Multiple sequence alignment - TraesCS2D01G344500

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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 TraesCS2D01G344500 chr2D 100.000 4538 0 0 1 4538 440607180 440611717 0.000000e+00 8381
1 TraesCS2D01G344500 chr2D 100.000 556 0 0 4944 5499 440612123 440612678 0.000000e+00 1027
2 TraesCS2D01G344500 chr2A 91.944 3637 184 49 143 3706 584062018 584065618 0.000000e+00 4992
3 TraesCS2D01G344500 chr2A 97.711 830 15 4 3711 4538 584065840 584066667 0.000000e+00 1424
4 TraesCS2D01G344500 chr2A 91.684 493 31 6 4944 5428 584066765 584067255 0.000000e+00 675
5 TraesCS2D01G344500 chr2B 95.312 2944 76 22 783 3706 518513499 518516400 0.000000e+00 4615
6 TraesCS2D01G344500 chr2B 98.552 829 9 2 3709 4535 518516620 518517447 0.000000e+00 1461
7 TraesCS2D01G344500 chr2B 92.381 210 13 1 5208 5414 518517906 518518115 4.170000e-76 296


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 TraesCS2D01G344500 chr2D 440607180 440612678 5498 False 4704.000000 8381 100.000000 1 5499 2 chr2D.!!$F1 5498
1 TraesCS2D01G344500 chr2A 584062018 584067255 5237 False 2363.666667 4992 93.779667 143 5428 3 chr2A.!!$F1 5285
2 TraesCS2D01G344500 chr2B 518513499 518518115 4616 False 2124.000000 4615 95.415000 783 5414 3 chr2B.!!$F1 4631

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
253 254 0.032515 TCGAAGAGGGCCATCTGGTA 60.033 55.0 22.78 6.20 37.57 3.25 F
1271 1314 0.178068 TTATTCTGTGCTCCGGGCTC 59.822 55.0 14.76 11.92 42.39 4.70 F
1927 1997 0.111061 AGCACCAGAATTGCAGTGGA 59.889 50.0 12.05 0.00 42.83 4.02 F
3129 3208 1.048601 GGAGCGAGATACCAATCCCA 58.951 55.0 0.00 0.00 31.98 4.37 F
3241 3320 5.006649 CGTCTTGACTTCTTGACATTTCACA 59.993 40.0 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 1977 0.242825 CCACTGCAATTCTGGTGCTG 59.757 55.000 0.0 2.26 42.69 4.41 R
2565 2641 6.487668 CCACATGAGAATGCACCTATAAATGA 59.512 38.462 0.0 0.00 0.00 2.57 R
3638 3717 0.813184 AAAACATGGCTGAGATGCGG 59.187 50.000 0.0 0.00 0.00 5.69 R
4426 4724 1.531602 GTTGCTTGGGCCCTTGTCT 60.532 57.895 25.7 0.00 37.74 3.41 R
5042 5341 4.219944 ACAGCCAGTACAAGATTAGAACGA 59.780 41.667 0.0 0.00 0.00 3.85 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
26 27 3.049674 CGGTCACGCATGTTGCCT 61.050 61.111 0.00 0.00 41.12 4.75
27 28 2.870372 GGTCACGCATGTTGCCTC 59.130 61.111 0.00 0.00 41.12 4.70
28 29 1.965930 GGTCACGCATGTTGCCTCA 60.966 57.895 0.00 0.00 41.12 3.86
29 30 1.207593 GTCACGCATGTTGCCTCAC 59.792 57.895 0.00 0.00 41.12 3.51
30 31 1.227793 TCACGCATGTTGCCTCACA 60.228 52.632 0.00 0.00 41.12 3.58
31 32 0.606130 TCACGCATGTTGCCTCACAT 60.606 50.000 0.00 0.00 41.12 3.21
37 38 2.668250 CATGTTGCCTCACATGTGTTG 58.332 47.619 24.63 17.29 46.20 3.33
38 39 1.761449 TGTTGCCTCACATGTGTTGT 58.239 45.000 24.63 0.00 39.91 3.32
46 47 2.811307 ACATGTGTTGTGCAAGGCT 58.189 47.368 0.00 0.00 37.11 4.58
47 48 0.386476 ACATGTGTTGTGCAAGGCTG 59.614 50.000 0.00 0.00 37.11 4.85
48 49 0.319211 CATGTGTTGTGCAAGGCTGG 60.319 55.000 0.00 0.00 0.00 4.85
49 50 1.466025 ATGTGTTGTGCAAGGCTGGG 61.466 55.000 0.00 0.00 0.00 4.45
50 51 3.225798 TGTTGTGCAAGGCTGGGC 61.226 61.111 4.59 4.59 0.00 5.36
62 63 3.699894 CTGGGCCGAGCTGTCTGT 61.700 66.667 0.21 0.00 0.00 3.41
63 64 3.947132 CTGGGCCGAGCTGTCTGTG 62.947 68.421 0.21 0.00 0.00 3.66
64 65 3.695606 GGGCCGAGCTGTCTGTGA 61.696 66.667 0.00 0.00 0.00 3.58
65 66 2.433318 GGCCGAGCTGTCTGTGAC 60.433 66.667 0.00 0.00 0.00 3.67
66 67 2.340078 GCCGAGCTGTCTGTGACA 59.660 61.111 0.00 0.37 40.50 3.58
67 68 1.079543 GCCGAGCTGTCTGTGACAT 60.080 57.895 0.00 0.00 41.94 3.06
68 69 0.671781 GCCGAGCTGTCTGTGACATT 60.672 55.000 0.00 0.00 41.94 2.71
69 70 1.354040 CCGAGCTGTCTGTGACATTC 58.646 55.000 0.00 2.51 41.94 2.67
70 71 1.337167 CCGAGCTGTCTGTGACATTCA 60.337 52.381 0.00 0.00 41.94 2.57
72 73 2.072298 GAGCTGTCTGTGACATTCACC 58.928 52.381 0.00 0.00 46.40 4.02
73 74 1.417517 AGCTGTCTGTGACATTCACCA 59.582 47.619 3.91 0.00 46.40 4.17
74 75 1.532868 GCTGTCTGTGACATTCACCAC 59.467 52.381 3.91 2.02 46.40 4.16
75 76 2.808202 GCTGTCTGTGACATTCACCACT 60.808 50.000 3.91 0.00 46.40 4.00
76 77 3.470709 CTGTCTGTGACATTCACCACTT 58.529 45.455 3.91 0.00 46.40 3.16
77 78 3.879295 CTGTCTGTGACATTCACCACTTT 59.121 43.478 3.91 0.00 46.40 2.66
78 79 3.627123 TGTCTGTGACATTCACCACTTTG 59.373 43.478 3.91 0.00 46.40 2.77
