Multiple sequence alignment - TraesCS7B01G409000

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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 TraesCS7B01G409000 chr7B 100.000 3525 0 0 1 3525 678296436 678292912 0.000000e+00 6510.0
1 TraesCS7B01G409000 chr7B 92.600 946 68 2 2582 3525 43251844 43250899 0.000000e+00 1358.0
2 TraesCS7B01G409000 chr7B 91.103 281 17 3 197 469 678359752 678359472 1.190000e-99 374.0
3 TraesCS7B01G409000 chr7B 88.793 116 12 1 548 662 677868644 677868529 1.320000e-29 141.0
4 TraesCS7B01G409000 chr7B 91.045 67 6 0 822 888 678835933 678835999 1.350000e-14 91.6
5 TraesCS7B01G409000 chr1B 94.609 946 49 2 2582 3525 41364132 41365077 0.000000e+00 1463.0
6 TraesCS7B01G409000 chr2B 93.136 947 61 4 2582 3525 9037940 9036995 0.000000e+00 1386.0
7 TraesCS7B01G409000 chrUn 92.925 947 63 4 2582 3525 42169134 42168189 0.000000e+00 1375.0
8 TraesCS7B01G409000 chr3B 91.958 945 71 5 2582 3522 753179873 753180816 0.000000e+00 1319.0
9 TraesCS7B01G409000 chr5D 90.592 946 87 2 2582 3525 393554997 393554052 0.000000e+00 1253.0
10 TraesCS7B01G409000 chr5D 89.083 229 21 2 98 326 446117985 446118209 7.450000e-72 281.0
11 TraesCS7B01G409000 chr5D 82.569 327 36 7 352 662 446118845 446119166 5.800000e-68 268.0
12 TraesCS7B01G409000 chr5D 92.982 57 4 0 723 779 446041611 446041555 2.250000e-12 84.2
13 TraesCS7B01G409000 chr3A 92.601 838 60 2 2690 3525 743123286 743124123 0.000000e+00 1203.0
14 TraesCS7B01G409000 chr3A 89.597 942 92 5 2582 3519 19772645 19773584 0.000000e+00 1192.0
15 TraesCS7B01G409000 chr5A 88.984 935 98 4 2582 3513 506343192 506344124 0.000000e+00 1151.0
16 TraesCS7B01G409000 chr7D 80.463 1597 162 83 950 2501 598697590 598696099 0.000000e+00 1083.0
17 TraesCS7B01G409000 chr7D 84.375 576 59 12 101 658 598698757 598698195 1.440000e-148 536.0
18 TraesCS7B01G409000 chr7D 87.541 305 30 7 1285 1584 598597633 598597934 2.600000e-91 346.0
19 TraesCS7B01G409000 chr7D 91.200 250 18 4 422 670 598505635 598505881 1.570000e-88 337.0
20 TraesCS7B01G409000 chr7D 85.520 221 21 5 1590 1803 598597974 598598190 1.650000e-53 220.0
21 TraesCS7B01G409000 chr7D 86.577 149 10 7 794 934 598698006 598697860 4.710000e-34 156.0
22 TraesCS7B01G409000 chr7D 88.281 128 10 3 546 670 598597084 598597209 7.880000e-32 148.0
23 TraesCS7B01G409000 chr7D 94.444 72 4 0 723 794 598698108 598698037 1.030000e-20 111.0
24 TraesCS7B01G409000 chr7D 93.243 74 3 1 723 794 598582388 598582461 1.340000e-19 108.0
25 TraesCS7B01G409000 chr7D 93.243 74 3 1 723 794 598582622 598582695 1.340000e-19 108.0
26 TraesCS7B01G409000 chr7D 92.982 57 4 0 723 779 598765888 598765944 2.250000e-12 84.2
27 TraesCS7B01G409000 chr7D 92.982 57 4 0 723 779 598766617 598766673 2.250000e-12 84.2
28 TraesCS7B01G409000 chr7A 87.542 899 61 15 1702 2582 691266948 691266083 0.000000e+00 992.0
29 TraesCS7B01G409000 chr7A 82.834 734 60 38 950 1660 691267635 691266945 6.510000e-167 597.0
30 TraesCS7B01G409000 chr7A 83.390 584 77 11 2013 2584 691263893 691263318 1.120000e-144 523.0
31 TraesCS7B01G409000 chr7A 77.891 882 126 40 1692 2551 691261802 691260968 5.290000e-133 484.0
32 TraesCS7B01G409000 chr7A 86.567 201 24 3 1951 2151 691264655 691264458 5.920000e-53 219.0
33 TraesCS7B01G409000 chr7A 85.116 215 19 7 438 642 691268465 691268254 1.280000e-49 207.0
34 TraesCS7B01G409000 chr7A 84.052 232 17 10 568 796 690993610 690993824 4.610000e-49 206.0
35 TraesCS7B01G409000 chr7A 92.793 111 3 5 561 669 691531115 691531008 4.710000e-34 156.0
36 TraesCS7B01G409000 chr7A 95.745 47 2 0 793 839 690993853 690993899 3.770000e-10 76.8
37 TraesCS7B01G409000 chr7A 85.000 80 5 1 1722 1794 691124776 691124855 1.360000e-09 75.0
38 TraesCS7B01G409000 chr2D 91.403 221 19 0 422 642 47789287 47789507 1.590000e-78 303.0
39 TraesCS7B01G409000 chr2D 79.396 364 51 14 1523 1874 47715488 47715839 5.880000e-58 235.0
40 TraesCS7B01G409000 chr2D 87.050 139 7 5 561 697 47646091 47646220 2.840000e-31 147.0
41 TraesCS7B01G409000 chr4A 88.571 210 15 6 1837 2042 370268719 370268515 2.720000e-61 246.0


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 TraesCS7B01G409000 chr7B 678292912 678296436 3524 True 6510.000000 6510 100.00000 1 3525 1 chr7B.!!$R3 3524
1 TraesCS7B01G409000 chr7B 43250899 43251844 945 True 1358.000000 1358 92.60000 2582 3525 1 chr7B.!!$R1 943
2 TraesCS7B01G409000 chr1B 41364132 41365077 945 False 1463.000000 1463 94.60900 2582 3525 1 chr1B.!!$F1 943
3 TraesCS7B01G409000 chr2B 9036995 9037940 945 True 1386.000000 1386 93.13600 2582 3525 1 chr2B.!!$R1 943
4 TraesCS7B01G409000 chrUn 42168189 42169134 945 True 1375.000000 1375 92.92500 2582 3525 1 chrUn.!!$R1 943
