Multiple sequence alignment - TraesCS3B01G019200

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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 TraesCS3B01G019200 chr3B 100.000 4397 0 0 1 4397 8129762 8134158 0.000000e+00 8120.0
1 TraesCS3B01G019200 chr3B 80.952 84 16 0 1158 1241 36492519 36492602 2.840000e-07 67.6
2 TraesCS3B01G019200 chr3A 88.844 4500 289 95 1 4397 13521625 13517236 0.000000e+00 5332.0
3 TraesCS3B01G019200 chr3A 82.918 281 29 12 987 1252 668027197 668026921 7.350000e-58 235.0
4 TraesCS3B01G019200 chr3D 87.684 4547 282 131 7 4397 6726366 6730790 0.000000e+00 5038.0
5 TraesCS3B01G019200 chr3D 89.941 338 21 7 1417 1750 57606535 57606863 1.460000e-114 424.0
6 TraesCS3B01G019200 chr3D 86.469 303 20 9 4096 4397 47796440 47796722 3.300000e-81 313.0
7 TraesCS3B01G019200 chr4A 92.557 309 16 5 1445 1753 433610604 433610303 1.880000e-118 436.0
8 TraesCS3B01G019200 chr4A 88.125 160 15 1 1417 1572 660540873 660541032 2.090000e-43 187.0
9 TraesCS3B01G019200 chr7D 90.237 338 22 7 1417 1750 103531853 103532183 8.740000e-117 431.0
10 TraesCS3B01G019200 chr2D 92.484 306 16 5 1445 1750 397123074 397123372 8.740000e-117 431.0
11 TraesCS3B01G019200 chr6D 91.909 309 18 5 1445 1753 46527890 46527589 4.060000e-115 425.0
12 TraesCS3B01G019200 chr5D 91.586 309 19 5 1445 1753 16496864 16496563 1.890000e-113 420.0
13 TraesCS3B01G019200 chr4D 91.262 309 20 5 1445 1753 222630707 222630406 8.800000e-112 414.0
14 TraesCS3B01G019200 chr6A 82.270 282 31 12 986 1252 577803247 577802970 4.420000e-55 226.0
15 TraesCS3B01G019200 chr1B 83.333 84 14 0 1158 1241 630060653 630060736 1.310000e-10 78.7
16 TraesCS3B01G019200 chr1B 100.000 29 0 0 3311 3339 647820399 647820427 2.000000e-03 54.7
17 TraesCS3B01G019200 chr7B 80.460 87 11 5 1158 1241 253370891 253370974 1.320000e-05 62.1
18 TraesCS3B01G019200 chr4B 100.000 29 0 0 3311 3339 463052549 463052577 2.000000e-03 54.7


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 TraesCS3B01G019200 chr3B 8129762 8134158 4396 False 8120 8120 100.000 1 4397 1 chr3B.!!$F1 4396
1 TraesCS3B01G019200 chr3A 13517236 13521625 4389 True 5332 5332 88.844 1 4397 1 chr3A.!!$R1 4396
2 TraesCS3B01G019200 chr3D 6726366 6730790 4424 False 5038 5038 87.684 7 4397 1 chr3D.!!$F1 4390

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
227 245 0.033405 GCCTTAACCCCTTCCCCTTC 60.033 60.0 0.00 0.00 0.00 3.46 F
678 722 0.100861 TTGCGTTTCCCGTCCAAAAC 59.899 50.0 0.00 0.00 39.32 2.43 F
956 1006 0.242286 CCCGAGACAGACAGAGTGTG 59.758 60.0 0.00 0.00 32.88 3.82 F
2220 2378 0.584396 TTTCCTTGTTGCAGTACGCG 59.416 50.0 3.53 3.53 46.97 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2359 0.584396 CGCGTACTGCAACAAGGAAA 59.416 50.000 0.00 0.00 46.97 3.13 R
2220 2378 0.803380 GCTGGATGCATTTTCGGTGC 60.803 55.000 0.00 0.00 42.31 5.01 R
2241 2399 1.576421 GCCTTTCTCGTTGCACCAG 59.424 57.895 0.00 0.00 0.00 4.00 R
4098 4313 0.036294 ACCAGAGAAAGTTAGGCGCC 60.036 55.000 21.89 21.89 0.00 6.53 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
24 27 1.293683 ACCCTCTCCTCCTCCTCCTC 61.294 65.000 0.00 0.00 0.00 3.71
25 28 1.541672 CCTCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
27 30 0.998945 CTCTCCTCCTCCTCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
28 31 1.232792 CTCCTCCTCCTCCTCCCTG 59.767 68.421 0.00 0.00 0.00 4.45
29 32 2.445654 CCTCCTCCTCCTCCCTGC 60.446 72.222 0.00 0.00 0.00 4.85
30 33 2.695597 CTCCTCCTCCTCCCTGCT 59.304 66.667 0.00 0.00 0.00 4.24
31 34 1.002792 CTCCTCCTCCTCCCTGCTT 59.997 63.158 0.00 0.00 0.00 3.91
33 36 1.306482 CCTCCTCCTCCCTGCTTGA 60.306 63.158 0.00 0.00 0.00 3.02
63 69 7.001073 CCTCTCTTCTAATTTAAATCCCAGGG 58.999 42.308 0.00 0.00 0.00 4.45
88 101 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
91 104 3.336676 AGGAAGGAAGGAAGGAAGGAAA 58.663 45.455 0.00 0.00 0.00 3.13
103 116 1.562008 GGAAGGAAAAGGAGGAGGAGG 59.438 57.143 0.00 0.00 0.00 4.30
104 117 2.270858 GAAGGAAAAGGAGGAGGAGGT 58.729 52.381 0.00 0.00 0.00 3.85
