Multiple sequence alignment - TraesCS4A01G087700

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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 TraesCS4A01G087700 chr4A 100.000 5498 0 0 1 5498 92221835 92216338 0.000000e+00 10154.0
1 TraesCS4A01G087700 chr4B 91.094 2998 151 41 217 3183 456593682 456596594 0.000000e+00 3951.0
2 TraesCS4A01G087700 chr4B 90.878 1732 104 16 3228 4939 456596780 456598477 0.000000e+00 2274.0
3 TraesCS4A01G087700 chr4B 88.592 561 23 13 4935 5461 456598501 456599054 1.290000e-180 643.0
4 TraesCS4A01G087700 chr4B 100.000 75 0 0 3189 3263 456596655 456596729 7.430000e-29 139.0
5 TraesCS4A01G087700 chr4B 97.436 39 1 0 3295 3333 456596731 456596769 3.550000e-07 67.6
6 TraesCS4A01G087700 chr4D 93.170 1713 62 16 493 2191 371789294 371790965 0.000000e+00 2464.0
7 TraesCS4A01G087700 chr4D 95.260 1308 44 7 3642 4939 371792616 371793915 0.000000e+00 2056.0
8 TraesCS4A01G087700 chr4D 96.953 919 27 1 2266 3183 371791092 371792010 0.000000e+00 1541.0
9 TraesCS4A01G087700 chr4D 98.065 465 9 0 3181 3645 371792072 371792536 0.000000e+00 809.0
10 TraesCS4A01G087700 chr4D 88.730 559 26 9 4935 5461 371793940 371794493 0.000000e+00 649.0
11 TraesCS4A01G087700 chr4D 91.273 275 19 3 201 474 371788968 371789238 2.420000e-98 370.0
12 TraesCS4A01G087700 chr4D 97.297 37 1 0 5462 5498 371794546 371794582 4.600000e-06 63.9
13 TraesCS4A01G087700 chr1B 90.446 157 13 2 3972 4128 634284941 634285095 7.220000e-49 206.0
14 TraesCS4A01G087700 chr2D 89.565 115 11 1 3816 3929 6750681 6750567 1.600000e-30 145.0
15 TraesCS4A01G087700 chr6B 82.653 98 9 6 1243 1336 626892255 626892162 4.570000e-11 80.5
16 TraesCS4A01G087700 chr6A 82.653 98 9 6 1243 1336 560574889 560574796 4.570000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G087700 chr4A 92216338 92221835 5497 True 10154.000000 10154 100.000000 1 5498 1 chr4A.!!$R1 5497
1 TraesCS4A01G087700 chr4B 456593682 456599054 5372 False 1414.920000 3951 93.600000 217 5461 5 chr4B.!!$F1 5244
2 TraesCS4A01G087700 chr4D 371788968 371794582 5614 False 1136.128571 2464 94.392571 201 5498 7 chr4D.!!$F1 5297

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
104 105 0.107654 GACGATGGTGAGGGAAAGGG 60.108 60.0 0.00 0.0 0.00 3.95 F
500 543 0.110823 GAGCAAACGTAACGCTGGTG 60.111 55.0 10.62 0.0 35.75 4.17 F
2213 2271 0.176910 GACTAGAAGCTCACTGGCCC 59.823 60.0 0.00 0.0 0.00 5.80 F
2908 3066 0.462759 CTCCCCGATCTTCCAGTTGC 60.463 60.0 0.00 0.0 0.00 4.17 F
4077 4479 0.818040 GAGTTTGGGTTGCACGGTCT 60.818 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2059 0.242286 CGCTGATCCCCTCATAGACG 59.758 60.000 0.00 0.0 32.10 4.18 R
2487 2643 0.381089 GATGCTGCAGTCCTTCATGC 59.619 55.000 16.64 0.0 42.86 4.06 R
3894 4292 1.666888 CCAAGAATGTCCGCAGCAAAC 60.667 52.381 0.00 0.0 0.00 2.93 R
4299 4702 0.255890 TAGGAATTGCTGGTGGCTCC 59.744 55.000 10.10 0.0 42.39 4.70 R
5442 5924 0.036306 AAGTCGGCGAAGTCCCAAAT 59.964 50.000 12.92 0.0 0.00 2.32 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 5.855740 TTCAAAACATCTTTTTACGGGGT 57.144 34.783 0.00 0.00 0.00 4.95
23 24 5.855740 TCAAAACATCTTTTTACGGGGTT 57.144 34.783 0.00 0.00 0.00 4.11
24 25 6.223351 TCAAAACATCTTTTTACGGGGTTT 57.777 33.333 0.00 0.00 0.00 3.27
25 26 6.641474 TCAAAACATCTTTTTACGGGGTTTT 58.359 32.000 0.00 0.00 37.43 2.43
26 27 6.757478 TCAAAACATCTTTTTACGGGGTTTTC 59.243 34.615 0.00 0.00 35.51 2.29
27 28 5.855740 AACATCTTTTTACGGGGTTTTCA 57.144 34.783 0.00 0.00 0.00 2.69
28 29 6.413783 AACATCTTTTTACGGGGTTTTCAT 57.586 33.333 0.00 0.00 0.00 2.57
29 30 6.020971 ACATCTTTTTACGGGGTTTTCATC 57.979 37.500 0.00 0.00 0.00 2.92
30 31 4.752661 TCTTTTTACGGGGTTTTCATCG 57.247 40.909 0.00 0.00 0.00 3.84
31 32 3.502979 TCTTTTTACGGGGTTTTCATCGG 59.497 43.478 0.00 0.00 0.00 4.18
32 33 2.565046 TTTACGGGGTTTTCATCGGT 57.435 45.000 0.00 0.00 0.00 4.69
33 34 2.565046 TTACGGGGTTTTCATCGGTT 57.435 45.000 0.00 0.00 0.00 4.44
34 35 2.565046 TACGGGGTTTTCATCGGTTT 57.435 45.000 0.00 0.00 0.00 3.27
35 36 1.241165 ACGGGGTTTTCATCGGTTTC 58.759 50.000 0.00 0.00 0.00 2.78
36 37 1.202842 ACGGGGTTTTCATCGGTTTCT 60.203 47.619 0.00 0.00 0.00 2.52
37 38 2.038820 ACGGGGTTTTCATCGGTTTCTA 59.961 45.455 0.00 0.00 0.00 2.10
38 39 2.417586 CGGGGTTTTCATCGGTTTCTAC 59.582 50.000 0.00 0.00 0.00 2.59
39 40 3.414269 GGGGTTTTCATCGGTTTCTACA 58.586 45.455 0.00 0.00 0.00 2.74
40 41 4.014406 GGGGTTTTCATCGGTTTCTACAT 58.986 43.478 0.00 0.00 0.00 2.29
41 42 4.142469 GGGGTTTTCATCGGTTTCTACATG 60.142 45.833 0.00 0.00 0.00 3.21
42 43 4.698304 GGGTTTTCATCGGTTTCTACATGA 59.302 41.667 0.00 0.00 0.00 3.07
43 44 5.357032 GGGTTTTCATCGGTTTCTACATGAT 59.643 40.000 0.00 0.00 0.00 2.45