79 80 2.618241 TCTGTGACATTCACCACTTTGC 59.382 45.455 3.91 0.00 46.40 3.68
80 81 1.680735 TGTGACATTCACCACTTTGCC 59.319 47.619 3.91 0.00 46.40 4.52
81 82 0.950836 TGACATTCACCACTTTGCCG 59.049 50.000 0.00 0.00 0.00 5.69
82 83 0.240945 GACATTCACCACTTTGCCGG 59.759 55.000 0.00 0.00 0.00 6.13
83 84 1.178534 ACATTCACCACTTTGCCGGG 61.179 55.000 2.18 0.00 0.00 5.73
84 85 2.275380 ATTCACCACTTTGCCGGGC 61.275 57.895 13.32 13.32 0.00 6.13
85 86 2.713531 ATTCACCACTTTGCCGGGCT 62.714 55.000 21.46 0.00 0.00 5.19
86 87 3.673484 CACCACTTTGCCGGGCTG 61.673 66.667 21.46 9.83 0.00 4.85
90 91 4.323477 ACTTTGCCGGGCTGCGTA 62.323 61.111 21.46 0.00 0.00 4.42
91 92 3.499737 CTTTGCCGGGCTGCGTAG 61.500 66.667 21.46 6.33 0.00 3.51
113 114 2.587194 CGCAGAGAGGGCCATTCG 60.587 66.667 6.18 0.90 0.00 3.34
114 115 2.203126 GCAGAGAGGGCCATTCGG 60.203 66.667 6.18 4.61 0.00 4.30
124 125 2.421739 CCATTCGGCTAGGGGTCG 59.578 66.667 0.00 0.00 45.40 4.79
125 126 2.280186 CATTCGGCTAGGGGTCGC 60.280 66.667 0.00 0.00 43.48 5.19
126 127 3.912907 ATTCGGCTAGGGGTCGCG 61.913 66.667 0.00 0.00 43.48 5.87
154 155 0.613260 TGACGGACCTGCTAGCATTT 59.387 50.000 19.72 8.00 0.00 2.32
155 156 1.009829 GACGGACCTGCTAGCATTTG 58.990 55.000 19.72 12.37 0.00 2.32
157 158 0.729116 CGGACCTGCTAGCATTTGTG 59.271 55.000 19.72 5.85 0.00 3.33
182 183 2.355445 CTATCGGGCTGCTTCGCTCA 62.355 60.000 0.00 0.00 0.00 4.26
190 191 1.153269 TGCTTCGCTCACACCAACA 60.153 52.632 0.00 0.00 0.00 3.33
192 193 0.380378 GCTTCGCTCACACCAACAAA 59.620 50.000 0.00 0.00 0.00 2.83
198 199 0.385390 CTCACACCAACAAAGCCCAC 59.615 55.000 0.00 0.00 0.00 4.61
204 205 1.437160 CAACAAAGCCCACGCACTT 59.563 52.632 0.00 0.00 37.52 3.16
207 208 3.605664 AAAGCCCACGCACTTGCC 61.606 61.111 0.00 0.00 37.91 4.52
209 210 4.892965 AGCCCACGCACTTGCCAA 62.893 61.111 0.00 0.00 37.91 4.52
215 216 4.093952 CGCACTTGCCAAGCTCGG 62.094 66.667 3.88 0.00 37.91 4.63
225 226 4.379243 AAGCTCGGCGGGTGACAG 62.379 66.667 9.26 0.00 0.00 3.51
252 253 1.306141 TCGAAGAGGGCCATCTGGT 60.306 57.895 22.78 5.88 37.57 4.00
253 254 0.032515 TCGAAGAGGGCCATCTGGTA 60.033 55.000 22.78 6.20 37.57 3.25
256 257 1.141858 GAAGAGGGCCATCTGGTAAGG 59.858 57.143 22.78 0.00 37.57 2.69
262 263 1.439543 GCCATCTGGTAAGGGATCCT 58.560 55.000 12.58 0.00 37.57 3.24
266 267 4.283363 CATCTGGTAAGGGATCCTGATG 57.717 50.000 12.58 13.53 45.90 3.07
268 269 3.309296 TCTGGTAAGGGATCCTGATGAC 58.691 50.000 12.58 1.51 32.13 3.06
284 285 1.376553 GACAAGAGGCCAGCTGGTC 60.377 63.158 30.54 30.54 40.99 4.02
299 300 2.676471 GTCCAGCGGCCAACCATT 60.676 61.111 2.24 0.00 34.57 3.16
303 304 2.117206 AGCGGCCAACCATTTCCA 59.883 55.556 2.24 0.00 34.57 3.53
314 315 3.038788 ACCATTTCCAAATGCGGTTTC 57.961 42.857 6.52 0.00 43.38 2.78
315 316 2.366916 ACCATTTCCAAATGCGGTTTCA 59.633 40.909 6.52 0.00 43.38 2.69
327 328 1.963747 CGGTTTCAAAGGATGTTCGC 58.036 50.000 0.00 0.00 0.00 4.70
329 330 2.665519 CGGTTTCAAAGGATGTTCGCTG 60.666 50.000 0.00 0.00 0.00 5.18
338 339 2.993899 AGGATGTTCGCTGTTTAAGACG 59.006 45.455 0.00 0.00 0.00 4.18
343 344 3.805422 TGTTCGCTGTTTAAGACGATTGT 59.195 39.130 0.00 0.00 35.41 2.71
344 345 4.141680 GTTCGCTGTTTAAGACGATTGTG 58.858 43.478 0.00 0.00 35.41 3.33
378 379 4.035909 AGTTTGTTGTTTTAGGCTACACGG 59.964 41.667 0.00 0.00 0.00 4.94
380 381 1.136169 GTTGTTTTAGGCTACACGGCG 60.136 52.381 4.80 4.80 44.22 6.46
381 382 0.671163 TGTTTTAGGCTACACGGCGG 60.671 55.000 13.24 2.35 44.22 6.13
383 384 0.538118 TTTTAGGCTACACGGCGGAT 59.462 50.000 13.24 0.09 44.22 4.18
385 386 0.670162 TTAGGCTACACGGCGGATAC 59.330 55.000 13.24 0.00 44.22 2.24
398 399 0.248054 CGGATACAACGCACATTGGC 60.248 55.000 0.00 0.00 33.63 4.52
406 407 2.409870 CGCACATTGGCCTTCCTCC 61.410 63.158 3.32 0.00 0.00 4.30
413 414 3.717294 GGCCTTCCTCCCGCTTCA 61.717 66.667 0.00 0.00 0.00 3.02
419 420 0.984230 TTCCTCCCGCTTCATCTTGT 59.016 50.000 0.00 0.00 0.00 3.16
440 441 1.881591 GCTCCTGCTCCAGATTGATC 58.118 55.000 0.00 0.00 32.44 2.92
447 448 1.680207 GCTCCAGATTGATCTTTGCCC 59.320 52.381 0.00 0.00 34.22 5.36
449 450 1.281867 TCCAGATTGATCTTTGCCCGT 59.718 47.619 0.00 0.00 34.22 5.28
450 451 2.094675 CCAGATTGATCTTTGCCCGTT 58.905 47.619 0.00 0.00 34.22 4.44
457 458 4.050934 CTTTGCCCGTTTCCCGCC 62.051 66.667 0.00 0.00 34.38 6.13
465 466 2.975799 GTTTCCCGCCAGCGACAA 60.976 61.111 14.67 2.49 42.83 3.18
