Multiple sequence alignment - TraesCS1D01G031200

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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 TraesCS1D01G031200 chr1D 100.000 4370 0 0 1 4370 12257587 12253218 0.000000e+00 8070.0
1 TraesCS1D01G031200 chr1D 92.605 2380 157 11 957 3320 12053221 12050845 0.000000e+00 3402.0
2 TraesCS1D01G031200 chr1D 89.411 2257 222 10 955 3211 12007129 12004890 0.000000e+00 2828.0
3 TraesCS1D01G031200 chr1D 85.914 2364 299 22 1023 3376 12039191 12036852 0.000000e+00 2490.0
4 TraesCS1D01G031200 chr1D 88.221 2012 231 1 1241 3252 12056829 12054824 0.000000e+00 2398.0
5 TraesCS1D01G031200 chr1D 86.617 2152 261 11 1109 3245 12296419 12294280 0.000000e+00 2353.0
6 TraesCS1D01G031200 chr1D 83.951 324 38 7 885 1195 12222874 12222552 9.190000e-77 298.0
7 TraesCS1D01G031200 chr1D 89.130 184 13 5 3450 3630 12226862 12226683 5.690000e-54 222.0
8 TraesCS1D01G031200 chr1D 95.455 44 1 1 3623 3665 12253932 12253889 7.840000e-08 69.4
9 TraesCS1D01G031200 chr1D 95.455 44 1 1 3656 3699 12253965 12253923 7.840000e-08 69.4
10 TraesCS1D01G031200 chr1A 94.392 2657 135 6 888 3537 14132765 14130116 0.000000e+00 4069.0
11 TraesCS1D01G031200 chr1A 87.200 2375 270 14 888 3252 14065472 14063122 0.000000e+00 2671.0
12 TraesCS1D01G031200 chr1A 86.217 2416 293 13 1025 3427 14084787 14082399 0.000000e+00 2580.0
13 TraesCS1D01G031200 chr1A 88.345 592 50 11 889 1464 14055558 14054970 0.000000e+00 693.0
14 TraesCS1D01G031200 chr1A 86.120 317 31 6 885 1190 14077523 14077209 3.260000e-86 329.0
15 TraesCS1D01G031200 chr1A 83.587 329 43 6 885 1202 14051559 14051231 9.190000e-77 298.0
16 TraesCS1D01G031200 chr1A 91.011 178 10 3 4199 4370 14111516 14111339 7.310000e-58 235.0
17 TraesCS1D01G031200 chr1A 87.923 207 12 7 3427 3630 14082304 14082108 9.450000e-57 231.0
18 TraesCS1D01G031200 chr1A 91.617 167 13 1 4199 4364 14129332 14129166 3.400000e-56 230.0
19 TraesCS1D01G031200 chr1A 88.953 172 18 1 4200 4370 14128678 14128507 1.230000e-50 211.0
20 TraesCS1D01G031200 chr1B 90.905 2485 132 21 888 3346 17782707 17780291 0.000000e+00 3251.0
21 TraesCS1D01G031200 chr1B 88.746 2257 237 10 955 3211 17737935 17735696 0.000000e+00 2745.0
22 TraesCS1D01G031200 chr1B 87.484 2373 274 11 885 3243 17746096 17743733 0.000000e+00 2715.0
23 TraesCS1D01G031200 chr1B 85.375 2523 305 20 1025 3514 17778150 17775659 0.000000e+00 2556.0
24 TraesCS1D01G031200 chr1B 85.957 235 30 1 956 1190 17770892 17770661 9.390000e-62 248.0
25 TraesCS1D01G031200 chr1B 93.333 90 5 1 261 350 17782818 17782730 9.860000e-27 132.0
26 TraesCS1D01G031200 chr1B 88.172 93 11 0 4116 4208 364125333 364125425 1.280000e-20 111.0
27 TraesCS1D01G031200 chr7A 94.118 476 18 5 379 853 668567623 668567157 0.000000e+00 715.0
28 TraesCS1D01G031200 chr7A 95.614 228 5 3 379 605 668564722 668564499 1.160000e-95 361.0
29 TraesCS1D01G031200 chr7A 91.176 170 10 2 684 853 668554760 668554596 4.400000e-55 226.0
30 TraesCS1D01G031200 chr7A 92.308 52 4 0 737 788 668567231 668567180 1.690000e-09 75.0
31 TraesCS1D01G031200 chr6B 90.709 409 31 6 479 882 643422344 643421938 4.970000e-149 538.0
32 TraesCS1D01G031200 chr6B 90.268 411 33 6 479 884 643425186 643424778 8.320000e-147 531.0
33 TraesCS1D01G031200 chr6B 87.500 88 11 0 4116 4203 462032316 462032229 7.730000e-18 102.0
34 TraesCS1D01G031200 chr6B 86.170 94 13 0 4115 4208 632889448 632889541 7.730000e-18 102.0
35 TraesCS1D01G031200 chr4B 92.582 364 22 4 522 882 20607158 20606797 6.480000e-143 518.0
36 TraesCS1D01G031200 chr2D 97.037 270 6 1 615 884 174334055 174334322 1.850000e-123 453.0
37 TraesCS1D01G031200 chr2D 95.897 195 6 1 688 882 174381868 174382060 9.120000e-82 315.0
38 TraesCS1D01G031200 chr2D 94.949 99 5 0 594 692 174338653 174338751 5.850000e-34 156.0
39 TraesCS1D01G031200 chr2D 88.764 89 9 1 4112 4200 528081790 528081703 1.660000e-19 108.0
40 TraesCS1D01G031200 chr2D 87.097 93 11 1 4112 4203 526080444 526080536 2.150000e-18 104.0
41 TraesCS1D01G031200 chr2B 97.419 155 3 1 732 886 8750819 8750666 3.350000e-66 263.0
42 TraesCS1D01G031200 chr2B 96.753 154 3 2 732 884 797176415 797176263 5.610000e-64 255.0
43 TraesCS1D01G031200 chr2B 95.425 153 7 0 732 884 8752140 8751988 1.210000e-60 244.0
44 TraesCS1D01G031200 chr2B 79.257 323 47 14 479 788 797176631 797176316 1.590000e-49 207.0
45 TraesCS1D01G031200 chr2B 83.575 207 29 4 479 680 8754392 8754186 5.770000e-44 189.0
46 TraesCS1D01G031200 chr5D 92.806 139 10 0 715 853 312078168 312078306 7.410000e-48 202.0
47 TraesCS1D01G031200 chr5D 94.231 52 3 0 737 788 312078232 312078283 3.620000e-11 80.5
48 TraesCS1D01G031200 chr3B 83.575 207 29 5 479 680 825750619 825750825 5.770000e-44 189.0
49 TraesCS1D01G031200 chr3B 86.184 152 3 5 731 882 825750834 825750967 9.790000e-32 148.0
50 TraesCS1D01G031200 chr6A 89.412 85 9 0 4116 4200 610131910 610131826 1.660000e-19 108.0
51 TraesCS1D01G031200 chr6D 89.286 84 8 1 4118 4200 462439499 462439582 2.150000e-18 104.0
52 TraesCS1D01G031200 chr6D 86.813 91 10 1 4110 4200 34581487 34581575 2.780000e-17 100.0