105 118 1.662686 AGGAAAAGGAGGAGGAGGTG 58.337 55.000 0.00 0.00 0.00 4.00
107 120 1.363246 GAAAAGGAGGAGGAGGTGGT 58.637 55.000 0.00 0.00 0.00 4.16
109 122 0.193574 AAAGGAGGAGGAGGTGGTGA 59.806 55.000 0.00 0.00 0.00 4.02
113 126 0.251832 GAGGAGGAGGTGGTGAGTGA 60.252 60.000 0.00 0.00 0.00 3.41
115 128 0.827368 GGAGGAGGTGGTGAGTGATC 59.173 60.000 0.00 0.00 0.00 2.92
116 129 0.457851 GAGGAGGTGGTGAGTGATCG 59.542 60.000 0.00 0.00 0.00 3.69
117 130 0.039764 AGGAGGTGGTGAGTGATCGA 59.960 55.000 0.00 0.00 0.00 3.59
118 131 0.457851 GGAGGTGGTGAGTGATCGAG 59.542 60.000 0.00 0.00 0.00 4.04
119 132 1.178276 GAGGTGGTGAGTGATCGAGT 58.822 55.000 0.00 0.00 0.00 4.18
120 133 0.891373 AGGTGGTGAGTGATCGAGTG 59.109 55.000 0.00 0.00 0.00 3.51
121 134 0.888619 GGTGGTGAGTGATCGAGTGA 59.111 55.000 0.00 0.00 0.00 3.41
122 135 1.135257 GGTGGTGAGTGATCGAGTGAG 60.135 57.143 0.00 0.00 0.00 3.51
123 136 0.528017 TGGTGAGTGATCGAGTGAGC 59.472 55.000 0.00 0.00 0.00 4.26
220 238 1.077169 CTTCCCAAGCCTTAACCCCTT 59.923 52.381 0.00 0.00 0.00 3.95
226 244 0.479789 AGCCTTAACCCCTTCCCCTT 60.480 55.000 0.00 0.00 0.00 3.95
227 245 0.033405 GCCTTAACCCCTTCCCCTTC 60.033 60.000 0.00 0.00 0.00 3.46
228 246 0.629596 CCTTAACCCCTTCCCCTTCC 59.370 60.000 0.00 0.00 0.00 3.46
229 247 0.629596 CTTAACCCCTTCCCCTTCCC 59.370 60.000 0.00 0.00 0.00 3.97
230 248 0.200260 TTAACCCCTTCCCCTTCCCT 59.800 55.000 0.00 0.00 0.00 4.20
231 249 0.200260 TAACCCCTTCCCCTTCCCTT 59.800 55.000 0.00 0.00 0.00 3.95
294 312 2.040947 CCTTCAAAGCTTTCCTCCTCCT 59.959 50.000 9.23 0.00 0.00 3.69
301 319 1.788229 CTTTCCTCCTCCTCCTCCTC 58.212 60.000 0.00 0.00 0.00 3.71
303 321 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
304 322 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
305 323 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
306 324 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
307 325 1.232792 CCTCCTCCTCCTCCTCCTG 59.767 68.421 0.00 0.00 0.00 3.86
308 326 1.457455 CTCCTCCTCCTCCTCCTGC 60.457 68.421 0.00 0.00 0.00 4.85
309 327 2.445654 CCTCCTCCTCCTCCTGCC 60.446 72.222 0.00 0.00 0.00 4.85
310 328 2.445654 CTCCTCCTCCTCCTGCCC 60.446 72.222 0.00 0.00 0.00 5.36
311 329 4.465446 TCCTCCTCCTCCTGCCCG 62.465 72.222 0.00 0.00 0.00 6.13
319 337 4.394712 CTCCTGCCCGCCGTCTTT 62.395 66.667 0.00 0.00 0.00 2.52
320 338 4.697756 TCCTGCCCGCCGTCTTTG 62.698 66.667 0.00 0.00 0.00 2.77
390 408 1.900016 TTGGGTTCTGCTGCTGCTG 60.900 57.895 17.00 15.94 40.48 4.41
391 409 3.745803 GGGTTCTGCTGCTGCTGC 61.746 66.667 22.51 22.51 40.48 5.25
392 410 2.672307 GGTTCTGCTGCTGCTGCT 60.672 61.111 27.67 0.00 40.48 4.24
453 471 2.158928 CCTCAGAGGCCTCTTCATTCAG 60.159 54.545 33.33 19.28 37.98 3.02
532 571 3.181482 TGGCTCTCGATTCATTGTCTCTC 60.181 47.826 0.00 0.00 0.00 3.20
533 572 3.042189 GCTCTCGATTCATTGTCTCTCG 58.958 50.000 0.00 0.00 0.00 4.04
534 573 3.488384 GCTCTCGATTCATTGTCTCTCGT 60.488 47.826 0.00 0.00 0.00 4.18
535 574 4.278858 CTCTCGATTCATTGTCTCTCGTC 58.721 47.826 0.00 0.00 0.00 4.20
536 575 3.065510 TCTCGATTCATTGTCTCTCGTCC 59.934 47.826 0.00 0.00 0.00 4.79
558 597 1.208535 CCCTTGCTCGGTGGTGTATTA 59.791 52.381 0.00 0.00 0.00 0.98
574 613 6.945435 TGGTGTATTATTTTCTGCTCCAAAGA 59.055 34.615 0.00 0.00 0.00 2.52
575 614 7.450014 TGGTGTATTATTTTCTGCTCCAAAGAA 59.550 33.333 0.00 0.00 31.85 2.52
576 615 8.470002 GGTGTATTATTTTCTGCTCCAAAGAAT 58.530 33.333 0.00 0.00 33.79 2.40
678 722 0.100861 TTGCGTTTCCCGTCCAAAAC 59.899 50.000 0.00 0.00 39.32 2.43
685 729 2.543777 TCCCGTCCAAAACTTCAGAG 57.456 50.000 0.00 0.00 0.00 3.35
724 768 1.373497 CTCGATGCCGATGCTACCC 60.373 63.158 0.00 0.00 44.62 3.69
758 802 4.380233 CCAGCTGCTTCCAATTAACAGAAG 60.380 45.833 8.66 6.60 39.99 2.85
759 803 4.456911 CAGCTGCTTCCAATTAACAGAAGA 59.543 41.667 0.00 1.55 39.50 2.87
760 804 5.048504 CAGCTGCTTCCAATTAACAGAAGAA 60.049 40.000 0.00 4.11 39.50 2.52
761 805 5.536161 AGCTGCTTCCAATTAACAGAAGAAA 59.464 36.000 12.74 2.70 39.50 2.52
