Multiple sequence alignment - TraesCS7D01G193100

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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 TraesCS7D01G193100 chr7D 100.000 3121 0 0 1 3121 149180075 149183195 0.000000e+00 5764.0
1 TraesCS7D01G193100 chr7D 90.410 2388 142 43 783 3087 149086248 149083865 0.000000e+00 3061.0
2 TraesCS7D01G193100 chr7D 100.000 496 0 0 3511 4006 149183585 149184080 0.000000e+00 917.0
3 TraesCS7D01G193100 chr7D 90.670 418 32 4 3511 3921 149083953 149083536 2.100000e-152 549.0
4 TraesCS7D01G193100 chr7D 100.000 35 0 0 3087 3121 149084021 149083987 9.290000e-07 65.8
5 TraesCS7D01G193100 chr7A 89.123 2611 170 46 570 3087 149863415 149860826 0.000000e+00 3144.0
6 TraesCS7D01G193100 chr7A 90.417 2181 132 46 685 2816 150021346 150023498 0.000000e+00 2798.0
7 TraesCS7D01G193100 chr7A 88.930 271 25 2 2822 3087 150023539 150023809 2.980000e-86 329.0
8 TraesCS7D01G193100 chr7A 88.780 205 18 4 174 376 150020703 150020904 3.090000e-61 246.0
9 TraesCS7D01G193100 chr7A 88.235 204 13 6 374 570 150020956 150021155 2.410000e-57 233.0
10 TraesCS7D01G193100 chr7A 87.919 149 13 3 3626 3770 149860828 149860681 1.910000e-38 171.0
11 TraesCS7D01G193100 chr7A 93.478 92 6 0 3511 3602 149860914 149860823 1.940000e-28 137.0
12 TraesCS7D01G193100 chr7B 94.370 1634 59 19 1192 2812 111942439 111944052 0.000000e+00 2477.0
13 TraesCS7D01G193100 chr7B 86.102 626 33 14 560 1136 111941576 111942196 3.400000e-175 625.0
14 TraesCS7D01G193100 chr7B 88.561 271 26 2 2822 3087 111944099 111944369 1.390000e-84 324.0
15 TraesCS7D01G193100 chr7B 82.418 364 27 16 221 570 111941210 111941550 2.360000e-72 283.0
16 TraesCS7D01G193100 chr7B 93.617 47 1 2 3754 3799 708834835 708834790 7.180000e-08 69.4
17 TraesCS7D01G193100 chr2B 83.479 2064 281 42 987 3015 232291538 232289500 0.000000e+00 1868.0
18 TraesCS7D01G193100 chr2B 83.765 1854 260 31 967 2800 232261280 232263112 0.000000e+00 1718.0
19 TraesCS7D01G193100 chr2A 85.149 1845 233 31 1201 3015 185364735 185362902 0.000000e+00 1851.0
20 TraesCS7D01G193100 chr2A 84.605 747 101 14 996 1734 185264710 185265450 0.000000e+00 730.0
21 TraesCS7D01G193100 chr3D 84.749 1213 156 19 1816 3004 464808960 464807753 0.000000e+00 1188.0
22 TraesCS7D01G193100 chr3A 84.289 1203 169 15 1816 3004 608195758 608194562 0.000000e+00 1157.0
23 TraesCS7D01G193100 chr3B 83.993 1212 168 18 1816 3004 618155766 618154558 0.000000e+00 1140.0
24 TraesCS7D01G193100 chr5B 82.014 1301 175 33 1746 3006 679312464 679313745 0.000000e+00 1051.0
25 TraesCS7D01G193100 chr5B 91.636 538 45 0 1197 1734 679311133 679311670 0.000000e+00 745.0
26 TraesCS7D01G193100 chr5B 80.469 128 18 3 3754 3880 567151820 567151699 1.530000e-14 91.6
27 TraesCS7D01G193100 chr2D 84.293 764 83 21 1002 1734 165485590 165484833 0.000000e+00 712.0
28 TraesCS7D01G193100 chr2D 93.478 46 3 0 3754 3799 591026535 591026490 7.180000e-08 69.4
29 TraesCS7D01G193100 chr5D 86.719 128 17 0 2878 3005 538262291 538262418 4.170000e-30 143.0
30 TraesCS7D01G193100 chr6D 77.660 188 35 4 3739 3921 66963203 66963388 1.520000e-19 108.0
31 TraesCS7D01G193100 chr6D 77.249 189 35 5 3739 3921 66615171 66615357 1.970000e-18 104.0
32 TraesCS7D01G193100 chr6D 86.585 82 5 4 3754 3831 112823892 112823813 7.130000e-13 86.1
33 TraesCS7D01G193100 chr1B 82.759 87 10 3 3754 3835 408654819 408654733 5.550000e-09 73.1
34 TraesCS7D01G193100 chr4D 89.362 47 3 2 3754 3799 313885345 313885390 1.560000e-04 58.4


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 TraesCS7D01G193100 chr7D 149180075 149184080 4005 False 3340.500000 5764 100.000000 1 4006 2 chr7D.!!$F1 4005
1 TraesCS7D01G193100 chr7D 149083536 149086248 2712 True 1225.266667 3061 93.693333 783 3921 3 chr7D.!!$R1 3138
2 TraesCS7D01G193100 chr7A 149860681 149863415 2734 True 1150.666667 3144 90.173333 570 3770 3 chr7A.!!$R1 3200
3 TraesCS7D01G193100 chr7A 150020703 150023809 3106 False 901.500000 2798 89.090500 174 3087 4 chr7A.!!$F1 2913
4 TraesCS7D01G193100 chr7B 111941210 111944369 3159 False 927.250000 2477 87.862750 221 3087 4 chr7B.!!$F1 2866
5 TraesCS7D01G193100 chr2B 232289500 232291538 2038 True 1868.000000 1868 83.479000 987 3015 1 chr2B.!!$R1 2028
6 TraesCS7D01G193100 chr2B 232261280 232263112 1832 False 1718.000000 1718 83.765000 967 2800 1 chr2B.!!$F1 1833
7 TraesCS7D01G193100 chr2A 185362902 185364735 1833 True 1851.000000 1851 85.149000 1201 3015 1 chr2A.!!$R1 1814
8 TraesCS7D01G193100 chr2A 185264710 185265450 740 False 730.000000 730 84.605000 996 1734 1 chr2A.!!$F1 738
9 TraesCS7D01G193100 chr3D 464807753 464808960 1207 True 1188.000000 1188 84.749000 1816 3004 1 chr3D.!!$R1 1188
10 TraesCS7D01G193100 chr3A 608194562 608195758 1196 True 1157.000000 1157 84.289000 1816 3004 1 chr3A.!!$R1 1188
