Multiple sequence alignment - TraesCS5B01G304700

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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 TraesCS5B01G304700 chr5B 100.000 2579 0 0 1 2579 488720957 488718379 0.000000e+00 4763
1 TraesCS5B01G304700 chr5B 77.778 630 108 22 1899 2503 488713483 488712861 2.440000e-95 359
2 TraesCS5B01G304700 chr1B 95.864 1209 31 4 712 1902 573369069 573367862 0.000000e+00 1938
3 TraesCS5B01G304700 chr1B 94.706 1209 27 10 708 1898 589496093 589497282 0.000000e+00 1844
4 TraesCS5B01G304700 chr7B 95.851 1205 30 7 712 1898 699151792 699150590 0.000000e+00 1930
5 TraesCS5B01G304700 chr7B 95.462 1212 34 7 708 1901 108496005 108494797 0.000000e+00 1914
6 TraesCS5B01G304700 chr7B 95.112 1207 31 6 709 1898 4607221 4608416 0.000000e+00 1877
7 TraesCS5B01G304700 chr7B 92.397 1210 63 10 709 1900 741362509 741363707 0.000000e+00 1698
8 TraesCS5B01G304700 chr6B 95.285 1209 36 6 712 1902 564315395 564316600 0.000000e+00 1897
9 TraesCS5B01G304700 chr6B 94.559 1213 35 4 709 1903 579213277 579214476 0.000000e+00 1845
10 TraesCS5B01G304700 chr3B 94.556 1194 42 17 712 1903 475262797 475263969 0.000000e+00 1823
11 TraesCS5B01G304700 chr4A 93.924 1185 54 6 732 1898 690151685 690152869 0.000000e+00 1773
12 TraesCS5B01G304700 chr2B 93.444 1205 42 10 712 1898 77815634 77816819 0.000000e+00 1753
13 TraesCS5B01G304700 chr5A 96.035 681 27 0 1899 2579 513211092 513210412 0.000000e+00 1109
14 TraesCS5B01G304700 chr5A 86.943 651 63 11 77 712 513211734 513211091 0.000000e+00 712
15 TraesCS5B01G304700 chr5A 82.707 399 56 7 310 705 513209055 513208667 2.460000e-90 342
16 TraesCS5B01G304700 chr5D 94.983 299 15 0 2281 2579 407709402 407709104 1.080000e-128 470
17 TraesCS5B01G304700 chr5D 76.485 421 68 17 1899 2297 407668531 407668942 1.570000e-47 200


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 TraesCS5B01G304700 chr5B 488718379 488720957 2578 True 4763 4763 100.000000 1 2579 1 chr5B.!!$R2 2578
1 TraesCS5B01G304700 chr5B 488712861 488713483 622 True 359 359 77.778000 1899 2503 1 chr5B.!!$R1 604
2 TraesCS5B01G304700 chr1B 573367862 573369069 1207 True 1938 1938 95.864000 712 1902 1 chr1B.!!$R1 1190
3 TraesCS5B01G304700 chr1B 589496093 589497282 1189 False 1844 1844 94.706000 708 1898 1 chr1B.!!$F1 1190
4 TraesCS5B01G304700 chr7B 699150590 699151792 1202 True 1930 1930 95.851000 712 1898 1 chr7B.!!$R2 1186
5 TraesCS5B01G304700 chr7B 108494797 108496005 1208 True 1914 1914 95.462000 708 1901 1 chr7B.!!$R1 1193
6 TraesCS5B01G304700 chr7B 4607221 4608416 1195 False 1877 1877 95.112000 709 1898 1 chr7B.!!$F1 1189
7 TraesCS5B01G304700 chr7B 741362509 741363707 1198 False 1698 1698 92.397000 709 1900 1 chr7B.!!$F2 1191
8 TraesCS5B01G304700 chr6B 564315395 564316600 1205 False 1897 1897 95.285000 712 1902 1 chr6B.!!$F1 1190
9 TraesCS5B01G304700 chr6B 579213277 579214476 1199 False 1845 1845 94.559000 709 1903 1 chr6B.!!$F2 1194
10 TraesCS5B01G304700 chr3B 475262797 475263969 1172 False 1823 1823 94.556000 712 1903 1 chr3B.!!$F1 1191
11 TraesCS5B01G304700 chr4A 690151685 690152869 1184 False 1773 1773 93.924000 732 1898 1 chr4A.!!$F1 1166
12 TraesCS5B01G304700 chr2B 77815634 77816819 1185 False 1753 1753 93.444000 712 1898 1 chr2B.!!$F1 1186
13 TraesCS5B01G304700 chr5A 513208667 513211734 3067 True 721 1109 88.561667 77 2579 3 chr5A.!!$R1 2502

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
534 546 0.172578 TTCTCTCGTACACGGCCATG 59.827 55.0 2.24 0.0 40.29 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 3818 0.038067 CGGTGACCGGAACATGTACA 60.038 55.0 17.8 0.0 44.15 2.9 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
21 22 4.972514 GGAAGATCTTAGCTTTTGGTGG 57.027 45.455 8.25 0.00 0.00 4.61
22 23 4.336280 GGAAGATCTTAGCTTTTGGTGGT 58.664 43.478 8.25 0.00 0.00 4.16
23 24 5.497474 GGAAGATCTTAGCTTTTGGTGGTA 58.503 41.667 8.25 0.00 0.00 3.25
24 25 6.122964 GGAAGATCTTAGCTTTTGGTGGTAT 58.877 40.000 8.25 0.00 0.00 2.73
25 26 6.261158 GGAAGATCTTAGCTTTTGGTGGTATC 59.739 42.308 8.25 0.00 0.00 2.24
26 27 6.567602 AGATCTTAGCTTTTGGTGGTATCT 57.432 37.500 0.00 0.00 0.00 1.98
27 28 6.963322 AGATCTTAGCTTTTGGTGGTATCTT 58.037 36.000 0.00 0.00 0.00 2.40
28 29 7.051000 AGATCTTAGCTTTTGGTGGTATCTTC 58.949 38.462 0.00 0.00 0.00 2.87
29 30 5.175859 TCTTAGCTTTTGGTGGTATCTTCG 58.824 41.667 0.00 0.00 0.00 3.79
30 31 3.695830 AGCTTTTGGTGGTATCTTCGA 57.304 42.857 0.00 0.00 0.00 3.71
31 32 4.222124 AGCTTTTGGTGGTATCTTCGAT 57.778 40.909 0.00 0.00 0.00 3.59
