Multiple sequence alignment - TraesCS3B01G176400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G176400 chr3B 100.000 4229 0 0 1 4229 179370096 179365868 0.000000e+00 7810.0
1 TraesCS3B01G176400 chr3D 95.246 1788 64 7 1738 3506 125481055 125479270 0.000000e+00 2811.0
2 TraesCS3B01G176400 chr3D 93.411 1715 56 17 1 1691 125482839 125481158 0.000000e+00 2488.0
3 TraesCS3B01G176400 chr3D 86.350 337 28 5 3534 3853 125479202 125478867 6.730000e-93 351.0
4 TraesCS3B01G176400 chr3D 90.000 90 7 1 4133 4222 125478672 125478585 9.610000e-22 115.0
5 TraesCS3B01G176400 chr3A 95.134 1788 64 11 1738 3506 134236415 134234632 0.000000e+00 2798.0
6 TraesCS3B01G176400 chr3A 93.395 1741 51 24 1 1691 134238243 134236517 0.000000e+00 2519.0
7 TraesCS3B01G176400 chr3A 86.921 367 32 12 3510 3874 134234595 134234243 8.520000e-107 398.0
8 TraesCS3B01G176400 chr7D 93.023 43 3 0 1215 1257 427631625 427631583 3.530000e-06 63.9
9 TraesCS3B01G176400 chr7B 94.872 39 2 0 1215 1253 445423203 445423165 1.270000e-05 62.1


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 TraesCS3B01G176400 chr3B 179365868 179370096 4228 True 7810.00 7810 100.000000 1 4229 1 chr3B.!!$R1 4228
1 TraesCS3B01G176400 chr3D 125478585 125482839 4254 True 1441.25 2811 91.251750 1 4222 4 chr3D.!!$R1 4221
2 TraesCS3B01G176400 chr3A 134234243 134238243 4000 True 1905.00 2798 91.816667 1 3874 3 chr3A.!!$R1 3873

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
530 549 0.179020 TCCATGCCGATCCAATCCAC 60.179 55.0 0.0 0.0 0.0 4.02 F
1680 1736 0.179192 CCATGTCGATGTTTGCACCG 60.179 55.0 0.0 0.0 0.0 4.94 F
1682 1738 0.605319 ATGTCGATGTTTGCACCGGT 60.605 50.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2166 1.568612 AATCACGGTGCAGACAAGCG 61.569 55.000 2.51 0.0 43.79 4.68 R
2548 2677 0.463116 ACTCGCCCAAACGTTCAGTT 60.463 50.000 0.00 0.0 46.76 3.16 R
3506 3636 1.072489 TGAACCGGGCAACAATGTAGA 59.928 47.619 6.32 0.0 39.74 2.59 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
44 45 4.625028 TGATCGGCAAGTTGATATCTCTG 58.375 43.478 7.16 0.00 0.00 3.35
48 49 3.282021 GGCAAGTTGATATCTCTGCCAA 58.718 45.455 22.29 1.84 40.57 4.52
105 106 3.486383 TGTTCCAACTGGACAAGGAATC 58.514 45.455 0.00 0.00 45.39 2.52
130 131 2.029739 TGACATGGTGCTCATTTTGCTG 60.030 45.455 0.00 0.00 32.92 4.41
189 190 1.781786 TGAGAGCTATGGAGTCCCAC 58.218 55.000 6.74 0.00 46.98 4.61
190 191 1.044611 GAGAGCTATGGAGTCCCACC 58.955 60.000 6.74 0.00 46.98 4.61
191 192 0.339859 AGAGCTATGGAGTCCCACCA 59.660 55.000 6.74 0.00 46.98 4.17
206 207 1.820519 CCACCACAATTGTCCATCCAG 59.179 52.381 8.48 0.00 0.00 3.86
214 215 4.281688 ACAATTGTCCATCCAGAAAACAGG 59.718 41.667 4.92 0.00 0.00 4.00
334 353 3.374988 TGTATCGGCAAGAATGAGCAAAG 59.625 43.478 0.00 0.00 0.00 2.77
351 370 1.106944 AAGGGTCCACCAAACGCAAG 61.107 55.000 0.00 0.00 43.89 4.01
530 549 0.179020 TCCATGCCGATCCAATCCAC 60.179 55.000 0.00 0.00 0.00 4.02
532 551 1.227943 ATGCCGATCCAATCCACCG 60.228 57.895 0.00 0.00 0.00 4.94
697 722 2.130073 GAAAGAAAACCAGCGGCGCT 62.130 55.000 31.35 31.35 40.77 5.92
790 815 1.127343 GCTAGAGCCCAGATCCAAGT 58.873 55.000 0.00 0.00 34.31 3.16
791 816 2.320781 GCTAGAGCCCAGATCCAAGTA 58.679 52.381 0.00 0.00 34.31 2.24
798 840 4.530875 AGCCCAGATCCAAGTAGAAAATG 58.469 43.478 0.00 0.00 0.00 2.32
818 860 2.302260 GAGGCCCAGAATTTAAGAGGC 58.698 52.381 0.00 0.00 39.73 4.70
822 864 1.064685 CCCAGAATTTAAGAGGCCCGT 60.065 52.381 0.00 0.00 0.00 5.28
823 865 2.620627 CCCAGAATTTAAGAGGCCCGTT 60.621 50.000 0.00 0.00 0.00 4.44
840 887 2.670905 CCGTTATGAATGTTGCAGACGA 59.329 45.455 0.00 0.00 33.41 4.20
878 929 3.528532 TGTCACTGTCAGCATCATCATC 58.471 45.455 0.00 0.00 0.00 2.92
879 930 3.055675 TGTCACTGTCAGCATCATCATCA 60.056 43.478 0.00 0.00 0.00 3.07
880 931 4.127907 GTCACTGTCAGCATCATCATCAT 58.872 43.478 0.00 0.00 0.00 2.45
1447 1503 2.300152 TCTGTAAACTGTGGAGAGGCTG 59.700 50.000 0.00 0.00 0.00 4.85
1482 1538 4.776795 ATGTTGGTAAATTCAACCGACC 57.223 40.909 20.15 8.94 46.81 4.79
1578 1634 2.879002 ATCTCGTAGTGTCCATGCTG 57.121 50.000 0.00 0.00 0.00 4.41
1629 1685 9.155975 GAACTAAATCTGCAGATAGTTCTTTCA 57.844 33.333 37.42 16.92 41.90 2.69
1637 1693 4.026145 GCAGATAGTTCTTTCAGACATCGC 60.026 45.833 0.00 0.00 0.00 4.58
1653 1709 1.717032 TCGCTAGTATGCCTTGGGAT 58.283 50.000 0.00 0.00 34.03 3.85
1680 1736 0.179192 CCATGTCGATGTTTGCACCG 60.179 55.000 0.00 0.00 0.00 4.94
1682 1738 0.605319 ATGTCGATGTTTGCACCGGT 60.605 50.000 0.00 0.00 0.00 5.28
1709 1793 5.128827 ACGATAGGTCTTTAATCAGCAAGGA 59.871 40.000 0.00 0.00 43.77 3.36
