Multiple sequence alignment - TraesCS1D01G350600

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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 TraesCS1D01G350600 chr1D 100.000 9819 0 0 1 9819 436198502 436188684 0.000000e+00 18133.0
1 TraesCS1D01G350600 chr1D 88.298 94 11 0 5829 5922 407217114 407217207 8.060000e-21 113.0
2 TraesCS1D01G350600 chr1D 88.679 53 6 0 7500 7552 387426651 387426703 2.290000e-06 65.8
3 TraesCS1D01G350600 chr1A 94.994 5753 188 51 4106 9819 533452655 533446964 0.000000e+00 8937.0
4 TraesCS1D01G350600 chr1A 88.393 2645 107 79 556 3145 533456315 533453816 0.000000e+00 3000.0
5 TraesCS1D01G350600 chr1A 92.748 717 31 9 3165 3867 533453719 533453010 0.000000e+00 1016.0
6 TraesCS1D01G350600 chr1A 93.891 311 15 3 3873 4179 533452961 533452651 5.370000e-127 466.0
7 TraesCS1D01G350600 chr1A 88.679 53 6 0 7500 7552 487092092 487092144 2.290000e-06 65.8
8 TraesCS1D01G350600 chr1B 92.742 5856 206 92 88 5847 591118668 591112936 0.000000e+00 8257.0
9 TraesCS1D01G350600 chr1B 93.481 3927 131 38 5976 9819 591112876 591108992 0.000000e+00 5718.0
10 TraesCS1D01G350600 chr1B 95.833 48 2 0 1 48 591118699 591118652 2.940000e-10 78.7
11 TraesCS1D01G350600 chr5B 84.029 407 35 17 1211 1617 383037789 383038165 2.020000e-96 364.0
12 TraesCS1D01G350600 chr3A 79.009 424 74 13 7176 7588 509421516 509421097 9.710000e-70 276.0
13 TraesCS1D01G350600 chr3A 82.819 227 37 2 7789 8015 509420957 509420733 1.670000e-47 202.0
14 TraesCS1D01G350600 chr3A 90.566 53 5 0 7512 7564 601557475 601557423 4.920000e-08 71.3
15 TraesCS1D01G350600 chr3D 82.379 227 38 2 7789 8015 388332532 388332308 7.780000e-46 196.0
16 TraesCS1D01G350600 chr3D 97.674 43 1 0 5836 5878 401895777 401895819 3.800000e-09 75.0
17 TraesCS1D01G350600 chr3B 81.938 227 39 2 7789 8015 504981488 504981264 3.620000e-44 191.0
18 TraesCS1D01G350600 chr3B 88.679 53 6 0 7512 7564 607383460 607383512 2.290000e-06 65.8
19 TraesCS1D01G350600 chr3B 96.875 32 1 0 5897 5928 803561998 803562029 5.000000e-03 54.7
20 TraesCS1D01G350600 chr2B 86.598 97 12 1 5833 5929 361575874 361575969 1.350000e-18 106.0
21 TraesCS1D01G350600 chr4D 86.316 95 6 4 5836 5930 388127917 388128004 8.120000e-16 97.1
22 TraesCS1D01G350600 chr4D 93.333 45 3 0 5834 5878 66786674 66786718 6.360000e-07 67.6
23 TraesCS1D01G350600 chr7B 85.227 88 10 3 5833 5918 556739228 556739142 4.890000e-13 87.9
24 TraesCS1D01G350600 chr5A 97.561 41 1 0 5836 5876 361711208 361711248 4.920000e-08 71.3
25 TraesCS1D01G350600 chr5D 80.000 95 17 2 5833 5926 448333801 448333708 1.770000e-07 69.4


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 TraesCS1D01G350600 chr1D 436188684 436198502 9818 True 18133.000000 18133 100.000000 1 9819 1 chr1D.!!$R1 9818
1 TraesCS1D01G350600 chr1A 533446964 533456315 9351 True 3354.750000 8937 92.506500 556 9819 4 chr1A.!!$R1 9263
2 TraesCS1D01G350600 chr1B 591108992 591118699 9707 True 4684.566667 8257 94.018667 1 9819 3 chr1B.!!$R1 9818
3 TraesCS1D01G350600 chr3A 509420733 509421516 783 True 239.000000 276 80.914000 7176 8015 2 chr3A.!!$R2 839

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
725 732 0.040958 CAGCTTGGCTTTGTCGTCAC 60.041 55.000 0.00 0.00 36.40 3.67 F
1838 1901 0.033699 GCTTCAAATCTCCCTGCCCT 60.034 55.000 0.00 0.00 0.00 5.19 F
2235 2304 0.108281 GCGGAGGTGAAAGAGGTACC 60.108 60.000 2.73 2.73 34.68 3.34 F
3237 3417 0.742281 CTTCTGCCCTCGTCCACATG 60.742 60.000 0.00 0.00 0.00 3.21 F
4117 4354 2.432510 GCCTCACTTCTGTGCTATACCT 59.567 50.000 0.00 0.00 43.49 3.08 F
4819 5132 0.790814 GCAGTTGGAGACGTTGCTAC 59.209 55.000 0.00 0.00 32.76 3.58 F
5776 6116 3.131709 ACACAAGCTAGTCATGCAAGT 57.868 42.857 0.00 0.00 0.00 3.16 F
6403 6779 3.264897 CGTATGCTCCACTGCGCC 61.265 66.667 4.18 0.00 35.36 6.53 F
6591 6967 3.274288 CTTCAATGCCTTCTGGTACTCC 58.726 50.000 0.00 0.00 35.27 3.85 F
8452 8897 2.159028 GCTGTCTAAGGTAGCCTCCAAG 60.159 54.545 0.00 0.00 30.89 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2141 0.033503 GGTTGGGGATTGTAGGGGTG 60.034 60.000 0.00 0.00 0.00 4.61 R
3041 3133 0.464554 CGGGAAGCCAGAAGGAATCC 60.465 60.000 0.00 0.00 39.31 3.01 R
3284 3464 0.911769 TTGTATCCCAGACTGGCCAG 59.088 55.000 31.60 31.60 35.79 4.85 R
4449 4762 0.762418 ATGACCCAACCAACAGTCGA 59.238 50.000 0.00 0.00 31.75 4.20 R
6048 6391 0.176680 GAAGAGCTTCGGATGAGCCA 59.823 55.000 0.00 0.00 35.94 4.75 R
6392 6768 0.737715 GAAGTACTGGCGCAGTGGAG 60.738 60.000 18.70 5.63 45.01 3.86 R
7673 8064 2.040178 AGGGTATAAGGAAGACGCCAG 58.960 52.381 0.00 0.00 0.00 4.85 R
8139 8584 3.005539 AGTGCTGACCGGGCATCT 61.006 61.111 12.52 7.28 41.86 2.90 R
8522 8979 3.667360 ACTAAAACGTGGTGATGGGTAC 58.333 45.455 0.00 0.00 0.00 3.34 R
9580 10069 0.103208 ATTCTGACGGCGAGGTGATC 59.897 55.000 16.62 0.00 0.00 2.92 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
35 36 2.970639 GTAGTGCACGCCCAGAGA 59.029 61.111 12.01 0.00 0.00 3.10
40 41 2.346541 TGCACGCCCAGAGAGAGAG 61.347 63.158 0.00 0.00 0.00 3.20
41 42 2.049185 GCACGCCCAGAGAGAGAGA 61.049 63.158 0.00 0.00 0.00 3.10
42 43 2.003658 GCACGCCCAGAGAGAGAGAG 62.004 65.000 0.00 0.00 0.00 3.20
