Multiple sequence alignment - TraesCS4B01G042400

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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 TraesCS4B01G042400 chr4B 100.000 5044 0 0 1 5044 29271732 29266689 0.000000e+00 9315.0
1 TraesCS4B01G042400 chr4B 100.000 268 0 0 5353 5620 29266380 29266113 3.910000e-136 496.0
2 TraesCS4B01G042400 chr4B 87.597 129 11 1 85 208 529207561 529207689 1.630000e-30 145.0
3 TraesCS4B01G042400 chr4B 91.304 92 6 2 1 91 652975199 652975109 2.130000e-24 124.0
4 TraesCS4B01G042400 chr4B 92.045 88 6 1 1 88 505207730 505207644 7.650000e-24 122.0
5 TraesCS4B01G042400 chr4D 92.444 4897 184 84 250 5044 17253805 17248993 0.000000e+00 6822.0
6 TraesCS4B01G042400 chr4D 84.249 273 19 15 5353 5613 17248912 17248652 1.560000e-60 244.0
7 TraesCS4B01G042400 chr4A 93.118 3618 167 39 250 3820 583418543 583422125 0.000000e+00 5227.0
8 TraesCS4B01G042400 chr4A 89.280 1222 65 35 3857 5044 583422129 583423318 0.000000e+00 1471.0
9 TraesCS4B01G042400 chr4A 84.727 275 10 16 5353 5613 583423414 583423670 4.350000e-61 246.0
10 TraesCS4B01G042400 chr4A 100.000 38 0 0 204 241 534232206 534232169 2.810000e-08 71.3
11 TraesCS4B01G042400 chr2B 75.849 530 117 10 1096 1620 119633722 119633199 5.590000e-65 259.0
12 TraesCS4B01G042400 chr2B 86.364 132 13 1 74 200 596776906 596776775 7.590000e-29 139.0
13 TraesCS4B01G042400 chr2B 91.398 93 6 2 1 92 7905417 7905326 5.910000e-25 126.0
14 TraesCS4B01G042400 chr2D 75.568 528 122 7 1096 1620 77383217 77382694 2.600000e-63 254.0
15 TraesCS4B01G042400 chr2D 84.783 138 13 4 94 225 565942939 565942804 1.270000e-26 132.0
16 TraesCS4B01G042400 chr3D 90.598 117 5 2 89 200 548254431 548254546 3.510000e-32 150.0
17 TraesCS4B01G042400 chr3D 85.507 138 14 2 84 216 210622422 210622558 7.590000e-29 139.0
18 TraesCS4B01G042400 chr6D 89.344 122 8 1 84 200 445850830 445850951 1.260000e-31 148.0
19 TraesCS4B01G042400 chr1D 89.256 121 8 1 85 200 255827882 255827762 4.540000e-31 147.0
20 TraesCS4B01G042400 chr1D 87.023 131 12 1 85 210 489112629 489112759 5.870000e-30 143.0
21 TraesCS4B01G042400 chr7A 83.784 148 15 4 85 227 220543623 220543480 1.270000e-26 132.0
22 TraesCS4B01G042400 chr7A 93.182 88 5 1 1 88 211679378 211679464 1.640000e-25 128.0
23 TraesCS4B01G042400 chr5A 93.182 88 5 1 1 88 635134909 635134823 1.640000e-25 128.0
24 TraesCS4B01G042400 chr2A 83.803 142 15 7 1133 1270 465364064 465363927 1.640000e-25 128.0
25 TraesCS4B01G042400 chr2A 94.595 37 2 0 204 240 726608252 726608288 2.190000e-04 58.4
26 TraesCS4B01G042400 chr6A 92.045 88 6 1 1 88 48881998 48882084 7.650000e-24 122.0
27 TraesCS4B01G042400 chr5B 92.045 88 6 1 1 88 46054282 46054368 7.650000e-24 122.0
28 TraesCS4B01G042400 chr5B 92.045 88 6 1 1 88 267776908 267776994 7.650000e-24 122.0
29 TraesCS4B01G042400 chr7B 82.857 140 19 5 1133 1270 197406610 197406474 2.750000e-23 121.0
30 TraesCS4B01G042400 chr3B 87.619 105 10 3 1 104 450837230 450837332 9.890000e-23 119.0
31 TraesCS4B01G042400 chrUn 100.000 34 0 0 204 237 367262326 367262359 4.700000e-06 63.9
32 TraesCS4B01G042400 chrUn 100.000 34 0 0 204 237 387888417 387888384 4.700000e-06 63.9
33 TraesCS4B01G042400 chr3A 97.222 36 1 0 204 239 8120713 8120748 1.690000e-05 62.1


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 TraesCS4B01G042400 chr4B 29266113 29271732 5619 True 4905.500000 9315 100.000000 1 5620 2 chr4B.!!$R3 5619
1 TraesCS4B01G042400 chr4D 17248652 17253805 5153 True 3533.000000 6822 88.346500 250 5613 2 chr4D.!!$R1 5363
2 TraesCS4B01G042400 chr4A 583418543 583423670 5127 False 2314.666667 5227 89.041667 250 5613 3 chr4A.!!$F1 5363
3 TraesCS4B01G042400 chr2B 119633199 119633722 523 True 259.000000 259 75.849000 1096 1620 1 chr2B.!!$R2 524
4 TraesCS4B01G042400 chr2D 77382694 77383217 523 True 254.000000 254 75.568000 1096 1620 1 chr2D.!!$R1 524

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
245 246 0.036105 ACGATCAGCCTCATGTGCAA 60.036 50.0 11.52 1.51 0.00 4.08 F
438 448 0.317479 GCCACAGTTGTAGACCGAGT 59.683 55.0 0.00 0.00 0.00 4.18 F
893 983 0.539669 AAACAGAGGCGAAAAGGGGG 60.540 55.0 0.00 0.00 0.00 5.40 F
2308 2422 0.108472 GCTTGCTTGCCATTCCTTCC 60.108 55.0 0.00 0.00 0.00 3.46 F
3471 3590 1.045350 TCTCTGCCTCGAAGATGGGG 61.045 60.0 0.00 0.00 33.89 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2154 3.123959 CACATTGCCAGCATTTTAGCAAC 59.876 43.478 0.00 0.00 46.98 4.17 R
2275 2389 0.675633 GCAAGCACCTGAACACCATT 59.324 50.000 0.00 0.00 0.00 3.16 R
2582 2698 1.318576 ACAGGCTGTAAACAAGTGCC 58.681 50.000 20.61 4.18 43.52 5.01 R
3865 3984 2.772568 TCCACAGCAAACAAATGTCG 57.227 45.000 0.00 0.00 0.00 4.35 R
4784 4950 0.389948 ATCGAGGTTCAACGGTGAGC 60.390 55.000 9.05 9.05 34.49 4.26 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
27 28 7.392766 TCATGATATGATACTCCACCCTTTT 57.607 36.000 0.00 0.00 33.59 2.27
28 29 7.815383 TCATGATATGATACTCCACCCTTTTT 58.185 34.615 0.00 0.00 33.59 1.94
54 55 9.851686 TTATCTTCATTTAATGCTATGACACCT 57.148 29.630 0.00 0.00 30.89 4.00
55 56 7.792374 TCTTCATTTAATGCTATGACACCTC 57.208 36.000 0.00 0.00 30.89 3.85
56 57 7.337938 TCTTCATTTAATGCTATGACACCTCA 58.662 34.615 0.00 0.00 30.89 3.86
57 58 7.994911 TCTTCATTTAATGCTATGACACCTCAT 59.005 33.333 0.00 0.00 40.47 2.90