1724 1808 5.013079 TCAGCAAGGATTTCTCTGAAGGTTA 59.987 40.000 0.00 0.00 31.62 2.85
1809 1920 6.769512 AGCACTGTTATTCTGTTAGAAGGAA 58.230 36.000 0.00 0.00 37.69 3.36
1961 2072 3.805207 GGTGTTCTTACCACACTGAACT 58.195 45.455 3.39 0.00 43.55 3.01
1963 2074 3.560068 GTGTTCTTACCACACTGAACTGG 59.440 47.826 0.00 0.00 41.25 4.00
1980 2091 7.339466 ACTGAACTGGTTGTTTAGAAGATTTGT 59.661 33.333 7.20 0.00 42.68 2.83
1989 2100 9.313118 GTTGTTTAGAAGATTTGTGTTTCCAAT 57.687 29.630 0.00 0.00 0.00 3.16
2002 2113 8.824159 TTGTGTTTCCAATGGTTATATTTGTG 57.176 30.769 0.00 0.00 0.00 3.33
2032 2143 1.438651 CACCGTCGACATGGACATTT 58.561 50.000 17.16 0.00 36.73 2.32
2120 2232 3.961849 TGCACCATGATTAACTAAGGCA 58.038 40.909 0.00 0.00 0.00 4.75
2137 2249 7.227156 ACTAAGGCAATATCTTTGTGATAGGG 58.773 38.462 0.00 0.00 40.58 3.53
2196 2308 4.036262 GTGTTTCTGCATGTTGTAGTTCCA 59.964 41.667 0.00 0.00 31.74 3.53
2203 2315 4.340666 TGCATGTTGTAGTTCCACAAATGT 59.659 37.500 0.00 0.00 39.98 2.71
2220 2332 6.349300 ACAAATGTGAATAGACCGCTAGATT 58.651 36.000 0.00 0.00 0.00 2.40
2403 2532 0.861837 GGAGTGTCTGACTTGCAACG 59.138 55.000 9.51 0.00 33.83 4.10
2521 2650 7.636150 AGTACTAGGTAGCGTTCTTTTATCA 57.364 36.000 0.00 0.00 0.00 2.15
2548 2677 3.630312 GGAAAGCACCAAGTTAGTCAACA 59.370 43.478 0.00 0.00 37.10 3.33
2562 2691 2.422127 AGTCAACAACTGAACGTTTGGG 59.578 45.455 0.46 0.00 36.65 4.12
2643 2773 6.060788 AGATTCTCTTTATGTTCAGGCATCC 58.939 40.000 0.00 0.00 0.00 3.51
2644 2774 3.797039 TCTCTTTATGTTCAGGCATCCG 58.203 45.455 0.00 0.00 0.00 4.18
2695 2825 6.524101 TCATGTCTGCACTGTGTACTTATA 57.476 37.500 9.86 0.00 0.00 0.98
2918 3048 5.444663 AACAAGCCTGAGAAATCAAGAAC 57.555 39.130 0.00 0.00 0.00 3.01
2962 3092 0.461961 GGAGACGGGAGATGGTTCAG 59.538 60.000 0.00 0.00 0.00 3.02
3058 3188 0.321671 TCTAGGGAACAGTGCAGTGC 59.678 55.000 21.57 8.58 0.00 4.40
3192 3322 1.739338 CTCTGGCAGGGCGTAGTAGG 61.739 65.000 15.73 0.00 0.00 3.18
3204 3334 3.570550 GGCGTAGTAGGATGAGTCATCTT 59.429 47.826 27.89 24.13 40.39 2.40
3269 3399 5.605327 CCTTTCTGATACGTTGTTTGTACG 58.395 41.667 0.00 0.00 44.20 3.67
3307 3437 7.686127 GCATCTTATCTGCCATTTTGAAGGAAT 60.686 37.037 0.00 0.00 33.44 3.01
3384 3514 3.252554 AGGCTAGCTTACCTCTGCTAT 57.747 47.619 15.72 0.00 40.43 2.97
3491 3621 3.260128 TGCCAGTATATGCAGATCTCTGG 59.740 47.826 27.05 27.05 43.94 3.86
3506 3636 4.098914 TCTCTGGCTTTGGTTGTACAAT 57.901 40.909 12.26 0.00 0.00 2.71
3507 3637 4.072131 TCTCTGGCTTTGGTTGTACAATC 58.928 43.478 12.26 12.19 0.00 2.67
3565 3736 2.429478 TCATGCTTGTGATGGTCTGTG 58.571 47.619 0.00 0.00 0.00 3.66
3567 3738 1.882912 TGCTTGTGATGGTCTGTGAC 58.117 50.000 0.00 0.00 0.00 3.67
3568 3739 1.417517 TGCTTGTGATGGTCTGTGACT 59.582 47.619 0.00 0.00 32.47 3.41
3700 3872 7.763985 CCAGATTATGTTGGATTTTTGTAACCC 59.236 37.037 0.00 0.00 36.55 4.11
3703 3875 7.604657 TTATGTTGGATTTTTGTAACCCTGT 57.395 32.000 0.00 0.00 0.00 4.00
3704 3876 5.269505 TGTTGGATTTTTGTAACCCTGTG 57.730 39.130 0.00 0.00 0.00 3.66
3708 3880 6.095432 TGGATTTTTGTAACCCTGTGAATG 57.905 37.500 0.00 0.00 0.00 2.67
3720 3892 3.747529 CCCTGTGAATGCAAATCAAAACC 59.252 43.478 7.09 0.00 0.00 3.27
3723 3912 4.297510 TGTGAATGCAAATCAAAACCTCG 58.702 39.130 7.09 0.00 0.00 4.63
3726 3915 4.278170 TGAATGCAAATCAAAACCTCGACT 59.722 37.500 3.28 0.00 0.00 4.18
3729 3918 3.820467 TGCAAATCAAAACCTCGACTCAT 59.180 39.130 0.00 0.00 0.00 2.90
3736 3925 5.227908 TCAAAACCTCGACTCATGAACTAC 58.772 41.667 0.00 0.00 0.00 2.73
3763 3953 6.531503 TTGTCAGGTTTTGTCCATGTTAAA 57.468 33.333 0.00 0.00 0.00 1.52
3767 3957 8.043710 TGTCAGGTTTTGTCCATGTTAAATTTT 58.956 29.630 0.00 0.00 0.00 1.82
3793 3983 4.121317 TGGGCGTTTTCATAGGTATTACG 58.879 43.478 0.00 0.00 0.00 3.18
3819 4009 2.325661 AGGCCTTTTGCATTAGGGTT 57.674 45.000 0.00 0.00 43.89 4.11
3826 4016 4.082571 CCTTTTGCATTAGGGTTCTGAGTG 60.083 45.833 6.71 0.00 0.00 3.51
3828 4018 3.334583 TGCATTAGGGTTCTGAGTGTC 57.665 47.619 0.00 0.00 0.00 3.67
3863 4053 2.391616 TGCAATCTAGGTGCAGAGTG 57.608 50.000 15.47 0.00 46.76 3.51
3864 4054 1.065926 TGCAATCTAGGTGCAGAGTGG 60.066 52.381 15.47 0.00 46.76 4.00
3866 4056 2.898705 CAATCTAGGTGCAGAGTGGAC 58.101 52.381 0.00 0.00 37.07 4.02
3869 4059 1.827344 TCTAGGTGCAGAGTGGACATG 59.173 52.381 0.86 0.00 40.73 3.21
3870 4060 0.904649 TAGGTGCAGAGTGGACATGG 59.095 55.000 0.00 0.00 40.73 3.66
3871 4061 1.130054 AGGTGCAGAGTGGACATGGT 61.130 55.000 0.00 0.00 40.73 3.55
3872 4062 0.613260 GGTGCAGAGTGGACATGGTA 59.387 55.000 0.00 0.00 40.73 3.25
3873 4063 1.676014 GGTGCAGAGTGGACATGGTAC 60.676 57.143 0.00 0.00 40.73 3.34
3874 4064 0.613260 TGCAGAGTGGACATGGTACC 59.387 55.000 4.43 4.43 0.00 3.34
