0.00 0.00 2.17
2329 2357 4.021719 CAGTGAGCCAAGGAATGTGAATTT 60.022 41.667 0.00 0.00 0.00 1.82
2330 2358 4.590222 AGTGAGCCAAGGAATGTGAATTTT 59.410 37.500 0.00 0.00 0.00 1.82
2331 2359 4.687483 GTGAGCCAAGGAATGTGAATTTTG 59.313 41.667 0.00 0.00 0.00 2.44
2332 2360 4.588106 TGAGCCAAGGAATGTGAATTTTGA 59.412 37.500 0.00 0.00 0.00 2.69
2333 2361 5.143376 AGCCAAGGAATGTGAATTTTGAG 57.857 39.130 0.00 0.00 0.00 3.02
2334 2362 3.681417 GCCAAGGAATGTGAATTTTGAGC 59.319 43.478 0.00 0.00 0.00 4.26
2335 2363 4.562143 GCCAAGGAATGTGAATTTTGAGCT 60.562 41.667 0.00 0.00 0.00 4.09
2336 2364 5.166398 CCAAGGAATGTGAATTTTGAGCTC 58.834 41.667 6.82 6.82 0.00 4.09
2337 2365 5.047519 CCAAGGAATGTGAATTTTGAGCTCT 60.048 40.000 16.19 0.00 0.00 4.09
2338 2366 5.640189 AGGAATGTGAATTTTGAGCTCTG 57.360 39.130 16.19 0.00 0.00 3.35
2339 2367 5.319453 AGGAATGTGAATTTTGAGCTCTGA 58.681 37.500 16.19 0.25 0.00 3.27
2340 2368 5.182760 AGGAATGTGAATTTTGAGCTCTGAC 59.817 40.000 16.19 0.00 0.00 3.51
2341 2369 4.675190 ATGTGAATTTTGAGCTCTGACG 57.325 40.909 16.19 0.00 0.00 4.35
2342 2370 2.807967 TGTGAATTTTGAGCTCTGACGG 59.192 45.455 16.19 0.00 0.00 4.79
2343 2371 1.806542 TGAATTTTGAGCTCTGACGGC 59.193 47.619 16.19 1.42 0.00 5.68
2344 2372 1.131315 GAATTTTGAGCTCTGACGGCC 59.869 52.381 16.19 0.00 0.00 6.13
2345 2373 1.021390 ATTTTGAGCTCTGACGGCCG 61.021 55.000 26.86 26.86 0.00 6.13
2346 2374 3.589654 TTTGAGCTCTGACGGCCGG 62.590 63.158 31.76 12.37 0.00 6.13
2348 2376 4.500116 GAGCTCTGACGGCCGGTC 62.500 72.222 31.76 23.40 46.27 4.79
2350 2378 4.803426 GCTCTGACGGCCGGTCTG 62.803 72.222 31.76 24.73 46.24 3.51
2351 2379 3.374402 CTCTGACGGCCGGTCTGT 61.374 66.667 31.76 7.71 46.24 3.41
2352 2380 3.633094 CTCTGACGGCCGGTCTGTG 62.633 68.421 31.76 21.61 46.24 3.66
2358 2386 4.314440 GGCCGGTCTGTGCTGACA 62.314 66.667 1.90 0.00 38.61 3.58
2360 2388 2.357517 CCGGTCTGTGCTGACACC 60.358 66.667 10.53 0.00 46.86 4.16
2361 2389 2.421314 CGGTCTGTGCTGACACCA 59.579 61.111 10.53 0.00 46.86 4.17
2362 2390 1.004560 CGGTCTGTGCTGACACCAT 60.005 57.895 10.53 0.00 46.86 3.55
2363 2391 0.246360 CGGTCTGTGCTGACACCATA 59.754 55.000 10.53 0.00 46.86 2.74
2364 2392 1.726853 GGTCTGTGCTGACACCATAC 58.273 55.000 10.53 0.00 46.86 2.39