58 59 7.734924 TCATTTAATGCTATGACACCTCATC 57.265 36.000 0.00 0.00 38.21 2.92
59 60 7.281841 TCATTTAATGCTATGACACCTCATCA 58.718 34.615 0.00 0.00 38.21 3.07
60 61 7.774625 TCATTTAATGCTATGACACCTCATCAA 59.225 33.333 0.00 0.00 38.21 2.57
61 62 7.936496 TTTAATGCTATGACACCTCATCAAA 57.064 32.000 0.00 0.00 38.21 2.69
62 63 7.936496 TTAATGCTATGACACCTCATCAAAA 57.064 32.000 0.00 0.00 38.21 2.44
63 64 8.523915 TTAATGCTATGACACCTCATCAAAAT 57.476 30.769 0.00 0.00 38.21 1.82
64 65 7.414222 AATGCTATGACACCTCATCAAAATT 57.586 32.000 0.00 0.00 38.21 1.82
65 66 6.198650 TGCTATGACACCTCATCAAAATTG 57.801 37.500 0.00 0.00 38.21 2.32
66 67 5.039333 GCTATGACACCTCATCAAAATTGC 58.961 41.667 0.00 0.00 38.21 3.56
67 68 3.557577 TGACACCTCATCAAAATTGCG 57.442 42.857 0.00 0.00 0.00 4.85
68 69 2.884012 TGACACCTCATCAAAATTGCGT 59.116 40.909 0.00 0.00 0.00 5.24
69 70 4.068599 TGACACCTCATCAAAATTGCGTA 58.931 39.130 0.00 0.00 0.00 4.42
70 71 4.154015 TGACACCTCATCAAAATTGCGTAG 59.846 41.667 0.00 0.00 0.00 3.51
71 72 4.072131 ACACCTCATCAAAATTGCGTAGT 58.928 39.130 0.00 0.00 0.00 2.73
72 73 4.518970 ACACCTCATCAAAATTGCGTAGTT 59.481 37.500 0.00 0.00 0.00 2.24
73 74 4.853196 CACCTCATCAAAATTGCGTAGTTG 59.147 41.667 0.00 0.00 0.00 3.16
74 75 4.082787 ACCTCATCAAAATTGCGTAGTTGG 60.083 41.667 0.00 0.00 0.00 3.77
75 76 3.832276 TCATCAAAATTGCGTAGTTGGC 58.168 40.909 0.00 0.00 0.00 4.52
76 77 2.323939 TCAAAATTGCGTAGTTGGCG 57.676 45.000 0.00 0.00 0.00 5.69
77 78 1.604755 TCAAAATTGCGTAGTTGGCGT 59.395 42.857 0.00 0.00 0.00 5.68
78 79 1.713404 CAAAATTGCGTAGTTGGCGTG 59.287 47.619 0.00 0.00 0.00 5.34
79 80 0.386731 AAATTGCGTAGTTGGCGTGC 60.387 50.000 0.00 0.00 0.00 5.34
80 81 1.511318 AATTGCGTAGTTGGCGTGCA 61.511 50.000 0.00 0.00 0.00 4.57
81 82 2.182614 ATTGCGTAGTTGGCGTGCAC 62.183 55.000 6.82 6.82 34.90 4.57
82 83 4.424430 GCGTAGTTGGCGTGCACG 62.424 66.667 34.01 34.01 43.27 5.34
83 84 3.773630 CGTAGTTGGCGTGCACGG 61.774 66.667 37.47 20.93 40.23 4.94
84 85 2.663852 GTAGTTGGCGTGCACGGT 60.664 61.111 37.47 7.54 40.23 4.83
85 86 1.373246 GTAGTTGGCGTGCACGGTA 60.373 57.895 37.47 11.51 40.23 4.02
86 87 1.373246 TAGTTGGCGTGCACGGTAC 60.373 57.895 37.47 22.34 40.23 3.34
87 88 1.808531 TAGTTGGCGTGCACGGTACT 61.809 55.000 37.47 22.31 40.23 2.73
88 89 2.356553 TTGGCGTGCACGGTACTC 60.357 61.111 37.47 21.61 40.23 2.59
89 90 3.869473 TTGGCGTGCACGGTACTCC 62.869 63.158 37.47 28.88 40.23 3.85
90 91 4.065281 GGCGTGCACGGTACTCCT 62.065 66.667 37.47 0.00 40.23 3.69
91 92 2.506438 GCGTGCACGGTACTCCTC 60.506 66.667 37.47 16.66 40.23 3.71
92 93 2.181021 CGTGCACGGTACTCCTCC 59.819 66.667 31.15 0.00 35.37 4.30
93 94 2.577593 GTGCACGGTACTCCTCCC 59.422 66.667 0.00 0.00 0.00 4.30
98 99 2.832201 CGGTACTCCTCCCGTCCC 60.832 72.222 0.00 0.00 39.38 4.46
99 100 2.361771 GGTACTCCTCCCGTCCCA 59.638 66.667 0.00 0.00 0.00 4.37
100 101 1.305549 GGTACTCCTCCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
101 102 0.906282 GGTACTCCTCCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
102 103 0.978907 GTACTCCTCCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
103 104 1.558294 GTACTCCTCCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
104 105 1.073098 ACTCCTCCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
105 106 1.004394 ACTCCTCCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
106 107 1.282157 CTCCTCCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
107 108 1.708551 TCCTCCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
108 109 1.818674 CCTCCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
109 110 2.514803 CTCCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
110 111 2.488153 CTCCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
111 112 2.107552 TCCCGTCCCAAAATTCTTGTCT 59.892 45.455 0.00 0.00 0.00 3.41
112 113 2.890945 CCCGTCCCAAAATTCTTGTCTT 59.109 45.455 0.00 0.00 0.00 3.01
113 114 4.076394 CCCGTCCCAAAATTCTTGTCTTA 58.924 43.478 0.00 0.00 0.00 2.10
114 115 4.156008 CCCGTCCCAAAATTCTTGTCTTAG 59.844 45.833 0.00 0.00 0.00 2.18
115 116 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
116 117 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
117 118 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
118 119 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
119 120 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
120 121 8.576442 GTCCCAAAATTCTTGTCTTAGATTTGA 58.424 33.333 4.41 0.00 30.83 2.69
121 122 8.576442 TCCCAAAATTCTTGTCTTAGATTTGAC 58.424 33.333 4.41 0.00 30.83 3.18
122 123 8.579863 CCCAAAATTCTTGTCTTAGATTTGACT 58.420 33.333 4.41 0.00 30.83 3.41
130 131 8.622157 TCTTGTCTTAGATTTGACTAGATACGG 58.378 37.037 0.00 0.00 39.05 4.02
131 132 8.515695 TTGTCTTAGATTTGACTAGATACGGA 57.484 34.615 0.00 0.00 34.57 4.69
132 133 8.693120 TGTCTTAGATTTGACTAGATACGGAT 57.307 34.615 0.00 0.00 34.57 4.18
133 134 8.568794 TGTCTTAGATTTGACTAGATACGGATG 58.431 37.037 0.00 0.00 34.57 3.51
134 135 8.569641 GTCTTAGATTTGACTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
135 136 9.788889 TCTTAGATTTGACTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
152 153 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
153 154 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
154 155 9.622004 CGGATGTATCTAATACTAAAACGTGAT 57.378 33.333 0.00 0.00 36.70 3.06
