Multiple sequence alignment - TraesCS4A01G180400

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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 TraesCS4A01G180400 chr4A 100.000 4208 0 0 1 4208 454606017 454601810 0.000000e+00 7771.0
1 TraesCS4A01G180400 chr4A 98.049 205 4 0 3 207 453695238 453695442 1.440000e-94 357.0
2 TraesCS4A01G180400 chr4A 96.651 209 6 1 3 210 78541229 78541437 3.110000e-91 346.0
3 TraesCS4A01G180400 chr4B 94.542 2730 78 20 1510 4208 181438327 181435638 0.000000e+00 4150.0
4 TraesCS4A01G180400 chr4B 92.257 607 21 10 887 1491 181438897 181438315 0.000000e+00 837.0
5 TraesCS4A01G180400 chr4D 92.520 2714 129 33 890 3587 119235516 119232861 0.000000e+00 3819.0
6 TraesCS4A01G180400 chr4D 94.004 517 8 5 3714 4208 119232690 119232175 0.000000e+00 761.0
7 TraesCS4A01G180400 chr6D 90.824 643 55 3 210 850 412287439 412288079 0.000000e+00 857.0
8 TraesCS4A01G180400 chr6D 100.000 29 0 0 3873 3901 42691223 42691251 2.000000e-03 54.7
9 TraesCS4A01G180400 chr6D 100.000 29 0 0 3873 3901 345417648 345417676 2.000000e-03 54.7
10 TraesCS4A01G180400 chr1D 88.992 645 66 4 210 852 112224277 112224918 0.000000e+00 793.0
11 TraesCS4A01G180400 chr1D 88.958 643 66 4 210 850 381372472 381373111 0.000000e+00 789.0
12 TraesCS4A01G180400 chr1D 85.556 90 8 5 3713 3799 86511952 86512039 5.790000e-14 89.8
13 TraesCS4A01G180400 chr6B 85.537 643 88 4 210 850 213627106 213627745 0.000000e+00 667.0
14 TraesCS4A01G180400 chr6B 85.358 642 86 7 213 850 658547235 658546598 0.000000e+00 658.0
15 TraesCS4A01G180400 chr6B 86.473 207 22 5 3895 4099 78227735 78227533 5.480000e-54 222.0
16 TraesCS4A01G180400 chr5D 82.884 631 100 7 223 850 434823882 434824507 1.020000e-155 560.0
17 TraesCS4A01G180400 chr5D 77.925 530 89 22 2153 2669 229188235 229187721 5.290000e-79 305.0
18 TraesCS4A01G180400 chr5D 74.368 277 60 8 3925 4199 243827687 243827954 1.600000e-19 108.0
19 TraesCS4A01G180400 chr3A 88.350 309 31 4 3863 4166 146596840 146597148 2.390000e-97 366.0
20 TraesCS4A01G180400 chr3A 97.596 208 5 0 3 210 273134663 273134870 1.440000e-94 357.0
21 TraesCS4A01G180400 chr3A 97.596 208 5 0 3 210 273223070 273223277 1.440000e-94 357.0
22 TraesCS4A01G180400 chr3A 87.912 91 10 1 3713 3802 75415576 75415666 5.750000e-19 106.0
23 TraesCS4A01G180400 chr3A 84.091 88 10 4 3713 3798 11779770 11779685 9.700000e-12 82.4
24 TraesCS4A01G180400 chr7A 98.030 203 3 1 3 204 398649756 398649958 6.690000e-93 351.0
25 TraesCS4A01G180400 chr7A 96.651 209 5 2 3 210 300386085 300386292 3.110000e-91 346.0
26 TraesCS4A01G180400 chr7A 87.912 91 10 1 3713 3802 125267732 125267822 5.750000e-19 106.0
27 TraesCS4A01G180400 chr7A 97.674 43 1 0 3872 3914 735859517 735859559 1.620000e-09 75.0
28 TraesCS4A01G180400 chr6A 97.129 209 5 1 3 211 220630358 220630151 6.690000e-93 351.0
29 TraesCS4A01G180400 chr5A 96.190 210 8 0 1 210 217617840 217617631 1.120000e-90 344.0
30 TraesCS4A01G180400 chr5A 78.339 554 90 22 2153 2692 327434071 327434608 8.720000e-87 331.0
31 TraesCS4A01G180400 chr5A 87.912 91 10 1 3713 3802 464180991 464181081 5.750000e-19 106.0
32 TraesCS4A01G180400 chr1A 97.059 204 6 0 3 206 342157227 342157430 1.120000e-90 344.0
33 TraesCS4A01G180400 chr1A 86.893 206 21 6 3892 4095 279838744 279838945 4.230000e-55 226.0
34 TraesCS4A01G180400 chr5B 78.080 552 93 22 2153 2691 276658562 276659098 1.460000e-84 324.0
35 TraesCS4A01G180400 chrUn 86.667 210 22 5 3892 4099 112546032 112546237 1.180000e-55 228.0
36 TraesCS4A01G180400 chrUn 100.000 29 0 0 3873 3901 69931920 69931948 2.000000e-03 54.7
37 TraesCS4A01G180400 chrUn 100.000 29 0 0 3873 3901 95362171 95362199 2.000000e-03 54.7
38 TraesCS4A01G180400 chr2D 86.813 91 11 1 3713 3802 540062248 540062338 2.680000e-17 100.0
39 TraesCS4A01G180400 chr7B 85.870 92 11 2 3713 3802 570103161 570103070 3.460000e-16 97.1
40 TraesCS4A01G180400 chr2B 97.674 43 1 0 3872 3914 253718771 253718729 1.620000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G180400 chr4A 454601810 454606017 4207 True 7771.0 7771 100.0000 1 4208 1 chr4A.!!$R1 4207
1 TraesCS4A01G180400 chr4B 181435638 181438897 3259 True 2493.5 4150 93.3995 887 4208 2 chr4B.!!$R1 3321
2 TraesCS4A01G180400 chr4D 119232175 119235516 3341 True 2290.0 3819 93.2620 890 4208 2 chr4D.!!$R1 3318
3 TraesCS4A01G180400 chr6D 412287439 412288079 640 False 857.0 857 90.8240 210 850 1 chr6D.!!$F3 640
4 TraesCS4A01G180400 chr1D 112224277 112224918 641 False 793.0 793 88.9920 210 852 1 chr1D.!!$F2 642
5 TraesCS4A01G180400 chr1D 381372472 381373111 639 False 789.0 789 88.9580 210 850 1 chr1D.!!$F3 640
6 TraesCS4A01G180400 chr6B 213627106 213627745 639 False 667.0 667 85.5370 210 850 1 chr6B.!!$F1 640
7 TraesCS4A01G180400 chr6B 658546598 658547235 637 True 658.0 658 85.3580 213 850 1 chr6B.!!$R2 637
8 TraesCS4A01G180400 chr5D 434823882 434824507 625 False 560.0 560 82.8840 223 850 1 chr5D.!!$F2 627
9 TraesCS4A01G180400 chr5D 229187721 229188235 514 True 305.0 305 77.9250 2153 2669 1 chr5D.!!$R1 516
10 TraesCS4A01G180400 chr5A 327434071 327434608 537 False 331.0 331 78.3390 2153 2692 1 chr5A.!!$F1 539
11 TraesCS4A01G180400 chr5B 276658562 276659098 536 False 324.0 324 78.0800 2153 2691 1 chr5B.!!$F1 538

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
