Multiple sequence alignment - TraesCS3A01G438000

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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 TraesCS3A01G438000 chr3A 100.000 3907 0 0 1 3907 681398122 681402028 0.000000e+00 7215.0
1 TraesCS3A01G438000 chr3A 88.827 1432 101 15 837 2250 681446851 681448241 0.000000e+00 1703.0
2 TraesCS3A01G438000 chr3A 89.798 892 62 17 2245 3135 681448335 681449198 0.000000e+00 1116.0
3 TraesCS3A01G438000 chr3A 85.517 290 39 3 186 474 638064723 638064436 2.280000e-77 300.0
4 TraesCS3A01G438000 chr3A 96.875 32 1 0 622 653 681406242 681406273 2.000000e-03 54.7
5 TraesCS3A01G438000 chr3D 91.638 2595 150 40 515 3086 544444306 544446856 0.000000e+00 3528.0
6 TraesCS3A01G438000 chr3D 89.483 1084 66 10 840 1901 544771462 544772519 0.000000e+00 1327.0
7 TraesCS3A01G438000 chr3D 81.754 992 117 39 2275 3257 544772890 544773826 0.000000e+00 771.0
8 TraesCS3A01G438000 chr3D 86.719 512 28 12 3198 3688 544446874 544447366 2.070000e-147 532.0
9 TraesCS3A01G438000 chr3D 86.150 426 47 7 59 475 544443820 544444242 2.140000e-122 449.0
10 TraesCS3A01G438000 chr3D 86.833 281 32 5 195 474 496742746 496743022 3.790000e-80 309.0
11 TraesCS3A01G438000 chr3D 91.549 213 16 1 190 402 536441507 536441717 3.820000e-75 292.0
12 TraesCS3A01G438000 chr3D 91.549 213 16 1 190 402 536590239 536590449 3.820000e-75 292.0
13 TraesCS3A01G438000 chr3D 90.960 177 13 3 2709 2884 544791297 544791471 6.530000e-58 235.0
14 TraesCS3A01G438000 chr3D 88.591 149 14 3 3448 3593 544773883 544774031 1.120000e-40 178.0
15 TraesCS3A01G438000 chr3B 94.571 1271 45 10 482 1749 720265237 720266486 0.000000e+00 1943.0
16 TraesCS3A01G438000 chr3B 87.940 1393 99 36 1818 3193 720266513 720267853 0.000000e+00 1578.0
17 TraesCS3A01G438000 chr3B 85.906 447 39 11 31 475 720264772 720265196 4.600000e-124 455.0
18 TraesCS3A01G438000 chr3B 81.651 218 28 9 1843 2050 720975639 720975854 1.870000e-38 171.0
19 TraesCS3A01G438000 chr7A 86.395 294 31 8 186 474 634709464 634709175 2.930000e-81 313.0
20 TraesCS3A01G438000 chr7A 100.000 97 0 0 3809 3905 359267692 359267788 3.100000e-41 180.0
21 TraesCS3A01G438000 chr7A 100.000 97 0 0 3809 3905 622802654 622802558 3.100000e-41 180.0
22 TraesCS3A01G438000 chr7A 99.000 100 0 1 3808 3907 198663435 198663337 1.120000e-40 178.0
23 TraesCS3A01G438000 chr7D 85.714 294 33 7 186 474 549284015 549283726 6.340000e-78 302.0
24 TraesCS3A01G438000 chr7B 85.135 296 36 8 184 474 593016262 593015970 2.950000e-76 296.0
25 TraesCS3A01G438000 chr1A 99.010 101 0 1 3807 3907 564568804 564568903 3.100000e-41 180.0
26 TraesCS3A01G438000 chr2A 100.000 96 0 0 3807 3902 12245910 12245815 1.120000e-40 178.0
27 TraesCS3A01G438000 chr2A 100.000 96 0 0 3808 3903 12332929 12333024 1.120000e-40 178.0
28 TraesCS3A01G438000 chr2A 98.020 101 1 1 3807 3907 510818546 510818645 1.440000e-39 174.0
29 TraesCS3A01G438000 chr2B 100.000 95 0 0 3808 3902 49090686 49090780 4.010000e-40 176.0
30 TraesCS3A01G438000 chr6B 94.595 111 6 0 3790 3900 664717908 664717798 5.190000e-39 172.0


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 TraesCS3A01G438000 chr3A 681398122 681402028 3906 False 7215.000000 7215 100.000000 1 3907 1 chr3A.!!$F1 3906
1 TraesCS3A01G438000 chr3A 681446851 681449198 2347 False 1409.500000 1703 89.312500 837 3135 2 chr3A.!!$F3 2298
2 TraesCS3A01G438000 chr3D 544443820 544447366 3546 False 1503.000000 3528 88.169000 59 3688 3 chr3D.!!$F5 3629
3 TraesCS3A01G438000 chr3D 544771462 544774031 2569 False 758.666667 1327 86.609333 840 3593 3 chr3D.!!$F6 2753
4 TraesCS3A01G438000 chr3B 720264772 720267853 3081 False 1325.333333 1943 89.472333 31 3193 3 chr3B.!!$F2 3162

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
19 20 0.178068 ACCGCATACTCCACACCATC 59.822 55.0 0.00 0.0 0.00 3.51 F
81 82 0.179020 CTCAGGCTGTGGTGACCAAA 60.179 55.0 15.27 0.0 34.18 3.28 F
87 88 0.182537 CTGTGGTGACCAAACCTGGA 59.817 55.0 5.57 0.0 46.92 3.86 F
269 279 0.251742 CTGAGGGTCCCAATGGCAAA 60.252 55.0 11.55 0.0 0.00 3.68 F
413 423 0.679960 AAGGTATGCTTCAACCCGCC 60.680 55.0 0.00 0.0 36.34 6.13 F
2182 2370 0.110486 TCCAACTCACCCAGCTTTCC 59.890 55.0 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1708 0.321653 AATCGAACACCCTGCTGACC 60.322 55.000 0.00 0.0 0.00 4.02 R
1772 1880 3.074390 TGTGAAATTCCAGGTGACATCCT 59.926 43.478 0.00 0.0 38.51 3.24 R
1856 1988 3.281341 TCATTTTGTTGCCGACATGAC 57.719 42.857 0.00 0.0 38.26 3.06 R
2088 2276 0.188342 ACAGAAGGCCACCAACCAAT 59.812 50.000 5.01 0.0 0.00 3.16 R
2240 2428 1.838077 ACCCTGCACTTATAGGACACC 59.162 52.381 0.00 0.0 36.11 4.16 R
3340 3655 0.039074 CACGGTTCTTCTCTCGTGCT 60.039 55.000 0.00 0.0 44.56 4.40 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 3.800188 ACCGCATACTCCACACCA 58.200 55.556 0.00 0.00 0.00 4.17
18 19 2.296920 ACCGCATACTCCACACCAT 58.703 52.632 0.00 0.00 0.00 3.55
19 20 0.178068 ACCGCATACTCCACACCATC 59.822 55.000 0.00 0.00 0.00 3.51
20 21 0.532862 CCGCATACTCCACACCATCC 60.533 60.000 0.00 0.00 0.00 3.51
21 22 0.532862 CGCATACTCCACACCATCCC 60.533 60.000 0.00 0.00 0.00 3.85
22 23 0.532862 GCATACTCCACACCATCCCG 60.533 60.000 0.00 0.00 0.00 5.14
23 24 0.830648 CATACTCCACACCATCCCGT 59.169 55.000 0.00 0.00 0.00 5.28
24 25 0.830648 ATACTCCACACCATCCCGTG 59.169 55.000 0.00 0.00 39.75 4.94