196 197 9.934641 CAAATTCAAAACAAAAATTTTGGAACG 57.065 25.926 20.79 8.23 45.59 3.95
197 198 8.680707 AATTCAAAACAAAAATTTTGGAACGG 57.319 26.923 20.79 7.88 45.59 4.44
198 199 7.435068 TTCAAAACAAAAATTTTGGAACGGA 57.565 28.000 20.79 9.77 45.59 4.69
199 200 7.066374 TCAAAACAAAAATTTTGGAACGGAG 57.934 32.000 20.79 5.96 45.59 4.63
200 201 6.874134 TCAAAACAAAAATTTTGGAACGGAGA 59.126 30.769 20.79 7.86 45.59 3.71
201 202 7.387948 TCAAAACAAAAATTTTGGAACGGAGAA 59.612 29.630 20.79 0.00 45.59 2.87
202 203 7.674471 AAACAAAAATTTTGGAACGGAGAAA 57.326 28.000 20.79 0.00 0.00 2.52
203 204 7.674471 AACAAAAATTTTGGAACGGAGAAAA 57.326 28.000 20.79 0.00 0.00 2.29
204 205 7.857734 ACAAAAATTTTGGAACGGAGAAAAT 57.142 28.000 20.79 0.00 32.01 1.82
205 206 8.950208 ACAAAAATTTTGGAACGGAGAAAATA 57.050 26.923 20.79 0.00 30.81 1.40
206 207 8.822855 ACAAAAATTTTGGAACGGAGAAAATAC 58.177 29.630 20.79 0.00 30.81 1.89
207 208 9.040939 CAAAAATTTTGGAACGGAGAAAATACT 57.959 29.630 10.41 0.00 30.81 2.12
210 211 9.687210 AAATTTTGGAACGGAGAAAATACTAAC 57.313 29.630 0.00 0.00 30.81 2.34
211 212 8.631480 ATTTTGGAACGGAGAAAATACTAACT 57.369 30.769 0.00 0.00 29.54 2.24
212 213 9.729281 ATTTTGGAACGGAGAAAATACTAACTA 57.271 29.630 0.00 0.00 29.54 2.24
213 214 9.729281 TTTTGGAACGGAGAAAATACTAACTAT 57.271 29.630 0.00 0.00 0.00 2.12
214 215 8.712285 TTGGAACGGAGAAAATACTAACTATG 57.288 34.615 0.00 0.00 0.00 2.23
215 216 8.070034 TGGAACGGAGAAAATACTAACTATGA 57.930 34.615 0.00 0.00 0.00 2.15
216 217 8.701895 TGGAACGGAGAAAATACTAACTATGAT 58.298 33.333 0.00 0.00 0.00 2.45
234 235 7.763356 ACTATGATACTACCATTACGATCAGC 58.237 38.462 0.00 0.00 0.00 4.26
235 236 5.386958 TGATACTACCATTACGATCAGCC 57.613 43.478 0.00 0.00 0.00 4.85
236 237 5.077564 TGATACTACCATTACGATCAGCCT 58.922 41.667 0.00 0.00 0.00 4.58
237 238 5.183331 TGATACTACCATTACGATCAGCCTC 59.817 44.000 0.00 0.00 0.00 4.70
238 239 3.296854 ACTACCATTACGATCAGCCTCA 58.703 45.455 0.00 0.00 0.00 3.86
239 240 3.898123 ACTACCATTACGATCAGCCTCAT 59.102 43.478 0.00 0.00 0.00 2.90
240 241 3.117491 ACCATTACGATCAGCCTCATG 57.883 47.619 0.00 0.00 0.00 3.07
241 242 2.435805 ACCATTACGATCAGCCTCATGT 59.564 45.455 0.00 0.00 0.00 3.21
242 243 2.804527 CCATTACGATCAGCCTCATGTG 59.195 50.000 0.00 0.00 0.00 3.21
243 244 1.939974 TTACGATCAGCCTCATGTGC 58.060 50.000 0.00 0.00 0.00 4.57
244 245 0.823460 TACGATCAGCCTCATGTGCA 59.177 50.000 11.52 0.00 0.00 4.57
245 246 0.036105 ACGATCAGCCTCATGTGCAA 60.036 50.000 11.52 1.51 0.00 4.08
246 247 0.656259 CGATCAGCCTCATGTGCAAG 59.344 55.000 11.52 4.97 0.00 4.01
247 248 1.747709 GATCAGCCTCATGTGCAAGT 58.252 50.000 11.52 0.00 0.00 3.16
248 249 1.669779 GATCAGCCTCATGTGCAAGTC 59.330 52.381 11.52 3.82 0.00 3.01
280 284 1.280746 CGCCAGTGACAAACAGCAG 59.719 57.895 0.00 0.00 32.19 4.24
287 292 2.594592 ACAAACAGCAGGTCGCCC 60.595 61.111 0.00 0.00 44.04 6.13
290 295 1.454847 AAACAGCAGGTCGCCCAAA 60.455 52.632 0.00 0.00 44.04 3.28
293 298 2.032681 AGCAGGTCGCCCAAACTC 59.967 61.111 0.00 0.00 44.04 3.01
336 341 1.333791 CCTCGAACAAAACGTGCCTTC 60.334 52.381 0.00 0.00 0.00 3.46
344 353 2.359570 AAACGTGCCTTCCGTCGTCT 62.360 55.000 0.00 0.00 37.61 4.18
404 414 1.081094 CAGTGAATGCATGCTCGTGA 58.919 50.000 20.33 0.00 0.00 4.35
427 437 3.586100 AAACAAAGAAACGCCACAGTT 57.414 38.095 0.00 0.00 35.59 3.16
437 447 0.732880 CGCCACAGTTGTAGACCGAG 60.733 60.000 0.00 0.00 0.00 4.63
438 448 0.317479 GCCACAGTTGTAGACCGAGT 59.683 55.000 0.00 0.00 0.00 4.18
455 465 0.832135 AGTCCACATGTCGGTGACCT 60.832 55.000 0.00 4.52 41.32 3.85
740 816 3.129502 GTAAAAGCGCCCGTCCCC 61.130 66.667 2.29 0.00 0.00 4.81
893 983 0.539669 AAACAGAGGCGAAAAGGGGG 60.540 55.000 0.00 0.00 0.00 5.40
894 984 1.423794 AACAGAGGCGAAAAGGGGGA 61.424 55.000 0.00 0.00 0.00 4.81
895 985 1.078143 CAGAGGCGAAAAGGGGGAG 60.078 63.158 0.00 0.00 0.00 4.30
896 986 2.438614 GAGGCGAAAAGGGGGAGC 60.439 66.667 0.00 0.00 0.00 4.70
1770 1884 4.951963 GAATCGGAGGGCGAGGCG 62.952 72.222 0.00 0.00 0.00 5.52
2040 2154 3.680937 TCCTCGTTATTTAGTTGTTGCCG 59.319 43.478 0.00 0.00 0.00 5.69
2041 2155 3.434299 CCTCGTTATTTAGTTGTTGCCGT 59.566 43.478 0.00 0.00 0.00 5.68
2140 2254 0.625849 ATTCGGTGGGGAAATCTGCT 59.374 50.000 0.00 0.00 0.00 4.24
2200 2314 2.382305 TCCTAGGGAGAAGTTCTGGACA 59.618 50.000 10.90 0.00 0.00 4.02
2275 2389 1.198759 GGTGGAAGGACTACTGCCCA 61.199 60.000 0.00 0.00 45.47 5.36
2308 2422 0.108472 GCTTGCTTGCCATTCCTTCC 60.108 55.000 0.00 0.00 0.00 3.46
2315 2431 3.359033 CTTGCCATTCCTTCCAATCAGA 58.641 45.455 0.00 0.00 0.00 3.27
2326 2442 5.071519 TCCTTCCAATCAGATCTCTGGATTC 59.928 44.000 15.31 0.00 43.91 2.52
2330 2446 5.071519 TCCAATCAGATCTCTGGATTCCTTC 59.928 44.000 11.93 0.00 43.91 3.46
2331 2447 5.072058 CCAATCAGATCTCTGGATTCCTTCT 59.928 44.000 8.72 0.00 43.91 2.85
2335 2451 6.413052 TCAGATCTCTGGATTCCTTCTTTTG 58.587 40.000 3.95 0.00 43.91 2.44
2336 2452 6.013032 TCAGATCTCTGGATTCCTTCTTTTGT 60.013 38.462 3.95 0.00 43.91 2.83
2339 2455 8.386264 AGATCTCTGGATTCCTTCTTTTGTTTA 58.614 33.333 3.95 0.00 31.46 2.01
2340 2456 8.940397 ATCTCTGGATTCCTTCTTTTGTTTAA 57.060 30.769 3.95 0.00 0.00 1.52
2343 2459 9.987272 CTCTGGATTCCTTCTTTTGTTTAATTT 57.013 29.630 3.95 0.00 0.00 1.82
2450 2566 2.874086 CGCTATCTGTGGAAATGATGCA 59.126 45.455 0.00 0.00 0.00 3.96