480 481 2.847901 CGACAATCGAACACGTCTACT 58.152 47.619 0.00 0.00 43.74 2.57
486 487 3.325293 TCGAACACGTCTACTACCTCT 57.675 47.619 0.00 0.00 0.00 3.69
496 497 4.017808 GTCTACTACCTCTGCCTTCTTGA 58.982 47.826 0.00 0.00 0.00 3.02
503 504 1.410517 CTCTGCCTTCTTGAGCGGATA 59.589 52.381 0.00 0.00 43.22 2.59
522 523 1.377725 CGCATCCTGCCCTGTTCTT 60.378 57.895 0.00 0.00 41.12 2.52
534 535 3.019564 CCCTGTTCTTTGGCCTCAATAG 58.980 50.000 3.32 0.00 32.28 1.73
549 550 2.287644 TCAATAGGCGTGCAATTCATCG 59.712 45.455 0.00 0.00 0.00 3.84
554 555 1.400888 GGCGTGCAATTCATCGTCAAA 60.401 47.619 0.00 0.00 0.00 2.69
555 556 2.518949 GCGTGCAATTCATCGTCAAAT 58.481 42.857 0.00 0.00 0.00 2.32
591 592 1.262640 TTCGGGTGGGTAGCTCCTTC 61.263 60.000 0.00 0.00 36.25 3.46
595 596 1.448013 GTGGGTAGCTCCTTCGTGC 60.448 63.158 0.00 0.00 36.25 5.34
597 598 1.192146 TGGGTAGCTCCTTCGTGCTT 61.192 55.000 0.00 0.00 39.48 3.91
614 615 4.213270 CGTGCTTGTGTTCTCTTCCATTTA 59.787 41.667 0.00 0.00 0.00 1.40
619 620 7.867403 TGCTTGTGTTCTCTTCCATTTAAAATC 59.133 33.333 0.00 0.00 0.00 2.17
620 621 7.329471 GCTTGTGTTCTCTTCCATTTAAAATCC 59.671 37.037 0.00 0.00 0.00 3.01
625 626 5.484715 TCTCTTCCATTTAAAATCCGTCGT 58.515 37.500 0.00 0.00 0.00 4.34
628 629 3.340034 TCCATTTAAAATCCGTCGTGCT 58.660 40.909 0.00 0.00 0.00 4.40
630 631 2.604969 TTTAAAATCCGTCGTGCTGC 57.395 45.000 0.00 0.00 0.00 5.25
664 692 3.656045 CGGCCCGTCACAAACCAC 61.656 66.667 0.00 0.00 0.00 4.16
667 695 2.203098 CCCGTCACAAACCACCGT 60.203 61.111 0.00 0.00 0.00 4.83
673 701 0.601576 TCACAAACCACCGTGATCCG 60.602 55.000 0.00 0.00 37.23 4.18
674 702 1.964373 ACAAACCACCGTGATCCGC 60.964 57.895 0.00 0.00 34.38 5.54
682 710 3.490759 CGTGATCCGCTGTGCACC 61.491 66.667 15.69 0.00 0.00 5.01
712 740 7.201401 GCACCATCGTCAAATACCATTTTTAAC 60.201 37.037 0.00 0.00 0.00 2.01
714 742 6.470877 CCATCGTCAAATACCATTTTTAACGG 59.529 38.462 0.00 0.00 31.26 4.44
729 758 2.801077 AACGGAGGATTTTTCGGGAT 57.199 45.000 0.00 0.00 0.00 3.85
752 781 1.565156 TAAAAGCAGCGCACCTGTCG 61.565 55.000 11.47 0.00 43.71 4.35
760 789 1.954382 AGCGCACCTGTCGATCTTATA 59.046 47.619 11.47 0.00 0.00 0.98
768 797 5.067936 CACCTGTCGATCTTATAGACACCTT 59.932 44.000 0.00 0.00 39.47 3.50
769 798 6.262496 CACCTGTCGATCTTATAGACACCTTA 59.738 42.308 0.00 0.00 39.47 2.69
824 853 3.270877 GAACGGTTGGTGATGCTCTTAT 58.729 45.455 0.00 0.00 0.00 1.73
825 854 4.439057 GAACGGTTGGTGATGCTCTTATA 58.561 43.478 0.00 0.00 0.00 0.98
854 885 6.987403 TTAGTTGCAGAAAAACCCCTAATT 57.013 33.333 0.00 0.00 0.00 1.40
855 886 5.468540 AGTTGCAGAAAAACCCCTAATTC 57.531 39.130 0.00 0.00 0.00 2.17
856 887 4.283467 AGTTGCAGAAAAACCCCTAATTCC 59.717 41.667 0.00 0.00 0.00 3.01
857 888 3.850752 TGCAGAAAAACCCCTAATTCCA 58.149 40.909 0.00 0.00 0.00 3.53
858 889 4.424842 TGCAGAAAAACCCCTAATTCCAT 58.575 39.130 0.00 0.00 0.00 3.41
859 890 4.843516 TGCAGAAAAACCCCTAATTCCATT 59.156 37.500 0.00 0.00 0.00 3.16
883 916 2.908626 GCTCTAACGAAAATGCCGTTTG 59.091 45.455 6.23 5.07 46.52 2.93
894 927 2.251642 GCCGTTTGGTTCTCTGCGT 61.252 57.895 0.00 0.00 37.67 5.24
923 956 4.207429 GTGAATCTAAACTCGGAATCGCTC 59.793 45.833 0.00 0.00 36.13 5.03
926 959 2.099263 TCTAAACTCGGAATCGCTCCTG 59.901 50.000 2.40 0.00 42.85 3.86
1068 1108 4.814294 GCCGTCGTCGCCATCCTT 62.814 66.667 0.00 0.00 35.54 3.36
1268 1311 2.917933 TCAATTATTCTGTGCTCCGGG 58.082 47.619 0.00 0.00 0.00 5.73
1269 1312 1.334869 CAATTATTCTGTGCTCCGGGC 59.665 52.381 0.00 4.52 42.22 6.13
1271 1314 0.178068 TTATTCTGTGCTCCGGGCTC 59.822 55.000 14.76 11.92 42.39 4.70
1272 1315 1.686325 TATTCTGTGCTCCGGGCTCC 61.686 60.000 14.76 7.17 42.39 4.70
1344 1397 8.996988 TTTTACTATTCAACTTGTTTGCTACG 57.003 30.769 0.00 0.00 34.88 3.51
1440 1499 2.544685 CCTCGACCTAATGCAGTTCAG 58.455 52.381 0.00 0.00 0.00 3.02
1448 1507 1.436600 AATGCAGTTCAGTCGAGCAG 58.563 50.000 0.00 0.00 38.75 4.24
1476 1535 2.293122 TGTGCTTGATTGTTAGGTGTGC 59.707 45.455 0.00 0.00 0.00 4.57
1486 1545 5.392767 TTGTTAGGTGTGCACTTTGAAAA 57.607 34.783 19.41 2.30 0.00 2.29
1548 1607 5.233988 AGTCTCTAATTGCAGAACACTGAC 58.766 41.667 0.00 0.00 33.94 3.51
1549 1608 5.011533 AGTCTCTAATTGCAGAACACTGACT 59.988 40.000 0.00 0.00 33.94 3.41
1550 1609 5.119898 GTCTCTAATTGCAGAACACTGACTG 59.880 44.000 0.00 0.00 37.22 3.51
1551 1610 5.011023 TCTCTAATTGCAGAACACTGACTGA 59.989 40.000 0.00 0.00 36.38 3.41