3875 4065 0.905357 GCAGAGTGGACATGGTACCT 59.095 55.000 14.36 0.00 0.00 3.08
3876 4066 2.108168 GCAGAGTGGACATGGTACCTA 58.892 52.381 14.36 0.00 0.00 3.08
3877 4067 2.101582 GCAGAGTGGACATGGTACCTAG 59.898 54.545 14.36 8.03 0.00 3.02
3880 4070 4.024670 AGAGTGGACATGGTACCTAGTTC 58.975 47.826 14.36 10.77 0.00 3.01
3881 4071 3.767673 GAGTGGACATGGTACCTAGTTCA 59.232 47.826 14.36 13.29 0.00 3.18
3882 4072 4.362677 AGTGGACATGGTACCTAGTTCAT 58.637 43.478 17.64 7.65 0.00 2.57
3883 4073 4.783227 AGTGGACATGGTACCTAGTTCATT 59.217 41.667 17.64 12.58 0.00 2.57
3885 4075 6.442564 AGTGGACATGGTACCTAGTTCATTAA 59.557 38.462 17.64 0.00 0.00 1.40
3888 4078 7.773224 TGGACATGGTACCTAGTTCATTAAATG 59.227 37.037 14.36 6.20 0.00 2.32
3889 4079 7.990886 GGACATGGTACCTAGTTCATTAAATGA 59.009 37.037 14.36 0.00 37.55 2.57
3890 4080 8.964476 ACATGGTACCTAGTTCATTAAATGAG 57.036 34.615 14.36 0.00 40.94 2.90
3892 4082 9.265901 CATGGTACCTAGTTCATTAAATGAGAG 57.734 37.037 14.36 0.00 40.94 3.20
3893 4083 7.272978 TGGTACCTAGTTCATTAAATGAGAGC 58.727 38.462 14.36 0.00 40.94 4.09
3894 4084 7.125811 TGGTACCTAGTTCATTAAATGAGAGCT 59.874 37.037 14.36 0.00 40.94 4.09
3896 4086 9.036671 GTACCTAGTTCATTAAATGAGAGCTTC 57.963 37.037 0.00 0.00 40.94 3.86
3897 4087 7.624549 ACCTAGTTCATTAAATGAGAGCTTCA 58.375 34.615 0.00 0.00 40.94 3.02
3898 4088 7.550906 ACCTAGTTCATTAAATGAGAGCTTCAC 59.449 37.037 0.00 0.00 40.94 3.18
3899 4089 6.414408 AGTTCATTAAATGAGAGCTTCACG 57.586 37.500 0.00 0.00 40.94 4.35
3900 4090 4.864916 TCATTAAATGAGAGCTTCACGC 57.135 40.909 0.00 0.00 38.99 5.34
3901 4091 4.507710 TCATTAAATGAGAGCTTCACGCT 58.492 39.130 0.00 0.00 42.91 5.07
3902 4092 5.660460 TCATTAAATGAGAGCTTCACGCTA 58.340 37.500 0.00 0.00 41.25 4.26
3904 4094 6.593770 TCATTAAATGAGAGCTTCACGCTAAA 59.406 34.615 0.00 0.00 41.25 1.85
3914 4104 4.168760 GCTTCACGCTAAAATTGCTCAAT 58.831 39.130 0.00 0.00 35.14 2.57
3915 4105 4.622740 GCTTCACGCTAAAATTGCTCAATT 59.377 37.500 2.24 2.24 37.89 2.32
3918 4108 4.922692 TCACGCTAAAATTGCTCAATTTGG 59.077 37.500 18.01 14.91 46.76 3.28
3920 4110 3.062504 CGCTAAAATTGCTCAATTTGGGC 59.937 43.478 14.48 14.48 46.76 5.36
3921 4111 4.256110 GCTAAAATTGCTCAATTTGGGCT 58.744 39.130 21.27 4.14 46.08 5.19
3922 4112 4.696877 GCTAAAATTGCTCAATTTGGGCTT 59.303 37.500 21.27 10.21 46.08 4.35
3923 4113 5.181811 GCTAAAATTGCTCAATTTGGGCTTT 59.818 36.000 21.27 15.34 46.08 3.51
3924 4114 5.441709 AAAATTGCTCAATTTGGGCTTTG 57.558 34.783 21.27 0.00 46.08 2.77
3925 4115 3.775261 ATTGCTCAATTTGGGCTTTGT 57.225 38.095 21.27 3.10 46.08 2.83
3927 4117 3.110447 TGCTCAATTTGGGCTTTGTTC 57.890 42.857 21.27 0.00 46.08 3.18
3928 4118 2.061028 GCTCAATTTGGGCTTTGTTCG 58.939 47.619 14.09 0.00 41.63 3.95
3929 4119 2.545742 GCTCAATTTGGGCTTTGTTCGT 60.546 45.455 14.09 0.00 41.63 3.85
3930 4120 3.716601 CTCAATTTGGGCTTTGTTCGTT 58.283 40.909 0.00 0.00 0.00 3.85
3932 4122 3.868077 TCAATTTGGGCTTTGTTCGTTTG 59.132 39.130 0.00 0.00 0.00 2.93
3934 4124 2.285827 TTGGGCTTTGTTCGTTTGTG 57.714 45.000 0.00 0.00 0.00 3.33
3935 4125 1.178276 TGGGCTTTGTTCGTTTGTGT 58.822 45.000 0.00 0.00 0.00 3.72
3936 4126 1.546476 TGGGCTTTGTTCGTTTGTGTT 59.454 42.857 0.00 0.00 0.00 3.32
3938 4128 3.192844 TGGGCTTTGTTCGTTTGTGTTAA 59.807 39.130 0.00 0.00 0.00 2.01
3946 4136 2.741122 CGTTTGTGTTAAACGGAGCA 57.259 45.000 14.94 0.00 46.39 4.26
3948 4138 3.033185 CGTTTGTGTTAAACGGAGCAAG 58.967 45.455 14.94 0.00 46.39 4.01
3950 4140 4.664188 GTTTGTGTTAAACGGAGCAAGAA 58.336 39.130 0.00 0.00 0.00 2.52
3951 4141 5.278604 GTTTGTGTTAAACGGAGCAAGAAT 58.721 37.500 0.00 0.00 0.00 2.40
4001 4191 4.680171 GTGCTTCACGTTAAGGCTAAAT 57.320 40.909 11.27 0.00 0.00 1.40
4002 4192 4.403453 GTGCTTCACGTTAAGGCTAAATG 58.597 43.478 11.27 0.00 0.00 2.32
4003 4193 4.069304 TGCTTCACGTTAAGGCTAAATGT 58.931 39.130 11.27 0.00 0.00 2.71
4004 4194 4.517453 TGCTTCACGTTAAGGCTAAATGTT 59.483 37.500 11.27 0.00 0.00 2.71
4005 4195 4.851558 GCTTCACGTTAAGGCTAAATGTTG 59.148 41.667 11.27 0.00 0.00 3.33
4008 4198 3.754323 CACGTTAAGGCTAAATGTTGGGA 59.246 43.478 0.00 0.00 0.00 4.37
4009 4199 4.007659 ACGTTAAGGCTAAATGTTGGGAG 58.992 43.478 0.00 0.00 0.00 4.30
4010 4200 4.007659 CGTTAAGGCTAAATGTTGGGAGT 58.992 43.478 0.00 0.00 0.00 3.85
4011 4201 4.142687 CGTTAAGGCTAAATGTTGGGAGTG 60.143 45.833 0.00 0.00 0.00 3.51
4012 4202 2.514458 AGGCTAAATGTTGGGAGTGG 57.486 50.000 0.00 0.00 0.00 4.00
4013 4203 1.710809 AGGCTAAATGTTGGGAGTGGT 59.289 47.619 0.00 0.00 0.00 4.16
4014 4204 2.110011 AGGCTAAATGTTGGGAGTGGTT 59.890 45.455 0.00 0.00 0.00 3.67
