Multiple sequence alignment - TraesCS1D01G099900

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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 TraesCS1D01G099900 chr1D 100.000 6614 0 0 1 6614 87097214 87090601 0.000000e+00 12214.0
1 TraesCS1D01G099900 chr1D 100.000 117 0 0 714 830 72884447 72884331 4.020000e-52 217.0
2 TraesCS1D01G099900 chr1D 100.000 117 0 0 714 830 481558212 481558096 4.020000e-52 217.0
3 TraesCS1D01G099900 chr1A 96.771 3531 85 11 2786 6314 82950517 82947014 0.000000e+00 5862.0
4 TraesCS1D01G099900 chr1A 94.678 1954 62 21 831 2769 82952647 82950721 0.000000e+00 2994.0
5 TraesCS1D01G099900 chr1A 90.323 434 29 7 282 712 82953080 82952657 2.080000e-154 556.0
6 TraesCS1D01G099900 chr1A 86.634 202 18 1 6311 6512 82946911 82946719 1.440000e-51 215.0
7 TraesCS1D01G099900 chr1A 94.737 38 2 0 6577 6614 82946713 82946676 7.160000e-05 60.2
8 TraesCS1D01G099900 chr1B 95.446 2723 86 16 3305 6015 140298220 140295524 0.000000e+00 4307.0
9 TraesCS1D01G099900 chr1B 92.445 1959 75 29 831 2769 140300772 140298867 0.000000e+00 2730.0
10 TraesCS1D01G099900 chr1B 92.623 488 25 8 2786 3272 140298698 140298221 0.000000e+00 691.0
11 TraesCS1D01G099900 chr1B 89.716 564 21 16 185 716 140301339 140300781 0.000000e+00 686.0
12 TraesCS1D01G099900 chr1B 95.033 302 14 1 6014 6314 140295442 140295141 2.160000e-129 473.0
13 TraesCS1D01G099900 chr1B 91.640 311 14 4 6311 6614 140295039 140294734 2.850000e-113 420.0
14 TraesCS1D01G099900 chr1B 86.842 114 10 2 31 140 140301443 140301331 9.010000e-24 122.0
15 TraesCS1D01G099900 chr6A 97.674 129 3 0 702 830 188742342 188742470 8.630000e-54 222.0
16 TraesCS1D01G099900 chr7B 100.000 117 0 0 714 830 336360962 336361078 4.020000e-52 217.0
17 TraesCS1D01G099900 chr7B 99.174 121 0 1 711 830 534538237 534538117 4.020000e-52 217.0
18 TraesCS1D01G099900 chr7B 100.000 117 0 0 714 830 733885648 733885532 4.020000e-52 217.0
19 TraesCS1D01G099900 chr4A 100.000 117 0 0 714 830 8592558 8592674 4.020000e-52 217.0
20 TraesCS1D01G099900 chr2D 100.000 117 0 0 714 830 405174463 405174347 4.020000e-52 217.0
21 TraesCS1D01G099900 chr5B 96.875 128 4 0 703 830 399041864 399041991 1.440000e-51 215.0


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 TraesCS1D01G099900 chr1D 87090601 87097214 6613 True 12214.00 12214 100.000000 1 6614 1 chr1D.!!$R2 6613
1 TraesCS1D01G099900 chr1A 82946676 82953080 6404 True 1937.44 5862 92.628600 282 6614 5 chr1A.!!$R1 6332
2 TraesCS1D01G099900 chr1B 140294734 140301443 6709 True 1347.00 4307 91.963571 31 6614 7 chr1B.!!$R1 6583

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
839 878 0.038310 TCAGAGGAGCGAGAAGACCA 59.962 55.000 0.00 0.00 0.00 4.02 F
2048 2105 2.224281 TGTGGGATTGGCAGACGATATC 60.224 50.000 0.00 0.00 0.00 1.63 F
3300 3564 0.865769 GTTGGTGTGTCCTGCGTAAG 59.134 55.000 0.00 0.00 37.07 2.34 F
4026 4298 0.106335 CCTACTCTCCATGCTGCAGG 59.894 60.000 17.12 8.11 0.00 4.85 F
5202 5478 1.622811 CTCTCTGTGTCTGGCCTTCTT 59.377 52.381 3.32 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2291 0.531974 AGTCCACAAACACACGCGAT 60.532 50.000 15.93 0.0 0.00 4.58 R
3683 3947 0.533531 TTGTGTGCTCACTGCTCAGG 60.534 55.000 18.85 0.0 44.44 3.86 R
5262 5538 1.108727 CACTGTTCCCAGCAAAGGCA 61.109 55.000 0.00 0.0 42.81 4.75 R
5318 5594 1.836166 TGATCTCCAGCTTCTTCAGGG 59.164 52.381 0.00 0.0 0.00 4.45 R
6124 6486 0.036577 ACAGCCAGCACTCAGATGTC 60.037 55.000 0.00 0.0 0.00 3.06 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
27 28 7.753659 TCGAAGCTCTGATTACTAGTATATGC 58.246 38.462 2.79 3.57 0.00 3.14
28 29 6.684979 CGAAGCTCTGATTACTAGTATATGCG 59.315 42.308 2.79 0.00 0.00 4.73
29 30 7.413109 CGAAGCTCTGATTACTAGTATATGCGA 60.413 40.741 2.79 0.00 0.00 5.10
60 61 9.303537 GTATGTTTGGTTTGTAAAAGCTTGTAA 57.696 29.630 0.00 0.00 0.00 2.41
75 76 6.111768 AGCTTGTAAAACATCTATTCGCAG 57.888 37.500 0.00 0.00 0.00 5.18
78 79 6.684555 GCTTGTAAAACATCTATTCGCAGAAG 59.315 38.462 0.00 0.00 45.90 2.85
84 85 8.733857 AAAACATCTATTCGCAGAAGAAAAAG 57.266 30.769 0.00 0.00 45.90 2.27
85 86 5.873732 ACATCTATTCGCAGAAGAAAAAGC 58.126 37.500 0.00 0.00 45.90 3.51
86 87 5.645497 ACATCTATTCGCAGAAGAAAAAGCT 59.355 36.000 0.00 0.00 45.90 3.74
87 88 6.150140 ACATCTATTCGCAGAAGAAAAAGCTT 59.850 34.615 0.00 0.00 45.90 3.74
103 108 9.435688 AGAAAAAGCTTGTAAAACATCAAAAGT 57.564 25.926 0.00 0.00 0.00 2.66
109 114 6.761242 GCTTGTAAAACATCAAAAGTTTCCCT 59.239 34.615 0.00 0.00 38.17 4.20
123 128 8.503196 CAAAAGTTTCCCTACAAAATTTATGCC 58.497 33.333 0.00 0.00 33.58 4.40
130 135 5.221342 CCCTACAAAATTTATGCCGGCAATA 60.221 40.000 36.33 21.77 0.00 1.90