44 45 6.540914 GGGTTTTCATCGGTTTCTACATGATA 59.459 38.462 0.00 0.00 0.00 2.15
45 46 7.228706 GGGTTTTCATCGGTTTCTACATGATAT 59.771 37.037 0.00 0.00 0.00 1.63
46 47 8.621286 GGTTTTCATCGGTTTCTACATGATATT 58.379 33.333 0.00 0.00 0.00 1.28
47 48 9.651718 GTTTTCATCGGTTTCTACATGATATTC 57.348 33.333 0.00 0.00 0.00 1.75
48 49 9.613428 TTTTCATCGGTTTCTACATGATATTCT 57.387 29.630 0.00 0.00 0.00 2.40
49 50 8.818141 TTCATCGGTTTCTACATGATATTCTC 57.182 34.615 0.00 0.00 0.00 2.87
50 51 7.378966 TCATCGGTTTCTACATGATATTCTCC 58.621 38.462 0.00 0.00 0.00 3.71
51 52 6.097915 TCGGTTTCTACATGATATTCTCCC 57.902 41.667 0.00 0.00 0.00 4.30
52 53 4.923871 CGGTTTCTACATGATATTCTCCCG 59.076 45.833 0.00 0.00 0.00 5.14
53 54 5.238583 GGTTTCTACATGATATTCTCCCGG 58.761 45.833 0.00 0.00 0.00 5.73
54 55 5.221661 GGTTTCTACATGATATTCTCCCGGT 60.222 44.000 0.00 0.00 0.00 5.28
55 56 6.289064 GTTTCTACATGATATTCTCCCGGTT 58.711 40.000 0.00 0.00 0.00 4.44
56 57 6.494666 TTCTACATGATATTCTCCCGGTTT 57.505 37.500 0.00 0.00 0.00 3.27
57 58 6.097915 TCTACATGATATTCTCCCGGTTTC 57.902 41.667 0.00 0.00 0.00 2.78
58 59 4.771114 ACATGATATTCTCCCGGTTTCA 57.229 40.909 0.00 0.00 0.00 2.69
59 60 5.310409 ACATGATATTCTCCCGGTTTCAT 57.690 39.130 0.00 0.00 0.00 2.57
60 61 5.308825 ACATGATATTCTCCCGGTTTCATC 58.691 41.667 0.00 0.00 0.00 2.92
61 62 5.072329 ACATGATATTCTCCCGGTTTCATCT 59.928 40.000 0.00 0.00 0.00 2.90
62 63 4.960938 TGATATTCTCCCGGTTTCATCTG 58.039 43.478 0.00 0.00 0.00 2.90
63 64 2.717639 ATTCTCCCGGTTTCATCTGG 57.282 50.000 0.00 0.00 0.00 3.86
64 65 1.651737 TTCTCCCGGTTTCATCTGGA 58.348 50.000 0.00 0.00 36.02 3.86
65 66 1.879575 TCTCCCGGTTTCATCTGGAT 58.120 50.000 0.00 0.00 36.02 3.41
66 67 2.196595 TCTCCCGGTTTCATCTGGATT 58.803 47.619 0.00 0.00 36.02 3.01
67 68 2.576191 TCTCCCGGTTTCATCTGGATTT 59.424 45.455 0.00 0.00 36.02 2.17
68 69 2.684881 CTCCCGGTTTCATCTGGATTTG 59.315 50.000 0.00 0.00 36.02 2.32
69 70 1.134946 CCCGGTTTCATCTGGATTTGC 59.865 52.381 0.00 0.00 36.02 3.68
70 71 1.202177 CCGGTTTCATCTGGATTTGCG 60.202 52.381 0.00 0.00 36.02 4.85
71 72 1.468520 CGGTTTCATCTGGATTTGCGT 59.531 47.619 0.00 0.00 0.00 5.24
72 73 2.675844 CGGTTTCATCTGGATTTGCGTA 59.324 45.455 0.00 0.00 0.00 4.42
73 74 3.242413 CGGTTTCATCTGGATTTGCGTAG 60.242 47.826 0.00 0.00 0.00 3.51
74 75 3.938963 GGTTTCATCTGGATTTGCGTAGA 59.061 43.478 0.00 0.00 0.00 2.59
75 76 4.034510 GGTTTCATCTGGATTTGCGTAGAG 59.965 45.833 0.00 0.00 0.00 2.43
76 77 3.459232 TCATCTGGATTTGCGTAGAGG 57.541 47.619 0.00 0.00 0.00 3.69
77 78 3.031013 TCATCTGGATTTGCGTAGAGGA 58.969 45.455 0.00 0.00 0.00 3.71
78 79 3.450817 TCATCTGGATTTGCGTAGAGGAA 59.549 43.478 0.00 0.00 28.39 3.36
79 80 3.526931 TCTGGATTTGCGTAGAGGAAG 57.473 47.619 0.00 0.00 0.00 3.46
80 81 2.168521 TCTGGATTTGCGTAGAGGAAGG 59.831 50.000 0.00 0.00 0.00 3.46
81 82 1.300481 GGATTTGCGTAGAGGAAGGC 58.700 55.000 0.00 0.00 0.00 4.35
82 83 0.931005 GATTTGCGTAGAGGAAGGCG 59.069 55.000 0.00 0.00 32.99 5.52
86 87 3.515286 CGTAGAGGAAGGCGCCGA 61.515 66.667 23.20 0.00 0.00 5.54
87 88 2.104530 GTAGAGGAAGGCGCCGAC 59.895 66.667 23.20 18.74 0.00 4.79
88 89 3.515286 TAGAGGAAGGCGCCGACG 61.515 66.667 23.20 0.00 44.07 5.12
89 90 3.982316 TAGAGGAAGGCGCCGACGA 62.982 63.158 23.20 5.48 43.93 4.20
90 91 4.208686 GAGGAAGGCGCCGACGAT 62.209 66.667 23.20 7.43 43.93 3.73
91 92 4.514577 AGGAAGGCGCCGACGATG 62.515 66.667 23.20 0.00 43.93 3.84
93 94 4.814294 GAAGGCGCCGACGATGGT 62.814 66.667 23.20 0.00 43.93 3.55
98 99 4.873129 CGCCGACGATGGTGAGGG 62.873 72.222 0.00 0.00 42.25 4.30
99 100 3.458163 GCCGACGATGGTGAGGGA 61.458 66.667 0.00 0.00 0.00 4.20
100 101 3.014085 GCCGACGATGGTGAGGGAA 62.014 63.158 0.00 0.00 0.00 3.97
101 102 1.594833 CCGACGATGGTGAGGGAAA 59.405 57.895 0.00 0.00 0.00 3.13
102 103 0.460284 CCGACGATGGTGAGGGAAAG 60.460 60.000 0.00 0.00 0.00 2.62
103 104 0.460284 CGACGATGGTGAGGGAAAGG 60.460 60.000 0.00 0.00 0.00 3.11
104 105 0.107654 GACGATGGTGAGGGAAAGGG 60.108 60.000 0.00 0.00 0.00 3.95
105 106 1.452108 CGATGGTGAGGGAAAGGGC 60.452 63.158 0.00 0.00 0.00 5.19
106 107 1.452108 GATGGTGAGGGAAAGGGCG 60.452 63.158 0.00 0.00 0.00 6.13
107 108 2.893682 GATGGTGAGGGAAAGGGCGG 62.894 65.000 0.00 0.00 0.00 6.13
108 109 4.426313 GGTGAGGGAAAGGGCGGG 62.426 72.222 0.00 0.00 0.00 6.13
109 110 4.426313 GTGAGGGAAAGGGCGGGG 62.426 72.222 0.00 0.00 0.00 5.73
110 111 4.667935 TGAGGGAAAGGGCGGGGA 62.668 66.667 0.00 0.00 0.00 4.81
111 112 3.798511 GAGGGAAAGGGCGGGGAG 61.799 72.222 0.00 0.00 0.00 4.30
114 115 3.798511 GGAAAGGGCGGGGAGGAG 61.799 72.222 0.00 0.00 0.00 3.69
115 116 3.798511 GAAAGGGCGGGGAGGAGG 61.799 72.222 0.00 0.00 0.00 4.30
120 121 4.250170 GGCGGGGAGGAGGGGATA 62.250 72.222 0.00 0.00 0.00 2.59
