Multiple sequence alignment - TraesCS4A01G097200

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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 TraesCS4A01G097200 chr4A 100.000 4604 0 0 1 4604 106913315 106908712 0.000000e+00 8503.0
1 TraesCS4A01G097200 chr4A 96.703 91 2 1 1 90 374662846 374662936 2.870000e-32 150.0
2 TraesCS4A01G097200 chr4A 95.556 90 3 1 1 89 374661009 374660920 4.800000e-30 143.0
3 TraesCS4A01G097200 chr4A 94.444 90 4 1 1 89 106914648 106914737 2.230000e-28 137.0
4 TraesCS4A01G097200 chr4A 98.485 66 1 0 1044 1109 106912242 106912177 2.910000e-22 117.0
5 TraesCS4A01G097200 chr4A 98.485 66 1 0 1074 1139 106912272 106912207 2.910000e-22 117.0
6 TraesCS4A01G097200 chr4A 97.222 36 1 0 1044 1079 106912212 106912177 1.380000e-05 62.1
7 TraesCS4A01G097200 chr4A 97.222 36 1 0 1104 1139 106912272 106912237 1.380000e-05 62.1
8 TraesCS4A01G097200 chr4B 94.537 3496 118 42 1146 4604 441670652 441674111 0.000000e+00 5330.0
9 TraesCS4A01G097200 chr4B 81.522 1012 68 35 96 1051 441669664 441670612 0.000000e+00 723.0
10 TraesCS4A01G097200 chr4D 94.357 3385 118 31 1117 4467 358468674 358472019 0.000000e+00 5125.0
11 TraesCS4A01G097200 chr4D 90.206 970 34 20 93 1051 358467730 358468649 0.000000e+00 1208.0
12 TraesCS4A01G097200 chr4D 91.489 141 9 2 4467 4604 358472215 358472355 1.690000e-44 191.0
13 TraesCS4A01G097200 chr4D 97.222 36 1 0 4144 4179 91055487 91055452 1.380000e-05 62.1
14 TraesCS4A01G097200 chr5D 95.604 91 3 1 1 90 36492271 36492181 1.340000e-30 145.0
15 TraesCS4A01G097200 chr5D 94.505 91 4 1 1 90 36536079 36536169 6.210000e-29 139.0
16 TraesCS4A01G097200 chr5D 93.750 48 2 1 4139 4185 255078237 255078190 2.300000e-08 71.3
17 TraesCS4A01G097200 chr5D 97.059 34 1 0 4145 4178 358219717 358219750 1.790000e-04 58.4
18 TraesCS4A01G097200 chr3D 95.604 91 3 1 1 90 467319986 467319896 1.340000e-30 145.0
19 TraesCS4A01G097200 chr6A 94.505 91 4 1 1 90 417300349 417300259 6.210000e-29 139.0
20 TraesCS4A01G097200 chrUn 93.407 91 5 1 1 90 82536946 82537036 2.890000e-27 134.0
21 TraesCS4A01G097200 chr3A 89.524 105 10 1 1 104 676845699 676845803 1.040000e-26 132.0
22 TraesCS4A01G097200 chr6B 97.561 41 0 1 4147 4186 289179293 289179333 8.270000e-08 69.4
23 TraesCS4A01G097200 chr7D 87.500 48 4 2 4007 4052 64443116 64443163 2.000000e-03 54.7


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 TraesCS4A01G097200 chr4A 106908712 106913315 4603 True 1772.240000 8503 98.282800 1 4604 5 chr4A.!!$R2 4603
1 TraesCS4A01G097200 chr4B 441669664 441674111 4447 False 3026.500000 5330 88.029500 96 4604 2 chr4B.!!$F1 4508
2 TraesCS4A01G097200 chr4D 358467730 358472355 4625 False 2174.666667 5125 92.017333 93 4604 3 chr4D.!!$F1 4511

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
861 919 0.466124 CCTCCTCCTCTAAAAGCCCG 59.534 60.0 0.0 0.0 0.00 6.13 F
1289 1354 0.108207 GGATCTCGACCTCCGGTAGA 59.892 60.0 0.0 0.0 35.25 2.59 F
1380 1446 0.181114 TGAAATCTCCGGGGCTCATG 59.819 55.0 0.0 0.0 0.00 3.07 F
1381 1447 0.181350 GAAATCTCCGGGGCTCATGT 59.819 55.0 0.0 0.0 0.00 3.21 F
3106 3178 0.035725 CACAGATGCTGGCTCTTCCA 60.036 55.0 0.0 0.0 44.18 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2431 0.111061 AGGCCTTGACACAATCAGCA 59.889 50.000 0.0 0.0 38.99 4.41 R
2575 2647 0.251634 CTTCCTCCTTGACAGGCTCC 59.748 60.000 0.0 0.0 40.58 4.70 R
2581 2653 0.979665 CTGGCTCTTCCTCCTTGACA 59.020 55.000 0.0 0.0 35.26 3.58 R
3109 3181 1.215382 CTGCATCGAACCGTCTGGA 59.785 57.895 0.0 0.0 39.21 3.86 R
4392 4502 0.606401 ACATCGGGGAGCAACAACTG 60.606 55.000 0.0 0.0 0.00 3.16 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
20 21 3.151542 AGTTGAGGGATTGGATAGGGT 57.848 47.619 0.00 0.00 0.00 4.34
21 22 3.049344 AGTTGAGGGATTGGATAGGGTC 58.951 50.000 0.00 0.00 0.00 4.46
22 23 2.777692 GTTGAGGGATTGGATAGGGTCA 59.222 50.000 0.00 0.00 0.00 4.02
23 24 3.144068 TGAGGGATTGGATAGGGTCAA 57.856 47.619 0.00 0.00 0.00 3.18
24 25 3.469859 TGAGGGATTGGATAGGGTCAAA 58.530 45.455 0.00 0.00 0.00 2.69
25 26 4.054369 TGAGGGATTGGATAGGGTCAAAT 58.946 43.478 0.00 0.00 32.98 2.32
26 27 4.482025 TGAGGGATTGGATAGGGTCAAATT 59.518 41.667 0.00 0.00 30.34 1.82
27 28 5.066913 AGGGATTGGATAGGGTCAAATTC 57.933 43.478 0.00 0.00 30.34 2.17
28 29 4.482025 AGGGATTGGATAGGGTCAAATTCA 59.518 41.667 0.00 0.00 30.34 2.57
29 30 5.043432 AGGGATTGGATAGGGTCAAATTCAA 60.043 40.000 0.00 0.00 30.34 2.69
