Multiple sequence alignment - TraesCS3B01G418000

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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 TraesCS3B01G418000 chr3B 100.000 4631 0 0 1 4631 655026672 655031302 0.000000e+00 8552.0
1 TraesCS3B01G418000 chr3D 85.071 3175 194 110 1 3021 496069800 496072848 0.000000e+00 2979.0
2 TraesCS3B01G418000 chr3D 84.693 1483 113 48 3015 4457 496072883 496074291 0.000000e+00 1376.0
3 TraesCS3B01G418000 chr3D 96.078 102 2 1 4532 4631 496096989 496097090 1.030000e-36 165.0
4 TraesCS3B01G418000 chr3A 88.949 2018 121 29 487 2435 635324863 635326847 0.000000e+00 2398.0
5 TraesCS3B01G418000 chr3A 85.865 1521 95 47 3018 4495 635327429 635328872 0.000000e+00 1507.0
6 TraesCS3B01G418000 chr3A 91.165 498 14 9 1 483 635322320 635322802 0.000000e+00 649.0
7 TraesCS3B01G418000 chr3A 83.828 674 64 26 3528 4175 648830575 648829921 2.380000e-167 599.0
8 TraesCS3B01G418000 chr3A 84.698 562 35 20 2479 3021 635326863 635327392 8.890000e-142 514.0
9 TraesCS3B01G418000 chr3A 94.872 78 3 1 4524 4600 635328960 635329037 2.260000e-23 121.0
10 TraesCS3B01G418000 chr3A 100.000 47 0 0 4585 4631 635329055 635329101 2.300000e-13 87.9
11 TraesCS3B01G418000 chr4B 85.373 670 57 26 3528 4175 147476477 147477127 0.000000e+00 656.0
12 TraesCS3B01G418000 chr1B 84.288 681 57 32 3520 4171 635834943 635835602 1.830000e-173 619.0
13 TraesCS3B01G418000 chr1B 89.352 216 20 2 1177 1389 486848846 486848631 7.640000e-68 268.0
14 TraesCS3B01G418000 chr1B 86.755 151 16 4 2478 2628 486847691 486847545 1.030000e-36 165.0
15 TraesCS3B01G418000 chr6B 84.148 675 62 28 3528 4175 606377059 606376403 3.060000e-171 612.0
16 TraesCS3B01G418000 chr7B 84.148 675 60 27 3528 4175 72009480 72008826 1.100000e-170 610.0
17 TraesCS3B01G418000 chr6A 83.673 686 61 32 3520 4175 152859235 152859899 2.380000e-167 599.0
18 TraesCS3B01G418000 chr7A 83.728 676 63 29 3528 4175 645837947 645838603 3.080000e-166 595.0
19 TraesCS3B01G418000 chr1A 83.007 306 38 11 1097 1389 462778467 462778163 9.880000e-67 265.0
20 TraesCS3B01G418000 chr1D 88.426 216 22 2 1177 1389 363621545 363621330 1.650000e-64 257.0
21 TraesCS3B01G418000 chr1D 88.722 133 13 2 2497 2628 363620382 363620251 1.330000e-35 161.0


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 TraesCS3B01G418000 chr3B 655026672 655031302 4630 False 8552.000000 8552 100.000000 1 4631 1 chr3B.!!$F1 4630
1 TraesCS3B01G418000 chr3D 496069800 496074291 4491 False 2177.500000 2979 84.882000 1 4457 2 chr3D.!!$F2 4456
2 TraesCS3B01G418000 chr3A 635322320 635329101 6781 False 879.483333 2398 90.924833 1 4631 6 chr3A.!!$F1 4630
3 TraesCS3B01G418000 chr3A 648829921 648830575 654 True 599.000000 599 83.828000 3528 4175 1 chr3A.!!$R1 647
4 TraesCS3B01G418000 chr4B 147476477 147477127 650 False 656.000000 656 85.373000 3528 4175 1 chr4B.!!$F1 647
5 TraesCS3B01G418000 chr1B 635834943 635835602 659 False 619.000000 619 84.288000 3520 4171 1 chr1B.!!$F1 651
6 TraesCS3B01G418000 chr1B 486847545 486848846 1301 True 216.500000 268 88.053500 1177 2628 2 chr1B.!!$R1 1451
7 TraesCS3B01G418000 chr6B 606376403 606377059 656 True 612.000000 612 84.148000 3528 4175 1 chr6B.!!$R1 647
8 TraesCS3B01G418000 chr7B 72008826 72009480 654 True 610.000000 610 84.148000 3528 4175 1 chr7B.!!$R1 647
9 TraesCS3B01G418000 chr6A 152859235 152859899 664 False 599.000000 599 83.673000 3520 4175 1 chr6A.!!$F1 655
10 TraesCS3B01G418000 chr7A 645837947 645838603 656 False 595.000000 595 83.728000 3528 4175 1 chr7A.!!$F1 647
11 TraesCS3B01G418000 chr1D 363620251 363621545 1294 True 209.000000 257 88.574000 1177 2628 2 chr1D.!!$R1 1451

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
236 252 0.319728 TGTCAGAGGCTTGAGTGAGC 59.680 55.0 0.0 0.0 41.96 4.26 F
1644 3858 0.608640 CAGTCTAGCTTGGTTCGGGT 59.391 55.0 0.0 0.0 0.00 5.28 F
2002 4359 0.181350 AATCCCGCCATCCTGAAGTC 59.819 55.0 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 3880 0.405198 TCTCTTGGGCATGCTTCCAA 59.595 50.0 22.29 22.29 40.36 3.53 R
3469 6131 0.098728 GTCAAGCTGCACACACGTTT 59.901 50.0 1.02 0.00 0.00 3.60 R
3730 6419 1.200519 TGGGACAGATTTACGGGGAG 58.799 55.0 0.00 0.00 0.00 4.30 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.067180 CGTTCGTATTGGTAGGGCTTAGA 59.933 47.826 0.00 0.00 0.00 2.10
109 122 1.373371 GTCCCGACCCAACACGTAC 60.373 63.158 0.00 0.00 0.00 3.67
161 177 0.389817 TCAACACCGCTCTCGAATGG 60.390 55.000 0.00 0.00 38.10 3.16
232 248 0.972883 GGACTGTCAGAGGCTTGAGT 59.027 55.000 6.91 0.00 0.00 3.41
236 252 0.319728 TGTCAGAGGCTTGAGTGAGC 59.680 55.000 0.00 0.00 41.96 4.26
240 256 0.897863 AGAGGCTTGAGTGAGCGAGT 60.898 55.000 0.00 0.00 43.62 4.18
241 257 0.735632 GAGGCTTGAGTGAGCGAGTG 60.736 60.000 0.00 0.00 43.62 3.51