43 44 0.393673 CACGCCCAGAGAGAGAGAGA 60.394 60.000 0.00 0.00 0.00 3.10
44 45 0.107214 ACGCCCAGAGAGAGAGAGAG 60.107 60.000 0.00 0.00 0.00 3.20
45 46 0.180171 CGCCCAGAGAGAGAGAGAGA 59.820 60.000 0.00 0.00 0.00 3.10
46 47 1.811558 CGCCCAGAGAGAGAGAGAGAG 60.812 61.905 0.00 0.00 0.00 3.20
47 48 1.490490 GCCCAGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
48 49 2.486191 GCCCAGAGAGAGAGAGAGAGAG 60.486 59.091 0.00 0.00 0.00 3.20
49 50 3.041211 CCCAGAGAGAGAGAGAGAGAGA 58.959 54.545 0.00 0.00 0.00 3.10
50 51 3.070734 CCCAGAGAGAGAGAGAGAGAGAG 59.929 56.522 0.00 0.00 0.00 3.20
51 52 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
52 53 4.039004 CCAGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
53 54 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
54 55 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
55 56 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
56 57 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
57 58 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
58 59 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
59 60 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
60 61 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
61 62 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
62 63 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
63 64 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
64 65 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
65 66 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
66 67 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
67 68 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
68 69 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
69 70 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
70 71 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
71 72 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
72 73 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
73 74 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
74 75 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
75 76 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
76 77 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
77 78 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
78 79 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
79 80 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
80 81 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
81 82 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
82 83 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
83 84 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
84 85 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
85 86 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
86 87 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
87 88 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
88 89 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
89 90 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
90 91 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
91 92 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
92 93 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
93 94 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
94 95 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
95 96 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
216 221 4.473520 AGCTCGCCCCCATGTTCG 62.474 66.667 0.00 0.00 0.00 3.95
239 244 3.233980 ATCATGGCGCGCCCTCTA 61.234 61.111 44.42 28.65 34.56 2.43
242 247 2.919856 ATGGCGCGCCCTCTATCT 60.920 61.111 44.42 18.76 34.56 1.98
245 250 2.257067 GCGCGCCCTCTATCTCTC 59.743 66.667 23.24 0.00 0.00 3.20
247 252 0.956410 GCGCGCCCTCTATCTCTCTA 60.956 60.000 23.24 0.00 0.00 2.43
249 254 1.668751 CGCGCCCTCTATCTCTCTATC 59.331 57.143 0.00 0.00 0.00 2.08
250 255 2.021457 GCGCCCTCTATCTCTCTATCC 58.979 57.143 0.00 0.00 0.00 2.59
251 256 2.619332 GCGCCCTCTATCTCTCTATCCA 60.619 54.545 0.00 0.00 0.00 3.41
252 257 3.897239 CGCCCTCTATCTCTCTATCCAT 58.103 50.000 0.00 0.00 0.00 3.41
253 258 3.882888 CGCCCTCTATCTCTCTATCCATC 59.117 52.174 0.00 0.00 0.00 3.51
254 259 3.882888 GCCCTCTATCTCTCTATCCATCG 59.117 52.174 0.00 0.00 0.00 3.84
255 260 3.882888 CCCTCTATCTCTCTATCCATCGC 59.117 52.174 0.00 0.00 0.00 4.58
256 261 4.385199 CCCTCTATCTCTCTATCCATCGCT 60.385 50.000 0.00 0.00 0.00 4.93
333 340 4.785453 CCCCGCCCACTCAAGCTC 62.785 72.222 0.00 0.00 0.00 4.09
342 349 2.268802 ACTCAAGCTCGCTGACCGA 61.269 57.895 0.00 0.00 45.15 4.69
344 351 2.811317 CAAGCTCGCTGACCGACC 60.811 66.667 0.00 0.00 41.89 4.79
345 352 4.421479 AAGCTCGCTGACCGACCG 62.421 66.667 0.00 0.00 41.89 4.79
352 359 4.308458 CTGACCGACCGGCAACCA 62.308 66.667 8.55 1.40 39.32 3.67
353 360 4.308458 TGACCGACCGGCAACCAG 62.308 66.667 8.55 0.00 39.32 4.00
364 371 3.043713 CAACCAGCTCGCTCGCAA 61.044 61.111 0.00 0.00 0.00 4.85
365 372 2.740055 AACCAGCTCGCTCGCAAG 60.740 61.111 0.00 0.00 0.00 4.01
366 373 3.521529 AACCAGCTCGCTCGCAAGT 62.522 57.895 0.00 0.00 39.48 3.16
367 374 3.184683 CCAGCTCGCTCGCAAGTC 61.185 66.667 0.00 0.00 39.48 3.01
368 375 3.540014 CAGCTCGCTCGCAAGTCG 61.540 66.667 0.00 0.00 40.15 4.18