121 122 2.122547 GCGGGGAGGAGGGGATAA 60.123 66.667 0.00 0.00 0.00 1.75
122 123 1.539124 GCGGGGAGGAGGGGATAAT 60.539 63.158 0.00 0.00 0.00 1.28
123 124 1.842381 GCGGGGAGGAGGGGATAATG 61.842 65.000 0.00 0.00 0.00 1.90
124 125 1.201429 CGGGGAGGAGGGGATAATGG 61.201 65.000 0.00 0.00 0.00 3.16
125 126 1.501654 GGGGAGGAGGGGATAATGGC 61.502 65.000 0.00 0.00 0.00 4.40
126 127 1.679898 GGAGGAGGGGATAATGGCG 59.320 63.158 0.00 0.00 0.00 5.69
127 128 1.679898 GAGGAGGGGATAATGGCGG 59.320 63.158 0.00 0.00 0.00 6.13
128 129 1.842381 GAGGAGGGGATAATGGCGGG 61.842 65.000 0.00 0.00 0.00 6.13
129 130 2.757077 GAGGGGATAATGGCGGGG 59.243 66.667 0.00 0.00 0.00 5.73
130 131 2.858974 AGGGGATAATGGCGGGGG 60.859 66.667 0.00 0.00 0.00 5.40
131 132 2.856988 GGGGATAATGGCGGGGGA 60.857 66.667 0.00 0.00 0.00 4.81
132 133 2.757077 GGGATAATGGCGGGGGAG 59.243 66.667 0.00 0.00 0.00 4.30
133 134 2.757077 GGATAATGGCGGGGGAGG 59.243 66.667 0.00 0.00 0.00 4.30
134 135 2.757077 GATAATGGCGGGGGAGGG 59.243 66.667 0.00 0.00 0.00 4.30
135 136 3.569200 GATAATGGCGGGGGAGGGC 62.569 68.421 0.00 0.00 0.00 5.19
187 188 4.279043 GCGGGCGTGTTTTTGGCT 62.279 61.111 0.00 0.00 0.00 4.75
188 189 2.415426 CGGGCGTGTTTTTGGCTT 59.585 55.556 0.00 0.00 0.00 4.35
189 190 1.227118 CGGGCGTGTTTTTGGCTTT 60.227 52.632 0.00 0.00 0.00 3.51
190 191 1.212455 CGGGCGTGTTTTTGGCTTTC 61.212 55.000 0.00 0.00 0.00 2.62
191 192 1.212455 GGGCGTGTTTTTGGCTTTCG 61.212 55.000 0.00 0.00 0.00 3.46
192 193 1.212455 GGCGTGTTTTTGGCTTTCGG 61.212 55.000 0.00 0.00 0.00 4.30
193 194 0.248702 GCGTGTTTTTGGCTTTCGGA 60.249 50.000 0.00 0.00 0.00 4.55
194 195 1.799548 GCGTGTTTTTGGCTTTCGGAA 60.800 47.619 0.00 0.00 0.00 4.30
195 196 2.116366 CGTGTTTTTGGCTTTCGGAAG 58.884 47.619 0.00 0.00 35.92 3.46
251 252 2.664851 CATGTGGGCGTGTCGTGT 60.665 61.111 0.00 0.00 0.00 4.49
252 253 2.110213 ATGTGGGCGTGTCGTGTT 59.890 55.556 0.00 0.00 0.00 3.32
253 254 0.946700 CATGTGGGCGTGTCGTGTTA 60.947 55.000 0.00 0.00 0.00 2.41
311 313 3.529634 TTTATGCTTTCGGTGTTGTCG 57.470 42.857 0.00 0.00 0.00 4.35
312 314 0.793861 TATGCTTTCGGTGTTGTCGC 59.206 50.000 0.00 0.00 0.00 5.19
346 352 4.276678 GCCATGCACAAGAGCTTTCATATA 59.723 41.667 0.00 0.00 34.99 0.86
347 353 5.048224 GCCATGCACAAGAGCTTTCATATAT 60.048 40.000 0.00 0.00 34.99 0.86
348 354 6.516194 GCCATGCACAAGAGCTTTCATATATT 60.516 38.462 0.00 0.00 34.99 1.28
349 355 7.308770 GCCATGCACAAGAGCTTTCATATATTA 60.309 37.037 0.00 0.00 34.99 0.98
350 356 8.570488 CCATGCACAAGAGCTTTCATATATTAA 58.430 33.333 0.00 0.00 34.99 1.40
365 371 7.460296 TCATATATTAATTAATGTGTGCCGCG 58.540 34.615 19.97 0.00 30.12 6.46
456 462 2.682856 CCGTATGTTTCTTGGGACATGG 59.317 50.000 0.00 0.00 39.30 3.66
474 480 0.804989 GGTGCTGCCTGTGTGATTAC 59.195 55.000 0.00 0.00 0.00 1.89
475 481 1.522668 GTGCTGCCTGTGTGATTACA 58.477 50.000 0.00 0.00 0.00 2.41
476 482 1.879380 GTGCTGCCTGTGTGATTACAA 59.121 47.619 0.00 0.00 38.82 2.41
477 483 2.095567 GTGCTGCCTGTGTGATTACAAG 60.096 50.000 0.00 0.00 38.82 3.16
479 485 3.244387 TGCTGCCTGTGTGATTACAAGTA 60.244 43.478 0.00 0.00 38.82 2.24
480 486 3.372206 GCTGCCTGTGTGATTACAAGTAG 59.628 47.826 0.00 0.00 38.82 2.57
481 487 3.935203 CTGCCTGTGTGATTACAAGTAGG 59.065 47.826 10.65 10.65 38.82 3.18
482 488 3.580895 TGCCTGTGTGATTACAAGTAGGA 59.419 43.478 16.34 4.21 38.82 2.94
483 489 4.184629 GCCTGTGTGATTACAAGTAGGAG 58.815 47.826 16.34 0.00 38.82 3.69
485 491 4.322725 CCTGTGTGATTACAAGTAGGAGCA 60.323 45.833 9.82 0.00 38.82 4.26
487 493 5.616270 TGTGTGATTACAAGTAGGAGCAAA 58.384 37.500 0.00 0.00 38.82 3.68
488 494 5.468746 TGTGTGATTACAAGTAGGAGCAAAC 59.531 40.000 0.00 0.00 38.82 2.93
489 495 4.688879 TGTGATTACAAGTAGGAGCAAACG 59.311 41.667 0.00 0.00 32.88 3.60
490 496 4.689345 GTGATTACAAGTAGGAGCAAACGT 59.311 41.667 0.00 0.00 0.00 3.99
491 497 5.865552 GTGATTACAAGTAGGAGCAAACGTA 59.134 40.000 0.00 0.00 0.00 3.57
500 543 0.110823 GAGCAAACGTAACGCTGGTG 60.111 55.000 10.62 0.00 35.75 4.17
522 565 1.656441 GTGTGCTGACTTGGCAAGG 59.344 57.895 29.26 14.06 41.54 3.61
617 665 1.405933 GCACCCATTCCATTCCAAAGC 60.406 52.381 0.00 0.00 0.00 3.51
768 816 2.990642 CCACCACAAAGGCAAAAGC 58.009 52.632 0.00 0.00 43.14 3.51
818 866 4.675303 CTCCCACTCCCACCCCCA 62.675 72.222 0.00 0.00 0.00 4.96
936 984 1.692121 CCAGAGAGCCCTCATCTCCTT 60.692 57.143 0.00 0.00 43.53 3.36
940 988 1.385206 AGCCCTCATCTCCTTCCCC 60.385 63.158 0.00 0.00 0.00 4.81
957 1005 3.339093 CCCTCGCCTTTTCCCCCT 61.339 66.667 0.00 0.00 0.00 4.79
959 1007 1.378646 CCTCGCCTTTTCCCCCTTC 60.379 63.158 0.00 0.00 0.00 3.46
962 1010 2.038975 GCCTTTTCCCCCTTCCCC 59.961 66.667 0.00 0.00 0.00 4.81
963 1011 2.359011 CCTTTTCCCCCTTCCCCG 59.641 66.667 0.00 0.00 0.00 5.73