4015 4205 3.332485 AGGCTAAATGTTGGGAGTGGTTA 59.668 43.478 0.00 0.00 0.00 2.85
4016 4206 4.083565 GGCTAAATGTTGGGAGTGGTTAA 58.916 43.478 0.00 0.00 0.00 2.01
4018 4208 4.380550 GCTAAATGTTGGGAGTGGTTAAGC 60.381 45.833 0.00 0.00 0.00 3.09
4019 4209 3.525800 AATGTTGGGAGTGGTTAAGCT 57.474 42.857 6.19 0.00 0.00 3.74
4020 4210 3.525800 ATGTTGGGAGTGGTTAAGCTT 57.474 42.857 3.48 3.48 0.00 3.74
4021 4211 4.650972 ATGTTGGGAGTGGTTAAGCTTA 57.349 40.909 0.86 0.86 0.00 3.09
4022 4212 4.015872 TGTTGGGAGTGGTTAAGCTTAG 57.984 45.455 6.24 0.00 0.00 2.18
4023 4213 3.649023 TGTTGGGAGTGGTTAAGCTTAGA 59.351 43.478 6.24 0.00 0.00 2.10
4024 4214 4.103469 TGTTGGGAGTGGTTAAGCTTAGAA 59.897 41.667 6.24 0.00 0.00 2.10
4026 4216 4.906618 TGGGAGTGGTTAAGCTTAGAAAG 58.093 43.478 6.24 0.00 0.00 2.62
4040 4230 4.836825 CTTAGAAAGCTTGACATCTCCCA 58.163 43.478 0.00 0.00 0.00 4.37
4041 4231 3.795688 AGAAAGCTTGACATCTCCCAA 57.204 42.857 0.00 0.00 0.00 4.12
4042 4232 4.313020 AGAAAGCTTGACATCTCCCAAT 57.687 40.909 0.00 0.00 0.00 3.16
4043 4233 4.015084 AGAAAGCTTGACATCTCCCAATG 58.985 43.478 0.00 0.00 0.00 2.82
4044 4234 3.726557 AAGCTTGACATCTCCCAATGA 57.273 42.857 0.00 0.00 0.00 2.57
4045 4235 3.278668 AGCTTGACATCTCCCAATGAG 57.721 47.619 0.00 0.00 42.90 2.90
4046 4236 1.674962 GCTTGACATCTCCCAATGAGC 59.325 52.381 0.00 0.00 41.18 4.26
4047 4237 1.938577 CTTGACATCTCCCAATGAGCG 59.061 52.381 0.00 0.00 41.18 5.03
4048 4238 0.178767 TGACATCTCCCAATGAGCGG 59.821 55.000 0.00 0.00 41.18 5.52
4049 4239 0.533755 GACATCTCCCAATGAGCGGG 60.534 60.000 0.00 0.00 46.03 6.13
4050 4240 1.895707 CATCTCCCAATGAGCGGGC 60.896 63.158 0.00 0.00 44.11 6.13
4051 4241 2.377810 ATCTCCCAATGAGCGGGCA 61.378 57.895 0.00 0.00 44.11 5.36
4052 4242 2.335092 ATCTCCCAATGAGCGGGCAG 62.335 60.000 0.00 0.00 44.11 4.85
4053 4243 3.329889 TCCCAATGAGCGGGCAGT 61.330 61.111 0.00 0.00 44.11 4.40
4054 4244 3.136123 CCCAATGAGCGGGCAGTG 61.136 66.667 0.00 0.00 36.72 3.66
4055 4245 3.136123 CCAATGAGCGGGCAGTGG 61.136 66.667 8.81 8.81 45.98 4.00
4056 4246 2.046023 CAATGAGCGGGCAGTGGA 60.046 61.111 0.00 0.00 30.79 4.02
4057 4247 2.110967 CAATGAGCGGGCAGTGGAG 61.111 63.158 0.00 0.00 30.79 3.86
4058 4248 3.335356 AATGAGCGGGCAGTGGAGG 62.335 63.158 0.00 0.00 0.00 4.30
4074 4264 2.035530 GAGGCCTCCATCAAAGACTG 57.964 55.000 23.19 0.00 0.00 3.51
4075 4265 0.622665 AGGCCTCCATCAAAGACTGG 59.377 55.000 0.00 0.00 0.00 4.00
4076 4266 0.329596 GGCCTCCATCAAAGACTGGT 59.670 55.000 0.00 0.00 34.03 4.00
4077 4267 1.457346 GCCTCCATCAAAGACTGGTG 58.543 55.000 0.00 0.00 35.74 4.17
4084 4274 4.691860 CATCAAAGACTGGTGGATCAAC 57.308 45.455 0.00 0.00 31.90 3.18
4085 4275 3.855255 TCAAAGACTGGTGGATCAACA 57.145 42.857 1.86 0.00 0.00 3.33
4086 4276 4.371624 TCAAAGACTGGTGGATCAACAT 57.628 40.909 1.86 0.00 27.67 2.71
4087 4277 4.074259 TCAAAGACTGGTGGATCAACATG 58.926 43.478 1.86 0.00 27.67 3.21
4088 4278 2.119801 AGACTGGTGGATCAACATGC 57.880 50.000 1.86 0.00 27.67 4.06
4089 4279 1.632409 AGACTGGTGGATCAACATGCT 59.368 47.619 1.86 0.00 27.67 3.79
4090 4280 2.840038 AGACTGGTGGATCAACATGCTA 59.160 45.455 1.86 0.00 27.67 3.49
4091 4281 3.118482 AGACTGGTGGATCAACATGCTAG 60.118 47.826 1.86 0.00 27.67 3.42
4092 4282 2.092753 ACTGGTGGATCAACATGCTAGG 60.093 50.000 1.86 0.00 27.67 3.02
4093 4283 1.212688 TGGTGGATCAACATGCTAGGG 59.787 52.381 1.86 0.00 0.00 3.53
4094 4284 1.312815 GTGGATCAACATGCTAGGGC 58.687 55.000 0.00 0.00 39.26 5.19
4095 4285 0.183492 TGGATCAACATGCTAGGGCC 59.817 55.000 0.00 0.00 37.74 5.80
4096 4286 0.475906 GGATCAACATGCTAGGGCCT 59.524 55.000 12.58 12.58 37.74 5.19
4097 4287 1.699634 GGATCAACATGCTAGGGCCTA 59.300 52.381 13.73 13.73 37.74 3.93
4098 4288 2.289945 GGATCAACATGCTAGGGCCTAG 60.290 54.545 32.12 32.12 37.16 3.02
4099 4289 1.131638 TCAACATGCTAGGGCCTAGG 58.868 55.000 35.37 23.70 34.88 3.02
4115 4305 2.627945 CTAGGGCACGCAACAAATCTA 58.372 47.619 0.00 0.00 0.00 1.98
4116 4306 1.165270 AGGGCACGCAACAAATCTAC 58.835 50.000 0.00 0.00 0.00 2.59
4117 4307 1.165270 GGGCACGCAACAAATCTACT 58.835 50.000 0.00 0.00 0.00 2.57
4118 4308 1.130561 GGGCACGCAACAAATCTACTC 59.869 52.381 0.00 0.00 0.00 2.59
4119 4309 1.804151 GGCACGCAACAAATCTACTCA 59.196 47.619 0.00 0.00 0.00 3.41
4120 4310 2.159653 GGCACGCAACAAATCTACTCAG 60.160 50.000 0.00 0.00 0.00 3.35
4121 4311 2.726066 GCACGCAACAAATCTACTCAGC 60.726 50.000 0.00 0.00 0.00 4.26
4122 4312 2.076863 ACGCAACAAATCTACTCAGCC 58.923 47.619 0.00 0.00 0.00 4.85
4123 4313 1.061131 CGCAACAAATCTACTCAGCCG 59.939 52.381 0.00 0.00 0.00 5.52
4124 4314 2.346803 GCAACAAATCTACTCAGCCGA 58.653 47.619 0.00 0.00 0.00 5.54
