Multiple sequence alignment - TraesCS1D01G204500

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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 TraesCS1D01G204500 chr1D 100.000 3478 0 0 1 3478 289773736 289777213 0.000000e+00 6423
1 TraesCS1D01G204500 chr1D 90.991 222 18 2 1 222 37440695 37440914 7.300000e-77 298
2 TraesCS1D01G204500 chr1D 78.099 242 37 13 1937 2176 238467441 238467668 4.680000e-29 139
3 TraesCS1D01G204500 chr1A 92.558 2150 115 21 221 2362 362190125 362192237 0.000000e+00 3042
4 TraesCS1D01G204500 chr1A 89.530 1127 74 26 2362 3477 362192273 362193366 0.000000e+00 1387
5 TraesCS1D01G204500 chr1A 94.048 84 5 0 1950 2033 302197298 302197381 1.010000e-25 128
6 TraesCS1D01G204500 chr1B 91.070 1075 59 17 221 1287 391066331 391067376 0.000000e+00 1419
7 TraesCS1D01G204500 chr1B 92.680 970 45 13 1403 2362 391067416 391068369 0.000000e+00 1375
8 TraesCS1D01G204500 chr1B 85.613 1126 69 39 2364 3478 391068407 391069450 0.000000e+00 1096
9 TraesCS1D01G204500 chr1B 78.509 228 35 11 1946 2172 335735971 335735757 1.680000e-28 137
10 TraesCS1D01G204500 chr3D 91.964 224 16 1 1 222 491992292 491992069 2.610000e-81 313
11 TraesCS1D01G204500 chr3D 90.625 224 21 0 1 224 495167529 495167306 7.300000e-77 298
12 TraesCS1D01G204500 chr3A 90.991 222 19 1 1 222 523610237 523610017 7.300000e-77 298
13 TraesCS1D01G204500 chr7D 90.583 223 21 0 1 223 506498866 506498644 2.620000e-76 296
14 TraesCS1D01G204500 chr5A 90.090 222 22 0 1 222 632833914 632834135 4.390000e-74 289
15 TraesCS1D01G204500 chr5A 80.889 225 35 7 363 583 409327921 409328141 1.660000e-38 171
16 TraesCS1D01G204500 chr5A 80.952 168 28 2 388 555 86668924 86668761 2.820000e-26 130
17 TraesCS1D01G204500 chr3B 89.640 222 21 1 1 222 763200316 763200097 7.350000e-72 281
18 TraesCS1D01G204500 chr3B 84.541 207 27 5 363 567 31521198 31521401 2.120000e-47 200
19 TraesCS1D01G204500 chr7B 88.739 222 25 0 2 223 616689278 616689499 4.420000e-69 272
20 TraesCS1D01G204500 chrUn 88.053 226 27 0 1 226 35417372 35417147 5.720000e-68 268
21 TraesCS1D01G204500 chr6B 84.490 245 33 4 343 583 650790901 650791144 1.610000e-58 237
22 TraesCS1D01G204500 chr5B 80.383 209 32 5 348 555 98675350 98675150 2.160000e-32 150


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 TraesCS1D01G204500 chr1D 289773736 289777213 3477 False 6423.000000 6423 100.000000 1 3478 1 chr1D.!!$F3 3477
1 TraesCS1D01G204500 chr1A 362190125 362193366 3241 False 2214.500000 3042 91.044000 221 3477 2 chr1A.!!$F2 3256
2 TraesCS1D01G204500 chr1B 391066331 391069450 3119 False 1296.666667 1419 89.787667 221 3478 3 chr1B.!!$F1 3257

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
200 201 0.334676 TGAGGCATTTTACCCCTGGG 59.665 55.000 5.5 5.5 42.03 4.45 F
1505 1520 1.362237 TCTTTGGCCCCTTTCCATCAT 59.638 47.619 0.0 0.0 32.92 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1715 1.050204 GATGATGCTCTCCTCTGCCT 58.950 55.0 0.00 0.0 0.0 4.75 R
2883 2950 0.106519 GTGAGCTATGCCCCATGGTT 60.107 55.0 11.73 0.0 0.0 3.67 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
31 32 4.201208 CGGTCAAAATCGGATGATCAAG 57.799 45.455 0.00 0.00 32.24 3.02
32 33 3.623060 CGGTCAAAATCGGATGATCAAGT 59.377 43.478 0.00 0.00 32.24 3.16
33 34 4.094887 CGGTCAAAATCGGATGATCAAGTT 59.905 41.667 0.00 0.00 32.24 2.66
34 35 5.391950 CGGTCAAAATCGGATGATCAAGTTT 60.392 40.000 0.00 0.00 32.24 2.66
35 36 6.389906 GGTCAAAATCGGATGATCAAGTTTT 58.610 36.000 0.00 0.74 32.24 2.43
36 37 7.535139 GGTCAAAATCGGATGATCAAGTTTTA 58.465 34.615 0.00 0.00 32.24 1.52
37 38 8.026607 GGTCAAAATCGGATGATCAAGTTTTAA 58.973 33.333 0.00 0.00 32.24 1.52
38 39 9.405587 GTCAAAATCGGATGATCAAGTTTTAAA 57.594 29.630 0.00 0.00 32.24 1.52
39 40 9.405587 TCAAAATCGGATGATCAAGTTTTAAAC 57.594 29.630 0.00 0.00 32.24 2.01
40 41 9.410556 CAAAATCGGATGATCAAGTTTTAAACT 57.589 29.630 4.30 4.30 37.27 2.66
41 42 8.970691 AAATCGGATGATCAAGTTTTAAACTG 57.029 30.769 11.35 6.11 36.29 3.16
42 43 7.921786 ATCGGATGATCAAGTTTTAAACTGA 57.078 32.000 11.35 10.89 41.91 3.41
43 44 7.737972 TCGGATGATCAAGTTTTAAACTGAA 57.262 32.000 11.35 3.21 41.91 3.02
