Multiple sequence alignment - TraesCS6A01G344800

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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 TraesCS6A01G344800 chr6A 100.000 6991 0 0 914 7904 578901732 578894742 0.000000e+00 12911.0
1 TraesCS6A01G344800 chr6A 100.000 385 0 0 1 385 578902645 578902261 0.000000e+00 712.0
2 TraesCS6A01G344800 chr6A 89.091 110 10 2 4610 4718 209837230 209837338 1.380000e-27 135.0
3 TraesCS6A01G344800 chr6D 94.819 3339 128 19 992 4327 432725351 432722055 0.000000e+00 5166.0
4 TraesCS6A01G344800 chr6D 93.546 3424 116 44 4506 7899 432721424 432718076 0.000000e+00 5001.0
5 TraesCS6A01G344800 chr6D 88.184 347 15 18 1 337 432725835 432725505 2.670000e-104 390.0
6 TraesCS6A01G344800 chr6D 93.529 170 8 2 4344 4513 432722071 432721905 4.740000e-62 250.0
7 TraesCS6A01G344800 chr6B 90.866 1905 100 30 6038 7899 652640549 652638676 0.000000e+00 2486.0
8 TraesCS6A01G344800 chr6B 91.988 1735 94 17 927 2637 652646223 652644510 0.000000e+00 2392.0
9 TraesCS6A01G344800 chr6B 97.002 1401 40 1 2927 4327 652644306 652642908 0.000000e+00 2353.0
10 TraesCS6A01G344800 chr6B 94.145 1486 68 11 4516 5987 652642307 652640827 0.000000e+00 2244.0
11 TraesCS6A01G344800 chr6B 98.565 209 3 0 2693 2901 652644510 652644302 3.480000e-98 370.0
12 TraesCS6A01G344800 chr6B 83.791 401 33 21 1 385 652646678 652646294 1.260000e-92 351.0
13 TraesCS6A01G344800 chr6B 90.449 178 12 4 4344 4517 652642924 652642748 6.170000e-56 230.0
14 TraesCS6A01G344800 chr3D 89.252 214 20 3 4610 4822 424217347 424217558 1.690000e-66 265.0
15 TraesCS6A01G344800 chr5B 88.182 110 11 2 4610 4718 491056871 491056979 6.440000e-26 130.0
16 TraesCS6A01G344800 chr4D 87.273 110 12 2 4610 4718 222200177 222200069 2.990000e-24 124.0
17 TraesCS6A01G344800 chr7B 81.034 116 22 0 4907 5022 46983831 46983946 8.450000e-15 93.5


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 TraesCS6A01G344800 chr6A 578894742 578902645 7903 True 6811.500000 12911 100.000000 1 7904 2 chr6A.!!$R1 7903
1 TraesCS6A01G344800 chr6D 432718076 432725835 7759 True 2701.750000 5166 92.519500 1 7899 4 chr6D.!!$R1 7898
2 TraesCS6A01G344800 chr6B 652638676 652646678 8002 True 1489.428571 2486 92.400857 1 7899 7 chr6B.!!$R1 7898

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
152 163 0.040246 GACGGCGTGATACCTAGAGC 60.040 60.000 21.19 0.0 0.00 4.09 F
279 302 0.338120 CTCCCCTCTCACCCTCTCTT 59.662 60.000 0.00 0.0 0.00 2.85 F
936 965 1.204062 CGAGCACGCACGAACAATT 59.796 52.632 2.55 0.0 32.00 2.32 F
1690 1745 0.178970 TATCCTACTCCGACCTGGCC 60.179 60.000 0.00 0.0 37.80 5.36 F
1744 1799 0.253044 TCATCAAGTACCAGCAGCCC 59.747 55.000 0.00 0.0 0.00 5.19 F
3537 3592 0.942962 GGAGCAGATGATGAAAGGCG 59.057 55.000 0.00 0.0 0.00 5.52 F
4274 4329 0.179100 GAGAGAGCGCTTGGTATGCA 60.179 55.000 13.26 0.0 0.00 3.96 F
5134 5972 0.175760 TCCTATCTGGACACTTGCGC 59.824 55.000 0.00 0.0 40.56 6.09 F
6361 7446 0.035630 CCTGACCAGAGGAAGGCAAG 60.036 60.000 0.00 0.0 34.69 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1072 1121 0.909623 AGGTCCTGTAATTCCCCACG 59.090 55.000 0.00 0.00 0.00 4.94 R
1415 1469 0.967380 GCCAATCCACCAGTCCCAAG 60.967 60.000 0.00 0.00 0.00 3.61 R
2691 2746 1.266867 ATGGCTTTGGTTGGGATGCC 61.267 55.000 0.00 0.00 40.62 4.40 R
3623 3678 0.847373 TGTTCTGTAGGTTTGCCCCA 59.153 50.000 0.00 0.00 34.57 4.96 R
3787 3842 8.584157 TCATTATCACAAACAGGTAAATTTGCT 58.416 29.630 6.23 0.00 39.03 3.91 R
5126 5964 1.210931 CCAATCTGGTGCGCAAGTG 59.789 57.895 14.00 5.87 33.64 3.16 R
6058 7143 1.901591 ACCACAAGGAGCAACATCTG 58.098 50.000 0.00 0.00 38.69 2.90 R
6564 7650 0.535797 CAGCTGATGACTCCTGCAGA 59.464 55.000 17.39 0.00 0.00 4.26 R
7760 8886 0.308684 CCCGTTGAATCATGCATCGG 59.691 55.000 8.07 8.07 44.23 4.18 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
52 53 2.343758 CCTCCACACGACACCCAG 59.656 66.667 0.00 0.00 0.00 4.45
53 54 2.343758 CTCCACACGACACCCAGG 59.656 66.667 0.00 0.00 0.00 4.45
