Multiple sequence alignment - TraesCS5A01G387000

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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 TraesCS5A01G387000 chr5A 100.000 3466 0 0 1 3466 584506906 584510371 0.000000e+00 6401.0
1 TraesCS5A01G387000 chr5B 91.875 2043 100 26 1200 3204 570935939 570937953 0.000000e+00 2793.0
2 TraesCS5A01G387000 chr5B 93.402 1167 52 5 1200 2353 571174097 571175251 0.000000e+00 1705.0
3 TraesCS5A01G387000 chr5B 87.212 1040 115 13 132 1166 570934736 570935762 0.000000e+00 1168.0
4 TraesCS5A01G387000 chr5B 85.697 825 103 10 158 976 571122770 571123585 0.000000e+00 856.0
5 TraesCS5A01G387000 chr5B 90.909 308 15 4 2344 2638 571175419 571175726 5.390000e-108 401.0
6 TraesCS5A01G387000 chr5B 90.055 181 10 3 2737 2909 571175771 571175951 9.680000e-56 228.0
7 TraesCS5A01G387000 chr5B 84.426 244 13 13 2946 3174 571175949 571176182 2.090000e-52 217.0
8 TraesCS5A01G387000 chr5B 95.556 135 3 2 3138 3270 570937945 570938078 2.710000e-51 213.0
9 TraesCS5A01G387000 chr5B 94.737 133 7 0 3138 3270 571176208 571176340 1.260000e-49 207.0
10 TraesCS5A01G387000 chr5B 100.000 28 0 0 2686 2713 571175743 571175770 6.000000e-03 52.8
11 TraesCS5A01G387000 chr5D 91.052 2034 113 31 1200 3204 464078500 464080493 0.000000e+00 2684.0
12 TraesCS5A01G387000 chr5D 86.654 1019 122 10 150 1163 464077311 464078320 0.000000e+00 1116.0
13 TraesCS5A01G387000 chr5D 98.649 74 1 0 3138 3211 464080485 464080558 7.810000e-27 132.0
14 TraesCS5A01G387000 chr3B 82.842 2407 315 58 140 2497 671747490 671745133 0.000000e+00 2067.0
15 TraesCS5A01G387000 chr3B 81.648 1068 176 7 1257 2305 13966279 13967345 0.000000e+00 869.0
16 TraesCS5A01G387000 chr3B 98.039 51 1 0 1 51 807814582 807814532 4.760000e-14 89.8
17 TraesCS5A01G387000 chr3B 98.000 50 1 0 1 50 60147548 60147499 1.710000e-13 87.9
18 TraesCS5A01G387000 chr2B 82.482 2329 329 53 135 2424 752830907 752828619 0.000000e+00 1967.0
19 TraesCS5A01G387000 chr2B 98.039 51 1 0 1 51 18738426 18738376 4.760000e-14 89.8
20 TraesCS5A01G387000 chr2D 82.163 2293 331 47 154 2403 617073881 617071624 0.000000e+00 1897.0
21 TraesCS5A01G387000 chr2D 83.939 716 90 11 1696 2394 616968288 616967581 0.000000e+00 662.0
22 TraesCS5A01G387000 chr2A 82.020 2297 328 59 154 2403 747144766 747142508 0.000000e+00 1875.0
23 TraesCS5A01G387000 chr2A 77.820 532 87 23 125 640 746977667 746977151 2.020000e-77 300.0
24 TraesCS5A01G387000 chrUn 81.947 1058 170 7 1289 2327 238784780 238785835 0.000000e+00 876.0
25 TraesCS5A01G387000 chrUn 81.947 1058 170 7 1289 2327 240351494 240350439 0.000000e+00 876.0
26 TraesCS5A01G387000 chrUn 81.182 1100 187 6 1247 2327 296501503 296500405 0.000000e+00 867.0
27 TraesCS5A01G387000 chr3D 81.261 1094 181 9 1255 2327 5007046 5005956 0.000000e+00 863.0
28 TraesCS5A01G387000 chr3D 81.569 1058 174 10 1289 2327 4967357 4966302 0.000000e+00 854.0
29 TraesCS5A01G387000 chr7B 100.000 50 0 0 1 50 709452974 709452925 3.680000e-15 93.5
30 TraesCS5A01G387000 chr7A 100.000 50 0 0 1 50 669085092 669085141 3.680000e-15 93.5
31 TraesCS5A01G387000 chr6A 100.000 50 0 0 1 50 46736184 46736233 3.680000e-15 93.5
32 TraesCS5A01G387000 chr6B 98.039 51 1 0 1 51 644402155 644402205 4.760000e-14 89.8
33 TraesCS5A01G387000 chr4A 98.039 51 1 0 1 51 723024114 723024064 4.760000e-14 89.8
34 TraesCS5A01G387000 chr4B 98.000 50 1 0 1 50 122657237 122657188 1.710000e-13 87.9


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 TraesCS5A01G387000 chr5A 584506906 584510371 3465 False 6401.000000 6401 100.000000 1 3466 1 chr5A.!!$F1 3465
1 TraesCS5A01G387000 chr5B 570934736 570938078 3342 False 1391.333333 2793 91.547667 132 3270 3 chr5B.!!$F2 3138
2 TraesCS5A01G387000 chr5B 571122770 571123585 815 False 856.000000 856 85.697000 158 976 1 chr5B.!!$F1 818
3 TraesCS5A01G387000 chr5B 571174097 571176340 2243 False 468.466667 1705 92.254833 1200 3270 6 chr5B.!!$F3 2070
4 TraesCS5A01G387000 chr5D 464077311 464080558 3247 False 1310.666667 2684 92.118333 150 3211 3 chr5D.!!$F1 3061
5 TraesCS5A01G387000 chr3B 671745133 671747490 2357 True 2067.000000 2067 82.842000 140 2497 1 chr3B.!!$R2 2357
6 TraesCS5A01G387000 chr3B 13966279 13967345 1066 False 869.000000 869 81.648000 1257 2305 1 chr3B.!!$F1 1048
7 TraesCS5A01G387000 chr2B 752828619 752830907 2288 True 1967.000000 1967 82.482000 135 2424 1 chr2B.!!$R2 2289
8 TraesCS5A01G387000 chr2D 617071624 617073881 2257 True 1897.000000 1897 82.163000 154 2403 1 chr2D.!!$R2 2249
9 TraesCS5A01G387000 chr2D 616967581 616968288 707 True 662.000000 662 83.939000 1696 2394 1 chr2D.!!$R1 698
10 TraesCS5A01G387000 chr2A 747142508 747144766 2258 True 1875.000000 1875 82.020000 154 2403 1 chr2A.!!$R2 2249
11 TraesCS5A01G387000 chr2A 746977151 746977667 516 True 300.000000 300 77.820000 125 640 1 chr2A.!!$R1 515
12 TraesCS5A01G387000 chrUn 238784780 238785835 1055 False 876.000000 876 81.947000 1289 2327 1 chrUn.!!$F1 1038
13 TraesCS5A01G387000 chrUn 240350439 240351494 1055 True 876.000000 876 81.947000 1289 2327 1 chrUn.!!$R1 1038
14 TraesCS5A01G387000 chrUn 296500405 296501503 1098 True 867.000000 867 81.182000 1247 2327 1 chrUn.!!$R2 1080
15 TraesCS5A01G387000 chr3D 5005956 5007046 1090 True 863.000000 863 81.261000 1255 2327 1 chr3D.!!$R2 1072
16 TraesCS5A01G387000 chr3D 4966302 4967357 1055 True 854.000000 854 81.569000 1289 2327 1 chr3D.!!$R1 1038