30 31 5.302823 GGGATTGGATAGGGTCAAATTCAAG 59.697 44.000 0.00 0.00 30.34 3.02
31 32 5.893824 GGATTGGATAGGGTCAAATTCAAGT 59.106 40.000 0.00 0.00 30.34 3.16
32 33 6.381133 GGATTGGATAGGGTCAAATTCAAGTT 59.619 38.462 0.00 0.00 30.34 2.66
33 34 6.588719 TTGGATAGGGTCAAATTCAAGTTG 57.411 37.500 0.00 0.00 0.00 3.16
34 35 5.640147 TGGATAGGGTCAAATTCAAGTTGT 58.360 37.500 2.11 0.00 0.00 3.32
35 36 6.785076 TGGATAGGGTCAAATTCAAGTTGTA 58.215 36.000 2.11 0.00 0.00 2.41
36 37 6.884295 TGGATAGGGTCAAATTCAAGTTGTAG 59.116 38.462 2.11 0.00 0.00 2.74
37 38 6.318900 GGATAGGGTCAAATTCAAGTTGTAGG 59.681 42.308 2.11 0.00 0.00 3.18
38 39 5.319043 AGGGTCAAATTCAAGTTGTAGGA 57.681 39.130 2.11 0.00 0.00 2.94
39 40 5.070685 AGGGTCAAATTCAAGTTGTAGGAC 58.929 41.667 2.11 5.32 0.00 3.85
40 41 5.070685 GGGTCAAATTCAAGTTGTAGGACT 58.929 41.667 2.11 0.00 0.00 3.85
41 42 6.043938 AGGGTCAAATTCAAGTTGTAGGACTA 59.956 38.462 2.11 0.00 0.00 2.59
42 43 6.713450 GGGTCAAATTCAAGTTGTAGGACTAA 59.287 38.462 2.11 0.00 0.00 2.24
43 44 7.229907 GGGTCAAATTCAAGTTGTAGGACTAAA 59.770 37.037 2.11 0.00 0.00 1.85
44 45 8.290325 GGTCAAATTCAAGTTGTAGGACTAAAG 58.710 37.037 2.11 0.00 0.00 1.85
45 46 7.803659 GTCAAATTCAAGTTGTAGGACTAAAGC 59.196 37.037 2.11 0.00 0.00 3.51
46 47 7.500892 TCAAATTCAAGTTGTAGGACTAAAGCA 59.499 33.333 2.11 0.00 0.00 3.91
47 48 8.299570 CAAATTCAAGTTGTAGGACTAAAGCAT 58.700 33.333 2.11 0.00 0.00 3.79
48 49 7.617041 ATTCAAGTTGTAGGACTAAAGCATC 57.383 36.000 2.11 0.00 0.00 3.91
49 50 6.109156 TCAAGTTGTAGGACTAAAGCATCA 57.891 37.500 2.11 0.00 0.00 3.07
50 51 5.932303 TCAAGTTGTAGGACTAAAGCATCAC 59.068 40.000 2.11 0.00 0.00 3.06
51 52 5.483685 AGTTGTAGGACTAAAGCATCACA 57.516 39.130 0.00 0.00 0.00 3.58
52 53 6.054860 AGTTGTAGGACTAAAGCATCACAT 57.945 37.500 0.00 0.00 0.00 3.21
53 54 6.476378 AGTTGTAGGACTAAAGCATCACATT 58.524 36.000 0.00 0.00 0.00 2.71
54 55 6.372659 AGTTGTAGGACTAAAGCATCACATTG 59.627 38.462 0.00 0.00 0.00 2.82
55 56 6.048732 TGTAGGACTAAAGCATCACATTGA 57.951 37.500 0.00 0.00 0.00 2.57
56 57 6.108687 TGTAGGACTAAAGCATCACATTGAG 58.891 40.000 0.00 0.00 0.00 3.02
57 58 5.426689 AGGACTAAAGCATCACATTGAGA 57.573 39.130 0.00 0.00 0.00 3.27
58 59 5.426504 AGGACTAAAGCATCACATTGAGAG 58.573 41.667 0.00 0.00 0.00 3.20
59 60 4.034975 GGACTAAAGCATCACATTGAGAGC 59.965 45.833 0.00 0.00 33.31 4.09
60 61 4.582869 ACTAAAGCATCACATTGAGAGCA 58.417 39.130 6.27 0.00 34.89 4.26
61 62 5.005740 ACTAAAGCATCACATTGAGAGCAA 58.994 37.500 6.27 0.00 34.89 3.91
62 63 4.436242 AAAGCATCACATTGAGAGCAAG 57.564 40.909 6.27 0.00 37.45 4.01
63 64 3.069079 AGCATCACATTGAGAGCAAGT 57.931 42.857 6.27 0.00 37.45 3.16
64 65 3.418995 AGCATCACATTGAGAGCAAGTT 58.581 40.909 6.27 0.00 37.45 2.66
65 66 3.439476 AGCATCACATTGAGAGCAAGTTC 59.561 43.478 6.27 0.00 37.45 3.01
66 67 3.439476 GCATCACATTGAGAGCAAGTTCT 59.561 43.478 0.00 0.00 37.45 3.01
67 68 4.633126 GCATCACATTGAGAGCAAGTTCTA 59.367 41.667 0.00 0.00 37.45 2.10
68 69 5.220624 GCATCACATTGAGAGCAAGTTCTAG 60.221 44.000 0.00 0.00 37.45 2.43
69 70 4.825422 TCACATTGAGAGCAAGTTCTAGG 58.175 43.478 0.00 0.00 37.45 3.02
70 71 4.528206 TCACATTGAGAGCAAGTTCTAGGA 59.472 41.667 0.00 0.00 37.45 2.94
71 72 4.629200 CACATTGAGAGCAAGTTCTAGGAC 59.371 45.833 0.00 0.00 37.45 3.85
72 73 4.530161 ACATTGAGAGCAAGTTCTAGGACT 59.470 41.667 0.00 0.00 37.45 3.85
73 74 4.792521 TTGAGAGCAAGTTCTAGGACTC 57.207 45.455 3.51 0.00 0.00 3.36
74 75 3.093057 TGAGAGCAAGTTCTAGGACTCC 58.907 50.000 3.51 0.00 0.00 3.85
75 76 3.245443 TGAGAGCAAGTTCTAGGACTCCT 60.245 47.826 3.51 4.06 37.71 3.69
76 77 3.096092 AGAGCAAGTTCTAGGACTCCTG 58.904 50.000 3.51 0.97 34.61 3.86
77 78 3.093057 GAGCAAGTTCTAGGACTCCTGA 58.907 50.000 3.51 0.84 34.61 3.86
78 79 3.704061 GAGCAAGTTCTAGGACTCCTGAT 59.296 47.826 3.51 0.00 34.61 2.90
79 80 3.450457 AGCAAGTTCTAGGACTCCTGATG 59.550 47.826 3.51 0.00 34.61 3.07
80 81 3.791245 CAAGTTCTAGGACTCCTGATGC 58.209 50.000 3.51 0.00 34.61 3.91
81 82 3.396685 AGTTCTAGGACTCCTGATGCT 57.603 47.619 7.98 0.00 34.61 3.79
82 83 3.718723 AGTTCTAGGACTCCTGATGCTT 58.281 45.455 7.98 0.00 34.61 3.91
83 84 4.100373 AGTTCTAGGACTCCTGATGCTTT 58.900 43.478 7.98 0.00 34.61 3.51
84 85 4.534103 AGTTCTAGGACTCCTGATGCTTTT 59.466 41.667 7.98 0.00 34.61 2.27
85 86 5.721960 AGTTCTAGGACTCCTGATGCTTTTA 59.278 40.000 7.98 0.00 34.61 1.52
86 87 6.213600 AGTTCTAGGACTCCTGATGCTTTTAA 59.786 38.462 7.98 0.00 34.61 1.52
87 88 5.978814 TCTAGGACTCCTGATGCTTTTAAC 58.021 41.667 7.98 0.00 34.61 2.01