55 56 4.248842 CCACACGACACCCAGGCA 62.249 66.667 0.00 0.00 0.00 4.75
56 57 2.666190 CACACGACACCCAGGCAG 60.666 66.667 0.00 0.00 0.00 4.85
57 58 4.626081 ACACGACACCCAGGCAGC 62.626 66.667 0.00 0.00 0.00 5.25
61 62 4.101448 GACACCCAGGCAGCCGAT 62.101 66.667 5.55 0.00 0.00 4.18
62 63 4.101448 ACACCCAGGCAGCCGATC 62.101 66.667 5.55 0.00 0.00 3.69
150 161 1.306148 CTGACGGCGTGATACCTAGA 58.694 55.000 21.19 0.00 0.00 2.43
151 162 1.264557 CTGACGGCGTGATACCTAGAG 59.735 57.143 21.19 0.00 0.00 2.43
152 163 0.040246 GACGGCGTGATACCTAGAGC 60.040 60.000 21.19 0.00 0.00 4.09
153 164 1.286260 CGGCGTGATACCTAGAGCC 59.714 63.158 0.00 0.00 41.03 4.70
200 218 2.123077 CCCCAACCCAGCCAACAA 60.123 61.111 0.00 0.00 0.00 2.83
270 293 1.758514 GACGCATCCTCCCCTCTCA 60.759 63.158 0.00 0.00 0.00 3.27
272 295 2.801631 CGCATCCTCCCCTCTCACC 61.802 68.421 0.00 0.00 0.00 4.02
274 297 1.316266 CATCCTCCCCTCTCACCCT 59.684 63.158 0.00 0.00 0.00 4.34
279 302 0.338120 CTCCCCTCTCACCCTCTCTT 59.662 60.000 0.00 0.00 0.00 2.85
300 323 4.468689 CCCCTCGTCGCCTTTCCC 62.469 72.222 0.00 0.00 0.00 3.97
301 324 4.814294 CCCTCGTCGCCTTTCCCG 62.814 72.222 0.00 0.00 0.00 5.14
936 965 1.204062 CGAGCACGCACGAACAATT 59.796 52.632 2.55 0.00 32.00 2.32
984 1014 2.031420 GGCAAGTTTGTTAGTTCGTCCC 60.031 50.000 0.00 0.00 0.00 4.46
986 1016 3.059120 GCAAGTTTGTTAGTTCGTCCCTC 60.059 47.826 0.00 0.00 0.00 4.30
1028 1058 2.732619 GGGGAGGAAACGGAGCGAT 61.733 63.158 0.00 0.00 0.00 4.58
1089 1138 3.471354 CCGTGGGGAATTACAGGAC 57.529 57.895 0.00 0.00 34.06 3.85
1127 1177 7.756558 AGATTCTGTTTCAGATTTCGAATTCC 58.243 34.615 14.71 0.92 40.39 3.01
1149 1199 2.827800 TTTTGCGGGCAAATCATTCA 57.172 40.000 18.43 1.13 44.14 2.57
1181 1231 1.539388 ACGCATTCTTCGAAATTGCCA 59.461 42.857 16.44 0.00 0.00 4.92
1182 1232 2.179589 CGCATTCTTCGAAATTGCCAG 58.820 47.619 16.44 4.85 0.00 4.85
1183 1233 2.159531 CGCATTCTTCGAAATTGCCAGA 60.160 45.455 16.44 0.00 0.00 3.86
1184 1234 3.488047 CGCATTCTTCGAAATTGCCAGAT 60.488 43.478 16.44 0.00 0.00 2.90
1185 1235 4.427312 GCATTCTTCGAAATTGCCAGATT 58.573 39.130 13.01 0.00 0.00 2.40
1186 1236 4.866486 GCATTCTTCGAAATTGCCAGATTT 59.134 37.500 13.01 0.00 32.16 2.17
1194 1244 4.809673 GAAATTGCCAGATTTCGAAAGGT 58.190 39.130 16.80 0.00 36.59 3.50
1266 1316 3.118038 GGGGCTGATCTGTGGTGTTATTA 60.118 47.826 1.27 0.00 0.00 0.98
1268 1318 4.130118 GGCTGATCTGTGGTGTTATTAGG 58.870 47.826 1.27 0.00 0.00 2.69
1276 1326 7.743116 TCTGTGGTGTTATTAGGGAAATCTA 57.257 36.000 0.00 0.00 0.00 1.98
1278 1328 8.210946 TCTGTGGTGTTATTAGGGAAATCTATG 58.789 37.037 0.00 0.00 0.00 2.23
1279 1329 7.287061 TGTGGTGTTATTAGGGAAATCTATGG 58.713 38.462 0.00 0.00 0.00 2.74
1280 1330 6.206829 GTGGTGTTATTAGGGAAATCTATGGC 59.793 42.308 0.00 0.00 0.00 4.40
1290 1340 4.499696 GGGAAATCTATGGCAAATTGTCCG 60.500 45.833 0.00 0.00 0.00 4.79
1291 1341 4.338118 GGAAATCTATGGCAAATTGTCCGA 59.662 41.667 0.00 0.00 0.00 4.55
1292 1342 5.010012 GGAAATCTATGGCAAATTGTCCGAT 59.990 40.000 0.00 0.00 0.00 4.18
1293 1343 6.461509 GGAAATCTATGGCAAATTGTCCGATT 60.462 38.462 0.00 0.00 0.00 3.34
1294 1344 6.469782 AATCTATGGCAAATTGTCCGATTT 57.530 33.333 0.00 0.00 0.00 2.17
1295 1345 5.499139 TCTATGGCAAATTGTCCGATTTC 57.501 39.130 0.00 0.00 0.00 2.17
1296 1346 2.627863 TGGCAAATTGTCCGATTTCG 57.372 45.000 0.00 0.00 39.44 3.46
1297 1347 1.883275 TGGCAAATTGTCCGATTTCGT 59.117 42.857 0.00 0.00 37.74 3.85
1298 1348 2.250188 GGCAAATTGTCCGATTTCGTG 58.750 47.619 0.00 0.00 37.74 4.35
1299 1349 2.351350 GGCAAATTGTCCGATTTCGTGT 60.351 45.455 0.00 0.00 37.74 4.49
1300 1350 2.908626 GCAAATTGTCCGATTTCGTGTC 59.091 45.455 0.00 0.00 37.74 3.67
1301 1351 3.488489 CAAATTGTCCGATTTCGTGTCC 58.512 45.455 0.00 0.00 37.74 4.02
1302 1352 1.355971 ATTGTCCGATTTCGTGTCCG 58.644 50.000 0.00 0.00 37.74 4.79
1316 1366 2.348666 CGTGTCCGGATTTCATGTCTTC 59.651 50.000 7.81 0.00 0.00 2.87
1336 1390 5.356190 TCTTCATTTGTCTGATGATGGAAGC 59.644 40.000 0.00 0.00 33.82 3.86
1402 1456 1.228429 CGACAGGAAGGGGCCAAAA 60.228 57.895 4.39 0.00 0.00 2.44
