Multiple sequence alignment - TraesCS1D01G101200

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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 TraesCS1D01G101200 chr1D 100.000 4473 0 0 1 4473 89122764 89127236 0.000000e+00 8261.0
1 TraesCS1D01G101200 chr1D 90.083 242 24 0 714 955 27881648 27881889 9.340000e-82 315.0
2 TraesCS1D01G101200 chr1A 96.209 2954 88 10 1031 3975 85032417 85035355 0.000000e+00 4813.0
3 TraesCS1D01G101200 chr1A 95.850 506 16 3 3968 4473 85035604 85036104 0.000000e+00 813.0
4 TraesCS1D01G101200 chr1A 84.326 638 73 16 89 713 85031431 85032054 2.300000e-167 599.0
5 TraesCS1D01G101200 chr1A 90.000 70 7 0 3939 4008 543475009 543475078 1.710000e-14 91.6
6 TraesCS1D01G101200 chr1B 96.638 2826 58 14 982 3793 142296457 142299259 0.000000e+00 4658.0
7 TraesCS1D01G101200 chr1B 97.804 683 15 0 3791 4473 142317443 142318125 0.000000e+00 1179.0
8 TraesCS1D01G101200 chr1B 87.408 683 74 9 19 692 142294490 142295169 0.000000e+00 774.0
9 TraesCS1D01G101200 chr1B 89.879 247 24 1 710 955 520524978 520524732 2.600000e-82 316.0
10 TraesCS1D01G101200 chr1B 86.957 207 27 0 1036 1242 142295184 142295390 2.690000e-57 233.0
11 TraesCS1D01G101200 chr1B 83.575 207 26 6 4107 4311 60057554 60057354 2.120000e-43 187.0
12 TraesCS1D01G101200 chr1B 91.860 86 7 0 4388 4473 60057349 60057264 2.190000e-23 121.0
13 TraesCS1D01G101200 chr1B 93.750 64 4 0 3945 4008 597156802 597156865 3.680000e-16 97.1
14 TraesCS1D01G101200 chr2A 90.496 242 22 1 715 955 362446136 362445895 7.220000e-83 318.0
15 TraesCS1D01G101200 chr2A 86.517 89 8 3 3921 4008 74145550 74145635 1.320000e-15 95.3
16 TraesCS1D01G101200 chr2A 90.541 74 3 4 3942 4013 182009054 182008983 1.320000e-15 95.3
17 TraesCS1D01G101200 chr2A 88.158 76 8 1 3933 4008 591279979 591280053 6.160000e-14 89.8
18 TraesCS1D01G101200 chr2B 90.164 244 23 1 714 957 399350442 399350684 2.600000e-82 316.0
19 TraesCS1D01G101200 chr2B 89.754 244 25 0 714 957 151649507 151649264 3.360000e-81 313.0
20 TraesCS1D01G101200 chr7D 89.837 246 24 1 711 955 31062087 31061842 9.340000e-82 315.0
21 TraesCS1D01G101200 chr6B 90.083 242 24 0 714 955 523343636 523343877 9.340000e-82 315.0
22 TraesCS1D01G101200 chr7B 89.474 247 25 1 712 957 570276696 570276942 1.210000e-80 311.0
23 TraesCS1D01G101200 chr7A 89.431 246 25 1 710 955 631367415 631367659 4.350000e-80 309.0
24 TraesCS1D01G101200 chr2D 84.475 219 26 6 4095 4311 78675785 78675573 4.530000e-50 209.0
25 TraesCS1D01G101200 chr2D 92.308 91 7 0 4383 4473 86508431 86508341 3.630000e-26 130.0
26 TraesCS1D01G101200 chr2D 91.304 92 8 0 4382 4473 78675570 78675479 4.700000e-25 126.0
27 TraesCS1D01G101200 chr2D 82.707 133 16 5 4181 4311 86508559 86508432 1.320000e-20 111.0
28 TraesCS1D01G101200 chr5A 91.304 92 8 0 4382 4473 691741764 691741855 4.700000e-25 126.0
29 TraesCS1D01G101200 chr3B 90.000 70 7 0 3939 4008 8721884 8721953 1.710000e-14 91.6


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 TraesCS1D01G101200 chr1D 89122764 89127236 4472 False 8261.000000 8261 100.000000 1 4473 1 chr1D.!!$F2 4472
1 TraesCS1D01G101200 chr1A 85031431 85036104 4673 False 2075.000000 4813 92.128333 89 4473 3 chr1A.!!$F2 4384
2 TraesCS1D01G101200 chr1B 142294490 142299259 4769 False 1888.333333 4658 90.334333 19 3793 3 chr1B.!!$F3 3774
3 TraesCS1D01G101200 chr1B 142317443 142318125 682 False 1179.000000 1179 97.804000 3791 4473 1 chr1B.!!$F1 682

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
797 2076 0.038892 TAACCAACGAGACCGACTGC 60.039 55.000 0.00 0.0 39.5 4.40 F
884 2163 0.175760 CCCGTCACAATCCGTCTCAT 59.824 55.000 0.00 0.0 0.0 2.90 F
1494 3066 0.394762 TGGGAGAACATGGATGCTGC 60.395 55.000 0.00 0.0 0.0 5.25 F
1953 3528 2.875933 TCTTAAGTTGTTTCAGGCGTGG 59.124 45.455 6.56 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2755 4331 0.874390 TGTTGAGAAATGCCGTGCTC 59.126 50.000 0.00 0.00 0.00 4.26 R
2944 4520 4.135493 GTCGCGTCCGCTTTCAGC 62.135 66.667 5.77 0.00 39.32 4.26 R
2959 4535 1.076533 AATGCACGATCGACACGGTC 61.077 55.000 24.34 2.89 33.21 4.79 R
3657 5237 0.512952 CGTGGTTTCTTCAGGCTTCG 59.487 55.000 0.00 0.00 0.00 3.79 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
17 18 2.962569 TTCGTCGCCTCTCACCAG 59.037 61.111 0.00 0.00 0.00 4.00
25 26 1.835927 GCCTCTCACCAGCACCTCTT 61.836 60.000 0.00 0.00 0.00 2.85
30 31 0.976641 TCACCAGCACCTCTTACCAG 59.023 55.000 0.00 0.00 0.00 4.00
53 54 2.434336 AGTGTGTGCAAGAGTTCCACTA 59.566 45.455 0.00 0.00 30.45 2.74
56 57 1.270094 TGTGCAAGAGTTCCACTACCG 60.270 52.381 0.00 0.00 0.00 4.02
58 59 1.272490 TGCAAGAGTTCCACTACCGAG 59.728 52.381 0.00 0.00 0.00 4.63
71 72 3.752665 ACTACCGAGTGAGAGAGAACAA 58.247 45.455 0.00 0.00 33.41 2.83
126 127 3.170490 ATCGAAGGGGATGGCGCTC 62.170 63.158 7.64 0.00 0.00 5.03
155 156 3.894547 GAGGCAACGCTCCCCGAAA 62.895 63.158 0.00 0.00 46.39 3.46