2365 2393 1.276421 GGTCTGTGCTGACACCATACT 59.724 52.381 10.53 0.00 46.86 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.844090 GGTCTCCGAGGCCAGAGC 61.844 72.222 14.53 4.67 40.51 4.09
92 94 1.449601 CAACGGAGGGGAATGGTCG 60.450 63.158 0.00 0.00 0.00 4.79
97 99 2.316586 ATGGCCAACGGAGGGGAAT 61.317 57.895 10.96 0.00 0.00 3.01
98 100 2.938798 ATGGCCAACGGAGGGGAA 60.939 61.111 10.96 0.00 0.00 3.97
99 101 3.727258 CATGGCCAACGGAGGGGA 61.727 66.667 10.96 0.00 0.00 4.81
102 104 4.738998 TGCCATGGCCAACGGAGG 62.739 66.667 33.44 15.83 41.09 4.30
108 110 0.468585 GATCCAGATGCCATGGCCAA 60.469 55.000 33.44 17.20 41.09 4.52
140 142 2.360483 AGGCATCGAGTATGTGACAGAG 59.640 50.000 0.00 0.00 37.93 3.35
173 175 4.047125 CCCAGGCCGGACACCATT 62.047 66.667 11.69 0.00 36.56 3.16
209 211 4.838486 GACGAGGAGCACGCCGAG 62.838 72.222 0.00 0.00 0.00 4.63
238 240 4.032452 TTGCCATCTCCGCCTGCA 62.032 61.111 0.00 0.00 0.00 4.41
249 251 1.978617 CCAAGCCCGAAGTTGCCAT 60.979 57.895 0.00 0.00 0.00 4.40
254 256 2.034221 GCCTCCAAGCCCGAAGTT 59.966 61.111 0.00 0.00 0.00 2.66
255 257 4.394712 CGCCTCCAAGCCCGAAGT 62.395 66.667 0.00 0.00 0.00 3.01
263 265 2.255252 CGCAAAACCGCCTCCAAG 59.745 61.111 0.00 0.00 0.00 3.61
293 299 2.353858 CCACATGGCCTTGCAAGAA 58.646 52.632 28.05 12.99 0.00 2.52
400 408 0.395311 AAGCCCGTAGAGATCCGACA 60.395 55.000 0.00 0.00 0.00 4.35
402 410 0.744874 CAAAGCCCGTAGAGATCCGA 59.255 55.000 0.00 0.00 0.00 4.55
458 466 0.319083 ACAGCGGGTCGTTCATACAA 59.681 50.000 0.00 0.00 0.00 2.41
463 471 3.529341 ATGCACAGCGGGTCGTTCA 62.529 57.895 0.00 0.00 0.00 3.18
485 493 3.410628 TGCCCCGACATCCTGCAT 61.411 61.111 0.00 0.00 0.00 3.96
489 497 3.771160 GACGTGCCCCGACATCCT 61.771 66.667 0.00 0.00 40.70 3.24
491 499 2.202756 GAGACGTGCCCCGACATC 60.203 66.667 0.00 0.00 40.70 3.06
492 500 4.129737 CGAGACGTGCCCCGACAT 62.130 66.667 0.00 0.00 40.70 3.06
518 527 2.494530 GGGACTCCTAGGCTGCGAG 61.495 68.421 2.96 10.20 0.00 5.03
533 542 2.040442 TCCTCCGCCAAGATGGGA 59.960 61.111 0.00 0.00 38.19 4.37
557 566 1.443407 CCTAGCGATGACCACCCTG 59.557 63.158 0.00 0.00 0.00 4.45
616 625 0.889186 CCAACAACAACCTCCCTCGG 60.889 60.000 0.00 0.00 0.00 4.63
619 628 0.178990 GCTCCAACAACAACCTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
