Multiple sequence alignment - TraesCS6B01G176800

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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 TraesCS6B01G176800 chr6B 100.000 3308 0 0 1 3308 193890456 193893763 0.000000e+00 6109.0
1 TraesCS6B01G176800 chr6B 100.000 38 0 0 152 189 169477548 169477511 1.650000e-08 71.3
2 TraesCS6B01G176800 chr6A 90.124 3220 166 65 191 3305 129932187 129935359 0.000000e+00 4045.0
3 TraesCS6B01G176800 chr6D 91.571 2800 110 48 577 3305 106696703 106699447 0.000000e+00 3747.0
4 TraesCS6B01G176800 chr5A 97.619 42 1 0 148 189 513224461 513224502 4.580000e-09 73.1
5 TraesCS6B01G176800 chr5A 87.931 58 6 1 1397 1454 42630239 42630295 2.130000e-07 67.6
6 TraesCS6B01G176800 chr7D 97.561 41 1 0 152 192 585547922 585547882 1.650000e-08 71.3
7 TraesCS6B01G176800 chr7D 100.000 38 0 0 152 189 632803272 632803309 1.650000e-08 71.3
8 TraesCS6B01G176800 chr7B 97.561 41 1 0 152 192 654862170 654862130 1.650000e-08 71.3
9 TraesCS6B01G176800 chr5B 97.500 40 1 0 152 191 275312044 275312005 5.920000e-08 69.4
10 TraesCS6B01G176800 chr3B 97.500 40 1 0 152 191 613873657 613873618 5.920000e-08 69.4
11 TraesCS6B01G176800 chrUn 90.385 52 4 1 1403 1454 262578062 262578112 2.130000e-07 67.6
12 TraesCS6B01G176800 chrUn 90.385 52 4 1 1403 1454 262587678 262587728 2.130000e-07 67.6
13 TraesCS6B01G176800 chrUn 90.385 52 4 1 1403 1454 271996380 271996430 2.130000e-07 67.6
14 TraesCS6B01G176800 chrUn 91.489 47 4 0 1977 2023 16442984 16442938 7.660000e-07 65.8
15 TraesCS6B01G176800 chrUn 100.000 32 0 0 1977 2008 16613652 16613683 3.560000e-05 60.2
16 TraesCS6B01G176800 chrUn 100.000 32 0 0 1977 2008 16658811 16658842 3.560000e-05 60.2
17 TraesCS6B01G176800 chrUn 89.362 47 5 0 1977 2023 266169913 266169867 3.560000e-05 60.2
18 TraesCS6B01G176800 chrUn 100.000 32 0 0 1977 2008 272512984 272513015 3.560000e-05 60.2
19 TraesCS6B01G176800 chrUn 100.000 32 0 0 1977 2008 288702109 288702140 3.560000e-05 60.2
20 TraesCS6B01G176800 chrUn 89.362 47 5 0 1977 2023 379210435 379210389 3.560000e-05 60.2
21 TraesCS6B01G176800 chr4A 90.385 52 4 1 1403 1454 639965840 639965890 2.130000e-07 67.6
22 TraesCS6B01G176800 chr3D 95.238 42 2 0 154 195 612675770 612675729 2.130000e-07 67.6
23 TraesCS6B01G176800 chr2A 93.182 44 3 0 146 189 18448170 18448213 7.660000e-07 65.8


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 TraesCS6B01G176800 chr6B 193890456 193893763 3307 False 6109 6109 100.000 1 3308 1 chr6B.!!$F1 3307
1 TraesCS6B01G176800 chr6A 129932187 129935359 3172 False 4045 4045 90.124 191 3305 1 chr6A.!!$F1 3114
2 TraesCS6B01G176800 chr6D 106696703 106699447 2744 False 3747 3747 91.571 577 3305 1 chr6D.!!$F1 2728

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
392 393 0.179111 ACATAGTCGGCATCACCACG 60.179 55.0 0.0 0.00 39.03 4.94 F
1325 1418 0.387112 CGATCTCTGCCGATCTCAGC 60.387 60.0 6.9 0.58 38.09 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1706 0.179009 ACCTTGAGCTGCAGCAAGAA 60.179 50.0 38.24 24.95 43.11 2.52 R
2493 2614 0.103715 ATCCATCCACCATAGGCCCT 60.104 55.0 0.00 0.00 0.00 5.19 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
18 19 3.989104 GTGCATAGTACTCGCCCAT 57.011 52.632 13.14 0.00 0.00 4.00
19 20 2.240493 GTGCATAGTACTCGCCCATT 57.760 50.000 13.14 0.00 0.00 3.16
20 21 3.380479 GTGCATAGTACTCGCCCATTA 57.620 47.619 13.14 0.00 0.00 1.90
21 22 3.724374 GTGCATAGTACTCGCCCATTAA 58.276 45.455 13.14 0.00 0.00 1.40
22 23 4.124238 GTGCATAGTACTCGCCCATTAAA 58.876 43.478 13.14 0.00 0.00 1.52
23 24 4.573201 GTGCATAGTACTCGCCCATTAAAA 59.427 41.667 13.14 0.00 0.00 1.52
24 25 5.065474 GTGCATAGTACTCGCCCATTAAAAA 59.935 40.000 13.14 0.00 0.00 1.94
25 26 5.825679 TGCATAGTACTCGCCCATTAAAAAT 59.174 36.000 13.14 0.00 0.00 1.82
26 27 6.320164 TGCATAGTACTCGCCCATTAAAAATT 59.680 34.615 13.14 0.00 0.00 1.82
27 28 7.499563 TGCATAGTACTCGCCCATTAAAAATTA 59.500 33.333 13.14 0.00 0.00 1.40
28 29 8.015658 GCATAGTACTCGCCCATTAAAAATTAG 58.984 37.037 0.00 0.00 0.00 1.73
29 30 9.268268 CATAGTACTCGCCCATTAAAAATTAGA 57.732 33.333 0.00 0.00 0.00 2.10
30 31 9.841295 ATAGTACTCGCCCATTAAAAATTAGAA 57.159 29.630 0.00 0.00 0.00 2.10
31 32 8.747538 AGTACTCGCCCATTAAAAATTAGAAT 57.252 30.769 0.00 0.00 0.00 2.40
32 33 8.837389 AGTACTCGCCCATTAAAAATTAGAATC 58.163 33.333 0.00 0.00 0.00 2.52
33 34 7.639113 ACTCGCCCATTAAAAATTAGAATCA 57.361 32.000 0.00 0.00 0.00 2.57
34 35 7.480810 ACTCGCCCATTAAAAATTAGAATCAC 58.519 34.615 0.00 0.00 0.00 3.06
35 36 7.122055 ACTCGCCCATTAAAAATTAGAATCACA 59.878 33.333 0.00 0.00 0.00 3.58
36 37 7.831753 TCGCCCATTAAAAATTAGAATCACAA 58.168 30.769 0.00 0.00 0.00 3.33
37 38 8.307483 TCGCCCATTAAAAATTAGAATCACAAA 58.693 29.630 0.00 0.00 0.00 2.83
38 39 8.594687 CGCCCATTAAAAATTAGAATCACAAAG 58.405 33.333 0.00 0.00 0.00 2.77
39 40 9.435688 GCCCATTAAAAATTAGAATCACAAAGT 57.564 29.630 0.00 0.00 0.00 2.66
44 45 9.691362 TTAAAAATTAGAATCACAAAGTCTGGC 57.309 29.630 0.00 0.00 0.00 4.85
45 46 5.904362 AATTAGAATCACAAAGTCTGGCC 57.096 39.130 0.00 0.00 0.00 5.36
46 47 1.813513 AGAATCACAAAGTCTGGCCG 58.186 50.000 0.00 0.00 0.00 6.13
