Multiple sequence alignment - TraesCS3A01G005600

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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 TraesCS3A01G005600 chr3A 100.000 2543 0 0 1 2543 7126703 7124161 0.000000e+00 4697.0
1 TraesCS3A01G005600 chr3D 93.884 1684 84 10 5 1684 1889016 1890684 0.000000e+00 2521.0
2 TraesCS3A01G005600 chr3D 93.182 264 12 2 1927 2190 269465490 269465747 1.430000e-102 383.0
3 TraesCS3A01G005600 chr3D 92.248 258 14 2 1933 2190 153750162 153750413 6.690000e-96 361.0
4 TraesCS3A01G005600 chr3D 91.860 258 15 2 1933 2190 563448930 563449181 3.110000e-94 355.0
5 TraesCS3A01G005600 chr3B 93.279 982 53 6 809 1790 5075579 5076547 0.000000e+00 1435.0
6 TraesCS3A01G005600 chr3B 93.177 982 54 6 809 1790 4220135 4221103 0.000000e+00 1430.0
7 TraesCS3A01G005600 chr3B 91.840 674 43 7 5 670 4219452 4220121 0.000000e+00 929.0
8 TraesCS3A01G005600 chr3B 91.543 674 45 7 5 670 5074897 5075566 0.000000e+00 918.0
9 TraesCS3A01G005600 chr3B 87.679 349 24 8 2191 2537 5076713 5077044 3.070000e-104 388.0
10 TraesCS3A01G005600 chr3B 87.106 349 26 8 2191 2537 4221269 4221600 6.640000e-101 377.0
11 TraesCS3A01G005600 chr3B 95.745 141 6 0 1784 1924 4221129 4221269 7.080000e-56 228.0
12 TraesCS3A01G005600 chr3B 95.745 141 6 0 1784 1924 5076573 5076713 7.080000e-56 228.0
13 TraesCS3A01G005600 chr2D 93.704 270 11 2 1926 2195 541547549 541547286 1.420000e-107 399.0
14 TraesCS3A01G005600 chr7A 91.697 277 13 5 1927 2201 103073289 103073021 2.390000e-100 375.0
15 TraesCS3A01G005600 chr6D 93.050 259 11 2 1937 2194 450269582 450269330 3.090000e-99 372.0
16 TraesCS3A01G005600 chr6D 84.146 82 12 1 2340 2420 35496062 35496143 7.540000e-11 78.7
17 TraesCS3A01G005600 chr4A 91.791 268 15 3 1927 2193 707022283 707022022 1.440000e-97 366.0
18 TraesCS3A01G005600 chr4A 91.892 259 15 2 1935 2193 443855283 443855031 8.650000e-95 357.0
19 TraesCS3A01G005600 chr7D 93.200 250 14 2 1945 2193 25492995 25492748 5.170000e-97 364.0
20 TraesCS3A01G005600 chr7D 93.023 43 2 1 2374 2415 244220440 244220398 7.600000e-06 62.1
21 TraesCS3A01G005600 chr4B 84.375 96 9 5 2329 2420 56269039 56269132 3.480000e-14 89.8
22 TraesCS3A01G005600 chr1A 87.692 65 6 2 2377 2440 561273621 561273558 9.760000e-10 75.0
23 TraesCS3A01G005600 chr1D 86.154 65 8 1 2377 2440 468341161 468341097 4.540000e-08 69.4
24 TraesCS3A01G005600 chr5D 86.792 53 6 1 2389 2440 43245511 43245563 9.830000e-05 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 TraesCS3A01G005600 chr3A 7124161 7126703 2542 True 4697.00 4697 100.0000 1 2543 1 chr3A.!!$R1 2542
1 TraesCS3A01G005600 chr3D 1889016 1890684 1668 False 2521.00 2521 93.8840 5 1684 1 chr3D.!!$F1 1679
2 TraesCS3A01G005600 chr3B 5074897 5077044 2147 False 742.25 1435 92.0615 5 2537 4 chr3B.!!$F2 2532
3 TraesCS3A01G005600 chr3B 4219452 4221600 2148 False 741.00 1430 91.9670 5 2537 4 chr3B.!!$F1 2532

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
968 976 1.209261 TGCACCAACAGAACAGAGACA 59.791 47.619 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 2409 0.183492 TGAGCAGGTAATCATGGGCC 59.817 55.0 0.0 0.0 0.0 5.8 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
130 137 2.607282 GCGAGTATGCGGCAACTAGTAT 60.607 50.000 6.82 0.00 0.00 2.12
219 226 7.180322 TGGCATAATTAAGGCAGATTTTTCA 57.820 32.000 12.36 0.00 35.21 2.69
221 228 7.548780 TGGCATAATTAAGGCAGATTTTTCAAC 59.451 33.333 12.36 0.00 35.21 3.18
222 229 7.548780 GGCATAATTAAGGCAGATTTTTCAACA 59.451 33.333 9.16 0.00 0.00 3.33
305 312 2.677337 GCAAAGTGCAAACAACAATGGT 59.323 40.909 0.00 0.00 44.26 3.55
360 367 3.249091 CTCATCTTCTTCATATCCGCCG 58.751 50.000 0.00 0.00 0.00 6.46
375 382 1.668419 CGCCGAATCATTCTTCCCTT 58.332 50.000 0.00 0.00 0.00 3.95
449 456 1.379146 GGTTTGTCCCCCTCACCTC 59.621 63.158 0.00 0.00 0.00 3.85
462 469 5.368989 CCCCTCACCTCTGAAACAATATAC 58.631 45.833 0.00 0.00 0.00 1.47
547 554 4.035558 ACTGTCGCATAATATTGGTTGCAG 59.964 41.667 15.63 11.01 34.80 4.41
610 618 8.995027 TTCCATTGCTGGTCATTTATAATACT 57.005 30.769 0.00 0.00 43.61 2.12
612 620 7.665559 TCCATTGCTGGTCATTTATAATACTCC 59.334 37.037 0.00 0.00 43.61 3.85
615 623 8.621532 TTGCTGGTCATTTATAATACTCCATC 57.378 34.615 0.00 0.00 0.00 3.51
617 625 8.097038 TGCTGGTCATTTATAATACTCCATCTC 58.903 37.037 0.00 0.00 0.00 2.75
618 626 8.097038 GCTGGTCATTTATAATACTCCATCTCA 58.903 37.037 0.00 0.00 0.00 3.27
619 627 9.429359 CTGGTCATTTATAATACTCCATCTCAC 57.571 37.037 0.00 0.00 0.00 3.51