4125 4315 2.349886 GCAACAAATCTACTCAGCCGAG 59.650 50.000 0.00 0.00 45.49 4.63
4126 4316 3.849911 CAACAAATCTACTCAGCCGAGA 58.150 45.455 3.36 0.00 42.34 4.04
4127 4317 4.245660 CAACAAATCTACTCAGCCGAGAA 58.754 43.478 3.36 0.00 42.34 2.87
4128 4318 4.744795 ACAAATCTACTCAGCCGAGAAT 57.255 40.909 3.36 0.00 42.34 2.40
4129 4319 4.688021 ACAAATCTACTCAGCCGAGAATC 58.312 43.478 3.36 0.00 42.34 2.52
4150 4340 2.469886 CGCCTTCGCCAAGTTTTAAAAC 59.530 45.455 21.06 21.06 39.17 2.43
4158 4348 3.638484 CCAAGTTTTAAAACGAGGCCAG 58.362 45.455 22.95 0.00 43.51 4.85
4222 4412 4.891756 CCATGCCAGGAGAGTATTCATTTT 59.108 41.667 0.00 0.00 0.00 1.82
4223 4413 5.361857 CCATGCCAGGAGAGTATTCATTTTT 59.638 40.000 0.00 0.00 0.00 1.94
4224 4414 5.902613 TGCCAGGAGAGTATTCATTTTTG 57.097 39.130 0.00 0.00 0.00 2.44
4225 4415 4.158394 TGCCAGGAGAGTATTCATTTTTGC 59.842 41.667 0.00 0.00 0.00 3.68
4226 4416 4.731773 GCCAGGAGAGTATTCATTTTTGCG 60.732 45.833 0.00 0.00 0.00 4.85
4227 4417 4.635765 CCAGGAGAGTATTCATTTTTGCGA 59.364 41.667 0.00 0.00 0.00 5.10
4228 4418 5.123820 CCAGGAGAGTATTCATTTTTGCGAA 59.876 40.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.867174 GGAATACATACTTTTGTTGGTTGGC 59.133 40.000 0.00 0.00 0.00 4.52
48 49 8.520351 GCTAAAGGAATACATACTTTTGTTGGT 58.480 33.333 0.00 0.00 36.07 3.67
105 106 3.861276 AAATGAGCACCATGTCACATG 57.139 42.857 11.18 11.18 35.24 3.21
130 131 3.438781 TCATGTGCTTCCGTGTAATTTCC 59.561 43.478 0.00 0.00 0.00 3.13
172 173 3.232279 GGTGGGACTCCATAGCTCT 57.768 57.895 0.00 0.00 46.09 4.09
189 190 4.039004 TGTTTTCTGGATGGACAATTGTGG 59.961 41.667 17.58 0.00 0.00 4.17
190 191 5.199024 TGTTTTCTGGATGGACAATTGTG 57.801 39.130 17.58 0.00 0.00 3.33
191 192 4.281688 CCTGTTTTCTGGATGGACAATTGT 59.718 41.667 11.78 11.78 40.71 2.71
206 207 6.430000 TCTTATCTTTGTGCCTACCTGTTTTC 59.570 38.462 0.00 0.00 0.00 2.29
214 215 7.982354 ACTGAGTAATCTTATCTTTGTGCCTAC 59.018 37.037 0.00 0.00 0.00 3.18
334 353 2.561037 CCTTGCGTTTGGTGGACCC 61.561 63.158 0.00 0.00 34.29 4.46
530 549 4.368808 CGCGTGCTGTTGGTTCGG 62.369 66.667 0.00 0.00 0.00 4.30
532 551 4.025401 CCCGCGTGCTGTTGGTTC 62.025 66.667 4.92 0.00 0.00 3.62
635 657 4.586235 ACCAAACCGGCAGCTGCT 62.586 61.111 35.82 16.13 41.70 4.24
708 733 4.637387 ATCCTTCCTTCTATGCCATCAG 57.363 45.455 0.00 0.00 0.00 2.90
790 815 7.410174 TCTTAAATTCTGGGCCTCATTTTCTA 58.590 34.615 4.53 0.00 0.00 2.10
791 816 6.256053 TCTTAAATTCTGGGCCTCATTTTCT 58.744 36.000 4.53 0.00 0.00 2.52
798 840 2.302260 GCCTCTTAAATTCTGGGCCTC 58.698 52.381 4.53 0.00 34.19 4.70
818 860 2.223021 CGTCTGCAACATTCATAACGGG 60.223 50.000 0.00 0.00 0.00 5.28
822 864 2.670905 CGGTCGTCTGCAACATTCATAA 59.329 45.455 0.00 0.00 0.00 1.90
823 865 2.094442 TCGGTCGTCTGCAACATTCATA 60.094 45.455 0.00 0.00 0.00 2.15
840 887 1.077501 CAAGACATGGGCCATCGGT 60.078 57.895 18.16 13.08 0.00 4.69
895 946 2.374170 GAGGGAGGAGAGAGGTAGGTAG 59.626 59.091 0.00 0.00 0.00 3.18
1209 1265 1.365633 GATAGCGTGGAGGCTCCTG 59.634 63.158 32.28 24.78 43.54 3.86
1395 1451 2.292292 CCAACCAAACTAACCACTTCGG 59.708 50.000 0.00 0.00 42.50 4.30
1447 1503 1.818674 CCAACATTTCTACCCACAGCC 59.181 52.381 0.00 0.00 0.00 4.85
1509 1565 8.143835 CAGATTGTAAATCATACCCCAAATTCC 58.856 37.037 3.03 0.00 0.00 3.01
1578 1634 3.258372 GGTGATTTCCCTCTTCCAAAACC 59.742 47.826 0.00 0.00 0.00 3.27
1629 1685 2.036475 CCAAGGCATACTAGCGATGTCT 59.964 50.000 6.53 6.53 40.98 3.41
1637 1693 4.763793 CCAAATCATCCCAAGGCATACTAG 59.236 45.833 0.00 0.00 0.00 2.57
1653 1709 2.127271 ACATCGACATGGCCAAATCA 57.873 45.000 10.96 1.95 33.82 2.57
1680 1736 5.234543 GCTGATTAAAGACCTATCGTCAACC 59.765 44.000 0.00 0.00 44.66 3.77
1682 1738 5.972935 TGCTGATTAAAGACCTATCGTCAA 58.027 37.500 0.00 0.00 44.66 3.18
1690 1774 6.488715 AGAAATCCTTGCTGATTAAAGACCT 58.511 36.000 0.00 0.00 33.91 3.85
1709 1793 7.547370 CGAGATGAGTTTAACCTTCAGAGAAAT 59.453 37.037 0.00 0.00 0.00 2.17
1751 1862 6.851609 TCGAGGTTGATTGGAAAACATATTG 58.148 36.000 0.00 0.00 0.00 1.90
1961 2072 7.093727 TGGAAACACAAATCTTCTAAACAACCA 60.094 33.333 0.00 0.00 33.40 3.67
1963 2074 8.696410 TTGGAAACACAAATCTTCTAAACAAC 57.304 30.769 0.00 0.00 42.67 3.32
1980 2091 8.303156 CAGACACAAATATAACCATTGGAAACA 58.697 33.333 10.37 0.00 39.83 2.83
1989 2100 2.680841 GCGGCAGACACAAATATAACCA 59.319 45.455 0.00 0.00 0.00 3.67
2017 2128 6.706270 ACAAGGATATAAATGTCCATGTCGAC 59.294 38.462 9.11 9.11 43.41 4.20
2032 2143 9.502091 AAGCGCATCTTATTTAACAAGGATATA 57.498 29.630 11.47 0.00 32.10 0.86
2046 2158 1.667724 GTGCAGACAAGCGCATCTTAT 59.332 47.619 11.47 0.00 44.15 1.73
2054 2166 1.568612 AATCACGGTGCAGACAAGCG 61.569 55.000 2.51 0.00 43.79 4.68