47 48 1.072331 AGAATCACAAAGTCTGGCCGT 59.928 47.619 0.00 0.00 0.00 5.68
48 49 1.197721 GAATCACAAAGTCTGGCCGTG 59.802 52.381 0.00 0.00 0.00 4.94
49 50 0.606401 ATCACAAAGTCTGGCCGTGG 60.606 55.000 0.00 0.00 0.00 4.94
50 51 1.227823 CACAAAGTCTGGCCGTGGA 60.228 57.895 0.00 0.00 0.00 4.02
51 52 1.227853 ACAAAGTCTGGCCGTGGAC 60.228 57.895 13.30 13.30 0.00 4.02
52 53 1.966451 CAAAGTCTGGCCGTGGACC 60.966 63.158 16.31 0.00 33.39 4.46
53 54 2.147387 AAAGTCTGGCCGTGGACCT 61.147 57.895 16.31 4.62 33.39 3.85
54 55 2.113243 AAAGTCTGGCCGTGGACCTC 62.113 60.000 16.31 0.00 33.39 3.85
55 56 3.311110 GTCTGGCCGTGGACCTCA 61.311 66.667 10.92 0.00 0.00 3.86
56 57 2.525629 TCTGGCCGTGGACCTCAA 60.526 61.111 0.00 0.00 0.00 3.02
57 58 1.918293 TCTGGCCGTGGACCTCAAT 60.918 57.895 0.00 0.00 0.00 2.57
58 59 1.450312 CTGGCCGTGGACCTCAATC 60.450 63.158 0.00 0.00 0.00 2.67
59 60 2.184020 CTGGCCGTGGACCTCAATCA 62.184 60.000 0.00 0.00 0.00 2.57
60 61 1.745489 GGCCGTGGACCTCAATCAC 60.745 63.158 0.00 0.00 0.00 3.06
61 62 1.296715 GCCGTGGACCTCAATCACT 59.703 57.895 0.00 0.00 0.00 3.41
62 63 0.535335 GCCGTGGACCTCAATCACTA 59.465 55.000 0.00 0.00 0.00 2.74
63 64 1.139058 GCCGTGGACCTCAATCACTAT 59.861 52.381 0.00 0.00 0.00 2.12
64 65 2.364324 GCCGTGGACCTCAATCACTATA 59.636 50.000 0.00 0.00 0.00 1.31
65 66 3.181469 GCCGTGGACCTCAATCACTATAA 60.181 47.826 0.00 0.00 0.00 0.98
66 67 4.621991 CCGTGGACCTCAATCACTATAAG 58.378 47.826 0.00 0.00 0.00 1.73
67 68 4.501571 CCGTGGACCTCAATCACTATAAGG 60.502 50.000 0.00 0.00 0.00 2.69
68 69 4.381411 GTGGACCTCAATCACTATAAGGC 58.619 47.826 0.00 0.00 0.00 4.35
69 70 4.037222 TGGACCTCAATCACTATAAGGCA 58.963 43.478 0.00 0.00 0.00 4.75
70 71 4.473196 TGGACCTCAATCACTATAAGGCAA 59.527 41.667 0.00 0.00 0.00 4.52
71 72 5.132648 TGGACCTCAATCACTATAAGGCAAT 59.867 40.000 0.00 0.00 0.00 3.56
72 73 5.471456 GGACCTCAATCACTATAAGGCAATG 59.529 44.000 0.00 0.00 0.00 2.82
73 74 4.823989 ACCTCAATCACTATAAGGCAATGC 59.176 41.667 0.00 0.00 0.00 3.56
74 75 4.823442 CCTCAATCACTATAAGGCAATGCA 59.177 41.667 7.79 0.00 0.00 3.96
75 76 5.300034 CCTCAATCACTATAAGGCAATGCAA 59.700 40.000 7.79 0.00 0.00 4.08
76 77 6.015688 CCTCAATCACTATAAGGCAATGCAAT 60.016 38.462 7.79 0.00 0.00 3.56
77 78 6.741109 TCAATCACTATAAGGCAATGCAATG 58.259 36.000 7.79 0.00 0.00 2.82
78 79 6.546772 TCAATCACTATAAGGCAATGCAATGA 59.453 34.615 5.79 0.00 0.00 2.57
79 80 6.964807 ATCACTATAAGGCAATGCAATGAA 57.035 33.333 5.79 0.00 0.00 2.57
80 81 6.772360 TCACTATAAGGCAATGCAATGAAA 57.228 33.333 5.79 0.00 0.00 2.69
81 82 6.563422 TCACTATAAGGCAATGCAATGAAAC 58.437 36.000 5.79 0.00 0.00 2.78
82 83 6.152492 TCACTATAAGGCAATGCAATGAAACA 59.848 34.615 5.79 0.00 0.00 2.83
83 84 6.982141 CACTATAAGGCAATGCAATGAAACAT 59.018 34.615 5.79 0.00 0.00 2.71
84 85 7.493320 CACTATAAGGCAATGCAATGAAACATT 59.507 33.333 5.79 0.00 36.96 2.71
92 93 7.372451 CAATGCAATGAAACATTGGAAATCT 57.628 32.000 18.82 4.07 46.01 2.40
93 94 6.978343 ATGCAATGAAACATTGGAAATCTG 57.022 33.333 18.82 0.00 33.26 2.90
94 95 4.691685 TGCAATGAAACATTGGAAATCTGC 59.308 37.500 20.76 9.24 0.00 4.26
95 96 4.933400 GCAATGAAACATTGGAAATCTGCT 59.067 37.500 20.76 0.00 0.00 4.24
96 97 5.410439 GCAATGAAACATTGGAAATCTGCTT 59.590 36.000 20.76 0.00 0.00 3.91
97 98 6.619874 GCAATGAAACATTGGAAATCTGCTTG 60.620 38.462 20.76 0.00 0.00 4.01
98 99 5.534207 TGAAACATTGGAAATCTGCTTGT 57.466 34.783 0.00 0.00 0.00 3.16
99 100 5.916318 TGAAACATTGGAAATCTGCTTGTT 58.084 33.333 0.00 0.00 0.00 2.83
100 101 6.347696 TGAAACATTGGAAATCTGCTTGTTT 58.652 32.000 0.00 0.00 38.21 2.83
101 102 6.479660 TGAAACATTGGAAATCTGCTTGTTTC 59.520 34.615 15.15 15.15 45.71 2.78
102 103 5.534207 ACATTGGAAATCTGCTTGTTTCA 57.466 34.783 9.37 0.00 36.34 2.69
103 104 5.916318 ACATTGGAAATCTGCTTGTTTCAA 58.084 33.333 9.37 0.00 36.34 2.69
104 105 6.347696 ACATTGGAAATCTGCTTGTTTCAAA 58.652 32.000 9.37 5.88 36.34 2.69
105 106 6.822676 ACATTGGAAATCTGCTTGTTTCAAAA 59.177 30.769 9.37 5.14 36.34 2.44
106 107 7.336427 ACATTGGAAATCTGCTTGTTTCAAAAA 59.664 29.630 9.37 3.43 36.34 1.94
131 132 9.546428 AAAGACAAAAGAAAAGGAAATATGTGG 57.454 29.630 0.00 0.00 0.00 4.17
132 133 7.670364 AGACAAAAGAAAAGGAAATATGTGGG 58.330 34.615 0.00 0.00 0.00 4.61
133 134 7.508977 AGACAAAAGAAAAGGAAATATGTGGGA 59.491 33.333 0.00 0.00 0.00 4.37
134 135 8.206126 ACAAAAGAAAAGGAAATATGTGGGAT 57.794 30.769 0.00 0.00 0.00 3.85
135 136 8.314021 ACAAAAGAAAAGGAAATATGTGGGATC 58.686 33.333 0.00 0.00 0.00 3.36
136 137 8.313292 CAAAAGAAAAGGAAATATGTGGGATCA 58.687 33.333 0.00 0.00 0.00 2.92
137 138 8.613922 AAAGAAAAGGAAATATGTGGGATCAT 57.386 30.769 0.00 0.00 0.00 2.45
138 139 7.592885 AGAAAAGGAAATATGTGGGATCATG 57.407 36.000 0.00 0.00 0.00 3.07
139 140 5.796424 AAAGGAAATATGTGGGATCATGC 57.204 39.130 0.00 0.00 0.00 4.06
140 141 4.736611 AGGAAATATGTGGGATCATGCT 57.263 40.909 0.00 0.00 0.00 3.79
141 142 5.070823 AGGAAATATGTGGGATCATGCTT 57.929 39.130 0.00 0.00 0.00 3.91
142 143 6.204852 AGGAAATATGTGGGATCATGCTTA 57.795 37.500 0.00 0.00 0.00 3.09
143 144 6.243900 AGGAAATATGTGGGATCATGCTTAG 58.756 40.000 0.00 0.00 0.00 2.18
144 145 5.105997 GGAAATATGTGGGATCATGCTTAGC 60.106 44.000 0.00 0.00 0.00 3.09
145 146 4.923516 ATATGTGGGATCATGCTTAGCT 57.076 40.909 5.60 0.00 0.00 3.32