964 1012 2.359011 CTTTTCCCCCTTCCCCGG 59.641 66.667 0.00 0.00 0.00 5.73
965 1013 2.121413 TTTTCCCCCTTCCCCGGA 60.121 61.111 0.73 0.00 0.00 5.14
1529 1587 1.705997 AAGGAAACTGCCAGGGACGT 61.706 55.000 0.00 0.00 42.68 4.34
1569 1627 2.275089 CCGGCATGGTTGGATCCA 59.725 61.111 11.44 11.44 42.01 3.41
1626 1684 1.054978 GCGAGGGAGGGATTAAGGGT 61.055 60.000 0.00 0.00 0.00 4.34
1881 1939 1.270826 ACAGGCACATCCTCGATATCG 59.729 52.381 19.14 19.14 45.52 2.92
1884 1942 1.402984 GGCACATCCTCGATATCGACC 60.403 57.143 23.48 16.75 44.22 4.79
2001 2059 1.002011 GAGTGGCTCCTTTGGGACC 60.002 63.158 0.00 0.00 36.57 4.46
2075 2133 5.657474 TCATCGTTCCTTGTATACTGGTTC 58.343 41.667 4.17 4.29 0.00 3.62
2077 2135 5.320549 TCGTTCCTTGTATACTGGTTCTC 57.679 43.478 4.17 0.36 0.00 2.87
2093 2151 4.693566 TGGTTCTCAACGTTATGCTTAAGG 59.306 41.667 0.00 9.72 0.00 2.69
2097 2155 7.412672 GGTTCTCAACGTTATGCTTAAGGTTAG 60.413 40.741 22.38 19.23 41.85 2.34
2100 2158 6.646267 TCAACGTTATGCTTAAGGTTAGGAT 58.354 36.000 22.38 5.65 41.85 3.24
2141 2199 3.240302 TCCAAGATAACCTAGGGCTAGC 58.760 50.000 14.81 6.04 31.95 3.42
2168 2226 1.272092 CCAGAAGCCTTGATCAACCCA 60.272 52.381 3.38 0.00 0.00 4.51
2170 2228 2.892852 CAGAAGCCTTGATCAACCCAAA 59.107 45.455 3.38 0.00 0.00 3.28
2213 2271 0.176910 GACTAGAAGCTCACTGGCCC 59.823 60.000 0.00 0.00 0.00 5.80
2257 2315 9.672673 AACTATTGAGTAGCAAAATACAGATGT 57.327 29.630 0.00 0.00 40.48 3.06
2258 2316 9.102757 ACTATTGAGTAGCAAAATACAGATGTG 57.897 33.333 0.00 0.00 40.48 3.21
2319 2472 6.377996 TGGTTTCATCTTCAACATAATCCTGG 59.622 38.462 0.00 0.00 0.00 4.45
2432 2585 2.867975 GCCAAAATATTGCACTGCATCC 59.132 45.455 4.10 0.00 38.76 3.51
2487 2643 2.867109 ATGGATATTCAGCTTCCGGG 57.133 50.000 0.00 0.00 31.90 5.73
2528 2684 5.253330 TCTGTTGTTCCTTTATTAGGCTGG 58.747 41.667 0.00 0.00 44.37 4.85
2656 2812 5.485353 AGAAGTGTCCTTACATGATCAAGGA 59.515 40.000 18.18 18.18 46.35 3.36
2707 2863 0.895559 AGCAGGTTGGTTTAGCTGGC 60.896 55.000 0.00 0.00 42.43 4.85
2731 2887 8.342634 GGCTGTTTGTGTTATTGATAATATCGT 58.657 33.333 0.00 0.00 0.00 3.73
2893 3051 3.075148 GGAACTGACAAAGTAAGCTCCC 58.925 50.000 0.00 0.00 38.56 4.30
2894 3052 2.861147 ACTGACAAAGTAAGCTCCCC 57.139 50.000 0.00 0.00 37.36 4.81
2908 3066 0.462759 CTCCCCGATCTTCCAGTTGC 60.463 60.000 0.00 0.00 0.00 4.17
3358 3663 1.172180 TGAAGCTTGCGGACTTTGGG 61.172 55.000 2.10 0.00 0.00 4.12
3417 3722 7.552330 ACCTGCATAATTTTGTGTTTGAACTTT 59.448 29.630 0.00 0.00 0.00 2.66
3548 3853 3.046283 TGGCACCTGAGGTATATCACT 57.954 47.619 2.59 0.00 32.11 3.41
3585 3890 7.277174 TCAGATTAGCATAGTCTCGAATTCA 57.723 36.000 6.22 0.00 35.25 2.57
3586 3891 7.366513 TCAGATTAGCATAGTCTCGAATTCAG 58.633 38.462 6.22 2.67 35.25 3.02
3664 4052 8.732531 GCAAGTAGTAGTATAATCCTGAGGTAG 58.267 40.741 0.00 0.00 0.00 3.18
3803 4201 7.834068 ACTATTAGTGACAACTATTGCACTG 57.166 36.000 19.68 11.05 43.09 3.66
3822 4220 4.923871 CACTGGTAGTTCACACTGTATGTC 59.076 45.833 0.00 0.00 40.64 3.06
3894 4292 4.701651 TGGATTGGTGCTCTATGTTCTTTG 59.298 41.667 0.00 0.00 0.00 2.77
3962 4361 5.299949 TGGCATAAGCATACTGTCATGTAG 58.700 41.667 0.00 0.00 44.61 2.74
4077 4479 0.818040 GAGTTTGGGTTGCACGGTCT 60.818 55.000 0.00 0.00 0.00 3.85
4163 4566 5.930569 TGAATCTAGTAATAGCTGCTGCATG 59.069 40.000 18.42 0.00 42.74 4.06
4214 4617 3.366052 AAAAGGTCTCTGGTGTGTGTT 57.634 42.857 0.00 0.00 0.00 3.32
4267 4670 3.068590 CCCATTCTTGCAACTTGTTCTGT 59.931 43.478 0.00 0.00 0.00 3.41
4281 4684 2.438021 TGTTCTGTAGACACAAGCCCTT 59.562 45.455 0.00 0.00 33.22 3.95
4293 4696 1.478105 CAAGCCCTTTACAGGATTGGC 59.522 52.381 0.00 0.00 44.19 4.52
4299 4702 2.102578 CTTTACAGGATTGGCAAGGGG 58.897 52.381 5.96 0.00 0.00 4.79
4302 4705 1.076485 CAGGATTGGCAAGGGGGAG 60.076 63.158 5.96 0.00 0.00 4.30
4323 4726 1.098050 CACCAGCAATTCCTAGTGGC 58.902 55.000 0.00 0.00 0.00 5.01
4446 4849 4.763874 GATCTATGCGATCTATACGGTCG 58.236 47.826 0.00 0.00 44.21 4.79
4513 4916 2.159028 GGATAGAGCTGTGGACAACTCC 60.159 54.545 6.58 0.00 39.28 3.85
4624 5027 2.622064 ATCGCCTGGTTAATCTGACC 57.378 50.000 0.00 0.00 37.69 4.02
4663 5066 6.993786 TCTATCTGCAGATATTAGTCCTCG 57.006 41.667 31.46 18.62 36.53 4.63
4751 5154 8.506168 TCTCTTGTGTTTTGTTAGTTGATTCT 57.494 30.769 0.00 0.00 0.00 2.40
4752 5155 8.956426 TCTCTTGTGTTTTGTTAGTTGATTCTT 58.044 29.630 0.00 0.00 0.00 2.52
4753 5156 9.573133 CTCTTGTGTTTTGTTAGTTGATTCTTT 57.427 29.630 0.00 0.00 0.00 2.52
4754 5157 9.921637 TCTTGTGTTTTGTTAGTTGATTCTTTT 57.078 25.926 0.00 0.00 0.00 2.27
4789 5197 6.222038 TCTGGTGATCCGGCTAATATTATC 57.778 41.667 0.00 0.00 39.81 1.75
4908 5323 2.568509 TGTCATGGTGCTGAATGAGAGA 59.431 45.455 0.00 0.00 33.58 3.10
4909 5324 3.196463 GTCATGGTGCTGAATGAGAGAG 58.804 50.000 0.00 0.00 33.58 3.20