53 TraesCS1D01G031200 chr4A 87.500 88 11 0 4113 4200 512025834 512025921 7.730000e-18 102.0
54 TraesCS1D01G031200 chr3A 100.000 28 0 0 4052 4079 746374828 746374855 8.000000e-03 52.8


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 TraesCS1D01G031200 chr1D 12253218 12257587 4369 True 2736.266667 8070 96.970000 1 4370 3 chr1D.!!$R6 4369
1 TraesCS1D01G031200 chr1D 12050845 12056829 5984 True 2900.000000 3402 90.413000 957 3320 2 chr1D.!!$R4 2363
2 TraesCS1D01G031200 chr1D 12004890 12007129 2239 True 2828.000000 2828 89.411000 955 3211 1 chr1D.!!$R1 2256
3 TraesCS1D01G031200 chr1D 12036852 12039191 2339 True 2490.000000 2490 85.914000 1023 3376 1 chr1D.!!$R2 2353
4 TraesCS1D01G031200 chr1D 12294280 12296419 2139 True 2353.000000 2353 86.617000 1109 3245 1 chr1D.!!$R3 2136
5 TraesCS1D01G031200 chr1D 12222552 12226862 4310 True 260.000000 298 86.540500 885 3630 2 chr1D.!!$R5 2745
6 TraesCS1D01G031200 chr1A 14063122 14065472 2350 True 2671.000000 2671 87.200000 888 3252 1 chr1A.!!$R1 2364
7 TraesCS1D01G031200 chr1A 14128507 14132765 4258 True 1503.333333 4069 91.654000 888 4370 3 chr1A.!!$R6 3482
8 TraesCS1D01G031200 chr1A 14082108 14084787 2679 True 1405.500000 2580 87.070000 1025 3630 2 chr1A.!!$R5 2605
9 TraesCS1D01G031200 chr1A 14051231 14055558 4327 True 495.500000 693 85.966000 885 1464 2 chr1A.!!$R4 579
10 TraesCS1D01G031200 chr1B 17735696 17737935 2239 True 2745.000000 2745 88.746000 955 3211 1 chr1B.!!$R1 2256
11 TraesCS1D01G031200 chr1B 17743733 17746096 2363 True 2715.000000 2715 87.484000 885 3243 1 chr1B.!!$R2 2358
12 TraesCS1D01G031200 chr1B 17775659 17782818 7159 True 1979.666667 3251 89.871000 261 3514 3 chr1B.!!$R4 3253
13 TraesCS1D01G031200 chr7A 668564499 668567623 3124 True 383.666667 715 94.013333 379 853 3 chr7A.!!$R2 474
14 TraesCS1D01G031200 chr6B 643421938 643425186 3248 True 534.500000 538 90.488500 479 884 2 chr6B.!!$R2 405
15 TraesCS1D01G031200 chr2B 8750666 8754392 3726 True 232.000000 263 92.139667 479 886 3 chr2B.!!$R1 407

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
172 173 0.107831 ACTGGCGGAGTTTAGTGCAA 59.892 50.0 0.00 0.00 0.00 4.08 F
174 175 0.887387 TGGCGGAGTTTAGTGCAACC 60.887 55.0 0.00 0.00 37.80 3.77 F
1283 5587 0.964358 AGTTCAGATTGCTGCAGGGC 60.964 55.0 17.12 2.89 42.01 5.19 F
2447 6775 0.740868 CATCGGCTTCGGCTTTCAGA 60.741 55.0 0.00 0.00 41.44 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 6485 1.302832 CTGGTGAGGAGTGTTGCCC 60.303 63.158 0.00 0.0 0.00 5.36 R
2238 6558 2.121963 TCCTGGTCCCAGCCAAGT 60.122 61.111 7.87 0.0 42.35 3.16 R
2893 7223 0.173255 CCCGTGGAACATTTGCATCC 59.827 55.000 0.00 0.0 44.52 3.51 R
3955 13650 0.107848 CTGTAAGGTGGGCCTAACCG 60.108 60.000 18.75 4.6 46.33 4.44 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
22 23 3.247006 ACAGTGGTATTAGGCTTGTCG 57.753 47.619 0.00 0.00 0.00 4.35
23 24 2.565834 ACAGTGGTATTAGGCTTGTCGT 59.434 45.455 0.00 0.00 0.00 4.34
25 26 4.142227 ACAGTGGTATTAGGCTTGTCGTAG 60.142 45.833 0.00 0.00 0.00 3.51
29 30 5.690857 GTGGTATTAGGCTTGTCGTAGATTC 59.309 44.000 0.00 0.00 40.67 2.52
30 31 5.361571 TGGTATTAGGCTTGTCGTAGATTCA 59.638 40.000 0.00 0.00 40.67 2.57
32 33 4.794278 TTAGGCTTGTCGTAGATTCACA 57.206 40.909 0.00 0.00 40.67 3.58
34 35 4.002906 AGGCTTGTCGTAGATTCACAAA 57.997 40.909 0.00 0.00 40.67 2.83
35 36 4.579869 AGGCTTGTCGTAGATTCACAAAT 58.420 39.130 0.00 0.00 40.67 2.32
36 37 4.631813 AGGCTTGTCGTAGATTCACAAATC 59.368 41.667 0.00 0.00 40.67 2.17
39 40 3.845178 TGTCGTAGATTCACAAATCGCT 58.155 40.909 0.00 0.00 45.01 4.93
48 49 3.610040 TCACAAATCGCTAGGTGTGAT 57.390 42.857 1.37 0.00 44.02 3.06
50 51 3.002791 CACAAATCGCTAGGTGTGATGT 58.997 45.455 0.00 0.00 44.32 3.06
53 54 4.154195 ACAAATCGCTAGGTGTGATGTTTC 59.846 41.667 0.00 0.00 44.32 2.78
55 56 2.959516 TCGCTAGGTGTGATGTTTCTG 58.040 47.619 0.00 0.00 0.00 3.02
56 57 2.299013 TCGCTAGGTGTGATGTTTCTGT 59.701 45.455 0.00 0.00 0.00 3.41
58 59 4.021807 TCGCTAGGTGTGATGTTTCTGTTA 60.022 41.667 0.00 0.00 0.00 2.41
60 61 5.351465 CGCTAGGTGTGATGTTTCTGTTATT 59.649 40.000 0.00 0.00 0.00 1.40
61 62 6.546395 GCTAGGTGTGATGTTTCTGTTATTG 58.454 40.000 0.00 0.00 0.00 1.90
63 64 7.066284 GCTAGGTGTGATGTTTCTGTTATTGAT 59.934 37.037 0.00 0.00 0.00 2.57
64 65 7.149569 AGGTGTGATGTTTCTGTTATTGATG 57.850 36.000 0.00 0.00 0.00 3.07
66 67 6.803320 GGTGTGATGTTTCTGTTATTGATGTG 59.197 38.462 0.00 0.00 0.00 3.21
69 70 8.795513 TGTGATGTTTCTGTTATTGATGTGAAT 58.204 29.630 0.00 0.00 0.00 2.57
111 112 7.833285 ACTGGGTAAAATAATGTTCTTGTGT 57.167 32.000 0.00 0.00 0.00 3.72
113 114 7.286775 ACTGGGTAAAATAATGTTCTTGTGTGT 59.713 33.333 0.00 0.00 0.00 3.72
115 116 6.364976 GGGTAAAATAATGTTCTTGTGTGTGC 59.635 38.462 0.00 0.00 0.00 4.57
117 118 7.436673 GGTAAAATAATGTTCTTGTGTGTGCAA 59.563 33.333 0.00 0.00 0.00 4.08
121 122 2.710377 TGTTCTTGTGTGTGCAAGTCT 58.290 42.857 0.00 0.00 44.41 3.24
122 123 3.081061 TGTTCTTGTGTGTGCAAGTCTT 58.919 40.909 0.00 0.00 44.41 3.01
126 127 2.401583 TGTGTGTGCAAGTCTTCAGT 57.598 45.000 0.00 0.00 0.00 3.41
129 130 3.505680 TGTGTGTGCAAGTCTTCAGTTTT 59.494 39.130 0.00 0.00 0.00 2.43
131 132 4.009675 TGTGTGCAAGTCTTCAGTTTTCT 58.990 39.130 0.00 0.00 0.00 2.52