131 136 6.454795 CCTACAAAATTTATGCCGGCAATAT 58.545 36.000 36.33 23.03 0.00 1.28
132 137 6.586082 CCTACAAAATTTATGCCGGCAATATC 59.414 38.462 36.33 0.00 0.00 1.63
133 138 5.911752 ACAAAATTTATGCCGGCAATATCA 58.088 33.333 36.33 16.37 0.00 2.15
134 139 6.344500 ACAAAATTTATGCCGGCAATATCAA 58.656 32.000 36.33 20.92 0.00 2.57
135 140 6.820656 ACAAAATTTATGCCGGCAATATCAAA 59.179 30.769 36.33 25.43 0.00 2.69
136 141 7.011295 ACAAAATTTATGCCGGCAATATCAAAG 59.989 33.333 36.33 22.11 0.00 2.77
137 142 3.641437 TTATGCCGGCAATATCAAAGC 57.359 42.857 36.33 0.00 0.00 3.51
138 143 0.311790 ATGCCGGCAATATCAAAGCG 59.688 50.000 36.33 0.00 0.00 4.68
139 144 0.746204 TGCCGGCAATATCAAAGCGA 60.746 50.000 30.74 0.00 0.00 4.93
140 145 0.040958 GCCGGCAATATCAAAGCGAG 60.041 55.000 24.80 0.00 0.00 5.03
141 146 1.581934 CCGGCAATATCAAAGCGAGA 58.418 50.000 0.00 0.00 0.00 4.04
142 147 1.261619 CCGGCAATATCAAAGCGAGAC 59.738 52.381 0.00 0.00 0.00 3.36
143 148 2.205074 CGGCAATATCAAAGCGAGACT 58.795 47.619 0.00 0.00 0.00 3.24
144 149 3.381045 CGGCAATATCAAAGCGAGACTA 58.619 45.455 0.00 0.00 0.00 2.59
145 150 3.182572 CGGCAATATCAAAGCGAGACTAC 59.817 47.826 0.00 0.00 0.00 2.73
146 151 4.372656 GGCAATATCAAAGCGAGACTACT 58.627 43.478 0.00 0.00 0.00 2.57
147 152 4.811557 GGCAATATCAAAGCGAGACTACTT 59.188 41.667 0.00 0.00 0.00 2.24
148 153 5.050702 GGCAATATCAAAGCGAGACTACTTC 60.051 44.000 0.00 0.00 0.00 3.01
149 154 5.331905 GCAATATCAAAGCGAGACTACTTCG 60.332 44.000 0.00 0.00 0.00 3.79
155 160 3.206348 CGAGACTACTTCGCAGACG 57.794 57.895 0.00 0.00 42.01 4.18
166 171 2.502213 TCGCAGACGACTTCTTTGAA 57.498 45.000 0.00 0.00 45.12 2.69
167 172 2.124903 TCGCAGACGACTTCTTTGAAC 58.875 47.619 0.00 0.00 45.12 3.18
168 173 1.192534 CGCAGACGACTTCTTTGAACC 59.807 52.381 0.00 0.00 43.93 3.62
169 174 1.192534 GCAGACGACTTCTTTGAACCG 59.807 52.381 0.00 0.00 28.96 4.44
170 175 2.739292 CAGACGACTTCTTTGAACCGA 58.261 47.619 0.00 0.00 28.96 4.69
171 176 2.471743 CAGACGACTTCTTTGAACCGAC 59.528 50.000 0.00 0.00 28.96 4.79
172 177 2.361438 AGACGACTTCTTTGAACCGACT 59.639 45.455 0.00 0.00 0.00 4.18
173 178 3.121544 GACGACTTCTTTGAACCGACTT 58.878 45.455 0.00 0.00 0.00 3.01
174 179 3.121544 ACGACTTCTTTGAACCGACTTC 58.878 45.455 0.00 0.00 0.00 3.01
175 180 3.120792 CGACTTCTTTGAACCGACTTCA 58.879 45.455 0.00 0.00 37.08 3.02
176 181 3.060473 CGACTTCTTTGAACCGACTTCAC 60.060 47.826 0.00 0.00 38.70 3.18
177 182 3.869065 ACTTCTTTGAACCGACTTCACA 58.131 40.909 0.00 0.00 38.70 3.58
178 183 3.871594 ACTTCTTTGAACCGACTTCACAG 59.128 43.478 3.71 3.71 38.70 3.66
179 184 3.812156 TCTTTGAACCGACTTCACAGA 57.188 42.857 7.28 7.28 41.47 3.41
180 185 3.454375 TCTTTGAACCGACTTCACAGAC 58.546 45.455 7.28 0.00 39.68 3.51
181 186 3.132289 TCTTTGAACCGACTTCACAGACT 59.868 43.478 7.28 0.00 39.68 3.24
182 187 4.340097 TCTTTGAACCGACTTCACAGACTA 59.660 41.667 7.28 0.00 39.68 2.59
183 188 3.637998 TGAACCGACTTCACAGACTAC 57.362 47.619 0.00 0.00 33.65 2.73
189 194 4.098960 ACCGACTTCACAGACTACTTCAAA 59.901 41.667 0.00 0.00 0.00 2.69
253 258 3.350219 TGAAGGCTGGGTTGAGTTATC 57.650 47.619 0.00 0.00 0.00 1.75
384 390 2.563427 GCTGAAACAAGCGCCTCC 59.437 61.111 2.29 0.00 32.56 4.30
444 450 2.123854 TCGCTCGCTCACCCCTAT 60.124 61.111 0.00 0.00 0.00 2.57
477 485 6.693113 CAGAGCAGTAAAAACAGTTCTTTTCC 59.307 38.462 0.00 0.00 0.00 3.13
483 491 7.067008 CAGTAAAAACAGTTCTTTTCCCTCTCA 59.933 37.037 0.00 0.00 0.00 3.27
598 633 3.043586 GACAACGACAGTACACACTCAG 58.956 50.000 0.00 0.00 30.46 3.35
682 721 6.535963 AATGAAAATAGAAAAGCAGAGGGG 57.464 37.500 0.00 0.00 0.00 4.79
689 728 1.209261 GAAAAGCAGAGGGGGAGAGAG 59.791 57.143 0.00 0.00 0.00 3.20
713 752 2.689034 GTGAGGGTGAGGGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
716 755 4.026357 AGGGTGAGGGGAGGGGAC 62.026 72.222 0.00 0.00 0.00 4.46
729 768 4.779733 GGGACTCGGCTCCCCTGA 62.780 72.222 7.00 0.00 44.12 3.86
730 769 3.462678 GGACTCGGCTCCCCTGAC 61.463 72.222 0.00 0.00 0.00 3.51
731 770 3.827898 GACTCGGCTCCCCTGACG 61.828 72.222 0.00 0.00 40.31 4.35
732 771 4.680537 ACTCGGCTCCCCTGACGT 62.681 66.667 0.00 0.00 39.83 4.34
733 772 2.439701 CTCGGCTCCCCTGACGTA 60.440 66.667 0.00 0.00 39.83 3.57
734 773 2.753043 TCGGCTCCCCTGACGTAC 60.753 66.667 0.00 0.00 39.83 3.67
735 774 2.754658 CGGCTCCCCTGACGTACT 60.755 66.667 0.00 0.00 33.11 2.73
736 775 2.893398 GGCTCCCCTGACGTACTG 59.107 66.667 0.00 0.00 0.00 2.74
737 776 2.184579 GCTCCCCTGACGTACTGC 59.815 66.667 0.00 0.00 0.00 4.40
738 777 2.646175 GCTCCCCTGACGTACTGCA 61.646 63.158 0.00 0.00 0.00 4.41
739 778 1.513158 CTCCCCTGACGTACTGCAG 59.487 63.158 13.48 13.48 0.00 4.41
