Multiple sequence alignment - TraesCS1A01G071500

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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 TraesCS1A01G071500 chr1A 100.000 3637 0 0 1 3637 53999915 54003551 0.000000e+00 6717.0
1 TraesCS1A01G071500 chr1D 89.823 1867 119 23 1164 2985 55409780 55411620 0.000000e+00 2329.0
2 TraesCS1A01G071500 chr1D 88.618 492 26 17 659 1126 55409293 55409778 4.070000e-159 571.0
3 TraesCS1A01G071500 chr1D 82.909 275 31 14 367 637 55408874 55409136 2.180000e-57 233.0
4 TraesCS1A01G071500 chr1B 91.365 1656 109 20 1980 3617 90878720 90880359 0.000000e+00 2235.0
5 TraesCS1A01G071500 chr1B 88.342 1707 167 17 1379 3066 90698036 90699729 0.000000e+00 2021.0
6 TraesCS1A01G071500 chr1B 82.520 1373 128 62 659 1983 90877154 90878462 0.000000e+00 1103.0
7 TraesCS1A01G071500 chr1B 86.188 724 51 14 659 1340 90697194 90697910 0.000000e+00 737.0
8 TraesCS1A01G071500 chr1B 89.787 235 21 3 3256 3489 90699845 90700077 7.630000e-77 298.0
9 TraesCS1A01G071500 chr1B 85.284 299 24 12 357 653 90696796 90697076 1.280000e-74 291.0
10 TraesCS1A01G071500 chr1B 93.162 117 8 0 3101 3217 90699729 90699845 4.830000e-39 172.0
11 TraesCS1A01G071500 chr1B 96.000 50 2 0 1 50 90696495 90696544 8.370000e-12 82.4
12 TraesCS1A01G071500 chr1B 100.000 31 0 0 294 324 90876274 90876304 1.410000e-04 58.4
13 TraesCS1A01G071500 chr6B 78.598 271 49 7 1598 1864 586649870 586650135 1.740000e-38 171.0
14 TraesCS1A01G071500 chr5B 83.439 157 19 3 1711 1866 548580763 548580913 4.900000e-29 139.0
15 TraesCS1A01G071500 chr5B 89.381 113 7 4 49 161 533892989 533893096 1.760000e-28 137.0
16 TraesCS1A01G071500 chr2B 85.455 110 10 4 56 160 670839992 670840100 3.840000e-20 110.0
17 TraesCS1A01G071500 chr6A 81.651 109 15 5 52 160 1744869 1744766 6.470000e-13 86.1
18 TraesCS1A01G071500 chr3A 71.986 282 67 10 1594 1866 477131492 477131770 5.040000e-09 73.1


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 TraesCS1A01G071500 chr1A 53999915 54003551 3636 False 6717.000000 6717 100.000000 1 3637 1 chr1A.!!$F1 3636
1 TraesCS1A01G071500 chr1D 55408874 55411620 2746 False 1044.333333 2329 87.116667 367 2985 3 chr1D.!!$F1 2618
2 TraesCS1A01G071500 chr1B 90876274 90880359 4085 False 1132.133333 2235 91.295000 294 3617 3 chr1B.!!$F2 3323
3 TraesCS1A01G071500 chr1B 90696495 90700077 3582 False 600.233333 2021 89.793833 1 3489 6 chr1B.!!$F1 3488

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
236 237 0.102300 GAAGGTGGCCAAACACACAC 59.898 55.0 7.24 0.00 43.08 3.82 F
677 1300 0.320421 TGTGGTAGGAACAAGAGCGC 60.320 55.0 0.00 0.00 0.00 5.92 F
1123 1776 0.631753 TCCACGATTCCCTCTCCTCT 59.368 55.0 0.00 0.00 0.00 3.69 F
1206 1896 0.997196 GTTGGTTGATCGCGACTACC 59.003 55.0 23.96 23.96 34.69 3.18 F
1497 2287 2.033424 TCTTCGGTGAGTCTATCATGCG 59.967 50.0 0.00 0.00 40.92 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1890 0.243907 TTCGCAGCACTCTGGTAGTC 59.756 55.000 0.00 0.0 40.65 2.59 R
1562 2352 0.898326 TGCAGTGGGTCGCTAAGAGA 60.898 55.000 0.00 0.0 0.00 3.10 R
2148 3201 2.363306 TCAGGTGGCTTGTTCATGTT 57.637 45.000 0.00 0.0 0.00 2.71 R
2522 3590 2.908916 GCCATGTTAGCATTTGGCAAT 58.091 42.857 16.67 0.0 45.44 3.56 R
3316 4402 2.630592 GAACGAGGGAGGCCGATCAC 62.631 65.000 0.00 0.0 0.00 3.06 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
51 52 9.959721 AAGTGAACAATCCATATAAGTTGTAGT 57.040 29.630 0.00 0.00 33.99 2.73
52 53 9.601217 AGTGAACAATCCATATAAGTTGTAGTC 57.399 33.333 0.00 0.00 33.99 2.59
53 54 8.827677 GTGAACAATCCATATAAGTTGTAGTCC 58.172 37.037 0.00 0.00 33.99 3.85
54 55 7.990886 TGAACAATCCATATAAGTTGTAGTCCC 59.009 37.037 0.00 0.00 33.99 4.46
55 56 7.691993 ACAATCCATATAAGTTGTAGTCCCT 57.308 36.000 0.00 0.00 33.39 4.20
56 57 7.736893 ACAATCCATATAAGTTGTAGTCCCTC 58.263 38.462 0.00 0.00 33.39 4.30
57 58 7.569111 ACAATCCATATAAGTTGTAGTCCCTCT 59.431 37.037 0.00 0.00 33.39 3.69
58 59 6.978674 TCCATATAAGTTGTAGTCCCTCTG 57.021 41.667 0.00 0.00 0.00 3.35
59 60 6.441222 TCCATATAAGTTGTAGTCCCTCTGT 58.559 40.000 0.00 0.00 0.00 3.41
60 61 6.901300 TCCATATAAGTTGTAGTCCCTCTGTT 59.099 38.462 0.00 0.00 0.00 3.16
61 62 7.069578 TCCATATAAGTTGTAGTCCCTCTGTTC 59.930 40.741 0.00 0.00 0.00 3.18
62 63 7.147724 CCATATAAGTTGTAGTCCCTCTGTTCA 60.148 40.741 0.00 0.00 0.00 3.18
63 64 4.338379 AAGTTGTAGTCCCTCTGTTCAC 57.662 45.455 0.00 0.00 0.00 3.18
64 65 3.577919 AGTTGTAGTCCCTCTGTTCACT 58.422 45.455 0.00 0.00 0.00 3.41