956 1006 0.242286 CCCGAGACAGACAGAGTGTG 59.758 60.000 0.00 0.00 32.88 3.82
975 1025 1.970114 CAGGCCGCCATGGATGATC 60.970 63.158 18.40 0.00 42.00 2.92
976 1026 3.052082 GGCCGCCATGGATGATCG 61.052 66.667 18.40 8.99 42.00 3.69
977 1027 3.730761 GCCGCCATGGATGATCGC 61.731 66.667 18.40 2.55 42.00 4.58
978 1028 3.052082 CCGCCATGGATGATCGCC 61.052 66.667 18.40 0.00 42.00 5.54
979 1029 2.031616 CGCCATGGATGATCGCCT 59.968 61.111 18.40 0.00 0.00 5.52
980 1030 2.322830 CGCCATGGATGATCGCCTG 61.323 63.158 18.40 2.71 0.00 4.85
981 1031 1.071987 GCCATGGATGATCGCCTGA 59.928 57.895 18.40 0.00 0.00 3.86
984 1043 1.271217 CCATGGATGATCGCCTGATGT 60.271 52.381 5.56 0.00 34.09 3.06
996 1055 2.936928 CTGATGTGTGCTTGCAGGA 58.063 52.632 0.00 0.00 0.00 3.86
997 1056 1.460504 CTGATGTGTGCTTGCAGGAT 58.539 50.000 0.00 0.00 0.00 3.24
1087 1146 3.132801 GCAGGAAGCAGGCTGAGC 61.133 66.667 20.86 3.12 44.79 4.26
1241 1300 1.452108 GCGGCAGCCTCAAGGTAAT 60.452 57.895 10.54 0.00 37.42 1.89
1242 1301 1.032114 GCGGCAGCCTCAAGGTAATT 61.032 55.000 10.54 0.00 37.42 1.40
1244 1303 2.639065 CGGCAGCCTCAAGGTAATTAA 58.361 47.619 10.54 0.00 37.57 1.40
1245 1304 2.614057 CGGCAGCCTCAAGGTAATTAAG 59.386 50.000 10.54 0.00 37.57 1.85
1328 1391 6.199342 GCAGTAATTTAACTTCGTTGGCAAAA 59.801 34.615 0.00 0.00 0.00 2.44
1386 1454 3.488355 ATGGGGTGGGAAATTTGATCA 57.512 42.857 0.00 0.00 0.00 2.92
1387 1455 3.488355 TGGGGTGGGAAATTTGATCAT 57.512 42.857 0.00 0.00 0.00 2.45
1390 1458 4.019501 TGGGGTGGGAAATTTGATCATTTG 60.020 41.667 0.00 0.00 0.00 2.32
1397 1465 9.921637 GTGGGAAATTTGATCATTTGTTAGTAA 57.078 29.630 0.00 0.00 0.00 2.24
1429 1510 6.116806 GGTTTCCAACTTTAATTTTGGGTGT 58.883 36.000 13.19 0.00 42.35 4.16
1433 1514 8.485578 TTCCAACTTTAATTTTGGGTGTCTAT 57.514 30.769 13.19 0.00 42.35 1.98
1440 1521 8.894768 TTTAATTTTGGGTGTCTATTTTGGTG 57.105 30.769 0.00 0.00 0.00 4.17
1442 1523 5.941555 TTTTGGGTGTCTATTTTGGTGTT 57.058 34.783 0.00 0.00 0.00 3.32
1494 1586 4.886579 ACTTGCCATGAGGAATTTTTGTC 58.113 39.130 0.00 0.00 36.89 3.18
1511 1603 3.828875 TGTCATTTTTGGTTGGGGTTC 57.171 42.857 0.00 0.00 0.00 3.62
1531 1623 4.307443 TCGATGCAGTAGGTTGTATCTG 57.693 45.455 0.00 0.00 37.84 2.90
1754 1860 5.905913 AGGGTTAGATGCAGTAGGTTCTATT 59.094 40.000 0.00 0.00 0.00 1.73
1865 1981 3.617288 GCCTAATGTTGGCCTTCCTTTTG 60.617 47.826 3.32 0.00 44.32 2.44
1869 1985 1.132881 TGTTGGCCTTCCTTTTGGGAT 60.133 47.619 3.32 0.00 44.66 3.85
1975 2110 2.545810 AGCAAGGGGGAGAGCTATATC 58.454 52.381 0.00 0.00 35.19 1.63
1976 2111 2.113414 AGCAAGGGGGAGAGCTATATCT 59.887 50.000 0.00 0.00 35.19 1.98
1977 2112 3.338214 AGCAAGGGGGAGAGCTATATCTA 59.662 47.826 0.00 0.00 35.19 1.98
1982 2117 6.524545 AGGGGGAGAGCTATATCTATAGAC 57.475 45.833 4.10 0.00 38.30 2.59
2017 2152 2.228103 TGCGTGAGACAACTACCTACAG 59.772 50.000 0.00 0.00 0.00 2.74
2018 2153 2.486982 GCGTGAGACAACTACCTACAGA 59.513 50.000 0.00 0.00 0.00 3.41
2019 2154 3.670091 GCGTGAGACAACTACCTACAGAC 60.670 52.174 0.00 0.00 0.00 3.51
2020 2155 3.501062 CGTGAGACAACTACCTACAGACA 59.499 47.826 0.00 0.00 0.00 3.41
2021 2156 4.613167 CGTGAGACAACTACCTACAGACAC 60.613 50.000 0.00 0.00 0.00 3.67
2022 2157 3.825014 TGAGACAACTACCTACAGACACC 59.175 47.826 0.00 0.00 0.00 4.16
2087 2222 4.164030 ACATTCTGGCCTTTTGTCCTTTTT 59.836 37.500 3.32 0.00 0.00 1.94
2143 2301 4.451629 TGGAATCGACTAAGAAGACACC 57.548 45.455 0.00 0.00 0.00 4.16
2176 2334 6.647895 GGTTGATTATACCGGTCGATTACATT 59.352 38.462 12.40 0.00 0.00 2.71
2178 2336 6.160684 TGATTATACCGGTCGATTACATTGG 58.839 40.000 12.40 0.00 0.00 3.16
2187 2345 6.292703 CCGGTCGATTACATTGGATTAAACTC 60.293 42.308 0.00 0.00 0.00 3.01
2193 2351 9.326413 CGATTACATTGGATTAAACTCTTACCT 57.674 33.333 0.00 0.00 0.00 3.08
2220 2378 0.584396 TTTCCTTGTTGCAGTACGCG 59.416 50.000 3.53 3.53 46.97 6.01
2256 2414 2.892334 GCGCTGGTGCAACGAGAAA 61.892 57.895 0.00 0.00 46.53 2.52
2318 2476 7.867445 AACAAACAAAAATTGCCTATCTACG 57.133 32.000 0.00 0.00 0.00 3.51
2321 2479 3.064820 ACAAAAATTGCCTATCTACGCGG 59.935 43.478 12.47 0.00 0.00 6.46
