Multiple sequence alignment - TraesCS2A01G512600

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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 TraesCS2A01G512600 chr2A 100.000 3227 0 0 1 3227 737641089 737644315 0.000000e+00 5960.0
1 TraesCS2A01G512600 chr2A 93.985 1463 64 6 612 2050 737806670 737808132 0.000000e+00 2193.0
2 TraesCS2A01G512600 chr2A 86.406 743 73 11 2047 2763 737825909 737826649 0.000000e+00 787.0
3 TraesCS2A01G512600 chr2D 88.832 2722 201 31 96 2765 606128703 606131373 0.000000e+00 3247.0
4 TraesCS2A01G512600 chr2B 88.921 2455 207 25 362 2763 737047043 737049485 0.000000e+00 2966.0
5 TraesCS2A01G512600 chr2B 94.297 263 15 0 611 873 737014826 737015088 1.390000e-108 403.0
6 TraesCS2A01G512600 chr2B 87.372 293 22 9 2764 3052 737049628 737049909 4.020000e-84 322.0
7 TraesCS2A01G512600 chr2B 90.612 245 13 2 101 343 737009352 737009588 1.870000e-82 316.0
8 TraesCS2A01G512600 chrUn 100.000 418 0 0 1031 1448 477045265 477045682 0.000000e+00 773.0
9 TraesCS2A01G512600 chr6D 91.111 180 15 1 3049 3227 454210928 454211107 3.220000e-60 243.0
10 TraesCS2A01G512600 chr7D 89.362 188 19 1 3041 3227 38726886 38727073 5.380000e-58 235.0
11 TraesCS2A01G512600 chr7B 88.043 184 20 2 3046 3227 64004839 64004656 1.950000e-52 217.0
12 TraesCS2A01G512600 chr7B 87.413 143 17 1 3042 3183 22714091 22714233 2.580000e-36 163.0
13 TraesCS2A01G512600 chr7B 84.906 159 23 1 3042 3199 22789204 22789362 3.330000e-35 159.0
14 TraesCS2A01G512600 chr7B 84.906 159 23 1 3042 3199 22966454 22966612 3.330000e-35 159.0
15 TraesCS2A01G512600 chr7B 84.277 159 24 1 3042 3199 22674770 22674928 1.550000e-33 154.0
16 TraesCS2A01G512600 chr7B 83.648 159 24 2 3042 3199 22715612 22715769 7.210000e-32 148.0
17 TraesCS2A01G512600 chr7B 83.019 159 26 1 3042 3199 22838291 22838449 3.360000e-30 143.0
18 TraesCS2A01G512600 chr1B 100.000 30 0 0 65 94 87966543 87966572 4.500000e-04 56.5
19 TraesCS2A01G512600 chr3B 92.105 38 1 1 58 95 72464424 72464459 6.000000e-03 52.8


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 TraesCS2A01G512600 chr2A 737641089 737644315 3226 False 5960 5960 100.0000 1 3227 1 chr2A.!!$F1 3226
1 TraesCS2A01G512600 chr2A 737806670 737808132 1462 False 2193 2193 93.9850 612 2050 1 chr2A.!!$F2 1438
2 TraesCS2A01G512600 chr2A 737825909 737826649 740 False 787 787 86.4060 2047 2763 1 chr2A.!!$F3 716
3 TraesCS2A01G512600 chr2D 606128703 606131373 2670 False 3247 3247 88.8320 96 2765 1 chr2D.!!$F1 2669
4 TraesCS2A01G512600 chr2B 737047043 737049909 2866 False 1644 2966 88.1465 362 3052 2 chr2B.!!$F3 2690

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
894 936 0.034616 GAGGCTTGATCTCCATCCGG 59.965 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2743 2859 0.108472 TCGCCATGAGTCTCTTGCTG 60.108 55.0 9.7 5.1 0.0 4.41 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 2.426023 ACAGTGTCTGTTCGGGCC 59.574 61.111 0.00 0.00 42.59 5.80
18 19 2.425592 CAGTGTCTGTTCGGGCCA 59.574 61.111 4.39 0.00 0.00 5.36
19 20 1.961277 CAGTGTCTGTTCGGGCCAC 60.961 63.158 4.39 0.00 0.00 5.01
20 21 2.140792 AGTGTCTGTTCGGGCCACT 61.141 57.895 4.39 0.00 0.00 4.00
21 22 1.227853 GTGTCTGTTCGGGCCACTT 60.228 57.895 4.39 0.00 0.00 3.16
22 23 0.818040 GTGTCTGTTCGGGCCACTTT 60.818 55.000 4.39 0.00 0.00 2.66
23 24 0.106918 TGTCTGTTCGGGCCACTTTT 60.107 50.000 4.39 0.00 0.00 2.27
24 25 1.029681 GTCTGTTCGGGCCACTTTTT 58.970 50.000 4.39 0.00 0.00 1.94
46 47 7.551035 TTTTCACTAAAACCGTAAACTAGCA 57.449 32.000 0.00 0.00 29.59 3.49
47 48 6.774354 TTCACTAAAACCGTAAACTAGCAG 57.226 37.500 0.00 0.00 0.00 4.24
48 49 4.687483 TCACTAAAACCGTAAACTAGCAGC 59.313 41.667 0.00 0.00 0.00 5.25
49 50 4.689345 CACTAAAACCGTAAACTAGCAGCT 59.311 41.667 0.00 0.00 0.00 4.24
50 51 5.178809 CACTAAAACCGTAAACTAGCAGCTT 59.821 40.000 0.00 0.00 0.00 3.74
51 52 5.761726 ACTAAAACCGTAAACTAGCAGCTTT 59.238 36.000 0.00 0.00 0.00 3.51
52 53 5.509716 AAAACCGTAAACTAGCAGCTTTT 57.490 34.783 0.00 0.00 0.00 2.27
53 54 5.509716 AAACCGTAAACTAGCAGCTTTTT 57.490 34.783 0.00 3.48 0.00 1.94
71 72 4.555348 TTTTTGTAGTTCGGCGTGATTT 57.445 36.364 6.85 0.00 0.00 2.17
72 73 5.670149 TTTTTGTAGTTCGGCGTGATTTA 57.330 34.783 6.85 0.00 0.00 1.40
73 74 5.670149 TTTTGTAGTTCGGCGTGATTTAA 57.330 34.783 6.85 0.00 0.00 1.52
74 75 4.914312 TTGTAGTTCGGCGTGATTTAAG 57.086 40.909 6.85 0.00 0.00 1.85
75 76 3.255725 TGTAGTTCGGCGTGATTTAAGG 58.744 45.455 6.85 0.00 0.00 2.69
76 77 1.734163 AGTTCGGCGTGATTTAAGGG 58.266 50.000 6.85 0.00 0.00 3.95
77 78 0.730840 GTTCGGCGTGATTTAAGGGG 59.269 55.000 6.85 0.00 0.00 4.79
78 79 0.325602 TTCGGCGTGATTTAAGGGGT 59.674 50.000 6.85 0.00 0.00 4.95
79 80 0.108041 TCGGCGTGATTTAAGGGGTC 60.108 55.000 6.85 0.00 0.00 4.46
80 81 0.107848 CGGCGTGATTTAAGGGGTCT 60.108 55.000 0.00 0.00 0.00 3.85
81 82 1.379527 GGCGTGATTTAAGGGGTCTG 58.620 55.000 0.00 0.00 0.00 3.51
82 83 0.733150 GCGTGATTTAAGGGGTCTGC 59.267 55.000 0.00 0.00 0.00 4.26
83 84 1.679032 GCGTGATTTAAGGGGTCTGCT 60.679 52.381 0.00 0.00 0.00 4.24
84 85 2.419574 GCGTGATTTAAGGGGTCTGCTA 60.420 50.000 0.00 0.00 0.00 3.49
85 86 3.458189 CGTGATTTAAGGGGTCTGCTAG 58.542 50.000 0.00 0.00 0.00 3.42
86 87 3.132289 CGTGATTTAAGGGGTCTGCTAGA 59.868 47.826 0.00 0.00 0.00 2.43
87 88 4.698575 GTGATTTAAGGGGTCTGCTAGAG 58.301 47.826 0.00 0.00 0.00 2.43