65 66 3.967987 AGTTGTAGTCCCTCTGTTCACTT 59.032 43.478 0.00 0.00 0.00 3.16
66 67 4.409247 AGTTGTAGTCCCTCTGTTCACTTT 59.591 41.667 0.00 0.00 0.00 2.66
67 68 5.104485 AGTTGTAGTCCCTCTGTTCACTTTT 60.104 40.000 0.00 0.00 0.00 2.27
68 69 6.099269 AGTTGTAGTCCCTCTGTTCACTTTTA 59.901 38.462 0.00 0.00 0.00 1.52
69 70 6.681729 TGTAGTCCCTCTGTTCACTTTTAT 57.318 37.500 0.00 0.00 0.00 1.40
70 71 7.786046 TGTAGTCCCTCTGTTCACTTTTATA 57.214 36.000 0.00 0.00 0.00 0.98
71 72 8.197592 TGTAGTCCCTCTGTTCACTTTTATAA 57.802 34.615 0.00 0.00 0.00 0.98
72 73 8.311836 TGTAGTCCCTCTGTTCACTTTTATAAG 58.688 37.037 0.00 0.00 37.40 1.73
73 74 7.554959 AGTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
74 75 8.152023 AGTCCCTCTGTTCACTTTTATAAGAT 57.848 34.615 0.00 0.00 35.30 2.40
75 76 9.268282 AGTCCCTCTGTTCACTTTTATAAGATA 57.732 33.333 0.00 0.00 35.30 1.98
76 77 9.315525 GTCCCTCTGTTCACTTTTATAAGATAC 57.684 37.037 0.00 0.00 35.30 2.24
77 78 9.268282 TCCCTCTGTTCACTTTTATAAGATACT 57.732 33.333 0.00 0.00 35.30 2.12
78 79 9.892130 CCCTCTGTTCACTTTTATAAGATACTT 57.108 33.333 0.00 0.00 35.30 2.24
105 106 7.624360 TTCATACAACTGAAAAGTGAACTGT 57.376 32.000 0.00 0.00 32.35 3.55
106 107 7.624360 TCATACAACTGAAAAGTGAACTGTT 57.376 32.000 0.00 0.00 0.00 3.16
107 108 8.050778 TCATACAACTGAAAAGTGAACTGTTT 57.949 30.769 0.00 0.00 0.00 2.83
108 109 8.519526 TCATACAACTGAAAAGTGAACTGTTTT 58.480 29.630 0.00 0.00 0.00 2.43
109 110 8.586273 CATACAACTGAAAAGTGAACTGTTTTG 58.414 33.333 0.00 0.00 0.00 2.44
110 111 5.925969 ACAACTGAAAAGTGAACTGTTTTGG 59.074 36.000 0.00 0.00 0.00 3.28
111 112 5.072040 ACTGAAAAGTGAACTGTTTTGGG 57.928 39.130 0.00 0.00 0.00 4.12
112 113 4.526650 ACTGAAAAGTGAACTGTTTTGGGT 59.473 37.500 0.00 0.00 0.00 4.51
113 114 5.712917 ACTGAAAAGTGAACTGTTTTGGGTA 59.287 36.000 0.00 0.00 0.00 3.69
114 115 6.379988 ACTGAAAAGTGAACTGTTTTGGGTAT 59.620 34.615 0.00 0.00 0.00 2.73
115 116 7.093509 ACTGAAAAGTGAACTGTTTTGGGTATT 60.094 33.333 0.00 0.00 0.00 1.89
116 117 7.038659 TGAAAAGTGAACTGTTTTGGGTATTG 58.961 34.615 0.00 0.00 0.00 1.90
117 118 6.538945 AAAGTGAACTGTTTTGGGTATTGT 57.461 33.333 0.00 0.00 0.00 2.71
118 119 5.767816 AGTGAACTGTTTTGGGTATTGTC 57.232 39.130 0.00 0.00 0.00 3.18
119 120 5.445964 AGTGAACTGTTTTGGGTATTGTCT 58.554 37.500 0.00 0.00 0.00 3.41
120 121 5.891551 AGTGAACTGTTTTGGGTATTGTCTT 59.108 36.000 0.00 0.00 0.00 3.01
121 122 7.057894 AGTGAACTGTTTTGGGTATTGTCTTA 58.942 34.615 0.00 0.00 0.00 2.10
122 123 7.558444 AGTGAACTGTTTTGGGTATTGTCTTAA 59.442 33.333 0.00 0.00 0.00 1.85
123 124 8.192110 GTGAACTGTTTTGGGTATTGTCTTAAA 58.808 33.333 0.00 0.00 0.00 1.52
124 125 8.919145 TGAACTGTTTTGGGTATTGTCTTAAAT 58.081 29.630 0.00 0.00 0.00 1.40
125 126 9.191995 GAACTGTTTTGGGTATTGTCTTAAATG 57.808 33.333 0.00 0.00 0.00 2.32
126 127 8.245195 ACTGTTTTGGGTATTGTCTTAAATGT 57.755 30.769 0.00 0.00 0.00 2.71
127 128 8.357402 ACTGTTTTGGGTATTGTCTTAAATGTC 58.643 33.333 0.00 0.00 0.00 3.06
128 129 8.472007 TGTTTTGGGTATTGTCTTAAATGTCT 57.528 30.769 0.00 0.00 0.00 3.41
129 130 9.575868 TGTTTTGGGTATTGTCTTAAATGTCTA 57.424 29.630 0.00 0.00 0.00 2.59
133 134 9.575868 TTGGGTATTGTCTTAAATGTCTAAACA 57.424 29.630 0.00 0.00 40.38 2.83
134 135 9.226606 TGGGTATTGTCTTAAATGTCTAAACAG 57.773 33.333 0.00 0.00 39.20 3.16
135 136 9.227777 GGGTATTGTCTTAAATGTCTAAACAGT 57.772 33.333 0.00 0.00 39.20 3.55
148 149 8.958119 ATGTCTAAACAGTCTTACAAAAGTGA 57.042 30.769 0.00 0.00 39.20 3.41
149 150 8.780846 TGTCTAAACAGTCTTACAAAAGTGAA 57.219 30.769 0.00 0.00 34.13 3.18
150 151 8.662141 TGTCTAAACAGTCTTACAAAAGTGAAC 58.338 33.333 0.00 0.00 34.13 3.18
151 152 7.844653 GTCTAAACAGTCTTACAAAAGTGAACG 59.155 37.037 0.00 0.00 34.13 3.95
152 153 5.479716 AACAGTCTTACAAAAGTGAACGG 57.520 39.130 0.00 0.00 34.13 4.44
153 154 4.761975 ACAGTCTTACAAAAGTGAACGGA 58.238 39.130 0.00 0.00 34.13 4.69
154 155 4.809426 ACAGTCTTACAAAAGTGAACGGAG 59.191 41.667 0.00 0.00 34.13 4.63
155 156 5.047847 CAGTCTTACAAAAGTGAACGGAGA 58.952 41.667 0.00 0.00 34.13 3.71
156 157 5.175856 CAGTCTTACAAAAGTGAACGGAGAG 59.824 44.000 0.00 0.00 34.13 3.20
157 158 5.068723 AGTCTTACAAAAGTGAACGGAGAGA 59.931 40.000 0.00 0.00 34.13 3.10
158 159 5.402867 GTCTTACAAAAGTGAACGGAGAGAG 59.597 44.000 0.00 0.00 34.13 3.20
159 160 3.821421 ACAAAAGTGAACGGAGAGAGT 57.179 42.857 0.00 0.00 0.00 3.24
160 161 3.458189 ACAAAAGTGAACGGAGAGAGTG 58.542 45.455 0.00 0.00 0.00 3.51
161 162 2.156343 AAAGTGAACGGAGAGAGTGC 57.844 50.000 0.00 0.00 0.00 4.40