1415 1469 1.370900 CCAAAACACGAGCAGCTGC 60.371 57.895 31.53 31.53 42.49 5.25
1458 1512 2.299013 TCGTGTGATGTACTTGGCTCTT 59.701 45.455 0.00 0.00 0.00 2.85
1529 1584 4.175489 CATCTGCTGCCGCTGCAC 62.175 66.667 19.80 0.00 44.23 4.57
1666 1721 3.740128 GATCGTCATGCTGCCCCGT 62.740 63.158 0.00 0.00 0.00 5.28
1690 1745 0.178970 TATCCTACTCCGACCTGGCC 60.179 60.000 0.00 0.00 37.80 5.36
1744 1799 0.253044 TCATCAAGTACCAGCAGCCC 59.747 55.000 0.00 0.00 0.00 5.19
1762 1817 1.347050 CCCGATGAGGATCTTGATGCT 59.653 52.381 4.33 4.33 45.00 3.79
1777 1832 1.476891 GATGCTCTGGTCTCGGTTGTA 59.523 52.381 0.00 0.00 0.00 2.41
1795 1850 6.498304 GGTTGTAAATGATGATGATGTGGTC 58.502 40.000 0.00 0.00 0.00 4.02
1810 1865 2.374839 TGTGGTCAACATGATGGAGGAA 59.625 45.455 0.00 0.00 32.36 3.36
1870 1925 3.181459 GGCTCAGGGTCTTCTTATTCTCC 60.181 52.174 0.00 0.00 0.00 3.71
1921 1976 1.392589 CTGTGCATTACCATGGGGAC 58.607 55.000 18.09 10.01 38.05 4.46
1948 2003 2.657143 GAGACGGAGAGGAGGTATGTT 58.343 52.381 0.00 0.00 0.00 2.71
2378 2433 2.362375 GGAATTTGGGCCGCTCCA 60.362 61.111 0.00 0.00 36.21 3.86
2402 2457 4.925646 GCAATTTCTTGGATGGAAACAGTC 59.074 41.667 0.00 0.00 36.91 3.51
2508 2563 6.088085 GTCCAACAACATTTTGATCAATCGAC 59.912 38.462 9.40 0.00 36.48 4.20
2620 2675 6.575162 AGACTGGAAAATGGTGTTTATGTC 57.425 37.500 0.00 0.00 0.00 3.06
2659 2714 2.304761 TCACCCTCCCATGTTCTACAAC 59.695 50.000 0.00 0.00 0.00 3.32
2680 2735 6.481313 ACAACGAATCACATTCTCATGATAGG 59.519 38.462 0.00 0.00 34.41 2.57
2691 2746 3.072038 TCTCATGATAGGTCTTGGCATGG 59.928 47.826 0.00 0.00 37.51 3.66
2906 2961 3.369787 CCAGGGCGAGCATATGAATGATA 60.370 47.826 6.97 0.00 34.84 2.15
3055 3110 1.135315 CTTGCCGCCACTTCAATCG 59.865 57.895 0.00 0.00 0.00 3.34
3183 3238 4.536090 AGGTGATGTTAGTCCAAGGATTCA 59.464 41.667 0.00 0.00 0.00 2.57
3237 3292 2.353610 GGCCTTCACCCAATGGCAG 61.354 63.158 0.00 0.00 46.53 4.85
3272 3327 1.349357 TCGTTGGACATGATGTTCCCA 59.651 47.619 0.58 1.46 0.00 4.37
3382 3437 2.435586 CAGCAACCAGGAGCTCCG 60.436 66.667 26.95 20.34 39.50 4.63
3502 3557 2.773487 TCCAGGTTGGACATTAACACG 58.227 47.619 0.00 0.00 42.67 4.49
3537 3592 0.942962 GGAGCAGATGATGAAAGGCG 59.057 55.000 0.00 0.00 0.00 5.52
3573 3628 3.504520 ACTGAAACAAAACCTTCACACGT 59.495 39.130 0.00 0.00 0.00 4.49
3843 3898 7.890127 TGATGGAAAGAAGTTTGATGAGGTAAT 59.110 33.333 0.00 0.00 0.00 1.89
3851 3906 6.299805 AGTTTGATGAGGTAATGTCTGCTA 57.700 37.500 0.00 0.00 0.00 3.49
3854 3909 5.876651 TGATGAGGTAATGTCTGCTATGT 57.123 39.130 0.00 0.00 0.00 2.29
3865 3920 7.792374 AATGTCTGCTATGTGTAATACTTGG 57.208 36.000 0.00 0.00 0.00 3.61
3904 3959 6.831976 CATTAAACTACCTAATGCTCTCCCT 58.168 40.000 0.00 0.00 31.80 4.20
4180 4235 3.181478 CGGGTACTTATGGGTCAGTCTTC 60.181 52.174 0.00 0.00 0.00 2.87
4274 4329 0.179100 GAGAGAGCGCTTGGTATGCA 60.179 55.000 13.26 0.00 0.00 3.96
4288 4343 6.256321 GCTTGGTATGCATTATTTCCTTGTTG 59.744 38.462 3.54 0.00 0.00 3.33
4327 4382 5.657826 TTGGCAGCATAGCAAAATTTCTA 57.342 34.783 0.00 0.00 35.83 2.10
4328 4383 4.997565 TGGCAGCATAGCAAAATTTCTAC 58.002 39.130 0.00 0.00 35.83 2.59
4329 4384 4.142182 TGGCAGCATAGCAAAATTTCTACC 60.142 41.667 0.00 0.00 35.83 3.18
4330 4385 4.363138 GCAGCATAGCAAAATTTCTACCC 58.637 43.478 0.00 0.00 0.00 3.69
4331 4386 4.601019 CAGCATAGCAAAATTTCTACCCG 58.399 43.478 0.00 0.00 0.00 5.28
4332 4387 3.066760 AGCATAGCAAAATTTCTACCCGC 59.933 43.478 0.00 0.00 0.00 6.13
4333 4388 3.181491 GCATAGCAAAATTTCTACCCGCA 60.181 43.478 0.00 0.00 0.00 5.69
4334 4389 4.676723 GCATAGCAAAATTTCTACCCGCAA 60.677 41.667 0.00 0.00 0.00 4.85
4335 4390 5.406649 CATAGCAAAATTTCTACCCGCAAA 58.593 37.500 0.00 0.00 0.00 3.68
4336 4391 4.329462 AGCAAAATTTCTACCCGCAAAA 57.671 36.364 0.00 0.00 0.00 2.44
4337 4392 4.698575 AGCAAAATTTCTACCCGCAAAAA 58.301 34.783 0.00 0.00 0.00 1.94
4455 4511 2.717639 AATGTGGCTGTGGATAGGTC 57.282 50.000 0.00 0.00 0.00 3.85
4462 4518 3.330701 TGGCTGTGGATAGGTCTCTTTTT 59.669 43.478 0.00 0.00 0.00 1.94
4503 4559 1.542915 GGCCTTGGCTGCATGTATATG 59.457 52.381 11.71 0.00 37.36 1.78