5 TraesCS7B01G409000 chr3B 753179873 753180816 943 False 1319.000000 1319 91.95800 2582 3522 1 chr3B.!!$F1 940
6 TraesCS7B01G409000 chr5D 393554052 393554997 945 True 1253.000000 1253 90.59200 2582 3525 1 chr5D.!!$R1 943
7 TraesCS7B01G409000 chr5D 446117985 446119166 1181 False 274.500000 281 85.82600 98 662 2 chr5D.!!$F1 564
8 TraesCS7B01G409000 chr3A 743123286 743124123 837 False 1203.000000 1203 92.60100 2690 3525 1 chr3A.!!$F2 835
9 TraesCS7B01G409000 chr3A 19772645 19773584 939 False 1192.000000 1192 89.59700 2582 3519 1 chr3A.!!$F1 937
10 TraesCS7B01G409000 chr5A 506343192 506344124 932 False 1151.000000 1151 88.98400 2582 3513 1 chr5A.!!$F1 931
11 TraesCS7B01G409000 chr7D 598696099 598698757 2658 True 471.500000 1083 86.46475 101 2501 4 chr7D.!!$R1 2400
12 TraesCS7B01G409000 chr7D 598597084 598598190 1106 False 238.000000 346 87.11400 546 1803 3 chr7D.!!$F3 1257
13 TraesCS7B01G409000 chr7A 691260968 691268465 7497 True 503.666667 992 83.89000 438 2584 6 chr7A.!!$R2 2146

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
943 1730 0.033781 ACACCGATCCCGTTCGAAAA 59.966 50.0 0.0 0.0 41.62 2.29 F
1535 2611 0.107268 GGTGACCCCGTTACAGTTGT 59.893 55.0 0.0 0.0 0.00 3.32 F
2048 3199 0.319405 GCTGCCCATTCTGCAAAACT 59.681 50.0 0.0 0.0 38.46 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 3424 0.343372 AGGCTTGGGACTCCTATGGA 59.657 55.000 0.0 0.0 0.00 3.41 R
2513 6414 0.405585 CACCAAATCCCCACTCCACT 59.594 55.000 0.0 0.0 0.00 4.00 R
2992 6903 1.997874 GCTCACCCCAGACCCATCT 60.998 63.158 0.0 0.0 34.57 2.90 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 3.256960 GGGCCCTCACCACCAAGA 61.257 66.667 17.04 0.00 0.00 3.02
18 19 2.352805 GGCCCTCACCACCAAGAG 59.647 66.667 0.00 0.00 0.00 2.85
21 22 3.081554 CCTCACCACCAAGAGGGG 58.918 66.667 0.00 0.00 46.11 4.79
27 28 3.322466 CACCAAGAGGGGGCGTCT 61.322 66.667 0.00 0.00 42.91 4.18
28 29 3.322466 ACCAAGAGGGGGCGTCTG 61.322 66.667 0.00 0.00 42.91 3.51
29 30 3.003173 CCAAGAGGGGGCGTCTGA 61.003 66.667 0.00 0.00 0.00 3.27
30 31 2.592993 CCAAGAGGGGGCGTCTGAA 61.593 63.158 0.00 0.00 0.00 3.02
31 32 1.078848 CAAGAGGGGGCGTCTGAAG 60.079 63.158 0.00 0.00 0.00 3.02
32 33 2.294078 AAGAGGGGGCGTCTGAAGG 61.294 63.158 0.00 0.00 0.00 3.46
33 34 3.787001 GAGGGGGCGTCTGAAGGG 61.787 72.222 0.00 0.00 0.00 3.95
36 37 3.090532 GGGGCGTCTGAAGGGGAT 61.091 66.667 0.00 0.00 0.00 3.85
37 38 2.506472 GGGCGTCTGAAGGGGATC 59.494 66.667 0.00 0.00 0.00 3.36
38 39 2.367202 GGGCGTCTGAAGGGGATCA 61.367 63.158 0.00 0.00 0.00 2.92
39 40 1.144936 GGCGTCTGAAGGGGATCAG 59.855 63.158 0.00 0.00 46.62 2.90
40 41 1.144936 GCGTCTGAAGGGGATCAGG 59.855 63.158 4.63 0.00 45.55 3.86
41 42 1.826024 CGTCTGAAGGGGATCAGGG 59.174 63.158 4.63 0.00 45.55 4.45
42 43 0.687757 CGTCTGAAGGGGATCAGGGA 60.688 60.000 4.63 0.00 45.55 4.20
43 44 0.833949 GTCTGAAGGGGATCAGGGAC 59.166 60.000 4.63 0.00 45.55 4.46
44 45 0.687757 TCTGAAGGGGATCAGGGACG 60.688 60.000 4.63 0.00 45.55 4.79
45 46 0.687757 CTGAAGGGGATCAGGGACGA 60.688 60.000 0.00 0.00 42.52 4.20
46 47 0.976073 TGAAGGGGATCAGGGACGAC 60.976 60.000 0.00 0.00 0.00 4.34
47 48 2.017559 GAAGGGGATCAGGGACGACG 62.018 65.000 0.00 0.00 0.00 5.12
48 49 3.537874 GGGGATCAGGGACGACGG 61.538 72.222 0.00 0.00 0.00 4.79
49 50 4.222847 GGGATCAGGGACGACGGC 62.223 72.222 0.00 0.00 0.00 5.68
50 51 4.570663 GGATCAGGGACGACGGCG 62.571 72.222 10.39 10.39 44.79 6.46
66 67 4.675029 CGCGACGGAACCCAAGGT 62.675 66.667 0.00 0.00 37.65 3.50
67 68 2.741211 GCGACGGAACCCAAGGTC 60.741 66.667 0.00 0.00 33.12 3.85
68 69 2.431942 CGACGGAACCCAAGGTCG 60.432 66.667 0.00 0.00 44.92 4.79
69 70 2.741211 GACGGAACCCAAGGTCGC 60.741 66.667 0.00 0.00 33.12 5.19
70 71 4.324991 ACGGAACCCAAGGTCGCC 62.325 66.667 0.00 0.00 33.12 5.54
72 73 3.647771 GGAACCCAAGGTCGCCCT 61.648 66.667 0.00 0.00 45.63 5.19
73 74 2.046217 GAACCCAAGGTCGCCCTC 60.046 66.667 0.00 0.00 41.56 4.30
74 75 3.952628 GAACCCAAGGTCGCCCTCG 62.953 68.421 0.00 0.00 41.56 4.63
78 79 4.148825 CAAGGTCGCCCTCGGGAG 62.149 72.222 6.08 2.12 41.56 4.30
79 80 4.377760 AAGGTCGCCCTCGGGAGA 62.378 66.667 6.08 5.06 41.56 3.71
91 92 4.200283 GGGAGAGCGGCGTGAGAG 62.200 72.222 9.37 0.00 0.00 3.20
92 93 3.134792 GGAGAGCGGCGTGAGAGA 61.135 66.667 9.37 0.00 0.00 3.10
93 94 2.407210 GAGAGCGGCGTGAGAGAG 59.593 66.667 9.37 0.00 0.00 3.20
94 95 2.045829 AGAGCGGCGTGAGAGAGA 60.046 61.111 9.37 0.00 0.00 3.10
95 96 2.047151 GAGAGCGGCGTGAGAGAGAG 62.047 65.000 9.37 0.00 0.00 3.20
96 97 2.360600 AGCGGCGTGAGAGAGAGT 60.361 61.111 9.37 0.00 0.00 3.24
115 116 7.203910 AGAGAGTACCGTAATCACATTCATTC 58.796 38.462 8.60 0.00 0.00 2.67
123 124 6.761242 CCGTAATCACATTCATTCCTTCAGTA 59.239 38.462 0.00 0.00 0.00 2.74
