Multiple sequence alignment - TraesCS1A01G115200

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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 TraesCS1A01G115200 chr1A 100.000 5959 0 0 1 5959 119702774 119708732 0.000000e+00 11005.0
1 TraesCS1A01G115200 chr1A 89.327 431 34 10 339 767 119629250 119629670 1.140000e-146 531.0
2 TraesCS1A01G115200 chr1A 79.462 409 67 13 2741 3149 566120259 566120650 2.120000e-69 274.0
3 TraesCS1A01G115200 chr1B 92.994 4125 196 52 1874 5959 172002167 172006237 0.000000e+00 5930.0
4 TraesCS1A01G115200 chr1B 91.064 1231 52 27 469 1664 172000958 172002165 0.000000e+00 1611.0
5 TraesCS1A01G115200 chr1B 94.512 164 8 1 1 164 453232265 453232103 9.910000e-63 252.0
6 TraesCS1A01G115200 chr1B 77.778 414 52 25 2583 2964 558505769 558506174 1.010000e-52 219.0
7 TraesCS1A01G115200 chr1B 89.080 174 17 2 165 337 34997851 34998023 1.300000e-51 215.0
8 TraesCS1A01G115200 chr1B 87.027 185 22 2 165 347 170882891 170883075 2.180000e-49 207.0
9 TraesCS1A01G115200 chr1B 87.302 126 7 4 339 458 172000311 172000433 1.040000e-27 135.0
10 TraesCS1A01G115200 chr1B 85.484 124 16 2 2736 2858 317842568 317842446 1.740000e-25 128.0
11 TraesCS1A01G115200 chr1B 92.857 42 3 0 3460 3501 249204259 249204218 1.790000e-05 62.1
12 TraesCS1A01G115200 chr1B 92.683 41 3 0 3461 3501 398155948 398155908 6.450000e-05 60.2
13 TraesCS1A01G115200 chr1D 95.577 2894 110 9 2594 5480 112463996 112466878 0.000000e+00 4619.0
14 TraesCS1A01G115200 chr1D 92.824 2160 75 24 483 2602 112461398 112463517 0.000000e+00 3057.0
15 TraesCS1A01G115200 chr1D 91.636 275 18 5 5686 5959 112467162 112467432 5.640000e-100 375.0
16 TraesCS1A01G115200 chr1D 95.161 62 3 0 339 400 112461022 112461083 1.370000e-16 99.0
17 TraesCS1A01G115200 chr1D 95.833 48 0 2 401 448 112461343 112461388 6.400000e-10 76.8
18 TraesCS1A01G115200 chr4D 76.730 838 144 38 2418 3228 469873501 469872688 2.570000e-113 420.0
19 TraesCS1A01G115200 chr4D 80.309 259 34 12 2127 2380 461230278 461230524 4.740000e-41 180.0
20 TraesCS1A01G115200 chr4D 80.309 259 34 12 2127 2380 462629843 462630089 4.740000e-41 180.0
21 TraesCS1A01G115200 chr4D 79.537 259 36 12 2127 2380 475143885 475144131 1.030000e-37 169.0
22 TraesCS1A01G115200 chr4A 76.082 832 140 39 2418 3222 1716133 1716932 4.360000e-101 379.0
23 TraesCS1A01G115200 chr4A 75.156 801 123 37 2418 3183 707867756 707868515 2.090000e-79 307.0
24 TraesCS1A01G115200 chr4A 93.902 164 10 0 1 164 604850749 604850912 1.280000e-61 248.0
25 TraesCS1A01G115200 chr4A 77.586 232 39 11 2486 2716 485716953 485716734 1.740000e-25 128.0
26 TraesCS1A01G115200 chr2D 81.148 488 66 17 4494 4974 58759222 58759690 9.430000e-98 368.0
27 TraesCS1A01G115200 chr2D 78.405 514 59 19 1159 1661 57963843 57963371 2.720000e-73 287.0
28 TraesCS1A01G115200 chr2D 77.672 524 66 24 1156 1661 58755459 58755949 7.610000e-69 272.0
29 TraesCS1A01G115200 chr2D 94.512 164 9 0 1 164 621724607 621724770 2.760000e-63 254.0
30 TraesCS1A01G115200 chr2D 93.902 164 10 0 1 164 91047157 91047320 1.280000e-61 248.0
31 TraesCS1A01G115200 chr2D 80.342 234 30 5 2100 2328 86155773 86155551 4.780000e-36 163.0
32 TraesCS1A01G115200 chr2D 92.857 112 7 1 3864 3975 91801331 91801441 1.720000e-35 161.0
33 TraesCS1A01G115200 chr2D 91.964 112 8 1 3864 3975 105649187 105649077 8.000000e-34 156.0
34 TraesCS1A01G115200 chr2B 80.943 488 67 17 4494 4974 91233316 91233784 4.390000e-96 363.0
35 TraesCS1A01G115200 chr2B 88.000 175 20 1 165 338 160434985 160434811 7.830000e-49 206.0
36 TraesCS1A01G115200 chr2B 88.000 175 20 1 165 338 399766088 399765914 7.830000e-49 206.0
37 TraesCS1A01G115200 chr2B 78.947 266 43 7 1156 1410 91226394 91226657 1.030000e-37 169.0
38 TraesCS1A01G115200 chr2B 95.050 101 4 1 3864 3964 155887741 155887840 2.220000e-34 158.0
39 TraesCS1A01G115200 chr2B 86.726 113 13 2 2747 2858 444507416 444507305 2.250000e-24 124.0
40 TraesCS1A01G115200 chr2A 81.087 460 65 11 4494 4949 58863630 58863189 1.230000e-91 348.0
41 TraesCS1A01G115200 chr2A 88.525 183 17 2 1479 1661 58905672 58905494 1.010000e-52 219.0
42 TraesCS1A01G115200 chr2A 84.302 172 21 6 1249 1420 58905863 58905698 4.780000e-36 163.0
43 TraesCS1A01G115200 chr5A 92.571 175 12 1 165 338 266516470 266516296 3.570000e-62 250.0
44 TraesCS1A01G115200 chr5A 93.902 164 10 0 1 164 266516582 266516419 1.280000e-61 248.0
45 TraesCS1A01G115200 chr5A 75.789 380 59 21 2742 3116 308541015 308541366 1.720000e-35 161.0
46 TraesCS1A01G115200 chr7B 93.902 164 10 0 1 164 8465604 8465767 1.280000e-61 248.0
47 TraesCS1A01G115200 chr7B 93.902 164 10 0 1 164 721551114 721551277 1.280000e-61 248.0
48 TraesCS1A01G115200 chr7B 78.133 407 75 11 3724 4125 502787776 502787379 4.610000e-61 246.0
49 TraesCS1A01G115200 chr7B 80.328 244 34 13 3660 3900 193805849 193805617 7.940000e-39 172.0
50 TraesCS1A01G115200 chr7B 92.857 112 7 1 3864 3975 610324922 610325032 1.720000e-35 161.0
51 TraesCS1A01G115200 chr7B 91.071 112 9 1 3864 3975 146977985 146978095 3.720000e-32 150.0