4600 5438 4.956075 GGTAATGGTTTGGTCTCATGGAAT 59.044 41.667 0.00 0.00 0.00 3.01
4732 5570 1.210478 GGTCCTGATGGAAGCTTAGCA 59.790 52.381 7.07 0.00 45.18 3.49
4759 5597 3.992943 ACCGAGTTTATGGTCAATGGA 57.007 42.857 0.00 0.00 31.16 3.41
4959 5797 5.010012 GCATGGGAAGAATATCGTCCATTTT 59.990 40.000 13.12 0.00 45.17 1.82
4968 5806 8.737168 AGAATATCGTCCATTTTGATCTCAAA 57.263 30.769 1.28 1.28 43.36 2.69
5027 5865 2.086869 ACCGATCTGCAAGGTTTGATG 58.913 47.619 0.00 0.00 33.96 3.07
5034 5872 0.681175 GCAAGGTTTGATGCCCACTT 59.319 50.000 0.00 0.00 36.56 3.16
5070 5908 5.189736 TGCTTCTCCTTCTCTATTTGCCTAA 59.810 40.000 0.00 0.00 0.00 2.69
5077 5915 5.819901 CCTTCTCTATTTGCCTAAACTCCTG 59.180 44.000 0.00 0.00 0.00 3.86
5078 5916 6.374417 TTCTCTATTTGCCTAAACTCCTGT 57.626 37.500 0.00 0.00 0.00 4.00
5083 5921 7.882179 TCTATTTGCCTAAACTCCTGTTTTTC 58.118 34.615 0.00 0.00 43.13 2.29
5088 5926 5.154222 GCCTAAACTCCTGTTTTTCGAATG 58.846 41.667 0.00 0.00 43.13 2.67
5134 5972 0.175760 TCCTATCTGGACACTTGCGC 59.824 55.000 0.00 0.00 40.56 6.09
5354 6195 7.573968 ACTCTTAATGTTCTGACAAAAAGCT 57.426 32.000 0.00 0.00 39.66 3.74
5357 6198 8.169977 TCTTAATGTTCTGACAAAAAGCTGAT 57.830 30.769 0.00 0.00 39.66 2.90
5495 6336 7.012943 TCGAAACTTAAGTTATGTTGATTGCG 58.987 34.615 20.83 6.73 37.25 4.85
5503 6344 7.566858 AAGTTATGTTGATTGCGACATTTTC 57.433 32.000 4.28 0.00 44.88 2.29
5510 6351 5.131594 TGATTGCGACATTTTCATTTCCA 57.868 34.783 0.00 0.00 0.00 3.53
5574 6415 8.223769 CACATGTATCAGTTTGAGTAACTTGTC 58.776 37.037 0.00 0.00 44.73 3.18
5593 6442 1.614903 TCTCAGGGCTGCAAAAACATG 59.385 47.619 0.50 0.00 0.00 3.21
5618 6467 6.537453 TTGTTGGACATTTTCTTCCTTTGA 57.463 33.333 0.00 0.00 32.55 2.69
5722 6571 6.122277 TGGAAATGGTCAGATGTAAATCTCC 58.878 40.000 0.00 0.00 0.00 3.71
5814 6666 5.511234 AGCTGTATGAAATTGGAATCAGC 57.489 39.130 13.56 13.56 44.61 4.26
5850 6702 1.072331 CAGTGCTGTTCCCCTACTTGT 59.928 52.381 0.00 0.00 0.00 3.16
6014 6936 3.302365 TGCTTGTTATTGCAAAGAGGC 57.698 42.857 1.71 0.00 36.15 4.70
6058 7143 5.793030 ATATTAGTCAGGCACCTGTAGTC 57.207 43.478 16.12 6.28 43.96 2.59
6067 7152 1.734465 GCACCTGTAGTCAGATGTTGC 59.266 52.381 0.00 0.00 43.76 4.17
6199 7284 4.889409 TGGAAATCATTGATGGAAGGTAGC 59.111 41.667 0.00 0.00 0.00 3.58
6287 7372 5.276348 GCCGCAGCAATGAATGTTAAATAAC 60.276 40.000 0.00 0.00 39.53 1.89
6310 7395 4.000988 AGGCTCAAGTTATTACAACGTGG 58.999 43.478 0.00 0.00 31.96 4.94
6335 7420 4.613437 AGGCATGTAAAGAATCCCATGTT 58.387 39.130 0.00 0.00 37.57 2.71
6361 7446 0.035630 CCTGACCAGAGGAAGGCAAG 60.036 60.000 0.00 0.00 34.69 4.01
6368 7453 3.689002 GAGGAAGGCAAGCCCGGAG 62.689 68.421 0.73 0.00 39.21 4.63
6475 7561 0.963962 TCACGGACGGTTCTAAAGCT 59.036 50.000 0.00 0.00 0.00 3.74
6535 7621 7.983307 TCCTTTGACAAAATTTTGAAATGGTG 58.017 30.769 32.20 16.45 40.55 4.17
6538 7624 6.998968 TGACAAAATTTTGAAATGGTGCTT 57.001 29.167 32.20 10.00 40.55 3.91
6554 7640 1.742831 TGCTTGCAAACGTGACTTCTT 59.257 42.857 0.00 0.00 0.00 2.52
6556 7642 2.629022 CTTGCAAACGTGACTTCTTCG 58.371 47.619 0.00 0.00 0.00 3.79
6564 7650 2.159142 ACGTGACTTCTTCGTTTCCTGT 60.159 45.455 0.00 0.00 34.07 4.00
6586 7672 1.600638 CAGGAGTCATCAGCTGCCA 59.399 57.895 9.47 0.00 0.00 4.92
6587 7673 0.180642 CAGGAGTCATCAGCTGCCAT 59.819 55.000 9.47 0.00 0.00 4.40
6588 7674 0.917533 AGGAGTCATCAGCTGCCATT 59.082 50.000 9.47 0.00 0.00 3.16
6601 7690 2.161855 CTGCCATTTGCCTTCAGTACA 58.838 47.619 0.00 0.00 40.16 2.90
6769 7861 3.801114 TCATACGATTGTGTCCTGAGG 57.199 47.619 0.00 0.00 0.00 3.86
6858 7950 3.518068 GGGCCGCCTCGAAAATGG 61.518 66.667 9.86 0.00 0.00 3.16
6953 8048 3.427503 CCAGTGGTAACCGATTTGAATGC 60.428 47.826 0.00 0.00 0.00 3.56
6965 8060 1.660167 TTGAATGCGCCTCTGATGAG 58.340 50.000 4.18 0.00 39.92 2.90
7041 8137 1.199327 CAAATCTGCACTGTGCTGGAG 59.801 52.381 30.67 21.51 45.31 3.86
7166 8267 3.944015 GCTCTGCTCCATGAAGTTTATGT 59.056 43.478 6.85 0.00 0.00 2.29
7370 8478 2.618241 TGGTTTTCAGTCTGATGTGCAC 59.382 45.455 10.75 10.75 0.00 4.57