242 258 1.181741 AGGCTTGAGTGAGCGAGTGA 61.182 55.000 0.00 0.00 43.62 3.41
243 259 0.735632 GGCTTGAGTGAGCGAGTGAG 60.736 60.000 0.00 0.00 43.62 3.51
333 364 3.822403 CTAGAGCCGCGCTGAGAGC 62.822 68.421 5.56 0.00 39.88 4.09
352 383 3.609853 AGCGAGATGGAGCAATGTTTAA 58.390 40.909 0.00 0.00 35.48 1.52
364 395 6.238593 GGAGCAATGTTTAATCCTAGCTTCAG 60.239 42.308 0.00 0.00 0.00 3.02
365 396 6.183347 AGCAATGTTTAATCCTAGCTTCAGT 58.817 36.000 0.00 0.00 0.00 3.41
366 397 7.338710 AGCAATGTTTAATCCTAGCTTCAGTA 58.661 34.615 0.00 0.00 0.00 2.74
386 417 2.742372 GCCCGAGATTGCACACGT 60.742 61.111 0.00 0.00 0.00 4.49
387 418 1.447140 GCCCGAGATTGCACACGTA 60.447 57.895 0.00 0.00 0.00 3.57
388 419 1.693083 GCCCGAGATTGCACACGTAC 61.693 60.000 0.00 0.00 0.00 3.67
389 420 1.410737 CCCGAGATTGCACACGTACG 61.411 60.000 15.01 15.01 0.00 3.67
399 430 1.959226 ACACGTACGCAAAGGGCTG 60.959 57.895 16.72 5.92 41.67 4.85
411 442 2.923035 GGGCTGGCCGGATAGCTA 60.923 66.667 23.90 0.00 39.80 3.32
415 446 2.962882 CTGGCCGGATAGCTAGCTA 58.037 57.895 26.09 26.09 34.39 3.32
416 447 0.814457 CTGGCCGGATAGCTAGCTAG 59.186 60.000 27.42 16.84 34.39 3.42
417 448 0.612174 TGGCCGGATAGCTAGCTAGG 60.612 60.000 27.42 23.13 31.45 3.02
418 449 0.612453 GGCCGGATAGCTAGCTAGGT 60.612 60.000 27.42 27.23 37.80 3.08
462 496 4.965814 ACAAGATCCACTGGTAGCATATG 58.034 43.478 0.00 0.00 29.80 1.78
479 520 6.961042 AGCATATGGAAACCATTTGGAATTT 58.039 32.000 17.75 0.00 42.23 1.82
485 526 6.405538 TGGAAACCATTTGGAATTTATGAGC 58.594 36.000 3.01 0.00 38.94 4.26
486 527 6.013898 TGGAAACCATTTGGAATTTATGAGCA 60.014 34.615 3.01 0.00 38.94 4.26
505 2607 4.965814 AGCACATGATAAGTATGGGAGTG 58.034 43.478 0.00 0.00 30.44 3.51
572 2684 2.989253 CCCGGTTTGGAGCCAACC 60.989 66.667 0.00 6.19 42.00 3.77
573 2685 2.203422 CCGGTTTGGAGCCAACCA 60.203 61.111 15.98 0.00 42.00 3.67
574 2686 1.606313 CCGGTTTGGAGCCAACCAT 60.606 57.895 15.98 0.00 42.00 3.55
575 2687 1.586028 CGGTTTGGAGCCAACCATG 59.414 57.895 15.98 0.00 39.82 3.66
658 2774 5.163141 ACCATGAAAATCATCCGTACCCATA 60.163 40.000 0.00 0.00 34.28 2.74
664 2780 4.537135 ATCATCCGTACCCATATGTGAC 57.463 45.455 1.24 0.00 0.00 3.67
716 2833 1.009829 GTGCAGCGATTCCCTTGTAG 58.990 55.000 0.00 0.00 0.00 2.74
725 2844 7.556844 CAGCGATTCCCTTGTAGGTATTATAT 58.443 38.462 0.00 0.00 31.93 0.86
731 2850 8.918202 TTCCCTTGTAGGTATTATATTTGCAG 57.082 34.615 0.00 0.00 31.93 4.41
754 2873 4.574013 GTGCATTATGCTCTCTGCTTAAGT 59.426 41.667 18.44 0.00 45.31 2.24
776 2911 2.808543 ACTTAAGCACGCTTTCTTCAGG 59.191 45.455 9.96 0.00 37.47 3.86
799 2941 2.100605 TTGTGTGTGTGTGTGCAGTA 57.899 45.000 0.00 0.00 0.00 2.74
826 2968 2.577112 CGCGCTCGTGACCACTAG 60.577 66.667 5.56 0.00 0.00 2.57
828 2970 2.566529 CGCTCGTGACCACTAGCA 59.433 61.111 21.23 0.00 46.62 3.49
861 3003 2.547642 CCGCTCCATGATTCCTCTCTTC 60.548 54.545 0.00 0.00 0.00 2.87
1308 3507 2.672908 CTGCTCCACATCCTGCCA 59.327 61.111 0.00 0.00 0.00 4.92
1438 3641 9.701098 TTAAGTTACGAGCATTCTTCTTTTCTA 57.299 29.630 0.00 0.00 0.00 2.10
1464 3667 4.282195 ACGAAAATACTTGCATTTTCCCCA 59.718 37.500 14.53 0.00 45.72 4.96
1497 3705 4.100084 CCCGGCCTCTGCATCACA 62.100 66.667 0.00 0.00 40.13 3.58
1566 3780 4.442733 CAGCACTATTTCGAGCTAGCTAAC 59.557 45.833 19.38 5.15 35.19 2.34
1578 3792 3.259374 AGCTAGCTAACTGTGCTTCTTCA 59.741 43.478 17.69 0.00 41.46 3.02
1644 3858 0.608640 CAGTCTAGCTTGGTTCGGGT 59.391 55.000 0.00 0.00 0.00 5.28
1660 3874 3.681473 GTTCCCCCTTTGGAAGCG 58.319 61.111 0.00 0.00 44.86 4.68
1692 3906 3.044156 AGCATGCCCAAGAGATTCTAGA 58.956 45.455 15.66 0.00 0.00 2.43
1873 4168 8.692110 TGCAAGCATGTTTCATTATCTAAAAG 57.308 30.769 0.00 0.00 0.00 2.27
1908 4203 7.594714 GCTTACTAGCAGCTCATACATACTTA 58.405 38.462 0.00 0.00 46.95 2.24
1913 4208 3.866449 GCAGCTCATACATACTTAGGCCC 60.866 52.174 0.00 0.00 0.00 5.80
1916 4211 3.578716 GCTCATACATACTTAGGCCCAGA 59.421 47.826 0.00 0.00 0.00 3.86
1917 4212 4.223923 GCTCATACATACTTAGGCCCAGAT 59.776 45.833 0.00 0.00 0.00 2.90
1948 4305 2.398554 AAGCATAGTGTTGCCGCCG 61.399 57.895 0.00 0.00 43.83 6.46
2002 4359 0.181350 AATCCCGCCATCCTGAAGTC 59.819 55.000 0.00 0.00 0.00 3.01
2047 4404 6.156519 CCTTCAGTACTTGGTTAAAAATGGC 58.843 40.000 0.00 0.00 0.00 4.40
2146 4579 2.275380 GCCCACTTTTCATGGCCGT 61.275 57.895 0.00 0.00 37.94 5.68
2293 4732 2.223876 ACATGGGCATTACTACGTACGG 60.224 50.000 21.06 5.00 0.00 4.02
2342 4781 3.815856 TTGCTTTGGTTGCTTGAATCA 57.184 38.095 0.00 0.00 0.00 2.57
2397 4836 2.713863 AGTACTCTACTCCCCTGTCG 57.286 55.000 0.00 0.00 32.47 4.35
2422 4861 1.003972 ACGTTGCATGAACTGTTCGTG 60.004 47.619 29.49 29.49 46.86 4.35
2430 4869 1.754803 TGAACTGTTCGTGTGTCCTCT 59.245 47.619 15.18 0.00 0.00 3.69
2436 4875 1.261619 GTTCGTGTGTCCTCTTGCTTG 59.738 52.381 0.00 0.00 0.00 4.01