162 163 1.040646 AAGTGAACGGAGAGAGTGCA 58.959 50.000 0.00 0.00 0.00 4.57
163 164 1.261480 AGTGAACGGAGAGAGTGCAT 58.739 50.000 0.00 0.00 28.63 3.96
164 165 2.447443 AGTGAACGGAGAGAGTGCATA 58.553 47.619 0.00 0.00 28.63 3.14
165 166 2.425312 AGTGAACGGAGAGAGTGCATAG 59.575 50.000 0.00 0.00 28.63 2.23
166 167 2.423892 GTGAACGGAGAGAGTGCATAGA 59.576 50.000 0.00 0.00 28.63 1.98
167 168 3.067461 GTGAACGGAGAGAGTGCATAGAT 59.933 47.826 0.00 0.00 28.63 1.98
168 169 3.067320 TGAACGGAGAGAGTGCATAGATG 59.933 47.826 0.00 0.00 0.00 2.90
169 170 2.660572 ACGGAGAGAGTGCATAGATGT 58.339 47.619 0.00 0.00 0.00 3.06
176 177 6.644592 GGAGAGAGTGCATAGATGTAATGAAC 59.355 42.308 0.00 0.00 33.66 3.18
204 205 5.921962 AAATGAAAATGCTCCTACCCTTC 57.078 39.130 0.00 0.00 0.00 3.46
236 237 0.102300 GAAGGTGGCCAAACACACAC 59.898 55.000 7.24 0.00 43.08 3.82
251 252 7.277539 CCAAACACACACTAATCAACATGTTTT 59.722 33.333 8.77 4.48 37.02 2.43
255 256 7.147312 CACACACTAATCAACATGTTTTCCAT 58.853 34.615 8.77 0.00 0.00 3.41
284 285 3.744238 AAAAAGGAAAACCGACCCATG 57.256 42.857 0.00 0.00 0.00 3.66
287 288 1.905637 AGGAAAACCGACCCATGTTC 58.094 50.000 0.00 0.00 0.00 3.18
288 289 1.423921 AGGAAAACCGACCCATGTTCT 59.576 47.619 0.00 0.00 0.00 3.01
340 383 4.499037 TCACCATACGTGATCTTATCCG 57.501 45.455 0.00 0.00 46.80 4.18
342 385 4.765339 TCACCATACGTGATCTTATCCGAT 59.235 41.667 0.00 0.00 46.80 4.18
358 401 3.374764 TCCGATCATCTCCTTCCTGAAA 58.625 45.455 0.00 0.00 0.00 2.69
359 402 3.774766 TCCGATCATCTCCTTCCTGAAAA 59.225 43.478 0.00 0.00 0.00 2.29
360 403 4.225042 TCCGATCATCTCCTTCCTGAAAAA 59.775 41.667 0.00 0.00 0.00 1.94
361 404 4.574013 CCGATCATCTCCTTCCTGAAAAAG 59.426 45.833 0.00 0.00 0.00 2.27
362 405 5.423015 CGATCATCTCCTTCCTGAAAAAGA 58.577 41.667 0.00 0.00 0.00 2.52
365 408 5.940617 TCATCTCCTTCCTGAAAAAGAACA 58.059 37.500 0.00 0.00 0.00 3.18
372 850 8.760980 TCCTTCCTGAAAAAGAACAAAGATTA 57.239 30.769 0.00 0.00 0.00 1.75
439 917 8.194769 GGTTATTCCAACGAATCCATTGTTTAT 58.805 33.333 0.00 0.00 39.49 1.40
440 918 9.019764 GTTATTCCAACGAATCCATTGTTTATG 57.980 33.333 0.00 0.00 39.49 1.90
473 952 3.401033 AGTCATTGTTCGACACATCCA 57.599 42.857 0.00 0.00 34.43 3.41
481 960 1.431845 CGACACATCCATCGTCGGA 59.568 57.895 3.37 0.00 46.59 4.55
483 962 0.527817 GACACATCCATCGTCGGACC 60.528 60.000 1.91 0.00 38.07 4.46
509 996 7.360946 CGGTCTCCCTTTCAGTTAAAAATACTG 60.361 40.741 0.00 0.00 43.41 2.74
510 997 7.447545 GGTCTCCCTTTCAGTTAAAAATACTGT 59.552 37.037 0.00 0.00 42.77 3.55
535 1022 7.661127 ACAAGCAATTAACTATCACGTACAA 57.339 32.000 0.00 0.00 0.00 2.41
537 1024 6.345920 AGCAATTAACTATCACGTACAAGC 57.654 37.500 0.00 0.00 0.00 4.01
538 1025 5.872617 AGCAATTAACTATCACGTACAAGCA 59.127 36.000 0.00 0.00 0.00 3.91
539 1026 6.036083 AGCAATTAACTATCACGTACAAGCAG 59.964 38.462 0.00 0.00 0.00 4.24
540 1027 6.035650 GCAATTAACTATCACGTACAAGCAGA 59.964 38.462 0.00 0.00 0.00 4.26
541 1028 7.391786 CAATTAACTATCACGTACAAGCAGAC 58.608 38.462 0.00 0.00 0.00 3.51
542 1029 4.514781 AACTATCACGTACAAGCAGACA 57.485 40.909 0.00 0.00 0.00 3.41
543 1030 4.098055 ACTATCACGTACAAGCAGACAG 57.902 45.455 0.00 0.00 0.00 3.51
545 1032 1.037493 TCACGTACAAGCAGACAGGT 58.963 50.000 0.00 0.00 0.00 4.00
546 1033 1.139989 CACGTACAAGCAGACAGGTG 58.860 55.000 0.00 0.00 0.00 4.00
547 1034 1.037493 ACGTACAAGCAGACAGGTGA 58.963 50.000 0.00 0.00 0.00 4.02
548 1035 1.618837 ACGTACAAGCAGACAGGTGAT 59.381 47.619 0.00 0.00 0.00 3.06
558 1045 3.607741 CAGACAGGTGATGAGAGCAAAT 58.392 45.455 0.00 0.00 0.00 2.32
568 1055 0.933796 GAGAGCAAATCCAGCTACGC 59.066 55.000 0.00 0.00 43.58 4.42
600 1087 2.976903 GCATGCCGATCTGCCCTC 60.977 66.667 6.36 0.00 32.15 4.30
601 1088 2.664185 CATGCCGATCTGCCCTCG 60.664 66.667 6.66 0.00 35.92 4.63
607 1094 1.299165 CGATCTGCCCTCGGTTACG 60.299 63.158 0.00 0.00 42.74 3.18
677 1300 0.320421 TGTGGTAGGAACAAGAGCGC 60.320 55.000 0.00 0.00 0.00 5.92
725 1353 4.444024 CATGCCACGAACGCGGTG 62.444 66.667 12.47 9.20 43.17 4.94
747 1375 1.432270 GCCTAATCAGCTCACGGTGC 61.432 60.000 2.51 0.00 38.50 5.01
851 1485 1.302752 TGCATGAGTGGGACAGTGC 60.303 57.895 0.00 0.00 45.14 4.40
855 1489 4.008933 GAGTGGGACAGTGCGCCT 62.009 66.667 4.18 0.00 45.14 5.52
856 1490 4.320456 AGTGGGACAGTGCGCCTG 62.320 66.667 20.07 20.07 42.47 4.85
883 1519 8.712285 TCCGTTAAATCATCTTCTTATTTCGT 57.288 30.769 0.00 0.00 0.00 3.85
946 1599 2.668550 GTTGGCCGTCCACTCCAC 60.669 66.667 0.00 0.00 43.33 4.02
992 1645 3.217743 CGTAGAGGGGGCGAGGTC 61.218 72.222 0.00 0.00 0.00 3.85