174 175 0.173708 CCTCTAAGTCGTGCCCTGAC 59.826 60.000 0.00 0.00 36.60 3.51 F
205 206 0.323360 ATAGCCGCATTGTGGGTGTT 60.323 50.000 26.86 13.84 44.01 3.32 F
430 431 0.324614 TGAGGCAGGTGTGGTACATG 59.675 55.000 0.00 0.00 44.52 3.21 F
502 503 0.524862 CAATCAGCAACTGGTGGAGC 59.475 55.000 8.91 0.00 43.23 4.70 F
1260 1267 1.066573 CCATCTTCAAGTCCGCTGTCT 60.067 52.381 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1434 0.036388 TGGCTGAATGAAGGGACGAC 60.036 55.000 0.00 0.0 0.00 4.34 R
1722 1748 0.893270 AGCATAAACAGCGGTGCCAA 60.893 50.000 15.82 0.0 38.31 4.52 R
1861 1887 1.433534 TCATGTAACGCATTGCACGA 58.566 45.000 9.69 0.0 35.19 4.35 R
2447 2490 2.670934 GTGTCCAGCCCAGCACAG 60.671 66.667 0.00 0.0 32.62 3.66 R
3242 3285 0.820871 GTCCTGGTTTGTTTGCACCA 59.179 50.000 0.00 0.0 40.98 4.17 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
24 25 6.732896 ATAGTCGGACCTTGATTGTATTCT 57.267 37.500 4.14 0.00 0.00 2.40
25 26 4.759782 AGTCGGACCTTGATTGTATTCTG 58.240 43.478 4.14 0.00 0.00 3.02
26 27 3.871594 GTCGGACCTTGATTGTATTCTGG 59.128 47.826 0.00 0.00 0.00 3.86
27 28 3.772572 TCGGACCTTGATTGTATTCTGGA 59.227 43.478 0.00 0.00 0.00 3.86
28 29 4.408921 TCGGACCTTGATTGTATTCTGGAT 59.591 41.667 0.00 0.00 0.00 3.41
29 30 4.512944 CGGACCTTGATTGTATTCTGGATG 59.487 45.833 0.00 0.00 0.00 3.51
30 31 5.684704 GGACCTTGATTGTATTCTGGATGA 58.315 41.667 0.00 0.00 0.00 2.92
31 32 6.302269 GGACCTTGATTGTATTCTGGATGAT 58.698 40.000 0.00 0.00 0.00 2.45
32 33 6.206243 GGACCTTGATTGTATTCTGGATGATG 59.794 42.308 0.00 0.00 0.00 3.07
33 34 6.666678 ACCTTGATTGTATTCTGGATGATGT 58.333 36.000 0.00 0.00 0.00 3.06
34 35 7.805163 ACCTTGATTGTATTCTGGATGATGTA 58.195 34.615 0.00 0.00 0.00 2.29
35 36 8.443176 ACCTTGATTGTATTCTGGATGATGTAT 58.557 33.333 0.00 0.00 0.00 2.29
36 37 8.727910 CCTTGATTGTATTCTGGATGATGTATG 58.272 37.037 0.00 0.00 0.00 2.39
37 38 9.498176 CTTGATTGTATTCTGGATGATGTATGA 57.502 33.333 0.00 0.00 0.00 2.15
64 65 4.937696 TTATGTATTGTGTGAAGTGGCG 57.062 40.909 0.00 0.00 0.00 5.69
65 66 2.535012 TGTATTGTGTGAAGTGGCGA 57.465 45.000 0.00 0.00 0.00 5.54
66 67 3.052455 TGTATTGTGTGAAGTGGCGAT 57.948 42.857 0.00 0.00 0.00 4.58
67 68 3.407698 TGTATTGTGTGAAGTGGCGATT 58.592 40.909 0.00 0.00 0.00 3.34
68 69 2.995466 ATTGTGTGAAGTGGCGATTG 57.005 45.000 0.00 0.00 0.00 2.67
69 70 1.674359 TTGTGTGAAGTGGCGATTGT 58.326 45.000 0.00 0.00 0.00 2.71
70 71 2.535012 TGTGTGAAGTGGCGATTGTA 57.465 45.000 0.00 0.00 0.00 2.41
71 72 2.839975 TGTGTGAAGTGGCGATTGTAA 58.160 42.857 0.00 0.00 0.00 2.41
72 73 2.805671 TGTGTGAAGTGGCGATTGTAAG 59.194 45.455 0.00 0.00 0.00 2.34
73 74 1.804151 TGTGAAGTGGCGATTGTAAGC 59.196 47.619 0.00 0.00 0.00 3.09
78 79 4.515404 GGCGATTGTAAGCCGACT 57.485 55.556 0.00 0.00 44.22 4.18
79 80 2.298593 GGCGATTGTAAGCCGACTC 58.701 57.895 0.00 0.00 44.22 3.36
80 81 0.179108 GGCGATTGTAAGCCGACTCT 60.179 55.000 0.00 0.00 44.22 3.24
81 82 1.641577 GCGATTGTAAGCCGACTCTT 58.358 50.000 0.00 0.00 0.00 2.85
82 83 2.000447 GCGATTGTAAGCCGACTCTTT 59.000 47.619 0.00 0.00 0.00 2.52
83 84 3.184541 GCGATTGTAAGCCGACTCTTTA 58.815 45.455 0.00 0.00 0.00 1.85
84 85 3.802685 GCGATTGTAAGCCGACTCTTTAT 59.197 43.478 0.00 0.00 0.00 1.40
85 86 4.085004 GCGATTGTAAGCCGACTCTTTATC 60.085 45.833 0.00 0.00 0.00 1.75
86 87 4.444720 CGATTGTAAGCCGACTCTTTATCC 59.555 45.833 0.00 0.00 0.00 2.59
87 88 3.814005 TGTAAGCCGACTCTTTATCCC 57.186 47.619 0.00 0.00 0.00 3.85
88 89 3.371965 TGTAAGCCGACTCTTTATCCCT 58.628 45.455 0.00 0.00 0.00 4.20
89 90 3.773119 TGTAAGCCGACTCTTTATCCCTT 59.227 43.478 0.00 0.00 0.00 3.95
90 91 4.224370 TGTAAGCCGACTCTTTATCCCTTT 59.776 41.667 0.00 0.00 0.00 3.11
91 92 3.545366 AGCCGACTCTTTATCCCTTTC 57.455 47.619 0.00 0.00 0.00 2.62
92 93 3.108376 AGCCGACTCTTTATCCCTTTCT 58.892 45.455 0.00 0.00 0.00 2.52
93 94 3.519913 AGCCGACTCTTTATCCCTTTCTT 59.480 43.478 0.00 0.00 0.00 2.52
94 95 4.715297 AGCCGACTCTTTATCCCTTTCTTA 59.285 41.667 0.00 0.00 0.00 2.10
95 96 5.367060 AGCCGACTCTTTATCCCTTTCTTAT 59.633 40.000 0.00 0.00 0.00 1.73
96 97 6.056236 GCCGACTCTTTATCCCTTTCTTATT 58.944 40.000 0.00 0.00 0.00 1.40
97 98 6.203145 GCCGACTCTTTATCCCTTTCTTATTC 59.797 42.308 0.00 0.00 0.00 1.75
98 99 7.272978 CCGACTCTTTATCCCTTTCTTATTCA 58.727 38.462 0.00 0.00 0.00 2.57
99 100 7.439655 CCGACTCTTTATCCCTTTCTTATTCAG 59.560 40.741 0.00 0.00 0.00 3.02
100 101 7.982354 CGACTCTTTATCCCTTTCTTATTCAGT 59.018 37.037 0.00 0.00 0.00 3.41
106 107 9.627123 TTTATCCCTTTCTTATTCAGTACATGG 57.373 33.333 0.00 0.00 0.00 3.66
107 108 6.001449 TCCCTTTCTTATTCAGTACATGGG 57.999 41.667 0.00 0.00 0.00 4.00
108 109 5.729229 TCCCTTTCTTATTCAGTACATGGGA 59.271 40.000 0.00 0.00 36.62 4.37
109 110 6.389869 TCCCTTTCTTATTCAGTACATGGGAT 59.610 38.462 0.00 0.00 34.37 3.85
110 111 6.488006 CCCTTTCTTATTCAGTACATGGGATG 59.512 42.308 0.00 0.00 31.98 3.51
111 112 7.056635 CCTTTCTTATTCAGTACATGGGATGT 58.943 38.462 0.00 0.00 46.92 3.06
112 113 7.012704 CCTTTCTTATTCAGTACATGGGATGTG 59.987 40.741 0.00 0.00 44.60 3.21
113 114 6.560003 TCTTATTCAGTACATGGGATGTGT 57.440 37.500 0.00 0.00 44.60 3.72
114 115 6.348498 TCTTATTCAGTACATGGGATGTGTG 58.652 40.000 0.00 0.00 44.60 3.82
115 116 4.842531 ATTCAGTACATGGGATGTGTGA 57.157 40.909 0.00 0.55 44.60 3.58
116 117 4.632327 TTCAGTACATGGGATGTGTGAA 57.368 40.909 0.00 10.19 44.60 3.18
117 118 4.206477 TCAGTACATGGGATGTGTGAAG 57.794 45.455 0.00 0.00 44.60 3.02