620 628 8.088365 TGGTCATTTATAATACTCCATCTCACG 58.912 37.037 0.00 0.00 0.00 4.35
621 629 7.545965 GGTCATTTATAATACTCCATCTCACGG 59.454 40.741 0.00 0.00 0.00 4.94
690 698 9.915629 ACATTTATTACTCGATCTGTAGGATTC 57.084 33.333 0.00 0.00 34.33 2.52
698 706 6.071334 ACTCGATCTGTAGGATTCTGTTTCAA 60.071 38.462 0.00 0.00 34.33 2.69
699 707 6.697395 TCGATCTGTAGGATTCTGTTTCAAA 58.303 36.000 0.00 0.00 34.33 2.69
700 708 7.158697 TCGATCTGTAGGATTCTGTTTCAAAA 58.841 34.615 0.00 0.00 34.33 2.44
758 766 5.221263 GGATCTAAACTCAGCGGAAGTATCA 60.221 44.000 0.00 0.00 0.00 2.15
791 799 2.136728 TGTTGCTGCATTGCACATTTC 58.863 42.857 7.38 6.10 43.20 2.17
875 883 8.651588 CAGCGAAAGAAATAGATATACCATCAC 58.348 37.037 0.00 0.00 0.00 3.06
876 884 7.542477 AGCGAAAGAAATAGATATACCATCACG 59.458 37.037 0.00 0.00 0.00 4.35
963 971 2.287915 GTGTACTGCACCAACAGAACAG 59.712 50.000 0.00 0.00 42.10 3.16
964 972 2.169561 TGTACTGCACCAACAGAACAGA 59.830 45.455 0.00 0.00 40.25 3.41
965 973 1.959042 ACTGCACCAACAGAACAGAG 58.041 50.000 0.00 0.00 40.25 3.35
966 974 1.486310 ACTGCACCAACAGAACAGAGA 59.514 47.619 0.00 0.00 40.25 3.10
967 975 1.869767 CTGCACCAACAGAACAGAGAC 59.130 52.381 0.00 0.00 40.25 3.36
968 976 1.209261 TGCACCAACAGAACAGAGACA 59.791 47.619 0.00 0.00 0.00 3.41
1042 1050 5.522460 TCCGTAGCTATTGTTCTTATTGTGC 59.478 40.000 0.00 0.00 0.00 4.57
1118 1126 1.671979 CGGATGTGCATGAAGACCAT 58.328 50.000 0.00 0.00 35.44 3.55
1170 1178 0.321298 TCAACCCAAAGAGCGCCTAC 60.321 55.000 2.29 0.00 0.00 3.18
1260 1268 3.009695 TCGGGGTCATCAACAACCTAAAT 59.990 43.478 0.00 0.00 35.78 1.40
1262 1270 4.574828 CGGGGTCATCAACAACCTAAATAG 59.425 45.833 0.00 0.00 35.78 1.73
1287 1295 3.083997 CTAGGCAAGCCCGAGGGT 61.084 66.667 7.62 0.00 39.21 4.34
1335 1343 0.036388 ATCAGGACGCCGACAACAAT 60.036 50.000 0.00 0.00 0.00 2.71
1576 1584 4.644103 AAATCTTGGCTCATATGTGTGC 57.356 40.909 7.87 7.87 42.55 4.57
1594 1602 3.876914 TGTGCGCTCCCTTCAATAATTAG 59.123 43.478 9.73 0.00 0.00 1.73
1596 1604 3.876914 TGCGCTCCCTTCAATAATTAGTG 59.123 43.478 9.73 6.58 0.00 2.74
1612 1620 6.408858 AATTAGTGAGTTGTTCATGTAGCG 57.591 37.500 0.00 0.00 38.29 4.26
1617 1625 4.862574 GTGAGTTGTTCATGTAGCGACATA 59.137 41.667 12.37 0.00 44.82 2.29
1623 1631 6.117911 TGTTCATGTAGCGACATATTTTGG 57.882 37.500 12.37 0.00 44.82 3.28
1698 1707 4.413760 ACCAAGTAGACAACTAGTGCCTA 58.586 43.478 0.00 0.00 37.50 3.93
1714 1723 0.729116 CCTACAAGCGACCAAGCATG 59.271 55.000 0.00 0.00 41.10 4.06
1715 1724 0.097674 CTACAAGCGACCAAGCATGC 59.902 55.000 10.51 10.51 39.18 4.06
1716 1725 0.605050 TACAAGCGACCAAGCATGCA 60.605 50.000 21.98 0.00 39.18 3.96
1717 1726 1.246056 ACAAGCGACCAAGCATGCAT 61.246 50.000 21.98 4.57 39.18 3.96
1758 1767 4.584743 TGACATATGTTCGCTCATCTAGGT 59.415 41.667 10.30 0.00 0.00 3.08
1767 1776 1.751924 GCTCATCTAGGTCACCGAACT 59.248 52.381 0.00 0.00 32.68 3.01
1772 1781 4.398358 TCATCTAGGTCACCGAACTAACAG 59.602 45.833 0.00 0.00 30.97 3.16
1779 1788 2.701951 TCACCGAACTAACAGGGTTTCT 59.298 45.455 0.00 0.00 0.00 2.52
1806 1847 7.077605 TGACAACAATTTCAATCTCGTCAATC 58.922 34.615 0.00 0.00 0.00 2.67
1894 1935 8.087750 TCGGCACAAATTAATTTCTTTGAGAAT 58.912 29.630 10.53 0.00 33.67 2.40
1924 1965 1.189884 CGGCTCGTGCAATTTTGTTTG 59.810 47.619 12.07 0.00 41.91 2.93
1984 2025 3.621419 CCAAAGGGGCAGATCCAAT 57.379 52.632 0.00 0.00 36.21 3.16
1985 2026 1.870064 CCAAAGGGGCAGATCCAATT 58.130 50.000 0.00 0.00 36.21 2.32
1986 2027 3.030873 CCAAAGGGGCAGATCCAATTA 57.969 47.619 0.00 0.00 36.21 1.40
1987 2028 3.373830 CCAAAGGGGCAGATCCAATTAA 58.626 45.455 0.00 0.00 36.21 1.40
1988 2029 3.969312 CCAAAGGGGCAGATCCAATTAAT 59.031 43.478 0.00 0.00 36.21 1.40
1989 2030 4.039609 CCAAAGGGGCAGATCCAATTAATC 59.960 45.833 0.00 0.00 36.21 1.75
1990 2031 4.821532 AAGGGGCAGATCCAATTAATCT 57.178 40.909 0.00 0.00 36.21 2.40
1991 2032 4.379302 AGGGGCAGATCCAATTAATCTC 57.621 45.455 0.62 0.00 36.21 2.75
1992 2033 3.077359 GGGGCAGATCCAATTAATCTCG 58.923 50.000 0.62 0.00 36.21 4.04
1993 2034 3.077359 GGGCAGATCCAATTAATCTCGG 58.923 50.000 0.62 0.00 36.21 4.63
1994 2035 3.496870 GGGCAGATCCAATTAATCTCGGT 60.497 47.826 0.62 0.00 36.21 4.69
1995 2036 3.748568 GGCAGATCCAATTAATCTCGGTC 59.251 47.826 0.62 0.00 31.05 4.79
1996 2037 4.380531 GCAGATCCAATTAATCTCGGTCA 58.619 43.478 0.62 0.00 31.05 4.02
1997 2038 4.999950 GCAGATCCAATTAATCTCGGTCAT 59.000 41.667 0.62 0.00 31.05 3.06
1998 2039 5.121454 GCAGATCCAATTAATCTCGGTCATC 59.879 44.000 0.62 0.00 31.05 2.92