623 630 1.889545 AAGTGAAACCTCAGCTGCTC 58.110 50.000 9.47 0.92 37.80 4.26
632 639 0.814457 CTCAGCTGCTCCTACGACTT 59.186 55.000 9.47 0.00 0.00 3.01
633 640 2.017782 CTCAGCTGCTCCTACGACTTA 58.982 52.381 9.47 0.00 0.00 2.24
634 641 1.743958 TCAGCTGCTCCTACGACTTAC 59.256 52.381 9.47 0.00 0.00 2.34
638 645 0.679002 TGCTCCTACGACTTACCGCT 60.679 55.000 0.00 0.00 0.00 5.52
639 646 1.303309 GCTCCTACGACTTACCGCTA 58.697 55.000 0.00 0.00 0.00 4.26
640 647 1.003008 GCTCCTACGACTTACCGCTAC 60.003 57.143 0.00 0.00 0.00 3.58
641 648 2.283298 CTCCTACGACTTACCGCTACA 58.717 52.381 0.00 0.00 0.00 2.74
642 649 2.877168 CTCCTACGACTTACCGCTACAT 59.123 50.000 0.00 0.00 0.00 2.29
643 650 2.615447 TCCTACGACTTACCGCTACATG 59.385 50.000 0.00 0.00 0.00 3.21
644 651 2.287427 CCTACGACTTACCGCTACATGG 60.287 54.545 0.00 0.00 0.00 3.66
645 652 1.180029 ACGACTTACCGCTACATGGT 58.820 50.000 0.00 0.00 43.62 3.55
722 729 3.749981 CCAGCTTGGCTTTGTCGT 58.250 55.556 0.00 0.00 36.40 4.34
723 730 1.576421 CCAGCTTGGCTTTGTCGTC 59.424 57.895 0.00 0.00 36.40 4.20
724 731 1.165907 CCAGCTTGGCTTTGTCGTCA 61.166 55.000 0.00 0.00 36.40 4.35
725 732 0.040958 CAGCTTGGCTTTGTCGTCAC 60.041 55.000 0.00 0.00 36.40 3.67
726 733 0.179045 AGCTTGGCTTTGTCGTCACT 60.179 50.000 0.00 0.00 33.89 3.41
727 734 1.070134 AGCTTGGCTTTGTCGTCACTA 59.930 47.619 0.00 0.00 33.89 2.74
728 735 1.461127 GCTTGGCTTTGTCGTCACTAG 59.539 52.381 0.00 0.00 0.00 2.57
729 736 2.755650 CTTGGCTTTGTCGTCACTAGT 58.244 47.619 0.00 0.00 0.00 2.57
730 737 3.859627 GCTTGGCTTTGTCGTCACTAGTA 60.860 47.826 0.00 0.00 0.00 1.82
731 738 3.293311 TGGCTTTGTCGTCACTAGTAC 57.707 47.619 0.00 0.00 0.00 2.73
732 739 2.029649 TGGCTTTGTCGTCACTAGTACC 60.030 50.000 0.00 0.00 0.00 3.34
733 740 2.029649 GGCTTTGTCGTCACTAGTACCA 60.030 50.000 0.00 0.00 0.00 3.25
734 741 2.985139 GCTTTGTCGTCACTAGTACCAC 59.015 50.000 0.00 0.00 0.00 4.16
735 742 3.572584 CTTTGTCGTCACTAGTACCACC 58.427 50.000 0.00 0.00 0.00 4.61
736 743 2.275134 TGTCGTCACTAGTACCACCA 57.725 50.000 0.00 0.00 0.00 4.17
737 744 1.881973 TGTCGTCACTAGTACCACCAC 59.118 52.381 0.00 0.00 0.00 4.16
738 745 2.157738 GTCGTCACTAGTACCACCACT 58.842 52.381 0.00 0.00 0.00 4.00
739 746 3.244526 TGTCGTCACTAGTACCACCACTA 60.245 47.826 0.00 0.00 0.00 2.74
758 765 6.094464 ACCACTATTAACCAATCTTTTACGGC 59.906 38.462 0.00 0.00 0.00 5.68
759 766 6.189567 CACTATTAACCAATCTTTTACGGCG 58.810 40.000 4.80 4.80 0.00 6.46
760 767 4.625972 ATTAACCAATCTTTTACGGCGG 57.374 40.909 13.24 0.00 0.00 6.13
761 768 0.524414 AACCAATCTTTTACGGCGGC 59.476 50.000 13.24 0.00 0.00 6.53
762 769 0.322187 ACCAATCTTTTACGGCGGCT 60.322 50.000 13.24 0.00 0.00 5.52
763 770 0.098728 CCAATCTTTTACGGCGGCTG 59.901 55.000 13.24 7.39 0.00 4.85
764 771 0.098728 CAATCTTTTACGGCGGCTGG 59.901 55.000 13.24 1.76 0.00 4.85
765 772 1.654023 AATCTTTTACGGCGGCTGGC 61.654 55.000 13.24 9.52 42.51 4.85
975 1010 1.223501 TATCACCCCTCTCGTCTCCT 58.776 55.000 0.00 0.00 0.00 3.69
976 1011 0.106419 ATCACCCCTCTCGTCTCCTC 60.106 60.000 0.00 0.00 0.00 3.71
977 1012 1.208844 TCACCCCTCTCGTCTCCTCT 61.209 60.000 0.00 0.00 0.00 3.69
978 1013 0.750182 CACCCCTCTCGTCTCCTCTC 60.750 65.000 0.00 0.00 0.00 3.20
979 1014 0.917333 ACCCCTCTCGTCTCCTCTCT 60.917 60.000 0.00 0.00 0.00 3.10
1688 1751 3.197790 CGCGCCATCAAGGGTCTG 61.198 66.667 0.00 0.00 38.09 3.51
1834 1897 2.517959 TGGTTGCTTCAAATCTCCCTG 58.482 47.619 0.00 0.00 0.00 4.45
1835 1898 1.203287 GGTTGCTTCAAATCTCCCTGC 59.797 52.381 0.00 0.00 0.00 4.85
1837 1900 0.323725 TGCTTCAAATCTCCCTGCCC 60.324 55.000 0.00 0.00 0.00 5.36
1838 1901 0.033699 GCTTCAAATCTCCCTGCCCT 60.034 55.000 0.00 0.00 0.00 5.19
1840 1903 0.625849 TTCAAATCTCCCTGCCCTCC 59.374 55.000 0.00 0.00 0.00 4.30
1843 1906 1.341156 AAATCTCCCTGCCCTCCTCG 61.341 60.000 0.00 0.00 0.00 4.63
1852 1915 2.906458 CCCTCCTCGCAGCAATCT 59.094 61.111 0.00 0.00 0.00 2.40
1864 1927 0.807496 AGCAATCTTCAAGCCGCTTC 59.193 50.000 1.56 0.00 0.00 3.86
2078 2141 3.395639 TCTTCGACATGTAACAACCCAC 58.604 45.455 0.00 0.00 0.00 4.61
2079 2142 2.912690 TCGACATGTAACAACCCACA 57.087 45.000 0.00 0.00 0.00 4.17
2143 2206 1.363744 CTCTGAGTCCGCACCATTTC 58.636 55.000 0.00 0.00 0.00 2.17
2145 2208 1.066858 TCTGAGTCCGCACCATTTCTC 60.067 52.381 0.00 0.00 0.00 2.87
2148 2211 2.435938 TCCGCACCATTTCTCGCC 60.436 61.111 0.00 0.00 0.00 5.54
2235 2304 0.108281 GCGGAGGTGAAAGAGGTACC 60.108 60.000 2.73 2.73 34.68 3.34
2245 2314 5.479724 GGTGAAAGAGGTACCACTACTTACT 59.520 44.000 15.94 0.00 34.61 2.24
2348 2423 9.802039 AGTACAAATTCTTCCATTTTGGTAGTA 57.198 29.630 0.00 0.00 39.03 1.82
2350 2425 7.602753 ACAAATTCTTCCATTTTGGTAGTAGC 58.397 34.615 0.89 0.00 39.03 3.58
2362 2437 6.474140 TTTGGTAGTAGCAGAATATTCGGA 57.526 37.500 18.32 0.00 0.00 4.55
2363 2438 5.449107 TGGTAGTAGCAGAATATTCGGAC 57.551 43.478 18.32 9.06 0.00 4.79
2364 2439 5.138276 TGGTAGTAGCAGAATATTCGGACT 58.862 41.667 18.32 14.93 0.00 3.85
2587 2668 7.967303 CCAATCTCTTTCTACATGAGCTTTTTC 59.033 37.037 0.00 0.00 0.00 2.29
2784 2875 9.878667 TTAATCTAATCTATTGTGTTCCGTTGA 57.121 29.630 0.00 0.00 0.00 3.18
2827 2918 2.257353 GCCTAGCCAGGTTGTGTTG 58.743 57.895 0.00 0.00 44.68 3.33