88 89 4.406003 GTGATTTAAGGGGTCTGCTAGAGA 59.594 45.833 0.00 0.00 0.00 3.10
89 90 5.071115 GTGATTTAAGGGGTCTGCTAGAGAT 59.929 44.000 0.00 0.00 31.63 2.75
90 91 5.070981 TGATTTAAGGGGTCTGCTAGAGATG 59.929 44.000 0.00 0.00 31.63 2.90
91 92 1.127343 AAGGGGTCTGCTAGAGATGC 58.873 55.000 0.00 0.00 31.63 3.91
92 93 0.264359 AGGGGTCTGCTAGAGATGCT 59.736 55.000 0.00 0.00 31.63 3.79
93 94 0.678950 GGGGTCTGCTAGAGATGCTC 59.321 60.000 0.00 0.00 31.63 4.26
94 95 1.407936 GGGTCTGCTAGAGATGCTCA 58.592 55.000 0.00 0.00 31.63 4.26
95 96 1.340889 GGGTCTGCTAGAGATGCTCAG 59.659 57.143 0.00 0.00 31.63 3.35
96 97 2.031120 GGTCTGCTAGAGATGCTCAGT 58.969 52.381 0.00 0.00 31.63 3.41
97 98 2.430332 GGTCTGCTAGAGATGCTCAGTT 59.570 50.000 0.00 0.00 31.63 3.16
98 99 3.118811 GGTCTGCTAGAGATGCTCAGTTT 60.119 47.826 0.00 0.00 31.63 2.66
99 100 4.111916 GTCTGCTAGAGATGCTCAGTTTC 58.888 47.826 0.00 0.00 31.63 2.78
100 101 4.022603 TCTGCTAGAGATGCTCAGTTTCT 58.977 43.478 0.00 0.00 32.06 2.52
101 102 4.097741 TCTGCTAGAGATGCTCAGTTTCTC 59.902 45.833 0.00 0.00 36.88 2.87
102 103 3.766051 TGCTAGAGATGCTCAGTTTCTCA 59.234 43.478 8.26 0.00 38.67 3.27
103 104 4.142204 TGCTAGAGATGCTCAGTTTCTCAG 60.142 45.833 8.26 5.50 38.67 3.35
112 113 8.481314 AGATGCTCAGTTTCTCAGATACAAATA 58.519 33.333 0.00 0.00 0.00 1.40
117 118 6.310467 TCAGTTTCTCAGATACAAATACGCAC 59.690 38.462 0.00 0.00 0.00 5.34
120 121 2.857748 CTCAGATACAAATACGCACGCA 59.142 45.455 0.00 0.00 0.00 5.24
147 148 7.663081 AGTGCATATATACACAAATCCAAGGAG 59.337 37.037 16.65 0.00 39.30 3.69
148 149 6.430925 TGCATATATACACAAATCCAAGGAGC 59.569 38.462 0.00 0.00 0.00 4.70
190 191 3.594568 GCAGCACTAGCCAATGCA 58.405 55.556 5.91 0.00 44.59 3.96
191 192 2.112898 GCAGCACTAGCCAATGCAT 58.887 52.632 5.91 0.00 44.59 3.96
192 193 1.311859 GCAGCACTAGCCAATGCATA 58.688 50.000 0.00 0.00 44.59 3.14
193 194 1.266175 GCAGCACTAGCCAATGCATAG 59.734 52.381 0.00 0.00 44.59 2.23
194 195 1.878088 CAGCACTAGCCAATGCATAGG 59.122 52.381 0.00 0.00 44.59 2.57
195 196 1.770658 AGCACTAGCCAATGCATAGGA 59.229 47.619 0.00 0.00 44.59 2.94
196 197 2.374504 AGCACTAGCCAATGCATAGGAT 59.625 45.455 0.00 0.00 44.59 3.24
197 198 2.486982 GCACTAGCCAATGCATAGGATG 59.513 50.000 0.00 0.00 41.65 3.51
240 241 5.812127 TGGTGATACACATGAGATTTTCTCG 59.188 40.000 0.00 0.00 40.12 4.04
413 414 1.066908 CACTTGCCATGTTTGAACCGT 59.933 47.619 0.00 0.00 0.00 4.83
518 529 3.084039 CTGTTTATTTCTGCTGCCTCCA 58.916 45.455 0.00 0.00 0.00 3.86
553 577 1.476891 CCTTCTTCGATCCGGACTCAA 59.523 52.381 6.12 0.00 0.00 3.02
555 579 0.815734 TCTTCGATCCGGACTCAACC 59.184 55.000 6.12 0.00 0.00 3.77
579 603 1.080772 CGTGAAGTGGCGCTAGACA 60.081 57.895 7.64 0.00 0.00 3.41
619 650 2.122167 GCGTCCAGATCTCGACCCT 61.122 63.158 13.98 0.00 0.00 4.34
706 737 1.259609 CTTCATTTGCTTGGCCTCCA 58.740 50.000 3.32 0.00 0.00 3.86
717 748 3.771160 GCCTCCACCCGTCGACAT 61.771 66.667 17.16 0.00 0.00 3.06
732 763 2.356793 CATCAGATCGGAGCGCCC 60.357 66.667 2.29 3.94 0.00 6.13
734 765 2.212811 ATCAGATCGGAGCGCCCAT 61.213 57.895 2.29 0.00 34.14 4.00
736 767 1.080230 CAGATCGGAGCGCCCATAG 60.080 63.158 2.29 0.00 34.14 2.23
759 790 2.249844 TCTTCGACCCAGAAACAACC 57.750 50.000 0.00 0.00 0.00 3.77
824 866 1.321074 GGAACCCCTCACTCGATCGT 61.321 60.000 15.94 0.00 0.00 3.73
838 880 0.249489 GATCGTGATCCTGGTTCGGG 60.249 60.000 0.00 0.00 31.76 5.14
888 930 2.911484 ACAAATCGAGGCTTGATCTCC 58.089 47.619 17.48 0.00 0.00 3.71
893 935 0.319383 CGAGGCTTGATCTCCATCCG 60.319 60.000 0.00 0.00 0.00 4.18
894 936 0.034616 GAGGCTTGATCTCCATCCGG 59.965 60.000 0.00 0.00 0.00 5.14
906 948 3.036091 CTCCATCCGGAAAGGTAGGTAA 58.964 50.000 21.69 4.97 42.21 2.85
909 955 4.134563 CCATCCGGAAAGGTAGGTAAATG 58.865 47.826 9.01 0.00 41.99 2.32
911 957 5.163280 CCATCCGGAAAGGTAGGTAAATGTA 60.163 44.000 9.01 0.00 41.99 2.29
933 979 8.641499 TGTATTTGTTGAGGTGTTCAATTTTC 57.359 30.769 0.00 0.00 46.85 2.29
942 988 4.646492 AGGTGTTCAATTTTCACTCTGCTT 59.354 37.500 0.00 0.00 33.30 3.91
943 989 4.741676 GGTGTTCAATTTTCACTCTGCTTG 59.258 41.667 0.00 0.00 33.30 4.01
944 990 5.343249 GTGTTCAATTTTCACTCTGCTTGT 58.657 37.500 0.00 0.00 0.00 3.16
945 991 5.807011 GTGTTCAATTTTCACTCTGCTTGTT 59.193 36.000 0.00 0.00 0.00 2.83
946 992 5.806502 TGTTCAATTTTCACTCTGCTTGTTG 59.193 36.000 0.00 0.00 0.00 3.33
947 993 4.362279 TCAATTTTCACTCTGCTTGTTGC 58.638 39.130 0.00 0.00 43.25 4.17
948 994 2.869233 TTTTCACTCTGCTTGTTGCC 57.131 45.000 0.00 0.00 42.00 4.52
949 995 1.032014 TTTCACTCTGCTTGTTGCCC 58.968 50.000 0.00 0.00 42.00 5.36
960 1014 0.961019 TTGTTGCCCTGTTCATCTGC 59.039 50.000 0.00 0.00 0.00 4.26
1570 1650 5.521010 AGTCATTGATTGCAAACACAACAAG 59.479 36.000 9.14 7.60 37.59 3.16
1828 1912 3.587506 TGCTGATGGATGATGATGAGGAT 59.412 43.478 0.00 0.00 0.00 3.24
1850 1934 1.911057 TCTTGCTGGAAGTCTCGAGA 58.089 50.000 12.08 12.08 35.30 4.04
1877 1961 6.605594 CCAAGAATTTAGTGGTAAAGCCCATA 59.394 38.462 0.00 0.00 36.74 2.74
1894 1978 5.299279 AGCCCATATACAGTGTTGTATTTGC 59.701 40.000 0.00 6.05 45.92 3.68
1994 2079 2.813061 GCAACAAGCAAAGAAGCAGAA 58.187 42.857 0.00 0.00 44.79 3.02
2014 2099 3.990318 AGAAACAAAGAAAGAAGCGGG 57.010 42.857 0.00 0.00 0.00 6.13
2044 2129 3.056607 AGAAAGCAAAACAGGCGCAATAT 60.057 39.130 10.83 0.00 36.08 1.28
2063 2148 1.517257 CTTGCCGCGGACTAGACTG 60.517 63.158 33.48 5.09 0.00 3.51