1999 2040 6.226052 CAGATCCAATTAATCTCGGTCATCA 58.774 40.000 0.62 0.00 31.05 3.07
2000 2041 6.707608 CAGATCCAATTAATCTCGGTCATCAA 59.292 38.462 0.62 0.00 31.05 2.57
2001 2042 7.227314 CAGATCCAATTAATCTCGGTCATCAAA 59.773 37.037 0.62 0.00 31.05 2.69
2002 2043 7.941238 AGATCCAATTAATCTCGGTCATCAAAT 59.059 33.333 0.00 0.00 0.00 2.32
2003 2044 7.496529 TCCAATTAATCTCGGTCATCAAATC 57.503 36.000 0.00 0.00 0.00 2.17
2004 2045 7.053498 TCCAATTAATCTCGGTCATCAAATCA 58.947 34.615 0.00 0.00 0.00 2.57
2005 2046 7.720957 TCCAATTAATCTCGGTCATCAAATCAT 59.279 33.333 0.00 0.00 0.00 2.45
2006 2047 7.806487 CCAATTAATCTCGGTCATCAAATCATG 59.194 37.037 0.00 0.00 0.00 3.07
2007 2048 8.347771 CAATTAATCTCGGTCATCAAATCATGT 58.652 33.333 0.00 0.00 0.00 3.21
2008 2049 5.998454 AATCTCGGTCATCAAATCATGTC 57.002 39.130 0.00 0.00 0.00 3.06
2009 2050 4.470334 TCTCGGTCATCAAATCATGTCA 57.530 40.909 0.00 0.00 0.00 3.58
2010 2051 4.831107 TCTCGGTCATCAAATCATGTCAA 58.169 39.130 0.00 0.00 0.00 3.18
2011 2052 5.430886 TCTCGGTCATCAAATCATGTCAAT 58.569 37.500 0.00 0.00 0.00 2.57
2012 2053 5.525012 TCTCGGTCATCAAATCATGTCAATC 59.475 40.000 0.00 0.00 0.00 2.67
2013 2054 4.576053 TCGGTCATCAAATCATGTCAATCC 59.424 41.667 0.00 0.00 0.00 3.01
2014 2055 4.336153 CGGTCATCAAATCATGTCAATCCA 59.664 41.667 0.00 0.00 0.00 3.41
2015 2056 5.163632 CGGTCATCAAATCATGTCAATCCAA 60.164 40.000 0.00 0.00 0.00 3.53
2016 2057 6.460537 CGGTCATCAAATCATGTCAATCCAAT 60.461 38.462 0.00 0.00 0.00 3.16
2017 2058 6.700081 GGTCATCAAATCATGTCAATCCAATG 59.300 38.462 0.00 0.00 0.00 2.82
2018 2059 7.417003 GGTCATCAAATCATGTCAATCCAATGA 60.417 37.037 0.00 0.00 0.00 2.57
2028 2069 5.091261 GTCAATCCAATGACCTAGACTGT 57.909 43.478 0.00 0.00 43.11 3.55
2029 2070 5.491982 GTCAATCCAATGACCTAGACTGTT 58.508 41.667 0.00 0.00 43.11 3.16
2030 2071 5.940470 GTCAATCCAATGACCTAGACTGTTT 59.060 40.000 0.00 0.00 43.11 2.83
2031 2072 6.092807 GTCAATCCAATGACCTAGACTGTTTC 59.907 42.308 0.00 0.00 43.11 2.78
2032 2073 5.762179 ATCCAATGACCTAGACTGTTTCA 57.238 39.130 0.00 0.00 0.00 2.69
2033 2074 5.560722 TCCAATGACCTAGACTGTTTCAA 57.439 39.130 0.00 0.00 0.00 2.69
2034 2075 6.126863 TCCAATGACCTAGACTGTTTCAAT 57.873 37.500 0.00 0.00 0.00 2.57
2035 2076 5.939883 TCCAATGACCTAGACTGTTTCAATG 59.060 40.000 0.00 0.00 0.00 2.82
2036 2077 5.707298 CCAATGACCTAGACTGTTTCAATGT 59.293 40.000 0.00 0.00 0.00 2.71
2037 2078 6.128172 CCAATGACCTAGACTGTTTCAATGTC 60.128 42.308 0.00 0.00 0.00 3.06
2038 2079 4.556233 TGACCTAGACTGTTTCAATGTCG 58.444 43.478 0.00 0.00 36.01 4.35
2039 2080 4.279922 TGACCTAGACTGTTTCAATGTCGA 59.720 41.667 0.00 0.00 36.01 4.20
2040 2081 4.810790 ACCTAGACTGTTTCAATGTCGAG 58.189 43.478 0.00 0.00 36.01 4.04
2041 2082 4.281182 ACCTAGACTGTTTCAATGTCGAGT 59.719 41.667 0.00 0.00 33.61 4.18
2042 2083 4.623167 CCTAGACTGTTTCAATGTCGAGTG 59.377 45.833 0.00 0.00 33.61 3.51
2043 2084 2.802816 AGACTGTTTCAATGTCGAGTGC 59.197 45.455 0.00 0.00 36.01 4.40
2044 2085 2.802816 GACTGTTTCAATGTCGAGTGCT 59.197 45.455 0.00 0.00 0.00 4.40
2045 2086 2.802816 ACTGTTTCAATGTCGAGTGCTC 59.197 45.455 0.00 0.00 0.00 4.26
2046 2087 2.802247 CTGTTTCAATGTCGAGTGCTCA 59.198 45.455 0.00 0.00 0.00 4.26
2047 2088 3.202097 TGTTTCAATGTCGAGTGCTCAA 58.798 40.909 0.00 0.00 0.00 3.02
2048 2089 3.002246 TGTTTCAATGTCGAGTGCTCAAC 59.998 43.478 0.00 0.00 0.00 3.18
2049 2090 2.524569 TCAATGTCGAGTGCTCAACA 57.475 45.000 0.00 0.00 0.00 3.33
2058 2099 3.345087 GTGCTCAACACGTTTAGCG 57.655 52.632 10.57 0.00 41.36 4.26
2072 2113 4.459606 CGTTTAGCGTGCAGTTAATTTCA 58.540 39.130 0.00 0.00 35.54 2.69
2073 2114 5.086058 CGTTTAGCGTGCAGTTAATTTCAT 58.914 37.500 0.00 0.00 35.54 2.57
2074 2115 5.002468 CGTTTAGCGTGCAGTTAATTTCATG 59.998 40.000 0.00 0.00 35.54 3.07
2075 2116 2.867429 AGCGTGCAGTTAATTTCATGC 58.133 42.857 6.69 6.69 40.63 4.06
2076 2117 1.919918 GCGTGCAGTTAATTTCATGCC 59.080 47.619 3.91 0.00 37.89 4.40
2077 2118 2.670789 GCGTGCAGTTAATTTCATGCCA 60.671 45.455 3.91 0.00 37.89 4.92
2078 2119 3.573598 CGTGCAGTTAATTTCATGCCAA 58.426 40.909 0.00 0.00 37.89 4.52
2079 2120 3.986572 CGTGCAGTTAATTTCATGCCAAA 59.013 39.130 0.00 0.00 37.89 3.28
2080 2121 4.626604 CGTGCAGTTAATTTCATGCCAAAT 59.373 37.500 0.00 0.00 37.89 2.32
2081 2122 5.804473 CGTGCAGTTAATTTCATGCCAAATA 59.196 36.000 0.00 0.00 37.89 1.40
2082 2123 6.476380 CGTGCAGTTAATTTCATGCCAAATAT 59.524 34.615 0.00 0.00 37.89 1.28
2083 2124 7.647318 CGTGCAGTTAATTTCATGCCAAATATA 59.353 33.333 0.00 0.00 37.89 0.86