2324 2482 0.317479 ATTGCCTATCTACGCGGTCC 59.683 55.000 12.47 0.00 0.00 4.46
2326 2484 1.286260 GCCTATCTACGCGGTCCAG 59.714 63.158 12.47 1.61 0.00 3.86
2327 2485 1.453762 GCCTATCTACGCGGTCCAGT 61.454 60.000 12.47 0.00 0.00 4.00
2328 2486 1.888215 CCTATCTACGCGGTCCAGTA 58.112 55.000 12.47 0.00 0.00 2.74
2371 2541 5.871834 ACAGGTAAGCATGTGTACCTTTAA 58.128 37.500 20.66 0.00 46.50 1.52
2384 2554 9.614792 ATGTGTACCTTTAATCTTATGAACTCC 57.385 33.333 0.00 0.00 0.00 3.85
2411 2581 1.980772 GCAGCAATTCAGGCCAGGT 60.981 57.895 5.01 0.00 0.00 4.00
2513 2683 3.700539 CCTGATGCAAAACCATGGTGATA 59.299 43.478 20.60 4.04 0.00 2.15
2515 2685 5.163385 CCTGATGCAAAACCATGGTGATATT 60.163 40.000 20.60 5.85 0.00 1.28
2519 2689 5.722263 TGCAAAACCATGGTGATATTTCTG 58.278 37.500 20.60 6.27 0.00 3.02
2520 2690 4.567959 GCAAAACCATGGTGATATTTCTGC 59.432 41.667 20.60 12.44 0.00 4.26
2521 2691 5.111293 CAAAACCATGGTGATATTTCTGCC 58.889 41.667 20.60 0.00 0.00 4.85
2559 2729 2.160171 CCACAGGGGGAACTGGGAA 61.160 63.158 0.00 0.00 44.71 3.97
2713 2883 5.448768 GCCATCATTGTGAGTTCATCAGAAG 60.449 44.000 0.00 0.00 43.73 2.85
2714 2884 5.646793 CCATCATTGTGAGTTCATCAGAAGT 59.353 40.000 0.00 0.00 43.73 3.01
2715 2885 6.150641 CCATCATTGTGAGTTCATCAGAAGTT 59.849 38.462 0.00 0.00 43.73 2.66
2716 2886 6.791887 TCATTGTGAGTTCATCAGAAGTTC 57.208 37.500 0.00 0.00 43.73 3.01
2717 2887 6.290605 TCATTGTGAGTTCATCAGAAGTTCA 58.709 36.000 5.50 0.00 43.73 3.18
2718 2888 6.426025 TCATTGTGAGTTCATCAGAAGTTCAG 59.574 38.462 5.50 0.00 43.73 3.02
2719 2889 5.535753 TGTGAGTTCATCAGAAGTTCAGA 57.464 39.130 5.50 2.64 39.07 3.27
2720 2890 5.917462 TGTGAGTTCATCAGAAGTTCAGAA 58.083 37.500 5.50 1.27 39.07 3.02
2721 2891 5.755375 TGTGAGTTCATCAGAAGTTCAGAAC 59.245 40.000 5.00 5.00 39.07 3.01
2750 2921 5.835819 TGTGTTTTGATCCATGAAGGGTTTA 59.164 36.000 0.00 0.00 38.24 2.01
2762 2933 9.403583 TCCATGAAGGGTTTATAATTAACAGAC 57.596 33.333 0.00 0.00 38.24 3.51
2819 2990 1.079750 GGTTCTCCGGCACACTCTC 60.080 63.158 0.00 0.00 0.00 3.20
2996 3182 8.325046 TCTTGAATTTTACCATTTTTATGGGGG 58.675 33.333 8.87 0.00 45.84 5.40
2999 3185 2.074729 TACCATTTTTATGGGGGCGG 57.925 50.000 8.87 0.00 45.84 6.13
3091 3277 1.872679 GACCTTCCATCGTCGTCGC 60.873 63.158 0.00 0.00 36.96 5.19
3106 3292 1.003112 TCGCCGCCAACAGGTAATT 60.003 52.632 0.00 0.00 0.00 1.40
3112 3298 1.330521 CGCCAACAGGTAATTCCATCG 59.669 52.381 0.00 0.00 39.02 3.84
3113 3299 2.365582 GCCAACAGGTAATTCCATCGT 58.634 47.619 0.00 0.00 39.02 3.73
3117 3303 4.142687 CCAACAGGTAATTCCATCGTTGAC 60.143 45.833 16.40 0.00 41.42 3.18
3118 3304 3.259064 ACAGGTAATTCCATCGTTGACG 58.741 45.455 0.00 0.00 39.02 4.35
3184 3375 2.093816 TGATACCAGTCAGCAGCAGAAG 60.094 50.000 0.00 0.00 0.00 2.85
3193 3384 2.827921 TCAGCAGCAGAAGACTGATACA 59.172 45.455 0.00 0.00 46.03 2.29
3217 3408 1.302366 TCACTTGCACTGCAGAGTTG 58.698 50.000 23.35 9.81 40.61 3.16
3345 3545 1.482593 GAGGAAGAAGAGGATGCCGAA 59.517 52.381 0.00 0.00 0.00 4.30
3346 3546 2.103941 GAGGAAGAAGAGGATGCCGAAT 59.896 50.000 0.00 0.00 0.00 3.34
3359 3559 3.398134 CGAATCCGATCCTGCGCG 61.398 66.667 0.00 0.00 38.22 6.86
3477 3677 5.069781 ACAGGGAGAAAGATACTGATGTAGC 59.930 44.000 0.00 0.00 35.48 3.58
3531 3731 7.877612 TGTGCACAAGAAATAGAAGAATGTAGA 59.122 33.333 19.28 0.00 0.00 2.59
3551 3751 4.033709 AGAGGCTCTGTACATACCACAAT 58.966 43.478 17.96 0.00 0.00 2.71
3658 3858 4.101585 TGGAATTACAGGCCTGTATCTGAG 59.898 45.833 39.32 13.48 44.54 3.35
3699 3907 5.645067 TCATGCTTGATCTACAGTTCTTTGG 59.355 40.000 0.00 0.00 0.00 3.28
3727 3936 1.817357 ACTGACATGTGCATGGACTG 58.183 50.000 18.75 15.27 42.91 3.51
3767 3976 7.823799 TGAGCATACAAATTTCTGTACATCTGA 59.176 33.333 0.00 0.00 34.68 3.27
3794 4003 6.831727 CAACATTTGCTTGACAAGATTTCA 57.168 33.333 19.51 4.33 40.06 2.69
3795 4004 7.236674 CAACATTTGCTTGACAAGATTTCAA 57.763 32.000 19.51 10.17 40.06 2.69
3796 4005 7.686519 CAACATTTGCTTGACAAGATTTCAAA 58.313 30.769 19.51 17.48 40.06 2.69
3797 4006 7.473027 ACATTTGCTTGACAAGATTTCAAAG 57.527 32.000 19.51 13.43 40.06 2.77