2438 4877 1.159713 CGTGTGTCCTCTTGCTTGCA 61.160 55.000 0.00 0.00 0.00 4.08
2440 4879 1.610522 GTGTGTCCTCTTGCTTGCATT 59.389 47.619 0.00 0.00 0.00 3.56
2442 4881 2.034939 TGTGTCCTCTTGCTTGCATTTG 59.965 45.455 0.00 0.00 0.00 2.32
2443 4882 2.035066 GTGTCCTCTTGCTTGCATTTGT 59.965 45.455 0.00 0.00 0.00 2.83
2450 4889 1.592064 TGCTTGCATTTGTCTGTCGA 58.408 45.000 0.00 0.00 0.00 4.20
2455 4894 3.624326 TGCATTTGTCTGTCGAAAAGG 57.376 42.857 0.00 0.00 0.00 3.11
2456 4895 3.210227 TGCATTTGTCTGTCGAAAAGGA 58.790 40.909 0.00 0.00 0.00 3.36
2460 4899 5.505654 GCATTTGTCTGTCGAAAAGGAAAGA 60.506 40.000 0.00 0.00 0.00 2.52
2491 4957 1.506309 GCTCATGGTGTTGCGTGTGA 61.506 55.000 0.00 0.00 0.00 3.58
2493 4959 0.660488 TCATGGTGTTGCGTGTGAAC 59.340 50.000 0.00 0.00 0.00 3.18
2649 5236 5.165911 CTGGTAAGCATACATTCTTGCAG 57.834 43.478 1.01 0.00 41.35 4.41
2652 5239 4.635765 GGTAAGCATACATTCTTGCAGACA 59.364 41.667 1.01 0.00 41.35 3.41
2653 5240 5.297776 GGTAAGCATACATTCTTGCAGACAT 59.702 40.000 1.01 0.00 41.35 3.06
2654 5241 4.895224 AGCATACATTCTTGCAGACATG 57.105 40.909 0.00 0.00 41.35 3.21
2655 5242 7.216867 GTAAGCATACATTCTTGCAGACATGC 61.217 42.308 0.00 0.00 41.35 4.06
2656 5243 9.479338 GTAAGCATACATTCTTGCAGACATGCA 62.479 40.741 13.93 0.00 44.89 3.96
2738 5325 9.862149 TGTGTCTATCTACCTTATCACTATTGA 57.138 33.333 0.00 0.00 35.73 2.57
2763 5358 3.740832 GCTTGTGTTAAAAATGTGAGGCC 59.259 43.478 0.00 0.00 0.00 5.19
2764 5359 4.739137 GCTTGTGTTAAAAATGTGAGGCCA 60.739 41.667 5.01 0.00 0.00 5.36
2853 5449 2.896854 AGTGCAGTGTGTGGTGCG 60.897 61.111 0.00 0.00 42.96 5.34
2866 5462 2.159085 TGTGGTGCGGTTTTTAAAAGGG 60.159 45.455 0.14 0.00 0.00 3.95
2877 5473 5.834742 GGTTTTTAAAAGGGGGTAGTTCAGA 59.165 40.000 0.14 0.00 0.00 3.27
2888 5484 5.453480 GGGGGTAGTTCAGAGTCATTCATAC 60.453 48.000 0.00 0.00 0.00 2.39
3000 5609 3.943671 TCCCTTCAGGAAAAGAACACA 57.056 42.857 0.00 0.00 43.78 3.72
3014 5623 1.600485 GAACACAGTAAACCACCACCG 59.400 52.381 0.00 0.00 0.00 4.94
3072 5724 0.976073 TTGATGAGAGGGTCCGGTCC 60.976 60.000 9.52 9.52 0.00 4.46
3078 5730 2.283966 AGGGTCCGGTCCAGTCAG 60.284 66.667 19.75 0.00 0.00 3.51
3101 5753 2.030562 ACAAACGACGGCTCCTGG 59.969 61.111 0.00 0.00 0.00 4.45
3102 5754 2.742372 CAAACGACGGCTCCTGGG 60.742 66.667 0.00 0.00 0.00 4.45
3103 5755 4.699522 AAACGACGGCTCCTGGGC 62.700 66.667 0.00 0.00 37.12 5.36
3142 5794 1.603455 ACACCCGTTCAATGGCAGG 60.603 57.895 0.00 0.00 0.00 4.85
3174 5833 0.309612 CTTTCCGGAAAACACCACCG 59.690 55.000 28.62 12.03 45.24 4.94
3195 5854 1.139654 GGCTAGTGCAGATCCATGTGA 59.860 52.381 0.00 0.00 41.91 3.58
3196 5855 2.224475 GGCTAGTGCAGATCCATGTGAT 60.224 50.000 0.00 0.00 41.91 3.06
3309 5968 5.743872 CGTTCATTCATGTCGACAAGAGATA 59.256 40.000 24.13 9.25 30.93 1.98
3311 5970 7.043125 CGTTCATTCATGTCGACAAGAGATAAT 60.043 37.037 24.13 10.90 30.93 1.28
3316 5975 8.634475 TTCATGTCGACAAGAGATAATAACAG 57.366 34.615 24.13 0.00 30.93 3.16
3383 6045 7.255451 GGTGGTTAACTTTTCATCTTGTCATCA 60.255 37.037 5.42 0.00 0.00 3.07
3384 6046 8.299570 GTGGTTAACTTTTCATCTTGTCATCAT 58.700 33.333 5.42 0.00 0.00 2.45
3385 6047 8.859090 TGGTTAACTTTTCATCTTGTCATCATT 58.141 29.630 5.42 0.00 0.00 2.57
3386 6048 9.346725 GGTTAACTTTTCATCTTGTCATCATTC 57.653 33.333 5.42 0.00 0.00 2.67
3387 6049 9.055248 GTTAACTTTTCATCTTGTCATCATTCG 57.945 33.333 0.00 0.00 0.00 3.34
3388 6050 6.808008 ACTTTTCATCTTGTCATCATTCGT 57.192 33.333 0.00 0.00 0.00 3.85
3389 6051 6.835914 ACTTTTCATCTTGTCATCATTCGTC 58.164 36.000 0.00 0.00 0.00 4.20
3397 6059 5.357032 TCTTGTCATCATTCGTCACTAGCTA 59.643 40.000 0.00 0.00 0.00 3.32
3406 6068 7.270779 TCATTCGTCACTAGCTACTTCTACTA 58.729 38.462 0.00 0.00 0.00 1.82
3407 6069 7.438757 TCATTCGTCACTAGCTACTTCTACTAG 59.561 40.741 0.00 0.00 39.44 2.57
3408 6070 6.462552 TCGTCACTAGCTACTTCTACTAGA 57.537 41.667 0.00 0.00 37.44 2.43
3409 6071 6.272318 TCGTCACTAGCTACTTCTACTAGAC 58.728 44.000 0.00 0.00 37.44 2.59
3410 6072 5.463061 CGTCACTAGCTACTTCTACTAGACC 59.537 48.000 0.00 0.00 37.44 3.85
3411 6073 6.585416 GTCACTAGCTACTTCTACTAGACCT 58.415 44.000 0.00 0.00 37.44 3.85
3412 6074 7.049754 GTCACTAGCTACTTCTACTAGACCTT 58.950 42.308 0.00 0.00 37.44 3.50
3413 6075 7.011669 GTCACTAGCTACTTCTACTAGACCTTG 59.988 44.444 0.00 0.00 37.44 3.61
3414 6076 6.824704 CACTAGCTACTTCTACTAGACCTTGT 59.175 42.308 0.00 0.00 37.44 3.16
3415 6077 7.011669 CACTAGCTACTTCTACTAGACCTTGTC 59.988 44.444 0.00 0.00 37.44 3.18
3416 6078 6.069705 AGCTACTTCTACTAGACCTTGTCT 57.930 41.667 0.00 1.94 45.54 3.41
3417 6079 5.883673 AGCTACTTCTACTAGACCTTGTCTG 59.116 44.000 7.00 0.63 43.30 3.51
3418 6080 5.881443 GCTACTTCTACTAGACCTTGTCTGA 59.119 44.000 7.00 0.00 43.30 3.27
3419 6081 6.374894 GCTACTTCTACTAGACCTTGTCTGAA 59.625 42.308 7.00 1.71 43.30 3.02
3420 6082 7.067737 GCTACTTCTACTAGACCTTGTCTGAAT 59.932 40.741 7.00 0.00 43.30 2.57