2832 2923 1.555967 AGCCAGGTTGTGTTGTTTGT 58.444 45.000 0.00 0.00 0.00 2.83
2865 2956 4.385358 TTTTCCAAGCTGTGAAAAGGAC 57.615 40.909 15.83 0.00 35.99 3.85
2985 3076 2.104331 CAGAGGAATACGCCGCGT 59.896 61.111 23.72 23.72 44.35 6.01
3041 3133 7.375834 TCGGCTACATTGAGGTATAAACTATG 58.624 38.462 0.00 0.00 0.00 2.23
3074 3166 2.379972 CTTCCCGTCACTATCCTCTGT 58.620 52.381 0.00 0.00 0.00 3.41
3075 3167 1.763968 TCCCGTCACTATCCTCTGTG 58.236 55.000 0.00 0.00 35.68 3.66
3108 3203 1.220529 TGCTTCTCAAGACAGCAACG 58.779 50.000 11.77 0.00 36.23 4.10
3124 3287 3.389687 CAACGCTATTGTTGCTACTGG 57.610 47.619 0.00 0.00 42.34 4.00
3229 3409 2.743636 TGTTTCTACTTCTGCCCTCG 57.256 50.000 0.00 0.00 0.00 4.63
3237 3417 0.742281 CTTCTGCCCTCGTCCACATG 60.742 60.000 0.00 0.00 0.00 3.21
3284 3464 6.509418 TGAACCAATAACCATCTTACTTGC 57.491 37.500 0.00 0.00 0.00 4.01
3770 3951 3.438087 GCACATCTGACTGTATGTTGCTT 59.562 43.478 0.00 0.00 34.12 3.91
3818 3999 2.622942 TCTTTGCCATCCACACTGAAAC 59.377 45.455 0.00 0.00 0.00 2.78
3825 4016 4.370917 CCATCCACACTGAAACCTTTTTG 58.629 43.478 0.00 0.00 0.00 2.44
3853 4044 6.700960 CCTATCAAGAATAGAGACTGTTGCTG 59.299 42.308 0.00 0.00 39.94 4.41
3971 4206 3.071580 GCTCAGTGCCCAGTATCAC 57.928 57.895 0.00 0.00 35.15 3.06
3994 4229 7.335673 TCACTTGTTGTAGAATTGTTGTTCTGA 59.664 33.333 0.00 0.00 38.79 3.27
4117 4354 2.432510 GCCTCACTTCTGTGCTATACCT 59.567 50.000 0.00 0.00 43.49 3.08
4126 4363 7.330454 CACTTCTGTGCTATACCTAATATGCAG 59.670 40.741 0.00 0.00 37.38 4.41
4264 4574 6.049149 TCTTTCTTAGGATGGAGTTATTGCG 58.951 40.000 0.00 0.00 0.00 4.85
4356 4666 4.665009 TCATAATCTTGTGGGGCCTTCTAT 59.335 41.667 0.84 0.00 0.00 1.98
4389 4699 5.473504 GGGCTATTTGACTTTCTGTTCTCAA 59.526 40.000 0.00 0.00 0.00 3.02
4459 4772 7.553881 ACTATGGATAATTTTCGACTGTTGG 57.446 36.000 0.00 0.00 0.00 3.77
4594 4907 8.113062 TGCTTTTAAAATTGAAATGTTCACACG 58.887 29.630 0.09 0.00 39.87 4.49
4763 5076 7.773224 CCATATTCTACTTAATGTTGGGACACA 59.227 37.037 0.00 0.00 39.29 3.72
4819 5132 0.790814 GCAGTTGGAGACGTTGCTAC 59.209 55.000 0.00 0.00 32.76 3.58
5040 5353 5.197451 TGGAAATTTATCCAGTACCGCAAT 58.803 37.500 0.00 0.00 44.52 3.56
5312 5625 7.678837 TGTCCAATAAATTTCCTGCAGAATTT 58.321 30.769 22.45 22.45 33.44 1.82
5314 5627 7.278646 GTCCAATAAATTTCCTGCAGAATTTCC 59.721 37.037 22.47 7.78 33.44 3.13
5315 5628 7.180766 TCCAATAAATTTCCTGCAGAATTTCCT 59.819 33.333 22.47 12.85 33.44 3.36
5384 5700 8.592809 AGATATCTCTCCACACTTTCATTATCC 58.407 37.037 0.00 0.00 0.00 2.59
5419 5735 3.195610 TGTAGACCGCAGTGATTGATCTT 59.804 43.478 0.00 0.00 0.00 2.40
5458 5774 8.020244 GCAACAAAATTTGGTTAAATACATGGG 58.980 33.333 10.64 0.00 35.50 4.00
5465 5781 4.862371 TGGTTAAATACATGGGTCCTTCC 58.138 43.478 0.00 0.00 0.00 3.46
5587 5914 4.000331 TCTGTCTGAAAGCTTTCTCTGG 58.000 45.455 33.03 21.65 38.02 3.86
5635 5962 9.974980 TTAGAAAATGGGTTATGAACTTGAAAC 57.025 29.630 0.00 0.00 0.00 2.78
5671 6011 6.716934 TTACCTGGTTGCTGTTTAAAATCA 57.283 33.333 3.84 0.00 0.00 2.57
5776 6116 3.131709 ACACAAGCTAGTCATGCAAGT 57.868 42.857 0.00 0.00 0.00 3.16
5932 6274 7.361971 GGAACGGAAGGAGTAGTATATAAGCTC 60.362 44.444 0.00 0.00 0.00 4.09
5972 6314 4.095946 AGAGGATGAGAGAAGCTGAAACT 58.904 43.478 0.00 0.00 0.00 2.66
6048 6391 5.186198 CAGTAATAGTTGGGCTGTAAAGCT 58.814 41.667 4.54 0.00 34.73 3.74
6087 6444 6.824553 TCTTCTCATCAGCTAACTAATGCAT 58.175 36.000 0.00 0.00 0.00 3.96
6140 6498 9.042632 CATTTGAACGCACAAAATGAAATAATG 57.957 29.630 10.67 0.00 41.88 1.90
6392 6768 3.717400 TTCCTCAGATGAGACGTATGC 57.283 47.619 11.44 0.00 44.74 3.14
6403 6779 3.264897 CGTATGCTCCACTGCGCC 61.265 66.667 4.18 0.00 35.36 6.53
6591 6967 3.274288 CTTCAATGCCTTCTGGTACTCC 58.726 50.000 0.00 0.00 35.27 3.85
6858 7234 4.956075 GGATATTGAAGGTCAACCCACATT 59.044 41.667 0.00 0.00 39.45 2.71
7673 8064 7.934457 ACTGCAATCTATATCATGTTTCCAAC 58.066 34.615 0.00 0.00 0.00 3.77
8023 8468 7.731054 AGATCAAAGGGTAACTATCAGCTAAG 58.269 38.462 0.00 0.00 0.00 2.18
8025 8470 4.691326 AAGGGTAACTATCAGCTAAGCC 57.309 45.455 0.00 0.00 0.00 4.35
8139 8584 5.306937 TCTCACAAGTGTTTATGAGGAAGGA 59.693 40.000 0.00 0.00 39.27 3.36
8227 8672 3.502979 AGTGTCTGGAACTCGAGTAAGTC 59.497 47.826 20.39 12.88 0.00 3.01
8452 8897 2.159028 GCTGTCTAAGGTAGCCTCCAAG 60.159 54.545 0.00 0.00 30.89 3.61
8522 8979 5.160699 TCATGCTTTTAGCTGCGAAATAG 57.839 39.130 8.71 9.85 42.97 1.73
8550 9013 5.107220 CCATCACCACGTTTTAGTACTTCAC 60.107 44.000 0.00 0.00 0.00 3.18
8551 9014 5.266733 TCACCACGTTTTAGTACTTCACT 57.733 39.130 0.00 0.00 41.62 3.41
8566 9029 6.815641 AGTACTTCACTCAAGATGCAATACAG 59.184 38.462 0.00 0.00 35.82 2.74
8750 9215 3.201290 TGGCAAATGCACGACAAAATTT 58.799 36.364 7.80 0.00 44.36 1.82
8804 9269 6.660094 AGGTAAACCGCACAATAGGAAATTAA 59.340 34.615 0.00 0.00 42.08 1.40
8850 9315 4.198890 TTTGCTTGTTGCGCGCCA 62.199 55.556 30.77 16.58 46.63 5.69
8889 9354 4.156739 GGGAAAGAATCACCTAGTGCTTTG 59.843 45.833 0.00 0.00 32.98 2.77
8903 9368 0.593128 GCTTTGTCGGTGCACTGATT 59.407 50.000 30.13 0.00 33.23 2.57
8937 9420 5.703876 CAATGTTACTCAAGAAAGGAAGCC 58.296 41.667 0.00 0.00 0.00 4.35
9003 9486 8.516234 GGATTCAGAAGTATATATCACTGTCGT 58.484 37.037 0.00 0.00 0.00 4.34