2507 2623 5.131067 AGTTTCTTTTACCTCACCCAAGAC 58.869 41.667 0.00 0.00 0.00 3.01
2582 2698 4.831669 TGCTCATGCCATCGTTATGAACG 61.832 47.826 5.40 5.40 46.79 3.95
2664 2783 4.992319 CACTTGTGAAATGATTGGCATTGT 59.008 37.500 0.00 0.00 46.25 2.71
2665 2784 5.467399 CACTTGTGAAATGATTGGCATTGTT 59.533 36.000 0.00 0.00 46.25 2.83
2666 2785 5.697633 ACTTGTGAAATGATTGGCATTGTTC 59.302 36.000 0.00 0.00 46.25 3.18
2670 2789 6.424509 TGTGAAATGATTGGCATTGTTCTTTC 59.575 34.615 0.00 0.00 46.25 2.62
2679 2798 5.064558 TGGCATTGTTCTTTCAATTGCATT 58.935 33.333 0.00 0.00 36.10 3.56
2683 2802 6.292973 GCATTGTTCTTTCAATTGCATTGTGA 60.293 34.615 0.00 0.00 41.02 3.58
2783 2902 7.201652 GGCATTGTCTTCTTAGTCCTTATGTTC 60.202 40.741 0.00 0.00 0.00 3.18
2823 2942 2.098117 GCTAAATGTGCTGCCAAGTAGG 59.902 50.000 0.00 0.00 41.84 3.18
2844 2963 5.480205 AGGAATACTTTGAGAGAAACGGTC 58.520 41.667 0.00 0.00 0.00 4.79
2905 3024 1.401552 TGCAGTTGCTTATTCGGATGC 59.598 47.619 5.62 0.00 42.66 3.91
2985 3104 1.235724 GTGTCCACTGTGTAAAGCCC 58.764 55.000 7.08 0.00 0.00 5.19
3471 3590 1.045350 TCTCTGCCTCGAAGATGGGG 61.045 60.000 0.00 0.00 33.89 4.96
3528 3647 6.096282 TCCTTGTTCTTTACCCAGAAAAGTTG 59.904 38.462 0.00 0.00 34.50 3.16
3694 3813 5.521544 GGTATGTTGCCGTGTTTTCTTTTA 58.478 37.500 0.00 0.00 0.00 1.52
3697 3816 7.170151 GGTATGTTGCCGTGTTTTCTTTTAAAT 59.830 33.333 0.00 0.00 0.00 1.40
3726 3845 6.981722 TCCTATCTTTTTCTTGCAAAACTCC 58.018 36.000 0.00 0.00 0.00 3.85
3780 3899 7.681679 TGGGTTCATGTTAGTGTAATTCTACA 58.318 34.615 0.00 0.00 35.61 2.74
3800 3919 8.251750 TCTACAAACTTATCTCAAAATGACCG 57.748 34.615 0.00 0.00 0.00 4.79
3836 3955 7.288810 AGTAATTCTTTGCATCCTTTCAACA 57.711 32.000 0.00 0.00 0.00 3.33
3853 3972 7.594758 CCTTTCAACATTATGTACCTTGTGTTG 59.405 37.037 17.88 17.88 44.57 3.33
3865 3984 7.703328 TGTACCTTGTGTTGAAGATTCTTTTC 58.297 34.615 0.00 0.00 0.00 2.29
3881 4003 4.992688 TCTTTTCGACATTTGTTTGCTGT 58.007 34.783 0.00 0.00 0.00 4.40
3882 4004 4.797868 TCTTTTCGACATTTGTTTGCTGTG 59.202 37.500 0.00 0.00 0.00 3.66
3891 4013 7.410728 CGACATTTGTTTGCTGTGGATAAAATC 60.411 37.037 0.00 0.00 0.00 2.17
3929 4051 6.151691 TGCATGTTAGAAAATTGAAGCAGAC 58.848 36.000 0.00 0.00 0.00 3.51
3933 4055 8.506437 CATGTTAGAAAATTGAAGCAGACAGTA 58.494 33.333 0.00 0.00 0.00 2.74
3935 4057 5.948992 AGAAAATTGAAGCAGACAGTACC 57.051 39.130 0.00 0.00 0.00 3.34
3936 4058 5.625150 AGAAAATTGAAGCAGACAGTACCT 58.375 37.500 0.00 0.00 0.00 3.08
3937 4059 6.064717 AGAAAATTGAAGCAGACAGTACCTT 58.935 36.000 0.00 0.00 0.00 3.50
3938 4060 7.224297 AGAAAATTGAAGCAGACAGTACCTTA 58.776 34.615 0.00 0.00 0.00 2.69
3939 4061 6.803154 AAATTGAAGCAGACAGTACCTTAC 57.197 37.500 0.00 0.00 0.00 2.34
3940 4062 5.746990 ATTGAAGCAGACAGTACCTTACT 57.253 39.130 0.00 0.00 40.28 2.24
3942 4064 5.899120 TGAAGCAGACAGTACCTTACTAG 57.101 43.478 0.00 0.00 37.23 2.57
3955 4080 4.518249 ACCTTACTAGCCTGAAAGCAATC 58.482 43.478 0.00 0.00 34.23 2.67
4015 4141 3.636300 TGTGCTTTGTCATGCCTAAAAGT 59.364 39.130 9.47 0.00 33.21 2.66
4036 4162 6.780457 AGTATGGCTTTTGTGCTTTATCAT 57.220 33.333 0.00 0.00 0.00 2.45
4050 4176 5.822519 TGCTTTATCATGGGTTCTACACATC 59.177 40.000 0.00 0.00 37.83 3.06
4051 4177 6.058183 GCTTTATCATGGGTTCTACACATCT 58.942 40.000 0.00 0.00 37.83 2.90
4056 4182 4.964897 TCATGGGTTCTACACATCTCTCAT 59.035 41.667 0.00 0.00 37.83 2.90
4072 4198 6.516739 TCTCTCATGCCCTTATATAACTCG 57.483 41.667 0.00 0.00 0.00 4.18
4382 4525 1.819288 TCCAGAAGAAGCGAGTTCGAT 59.181 47.619 5.60 0.00 43.02 3.59
4400 4543 0.250513 ATCCGTTTCTCCTCAGTGGC 59.749 55.000 0.00 0.00 35.26 5.01
4433 4576 4.796231 CCGAACCAGACCGGCGAG 62.796 72.222 9.30 0.06 39.22 5.03
4448 4591 2.152699 CGAGGTGCACGACGTGATC 61.153 63.158 31.08 20.42 35.23 2.92
4502 4645 4.012374 ACTATGACATCACCAAAAGGCTG 58.988 43.478 0.00 0.00 0.00 4.85
4529 4672 2.610374 TGTTTACAAGTCGTTGCAGACC 59.390 45.455 2.65 0.00 41.83 3.85
4535 4678 3.228017 TCGTTGCAGACCGACCCA 61.228 61.111 1.67 0.00 0.00 4.51
4550 4693 2.480419 CGACCCAAATTCGATATCTGCC 59.520 50.000 0.34 0.00 38.85 4.85
4624 4768 6.515272 TTTTGTGGAAGATGGCTAAGAATC 57.485 37.500 0.00 0.00 0.00 2.52
4641 4787 2.442236 ATCGGGGTCAAAGATGCATT 57.558 45.000 0.00 0.00 0.00 3.56
4686 4852 4.051932 GGAGGATTCCGAGGTGGT 57.948 61.111 0.00 0.00 39.52 4.16
4717 4883 4.673580 CGATTTTCTGCATGGTCAAAGGAG 60.674 45.833 0.00 0.00 0.00 3.69
4749 4915 6.092944 TGTTAAATACCACCAACGATCATCAC 59.907 38.462 0.00 0.00 0.00 3.06
4768 4934 4.473520 AGCCGCTGGAATCCGGTG 62.474 66.667 14.51 14.51 45.98 4.94
4784 4950 0.721718 GGTGAAAATCAGCTCGTCGG 59.278 55.000 2.49 0.00 41.34 4.79
4786 4952 0.037326 TGAAAATCAGCTCGTCGGCT 60.037 50.000 2.81 2.81 44.10 5.52
4787 4953 0.647925 GAAAATCAGCTCGTCGGCTC 59.352 55.000 5.39 0.00 41.00 4.70
4788 4954 0.037326 AAAATCAGCTCGTCGGCTCA 60.037 50.000 5.39 0.00 41.00 4.26
4789 4955 0.737715 AAATCAGCTCGTCGGCTCAC 60.738 55.000 5.39 0.00 41.00 3.51
4790 4956 2.564553 AATCAGCTCGTCGGCTCACC 62.565 60.000 5.39 0.00 41.00 4.02
4807 4984 0.966920 ACCGTTGAACCTCGATCAGT 59.033 50.000 0.00 0.00 0.00 3.41
4811 4988 3.172050 CGTTGAACCTCGATCAGTAGTG 58.828 50.000 0.00 0.00 0.00 2.74
4880 5057 1.815003 GACTGTGGCTGGATTTTGGAG 59.185 52.381 0.00 0.00 0.00 3.86
4971 5149 1.613630 TGGTCCTTCCAGCTCCCTC 60.614 63.158 0.00 0.00 41.93 4.30