88 89 4.917906 AGGACTCCTGATGCTTTTAACT 57.082 40.909 0.00 0.00 29.57 2.24
89 90 4.837972 AGGACTCCTGATGCTTTTAACTC 58.162 43.478 0.00 0.00 29.57 3.01
90 91 3.619038 GGACTCCTGATGCTTTTAACTCG 59.381 47.826 0.00 0.00 0.00 4.18
91 92 3.600388 ACTCCTGATGCTTTTAACTCGG 58.400 45.455 0.00 0.00 0.00 4.63
208 215 4.913924 CGAAAGGAAAGAAATGCTTGACAG 59.086 41.667 0.00 0.00 36.80 3.51
224 231 1.933853 GACAGCGAAAACAGTCACAGT 59.066 47.619 0.00 0.00 0.00 3.55
258 265 1.272769 GGAACGAACCAGCTACTGACT 59.727 52.381 0.00 0.00 32.44 3.41
259 266 2.597520 GAACGAACCAGCTACTGACTC 58.402 52.381 0.00 0.00 32.44 3.36
270 277 4.624882 CAGCTACTGACTCTGTTCATTCAC 59.375 45.833 0.00 0.00 32.44 3.18
285 292 4.326826 TCATTCACAAATGGACAGTCTCC 58.673 43.478 0.00 0.00 42.19 3.71
317 324 2.292794 ATCAATGGTCCGTCGGTCCG 62.293 60.000 20.45 4.39 33.66 4.79
330 337 1.519455 GGTCCGAAGCACCAGATCG 60.519 63.158 0.00 0.00 38.97 3.69
488 501 0.521291 ACCGTTTTGCATGATCACCG 59.479 50.000 0.00 0.00 0.00 4.94
572 590 1.244816 GGCGCAAGGAGGTAAAAAGT 58.755 50.000 10.83 0.00 38.28 2.66
574 592 2.418976 GGCGCAAGGAGGTAAAAAGTAG 59.581 50.000 10.83 0.00 38.28 2.57
680 725 2.873288 CTCGCTGCTTTCCTTGCC 59.127 61.111 0.00 0.00 0.00 4.52
779 837 1.077169 ACACCATTTCTTCCCCCTTCC 59.923 52.381 0.00 0.00 0.00 3.46
823 881 4.162690 CCACCTCAGCCGGCCTAC 62.163 72.222 26.15 0.00 0.00 3.18
824 882 4.162690 CACCTCAGCCGGCCTACC 62.163 72.222 26.15 0.00 0.00 3.18
827 885 3.541713 CTCAGCCGGCCTACCCTC 61.542 72.222 26.15 0.00 0.00 4.30
861 919 0.466124 CCTCCTCCTCTAAAAGCCCG 59.534 60.000 0.00 0.00 0.00 6.13
905 963 1.152839 GAGACGGGGGAGAGAGAGG 60.153 68.421 0.00 0.00 0.00 3.69
906 964 2.123640 GACGGGGGAGAGAGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
907 965 2.617538 ACGGGGGAGAGAGAGGGA 60.618 66.667 0.00 0.00 0.00 4.20
908 966 2.197324 CGGGGGAGAGAGAGGGAG 59.803 72.222 0.00 0.00 0.00 4.30
912 970 1.541672 GGGAGAGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
1027 1087 1.208776 AGGTATTCCCTTTTCCGTCCG 59.791 52.381 0.00 0.00 42.73 4.79
1051 1111 4.598894 CTCCCTGGATCTGCGCCG 62.599 72.222 4.18 0.00 0.00 6.46
1054 1114 4.598894 CCTGGATCTGCGCCGGAG 62.599 72.222 5.05 1.55 33.45 4.63
1067 1127 4.285851 CGGAGGTGGCTTCTGTTC 57.714 61.111 0.00 0.00 0.00 3.18
1068 1128 1.376037 CGGAGGTGGCTTCTGTTCC 60.376 63.158 0.00 0.00 0.00 3.62
1069 1129 1.831652 CGGAGGTGGCTTCTGTTCCT 61.832 60.000 0.00 0.00 0.00 3.36
1070 1130 1.276622 GGAGGTGGCTTCTGTTCCTA 58.723 55.000 0.00 0.00 0.00 2.94
1071 1131 1.208293 GGAGGTGGCTTCTGTTCCTAG 59.792 57.143 0.00 0.00 0.00 3.02
1072 1132 0.615850 AGGTGGCTTCTGTTCCTAGC 59.384 55.000 0.00 0.00 0.00 3.42
1073 1133 0.615850 GGTGGCTTCTGTTCCTAGCT 59.384 55.000 0.00 0.00 35.30 3.32
1074 1134 1.406205 GGTGGCTTCTGTTCCTAGCTC 60.406 57.143 0.00 0.00 35.30 4.09
1075 1135 1.552792 GTGGCTTCTGTTCCTAGCTCT 59.447 52.381 0.00 0.00 35.30 4.09
1076 1136 1.552337 TGGCTTCTGTTCCTAGCTCTG 59.448 52.381 0.00 0.00 35.30 3.35
1077 1137 1.650825 GCTTCTGTTCCTAGCTCTGC 58.349 55.000 0.00 0.00 32.26 4.26
1078 1138 1.919918 CTTCTGTTCCTAGCTCTGCG 58.080 55.000 0.00 0.00 0.00 5.18
1079 1139 0.108615 TTCTGTTCCTAGCTCTGCGC 60.109 55.000 0.00 0.00 39.57 6.09
1080 1140 1.520342 CTGTTCCTAGCTCTGCGCC 60.520 63.158 4.18 0.00 40.39 6.53
1081 1141 2.583593 GTTCCTAGCTCTGCGCCG 60.584 66.667 4.18 0.00 40.39 6.46
1082 1142 3.838271 TTCCTAGCTCTGCGCCGG 61.838 66.667 4.18 0.00 40.39 6.13
1083 1143 4.815108 TCCTAGCTCTGCGCCGGA 62.815 66.667 5.05 1.93 40.39 5.14
1084 1144 4.277593 CCTAGCTCTGCGCCGGAG 62.278 72.222 19.01 19.01 40.39 4.63
1097 1157 4.285851 CGGAGGTGGCTTCTGTTC 57.714 61.111 0.00 0.00 0.00 3.18
1098 1158 1.376037 CGGAGGTGGCTTCTGTTCC 60.376 63.158 0.00 0.00 0.00 3.62
1099 1159 1.831652 CGGAGGTGGCTTCTGTTCCT 61.832 60.000 0.00 0.00 0.00 3.36
1100 1160 1.276622 GGAGGTGGCTTCTGTTCCTA 58.723 55.000 0.00 0.00 0.00 2.94
1101 1161 1.066071 GGAGGTGGCTTCTGTTCCTAC 60.066 57.143 0.00 0.00 0.00 3.18
1102 1162 0.984995 AGGTGGCTTCTGTTCCTACC 59.015 55.000 0.00 0.00 0.00 3.18
1103 1163 0.984995 GGTGGCTTCTGTTCCTACCT 59.015 55.000 0.00 0.00 0.00 3.08
1104 1164 1.066071 GGTGGCTTCTGTTCCTACCTC 60.066 57.143 0.00 0.00 0.00 3.85
1105 1165 1.903183 GTGGCTTCTGTTCCTACCTCT 59.097 52.381 0.00 0.00 0.00 3.69
1106 1166 1.902508 TGGCTTCTGTTCCTACCTCTG 59.097 52.381 0.00 0.00 0.00 3.35
1107 1167 1.406205 GGCTTCTGTTCCTACCTCTGC 60.406 57.143 0.00 0.00 0.00 4.26