2090 2175 1.337071 CCATGACAGATCAAGCCATGC 59.663 52.381 8.35 0.00 38.69 4.06
2099 2184 0.405198 TCAAGCCATGCCTTCCTCAA 59.595 50.000 0.00 0.00 0.00 3.02
2159 2244 8.713971 TGGTGTTAAGATCACTCATGGTAATAT 58.286 33.333 0.00 0.00 36.25 1.28
2222 2307 1.015109 CAGGATGCATCTGTGTCAGC 58.985 55.000 25.28 6.91 0.00 4.26
2243 2328 3.294493 GCATGTGGGTGCACCGTT 61.294 61.111 29.08 11.01 44.43 4.44
2244 2329 2.953821 CATGTGGGTGCACCGTTC 59.046 61.111 29.08 20.54 44.64 3.95
2261 2346 2.964768 CGTTCGTTGTAGCTTCTTTTGC 59.035 45.455 0.00 0.00 0.00 3.68
2282 2367 1.173913 GCGGCAGATGTAACCCTTTT 58.826 50.000 0.00 0.00 0.00 2.27
2303 2388 2.504175 TGATTAGGGGAACACTAGCCAC 59.496 50.000 0.00 0.00 0.00 5.01
2368 2453 8.204160 AGCCTTTAGTTTAAATTGCAAAGTCTT 58.796 29.630 1.71 0.00 31.57 3.01
2369 2454 8.826710 GCCTTTAGTTTAAATTGCAAAGTCTTT 58.173 29.630 1.71 1.72 0.00 2.52
2379 2464 4.903638 TGCAAAGTCTTTATCGTTCGAG 57.096 40.909 0.00 0.00 0.00 4.04
2392 2477 1.332640 CGTTCGAGCATTGCAGCATAG 60.333 52.381 11.91 0.00 36.85 2.23
2401 2486 2.472695 TTGCAGCATAGAACTTCCGT 57.527 45.000 0.00 0.00 0.00 4.69
2405 2490 1.929836 CAGCATAGAACTTCCGTGCTC 59.070 52.381 13.05 0.00 43.68 4.26
2413 2498 4.642429 AGAACTTCCGTGCTCTACATTTT 58.358 39.130 0.00 0.00 0.00 1.82
2420 2505 4.154015 TCCGTGCTCTACATTTTCAACATG 59.846 41.667 0.00 0.00 0.00 3.21
2427 2512 6.349280 GCTCTACATTTTCAACATGGTAGCAA 60.349 38.462 0.00 0.00 30.81 3.91
2459 2544 6.097554 TGTTGTGGTGTGTCAAAAATAAGGAT 59.902 34.615 0.00 0.00 0.00 3.24
2506 2602 3.244181 ACAACCATGCATGACCTTTTTCC 60.244 43.478 28.31 0.00 0.00 3.13
2508 2604 4.046286 ACCATGCATGACCTTTTTCCTA 57.954 40.909 28.31 0.00 0.00 2.94
2517 2613 6.555315 CATGACCTTTTTCCTAGTATGCAAC 58.445 40.000 0.00 0.00 0.00 4.17
2612 2726 3.379688 TCAGCAACACAACATTTGTAGCA 59.620 39.130 10.81 0.00 43.23 3.49
2632 2746 5.999044 AGCAGACCTTAAGAATCATCACAT 58.001 37.500 3.36 0.00 0.00 3.21
2640 2754 7.830697 ACCTTAAGAATCATCACATCATGTTGA 59.169 33.333 10.74 4.07 40.50 3.18
2641 2755 8.127327 CCTTAAGAATCATCACATCATGTTGAC 58.873 37.037 10.74 0.00 39.34 3.18
2668 2783 7.748241 GTGTGTTTGCAACAACATAAAAACAAT 59.252 29.630 14.60 0.00 44.16 2.71
2674 2789 6.039047 TGCAACAACATAAAAACAATGCCATT 59.961 30.769 0.00 0.00 0.00 3.16
2694 2810 0.521242 GCATGTCGGACGAATGTTGC 60.521 55.000 3.34 0.26 0.00 4.17
2721 2837 4.510571 TCGAATAACCCAAAGCTAACCTC 58.489 43.478 0.00 0.00 0.00 3.85
2732 2848 1.819903 AGCTAACCTCTGTCCTCGAAC 59.180 52.381 0.00 0.00 0.00 3.95
2734 2850 1.811359 CTAACCTCTGTCCTCGAACGT 59.189 52.381 0.00 0.00 0.00 3.99
2740 2856 1.955778 TCTGTCCTCGAACGTAAACCA 59.044 47.619 0.00 0.00 0.00 3.67
2743 2859 1.788886 GTCCTCGAACGTAAACCACAC 59.211 52.381 0.00 0.00 0.00 3.82
2747 2863 0.931702 CGAACGTAAACCACACAGCA 59.068 50.000 0.00 0.00 0.00 4.41
2756 2872 1.123077 ACCACACAGCAAGAGACTCA 58.877 50.000 5.02 0.00 0.00 3.41
2765 2881 0.109086 CAAGAGACTCATGGCGACGT 60.109 55.000 5.02 0.00 0.00 4.34
2784 3042 2.502142 TGGAGAAGTGCTGCATCAAT 57.498 45.000 5.27 0.00 40.31 2.57
2785 3043 2.362736 TGGAGAAGTGCTGCATCAATC 58.637 47.619 5.27 2.52 40.31 2.67
2786 3044 2.290450 TGGAGAAGTGCTGCATCAATCA 60.290 45.455 5.27 0.00 40.31 2.57
2787 3045 2.751259 GGAGAAGTGCTGCATCAATCAA 59.249 45.455 5.27 0.00 34.66 2.57
2788 3046 3.181499 GGAGAAGTGCTGCATCAATCAAG 60.181 47.826 5.27 0.00 34.66 3.02
2795 3053 5.009911 AGTGCTGCATCAATCAAGTAAACAA 59.990 36.000 5.27 0.00 0.00 2.83
2798 3056 5.164022 GCTGCATCAATCAAGTAAACAAAGC 60.164 40.000 0.00 0.00 0.00 3.51
2804 3062 7.985634 TCAATCAAGTAAACAAAGCAGAAAC 57.014 32.000 0.00 0.00 0.00 2.78
2816 3074 2.693069 AGCAGAAACACGAGAGGAATG 58.307 47.619 0.00 0.00 0.00 2.67
2883 3141 7.334921 CGGTGGAAAGGTATCATTTACTGTTTA 59.665 37.037 0.00 0.00 0.00 2.01
2929 3187 8.274322 TGTTTGGTTATATCTCATCATTGGTCT 58.726 33.333 0.00 0.00 0.00 3.85
2951 3211 1.445871 AAAAGACGAATACCACGGGC 58.554 50.000 0.00 0.00 34.93 6.13
2962 3222 1.480789 ACCACGGGCTTTGTCTTTTT 58.519 45.000 0.00 0.00 0.00 1.94
2964 3224 1.269569 CCACGGGCTTTGTCTTTTTCC 60.270 52.381 0.00 0.00 0.00 3.13
2968 3228 3.196901 ACGGGCTTTGTCTTTTTCCTTTT 59.803 39.130 0.00 0.00 0.00 2.27
2990 3250 6.613153 TTTTTGGGGGTGAAAACCATATAG 57.387 37.500 0.00 0.00 33.63 1.31
2991 3251 3.963476 TGGGGGTGAAAACCATATAGG 57.037 47.619 0.00 0.00 45.67 2.57
2992 3252 3.475936 TGGGGGTGAAAACCATATAGGA 58.524 45.455 0.00 0.00 41.22 2.94
2996 3256 5.454966 GGGGTGAAAACCATATAGGATTGT 58.545 41.667 0.00 0.00 41.22 2.71
3006 3266 5.132502 CCATATAGGATTGTCAAGTGGCAA 58.867 41.667 0.03 0.03 44.39 4.52
3032 3292 0.532862 CACGGGTGCTTTGAGACACT 60.533 55.000 0.00 0.00 36.99 3.55
3033 3293 0.532862 ACGGGTGCTTTGAGACACTG 60.533 55.000 0.00 0.00 36.99 3.66
3039 3299 1.684450 TGCTTTGAGACACTGGTACGA 59.316 47.619 0.00 0.00 0.00 3.43
3048 3308 4.913126 CTGGTACGAGTTCCAGCC 57.087 61.111 14.39 0.00 43.45 4.85
3049 3309 1.972198 CTGGTACGAGTTCCAGCCA 59.028 57.895 14.39 1.02 43.45 4.75
3051 3311 0.034337 TGGTACGAGTTCCAGCCAAC 59.966 55.000 0.00 0.00 0.00 3.77
3052 3312 1.012486 GGTACGAGTTCCAGCCAACG 61.012 60.000 0.00 0.00 0.00 4.10
3053 3313 0.319297 GTACGAGTTCCAGCCAACGT 60.319 55.000 0.00 0.00 37.68 3.99
3054 3314 0.390124 TACGAGTTCCAGCCAACGTT 59.610 50.000 0.00 0.00 35.66 3.99
3055 3315 0.463116 ACGAGTTCCAGCCAACGTTT 60.463 50.000 0.00 0.00 0.00 3.60
3056 3316 0.661020 CGAGTTCCAGCCAACGTTTT 59.339 50.000 0.00 0.00 0.00 2.43