742 781 3.377656 CCTGACGTACTGCAGGGT 58.622 61.111 19.93 12.80 46.24 4.34
743 782 1.079819 CCTGACGTACTGCAGGGTG 60.080 63.158 19.93 9.21 46.24 4.61
744 783 1.738099 CTGACGTACTGCAGGGTGC 60.738 63.158 19.93 0.92 45.29 5.01
753 792 2.985847 GCAGGGTGCAGTTGGGTC 60.986 66.667 0.00 0.00 44.26 4.46
754 793 2.515398 CAGGGTGCAGTTGGGTCA 59.485 61.111 0.00 0.00 0.00 4.02
755 794 1.898574 CAGGGTGCAGTTGGGTCAC 60.899 63.158 0.00 0.00 0.00 3.67
756 795 2.078665 AGGGTGCAGTTGGGTCACT 61.079 57.895 0.00 0.00 0.00 3.41
757 796 1.898574 GGGTGCAGTTGGGTCACTG 60.899 63.158 0.00 0.00 46.15 3.66
758 797 1.148273 GGTGCAGTTGGGTCACTGA 59.852 57.895 5.01 0.00 46.29 3.41
759 798 1.166531 GGTGCAGTTGGGTCACTGAC 61.167 60.000 5.01 0.00 46.29 3.51
760 799 0.463654 GTGCAGTTGGGTCACTGACA 60.464 55.000 11.34 0.35 46.29 3.58
761 800 0.179048 TGCAGTTGGGTCACTGACAG 60.179 55.000 11.34 0.00 46.29 3.51
762 801 0.886490 GCAGTTGGGTCACTGACAGG 60.886 60.000 11.34 0.00 46.29 4.00
763 802 0.469917 CAGTTGGGTCACTGACAGGT 59.530 55.000 11.34 0.00 46.29 4.00
764 803 0.469917 AGTTGGGTCACTGACAGGTG 59.530 55.000 11.34 3.26 38.44 4.00
765 804 0.535102 GTTGGGTCACTGACAGGTGG 60.535 60.000 11.34 0.00 37.75 4.61
766 805 1.705002 TTGGGTCACTGACAGGTGGG 61.705 60.000 11.34 0.00 37.75 4.61
767 806 2.032681 GGTCACTGACAGGTGGGC 59.967 66.667 11.34 0.00 37.75 5.36
768 807 2.032681 GTCACTGACAGGTGGGCC 59.967 66.667 7.51 0.00 37.75 5.80
769 808 2.447572 TCACTGACAGGTGGGCCA 60.448 61.111 0.00 0.00 37.75 5.36
770 809 2.075566 TCACTGACAGGTGGGCCAA 61.076 57.895 8.40 0.00 37.75 4.52
771 810 1.898574 CACTGACAGGTGGGCCAAC 60.899 63.158 15.52 15.52 37.19 3.77
772 811 2.078665 ACTGACAGGTGGGCCAACT 61.079 57.895 21.01 21.01 37.19 3.16
773 812 1.151450 CTGACAGGTGGGCCAACTT 59.849 57.895 24.60 13.86 37.19 2.66
774 813 1.152777 TGACAGGTGGGCCAACTTG 60.153 57.895 24.60 20.50 37.19 3.16
775 814 2.521708 ACAGGTGGGCCAACTTGC 60.522 61.111 24.60 0.90 37.19 4.01
776 815 2.203538 CAGGTGGGCCAACTTGCT 60.204 61.111 24.60 0.00 37.19 3.91
777 816 1.833934 CAGGTGGGCCAACTTGCTT 60.834 57.895 24.60 0.00 37.19 3.91
778 817 1.075301 AGGTGGGCCAACTTGCTTT 60.075 52.632 21.01 0.00 37.19 3.51
779 818 1.115326 AGGTGGGCCAACTTGCTTTC 61.115 55.000 21.01 0.00 37.19 2.62
780 819 1.007387 GTGGGCCAACTTGCTTTCG 60.007 57.895 8.40 0.00 0.00 3.46
781 820 2.199652 TGGGCCAACTTGCTTTCGG 61.200 57.895 2.13 0.00 0.00 4.30
782 821 2.650778 GGCCAACTTGCTTTCGGG 59.349 61.111 0.00 0.00 0.00 5.14
783 822 2.049156 GCCAACTTGCTTTCGGGC 60.049 61.111 0.00 0.00 0.00 6.13
784 823 2.650778 CCAACTTGCTTTCGGGCC 59.349 61.111 0.00 0.00 0.00 5.80
785 824 2.650778 CAACTTGCTTTCGGGCCC 59.349 61.111 13.57 13.57 0.00 5.80
786 825 2.197324 AACTTGCTTTCGGGCCCA 59.803 55.556 24.92 6.15 0.00 5.36
787 826 2.200337 AACTTGCTTTCGGGCCCAC 61.200 57.895 24.92 5.64 0.00 4.61
788 827 3.373565 CTTGCTTTCGGGCCCACC 61.374 66.667 24.92 4.81 0.00 4.61
789 828 3.868200 CTTGCTTTCGGGCCCACCT 62.868 63.158 24.92 0.00 36.97 4.00
790 829 4.659172 TGCTTTCGGGCCCACCTG 62.659 66.667 24.92 10.12 44.63 4.00
791 830 4.660938 GCTTTCGGGCCCACCTGT 62.661 66.667 24.92 0.00 43.58 4.00
792 831 2.359975 CTTTCGGGCCCACCTGTC 60.360 66.667 24.92 0.00 43.58 3.51
793 832 3.172106 TTTCGGGCCCACCTGTCA 61.172 61.111 24.92 0.00 43.58 3.58
794 833 3.190738 TTTCGGGCCCACCTGTCAG 62.191 63.158 24.92 1.98 43.58 3.51
795 834 4.954118 TCGGGCCCACCTGTCAGT 62.954 66.667 24.92 0.00 43.58 3.41
796 835 4.704833 CGGGCCCACCTGTCAGTG 62.705 72.222 24.92 0.00 37.57 3.66
802 841 2.515398 CACCTGTCAGTGGCCCAA 59.485 61.111 0.00 0.00 33.95 4.12
803 842 1.898574 CACCTGTCAGTGGCCCAAC 60.899 63.158 0.00 0.00 33.95 3.77
804 843 2.078665 ACCTGTCAGTGGCCCAACT 61.079 57.895 0.00 0.00 0.00 3.16
806 845 2.203337 TGTCAGTGGCCCAACTGC 60.203 61.111 16.60 12.53 45.93 4.40
807 846 2.203337 GTCAGTGGCCCAACTGCA 60.203 61.111 16.60 5.16 45.93 4.41
808 847 2.203337 TCAGTGGCCCAACTGCAC 60.203 61.111 16.60 0.00 45.93 4.57
809 848 3.297620 CAGTGGCCCAACTGCACC 61.298 66.667 10.07 0.00 41.05 5.01
810 849 4.603535 AGTGGCCCAACTGCACCC 62.604 66.667 0.00 0.00 0.00 4.61
811 850 4.603535 GTGGCCCAACTGCACCCT 62.604 66.667 0.00 0.00 0.00 4.34
812 851 4.601794 TGGCCCAACTGCACCCTG 62.602 66.667 0.00 0.00 0.00 4.45
822 861 2.342279 GCACCCTGCAGTACGTCA 59.658 61.111 13.81 0.00 44.26 4.35
823 862 1.738099 GCACCCTGCAGTACGTCAG 60.738 63.158 13.81 9.54 44.26 3.51
826 865 1.251527 ACCCTGCAGTACGTCAGAGG 61.252 60.000 13.81 15.90 32.26 3.69
829 868 0.179150 CTGCAGTACGTCAGAGGAGC 60.179 60.000 5.25 0.00 32.26 4.70
839 878 0.038310 TCAGAGGAGCGAGAAGACCA 59.962 55.000 0.00 0.00 0.00 4.02
1597 1652 2.560105 AGATTTGGGTGCTTCTTTGCTC 59.440 45.455 0.00 0.00 0.00 4.26