1552 1611 5.233225 TCTAATTGCAGAACACTGACTGAG 58.767 41.667 0.00 0.00 36.38 3.35
1816 1886 8.515695 TCTGCTACAATGATTTCATTCAGAAT 57.484 30.769 14.90 0.00 44.10 2.40
1907 1977 1.291184 GCCACTTTTGCGGATTTGCC 61.291 55.000 0.00 0.00 0.00 4.52
1927 1997 0.111061 AGCACCAGAATTGCAGTGGA 59.889 50.000 12.05 0.00 42.83 4.02
2398 2474 8.777865 TGCATGACCTCATTATAAATAGCTAC 57.222 34.615 0.00 0.00 33.61 3.58
2516 2592 6.740960 GCAGAACAGCAGAGGTCTATCATTAT 60.741 42.308 0.00 0.00 0.00 1.28
2560 2636 8.307483 CAAGTTAACTCTTGAGACCTTCTGATA 58.693 37.037 8.95 0.00 45.11 2.15
2826 2902 7.816031 CCTAGGTACGAGTCTTGTTTCATTTTA 59.184 37.037 0.00 0.00 0.00 1.52
3129 3208 1.048601 GGAGCGAGATACCAATCCCA 58.951 55.000 0.00 0.00 31.98 4.37
3241 3320 5.006649 CGTCTTGACTTCTTGACATTTCACA 59.993 40.000 0.00 0.00 0.00 3.58
3370 3449 5.309323 TGCACAGTATACAAAATTGAGGC 57.691 39.130 5.50 4.96 0.00 4.70
3706 3785 5.688807 ACATTGAATACCTAGCATGCTTCT 58.311 37.500 28.02 10.98 0.00 2.85
3707 3786 6.125029 ACATTGAATACCTAGCATGCTTCTT 58.875 36.000 28.02 12.49 0.00 2.52
3708 3787 7.282585 ACATTGAATACCTAGCATGCTTCTTA 58.717 34.615 28.02 14.33 0.00 2.10
3709 3788 7.775093 ACATTGAATACCTAGCATGCTTCTTAA 59.225 33.333 28.02 6.18 0.00 1.85
4290 4588 5.893687 AGCATTCGTAAATCATGAATTGCA 58.106 33.333 11.46 0.00 40.27 4.08
5060 5359 7.993821 ATGATGTCGTTCTAATCTTGTACTG 57.006 36.000 0.00 0.00 0.00 2.74
5075 5377 5.479027 TCTTGTACTGGCTGTAACAGATACA 59.521 40.000 5.77 0.00 42.22 2.29
5082 5384 6.149129 TGGCTGTAACAGATACATCTACTG 57.851 41.667 0.00 0.00 43.42 2.74
5083 5385 5.891551 TGGCTGTAACAGATACATCTACTGA 59.108 40.000 0.00 0.00 43.42 3.41
5180 5483 5.439721 TGCTAGCCACATCAGTATTGAAAT 58.560 37.500 13.29 0.00 36.78 2.17
5248 5656 1.052694 AAGGGGTATCCGGCAGGTAC 61.053 60.000 1.81 5.06 41.52 3.34
5305 5713 2.289694 ACCTCTCATCCAAACACCTTCG 60.290 50.000 0.00 0.00 0.00 3.79
5355 5766 4.826556 CCTCTGCAGTAGCTTCTAAACTT 58.173 43.478 14.67 0.00 42.74 2.66
5371 5782 8.463930 TTCTAAACTTGATGTGAATCCAGTTT 57.536 30.769 17.06 17.06 43.98 2.66
5384 5795 5.485353 TGAATCCAGTTTGTATCCTCTGAGT 59.515 40.000 3.66 0.00 0.00 3.41
5399 5810 4.336713 CCTCTGAGTCATCAACGTCATCTA 59.663 45.833 3.66 0.00 34.23 1.98
5407 5818 7.225011 AGTCATCAACGTCATCTAGACCTATA 58.775 38.462 0.00 0.00 44.66 1.31
5409 5820 5.919272 TCAACGTCATCTAGACCTATACG 57.081 43.478 0.00 3.73 44.66 3.06
5414 5825 6.283694 ACGTCATCTAGACCTATACGTACAA 58.716 40.000 14.40 0.00 44.66 2.41
5415 5826 6.763135 ACGTCATCTAGACCTATACGTACAAA 59.237 38.462 14.40 0.00 44.66 2.83
5440 5851 2.423446 TTTTGCGGGGGTTCCTATAC 57.577 50.000 0.00 0.00 0.00 1.47
5441 5852 0.547553 TTTGCGGGGGTTCCTATACC 59.452 55.000 0.00 0.00 37.47 2.73
5442 5853 0.326808 TTGCGGGGGTTCCTATACCT 60.327 55.000 0.00 0.00 38.30 3.08
5443 5854 0.562177 TGCGGGGGTTCCTATACCTA 59.438 55.000 0.00 0.00 38.30 3.08
5444 5855 0.972134 GCGGGGGTTCCTATACCTAC 59.028 60.000 0.00 0.00 38.30 3.18
5445 5856 1.758841 GCGGGGGTTCCTATACCTACA 60.759 57.143 0.00 0.00 38.30 2.74
5446 5857 2.245582 CGGGGGTTCCTATACCTACAG 58.754 57.143 0.00 0.00 38.30 2.74
5447 5858 2.425392 CGGGGGTTCCTATACCTACAGT 60.425 54.545 0.00 0.00 38.30 3.55
5448 5859 3.662078 GGGGGTTCCTATACCTACAGTT 58.338 50.000 0.00 0.00 38.30 3.16
5449 5860 3.390311 GGGGGTTCCTATACCTACAGTTG 59.610 52.174 0.00 0.00 38.30 3.16
5450 5861 4.292643 GGGGTTCCTATACCTACAGTTGA 58.707 47.826 0.00 0.00 38.30 3.18
5451 5862 4.100653 GGGGTTCCTATACCTACAGTTGAC 59.899 50.000 0.00 0.00 38.30 3.18
5452 5863 4.100653 GGGTTCCTATACCTACAGTTGACC 59.899 50.000 0.00 0.00 38.30 4.02
5453 5864 4.961099 GGTTCCTATACCTACAGTTGACCT 59.039 45.833 0.00 0.00 35.23 3.85
5454 5865 5.163437 GGTTCCTATACCTACAGTTGACCTG 60.163 48.000 0.00 0.00 39.91 4.00
5455 5866 5.461516 TCCTATACCTACAGTTGACCTGA 57.538 43.478 0.00 0.00 44.49 3.86
5456 5867 5.446860 TCCTATACCTACAGTTGACCTGAG 58.553 45.833 0.00 0.00 44.49 3.35
5457 5868 4.038162 CCTATACCTACAGTTGACCTGAGC 59.962 50.000 0.00 0.00 44.49 4.26
5458 5869 2.016905 ACCTACAGTTGACCTGAGCT 57.983 50.000 0.00 0.00 44.49 4.09
5459 5870 1.896465 ACCTACAGTTGACCTGAGCTC 59.104 52.381 6.82 6.82 44.49 4.09
5460 5871 2.175202 CCTACAGTTGACCTGAGCTCT 58.825 52.381 16.19 0.00 44.49 4.09
5461 5872 2.564947 CCTACAGTTGACCTGAGCTCTT 59.435 50.000 16.19 0.00 44.49 2.85
5462 5873 3.007398 CCTACAGTTGACCTGAGCTCTTT 59.993 47.826 16.19 0.00 44.49 2.52