124 125 7.254455 CCGTAATCACATTCATTCCTTCAGTAC 60.254 40.741 0.00 0.00 0.00 2.73
125 126 7.492669 CGTAATCACATTCATTCCTTCAGTACT 59.507 37.037 0.00 0.00 0.00 2.73
126 127 7.621428 AATCACATTCATTCCTTCAGTACTG 57.379 36.000 17.17 17.17 0.00 2.74
127 128 6.114187 TCACATTCATTCCTTCAGTACTGT 57.886 37.500 21.99 0.00 0.00 3.55
128 129 6.533730 TCACATTCATTCCTTCAGTACTGTT 58.466 36.000 21.99 0.00 0.00 3.16
129 130 7.676004 TCACATTCATTCCTTCAGTACTGTTA 58.324 34.615 21.99 10.87 0.00 2.41
130 131 8.154203 TCACATTCATTCCTTCAGTACTGTTAA 58.846 33.333 21.99 9.55 0.00 2.01
132 133 8.375506 ACATTCATTCCTTCAGTACTGTTAAGA 58.624 33.333 21.99 12.06 0.00 2.10
133 134 8.660373 CATTCATTCCTTCAGTACTGTTAAGAC 58.340 37.037 21.99 0.00 0.00 3.01
134 135 6.698380 TCATTCCTTCAGTACTGTTAAGACC 58.302 40.000 21.99 0.00 0.00 3.85
135 136 6.269077 TCATTCCTTCAGTACTGTTAAGACCA 59.731 38.462 21.99 7.41 0.00 4.02
136 137 6.681729 TTCCTTCAGTACTGTTAAGACCAT 57.318 37.500 21.99 0.00 0.00 3.55
137 138 7.786046 TTCCTTCAGTACTGTTAAGACCATA 57.214 36.000 21.99 0.00 0.00 2.74
138 139 7.786046 TCCTTCAGTACTGTTAAGACCATAA 57.214 36.000 21.99 4.66 0.00 1.90
146 147 8.915036 AGTACTGTTAAGACCATAAGATGTAGG 58.085 37.037 0.00 0.00 0.00 3.18
183 184 5.293814 CAGTTGGAGATATCTTTCTGCAGTG 59.706 44.000 14.67 5.73 43.66 3.66
184 185 5.046014 AGTTGGAGATATCTTTCTGCAGTGT 60.046 40.000 14.67 0.00 43.66 3.55
188 189 5.396213 GGAGATATCTTTCTGCAGTGTTCCT 60.396 44.000 14.67 2.26 34.50 3.36
197 198 2.098614 TGCAGTGTTCCTTGAAAGCAA 58.901 42.857 0.00 0.00 0.00 3.91
200 201 3.932089 GCAGTGTTCCTTGAAAGCAAAAA 59.068 39.130 0.00 0.00 32.73 1.94
201 202 4.201714 GCAGTGTTCCTTGAAAGCAAAAAC 60.202 41.667 0.00 0.00 33.58 2.43
205 206 5.411361 GTGTTCCTTGAAAGCAAAAACCTTT 59.589 36.000 0.00 0.00 35.36 3.11
233 234 7.166167 AGATAAACATGATGCATGATGAGCTA 58.834 34.615 29.50 17.42 43.81 3.32
234 235 7.829706 AGATAAACATGATGCATGATGAGCTAT 59.170 33.333 29.50 20.51 43.81 2.97
245 246 6.259387 TGCATGATGAGCTATTGACTAGTTTG 59.741 38.462 0.00 0.00 0.00 2.93
251 252 5.011635 TGAGCTATTGACTAGTTTGTGGTGA 59.988 40.000 0.00 0.00 0.00 4.02
253 254 5.877012 AGCTATTGACTAGTTTGTGGTGATG 59.123 40.000 0.00 0.00 0.00 3.07
274 275 8.589629 GTGATGTTTGAATATTTGATCAGTTGC 58.410 33.333 0.00 0.00 0.00 4.17
280 281 5.006261 TGAATATTTGATCAGTTGCGTACCG 59.994 40.000 0.00 0.00 0.00 4.02
326 327 0.545646 GGAGGCAGGCAGATTTCTCT 59.454 55.000 0.00 0.00 0.00 3.10
375 997 2.807967 CGAGTTGGCTTGAATTCTCACA 59.192 45.455 7.05 0.00 0.00 3.58
407 1029 7.040478 CCTTGTCTGAATTTTCAACAGTCCATA 60.040 37.037 0.00 0.00 36.64 2.74
411 1033 7.965107 GTCTGAATTTTCAACAGTCCATATGTC 59.035 37.037 1.24 0.00 36.64 3.06
440 1071 2.346099 ACACGGCGGAATTTGAAATG 57.654 45.000 13.24 0.00 0.00 2.32
443 1074 2.099405 ACGGCGGAATTTGAAATGGAT 58.901 42.857 13.24 0.00 0.00 3.41
501 1139 2.707791 TCAGCTTATGCCCAGCTCTATT 59.292 45.455 0.00 0.00 44.77 1.73
505 1143 3.004106 GCTTATGCCCAGCTCTATTGTTG 59.996 47.826 0.00 0.00 34.15 3.33
510 1148 1.098050 CCAGCTCTATTGTTGGTGCC 58.902 55.000 0.00 0.00 0.00 5.01
529 1167 2.649516 CCGTTTGTGTGTGCTGTAATG 58.350 47.619 0.00 0.00 0.00 1.90
534 1172 2.217750 TGTGTGTGCTGTAATGGTGAC 58.782 47.619 0.00 0.00 0.00 3.67
540 1178 2.679837 GTGCTGTAATGGTGACCAGATG 59.320 50.000 11.23 0.00 36.75 2.90
543 1181 2.679837 CTGTAATGGTGACCAGATGTGC 59.320 50.000 11.23 0.00 36.75 4.57
544 1182 2.017049 GTAATGGTGACCAGATGTGCC 58.983 52.381 11.23 0.00 36.75 5.01
555 1193 5.193099 ACCAGATGTGCCCTAGTATTTTT 57.807 39.130 0.00 0.00 0.00 1.94
566 1204 6.770785 TGCCCTAGTATTTTTATCATCACCAC 59.229 38.462 0.00 0.00 0.00 4.16
651 1307 3.833442 GGCGACGGAAATTCAATCTTTT 58.167 40.909 0.00 0.00 0.00 2.27
652 1308 4.234574 GGCGACGGAAATTCAATCTTTTT 58.765 39.130 0.00 0.00 0.00 1.94
653 1309 4.089923 GGCGACGGAAATTCAATCTTTTTG 59.910 41.667 0.00 0.00 0.00 2.44
671 1333 9.607988 ATCTTTTTGTTTTTCTATTTTTCCCGT 57.392 25.926 0.00 0.00 0.00 5.28
674 1336 9.872721 TTTTTGTTTTTCTATTTTTCCCGTACT 57.127 25.926 0.00 0.00 0.00 2.73
696 1395 6.939132 CTTCTCAGTGAAGGATAAATGCAT 57.061 37.500 0.00 0.00 46.25 3.96
697 1396 6.688637 TTCTCAGTGAAGGATAAATGCATG 57.311 37.500 0.00 0.00 0.00 4.06
698 1397 5.748402 TCTCAGTGAAGGATAAATGCATGT 58.252 37.500 0.00 0.00 0.00 3.21
699 1398 5.587443 TCTCAGTGAAGGATAAATGCATGTG 59.413 40.000 0.00 0.00 0.00 3.21
700 1399 4.641541 TCAGTGAAGGATAAATGCATGTGG 59.358 41.667 0.00 0.00 0.00 4.17
701 1400 4.400251 CAGTGAAGGATAAATGCATGTGGT 59.600 41.667 0.00 0.00 0.00 4.16
702 1401 5.018809 AGTGAAGGATAAATGCATGTGGTT 58.981 37.500 0.00 0.00 0.00 3.67
703 1402 5.481473 AGTGAAGGATAAATGCATGTGGTTT 59.519 36.000 0.00 0.00 0.00 3.27