52 TraesCS1A01G115200 chr7B 97.222 36 1 0 3460 3495 8639909 8639944 1.790000e-05 62.1
53 TraesCS1A01G115200 chr7B 92.683 41 3 0 3461 3501 627033045 627033005 6.450000e-05 60.2
54 TraesCS1A01G115200 chr5B 93.902 164 10 0 1 164 100353253 100353090 1.280000e-61 248.0
55 TraesCS1A01G115200 chr5B 93.902 164 10 0 1 164 350492521 350492684 1.280000e-61 248.0
56 TraesCS1A01G115200 chr5B 88.372 172 18 2 165 335 710807759 710807589 7.830000e-49 206.0
57 TraesCS1A01G115200 chr5B 80.695 259 33 13 2127 2380 703101347 703101101 1.020000e-42 185.0
58 TraesCS1A01G115200 chr5B 80.500 200 30 9 1674 1870 276914553 276914360 1.730000e-30 145.0
59 TraesCS1A01G115200 chrUn 89.080 174 17 2 165 337 290065346 290065518 1.300000e-51 215.0
60 TraesCS1A01G115200 chr6D 85.854 205 25 4 1674 1875 303623276 303623073 1.300000e-51 215.0
61 TraesCS1A01G115200 chr6D 75.429 350 57 18 2741 3087 420940126 420939803 6.230000e-30 143.0
62 TraesCS1A01G115200 chr6B 89.080 174 18 1 165 337 644650362 644650189 1.300000e-51 215.0
63 TraesCS1A01G115200 chr6B 84.390 205 28 4 1674 1875 469288131 469287928 1.310000e-46 198.0
64 TraesCS1A01G115200 chr6B 81.467 259 31 6 2127 2380 33647222 33646976 4.710000e-46 196.0
65 TraesCS1A01G115200 chr4B 82.996 247 25 10 2139 2380 617870839 617870605 2.180000e-49 207.0
66 TraesCS1A01G115200 chr7A 86.339 183 23 2 165 346 670537998 670537817 1.310000e-46 198.0
67 TraesCS1A01G115200 chr5D 81.405 242 34 10 3660 3900 565213600 565213369 2.840000e-43 187.0
68 TraesCS1A01G115200 chr5D 75.538 372 62 22 2741 3106 243077951 243077603 8.000000e-34 156.0
69 TraesCS1A01G115200 chr5D 73.890 383 67 21 2741 3121 505805981 505805630 8.110000e-24 122.0
70 TraesCS1A01G115200 chr5D 97.222 36 1 0 3460 3495 378337366 378337401 1.790000e-05 62.1
71 TraesCS1A01G115200 chr3D 80.309 259 32 14 2127 2380 459315198 459315442 1.710000e-40 178.0
72 TraesCS1A01G115200 chr3D 80.383 209 37 4 1666 1872 91675673 91675879 8.000000e-34 156.0
73 TraesCS1A01G115200 chr3D 81.977 172 25 6 1706 1873 231161572 231161403 2.240000e-29 141.0
74 TraesCS1A01G115200 chr3D 92.553 94 4 3 1291 1383 91225787 91225696 1.350000e-26 132.0
75 TraesCS1A01G115200 chr3A 82.759 203 30 5 1674 1873 298154814 298155014 6.140000e-40 176.0
76 TraesCS1A01G115200 chr3A 80.383 209 37 4 1666 1872 107741159 107741365 8.000000e-34 156.0
77 TraesCS1A01G115200 chr3A 84.921 126 17 2 2027 2151 107404406 107404282 6.270000e-25 126.0
78 TraesCS1A01G115200 chr3A 92.045 88 5 2 1297 1383 107404842 107404756 8.110000e-24 122.0
79 TraesCS1A01G115200 chr7D 80.508 236 36 7 3864 4095 22857702 22857473 7.940000e-39 172.0
80 TraesCS1A01G115200 chr7D 75.799 219 34 14 3239 3447 111790331 111790122 6.360000e-15 93.5
81 TraesCS1A01G115200 chr3B 79.424 243 38 11 3660 3900 242235381 242235149 1.720000e-35 161.0
82 TraesCS1A01G115200 chr3B 81.921 177 25 7 1698 1869 283599211 283599037 6.230000e-30 143.0
83 TraesCS1A01G115200 chr3B 91.489 94 5 3 1291 1383 140857532 140857441 6.270000e-25 126.0
84 TraesCS1A01G115200 chr3B 92.857 42 3 0 3460 3501 768985717 768985676 1.790000e-05 62.1


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 TraesCS1A01G115200 chr1A 119702774 119708732 5958 False 11005.000000 11005 100.000000 1 5959 1 chr1A.!!$F2 5958
1 TraesCS1A01G115200 chr1B 172000311 172006237 5926 False 2558.666667 5930 90.453333 339 5959 3 chr1B.!!$F4 5620
2 TraesCS1A01G115200 chr1D 112461022 112467432 6410 False 1645.360000 4619 94.206200 339 5959 5 chr1D.!!$F1 5620
3 TraesCS1A01G115200 chr4D 469872688 469873501 813 True 420.000000 420 76.730000 2418 3228 1 chr4D.!!$R1 810
4 TraesCS1A01G115200 chr4A 1716133 1716932 799 False 379.000000 379 76.082000 2418 3222 1 chr4A.!!$F1 804
5 TraesCS1A01G115200 chr4A 707867756 707868515 759 False 307.000000 307 75.156000 2418 3183 1 chr4A.!!$F3 765
6 TraesCS1A01G115200 chr2D 58755459 58759690 4231 False 320.000000 368 79.410000 1156 4974 2 chr2D.!!$F4 3818

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
449 716 0.168128 GGACGAAAACATGCGGAAGG 59.832 55.0 0.00 0.0 0.00 3.46 F
688 1470 0.179043 TCGACGAGAGAGGGAGATGG 60.179 60.0 0.00 0.0 0.00 3.51 F
883 1687 0.521291 CATTTCCAACGACGGCACAT 59.479 50.0 0.00 0.0 0.00 3.21 F
2276 3898 0.889306 AGTAGGTTCTCTCGTGCCAC 59.111 55.0 0.00 0.0 0.00 5.01 F
2947 5122 0.035725 TGTTGCTCTGCATCCTCCTG 60.036 55.0 0.00 0.0 38.76 3.86 F
3371 5546 0.038343 CCGGCTGGGTCATGTTTTTG 60.038 55.0 2.57 0.0 0.00 2.44 F
3977 6163 0.113972 TCCATTGGGCATTCACACCA 59.886 50.0 2.09 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 3897 0.539986 ACACAACTCCACCGACAAGT 59.460 50.000 0.0 0.0 0.00 3.16 R
2276 3898 1.330521 CAACACAACTCCACCGACAAG 59.669 52.381 0.0 0.0 0.00 3.16 R
2478 4101 2.203788 AAGGCCCTCTCGGACACA 60.204 61.111 0.0 0.0 45.73 3.72 R
3303 5478 0.034059 CTGACCGGCATCCCTCATAC 59.966 60.000 0.0 0.0 0.00 2.39 R
4271 6458 0.318869 CAATGGCTGCTTTCACGCAA 60.319 50.000 0.0 0.0 39.80 4.85 R
4721 7779 2.159627 GGATGACACGATGACAACAACC 59.840 50.000 0.0 0.0 0.00 3.77 R
5300 8360 2.189594 TCTGGATGCACTTGACTTGG 57.810 50.000 0.0 0.0 0.00 3.61 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
