Multiple sequence alignment - TraesCS5A01G145200

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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 TraesCS5A01G145200 chr5A 100.000 2693 0 0 1 2693 321050948 321053640 0.000000e+00 4974
1 TraesCS5A01G145200 chr5A 76.514 545 119 8 2151 2691 394994852 394994313 3.390000e-74 289
2 TraesCS5A01G145200 chr5D 89.944 2128 156 21 597 2691 233689642 233687540 0.000000e+00 2691
3 TraesCS5A01G145200 chr5D 89.091 330 18 8 272 598 233690046 233689732 6.990000e-106 394
4 TraesCS5A01G145200 chr5B 89.347 1408 64 21 605 1991 271181596 271182938 0.000000e+00 1690
5 TraesCS5A01G145200 chr5B 90.455 440 23 7 173 598 271180835 271181269 1.810000e-156 562
6 TraesCS5A01G145200 chr5B 78.608 589 109 13 2109 2690 548156585 548156007 9.100000e-100 374
7 TraesCS5A01G145200 chr1B 80.290 482 88 5 2214 2691 496196582 496197060 9.170000e-95 357
8 TraesCS5A01G145200 chr7D 79.175 509 101 5 2186 2691 185369807 185370313 5.520000e-92 348
9 TraesCS5A01G145200 chr4D 78.727 597 68 33 1077 1645 102534320 102533755 7.140000e-91 344
10 TraesCS5A01G145200 chr1A 78.506 549 97 10 2153 2691 535293568 535294105 9.230000e-90 340
11 TraesCS5A01G145200 chr4B 79.583 480 91 7 2216 2691 168140695 168140219 1.190000e-88 337
12 TraesCS5A01G145200 chr4B 78.020 596 74 30 1077 1645 147066781 147066216 3.340000e-84 322
13 TraesCS5A01G145200 chr4A 78.108 539 112 6 2154 2688 532593803 532594339 1.190000e-88 337
14 TraesCS5A01G145200 chr4A 77.737 548 108 13 2151 2690 478577496 478576955 9.300000e-85 324
15 TraesCS5A01G145200 chr2B 80.526 190 30 6 2177 2362 142383882 142384068 3.620000e-29 139


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 TraesCS5A01G145200 chr5A 321050948 321053640 2692 False 4974.0 4974 100.0000 1 2693 1 chr5A.!!$F1 2692
1 TraesCS5A01G145200 chr5A 394994313 394994852 539 True 289.0 289 76.5140 2151 2691 1 chr5A.!!$R1 540
2 TraesCS5A01G145200 chr5D 233687540 233690046 2506 True 1542.5 2691 89.5175 272 2691 2 chr5D.!!$R1 2419
3 TraesCS5A01G145200 chr5B 271180835 271182938 2103 False 1126.0 1690 89.9010 173 1991 2 chr5B.!!$F1 1818
4 TraesCS5A01G145200 chr5B 548156007 548156585 578 True 374.0 374 78.6080 2109 2690 1 chr5B.!!$R1 581
5 TraesCS5A01G145200 chr7D 185369807 185370313 506 False 348.0 348 79.1750 2186 2691 1 chr7D.!!$F1 505
6 TraesCS5A01G145200 chr4D 102533755 102534320 565 True 344.0 344 78.7270 1077 1645 1 chr4D.!!$R1 568
7 TraesCS5A01G145200 chr1A 535293568 535294105 537 False 340.0 340 78.5060 2153 2691 1 chr1A.!!$F1 538
8 TraesCS5A01G145200 chr4B 147066216 147066781 565 True 322.0 322 78.0200 1077 1645 1 chr4B.!!$R1 568
9 TraesCS5A01G145200 chr4A 532593803 532594339 536 False 337.0 337 78.1080 2154 2688 1 chr4A.!!$F1 534
10 TraesCS5A01G145200 chr4A 478576955 478577496 541 True 324.0 324 77.7370 2151 2690 1 chr4A.!!$R1 539

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
72 73 0.039437 CGGTATAGGCTAGTGTGGCG 60.039 60.0 0.0 0.0 37.59 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2450 0.104304 GATGCCCTTACACGATCGGT 59.896 55.0 20.98 16.2 0.0 4.69 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
22 23 2.484889 GCATACTTGCCCTAGTGTAGC 58.515 52.381 0.00 0.00 43.38 3.58
23 24 2.103263 GCATACTTGCCCTAGTGTAGCT 59.897 50.000 0.00 0.00 43.38 3.32
24 25 3.432326 GCATACTTGCCCTAGTGTAGCTT 60.432 47.826 0.00 0.00 43.38 3.74
25 26 4.372656 CATACTTGCCCTAGTGTAGCTTC 58.627 47.826 0.00 0.00 0.00 3.86
26 27 2.541466 ACTTGCCCTAGTGTAGCTTCT 58.459 47.619 0.00 0.00 0.00 2.85
27 28 3.709587 ACTTGCCCTAGTGTAGCTTCTA 58.290 45.455 0.00 0.00 0.00 2.10
28 29 3.702045 ACTTGCCCTAGTGTAGCTTCTAG 59.298 47.826 0.00 2.41 34.98 2.43
29 30 3.383698 TGCCCTAGTGTAGCTTCTAGT 57.616 47.619 14.62 0.35 33.81 2.57
30 31 3.709587 TGCCCTAGTGTAGCTTCTAGTT 58.290 45.455 14.62 0.00 33.81 2.24
31 32 4.094476 TGCCCTAGTGTAGCTTCTAGTTT 58.906 43.478 14.62 0.00 33.81 2.66
32 33 4.159879 TGCCCTAGTGTAGCTTCTAGTTTC 59.840 45.833 14.62 7.50 33.81 2.78