662 672 4.697756 CGCAACCGGCAAGGGAGA 62.698 66.667 0.00 0.00 46.96 3.71
704 714 1.966901 TACCACGGCGATGGCATCTT 61.967 55.000 23.97 9.89 44.33 2.40
708 718 3.071837 TCTACCACGGCGATGGCA 61.072 61.111 22.50 12.89 44.33 4.92
712 722 1.076923 AGACCTCTACCACGGCGAT 60.077 57.895 16.62 0.25 0.00 4.58
817 833 1.202533 CCGCCGTATCACAGGAAATCT 60.203 52.381 0.00 0.00 0.00 2.40
846 862 1.520174 CATGTCAAGCTGCGTCGATAG 59.480 52.381 0.00 0.00 0.00 2.08
848 864 1.699656 GCATGTCAAGCTGCGTCGAT 61.700 55.000 0.00 0.00 0.00 3.59
852 868 3.425713 CGGCATGTCAAGCTGCGT 61.426 61.111 0.00 0.00 39.30 5.24
890 906 3.555117 AAGTCCTCCAGGTGGTACTTA 57.445 47.619 17.24 0.00 34.51 2.24
908 924 0.593773 CCGCGAACACCACCAAAAAG 60.594 55.000 8.23 0.00 0.00 2.27
941 957 6.151144 CGGAAGGGATAACAAGATCTTTGTTT 59.849 38.462 20.73 11.65 42.10 2.83
949 965 3.388350 GGAGACGGAAGGGATAACAAGAT 59.612 47.826 0.00 0.00 0.00 2.40
957 973 1.056700 CCATGGGAGACGGAAGGGAT 61.057 60.000 2.85 0.00 0.00 3.85
1018 1035 0.452987 TCATCAGCTTGCAATTCGCC 59.547 50.000 0.00 0.00 41.33 5.54
1024 1041 2.793288 TCATCCTCATCAGCTTGCAA 57.207 45.000 0.00 0.00 0.00 4.08
1026 1043 1.948145 CCTTCATCCTCATCAGCTTGC 59.052 52.381 0.00 0.00 0.00 4.01
1043 1060 4.284178 CCCTTCAATCATCAATCCACCTT 58.716 43.478 0.00 0.00 0.00 3.50
1102 1120 1.308998 CACGAACTGCCCAGAAGTTT 58.691 50.000 1.69 0.00 37.98 2.66
1104 1122 1.045407 TACACGAACTGCCCAGAAGT 58.955 50.000 1.69 0.00 0.00 3.01
1123 1141 2.832931 GCGCCAAGCTATCGATCAT 58.167 52.632 0.00 0.00 44.04 2.45
1179 1197 1.149174 CACACACCAGGCCTTGAGT 59.851 57.895 11.55 5.89 0.00 3.41
1184 1202 2.606587 GGATCCACACACCAGGCCT 61.607 63.158 6.95 0.00 0.00 5.19
1204 1224 1.230635 CGAAACACTGGCACCTCCTG 61.231 60.000 0.00 0.00 39.46 3.86
1279 1299 4.706035 TCAAGCAATTGCCAGAATGTTTT 58.294 34.783 26.45 8.31 43.38 2.43
1305 1325 1.612991 CCAACATGGATGAACGTGGGA 60.613 52.381 0.00 0.00 40.96 4.37
1311 1331 2.163010 CACTCTGCCAACATGGATGAAC 59.837 50.000 0.00 0.00 40.96 3.18
1312 1332 2.224843 ACACTCTGCCAACATGGATGAA 60.225 45.455 0.00 0.00 40.96 2.57
1333 1353 2.813726 CCGGTGGTGTGAAGTCCCA 61.814 63.158 0.00 0.00 0.00 4.37
1338 1358 0.535102 AAAGCTCCGGTGGTGTGAAG 60.535 55.000 9.27 0.00 0.00 3.02
1362 1382 1.326213 CCTCCTCACTGTCCGCTCAT 61.326 60.000 0.00 0.00 0.00 2.90