32 33 4.589908 AGCTTTTGGTGGTATCTTCGATT 58.410 39.130 0.00 0.00 0.00 3.34
33 34 4.396166 AGCTTTTGGTGGTATCTTCGATTG 59.604 41.667 0.00 0.00 0.00 2.67
34 35 4.662145 CTTTTGGTGGTATCTTCGATTGC 58.338 43.478 0.00 0.00 0.00 3.56
35 36 3.342377 TTGGTGGTATCTTCGATTGCA 57.658 42.857 0.00 0.00 0.00 4.08
36 37 2.627945 TGGTGGTATCTTCGATTGCAC 58.372 47.619 0.00 0.00 0.00 4.57
37 38 2.027653 TGGTGGTATCTTCGATTGCACA 60.028 45.455 0.00 0.00 0.00 4.57
38 39 3.206150 GGTGGTATCTTCGATTGCACAT 58.794 45.455 0.00 0.00 0.00 3.21
39 40 3.627577 GGTGGTATCTTCGATTGCACATT 59.372 43.478 0.00 0.00 0.00 2.71
40 41 4.096382 GGTGGTATCTTCGATTGCACATTT 59.904 41.667 0.00 0.00 0.00 2.32
41 42 5.266242 GTGGTATCTTCGATTGCACATTTC 58.734 41.667 0.00 0.00 0.00 2.17
42 43 5.065218 GTGGTATCTTCGATTGCACATTTCT 59.935 40.000 0.00 0.00 0.00 2.52
43 44 5.647658 TGGTATCTTCGATTGCACATTTCTT 59.352 36.000 0.00 0.00 0.00 2.52
44 45 6.150976 TGGTATCTTCGATTGCACATTTCTTT 59.849 34.615 0.00 0.00 0.00 2.52
45 46 7.335673 TGGTATCTTCGATTGCACATTTCTTTA 59.664 33.333 0.00 0.00 0.00 1.85
46 47 7.640240 GGTATCTTCGATTGCACATTTCTTTAC 59.360 37.037 0.00 0.00 0.00 2.01
47 48 6.552859 TCTTCGATTGCACATTTCTTTACA 57.447 33.333 0.00 0.00 0.00 2.41
48 49 6.964908 TCTTCGATTGCACATTTCTTTACAA 58.035 32.000 0.00 0.00 0.00 2.41
49 50 7.592938 TCTTCGATTGCACATTTCTTTACAAT 58.407 30.769 0.00 0.00 0.00 2.71
50 51 8.081633 TCTTCGATTGCACATTTCTTTACAATT 58.918 29.630 0.00 0.00 0.00 2.32
51 52 7.565450 TCGATTGCACATTTCTTTACAATTG 57.435 32.000 3.24 3.24 32.55 2.32
52 53 7.144661 TCGATTGCACATTTCTTTACAATTGT 58.855 30.769 16.68 16.68 32.92 2.71
53 54 7.325821 TCGATTGCACATTTCTTTACAATTGTC 59.674 33.333 15.85 0.00 32.92 3.18
54 55 7.410728 CGATTGCACATTTCTTTACAATTGTCC 60.411 37.037 15.85 0.00 0.00 4.02
55 56 6.154203 TGCACATTTCTTTACAATTGTCCA 57.846 33.333 15.85 0.00 0.00 4.02
56 57 5.982516 TGCACATTTCTTTACAATTGTCCAC 59.017 36.000 15.85 0.00 0.00 4.02
57 58 6.183360 TGCACATTTCTTTACAATTGTCCACT 60.183 34.615 15.85 0.00 0.00 4.00
58 59 6.144402 GCACATTTCTTTACAATTGTCCACTG 59.856 38.462 15.85 7.47 0.00 3.66
59 60 7.424803 CACATTTCTTTACAATTGTCCACTGA 58.575 34.615 15.85 5.11 0.00 3.41
60 61 7.920151 CACATTTCTTTACAATTGTCCACTGAA 59.080 33.333 15.85 10.60 0.00 3.02
61 62 8.474025 ACATTTCTTTACAATTGTCCACTGAAA 58.526 29.630 15.85 17.55 0.00 2.69
62 63 9.480053 CATTTCTTTACAATTGTCCACTGAAAT 57.520 29.630 15.85 18.74 32.76 2.17
63 64 9.696917 ATTTCTTTACAATTGTCCACTGAAATC 57.303 29.630 15.85 0.00 0.00 2.17
64 65 8.463930 TTCTTTACAATTGTCCACTGAAATCT 57.536 30.769 15.85 0.00 0.00 2.40
65 66 9.567776 TTCTTTACAATTGTCCACTGAAATCTA 57.432 29.630 15.85 0.00 0.00 1.98
66 67 9.567776 TCTTTACAATTGTCCACTGAAATCTAA 57.432 29.630 15.85 0.00 0.00 2.10
70 71 8.237811 ACAATTGTCCACTGAAATCTAAAAGT 57.762 30.769 4.92 0.00 0.00 2.66
71 72 8.695456 ACAATTGTCCACTGAAATCTAAAAGTT 58.305 29.630 4.92 0.00 0.00 2.66
72 73 9.185192 CAATTGTCCACTGAAATCTAAAAGTTC 57.815 33.333 0.00 0.00 0.00 3.01
73 74 7.873719 TTGTCCACTGAAATCTAAAAGTTCA 57.126 32.000 0.00 0.00 0.00 3.18
74 75 8.463930 TTGTCCACTGAAATCTAAAAGTTCAT 57.536 30.769 0.00 0.00 31.21 2.57
75 76 9.567776 TTGTCCACTGAAATCTAAAAGTTCATA 57.432 29.630 0.00 0.00 31.21 2.15
98 99 6.420913 AATAGTTAGATACCAGCGGAACAT 57.579 37.500 1.50 0.00 0.00 2.71
104 105 1.053424 TACCAGCGGAACATATCCCC 58.947 55.000 1.50 0.00 46.39 4.81
112 118 1.160137 GAACATATCCCCGCATGAGC 58.840 55.000 0.00 0.00 37.42 4.26
114 120 1.376086 CATATCCCCGCATGAGCCA 59.624 57.895 0.00 0.00 37.52 4.75
118 124 0.397535 ATCCCCGCATGAGCCAAATT 60.398 50.000 0.00 0.00 37.52 1.82
120 126 1.142314 CCCGCATGAGCCAAATTGG 59.858 57.895 7.84 7.84 41.55 3.16
121 127 1.606885 CCCGCATGAGCCAAATTGGT 61.607 55.000 14.17 0.20 40.46 3.67
127 133 2.079170 TGAGCCAAATTGGTTCCACA 57.921 45.000 23.01 5.63 45.78 4.17
129 135 0.673437 AGCCAAATTGGTTCCACACG 59.327 50.000 14.17 0.00 40.46 4.49
133 139 3.305744 GCCAAATTGGTTCCACACGTAAT 60.306 43.478 14.17 0.00 40.46 1.89
135 141 5.565045 GCCAAATTGGTTCCACACGTAATAA 60.565 40.000 14.17 0.00 40.46 1.40
136 142 6.626302 CCAAATTGGTTCCACACGTAATAAT 58.374 36.000 3.34 0.00 31.35 1.28
144 150 7.279090 TGGTTCCACACGTAATAATAGATGTTG 59.721 37.037 0.00 0.00 0.00 3.33
148 154 6.204688 CCACACGTAATAATAGATGTTGCCAT 59.795 38.462 0.00 0.00 0.00 4.40
153 159 7.042051 ACGTAATAATAGATGTTGCCATGACAC 60.042 37.037 0.00 0.00 0.00 3.67
159 165 4.084287 AGATGTTGCCATGACACAAGATT 58.916 39.130 0.00 0.00 30.68 2.40
164 170 1.678101 GCCATGACACAAGATTAGGGC 59.322 52.381 0.00 0.00 0.00 5.19