2084 2125 8.755018 GTGCAGTTAATTTCATGCCAAATATAC 58.245 33.333 0.00 0.00 37.89 1.47
2085 2126 8.694540 TGCAGTTAATTTCATGCCAAATATACT 58.305 29.630 6.13 0.00 37.89 2.12
2086 2127 9.185192 GCAGTTAATTTCATGCCAAATATACTC 57.815 33.333 0.00 0.00 32.49 2.59
2087 2128 9.683069 CAGTTAATTTCATGCCAAATATACTCC 57.317 33.333 0.00 0.00 0.00 3.85
2088 2129 9.646522 AGTTAATTTCATGCCAAATATACTCCT 57.353 29.630 0.00 0.00 0.00 3.69
2089 2130 9.683069 GTTAATTTCATGCCAAATATACTCCTG 57.317 33.333 0.00 0.00 0.00 3.86
2090 2131 9.639563 TTAATTTCATGCCAAATATACTCCTGA 57.360 29.630 0.00 0.00 0.00 3.86
2091 2132 8.716674 AATTTCATGCCAAATATACTCCTGAT 57.283 30.769 0.00 0.00 0.00 2.90
2092 2133 7.514784 TTTCATGCCAAATATACTCCTGATG 57.485 36.000 0.00 0.00 0.00 3.07
2093 2134 6.191657 TCATGCCAAATATACTCCTGATGT 57.808 37.500 0.00 0.00 0.00 3.06
2094 2135 6.604171 TCATGCCAAATATACTCCTGATGTT 58.396 36.000 0.00 0.00 0.00 2.71
2095 2136 7.744733 TCATGCCAAATATACTCCTGATGTTA 58.255 34.615 0.00 0.00 0.00 2.41
2096 2137 8.217111 TCATGCCAAATATACTCCTGATGTTAA 58.783 33.333 0.00 0.00 0.00 2.01
2097 2138 9.017509 CATGCCAAATATACTCCTGATGTTAAT 57.982 33.333 0.00 0.00 0.00 1.40
2098 2139 8.621532 TGCCAAATATACTCCTGATGTTAATC 57.378 34.615 0.00 0.00 0.00 1.75
2099 2140 8.217111 TGCCAAATATACTCCTGATGTTAATCA 58.783 33.333 0.00 0.00 40.61 2.57
2100 2141 8.507249 GCCAAATATACTCCTGATGTTAATCAC 58.493 37.037 0.00 0.00 37.91 3.06
2101 2142 9.559732 CCAAATATACTCCTGATGTTAATCACA 57.440 33.333 0.00 0.00 37.91 3.58
2111 2152 9.898152 TCCTGATGTTAATCACATAATAACACA 57.102 29.630 0.20 1.66 46.96 3.72
2112 2153 9.935682 CCTGATGTTAATCACATAATAACACAC 57.064 33.333 0.20 0.29 46.96 3.82
2143 2184 6.727824 ATCTTACTTAATATCCGCATGCAC 57.272 37.500 19.57 0.00 0.00 4.57
2144 2185 5.853936 TCTTACTTAATATCCGCATGCACT 58.146 37.500 19.57 3.59 0.00 4.40
2145 2186 6.288294 TCTTACTTAATATCCGCATGCACTT 58.712 36.000 19.57 3.39 0.00 3.16
2146 2187 7.438564 TCTTACTTAATATCCGCATGCACTTA 58.561 34.615 19.57 5.72 0.00 2.24
2147 2188 7.929245 TCTTACTTAATATCCGCATGCACTTAA 59.071 33.333 19.57 11.55 0.00 1.85
2148 2189 8.615878 TTACTTAATATCCGCATGCACTTAAT 57.384 30.769 19.57 5.58 0.00 1.40
2149 2190 9.713713 TTACTTAATATCCGCATGCACTTAATA 57.286 29.630 19.57 7.60 0.00 0.98
2150 2191 8.792830 ACTTAATATCCGCATGCACTTAATAT 57.207 30.769 19.57 9.48 0.00 1.28
2151 2192 9.884636 ACTTAATATCCGCATGCACTTAATATA 57.115 29.630 19.57 4.53 0.00 0.86
2153 2194 9.884636 TTAATATCCGCATGCACTTAATATACT 57.115 29.630 19.57 2.37 0.00 2.12
2154 2195 8.792830 AATATCCGCATGCACTTAATATACTT 57.207 30.769 19.57 0.00 0.00 2.24
2155 2196 8.792830 ATATCCGCATGCACTTAATATACTTT 57.207 30.769 19.57 0.00 0.00 2.66
2156 2197 6.539649 TCCGCATGCACTTAATATACTTTC 57.460 37.500 19.57 0.00 0.00 2.62
2157 2198 6.052360 TCCGCATGCACTTAATATACTTTCA 58.948 36.000 19.57 0.00 0.00 2.69
2158 2199 6.540551 TCCGCATGCACTTAATATACTTTCAA 59.459 34.615 19.57 0.00 0.00 2.69
2159 2200 7.066404 TCCGCATGCACTTAATATACTTTCAAA 59.934 33.333 19.57 0.00 0.00 2.69
2160 2201 7.862372 CCGCATGCACTTAATATACTTTCAAAT 59.138 33.333 19.57 0.00 0.00 2.32
2161 2202 9.236691 CGCATGCACTTAATATACTTTCAAATT 57.763 29.630 19.57 0.00 0.00 1.82
2175 2216 7.160633 ACTTTCAAATTAACGTTCATTGCAC 57.839 32.000 2.82 0.00 0.00 4.57
2176 2217 5.797909 TTCAAATTAACGTTCATTGCACG 57.202 34.783 2.82 7.30 43.52 5.34
2183 2224 2.873170 CGTTCATTGCACGTACACAT 57.127 45.000 0.47 0.00 32.80 3.21
2184 2225 3.181826 CGTTCATTGCACGTACACATT 57.818 42.857 0.47 0.00 32.80 2.71
2185 2226 2.901873 CGTTCATTGCACGTACACATTG 59.098 45.455 0.47 0.00 32.80 2.82
2186 2227 3.363477 CGTTCATTGCACGTACACATTGA 60.363 43.478 0.47 0.00 32.80 2.57
2187 2228 3.804518 TCATTGCACGTACACATTGAC 57.195 42.857 0.00 0.00 0.00 3.18
2188 2229 3.398406 TCATTGCACGTACACATTGACT 58.602 40.909 0.00 0.00 0.00 3.41
2189 2230 4.561105 TCATTGCACGTACACATTGACTA 58.439 39.130 0.00 0.00 0.00 2.59
2190 2231 5.175127 TCATTGCACGTACACATTGACTAT 58.825 37.500 0.00 0.00 0.00 2.12
2191 2232 5.641636 TCATTGCACGTACACATTGACTATT 59.358 36.000 0.00 0.00 0.00 1.73
2192 2233 6.814146 TCATTGCACGTACACATTGACTATTA 59.186 34.615 0.00 0.00 0.00 0.98
2193 2234 6.397831 TTGCACGTACACATTGACTATTAC 57.602 37.500 0.00 0.00 0.00 1.89
2197 2238 7.977293 TGCACGTACACATTGACTATTACTATT 59.023 33.333 0.00 0.00 0.00 1.73
2223 2265 3.448093 TGAAAGAATGTGTGGGCCATA 57.552 42.857 10.70 3.21 0.00 2.74
2229 2271 0.679640 ATGTGTGGGCCATACGGTTG 60.680 55.000 25.57 0.00 33.28 3.77