44 45 7.806690 TCGGATGATCAAGTTTTAAACTGAAG 58.193 34.615 11.35 5.18 41.91 3.02
45 46 7.659799 TCGGATGATCAAGTTTTAAACTGAAGA 59.340 33.333 11.35 10.09 41.91 2.87
46 47 7.746475 CGGATGATCAAGTTTTAAACTGAAGAC 59.254 37.037 11.35 3.81 41.91 3.01
47 48 8.023706 GGATGATCAAGTTTTAAACTGAAGACC 58.976 37.037 11.35 2.38 41.91 3.85
48 49 8.697507 ATGATCAAGTTTTAAACTGAAGACCT 57.302 30.769 11.35 0.00 41.91 3.85
49 50 8.154649 TGATCAAGTTTTAAACTGAAGACCTC 57.845 34.615 11.35 6.52 41.91 3.85
50 51 7.773224 TGATCAAGTTTTAAACTGAAGACCTCA 59.227 33.333 11.35 8.60 41.91 3.86
51 52 7.931578 TCAAGTTTTAAACTGAAGACCTCAA 57.068 32.000 11.35 0.00 41.91 3.02
52 53 8.519799 TCAAGTTTTAAACTGAAGACCTCAAT 57.480 30.769 11.35 0.00 41.91 2.57
53 54 9.621629 TCAAGTTTTAAACTGAAGACCTCAATA 57.378 29.630 11.35 0.00 41.91 1.90
59 60 8.974060 TTAAACTGAAGACCTCAATAAACTGT 57.026 30.769 0.00 0.00 32.17 3.55
60 61 6.867662 AACTGAAGACCTCAATAAACTGTG 57.132 37.500 0.00 0.00 32.17 3.66
61 62 6.174720 ACTGAAGACCTCAATAAACTGTGA 57.825 37.500 0.00 0.00 32.17 3.58
62 63 6.226787 ACTGAAGACCTCAATAAACTGTGAG 58.773 40.000 0.00 0.00 40.84 3.51
134 135 9.950680 TTAGAGCTTTAAGAAATTGTTGACTTG 57.049 29.630 0.00 0.00 0.00 3.16
135 136 7.428826 AGAGCTTTAAGAAATTGTTGACTTGG 58.571 34.615 0.00 0.00 0.00 3.61
136 137 7.068716 AGAGCTTTAAGAAATTGTTGACTTGGT 59.931 33.333 0.00 0.00 0.00 3.67
137 138 7.203218 AGCTTTAAGAAATTGTTGACTTGGTC 58.797 34.615 0.00 0.00 0.00 4.02
138 139 6.978080 GCTTTAAGAAATTGTTGACTTGGTCA 59.022 34.615 0.00 0.00 41.09 4.02
149 150 3.636679 TGACTTGGTCAAAATTGGGTGA 58.363 40.909 0.00 0.00 39.78 4.02
150 151 3.383185 TGACTTGGTCAAAATTGGGTGAC 59.617 43.478 8.11 8.11 39.78 3.67
182 183 4.852134 TTGGACACCTCAATTGATTGTG 57.148 40.909 25.27 25.27 38.84 3.33
183 184 4.097551 TGGACACCTCAATTGATTGTGA 57.902 40.909 30.09 15.05 38.84 3.58
184 185 4.074259 TGGACACCTCAATTGATTGTGAG 58.926 43.478 30.09 12.38 40.84 3.51
193 194 7.515957 CTCAATTGATTGTGAGGCATTTTAC 57.484 36.000 8.96 0.00 38.08 2.01
194 195 6.397272 TCAATTGATTGTGAGGCATTTTACC 58.603 36.000 3.38 0.00 38.84 2.85
195 196 4.799564 TTGATTGTGAGGCATTTTACCC 57.200 40.909 0.00 0.00 0.00 3.69
196 197 3.096092 TGATTGTGAGGCATTTTACCCC 58.904 45.455 0.00 0.00 0.00 4.95
197 198 2.990740 TTGTGAGGCATTTTACCCCT 57.009 45.000 0.00 0.00 0.00 4.79
198 199 2.214376 TGTGAGGCATTTTACCCCTG 57.786 50.000 0.00 0.00 0.00 4.45
199 200 1.272425 TGTGAGGCATTTTACCCCTGG 60.272 52.381 0.00 0.00 0.00 4.45
200 201 0.334676 TGAGGCATTTTACCCCTGGG 59.665 55.000 5.50 5.50 42.03 4.45
211 212 4.480480 CCCTGGGGAGCTTAGTGA 57.520 61.111 4.27 0.00 37.50 3.41
212 213 2.936823 CCCTGGGGAGCTTAGTGAT 58.063 57.895 4.27 0.00 37.50 3.06
213 214 2.103153 CCCTGGGGAGCTTAGTGATA 57.897 55.000 4.27 0.00 37.50 2.15
214 215 2.625639 CCCTGGGGAGCTTAGTGATAT 58.374 52.381 4.27 0.00 37.50 1.63
215 216 3.791320 CCCTGGGGAGCTTAGTGATATA 58.209 50.000 4.27 0.00 37.50 0.86
216 217 3.772025 CCCTGGGGAGCTTAGTGATATAG 59.228 52.174 4.27 0.00 37.50 1.31
217 218 4.421131 CCTGGGGAGCTTAGTGATATAGT 58.579 47.826 0.00 0.00 0.00 2.12
218 219 5.518546 CCCTGGGGAGCTTAGTGATATAGTA 60.519 48.000 4.27 0.00 37.50 1.82
219 220 5.654650 CCTGGGGAGCTTAGTGATATAGTAG 59.345 48.000 0.00 0.00 0.00 2.57
244 245 8.943085 AGATTAGGAAAACCATCTGATAGACAT 58.057 33.333 0.00 0.00 0.00 3.06
262 263 6.391227 AGACATAAACAGAAACAAACAGGG 57.609 37.500 0.00 0.00 0.00 4.45
273 274 4.584327 AACAAACAGGGTCATGTAAAGC 57.416 40.909 0.00 0.00 31.70 3.51
280 281 3.879295 CAGGGTCATGTAAAGCATACCAG 59.121 47.826 0.00 0.00 35.74 4.00
282 283 4.130118 GGGTCATGTAAAGCATACCAGAG 58.870 47.826 0.00 0.00 35.74 3.35
358 359 8.909923 TCGTTTCATAATCATCTACTACCTTCA 58.090 33.333 0.00 0.00 0.00 3.02
365 366 6.831664 ATCATCTACTACCTTCATTTGGGT 57.168 37.500 0.00 0.00 39.40 4.51
386 387 9.548631 TTGGGTTTATTGGTTCCTTTCATATTA 57.451 29.630 0.00 0.00 0.00 0.98
401 402 8.124199 CCTTTCATATTATGTGCCAAATTTTGC 58.876 33.333 7.29 7.29 0.00 3.68
410 411 3.928375 GTGCCAAATTTTGCCTGTAGATG 59.072 43.478 11.39 0.00 0.00 2.90
426 427 8.893727 GCCTGTAGATGTGACTAACAAAATATT 58.106 33.333 0.00 0.00 43.61 1.28