183 184 2.285668 CTTGGGGAGAGAGGGGCA 60.286 66.667 0.00 0.00 0.00 5.36
184 185 1.925455 CTTGGGGAGAGAGGGGCAA 60.925 63.158 0.00 0.00 0.00 4.52
201 202 1.745653 GCAAAGGGGATCGAAAGGAAG 59.254 52.381 0.00 0.00 0.00 3.46
239 240 2.637872 CTGGGCCGGGAAGATAAGATAA 59.362 50.000 3.77 0.00 0.00 1.75
269 270 1.206578 GCGATGTGTTTGTCCCACG 59.793 57.895 0.00 0.00 35.56 4.94
294 295 2.196595 CACATGGAGTAAGGGGAAGGA 58.803 52.381 0.00 0.00 0.00 3.36
345 347 9.088987 TGGTCTAAAAGAAGCATTTTCCTAAAT 57.911 29.630 0.00 0.00 34.35 1.40
404 406 0.593128 GTTGGACGCTCACAGCAAAT 59.407 50.000 0.00 0.00 42.58 2.32
408 410 2.093500 TGGACGCTCACAGCAAATCTAT 60.093 45.455 0.00 0.00 42.58 1.98
459 462 9.520204 AGAACAACATTCTGTTAACTTCAATTG 57.480 29.630 7.22 0.00 38.77 2.32
474 477 8.953368 AACTTCAATTGAGAAATTTTTCTGCT 57.047 26.923 8.41 0.00 46.84 4.24
478 486 9.991388 TTCAATTGAGAAATTTTTCTGCTTTTG 57.009 25.926 8.41 8.53 46.84 2.44
617 632 7.744087 TTTATGAAACACAGTACAGAAGCAT 57.256 32.000 0.00 0.00 0.00 3.79
650 665 5.298527 GCCTATTTACGTAGAAAGCCCAATT 59.701 40.000 0.00 0.00 0.00 2.32
656 671 8.570068 TTTACGTAGAAAGCCCAATTAGAAAT 57.430 30.769 0.00 0.00 0.00 2.17
658 673 9.669887 TTACGTAGAAAGCCCAATTAGAAATAA 57.330 29.630 0.00 0.00 0.00 1.40
662 1940 7.978099 AGAAAGCCCAATTAGAAATAACCAT 57.022 32.000 0.00 0.00 0.00 3.55
698 1977 5.294552 GCTCAGAATTATCTAACCCACACAC 59.705 44.000 0.00 0.00 33.50 3.82
703 1982 2.859165 ATCTAACCCACACACCACTG 57.141 50.000 0.00 0.00 0.00 3.66
706 1985 1.142060 CTAACCCACACACCACTGGAA 59.858 52.381 0.71 0.00 0.00 3.53
714 1993 5.071788 CCCACACACCACTGGAATACTATAT 59.928 44.000 0.71 0.00 0.00 0.86
715 1994 6.269077 CCCACACACCACTGGAATACTATATA 59.731 42.308 0.71 0.00 0.00 0.86
716 1995 7.152645 CCACACACCACTGGAATACTATATAC 58.847 42.308 0.71 0.00 0.00 1.47
717 1996 7.015292 CCACACACCACTGGAATACTATATACT 59.985 40.741 0.71 0.00 0.00 2.12
718 1997 8.082852 CACACACCACTGGAATACTATATACTC 58.917 40.741 0.71 0.00 0.00 2.59
721 2000 6.954684 CACCACTGGAATACTATATACTCCCT 59.045 42.308 0.71 0.00 0.00 4.20
722 2001 7.122948 CACCACTGGAATACTATATACTCCCTC 59.877 44.444 0.71 0.00 0.00 4.30
723 2002 6.608002 CCACTGGAATACTATATACTCCCTCC 59.392 46.154 0.00 0.00 0.00 4.30
724 2003 7.182760 CACTGGAATACTATATACTCCCTCCA 58.817 42.308 0.00 0.00 0.00 3.86
725 2004 7.841729 CACTGGAATACTATATACTCCCTCCAT 59.158 40.741 0.00 0.00 30.41 3.41
726 2005 8.410623 ACTGGAATACTATATACTCCCTCCATT 58.589 37.037 0.00 0.00 30.41 3.16
727 2006 8.840200 TGGAATACTATATACTCCCTCCATTC 57.160 38.462 0.00 0.00 0.00 2.67
728 2007 7.844779 TGGAATACTATATACTCCCTCCATTCC 59.155 40.741 0.00 0.00 38.65 3.01
729 2008 7.844779 GGAATACTATATACTCCCTCCATTCCA 59.155 40.741 0.00 0.00 38.26 3.53
730 2009 9.268282 GAATACTATATACTCCCTCCATTCCAA 57.732 37.037 0.00 0.00 0.00 3.53
731 2010 9.629649 AATACTATATACTCCCTCCATTCCAAA 57.370 33.333 0.00 0.00 0.00 3.28
732 2011 7.947782 ACTATATACTCCCTCCATTCCAAAA 57.052 36.000 0.00 0.00 0.00 2.44
733 2012 8.525729 ACTATATACTCCCTCCATTCCAAAAT 57.474 34.615 0.00 0.00 0.00 1.82
734 2013 9.629649 ACTATATACTCCCTCCATTCCAAAATA 57.370 33.333 0.00 0.00 0.00 1.40
738 2017 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
739 2018 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
740 2019 5.385198 TCCCTCCATTCCAAAATATAGTGC 58.615 41.667 0.00 0.00 0.00 4.40
741 2020 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
742 2021 4.320494 CCTCCATTCCAAAATATAGTGCGC 60.320 45.833 0.00 0.00 0.00 6.09
743 2022 3.568007 TCCATTCCAAAATATAGTGCGCC 59.432 43.478 4.18 0.00 0.00 6.53
744 2023 3.305335 CCATTCCAAAATATAGTGCGCCC 60.305 47.826 4.18 0.00 0.00 6.13
745 2024 2.719531 TCCAAAATATAGTGCGCCCA 57.280 45.000 4.18 0.00 0.00 5.36
746 2025 2.294074 TCCAAAATATAGTGCGCCCAC 58.706 47.619 4.18 0.00 42.39 4.61
747 2026 1.002900 CCAAAATATAGTGCGCCCACG 60.003 52.381 4.18 0.00 46.62 4.94
757 2036 3.486263 CGCCCACGCTTTCTAAGG 58.514 61.111 0.00 0.00 0.00 2.69
758 2037 1.375523 CGCCCACGCTTTCTAAGGT 60.376 57.895 0.00 0.00 0.00 3.50
759 2038 1.359459 CGCCCACGCTTTCTAAGGTC 61.359 60.000 0.00 0.00 0.00 3.85
760 2039 1.025113 GCCCACGCTTTCTAAGGTCC 61.025 60.000 0.00 0.00 0.00 4.46
761 2040 0.323629 CCCACGCTTTCTAAGGTCCA 59.676 55.000 0.00 0.00 0.00 4.02
762 2041 1.271163 CCCACGCTTTCTAAGGTCCAA 60.271 52.381 0.00 0.00 0.00 3.53
763 2042 1.804748 CCACGCTTTCTAAGGTCCAAC 59.195 52.381 0.00 0.00 0.00 3.77
764 2043 2.550208 CCACGCTTTCTAAGGTCCAACT 60.550 50.000 0.00 0.00 0.00 3.16
765 2044 3.139077 CACGCTTTCTAAGGTCCAACTT 58.861 45.455 0.00 0.00 34.52 2.66
766 2045 3.564225 CACGCTTTCTAAGGTCCAACTTT 59.436 43.478 0.00 0.00 32.02 2.66
767 2046 4.753107 CACGCTTTCTAAGGTCCAACTTTA 59.247 41.667 0.00 0.00 32.02 1.85
768 2047 5.237779 CACGCTTTCTAAGGTCCAACTTTAA 59.762 40.000 0.00 0.00 32.02 1.52