7425 8533 4.694509 AGTGCATTTTCTTCAGAGCTACTG 59.305 41.667 0.00 6.79 46.97 2.74
7449 8559 0.670162 GTTGACATTGCAGGCAGTGT 59.330 50.000 20.24 20.24 46.92 3.55
7453 8563 1.171308 ACATTGCAGGCAGTGTCATC 58.829 50.000 15.49 0.00 41.94 2.92
7494 8605 4.164221 TCCTTGTCCTTAACCATCTCATCC 59.836 45.833 0.00 0.00 0.00 3.51
7610 8727 2.898920 GATTAGCCAGGCCTGCAGCA 62.899 60.000 28.76 14.53 46.50 4.41
7611 8728 2.905935 ATTAGCCAGGCCTGCAGCAG 62.906 60.000 28.76 16.23 46.50 4.24
7740 8866 1.325943 CGCTTTTCGATCTCTTCTGCC 59.674 52.381 0.00 0.00 41.67 4.85
7747 8873 3.417275 ATCTCTTCTGCCCGTCGCG 62.417 63.158 0.00 0.00 42.08 5.87
7796 8924 2.780010 ACGGGAGGAGGAATTTCATGAT 59.220 45.455 0.00 0.00 0.00 2.45
7799 8927 4.506271 CGGGAGGAGGAATTTCATGATGAT 60.506 45.833 0.00 0.00 0.00 2.45
7899 9036 2.869801 CGTAGGTGACAAGTCAAAAGCA 59.130 45.455 4.20 0.00 41.85 3.91
7900 9037 3.311322 CGTAGGTGACAAGTCAAAAGCAA 59.689 43.478 4.20 0.00 41.85 3.91
7901 9038 4.201871 CGTAGGTGACAAGTCAAAAGCAAA 60.202 41.667 4.20 0.00 41.85 3.68
7902 9039 4.376340 AGGTGACAAGTCAAAAGCAAAG 57.624 40.909 4.20 0.00 41.85 2.77
7903 9040 2.860136 GGTGACAAGTCAAAAGCAAAGC 59.140 45.455 4.20 0.00 41.85 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.626081 GCTGCCTGGGTGTCGTGT 62.626 66.667 0.00 0.00 0.00 4.49
44 45 4.101448 ATCGGCTGCCTGGGTGTC 62.101 66.667 17.92 0.00 0.00 3.67
45 46 4.101448 GATCGGCTGCCTGGGTGT 62.101 66.667 17.92 0.00 0.00 4.16
46 47 4.864334 GGATCGGCTGCCTGGGTG 62.864 72.222 17.92 0.05 0.00 4.61
50 51 3.764160 GAAGGGGATCGGCTGCCTG 62.764 68.421 17.92 10.52 35.23 4.85
52 53 4.570874 GGAAGGGGATCGGCTGCC 62.571 72.222 9.11 9.11 33.75 4.85
53 54 3.797353 TGGAAGGGGATCGGCTGC 61.797 66.667 0.00 0.00 0.00 5.25
55 56 2.285368 TGTGGAAGGGGATCGGCT 60.285 61.111 0.00 0.00 0.00 5.52
56 57 2.124695 GTGTGGAAGGGGATCGGC 60.125 66.667 0.00 0.00 0.00 5.54
57 58 1.995626 AGGTGTGGAAGGGGATCGG 60.996 63.158 0.00 0.00 0.00 4.18
59 60 0.253327 GTCAGGTGTGGAAGGGGATC 59.747 60.000 0.00 0.00 0.00 3.36
60 61 1.553690 CGTCAGGTGTGGAAGGGGAT 61.554 60.000 0.00 0.00 0.00 3.85
61 62 2.214216 CGTCAGGTGTGGAAGGGGA 61.214 63.158 0.00 0.00 0.00 4.81
62 63 2.347490 CGTCAGGTGTGGAAGGGG 59.653 66.667 0.00 0.00 0.00 4.79
150 161 1.072159 GGATATTCGCTGGCTGGCT 59.928 57.895 2.00 0.00 0.00 4.75
151 162 2.320587 CGGATATTCGCTGGCTGGC 61.321 63.158 0.00 0.00 0.00 4.85
152 163 3.957260 CGGATATTCGCTGGCTGG 58.043 61.111 0.00 0.00 0.00 4.85
257 277 0.933791 AGAGGGTGAGAGGGGAGGAT 60.934 60.000 0.00 0.00 0.00 3.24
913 942 2.582265 TTCGTGCGTGCTCGTGTTC 61.582 57.895 14.82 0.00 39.49 3.18
914 943 2.583868 TTCGTGCGTGCTCGTGTT 60.584 55.556 14.82 0.00 39.49 3.32
915 944 3.327754 GTTCGTGCGTGCTCGTGT 61.328 61.111 14.82 0.00 39.49 4.49
916 945 2.158058 ATTGTTCGTGCGTGCTCGTG 62.158 55.000 14.82 0.79 39.49 4.35
917 946 1.495584 AATTGTTCGTGCGTGCTCGT 61.496 50.000 14.82 0.00 39.49 4.18
918 947 1.054348 CAATTGTTCGTGCGTGCTCG 61.054 55.000 9.79 9.79 40.37 5.03
919 948 0.725784 CCAATTGTTCGTGCGTGCTC 60.726 55.000 4.43 0.00 0.00 4.26
920 949 1.282570 CCAATTGTTCGTGCGTGCT 59.717 52.632 4.43 0.00 0.00 4.40
921 950 2.364311 GCCAATTGTTCGTGCGTGC 61.364 57.895 4.43 0.00 0.00 5.34
922 951 0.998226 CAGCCAATTGTTCGTGCGTG 60.998 55.000 4.43 0.00 0.00 5.34
923 952 1.282570 CAGCCAATTGTTCGTGCGT 59.717 52.632 4.43 0.00 0.00 5.24
924 953 1.442520 CCAGCCAATTGTTCGTGCG 60.443 57.895 4.43 0.00 0.00 5.34
925 954 0.031994 AACCAGCCAATTGTTCGTGC 59.968 50.000 4.43 0.00 0.00 5.34
936 965 2.452600 AAACAGGAGAAAACCAGCCA 57.547 45.000 0.00 0.00 0.00 4.75
960 989 4.439016 GGACGAACTAACAAACTTGCCAAA 60.439 41.667 0.00 0.00 0.00 3.28
961 990 3.065648 GGACGAACTAACAAACTTGCCAA 59.934 43.478 0.00 0.00 0.00 4.52
962 991 2.614983 GGACGAACTAACAAACTTGCCA 59.385 45.455 0.00 0.00 0.00 4.92
963 992 2.031420 GGGACGAACTAACAAACTTGCC 60.031 50.000 0.00 0.00 0.00 4.52
965 994 3.497262 GGAGGGACGAACTAACAAACTTG 59.503 47.826 0.00 0.00 0.00 3.16
971 1001 3.703052 GGATAAGGAGGGACGAACTAACA 59.297 47.826 0.00 0.00 0.00 2.41