25 26 3.952174 GAACATTTTATGTGCGTGCAC 57.048 42.857 17.72 17.72 44.07 4.57
33 34 4.302154 GTGCGTGCACAAGGTTTC 57.698 55.556 19.45 0.00 45.53 2.78
34 35 1.654137 GTGCGTGCACAAGGTTTCG 60.654 57.895 19.45 0.61 45.53 3.46
35 36 2.051345 GCGTGCACAAGGTTTCGG 60.051 61.111 18.64 0.00 0.00 4.30
36 37 2.830285 GCGTGCACAAGGTTTCGGT 61.830 57.895 18.64 0.00 0.00 4.69
37 38 1.010125 CGTGCACAAGGTTTCGGTG 60.010 57.895 18.64 0.00 35.68 4.94
38 39 1.433053 CGTGCACAAGGTTTCGGTGA 61.433 55.000 18.64 0.00 34.52 4.02
39 40 0.736053 GTGCACAAGGTTTCGGTGAA 59.264 50.000 13.17 0.00 34.52 3.18
40 41 1.133407 GTGCACAAGGTTTCGGTGAAA 59.867 47.619 13.17 0.00 34.52 2.69
41 42 1.819288 TGCACAAGGTTTCGGTGAAAA 59.181 42.857 0.00 0.00 33.14 2.29
42 43 2.231478 TGCACAAGGTTTCGGTGAAAAA 59.769 40.909 0.00 0.00 33.14 1.94
43 44 2.601314 GCACAAGGTTTCGGTGAAAAAC 59.399 45.455 0.00 0.00 33.14 2.43
44 45 2.849473 CACAAGGTTTCGGTGAAAAACG 59.151 45.455 0.00 0.00 37.46 3.60
45 46 2.748532 ACAAGGTTTCGGTGAAAAACGA 59.251 40.909 0.00 0.00 37.46 3.85
46 47 3.103007 CAAGGTTTCGGTGAAAAACGAC 58.897 45.455 0.00 0.00 39.04 4.34
47 48 1.328374 AGGTTTCGGTGAAAAACGACG 59.672 47.619 0.00 0.00 39.04 5.12
48 49 1.062440 GGTTTCGGTGAAAAACGACGT 59.938 47.619 0.00 0.00 39.04 4.34
49 50 2.476018 GGTTTCGGTGAAAAACGACGTT 60.476 45.455 7.57 7.57 39.04 3.99
50 51 3.162831 GTTTCGGTGAAAAACGACGTTT 58.837 40.909 19.83 19.83 39.04 3.60
51 52 3.468304 TTCGGTGAAAAACGACGTTTT 57.532 38.095 28.19 28.19 45.94 2.43
95 96 9.638176 AAGATAAAGAAATGCCTCATGAATAGT 57.362 29.630 0.00 0.00 0.00 2.12
96 97 9.638176 AGATAAAGAAATGCCTCATGAATAGTT 57.362 29.630 0.00 0.00 0.00 2.24
106 107 7.483307 TGCCTCATGAATAGTTAAAATGAAGC 58.517 34.615 0.00 0.00 35.97 3.86
107 108 7.122501 TGCCTCATGAATAGTTAAAATGAAGCA 59.877 33.333 0.00 3.73 40.55 3.91
108 109 8.139989 GCCTCATGAATAGTTAAAATGAAGCAT 58.860 33.333 0.00 0.00 35.65 3.79
109 110 9.674824 CCTCATGAATAGTTAAAATGAAGCATC 57.325 33.333 0.00 0.00 0.00 3.91
110 111 9.674824 CTCATGAATAGTTAAAATGAAGCATCC 57.325 33.333 0.00 0.00 0.00 3.51
111 112 9.187996 TCATGAATAGTTAAAATGAAGCATCCA 57.812 29.630 0.00 0.00 0.00 3.41
112 113 9.806203 CATGAATAGTTAAAATGAAGCATCCAA 57.194 29.630 0.00 0.00 0.00 3.53
118 119 8.907222 AGTTAAAATGAAGCATCCAAAATTGT 57.093 26.923 0.00 0.00 0.00 2.71
119 120 8.992073 AGTTAAAATGAAGCATCCAAAATTGTC 58.008 29.630 0.00 0.00 0.00 3.18
120 121 8.992073 GTTAAAATGAAGCATCCAAAATTGTCT 58.008 29.630 0.00 0.00 0.00 3.41
121 122 9.558396 TTAAAATGAAGCATCCAAAATTGTCTT 57.442 25.926 0.00 0.00 0.00 3.01
122 123 8.454570 AAAATGAAGCATCCAAAATTGTCTTT 57.545 26.923 0.00 0.00 0.00 2.52
123 124 8.454570 AAATGAAGCATCCAAAATTGTCTTTT 57.545 26.923 0.00 0.00 0.00 2.27
124 125 8.454570 AATGAAGCATCCAAAATTGTCTTTTT 57.545 26.923 0.00 0.00 0.00 1.94
162 163 6.641176 AAAACATCGTTTTTCACTGAAACC 57.359 33.333 3.56 0.00 34.35 3.27
163 164 5.576447 AACATCGTTTTTCACTGAAACCT 57.424 34.783 3.56 0.00 34.35 3.50
164 165 6.687081 AACATCGTTTTTCACTGAAACCTA 57.313 33.333 3.56 0.00 34.35 3.08
165 166 6.687081 ACATCGTTTTTCACTGAAACCTAA 57.313 33.333 3.56 0.00 34.35 2.69
166 167 7.090953 ACATCGTTTTTCACTGAAACCTAAA 57.909 32.000 3.56 0.00 34.35 1.85
167 168 7.712797 ACATCGTTTTTCACTGAAACCTAAAT 58.287 30.769 3.56 0.00 34.35 1.40
168 169 8.194769 ACATCGTTTTTCACTGAAACCTAAATT 58.805 29.630 3.56 0.00 34.35 1.82
169 170 9.672086 CATCGTTTTTCACTGAAACCTAAATTA 57.328 29.630 3.56 0.00 34.35 1.40
222 223 3.423996 TTTTACCGAAACCTTGTGCAC 57.576 42.857 10.75 10.75 0.00 4.57
223 224 2.039818 TTACCGAAACCTTGTGCACA 57.960 45.000 17.42 17.42 0.00 4.57
224 225 1.301423 TACCGAAACCTTGTGCACAC 58.699 50.000 21.56 5.87 0.00 3.82
225 226 0.678366 ACCGAAACCTTGTGCACACA 60.678 50.000 21.56 10.18 39.98 3.72
238 239 3.233578 GTGCACACACATAAAATGTCCG 58.766 45.455 13.17 0.00 46.61 4.79
239 240 2.227626 TGCACACACATAAAATGTCCGG 59.772 45.455 0.00 0.00 42.70 5.14
240 241 2.486203 GCACACACATAAAATGTCCGGA 59.514 45.455 0.00 0.00 42.70 5.14
241 242 3.128589 GCACACACATAAAATGTCCGGAT 59.871 43.478 7.81 0.00 42.70 4.18
242 243 4.334203 GCACACACATAAAATGTCCGGATA 59.666 41.667 7.81 4.93 42.70 2.59
243 244 5.008613 GCACACACATAAAATGTCCGGATAT 59.991 40.000 7.81 7.95 42.70 1.63
244 245 6.203915 GCACACACATAAAATGTCCGGATATA 59.796 38.462 14.71 0.00 42.70 0.86
245 246 7.571244 GCACACACATAAAATGTCCGGATATAG 60.571 40.741 14.71 5.25 42.70 1.31
246 247 7.655732 CACACACATAAAATGTCCGGATATAGA 59.344 37.037 14.71 3.23 42.70 1.98
247 248 8.375506 ACACACATAAAATGTCCGGATATAGAT 58.624 33.333 14.71 5.46 42.70 1.98
248 249 8.659491 CACACATAAAATGTCCGGATATAGATG 58.341 37.037 14.71 17.87 42.70 2.90
249 250 7.334421 ACACATAAAATGTCCGGATATAGATGC 59.666 37.037 14.71 0.00 42.70 3.91
250 251 7.334171 CACATAAAATGTCCGGATATAGATGCA 59.666 37.037 14.71 1.47 42.70 3.96
251 252 7.882791 ACATAAAATGTCCGGATATAGATGCAA 59.117 33.333 14.71 0.00 39.92 4.08
252 253 6.808008 AAAATGTCCGGATATAGATGCAAG 57.192 37.500 14.71 0.00 0.00 4.01
253 254 5.745312 AATGTCCGGATATAGATGCAAGA 57.255 39.130 14.71 0.00 0.00 3.02
254 255 5.946942 ATGTCCGGATATAGATGCAAGAT 57.053 39.130 12.63 0.00 0.00 2.40