769 2048 5.237996 ACGCTTTCTAAGGTCCAACTTTAAC 59.762 40.000 0.00 0.00 32.02 2.01
770 2049 5.334646 CGCTTTCTAAGGTCCAACTTTAACC 60.335 44.000 0.00 0.00 32.02 2.85
771 2050 5.533528 GCTTTCTAAGGTCCAACTTTAACCA 59.466 40.000 0.00 0.00 35.43 3.67
772 2051 6.208797 GCTTTCTAAGGTCCAACTTTAACCAT 59.791 38.462 0.00 0.00 35.43 3.55
773 2052 7.392393 GCTTTCTAAGGTCCAACTTTAACCATA 59.608 37.037 0.00 0.00 35.43 2.74
774 2053 9.292195 CTTTCTAAGGTCCAACTTTAACCATAA 57.708 33.333 0.00 0.00 35.43 1.90
775 2054 9.643735 TTTCTAAGGTCCAACTTTAACCATAAA 57.356 29.630 0.00 0.00 35.43 1.40
776 2055 9.816787 TTCTAAGGTCCAACTTTAACCATAAAT 57.183 29.630 0.00 0.00 35.43 1.40
777 2056 9.816787 TCTAAGGTCCAACTTTAACCATAAATT 57.183 29.630 0.00 0.00 35.43 1.82
782 2061 9.426837 GGTCCAACTTTAACCATAAATTTAACC 57.573 33.333 1.21 0.00 30.46 2.85
783 2062 9.984190 GTCCAACTTTAACCATAAATTTAACCA 57.016 29.630 1.21 0.00 30.88 3.67
788 2067 9.902196 ACTTTAACCATAAATTTAACCAACGAG 57.098 29.630 1.21 0.01 30.88 4.18
790 2069 9.896263 TTTAACCATAAATTTAACCAACGAGAC 57.104 29.630 1.21 0.00 0.00 3.36
791 2070 6.505044 ACCATAAATTTAACCAACGAGACC 57.495 37.500 1.21 0.00 0.00 3.85
792 2071 5.122711 ACCATAAATTTAACCAACGAGACCG 59.877 40.000 1.21 0.00 42.50 4.79
793 2072 5.352016 CCATAAATTTAACCAACGAGACCGA 59.648 40.000 1.21 0.00 39.50 4.69
794 2073 4.737353 AAATTTAACCAACGAGACCGAC 57.263 40.909 0.00 0.00 39.50 4.79
795 2074 3.672767 ATTTAACCAACGAGACCGACT 57.327 42.857 0.00 0.00 39.50 4.18
796 2075 2.427232 TTAACCAACGAGACCGACTG 57.573 50.000 0.00 0.00 39.50 3.51
797 2076 0.038892 TAACCAACGAGACCGACTGC 60.039 55.000 0.00 0.00 39.50 4.40
798 2077 2.805353 CCAACGAGACCGACTGCG 60.805 66.667 0.00 0.00 39.50 5.18
808 2087 3.711842 CGACTGCGGCGCAAGAAA 61.712 61.111 35.41 12.74 38.41 2.52
809 2088 2.637025 GACTGCGGCGCAAGAAAA 59.363 55.556 35.41 11.92 38.41 2.29
810 2089 1.008995 GACTGCGGCGCAAGAAAAA 60.009 52.632 35.41 11.10 38.41 1.94
865 2144 9.783256 ACGAATTTACTGGTATAATTTTTGCTC 57.217 29.630 0.00 0.00 0.00 4.26
866 2145 9.233232 CGAATTTACTGGTATAATTTTTGCTCC 57.767 33.333 0.00 0.00 0.00 4.70
867 2146 9.529325 GAATTTACTGGTATAATTTTTGCTCCC 57.471 33.333 0.00 0.00 0.00 4.30
868 2147 6.687081 TTACTGGTATAATTTTTGCTCCCG 57.313 37.500 0.00 0.00 0.00 5.14
869 2148 4.595986 ACTGGTATAATTTTTGCTCCCGT 58.404 39.130 0.00 0.00 0.00 5.28
870 2149 4.638865 ACTGGTATAATTTTTGCTCCCGTC 59.361 41.667 0.00 0.00 0.00 4.79
871 2150 4.590918 TGGTATAATTTTTGCTCCCGTCA 58.409 39.130 0.00 0.00 0.00 4.35
872 2151 4.396790 TGGTATAATTTTTGCTCCCGTCAC 59.603 41.667 0.00 0.00 0.00 3.67
873 2152 4.396790 GGTATAATTTTTGCTCCCGTCACA 59.603 41.667 0.00 0.00 0.00 3.58
874 2153 5.106078 GGTATAATTTTTGCTCCCGTCACAA 60.106 40.000 0.00 0.00 0.00 3.33
875 2154 5.659440 ATAATTTTTGCTCCCGTCACAAT 57.341 34.783 0.00 0.00 0.00 2.71
876 2155 3.575965 ATTTTTGCTCCCGTCACAATC 57.424 42.857 0.00 0.00 0.00 2.67
877 2156 1.243902 TTTTGCTCCCGTCACAATCC 58.756 50.000 0.00 0.00 0.00 3.01
878 2157 0.953471 TTTGCTCCCGTCACAATCCG 60.953 55.000 0.00 0.00 0.00 4.18
879 2158 2.107041 TTGCTCCCGTCACAATCCGT 62.107 55.000 0.00 0.00 0.00 4.69
880 2159 1.810030 GCTCCCGTCACAATCCGTC 60.810 63.158 0.00 0.00 0.00 4.79
881 2160 1.890894 CTCCCGTCACAATCCGTCT 59.109 57.895 0.00 0.00 0.00 4.18
882 2161 0.179134 CTCCCGTCACAATCCGTCTC 60.179 60.000 0.00 0.00 0.00 3.36
883 2162 0.896479 TCCCGTCACAATCCGTCTCA 60.896 55.000 0.00 0.00 0.00 3.27
884 2163 0.175760 CCCGTCACAATCCGTCTCAT 59.824 55.000 0.00 0.00 0.00 2.90
885 2164 1.405526 CCCGTCACAATCCGTCTCATT 60.406 52.381 0.00 0.00 0.00 2.57
886 2165 1.660607 CCGTCACAATCCGTCTCATTG 59.339 52.381 0.00 0.00 37.29 2.82
887 2166 1.660607 CGTCACAATCCGTCTCATTGG 59.339 52.381 0.00 0.00 35.82 3.16
888 2167 1.398390 GTCACAATCCGTCTCATTGGC 59.602 52.381 0.00 0.00 35.82 4.52
889 2168 1.278985 TCACAATCCGTCTCATTGGCT 59.721 47.619 0.00 0.00 35.82 4.75
890 2169 2.499693 TCACAATCCGTCTCATTGGCTA 59.500 45.455 0.00 0.00 35.82 3.93
891 2170 3.055458 TCACAATCCGTCTCATTGGCTAA 60.055 43.478 0.00 0.00 35.82 3.09
892 2171 3.689161 CACAATCCGTCTCATTGGCTAAA 59.311 43.478 0.00 0.00 35.82 1.85
893 2172 4.336433 CACAATCCGTCTCATTGGCTAAAT 59.664 41.667 0.00 0.00 35.82 1.40
894 2173 4.949856 ACAATCCGTCTCATTGGCTAAATT 59.050 37.500 0.00 0.00 35.82 1.82
895 2174 5.418840 ACAATCCGTCTCATTGGCTAAATTT 59.581 36.000 0.00 0.00 35.82 1.82
896 2175 6.601613 ACAATCCGTCTCATTGGCTAAATTTA 59.398 34.615 0.00 0.00 35.82 1.40
897 2176 7.285401 ACAATCCGTCTCATTGGCTAAATTTAT 59.715 33.333 0.00 0.00 35.82 1.40
898 2177 6.618287 TCCGTCTCATTGGCTAAATTTATG 57.382 37.500 0.00 0.00 0.00 1.90
899 2178 5.530915 TCCGTCTCATTGGCTAAATTTATGG 59.469 40.000 0.00 0.00 0.00 2.74
900 2179 5.299279 CCGTCTCATTGGCTAAATTTATGGT 59.701 40.000 0.00 0.00 0.00 3.55
901 2180 6.183360 CCGTCTCATTGGCTAAATTTATGGTT 60.183 38.462 0.00 0.00 0.00 3.67
902 2181 7.012894 CCGTCTCATTGGCTAAATTTATGGTTA 59.987 37.037 0.00 0.00 0.00 2.85