118 119 3.837731 TCAGTACATGGGATGTGTGAAGA 59.162 43.478 0.00 0.00 44.60 2.87
119 120 4.471025 TCAGTACATGGGATGTGTGAAGAT 59.529 41.667 0.00 0.00 44.60 2.40
120 121 5.045651 TCAGTACATGGGATGTGTGAAGATT 60.046 40.000 0.00 0.00 44.60 2.40
121 122 6.156083 TCAGTACATGGGATGTGTGAAGATTA 59.844 38.462 0.00 0.00 44.60 1.75
122 123 6.258727 CAGTACATGGGATGTGTGAAGATTAC 59.741 42.308 0.00 0.00 44.60 1.89
123 124 4.526970 ACATGGGATGTGTGAAGATTACC 58.473 43.478 0.00 0.00 43.01 2.85
124 125 3.644966 TGGGATGTGTGAAGATTACCC 57.355 47.619 0.00 0.00 36.92 3.69
125 126 2.241176 TGGGATGTGTGAAGATTACCCC 59.759 50.000 0.00 0.00 35.69 4.95
126 127 2.509964 GGGATGTGTGAAGATTACCCCT 59.490 50.000 0.00 0.00 0.00 4.79
127 128 3.053619 GGGATGTGTGAAGATTACCCCTT 60.054 47.826 0.00 0.00 0.00 3.95
128 129 4.569865 GGGATGTGTGAAGATTACCCCTTT 60.570 45.833 0.00 0.00 0.00 3.11
129 130 5.016831 GGATGTGTGAAGATTACCCCTTTT 58.983 41.667 0.00 0.00 0.00 2.27
130 131 5.105756 GGATGTGTGAAGATTACCCCTTTTG 60.106 44.000 0.00 0.00 0.00 2.44
131 132 3.572255 TGTGTGAAGATTACCCCTTTTGC 59.428 43.478 0.00 0.00 0.00 3.68
132 133 2.817258 TGTGAAGATTACCCCTTTTGCG 59.183 45.455 0.00 0.00 0.00 4.85
133 134 3.078837 GTGAAGATTACCCCTTTTGCGA 58.921 45.455 0.00 0.00 0.00 5.10
134 135 3.078837 TGAAGATTACCCCTTTTGCGAC 58.921 45.455 0.00 0.00 0.00 5.19
135 136 2.871096 AGATTACCCCTTTTGCGACA 57.129 45.000 0.00 0.00 0.00 4.35
136 137 3.149005 AGATTACCCCTTTTGCGACAA 57.851 42.857 0.00 0.00 0.00 3.18
137 138 3.492337 AGATTACCCCTTTTGCGACAAA 58.508 40.909 1.63 1.63 0.00 2.83
138 139 3.254903 AGATTACCCCTTTTGCGACAAAC 59.745 43.478 4.80 0.00 0.00 2.93
139 140 1.320507 TACCCCTTTTGCGACAAACC 58.679 50.000 4.80 0.00 0.00 3.27
140 141 0.396556 ACCCCTTTTGCGACAAACCT 60.397 50.000 4.80 0.00 0.00 3.50
141 142 1.133730 ACCCCTTTTGCGACAAACCTA 60.134 47.619 4.80 0.00 0.00 3.08
142 143 1.268625 CCCCTTTTGCGACAAACCTAC 59.731 52.381 4.80 0.00 0.00 3.18
143 144 1.268625 CCCTTTTGCGACAAACCTACC 59.731 52.381 4.80 0.00 0.00 3.18
144 145 1.950909 CCTTTTGCGACAAACCTACCA 59.049 47.619 4.80 0.00 0.00 3.25
145 146 2.556622 CCTTTTGCGACAAACCTACCAT 59.443 45.455 4.80 0.00 0.00 3.55
146 147 3.564511 CTTTTGCGACAAACCTACCATG 58.435 45.455 4.80 0.00 0.00 3.66
147 148 0.878416 TTGCGACAAACCTACCATGC 59.122 50.000 0.00 0.00 0.00 4.06
148 149 1.295357 TGCGACAAACCTACCATGCG 61.295 55.000 0.00 0.00 0.00 4.73
149 150 1.977594 GCGACAAACCTACCATGCGG 61.978 60.000 0.00 0.00 38.77 5.69
150 151 1.800681 GACAAACCTACCATGCGGC 59.199 57.895 0.00 0.00 34.57 6.53
151 152 0.676782 GACAAACCTACCATGCGGCT 60.677 55.000 0.00 0.00 34.57 5.52
152 153 0.616371 ACAAACCTACCATGCGGCTA 59.384 50.000 0.00 0.00 34.57 3.93
153 154 1.211949 ACAAACCTACCATGCGGCTAT 59.788 47.619 0.00 0.00 34.57 2.97
154 155 1.603802 CAAACCTACCATGCGGCTATG 59.396 52.381 0.00 3.60 34.57 2.23
155 156 0.535102 AACCTACCATGCGGCTATGC 60.535 55.000 0.00 0.00 34.57 3.14
156 157 1.672356 CCTACCATGCGGCTATGCC 60.672 63.158 0.00 0.00 46.75 4.40
167 168 2.141535 GGCTATGCCTCTAAGTCGTG 57.858 55.000 0.73 0.00 46.69 4.35
168 169 1.492720 GCTATGCCTCTAAGTCGTGC 58.507 55.000 0.00 0.00 0.00 5.34
169 170 1.870167 GCTATGCCTCTAAGTCGTGCC 60.870 57.143 0.00 0.00 0.00 5.01
170 171 0.750850 TATGCCTCTAAGTCGTGCCC 59.249 55.000 0.00 0.00 0.00 5.36
171 172 0.978146 ATGCCTCTAAGTCGTGCCCT 60.978 55.000 0.00 0.00 0.00 5.19
172 173 1.153549 GCCTCTAAGTCGTGCCCTG 60.154 63.158 0.00 0.00 0.00 4.45
173 174 1.605058 GCCTCTAAGTCGTGCCCTGA 61.605 60.000 0.00 0.00 0.00 3.86
174 175 0.173708 CCTCTAAGTCGTGCCCTGAC 59.826 60.000 0.00 0.00 36.60 3.51
175 176 0.888619 CTCTAAGTCGTGCCCTGACA 59.111 55.000 3.38 0.00 38.83 3.58
176 177 0.601558 TCTAAGTCGTGCCCTGACAC 59.398 55.000 3.38 0.00 38.83 3.67
182 183 3.936203 GTGCCCTGACACGTGGGA 61.936 66.667 21.57 4.43 46.15 4.37
183 184 3.625897 TGCCCTGACACGTGGGAG 61.626 66.667 21.57 14.30 46.15 4.30
184 185 3.311110 GCCCTGACACGTGGGAGA 61.311 66.667 21.57 0.00 46.15 3.71
185 186 2.660064 GCCCTGACACGTGGGAGAT 61.660 63.158 21.57 0.00 46.15 2.75
186 187 1.327690 GCCCTGACACGTGGGAGATA 61.328 60.000 21.57 0.00 46.15 1.98
187 188 1.414158 CCCTGACACGTGGGAGATAT 58.586 55.000 21.57 0.00 46.15 1.63
188 189 2.594131 CCCTGACACGTGGGAGATATA 58.406 52.381 21.57 0.00 46.15 0.86
189 190 2.558795 CCCTGACACGTGGGAGATATAG 59.441 54.545 21.57 5.71 46.15 1.31
190 191 2.029828 CCTGACACGTGGGAGATATAGC 60.030 54.545 21.57 0.00 0.00 2.97
191 192 1.961394 TGACACGTGGGAGATATAGCC 59.039 52.381 21.57 0.00 0.00 3.93
192 193 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
193 194 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
194 195 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
195 196 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
196 197 1.066858 CGTGGGAGATATAGCCGCATT 60.067 52.381 0.00 0.00 0.00 3.56
197 198 2.350522 GTGGGAGATATAGCCGCATTG 58.649 52.381 0.00 0.00 0.00 2.82
198 199 1.977854 TGGGAGATATAGCCGCATTGT 59.022 47.619 0.00 0.00 0.00 2.71
199 200 2.289631 TGGGAGATATAGCCGCATTGTG 60.290 50.000 0.00 0.00 0.00 3.33
200 201 2.350522 GGAGATATAGCCGCATTGTGG 58.649 52.381 12.04 12.04 36.10 4.17
201 202 2.350522 GAGATATAGCCGCATTGTGGG 58.649 52.381 17.65 5.07 33.18 4.61
202 203 1.699634 AGATATAGCCGCATTGTGGGT 59.300 47.619 23.14 23.14 46.10 4.51