11 TraesCS7D01G193100 chr3B 618154558 618155766 1208 True 1140.000000 1140 83.993000 1816 3004 1 chr3B.!!$R1 1188
12 TraesCS7D01G193100 chr5B 679311133 679313745 2612 False 898.000000 1051 86.825000 1197 3006 2 chr5B.!!$F1 1809
13 TraesCS7D01G193100 chr2D 165484833 165485590 757 True 712.000000 712 84.293000 1002 1734 1 chr2D.!!$R1 732

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
847 1035 0.032403 TGCATGCACCTCAAGCAAAC 59.968 50.0 18.46 0.0 45.17 2.93 F
1776 2990 0.250858 TGTCCAGCCAATGTCACAGG 60.251 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 3058 0.774908 TTTCCGGGTTCCACCTTCAT 59.225 50.0 0.00 0.00 38.64 2.57 R
3097 4437 0.036306 TTCTGGTTCGGAAGGCTTCC 59.964 55.0 32.12 32.12 46.62 3.46 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 9.892130 AGTCCGATATCTTTTAAAATGTCTTCT 57.108 29.630 0.09 0.00 0.00 2.85
61 62 9.793259 TTTTTGTCAACCTATTCTAGTCAAGAT 57.207 29.630 0.00 0.00 33.05 2.40
62 63 9.793259 TTTTGTCAACCTATTCTAGTCAAGATT 57.207 29.630 0.00 0.00 33.05 2.40
63 64 9.793259 TTTGTCAACCTATTCTAGTCAAGATTT 57.207 29.630 0.00 0.00 33.05 2.17
64 65 9.793259 TTGTCAACCTATTCTAGTCAAGATTTT 57.207 29.630 0.00 0.00 33.05 1.82
65 66 9.219603 TGTCAACCTATTCTAGTCAAGATTTTG 57.780 33.333 0.00 0.00 33.05 2.44
66 67 9.220767 GTCAACCTATTCTAGTCAAGATTTTGT 57.779 33.333 0.00 0.00 35.73 2.83
67 68 9.219603 TCAACCTATTCTAGTCAAGATTTTGTG 57.780 33.333 0.00 0.00 35.73 3.33
68 69 9.219603 CAACCTATTCTAGTCAAGATTTTGTGA 57.780 33.333 0.00 0.00 35.73 3.58
69 70 9.793259 AACCTATTCTAGTCAAGATTTTGTGAA 57.207 29.630 0.00 0.00 35.73 3.18
70 71 9.965902 ACCTATTCTAGTCAAGATTTTGTGAAT 57.034 29.630 0.00 5.57 35.73 2.57
75 76 9.778741 TTCTAGTCAAGATTTTGTGAATGTACT 57.221 29.630 0.00 0.00 35.73 2.73
76 77 9.424319 TCTAGTCAAGATTTTGTGAATGTACTC 57.576 33.333 0.00 0.00 35.73 2.59
77 78 7.440523 AGTCAAGATTTTGTGAATGTACTCC 57.559 36.000 0.00 0.00 35.73 3.85
78 79 6.147821 AGTCAAGATTTTGTGAATGTACTCCG 59.852 38.462 0.00 0.00 35.73 4.63
79 80 6.147164 GTCAAGATTTTGTGAATGTACTCCGA 59.853 38.462 0.00 0.00 35.73 4.55
80 81 6.878923 TCAAGATTTTGTGAATGTACTCCGAT 59.121 34.615 0.00 0.00 35.73 4.18
81 82 6.668541 AGATTTTGTGAATGTACTCCGATG 57.331 37.500 0.00 0.00 0.00 3.84
82 83 6.173339 AGATTTTGTGAATGTACTCCGATGT 58.827 36.000 0.00 0.00 0.00 3.06
83 84 7.327975 AGATTTTGTGAATGTACTCCGATGTA 58.672 34.615 0.00 0.00 0.00 2.29
84 85 7.987458 AGATTTTGTGAATGTACTCCGATGTAT 59.013 33.333 0.00 0.00 0.00 2.29
85 86 7.534085 TTTTGTGAATGTACTCCGATGTATC 57.466 36.000 0.00 0.00 0.00 2.24
86 87 5.845391 TGTGAATGTACTCCGATGTATCA 57.155 39.130 0.00 0.00 0.00 2.15
87 88 6.215495 TGTGAATGTACTCCGATGTATCAA 57.785 37.500 0.00 0.00 0.00 2.57
88 89 6.816136 TGTGAATGTACTCCGATGTATCAAT 58.184 36.000 0.00 0.00 0.00 2.57
89 90 7.947282 TGTGAATGTACTCCGATGTATCAATA 58.053 34.615 0.00 0.00 0.00 1.90
90 91 8.417884 TGTGAATGTACTCCGATGTATCAATAA 58.582 33.333 0.00 0.00 0.00 1.40
91 92 9.256477 GTGAATGTACTCCGATGTATCAATAAA 57.744 33.333 0.00 0.00 0.00 1.40
92 93 9.825109 TGAATGTACTCCGATGTATCAATAAAA 57.175 29.630 0.00 0.00 0.00 1.52
96 97 9.825109 TGTACTCCGATGTATCAATAAAATTGA 57.175 29.630 4.90 4.90 0.00 2.57
99 100 9.559732 ACTCCGATGTATCAATAAAATTGATGA 57.440 29.630 20.24 10.42 39.30 2.92
119 120 8.397215 TGATGATGAAAACAATAAGAAATGCG 57.603 30.769 0.00 0.00 0.00 4.73
120 121 8.028354 TGATGATGAAAACAATAAGAAATGCGT 58.972 29.630 0.00 0.00 0.00 5.24
121 122 7.795431 TGATGAAAACAATAAGAAATGCGTC 57.205 32.000 0.00 0.00 0.00 5.19
122 123 7.366513 TGATGAAAACAATAAGAAATGCGTCA 58.633 30.769 0.00 0.00 0.00 4.35
123 124 7.864882 TGATGAAAACAATAAGAAATGCGTCAA 59.135 29.630 0.00 0.00 0.00 3.18
124 125 7.993821 TGAAAACAATAAGAAATGCGTCAAA 57.006 28.000 0.00 0.00 0.00 2.69
125 126 8.412608 TGAAAACAATAAGAAATGCGTCAAAA 57.587 26.923 0.00 0.00 0.00 2.44
126 127 8.873830 TGAAAACAATAAGAAATGCGTCAAAAA 58.126 25.926 0.00 0.00 0.00 1.94
148 149 5.618056 AAATATATGCAGACAAGATGCGG 57.382 39.130 0.00 0.00 46.87 5.69
149 150 1.233019 ATATGCAGACAAGATGCGGC 58.767 50.000 0.00 0.00 46.87 6.53
150 151 0.815213 TATGCAGACAAGATGCGGCC 60.815 55.000 0.00 0.00 46.87 6.13
151 152 3.869272 GCAGACAAGATGCGGCCG 61.869 66.667 24.05 24.05 33.31 6.13
152 153 2.125552 CAGACAAGATGCGGCCGA 60.126 61.111 33.48 15.19 0.00 5.54
153 154 1.741401 CAGACAAGATGCGGCCGAA 60.741 57.895 33.48 22.91 0.00 4.30
154 155 1.003839 AGACAAGATGCGGCCGAAA 60.004 52.632 33.48 17.52 0.00 3.46
155 156 0.392998 AGACAAGATGCGGCCGAAAT 60.393 50.000 33.48 22.03 0.00 2.17
156 157 0.248215 GACAAGATGCGGCCGAAATG 60.248 55.000 33.48 21.71 0.00 2.32
157 158 1.587088 CAAGATGCGGCCGAAATGC 60.587 57.895 33.48 13.08 0.00 3.56
158 159 3.112126 AAGATGCGGCCGAAATGCG 62.112 57.895 33.48 0.00 40.47 4.73
185 186 2.024319 GCCGGCGCTGATCTATGTC 61.024 63.158 20.25 0.00 0.00 3.06