174 180 5.484998 ACACAAGATTAGGGCCAATCAAATT 59.515 36.000 22.28 11.14 37.38 1.82
176 182 5.129320 ACAAGATTAGGGCCAATCAAATTCC 59.871 40.000 22.28 3.65 37.38 3.01
178 184 1.398692 TAGGGCCAATCAAATTCCGC 58.601 50.000 6.18 0.00 0.00 5.54
179 185 1.143838 GGGCCAATCAAATTCCGCC 59.856 57.895 4.39 0.00 35.14 6.13
183 189 1.204467 GCCAATCAAATTCCGCCTGAA 59.796 47.619 0.00 0.00 37.38 3.02
184 190 2.159057 GCCAATCAAATTCCGCCTGAAT 60.159 45.455 0.00 0.00 45.75 2.57
185 191 3.450578 CCAATCAAATTCCGCCTGAATG 58.549 45.455 0.00 0.00 42.97 2.67
197 203 3.185188 CCGCCTGAATGAATATTCGACAG 59.815 47.826 19.88 19.88 44.55 3.51
202 208 5.221521 CCTGAATGAATATTCGACAGGGAGA 60.222 44.000 28.39 7.71 44.55 3.71
208 214 0.970937 ATTCGACAGGGAGAAGCCGA 60.971 55.000 0.00 0.00 37.63 5.54
209 215 1.595993 TTCGACAGGGAGAAGCCGAG 61.596 60.000 0.00 0.00 37.63 4.63
210 216 2.185608 GACAGGGAGAAGCCGAGC 59.814 66.667 0.00 0.00 37.63 5.03
211 217 2.604686 ACAGGGAGAAGCCGAGCA 60.605 61.111 0.00 0.00 37.63 4.26
213 219 2.604686 AGGGAGAAGCCGAGCACA 60.605 61.111 0.00 0.00 37.63 4.57
214 220 1.992277 AGGGAGAAGCCGAGCACAT 60.992 57.895 0.00 0.00 37.63 3.21
216 222 2.467826 GGAGAAGCCGAGCACATGC 61.468 63.158 0.00 0.00 42.49 4.06
227 239 2.377310 GCACATGCGCAAGGCTTTG 61.377 57.895 17.11 9.94 44.05 2.77
229 241 0.598158 CACATGCGCAAGGCTTTGTT 60.598 50.000 17.11 0.00 44.05 2.83
234 246 0.854705 GCGCAAGGCTTTGTTCTTTG 59.145 50.000 10.54 0.00 39.11 2.77
236 248 1.854126 CGCAAGGCTTTGTTCTTTGTG 59.146 47.619 10.54 0.00 36.65 3.33
239 251 3.260740 CAAGGCTTTGTTCTTTGTGCAA 58.739 40.909 0.00 0.00 0.00 4.08
241 253 1.933181 GGCTTTGTTCTTTGTGCAACC 59.067 47.619 0.00 0.00 34.36 3.77
259 271 7.151976 GTGCAACCTGTAAATAATGGAACTTT 58.848 34.615 0.00 0.00 0.00 2.66
260 272 7.116233 GTGCAACCTGTAAATAATGGAACTTTG 59.884 37.037 0.00 0.00 0.00 2.77
263 275 8.356657 CAACCTGTAAATAATGGAACTTTGACA 58.643 33.333 0.00 0.00 0.00 3.58
266 278 7.807907 CCTGTAAATAATGGAACTTTGACACAC 59.192 37.037 0.00 0.00 0.00 3.82
267 279 8.226819 TGTAAATAATGGAACTTTGACACACA 57.773 30.769 0.00 0.00 0.00 3.72
268 280 8.687242 TGTAAATAATGGAACTTTGACACACAA 58.313 29.630 0.00 0.00 36.65 3.33
269 281 8.964150 GTAAATAATGGAACTTTGACACACAAC 58.036 33.333 0.00 0.00 38.29 3.32
271 283 2.796557 TGGAACTTTGACACACAACCA 58.203 42.857 0.00 0.00 38.29 3.67
272 284 2.490115 TGGAACTTTGACACACAACCAC 59.510 45.455 0.00 0.00 38.29 4.16
273 285 2.752903 GGAACTTTGACACACAACCACT 59.247 45.455 0.00 0.00 38.29 4.00
274 286 3.427503 GGAACTTTGACACACAACCACTG 60.428 47.826 0.00 0.00 38.29 3.66
287 299 5.702670 ACACAACCACTGATATTGTTCAGAG 59.297 40.000 8.36 0.70 44.88 3.35
297 309 5.920840 TGATATTGTTCAGAGCTATACACGC 59.079 40.000 0.00 0.00 0.00 5.34
299 311 3.150848 TGTTCAGAGCTATACACGCAG 57.849 47.619 0.00 0.00 0.00 5.18
303 315 0.671251 AGAGCTATACACGCAGAGGC 59.329 55.000 0.00 0.00 0.00 4.70
304 316 0.319125 GAGCTATACACGCAGAGGCC 60.319 60.000 0.00 0.00 36.38 5.19
312 324 1.228552 ACGCAGAGGCCCACAAATT 60.229 52.632 0.00 0.00 36.38 1.82
319 331 4.060205 CAGAGGCCCACAAATTCTTTTTG 58.940 43.478 0.00 0.00 35.64 2.44
327 339 4.270808 CCACAAATTCTTTTTGACAGTGGC 59.729 41.667 5.17 0.00 33.83 5.01
344 356 0.592247 GGCTTTGACACACAAGCACG 60.592 55.000 11.44 0.00 39.77 5.34
349 361 0.809636 TGACACACAAGCACGACCTG 60.810 55.000 0.00 0.00 0.00 4.00
359 371 1.497278 CACGACCTGGCAAACGATG 59.503 57.895 12.91 0.00 0.00 3.84
360 372 1.671054 ACGACCTGGCAAACGATGG 60.671 57.895 12.91 1.06 0.00 3.51
366 378 0.734889 CTGGCAAACGATGGTCCATC 59.265 55.000 20.45 20.45 37.50 3.51
420 432 4.609995 GCAGCAAGCAATGGCATT 57.390 50.000 6.96 6.96 44.61 3.56
458 470 0.248417 CATCACTGAGCGTCTCTCCG 60.248 60.000 8.07 0.00 41.18 4.63
473 485 1.450531 CTCCGCCTCAATCCATTGGC 61.451 60.000 0.00 0.00 41.76 4.52
492 504 1.744368 ACTCATGCTTCGCAGCCAG 60.744 57.895 4.17 0.40 46.74 4.85
506 518 2.363172 GCCAGAGTCTCCCAGTCCC 61.363 68.421 0.00 0.00 0.00 4.46
534 546 0.172578 TTCTCTCGTACACGGCCATG 59.827 55.000 2.24 0.00 40.29 3.66
535 547 0.678684 TCTCTCGTACACGGCCATGA 60.679 55.000 5.45 0.00 40.29 3.07
553 565 2.807045 CTGAGCAGCACGACGTCC 60.807 66.667 10.58 0.00 0.00 4.79
610 622 4.314440 TGCACCTGCCTCCACGTC 62.314 66.667 0.00 0.00 41.18 4.34
622 634 2.742372 CACGTCCCCTTGAAGCCG 60.742 66.667 0.00 0.00 0.00 5.52
629 641 2.620112 CCCTTGAAGCCGCACACTG 61.620 63.158 0.00 0.00 0.00 3.66
662 674 3.423154 GCCGGTGCTTGAACTCCG 61.423 66.667 1.90 0.00 44.28 4.63
691 706 2.908015 GGCCACCGGATCAGCTTA 59.092 61.111 9.46 0.00 0.00 3.09