1363 1383 1.979155 CCTCCTCACTGTCCGCTCA 60.979 63.158 0.00 0.00 0.00 4.26
1368 1388 0.894184 TGTCGTCCTCCTCACTGTCC 60.894 60.000 0.00 0.00 0.00 4.02
1370 1390 0.674534 GTTGTCGTCCTCCTCACTGT 59.325 55.000 0.00 0.00 0.00 3.55
1380 1400 0.946221 CACTCTGCCTGTTGTCGTCC 60.946 60.000 0.00 0.00 0.00 4.79
1382 1402 1.069765 CCACTCTGCCTGTTGTCGT 59.930 57.895 0.00 0.00 0.00 4.34
1383 1403 2.320587 GCCACTCTGCCTGTTGTCG 61.321 63.158 0.00 0.00 0.00 4.35
1388 1408 2.282040 GCAAGCCACTCTGCCTGT 60.282 61.111 0.00 0.00 0.00 4.00
1390 1410 4.711949 CGGCAAGCCACTCTGCCT 62.712 66.667 12.19 0.00 44.65 4.75
1392 1412 3.123620 CTCGGCAAGCCACTCTGC 61.124 66.667 12.19 0.00 35.37 4.26
1408 1428 1.065854 CCCCAAATCTCGAGAACTGCT 60.066 52.381 20.91 0.00 0.00 4.24
1413 1433 0.253044 CAGGCCCCAAATCTCGAGAA 59.747 55.000 20.91 2.87 0.00 2.87
1419 1439 2.772924 CCACCAGGCCCCAAATCT 59.227 61.111 0.00 0.00 0.00 2.40
1431 1451 1.302949 GACCTGCTAATGGCCACCA 59.697 57.895 8.16 1.83 40.92 4.17
1465 1485 3.305676 GCACCATAGTCATCATAGACGCT 60.306 47.826 0.00 0.00 43.24 5.07
1472 1492 0.250467 GCCCGCACCATAGTCATCAT 60.250 55.000 0.00 0.00 0.00 2.45
1527 1547 3.289834 TACGATCTACCGGCGCCC 61.290 66.667 23.46 3.25 0.00 6.13
1536 1556 0.744874 GCACCTGCCAGTACGATCTA 59.255 55.000 0.00 0.00 34.31 1.98
1537 1557 0.972983 AGCACCTGCCAGTACGATCT 60.973 55.000 0.00 0.00 43.38 2.75
1539 1559 1.219124 CAGCACCTGCCAGTACGAT 59.781 57.895 0.00 0.00 43.38 3.73
1602 1622 4.024984 TCTAGGGCCCCACCAGCT 62.025 66.667 21.43 0.00 42.05 4.24
1603 1623 3.483869 CTCTAGGGCCCCACCAGC 61.484 72.222 21.43 0.00 42.05 4.85
1607 1627 2.998949 CCAACTCTAGGGCCCCAC 59.001 66.667 21.43 0.00 0.00 4.61
1633 1653 3.246880 ACCCACGACCCTTGTCCC 61.247 66.667 0.00 0.00 38.32 4.46
1638 1658 1.052124 TTGACTGACCCACGACCCTT 61.052 55.000 0.00 0.00 0.00 3.95
1642 1662 1.658994 TTGTTTGACTGACCCACGAC 58.341 50.000 0.00 0.00 0.00 4.34
1650 1670 5.124776 AGGAACGTTTGAATTGTTTGACTGA 59.875 36.000 0.46 0.00 0.00 3.41
1658 1678 3.687698 CCGGATAGGAACGTTTGAATTGT 59.312 43.478 0.46 0.00 45.00 2.71
1659 1679 3.687698 ACCGGATAGGAACGTTTGAATTG 59.312 43.478 9.46 0.00 45.00 2.32
1669 1689 4.262079 CCTCATTGTAGACCGGATAGGAAC 60.262 50.000 9.46 0.00 45.00 3.62