146 147 2.336945 TGTGGGATCATGCTTAGCTG 57.663 50.000 5.60 1.56 0.00 4.24
147 148 1.134007 TGTGGGATCATGCTTAGCTGG 60.134 52.381 5.60 0.00 0.00 4.85
148 149 1.133976 GTGGGATCATGCTTAGCTGGT 60.134 52.381 5.60 0.00 0.00 4.00
149 150 1.565759 TGGGATCATGCTTAGCTGGTT 59.434 47.619 5.60 0.00 0.00 3.67
150 151 2.777114 TGGGATCATGCTTAGCTGGTTA 59.223 45.455 5.60 0.00 0.00 2.85
151 152 3.142174 GGGATCATGCTTAGCTGGTTAC 58.858 50.000 5.60 0.00 0.00 2.50
152 153 3.433598 GGGATCATGCTTAGCTGGTTACA 60.434 47.826 5.60 0.00 0.00 2.41
153 154 4.199310 GGATCATGCTTAGCTGGTTACAA 58.801 43.478 5.60 0.00 0.00 2.41
154 155 4.823989 GGATCATGCTTAGCTGGTTACAAT 59.176 41.667 5.60 0.00 0.00 2.71
155 156 5.997746 GGATCATGCTTAGCTGGTTACAATA 59.002 40.000 5.60 0.00 0.00 1.90
156 157 6.656693 GGATCATGCTTAGCTGGTTACAATAT 59.343 38.462 5.60 0.00 0.00 1.28
157 158 7.175641 GGATCATGCTTAGCTGGTTACAATATT 59.824 37.037 5.60 0.00 0.00 1.28
158 159 7.880160 TCATGCTTAGCTGGTTACAATATTT 57.120 32.000 5.60 0.00 0.00 1.40
159 160 8.292444 TCATGCTTAGCTGGTTACAATATTTT 57.708 30.769 5.60 0.00 0.00 1.82
160 161 8.748412 TCATGCTTAGCTGGTTACAATATTTTT 58.252 29.630 5.60 0.00 0.00 1.94
161 162 8.810427 CATGCTTAGCTGGTTACAATATTTTTG 58.190 33.333 5.60 0.00 0.00 2.44
162 163 7.891561 TGCTTAGCTGGTTACAATATTTTTGT 58.108 30.769 5.60 0.00 36.49 2.83
163 164 8.364142 TGCTTAGCTGGTTACAATATTTTTGTT 58.636 29.630 5.60 0.00 34.11 2.83
164 165 8.647226 GCTTAGCTGGTTACAATATTTTTGTTG 58.353 33.333 0.00 0.00 34.11 3.33
165 166 9.906660 CTTAGCTGGTTACAATATTTTTGTTGA 57.093 29.630 0.00 0.00 34.11 3.18
169 170 8.807581 GCTGGTTACAATATTTTTGTTGATAGC 58.192 33.333 0.00 2.02 34.11 2.97
189 190 3.126001 CTTACCAAGCTGACCACTTGA 57.874 47.619 5.12 0.00 45.99 3.02
209 210 1.216064 TGGGATCATGCTTAGCTGGT 58.784 50.000 5.60 0.00 0.00 4.00
211 212 1.141657 GGGATCATGCTTAGCTGGTCA 59.858 52.381 15.08 0.00 0.00 4.02
223 224 5.592688 GCTTAGCTGGTCACCCATAAATTAA 59.407 40.000 0.00 0.00 40.90 1.40
224 225 6.459710 GCTTAGCTGGTCACCCATAAATTAAC 60.460 42.308 0.00 0.00 40.90 2.01
232 233 5.185056 GTCACCCATAAATTAACCAAGCAGT 59.815 40.000 0.00 0.00 0.00 4.40
235 236 7.451877 TCACCCATAAATTAACCAAGCAGTTAA 59.548 33.333 8.57 8.57 44.12 2.01
304 305 9.205513 ACCATATTTCTTTAATGGCAGAGATTT 57.794 29.630 0.00 0.00 43.33 2.17
305 306 9.472361 CCATATTTCTTTAATGGCAGAGATTTG 57.528 33.333 0.00 0.00 34.19 2.32
306 307 8.975439 CATATTTCTTTAATGGCAGAGATTTGC 58.025 33.333 0.00 0.00 43.34 3.68
310 311 4.621068 TTAATGGCAGAGATTTGCTTCG 57.379 40.909 0.00 0.00 43.57 3.79
324 325 6.863126 AGATTTGCTTCGAAACAAACCATAAG 59.137 34.615 24.55 0.00 38.50 1.73
340 341 7.748691 AACCATAAGTTACCGTTTTACATGT 57.251 32.000 2.69 2.69 36.74 3.21
342 343 9.452287 AACCATAAGTTACCGTTTTACATGTAT 57.548 29.630 6.36 0.00 36.74 2.29
351 352 9.887629 TTACCGTTTTACATGTATCCTGAATAA 57.112 29.630 6.36 0.00 0.00 1.40
381 382 3.487942 TCAACGTTGTCACAACATAGTCG 59.512 43.478 26.47 7.88 34.73 4.18
383 384 1.126113 CGTTGTCACAACATAGTCGGC 59.874 52.381 20.58 0.00 34.73 5.54
384 385 2.139917 GTTGTCACAACATAGTCGGCA 58.860 47.619 16.14 0.00 34.73 5.69
385 386 2.742053 GTTGTCACAACATAGTCGGCAT 59.258 45.455 16.14 0.00 34.73 4.40
390 391 1.277842 ACAACATAGTCGGCATCACCA 59.722 47.619 0.00 0.00 39.03 4.17
392 393 0.179111 ACATAGTCGGCATCACCACG 60.179 55.000 0.00 0.00 39.03 4.94
404 405 2.203294 ACCACGGCCAAGGACAAC 60.203 61.111 16.90 0.00 0.00 3.32
428 429 1.790387 GCACGCCATCACTCTTCAC 59.210 57.895 0.00 0.00 0.00 3.18
455 457 6.979817 TGTTATTTCATTCCATAGCAATGCAC 59.020 34.615 8.35 0.00 32.17 4.57
456 458 3.696281 TTCATTCCATAGCAATGCACG 57.304 42.857 8.35 0.00 32.17 5.34
457 459 2.916640 TCATTCCATAGCAATGCACGA 58.083 42.857 8.35 0.00 32.17 4.35
458 460 2.613595 TCATTCCATAGCAATGCACGAC 59.386 45.455 8.35 0.00 32.17 4.34
477 480 3.067180 CGACGGGTATTTGGCTAGTTAGA 59.933 47.826 0.00 0.00 0.00 2.10
478 481 4.618965 GACGGGTATTTGGCTAGTTAGAG 58.381 47.826 0.00 0.00 0.00 2.43
485 488 7.496263 GGGTATTTGGCTAGTTAGAGAAAAGAG 59.504 40.741 0.00 0.00 0.00 2.85
487 490 5.422214 TTGGCTAGTTAGAGAAAAGAGGG 57.578 43.478 0.00 0.00 0.00 4.30
488 491 3.197983 TGGCTAGTTAGAGAAAAGAGGGC 59.802 47.826 0.00 0.00 0.00 5.19
489 492 3.432467 GGCTAGTTAGAGAAAAGAGGGCC 60.432 52.174 0.00 0.00 0.00 5.80
490 493 3.452990 GCTAGTTAGAGAAAAGAGGGCCT 59.547 47.826 5.25 5.25 0.00 5.19
491 494 4.442332 GCTAGTTAGAGAAAAGAGGGCCTC 60.442 50.000 26.42 26.42 0.00 4.70
492 495 3.797312 AGTTAGAGAAAAGAGGGCCTCT 58.203 45.455 30.46 30.46 43.37 3.69
499 508 1.307430 AAGAGGGCCTCTTCCTCCC 60.307 63.158 37.31 9.74 46.42 4.30
500 509 3.157949 GAGGGCCTCTTCCTCCCG 61.158 72.222 26.44 0.00 43.71 5.14
506 515 1.308783 GCCTCTTCCTCCCGCAAAAG 61.309 60.000 0.00 0.00 0.00 2.27
509 518 2.619074 CCTCTTCCTCCCGCAAAAGAAT 60.619 50.000 0.00 0.00 0.00 2.40
510 519 3.084786 CTCTTCCTCCCGCAAAAGAATT 58.915 45.455 0.00 0.00 0.00 2.17
526 535 6.045350 AAAGAATTTGGCACGAGTGGTGAG 62.045 45.833 9.74 0.00 43.09 3.51
534 543 2.130272 ACGAGTGGTGAGCTATCTGA 57.870 50.000 0.00 0.00 0.00 3.27
543 584 7.168219 AGTGGTGAGCTATCTGAAAAACAATA 58.832 34.615 0.00 0.00 0.00 1.90
546 587 8.296713 TGGTGAGCTATCTGAAAAACAATAAAC 58.703 33.333 0.00 0.00 0.00 2.01