255 256 5.745312 TGTCCGGATATAGATGCAAGATT 57.255 39.130 7.81 0.00 0.00 2.40
256 257 6.114187 TGTCCGGATATAGATGCAAGATTT 57.886 37.500 7.81 0.00 0.00 2.17
257 258 6.533730 TGTCCGGATATAGATGCAAGATTTT 58.466 36.000 7.81 0.00 0.00 1.82
258 259 6.998074 TGTCCGGATATAGATGCAAGATTTTT 59.002 34.615 7.81 0.00 0.00 1.94
259 260 8.154203 TGTCCGGATATAGATGCAAGATTTTTA 58.846 33.333 7.81 0.00 0.00 1.52
260 261 9.167311 GTCCGGATATAGATGCAAGATTTTTAT 57.833 33.333 7.81 0.00 0.00 1.40
261 262 9.739276 TCCGGATATAGATGCAAGATTTTTATT 57.261 29.630 0.00 0.00 0.00 1.40
306 307 9.531942 TGAAATGTGTATTTTGATAATGGATGC 57.468 29.630 0.00 0.00 36.66 3.91
307 308 9.531942 GAAATGTGTATTTTGATAATGGATGCA 57.468 29.630 0.00 0.00 36.66 3.96
308 309 9.887629 AAATGTGTATTTTGATAATGGATGCAA 57.112 25.926 0.00 0.00 32.70 4.08
310 311 8.874744 TGTGTATTTTGATAATGGATGCAATG 57.125 30.769 0.00 0.00 0.00 2.82
311 312 7.927092 TGTGTATTTTGATAATGGATGCAATGG 59.073 33.333 0.00 0.00 0.00 3.16
312 313 8.143193 GTGTATTTTGATAATGGATGCAATGGA 58.857 33.333 0.00 0.00 0.00 3.41
313 314 8.872134 TGTATTTTGATAATGGATGCAATGGAT 58.128 29.630 0.00 0.00 0.00 3.41
314 315 9.362539 GTATTTTGATAATGGATGCAATGGATC 57.637 33.333 6.17 6.17 0.00 3.36
315 316 7.606135 TTTTGATAATGGATGCAATGGATCT 57.394 32.000 14.21 0.00 0.00 2.75
316 317 8.709272 TTTTGATAATGGATGCAATGGATCTA 57.291 30.769 14.21 8.98 0.00 1.98
317 318 7.933215 TTGATAATGGATGCAATGGATCTAG 57.067 36.000 14.21 0.00 0.00 2.43
318 319 6.420638 TGATAATGGATGCAATGGATCTAGG 58.579 40.000 14.21 0.00 0.00 3.02
319 320 6.216046 TGATAATGGATGCAATGGATCTAGGA 59.784 38.462 14.21 1.45 0.00 2.94
320 321 4.571369 ATGGATGCAATGGATCTAGGAG 57.429 45.455 14.21 0.00 0.00 3.69
321 322 2.039480 TGGATGCAATGGATCTAGGAGC 59.961 50.000 14.21 0.00 0.00 4.70
322 323 2.617532 GGATGCAATGGATCTAGGAGCC 60.618 54.545 14.21 0.00 38.78 4.70
328 329 0.839946 TGGATCTAGGAGCCAAAGGC 59.160 55.000 1.81 0.00 45.57 4.35
354 355 8.383619 CAATTACCGTCTCTCTTCATAGTTTTG 58.616 37.037 0.00 0.00 0.00 2.44
404 671 3.733024 TGATACACGCGGCTTAAAAAG 57.267 42.857 12.47 0.00 0.00 2.27
406 673 3.747010 TGATACACGCGGCTTAAAAAGAA 59.253 39.130 12.47 0.00 0.00 2.52
407 674 4.213694 TGATACACGCGGCTTAAAAAGAAA 59.786 37.500 12.47 0.00 0.00 2.52
408 675 2.994849 ACACGCGGCTTAAAAAGAAAG 58.005 42.857 12.47 0.00 0.00 2.62
449 716 0.168128 GGACGAAAACATGCGGAAGG 59.832 55.000 0.00 0.00 0.00 3.46
458 725 2.616458 ATGCGGAAGGGGAAGCCTT 61.616 57.895 0.00 0.00 0.00 4.35
460 727 1.451567 GCGGAAGGGGAAGCCTTAC 60.452 63.158 0.00 0.00 0.00 2.34
461 728 1.988015 CGGAAGGGGAAGCCTTACA 59.012 57.895 0.00 0.00 0.00 2.41
462 729 0.546598 CGGAAGGGGAAGCCTTACAT 59.453 55.000 0.00 0.00 0.00 2.29
463 730 1.747206 CGGAAGGGGAAGCCTTACATG 60.747 57.143 0.00 0.00 0.00 3.21
464 731 1.393603 GAAGGGGAAGCCTTACATGC 58.606 55.000 0.00 0.00 0.00 4.06
465 732 1.002857 AAGGGGAAGCCTTACATGCT 58.997 50.000 0.00 0.00 41.89 3.79
466 733 0.548510 AGGGGAAGCCTTACATGCTC 59.451 55.000 0.00 0.00 38.34 4.26
467 734 0.548510 GGGGAAGCCTTACATGCTCT 59.451 55.000 0.00 0.00 38.34 4.09
477 1258 1.725557 TACATGCTCTCCTCCGACGC 61.726 60.000 0.00 0.00 0.00 5.19
531 1313 5.713792 TGGCGGAATTTCAGTTTTTATCA 57.286 34.783 0.00 0.00 0.00 2.15
568 1350 1.332195 AAGTTCCAAGAAAGGGCTGC 58.668 50.000 0.00 0.00 0.00 5.25
570 1352 0.827507 GTTCCAAGAAAGGGCTGCCA 60.828 55.000 22.05 0.00 0.00 4.92
575 1357 0.618458 AAGAAAGGGCTGCCATCGTA 59.382 50.000 22.05 0.00 0.00 3.43
596 1378 1.071567 GAGAAAACCCGAGCGACGAG 61.072 60.000 0.00 0.00 45.77 4.18
652 1434 3.758973 TTTCCGCACCCGCACAAGA 62.759 57.895 0.00 0.00 38.40 3.02
687 1469 3.388272 TCGACGAGAGAGGGAGATG 57.612 57.895 0.00 0.00 0.00 2.90
688 1470 0.179043 TCGACGAGAGAGGGAGATGG 60.179 60.000 0.00 0.00 0.00 3.51
689 1471 1.791103 CGACGAGAGAGGGAGATGGC 61.791 65.000 0.00 0.00 0.00 4.40
693 1475 2.841988 GAGAGGGAGATGGCGGCT 60.842 66.667 11.43 0.00 0.00 5.52
695 1477 3.157252 GAGGGAGATGGCGGCTGA 61.157 66.667 11.43 0.00 0.00 4.26
723 1505 2.689771 TTTACCCCGCTCCCTCCC 60.690 66.667 0.00 0.00 0.00 4.30
724 1506 3.262778 TTTACCCCGCTCCCTCCCT 62.263 63.158 0.00 0.00 0.00 4.20
725 1507 3.691297 TTACCCCGCTCCCTCCCTC 62.691 68.421 0.00 0.00 0.00 4.30
883 1687 0.521291 CATTTCCAACGACGGCACAT 59.479 50.000 0.00 0.00 0.00 3.21
935 1739 3.785189 TAGATTTCCTCGCCGCGCC 62.785 63.158 8.21 0.00 0.00 6.53
975 1779 1.341531 CCGTGTGAGAGTCCAAGAACT 59.658 52.381 0.00 0.00 0.00 3.01
992 1796 4.316823 TGGACGGAGGAGCCAGGT 62.317 66.667 0.00 0.00 35.94 4.00
1039 1843 1.476110 CCTCCTCGTCCTACTCCTCTG 60.476 61.905 0.00 0.00 0.00 3.35
1421 2234 9.387397 ACATTTATTTCCCCTTTCTTCCTTTAA 57.613 29.630 0.00 0.00 0.00 1.52
1428 2241 6.499436 TCCCCTTTCTTCCTTTAATTTAGGG 58.501 40.000 0.00 0.00 39.59 3.53
1439 2252 8.801882 TCCTTTAATTTAGGGTTATCACACAG 57.198 34.615 6.49 0.00 33.41 3.66
1475 2288 5.474578 TGATCCTCCTAATCCAATCTTCG 57.525 43.478 0.00 0.00 0.00 3.79
1496 2323 3.120095 CGTTTGCATGTGACTGATGATGT 60.120 43.478 0.00 0.00 0.00 3.06
1649 2482 7.176690 CCTTCAACAGGTAACAACAAGGATAAT 59.823 37.037 0.00 0.00 37.99 1.28