203 204 1.806542 GATATAGCCGCATTGTGGGTG 59.193 52.381 26.86 0.00 44.01 4.61
204 205 0.544223 TATAGCCGCATTGTGGGTGT 59.456 50.000 26.86 23.05 44.01 4.16
205 206 0.323360 ATAGCCGCATTGTGGGTGTT 60.323 50.000 26.86 13.84 44.01 3.32
206 207 0.538516 TAGCCGCATTGTGGGTGTTT 60.539 50.000 26.86 1.89 44.01 2.83
207 208 1.372872 GCCGCATTGTGGGTGTTTC 60.373 57.895 17.65 0.00 33.18 2.78
208 209 2.037053 CCGCATTGTGGGTGTTTCA 58.963 52.632 8.45 0.00 0.00 2.69
227 228 8.296713 GTGTTTCAATCAGGTTTCAAGCTTATA 58.703 33.333 0.00 0.00 33.87 0.98
250 251 1.686115 GCCATATGGAAGTGTTGGGCT 60.686 52.381 26.47 0.00 37.22 5.19
253 254 1.367346 TATGGAAGTGTTGGGCTCCA 58.633 50.000 0.00 0.00 0.00 3.86
254 255 0.706433 ATGGAAGTGTTGGGCTCCAT 59.294 50.000 0.00 0.00 31.53 3.41
302 303 0.749454 GGTGCAATACAGGCTCTGGG 60.749 60.000 7.06 0.00 35.51 4.45
322 323 3.110178 GCGGACAGACGGTTTCGG 61.110 66.667 0.00 0.00 41.39 4.30
367 368 3.081061 ACCATGTTATCTTTGCGAGCAA 58.919 40.909 6.39 6.39 0.00 3.91
376 377 2.146342 CTTTGCGAGCAAGAGGAAGAA 58.854 47.619 10.52 0.00 37.24 2.52
388 389 5.126707 GCAAGAGGAAGAAATTGTGGATCAT 59.873 40.000 0.00 0.00 0.00 2.45
411 412 3.969117 CACTATGCAGTGTGTGTTTGT 57.031 42.857 12.14 0.00 46.03 2.83
430 431 0.324614 TGAGGCAGGTGTGGTACATG 59.675 55.000 0.00 0.00 44.52 3.21
491 492 1.542472 CACAGCATTCCACAATCAGCA 59.458 47.619 0.00 0.00 0.00 4.41
501 502 1.538512 CACAATCAGCAACTGGTGGAG 59.461 52.381 8.91 2.69 43.23 3.86
502 503 0.524862 CAATCAGCAACTGGTGGAGC 59.475 55.000 8.91 0.00 43.23 4.70
570 571 1.476891 GGTGGTCACTTCGATCTGCTA 59.523 52.381 0.93 0.00 0.00 3.49
595 596 2.121291 TATGGAAGCAACGCAATGGA 57.879 45.000 0.00 0.00 0.00 3.41
628 632 3.769844 GGAGGACTGACTAAGGAATGTCA 59.230 47.826 0.00 0.00 40.39 3.58
657 661 1.815003 GTGGACCTGATTTGGCAAGAG 59.185 52.381 0.00 0.00 0.00 2.85
664 668 5.574188 ACCTGATTTGGCAAGAGTTAGAAT 58.426 37.500 0.00 0.00 0.00 2.40
672 676 3.440522 GGCAAGAGTTAGAATTGTGGTCC 59.559 47.826 0.00 0.00 0.00 4.46
707 711 2.035961 CCGGAGTATCTACATGGTGTGG 59.964 54.545 0.00 0.00 33.73 4.17
719 723 3.109151 CATGGTGTGGGTAGTAGGGTAA 58.891 50.000 0.00 0.00 0.00 2.85
720 724 2.539302 TGGTGTGGGTAGTAGGGTAAC 58.461 52.381 0.00 0.00 0.00 2.50
729 733 4.578928 GGGTAGTAGGGTAACGTTTCGATA 59.421 45.833 5.91 0.00 35.44 2.92
730 734 5.241728 GGGTAGTAGGGTAACGTTTCGATAT 59.758 44.000 5.91 0.00 35.44 1.63
748 752 2.482414 ATACGGAGGGTATGGTGGAA 57.518 50.000 0.00 0.00 40.34 3.53
784 789 7.559335 TGCCATCTATCTACCATGTAATCTT 57.441 36.000 0.00 0.00 0.00 2.40
785 790 7.977818 TGCCATCTATCTACCATGTAATCTTT 58.022 34.615 0.00 0.00 0.00 2.52
786 791 8.439971 TGCCATCTATCTACCATGTAATCTTTT 58.560 33.333 0.00 0.00 0.00 2.27
828 833 8.028938 TCTTTTTCTATAAAGTTACGGTACGCT 58.971 33.333 0.00 0.00 44.72 5.07
906 911 4.483476 AAAGTACTAAAAAGCCACAGCG 57.517 40.909 0.00 0.00 46.67 5.18
907 912 1.804748 AGTACTAAAAAGCCACAGCGC 59.195 47.619 0.00 0.00 46.67 5.92
908 913 1.533731 GTACTAAAAAGCCACAGCGCA 59.466 47.619 11.47 0.00 46.67 6.09
1070 1077 2.362369 CCTCTGCTCCCGTGTCCAT 61.362 63.158 0.00 0.00 0.00 3.41
1256 1263 1.078143 GCCCATCTTCAAGTCCGCT 60.078 57.895 0.00 0.00 0.00 5.52
1260 1267 1.066573 CCATCTTCAAGTCCGCTGTCT 60.067 52.381 0.00 0.00 0.00 3.41
1402 1416 2.233922 TCCCAGCAGCTGTAAGTTACTC 59.766 50.000 21.26 6.24 35.30 2.59
1403 1417 2.622436 CCAGCAGCTGTAAGTTACTCC 58.378 52.381 21.26 5.22 35.30 3.85
1404 1418 2.234908 CCAGCAGCTGTAAGTTACTCCT 59.765 50.000 21.26 7.27 35.30 3.69
1405 1419 3.516615 CAGCAGCTGTAAGTTACTCCTC 58.483 50.000 16.64 0.00 35.30 3.71
1406 1420 2.498078 AGCAGCTGTAAGTTACTCCTCC 59.502 50.000 16.64 1.29 35.30 4.30
1407 1421 2.735762 GCAGCTGTAAGTTACTCCTCCG 60.736 54.545 16.64 1.90 35.30 4.63
1408 1422 2.492484 CAGCTGTAAGTTACTCCTCCGT 59.508 50.000 14.00 0.00 35.30 4.69
1420 1434 7.042335 AGTTACTCCTCCGTATTTGATTTGAG 58.958 38.462 0.00 0.00 0.00 3.02
1454 1468 4.811969 TCAGCCAAGAACCGTTTCTATA 57.188 40.909 0.00 0.00 41.56 1.31
1498 1512 7.886338 AGGTAAGAATGTGGAATTGTCTTTTC 58.114 34.615 0.00 0.00 31.28 2.29
1505 1519 8.421249 AATGTGGAATTGTCTTTTCCTGAATA 57.579 30.769 4.28 0.00 42.63 1.75
1583 1597 2.087646 GAAGAAGCTGATCACCCCAAC 58.912 52.381 0.00 0.00 0.00 3.77
1700 1726 5.484173 TCTGCCTGTAATAATGCGAAAAG 57.516 39.130 0.00 0.00 0.00 2.27
1701 1727 4.941263 TCTGCCTGTAATAATGCGAAAAGT 59.059 37.500 0.00 0.00 0.00 2.66
1722 1748 4.021016 AGTTAGAAATCTGCTTCGTGGTCT 60.021 41.667 0.00 0.00 0.00 3.85
1739 1765 1.135689 GTCTTGGCACCGCTGTTTATG 60.136 52.381 0.00 0.00 0.00 1.90
1749 1775 2.029244 CCGCTGTTTATGCTTCGTACAG 59.971 50.000 0.00 0.00 39.29 2.74
1861 1887 7.803279 AATCTTTTTCGTAAGGTGAAGTCTT 57.197 32.000 0.00 0.00 38.47 3.01
1917 1943 1.340017 TGCTCCTTGGTGTTATCAGCC 60.340 52.381 0.74 0.00 40.84 4.85
1947 1973 9.277783 GAGTAATGTCTGCTAATTTGACCATAT 57.722 33.333 0.00 0.00 0.00 1.78
2009 2035 2.967270 GGCTTTGCCCAAGTCTGAT 58.033 52.632 0.00 0.00 44.06 2.90
2015 2041 4.023365 GCTTTGCCCAAGTCTGATATCATC 60.023 45.833 5.72 3.07 34.56 2.92
2118 2151 7.064134 CGTGGAATATGCTTAGTTCACAAGTAA 59.936 37.037 16.07 0.00 0.00 2.24
2126 2159 8.492673 TGCTTAGTTCACAAGTAATAGAATGG 57.507 34.615 0.00 0.00 0.00 3.16
2380 2416 1.069636 CCGAACTGCTCTTCTTGCAAC 60.070 52.381 0.00 0.00 40.13 4.17
2447 2490 2.540515 TGCATCGATTTCTTCCTCGTC 58.459 47.619 0.00 0.00 36.33 4.20
2728 2771 2.465860 TGTCATTAACCCAGTGTCCG 57.534 50.000 0.00 0.00 0.00 4.79