548 589 9.334693 GTGAGCTATCTGAAAAACAATAAACAG 57.665 33.333 0.00 0.00 0.00 3.16
559 600 5.362556 AACAATAAACAGTAGCTGTGCTG 57.637 39.130 0.00 4.81 44.62 4.41
560 601 3.189287 ACAATAAACAGTAGCTGTGCTGC 59.811 43.478 12.63 0.66 44.62 5.25
561 602 1.808411 TAAACAGTAGCTGTGCTGCC 58.192 50.000 12.63 0.00 44.62 4.85
562 603 1.230635 AAACAGTAGCTGTGCTGCCG 61.231 55.000 12.63 0.00 44.62 5.69
563 604 2.047844 CAGTAGCTGTGCTGCCGT 60.048 61.111 0.00 0.00 42.06 5.68
564 605 2.047844 AGTAGCTGTGCTGCCGTG 60.048 61.111 0.00 0.00 42.06 4.94
565 606 3.121030 GTAGCTGTGCTGCCGTGG 61.121 66.667 0.00 0.00 40.10 4.94
566 607 3.625897 TAGCTGTGCTGCCGTGGT 61.626 61.111 0.00 0.00 40.10 4.16
567 608 3.589654 TAGCTGTGCTGCCGTGGTC 62.590 63.158 0.00 0.00 40.10 4.02
595 638 3.920196 GGTCCACGGTGTCCACGT 61.920 66.667 7.45 0.00 46.82 4.49
700 743 0.399075 ACATCCCCGACCGACTTTTT 59.601 50.000 0.00 0.00 0.00 1.94
745 789 1.303317 ACCTTCCATTCCACGTGCC 60.303 57.895 10.91 0.00 0.00 5.01
747 791 0.609131 CCTTCCATTCCACGTGCCTT 60.609 55.000 10.91 0.00 0.00 4.35
796 855 3.556999 CGTGATAAGAGGAGGAGAAGGA 58.443 50.000 0.00 0.00 0.00 3.36
797 856 3.568007 CGTGATAAGAGGAGGAGAAGGAG 59.432 52.174 0.00 0.00 0.00 3.69
798 857 3.895041 GTGATAAGAGGAGGAGAAGGAGG 59.105 52.174 0.00 0.00 0.00 4.30
799 858 3.794399 TGATAAGAGGAGGAGAAGGAGGA 59.206 47.826 0.00 0.00 0.00 3.71
800 859 4.233053 TGATAAGAGGAGGAGAAGGAGGAA 59.767 45.833 0.00 0.00 0.00 3.36
801 860 2.846665 AGAGGAGGAGAAGGAGGAAG 57.153 55.000 0.00 0.00 0.00 3.46
802 861 2.293246 AGAGGAGGAGAAGGAGGAAGA 58.707 52.381 0.00 0.00 0.00 2.87
832 891 3.958860 AGCGGGCCAGCTCTTTGT 61.959 61.111 25.87 1.14 45.67 2.83
1076 1161 1.078918 CAGGAATCGCAGGTCAGCA 60.079 57.895 0.00 0.00 0.00 4.41
1139 1225 2.899339 GAGCAGGCGGCCAGATTC 60.899 66.667 23.09 10.86 46.50 2.52
1143 1229 4.162690 AGGCGGCCAGATTCGGTC 62.163 66.667 23.09 0.00 0.00 4.79
1202 1288 2.158325 TCCAGGGAACATCTTTGCCTTT 60.158 45.455 0.00 0.00 38.23 3.11
1228 1314 1.482593 CTTCATCTCCCCGCTGTAAGT 59.517 52.381 0.00 0.00 35.30 2.24
1237 1325 4.832608 GCTGTAAGTCCGCCCCCG 62.833 72.222 0.00 0.00 35.30 5.73
1241 1329 1.190833 TGTAAGTCCGCCCCCGTTTA 61.191 55.000 0.00 0.00 0.00 2.01
1325 1418 0.387112 CGATCTCTGCCGATCTCAGC 60.387 60.000 6.90 0.58 38.09 4.26
1570 1663 0.391263 CTACCCACCGCTTGTCCTTC 60.391 60.000 0.00 0.00 0.00 3.46
1589 1682 1.452651 GCTGCCTTGCCTGCATCTA 60.453 57.895 0.00 0.00 38.22 1.98
1610 1703 9.599866 CATCTATAAGTTTGACTGATGTGGTTA 57.400 33.333 0.00 0.00 0.00 2.85
1611 1704 8.997621 TCTATAAGTTTGACTGATGTGGTTAC 57.002 34.615 0.00 0.00 0.00 2.50
1612 1705 8.812972 TCTATAAGTTTGACTGATGTGGTTACT 58.187 33.333 0.00 0.00 0.00 2.24
1613 1706 9.436957 CTATAAGTTTGACTGATGTGGTTACTT 57.563 33.333 0.00 0.00 0.00 2.24
1660 1753 2.839098 CTGGCAGGGGTGTTCTGT 59.161 61.111 6.61 0.00 34.89 3.41
1802 1895 9.123902 CCATCATTGTGAGTCCTGAAATATTTA 57.876 33.333 0.00 0.00 0.00 1.40
1809 1902 9.177608 TGTGAGTCCTGAAATATTTATTTCCTG 57.822 33.333 16.53 11.04 46.80 3.86
1810 1903 8.131731 GTGAGTCCTGAAATATTTATTTCCTGC 58.868 37.037 16.53 7.67 46.80 4.85
1872 1992 6.214615 TCTTCTGGTGTATAATTGGTCCTTCA 59.785 38.462 0.00 0.00 0.00 3.02
1923 2043 7.496920 TGATCTCATCTGACCATGTTTGTTATC 59.503 37.037 0.00 0.00 0.00 1.75
1993 2113 2.030027 TGGTGATCAGGACCAAGAGT 57.970 50.000 0.00 0.00 40.65 3.24
2064 2184 0.320596 TCGTTTTTCGCATACGGGGT 60.321 50.000 0.00 0.00 40.63 4.95
2175 2295 3.132111 TGTTTGGCCCTTCTTTCTTGTTC 59.868 43.478 0.00 0.00 0.00 3.18
2310 2430 6.524101 TTACTAGTCACACATACATGAGCA 57.476 37.500 0.00 0.00 0.00 4.26
2318 2438 3.376234 ACACATACATGAGCATGCAAGAC 59.624 43.478 21.98 8.73 42.39 3.01
2321 2441 4.095932 ACATACATGAGCATGCAAGACAAG 59.904 41.667 21.98 12.99 42.39 3.16
2366 2487 2.572290 ACTGTTATATGCGGCTTTCCC 58.428 47.619 0.00 0.00 0.00 3.97
2396 2517 4.216257 CGTTGAGTTTCCTGATCATGGTTT 59.784 41.667 0.00 0.00 0.00 3.27
2399 2520 2.827921 AGTTTCCTGATCATGGTTTGCC 59.172 45.455 0.00 0.00 0.00 4.52
2493 2614 6.183360 TGTCACATTCGTTAAACAAACATGGA 60.183 34.615 0.00 0.00 38.03 3.41
2632 2759 5.971763 ACTTGTAATGTTTGCCAAGTTCAA 58.028 33.333 0.00 0.00 43.59 2.69
2648 2775 7.382110 CCAAGTTCAAGAGTGAAGATCTCTAA 58.618 38.462 0.00 0.00 44.44 2.10
2655 2782 8.085296 TCAAGAGTGAAGATCTCTAACAAGTTC 58.915 37.037 0.00 0.00 40.79 3.01
2742 2870 0.752054 CTTGCAACAAAAGGAGGCCA 59.248 50.000 5.01 0.00 0.00 5.36
2744 2872 1.114722 TGCAACAAAAGGAGGCCAGG 61.115 55.000 5.01 0.00 0.00 4.45
2794 2922 0.663153 AAGCGTCAACTTCTTGTGCC 59.337 50.000 0.00 0.00 33.21 5.01
2813 2941 5.694006 TGTGCCAACAAATACATTTTAGCAC 59.306 36.000 14.84 14.84 31.82 4.40
2817 2945 6.144724 GCCAACAAATACATTTTAGCACGAAA 59.855 34.615 0.00 0.00 0.00 3.46
2828 2970 9.030301 ACATTTTAGCACGAAATATAATTTGGC 57.970 29.630 0.00 0.00 0.00 4.52
2854 2996 3.576078 ATGGTGGTGTCACTTTCTTGA 57.424 42.857 2.35 0.00 43.17 3.02
2909 3054 3.564511 CGCGGAAAATTGATGTTTGAGT 58.435 40.909 0.00 0.00 0.00 3.41
2944 3089 4.929819 TTTGTGGTTTTTCTAGAAGGCC 57.070 40.909 5.12 9.64 0.00 5.19
2949 3094 2.820197 GGTTTTTCTAGAAGGCCACAGG 59.180 50.000 5.01 0.00 0.00 4.00