1690 2523 6.866248 ACCCTTATTAAAAGTTTGCACGAATG 59.134 34.615 0.00 0.00 0.00 2.67
1703 2536 8.614346 AGTTTGCACGAATGTTAAAGTTACTTA 58.386 29.630 0.00 0.00 0.00 2.24
1744 3360 1.195448 GCCGGCAGATCAAATGTATCG 59.805 52.381 24.80 0.00 0.00 2.92
1797 3413 9.887862 ATATTATCATTTCTGATTGAAGGGGTT 57.112 29.630 0.00 0.00 42.23 4.11
1802 3418 7.010160 TCATTTCTGATTGAAGGGGTTAACTT 58.990 34.615 5.42 0.00 35.89 2.66
1854 3470 3.914435 TCTGTAAGCTTTTCTAGGGGGTT 59.086 43.478 3.20 0.00 0.00 4.11
2208 3830 5.874895 TGAAATGTGCAGAAAGAGATGAG 57.125 39.130 0.00 0.00 0.00 2.90
2275 3897 2.089980 GTAGTAGGTTCTCTCGTGCCA 58.910 52.381 0.00 0.00 0.00 4.92
2276 3898 0.889306 AGTAGGTTCTCTCGTGCCAC 59.111 55.000 0.00 0.00 0.00 5.01
2376 3998 3.959535 TCCAAATGTCAAAGGATTGGC 57.040 42.857 0.00 0.00 41.62 4.52
2398 4020 6.419413 TGGCGAAACATTGACTTTTTGATTAC 59.581 34.615 0.00 0.00 0.00 1.89
2723 4848 1.979693 GTCAGACTCCACCTCCGCT 60.980 63.158 0.00 0.00 0.00 5.52
2947 5122 0.035725 TGTTGCTCTGCATCCTCCTG 60.036 55.000 0.00 0.00 38.76 3.86
3011 5186 4.039092 AGGCCAGCTGCAATCCGT 62.039 61.111 8.66 0.00 43.89 4.69
3055 5230 0.756294 TCAAGGAGCTTGAACCGACA 59.244 50.000 0.00 0.00 45.84 4.35
3116 5291 2.758327 ATGGCTACAGGCGGACGA 60.758 61.111 0.00 0.00 44.42 4.20
3284 5459 3.177228 GTGTCTGGGCCTCCTCATATAT 58.823 50.000 4.53 0.00 0.00 0.86
3370 5545 2.350738 CCGGCTGGGTCATGTTTTT 58.649 52.632 2.57 0.00 0.00 1.94
3371 5546 0.038343 CCGGCTGGGTCATGTTTTTG 60.038 55.000 2.57 0.00 0.00 2.44
3416 5593 2.129146 CGTGGGCGTATAGGGGACA 61.129 63.158 0.00 0.00 0.00 4.02
3485 5662 9.561069 GGAATGTATCACACTATCCATTAGTTT 57.439 33.333 0.00 0.00 39.19 2.66
3528 5706 6.768381 CCACTCTGGAAAGAAAGAAACTAGTT 59.232 38.462 1.12 1.12 40.96 2.24
3618 5796 7.227512 GGAAGTGAGGTGTCAATTATGAATAGG 59.772 40.741 0.00 0.00 41.01 2.57
3651 5829 6.044682 AGGTTACAACTGTATACATTACCGC 58.955 40.000 5.91 0.00 32.20 5.68
3764 5942 5.654650 TCAAAACATTGGTTGTACTTCAGGT 59.345 36.000 0.00 0.00 37.68 4.00
3846 6032 4.165950 TGACTGCATATGTACTTTGGGGAT 59.834 41.667 4.29 0.00 0.00 3.85
3977 6163 0.113972 TCCATTGGGCATTCACACCA 59.886 50.000 2.09 0.00 0.00 4.17
4016 6202 3.265489 TCCTGAACCACTTTCCCCTTAT 58.735 45.455 0.00 0.00 32.58 1.73
4271 6458 4.652822 AGGGCGTAAATCTTCAAGAACTT 58.347 39.130 0.00 0.00 0.00 2.66
4484 7540 3.211045 ACCGCTTTCAGTGTACATGTTT 58.789 40.909 2.30 0.00 0.00 2.83
4565 7621 9.220767 GAAATTCAACTTCTACCACTTATCTGT 57.779 33.333 0.00 0.00 0.00 3.41
4721 7779 2.450160 GTTGCAAACTCTGTCAAACGG 58.550 47.619 0.00 0.00 45.32 4.44
4815 7873 9.838339 ACTTCATGACTAACCAATCCTATTTAG 57.162 33.333 0.00 0.00 0.00 1.85
5209 8269 5.064452 GCATGTACTCCTGAAAGTTCTGATG 59.936 44.000 0.00 0.00 0.00 3.07
5242 8302 5.072741 AGCCTTTTTGCAGTGATTCTCTTA 58.927 37.500 0.00 0.00 0.00 2.10
5251 8311 5.181811 TGCAGTGATTCTCTTAACATGTTGG 59.818 40.000 21.42 13.24 0.00 3.77
5254 8314 5.182001 AGTGATTCTCTTAACATGTTGGTGC 59.818 40.000 21.42 3.30 0.00 5.01
5424 8487 6.541111 AACGTTCAAGATTCTAACTTCCAC 57.459 37.500 0.00 0.00 0.00 4.02
5520 8602 8.727149 TCCCTAAAGATCAGTATCAATGGAATT 58.273 33.333 0.00 0.00 36.63 2.17
5536 8618 6.745794 ATGGAATTGAAAAGAAAACAGGGA 57.254 33.333 0.00 0.00 0.00 4.20
5537 8619 6.552445 TGGAATTGAAAAGAAAACAGGGAA 57.448 33.333 0.00 0.00 0.00 3.97
5538 8620 7.135591 TGGAATTGAAAAGAAAACAGGGAAT 57.864 32.000 0.00 0.00 0.00 3.01
5539 8621 6.991531 TGGAATTGAAAAGAAAACAGGGAATG 59.008 34.615 0.00 0.00 0.00 2.67
5540 8622 6.427853 GGAATTGAAAAGAAAACAGGGAATGG 59.572 38.462 0.00 0.00 0.00 3.16
5543 8625 6.745794 TGAAAAGAAAACAGGGAATGGAAT 57.254 33.333 0.00 0.00 0.00 3.01
5544 8626 7.135591 TGAAAAGAAAACAGGGAATGGAATT 57.864 32.000 0.00 0.00 40.93 2.17
5545 8627 7.572814 TGAAAAGAAAACAGGGAATGGAATTT 58.427 30.769 0.00 0.00 36.07 1.82
5546 8628 8.052141 TGAAAAGAAAACAGGGAATGGAATTTT 58.948 29.630 0.00 0.00 36.07 1.82
5547 8629 8.821686 AAAAGAAAACAGGGAATGGAATTTTT 57.178 26.923 0.00 0.00 36.07 1.94
5605 8719 8.597662 AAAACTGCGTATCTTGTAGAAAACTA 57.402 30.769 0.00 0.00 0.00 2.24
5940 9081 3.323979 AGGTGAGGCGAGAAAGAACTTTA 59.676 43.478 0.00 0.00 32.11 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.952174 GTGCACGCACATAAAATGTTC 57.048 42.857 17.03 0.00 45.53 3.18
16 17 1.654137 CGAAACCTTGTGCACGCAC 60.654 57.895 15.20 15.20 46.33 5.34
17 18 2.712539 CGAAACCTTGTGCACGCA 59.287 55.556 13.13 0.00 0.00 5.24
18 19 2.051345 CCGAAACCTTGTGCACGC 60.051 61.111 13.13 0.00 0.00 5.34
19 20 1.010125 CACCGAAACCTTGTGCACG 60.010 57.895 13.13 0.00 0.00 5.34
20 21 0.736053 TTCACCGAAACCTTGTGCAC 59.264 50.000 10.75 10.75 0.00 4.57
21 22 1.464734 TTTCACCGAAACCTTGTGCA 58.535 45.000 0.00 0.00 0.00 4.57
22 23 2.570442 TTTTCACCGAAACCTTGTGC 57.430 45.000 0.00 0.00 30.83 4.57
23 24 2.849473 CGTTTTTCACCGAAACCTTGTG 59.151 45.455 0.00 0.00 34.35 3.33
24 25 2.748532 TCGTTTTTCACCGAAACCTTGT 59.251 40.909 0.00 0.00 34.35 3.16
25 26 3.103007 GTCGTTTTTCACCGAAACCTTG 58.897 45.455 0.00 0.00 34.35 3.61
26 27 2.223089 CGTCGTTTTTCACCGAAACCTT 60.223 45.455 0.00 0.00 34.35 3.50
27 28 1.328374 CGTCGTTTTTCACCGAAACCT 59.672 47.619 0.00 0.00 34.35 3.50