993 1646 2.043248 GTAGAGGGGGCGAGGTCA 60.043 66.667 0.00 0.00 0.00 4.02
1120 1773 1.443828 GCTCCACGATTCCCTCTCC 59.556 63.158 0.00 0.00 0.00 3.71
1121 1774 1.045911 GCTCCACGATTCCCTCTCCT 61.046 60.000 0.00 0.00 0.00 3.69
1122 1775 1.036707 CTCCACGATTCCCTCTCCTC 58.963 60.000 0.00 0.00 0.00 3.71
1123 1776 0.631753 TCCACGATTCCCTCTCCTCT 59.368 55.000 0.00 0.00 0.00 3.69
1124 1777 1.036707 CCACGATTCCCTCTCCTCTC 58.963 60.000 0.00 0.00 0.00 3.20
1125 1778 1.410932 CCACGATTCCCTCTCCTCTCT 60.411 57.143 0.00 0.00 0.00 3.10
1126 1779 1.953686 CACGATTCCCTCTCCTCTCTC 59.046 57.143 0.00 0.00 0.00 3.20
1127 1780 1.850345 ACGATTCCCTCTCCTCTCTCT 59.150 52.381 0.00 0.00 0.00 3.10
1128 1781 2.158667 ACGATTCCCTCTCCTCTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
1129 1782 2.106511 CGATTCCCTCTCCTCTCTCTCT 59.893 54.545 0.00 0.00 0.00 3.10
1130 1783 3.756117 GATTCCCTCTCCTCTCTCTCTC 58.244 54.545 0.00 0.00 0.00 3.20
1159 1812 7.127493 TCTCTCTCTCTGTACCTGGTTTATCTA 59.873 40.741 3.84 0.00 0.00 1.98
1200 1890 1.154413 GTGCTGTTGGTTGATCGCG 60.154 57.895 0.00 0.00 0.00 5.87
1203 1893 1.291877 GCTGTTGGTTGATCGCGACT 61.292 55.000 12.93 0.00 0.00 4.18
1206 1896 0.997196 GTTGGTTGATCGCGACTACC 59.003 55.000 23.96 23.96 34.69 3.18
1238 1936 2.762535 ATTCCTAGTGACACCGGTTG 57.237 50.000 2.97 2.94 0.00 3.77
1251 1954 2.746904 CACCGGTTGCAGTTTATGATCA 59.253 45.455 2.97 0.00 0.00 2.92
1252 1955 3.378112 CACCGGTTGCAGTTTATGATCAT 59.622 43.478 13.81 13.81 0.00 2.45
1253 1956 3.627577 ACCGGTTGCAGTTTATGATCATC 59.372 43.478 12.53 0.00 0.00 2.92
1254 1957 3.879295 CCGGTTGCAGTTTATGATCATCT 59.121 43.478 12.53 0.00 0.00 2.90
1277 1980 8.763984 TCTATCTATATACGGGGAATTTCTCC 57.236 38.462 5.12 5.12 44.54 3.71
1302 2005 7.416213 CCCGTGCTCTCCATTTCAAATTAATTA 60.416 37.037 0.01 0.00 0.00 1.40
1385 2175 7.581476 TCCGAAATTAATTATCTTCCAATCGC 58.419 34.615 0.01 0.00 0.00 4.58
1487 2277 5.661056 TGATAATGTTCTCTTCGGTGAGT 57.339 39.130 5.71 0.00 35.68 3.41
1497 2287 2.033424 TCTTCGGTGAGTCTATCATGCG 59.967 50.000 0.00 0.00 40.92 4.73
1613 2403 5.890424 TTTAAGGCCTCCTTTGATTTACG 57.110 39.130 5.23 0.00 41.69 3.18
1614 2404 2.420058 AGGCCTCCTTTGATTTACGG 57.580 50.000 0.00 0.00 0.00 4.02
1621 2411 4.395231 CCTCCTTTGATTTACGGGAACTTC 59.605 45.833 0.00 0.00 0.00 3.01
1630 2420 5.913137 TTTACGGGAACTTCGTAGGAATA 57.087 39.130 0.00 0.00 42.78 1.75
1638 2428 6.127225 GGGAACTTCGTAGGAATACTAAAGGT 60.127 42.308 0.00 0.00 32.37 3.50
1640 2430 7.821359 GGAACTTCGTAGGAATACTAAAGGTTT 59.179 37.037 0.00 0.00 32.37 3.27
1762 2552 9.535878 AGAAAAAGAAATATTAGCCTAGACTCG 57.464 33.333 0.00 0.00 0.00 4.18
1800 2590 5.551305 TCCTATCCATCAAATCACATCGT 57.449 39.130 0.00 0.00 0.00 3.73
1802 2592 5.991606 TCCTATCCATCAAATCACATCGTTC 59.008 40.000 0.00 0.00 0.00 3.95
1946 2738 7.307573 CGATTCATATGCATCAGTGTTGTATGT 60.308 37.037 14.47 5.59 0.00 2.29
1949 2741 6.480981 TCATATGCATCAGTGTTGTATGTCTG 59.519 38.462 0.19 8.91 0.00 3.51
1957 2749 6.993079 TCAGTGTTGTATGTCTGTTACTCAT 58.007 36.000 0.00 0.00 0.00 2.90
2048 3101 6.868864 TCTCTTTCTAGGAAGTTCATGAAACG 59.131 38.462 10.35 6.46 43.02 3.60
2052 3105 3.208747 AGGAAGTTCATGAAACGGTGT 57.791 42.857 10.35 0.00 43.02 4.16
2080 3133 9.831737 AATGAATAATCTTTTCAAGTTCGTCTG 57.168 29.630 0.00 0.00 36.72 3.51
2095 3148 8.895845 CAAGTTCGTCTGTCATTAAATTCTTTG 58.104 33.333 0.00 0.00 0.00 2.77
2099 3152 7.572759 TCGTCTGTCATTAAATTCTTTGACAC 58.427 34.615 11.23 5.01 42.46 3.67
2136 3189 4.469945 TCCCTCGGTTGTTATTTCATCTCT 59.530 41.667 0.00 0.00 0.00 3.10
2148 3201 7.733047 TGTTATTTCATCTCTAGGGTATGGCTA 59.267 37.037 0.00 0.00 0.00 3.93
2468 3530 8.902540 TTTCTTGCCATATTACTATACCACAG 57.097 34.615 0.00 0.00 0.00 3.66
2633 3701 0.407139 AAGAGCCTGAAGCCCAACAT 59.593 50.000 0.00 0.00 45.47 2.71
2709 3777 2.667481 CGGGCAATTTGTAATGCTTGTG 59.333 45.455 0.00 0.00 42.20 3.33
2716 3784 6.526325 GCAATTTGTAATGCTTGTGATCGTAA 59.474 34.615 0.00 0.00 39.46 3.18
2717 3785 7.061673 GCAATTTGTAATGCTTGTGATCGTAAA 59.938 33.333 0.00 0.00 39.46 2.01
2799 3867 3.969976 TGAGATCCTTTGACATAGGAGGG 59.030 47.826 18.05 0.00 44.63 4.30
2848 3916 0.747644 TCCATGCCGCATTCGACAAT 60.748 50.000 2.16 0.00 38.10 2.71
2851 3919 0.381801 ATGCCGCATTCGACAATTCC 59.618 50.000 0.00 0.00 38.10 3.01
2858 3926 2.797087 GCATTCGACAATTCCAGGCATG 60.797 50.000 0.00 0.00 0.00 4.06
2937 4021 4.096081 CGAAGGTCGTCTGGTCTACTAATT 59.904 45.833 0.00 0.00 34.72 1.40
2947 4031 5.486063 TCTGGTCTACTAATTAAGCCCACAA 59.514 40.000 0.00 0.00 0.00 3.33