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
764 802 0.033228 CTCTGGGTGATCGGAGCATC 59.967 60.0 0.0 0.0 33.93 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2680 3135 1.227793 GCCATCAGGAGCTACAGGC 60.228 63.158 0.0 1.9 36.89 4.85 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 1.941812 CCGTCGGCATAGATTTGGC 59.058 57.895 0.00 0.00 38.71 4.52
21 22 1.507141 CCGTCGGCATAGATTTGGCC 61.507 60.000 0.00 0.00 44.27 5.36
25 26 1.941812 GGCATAGATTTGGCCGTCG 59.058 57.895 0.00 0.00 38.04 5.12
26 27 1.507141 GGCATAGATTTGGCCGTCGG 61.507 60.000 6.99 6.99 38.04 4.79
43 44 2.203209 GCATAGGGCCCTGTTCCG 60.203 66.667 35.81 17.20 36.11 4.30
44 45 2.510906 CATAGGGCCCTGTTCCGG 59.489 66.667 35.81 12.16 0.00 5.14
45 46 2.042261 ATAGGGCCCTGTTCCGGT 59.958 61.111 35.81 8.02 0.00 5.28
46 47 1.052124 CATAGGGCCCTGTTCCGGTA 61.052 60.000 35.81 12.49 0.00 4.02
47 48 0.763223 ATAGGGCCCTGTTCCGGTAG 60.763 60.000 35.81 0.00 0.00 3.18
48 49 2.172229 TAGGGCCCTGTTCCGGTAGT 62.172 60.000 35.81 5.66 0.00 2.73
49 50 2.267961 GGCCCTGTTCCGGTAGTG 59.732 66.667 0.00 0.00 0.00 2.74
50 51 2.590114 GGCCCTGTTCCGGTAGTGT 61.590 63.158 0.00 0.00 0.00 3.55
51 52 1.373812 GCCCTGTTCCGGTAGTGTT 59.626 57.895 0.00 0.00 0.00 3.32
52 53 0.250597 GCCCTGTTCCGGTAGTGTTT 60.251 55.000 0.00 0.00 0.00 2.83
53 54 1.804601 CCCTGTTCCGGTAGTGTTTC 58.195 55.000 0.00 0.00 0.00 2.78
54 55 1.609841 CCCTGTTCCGGTAGTGTTTCC 60.610 57.143 0.00 0.00 0.00 3.13
55 56 1.071071 CCTGTTCCGGTAGTGTTTCCA 59.929 52.381 0.00 0.00 0.00 3.53
56 57 2.140717 CTGTTCCGGTAGTGTTTCCAC 58.859 52.381 0.00 0.00 42.17 4.02
78 79 3.986442 GCAATGTGGGTGCAAATTTTT 57.014 38.095 0.00 0.00 41.80 1.94
79 80 3.630101 GCAATGTGGGTGCAAATTTTTG 58.370 40.909 0.00 0.00 41.80 2.44
93 94 6.682423 CAAATTTTTGCTCCTGGAACTTTT 57.318 33.333 0.00 0.00 0.00 2.27
94 95 7.784633 CAAATTTTTGCTCCTGGAACTTTTA 57.215 32.000 0.00 0.00 0.00 1.52
95 96 8.207521 CAAATTTTTGCTCCTGGAACTTTTAA 57.792 30.769 0.00 0.00 0.00 1.52
96 97 8.839343 CAAATTTTTGCTCCTGGAACTTTTAAT 58.161 29.630 0.00 0.00 0.00 1.40
97 98 8.978874 AATTTTTGCTCCTGGAACTTTTAATT 57.021 26.923 0.00 0.00 0.00 1.40
100 101 9.892130 TTTTTGCTCCTGGAACTTTTAATTAAA 57.108 25.926 6.54 6.54 0.00 1.52
102 103 7.227049 TGCTCCTGGAACTTTTAATTAAAGG 57.773 36.000 16.18 16.18 46.16 3.11
103 104 7.007723 TGCTCCTGGAACTTTTAATTAAAGGA 58.992 34.615 22.62 16.28 46.16 3.36
104 105 7.039993 TGCTCCTGGAACTTTTAATTAAAGGAC 60.040 37.037 22.62 15.86 46.16 3.85
105 106 7.443259 TCCTGGAACTTTTAATTAAAGGACG 57.557 36.000 22.62 10.57 46.16 4.79
106 107 7.225725 TCCTGGAACTTTTAATTAAAGGACGA 58.774 34.615 22.62 13.37 46.16 4.20
107 108 7.389607 TCCTGGAACTTTTAATTAAAGGACGAG 59.610 37.037 22.62 19.18 46.16 4.18
108 109 7.174426 CCTGGAACTTTTAATTAAAGGACGAGT 59.826 37.037 22.62 14.37 46.16 4.18
109 110 8.454570 TGGAACTTTTAATTAAAGGACGAGTT 57.545 30.769 22.62 20.28 46.16 3.01
110 111 8.347035 TGGAACTTTTAATTAAAGGACGAGTTG 58.653 33.333 22.62 5.32 46.16 3.16
111 112 8.562052 GGAACTTTTAATTAAAGGACGAGTTGA 58.438 33.333 22.62 0.41 46.16 3.18
114 115 9.893305 ACTTTTAATTAAAGGACGAGTTGATTG 57.107 29.630 22.62 0.00 46.16 2.67
115 116 9.893305 CTTTTAATTAAAGGACGAGTTGATTGT 57.107 29.630 13.33 0.00 39.68 2.71
116 117 9.672086 TTTTAATTAAAGGACGAGTTGATTGTG 57.328 29.630 10.40 0.00 0.00 3.33
117 118 4.742438 TTAAAGGACGAGTTGATTGTGC 57.258 40.909 0.00 0.00 33.88 4.57
118 119 1.523758 AAGGACGAGTTGATTGTGCC 58.476 50.000 0.00 0.00 34.19 5.01
119 120 0.321653 AGGACGAGTTGATTGTGCCC 60.322 55.000 0.00 0.00 34.19 5.36
120 121 1.305930 GGACGAGTTGATTGTGCCCC 61.306 60.000 0.00 0.00 0.00 5.80
121 122 1.635663 GACGAGTTGATTGTGCCCCG 61.636 60.000 0.00 0.00 0.00 5.73
122 123 2.877691 GAGTTGATTGTGCCCCGC 59.122 61.111 0.00 0.00 0.00 6.13
123 124 1.971167 GAGTTGATTGTGCCCCGCA 60.971 57.895 0.00 0.00 35.60 5.69
124 125 1.926511 GAGTTGATTGTGCCCCGCAG 61.927 60.000 0.00 0.00 40.08 5.18
125 126 3.372730 TTGATTGTGCCCCGCAGC 61.373 61.111 0.00 0.00 40.08 5.25
137 138 1.594833 CCGCAGCCCAGTACTACAA 59.405 57.895 0.00 0.00 0.00 2.41
178 179 4.161377 ACCAAGCCAAAACAAGAGCTAAAA 59.839 37.500 0.00 0.00 34.49 1.52
260 268 3.134127 GCCGTGGATGTTGAGGGC 61.134 66.667 0.00 0.00 36.08 5.19
310 345 4.113815 TTGCGGCCATCTCCAGGG 62.114 66.667 2.24 0.00 0.00 4.45
486 521 2.034066 ACGCCAACCTGGACATGG 59.966 61.111 0.00 7.13 40.96 3.66
552 587 2.041686 GGTCTCCAGCGACTCGACT 61.042 63.158 1.63 0.00 34.38 4.18
570 605 1.204704 ACTGCCTCGTCGAATTGATGA 59.795 47.619 0.00 0.00 40.34 2.92
689 727 5.410924 TCTTCCTTCGTCTATGTGTTGATG 58.589 41.667 0.00 0.00 0.00 3.07
717 755 6.180472 TCTTATTCTGTTGGGAAGCTTAAGG 58.820 40.000 0.00 0.00 0.00 2.69
728 766 1.137614 GCTTAAGGCTTCTTGCGGC 59.862 57.895 1.30 0.00 44.05 6.53
747 785 1.077501 TACTTGGCCATGGCTGCTC 60.078 57.895 34.70 19.38 41.60 4.26
764 802 0.033228 CTCTGGGTGATCGGAGCATC 59.967 60.000 0.00 0.00 33.93 3.91
792 830 0.584396 TAACGCAAGCCACGAAACTG 59.416 50.000 0.00 0.00 45.62 3.16
845 883 7.362401 CCTGTTTGGTTTCCTTTCAGATATGAG 60.362 40.741 0.00 0.00 0.00 2.90
934 985 2.227388 CACCATGCTTCTGTTCTGGAAC 59.773 50.000 6.53 6.53 41.50 3.62
976 1027 9.965902 ACTTCTCTACATTTTCTCCATTGTATT 57.034 29.630 0.00 0.00 0.00 1.89
981 1032 6.594788 ACATTTTCTCCATTGTATTGCAGT 57.405 33.333 0.00 0.00 0.00 4.40
1004 1061 0.394216 CGCCCTGGACAATCAATGGA 60.394 55.000 0.00 0.00 0.00 3.41
1061 1118 5.613358 ACGGTTGATTCTGAAATCTTGTC 57.387 39.130 0.00 0.00 41.63 3.18
1073 1130 3.648339 AATCTTGTCTTGCGCATTTGT 57.352 38.095 12.75 0.00 0.00 2.83