4979 5157 2.359169 CCAGCTCCCTCGGTAGCAA 61.359 63.158 3.29 0.00 41.32 3.91
5035 5224 6.326323 AGGATTCTTTTCTTGGCTGGTTTAAA 59.674 34.615 0.00 0.00 0.00 1.52
5038 5227 8.978874 ATTCTTTTCTTGGCTGGTTTAAATTT 57.021 26.923 0.00 0.00 0.00 1.82
5431 5620 3.947834 GGTGGATCAGAATTGAATTCGGT 59.052 43.478 15.68 6.59 43.92 4.69
5442 5631 7.497249 CAGAATTGAATTCGGTATCTTCTTCCT 59.503 37.037 11.83 0.00 43.92 3.36
5447 5636 5.538849 ATTCGGTATCTTCTTCCTCTTCC 57.461 43.478 0.00 0.00 0.00 3.46
5459 5648 0.615331 CCTCTTCCCTGCACTGCTTA 59.385 55.000 1.98 0.00 0.00 3.09
5485 5680 0.306533 TCTTTTGCGTCGTTGGCTTC 59.693 50.000 0.00 0.00 0.00 3.86
5486 5681 0.307760 CTTTTGCGTCGTTGGCTTCT 59.692 50.000 0.00 0.00 0.00 2.85
5487 5682 0.736053 TTTTGCGTCGTTGGCTTCTT 59.264 45.000 0.00 0.00 0.00 2.52
5488 5683 0.306533 TTTGCGTCGTTGGCTTCTTC 59.693 50.000 0.00 0.00 0.00 2.87
5514 5709 3.317993 CCTTTCCCAGTATTTATTGGCCG 59.682 47.826 0.00 0.00 32.26 6.13
5515 5710 1.975660 TCCCAGTATTTATTGGCCGC 58.024 50.000 0.00 0.00 32.26 6.53
5516 5711 1.493022 TCCCAGTATTTATTGGCCGCT 59.507 47.619 0.00 0.00 32.26 5.52
5517 5712 1.880027 CCCAGTATTTATTGGCCGCTC 59.120 52.381 0.00 0.00 32.26 5.03
5518 5713 1.880027 CCAGTATTTATTGGCCGCTCC 59.120 52.381 0.00 0.00 0.00 4.70
5519 5714 1.880027 CAGTATTTATTGGCCGCTCCC 59.120 52.381 0.00 0.00 0.00 4.30
5520 5715 1.774856 AGTATTTATTGGCCGCTCCCT 59.225 47.619 0.00 0.00 0.00 4.20
5521 5716 2.152016 GTATTTATTGGCCGCTCCCTC 58.848 52.381 0.00 0.00 0.00 4.30
5536 5735 0.106894 CCCTCCCACGGATAGCTTTC 59.893 60.000 0.00 0.00 0.00 2.62
5555 5754 1.892819 CTGCAGGCCGGAGAGAGAAA 61.893 60.000 5.05 0.00 34.28 2.52
5571 5777 0.169009 GAAAGTAGGCTTGGCTTGCG 59.831 55.000 1.22 0.00 34.71 4.85
5572 5778 1.244019 AAAGTAGGCTTGGCTTGCGG 61.244 55.000 1.22 0.00 34.71 5.69
5617 5829 3.138798 GCCTGCCTGCCTGTGATG 61.139 66.667 0.00 0.00 0.00 3.07
5618 5830 2.353958 CCTGCCTGCCTGTGATGT 59.646 61.111 0.00 0.00 0.00 3.06
5619 5831 1.748122 CCTGCCTGCCTGTGATGTC 60.748 63.158 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.392766 AAAAGGGTGGAGTATCATATCATGA 57.607 36.000 0.00 0.00 44.55 3.07
28 29 9.851686 AGGTGTCATAGCATTAAATGAAGATAA 57.148 29.630 0.00 0.00 34.06 1.75
29 30 9.494271 GAGGTGTCATAGCATTAAATGAAGATA 57.506 33.333 0.00 0.00 34.06 1.98
30 31 7.994911 TGAGGTGTCATAGCATTAAATGAAGAT 59.005 33.333 0.00 0.00 34.06 2.40
31 32 7.337938 TGAGGTGTCATAGCATTAAATGAAGA 58.662 34.615 0.00 0.00 34.06 2.87
32 33 7.558161 TGAGGTGTCATAGCATTAAATGAAG 57.442 36.000 0.00 0.00 34.06 3.02
33 34 7.774625 TGATGAGGTGTCATAGCATTAAATGAA 59.225 33.333 0.00 0.00 43.92 2.57
34 35 7.281841 TGATGAGGTGTCATAGCATTAAATGA 58.718 34.615 0.00 0.00 43.92 2.57
35 36 7.500720 TGATGAGGTGTCATAGCATTAAATG 57.499 36.000 0.00 0.00 43.92 2.32
36 37 8.523915 TTTGATGAGGTGTCATAGCATTAAAT 57.476 30.769 0.00 0.00 43.92 1.40
37 38 7.936496 TTTGATGAGGTGTCATAGCATTAAA 57.064 32.000 0.00 0.00 43.92 1.52
38 39 7.936496 TTTTGATGAGGTGTCATAGCATTAA 57.064 32.000 0.00 0.00 43.92 1.40
39 40 8.407832 CAATTTTGATGAGGTGTCATAGCATTA 58.592 33.333 0.00 0.00 43.92 1.90
40 41 7.262772 CAATTTTGATGAGGTGTCATAGCATT 58.737 34.615 0.00 0.00 43.92 3.56
41 42 6.682113 GCAATTTTGATGAGGTGTCATAGCAT 60.682 38.462 0.00 0.00 43.92 3.79
42 43 5.393352 GCAATTTTGATGAGGTGTCATAGCA 60.393 40.000 0.00 0.00 43.92 3.49
43 44 5.039333 GCAATTTTGATGAGGTGTCATAGC 58.961 41.667 0.00 0.00 43.92 2.97
44 45 5.163723 ACGCAATTTTGATGAGGTGTCATAG 60.164 40.000 0.00 0.00 43.92 2.23
45 46 4.699735 ACGCAATTTTGATGAGGTGTCATA 59.300 37.500 0.00 0.00 43.92 2.15
46 47 3.507233 ACGCAATTTTGATGAGGTGTCAT 59.493 39.130 0.00 0.00 46.75 3.06
47 48 2.884012 ACGCAATTTTGATGAGGTGTCA 59.116 40.909 0.00 0.00 37.02 3.58
48 49 3.559238 ACGCAATTTTGATGAGGTGTC 57.441 42.857 0.00 0.00 0.00 3.67
49 50 4.072131 ACTACGCAATTTTGATGAGGTGT 58.928 39.130 0.00 0.00 0.00 4.16
50 51 4.685169 ACTACGCAATTTTGATGAGGTG 57.315 40.909 0.00 0.00 0.00 4.00
51 52 4.082787 CCAACTACGCAATTTTGATGAGGT 60.083 41.667 0.00 0.00 0.00 3.85
52 53 4.414852 CCAACTACGCAATTTTGATGAGG 58.585 43.478 0.00 0.00 0.00 3.86
53 54 3.853671 GCCAACTACGCAATTTTGATGAG 59.146 43.478 0.00 0.00 0.00 2.90
54 55 3.669290 CGCCAACTACGCAATTTTGATGA 60.669 43.478 0.00 0.00 0.00 2.92
55 56 2.593775 CGCCAACTACGCAATTTTGATG 59.406 45.455 0.00 0.00 0.00 3.07
56 57 2.227865 ACGCCAACTACGCAATTTTGAT 59.772 40.909 0.00 0.00 0.00 2.57
57 58 1.604755 ACGCCAACTACGCAATTTTGA 59.395 42.857 0.00 0.00 0.00 2.69
58 59 1.713404 CACGCCAACTACGCAATTTTG 59.287 47.619 0.00 0.00 0.00 2.44
59 60 1.928595 GCACGCCAACTACGCAATTTT 60.929 47.619 0.00 0.00 0.00 1.82
60 61 0.386731 GCACGCCAACTACGCAATTT 60.387 50.000 0.00 0.00 0.00 1.82
61 62 1.209127 GCACGCCAACTACGCAATT 59.791 52.632 0.00 0.00 0.00 2.32
62 63 1.963855 TGCACGCCAACTACGCAAT 60.964 52.632 0.00 0.00 0.00 3.56
63 64 2.589159 TGCACGCCAACTACGCAA 60.589 55.556 0.00 0.00 0.00 4.85
64 65 3.342627 GTGCACGCCAACTACGCA 61.343 61.111 0.00 0.00 0.00 5.24
65 66 4.424430 CGTGCACGCCAACTACGC 62.424 66.667 28.16 0.00 0.00 4.42
66 67 3.773630 CCGTGCACGCCAACTACG 61.774 66.667 33.17 13.44 38.18 3.51
67 68 1.373246 TACCGTGCACGCCAACTAC 60.373 57.895 33.17 0.00 38.18 2.73
68 69 1.373246 GTACCGTGCACGCCAACTA 60.373 57.895 33.17 13.19 38.18 2.24
69 70 2.663852 GTACCGTGCACGCCAACT 60.664 61.111 33.17 14.16 38.18 3.16