903 2182 8.402472 CGTCTCATTGGCTAAATTTATGGTTAA 58.598 33.333 0.00 0.00 0.00 2.01
911 2190 9.921637 TGGCTAAATTTATGGTTAAAGTTGAAG 57.078 29.630 0.00 0.00 36.56 3.02
912 2191 8.869897 GGCTAAATTTATGGTTAAAGTTGAAGC 58.130 33.333 0.00 0.00 36.82 3.86
913 2192 9.418045 GCTAAATTTATGGTTAAAGTTGAAGCA 57.582 29.630 7.30 7.30 37.16 3.91
916 2195 8.776376 AATTTATGGTTAAAGTTGAAGCATGG 57.224 30.769 22.70 0.00 43.09 3.66
917 2196 4.806640 ATGGTTAAAGTTGAAGCATGGG 57.193 40.909 15.49 0.00 42.00 4.00
918 2197 3.838565 TGGTTAAAGTTGAAGCATGGGA 58.161 40.909 0.41 0.00 29.71 4.37
919 2198 4.219115 TGGTTAAAGTTGAAGCATGGGAA 58.781 39.130 0.41 0.00 29.71 3.97
920 2199 4.837860 TGGTTAAAGTTGAAGCATGGGAAT 59.162 37.500 0.41 0.00 29.71 3.01
921 2200 6.013379 TGGTTAAAGTTGAAGCATGGGAATA 58.987 36.000 0.41 0.00 29.71 1.75
922 2201 6.152661 TGGTTAAAGTTGAAGCATGGGAATAG 59.847 38.462 0.41 0.00 29.71 1.73
923 2202 6.377146 GGTTAAAGTTGAAGCATGGGAATAGA 59.623 38.462 0.00 0.00 0.00 1.98
924 2203 7.415653 GGTTAAAGTTGAAGCATGGGAATAGAG 60.416 40.741 0.00 0.00 0.00 2.43
925 2204 5.441718 AAGTTGAAGCATGGGAATAGAGA 57.558 39.130 0.00 0.00 0.00 3.10
926 2205 5.441718 AGTTGAAGCATGGGAATAGAGAA 57.558 39.130 0.00 0.00 0.00 2.87
927 2206 5.819991 AGTTGAAGCATGGGAATAGAGAAA 58.180 37.500 0.00 0.00 0.00 2.52
928 2207 6.248433 AGTTGAAGCATGGGAATAGAGAAAA 58.752 36.000 0.00 0.00 0.00 2.29
929 2208 6.151817 AGTTGAAGCATGGGAATAGAGAAAAC 59.848 38.462 0.00 0.00 0.00 2.43
930 2209 5.569355 TGAAGCATGGGAATAGAGAAAACA 58.431 37.500 0.00 0.00 0.00 2.83
931 2210 5.415701 TGAAGCATGGGAATAGAGAAAACAC 59.584 40.000 0.00 0.00 0.00 3.32
932 2211 5.184892 AGCATGGGAATAGAGAAAACACT 57.815 39.130 0.00 0.00 0.00 3.55
933 2212 6.313519 AGCATGGGAATAGAGAAAACACTA 57.686 37.500 0.00 0.00 0.00 2.74
934 2213 6.904626 AGCATGGGAATAGAGAAAACACTAT 58.095 36.000 0.00 0.00 0.00 2.12
935 2214 8.034313 AGCATGGGAATAGAGAAAACACTATA 57.966 34.615 0.00 0.00 0.00 1.31
936 2215 8.664079 AGCATGGGAATAGAGAAAACACTATAT 58.336 33.333 0.00 0.00 0.00 0.86
937 2216 9.289782 GCATGGGAATAGAGAAAACACTATATT 57.710 33.333 0.00 0.00 37.12 1.28
946 2225 8.040716 AGAGAAAACACTATATTTTGGAACGG 57.959 34.615 0.00 0.00 29.44 4.44
947 2226 7.881232 AGAGAAAACACTATATTTTGGAACGGA 59.119 33.333 0.00 0.00 29.44 4.69
948 2227 8.575649 AGAAAACACTATATTTTGGAACGGAT 57.424 30.769 0.00 0.00 29.44 4.18
949 2228 8.458843 AGAAAACACTATATTTTGGAACGGATG 58.541 33.333 0.00 0.00 29.44 3.51
950 2229 6.693315 AACACTATATTTTGGAACGGATGG 57.307 37.500 0.00 0.00 0.00 3.51
951 2230 5.996644 ACACTATATTTTGGAACGGATGGA 58.003 37.500 0.00 0.00 0.00 3.41
952 2231 6.055588 ACACTATATTTTGGAACGGATGGAG 58.944 40.000 0.00 0.00 0.00 3.86
953 2232 6.055588 CACTATATTTTGGAACGGATGGAGT 58.944 40.000 0.00 0.00 0.00 3.85
954 2233 7.147620 ACACTATATTTTGGAACGGATGGAGTA 60.148 37.037 0.00 0.00 0.00 2.59
955 2234 7.170998 CACTATATTTTGGAACGGATGGAGTAC 59.829 40.741 0.00 0.00 0.00 2.73
956 2235 4.569719 ATTTTGGAACGGATGGAGTACT 57.430 40.909 0.00 0.00 0.00 2.73
957 2236 3.328382 TTTGGAACGGATGGAGTACTG 57.672 47.619 0.00 0.00 0.00 2.74
958 2237 1.933021 TGGAACGGATGGAGTACTGT 58.067 50.000 0.00 0.00 0.00 3.55
959 2238 3.090210 TGGAACGGATGGAGTACTGTA 57.910 47.619 0.00 0.00 0.00 2.74
960 2239 3.638860 TGGAACGGATGGAGTACTGTAT 58.361 45.455 0.00 0.00 0.00 2.29
961 2240 4.795469 TGGAACGGATGGAGTACTGTATA 58.205 43.478 0.00 0.00 0.00 1.47
962 2241 5.391256 TGGAACGGATGGAGTACTGTATAT 58.609 41.667 0.00 0.00 0.00 0.86
963 2242 5.836898 TGGAACGGATGGAGTACTGTATATT 59.163 40.000 0.00 0.00 0.00 1.28
964 2243 7.005902 TGGAACGGATGGAGTACTGTATATTA 58.994 38.462 0.00 0.00 0.00 0.98
965 2244 7.176165 TGGAACGGATGGAGTACTGTATATTAG 59.824 40.741 0.00 0.00 0.00 1.73
966 2245 6.512342 ACGGATGGAGTACTGTATATTAGC 57.488 41.667 0.00 0.00 0.00 3.09
967 2246 5.418209 ACGGATGGAGTACTGTATATTAGCC 59.582 44.000 0.00 0.00 0.00 3.93
968 2247 5.652891 CGGATGGAGTACTGTATATTAGCCT 59.347 44.000 0.00 0.00 0.00 4.58
995 2274 3.006940 ACAACAGAAAACAGCACTCGAA 58.993 40.909 0.00 0.00 0.00 3.71
1009 2288 1.394227 ACTCGAATCTCAGTCGTCGTC 59.606 52.381 0.00 0.00 39.52 4.20
1018 2297 3.470567 GTCGTCGTCGCTGCAAGG 61.471 66.667 0.00 0.00 36.96 3.61
1024 2303 1.515952 CGTCGCTGCAAGGAGAGAG 60.516 63.158 0.00 0.00 0.00 3.20
1025 2304 1.886585 GTCGCTGCAAGGAGAGAGA 59.113 57.895 0.00 0.00 0.00 3.10
1220 2792 2.545952 GGATAATGTCCGTGACGCTGAT 60.546 50.000 0.00 0.00 37.23 2.90
1457 3029 5.616204 CGCAGTCGAATCGGATATACAGTAA 60.616 44.000 1.76 0.00 38.10 2.24
1494 3066 0.394762 TGGGAGAACATGGATGCTGC 60.395 55.000 0.00 0.00 0.00 5.25
1659 3233 4.414852 CATTCGTTTACTGCTTGGGATTG 58.585 43.478 0.00 0.00 0.00 2.67
1847 3422 7.173218 CAGTACTCACCATTATGTGTGTTTTCT 59.827 37.037 11.51 6.31 41.61 2.52
1953 3528 2.875933 TCTTAAGTTGTTTCAGGCGTGG 59.124 45.455 6.56 0.00 0.00 4.94