1078 1135 1.069296 TGTCTTGCGCATTTGTAGCAC 60.069 47.619 12.75 6.33 40.92 4.40
1092 1149 8.103924 GCATTTGTAGCACATAATTTTTCTTCG 58.896 33.333 0.00 0.00 0.00 3.79
1094 1151 8.948853 TTTGTAGCACATAATTTTTCTTCGAG 57.051 30.769 0.00 0.00 0.00 4.04
1108 1165 0.599204 TTCGAGTGAACACCTTCGCC 60.599 55.000 10.30 0.00 37.59 5.54
1109 1166 1.006102 CGAGTGAACACCTTCGCCT 60.006 57.895 1.11 0.00 37.59 5.52
1110 1167 1.284982 CGAGTGAACACCTTCGCCTG 61.285 60.000 1.11 0.00 37.59 4.85
1120 1177 1.621814 ACCTTCGCCTGCTACACTTTA 59.378 47.619 0.00 0.00 0.00 1.85
1121 1178 2.236395 ACCTTCGCCTGCTACACTTTAT 59.764 45.455 0.00 0.00 0.00 1.40
1166 1223 1.804151 GAAGTTCATTGCTGGTACGCA 59.196 47.619 0.00 0.00 36.27 5.24
1167 1224 1.156736 AGTTCATTGCTGGTACGCAC 58.843 50.000 0.00 0.00 37.56 5.34
1168 1225 0.179225 GTTCATTGCTGGTACGCACG 60.179 55.000 0.00 0.00 37.56 5.34
1169 1226 1.906994 TTCATTGCTGGTACGCACGC 61.907 55.000 0.00 0.00 37.56 5.34
1171 1228 3.892740 ATTGCTGGTACGCACGCCA 62.893 57.895 0.00 0.00 37.56 5.69
1178 1235 3.680786 TACGCACGCCAGCAGAGT 61.681 61.111 0.00 0.00 0.00 3.24
1179 1236 3.220999 TACGCACGCCAGCAGAGTT 62.221 57.895 0.00 0.00 0.00 3.01
1180 1237 1.868987 TACGCACGCCAGCAGAGTTA 61.869 55.000 0.00 0.00 0.00 2.24
1181 1238 2.730672 CGCACGCCAGCAGAGTTAC 61.731 63.158 0.00 0.00 0.00 2.50
1182 1239 1.667830 GCACGCCAGCAGAGTTACA 60.668 57.895 0.00 0.00 0.00 2.41
1183 1240 1.901650 GCACGCCAGCAGAGTTACAC 61.902 60.000 0.00 0.00 0.00 2.90
1185 1245 0.321671 ACGCCAGCAGAGTTACACAT 59.678 50.000 0.00 0.00 0.00 3.21
1188 1248 2.541346 CGCCAGCAGAGTTACACATATG 59.459 50.000 0.00 0.00 0.00 1.78
1198 1258 8.516234 GCAGAGTTACACATATGTACTAGCTAT 58.484 37.037 8.32 3.39 41.12 2.97
1200 1260 9.015367 AGAGTTACACATATGTACTAGCTATGG 57.985 37.037 8.32 0.00 41.12 2.74
1288 1504 0.117541 TTGCTCCCCTGGTGGTACTA 59.882 55.000 0.00 0.00 0.00 1.82
1321 1537 5.512232 GGCCCACAAATATTGGAAAACAAGA 60.512 40.000 0.00 0.00 43.48 3.02
1349 1565 3.723554 GATGCGGTCGAGAAGTTCT 57.276 52.632 4.68 4.68 0.00 3.01
1364 1580 5.766222 AGAAGTTCTTACAAATGCAGCAAG 58.234 37.500 0.00 0.00 0.00 4.01
1387 1603 1.378514 CGGCCCAACAAGGTATGCT 60.379 57.895 0.00 0.00 34.66 3.79
1678 1894 7.923878 GGTTCTCTTGATAAGTACATCTTCTCC 59.076 40.741 0.00 0.00 37.56 3.71
1957 2173 2.551721 CCGGAGCTTTGGCATCATATCT 60.552 50.000 0.00 0.00 41.70 1.98
1966 2182 4.961438 TGGCATCATATCTAGCAAGTCA 57.039 40.909 0.00 0.00 0.00 3.41
2222 2459 0.179111 CGAAGGGAGCGTTGATAGCA 60.179 55.000 0.00 0.00 37.01 3.49
2368 2783 7.633361 TCGATGAAGTAAATTATTACGAGGC 57.367 36.000 0.00 0.00 44.97 4.70
2435 2857 9.669353 CTATGGAATGTGAATGTTTTATACAGC 57.331 33.333 0.00 0.00 40.83 4.40
2488 2918 4.678509 TGTTCATCCGAAATACAAGCAC 57.321 40.909 0.00 0.00 31.43 4.40
2509 2939 6.502195 CACATTATGTGTATCGAGTGTGAG 57.498 41.667 16.45 0.00 43.08 3.51
2543 2973 1.415659 CATTGCCCAAAAGGGTGTGAA 59.584 47.619 2.03 0.00 35.41 3.18
2679 3134 2.820330 CGCTGTTTGTTGGTTTCCAAT 58.180 42.857 4.51 0.00 45.80 3.16
2680 3135 2.539274 CGCTGTTTGTTGGTTTCCAATG 59.461 45.455 4.51 0.00 45.80 2.82
2713 3173 2.362120 GGCACATCCTTGCAGCCT 60.362 61.111 3.76 0.00 44.94 4.58
2738 3198 4.828939 ACTGAAGAAGCATGAAACCATGAA 59.171 37.500 9.35 0.00 43.04 2.57
2742 3202 6.489700 TGAAGAAGCATGAAACCATGAAACTA 59.510 34.615 9.35 0.00 43.04 2.24
2840 3312 6.088824 GCAATTACTTTCAACAGATCAGGTG 58.911 40.000 0.00 0.00 0.00 4.00
2996 3475 7.573968 TCATCACGTATAGATCCCATAGATG 57.426 40.000 0.00 0.00 34.42 2.90
2997 3476 7.346471 TCATCACGTATAGATCCCATAGATGA 58.654 38.462 0.00 0.00 36.70 2.92
2998 3477 8.001292 TCATCACGTATAGATCCCATAGATGAT 58.999 37.037 0.00 7.50 34.84 2.45
3017 3496 5.627499 TGATTAAAGAGCGCTTGAATGTT 57.373 34.783 16.69 2.39 35.69 2.71
3018 3497 5.393124 TGATTAAAGAGCGCTTGAATGTTG 58.607 37.500 16.69 0.00 35.69 3.33
3019 3498 2.712057 AAAGAGCGCTTGAATGTTGG 57.288 45.000 13.26 0.00 33.79 3.77
3079 3572 0.248377 GCAGCTTGCCTCTAATTGCG 60.248 55.000 0.00 0.00 37.42 4.85
3081 3574 2.279741 CAGCTTGCCTCTAATTGCGTA 58.720 47.619 0.00 0.00 0.00 4.42
3082 3575 2.030946 CAGCTTGCCTCTAATTGCGTAC 59.969 50.000 0.00 0.00 0.00 3.67
3083 3576 2.006888 GCTTGCCTCTAATTGCGTACA 58.993 47.619 0.00 0.00 0.00 2.90
3084 3577 2.614057 GCTTGCCTCTAATTGCGTACAT 59.386 45.455 0.00 0.00 0.00 2.29
3085 3578 3.546815 GCTTGCCTCTAATTGCGTACATG 60.547 47.826 0.00 0.00 0.00 3.21
3221 3779 2.124819 CATTGGCCTGCTCTCGCT 60.125 61.111 3.32 0.00 36.97 4.93
3270 3830 0.683504 AGTCCCGACGGCAGATTACT 60.684 55.000 8.86 1.62 36.20 2.24
3271 3831 0.527817 GTCCCGACGGCAGATTACTG 60.528 60.000 8.86 0.00 45.91 2.74
3272 3832 0.681887 TCCCGACGGCAGATTACTGA 60.682 55.000 8.86 0.00 46.03 3.41
3273 3833 0.249073 CCCGACGGCAGATTACTGAG 60.249 60.000 8.86 0.00 46.03 3.35
3274 3834 0.872021 CCGACGGCAGATTACTGAGC 60.872 60.000 0.00 0.00 46.03 4.26
3275 3835 0.101399 CGACGGCAGATTACTGAGCT 59.899 55.000 0.00 0.00 46.03 4.09
3276 3836 1.565305 GACGGCAGATTACTGAGCTG 58.435 55.000 0.00 0.00 46.03 4.24
3281 3841 2.859526 CAGATTACTGAGCTGCTCGA 57.140 50.000 23.35 12.33 46.03 4.04
3282 3842 2.730069 CAGATTACTGAGCTGCTCGAG 58.270 52.381 23.35 21.53 46.03 4.04
3283 3843 3.111422 CAGATTACTGAGCTGCTCGAGC 61.111 54.545 30.42 30.42 46.03 5.03
3300 3860 4.514577 CGGCGGCGGATCTCACTT 62.515 66.667 25.36 0.00 0.00 3.16
3301 3861 2.892425 GGCGGCGGATCTCACTTG 60.892 66.667 9.78 0.00 0.00 3.16
3302 3862 3.567797 GCGGCGGATCTCACTTGC 61.568 66.667 9.78 0.00 0.00 4.01
3303 3863 2.892425 CGGCGGATCTCACTTGCC 60.892 66.667 0.00 0.00 42.29 4.52