704 1403 6.014327 AGTGAAGGATAAATGCATGTGGTTTT 60.014 34.615 0.00 0.00 0.00 2.43
705 1404 6.650390 GTGAAGGATAAATGCATGTGGTTTTT 59.350 34.615 0.00 0.00 0.00 1.94
734 1433 7.522901 TTTTGATCAAACGGATAAATGCATG 57.477 32.000 20.35 0.00 36.00 4.06
747 1446 6.016360 GGATAAATGCATGTGGTAATGTGCTA 60.016 38.462 0.00 0.00 38.37 3.49
796 1495 7.285566 ACATGCTCACTGTTGATATAGGAAAT 58.714 34.615 0.00 0.00 0.00 2.17
797 1496 7.443575 ACATGCTCACTGTTGATATAGGAAATC 59.556 37.037 0.00 0.00 0.00 2.17
934 1721 2.108970 ACCTTTAGAGACACCGATCCC 58.891 52.381 0.00 0.00 0.00 3.85
935 1722 1.067212 CCTTTAGAGACACCGATCCCG 59.933 57.143 0.00 0.00 0.00 5.14
937 1724 1.843368 TTAGAGACACCGATCCCGTT 58.157 50.000 0.00 0.00 0.00 4.44
938 1725 1.386533 TAGAGACACCGATCCCGTTC 58.613 55.000 0.00 0.00 0.00 3.95
941 1728 1.213537 GACACCGATCCCGTTCGAA 59.786 57.895 0.00 0.00 41.62 3.71
942 1729 0.388907 GACACCGATCCCGTTCGAAA 60.389 55.000 0.00 0.00 41.62 3.46
943 1730 0.033781 ACACCGATCCCGTTCGAAAA 59.966 50.000 0.00 0.00 41.62 2.29
944 1731 0.719465 CACCGATCCCGTTCGAAAAG 59.281 55.000 0.00 0.00 41.62 2.27
945 1732 0.604578 ACCGATCCCGTTCGAAAAGA 59.395 50.000 0.00 0.00 41.62 2.52
946 1733 1.278238 CCGATCCCGTTCGAAAAGAG 58.722 55.000 0.00 0.00 41.62 2.85
947 1734 1.278238 CGATCCCGTTCGAAAAGAGG 58.722 55.000 0.00 1.15 41.62 3.69
982 2031 1.657804 TCTTCCTTCCCTCCACTTCC 58.342 55.000 0.00 0.00 0.00 3.46
988 2037 1.429299 CTTCCCTCCACTTCCCCTTTT 59.571 52.381 0.00 0.00 0.00 2.27
995 2044 0.690762 CACTTCCCCTTTTCCTCCGA 59.309 55.000 0.00 0.00 0.00 4.55
1010 2059 0.796312 TCCGACGATCAAAAAGCAGC 59.204 50.000 0.00 0.00 0.00 5.25
1011 2060 0.179189 CCGACGATCAAAAAGCAGCC 60.179 55.000 0.00 0.00 0.00 4.85
1012 2061 0.516877 CGACGATCAAAAAGCAGCCA 59.483 50.000 0.00 0.00 0.00 4.75
1013 2062 1.464687 CGACGATCAAAAAGCAGCCAG 60.465 52.381 0.00 0.00 0.00 4.85
1014 2063 0.242017 ACGATCAAAAAGCAGCCAGC 59.758 50.000 0.00 0.00 46.19 4.85
1058 2125 0.822811 CTCTGCTGCTCTGCTCCTTA 59.177 55.000 0.00 0.00 0.00 2.69
1112 2179 1.066918 ACGGCGAGGCTATAAACCG 59.933 57.895 16.62 10.42 45.86 4.44
1137 2204 3.775654 GGCCGTAGCTGACAGCCT 61.776 66.667 23.74 13.34 46.72 4.58
1138 2205 2.266055 GCCGTAGCTGACAGCCTT 59.734 61.111 23.74 9.13 43.77 4.35
1139 2206 1.811679 GCCGTAGCTGACAGCCTTC 60.812 63.158 23.74 12.94 43.77 3.46
1140 2207 1.893786 CCGTAGCTGACAGCCTTCT 59.106 57.895 23.74 7.98 43.77 2.85
1141 2208 1.103803 CCGTAGCTGACAGCCTTCTA 58.896 55.000 23.74 6.93 43.77 2.10
1142 2209 1.202313 CCGTAGCTGACAGCCTTCTAC 60.202 57.143 23.74 17.17 43.77 2.59
1143 2210 1.746220 CGTAGCTGACAGCCTTCTACT 59.254 52.381 23.74 6.09 43.77 2.57
1144 2211 2.223386 CGTAGCTGACAGCCTTCTACTC 60.223 54.545 23.74 5.06 43.77 2.59
1161 2233 3.465403 CCTCCCACTCCTCGGCAG 61.465 72.222 0.00 0.00 0.00 4.85
1383 2455 6.194031 CGTACGTACGCTTTATCATTCATT 57.806 37.500 32.36 0.00 43.14 2.57
1389 2461 5.741388 ACGCTTTATCATTCATTCCACTC 57.259 39.130 0.00 0.00 0.00 3.51
1390 2462 4.271049 ACGCTTTATCATTCATTCCACTCG 59.729 41.667 0.00 0.00 0.00 4.18
1458 2534 0.744874 TGTCCTCCGTTGATCGATCC 59.255 55.000 22.31 7.25 42.86 3.36
1531 2607 0.320421 CACAGGTGACCCCGTTACAG 60.320 60.000 0.00 0.00 38.74 2.74
1534 2610 0.395312 AGGTGACCCCGTTACAGTTG 59.605 55.000 0.00 0.00 38.74 3.16
1535 2611 0.107268 GGTGACCCCGTTACAGTTGT 59.893 55.000 0.00 0.00 0.00 3.32
1541 2626 1.202842 CCCCGTTACAGTTGTCCCTTT 60.203 52.381 0.00 0.00 0.00 3.11
1542 2627 1.877443 CCCGTTACAGTTGTCCCTTTG 59.123 52.381 0.00 0.00 0.00 2.77
1550 2635 4.086457 ACAGTTGTCCCTTTGTTTCTGTT 58.914 39.130 0.00 0.00 32.15 3.16
1551 2636 4.526650 ACAGTTGTCCCTTTGTTTCTGTTT 59.473 37.500 0.00 0.00 32.15 2.83
1553 2638 6.209788 ACAGTTGTCCCTTTGTTTCTGTTTAA 59.790 34.615 0.00 0.00 32.15 1.52
1628 2747 2.547211 CCAAGTGAACTGAGAACTGCAG 59.453 50.000 13.48 13.48 39.26 4.41
1666 2789 1.259609 AACACATGGTCCATGCCTTG 58.740 50.000 28.57 21.67 44.80 3.61
1731 2861 2.838736 TGACTCTGCCAAGTTCTCAAC 58.161 47.619 0.00 0.00 0.00 3.18
1813 2943 1.411977 CCAGAGCTGTCCAGTATCCTG 59.588 57.143 0.00 0.00 38.50 3.86
1869 3013 7.601508 TGTGCATATGTATCTCATGAACATCTC 59.398 37.037 13.49 6.50 37.91 2.75
1916 3066 3.189910 TGTTCTGTGATTCATGCTTCTGC 59.810 43.478 0.00 0.00 40.20 4.26
1962 3112 1.757682 TTCGTTCATGTATTGGGCCC 58.242 50.000 17.59 17.59 0.00 5.80
1970 3120 3.960102 TCATGTATTGGGCCCAAAATCTC 59.040 43.478 40.00 25.55 39.55 2.75
2048 3199 0.319405 GCTGCCCATTCTGCAAAACT 59.681 50.000 0.00 0.00 38.46 2.66
2136 3287 3.110705 AGCTTTCAGCCCAGAGATTCTA 58.889 45.455 0.00 0.00 43.77 2.10
2151 3302 7.496920 CCAGAGATTCTAATCAACATACAGCAA 59.503 37.037 5.55 0.00 37.89 3.91
2152 3303 9.053840 CAGAGATTCTAATCAACATACAGCAAT 57.946 33.333 5.55 0.00 37.89 3.56