5463 5874 3.118905 ACAGTTGACCTGAGCTCTTTC 57.881 47.619 16.19 8.88 44.49 2.62
5464 5875 2.435805 ACAGTTGACCTGAGCTCTTTCA 59.564 45.455 16.19 11.40 44.49 2.69
5465 5876 3.118261 ACAGTTGACCTGAGCTCTTTCAA 60.118 43.478 16.19 16.38 44.49 2.69
5466 5877 3.249559 CAGTTGACCTGAGCTCTTTCAAC 59.750 47.826 29.27 29.27 44.49 3.18
5467 5878 3.471680 GTTGACCTGAGCTCTTTCAACT 58.528 45.455 29.21 6.44 41.78 3.16
5468 5879 3.393089 TGACCTGAGCTCTTTCAACTC 57.607 47.619 16.19 0.79 0.00 3.01
5469 5880 2.968574 TGACCTGAGCTCTTTCAACTCT 59.031 45.455 16.19 0.00 0.00 3.24
5470 5881 3.006323 TGACCTGAGCTCTTTCAACTCTC 59.994 47.826 16.19 0.00 0.00 3.20
5471 5882 2.968574 ACCTGAGCTCTTTCAACTCTCA 59.031 45.455 16.19 0.00 33.35 3.27
5472 5883 3.244044 ACCTGAGCTCTTTCAACTCTCAC 60.244 47.826 16.19 0.00 31.36 3.51
5473 5884 3.244009 CCTGAGCTCTTTCAACTCTCACA 60.244 47.826 16.19 0.00 31.36 3.58
5474 5885 4.563168 CCTGAGCTCTTTCAACTCTCACAT 60.563 45.833 16.19 0.00 31.36 3.21
5475 5886 4.313282 TGAGCTCTTTCAACTCTCACATG 58.687 43.478 16.19 0.00 0.00 3.21
5476 5887 3.072944 AGCTCTTTCAACTCTCACATGC 58.927 45.455 0.00 0.00 0.00 4.06
5477 5888 2.161211 GCTCTTTCAACTCTCACATGCC 59.839 50.000 0.00 0.00 0.00 4.40
5478 5889 3.672808 CTCTTTCAACTCTCACATGCCT 58.327 45.455 0.00 0.00 0.00 4.75
5479 5890 4.070716 CTCTTTCAACTCTCACATGCCTT 58.929 43.478 0.00 0.00 0.00 4.35
5480 5891 4.067896 TCTTTCAACTCTCACATGCCTTC 58.932 43.478 0.00 0.00 0.00 3.46
5481 5892 3.777106 TTCAACTCTCACATGCCTTCT 57.223 42.857 0.00 0.00 0.00 2.85
5482 5893 3.049708 TCAACTCTCACATGCCTTCTG 57.950 47.619 0.00 0.00 0.00 3.02
5483 5894 2.369860 TCAACTCTCACATGCCTTCTGT 59.630 45.455 0.00 0.00 0.00 3.41
5484 5895 2.469274 ACTCTCACATGCCTTCTGTG 57.531 50.000 0.00 0.00 44.26 3.66
5489 5900 2.983402 CACATGCCTTCTGTGAAGTG 57.017 50.000 6.57 1.90 45.44 3.16
5490 5901 1.538512 CACATGCCTTCTGTGAAGTGG 59.461 52.381 6.57 0.00 45.44 4.00
5491 5902 0.524862 CATGCCTTCTGTGAAGTGGC 59.475 55.000 6.57 0.00 43.49 5.01
5492 5903 4.481195 GCCTTCTGTGAAGTGGCA 57.519 55.556 6.57 0.00 42.79 4.92
5493 5904 2.719376 GCCTTCTGTGAAGTGGCAA 58.281 52.632 6.57 0.00 42.79 4.52
5494 5905 0.595095 GCCTTCTGTGAAGTGGCAAG 59.405 55.000 6.57 0.00 42.79 4.01
5495 5906 1.972872 CCTTCTGTGAAGTGGCAAGT 58.027 50.000 6.57 0.00 0.00 3.16
5496 5907 1.605710 CCTTCTGTGAAGTGGCAAGTG 59.394 52.381 6.57 0.00 0.00 3.16
5497 5908 2.292267 CTTCTGTGAAGTGGCAAGTGT 58.708 47.619 0.00 0.00 0.00 3.55
5498 5909 2.418368 TCTGTGAAGTGGCAAGTGTT 57.582 45.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.027170 GAGGCAACATGCGTGACCG 62.027 63.158 14.17 1.20 46.21 4.79
10 11 1.965930 TGAGGCAACATGCGTGACC 60.966 57.895 14.17 10.85 46.21 4.02
11 12 1.207593 GTGAGGCAACATGCGTGAC 59.792 57.895 14.17 0.54 46.21 3.67
12 13 0.606130 ATGTGAGGCAACATGCGTGA 60.606 50.000 14.17 0.00 46.21 4.35
13 14 1.878070 ATGTGAGGCAACATGCGTG 59.122 52.632 3.82 3.82 46.21 5.34
14 15 4.402851 ATGTGAGGCAACATGCGT 57.597 50.000 5.18 0.00 46.21 5.24
18 19 2.309613 ACAACACATGTGAGGCAACAT 58.690 42.857 31.94 4.03 41.93 2.71
19 20 1.761449 ACAACACATGTGAGGCAACA 58.239 45.000 31.94 0.00 41.93 3.33
28 29 0.386476 CAGCCTTGCACAACACATGT 59.614 50.000 0.00 0.00 45.34 3.21
29 30 0.319211 CCAGCCTTGCACAACACATG 60.319 55.000 0.00 0.00 0.00 3.21
30 31 1.466025 CCCAGCCTTGCACAACACAT 61.466 55.000 0.00 0.00 0.00 3.21
31 32 2.126596 CCCAGCCTTGCACAACACA 61.127 57.895 0.00 0.00 0.00 3.72
32 33 2.730094 CCCAGCCTTGCACAACAC 59.270 61.111 0.00 0.00 0.00 3.32
33 34 3.225798 GCCCAGCCTTGCACAACA 61.226 61.111 0.00 0.00 0.00 3.33
34 35 3.994853 GGCCCAGCCTTGCACAAC 61.995 66.667 0.00 0.00 46.69 3.32
45 46 3.699894 ACAGACAGCTCGGCCCAG 61.700 66.667 0.00 0.00 0.00 4.45
46 47 4.007644 CACAGACAGCTCGGCCCA 62.008 66.667 0.00 0.00 0.00 5.36
47 48 3.695606 TCACAGACAGCTCGGCCC 61.696 66.667 0.00 0.00 0.00 5.80
48 49 2.433318 GTCACAGACAGCTCGGCC 60.433 66.667 0.00 0.00 32.09 6.13
49 50 0.671781 AATGTCACAGACAGCTCGGC 60.672 55.000 6.01 0.00 46.04 5.54
50 51 1.337167 TGAATGTCACAGACAGCTCGG 60.337 52.381 6.01 0.00 46.04 4.63
51 52 1.723542 GTGAATGTCACAGACAGCTCG 59.276 52.381 6.01 0.00 46.04 5.03
61 62 1.334960 CGGCAAAGTGGTGAATGTCAC 60.335 52.381 0.00 0.00 46.23 3.67
62 63 0.950836 CGGCAAAGTGGTGAATGTCA 59.049 50.000 0.00 0.00 0.00 3.58
63 64 0.240945 CCGGCAAAGTGGTGAATGTC 59.759 55.000 0.00 0.00 0.00 3.06