975 1005 2.668625 GAGGATAAGGAGGGACGAACT 58.331 52.381 0.00 0.00 0.00 3.01
984 1014 1.333177 CAGACGGGGAGGATAAGGAG 58.667 60.000 0.00 0.00 0.00 3.69
986 1016 1.497161 AACAGACGGGGAGGATAAGG 58.503 55.000 0.00 0.00 0.00 2.69
1024 1054 4.562789 GGCCAGATAAAAACAGAAAATCGC 59.437 41.667 0.00 0.00 0.00 4.58
1028 1058 6.723298 TCTTGGCCAGATAAAAACAGAAAA 57.277 33.333 5.11 0.00 0.00 2.29
1072 1121 0.909623 AGGTCCTGTAATTCCCCACG 59.090 55.000 0.00 0.00 0.00 4.94
1074 1123 2.196595 CTGAGGTCCTGTAATTCCCCA 58.803 52.381 0.00 0.00 0.00 4.96
1188 1238 4.505313 AAAAAGAATGAGCCGACCTTTC 57.495 40.909 0.00 0.00 0.00 2.62
1223 1273 1.201181 CCACCGTCAGAGAAGAGACAG 59.799 57.143 0.00 0.00 34.48 3.51
1228 1278 1.609501 CCCCCACCGTCAGAGAAGA 60.610 63.158 0.00 0.00 0.00 2.87
1229 1279 2.982130 CCCCCACCGTCAGAGAAG 59.018 66.667 0.00 0.00 0.00 2.85
1256 1306 6.126332 TGCCATAGATTTCCCTAATAACACCA 60.126 38.462 0.00 0.00 0.00 4.17
1266 1316 4.651045 GGACAATTTGCCATAGATTTCCCT 59.349 41.667 0.00 0.00 0.00 4.20
1268 1318 4.338118 TCGGACAATTTGCCATAGATTTCC 59.662 41.667 0.00 0.00 0.00 3.13
1276 1326 2.491693 ACGAAATCGGACAATTTGCCAT 59.508 40.909 7.81 0.00 44.95 4.40
1278 1328 2.250188 CACGAAATCGGACAATTTGCC 58.750 47.619 7.81 0.00 44.95 4.52
1279 1329 2.908626 GACACGAAATCGGACAATTTGC 59.091 45.455 7.81 0.00 44.95 3.68
1280 1330 3.488489 GGACACGAAATCGGACAATTTG 58.512 45.455 7.81 0.00 44.95 2.32
1290 1340 3.374058 ACATGAAATCCGGACACGAAATC 59.626 43.478 6.12 0.00 44.60 2.17
1291 1341 3.343617 ACATGAAATCCGGACACGAAAT 58.656 40.909 6.12 0.00 44.60 2.17
1292 1342 2.739913 GACATGAAATCCGGACACGAAA 59.260 45.455 6.12 0.00 44.60 3.46
1293 1343 2.028476 AGACATGAAATCCGGACACGAA 60.028 45.455 6.12 0.00 44.60 3.85
1294 1344 1.548719 AGACATGAAATCCGGACACGA 59.451 47.619 6.12 0.00 44.60 4.35
1295 1345 2.010145 AGACATGAAATCCGGACACG 57.990 50.000 6.12 0.00 40.55 4.49
1296 1346 3.334691 TGAAGACATGAAATCCGGACAC 58.665 45.455 6.12 1.22 0.00 3.67
1297 1347 3.694043 TGAAGACATGAAATCCGGACA 57.306 42.857 6.12 0.00 0.00 4.02
1298 1348 5.106157 ACAAATGAAGACATGAAATCCGGAC 60.106 40.000 6.12 0.00 36.79 4.79
1299 1349 5.009631 ACAAATGAAGACATGAAATCCGGA 58.990 37.500 6.61 6.61 36.79 5.14
1300 1350 5.124457 AGACAAATGAAGACATGAAATCCGG 59.876 40.000 0.00 0.00 36.79 5.14
1301 1351 6.025896 CAGACAAATGAAGACATGAAATCCG 58.974 40.000 0.00 0.00 36.79 4.18
1302 1352 7.149569 TCAGACAAATGAAGACATGAAATCC 57.850 36.000 0.00 0.00 36.79 3.01
1316 1366 4.733815 GCAGCTTCCATCATCAGACAAATG 60.734 45.833 0.00 0.00 0.00 2.32
1415 1469 0.967380 GCCAATCCACCAGTCCCAAG 60.967 60.000 0.00 0.00 0.00 3.61
1458 1512 1.741401 CTTGAGTTGGATCGGCGCA 60.741 57.895 10.83 0.00 0.00 6.09
1493 1547 3.190849 CGCCATGTGTGCCGAGAG 61.191 66.667 0.00 0.00 0.00 3.20
1636 1691 3.718210 GACGATCCTGGTGTCGCCC 62.718 68.421 18.93 10.78 41.31 6.13
1666 1721 3.487372 CAGGTCGGAGTAGGATATGTCA 58.513 50.000 0.00 0.00 0.00 3.58
1744 1799 3.318886 CAGAGCATCAAGATCCTCATCG 58.681 50.000 3.99 0.00 37.82 3.84
1762 1817 4.221924 TCATCATTTACAACCGAGACCAGA 59.778 41.667 0.00 0.00 0.00 3.86
1777 1832 6.378848 TCATGTTGACCACATCATCATCATTT 59.621 34.615 0.00 0.00 43.17 2.32
1795 1850 6.514541 GCTTGTCATATTCCTCCATCATGTTG 60.515 42.308 0.00 0.00 0.00 3.33
1921 1976 3.578272 CTCTCCGTCTCCCGCTCG 61.578 72.222 0.00 0.00 34.38 5.03
1981 2036 1.277557 ACTGACACAGGAGATGAAGGC 59.722 52.381 0.00 0.00 35.51 4.35
2378 2433 4.590222 ACTGTTTCCATCCAAGAAATTGCT 59.410 37.500 0.00 0.00 35.77 3.91
2508 2563 2.357009 GCAGAATACTCACTTGCCATGG 59.643 50.000 7.63 7.63 0.00 3.66
2620 2675 2.023673 TGACCACCAGTTTGCTCTTTG 58.976 47.619 0.00 0.00 0.00 2.77
2659 2714 6.453943 AGACCTATCATGAGAATGTGATTCG 58.546 40.000 0.09 0.00 43.92 3.34
2680 2735 3.530067 GGATGCCCATGCCAAGAC 58.470 61.111 0.00 0.00 36.33 3.01
2691 2746 1.266867 ATGGCTTTGGTTGGGATGCC 61.267 55.000 0.00 0.00 40.62 4.40
2906 2961 9.515226 ACTTACAACTTGTTGGTTATGATATGT 57.485 29.630 16.48 5.15 0.00 2.29
3055 3110 2.553086 CTGCTTGCTCTCCTTCTCATC 58.447 52.381 0.00 0.00 0.00 2.92