3421 6083 7.399245 ACTTCTACTAGACCTTGTCTGAATC 57.601 40.000 7.00 0.00 43.30 2.52
3422 6084 6.378848 ACTTCTACTAGACCTTGTCTGAATCC 59.621 42.308 7.00 0.00 43.30 3.01
3423 6085 5.202004 TCTACTAGACCTTGTCTGAATCCC 58.798 45.833 7.00 0.00 43.30 3.85
3424 6086 3.108376 ACTAGACCTTGTCTGAATCCCC 58.892 50.000 7.00 0.00 43.30 4.81
3425 6087 2.350863 AGACCTTGTCTGAATCCCCT 57.649 50.000 0.00 0.00 41.76 4.79
3426 6088 3.491766 AGACCTTGTCTGAATCCCCTA 57.508 47.619 0.00 0.00 41.76 3.53
3427 6089 3.803340 AGACCTTGTCTGAATCCCCTAA 58.197 45.455 0.00 0.00 41.76 2.69
3428 6090 4.175962 AGACCTTGTCTGAATCCCCTAAA 58.824 43.478 0.00 0.00 41.76 1.85
3429 6091 4.601857 AGACCTTGTCTGAATCCCCTAAAA 59.398 41.667 0.00 0.00 41.76 1.52
3430 6092 5.074515 AGACCTTGTCTGAATCCCCTAAAAA 59.925 40.000 0.00 0.00 41.76 1.94
3469 6131 5.634118 ACCTTGTCTGAATGAAGAAATGGA 58.366 37.500 6.90 0.00 34.00 3.41
3487 6168 0.376852 GAAACGTGTGTGCAGCTTGA 59.623 50.000 0.00 0.00 0.00 3.02
3606 6287 4.947147 GTCAGCACCCGGTGGCAA 62.947 66.667 19.41 2.11 44.69 4.52
3635 6316 4.803426 GCTCCTCGCCTGACCGTG 62.803 72.222 0.00 0.00 0.00 4.94
3636 6317 3.062466 CTCCTCGCCTGACCGTGA 61.062 66.667 0.00 0.00 0.00 4.35
3638 6319 4.436998 CCTCGCCTGACCGTGACC 62.437 72.222 0.00 0.00 0.00 4.02
3643 6324 2.660064 GCCTGACCGTGACCTCCAT 61.660 63.158 0.00 0.00 0.00 3.41
3652 6337 2.592861 GACCTCCATCCGCCATGC 60.593 66.667 0.00 0.00 0.00 4.06
3675 6362 4.025979 CCCACGACGATGTTTTTATAGAGC 60.026 45.833 0.00 0.00 0.00 4.09
3720 6409 0.965866 TCGTTCCTGCGTGATCCTCT 60.966 55.000 0.00 0.00 0.00 3.69
3721 6410 0.526524 CGTTCCTGCGTGATCCTCTC 60.527 60.000 0.00 0.00 0.00 3.20
3724 6413 2.362397 GTTCCTGCGTGATCCTCTCATA 59.638 50.000 0.00 0.00 35.97 2.15
3727 6416 3.643320 TCCTGCGTGATCCTCTCATATTT 59.357 43.478 0.00 0.00 35.97 1.40
3728 6417 4.101585 TCCTGCGTGATCCTCTCATATTTT 59.898 41.667 0.00 0.00 35.97 1.82
3729 6418 5.304357 TCCTGCGTGATCCTCTCATATTTTA 59.696 40.000 0.00 0.00 35.97 1.52
3730 6419 5.406780 CCTGCGTGATCCTCTCATATTTTAC 59.593 44.000 0.00 0.00 35.97 2.01
3731 6420 6.161855 TGCGTGATCCTCTCATATTTTACT 57.838 37.500 0.00 0.00 35.97 2.24
3732 6421 6.216569 TGCGTGATCCTCTCATATTTTACTC 58.783 40.000 0.00 0.00 35.97 2.59
3739 6428 6.138263 TCCTCTCATATTTTACTCCCCGTAA 58.862 40.000 0.00 0.00 36.34 3.18
3773 6462 1.868498 TGTGCTTTTTAACCCGTCGAG 59.132 47.619 0.00 0.00 0.00 4.04
3774 6463 1.869132 GTGCTTTTTAACCCGTCGAGT 59.131 47.619 0.00 0.00 0.00 4.18
3777 6467 4.864247 GTGCTTTTTAACCCGTCGAGTATA 59.136 41.667 0.00 0.00 0.00 1.47
3779 6469 5.931146 TGCTTTTTAACCCGTCGAGTATAAA 59.069 36.000 0.00 0.00 0.00 1.40
3892 6600 7.172532 TCGTGCTGTAAAATGTAAAGTCTGAAT 59.827 33.333 0.00 0.00 0.00 2.57
3953 6664 7.642586 GTCTTTTCAGTGTGTGTAATTTGTACC 59.357 37.037 0.00 0.00 0.00 3.34
3994 6716 4.464244 TCTGCAAGACTGTAATCTGTAGCT 59.536 41.667 0.00 0.00 38.67 3.32
4036 6760 3.693578 TGTGTTGCACAAAAGACTGATGA 59.306 39.130 0.00 0.00 41.69 2.92
4072 6796 5.277731 GCTCCTTGCTTGCTCAAGTATATTC 60.278 44.000 10.86 0.00 41.29 1.75
4091 6815 7.865706 ATATTCGAGGTTTTCTTTACTGCAT 57.134 32.000 0.00 0.00 0.00 3.96
4092 6816 5.356882 TTCGAGGTTTTCTTTACTGCATG 57.643 39.130 0.00 0.00 0.00 4.06
4114 6846 0.113972 TTGCACCCATGTCCCAATGA 59.886 50.000 0.00 0.00 0.00 2.57
4121 6853 1.894466 CCATGTCCCAATGACTTGCAA 59.106 47.619 0.00 0.00 44.01 4.08
4124 6856 0.603065 GTCCCAATGACTTGCAACCC 59.397 55.000 0.00 0.00 41.03 4.11
4127 6859 0.039256 CCAATGACTTGCAACCCACG 60.039 55.000 0.00 0.00 0.00 4.94
4142 6875 0.530650 CCACGAAGTCACTGCAGTGT 60.531 55.000 38.41 24.67 41.61 3.55
4154 6887 3.814842 CACTGCAGTGTCAGGTGAAAATA 59.185 43.478 34.04 0.00 40.96 1.40
4165 6898 8.669243 GTGTCAGGTGAAAATAGGAAATCTAAG 58.331 37.037 0.00 0.00 0.00 2.18
4199 6932 0.096976 CATCGCGGTGACATCCAAAC 59.903 55.000 15.97 0.00 0.00 2.93
4203 6936 0.951558 GCGGTGACATCCAAACAACT 59.048 50.000 0.00 0.00 0.00 3.16
4204 6937 1.334960 GCGGTGACATCCAAACAACTG 60.335 52.381 0.00 0.00 0.00 3.16
4205 6938 2.217750 CGGTGACATCCAAACAACTGA 58.782 47.619 0.00 0.00 0.00 3.41
4206 6939 2.032030 CGGTGACATCCAAACAACTGAC 60.032 50.000 0.00 0.00 0.00 3.51
4207 6940 2.293399 GGTGACATCCAAACAACTGACC 59.707 50.000 0.00 0.00 0.00 4.02
4208 6941 2.293399 GTGACATCCAAACAACTGACCC 59.707 50.000 0.00 0.00 0.00 4.46
4228 6967 2.281553 GCCGGGGCCTGCTATAAC 60.282 66.667 6.91 0.00 34.56 1.89
4238 6977 2.548920 GCCTGCTATAACTCGCTCCAAT 60.549 50.000 0.00 0.00 0.00 3.16
4243 6982 6.428159 CCTGCTATAACTCGCTCCAATTTTAT 59.572 38.462 0.00 0.00 0.00 1.40
4244 6983 7.041098 CCTGCTATAACTCGCTCCAATTTTATT 60.041 37.037 0.00 0.00 0.00 1.40
4245 6984 8.220755 TGCTATAACTCGCTCCAATTTTATTT 57.779 30.769 0.00 0.00 0.00 1.40
4246 6985 9.332502 TGCTATAACTCGCTCCAATTTTATTTA 57.667 29.630 0.00 0.00 0.00 1.40