2008 3583 7.227049 TCAGTACTCATCATCTTGTGTGTTA 57.773 36.000 0.00 0.00 0.00 2.41
2052 3627 7.203218 GGATTAGCTTTGATTGGGAATGTAAC 58.797 38.462 0.00 0.00 0.00 2.50
2755 4331 4.685169 AAGGTATCGATTGCAACACTTG 57.315 40.909 1.71 0.00 0.00 3.16
2944 4520 4.141688 GGTTTACCAGTATCCCTTCTCCTG 60.142 50.000 0.00 0.00 35.64 3.86
3095 4671 2.585432 AGCCCACCCTATTTTATGGTGT 59.415 45.455 7.10 0.00 46.49 4.16
3096 4672 3.012388 AGCCCACCCTATTTTATGGTGTT 59.988 43.478 7.10 0.00 46.49 3.32
3097 4673 3.132111 GCCCACCCTATTTTATGGTGTTG 59.868 47.826 7.10 0.00 46.49 3.33
3098 4674 3.132111 CCCACCCTATTTTATGGTGTTGC 59.868 47.826 7.10 0.00 46.49 4.17
3547 5127 3.368571 GCTTTGGCTGGCGCTCTT 61.369 61.111 7.64 0.00 36.09 2.85
3571 5151 4.129737 ATACGCAGTCGCCGCTGT 62.130 61.111 9.59 0.00 43.93 4.40
3613 5193 1.268079 CCAGATGCGCTCGAGATAGAA 59.732 52.381 18.75 0.79 0.00 2.10
3617 5197 3.376859 AGATGCGCTCGAGATAGAATAGG 59.623 47.826 18.75 0.00 0.00 2.57
3657 5237 1.789078 CTGCTCAGCAACCACACACC 61.789 60.000 0.00 0.00 38.41 4.16
3820 5403 1.375908 GCTGCTGACCGTTGGATCA 60.376 57.895 0.00 0.00 0.00 2.92
3889 5472 7.801104 TCAATCAATTTACCTGTAGCCTATCA 58.199 34.615 0.00 0.00 0.00 2.15
3933 5516 8.340230 AGACGCTTTTTCAGTTCAATTTAAAG 57.660 30.769 0.00 0.00 0.00 1.85
3942 5525 8.715191 TTCAGTTCAATTTAAAGTGCAAACAT 57.285 26.923 17.24 5.36 0.00 2.71
3973 5813 6.953101 TGCCTCTGTACCAAAATATAAGACA 58.047 36.000 0.00 0.00 0.00 3.41
4109 5949 2.778299 TCCACCAAGCACTCAACATAC 58.222 47.619 0.00 0.00 0.00 2.39
4206 6046 3.591023 CATCAGCAAAATGGATGCACAA 58.409 40.909 0.00 0.00 46.22 3.33
4242 6082 0.037697 GTATCGCCCAGTCACACACA 60.038 55.000 0.00 0.00 0.00 3.72
4256 6096 5.635280 AGTCACACACATTCTACATCTTTCG 59.365 40.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.962569 CTGGTGAGAGGCGACGAA 59.037 61.111 0.00 0.00 0.00 3.85
1 2 3.749064 GCTGGTGAGAGGCGACGA 61.749 66.667 0.00 0.00 0.00 4.20
2 3 4.056125 TGCTGGTGAGAGGCGACG 62.056 66.667 0.00 0.00 0.00 5.12
3 4 2.433318 GTGCTGGTGAGAGGCGAC 60.433 66.667 0.00 0.00 0.00 5.19
4 5 3.695606 GGTGCTGGTGAGAGGCGA 61.696 66.667 0.00 0.00 0.00 5.54
5 6 3.655810 GAGGTGCTGGTGAGAGGCG 62.656 68.421 0.00 0.00 0.00 5.52
6 7 1.835927 AAGAGGTGCTGGTGAGAGGC 61.836 60.000 0.00 0.00 0.00 4.70
7 8 1.205893 GTAAGAGGTGCTGGTGAGAGG 59.794 57.143 0.00 0.00 0.00 3.69
8 9 1.205893 GGTAAGAGGTGCTGGTGAGAG 59.794 57.143 0.00 0.00 0.00 3.20
9 10 1.267121 GGTAAGAGGTGCTGGTGAGA 58.733 55.000 0.00 0.00 0.00 3.27
10 11 0.976641 TGGTAAGAGGTGCTGGTGAG 59.023 55.000 0.00 0.00 0.00 3.51
11 12 0.976641 CTGGTAAGAGGTGCTGGTGA 59.023 55.000 0.00 0.00 0.00 4.02
12 13 0.674895 GCTGGTAAGAGGTGCTGGTG 60.675 60.000 0.00 0.00 0.00 4.17
13 14 1.127567 TGCTGGTAAGAGGTGCTGGT 61.128 55.000 0.00 0.00 0.00 4.00
14 15 0.392193 CTGCTGGTAAGAGGTGCTGG 60.392 60.000 0.00 0.00 0.00 4.85
15 16 0.322975 ACTGCTGGTAAGAGGTGCTG 59.677 55.000 0.00 0.00 0.00 4.41
16 17 0.322975 CACTGCTGGTAAGAGGTGCT 59.677 55.000 0.00 0.00 0.00 4.40
17 18 0.035458 ACACTGCTGGTAAGAGGTGC 59.965 55.000 0.00 0.00 33.53 5.01
53 54 1.889829 CCTTGTTCTCTCTCACTCGGT 59.110 52.381 0.00 0.00 0.00 4.69
56 57 2.495669 CCCTCCTTGTTCTCTCTCACTC 59.504 54.545 0.00 0.00 0.00 3.51
58 59 2.530701 TCCCTCCTTGTTCTCTCTCAC 58.469 52.381 0.00 0.00 0.00 3.51
68 69 0.038744 CATGCACCTTCCCTCCTTGT 59.961 55.000 0.00 0.00 0.00 3.16
71 72 1.213926 GAATCATGCACCTTCCCTCCT 59.786 52.381 0.00 0.00 0.00 3.69
109 110 3.849951 GAGCGCCATCCCCTTCGA 61.850 66.667 2.29 0.00 0.00 3.71
126 127 0.737715 CGTTGCCTCTTTCTCCTCGG 60.738 60.000 0.00 0.00 0.00 4.63
151 152 2.359975 AAGCGCCCCTTCCTTTCG 60.360 61.111 2.29 0.00 0.00 3.46
163 164 4.168291 CCCTCTCTCCCCAAGCGC 62.168 72.222 0.00 0.00 0.00 5.92
183 184 2.239907 CTCCTTCCTTTCGATCCCCTTT 59.760 50.000 0.00 0.00 0.00 3.11
184 185 1.840635 CTCCTTCCTTTCGATCCCCTT 59.159 52.381 0.00 0.00 0.00 3.95
218 219 1.059913 ATCTTATCTTCCCGGCCCAG 58.940 55.000 0.00 0.00 0.00 4.45
226 227 8.300286 GCTTATGCCCTTTTTATCTTATCTTCC 58.700 37.037 0.00 0.00 0.00 3.46
239 240 2.446435 ACACATCGCTTATGCCCTTTT 58.554 42.857 0.00 0.00 39.39 2.27
269 270 0.546598 CCCTTACTCCATGTGTCCCC 59.453 60.000 0.00 0.00 0.00 4.81
294 295 5.592282 ACTGATTCTCACGTATCATCTGTCT 59.408 40.000 0.00 0.00 30.91 3.41
317 318 6.749139 AGGAAAATGCTTCTTTTAGACCAAC 58.251 36.000 0.00 0.00 0.00 3.77
319 320 8.472007 TTTAGGAAAATGCTTCTTTTAGACCA 57.528 30.769 0.00 0.00 0.00 4.02
397 399 4.701651 TGAAGTGAACCCATAGATTTGCTG 59.298 41.667 0.00 0.00 0.00 4.41
458 461 9.598517 ACAATACAAAAGCAGAAAAATTTCTCA 57.401 25.926 5.45 0.00 45.23 3.27
486 494 9.783081 ACATATGAAGCATGTGACAGAATATTA 57.217 29.630 10.38 0.00 36.65 0.98
593 608 7.308529 CCATGCTTCTGTACTGTGTTTCATAAA 60.309 37.037 0.00 0.00 0.00 1.40
662 1940 7.527796 AGATAATTCTGAGCCTACTACCTACA 58.472 38.462 0.00 0.00 0.00 2.74
698 1977 6.608002 GGAGGGAGTATATAGTATTCCAGTGG 59.392 46.154 1.40 1.40 0.00 4.00