25 26 1.895020 TACTCCACACCATCCCGTGC 61.895 60.000 0.00 0.00 37.25 5.34
26 27 2.927856 TCCACACCATCCCGTGCT 60.928 61.111 0.00 0.00 37.25 4.40
27 28 2.034066 CCACACCATCCCGTGCTT 59.966 61.111 0.00 0.00 37.25 3.91
28 29 2.040544 CCACACCATCCCGTGCTTC 61.041 63.158 0.00 0.00 37.25 3.86
29 30 1.003355 CACACCATCCCGTGCTTCT 60.003 57.895 0.00 0.00 37.25 2.85
43 44 1.298014 CTTCTCCCAGGAGCACCAC 59.702 63.158 8.95 0.00 41.71 4.16
46 47 3.249189 TCCCAGGAGCACCACCAC 61.249 66.667 2.07 0.00 38.94 4.16
47 48 4.351054 CCCAGGAGCACCACCACC 62.351 72.222 2.07 0.00 38.94 4.61
48 49 3.252284 CCAGGAGCACCACCACCT 61.252 66.667 2.07 0.00 38.94 4.00
49 50 2.033141 CAGGAGCACCACCACCTG 59.967 66.667 2.07 0.00 42.71 4.00
51 52 4.269523 GGAGCACCACCACCTGCA 62.270 66.667 0.00 0.00 35.73 4.41
52 53 2.034687 GAGCACCACCACCTGCAT 59.965 61.111 0.00 0.00 35.73 3.96
53 54 2.282674 AGCACCACCACCTGCATG 60.283 61.111 0.00 0.00 35.73 4.06
56 57 1.747325 GCACCACCACCTGCATGTTT 61.747 55.000 0.00 0.00 33.31 2.83
57 58 0.314935 CACCACCACCTGCATGTTTC 59.685 55.000 0.00 0.00 0.00 2.78
58 59 0.185901 ACCACCACCTGCATGTTTCT 59.814 50.000 0.00 0.00 0.00 2.52
59 60 0.883833 CCACCACCTGCATGTTTCTC 59.116 55.000 0.00 0.00 0.00 2.87
60 61 0.518636 CACCACCTGCATGTTTCTCG 59.481 55.000 0.00 0.00 0.00 4.04
61 62 0.396435 ACCACCTGCATGTTTCTCGA 59.604 50.000 0.00 0.00 0.00 4.04
62 63 0.798776 CCACCTGCATGTTTCTCGAC 59.201 55.000 0.00 0.00 0.00 4.20
63 64 1.609061 CCACCTGCATGTTTCTCGACT 60.609 52.381 0.00 0.00 0.00 4.18
69 70 1.674221 GCATGTTTCTCGACTCAGGCT 60.674 52.381 0.00 0.00 35.27 4.58
70 71 1.998315 CATGTTTCTCGACTCAGGCTG 59.002 52.381 8.58 8.58 0.00 4.85
81 82 0.179020 CTCAGGCTGTGGTGACCAAA 60.179 55.000 15.27 0.00 34.18 3.28
83 84 1.152756 AGGCTGTGGTGACCAAACC 60.153 57.895 5.57 8.39 40.94 3.27
84 85 1.152756 GGCTGTGGTGACCAAACCT 60.153 57.895 5.57 0.00 41.16 3.50
85 86 1.455383 GGCTGTGGTGACCAAACCTG 61.455 60.000 5.57 0.00 41.16 4.00
87 88 0.182537 CTGTGGTGACCAAACCTGGA 59.817 55.000 5.57 0.00 46.92 3.86
88 89 0.626382 TGTGGTGACCAAACCTGGAA 59.374 50.000 5.57 0.00 46.92 3.53
89 90 1.318576 GTGGTGACCAAACCTGGAAG 58.681 55.000 5.57 0.00 46.92 3.46
90 91 1.133915 GTGGTGACCAAACCTGGAAGA 60.134 52.381 5.57 0.00 46.92 2.87
91 92 1.133915 TGGTGACCAAACCTGGAAGAC 60.134 52.381 0.00 0.00 46.92 3.01
92 93 1.226746 GTGACCAAACCTGGAAGACG 58.773 55.000 0.00 0.00 46.92 4.18
93 94 0.534203 TGACCAAACCTGGAAGACGC 60.534 55.000 0.00 0.00 46.92 5.19
95 96 2.556287 CAAACCTGGAAGACGCGC 59.444 61.111 5.73 0.00 34.07 6.86
107 108 4.419939 ACGCGCACGAGCAGATCA 62.420 61.111 5.73 0.00 43.93 2.92
116 117 3.088500 GAGCAGATCAACACGGCGC 62.089 63.158 6.90 0.00 34.06 6.53
126 127 4.504916 CACGGCGCTGAGGGAGAG 62.505 72.222 25.98 0.00 0.00 3.20
158 166 1.471287 TGCATGTCAGCAGCTTCAATC 59.529 47.619 0.00 0.00 40.11 2.67
165 173 2.551032 TCAGCAGCTTCAATCAACACTG 59.449 45.455 0.00 0.00 0.00 3.66
170 178 5.474532 AGCAGCTTCAATCAACACTGAATTA 59.525 36.000 0.00 0.00 34.49 1.40
171 179 6.016024 AGCAGCTTCAATCAACACTGAATTAA 60.016 34.615 0.00 0.00 34.49 1.40
181 189 7.213216 TCAACACTGAATTAAAGCTGCATTA 57.787 32.000 1.02 0.00 0.00 1.90
182 190 7.083858 TCAACACTGAATTAAAGCTGCATTAC 58.916 34.615 1.02 0.00 0.00 1.89
184 192 7.161773 ACACTGAATTAAAGCTGCATTACAT 57.838 32.000 1.02 0.00 0.00 2.29
245 255 0.964860 ATAATGCAACGCACTGGGCA 60.965 50.000 1.50 0.00 43.04 5.36
269 279 0.251742 CTGAGGGTCCCAATGGCAAA 60.252 55.000 11.55 0.00 0.00 3.68
413 423 0.679960 AAGGTATGCTTCAACCCGCC 60.680 55.000 0.00 0.00 36.34 6.13
477 487 2.359850 GCCAAGCGATGTGGGTCA 60.360 61.111 4.48 0.00 36.58 4.02
478 488 1.750399 GCCAAGCGATGTGGGTCAT 60.750 57.895 4.48 0.00 39.77 3.06
479 489 1.996786 GCCAAGCGATGTGGGTCATG 61.997 60.000 4.48 0.00 36.83 3.07
486 530 3.704231 ATGTGGGTCATGGGCTCGC 62.704 63.158 0.00 0.00 35.19 5.03
511 555 2.180204 CCTCGCATGGGCCGTAAAG 61.180 63.158 4.59 0.00 36.38 1.85
523 567 1.470979 GCCGTAAAGATCCTGAAGCGA 60.471 52.381 0.00 0.00 0.00 4.93
537 581 2.155279 GAAGCGAGCCTTTCTTTCCTT 58.845 47.619 0.00 0.00 32.78 3.36
660 732 4.878397 GGCAGTCAGTAAAGTATGCTTCAT 59.122 41.667 0.00 0.00 33.01 2.57
722 794 4.551603 CGCTGTGAAAAGAACAAGACTGAG 60.552 45.833 0.00 0.00 0.00 3.35
773 845 1.588861 GCATCGTTAGGAGCTTTCGAC 59.411 52.381 0.00 0.00 33.55 4.20
780 852 4.174762 GTTAGGAGCTTTCGACAGGTTAG 58.825 47.826 4.56 0.00 0.00 2.34
868 941 4.279145 ACAAGAGAGGATTAGCTTCGGTA 58.721 43.478 0.00 0.00 0.00 4.02
876 955 5.608449 AGGATTAGCTTCGGTATTTACCAC 58.392 41.667 7.50 0.00 46.80 4.16
877 956 5.365895 AGGATTAGCTTCGGTATTTACCACT 59.634 40.000 7.50 1.82 46.80 4.00
900 980 2.092212 TGATGATGGCTTCCTTCCTTCC 60.092 50.000 0.00 0.00 0.00 3.46
902 982 1.995542 TGATGGCTTCCTTCCTTCCTT 59.004 47.619 0.00 0.00 0.00 3.36
903 983 2.025887 TGATGGCTTCCTTCCTTCCTTC 60.026 50.000 0.00 0.00 0.00 3.46
904 984 1.444933 TGGCTTCCTTCCTTCCTTCA 58.555 50.000 0.00 0.00 0.00 3.02
905 985 1.995542 TGGCTTCCTTCCTTCCTTCAT 59.004 47.619 0.00 0.00 0.00 2.57
906 986 3.189606 TGGCTTCCTTCCTTCCTTCATA 58.810 45.455 0.00 0.00 0.00 2.15
907 987 3.788142 TGGCTTCCTTCCTTCCTTCATAT 59.212 43.478 0.00 0.00 0.00 1.78
908 988 4.230502 TGGCTTCCTTCCTTCCTTCATATT 59.769 41.667 0.00 0.00 0.00 1.28
909 989 5.431731 TGGCTTCCTTCCTTCCTTCATATTA 59.568 40.000 0.00 0.00 0.00 0.98
910 990 6.000840 GGCTTCCTTCCTTCCTTCATATTAG 58.999 44.000 0.00 0.00 0.00 1.73