2963 3108 1.608055 CACAGGCAGAACATGAACCA 58.392 50.000 0.00 0.00 0.00 3.67
2994 3144 7.649705 ACAGATGTATTTCAGACGCAATACTAG 59.350 37.037 5.47 0.00 36.97 2.57
2996 3146 8.847196 AGATGTATTTCAGACGCAATACTAGTA 58.153 33.333 4.77 4.77 36.97 1.82
3042 3192 5.599656 TCCCAAATTTCAGATGGATGATTCC 59.400 40.000 0.00 0.00 42.94 3.01
3092 3242 2.124819 CCTACAGCCTGCCTGCAG 60.125 66.667 12.17 12.17 45.78 4.41
3123 3273 6.294731 GGTTGAGGTTCTCTGCATTATTTTGT 60.295 38.462 0.00 0.00 0.00 2.83
3192 3344 9.843334 TCATTTGTTTATATTGTTTTACCGGTC 57.157 29.630 12.40 0.00 0.00 4.79
3227 3379 1.683943 ATTTGATGCTATGTGCGGCT 58.316 45.000 0.00 0.00 46.63 5.52
3251 3403 7.173907 GCTAGCATTAATGGATTACTGATGTGT 59.826 37.037 17.02 0.00 0.00 3.72
3252 3404 7.268199 AGCATTAATGGATTACTGATGTGTG 57.732 36.000 17.02 0.00 0.00 3.82
3253 3405 6.830324 AGCATTAATGGATTACTGATGTGTGT 59.170 34.615 17.02 0.00 0.00 3.72
3255 3407 8.786898 GCATTAATGGATTACTGATGTGTGTAT 58.213 33.333 17.02 0.00 0.00 2.29
3286 3438 8.255905 TGATGGATGTATCATGTATGTGATCTC 58.744 37.037 0.00 0.00 39.45 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.240493 AATGGGCGAGTACTATGCAC 57.760 50.000 18.28 16.02 0.00 4.57
1 2 4.409718 TTTAATGGGCGAGTACTATGCA 57.590 40.909 18.28 0.00 0.00 3.96
2 3 5.744666 TTTTTAATGGGCGAGTACTATGC 57.255 39.130 10.39 10.39 0.00 3.14
3 4 9.268268 TCTAATTTTTAATGGGCGAGTACTATG 57.732 33.333 0.00 0.00 0.00 2.23
4 5 9.841295 TTCTAATTTTTAATGGGCGAGTACTAT 57.159 29.630 0.00 0.00 0.00 2.12
5 6 9.841295 ATTCTAATTTTTAATGGGCGAGTACTA 57.159 29.630 0.00 0.00 0.00 1.82
6 7 8.747538 ATTCTAATTTTTAATGGGCGAGTACT 57.252 30.769 0.00 0.00 0.00 2.73
7 8 8.617809 TGATTCTAATTTTTAATGGGCGAGTAC 58.382 33.333 0.00 0.00 0.00 2.73
8 9 8.617809 GTGATTCTAATTTTTAATGGGCGAGTA 58.382 33.333 0.00 0.00 0.00 2.59
9 10 7.122055 TGTGATTCTAATTTTTAATGGGCGAGT 59.878 33.333 0.00 0.00 0.00 4.18
10 11 7.479980 TGTGATTCTAATTTTTAATGGGCGAG 58.520 34.615 0.00 0.00 0.00 5.03
11 12 7.397892 TGTGATTCTAATTTTTAATGGGCGA 57.602 32.000 0.00 0.00 0.00 5.54
12 13 8.472683 TTTGTGATTCTAATTTTTAATGGGCG 57.527 30.769 0.00 0.00 0.00 6.13
13 14 9.435688 ACTTTGTGATTCTAATTTTTAATGGGC 57.564 29.630 0.00 0.00 0.00 5.36
18 19 9.691362 GCCAGACTTTGTGATTCTAATTTTTAA 57.309 29.630 0.00 0.00 0.00 1.52
19 20 8.303876 GGCCAGACTTTGTGATTCTAATTTTTA 58.696 33.333 0.00 0.00 0.00 1.52
20 21 7.154656 GGCCAGACTTTGTGATTCTAATTTTT 58.845 34.615 0.00 0.00 0.00 1.94
21 22 6.570378 CGGCCAGACTTTGTGATTCTAATTTT 60.570 38.462 2.24 0.00 0.00 1.82
22 23 5.106157 CGGCCAGACTTTGTGATTCTAATTT 60.106 40.000 2.24 0.00 0.00 1.82
23 24 4.396166 CGGCCAGACTTTGTGATTCTAATT 59.604 41.667 2.24 0.00 0.00 1.40
24 25 3.941483 CGGCCAGACTTTGTGATTCTAAT 59.059 43.478 2.24 0.00 0.00 1.73
25 26 3.244422 ACGGCCAGACTTTGTGATTCTAA 60.244 43.478 2.24 0.00 0.00 2.10
26 27 2.301870 ACGGCCAGACTTTGTGATTCTA 59.698 45.455 2.24 0.00 0.00 2.10
27 28 1.072331 ACGGCCAGACTTTGTGATTCT 59.928 47.619 2.24 0.00 0.00 2.40
28 29 1.197721 CACGGCCAGACTTTGTGATTC 59.802 52.381 2.24 0.00 32.39 2.52
29 30 1.238439 CACGGCCAGACTTTGTGATT 58.762 50.000 2.24 0.00 32.39 2.57
30 31 0.606401 CCACGGCCAGACTTTGTGAT 60.606 55.000 2.24 0.00 32.39 3.06
31 32 1.227823 CCACGGCCAGACTTTGTGA 60.228 57.895 2.24 0.00 32.39 3.58
32 33 1.227823 TCCACGGCCAGACTTTGTG 60.228 57.895 2.24 0.00 0.00 3.33
33 34 1.227853 GTCCACGGCCAGACTTTGT 60.228 57.895 2.24 0.00 0.00 2.83
34 35 1.966451 GGTCCACGGCCAGACTTTG 60.966 63.158 15.08 0.00 33.39 2.77
35 36 2.113243 GAGGTCCACGGCCAGACTTT 62.113 60.000 15.08 6.28 33.39 2.66
36 37 2.526873 AGGTCCACGGCCAGACTT 60.527 61.111 15.08 6.89 33.39 3.01
37 38 2.997897 GAGGTCCACGGCCAGACT 60.998 66.667 15.08 4.12 33.39 3.24
38 39 2.185310 ATTGAGGTCCACGGCCAGAC 62.185 60.000 2.24 6.26 0.00 3.51
39 40 1.899437 GATTGAGGTCCACGGCCAGA 61.899 60.000 2.24 0.00 0.00 3.86
40 41 1.450312 GATTGAGGTCCACGGCCAG 60.450 63.158 2.24 0.00 0.00 4.85
41 42 2.220586 TGATTGAGGTCCACGGCCA 61.221 57.895 2.24 0.00 0.00 5.36
42 43 1.745489 GTGATTGAGGTCCACGGCC 60.745 63.158 0.00 0.00 0.00 6.13
43 44 0.535335 TAGTGATTGAGGTCCACGGC 59.465 55.000 0.00 0.00 36.06 5.68
44 45 4.501571 CCTTATAGTGATTGAGGTCCACGG 60.502 50.000 0.00 0.00 36.06 4.94
45 46 4.621991 CCTTATAGTGATTGAGGTCCACG 58.378 47.826 0.00 0.00 36.06 4.94
46 47 4.141711 TGCCTTATAGTGATTGAGGTCCAC 60.142 45.833 0.00 0.00 0.00 4.02
47 48 4.037222 TGCCTTATAGTGATTGAGGTCCA 58.963 43.478 0.00 0.00 0.00 4.02
48 49 4.689612 TGCCTTATAGTGATTGAGGTCC 57.310 45.455 0.00 0.00 0.00 4.46
49 50 5.049129 GCATTGCCTTATAGTGATTGAGGTC 60.049 44.000 0.00 0.00 0.00 3.85
50 51 4.823989 GCATTGCCTTATAGTGATTGAGGT 59.176 41.667 0.00 0.00 0.00 3.85
51 52 4.823442 TGCATTGCCTTATAGTGATTGAGG 59.177 41.667 6.12 0.00 0.00 3.86
52 53 6.381481 TTGCATTGCCTTATAGTGATTGAG 57.619 37.500 6.12 0.00 0.00 3.02
53 54 6.546772 TCATTGCATTGCCTTATAGTGATTGA 59.453 34.615 6.12 0.00 0.00 2.57
54 55 6.741109 TCATTGCATTGCCTTATAGTGATTG 58.259 36.000 6.12 0.00 0.00 2.67
55 56 6.964807 TCATTGCATTGCCTTATAGTGATT 57.035 33.333 6.12 0.00 0.00 2.57
56 57 6.964807 TTCATTGCATTGCCTTATAGTGAT 57.035 33.333 6.12 0.00 0.00 3.06
57 58 6.152492 TGTTTCATTGCATTGCCTTATAGTGA 59.848 34.615 6.12 0.00 0.00 3.41