1131 1196 1.066071 GGAGGTGGCTTCTGTTCCTAC 60.066 57.143 0.00 0.00 0.00 3.18
1135 1200 1.903183 GTGGCTTCTGTTCCTACCTCT 59.097 52.381 0.00 0.00 0.00 3.69
1178 1243 4.064388 GGAGTAGGAGTAGCTACCTAACG 58.936 52.174 20.31 0.00 39.93 3.18
1264 1329 1.884926 GCAAATCTCGCCTCTCGGG 60.885 63.158 0.00 0.00 40.87 5.14
1287 1352 1.150081 GGGATCTCGACCTCCGGTA 59.850 63.158 0.00 0.00 35.25 4.02
1288 1353 0.890090 GGGATCTCGACCTCCGGTAG 60.890 65.000 0.00 0.00 35.25 3.18
1289 1354 0.108207 GGATCTCGACCTCCGGTAGA 59.892 60.000 0.00 0.00 35.25 2.59
1291 1356 4.959399 CTCGACCTCCGGTAGAGT 57.041 61.111 13.06 0.00 45.84 3.24
1372 1438 2.357009 CTGGCTTTGATGAAATCTCCGG 59.643 50.000 0.00 0.00 45.81 5.14
1374 1440 1.678101 GCTTTGATGAAATCTCCGGGG 59.322 52.381 0.00 0.00 45.81 5.73
1380 1446 0.181114 TGAAATCTCCGGGGCTCATG 59.819 55.000 0.00 0.00 0.00 3.07
1381 1447 0.181350 GAAATCTCCGGGGCTCATGT 59.819 55.000 0.00 0.00 0.00 3.21
1383 1449 1.051812 AATCTCCGGGGCTCATGTAG 58.948 55.000 0.00 0.00 0.00 2.74
1389 1455 0.811616 CGGGGCTCATGTAGTGCTTC 60.812 60.000 0.00 0.00 36.95 3.86
1447 1513 3.670377 GCCGCTGGTGGTTGGTTC 61.670 66.667 2.05 0.00 0.00 3.62
1453 1519 0.750182 CTGGTGGTTGGTTCGTTGGT 60.750 55.000 0.00 0.00 0.00 3.67
1861 1933 2.126031 GACTTCCGTGACGAGGCC 60.126 66.667 6.54 0.00 0.00 5.19
2062 2134 1.000019 CTCGTACACCTCCCCTCCA 60.000 63.158 0.00 0.00 0.00 3.86
2112 2184 2.747460 TGACAGCAGGAATGGCGC 60.747 61.111 0.00 0.00 36.08 6.53
2113 2185 3.512516 GACAGCAGGAATGGCGCC 61.513 66.667 22.73 22.73 36.08 6.53
2134 2206 1.649321 ACTCTGATGACAAGAGGCCA 58.351 50.000 5.01 0.00 34.25 5.36
2137 2209 0.617413 CTGATGACAAGAGGCCACCT 59.383 55.000 5.01 0.00 36.03 4.00
2359 2431 5.359194 ACAGGTTCTTCGACATGGAATAT 57.641 39.130 0.00 0.00 35.75 1.28
2380 2452 1.615392 GCTGATTGTGTCAAGGCCTTT 59.385 47.619 17.61 0.00 36.14 3.11
2513 2585 6.094061 GTCACTGATAAGTTACTGGAGACAC 58.906 44.000 0.00 0.00 35.60 3.67
2562 2634 3.579302 CCCCAAGAGCCCACCACA 61.579 66.667 0.00 0.00 0.00 4.17
2575 2647 4.463879 CCACAGGAGCCTGAGCCG 62.464 72.222 22.62 7.99 46.30 5.52
2791 2863 0.911525 CTCTGGCCCTCTTCCAAGGA 60.912 60.000 0.00 0.00 38.87 3.36
3106 3178 0.035725 CACAGATGCTGGCTCTTCCA 60.036 55.000 0.00 0.00 44.18 3.53
3139 3211 0.948623 CGATGCAGAACGTTGGTGGA 60.949 55.000 5.00 4.52 0.00 4.02
3148 3220 2.474410 ACGTTGGTGGAGATCCTTTC 57.526 50.000 0.00 0.00 36.82 2.62
3193 3265 2.563261 CATCCTATGTGCAGATGGCT 57.437 50.000 6.60 0.00 45.15 4.75
3259 3331 1.078426 GCAGCAGTACCAACGGGAT 60.078 57.895 0.00 0.00 38.05 3.85
3449 3521 7.306749 GCTGTGAATTTTGTTCTGTATTTGTGG 60.307 37.037 0.00 0.00 0.00 4.17
3608 3682 7.658982 TGAATACATAATCTGAGCTGATGTTCC 59.341 37.037 0.00 0.00 33.05 3.62
3619 3693 5.163405 TGAGCTGATGTTCCTTCATAGTACC 60.163 44.000 0.00 0.00 0.00 3.34
3652 3726 0.657840 GACCTGTGCATATTGTCGGC 59.342 55.000 0.00 0.00 0.00 5.54
3665 3739 4.752879 TCGGCCGCTTGGTGCTAC 62.753 66.667 23.51 0.00 40.11 3.58
3666 3740 4.760047 CGGCCGCTTGGTGCTACT 62.760 66.667 14.67 0.00 40.11 2.57
3667 3741 2.359975 GGCCGCTTGGTGCTACTT 60.360 61.111 0.00 0.00 40.11 2.24
3668 3742 2.399356 GGCCGCTTGGTGCTACTTC 61.399 63.158 0.00 0.00 40.11 3.01
3669 3743 2.399356 GCCGCTTGGTGCTACTTCC 61.399 63.158 0.00 0.00 40.11 3.46
3692 3766 4.186159 CCCGGTTGTTGTTAGTATACCTG 58.814 47.826 0.00 0.00 0.00 4.00
3800 3877 3.565902 GCTGGAGAAGTTTGTTGCTAGTT 59.434 43.478 0.00 0.00 0.00 2.24
3903 3980 1.691196 TGGAGCAAAGTTCCCTTGTG 58.309 50.000 0.00 0.00 33.62 3.33
3924 4006 7.615582 TGTGAAAATAGAGCTCGAATGATTT 57.384 32.000 8.37 7.73 0.00 2.17
3954 4036 5.196341 TGCTCGTCGAAGTTATGGAATAT 57.804 39.130 0.00 0.00 0.00 1.28
3964 4046 6.293081 CGAAGTTATGGAATATCTGTTGCTGG 60.293 42.308 0.00 0.00 29.66 4.85
3968 4050 8.600665 AGTTATGGAATATCTGTTGCTGGAAGC 61.601 40.741 0.00 0.00 43.02 3.86
3980 4062 2.629336 CTGGAAGCCTGGAACCTATC 57.371 55.000 0.00 0.00 0.00 2.08
3981 4063 1.839994 CTGGAAGCCTGGAACCTATCA 59.160 52.381 0.00 0.00 0.00 2.15
3982 4064 2.239654 CTGGAAGCCTGGAACCTATCAA 59.760 50.000 0.00 0.00 0.00 2.57
3995 4077 7.168219 TGGAACCTATCAACTATCATAATGCC 58.832 38.462 0.00 0.00 0.00 4.40
3996 4078 7.168219 GGAACCTATCAACTATCATAATGCCA 58.832 38.462 0.00 0.00 0.00 4.92
4038 4127 5.840243 TGCATGATTCTCAAAATGTAGGG 57.160 39.130 0.00 0.00 0.00 3.53
4086 4178 2.821969 GTGACATTGCCCACTTGAATCT 59.178 45.455 3.40 0.00 0.00 2.40
4087 4179 3.256631 GTGACATTGCCCACTTGAATCTT 59.743 43.478 3.40 0.00 0.00 2.40