703 1982 7.844779 TGGAATGGAGGGAGTATATAGTATTCC 59.155 40.741 15.11 15.11 39.94 3.01
706 1985 9.629649 TTTTGGAATGGAGGGAGTATATAGTAT 57.370 33.333 0.00 0.00 0.00 2.12
714 1993 7.691791 GCACTATATTTTGGAATGGAGGGAGTA 60.692 40.741 0.00 0.00 0.00 2.59
715 1994 6.605119 CACTATATTTTGGAATGGAGGGAGT 58.395 40.000 0.00 0.00 0.00 3.85
716 1995 5.474876 GCACTATATTTTGGAATGGAGGGAG 59.525 44.000 0.00 0.00 0.00 4.30
717 1996 5.385198 GCACTATATTTTGGAATGGAGGGA 58.615 41.667 0.00 0.00 0.00 4.20
718 1997 4.216257 CGCACTATATTTTGGAATGGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
721 2000 3.568007 GGCGCACTATATTTTGGAATGGA 59.432 43.478 10.83 0.00 0.00 3.41
722 2001 3.305335 GGGCGCACTATATTTTGGAATGG 60.305 47.826 10.83 0.00 0.00 3.16
723 2002 3.317711 TGGGCGCACTATATTTTGGAATG 59.682 43.478 12.74 0.00 0.00 2.67
724 2003 3.317993 GTGGGCGCACTATATTTTGGAAT 59.682 43.478 25.28 0.00 0.00 3.01
725 2004 2.685897 GTGGGCGCACTATATTTTGGAA 59.314 45.455 25.28 0.00 0.00 3.53
726 2005 2.294074 GTGGGCGCACTATATTTTGGA 58.706 47.619 25.28 0.00 0.00 3.53
727 2006 1.002900 CGTGGGCGCACTATATTTTGG 60.003 52.381 28.52 8.56 0.00 3.28
728 2007 2.383298 CGTGGGCGCACTATATTTTG 57.617 50.000 28.52 9.25 0.00 2.44
740 2019 1.359459 GACCTTAGAAAGCGTGGGCG 61.359 60.000 0.00 0.00 46.35 6.13
741 2020 1.025113 GGACCTTAGAAAGCGTGGGC 61.025 60.000 0.00 0.00 40.37 5.36
742 2021 0.323629 TGGACCTTAGAAAGCGTGGG 59.676 55.000 0.00 0.00 0.00 4.61
743 2022 1.804748 GTTGGACCTTAGAAAGCGTGG 59.195 52.381 0.00 0.00 0.00 4.94
744 2023 2.767505 AGTTGGACCTTAGAAAGCGTG 58.232 47.619 0.00 0.00 0.00 5.34
745 2024 3.487120 AAGTTGGACCTTAGAAAGCGT 57.513 42.857 0.00 0.00 0.00 5.07
746 2025 5.334646 GGTTAAAGTTGGACCTTAGAAAGCG 60.335 44.000 0.00 0.00 0.00 4.68
747 2026 5.533528 TGGTTAAAGTTGGACCTTAGAAAGC 59.466 40.000 8.80 0.00 34.52 3.51
748 2027 7.761038 ATGGTTAAAGTTGGACCTTAGAAAG 57.239 36.000 8.80 0.00 34.52 2.62
749 2028 9.643735 TTTATGGTTAAAGTTGGACCTTAGAAA 57.356 29.630 8.80 0.00 34.52 2.52
750 2029 9.816787 ATTTATGGTTAAAGTTGGACCTTAGAA 57.183 29.630 8.80 5.74 34.52 2.10
751 2030 9.816787 AATTTATGGTTAAAGTTGGACCTTAGA 57.183 29.630 8.80 4.05 34.52 2.10
756 2035 9.426837 GGTTAAATTTATGGTTAAAGTTGGACC 57.573 33.333 0.00 1.82 36.56 4.46
757 2036 9.984190 TGGTTAAATTTATGGTTAAAGTTGGAC 57.016 29.630 0.00 2.05 36.56 4.02
762 2041 9.902196 CTCGTTGGTTAAATTTATGGTTAAAGT 57.098 29.630 0.00 0.00 31.07 2.66
764 2043 9.896263 GTCTCGTTGGTTAAATTTATGGTTAAA 57.104 29.630 0.00 0.00 0.00 1.52
765 2044 8.513774 GGTCTCGTTGGTTAAATTTATGGTTAA 58.486 33.333 0.00 0.00 0.00 2.01
766 2045 7.148440 CGGTCTCGTTGGTTAAATTTATGGTTA 60.148 37.037 0.00 0.00 0.00 2.85
767 2046 6.348704 CGGTCTCGTTGGTTAAATTTATGGTT 60.349 38.462 0.00 0.00 0.00 3.67
768 2047 5.122711 CGGTCTCGTTGGTTAAATTTATGGT 59.877 40.000 0.00 0.00 0.00 3.55
769 2048 5.352016 TCGGTCTCGTTGGTTAAATTTATGG 59.648 40.000 0.00 0.00 37.69 2.74
770 2049 6.091713 AGTCGGTCTCGTTGGTTAAATTTATG 59.908 38.462 0.00 0.00 37.69 1.90
771 2050 6.091713 CAGTCGGTCTCGTTGGTTAAATTTAT 59.908 38.462 0.00 0.00 37.69 1.40
772 2051 5.406175 CAGTCGGTCTCGTTGGTTAAATTTA 59.594 40.000 0.00 0.00 37.69 1.40
773 2052 4.212636 CAGTCGGTCTCGTTGGTTAAATTT 59.787 41.667 0.00 0.00 37.69 1.82
774 2053 3.744426 CAGTCGGTCTCGTTGGTTAAATT 59.256 43.478 0.00 0.00 37.69 1.82
775 2054 3.323243 CAGTCGGTCTCGTTGGTTAAAT 58.677 45.455 0.00 0.00 37.69 1.40
776 2055 2.746269 CAGTCGGTCTCGTTGGTTAAA 58.254 47.619 0.00 0.00 37.69 1.52
777 2056 1.603678 GCAGTCGGTCTCGTTGGTTAA 60.604 52.381 0.00 0.00 37.69 2.01
778 2057 0.038892 GCAGTCGGTCTCGTTGGTTA 60.039 55.000 0.00 0.00 37.69 2.85
779 2058 1.300697 GCAGTCGGTCTCGTTGGTT 60.301 57.895 0.00 0.00 37.69 3.67
780 2059 2.338984 GCAGTCGGTCTCGTTGGT 59.661 61.111 0.00 0.00 37.69 3.67
781 2060 2.805353 CGCAGTCGGTCTCGTTGG 60.805 66.667 0.00 0.00 37.69 3.77
791 2070 2.709629 TTTTTCTTGCGCCGCAGTCG 62.710 55.000 13.13 5.28 40.61 4.18
792 2071 1.008995 TTTTTCTTGCGCCGCAGTC 60.009 52.632 13.13 0.00 40.61 3.51
793 2072 3.115556 TTTTTCTTGCGCCGCAGT 58.884 50.000 13.13 0.00 40.61 4.40
839 2118 9.783256 GAGCAAAAATTATACCAGTAAATTCGT 57.217 29.630 0.00 0.00 0.00 3.85
840 2119 9.233232 GGAGCAAAAATTATACCAGTAAATTCG 57.767 33.333 0.00 0.00 0.00 3.34
841 2120 9.529325 GGGAGCAAAAATTATACCAGTAAATTC 57.471 33.333 0.00 0.00 0.00 2.17
842 2121 8.194769 CGGGAGCAAAAATTATACCAGTAAATT 58.805 33.333 0.00 0.00 0.00 1.82
843 2122 7.340999 ACGGGAGCAAAAATTATACCAGTAAAT 59.659 33.333 0.00 0.00 0.00 1.40
844 2123 6.660094 ACGGGAGCAAAAATTATACCAGTAAA 59.340 34.615 0.00 0.00 0.00 2.01
845 2124 6.181908 ACGGGAGCAAAAATTATACCAGTAA 58.818 36.000 0.00 0.00 0.00 2.24
846 2125 5.747342 ACGGGAGCAAAAATTATACCAGTA 58.253 37.500 0.00 0.00 0.00 2.74
847 2126 4.595986 ACGGGAGCAAAAATTATACCAGT 58.404 39.130 0.00 0.00 0.00 4.00
848 2127 4.638421 TGACGGGAGCAAAAATTATACCAG 59.362 41.667 0.00 0.00 0.00 4.00