911 991 5.471797 GCTTCCTTCCTTCCTTCATATTAGC 59.528 44.000 0.00 0.00 0.00 3.09
1461 1549 3.918102 CGACATACGCTACTGCTCA 57.082 52.632 0.00 0.00 36.97 4.26
1506 1594 1.378514 GGTGGACATGGCCATCGTT 60.379 57.895 26.67 2.41 40.68 3.85
1569 1657 3.766691 GGGAACGCCGCAGACCTA 61.767 66.667 0.00 0.00 33.83 3.08
1578 1666 2.496817 GCAGACCTAGCCCTCACG 59.503 66.667 0.00 0.00 0.00 4.35
1620 1708 2.123982 GCCAAGGAGATGGGGCTG 60.124 66.667 0.00 0.00 43.09 4.85
1772 1880 9.255304 GTGCAATTCCAAGTTCAAACTAATAAA 57.745 29.630 0.00 0.00 38.57 1.40
1805 1914 5.983118 CCTGGAATTTCACAACCTACAAAAC 59.017 40.000 0.00 0.00 0.00 2.43
1841 1973 5.350914 GGAGTTGAGAACTTGAGATGTCATG 59.649 44.000 4.40 4.40 43.03 3.07
1866 1998 3.990092 TCATTATGTAGGTCATGTCGGC 58.010 45.455 0.00 0.00 37.91 5.54
2015 2189 8.918202 ATTTTATGTTAGTCAGAACCTGTTGA 57.082 30.769 0.00 0.00 32.61 3.18
2027 2215 6.752168 CAGAACCTGTTGATTCTGGAAAAAT 58.248 36.000 6.16 0.00 45.35 1.82
2028 2216 7.212274 CAGAACCTGTTGATTCTGGAAAAATT 58.788 34.615 6.16 0.00 45.35 1.82
2088 2276 8.079203 ACGCATGAATTGTGTCTTTAAATACAA 58.921 29.630 7.88 10.48 45.95 2.41
2096 2284 8.879342 TTGTGTCTTTAAATACAATTGGTTGG 57.121 30.769 10.83 0.00 39.70 3.77
2097 2285 8.012957 TGTGTCTTTAAATACAATTGGTTGGT 57.987 30.769 10.83 0.00 39.70 3.67
2099 2287 7.383843 GTGTCTTTAAATACAATTGGTTGGTGG 59.616 37.037 10.83 0.00 39.70 4.61
2103 2291 2.390225 TACAATTGGTTGGTGGCCTT 57.610 45.000 10.83 0.00 39.70 4.35
2107 2295 0.188342 ATTGGTTGGTGGCCTTCTGT 59.812 50.000 3.32 0.00 0.00 3.41
2116 2304 3.761752 TGGTGGCCTTCTGTTATTTTAGC 59.238 43.478 3.32 0.00 0.00 3.09
2171 2359 5.221925 ACAGGCTTTCTAGAATTCCAACTCA 60.222 40.000 19.61 0.00 0.00 3.41
2182 2370 0.110486 TCCAACTCACCCAGCTTTCC 59.890 55.000 0.00 0.00 0.00 3.13
2240 2428 4.100529 GTGCATTTGCTATAGTGTGCTTG 58.899 43.478 16.15 4.68 42.66 4.01
2351 2638 3.067742 GCTCCATTTCCCAACATCATGAG 59.932 47.826 0.09 0.00 0.00 2.90
2357 2644 4.371624 TTCCCAACATCATGAGAAGTGT 57.628 40.909 0.09 0.00 0.00 3.55
2387 2674 7.827729 GGAAAGTTTGGGTCATATAGTTAGTGT 59.172 37.037 0.00 0.00 0.00 3.55
2472 2759 3.432252 GGGTTCACAATTCACTAGTGTCG 59.568 47.826 21.99 11.41 31.58 4.35
2486 2773 2.194212 TGTCGCCCCTCTATCGAGC 61.194 63.158 0.00 0.00 35.90 5.03
2603 2890 0.603707 CATGCACAAGACGTCCCTGT 60.604 55.000 13.01 13.38 0.00 4.00
2676 2975 0.179045 AACTCAACAAGCTGCGACCT 60.179 50.000 0.00 0.00 0.00 3.85
2686 2985 0.601311 GCTGCGACCTATGATGGACC 60.601 60.000 0.00 0.00 0.00 4.46
3089 3390 9.958180 AAAGGGAATAAAACAAGGATTTTATGG 57.042 29.630 4.68 0.00 41.66 2.74
3090 3391 8.679344 AGGGAATAAAACAAGGATTTTATGGT 57.321 30.769 4.68 0.00 41.66 3.55
3115 3416 2.688446 TCCTTAGCACTACTGATGTCCG 59.312 50.000 0.00 0.00 0.00 4.79
3128 3430 6.465439 ACTGATGTCCGTATTGATTAGTGA 57.535 37.500 0.00 0.00 0.00 3.41
3144 3446 7.734942 TGATTAGTGATATGTTGTGATGCCTA 58.265 34.615 0.00 0.00 0.00 3.93
3151 3460 9.875691 GTGATATGTTGTGATGCCTATAGATTA 57.124 33.333 0.00 0.00 0.00 1.75
3165 3474 6.431234 GCCTATAGATTAACCATTCCCACTTG 59.569 42.308 0.00 0.00 0.00 3.16
3166 3475 7.518188 CCTATAGATTAACCATTCCCACTTGT 58.482 38.462 0.00 0.00 0.00 3.16
3258 3570 4.452455 ACTGGAAAGTTCACGAGCTTATTG 59.548 41.667 0.00 0.00 31.49 1.90
3264 3576 7.064728 GGAAAGTTCACGAGCTTATTGTATCTT 59.935 37.037 0.00 0.00 31.49 2.40
3307 3622 8.139350 CCATGCATATGTTCATAGAACAACAAT 58.861 33.333 15.54 7.91 36.14 2.71
3327 3642 3.195471 TGTTACAACCAATCCACGTGA 57.805 42.857 19.30 3.36 0.00 4.35
3334 3649 3.430333 ACCAATCCACGTGAAAACAAC 57.570 42.857 19.30 0.00 0.00 3.32
3335 3650 2.755655 ACCAATCCACGTGAAAACAACA 59.244 40.909 19.30 0.00 0.00 3.33
3339 3654 4.974368 ATCCACGTGAAAACAACAAGAA 57.026 36.364 19.30 0.00 0.00 2.52
3340 3655 4.768130 TCCACGTGAAAACAACAAGAAA 57.232 36.364 19.30 0.00 0.00 2.52
3341 3656 4.728534 TCCACGTGAAAACAACAAGAAAG 58.271 39.130 19.30 0.00 0.00 2.62
3343 3658 3.917380 CACGTGAAAACAACAAGAAAGCA 59.083 39.130 10.90 0.00 0.00 3.91
3344 3659 3.917985 ACGTGAAAACAACAAGAAAGCAC 59.082 39.130 0.00 0.00 0.00 4.40
3349 3664 3.951979 AACAACAAGAAAGCACGAGAG 57.048 42.857 0.00 0.00 0.00 3.20
3352 3667 3.557595 ACAACAAGAAAGCACGAGAGAAG 59.442 43.478 0.00 0.00 0.00 2.85
3361 3676 1.009389 CACGAGAGAAGAACCGTGCC 61.009 60.000 0.00 0.00 44.24 5.01
3368 3683 1.947456 AGAAGAACCGTGCCAAAACTC 59.053 47.619 0.00 0.00 0.00 3.01
3374 3689 1.165907 CCGTGCCAAAACTCTGCAGA 61.166 55.000 17.19 17.19 35.33 4.26
3402 3717 2.356535 CCTCCAGCAAGAAATAGCCACT 60.357 50.000 0.00 0.00 0.00 4.00
3443 3759 5.296780 TGAACAAGACCAATGAGAAACTGAC 59.703 40.000 0.00 0.00 0.00 3.51
3539 3872 6.765512 CCTTTGGTTACCATGTCAATTTGTTT 59.234 34.615 4.38 0.00 31.53 2.83
3542 3875 9.667107 TTTGGTTACCATGTCAATTTGTTTTTA 57.333 25.926 4.38 0.00 31.53 1.52
3543 3876 9.838339 TTGGTTACCATGTCAATTTGTTTTTAT 57.162 25.926 4.38 0.00 31.53 1.40
3544 3877 9.482627 TGGTTACCATGTCAATTTGTTTTTATC 57.517 29.630 0.00 0.00 0.00 1.75
3602 3936 3.670627 GCTTACAGCATTTTCAAGTCCGG 60.671 47.826 0.00 0.00 41.89 5.14
3607 3941 4.522789 ACAGCATTTTCAAGTCCGGTTATT 59.477 37.500 0.00 0.00 0.00 1.40
3637 3971 7.535489 AACCAGAAATTAGTACATCGCTTAC 57.465 36.000 0.00 0.00 0.00 2.34
3638 3972 6.875076 ACCAGAAATTAGTACATCGCTTACT 58.125 36.000 0.00 0.00 34.15 2.24
3651 3985 4.301637 TCGCTTACTTAATCGATCTGCA 57.698 40.909 0.00 0.00 30.13 4.41