3183 3238 3.198417 TCGATCATATGCAGGCATACCAT 59.802 43.478 15.59 10.48 41.09 3.55
3237 3292 6.163476 TGTCCAACGATTCTATATGGTATGC 58.837 40.000 0.00 0.00 32.90 3.14
3272 3327 4.159693 GGAAGAAGGGTTTTCAACAACAGT 59.840 41.667 0.00 0.00 0.00 3.55
3382 3437 7.382488 GCTCTTTCAGGAAAAATTTCTACCAAC 59.618 37.037 5.91 0.00 37.35 3.77
3502 3557 6.076981 TCTGCTCCTTCAAATTTCTTTGTC 57.923 37.500 0.00 0.00 42.02 3.18
3573 3628 3.785982 TGCTAGGGTCACTCGCAA 58.214 55.556 0.00 0.00 43.94 4.85
3623 3678 0.847373 TGTTCTGTAGGTTTGCCCCA 59.153 50.000 0.00 0.00 34.57 4.96
3787 3842 8.584157 TCATTATCACAAACAGGTAAATTTGCT 58.416 29.630 6.23 0.00 39.03 3.91
3795 3850 8.676401 CATCATTGTCATTATCACAAACAGGTA 58.324 33.333 0.00 0.00 37.30 3.08
3843 3898 6.071051 TGTCCAAGTATTACACATAGCAGACA 60.071 38.462 0.00 0.00 0.00 3.41
3851 3906 7.759489 ATGTGTTTGTCCAAGTATTACACAT 57.241 32.000 16.14 16.14 45.35 3.21
3854 3909 8.293867 GCTTAATGTGTTTGTCCAAGTATTACA 58.706 33.333 0.00 0.00 0.00 2.41
3865 3920 9.124807 GGTAGTTTAATGCTTAATGTGTTTGTC 57.875 33.333 0.00 0.00 0.00 3.18
3903 3958 6.111382 TCTGCAGATGAAAGGATTTGAGTAG 58.889 40.000 13.74 0.00 39.27 2.57
3904 3959 6.053632 TCTGCAGATGAAAGGATTTGAGTA 57.946 37.500 13.74 0.00 39.27 2.59
4180 4235 2.177669 ACATCCCCTCCATTTACCATGG 59.822 50.000 11.19 11.19 40.48 3.66
4274 4329 5.768164 AGTCGACAACCAACAAGGAAATAAT 59.232 36.000 19.50 0.00 41.22 1.28
4288 4343 2.418976 GCCAATCCTTAAGTCGACAACC 59.581 50.000 19.50 0.00 0.00 3.77
4336 4391 9.551734 AAGAGAAATTTTGCTATGCTTCTTTTT 57.448 25.926 0.00 0.00 0.00 1.94
4337 4392 9.551734 AAAGAGAAATTTTGCTATGCTTCTTTT 57.448 25.926 0.00 0.00 0.00 2.27
4339 4394 9.631452 GTAAAGAGAAATTTTGCTATGCTTCTT 57.369 29.630 0.00 0.00 0.00 2.52
4340 4395 8.246871 GGTAAAGAGAAATTTTGCTATGCTTCT 58.753 33.333 0.00 0.00 0.00 2.85
4341 4396 8.246871 AGGTAAAGAGAAATTTTGCTATGCTTC 58.753 33.333 0.00 0.00 0.00 3.86
4342 4397 8.127150 AGGTAAAGAGAAATTTTGCTATGCTT 57.873 30.769 0.00 0.00 0.00 3.91
4343 4398 7.709149 AGGTAAAGAGAAATTTTGCTATGCT 57.291 32.000 0.00 0.00 0.00 3.79
4349 4404 9.358872 CCTGAAATAGGTAAAGAGAAATTTTGC 57.641 33.333 0.00 0.00 42.00 3.68
4350 4405 9.860898 CCCTGAAATAGGTAAAGAGAAATTTTG 57.139 33.333 0.00 0.00 45.80 2.44
4351 4406 9.601810 ACCCTGAAATAGGTAAAGAGAAATTTT 57.398 29.630 0.00 0.00 45.80 1.82
4352 4407 9.244292 GACCCTGAAATAGGTAAAGAGAAATTT 57.756 33.333 0.00 0.00 45.80 1.82
4353 4408 8.390921 TGACCCTGAAATAGGTAAAGAGAAATT 58.609 33.333 0.00 0.00 45.80 1.82
4354 4409 7.928873 TGACCCTGAAATAGGTAAAGAGAAAT 58.071 34.615 0.00 0.00 45.80 2.17
4355 4410 7.324388 TGACCCTGAAATAGGTAAAGAGAAA 57.676 36.000 0.00 0.00 45.80 2.52
4356 4411 6.945636 TGACCCTGAAATAGGTAAAGAGAA 57.054 37.500 0.00 0.00 45.80 2.87
4357 4412 6.945636 TTGACCCTGAAATAGGTAAAGAGA 57.054 37.500 0.00 0.00 45.80 3.10
4358 4413 7.094334 GGTTTTGACCCTGAAATAGGTAAAGAG 60.094 40.741 0.00 0.00 45.80 2.85
4359 4414 6.717997 GGTTTTGACCCTGAAATAGGTAAAGA 59.282 38.462 0.00 0.00 45.80 2.52
4568 5406 2.491693 CCAAACCATTACCACAGCGAAT 59.508 45.455 0.00 0.00 0.00 3.34
4600 5438 1.896220 AAATCAGAACTTGAGGCGCA 58.104 45.000 10.83 0.00 39.68 6.09
4601 5439 4.622701 AATAAATCAGAACTTGAGGCGC 57.377 40.909 0.00 0.00 39.68 6.53
4732 5570 5.217978 TGACCATAAACTCGGTAACAGTT 57.782 39.130 0.00 0.00 38.85 3.16
4759 5597 5.768980 TCCTCAGGAATTGTTTGAGAGAT 57.231 39.130 0.00 0.00 40.54 2.75
5027 5865 1.273327 CAATGAAGGGAACAAGTGGGC 59.727 52.381 0.00 0.00 0.00 5.36
5034 5872 2.376518 AGGAGAAGCAATGAAGGGAACA 59.623 45.455 0.00 0.00 0.00 3.18
5070 5908 4.647424 TTGCATTCGAAAAACAGGAGTT 57.353 36.364 0.00 0.00 40.40 3.01
5126 5964 1.210931 CCAATCTGGTGCGCAAGTG 59.789 57.895 14.00 5.87 33.64 3.16
5333 6174 8.807667 AATCAGCTTTTTGTCAGAACATTAAG 57.192 30.769 0.00 0.00 34.73 1.85
5452 6293 8.889849 AGTTTCGAATGTTACCAATAATTTCG 57.110 30.769 0.00 0.00 38.65 3.46
5468 6309 9.341899 GCAATCAACATAACTTAAGTTTCGAAT 57.658 29.630 25.07 10.47 39.31 3.34
5495 6336 6.928520 AGGTCTCATTGGAAATGAAAATGTC 58.071 36.000 4.38 0.00 33.84 3.06