28 29 1.062440 ACGTCGTTTTTCACCGAAACC 59.938 47.619 0.00 0.00 34.35 3.27
29 30 2.440560 ACGTCGTTTTTCACCGAAAC 57.559 45.000 0.00 0.00 34.47 2.78
30 31 3.468304 AAACGTCGTTTTTCACCGAAA 57.532 38.095 17.41 0.00 31.10 3.46
31 32 3.468304 AAAACGTCGTTTTTCACCGAA 57.532 38.095 26.23 0.00 42.11 4.30
69 70 9.638176 ACTATTCATGAGGCATTTCTTTATCTT 57.362 29.630 0.00 0.00 0.00 2.40
70 71 9.638176 AACTATTCATGAGGCATTTCTTTATCT 57.362 29.630 0.00 0.00 0.00 1.98
80 81 8.139989 GCTTCATTTTAACTATTCATGAGGCAT 58.860 33.333 9.05 0.00 43.11 4.40
81 82 7.483307 GCTTCATTTTAACTATTCATGAGGCA 58.517 34.615 9.05 0.00 43.11 4.75
82 83 7.483307 TGCTTCATTTTAACTATTCATGAGGC 58.517 34.615 7.42 7.42 43.61 4.70
83 84 9.674824 GATGCTTCATTTTAACTATTCATGAGG 57.325 33.333 0.00 0.00 0.00 3.86
84 85 9.674824 GGATGCTTCATTTTAACTATTCATGAG 57.325 33.333 0.00 0.00 0.00 2.90
85 86 9.187996 TGGATGCTTCATTTTAACTATTCATGA 57.812 29.630 1.64 0.00 0.00 3.07
86 87 9.806203 TTGGATGCTTCATTTTAACTATTCATG 57.194 29.630 1.64 0.00 0.00 3.07
92 93 9.995003 ACAATTTTGGATGCTTCATTTTAACTA 57.005 25.926 1.64 0.00 0.00 2.24
93 94 8.907222 ACAATTTTGGATGCTTCATTTTAACT 57.093 26.923 1.64 0.00 0.00 2.24
94 95 8.992073 AGACAATTTTGGATGCTTCATTTTAAC 58.008 29.630 1.64 0.00 0.00 2.01
95 96 9.558396 AAGACAATTTTGGATGCTTCATTTTAA 57.442 25.926 1.64 0.00 0.00 1.52
96 97 9.558396 AAAGACAATTTTGGATGCTTCATTTTA 57.442 25.926 1.64 0.00 0.00 1.52
97 98 8.454570 AAAGACAATTTTGGATGCTTCATTTT 57.545 26.923 1.64 0.00 0.00 1.82
98 99 8.454570 AAAAGACAATTTTGGATGCTTCATTT 57.545 26.923 1.64 0.00 0.00 2.32
99 100 8.454570 AAAAAGACAATTTTGGATGCTTCATT 57.545 26.923 1.64 0.00 31.55 2.57
138 139 6.871492 AGGTTTCAGTGAAAAACGATGTTTTT 59.129 30.769 19.63 17.47 37.46 1.94
139 140 6.394809 AGGTTTCAGTGAAAAACGATGTTTT 58.605 32.000 19.63 2.00 37.46 2.43
140 141 5.961272 AGGTTTCAGTGAAAAACGATGTTT 58.039 33.333 19.63 0.00 37.46 2.83
141 142 5.576447 AGGTTTCAGTGAAAAACGATGTT 57.424 34.783 19.63 0.00 37.46 2.71
142 143 6.687081 TTAGGTTTCAGTGAAAAACGATGT 57.313 33.333 19.63 3.71 37.46 3.06
143 144 8.574196 AATTTAGGTTTCAGTGAAAAACGATG 57.426 30.769 19.63 0.00 37.46 3.84
201 202 3.192844 TGTGCACAAGGTTTCGGTAAAAA 59.807 39.130 19.28 0.00 0.00 1.94
202 203 2.753452 TGTGCACAAGGTTTCGGTAAAA 59.247 40.909 19.28 0.00 0.00 1.52
203 204 2.097791 GTGTGCACAAGGTTTCGGTAAA 59.902 45.455 23.59 0.00 0.00 2.01
204 205 1.671845 GTGTGCACAAGGTTTCGGTAA 59.328 47.619 23.59 0.00 0.00 2.85
205 206 1.301423 GTGTGCACAAGGTTTCGGTA 58.699 50.000 23.59 0.00 0.00 4.02
206 207 0.678366 TGTGTGCACAAGGTTTCGGT 60.678 50.000 23.59 0.00 38.56 4.69
207 208 0.248458 GTGTGTGCACAAGGTTTCGG 60.248 55.000 23.59 0.00 43.77 4.30
208 209 3.234368 GTGTGTGCACAAGGTTTCG 57.766 52.632 23.59 0.00 43.77 3.46
217 218 3.233578 CGGACATTTTATGTGTGTGCAC 58.766 45.455 10.75 10.75 45.03 4.57
218 219 2.227626 CCGGACATTTTATGTGTGTGCA 59.772 45.455 0.00 0.00 45.03 4.57
219 220 2.486203 TCCGGACATTTTATGTGTGTGC 59.514 45.455 0.00 0.00 45.03 4.57
220 221 4.963276 ATCCGGACATTTTATGTGTGTG 57.037 40.909 6.12 0.00 45.03 3.82
221 222 7.732025 TCTATATCCGGACATTTTATGTGTGT 58.268 34.615 6.12 0.00 45.03 3.72
222 223 8.659491 CATCTATATCCGGACATTTTATGTGTG 58.341 37.037 6.12 0.00 45.03 3.82
223 224 7.334421 GCATCTATATCCGGACATTTTATGTGT 59.666 37.037 6.12 0.00 45.03 3.72
224 225 7.334171 TGCATCTATATCCGGACATTTTATGTG 59.666 37.037 6.12 3.32 45.03 3.21
226 227 7.848223 TGCATCTATATCCGGACATTTTATG 57.152 36.000 6.12 6.78 0.00 1.90
227 228 8.321353 TCTTGCATCTATATCCGGACATTTTAT 58.679 33.333 6.12 2.53 0.00 1.40
228 229 7.676004 TCTTGCATCTATATCCGGACATTTTA 58.324 34.615 6.12 0.00 0.00 1.52
229 230 6.533730 TCTTGCATCTATATCCGGACATTTT 58.466 36.000 6.12 0.00 0.00 1.82
230 231 6.114187 TCTTGCATCTATATCCGGACATTT 57.886 37.500 6.12 0.00 0.00 2.32
231 232 5.745312 TCTTGCATCTATATCCGGACATT 57.255 39.130 6.12 0.00 0.00 2.71
232 233 5.946942 ATCTTGCATCTATATCCGGACAT 57.053 39.130 6.12 2.01 0.00 3.06
233 234 5.745312 AATCTTGCATCTATATCCGGACA 57.255 39.130 6.12 0.00 0.00 4.02
234 235 7.440523 AAAAATCTTGCATCTATATCCGGAC 57.559 36.000 6.12 0.00 0.00 4.79
235 236 9.739276 AATAAAAATCTTGCATCTATATCCGGA 57.261 29.630 6.61 6.61 0.00 5.14
280 281 9.531942 GCATCCATTATCAAAATACACATTTCA 57.468 29.630 0.00 0.00 33.09 2.69
281 282 9.531942 TGCATCCATTATCAAAATACACATTTC 57.468 29.630 0.00 0.00 33.09 2.17
282 283 9.887629 TTGCATCCATTATCAAAATACACATTT 57.112 25.926 0.00 0.00 35.84 2.32
284 285 9.483916 CATTGCATCCATTATCAAAATACACAT 57.516 29.630 0.00 0.00 0.00 3.21
285 286 7.927092 CCATTGCATCCATTATCAAAATACACA 59.073 33.333 0.00 0.00 0.00 3.72
286 287 8.143193 TCCATTGCATCCATTATCAAAATACAC 58.857 33.333 0.00 0.00 0.00 2.90
287 288 8.247666 TCCATTGCATCCATTATCAAAATACA 57.752 30.769 0.00 0.00 0.00 2.29
288 289 9.362539 GATCCATTGCATCCATTATCAAAATAC 57.637 33.333 0.00 0.00 0.00 1.89
289 290 9.316594 AGATCCATTGCATCCATTATCAAAATA 57.683 29.630 0.00 0.00 0.00 1.40
290 291 8.202461 AGATCCATTGCATCCATTATCAAAAT 57.798 30.769 0.00 0.00 0.00 1.82
291 292 7.606135 AGATCCATTGCATCCATTATCAAAA 57.394 32.000 0.00 0.00 0.00 2.44
292 293 7.395206 CCTAGATCCATTGCATCCATTATCAAA 59.605 37.037 0.00 0.00 0.00 2.69