190 191 1.124462 GCGCTGATCTATGTCGTGTC 58.876 55.000 0.00 0.00 0.00 3.67
194 195 4.399112 CGCTGATCTATGTCGTGTCTATC 58.601 47.826 0.00 0.00 0.00 2.08
206 207 3.873361 TCGTGTCTATCGGGTGTAAGTAG 59.127 47.826 0.00 0.00 0.00 2.57
259 260 3.827722 TCCTTCTGTTCGTTGGGAATTT 58.172 40.909 0.00 0.00 36.92 1.82
260 261 3.568007 TCCTTCTGTTCGTTGGGAATTTG 59.432 43.478 0.00 0.00 36.92 2.32
261 262 3.317993 CCTTCTGTTCGTTGGGAATTTGT 59.682 43.478 0.00 0.00 36.92 2.83
262 263 4.517453 CCTTCTGTTCGTTGGGAATTTGTA 59.483 41.667 0.00 0.00 36.92 2.41
263 264 5.183140 CCTTCTGTTCGTTGGGAATTTGTAT 59.817 40.000 0.00 0.00 36.92 2.29
264 265 6.294508 CCTTCTGTTCGTTGGGAATTTGTATT 60.295 38.462 0.00 0.00 36.92 1.89
265 266 7.094549 CCTTCTGTTCGTTGGGAATTTGTATTA 60.095 37.037 0.00 0.00 36.92 0.98
266 267 7.931578 TCTGTTCGTTGGGAATTTGTATTAT 57.068 32.000 0.00 0.00 36.92 1.28
267 268 8.343168 TCTGTTCGTTGGGAATTTGTATTATT 57.657 30.769 0.00 0.00 36.92 1.40
268 269 8.240682 TCTGTTCGTTGGGAATTTGTATTATTG 58.759 33.333 0.00 0.00 36.92 1.90
269 270 7.887381 TGTTCGTTGGGAATTTGTATTATTGT 58.113 30.769 0.00 0.00 36.92 2.71
270 271 9.011095 TGTTCGTTGGGAATTTGTATTATTGTA 57.989 29.630 0.00 0.00 36.92 2.41
271 272 9.281075 GTTCGTTGGGAATTTGTATTATTGTAC 57.719 33.333 0.00 0.00 36.92 2.90
329 341 2.017049 CAACAACTAGGTAGGCATGCC 58.983 52.381 30.12 30.12 0.00 4.40
337 349 1.071471 GTAGGCATGCCGCACCTAT 59.929 57.895 30.50 14.22 45.17 2.57
381 447 9.094459 CAAAATTTTCAAGTCATTATGCAAACG 57.906 29.630 0.00 0.00 0.00 3.60
387 454 5.470437 TCAAGTCATTATGCAAACGTTGGTA 59.530 36.000 0.00 0.00 0.00 3.25
390 457 7.011828 AGTCATTATGCAAACGTTGGTATAC 57.988 36.000 12.44 4.88 0.00 1.47
396 467 4.783055 TGCAAACGTTGGTATACCCATAT 58.217 39.130 19.42 0.00 44.74 1.78
548 628 1.686587 TGGTGTGGTGACAGTGACTAG 59.313 52.381 0.00 0.00 44.46 2.57
558 642 5.336849 GGTGACAGTGACTAGCAGAAGTAAT 60.337 44.000 0.00 0.00 0.00 1.89
561 654 7.813148 GTGACAGTGACTAGCAGAAGTAATTAA 59.187 37.037 0.00 0.00 0.00 1.40
598 721 6.160576 TGCTGCAGTATCATACAAGTGATA 57.839 37.500 16.64 0.00 39.45 2.15
606 729 8.012809 CAGTATCATACAAGTGATAGTCTCGAC 58.987 40.741 0.00 0.00 40.85 4.20
796 983 0.808755 ACGAAAATTGCCGCCTAAGG 59.191 50.000 0.00 0.00 0.00 2.69
847 1035 0.032403 TGCATGCACCTCAAGCAAAC 59.968 50.000 18.46 0.00 45.17 2.93
920 1108 7.047271 TGTTCAGTGCATATATAAACTCAGCA 58.953 34.615 0.00 0.00 0.00 4.41
973 1162 1.039068 ATCATCTGGTCCTCTGCTCG 58.961 55.000 0.00 0.00 0.00 5.03
1016 1224 1.747709 GCTATGGCCATGGCTATCTG 58.252 55.000 38.48 28.33 41.38 2.90
1029 1237 1.422531 CTATCTGCTCTGGCCTTCCT 58.577 55.000 3.32 0.00 37.74 3.36
1048 1256 1.752694 GCTCCGTGCTCTCTCCTCT 60.753 63.158 0.00 0.00 38.95 3.69
1080 1291 2.806856 GCTGCTCATCGTCCAAGCG 61.807 63.158 0.00 0.00 38.90 4.68
1122 1348 5.801350 ACGATTTCAATGTATGTCCACAG 57.199 39.130 0.00 0.00 0.00 3.66
1136 1362 7.765819 TGTATGTCCACAGTTCATTTCATCTAG 59.234 37.037 0.00 0.00 0.00 2.43
1137 1363 6.114187 TGTCCACAGTTCATTTCATCTAGT 57.886 37.500 0.00 0.00 0.00 2.57
1158 1559 9.152327 TCTAGTATCTTGATTTGATCACATCCT 57.848 33.333 17.19 9.44 39.39 3.24
1160 1561 8.447924 AGTATCTTGATTTGATCACATCCTTG 57.552 34.615 17.19 8.74 39.39 3.61
1170 1575 0.529773 CACATCCTTGCATGCATGGC 60.530 55.000 36.10 19.18 40.01 4.40
1172 1577 1.755395 ATCCTTGCATGCATGGCGT 60.755 52.632 36.10 26.88 40.01 5.68
1186 1597 4.072088 GCGTTCGCCTTGACCACG 62.072 66.667 5.87 0.00 34.66 4.94
1199 1623 3.807538 CCACGCCTCTGCATGCAC 61.808 66.667 18.46 6.07 37.32 4.57
1463 1887 2.462255 TACGACTTCACCGTCACCGC 62.462 60.000 0.00 0.00 40.95 5.68
1590 2014 4.410400 CCGCACAAGGAGGTCCCC 62.410 72.222 0.00 0.00 36.42 4.81
1735 2159 1.002544 ACTGCTCTGCCAAAGGTACTC 59.997 52.381 0.00 0.00 38.49 2.59
1739 2163 2.418884 GCTCTGCCAAAGGTACTCCTAC 60.419 54.545 0.00 0.00 44.35 3.18
1756 2962 6.125029 ACTCCTACCTACGTGCTTTCTATTA 58.875 40.000 0.00 0.00 0.00 0.98
1761 2967 5.598769 ACCTACGTGCTTTCTATTATGTCC 58.401 41.667 0.00 0.00 0.00 4.02
1776 2990 0.250858 TGTCCAGCCAATGTCACAGG 60.251 55.000 0.00 0.00 0.00 4.00
1804 3018 8.331730 AGAAAACGTGCTAACTAATATTTGGT 57.668 30.769 0.00 0.00 0.00 3.67
1807 3021 7.443259 AACGTGCTAACTAATATTTGGTGTT 57.557 32.000 0.00 0.00 0.00 3.32
1808 3022 6.837992 ACGTGCTAACTAATATTTGGTGTTG 58.162 36.000 0.00 0.00 0.00 3.33
1832 3058 4.300803 GCATGATGCAGACACTTTCAAAA 58.699 39.130 13.36 0.00 44.26 2.44
2239 3486 1.215423 ACCAACTTCACCTCCAAGCTT 59.785 47.619 0.00 0.00 0.00 3.74
2311 3558 0.600255 AGCGGTTCTTCTTCACGGTG 60.600 55.000 0.56 0.56 33.76 4.94
2686 3933 2.159382 CAAGGGTTTGGCAACTACGAT 58.841 47.619 0.00 0.00 32.90 3.73
2731 3978 1.746615 CCTCGTCGACCCGGTAGAA 60.747 63.158 10.58 0.00 0.00 2.10
2825 4134 4.574828 ACAGTTTAGTACAAGTTGCACTGG 59.425 41.667 17.45 5.82 35.69 4.00
2828 4137 6.017109 CAGTTTAGTACAAGTTGCACTGGAAT 60.017 38.462 17.45 3.95 0.00 3.01