3652 3986 4.678622 TCGCTTACTTAATCGATCTGCAA 58.321 39.130 0.00 0.00 30.13 4.08
3657 3991 7.570140 CGCTTACTTAATCGATCTGCAATGAAT 60.570 37.037 0.00 0.00 0.00 2.57
3688 4022 5.686753 TGTGGTTTAACAAGGTCACATACT 58.313 37.500 0.00 0.00 31.33 2.12
3689 4023 5.529430 TGTGGTTTAACAAGGTCACATACTG 59.471 40.000 0.00 0.00 31.33 2.74
3690 4024 5.761234 GTGGTTTAACAAGGTCACATACTGA 59.239 40.000 0.00 0.00 0.00 3.41
3691 4025 6.261381 GTGGTTTAACAAGGTCACATACTGAA 59.739 38.462 0.00 0.00 0.00 3.02
3692 4026 6.829298 TGGTTTAACAAGGTCACATACTGAAA 59.171 34.615 0.00 0.00 0.00 2.69
3693 4027 7.339721 TGGTTTAACAAGGTCACATACTGAAAA 59.660 33.333 0.00 0.00 0.00 2.29
3694 4028 8.192110 GGTTTAACAAGGTCACATACTGAAAAA 58.808 33.333 0.00 0.00 0.00 1.94
3695 4029 9.016623 GTTTAACAAGGTCACATACTGAAAAAC 57.983 33.333 0.00 0.00 0.00 2.43
3696 4030 6.767524 AACAAGGTCACATACTGAAAAACA 57.232 33.333 0.00 0.00 0.00 2.83
3697 4031 6.767524 ACAAGGTCACATACTGAAAAACAA 57.232 33.333 0.00 0.00 0.00 2.83
3698 4032 7.164230 ACAAGGTCACATACTGAAAAACAAA 57.836 32.000 0.00 0.00 0.00 2.83
3699 4033 7.781056 ACAAGGTCACATACTGAAAAACAAAT 58.219 30.769 0.00 0.00 0.00 2.32
3700 4034 8.257306 ACAAGGTCACATACTGAAAAACAAATT 58.743 29.630 0.00 0.00 0.00 1.82
3701 4035 9.743057 CAAGGTCACATACTGAAAAACAAATTA 57.257 29.630 0.00 0.00 0.00 1.40
3703 4037 9.744468 AGGTCACATACTGAAAAACAAATTAAC 57.256 29.630 0.00 0.00 0.00 2.01
3704 4038 8.974408 GGTCACATACTGAAAAACAAATTAACC 58.026 33.333 0.00 0.00 0.00 2.85
3705 4039 8.974408 GTCACATACTGAAAAACAAATTAACCC 58.026 33.333 0.00 0.00 0.00 4.11
3706 4040 8.696374 TCACATACTGAAAAACAAATTAACCCA 58.304 29.630 0.00 0.00 0.00 4.51
3707 4041 8.760569 CACATACTGAAAAACAAATTAACCCAC 58.239 33.333 0.00 0.00 0.00 4.61
3708 4042 7.650104 ACATACTGAAAAACAAATTAACCCACG 59.350 33.333 0.00 0.00 0.00 4.94
3709 4043 5.968254 ACTGAAAAACAAATTAACCCACGT 58.032 33.333 0.00 0.00 0.00 4.49
3710 4044 6.037726 ACTGAAAAACAAATTAACCCACGTC 58.962 36.000 0.00 0.00 0.00 4.34
3711 4045 6.127563 ACTGAAAAACAAATTAACCCACGTCT 60.128 34.615 0.00 0.00 0.00 4.18
3712 4046 7.067251 ACTGAAAAACAAATTAACCCACGTCTA 59.933 33.333 0.00 0.00 0.00 2.59
3713 4047 7.769220 TGAAAAACAAATTAACCCACGTCTAA 58.231 30.769 0.00 0.00 0.00 2.10
3714 4048 8.248945 TGAAAAACAAATTAACCCACGTCTAAA 58.751 29.630 0.00 0.00 0.00 1.85
3715 4049 7.990541 AAAACAAATTAACCCACGTCTAAAC 57.009 32.000 0.00 0.00 0.00 2.01
3725 4059 3.786809 CGTCTAAACGCCTGTCTGA 57.213 52.632 0.00 0.00 42.82 3.27
3726 4060 2.060326 CGTCTAAACGCCTGTCTGAA 57.940 50.000 0.00 0.00 42.82 3.02
3727 4061 2.400399 CGTCTAAACGCCTGTCTGAAA 58.600 47.619 0.00 0.00 42.82 2.69
3728 4062 2.798283 CGTCTAAACGCCTGTCTGAAAA 59.202 45.455 0.00 0.00 42.82 2.29
3729 4063 3.432252 CGTCTAAACGCCTGTCTGAAAAT 59.568 43.478 0.00 0.00 42.82 1.82
3730 4064 4.624024 CGTCTAAACGCCTGTCTGAAAATA 59.376 41.667 0.00 0.00 42.82 1.40
3731 4065 5.220228 CGTCTAAACGCCTGTCTGAAAATAG 60.220 44.000 0.00 0.00 42.82 1.73
3732 4066 3.831715 AAACGCCTGTCTGAAAATAGC 57.168 42.857 0.00 0.00 0.00 2.97
3733 4067 2.770164 ACGCCTGTCTGAAAATAGCT 57.230 45.000 0.00 0.00 0.00 3.32
3734 4068 2.622436 ACGCCTGTCTGAAAATAGCTC 58.378 47.619 0.00 0.00 0.00 4.09
3735 4069 1.936547 CGCCTGTCTGAAAATAGCTCC 59.063 52.381 0.00 0.00 0.00 4.70
3736 4070 2.677902 CGCCTGTCTGAAAATAGCTCCA 60.678 50.000 0.00 0.00 0.00 3.86
3737 4071 3.347216 GCCTGTCTGAAAATAGCTCCAA 58.653 45.455 0.00 0.00 0.00 3.53
3738 4072 3.758554 GCCTGTCTGAAAATAGCTCCAAA 59.241 43.478 0.00 0.00 0.00 3.28
3739 4073 4.218417 GCCTGTCTGAAAATAGCTCCAAAA 59.782 41.667 0.00 0.00 0.00 2.44
3740 4074 5.105595 GCCTGTCTGAAAATAGCTCCAAAAT 60.106 40.000 0.00 0.00 0.00 1.82
3741 4075 6.095440 GCCTGTCTGAAAATAGCTCCAAAATA 59.905 38.462 0.00 0.00 0.00 1.40
3742 4076 7.362920 GCCTGTCTGAAAATAGCTCCAAAATAA 60.363 37.037 0.00 0.00 0.00 1.40
3743 4077 8.689972 CCTGTCTGAAAATAGCTCCAAAATAAT 58.310 33.333 0.00 0.00 0.00 1.28
3765 4099 3.987404 GTGACTCCCACATGCACC 58.013 61.111 0.00 0.00 45.03 5.01
3766 4100 1.675641 GTGACTCCCACATGCACCC 60.676 63.158 0.00 0.00 45.03 4.61
3767 4101 1.847506 TGACTCCCACATGCACCCT 60.848 57.895 0.00 0.00 0.00 4.34
3768 4102 1.078143 GACTCCCACATGCACCCTC 60.078 63.158 0.00 0.00 0.00 4.30
3769 4103 1.539869 ACTCCCACATGCACCCTCT 60.540 57.895 0.00 0.00 0.00 3.69
3770 4104 1.077930 CTCCCACATGCACCCTCTG 60.078 63.158 0.00 0.00 0.00 3.35
3771 4105 1.845627 CTCCCACATGCACCCTCTGT 61.846 60.000 0.00 0.00 0.00 3.41
3772 4106 0.546507 TCCCACATGCACCCTCTGTA 60.547 55.000 0.00 0.00 0.00 2.74
3773 4107 0.327924 CCCACATGCACCCTCTGTAA 59.672 55.000 0.00 0.00 0.00 2.41
3774 4108 1.271871 CCCACATGCACCCTCTGTAAA 60.272 52.381 0.00 0.00 0.00 2.01
3775 4109 2.513753 CCACATGCACCCTCTGTAAAA 58.486 47.619 0.00 0.00 0.00 1.52
3776 4110 2.890311 CCACATGCACCCTCTGTAAAAA 59.110 45.455 0.00 0.00 0.00 1.94
3777 4111 3.511146 CCACATGCACCCTCTGTAAAAAT 59.489 43.478 0.00 0.00 0.00 1.82
3778 4112 4.704540 CCACATGCACCCTCTGTAAAAATA 59.295 41.667 0.00 0.00 0.00 1.40
3779 4113 5.360714 CCACATGCACCCTCTGTAAAAATAT 59.639 40.000 0.00 0.00 0.00 1.28
3780 4114 6.127366 CCACATGCACCCTCTGTAAAAATATT 60.127 38.462 0.00 0.00 0.00 1.28
3781 4115 7.068103 CCACATGCACCCTCTGTAAAAATATTA 59.932 37.037 0.00 0.00 0.00 0.98
3782 4116 8.131100 CACATGCACCCTCTGTAAAAATATTAG 58.869 37.037 0.00 0.00 0.00 1.73