293 294 6.888088 CCTAGATCCATTGCATCCATTATCAA 59.112 38.462 0.00 0.00 0.00 2.57
294 295 6.216046 TCCTAGATCCATTGCATCCATTATCA 59.784 38.462 0.00 0.00 0.00 2.15
295 296 6.656902 TCCTAGATCCATTGCATCCATTATC 58.343 40.000 0.00 0.00 0.00 1.75
296 297 6.647461 TCCTAGATCCATTGCATCCATTAT 57.353 37.500 0.00 0.00 0.00 1.28
297 298 5.572271 GCTCCTAGATCCATTGCATCCATTA 60.572 44.000 0.00 0.00 0.00 1.90
298 299 4.810033 GCTCCTAGATCCATTGCATCCATT 60.810 45.833 0.00 0.00 0.00 3.16
299 300 3.308259 GCTCCTAGATCCATTGCATCCAT 60.308 47.826 0.00 0.00 0.00 3.41
300 301 2.039480 GCTCCTAGATCCATTGCATCCA 59.961 50.000 0.00 0.00 0.00 3.41
301 302 2.617532 GGCTCCTAGATCCATTGCATCC 60.618 54.545 0.00 0.00 0.00 3.51
302 303 2.039480 TGGCTCCTAGATCCATTGCATC 59.961 50.000 0.00 0.00 0.00 3.91
303 304 2.060275 TGGCTCCTAGATCCATTGCAT 58.940 47.619 0.00 0.00 0.00 3.96
304 305 1.510492 TGGCTCCTAGATCCATTGCA 58.490 50.000 0.00 0.00 0.00 4.08
305 306 2.645838 TTGGCTCCTAGATCCATTGC 57.354 50.000 0.00 0.00 27.57 3.56
306 307 3.484407 CCTTTGGCTCCTAGATCCATTG 58.516 50.000 0.00 0.00 27.57 2.82
307 308 2.158549 GCCTTTGGCTCCTAGATCCATT 60.159 50.000 0.73 0.00 46.69 3.16
308 309 1.423161 GCCTTTGGCTCCTAGATCCAT 59.577 52.381 0.73 0.00 46.69 3.41
309 310 0.839946 GCCTTTGGCTCCTAGATCCA 59.160 55.000 0.73 0.00 46.69 3.41
310 311 3.715871 GCCTTTGGCTCCTAGATCC 57.284 57.895 0.73 0.00 46.69 3.36
321 322 2.678336 GAGAGACGGTAATTGCCTTTGG 59.322 50.000 11.07 0.00 0.00 3.28
322 323 3.600388 AGAGAGACGGTAATTGCCTTTG 58.400 45.455 11.07 0.00 0.00 2.77
323 324 3.983044 AGAGAGACGGTAATTGCCTTT 57.017 42.857 11.07 0.00 0.00 3.11
324 325 3.260884 TGAAGAGAGACGGTAATTGCCTT 59.739 43.478 11.07 0.38 0.00 4.35
325 326 2.832129 TGAAGAGAGACGGTAATTGCCT 59.168 45.455 11.07 0.00 0.00 4.75
326 327 3.247006 TGAAGAGAGACGGTAATTGCC 57.753 47.619 1.83 1.83 0.00 4.52
327 328 5.593010 ACTATGAAGAGAGACGGTAATTGC 58.407 41.667 0.00 0.00 0.00 3.56
328 329 8.383619 CAAAACTATGAAGAGAGACGGTAATTG 58.616 37.037 0.00 0.00 0.00 2.32
329 330 8.311836 TCAAAACTATGAAGAGAGACGGTAATT 58.688 33.333 0.00 0.00 0.00 1.40
330 331 7.837863 TCAAAACTATGAAGAGAGACGGTAAT 58.162 34.615 0.00 0.00 0.00 1.89
331 332 7.223260 TCAAAACTATGAAGAGAGACGGTAA 57.777 36.000 0.00 0.00 0.00 2.85
332 333 6.127703 CCTCAAAACTATGAAGAGAGACGGTA 60.128 42.308 0.00 0.00 0.00 4.02
333 334 5.336849 CCTCAAAACTATGAAGAGAGACGGT 60.337 44.000 0.00 0.00 0.00 4.83
334 335 5.105752 CCTCAAAACTATGAAGAGAGACGG 58.894 45.833 0.00 0.00 0.00 4.79
335 336 4.564769 GCCTCAAAACTATGAAGAGAGACG 59.435 45.833 0.00 0.00 0.00 4.18
336 337 5.482908 TGCCTCAAAACTATGAAGAGAGAC 58.517 41.667 0.00 0.00 0.00 3.36
337 338 5.745312 TGCCTCAAAACTATGAAGAGAGA 57.255 39.130 0.00 0.00 0.00 3.10
354 355 4.256920 ACAATCAGAGTAACACATGCCTC 58.743 43.478 0.00 0.00 0.00 4.70
458 725 1.725557 GCGTCGGAGGAGAGCATGTA 61.726 60.000 1.18 0.00 0.00 2.29
460 727 2.279120 GCGTCGGAGGAGAGCATG 60.279 66.667 1.18 0.00 0.00 4.06
461 728 3.893763 CGCGTCGGAGGAGAGCAT 61.894 66.667 0.00 0.00 0.00 3.79
466 733 4.965858 GATCGCGCGTCGGAGGAG 62.966 72.222 30.98 0.00 39.05 3.69
568 1350 1.479323 TCGGGTTTTCTCCTACGATGG 59.521 52.381 0.00 0.00 0.00 3.51
570 1352 1.136500 GCTCGGGTTTTCTCCTACGAT 59.864 52.381 0.00 0.00 0.00 3.73
575 1357 1.292541 GTCGCTCGGGTTTTCTCCT 59.707 57.895 0.00 0.00 0.00 3.69
596 1378 1.172812 ACACTCGCTTTTTCTGGCCC 61.173 55.000 0.00 0.00 0.00 5.80
679 1461 3.474570 GTCAGCCGCCATCTCCCT 61.475 66.667 0.00 0.00 0.00 4.20
681 1463 3.453070 GAGGTCAGCCGCCATCTCC 62.453 68.421 0.00 0.00 40.50 3.71
688 1470 4.500116 GACGAGGAGGTCAGCCGC 62.500 72.222 0.00 0.00 40.50 6.53
689 1471 1.878656 AAAGACGAGGAGGTCAGCCG 61.879 60.000 0.00 0.00 39.42 5.52
693 1475 1.553706 GGGTAAAGACGAGGAGGTCA 58.446 55.000 0.00 0.00 39.42 4.02
695 1477 0.969409 CGGGGTAAAGACGAGGAGGT 60.969 60.000 0.00 0.00 0.00 3.85
853 1646 0.742990 TTGGAAATGCGGTAGAGGCG 60.743 55.000 0.00 0.00 0.00 5.52
883 1687 1.307953 TCCTCTCTCTCCCTCCCGA 60.308 63.158 0.00 0.00 0.00 5.14
935 1739 2.629763 GCCGCGCTAATTAACGGG 59.370 61.111 15.95 15.95 45.72 5.28
975 1779 4.316823 ACCTGGCTCCTCCGTCCA 62.317 66.667 0.00 0.00 37.80 4.02
1017 1821 1.422402 GAGGAGTAGGACGAGGAGGAT 59.578 57.143 0.00 0.00 0.00 3.24
1421 2234 7.065803 CGATTTGTCTGTGTGATAACCCTAAAT 59.934 37.037 0.00 0.00 0.00 1.40
1422 2235 6.370442 CGATTTGTCTGTGTGATAACCCTAAA 59.630 38.462 0.00 0.00 0.00 1.85
1423 2236 5.872617 CGATTTGTCTGTGTGATAACCCTAA 59.127 40.000 0.00 0.00 0.00 2.69
1428 2241 6.888430 AGAAACGATTTGTCTGTGTGATAAC 58.112 36.000 0.00 0.00 0.00 1.89
1433 2246 5.155509 TCAAGAAACGATTTGTCTGTGTG 57.844 39.130 0.00 0.00 0.00 3.82
1439 2252 4.938226 AGGAGGATCAAGAAACGATTTGTC 59.062 41.667 0.00 0.00 36.25 3.18
1475 2288 4.430137 ACATCATCAGTCACATGCAAAC 57.570 40.909 0.00 0.00 0.00 2.93
1496 2323 4.948341 TTCAGAACCTGTGTAGTAGCAA 57.052 40.909 0.00 0.00 32.61 3.91
1672 2505 8.690680 ACTTTAACATTCGTGCAAACTTTTAA 57.309 26.923 0.00 0.00 0.00 1.52
1673 2506 8.690680 AACTTTAACATTCGTGCAAACTTTTA 57.309 26.923 0.00 0.00 0.00 1.52
1674 2507 7.589574 AACTTTAACATTCGTGCAAACTTTT 57.410 28.000 0.00 0.00 0.00 2.27