2230 2272 2.360600 TGTGGGCCATACGGTTGC 60.361 61.111 10.70 0.00 33.28 4.17
2234 2276 2.414785 GGGCCATACGGTTGCCTTG 61.415 63.158 4.39 0.00 44.71 3.61
2277 2319 1.733912 GCAGTCACTCAAATCGCATCA 59.266 47.619 0.00 0.00 0.00 3.07
2279 2321 1.995484 AGTCACTCAAATCGCATCACG 59.005 47.619 0.00 0.00 45.62 4.35
2280 2322 1.061131 GTCACTCAAATCGCATCACGG 59.939 52.381 0.00 0.00 43.89 4.94
2286 2328 1.735018 CAAATCGCATCACGGTGGTTA 59.265 47.619 8.50 0.00 43.89 2.85
2287 2329 1.651987 AATCGCATCACGGTGGTTAG 58.348 50.000 8.50 0.00 43.89 2.34
2289 2331 0.108992 TCGCATCACGGTGGTTAGAC 60.109 55.000 8.50 0.00 43.89 2.59
2299 2341 2.094338 CGGTGGTTAGACCCAAGTAGTC 60.094 54.545 0.00 0.00 37.50 2.59
2372 2414 8.499406 ACATAAATATTCTAGTAAGTTGGCCCA 58.501 33.333 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 312 1.965930 GTGGATGTTGTGGCGCTCA 60.966 57.895 7.64 4.33 0.00 4.26
336 343 3.993081 GCGGATATGAAGAAGATGAGGTG 59.007 47.826 0.00 0.00 0.00 4.00
387 394 5.616986 AGAGACCAAATATATTCCCCCACAT 59.383 40.000 0.00 0.00 0.00 3.21
449 456 4.876107 AGGGTCAAGCGTATATTGTTTCAG 59.124 41.667 0.00 0.00 0.00 3.02
462 469 1.808411 TGAAAGCTAAGGGTCAAGCG 58.192 50.000 0.00 0.00 43.63 4.68
568 575 6.128227 GCAATGGAATAGCAAATCAGCAAAAA 60.128 34.615 0.00 0.00 36.85 1.94
569 576 5.352016 GCAATGGAATAGCAAATCAGCAAAA 59.648 36.000 0.00 0.00 36.85 2.44
609 617 4.023707 GCCATTAATTTCCGTGAGATGGAG 60.024 45.833 3.80 0.00 34.21 3.86
610 618 3.882888 GCCATTAATTTCCGTGAGATGGA 59.117 43.478 3.80 0.00 35.68 3.41
612 620 4.336433 ACTGCCATTAATTTCCGTGAGATG 59.664 41.667 0.00 0.00 0.00 2.90
615 623 4.634004 TGTACTGCCATTAATTTCCGTGAG 59.366 41.667 0.00 0.00 0.00 3.51
617 625 4.955925 TGTACTGCCATTAATTTCCGTG 57.044 40.909 0.00 0.00 0.00 4.94
618 626 5.650266 TGAATGTACTGCCATTAATTTCCGT 59.350 36.000 0.00 0.00 35.24 4.69
619 627 5.971202 GTGAATGTACTGCCATTAATTTCCG 59.029 40.000 0.00 0.00 35.24 4.30
620 628 7.100458 AGTGAATGTACTGCCATTAATTTCC 57.900 36.000 0.00 0.00 35.24 3.13
726 734 5.411781 CGCTGAGTTTAGATCCAAGTTACT 58.588 41.667 0.00 0.00 0.00 2.24
727 735 4.567159 CCGCTGAGTTTAGATCCAAGTTAC 59.433 45.833 0.00 0.00 0.00 2.50
728 736 4.464951 TCCGCTGAGTTTAGATCCAAGTTA 59.535 41.667 0.00 0.00 0.00 2.24
729 737 3.260884 TCCGCTGAGTTTAGATCCAAGTT 59.739 43.478 0.00 0.00 0.00 2.66
730 738 2.832129 TCCGCTGAGTTTAGATCCAAGT 59.168 45.455 0.00 0.00 0.00 3.16
731 739 3.526931 TCCGCTGAGTTTAGATCCAAG 57.473 47.619 0.00 0.00 0.00 3.61
732 740 3.260884 ACTTCCGCTGAGTTTAGATCCAA 59.739 43.478 0.00 0.00 0.00 3.53
733 741 2.832129 ACTTCCGCTGAGTTTAGATCCA 59.168 45.455 0.00 0.00 0.00 3.41
734 742 3.528597 ACTTCCGCTGAGTTTAGATCC 57.471 47.619 0.00 0.00 0.00 3.36
735 743 5.833082 TGATACTTCCGCTGAGTTTAGATC 58.167 41.667 0.00 0.00 0.00 2.75
736 744 5.854010 TGATACTTCCGCTGAGTTTAGAT 57.146 39.130 0.00 0.00 0.00 1.98
758 766 4.378774 TGCAGCAACAAATAAATGCACTT 58.621 34.783 0.00 0.00 42.45 3.16
791 799 6.965500 GCTCATCAAACAGTGATTTAGTCATG 59.035 38.462 0.00 0.00 45.13 3.07
875 883 4.627035 TCTTTATGATATGATGCGCCTTCG 59.373 41.667 4.18 0.00 39.07 3.79
876 884 6.674694 ATCTTTATGATATGATGCGCCTTC 57.325 37.500 4.18 2.11 32.79 3.46
963 971 2.531206 CAACTAGCTAGGCGTTGTCTC 58.469 52.381 24.35 0.00 34.77 3.36
964 972 1.404315 GCAACTAGCTAGGCGTTGTCT 60.404 52.381 24.35 0.00 39.98 3.41
965 973 1.000145 GCAACTAGCTAGGCGTTGTC 59.000 55.000 24.35 12.42 39.98 3.18
966 974 0.320374 TGCAACTAGCTAGGCGTTGT 59.680 50.000 24.35 0.18 45.94 3.32
967 975 1.438651 TTGCAACTAGCTAGGCGTTG 58.561 50.000 24.35 19.77 45.94 4.10
968 976 1.804748 GTTTGCAACTAGCTAGGCGTT 59.195 47.619 24.35 8.29 45.94 4.84
989 997 1.139163 GCTTGCCATTGTGGTTTTCG 58.861 50.000 0.00 0.00 40.46 3.46
1118 1126 2.519949 TGCACAGCATGGGGTTCA 59.480 55.556 0.00 0.00 42.43 3.18
1260 1268 2.042095 TTGCCTAGGCTGCCCCTA 59.958 61.111 33.07 9.58 44.08 3.53
1335 1343 0.462225 TTCGGGCGTTGTGTTTGAGA 60.462 50.000 0.00 0.00 0.00 3.27
1576 1584 5.360591 ACTCACTAATTATTGAAGGGAGCG 58.639 41.667 6.85 0.00 43.27 5.03
1594 1602 3.057019 TGTCGCTACATGAACAACTCAC 58.943 45.455 0.00 0.00 36.69 3.51
1596 1604 6.589830 AATATGTCGCTACATGAACAACTC 57.410 37.500 13.77 0.00 45.99 3.01
1612 1620 8.885722 ACAATTTCATCAATGCCAAAATATGTC 58.114 29.630 0.00 0.00 0.00 3.06
1617 1625 7.747155 TTCACAATTTCATCAATGCCAAAAT 57.253 28.000 0.00 0.00 0.00 1.82
1623 1631 8.564648 TCGATAATTCACAATTTCATCAATGC 57.435 30.769 0.00 0.00 32.38 3.56
1698 1707 1.246056 ATGCATGCTTGGTCGCTTGT 61.246 50.000 20.33 0.00 37.38 3.16