1670 1690 3.895656 CCTCATTGTAGACCGGATAGGAA 59.104 47.826 9.46 0.00 45.00 3.36
1687 1707 1.281925 AACAGAATCCCGCCCCTCAT 61.282 55.000 0.00 0.00 0.00 2.90
1688 1708 1.923395 AACAGAATCCCGCCCCTCA 60.923 57.895 0.00 0.00 0.00 3.86
1692 1712 2.361104 TGCAACAGAATCCCGCCC 60.361 61.111 0.00 0.00 0.00 6.13
1699 1719 1.421268 TCCAGGTGTCTGCAACAGAAT 59.579 47.619 0.00 0.00 42.46 2.40
1700 1720 0.836606 TCCAGGTGTCTGCAACAGAA 59.163 50.000 0.00 0.00 42.46 3.02
1701 1721 0.394192 CTCCAGGTGTCTGCAACAGA 59.606 55.000 2.52 0.00 38.97 3.41
1703 1723 1.451504 CCTCCAGGTGTCTGCAACA 59.548 57.895 0.00 0.00 39.61 3.33
1708 1728 1.002868 CAAGCCCTCCAGGTGTCTG 60.003 63.158 0.00 0.00 40.59 3.51
1709 1729 1.462238 ACAAGCCCTCCAGGTGTCT 60.462 57.895 0.00 0.00 38.26 3.41
1714 1734 0.179936 GATGAGACAAGCCCTCCAGG 59.820 60.000 0.00 0.00 39.47 4.45
1719 1739 0.755686 GATCCGATGAGACAAGCCCT 59.244 55.000 0.00 0.00 0.00 5.19
1744 1764 0.035915 GTCACCCCTCTCTCCTTTGC 60.036 60.000 0.00 0.00 0.00 3.68
1768 1788 1.486310 TCCTGATCTCATTGTTCGGGG 59.514 52.381 0.00 0.00 39.98 5.73
1772 1792 4.999950 ACAGTTGTCCTGATCTCATTGTTC 59.000 41.667 0.00 0.00 44.49 3.18
1773 1793 4.978099 ACAGTTGTCCTGATCTCATTGTT 58.022 39.130 0.00 0.00 44.49 2.83
1790 1811 0.318762 GCTCGAGAACCTGGACAGTT 59.681 55.000 18.75 0.00 0.00 3.16
1791 1812 1.536943 GGCTCGAGAACCTGGACAGT 61.537 60.000 18.75 0.00 0.00 3.55
1793 1814 0.832135 AAGGCTCGAGAACCTGGACA 60.832 55.000 18.75 0.00 36.07 4.02
1800 1821 1.137086 TGGCATAGAAGGCTCGAGAAC 59.863 52.381 18.75 8.13 34.73 3.01
1827 1848 2.930019 CCTCTCCACCCCTGCACA 60.930 66.667 0.00 0.00 0.00 4.57
1843 1864 2.757099 CTGCCTGATTGGTGCCCC 60.757 66.667 0.00 0.00 38.35 5.80
1847 1868 0.524862 GTGCTTCTGCCTGATTGGTG 59.475 55.000 0.00 0.00 38.71 4.17
1876 1897 1.154205 GGATCACCAGATTGTCGCGG 61.154 60.000 6.13 0.00 33.72 6.46
1877 1898 1.154205 GGGATCACCAGATTGTCGCG 61.154 60.000 0.00 0.00 39.85 5.87
1878 1899 0.107703 TGGGATCACCAGATTGTCGC 60.108 55.000 0.00 0.00 46.80 5.19
1888 1909 2.438434 CCTTGCCGTGGGATCACC 60.438 66.667 0.00 0.00 40.65 4.02
1895 1916 4.047125 ATGTCCCCCTTGCCGTGG 62.047 66.667 0.00 0.00 0.00 4.94
1896 1917 2.191786 TACATGTCCCCCTTGCCGTG 62.192 60.000 0.00 0.00 0.00 4.94