64 65 1.178534 CCCGGCAAAGTGGTGAATGT 61.179 55.000 0.00 0.00 0.00 2.71
65 66 1.586028 CCCGGCAAAGTGGTGAATG 59.414 57.895 0.00 0.00 0.00 2.67
66 67 2.275380 GCCCGGCAAAGTGGTGAAT 61.275 57.895 3.91 0.00 0.00 2.57
67 68 2.909965 GCCCGGCAAAGTGGTGAA 60.910 61.111 3.91 0.00 0.00 3.18
68 69 3.884774 AGCCCGGCAAAGTGGTGA 61.885 61.111 13.15 0.00 0.00 4.02
69 70 3.673484 CAGCCCGGCAAAGTGGTG 61.673 66.667 13.15 0.00 0.00 4.17
73 74 4.323477 TACGCAGCCCGGCAAAGT 62.323 61.111 13.15 10.29 42.52 2.66
74 75 3.499737 CTACGCAGCCCGGCAAAG 61.500 66.667 13.15 4.30 42.52 2.77
94 95 4.845580 AATGGCCCTCTCTGCGCG 62.846 66.667 0.00 0.00 0.00 6.86
95 96 2.899339 GAATGGCCCTCTCTGCGC 60.899 66.667 0.00 0.00 0.00 6.09
96 97 2.587194 CGAATGGCCCTCTCTGCG 60.587 66.667 0.00 0.00 0.00 5.18
97 98 2.203126 CCGAATGGCCCTCTCTGC 60.203 66.667 0.00 0.00 0.00 4.26
107 108 2.421739 CGACCCCTAGCCGAATGG 59.578 66.667 0.00 0.00 38.77 3.16
108 109 2.280186 GCGACCCCTAGCCGAATG 60.280 66.667 0.00 0.00 0.00 2.67
109 110 3.912907 CGCGACCCCTAGCCGAAT 61.913 66.667 0.00 0.00 0.00 3.34
134 135 0.108138 AATGCTAGCAGGTCCGTCAC 60.108 55.000 23.89 0.00 0.00 3.67
135 136 0.613260 AAATGCTAGCAGGTCCGTCA 59.387 50.000 23.89 0.00 0.00 4.35
136 137 1.009829 CAAATGCTAGCAGGTCCGTC 58.990 55.000 23.89 0.00 0.00 4.79
137 138 0.324943 ACAAATGCTAGCAGGTCCGT 59.675 50.000 23.89 12.23 0.00 4.69
138 139 0.729116 CACAAATGCTAGCAGGTCCG 59.271 55.000 23.89 11.60 0.00 4.79
139 140 1.098050 CCACAAATGCTAGCAGGTCC 58.902 55.000 23.89 0.00 0.00 4.46
140 141 0.453390 GCCACAAATGCTAGCAGGTC 59.547 55.000 23.89 10.38 0.00 3.85
141 142 0.967380 GGCCACAAATGCTAGCAGGT 60.967 55.000 23.89 17.35 0.00 4.00
182 183 2.781158 GCGTGGGCTTTGTTGGTGT 61.781 57.895 0.00 0.00 35.83 4.16
184 185 2.441164 TGCGTGGGCTTTGTTGGT 60.441 55.556 0.00 0.00 40.82 3.67
190 191 3.605664 GGCAAGTGCGTGGGCTTT 61.606 61.111 0.00 0.00 43.26 3.51
192 193 4.892965 TTGGCAAGTGCGTGGGCT 62.893 61.111 0.00 0.00 43.26 5.19
198 199 4.093952 CCGAGCTTGGCAAGTGCG 62.094 66.667 26.71 26.26 43.26 5.34
207 208 4.680237 TGTCACCCGCCGAGCTTG 62.680 66.667 0.00 0.00 0.00 4.01
225 226 2.266055 CCTCTTCGACCACCAGGC 59.734 66.667 0.00 0.00 39.06 4.85
252 253 3.969976 CCTCTTGTCATCAGGATCCCTTA 59.030 47.826 8.55 0.00 0.00 2.69
253 254 2.776536 CCTCTTGTCATCAGGATCCCTT 59.223 50.000 8.55 0.00 0.00 3.95
256 257 1.202746 GGCCTCTTGTCATCAGGATCC 60.203 57.143 2.48 2.48 0.00 3.36
262 263 0.035725 CAGCTGGCCTCTTGTCATCA 60.036 55.000 5.57 0.00 0.00 3.07
266 267 1.376553 GACCAGCTGGCCTCTTGTC 60.377 63.158 33.06 16.75 39.32 3.18
268 269 2.045536 GGACCAGCTGGCCTCTTG 60.046 66.667 33.06 7.55 39.32 3.02
284 285 2.573340 GAAATGGTTGGCCGCTGG 59.427 61.111 0.00 0.00 37.67 4.85
299 300 2.695666 TCCTTTGAAACCGCATTTGGAA 59.304 40.909 0.00 0.00 0.00 3.53
303 304 4.306600 GAACATCCTTTGAAACCGCATTT 58.693 39.130 0.00 0.00 0.00 2.32
314 315 5.147162 GTCTTAAACAGCGAACATCCTTTG 58.853 41.667 0.00 0.00 0.00 2.77
315 316 4.084013 CGTCTTAAACAGCGAACATCCTTT 60.084 41.667 0.00 0.00 0.00 3.11
359 360 1.874872 GCCGTGTAGCCTAAAACAACA 59.125 47.619 0.00 0.00 0.00 3.33
380 381 0.100503 GGCCAATGTGCGTTGTATCC 59.899 55.000 0.00 0.00 0.00 2.59
381 382 1.094785 AGGCCAATGTGCGTTGTATC 58.905 50.000 5.01 0.00 0.00 2.24
383 384 0.878416 GAAGGCCAATGTGCGTTGTA 59.122 50.000 5.01 0.00 39.26 2.41
385 386 1.080569 GGAAGGCCAATGTGCGTTG 60.081 57.895 5.01 0.00 39.26 4.10
394 395 3.256960 AAGCGGGAGGAAGGCCAA 61.257 61.111 5.01 0.00 36.29 4.52
395 396 3.717294 GAAGCGGGAGGAAGGCCA 61.717 66.667 5.01 0.00 36.29 5.36
398 399 0.543749 AAGATGAAGCGGGAGGAAGG 59.456 55.000 0.00 0.00 0.00 3.46
406 407 1.137872 AGGAGCTACAAGATGAAGCGG 59.862 52.381 0.00 0.00 41.19 5.52
419 420 3.693653 AGATCAATCTGGAGCAGGAGCTA 60.694 47.826 0.00 0.00 43.31 3.32
431 432 3.428045 GGAAACGGGCAAAGATCAATCTG 60.428 47.826 0.00 0.00 37.19 2.90
436 437 0.958382 CGGGAAACGGGCAAAGATCA 60.958 55.000 0.00 0.00 39.42 2.92
438 439 2.340328 GCGGGAAACGGGCAAAGAT 61.340 57.895 0.00 0.00 44.51 2.40
439 440 2.981350 GCGGGAAACGGGCAAAGA 60.981 61.111 0.00 0.00 44.51 2.52
449 450 2.033448 ATTGTCGCTGGCGGGAAA 59.967 55.556 14.94 7.57 40.25 3.13
450 451 2.435938 GATTGTCGCTGGCGGGAA 60.436 61.111 14.94 8.32 40.25 3.97
457 458 0.091344 GACGTGTTCGATTGTCGCTG 59.909 55.000 0.00 0.00 40.21 5.18