4913 5328 4.134379 TGGTGCTGAATGAGAGAGATTC 57.866 45.455 0.00 0.00 0.00 2.52
4939 5354 1.069049 GTTGTTCCAACTGCAAGGCAT 59.931 47.619 0.00 0.00 38.13 4.40
4940 5355 0.675083 TGTTCCAACTGCAAGGCATG 59.325 50.000 0.00 0.00 38.13 4.06
4954 5404 4.320870 CAAGGCATGCTCTGGAAAATTTT 58.679 39.130 18.92 2.28 0.00 1.82
4955 5405 4.198028 AGGCATGCTCTGGAAAATTTTC 57.802 40.909 20.51 20.51 36.46 2.29
4958 5408 4.999311 GGCATGCTCTGGAAAATTTTCTTT 59.001 37.500 25.86 0.00 37.35 2.52
5011 5461 5.992217 GGTATGCTCTGGAACTTTCGATAAT 59.008 40.000 0.00 0.00 0.00 1.28
5018 5469 3.279434 GGAACTTTCGATAATGGTGGCT 58.721 45.455 0.00 0.00 0.00 4.75
5020 5471 3.627395 ACTTTCGATAATGGTGGCTGA 57.373 42.857 0.00 0.00 0.00 4.26
5046 5497 0.390472 CTGGAACTGCGTCCCTTCTC 60.390 60.000 0.00 0.00 36.80 2.87
5201 5655 7.162062 CGCGTATTTGCTGACTTATTAGTTTTC 59.838 37.037 0.00 0.00 33.84 2.29
5236 5690 3.709987 CCTGCTTTGTTTCTTTGTGAGG 58.290 45.455 0.00 0.00 0.00 3.86
5241 5696 6.226787 TGCTTTGTTTCTTTGTGAGGAAAAA 58.773 32.000 0.00 0.00 33.97 1.94
5298 5753 7.970384 ACGTGTATACAGTTCAACCATAAATG 58.030 34.615 5.62 0.00 0.00 2.32
5381 5861 1.073923 AGATTGGTGTTCCCAGGTGTC 59.926 52.381 0.00 0.00 46.31 3.67
5392 5872 1.656652 CCAGGTGTCGAAAGCATAGG 58.343 55.000 7.67 2.15 0.00 2.57
5435 5917 2.072298 CGAACTGAGGAAGGAAGCAAG 58.928 52.381 0.00 0.00 0.00 4.01
5436 5918 1.809547 GAACTGAGGAAGGAAGCAAGC 59.190 52.381 0.00 0.00 0.00 4.01
5442 5924 0.250901 GGAAGGAAGCAAGCACCTGA 60.251 55.000 10.54 0.00 34.03 3.86
5457 5939 1.369091 CCTGATTTGGGACTTCGCCG 61.369 60.000 0.00 0.00 0.00 6.46
5491 6024 3.520290 TGAGCTCACAAGTAATACGGG 57.480 47.619 13.74 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.855740 AACCCCGTAAAAAGATGTTTTGA 57.144 34.783 0.71 0.00 35.96 2.69
2 3 6.535508 TGAAAACCCCGTAAAAAGATGTTTTG 59.464 34.615 0.71 0.00 35.96 2.44
3 4 6.641474 TGAAAACCCCGTAAAAAGATGTTTT 58.359 32.000 0.00 0.00 37.48 2.43
4 5 6.223351 TGAAAACCCCGTAAAAAGATGTTT 57.777 33.333 0.00 0.00 0.00 2.83
5 6 5.855740 TGAAAACCCCGTAAAAAGATGTT 57.144 34.783 0.00 0.00 0.00 2.71
6 7 5.335348 CGATGAAAACCCCGTAAAAAGATGT 60.335 40.000 0.00 0.00 0.00 3.06
7 8 5.092781 CGATGAAAACCCCGTAAAAAGATG 58.907 41.667 0.00 0.00 0.00 2.90
8 9 4.157105 CCGATGAAAACCCCGTAAAAAGAT 59.843 41.667 0.00 0.00 0.00 2.40
11 12 3.220940 ACCGATGAAAACCCCGTAAAAA 58.779 40.909 0.00 0.00 0.00 1.94
12 13 2.861274 ACCGATGAAAACCCCGTAAAA 58.139 42.857 0.00 0.00 0.00 1.52
13 14 2.565046 ACCGATGAAAACCCCGTAAA 57.435 45.000 0.00 0.00 0.00 2.01
14 15 2.565046 AACCGATGAAAACCCCGTAA 57.435 45.000 0.00 0.00 0.00 3.18
15 16 2.038820 AGAAACCGATGAAAACCCCGTA 59.961 45.455 0.00 0.00 0.00 4.02
16 17 1.202842 AGAAACCGATGAAAACCCCGT 60.203 47.619 0.00 0.00 0.00 5.28
17 18 1.530323 AGAAACCGATGAAAACCCCG 58.470 50.000 0.00 0.00 0.00 5.73
18 19 3.414269 TGTAGAAACCGATGAAAACCCC 58.586 45.455 0.00 0.00 0.00 4.95
19 20 4.698304 TCATGTAGAAACCGATGAAAACCC 59.302 41.667 0.00 0.00 0.00 4.11
20 21 5.873179 TCATGTAGAAACCGATGAAAACC 57.127 39.130 0.00 0.00 0.00 3.27
21 22 9.651718 GAATATCATGTAGAAACCGATGAAAAC 57.348 33.333 0.00 0.00 0.00 2.43
22 23 9.613428 AGAATATCATGTAGAAACCGATGAAAA 57.387 29.630 0.00 0.00 0.00 2.29
23 24 9.261180 GAGAATATCATGTAGAAACCGATGAAA 57.739 33.333 0.00 0.00 0.00 2.69
24 25 7.872993 GGAGAATATCATGTAGAAACCGATGAA 59.127 37.037 0.00 0.00 0.00 2.57
25 26 7.378966 GGAGAATATCATGTAGAAACCGATGA 58.621 38.462 0.00 0.00 0.00 2.92
26 27 6.591834 GGGAGAATATCATGTAGAAACCGATG 59.408 42.308 0.00 0.00 0.00 3.84
27 28 6.572509 CGGGAGAATATCATGTAGAAACCGAT 60.573 42.308 0.00 0.00 37.43 4.18
28 29 5.278808 CGGGAGAATATCATGTAGAAACCGA 60.279 44.000 0.00 0.00 37.43 4.69
29 30 4.923871 CGGGAGAATATCATGTAGAAACCG 59.076 45.833 0.00 0.00 0.00 4.44
30 31 5.221661 ACCGGGAGAATATCATGTAGAAACC 60.222 44.000 6.32 0.00 0.00 3.27
31 32 5.855045 ACCGGGAGAATATCATGTAGAAAC 58.145 41.667 6.32 0.00 0.00 2.78
32 33 6.494666 AACCGGGAGAATATCATGTAGAAA 57.505 37.500 6.32 0.00 0.00 2.52
33 34 6.099125 TGAAACCGGGAGAATATCATGTAGAA 59.901 38.462 6.32 0.00 0.00 2.10
34 35 5.600898 TGAAACCGGGAGAATATCATGTAGA 59.399 40.000 6.32 0.00 0.00 2.59
35 36 5.853936 TGAAACCGGGAGAATATCATGTAG 58.146 41.667 6.32 0.00 0.00 2.74
36 37 5.880164 TGAAACCGGGAGAATATCATGTA 57.120 39.130 6.32 0.00 0.00 2.29
37 38 4.771114 TGAAACCGGGAGAATATCATGT 57.229 40.909 6.32 0.00 0.00 3.21
38 39 5.410746 CAGATGAAACCGGGAGAATATCATG 59.589 44.000 6.32 0.00 0.00 3.07
39 40 5.513788 CCAGATGAAACCGGGAGAATATCAT 60.514 44.000 6.32 4.53 0.00 2.45
40 41 4.202357 CCAGATGAAACCGGGAGAATATCA 60.202 45.833 6.32 0.00 0.00 2.15
41 42 4.040461 TCCAGATGAAACCGGGAGAATATC 59.960 45.833 6.32 1.94 0.00 1.63
42 43 3.973973 TCCAGATGAAACCGGGAGAATAT 59.026 43.478 6.32 0.00 0.00 1.28