33 34 4.441773 GCCCTAGTGTAGCTTCTAGTTTCC 60.442 50.000 14.62 2.77 33.81 3.13
34 35 4.099727 CCCTAGTGTAGCTTCTAGTTTCCC 59.900 50.000 14.62 0.00 33.81 3.97
35 36 4.710375 CCTAGTGTAGCTTCTAGTTTCCCA 59.290 45.833 14.62 0.00 33.81 4.37
36 37 5.364157 CCTAGTGTAGCTTCTAGTTTCCCAT 59.636 44.000 14.62 0.00 33.81 4.00
37 38 5.346181 AGTGTAGCTTCTAGTTTCCCATC 57.654 43.478 0.00 0.00 0.00 3.51
38 39 4.162509 AGTGTAGCTTCTAGTTTCCCATCC 59.837 45.833 0.00 0.00 0.00 3.51
39 40 4.081087 GTGTAGCTTCTAGTTTCCCATCCA 60.081 45.833 0.00 0.00 0.00 3.41
40 41 4.534500 TGTAGCTTCTAGTTTCCCATCCAA 59.466 41.667 0.00 0.00 0.00 3.53
41 42 4.870021 AGCTTCTAGTTTCCCATCCAAT 57.130 40.909 0.00 0.00 0.00 3.16
42 43 4.530875 AGCTTCTAGTTTCCCATCCAATG 58.469 43.478 0.00 0.00 0.00 2.82
43 44 4.228210 AGCTTCTAGTTTCCCATCCAATGA 59.772 41.667 0.00 0.00 0.00 2.57
44 45 4.949856 GCTTCTAGTTTCCCATCCAATGAA 59.050 41.667 0.00 0.00 0.00 2.57
45 46 5.163612 GCTTCTAGTTTCCCATCCAATGAAC 60.164 44.000 0.00 0.00 0.00 3.18
46 47 5.779241 TCTAGTTTCCCATCCAATGAACT 57.221 39.130 0.00 0.00 32.04 3.01
47 48 5.500234 TCTAGTTTCCCATCCAATGAACTG 58.500 41.667 0.00 0.00 30.50 3.16
48 49 4.387026 AGTTTCCCATCCAATGAACTGA 57.613 40.909 0.00 0.00 0.00 3.41
49 50 4.082125 AGTTTCCCATCCAATGAACTGAC 58.918 43.478 0.00 0.00 0.00 3.51
50 51 2.806945 TCCCATCCAATGAACTGACC 57.193 50.000 0.00 0.00 0.00 4.02
51 52 1.991813 TCCCATCCAATGAACTGACCA 59.008 47.619 0.00 0.00 0.00 4.02
52 53 2.025981 TCCCATCCAATGAACTGACCAG 60.026 50.000 0.00 0.00 0.00 4.00
53 54 1.747355 CCATCCAATGAACTGACCAGC 59.253 52.381 0.00 0.00 0.00 4.85
54 55 1.399440 CATCCAATGAACTGACCAGCG 59.601 52.381 0.00 0.00 0.00 5.18
55 56 0.321564 TCCAATGAACTGACCAGCGG 60.322 55.000 0.00 0.00 0.00 5.52
56 57 0.606401 CCAATGAACTGACCAGCGGT 60.606 55.000 0.00 0.00 39.44 5.68
57 58 1.338674 CCAATGAACTGACCAGCGGTA 60.339 52.381 0.09 0.00 35.25 4.02
58 59 2.632377 CAATGAACTGACCAGCGGTAT 58.368 47.619 0.09 0.00 35.25 2.73
59 60 3.431626 CCAATGAACTGACCAGCGGTATA 60.432 47.826 0.09 0.00 35.25 1.47
60 61 3.735237 ATGAACTGACCAGCGGTATAG 57.265 47.619 0.09 5.40 35.25 1.31
61 62 1.754803 TGAACTGACCAGCGGTATAGG 59.245 52.381 0.09 0.00 35.25 2.57
62 63 0.464452 AACTGACCAGCGGTATAGGC 59.536 55.000 0.09 0.00 35.25 3.93
63 64 0.397254 ACTGACCAGCGGTATAGGCT 60.397 55.000 0.09 0.00 42.61 4.58
64 65 1.133575 ACTGACCAGCGGTATAGGCTA 60.134 52.381 0.00 0.00 39.08 3.93
65 66 1.542030 CTGACCAGCGGTATAGGCTAG 59.458 57.143 0.00 0.00 39.08 3.42
66 67 1.133575 TGACCAGCGGTATAGGCTAGT 60.134 52.381 0.00 0.00 39.08 2.57
67 68 1.269998 GACCAGCGGTATAGGCTAGTG 59.730 57.143 0.00 0.00 39.08 2.74
68 69 1.329256 CCAGCGGTATAGGCTAGTGT 58.671 55.000 0.00 0.00 39.08 3.55
69 70 1.000163 CCAGCGGTATAGGCTAGTGTG 60.000 57.143 0.00 0.00 39.08 3.82
70 71 1.000163 CAGCGGTATAGGCTAGTGTGG 60.000 57.143 0.00 0.00 39.08 4.17
71 72 0.319641 GCGGTATAGGCTAGTGTGGC 60.320 60.000 0.00 0.00 0.00 5.01
72 73 0.039437 CGGTATAGGCTAGTGTGGCG 60.039 60.000 0.00 0.00 37.59 5.69
73 74 1.325355 GGTATAGGCTAGTGTGGCGA 58.675 55.000 0.00 0.00 37.59 5.54
74 75 1.269998 GGTATAGGCTAGTGTGGCGAG 59.730 57.143 0.00 0.00 37.59 5.03
75 76 0.959553 TATAGGCTAGTGTGGCGAGC 59.040 55.000 0.00 0.00 43.77 5.03
76 77 0.757188 ATAGGCTAGTGTGGCGAGCT 60.757 55.000 0.00 0.00 43.93 4.09
77 78 0.106868 TAGGCTAGTGTGGCGAGCTA 60.107 55.000 0.00 0.00 43.93 3.32
78 79 1.227002 GGCTAGTGTGGCGAGCTAC 60.227 63.158 4.58 4.58 43.93 3.58
79 80 1.511305 GCTAGTGTGGCGAGCTACA 59.489 57.895 10.19 10.19 41.70 2.74
80 81 0.103208 GCTAGTGTGGCGAGCTACAT 59.897 55.000 16.78 9.01 41.70 2.29
81 82 1.337071 GCTAGTGTGGCGAGCTACATA 59.663 52.381 16.78 9.58 41.70 2.29
82 83 2.859032 GCTAGTGTGGCGAGCTACATAC 60.859 54.545 16.78 5.90 41.70 2.39
83 84 1.475403 AGTGTGGCGAGCTACATACT 58.525 50.000 16.78 8.02 39.50 2.12
84 85 1.135139 AGTGTGGCGAGCTACATACTG 59.865 52.381 16.78 0.00 39.50 2.74
85 86 0.179111 TGTGGCGAGCTACATACTGC 60.179 55.000 10.19 0.00 32.53 4.40
86 87 0.103208 GTGGCGAGCTACATACTGCT 59.897 55.000 6.71 0.00 42.82 4.24