2137 2249 3.812053 CCTGCTGAGAGGCAATAACATAC 59.188 47.826 0.00 0.00 41.94 2.39
2196 2308 5.339008 TCTAGCGGTCTATTCACATTTGT 57.661 39.130 0.00 0.00 0.00 2.83
2203 2315 6.929049 CCAATTGTAATCTAGCGGTCTATTCA 59.071 38.462 4.43 0.00 0.00 2.57
2220 2332 4.460263 GGTGATAGATGTGCCCAATTGTA 58.540 43.478 4.43 0.00 0.00 2.41
2345 2474 5.353111 TGCATGCATTATGAAATTCCACAG 58.647 37.500 18.46 0.00 39.21 3.66
2403 2532 1.909700 TCAACCAGGAACTTGCATCC 58.090 50.000 0.00 0.00 34.60 3.51
2461 2590 7.885297 TCTGCAAAAGCTTGACAAATTAGTAT 58.115 30.769 0.00 0.00 34.14 2.12
2463 2592 6.147864 TCTGCAAAAGCTTGACAAATTAGT 57.852 33.333 0.00 0.00 34.14 2.24
2521 2650 4.286707 ACTAACTTGGTGCTTTCCCTTTT 58.713 39.130 0.00 0.00 0.00 2.27
2548 2677 0.463116 ACTCGCCCAAACGTTCAGTT 60.463 50.000 0.00 0.00 46.76 3.16
2643 2773 5.991328 AGCATTAATCATGGTACTTCACG 57.009 39.130 0.00 0.00 42.07 4.35
2644 2774 7.320443 TCAAGCATTAATCATGGTACTTCAC 57.680 36.000 0.00 0.00 43.13 3.18
2695 2825 7.941238 AGCCTGCAAGAACATTGAGTATAATAT 59.059 33.333 0.00 0.00 34.07 1.28
2767 2897 2.984471 GCATGATGTGACTTTGTTGCAG 59.016 45.455 0.00 0.00 0.00 4.41
2918 3048 2.015736 ACTGTTAGCGCCAGAATGAG 57.984 50.000 17.44 6.87 39.69 2.90
2962 3092 5.510430 AGAAACCATCCACCCTAAGAAATC 58.490 41.667 0.00 0.00 0.00 2.17
3098 3228 4.119862 TGAACTTTGTTCTCCAGAAGACG 58.880 43.478 11.06 0.00 34.27 4.18
3192 3322 6.981762 AAGAACACATCAAGATGACTCATC 57.018 37.500 16.39 10.65 41.20 2.92
3204 3334 5.592282 TCAACTTTTGGCTAAGAACACATCA 59.408 36.000 6.89 0.00 0.00 3.07
3269 3399 8.405531 TGGCAGATAAGATGCTAACAAAAATAC 58.594 33.333 0.00 0.00 43.35 1.89
3272 3402 6.832520 TGGCAGATAAGATGCTAACAAAAA 57.167 33.333 0.00 0.00 43.35 1.94
3506 3636 1.072489 TGAACCGGGCAACAATGTAGA 59.928 47.619 6.32 0.00 39.74 2.59
3507 3637 1.529226 TGAACCGGGCAACAATGTAG 58.471 50.000 6.32 0.00 39.74 2.74
3521 3684 8.141268 TGAAACCAGAAAACAATCTAATGAACC 58.859 33.333 0.00 0.00 0.00 3.62
3565 3736 5.679734 ATCACATGATCCGCAATTAAGTC 57.320 39.130 0.00 0.00 0.00 3.01
3567 3738 6.267817 ACAAATCACATGATCCGCAATTAAG 58.732 36.000 0.00 0.00 32.75 1.85
3568 3739 6.206395 ACAAATCACATGATCCGCAATTAA 57.794 33.333 0.00 0.00 32.75 1.40
3619 3790 2.176889 TCCTCACCTGGTTAGCTGTAC 58.823 52.381 0.00 0.00 0.00 2.90
3629 3801 2.875296 TCCAACAAAATCCTCACCTGG 58.125 47.619 0.00 0.00 0.00 4.45
3700 3872 4.383649 CGAGGTTTTGATTTGCATTCACAG 59.616 41.667 0.00 0.00 0.00 3.66
3703 3875 4.278170 AGTCGAGGTTTTGATTTGCATTCA 59.722 37.500 0.00 0.00 0.00 2.57
3704 3876 4.798574 AGTCGAGGTTTTGATTTGCATTC 58.201 39.130 0.00 0.00 0.00 2.67
3708 3880 3.896648 TGAGTCGAGGTTTTGATTTGC 57.103 42.857 0.00 0.00 0.00 3.68
3720 3892 6.420903 TGACAAAAAGTAGTTCATGAGTCGAG 59.579 38.462 0.00 0.00 0.00 4.04
3723 3912 6.483640 ACCTGACAAAAAGTAGTTCATGAGTC 59.516 38.462 0.00 0.00 0.00 3.36
3726 3915 7.639113 AAACCTGACAAAAAGTAGTTCATGA 57.361 32.000 0.00 0.00 0.00 3.07
3729 3918 7.222000 ACAAAACCTGACAAAAAGTAGTTCA 57.778 32.000 0.00 0.00 0.00 3.18
3736 3925 5.418676 ACATGGACAAAACCTGACAAAAAG 58.581 37.500 0.00 0.00 0.00 2.27
3763 3953 5.479027 ACCTATGAAAACGCCCAAGTAAAAT 59.521 36.000 0.00 0.00 0.00 1.82
3767 3957 3.706600 ACCTATGAAAACGCCCAAGTA 57.293 42.857 0.00 0.00 0.00 2.24
3793 3983 4.279420 CCTAATGCAAAAGGCCTTATCCTC 59.721 45.833 20.84 7.28 43.89 3.71
3819 4009 1.040646 AACTTCAGCCGACACTCAGA 58.959 50.000 0.00 0.00 0.00 3.27
3826 4016 0.514691 CAAGCTCAACTTCAGCCGAC 59.485 55.000 0.00 0.00 36.04 4.79
3828 4018 1.208614 GCAAGCTCAACTTCAGCCG 59.791 57.895 0.00 0.00 36.04 5.52
3860 4050 3.786553 TGAACTAGGTACCATGTCCACT 58.213 45.455 15.94 0.00 0.00 4.00
3863 4053 7.990886 TCATTTAATGAACTAGGTACCATGTCC 59.009 37.037 15.94 0.21 36.11 4.02
3864 4054 8.958119 TCATTTAATGAACTAGGTACCATGTC 57.042 34.615 15.94 6.32 36.11 3.06
3866 4056 9.265901 CTCTCATTTAATGAACTAGGTACCATG 57.734 37.037 15.94 8.66 39.11 3.66
3869 4059 7.501844 AGCTCTCATTTAATGAACTAGGTACC 58.498 38.462 2.73 2.73 39.11 3.34
3870 4060 8.950208 AAGCTCTCATTTAATGAACTAGGTAC 57.050 34.615 9.05 0.00 39.11 3.34
3871 4061 8.758829 TGAAGCTCTCATTTAATGAACTAGGTA 58.241 33.333 9.05 0.00 39.11 3.08
3872 4062 7.550906 GTGAAGCTCTCATTTAATGAACTAGGT 59.449 37.037 9.05 9.13 39.11 3.08
3873 4063 7.254252 CGTGAAGCTCTCATTTAATGAACTAGG 60.254 40.741 9.05 0.00 39.11 3.02
3874 4064 7.616673 CGTGAAGCTCTCATTTAATGAACTAG 58.383 38.462 9.05 7.87 39.11 2.57
3875 4065 6.036083 GCGTGAAGCTCTCATTTAATGAACTA 59.964 38.462 9.05 0.00 44.04 2.24
3876 4066 5.163814 GCGTGAAGCTCTCATTTAATGAACT 60.164 40.000 9.05 4.38 44.04 3.01