3800 4009 7.524294 TTTGCTTGACAAGATTTCAAAGTTC 57.476 32.000 19.51 0.00 40.06 3.01
3814 4023 9.434559 GATTTCAAAGTTCAAACAGTACAGTAC 57.565 33.333 2.05 2.05 0.00 2.73
3818 4027 2.054687 TCAAACAGTACAGTACCGCG 57.945 50.000 7.13 0.00 0.00 6.46
3824 4033 2.614057 ACAGTACAGTACCGCGGTATAC 59.386 50.000 38.22 32.46 32.82 1.47
3974 4189 6.735704 GGGGGCAGGGATACATATACATATAT 59.264 42.308 0.00 0.00 39.74 0.86
3975 4190 7.239773 GGGGGCAGGGATACATATACATATATT 59.760 40.741 0.00 0.00 39.74 1.28
4065 4280 2.519377 CGAGGTACTTGAACACCACA 57.481 50.000 0.00 0.00 44.22 4.17
4092 4307 2.188994 GCCAGCGCTCCTTCAGAT 59.811 61.111 7.13 0.00 0.00 2.90
4094 4309 0.599728 GCCAGCGCTCCTTCAGATAG 60.600 60.000 7.13 0.00 0.00 2.08
4095 4310 0.749649 CCAGCGCTCCTTCAGATAGT 59.250 55.000 7.13 0.00 0.00 2.12
4096 4311 1.537776 CCAGCGCTCCTTCAGATAGTG 60.538 57.143 7.13 0.00 0.00 2.74
4098 4313 1.135915 AGCGCTCCTTCAGATAGTGTG 59.864 52.381 2.64 0.00 0.00 3.82
4104 4319 0.176680 CTTCAGATAGTGTGGCGCCT 59.823 55.000 29.70 9.99 0.00 5.52
4152 4367 1.759445 TCCTGCACTAGCTCATCCTTC 59.241 52.381 0.00 0.00 42.74 3.46
4206 4421 2.028112 TGCACAGGTAACATCAGAGGAC 60.028 50.000 0.00 0.00 41.41 3.85
4216 4431 3.894759 ACATCAGAGGACAATCCATTGG 58.105 45.455 4.36 0.00 41.96 3.16
4222 4437 3.758554 AGAGGACAATCCATTGGTTTTCG 59.241 43.478 1.86 0.00 41.96 3.46
4224 4439 2.231235 GGACAATCCATTGGTTTTCGCT 59.769 45.455 1.86 0.00 41.96 4.93
4225 4440 3.306019 GGACAATCCATTGGTTTTCGCTT 60.306 43.478 1.86 0.00 41.96 4.68
4228 4443 4.764823 ACAATCCATTGGTTTTCGCTTAGA 59.235 37.500 1.86 0.00 41.96 2.10
4355 4570 6.183360 TGCCAATACATCATTCTGAAATGCAT 60.183 34.615 0.00 0.00 41.76 3.96
4356 4571 6.365247 GCCAATACATCATTCTGAAATGCATC 59.635 38.462 0.00 0.00 41.76 3.91
4360 4575 6.275494 ACATCATTCTGAAATGCATCAACA 57.725 33.333 0.00 0.00 41.76 3.33
4368 4584 6.571605 TCTGAAATGCATCAACAGAAACAAA 58.428 32.000 20.30 4.99 35.20 2.83
4370 4586 7.711772 TCTGAAATGCATCAACAGAAACAAATT 59.288 29.630 20.30 0.29 35.20 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.230819 AGGAGGAGGAGGAGAGGGT 60.231 63.158 0.00 0.00 0.00 4.34
63 69 2.025793 CCTTCCTTCCTTCCTTCCTTCC 60.026 54.545 0.00 0.00 0.00 3.46
88 101 1.003696 CACCACCTCCTCCTCCTTTTC 59.996 57.143 0.00 0.00 0.00 2.29
91 104 0.252467 CTCACCACCTCCTCCTCCTT 60.252 60.000 0.00 0.00 0.00 3.36
103 116 1.734047 GCTCACTCGATCACTCACCAC 60.734 57.143 0.00 0.00 0.00 4.16
104 117 0.528017 GCTCACTCGATCACTCACCA 59.472 55.000 0.00 0.00 0.00 4.17
105 118 0.179124 GGCTCACTCGATCACTCACC 60.179 60.000 0.00 0.00 0.00 4.02
107 120 1.550327 AAGGCTCACTCGATCACTCA 58.450 50.000 0.00 0.00 0.00 3.41
109 122 2.165437 GAGAAAGGCTCACTCGATCACT 59.835 50.000 5.42 0.00 43.38 3.41
113 126 1.561643 TGGAGAAAGGCTCACTCGAT 58.438 50.000 12.43 0.00 45.81 3.59
115 128 2.005451 CAATGGAGAAAGGCTCACTCG 58.995 52.381 12.43 0.00 45.81 4.18
116 129 1.742268 GCAATGGAGAAAGGCTCACTC 59.258 52.381 10.96 10.96 45.81 3.51
117 130 1.831580 GCAATGGAGAAAGGCTCACT 58.168 50.000 0.00 0.00 45.81 3.41
118 131 0.449388 CGCAATGGAGAAAGGCTCAC 59.551 55.000 0.00 0.00 45.81 3.51
119 132 1.308069 GCGCAATGGAGAAAGGCTCA 61.308 55.000 0.30 0.00 45.81 4.26
120 133 1.028868 AGCGCAATGGAGAAAGGCTC 61.029 55.000 11.47 0.00 43.17 4.70
121 134 0.610232 AAGCGCAATGGAGAAAGGCT 60.610 50.000 11.47 0.00 0.00 4.58
122 135 0.179153 GAAGCGCAATGGAGAAAGGC 60.179 55.000 11.47 0.00 0.00 4.35
123 136 1.399791 GAGAAGCGCAATGGAGAAAGG 59.600 52.381 11.47 0.00 0.00 3.11
208 226 0.033405 GAAGGGGAAGGGGTTAAGGC 60.033 60.000 0.00 0.00 0.00 4.35
220 238 1.230182 GGAGGGAAAGGGAAGGGGA 60.230 63.158 0.00 0.00 0.00 4.81
226 244 2.238701 GGCAAGGGAGGGAAAGGGA 61.239 63.158 0.00 0.00 0.00 4.20
227 245 1.804530 AAGGCAAGGGAGGGAAAGGG 61.805 60.000 0.00 0.00 0.00 3.95
228 246 0.999712 TAAGGCAAGGGAGGGAAAGG 59.000 55.000 0.00 0.00 0.00 3.11
229 247 1.683319 GCTAAGGCAAGGGAGGGAAAG 60.683 57.143 0.00 0.00 38.54 2.62
230 248 0.331616 GCTAAGGCAAGGGAGGGAAA 59.668 55.000 0.00 0.00 38.54 3.13