96 97 4.992319 AGCTACATACTGCTCTAGTCTACG 59.008 45.833 0.00 0.00 40.89 3.51
97 98 4.751098 GCTACATACTGCTCTAGTCTACGT 59.249 45.833 0.00 0.00 40.89 3.57
98 99 5.925397 GCTACATACTGCTCTAGTCTACGTA 59.075 44.000 0.00 0.00 40.89 3.57
99 100 6.128849 GCTACATACTGCTCTAGTCTACGTAC 60.129 46.154 0.00 0.00 40.89 3.67
100 101 5.668471 ACATACTGCTCTAGTCTACGTACA 58.332 41.667 0.00 0.00 40.89 2.90
101 102 6.289834 ACATACTGCTCTAGTCTACGTACAT 58.710 40.000 0.00 0.00 40.89 2.29
102 103 6.203145 ACATACTGCTCTAGTCTACGTACATG 59.797 42.308 0.00 0.00 40.89 3.21
103 104 3.312973 ACTGCTCTAGTCTACGTACATGC 59.687 47.826 0.00 0.00 33.17 4.06
104 105 3.275999 TGCTCTAGTCTACGTACATGCA 58.724 45.455 0.00 0.00 0.00 3.96
105 106 3.883489 TGCTCTAGTCTACGTACATGCAT 59.117 43.478 0.00 0.00 0.00 3.96
106 107 4.222886 GCTCTAGTCTACGTACATGCATG 58.777 47.826 25.09 25.09 0.00 4.06
107 108 4.023963 GCTCTAGTCTACGTACATGCATGA 60.024 45.833 32.75 13.72 0.00 3.07
108 109 5.674933 TCTAGTCTACGTACATGCATGAG 57.325 43.478 32.75 22.93 0.00 2.90
109 110 5.123936 TCTAGTCTACGTACATGCATGAGT 58.876 41.667 32.75 26.64 0.00 3.41
110 111 4.720649 AGTCTACGTACATGCATGAGTT 57.279 40.909 32.75 13.48 0.00 3.01
111 112 5.830000 AGTCTACGTACATGCATGAGTTA 57.170 39.130 32.75 12.40 0.00 2.24
112 113 6.392625 AGTCTACGTACATGCATGAGTTAT 57.607 37.500 32.75 12.71 0.00 1.89
113 114 7.506328 AGTCTACGTACATGCATGAGTTATA 57.494 36.000 32.75 11.63 0.00 0.98
114 115 8.112016 AGTCTACGTACATGCATGAGTTATAT 57.888 34.615 32.75 11.20 0.00 0.86
115 116 8.023706 AGTCTACGTACATGCATGAGTTATATG 58.976 37.037 32.75 19.91 0.00 1.78
126 127 6.490721 TGCATGAGTTATATGCCATGAAATGA 59.509 34.615 0.00 0.00 46.67 2.57
127 128 7.014422 TGCATGAGTTATATGCCATGAAATGAA 59.986 33.333 0.00 0.00 46.67 2.57
128 129 7.868922 GCATGAGTTATATGCCATGAAATGAAA 59.131 33.333 0.00 0.00 46.28 2.69
146 147 9.651718 GAAATGAAATTCACGAGTTATATGACC 57.348 33.333 0.00 0.00 33.67 4.02
147 148 8.731275 AATGAAATTCACGAGTTATATGACCA 57.269 30.769 0.00 0.00 0.00 4.02
148 149 8.731275 ATGAAATTCACGAGTTATATGACCAA 57.269 30.769 0.00 0.00 0.00 3.67
149 150 8.196802 TGAAATTCACGAGTTATATGACCAAG 57.803 34.615 0.00 0.00 0.00 3.61
150 151 8.038351 TGAAATTCACGAGTTATATGACCAAGA 58.962 33.333 0.00 0.00 0.00 3.02
151 152 7.772332 AATTCACGAGTTATATGACCAAGAC 57.228 36.000 0.00 0.00 0.00 3.01
152 153 5.907866 TCACGAGTTATATGACCAAGACA 57.092 39.130 0.00 0.00 0.00 3.41
153 154 5.647589 TCACGAGTTATATGACCAAGACAC 58.352 41.667 0.00 0.00 0.00 3.67
154 155 5.184287 TCACGAGTTATATGACCAAGACACA 59.816 40.000 0.00 0.00 0.00 3.72
155 156 6.042777 CACGAGTTATATGACCAAGACACAT 58.957 40.000 0.00 0.00 0.00 3.21
156 157 7.067737 TCACGAGTTATATGACCAAGACACATA 59.932 37.037 0.00 0.00 0.00 2.29
157 158 7.867909 CACGAGTTATATGACCAAGACACATAT 59.132 37.037 0.00 0.00 39.49 1.78
158 159 8.421784 ACGAGTTATATGACCAAGACACATATT 58.578 33.333 0.00 0.00 37.98 1.28
159 160 9.261180 CGAGTTATATGACCAAGACACATATTT 57.739 33.333 0.00 0.00 37.98 1.40
163 164 7.823745 ATATGACCAAGACACATATTTTCCC 57.176 36.000 0.00 0.00 34.79 3.97
164 165 4.340617 TGACCAAGACACATATTTTCCCC 58.659 43.478 0.00 0.00 0.00 4.81
165 166 3.352648 ACCAAGACACATATTTTCCCCG 58.647 45.455 0.00 0.00 0.00 5.73
166 167 2.099098 CCAAGACACATATTTTCCCCGC 59.901 50.000 0.00 0.00 0.00 6.13
167 168 2.052782 AGACACATATTTTCCCCGCC 57.947 50.000 0.00 0.00 0.00 6.13
168 169 1.564348 AGACACATATTTTCCCCGCCT 59.436 47.619 0.00 0.00 0.00 5.52
169 170 1.676006 GACACATATTTTCCCCGCCTG 59.324 52.381 0.00 0.00 0.00 4.85
170 171 1.283613 ACACATATTTTCCCCGCCTGA 59.716 47.619 0.00 0.00 0.00 3.86
171 172 2.291282 ACACATATTTTCCCCGCCTGAA 60.291 45.455 0.00 0.00 0.00 3.02
201 202 4.471386 ACAGTTCATTACACTATGGCTCCT 59.529 41.667 0.00 0.00 0.00 3.69
207 208 5.540337 TCATTACACTATGGCTCCTTCTAGG 59.460 44.000 0.00 0.00 36.46 3.02
212 213 5.128991 ACACTATGGCTCCTTCTAGGTTAAC 59.871 44.000 0.00 0.00 36.53 2.01
217 218 9.310449 CTATGGCTCCTTCTAGGTTAACTATTA 57.690 37.037 5.42 0.00 36.53 0.98