3261 4345 6.040842 AGGACAGTGCACAAATGAAGTAAAAT 59.959 34.615 21.04 0.00 0.00 1.82
3262 4346 7.230510 AGGACAGTGCACAAATGAAGTAAAATA 59.769 33.333 21.04 0.00 0.00 1.40
3395 4481 8.299570 ACTATGATCTTGTTGAAACCAATTGTC 58.700 33.333 4.43 0.00 0.00 3.18
3455 4541 5.546526 TCAACAAAAATAAACATCAGGGCC 58.453 37.500 0.00 0.00 0.00 5.80
3507 4593 9.753674 TTAATAAAGTTCATCTTCTCAACCCAT 57.246 29.630 0.00 0.00 35.02 4.00
3526 4612 6.218053 ACCCATATAATAGGTATTCCCCTCC 58.782 44.000 0.00 0.00 35.97 4.30
3541 4627 2.486191 CCCCTCCAGGAAATCTTGATCG 60.486 54.545 0.00 0.00 38.24 3.69
3546 4632 4.454678 TCCAGGAAATCTTGATCGAATGG 58.545 43.478 0.00 0.00 0.00 3.16
3573 4659 4.878397 GTCTACATTAAGCTTCACATGGCT 59.122 41.667 0.00 0.00 40.85 4.75
3588 4674 2.634639 TGGCTCCTAGGAGGTAACAA 57.365 50.000 34.75 13.28 42.19 2.83
3594 4680 5.339282 GGCTCCTAGGAGGTAACAAATTTCT 60.339 44.000 34.75 0.00 42.19 2.52
3610 4696 3.744238 TTTCTTTGTTGCTTTAGGGGC 57.256 42.857 0.00 0.00 0.00 5.80
3613 4699 1.963515 CTTTGTTGCTTTAGGGGCTGT 59.036 47.619 0.00 0.00 0.00 4.40
3617 4703 2.084546 GTTGCTTTAGGGGCTGTAGTG 58.915 52.381 0.00 0.00 0.00 2.74
3618 4704 1.358152 TGCTTTAGGGGCTGTAGTGT 58.642 50.000 0.00 0.00 0.00 3.55
3619 4705 1.702957 TGCTTTAGGGGCTGTAGTGTT 59.297 47.619 0.00 0.00 0.00 3.32
3620 4706 2.084546 GCTTTAGGGGCTGTAGTGTTG 58.915 52.381 0.00 0.00 0.00 3.33
3621 4707 2.711542 CTTTAGGGGCTGTAGTGTTGG 58.288 52.381 0.00 0.00 0.00 3.77
3622 4708 2.032965 TTAGGGGCTGTAGTGTTGGA 57.967 50.000 0.00 0.00 0.00 3.53
3623 4709 2.032965 TAGGGGCTGTAGTGTTGGAA 57.967 50.000 0.00 0.00 0.00 3.53
3624 4710 1.372501 AGGGGCTGTAGTGTTGGAAT 58.627 50.000 0.00 0.00 0.00 3.01
3625 4711 1.710809 AGGGGCTGTAGTGTTGGAATT 59.289 47.619 0.00 0.00 0.00 2.17
3626 4712 2.110011 AGGGGCTGTAGTGTTGGAATTT 59.890 45.455 0.00 0.00 0.00 1.82
3627 4713 2.897326 GGGGCTGTAGTGTTGGAATTTT 59.103 45.455 0.00 0.00 0.00 1.82
3628 4714 3.306019 GGGGCTGTAGTGTTGGAATTTTG 60.306 47.826 0.00 0.00 0.00 2.44
3629 4715 3.320826 GGGCTGTAGTGTTGGAATTTTGT 59.679 43.478 0.00 0.00 0.00 2.83
3630 4716 4.546570 GGCTGTAGTGTTGGAATTTTGTC 58.453 43.478 0.00 0.00 0.00 3.18
3631 4717 4.278419 GGCTGTAGTGTTGGAATTTTGTCT 59.722 41.667 0.00 0.00 0.00 3.41
3632 4718 5.472137 GGCTGTAGTGTTGGAATTTTGTCTA 59.528 40.000 0.00 0.00 0.00 2.59
3633 4719 6.371389 GCTGTAGTGTTGGAATTTTGTCTAC 58.629 40.000 0.00 0.00 0.00 2.59
3634 4720 6.204882 GCTGTAGTGTTGGAATTTTGTCTACT 59.795 38.462 0.00 0.00 0.00 2.57
3635 4721 7.255139 GCTGTAGTGTTGGAATTTTGTCTACTT 60.255 37.037 0.00 0.00 0.00 2.24
3636 4722 8.514330 TGTAGTGTTGGAATTTTGTCTACTTT 57.486 30.769 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.748630 GGATTGTTCACTTTGTCCTTTTCAC 59.251 40.000 0.00 0.00 0.00 3.18
14 15 5.420421 TGGATTGTTCACTTTGTCCTTTTCA 59.580 36.000 0.00 0.00 0.00 2.69
50 51 9.315525 GTATCTTATAAAAGTGAACAGAGGGAC 57.684 37.037 0.00 0.00 34.13 4.46
51 52 9.268282 AGTATCTTATAAAAGTGAACAGAGGGA 57.732 33.333 0.00 0.00 34.13 4.20
52 53 9.892130 AAGTATCTTATAAAAGTGAACAGAGGG 57.108 33.333 0.00 0.00 34.13 4.30
79 80 8.686334 ACAGTTCACTTTTCAGTTGTATGAAAT 58.314 29.630 3.00 0.00 45.83 2.17
80 81 8.050778 ACAGTTCACTTTTCAGTTGTATGAAA 57.949 30.769 0.00 0.00 45.12 2.69
81 82 7.624360 ACAGTTCACTTTTCAGTTGTATGAA 57.376 32.000 0.00 0.00 37.41 2.57
82 83 7.624360 AACAGTTCACTTTTCAGTTGTATGA 57.376 32.000 0.00 0.00 0.00 2.15
83 84 8.586273 CAAAACAGTTCACTTTTCAGTTGTATG 58.414 33.333 0.00 0.00 0.00 2.39
84 85 7.759433 CCAAAACAGTTCACTTTTCAGTTGTAT 59.241 33.333 0.00 0.00 0.00 2.29
85 86 7.087639 CCAAAACAGTTCACTTTTCAGTTGTA 58.912 34.615 0.00 0.00 0.00 2.41
86 87 5.925969 CCAAAACAGTTCACTTTTCAGTTGT 59.074 36.000 0.00 0.00 0.00 3.32
87 88 5.348451 CCCAAAACAGTTCACTTTTCAGTTG 59.652 40.000 0.00 0.00 0.00 3.16
88 89 5.011635 ACCCAAAACAGTTCACTTTTCAGTT 59.988 36.000 0.00 0.00 0.00 3.16
89 90 4.526650 ACCCAAAACAGTTCACTTTTCAGT 59.473 37.500 0.00 0.00 0.00 3.41
90 91 5.072040 ACCCAAAACAGTTCACTTTTCAG 57.928 39.130 0.00 0.00 0.00 3.02
91 92 6.783708 ATACCCAAAACAGTTCACTTTTCA 57.216 33.333 0.00 0.00 0.00 2.69
92 93 7.039270 ACAATACCCAAAACAGTTCACTTTTC 58.961 34.615 0.00 0.00 0.00 2.29
93 94 6.941857 ACAATACCCAAAACAGTTCACTTTT 58.058 32.000 0.00 0.00 0.00 2.27
94 95 6.379988 AGACAATACCCAAAACAGTTCACTTT 59.620 34.615 0.00 0.00 0.00 2.66
95 96 5.891551 AGACAATACCCAAAACAGTTCACTT 59.108 36.000 0.00 0.00 0.00 3.16
96 97 5.445964 AGACAATACCCAAAACAGTTCACT 58.554 37.500 0.00 0.00 0.00 3.41