647 651 4.836125 TCAAACAACAGGCAGATTCTTC 57.164 40.909 0.00 0.00 0.00 2.87
675 679 7.408756 ACACCAAATGTAATATTGATGTGCT 57.591 32.000 0.00 0.00 40.88 4.40
711 715 8.135382 TCTCTTTGTAGCTTTTCACCTATACT 57.865 34.615 0.00 0.00 0.00 2.12
715 719 5.647589 TGTAGCTTTTCACCTATACTGTCG 58.352 41.667 0.00 0.00 0.00 4.35
716 720 4.803098 AGCTTTTCACCTATACTGTCGT 57.197 40.909 0.00 0.00 0.00 4.34
913 919 4.093998 CACAAGCAGCTACTCCAGTATTTG 59.906 45.833 0.00 0.00 0.00 2.32
1041 1047 2.573915 GTCCAGGGAAGAGGATGACTTT 59.426 50.000 0.00 0.00 36.11 2.66
1132 1138 2.611225 TTTTTGCTTTTGCCCATCGT 57.389 40.000 0.00 0.00 46.87 3.73
1155 1161 6.963242 CGTCTTCATTCAACTGTTCATATTGG 59.037 38.462 0.00 0.00 0.00 3.16
1161 1167 9.952030 TCATTCAACTGTTCATATTGGTACTAA 57.048 29.630 0.00 0.00 0.00 2.24
1165 1171 9.787435 TCAACTGTTCATATTGGTACTAAGTTT 57.213 29.630 0.00 0.00 0.00 2.66
1178 1186 8.439964 TGGTACTAAGTTTACCTCCATTAACT 57.560 34.615 5.55 0.00 39.94 2.24
1181 1189 6.637657 ACTAAGTTTACCTCCATTAACTCCG 58.362 40.000 0.00 0.00 30.92 4.63
1249 1264 2.287769 GGTTGTTTGTTTGGCTTGCAT 58.712 42.857 0.00 0.00 0.00 3.96
1257 1272 4.642445 TGTTTGGCTTGCATATGATCTG 57.358 40.909 6.97 0.00 0.00 2.90
1269 1284 9.499585 CTTGCATATGATCTGTCTAAAAAGTTG 57.500 33.333 6.97 0.00 0.00 3.16
1271 1286 6.630443 GCATATGATCTGTCTAAAAAGTTGCG 59.370 38.462 6.97 0.00 0.00 4.85
1272 1287 4.404507 TGATCTGTCTAAAAAGTTGCGC 57.595 40.909 0.00 0.00 0.00 6.09
1297 1312 8.864024 GCTTGTTAATTTAGAAGAAAGATTGGC 58.136 33.333 5.61 0.00 0.00 4.52
1298 1313 9.358872 CTTGTTAATTTAGAAGAAAGATTGGCC 57.641 33.333 0.00 0.00 0.00 5.36
1314 1329 5.670361 AGATTGGCCCAACTTATAAGGTCTA 59.330 40.000 16.73 0.00 0.00 2.59
1445 1460 7.006210 GCACGTTTCTTATCGATTTTGTACTTG 59.994 37.037 1.71 2.90 0.00 3.16
1447 1462 8.553696 ACGTTTCTTATCGATTTTGTACTTGTT 58.446 29.630 1.71 0.00 0.00 2.83
1494 1509 1.886542 CCTAGTGTTGTTCTTTGGCCC 59.113 52.381 0.00 0.00 0.00 5.80
1495 1510 1.886542 CTAGTGTTGTTCTTTGGCCCC 59.113 52.381 0.00 0.00 0.00 5.80
1503 1518 1.550524 GTTCTTTGGCCCCTTTCCATC 59.449 52.381 0.00 0.00 32.92 3.51
1505 1520 1.362237 TCTTTGGCCCCTTTCCATCAT 59.638 47.619 0.00 0.00 32.92 2.45
1543 1558 2.293122 TGCACAGAAACAACTACCATGC 59.707 45.455 0.00 0.00 0.00 4.06
1545 1560 3.365364 GCACAGAAACAACTACCATGCTC 60.365 47.826 0.00 0.00 0.00 4.26
1546 1561 3.814842 CACAGAAACAACTACCATGCTCA 59.185 43.478 0.00 0.00 0.00 4.26
1547 1562 4.456911 CACAGAAACAACTACCATGCTCAT 59.543 41.667 0.00 0.00 0.00 2.90
1548 1563 4.697352 ACAGAAACAACTACCATGCTCATC 59.303 41.667 0.00 0.00 0.00 2.92
1557 1572 4.526262 ACTACCATGCTCATCCATACTCTC 59.474 45.833 0.00 0.00 0.00 3.20
1700 1715 3.947841 GCACGGCAACTTCACGCA 61.948 61.111 0.00 0.00 0.00 5.24
1848 1870 1.812571 GTCACACCAATGTCCATCACC 59.187 52.381 0.00 0.00 36.72 4.02
1849 1871 1.176527 CACACCAATGTCCATCACCC 58.823 55.000 0.00 0.00 36.72 4.61
1850 1872 0.039618 ACACCAATGTCCATCACCCC 59.960 55.000 0.00 0.00 31.55 4.95
1858 1880 1.075374 TGTCCATCACCCCTTTTCCAG 59.925 52.381 0.00 0.00 0.00 3.86
1860 1882 2.024941 GTCCATCACCCCTTTTCCAGAT 60.025 50.000 0.00 0.00 0.00 2.90
1948 1970 0.752743 TCTGGCACTGCTTTGCTTGT 60.753 50.000 9.55 0.00 42.56 3.16
2386 2447 4.415150 CTGCGCCCCCATGACTGT 62.415 66.667 4.18 0.00 0.00 3.55
2390 2451 1.077501 CGCCCCCATGACTGTGATT 60.078 57.895 0.00 0.00 0.00 2.57
2490 2551 4.401202 TCGATGACTAGTAATCAAGTGGCA 59.599 41.667 18.64 0.00 0.00 4.92
2519 2582 5.130477 AGGTAGAATGGTTATCGTCAATGGT 59.870 40.000 0.00 0.00 0.00 3.55
2564 2629 3.436704 CCGCAAGATTGTCATGTACTGTT 59.563 43.478 0.00 0.00 43.02 3.16
2583 2648 9.429600 GTACTGTTAAACATTTACTGTGTTGTC 57.570 33.333 0.00 0.00 39.57 3.18
2647 2712 2.241176 TGAGCGGAAAGGTAATTCCCAT 59.759 45.455 0.74 0.00 45.03 4.00
2667 2732 4.353737 CATTTGAATCATAACTGGGCGTG 58.646 43.478 0.00 0.00 0.00 5.34
2714 2779 4.641989 AGACATTGCACAAGTTTCTTCAGT 59.358 37.500 0.00 0.00 0.00 3.41
2730 2795 8.728833 GTTTCTTCAGTGATGATCATCTTTTCT 58.271 33.333 30.65 20.95 38.60 2.52
2800 2867 4.502259 CCAGACCATATACTCAGTTCAGCC 60.502 50.000 0.00 0.00 0.00 4.85