1633 1688 3.896648 TTGAGCTTTGTTCGGTCATTC 57.103 42.857 0.00 0.00 38.51 2.67
1659 1714 4.915667 GCTTTCGGTTTTTGTGATCTAACC 59.084 41.667 0.00 0.00 37.31 2.85
1675 1730 3.668386 CCAGTTCTTGGTTCGGCC 58.332 61.111 0.00 0.00 42.41 6.13
1729 1786 4.582701 AATGGTTCAACGATTTTGAGCA 57.417 36.364 0.00 0.00 32.32 4.26
1775 1832 5.147162 CGCTTCATTTGGTACTTCTTTGAC 58.853 41.667 0.00 0.00 0.00 3.18
1778 1835 7.147976 GCTTCATTTGGTACTTCTTTGACATT 58.852 34.615 0.00 0.00 0.00 2.71
1794 1851 5.112220 TGACATTGATGCAAGTTTCAGTC 57.888 39.130 0.00 0.00 0.00 3.51
1827 1884 8.421784 TGATCTATTCCTAGTTTAAGCGTGAAT 58.578 33.333 0.00 8.29 0.00 2.57
1966 2023 4.917906 AACTAGCCTTCATCCTGTTCTT 57.082 40.909 0.00 0.00 0.00 2.52
1974 2031 4.565236 CCTTCATCCTGTTCTTCAGAAGCT 60.565 45.833 5.15 0.00 46.27 3.74
2048 2105 2.224281 TGTGGGATTGGCAGACGATATC 60.224 50.000 0.00 0.00 0.00 1.63
2233 2291 5.947663 TCTCCTTTCCATTTTCAGTTACCA 58.052 37.500 0.00 0.00 0.00 3.25
2386 2446 5.503927 AGAATGTGATATTTGCTCCAGTGT 58.496 37.500 0.00 0.00 0.00 3.55
2446 2506 5.335976 GCAACTTTGATCCCTTCCTTTGTAG 60.336 44.000 0.00 0.00 0.00 2.74
2467 2530 2.996621 GTCTGATTAGTTGAGCTTGCGT 59.003 45.455 0.00 0.00 0.00 5.24
2594 2661 3.120649 GCACAACCAGTACTGTTTCGATC 60.121 47.826 21.18 1.86 0.00 3.69
2645 2712 3.440522 GTGAGGAAAGGCTAATGGTGTTC 59.559 47.826 0.00 0.00 0.00 3.18
2663 2733 6.147164 TGGTGTTCGATCAGTTTTTGATACTC 59.853 38.462 0.00 0.00 46.51 2.59
2692 2762 3.937706 CCTGTGCAAACATAGAAGAGAGG 59.062 47.826 0.00 0.00 37.20 3.69
2712 2789 3.077359 GGCTGAAGTAACTGAATGTGCT 58.923 45.455 0.00 0.00 0.00 4.40
2716 2793 5.437289 TGAAGTAACTGAATGTGCTTTGG 57.563 39.130 0.00 0.00 0.00 3.28
2747 2824 4.645863 AGTCCAATGCCATATATGCAGA 57.354 40.909 7.24 0.00 42.92 4.26
2769 2846 7.802251 GCAGATGCATAACAAATCATTAGACTC 59.198 37.037 0.00 0.00 41.59 3.36
2770 2847 9.053840 CAGATGCATAACAAATCATTAGACTCT 57.946 33.333 0.00 0.00 0.00 3.24
2774 3029 9.665719 TGCATAACAAATCATTAGACTCTGTTA 57.334 29.630 0.00 0.00 0.00 2.41
2822 3086 9.495754 GAAAATTTTGACTACATAGATGTGAGC 57.504 33.333 8.47 0.00 41.89 4.26
2876 3140 6.435430 TGACATGGTAATGCAATGTAGTTC 57.565 37.500 1.02 0.00 41.63 3.01
2985 3249 6.978343 TTTGGATGAGGTTGATAGTTAACG 57.022 37.500 0.00 0.00 0.00 3.18
3017 3281 9.646427 GAATCTAAGCTGGGTAGTTCATATTAG 57.354 37.037 0.00 0.00 0.00 1.73
3022 3286 8.879427 AAGCTGGGTAGTTCATATTAGTTTTT 57.121 30.769 0.00 0.00 0.00 1.94
3023 3287 8.507524 AGCTGGGTAGTTCATATTAGTTTTTC 57.492 34.615 0.00 0.00 0.00 2.29
3028 3292 8.188799 GGGTAGTTCATATTAGTTTTTCTTGCC 58.811 37.037 0.00 0.00 0.00 4.52
3029 3293 8.957466 GGTAGTTCATATTAGTTTTTCTTGCCT 58.043 33.333 0.00 0.00 0.00 4.75
3273 3537 5.699458 ACTTTAGGTGTGTGCTGTTATACAC 59.301 40.000 0.00 0.00 45.57 2.90
3285 3549 7.119116 TGTGCTGTTATACACTATTGAAGTTGG 59.881 37.037 0.00 0.00 35.76 3.77
3300 3564 0.865769 GTTGGTGTGTCCTGCGTAAG 59.134 55.000 0.00 0.00 37.07 2.34
3396 3660 3.146066 TCGGTTTGCTTGTGCTTTATCT 58.854 40.909 0.00 0.00 40.48 1.98
3462 3726 9.409312 CTGTTGATCTAGTATGCTTGAGAATAG 57.591 37.037 1.30 1.63 30.64 1.73
3468 3732 5.559148 AGTATGCTTGAGAATAGGGGAAG 57.441 43.478 0.00 0.00 0.00 3.46
3577 3841 5.008613 GCTTTACACTGATGTTCCTGTGAAA 59.991 40.000 0.00 0.00 40.48 2.69
3683 3947 8.185003 ACTGCAAATGTTGACTTTAAAGTTTC 57.815 30.769 21.40 14.49 39.88 2.78
3757 4021 8.934023 AACAAAGATTAGTTGAACCCTGAATA 57.066 30.769 0.00 0.00 0.00 1.75
3875 4147 7.121382 TCTCATAAATTGCCTTGATTCTTCCT 58.879 34.615 0.00 0.00 0.00 3.36
4007 4279 8.766151 CGCCTATCCTTAAGTTCTAATTTCTTC 58.234 37.037 0.97 0.00 0.00 2.87
4026 4298 0.106335 CCTACTCTCCATGCTGCAGG 59.894 60.000 17.12 8.11 0.00 4.85
4047 4319 6.128145 GCAGGAATTTAAGAGAACTTGACCTC 60.128 42.308 0.00 0.00 37.53 3.85
4563 4835 4.433186 TTTATCAACTTCAATGCCCACG 57.567 40.909 0.00 0.00 0.00 4.94
4610 4882 8.136800 CACATTGCTTAAGTGAATATTGCCATA 58.863 33.333 4.02 0.00 35.33 2.74
4684 4960 9.040939 GCATAAACAGAAACAACTATGGTTTTT 57.959 29.630 0.00 0.00 36.33 1.94
4751 5027 2.878406 CCCCACAACAGTGTAGTTCTTG 59.122 50.000 0.00 0.00 35.72 3.02
4790 5066 7.815840 TCAATGTCTCACTTTCCATGTTTTA 57.184 32.000 0.00 0.00 0.00 1.52
4965 5241 5.474876 AGTTTTATTGACTGAAAGAGGCCTG 59.525 40.000 12.00 0.00 37.43 4.85
5202 5478 1.622811 CTCTCTGTGTCTGGCCTTCTT 59.377 52.381 3.32 0.00 0.00 2.52
5262 5538 6.585695 AATTGTCTTGAGATGCTGTCAATT 57.414 33.333 0.00 0.00 33.49 2.32
5559 5835 4.499188 CCGGTCGAGACATTGTATGTGTAT 60.499 45.833 5.55 0.00 45.03 2.29
5598 5874 2.467880 AGGTCCGACACACCAGATTAT 58.532 47.619 0.00 0.00 36.23 1.28
5742 6018 4.552355 TGAAGCTGTCGTAAAATCTCGAA 58.448 39.130 0.00 0.00 37.81 3.71