58 59 6.331845 TGTTTCATTGCATTGCCTTATAGTG 58.668 36.000 6.12 0.00 0.00 2.74
59 60 6.528537 TGTTTCATTGCATTGCCTTATAGT 57.471 33.333 6.12 0.00 0.00 2.12
60 61 7.042321 CCAATGTTTCATTGCATTGCCTTATAG 60.042 37.037 14.59 0.00 46.15 1.31
61 62 6.762187 CCAATGTTTCATTGCATTGCCTTATA 59.238 34.615 14.59 0.00 46.15 0.98
62 63 5.587043 CCAATGTTTCATTGCATTGCCTTAT 59.413 36.000 14.59 0.00 46.15 1.73
63 64 4.936411 CCAATGTTTCATTGCATTGCCTTA 59.064 37.500 14.59 0.00 46.15 2.69
64 65 3.754323 CCAATGTTTCATTGCATTGCCTT 59.246 39.130 14.59 0.00 46.15 4.35
65 66 3.008157 TCCAATGTTTCATTGCATTGCCT 59.992 39.130 14.59 0.00 46.15 4.75
66 67 3.336468 TCCAATGTTTCATTGCATTGCC 58.664 40.909 14.59 0.00 46.15 4.52
67 68 5.359716 TTTCCAATGTTTCATTGCATTGC 57.640 34.783 14.59 0.46 46.15 3.56
68 69 7.240674 CAGATTTCCAATGTTTCATTGCATTG 58.759 34.615 14.59 9.51 46.71 2.82
69 70 6.128117 GCAGATTTCCAATGTTTCATTGCATT 60.128 34.615 14.59 0.00 35.91 3.56
70 71 5.353123 GCAGATTTCCAATGTTTCATTGCAT 59.647 36.000 14.59 7.83 0.00 3.96
71 72 4.691685 GCAGATTTCCAATGTTTCATTGCA 59.308 37.500 14.59 0.17 0.00 4.08
72 73 4.933400 AGCAGATTTCCAATGTTTCATTGC 59.067 37.500 14.59 4.44 0.00 3.56
73 74 6.425721 ACAAGCAGATTTCCAATGTTTCATTG 59.574 34.615 13.47 13.47 0.00 2.82
74 75 6.527423 ACAAGCAGATTTCCAATGTTTCATT 58.473 32.000 0.00 0.00 0.00 2.57
75 76 6.105397 ACAAGCAGATTTCCAATGTTTCAT 57.895 33.333 0.00 0.00 0.00 2.57
76 77 5.534207 ACAAGCAGATTTCCAATGTTTCA 57.466 34.783 0.00 0.00 0.00 2.69
77 78 6.849588 AAACAAGCAGATTTCCAATGTTTC 57.150 33.333 0.00 0.00 35.31 2.78
78 79 6.347696 TGAAACAAGCAGATTTCCAATGTTT 58.652 32.000 0.00 0.00 40.89 2.83
79 80 5.916318 TGAAACAAGCAGATTTCCAATGTT 58.084 33.333 4.69 0.00 34.52 2.71
80 81 5.534207 TGAAACAAGCAGATTTCCAATGT 57.466 34.783 4.69 0.00 34.52 2.71
81 82 6.847956 TTTGAAACAAGCAGATTTCCAATG 57.152 33.333 4.69 0.00 34.52 2.82
82 83 7.862512 TTTTTGAAACAAGCAGATTTCCAAT 57.137 28.000 4.69 0.00 34.52 3.16
105 106 9.546428 CCACATATTTCCTTTTCTTTTGTCTTT 57.454 29.630 0.00 0.00 0.00 2.52
106 107 8.150296 CCCACATATTTCCTTTTCTTTTGTCTT 58.850 33.333 0.00 0.00 0.00 3.01
107 108 7.508977 TCCCACATATTTCCTTTTCTTTTGTCT 59.491 33.333 0.00 0.00 0.00 3.41
108 109 7.666623 TCCCACATATTTCCTTTTCTTTTGTC 58.333 34.615 0.00 0.00 0.00 3.18
109 110 7.610580 TCCCACATATTTCCTTTTCTTTTGT 57.389 32.000 0.00 0.00 0.00 2.83
110 111 8.313292 TGATCCCACATATTTCCTTTTCTTTTG 58.687 33.333 0.00 0.00 0.00 2.44
111 112 8.434589 TGATCCCACATATTTCCTTTTCTTTT 57.565 30.769 0.00 0.00 0.00 2.27
112 113 8.480501 CATGATCCCACATATTTCCTTTTCTTT 58.519 33.333 0.00 0.00 0.00 2.52
113 114 7.418254 GCATGATCCCACATATTTCCTTTTCTT 60.418 37.037 0.00 0.00 0.00 2.52
114 115 6.041296 GCATGATCCCACATATTTCCTTTTCT 59.959 38.462 0.00 0.00 0.00 2.52
115 116 6.041296 AGCATGATCCCACATATTTCCTTTTC 59.959 38.462 0.00 0.00 0.00 2.29
116 117 5.901276 AGCATGATCCCACATATTTCCTTTT 59.099 36.000 0.00 0.00 0.00 2.27
117 118 5.461327 AGCATGATCCCACATATTTCCTTT 58.539 37.500 0.00 0.00 0.00 3.11
118 119 5.070823 AGCATGATCCCACATATTTCCTT 57.929 39.130 0.00 0.00 0.00 3.36
119 120 4.736611 AGCATGATCCCACATATTTCCT 57.263 40.909 0.00 0.00 0.00 3.36
120 121 5.105997 GCTAAGCATGATCCCACATATTTCC 60.106 44.000 0.00 0.00 0.00 3.13
121 122 5.709164 AGCTAAGCATGATCCCACATATTTC 59.291 40.000 0.00 0.00 0.00 2.17
122 123 5.475909 CAGCTAAGCATGATCCCACATATTT 59.524 40.000 0.00 0.00 0.00 1.40
123 124 5.008331 CAGCTAAGCATGATCCCACATATT 58.992 41.667 0.00 0.00 0.00 1.28
124 125 4.567116 CCAGCTAAGCATGATCCCACATAT 60.567 45.833 0.00 0.00 0.00 1.78
125 126 3.244665 CCAGCTAAGCATGATCCCACATA 60.245 47.826 0.00 0.00 0.00 2.29
126 127 2.488528 CCAGCTAAGCATGATCCCACAT 60.489 50.000 0.00 0.00 0.00 3.21
127 128 1.134007 CCAGCTAAGCATGATCCCACA 60.134 52.381 0.00 0.00 0.00 4.17
128 129 1.133976 ACCAGCTAAGCATGATCCCAC 60.134 52.381 0.00 0.00 0.00 4.61
129 130 1.216064 ACCAGCTAAGCATGATCCCA 58.784 50.000 0.00 0.00 0.00 4.37
130 131 2.355010 AACCAGCTAAGCATGATCCC 57.645 50.000 0.00 0.00 0.00 3.85
131 132 3.808728 TGTAACCAGCTAAGCATGATCC 58.191 45.455 0.00 0.00 0.00 3.36
132 133 7.678947 ATATTGTAACCAGCTAAGCATGATC 57.321 36.000 0.00 0.00 0.00 2.92
133 134 8.469309 AAATATTGTAACCAGCTAAGCATGAT 57.531 30.769 0.00 0.00 0.00 2.45
134 135 7.880160 AAATATTGTAACCAGCTAAGCATGA 57.120 32.000 0.00 0.00 0.00 3.07
135 136 8.810427 CAAAAATATTGTAACCAGCTAAGCATG 58.190 33.333 0.00 0.00 0.00 4.06
136 137 8.531146 ACAAAAATATTGTAACCAGCTAAGCAT 58.469 29.630 0.00 0.00 0.00 3.79
137 138 7.891561 ACAAAAATATTGTAACCAGCTAAGCA 58.108 30.769 0.00 0.00 0.00 3.91
138 139 8.647226 CAACAAAAATATTGTAACCAGCTAAGC 58.353 33.333 0.00 0.00 31.50 3.09
139 140 9.906660 TCAACAAAAATATTGTAACCAGCTAAG 57.093 29.630 0.00 0.00 31.50 2.18
143 144 8.807581 GCTATCAACAAAAATATTGTAACCAGC 58.192 33.333 0.00 0.00 31.50 4.85
169 170 3.126001 TCAAGTGGTCAGCTTGGTAAG 57.874 47.619 5.39 0.00 42.44 2.34
170 171 3.411446 CATCAAGTGGTCAGCTTGGTAA 58.589 45.455 5.39 0.00 42.44 2.85
171 172 2.290260 CCATCAAGTGGTCAGCTTGGTA 60.290 50.000 5.39 0.00 43.44 3.25
172 173 1.546323 CCATCAAGTGGTCAGCTTGGT 60.546 52.381 5.39 0.00 43.44 3.67
173 174 1.171308 CCATCAAGTGGTCAGCTTGG 58.829 55.000 5.39 0.00 43.44 3.61