239 244 7.654022 TTAAGCGAATTTAGGGAATGGAATT 57.346 32.000 0.00 0.00 40.93 2.17
251 256 3.002862 GGAATGGAATTTATACGCGCACA 59.997 43.478 5.73 0.00 36.07 4.57
329 344 1.876497 TTTCATTCCTTGCCGCAGCC 61.876 55.000 0.00 0.00 38.69 4.85
374 389 9.866936 CACTACGACTTTATCTATCTACACTTC 57.133 37.037 0.00 0.00 0.00 3.01
504 519 3.973973 TCCACGATTTATCCTGATTCCCT 59.026 43.478 0.00 0.00 0.00 4.20
542 557 4.041567 AGCCCGTCATTCATACATCCAATA 59.958 41.667 0.00 0.00 0.00 1.90
561 576 5.939296 CCAATAACAGCAACAAATGGGAAAT 59.061 36.000 0.00 0.00 0.00 2.17
616 952 9.277565 CTTTGATAGTTTCGTTATTTCCATGTG 57.722 33.333 0.00 0.00 0.00 3.21
651 991 5.738370 CGAAATTCCTATTTCCATGTCGAC 58.262 41.667 9.11 9.11 44.40 4.20
670 1010 6.479990 TGTCGACCAATCAAGAATAATGCTAG 59.520 38.462 14.12 0.00 0.00 3.42
672 1012 5.237127 CGACCAATCAAGAATAATGCTAGCA 59.763 40.000 21.85 21.85 0.00 3.49
673 1013 6.072838 CGACCAATCAAGAATAATGCTAGCAT 60.073 38.462 24.67 24.67 38.46 3.79
674 1014 6.978338 ACCAATCAAGAATAATGCTAGCATG 58.022 36.000 30.19 17.47 36.68 4.06
675 1015 5.862323 CCAATCAAGAATAATGCTAGCATGC 59.138 40.000 30.19 18.79 36.68 4.06
676 1016 6.294564 CCAATCAAGAATAATGCTAGCATGCT 60.295 38.462 30.19 25.99 36.68 3.79
677 1017 7.094506 CCAATCAAGAATAATGCTAGCATGCTA 60.095 37.037 30.19 25.40 36.68 3.49
678 1018 7.612668 ATCAAGAATAATGCTAGCATGCTAG 57.387 36.000 39.05 39.05 46.41 3.42
699 1039 0.812014 TTGCAACTGCCGAGACGAAA 60.812 50.000 0.00 0.00 41.18 3.46
700 1040 0.812014 TGCAACTGCCGAGACGAAAA 60.812 50.000 0.00 0.00 41.18 2.29
701 1041 0.306533 GCAACTGCCGAGACGAAAAA 59.693 50.000 0.00 0.00 34.31 1.94
727 1070 7.785033 AGAAAAGAAAATGTCCATTGTTGTCT 58.215 30.769 0.00 0.00 0.00 3.41
745 1088 4.733972 GTCTAGTGACAAAAAGCAGGTC 57.266 45.455 0.00 0.00 42.48 3.85
746 1089 3.498777 GTCTAGTGACAAAAAGCAGGTCC 59.501 47.826 0.00 0.00 42.48 4.46
747 1090 2.736670 AGTGACAAAAAGCAGGTCCT 57.263 45.000 0.00 0.00 0.00 3.85
748 1091 2.576615 AGTGACAAAAAGCAGGTCCTC 58.423 47.619 0.00 0.00 0.00 3.71
749 1092 1.264288 GTGACAAAAAGCAGGTCCTCG 59.736 52.381 0.00 0.00 0.00 4.63
750 1093 1.140052 TGACAAAAAGCAGGTCCTCGA 59.860 47.619 0.00 0.00 0.00 4.04
751 1094 1.801178 GACAAAAAGCAGGTCCTCGAG 59.199 52.381 5.13 5.13 0.00 4.04
752 1095 1.160137 CAAAAAGCAGGTCCTCGAGG 58.840 55.000 26.32 26.32 0.00 4.63
753 1096 1.056660 AAAAAGCAGGTCCTCGAGGA 58.943 50.000 30.49 30.49 43.08 3.71
785 1128 9.140286 TCTGATAAACTGAAAAGTATTCTCACG 57.860 33.333 0.00 0.00 0.00 4.35
833 1184 1.134491 CCGTCCACCTCACCTTATTCC 60.134 57.143 0.00 0.00 0.00 3.01
840 1191 2.959707 ACCTCACCTTATTCCTAGCTCG 59.040 50.000 0.00 0.00 0.00 5.03
879 1240 1.741327 CGGCCGGTATATATCCCCCG 61.741 65.000 20.10 10.08 40.12 5.73
927 1288 0.252467 ACCTCTCCTCCAACCTCCTG 60.252 60.000 0.00 0.00 0.00 3.86
933 1320 2.525629 TCCAACCTCCTGACCGCA 60.526 61.111 0.00 0.00 0.00 5.69
934 1321 2.111999 CTCCAACCTCCTGACCGCAA 62.112 60.000 0.00 0.00 0.00 4.85
935 1322 1.672356 CCAACCTCCTGACCGCAAG 60.672 63.158 0.00 0.00 0.00 4.01
936 1323 2.032681 AACCTCCTGACCGCAAGC 59.967 61.111 0.00 0.00 0.00 4.01
937 1324 2.818169 AACCTCCTGACCGCAAGCA 61.818 57.895 0.00 0.00 0.00 3.91
938 1325 2.743928 CCTCCTGACCGCAAGCAC 60.744 66.667 0.00 0.00 0.00 4.40
939 1326 3.114616 CTCCTGACCGCAAGCACG 61.115 66.667 0.00 0.00 0.00 5.34
1017 1410 4.702274 ATGGCCAAGGTGCACCCC 62.702 66.667 32.29 24.96 36.42 4.95
1272 1665 2.705826 CGGCGCAAGATCAAGCTC 59.294 61.111 10.83 0.14 43.02 4.09
1273 1666 2.705826 GGCGCAAGATCAAGCTCG 59.294 61.111 10.83 0.00 43.02 5.03
1308 1701 1.374252 GCACTGGGTGGTGTACGAG 60.374 63.158 0.00 0.00 39.21 4.18
1779 2196 0.250727 CAAGGTTCTTCGCAAGGGGA 60.251 55.000 0.00 0.00 38.47 4.81
1867 2284 7.751768 AGTAGCAAAGCAGAAGAGTAATTTT 57.248 32.000 0.00 0.00 0.00 1.82
1914 2331 0.822121 GAGGCTGGATGCATGCATGA 60.822 55.000 36.73 21.23 45.15 3.07
1936 2353 7.137490 TGACTTAGGAATCGGTGTATATACG 57.863 40.000 8.33 0.00 0.00 3.06
1966 2385 5.106396 CCTCTGAAACTTGTTCATGGATGAC 60.106 44.000 0.00 0.00 36.36 3.06