9006 9489 6.486993 TCAGAAGTATATATCACTGTCGTGCT 59.513 38.462 0.00 0.00 40.99 4.40
9009 9492 4.827835 AGTATATATCACTGTCGTGCTGGT 59.172 41.667 0.00 0.00 40.99 4.00
9010 9493 2.299993 ATATCACTGTCGTGCTGGTG 57.700 50.000 0.00 0.00 40.99 4.17
9012 9495 0.610174 ATCACTGTCGTGCTGGTGAT 59.390 50.000 0.00 0.00 42.34 3.06
9014 9497 0.319813 CACTGTCGTGCTGGTGATGA 60.320 55.000 0.00 0.00 33.82 2.92
9016 9499 1.005037 TGTCGTGCTGGTGATGACC 60.005 57.895 0.00 0.00 43.48 4.02
9019 9502 2.358615 GTGCTGGTGATGACCGCA 60.359 61.111 14.56 14.56 46.62 5.69
9064 9547 0.317160 ATGCGGAGTCGACACAAAGA 59.683 50.000 19.50 0.00 39.00 2.52
9065 9548 0.596600 TGCGGAGTCGACACAAAGAC 60.597 55.000 19.50 0.73 39.00 3.01
9206 9691 1.110442 TTGTCAGGCCACAAGTTTGG 58.890 50.000 5.01 1.09 39.98 3.28
9209 9694 1.067060 GTCAGGCCACAAGTTTGGTTC 59.933 52.381 5.01 1.24 39.09 3.62
9250 9737 2.672996 CGGAAACACAGGCAGGGG 60.673 66.667 0.00 0.00 0.00 4.79
9423 9910 1.880027 GGTTGTGTGATGTTGAGACCC 59.120 52.381 0.00 0.00 0.00 4.46
9424 9911 1.880027 GTTGTGTGATGTTGAGACCCC 59.120 52.381 0.00 0.00 0.00 4.95
9426 9913 1.774254 TGTGTGATGTTGAGACCCCTT 59.226 47.619 0.00 0.00 0.00 3.95
9456 9943 6.371809 TTTGTTTGGACTTCTGTGTGATAC 57.628 37.500 0.00 0.00 0.00 2.24
9466 9953 4.270245 TCTGTGTGATACATGTTGCTGA 57.730 40.909 2.30 0.00 38.92 4.26
9517 10004 0.328592 GGGGTCAAGTTCTTCCTCCC 59.671 60.000 0.00 0.00 0.00 4.30
9521 10008 1.636003 GTCAAGTTCTTCCTCCCCCAT 59.364 52.381 0.00 0.00 0.00 4.00
9524 10011 2.041620 CAAGTTCTTCCTCCCCCATGAA 59.958 50.000 0.00 0.00 0.00 2.57
9563 10052 1.278238 GTTCGACGGCTATCACCTTG 58.722 55.000 0.00 0.00 0.00 3.61
9564 10053 0.459585 TTCGACGGCTATCACCTTGC 60.460 55.000 0.00 0.00 0.00 4.01
9565 10054 1.883084 CGACGGCTATCACCTTGCC 60.883 63.158 0.00 0.00 41.76 4.52
9568 10057 4.126524 GGCTATCACCTTGCCGTC 57.873 61.111 0.00 0.00 36.02 4.79
9569 10058 1.220749 GGCTATCACCTTGCCGTCA 59.779 57.895 0.00 0.00 36.02 4.35
9570 10059 1.090052 GGCTATCACCTTGCCGTCAC 61.090 60.000 0.00 0.00 36.02 3.67
9571 10060 1.090052 GCTATCACCTTGCCGTCACC 61.090 60.000 0.00 0.00 0.00 4.02
9572 10061 0.806102 CTATCACCTTGCCGTCACCG 60.806 60.000 0.00 0.00 0.00 4.94
9573 10062 2.845752 TATCACCTTGCCGTCACCGC 62.846 60.000 0.00 0.00 0.00 5.68
9625 10117 9.961265 TTCATCGACGATAATCTAAGTTATGTT 57.039 29.630 10.57 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.963374 TCTCTCTCTCTCTCTCTCTCTGG 59.037 52.174 0.00 0.00 0.00 3.86
35 36 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
40 41 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
41 42 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
42 43 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
43 44 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
44 45 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
45 46 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
46 47 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
47 48 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
48 49 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
49 50 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
50 51 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
51 52 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
52 53 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
53 54 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
54 55 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
55 56 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
56 57 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
57 58 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
58 59 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
59 60 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
60 61 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
61 62 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
62 63 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
63 64 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
64 65 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
65 66 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
66 67 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
67 68 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
68 69 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
69 70 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
70 71 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
71 72 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
72 73 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
73 74 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
74 75 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
75 76 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
76 77 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
77 78 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
78 79 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
79 80 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
80 81 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
81 82 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
82 83 4.038642 GGTCTCTCTCTCTCTCTCTCTCTC 59.961 54.167 0.00 0.00 0.00 3.20