1897 1918 1.910580 CTACATGTCCCCCTTGCCGT 61.911 60.000 0.00 0.00 0.00 5.68
1901 1922 1.765314 CTCCTCTACATGTCCCCCTTG 59.235 57.143 0.00 0.00 0.00 3.61
1902 1923 1.366435 ACTCCTCTACATGTCCCCCTT 59.634 52.381 0.00 0.00 0.00 3.95
1903 1924 1.019650 ACTCCTCTACATGTCCCCCT 58.980 55.000 0.00 0.00 0.00 4.79
1904 1925 1.486726 CAACTCCTCTACATGTCCCCC 59.513 57.143 0.00 0.00 0.00 5.40
1905 1926 1.486726 CCAACTCCTCTACATGTCCCC 59.513 57.143 0.00 0.00 0.00 4.81
1906 1927 1.486726 CCCAACTCCTCTACATGTCCC 59.513 57.143 0.00 0.00 0.00 4.46
1908 1929 2.188817 ACCCCAACTCCTCTACATGTC 58.811 52.381 0.00 0.00 0.00 3.06
1910 1931 2.356125 CCAACCCCAACTCCTCTACATG 60.356 54.545 0.00 0.00 0.00 3.21
1911 1932 1.916181 CCAACCCCAACTCCTCTACAT 59.084 52.381 0.00 0.00 0.00 2.29
1912 1933 1.132657 TCCAACCCCAACTCCTCTACA 60.133 52.381 0.00 0.00 0.00 2.74
1915 1936 1.492993 GCTCCAACCCCAACTCCTCT 61.493 60.000 0.00 0.00 0.00 3.69
1927 1955 1.302832 CTCCACCACCTGCTCCAAC 60.303 63.158 0.00 0.00 0.00 3.77
1951 1979 0.165944 GGATCACCAAAGTTGTCGCG 59.834 55.000 0.00 0.00 35.97 5.87
1988 2016 3.164268 CTCCATTCCCAATTCCACAACA 58.836 45.455 0.00 0.00 0.00 3.33
1989 2017 2.094026 GCTCCATTCCCAATTCCACAAC 60.094 50.000 0.00 0.00 0.00 3.32
1991 2019 1.076841 TGCTCCATTCCCAATTCCACA 59.923 47.619 0.00 0.00 0.00 4.17
1994 2022 1.482182 GGTTGCTCCATTCCCAATTCC 59.518 52.381 0.00 0.00 35.97 3.01
1996 2024 1.079323 AGGGTTGCTCCATTCCCAATT 59.921 47.619 0.00 0.00 42.12 2.32
2004 2032 1.377725 CAAGCGAGGGTTGCTCCAT 60.378 57.895 0.00 0.00 43.14 3.41
2012 2040 1.488705 TTGGATCCACAAGCGAGGGT 61.489 55.000 15.91 0.00 0.00 4.34
2013 2041 0.107017 ATTGGATCCACAAGCGAGGG 60.107 55.000 15.91 0.00 33.23 4.30
2014 2042 1.019673 CATTGGATCCACAAGCGAGG 58.980 55.000 15.91 0.00 33.23 4.63
2019 2047 0.680921 ACCCGCATTGGATCCACAAG 60.681 55.000 15.91 8.45 42.00 3.16
2021 2049 1.378382 CACCCGCATTGGATCCACA 60.378 57.895 15.91 6.51 42.00 4.17
2023 2051 2.275089 CCACCCGCATTGGATCCA 59.725 61.111 11.44 11.44 42.00 3.41
2031 2059 1.077501 CCAAGTCATCCACCCGCAT 60.078 57.895 0.00 0.00 0.00 4.73
2041 2069 2.863484 TGGGGGCCACCAAGTCAT 60.863 61.111 29.27 0.00 42.91 3.06
2052 2080 2.753043 CATCAGTGTGCTGGGGGC 60.753 66.667 0.00 0.00 42.78 5.80