132 133 4.458989 TGTGTGCAAGTCTTCAGTTTTCTT 59.541 37.500 0.00 0.00 0.00 2.52
133 134 5.048083 TGTGTGCAAGTCTTCAGTTTTCTTT 60.048 36.000 0.00 0.00 0.00 2.52
135 136 6.033937 GTGTGCAAGTCTTCAGTTTTCTTTTC 59.966 38.462 0.00 0.00 0.00 2.29
136 137 5.516696 GTGCAAGTCTTCAGTTTTCTTTTCC 59.483 40.000 0.00 0.00 0.00 3.13
137 138 5.184864 TGCAAGTCTTCAGTTTTCTTTTCCA 59.815 36.000 0.00 0.00 0.00 3.53
138 139 6.099341 GCAAGTCTTCAGTTTTCTTTTCCAA 58.901 36.000 0.00 0.00 0.00 3.53
139 140 6.758416 GCAAGTCTTCAGTTTTCTTTTCCAAT 59.242 34.615 0.00 0.00 0.00 3.16
140 141 7.043125 GCAAGTCTTCAGTTTTCTTTTCCAATC 60.043 37.037 0.00 0.00 0.00 2.67
144 145 8.621286 GTCTTCAGTTTTCTTTTCCAATCAGTA 58.379 33.333 0.00 0.00 0.00 2.74
148 149 6.587608 CAGTTTTCTTTTCCAATCAGTATGGC 59.412 38.462 0.00 0.00 37.88 4.40
149 150 6.267471 AGTTTTCTTTTCCAATCAGTATGGCA 59.733 34.615 0.00 0.00 37.88 4.92
153 154 2.732844 TCCAATCAGTATGGCATGCA 57.267 45.000 21.36 6.13 37.88 3.96
156 157 2.034179 CCAATCAGTATGGCATGCACTG 59.966 50.000 23.81 23.81 40.83 3.66
157 158 1.977056 ATCAGTATGGCATGCACTGG 58.023 50.000 27.11 14.50 40.08 4.00
164 165 3.058160 GCATGCACTGGCGGAGTT 61.058 61.111 14.21 0.00 45.35 3.01
166 167 1.305219 GCATGCACTGGCGGAGTTTA 61.305 55.000 14.21 0.00 45.35 2.01
167 168 0.729116 CATGCACTGGCGGAGTTTAG 59.271 55.000 0.00 0.00 45.35 1.85
169 170 0.602638 TGCACTGGCGGAGTTTAGTG 60.603 55.000 0.00 0.00 45.35 2.74
170 171 2.162716 CACTGGCGGAGTTTAGTGC 58.837 57.895 0.00 0.00 34.78 4.40
172 173 0.107831 ACTGGCGGAGTTTAGTGCAA 59.892 50.000 0.00 0.00 0.00 4.08
174 175 0.887387 TGGCGGAGTTTAGTGCAACC 60.887 55.000 0.00 0.00 37.80 3.77
175 176 1.583495 GGCGGAGTTTAGTGCAACCC 61.583 60.000 0.00 0.00 37.80 4.11
177 178 1.156736 CGGAGTTTAGTGCAACCCTG 58.843 55.000 0.00 0.00 37.80 4.45
202 203 3.966543 CACCGCCCTCCCAGGTTT 61.967 66.667 0.00 0.00 35.85 3.27
203 204 3.966543 ACCGCCCTCCCAGGTTTG 61.967 66.667 0.00 0.00 33.96 2.93
219 220 6.007703 CCAGGTTTGGGTAAATTACTGAAGA 58.992 40.000 2.96 0.00 41.05 2.87
220 221 6.492087 CCAGGTTTGGGTAAATTACTGAAGAA 59.508 38.462 2.96 0.00 41.05 2.52
221 222 7.014808 CCAGGTTTGGGTAAATTACTGAAGAAA 59.985 37.037 2.96 0.00 41.05 2.52
222 223 8.417884 CAGGTTTGGGTAAATTACTGAAGAAAA 58.582 33.333 2.96 0.00 31.92 2.29
223 224 9.154632 AGGTTTGGGTAAATTACTGAAGAAAAT 57.845 29.630 2.96 0.00 0.00 1.82
224 225 9.772973 GGTTTGGGTAAATTACTGAAGAAAATT 57.227 29.630 2.96 0.00 0.00 1.82
246 247 3.422204 TGGGACAGCATTACCCCC 58.578 61.111 0.00 0.00 42.65 5.40
261 262 2.518349 CCCCCACCACACACACAC 60.518 66.667 0.00 0.00 0.00 3.82
263 264 2.118404 CCCCACCACACACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
264 265 1.377856 CCCACCACACACACACACA 60.378 57.895 0.00 0.00 0.00 3.72
307 308 2.950433 CCACTGATGGCATGTCAAAAC 58.050 47.619 3.01 0.00 39.82 2.43
350 351 5.763876 ATAAACAGCAAGAAGTAGAGGGT 57.236 39.130 0.00 0.00 0.00 4.34
375 376 3.078837 GGAAGCAGAATTCCGGTTTACA 58.921 45.455 7.50 0.00 39.47 2.41
379 380 2.161609 GCAGAATTCCGGTTTACAGGTG 59.838 50.000 0.00 0.00 32.79 4.00
382 383 3.818773 AGAATTCCGGTTTACAGGTGTTG 59.181 43.478 0.00 0.00 32.79 3.33
396 397 2.092103 AGGTGTTGCCCAAAACTACTGA 60.092 45.455 1.72 0.00 38.26 3.41
406 407 4.464597 CCCAAAACTACTGACTAGCTCTCT 59.535 45.833 0.00 0.00 0.00 3.10
457 458 2.668889 GCAGCTGCACACTGAGCT 60.669 61.111 33.36 3.19 46.73 4.09
584 589 1.480954 AGGCTCGTGGTAGTGGTAATG 59.519 52.381 0.00 0.00 0.00 1.90
706 712 5.806654 TGCATAGCACATTCCTATCTACA 57.193 39.130 0.00 0.00 31.71 2.74
707 713 5.787380 TGCATAGCACATTCCTATCTACAG 58.213 41.667 0.00 0.00 31.71 2.74
804 5074 5.069251 CAGCCTTTCTACTAGCTAAAGCCTA 59.931 44.000 0.00 0.00 43.38 3.93
807 5077 6.425417 GCCTTTCTACTAGCTAAAGCCTAATG 59.575 42.308 0.00 0.00 43.38 1.90
882 5152 4.504864 CCTGTAGACTGGGTTGATCAACAA 60.505 45.833 33.42 22.21 42.85 2.83
883 5153 5.241403 TGTAGACTGGGTTGATCAACAAT 57.759 39.130 33.42 18.64 42.85 2.71
920 5190 1.915614 GCACATGAGCAAGGTGGACG 61.916 60.000 10.48 0.00 33.25 4.79
938 5212 3.550678 GGACGGTCGTCTCACATAATTTC 59.449 47.826 20.55 0.00 44.04 2.17
1283 5587 0.964358 AGTTCAGATTGCTGCAGGGC 60.964 55.000 17.12 2.89 42.01 5.19
1316 5620 3.678289 CACCACCAGATCAGATCAAACA 58.322 45.455 13.14 0.00 0.00 2.83
1336 5640 7.661437 TCAAACAATGCTCTTCACTACATAAGT 59.339 33.333 0.00 0.00 39.81 2.24
1388 5696 1.672854 CGACGTATGCCAAGGGGAGA 61.673 60.000 0.00 0.00 35.59 3.71
1393 5701 1.635817 TATGCCAAGGGGAGACTGCC 61.636 60.000 4.00 4.00 35.59 4.85
1438 5746 1.826385 GTGACATTCTTGGGGAGGTG 58.174 55.000 0.00 0.00 0.00 4.00
1447 5755 1.195442 TTGGGGAGGTGTACGCATCA 61.195 55.000 21.28 0.25 0.00 3.07
1474 5782 1.526686 CTGGCCGCCATTGCATAGA 60.527 57.895 13.86 0.00 37.32 1.98
1702 6016 2.936919 TGCATTGTCAGAGAGGTGTT 57.063 45.000 0.00 0.00 0.00 3.32
1714 6028 3.716872 AGAGAGGTGTTGAGGAGGAAAAA 59.283 43.478 0.00 0.00 0.00 1.94
1866 6183 2.443255 GGGGCTGGGATATCTTTCAAGA 59.557 50.000 2.05 0.00 39.78 3.02
1867 6184 3.075134 GGGGCTGGGATATCTTTCAAGAT 59.925 47.826 7.22 7.22 46.85 2.40
2127 6445 1.584380 GCAGAAGCTGTGGCAGAAGG 61.584 60.000 0.00 0.00 41.70 3.46
2165 6485 6.484977 GGCCAGTGAAATCCTAAAGAAGATAG 59.515 42.308 0.00 0.00 0.00 2.08