2820 2887 3.860754 GCCAGTGGTTGCATAAAAGAACC 60.861 47.826 11.74 0.00 39.77 3.62
2825 2892 3.637229 TGGTTGCATAAAAGAACCGGAAA 59.363 39.130 9.46 0.00 41.85 3.13
2833 2900 1.021968 AAGAACCGGAAACTGCACAC 58.978 50.000 9.46 0.00 0.00 3.82
2866 2933 0.740868 AACCGTGTCAGGCATGATCG 60.741 55.000 17.38 17.38 37.87 3.69
2873 2940 1.590238 GTCAGGCATGATCGAAACTCG 59.410 52.381 3.55 0.00 42.10 4.18
2876 2943 2.791560 CAGGCATGATCGAAACTCGTAG 59.208 50.000 0.00 0.00 41.35 3.51
2878 2945 3.119101 AGGCATGATCGAAACTCGTAGTT 60.119 43.478 0.00 0.00 40.80 2.24
2879 2946 3.243177 GGCATGATCGAAACTCGTAGTTC 59.757 47.826 0.00 0.00 37.47 3.01
2880 2947 4.106197 GCATGATCGAAACTCGTAGTTCT 58.894 43.478 0.00 0.00 37.47 3.01
2881 2948 4.563184 GCATGATCGAAACTCGTAGTTCTT 59.437 41.667 0.00 0.00 37.47 2.52
2882 2949 5.062308 GCATGATCGAAACTCGTAGTTCTTT 59.938 40.000 0.00 0.00 37.47 2.52
2883 2950 6.252869 GCATGATCGAAACTCGTAGTTCTTTA 59.747 38.462 0.00 0.00 37.47 1.85
2884 2951 7.201410 GCATGATCGAAACTCGTAGTTCTTTAA 60.201 37.037 0.00 0.00 37.47 1.52
2885 2952 7.558435 TGATCGAAACTCGTAGTTCTTTAAC 57.442 36.000 0.00 0.00 37.47 2.01
2886 2953 6.583806 TGATCGAAACTCGTAGTTCTTTAACC 59.416 38.462 0.00 0.00 37.47 2.85
2887 2954 5.830912 TCGAAACTCGTAGTTCTTTAACCA 58.169 37.500 1.58 0.00 37.47 3.67
2888 2955 6.449698 TCGAAACTCGTAGTTCTTTAACCAT 58.550 36.000 1.58 0.00 37.47 3.55
2889 2956 6.364165 TCGAAACTCGTAGTTCTTTAACCATG 59.636 38.462 1.58 0.00 37.47 3.66
2890 2957 6.400727 CGAAACTCGTAGTTCTTTAACCATGG 60.401 42.308 11.19 11.19 37.47 3.66
2891 2958 4.828829 ACTCGTAGTTCTTTAACCATGGG 58.171 43.478 18.09 0.00 36.15 4.00
2892 2959 4.189231 CTCGTAGTTCTTTAACCATGGGG 58.811 47.826 18.09 0.71 36.15 4.96
2893 2960 2.681344 CGTAGTTCTTTAACCATGGGGC 59.319 50.000 18.09 0.00 37.90 5.80
2894 2961 2.990740 AGTTCTTTAACCATGGGGCA 57.009 45.000 18.09 0.00 37.90 5.36
2895 2962 3.473113 AGTTCTTTAACCATGGGGCAT 57.527 42.857 18.09 1.59 37.90 4.40
2896 2963 4.601406 AGTTCTTTAACCATGGGGCATA 57.399 40.909 18.09 0.55 37.90 3.14
2897 2964 4.536765 AGTTCTTTAACCATGGGGCATAG 58.463 43.478 18.09 6.75 37.90 2.23
2898 2965 2.944129 TCTTTAACCATGGGGCATAGC 58.056 47.619 18.09 0.00 37.90 2.97
2899 2966 2.513738 TCTTTAACCATGGGGCATAGCT 59.486 45.455 18.09 0.00 37.90 3.32
2917 2984 6.073873 GCATAGCTCACATCAGATTCAAGTAC 60.074 42.308 0.00 0.00 0.00 2.73
2920 2987 6.804677 AGCTCACATCAGATTCAAGTACTAG 58.195 40.000 0.00 0.00 0.00 2.57
2922 2989 6.917477 GCTCACATCAGATTCAAGTACTAGAG 59.083 42.308 0.00 0.00 0.00 2.43
2923 2990 7.416213 GCTCACATCAGATTCAAGTACTAGAGT 60.416 40.741 0.00 0.00 0.00 3.24
2925 2992 9.634021 TCACATCAGATTCAAGTACTAGAGTAT 57.366 33.333 0.00 0.00 32.54 2.12
2988 3071 2.433239 GGGACCTAAAATCCAGAGCGTA 59.567 50.000 0.00 0.00 38.06 4.42
2991 3074 4.039366 GGACCTAAAATCCAGAGCGTAGAT 59.961 45.833 0.00 0.00 36.15 1.98
2996 3079 1.476007 ATCCAGAGCGTAGATGGGGC 61.476 60.000 0.00 0.00 34.71 5.80
3000 3083 1.182385 AGAGCGTAGATGGGGCTAGC 61.182 60.000 6.04 6.04 37.10 3.42
3011 3094 1.343985 TGGGGCTAGCTAACAGGATCA 60.344 52.381 15.72 0.00 0.00 2.92
3020 3103 4.387598 AGCTAACAGGATCATGATGCTTC 58.612 43.478 25.46 12.75 37.39 3.86
3027 3110 5.104444 ACAGGATCATGATGCTTCTCTTCTT 60.104 40.000 25.46 0.57 37.39 2.52
3029 3112 4.515944 GGATCATGATGCTTCTCTTCTTGG 59.484 45.833 19.05 0.00 0.00 3.61
3054 3137 1.153647 CGAATGCGTCAGCCCTGTA 60.154 57.895 0.00 0.00 44.33 2.74
3065 3148 0.838122 AGCCCTGTACTGCTGACCTT 60.838 55.000 0.00 0.00 36.23 3.50
3066 3149 0.674895 GCCCTGTACTGCTGACCTTG 60.675 60.000 0.00 0.00 0.00 3.61
3067 3150 0.674895 CCCTGTACTGCTGACCTTGC 60.675 60.000 0.00 0.00 0.00 4.01
3068 3151 0.674895 CCTGTACTGCTGACCTTGCC 60.675 60.000 0.00 0.00 0.00 4.52
3069 3152 0.035317 CTGTACTGCTGACCTTGCCA 59.965 55.000 0.00 0.00 0.00 4.92
3083 3166 2.290514 CCTTGCCATCAGAGGTTCAGAA 60.291 50.000 0.00 0.00 0.00 3.02
3109 3192 2.290323 CCGGTTTCTTCTTGGAGTCCAT 60.290 50.000 14.00 0.00 31.53 3.41
3163 3246 4.822026 CACTTAACAAGGTGAGGACTAGG 58.178 47.826 0.00 0.00 35.69 3.02
3371 3456 9.887406 CTAGTTTCCTTTTAACAAAGCGAATAA 57.113 29.630 0.00 0.00 38.53 1.40
3398 3483 8.291191 TGAACTGCATGATGTTCCAATATTTA 57.709 30.769 20.76 4.96 41.10 1.40