2769 2812 2.512515 GAGCCATCCAGCGACACC 60.513 66.667 0.00 0.00 38.01 4.16
2794 2837 5.831702 AATGCTGAAAGATGATGAGGAAC 57.168 39.130 0.00 0.00 34.07 3.62
2798 2841 5.055812 GCTGAAAGATGATGAGGAACCTAG 58.944 45.833 0.00 0.00 34.07 3.02
2799 2842 5.396213 GCTGAAAGATGATGAGGAACCTAGT 60.396 44.000 0.00 0.00 34.07 2.57
2800 2843 6.183360 GCTGAAAGATGATGAGGAACCTAGTA 60.183 42.308 0.00 0.00 34.07 1.82
2801 2844 7.633772 GCTGAAAGATGATGAGGAACCTAGTAA 60.634 40.741 0.00 0.00 34.07 2.24
2802 2845 7.786030 TGAAAGATGATGAGGAACCTAGTAAG 58.214 38.462 0.00 0.00 0.00 2.34
2833 2876 0.041238 AGTAGTACAGGAGCCAGGCA 59.959 55.000 15.80 0.00 0.00 4.75
3003 3046 4.929808 ACTAGAAGAGTAAAACATGTGCCG 59.070 41.667 0.00 0.00 36.27 5.69
3140 3183 1.983972 CTACTCGGTGAGACTGCAAC 58.016 55.000 0.00 0.00 33.32 4.17
3191 3234 1.814394 GAAGCATGATTCACAGCACCA 59.186 47.619 18.52 0.00 0.00 4.17
3342 3385 2.663602 CTCTTCGACCACAGAACGAATG 59.336 50.000 0.00 0.00 43.22 2.67
3346 3389 2.094906 TCGACCACAGAACGAATGGTAG 60.095 50.000 0.00 0.00 46.86 3.18
3375 3419 3.531814 AGGGGTAGCCTTGGAATGTTTAT 59.468 43.478 11.48 0.00 0.00 1.40
3376 3420 4.016572 AGGGGTAGCCTTGGAATGTTTATT 60.017 41.667 11.48 0.00 0.00 1.40
3377 3421 5.194942 AGGGGTAGCCTTGGAATGTTTATTA 59.805 40.000 11.48 0.00 0.00 0.98
3414 3458 5.415701 TGAAAGAAGTGGAACCTGAATATGC 59.584 40.000 0.00 0.00 37.80 3.14
3586 3630 4.673580 GCATGCATGTCTCTTCGTTTTGAT 60.674 41.667 26.79 0.00 0.00 2.57
3588 3632 3.814842 TGCATGTCTCTTCGTTTTGATGT 59.185 39.130 0.00 0.00 0.00 3.06
3613 3657 5.749596 TCACCGGATTATTGTTAATGCAG 57.250 39.130 9.46 0.00 36.29 4.41
3657 3702 5.221722 TGGCACTGATAGATCTATTTGGACC 60.222 44.000 16.37 14.86 0.00 4.46
3791 3983 5.523916 GCCGAATTAGAAAGCATTACTCTCA 59.476 40.000 0.00 0.00 0.00 3.27
3865 4064 5.360714 TCCACCCTAGTTACCAAACTATACG 59.639 44.000 0.00 0.00 45.03 3.06
3926 4136 0.537188 AGTAGACCTGAATGCCACCG 59.463 55.000 0.00 0.00 0.00 4.94
4191 4406 2.649742 TTCTCCTGAAGGACCCAGAT 57.350 50.000 0.00 0.00 39.78 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.255836 CCAGAATACAATCAAGGTCCGACTATA 60.256 40.741 0.00 0.00 0.00 1.31
1 2 6.463049 CCAGAATACAATCAAGGTCCGACTAT 60.463 42.308 0.00 0.00 0.00 2.12
3 4 4.383118 CCAGAATACAATCAAGGTCCGACT 60.383 45.833 0.00 0.00 0.00 4.18
4 5 3.871594 CCAGAATACAATCAAGGTCCGAC 59.128 47.826 0.00 0.00 0.00 4.79
5 6 3.772572 TCCAGAATACAATCAAGGTCCGA 59.227 43.478 0.00 0.00 0.00 4.55
6 7 4.137116 TCCAGAATACAATCAAGGTCCG 57.863 45.455 0.00 0.00 0.00 4.79
7 8 5.684704 TCATCCAGAATACAATCAAGGTCC 58.315 41.667 0.00 0.00 0.00 4.46
8 9 6.769822 ACATCATCCAGAATACAATCAAGGTC 59.230 38.462 0.00 0.00 0.00 3.85
9 10 6.666678 ACATCATCCAGAATACAATCAAGGT 58.333 36.000 0.00 0.00 0.00 3.50
10 11 8.727910 CATACATCATCCAGAATACAATCAAGG 58.272 37.037 0.00 0.00 0.00 3.61
11 12 9.498176 TCATACATCATCCAGAATACAATCAAG 57.502 33.333 0.00 0.00 0.00 3.02
38 39 8.769891 CGCCACTTCACACAATACATAAATATA 58.230 33.333 0.00 0.00 0.00 0.86
39 40 7.497579 TCGCCACTTCACACAATACATAAATAT 59.502 33.333 0.00 0.00 0.00 1.28
40 41 6.819146 TCGCCACTTCACACAATACATAAATA 59.181 34.615 0.00 0.00 0.00 1.40
41 42 5.645929 TCGCCACTTCACACAATACATAAAT 59.354 36.000 0.00 0.00 0.00 1.40
42 43 4.998033 TCGCCACTTCACACAATACATAAA 59.002 37.500 0.00 0.00 0.00 1.40
43 44 4.570930 TCGCCACTTCACACAATACATAA 58.429 39.130 0.00 0.00 0.00 1.90
44 45 4.195225 TCGCCACTTCACACAATACATA 57.805 40.909 0.00 0.00 0.00 2.29
45 46 3.052455 TCGCCACTTCACACAATACAT 57.948 42.857 0.00 0.00 0.00 2.29
46 47 2.535012 TCGCCACTTCACACAATACA 57.465 45.000 0.00 0.00 0.00 2.29
47 48 3.188460 ACAATCGCCACTTCACACAATAC 59.812 43.478 0.00 0.00 0.00 1.89
48 49 3.407698 ACAATCGCCACTTCACACAATA 58.592 40.909 0.00 0.00 0.00 1.90
49 50 2.229792 ACAATCGCCACTTCACACAAT 58.770 42.857 0.00 0.00 0.00 2.71
50 51 1.674359 ACAATCGCCACTTCACACAA 58.326 45.000 0.00 0.00 0.00 3.33
51 52 2.535012 TACAATCGCCACTTCACACA 57.465 45.000 0.00 0.00 0.00 3.72
52 53 2.412847 GCTTACAATCGCCACTTCACAC 60.413 50.000 0.00 0.00 0.00 3.82
53 54 1.804151 GCTTACAATCGCCACTTCACA 59.196 47.619 0.00 0.00 0.00 3.58
54 55 1.130561 GGCTTACAATCGCCACTTCAC 59.869 52.381 0.00 0.00 45.59 3.18
55 56 1.448985 GGCTTACAATCGCCACTTCA 58.551 50.000 0.00 0.00 45.59 3.02
56 57 0.373716 CGGCTTACAATCGCCACTTC 59.626 55.000 0.00 0.00 46.62 3.01
57 58 0.036765 TCGGCTTACAATCGCCACTT 60.037 50.000 0.00 0.00 46.62 3.16
58 59 0.739813 GTCGGCTTACAATCGCCACT 60.740 55.000 0.00 0.00 46.62 4.00
59 60 0.739813 AGTCGGCTTACAATCGCCAC 60.740 55.000 0.00 0.00 46.62 5.01
60 61 0.459585 GAGTCGGCTTACAATCGCCA 60.460 55.000 0.00 0.00 46.62 5.69
61 62 0.179108 AGAGTCGGCTTACAATCGCC 60.179 55.000 0.00 0.00 42.86 5.54
62 63 1.641577 AAGAGTCGGCTTACAATCGC 58.358 50.000 0.00 0.00 0.00 4.58
63 64 4.444720 GGATAAAGAGTCGGCTTACAATCG 59.555 45.833 0.00 0.00 0.00 3.34
64 65 4.750598 GGGATAAAGAGTCGGCTTACAATC 59.249 45.833 0.00 0.00 0.00 2.67
65 66 4.409247 AGGGATAAAGAGTCGGCTTACAAT 59.591 41.667 0.00 0.00 0.00 2.71
66 67 3.773119 AGGGATAAAGAGTCGGCTTACAA 59.227 43.478 0.00 0.00 0.00 2.41
67 68 3.371965 AGGGATAAAGAGTCGGCTTACA 58.628 45.455 0.00 0.00 0.00 2.41
68 69 4.403585 AAGGGATAAAGAGTCGGCTTAC 57.596 45.455 0.00 0.00 0.00 2.34
69 70 4.715297 AGAAAGGGATAAAGAGTCGGCTTA 59.285 41.667 0.00 0.00 0.00 3.09