5800 6076 5.030820 AGGTGTTAATAACTGTAGGAGGCT 58.969 41.667 4.67 0.00 0.00 4.58
5801 6077 5.104900 AGGTGTTAATAACTGTAGGAGGCTG 60.105 44.000 4.67 0.00 0.00 4.85
6002 6280 3.443681 CCCGCCTTTCAGATTATGTGTTT 59.556 43.478 0.00 0.00 0.00 2.83
6048 6409 4.214332 GTCATCTGGTGTTCTCTTTGTTCC 59.786 45.833 0.00 0.00 0.00 3.62
6124 6486 3.365820 GCACAAATTTCTCCTTGATTGCG 59.634 43.478 0.00 0.00 0.00 4.85
6143 6505 0.036577 GACATCTGAGTGCTGGCTGT 60.037 55.000 0.00 0.00 0.00 4.40
6175 6537 7.918536 ATGTAGCAAAATATGGATAGAGCTG 57.081 36.000 0.00 0.00 32.70 4.24
6187 6549 3.509575 GGATAGAGCTGTATGTCAGAGGG 59.490 52.174 8.33 0.00 46.27 4.30
6342 6810 3.406764 AGAGAAACATCTGCAGTTCACC 58.593 45.455 14.67 6.39 0.00 4.02
6343 6811 3.072184 AGAGAAACATCTGCAGTTCACCT 59.928 43.478 14.67 8.40 0.00 4.00
6356 6824 6.530120 TGCAGTTCACCTTTACTTGAGATTA 58.470 36.000 0.00 0.00 0.00 1.75
6370 6838 5.587844 ACTTGAGATTAATTGCGATTGAGCT 59.412 36.000 8.83 8.83 38.13 4.09
6417 6885 8.533737 CAACAATGCATTTAACTGATACTACG 57.466 34.615 9.83 0.00 0.00 3.51
6605 7080 4.967036 TCTGACACCAACAATATCACACA 58.033 39.130 0.00 0.00 0.00 3.72
6610 7085 5.069318 ACACCAACAATATCACACATGTCA 58.931 37.500 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.237949 GCATATACTAGTAATCAGAGCTTCGAA 58.762 37.037 6.70 0.00 0.00 3.71
3 4 6.684979 CGCATATACTAGTAATCAGAGCTTCG 59.315 42.308 6.70 0.00 0.00 3.79
4 5 7.694784 GTCGCATATACTAGTAATCAGAGCTTC 59.305 40.741 6.70 0.00 0.00 3.86
6 7 6.655425 TGTCGCATATACTAGTAATCAGAGCT 59.345 38.462 6.70 0.00 0.00 4.09
7 8 6.843208 TGTCGCATATACTAGTAATCAGAGC 58.157 40.000 6.70 5.11 0.00 4.09
8 9 7.965655 CCTTGTCGCATATACTAGTAATCAGAG 59.034 40.741 6.70 0.19 0.00 3.35
9 10 7.447545 ACCTTGTCGCATATACTAGTAATCAGA 59.552 37.037 6.70 0.99 0.00 3.27
10 11 7.594714 ACCTTGTCGCATATACTAGTAATCAG 58.405 38.462 6.70 0.00 0.00 2.90
11 12 7.520451 ACCTTGTCGCATATACTAGTAATCA 57.480 36.000 6.70 0.00 0.00 2.57
12 13 9.504710 CATACCTTGTCGCATATACTAGTAATC 57.495 37.037 6.70 0.00 0.00 1.75
13 14 9.021807 ACATACCTTGTCGCATATACTAGTAAT 57.978 33.333 6.70 0.00 30.89 1.89
14 15 8.400184 ACATACCTTGTCGCATATACTAGTAA 57.600 34.615 6.70 0.00 30.89 2.24
15 16 7.991084 ACATACCTTGTCGCATATACTAGTA 57.009 36.000 4.77 4.77 30.89 1.82
16 17 6.896021 ACATACCTTGTCGCATATACTAGT 57.104 37.500 0.00 0.00 30.89 2.57
17 18 7.116376 CCAAACATACCTTGTCGCATATACTAG 59.884 40.741 0.00 0.00 37.68 2.57
18 19 6.926826 CCAAACATACCTTGTCGCATATACTA 59.073 38.462 0.00 0.00 37.68 1.82
19 20 5.758296 CCAAACATACCTTGTCGCATATACT 59.242 40.000 0.00 0.00 37.68 2.12
20 21 5.526111 ACCAAACATACCTTGTCGCATATAC 59.474 40.000 0.00 0.00 37.68 1.47
21 22 5.676552 ACCAAACATACCTTGTCGCATATA 58.323 37.500 0.00 0.00 37.68 0.86
22 23 4.523083 ACCAAACATACCTTGTCGCATAT 58.477 39.130 0.00 0.00 37.68 1.78
23 24 3.945346 ACCAAACATACCTTGTCGCATA 58.055 40.909 0.00 0.00 37.68 3.14
24 25 2.790433 ACCAAACATACCTTGTCGCAT 58.210 42.857 0.00 0.00 37.68 4.73
25 26 2.264005 ACCAAACATACCTTGTCGCA 57.736 45.000 0.00 0.00 37.68 5.10
26 27 3.243267 ACAAACCAAACATACCTTGTCGC 60.243 43.478 0.00 0.00 37.68 5.19
27 28 4.561735 ACAAACCAAACATACCTTGTCG 57.438 40.909 0.00 0.00 37.68 4.35
28 29 7.042992 GCTTTTACAAACCAAACATACCTTGTC 60.043 37.037 0.00 0.00 37.68 3.18
29 30 6.759356 GCTTTTACAAACCAAACATACCTTGT 59.241 34.615 0.00 0.00 41.53 3.16
60 61 6.803807 GCTTTTTCTTCTGCGAATAGATGTTT 59.196 34.615 0.00 0.00 0.00 2.83
84 85 6.761242 AGGGAAACTTTTGATGTTTTACAAGC 59.239 34.615 0.00 0.00 37.70 4.01
85 86 9.244799 GTAGGGAAACTTTTGATGTTTTACAAG 57.755 33.333 0.00 0.00 37.70 3.16
86 87 8.750298 TGTAGGGAAACTTTTGATGTTTTACAA 58.250 29.630 0.00 0.00 37.70 2.41
87 88 8.294954 TGTAGGGAAACTTTTGATGTTTTACA 57.705 30.769 0.00 0.00 37.70 2.41
102 107 5.106442 CCGGCATAAATTTTGTAGGGAAAC 58.894 41.667 0.00 0.00 0.00 2.78
103 108 4.382147 GCCGGCATAAATTTTGTAGGGAAA 60.382 41.667 24.80 0.00 0.00 3.13
109 114 7.043961 TGATATTGCCGGCATAAATTTTGTA 57.956 32.000 33.25 11.88 0.00 2.41
123 128 2.205074 AGTCTCGCTTTGATATTGCCG 58.795 47.619 0.00 0.00 0.00 5.69
137 142 0.720027 TCGTCTGCGAAGTAGTCTCG 59.280 55.000 0.00 0.00 44.92 4.04
147 152 2.124903 GTTCAAAGAAGTCGTCTGCGA 58.875 47.619 0.00 0.00 45.79 5.10
148 153 1.192534 GGTTCAAAGAAGTCGTCTGCG 59.807 52.381 0.00 0.00 36.40 5.18
149 154 1.192534 CGGTTCAAAGAAGTCGTCTGC 59.807 52.381 0.00 0.00 36.40 4.26
150 155 2.471743 GTCGGTTCAAAGAAGTCGTCTG 59.528 50.000 0.00 0.00 36.40 3.51
151 156 2.361438 AGTCGGTTCAAAGAAGTCGTCT 59.639 45.455 0.00 0.00 38.69 4.18
152 157 2.740452 AGTCGGTTCAAAGAAGTCGTC 58.260 47.619 0.00 0.00 0.00 4.20
153 158 2.884894 AGTCGGTTCAAAGAAGTCGT 57.115 45.000 0.00 0.00 0.00 4.34