3469 3557 1.339535 TGAAACGACATATGGGCAGCA 60.340 47.619 7.80 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.689383 CCGATTTTGACCGGATCAATAAT 57.311 39.130 9.46 15.00 46.80 1.28
9 10 2.560504 TGATCATCCGATTTTGACCGG 58.439 47.619 0.00 0.00 46.57 5.28
10 11 3.623060 ACTTGATCATCCGATTTTGACCG 59.377 43.478 0.00 0.00 29.66 4.79
11 12 5.567138 AACTTGATCATCCGATTTTGACC 57.433 39.130 0.00 0.00 29.66 4.02
12 13 8.964420 TTAAAACTTGATCATCCGATTTTGAC 57.036 30.769 0.00 0.00 29.66 3.18
13 14 9.405587 GTTTAAAACTTGATCATCCGATTTTGA 57.594 29.630 0.00 0.00 29.66 2.69
14 15 9.410556 AGTTTAAAACTTGATCATCCGATTTTG 57.589 29.630 0.00 0.00 39.04 2.44
15 16 9.410556 CAGTTTAAAACTTGATCATCCGATTTT 57.589 29.630 0.00 2.68 40.46 1.82
16 17 8.792633 TCAGTTTAAAACTTGATCATCCGATTT 58.207 29.630 0.00 0.00 40.46 2.17
17 18 8.335532 TCAGTTTAAAACTTGATCATCCGATT 57.664 30.769 0.00 0.00 40.46 3.34
18 19 7.921786 TCAGTTTAAAACTTGATCATCCGAT 57.078 32.000 0.00 0.00 40.46 4.18
19 20 7.659799 TCTTCAGTTTAAAACTTGATCATCCGA 59.340 33.333 0.00 0.00 40.46 4.55
20 21 7.746475 GTCTTCAGTTTAAAACTTGATCATCCG 59.254 37.037 0.00 0.00 40.46 4.18
21 22 8.023706 GGTCTTCAGTTTAAAACTTGATCATCC 58.976 37.037 0.00 0.00 40.46 3.51
22 23 8.787852 AGGTCTTCAGTTTAAAACTTGATCATC 58.212 33.333 0.00 0.00 40.46 2.92
23 24 8.697507 AGGTCTTCAGTTTAAAACTTGATCAT 57.302 30.769 0.00 0.00 40.46 2.45
24 25 7.773224 TGAGGTCTTCAGTTTAAAACTTGATCA 59.227 33.333 0.00 0.00 40.46 2.92
25 26 8.154649 TGAGGTCTTCAGTTTAAAACTTGATC 57.845 34.615 0.00 0.00 40.46 2.92
26 27 8.519799 TTGAGGTCTTCAGTTTAAAACTTGAT 57.480 30.769 0.00 0.00 40.46 2.57
27 28 7.931578 TTGAGGTCTTCAGTTTAAAACTTGA 57.068 32.000 0.00 0.00 40.46 3.02
33 34 9.403583 ACAGTTTATTGAGGTCTTCAGTTTAAA 57.596 29.630 0.00 0.00 37.07 1.52
34 35 8.836413 CACAGTTTATTGAGGTCTTCAGTTTAA 58.164 33.333 0.00 0.00 37.07 1.52
35 36 8.208224 TCACAGTTTATTGAGGTCTTCAGTTTA 58.792 33.333 0.00 0.00 37.07 2.01
36 37 7.054124 TCACAGTTTATTGAGGTCTTCAGTTT 58.946 34.615 0.00 0.00 37.07 2.66
37 38 6.591935 TCACAGTTTATTGAGGTCTTCAGTT 58.408 36.000 0.00 0.00 37.07 3.16
38 39 6.174720 TCACAGTTTATTGAGGTCTTCAGT 57.825 37.500 0.00 0.00 37.07 3.41
39 40 6.718454 CTCACAGTTTATTGAGGTCTTCAG 57.282 41.667 0.00 0.00 37.07 3.02
108 109 9.950680 CAAGTCAACAATTTCTTAAAGCTCTAA 57.049 29.630 0.00 0.00 0.00 2.10
109 110 8.567948 CCAAGTCAACAATTTCTTAAAGCTCTA 58.432 33.333 0.00 0.00 0.00 2.43
110 111 7.068716 ACCAAGTCAACAATTTCTTAAAGCTCT 59.931 33.333 0.00 0.00 0.00 4.09
111 112 7.203218 ACCAAGTCAACAATTTCTTAAAGCTC 58.797 34.615 0.00 0.00 0.00 4.09
112 113 7.112452 ACCAAGTCAACAATTTCTTAAAGCT 57.888 32.000 0.00 0.00 0.00 3.74
113 114 6.978080 TGACCAAGTCAACAATTTCTTAAAGC 59.022 34.615 0.00 0.00 39.78 3.51
114 115 8.925161 TTGACCAAGTCAACAATTTCTTAAAG 57.075 30.769 6.08 0.00 45.88 1.85
128 129 3.383185 GTCACCCAATTTTGACCAAGTCA 59.617 43.478 0.00 0.00 41.09 3.41
129 130 3.977427 GTCACCCAATTTTGACCAAGTC 58.023 45.455 1.61 0.00 36.85 3.01
159 160 5.539574 TCACAATCAATTGAGGTGTCCAATT 59.460 36.000 28.21 9.99 42.88 2.32
160 161 5.078949 TCACAATCAATTGAGGTGTCCAAT 58.921 37.500 28.21 8.63 40.14 3.16
161 162 4.468713 TCACAATCAATTGAGGTGTCCAA 58.531 39.130 28.21 15.46 40.14 3.53
162 163 4.074259 CTCACAATCAATTGAGGTGTCCA 58.926 43.478 28.21 16.61 40.14 4.02
163 164 4.691860 CTCACAATCAATTGAGGTGTCC 57.308 45.455 28.21 0.00 40.14 4.02
169 170 6.532657 GGTAAAATGCCTCACAATCAATTGAG 59.467 38.462 14.54 3.71 40.14 3.02
170 171 6.397272 GGTAAAATGCCTCACAATCAATTGA 58.603 36.000 11.26 11.26 40.14 2.57
171 172 5.581874 GGGTAAAATGCCTCACAATCAATTG 59.418 40.000 0.00 0.00 43.26 2.32
172 173 5.338300 GGGGTAAAATGCCTCACAATCAATT 60.338 40.000 0.00 0.00 0.00 2.32
173 174 4.162131 GGGGTAAAATGCCTCACAATCAAT 59.838 41.667 0.00 0.00 0.00 2.57
174 175 3.513515 GGGGTAAAATGCCTCACAATCAA 59.486 43.478 0.00 0.00 0.00 2.57
175 176 3.096092 GGGGTAAAATGCCTCACAATCA 58.904 45.455 0.00 0.00 0.00 2.57
176 177 3.131046 CAGGGGTAAAATGCCTCACAATC 59.869 47.826 0.00 0.00 0.00 2.67
177 178 3.099141 CAGGGGTAAAATGCCTCACAAT 58.901 45.455 0.00 0.00 0.00 2.71