4091 4183 4.702131 ACATTGCCCACTTGAATCTTACTC 59.298 41.667 0.00 0.00 0.00 2.59
4096 4188 3.118223 CCCACTTGAATCTTACTCCCTCC 60.118 52.174 0.00 0.00 0.00 4.30
4105 4197 5.896073 ATCTTACTCCCTCCGATTCAAAT 57.104 39.130 0.00 0.00 0.00 2.32
4181 4275 4.062293 TGCGATACTTATTTTGGATCGGG 58.938 43.478 9.86 0.00 39.74 5.14
4207 4313 4.637534 AGCATAGAATGGTTGATGTCACAC 59.362 41.667 0.00 0.00 37.84 3.82
4208 4314 4.395854 GCATAGAATGGTTGATGTCACACA 59.604 41.667 0.00 0.00 0.00 3.72
4209 4315 5.674569 GCATAGAATGGTTGATGTCACACAC 60.675 44.000 0.00 0.00 0.00 3.82
4211 4317 3.565482 AGAATGGTTGATGTCACACACAC 59.435 43.478 0.00 0.00 38.04 3.82
4242 4348 9.642343 AAAAAGAGATTGTAAAAAGAGGGTACT 57.358 29.630 0.00 0.00 0.00 2.73
4243 4349 8.622948 AAAGAGATTGTAAAAAGAGGGTACTG 57.377 34.615 0.00 0.00 0.00 2.74
4262 4370 4.521146 ACTGGATGCTAGATTTCCAACAG 58.479 43.478 9.26 0.00 38.99 3.16
4265 4373 3.563390 GGATGCTAGATTTCCAACAGAGC 59.437 47.826 0.00 0.00 0.00 4.09
4271 4379 3.326747 AGATTTCCAACAGAGCGTACAC 58.673 45.455 0.00 0.00 0.00 2.90
4282 4391 3.553511 CAGAGCGTACACATGATTCCTTC 59.446 47.826 0.00 0.00 0.00 3.46
4328 4437 4.155826 GTCCGATGAATCAAATGACCAACA 59.844 41.667 0.00 0.00 0.00 3.33
4337 4446 8.469200 TGAATCAAATGACCAACATAGAATTCC 58.531 33.333 0.65 0.00 38.38 3.01
4341 4450 9.527157 TCAAATGACCAACATAGAATTCCTTTA 57.473 29.630 0.65 0.00 38.38 1.85
4392 4502 2.558380 AATCAAAGGAGCCCGCCCTC 62.558 60.000 0.00 0.00 32.57 4.30
4404 4514 2.328099 CGCCCTCAGTTGTTGCTCC 61.328 63.158 0.00 0.00 0.00 4.70
4421 4531 3.321111 TGCTCCCCGATGTATAAGTTCTC 59.679 47.826 0.00 0.00 0.00 2.87
4431 4541 9.698309 CCGATGTATAAGTTCTCAATATCAACT 57.302 33.333 0.00 0.00 31.48 3.16
4454 4564 2.813754 CGTCAACAGGATGAAACATGGT 59.186 45.455 0.00 0.00 39.69 3.55
4591 4900 1.387084 GTCGTGCGTGATTGACTCTTC 59.613 52.381 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.777692 TGACCCTATCCAATCCCTCAAC 59.222 50.000 0.00 0.00 0.00 3.18
2 3 3.144068 TGACCCTATCCAATCCCTCAA 57.856 47.619 0.00 0.00 0.00 3.02
3 4 2.887454 TGACCCTATCCAATCCCTCA 57.113 50.000 0.00 0.00 0.00 3.86
4 5 4.731313 ATTTGACCCTATCCAATCCCTC 57.269 45.455 0.00 0.00 0.00 4.30
5 6 4.482025 TGAATTTGACCCTATCCAATCCCT 59.518 41.667 0.00 0.00 0.00 4.20
6 7 4.803452 TGAATTTGACCCTATCCAATCCC 58.197 43.478 0.00 0.00 0.00 3.85
7 8 5.893824 ACTTGAATTTGACCCTATCCAATCC 59.106 40.000 0.00 0.00 0.00 3.01
8 9 7.093771 ACAACTTGAATTTGACCCTATCCAATC 60.094 37.037 2.14 0.00 0.00 2.67
9 10 6.725834 ACAACTTGAATTTGACCCTATCCAAT 59.274 34.615 2.14 0.00 0.00 3.16
10 11 6.074648 ACAACTTGAATTTGACCCTATCCAA 58.925 36.000 2.14 0.00 0.00 3.53
11 12 5.640147 ACAACTTGAATTTGACCCTATCCA 58.360 37.500 2.14 0.00 0.00 3.41
12 13 6.318900 CCTACAACTTGAATTTGACCCTATCC 59.681 42.308 2.14 0.00 0.00 2.59
13 14 7.065923 GTCCTACAACTTGAATTTGACCCTATC 59.934 40.741 2.14 0.00 0.00 2.08
14 15 6.884836 GTCCTACAACTTGAATTTGACCCTAT 59.115 38.462 2.14 0.00 0.00 2.57
15 16 6.043938 AGTCCTACAACTTGAATTTGACCCTA 59.956 38.462 2.14 0.00 0.00 3.53
16 17 5.070685 GTCCTACAACTTGAATTTGACCCT 58.929 41.667 2.14 0.00 0.00 4.34
17 18 5.070685 AGTCCTACAACTTGAATTTGACCC 58.929 41.667 2.14 0.00 0.00 4.46
18 19 7.739498 TTAGTCCTACAACTTGAATTTGACC 57.261 36.000 2.14 0.00 0.00 4.02
19 20 7.803659 GCTTTAGTCCTACAACTTGAATTTGAC 59.196 37.037 2.14 0.00 0.00 3.18
20 21 7.500892 TGCTTTAGTCCTACAACTTGAATTTGA 59.499 33.333 2.14 0.00 0.00 2.69
21 22 7.648142 TGCTTTAGTCCTACAACTTGAATTTG 58.352 34.615 0.00 0.00 0.00 2.32
22 23 7.817418 TGCTTTAGTCCTACAACTTGAATTT 57.183 32.000 0.00 0.00 0.00 1.82
23 24 7.665559 TGATGCTTTAGTCCTACAACTTGAATT 59.334 33.333 0.00 0.00 0.00 2.17
24 25 7.119846 GTGATGCTTTAGTCCTACAACTTGAAT 59.880 37.037 0.00 0.00 0.00 2.57
25 26 6.426937 GTGATGCTTTAGTCCTACAACTTGAA 59.573 38.462 0.00 0.00 0.00 2.69
26 27 5.932303 GTGATGCTTTAGTCCTACAACTTGA 59.068 40.000 0.00 0.00 0.00 3.02
27 28 5.700832 TGTGATGCTTTAGTCCTACAACTTG 59.299 40.000 0.00 0.00 0.00 3.16
28 29 5.865085 TGTGATGCTTTAGTCCTACAACTT 58.135 37.500 0.00 0.00 0.00 2.66
29 30 5.483685 TGTGATGCTTTAGTCCTACAACT 57.516 39.130 0.00 0.00 0.00 3.16
30 31 6.371548 TCAATGTGATGCTTTAGTCCTACAAC 59.628 38.462 0.00 0.00 0.00 3.32
31 32 6.472016 TCAATGTGATGCTTTAGTCCTACAA 58.528 36.000 0.00 0.00 0.00 2.41
32 33 6.048732 TCAATGTGATGCTTTAGTCCTACA 57.951 37.500 0.00 0.00 0.00 2.74
33 34 6.341316 TCTCAATGTGATGCTTTAGTCCTAC 58.659 40.000 0.00 0.00 0.00 3.18