4247 6986 9.813080 GCTATAACTCGCTCCAATTTTATTTAG 57.187 33.333 0.00 0.00 0.00 1.85
4249 6988 8.974060 ATAACTCGCTCCAATTTTATTTAGGA 57.026 30.769 0.00 0.00 0.00 2.94
4256 6995 7.269477 CTCCAATTTTATTTAGGAGCAGGAG 57.731 40.000 0.00 0.00 39.39 3.69
4257 6996 5.594317 TCCAATTTTATTTAGGAGCAGGAGC 59.406 40.000 0.00 0.00 42.56 4.70
4258 6997 5.221322 CCAATTTTATTTAGGAGCAGGAGCC 60.221 44.000 0.00 0.00 43.56 4.70
4259 6998 4.584638 TTTTATTTAGGAGCAGGAGCCA 57.415 40.909 0.00 0.00 43.56 4.75
4262 7001 0.252696 TTTAGGAGCAGGAGCCAGGA 60.253 55.000 0.00 0.00 43.56 3.86
4263 7002 0.689080 TTAGGAGCAGGAGCCAGGAG 60.689 60.000 0.00 0.00 43.56 3.69
4264 7003 2.595954 TAGGAGCAGGAGCCAGGAGG 62.596 65.000 0.00 0.00 43.56 4.30
4278 7017 2.286872 CAGGAGGTGCATCATTGTCTC 58.713 52.381 0.00 0.00 0.00 3.36
4330 7069 1.673665 GGCTGTTGTCTGCAGGGAG 60.674 63.158 15.13 4.11 39.69 4.30
4349 7088 3.244911 GGAGTCCTTCACTGAAATCCCAA 60.245 47.826 0.41 0.00 34.41 4.12
4356 7095 1.266718 CACTGAAATCCCAACACACCG 59.733 52.381 0.00 0.00 0.00 4.94
4511 7325 1.135527 TCGGTAAACATACGGCTGAGG 59.864 52.381 0.00 0.00 0.00 3.86
4515 7329 4.117685 GGTAAACATACGGCTGAGGTAAG 58.882 47.826 0.00 0.00 0.00 2.34
4516 7330 4.142093 GGTAAACATACGGCTGAGGTAAGA 60.142 45.833 0.00 0.00 0.00 2.10
4518 7332 4.755266 AACATACGGCTGAGGTAAGATT 57.245 40.909 0.00 0.00 0.00 2.40
4519 7333 4.323553 ACATACGGCTGAGGTAAGATTC 57.676 45.455 0.00 0.00 0.00 2.52
4520 7334 3.704566 ACATACGGCTGAGGTAAGATTCA 59.295 43.478 0.00 0.00 0.00 2.57
4521 7335 2.674796 ACGGCTGAGGTAAGATTCAC 57.325 50.000 0.00 0.00 0.00 3.18
4522 7336 1.135083 ACGGCTGAGGTAAGATTCACG 60.135 52.381 0.00 0.00 0.00 4.35
4523 7337 1.135083 CGGCTGAGGTAAGATTCACGT 60.135 52.381 0.00 0.00 0.00 4.49
4524 7338 2.098607 CGGCTGAGGTAAGATTCACGTA 59.901 50.000 0.00 0.00 0.00 3.57
4525 7339 3.428452 CGGCTGAGGTAAGATTCACGTAA 60.428 47.826 0.00 0.00 0.00 3.18
4526 7340 3.864003 GGCTGAGGTAAGATTCACGTAAC 59.136 47.826 0.00 0.00 0.00 2.50
4527 7341 4.381718 GGCTGAGGTAAGATTCACGTAACT 60.382 45.833 0.00 0.00 33.52 2.24
4528 7342 5.169295 GCTGAGGTAAGATTCACGTAACTT 58.831 41.667 0.00 0.00 31.19 2.66
4529 7343 5.638234 GCTGAGGTAAGATTCACGTAACTTT 59.362 40.000 0.00 0.00 31.19 2.66
4530 7344 6.810182 GCTGAGGTAAGATTCACGTAACTTTA 59.190 38.462 0.00 0.00 31.19 1.85
4586 7400 2.333225 CGGCGACAGCTAGCTAGG 59.667 66.667 18.86 8.88 44.37 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.322277 TCGTCCGCTTCTACAGTCCT 60.322 55.000 0.00 0.00 0.00 3.85
109 122 1.135916 GCGATGGAGCTAGCGTAGTAG 60.136 57.143 9.55 2.55 0.00 2.57
232 248 2.049156 CAACGCCTCACTCGCTCA 60.049 61.111 0.00 0.00 0.00 4.26
236 252 2.372690 CGAACCAACGCCTCACTCG 61.373 63.158 0.00 0.00 0.00 4.18
240 256 0.745128 AACAACGAACCAACGCCTCA 60.745 50.000 0.00 0.00 36.70 3.86
241 257 1.193874 CTAACAACGAACCAACGCCTC 59.806 52.381 0.00 0.00 36.70 4.70
242 258 1.223187 CTAACAACGAACCAACGCCT 58.777 50.000 0.00 0.00 36.70 5.52
243 259 0.385098 GCTAACAACGAACCAACGCC 60.385 55.000 0.00 0.00 36.70 5.68
333 364 4.818546 AGGATTAAACATTGCTCCATCTCG 59.181 41.667 0.00 0.00 0.00 4.04
339 370 5.590259 TGAAGCTAGGATTAAACATTGCTCC 59.410 40.000 6.77 0.00 32.61 4.70
352 383 2.043227 GGGCAGTACTGAAGCTAGGAT 58.957 52.381 27.08 0.00 0.00 3.24
364 395 0.391130 TGTGCAATCTCGGGCAGTAC 60.391 55.000 0.00 0.00 41.35 2.73
365 396 0.391130 GTGTGCAATCTCGGGCAGTA 60.391 55.000 0.00 0.00 41.35 2.74
366 397 1.672356 GTGTGCAATCTCGGGCAGT 60.672 57.895 0.00 0.00 41.35 4.40
389 420 3.714487 TATCCGGCCAGCCCTTTGC 62.714 63.158 2.24 0.00 41.71 3.68
399 430 0.612453 ACCTAGCTAGCTATCCGGCC 60.612 60.000 24.36 0.00 0.00 6.13
411 442 0.903454 ACGTGCTAACCCACCTAGCT 60.903 55.000 0.00 0.00 41.96 3.32
413 444 0.892755 TCACGTGCTAACCCACCTAG 59.107 55.000 11.67 0.00 32.10 3.02
415 446 0.690762 ATTCACGTGCTAACCCACCT 59.309 50.000 11.67 0.00 32.10 4.00
416 447 2.389962 TATTCACGTGCTAACCCACC 57.610 50.000 11.67 0.00 32.10 4.61
417 448 3.592059 TCTTATTCACGTGCTAACCCAC 58.408 45.455 11.67 0.00 0.00 4.61
418 449 3.965379 TCTTATTCACGTGCTAACCCA 57.035 42.857 11.67 0.00 0.00 4.51
462 496 6.313658 GTGCTCATAAATTCCAAATGGTTTCC 59.686 38.462 0.00 0.00 36.34 3.13
479 520 6.498303 ACTCCCATACTTATCATGTGCTCATA 59.502 38.462 0.04 0.00 32.47 2.15
483 524 4.202398 CCACTCCCATACTTATCATGTGCT 60.202 45.833 0.00 0.00 0.00 4.40
485 526 4.067896 GCCACTCCCATACTTATCATGTG 58.932 47.826 0.00 0.00 0.00 3.21
486 527 3.244215 CGCCACTCCCATACTTATCATGT 60.244 47.826 0.00 0.00 0.00 3.21
524 2627 4.318546 GGTCAATACGGCATCAATCGTAAC 60.319 45.833 0.00 0.00 43.58 2.50
568 2680 0.795698 TTCGTCGACATGCATGGTTG 59.204 50.000 29.41 18.20 0.00 3.77
572 2684 1.078709 AGGTTTCGTCGACATGCATG 58.921 50.000 25.09 25.09 0.00 4.06
573 2685 1.078709 CAGGTTTCGTCGACATGCAT 58.921 50.000 17.16 0.00 0.00 3.96