178 179 2.524306 CAGGGGTAAAATGCCTCACAA 58.476 47.619 0.00 0.00 0.00 3.33
179 180 1.272425 CCAGGGGTAAAATGCCTCACA 60.272 52.381 0.00 0.00 0.00 3.58
180 181 1.474330 CCAGGGGTAAAATGCCTCAC 58.526 55.000 0.00 0.00 0.00 3.51
181 182 0.334676 CCCAGGGGTAAAATGCCTCA 59.665 55.000 0.00 0.00 0.00 3.86
182 183 0.397114 CCCCAGGGGTAAAATGCCTC 60.397 60.000 18.09 0.00 38.25 4.70
183 184 0.853586 TCCCCAGGGGTAAAATGCCT 60.854 55.000 25.52 0.00 44.74 4.75
184 185 0.397114 CTCCCCAGGGGTAAAATGCC 60.397 60.000 25.52 0.00 44.74 4.40
185 186 1.043116 GCTCCCCAGGGGTAAAATGC 61.043 60.000 25.52 15.33 44.74 3.56
186 187 0.631212 AGCTCCCCAGGGGTAAAATG 59.369 55.000 25.52 9.76 44.74 2.32
187 188 1.393468 AAGCTCCCCAGGGGTAAAAT 58.607 50.000 25.52 5.60 44.74 1.82
188 189 1.920351 CTAAGCTCCCCAGGGGTAAAA 59.080 52.381 25.52 3.59 44.74 1.52
189 190 1.203518 ACTAAGCTCCCCAGGGGTAAA 60.204 52.381 25.52 4.02 44.74 2.01
190 191 0.420272 ACTAAGCTCCCCAGGGGTAA 59.580 55.000 25.52 4.87 44.74 2.85
191 192 0.326238 CACTAAGCTCCCCAGGGGTA 60.326 60.000 25.52 8.46 44.74 3.69
192 193 1.616628 CACTAAGCTCCCCAGGGGT 60.617 63.158 25.52 7.60 44.74 4.95
193 194 0.695803 ATCACTAAGCTCCCCAGGGG 60.696 60.000 20.55 20.55 46.11 4.79
194 195 2.103153 TATCACTAAGCTCCCCAGGG 57.897 55.000 0.00 0.00 0.00 4.45
195 196 4.421131 ACTATATCACTAAGCTCCCCAGG 58.579 47.826 0.00 0.00 0.00 4.45
196 197 6.486056 TCTACTATATCACTAAGCTCCCCAG 58.514 44.000 0.00 0.00 0.00 4.45
197 198 6.464530 TCTACTATATCACTAAGCTCCCCA 57.535 41.667 0.00 0.00 0.00 4.96
198 199 7.964666 AATCTACTATATCACTAAGCTCCCC 57.035 40.000 0.00 0.00 0.00 4.81
199 200 9.127277 CCTAATCTACTATATCACTAAGCTCCC 57.873 40.741 0.00 0.00 0.00 4.30
200 201 9.908747 TCCTAATCTACTATATCACTAAGCTCC 57.091 37.037 0.00 0.00 0.00 4.70
215 216 9.661954 TCTATCAGATGGTTTTCCTAATCTACT 57.338 33.333 0.00 0.00 41.38 2.57
216 217 9.699703 GTCTATCAGATGGTTTTCCTAATCTAC 57.300 37.037 0.00 0.00 41.38 2.59
217 218 9.434275 TGTCTATCAGATGGTTTTCCTAATCTA 57.566 33.333 0.00 0.00 41.38 1.98
218 219 8.324191 TGTCTATCAGATGGTTTTCCTAATCT 57.676 34.615 0.00 0.00 41.38 2.40
244 245 5.654650 ACATGACCCTGTTTGTTTCTGTTTA 59.345 36.000 0.00 0.00 0.00 2.01
262 263 5.053145 CCTCTCTGGTATGCTTTACATGAC 58.947 45.833 0.00 0.00 40.06 3.06
273 274 4.837093 TTGGTTTACCCTCTCTGGTATG 57.163 45.455 0.00 0.00 40.49 2.39
309 310 6.197468 CGACACCGACAATGTGTTTAATTTTT 59.803 34.615 0.00 0.00 46.43 1.94
358 359 6.755542 TGAAAGGAACCAATAAACCCAAAT 57.244 33.333 0.00 0.00 0.00 2.32
670 674 2.603021 AGAGAAGTGGAGAGAAGCACA 58.397 47.619 0.00 0.00 0.00 4.57
671 675 3.676291 AAGAGAAGTGGAGAGAAGCAC 57.324 47.619 0.00 0.00 0.00 4.40
675 679 4.835615 AGCTACAAAGAGAAGTGGAGAGAA 59.164 41.667 0.00 0.00 0.00 2.87
711 715 1.960417 TTCCTGCACATGAAACGACA 58.040 45.000 0.00 0.00 0.00 4.35
715 719 2.744202 AGACGATTCCTGCACATGAAAC 59.256 45.455 0.00 0.00 0.00 2.78
716 720 2.743664 CAGACGATTCCTGCACATGAAA 59.256 45.455 0.00 0.00 0.00 2.69
913 919 3.118223 AGAGACCCAATGCCTTAGCTTAC 60.118 47.826 0.00 0.00 40.80 2.34
1123 1129 2.083774 GTTGAATGAAGACGATGGGCA 58.916 47.619 0.00 0.00 0.00 5.36
1132 1138 8.946085 GTACCAATATGAACAGTTGAATGAAGA 58.054 33.333 0.00 0.00 0.00 2.87
1155 1161 7.704047 CGGAGTTAATGGAGGTAAACTTAGTAC 59.296 40.741 0.00 0.00 32.51 2.73
1161 1167 5.952347 ATCGGAGTTAATGGAGGTAAACT 57.048 39.130 0.00 0.00 34.96 2.66
1165 1171 6.097839 GGCATATATCGGAGTTAATGGAGGTA 59.902 42.308 0.00 0.00 0.00 3.08
1167 1173 5.129485 AGGCATATATCGGAGTTAATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
1178 1186 7.665145 TCATTTTGAATGAAGGCATATATCGGA 59.335 33.333 1.10 0.00 33.44 4.55
1249 1264 5.874810 AGCGCAACTTTTTAGACAGATCATA 59.125 36.000 11.47 0.00 0.00 2.15
1257 1272 6.986424 ATTAACAAGCGCAACTTTTTAGAC 57.014 33.333 11.47 0.00 36.04 2.59
1269 1284 8.578769 CAATCTTTCTTCTAAATTAACAAGCGC 58.421 33.333 0.00 0.00 0.00 5.92
1271 1286 8.864024 GCCAATCTTTCTTCTAAATTAACAAGC 58.136 33.333 0.00 0.00 0.00 4.01
1272 1287 9.358872 GGCCAATCTTTCTTCTAAATTAACAAG 57.641 33.333 0.00 0.00 0.00 3.16
1297 1312 6.793505 ACTGACTAGACCTTATAAGTTGGG 57.206 41.667 11.50 0.00 0.00 4.12