231 249 1.571773 GGCTAAGGCAAGGGAGGGAA 61.572 60.000 0.00 0.00 40.87 3.97
294 312 4.465446 CGGGCAGGAGGAGGAGGA 62.465 72.222 0.00 0.00 0.00 3.71
303 321 4.697756 CAAAGACGGCGGGCAGGA 62.698 66.667 13.24 0.00 0.00 3.86
311 329 0.743345 AGTTATCGCCCAAAGACGGC 60.743 55.000 0.00 0.00 43.38 5.68
312 330 2.589798 TAGTTATCGCCCAAAGACGG 57.410 50.000 0.00 0.00 0.00 4.79
313 331 2.606272 GGTTAGTTATCGCCCAAAGACG 59.394 50.000 0.00 0.00 0.00 4.18
314 332 3.869832 GAGGTTAGTTATCGCCCAAAGAC 59.130 47.826 0.00 0.00 0.00 3.01
315 333 3.118519 GGAGGTTAGTTATCGCCCAAAGA 60.119 47.826 0.00 0.00 0.00 2.52
316 334 3.203716 GGAGGTTAGTTATCGCCCAAAG 58.796 50.000 0.00 0.00 0.00 2.77
317 335 2.419021 CGGAGGTTAGTTATCGCCCAAA 60.419 50.000 0.00 0.00 0.00 3.28
318 336 1.137479 CGGAGGTTAGTTATCGCCCAA 59.863 52.381 0.00 0.00 0.00 4.12
319 337 0.748450 CGGAGGTTAGTTATCGCCCA 59.252 55.000 0.00 0.00 0.00 5.36
320 338 0.599466 GCGGAGGTTAGTTATCGCCC 60.599 60.000 0.00 0.00 37.62 6.13
321 339 0.103572 TGCGGAGGTTAGTTATCGCC 59.896 55.000 0.00 0.00 42.07 5.54
322 340 1.859080 CTTGCGGAGGTTAGTTATCGC 59.141 52.381 0.00 0.00 42.90 4.58
323 341 2.470821 CCTTGCGGAGGTTAGTTATCG 58.529 52.381 0.00 0.00 40.95 2.92
354 372 3.372206 CCCAACGAAAATGAGCAGTAGAG 59.628 47.826 0.00 0.00 0.00 2.43
418 436 2.918712 CTGAGGTTTCAGTGGTCTGT 57.081 50.000 0.00 0.00 44.74 3.41
453 471 7.064490 GGAGAAATCAAGAAGAGATCAACTGAC 59.936 40.741 0.00 0.00 0.00 3.51
678 722 5.008980 AGAAGAGGCCAAAATTCTCTGAAG 58.991 41.667 5.01 0.00 37.85 3.02
685 729 2.964740 GCCAAGAAGAGGCCAAAATTC 58.035 47.619 5.01 3.15 46.50 2.17
724 768 2.758089 GCAGCTGGAATCAGTGGCG 61.758 63.158 17.12 0.00 42.78 5.69
761 805 5.543790 ACTGGGAGTTGATAAAGCCATTTTT 59.456 36.000 0.00 0.00 0.00 1.94
773 817 2.154462 CGCAAGAAACTGGGAGTTGAT 58.846 47.619 0.00 0.00 38.66 2.57
775 819 0.593128 CCGCAAGAAACTGGGAGTTG 59.407 55.000 0.00 0.00 38.66 3.16
849 896 3.584406 ATTCTGTCAGTCAGGAAGTCG 57.416 47.619 0.00 0.00 43.76 4.18
851 898 7.038302 TGGTATTTATTCTGTCAGTCAGGAAGT 60.038 37.037 0.00 0.00 43.76 3.01
852 899 7.331026 TGGTATTTATTCTGTCAGTCAGGAAG 58.669 38.462 0.00 0.00 43.76 3.46
854 901 6.667848 TCTGGTATTTATTCTGTCAGTCAGGA 59.332 38.462 0.00 0.00 43.76 3.86
855 902 6.878317 TCTGGTATTTATTCTGTCAGTCAGG 58.122 40.000 0.00 0.00 43.76 3.86
856 903 7.010923 GCTTCTGGTATTTATTCTGTCAGTCAG 59.989 40.741 0.00 0.00 44.85 3.51
857 904 6.818644 GCTTCTGGTATTTATTCTGTCAGTCA 59.181 38.462 0.00 0.00 0.00 3.41
858 905 6.818644 TGCTTCTGGTATTTATTCTGTCAGTC 59.181 38.462 0.00 0.00 0.00 3.51
859 906 6.711277 TGCTTCTGGTATTTATTCTGTCAGT 58.289 36.000 0.00 0.00 0.00 3.41
956 1006 4.881440 TCATCCATGGCGGCCTGC 62.881 66.667 21.46 10.60 45.38 4.85
975 1025 2.177531 GCAAGCACACATCAGGCG 59.822 61.111 0.00 0.00 0.00 5.52
976 1026 1.211969 CTGCAAGCACACATCAGGC 59.788 57.895 0.00 0.00 0.00 4.85
977 1027 0.607217 TCCTGCAAGCACACATCAGG 60.607 55.000 0.00 0.00 44.18 3.86
978 1028 1.400846 GATCCTGCAAGCACACATCAG 59.599 52.381 0.00 0.00 0.00 2.90
979 1029 1.456296 GATCCTGCAAGCACACATCA 58.544 50.000 0.00 0.00 0.00 3.07
980 1030 0.737219 GGATCCTGCAAGCACACATC 59.263 55.000 3.84 0.00 0.00 3.06
981 1031 0.038599 TGGATCCTGCAAGCACACAT 59.961 50.000 14.23 0.00 0.00 3.21
984 1043 0.681887 CCATGGATCCTGCAAGCACA 60.682 55.000 14.23 0.00 0.00 4.57
996 1055 0.253044 CGAGGTGTTCACCCATGGAT 59.747 55.000 15.22 0.00 0.00 3.41
997 1056 1.676968 CGAGGTGTTCACCCATGGA 59.323 57.895 15.22 0.00 0.00 3.41
1241 1300 5.270083 CGTTCTGAACATTGTTGTGCTTAA 58.730 37.500 19.56 0.00 35.83 1.85
1242 1301 4.788201 GCGTTCTGAACATTGTTGTGCTTA 60.788 41.667 19.56 0.00 35.83 3.09
1244 1303 2.541588 GCGTTCTGAACATTGTTGTGCT 60.542 45.455 19.56 0.00 35.83 4.40
1245 1304 1.780860 GCGTTCTGAACATTGTTGTGC 59.219 47.619 19.56 8.80 35.83 4.57
1335 1398 3.005155 ACTTCTGCAGCTTTTGTGAATCC 59.995 43.478 9.47 0.00 0.00 3.01
1338 1401 4.454728 AAACTTCTGCAGCTTTTGTGAA 57.545 36.364 9.47 0.00 0.00 3.18
1371 1439 9.921637 TTACTAACAAATGATCAAATTTCCCAC 57.078 29.630 0.00 0.00 0.00 4.61