43 44 3.380393 TCCAGATGAAACCGGGAGAATA 58.620 45.455 6.32 0.00 0.00 1.75
44 45 2.196595 TCCAGATGAAACCGGGAGAAT 58.803 47.619 6.32 0.00 0.00 2.40
45 46 1.651737 TCCAGATGAAACCGGGAGAA 58.348 50.000 6.32 0.00 0.00 2.87
46 47 1.879575 ATCCAGATGAAACCGGGAGA 58.120 50.000 6.32 0.00 0.00 3.71
47 48 2.684881 CAAATCCAGATGAAACCGGGAG 59.315 50.000 6.32 0.00 0.00 4.30
48 49 2.722094 CAAATCCAGATGAAACCGGGA 58.278 47.619 6.32 0.00 0.00 5.14
49 50 1.134946 GCAAATCCAGATGAAACCGGG 59.865 52.381 6.32 0.00 0.00 5.73
50 51 1.202177 CGCAAATCCAGATGAAACCGG 60.202 52.381 0.00 0.00 0.00 5.28
51 52 1.468520 ACGCAAATCCAGATGAAACCG 59.531 47.619 0.00 0.00 0.00 4.44
52 53 3.938963 TCTACGCAAATCCAGATGAAACC 59.061 43.478 0.00 0.00 0.00 3.27
53 54 4.034510 CCTCTACGCAAATCCAGATGAAAC 59.965 45.833 0.00 0.00 0.00 2.78
54 55 4.081142 TCCTCTACGCAAATCCAGATGAAA 60.081 41.667 0.00 0.00 0.00 2.69
55 56 3.450817 TCCTCTACGCAAATCCAGATGAA 59.549 43.478 0.00 0.00 0.00 2.57
56 57 3.031013 TCCTCTACGCAAATCCAGATGA 58.969 45.455 0.00 0.00 0.00 2.92
57 58 3.459232 TCCTCTACGCAAATCCAGATG 57.541 47.619 0.00 0.00 0.00 2.90
58 59 3.181461 CCTTCCTCTACGCAAATCCAGAT 60.181 47.826 0.00 0.00 0.00 2.90
59 60 2.168521 CCTTCCTCTACGCAAATCCAGA 59.831 50.000 0.00 0.00 0.00 3.86
60 61 2.555199 CCTTCCTCTACGCAAATCCAG 58.445 52.381 0.00 0.00 0.00 3.86
61 62 1.406887 GCCTTCCTCTACGCAAATCCA 60.407 52.381 0.00 0.00 0.00 3.41
62 63 1.300481 GCCTTCCTCTACGCAAATCC 58.700 55.000 0.00 0.00 0.00 3.01
63 64 0.931005 CGCCTTCCTCTACGCAAATC 59.069 55.000 0.00 0.00 0.00 2.17
64 65 3.065575 CGCCTTCCTCTACGCAAAT 57.934 52.632 0.00 0.00 0.00 2.32
65 66 4.590487 CGCCTTCCTCTACGCAAA 57.410 55.556 0.00 0.00 0.00 3.68
69 70 3.515286 TCGGCGCCTTCCTCTACG 61.515 66.667 26.68 7.80 0.00 3.51
70 71 2.104530 GTCGGCGCCTTCCTCTAC 59.895 66.667 26.68 7.08 0.00 2.59
71 72 3.515286 CGTCGGCGCCTTCCTCTA 61.515 66.667 26.68 0.00 0.00 2.43
73 74 4.208686 ATCGTCGGCGCCTTCCTC 62.209 66.667 26.68 8.86 38.14 3.71
74 75 4.514577 CATCGTCGGCGCCTTCCT 62.515 66.667 26.68 1.80 38.14 3.36
76 77 4.814294 ACCATCGTCGGCGCCTTC 62.814 66.667 26.68 15.95 38.14 3.46
81 82 4.873129 CCCTCACCATCGTCGGCG 62.873 72.222 1.15 1.15 39.92 6.46
82 83 2.515996 TTTCCCTCACCATCGTCGGC 62.516 60.000 0.00 0.00 0.00 5.54
83 84 0.460284 CTTTCCCTCACCATCGTCGG 60.460 60.000 0.00 0.00 0.00 4.79
84 85 0.460284 CCTTTCCCTCACCATCGTCG 60.460 60.000 0.00 0.00 0.00 5.12
85 86 0.107654 CCCTTTCCCTCACCATCGTC 60.108 60.000 0.00 0.00 0.00 4.20
86 87 1.991230 CCCTTTCCCTCACCATCGT 59.009 57.895 0.00 0.00 0.00 3.73
87 88 1.452108 GCCCTTTCCCTCACCATCG 60.452 63.158 0.00 0.00 0.00 3.84
88 89 1.452108 CGCCCTTTCCCTCACCATC 60.452 63.158 0.00 0.00 0.00 3.51
89 90 2.677228 CGCCCTTTCCCTCACCAT 59.323 61.111 0.00 0.00 0.00 3.55
90 91 3.646715 CCGCCCTTTCCCTCACCA 61.647 66.667 0.00 0.00 0.00 4.17
91 92 4.426313 CCCGCCCTTTCCCTCACC 62.426 72.222 0.00 0.00 0.00 4.02
92 93 4.426313 CCCCGCCCTTTCCCTCAC 62.426 72.222 0.00 0.00 0.00 3.51
93 94 4.667935 TCCCCGCCCTTTCCCTCA 62.668 66.667 0.00 0.00 0.00 3.86
94 95 3.798511 CTCCCCGCCCTTTCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
97 98 3.798511 CTCCTCCCCGCCCTTTCC 61.799 72.222 0.00 0.00 0.00 3.13
98 99 3.798511 CCTCCTCCCCGCCCTTTC 61.799 72.222 0.00 0.00 0.00 2.62
103 104 3.786866 TTATCCCCTCCTCCCCGCC 62.787 68.421 0.00 0.00 0.00 6.13
104 105 1.539124 ATTATCCCCTCCTCCCCGC 60.539 63.158 0.00 0.00 0.00 6.13
105 106 1.201429 CCATTATCCCCTCCTCCCCG 61.201 65.000 0.00 0.00 0.00 5.73
106 107 1.501654 GCCATTATCCCCTCCTCCCC 61.502 65.000 0.00 0.00 0.00 4.81
107 108 1.842381 CGCCATTATCCCCTCCTCCC 61.842 65.000 0.00 0.00 0.00 4.30
108 109 1.679898 CGCCATTATCCCCTCCTCC 59.320 63.158 0.00 0.00 0.00 4.30
109 110 1.679898 CCGCCATTATCCCCTCCTC 59.320 63.158 0.00 0.00 0.00 3.71
110 111 1.847968 CCCGCCATTATCCCCTCCT 60.848 63.158 0.00 0.00 0.00 3.69
111 112 2.757077 CCCGCCATTATCCCCTCC 59.243 66.667 0.00 0.00 0.00 4.30
112 113 2.757077 CCCCGCCATTATCCCCTC 59.243 66.667 0.00 0.00 0.00 4.30
113 114 2.858974 CCCCCGCCATTATCCCCT 60.859 66.667 0.00 0.00 0.00 4.79
114 115 2.856988 TCCCCCGCCATTATCCCC 60.857 66.667 0.00 0.00 0.00 4.81
115 116 2.757077 CTCCCCCGCCATTATCCC 59.243 66.667 0.00 0.00 0.00 3.85
116 117 2.757077 CCTCCCCCGCCATTATCC 59.243 66.667 0.00 0.00 0.00 2.59
117 118 2.757077 CCCTCCCCCGCCATTATC 59.243 66.667 0.00 0.00 0.00 1.75
118 119 3.580319 GCCCTCCCCCGCCATTAT 61.580 66.667 0.00 0.00 0.00 1.28
170 171 3.783478 AAGCCAAAAACACGCCCGC 62.783 57.895 0.00 0.00 0.00 6.13
171 172 1.212455 GAAAGCCAAAAACACGCCCG 61.212 55.000 0.00 0.00 0.00 6.13
172 173 1.212455 CGAAAGCCAAAAACACGCCC 61.212 55.000 0.00 0.00 0.00 6.13