97 98 5.767816 AGACAATACCCAAAACAGTTCAC 57.232 39.130 0.00 0.00 0.00 3.18
98 99 7.883391 TTAAGACAATACCCAAAACAGTTCA 57.117 32.000 0.00 0.00 0.00 3.18
99 100 9.191995 CATTTAAGACAATACCCAAAACAGTTC 57.808 33.333 0.00 0.00 0.00 3.01
100 101 8.700973 ACATTTAAGACAATACCCAAAACAGTT 58.299 29.630 0.00 0.00 0.00 3.16
101 102 8.245195 ACATTTAAGACAATACCCAAAACAGT 57.755 30.769 0.00 0.00 0.00 3.55
102 103 8.576442 AGACATTTAAGACAATACCCAAAACAG 58.424 33.333 0.00 0.00 0.00 3.16
103 104 8.472007 AGACATTTAAGACAATACCCAAAACA 57.528 30.769 0.00 0.00 0.00 2.83
107 108 9.575868 TGTTTAGACATTTAAGACAATACCCAA 57.424 29.630 0.00 0.00 0.00 4.12
108 109 9.226606 CTGTTTAGACATTTAAGACAATACCCA 57.773 33.333 0.00 0.00 34.72 4.51
109 110 9.227777 ACTGTTTAGACATTTAAGACAATACCC 57.772 33.333 0.00 0.00 34.72 3.69
122 123 9.391006 TCACTTTTGTAAGACTGTTTAGACATT 57.609 29.630 0.00 0.00 33.72 2.71
123 124 8.958119 TCACTTTTGTAAGACTGTTTAGACAT 57.042 30.769 0.00 0.00 33.72 3.06
124 125 8.662141 GTTCACTTTTGTAAGACTGTTTAGACA 58.338 33.333 0.00 0.00 35.30 3.41
125 126 7.844653 CGTTCACTTTTGTAAGACTGTTTAGAC 59.155 37.037 0.00 0.00 35.30 2.59
126 127 7.010738 CCGTTCACTTTTGTAAGACTGTTTAGA 59.989 37.037 0.00 0.00 35.30 2.10
127 128 7.010738 TCCGTTCACTTTTGTAAGACTGTTTAG 59.989 37.037 0.00 0.00 35.30 1.85
128 129 6.817641 TCCGTTCACTTTTGTAAGACTGTTTA 59.182 34.615 0.00 0.00 35.30 2.01
129 130 5.644636 TCCGTTCACTTTTGTAAGACTGTTT 59.355 36.000 0.00 0.00 35.30 2.83
130 131 5.180271 TCCGTTCACTTTTGTAAGACTGTT 58.820 37.500 0.00 0.00 35.30 3.16
131 132 4.761975 TCCGTTCACTTTTGTAAGACTGT 58.238 39.130 0.00 0.00 35.30 3.55
132 133 5.047847 TCTCCGTTCACTTTTGTAAGACTG 58.952 41.667 0.00 0.00 35.30 3.51
133 134 5.068723 TCTCTCCGTTCACTTTTGTAAGACT 59.931 40.000 0.00 0.00 35.30 3.24
134 135 5.287226 TCTCTCCGTTCACTTTTGTAAGAC 58.713 41.667 0.00 0.00 35.30 3.01
135 136 5.068723 ACTCTCTCCGTTCACTTTTGTAAGA 59.931 40.000 0.00 0.00 35.30 2.10
136 137 5.175856 CACTCTCTCCGTTCACTTTTGTAAG 59.824 44.000 0.00 0.00 37.40 2.34
137 138 5.047847 CACTCTCTCCGTTCACTTTTGTAA 58.952 41.667 0.00 0.00 0.00 2.41
138 139 4.617959 CACTCTCTCCGTTCACTTTTGTA 58.382 43.478 0.00 0.00 0.00 2.41
139 140 3.458189 CACTCTCTCCGTTCACTTTTGT 58.542 45.455 0.00 0.00 0.00 2.83
140 141 2.221981 GCACTCTCTCCGTTCACTTTTG 59.778 50.000 0.00 0.00 0.00 2.44
141 142 2.158957 TGCACTCTCTCCGTTCACTTTT 60.159 45.455 0.00 0.00 0.00 2.27
142 143 1.412710 TGCACTCTCTCCGTTCACTTT 59.587 47.619 0.00 0.00 0.00 2.66
143 144 1.040646 TGCACTCTCTCCGTTCACTT 58.959 50.000 0.00 0.00 0.00 3.16
144 145 1.261480 ATGCACTCTCTCCGTTCACT 58.739 50.000 0.00 0.00 0.00 3.41
145 146 2.423892 TCTATGCACTCTCTCCGTTCAC 59.576 50.000 0.00 0.00 0.00 3.18
146 147 2.723273 TCTATGCACTCTCTCCGTTCA 58.277 47.619 0.00 0.00 0.00 3.18
147 148 3.067461 ACATCTATGCACTCTCTCCGTTC 59.933 47.826 0.00 0.00 0.00 3.95
148 149 3.027412 ACATCTATGCACTCTCTCCGTT 58.973 45.455 0.00 0.00 0.00 4.44
149 150 2.660572 ACATCTATGCACTCTCTCCGT 58.339 47.619 0.00 0.00 0.00 4.69
150 151 4.837896 TTACATCTATGCACTCTCTCCG 57.162 45.455 0.00 0.00 0.00 4.63
151 152 6.338214 TCATTACATCTATGCACTCTCTCC 57.662 41.667 0.00 0.00 0.00 3.71
152 153 7.432869 AGTTCATTACATCTATGCACTCTCTC 58.567 38.462 0.00 0.00 25.54 3.20
153 154 7.358770 AGTTCATTACATCTATGCACTCTCT 57.641 36.000 0.00 0.00 25.54 3.10
176 177 9.136323 AGGGTAGGAGCATTTTCATTTTTATAG 57.864 33.333 0.00 0.00 0.00 1.31
204 205 0.178068 CACCTTCCCACATCTACCCG 59.822 60.000 0.00 0.00 0.00 5.28
209 210 1.434513 TTGGCCACCTTCCCACATCT 61.435 55.000 3.88 0.00 0.00 2.90
269 270 1.810755 GAGAACATGGGTCGGTTTTCC 59.189 52.381 0.00 0.00 0.00 3.13
283 284 1.080093 GCGGACGATGTGGAGAACA 60.080 57.895 0.00 0.00 44.79 3.18
284 285 1.810030 GGCGGACGATGTGGAGAAC 60.810 63.158 0.00 0.00 0.00 3.01
340 383 6.656693 TGTTCTTTTTCAGGAAGGAGATGATC 59.343 38.462 0.00 0.00 0.00 2.92
342 385 5.940617 TGTTCTTTTTCAGGAAGGAGATGA 58.059 37.500 0.00 0.00 0.00 2.92
358 401 5.929992 TGACGTCCGATAATCTTTGTTCTTT 59.070 36.000 14.12 0.00 0.00 2.52
359 402 5.347907 GTGACGTCCGATAATCTTTGTTCTT 59.652 40.000 14.12 0.00 0.00 2.52
360 403 4.863131 GTGACGTCCGATAATCTTTGTTCT 59.137 41.667 14.12 0.00 0.00 3.01
361 404 4.259292 CGTGACGTCCGATAATCTTTGTTC 60.259 45.833 14.12 0.00 0.00 3.18
362 405 3.611113 CGTGACGTCCGATAATCTTTGTT 59.389 43.478 14.12 0.00 0.00 2.83
365 408 3.770263 TCGTGACGTCCGATAATCTTT 57.230 42.857 20.37 0.00 0.00 2.52
372 850 2.104331 GGCATCGTGACGTCCGAT 59.896 61.111 26.04 26.04 45.31 4.18