2864 4203 7.281549 GTCCATGCTCATATGTATCATATGCAA 59.718 37.037 19.00 10.75 33.29 4.08
3033 4373 2.331809 GCTTAGAGCCGTTGGTTTTG 57.668 50.000 0.00 0.00 34.48 2.44
3034 4374 1.607148 GCTTAGAGCCGTTGGTTTTGT 59.393 47.619 0.00 0.00 34.48 2.83
3036 4376 3.490249 GCTTAGAGCCGTTGGTTTTGTTT 60.490 43.478 0.00 0.00 34.48 2.83
3037 4377 2.577449 AGAGCCGTTGGTTTTGTTTG 57.423 45.000 0.00 0.00 0.00 2.93
3038 4378 2.096248 AGAGCCGTTGGTTTTGTTTGA 58.904 42.857 0.00 0.00 0.00 2.69
3039 4379 2.693074 AGAGCCGTTGGTTTTGTTTGAT 59.307 40.909 0.00 0.00 0.00 2.57
3040 4380 3.132111 AGAGCCGTTGGTTTTGTTTGATT 59.868 39.130 0.00 0.00 0.00 2.57
3041 4381 3.867857 AGCCGTTGGTTTTGTTTGATTT 58.132 36.364 0.00 0.00 0.00 2.17
3042 4382 3.620821 AGCCGTTGGTTTTGTTTGATTTG 59.379 39.130 0.00 0.00 0.00 2.32
3043 4383 3.372514 GCCGTTGGTTTTGTTTGATTTGT 59.627 39.130 0.00 0.00 0.00 2.83
3044 4384 4.142795 GCCGTTGGTTTTGTTTGATTTGTT 60.143 37.500 0.00 0.00 0.00 2.83
3045 4385 5.555552 CCGTTGGTTTTGTTTGATTTGTTC 58.444 37.500 0.00 0.00 0.00 3.18
3046 4386 5.244362 CGTTGGTTTTGTTTGATTTGTTCG 58.756 37.500 0.00 0.00 0.00 3.95
3047 4387 4.849111 TGGTTTTGTTTGATTTGTTCGC 57.151 36.364 0.00 0.00 0.00 4.70
3048 4388 4.245660 TGGTTTTGTTTGATTTGTTCGCA 58.754 34.783 0.00 0.00 0.00 5.10
3049 4389 4.690748 TGGTTTTGTTTGATTTGTTCGCAA 59.309 33.333 0.00 0.00 34.91 4.85
3062 4402 6.427300 TTTGTTCGCAAATTTACGATTGAC 57.573 33.333 13.96 10.08 41.66 3.18
3063 4403 5.351233 TGTTCGCAAATTTACGATTGACT 57.649 34.783 13.96 0.00 38.25 3.41
3064 4404 5.753744 TGTTCGCAAATTTACGATTGACTT 58.246 33.333 13.96 0.00 38.25 3.01
3065 4405 5.849081 TGTTCGCAAATTTACGATTGACTTC 59.151 36.000 13.96 1.68 38.25 3.01
3066 4406 5.856126 TCGCAAATTTACGATTGACTTCT 57.144 34.783 9.42 0.00 32.45 2.85
3067 4407 5.854157 TCGCAAATTTACGATTGACTTCTC 58.146 37.500 9.42 0.00 32.45 2.87
3068 4408 5.637810 TCGCAAATTTACGATTGACTTCTCT 59.362 36.000 9.42 0.00 32.45 3.10
3069 4409 6.147164 TCGCAAATTTACGATTGACTTCTCTT 59.853 34.615 9.42 0.00 32.45 2.85
3070 4410 6.247165 CGCAAATTTACGATTGACTTCTCTTG 59.753 38.462 4.77 0.00 0.00 3.02
3071 4411 7.078228 GCAAATTTACGATTGACTTCTCTTGT 58.922 34.615 0.00 0.00 0.00 3.16
3072 4412 7.591426 GCAAATTTACGATTGACTTCTCTTGTT 59.409 33.333 0.00 0.00 0.00 2.83
3073 4413 8.895845 CAAATTTACGATTGACTTCTCTTGTTG 58.104 33.333 0.00 0.00 0.00 3.33
3074 4414 7.962964 ATTTACGATTGACTTCTCTTGTTGA 57.037 32.000 0.00 0.00 0.00 3.18
3075 4415 7.408132 TTTACGATTGACTTCTCTTGTTGAG 57.592 36.000 0.00 0.00 43.96 3.02
3076 4416 4.310769 ACGATTGACTTCTCTTGTTGAGG 58.689 43.478 0.00 0.00 42.86 3.86
3077 4417 3.681897 CGATTGACTTCTCTTGTTGAGGG 59.318 47.826 0.00 0.00 42.86 4.30
3078 4418 2.550830 TGACTTCTCTTGTTGAGGGC 57.449 50.000 0.00 0.00 42.86 5.19
3079 4419 2.050144 TGACTTCTCTTGTTGAGGGCT 58.950 47.619 0.00 0.00 42.86 5.19
3080 4420 2.037772 TGACTTCTCTTGTTGAGGGCTC 59.962 50.000 0.00 0.00 42.86 4.70
3081 4421 2.301583 GACTTCTCTTGTTGAGGGCTCT 59.698 50.000 0.00 0.00 42.86 4.09
3082 4422 3.511477 ACTTCTCTTGTTGAGGGCTCTA 58.489 45.455 0.00 0.00 42.86 2.43
3083 4423 3.513515 ACTTCTCTTGTTGAGGGCTCTAG 59.486 47.826 0.00 0.00 42.86 2.43
3084 4424 3.176924 TCTCTTGTTGAGGGCTCTAGT 57.823 47.619 0.00 0.00 42.86 2.57
3085 4425 3.511477 TCTCTTGTTGAGGGCTCTAGTT 58.489 45.455 0.00 0.00 42.86 2.24
3086 4426 3.904339 TCTCTTGTTGAGGGCTCTAGTTT 59.096 43.478 0.00 0.00 42.86 2.66
3087 4427 3.999663 CTCTTGTTGAGGGCTCTAGTTTG 59.000 47.826 0.00 0.00 39.08 2.93
3088 4428 2.859165 TGTTGAGGGCTCTAGTTTGG 57.141 50.000 0.00 0.00 0.00 3.28
3089 4429 2.054799 TGTTGAGGGCTCTAGTTTGGT 58.945 47.619 0.00 0.00 0.00 3.67
3090 4430 3.244582 TGTTGAGGGCTCTAGTTTGGTA 58.755 45.455 0.00 0.00 0.00 3.25
3091 4431 3.007614 TGTTGAGGGCTCTAGTTTGGTAC 59.992 47.826 0.00 0.00 0.00 3.34
3092 4432 3.185880 TGAGGGCTCTAGTTTGGTACT 57.814 47.619 0.00 0.00 41.04 2.73
3093 4433 4.326600 TGAGGGCTCTAGTTTGGTACTA 57.673 45.455 0.00 0.00 38.33 1.82
3102 4442 3.589495 AGTTTGGTACTAGACGGAAGC 57.411 47.619 0.00 0.00 34.56 3.86
3103 4443 2.233186 AGTTTGGTACTAGACGGAAGCC 59.767 50.000 0.00 0.00 34.56 4.35
3104 4444 2.226962 TTGGTACTAGACGGAAGCCT 57.773 50.000 0.00 0.00 0.00 4.58
3105 4445 2.226962 TGGTACTAGACGGAAGCCTT 57.773 50.000 0.00 0.00 0.00 4.35
3106 4446 2.097825 TGGTACTAGACGGAAGCCTTC 58.902 52.381 0.00 0.00 0.00 3.46
3107 4447 1.408340 GGTACTAGACGGAAGCCTTCC 59.592 57.143 13.77 13.77 46.62 3.46
3114 4454 4.303257 GGAAGCCTTCCGAACCAG 57.697 61.111 7.93 0.00 40.59 4.00
3115 4455 1.677552 GGAAGCCTTCCGAACCAGA 59.322 57.895 7.93 0.00 40.59 3.86
3116 4456 0.036306 GGAAGCCTTCCGAACCAGAA 59.964 55.000 7.93 0.00 40.59 3.02
3117 4457 1.443802 GAAGCCTTCCGAACCAGAAG 58.556 55.000 0.00 0.00 40.39 2.85
3118 4458 0.765510 AAGCCTTCCGAACCAGAAGT 59.234 50.000 0.00 0.00 39.29 3.01