70 71 2.663852 AGTACCGTGCACGCCAAC 60.664 61.111 33.17 26.46 38.18 3.77
71 72 2.356553 GAGTACCGTGCACGCCAA 60.357 61.111 33.17 17.26 38.18 4.52
72 73 4.367023 GGAGTACCGTGCACGCCA 62.367 66.667 33.17 19.55 36.05 5.69
73 74 3.984200 GAGGAGTACCGTGCACGCC 62.984 68.421 33.17 26.38 41.83 5.68
74 75 2.506438 GAGGAGTACCGTGCACGC 60.506 66.667 33.17 19.77 41.83 5.34
75 76 2.181021 GGAGGAGTACCGTGCACG 59.819 66.667 31.77 31.77 41.83 5.34
76 77 2.577593 GGGAGGAGTACCGTGCAC 59.422 66.667 6.82 6.82 41.83 4.57
77 78 3.066190 CGGGAGGAGTACCGTGCA 61.066 66.667 0.00 0.00 44.85 4.57
82 83 0.906282 TTTGGGACGGGAGGAGTACC 60.906 60.000 0.00 0.00 42.94 3.34
83 84 0.978907 TTTTGGGACGGGAGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
84 85 1.961133 ATTTTGGGACGGGAGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
85 86 1.004394 GAATTTTGGGACGGGAGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
86 87 1.282157 AGAATTTTGGGACGGGAGGAG 59.718 52.381 0.00 0.00 0.00 3.69
87 88 1.368374 AGAATTTTGGGACGGGAGGA 58.632 50.000 0.00 0.00 0.00 3.71
88 89 1.818674 CAAGAATTTTGGGACGGGAGG 59.181 52.381 0.00 0.00 0.00 4.30
89 90 2.488153 GACAAGAATTTTGGGACGGGAG 59.512 50.000 0.00 0.00 0.00 4.30
90 91 2.107552 AGACAAGAATTTTGGGACGGGA 59.892 45.455 0.00 0.00 0.00 5.14
91 92 2.514803 AGACAAGAATTTTGGGACGGG 58.485 47.619 0.00 0.00 0.00 5.28
92 93 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
93 94 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
94 95 8.576442 TCAAATCTAAGACAAGAATTTTGGGAC 58.424 33.333 0.00 0.00 31.13 4.46
95 96 8.576442 GTCAAATCTAAGACAAGAATTTTGGGA 58.424 33.333 0.00 0.00 31.13 4.37
96 97 8.579863 AGTCAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 37.23 4.12
104 105 8.622157 CCGTATCTAGTCAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 37.23 3.02
105 106 8.622157 TCCGTATCTAGTCAAATCTAAGACAAG 58.378 37.037 0.00 0.00 37.23 3.16
106 107 8.515695 TCCGTATCTAGTCAAATCTAAGACAA 57.484 34.615 0.00 0.00 37.23 3.18
107 108 8.568794 CATCCGTATCTAGTCAAATCTAAGACA 58.431 37.037 0.00 0.00 37.23 3.41
108 109 8.569641 ACATCCGTATCTAGTCAAATCTAAGAC 58.430 37.037 0.00 0.00 35.02 3.01
109 110 8.693120 ACATCCGTATCTAGTCAAATCTAAGA 57.307 34.615 0.00 0.00 0.00 2.10
126 127 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
127 128 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
128 129 9.622004 ATCACGTTTTAGTATTAGATACATCCG 57.378 33.333 0.00 0.00 38.21 4.18
170 171 9.934641 CGTTCCAAAATTTTTGTTTTGAATTTG 57.065 25.926 18.05 7.24 46.78 2.32
171 172 9.133627 CCGTTCCAAAATTTTTGTTTTGAATTT 57.866 25.926 18.05 0.00 46.78 1.82
172 173 8.515414 TCCGTTCCAAAATTTTTGTTTTGAATT 58.485 25.926 18.05 0.00 46.78 2.17
173 174 8.045176 TCCGTTCCAAAATTTTTGTTTTGAAT 57.955 26.923 18.05 0.00 46.78 2.57
174 175 7.387948 TCTCCGTTCCAAAATTTTTGTTTTGAA 59.612 29.630 18.05 12.11 46.78 2.69
175 176 6.874134 TCTCCGTTCCAAAATTTTTGTTTTGA 59.126 30.769 18.05 7.53 46.78 2.69
176 177 7.066374 TCTCCGTTCCAAAATTTTTGTTTTG 57.934 32.000 18.05 5.39 44.63 2.44
177 178 7.674471 TTCTCCGTTCCAAAATTTTTGTTTT 57.326 28.000 18.05 0.00 0.00 2.43
178 179 7.674471 TTTCTCCGTTCCAAAATTTTTGTTT 57.326 28.000 18.05 0.00 0.00 2.83
179 180 7.674471 TTTTCTCCGTTCCAAAATTTTTGTT 57.326 28.000 18.05 0.00 0.00 2.83
180 181 7.857734 ATTTTCTCCGTTCCAAAATTTTTGT 57.142 28.000 18.05 0.00 0.00 2.83
181 182 9.040939 AGTATTTTCTCCGTTCCAAAATTTTTG 57.959 29.630 13.76 13.76 33.02 2.44
184 185 9.687210 GTTAGTATTTTCTCCGTTCCAAAATTT 57.313 29.630 0.00 0.00 33.02 1.82
185 186 9.074576 AGTTAGTATTTTCTCCGTTCCAAAATT 57.925 29.630 0.00 0.00 33.02 1.82
186 187 8.631480 AGTTAGTATTTTCTCCGTTCCAAAAT 57.369 30.769 0.00 0.00 34.75 1.82
187 188 9.729281 ATAGTTAGTATTTTCTCCGTTCCAAAA 57.271 29.630 0.00 0.00 0.00 2.44
188 189 9.158233 CATAGTTAGTATTTTCTCCGTTCCAAA 57.842 33.333 0.00 0.00 0.00 3.28
189 190 8.533657 TCATAGTTAGTATTTTCTCCGTTCCAA 58.466 33.333 0.00 0.00 0.00 3.53
190 191 8.070034 TCATAGTTAGTATTTTCTCCGTTCCA 57.930 34.615 0.00 0.00 0.00 3.53
208 209 8.244802 GCTGATCGTAATGGTAGTATCATAGTT 58.755 37.037 0.00 0.00 0.00 2.24
209 210 7.148052 GGCTGATCGTAATGGTAGTATCATAGT 60.148 40.741 0.00 0.00 0.00 2.12
210 211 7.067615 AGGCTGATCGTAATGGTAGTATCATAG 59.932 40.741 0.00 0.00 0.00 2.23
211 212 6.890268 AGGCTGATCGTAATGGTAGTATCATA 59.110 38.462 0.00 0.00 0.00 2.15
212 213 5.717178 AGGCTGATCGTAATGGTAGTATCAT 59.283 40.000 0.00 0.00 0.00 2.45
213 214 5.077564 AGGCTGATCGTAATGGTAGTATCA 58.922 41.667 0.00 0.00 0.00 2.15
214 215 5.183331 TGAGGCTGATCGTAATGGTAGTATC 59.817 44.000 0.00 0.00 0.00 2.24
215 216 5.077564 TGAGGCTGATCGTAATGGTAGTAT 58.922 41.667 0.00 0.00 0.00 2.12
216 217 4.466827 TGAGGCTGATCGTAATGGTAGTA 58.533 43.478 0.00 0.00 0.00 1.82
217 218 3.296854 TGAGGCTGATCGTAATGGTAGT 58.703 45.455 0.00 0.00 0.00 2.73
218 219 4.240888 CATGAGGCTGATCGTAATGGTAG 58.759 47.826 0.00 0.00 0.00 3.18
219 220 3.641436 ACATGAGGCTGATCGTAATGGTA 59.359 43.478 0.00 0.00 0.00 3.25
220 221 2.435805 ACATGAGGCTGATCGTAATGGT 59.564 45.455 0.00 0.00 0.00 3.55
221 222 2.804527 CACATGAGGCTGATCGTAATGG 59.195 50.000 0.00 0.00 0.00 3.16
222 223 2.222678 GCACATGAGGCTGATCGTAATG 59.777 50.000 0.00 0.00 0.00 1.90
223 224 2.158914 TGCACATGAGGCTGATCGTAAT 60.159 45.455 0.00 0.00 0.00 1.89
224 225 1.206849 TGCACATGAGGCTGATCGTAA 59.793 47.619 0.00 0.00 0.00 3.18