34 35 6.544928 TCTCAATGTGATGCTTTAGTCCTA 57.455 37.500 0.00 0.00 0.00 2.94
35 36 5.426504 CTCTCAATGTGATGCTTTAGTCCT 58.573 41.667 0.00 0.00 0.00 3.85
36 37 4.034975 GCTCTCAATGTGATGCTTTAGTCC 59.965 45.833 0.00 0.00 0.00 3.85
37 38 4.633126 TGCTCTCAATGTGATGCTTTAGTC 59.367 41.667 7.73 0.00 30.64 2.59
38 39 4.582869 TGCTCTCAATGTGATGCTTTAGT 58.417 39.130 7.73 0.00 30.64 2.24
39 40 5.123502 ACTTGCTCTCAATGTGATGCTTTAG 59.876 40.000 7.73 0.00 30.64 1.85
40 41 5.005740 ACTTGCTCTCAATGTGATGCTTTA 58.994 37.500 7.73 0.00 30.64 1.85
41 42 3.825014 ACTTGCTCTCAATGTGATGCTTT 59.175 39.130 7.73 0.00 30.64 3.51
42 43 3.418995 ACTTGCTCTCAATGTGATGCTT 58.581 40.909 7.73 0.00 30.64 3.91
43 44 3.069079 ACTTGCTCTCAATGTGATGCT 57.931 42.857 7.73 0.00 30.64 3.79
44 45 3.439476 AGAACTTGCTCTCAATGTGATGC 59.561 43.478 0.00 0.00 0.00 3.91
45 46 5.293814 CCTAGAACTTGCTCTCAATGTGATG 59.706 44.000 0.00 0.00 0.00 3.07
46 47 5.188555 TCCTAGAACTTGCTCTCAATGTGAT 59.811 40.000 0.00 0.00 0.00 3.06
47 48 4.528206 TCCTAGAACTTGCTCTCAATGTGA 59.472 41.667 0.00 0.00 0.00 3.58
48 49 4.629200 GTCCTAGAACTTGCTCTCAATGTG 59.371 45.833 0.00 0.00 0.00 3.21
49 50 4.530161 AGTCCTAGAACTTGCTCTCAATGT 59.470 41.667 0.00 0.00 0.00 2.71
50 51 5.083533 AGTCCTAGAACTTGCTCTCAATG 57.916 43.478 0.00 0.00 0.00 2.82
51 52 4.161377 GGAGTCCTAGAACTTGCTCTCAAT 59.839 45.833 0.41 0.00 0.00 2.57
52 53 3.511934 GGAGTCCTAGAACTTGCTCTCAA 59.488 47.826 0.41 0.00 0.00 3.02
53 54 3.093057 GGAGTCCTAGAACTTGCTCTCA 58.907 50.000 0.41 0.00 0.00 3.27
54 55 3.130340 CAGGAGTCCTAGAACTTGCTCTC 59.870 52.174 12.53 0.00 29.64 3.20
55 56 3.096092 CAGGAGTCCTAGAACTTGCTCT 58.904 50.000 12.53 0.00 29.64 4.09
56 57 3.093057 TCAGGAGTCCTAGAACTTGCTC 58.907 50.000 12.53 0.00 29.64 4.26
57 58 3.176924 TCAGGAGTCCTAGAACTTGCT 57.823 47.619 12.53 0.00 29.64 3.91
58 59 3.791245 CATCAGGAGTCCTAGAACTTGC 58.209 50.000 12.53 0.00 29.64 4.01
59 60 3.450457 AGCATCAGGAGTCCTAGAACTTG 59.550 47.826 12.53 8.48 29.64 3.16
60 61 3.718723 AGCATCAGGAGTCCTAGAACTT 58.281 45.455 12.53 0.00 29.64 2.66
61 62 3.396685 AGCATCAGGAGTCCTAGAACT 57.603 47.619 12.53 10.60 29.64 3.01
62 63 4.479786 AAAGCATCAGGAGTCCTAGAAC 57.520 45.455 12.53 8.69 29.64 3.01
63 64 6.213600 AGTTAAAAGCATCAGGAGTCCTAGAA 59.786 38.462 12.53 0.51 29.64 2.10
64 65 5.721960 AGTTAAAAGCATCAGGAGTCCTAGA 59.278 40.000 12.53 12.23 29.64 2.43
65 66 5.983540 AGTTAAAAGCATCAGGAGTCCTAG 58.016 41.667 12.53 6.83 29.64 3.02
66 67 5.394224 CGAGTTAAAAGCATCAGGAGTCCTA 60.394 44.000 12.53 0.85 29.64 2.94
67 68 4.621747 CGAGTTAAAAGCATCAGGAGTCCT 60.622 45.833 5.62 5.62 0.00 3.85
68 69 3.619038 CGAGTTAAAAGCATCAGGAGTCC 59.381 47.826 0.00 0.00 0.00 3.85
69 70 3.619038 CCGAGTTAAAAGCATCAGGAGTC 59.381 47.826 0.00 0.00 0.00 3.36
70 71 3.260884 TCCGAGTTAAAAGCATCAGGAGT 59.739 43.478 0.00 0.00 0.00 3.85
71 72 3.861840 TCCGAGTTAAAAGCATCAGGAG 58.138 45.455 0.00 0.00 0.00 3.69
72 73 3.973206 TCCGAGTTAAAAGCATCAGGA 57.027 42.857 0.00 0.00 0.00 3.86
73 74 5.371115 TTTTCCGAGTTAAAAGCATCAGG 57.629 39.130 0.00 0.00 0.00 3.86
117 118 1.093496 TGCATGCCGCTGATGAGAAG 61.093 55.000 16.68 0.00 43.06 2.85
178 184 1.837538 TTCTTTCCTTTCGCGCGGTG 61.838 55.000 31.69 19.15 0.00 4.94
182 188 0.984829 GCATTTCTTTCCTTTCGCGC 59.015 50.000 0.00 0.00 0.00 6.86
208 215 1.261619 CAGGACTGTGACTGTTTTCGC 59.738 52.381 0.00 0.00 0.00 4.70
224 231 0.250727 CGTTCCTCTTTTGCCCAGGA 60.251 55.000 0.00 0.00 34.31 3.86
306 313 4.047059 GTGCTTCGGACCGACGGA 62.047 66.667 23.38 14.04 34.89 4.69
317 324 0.530870 GTAGGGCGATCTGGTGCTTC 60.531 60.000 0.00 0.00 0.00 3.86
330 337 4.814294 CGCTGTCGTGGGTAGGGC 62.814 72.222 0.00 0.00 0.00 5.19
572 590 2.519302 GCGCCTACCCCCGTACTA 60.519 66.667 0.00 0.00 0.00 1.82
841 899 0.181587 GGGCTTTTAGAGGAGGAGGC 59.818 60.000 0.00 0.00 0.00 4.70
861 919 4.735358 GCCGGGGGAGTTTGACCC 62.735 72.222 2.18 0.00 46.59 4.46
905 963 1.152546 GAGAGCCTCTCCCCTCTCC 60.153 68.421 10.79 0.00 45.24 3.71
906 964 1.528309 CGAGAGCCTCTCCCCTCTC 60.528 68.421 15.93 7.43 46.67 3.20
907 965 2.600731 CGAGAGCCTCTCCCCTCT 59.399 66.667 15.93 0.00 40.34 3.69
908 966 2.366153 ATCCGAGAGCCTCTCCCCTC 62.366 65.000 15.93 0.00 40.34 4.30
912 970 2.265182 CGGATCCGAGAGCCTCTCC 61.265 68.421 30.62 1.54 40.34 3.71
985 1043 3.838271 GACAGGCGCAGATCCGGA 61.838 66.667 6.61 6.61 0.00 5.14
1027 1087 0.602562 CAGATCCAGGGAGCGAGATC 59.397 60.000 0.00 0.00 35.44 2.75