70 71 3.519913 AGAAAGGGATAAAGAGTCGGCTT 59.480 43.478 0.00 0.00 0.00 4.35
71 72 3.108376 AGAAAGGGATAAAGAGTCGGCT 58.892 45.455 0.00 0.00 0.00 5.52
72 73 3.545366 AGAAAGGGATAAAGAGTCGGC 57.455 47.619 0.00 0.00 0.00 5.54
73 74 7.272978 TGAATAAGAAAGGGATAAAGAGTCGG 58.727 38.462 0.00 0.00 0.00 4.79
74 75 7.982354 ACTGAATAAGAAAGGGATAAAGAGTCG 59.018 37.037 0.00 0.00 0.00 4.18
80 81 9.627123 CCATGTACTGAATAAGAAAGGGATAAA 57.373 33.333 0.00 0.00 0.00 1.40
81 82 8.217799 CCCATGTACTGAATAAGAAAGGGATAA 58.782 37.037 0.00 0.00 33.23 1.75
82 83 7.570982 TCCCATGTACTGAATAAGAAAGGGATA 59.429 37.037 0.00 0.00 35.62 2.59
83 84 6.389869 TCCCATGTACTGAATAAGAAAGGGAT 59.610 38.462 0.00 0.00 35.62 3.85
84 85 5.729229 TCCCATGTACTGAATAAGAAAGGGA 59.271 40.000 0.00 0.00 38.05 4.20
85 86 6.001449 TCCCATGTACTGAATAAGAAAGGG 57.999 41.667 0.00 0.00 0.00 3.95
86 87 7.012704 CACATCCCATGTACTGAATAAGAAAGG 59.987 40.741 0.00 0.00 42.70 3.11
87 88 7.554118 ACACATCCCATGTACTGAATAAGAAAG 59.446 37.037 0.00 0.00 42.70 2.62
88 89 7.336679 CACACATCCCATGTACTGAATAAGAAA 59.663 37.037 0.00 0.00 42.70 2.52
89 90 6.823182 CACACATCCCATGTACTGAATAAGAA 59.177 38.462 0.00 0.00 42.70 2.52
90 91 6.156083 TCACACATCCCATGTACTGAATAAGA 59.844 38.462 0.00 0.00 42.70 2.10
91 92 6.348498 TCACACATCCCATGTACTGAATAAG 58.652 40.000 0.00 0.00 42.70 1.73
92 93 6.306643 TCACACATCCCATGTACTGAATAA 57.693 37.500 0.00 0.00 42.70 1.40
93 94 5.948742 TCACACATCCCATGTACTGAATA 57.051 39.130 0.00 0.00 42.70 1.75
94 95 4.842531 TCACACATCCCATGTACTGAAT 57.157 40.909 0.00 0.00 42.70 2.57
95 96 4.285775 TCTTCACACATCCCATGTACTGAA 59.714 41.667 0.00 7.93 42.70 3.02
96 97 3.837731 TCTTCACACATCCCATGTACTGA 59.162 43.478 0.00 0.00 42.70 3.41
97 98 4.206477 TCTTCACACATCCCATGTACTG 57.794 45.455 0.00 0.00 42.70 2.74
98 99 5.441718 AATCTTCACACATCCCATGTACT 57.558 39.130 0.00 0.00 42.70 2.73
99 100 5.527582 GGTAATCTTCACACATCCCATGTAC 59.472 44.000 0.00 0.00 42.70 2.90
100 101 5.397447 GGGTAATCTTCACACATCCCATGTA 60.397 44.000 0.00 0.00 42.70 2.29
101 102 4.526970 GGTAATCTTCACACATCCCATGT 58.473 43.478 0.00 0.00 46.22 3.21
102 103 3.885297 GGGTAATCTTCACACATCCCATG 59.115 47.826 0.00 0.00 34.39 3.66
103 104 3.117512 GGGGTAATCTTCACACATCCCAT 60.118 47.826 0.00 0.00 35.77 4.00
104 105 2.241176 GGGGTAATCTTCACACATCCCA 59.759 50.000 0.00 0.00 35.77 4.37
105 106 2.509964 AGGGGTAATCTTCACACATCCC 59.490 50.000 0.00 0.00 0.00 3.85
106 107 3.933861 AGGGGTAATCTTCACACATCC 57.066 47.619 0.00 0.00 0.00 3.51
107 108 5.622233 GCAAAAGGGGTAATCTTCACACATC 60.622 44.000 0.00 0.00 0.00 3.06
108 109 4.220602 GCAAAAGGGGTAATCTTCACACAT 59.779 41.667 0.00 0.00 0.00 3.21
109 110 3.572255 GCAAAAGGGGTAATCTTCACACA 59.428 43.478 0.00 0.00 0.00 3.72
110 111 3.365969 CGCAAAAGGGGTAATCTTCACAC 60.366 47.826 0.00 0.00 0.00 3.82
111 112 2.817258 CGCAAAAGGGGTAATCTTCACA 59.183 45.455 0.00 0.00 0.00 3.58
112 113 3.078837 TCGCAAAAGGGGTAATCTTCAC 58.921 45.455 0.00 0.00 0.00 3.18
113 114 3.078837 GTCGCAAAAGGGGTAATCTTCA 58.921 45.455 0.00 0.00 0.00 3.02
114 115 3.078837 TGTCGCAAAAGGGGTAATCTTC 58.921 45.455 0.00 0.00 0.00 2.87
115 116 3.149005 TGTCGCAAAAGGGGTAATCTT 57.851 42.857 0.00 0.00 0.00 2.40
116 117 2.871096 TGTCGCAAAAGGGGTAATCT 57.129 45.000 0.00 0.00 0.00 2.40
117 118 3.571571 GTTTGTCGCAAAAGGGGTAATC 58.428 45.455 6.59 0.00 0.00 1.75
118 119 2.297880 GGTTTGTCGCAAAAGGGGTAAT 59.702 45.455 6.59 0.00 0.00 1.89
119 120 1.682323 GGTTTGTCGCAAAAGGGGTAA 59.318 47.619 6.59 0.00 0.00 2.85
120 121 1.133730 AGGTTTGTCGCAAAAGGGGTA 60.134 47.619 6.59 0.00 0.00 3.69
121 122 0.396556 AGGTTTGTCGCAAAAGGGGT 60.397 50.000 6.59 0.00 0.00 4.95
122 123 1.268625 GTAGGTTTGTCGCAAAAGGGG 59.731 52.381 6.59 0.00 0.00 4.79
123 124 1.268625 GGTAGGTTTGTCGCAAAAGGG 59.731 52.381 6.59 0.00 0.00 3.95
124 125 1.950909 TGGTAGGTTTGTCGCAAAAGG 59.049 47.619 6.59 0.00 0.00 3.11
125 126 3.564511 CATGGTAGGTTTGTCGCAAAAG 58.435 45.455 6.59 0.00 0.00 2.27
126 127 2.287909 GCATGGTAGGTTTGTCGCAAAA 60.288 45.455 6.59 0.00 0.00 2.44
127 128 1.268352 GCATGGTAGGTTTGTCGCAAA 59.732 47.619 0.00 1.63 0.00 3.68
128 129 0.878416 GCATGGTAGGTTTGTCGCAA 59.122 50.000 0.00 0.00 0.00 4.85
129 130 1.295357 CGCATGGTAGGTTTGTCGCA 61.295 55.000 0.00 0.00 0.00 5.10
130 131 1.423845 CGCATGGTAGGTTTGTCGC 59.576 57.895 0.00 0.00 0.00 5.19
131 132 1.977594 GCCGCATGGTAGGTTTGTCG 61.978 60.000 0.00 0.00 37.67 4.35
132 133 0.676782 AGCCGCATGGTAGGTTTGTC 60.677 55.000 0.00 0.00 37.67 3.18
133 134 0.616371 TAGCCGCATGGTAGGTTTGT 59.384 50.000 0.00 0.00 37.67 2.83
134 135 1.603802 CATAGCCGCATGGTAGGTTTG 59.396 52.381 0.00 0.00 37.67 2.93
135 136 1.967319 CATAGCCGCATGGTAGGTTT 58.033 50.000 0.00 0.00 37.67 3.27
136 137 0.535102 GCATAGCCGCATGGTAGGTT 60.535 55.000 0.00 0.00 37.67 3.50
137 138 1.071471 GCATAGCCGCATGGTAGGT 59.929 57.895 0.00 0.00 37.67 3.08
138 139 1.672356 GGCATAGCCGCATGGTAGG 60.672 63.158 0.00 0.00 39.62 3.18
139 140 3.972227 GGCATAGCCGCATGGTAG 58.028 61.111 0.00 0.00 39.62 3.18
149 150 1.492720 GCACGACTTAGAGGCATAGC 58.507 55.000 0.00 0.00 0.00 2.97
150 151 1.269831 GGGCACGACTTAGAGGCATAG 60.270 57.143 0.00 0.00 0.00 2.23
151 152 0.750850 GGGCACGACTTAGAGGCATA 59.249 55.000 0.00 0.00 0.00 3.14
152 153 0.978146 AGGGCACGACTTAGAGGCAT 60.978 55.000 0.00 0.00 0.00 4.40
153 154 1.609501 AGGGCACGACTTAGAGGCA 60.610 57.895 0.00 0.00 0.00 4.75