2063 2091 3.424703 CATTGACTGGTTTCCCATCAGT 58.575 45.455 0.00 0.00 43.50 3.41
2071 2099 1.464997 GCGTCTCCATTGACTGGTTTC 59.535 52.381 0.00 0.00 46.08 2.78
2078 2106 2.370281 TCTTCTGCGTCTCCATTGAC 57.630 50.000 0.00 0.00 0.00 3.18
2086 2114 1.021202 CGAGGAGATCTTCTGCGTCT 58.979 55.000 8.74 0.00 40.01 4.18
2088 2116 0.394488 TCCGAGGAGATCTTCTGCGT 60.394 55.000 8.74 0.00 40.01 5.24
2107 2135 0.757188 CTCTCCATACGTCCCTGGCT 60.757 60.000 0.00 0.00 32.30 4.75
2115 2143 1.342076 TGCTCCCTTCTCTCCATACGT 60.342 52.381 0.00 0.00 0.00 3.57
2118 2146 3.116977 TGATCTGCTCCCTTCTCTCCATA 60.117 47.826 0.00 0.00 0.00 2.74
2119 2147 2.328319 GATCTGCTCCCTTCTCTCCAT 58.672 52.381 0.00 0.00 0.00 3.41
2139 2167 2.562635 CCATCCATCAGTCAAGAGCTG 58.437 52.381 0.00 0.00 35.43 4.24
2141 2169 1.964552 CCCATCCATCAGTCAAGAGC 58.035 55.000 0.00 0.00 0.00 4.09
2143 2171 0.548031 GGCCCATCCATCAGTCAAGA 59.452 55.000 0.00 0.00 34.01 3.02
2144 2172 0.466922 GGGCCCATCCATCAGTCAAG 60.467 60.000 19.95 0.00 36.21 3.02
2156 2184 2.284211 TATCCTCCACTGGGGCCCAT 62.284 60.000 28.95 13.90 36.21 4.00
2166 2194 3.759581 TGGACCGTAGTATATCCTCCAC 58.240 50.000 0.00 0.00 32.06 4.02
2177 2205 1.275291 CCATCTGTGTTGGACCGTAGT 59.725 52.381 0.00 0.00 36.26 2.73
2180 2208 1.374947 CCCATCTGTGTTGGACCGT 59.625 57.895 0.00 0.00 36.26 4.83
2204 2232 3.947132 CTCCTCCACCAGCGCACTG 62.947 68.421 11.47 0.00 44.05 3.66
2215 2243 2.611800 ATGTGGCTGCCTCCTCCA 60.612 61.111 21.03 8.88 0.00 3.86
2236 2264 2.752807 GGGTGGATGGGCACGGTAT 61.753 63.158 0.00 0.00 0.00 2.73
2237 2265 3.404438 GGGTGGATGGGCACGGTA 61.404 66.667 0.00 0.00 0.00 4.02
2239 2267 3.660422 ATTGGGTGGATGGGCACGG 62.660 63.158 0.00 0.00 0.00 4.94
2240 2268 2.044053 ATTGGGTGGATGGGCACG 60.044 61.111 0.00 0.00 0.00 5.34
2260 2288 1.418637 GTACAGTGGTCTCCAAACCCA 59.581 52.381 0.00 0.00 38.65 4.51
2265 2293 3.582647 ACATCATGTACAGTGGTCTCCAA 59.417 43.478 0.33 0.00 34.18 3.53
2273 2301 2.667969 CGTGGTCACATCATGTACAGTG 59.332 50.000 0.33 4.13 0.00 3.66
2277 2305 1.917955 CGACGTGGTCACATCATGTAC 59.082 52.381 0.00 0.00 34.84 2.90
2279 2307 0.601057 TCGACGTGGTCACATCATGT 59.399 50.000 0.00 0.00 37.10 3.21
2282 2310 0.172578 GGATCGACGTGGTCACATCA 59.827 55.000 0.00 0.00 32.09 3.07