183 184 3.252701 GCTAAGCATGATCCCATCAAGTG 59.747 47.826 0.00 0.00 43.50 3.16
184 185 3.137913 AGCTAAGCATGATCCCATCAAGT 59.862 43.478 0.00 0.00 43.50 3.16
185 186 3.502595 CAGCTAAGCATGATCCCATCAAG 59.497 47.826 0.00 0.00 43.50 3.02
186 187 3.483421 CAGCTAAGCATGATCCCATCAA 58.517 45.455 0.00 0.00 43.50 2.57
187 188 2.224695 CCAGCTAAGCATGATCCCATCA 60.225 50.000 0.00 0.00 44.55 3.07
188 189 2.224719 ACCAGCTAAGCATGATCCCATC 60.225 50.000 0.00 0.00 0.00 3.51
189 190 1.779092 ACCAGCTAAGCATGATCCCAT 59.221 47.619 0.00 0.00 0.00 4.00
194 195 2.338577 GGTGACCAGCTAAGCATGAT 57.661 50.000 0.00 0.00 0.00 2.45
209 210 5.329399 ACTGCTTGGTTAATTTATGGGTGA 58.671 37.500 0.00 0.00 0.00 4.02
211 212 7.784470 TTAACTGCTTGGTTAATTTATGGGT 57.216 32.000 6.28 0.00 36.93 4.51
223 224 4.860022 AGAGGCATAATTAACTGCTTGGT 58.140 39.130 10.15 0.00 38.45 3.67
224 225 6.942532 TTAGAGGCATAATTAACTGCTTGG 57.057 37.500 10.15 0.00 38.45 3.61
287 288 5.032863 CGAAGCAAATCTCTGCCATTAAAG 58.967 41.667 0.00 0.00 43.73 1.85
304 305 5.508200 AACTTATGGTTTGTTTCGAAGCA 57.492 34.783 10.92 10.92 39.17 3.91
305 306 5.854866 GGTAACTTATGGTTTGTTTCGAAGC 59.145 40.000 4.89 4.89 39.17 3.86
306 307 6.075280 CGGTAACTTATGGTTTGTTTCGAAG 58.925 40.000 0.00 0.00 39.17 3.79
310 311 7.990541 AAAACGGTAACTTATGGTTTGTTTC 57.009 32.000 0.00 0.00 36.49 2.78
324 325 7.599630 TTCAGGATACATGTAAAACGGTAAC 57.400 36.000 10.14 0.00 41.41 2.50
342 343 7.822334 ACAACGTTGATGACTAATTATTCAGGA 59.178 33.333 33.66 0.00 0.00 3.86
351 352 5.525745 TGTTGTGACAACGTTGATGACTAAT 59.474 36.000 33.66 9.45 31.49 1.73
381 382 3.443045 CTTGGCCGTGGTGATGCC 61.443 66.667 0.00 0.00 45.56 4.40
383 384 2.040544 GTCCTTGGCCGTGGTGATG 61.041 63.158 12.75 0.00 0.00 3.07
384 385 2.063015 TTGTCCTTGGCCGTGGTGAT 62.063 55.000 12.75 0.00 0.00 3.06
385 386 2.747443 TTGTCCTTGGCCGTGGTGA 61.747 57.895 12.75 0.00 0.00 4.02
390 391 4.636435 CCGGTTGTCCTTGGCCGT 62.636 66.667 0.00 0.00 42.36 5.68
392 393 2.671963 GACCGGTTGTCCTTGGCC 60.672 66.667 9.42 0.00 38.09 5.36
396 397 2.280592 GTGCGACCGGTTGTCCTT 60.281 61.111 22.97 0.00 41.18 3.36
410 411 0.950555 TGTGAAGAGTGATGGCGTGC 60.951 55.000 0.00 0.00 0.00 5.34
428 429 7.654116 TGCATTGCTATGGAATGAAATAACATG 59.346 33.333 14.33 0.00 33.36 3.21
455 457 2.304751 AACTAGCCAAATACCCGTCG 57.695 50.000 0.00 0.00 0.00 5.12
456 458 4.340381 TCTCTAACTAGCCAAATACCCGTC 59.660 45.833 0.00 0.00 0.00 4.79
457 459 4.284178 TCTCTAACTAGCCAAATACCCGT 58.716 43.478 0.00 0.00 0.00 5.28
458 460 4.931661 TCTCTAACTAGCCAAATACCCG 57.068 45.455 0.00 0.00 0.00 5.28
487 490 1.303317 TTTTGCGGGAGGAAGAGGC 60.303 57.895 0.00 0.00 42.50 4.70
488 491 0.324943 TCTTTTGCGGGAGGAAGAGG 59.675 55.000 0.00 0.00 41.66 3.69
489 492 2.185004 TTCTTTTGCGGGAGGAAGAG 57.815 50.000 0.00 0.00 42.50 2.85
490 493 2.879103 ATTCTTTTGCGGGAGGAAGA 57.121 45.000 0.00 0.00 42.50 2.87
491 494 3.578688 CAAATTCTTTTGCGGGAGGAAG 58.421 45.455 0.00 0.00 42.50 3.46
492 495 2.298729 CCAAATTCTTTTGCGGGAGGAA 59.701 45.455 0.00 0.00 40.77 3.36
495 498 1.000731 TGCCAAATTCTTTTGCGGGAG 59.999 47.619 0.00 0.00 40.77 4.30
499 508 1.715519 CTCGTGCCAAATTCTTTTGCG 59.284 47.619 0.00 0.00 40.77 4.85
500 509 2.472488 CACTCGTGCCAAATTCTTTTGC 59.528 45.455 0.00 0.00 40.77 3.68
501 510 3.052036 CCACTCGTGCCAAATTCTTTTG 58.948 45.455 0.00 0.00 41.59 2.44
502 511 2.693074 ACCACTCGTGCCAAATTCTTTT 59.307 40.909 0.00 0.00 0.00 2.27
506 515 1.197721 CTCACCACTCGTGCCAAATTC 59.802 52.381 0.00 0.00 42.69 2.17
509 518 1.891919 GCTCACCACTCGTGCCAAA 60.892 57.895 0.00 0.00 42.69 3.28
510 519 1.468506 TAGCTCACCACTCGTGCCAA 61.469 55.000 0.00 0.00 42.69 4.52
516 525 3.510388 TTTCAGATAGCTCACCACTCG 57.490 47.619 0.00 0.00 0.00 4.18
519 528 5.689383 TTGTTTTTCAGATAGCTCACCAC 57.311 39.130 0.00 0.00 0.00 4.16
521 530 8.296713 TGTTTATTGTTTTTCAGATAGCTCACC 58.703 33.333 0.00 0.00 0.00 4.02
526 535 9.278734 GCTACTGTTTATTGTTTTTCAGATAGC 57.721 33.333 0.00 0.00 32.21 2.97
529 538 8.850156 ACAGCTACTGTTTATTGTTTTTCAGAT 58.150 29.630 0.00 0.00 42.59 2.90
533 542 6.918022 AGCACAGCTACTGTTTATTGTTTTTC 59.082 34.615 0.00 0.00 42.59 2.29
534 543 6.697019 CAGCACAGCTACTGTTTATTGTTTTT 59.303 34.615 0.00 0.00 42.59 1.94
543 584 1.230635 CGGCAGCACAGCTACTGTTT 61.231 55.000 11.06 0.00 42.59 2.83
546 587 2.047844 ACGGCAGCACAGCTACTG 60.048 61.111 6.28 6.28 36.40 2.74
548 589 3.121030 CCACGGCAGCACAGCTAC 61.121 66.667 0.00 0.00 36.40 3.58
700 743 7.037297 GGATATCCTGGGATCTTATTCCTTGAA 60.037 40.741 14.97 0.00 35.97 2.69
703 746 6.216456 GTGGATATCCTGGGATCTTATTCCTT 59.784 42.308 22.35 0.00 36.17 3.36
712 755 2.573915 GGAAGGTGGATATCCTGGGATC 59.426 54.545 22.35 13.23 36.17 3.36
796 855 1.290732 CTTCCTCCTCCTCCTCTTCCT 59.709 57.143 0.00 0.00 0.00 3.36
797 856 1.788229 CTTCCTCCTCCTCCTCTTCC 58.212 60.000 0.00 0.00 0.00 3.46
798 857 1.119684 GCTTCCTCCTCCTCCTCTTC 58.880 60.000 0.00 0.00 0.00 2.87
799 858 0.686112 CGCTTCCTCCTCCTCCTCTT 60.686 60.000 0.00 0.00 0.00 2.85
800 859 1.076339 CGCTTCCTCCTCCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
801 860 2.131067 CCGCTTCCTCCTCCTCCTC 61.131 68.421 0.00 0.00 0.00 3.71