154 155 1.153549 CAGGGCACGACTTAGAGGC 60.154 63.158 0.00 0.00 0.00 4.70
155 156 0.173708 GTCAGGGCACGACTTAGAGG 59.826 60.000 4.06 0.00 0.00 3.69
156 157 0.888619 TGTCAGGGCACGACTTAGAG 59.111 55.000 11.28 0.00 34.37 2.43
157 158 0.601558 GTGTCAGGGCACGACTTAGA 59.398 55.000 11.28 0.00 34.37 2.10
158 159 3.123674 GTGTCAGGGCACGACTTAG 57.876 57.895 11.28 0.00 34.37 2.18
165 166 3.883744 CTCCCACGTGTCAGGGCAC 62.884 68.421 15.65 0.00 45.07 5.01
166 167 3.625897 CTCCCACGTGTCAGGGCA 61.626 66.667 15.65 0.00 45.07 5.36
167 168 1.327690 TATCTCCCACGTGTCAGGGC 61.328 60.000 15.65 0.00 45.07 5.19
168 169 1.414158 ATATCTCCCACGTGTCAGGG 58.586 55.000 15.65 8.71 46.90 4.45
169 170 2.029828 GCTATATCTCCCACGTGTCAGG 60.030 54.545 15.65 8.95 0.00 3.86
170 171 2.029828 GGCTATATCTCCCACGTGTCAG 60.030 54.545 15.65 9.65 0.00 3.51
171 172 1.961394 GGCTATATCTCCCACGTGTCA 59.039 52.381 15.65 0.00 0.00 3.58
172 173 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
173 174 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
174 175 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
175 176 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
176 177 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
177 178 2.289694 ACAATGCGGCTATATCTCCCAC 60.290 50.000 0.00 0.00 0.00 4.61
178 179 1.977854 ACAATGCGGCTATATCTCCCA 59.022 47.619 0.00 0.00 0.00 4.37
179 180 2.350522 CACAATGCGGCTATATCTCCC 58.649 52.381 0.00 0.00 0.00 4.30
180 181 2.350522 CCACAATGCGGCTATATCTCC 58.649 52.381 0.00 0.00 0.00 3.71
181 182 2.289694 ACCCACAATGCGGCTATATCTC 60.290 50.000 0.00 0.00 0.00 2.75
182 183 1.699634 ACCCACAATGCGGCTATATCT 59.300 47.619 0.00 0.00 0.00 1.98
183 184 1.806542 CACCCACAATGCGGCTATATC 59.193 52.381 0.00 0.00 0.00 1.63
184 185 1.142870 ACACCCACAATGCGGCTATAT 59.857 47.619 0.00 0.00 0.00 0.86
185 186 0.544223 ACACCCACAATGCGGCTATA 59.456 50.000 0.00 0.00 0.00 1.31
186 187 0.323360 AACACCCACAATGCGGCTAT 60.323 50.000 0.00 0.00 0.00 2.97
187 188 0.538516 AAACACCCACAATGCGGCTA 60.539 50.000 0.00 0.00 0.00 3.93
188 189 1.805428 GAAACACCCACAATGCGGCT 61.805 55.000 0.00 0.00 0.00 5.52
189 190 1.372872 GAAACACCCACAATGCGGC 60.373 57.895 0.00 0.00 0.00 6.53
190 191 0.387202 TTGAAACACCCACAATGCGG 59.613 50.000 0.00 0.00 0.00 5.69
191 192 2.288091 TGATTGAAACACCCACAATGCG 60.288 45.455 0.00 0.00 34.94 4.73
192 193 3.319755 CTGATTGAAACACCCACAATGC 58.680 45.455 0.00 0.00 34.94 3.56
193 194 3.321682 ACCTGATTGAAACACCCACAATG 59.678 43.478 0.00 0.00 34.94 2.82
194 195 3.575805 ACCTGATTGAAACACCCACAAT 58.424 40.909 0.00 0.00 37.03 2.71
195 196 3.025322 ACCTGATTGAAACACCCACAA 57.975 42.857 0.00 0.00 0.00 3.33
196 197 2.746279 ACCTGATTGAAACACCCACA 57.254 45.000 0.00 0.00 0.00 4.17
197 198 3.383185 TGAAACCTGATTGAAACACCCAC 59.617 43.478 0.00 0.00 0.00 4.61
198 199 3.636679 TGAAACCTGATTGAAACACCCA 58.363 40.909 0.00 0.00 0.00 4.51
199 200 4.620982 CTTGAAACCTGATTGAAACACCC 58.379 43.478 0.00 0.00 0.00 4.61
200 201 4.051237 GCTTGAAACCTGATTGAAACACC 58.949 43.478 0.00 0.00 0.00 4.16
201 202 4.936891 AGCTTGAAACCTGATTGAAACAC 58.063 39.130 0.00 0.00 0.00 3.32
202 203 5.596836 AAGCTTGAAACCTGATTGAAACA 57.403 34.783 0.00 0.00 0.00 2.83
203 204 7.481798 CGTATAAGCTTGAAACCTGATTGAAAC 59.518 37.037 9.86 0.00 0.00 2.78
204 205 7.361713 CCGTATAAGCTTGAAACCTGATTGAAA 60.362 37.037 9.86 0.00 0.00 2.69
205 206 6.093495 CCGTATAAGCTTGAAACCTGATTGAA 59.907 38.462 9.86 0.00 0.00 2.69
206 207 5.584649 CCGTATAAGCTTGAAACCTGATTGA 59.415 40.000 9.86 0.00 0.00 2.57
207 208 5.730568 GCCGTATAAGCTTGAAACCTGATTG 60.731 44.000 9.86 0.00 0.00 2.67
208 209 4.335594 GCCGTATAAGCTTGAAACCTGATT 59.664 41.667 9.86 0.00 0.00 2.57
227 228 1.681780 CCAACACTTCCATATGGCCGT 60.682 52.381 17.58 12.78 34.44 5.68
250 251 1.412079 AAAGCTTGCACACCAATGGA 58.588 45.000 6.16 0.00 31.91 3.41
253 254 3.181463 ACATGAAAAGCTTGCACACCAAT 60.181 39.130 0.00 0.00 31.91 3.16
254 255 2.168106 ACATGAAAAGCTTGCACACCAA 59.832 40.909 0.00 0.00 0.00 3.67
322 323 3.153919 TCTTTGGTCCTGTAAACCATGC 58.846 45.455 0.00 0.00 45.89 4.06
367 368 7.718753 GTGATATGATCCACAATTTCTTCCTCT 59.281 37.037 0.00 0.00 33.72 3.69
376 377 7.229308 ACTGCATAGTGATATGATCCACAATT 58.771 34.615 0.00 0.00 35.34 2.32
411 412 0.324614 CATGTACCACACCTGCCTCA 59.675 55.000 0.00 0.00 0.00 3.86
448 449 0.898326 GGCAAAGGTCCGGGTTGATT 60.898 55.000 0.00 0.00 0.00 2.57
501 502 1.221414 GATATGCTTCCTCGTGGTGC 58.779 55.000 14.08 14.08 35.63 5.01
502 503 1.541233 GGGATATGCTTCCTCGTGGTG 60.541 57.143 2.99 0.00 35.97 4.17
570 571 2.710377 TGCGTTGCTTCCATATGTTCT 58.290 42.857 1.24 0.00 0.00 3.01
595 596 1.068121 CAGTCCTCCCAAAGACCCTT 58.932 55.000 0.00 0.00 33.29 3.95
628 632 0.836400 ATCAGGTCCACGGTTCCACT 60.836 55.000 0.00 0.00 0.00 4.00
657 661 3.674997 TGCTCTGGACCACAATTCTAAC 58.325 45.455 0.00 0.00 0.00 2.34
664 668 2.061220 CTCCTGCTCTGGACCACAA 58.939 57.895 0.00 0.00 31.94 3.33
672 676 4.463879 CCGGTGGCTCCTGCTCTG 62.464 72.222 3.83 0.00 39.59 3.35
707 711 4.639135 ATCGAAACGTTACCCTACTACC 57.361 45.455 0.00 0.00 0.00 3.18
719 723 2.301346 ACCCTCCGTATATCGAAACGT 58.699 47.619 14.56 0.00 42.86 3.99
720 724 4.409570 CATACCCTCCGTATATCGAAACG 58.590 47.826 10.35 10.35 42.86 3.60
729 733 2.326428 CTTCCACCATACCCTCCGTAT 58.674 52.381 0.00 0.00 38.24 3.06
730 734 1.784358 CTTCCACCATACCCTCCGTA 58.216 55.000 0.00 0.00 0.00 4.02