3057 3317 1.596954 CGAGTTCCAGCCAACGTTTTG 60.597 52.381 0.00 0.00 0.00 2.44
3067 3327 3.757745 CCAACGTTTTGGCTATCGAAT 57.242 42.857 0.00 0.00 46.09 3.34
3068 3328 3.680789 CCAACGTTTTGGCTATCGAATC 58.319 45.455 0.00 0.00 46.09 2.52
3069 3329 3.486875 CCAACGTTTTGGCTATCGAATCC 60.487 47.826 0.00 0.00 46.09 3.01
3070 3330 2.285977 ACGTTTTGGCTATCGAATCCC 58.714 47.619 0.00 0.00 0.00 3.85
3071 3331 2.285083 CGTTTTGGCTATCGAATCCCA 58.715 47.619 0.00 0.00 0.00 4.37
3072 3332 2.680841 CGTTTTGGCTATCGAATCCCAA 59.319 45.455 9.21 9.21 35.68 4.12
3073 3333 3.486875 CGTTTTGGCTATCGAATCCCAAC 60.487 47.826 11.96 7.76 37.10 3.77
3074 3334 3.358111 TTTGGCTATCGAATCCCAACA 57.642 42.857 11.96 3.97 37.10 3.33
3075 3335 3.358111 TTGGCTATCGAATCCCAACAA 57.642 42.857 9.21 0.00 32.73 2.83
3076 3336 3.358111 TGGCTATCGAATCCCAACAAA 57.642 42.857 0.00 0.00 0.00 2.83
3077 3337 3.691575 TGGCTATCGAATCCCAACAAAA 58.308 40.909 0.00 0.00 0.00 2.44
3078 3338 4.277476 TGGCTATCGAATCCCAACAAAAT 58.723 39.130 0.00 0.00 0.00 1.82
3079 3339 4.709397 TGGCTATCGAATCCCAACAAAATT 59.291 37.500 0.00 0.00 0.00 1.82
3080 3340 5.163561 TGGCTATCGAATCCCAACAAAATTC 60.164 40.000 0.00 0.00 0.00 2.17
3081 3341 5.281727 GCTATCGAATCCCAACAAAATTCC 58.718 41.667 0.00 0.00 0.00 3.01
3082 3342 3.840890 TCGAATCCCAACAAAATTCCG 57.159 42.857 0.00 0.00 0.00 4.30
3083 3343 3.413327 TCGAATCCCAACAAAATTCCGA 58.587 40.909 0.00 0.00 0.00 4.55
3084 3344 3.438781 TCGAATCCCAACAAAATTCCGAG 59.561 43.478 0.00 0.00 0.00 4.63
3085 3345 3.427503 CGAATCCCAACAAAATTCCGAGG 60.428 47.826 0.00 0.00 0.00 4.63
3086 3346 1.917872 TCCCAACAAAATTCCGAGGG 58.082 50.000 0.00 0.00 36.15 4.30
3087 3347 1.146152 TCCCAACAAAATTCCGAGGGT 59.854 47.619 0.00 0.00 36.24 4.34
3088 3348 1.272212 CCCAACAAAATTCCGAGGGTG 59.728 52.381 0.00 0.00 0.00 4.61
3089 3349 1.272212 CCAACAAAATTCCGAGGGTGG 59.728 52.381 0.00 0.00 0.00 4.61
3090 3350 1.272212 CAACAAAATTCCGAGGGTGGG 59.728 52.381 0.00 0.00 0.00 4.61
3091 3351 0.898326 ACAAAATTCCGAGGGTGGGC 60.898 55.000 0.00 0.00 0.00 5.36
3092 3352 1.677633 AAAATTCCGAGGGTGGGCG 60.678 57.895 0.00 0.00 0.00 6.13
3093 3353 2.132089 AAAATTCCGAGGGTGGGCGA 62.132 55.000 0.00 0.00 0.00 5.54
3094 3354 2.536997 AAATTCCGAGGGTGGGCGAG 62.537 60.000 0.00 0.00 0.00 5.03
3095 3355 3.976490 ATTCCGAGGGTGGGCGAGA 62.976 63.158 0.00 0.00 0.00 4.04
3096 3356 4.689549 TCCGAGGGTGGGCGAGAA 62.690 66.667 0.00 0.00 0.00 2.87
3097 3357 3.702048 CCGAGGGTGGGCGAGAAA 61.702 66.667 0.00 0.00 0.00 2.52
3098 3358 2.434359 CGAGGGTGGGCGAGAAAC 60.434 66.667 0.00 0.00 0.00 2.78
3099 3359 2.434359 GAGGGTGGGCGAGAAACG 60.434 66.667 0.00 0.00 45.66 3.60
3121 3381 2.806244 CGGATACCGCAAAATTAGGAGG 59.194 50.000 0.00 0.00 41.17 4.30
3122 3382 3.493699 CGGATACCGCAAAATTAGGAGGA 60.494 47.826 6.13 0.00 41.17 3.71
3123 3383 4.457466 GGATACCGCAAAATTAGGAGGAA 58.543 43.478 6.13 0.00 0.00 3.36
3124 3384 4.885325 GGATACCGCAAAATTAGGAGGAAA 59.115 41.667 6.13 0.00 0.00 3.13
3125 3385 5.358725 GGATACCGCAAAATTAGGAGGAAAA 59.641 40.000 6.13 0.00 0.00 2.29
3126 3386 6.127563 GGATACCGCAAAATTAGGAGGAAAAA 60.128 38.462 6.13 0.00 0.00 1.94
3127 3387 4.878439 ACCGCAAAATTAGGAGGAAAAAC 58.122 39.130 6.13 0.00 0.00 2.43
3128 3388 4.242475 CCGCAAAATTAGGAGGAAAAACC 58.758 43.478 0.00 0.00 39.35 3.27
3129 3389 3.917985 CGCAAAATTAGGAGGAAAAACCG 59.082 43.478 0.00 0.00 44.74 4.44
3130 3390 4.557895 CGCAAAATTAGGAGGAAAAACCGT 60.558 41.667 0.00 0.00 44.74 4.83
3131 3391 5.294356 GCAAAATTAGGAGGAAAAACCGTT 58.706 37.500 0.00 0.00 44.74 4.44
3132 3392 5.404366 GCAAAATTAGGAGGAAAAACCGTTC 59.596 40.000 0.00 0.00 44.74 3.95
3133 3393 5.366829 AAATTAGGAGGAAAAACCGTTCG 57.633 39.130 0.00 0.00 44.74 3.95
3134 3394 3.749665 TTAGGAGGAAAAACCGTTCGA 57.250 42.857 0.00 0.00 44.74 3.71
3135 3395 2.625695 AGGAGGAAAAACCGTTCGAA 57.374 45.000 0.00 0.00 44.74 3.71
3136 3396 3.136009 AGGAGGAAAAACCGTTCGAAT 57.864 42.857 0.00 0.00 44.74 3.34
3137 3397 3.483421 AGGAGGAAAAACCGTTCGAATT 58.517 40.909 0.00 0.00 44.74 2.17
3138 3398 3.887110 AGGAGGAAAAACCGTTCGAATTT 59.113 39.130 0.00 0.00 44.74 1.82
3139 3399 4.340097 AGGAGGAAAAACCGTTCGAATTTT 59.660 37.500 0.00 3.88 44.74 1.82
3140 3400 5.532032 AGGAGGAAAAACCGTTCGAATTTTA 59.468 36.000 0.00 0.00 44.74 1.52
3141 3401 6.039605 AGGAGGAAAAACCGTTCGAATTTTAA 59.960 34.615 0.00 0.00 44.74 1.52
3142 3402 6.696583 GGAGGAAAAACCGTTCGAATTTTAAA 59.303 34.615 0.00 0.00 44.74 1.52
3143 3403 7.222417 GGAGGAAAAACCGTTCGAATTTTAAAA 59.778 33.333 0.00 2.51 44.74 1.52
3144 3404 7.897920 AGGAAAAACCGTTCGAATTTTAAAAC 58.102 30.769 0.00 0.00 44.74 2.43
3145 3405 7.544915 AGGAAAAACCGTTCGAATTTTAAAACA 59.455 29.630 0.00 0.00 44.74 2.83
3146 3406 8.329583 GGAAAAACCGTTCGAATTTTAAAACAT 58.670 29.630 0.00 0.00 0.00 2.71
3193 3453 9.015367 TGATATAGGAATATATTAGCTCGGAGC 57.985 37.037 22.13 22.13 42.84 4.70
3203 3463 3.523806 GCTCGGAGCTCAAGAAGTT 57.476 52.632 22.32 0.00 38.45 2.66
3204 3464 1.802069 GCTCGGAGCTCAAGAAGTTT 58.198 50.000 22.32 0.00 38.45 2.66
3205 3465 2.960819 GCTCGGAGCTCAAGAAGTTTA 58.039 47.619 22.32 0.00 38.45 2.01
3206 3466 3.526534 GCTCGGAGCTCAAGAAGTTTAT 58.473 45.455 22.32 0.00 38.45 1.40
3207 3467 4.683832 GCTCGGAGCTCAAGAAGTTTATA 58.316 43.478 22.32 0.00 38.45 0.98
3208 3468 5.109903 GCTCGGAGCTCAAGAAGTTTATAA 58.890 41.667 22.32 0.00 38.45 0.98