2252 6574 2.515398 CACACTTGGCTGGGACCA 59.485 61.111 0.00 0.00 38.16 4.02
2447 6775 0.740868 CATCGGCTTCGGCTTTCAGA 60.741 55.000 0.00 0.00 41.44 3.27
2569 6897 4.934797 AATGATCAAGGAGACAGGGAAA 57.065 40.909 0.00 0.00 0.00 3.13
2893 7223 9.285770 CATTACTCTTCAATGTTTGACATGATG 57.714 33.333 0.00 0.00 37.97 3.07
3127 7465 9.739276 AAGAACACACTTTATCATGAGGAATTA 57.261 29.630 0.09 0.00 0.00 1.40
3143 11964 7.541162 TGAGGAATTATTTGCTGTTGAAGATG 58.459 34.615 0.00 0.00 33.10 2.90
3308 12139 5.297278 TGTGTACCTGGTCATTGTTTTGTAC 59.703 40.000 0.63 0.00 0.00 2.90
3324 12291 5.652994 TTTGTACAGTGAACAAAAAGGCT 57.347 34.783 0.00 0.00 42.28 4.58
3429 12495 5.163343 TGGAAATACCATACCTAGACACTGC 60.163 44.000 0.00 0.00 44.64 4.40
3445 12514 4.451900 ACACTGCTTTGCTGTAAAGTACT 58.548 39.130 17.49 0.00 46.05 2.73
3446 12515 4.273480 ACACTGCTTTGCTGTAAAGTACTG 59.727 41.667 17.49 14.23 46.05 2.74
3447 12516 4.273480 CACTGCTTTGCTGTAAAGTACTGT 59.727 41.667 17.49 10.05 46.05 3.55
3467 12536 5.994054 ACTGTAGATCATTGCGCTGAATATT 59.006 36.000 9.73 0.00 0.00 1.28
3562 12988 9.872684 ACATAACAGGAATCCAATAGAATGAAT 57.127 29.630 0.61 0.00 0.00 2.57
3602 13070 6.215845 ACAAATAAGTGGAGTTTGAACATGC 58.784 36.000 0.00 0.00 36.58 4.06
3619 13089 5.344207 ACATGCGTCTTCTGTAAAACTTC 57.656 39.130 0.00 0.00 0.00 3.01
3642 13190 6.739112 TCTACTTCAATCATACATGGACGAG 58.261 40.000 0.00 0.00 0.00 4.18
3646 13194 6.481313 ACTTCAATCATACATGGACGAGATTG 59.519 38.462 17.44 17.44 42.06 2.67
3651 13199 0.914417 ACATGGACGAGATTGGGGGT 60.914 55.000 0.00 0.00 0.00 4.95
3652 13200 0.464373 CATGGACGAGATTGGGGGTG 60.464 60.000 0.00 0.00 0.00 4.61
3653 13201 0.620410 ATGGACGAGATTGGGGGTGA 60.620 55.000 0.00 0.00 0.00 4.02
3654 13202 1.264749 TGGACGAGATTGGGGGTGAG 61.265 60.000 0.00 0.00 0.00 3.51
3655 13203 1.153349 GACGAGATTGGGGGTGAGC 60.153 63.158 0.00 0.00 0.00 4.26
3656 13204 1.613630 ACGAGATTGGGGGTGAGCT 60.614 57.895 0.00 0.00 0.00 4.09
3664 13279 0.776810 TGGGGGTGAGCTTCAAATCA 59.223 50.000 0.00 0.00 0.00 2.57
3668 13283 3.620488 GGGGTGAGCTTCAAATCATACA 58.380 45.455 0.00 0.00 0.00 2.29
3673 13288 5.220931 GGTGAGCTTCAAATCATACATGGAC 60.221 44.000 0.00 0.00 0.00 4.02
3680 13295 6.849588 TCAAATCATACATGGACGAGATTG 57.150 37.500 0.00 0.00 0.00 2.67
3681 13296 5.759763 TCAAATCATACATGGACGAGATTGG 59.240 40.000 0.00 0.00 0.00 3.16
3684 13299 1.128200 TACATGGACGAGATTGGGGG 58.872 55.000 0.00 0.00 0.00 5.40
3685 13300 0.914417 ACATGGACGAGATTGGGGGT 60.914 55.000 0.00 0.00 0.00 4.95
3686 13301 0.464373 CATGGACGAGATTGGGGGTG 60.464 60.000 0.00 0.00 0.00 4.61
3687 13302 0.620410 ATGGACGAGATTGGGGGTGA 60.620 55.000 0.00 0.00 0.00 4.02
3688 13303 1.264749 TGGACGAGATTGGGGGTGAG 61.265 60.000 0.00 0.00 0.00 3.51
3689 13304 1.153349 GACGAGATTGGGGGTGAGC 60.153 63.158 0.00 0.00 0.00 4.26
3690 13305 1.613630 ACGAGATTGGGGGTGAGCT 60.614 57.895 0.00 0.00 0.00 4.09
3691 13306 1.144936 CGAGATTGGGGGTGAGCTC 59.855 63.158 6.82 6.82 0.00 4.09
3693 13308 1.229951 AGATTGGGGGTGAGCTCCA 60.230 57.895 12.15 0.00 36.82 3.86
3694 13309 0.846427 AGATTGGGGGTGAGCTCCAA 60.846 55.000 19.38 19.38 43.62 3.53
3696 13311 0.712380 ATTGGGGGTGAGCTCCAAAT 59.288 50.000 20.99 6.25 42.86 2.32
3697 13312 0.039618 TTGGGGGTGAGCTCCAAATC 59.960 55.000 14.53 0.00 37.58 2.17
3698 13313 1.139498 TGGGGGTGAGCTCCAAATCA 61.139 55.000 12.15 1.62 36.82 2.57
3709 13351 2.342650 CCAAATCACCAGGGCCACG 61.343 63.158 6.18 0.00 0.00 4.94
3733 13375 2.283809 CGGGGGATCAGAGAGGGT 59.716 66.667 0.00 0.00 0.00 4.34
3739 13387 1.406860 GGATCAGAGAGGGTGAGGGC 61.407 65.000 0.00 0.00 0.00 5.19
3742 13390 4.787280 AGAGAGGGTGAGGGCGGG 62.787 72.222 0.00 0.00 0.00 6.13
3743 13391 4.779733 GAGAGGGTGAGGGCGGGA 62.780 72.222 0.00 0.00 0.00 5.14
3755 13403 2.683933 GCGGGAGGACCTTGGAGA 60.684 66.667 0.00 0.00 36.97 3.71
3760 13408 1.324005 GGAGGACCTTGGAGACCGAG 61.324 65.000 0.00 0.00 34.87 4.63
3779 13436 1.448717 GTCGGCCAAGGAGAAGAGC 60.449 63.158 2.24 0.00 0.00 4.09
3786 13443 0.461961 CAAGGAGAAGAGCCCCTACG 59.538 60.000 0.00 0.00 0.00 3.51
3803 13460 3.179939 GCGTCGTCTTCCTTCGCC 61.180 66.667 0.00 0.00 40.83 5.54
3804 13461 2.874780 CGTCGTCTTCCTTCGCCG 60.875 66.667 0.00 0.00 0.00 6.46
3805 13462 2.564975 GTCGTCTTCCTTCGCCGA 59.435 61.111 0.00 0.00 0.00 5.54
3806 13463 1.514443 GTCGTCTTCCTTCGCCGAG 60.514 63.158 0.00 0.00 0.00 4.63
3808 13465 2.509561 GTCTTCCTTCGCCGAGGC 60.510 66.667 3.59 3.59 36.71 4.70
3810 13467 3.775654 CTTCCTTCGCCGAGGCCT 61.776 66.667 3.86 3.86 36.71 5.19
3812 13469 3.310860 TTCCTTCGCCGAGGCCTTC 62.311 63.158 6.77 0.00 36.71 3.46
3838 13507 1.819229 CCATGGAGAGGTCACGGAG 59.181 63.158 5.56 0.00 0.00 4.63
3839 13508 1.680522 CCATGGAGAGGTCACGGAGG 61.681 65.000 5.56 0.00 0.00 4.30
3844 13513 0.750182 GAGAGGTCACGGAGGAGAGG 60.750 65.000 0.00 0.00 0.00 3.69
3846 13515 1.000646 AGGTCACGGAGGAGAGGAC 60.001 63.158 0.00 0.00 0.00 3.85
3847 13516 2.408241 GGTCACGGAGGAGAGGACG 61.408 68.421 0.00 0.00 0.00 4.79
3848 13517 2.045242 TCACGGAGGAGAGGACGG 60.045 66.667 0.00 0.00 0.00 4.79
3849 13518 2.045242 CACGGAGGAGAGGACGGA 60.045 66.667 0.00 0.00 0.00 4.69