2179 3330 9.998106 ATACTACCTAATACTATTTGCCAACAG 57.002 33.333 0.00 0.00 0.00 3.16
2185 3336 8.398665 CCTAATACTATTTGCCAACAGAACTTC 58.601 37.037 0.00 0.00 0.00 3.01
2273 3424 1.692519 GCCGGTGGACATATCCTACTT 59.307 52.381 1.90 0.00 46.43 2.24
2292 3443 0.343372 TCCATAGGAGTCCCAAGCCT 59.657 55.000 5.25 0.00 35.82 4.58
2310 3461 3.057033 AGCCTGATTTTGCAGTGCTAAAG 60.057 43.478 24.89 14.34 39.20 1.85
2313 3464 6.352729 CCTGATTTTGCAGTGCTAAAGGCA 62.353 45.833 24.89 22.39 36.82 4.75
2338 3489 5.220567 CCCAAACCAAACTGTTGATTTTTCG 60.221 40.000 0.00 0.00 36.83 3.46
2346 3497 3.568430 ACTGTTGATTTTTCGGACCCTTC 59.432 43.478 0.00 0.00 0.00 3.46
2365 3516 4.874966 CCTTCGAGAGAGATTTCATTGCTT 59.125 41.667 0.00 0.00 43.69 3.91
2368 3519 4.081476 TCGAGAGAGATTTCATTGCTTCCA 60.081 41.667 0.00 0.00 34.84 3.53
2475 3634 6.333416 TGCAGAACAGAGTAAATGCTAGTAG 58.667 40.000 0.00 0.00 34.80 2.57
2482 3641 7.106239 ACAGAGTAAATGCTAGTAGTGCAAAT 58.894 34.615 0.00 0.00 44.01 2.32
2512 6413 2.401583 AATATTCTGTCAGCGGCACA 57.598 45.000 1.45 0.00 0.00 4.57
2513 6414 2.401583 ATATTCTGTCAGCGGCACAA 57.598 45.000 1.45 0.00 0.00 3.33
2516 6417 1.159713 TTCTGTCAGCGGCACAAGTG 61.160 55.000 1.45 0.00 0.00 3.16
2522 6428 3.357079 GCGGCACAAGTGGAGTGG 61.357 66.667 2.00 0.00 37.46 4.00
2540 6446 0.890683 GGGGATTTGGTGCAGAAGTG 59.109 55.000 0.00 0.00 0.00 3.16
2556 6462 5.513495 GCAGAAGTGTAGAACGATTCTGTAG 59.487 44.000 17.85 2.88 41.45 2.74
2575 6481 0.520847 GCTGGCTCTGAAGACAAAGC 59.479 55.000 0.00 0.00 41.06 3.51
2577 6483 2.613977 GCTGGCTCTGAAGACAAAGCTA 60.614 50.000 0.00 0.00 41.06 3.32
2628 6534 3.726517 CCAACCGCAAGCTCACCG 61.727 66.667 0.00 0.00 0.00 4.94
2750 6657 2.997315 CTGGACGCTCTCCCCACA 60.997 66.667 0.00 0.00 38.49 4.17
2931 6842 3.090532 GCCCTCCCGGTCCAGAAT 61.091 66.667 0.00 0.00 0.00 2.40
2940 6851 1.672854 CGGTCCAGAATCGGTGCCTA 61.673 60.000 0.00 0.00 0.00 3.93
3121 7801 2.523168 TCACCGCTGTCACCCTCA 60.523 61.111 0.00 0.00 0.00 3.86
3422 8477 1.041447 GCCGGCCTCTACCAACTCTA 61.041 60.000 18.11 0.00 0.00 2.43
3432 8487 2.271944 ACCAACTCTACCACTTTGGC 57.728 50.000 0.00 0.00 42.67 4.52
3486 9150 1.245732 AGAACTACGCTCCAAGTCGT 58.754 50.000 0.00 0.00 42.09 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.256960 TCTTGGTGGTGAGGGCCC 61.257 66.667 16.46 16.46 0.00 5.80
1 2 2.352805 CTCTTGGTGGTGAGGGCC 59.647 66.667 0.00 0.00 0.00 5.80
2 3 2.352805 CCTCTTGGTGGTGAGGGC 59.647 66.667 0.00 0.00 44.44 5.19
4 5 2.606587 CCCCCTCTTGGTGGTGAGG 61.607 68.421 0.00 0.00 46.91 3.86
5 6 3.081554 CCCCCTCTTGGTGGTGAG 58.918 66.667 0.00 0.00 0.00 3.51
9 10 4.410400 GACGCCCCCTCTTGGTGG 62.410 72.222 0.00 0.00 37.71 4.61
10 11 3.322466 AGACGCCCCCTCTTGGTG 61.322 66.667 0.00 0.00 39.33 4.17
11 12 3.322466 CAGACGCCCCCTCTTGGT 61.322 66.667 0.00 0.00 0.00 3.67
12 13 2.527951 CTTCAGACGCCCCCTCTTGG 62.528 65.000 0.00 0.00 0.00 3.61
13 14 1.078848 CTTCAGACGCCCCCTCTTG 60.079 63.158 0.00 0.00 0.00 3.02
14 15 2.294078 CCTTCAGACGCCCCCTCTT 61.294 63.158 0.00 0.00 0.00 2.85
15 16 2.685380 CCTTCAGACGCCCCCTCT 60.685 66.667 0.00 0.00 0.00 3.69
16 17 3.787001 CCCTTCAGACGCCCCCTC 61.787 72.222 0.00 0.00 0.00 4.30
19 20 3.090532 ATCCCCTTCAGACGCCCC 61.091 66.667 0.00 0.00 0.00 5.80
20 21 2.317149 CTGATCCCCTTCAGACGCCC 62.317 65.000 0.00 0.00 44.88 6.13
21 22 1.144936 CTGATCCCCTTCAGACGCC 59.855 63.158 0.00 0.00 44.88 5.68
22 23 1.144936 CCTGATCCCCTTCAGACGC 59.855 63.158 3.10 0.00 44.88 5.19
23 24 0.687757 TCCCTGATCCCCTTCAGACG 60.688 60.000 3.10 0.00 44.88 4.18
24 25 0.833949 GTCCCTGATCCCCTTCAGAC 59.166 60.000 3.10 0.00 44.88 3.51
25 26 0.687757 CGTCCCTGATCCCCTTCAGA 60.688 60.000 3.10 0.00 44.88 3.27
26 27 0.687757 TCGTCCCTGATCCCCTTCAG 60.688 60.000 0.00 0.00 42.31 3.02
27 28 0.976073 GTCGTCCCTGATCCCCTTCA 60.976 60.000 0.00 0.00 0.00 3.02
28 29 1.823976 GTCGTCCCTGATCCCCTTC 59.176 63.158 0.00 0.00 0.00 3.46
29 30 2.058595 CGTCGTCCCTGATCCCCTT 61.059 63.158 0.00 0.00 0.00 3.95
30 31 2.442272 CGTCGTCCCTGATCCCCT 60.442 66.667 0.00 0.00 0.00 4.79
31 32 3.537874 CCGTCGTCCCTGATCCCC 61.538 72.222 0.00 0.00 0.00 4.81
32 33 4.222847 GCCGTCGTCCCTGATCCC 62.223 72.222 0.00 0.00 0.00 3.85
33 34 4.570663 CGCCGTCGTCCCTGATCC 62.571 72.222 0.00 0.00 0.00 3.36
49 50 4.675029 ACCTTGGGTTCCGTCGCG 62.675 66.667 0.00 0.00 27.29 5.87
50 51 2.741211 GACCTTGGGTTCCGTCGC 60.741 66.667 0.00 0.00 35.25 5.19
51 52 2.431942 CGACCTTGGGTTCCGTCG 60.432 66.667 0.00 0.00 41.70 5.12
52 53 2.741211 GCGACCTTGGGTTCCGTC 60.741 66.667 0.00 0.00 35.25 4.79
53 54 4.324991 GGCGACCTTGGGTTCCGT 62.325 66.667 0.00 0.00 35.25 4.69
74 75 4.200283 CTCTCACGCCGCTCTCCC 62.200 72.222 0.00 0.00 0.00 4.30