3304 3864 2.268920 GGCGGATCTCACTTGCCA 59.731 61.111 0.00 0.00 45.06 4.92
3305 3865 2.109126 GGCGGATCTCACTTGCCAC 61.109 63.158 0.00 0.00 45.06 5.01
3306 3866 1.078848 GCGGATCTCACTTGCCACT 60.079 57.895 0.00 0.00 0.00 4.00
3307 3867 1.364626 GCGGATCTCACTTGCCACTG 61.365 60.000 0.00 0.00 0.00 3.66
3308 3868 0.742281 CGGATCTCACTTGCCACTGG 60.742 60.000 0.00 0.00 0.00 4.00
3309 3869 0.393537 GGATCTCACTTGCCACTGGG 60.394 60.000 0.00 0.00 37.18 4.45
3310 3870 0.393537 GATCTCACTTGCCACTGGGG 60.394 60.000 0.00 0.00 40.85 4.96
3319 3879 2.750350 CCACTGGGGCGAAGTCTT 59.250 61.111 0.00 0.00 0.00 3.01
3320 3880 1.980052 CCACTGGGGCGAAGTCTTA 59.020 57.895 0.00 0.00 0.00 2.10
3321 3881 0.391263 CCACTGGGGCGAAGTCTTAC 60.391 60.000 0.00 0.00 0.00 2.34
3322 3882 0.608640 CACTGGGGCGAAGTCTTACT 59.391 55.000 0.00 0.00 0.00 2.24
3323 3883 0.608640 ACTGGGGCGAAGTCTTACTG 59.391 55.000 0.00 0.00 0.00 2.74
3324 3884 0.895530 CTGGGGCGAAGTCTTACTGA 59.104 55.000 0.00 0.00 0.00 3.41
3325 3885 0.895530 TGGGGCGAAGTCTTACTGAG 59.104 55.000 0.00 0.00 0.00 3.35
3326 3886 0.460459 GGGGCGAAGTCTTACTGAGC 60.460 60.000 0.00 0.00 32.84 4.26
3327 3887 0.802607 GGGCGAAGTCTTACTGAGCG 60.803 60.000 0.00 0.00 33.91 5.03
3328 3888 0.802607 GGCGAAGTCTTACTGAGCGG 60.803 60.000 0.00 0.00 33.91 5.52
3329 3889 1.414527 GCGAAGTCTTACTGAGCGGC 61.415 60.000 0.00 0.00 0.00 6.53
3330 3890 1.134530 CGAAGTCTTACTGAGCGGCG 61.135 60.000 0.51 0.51 0.00 6.46
3331 3891 0.802607 GAAGTCTTACTGAGCGGCGG 60.803 60.000 9.78 0.00 0.00 6.13
3332 3892 2.837371 AAGTCTTACTGAGCGGCGGC 62.837 60.000 9.78 8.43 40.37 6.53
3333 3893 4.492160 TCTTACTGAGCGGCGGCG 62.492 66.667 28.70 28.70 46.35 6.46
3340 3900 4.280494 GAGCGGCGGCGGATCTTA 62.280 66.667 33.02 0.00 46.35 2.10
3341 3901 4.587189 AGCGGCGGCGGATCTTAC 62.587 66.667 33.02 14.10 46.35 2.34
3342 3902 4.587189 GCGGCGGCGGATCTTACT 62.587 66.667 33.02 0.00 0.00 2.24
3343 3903 2.658593 CGGCGGCGGATCTTACTG 60.659 66.667 25.36 0.00 0.00 2.74
3344 3904 2.812499 GGCGGCGGATCTTACTGA 59.188 61.111 9.78 0.00 0.00 3.41
3345 3905 1.300233 GGCGGCGGATCTTACTGAG 60.300 63.158 9.78 0.00 0.00 3.35
3346 3906 1.951631 GCGGCGGATCTTACTGAGC 60.952 63.158 9.78 0.00 0.00 4.26
3347 3907 1.658717 CGGCGGATCTTACTGAGCG 60.659 63.158 0.00 0.00 30.59 5.03
3348 3908 1.300233 GGCGGATCTTACTGAGCGG 60.300 63.158 0.00 0.00 35.02 5.52
3349 3909 1.951631 GCGGATCTTACTGAGCGGC 60.952 63.158 0.00 0.00 46.74 6.53
3350 3910 1.658717 CGGATCTTACTGAGCGGCG 60.659 63.158 0.51 0.51 30.59 6.46
3351 3911 1.300233 GGATCTTACTGAGCGGCGG 60.300 63.158 9.78 0.00 30.59 6.13
3352 3912 1.951631 GATCTTACTGAGCGGCGGC 60.952 63.158 9.78 8.43 40.37 6.53
3353 3913 2.629050 GATCTTACTGAGCGGCGGCA 62.629 60.000 19.21 0.00 43.41 5.69
3354 3914 2.635229 ATCTTACTGAGCGGCGGCAG 62.635 60.000 19.21 19.51 43.41 4.85
3355 3915 3.356639 CTTACTGAGCGGCGGCAGA 62.357 63.158 25.28 11.34 43.41 4.26
3356 3916 2.635229 CTTACTGAGCGGCGGCAGAT 62.635 60.000 25.28 15.09 43.41 2.90
3357 3917 2.238847 TTACTGAGCGGCGGCAGATT 62.239 55.000 25.28 11.63 43.41 2.40
3358 3918 1.388837 TACTGAGCGGCGGCAGATTA 61.389 55.000 25.28 10.84 43.41 1.75
3359 3919 2.202878 TGAGCGGCGGCAGATTAC 60.203 61.111 19.21 3.35 43.41 1.89
3360 3920 2.107141 GAGCGGCGGCAGATTACT 59.893 61.111 19.21 0.00 43.41 2.24
3361 3921 2.202932 AGCGGCGGCAGATTACTG 60.203 61.111 19.21 0.00 45.91 2.74
3362 3922 2.202878 GCGGCGGCAGATTACTGA 60.203 61.111 9.78 0.00 46.03 3.41
3363 3923 1.813753 GCGGCGGCAGATTACTGAA 60.814 57.895 9.78 0.00 46.03 3.02
3364 3924 2.006772 CGGCGGCAGATTACTGAAC 58.993 57.895 10.53 0.00 46.03 3.18
3365 3925 0.739462 CGGCGGCAGATTACTGAACA 60.739 55.000 10.53 0.00 46.03 3.18
3366 3926 1.668419 GGCGGCAGATTACTGAACAT 58.332 50.000 3.07 0.00 46.03 2.71
3367 3927 1.331756 GGCGGCAGATTACTGAACATG 59.668 52.381 3.07 0.00 46.03 3.21
3368 3928 1.331756 GCGGCAGATTACTGAACATGG 59.668 52.381 0.00 0.00 46.03 3.66
3369 3929 2.632377 CGGCAGATTACTGAACATGGT 58.368 47.619 0.00 0.00 46.03 3.55
3370 3930 2.352651 CGGCAGATTACTGAACATGGTG 59.647 50.000 0.00 0.00 46.03 4.17
3371 3931 2.684881 GGCAGATTACTGAACATGGTGG 59.315 50.000 0.00 0.00 46.03 4.61
3372 3932 2.684881 GCAGATTACTGAACATGGTGGG 59.315 50.000 0.00 0.00 46.03 4.61
3373 3933 2.684881 CAGATTACTGAACATGGTGGGC 59.315 50.000 0.00 0.00 46.03 5.36
3374 3934 2.024414 GATTACTGAACATGGTGGGCC 58.976 52.381 0.00 0.00 0.00 5.80
3375 3935 1.072266 TTACTGAACATGGTGGGCCT 58.928 50.000 4.53 0.00 35.27 5.19
3376 3936 1.072266 TACTGAACATGGTGGGCCTT 58.928 50.000 4.53 0.00 35.27 4.35
3377 3937 0.188342 ACTGAACATGGTGGGCCTTT 59.812 50.000 4.53 0.00 35.27 3.11
3378 3938 1.341080 CTGAACATGGTGGGCCTTTT 58.659 50.000 4.53 0.00 35.27 2.27
3379 3939 1.273327 CTGAACATGGTGGGCCTTTTC 59.727 52.381 4.53 0.00 35.27 2.29
3380 3940 1.337118 GAACATGGTGGGCCTTTTCA 58.663 50.000 4.53 0.00 35.27 2.69
3381 3941 1.691434 GAACATGGTGGGCCTTTTCAA 59.309 47.619 4.53 0.00 35.27 2.69
3382 3942 1.799933 ACATGGTGGGCCTTTTCAAA 58.200 45.000 4.53 0.00 35.27 2.69
3383 3943 1.693606 ACATGGTGGGCCTTTTCAAAG 59.306 47.619 4.53 0.00 35.27 2.77
3384 3944 1.969923 CATGGTGGGCCTTTTCAAAGA 59.030 47.619 4.53 0.00 38.28 2.52
3385 3945 1.703411 TGGTGGGCCTTTTCAAAGAG 58.297 50.000 4.53 0.00 38.28 2.85
3386 3946 1.063266 TGGTGGGCCTTTTCAAAGAGT 60.063 47.619 4.53 0.00 38.28 3.24
3387 3947 2.175931 TGGTGGGCCTTTTCAAAGAGTA 59.824 45.455 4.53 0.00 38.28 2.59
3388 3948 2.820197 GGTGGGCCTTTTCAAAGAGTAG 59.180 50.000 4.53 0.00 38.28 2.57