3850 13519 2.115911 CACGGAGGAGAGGACGGAG 61.116 68.421 0.00 0.00 0.00 4.63
3851 13520 2.299429 ACGGAGGAGAGGACGGAGA 61.299 63.158 0.00 0.00 0.00 3.71
3852 13521 1.077644 CGGAGGAGAGGACGGAGAA 60.078 63.158 0.00 0.00 0.00 2.87
3853 13522 1.378124 CGGAGGAGAGGACGGAGAAC 61.378 65.000 0.00 0.00 0.00 3.01
3854 13523 1.038681 GGAGGAGAGGACGGAGAACC 61.039 65.000 0.00 0.00 0.00 3.62
3876 13545 3.367498 CGAACAGAAAGAGAGGGACGAAT 60.367 47.826 0.00 0.00 0.00 3.34
3894 13563 2.781595 ATTCCGCCTTCGTGAAGCGT 62.782 55.000 18.16 4.87 42.13 5.07
3921 13616 1.079612 TGGCTGATGTGCTGAGTCG 60.080 57.895 0.00 0.00 0.00 4.18
3930 13625 4.754618 TGATGTGCTGAGTCGTGTTTTAAT 59.245 37.500 0.00 0.00 0.00 1.40
3944 13639 0.041982 TTTAATTGGACCTGGGCCCC 59.958 55.000 22.27 2.51 0.00 5.80
3958 13653 3.953775 CCCCAAGCTGTGTCCGGT 61.954 66.667 0.00 0.00 0.00 5.28
3980 13676 2.584608 CCCACCTTACAGGCCTCG 59.415 66.667 0.00 0.52 39.63 4.63
4003 13699 4.792704 GCCTCGCAGAAAACAAAAGAATCA 60.793 41.667 0.00 0.00 34.09 2.57
4004 13700 4.676924 CCTCGCAGAAAACAAAAGAATCAC 59.323 41.667 0.00 0.00 34.09 3.06
4006 13702 3.735746 CGCAGAAAACAAAAGAATCACCC 59.264 43.478 0.00 0.00 0.00 4.61
4008 13704 4.507756 GCAGAAAACAAAAGAATCACCCAC 59.492 41.667 0.00 0.00 0.00 4.61
4009 13705 5.682212 GCAGAAAACAAAAGAATCACCCACT 60.682 40.000 0.00 0.00 0.00 4.00
4010 13706 6.340522 CAGAAAACAAAAGAATCACCCACTT 58.659 36.000 0.00 0.00 0.00 3.16
4011 13707 6.818142 CAGAAAACAAAAGAATCACCCACTTT 59.182 34.615 0.00 0.00 35.74 2.66
4012 13708 7.010460 CAGAAAACAAAAGAATCACCCACTTTC 59.990 37.037 0.00 0.00 33.58 2.62
4013 13709 4.568152 ACAAAAGAATCACCCACTTTCG 57.432 40.909 0.00 0.00 33.58 3.46
4014 13710 3.951680 ACAAAAGAATCACCCACTTTCGT 59.048 39.130 0.00 0.00 33.58 3.85
4018 13714 2.372172 AGAATCACCCACTTTCGTCCTT 59.628 45.455 0.00 0.00 0.00 3.36
4019 13715 2.951229 ATCACCCACTTTCGTCCTTT 57.049 45.000 0.00 0.00 0.00 3.11
4020 13716 1.961793 TCACCCACTTTCGTCCTTTG 58.038 50.000 0.00 0.00 0.00 2.77
4021 13717 1.210967 TCACCCACTTTCGTCCTTTGT 59.789 47.619 0.00 0.00 0.00 2.83
4022 13718 1.602377 CACCCACTTTCGTCCTTTGTC 59.398 52.381 0.00 0.00 0.00 3.18
4023 13719 1.489230 ACCCACTTTCGTCCTTTGTCT 59.511 47.619 0.00 0.00 0.00 3.41
4024 13720 2.701951 ACCCACTTTCGTCCTTTGTCTA 59.298 45.455 0.00 0.00 0.00 2.59
4025 13721 3.135167 ACCCACTTTCGTCCTTTGTCTAA 59.865 43.478 0.00 0.00 0.00 2.10
4026 13722 4.131596 CCCACTTTCGTCCTTTGTCTAAA 58.868 43.478 0.00 0.00 0.00 1.85
4027 13723 4.760204 CCCACTTTCGTCCTTTGTCTAAAT 59.240 41.667 0.00 0.00 0.00 1.40
4028 13724 5.935789 CCCACTTTCGTCCTTTGTCTAAATA 59.064 40.000 0.00 0.00 0.00 1.40
4029 13725 6.598064 CCCACTTTCGTCCTTTGTCTAAATAT 59.402 38.462 0.00 0.00 0.00 1.28
4030 13726 7.767198 CCCACTTTCGTCCTTTGTCTAAATATA 59.233 37.037 0.00 0.00 0.00 0.86
4031 13727 9.326413 CCACTTTCGTCCTTTGTCTAAATATAT 57.674 33.333 0.00 0.00 0.00 0.86
4055 13751 4.797800 AAAACCTACTTCCGTCCTACTC 57.202 45.455 0.00 0.00 0.00 2.59
4057 13753 3.280197 ACCTACTTCCGTCCTACTCTC 57.720 52.381 0.00 0.00 0.00 3.20
4059 13755 3.266513 ACCTACTTCCGTCCTACTCTCTT 59.733 47.826 0.00 0.00 0.00 2.85
4065 13761 4.985538 TCCGTCCTACTCTCTTCATTTC 57.014 45.455 0.00 0.00 0.00 2.17
4127 13823 4.778213 AAAGCATATTACTCCCTCTGCA 57.222 40.909 0.00 0.00 32.18 4.41
4130 13826 2.810852 GCATATTACTCCCTCTGCAAGC 59.189 50.000 0.00 0.00 0.00 4.01
4131 13827 3.495806 GCATATTACTCCCTCTGCAAGCT 60.496 47.826 0.00 0.00 0.00 3.74
4132 13828 4.262635 GCATATTACTCCCTCTGCAAGCTA 60.263 45.833 0.00 0.00 0.00 3.32
4136 13832 6.694445 ATTACTCCCTCTGCAAGCTAATAT 57.306 37.500 0.00 0.00 0.00 1.28
4137 13833 7.798710 ATTACTCCCTCTGCAAGCTAATATA 57.201 36.000 0.00 0.00 0.00 0.86
4138 13834 7.612065 TTACTCCCTCTGCAAGCTAATATAA 57.388 36.000 0.00 0.00 0.00 0.98
4139 13835 6.694445 ACTCCCTCTGCAAGCTAATATAAT 57.306 37.500 0.00 0.00 0.00 1.28
4140 13836 7.798710 ACTCCCTCTGCAAGCTAATATAATA 57.201 36.000 0.00 0.00 0.00 0.98
4141 13837 7.846066 ACTCCCTCTGCAAGCTAATATAATAG 58.154 38.462 0.00 0.00 0.00 1.73
4142 13838 6.644347 TCCCTCTGCAAGCTAATATAATAGC 58.356 40.000 11.26 11.26 46.94 2.97
4196 13949 9.871238 ACGCTTTTATATTTCTTTACTGAGAGA 57.129 29.630 0.00 0.00 0.00 3.10
4243 14179 5.971895 AAGCACTAACGAAAACTTAACGA 57.028 34.783 0.00 0.00 0.00 3.85
4364 14564 1.666700 TGTAGGTGCAACAACGTTGTC 59.333 47.619 32.36 21.54 41.31 3.18
4366 14566 0.732571 AGGTGCAACAACGTTGTCAG 59.267 50.000 32.36 26.65 41.31 3.51
4369 14569 0.179176 TGCAACAACGTTGTCAGCAC 60.179 50.000 36.83 24.49 42.89 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.459670 TGTGAATCTACGACAAGCCTAATA 57.540 37.500 0.00 0.00 0.00 0.98
10 11 5.339008 TGTGAATCTACGACAAGCCTAAT 57.661 39.130 0.00 0.00 0.00 1.73
15 16 4.569029 CGATTTGTGAATCTACGACAAGC 58.431 43.478 0.00 0.00 39.61 4.01
18 19 3.845178 AGCGATTTGTGAATCTACGACA 58.155 40.909 0.00 0.00 39.61 4.35
19 20 4.441415 CCTAGCGATTTGTGAATCTACGAC 59.559 45.833 0.00 0.00 39.61 4.34
20 21 4.097437 ACCTAGCGATTTGTGAATCTACGA 59.903 41.667 0.00 0.00 39.61 3.43
22 23 5.005779 CACACCTAGCGATTTGTGAATCTAC 59.994 44.000 8.92 0.00 41.61 2.59
23 24 5.105513 TCACACCTAGCGATTTGTGAATCTA 60.106 40.000 9.26 0.00 44.09 1.98