1298 1313 9.503399 AAAAACTGACTAGACCTTATAAGTTGG 57.497 33.333 11.50 0.00 0.00 3.77
1314 1329 4.883083 TCTGCGACTATGAAAAACTGACT 58.117 39.130 0.00 0.00 0.00 3.41
1394 1409 8.251721 GCCAAAGTAGTTCTAAGATAACTGAGA 58.748 37.037 0.00 0.00 37.71 3.27
1395 1410 8.035394 TGCCAAAGTAGTTCTAAGATAACTGAG 58.965 37.037 0.00 0.00 37.71 3.35
1396 1411 7.817962 GTGCCAAAGTAGTTCTAAGATAACTGA 59.182 37.037 0.00 0.00 37.71 3.41
1397 1412 7.201444 CGTGCCAAAGTAGTTCTAAGATAACTG 60.201 40.741 0.00 0.00 37.71 3.16
1398 1413 6.812160 CGTGCCAAAGTAGTTCTAAGATAACT 59.188 38.462 0.00 0.00 40.25 2.24
1399 1414 6.589139 ACGTGCCAAAGTAGTTCTAAGATAAC 59.411 38.462 0.00 0.00 0.00 1.89
1411 1426 4.624024 TCGATAAGAAACGTGCCAAAGTAG 59.376 41.667 0.00 0.00 0.00 2.57
1445 1460 3.247886 GTCCGAACTCTCCACAGAAAAAC 59.752 47.826 0.00 0.00 0.00 2.43
1447 1462 2.432874 TGTCCGAACTCTCCACAGAAAA 59.567 45.455 0.00 0.00 0.00 2.29
1494 1509 5.220854 CGCTACTGGTTTTATGATGGAAAGG 60.221 44.000 0.00 0.00 0.00 3.11
1495 1510 5.354234 ACGCTACTGGTTTTATGATGGAAAG 59.646 40.000 0.00 0.00 0.00 2.62
1503 1518 2.351726 GCAGGACGCTACTGGTTTTATG 59.648 50.000 4.15 0.00 37.77 1.90
1505 1520 1.345089 TGCAGGACGCTACTGGTTTTA 59.655 47.619 4.15 0.00 43.06 1.52
1528 1543 4.009675 TGGATGAGCATGGTAGTTGTTTC 58.990 43.478 0.00 0.00 0.00 2.78
1543 1558 6.159299 AGTGACAATGAGAGTATGGATGAG 57.841 41.667 0.00 0.00 0.00 2.90
1545 1560 5.752472 GTGAGTGACAATGAGAGTATGGATG 59.248 44.000 0.00 0.00 0.00 3.51
1546 1561 5.163364 GGTGAGTGACAATGAGAGTATGGAT 60.163 44.000 0.00 0.00 0.00 3.41
1547 1562 4.160439 GGTGAGTGACAATGAGAGTATGGA 59.840 45.833 0.00 0.00 0.00 3.41
1548 1563 4.081476 TGGTGAGTGACAATGAGAGTATGG 60.081 45.833 0.00 0.00 0.00 2.74
1700 1715 1.050204 GATGATGCTCTCCTCTGCCT 58.950 55.000 0.00 0.00 0.00 4.75
1848 1870 6.071165 AGCTAATTTGAACATCTGGAAAAGGG 60.071 38.462 0.00 0.00 0.00 3.95
1849 1871 6.810182 CAGCTAATTTGAACATCTGGAAAAGG 59.190 38.462 0.00 0.00 0.00 3.11
1850 1872 7.596494 TCAGCTAATTTGAACATCTGGAAAAG 58.404 34.615 0.00 0.00 0.00 2.27
1948 1970 1.278985 ACCAGCTGTTCGATCCAATGA 59.721 47.619 13.81 0.00 0.00 2.57
2386 2447 2.000701 ATGGACGCCAGGGGAATCA 61.001 57.895 11.28 5.66 36.75 2.57
2490 2551 5.357878 TGACGATAACCATTCTACCTACGTT 59.642 40.000 0.00 0.00 0.00 3.99
2519 2582 1.535444 TCCTGAACCAAGGAGCCGA 60.535 57.895 0.00 0.00 41.60 5.54
2564 2629 6.762187 TCGGAAGACAACACAGTAAATGTTTA 59.238 34.615 0.00 0.00 35.64 2.01
2583 2648 7.145323 ACAACATGGTAAATCTTTTTCGGAAG 58.855 34.615 0.00 0.00 0.00 3.46
2647 2712 2.752354 CCACGCCCAGTTATGATTCAAA 59.248 45.455 0.00 0.00 0.00 2.69
2667 2732 2.706339 ATCACATCAACAGAGAGGCC 57.294 50.000 0.00 0.00 0.00 5.19
2714 2779 5.816258 GCTCTGTCAGAAAAGATGATCATCA 59.184 40.000 31.99 11.35 40.22 3.07
2730 2795 1.627329 AGCTTCCAGAATGCTCTGTCA 59.373 47.619 2.63 0.00 46.71 3.58
2748 2813 1.403323 GGCACAGATTAAGCCTTGAGC 59.597 52.381 0.00 0.00 44.92 4.26
2800 2867 3.564511 CGGTTCTTTTATGCAACCACTG 58.435 45.455 0.00 0.00 39.79 3.66
2820 2887 0.165944 GGATTCGTGTGCAGTTTCCG 59.834 55.000 0.00 0.00 0.00 4.30
2825 2892 1.676916 CCAGATGGATTCGTGTGCAGT 60.677 52.381 0.00 0.00 37.39 4.40
2833 2900 0.744414 ACGGTTGCCAGATGGATTCG 60.744 55.000 2.18 3.26 37.39 3.34
2866 2933 6.128363 CCCATGGTTAAAGAACTACGAGTTTC 60.128 42.308 11.73 0.00 38.80 2.78
2873 2940 3.692690 TGCCCCATGGTTAAAGAACTAC 58.307 45.455 11.73 0.00 35.74 2.73
2876 2943 3.068165 GCTATGCCCCATGGTTAAAGAAC 59.932 47.826 11.73 0.00 34.56 3.01
2878 2945 2.513738 AGCTATGCCCCATGGTTAAAGA 59.486 45.455 11.73 0.00 0.00 2.52
2879 2946 2.887152 GAGCTATGCCCCATGGTTAAAG 59.113 50.000 11.73 2.62 0.00 1.85
2880 2947 2.243478 TGAGCTATGCCCCATGGTTAAA 59.757 45.455 11.73 0.00 0.00 1.52
2881 2948 1.849692 TGAGCTATGCCCCATGGTTAA 59.150 47.619 11.73 0.00 0.00 2.01
2882 2949 1.142870 GTGAGCTATGCCCCATGGTTA 59.857 52.381 11.73 0.00 0.00 2.85
2883 2950 0.106519 GTGAGCTATGCCCCATGGTT 60.107 55.000 11.73 0.00 0.00 3.67
2884 2951 1.281199 TGTGAGCTATGCCCCATGGT 61.281 55.000 11.73 0.00 0.00 3.55
2885 2952 0.111832 ATGTGAGCTATGCCCCATGG 59.888 55.000 4.14 4.14 0.00 3.66
2886 2953 1.202842 TGATGTGAGCTATGCCCCATG 60.203 52.381 0.00 0.00 0.00 3.66