574 2686 0.032815 TCAGGTTTCGTCGACATGCA 59.967 50.000 17.16 0.00 0.00 3.96
575 2687 0.438830 GTCAGGTTTCGTCGACATGC 59.561 55.000 17.16 2.18 0.00 4.06
620 2736 2.136878 ATGGTCTCAGCTAGCCGGG 61.137 63.158 12.13 0.00 0.00 5.73
621 2737 1.068753 CATGGTCTCAGCTAGCCGG 59.931 63.158 12.13 4.14 0.00 6.13
622 2738 0.461548 TTCATGGTCTCAGCTAGCCG 59.538 55.000 12.13 0.00 0.00 5.52
623 2739 2.698855 TTTCATGGTCTCAGCTAGCC 57.301 50.000 12.13 0.00 0.00 3.93
624 2740 4.194640 TGATTTTCATGGTCTCAGCTAGC 58.805 43.478 6.62 6.62 0.00 3.42
627 2743 4.205587 GGATGATTTTCATGGTCTCAGCT 58.794 43.478 0.00 0.00 37.20 4.24
658 2774 3.794270 GCGTATGCACCGTCACAT 58.206 55.556 0.89 0.00 42.15 3.21
716 2833 8.398491 GCATAATGCACTGCAAATATAATACC 57.602 34.615 8.03 0.00 43.62 2.73
754 2873 3.994392 CCTGAAGAAAGCGTGCTTAAGTA 59.006 43.478 7.64 0.00 34.84 2.24
763 2898 3.192633 ACACAAAAACCTGAAGAAAGCGT 59.807 39.130 0.00 0.00 0.00 5.07
765 2900 4.327087 CACACACAAAAACCTGAAGAAAGC 59.673 41.667 0.00 0.00 0.00 3.51
766 2901 5.345741 CACACACACAAAAACCTGAAGAAAG 59.654 40.000 0.00 0.00 0.00 2.62
776 2911 2.398498 TGCACACACACACACAAAAAC 58.602 42.857 0.00 0.00 0.00 2.43
824 2966 2.133195 CGGGTGGATTAGCCTGCTA 58.867 57.895 0.00 0.00 44.97 3.49
828 2970 2.444256 GGAGCGGGTGGATTAGCCT 61.444 63.158 0.00 0.00 44.97 4.58
861 3003 1.087501 GAAAGGACAAGGCCGCTTAG 58.912 55.000 0.00 0.00 0.00 2.18
897 3039 1.287815 CACGGCCGGAGCGATATAA 59.712 57.895 31.76 0.00 41.24 0.98
1107 3303 1.376037 CTTCTTGGACCACCGCCTC 60.376 63.158 0.00 0.00 39.42 4.70
1476 3679 1.053835 TGATGCAGAGGCCGGGATAA 61.054 55.000 2.18 0.00 40.13 1.75
1497 3705 1.965643 TGTACTACTTCCGTTGGCTGT 59.034 47.619 0.00 0.00 0.00 4.40
1566 3780 5.045215 TGAAGCAAAAATGAAGAAGCACAG 58.955 37.500 0.00 0.00 0.00 3.66
1578 3792 5.945466 AAATGGCGATTTGAAGCAAAAAT 57.055 30.435 5.83 0.00 36.90 1.82
1644 3858 1.228429 CACGCTTCCAAAGGGGGAA 60.228 57.895 8.38 0.00 46.90 3.97
1666 3880 0.405198 TCTCTTGGGCATGCTTCCAA 59.595 50.000 22.29 22.29 40.36 3.53
1672 3886 3.482156 TCTAGAATCTCTTGGGCATGC 57.518 47.619 9.90 9.90 0.00 4.06
1884 4179 8.240682 CCTAAGTATGTATGAGCTGCTAGTAAG 58.759 40.741 0.15 0.00 0.00 2.34
1903 4198 7.208064 ACATTTTCTTATCTGGGCCTAAGTA 57.792 36.000 4.53 0.00 0.00 2.24
1908 4203 4.934356 TGAACATTTTCTTATCTGGGCCT 58.066 39.130 4.53 0.00 32.36 5.19
1913 4208 9.499585 CACTATGCTTGAACATTTTCTTATCTG 57.500 33.333 0.00 0.00 32.36 2.90
1916 4211 9.630098 CAACACTATGCTTGAACATTTTCTTAT 57.370 29.630 0.00 0.00 32.36 1.73
1917 4212 7.594758 GCAACACTATGCTTGAACATTTTCTTA 59.405 33.333 0.00 0.00 43.06 2.10
1948 4305 5.004535 CCGAAACTTTACGCTATTGACTCTC 59.995 44.000 0.00 0.00 0.00 3.20
2002 4359 2.113807 TGTCTCTCCCTCATCATGTGG 58.886 52.381 0.00 0.00 0.00 4.17
2047 4404 1.270518 CCAACCAGATGGATAGGCTCG 60.271 57.143 5.72 0.00 43.54 5.03
2146 4579 2.142761 CCTGCCGAGATCCATCCCA 61.143 63.158 0.00 0.00 0.00 4.37
2342 4781 3.152341 CCACATTGAGGCTCTGACTTTT 58.848 45.455 16.72 0.00 0.00 2.27
2397 4836 0.179225 CAGTTCATGCAACGTACGGC 60.179 55.000 21.06 14.66 40.32 5.68
2422 4861 2.035066 ACAAATGCAAGCAAGAGGACAC 59.965 45.455 0.00 0.00 0.00 3.67
2430 4869 1.946081 TCGACAGACAAATGCAAGCAA 59.054 42.857 0.00 0.00 0.00 3.91
2436 4875 3.896648 TCCTTTTCGACAGACAAATGC 57.103 42.857 0.00 0.00 0.00 3.56
2438 4877 6.693315 TTCTTTCCTTTTCGACAGACAAAT 57.307 33.333 0.00 0.00 0.00 2.32
2440 4879 6.503589 TTTTCTTTCCTTTTCGACAGACAA 57.496 33.333 0.00 0.00 0.00 3.18
2491 4957 0.395312 CACCTCCACCTACCAACGTT 59.605 55.000 0.00 0.00 0.00 3.99
2493 4959 1.189524 TCCACCTCCACCTACCAACG 61.190 60.000 0.00 0.00 0.00 4.10
2646 5233 5.333645 GCTGTATACAGTAATGCATGTCTGC 60.334 44.000 28.95 10.68 45.88 4.26
2648 5235 5.917462 TGCTGTATACAGTAATGCATGTCT 58.083 37.500 28.95 0.00 45.45 3.41
2649 5236 6.791887 ATGCTGTATACAGTAATGCATGTC 57.208 37.500 28.95 12.30 45.45 3.06
2652 5239 7.895975 CAGTATGCTGTATACAGTAATGCAT 57.104 36.000 28.95 26.41 45.45 3.96
2668 5255 6.603997 GGTAGGCAGTAGATATACAGTATGCT 59.396 42.308 3.03 3.58 42.53 3.79
2669 5256 6.603997 AGGTAGGCAGTAGATATACAGTATGC 59.396 42.308 3.03 0.87 42.53 3.14
2673 5260 7.785506 AGAAAAGGTAGGCAGTAGATATACAGT 59.214 37.037 0.00 0.00 0.00 3.55
2674 5261 8.184304 AGAAAAGGTAGGCAGTAGATATACAG 57.816 38.462 0.00 0.00 0.00 2.74
2675 5262 8.548880 AAGAAAAGGTAGGCAGTAGATATACA 57.451 34.615 0.00 0.00 0.00 2.29
2676 5263 9.833917 AAAAGAAAAGGTAGGCAGTAGATATAC 57.166 33.333 0.00 0.00 0.00 1.47
2680 5267 9.232473 CTTAAAAAGAAAAGGTAGGCAGTAGAT 57.768 33.333 0.00 0.00 0.00 1.98
2681 5268 8.434392 TCTTAAAAAGAAAAGGTAGGCAGTAGA 58.566 33.333 0.00 0.00 33.83 2.59
2682 5269 8.617290 TCTTAAAAAGAAAAGGTAGGCAGTAG 57.383 34.615 0.00 0.00 33.83 2.57
2683 5270 8.983702 TTCTTAAAAAGAAAAGGTAGGCAGTA 57.016 30.769 0.00 0.00 44.10 2.74