849 2128 4.396790 GTGACGGGAGCAAAAATTATACCA 59.603 41.667 0.00 0.00 0.00 3.25
850 2129 4.396790 TGTGACGGGAGCAAAAATTATACC 59.603 41.667 0.00 0.00 0.00 2.73
851 2130 5.554822 TGTGACGGGAGCAAAAATTATAC 57.445 39.130 0.00 0.00 0.00 1.47
852 2131 6.183360 GGATTGTGACGGGAGCAAAAATTATA 60.183 38.462 0.00 0.00 0.00 0.98
853 2132 5.394115 GGATTGTGACGGGAGCAAAAATTAT 60.394 40.000 0.00 0.00 0.00 1.28
854 2133 4.082463 GGATTGTGACGGGAGCAAAAATTA 60.082 41.667 0.00 0.00 0.00 1.40
855 2134 3.306019 GGATTGTGACGGGAGCAAAAATT 60.306 43.478 0.00 0.00 0.00 1.82
856 2135 2.231235 GGATTGTGACGGGAGCAAAAAT 59.769 45.455 0.00 0.00 0.00 1.82
857 2136 1.611491 GGATTGTGACGGGAGCAAAAA 59.389 47.619 0.00 0.00 0.00 1.94
858 2137 1.243902 GGATTGTGACGGGAGCAAAA 58.756 50.000 0.00 0.00 0.00 2.44
859 2138 0.953471 CGGATTGTGACGGGAGCAAA 60.953 55.000 0.00 0.00 0.00 3.68
860 2139 1.375396 CGGATTGTGACGGGAGCAA 60.375 57.895 0.00 0.00 0.00 3.91
861 2140 2.264480 CGGATTGTGACGGGAGCA 59.736 61.111 0.00 0.00 0.00 4.26
862 2141 1.810030 GACGGATTGTGACGGGAGC 60.810 63.158 0.00 0.00 0.00 4.70
863 2142 0.179134 GAGACGGATTGTGACGGGAG 60.179 60.000 0.00 0.00 0.00 4.30
864 2143 0.896479 TGAGACGGATTGTGACGGGA 60.896 55.000 0.00 0.00 0.00 5.14
865 2144 0.175760 ATGAGACGGATTGTGACGGG 59.824 55.000 0.00 0.00 0.00 5.28
866 2145 1.660607 CAATGAGACGGATTGTGACGG 59.339 52.381 0.00 0.00 0.00 4.79
867 2146 1.660607 CCAATGAGACGGATTGTGACG 59.339 52.381 0.00 0.00 0.00 4.35
868 2147 1.398390 GCCAATGAGACGGATTGTGAC 59.602 52.381 0.00 0.00 0.00 3.67
869 2148 1.278985 AGCCAATGAGACGGATTGTGA 59.721 47.619 0.00 0.00 0.00 3.58
870 2149 1.742761 AGCCAATGAGACGGATTGTG 58.257 50.000 0.00 0.00 0.00 3.33
871 2150 3.627395 TTAGCCAATGAGACGGATTGT 57.373 42.857 0.00 0.00 0.00 2.71
872 2151 5.505173 AATTTAGCCAATGAGACGGATTG 57.495 39.130 0.00 0.00 0.00 2.67
873 2152 7.255590 CCATAAATTTAGCCAATGAGACGGATT 60.256 37.037 3.94 0.00 0.00 3.01
874 2153 6.207417 CCATAAATTTAGCCAATGAGACGGAT 59.793 38.462 3.94 0.00 0.00 4.18
875 2154 5.530915 CCATAAATTTAGCCAATGAGACGGA 59.469 40.000 3.94 0.00 0.00 4.69
876 2155 5.299279 ACCATAAATTTAGCCAATGAGACGG 59.701 40.000 3.94 0.00 0.00 4.79
877 2156 6.377327 ACCATAAATTTAGCCAATGAGACG 57.623 37.500 3.94 0.00 0.00 4.18
885 2164 9.921637 CTTCAACTTTAACCATAAATTTAGCCA 57.078 29.630 3.94 0.00 30.88 4.75
886 2165 8.869897 GCTTCAACTTTAACCATAAATTTAGCC 58.130 33.333 3.94 0.00 30.88 3.93
887 2166 9.418045 TGCTTCAACTTTAACCATAAATTTAGC 57.582 29.630 3.94 0.00 30.88 3.09
890 2169 9.218440 CCATGCTTCAACTTTAACCATAAATTT 57.782 29.630 0.00 0.00 30.88 1.82
891 2170 7.823799 CCCATGCTTCAACTTTAACCATAAATT 59.176 33.333 0.00 0.00 30.88 1.82
892 2171 7.180051 TCCCATGCTTCAACTTTAACCATAAAT 59.820 33.333 0.00 0.00 30.88 1.40
893 2172 6.495181 TCCCATGCTTCAACTTTAACCATAAA 59.505 34.615 0.00 0.00 0.00 1.40
894 2173 6.013379 TCCCATGCTTCAACTTTAACCATAA 58.987 36.000 0.00 0.00 0.00 1.90
895 2174 5.575157 TCCCATGCTTCAACTTTAACCATA 58.425 37.500 0.00 0.00 0.00 2.74
896 2175 4.415596 TCCCATGCTTCAACTTTAACCAT 58.584 39.130 0.00 0.00 0.00 3.55
897 2176 3.838565 TCCCATGCTTCAACTTTAACCA 58.161 40.909 0.00 0.00 0.00 3.67
898 2177 4.864704 TTCCCATGCTTCAACTTTAACC 57.135 40.909 0.00 0.00 0.00 2.85
899 2178 7.336931 TCTCTATTCCCATGCTTCAACTTTAAC 59.663 37.037 0.00 0.00 0.00 2.01
900 2179 7.402054 TCTCTATTCCCATGCTTCAACTTTAA 58.598 34.615 0.00 0.00 0.00 1.52
901 2180 6.957631 TCTCTATTCCCATGCTTCAACTTTA 58.042 36.000 0.00 0.00 0.00 1.85
902 2181 5.819991 TCTCTATTCCCATGCTTCAACTTT 58.180 37.500 0.00 0.00 0.00 2.66
903 2182 5.441718 TCTCTATTCCCATGCTTCAACTT 57.558 39.130 0.00 0.00 0.00 2.66
904 2183 5.441718 TTCTCTATTCCCATGCTTCAACT 57.558 39.130 0.00 0.00 0.00 3.16
905 2184 6.071952 TGTTTTCTCTATTCCCATGCTTCAAC 60.072 38.462 0.00 0.00 0.00 3.18
906 2185 6.009589 TGTTTTCTCTATTCCCATGCTTCAA 58.990 36.000 0.00 0.00 0.00 2.69
907 2186 5.415701 GTGTTTTCTCTATTCCCATGCTTCA 59.584 40.000 0.00 0.00 0.00 3.02
908 2187 5.649831 AGTGTTTTCTCTATTCCCATGCTTC 59.350 40.000 0.00 0.00 0.00 3.86
909 2188 5.574188 AGTGTTTTCTCTATTCCCATGCTT 58.426 37.500 0.00 0.00 0.00 3.91
910 2189 5.184892 AGTGTTTTCTCTATTCCCATGCT 57.815 39.130 0.00 0.00 0.00 3.79
911 2190 8.854614 ATATAGTGTTTTCTCTATTCCCATGC 57.145 34.615 0.00 0.00 37.63 4.06
920 2199 9.158233 CCGTTCCAAAATATAGTGTTTTCTCTA 57.842 33.333 0.00 0.00 0.00 2.43
921 2200 7.881232 TCCGTTCCAAAATATAGTGTTTTCTCT 59.119 33.333 0.00 0.00 0.00 3.10
922 2201 8.036273 TCCGTTCCAAAATATAGTGTTTTCTC 57.964 34.615 0.00 0.00 0.00 2.87
923 2202 7.989416 TCCGTTCCAAAATATAGTGTTTTCT 57.011 32.000 0.00 0.00 0.00 2.52
924 2203 7.700656 CCATCCGTTCCAAAATATAGTGTTTTC 59.299 37.037 0.00 0.00 0.00 2.29
925 2204 7.394923 TCCATCCGTTCCAAAATATAGTGTTTT 59.605 33.333 0.00 0.00 0.00 2.43
926 2205 6.887545 TCCATCCGTTCCAAAATATAGTGTTT 59.112 34.615 0.00 0.00 0.00 2.83