5503 6344 4.606457 GACGAAGGTCTCATTGGAAATG 57.394 45.455 0.00 0.00 40.15 2.32
5530 6371 5.105146 ACATGTGCACCCAAAAAGAACTTAA 60.105 36.000 15.69 0.00 0.00 1.85
5537 6378 4.022068 ACTGATACATGTGCACCCAAAAAG 60.022 41.667 15.69 6.63 0.00 2.27
5574 6415 1.938016 GCATGTTTTTGCAGCCCTGAG 60.938 52.381 0.00 0.00 42.31 3.35
5593 6442 4.590850 AGGAAGAAAATGTCCAACAAGC 57.409 40.909 0.00 0.00 36.28 4.01
5642 6491 6.986817 TCCCGCAAATAAGTTTTTCAAAATCA 59.013 30.769 0.00 0.00 0.00 2.57
5643 6492 7.414814 TCCCGCAAATAAGTTTTTCAAAATC 57.585 32.000 0.00 0.00 0.00 2.17
5722 6571 4.274069 CATTTATCACTGAAACGCATCCG 58.726 43.478 0.00 0.00 41.14 4.18
5787 6638 7.669427 TGATTCCAATTTCATACAGCTTGTTT 58.331 30.769 0.00 0.00 0.00 2.83
5790 6641 5.747197 GCTGATTCCAATTTCATACAGCTTG 59.253 40.000 0.00 0.00 43.69 4.01
5791 6642 5.449588 CGCTGATTCCAATTTCATACAGCTT 60.450 40.000 0.00 0.00 44.48 3.74
5912 6765 5.506708 TCTTACTACAGGTGCATGACTAGA 58.493 41.667 0.00 0.00 0.00 2.43
6014 6936 9.950680 AATATTTGATAAGCACAAAAGGTATCG 57.049 29.630 0.00 0.00 39.95 2.92
6058 7143 1.901591 ACCACAAGGAGCAACATCTG 58.098 50.000 0.00 0.00 38.69 2.90
6095 7180 8.477256 CCCTACAAAATGGACATGACAATTAAT 58.523 33.333 0.00 0.00 0.00 1.40
6102 7187 3.023832 CCCCCTACAAAATGGACATGAC 58.976 50.000 0.00 0.00 0.00 3.06
6287 7372 4.142902 CCACGTTGTAATAACTTGAGCCTG 60.143 45.833 0.00 0.00 0.00 4.85
6310 7395 4.156455 TGGGATTCTTTACATGCCTCTC 57.844 45.455 0.00 0.00 33.34 3.20
6348 7433 2.437359 CGGGCTTGCCTTCCTCTG 60.437 66.667 11.71 0.00 0.00 3.35
6361 7446 3.994392 CACATGTAACATATACTCCGGGC 59.006 47.826 0.00 0.00 0.00 6.13
6368 7453 6.511767 GCTGCCAAGACACATGTAACATATAC 60.512 42.308 0.00 0.00 0.00 1.47
6452 7537 2.642139 TTAGAACCGTCCGTGATGAC 57.358 50.000 0.00 0.00 0.00 3.06
6475 7561 2.290641 ACCACCCGCTCACATCAAATAA 60.291 45.455 0.00 0.00 0.00 1.40
6535 7621 2.376032 GAAGAAGTCACGTTTGCAAGC 58.624 47.619 2.75 2.75 0.00 4.01
6538 7624 1.647346 ACGAAGAAGTCACGTTTGCA 58.353 45.000 0.00 0.00 36.91 4.08
6564 7650 0.535797 CAGCTGATGACTCCTGCAGA 59.464 55.000 17.39 0.00 0.00 4.26
6587 7673 9.348476 TGCAATATATATTGTACTGAAGGCAAA 57.652 29.630 28.02 2.38 43.72 3.68
6588 7674 8.916628 TGCAATATATATTGTACTGAAGGCAA 57.083 30.769 28.02 6.87 43.72 4.52
6601 7690 9.624373 GAGGAATGGACAGATGCAATATATATT 57.376 33.333 1.91 1.91 0.00 1.28
6746 7838 4.935205 CCTCAGGACACAATCGTATGAAAA 59.065 41.667 0.00 0.00 0.00 2.29
6769 7861 5.357032 TGTTCAGAGTTTGTTCCCTCTTTTC 59.643 40.000 0.00 0.00 35.90 2.29
6879 7971 1.848388 TGGGATCATGGCAGTGAAGAT 59.152 47.619 0.00 0.00 0.00 2.40
6880 7972 1.065199 GTGGGATCATGGCAGTGAAGA 60.065 52.381 0.00 0.00 0.00 2.87
6965 8060 2.670934 CTGGTGGCCACACTGAGC 60.671 66.667 35.78 18.50 46.85 4.26
7041 8137 6.868864 TCTCAGTAGACACATTTTCTAAGTGC 59.131 38.462 0.00 0.00 36.76 4.40
7166 8267 1.136690 CGAGACAGCAAGCGTACAAA 58.863 50.000 0.00 0.00 0.00 2.83
7347 8453 3.890756 TGCACATCAGACTGAAAACCATT 59.109 39.130 9.70 0.00 0.00 3.16
7370 8478 3.881688 CTGCATTATTGAAGACAGGGAGG 59.118 47.826 0.00 0.00 28.60 4.30
7425 8533 1.473677 TGCCTGCAATGTCAACATAGC 59.526 47.619 0.00 0.00 35.10 2.97
7443 8553 3.069289 TGTGATGAGTTGATGACACTGC 58.931 45.455 0.00 0.00 0.00 4.40
7449 8559 3.069289 GCAGTGTGTGATGAGTTGATGA 58.931 45.455 0.00 0.00 0.00 2.92
7453 8563 1.802960 GGAGCAGTGTGTGATGAGTTG 59.197 52.381 0.00 0.00 0.00 3.16
7610 8727 1.303317 GGAATTGTGACGGGTGCCT 60.303 57.895 0.00 0.00 0.00 4.75
7611 8728 1.303317 AGGAATTGTGACGGGTGCC 60.303 57.895 0.00 0.00 0.00 5.01
7759 8885 0.317269 CCGTTGAATCATGCATCGGC 60.317 55.000 1.95 0.00 40.42 5.54
7760 8886 0.308684 CCCGTTGAATCATGCATCGG 59.691 55.000 8.07 8.07 44.23 4.18
7761 8887 1.262417 CTCCCGTTGAATCATGCATCG 59.738 52.381 0.00 0.00 0.00 3.84
7796 8924 6.763135 CGGACCATTCTGAAATTCTCTTATCA 59.237 38.462 0.00 0.00 0.00 2.15
7799 8927 6.049955 ACGGACCATTCTGAAATTCTCTTA 57.950 37.500 0.00 0.00 31.76 2.10
7817 8945 4.933330 ACAGATCACACATACATACGGAC 58.067 43.478 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.