154 159 3.120792 TGAAGTCGGTTCAAAGAAGTCG 58.879 45.455 0.00 0.00 42.49 4.18
163 168 3.220110 AGTAGTCTGTGAAGTCGGTTCA 58.780 45.455 0.00 0.00 43.26 3.18
164 169 3.919223 AGTAGTCTGTGAAGTCGGTTC 57.081 47.619 0.00 0.00 35.48 3.62
165 170 3.635373 TGAAGTAGTCTGTGAAGTCGGTT 59.365 43.478 0.00 0.00 0.00 4.44
166 171 3.220110 TGAAGTAGTCTGTGAAGTCGGT 58.780 45.455 0.00 0.00 0.00 4.69
167 172 3.917329 TGAAGTAGTCTGTGAAGTCGG 57.083 47.619 0.00 0.00 0.00 4.79
168 173 4.146616 CGTTTGAAGTAGTCTGTGAAGTCG 59.853 45.833 0.00 0.00 0.00 4.18
169 174 5.173492 GTCGTTTGAAGTAGTCTGTGAAGTC 59.827 44.000 0.00 0.00 0.00 3.01
170 175 5.041940 GTCGTTTGAAGTAGTCTGTGAAGT 58.958 41.667 0.00 0.00 0.00 3.01
171 176 5.041287 TGTCGTTTGAAGTAGTCTGTGAAG 58.959 41.667 0.00 0.00 0.00 3.02
172 177 5.001237 TGTCGTTTGAAGTAGTCTGTGAA 57.999 39.130 0.00 0.00 0.00 3.18
173 178 4.642445 TGTCGTTTGAAGTAGTCTGTGA 57.358 40.909 0.00 0.00 0.00 3.58
174 179 4.745125 ACATGTCGTTTGAAGTAGTCTGTG 59.255 41.667 0.00 0.00 0.00 3.66
175 180 4.745125 CACATGTCGTTTGAAGTAGTCTGT 59.255 41.667 0.00 0.00 0.00 3.41
176 181 4.982295 TCACATGTCGTTTGAAGTAGTCTG 59.018 41.667 0.00 0.00 0.00 3.51
177 182 5.196341 TCACATGTCGTTTGAAGTAGTCT 57.804 39.130 0.00 0.00 0.00 3.24
178 183 5.062308 GGATCACATGTCGTTTGAAGTAGTC 59.938 44.000 0.00 0.00 0.00 2.59
179 184 4.929808 GGATCACATGTCGTTTGAAGTAGT 59.070 41.667 0.00 0.00 0.00 2.73
180 185 4.929211 TGGATCACATGTCGTTTGAAGTAG 59.071 41.667 0.00 0.00 0.00 2.57
181 186 4.888917 TGGATCACATGTCGTTTGAAGTA 58.111 39.130 0.00 0.00 0.00 2.24
182 187 3.738982 TGGATCACATGTCGTTTGAAGT 58.261 40.909 0.00 0.00 0.00 3.01
183 188 4.466828 GTTGGATCACATGTCGTTTGAAG 58.533 43.478 0.00 0.00 0.00 3.02
189 194 2.540515 GATCGTTGGATCACATGTCGT 58.459 47.619 0.00 0.00 46.81 4.34
253 258 2.383298 AGTTGAACGATTTGTGCACG 57.617 45.000 13.13 1.70 35.17 5.34
361 367 1.372128 CGCTTGTTTCAGCTTGGGC 60.372 57.895 0.00 0.00 37.68 5.36
384 390 4.102210 AGTGATGGAACTGATGGTAGGATG 59.898 45.833 0.00 0.00 0.00 3.51
444 450 3.751479 TTTTACTGCTCTGTGCTGAGA 57.249 42.857 14.17 1.04 42.27 3.27
477 485 9.748708 TGTTTCAGATTTATTTGTTTTGAGAGG 57.251 29.630 0.00 0.00 0.00 3.69
558 567 7.334921 TCGTTGTCCTTTTGTTTTCTTTCTAGA 59.665 33.333 0.00 0.00 0.00 2.43
598 633 3.350219 AGACAGTGAGAGAGAGAGGAC 57.650 52.381 0.00 0.00 0.00 3.85
680 719 0.923358 TCACCTCTCTCTCTCTCCCC 59.077 60.000 0.00 0.00 0.00 4.81
682 721 1.133792 CCCTCACCTCTCTCTCTCTCC 60.134 61.905 0.00 0.00 0.00 3.71
689 728 0.686112 CCCTCACCCTCACCTCTCTC 60.686 65.000 0.00 0.00 0.00 3.20
713 752 3.462678 GTCAGGGGAGCCGAGTCC 61.463 72.222 0.00 0.00 35.64 3.85
716 755 2.439701 TACGTCAGGGGAGCCGAG 60.440 66.667 0.00 0.00 0.00 4.63
717 756 2.753043 GTACGTCAGGGGAGCCGA 60.753 66.667 0.00 0.00 0.00 5.54
718 757 2.754658 AGTACGTCAGGGGAGCCG 60.755 66.667 0.00 0.00 0.00 5.52
719 758 2.893398 CAGTACGTCAGGGGAGCC 59.107 66.667 0.00 0.00 0.00 4.70
720 759 2.184579 GCAGTACGTCAGGGGAGC 59.815 66.667 0.00 0.00 0.00 4.70
721 760 1.513158 CTGCAGTACGTCAGGGGAG 59.487 63.158 5.25 0.00 0.00 4.30
722 761 1.982395 CCTGCAGTACGTCAGGGGA 60.982 63.158 21.58 0.00 44.64 4.81
723 762 2.579201 CCTGCAGTACGTCAGGGG 59.421 66.667 21.58 5.35 44.64 4.79
726 765 1.738099 GCACCCTGCAGTACGTCAG 60.738 63.158 13.81 9.54 44.26 3.51
727 766 2.342279 GCACCCTGCAGTACGTCA 59.658 61.111 13.81 0.00 44.26 4.35
736 775 2.985847 GACCCAACTGCACCCTGC 60.986 66.667 0.00 0.00 45.29 4.85
737 776 1.898574 GTGACCCAACTGCACCCTG 60.899 63.158 0.00 0.00 0.00 4.45
738 777 2.078665 AGTGACCCAACTGCACCCT 61.079 57.895 0.00 0.00 33.14 4.34
739 778 1.898574 CAGTGACCCAACTGCACCC 60.899 63.158 0.00 0.00 41.05 4.61
740 779 1.148273 TCAGTGACCCAACTGCACC 59.852 57.895 0.00 0.00 45.93 5.01
741 780 0.463654 TGTCAGTGACCCAACTGCAC 60.464 55.000 20.43 0.00 45.93 4.57
742 781 0.179048 CTGTCAGTGACCCAACTGCA 60.179 55.000 20.43 0.00 45.93 4.41
743 782 0.886490 CCTGTCAGTGACCCAACTGC 60.886 60.000 20.43 0.00 45.93 4.40
745 784 0.469917 CACCTGTCAGTGACCCAACT 59.530 55.000 20.43 0.00 40.34 3.16
746 785 0.535102 CCACCTGTCAGTGACCCAAC 60.535 60.000 20.43 0.00 40.34 3.77
747 786 1.705002 CCCACCTGTCAGTGACCCAA 61.705 60.000 20.43 1.10 40.34 4.12
748 787 2.146724 CCCACCTGTCAGTGACCCA 61.147 63.158 20.43 1.94 40.34 4.51
749 788 2.750350 CCCACCTGTCAGTGACCC 59.250 66.667 20.43 0.00 40.34 4.46
750 789 2.032681 GCCCACCTGTCAGTGACC 59.967 66.667 20.43 3.45 40.34 4.02
751 790 2.032681 GGCCCACCTGTCAGTGAC 59.967 66.667 16.68 16.68 40.34 3.67
752 791 2.075566 TTGGCCCACCTGTCAGTGA 61.076 57.895 0.00 0.00 40.34 3.41
753 792 1.898574 GTTGGCCCACCTGTCAGTG 60.899 63.158 0.00 0.00 36.63 3.66