75 76 3.119709 CTCTCTCACGCCGCTCTCC 62.120 68.421 0.00 0.00 0.00 3.71
76 77 2.047151 CTCTCTCTCACGCCGCTCTC 62.047 65.000 0.00 0.00 0.00 3.20
77 78 2.045829 TCTCTCTCACGCCGCTCT 60.046 61.111 0.00 0.00 0.00 4.09
78 79 1.090625 TACTCTCTCTCACGCCGCTC 61.091 60.000 0.00 0.00 0.00 5.03
79 80 1.078356 TACTCTCTCTCACGCCGCT 60.078 57.895 0.00 0.00 0.00 5.52
80 81 1.062845 GTACTCTCTCTCACGCCGC 59.937 63.158 0.00 0.00 0.00 6.53
81 82 1.722677 GGTACTCTCTCTCACGCCG 59.277 63.158 0.00 0.00 0.00 6.46
82 83 1.025647 ACGGTACTCTCTCTCACGCC 61.026 60.000 0.00 0.00 0.00 5.68
83 84 1.649664 TACGGTACTCTCTCTCACGC 58.350 55.000 0.00 0.00 0.00 5.34
84 85 3.869832 TGATTACGGTACTCTCTCTCACG 59.130 47.826 7.00 0.00 0.00 4.35
85 86 4.634883 TGTGATTACGGTACTCTCTCTCAC 59.365 45.833 7.00 1.05 0.00 3.51
86 87 4.840271 TGTGATTACGGTACTCTCTCTCA 58.160 43.478 7.00 0.00 0.00 3.27
87 88 6.038382 TGAATGTGATTACGGTACTCTCTCTC 59.962 42.308 7.00 5.37 0.00 3.20
88 89 5.886474 TGAATGTGATTACGGTACTCTCTCT 59.114 40.000 7.00 0.00 0.00 3.10
89 90 6.132791 TGAATGTGATTACGGTACTCTCTC 57.867 41.667 7.00 0.53 0.00 3.20
90 91 6.716934 ATGAATGTGATTACGGTACTCTCT 57.283 37.500 7.00 0.00 0.00 3.10
91 92 6.421202 GGAATGAATGTGATTACGGTACTCTC 59.579 42.308 7.00 4.36 0.00 3.20
92 93 6.098409 AGGAATGAATGTGATTACGGTACTCT 59.902 38.462 7.00 0.00 0.00 3.24
93 94 6.281405 AGGAATGAATGTGATTACGGTACTC 58.719 40.000 0.00 0.00 0.00 2.59
94 95 6.235231 AGGAATGAATGTGATTACGGTACT 57.765 37.500 0.00 0.00 0.00 2.73
95 96 6.537301 TGAAGGAATGAATGTGATTACGGTAC 59.463 38.462 0.00 0.00 0.00 3.34
96 97 6.645306 TGAAGGAATGAATGTGATTACGGTA 58.355 36.000 0.00 0.00 0.00 4.02
115 116 7.837863 TCTTATGGTCTTAACAGTACTGAAGG 58.162 38.462 29.30 16.05 0.00 3.46
123 124 6.672657 ACCCTACATCTTATGGTCTTAACAGT 59.327 38.462 0.00 0.00 33.60 3.55
124 125 7.125792 ACCCTACATCTTATGGTCTTAACAG 57.874 40.000 0.00 0.00 33.60 3.16
125 126 7.504926 AACCCTACATCTTATGGTCTTAACA 57.495 36.000 0.00 0.00 33.60 2.41
126 127 8.702819 ACTAACCCTACATCTTATGGTCTTAAC 58.297 37.037 0.00 0.00 33.60 2.01
127 128 8.849543 ACTAACCCTACATCTTATGGTCTTAA 57.150 34.615 0.00 0.00 33.60 1.85
128 129 9.940974 TTACTAACCCTACATCTTATGGTCTTA 57.059 33.333 0.00 0.00 33.60 2.10
129 130 8.702819 GTTACTAACCCTACATCTTATGGTCTT 58.297 37.037 0.00 0.00 33.60 3.01
130 131 7.842743 TGTTACTAACCCTACATCTTATGGTCT 59.157 37.037 0.00 0.00 33.60 3.85
132 133 7.983166 TGTTACTAACCCTACATCTTATGGT 57.017 36.000 0.00 0.00 33.60 3.55
133 134 9.106070 GTTTGTTACTAACCCTACATCTTATGG 57.894 37.037 0.00 0.00 33.60 2.74
134 135 9.661563 TGTTTGTTACTAACCCTACATCTTATG 57.338 33.333 7.16 0.00 0.00 1.90
135 136 9.886132 CTGTTTGTTACTAACCCTACATCTTAT 57.114 33.333 7.16 0.00 0.00 1.73
136 137 8.873144 ACTGTTTGTTACTAACCCTACATCTTA 58.127 33.333 7.16 0.00 0.00 2.10
137 138 7.742767 ACTGTTTGTTACTAACCCTACATCTT 58.257 34.615 7.16 0.00 0.00 2.40
138 139 7.312415 ACTGTTTGTTACTAACCCTACATCT 57.688 36.000 7.16 0.00 0.00 2.90
146 147 8.788325 ATATCTCCAACTGTTTGTTACTAACC 57.212 34.615 7.16 0.00 37.07 2.85
183 184 5.641636 TGAAAGGTTTTTGCTTTCAAGGAAC 59.358 36.000 0.00 1.18 42.02 3.62
184 185 5.799213 TGAAAGGTTTTTGCTTTCAAGGAA 58.201 33.333 0.00 0.00 42.02 3.36
197 198 8.149647 TGCATCATGTTTATCTTGAAAGGTTTT 58.850 29.630 0.00 0.00 34.65 2.43
200 201 6.839124 TGCATCATGTTTATCTTGAAAGGT 57.161 33.333 0.00 0.00 34.65 3.50
201 202 7.485810 TCATGCATCATGTTTATCTTGAAAGG 58.514 34.615 0.00 0.00 41.98 3.11
205 206 7.521585 GCTCATCATGCATCATGTTTATCTTGA 60.522 37.037 10.58 0.00 41.98 3.02
233 234 6.545666 TCAAACATCACCACAAACTAGTCAAT 59.454 34.615 0.00 0.00 0.00 2.57
234 235 5.883115 TCAAACATCACCACAAACTAGTCAA 59.117 36.000 0.00 0.00 0.00 3.18
245 246 8.246180 ACTGATCAAATATTCAAACATCACCAC 58.754 33.333 0.00 0.00 0.00 4.16
251 252 7.315142 ACGCAACTGATCAAATATTCAAACAT 58.685 30.769 0.00 0.00 0.00 2.71
253 254 7.218204 GGTACGCAACTGATCAAATATTCAAAC 59.782 37.037 0.00 0.00 0.00 2.93
280 281 3.728076 TGAGGAGATAACCATACACGC 57.272 47.619 0.00 0.00 0.00 5.34
326 327 5.221048 GCTCTGCTTTTCTTGGACAAAGTTA 60.221 40.000 0.00 0.00 37.18 2.24
375 997 3.826157 TGAAAATTCAGACAAGGCGGATT 59.174 39.130 0.00 0.00 32.50 3.01
407 1029 1.640428 CCGTGTATCAACGCAGACAT 58.360 50.000 0.00 0.00 42.23 3.06
411 1033 2.695055 CGCCGTGTATCAACGCAG 59.305 61.111 0.00 0.00 42.23 5.18
440 1071 5.875359 ACCGAGAGAAAACTACATTTGATCC 59.125 40.000 0.00 0.00 0.00 3.36
443 1074 6.540914 ACAAACCGAGAGAAAACTACATTTGA 59.459 34.615 0.00 0.00 0.00 2.69
501 1139 1.244697 ACACACAAACGGCACCAACA 61.245 50.000 0.00 0.00 0.00 3.33
505 1143 2.278531 GCACACACAAACGGCACC 60.279 61.111 0.00 0.00 0.00 5.01
510 1148 2.032799 ACCATTACAGCACACACAAACG 59.967 45.455 0.00 0.00 0.00 3.60