3783 4117 7.834181 ACATGCACCCTCTGTAAAAATATTAGT 59.166 33.333 0.00 0.00 0.00 2.24
3784 4118 9.337396 CATGCACCCTCTGTAAAAATATTAGTA 57.663 33.333 0.00 0.00 0.00 1.82
3785 4119 8.958119 TGCACCCTCTGTAAAAATATTAGTAG 57.042 34.615 0.00 0.00 0.00 2.57
3786 4120 8.764558 TGCACCCTCTGTAAAAATATTAGTAGA 58.235 33.333 0.00 0.00 0.00 2.59
3787 4121 9.262358 GCACCCTCTGTAAAAATATTAGTAGAG 57.738 37.037 0.00 0.00 0.00 2.43
3788 4122 9.765795 CACCCTCTGTAAAAATATTAGTAGAGG 57.234 37.037 18.17 18.17 46.02 3.69
3798 4132 9.774413 AAAAATATTAGTAGAGGGAATACCACG 57.226 33.333 0.00 0.00 43.89 4.94
3799 4133 8.488308 AAATATTAGTAGAGGGAATACCACGT 57.512 34.615 0.00 0.00 43.89 4.49
3800 4134 8.488308 AATATTAGTAGAGGGAATACCACGTT 57.512 34.615 0.00 0.00 43.89 3.99
3801 4135 9.592196 AATATTAGTAGAGGGAATACCACGTTA 57.408 33.333 0.00 0.00 43.89 3.18
3802 4136 9.765295 ATATTAGTAGAGGGAATACCACGTTAT 57.235 33.333 0.00 0.00 43.89 1.89
3803 4137 5.786264 AGTAGAGGGAATACCACGTTATG 57.214 43.478 0.00 0.00 43.89 1.90
3804 4138 5.452255 AGTAGAGGGAATACCACGTTATGA 58.548 41.667 0.00 0.00 43.89 2.15
3805 4139 4.667519 AGAGGGAATACCACGTTATGAC 57.332 45.455 0.00 0.00 43.89 3.06
3806 4140 4.287552 AGAGGGAATACCACGTTATGACT 58.712 43.478 0.00 0.00 43.89 3.41
3807 4141 4.341520 AGAGGGAATACCACGTTATGACTC 59.658 45.833 0.00 0.00 43.89 3.36
3808 4142 3.067742 AGGGAATACCACGTTATGACTCG 59.932 47.826 0.00 0.00 43.89 4.18
3809 4143 3.067180 GGGAATACCACGTTATGACTCGA 59.933 47.826 0.00 0.00 39.85 4.04
3810 4144 4.440525 GGGAATACCACGTTATGACTCGAA 60.441 45.833 0.00 0.00 39.85 3.71
3811 4145 5.104374 GGAATACCACGTTATGACTCGAAA 58.896 41.667 0.00 0.00 35.97 3.46
3812 4146 5.577945 GGAATACCACGTTATGACTCGAAAA 59.422 40.000 0.00 0.00 35.97 2.29
3813 4147 6.257193 GGAATACCACGTTATGACTCGAAAAT 59.743 38.462 0.00 0.00 35.97 1.82
3814 4148 7.201582 GGAATACCACGTTATGACTCGAAAATT 60.202 37.037 0.00 0.00 35.97 1.82
3815 4149 5.526010 ACCACGTTATGACTCGAAAATTC 57.474 39.130 0.00 0.00 0.00 2.17
3828 4162 3.325230 GAAAATTCGAATCTGAGCCCG 57.675 47.619 11.83 0.00 0.00 6.13
3829 4163 2.691409 AAATTCGAATCTGAGCCCGA 57.309 45.000 11.83 0.00 0.00 5.14
3830 4164 2.231215 AATTCGAATCTGAGCCCGAG 57.769 50.000 11.83 0.00 32.41 4.63
3831 4165 0.249657 ATTCGAATCTGAGCCCGAGC 60.250 55.000 4.39 0.00 40.32 5.03
3841 4175 2.894387 GCCCGAGCTCATCTGCAC 60.894 66.667 15.40 0.00 35.50 4.57
3842 4176 2.202987 CCCGAGCTCATCTGCACC 60.203 66.667 15.40 0.00 34.99 5.01
3843 4177 2.729479 CCCGAGCTCATCTGCACCT 61.729 63.158 15.40 0.00 34.99 4.00
3844 4178 1.521010 CCGAGCTCATCTGCACCTG 60.521 63.158 15.40 0.00 34.99 4.00
3845 4179 2.172372 CGAGCTCATCTGCACCTGC 61.172 63.158 15.40 0.00 42.50 4.85
3846 4180 2.125229 AGCTCATCTGCACCTGCG 60.125 61.111 0.00 0.00 45.83 5.18
3847 4181 3.873883 GCTCATCTGCACCTGCGC 61.874 66.667 0.00 0.00 45.83 6.09
3848 4182 2.125229 CTCATCTGCACCTGCGCT 60.125 61.111 9.73 0.00 45.83 5.92
3849 4183 2.125391 TCATCTGCACCTGCGCTC 60.125 61.111 9.73 0.00 45.83 5.03
3850 4184 2.435410 CATCTGCACCTGCGCTCA 60.435 61.111 9.73 0.00 45.83 4.26
3851 4185 2.435586 ATCTGCACCTGCGCTCAC 60.436 61.111 9.73 0.00 45.83 3.51
3854 4188 4.600576 TGCACCTGCGCTCACGAA 62.601 61.111 9.73 0.00 45.83 3.85
3855 4189 3.345808 GCACCTGCGCTCACGAAA 61.346 61.111 9.73 0.00 43.93 3.46
3856 4190 2.892334 GCACCTGCGCTCACGAAAA 61.892 57.895 9.73 0.00 43.93 2.29
3857 4191 1.646540 CACCTGCGCTCACGAAAAA 59.353 52.632 9.73 0.00 43.93 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.178068 GATGGTGTGGAGTATGCGGT 59.822 55.000 0.00 0.00 0.00 5.68
2 3 0.532862 GGGATGGTGTGGAGTATGCG 60.533 60.000 0.00 0.00 0.00 4.73
3 4 0.532862 CGGGATGGTGTGGAGTATGC 60.533 60.000 0.00 0.00 0.00 3.14
4 5 0.830648 ACGGGATGGTGTGGAGTATG 59.169 55.000 0.00 0.00 0.00 2.39
5 6 0.830648 CACGGGATGGTGTGGAGTAT 59.169 55.000 0.00 0.00 33.24 2.12
6 7 1.895020 GCACGGGATGGTGTGGAGTA 61.895 60.000 0.00 0.00 40.08 2.59
7 8 3.068881 CACGGGATGGTGTGGAGT 58.931 61.111 0.00 0.00 33.24 3.85
8 9 2.436646 GCACGGGATGGTGTGGAG 60.437 66.667 0.00 0.00 40.08 3.86
9 10 2.463589 GAAGCACGGGATGGTGTGGA 62.464 60.000 0.00 0.00 39.59 4.02
10 11 2.034066 AAGCACGGGATGGTGTGG 59.966 61.111 0.00 0.00 39.59 4.17
11 12 1.003355 AGAAGCACGGGATGGTGTG 60.003 57.895 0.00 0.00 39.59 3.82
12 13 1.296715 GAGAAGCACGGGATGGTGT 59.703 57.895 0.00 0.00 39.59 4.16
13 14 1.450312 GGAGAAGCACGGGATGGTG 60.450 63.158 0.00 0.00 39.59 4.17
14 15 2.670148 GGGAGAAGCACGGGATGGT 61.670 63.158 0.00 0.00 42.22 3.55
15 16 2.190578 GGGAGAAGCACGGGATGG 59.809 66.667 0.00 0.00 0.00 3.51
16 17 1.153289 CTGGGAGAAGCACGGGATG 60.153 63.158 0.00 0.00 0.00 3.51
17 18 3.313874 CTGGGAGAAGCACGGGAT 58.686 61.111 0.00 0.00 0.00 3.85
20 21 2.581354 CTCCTGGGAGAAGCACGG 59.419 66.667 10.92 0.00 44.53 4.94
21 22 2.125350 GCTCCTGGGAGAAGCACG 60.125 66.667 19.64 0.00 44.53 5.34
22 23 1.376553 GTGCTCCTGGGAGAAGCAC 60.377 63.158 18.71 18.71 46.74 4.40
23 24 2.596851 GGTGCTCCTGGGAGAAGCA 61.597 63.158 19.64 8.90 45.15 3.91
24 25 2.270527 GGTGCTCCTGGGAGAAGC 59.729 66.667 19.64 15.09 44.53 3.86
25 26 1.298014 GTGGTGCTCCTGGGAGAAG 59.702 63.158 19.64 0.00 44.53 2.85
26 27 2.224159 GGTGGTGCTCCTGGGAGAA 61.224 63.158 19.64 7.04 44.53 2.87
27 28 2.607750 GGTGGTGCTCCTGGGAGA 60.608 66.667 19.64 3.22 44.53 3.71
28 29 2.930019 TGGTGGTGCTCCTGGGAG 60.930 66.667 11.97 11.97 44.56 4.30
29 30 3.249189 GTGGTGGTGCTCCTGGGA 61.249 66.667 6.34 0.00 34.23 4.37