1714 1723 5.800438 GTCATCATTGATACATGCATCATGC 59.200 40.000 9.44 1.35 38.55 4.06
1715 1724 6.908825 TGTCATCATTGATACATGCATCATG 58.091 36.000 9.44 9.80 39.72 3.07
1716 1725 7.703058 ATGTCATCATTGATACATGCATCAT 57.297 32.000 9.44 0.00 34.95 2.45
1717 1726 8.673711 CATATGTCATCATTGATACATGCATCA 58.326 33.333 20.33 4.40 35.70 3.07
1723 1732 7.605309 AGCGAACATATGTCATCATTGATACAT 59.395 33.333 9.23 17.80 35.70 2.29
1758 1767 2.701951 AGAAACCCTGTTAGTTCGGTGA 59.298 45.455 0.00 0.00 0.00 4.02
1767 1776 6.783708 ATTGTTGTCAAAGAAACCCTGTTA 57.216 33.333 0.00 0.00 37.11 2.41
1772 1781 6.976636 TTGAAATTGTTGTCAAAGAAACCC 57.023 33.333 0.00 0.00 37.11 4.11
1779 1788 6.790282 TGACGAGATTGAAATTGTTGTCAAA 58.210 32.000 0.00 0.00 37.31 2.69
1870 1911 9.815936 CAATTCTCAAAGAAATTAATTTGTGCC 57.184 29.630 17.98 3.92 37.82 5.01
1894 1935 2.110213 ACGAGCCGGCAGAAACAA 59.890 55.556 31.54 0.00 0.00 2.83
1947 1988 9.649316 CCCTTTGGGTCTTTTTATATTGGTATA 57.351 33.333 0.00 0.00 38.25 1.47
1948 1989 8.547481 CCCTTTGGGTCTTTTTATATTGGTAT 57.453 34.615 0.00 0.00 38.25 2.73
1949 1990 7.964666 CCCTTTGGGTCTTTTTATATTGGTA 57.035 36.000 0.00 0.00 38.25 3.25
1950 1991 6.867519 CCCTTTGGGTCTTTTTATATTGGT 57.132 37.500 0.00 0.00 38.25 3.67
1966 2007 1.870064 AATTGGATCTGCCCCTTTGG 58.130 50.000 0.00 0.00 34.97 3.28
1967 2008 4.897670 AGATTAATTGGATCTGCCCCTTTG 59.102 41.667 5.62 0.00 32.79 2.77
1968 2009 5.143369 GAGATTAATTGGATCTGCCCCTTT 58.857 41.667 9.96 0.00 34.13 3.11
1969 2010 4.734266 GAGATTAATTGGATCTGCCCCTT 58.266 43.478 9.96 0.00 34.13 3.95
1970 2011 3.244700 CGAGATTAATTGGATCTGCCCCT 60.245 47.826 9.96 0.00 34.13 4.79
1971 2012 3.077359 CGAGATTAATTGGATCTGCCCC 58.923 50.000 9.96 0.00 34.13 5.80
1972 2013 3.077359 CCGAGATTAATTGGATCTGCCC 58.923 50.000 9.96 0.00 34.13 5.36
1973 2014 3.744660 ACCGAGATTAATTGGATCTGCC 58.255 45.455 9.96 0.00 34.13 4.85
1974 2015 4.380531 TGACCGAGATTAATTGGATCTGC 58.619 43.478 9.96 3.47 34.13 4.26
1975 2016 6.226052 TGATGACCGAGATTAATTGGATCTG 58.774 40.000 9.96 1.90 34.13 2.90
1976 2017 6.425210 TGATGACCGAGATTAATTGGATCT 57.575 37.500 8.74 6.01 36.60 2.75
1977 2018 7.496529 TTTGATGACCGAGATTAATTGGATC 57.503 36.000 8.74 0.00 0.00 3.36
1978 2019 7.720957 TGATTTGATGACCGAGATTAATTGGAT 59.279 33.333 8.74 0.00 0.00 3.41
1979 2020 7.053498 TGATTTGATGACCGAGATTAATTGGA 58.947 34.615 8.74 0.00 0.00 3.53
1980 2021 7.263100 TGATTTGATGACCGAGATTAATTGG 57.737 36.000 0.00 0.00 0.00 3.16
1981 2022 8.347771 ACATGATTTGATGACCGAGATTAATTG 58.652 33.333 0.00 0.00 0.00 2.32
1982 2023 8.455903 ACATGATTTGATGACCGAGATTAATT 57.544 30.769 0.00 0.00 0.00 1.40
1983 2024 7.716560 TGACATGATTTGATGACCGAGATTAAT 59.283 33.333 0.00 0.00 0.00 1.40
1984 2025 7.047271 TGACATGATTTGATGACCGAGATTAA 58.953 34.615 0.00 0.00 0.00 1.40
1985 2026 6.581712 TGACATGATTTGATGACCGAGATTA 58.418 36.000 0.00 0.00 0.00 1.75
1986 2027 5.430886 TGACATGATTTGATGACCGAGATT 58.569 37.500 0.00 0.00 0.00 2.40
1987 2028 5.027293 TGACATGATTTGATGACCGAGAT 57.973 39.130 0.00 0.00 0.00 2.75
1988 2029 4.470334 TGACATGATTTGATGACCGAGA 57.530 40.909 0.00 0.00 0.00 4.04
1989 2030 5.277683 GGATTGACATGATTTGATGACCGAG 60.278 44.000 0.00 0.00 0.00 4.63
1990 2031 4.576053 GGATTGACATGATTTGATGACCGA 59.424 41.667 0.00 0.00 0.00 4.69
1991 2032 4.336153 TGGATTGACATGATTTGATGACCG 59.664 41.667 0.00 0.00 0.00 4.79
1992 2033 5.840243 TGGATTGACATGATTTGATGACC 57.160 39.130 0.00 0.00 0.00 4.02
1993 2034 7.434307 GTCATTGGATTGACATGATTTGATGAC 59.566 37.037 0.00 5.28 44.38 3.06
1994 2035 7.417003 GGTCATTGGATTGACATGATTTGATGA 60.417 37.037 0.00 0.00 46.32 2.92
1995 2036 6.700081 GGTCATTGGATTGACATGATTTGATG 59.300 38.462 0.00 0.00 46.32 3.07
1996 2037 6.610020 AGGTCATTGGATTGACATGATTTGAT 59.390 34.615 0.00 0.00 46.32 2.57
1997 2038 5.953548 AGGTCATTGGATTGACATGATTTGA 59.046 36.000 0.00 0.00 46.32 2.69
1998 2039 6.216801 AGGTCATTGGATTGACATGATTTG 57.783 37.500 0.00 0.00 46.32 2.32
1999 2040 7.284034 GTCTAGGTCATTGGATTGACATGATTT 59.716 37.037 0.00 0.00 46.32 2.17
2000 2041 6.769822 GTCTAGGTCATTGGATTGACATGATT 59.230 38.462 0.00 0.00 46.32 2.57
2001 2042 6.100859 AGTCTAGGTCATTGGATTGACATGAT 59.899 38.462 0.00 0.00 46.32 2.45
2002 2043 5.426509 AGTCTAGGTCATTGGATTGACATGA 59.573 40.000 0.00 0.00 46.32 3.07
2003 2044 5.526479 CAGTCTAGGTCATTGGATTGACATG 59.474 44.000 6.88 0.00 46.32 3.21
2004 2045 5.190528 ACAGTCTAGGTCATTGGATTGACAT 59.809 40.000 6.88 2.33 46.32 3.06