3389 3949 2.820197 GTGGGCCTTTTCAAAGAGTAGG 59.180 50.000 4.53 0.00 38.28 3.18
3390 3950 2.225017 TGGGCCTTTTCAAAGAGTAGGG 60.225 50.000 4.53 0.00 38.28 3.53
3391 3951 1.819288 GGCCTTTTCAAAGAGTAGGGC 59.181 52.381 0.00 0.00 43.11 5.19
3392 3952 1.468914 GCCTTTTCAAAGAGTAGGGCG 59.531 52.381 0.56 0.00 38.28 6.13
3393 3953 2.874457 GCCTTTTCAAAGAGTAGGGCGA 60.874 50.000 0.56 0.00 38.28 5.54
3394 3954 2.742589 CCTTTTCAAAGAGTAGGGCGAC 59.257 50.000 0.56 0.00 38.28 5.19
3395 3955 3.557264 CCTTTTCAAAGAGTAGGGCGACT 60.557 47.826 0.56 0.00 38.28 4.18
3396 3956 3.764237 TTTCAAAGAGTAGGGCGACTT 57.236 42.857 0.00 0.00 0.00 3.01
3397 3957 2.743636 TCAAAGAGTAGGGCGACTTG 57.256 50.000 0.00 0.00 0.00 3.16
3398 3958 1.275291 TCAAAGAGTAGGGCGACTTGG 59.725 52.381 0.00 0.00 0.00 3.61
3399 3959 1.275291 CAAAGAGTAGGGCGACTTGGA 59.725 52.381 0.00 0.00 0.00 3.53
3400 3960 1.867363 AAGAGTAGGGCGACTTGGAT 58.133 50.000 0.00 0.00 0.00 3.41
3401 3961 1.404843 AGAGTAGGGCGACTTGGATC 58.595 55.000 0.00 0.00 0.00 3.36
3402 3962 1.063567 AGAGTAGGGCGACTTGGATCT 60.064 52.381 0.00 0.00 0.00 2.75
3403 3963 1.338655 GAGTAGGGCGACTTGGATCTC 59.661 57.143 0.00 0.00 0.00 2.75
3404 3964 0.030908 GTAGGGCGACTTGGATCTCG 59.969 60.000 0.00 0.00 0.00 4.04
3405 3965 1.107538 TAGGGCGACTTGGATCTCGG 61.108 60.000 4.51 0.00 0.00 4.63
3406 3966 2.586357 GGCGACTTGGATCTCGGC 60.586 66.667 11.85 11.85 46.42 5.54
3407 3967 2.586357 GCGACTTGGATCTCGGCC 60.586 66.667 0.00 0.00 0.00 6.13
3408 3968 2.892640 CGACTTGGATCTCGGCCA 59.107 61.111 2.24 0.00 0.00 5.36
3409 3969 1.218047 CGACTTGGATCTCGGCCAA 59.782 57.895 2.24 0.00 42.81 4.52
3410 3970 0.391130 CGACTTGGATCTCGGCCAAA 60.391 55.000 2.24 0.00 44.23 3.28
3411 3971 1.743772 CGACTTGGATCTCGGCCAAAT 60.744 52.381 2.24 0.00 44.23 2.32
3412 3972 2.369394 GACTTGGATCTCGGCCAAATT 58.631 47.619 2.24 0.00 44.23 1.82
3413 3973 2.755103 GACTTGGATCTCGGCCAAATTT 59.245 45.455 2.24 0.00 44.23 1.82
3414 3974 3.165071 ACTTGGATCTCGGCCAAATTTT 58.835 40.909 2.24 0.00 44.23 1.82
3415 3975 3.578282 ACTTGGATCTCGGCCAAATTTTT 59.422 39.130 2.24 0.00 44.23 1.94
3416 3976 3.591196 TGGATCTCGGCCAAATTTTTG 57.409 42.857 2.24 0.00 37.90 2.44
3417 3977 3.161067 TGGATCTCGGCCAAATTTTTGA 58.839 40.909 2.24 0.00 40.55 2.69
3418 3978 3.576118 TGGATCTCGGCCAAATTTTTGAA 59.424 39.130 2.24 0.00 40.55 2.69
3419 3979 4.039730 TGGATCTCGGCCAAATTTTTGAAA 59.960 37.500 2.24 0.00 40.55 2.69
3420 3980 4.994217 GGATCTCGGCCAAATTTTTGAAAA 59.006 37.500 2.24 0.00 40.55 2.29
3421 3981 5.468409 GGATCTCGGCCAAATTTTTGAAAAA 59.532 36.000 5.47 5.47 40.55 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.941812 GCCGACGGCCAAATCTATG 59.058 57.895 28.74 0.00 44.06 2.23
10 11 4.456806 GCCGACGGCCAAATCTAT 57.543 55.556 28.74 0.00 44.06 1.98
26 27 2.203209 CGGAACAGGGCCCTATGC 60.203 66.667 28.13 20.74 40.16 3.14
27 28 1.052124 TACCGGAACAGGGCCCTATG 61.052 60.000 28.13 17.80 35.02 2.23
28 29 0.763223 CTACCGGAACAGGGCCCTAT 60.763 60.000 28.13 12.06 35.02 2.57
29 30 1.382146 CTACCGGAACAGGGCCCTA 60.382 63.158 28.13 4.94 35.02 3.53
30 31 2.687566 CTACCGGAACAGGGCCCT 60.688 66.667 22.28 22.28 35.02 5.19
31 32 3.007323 ACTACCGGAACAGGGCCC 61.007 66.667 16.46 16.46 35.02 5.80
32 33 2.120737 AACACTACCGGAACAGGGCC 62.121 60.000 9.46 0.00 35.02 5.80
33 34 0.250597 AAACACTACCGGAACAGGGC 60.251 55.000 9.46 0.00 35.02 5.19
34 35 1.609841 GGAAACACTACCGGAACAGGG 60.610 57.143 9.46 5.74 35.02 4.45
35 36 1.071071 TGGAAACACTACCGGAACAGG 59.929 52.381 9.46 0.00 33.40 4.00
36 37 2.536761 TGGAAACACTACCGGAACAG 57.463 50.000 9.46 4.49 33.40 3.16
54 55 3.445888 TGCACCCACATTGCAGTG 58.554 55.556 7.79 7.79 45.06 3.66
58 59 3.630101 CAAAAATTTGCACCCACATTGC 58.370 40.909 0.00 0.00 40.63 3.56
70 71 6.682423 AAAAGTTCCAGGAGCAAAAATTTG 57.318 33.333 6.02 1.52 41.03 2.32
71 72 8.978874 ATTAAAAGTTCCAGGAGCAAAAATTT 57.021 26.923 6.02 2.10 0.00 1.82
72 73 8.978874 AATTAAAAGTTCCAGGAGCAAAAATT 57.021 26.923 6.02 3.66 0.00 1.82
74 75 9.892130 TTTAATTAAAAGTTCCAGGAGCAAAAA 57.108 25.926 8.20 0.00 0.00 1.94
75 76 9.541143 CTTTAATTAAAAGTTCCAGGAGCAAAA 57.459 29.630 11.62 0.00 39.87 2.44
76 77 8.147704 CCTTTAATTAAAAGTTCCAGGAGCAAA 58.852 33.333 11.62 0.00 42.68 3.68
77 78 7.507616 TCCTTTAATTAAAAGTTCCAGGAGCAA 59.492 33.333 11.62 0.00 42.68 3.91
78 79 7.007723 TCCTTTAATTAAAAGTTCCAGGAGCA 58.992 34.615 11.62 0.00 42.68 4.26
79 80 7.313646 GTCCTTTAATTAAAAGTTCCAGGAGC 58.686 38.462 11.62 0.00 42.68 4.70
80 81 7.389607 TCGTCCTTTAATTAAAAGTTCCAGGAG 59.610 37.037 11.62 7.26 42.68 3.69
81 82 7.225725 TCGTCCTTTAATTAAAAGTTCCAGGA 58.774 34.615 11.62 9.64 42.68 3.86
82 83 7.174426 ACTCGTCCTTTAATTAAAAGTTCCAGG 59.826 37.037 11.62 7.62 42.68 4.45
83 84 8.095937 ACTCGTCCTTTAATTAAAAGTTCCAG 57.904 34.615 11.62 6.53 42.68 3.86
84 85 8.347035 CAACTCGTCCTTTAATTAAAAGTTCCA 58.653 33.333 16.61 0.85 42.68 3.53
85 86 8.562052 TCAACTCGTCCTTTAATTAAAAGTTCC 58.438 33.333 16.61 4.06 42.68 3.62
88 89 9.893305 CAATCAACTCGTCCTTTAATTAAAAGT 57.107 29.630 11.62 8.79 42.68 2.66
89 90 9.893305 ACAATCAACTCGTCCTTTAATTAAAAG 57.107 29.630 11.62 6.20 43.66 2.27
90 91 9.672086 CACAATCAACTCGTCCTTTAATTAAAA 57.328 29.630 11.62 0.00 0.00 1.52
91 92 7.806014 GCACAATCAACTCGTCCTTTAATTAAA 59.194 33.333 10.16 10.16 0.00 1.52
92 93 7.302524 GCACAATCAACTCGTCCTTTAATTAA 58.697 34.615 0.00 0.00 0.00 1.40
93 94 6.128117 GGCACAATCAACTCGTCCTTTAATTA 60.128 38.462 0.00 0.00 0.00 1.40
94 95 5.335661 GGCACAATCAACTCGTCCTTTAATT 60.336 40.000 0.00 0.00 0.00 1.40