859 962 2.890474 CGGCGCGCTAGATTTGGT 60.890 61.111 32.29 0.00 0.00 3.67
887 991 2.354773 GCGCGCGCCTATAAGTCT 60.355 61.111 42.83 0.00 34.56 3.24
963 1067 3.158537 TTCGCACTCCACCGCTTCA 62.159 57.895 0.00 0.00 0.00 3.02
1912 3591 2.202610 TCTGAAGCCGCGTCATCG 60.203 61.111 9.53 0.00 40.37 3.84
1919 3598 2.503158 CCGCGTCATCGTCGTCAA 60.503 61.111 4.92 0.00 39.49 3.18
1939 3618 1.074319 CGGCAACATGAATGTGCAGC 61.074 55.000 0.00 11.31 41.61 5.25
1942 3621 1.333115 CAACATGAATGTGCAGCGTG 58.667 50.000 0.00 0.00 41.61 5.34
1945 3624 0.519792 CATGAATGTGCAGCGTGTCG 60.520 55.000 0.00 0.00 0.00 4.35
1949 3628 2.434658 AATGTGCAGCGTGTCGAGGA 62.435 55.000 0.00 0.00 0.00 3.71
1972 3651 4.537433 GCGGCCTCCAGCAGGTAG 62.537 72.222 0.00 0.00 45.61 3.18
2032 3711 3.175724 CGCAGCCTCTTCAGCTTG 58.824 61.111 0.00 0.00 38.95 4.01
2070 3749 4.760047 GCTCGGCGTGACCCACAT 62.760 66.667 13.77 0.00 33.40 3.21
2071 3750 2.047274 CTCGGCGTGACCCACATT 60.047 61.111 6.85 0.00 33.40 2.71
2072 3751 1.671054 CTCGGCGTGACCCACATTT 60.671 57.895 6.85 0.00 33.40 2.32
2073 3752 1.911293 CTCGGCGTGACCCACATTTG 61.911 60.000 6.85 0.00 33.40 2.32
2074 3753 2.961768 GGCGTGACCCACATTTGG 59.038 61.111 0.00 0.00 43.50 3.28
2088 3770 3.801068 TTTGGGGCCCAGTGAACCG 62.801 63.158 27.05 0.00 33.81 4.44
2091 3773 3.728373 GGGCCCAGTGAACCGGAT 61.728 66.667 19.95 0.00 0.00 4.18
2109 3791 0.553819 ATGACGAGGTCCTCTAGGCT 59.446 55.000 17.00 0.00 34.44 4.58
2110 3792 0.331954 TGACGAGGTCCTCTAGGCTT 59.668 55.000 17.00 0.00 34.44 4.35
2112 3794 0.684805 ACGAGGTCCTCTAGGCTTGG 60.685 60.000 17.00 1.21 34.44 3.61
2118 3800 0.032017 TCCTCTAGGCTTGGGAGGTC 60.032 60.000 21.64 0.00 44.85 3.85
2119 3801 1.051556 CCTCTAGGCTTGGGAGGTCC 61.052 65.000 17.24 0.00 41.04 4.46
2120 3802 0.325671 CTCTAGGCTTGGGAGGTCCA 60.326 60.000 0.00 0.00 45.43 4.02
2122 3804 0.471617 CTAGGCTTGGGAGGTCCATG 59.528 60.000 0.00 0.00 46.52 3.66
2125 3807 0.681243 GGCTTGGGAGGTCCATGAAC 60.681 60.000 0.00 0.00 46.52 3.18
2126 3808 0.329596 GCTTGGGAGGTCCATGAACT 59.670 55.000 0.00 0.00 46.52 3.01
2127 3809 1.272147 GCTTGGGAGGTCCATGAACTT 60.272 52.381 0.00 0.00 46.52 2.66
2129 3811 0.698238 TGGGAGGTCCATGAACTTGG 59.302 55.000 0.00 0.00 41.46 3.61
2130 3812 0.991920 GGGAGGTCCATGAACTTGGA 59.008 55.000 0.00 5.51 43.56 3.53
2132 3814 1.909302 GGAGGTCCATGAACTTGGAGA 59.091 52.381 9.22 0.00 46.31 3.71
2133 3815 2.093235 GGAGGTCCATGAACTTGGAGAG 60.093 54.545 9.22 0.00 46.31 3.20
2135 3817 1.065126 GGTCCATGAACTTGGAGAGGG 60.065 57.143 9.22 0.00 46.31 4.30
2136 3818 1.630878 GTCCATGAACTTGGAGAGGGT 59.369 52.381 9.22 0.00 46.31 4.34
2137 3819 1.630369 TCCATGAACTTGGAGAGGGTG 59.370 52.381 0.00 0.00 40.90 4.61
2138 3820 1.352352 CCATGAACTTGGAGAGGGTGT 59.648 52.381 0.00 0.00 39.25 4.16
2139 3821 2.571653 CCATGAACTTGGAGAGGGTGTA 59.428 50.000 0.00 0.00 39.25 2.90
2140 3822 3.600388 CATGAACTTGGAGAGGGTGTAC 58.400 50.000 0.00 0.00 0.00 2.90
2141 3823 2.684943 TGAACTTGGAGAGGGTGTACA 58.315 47.619 0.00 0.00 0.00 2.90
2142 3824 3.248024 TGAACTTGGAGAGGGTGTACAT 58.752 45.455 0.00 0.00 0.00 2.29
2143 3825 3.007940 TGAACTTGGAGAGGGTGTACATG 59.992 47.826 0.00 0.00 0.00 3.21
2144 3826 2.621070 ACTTGGAGAGGGTGTACATGT 58.379 47.619 2.69 2.69 0.00 3.21
2146 3828 3.008049 ACTTGGAGAGGGTGTACATGTTC 59.992 47.826 2.30 0.00 0.00 3.18
2147 3829 1.906574 TGGAGAGGGTGTACATGTTCC 59.093 52.381 2.30 2.46 0.00 3.62
2148 3830 1.134788 GGAGAGGGTGTACATGTTCCG 60.135 57.143 2.30 0.00 0.00 4.30
2149 3831 0.902531 AGAGGGTGTACATGTTCCGG 59.097 55.000 2.30 0.00 0.00 5.14
2150 3832 0.611714 GAGGGTGTACATGTTCCGGT 59.388 55.000 2.30 0.00 0.00 5.28
2151 3833 0.611714 AGGGTGTACATGTTCCGGTC 59.388 55.000 2.30 0.00 0.00 4.79
2152 3834 0.322322 GGGTGTACATGTTCCGGTCA 59.678 55.000 2.30 2.56 0.00 4.02
2153 3835 1.435577 GGTGTACATGTTCCGGTCAC 58.564 55.000 2.30 0.00 0.00 3.67
2165 3847 4.530857 GGTCACCGGGAGCGATGG 62.531 72.222 6.32 0.00 33.78 3.51
2166 3848 3.771160 GTCACCGGGAGCGATGGT 61.771 66.667 6.32 0.00 36.10 3.55
2186 3886 3.109612 CTGGCGTCCTCGTCGTAGG 62.110 68.421 4.82 4.82 45.30 3.18
2199 3899 1.153823 CGTAGGTGAGGTTGAGGCG 60.154 63.158 0.00 0.00 0.00 5.52
2230 3930 2.048127 ACGGAGCCGAACTTGAGC 60.048 61.111 16.83 0.00 42.83 4.26
2232 3932 2.097038 CGGAGCCGAACTTGAGCTG 61.097 63.158 2.00 0.00 42.83 4.24
2236 3936 1.743252 GCCGAACTTGAGCTGGAGG 60.743 63.158 0.00 0.00 0.00 4.30
2297 3997 2.845550 CGCAGGTCGATCATCCCGA 61.846 63.158 0.00 0.00 41.67 5.14
2298 3998 1.006805 GCAGGTCGATCATCCCGAG 60.007 63.158 0.00 0.00 36.66 4.63