754 793 1.645402 AAGTTGGCCCACCTGTCAGT 61.645 55.000 2.72 0.00 36.63 3.41
755 794 1.151450 AAGTTGGCCCACCTGTCAG 59.849 57.895 2.72 0.00 36.63 3.51
756 795 1.152777 CAAGTTGGCCCACCTGTCA 60.153 57.895 2.72 0.00 36.63 3.58
757 796 2.564721 GCAAGTTGGCCCACCTGTC 61.565 63.158 2.72 0.00 36.63 3.51
758 797 2.521708 GCAAGTTGGCCCACCTGT 60.522 61.111 2.72 0.00 36.63 4.00
759 798 1.402107 AAAGCAAGTTGGCCCACCTG 61.402 55.000 2.72 1.84 36.63 4.00
760 799 1.075301 AAAGCAAGTTGGCCCACCT 60.075 52.632 2.72 0.00 36.63 4.00
761 800 1.367471 GAAAGCAAGTTGGCCCACC 59.633 57.895 2.72 0.00 0.00 4.61
762 801 1.007387 CGAAAGCAAGTTGGCCCAC 60.007 57.895 0.00 0.00 0.00 4.61
763 802 2.199652 CCGAAAGCAAGTTGGCCCA 61.200 57.895 0.00 0.00 0.00 5.36
764 803 2.650778 CCGAAAGCAAGTTGGCCC 59.349 61.111 0.00 0.00 0.00 5.80
765 804 2.650778 CCCGAAAGCAAGTTGGCC 59.349 61.111 4.75 0.00 0.00 5.36
766 805 2.049156 GCCCGAAAGCAAGTTGGC 60.049 61.111 4.75 0.00 0.00 4.52
767 806 2.650778 GGCCCGAAAGCAAGTTGG 59.349 61.111 4.75 0.00 0.00 3.77
768 807 2.199652 TGGGCCCGAAAGCAAGTTG 61.200 57.895 19.37 0.00 0.00 3.16
769 808 2.197324 TGGGCCCGAAAGCAAGTT 59.803 55.556 19.37 0.00 0.00 2.66
770 809 2.597510 GTGGGCCCGAAAGCAAGT 60.598 61.111 19.37 0.00 0.00 3.16
771 810 3.373565 GGTGGGCCCGAAAGCAAG 61.374 66.667 19.37 0.00 0.00 4.01
772 811 3.897122 AGGTGGGCCCGAAAGCAA 61.897 61.111 19.37 0.00 38.74 3.91
773 812 4.659172 CAGGTGGGCCCGAAAGCA 62.659 66.667 19.37 0.00 38.74 3.91
774 813 4.660938 ACAGGTGGGCCCGAAAGC 62.661 66.667 19.37 9.80 38.74 3.51
775 814 2.359975 GACAGGTGGGCCCGAAAG 60.360 66.667 19.37 10.07 38.74 2.62
776 815 3.172106 TGACAGGTGGGCCCGAAA 61.172 61.111 19.37 0.00 38.74 3.46
777 816 3.636231 CTGACAGGTGGGCCCGAA 61.636 66.667 19.37 0.00 38.74 4.30
778 817 4.954118 ACTGACAGGTGGGCCCGA 62.954 66.667 19.37 3.06 38.74 5.14
779 818 4.704833 CACTGACAGGTGGGCCCG 62.705 72.222 19.37 4.81 38.74 6.13
785 824 1.898574 GTTGGGCCACTGACAGGTG 60.899 63.158 5.23 2.99 37.00 4.00
786 825 2.078665 AGTTGGGCCACTGACAGGT 61.079 57.895 5.23 0.00 0.00 4.00
787 826 1.601759 CAGTTGGGCCACTGACAGG 60.602 63.158 23.45 7.08 46.29 4.00
788 827 2.263741 GCAGTTGGGCCACTGACAG 61.264 63.158 28.71 15.14 46.29 3.51
789 828 2.203337 GCAGTTGGGCCACTGACA 60.203 61.111 28.71 5.60 46.29 3.58
790 829 2.203337 TGCAGTTGGGCCACTGAC 60.203 61.111 28.71 21.80 46.29 3.51
791 830 2.203337 GTGCAGTTGGGCCACTGA 60.203 61.111 28.71 16.56 46.29 3.41
792 831 3.297620 GGTGCAGTTGGGCCACTG 61.298 66.667 23.47 23.47 46.15 3.66
793 832 4.603535 GGGTGCAGTTGGGCCACT 62.604 66.667 5.23 3.94 0.00 4.00
794 833 4.603535 AGGGTGCAGTTGGGCCAC 62.604 66.667 5.23 1.08 0.00 5.01
795 834 4.601794 CAGGGTGCAGTTGGGCCA 62.602 66.667 0.00 0.00 0.00 5.36
805 844 1.738099 CTGACGTACTGCAGGGTGC 60.738 63.158 19.93 0.92 45.29 5.01
806 845 0.109086 CTCTGACGTACTGCAGGGTG 60.109 60.000 19.93 9.21 33.05 4.61
807 846 1.251527 CCTCTGACGTACTGCAGGGT 61.252 60.000 19.93 12.80 30.57 4.34
808 847 0.965866 TCCTCTGACGTACTGCAGGG 60.966 60.000 19.93 9.39 33.05 4.45
809 848 0.453793 CTCCTCTGACGTACTGCAGG 59.546 60.000 19.93 2.38 33.05 4.85
810 849 0.179150 GCTCCTCTGACGTACTGCAG 60.179 60.000 13.48 13.48 0.00 4.41
811 850 1.883732 GCTCCTCTGACGTACTGCA 59.116 57.895 0.00 0.00 0.00 4.41
812 851 1.226435 CGCTCCTCTGACGTACTGC 60.226 63.158 0.00 0.00 0.00 4.40
813 852 0.375454 CTCGCTCCTCTGACGTACTG 59.625 60.000 0.00 0.00 0.00 2.74
814 853 0.249676 TCTCGCTCCTCTGACGTACT 59.750 55.000 0.00 0.00 0.00 2.73
815 854 1.062880 CTTCTCGCTCCTCTGACGTAC 59.937 57.143 0.00 0.00 0.00 3.67
816 855 1.066358 TCTTCTCGCTCCTCTGACGTA 60.066 52.381 0.00 0.00 0.00 3.57
817 856 0.321741 TCTTCTCGCTCCTCTGACGT 60.322 55.000 0.00 0.00 0.00 4.34
818 857 0.098025 GTCTTCTCGCTCCTCTGACG 59.902 60.000 0.00 0.00 0.00 4.35
819 858 0.454196 GGTCTTCTCGCTCCTCTGAC 59.546 60.000 0.00 0.00 0.00 3.51
820 859 0.038310 TGGTCTTCTCGCTCCTCTGA 59.962 55.000 0.00 0.00 0.00 3.27
821 860 0.455410 CTGGTCTTCTCGCTCCTCTG 59.545 60.000 0.00 0.00 0.00 3.35
822 861 0.682855 CCTGGTCTTCTCGCTCCTCT 60.683 60.000 0.00 0.00 0.00 3.69
823 862 1.671901 CCCTGGTCTTCTCGCTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
826 865 2.726351 CCCCCTGGTCTTCTCGCTC 61.726 68.421 0.00 0.00 0.00 5.03
1633 1688 2.748461 TCACAAAAACCGAAAGCTCG 57.252 45.000 0.00 0.00 45.02 5.03
1697 1752 3.735746 CGTTGAACCATTTTGAGGAAAGC 59.264 43.478 0.00 0.00 0.00 3.51
1698 1753 5.181690 TCGTTGAACCATTTTGAGGAAAG 57.818 39.130 0.00 0.00 0.00 2.62
1775 1832 5.765176 TCTTGACTGAAACTTGCATCAATG 58.235 37.500 0.00 0.00 0.00 2.82
1778 1835 6.039605 TCAAATCTTGACTGAAACTTGCATCA 59.960 34.615 0.00 0.00 34.08 3.07