225 226 0.823460 TGCACATGAGGCTGATCGTA 59.177 50.000 0.00 0.00 0.00 3.43
226 227 0.036105 TTGCACATGAGGCTGATCGT 60.036 50.000 0.00 0.00 0.00 3.73
227 228 0.656259 CTTGCACATGAGGCTGATCG 59.344 55.000 0.00 0.00 0.00 3.69
228 229 1.669779 GACTTGCACATGAGGCTGATC 59.330 52.381 0.00 0.00 0.00 2.92
229 230 1.003928 TGACTTGCACATGAGGCTGAT 59.996 47.619 0.00 0.00 0.00 2.90
230 231 0.397564 TGACTTGCACATGAGGCTGA 59.602 50.000 0.00 0.00 0.00 4.26
231 232 1.460504 ATGACTTGCACATGAGGCTG 58.539 50.000 0.00 3.30 0.00 4.85
232 233 2.211250 AATGACTTGCACATGAGGCT 57.789 45.000 0.00 0.00 0.00 4.58
233 234 3.308438 AAAATGACTTGCACATGAGGC 57.692 42.857 0.00 3.11 0.00 4.70
234 235 5.181811 TCAGTAAAATGACTTGCACATGAGG 59.818 40.000 0.00 0.00 0.00 3.86
235 236 6.082338 GTCAGTAAAATGACTTGCACATGAG 58.918 40.000 0.00 0.00 45.03 2.90
236 237 6.000891 GTCAGTAAAATGACTTGCACATGA 57.999 37.500 0.00 0.00 45.03 3.07
247 248 2.422597 CTGGCGTGGTCAGTAAAATGA 58.577 47.619 0.00 0.00 29.72 2.57
248 249 2.900122 CTGGCGTGGTCAGTAAAATG 57.100 50.000 0.00 0.00 29.72 2.32
287 292 1.843734 TTTTACCGCGGCCGAGTTTG 61.844 55.000 33.48 16.18 36.29 2.93
290 295 1.812507 GATTTTACCGCGGCCGAGT 60.813 57.895 33.48 26.97 36.29 4.18
293 298 0.099791 ATTTGATTTTACCGCGGCCG 59.900 50.000 28.58 24.05 0.00 6.13
437 447 0.389948 GAGGTCACCGACATGTGGAC 60.390 60.000 17.76 12.56 36.87 4.02
438 448 1.541310 GGAGGTCACCGACATGTGGA 61.541 60.000 17.76 2.42 36.87 4.02
566 612 3.009714 GGGTCTGGGTCCAGGTCC 61.010 72.222 16.15 16.78 43.75 4.46
571 617 0.545309 CTCTTCTGGGTCTGGGTCCA 60.545 60.000 0.00 0.00 0.00 4.02
572 618 1.268283 CCTCTTCTGGGTCTGGGTCC 61.268 65.000 0.00 0.00 0.00 4.46
573 619 0.545548 ACCTCTTCTGGGTCTGGGTC 60.546 60.000 0.00 0.00 30.15 4.46
574 620 0.545548 GACCTCTTCTGGGTCTGGGT 60.546 60.000 5.72 0.00 46.89 4.51
575 621 2.291856 GACCTCTTCTGGGTCTGGG 58.708 63.158 5.72 0.00 46.89 4.45
645 700 1.277273 AGTTTACGGAACTGCCCCTAC 59.723 52.381 5.75 0.00 46.66 3.18
747 823 2.038659 GGATGGAAGAGGAGTGAGGAG 58.961 57.143 0.00 0.00 0.00 3.69
748 824 1.362584 TGGATGGAAGAGGAGTGAGGA 59.637 52.381 0.00 0.00 0.00 3.71
838 928 1.591183 CTGGCGGTTTGATTTGGGG 59.409 57.895 0.00 0.00 0.00 4.96
893 983 0.387565 CCTAAAGCCTCTCTCCGCTC 59.612 60.000 0.00 0.00 33.09 5.03
894 984 0.033011 TCCTAAAGCCTCTCTCCGCT 60.033 55.000 0.00 0.00 36.74 5.52
895 985 0.387565 CTCCTAAAGCCTCTCTCCGC 59.612 60.000 0.00 0.00 0.00 5.54
896 986 1.036707 CCTCCTAAAGCCTCTCTCCG 58.963 60.000 0.00 0.00 0.00 4.63
934 1024 4.174129 GTTTGCGATTCGGGGCCG 62.174 66.667 8.34 0.00 41.35 6.13
935 1025 3.822192 GGTTTGCGATTCGGGGCC 61.822 66.667 8.34 0.00 0.00 5.80
1770 1884 3.399181 TCGCAGGTGATGTCCCCC 61.399 66.667 0.00 0.00 0.00 5.40
2040 2154 3.123959 CACATTGCCAGCATTTTAGCAAC 59.876 43.478 0.00 0.00 46.98 4.17
2275 2389 0.675633 GCAAGCACCTGAACACCATT 59.324 50.000 0.00 0.00 0.00 3.16
2308 2422 6.177310 AGAAGGAATCCAGAGATCTGATTG 57.823 41.667 11.44 2.34 46.59 2.67
2315 2431 8.940397 TTAAACAAAAGAAGGAATCCAGAGAT 57.060 30.769 0.61 0.00 0.00 2.75
2346 2462 9.866655 AGCATCCCAGTCAATAATAAAGATTAA 57.133 29.630 0.00 0.00 31.28 1.40
2349 2465 6.718454 CCAGCATCCCAGTCAATAATAAAGAT 59.282 38.462 0.00 0.00 0.00 2.40
2359 2475 3.824133 CATAATCCAGCATCCCAGTCAA 58.176 45.455 0.00 0.00 0.00 3.18
2450 2566 1.882989 GCGAAGACAGCTCCCTCAGT 61.883 60.000 0.00 0.00 0.00 3.41
2507 2623 5.563751 CACTGTTTTAATCATGAAACGGTCG 59.436 40.000 16.20 10.32 46.03 4.79
2582 2698 1.318576 ACAGGCTGTAAACAAGTGCC 58.681 50.000 20.61 4.18 43.52 5.01
2679 2798 9.784531 TTTTCCTAATTTAATGCCATTTTCACA 57.215 25.926 0.00 0.00 0.00 3.58
2823 2942 5.927115 ACAGACCGTTTCTCTCAAAGTATTC 59.073 40.000 0.00 0.00 28.96 1.75
2844 2963 8.184192 GGTGATGAGATACCATTTAACAAACAG 58.816 37.037 0.00 0.00 36.94 3.16
2905 3024 3.201290 CATGTTGGAAGTAGCTAGGCAG 58.799 50.000 0.00 0.00 0.00 4.85
2918 3037 8.638873 AGTAATCATATCGACTAACATGTTGGA 58.361 33.333 26.56 15.33 0.00 3.53
2985 3104 2.201732 CGTACCTTCGGTCCATTGATG 58.798 52.381 0.00 0.00 37.09 3.07
3214 3333 6.348540 GCAACCGAAATACAAAGTTGAGATCT 60.349 38.462 0.00 0.00 40.12 2.75
3217 3336 4.319190 CGCAACCGAAATACAAAGTTGAGA 60.319 41.667 5.43 0.00 39.60 3.27
3471 3590 4.524749 GAGAAGCGGTAAAAGTTGACAAC 58.475 43.478 10.47 10.47 0.00 3.32
3694 3813 9.612066 TTGCAAGAAAAAGATAGGAAACAATTT 57.388 25.926 0.00 0.00 0.00 1.82
3697 3816 8.878769 GTTTTGCAAGAAAAAGATAGGAAACAA 58.121 29.630 0.00 0.00 29.93 2.83
3726 3845 7.192148 TGTTTGGAATGCATGAATTTCAAAG 57.808 32.000 27.07 0.82 42.81 2.77
3780 3899 5.957842 TGCGGTCATTTTGAGATAAGTTT 57.042 34.783 0.00 0.00 0.00 2.66
3786 3905 4.672542 CGTTTCATGCGGTCATTTTGAGAT 60.673 41.667 0.00 0.00 0.00 2.75
3800 3919 5.060940 GCAAAGAATTACTTCCGTTTCATGC 59.939 40.000 0.00 0.00 37.93 4.06
3836 3955 9.520515 AAGAATCTTCAACACAAGGTACATAAT 57.479 29.630 0.00 0.00 0.00 1.28
3853 3972 7.168135 AGCAAACAAATGTCGAAAAGAATCTTC 59.832 33.333 0.00 0.00 0.00 2.87
3855 3974 6.418819 CAGCAAACAAATGTCGAAAAGAATCT 59.581 34.615 0.00 0.00 0.00 2.40
3865 3984 2.772568 TCCACAGCAAACAAATGTCG 57.227 45.000 0.00 0.00 0.00 4.35
3881 4003 7.434897 GCAATTGTAATCTTGCGATTTTATCCA 59.565 33.333 7.40 0.00 40.28 3.41
3882 4004 7.777425 GCAATTGTAATCTTGCGATTTTATCC 58.223 34.615 7.40 0.00 40.28 2.59