2684 5271 7.891498 TTCTTAAAAAGAAAAGGTAGGCAGT 57.109 32.000 0.00 0.00 44.10 4.40
2738 5325 5.591099 CCTCACATTTTTAACACAAGCACT 58.409 37.500 0.00 0.00 0.00 4.40
2763 5358 6.516739 TCTATCTACTCACAGTTGACCTTG 57.483 41.667 0.00 0.00 33.15 3.61
2764 5359 7.379750 GTTTCTATCTACTCACAGTTGACCTT 58.620 38.462 0.00 0.00 33.15 3.50
2853 5449 5.834742 TCTGAACTACCCCCTTTTAAAAACC 59.165 40.000 1.66 0.00 0.00 3.27
2866 5462 5.364157 AGGTATGAATGACTCTGAACTACCC 59.636 44.000 0.00 0.00 0.00 3.69
2877 5473 2.634940 CGGGATCCAGGTATGAATGACT 59.365 50.000 15.23 0.00 0.00 3.41
2917 5513 1.215244 CAGATGTAGCAGTGCGGATG 58.785 55.000 10.00 0.61 0.00 3.51
2919 5515 1.470051 TACAGATGTAGCAGTGCGGA 58.530 50.000 10.00 0.00 0.00 5.54
2921 5517 3.190079 ACAATACAGATGTAGCAGTGCG 58.810 45.455 10.00 0.00 33.52 5.34
2957 5559 1.480954 GGCTCAAGGGAACTGATACGA 59.519 52.381 0.00 0.00 42.68 3.43
2958 5560 1.482593 AGGCTCAAGGGAACTGATACG 59.517 52.381 0.00 0.00 42.68 3.06
3000 5609 1.072505 CTGCCGGTGGTGGTTTACT 59.927 57.895 1.90 0.00 0.00 2.24
3014 5623 0.599558 TTGCTTGCACAAGATCTGCC 59.400 50.000 14.44 0.00 40.79 4.85
3061 5713 2.283966 CTGACTGGACCGGACCCT 60.284 66.667 20.56 5.18 0.00 4.34
3072 5724 2.128035 GTCGTTTGTGAGTCCTGACTG 58.872 52.381 4.19 0.00 42.66 3.51
3078 5730 1.282930 GAGCCGTCGTTTGTGAGTCC 61.283 60.000 0.00 0.00 0.00 3.85
3103 5755 4.598894 CCCGATCGAGCCTGCCTG 62.599 72.222 18.66 0.00 0.00 4.85
3142 5794 1.635663 CGGAAAGACACGCATGGACC 61.636 60.000 0.00 0.00 0.00 4.46
3143 5795 1.635663 CCGGAAAGACACGCATGGAC 61.636 60.000 0.00 0.00 0.00 4.02
3174 5833 0.471617 ACATGGATCTGCACTAGCCC 59.528 55.000 0.00 0.00 41.13 5.19
3176 5835 2.609427 TCACATGGATCTGCACTAGC 57.391 50.000 0.00 0.00 42.57 3.42
3195 5854 4.736611 AGCATCTGGGATTTATGGACAT 57.263 40.909 0.00 0.00 0.00 3.06
3196 5855 4.524802 AAGCATCTGGGATTTATGGACA 57.475 40.909 0.00 0.00 0.00 4.02
3309 5968 5.263968 ACTAGCACTACATCGCTGTTATT 57.736 39.130 0.00 0.00 39.30 1.40
3311 5970 5.823209 TTACTAGCACTACATCGCTGTTA 57.177 39.130 0.00 0.00 39.30 2.41
3316 5975 6.436261 TGATACTTTACTAGCACTACATCGC 58.564 40.000 0.00 0.00 0.00 4.58
3383 6045 7.439056 GTCTAGTAGAAGTAGCTAGTGACGAAT 59.561 40.741 0.73 0.00 35.14 3.34
3384 6046 6.756074 GTCTAGTAGAAGTAGCTAGTGACGAA 59.244 42.308 0.73 0.00 35.14 3.85
3385 6047 6.272318 GTCTAGTAGAAGTAGCTAGTGACGA 58.728 44.000 0.73 0.00 35.14 4.20
3386 6048 5.463061 GGTCTAGTAGAAGTAGCTAGTGACG 59.537 48.000 0.73 0.00 35.14 4.35
3387 6049 6.585416 AGGTCTAGTAGAAGTAGCTAGTGAC 58.415 44.000 0.73 3.39 35.14 3.67
3388 6050 6.811634 AGGTCTAGTAGAAGTAGCTAGTGA 57.188 41.667 0.73 0.00 35.14 3.41
3389 6051 6.824704 ACAAGGTCTAGTAGAAGTAGCTAGTG 59.175 42.308 0.73 0.00 35.14 2.74
3397 6059 6.378848 GGATTCAGACAAGGTCTAGTAGAAGT 59.621 42.308 0.17 0.00 41.37 3.01
3406 6068 2.350863 AGGGGATTCAGACAAGGTCT 57.649 50.000 0.00 0.00 44.44 3.85
3407 6069 4.569719 TTTAGGGGATTCAGACAAGGTC 57.430 45.455 0.00 0.00 0.00 3.85
3408 6070 5.333566 TTTTTAGGGGATTCAGACAAGGT 57.666 39.130 0.00 0.00 0.00 3.50
3430 6092 6.318900 CAGACAAGGTCTAGTGGTTTCTTTTT 59.681 38.462 0.00 0.00 41.37 1.94
3431 6093 5.823045 CAGACAAGGTCTAGTGGTTTCTTTT 59.177 40.000 0.00 0.00 41.37 2.27
3432 6094 5.130477 TCAGACAAGGTCTAGTGGTTTCTTT 59.870 40.000 0.00 0.00 41.37 2.52
3433 6095 4.654262 TCAGACAAGGTCTAGTGGTTTCTT 59.346 41.667 0.00 0.00 41.37 2.52
3434 6096 4.223953 TCAGACAAGGTCTAGTGGTTTCT 58.776 43.478 0.00 0.00 41.37 2.52
3435 6097 4.602340 TCAGACAAGGTCTAGTGGTTTC 57.398 45.455 0.00 0.00 41.37 2.78
3436 6098 5.071788 TCATTCAGACAAGGTCTAGTGGTTT 59.928 40.000 0.00 0.00 41.37 3.27
3437 6099 4.593206 TCATTCAGACAAGGTCTAGTGGTT 59.407 41.667 0.00 0.00 41.37 3.67
3438 6100 4.160329 TCATTCAGACAAGGTCTAGTGGT 58.840 43.478 0.00 0.00 41.37 4.16
3439 6101 4.808414 TCATTCAGACAAGGTCTAGTGG 57.192 45.455 0.00 0.00 41.37 4.00
3440 6102 6.030548 TCTTCATTCAGACAAGGTCTAGTG 57.969 41.667 0.00 0.00 41.37 2.74
3469 6131 0.098728 GTCAAGCTGCACACACGTTT 59.901 50.000 1.02 0.00 0.00 3.60
3576 6257 4.208686 CTGACGAGGTAGCCGCCC 62.209 72.222 0.00 0.00 0.00 6.13
3606 6287 1.609320 GCGAGGAGCCAGAAGTTCTTT 60.609 52.381 1.56 0.00 40.81 2.52
3633 6314 1.524621 CATGGCGGATGGAGGTCAC 60.525 63.158 0.00 0.00 0.00 3.67
3635 6316 2.592861 GCATGGCGGATGGAGGTC 60.593 66.667 0.00 0.00 31.99 3.85
3636 6317 4.195334 GGCATGGCGGATGGAGGT 62.195 66.667 2.41 0.00 31.99 3.85
3638 6319 4.193893 TGGGCATGGCGGATGGAG 62.194 66.667 13.76 0.00 31.99 3.86
3652 6337 4.025979 GCTCTATAAAAACATCGTCGTGGG 60.026 45.833 0.00 0.00 0.00 4.61
3675 6362 1.945394 ACAGACAAACTCAGCAGCAAG 59.055 47.619 0.00 0.00 0.00 4.01
3727 6416 2.767960 GGGACAGATTTACGGGGAGTAA 59.232 50.000 0.00 0.00 43.05 2.24
3728 6417 2.292389 TGGGACAGATTTACGGGGAGTA 60.292 50.000 0.00 0.00 0.00 2.59