2030 2450 3.138304 ACTAAAGTGAATGCTTGCGTCA 58.862 40.909 0.00 0.00 0.00 4.35
2046 2466 0.804933 GTCACCGATCGTGTAAGGGC 60.805 60.000 15.09 0.00 43.51 5.19
2052 2472 1.860950 CGATCGTGTAAGGGCATCTTG 59.139 52.381 7.03 0.00 36.93 3.02
2065 2485 0.673644 CATCTTGAACGCCGACCCTT 60.674 55.000 0.00 0.00 0.00 3.95
2073 2493 1.294138 CGCCGACCCTTAAACCTCA 59.706 57.895 0.00 0.00 0.00 3.86
2083 2503 3.633986 CCCTTAAACCTCATGCATCCTTC 59.366 47.826 0.00 0.00 0.00 3.46
2085 2505 2.905415 AAACCTCATGCATCCTTCCA 57.095 45.000 0.00 0.00 0.00 3.53
2089 2509 2.042162 ACCTCATGCATCCTTCCAAACT 59.958 45.455 0.00 0.00 0.00 2.66
2095 2515 1.200948 GCATCCTTCCAAACTGCACTC 59.799 52.381 0.00 0.00 33.13 3.51
2098 2518 2.851195 TCCTTCCAAACTGCACTCTTC 58.149 47.619 0.00 0.00 0.00 2.87
2099 2519 2.172505 TCCTTCCAAACTGCACTCTTCA 59.827 45.455 0.00 0.00 0.00 3.02
2107 2527 1.221466 CTGCACTCTTCAAACCGCGA 61.221 55.000 8.23 0.00 0.00 5.87
2134 2554 4.875536 CCATCCAACGTGATTCTGTATCAA 59.124 41.667 0.00 0.00 44.62 2.57
2137 2557 5.977635 TCCAACGTGATTCTGTATCAATCT 58.022 37.500 0.00 0.00 44.62 2.40
2172 2592 4.202101 TGAACGTACTTTCTCCCGTAAACA 60.202 41.667 12.72 0.00 32.49 2.83
2202 2624 2.034221 GGGAGCTTTGCGGGAGTT 59.966 61.111 0.00 0.00 0.00 3.01
2236 2658 1.875488 GCCCTCTTCTAACCACCCTA 58.125 55.000 0.00 0.00 0.00 3.53
2255 2680 3.160478 GCCCACCCAAACCCTCCTT 62.160 63.158 0.00 0.00 0.00 3.36
2263 2688 0.685097 CAAACCCTCCTTCCTCGTCA 59.315 55.000 0.00 0.00 0.00 4.35
2342 2767 1.278985 TCCACATTGAAGACGGCTCAT 59.721 47.619 0.00 0.00 0.00 2.90
2367 2792 1.194781 ACATGACCTCTCACCGCCTT 61.195 55.000 0.00 0.00 0.00 4.35
2423 2848 1.878522 GCGACGCATCTCCGATGTT 60.879 57.895 16.42 0.00 0.00 2.71
2429 2854 1.083806 GCATCTCCGATGTTCGTGCA 61.084 55.000 5.81 0.00 37.84 4.57
2501 2926 1.002134 CCCGTTCAATGCCCTGTCT 60.002 57.895 0.00 0.00 0.00 3.41
2550 2979 0.605589 CGACCAAGAAACCCACTCCC 60.606 60.000 0.00 0.00 0.00 4.30
2574 3004 2.096406 CGCATTGACGCACCGAAG 59.904 61.111 0.00 0.00 0.00 3.79
2602 3032 2.287915 CCTCACCGAAATCCGCTATTTG 59.712 50.000 0.00 0.00 37.93 2.32
2616 3047 2.699954 CTATTTGAAGGCGACCACACT 58.300 47.619 0.00 0.00 0.00 3.55
2624 3055 1.805945 GCGACCACACTCGGCTAAG 60.806 63.158 0.00 0.00 34.06 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.100189 AGAAGCTACACTAGGGCAAGTATG 59.900 45.833 0.00 0.00 0.00 2.39
4 5 4.290942 AGAAGCTACACTAGGGCAAGTAT 58.709 43.478 0.00 0.00 0.00 2.12
5 6 3.709587 AGAAGCTACACTAGGGCAAGTA 58.290 45.455 0.00 0.00 0.00 2.24
6 7 2.541466 AGAAGCTACACTAGGGCAAGT 58.459 47.619 0.00 0.00 0.00 3.16
7 8 3.702045 ACTAGAAGCTACACTAGGGCAAG 59.298 47.826 19.45 0.00 39.97 4.01
8 9 3.709587 ACTAGAAGCTACACTAGGGCAA 58.290 45.455 19.45 0.00 39.97 4.52
9 10 3.383698 ACTAGAAGCTACACTAGGGCA 57.616 47.619 19.45 0.00 39.97 5.36
10 11 4.441773 GGAAACTAGAAGCTACACTAGGGC 60.442 50.000 19.45 11.66 39.97 5.19
11 12 4.099727 GGGAAACTAGAAGCTACACTAGGG 59.900 50.000 19.45 0.00 39.97 3.53
12 13 4.710375 TGGGAAACTAGAAGCTACACTAGG 59.290 45.833 19.45 8.04 39.97 3.02
13 14 5.916661 TGGGAAACTAGAAGCTACACTAG 57.083 43.478 16.00 16.00 41.01 2.57
14 15 5.363005 GGATGGGAAACTAGAAGCTACACTA 59.637 44.000 0.00 0.00 0.00 2.74
15 16 4.162509 GGATGGGAAACTAGAAGCTACACT 59.837 45.833 0.00 0.00 0.00 3.55
16 17 4.081087 TGGATGGGAAACTAGAAGCTACAC 60.081 45.833 0.00 0.00 0.00 2.90
17 18 4.101114 TGGATGGGAAACTAGAAGCTACA 58.899 43.478 0.00 0.00 0.00 2.74
18 19 4.755266 TGGATGGGAAACTAGAAGCTAC 57.245 45.455 0.00 0.00 0.00 3.58
19 20 5.428457 TCATTGGATGGGAAACTAGAAGCTA 59.572 40.000 0.00 0.00 0.00 3.32
20 21 4.228210 TCATTGGATGGGAAACTAGAAGCT 59.772 41.667 0.00 0.00 0.00 3.74
21 22 4.526970 TCATTGGATGGGAAACTAGAAGC 58.473 43.478 0.00 0.00 0.00 3.86
22 23 6.094603 CAGTTCATTGGATGGGAAACTAGAAG 59.905 42.308 0.00 0.00 0.00 2.85
23 24 5.945784 CAGTTCATTGGATGGGAAACTAGAA 59.054 40.000 0.00 0.00 0.00 2.10
24 25 5.250543 TCAGTTCATTGGATGGGAAACTAGA 59.749 40.000 0.00 0.00 0.00 2.43
25 26 5.355350 GTCAGTTCATTGGATGGGAAACTAG 59.645 44.000 0.00 0.00 0.00 2.57