1051 1111 1.208293 CTAGGAACAGAAGCCACCTCC 59.792 57.143 0.00 0.00 32.90 4.30
1052 1112 1.406205 GCTAGGAACAGAAGCCACCTC 60.406 57.143 0.00 0.00 32.90 3.85
1053 1113 0.615850 GCTAGGAACAGAAGCCACCT 59.384 55.000 0.00 0.00 35.11 4.00
1054 1114 0.615850 AGCTAGGAACAGAAGCCACC 59.384 55.000 0.00 0.00 36.92 4.61
1055 1115 1.552792 AGAGCTAGGAACAGAAGCCAC 59.447 52.381 0.00 0.00 36.92 5.01
1056 1116 1.552337 CAGAGCTAGGAACAGAAGCCA 59.448 52.381 0.00 0.00 36.92 4.75
1057 1117 1.742071 GCAGAGCTAGGAACAGAAGCC 60.742 57.143 0.00 0.00 36.92 4.35
1058 1118 1.650825 GCAGAGCTAGGAACAGAAGC 58.349 55.000 0.00 0.00 36.48 3.86
1059 1119 1.919918 CGCAGAGCTAGGAACAGAAG 58.080 55.000 0.00 0.00 0.00 2.85
1060 1120 0.108615 GCGCAGAGCTAGGAACAGAA 60.109 55.000 0.30 0.00 44.04 3.02
1061 1121 1.513158 GCGCAGAGCTAGGAACAGA 59.487 57.895 0.30 0.00 44.04 3.41
1062 1122 4.100981 GCGCAGAGCTAGGAACAG 57.899 61.111 0.30 0.00 44.04 3.16
1079 1139 1.376037 GAACAGAAGCCACCTCCGG 60.376 63.158 0.00 0.00 0.00 5.14
1080 1140 1.376037 GGAACAGAAGCCACCTCCG 60.376 63.158 0.00 0.00 0.00 4.63
1081 1141 1.066071 GTAGGAACAGAAGCCACCTCC 60.066 57.143 0.00 0.00 32.90 4.30
1082 1142 1.066071 GGTAGGAACAGAAGCCACCTC 60.066 57.143 0.00 0.00 32.90 3.85
1083 1143 0.984995 GGTAGGAACAGAAGCCACCT 59.015 55.000 0.00 0.00 35.11 4.00
1084 1144 0.984995 AGGTAGGAACAGAAGCCACC 59.015 55.000 0.00 0.00 0.00 4.61
1085 1145 1.903183 AGAGGTAGGAACAGAAGCCAC 59.097 52.381 0.00 0.00 0.00 5.01
1086 1146 1.902508 CAGAGGTAGGAACAGAAGCCA 59.097 52.381 0.00 0.00 0.00 4.75
1087 1147 1.406205 GCAGAGGTAGGAACAGAAGCC 60.406 57.143 0.00 0.00 0.00 4.35
1088 1148 1.737363 CGCAGAGGTAGGAACAGAAGC 60.737 57.143 0.00 0.00 0.00 3.86
1089 1149 1.737363 GCGCAGAGGTAGGAACAGAAG 60.737 57.143 0.30 0.00 0.00 2.85
1090 1150 0.246635 GCGCAGAGGTAGGAACAGAA 59.753 55.000 0.30 0.00 0.00 3.02
1091 1151 1.605058 GGCGCAGAGGTAGGAACAGA 61.605 60.000 10.83 0.00 0.00 3.41
1092 1152 1.153549 GGCGCAGAGGTAGGAACAG 60.154 63.158 10.83 0.00 0.00 3.16
1093 1153 2.978824 GGCGCAGAGGTAGGAACA 59.021 61.111 10.83 0.00 0.00 3.18
1094 1154 2.202756 CGGCGCAGAGGTAGGAAC 60.203 66.667 10.83 0.00 0.00 3.62
1095 1155 3.458163 CCGGCGCAGAGGTAGGAA 61.458 66.667 10.83 0.00 0.00 3.36
1096 1156 4.435970 TCCGGCGCAGAGGTAGGA 62.436 66.667 10.83 2.81 0.00 2.94
1097 1157 3.905678 CTCCGGCGCAGAGGTAGG 61.906 72.222 10.83 0.14 0.00 3.18
1098 1158 3.905678 CCTCCGGCGCAGAGGTAG 61.906 72.222 28.66 17.44 45.05 3.18
1123 1188 1.609501 AGCCGCAGAGGTAGGAACA 60.610 57.895 0.00 0.00 43.70 3.18
1147 1212 3.127352 CTCCTACTCCGCAGCCGAC 62.127 68.421 0.00 0.00 36.29 4.79
1178 1243 7.982919 TCATCTAATCTAGACTAGATCGGCTAC 59.017 40.741 22.45 0.00 44.44 3.58
1264 1329 2.123812 AGGTCGAGATCCCCGGAC 60.124 66.667 0.73 0.00 0.00 4.79
1287 1352 8.289939 TGGAAACACGTAAAGATATCTACTCT 57.710 34.615 5.46 0.00 33.40 3.24
1288 1353 8.922058 TTGGAAACACGTAAAGATATCTACTC 57.078 34.615 5.46 0.00 42.67 2.59
1289 1354 9.886132 AATTGGAAACACGTAAAGATATCTACT 57.114 29.630 5.46 0.00 42.67 2.57
1372 1438 2.409948 AAGAAGCACTACATGAGCCC 57.590 50.000 0.00 0.00 32.56 5.19
1374 1440 4.022849 ACCAAAAAGAAGCACTACATGAGC 60.023 41.667 0.00 0.00 0.00 4.26
1380 1446 5.703130 AGATCTGACCAAAAAGAAGCACTAC 59.297 40.000 0.00 0.00 0.00 2.73
1381 1447 5.869579 AGATCTGACCAAAAAGAAGCACTA 58.130 37.500 0.00 0.00 0.00 2.74
1383 1449 5.470098 TGTAGATCTGACCAAAAAGAAGCAC 59.530 40.000 5.18 0.00 0.00 4.40
1389 1455 4.690748 TCGCTTGTAGATCTGACCAAAAAG 59.309 41.667 5.18 0.00 0.00 2.27
1431 1497 3.353836 CGAACCAACCACCAGCGG 61.354 66.667 0.00 0.00 0.00 5.52
1447 1513 0.905357 AATCCTCCTCCTCACCAACG 59.095 55.000 0.00 0.00 0.00 4.10
1453 1519 0.470080 CCGCCTAATCCTCCTCCTCA 60.470 60.000 0.00 0.00 0.00 3.86
1909 1981 3.127352 GAGGCGCTGGTCGAGGTAG 62.127 68.421 7.64 0.00 41.67 3.18
2014 2086 1.742768 GCCATACGGGTCAGGAGAG 59.257 63.158 0.00 0.00 39.65 3.20
2047 2119 4.051932 CCTGGAGGGGAGGTGTAC 57.948 66.667 0.00 0.00 0.00 2.90
2062 2134 0.350541 ACCCTCCATACCCATTCCCT 59.649 55.000 0.00 0.00 0.00 4.20
2112 2184 2.354259 GCCTCTTGTCATCAGAGTTGG 58.646 52.381 1.75 0.00 0.00 3.77
2113 2185 2.289882 TGGCCTCTTGTCATCAGAGTTG 60.290 50.000 3.32 0.00 0.00 3.16
2174 2246 2.268920 CAGGTGGTGCATACGGCT 59.731 61.111 0.00 0.00 45.15 5.52
2347 2419 4.274214 ACACAATCAGCATATTCCATGTCG 59.726 41.667 0.00 0.00 0.00 4.35
2359 2431 0.111061 AGGCCTTGACACAATCAGCA 59.889 50.000 0.00 0.00 38.99 4.41