173 174 1.212455 CCGAAAGCCAAAAACACGCC 61.212 55.000 0.00 0.00 0.00 5.68
174 175 0.248702 TCCGAAAGCCAAAAACACGC 60.249 50.000 0.00 0.00 0.00 5.34
175 176 2.116366 CTTCCGAAAGCCAAAAACACG 58.884 47.619 0.00 0.00 0.00 4.49
186 187 4.357018 GGAAACTAATGGCTTCCGAAAG 57.643 45.455 0.00 0.00 35.47 2.62
191 192 2.606272 CGTACGGAAACTAATGGCTTCC 59.394 50.000 7.57 0.00 36.12 3.46
192 193 2.030091 GCGTACGGAAACTAATGGCTTC 59.970 50.000 18.39 0.00 0.00 3.86
193 194 2.004733 GCGTACGGAAACTAATGGCTT 58.995 47.619 18.39 0.00 0.00 4.35
194 195 1.066716 TGCGTACGGAAACTAATGGCT 60.067 47.619 18.39 0.00 0.00 4.75
195 196 1.361793 TGCGTACGGAAACTAATGGC 58.638 50.000 18.39 0.00 0.00 4.40
196 197 4.609691 AAATGCGTACGGAAACTAATGG 57.390 40.909 15.02 0.00 0.00 3.16
197 198 5.185341 CGTAAATGCGTACGGAAACTAATG 58.815 41.667 15.02 0.00 42.47 1.90
198 199 5.379757 CGTAAATGCGTACGGAAACTAAT 57.620 39.130 15.02 0.00 42.47 1.73
199 200 4.821414 CGTAAATGCGTACGGAAACTAA 57.179 40.909 15.02 0.00 42.47 2.24
200 201 5.394802 TTACGTAAATGCGTACGGAAACTA 58.605 37.500 15.02 2.63 45.06 2.24
201 202 4.233789 TTACGTAAATGCGTACGGAAACT 58.766 39.130 15.02 3.67 45.06 2.66
202 203 4.560396 TTACGTAAATGCGTACGGAAAC 57.440 40.909 15.02 11.46 45.06 2.78
208 209 5.308147 GTTGAGGTTTACGTAAATGCGTAC 58.692 41.667 22.65 14.42 45.40 3.67
209 210 4.388469 GGTTGAGGTTTACGTAAATGCGTA 59.612 41.667 22.65 7.38 45.06 4.42
251 252 8.777413 CATTCTTGATTCACTGTTGACTCTTAA 58.223 33.333 0.00 0.00 33.54 1.85
252 253 7.933577 ACATTCTTGATTCACTGTTGACTCTTA 59.066 33.333 0.00 0.00 33.54 2.10
253 254 6.769822 ACATTCTTGATTCACTGTTGACTCTT 59.230 34.615 0.00 0.00 33.54 2.85
346 352 2.357637 AGCGCGGCACACATTAATTAAT 59.642 40.909 8.83 4.81 0.00 1.40
347 353 1.740585 AGCGCGGCACACATTAATTAA 59.259 42.857 8.83 0.00 0.00 1.40
348 354 1.374560 AGCGCGGCACACATTAATTA 58.625 45.000 8.83 0.00 0.00 1.40
349 355 0.525761 AAGCGCGGCACACATTAATT 59.474 45.000 8.83 0.00 0.00 1.40
350 356 0.525761 AAAGCGCGGCACACATTAAT 59.474 45.000 8.83 0.00 0.00 1.40
351 357 0.386605 CAAAGCGCGGCACACATTAA 60.387 50.000 8.83 0.00 0.00 1.40
352 358 1.208870 CAAAGCGCGGCACACATTA 59.791 52.632 8.83 0.00 0.00 1.90
354 360 4.705519 GCAAAGCGCGGCACACAT 62.706 61.111 8.83 0.00 0.00 3.21
392 398 1.134226 CGAACGACCCTTGTGTGTAC 58.866 55.000 0.00 0.00 0.00 2.90
398 404 1.269936 ACGAAATCGAACGACCCTTGT 60.270 47.619 10.16 0.00 43.02 3.16
400 406 1.000060 TCACGAAATCGAACGACCCTT 60.000 47.619 10.16 0.00 43.02 3.95
456 462 1.522668 TGTAATCACACAGGCAGCAC 58.477 50.000 0.00 0.00 0.00 4.40
474 480 2.159881 GCGTTACGTTTGCTCCTACTTG 60.160 50.000 6.63 0.00 0.00 3.16
475 481 2.064014 GCGTTACGTTTGCTCCTACTT 58.936 47.619 6.63 0.00 0.00 2.24
476 482 1.271656 AGCGTTACGTTTGCTCCTACT 59.728 47.619 6.63 0.00 32.44 2.57
477 483 1.389106 CAGCGTTACGTTTGCTCCTAC 59.611 52.381 6.63 0.00 36.69 3.18
479 485 0.949105 CCAGCGTTACGTTTGCTCCT 60.949 55.000 6.63 0.00 36.69 3.69
480 486 1.226030 ACCAGCGTTACGTTTGCTCC 61.226 55.000 6.63 0.00 36.69 4.70
481 487 0.110823 CACCAGCGTTACGTTTGCTC 60.111 55.000 6.63 0.00 36.69 4.26
482 488 0.531090 TCACCAGCGTTACGTTTGCT 60.531 50.000 6.63 0.00 40.16 3.91
483 489 0.383860 GTCACCAGCGTTACGTTTGC 60.384 55.000 6.63 0.00 0.00 3.68
485 491 1.216941 CGGTCACCAGCGTTACGTTT 61.217 55.000 6.63 0.00 38.76 3.60
487 493 2.049802 CGGTCACCAGCGTTACGT 60.050 61.111 6.63 0.00 38.76 3.57
500 543 2.607892 GCCAAGTCAGCACACGGTC 61.608 63.158 0.00 0.00 0.00 4.79
565 608 2.126424 GGCGGACGTGTGACTCTC 60.126 66.667 0.00 0.00 0.00 3.20
568 611 4.295119 GTGGGCGGACGTGTGACT 62.295 66.667 0.00 0.00 0.00 3.41
763 811 0.110056 CGCATTGACTCGCAGCTTTT 60.110 50.000 0.00 0.00 0.00 2.27
817 865 1.894756 TTTTTCGGTGGGCGAGGTG 60.895 57.895 0.00 0.00 0.00 4.00
818 866 2.511900 TTTTTCGGTGGGCGAGGT 59.488 55.556 0.00 0.00 0.00 3.85
913 961 0.760189 AGATGAGGGCTCTCTGGCTC 60.760 60.000 16.21 6.55 40.58 4.70
940 988 2.838748 GAAGGGGGAAAAGGCGAGGG 62.839 65.000 0.00 0.00 0.00 4.30
1484 1542 2.512515 GCTCGAAATCAGCGGCCT 60.513 61.111 0.00 0.00 0.00 5.19
1881 1939 1.719780 GTCTCATCGTCGTTTGTGGTC 59.280 52.381 0.00 0.00 0.00 4.02
1884 1942 2.096909 GGTTGTCTCATCGTCGTTTGTG 60.097 50.000 0.00 0.00 0.00 3.33
1946 2004 0.323542 ACTCCACGACCGGATCTTCT 60.324 55.000 9.46 0.00 33.56 2.85
2001 2059 0.242286 CGCTGATCCCCTCATAGACG 59.758 60.000 0.00 0.00 32.10 4.18
2064 2122 6.040878 AGCATAACGTTGAGAACCAGTATAC 58.959 40.000 11.99 0.00 0.00 1.47
2068 2126 3.402628 AGCATAACGTTGAGAACCAGT 57.597 42.857 11.99 0.00 0.00 4.00
2075 2133 6.103997 TCCTAACCTTAAGCATAACGTTGAG 58.896 40.000 11.99 4.14 0.00 3.02
2077 2135 6.761714 AGATCCTAACCTTAAGCATAACGTTG 59.238 38.462 11.99 0.00 0.00 4.10