26 27 5.253330 GTCAGTTCATTGGATGGGAAACTA 58.747 41.667 0.00 0.00 0.00 2.24
27 28 4.082125 GTCAGTTCATTGGATGGGAAACT 58.918 43.478 0.00 0.00 0.00 2.66
28 29 3.193479 GGTCAGTTCATTGGATGGGAAAC 59.807 47.826 0.00 0.00 0.00 2.78
29 30 3.181424 TGGTCAGTTCATTGGATGGGAAA 60.181 43.478 0.00 0.00 0.00 3.13
30 31 2.378208 TGGTCAGTTCATTGGATGGGAA 59.622 45.455 0.00 0.00 0.00 3.97
31 32 1.991813 TGGTCAGTTCATTGGATGGGA 59.008 47.619 0.00 0.00 0.00 4.37
32 33 2.372264 CTGGTCAGTTCATTGGATGGG 58.628 52.381 0.00 0.00 0.00 4.00
33 34 1.747355 GCTGGTCAGTTCATTGGATGG 59.253 52.381 0.00 0.00 0.00 3.51
34 35 1.399440 CGCTGGTCAGTTCATTGGATG 59.601 52.381 0.00 0.00 0.00 3.51
35 36 1.679944 CCGCTGGTCAGTTCATTGGAT 60.680 52.381 0.00 0.00 0.00 3.41
36 37 0.321564 CCGCTGGTCAGTTCATTGGA 60.322 55.000 0.00 0.00 0.00 3.53
37 38 0.606401 ACCGCTGGTCAGTTCATTGG 60.606 55.000 0.00 0.00 0.00 3.16
38 39 2.093306 TACCGCTGGTCAGTTCATTG 57.907 50.000 3.45 0.00 37.09 2.82
39 40 3.181465 CCTATACCGCTGGTCAGTTCATT 60.181 47.826 3.45 0.00 37.09 2.57
40 41 2.365617 CCTATACCGCTGGTCAGTTCAT 59.634 50.000 3.45 0.00 37.09 2.57
41 42 1.754803 CCTATACCGCTGGTCAGTTCA 59.245 52.381 3.45 0.00 37.09 3.18
42 43 1.538419 GCCTATACCGCTGGTCAGTTC 60.538 57.143 3.45 0.00 37.09 3.01
43 44 0.464452 GCCTATACCGCTGGTCAGTT 59.536 55.000 3.45 0.00 37.09 3.16
44 45 0.397254 AGCCTATACCGCTGGTCAGT 60.397 55.000 3.45 0.00 37.09 3.41
45 46 1.542030 CTAGCCTATACCGCTGGTCAG 59.458 57.143 3.45 3.61 37.09 3.51
46 47 1.133575 ACTAGCCTATACCGCTGGTCA 60.134 52.381 3.45 0.00 43.72 4.02
47 48 1.269998 CACTAGCCTATACCGCTGGTC 59.730 57.143 3.45 0.00 43.72 4.02
48 49 3.844161 ACTAGCCTATACCGCTGGT 57.156 52.632 5.58 5.58 42.51 4.00
49 50 1.000163 CACACTAGCCTATACCGCTGG 60.000 57.143 0.00 0.48 40.40 4.85
50 51 1.000163 CCACACTAGCCTATACCGCTG 60.000 57.143 0.00 0.00 37.12 5.18
51 52 1.329256 CCACACTAGCCTATACCGCT 58.671 55.000 0.00 0.00 40.45 5.52
52 53 0.319641 GCCACACTAGCCTATACCGC 60.320 60.000 0.00 0.00 0.00 5.68
53 54 0.039437 CGCCACACTAGCCTATACCG 60.039 60.000 0.00 0.00 0.00 4.02
54 55 1.269998 CTCGCCACACTAGCCTATACC 59.730 57.143 0.00 0.00 0.00 2.73
55 56 1.336056 GCTCGCCACACTAGCCTATAC 60.336 57.143 0.00 0.00 30.94 1.47
56 57 0.959553 GCTCGCCACACTAGCCTATA 59.040 55.000 0.00 0.00 30.94 1.31
57 58 0.757188 AGCTCGCCACACTAGCCTAT 60.757 55.000 0.00 0.00 37.81 2.57
58 59 0.106868 TAGCTCGCCACACTAGCCTA 60.107 55.000 0.00 0.00 37.81 3.93
59 60 1.379977 TAGCTCGCCACACTAGCCT 60.380 57.895 0.00 0.00 37.81 4.58
60 61 1.227002 GTAGCTCGCCACACTAGCC 60.227 63.158 0.00 0.00 37.81 3.93
61 62 0.103208 ATGTAGCTCGCCACACTAGC 59.897 55.000 0.00 0.00 37.35 3.42
62 63 2.619177 AGTATGTAGCTCGCCACACTAG 59.381 50.000 0.00 0.00 0.00 2.57
63 64 2.357952 CAGTATGTAGCTCGCCACACTA 59.642 50.000 0.00 0.00 0.00 2.74
64 65 1.135139 CAGTATGTAGCTCGCCACACT 59.865 52.381 0.00 0.00 0.00 3.55
65 66 1.560923 CAGTATGTAGCTCGCCACAC 58.439 55.000 0.00 0.00 0.00 3.82
66 67 0.179111 GCAGTATGTAGCTCGCCACA 60.179 55.000 0.00 0.00 39.31 4.17
67 68 0.103208 AGCAGTATGTAGCTCGCCAC 59.897 55.000 0.00 0.00 36.00 5.01
68 69 0.385751 GAGCAGTATGTAGCTCGCCA 59.614 55.000 0.00 0.00 46.53 5.69
69 70 3.187211 GAGCAGTATGTAGCTCGCC 57.813 57.895 0.00 0.00 46.53 5.54
73 74 4.992319 CGTAGACTAGAGCAGTATGTAGCT 59.008 45.833 0.00 0.00 45.25 3.32
74 75 4.751098 ACGTAGACTAGAGCAGTATGTAGC 59.249 45.833 0.00 0.00 37.72 3.58
75 76 6.922407 TGTACGTAGACTAGAGCAGTATGTAG 59.078 42.308 0.00 0.00 37.72 2.74
76 77 6.809869 TGTACGTAGACTAGAGCAGTATGTA 58.190 40.000 0.00 0.00 37.72 2.29
77 78 5.668471 TGTACGTAGACTAGAGCAGTATGT 58.332 41.667 0.00 0.00 37.72 2.29
78 79 6.594886 CATGTACGTAGACTAGAGCAGTATG 58.405 44.000 0.00 0.00 37.72 2.39
79 80 5.179742 GCATGTACGTAGACTAGAGCAGTAT 59.820 44.000 0.00 0.00 37.72 2.12
80 81 4.510711 GCATGTACGTAGACTAGAGCAGTA 59.489 45.833 0.00 0.00 37.72 2.74
81 82 3.312973 GCATGTACGTAGACTAGAGCAGT 59.687 47.826 0.00 0.00 41.47 4.40
82 83 3.312697 TGCATGTACGTAGACTAGAGCAG 59.687 47.826 0.00 0.00 0.00 4.24