83 84 3.964031 GGTCTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
84 85 3.964031 AGGTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
85 86 3.964031 GAGGTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 37.07 3.10
86 87 3.243569 CGAGGTCTCTCTCTCTCTCTCTC 60.244 56.522 0.00 0.00 37.86 3.20
87 88 2.695666 CGAGGTCTCTCTCTCTCTCTCT 59.304 54.545 0.00 0.00 37.86 3.10
88 89 2.803492 GCGAGGTCTCTCTCTCTCTCTC 60.803 59.091 0.00 0.00 37.86 3.20
89 90 1.139058 GCGAGGTCTCTCTCTCTCTCT 59.861 57.143 0.00 0.00 37.86 3.10
90 91 1.139058 AGCGAGGTCTCTCTCTCTCTC 59.861 57.143 0.00 0.00 37.86 3.20
91 92 1.134401 CAGCGAGGTCTCTCTCTCTCT 60.134 57.143 0.00 0.00 33.20 3.10
92 93 1.299541 CAGCGAGGTCTCTCTCTCTC 58.700 60.000 0.00 0.00 33.20 3.20
93 94 0.107214 CCAGCGAGGTCTCTCTCTCT 60.107 60.000 0.00 0.00 33.20 3.10
94 95 1.101049 CCCAGCGAGGTCTCTCTCTC 61.101 65.000 0.00 0.00 33.20 3.20
95 96 1.077068 CCCAGCGAGGTCTCTCTCT 60.077 63.158 0.00 0.00 35.64 3.10
230 235 2.021457 GGATAGAGAGATAGAGGGCGC 58.979 57.143 0.00 0.00 0.00 6.53
231 236 3.358111 TGGATAGAGAGATAGAGGGCG 57.642 52.381 0.00 0.00 0.00 6.13
234 239 4.780815 AGCGATGGATAGAGAGATAGAGG 58.219 47.826 0.00 0.00 0.00 3.69
239 244 5.827797 GGATAGAAGCGATGGATAGAGAGAT 59.172 44.000 0.00 0.00 0.00 2.75
242 247 4.946772 CAGGATAGAAGCGATGGATAGAGA 59.053 45.833 0.00 0.00 0.00 3.10
245 250 3.430098 GCCAGGATAGAAGCGATGGATAG 60.430 52.174 0.00 0.00 0.00 2.08
247 252 1.277557 GCCAGGATAGAAGCGATGGAT 59.722 52.381 0.00 0.00 0.00 3.41
249 254 0.394192 TGCCAGGATAGAAGCGATGG 59.606 55.000 0.00 0.00 0.00 3.51
250 255 1.607509 CCTGCCAGGATAGAAGCGATG 60.608 57.143 4.15 0.00 37.67 3.84
251 256 0.683973 CCTGCCAGGATAGAAGCGAT 59.316 55.000 4.15 0.00 37.67 4.58
252 257 2.032860 GCCTGCCAGGATAGAAGCGA 62.033 60.000 16.85 0.00 37.67 4.93
253 258 1.596477 GCCTGCCAGGATAGAAGCG 60.596 63.158 16.85 0.00 37.67 4.68
254 259 0.534652 CTGCCTGCCAGGATAGAAGC 60.535 60.000 16.85 0.00 37.67 3.86
255 260 0.534652 GCTGCCTGCCAGGATAGAAG 60.535 60.000 16.85 4.29 42.03 2.85
256 261 1.528824 GCTGCCTGCCAGGATAGAA 59.471 57.895 16.85 0.00 42.03 2.10
348 355 2.740055 CTTGCGAGCGAGCTGGTT 60.740 61.111 0.84 0.00 38.13 3.67
349 356 3.923563 GACTTGCGAGCGAGCTGGT 62.924 63.158 11.96 6.36 38.13 4.00
350 357 3.184683 GACTTGCGAGCGAGCTGG 61.185 66.667 11.96 1.87 38.13 4.85
351 358 3.540014 CGACTTGCGAGCGAGCTG 61.540 66.667 11.96 1.62 44.57 4.24
513 520 4.246206 CGCTCGTGGCCATGCATG 62.246 66.667 20.86 20.19 37.74 4.06
623 630 2.287427 CCATGTAGCGGTAAGTCGTAGG 60.287 54.545 0.00 0.00 0.00 3.18
632 639 1.261938 ACCAGCACCATGTAGCGGTA 61.262 55.000 15.82 0.00 36.44 4.02
633 640 2.268920 CCAGCACCATGTAGCGGT 59.731 61.111 0.00 0.00 37.16 5.68
634 641 1.815421 GACCAGCACCATGTAGCGG 60.815 63.158 12.44 12.44 35.48 5.52
678 685 2.623889 CCGATCTCCAGGAAATACGAGT 59.376 50.000 0.00 0.00 0.00 4.18
706 713 0.040958 GTGACGACAAAGCCAAGCTG 60.041 55.000 0.00 0.00 39.62 4.24
710 717 2.902705 ACTAGTGACGACAAAGCCAA 57.097 45.000 0.00 0.00 0.00 4.52
722 729 6.255287 TGGTTAATAGTGGTGGTACTAGTGA 58.745 40.000 5.39 0.00 36.66 3.41
723 730 6.534475 TGGTTAATAGTGGTGGTACTAGTG 57.466 41.667 5.39 0.00 36.66 2.74
724 731 7.622479 AGATTGGTTAATAGTGGTGGTACTAGT 59.378 37.037 0.00 0.00 36.66 2.57
725 732 8.019656 AGATTGGTTAATAGTGGTGGTACTAG 57.980 38.462 0.00 0.00 36.66 2.57
726 733 7.983166 AGATTGGTTAATAGTGGTGGTACTA 57.017 36.000 0.00 0.00 37.54 1.82
727 734 6.886178 AGATTGGTTAATAGTGGTGGTACT 57.114 37.500 0.00 0.00 34.71 2.73
728 735 7.933215 AAAGATTGGTTAATAGTGGTGGTAC 57.067 36.000 0.00 0.00 0.00 3.34
729 736 9.452287 GTAAAAGATTGGTTAATAGTGGTGGTA 57.548 33.333 0.00 0.00 0.00 3.25
730 737 7.120138 CGTAAAAGATTGGTTAATAGTGGTGGT 59.880 37.037 0.00 0.00 0.00 4.16
731 738 7.414762 CCGTAAAAGATTGGTTAATAGTGGTGG 60.415 40.741 0.00 0.00 0.00 4.61
732 739 7.469260 CCGTAAAAGATTGGTTAATAGTGGTG 58.531 38.462 0.00 0.00 0.00 4.17
733 740 6.094464 GCCGTAAAAGATTGGTTAATAGTGGT 59.906 38.462 0.00 0.00 0.00 4.16
734 741 6.492254 GCCGTAAAAGATTGGTTAATAGTGG 58.508 40.000 0.00 0.00 0.00 4.00
735 742 6.189567 CGCCGTAAAAGATTGGTTAATAGTG 58.810 40.000 0.00 0.00 0.00 2.74
736 743 5.295045 CCGCCGTAAAAGATTGGTTAATAGT 59.705 40.000 0.00 0.00 0.00 2.12
737 744 5.744490 CCGCCGTAAAAGATTGGTTAATAG 58.256 41.667 0.00 0.00 0.00 1.73
738 745 4.035441 GCCGCCGTAAAAGATTGGTTAATA 59.965 41.667 0.00 0.00 0.00 0.98
739 746 3.181494 GCCGCCGTAAAAGATTGGTTAAT 60.181 43.478 0.00 0.00 0.00 1.40
763 770 4.717313 GAATATCCCGGGCCGGCC 62.717 72.222 39.24 38.57 46.86 6.13
764 771 3.268103 ATGAATATCCCGGGCCGGC 62.268 63.158 39.24 24.18 46.86 6.13
766 773 0.673644 GACATGAATATCCCGGGCCG 60.674 60.000 21.46 21.46 0.00 6.13
767 774 0.693049 AGACATGAATATCCCGGGCC 59.307 55.000 18.49 0.00 0.00 5.80
768 775 1.813513 CAGACATGAATATCCCGGGC 58.186 55.000 18.49 0.73 0.00 6.13
769 776 1.349026 AGCAGACATGAATATCCCGGG 59.651 52.381 16.85 16.85 0.00 5.73
830 859 1.898574 CCAGCCAGGCTTTGTCGTT 60.899 57.895 12.86 0.00 36.40 3.85
1066 1105 1.962321 GACGGCTCCTTCCTTCCCTC 61.962 65.000 0.00 0.00 0.00 4.30
1834 1897 2.883267 AAGATTGCTGCGAGGAGGGC 62.883 60.000 0.00 0.00 0.00 5.19