397 875 1.538047 AACCATAGCAGCCACTTGTG 58.462 50.000 0.00 0.00 0.00 3.33
439 917 4.776349 ACAATGACTTGGTAACTGACACA 58.224 39.130 0.00 0.00 36.64 3.72
440 918 5.558273 CGAACAATGACTTGGTAACTGACAC 60.558 44.000 0.00 0.00 36.64 3.67
473 952 2.827642 GGAGACCGGTCCGACGAT 60.828 66.667 30.82 11.57 35.47 3.73
509 996 8.176814 TGTACGTGATAGTTAATTGCTTGTAC 57.823 34.615 0.00 0.00 0.00 2.90
510 997 8.760103 TTGTACGTGATAGTTAATTGCTTGTA 57.240 30.769 0.00 0.00 0.00 2.41
527 1014 1.139989 CACCTGTCTGCTTGTACGTG 58.860 55.000 0.00 0.00 0.00 4.49
528 1015 1.037493 TCACCTGTCTGCTTGTACGT 58.963 50.000 0.00 0.00 0.00 3.57
535 1022 0.536260 GCTCTCATCACCTGTCTGCT 59.464 55.000 0.00 0.00 0.00 4.24
537 1024 2.756840 TTGCTCTCATCACCTGTCTG 57.243 50.000 0.00 0.00 0.00 3.51
538 1025 3.370315 GGATTTGCTCTCATCACCTGTCT 60.370 47.826 0.00 0.00 0.00 3.41
539 1026 2.941720 GGATTTGCTCTCATCACCTGTC 59.058 50.000 0.00 0.00 0.00 3.51
540 1027 2.306805 TGGATTTGCTCTCATCACCTGT 59.693 45.455 0.00 0.00 0.00 4.00
541 1028 2.943690 CTGGATTTGCTCTCATCACCTG 59.056 50.000 0.00 0.00 0.00 4.00
542 1029 2.683152 GCTGGATTTGCTCTCATCACCT 60.683 50.000 0.00 0.00 0.00 4.00
543 1030 1.674962 GCTGGATTTGCTCTCATCACC 59.325 52.381 0.00 0.00 0.00 4.02
545 1032 3.739209 CGTAGCTGGATTTGCTCTCATCA 60.739 47.826 0.00 0.00 41.46 3.07
546 1033 2.799412 CGTAGCTGGATTTGCTCTCATC 59.201 50.000 0.00 0.00 41.46 2.92
547 1034 2.831333 CGTAGCTGGATTTGCTCTCAT 58.169 47.619 0.00 0.00 41.46 2.90
548 1035 2.299993 CGTAGCTGGATTTGCTCTCA 57.700 50.000 0.00 0.00 41.46 3.27
579 1066 3.963222 GCAGATCGGCATGCCTAG 58.037 61.111 33.07 19.53 36.41 3.02
589 1076 1.299165 CGTAACCGAGGGCAGATCG 60.299 63.158 0.00 0.00 39.86 3.69
599 1086 0.673333 TACTCGCTCCACGTAACCGA 60.673 55.000 0.00 0.00 44.19 4.69
600 1087 0.168788 TTACTCGCTCCACGTAACCG 59.831 55.000 0.00 0.00 44.19 4.44
601 1088 2.573941 ATTACTCGCTCCACGTAACC 57.426 50.000 0.00 0.00 44.19 2.85
607 1094 3.375299 AGCATTTGAATTACTCGCTCCAC 59.625 43.478 0.00 0.00 0.00 4.02
653 1160 3.119245 GCTCTTGTTCCTACCACATACGA 60.119 47.826 0.00 0.00 0.00 3.43
677 1300 2.854777 CTCGAATACTTTGAGGTGAGCG 59.145 50.000 0.00 0.00 37.50 5.03
747 1375 3.204306 ACATGGAGTGGATATGCACTG 57.796 47.619 31.59 20.56 0.00 3.66
851 1485 1.261619 GATGATTTAACGGAGCAGGCG 59.738 52.381 0.00 0.00 0.00 5.52
855 1489 8.506168 AAATAAGAAGATGATTTAACGGAGCA 57.494 30.769 0.00 0.00 0.00 4.26
856 1490 7.794349 CGAAATAAGAAGATGATTTAACGGAGC 59.206 37.037 0.00 0.00 0.00 4.70
916 1560 2.742372 CCAACGGCTGAGGAACGG 60.742 66.667 0.00 0.00 0.00 4.44
965 1618 2.581354 CCTCTACGGCTGCTTGCT 59.419 61.111 0.00 0.00 42.39 3.91
1114 1767 3.312890 AGAGAGAGAGAGAGAGGAGAGG 58.687 54.545 0.00 0.00 0.00 3.69
1115 1768 4.222336 AGAGAGAGAGAGAGAGAGGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
1116 1769 4.078922 AGAGAGAGAGAGAGAGAGAGGAGA 60.079 50.000 0.00 0.00 0.00 3.71
1117 1770 4.222336 AGAGAGAGAGAGAGAGAGAGGAG 58.778 52.174 0.00 0.00 0.00 3.69
1118 1771 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
1119 1772 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1120 1773 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1121 1774 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1122 1775 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1123 1776 4.614475 ACAGAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
1124 1777 5.221342 GGTACAGAGAGAGAGAGAGAGAGAG 60.221 52.000 0.00 0.00 0.00 3.20
1125 1778 4.649674 GGTACAGAGAGAGAGAGAGAGAGA 59.350 50.000 0.00 0.00 0.00 3.10
1126 1779 4.651503 AGGTACAGAGAGAGAGAGAGAGAG 59.348 50.000 0.00 0.00 0.00 3.20
1127 1780 4.405680 CAGGTACAGAGAGAGAGAGAGAGA 59.594 50.000 0.00 0.00 0.00 3.10
1128 1781 4.443457 CCAGGTACAGAGAGAGAGAGAGAG 60.443 54.167 0.00 0.00 0.00 3.20
1129 1782 3.454447 CCAGGTACAGAGAGAGAGAGAGA 59.546 52.174 0.00 0.00 0.00 3.10
1130 1783 3.199946 ACCAGGTACAGAGAGAGAGAGAG 59.800 52.174 0.00 0.00 0.00 3.20
1159 1812 5.016831 CAGGTTAATTTGGGAAAGCTAGGT 58.983 41.667 0.00 0.00 30.29 3.08
1200 1890 0.243907 TTCGCAGCACTCTGGTAGTC 59.756 55.000 0.00 0.00 40.65 2.59
1203 1893 1.405526 GGAATTCGCAGCACTCTGGTA 60.406 52.381 0.00 0.00 40.65 3.25
1206 1896 2.200067 CTAGGAATTCGCAGCACTCTG 58.800 52.381 0.00 0.00 43.16 3.35
1251 1954 9.369672 GGAGAAATTCCCCGTATATAGATAGAT 57.630 37.037 0.00 0.00 40.37 1.98
1252 1955 8.763984 GGAGAAATTCCCCGTATATAGATAGA 57.236 38.462 0.00 0.00 40.37 1.98
1277 1980 3.855689 AATTTGAAATGGAGAGCACGG 57.144 42.857 0.00 0.00 0.00 4.94