2304 4004 4.327885 GATCATCCCGAGCGTGTC 57.672 61.111 0.00 0.00 0.00 3.67
2332 4032 1.515952 CTCGACGAGCAGCTCCTTG 60.516 63.158 17.16 9.40 0.00 3.61
2338 4038 1.519719 GAGCAGCTCCTTGATCCGT 59.480 57.895 11.84 0.00 0.00 4.69
2342 4042 4.116878 GCTCCTTGATCCGTGAGC 57.883 61.111 10.49 10.49 42.89 4.26
2370 4070 2.479650 GACGACGAGACACCTCCG 59.520 66.667 0.00 0.00 36.04 4.63
2372 4072 3.054503 CGACGAGACACCTCCGGT 61.055 66.667 0.00 0.00 36.04 5.28
2373 4073 2.876219 GACGAGACACCTCCGGTC 59.124 66.667 0.00 0.00 36.04 4.79
2377 4077 3.343788 GAGACACCTCCGGTCGCAG 62.344 68.421 0.00 0.00 40.20 5.18
2429 4154 4.166011 GGCACGCCAAGATGACGC 62.166 66.667 2.36 0.00 35.81 5.19
2431 4156 2.434884 CACGCCAAGATGACGCCT 60.435 61.111 0.00 0.00 0.00 5.52
2484 4209 1.136147 CTTGCAAGACGAGCATGGC 59.864 57.895 22.31 0.00 42.33 4.40
2488 4213 2.169789 CAAGACGAGCATGGCGAGG 61.170 63.158 0.00 0.00 0.00 4.63
2527 4252 3.723348 GGCAGGTTCGCGTCCAAC 61.723 66.667 20.57 12.11 0.00 3.77
2528 4253 3.723348 GCAGGTTCGCGTCCAACC 61.723 66.667 17.85 17.85 43.38 3.77
2529 4254 3.047877 CAGGTTCGCGTCCAACCC 61.048 66.667 20.84 7.31 44.01 4.11
2530 4255 4.675029 AGGTTCGCGTCCAACCCG 62.675 66.667 20.84 0.00 44.01 5.28
2531 4256 4.668118 GGTTCGCGTCCAACCCGA 62.668 66.667 15.38 0.00 37.88 5.14
2532 4257 2.662527 GTTCGCGTCCAACCCGAA 60.663 61.111 5.77 0.00 38.49 4.30
2533 4258 2.356553 TTCGCGTCCAACCCGAAG 60.357 61.111 5.77 0.00 36.23 3.79
2556 4281 3.121030 CGGGGCGAAGTTGCTGAG 61.121 66.667 0.00 0.00 34.52 3.35
2557 4282 3.435186 GGGGCGAAGTTGCTGAGC 61.435 66.667 0.00 0.00 34.52 4.26
2558 4283 2.359230 GGGCGAAGTTGCTGAGCT 60.359 61.111 5.83 0.00 34.52 4.09
2559 4284 1.968540 GGGCGAAGTTGCTGAGCTT 60.969 57.895 5.83 0.00 34.52 3.74
2560 4285 1.518903 GGGCGAAGTTGCTGAGCTTT 61.519 55.000 5.83 0.00 34.52 3.51
2561 4286 1.156736 GGCGAAGTTGCTGAGCTTTA 58.843 50.000 5.83 0.00 34.52 1.85
2562 4287 1.129437 GGCGAAGTTGCTGAGCTTTAG 59.871 52.381 5.83 0.00 34.52 1.85
2563 4288 1.129437 GCGAAGTTGCTGAGCTTTAGG 59.871 52.381 5.83 0.00 0.00 2.69
2564 4289 1.129437 CGAAGTTGCTGAGCTTTAGGC 59.871 52.381 5.83 0.00 42.19 3.93
2576 4301 3.923017 GCTTTAGGCTTTTGAGCTTCA 57.077 42.857 0.00 0.00 38.06 3.02
2577 4302 3.569548 GCTTTAGGCTTTTGAGCTTCAC 58.430 45.455 0.00 0.00 38.06 3.18
2578 4303 3.254411 GCTTTAGGCTTTTGAGCTTCACT 59.746 43.478 0.00 0.00 38.06 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.336280 ACCACCAAAAGCTAAGATCTTCC 58.664 43.478 12.24 4.57 0.00 3.46
1 2 7.051000 AGATACCACCAAAAGCTAAGATCTTC 58.949 38.462 12.24 0.00 0.00 2.87
3 4 6.567602 AGATACCACCAAAAGCTAAGATCT 57.432 37.500 0.00 0.00 0.00 2.75
4 5 6.018669 CGAAGATACCACCAAAAGCTAAGATC 60.019 42.308 0.00 0.00 0.00 2.75
5 6 5.817816 CGAAGATACCACCAAAAGCTAAGAT 59.182 40.000 0.00 0.00 0.00 2.40
6 7 5.046878 TCGAAGATACCACCAAAAGCTAAGA 60.047 40.000 0.00 0.00 0.00 2.10
7 8 5.175859 TCGAAGATACCACCAAAAGCTAAG 58.824 41.667 0.00 0.00 0.00 2.18
8 9 5.155278 TCGAAGATACCACCAAAAGCTAA 57.845 39.130 0.00 0.00 0.00 3.09
9 10 4.811969 TCGAAGATACCACCAAAAGCTA 57.188 40.909 0.00 0.00 0.00 3.32
10 11 3.695830 TCGAAGATACCACCAAAAGCT 57.304 42.857 0.00 0.00 0.00 3.74
11 12 4.662145 CAATCGAAGATACCACCAAAAGC 58.338 43.478 0.00 0.00 45.12 3.51
12 13 4.155826 TGCAATCGAAGATACCACCAAAAG 59.844 41.667 0.00 0.00 45.12 2.27
13 14 4.075682 TGCAATCGAAGATACCACCAAAA 58.924 39.130 0.00 0.00 45.12 2.44
14 15 3.438781 GTGCAATCGAAGATACCACCAAA 59.561 43.478 0.00 0.00 45.12 3.28
15 16 3.006940 GTGCAATCGAAGATACCACCAA 58.993 45.455 0.00 0.00 45.12 3.67
16 17 2.027653 TGTGCAATCGAAGATACCACCA 60.028 45.455 0.00 0.00 45.12 4.17
17 18 2.627945 TGTGCAATCGAAGATACCACC 58.372 47.619 0.00 0.00 45.12 4.61
18 19 4.882671 AATGTGCAATCGAAGATACCAC 57.117 40.909 0.00 6.22 45.12 4.16
19 20 5.185454 AGAAATGTGCAATCGAAGATACCA 58.815 37.500 0.00 0.00 45.12 3.25
20 21 5.741388 AGAAATGTGCAATCGAAGATACC 57.259 39.130 0.00 0.00 45.12 2.73
21 22 8.175069 TGTAAAGAAATGTGCAATCGAAGATAC 58.825 33.333 0.00 0.00 45.12 2.24
22 23 8.262715 TGTAAAGAAATGTGCAATCGAAGATA 57.737 30.769 0.00 0.00 45.12 1.98
23 24 7.144722 TGTAAAGAAATGTGCAATCGAAGAT 57.855 32.000 0.00 0.00 45.12 2.40
24 25 6.552859 TGTAAAGAAATGTGCAATCGAAGA 57.447 33.333 0.00 0.00 45.75 2.87
25 26 7.801547 ATTGTAAAGAAATGTGCAATCGAAG 57.198 32.000 0.00 0.00 0.00 3.79
26 27 7.651304 ACAATTGTAAAGAAATGTGCAATCGAA 59.349 29.630 9.97 0.00 0.00 3.71
27 28 7.144661 ACAATTGTAAAGAAATGTGCAATCGA 58.855 30.769 9.97 0.00 0.00 3.59