3119 4459 0.765510 AGCCTTCCGAACCAGAAGTT 59.234 50.000 0.00 0.00 43.07 2.66
3120 4460 0.875059 GCCTTCCGAACCAGAAGTTG 59.125 55.000 0.00 0.00 39.40 3.16
3558 4898 6.985188 TCCTCTCTAATTTGATTTGTTCGG 57.015 37.500 0.00 0.00 0.00 4.30
3575 4915 3.332761 TCGGTAATTTGCGATTGATGC 57.667 42.857 0.00 0.00 0.00 3.91
3580 4920 3.872511 AATTTGCGATTGATGCCTTCA 57.127 38.095 0.00 0.00 0.00 3.02
3763 5107 6.282199 TGAAGGGACTCTAATAAGTGTCAC 57.718 41.667 9.14 0.00 45.80 3.67
3789 5133 2.976840 GCACGAAGCAATTCCGGCA 61.977 57.895 0.00 0.00 44.79 5.69
3795 5139 0.960364 AAGCAATTCCGGCATGACGT 60.960 50.000 21.63 0.00 0.00 4.34
3799 5143 1.984990 CAATTCCGGCATGACGTTTTG 59.015 47.619 21.63 15.74 0.00 2.44
3816 5164 8.071368 TGACGTTTTGGCAAGTTTAGTTATAAG 58.929 33.333 0.00 0.00 0.00 1.73
3819 5167 7.325097 CGTTTTGGCAAGTTTAGTTATAAGTGG 59.675 37.037 0.00 0.00 0.00 4.00
3823 5171 6.601613 TGGCAAGTTTAGTTATAAGTGGATGG 59.398 38.462 2.90 0.00 0.00 3.51
3864 5212 4.916983 TGACAACTTTCTGTTTGGATGG 57.083 40.909 0.00 0.00 36.63 3.51
3865 5213 3.636300 TGACAACTTTCTGTTTGGATGGG 59.364 43.478 0.00 0.00 36.63 4.00
3880 5228 8.759782 TGTTTGGATGGGAAGTTTTAGTTTTTA 58.240 29.630 0.00 0.00 0.00 1.52
3930 5280 2.046108 AAAAACATCCGGGTGGTGC 58.954 52.632 21.19 0.00 36.30 5.01
3931 5281 1.468506 AAAAACATCCGGGTGGTGCC 61.469 55.000 21.19 0.00 36.30 5.01
3932 5282 4.715523 AACATCCGGGTGGTGCCG 62.716 66.667 21.19 0.00 38.44 5.69
3949 5299 2.346365 GGTGACCACCGGGAGTTC 59.654 66.667 6.32 0.00 42.29 3.01
3950 5300 2.346365 GTGACCACCGGGAGTTCC 59.654 66.667 6.32 0.00 38.05 3.62
3960 5310 4.972875 GGAGTTCCCCTGCTCATG 57.027 61.111 0.00 0.00 33.66 3.07
3961 5311 1.225704 GGAGTTCCCCTGCTCATGG 59.774 63.158 0.00 0.00 33.66 3.66
3962 5312 1.274703 GGAGTTCCCCTGCTCATGGA 61.275 60.000 0.00 0.00 33.66 3.41
3963 5313 0.620556 GAGTTCCCCTGCTCATGGAA 59.379 55.000 0.00 0.00 35.84 3.53
3964 5314 0.622665 AGTTCCCCTGCTCATGGAAG 59.377 55.000 0.00 0.00 38.77 3.46
3965 5315 1.034292 GTTCCCCTGCTCATGGAAGC 61.034 60.000 0.00 0.00 38.77 3.86
3967 5317 1.751927 CCCCTGCTCATGGAAGCAC 60.752 63.158 5.04 0.00 47.00 4.40
3968 5318 1.751927 CCCTGCTCATGGAAGCACC 60.752 63.158 5.04 0.00 47.00 5.01
3976 5326 3.164977 TGGAAGCACCACCGACCA 61.165 61.111 0.00 0.00 44.64 4.02
3977 5327 2.668550 GGAAGCACCACCGACCAC 60.669 66.667 0.00 0.00 38.79 4.16
3978 5328 2.426023 GAAGCACCACCGACCACT 59.574 61.111 0.00 0.00 0.00 4.00
3979 5329 1.961277 GAAGCACCACCGACCACTG 60.961 63.158 0.00 0.00 0.00 3.66
3980 5330 3.476031 AAGCACCACCGACCACTGG 62.476 63.158 0.00 0.00 0.00 4.00
3982 5332 3.238497 CACCACCGACCACTGGGA 61.238 66.667 0.00 0.00 38.05 4.37
3983 5333 2.923035 ACCACCGACCACTGGGAG 60.923 66.667 0.00 0.00 38.05 4.30
3984 5334 2.603473 CCACCGACCACTGGGAGA 60.603 66.667 0.00 0.00 38.05 3.71
3985 5335 2.214216 CCACCGACCACTGGGAGAA 61.214 63.158 0.00 0.00 38.05 2.87
3986 5336 1.293498 CACCGACCACTGGGAGAAG 59.707 63.158 0.00 0.00 38.05 2.85
3987 5337 1.913762 ACCGACCACTGGGAGAAGG 60.914 63.158 0.00 0.00 38.05 3.46
3988 5338 2.266055 CGACCACTGGGAGAAGGC 59.734 66.667 0.00 0.00 38.05 4.35
3989 5339 2.671682 GACCACTGGGAGAAGGCC 59.328 66.667 0.00 0.00 38.05 5.19
3996 5346 4.811364 GGGAGAAGGCCCTGCAGC 62.811 72.222 8.66 0.00 45.12 5.25
3997 5347 3.726144 GGAGAAGGCCCTGCAGCT 61.726 66.667 8.66 0.00 0.00 4.24
3998 5348 2.438075 GAGAAGGCCCTGCAGCTG 60.438 66.667 10.11 10.11 0.00 4.24
3999 5349 4.737177 AGAAGGCCCTGCAGCTGC 62.737 66.667 31.89 31.89 42.50 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.892130 AGAAGACATTTTAAAAGATATCGGACT 57.108 29.630 6.79 2.30 0.00 3.85
35 36 9.793259 ATCTTGACTAGAATAGGTTGACAAAAA 57.207 29.630 0.00 0.00 44.97 1.94
36 37 9.793259 AATCTTGACTAGAATAGGTTGACAAAA 57.207 29.630 0.00 0.00 44.97 2.44
37 38 9.793259 AAATCTTGACTAGAATAGGTTGACAAA 57.207 29.630 0.00 0.00 44.97 2.83
38 39 9.793259 AAAATCTTGACTAGAATAGGTTGACAA 57.207 29.630 0.00 0.00 44.97 3.18
39 40 9.219603 CAAAATCTTGACTAGAATAGGTTGACA 57.780 33.333 0.00 0.00 44.97 3.58
40 41 9.220767 ACAAAATCTTGACTAGAATAGGTTGAC 57.779 33.333 0.00 0.00 38.34 3.18
41 42 9.219603 CACAAAATCTTGACTAGAATAGGTTGA 57.780 33.333 0.00 0.00 38.34 3.18
42 43 9.219603 TCACAAAATCTTGACTAGAATAGGTTG 57.780 33.333 0.00 0.00 38.34 3.77
43 44 9.793259 TTCACAAAATCTTGACTAGAATAGGTT 57.207 29.630 0.00 0.00 38.34 3.50
44 45 9.965902 ATTCACAAAATCTTGACTAGAATAGGT 57.034 29.630 0.00 0.00 38.34 3.08
49 50 9.778741 AGTACATTCACAAAATCTTGACTAGAA 57.221 29.630 0.00 0.00 36.22 2.10
50 51 9.424319 GAGTACATTCACAAAATCTTGACTAGA 57.576 33.333 0.00 0.00 36.33 2.43
51 52 8.660373 GGAGTACATTCACAAAATCTTGACTAG 58.340 37.037 0.00 0.00 36.33 2.57
52 53 7.330946 CGGAGTACATTCACAAAATCTTGACTA 59.669 37.037 0.00 0.00 36.33 2.59
53 54 6.147821 CGGAGTACATTCACAAAATCTTGACT 59.852 38.462 0.00 0.00 36.33 3.41