3929 4051 4.081642 TGCTTTCAGGCTAGTAAGGTACTG 60.082 45.833 0.00 0.00 40.86 2.74
3933 4055 4.019321 TGATTGCTTTCAGGCTAGTAAGGT 60.019 41.667 0.00 0.00 0.00 3.50
3935 4057 5.181748 ACTGATTGCTTTCAGGCTAGTAAG 58.818 41.667 17.18 0.00 46.04 2.34
3936 4058 5.165961 ACTGATTGCTTTCAGGCTAGTAA 57.834 39.130 17.18 0.00 46.04 2.24
3937 4059 4.826274 ACTGATTGCTTTCAGGCTAGTA 57.174 40.909 17.18 0.00 46.04 1.82
3938 4060 3.710209 ACTGATTGCTTTCAGGCTAGT 57.290 42.857 17.18 0.00 46.04 2.57
3939 4061 4.005650 TCAACTGATTGCTTTCAGGCTAG 58.994 43.478 17.18 7.14 46.04 3.42
3940 4062 4.019792 TCAACTGATTGCTTTCAGGCTA 57.980 40.909 17.18 3.38 46.04 3.93
3942 4064 3.863142 ATCAACTGATTGCTTTCAGGC 57.137 42.857 17.18 0.00 46.04 4.85
4015 4141 5.163426 CCCATGATAAAGCACAAAAGCCATA 60.163 40.000 0.00 0.00 34.23 2.74
4032 4158 4.964897 TGAGAGATGTGTAGAACCCATGAT 59.035 41.667 0.00 0.00 0.00 2.45
4036 4162 3.118629 GCATGAGAGATGTGTAGAACCCA 60.119 47.826 0.00 0.00 0.00 4.51
4050 4176 6.274157 ACGAGTTATATAAGGGCATGAGAG 57.726 41.667 0.00 0.00 0.00 3.20
4051 4177 6.717997 TGTACGAGTTATATAAGGGCATGAGA 59.282 38.462 0.00 0.00 0.00 3.27
4056 4182 5.303589 AGCTTGTACGAGTTATATAAGGGCA 59.696 40.000 11.83 0.00 0.00 5.36
4101 4227 4.400884 TGGCTGCTCAAAGTTTCAACTAAA 59.599 37.500 0.00 0.00 38.57 1.85
4348 4491 1.077644 CTGGATGCTTGCTCTGCCT 60.078 57.895 0.00 0.00 0.00 4.75
4382 4525 1.671742 GCCACTGAGGAGAAACGGA 59.328 57.895 0.00 0.00 41.22 4.69
4433 4576 2.094659 CAGGATCACGTCGTGCACC 61.095 63.158 20.56 22.27 36.09 5.01
4448 4591 4.878439 TGTCGATTATCCCGAAATACAGG 58.122 43.478 0.00 0.00 37.81 4.00
4502 4645 3.810373 CAACGACTTGTAAACATGCTCC 58.190 45.455 0.00 0.00 0.00 4.70
4529 4672 2.480419 GGCAGATATCGAATTTGGGTCG 59.520 50.000 0.00 0.00 39.88 4.79
4535 4678 3.131396 GTCCACGGCAGATATCGAATTT 58.869 45.455 0.00 0.00 0.00 1.82
4550 4693 1.139095 GTAGAGCTTCGGGTCCACG 59.861 63.158 0.00 0.00 42.85 4.94
4624 4768 1.462616 TGAATGCATCTTTGACCCCG 58.537 50.000 0.00 0.00 0.00 5.73
4686 4852 4.202202 ACCATGCAGAAAATCGACCAAAAA 60.202 37.500 0.00 0.00 0.00 1.94
4717 4883 5.407502 GTTGGTGGTATTTAACAATGGAGC 58.592 41.667 0.00 0.00 0.00 4.70
4768 4934 0.647925 GAGCCGACGAGCTGATTTTC 59.352 55.000 14.30 0.00 45.15 2.29
4784 4950 0.389948 ATCGAGGTTCAACGGTGAGC 60.390 55.000 9.05 9.05 34.49 4.26
4786 4952 0.963225 TGATCGAGGTTCAACGGTGA 59.037 50.000 0.00 0.00 0.00 4.02
4787 4953 1.336887 ACTGATCGAGGTTCAACGGTG 60.337 52.381 0.00 0.00 0.00 4.94
4788 4954 0.966920 ACTGATCGAGGTTCAACGGT 59.033 50.000 0.00 0.00 0.00 4.83
4789 4955 2.163815 ACTACTGATCGAGGTTCAACGG 59.836 50.000 0.00 0.00 0.00 4.44
4790 4956 3.172050 CACTACTGATCGAGGTTCAACG 58.828 50.000 0.00 0.00 0.00 4.10
4791 4957 3.192844 TCCACTACTGATCGAGGTTCAAC 59.807 47.826 0.00 0.00 0.00 3.18
4792 4958 3.427573 TCCACTACTGATCGAGGTTCAA 58.572 45.455 0.00 0.00 0.00 2.69
4807 4984 0.702902 ACCTCGTCTCCCTTCCACTA 59.297 55.000 0.00 0.00 0.00 2.74
4811 4988 1.079057 GCAACCTCGTCTCCCTTCC 60.079 63.158 0.00 0.00 0.00 3.46
4904 5082 3.101643 TGTACAGATGCCTACTGGAGT 57.898 47.619 0.00 0.00 39.38 3.85
4905 5083 4.679373 AATGTACAGATGCCTACTGGAG 57.321 45.455 0.33 0.00 39.38 3.86
4906 5084 5.185454 CAAAATGTACAGATGCCTACTGGA 58.815 41.667 0.33 0.00 39.38 3.86
4907 5085 4.943705 ACAAAATGTACAGATGCCTACTGG 59.056 41.667 0.33 0.00 39.38 4.00
4908 5086 5.643348 TCACAAAATGTACAGATGCCTACTG 59.357 40.000 0.33 0.00 40.68 2.74
4971 5149 2.457366 AAAGGACTGACTTGCTACCG 57.543 50.000 0.00 0.00 0.00 4.02
4999 5188 9.467796 CCAAGAAAAGAATCCTAATCCTAACTT 57.532 33.333 0.00 0.00 0.00 2.66
5360 5549 7.043961 TGTTGTATCTGTACATGATCTCTCC 57.956 40.000 0.00 0.94 40.35 3.71
5431 5620 3.452627 GTGCAGGGAAGAGGAAGAAGATA 59.547 47.826 0.00 0.00 0.00 1.98
5442 5631 1.210478 GGATAAGCAGTGCAGGGAAGA 59.790 52.381 19.20 0.00 0.00 2.87
5447 5636 0.835941 AGAGGGATAAGCAGTGCAGG 59.164 55.000 19.20 0.00 0.00 4.85
5459 5648 0.608640 ACGACGCAAAAGAGAGGGAT 59.391 50.000 0.00 0.00 0.00 3.85
5485 5680 7.068716 CCAATAAATACTGGGAAAGGAAGGAAG 59.931 40.741 0.00 0.00 0.00 3.46
5486 5681 6.895204 CCAATAAATACTGGGAAAGGAAGGAA 59.105 38.462 0.00 0.00 0.00 3.36
5487 5682 6.431722 CCAATAAATACTGGGAAAGGAAGGA 58.568 40.000 0.00 0.00 0.00 3.36
5488 5683 5.069119 GCCAATAAATACTGGGAAAGGAAGG 59.931 44.000 0.00 0.00 32.95 3.46
5514 5709 2.873525 GCTATCCGTGGGAGGGAGC 61.874 68.421 0.00 1.69 35.39 4.70
5515 5710 0.760945 AAGCTATCCGTGGGAGGGAG 60.761 60.000 0.00 0.00 35.39 4.30
5516 5711 0.326238 AAAGCTATCCGTGGGAGGGA 60.326 55.000 0.00 0.00 36.49 4.20
5517 5712 0.106894 GAAAGCTATCCGTGGGAGGG 59.893 60.000 0.00 0.00 34.05 4.30
5518 5713 1.123928 AGAAAGCTATCCGTGGGAGG 58.876 55.000 0.00 0.00 34.05 4.30
5519 5714 1.808133 GCAGAAAGCTATCCGTGGGAG 60.808 57.143 0.00 0.00 41.15 4.30
5520 5715 0.178068 GCAGAAAGCTATCCGTGGGA 59.822 55.000 0.00 0.00 41.15 4.37
5521 5716 0.107703 TGCAGAAAGCTATCCGTGGG 60.108 55.000 0.00 0.00 45.94 4.61
5524 5719 0.462759 GCCTGCAGAAAGCTATCCGT 60.463 55.000 17.39 0.00 45.94 4.69
5536 5735 1.892819 TTTCTCTCTCCGGCCTGCAG 61.893 60.000 6.78 6.78 0.00 4.41
5555 5754 2.045926 CCGCAAGCCAAGCCTACT 60.046 61.111 0.00 0.00 0.00 2.57
5571 5777 2.993853 CAGGTCAAGGGGAGAGCC 59.006 66.667 0.00 0.00 34.17 4.70
5572 5778 2.270527 GCAGGTCAAGGGGAGAGC 59.729 66.667 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.