2312 2340 3.681417 GCTCAAAATTCACATTCCTTGGC 59.319 43.478 0.00 0.00 0.00 4.52
2313 2341 5.047519 AGAGCTCAAAATTCACATTCCTTGG 60.048 40.000 17.77 0.00 0.00 3.61
2314 2342 5.862323 CAGAGCTCAAAATTCACATTCCTTG 59.138 40.000 17.77 0.00 0.00 3.61
2315 2343 5.771666 TCAGAGCTCAAAATTCACATTCCTT 59.228 36.000 17.77 0.00 0.00 3.36
2316 2344 5.182760 GTCAGAGCTCAAAATTCACATTCCT 59.817 40.000 17.77 0.00 0.00 3.36
2317 2345 5.397326 GTCAGAGCTCAAAATTCACATTCC 58.603 41.667 17.77 0.00 0.00 3.01
2318 2346 5.084722 CGTCAGAGCTCAAAATTCACATTC 58.915 41.667 17.77 0.00 0.00 2.67
2319 2347 4.083110 CCGTCAGAGCTCAAAATTCACATT 60.083 41.667 17.77 0.00 0.00 2.71
2320 2348 3.438087 CCGTCAGAGCTCAAAATTCACAT 59.562 43.478 17.77 0.00 0.00 3.21
2321 2349 2.807967 CCGTCAGAGCTCAAAATTCACA 59.192 45.455 17.77 0.00 0.00 3.58
2322 2350 2.413371 GCCGTCAGAGCTCAAAATTCAC 60.413 50.000 17.77 0.43 0.00 3.18
2323 2351 1.806542 GCCGTCAGAGCTCAAAATTCA 59.193 47.619 17.77 0.00 0.00 2.57
2324 2352 1.131315 GGCCGTCAGAGCTCAAAATTC 59.869 52.381 17.77 0.45 0.00 2.17
2325 2353 1.168714 GGCCGTCAGAGCTCAAAATT 58.831 50.000 17.77 0.00 0.00 1.82
2326 2354 1.021390 CGGCCGTCAGAGCTCAAAAT 61.021 55.000 19.50 0.00 0.00 1.82
2327 2355 1.667830 CGGCCGTCAGAGCTCAAAA 60.668 57.895 19.50 0.00 0.00 2.44
2328 2356 2.048222 CGGCCGTCAGAGCTCAAA 60.048 61.111 19.50 0.00 0.00 2.69
2329 2357 4.069232 CCGGCCGTCAGAGCTCAA 62.069 66.667 26.12 0.00 0.00 3.02
2331 2359 4.500116 GACCGGCCGTCAGAGCTC 62.500 72.222 26.12 5.27 41.54 4.09
2333 2361 4.803426 CAGACCGGCCGTCAGAGC 62.803 72.222 26.12 6.22 44.66 4.09
2334 2362 3.374402 ACAGACCGGCCGTCAGAG 61.374 66.667 26.12 10.93 44.66 3.35
2335 2363 3.680786 CACAGACCGGCCGTCAGA 61.681 66.667 26.12 0.00 44.66 3.27
2341 2369 4.314440 TGTCAGCACAGACCGGCC 62.314 66.667 0.00 0.00 37.73 6.13
2342 2370 3.044305 GTGTCAGCACAGACCGGC 61.044 66.667 0.00 0.00 44.64 6.13
2343 2371 2.357517 GGTGTCAGCACAGACCGG 60.358 66.667 0.00 0.00 46.95 5.28
2344 2372 0.246360 TATGGTGTCAGCACAGACCG 59.754 55.000 6.92 0.00 46.95 4.79
2345 2373 1.276421 AGTATGGTGTCAGCACAGACC 59.724 52.381 6.92 0.00 46.95 3.85
2346 2374 2.751166 AGTATGGTGTCAGCACAGAC 57.249 50.000 6.92 6.20 46.95 3.51


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

AutoCloner maintained by Alex Coulton.