3209 3469 5.581085 GCTCGGAGCTCAAGAAGTTTATAAA 59.419 40.000 22.32 0.00 38.45 1.40
3210 3470 6.258947 GCTCGGAGCTCAAGAAGTTTATAAAT 59.741 38.462 22.32 0.00 38.45 1.40
3211 3471 7.201652 GCTCGGAGCTCAAGAAGTTTATAAATT 60.202 37.037 22.32 0.00 38.45 1.82
3212 3472 8.197988 TCGGAGCTCAAGAAGTTTATAAATTC 57.802 34.615 17.19 6.70 0.00 2.17
3213 3473 7.822334 TCGGAGCTCAAGAAGTTTATAAATTCA 59.178 33.333 17.19 3.21 0.00 2.57
3214 3474 7.905493 CGGAGCTCAAGAAGTTTATAAATTCAC 59.095 37.037 17.19 6.51 0.00 3.18
3215 3475 8.951243 GGAGCTCAAGAAGTTTATAAATTCACT 58.049 33.333 17.19 8.05 0.00 3.41
3216 3476 9.766277 GAGCTCAAGAAGTTTATAAATTCACTG 57.234 33.333 9.40 13.52 0.00 3.66
3217 3477 9.289782 AGCTCAAGAAGTTTATAAATTCACTGT 57.710 29.630 16.12 0.00 0.00 3.55
3218 3478 9.899226 GCTCAAGAAGTTTATAAATTCACTGTT 57.101 29.630 16.12 2.34 0.00 3.16
3221 3481 9.965824 CAAGAAGTTTATAAATTCACTGTTGGT 57.034 29.630 16.12 0.00 0.00 3.67
3222 3482 9.965824 AAGAAGTTTATAAATTCACTGTTGGTG 57.034 29.630 16.12 0.00 46.60 4.17
3223 3483 8.082242 AGAAGTTTATAAATTCACTGTTGGTGC 58.918 33.333 16.12 0.00 44.98 5.01
3224 3484 7.283625 AGTTTATAAATTCACTGTTGGTGCA 57.716 32.000 0.31 0.00 44.98 4.57
3225 3485 7.370383 AGTTTATAAATTCACTGTTGGTGCAG 58.630 34.615 0.31 0.00 44.98 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.961277 GTGGCCCGAACAGACACTG 60.961 63.158 0.00 0.00 37.52 3.66
2 3 1.696097 AAGTGGCCCGAACAGACACT 61.696 55.000 0.00 0.00 43.61 3.55
3 4 0.818040 AAAGTGGCCCGAACAGACAC 60.818 55.000 0.00 0.00 0.00 3.67
4 5 0.106918 AAAAGTGGCCCGAACAGACA 60.107 50.000 0.00 0.00 0.00 3.41
5 6 1.029681 AAAAAGTGGCCCGAACAGAC 58.970 50.000 0.00 0.00 0.00 3.51
6 7 3.505835 AAAAAGTGGCCCGAACAGA 57.494 47.368 0.00 0.00 0.00 3.41
21 22 7.983307 TGCTAGTTTACGGTTTTAGTGAAAAA 58.017 30.769 0.00 0.00 36.32 1.94
22 23 7.551035 TGCTAGTTTACGGTTTTAGTGAAAA 57.449 32.000 0.00 0.00 32.00 2.29
23 24 6.293027 GCTGCTAGTTTACGGTTTTAGTGAAA 60.293 38.462 0.00 0.00 0.00 2.69
24 25 5.178067 GCTGCTAGTTTACGGTTTTAGTGAA 59.822 40.000 0.00 0.00 0.00 3.18
25 26 4.687483 GCTGCTAGTTTACGGTTTTAGTGA 59.313 41.667 0.00 0.00 0.00 3.41
26 27 4.689345 AGCTGCTAGTTTACGGTTTTAGTG 59.311 41.667 0.00 0.00 0.00 2.74
27 28 4.891260 AGCTGCTAGTTTACGGTTTTAGT 58.109 39.130 0.00 0.00 0.00 2.24
28 29 5.857822 AAGCTGCTAGTTTACGGTTTTAG 57.142 39.130 0.90 0.00 0.00 1.85
29 30 6.622833 AAAAGCTGCTAGTTTACGGTTTTA 57.377 33.333 0.90 0.00 34.67 1.52
30 31 5.509716 AAAAGCTGCTAGTTTACGGTTTT 57.490 34.783 0.90 0.00 32.47 2.43
31 32 5.509716 AAAAAGCTGCTAGTTTACGGTTT 57.490 34.783 0.90 0.00 0.00 3.27
50 51 4.555348 AAATCACGCCGAACTACAAAAA 57.445 36.364 0.00 0.00 0.00 1.94
51 52 5.334260 CCTTAAATCACGCCGAACTACAAAA 60.334 40.000 0.00 0.00 0.00 2.44
52 53 4.152759 CCTTAAATCACGCCGAACTACAAA 59.847 41.667 0.00 0.00 0.00 2.83
53 54 3.680937 CCTTAAATCACGCCGAACTACAA 59.319 43.478 0.00 0.00 0.00 2.41
54 55 3.255725 CCTTAAATCACGCCGAACTACA 58.744 45.455 0.00 0.00 0.00 2.74
55 56 2.606272 CCCTTAAATCACGCCGAACTAC 59.394 50.000 0.00 0.00 0.00 2.73
56 57 2.419021 CCCCTTAAATCACGCCGAACTA 60.419 50.000 0.00 0.00 0.00 2.24
57 58 1.677820 CCCCTTAAATCACGCCGAACT 60.678 52.381 0.00 0.00 0.00 3.01
58 59 0.730840 CCCCTTAAATCACGCCGAAC 59.269 55.000 0.00 0.00 0.00 3.95
59 60 0.325602 ACCCCTTAAATCACGCCGAA 59.674 50.000 0.00 0.00 0.00 4.30
60 61 0.108041 GACCCCTTAAATCACGCCGA 60.108 55.000 0.00 0.00 0.00 5.54
61 62 0.107848 AGACCCCTTAAATCACGCCG 60.108 55.000 0.00 0.00 0.00 6.46
62 63 1.379527 CAGACCCCTTAAATCACGCC 58.620 55.000 0.00 0.00 0.00 5.68
63 64 0.733150 GCAGACCCCTTAAATCACGC 59.267 55.000 0.00 0.00 0.00 5.34
64 65 2.403252 AGCAGACCCCTTAAATCACG 57.597 50.000 0.00 0.00 0.00 4.35
65 66 4.406003 TCTCTAGCAGACCCCTTAAATCAC 59.594 45.833 0.00 0.00 0.00 3.06
66 67 4.620723 TCTCTAGCAGACCCCTTAAATCA 58.379 43.478 0.00 0.00 0.00 2.57
67 68 5.546526 CATCTCTAGCAGACCCCTTAAATC 58.453 45.833 0.00 0.00 32.26 2.17
68 69 4.202409 GCATCTCTAGCAGACCCCTTAAAT 60.202 45.833 0.00 0.00 32.26 1.40
69 70 3.134804 GCATCTCTAGCAGACCCCTTAAA 59.865 47.826 0.00 0.00 32.26 1.52
70 71 2.700897 GCATCTCTAGCAGACCCCTTAA 59.299 50.000 0.00 0.00 32.26 1.85
71 72 2.091055 AGCATCTCTAGCAGACCCCTTA 60.091 50.000 0.00 0.00 32.26 2.69
72 73 1.127343 GCATCTCTAGCAGACCCCTT 58.873 55.000 0.00 0.00 32.26 3.95
73 74 0.264359 AGCATCTCTAGCAGACCCCT 59.736 55.000 0.00 0.00 32.26 4.79
74 75 0.678950 GAGCATCTCTAGCAGACCCC 59.321 60.000 0.00 0.00 32.26 4.95
75 76 1.340889 CTGAGCATCTCTAGCAGACCC 59.659 57.143 0.00 0.00 32.26 4.46
76 77 2.031120 ACTGAGCATCTCTAGCAGACC 58.969 52.381 0.00 0.00 32.26 3.85
77 78 3.799281 AACTGAGCATCTCTAGCAGAC 57.201 47.619 0.00 0.00 32.26 3.51
78 79 4.022603 AGAAACTGAGCATCTCTAGCAGA 58.977 43.478 0.00 0.00 34.92 4.26
79 80 4.142204 TGAGAAACTGAGCATCTCTAGCAG 60.142 45.833 13.90 0.00 40.18 4.24
80 81 3.766051 TGAGAAACTGAGCATCTCTAGCA 59.234 43.478 13.90 0.00 40.18 3.49
81 82 4.097741 TCTGAGAAACTGAGCATCTCTAGC 59.902 45.833 13.90 0.00 40.18 3.42
82 83 5.833406 TCTGAGAAACTGAGCATCTCTAG 57.167 43.478 13.90 10.37 40.18 2.43
83 84 6.830838 TGTATCTGAGAAACTGAGCATCTCTA 59.169 38.462 13.90 5.41 40.18 2.43
84 85 5.655974 TGTATCTGAGAAACTGAGCATCTCT 59.344 40.000 13.90 0.00 40.18 3.10
85 86 5.900425 TGTATCTGAGAAACTGAGCATCTC 58.100 41.667 7.84 7.84 39.98 2.75