529 1167 0.179000 CTAGGGCACATCTGGTCACC 59.821 60.000 0.00 0.00 0.00 4.02
534 1172 6.998074 TGATAAAAATACTAGGGCACATCTGG 59.002 38.462 0.00 0.00 0.00 3.86
540 1178 6.770785 TGGTGATGATAAAAATACTAGGGCAC 59.229 38.462 0.00 0.00 0.00 5.01
543 1181 7.661847 GGAGTGGTGATGATAAAAATACTAGGG 59.338 40.741 0.00 0.00 0.00 3.53
544 1182 7.385205 CGGAGTGGTGATGATAAAAATACTAGG 59.615 40.741 0.00 0.00 0.00 3.02
566 1204 1.297664 CCACCTAGACTACGACGGAG 58.702 60.000 5.27 5.27 0.00 4.63
651 1307 8.905850 AGAAGTACGGGAAAAATAGAAAAACAA 58.094 29.630 0.00 0.00 0.00 2.83
652 1308 8.454570 AGAAGTACGGGAAAAATAGAAAAACA 57.545 30.769 0.00 0.00 0.00 2.83
653 1309 8.562052 TGAGAAGTACGGGAAAAATAGAAAAAC 58.438 33.333 0.00 0.00 0.00 2.43
661 1321 5.223449 TCACTGAGAAGTACGGGAAAAAT 57.777 39.130 0.00 0.00 0.00 1.82
674 1336 6.094464 CACATGCATTTATCCTTCACTGAGAA 59.906 38.462 0.00 0.00 34.41 2.87
709 1408 7.601886 ACATGCATTTATCCGTTTGATCAAAAA 59.398 29.630 22.07 12.12 34.76 1.94
710 1409 7.063191 CACATGCATTTATCCGTTTGATCAAAA 59.937 33.333 22.07 7.95 34.76 2.44
711 1410 6.530887 CACATGCATTTATCCGTTTGATCAAA 59.469 34.615 16.91 16.91 34.76 2.69
712 1411 6.035217 CACATGCATTTATCCGTTTGATCAA 58.965 36.000 3.38 3.38 34.76 2.57
713 1412 5.450274 CCACATGCATTTATCCGTTTGATCA 60.450 40.000 0.00 0.00 34.76 2.92
714 1413 4.977963 CCACATGCATTTATCCGTTTGATC 59.022 41.667 0.00 0.00 34.76 2.92
715 1414 4.402155 ACCACATGCATTTATCCGTTTGAT 59.598 37.500 0.00 0.00 37.49 2.57
716 1415 3.761218 ACCACATGCATTTATCCGTTTGA 59.239 39.130 0.00 0.00 0.00 2.69
717 1416 4.108699 ACCACATGCATTTATCCGTTTG 57.891 40.909 0.00 0.00 0.00 2.93
718 1417 5.906113 TTACCACATGCATTTATCCGTTT 57.094 34.783 0.00 0.00 0.00 3.60
719 1418 5.359576 ACATTACCACATGCATTTATCCGTT 59.640 36.000 0.00 0.00 0.00 4.44
720 1419 4.887071 ACATTACCACATGCATTTATCCGT 59.113 37.500 0.00 0.00 0.00 4.69
721 1420 5.214417 CACATTACCACATGCATTTATCCG 58.786 41.667 0.00 0.00 0.00 4.18
734 1433 7.622256 GCTTCGATATGAATAGCACATTACCAC 60.622 40.741 0.00 0.00 35.63 4.16
747 1446 5.543507 ACAGAAGGAGCTTCGATATGAAT 57.456 39.130 2.93 0.00 44.34 2.57
796 1495 7.954835 ACAAAACAATCTCCAAATGAAGATGA 58.045 30.769 0.00 0.00 0.00 2.92
797 1496 9.350357 CTACAAAACAATCTCCAAATGAAGATG 57.650 33.333 0.00 0.00 0.00 2.90
808 1541 7.262048 TCACCAAAAACTACAAAACAATCTCC 58.738 34.615 0.00 0.00 0.00 3.71
844 1583 4.507710 TGCTCAGATTTACTACCTTGCAG 58.492 43.478 0.00 0.00 0.00 4.41
902 1643 4.930405 GTCTCTAAAGGTTAAGACTGCCAC 59.070 45.833 0.00 0.00 36.16 5.01
934 1721 5.103290 TCAATTTTCCCTCTTTTCGAACG 57.897 39.130 0.00 0.00 0.00 3.95
935 1722 6.586463 GGAATCAATTTTCCCTCTTTTCGAAC 59.414 38.462 0.00 0.00 39.46 3.95
937 1724 6.010219 AGGAATCAATTTTCCCTCTTTTCGA 58.990 36.000 5.45 0.00 45.32 3.71
938 1725 6.272822 AGGAATCAATTTTCCCTCTTTTCG 57.727 37.500 5.45 0.00 45.32 3.46
941 1728 7.862274 AGAAAGGAATCAATTTTCCCTCTTT 57.138 32.000 5.45 1.17 45.32 2.52
942 1729 7.038729 GGAAGAAAGGAATCAATTTTCCCTCTT 60.039 37.037 16.57 16.57 45.32 2.85
943 1730 6.438741 GGAAGAAAGGAATCAATTTTCCCTCT 59.561 38.462 5.45 5.61 45.32 3.69
944 1731 6.438741 AGGAAGAAAGGAATCAATTTTCCCTC 59.561 38.462 5.45 3.74 45.32 4.30
945 1732 6.326161 AGGAAGAAAGGAATCAATTTTCCCT 58.674 36.000 5.45 0.00 45.32 4.20
946 1733 6.611613 AGGAAGAAAGGAATCAATTTTCCC 57.388 37.500 5.45 0.00 45.32 3.97
947 1734 7.099764 GGAAGGAAGAAAGGAATCAATTTTCC 58.900 38.462 1.21 1.21 44.67 3.13
982 2031 0.535335 TGATCGTCGGAGGAAAAGGG 59.465 55.000 4.32 0.00 0.00 3.95
988 2037 1.001520 TGCTTTTTGATCGTCGGAGGA 59.998 47.619 2.53 2.53 0.00 3.71
995 2044 0.242017 GCTGGCTGCTTTTTGATCGT 59.758 50.000 9.31 0.00 38.95 3.73
1071 2138 4.794439 CATCGTCGTGGCCTGCGA 62.794 66.667 16.76 16.76 37.76 5.10
1094 2161 1.066918 CGGTTTATAGCCTCGCCGT 59.933 57.895 0.00 0.00 35.11 5.68
1100 2167 0.532196 GGAAGCGCGGTTTATAGCCT 60.532 55.000 25.80 0.00 0.00 4.58
1129 2196 1.619977 GGGAGGAGTAGAAGGCTGTCA 60.620 57.143 0.00 0.00 0.00 3.58
1131 2198 0.413832 TGGGAGGAGTAGAAGGCTGT 59.586 55.000 0.00 0.00 0.00 4.40
1133 2200 0.713579 AGTGGGAGGAGTAGAAGGCT 59.286 55.000 0.00 0.00 0.00 4.58
1134 2201 1.116308 GAGTGGGAGGAGTAGAAGGC 58.884 60.000 0.00 0.00 0.00 4.35
1135 2202 1.289530 AGGAGTGGGAGGAGTAGAAGG 59.710 57.143 0.00 0.00 0.00 3.46
1137 2204 1.064611 CGAGGAGTGGGAGGAGTAGAA 60.065 57.143 0.00 0.00 0.00 2.10
1138 2205 0.547075 CGAGGAGTGGGAGGAGTAGA 59.453 60.000 0.00 0.00 0.00 2.59
1139 2206 0.466555 CCGAGGAGTGGGAGGAGTAG 60.467 65.000 0.00 0.00 0.00 2.57
1140 2207 1.613610 CCGAGGAGTGGGAGGAGTA 59.386 63.158 0.00 0.00 0.00 2.59
1141 2208 2.360980 CCGAGGAGTGGGAGGAGT 59.639 66.667 0.00 0.00 0.00 3.85
1142 2209 3.151022 GCCGAGGAGTGGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