43 44 0.798776 GTCGAGAAACATGCAGGTGG 59.201 55.000 4.03 0.00 0.00 4.61
46 47 1.998315 CTGAGTCGAGAAACATGCAGG 59.002 52.381 0.00 0.00 0.00 4.85
47 48 1.998315 CCTGAGTCGAGAAACATGCAG 59.002 52.381 0.00 0.00 0.00 4.41
48 49 1.941209 GCCTGAGTCGAGAAACATGCA 60.941 52.381 0.00 0.00 0.00 3.96
49 50 0.723981 GCCTGAGTCGAGAAACATGC 59.276 55.000 0.00 0.00 0.00 4.06
51 52 1.620819 ACAGCCTGAGTCGAGAAACAT 59.379 47.619 0.00 0.00 0.00 2.71
52 53 1.040646 ACAGCCTGAGTCGAGAAACA 58.959 50.000 0.00 0.00 0.00 2.83
53 54 1.423395 CACAGCCTGAGTCGAGAAAC 58.577 55.000 0.00 0.00 0.00 2.78
56 57 1.228583 ACCACAGCCTGAGTCGAGA 60.229 57.895 0.00 0.00 0.00 4.04
57 58 1.080230 CACCACAGCCTGAGTCGAG 60.080 63.158 0.00 0.00 0.00 4.04
58 59 1.530655 TCACCACAGCCTGAGTCGA 60.531 57.895 0.00 0.00 0.00 4.20
59 60 1.373497 GTCACCACAGCCTGAGTCG 60.373 63.158 0.00 0.00 0.00 4.18
60 61 1.004440 GGTCACCACAGCCTGAGTC 60.004 63.158 0.00 0.00 0.00 3.36
61 62 1.344953 TTGGTCACCACAGCCTGAGT 61.345 55.000 0.00 0.00 30.78 3.41
62 63 0.179020 TTTGGTCACCACAGCCTGAG 60.179 55.000 0.00 0.00 30.78 3.35
63 64 0.465460 GTTTGGTCACCACAGCCTGA 60.465 55.000 0.00 0.00 30.78 3.86
69 70 0.626382 TTCCAGGTTTGGTCACCACA 59.374 50.000 0.00 0.00 45.26 4.17
70 71 1.133915 TCTTCCAGGTTTGGTCACCAC 60.134 52.381 0.00 0.00 45.26 4.16
83 84 3.175240 CTCGTGCGCGTCTTCCAG 61.175 66.667 20.50 4.35 39.49 3.86
86 87 3.832171 CTGCTCGTGCGCGTCTTC 61.832 66.667 20.50 7.78 43.34 2.87
87 88 3.633094 ATCTGCTCGTGCGCGTCTT 62.633 57.895 20.50 0.00 43.34 3.01
88 89 4.121669 ATCTGCTCGTGCGCGTCT 62.122 61.111 20.50 0.00 43.34 4.18
89 90 3.611792 GATCTGCTCGTGCGCGTC 61.612 66.667 20.50 13.08 43.34 5.19
90 91 3.914605 TTGATCTGCTCGTGCGCGT 62.915 57.895 20.50 0.00 43.34 6.01
91 92 3.181290 TTGATCTGCTCGTGCGCG 61.181 61.111 14.79 14.79 43.34 6.86
92 93 2.382746 TGTTGATCTGCTCGTGCGC 61.383 57.895 0.00 0.00 43.34 6.09
93 94 1.417592 GTGTTGATCTGCTCGTGCG 59.582 57.895 4.84 0.23 43.34 5.34
95 96 1.959899 GCCGTGTTGATCTGCTCGTG 61.960 60.000 0.00 0.00 0.00 4.35
107 108 4.379243 CTCCCTCAGCGCCGTGTT 62.379 66.667 2.29 0.00 0.00 3.32
116 117 2.186384 CGGCTTGCTCTCCCTCAG 59.814 66.667 0.00 0.00 0.00 3.35
138 139 1.471287 GATTGAAGCTGCTGACATGCA 59.529 47.619 1.35 0.00 41.05 3.96
139 140 1.471287 TGATTGAAGCTGCTGACATGC 59.529 47.619 1.35 3.36 0.00 4.06
140 141 3.057806 TGTTGATTGAAGCTGCTGACATG 60.058 43.478 1.35 0.00 0.00 3.21
141 142 3.057736 GTGTTGATTGAAGCTGCTGACAT 60.058 43.478 1.35 0.00 0.00 3.06
158 166 6.862608 TGTAATGCAGCTTTAATTCAGTGTTG 59.137 34.615 2.39 0.00 0.00 3.33
226 236 0.964860 TGCCCAGTGCGTTGCATTAT 60.965 50.000 0.00 0.00 45.60 1.28
229 239 2.911509 TTGCCCAGTGCGTTGCAT 60.912 55.556 0.00 0.00 45.60 3.96
313 323 1.354031 TGTGGGCCATGTGTCTACAAT 59.646 47.619 10.70 0.00 40.84 2.71
318 328 1.845791 TGATATGTGGGCCATGTGTCT 59.154 47.619 10.70 0.00 34.86 3.41
413 423 2.270874 ATAAAGAGCAGGGGTGGCCG 62.271 60.000 0.00 0.00 0.00 6.13
475 485 2.192979 GGATTGGCGAGCCCATGA 59.807 61.111 12.05 0.00 44.89 3.07
511 555 1.134551 AGAAAGGCTCGCTTCAGGATC 60.135 52.381 0.68 0.00 0.00 3.36
523 567 2.772287 CGTCTCAAGGAAAGAAAGGCT 58.228 47.619 0.00 0.00 0.00 4.58
537 581 4.314440 GCCCACCTGTGCGTCTCA 62.314 66.667 0.00 0.00 0.00 3.27
574 623 3.860930 AACCATGACCCACCGGTGC 62.861 63.158 29.75 16.21 44.88 5.01
616 666 1.687840 CGGGACCCATGACCCACTA 60.688 63.158 12.15 0.00 45.64 2.74
619 669 4.667935 ACCGGGACCCATGACCCA 62.668 66.667 12.15 0.00 45.64 4.51
722 794 2.472909 GCCGCAGTACAATCCAGCC 61.473 63.158 0.00 0.00 0.00 4.85
786 859 1.483827 AGCAGCTCGGAAATCATCAGA 59.516 47.619 0.00 0.00 0.00 3.27
844 917 4.020128 ACCGAAGCTAATCCTCTCTTGTTT 60.020 41.667 0.00 0.00 0.00 2.83
868 941 6.006449 GGAAGCCATCATCATAGTGGTAAAT 58.994 40.000 0.00 0.00 35.44 1.40
876 955 4.637387 AGGAAGGAAGCCATCATCATAG 57.363 45.455 0.00 0.00 0.00 2.23
877 956 4.202503 GGAAGGAAGGAAGCCATCATCATA 60.203 45.833 0.00 0.00 0.00 2.15
900 980 2.876550 TGCTGCTGCTGCTAATATGAAG 59.123 45.455 27.67 4.20 40.48 3.02
902 982 2.490991 CTGCTGCTGCTGCTAATATGA 58.509 47.619 27.67 8.77 40.48 2.15
903 983 2.971430 CTGCTGCTGCTGCTAATATG 57.029 50.000 27.67 10.52 40.48 1.78
911 991 2.258726 TTGACTGCTGCTGCTGCTG 61.259 57.895 27.75 27.75 41.07 4.41
988 1076 2.042404 CTGGCCATCTGAGCTCCTCC 62.042 65.000 5.51 3.86 0.00 4.30
1461 1549 2.107546 ACGAACGTGGCGTCCTTT 59.892 55.556 10.48 0.00 39.99 3.11
1620 1708 0.321653 AATCGAACACCCTGCTGACC 60.322 55.000 0.00 0.00 0.00 4.02
1755 1863 9.612620 GTGACATCCTTTATTAGTTTGAACTTG 57.387 33.333 1.20 0.00 40.37 3.16
1772 1880 3.074390 TGTGAAATTCCAGGTGACATCCT 59.926 43.478 0.00 0.00 38.51 3.24
1805 1914 3.808728 TCTCAACTCCAAACAAGGACTG 58.191 45.455 0.00 0.00 33.19 3.51
1841 1973 5.635280 CCGACATGACCTACATAATGATGTC 59.365 44.000 0.00 0.00 43.01 3.06
1856 1988 3.281341 TCATTTTGTTGCCGACATGAC 57.719 42.857 0.00 0.00 38.26 3.06
1866 1998 5.009854 AGACACCCTTGTTCATTTTGTTG 57.990 39.130 0.00 0.00 35.47 3.33
1929 2102 7.790027 AGTTAGATCAACTGCAATCAGAGTAT 58.210 34.615 9.00 0.00 46.01 2.12
2010 2184 6.729690 ACCTCAATTTTTCCAGAATCAACA 57.270 33.333 0.00 0.00 0.00 3.33
2015 2189 9.764363 GAAGTTTAACCTCAATTTTTCCAGAAT 57.236 29.630 0.00 0.00 0.00 2.40
2027 2215 9.616156 TGTTACTAACATGAAGTTTAACCTCAA 57.384 29.630 0.00 0.00 41.64 3.02
2088 2276 0.188342 ACAGAAGGCCACCAACCAAT 59.812 50.000 5.01 0.00 0.00 3.16