927 2206 6.419791 TCCATCCGTTCCAAAATATAGTGTT 58.580 36.000 0.00 0.00 0.00 3.32
928 2207 5.996644 TCCATCCGTTCCAAAATATAGTGT 58.003 37.500 0.00 0.00 0.00 3.55
929 2208 6.055588 ACTCCATCCGTTCCAAAATATAGTG 58.944 40.000 0.00 0.00 0.00 2.74
930 2209 6.248569 ACTCCATCCGTTCCAAAATATAGT 57.751 37.500 0.00 0.00 0.00 2.12
931 2210 7.385205 CAGTACTCCATCCGTTCCAAAATATAG 59.615 40.741 0.00 0.00 0.00 1.31
932 2211 7.147620 ACAGTACTCCATCCGTTCCAAAATATA 60.148 37.037 0.00 0.00 0.00 0.86
933 2212 6.055588 CAGTACTCCATCCGTTCCAAAATAT 58.944 40.000 0.00 0.00 0.00 1.28
934 2213 5.046159 ACAGTACTCCATCCGTTCCAAAATA 60.046 40.000 0.00 0.00 0.00 1.40
935 2214 4.261801 CAGTACTCCATCCGTTCCAAAAT 58.738 43.478 0.00 0.00 0.00 1.82
936 2215 3.071892 ACAGTACTCCATCCGTTCCAAAA 59.928 43.478 0.00 0.00 0.00 2.44
937 2216 2.635915 ACAGTACTCCATCCGTTCCAAA 59.364 45.455 0.00 0.00 0.00 3.28
938 2217 2.253610 ACAGTACTCCATCCGTTCCAA 58.746 47.619 0.00 0.00 0.00 3.53
939 2218 1.933021 ACAGTACTCCATCCGTTCCA 58.067 50.000 0.00 0.00 0.00 3.53
940 2219 5.979288 ATATACAGTACTCCATCCGTTCC 57.021 43.478 0.00 0.00 0.00 3.62
941 2220 7.028361 GCTAATATACAGTACTCCATCCGTTC 58.972 42.308 0.00 0.00 0.00 3.95
942 2221 6.071503 GGCTAATATACAGTACTCCATCCGTT 60.072 42.308 0.00 0.00 0.00 4.44
943 2222 5.418209 GGCTAATATACAGTACTCCATCCGT 59.582 44.000 0.00 0.00 0.00 4.69
944 2223 5.652891 AGGCTAATATACAGTACTCCATCCG 59.347 44.000 0.00 0.00 0.00 4.18
945 2224 7.483580 AAGGCTAATATACAGTACTCCATCC 57.516 40.000 0.00 0.00 0.00 3.51
961 2240 9.313118 CTGTTTTCTGTTGTTTTTAAGGCTAAT 57.687 29.630 0.00 0.00 0.00 1.73
962 2241 7.276878 GCTGTTTTCTGTTGTTTTTAAGGCTAA 59.723 33.333 0.00 0.00 0.00 3.09
963 2242 6.754675 GCTGTTTTCTGTTGTTTTTAAGGCTA 59.245 34.615 0.00 0.00 0.00 3.93
964 2243 5.580691 GCTGTTTTCTGTTGTTTTTAAGGCT 59.419 36.000 0.00 0.00 0.00 4.58
965 2244 5.350091 TGCTGTTTTCTGTTGTTTTTAAGGC 59.650 36.000 0.00 0.00 0.00 4.35
966 2245 6.589907 AGTGCTGTTTTCTGTTGTTTTTAAGG 59.410 34.615 0.00 0.00 0.00 2.69
967 2246 7.461416 CGAGTGCTGTTTTCTGTTGTTTTTAAG 60.461 37.037 0.00 0.00 0.00 1.85
968 2247 6.306837 CGAGTGCTGTTTTCTGTTGTTTTTAA 59.693 34.615 0.00 0.00 0.00 1.52
973 2252 3.006940 TCGAGTGCTGTTTTCTGTTGTT 58.993 40.909 0.00 0.00 0.00 2.83
974 2253 2.627945 TCGAGTGCTGTTTTCTGTTGT 58.372 42.857 0.00 0.00 0.00 3.32
995 2274 1.425825 CAGCGACGACGACTGAGAT 59.574 57.895 19.99 0.00 41.93 2.75
1009 2288 0.101040 CTCTCTCTCTCCTTGCAGCG 59.899 60.000 0.00 0.00 0.00 5.18
1018 2297 5.698545 GCACTAGATTCTCTCTCTCTCTCTC 59.301 48.000 0.00 0.00 35.28 3.20
1024 2303 4.760204 GGGTAGCACTAGATTCTCTCTCTC 59.240 50.000 0.00 0.00 35.28 3.20
1025 2304 4.447180 GGGGTAGCACTAGATTCTCTCTCT 60.447 50.000 0.00 0.00 35.28 3.10
1170 2742 1.599047 CTGGTCGATTGGTCCAGCT 59.401 57.895 6.12 0.00 41.46 4.24
1457 3029 2.236395 CCCAGTACCACGAAAGGAAGAT 59.764 50.000 0.00 0.00 0.00 2.40
1494 3066 3.364964 GGAGTGAATTACAGTGCCAAACG 60.365 47.826 0.00 0.00 34.82 3.60
1659 3233 3.521796 GAGCAAATCCGGCCAGGC 61.522 66.667 1.26 1.26 40.77 4.85
1794 3369 1.842052 TCCGGGCTAAAATTTGGGAC 58.158 50.000 0.00 0.00 0.00 4.46
1847 3422 5.776716 AGCAAATCTCTCAGAAATTGGGAAA 59.223 36.000 0.00 0.00 35.37 3.13
2052 3627 2.480419 CCAGTGAAGCGACCACTTAAAG 59.520 50.000 6.05 0.00 42.44 1.85
2755 4331 0.874390 TGTTGAGAAATGCCGTGCTC 59.126 50.000 0.00 0.00 0.00 4.26
2944 4520 4.135493 GTCGCGTCCGCTTTCAGC 62.135 66.667 5.77 0.00 39.32 4.26
2959 4535 1.076533 AATGCACGATCGACACGGTC 61.077 55.000 24.34 2.89 33.21 4.79
3095 4671 3.057315 GCAGTCAGAATTAAGGCAAGCAA 60.057 43.478 0.00 0.00 0.00 3.91
3096 4672 2.489329 GCAGTCAGAATTAAGGCAAGCA 59.511 45.455 0.00 0.00 0.00 3.91
3097 4673 2.751806 AGCAGTCAGAATTAAGGCAAGC 59.248 45.455 0.00 0.00 0.00 4.01
3098 4674 3.755378 ACAGCAGTCAGAATTAAGGCAAG 59.245 43.478 0.00 0.00 0.00 4.01
3176 4752 1.111116 TGGAGTTTGTCCCGACGTCT 61.111 55.000 14.70 0.00 46.31 4.18
3547 5127 1.731433 GGCGACTGCGTATGTAGGGA 61.731 60.000 4.98 0.00 44.10 4.20
3571 5151 3.760035 GCTTCGTCCCTGCCTCGA 61.760 66.667 0.00 0.00 0.00 4.04
3617 5197 2.359230 GGTGCTCAGAGGCCACAC 60.359 66.667 5.01 2.91 0.00 3.82
3657 5237 0.512952 CGTGGTTTCTTCAGGCTTCG 59.487 55.000 0.00 0.00 0.00 3.79
3756 5336 3.697747 CCCCAGCCGAACGTACCA 61.698 66.667 0.00 0.00 0.00 3.25
3820 5403 4.771114 TTCATTTGGGACATCGGATACT 57.229 40.909 0.00 0.00 39.30 2.12
3889 5472 5.583457 GCGTCTTATATTTTGGTACAGTGGT 59.417 40.000 0.00 0.00 42.39 4.16
3933 5516 4.003648 AGAGGCAGTAGTAATGTTTGCAC 58.996 43.478 0.00 0.00 36.53 4.57
3942 5525 5.811796 TTTTGGTACAGAGGCAGTAGTAA 57.188 39.130 0.00 0.00 42.39 2.24
4109 5949 5.122082 ACAAATTGTTTGAACTGTTGCCTTG 59.878 36.000 9.21 0.00 43.26 3.61
4206 6046 5.277601 CGATACATCGTTGTTGGTTTTCT 57.722 39.130 4.14 0.00 44.74 2.52


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

AutoCloner maintained by Alex Coulton.