2093 2151 6.019479 CGAACATAGCAAGTTGAGATCCTAAC 60.019 42.308 7.16 2.34 0.00 2.34
2097 2155 4.184629 ACGAACATAGCAAGTTGAGATCC 58.815 43.478 7.16 0.00 0.00 3.36
2100 2158 3.994392 GGAACGAACATAGCAAGTTGAGA 59.006 43.478 7.16 0.00 0.00 3.27
2141 2199 5.139435 TGATCAAGGCTTCTGGATATACG 57.861 43.478 0.00 0.00 31.51 3.06
2191 2249 1.134848 GCCAGTGAGCTTCTAGTCAGG 60.135 57.143 0.00 0.00 0.00 3.86
2192 2250 1.134848 GGCCAGTGAGCTTCTAGTCAG 60.135 57.143 0.00 0.00 0.00 3.51
2196 2254 1.267574 TGGGGCCAGTGAGCTTCTAG 61.268 60.000 4.39 0.00 0.00 2.43
2239 2297 5.817816 GGCTACACATCTGTATTTTGCTACT 59.182 40.000 0.00 0.00 32.21 2.57
2432 2585 4.695455 ACCACATAATTCAGAACTGGAACG 59.305 41.667 1.93 0.00 0.00 3.95
2487 2643 0.381089 GATGCTGCAGTCCTTCATGC 59.619 55.000 16.64 0.00 42.86 4.06
2656 2812 2.717485 CACTGCTGTGCGTTGCTT 59.283 55.556 11.01 0.00 37.38 3.91
2731 2887 6.645790 AGAAGTCGTAAAAGACAAGGTCTA 57.354 37.500 0.00 0.00 42.59 2.59
2801 2959 6.575162 TTTCCTGAAAAGTAGAATGGAAGC 57.425 37.500 0.00 0.00 34.25 3.86
2893 3051 1.091771 ATGCGCAACTGGAAGATCGG 61.092 55.000 17.11 0.00 37.43 4.18
2894 3052 0.302890 GATGCGCAACTGGAAGATCG 59.697 55.000 17.11 0.00 37.43 3.69
2908 3066 4.297510 TCAACAATGGAAAAAGTGATGCG 58.702 39.130 0.00 0.00 0.00 4.73
3375 3680 8.911918 TTATGCAGGTTTTACAAGAAAGTAGA 57.088 30.769 0.00 0.00 0.00 2.59
3417 3722 7.564793 AGTTAGTGCATGGATAACTACATTCA 58.435 34.615 15.32 0.00 37.84 2.57
3585 3890 9.826574 GAAGGAAAAGGGTAAAAATAAACAACT 57.173 29.630 0.00 0.00 0.00 3.16
3586 3891 9.602568 TGAAGGAAAAGGGTAAAAATAAACAAC 57.397 29.630 0.00 0.00 0.00 3.32
3731 4119 3.502211 GGCAAAGCAAGCTAACTGAACTA 59.498 43.478 0.00 0.00 0.00 2.24
3803 4201 4.430137 TCGACATACAGTGTGAACTACC 57.570 45.455 5.88 0.00 42.36 3.18
3822 4220 6.200286 ACACGTAATTATTCCACTAAGCATCG 59.800 38.462 0.00 0.00 0.00 3.84
3894 4292 1.666888 CCAAGAATGTCCGCAGCAAAC 60.667 52.381 0.00 0.00 0.00 2.93
3962 4361 9.449719 AATAATCGAAAAGGTATGGACATATCC 57.550 33.333 0.00 2.00 46.48 2.59
4163 4566 7.835634 TTTAAACCAACACTGGAATTCAAAC 57.164 32.000 7.93 0.00 46.92 2.93
4267 4670 3.244582 TCCTGTAAAGGGCTTGTGTCTA 58.755 45.455 0.00 0.00 0.00 2.59
4281 4684 0.334676 CCCCCTTGCCAATCCTGTAA 59.665 55.000 0.00 0.00 0.00 2.41
4293 4696 4.748144 GCTGGTGGCTCCCCCTTG 62.748 72.222 2.66 0.00 38.06 3.61
4299 4702 0.255890 TAGGAATTGCTGGTGGCTCC 59.744 55.000 10.10 0.00 42.39 4.70
4302 4705 1.098050 CACTAGGAATTGCTGGTGGC 58.902 55.000 28.40 0.00 42.22 5.01
4446 4849 2.299013 TGGGCGTGTATATGTCCTCATC 59.701 50.000 3.82 0.00 38.45 2.92
4513 4916 4.512944 ACTTACAATTCTGCCGATATGCTG 59.487 41.667 0.00 0.00 0.00 4.41
4576 4979 0.622665 AACAGATGGCAGCCTAGCTT 59.377 50.000 14.15 0.00 36.40 3.74
4624 5027 5.404968 GCAGATAGAATAAGCAGCACTACAG 59.595 44.000 0.00 0.00 0.00 2.74
4663 5066 0.950116 GCCAGCTCCACATGATTAGC 59.050 55.000 0.00 4.73 35.16 3.09
4710 5113 3.498774 AGAGATGCTGGTTGACAACTT 57.501 42.857 17.52 0.00 0.00 2.66
4751 5154 6.150474 GGATCACCAGAATTCGGTAAAGAAAA 59.850 38.462 17.67 3.62 34.02 2.29
4752 5155 5.646360 GGATCACCAGAATTCGGTAAAGAAA 59.354 40.000 17.67 4.86 34.02 2.52
4753 5156 5.183228 GGATCACCAGAATTCGGTAAAGAA 58.817 41.667 17.67 6.13 34.02 2.52
4754 5157 4.679639 CGGATCACCAGAATTCGGTAAAGA 60.680 45.833 17.67 12.98 34.02 2.52
4755 5158 3.555956 CGGATCACCAGAATTCGGTAAAG 59.444 47.826 17.67 9.20 34.02 1.85
4789 5197 2.294170 TACTCTACTCCCCGGGCAGG 62.294 65.000 17.99 10.17 40.63 4.85
4958 5408 6.889177 TGATCTATGTGGTAAGCAATCCAAAA 59.111 34.615 0.00 0.00 35.38 2.44
4979 5429 1.409064 TCCAGAGCATACCACGTGATC 59.591 52.381 19.30 0.00 32.41 2.92
5018 5469 0.179048 CGCAGTTCCAGGCCATATCA 60.179 55.000 5.01 0.00 0.00 2.15
5020 5471 1.915228 ACGCAGTTCCAGGCCATAT 59.085 52.632 5.01 0.00 37.78 1.78
5046 5497 0.647410 CAGCATAGAAGTCGCCAACG 59.353 55.000 0.00 0.00 42.01 4.10
5113 5564 1.312815 CCAGCGGAGGAATTTCCATC 58.687 55.000 17.57 11.20 39.61 3.51
5201 5655 1.602311 AGCAGGCACAGAGACAAAAG 58.398 50.000 0.00 0.00 0.00 2.27
5236 5690 4.356289 ACTTGTACACGGCATTGTTTTTC 58.644 39.130 4.21 0.00 0.00 2.29
5241 5696 1.144969 CGACTTGTACACGGCATTGT 58.855 50.000 5.98 0.00 0.00 2.71
5298 5753 4.111375 TCTTAACAGAATGGCGAGACTC 57.889 45.455 0.00 0.00 43.62 3.36
5381 5861 3.997021 ACTTCAGTGTTCCTATGCTTTCG 59.003 43.478 0.00 0.00 0.00 3.46
5392 5872 2.298729 AGCTCTCCTCACTTCAGTGTTC 59.701 50.000 6.84 0.00 45.76 3.18
5435 5917 0.804989 CGAAGTCCCAAATCAGGTGC 59.195 55.000 0.00 0.00 0.00 5.01
5436 5918 0.804989 GCGAAGTCCCAAATCAGGTG 59.195 55.000 0.00 0.00 0.00 4.00
5442 5924 0.036306 AAGTCGGCGAAGTCCCAAAT 59.964 50.000 12.92 0.00 0.00 2.32
5457 5939 3.368236 GTGAGCTCAAACGGATGTAAGTC 59.632 47.826 20.19 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.