802 861 2.042435 CCGCTTCCTCCTCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
832 891 2.530151 AGCAGGAACAGCAGGGGA 60.530 61.111 0.00 0.00 45.86 4.81
913 998 3.019564 CCTCCGGCAGATGATTCTTTTT 58.980 45.455 0.00 0.00 0.00 1.94
914 999 2.239654 TCCTCCGGCAGATGATTCTTTT 59.760 45.455 0.00 0.00 0.00 2.27
915 1000 1.839994 TCCTCCGGCAGATGATTCTTT 59.160 47.619 0.00 0.00 0.00 2.52
916 1001 1.415659 CTCCTCCGGCAGATGATTCTT 59.584 52.381 0.00 0.00 0.00 2.52
1076 1161 1.606313 CAAAGGGAATGGCGGTGGT 60.606 57.895 0.00 0.00 0.00 4.16
1125 1211 4.473520 ACCGAATCTGGCCGCCTG 62.474 66.667 11.61 10.74 0.00 4.85
1139 1225 2.742372 CAAGAACTGGCCGGACCG 60.742 66.667 21.41 6.99 43.94 4.79
1202 1288 1.900351 CGGGGAGATGAAGAGCACA 59.100 57.895 0.00 0.00 0.00 4.57
1228 1314 0.677414 GAAATGTAAACGGGGGCGGA 60.677 55.000 0.00 0.00 0.00 5.54
1237 1325 7.368059 AGAAGAAATCGGGTTGAAATGTAAAC 58.632 34.615 0.00 0.00 0.00 2.01
1241 1329 5.278957 CCAAGAAGAAATCGGGTTGAAATGT 60.279 40.000 0.00 0.00 0.00 2.71
1325 1418 1.210478 ACGATCCTCCTGAATGTTGGG 59.790 52.381 0.00 0.00 0.00 4.12
1570 1663 4.189188 GATGCAGGCAAGGCAGCG 62.189 66.667 0.00 0.00 45.68 5.18
1589 1682 8.691661 AAAGTAACCACATCAGTCAAACTTAT 57.308 30.769 0.00 0.00 0.00 1.73
1610 1703 1.607628 CTTGAGCTGCAGCAAGAAAGT 59.392 47.619 38.24 17.87 43.11 2.66
1611 1704 1.068472 CCTTGAGCTGCAGCAAGAAAG 60.068 52.381 38.24 29.91 43.11 2.62
1612 1705 0.956633 CCTTGAGCTGCAGCAAGAAA 59.043 50.000 38.24 23.94 43.11 2.52
1613 1706 0.179009 ACCTTGAGCTGCAGCAAGAA 60.179 50.000 38.24 24.95 43.11 2.52
1660 1753 0.179032 ACACAATCAGGCCGAACACA 60.179 50.000 0.00 0.00 0.00 3.72
1803 1896 8.789762 GGTTTGAGTTAGTTATAAAGCAGGAAA 58.210 33.333 0.00 0.00 0.00 3.13
1805 1898 7.606456 CAGGTTTGAGTTAGTTATAAAGCAGGA 59.394 37.037 0.00 0.00 32.80 3.86
1807 1900 8.324163 ACAGGTTTGAGTTAGTTATAAAGCAG 57.676 34.615 0.00 0.00 32.80 4.24
1841 1961 5.009010 CCAATTATACACCAGAAGATGTGGC 59.991 44.000 0.00 0.00 38.83 5.01
1872 1992 2.099405 CGCCAAACCCATCAAACCTAT 58.901 47.619 0.00 0.00 0.00 2.57
1993 2113 2.969821 AAAAGGGCATGTACTCCACA 57.030 45.000 0.00 0.00 42.69 4.17
2064 2184 4.564782 ATGAAGAAGTCATCCAGAAGCA 57.435 40.909 0.00 0.00 44.01 3.91
2175 2295 2.941428 GGAACCTGTAATTGGCAAACG 58.059 47.619 3.01 0.00 0.00 3.60
2310 2430 3.825328 ACTCAACCTTCTTGTCTTGCAT 58.175 40.909 0.00 0.00 0.00 3.96
2318 2438 5.654497 AGCTTTTCAAACTCAACCTTCTTG 58.346 37.500 0.00 0.00 0.00 3.02
2321 2441 9.181805 GTAAATAGCTTTTCAAACTCAACCTTC 57.818 33.333 0.00 0.00 0.00 3.46
2366 2487 5.409520 TGATCAGGAAACTCAACGAGAAATG 59.590 40.000 0.00 0.00 40.21 2.32
2396 2517 0.396435 AAACGTGTGATGGAGAGGCA 59.604 50.000 0.00 0.00 0.00 4.75
2399 2520 3.181530 CGCTTTAAACGTGTGATGGAGAG 60.182 47.826 0.00 0.00 0.00 3.20
2493 2614 0.103715 ATCCATCCACCATAGGCCCT 60.104 55.000 0.00 0.00 0.00 5.19
2632 2759 7.775053 AGAACTTGTTAGAGATCTTCACTCT 57.225 36.000 0.00 0.00 45.15 3.24
2706 2834 5.181690 TGCAAGACACCATTTCTTACAAC 57.818 39.130 0.00 0.00 31.86 3.32
2722 2850 1.039856 GGCCTCCTTTTGTTGCAAGA 58.960 50.000 0.00 0.00 0.00 3.02
2773 2901 1.334149 GCACAAGAAGTTGACGCTTCC 60.334 52.381 2.63 0.00 44.27 3.46
2813 2941 5.629020 CCATTGACCGCCAAATTATATTTCG 59.371 40.000 0.00 0.00 38.43 3.46
2817 2945 4.280677 CCACCATTGACCGCCAAATTATAT 59.719 41.667 0.00 0.00 38.43 0.86
2823 2951 1.152652 ACCACCATTGACCGCCAAA 60.153 52.632 0.00 0.00 38.43 3.28
2828 2970 0.250295 AGTGACACCACCATTGACCG 60.250 55.000 0.84 0.00 44.22 4.79
2909 3054 1.000827 CCACAAAACGTGCAAGCCATA 60.001 47.619 0.00 0.00 44.91 2.74
2944 3089 1.538512 CTGGTTCATGTTCTGCCTGTG 59.461 52.381 0.00 0.00 0.00 3.66
2949 3094 2.618241 TGTTGACTGGTTCATGTTCTGC 59.382 45.455 0.00 0.00 32.84 4.26
2959 3104 6.428159 GTCTGAAATACATCTGTTGACTGGTT 59.572 38.462 0.00 0.00 0.00 3.67
2963 3108 4.627467 GCGTCTGAAATACATCTGTTGACT 59.373 41.667 0.00 0.00 0.00 3.41
2994 3144 5.998363 AGAGGAAAAAGTTCAGACCATGTAC 59.002 40.000 0.00 0.00 35.25 2.90
2996 3146 5.053978 AGAGGAAAAAGTTCAGACCATGT 57.946 39.130 0.00 0.00 35.25 3.21
3042 3192 2.224066 GGCTGTACTGTACATGCCCTAG 60.224 54.545 30.39 17.52 42.23 3.02
3092 3242 0.980423 AGAGAACCTCAACCCTGAGC 59.020 55.000 0.00 0.00 46.76 4.26
3123 3273 6.940298 AGCACTACTCCAGCTTTTTACATAAA 59.060 34.615 0.00 0.00 34.37 1.40
3136 3286 5.394333 GGACCTTAAACTAGCACTACTCCAG 60.394 48.000 0.00 0.00 0.00 3.86
3186 3338 2.507407 ACAAATAATGGCTGACCGGT 57.493 45.000 6.92 6.92 39.70 5.28
3192 3344 8.428186 AGCATCAAATAAACAAATAATGGCTG 57.572 30.769 0.00 0.00 0.00 4.85
3222 3374 4.003648 AGTAATCCATTAATGCTAGCCGC 58.996 43.478 13.29 0.00 39.77 6.53
3227 3379 7.992608 ACACACATCAGTAATCCATTAATGCTA 59.007 33.333 10.11 0.67 38.00 3.49
3241 3393 8.073467 TCCATCAAAGTATACACACATCAGTA 57.927 34.615 5.50 0.00 0.00 2.74
3255 3407 9.492973 CACATACATGATACATCCATCAAAGTA 57.507 33.333 0.00 0.00 38.39 2.24
3256 3408 8.212995 TCACATACATGATACATCCATCAAAGT 58.787 33.333 0.00 0.00 38.39 2.66
3257 3409 8.611654 TCACATACATGATACATCCATCAAAG 57.388 34.615 0.00 0.00 38.39 2.77
3258 3410 9.223099 GATCACATACATGATACATCCATCAAA 57.777 33.333 0.00 0.00 39.48 2.69


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

AutoCloner maintained by Alex Coulton.