3729 6418 1.201424 GGGACAGATTTACGGGGAGT 58.799 55.000 0.00 0.00 0.00 3.85
3730 6419 1.200519 TGGGACAGATTTACGGGGAG 58.799 55.000 0.00 0.00 0.00 4.30
3731 6420 3.402833 TGGGACAGATTTACGGGGA 57.597 52.632 0.00 0.00 0.00 4.81
3892 6600 3.375699 GAGGGTCAAATCCTAGGACTCA 58.624 50.000 15.42 0.00 34.46 3.41
3964 6686 9.236006 ACAGATTACAGTCTTGCAGAAAAATAT 57.764 29.630 0.00 0.00 0.00 1.28
3966 6688 7.516198 ACAGATTACAGTCTTGCAGAAAAAT 57.484 32.000 0.00 0.00 0.00 1.82
3969 6691 5.639506 GCTACAGATTACAGTCTTGCAGAAA 59.360 40.000 0.00 0.00 0.00 2.52
3971 6693 4.464244 AGCTACAGATTACAGTCTTGCAGA 59.536 41.667 0.00 0.00 0.00 4.26
3992 6714 2.742053 ACACGATGATGGTACAACAAGC 59.258 45.455 0.00 0.00 46.01 4.01
3994 6716 4.024472 CACAACACGATGATGGTACAACAA 60.024 41.667 0.00 0.00 46.01 2.83
4036 6760 1.610522 GCAAGGAGCACTCAACAACAT 59.389 47.619 0.00 0.00 44.79 2.71
4072 6796 3.502211 ACCATGCAGTAAAGAAAACCTCG 59.498 43.478 0.00 0.00 0.00 4.63
4091 6815 1.532794 GGGACATGGGTGCAAACCA 60.533 57.895 13.22 13.22 43.22 3.67
4092 6816 1.118356 TTGGGACATGGGTGCAAACC 61.118 55.000 0.00 1.78 39.30 3.27
4114 6846 0.107410 TGACTTCGTGGGTTGCAAGT 60.107 50.000 0.00 0.00 0.00 3.16
4121 6853 1.069765 CTGCAGTGACTTCGTGGGT 59.930 57.895 5.25 0.00 0.00 4.51
4142 6875 8.267894 CCTCTTAGATTTCCTATTTTCACCTGA 58.732 37.037 0.00 0.00 0.00 3.86
4154 6887 6.166982 CAAACTCGTTCCTCTTAGATTTCCT 58.833 40.000 0.00 0.00 0.00 3.36
4165 6898 0.721718 CGATGCCAAACTCGTTCCTC 59.278 55.000 0.00 0.00 0.00 3.71
4238 6977 4.526970 CTGGCTCCTGCTCCTAAATAAAA 58.473 43.478 0.00 0.00 39.59 1.52
4243 6982 0.252696 TCCTGGCTCCTGCTCCTAAA 60.253 55.000 0.00 0.00 39.59 1.85
4244 6983 0.689080 CTCCTGGCTCCTGCTCCTAA 60.689 60.000 0.00 0.00 39.59 2.69
4245 6984 1.075674 CTCCTGGCTCCTGCTCCTA 60.076 63.158 0.00 0.00 39.59 2.94
4246 6985 2.365370 CTCCTGGCTCCTGCTCCT 60.365 66.667 0.00 0.00 39.59 3.69
4247 6986 3.478274 CCTCCTGGCTCCTGCTCC 61.478 72.222 0.00 0.00 39.59 4.70
4248 6987 2.686835 ACCTCCTGGCTCCTGCTC 60.687 66.667 0.00 0.00 39.59 4.26
4249 6988 3.007920 CACCTCCTGGCTCCTGCT 61.008 66.667 0.00 0.00 39.59 4.24
4251 6990 2.605854 GATGCACCTCCTGGCTCCTG 62.606 65.000 0.00 0.00 36.63 3.86
4252 6991 2.285969 ATGCACCTCCTGGCTCCT 60.286 61.111 0.00 0.00 36.63 3.69
4254 6993 0.106819 AATGATGCACCTCCTGGCTC 60.107 55.000 0.00 0.00 36.63 4.70
4255 6994 0.395311 CAATGATGCACCTCCTGGCT 60.395 55.000 0.00 0.00 36.63 4.75
4256 6995 0.682209 ACAATGATGCACCTCCTGGC 60.682 55.000 0.00 0.00 36.63 4.85
4257 6996 1.064906 AGACAATGATGCACCTCCTGG 60.065 52.381 0.00 0.00 39.83 4.45
4258 6997 2.286872 GAGACAATGATGCACCTCCTG 58.713 52.381 0.00 0.00 0.00 3.86
4259 6998 1.134580 CGAGACAATGATGCACCTCCT 60.135 52.381 0.00 0.00 0.00 3.69
4262 7001 0.745845 GCCGAGACAATGATGCACCT 60.746 55.000 0.00 0.00 0.00 4.00
4263 7002 0.745845 AGCCGAGACAATGATGCACC 60.746 55.000 0.00 0.00 0.00 5.01
4264 7003 1.863454 CTAGCCGAGACAATGATGCAC 59.137 52.381 0.00 0.00 0.00 4.57
4278 7017 2.345244 CATGCCTAGCCCTAGCCG 59.655 66.667 0.00 0.00 41.25 5.52
4299 7038 0.700564 AACAGCCTCATGTGGACCAT 59.299 50.000 17.98 0.00 32.52 3.55
4311 7050 2.121992 CTCCCTGCAGACAACAGCCT 62.122 60.000 17.39 0.00 33.65 4.58
4330 7069 3.253432 GTGTTGGGATTTCAGTGAAGGAC 59.747 47.826 5.56 2.09 0.00 3.85
4495 7239 5.864418 ATCTTACCTCAGCCGTATGTTTA 57.136 39.130 0.00 0.00 0.00 2.01
4496 7240 4.755266 ATCTTACCTCAGCCGTATGTTT 57.245 40.909 0.00 0.00 0.00 2.83
4515 7329 7.674240 GCAGGATCTTGTAAAGTTACGTGAATC 60.674 40.741 6.70 0.00 46.34 2.52
4516 7330 6.092259 GCAGGATCTTGTAAAGTTACGTGAAT 59.908 38.462 6.70 0.00 46.34 2.57
4518 7332 4.927425 GCAGGATCTTGTAAAGTTACGTGA 59.073 41.667 6.70 0.00 46.34 4.35
4519 7333 4.201589 CGCAGGATCTTGTAAAGTTACGTG 60.202 45.833 6.70 0.00 46.34 4.49
4520 7334 3.924686 CGCAGGATCTTGTAAAGTTACGT 59.075 43.478 6.70 0.00 46.34 3.57
4521 7335 3.241995 GCGCAGGATCTTGTAAAGTTACG 60.242 47.826 0.30 0.23 46.34 3.18
4522 7336 3.682858 TGCGCAGGATCTTGTAAAGTTAC 59.317 43.478 5.66 0.00 46.34 2.50
4523 7337 3.932822 TGCGCAGGATCTTGTAAAGTTA 58.067 40.909 5.66 0.00 46.34 2.24
4524 7338 2.778299 TGCGCAGGATCTTGTAAAGTT 58.222 42.857 5.66 0.00 46.34 2.66
4525 7339 2.472695 TGCGCAGGATCTTGTAAAGT 57.527 45.000 5.66 0.00 46.34 2.66
4527 7341 2.423185 CCATTGCGCAGGATCTTGTAAA 59.577 45.455 11.31 0.00 0.00 2.01
4528 7342 2.016318 CCATTGCGCAGGATCTTGTAA 58.984 47.619 11.31 0.00 0.00 2.41
4529 7343 1.667236 CCATTGCGCAGGATCTTGTA 58.333 50.000 11.31 0.00 0.00 2.41
4530 7344 1.033746 CCCATTGCGCAGGATCTTGT 61.034 55.000 16.78 0.00 0.00 3.16
4551 7365 1.578583 CGTGTTCGTTTCCTTGTCCT 58.421 50.000 0.00 0.00 0.00 3.85
4586 7400 2.623416 GCCAAGTTATTATGGTCCCTGC 59.377 50.000 0.00 0.00 39.00 4.85


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

AutoCloner maintained by Alex Coulton.