1712 2545 1.344438 TCTGCCGGCTAATATGGTGAG 59.656 52.381 29.70 12.52 0.00 3.51
1714 2547 2.289631 TGATCTGCCGGCTAATATGGTG 60.290 50.000 29.70 6.34 0.00 4.17
1744 3360 8.616076 AGTCTTTTGTATCCAAATCAATCGATC 58.384 33.333 0.00 0.00 40.14 3.69
1783 3399 7.283354 GGATTAGAAGTTAACCCCTTCAATCAG 59.717 40.741 18.95 0.00 40.62 2.90
1785 3401 7.347252 AGGATTAGAAGTTAACCCCTTCAATC 58.653 38.462 0.88 10.63 40.62 2.67
1798 3414 8.951243 GCAGATTAAAAGTGAGGATTAGAAGTT 58.049 33.333 0.00 0.00 0.00 2.66
1802 3418 7.439356 CGATGCAGATTAAAAGTGAGGATTAGA 59.561 37.037 0.00 0.00 0.00 2.10
1854 3470 9.101655 GGTATAATAAGAACTTTGCTTCGGTAA 57.898 33.333 0.00 0.00 0.00 2.85
2073 3691 2.022129 GGTGTGCGTGAAGGAGACG 61.022 63.158 0.00 0.00 35.28 4.18
2208 3830 8.076178 AGAACAGCACAATTAAGAACAACATAC 58.924 33.333 0.00 0.00 0.00 2.39
2275 3897 0.539986 ACACAACTCCACCGACAAGT 59.460 50.000 0.00 0.00 0.00 3.16
2276 3898 1.330521 CAACACAACTCCACCGACAAG 59.669 52.381 0.00 0.00 0.00 3.16
2376 3998 7.145323 AGGGTAATCAAAAAGTCAATGTTTCG 58.855 34.615 0.00 0.00 0.00 3.46
2398 4020 9.434420 GATGATCTTACAAATATCTGAAGAGGG 57.566 37.037 0.00 0.00 30.14 4.30
2478 4101 2.203788 AAGGCCCTCTCGGACACA 60.204 61.111 0.00 0.00 45.73 3.72
2495 4121 3.680156 GCAAAATGAGGGGCGACA 58.320 55.556 0.00 0.00 0.00 4.35
2499 4125 2.885113 GGACGCAAAATGAGGGGC 59.115 61.111 0.00 0.00 0.00 5.80
2653 4778 4.316823 AGGAGGCAGGTCCGTCCA 62.317 66.667 5.43 0.00 42.05 4.02
2744 4898 4.475135 GAGGCGAAGGTGGAGGCC 62.475 72.222 0.00 0.00 45.91 5.19
2947 5122 2.042025 AGGAGGAGGAGCAGGAGC 60.042 66.667 0.00 0.00 42.56 4.70
3064 5239 1.078426 ACCACCTACGCAATGCTCC 60.078 57.895 2.94 0.00 0.00 4.70
3126 5301 2.046023 CCCCATTCACTCGCAGCA 60.046 61.111 0.00 0.00 0.00 4.41
3159 5334 2.787994 CTGCACTCACATTTCCTTCCT 58.212 47.619 0.00 0.00 0.00 3.36
3264 5439 3.176411 CATATATGAGGAGGCCCAGACA 58.824 50.000 6.92 0.00 33.88 3.41
3303 5478 0.034059 CTGACCGGCATCCCTCATAC 59.966 60.000 0.00 0.00 0.00 2.39
3399 5576 0.763035 AATGTCCCCTATACGCCCAC 59.237 55.000 0.00 0.00 0.00 4.61
3400 5577 1.142060 CAAATGTCCCCTATACGCCCA 59.858 52.381 0.00 0.00 0.00 5.36
3416 5593 3.591789 TCTATAGCTGGGCTCCTCAAAT 58.408 45.455 0.00 0.00 40.44 2.32
3485 5662 6.095580 CAGAGTGGTAGTGATAAGCTTGACTA 59.904 42.308 9.86 9.66 0.00 2.59
3528 5706 2.697229 TGGATTGCCAACAATGTGAACA 59.303 40.909 0.00 0.00 46.59 3.18
3618 5796 4.004196 ACAGTTGTAACCTAACCAGAGC 57.996 45.455 0.00 0.00 0.00 4.09
3732 5910 6.506500 ACAACCAATGTTTTGAATTGCAAA 57.493 29.167 1.71 0.00 44.38 3.68
3733 5911 6.820656 AGTACAACCAATGTTTTGAATTGCAA 59.179 30.769 0.00 0.00 43.63 4.08
3734 5912 6.344500 AGTACAACCAATGTTTTGAATTGCA 58.656 32.000 0.00 0.00 43.63 4.08
3740 5918 5.654650 ACCTGAAGTACAACCAATGTTTTGA 59.345 36.000 0.00 0.00 43.63 2.69
3764 5942 3.512496 GGAAATAAACCAGTTGGGGGAA 58.488 45.455 2.79 0.00 42.91 3.97
3846 6032 4.016444 GCACTCCAAAATCCAATCCTGTA 58.984 43.478 0.00 0.00 0.00 2.74
3977 6163 9.561069 GGTTCAGGATAGTTATCATGTTTGTAT 57.439 33.333 12.02 0.00 43.01 2.29
4016 6202 6.183360 ACGTTTCCTGTAAGAAAAGAAATGCA 60.183 34.615 6.89 0.00 37.40 3.96
4271 6458 0.318869 CAATGGCTGCTTTCACGCAA 60.319 50.000 0.00 0.00 39.80 4.85
4484 7540 9.219603 CTCATCTAACATCACTGAAGGTAAAAA 57.780 33.333 0.00 0.00 0.00 1.94
4721 7779 2.159627 GGATGACACGATGACAACAACC 59.840 50.000 0.00 0.00 0.00 3.77
4814 7872 4.022849 GTGAATTGTTAGAACTTGCTGGCT 60.023 41.667 0.00 0.00 0.00 4.75
4815 7873 4.022849 AGTGAATTGTTAGAACTTGCTGGC 60.023 41.667 0.00 0.00 0.00 4.85
5174 8234 5.183713 TCAGGAGTACATGCCAAAATTCTTG 59.816 40.000 0.00 0.00 0.00 3.02
5209 8269 5.517770 CACTGCAAAAAGGCTAATATTCTGC 59.482 40.000 0.00 0.00 34.04 4.26
5242 8302 5.076873 AGGTATAAGTTGCACCAACATGTT 58.923 37.500 4.92 4.92 45.66 2.71
5251 8311 2.678336 GCACCAGAGGTATAAGTTGCAC 59.322 50.000 0.00 0.00 32.11 4.57
5254 8314 4.081420 AGAGTGCACCAGAGGTATAAGTTG 60.081 45.833 14.63 0.00 32.11 3.16
5300 8360 2.189594 TCTGGATGCACTTGACTTGG 57.810 50.000 0.00 0.00 0.00 3.61
5392 8455 9.512435 GTTAGAATCTTGAACGTTATAGCACTA 57.488 33.333 0.00 3.90 0.00 2.74
5436 8499 9.834628 CTACCGCTTTTTGAGATTTAATGTTTA 57.165 29.630 0.00 0.00 0.00 2.01
5439 8502 7.040686 ACACTACCGCTTTTTGAGATTTAATGT 60.041 33.333 0.00 0.00 0.00 2.71
5440 8503 7.305474 ACACTACCGCTTTTTGAGATTTAATG 58.695 34.615 0.00 0.00 0.00 1.90
5453 8516 6.811253 TTCAAATGATAACACTACCGCTTT 57.189 33.333 0.00 0.00 0.00 3.51
5520 8602 6.745794 ATTCCATTCCCTGTTTTCTTTTCA 57.254 33.333 0.00 0.00 0.00 2.69
5521 8603 8.450578 AAAATTCCATTCCCTGTTTTCTTTTC 57.549 30.769 0.00 0.00 0.00 2.29
5605 8719 7.336427 TGAAAAGGCAATCTCAAACAAAATTGT 59.664 29.630 0.00 0.00 44.72 2.71
5616 8730 5.649395 CCTCATAAGTGAAAAGGCAATCTCA 59.351 40.000 0.00 0.00 33.05 3.27
5719 8859 9.295825 TCCAGAATGTTCTATTCTTTTTAAGCA 57.704 29.630 0.00 0.00 36.32 3.91
5861 9002 7.100409 TGAATTCACGTATGTTTCCTGTGATA 58.900 34.615 3.38 0.00 39.13 2.15
5873 9014 5.595885 AGATCCACTCTGAATTCACGTATG 58.404 41.667 3.38 1.01 31.12 2.39


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

AutoCloner maintained by Alex Coulton.