54 55 6.147164 TCGGAGTACATTCACAAAATCTTGAC 59.853 38.462 0.00 0.00 36.33 3.18
55 56 6.227522 TCGGAGTACATTCACAAAATCTTGA 58.772 36.000 0.00 0.00 36.33 3.02
56 57 6.480524 TCGGAGTACATTCACAAAATCTTG 57.519 37.500 0.00 0.00 38.61 3.02
57 58 6.655003 ACATCGGAGTACATTCACAAAATCTT 59.345 34.615 0.00 0.00 0.00 2.40
58 59 6.173339 ACATCGGAGTACATTCACAAAATCT 58.827 36.000 0.00 0.00 0.00 2.40
59 60 6.422776 ACATCGGAGTACATTCACAAAATC 57.577 37.500 0.00 0.00 0.00 2.17
60 61 7.768582 TGATACATCGGAGTACATTCACAAAAT 59.231 33.333 0.00 0.00 0.00 1.82
61 62 7.100409 TGATACATCGGAGTACATTCACAAAA 58.900 34.615 0.00 0.00 0.00 2.44
62 63 6.635755 TGATACATCGGAGTACATTCACAAA 58.364 36.000 0.00 0.00 0.00 2.83
63 64 6.215495 TGATACATCGGAGTACATTCACAA 57.785 37.500 0.00 0.00 0.00 3.33
64 65 5.845391 TGATACATCGGAGTACATTCACA 57.155 39.130 0.00 0.00 0.00 3.58
65 66 8.812147 TTATTGATACATCGGAGTACATTCAC 57.188 34.615 0.00 0.00 0.00 3.18
66 67 9.825109 TTTTATTGATACATCGGAGTACATTCA 57.175 29.630 0.00 0.00 0.00 2.57
70 71 9.825109 TCAATTTTATTGATACATCGGAGTACA 57.175 29.630 0.00 0.00 0.00 2.90
73 74 9.559732 TCATCAATTTTATTGATACATCGGAGT 57.440 29.630 12.99 0.00 37.06 3.85
93 94 8.862074 CGCATTTCTTATTGTTTTCATCATCAA 58.138 29.630 0.00 0.00 0.00 2.57
94 95 8.028354 ACGCATTTCTTATTGTTTTCATCATCA 58.972 29.630 0.00 0.00 0.00 3.07
95 96 8.398491 ACGCATTTCTTATTGTTTTCATCATC 57.602 30.769 0.00 0.00 0.00 2.92
96 97 8.028354 TGACGCATTTCTTATTGTTTTCATCAT 58.972 29.630 0.00 0.00 0.00 2.45
97 98 7.366513 TGACGCATTTCTTATTGTTTTCATCA 58.633 30.769 0.00 0.00 0.00 3.07
98 99 7.795431 TGACGCATTTCTTATTGTTTTCATC 57.205 32.000 0.00 0.00 0.00 2.92
99 100 8.586570 TTTGACGCATTTCTTATTGTTTTCAT 57.413 26.923 0.00 0.00 0.00 2.57
100 101 7.993821 TTTGACGCATTTCTTATTGTTTTCA 57.006 28.000 0.00 0.00 0.00 2.69
124 125 6.441274 CCGCATCTTGTCTGCATATATTTTT 58.559 36.000 0.00 0.00 39.64 1.94
125 126 5.563475 GCCGCATCTTGTCTGCATATATTTT 60.563 40.000 0.00 0.00 39.64 1.82
126 127 4.083110 GCCGCATCTTGTCTGCATATATTT 60.083 41.667 0.00 0.00 39.64 1.40
127 128 3.438087 GCCGCATCTTGTCTGCATATATT 59.562 43.478 0.00 0.00 39.64 1.28
128 129 3.005554 GCCGCATCTTGTCTGCATATAT 58.994 45.455 0.00 0.00 39.64 0.86
129 130 2.416747 GCCGCATCTTGTCTGCATATA 58.583 47.619 0.00 0.00 39.64 0.86
130 131 1.233019 GCCGCATCTTGTCTGCATAT 58.767 50.000 0.00 0.00 39.64 1.78
131 132 0.815213 GGCCGCATCTTGTCTGCATA 60.815 55.000 0.00 0.00 39.64 3.14
132 133 2.117156 GGCCGCATCTTGTCTGCAT 61.117 57.895 0.00 0.00 39.64 3.96
133 134 2.747460 GGCCGCATCTTGTCTGCA 60.747 61.111 0.00 0.00 39.64 4.41
134 135 3.869272 CGGCCGCATCTTGTCTGC 61.869 66.667 14.67 0.00 36.26 4.26
135 136 1.298157 TTTCGGCCGCATCTTGTCTG 61.298 55.000 23.51 0.00 0.00 3.51
136 137 0.392998 ATTTCGGCCGCATCTTGTCT 60.393 50.000 23.51 0.00 0.00 3.41
137 138 0.248215 CATTTCGGCCGCATCTTGTC 60.248 55.000 23.51 0.00 0.00 3.18
138 139 1.802636 CATTTCGGCCGCATCTTGT 59.197 52.632 23.51 0.00 0.00 3.16
139 140 1.587088 GCATTTCGGCCGCATCTTG 60.587 57.895 23.51 14.12 0.00 3.02
140 141 2.800736 GCATTTCGGCCGCATCTT 59.199 55.556 23.51 0.00 0.00 2.40
141 142 3.576356 CGCATTTCGGCCGCATCT 61.576 61.111 23.51 1.22 33.78 2.90
165 166 4.363990 ATAGATCAGCGCCGGCCG 62.364 66.667 23.46 21.04 41.24 6.13
166 167 2.740055 CATAGATCAGCGCCGGCC 60.740 66.667 23.46 14.23 41.24 6.13
167 168 2.024319 GACATAGATCAGCGCCGGC 61.024 63.158 19.07 19.07 40.37 6.13
168 169 1.730902 CGACATAGATCAGCGCCGG 60.731 63.158 2.29 0.00 0.00 6.13
169 170 1.008424 ACGACATAGATCAGCGCCG 60.008 57.895 2.29 0.00 0.00 6.46
170 171 0.249073 ACACGACATAGATCAGCGCC 60.249 55.000 2.29 0.00 0.00 6.53
171 172 1.124462 GACACGACATAGATCAGCGC 58.876 55.000 0.00 0.00 0.00 5.92
172 173 2.765108 AGACACGACATAGATCAGCG 57.235 50.000 0.00 0.00 0.00 5.18
185 186 3.873361 TCTACTTACACCCGATAGACACG 59.127 47.826 0.00 0.00 39.76 4.49
190 191 6.446781 TTCACTTCTACTTACACCCGATAG 57.553 41.667 0.00 0.00 0.00 2.08
194 195 5.235516 ACAATTCACTTCTACTTACACCCG 58.764 41.667 0.00 0.00 0.00 5.28
206 207 5.931724 CCCAACCCAATTAACAATTCACTTC 59.068 40.000 0.00 0.00 0.00 3.01
222 223 1.076549 GGATGCTTGACCCAACCCA 59.923 57.895 0.00 0.00 0.00 4.51
259 260 9.880157 GTTCTTCCCTTGTAGTACAATAATACA 57.120 33.333 15.91 0.00 37.48 2.29
262 263 7.980099 CGAGTTCTTCCCTTGTAGTACAATAAT 59.020 37.037 15.91 0.00 37.48 1.28
263 264 7.177216 TCGAGTTCTTCCCTTGTAGTACAATAA 59.823 37.037 15.91 9.92 37.48 1.40
264 265 6.660521 TCGAGTTCTTCCCTTGTAGTACAATA 59.339 38.462 15.91 2.91 37.48 1.90
265 266 5.479375 TCGAGTTCTTCCCTTGTAGTACAAT 59.521 40.000 15.91 0.00 37.48 2.71
266 267 4.828939 TCGAGTTCTTCCCTTGTAGTACAA 59.171 41.667 14.85 14.85 36.54 2.41
267 268 4.401022 TCGAGTTCTTCCCTTGTAGTACA 58.599 43.478 0.00 0.00 0.00 2.90
268 269 4.142425 CCTCGAGTTCTTCCCTTGTAGTAC 60.142 50.000 12.31 0.00 0.00 2.73
269 270 4.015084 CCTCGAGTTCTTCCCTTGTAGTA 58.985 47.826 12.31 0.00 0.00 1.82