2005 2046 4.532126 ACAGTCTAGGTCATTGGATTGACA 59.468 41.667 6.88 0.00 46.32 3.58
2006 2047 5.091261 ACAGTCTAGGTCATTGGATTGAC 57.909 43.478 0.00 0.00 44.27 3.18
2007 2048 5.762179 AACAGTCTAGGTCATTGGATTGA 57.238 39.130 0.00 0.00 0.00 2.57
2008 2049 5.939883 TGAAACAGTCTAGGTCATTGGATTG 59.060 40.000 0.00 0.00 0.00 2.67
2009 2050 6.126863 TGAAACAGTCTAGGTCATTGGATT 57.873 37.500 0.00 0.00 0.00 3.01
2010 2051 5.762179 TGAAACAGTCTAGGTCATTGGAT 57.238 39.130 0.00 0.00 0.00 3.41
2011 2052 5.560722 TTGAAACAGTCTAGGTCATTGGA 57.439 39.130 0.00 0.00 0.00 3.53
2012 2053 5.707298 ACATTGAAACAGTCTAGGTCATTGG 59.293 40.000 0.00 0.00 0.00 3.16
2013 2054 6.401474 CGACATTGAAACAGTCTAGGTCATTG 60.401 42.308 0.00 0.00 41.10 2.82
2014 2055 5.639506 CGACATTGAAACAGTCTAGGTCATT 59.360 40.000 0.00 0.00 41.10 2.57
2015 2056 5.047306 TCGACATTGAAACAGTCTAGGTCAT 60.047 40.000 0.00 0.00 41.10 3.06
2016 2057 4.279922 TCGACATTGAAACAGTCTAGGTCA 59.720 41.667 0.00 0.00 41.10 4.02
2017 2058 4.806330 TCGACATTGAAACAGTCTAGGTC 58.194 43.478 0.00 0.00 38.76 3.85
2018 2059 4.281182 ACTCGACATTGAAACAGTCTAGGT 59.719 41.667 0.00 0.00 31.58 3.08
2019 2060 4.623167 CACTCGACATTGAAACAGTCTAGG 59.377 45.833 0.00 0.00 31.58 3.02
2020 2061 4.090642 GCACTCGACATTGAAACAGTCTAG 59.909 45.833 0.00 0.00 33.02 2.43
2021 2062 3.987868 GCACTCGACATTGAAACAGTCTA 59.012 43.478 0.00 0.00 0.00 2.59
2022 2063 2.802816 GCACTCGACATTGAAACAGTCT 59.197 45.455 0.00 0.00 0.00 3.24
2023 2064 2.802816 AGCACTCGACATTGAAACAGTC 59.197 45.455 0.00 0.00 0.00 3.51
2024 2065 2.802816 GAGCACTCGACATTGAAACAGT 59.197 45.455 0.00 0.00 0.00 3.55
2025 2066 2.802247 TGAGCACTCGACATTGAAACAG 59.198 45.455 0.00 0.00 0.00 3.16
2026 2067 2.832563 TGAGCACTCGACATTGAAACA 58.167 42.857 0.00 0.00 0.00 2.83
2027 2068 3.002246 TGTTGAGCACTCGACATTGAAAC 59.998 43.478 15.31 2.28 46.09 2.78
2028 2069 3.202097 TGTTGAGCACTCGACATTGAAA 58.798 40.909 15.31 0.00 46.09 2.69
2029 2070 2.832563 TGTTGAGCACTCGACATTGAA 58.167 42.857 15.31 0.00 46.09 2.69
2030 2071 2.524569 TGTTGAGCACTCGACATTGA 57.475 45.000 15.31 0.00 46.09 2.57
2035 2076 0.928229 AAACGTGTTGAGCACTCGAC 59.072 50.000 10.58 10.58 43.66 4.20
2036 2077 2.390938 CTAAACGTGTTGAGCACTCGA 58.609 47.619 4.43 0.00 43.66 4.04
2037 2078 1.136611 GCTAAACGTGTTGAGCACTCG 60.137 52.381 15.69 0.00 44.65 4.18
2038 2079 1.136611 CGCTAAACGTGTTGAGCACTC 60.137 52.381 19.45 0.00 45.37 3.51
2039 2080 0.859232 CGCTAAACGTGTTGAGCACT 59.141 50.000 19.45 0.00 45.37 4.40
2040 2081 3.345087 CGCTAAACGTGTTGAGCAC 57.655 52.632 19.45 0.00 45.37 4.40
2051 2092 5.220024 GCATGAAATTAACTGCACGCTAAAC 60.220 40.000 0.00 0.00 34.77 2.01
2052 2093 4.856487 GCATGAAATTAACTGCACGCTAAA 59.144 37.500 0.00 0.00 34.77 1.85
2053 2094 4.411327 GCATGAAATTAACTGCACGCTAA 58.589 39.130 0.00 0.00 34.77 3.09
2054 2095 3.181501 GGCATGAAATTAACTGCACGCTA 60.182 43.478 0.00 0.00 36.34 4.26
2055 2096 2.415893 GGCATGAAATTAACTGCACGCT 60.416 45.455 0.00 0.00 36.34 5.07
2056 2097 1.919918 GGCATGAAATTAACTGCACGC 59.080 47.619 0.00 0.00 36.34 5.34
2057 2098 3.214697 TGGCATGAAATTAACTGCACG 57.785 42.857 0.00 0.00 36.34 5.34
2058 2099 7.775397 ATATTTGGCATGAAATTAACTGCAC 57.225 32.000 0.00 0.53 36.34 4.57
2059 2100 8.694540 AGTATATTTGGCATGAAATTAACTGCA 58.305 29.630 0.00 0.00 36.34 4.41
2060 2101 9.185192 GAGTATATTTGGCATGAAATTAACTGC 57.815 33.333 0.00 0.00 0.00 4.40
2061 2102 9.683069 GGAGTATATTTGGCATGAAATTAACTG 57.317 33.333 0.00 0.00 0.00 3.16
2062 2103 9.646522 AGGAGTATATTTGGCATGAAATTAACT 57.353 29.630 0.00 2.22 0.00 2.24
2063 2104 9.683069 CAGGAGTATATTTGGCATGAAATTAAC 57.317 33.333 0.00 0.00 0.00 2.01
2064 2105 9.639563 TCAGGAGTATATTTGGCATGAAATTAA 57.360 29.630 0.00 0.00 0.00 1.40
2065 2106 9.812347 ATCAGGAGTATATTTGGCATGAAATTA 57.188 29.630 0.00 0.00 0.00 1.40
2066 2107 8.582437 CATCAGGAGTATATTTGGCATGAAATT 58.418 33.333 0.00 0.00 0.00 1.82
2067 2108 7.727186 ACATCAGGAGTATATTTGGCATGAAAT 59.273 33.333 0.00 0.00 0.00 2.17
2068 2109 7.062322 ACATCAGGAGTATATTTGGCATGAAA 58.938 34.615 0.00 0.00 0.00 2.69
2069 2110 6.604171 ACATCAGGAGTATATTTGGCATGAA 58.396 36.000 0.00 0.00 0.00 2.57
2070 2111 6.191657 ACATCAGGAGTATATTTGGCATGA 57.808 37.500 0.00 0.00 0.00 3.07
2071 2112 6.889301 AACATCAGGAGTATATTTGGCATG 57.111 37.500 0.00 0.00 0.00 4.06
2072 2113 9.236006 GATTAACATCAGGAGTATATTTGGCAT 57.764 33.333 0.00 0.00 0.00 4.40
2073 2114 8.217111 TGATTAACATCAGGAGTATATTTGGCA 58.783 33.333 0.00 0.00 34.22 4.92
2074 2115 8.507249 GTGATTAACATCAGGAGTATATTTGGC 58.493 37.037 0.00 0.00 40.28 4.52