459 460 1.316735 GTAGACGTGTTCGATTGTCGC 59.683 52.381 0.00 0.00 40.21 5.19
465 466 3.622163 CAGAGGTAGTAGACGTGTTCGAT 59.378 47.826 0.00 0.00 40.62 3.59
480 481 0.532573 CGCTCAAGAAGGCAGAGGTA 59.467 55.000 0.00 0.00 0.00 3.08
486 487 0.179111 CGTATCCGCTCAAGAAGGCA 60.179 55.000 0.00 0.00 0.00 4.75
534 535 0.167908 TTGACGATGAATTGCACGCC 59.832 50.000 0.00 0.00 0.00 5.68
591 592 1.581934 TGGAAGAGAACACAAGCACG 58.418 50.000 0.00 0.00 0.00 5.34
595 596 7.538678 CGGATTTTAAATGGAAGAGAACACAAG 59.461 37.037 0.00 0.00 0.00 3.16
597 598 6.488683 ACGGATTTTAAATGGAAGAGAACACA 59.511 34.615 0.00 0.00 0.00 3.72
614 615 1.868997 CAGCAGCACGACGGATTTT 59.131 52.632 0.00 0.00 0.00 1.82
657 685 2.867472 GCGGATCACGGTGGTTTG 59.133 61.111 8.50 0.00 44.51 2.93
664 692 3.490759 GTGCACAGCGGATCACGG 61.491 66.667 13.17 0.00 44.51 4.94
682 710 1.006086 TATTTGACGATGGTGCTGCG 58.994 50.000 0.00 0.00 0.00 5.18
685 713 2.779755 TGGTATTTGACGATGGTGCT 57.220 45.000 0.00 0.00 0.00 4.40
688 716 7.024768 CGTTAAAAATGGTATTTGACGATGGT 58.975 34.615 9.73 0.00 46.37 3.55
695 723 7.948034 ATCCTCCGTTAAAAATGGTATTTGA 57.052 32.000 0.00 0.00 38.73 2.69
712 740 2.213499 CAGATCCCGAAAAATCCTCCG 58.787 52.381 0.00 0.00 0.00 4.63
714 742 6.678164 GCTTTTACAGATCCCGAAAAATCCTC 60.678 42.308 0.00 0.00 0.00 3.71
723 752 1.739035 CGCTGCTTTTACAGATCCCGA 60.739 52.381 0.00 0.00 40.25 5.14
729 758 0.250295 AGGTGCGCTGCTTTTACAGA 60.250 50.000 9.73 0.00 40.25 3.41
760 789 9.354673 CCATAAATATGGTTTCATAAGGTGTCT 57.645 33.333 10.71 0.00 46.42 3.41
797 826 2.773487 CATCACCAACCGTTCCTGTAA 58.227 47.619 0.00 0.00 0.00 2.41
798 827 1.609580 GCATCACCAACCGTTCCTGTA 60.610 52.381 0.00 0.00 0.00 2.74
799 828 0.889186 GCATCACCAACCGTTCCTGT 60.889 55.000 0.00 0.00 0.00 4.00
800 829 0.606401 AGCATCACCAACCGTTCCTG 60.606 55.000 0.00 0.00 0.00 3.86
801 830 0.321653 GAGCATCACCAACCGTTCCT 60.322 55.000 0.00 0.00 33.17 3.36
802 831 0.321653 AGAGCATCACCAACCGTTCC 60.322 55.000 0.00 0.00 37.82 3.62
803 832 1.523758 AAGAGCATCACCAACCGTTC 58.476 50.000 0.00 0.00 37.82 3.95
824 853 9.095700 AGGGGTTTTTCTGCAACTAAATTATTA 57.904 29.630 0.00 0.00 0.00 0.98
825 854 7.973402 AGGGGTTTTTCTGCAACTAAATTATT 58.027 30.769 0.00 0.00 0.00 1.40
840 869 5.187772 AGCTCAATGGAATTAGGGGTTTTTC 59.812 40.000 0.00 0.00 32.46 2.29
846 875 3.872459 AGAGCTCAATGGAATTAGGGG 57.128 47.619 17.77 0.00 32.46 4.79
854 885 4.094887 GCATTTTCGTTAGAGCTCAATGGA 59.905 41.667 17.77 5.80 0.00 3.41
855 886 4.346129 GCATTTTCGTTAGAGCTCAATGG 58.654 43.478 17.77 2.40 0.00 3.16
856 887 4.346129 GGCATTTTCGTTAGAGCTCAATG 58.654 43.478 17.77 15.19 0.00 2.82
857 888 3.063997 CGGCATTTTCGTTAGAGCTCAAT 59.936 43.478 17.77 1.71 0.00 2.57
858 889 2.415168 CGGCATTTTCGTTAGAGCTCAA 59.585 45.455 17.77 5.49 0.00 3.02
859 890 1.999735 CGGCATTTTCGTTAGAGCTCA 59.000 47.619 17.77 0.00 0.00 4.26
883 916 3.414700 CGGCACACGCAGAGAACC 61.415 66.667 0.00 0.00 41.24 3.62
894 927 2.333926 CGAGTTTAGATTCACGGCACA 58.666 47.619 0.00 0.00 0.00 4.57
923 956 2.108566 CATCAGCCGAGGAGCAGG 59.891 66.667 0.00 0.00 34.23 4.85
926 959 1.520342 GTGACATCAGCCGAGGAGC 60.520 63.158 0.00 0.00 0.00 4.70
1412 1471 2.433239 GCATTAGGTCGAGGGGAAGTTA 59.567 50.000 0.00 0.00 0.00 2.24
1440 1499 2.125912 ACACGATGGCTGCTCGAC 60.126 61.111 16.68 0.00 39.38 4.20
1448 1507 0.523072 ACAATCAAGCACACGATGGC 59.477 50.000 0.00 0.00 0.00 4.40
1476 1535 6.203338 AGCAAGCATAACCAATTTTCAAAGTG 59.797 34.615 0.00 0.00 34.07 3.16
1486 1545 2.819608 ACACGAAGCAAGCATAACCAAT 59.180 40.909 0.00 0.00 0.00 3.16
1548 1607 3.131709 ACATGACCAACCAGAACTCAG 57.868 47.619 0.00 0.00 0.00 3.35
1549 1608 3.576078 AACATGACCAACCAGAACTCA 57.424 42.857 0.00 0.00 0.00 3.41
1550 1609 3.432252 CGTAACATGACCAACCAGAACTC 59.568 47.826 0.00 0.00 0.00 3.01
1551 1610 3.399330 CGTAACATGACCAACCAGAACT 58.601 45.455 0.00 0.00 0.00 3.01
1552 1611 2.482721 CCGTAACATGACCAACCAGAAC 59.517 50.000 0.00 0.00 0.00 3.01
1707 1771 8.177663 GTCACAACATAGGTCATGACAATTAAG 58.822 37.037 26.47 14.35 39.66 1.85
1907 1977 0.242825 CCACTGCAATTCTGGTGCTG 59.757 55.000 0.00 2.26 42.69 4.41
2398 2474 8.454293 AACTCAGCAATATTTATCGACTATCG 57.546 34.615 0.00 0.00 42.10 2.92
2565 2641 6.487668 CCACATGAGAATGCACCTATAAATGA 59.512 38.462 0.00 0.00 0.00 2.57
3241 3320 8.749354 ACAAAAAGAGTTTAAAGACACCAGAAT 58.251 29.630 0.00 0.00 0.00 2.40