95 96 4.156008 GGCACAATCAACTCGTCCTTTAAT 59.844 41.667 0.00 0.00 0.00 1.40
96 97 3.500680 GGCACAATCAACTCGTCCTTTAA 59.499 43.478 0.00 0.00 0.00 1.52
97 98 3.071479 GGCACAATCAACTCGTCCTTTA 58.929 45.455 0.00 0.00 0.00 1.85
98 99 1.880027 GGCACAATCAACTCGTCCTTT 59.120 47.619 0.00 0.00 0.00 3.11
99 100 1.523758 GGCACAATCAACTCGTCCTT 58.476 50.000 0.00 0.00 0.00 3.36
100 101 0.321653 GGGCACAATCAACTCGTCCT 60.322 55.000 0.00 0.00 0.00 3.85
101 102 1.305930 GGGGCACAATCAACTCGTCC 61.306 60.000 0.00 0.00 0.00 4.79
102 103 1.635663 CGGGGCACAATCAACTCGTC 61.636 60.000 0.00 0.00 0.00 4.20
103 104 1.671054 CGGGGCACAATCAACTCGT 60.671 57.895 0.00 0.00 0.00 4.18
104 105 3.039202 GCGGGGCACAATCAACTCG 62.039 63.158 0.00 0.00 0.00 4.18
105 106 1.926511 CTGCGGGGCACAATCAACTC 61.927 60.000 0.00 0.00 33.79 3.01
106 107 1.973281 CTGCGGGGCACAATCAACT 60.973 57.895 0.00 0.00 33.79 3.16
107 108 2.568090 CTGCGGGGCACAATCAAC 59.432 61.111 0.00 0.00 33.79 3.18
108 109 3.372730 GCTGCGGGGCACAATCAA 61.373 61.111 0.00 0.00 33.79 2.57
117 118 2.762459 TAGTACTGGGCTGCGGGG 60.762 66.667 5.39 0.00 0.00 5.73
118 119 1.895020 TTGTAGTACTGGGCTGCGGG 61.895 60.000 5.39 0.00 0.00 6.13
119 120 0.460284 CTTGTAGTACTGGGCTGCGG 60.460 60.000 5.39 0.00 0.00 5.69
120 121 0.530744 TCTTGTAGTACTGGGCTGCG 59.469 55.000 5.39 0.00 0.00 5.18
121 122 1.825474 TCTCTTGTAGTACTGGGCTGC 59.175 52.381 5.39 0.00 0.00 5.25
122 123 3.118956 CCTTCTCTTGTAGTACTGGGCTG 60.119 52.174 5.39 0.00 0.00 4.85
123 124 3.100671 CCTTCTCTTGTAGTACTGGGCT 58.899 50.000 5.39 0.00 0.00 5.19
124 125 3.097614 TCCTTCTCTTGTAGTACTGGGC 58.902 50.000 5.39 0.00 0.00 5.36
125 126 5.246429 ACTTTCCTTCTCTTGTAGTACTGGG 59.754 44.000 5.39 0.00 0.00 4.45
126 127 6.209788 AGACTTTCCTTCTCTTGTAGTACTGG 59.790 42.308 5.39 0.00 0.00 4.00
127 128 7.222000 AGACTTTCCTTCTCTTGTAGTACTG 57.778 40.000 5.39 0.00 0.00 2.74
128 129 7.943447 TGTAGACTTTCCTTCTCTTGTAGTACT 59.057 37.037 0.00 0.00 0.00 2.73
129 130 8.108551 TGTAGACTTTCCTTCTCTTGTAGTAC 57.891 38.462 0.00 0.00 0.00 2.73
130 131 8.574737 GTTGTAGACTTTCCTTCTCTTGTAGTA 58.425 37.037 0.00 0.00 0.00 1.82
131 132 7.435305 GTTGTAGACTTTCCTTCTCTTGTAGT 58.565 38.462 0.00 0.00 0.00 2.73
132 133 6.869388 GGTTGTAGACTTTCCTTCTCTTGTAG 59.131 42.308 0.00 0.00 0.00 2.74
137 138 5.743422 GCTTGGTTGTAGACTTTCCTTCTCT 60.743 44.000 0.00 0.00 0.00 3.10
178 179 4.867047 GCATCGACGGATATCTGATCATTT 59.133 41.667 18.63 0.00 0.00 2.32
182 183 2.425312 AGGCATCGACGGATATCTGATC 59.575 50.000 18.63 10.51 0.00 2.92
184 185 1.813178 GAGGCATCGACGGATATCTGA 59.187 52.381 18.63 4.48 0.00 3.27
185 186 1.135257 GGAGGCATCGACGGATATCTG 60.135 57.143 10.14 10.14 0.00 2.90
186 187 1.178276 GGAGGCATCGACGGATATCT 58.822 55.000 2.05 0.00 0.00 1.98
190 191 1.368950 CATGGAGGCATCGACGGAT 59.631 57.895 0.00 0.00 0.00 4.18
191 192 2.796193 CCATGGAGGCATCGACGGA 61.796 63.158 5.56 0.00 0.00 4.69
192 193 2.280389 CCATGGAGGCATCGACGG 60.280 66.667 5.56 0.00 0.00 4.79
260 268 3.491581 GGCGTACCTATCATGTCGG 57.508 57.895 0.00 0.00 0.00 4.79
310 345 1.447314 CGGAAAGGGTAGTGGACGC 60.447 63.158 0.00 0.00 41.29 5.19
451 486 0.391597 GTCCACGACCCAGAAGTTCA 59.608 55.000 5.50 0.00 0.00 3.18
453 488 1.366366 CGTCCACGACCCAGAAGTT 59.634 57.895 0.00 0.00 43.02 2.66
552 587 1.640428 GTCATCAATTCGACGAGGCA 58.360 50.000 0.00 0.00 0.00 4.75
671 709 4.748892 AGTCCATCAACACATAGACGAAG 58.251 43.478 0.00 0.00 0.00 3.79
689 727 3.942115 GCTTCCCAACAGAATAAGAGTCC 59.058 47.826 0.00 0.00 0.00 3.85
717 755 1.796796 CCAAGTAGCCGCAAGAAGC 59.203 57.895 0.00 0.00 43.02 3.86
728 766 1.077212 AGCAGCCATGGCCAAGTAG 60.077 57.895 33.14 16.43 43.17 2.57
747 785 1.070445 GGATGCTCCGATCACCCAG 59.930 63.158 0.00 0.00 0.00 4.45
764 802 2.226437 GTGGCTTGCGTTATCATATGGG 59.774 50.000 2.13 0.00 0.00 4.00
766 804 2.799978 TCGTGGCTTGCGTTATCATATG 59.200 45.455 0.00 0.00 0.00 1.78
845 883 1.144936 CATGAAGCCCGACCTCCTC 59.855 63.158 0.00 0.00 0.00 3.71
871 912 6.147821 ACAAACTCACACAATCTTATCCTTCG 59.852 38.462 0.00 0.00 0.00 3.79
994 1045 7.430441 TGCATGACAAGATAATCCATTGATTG 58.570 34.615 0.00 0.00 41.31 2.67
1004 1061 5.864418 AAGCCAATGCATGACAAGATAAT 57.136 34.783 0.00 0.00 41.13 1.28
1061 1118 3.771171 TGTGCTACAAATGCGCAAG 57.229 47.368 17.11 8.15 46.07 4.01
1073 1130 7.899178 TCACTCGAAGAAAAATTATGTGCTA 57.101 32.000 0.00 0.00 34.09 3.49
1078 1135 7.584987 AGGTGTTCACTCGAAGAAAAATTATG 58.415 34.615 1.92 0.00 34.09 1.90
1092 1149 1.569479 GCAGGCGAAGGTGTTCACTC 61.569 60.000 2.98 0.00 32.36 3.51
1094 1151 0.320421 TAGCAGGCGAAGGTGTTCAC 60.320 55.000 0.00 0.00 32.36 3.18
1120 1177 9.064706 CAATATCGACGGGGAGTATACTATTAT 57.935 37.037 5.09 0.00 0.00 1.28
1121 1178 8.267183 TCAATATCGACGGGGAGTATACTATTA 58.733 37.037 5.09 0.00 0.00 0.98
1166 1223 0.321671 ATGTGTAACTCTGCTGGCGT 59.678 50.000 0.00 0.00 38.04 5.68
1167 1224 2.293677 TATGTGTAACTCTGCTGGCG 57.706 50.000 0.00 0.00 38.04 5.69
1168 1225 3.535561 ACATATGTGTAACTCTGCTGGC 58.464 45.455 7.78 0.00 36.63 4.85
1169 1226 5.907207 AGTACATATGTGTAACTCTGCTGG 58.093 41.667 18.81 0.00 42.18 4.85
1171 1228 6.547880 AGCTAGTACATATGTGTAACTCTGCT 59.452 38.462 18.81 19.85 42.18 4.24
1172 1229 6.740110 AGCTAGTACATATGTGTAACTCTGC 58.260 40.000 18.81 18.31 42.18 4.26
1173 1230 9.833182 CATAGCTAGTACATATGTGTAACTCTG 57.167 37.037 18.81 10.93 42.18 3.35
1175 1232 8.794553 ACCATAGCTAGTACATATGTGTAACTC 58.205 37.037 18.81 3.66 42.18 3.01