2094 2282 3.761752 GCTAAAATAACAGAAGGCCACCA 59.238 43.478 5.01 0.00 0.00 4.17
2095 2283 3.761752 TGCTAAAATAACAGAAGGCCACC 59.238 43.478 5.01 0.00 0.00 4.61
2096 2284 5.582689 ATGCTAAAATAACAGAAGGCCAC 57.417 39.130 5.01 0.00 0.00 5.01
2097 2285 6.423182 ACTATGCTAAAATAACAGAAGGCCA 58.577 36.000 5.01 0.00 0.00 5.36
2099 2287 9.495572 AGATACTATGCTAAAATAACAGAAGGC 57.504 33.333 0.00 0.00 0.00 4.35
2126 2314 7.355778 CCTGTGAAAAGTTTAAGCTGAACTAG 58.644 38.462 14.15 8.18 36.38 2.57
2127 2315 6.238648 GCCTGTGAAAAGTTTAAGCTGAACTA 60.239 38.462 14.15 0.00 36.38 2.24
2171 2359 2.919602 TGGATCTTTAGGAAAGCTGGGT 59.080 45.455 0.00 0.00 38.39 4.51
2240 2428 1.838077 ACCCTGCACTTATAGGACACC 59.162 52.381 0.00 0.00 36.11 4.16
2351 2638 4.204799 ACCCAAACTTTCCAGTACACTTC 58.795 43.478 0.00 0.00 30.68 3.01
2357 2644 7.504926 ACTATATGACCCAAACTTTCCAGTA 57.495 36.000 0.00 0.00 30.68 2.74
2387 2674 5.822519 AGTGCATCTGACTTCAAACTAACAA 59.177 36.000 0.00 0.00 0.00 2.83
2445 2732 6.379988 ACACTAGTGAATTGTGAACCCTTTTT 59.620 34.615 29.30 0.00 37.96 1.94
2450 2737 3.432252 CGACACTAGTGAATTGTGAACCC 59.568 47.826 29.30 2.90 37.96 4.11
2456 2743 1.338769 GGGGCGACACTAGTGAATTGT 60.339 52.381 29.30 6.23 0.00 2.71
2486 2773 4.202141 TGAACAAATCCAACTTGCTTCTGG 60.202 41.667 0.00 0.00 0.00 3.86
2603 2890 5.652994 AGTTAACAAGAAACTGGTTTGCA 57.347 34.783 8.61 0.00 35.87 4.08
2705 3004 9.985318 GACTTCTCTGATATTTCTGAAACAATG 57.015 33.333 4.73 0.00 30.48 2.82
3077 3378 8.914011 GTGCTAAGGAAATACCATAAAATCCTT 58.086 33.333 9.55 9.55 46.19 3.36
3082 3383 9.391006 CAGTAGTGCTAAGGAAATACCATAAAA 57.609 33.333 0.00 0.00 42.04 1.52
3083 3384 8.764558 TCAGTAGTGCTAAGGAAATACCATAAA 58.235 33.333 0.00 0.00 42.04 1.40
3084 3385 8.313944 TCAGTAGTGCTAAGGAAATACCATAA 57.686 34.615 0.00 0.00 42.04 1.90
3085 3386 7.907841 TCAGTAGTGCTAAGGAAATACCATA 57.092 36.000 0.00 0.00 42.04 2.74
3086 3387 6.808321 TCAGTAGTGCTAAGGAAATACCAT 57.192 37.500 0.00 0.00 42.04 3.55
3087 3388 6.156256 ACATCAGTAGTGCTAAGGAAATACCA 59.844 38.462 0.00 0.00 42.04 3.25
3088 3389 6.583562 ACATCAGTAGTGCTAAGGAAATACC 58.416 40.000 0.00 0.00 39.35 2.73
3089 3390 6.702282 GGACATCAGTAGTGCTAAGGAAATAC 59.298 42.308 0.00 0.00 0.00 1.89
3090 3391 6.461092 CGGACATCAGTAGTGCTAAGGAAATA 60.461 42.308 0.00 0.00 0.00 1.40
3115 3416 9.817365 GCATCACAACATATCACTAATCAATAC 57.183 33.333 0.00 0.00 0.00 1.89
3128 3430 9.672673 GGTTAATCTATAGGCATCACAACATAT 57.327 33.333 0.00 0.00 0.00 1.78
3144 3446 7.993183 CACTACAAGTGGGAATGGTTAATCTAT 59.007 37.037 0.00 0.00 42.35 1.98
3165 3474 1.069296 TGCAAAAGCGCATCACACTAC 60.069 47.619 11.47 0.00 36.86 2.73
3166 3475 1.197492 CTGCAAAAGCGCATCACACTA 59.803 47.619 11.47 0.00 42.06 2.74
3190 3500 5.869888 CACTCCTATTGTGAAGGTACTCAAC 59.130 44.000 0.00 0.00 38.49 3.18
3220 3530 3.199442 TCCAGTCCCTCAAATCAGGTA 57.801 47.619 0.00 0.00 0.00 3.08
3284 3599 8.054152 ACATTGTTGTTCTATGAACATATGCA 57.946 30.769 12.95 0.00 34.38 3.96
3291 3606 8.132362 TGGTTGTAACATTGTTGTTCTATGAAC 58.868 33.333 12.30 3.74 42.43 3.18
3307 3622 3.195471 TCACGTGGATTGGTTGTAACA 57.805 42.857 17.00 0.00 0.00 2.41
3327 3642 4.394920 TCTCTCGTGCTTTCTTGTTGTTTT 59.605 37.500 0.00 0.00 0.00 2.43
3334 3649 3.185391 GGTTCTTCTCTCGTGCTTTCTTG 59.815 47.826 0.00 0.00 0.00 3.02
3335 3650 3.394719 GGTTCTTCTCTCGTGCTTTCTT 58.605 45.455 0.00 0.00 0.00 2.52
3339 3654 0.674534 ACGGTTCTTCTCTCGTGCTT 59.325 50.000 0.00 0.00 34.40 3.91
3340 3655 0.039074 CACGGTTCTTCTCTCGTGCT 60.039 55.000 0.00 0.00 44.56 4.40
3341 3656 2.435741 CACGGTTCTTCTCTCGTGC 58.564 57.895 0.00 0.00 44.56 5.34
3343 3658 1.289380 GGCACGGTTCTTCTCTCGT 59.711 57.895 0.00 0.00 36.19 4.18
3344 3659 0.319555 TTGGCACGGTTCTTCTCTCG 60.320 55.000 0.00 0.00 0.00 4.04
3349 3664 1.947456 AGAGTTTTGGCACGGTTCTTC 59.053 47.619 0.00 0.00 0.00 2.87
3352 3667 0.317854 GCAGAGTTTTGGCACGGTTC 60.318 55.000 0.00 0.00 0.00 3.62
3361 3676 4.747810 AGGTGTTTTTCTGCAGAGTTTTG 58.252 39.130 17.43 0.00 0.00 2.44
3374 3689 5.509670 GCTATTTCTTGCTGGAGGTGTTTTT 60.510 40.000 0.00 0.00 0.00 1.94
3402 3717 3.911260 TGTTCACCCAACCCAGATACTTA 59.089 43.478 0.00 0.00 33.51 2.24
3443 3759 4.331717 ACTGAAATTCAACTTATACCGCCG 59.668 41.667 0.00 0.00 0.00 6.46
3651 3985 8.218338 TGTTAAACCACATGCAAAAATTCATT 57.782 26.923 0.00 0.00 0.00 2.57
3652 3986 7.798596 TGTTAAACCACATGCAAAAATTCAT 57.201 28.000 0.00 0.00 0.00 2.57
3657 3991 5.491982 ACCTTGTTAAACCACATGCAAAAA 58.508 33.333 0.00 0.00 0.00 1.94
3688 4022 6.210287 AGACGTGGGTTAATTTGTTTTTCA 57.790 33.333 0.00 0.00 0.00 2.69
3689 4023 8.533965 GTTTAGACGTGGGTTAATTTGTTTTTC 58.466 33.333 0.00 0.00 0.00 2.29
3690 4024 7.220491 CGTTTAGACGTGGGTTAATTTGTTTTT 59.780 33.333 0.00 0.00 44.08 1.94
3691 4025 6.692249 CGTTTAGACGTGGGTTAATTTGTTTT 59.308 34.615 0.00 0.00 44.08 2.43
3692 4026 6.200808 CGTTTAGACGTGGGTTAATTTGTTT 58.799 36.000 0.00 0.00 44.08 2.83
3693 4027 5.750650 CGTTTAGACGTGGGTTAATTTGTT 58.249 37.500 0.00 0.00 44.08 2.83
3694 4028 5.347012 CGTTTAGACGTGGGTTAATTTGT 57.653 39.130 0.00 0.00 44.08 2.83
3708 4042 5.446073 GCTATTTTCAGACAGGCGTTTAGAC 60.446 44.000 0.00 0.00 0.00 2.59
3709 4043 4.630069 GCTATTTTCAGACAGGCGTTTAGA 59.370 41.667 0.00 0.00 0.00 2.10
3710 4044 4.631813 AGCTATTTTCAGACAGGCGTTTAG 59.368 41.667 0.00 0.00 0.00 1.85
3711 4045 4.575885 AGCTATTTTCAGACAGGCGTTTA 58.424 39.130 0.00 0.00 0.00 2.01