1966 2023 1.259609 CATGGGCCAAAAGCTTCTGA 58.740 50.000 11.89 0.00 43.05 3.27
1974 2031 2.158711 TGCAATCAAACATGGGCCAAAA 60.159 40.909 11.89 0.00 0.00 2.44
2048 2105 8.127150 TCCATCATTGGTACACAGATAGATAG 57.873 38.462 0.00 0.00 44.06 2.08
2233 2291 0.531974 AGTCCACAAACACACGCGAT 60.532 50.000 15.93 0.00 0.00 4.58
2386 2446 7.177184 AGTCCATTATATGCAGGCATTATGAA 58.823 34.615 12.54 2.72 37.82 2.57
2446 2506 2.996621 ACGCAAGCTCAACTAATCAGAC 59.003 45.455 0.00 0.00 45.62 3.51
2467 2530 6.261435 TCCTACTTTCTGTCTAAGGGATTCA 58.739 40.000 0.00 0.00 0.00 2.57
2505 2568 9.429109 TCCTTCAAGTTCCTTTTTAAAAGGTAT 57.571 29.630 28.90 16.81 38.55 2.73
2645 2712 8.543774 GGATAACAGAGTATCAAAAACTGATCG 58.456 37.037 0.00 0.00 44.05 3.69
2663 2733 6.595326 TCTTCTATGTTTGCACAGGATAACAG 59.405 38.462 5.69 0.00 35.94 3.16
2692 2762 4.756084 AAGCACATTCAGTTACTTCAGC 57.244 40.909 0.00 0.00 0.00 4.26
2712 2789 7.350382 TGGCATTGGACTAGAATATAACCAAA 58.650 34.615 0.00 0.00 40.06 3.28
2747 2824 8.743085 ACAGAGTCTAATGATTTGTTATGCAT 57.257 30.769 3.79 3.79 0.00 3.96
2769 2846 4.499183 ACGAAGAAGCTCAAGGATAACAG 58.501 43.478 0.00 0.00 0.00 3.16
2770 2847 4.495422 GACGAAGAAGCTCAAGGATAACA 58.505 43.478 0.00 0.00 0.00 2.41
2774 3029 2.183679 AGGACGAAGAAGCTCAAGGAT 58.816 47.619 0.00 0.00 0.00 3.24
2822 3086 2.525750 AATGATACAAAGTGTGCGCG 57.474 45.000 0.00 0.00 0.00 6.86
2876 3140 2.213499 ACAAGGAAAGTGCTTCTGACG 58.787 47.619 0.00 0.00 34.17 4.35
2985 3249 7.769044 TGAACTACCCAGCTTAGATTCAATTAC 59.231 37.037 0.00 0.00 0.00 1.89
3037 3301 4.158764 CCAACTACTTCCAAACCACAACAA 59.841 41.667 0.00 0.00 0.00 2.83
3040 3304 3.292460 CCCAACTACTTCCAAACCACAA 58.708 45.455 0.00 0.00 0.00 3.33
3273 3537 3.189287 GCAGGACACACCAACTTCAATAG 59.811 47.826 0.00 0.00 42.04 1.73
3285 3549 1.128692 GCAATCTTACGCAGGACACAC 59.871 52.381 0.00 0.00 0.00 3.82
3300 3564 5.407387 ACTTCAATGCTCACAAAATGCAATC 59.593 36.000 0.00 0.00 40.24 2.67
3396 3660 7.093727 ACAGCAGCAACTAGAAGAGAATTACTA 60.094 37.037 0.00 0.00 0.00 1.82
3411 3675 1.673665 GCTAGCCACAGCAGCAACT 60.674 57.895 2.29 0.00 43.56 3.16
3462 3726 4.857130 ACTATTTTAGTGTCCCTTCCCC 57.143 45.455 0.00 0.00 37.69 4.81
3577 3841 9.528489 AGTTATATGATTTACAAACCAAGGTGT 57.472 29.630 0.00 0.00 0.00 4.16
3657 3921 7.755582 AACTTTAAAGTCAACATTTGCAGTC 57.244 32.000 20.78 0.00 38.57 3.51
3683 3947 0.533531 TTGTGTGCTCACTGCTCAGG 60.534 55.000 18.85 0.00 44.44 3.86
3757 4021 9.054922 ACAGCAAATAAAACATTGTATTGCTTT 57.945 25.926 16.92 11.91 29.51 3.51
3875 4147 8.877864 AAACAAAGTCCATATGAGTATTTGGA 57.122 30.769 18.41 0.00 40.65 3.53
4026 4298 7.745620 TTGGAGGTCAAGTTCTCTTAAATTC 57.254 36.000 0.00 0.00 32.07 2.17
4047 4319 6.176183 ACAATCCTCAATGTAGTTCTCTTGG 58.824 40.000 0.00 0.00 0.00 3.61
4311 4583 2.350522 TCGAGCTTTGCAAAGAGATCC 58.649 47.619 37.14 21.30 38.28 3.36
4563 4835 9.520204 AATGTGAGTGTATATTTGCAAAATAGC 57.480 29.630 17.19 7.95 0.00 2.97
4610 4882 6.855763 TCAAAGGGACATTATCAAGCATTT 57.144 33.333 0.00 0.00 0.00 2.32
4684 4960 2.038659 CAAAGAACTGGAAAGGGGCAA 58.961 47.619 0.00 0.00 0.00 4.52
4751 5027 9.713740 GTGAGACATTGATCATAATTCAGTTTC 57.286 33.333 0.00 0.00 0.00 2.78
4804 5080 7.547227 ACACAGCTTAAACTTTTCAATGAAGT 58.453 30.769 0.00 0.00 38.92 3.01
4965 5241 2.863704 GCAACTGGCAGAAACATCAACC 60.864 50.000 23.66 0.00 43.97 3.77
5202 5478 6.253512 CGATTGATTTGAACACGAGATCTGTA 59.746 38.462 0.00 0.00 0.00 2.74
5262 5538 1.108727 CACTGTTCCCAGCAAAGGCA 61.109 55.000 0.00 0.00 42.81 4.75
5318 5594 1.836166 TGATCTCCAGCTTCTTCAGGG 59.164 52.381 0.00 0.00 0.00 4.45
5598 5874 5.072600 ACTGTACCCTTAAACAATCTGGACA 59.927 40.000 0.00 0.00 0.00 4.02
5742 6018 2.101582 GTCTCATCCTACACTTGCCGAT 59.898 50.000 0.00 0.00 0.00 4.18
5800 6076 3.750371 CAGTTTCTGTAATCCACCCACA 58.250 45.455 0.00 0.00 0.00 4.17
5801 6077 2.488153 GCAGTTTCTGTAATCCACCCAC 59.512 50.000 0.00 0.00 33.43 4.61
6002 6280 9.639563 TGACCATAATTATTTAGCATCCAGAAA 57.360 29.630 0.00 0.00 0.00 2.52
6048 6409 3.744942 CACTCAGATGTCACAGTTTCCAG 59.255 47.826 0.00 0.00 0.00 3.86
6124 6486 0.036577 ACAGCCAGCACTCAGATGTC 60.037 55.000 0.00 0.00 0.00 3.06
6175 6537 5.938125 TCAAAAGTTAAGCCCTCTGACATAC 59.062 40.000 0.00 0.00 0.00 2.39
6187 6549 4.309933 AGCCAAGCAATCAAAAGTTAAGC 58.690 39.130 0.00 0.00 0.00 3.09
6342 6810 9.430838 CTCAATCGCAATTAATCTCAAGTAAAG 57.569 33.333 0.00 0.00 0.00 1.85
6343 6811 7.910162 GCTCAATCGCAATTAATCTCAAGTAAA 59.090 33.333 0.00 0.00 0.00 2.01
6417 6885 2.408050 CAGCAGGCGACATCCTATTAC 58.592 52.381 0.00 0.00 33.95 1.89
6490 6958 8.316640 AGAGATGAAAATACGATCCTAAATGC 57.683 34.615 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.