86 87 5.929058 TGTATCTGAGAAACTGAGCATCT 57.071 39.130 0.00 0.00 34.92 2.90
87 88 6.974932 TTTGTATCTGAGAAACTGAGCATC 57.025 37.500 0.00 0.00 0.00 3.91
88 89 7.223582 CGTATTTGTATCTGAGAAACTGAGCAT 59.776 37.037 0.00 0.00 0.00 3.79
89 90 6.531594 CGTATTTGTATCTGAGAAACTGAGCA 59.468 38.462 0.00 0.00 0.00 4.26
90 91 6.508721 GCGTATTTGTATCTGAGAAACTGAGC 60.509 42.308 0.00 0.00 0.00 4.26
91 92 6.531594 TGCGTATTTGTATCTGAGAAACTGAG 59.468 38.462 0.00 0.00 0.00 3.35
92 93 6.310467 GTGCGTATTTGTATCTGAGAAACTGA 59.690 38.462 0.00 0.00 0.00 3.41
93 94 6.470160 GTGCGTATTTGTATCTGAGAAACTG 58.530 40.000 0.00 0.00 0.00 3.16
94 95 5.288712 CGTGCGTATTTGTATCTGAGAAACT 59.711 40.000 0.00 0.00 0.00 2.66
95 96 5.481472 CGTGCGTATTTGTATCTGAGAAAC 58.519 41.667 0.00 0.00 0.00 2.78
96 97 4.032445 GCGTGCGTATTTGTATCTGAGAAA 59.968 41.667 0.00 0.00 0.00 2.52
97 98 3.550275 GCGTGCGTATTTGTATCTGAGAA 59.450 43.478 0.00 0.00 0.00 2.87
98 99 3.113322 GCGTGCGTATTTGTATCTGAGA 58.887 45.455 0.00 0.00 0.00 3.27
99 100 2.857748 TGCGTGCGTATTTGTATCTGAG 59.142 45.455 0.00 0.00 0.00 3.35
100 101 2.882324 TGCGTGCGTATTTGTATCTGA 58.118 42.857 0.00 0.00 0.00 3.27
101 102 3.062099 ACTTGCGTGCGTATTTGTATCTG 59.938 43.478 0.00 0.00 0.00 2.90
102 103 3.062099 CACTTGCGTGCGTATTTGTATCT 59.938 43.478 0.00 0.00 33.82 1.98
103 104 3.342269 CACTTGCGTGCGTATTTGTATC 58.658 45.455 0.00 0.00 33.82 2.24
117 118 6.079763 GGATTTGTGTATATATGCACTTGCG 58.920 40.000 27.35 0.00 45.83 4.85
120 121 7.998383 TCCTTGGATTTGTGTATATATGCACTT 59.002 33.333 27.35 16.06 42.76 3.16
190 191 6.857848 TCAGAACTCACTCCTATCATCCTAT 58.142 40.000 0.00 0.00 0.00 2.57
191 192 6.267492 TCAGAACTCACTCCTATCATCCTA 57.733 41.667 0.00 0.00 0.00 2.94
192 193 5.136068 TCAGAACTCACTCCTATCATCCT 57.864 43.478 0.00 0.00 0.00 3.24
193 194 5.860941 TTCAGAACTCACTCCTATCATCC 57.139 43.478 0.00 0.00 0.00 3.51
194 195 6.183360 ACCATTCAGAACTCACTCCTATCATC 60.183 42.308 0.00 0.00 0.00 2.92
195 196 5.664908 ACCATTCAGAACTCACTCCTATCAT 59.335 40.000 0.00 0.00 0.00 2.45
196 197 5.026121 ACCATTCAGAACTCACTCCTATCA 58.974 41.667 0.00 0.00 0.00 2.15
197 198 5.127845 TCACCATTCAGAACTCACTCCTATC 59.872 44.000 0.00 0.00 0.00 2.08
276 277 6.976925 CACATCTTTCTTTGCAGAGAAACTTT 59.023 34.615 24.25 11.75 39.90 2.66
279 280 5.825507 ACACATCTTTCTTTGCAGAGAAAC 58.174 37.500 24.25 0.00 39.90 2.78
413 414 2.822643 ATCGGGGCAGGAGAAGTCCA 62.823 60.000 0.00 0.00 46.80 4.02
481 492 4.699522 AGCGACGGTGGGGAAAGC 62.700 66.667 0.00 0.00 0.00 3.51
553 577 4.657824 CCACTTCACGTCCGCGGT 62.658 66.667 27.15 1.97 43.45 5.68
560 584 1.080705 GTCTAGCGCCACTTCACGT 60.081 57.895 2.29 0.00 0.00 4.49
604 630 3.811031 GAGAGGGTCGAGATCTGGA 57.189 57.895 0.00 0.05 0.00 3.86
706 737 1.725557 CCGATCTGATGTCGACGGGT 61.726 60.000 11.62 0.00 41.40 5.28
716 747 0.900182 TATGGGCGCTCCGATCTGAT 60.900 55.000 3.94 0.00 38.76 2.90
717 748 1.527433 CTATGGGCGCTCCGATCTGA 61.527 60.000 3.94 0.00 38.76 3.27
732 763 1.757118 TCTGGGTCGAAGAAGGCTATG 59.243 52.381 0.00 0.00 39.69 2.23
734 765 1.933021 TTCTGGGTCGAAGAAGGCTA 58.067 50.000 0.00 0.00 39.69 3.93
736 767 1.157585 GTTTCTGGGTCGAAGAAGGC 58.842 55.000 0.00 0.00 39.69 4.35
838 880 4.570874 GGATTCGCTCCAGCCCCC 62.571 72.222 0.00 0.00 44.26 5.40
888 930 4.777463 ACATTTACCTACCTTTCCGGATG 58.223 43.478 4.15 0.69 36.31 3.51
893 935 9.016438 TCAACAAATACATTTACCTACCTTTCC 57.984 33.333 0.00 0.00 0.00 3.13
906 948 9.612066 AAAATTGAACACCTCAACAAATACATT 57.388 25.926 0.00 0.00 46.80 2.71
909 955 8.539674 GTGAAAATTGAACACCTCAACAAATAC 58.460 33.333 0.00 0.00 46.80 1.89
911 957 7.330262 AGTGAAAATTGAACACCTCAACAAAT 58.670 30.769 0.00 0.00 46.80 2.32
942 988 0.178995 TGCAGATGAACAGGGCAACA 60.179 50.000 0.00 0.00 39.74 3.33
943 989 0.961019 TTGCAGATGAACAGGGCAAC 59.039 50.000 0.00 0.00 39.33 4.17
944 990 1.702182 TTTGCAGATGAACAGGGCAA 58.298 45.000 0.00 0.00 42.15 4.52
945 991 1.702182 TTTTGCAGATGAACAGGGCA 58.298 45.000 0.00 0.00 0.00 5.36
946 992 3.429410 GGTATTTTGCAGATGAACAGGGC 60.429 47.826 0.00 0.00 0.00 5.19
947 993 3.763360 TGGTATTTTGCAGATGAACAGGG 59.237 43.478 0.00 0.00 0.00 4.45
948 994 4.218200 TGTGGTATTTTGCAGATGAACAGG 59.782 41.667 0.00 0.00 0.00 4.00
949 995 5.375417 TGTGGTATTTTGCAGATGAACAG 57.625 39.130 0.00 0.00 0.00 3.16
1005 1067 6.618287 TTCAGCTTCTTCTCGAAAAATTCA 57.382 33.333 0.00 0.00 0.00 2.57
1570 1650 0.324275 TGGGGGCTGCTTCAAATACC 60.324 55.000 0.00 0.00 0.00 2.73
1828 1912 2.165234 CTCGAGACTTCCAGCAAGATGA 59.835 50.000 6.58 0.00 35.82 2.92
1850 1934 4.770531 GGCTTTACCACTAAATTCTTGGGT 59.229 41.667 5.25 0.00 38.86 4.51
1894 1978 8.696043 TCCAAGAGATGAATATGTTATTTGGG 57.304 34.615 0.00 0.00 33.83 4.12
1994 2079 2.623416 CCCCGCTTCTTTCTTTGTTTCT 59.377 45.455 0.00 0.00 0.00 2.52
2014 2099 3.243873 CCTGTTTTGCTTTCTTCCTTCCC 60.244 47.826 0.00 0.00 0.00 3.97
2044 2129 1.677966 AGTCTAGTCCGCGGCAAGA 60.678 57.895 23.51 19.33 0.00 3.02
2063 2148 0.543277 TGATCTGTCATGGCCCTGAC 59.457 55.000 28.55 28.55 44.70 3.51
2090 2175 7.387948 TCTTCTTAATTTCTTCGTTGAGGAAGG 59.612 37.037 12.04 0.00 42.88 3.46
2099 2184 7.805071 CACTTGCAATCTTCTTAATTTCTTCGT 59.195 33.333 0.00 0.00 0.00 3.85
2159 2244 2.158370 TGAGCTACCCTATTCCGATCCA 60.158 50.000 0.00 0.00 0.00 3.41
2222 2307 1.647545 CGGTGCACCCACATGCTAAG 61.648 60.000 29.95 8.00 46.28 2.18
2243 2328 1.529438 CGGCAAAAGAAGCTACAACGA 59.471 47.619 0.00 0.00 0.00 3.85