270 271 2.826725 CCTCGAGTTCTTCCCTTGTAGT 59.173 50.000 12.31 0.00 0.00 2.73
271 272 2.166664 CCCTCGAGTTCTTCCCTTGTAG 59.833 54.545 12.31 0.00 0.00 2.74
329 341 2.540101 GGAACTCGATTCAATAGGTGCG 59.460 50.000 8.98 0.00 39.30 5.34
337 349 6.573664 ATTTTGACATGGAACTCGATTCAA 57.426 33.333 0.00 0.00 39.30 2.69
381 447 8.780249 GTGTGAATACAATATGGGTATACCAAC 58.220 37.037 23.33 7.69 45.80 3.77
387 454 7.224297 GTCCAGTGTGAATACAATATGGGTAT 58.776 38.462 0.00 0.00 38.82 2.73
390 457 4.821805 GGTCCAGTGTGAATACAATATGGG 59.178 45.833 0.00 0.00 38.82 4.00
396 467 3.056393 CCTACGGTCCAGTGTGAATACAA 60.056 47.826 0.00 0.00 38.82 2.41
422 493 2.672714 GTGATGCCGAAAAAGGGTTTC 58.327 47.619 0.00 0.00 0.00 2.78
424 495 0.596082 CGTGATGCCGAAAAAGGGTT 59.404 50.000 0.00 0.00 0.00 4.11
426 497 0.878416 TTCGTGATGCCGAAAAAGGG 59.122 50.000 0.00 0.00 43.28 3.95
432 503 1.006825 CGTCAGTTCGTGATGCCGAA 61.007 55.000 0.00 0.00 43.96 4.30
433 504 1.443702 CGTCAGTTCGTGATGCCGA 60.444 57.895 0.00 0.00 37.56 5.54
435 506 0.865769 AAACGTCAGTTCGTGATGCC 59.134 50.000 0.00 0.00 45.05 4.40
436 507 2.159881 GGTAAACGTCAGTTCGTGATGC 60.160 50.000 0.00 0.00 45.05 3.91
561 654 8.642432 TGATACTGCAGCAAGTTTATAGATAGT 58.358 33.333 15.27 0.00 0.00 2.12
568 661 7.554118 ACTTGTATGATACTGCAGCAAGTTTAT 59.446 33.333 20.89 9.22 41.12 1.40
580 703 8.012809 GTCGAGACTATCACTTGTATGATACTG 58.987 40.741 4.03 0.04 39.97 2.74
598 721 3.315470 TGCGCATCTAATTAGTCGAGACT 59.685 43.478 5.66 10.80 45.02 3.24
606 729 3.548587 GCACACATGCGCATCTAATTAG 58.451 45.455 22.51 10.15 43.33 1.73
670 806 3.794028 CAGTGCACTCGATCTAGTTTAGC 59.206 47.826 18.64 0.00 0.00 3.09
796 983 2.034687 ACAGACAGGTGCCCATGC 59.965 61.111 0.00 0.00 38.26 4.06
939 1128 2.709934 AGATGATGGAGGGTGGAATGAG 59.290 50.000 0.00 0.00 0.00 2.90
973 1162 5.584253 TGTATCTTGAGGTAGCTCTTGAC 57.416 43.478 21.80 12.83 0.00 3.18
1016 1224 2.124778 GAGCAGGAAGGCCAGAGC 60.125 66.667 5.01 0.89 36.29 4.09
1080 1291 2.024319 GTGTCTGGTGACGCTCTGC 61.024 63.158 2.90 0.00 46.77 4.26
1136 1362 7.137426 GCAAGGATGTGATCAAATCAAGATAC 58.863 38.462 24.24 8.46 41.69 2.24
1137 1363 6.829811 TGCAAGGATGTGATCAAATCAAGATA 59.170 34.615 24.24 7.53 41.69 1.98
1158 1559 2.178769 CGAACGCCATGCATGCAA 59.821 55.556 26.68 8.49 0.00 4.08
1170 1575 4.072088 GCGTGGTCAAGGCGAACG 62.072 66.667 0.00 0.00 32.01 3.95
1172 1577 3.876589 GAGGCGTGGTCAAGGCGAA 62.877 63.158 5.04 0.00 40.69 4.70
1199 1623 3.266230 TTCGCCATTTGCACCTGCG 62.266 57.895 11.54 11.54 45.83 5.18
1590 2014 2.870161 CACTCGCCGAAGACGACG 60.870 66.667 0.00 0.00 45.70 5.12
1735 2159 6.746120 ACATAATAGAAAGCACGTAGGTAGG 58.254 40.000 0.00 0.00 0.00 3.18
1737 2161 6.321945 TGGACATAATAGAAAGCACGTAGGTA 59.678 38.462 0.00 0.00 0.00 3.08
1739 2163 5.597806 TGGACATAATAGAAAGCACGTAGG 58.402 41.667 0.00 0.00 0.00 3.18
1756 2962 1.615116 CCTGTGACATTGGCTGGACAT 60.615 52.381 0.00 0.00 0.00 3.06
1761 2967 3.057969 TCTAACCTGTGACATTGGCTG 57.942 47.619 0.00 0.00 0.00 4.85
1832 3058 0.774908 TTTCCGGGTTCCACCTTCAT 59.225 50.000 0.00 0.00 38.64 2.57
2816 4063 6.073819 GGACAAAAACATTATTCCAGTGCAAC 60.074 38.462 0.00 0.00 0.00 4.17
2819 4066 5.537188 TGGACAAAAACATTATTCCAGTGC 58.463 37.500 0.00 0.00 0.00 4.40
2825 4134 9.754382 ATATGAGCATGGACAAAAACATTATTC 57.246 29.630 0.00 0.00 0.00 1.75
2828 4137 8.065473 ACATATGAGCATGGACAAAAACATTA 57.935 30.769 10.38 0.00 0.00 1.90
2864 4203 1.375908 CCATACACCTGCACACGCT 60.376 57.895 0.00 0.00 39.64 5.07
3017 4357 3.280295 TCAAACAAAACCAACGGCTCTA 58.720 40.909 0.00 0.00 0.00 2.43
3045 4385 5.858475 AGAGAAGTCAATCGTAAATTTGCG 58.142 37.500 20.82 20.82 37.63 4.85
3046 4386 7.078228 ACAAGAGAAGTCAATCGTAAATTTGC 58.922 34.615 0.00 0.00 0.00 3.68
3047 4387 8.895845 CAACAAGAGAAGTCAATCGTAAATTTG 58.104 33.333 0.00 0.00 0.00 2.32
3048 4388 8.836413 TCAACAAGAGAAGTCAATCGTAAATTT 58.164 29.630 0.00 0.00 0.00 1.82
3049 4389 8.378172 TCAACAAGAGAAGTCAATCGTAAATT 57.622 30.769 0.00 0.00 0.00 1.82
3050 4390 7.962964 TCAACAAGAGAAGTCAATCGTAAAT 57.037 32.000 0.00 0.00 0.00 1.40
3065 4405 3.971245 AACTAGAGCCCTCAACAAGAG 57.029 47.619 0.00 0.00 44.31 2.85
3066 4406 3.244561 CCAAACTAGAGCCCTCAACAAGA 60.245 47.826 0.00 0.00 0.00 3.02
3067 4407 3.077359 CCAAACTAGAGCCCTCAACAAG 58.923 50.000 0.00 0.00 0.00 3.16
3068 4408 2.441750 ACCAAACTAGAGCCCTCAACAA 59.558 45.455 0.00 0.00 0.00 2.83
3069 4409 2.054799 ACCAAACTAGAGCCCTCAACA 58.945 47.619 0.00 0.00 0.00 3.33
3070 4410 2.861147 ACCAAACTAGAGCCCTCAAC 57.139 50.000 0.00 0.00 0.00 3.18
3071 4411 3.517612 AGTACCAAACTAGAGCCCTCAA 58.482 45.455 0.00 0.00 36.36 3.02
3072 4412 3.185880 AGTACCAAACTAGAGCCCTCA 57.814 47.619 0.00 0.00 36.36 3.86
3081 4421 3.445096 GGCTTCCGTCTAGTACCAAACTA 59.555 47.826 0.00 0.00 39.80 2.24
3082 4422 2.233186 GGCTTCCGTCTAGTACCAAACT 59.767 50.000 0.00 0.00 42.62 2.66