1412 1493 9.554395 CCAAAATAGACACCCAAAATTAAAGTT 57.446 29.630 0.00 0.00 0.00 2.66
1414 1495 8.987890 CACCAAAATAGACACCCAAAATTAAAG 58.012 33.333 0.00 0.00 0.00 1.85
1415 1496 8.487028 ACACCAAAATAGACACCCAAAATTAAA 58.513 29.630 0.00 0.00 0.00 1.52
1455 1546 3.139077 CAAGTCAAACCTACACTCCACC 58.861 50.000 0.00 0.00 0.00 4.61
1494 1586 3.324993 CATCGAACCCCAACCAAAAATG 58.675 45.455 0.00 0.00 0.00 2.32
1511 1603 4.307443 TCAGATACAACCTACTGCATCG 57.693 45.455 0.00 0.00 0.00 3.84
1531 1623 7.766278 TCACTGAGCTTTCCTGATACTTTAATC 59.234 37.037 0.00 0.00 0.00 1.75
1657 1762 8.123639 TCACTTCTACTACTTTTCAGCACTAT 57.876 34.615 0.00 0.00 0.00 2.12
1674 1779 5.353394 AGTCAAAACCACACTCACTTCTA 57.647 39.130 0.00 0.00 0.00 2.10
1675 1780 4.222124 AGTCAAAACCACACTCACTTCT 57.778 40.909 0.00 0.00 0.00 2.85
1676 1781 4.662145 CAAGTCAAAACCACACTCACTTC 58.338 43.478 0.00 0.00 0.00 3.01
1730 1836 3.725634 AGAACCTACTGCATCTAACCCT 58.274 45.455 0.00 0.00 0.00 4.34
1769 1882 4.961438 AATTGCTGACCCTTTTTCACAT 57.039 36.364 0.00 0.00 0.00 3.21
1865 1981 9.371136 CACACTATATATACATGTCACAATCCC 57.629 37.037 0.00 0.00 0.00 3.85
1869 1985 8.200792 TGCACACACTATATATACATGTCACAA 58.799 33.333 0.00 0.00 0.00 3.33
1963 2098 9.231297 GATGATGGTCTATAGATATAGCTCTCC 57.769 40.741 5.57 0.00 36.47 3.71
1975 2110 5.119743 CGCATTGTGTGATGATGGTCTATAG 59.880 44.000 0.00 0.00 0.00 1.31
1976 2111 4.990426 CGCATTGTGTGATGATGGTCTATA 59.010 41.667 0.00 0.00 0.00 1.31
1977 2112 3.811497 CGCATTGTGTGATGATGGTCTAT 59.189 43.478 0.00 0.00 0.00 1.98
1982 2117 1.738908 TCACGCATTGTGTGATGATGG 59.261 47.619 25.11 2.55 46.14 3.51
2154 2312 6.015265 TCCAATGTAATCGACCGGTATAATCA 60.015 38.462 7.34 3.52 0.00 2.57
2160 2318 4.675976 AATCCAATGTAATCGACCGGTA 57.324 40.909 7.34 0.00 0.00 4.02
2167 2325 9.326413 AGGTAAGAGTTTAATCCAATGTAATCG 57.674 33.333 0.00 0.00 0.00 3.34
2201 2359 0.584396 CGCGTACTGCAACAAGGAAA 59.416 50.000 0.00 0.00 46.97 3.13
2202 2360 1.837538 GCGCGTACTGCAACAAGGAA 61.838 55.000 8.43 0.00 46.97 3.36
2208 2366 4.424430 CGGTGCGCGTACTGCAAC 62.424 66.667 26.14 13.31 46.47 4.17
2220 2378 0.803380 GCTGGATGCATTTTCGGTGC 60.803 55.000 0.00 0.00 42.31 5.01
2241 2399 1.576421 GCCTTTCTCGTTGCACCAG 59.424 57.895 0.00 0.00 0.00 4.00
2294 2452 6.364976 GCGTAGATAGGCAATTTTTGTTTGTT 59.635 34.615 0.00 0.00 37.08 2.83
2318 2476 4.364860 ACAAAACAAAAATACTGGACCGC 58.635 39.130 0.00 0.00 0.00 5.68
2356 2526 8.893727 AGTTCATAAGATTAAAGGTACACATGC 58.106 33.333 0.00 0.00 0.00 4.06
2371 2541 5.189180 GCAGAAACAGGGAGTTCATAAGAT 58.811 41.667 0.00 0.00 40.26 2.40
2384 2554 2.352421 CCTGAATTGCTGCAGAAACAGG 60.352 50.000 23.19 23.19 38.16 4.00
2411 2581 3.245650 TGCTGTGGGGCAGTGTAA 58.754 55.556 0.00 0.00 46.64 2.41
2513 2683 4.642429 AGAGACGTTTTACAGGCAGAAAT 58.358 39.130 0.00 0.00 0.00 2.17
2515 2685 3.650139 GAGAGACGTTTTACAGGCAGAA 58.350 45.455 0.00 0.00 0.00 3.02
2559 2729 4.742201 AGATCGTGCCGCGCAACT 62.742 61.111 8.75 0.00 41.47 3.16
2671 2841 1.667830 CGACTGTCCGGCAACACAT 60.668 57.895 0.00 0.00 0.00 3.21
2713 2883 3.128589 TCAAAACACAGCCTGTTCTGAAC 59.871 43.478 13.49 13.49 42.70 3.18
2714 2884 3.351740 TCAAAACACAGCCTGTTCTGAA 58.648 40.909 0.00 0.00 42.70 3.02
2715 2885 2.997980 TCAAAACACAGCCTGTTCTGA 58.002 42.857 0.00 0.00 42.70 3.27
2716 2886 3.304928 GGATCAAAACACAGCCTGTTCTG 60.305 47.826 0.00 0.00 42.70 3.02
2717 2887 2.887152 GGATCAAAACACAGCCTGTTCT 59.113 45.455 0.00 0.00 42.70 3.01
2718 2888 2.622942 TGGATCAAAACACAGCCTGTTC 59.377 45.455 0.00 0.00 42.70 3.18
2719 2889 2.665165 TGGATCAAAACACAGCCTGTT 58.335 42.857 0.00 0.00 45.68 3.16
2720 2890 2.363306 TGGATCAAAACACAGCCTGT 57.637 45.000 0.00 0.00 32.89 4.00
2721 2891 2.821378 TCATGGATCAAAACACAGCCTG 59.179 45.455 0.00 0.00 0.00 4.85
2733 2903 9.928618 TGTTAATTATAAACCCTTCATGGATCA 57.071 29.630 0.00 0.00 38.35 2.92
2761 2932 4.492494 TGGATCACAATGACATAGCTGT 57.508 40.909 0.00 0.00 38.67 4.40
2762 2933 4.637091 TGTTGGATCACAATGACATAGCTG 59.363 41.667 0.00 0.00 41.95 4.24