2075 2116 9.559732 TGTGATTAACATCAGGAGTATATTTGG 57.440 33.333 0.00 0.00 40.28 3.28
2117 2158 8.883731 GTGCATGCGGATATTAAGTAAGATATT 58.116 33.333 14.09 0.00 0.00 1.28
2118 2159 8.260818 AGTGCATGCGGATATTAAGTAAGATAT 58.739 33.333 14.09 0.00 0.00 1.63
2119 2160 7.611770 AGTGCATGCGGATATTAAGTAAGATA 58.388 34.615 14.09 0.00 0.00 1.98
2120 2161 6.467677 AGTGCATGCGGATATTAAGTAAGAT 58.532 36.000 14.09 0.00 0.00 2.40
2121 2162 5.853936 AGTGCATGCGGATATTAAGTAAGA 58.146 37.500 14.09 0.00 0.00 2.10
2122 2163 6.545504 AAGTGCATGCGGATATTAAGTAAG 57.454 37.500 14.09 0.00 0.00 2.34
2123 2164 8.615878 ATTAAGTGCATGCGGATATTAAGTAA 57.384 30.769 14.09 0.49 0.00 2.24
2124 2165 9.884636 ATATTAAGTGCATGCGGATATTAAGTA 57.115 29.630 14.09 8.17 0.00 2.24
2125 2166 8.792830 ATATTAAGTGCATGCGGATATTAAGT 57.207 30.769 14.09 4.58 0.00 2.24
2127 2168 9.884636 AGTATATTAAGTGCATGCGGATATTAA 57.115 29.630 14.09 12.83 0.00 1.40
2128 2169 9.884636 AAGTATATTAAGTGCATGCGGATATTA 57.115 29.630 14.09 4.65 0.00 0.98
2129 2170 8.792830 AAGTATATTAAGTGCATGCGGATATT 57.207 30.769 14.09 5.62 0.00 1.28
2130 2171 8.792830 AAAGTATATTAAGTGCATGCGGATAT 57.207 30.769 14.09 13.06 0.00 1.63
2131 2172 7.875554 TGAAAGTATATTAAGTGCATGCGGATA 59.124 33.333 14.09 6.94 0.00 2.59
2132 2173 6.710295 TGAAAGTATATTAAGTGCATGCGGAT 59.290 34.615 14.09 3.59 0.00 4.18
2133 2174 6.052360 TGAAAGTATATTAAGTGCATGCGGA 58.948 36.000 14.09 0.00 0.00 5.54
2134 2175 6.299023 TGAAAGTATATTAAGTGCATGCGG 57.701 37.500 14.09 0.00 0.00 5.69
2135 2176 8.786937 ATTTGAAAGTATATTAAGTGCATGCG 57.213 30.769 14.09 0.00 0.00 4.73
2149 2190 8.911662 GTGCAATGAACGTTAATTTGAAAGTAT 58.088 29.630 8.23 0.00 0.00 2.12
2150 2191 7.112287 CGTGCAATGAACGTTAATTTGAAAGTA 59.888 33.333 8.23 0.00 36.31 2.24
2151 2192 6.075099 CGTGCAATGAACGTTAATTTGAAAGT 60.075 34.615 8.23 0.00 36.31 2.66
2152 2193 6.281056 CGTGCAATGAACGTTAATTTGAAAG 58.719 36.000 8.23 3.08 36.31 2.62
2153 2194 6.191534 CGTGCAATGAACGTTAATTTGAAA 57.808 33.333 8.23 0.00 36.31 2.69
2154 2195 5.797909 CGTGCAATGAACGTTAATTTGAA 57.202 34.783 8.23 1.38 36.31 2.69
2164 2205 2.873170 ATGTGTACGTGCAATGAACG 57.127 45.000 12.90 12.90 46.32 3.95
2165 2206 3.906008 GTCAATGTGTACGTGCAATGAAC 59.094 43.478 8.25 0.00 0.00 3.18
2166 2207 3.812609 AGTCAATGTGTACGTGCAATGAA 59.187 39.130 8.25 0.00 0.00 2.57
2167 2208 3.398406 AGTCAATGTGTACGTGCAATGA 58.602 40.909 8.25 10.60 0.00 2.57
2168 2209 3.811722 AGTCAATGTGTACGTGCAATG 57.188 42.857 8.25 8.35 0.00 2.82
2169 2210 6.816640 AGTAATAGTCAATGTGTACGTGCAAT 59.183 34.615 8.25 1.77 0.00 3.56
2170 2211 6.160684 AGTAATAGTCAATGTGTACGTGCAA 58.839 36.000 8.25 0.00 0.00 4.08
2171 2212 5.716094 AGTAATAGTCAATGTGTACGTGCA 58.284 37.500 0.82 0.82 0.00 4.57
2172 2213 7.925703 ATAGTAATAGTCAATGTGTACGTGC 57.074 36.000 0.00 0.00 0.00 5.34
2192 2233 8.960591 CCCACACATTCTTTCATTTCTAATAGT 58.039 33.333 0.00 0.00 0.00 2.12
2193 2234 7.917505 GCCCACACATTCTTTCATTTCTAATAG 59.082 37.037 0.00 0.00 0.00 1.73
2197 2238 4.462483 GGCCCACACATTCTTTCATTTCTA 59.538 41.667 0.00 0.00 0.00 2.10
2203 2244 2.307496 ATGGCCCACACATTCTTTCA 57.693 45.000 0.00 0.00 0.00 2.69
2212 2253 2.696759 GCAACCGTATGGCCCACAC 61.697 63.158 0.00 0.00 39.70 3.82
2217 2258 3.063743 GCAAGGCAACCGTATGGCC 62.064 63.158 0.00 0.00 46.33 5.36
2277 2319 1.897802 CTACTTGGGTCTAACCACCGT 59.102 52.381 0.00 0.00 41.02 4.83
2279 2321 2.235650 GGACTACTTGGGTCTAACCACC 59.764 54.545 0.00 0.00 41.02 4.61
2280 2322 2.235650 GGGACTACTTGGGTCTAACCAC 59.764 54.545 0.00 0.00 41.02 4.16
2323 2365 1.793714 CGTTGCAACGCACAGAAAACT 60.794 47.619 35.89 0.00 46.06 2.66
2347 2389 8.918202 TGGGCCAACTTACTAGAATATTTATG 57.082 34.615 2.13 0.00 0.00 1.90
2363 2405 1.686115 GCAGGTAATCATGGGCCAACT 60.686 52.381 11.89 0.00 0.00 3.16
2364 2406 0.746659 GCAGGTAATCATGGGCCAAC 59.253 55.000 11.89 2.89 0.00 3.77
2367 2409 0.183492 TGAGCAGGTAATCATGGGCC 59.817 55.000 0.00 0.00 0.00 5.80
2372 2414 9.970553 ATCACATTAATATGAGCAGGTAATCAT 57.029 29.630 2.43 0.00 39.44 2.45
2417 2460 9.170890 AGGTAGGTAAATCATTGAAGGATATGA 57.829 33.333 0.00 0.00 35.43 2.15
2487 2530 9.769093 CCACCTTTTATCGACTTACTTTTTATG 57.231 33.333 0.00 0.00 0.00 1.90
2488 2531 8.953313 CCCACCTTTTATCGACTTACTTTTTAT 58.047 33.333 0.00 0.00 0.00 1.40
2489 2532 8.156165 TCCCACCTTTTATCGACTTACTTTTTA 58.844 33.333 0.00 0.00 0.00 1.52
2502 2545 6.235664 TGTCTTAACTGTCCCACCTTTTATC 58.764 40.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.