1302 2005 9.654663 AGAATTTTGACGTAAAGCTAGAACTAT 57.345 29.630 0.00 0.00 0.00 2.12
1363 2080 7.090808 GGGGCGATTGGAAGATAATTAATTTC 58.909 38.462 5.91 4.44 0.00 2.17
1385 2175 1.630369 TCTCTGGTCACTCATTTGGGG 59.370 52.381 0.00 0.00 0.00 4.96
1487 2277 4.456280 AATAGATTCGGCGCATGATAGA 57.544 40.909 10.83 0.00 0.00 1.98
1497 2287 4.815269 AGTCATGCTCTAATAGATTCGGC 58.185 43.478 0.00 0.00 0.00 5.54
1535 2325 6.747414 ATTAGGTTGGCTATAGATGACACA 57.253 37.500 3.21 0.00 0.00 3.72
1562 2352 0.898326 TGCAGTGGGTCGCTAAGAGA 60.898 55.000 0.00 0.00 0.00 3.10
1613 2403 6.127225 ACCTTTAGTATTCCTACGAAGTTCCC 60.127 42.308 0.00 0.00 37.78 3.97
1614 2404 6.871844 ACCTTTAGTATTCCTACGAAGTTCC 58.128 40.000 0.00 0.00 37.78 3.62
1658 2448 4.489679 AATGAAAGAGCTTTGGACGAAC 57.510 40.909 0.00 0.00 32.11 3.95
1664 2454 5.964958 TCCTACAAATGAAAGAGCTTTGG 57.035 39.130 0.00 0.00 34.86 3.28
1667 2457 6.248433 TCCATTCCTACAAATGAAAGAGCTT 58.752 36.000 0.00 0.00 38.64 3.74
1793 2583 5.470368 TCTACAAGGAAAGAGAACGATGTG 58.530 41.667 0.00 0.00 0.00 3.21
1802 2592 9.658799 TGTATCTCAATTTCTACAAGGAAAGAG 57.341 33.333 0.00 0.00 38.38 2.85
2004 3057 5.374921 AGAGATCATGCTTCAAAATCCGAT 58.625 37.500 0.00 0.00 0.00 4.18
2021 3074 8.878769 GTTTCATGAACTTCCTAGAAAGAGATC 58.121 37.037 7.89 0.00 35.31 2.75
2095 3148 6.700520 CCGAGGGATTATTAAGTTACAGTGTC 59.299 42.308 0.00 0.00 0.00 3.67
2099 3152 7.046033 ACAACCGAGGGATTATTAAGTTACAG 58.954 38.462 0.00 0.00 0.00 2.74
2107 3160 9.280174 GATGAAATAACAACCGAGGGATTATTA 57.720 33.333 0.00 0.00 0.00 0.98
2136 3189 5.680619 CTTGTTCATGTTAGCCATACCCTA 58.319 41.667 0.00 0.00 30.71 3.53
2148 3201 2.363306 TCAGGTGGCTTGTTCATGTT 57.637 45.000 0.00 0.00 0.00 2.71
2262 3315 4.750098 ACTGCACAACACAATAGTAGTCAC 59.250 41.667 0.00 0.00 0.00 3.67
2337 3390 4.893424 TGCCATAAGAAAATAGTTCCGC 57.107 40.909 0.00 0.00 0.00 5.54
2385 3438 4.216687 GCATAGCGAGATAACTGGTAGAGT 59.783 45.833 0.00 0.00 35.94 3.24
2468 3530 8.137437 CCATGTTTATGATCTTTTGGTGGATAC 58.863 37.037 0.00 0.00 36.36 2.24
2499 3567 7.945033 ATTATGCAACAAACAAGAAAACGAT 57.055 28.000 0.00 0.00 0.00 3.73
2500 3568 7.616673 CAATTATGCAACAAACAAGAAAACGA 58.383 30.769 0.00 0.00 0.00 3.85
2501 3569 7.804392 CAATTATGCAACAAACAAGAAAACG 57.196 32.000 0.00 0.00 0.00 3.60
2522 3590 2.908916 GCCATGTTAGCATTTGGCAAT 58.091 42.857 16.67 0.00 45.44 3.56
2633 3701 4.638421 CAGTATTCTTCGGGCCATTGTTAA 59.362 41.667 4.39 0.00 0.00 2.01
2799 3867 3.932710 TGCACATTGACGTCCTTCTAATC 59.067 43.478 14.12 0.00 0.00 1.75
2851 3919 4.679373 AAGTATCTACAGTCCATGCCTG 57.321 45.455 8.58 8.58 36.01 4.85
2858 3926 7.661968 TGATAGATGCAAAGTATCTACAGTCC 58.338 38.462 6.92 0.00 39.28 3.85
2927 4011 6.875076 TCTCTTGTGGGCTTAATTAGTAGAC 58.125 40.000 0.00 0.00 0.00 2.59
2937 4021 4.724399 TCAACAAATCTCTTGTGGGCTTA 58.276 39.130 0.00 0.00 32.22 3.09
2947 4031 6.530019 AACAAACCAACTCAACAAATCTCT 57.470 33.333 0.00 0.00 0.00 3.10
2987 4071 4.530946 AGTCTGGTCGAAGGAGGAATAAAA 59.469 41.667 0.00 0.00 0.00 1.52
3108 4192 7.590322 GCTAAATGATGTAGCATTGATCACAAG 59.410 37.037 9.71 0.00 42.93 3.16
3261 4345 4.261155 GCTATCAATGGCGTGCAAATTCTA 60.261 41.667 0.00 0.00 0.00 2.10
3262 4346 3.489738 GCTATCAATGGCGTGCAAATTCT 60.490 43.478 0.00 0.00 0.00 2.40
3306 4392 4.082523 CCGATCACTGCACCCCGT 62.083 66.667 0.00 0.00 0.00 5.28
3316 4402 2.630592 GAACGAGGGAGGCCGATCAC 62.631 65.000 0.00 0.00 0.00 3.06
3395 4481 3.686726 GGTATGGACTTTCTCTTGCACAG 59.313 47.826 0.00 0.00 0.00 3.66
3455 4541 7.944061 TGCAAGTAATTGGAGAATTGATATGG 58.056 34.615 4.91 0.00 33.63 2.74
3502 4588 6.218053 GGAGGGGAATACCTATTATATGGGT 58.782 44.000 0.34 0.34 46.69 4.51
3507 4593 6.763097 TCCTGGAGGGGAATACCTATTATA 57.237 41.667 0.00 0.00 42.10 0.98
3526 4612 3.567164 CCCCATTCGATCAAGATTTCCTG 59.433 47.826 0.00 0.00 0.00 3.86
3531 4617 1.134098 ACGCCCCATTCGATCAAGATT 60.134 47.619 0.00 0.00 0.00 2.40
3541 4627 2.548480 GCTTAATGTAGACGCCCCATTC 59.452 50.000 0.00 0.00 31.63 2.67
3546 4632 2.608090 GTGAAGCTTAATGTAGACGCCC 59.392 50.000 0.00 0.00 0.00 6.13
3573 4659 7.523415 ACAAAGAAATTTGTTACCTCCTAGGA 58.477 34.615 11.98 11.98 41.95 2.94
3588 4674 4.347876 AGCCCCTAAAGCAACAAAGAAATT 59.652 37.500 0.00 0.00 0.00 1.82
3594 4680 2.080654 ACAGCCCCTAAAGCAACAAA 57.919 45.000 0.00 0.00 0.00 2.83
3610 4696 7.730364 AGTAGACAAAATTCCAACACTACAG 57.270 36.000 0.00 0.00 33.72 2.74


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

AutoCloner maintained by Alex Coulton.