1178 1235 9.803507 ACTACCATAGCTAGTACATATGTGTAA 57.196 33.333 18.81 2.45 42.18 2.41
1180 1237 9.451002 CTACTACCATAGCTAGTACATATGTGT 57.549 37.037 18.81 8.09 42.39 3.72
1181 1238 9.451002 ACTACTACCATAGCTAGTACATATGTG 57.549 37.037 18.81 2.54 0.00 3.21
1188 1248 8.351461 CCAAGAAACTACTACCATAGCTAGTAC 58.649 40.741 0.00 0.00 0.00 2.73
1198 1258 4.566907 GGGATTGCCAAGAAACTACTACCA 60.567 45.833 0.00 0.00 35.15 3.25
1200 1260 4.395231 GTGGGATTGCCAAGAAACTACTAC 59.605 45.833 0.00 0.00 35.15 2.73
1288 1504 2.629017 ATTTGTGGGCCAGGAAGAAT 57.371 45.000 6.40 0.00 0.00 2.40
1349 1565 3.119884 CCGATCACTTGCTGCATTTGTAA 60.120 43.478 1.84 0.00 0.00 2.41
1364 1580 0.035820 TACCTTGTTGGGCCGATCAC 60.036 55.000 0.00 0.00 41.11 3.06
1387 1603 3.119424 TGACCGCGACAATATCTGTGTAA 60.119 43.478 8.23 0.00 38.84 2.41
1957 2173 5.152623 AGCTGTAAACATCTGACTTGCTA 57.847 39.130 0.00 0.00 0.00 3.49
1966 2182 3.535561 CATCCCGAAGCTGTAAACATCT 58.464 45.455 0.00 0.00 0.00 2.90
2222 2459 4.428845 CCTTGAAGGCACCTGCAT 57.571 55.556 0.00 0.00 44.36 3.96
2368 2783 4.797868 TGCAACTTTTCACAAGATTTGTCG 59.202 37.500 0.00 0.00 43.23 4.35
2432 2854 7.046652 AGCATGGCTTATAATATAGAGTGCTG 58.953 38.462 0.00 0.00 33.89 4.41
2433 2855 7.192852 AGCATGGCTTATAATATAGAGTGCT 57.807 36.000 0.00 0.00 33.89 4.40
2459 2889 6.169800 TGTATTTCGGATGAACATTCACAGA 58.830 36.000 0.00 0.00 40.49 3.41
2488 2918 7.936950 AATCTCACACTCGATACACATAATG 57.063 36.000 0.00 0.00 0.00 1.90
2509 2939 5.549742 TGGGCAATGGGATAAATGAAATC 57.450 39.130 0.00 0.00 0.00 2.17
2576 3008 5.582950 TTTCCCCATGTATAATCCTCTGG 57.417 43.478 0.00 0.00 0.00 3.86
2679 3134 1.976132 GCCATCAGGAGCTACAGGCA 61.976 60.000 14.57 0.00 40.29 4.75
2680 3135 1.227793 GCCATCAGGAGCTACAGGC 60.228 63.158 0.00 1.90 36.89 4.85
2713 3173 6.258230 CATGGTTTCATGCTTCTTCAGTTA 57.742 37.500 0.00 0.00 43.44 2.24
2728 3188 6.435428 ACGTGTTGAATAGTTTCATGGTTTC 58.565 36.000 0.00 0.00 41.38 2.78
2738 3198 9.393249 CATTTTGTCATAACGTGTTGAATAGTT 57.607 29.630 2.54 0.00 0.00 2.24
2742 3202 5.633182 GCCATTTTGTCATAACGTGTTGAAT 59.367 36.000 2.54 0.00 0.00 2.57
2774 3237 3.322254 CCTAGTAGGTTGCAGATTCCGAT 59.678 47.826 8.17 0.00 0.00 4.18
2840 3312 3.119495 ACCTCACTGAAAAACAAGTGCAC 60.119 43.478 9.40 9.40 32.16 4.57
2970 3444 8.470002 CATCTATGGGATCTATACGTGATGAAA 58.530 37.037 0.00 0.00 32.05 2.69
2973 3447 7.573968 TCATCTATGGGATCTATACGTGATG 57.426 40.000 0.00 0.00 31.27 3.07
2996 3475 4.795278 CCAACATTCAAGCGCTCTTTAATC 59.205 41.667 12.06 0.00 26.92 1.75
2997 3476 4.458989 TCCAACATTCAAGCGCTCTTTAAT 59.541 37.500 12.06 5.49 28.89 1.40
2998 3477 3.818210 TCCAACATTCAAGCGCTCTTTAA 59.182 39.130 12.06 2.97 0.00 1.52
3017 3496 8.802267 CAAGTTTCCTCCAAATTTATTACTCCA 58.198 33.333 0.00 0.00 0.00 3.86
3018 3497 8.803235 ACAAGTTTCCTCCAAATTTATTACTCC 58.197 33.333 0.00 0.00 0.00 3.85
3019 3498 9.626045 CACAAGTTTCCTCCAAATTTATTACTC 57.374 33.333 0.00 0.00 0.00 2.59
3079 3572 3.131478 GGCGCCCCACACATGTAC 61.131 66.667 18.11 0.00 0.00 2.90
3248 3808 3.663815 ATCTGCCGTCGGGACTCCT 62.664 63.158 14.38 0.00 34.06 3.69
3283 3843 4.514577 AAGTGAGATCCGCCGCCG 62.515 66.667 0.00 0.00 0.00 6.46
3284 3844 2.892425 CAAGTGAGATCCGCCGCC 60.892 66.667 0.00 0.00 0.00 6.13
3285 3845 3.567797 GCAAGTGAGATCCGCCGC 61.568 66.667 0.00 0.00 0.00 6.53
3286 3846 2.892425 GGCAAGTGAGATCCGCCG 60.892 66.667 0.00 0.00 32.14 6.46
3287 3847 2.109126 GTGGCAAGTGAGATCCGCC 61.109 63.158 0.00 0.00 43.28 6.13
3288 3848 1.078848 AGTGGCAAGTGAGATCCGC 60.079 57.895 0.00 0.00 0.00 5.54
3289 3849 0.742281 CCAGTGGCAAGTGAGATCCG 60.742 60.000 0.00 0.00 0.00 4.18
3290 3850 0.393537 CCCAGTGGCAAGTGAGATCC 60.394 60.000 2.61 0.00 0.00 3.36
3291 3851 0.393537 CCCCAGTGGCAAGTGAGATC 60.394 60.000 2.61 0.00 0.00 2.75
3292 3852 1.687612 CCCCAGTGGCAAGTGAGAT 59.312 57.895 2.61 0.00 0.00 2.75
3293 3853 3.160585 CCCCAGTGGCAAGTGAGA 58.839 61.111 2.61 0.00 0.00 3.27
3302 3862 0.391263 GTAAGACTTCGCCCCAGTGG 60.391 60.000 0.63 0.63 37.09 4.00
3303 3863 0.608640 AGTAAGACTTCGCCCCAGTG 59.391 55.000 0.00 0.00 0.00 3.66
3304 3864 0.608640 CAGTAAGACTTCGCCCCAGT 59.391 55.000 0.00 0.00 0.00 4.00
3305 3865 0.895530 TCAGTAAGACTTCGCCCCAG 59.104 55.000 0.00 0.00 0.00 4.45
3306 3866 0.895530 CTCAGTAAGACTTCGCCCCA 59.104 55.000 0.00 0.00 0.00 4.96
3307 3867 0.460459 GCTCAGTAAGACTTCGCCCC 60.460 60.000 0.00 0.00 0.00 5.80
3308 3868 0.802607 CGCTCAGTAAGACTTCGCCC 60.803 60.000 0.00 0.00 0.00 6.13
3309 3869 0.802607 CCGCTCAGTAAGACTTCGCC 60.803 60.000 0.00 0.00 0.00 5.54
3310 3870 1.414527 GCCGCTCAGTAAGACTTCGC 61.415 60.000 0.00 0.00 0.00 4.70
3311 3871 1.134530 CGCCGCTCAGTAAGACTTCG 61.135 60.000 0.00 0.00 0.00 3.79
3312 3872 0.802607 CCGCCGCTCAGTAAGACTTC 60.803 60.000 0.00 0.00 0.00 3.01
3313 3873 1.215647 CCGCCGCTCAGTAAGACTT 59.784 57.895 0.00 0.00 0.00 3.01
3314 3874 2.885861 CCGCCGCTCAGTAAGACT 59.114 61.111 0.00 0.00 0.00 3.24
3315 3875 2.886124 GCCGCCGCTCAGTAAGAC 60.886 66.667 0.00 0.00 0.00 3.01
3316 3876 4.492160 CGCCGCCGCTCAGTAAGA 62.492 66.667 0.00 0.00 0.00 2.10
3323 3883 4.280494 TAAGATCCGCCGCCGCTC 62.280 66.667 0.00 0.00 0.00 5.03
3324 3884 4.587189 GTAAGATCCGCCGCCGCT 62.587 66.667 0.00 0.00 0.00 5.52
3325 3885 4.587189 AGTAAGATCCGCCGCCGC 62.587 66.667 0.00 0.00 0.00 6.53
3326 3886 2.658593 CAGTAAGATCCGCCGCCG 60.659 66.667 0.00 0.00 0.00 6.46
3327 3887 1.300233 CTCAGTAAGATCCGCCGCC 60.300 63.158 0.00 0.00 0.00 6.13
3328 3888 1.951631 GCTCAGTAAGATCCGCCGC 60.952 63.158 0.00 0.00 0.00 6.53