28 29 7.337150 ACAATTGTAAAGAAATGTGCAATCG 57.663 32.000 9.97 0.00 0.00 3.34
29 30 7.384660 TGGACAATTGTAAAGAAATGTGCAATC 59.615 33.333 11.95 0.00 0.00 2.67
30 31 7.171337 GTGGACAATTGTAAAGAAATGTGCAAT 59.829 33.333 11.95 0.00 0.00 3.56
31 32 6.478344 GTGGACAATTGTAAAGAAATGTGCAA 59.522 34.615 11.95 0.00 0.00 4.08
32 33 5.982516 GTGGACAATTGTAAAGAAATGTGCA 59.017 36.000 11.95 0.00 0.00 4.57
33 34 6.144402 CAGTGGACAATTGTAAAGAAATGTGC 59.856 38.462 11.95 0.00 0.00 4.57
34 35 7.424803 TCAGTGGACAATTGTAAAGAAATGTG 58.575 34.615 11.95 0.57 0.00 3.21
35 36 7.581213 TCAGTGGACAATTGTAAAGAAATGT 57.419 32.000 11.95 0.00 0.00 2.71
36 37 8.870160 TTTCAGTGGACAATTGTAAAGAAATG 57.130 30.769 11.95 5.47 0.00 2.32
37 38 9.696917 GATTTCAGTGGACAATTGTAAAGAAAT 57.303 29.630 22.83 22.83 35.43 2.17
38 39 8.912988 AGATTTCAGTGGACAATTGTAAAGAAA 58.087 29.630 11.95 16.17 0.00 2.52
39 40 8.463930 AGATTTCAGTGGACAATTGTAAAGAA 57.536 30.769 11.95 8.86 0.00 2.52
40 41 9.567776 TTAGATTTCAGTGGACAATTGTAAAGA 57.432 29.630 11.95 3.02 0.00 2.52
44 45 9.349713 ACTTTTAGATTTCAGTGGACAATTGTA 57.650 29.630 11.95 0.00 0.00 2.41
45 46 8.237811 ACTTTTAGATTTCAGTGGACAATTGT 57.762 30.769 11.78 11.78 0.00 2.71
46 47 9.185192 GAACTTTTAGATTTCAGTGGACAATTG 57.815 33.333 3.24 3.24 0.00 2.32
47 48 8.912988 TGAACTTTTAGATTTCAGTGGACAATT 58.087 29.630 0.00 0.00 0.00 2.32
48 49 8.463930 TGAACTTTTAGATTTCAGTGGACAAT 57.536 30.769 0.00 0.00 0.00 2.71
49 50 7.873719 TGAACTTTTAGATTTCAGTGGACAA 57.126 32.000 0.00 0.00 0.00 3.18
50 51 9.567776 TTATGAACTTTTAGATTTCAGTGGACA 57.432 29.630 0.00 0.00 32.91 4.02
66 67 9.477484 CGCTGGTATCTAACTATTATGAACTTT 57.523 33.333 0.00 0.00 0.00 2.66
67 68 8.088981 CCGCTGGTATCTAACTATTATGAACTT 58.911 37.037 0.00 0.00 0.00 2.66
68 69 7.450634 TCCGCTGGTATCTAACTATTATGAACT 59.549 37.037 0.00 0.00 0.00 3.01
69 70 7.600065 TCCGCTGGTATCTAACTATTATGAAC 58.400 38.462 0.00 0.00 0.00 3.18
70 71 7.770366 TCCGCTGGTATCTAACTATTATGAA 57.230 36.000 0.00 0.00 0.00 2.57
71 72 7.231925 TGTTCCGCTGGTATCTAACTATTATGA 59.768 37.037 0.00 0.00 0.00 2.15
72 73 7.375834 TGTTCCGCTGGTATCTAACTATTATG 58.624 38.462 0.00 0.00 0.00 1.90
73 74 7.534723 TGTTCCGCTGGTATCTAACTATTAT 57.465 36.000 0.00 0.00 0.00 1.28
74 75 6.964807 TGTTCCGCTGGTATCTAACTATTA 57.035 37.500 0.00 0.00 0.00 0.98
75 76 5.864418 TGTTCCGCTGGTATCTAACTATT 57.136 39.130 0.00 0.00 0.00 1.73
81 82 3.767673 GGGATATGTTCCGCTGGTATCTA 59.232 47.826 0.00 0.00 46.52 1.98
91 92 0.034756 TCATGCGGGGATATGTTCCG 59.965 55.000 0.00 0.00 46.52 4.30
98 99 0.478072 ATTTGGCTCATGCGGGGATA 59.522 50.000 0.00 0.00 40.82 2.59
104 105 1.632422 GAACCAATTTGGCTCATGCG 58.368 50.000 15.49 0.00 42.67 4.73
107 113 2.299867 GTGTGGAACCAATTTGGCTCAT 59.700 45.455 18.14 2.85 42.67 2.90
112 118 3.992260 TTACGTGTGGAACCAATTTGG 57.008 42.857 14.02 14.02 45.02 3.28
114 120 8.795842 TCTATTATTACGTGTGGAACCAATTT 57.204 30.769 0.00 0.00 34.36 1.82
118 124 6.880484 ACATCTATTATTACGTGTGGAACCA 58.120 36.000 0.00 0.00 34.36 3.67
120 126 7.123830 GCAACATCTATTATTACGTGTGGAAC 58.876 38.462 0.00 0.00 37.35 3.62
121 127 6.259167 GGCAACATCTATTATTACGTGTGGAA 59.741 38.462 0.00 0.00 0.00 3.53
144 150 1.678101 GCCCTAATCTTGTGTCATGGC 59.322 52.381 0.00 0.00 0.00 4.40
148 154 3.010027 TGATTGGCCCTAATCTTGTGTCA 59.990 43.478 14.92 0.00 37.81 3.58
153 159 5.604565 GGAATTTGATTGGCCCTAATCTTG 58.395 41.667 14.92 0.00 37.81 3.02
159 165 1.398692 GCGGAATTTGATTGGCCCTA 58.601 50.000 0.00 0.00 0.00 3.53
164 170 3.130869 TCATTCAGGCGGAATTTGATTGG 59.869 43.478 10.25 0.00 43.76 3.16
174 180 3.181470 TGTCGAATATTCATTCAGGCGGA 60.181 43.478 15.57 0.00 40.61 5.54
176 182 3.185188 CCTGTCGAATATTCATTCAGGCG 59.815 47.826 24.38 9.13 40.61 5.52
178 184 4.960938 TCCCTGTCGAATATTCATTCAGG 58.039 43.478 26.58 26.58 40.61 3.86
179 185 5.847304 TCTCCCTGTCGAATATTCATTCAG 58.153 41.667 15.57 16.63 40.61 3.02
183 189 4.503991 GGCTTCTCCCTGTCGAATATTCAT 60.504 45.833 15.57 0.00 0.00 2.57
184 190 3.181465 GGCTTCTCCCTGTCGAATATTCA 60.181 47.826 15.57 0.39 0.00 2.57
185 191 3.394719 GGCTTCTCCCTGTCGAATATTC 58.605 50.000 5.30 5.30 0.00 1.75
197 203 1.817099 CATGTGCTCGGCTTCTCCC 60.817 63.158 0.00 0.00 0.00 4.30
208 214 2.567497 AAAGCCTTGCGCATGTGCT 61.567 52.632 29.79 23.83 41.38 4.40
209 215 2.048877 AAAGCCTTGCGCATGTGC 60.049 55.556 24.25 24.25 41.38 4.57
210 216 0.598158 AACAAAGCCTTGCGCATGTG 60.598 50.000 12.75 10.47 39.08 3.21
211 217 0.318955 GAACAAAGCCTTGCGCATGT 60.319 50.000 12.75 8.90 40.35 3.21
213 219 0.675633 AAGAACAAAGCCTTGCGCAT 59.324 45.000 12.75 0.00 41.38 4.73