83 84 3.275999 TGCATGTACGTAGACTAGAGCA 58.724 45.455 0.00 0.00 0.00 4.26
84 85 3.965292 TGCATGTACGTAGACTAGAGC 57.035 47.619 0.00 0.00 0.00 4.09
85 86 5.237561 ACTCATGCATGTACGTAGACTAGAG 59.762 44.000 25.43 13.08 0.00 2.43
86 87 5.123936 ACTCATGCATGTACGTAGACTAGA 58.876 41.667 25.43 1.25 0.00 2.43
87 88 5.425577 ACTCATGCATGTACGTAGACTAG 57.574 43.478 25.43 13.75 0.00 2.57
88 89 5.830000 AACTCATGCATGTACGTAGACTA 57.170 39.130 25.43 1.98 0.00 2.59
89 90 4.720649 AACTCATGCATGTACGTAGACT 57.279 40.909 25.43 6.29 0.00 3.24
90 91 7.201359 GCATATAACTCATGCATGTACGTAGAC 60.201 40.741 25.43 7.06 46.47 2.59
91 92 6.806739 GCATATAACTCATGCATGTACGTAGA 59.193 38.462 25.43 11.67 46.47 2.59
92 93 6.982809 GCATATAACTCATGCATGTACGTAG 58.017 40.000 25.43 17.18 46.47 3.51
93 94 6.944557 GCATATAACTCATGCATGTACGTA 57.055 37.500 25.43 13.89 46.47 3.57
94 95 5.845985 GCATATAACTCATGCATGTACGT 57.154 39.130 25.43 17.48 46.47 3.57
102 103 6.916440 TCATTTCATGGCATATAACTCATGC 58.084 36.000 0.00 0.00 46.50 4.06
103 104 9.923143 ATTTCATTTCATGGCATATAACTCATG 57.077 29.630 0.00 0.00 38.54 3.07
105 106 9.970395 GAATTTCATTTCATGGCATATAACTCA 57.030 29.630 0.00 0.00 0.00 3.41
106 107 9.970395 TGAATTTCATTTCATGGCATATAACTC 57.030 29.630 0.00 0.00 30.82 3.01
107 108 9.754382 GTGAATTTCATTTCATGGCATATAACT 57.246 29.630 0.00 0.00 37.88 2.24
108 109 8.693504 CGTGAATTTCATTTCATGGCATATAAC 58.306 33.333 0.00 0.00 38.43 1.89
109 110 8.628280 TCGTGAATTTCATTTCATGGCATATAA 58.372 29.630 0.00 0.00 41.12 0.98
110 111 8.164058 TCGTGAATTTCATTTCATGGCATATA 57.836 30.769 0.00 0.00 41.12 0.86
111 112 7.041635 TCGTGAATTTCATTTCATGGCATAT 57.958 32.000 0.00 0.00 41.12 1.78
112 113 6.095300 ACTCGTGAATTTCATTTCATGGCATA 59.905 34.615 0.00 0.00 41.12 3.14
113 114 5.105635 ACTCGTGAATTTCATTTCATGGCAT 60.106 36.000 1.78 0.00 41.12 4.40
114 115 4.218200 ACTCGTGAATTTCATTTCATGGCA 59.782 37.500 1.78 0.00 41.12 4.92
115 116 4.737054 ACTCGTGAATTTCATTTCATGGC 58.263 39.130 1.78 0.00 41.12 4.40
120 121 9.651718 GGTCATATAACTCGTGAATTTCATTTC 57.348 33.333 1.78 0.00 0.00 2.17
121 122 9.173021 TGGTCATATAACTCGTGAATTTCATTT 57.827 29.630 1.78 0.00 0.00 2.32
122 123 8.731275 TGGTCATATAACTCGTGAATTTCATT 57.269 30.769 1.78 0.00 0.00 2.57
123 124 8.731275 TTGGTCATATAACTCGTGAATTTCAT 57.269 30.769 1.78 0.00 0.00 2.57
124 125 8.038351 TCTTGGTCATATAACTCGTGAATTTCA 58.962 33.333 0.00 0.00 0.00 2.69
125 126 8.328864 GTCTTGGTCATATAACTCGTGAATTTC 58.671 37.037 0.00 0.00 0.00 2.17
126 127 7.822334 TGTCTTGGTCATATAACTCGTGAATTT 59.178 33.333 0.00 0.00 0.00 1.82
127 128 7.277981 GTGTCTTGGTCATATAACTCGTGAATT 59.722 37.037 0.00 0.00 0.00 2.17
128 129 6.757010 GTGTCTTGGTCATATAACTCGTGAAT 59.243 38.462 0.00 0.00 0.00 2.57
129 130 6.097356 GTGTCTTGGTCATATAACTCGTGAA 58.903 40.000 0.00 0.00 0.00 3.18
130 131 5.184287 TGTGTCTTGGTCATATAACTCGTGA 59.816 40.000 0.00 0.00 0.00 4.35
131 132 5.407502 TGTGTCTTGGTCATATAACTCGTG 58.592 41.667 0.00 0.00 0.00 4.35
132 133 5.654603 TGTGTCTTGGTCATATAACTCGT 57.345 39.130 0.00 0.00 0.00 4.18
133 134 8.818141 AATATGTGTCTTGGTCATATAACTCG 57.182 34.615 0.00 0.00 34.85 4.18
137 138 9.349713 GGGAAAATATGTGTCTTGGTCATATAA 57.650 33.333 0.00 0.00 34.85 0.98
138 139 7.942341 GGGGAAAATATGTGTCTTGGTCATATA 59.058 37.037 0.00 0.00 34.85 0.86
139 140 6.777580 GGGGAAAATATGTGTCTTGGTCATAT 59.222 38.462 0.00 0.00 36.66 1.78
140 141 6.126409 GGGGAAAATATGTGTCTTGGTCATA 58.874 40.000 0.00 0.00 0.00 2.15
141 142 4.956075 GGGGAAAATATGTGTCTTGGTCAT 59.044 41.667 0.00 0.00 0.00 3.06
142 143 4.340617 GGGGAAAATATGTGTCTTGGTCA 58.659 43.478 0.00 0.00 0.00 4.02
143 144 3.377172 CGGGGAAAATATGTGTCTTGGTC 59.623 47.826 0.00 0.00 0.00 4.02
144 145 3.352648 CGGGGAAAATATGTGTCTTGGT 58.647 45.455 0.00 0.00 0.00 3.67
145 146 2.099098 GCGGGGAAAATATGTGTCTTGG 59.901 50.000 0.00 0.00 0.00 3.61
146 147 2.099098 GGCGGGGAAAATATGTGTCTTG 59.901 50.000 0.00 0.00 0.00 3.02
147 148 2.025321 AGGCGGGGAAAATATGTGTCTT 60.025 45.455 0.00 0.00 0.00 3.01