2819 2990 4.227134 CCGCCGACCATGAGAGGG 62.227 72.222 0.00 0.00 0.00 4.30
3025 3211 0.879090 GAAACAGAATTCCGGCGGTT 59.121 50.000 27.32 14.32 0.00 4.44
3073 3259 1.872679 GCGACGACGATGGAAGGTC 60.873 63.158 12.29 0.00 42.66 3.85
3091 3277 1.676006 GATGGAATTACCTGTTGGCGG 59.324 52.381 0.00 0.00 39.86 6.13
3112 3298 2.414559 CCAACAATGGCTGATCGTCAAC 60.415 50.000 0.00 0.00 40.58 3.18
3113 3299 1.811965 CCAACAATGGCTGATCGTCAA 59.188 47.619 0.00 0.00 40.58 3.18
3117 3303 1.176527 AACCCAACAATGGCTGATCG 58.823 50.000 0.00 0.00 46.09 3.69
3118 3304 2.354003 CCAAACCCAACAATGGCTGATC 60.354 50.000 0.00 0.00 46.09 2.92
3119 3305 1.624813 CCAAACCCAACAATGGCTGAT 59.375 47.619 0.00 0.00 46.09 2.90
3120 3306 1.047002 CCAAACCCAACAATGGCTGA 58.953 50.000 0.00 0.00 46.09 4.26
3193 3384 5.642117 AACTCTGCAGTGCAAGTGAAACTT 61.642 41.667 24.19 11.49 46.37 2.66
3217 3408 6.525121 TGCATCAGAAAATAGTATACGCAC 57.475 37.500 0.00 0.00 0.00 5.34
3359 3559 2.436115 GTGGTTGGTAGCGAGGCC 60.436 66.667 0.00 0.00 0.00 5.19
3421 3621 4.523083 TCTTTGCTTCTGTTAACCACACT 58.477 39.130 2.48 0.00 0.00 3.55
3460 3660 7.891561 ACTATCCTGCTACATCAGTATCTTTC 58.108 38.462 0.00 0.00 32.32 2.62
3477 3677 2.223688 CGAGTGGCTTCAGACTATCCTG 60.224 54.545 0.00 0.00 35.55 3.86
3531 3731 4.962995 AGTATTGTGGTATGTACAGAGCCT 59.037 41.667 16.42 3.03 0.00 4.58
3551 3751 3.693807 AGTTACATCGTCTGGGTCAGTA 58.306 45.455 0.00 0.00 32.61 2.74
3727 3936 6.486253 TGTATGCTCAGAAAACTGATCAAC 57.514 37.500 7.62 7.94 33.92 3.18
3785 3994 8.909708 TGTACTGTTTGAACTTTGAAATCTTG 57.090 30.769 0.00 0.00 0.00 3.02
3789 3998 8.403236 GGTACTGTACTGTTTGAACTTTGAAAT 58.597 33.333 16.79 0.00 0.00 2.17
3791 4000 6.036300 CGGTACTGTACTGTTTGAACTTTGAA 59.964 38.462 16.84 0.00 0.00 2.69
3792 4001 5.521010 CGGTACTGTACTGTTTGAACTTTGA 59.479 40.000 16.84 0.00 0.00 2.69
3793 4002 5.734311 CGGTACTGTACTGTTTGAACTTTG 58.266 41.667 16.84 0.00 0.00 2.77
3794 4003 4.271776 GCGGTACTGTACTGTTTGAACTTT 59.728 41.667 23.65 0.00 37.38 2.66
3795 4004 3.805971 GCGGTACTGTACTGTTTGAACTT 59.194 43.478 23.65 0.00 37.38 2.66
3796 4005 3.387397 GCGGTACTGTACTGTTTGAACT 58.613 45.455 23.65 0.00 37.38 3.01
3797 4006 2.154389 CGCGGTACTGTACTGTTTGAAC 59.846 50.000 23.65 8.64 37.38 3.18
3800 4009 1.065358 CCGCGGTACTGTACTGTTTG 58.935 55.000 23.65 15.29 37.38 2.93
3814 4023 1.537814 TATGGCTGGGTATACCGCGG 61.538 60.000 26.86 26.86 44.64 6.46
3818 4027 3.568430 GCTTTGTTATGGCTGGGTATACC 59.432 47.826 13.99 13.99 40.81 2.73
3824 4033 0.532115 GGTGCTTTGTTATGGCTGGG 59.468 55.000 0.00 0.00 0.00 4.45
3868 4077 9.377312 GCTCTTCTATGGATGATAATTTACCTC 57.623 37.037 0.00 0.00 0.00 3.85
3974 4189 5.465532 TGCTTTCCTGCATACATGAAAAA 57.534 34.783 0.00 0.00 39.12 1.94
3975 4190 5.229423 GTTGCTTTCCTGCATACATGAAAA 58.771 37.500 0.00 0.00 42.96 2.29
4077 4292 1.135915 ACACTATCTGAAGGAGCGCTG 59.864 52.381 18.48 0.00 0.00 5.18
4080 4295 1.804372 GCCACACTATCTGAAGGAGCG 60.804 57.143 0.00 0.00 0.00 5.03
4092 4307 1.621814 AGAAAGTTAGGCGCCACACTA 59.378 47.619 31.54 9.48 0.00 2.74
4094 4309 0.796927 GAGAAAGTTAGGCGCCACAC 59.203 55.000 31.54 23.92 0.00 3.82
4095 4310 0.685097 AGAGAAAGTTAGGCGCCACA 59.315 50.000 31.54 13.75 0.00 4.17
4096 4311 1.079503 CAGAGAAAGTTAGGCGCCAC 58.920 55.000 31.54 19.69 0.00 5.01
4098 4313 0.036294 ACCAGAGAAAGTTAGGCGCC 60.036 55.000 21.89 21.89 0.00 6.53
4104 4319 6.126883 TGGAGAACTTCAACCAGAGAAAGTTA 60.127 38.462 0.00 0.00 0.00 2.24
4206 4421 5.095490 GTCTAAGCGAAAACCAATGGATTG 58.905 41.667 6.16 0.00 37.52 2.67
4216 4431 6.467723 TGAGAAAGATGTCTAAGCGAAAAC 57.532 37.500 0.00 0.00 0.00 2.43
4360 4575 9.435688 GGTTGCTTCCATTTATAATTTGTTTCT 57.564 29.630 0.00 0.00 0.00 2.52
4368 4584 7.716799 TCACTTGGTTGCTTCCATTTATAAT 57.283 32.000 1.66 0.00 37.33 1.28
4370 4586 6.321181 GGATCACTTGGTTGCTTCCATTTATA 59.679 38.462 0.00 0.00 37.33 0.98
4374 4590 2.827921 GGATCACTTGGTTGCTTCCATT 59.172 45.455 0.00 0.00 37.33 3.16


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

AutoCloner maintained by Alex Coulton.