1835 1898 0.813210 GAAGATTGCTGCGAGGAGGG 60.813 60.000 0.00 0.00 0.00 4.30
1837 1900 1.664659 CTTGAAGATTGCTGCGAGGAG 59.335 52.381 0.00 0.00 28.51 3.69
1838 1901 1.730501 CTTGAAGATTGCTGCGAGGA 58.269 50.000 0.00 0.00 28.51 3.71
1840 1903 0.098376 GGCTTGAAGATTGCTGCGAG 59.902 55.000 0.00 0.00 34.62 5.03
1843 1906 4.779819 CGGCTTGAAGATTGCTGC 57.220 55.556 0.00 0.00 0.00 5.25
1846 1909 0.522076 CGAAGCGGCTTGAAGATTGC 60.522 55.000 21.70 1.69 0.00 3.56
1864 1927 4.896829 TAGGAGGGGGAGCGAGCG 62.897 72.222 0.00 0.00 0.00 5.03
2078 2141 0.033503 GGTTGGGGATTGTAGGGGTG 60.034 60.000 0.00 0.00 0.00 4.61
2079 2142 0.478789 TGGTTGGGGATTGTAGGGGT 60.479 55.000 0.00 0.00 0.00 4.95
2235 2304 4.442375 ACAGCAGCAGTAGTAAGTAGTG 57.558 45.455 0.00 0.00 35.40 2.74
2245 2314 3.056821 ACGTATGAAGAACAGCAGCAGTA 60.057 43.478 0.00 0.00 0.00 2.74
2273 2348 2.224942 ACCGGGGTAAAAAGGAAAGGAG 60.225 50.000 6.32 0.00 0.00 3.69
2348 2423 9.908747 ATATACTAGTAGTCCGAATATTCTGCT 57.091 33.333 13.45 10.33 0.00 4.24
2362 2437 9.726438 GCCCAATCATCAAAATATACTAGTAGT 57.274 33.333 8.85 8.14 0.00 2.73
2363 2438 9.167311 GGCCCAATCATCAAAATATACTAGTAG 57.833 37.037 8.85 0.00 0.00 2.57
2364 2439 7.822334 CGGCCCAATCATCAAAATATACTAGTA 59.178 37.037 4.77 4.77 0.00 1.82
2587 2668 2.561419 TCCTCCCGTGTTTCTAGAACAG 59.439 50.000 4.18 0.00 0.00 3.16
2775 2866 3.249799 TGTCACAATCACATCAACGGAAC 59.750 43.478 0.00 0.00 0.00 3.62
2777 2868 3.118905 TGTCACAATCACATCAACGGA 57.881 42.857 0.00 0.00 0.00 4.69
2779 2870 4.613866 CACAATGTCACAATCACATCAACG 59.386 41.667 0.00 0.00 33.12 4.10
2780 2871 5.522456 ACACAATGTCACAATCACATCAAC 58.478 37.500 0.00 0.00 33.12 3.18
2782 2873 6.874288 TTACACAATGTCACAATCACATCA 57.126 33.333 0.00 0.00 33.12 3.07
2783 2874 6.803320 CCTTTACACAATGTCACAATCACATC 59.197 38.462 0.00 0.00 33.12 3.06
2784 2875 6.294675 CCCTTTACACAATGTCACAATCACAT 60.295 38.462 0.00 0.00 35.94 3.21
2827 2918 3.489416 GGAAAAAGGCACGATGAACAAAC 59.511 43.478 0.00 0.00 0.00 2.93
2832 2923 2.288152 GCTTGGAAAAAGGCACGATGAA 60.288 45.455 0.00 0.00 0.00 2.57
2865 2956 2.988010 TCATCAGGATTCAGGAACCG 57.012 50.000 0.00 0.00 0.00 4.44
2985 3076 2.968574 GGTCTAGCTCCTCCATGATCAA 59.031 50.000 0.00 0.00 0.00 2.57
3041 3133 0.464554 CGGGAAGCCAGAAGGAATCC 60.465 60.000 0.00 0.00 39.31 3.01
3074 3166 6.219417 TGAGAAGCAAAATTTCAAGGAACA 57.781 33.333 0.00 0.00 0.00 3.18
3075 3167 6.980397 TCTTGAGAAGCAAAATTTCAAGGAAC 59.020 34.615 11.83 0.00 42.96 3.62
3108 3203 5.371115 TGTTTTCCAGTAGCAACAATAGC 57.629 39.130 0.00 0.00 0.00 2.97
3155 3321 1.822990 AGAGCAATGGCATTTGACTGG 59.177 47.619 10.65 0.00 44.61 4.00
3229 3409 7.554835 TGGGTATGTTAAAATAGACATGTGGAC 59.445 37.037 1.15 0.00 37.12 4.02
3237 3417 9.016438 TCAACCTTTGGGTATGTTAAAATAGAC 57.984 33.333 0.00 0.00 46.67 2.59
3284 3464 0.911769 TTGTATCCCAGACTGGCCAG 59.088 55.000 31.60 31.60 35.79 4.85
3491 3672 1.604604 CCCTTCTTCAGCGAACCAAA 58.395 50.000 0.00 0.00 0.00 3.28
3608 3789 4.702131 AGCATGATCAGGGTTCTTTGTTAC 59.298 41.667 6.19 0.00 0.00 2.50
3787 3968 5.414454 TGTGGATGGCAAAGATAAACTACAC 59.586 40.000 0.00 0.00 0.00 2.90
3825 4016 7.598493 GCAACAGTCTCTATTCTTGATAGGATC 59.402 40.741 0.00 0.00 38.62 3.36
3844 4035 2.282040 GCTCCTGCCAGCAACAGT 60.282 61.111 0.00 0.00 39.43 3.55
3867 4058 8.040727 CGGTGGATATAATTTGACTATGGATGA 58.959 37.037 0.00 0.00 0.00 2.92
3994 4229 5.562298 AGTAATTGTAACCCTGGCGATAT 57.438 39.130 0.00 0.00 0.00 1.63
4117 4354 7.880160 AATGGAACTAAAGCACTGCATATTA 57.120 32.000 3.30 0.00 0.00 0.98
4264 4574 3.429410 GCTAAATCTTGGGGAACATGCAC 60.429 47.826 0.00 0.00 0.00 4.57
4356 4666 4.650972 AGTCAAATAGCCCACCAAACTA 57.349 40.909 0.00 0.00 0.00 2.24
4389 4699 1.877443 GGTTAACGGTGCACATCAGTT 59.123 47.619 20.43 19.09 0.00 3.16
4444 4754 3.028130 ACCCAACCAACAGTCGAAAATT 58.972 40.909 0.00 0.00 0.00 1.82
4445 4755 2.621526 GACCCAACCAACAGTCGAAAAT 59.378 45.455 0.00 0.00 0.00 1.82
4449 4762 0.762418 ATGACCCAACCAACAGTCGA 59.238 50.000 0.00 0.00 31.75 4.20
4459 4772 5.897377 ACTAAAACAGCATATGACCCAAC 57.103 39.130 6.97 0.00 0.00 3.77
4546 4859 5.519722 CACAGAACACACTTTTATCCAACC 58.480 41.667 0.00 0.00 0.00 3.77
4659 4972 5.530915 TCAATTTGGCCTATCGATAAACCAG 59.469 40.000 19.83 12.21 0.00 4.00
4668 4981 2.554032 GTCCCATCAATTTGGCCTATCG 59.446 50.000 3.32 0.00 35.29 2.92
4819 5132 4.307443 TCACGTATGTATCCTTCTGCAG 57.693 45.455 7.63 7.63 0.00 4.41
4905 5218 1.448985 TTTTTCGGATCGGGCTCTTG 58.551 50.000 0.00 0.00 0.00 3.02
5040 5353 4.202040 CCCATCACACTAAATACGTACCGA 60.202 45.833 0.00 0.00 0.00 4.69
5312 5625 2.104792 CTGGGTCTGTTCAGAACAAGGA 59.895 50.000 16.85 9.03 41.61 3.36
5314 5627 2.104792 TCCTGGGTCTGTTCAGAACAAG 59.895 50.000 16.85 15.69 41.61 3.16
5315 5628 2.123589 TCCTGGGTCTGTTCAGAACAA 58.876 47.619 16.85 7.40 41.61 2.83
5328 5641 8.912988 CAACACATACAAAAATATATCCTGGGT 58.087 33.333 0.00 0.00 0.00 4.51
5384 5700 3.486542 GCGGTCTACAGAAACTAGGTACG 60.487 52.174 0.00 0.00 0.00 3.67
5419 5735 8.933807 CCAAATTTTGTTGCATCACATGTATTA 58.066 29.630 0.00 0.00 0.00 0.98
5635 5962 7.276218 CAGCAACCAGGTAAAATATGATTGTTG 59.724 37.037 0.00 0.00 34.15 3.33
5650 5977 5.806654 ATGATTTTAAACAGCAACCAGGT 57.193 34.783 0.00 0.00 0.00 4.00