2244 2329 1.950472 CGGCAAAAGAAGCTACAACG 58.050 50.000 0.00 0.00 0.00 4.10
2261 2346 2.869503 AAGGGTTACATCTGCCGCGG 62.870 60.000 24.05 24.05 0.00 6.46
2282 2367 2.504175 GTGGCTAGTGTTCCCCTAATCA 59.496 50.000 0.00 0.00 0.00 2.57
2291 2376 0.389948 CCGACCAGTGGCTAGTGTTC 60.390 60.000 9.78 0.00 0.00 3.18
2368 2453 1.327460 GCTGCAATGCTCGAACGATAA 59.673 47.619 6.82 0.00 0.00 1.75
2369 2454 0.930310 GCTGCAATGCTCGAACGATA 59.070 50.000 6.82 0.00 0.00 2.92
2379 2464 2.540361 CGGAAGTTCTATGCTGCAATGC 60.540 50.000 6.36 0.00 0.00 3.56
2392 2477 4.451096 TGAAAATGTAGAGCACGGAAGTTC 59.549 41.667 0.00 0.00 46.40 3.01
2401 2486 5.123820 GCTACCATGTTGAAAATGTAGAGCA 59.876 40.000 7.91 0.00 0.00 4.26
2405 2490 7.867403 AGTTTTGCTACCATGTTGAAAATGTAG 59.133 33.333 0.00 0.00 0.00 2.74
2413 2498 4.887071 ACAGAAGTTTTGCTACCATGTTGA 59.113 37.500 0.00 0.00 0.00 3.18
2420 2505 3.380320 ACCACAACAGAAGTTTTGCTACC 59.620 43.478 0.00 0.00 34.79 3.18
2427 2512 3.417101 TGACACACCACAACAGAAGTTT 58.583 40.909 0.00 0.00 35.28 2.66
2468 2553 3.254657 TGGTTGTGCTTTACATGGCTAAC 59.745 43.478 0.00 1.49 39.48 2.34
2473 2561 2.029200 TGCATGGTTGTGCTTTACATGG 60.029 45.455 0.00 0.00 45.27 3.66
2479 2567 1.001181 GGTCATGCATGGTTGTGCTTT 59.999 47.619 25.97 0.00 45.27 3.51
2506 2602 6.319658 ACCAATGAGGATTTGTTGCATACTAG 59.680 38.462 0.00 0.00 41.22 2.57
2508 2604 5.018809 ACCAATGAGGATTTGTTGCATACT 58.981 37.500 0.00 0.00 41.22 2.12
2517 2613 1.672881 GCTCCGACCAATGAGGATTTG 59.327 52.381 0.00 0.00 41.22 2.32
2612 2726 7.571919 ACATGATGTGATGATTCTTAAGGTCT 58.428 34.615 0.00 0.00 0.00 3.85
2632 2746 1.740025 TGCAAACACACGTCAACATGA 59.260 42.857 0.00 0.00 0.00 3.07
2674 2789 0.795698 CAACATTCGTCCGACATGCA 59.204 50.000 0.00 0.00 0.00 3.96
2694 2810 4.701956 AGCTTTGGGTTATTCGATGTTG 57.298 40.909 0.00 0.00 0.00 3.33
2721 2837 2.056577 GTGGTTTACGTTCGAGGACAG 58.943 52.381 0.00 0.00 0.00 3.51
2732 2848 2.221055 GTCTCTTGCTGTGTGGTTTACG 59.779 50.000 0.00 0.00 0.00 3.18
2734 2850 3.133901 TGAGTCTCTTGCTGTGTGGTTTA 59.866 43.478 0.65 0.00 0.00 2.01
2740 2856 1.610102 GCCATGAGTCTCTTGCTGTGT 60.610 52.381 9.70 0.00 0.00 3.72
2743 2859 0.108472 TCGCCATGAGTCTCTTGCTG 60.108 55.000 9.70 5.10 0.00 4.41
2747 2863 0.109086 CACGTCGCCATGAGTCTCTT 60.109 55.000 0.65 0.00 0.00 2.85
2756 2872 1.079819 CACTTCTCCACGTCGCCAT 60.080 57.895 0.00 0.00 0.00 4.40
2765 2881 2.290450 TGATTGATGCAGCACTTCTCCA 60.290 45.455 2.94 0.00 0.00 3.86
2784 3042 5.122554 TCGTGTTTCTGCTTTGTTTACTTGA 59.877 36.000 0.00 0.00 0.00 3.02
2785 3043 5.328691 TCGTGTTTCTGCTTTGTTTACTTG 58.671 37.500 0.00 0.00 0.00 3.16
2786 3044 5.353123 TCTCGTGTTTCTGCTTTGTTTACTT 59.647 36.000 0.00 0.00 0.00 2.24
2787 3045 4.873827 TCTCGTGTTTCTGCTTTGTTTACT 59.126 37.500 0.00 0.00 0.00 2.24
2788 3046 5.151632 TCTCGTGTTTCTGCTTTGTTTAC 57.848 39.130 0.00 0.00 0.00 2.01
2795 3053 2.910688 TTCCTCTCGTGTTTCTGCTT 57.089 45.000 0.00 0.00 0.00 3.91
2798 3056 4.560128 TCTTCATTCCTCTCGTGTTTCTG 58.440 43.478 0.00 0.00 0.00 3.02
2804 3062 2.928757 CAGCTTCTTCATTCCTCTCGTG 59.071 50.000 0.00 0.00 0.00 4.35
2816 3074 3.087781 AGCATTTCCTTCCAGCTTCTTC 58.912 45.455 0.00 0.00 29.98 2.87
2902 3160 8.455903 ACCAATGATGAGATATAACCAAACAG 57.544 34.615 0.00 0.00 0.00 3.16
2939 3199 2.109425 AGACAAAGCCCGTGGTATTC 57.891 50.000 0.00 0.00 0.00 1.75
2945 3205 1.681264 AGGAAAAAGACAAAGCCCGTG 59.319 47.619 0.00 0.00 0.00 4.94
2947 3207 3.452755 AAAGGAAAAAGACAAAGCCCG 57.547 42.857 0.00 0.00 0.00 6.13
2968 3228 5.026790 CCTATATGGTTTTCACCCCCAAAA 58.973 41.667 0.00 0.00 43.49 2.44
2970 3230 3.859248 TCCTATATGGTTTTCACCCCCAA 59.141 43.478 0.00 0.00 43.49 4.12
2971 3231 3.475936 TCCTATATGGTTTTCACCCCCA 58.524 45.455 0.00 0.00 43.49 4.96
2972 3232 4.741928 ATCCTATATGGTTTTCACCCCC 57.258 45.455 0.00 0.00 43.49 5.40
2973 3233 5.454966 ACAATCCTATATGGTTTTCACCCC 58.545 41.667 0.00 0.00 43.49 4.95
2974 3234 6.126409 TGACAATCCTATATGGTTTTCACCC 58.874 40.000 0.00 0.00 43.49 4.61
2975 3235 7.339466 ACTTGACAATCCTATATGGTTTTCACC 59.661 37.037 0.00 0.00 44.56 4.02
2976 3236 8.184192 CACTTGACAATCCTATATGGTTTTCAC 58.816 37.037 0.00 0.00 37.07 3.18
2977 3237 7.339212 CCACTTGACAATCCTATATGGTTTTCA 59.661 37.037 0.00 0.00 37.07 2.69
2978 3238 7.682021 GCCACTTGACAATCCTATATGGTTTTC 60.682 40.741 0.00 0.00 37.07 2.29
2979 3239 6.096846 GCCACTTGACAATCCTATATGGTTTT 59.903 38.462 0.00 0.00 37.07 2.43
2980 3240 5.594317 GCCACTTGACAATCCTATATGGTTT 59.406 40.000 0.00 0.00 37.07 3.27
2981 3241 5.133221 GCCACTTGACAATCCTATATGGTT 58.867 41.667 0.00 0.00 37.07 3.67
2983 3243 4.717877 TGCCACTTGACAATCCTATATGG 58.282 43.478 0.00 0.00 37.10 2.74
2984 3244 6.263842 ACATTGCCACTTGACAATCCTATATG 59.736 38.462 0.00 0.00 34.32 1.78
2987 3247 4.400251 CACATTGCCACTTGACAATCCTAT 59.600 41.667 0.00 0.00 34.32 2.57
2988 3248 3.758023 CACATTGCCACTTGACAATCCTA 59.242 43.478 0.00 0.00 34.32 2.94
2989 3249 2.559668 CACATTGCCACTTGACAATCCT 59.440 45.455 0.00 0.00 34.32 3.24
2990 3250 2.353011 CCACATTGCCACTTGACAATCC 60.353 50.000 0.00 0.00 34.32 3.01
2991 3251 2.353011 CCCACATTGCCACTTGACAATC 60.353 50.000 0.00 0.00 34.32 2.67
2992 3252 1.619827 CCCACATTGCCACTTGACAAT 59.380 47.619 0.00 0.00 36.96 2.71
2996 3256 1.152589 TGCCCACATTGCCACTTGA 60.153 52.632 0.00 0.00 0.00 3.02
3032 3292 0.034337 GTTGGCTGGAACTCGTACCA 59.966 55.000 0.00 0.00 34.81 3.25