1143 2210 3.965026 CTGCCGAGGAGTGGGAGGA 62.965 68.421 0.00 0.00 40.91 3.71
1144 2211 3.465403 CTGCCGAGGAGTGGGAGG 61.465 72.222 0.00 0.00 40.91 4.30
1161 2233 0.879839 GTTGCCCATTGTGGTTGTGC 60.880 55.000 0.00 0.00 35.17 4.57
1163 2235 1.739049 CGTTGCCCATTGTGGTTGT 59.261 52.632 0.00 0.00 35.17 3.32
1339 2411 1.817099 GAAGCAGATGGGGCACTCG 60.817 63.158 0.00 0.00 0.00 4.18
1383 2455 0.895559 TCTCTGAAGCAGCGAGTGGA 60.896 55.000 0.00 0.00 0.00 4.02
1389 2461 0.320247 ACCAACTCTCTGAAGCAGCG 60.320 55.000 0.00 0.00 0.00 5.18
1390 2462 1.001860 AGACCAACTCTCTGAAGCAGC 59.998 52.381 0.00 0.00 0.00 5.25
1458 2534 2.386661 AACTCGGGTAGAACTGCATG 57.613 50.000 0.00 0.00 0.00 4.06
1531 2607 7.547722 ACAATTAAACAGAAACAAAGGGACAAC 59.452 33.333 0.00 0.00 0.00 3.32
1534 2610 8.387354 CAAACAATTAAACAGAAACAAAGGGAC 58.613 33.333 0.00 0.00 0.00 4.46
1535 2611 7.065204 GCAAACAATTAAACAGAAACAAAGGGA 59.935 33.333 0.00 0.00 0.00 4.20
1541 2626 6.556212 TCGAGCAAACAATTAAACAGAAACA 58.444 32.000 0.00 0.00 0.00 2.83
1542 2627 7.444558 TTCGAGCAAACAATTAAACAGAAAC 57.555 32.000 0.00 0.00 0.00 2.78
1550 2635 8.346300 TCAGTACAAATTCGAGCAAACAATTAA 58.654 29.630 0.00 0.00 0.00 1.40
1551 2636 7.866729 TCAGTACAAATTCGAGCAAACAATTA 58.133 30.769 0.00 0.00 0.00 1.40
1553 2638 6.312399 TCAGTACAAATTCGAGCAAACAAT 57.688 33.333 0.00 0.00 0.00 2.71
1628 2747 9.277565 CATGTGTTTATAAGTGCAGTGTAATTC 57.722 33.333 0.00 0.00 0.00 2.17
1639 2758 5.450412 GGCATGGACCATGTGTTTATAAGTG 60.450 44.000 30.55 7.35 43.10 3.16
1649 2772 1.259609 AACAAGGCATGGACCATGTG 58.740 50.000 30.55 23.78 40.61 3.21
1675 2798 3.840124 TCTCTCGGATGTAGAGTAGCA 57.160 47.619 0.00 0.00 41.11 3.49
1676 2799 4.131596 ACTTCTCTCGGATGTAGAGTAGC 58.868 47.826 6.64 0.00 40.33 3.58
1677 2800 6.687081 AAACTTCTCTCGGATGTAGAGTAG 57.313 41.667 0.00 0.00 41.62 2.57
1678 2801 7.176165 TGAAAAACTTCTCTCGGATGTAGAGTA 59.824 37.037 0.00 0.00 41.11 2.59
1680 2803 6.309251 GTGAAAAACTTCTCTCGGATGTAGAG 59.691 42.308 0.00 0.00 41.59 2.43
1690 2820 8.371770 AGTCATTACAGTGAAAAACTTCTCTC 57.628 34.615 0.00 0.00 36.83 3.20
1731 2861 3.624777 ACAATGAAACAGGGCAGGATAG 58.375 45.455 0.00 0.00 0.00 2.08
1830 2960 1.012086 ATGCACAGAGTATTGCGCAG 58.988 50.000 11.31 0.00 39.24 5.18
1833 2963 5.866092 AGATACATATGCACAGAGTATTGCG 59.134 40.000 1.58 0.00 41.96 4.85
1943 3093 1.004862 TGGGCCCAATACATGAACGAA 59.995 47.619 26.33 0.00 0.00 3.85
1962 3112 7.194607 TCAGCTAGAAAACAGTGAGATTTTG 57.805 36.000 0.00 0.00 0.00 2.44
1970 3120 5.978919 TGCAAAATTCAGCTAGAAAACAGTG 59.021 36.000 0.00 0.00 40.22 3.66
2162 3313 9.686683 ATAGAAGTTCTGTTGGCAAATAGTATT 57.313 29.630 15.90 1.33 0.00 1.89
2166 3317 8.180267 CAGAATAGAAGTTCTGTTGGCAAATAG 58.820 37.037 18.41 3.81 46.30 1.73
2167 3318 8.044060 CAGAATAGAAGTTCTGTTGGCAAATA 57.956 34.615 18.41 0.00 46.30 1.40
2168 3319 6.917533 CAGAATAGAAGTTCTGTTGGCAAAT 58.082 36.000 18.41 0.00 46.30 2.32
2215 3366 1.227999 CGTTGCACCCTCATGAACGT 61.228 55.000 0.00 0.00 35.75 3.99
2273 3424 0.343372 AGGCTTGGGACTCCTATGGA 59.657 55.000 0.00 0.00 0.00 3.41
2285 3436 1.938016 GCACTGCAAAATCAGGCTTGG 60.938 52.381 0.00 0.00 38.36 3.61
2292 3443 3.302365 GCCTTTAGCACTGCAAAATCA 57.698 42.857 3.30 0.00 42.97 2.57
2310 3461 0.539518 AACAGTTTGGTTTGGGTGCC 59.460 50.000 0.00 0.00 0.00 5.01
2313 3464 4.835284 AAATCAACAGTTTGGTTTGGGT 57.165 36.364 0.00 0.00 43.19 4.51
2338 3489 2.761208 TGAAATCTCTCTCGAAGGGTCC 59.239 50.000 0.00 0.00 0.00 4.46
2346 3497 4.186926 TGGAAGCAATGAAATCTCTCTCG 58.813 43.478 0.00 0.00 0.00 4.04
2445 3596 5.922544 GCATTTACTCTGTTCTGCAAACATT 59.077 36.000 12.68 5.82 0.00 2.71
2502 3661 2.031012 CTCCACTTGTGCCGCTGA 59.969 61.111 0.00 0.00 0.00 4.26
2512 6413 1.158007 ACCAAATCCCCACTCCACTT 58.842 50.000 0.00 0.00 0.00 3.16
2513 6414 0.405585 CACCAAATCCCCACTCCACT 59.594 55.000 0.00 0.00 0.00 4.00
2516 6417 0.967380 CTGCACCAAATCCCCACTCC 60.967 60.000 0.00 0.00 0.00 3.85
2522 6428 1.620822 ACACTTCTGCACCAAATCCC 58.379 50.000 0.00 0.00 0.00 3.85
2540 6446 3.117046 GCCAGCTACAGAATCGTTCTAC 58.883 50.000 0.00 0.00 38.11 2.59
2556 6462 0.520847 GCTTTGTCTTCAGAGCCAGC 59.479 55.000 0.27 0.00 43.25 4.85
2575 6481 5.452077 CCGAGGTAGATTTGAGGGACTTTAG 60.452 48.000 0.00 0.00 41.55 1.85
2577 6483 3.197983 CCGAGGTAGATTTGAGGGACTTT 59.802 47.826 0.00 0.00 41.55 2.66
2750 6657 1.348696 TCCATCGCAGACATGGCATAT 59.651 47.619 0.00 0.00 42.51 1.78
2992 6903 1.997874 GCTCACCCCAGACCCATCT 60.998 63.158 0.00 0.00 34.57 2.90
2994 6905 2.125912 AGCTCACCCCAGACCCAT 59.874 61.111 0.00 0.00 0.00 4.00
3486 9150 2.048222 CAGGCGAAGAAGCGGACA 60.048 61.111 0.00 0.00 38.18 4.02


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

AutoCloner maintained by Alex Coulton.