5671 6011 9.646522 ACATAAGATAACAGGAGCCAATAAAAT 57.353 29.630 0.00 0.00 0.00 1.82
5731 6071 6.506500 AGTCAAATACTGCTGATGGAAAAG 57.493 37.500 0.00 0.00 36.93 2.27
5776 6116 1.562942 AGCATGCCTTCAGGATCTGAA 59.437 47.619 15.66 9.60 46.50 3.02
5932 6274 6.555463 TCCTCTTAATTTAGGTGGGTACAG 57.445 41.667 6.76 0.00 34.30 2.74
5972 6314 3.433343 TCCGACTTCTGTATGGTACCAA 58.567 45.455 20.76 5.65 0.00 3.67
6048 6391 0.176680 GAAGAGCTTCGGATGAGCCA 59.823 55.000 0.00 0.00 35.94 4.75
6392 6768 0.737715 GAAGTACTGGCGCAGTGGAG 60.738 60.000 18.70 5.63 45.01 3.86
6403 6779 1.204941 CTTGGTCTCCCCGAAGTACTG 59.795 57.143 0.00 0.00 35.15 2.74
6438 6814 2.111972 ACCCTCCACTCCTCTGACTAAA 59.888 50.000 0.00 0.00 0.00 1.85
6465 6841 4.188462 TGCAGACAACCATAATAACTCCG 58.812 43.478 0.00 0.00 0.00 4.63
6591 6967 8.611654 TGTATACAATGATGAACAGATGATGG 57.388 34.615 2.20 0.00 0.00 3.51
7468 7852 9.672673 AAAACATCATACTTGCTATAGTCTTGT 57.327 29.630 0.84 0.00 0.00 3.16
7673 8064 2.040178 AGGGTATAAGGAAGACGCCAG 58.960 52.381 0.00 0.00 0.00 4.85
7751 8142 9.752961 GCCTAGTTTTTCATAGTTTTGGTAAAA 57.247 29.630 0.00 0.00 0.00 1.52
8023 8468 3.119495 ACAGTGTGTCACTTGAAAAAGGC 60.119 43.478 12.92 0.00 42.59 4.35
8025 8470 5.046910 ACACAGTGTGTCACTTGAAAAAG 57.953 39.130 23.27 0.00 43.92 2.27
8139 8584 3.005539 AGTGCTGACCGGGCATCT 61.006 61.111 12.52 7.28 41.86 2.90
8227 8672 4.865925 CCAATTGGCATGTCATAACTTGTG 59.134 41.667 12.53 0.00 34.04 3.33
8493 8938 3.861886 GCAGCTAAAAGCATGAAAAGGCA 60.862 43.478 0.00 0.00 45.56 4.75
8522 8979 3.667360 ACTAAAACGTGGTGATGGGTAC 58.333 45.455 0.00 0.00 0.00 3.34
8550 9013 4.690184 TGTTGCTGTATTGCATCTTGAG 57.310 40.909 0.00 0.00 42.96 3.02
8551 9014 6.756299 TTATGTTGCTGTATTGCATCTTGA 57.244 33.333 0.00 0.00 42.96 3.02
8566 9029 5.335127 CCAGAACTGTGCTATTTATGTTGC 58.665 41.667 0.00 0.00 0.00 4.17
8624 9087 6.088824 CAGTTACCTTCTTTGCAATGATCAC 58.911 40.000 15.04 8.24 0.00 3.06
8657 9120 3.338249 GCAATAGAACACTCCTGCAAGA 58.662 45.455 0.00 0.00 34.07 3.02
8750 9215 4.219070 CAGAAATGCTCCTTGTGGAATTCA 59.781 41.667 7.93 0.00 42.66 2.57
8850 9315 0.772124 TCCCTTGCTCCCCAAAGTCT 60.772 55.000 0.00 0.00 31.94 3.24
8859 9324 2.095461 GGTGATTCTTTCCCTTGCTCC 58.905 52.381 0.00 0.00 0.00 4.70
8903 9368 2.739913 GAGTAACATTGCGTAACTGGCA 59.260 45.455 0.00 0.00 38.93 4.92
8919 9384 2.290071 CCCGGCTTCCTTTCTTGAGTAA 60.290 50.000 0.00 0.00 0.00 2.24
8937 9420 0.674534 GTACTACCAGCTGATCCCCG 59.325 60.000 17.39 0.00 0.00 5.73
8998 9481 1.005037 GGTCATCACCAGCACGACA 60.005 57.895 0.00 0.00 43.17 4.35
9003 9486 2.358615 GTGCGGTCATCACCAGCA 60.359 61.111 1.51 1.51 44.02 4.41
9009 9492 1.262417 TTACAGAGGTGCGGTCATCA 58.738 50.000 0.00 0.00 0.00 3.07
9010 9493 2.380084 TTTACAGAGGTGCGGTCATC 57.620 50.000 0.00 0.00 0.00 2.92
9012 9495 2.301870 AGATTTTACAGAGGTGCGGTCA 59.698 45.455 0.00 0.00 0.00 4.02
9014 9497 2.354805 GGAGATTTTACAGAGGTGCGGT 60.355 50.000 0.00 0.00 0.00 5.68
9016 9499 3.252974 AGGAGATTTTACAGAGGTGCG 57.747 47.619 0.00 0.00 0.00 5.34
9019 9502 6.295349 CCGCATATAGGAGATTTTACAGAGGT 60.295 42.308 0.00 0.00 0.00 3.85
9064 9547 5.965033 AACCATATTCAGGAGATCAGTGT 57.035 39.130 0.00 0.00 0.00 3.55
9065 9548 7.389884 CCATAAACCATATTCAGGAGATCAGTG 59.610 40.741 0.00 0.00 0.00 3.66
9209 9694 8.808529 CCGTCTGTATAATTACAAAGTGAGAAG 58.191 37.037 0.00 0.00 37.86 2.85
9250 9737 7.964604 AAAGAATCAAACTGTACTGTACTCC 57.035 36.000 17.98 0.00 0.00 3.85
9423 9910 4.632538 AGTCCAAACAAAAACGAGAAGG 57.367 40.909 0.00 0.00 0.00 3.46
9424 9911 5.739161 CAGAAGTCCAAACAAAAACGAGAAG 59.261 40.000 0.00 0.00 0.00 2.85
9426 9913 4.698304 ACAGAAGTCCAAACAAAAACGAGA 59.302 37.500 0.00 0.00 0.00 4.04
9456 9943 5.761165 TTCCATACATCATCAGCAACATG 57.239 39.130 0.00 0.00 0.00 3.21
9481 9968 4.202357 TGACCCCCTTCTCAAATATGATCG 60.202 45.833 0.00 0.00 34.37 3.69
9497 9984 0.328592 GGAGGAAGAACTTGACCCCC 59.671 60.000 0.00 0.00 0.00 5.40
9517 10004 0.179067 GCAATGGCCATGTTCATGGG 60.179 55.000 26.55 14.41 41.94 4.00
9521 10008 0.889994 GACAGCAATGGCCATGTTCA 59.110 50.000 21.63 0.00 42.56 3.18
9524 10011 2.703798 GCGACAGCAATGGCCATGT 61.704 57.895 21.63 15.03 44.35 3.21
9531 10018 2.096406 CGAACCGCGACAGCAATG 59.904 61.111 8.23 0.00 45.49 2.82
9532 10019 2.048597 TCGAACCGCGACAGCAAT 60.049 55.556 8.23 0.00 45.59 3.56
9572 10061 2.951745 CGAGGTGATCGCTGTCGC 60.952 66.667 15.34 0.00 45.98 5.19
9580 10069 0.103208 ATTCTGACGGCGAGGTGATC 59.897 55.000 16.62 0.00 0.00 2.92
9581 10070 0.537188 AATTCTGACGGCGAGGTGAT 59.463 50.000 16.62 0.00 0.00 3.06
9582 10071 0.108804 GAATTCTGACGGCGAGGTGA 60.109 55.000 16.62 3.02 0.00 4.02
9583 10072 0.389817 TGAATTCTGACGGCGAGGTG 60.390 55.000 16.62 0.26 0.00 4.00
9584 10073 0.537188 ATGAATTCTGACGGCGAGGT 59.463 50.000 16.62 0.00 0.00 3.85
9585 10074 1.212616 GATGAATTCTGACGGCGAGG 58.787 55.000 16.62 2.73 0.00 4.63
9586 10075 0.848942 CGATGAATTCTGACGGCGAG 59.151 55.000 16.62 0.25 0.00 5.03
9683 10175 9.855021 GATCTTTAGAGCCTGATATAGAACTTC 57.145 37.037 0.00 0.00 0.00 3.01
9694 10186 7.617723 AGTTTCTTAGAGATCTTTAGAGCCTGA 59.382 37.037 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.