25 26 3.932710 TCACACCTAGCGATTTGTGAATC 59.067 43.478 9.26 0.00 44.09 2.52
29 30 3.002791 ACATCACACCTAGCGATTTGTG 58.997 45.455 4.00 4.00 40.64 3.33
30 31 3.334583 ACATCACACCTAGCGATTTGT 57.665 42.857 0.00 0.00 0.00 2.83
32 33 4.393062 CAGAAACATCACACCTAGCGATTT 59.607 41.667 0.00 0.00 0.00 2.17
34 35 3.055819 ACAGAAACATCACACCTAGCGAT 60.056 43.478 0.00 0.00 0.00 4.58
35 36 2.299013 ACAGAAACATCACACCTAGCGA 59.701 45.455 0.00 0.00 0.00 4.93
36 37 2.688507 ACAGAAACATCACACCTAGCG 58.311 47.619 0.00 0.00 0.00 4.26
39 40 7.882791 ACATCAATAACAGAAACATCACACCTA 59.117 33.333 0.00 0.00 0.00 3.08
89 90 7.429633 CACACACAAGAACATTATTTTACCCA 58.570 34.615 0.00 0.00 0.00 4.51
90 91 6.364976 GCACACACAAGAACATTATTTTACCC 59.635 38.462 0.00 0.00 0.00 3.69
91 92 6.920758 TGCACACACAAGAACATTATTTTACC 59.079 34.615 0.00 0.00 0.00 2.85
92 93 7.922505 TGCACACACAAGAACATTATTTTAC 57.077 32.000 0.00 0.00 0.00 2.01
106 107 2.710377 ACTGAAGACTTGCACACACAA 58.290 42.857 0.00 0.00 0.00 3.33
111 112 5.643379 AAAGAAAACTGAAGACTTGCACA 57.357 34.783 0.00 0.00 0.00 4.57
113 114 5.184864 TGGAAAAGAAAACTGAAGACTTGCA 59.815 36.000 0.00 0.00 0.00 4.08
115 116 7.975616 TGATTGGAAAAGAAAACTGAAGACTTG 59.024 33.333 0.00 0.00 0.00 3.16
117 118 7.340487 ACTGATTGGAAAAGAAAACTGAAGACT 59.660 33.333 0.00 0.00 0.00 3.24
121 122 8.359642 CCATACTGATTGGAAAAGAAAACTGAA 58.640 33.333 0.00 0.00 36.26 3.02
122 123 7.523709 GCCATACTGATTGGAAAAGAAAACTGA 60.524 37.037 5.10 0.00 36.26 3.41
126 127 6.662865 TGCCATACTGATTGGAAAAGAAAA 57.337 33.333 5.10 0.00 36.26 2.29
129 130 4.098349 GCATGCCATACTGATTGGAAAAGA 59.902 41.667 6.36 0.00 36.26 2.52
131 132 3.768215 TGCATGCCATACTGATTGGAAAA 59.232 39.130 16.68 0.00 36.26 2.29
132 133 3.130869 GTGCATGCCATACTGATTGGAAA 59.869 43.478 16.68 0.00 36.26 3.13
133 134 2.689471 GTGCATGCCATACTGATTGGAA 59.311 45.455 16.68 0.00 36.26 3.53
135 136 2.034179 CAGTGCATGCCATACTGATTGG 59.966 50.000 24.96 4.21 43.35 3.16
136 137 2.034179 CCAGTGCATGCCATACTGATTG 59.966 50.000 28.79 14.46 43.35 2.67
137 138 2.304092 CCAGTGCATGCCATACTGATT 58.696 47.619 28.79 0.19 43.35 2.57
138 139 1.977056 CCAGTGCATGCCATACTGAT 58.023 50.000 28.79 0.56 43.35 2.90
139 140 0.749091 GCCAGTGCATGCCATACTGA 60.749 55.000 28.79 3.04 43.35 3.41
140 141 1.731700 GCCAGTGCATGCCATACTG 59.268 57.895 23.17 23.17 41.04 2.74
144 145 4.429522 TCCGCCAGTGCATGCCAT 62.430 61.111 16.68 0.00 37.32 4.40
148 149 0.729116 CTAAACTCCGCCAGTGCATG 59.271 55.000 0.00 0.00 34.56 4.06
149 150 0.324943 ACTAAACTCCGCCAGTGCAT 59.675 50.000 0.00 0.00 34.56 3.96
153 154 0.107831 TTGCACTAAACTCCGCCAGT 59.892 50.000 0.00 0.00 36.64 4.00
156 157 1.583495 GGGTTGCACTAAACTCCGCC 61.583 60.000 0.00 0.00 0.00 6.13
157 158 0.605589 AGGGTTGCACTAAACTCCGC 60.606 55.000 0.00 0.00 30.25 5.54
158 159 1.156736 CAGGGTTGCACTAAACTCCG 58.843 55.000 0.00 0.00 30.25 4.63
185 186 3.966543 AAACCTGGGAGGGCGGTG 61.967 66.667 0.00 0.00 40.58 4.94
186 187 3.966543 CAAACCTGGGAGGGCGGT 61.967 66.667 0.00 0.00 40.58 5.68
196 197 7.519032 TTCTTCAGTAATTTACCCAAACCTG 57.481 36.000 2.92 0.00 0.00 4.00
198 199 9.772973 AATTTTCTTCAGTAATTTACCCAAACC 57.227 29.630 2.92 0.00 0.00 3.27
211 212 8.303876 GCTGTCCCATAAAAATTTTCTTCAGTA 58.696 33.333 3.41 0.00 0.00 2.74
214 215 7.060383 TGCTGTCCCATAAAAATTTTCTTCA 57.940 32.000 3.41 0.00 0.00 3.02
215 216 8.552083 AATGCTGTCCCATAAAAATTTTCTTC 57.448 30.769 3.41 0.00 0.00 2.87
216 217 9.435688 GTAATGCTGTCCCATAAAAATTTTCTT 57.564 29.630 3.41 0.00 0.00 2.52
219 220 7.109501 GGGTAATGCTGTCCCATAAAAATTTT 58.890 34.615 0.00 0.00 40.79 1.82
220 221 6.352651 GGGGTAATGCTGTCCCATAAAAATTT 60.353 38.462 0.00 0.00 42.71 1.82
221 222 5.130311 GGGGTAATGCTGTCCCATAAAAATT 59.870 40.000 0.00 0.00 42.71 1.82
222 223 4.653801 GGGGTAATGCTGTCCCATAAAAAT 59.346 41.667 0.00 0.00 42.71 1.82
223 224 4.027437 GGGGTAATGCTGTCCCATAAAAA 58.973 43.478 0.00 0.00 42.71 1.94
224 225 3.628769 GGGGGTAATGCTGTCCCATAAAA 60.629 47.826 0.00 0.00 42.71 1.52
225 226 2.091555 GGGGGTAATGCTGTCCCATAAA 60.092 50.000 0.00 0.00 42.71 1.40
228 229 1.930520 GGGGGTAATGCTGTCCCAT 59.069 57.895 0.00 0.00 42.71 4.00
229 230 3.422204 GGGGGTAATGCTGTCCCA 58.578 61.111 0.00 0.00 42.71 4.37
246 247 1.377856 TGTGTGTGTGTGTGGTGGG 60.378 57.895 0.00 0.00 0.00 4.61
248 249 1.093972 ATGTGTGTGTGTGTGTGGTG 58.906 50.000 0.00 0.00 0.00 4.17
253 254 2.423185 AGGTTCAATGTGTGTGTGTGTG 59.577 45.455 0.00 0.00 0.00 3.82
255 256 3.119531 ACAAGGTTCAATGTGTGTGTGTG 60.120 43.478 0.00 0.00 0.00 3.82
256 257 3.088532 ACAAGGTTCAATGTGTGTGTGT 58.911 40.909 0.00 0.00 0.00 3.72
257 258 3.128415 TCACAAGGTTCAATGTGTGTGTG 59.872 43.478 5.88 0.00 45.52 3.82
258 259 3.351740 TCACAAGGTTCAATGTGTGTGT 58.648 40.909 5.88 0.00 45.52 3.72
259 260 4.353737 CTTCACAAGGTTCAATGTGTGTG 58.646 43.478 5.88 0.00 45.52 3.82
261 262 3.067180 AGCTTCACAAGGTTCAATGTGTG 59.933 43.478 5.88 0.00 45.52 3.82
263 264 3.304928 GGAGCTTCACAAGGTTCAATGTG 60.305 47.826 0.00 0.00 46.44 3.21
264 265 2.887152 GGAGCTTCACAAGGTTCAATGT 59.113 45.455 0.00 0.00 39.77 2.71
336 337 2.821437 TCCCTCACCCTCTACTTCTTG 58.179 52.381 0.00 0.00 0.00 3.02
343 344 0.710588 TCTGCTTCCCTCACCCTCTA 59.289 55.000 0.00 0.00 0.00 2.43