3083 4423 2.233186 AGGCTTCCGTCTAGTACCAAAC 59.767 50.000 0.00 0.00 0.00 2.93
3084 4424 2.532843 AGGCTTCCGTCTAGTACCAAA 58.467 47.619 0.00 0.00 0.00 3.28
3085 4425 2.226962 AGGCTTCCGTCTAGTACCAA 57.773 50.000 0.00 0.00 0.00 3.67
3086 4426 2.097825 GAAGGCTTCCGTCTAGTACCA 58.902 52.381 16.50 0.00 0.00 3.25
3087 4427 1.408340 GGAAGGCTTCCGTCTAGTACC 59.592 57.143 29.19 4.52 40.59 3.34
3088 4428 2.867287 GGAAGGCTTCCGTCTAGTAC 57.133 55.000 29.19 4.62 40.59 2.73
3097 4437 0.036306 TTCTGGTTCGGAAGGCTTCC 59.964 55.000 32.12 32.12 46.62 3.46
3098 4438 1.443802 CTTCTGGTTCGGAAGGCTTC 58.556 55.000 18.98 18.98 41.61 3.86
3099 4439 3.633361 CTTCTGGTTCGGAAGGCTT 57.367 52.632 0.00 0.00 41.61 4.35
3510 4850 0.323816 ACGGCTCTGATCCTCTGTGA 60.324 55.000 0.00 0.00 0.00 3.58
3511 4851 0.534412 AACGGCTCTGATCCTCTGTG 59.466 55.000 0.00 0.00 0.00 3.66
3512 4852 0.534412 CAACGGCTCTGATCCTCTGT 59.466 55.000 0.00 0.00 0.00 3.41
3513 4853 0.179089 CCAACGGCTCTGATCCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
3514 4854 0.616111 ACCAACGGCTCTGATCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
3515 4855 0.250513 AACCAACGGCTCTGATCCTC 59.749 55.000 0.00 0.00 0.00 3.71
3516 4856 0.693049 AAACCAACGGCTCTGATCCT 59.307 50.000 0.00 0.00 0.00 3.24
3517 4857 1.087501 GAAACCAACGGCTCTGATCC 58.912 55.000 0.00 0.00 0.00 3.36
3558 4898 4.671377 TGAAGGCATCAATCGCAAATTAC 58.329 39.130 0.00 0.00 34.30 1.89
3575 4915 1.404315 GCTACAACCCTCGACTGAAGG 60.404 57.143 0.00 0.00 0.00 3.46
3580 4920 3.487120 AAAAAGCTACAACCCTCGACT 57.513 42.857 0.00 0.00 0.00 4.18
3605 4945 5.362430 AGAAAATTGTAAGGTCAGCAAACCA 59.638 36.000 9.87 0.00 42.12 3.67
3647 4988 9.630098 CATTACAAACTGCTAATCAAGTGAAAT 57.370 29.630 0.00 0.00 0.00 2.17
3740 5084 5.778241 TGTGACACTTATTAGAGTCCCTTCA 59.222 40.000 7.20 0.34 40.13 3.02
3779 5123 1.984990 CAAAACGTCATGCCGGAATTG 59.015 47.619 5.05 0.00 0.00 2.32
3787 5131 1.851658 AACTTGCCAAAACGTCATGC 58.148 45.000 0.00 0.00 0.00 4.06
3789 5133 4.911514 ACTAAACTTGCCAAAACGTCAT 57.088 36.364 0.00 0.00 0.00 3.06
3795 5139 8.466617 TCCACTTATAACTAAACTTGCCAAAA 57.533 30.769 0.00 0.00 0.00 2.44
3799 5143 6.826741 TCCATCCACTTATAACTAAACTTGCC 59.173 38.462 0.00 0.00 0.00 4.52
3816 5164 7.870445 TGCTTTACAATTAAAGTTTCCATCCAC 59.130 33.333 0.00 0.00 44.30 4.02
3819 5167 9.638239 TCATGCTTTACAATTAAAGTTTCCATC 57.362 29.630 0.00 0.00 44.30 3.51
3830 5178 8.629158 ACAGAAAGTTGTCATGCTTTACAATTA 58.371 29.630 3.04 0.00 37.87 1.40
3832 5180 7.042797 ACAGAAAGTTGTCATGCTTTACAAT 57.957 32.000 3.04 0.00 37.87 2.71
3834 5182 6.449635 AACAGAAAGTTGTCATGCTTTACA 57.550 33.333 3.74 0.00 39.49 2.41
3837 5185 5.105392 TCCAAACAGAAAGTTGTCATGCTTT 60.105 36.000 3.46 3.46 41.19 3.51
3849 5197 5.535753 AAACTTCCCATCCAAACAGAAAG 57.464 39.130 0.00 0.00 0.00 2.62
3933 5283 2.346365 GGAACTCCCGGTGGTCAC 59.654 66.667 11.15 0.00 0.00 3.67
3943 5293 1.225704 CCATGAGCAGGGGAACTCC 59.774 63.158 0.00 0.00 31.65 3.85
3944 5294 0.620556 TTCCATGAGCAGGGGAACTC 59.379 55.000 0.92 0.00 35.84 3.01
3945 5295 0.622665 CTTCCATGAGCAGGGGAACT 59.377 55.000 0.92 0.00 35.84 3.01
3946 5296 1.034292 GCTTCCATGAGCAGGGGAAC 61.034 60.000 0.92 0.00 42.25 3.62
3947 5297 1.304282 GCTTCCATGAGCAGGGGAA 59.696 57.895 0.92 4.15 42.25 3.97
3948 5298 3.001514 GCTTCCATGAGCAGGGGA 58.998 61.111 0.92 0.00 42.25 4.81
3959 5309 3.164977 TGGTCGGTGGTGCTTCCA 61.165 61.111 0.00 0.00 45.01 3.53
3960 5310 2.668550 GTGGTCGGTGGTGCTTCC 60.669 66.667 0.00 0.00 0.00 3.46
3961 5311 1.961277 CAGTGGTCGGTGGTGCTTC 60.961 63.158 0.00 0.00 0.00 3.86
3962 5312 2.111043 CAGTGGTCGGTGGTGCTT 59.889 61.111 0.00 0.00 0.00 3.91
3963 5313 3.941188 CCAGTGGTCGGTGGTGCT 61.941 66.667 0.00 0.00 0.00 4.40
3965 5315 3.238497 TCCCAGTGGTCGGTGGTG 61.238 66.667 8.74 0.00 31.17 4.17
3966 5316 2.923035 CTCCCAGTGGTCGGTGGT 60.923 66.667 8.74 0.00 31.17 4.16
3967 5317 2.172483 CTTCTCCCAGTGGTCGGTGG 62.172 65.000 8.74 0.00 0.00 4.61
3968 5318 1.293498 CTTCTCCCAGTGGTCGGTG 59.707 63.158 8.74 0.00 0.00 4.94
3969 5319 1.913762 CCTTCTCCCAGTGGTCGGT 60.914 63.158 8.74 0.00 0.00 4.69
3970 5320 2.982130 CCTTCTCCCAGTGGTCGG 59.018 66.667 8.74 0.00 0.00 4.79
3971 5321 2.266055 GCCTTCTCCCAGTGGTCG 59.734 66.667 8.74 0.00 0.00 4.79
3972 5322 2.671682 GGCCTTCTCCCAGTGGTC 59.328 66.667 8.74 0.00 0.00 4.02
3973 5323 2.936032 GGGCCTTCTCCCAGTGGT 60.936 66.667 8.74 0.00 45.82 4.16
3979 5329 4.811364 GCTGCAGGGCCTTCTCCC 62.811 72.222 17.12 0.00 46.93 4.30
3980 5330 3.726144 AGCTGCAGGGCCTTCTCC 61.726 66.667 17.12 0.00 0.00 3.71
3981 5331 2.438075 CAGCTGCAGGGCCTTCTC 60.438 66.667 17.12 0.00 0.00 2.87
3982 5332 4.737177 GCAGCTGCAGGGCCTTCT 62.737 66.667 33.36 0.00 41.59 2.85


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

AutoCloner maintained by Alex Coulton.