2513 2585 2.436173 GGTCCCTCATAAACTCCTCCAG 59.564 54.545 0.00 0.00 0.00 3.86
2575 2647 0.251634 CTTCCTCCTTGACAGGCTCC 59.748 60.000 0.00 0.00 40.58 4.70
2581 2653 0.979665 CTGGCTCTTCCTCCTTGACA 59.020 55.000 0.00 0.00 35.26 3.58
3040 3112 1.845205 ACTGCTGGAGCTCCCACTT 60.845 57.895 29.95 7.72 40.82 3.16
3106 3178 1.513158 CATCGAACCGTCTGGAGCT 59.487 57.895 0.00 0.00 39.21 4.09
3109 3181 1.215382 CTGCATCGAACCGTCTGGA 59.785 57.895 0.00 0.00 39.21 3.86
3139 3211 1.227674 GGATGCCGCGAAAGGATCT 60.228 57.895 8.23 0.00 0.00 2.75
3148 3220 1.451387 AAAGGTAAGGGATGCCGCG 60.451 57.895 0.00 0.00 39.12 6.46
3193 3265 1.904537 TGCTGCTTCTTCTCCATCTCA 59.095 47.619 0.00 0.00 0.00 3.27
3449 3521 0.971447 ACAGCCCCGAGGAGTAAGAC 60.971 60.000 0.00 0.00 33.47 3.01
3619 3693 5.126779 TGCACAGGTCTCTAGTACTATCAG 58.873 45.833 2.33 3.05 0.00 2.90
3636 3710 1.643292 CGGCCGACAATATGCACAG 59.357 57.895 24.07 0.00 0.00 3.66
3665 3739 1.202842 ACTAACAACAACCGGGGGAAG 60.203 52.381 6.32 0.00 0.00 3.46
3666 3740 0.845337 ACTAACAACAACCGGGGGAA 59.155 50.000 6.32 0.00 0.00 3.97
3667 3741 1.727062 TACTAACAACAACCGGGGGA 58.273 50.000 6.32 0.00 0.00 4.81
3668 3742 2.793288 ATACTAACAACAACCGGGGG 57.207 50.000 6.32 0.00 0.00 5.40
3669 3743 3.198417 AGGTATACTAACAACAACCGGGG 59.802 47.826 6.32 0.00 32.18 5.73
3800 3877 1.349688 AGGACGTCCTTAATGCCAACA 59.650 47.619 31.69 0.00 46.09 3.33
3903 3980 5.911838 GGCAAATCATTCGAGCTCTATTTTC 59.088 40.000 12.85 4.73 0.00 2.29
3924 4006 3.513768 TTCGACGAGCAGCAAGGCA 62.514 57.895 0.00 0.00 35.83 4.75
3954 4036 1.073722 CCAGGCTTCCAGCAACAGA 59.926 57.895 0.00 0.00 44.75 3.41
3964 4046 3.636153 AGTTGATAGGTTCCAGGCTTC 57.364 47.619 0.00 0.00 0.00 3.86
3968 4050 7.335422 GCATTATGATAGTTGATAGGTTCCAGG 59.665 40.741 0.00 0.00 0.00 4.45
3976 4058 7.384932 TGAACGTGGCATTATGATAGTTGATAG 59.615 37.037 0.00 0.00 0.00 2.08
3977 4059 7.170828 GTGAACGTGGCATTATGATAGTTGATA 59.829 37.037 0.00 0.00 0.00 2.15
3978 4060 6.017934 GTGAACGTGGCATTATGATAGTTGAT 60.018 38.462 0.00 0.00 0.00 2.57
3979 4061 5.293324 GTGAACGTGGCATTATGATAGTTGA 59.707 40.000 0.00 0.00 0.00 3.18
3980 4062 5.064579 TGTGAACGTGGCATTATGATAGTTG 59.935 40.000 0.00 0.00 0.00 3.16
3981 4063 5.182487 TGTGAACGTGGCATTATGATAGTT 58.818 37.500 0.00 0.00 0.00 2.24
3982 4064 4.765273 TGTGAACGTGGCATTATGATAGT 58.235 39.130 0.00 0.00 0.00 2.12
3995 4077 4.614284 GCAAATCAAAGAGATGTGAACGTG 59.386 41.667 0.00 0.00 43.53 4.49
3996 4078 4.275689 TGCAAATCAAAGAGATGTGAACGT 59.724 37.500 0.00 0.00 43.53 3.99
4052 4144 4.458989 GGCAATGTCACTTCAATCCTGTAA 59.541 41.667 0.00 0.00 0.00 2.41
4072 4164 2.026262 GGGAGTAAGATTCAAGTGGGCA 60.026 50.000 0.00 0.00 0.00 5.36
4086 4178 5.659525 TCACTATTTGAATCGGAGGGAGTAA 59.340 40.000 0.00 0.00 0.00 2.24
4087 4179 5.205821 TCACTATTTGAATCGGAGGGAGTA 58.794 41.667 0.00 0.00 0.00 2.59
4091 4183 4.408182 ACTCACTATTTGAATCGGAGGG 57.592 45.455 0.00 0.00 32.21 4.30
4096 4188 6.368791 TGAGGTTGAACTCACTATTTGAATCG 59.631 38.462 0.00 0.00 42.26 3.34
4105 4197 7.054124 ACTTTGAATTGAGGTTGAACTCACTA 58.946 34.615 0.00 0.00 46.44 2.74
4181 4275 3.817647 GACATCAACCATTCTATGCTCCC 59.182 47.826 0.00 0.00 0.00 4.30
4238 4344 5.428253 TGTTGGAAATCTAGCATCCAGTAC 58.572 41.667 9.85 7.96 43.69 2.73
4240 4346 4.225942 TCTGTTGGAAATCTAGCATCCAGT 59.774 41.667 9.85 0.00 43.69 4.00
4241 4347 4.774124 TCTGTTGGAAATCTAGCATCCAG 58.226 43.478 9.85 0.00 43.69 3.86
4242 4348 4.774124 CTCTGTTGGAAATCTAGCATCCA 58.226 43.478 6.82 6.82 41.36 3.41
4243 4349 3.563390 GCTCTGTTGGAAATCTAGCATCC 59.437 47.826 0.00 2.37 0.00 3.51
4262 4370 2.535984 CGAAGGAATCATGTGTACGCTC 59.464 50.000 8.10 0.00 0.00 5.03
4265 4373 4.862574 TCTTTCGAAGGAATCATGTGTACG 59.137 41.667 7.61 0.00 30.88 3.67
4271 4379 6.690194 AGGAATTCTTTCGAAGGAATCATG 57.310 37.500 28.93 0.00 31.87 3.07
4392 4502 0.606401 ACATCGGGGAGCAACAACTG 60.606 55.000 0.00 0.00 0.00 3.16
4404 4514 8.926710 GTTGATATTGAGAACTTATACATCGGG 58.073 37.037 0.00 0.00 0.00 5.14
4431 4541 2.920724 TGTTTCATCCTGTTGACGGA 57.079 45.000 0.00 0.00 34.52 4.69
4467 4577 2.125326 CGAGCACCGTCCCCTCATA 61.125 63.158 0.00 0.00 0.00 2.15
4468 4578 3.461773 CGAGCACCGTCCCCTCAT 61.462 66.667 0.00 0.00 0.00 2.90
4487 4794 3.560251 CATCCCTAGCCCCCACCG 61.560 72.222 0.00 0.00 0.00 4.94
4534 4843 2.288961 TTTGATCGTCCTTAGCGACC 57.711 50.000 0.00 0.00 41.33 4.79
4539 4848 4.566759 TCGCTTTGATTTGATCGTCCTTAG 59.433 41.667 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.