214 220 0.459489 AAAGAACAAAGCCTTGCGCA 59.541 45.000 5.66 5.66 41.38 6.09
216 222 1.854126 CACAAAGAACAAAGCCTTGCG 59.146 47.619 0.00 0.00 35.84 4.85
223 235 3.848726 ACAGGTTGCACAAAGAACAAAG 58.151 40.909 0.00 0.00 0.00 2.77
227 239 7.116233 CCATTATTTACAGGTTGCACAAAGAAC 59.884 37.037 0.00 0.00 0.00 3.01
229 241 6.491745 TCCATTATTTACAGGTTGCACAAAGA 59.508 34.615 0.00 0.00 0.00 2.52
234 246 6.267496 AGTTCCATTATTTACAGGTTGCAC 57.733 37.500 0.00 0.00 0.00 4.57
236 248 7.328493 GTCAAAGTTCCATTATTTACAGGTTGC 59.672 37.037 0.00 0.00 0.00 4.17
239 251 7.504238 TGTGTCAAAGTTCCATTATTTACAGGT 59.496 33.333 0.00 0.00 0.00 4.00
241 253 8.349245 TGTGTGTCAAAGTTCCATTATTTACAG 58.651 33.333 0.00 0.00 0.00 2.74
259 271 4.713553 ACAATATCAGTGGTTGTGTGTCA 58.286 39.130 8.13 0.00 34.98 3.58
260 272 5.238432 TGAACAATATCAGTGGTTGTGTGTC 59.762 40.000 9.25 5.69 36.31 3.67
263 275 5.620206 TCTGAACAATATCAGTGGTTGTGT 58.380 37.500 9.25 0.00 45.65 3.72
266 278 4.940046 AGCTCTGAACAATATCAGTGGTTG 59.060 41.667 4.41 0.00 44.57 3.77
267 279 5.171339 AGCTCTGAACAATATCAGTGGTT 57.829 39.130 4.41 0.00 44.57 3.67
268 280 4.833478 AGCTCTGAACAATATCAGTGGT 57.167 40.909 4.41 5.01 45.65 4.16
269 281 7.383572 GTGTATAGCTCTGAACAATATCAGTGG 59.616 40.741 0.00 1.37 45.65 4.00
271 283 7.142021 CGTGTATAGCTCTGAACAATATCAGT 58.858 38.462 0.00 0.00 45.65 3.41
272 284 6.088749 GCGTGTATAGCTCTGAACAATATCAG 59.911 42.308 0.00 0.00 46.62 2.90
273 285 5.920840 GCGTGTATAGCTCTGAACAATATCA 59.079 40.000 0.00 0.00 0.00 2.15
274 286 5.920840 TGCGTGTATAGCTCTGAACAATATC 59.079 40.000 0.00 0.00 35.28 1.63
287 299 1.301009 GGGCCTCTGCGTGTATAGC 60.301 63.158 0.84 0.00 38.85 2.97
297 309 4.060205 CAAAAAGAATTTGTGGGCCTCTG 58.940 43.478 4.53 0.00 39.65 3.35
299 311 4.058124 GTCAAAAAGAATTTGTGGGCCTC 58.942 43.478 4.53 0.49 43.53 4.70
303 315 4.810491 CCACTGTCAAAAAGAATTTGTGGG 59.190 41.667 0.00 0.00 43.53 4.61
304 316 4.270808 GCCACTGTCAAAAAGAATTTGTGG 59.729 41.667 0.00 0.00 43.53 4.17
312 324 3.761218 TGTCAAAGCCACTGTCAAAAAGA 59.239 39.130 0.00 0.00 0.00 2.52
319 331 1.378531 TGTGTGTCAAAGCCACTGTC 58.621 50.000 0.00 0.00 33.92 3.51
327 339 1.268032 GGTCGTGCTTGTGTGTCAAAG 60.268 52.381 0.00 0.00 35.48 2.77
344 356 1.305930 GGACCATCGTTTGCCAGGTC 61.306 60.000 0.00 0.00 46.16 3.85
368 380 0.676736 TTGCGGTGATTTTTCCCCAC 59.323 50.000 0.00 0.00 0.00 4.61
384 396 4.337763 CTGCACATCTCGAATAGTTTTGC 58.662 43.478 0.00 0.00 0.00 3.68
420 432 1.063190 TGAGAAAGATCGAGGGGGCTA 60.063 52.381 0.00 0.00 0.00 3.93
492 504 0.321996 GTTGTGGGACTGGGAGACTC 59.678 60.000 0.00 0.00 0.00 3.36
506 518 1.616865 TGTACGAGAGAAGGGGTTGTG 59.383 52.381 0.00 0.00 0.00 3.33
534 546 2.049985 ACGTCGTGCTGCTCAGTC 60.050 61.111 0.00 0.00 0.00 3.51
535 547 2.049985 GACGTCGTGCTGCTCAGT 60.050 61.111 0.63 0.00 0.00 3.41
610 622 3.365265 GTGTGCGGCTTCAAGGGG 61.365 66.667 0.00 0.00 0.00 4.79
675 690 0.811616 CAGTAAGCTGATCCGGTGGC 60.812 60.000 0.00 1.78 45.28 5.01
1912 3591 0.584396 TTCATGTTGCCGTTGACGAC 59.416 50.000 4.91 0.00 43.02 4.34
1918 3597 0.672889 TGCACATTCATGTTGCCGTT 59.327 45.000 10.11 0.00 39.39 4.44
1919 3598 0.241749 CTGCACATTCATGTTGCCGT 59.758 50.000 10.11 0.00 39.39 5.68
1922 3601 0.387622 ACGCTGCACATTCATGTTGC 60.388 50.000 0.00 0.00 39.39 4.17
1924 3603 0.953727 ACACGCTGCACATTCATGTT 59.046 45.000 0.00 0.00 39.39 2.71
1925 3604 0.518636 GACACGCTGCACATTCATGT 59.481 50.000 0.00 0.00 42.84 3.21
1926 3605 0.519792 CGACACGCTGCACATTCATG 60.520 55.000 0.00 0.00 0.00 3.07
1927 3606 0.670239 TCGACACGCTGCACATTCAT 60.670 50.000 0.00 0.00 0.00 2.57
1939 3618 3.479269 GCGCCTTTCCTCGACACG 61.479 66.667 0.00 0.00 0.00 4.49
1966 3645 4.415332 ACGTGGACGCGCTACCTG 62.415 66.667 5.73 13.32 44.43 4.00
1968 3647 3.695022 ATCACGTGGACGCGCTACC 62.695 63.158 17.00 8.47 44.43 3.18
1972 3651 3.838795 GACATCACGTGGACGCGC 61.839 66.667 17.00 0.00 44.43 6.86
1975 3654 1.736645 GTGGGACATCACGTGGACG 60.737 63.158 17.00 6.97 44.52 4.79
1976 3655 4.278956 GTGGGACATCACGTGGAC 57.721 61.111 17.00 0.46 44.52 4.02
2015 3694 3.036783 GCAAGCTGAAGAGGCTGCG 62.037 63.158 0.00 0.00 40.19 5.18
2017 3696 2.045131 GGGCAAGCTGAAGAGGCTG 61.045 63.158 0.00 0.00 40.19 4.85
2020 3699 0.251077 AGTTGGGCAAGCTGAAGAGG 60.251 55.000 0.00 0.00 0.00 3.69
2054 3733 1.671054 AAATGTGGGTCACGCCGAG 60.671 57.895 0.00 0.00 37.14 4.63
2055 3734 1.963855 CAAATGTGGGTCACGCCGA 60.964 57.895 0.00 0.00 37.14 5.54
2056 3735 2.560861 CAAATGTGGGTCACGCCG 59.439 61.111 0.00 0.00 37.14 6.46
2065 3744 2.120274 ACTGGGCCCCAAATGTGG 59.880 61.111 22.27 0.00 45.53 4.17