3329 3889 1.658717 CGCTCAGTAAGATCCGCCG 60.659 63.158 0.00 0.00 0.00 6.46
3330 3890 1.300233 CCGCTCAGTAAGATCCGCC 60.300 63.158 0.00 0.00 0.00 6.13
3331 3891 1.951631 GCCGCTCAGTAAGATCCGC 60.952 63.158 0.00 0.00 0.00 5.54
3332 3892 1.658717 CGCCGCTCAGTAAGATCCG 60.659 63.158 0.00 0.00 0.00 4.18
3333 3893 1.300233 CCGCCGCTCAGTAAGATCC 60.300 63.158 0.00 0.00 0.00 3.36
3334 3894 1.951631 GCCGCCGCTCAGTAAGATC 60.952 63.158 0.00 0.00 0.00 2.75
3335 3895 2.107141 GCCGCCGCTCAGTAAGAT 59.893 61.111 0.00 0.00 0.00 2.40
3336 3896 3.356639 CTGCCGCCGCTCAGTAAGA 62.357 63.158 0.00 0.00 35.36 2.10
3337 3897 2.635229 ATCTGCCGCCGCTCAGTAAG 62.635 60.000 0.00 0.00 35.36 2.34
3338 3898 2.238847 AATCTGCCGCCGCTCAGTAA 62.239 55.000 0.00 0.00 35.36 2.24
3339 3899 1.388837 TAATCTGCCGCCGCTCAGTA 61.389 55.000 0.00 0.00 35.36 2.74
3340 3900 2.721167 TAATCTGCCGCCGCTCAGT 61.721 57.895 0.00 0.00 35.36 3.41
3341 3901 2.106938 TAATCTGCCGCCGCTCAG 59.893 61.111 0.00 3.82 35.36 3.35
3342 3902 2.202878 GTAATCTGCCGCCGCTCA 60.203 61.111 0.00 0.00 35.36 4.26
3343 3903 2.107141 AGTAATCTGCCGCCGCTC 59.893 61.111 0.00 0.00 35.36 5.03
3344 3904 2.202932 CAGTAATCTGCCGCCGCT 60.203 61.111 0.00 0.00 34.79 5.52
3345 3905 1.813753 TTCAGTAATCTGCCGCCGC 60.814 57.895 0.00 0.00 41.10 6.53
3346 3906 0.739462 TGTTCAGTAATCTGCCGCCG 60.739 55.000 0.00 0.00 41.10 6.46
3347 3907 1.331756 CATGTTCAGTAATCTGCCGCC 59.668 52.381 0.00 0.00 41.10 6.13
3348 3908 1.331756 CCATGTTCAGTAATCTGCCGC 59.668 52.381 0.00 0.00 41.10 6.53
3349 3909 2.352651 CACCATGTTCAGTAATCTGCCG 59.647 50.000 0.00 0.00 41.10 5.69
3350 3910 2.684881 CCACCATGTTCAGTAATCTGCC 59.315 50.000 0.00 0.00 41.10 4.85
3351 3911 2.684881 CCCACCATGTTCAGTAATCTGC 59.315 50.000 0.00 0.00 41.10 4.26
3352 3912 2.684881 GCCCACCATGTTCAGTAATCTG 59.315 50.000 0.00 0.00 42.54 2.90
3353 3913 2.357154 GGCCCACCATGTTCAGTAATCT 60.357 50.000 0.00 0.00 35.26 2.40
3354 3914 2.024414 GGCCCACCATGTTCAGTAATC 58.976 52.381 0.00 0.00 35.26 1.75
3355 3915 1.640670 AGGCCCACCATGTTCAGTAAT 59.359 47.619 0.00 0.00 39.06 1.89
3356 3916 1.072266 AGGCCCACCATGTTCAGTAA 58.928 50.000 0.00 0.00 39.06 2.24
3357 3917 1.072266 AAGGCCCACCATGTTCAGTA 58.928 50.000 0.00 0.00 39.06 2.74
3358 3918 0.188342 AAAGGCCCACCATGTTCAGT 59.812 50.000 0.00 0.00 39.06 3.41
3359 3919 1.273327 GAAAAGGCCCACCATGTTCAG 59.727 52.381 0.00 0.00 39.06 3.02
3360 3920 1.337118 GAAAAGGCCCACCATGTTCA 58.663 50.000 0.00 0.00 39.06 3.18
3361 3921 1.337118 TGAAAAGGCCCACCATGTTC 58.663 50.000 0.00 0.00 39.06 3.18
3362 3922 1.799933 TTGAAAAGGCCCACCATGTT 58.200 45.000 0.00 0.00 39.06 2.71
3363 3923 1.693606 CTTTGAAAAGGCCCACCATGT 59.306 47.619 0.00 0.00 39.06 3.21
3364 3924 1.969923 TCTTTGAAAAGGCCCACCATG 59.030 47.619 0.00 0.00 39.06 3.66
3365 3925 2.250924 CTCTTTGAAAAGGCCCACCAT 58.749 47.619 0.00 0.00 39.06 3.55
3366 3926 1.063266 ACTCTTTGAAAAGGCCCACCA 60.063 47.619 0.00 0.00 39.06 4.17
3367 3927 1.704641 ACTCTTTGAAAAGGCCCACC 58.295 50.000 0.00 0.00 36.67 4.61
3368 3928 2.820197 CCTACTCTTTGAAAAGGCCCAC 59.180 50.000 0.00 0.00 36.67 4.61
3369 3929 2.225017 CCCTACTCTTTGAAAAGGCCCA 60.225 50.000 0.00 0.00 36.67 5.36
3370 3930 2.447443 CCCTACTCTTTGAAAAGGCCC 58.553 52.381 0.00 0.00 36.67 5.80
3371 3931 1.819288 GCCCTACTCTTTGAAAAGGCC 59.181 52.381 0.00 0.00 36.67 5.19
3372 3932 1.468914 CGCCCTACTCTTTGAAAAGGC 59.531 52.381 3.08 0.00 36.67 4.35
3373 3933 2.742589 GTCGCCCTACTCTTTGAAAAGG 59.257 50.000 3.08 0.00 36.67 3.11
3374 3934 3.665190 AGTCGCCCTACTCTTTGAAAAG 58.335 45.455 0.00 0.00 37.36 2.27
3375 3935 3.764237 AGTCGCCCTACTCTTTGAAAA 57.236 42.857 0.00 0.00 0.00 2.29
3376 3936 3.399330 CAAGTCGCCCTACTCTTTGAAA 58.601 45.455 0.00 0.00 0.00 2.69
3377 3937 2.289444 CCAAGTCGCCCTACTCTTTGAA 60.289 50.000 0.00 0.00 0.00 2.69
3378 3938 1.275291 CCAAGTCGCCCTACTCTTTGA 59.725 52.381 0.00 0.00 0.00 2.69
3379 3939 1.275291 TCCAAGTCGCCCTACTCTTTG 59.725 52.381 0.00 0.00 0.00 2.77
3380 3940 1.640917 TCCAAGTCGCCCTACTCTTT 58.359 50.000 0.00 0.00 0.00 2.52
3381 3941 1.757699 GATCCAAGTCGCCCTACTCTT 59.242 52.381 0.00 0.00 0.00 2.85
3382 3942 1.063567 AGATCCAAGTCGCCCTACTCT 60.064 52.381 0.00 0.00 0.00 3.24
3383 3943 1.338655 GAGATCCAAGTCGCCCTACTC 59.661 57.143 0.00 0.00 0.00 2.59
3384 3944 1.404843 GAGATCCAAGTCGCCCTACT 58.595 55.000 0.00 0.00 0.00 2.57
3385 3945 0.030908 CGAGATCCAAGTCGCCCTAC 59.969 60.000 0.00 0.00 0.00 3.18
3386 3946 1.107538 CCGAGATCCAAGTCGCCCTA 61.108 60.000 0.00 0.00 34.78 3.53
3387 3947 2.427245 CCGAGATCCAAGTCGCCCT 61.427 63.158 0.00 0.00 34.78 5.19
3388 3948 2.107141 CCGAGATCCAAGTCGCCC 59.893 66.667 0.00 0.00 34.78 6.13
3389 3949 2.586357 GCCGAGATCCAAGTCGCC 60.586 66.667 0.00 0.00 34.78 5.54
3390 3950 2.586357 GGCCGAGATCCAAGTCGC 60.586 66.667 0.00 0.00 34.78 5.19
3391 3951 0.391130 TTTGGCCGAGATCCAAGTCG 60.391 55.000 0.00 0.00 43.67 4.18
3392 3952 2.044123 ATTTGGCCGAGATCCAAGTC 57.956 50.000 0.00 0.00 43.67 3.01
3393 3953 2.514458 AATTTGGCCGAGATCCAAGT 57.486 45.000 0.00 0.00 43.67 3.16
3394 3954 3.874392 AAAATTTGGCCGAGATCCAAG 57.126 42.857 0.00 0.00 43.67 3.61
3395 3955 3.576118 TCAAAAATTTGGCCGAGATCCAA 59.424 39.130 0.00 0.00 41.47 3.53
3396 3956 3.161067 TCAAAAATTTGGCCGAGATCCA 58.839 40.909 0.00 0.00 38.66 3.41
3397 3957 3.866883 TCAAAAATTTGGCCGAGATCC 57.133 42.857 0.00 0.00 38.66 3.36
3398 3958 6.538189 TTTTTCAAAAATTTGGCCGAGATC 57.462 33.333 0.00 0.00 38.66 2.75


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

AutoCloner maintained by Alex Coulton.