760 764 7.559335 AAGATTACATGGTAGATAGATGGCA 57.441 36.000 0.00 0.00 0.00 4.92
801 806 8.647226 GCGTACCGTAACTTTATAGAAAAAGAA 58.353 33.333 3.51 0.00 38.50 2.52
806 811 8.434661 CAAAAGCGTACCGTAACTTTATAGAAA 58.565 33.333 7.79 0.00 32.28 2.52
883 888 5.278604 CGCTGTGGCTTTTTAGTACTTTTT 58.721 37.500 0.00 0.00 36.09 1.94
884 889 4.791734 GCGCTGTGGCTTTTTAGTACTTTT 60.792 41.667 0.00 0.00 36.09 2.27
885 890 3.304458 GCGCTGTGGCTTTTTAGTACTTT 60.304 43.478 0.00 0.00 36.09 2.66
907 912 2.229062 TCTTCTCTAGCACCAAGACGTG 59.771 50.000 0.00 0.00 36.80 4.49
908 913 2.515854 TCTTCTCTAGCACCAAGACGT 58.484 47.619 0.00 0.00 0.00 4.34
1070 1077 1.953686 GAACCAGCAACCTGTAGCAAA 59.046 47.619 0.00 0.00 37.38 3.68
1097 1104 2.349532 GCGCACCAAAACTCAGAACTAC 60.350 50.000 0.30 0.00 0.00 2.73
1256 1263 2.506217 GCGCCGTCGATCAAGACA 60.506 61.111 0.00 0.00 40.98 3.41
1260 1267 2.813474 CTTGGCGCCGTCGATCAA 60.813 61.111 23.90 7.51 38.10 2.57
1402 1416 4.181578 ACGACTCAAATCAAATACGGAGG 58.818 43.478 0.00 0.00 0.00 4.30
1403 1417 4.267928 GGACGACTCAAATCAAATACGGAG 59.732 45.833 0.00 0.00 0.00 4.63
1404 1418 4.178540 GGACGACTCAAATCAAATACGGA 58.821 43.478 0.00 0.00 0.00 4.69
1405 1419 3.308866 GGGACGACTCAAATCAAATACGG 59.691 47.826 0.00 0.00 0.00 4.02
1406 1420 4.181578 AGGGACGACTCAAATCAAATACG 58.818 43.478 0.00 0.00 0.00 3.06
1407 1421 5.642063 TGAAGGGACGACTCAAATCAAATAC 59.358 40.000 0.00 0.00 0.00 1.89
1408 1422 5.800296 TGAAGGGACGACTCAAATCAAATA 58.200 37.500 0.00 0.00 0.00 1.40
1420 1434 0.036388 TGGCTGAATGAAGGGACGAC 60.036 55.000 0.00 0.00 0.00 4.34
1469 1483 9.533831 AAGACAATTCCACATTCTTACCTTTAT 57.466 29.630 0.00 0.00 0.00 1.40
1472 1486 7.839680 AAAGACAATTCCACATTCTTACCTT 57.160 32.000 0.00 0.00 0.00 3.50
1505 1519 6.740401 GCCATCCATAATTGCACATTCTGAAT 60.740 38.462 0.00 0.00 0.00 2.57
1700 1726 4.246458 AGACCACGAAGCAGATTTCTAAC 58.754 43.478 0.00 0.00 0.00 2.34
1701 1727 4.537135 AGACCACGAAGCAGATTTCTAA 57.463 40.909 0.00 0.00 0.00 2.10
1722 1748 0.893270 AGCATAAACAGCGGTGCCAA 60.893 50.000 15.82 0.00 38.31 4.52
1739 1765 3.129109 GCCCCTAAATACTGTACGAAGC 58.871 50.000 0.00 0.00 0.00 3.86
1749 1775 7.039714 CCATAATTTCAGGAAGCCCCTAAATAC 60.040 40.741 0.00 0.00 45.60 1.89
1861 1887 1.433534 TCATGTAACGCATTGCACGA 58.566 45.000 9.69 0.00 35.19 4.35
1917 1943 7.965107 GGTCAAATTAGCAGACATTACTCAAAG 59.035 37.037 0.00 0.00 34.04 2.77
1947 1973 4.949238 AGCTTACATATCCACATGCAACAA 59.051 37.500 0.00 0.00 0.00 2.83
2009 2035 7.013220 ACAAGCCAATAGAGAGTAGGATGATA 58.987 38.462 0.00 0.00 0.00 2.15
2447 2490 2.670934 GTGTCCAGCCCAGCACAG 60.671 66.667 0.00 0.00 32.62 3.66
2769 2812 5.052481 TCCTCATCATCTTTCAGCATTACG 58.948 41.667 0.00 0.00 0.00 3.18
2794 2837 7.284820 ACTACTCTTCTAGCTTCCTTACTAGG 58.715 42.308 0.00 0.00 43.46 3.02
2798 2841 7.012610 CCTGTACTACTCTTCTAGCTTCCTTAC 59.987 44.444 0.00 0.00 0.00 2.34
2799 2842 7.055378 CCTGTACTACTCTTCTAGCTTCCTTA 58.945 42.308 0.00 0.00 0.00 2.69
2800 2843 5.889289 CCTGTACTACTCTTCTAGCTTCCTT 59.111 44.000 0.00 0.00 0.00 3.36
2801 2844 5.192121 TCCTGTACTACTCTTCTAGCTTCCT 59.808 44.000 0.00 0.00 0.00 3.36
2802 2845 5.438833 TCCTGTACTACTCTTCTAGCTTCC 58.561 45.833 0.00 0.00 0.00 3.46
2803 2846 5.008316 GCTCCTGTACTACTCTTCTAGCTTC 59.992 48.000 0.00 0.00 0.00 3.86
2804 2847 4.885325 GCTCCTGTACTACTCTTCTAGCTT 59.115 45.833 0.00 0.00 0.00 3.74
2805 2848 4.457466 GCTCCTGTACTACTCTTCTAGCT 58.543 47.826 0.00 0.00 0.00 3.32
2806 2849 3.566742 GGCTCCTGTACTACTCTTCTAGC 59.433 52.174 0.00 0.00 0.00 3.42
2807 2850 4.783055 TGGCTCCTGTACTACTCTTCTAG 58.217 47.826 0.00 0.00 0.00 2.43
2808 2851 4.385421 CCTGGCTCCTGTACTACTCTTCTA 60.385 50.000 0.00 0.00 0.00 2.10
2809 2852 3.626222 CCTGGCTCCTGTACTACTCTTCT 60.626 52.174 0.00 0.00 0.00 2.85
2833 2876 0.948623 TGCAGCATTACAACGTCGCT 60.949 50.000 0.00 0.00 0.00 4.93
2840 2883 4.941263 CCTTACTAGGTTGCAGCATTACAA 59.059 41.667 2.05 0.00 36.74 2.41
3032 3075 5.862323 TGTTCTACGCTTCTAGCTTTGTTAG 59.138 40.000 0.00 0.00 39.60 2.34
3140 3183 1.466167 CTTTCCTGACATTGTGAGGCG 59.534 52.381 16.61 4.88 36.87 5.52
3191 3234 2.437281 AGCATCTACATTAGGCTGCACT 59.563 45.455 0.50 0.00 37.34 4.40
3239 3282 3.068873 GTCCTGGTTTGTTTGCACCATTA 59.931 43.478 0.00 0.00 42.35 1.90
3242 3285 0.820871 GTCCTGGTTTGTTTGCACCA 59.179 50.000 0.00 0.00 40.98 4.17
3342 3385 1.117994 GCTACCCCTACCACACTACC 58.882 60.000 0.00 0.00 0.00 3.18
3346 3389 0.252197 CAAGGCTACCCCTACCACAC 59.748 60.000 0.00 0.00 45.62 3.82
3375 3419 8.352201 CCACTTCTTTCAAGATCAACACATTAA 58.648 33.333 0.00 0.00 34.49 1.40
3376 3420 7.719193 TCCACTTCTTTCAAGATCAACACATTA 59.281 33.333 0.00 0.00 34.49 1.90
3377 3421 6.547141 TCCACTTCTTTCAAGATCAACACATT 59.453 34.615 0.00 0.00 34.49 2.71
3586 3630 6.238621 GCATTAACAATAATCCGGTGATGACA 60.239 38.462 0.00 0.00 29.08 3.58
3588 3632 5.825151 TGCATTAACAATAATCCGGTGATGA 59.175 36.000 0.00 0.00 29.08 2.92
3613 3657 4.003648 CCAAGAATGACTACCACTGAACC 58.996 47.826 0.00 0.00 0.00 3.62
3657 3702 3.784338 TCTTTGCTGCTTTCACCAAAAG 58.216 40.909 0.00 0.00 46.05 2.27
3791 3983 4.272504 GTGCAGTATGTTTATGTATGCCGT 59.727 41.667 0.00 0.00 39.31 5.68
3865 4064 3.125316 CGAACTAATGGTCAGAAAGGTGC 59.875 47.826 0.00 0.00 0.00 5.01
3926 4136 2.774774 CGAAGAGAGCAGCGCAAC 59.225 61.111 11.47 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.