3877 4067 5.024555 GCGTGAAGCTCTCATTTAATGAAC 58.975 41.667 9.05 1.96 44.04 3.18
3889 4079 9.387405 AATTGAGCAATTTTAGCGTGAAGCTCT 62.387 37.037 11.67 0.00 44.86 4.09
3890 4080 7.329961 AATTGAGCAATTTTAGCGTGAAGCTC 61.330 38.462 0.00 0.00 44.86 4.09
3892 4082 4.622740 AATTGAGCAATTTTAGCGTGAAGC 59.377 37.500 2.74 0.00 41.15 3.86
3893 4083 6.400303 CCAAATTGAGCAATTTTAGCGTGAAG 60.400 38.462 16.21 4.79 45.67 3.02
3894 4084 5.404968 CCAAATTGAGCAATTTTAGCGTGAA 59.595 36.000 16.21 0.00 45.67 3.18
3896 4086 4.091800 CCCAAATTGAGCAATTTTAGCGTG 59.908 41.667 16.21 7.11 45.67 5.34
3897 4087 4.244862 CCCAAATTGAGCAATTTTAGCGT 58.755 39.130 16.21 0.00 45.67 5.07
3898 4088 3.062504 GCCCAAATTGAGCAATTTTAGCG 59.937 43.478 16.21 7.36 45.67 4.26
3899 4089 4.256110 AGCCCAAATTGAGCAATTTTAGC 58.744 39.130 20.93 20.93 45.67 3.09
3900 4090 6.205270 ACAAAGCCCAAATTGAGCAATTTTAG 59.795 34.615 16.21 12.17 45.67 1.85
3901 4091 6.060788 ACAAAGCCCAAATTGAGCAATTTTA 58.939 32.000 16.21 0.00 45.67 1.52
3902 4092 4.888823 ACAAAGCCCAAATTGAGCAATTTT 59.111 33.333 16.21 2.50 45.67 1.82
3904 4094 4.089408 ACAAAGCCCAAATTGAGCAATT 57.911 36.364 1.68 2.74 42.35 2.32
3906 4096 3.465871 GAACAAAGCCCAAATTGAGCAA 58.534 40.909 1.68 0.00 0.00 3.91
3908 4098 2.061028 CGAACAAAGCCCAAATTGAGC 58.939 47.619 0.00 0.00 0.00 4.26
3909 4099 3.369546 ACGAACAAAGCCCAAATTGAG 57.630 42.857 0.00 0.00 0.00 3.02
3910 4100 3.810310 AACGAACAAAGCCCAAATTGA 57.190 38.095 0.00 0.00 0.00 2.57
3914 4104 2.028930 ACACAAACGAACAAAGCCCAAA 60.029 40.909 0.00 0.00 0.00 3.28
3915 4105 1.546476 ACACAAACGAACAAAGCCCAA 59.454 42.857 0.00 0.00 0.00 4.12
3918 4108 5.121071 GTTTAACACAAACGAACAAAGCC 57.879 39.130 0.00 0.00 0.00 4.35
3928 4118 4.281525 TCTTGCTCCGTTTAACACAAAC 57.718 40.909 0.00 0.00 0.00 2.93
3929 4119 4.966965 TTCTTGCTCCGTTTAACACAAA 57.033 36.364 0.00 0.00 0.00 2.83
3930 4120 5.066634 TCAATTCTTGCTCCGTTTAACACAA 59.933 36.000 0.00 0.00 0.00 3.33
3932 4122 5.103290 TCAATTCTTGCTCCGTTTAACAC 57.897 39.130 0.00 0.00 0.00 3.32
3934 4124 5.095490 CCATCAATTCTTGCTCCGTTTAAC 58.905 41.667 0.00 0.00 0.00 2.01
3935 4125 4.157656 CCCATCAATTCTTGCTCCGTTTAA 59.842 41.667 0.00 0.00 0.00 1.52
3936 4126 3.694072 CCCATCAATTCTTGCTCCGTTTA 59.306 43.478 0.00 0.00 0.00 2.01
3938 4128 2.094675 CCCATCAATTCTTGCTCCGTT 58.905 47.619 0.00 0.00 0.00 4.44
3941 4131 2.726821 TGACCCATCAATTCTTGCTCC 58.273 47.619 0.00 0.00 0.00 4.70
3942 4132 3.317430 GGATGACCCATCAATTCTTGCTC 59.683 47.826 8.91 0.00 42.13 4.26
3943 4133 3.053095 AGGATGACCCATCAATTCTTGCT 60.053 43.478 8.91 0.00 42.13 3.91
3944 4134 3.294214 AGGATGACCCATCAATTCTTGC 58.706 45.455 8.91 0.00 42.13 4.01
3945 4135 5.927281 AAAGGATGACCCATCAATTCTTG 57.073 39.130 8.91 0.00 42.13 3.02
3946 4136 6.940430 AAAAAGGATGACCCATCAATTCTT 57.060 33.333 8.91 1.17 42.13 2.52
3967 4157 2.863137 GTGAAGCACGGCATTTGAAAAA 59.137 40.909 0.00 0.00 0.00 1.94
3968 4158 2.468831 GTGAAGCACGGCATTTGAAAA 58.531 42.857 0.00 0.00 0.00 2.29
3980 4170 4.083484 ACATTTAGCCTTAACGTGAAGCAC 60.083 41.667 7.19 1.61 0.00 4.40
3982 4172 4.680171 ACATTTAGCCTTAACGTGAAGC 57.320 40.909 7.19 3.27 0.00 3.86
3983 4173 5.390613 CCAACATTTAGCCTTAACGTGAAG 58.609 41.667 5.59 5.59 0.00 3.02
3984 4174 4.216687 CCCAACATTTAGCCTTAACGTGAA 59.783 41.667 0.00 0.00 0.00 3.18
3985 4175 3.754323 CCCAACATTTAGCCTTAACGTGA 59.246 43.478 0.00 0.00 0.00 4.35
3986 4176 3.754323 TCCCAACATTTAGCCTTAACGTG 59.246 43.478 0.00 0.00 0.00 4.49
3989 4179 4.157840 CCACTCCCAACATTTAGCCTTAAC 59.842 45.833 0.00 0.00 0.00 2.01
3991 4181 3.332485 ACCACTCCCAACATTTAGCCTTA 59.668 43.478 0.00 0.00 0.00 2.69
3992 4182 2.110011 ACCACTCCCAACATTTAGCCTT 59.890 45.455 0.00 0.00 0.00 4.35
3994 4184 2.215942 ACCACTCCCAACATTTAGCC 57.784 50.000 0.00 0.00 0.00 3.93
3995 4185 4.380550 GCTTAACCACTCCCAACATTTAGC 60.381 45.833 0.00 0.00 0.00 3.09
3996 4186 5.010282 AGCTTAACCACTCCCAACATTTAG 58.990 41.667 0.00 0.00 0.00 1.85
3997 4187 4.993028 AGCTTAACCACTCCCAACATTTA 58.007 39.130 0.00 0.00 0.00 1.40
3998 4188 3.844640 AGCTTAACCACTCCCAACATTT 58.155 40.909 0.00 0.00 0.00 2.32
3999 4189 3.525800 AGCTTAACCACTCCCAACATT 57.474 42.857 0.00 0.00 0.00 2.71
4001 4191 3.649023 TCTAAGCTTAACCACTCCCAACA 59.351 43.478 7.74 0.00 0.00 3.33
4002 4192 4.281898 TCTAAGCTTAACCACTCCCAAC 57.718 45.455 7.74 0.00 0.00 3.77
4003 4193 4.986054 TTCTAAGCTTAACCACTCCCAA 57.014 40.909 7.74 0.00 0.00 4.12
4004 4194 4.906618 CTTTCTAAGCTTAACCACTCCCA 58.093 43.478 7.74 0.00 0.00 4.37
4018 4208 4.836825 TGGGAGATGTCAAGCTTTCTAAG 58.163 43.478 0.00 0.00 0.00 2.18