3712 4046 3.412386 AGCTATTTTCAGACAGGCGTTT 58.588 40.909 0.00 0.00 0.00 3.60
3713 4047 3.003480 GAGCTATTTTCAGACAGGCGTT 58.997 45.455 0.00 0.00 0.00 4.84
3714 4048 2.622436 GAGCTATTTTCAGACAGGCGT 58.378 47.619 0.00 0.00 0.00 5.68
3715 4049 1.936547 GGAGCTATTTTCAGACAGGCG 59.063 52.381 0.00 0.00 0.00 5.52
3716 4050 2.991250 TGGAGCTATTTTCAGACAGGC 58.009 47.619 0.00 0.00 0.00 4.85
3717 4051 5.964958 TTTTGGAGCTATTTTCAGACAGG 57.035 39.130 0.00 0.00 0.00 4.00
3747 4081 1.675641 GGTGCATGTGGGAGTCACC 60.676 63.158 0.00 0.00 45.48 4.02
3748 4082 1.675641 GGGTGCATGTGGGAGTCAC 60.676 63.158 0.00 0.00 46.23 3.67
3749 4083 1.841302 GAGGGTGCATGTGGGAGTCA 61.841 60.000 0.00 0.00 0.00 3.41
3750 4084 1.078143 GAGGGTGCATGTGGGAGTC 60.078 63.158 0.00 0.00 0.00 3.36
3751 4085 1.539869 AGAGGGTGCATGTGGGAGT 60.540 57.895 0.00 0.00 0.00 3.85
3752 4086 1.077930 CAGAGGGTGCATGTGGGAG 60.078 63.158 0.00 0.00 0.00 4.30
3753 4087 0.546507 TACAGAGGGTGCATGTGGGA 60.547 55.000 0.12 0.00 0.00 4.37
3754 4088 0.327924 TTACAGAGGGTGCATGTGGG 59.672 55.000 0.12 0.00 0.00 4.61
3755 4089 2.198827 TTTACAGAGGGTGCATGTGG 57.801 50.000 0.12 0.00 0.00 4.17
3756 4090 4.789012 ATTTTTACAGAGGGTGCATGTG 57.211 40.909 0.12 0.00 0.00 3.21
3757 4091 7.834181 ACTAATATTTTTACAGAGGGTGCATGT 59.166 33.333 0.00 0.00 0.00 3.21
3758 4092 8.225603 ACTAATATTTTTACAGAGGGTGCATG 57.774 34.615 0.00 0.00 0.00 4.06
3759 4093 9.561069 CTACTAATATTTTTACAGAGGGTGCAT 57.439 33.333 0.00 0.00 0.00 3.96
3760 4094 8.764558 TCTACTAATATTTTTACAGAGGGTGCA 58.235 33.333 0.00 0.00 0.00 4.57
3761 4095 9.262358 CTCTACTAATATTTTTACAGAGGGTGC 57.738 37.037 0.00 0.00 0.00 5.01
3762 4096 9.765795 CCTCTACTAATATTTTTACAGAGGGTG 57.234 37.037 16.19 0.00 42.72 4.61
3772 4106 9.774413 CGTGGTATTCCCTCTACTAATATTTTT 57.226 33.333 0.00 0.00 0.00 1.94
3773 4107 8.931568 ACGTGGTATTCCCTCTACTAATATTTT 58.068 33.333 0.00 0.00 0.00 1.82
3774 4108 8.488308 ACGTGGTATTCCCTCTACTAATATTT 57.512 34.615 0.00 0.00 0.00 1.40
3775 4109 8.488308 AACGTGGTATTCCCTCTACTAATATT 57.512 34.615 0.00 0.00 0.00 1.28
3776 4110 9.765295 ATAACGTGGTATTCCCTCTACTAATAT 57.235 33.333 0.00 0.00 0.00 1.28
3777 4111 9.017509 CATAACGTGGTATTCCCTCTACTAATA 57.982 37.037 0.00 0.00 0.00 0.98
3778 4112 7.727186 TCATAACGTGGTATTCCCTCTACTAAT 59.273 37.037 0.00 0.00 0.00 1.73
3779 4113 7.013655 GTCATAACGTGGTATTCCCTCTACTAA 59.986 40.741 0.00 0.00 0.00 2.24
3780 4114 6.488006 GTCATAACGTGGTATTCCCTCTACTA 59.512 42.308 0.00 0.00 0.00 1.82
3781 4115 5.301298 GTCATAACGTGGTATTCCCTCTACT 59.699 44.000 0.00 0.00 0.00 2.57
3782 4116 5.301298 AGTCATAACGTGGTATTCCCTCTAC 59.699 44.000 0.00 0.00 0.00 2.59
3783 4117 5.452255 AGTCATAACGTGGTATTCCCTCTA 58.548 41.667 0.00 0.00 0.00 2.43
3784 4118 4.287552 AGTCATAACGTGGTATTCCCTCT 58.712 43.478 0.00 0.00 0.00 3.69
3785 4119 4.618965 GAGTCATAACGTGGTATTCCCTC 58.381 47.826 0.00 0.00 0.00 4.30
3786 4120 3.067742 CGAGTCATAACGTGGTATTCCCT 59.932 47.826 0.00 0.00 0.00 4.20
3787 4121 3.067180 TCGAGTCATAACGTGGTATTCCC 59.933 47.826 0.00 0.00 0.00 3.97
3788 4122 4.297299 TCGAGTCATAACGTGGTATTCC 57.703 45.455 0.00 0.00 0.00 3.01
3789 4123 6.636666 TTTTCGAGTCATAACGTGGTATTC 57.363 37.500 0.00 0.00 0.00 1.75
3790 4124 7.605410 AATTTTCGAGTCATAACGTGGTATT 57.395 32.000 0.00 0.00 0.00 1.89
3791 4125 7.230466 GAATTTTCGAGTCATAACGTGGTAT 57.770 36.000 0.00 0.00 0.00 2.73
3792 4126 6.636666 GAATTTTCGAGTCATAACGTGGTA 57.363 37.500 0.00 0.00 0.00 3.25
3793 4127 5.526010 GAATTTTCGAGTCATAACGTGGT 57.474 39.130 0.00 0.00 0.00 4.16
3808 4142 2.936498 TCGGGCTCAGATTCGAATTTTC 59.064 45.455 12.81 0.03 0.00 2.29
3809 4143 2.939103 CTCGGGCTCAGATTCGAATTTT 59.061 45.455 12.81 1.04 0.00 1.82
3810 4144 2.555199 CTCGGGCTCAGATTCGAATTT 58.445 47.619 12.81 3.29 0.00 1.82
3811 4145 1.808133 GCTCGGGCTCAGATTCGAATT 60.808 52.381 12.81 0.00 35.22 2.17
3812 4146 0.249657 GCTCGGGCTCAGATTCGAAT 60.250 55.000 11.20 11.20 35.22 3.34
3813 4147 1.141881 GCTCGGGCTCAGATTCGAA 59.858 57.895 0.00 0.00 35.22 3.71
3814 4148 2.808315 GCTCGGGCTCAGATTCGA 59.192 61.111 0.00 0.00 35.22 3.71
3824 4158 2.894387 GTGCAGATGAGCTCGGGC 60.894 66.667 9.64 0.00 39.06 6.13
3825 4159 2.202987 GGTGCAGATGAGCTCGGG 60.203 66.667 9.64 0.00 34.99 5.14
3826 4160 1.521010 CAGGTGCAGATGAGCTCGG 60.521 63.158 9.64 0.00 34.99 4.63
3827 4161 2.172372 GCAGGTGCAGATGAGCTCG 61.172 63.158 9.64 0.00 41.59 5.03
3828 4162 2.172372 CGCAGGTGCAGATGAGCTC 61.172 63.158 6.82 6.82 42.21 4.09
3829 4163 2.125229 CGCAGGTGCAGATGAGCT 60.125 61.111 2.33 0.00 42.21 4.09
3830 4164 3.873883 GCGCAGGTGCAGATGAGC 61.874 66.667 0.30 10.34 42.21 4.26
3831 4165 2.125229 AGCGCAGGTGCAGATGAG 60.125 61.111 11.47 0.18 42.21 2.90
3832 4166 2.125391 GAGCGCAGGTGCAGATGA 60.125 61.111 11.47 0.00 39.88 2.92
3833 4167 2.435410 TGAGCGCAGGTGCAGATG 60.435 61.111 11.47 0.00 39.88 2.90
3834 4168 2.435586 GTGAGCGCAGGTGCAGAT 60.436 61.111 11.47 0.00 39.88 2.90
3837 4171 4.600576 TTCGTGAGCGCAGGTGCA 62.601 61.111 11.47 0.00 39.88 4.57
3838 4172 2.387125 TTTTTCGTGAGCGCAGGTGC 62.387 55.000 11.47 0.00 39.88 5.01
3839 4173 1.646540 TTTTTCGTGAGCGCAGGTG 59.353 52.632 11.47 0.00 39.88 4.00
3840 4174 4.134623 TTTTTCGTGAGCGCAGGT 57.865 50.000 11.47 0.00 46.54 4.00


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

AutoCloner maintained by Alex Coulton.