2066 3745 0.831288 TTCACTGGGCCCCAAATGTG 60.831 55.000 22.27 19.11 30.80 3.21
2067 3746 0.831711 GTTCACTGGGCCCCAAATGT 60.832 55.000 22.27 7.51 30.80 2.71
2069 3748 1.229177 GGTTCACTGGGCCCCAAAT 60.229 57.895 22.27 0.00 30.80 2.32
2070 3749 2.200092 GGTTCACTGGGCCCCAAA 59.800 61.111 22.27 5.12 30.80 3.28
2071 3750 4.278513 CGGTTCACTGGGCCCCAA 62.279 66.667 22.27 3.59 30.80 4.12
2074 3753 3.728373 ATCCGGTTCACTGGGCCC 61.728 66.667 17.59 17.59 42.72 5.80
2075 3754 2.438434 CATCCGGTTCACTGGGCC 60.438 66.667 0.00 0.00 42.72 5.80
2076 3755 1.745489 GTCATCCGGTTCACTGGGC 60.745 63.158 0.00 0.00 42.72 5.36
2077 3756 1.447838 CGTCATCCGGTTCACTGGG 60.448 63.158 0.00 0.00 42.72 4.45
2080 3762 0.898789 ACCTCGTCATCCGGTTCACT 60.899 55.000 0.00 0.00 37.11 3.41
2088 3770 1.611519 CCTAGAGGACCTCGTCATCC 58.388 60.000 15.97 0.00 43.24 3.51
2091 3773 0.331954 AAGCCTAGAGGACCTCGTCA 59.668 55.000 15.97 4.73 37.39 4.35
2112 3794 1.909302 TCTCCAAGTTCATGGACCTCC 59.091 52.381 0.00 0.00 44.52 4.30
2118 3800 1.352352 ACACCCTCTCCAAGTTCATGG 59.648 52.381 0.00 0.00 42.12 3.66
2119 3801 2.867109 ACACCCTCTCCAAGTTCATG 57.133 50.000 0.00 0.00 0.00 3.07
2120 3802 3.248024 TGTACACCCTCTCCAAGTTCAT 58.752 45.455 0.00 0.00 0.00 2.57
2122 3804 3.008049 ACATGTACACCCTCTCCAAGTTC 59.992 47.826 0.00 0.00 0.00 3.01
2125 3807 3.600388 GAACATGTACACCCTCTCCAAG 58.400 50.000 0.00 0.00 0.00 3.61
2126 3808 2.304761 GGAACATGTACACCCTCTCCAA 59.695 50.000 0.00 0.00 0.00 3.53
2127 3809 1.906574 GGAACATGTACACCCTCTCCA 59.093 52.381 0.00 0.00 0.00 3.86
2129 3811 1.134788 CCGGAACATGTACACCCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
2130 3812 0.902531 CCGGAACATGTACACCCTCT 59.097 55.000 0.00 0.00 0.00 3.69
2132 3814 0.611714 GACCGGAACATGTACACCCT 59.388 55.000 9.46 0.00 0.00 4.34
2133 3815 0.322322 TGACCGGAACATGTACACCC 59.678 55.000 9.46 0.00 0.00 4.61
2135 3817 1.435577 GGTGACCGGAACATGTACAC 58.564 55.000 9.46 5.00 0.00 2.90
2136 3818 0.038067 CGGTGACCGGAACATGTACA 60.038 55.000 17.80 0.00 44.15 2.90
2137 3819 2.745728 CGGTGACCGGAACATGTAC 58.254 57.895 17.80 0.00 44.15 2.90
2160 3842 4.457496 AGGACGCCAGCACCATCG 62.457 66.667 5.81 0.00 0.00 3.84
2161 3843 2.512515 GAGGACGCCAGCACCATC 60.513 66.667 5.81 0.00 0.00 3.51
2168 3850 2.403987 CTACGACGAGGACGCCAG 59.596 66.667 0.00 0.00 43.96 4.85
2176 3876 1.130749 CTCAACCTCACCTACGACGAG 59.869 57.143 0.00 0.00 0.00 4.18
2210 3910 2.664851 CAAGTTCGGCTCCGTGCA 60.665 61.111 8.28 0.00 45.15 4.57
2216 3916 0.739112 CTCCAGCTCAAGTTCGGCTC 60.739 60.000 0.00 0.00 33.74 4.70
2246 3946 2.807045 CGAGAGGCTGACGTGCAC 60.807 66.667 6.82 6.82 34.04 4.57
2284 3984 1.658717 CACGCTCGGGATGATCGAC 60.659 63.158 0.00 0.00 38.45 4.20
2319 4019 1.591059 CGGATCAAGGAGCTGCTCG 60.591 63.158 22.25 3.19 0.00 5.03
2323 4023 0.809241 GCTCACGGATCAAGGAGCTG 60.809 60.000 18.80 0.00 46.95 4.24
2353 4053 2.479650 CGGAGGTGTCTCGTCGTC 59.520 66.667 0.00 0.00 40.85 4.20
2377 4077 0.104855 TGTATCTCATGTCCTGCGGC 59.895 55.000 0.00 0.00 0.00 6.53
2383 4083 2.224161 GGAGGTGCTGTATCTCATGTCC 60.224 54.545 8.29 0.00 38.35 4.02
2387 4087 1.415659 GCTGGAGGTGCTGTATCTCAT 59.584 52.381 8.29 0.00 38.35 2.90
2392 4117 2.187946 GCGCTGGAGGTGCTGTAT 59.812 61.111 0.00 0.00 46.82 2.29
2447 4172 3.630148 CATGCCGATGTCGACGCC 61.630 66.667 11.62 3.96 43.02 5.68
2449 4174 3.299585 GACATGCCGATGTCGACG 58.700 61.111 11.62 0.00 46.95 5.12
2472 4197 3.842923 CCCTCGCCATGCTCGTCT 61.843 66.667 5.68 0.00 0.00 4.18
2510 4235 3.723348 GTTGGACGCGAACCTGCC 61.723 66.667 15.93 4.49 0.00 4.85
2511 4236 3.723348 GGTTGGACGCGAACCTGC 61.723 66.667 15.93 12.07 38.81 4.85
2512 4237 3.047877 GGGTTGGACGCGAACCTG 61.048 66.667 22.76 0.00 41.07 4.00
2520 4245 4.675029 ACGCCTTCGGGTTGGACG 62.675 66.667 0.00 0.00 40.69 4.79
2521 4246 3.047877 CACGCCTTCGGGTTGGAC 61.048 66.667 0.00 0.00 40.69 4.02
2539 4264 3.121030 CTCAGCAACTTCGCCCCG 61.121 66.667 0.00 0.00 0.00 5.73
2540 4265 3.435186 GCTCAGCAACTTCGCCCC 61.435 66.667 0.00 0.00 0.00 5.80
2541 4266 1.518903 AAAGCTCAGCAACTTCGCCC 61.519 55.000 0.00 0.00 0.00 6.13
2542 4267 1.129437 CTAAAGCTCAGCAACTTCGCC 59.871 52.381 0.00 0.00 0.00 5.54
2543 4268 1.129437 CCTAAAGCTCAGCAACTTCGC 59.871 52.381 0.00 0.00 0.00 4.70
2544 4269 1.129437 GCCTAAAGCTCAGCAACTTCG 59.871 52.381 0.00 0.00 38.99 3.79
2545 4270 2.909863 GCCTAAAGCTCAGCAACTTC 57.090 50.000 0.00 0.00 38.99 3.01


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

AutoCloner maintained by Alex Coulton.