3307 3386 9.722056 CCAGAACTTATTCTTCGAAATAATTGG 57.278 33.333 9.85 7.36 42.91 3.16
3317 3396 4.253685 TCTTGCCCAGAACTTATTCTTCG 58.746 43.478 0.00 0.00 42.91 3.79
3613 3692 8.677300 GGAACTAATGCAATAAACTGATCTGAA 58.323 33.333 6.60 0.00 0.00 3.02
3638 3717 0.813184 AAAACATGGCTGAGATGCGG 59.187 50.000 0.00 0.00 0.00 5.69
4426 4724 1.531602 GTTGCTTGGGCCCTTGTCT 60.532 57.895 25.70 0.00 37.74 3.41
4993 5291 8.311109 TGTGTAAAAGTGAGCTATTCTGTGATA 58.689 33.333 0.00 0.00 0.00 2.15
5033 5332 9.121658 AGTACAAGATTAGAACGACATCATAGA 57.878 33.333 0.00 0.00 0.00 1.98
5039 5338 5.105310 AGCCAGTACAAGATTAGAACGACAT 60.105 40.000 0.00 0.00 0.00 3.06
5042 5341 4.219944 ACAGCCAGTACAAGATTAGAACGA 59.780 41.667 0.00 0.00 0.00 3.85
5043 5342 4.495422 ACAGCCAGTACAAGATTAGAACG 58.505 43.478 0.00 0.00 0.00 3.95
5060 5359 6.392625 TCAGTAGATGTATCTGTTACAGCC 57.607 41.667 7.61 0.00 46.21 4.85
5075 5377 7.335422 GGAACATCAAGAAACACATCAGTAGAT 59.665 37.037 0.00 0.00 33.87 1.98
5083 5385 9.911788 AGAATATAGGAACATCAAGAAACACAT 57.088 29.630 0.00 0.00 0.00 3.21
5248 5656 7.715265 ACTAATACGGAGTGCATATGAAAAG 57.285 36.000 6.97 0.00 45.73 2.27
5305 5713 8.967552 TGAGAGAAAAATACGTCTTAGTCTTC 57.032 34.615 0.00 0.00 0.00 2.87
5355 5766 6.065976 AGGATACAAACTGGATTCACATCA 57.934 37.500 0.00 0.00 41.41 3.07
5371 5782 4.017126 ACGTTGATGACTCAGAGGATACA 58.983 43.478 1.53 0.00 32.90 2.29
5384 5795 6.147328 CGTATAGGTCTAGATGACGTTGATGA 59.853 42.308 0.00 0.00 46.24 2.92
5424 5835 0.562177 TAGGTATAGGAACCCCCGCA 59.438 55.000 0.00 0.00 40.71 5.69
5425 5836 0.972134 GTAGGTATAGGAACCCCCGC 59.028 60.000 0.00 0.00 40.71 6.13
5426 5837 2.245582 CTGTAGGTATAGGAACCCCCG 58.754 57.143 0.00 0.00 40.71 5.73
5427 5838 3.341318 ACTGTAGGTATAGGAACCCCC 57.659 52.381 0.00 0.00 40.71 5.40
5428 5839 4.100653 GTCAACTGTAGGTATAGGAACCCC 59.899 50.000 0.00 0.00 40.71 4.95
5429 5840 4.100653 GGTCAACTGTAGGTATAGGAACCC 59.899 50.000 0.00 0.00 40.71 4.11
5430 5841 4.961099 AGGTCAACTGTAGGTATAGGAACC 59.039 45.833 0.00 0.00 40.06 3.62
5431 5842 5.903810 CAGGTCAACTGTAGGTATAGGAAC 58.096 45.833 0.00 0.00 42.42 3.62
5445 5856 3.471680 GTTGAAAGAGCTCAGGTCAACT 58.528 45.455 30.42 6.10 42.96 3.16
5446 5857 3.471680 AGTTGAAAGAGCTCAGGTCAAC 58.528 45.455 30.50 30.50 45.37 3.18
5447 5858 3.389329 AGAGTTGAAAGAGCTCAGGTCAA 59.611 43.478 17.77 17.76 31.89 3.18
5448 5859 2.968574 AGAGTTGAAAGAGCTCAGGTCA 59.031 45.455 17.77 12.80 31.89 4.02
5449 5860 3.006323 TGAGAGTTGAAAGAGCTCAGGTC 59.994 47.826 17.77 10.23 32.36 3.85
5450 5861 2.968574 TGAGAGTTGAAAGAGCTCAGGT 59.031 45.455 17.77 0.00 32.36 4.00
5451 5862 3.244009 TGTGAGAGTTGAAAGAGCTCAGG 60.244 47.826 17.77 0.00 36.39 3.86
5452 5863 3.987547 TGTGAGAGTTGAAAGAGCTCAG 58.012 45.455 17.77 0.00 36.39 3.35
5453 5864 4.313282 CATGTGAGAGTTGAAAGAGCTCA 58.687 43.478 17.77 0.00 33.58 4.26
5454 5865 3.124976 GCATGTGAGAGTTGAAAGAGCTC 59.875 47.826 5.27 5.27 0.00 4.09
5455 5866 3.072944 GCATGTGAGAGTTGAAAGAGCT 58.927 45.455 0.00 0.00 0.00 4.09
5456 5867 2.161211 GGCATGTGAGAGTTGAAAGAGC 59.839 50.000 0.00 0.00 0.00 4.09
5457 5868 3.672808 AGGCATGTGAGAGTTGAAAGAG 58.327 45.455 0.00 0.00 0.00 2.85
5458 5869 3.777106 AGGCATGTGAGAGTTGAAAGA 57.223 42.857 0.00 0.00 0.00 2.52
5459 5870 4.070716 AGAAGGCATGTGAGAGTTGAAAG 58.929 43.478 0.00 0.00 0.00 2.62
5460 5871 3.817084 CAGAAGGCATGTGAGAGTTGAAA 59.183 43.478 0.00 0.00 0.00 2.69
5461 5872 3.181451 ACAGAAGGCATGTGAGAGTTGAA 60.181 43.478 0.00 0.00 0.00 2.69
5462 5873 2.369860 ACAGAAGGCATGTGAGAGTTGA 59.630 45.455 0.00 0.00 0.00 3.18
5463 5874 2.775890 ACAGAAGGCATGTGAGAGTTG 58.224 47.619 0.00 0.00 0.00 3.16
5471 5882 1.901591 CCACTTCACAGAAGGCATGT 58.098 50.000 11.08 0.00 0.00 3.21
5472 5883 0.524862 GCCACTTCACAGAAGGCATG 59.475 55.000 11.08 0.00 41.52 4.06
5473 5884 0.111061 TGCCACTTCACAGAAGGCAT 59.889 50.000 11.08 0.00 44.42 4.40
5474 5885 0.106769 TTGCCACTTCACAGAAGGCA 60.107 50.000 11.08 9.56 46.21 4.75
5475 5886 0.595095 CTTGCCACTTCACAGAAGGC 59.405 55.000 11.08 7.26 41.94 4.35
5476 5887 1.605710 CACTTGCCACTTCACAGAAGG 59.394 52.381 11.08 0.00 0.00 3.46
5477 5888 2.292267 ACACTTGCCACTTCACAGAAG 58.708 47.619 5.28 5.28 0.00 2.85
5478 5889 2.418368 ACACTTGCCACTTCACAGAA 57.582 45.000 0.00 0.00 0.00 3.02
5479 5890 2.418368 AACACTTGCCACTTCACAGA 57.582 45.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.