347 348 1.683319 GGAATTCTGCTTCCCTCACCC 60.683 57.143 5.23 0.00 39.06 4.61
348 349 1.756430 GGAATTCTGCTTCCCTCACC 58.244 55.000 5.23 0.00 39.06 4.02
350 351 0.253044 CCGGAATTCTGCTTCCCTCA 59.747 55.000 8.91 0.00 41.46 3.86
369 370 3.118920 AGTTTTGGGCAACACCTGTAAAC 60.119 43.478 0.00 0.00 39.10 2.01
375 376 2.092103 TCAGTAGTTTTGGGCAACACCT 60.092 45.455 0.00 0.00 39.10 4.00
379 380 3.188667 GCTAGTCAGTAGTTTTGGGCAAC 59.811 47.826 0.00 0.00 0.00 4.17
382 383 3.055747 AGAGCTAGTCAGTAGTTTTGGGC 60.056 47.826 0.00 0.00 0.00 5.36
396 397 6.715718 TGTTAGTGTACAAGAAGAGAGCTAGT 59.284 38.462 0.00 0.00 0.00 2.57
406 407 7.350744 TGGTAACTCTGTTAGTGTACAAGAA 57.649 36.000 0.00 0.00 38.88 2.52
584 589 6.252228 GCAAATAGCAATCAAAGTGAAGTAGC 59.748 38.462 0.00 0.00 44.79 3.58
804 5074 0.615331 TGAGGCGGAGAAAGAGCATT 59.385 50.000 0.00 0.00 0.00 3.56
807 5077 1.813337 GCTGAGGCGGAGAAAGAGC 60.813 63.158 0.00 0.00 0.00 4.09
882 5152 4.141413 TGTGCTACAATCTAGAATGCCCAT 60.141 41.667 7.75 0.00 0.00 4.00
883 5153 3.199727 TGTGCTACAATCTAGAATGCCCA 59.800 43.478 7.75 0.27 0.00 5.36
920 5190 7.787725 AATTAGGAAATTATGTGAGACGACC 57.212 36.000 0.00 0.00 33.45 4.79
938 5212 5.767168 CCTGGAAGATGGAAGCTAAATTAGG 59.233 44.000 1.88 0.00 34.07 2.69
1283 5587 2.125512 GTGGTGCTCAGGGCTACG 60.126 66.667 0.00 0.00 42.39 3.51
1316 5620 7.175347 TCTGACTTATGTAGTGAAGAGCATT 57.825 36.000 0.00 0.00 37.17 3.56
1336 5640 1.827344 ACGTCTTCCATCAGCATCTGA 59.173 47.619 0.00 0.00 44.99 3.27
1393 5701 3.382803 CTTCTCAGCGGCCTGGAGG 62.383 68.421 13.24 0.00 39.61 4.30
1438 5746 2.455032 CAGTCAGTAGCTGATGCGTAC 58.545 52.381 0.00 0.00 42.73 3.67
1447 5755 3.775654 GGCGGCCAGTCAGTAGCT 61.776 66.667 15.62 0.00 0.00 3.32
1474 5782 2.230266 AGCGTTGTCTGGTTTGTTGTTT 59.770 40.909 0.00 0.00 0.00 2.83
1714 6028 6.183360 GCTTATCAATACTTGGAGCACACATT 60.183 38.462 0.00 0.00 34.21 2.71
1719 6036 4.274459 CCAGCTTATCAATACTTGGAGCAC 59.726 45.833 0.00 0.00 35.47 4.40
1866 6183 4.202493 TGGCATGATGTGTATTGCTCCTAT 60.202 41.667 0.00 0.00 35.46 2.57
1867 6184 3.136260 TGGCATGATGTGTATTGCTCCTA 59.864 43.478 0.00 0.00 35.46 2.94
1878 6195 3.057104 ACAAGTTGTGATGGCATGATGTG 60.057 43.478 7.96 0.00 0.00 3.21
2165 6485 1.302832 CTGGTGAGGAGTGTTGCCC 60.303 63.158 0.00 0.00 0.00 5.36
2238 6558 2.121963 TCCTGGTCCCAGCCAAGT 60.122 61.111 7.87 0.00 42.35 3.16
2252 6574 7.020827 TGAGATTTTGATAAACCTGACTCCT 57.979 36.000 0.00 0.00 0.00 3.69
2447 6775 4.803329 ACCTCTGAATCATTAATGGCCT 57.197 40.909 15.36 0.44 0.00 5.19
2542 6870 3.875727 CTGTCTCCTTGATCATTTCGCAT 59.124 43.478 0.00 0.00 0.00 4.73
2569 6897 1.832883 TTGCATAATCAGCCAACCGT 58.167 45.000 0.00 0.00 0.00 4.83
2893 7223 0.173255 CCCGTGGAACATTTGCATCC 59.827 55.000 0.00 0.00 44.52 3.51
2947 7283 2.361610 AGTGCATCCCGCCCAAAG 60.362 61.111 0.00 0.00 41.33 2.77
2965 7302 2.635714 TCCTCACATGCTATGCTGTTG 58.364 47.619 0.00 0.00 0.00 3.33
3127 7465 3.233507 ACCACCATCTTCAACAGCAAAT 58.766 40.909 0.00 0.00 0.00 2.32
3143 11964 1.244019 CCTTGCAGTAGCCAACCACC 61.244 60.000 0.00 0.00 41.13 4.61
3237 12058 5.652014 ACACCAGATTCACTTGAAAAACTGA 59.348 36.000 17.69 0.00 37.61 3.41
3308 12139 4.900635 ACAGTAGCCTTTTTGTTCACTG 57.099 40.909 0.00 0.00 38.26 3.66
3324 12291 6.128391 CGGCAGAAGCAAAGTATTTTACAGTA 60.128 38.462 0.00 0.00 44.61 2.74
3445 12514 6.707608 AGAAATATTCAGCGCAATGATCTACA 59.292 34.615 11.47 0.00 0.00 2.74
3446 12515 7.095481 TGAGAAATATTCAGCGCAATGATCTAC 60.095 37.037 11.47 1.13 0.00 2.59
3447 12516 6.930722 TGAGAAATATTCAGCGCAATGATCTA 59.069 34.615 11.47 1.21 0.00 1.98
3467 12536 4.842531 TCCATATCACCAGCTTTGAGAA 57.157 40.909 1.46 0.00 0.00 2.87
3572 12998 7.517614 TCAAACTCCACTTATTTGTTGCATA 57.482 32.000 0.00 0.00 35.33 3.14
3575 13001 6.039616 TGTTCAAACTCCACTTATTTGTTGC 58.960 36.000 0.00 0.00 35.33 4.17
3576 13002 7.306749 GCATGTTCAAACTCCACTTATTTGTTG 60.307 37.037 0.00 0.00 35.33 3.33
3577 13003 6.701400 GCATGTTCAAACTCCACTTATTTGTT 59.299 34.615 0.00 0.00 35.33 2.83
3602 13070 7.925703 TGAAGTAGAAGTTTTACAGAAGACG 57.074 36.000 6.36 0.00 0.00 4.18
3619 13089 6.739112 TCTCGTCCATGTATGATTGAAGTAG 58.261 40.000 0.00 0.00 0.00 2.57
3631 13179 1.128200 CCCCCAATCTCGTCCATGTA 58.872 55.000 0.00 0.00 0.00 2.29
3634 13182 0.620410 TCACCCCCAATCTCGTCCAT 60.620 55.000 0.00 0.00 0.00 3.41
3642 13190 1.923356 TTTGAAGCTCACCCCCAATC 58.077 50.000 0.00 0.00 0.00 2.67
3646 13194 2.149973 ATGATTTGAAGCTCACCCCC 57.850 50.000 0.00 0.00 0.00 5.40
3651 13199 4.571984 CGTCCATGTATGATTTGAAGCTCA 59.428 41.667 0.00 0.00 0.00 4.26
3652 13200 4.811024 TCGTCCATGTATGATTTGAAGCTC 59.189 41.667 0.00 0.00 0.00 4.09
3653 13201 4.769688 TCGTCCATGTATGATTTGAAGCT 58.230 39.130 0.00 0.00 0.00 3.74
3654 13202 4.811024 TCTCGTCCATGTATGATTTGAAGC 59.189 41.667 0.00 0.00 0.00 3.86
3655 13203 7.350467 CAATCTCGTCCATGTATGATTTGAAG 58.650 38.462 0.00 0.00 0.00 3.02
3656 13204 6.260714 CCAATCTCGTCCATGTATGATTTGAA 59.739 38.462 0.00 0.00 0.00 2.69
3664 13279 1.699634 CCCCCAATCTCGTCCATGTAT 59.300 52.381 0.00 0.00 0.00 2.29
3668 13283 0.620410 TCACCCCCAATCTCGTCCAT 60.620 55.000 0.00 0.00 0.00 3.41
3673 13288 1.144936 GAGCTCACCCCCAATCTCG 59.855 63.158 9.40 0.00 0.00 4.04