2887 2954 1.073444 CTGATGTGAGCTATGCCCCAT 59.927 52.381 0.00 0.00 0.00 4.00
2888 2955 0.471191 CTGATGTGAGCTATGCCCCA 59.529 55.000 0.00 0.00 0.00 4.96
2889 2956 0.761187 TCTGATGTGAGCTATGCCCC 59.239 55.000 0.00 0.00 0.00 5.80
2890 2957 2.855209 ATCTGATGTGAGCTATGCCC 57.145 50.000 0.00 0.00 0.00 5.36
2891 2958 3.736720 TGAATCTGATGTGAGCTATGCC 58.263 45.455 0.00 0.00 0.00 4.40
2892 2959 4.815308 ACTTGAATCTGATGTGAGCTATGC 59.185 41.667 0.00 0.00 0.00 3.14
2893 2960 7.208777 AGTACTTGAATCTGATGTGAGCTATG 58.791 38.462 0.00 0.00 0.00 2.23
2894 2961 7.358770 AGTACTTGAATCTGATGTGAGCTAT 57.641 36.000 0.00 0.00 0.00 2.97
2895 2962 6.782082 AGTACTTGAATCTGATGTGAGCTA 57.218 37.500 0.00 0.00 0.00 3.32
2896 2963 5.674052 AGTACTTGAATCTGATGTGAGCT 57.326 39.130 0.00 0.00 0.00 4.09
2897 2964 6.800543 TCTAGTACTTGAATCTGATGTGAGC 58.199 40.000 0.00 0.00 0.00 4.26
2898 2965 7.995289 ACTCTAGTACTTGAATCTGATGTGAG 58.005 38.462 0.00 0.00 0.00 3.51
2899 2966 7.946381 ACTCTAGTACTTGAATCTGATGTGA 57.054 36.000 0.00 0.00 0.00 3.58
2920 2987 8.505625 CCGAAGTTCAAGGTATACTCTATACTC 58.494 40.741 3.32 0.00 40.61 2.59
2922 2989 8.388484 TCCGAAGTTCAAGGTATACTCTATAC 57.612 38.462 3.32 0.00 40.18 1.47
2923 2990 7.174599 GCTCCGAAGTTCAAGGTATACTCTATA 59.825 40.741 3.32 0.00 0.00 1.31
2925 2992 5.298777 GCTCCGAAGTTCAAGGTATACTCTA 59.701 44.000 3.32 0.00 0.00 2.43
2926 2993 4.098196 GCTCCGAAGTTCAAGGTATACTCT 59.902 45.833 3.32 0.00 0.00 3.24
2927 2994 4.142227 TGCTCCGAAGTTCAAGGTATACTC 60.142 45.833 3.32 0.00 0.00 2.59
2928 2995 3.767673 TGCTCCGAAGTTCAAGGTATACT 59.232 43.478 3.32 0.00 0.00 2.12
2929 2996 4.119442 TGCTCCGAAGTTCAAGGTATAC 57.881 45.455 3.32 0.00 0.00 1.47
2931 2998 3.197766 TGATGCTCCGAAGTTCAAGGTAT 59.802 43.478 3.32 0.00 0.00 2.73
2932 2999 2.565391 TGATGCTCCGAAGTTCAAGGTA 59.435 45.455 3.32 0.00 0.00 3.08
2934 3001 2.099141 TGATGCTCCGAAGTTCAAGG 57.901 50.000 3.32 0.00 0.00 3.61
2935 3002 2.159787 CGTTGATGCTCCGAAGTTCAAG 60.160 50.000 3.32 0.93 31.64 3.02
2937 3004 1.270094 ACGTTGATGCTCCGAAGTTCA 60.270 47.619 3.32 0.00 0.00 3.18
2944 3027 1.349627 GATGCACGTTGATGCTCCG 59.650 57.895 0.00 0.00 46.28 4.63
2965 3048 2.698797 CGCTCTGGATTTTAGGTCCCTA 59.301 50.000 0.00 0.00 34.76 3.53
2972 3055 4.310769 CCCATCTACGCTCTGGATTTTAG 58.689 47.826 0.00 0.00 31.38 1.85
2988 3071 1.062121 TCCTGTTAGCTAGCCCCATCT 60.062 52.381 12.13 0.00 0.00 2.90
2991 3074 1.343985 TGATCCTGTTAGCTAGCCCCA 60.344 52.381 12.13 4.72 0.00 4.96
2996 3079 5.149973 AGCATCATGATCCTGTTAGCTAG 57.850 43.478 4.86 0.00 0.00 3.42
3000 3083 5.856156 AGAGAAGCATCATGATCCTGTTAG 58.144 41.667 4.86 0.00 0.00 2.34
3011 3094 4.165565 TGATCCCAAGAAGAGAAGCATCAT 59.834 41.667 0.00 0.00 0.00 2.45
3020 3103 2.680312 TTCGCTGATCCCAAGAAGAG 57.320 50.000 0.00 0.00 0.00 2.85
3027 3110 1.521457 GACGCATTCGCTGATCCCA 60.521 57.895 0.00 0.00 39.84 4.37
3029 3112 1.930100 CTGACGCATTCGCTGATCC 59.070 57.895 0.00 0.00 39.84 3.36
3054 3137 0.322277 CTGATGGCAAGGTCAGCAGT 60.322 55.000 7.84 0.00 45.05 4.40
3065 3148 2.027745 GTCTTCTGAACCTCTGATGGCA 60.028 50.000 0.00 0.00 29.08 4.92
3066 3149 2.626840 GTCTTCTGAACCTCTGATGGC 58.373 52.381 0.00 0.00 0.00 4.40
3067 3150 2.093235 GGGTCTTCTGAACCTCTGATGG 60.093 54.545 0.00 0.00 46.38 3.51
3068 3151 3.258971 GGGTCTTCTGAACCTCTGATG 57.741 52.381 0.00 0.00 46.38 3.07
3083 3166 0.400594 CCAAGAAGAAACCGGGGTCT 59.599 55.000 6.32 4.61 0.00 3.85
3140 3223 3.127425 AGTCCTCACCTTGTTAAGTGC 57.873 47.619 0.00 0.00 0.00 4.40
3163 3246 4.795278 GCGAATGTGTCATTTCATTTCTCC 59.205 41.667 0.00 0.00 34.92 3.71
3271 3356 7.559897 TGAAGTTTCCTTGTTTTCCTAGTTCAT 59.440 33.333 0.00 0.00 0.00 2.57
3371 3456 5.670792 ATTGGAACATCATGCAGTTCATT 57.329 34.783 22.86 10.44 44.46 2.57
3423 3508 8.067751 TGCATCTCTATAGTACAGTTTGAGTT 57.932 34.615 0.00 0.00 0.00 3.01
3435 3520 6.149129 TGTCGTTTCATGCATCTCTATAGT 57.851 37.500 0.00 0.00 0.00 2.12
3436 3521 8.805688 CATATGTCGTTTCATGCATCTCTATAG 58.194 37.037 0.00 0.00 0.00 1.31
3437 3522 7.761249 CCATATGTCGTTTCATGCATCTCTATA 59.239 37.037 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.