4019 4209 4.908601 TGGGAGATGTCAAGCTTTCTAA 57.091 40.909 0.00 0.00 0.00 2.10
4020 4210 4.908601 TTGGGAGATGTCAAGCTTTCTA 57.091 40.909 0.00 0.00 0.00 2.10
4021 4211 3.795688 TTGGGAGATGTCAAGCTTTCT 57.204 42.857 0.00 0.00 0.00 2.52
4022 4212 4.012374 TCATTGGGAGATGTCAAGCTTTC 58.988 43.478 0.00 0.00 0.00 2.62
4023 4213 4.038271 TCATTGGGAGATGTCAAGCTTT 57.962 40.909 0.00 0.00 0.00 3.51
4024 4214 3.726557 TCATTGGGAGATGTCAAGCTT 57.273 42.857 0.00 0.00 0.00 3.74
4038 4228 3.136123 CCACTGCCCGCTCATTGG 61.136 66.667 0.00 0.00 31.80 3.16
4039 4229 2.046023 TCCACTGCCCGCTCATTG 60.046 61.111 0.00 0.00 0.00 2.82
4040 4230 2.270205 CTCCACTGCCCGCTCATT 59.730 61.111 0.00 0.00 0.00 2.57
4041 4231 3.790437 CCTCCACTGCCCGCTCAT 61.790 66.667 0.00 0.00 0.00 2.90
4055 4245 1.407989 CCAGTCTTTGATGGAGGCCTC 60.408 57.143 25.59 25.59 39.02 4.70
4056 4246 0.622665 CCAGTCTTTGATGGAGGCCT 59.377 55.000 3.86 3.86 39.02 5.19
4057 4247 0.329596 ACCAGTCTTTGATGGAGGCC 59.670 55.000 0.00 0.00 39.02 5.19
4058 4248 1.457346 CACCAGTCTTTGATGGAGGC 58.543 55.000 0.00 0.00 39.02 4.70
4059 4249 1.630369 TCCACCAGTCTTTGATGGAGG 59.370 52.381 1.70 1.70 45.66 4.30
4060 4250 3.054875 TGATCCACCAGTCTTTGATGGAG 60.055 47.826 0.00 0.00 42.56 3.86
4061 4251 2.912295 TGATCCACCAGTCTTTGATGGA 59.088 45.455 0.00 0.00 43.42 3.41
4062 4252 3.354948 TGATCCACCAGTCTTTGATGG 57.645 47.619 0.00 0.00 42.60 3.51
4063 4253 4.074259 TGTTGATCCACCAGTCTTTGATG 58.926 43.478 0.00 0.00 0.00 3.07
4064 4254 4.371624 TGTTGATCCACCAGTCTTTGAT 57.628 40.909 0.00 0.00 0.00 2.57
4065 4255 3.855255 TGTTGATCCACCAGTCTTTGA 57.145 42.857 0.00 0.00 0.00 2.69
4066 4256 3.366679 GCATGTTGATCCACCAGTCTTTG 60.367 47.826 0.00 0.00 0.00 2.77
4067 4257 2.821969 GCATGTTGATCCACCAGTCTTT 59.178 45.455 0.00 0.00 0.00 2.52
4068 4258 2.040813 AGCATGTTGATCCACCAGTCTT 59.959 45.455 0.00 0.00 0.00 3.01
4069 4259 1.632409 AGCATGTTGATCCACCAGTCT 59.368 47.619 0.00 0.00 0.00 3.24
4070 4260 2.119801 AGCATGTTGATCCACCAGTC 57.880 50.000 0.00 0.00 0.00 3.51
4071 4261 2.092753 CCTAGCATGTTGATCCACCAGT 60.093 50.000 0.00 0.00 0.00 4.00
4072 4262 2.569059 CCTAGCATGTTGATCCACCAG 58.431 52.381 0.00 0.00 0.00 4.00
4073 4263 1.212688 CCCTAGCATGTTGATCCACCA 59.787 52.381 0.00 0.00 0.00 4.17
4074 4264 1.972872 CCCTAGCATGTTGATCCACC 58.027 55.000 0.00 0.00 0.00 4.61
4075 4265 1.312815 GCCCTAGCATGTTGATCCAC 58.687 55.000 0.00 0.00 39.53 4.02
4076 4266 0.183492 GGCCCTAGCATGTTGATCCA 59.817 55.000 0.00 0.00 42.56 3.41
4077 4267 0.475906 AGGCCCTAGCATGTTGATCC 59.524 55.000 0.00 0.00 42.56 3.36
4078 4268 2.289945 CCTAGGCCCTAGCATGTTGATC 60.290 54.545 12.62 0.00 42.56 2.92
4079 4269 1.701847 CCTAGGCCCTAGCATGTTGAT 59.298 52.381 12.62 0.00 42.56 2.57
4080 4270 1.131638 CCTAGGCCCTAGCATGTTGA 58.868 55.000 12.62 0.00 42.56 3.18
4081 4271 0.109342 CCCTAGGCCCTAGCATGTTG 59.891 60.000 12.62 0.00 42.56 3.33
4082 4272 1.709994 GCCCTAGGCCCTAGCATGTT 61.710 60.000 12.62 0.00 44.06 2.71
4083 4273 2.150051 GCCCTAGGCCCTAGCATGT 61.150 63.158 12.62 0.00 44.06 3.21
4084 4274 2.753029 GCCCTAGGCCCTAGCATG 59.247 66.667 12.62 4.24 44.06 4.06
4094 4284 0.451783 GATTTGTTGCGTGCCCTAGG 59.548 55.000 0.06 0.06 0.00 3.02
4095 4285 1.453155 AGATTTGTTGCGTGCCCTAG 58.547 50.000 0.00 0.00 0.00 3.02
4096 4286 2.027561 AGTAGATTTGTTGCGTGCCCTA 60.028 45.455 0.00 0.00 0.00 3.53
4097 4287 1.165270 GTAGATTTGTTGCGTGCCCT 58.835 50.000 0.00 0.00 0.00 5.19
4098 4288 1.130561 GAGTAGATTTGTTGCGTGCCC 59.869 52.381 0.00 0.00 0.00 5.36
4099 4289 1.804151 TGAGTAGATTTGTTGCGTGCC 59.196 47.619 0.00 0.00 0.00 5.01
4128 4318 3.792794 GTTTTAAAACTTGGCGAAGGCGA 60.793 43.478 21.27 0.00 45.73 5.54
4129 4319 2.469886 GTTTTAAAACTTGGCGAAGGCG 59.530 45.455 21.27 0.00 45.73 5.52
4130 4320 2.469886 CGTTTTAAAACTTGGCGAAGGC 59.530 45.455 24.57 0.00 44.90 4.35
4131 4321 3.954999 TCGTTTTAAAACTTGGCGAAGG 58.045 40.909 24.57 9.29 36.77 3.46
4158 4348 2.568090 CCGCAATTGTCCAGGTGC 59.432 61.111 7.40 0.00 0.00 5.01
4181 4371 3.241530 TGTCTCCCTGGTGCGCTT 61.242 61.111 9.73 0.00 0.00 4.68
4185 4375 1.377725 CATGGTGTCTCCCTGGTGC 60.378 63.158 0.00 0.00 34.77 5.01
4186 4376 1.377725 GCATGGTGTCTCCCTGGTG 60.378 63.158 0.00 0.00 33.37 4.17
4187 4377 2.606587 GGCATGGTGTCTCCCTGGT 61.607 63.158 0.00 0.00 33.37 4.00
4188 4378 2.273449 GGCATGGTGTCTCCCTGG 59.727 66.667 0.00 0.00 33.37 4.45
4189 4379 1.077930 CTGGCATGGTGTCTCCCTG 60.078 63.158 0.00 0.00 35.40 4.45
4191 4381 2.262774 CTCCTGGCATGGTGTCTCCC 62.263 65.000 0.00 0.00 34.77 4.30
4192 4382 1.222936 CTCCTGGCATGGTGTCTCC 59.777 63.158 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.