3680 13295 0.681243 GTGATTTGGAGCTCACCCCC 60.681 60.000 17.19 0.00 36.59 5.40
3681 13296 2.873797 GTGATTTGGAGCTCACCCC 58.126 57.895 17.19 0.00 36.59 4.95
3684 13299 1.457346 CCTGGTGATTTGGAGCTCAC 58.543 55.000 17.19 4.40 40.82 3.51
3685 13300 0.329261 CCCTGGTGATTTGGAGCTCA 59.671 55.000 17.19 0.00 0.00 4.26
3686 13301 1.034292 GCCCTGGTGATTTGGAGCTC 61.034 60.000 4.71 4.71 0.00 4.09
3687 13302 1.000396 GCCCTGGTGATTTGGAGCT 60.000 57.895 0.00 0.00 0.00 4.09
3688 13303 2.054453 GGCCCTGGTGATTTGGAGC 61.054 63.158 0.00 0.00 0.00 4.70
3689 13304 0.967380 GTGGCCCTGGTGATTTGGAG 60.967 60.000 0.00 0.00 0.00 3.86
3690 13305 1.076549 GTGGCCCTGGTGATTTGGA 59.923 57.895 0.00 0.00 0.00 3.53
3691 13306 2.342650 CGTGGCCCTGGTGATTTGG 61.343 63.158 0.00 0.00 0.00 3.28
3693 13308 2.035626 CCGTGGCCCTGGTGATTT 59.964 61.111 0.00 0.00 0.00 2.17
3694 13309 2.933287 TCCGTGGCCCTGGTGATT 60.933 61.111 0.00 0.00 0.00 2.57
3696 13311 4.631740 TCTCCGTGGCCCTGGTGA 62.632 66.667 0.00 5.59 0.00 4.02
3697 13312 4.394712 GTCTCCGTGGCCCTGGTG 62.395 72.222 0.00 2.85 0.00 4.17
3698 13313 4.954118 TGTCTCCGTGGCCCTGGT 62.954 66.667 0.00 0.00 0.00 4.00
3709 13351 1.381327 TCTGATCCCCCGTGTCTCC 60.381 63.158 0.00 0.00 0.00 3.71
3721 13363 1.743321 CGCCCTCACCCTCTCTGATC 61.743 65.000 0.00 0.00 0.00 2.92
3733 13375 4.332543 AAGGTCCTCCCGCCCTCA 62.333 66.667 0.00 0.00 38.74 3.86
3739 13387 2.359967 GGTCTCCAAGGTCCTCCCG 61.360 68.421 0.00 0.00 38.74 5.14
3742 13390 1.324005 CCTCGGTCTCCAAGGTCCTC 61.324 65.000 0.00 0.00 0.00 3.71
3743 13391 1.305381 CCTCGGTCTCCAAGGTCCT 60.305 63.158 0.00 0.00 0.00 3.85
3746 13394 1.977544 CGACCTCGGTCTCCAAGGT 60.978 63.158 13.74 0.00 46.03 3.50
3747 13395 2.885861 CGACCTCGGTCTCCAAGG 59.114 66.667 13.74 0.00 42.54 3.61
3760 13408 1.219393 CTCTTCTCCTTGGCCGACC 59.781 63.158 0.00 0.00 0.00 4.79
3767 13415 0.461961 CGTAGGGGCTCTTCTCCTTG 59.538 60.000 0.00 0.00 32.46 3.61
3786 13443 3.179939 GGCGAAGGAAGACGACGC 61.180 66.667 0.00 0.00 43.52 5.19
3815 13472 3.474570 GACCTCTCCATGGCGGCT 61.475 66.667 11.43 0.00 33.14 5.52
3818 13487 2.202797 CGTGACCTCTCCATGGCG 60.203 66.667 6.96 0.00 0.00 5.69
3847 13516 3.580731 CTCTCTTTCTGTTCGGTTCTCC 58.419 50.000 0.00 0.00 0.00 3.71
3848 13517 3.580731 CCTCTCTTTCTGTTCGGTTCTC 58.419 50.000 0.00 0.00 0.00 2.87
3849 13518 2.300437 CCCTCTCTTTCTGTTCGGTTCT 59.700 50.000 0.00 0.00 0.00 3.01
3850 13519 2.299297 TCCCTCTCTTTCTGTTCGGTTC 59.701 50.000 0.00 0.00 0.00 3.62
3851 13520 2.037381 GTCCCTCTCTTTCTGTTCGGTT 59.963 50.000 0.00 0.00 0.00 4.44
3852 13521 1.619332 GTCCCTCTCTTTCTGTTCGGT 59.381 52.381 0.00 0.00 0.00 4.69
3853 13522 1.402984 CGTCCCTCTCTTTCTGTTCGG 60.403 57.143 0.00 0.00 0.00 4.30
3854 13523 1.540267 TCGTCCCTCTCTTTCTGTTCG 59.460 52.381 0.00 0.00 0.00 3.95
3855 13524 3.662247 TTCGTCCCTCTCTTTCTGTTC 57.338 47.619 0.00 0.00 0.00 3.18
3856 13525 4.563786 GGAATTCGTCCCTCTCTTTCTGTT 60.564 45.833 0.00 0.00 41.10 3.16
3857 13526 3.055747 GGAATTCGTCCCTCTCTTTCTGT 60.056 47.826 0.00 0.00 41.10 3.41
3858 13527 3.526534 GGAATTCGTCCCTCTCTTTCTG 58.473 50.000 0.00 0.00 41.10 3.02
3859 13528 2.166664 CGGAATTCGTCCCTCTCTTTCT 59.833 50.000 0.00 0.00 44.60 2.52
3860 13529 2.541556 CGGAATTCGTCCCTCTCTTTC 58.458 52.381 0.00 0.00 44.60 2.62
3861 13530 1.405661 GCGGAATTCGTCCCTCTCTTT 60.406 52.381 0.00 0.00 44.60 2.52
3862 13531 0.175989 GCGGAATTCGTCCCTCTCTT 59.824 55.000 0.00 0.00 44.60 2.85
3894 13563 1.155889 CACATCAGCCAGTGCGTAAA 58.844 50.000 0.00 0.00 44.33 2.01
3904 13573 1.079543 ACGACTCAGCACATCAGCC 60.080 57.895 0.00 0.00 34.23 4.85
3916 13611 4.083484 CCAGGTCCAATTAAAACACGACTC 60.083 45.833 0.00 0.00 0.00 3.36
3921 13616 2.028476 GGCCCAGGTCCAATTAAAACAC 60.028 50.000 0.00 0.00 0.00 3.32
3930 13625 3.589542 CTTGGGGCCCAGGTCCAA 61.590 66.667 27.05 16.99 42.75 3.53
3944 13639 1.298859 GCCTAACCGGACACAGCTTG 61.299 60.000 9.46 0.00 33.16 4.01
3955 13650 0.107848 CTGTAAGGTGGGCCTAACCG 60.108 60.000 18.75 4.60 46.33 4.44
3980 13676 2.774439 TCTTTTGTTTTCTGCGAGGC 57.226 45.000 0.00 0.00 0.00 4.70
4107 13803 4.712476 CTTGCAGAGGGAGTAATATGCTT 58.288 43.478 0.00 0.00 34.80 3.91
4109 13805 2.810852 GCTTGCAGAGGGAGTAATATGC 59.189 50.000 0.00 0.00 0.00 3.14
4117 13813 6.760770 GCTATTATATTAGCTTGCAGAGGGAG 59.239 42.308 16.07 0.00 41.15 4.30
4119 13815 6.409704 TGCTATTATATTAGCTTGCAGAGGG 58.590 40.000 21.32 0.00 44.03 4.30
4188 13941 9.091220 AGTAACCTTAACAATTACTCTCTCAGT 57.909 33.333 0.00 0.00 34.77 3.41
4189 13942 9.575783 GAGTAACCTTAACAATTACTCTCTCAG 57.424 37.037 13.55 0.00 45.94 3.35
4200 13953 9.379791 GTGCTTATGTAGAGTAACCTTAACAAT 57.620 33.333 0.00 0.00 0.00 2.71
4201 13954 8.591072 AGTGCTTATGTAGAGTAACCTTAACAA 58.409 33.333 0.00 0.00 0.00 2.83
4202 13955 8.130671 AGTGCTTATGTAGAGTAACCTTAACA 57.869 34.615 0.00 0.00 0.00 2.41
4230 13983 5.734311 ACAATGACAGTCGTTAAGTTTTCG 58.266 37.500 7.73 0.00 0.00 3.46
4318 14517 7.274447 TCTGGCAATGACTTTTCAGAAATTTT 58.726 30.769 0.00 0.00 34.35 1.82
4325 14524 4.778534 ACATCTGGCAATGACTTTTCAG 57.221 40.909 13.95 0.00 34.35 3.02


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

AutoCloner maintained by Alex Coulton.