3033 3293 1.012486 CGTTGGCTGGAACTCGTACC 61.012 60.000 0.00 0.00 0.00 3.34
3048 3308 3.486875 GGGATTCGATAGCCAAAACGTTG 60.487 47.826 0.00 0.00 34.25 4.10
3049 3309 2.681344 GGGATTCGATAGCCAAAACGTT 59.319 45.455 0.00 0.00 0.00 3.99
3051 3311 2.285083 TGGGATTCGATAGCCAAAACG 58.715 47.619 4.67 0.00 0.00 3.60
3052 3312 3.442273 TGTTGGGATTCGATAGCCAAAAC 59.558 43.478 0.00 7.87 36.49 2.43
3053 3313 3.691575 TGTTGGGATTCGATAGCCAAAA 58.308 40.909 0.00 0.00 36.49 2.44
3054 3314 3.358111 TGTTGGGATTCGATAGCCAAA 57.642 42.857 0.00 0.00 36.49 3.28
3055 3315 3.358111 TTGTTGGGATTCGATAGCCAA 57.642 42.857 4.67 0.00 33.08 4.52
3056 3316 3.358111 TTTGTTGGGATTCGATAGCCA 57.642 42.857 4.67 0.00 0.00 4.75
3057 3317 4.918810 ATTTTGTTGGGATTCGATAGCC 57.081 40.909 0.00 0.00 0.00 3.93
3058 3318 5.281727 GGAATTTTGTTGGGATTCGATAGC 58.718 41.667 0.00 0.00 32.03 2.97
3059 3319 5.295787 TCGGAATTTTGTTGGGATTCGATAG 59.704 40.000 0.00 0.00 32.03 2.08
3060 3320 5.186942 TCGGAATTTTGTTGGGATTCGATA 58.813 37.500 0.00 0.00 32.03 2.92
3061 3321 4.013728 TCGGAATTTTGTTGGGATTCGAT 58.986 39.130 0.00 0.00 32.03 3.59
3062 3322 3.413327 TCGGAATTTTGTTGGGATTCGA 58.587 40.909 0.00 0.00 32.03 3.71
3063 3323 3.427503 CCTCGGAATTTTGTTGGGATTCG 60.428 47.826 0.00 0.00 32.03 3.34
3064 3324 3.119137 CCCTCGGAATTTTGTTGGGATTC 60.119 47.826 0.00 0.00 35.40 2.52
3065 3325 2.831526 CCCTCGGAATTTTGTTGGGATT 59.168 45.455 0.00 0.00 35.40 3.01
3066 3326 2.225267 ACCCTCGGAATTTTGTTGGGAT 60.225 45.455 0.00 0.00 37.06 3.85
3067 3327 1.146152 ACCCTCGGAATTTTGTTGGGA 59.854 47.619 0.00 0.00 37.06 4.37
3068 3328 1.272212 CACCCTCGGAATTTTGTTGGG 59.728 52.381 0.00 0.00 39.06 4.12
3069 3329 1.272212 CCACCCTCGGAATTTTGTTGG 59.728 52.381 0.00 0.00 0.00 3.77
3070 3330 1.272212 CCCACCCTCGGAATTTTGTTG 59.728 52.381 0.00 0.00 0.00 3.33
3071 3331 1.627864 CCCACCCTCGGAATTTTGTT 58.372 50.000 0.00 0.00 0.00 2.83
3072 3332 0.898326 GCCCACCCTCGGAATTTTGT 60.898 55.000 0.00 0.00 0.00 2.83
3073 3333 1.890174 GCCCACCCTCGGAATTTTG 59.110 57.895 0.00 0.00 0.00 2.44
3074 3334 1.677633 CGCCCACCCTCGGAATTTT 60.678 57.895 0.00 0.00 0.00 1.82
3075 3335 2.045340 CGCCCACCCTCGGAATTT 60.045 61.111 0.00 0.00 0.00 1.82
3076 3336 3.006728 TCGCCCACCCTCGGAATT 61.007 61.111 0.00 0.00 0.00 2.17
3077 3337 3.470888 CTCGCCCACCCTCGGAAT 61.471 66.667 0.00 0.00 0.00 3.01
3078 3338 4.689549 TCTCGCCCACCCTCGGAA 62.690 66.667 0.00 0.00 0.00 4.30
3079 3339 4.689549 TTCTCGCCCACCCTCGGA 62.690 66.667 0.00 0.00 0.00 4.55
3080 3340 3.702048 TTTCTCGCCCACCCTCGG 61.702 66.667 0.00 0.00 0.00 4.63
3081 3341 2.434359 GTTTCTCGCCCACCCTCG 60.434 66.667 0.00 0.00 0.00 4.63
3082 3342 2.434359 CGTTTCTCGCCCACCCTC 60.434 66.667 0.00 0.00 0.00 4.30
3091 3351 3.597162 CGGTATCCGCGTTTCTCG 58.403 61.111 4.92 0.00 41.17 4.04
3101 3361 4.081322 TCCTCCTAATTTTGCGGTATCC 57.919 45.455 0.00 0.00 0.00 2.59
3102 3362 6.445357 TTTTCCTCCTAATTTTGCGGTATC 57.555 37.500 0.00 0.00 0.00 2.24
3103 3363 6.350696 GGTTTTTCCTCCTAATTTTGCGGTAT 60.351 38.462 0.00 0.00 0.00 2.73
3104 3364 5.047872 GGTTTTTCCTCCTAATTTTGCGGTA 60.048 40.000 0.00 0.00 0.00 4.02
3105 3365 4.262292 GGTTTTTCCTCCTAATTTTGCGGT 60.262 41.667 0.00 0.00 0.00 5.68
3106 3366 4.242475 GGTTTTTCCTCCTAATTTTGCGG 58.758 43.478 0.00 0.00 0.00 5.69
3107 3367 3.917985 CGGTTTTTCCTCCTAATTTTGCG 59.082 43.478 0.00 0.00 0.00 4.85
3108 3368 4.878439 ACGGTTTTTCCTCCTAATTTTGC 58.122 39.130 0.00 0.00 0.00 3.68
3109 3369 5.627780 CGAACGGTTTTTCCTCCTAATTTTG 59.372 40.000 0.00 0.00 0.00 2.44
3110 3370 5.532032 TCGAACGGTTTTTCCTCCTAATTTT 59.468 36.000 0.00 0.00 0.00 1.82
3111 3371 5.065235 TCGAACGGTTTTTCCTCCTAATTT 58.935 37.500 0.00 0.00 0.00 1.82
3112 3372 4.644498 TCGAACGGTTTTTCCTCCTAATT 58.356 39.130 0.00 0.00 0.00 1.40
3113 3373 4.276058 TCGAACGGTTTTTCCTCCTAAT 57.724 40.909 0.00 0.00 0.00 1.73
3114 3374 3.749665 TCGAACGGTTTTTCCTCCTAA 57.250 42.857 0.00 0.00 0.00 2.69
3115 3375 3.749665 TTCGAACGGTTTTTCCTCCTA 57.250 42.857 0.00 0.00 0.00 2.94
3116 3376 2.625695 TTCGAACGGTTTTTCCTCCT 57.374 45.000 0.00 0.00 0.00 3.69
3117 3377 3.909776 AATTCGAACGGTTTTTCCTCC 57.090 42.857 0.00 0.00 0.00 4.30
3118 3378 7.682593 TTTAAAATTCGAACGGTTTTTCCTC 57.317 32.000 11.90 0.00 0.00 3.71
3119 3379 7.544915 TGTTTTAAAATTCGAACGGTTTTTCCT 59.455 29.630 11.90 0.00 0.00 3.36
3120 3380 7.673651 TGTTTTAAAATTCGAACGGTTTTTCC 58.326 30.769 11.90 1.98 0.00 3.13
3167 3427 9.015367 GCTCCGAGCTAATATATTCCTATATCA 57.985 37.037 13.42 0.00 38.45 2.15
3185 3445 1.802069 AAACTTCTTGAGCTCCGAGC 58.198 50.000 12.80 12.80 42.84 5.03
3186 3446 7.778470 ATTTATAAACTTCTTGAGCTCCGAG 57.222 36.000 12.15 9.52 0.00 4.63
3187 3447 7.822334 TGAATTTATAAACTTCTTGAGCTCCGA 59.178 33.333 12.15 4.90 0.00 4.55
3188 3448 7.905493 GTGAATTTATAAACTTCTTGAGCTCCG 59.095 37.037 12.15 2.20 0.00 4.63
3189 3449 8.951243 AGTGAATTTATAAACTTCTTGAGCTCC 58.049 33.333 12.15 0.00 0.00 4.70
3190 3450 9.766277 CAGTGAATTTATAAACTTCTTGAGCTC 57.234 33.333 6.82 6.82 0.00 4.09
3191 3451 9.289782 ACAGTGAATTTATAAACTTCTTGAGCT 57.710 29.630 0.00 0.00 0.00 4.09
3192 3452 9.899226 AACAGTGAATTTATAAACTTCTTGAGC 57.101 29.630 0.00 0.00 0.00 4.26
3195 3455 9.965824 ACCAACAGTGAATTTATAAACTTCTTG 57.034 29.630 0.00 10.20 0.00 3.02


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

AutoCloner maintained by Alex Coulton.