148 149 1.564348 AGGCGGGGAAAATATGTGTCT 59.436 47.619 0.00 0.00 0.00 3.41
149 150 1.676006 CAGGCGGGGAAAATATGTGTC 59.324 52.381 0.00 0.00 0.00 3.67
150 151 1.283613 TCAGGCGGGGAAAATATGTGT 59.716 47.619 0.00 0.00 0.00 3.72
151 152 2.051334 TCAGGCGGGGAAAATATGTG 57.949 50.000 0.00 0.00 0.00 3.21
152 153 2.818751 TTCAGGCGGGGAAAATATGT 57.181 45.000 0.00 0.00 0.00 2.29
153 154 4.464069 TTTTTCAGGCGGGGAAAATATG 57.536 40.909 12.95 0.00 42.08 1.78
176 177 5.648092 GGAGCCATAGTGTAATGAACTGTTT 59.352 40.000 0.00 0.00 0.00 2.83
183 184 5.540337 CCTAGAAGGAGCCATAGTGTAATGA 59.460 44.000 0.00 0.00 37.67 2.57
184 185 5.305644 ACCTAGAAGGAGCCATAGTGTAATG 59.694 44.000 0.00 0.00 37.67 1.90
189 190 5.364157 AGTTAACCTAGAAGGAGCCATAGTG 59.636 44.000 0.88 0.00 37.67 2.74
196 197 6.641723 CGCTTAATAGTTAACCTAGAAGGAGC 59.358 42.308 0.88 1.98 37.67 4.70
212 213 7.979444 TCCATTCCCTAAATTCGCTTAATAG 57.021 36.000 0.00 0.00 0.00 1.73
217 218 6.544928 AAATTCCATTCCCTAAATTCGCTT 57.455 33.333 0.00 0.00 0.00 4.68
239 244 1.334556 AGGACGTATGTGCGCGTATAA 59.665 47.619 8.43 0.00 42.00 0.98
251 256 1.339929 TCGCATGCATGTAGGACGTAT 59.660 47.619 26.79 0.00 0.00 3.06
374 389 5.869344 TGATCACTTTGTTGTAATCTCCTCG 59.131 40.000 0.00 0.00 0.00 4.63
475 490 1.219522 GATAAATCGTGGACGGGCGG 61.220 60.000 0.00 0.00 40.29 6.13
476 491 1.219522 GGATAAATCGTGGACGGGCG 61.220 60.000 0.00 0.00 40.29 6.13
534 549 4.871557 CCCATTTGTTGCTGTTATTGGATG 59.128 41.667 0.00 0.00 0.00 3.51
542 557 8.133024 TCTAATATTTCCCATTTGTTGCTGTT 57.867 30.769 0.00 0.00 0.00 3.16
561 576 8.750298 ACGACAAATCTCTCTCCTTTTCTAATA 58.250 33.333 0.00 0.00 0.00 0.98
616 952 2.030805 AGGAATTTCGCAAACACAGAGC 60.031 45.455 0.00 0.00 0.00 4.09
651 991 5.862323 GCATGCTAGCATTATTCTTGATTGG 59.138 40.000 27.59 12.33 33.90 3.16
670 1010 0.801067 GCAGTTGCAAGCTAGCATGC 60.801 55.000 32.32 32.32 45.19 4.06
672 1012 1.651240 CGGCAGTTGCAAGCTAGCAT 61.651 55.000 18.83 0.65 45.19 3.79
673 1013 2.327343 CGGCAGTTGCAAGCTAGCA 61.327 57.895 18.83 0.00 44.36 3.49
674 1014 1.975363 CTCGGCAGTTGCAAGCTAGC 61.975 60.000 6.62 6.62 44.36 3.42
675 1015 0.390340 TCTCGGCAGTTGCAAGCTAG 60.390 55.000 0.00 3.53 44.36 3.42
676 1016 0.670546 GTCTCGGCAGTTGCAAGCTA 60.671 55.000 0.00 0.00 44.36 3.32
677 1017 1.963338 GTCTCGGCAGTTGCAAGCT 60.963 57.895 0.00 0.00 44.36 3.74
678 1018 2.558313 GTCTCGGCAGTTGCAAGC 59.442 61.111 0.00 0.00 44.36 4.01
679 1019 1.221466 TTCGTCTCGGCAGTTGCAAG 61.221 55.000 0.00 3.22 44.36 4.01
680 1020 0.812014 TTTCGTCTCGGCAGTTGCAA 60.812 50.000 6.43 0.00 44.36 4.08
699 1039 9.230122 ACAACAATGGACATTTTCTTTTCTTTT 57.770 25.926 0.00 0.00 0.00 2.27
700 1040 8.791327 ACAACAATGGACATTTTCTTTTCTTT 57.209 26.923 0.00 0.00 0.00 2.52
701 1041 8.260114 AGACAACAATGGACATTTTCTTTTCTT 58.740 29.630 0.00 0.00 0.00 2.52
702 1042 7.785033 AGACAACAATGGACATTTTCTTTTCT 58.215 30.769 0.00 0.00 0.00 2.52
727 1070 3.740115 GAGGACCTGCTTTTTGTCACTA 58.260 45.455 0.00 0.00 0.00 2.74
740 1083 2.300437 AGAGTTTTTCCTCGAGGACCTG 59.700 50.000 33.75 6.47 45.39 4.00
744 1087 5.995565 TTATCAGAGTTTTTCCTCGAGGA 57.004 39.130 30.49 30.49 43.73 3.71
745 1088 6.091441 CAGTTTATCAGAGTTTTTCCTCGAGG 59.909 42.308 26.32 26.32 36.56 4.63
746 1089 6.868864 TCAGTTTATCAGAGTTTTTCCTCGAG 59.131 38.462 5.13 5.13 36.56 4.04
747 1090 6.755206 TCAGTTTATCAGAGTTTTTCCTCGA 58.245 36.000 0.00 0.00 36.56 4.04
748 1091 7.421530 TTCAGTTTATCAGAGTTTTTCCTCG 57.578 36.000 0.00 0.00 36.56 4.63
749 1092 9.670719 CTTTTCAGTTTATCAGAGTTTTTCCTC 57.329 33.333 0.00 0.00 0.00 3.71
750 1093 9.190317 ACTTTTCAGTTTATCAGAGTTTTTCCT 57.810 29.630 0.00 0.00 0.00 3.36
761 1104 8.827177 ACGTGAGAATACTTTTCAGTTTATCA 57.173 30.769 0.00 0.00 34.06 2.15
778 1121 3.005367 TGCATGTCTTGTCTACGTGAGAA 59.995 43.478 0.00 0.00 36.20 2.87
781 1124 3.511699 GATGCATGTCTTGTCTACGTGA 58.488 45.455 2.46 0.00 36.20 4.35
783 1126 2.735444 CGGATGCATGTCTTGTCTACGT 60.735 50.000 2.46 0.00 0.00 3.57
785 1128 2.205074 CCGGATGCATGTCTTGTCTAC 58.795 52.381 2.46 0.00 0.00 2.59
812 1155 0.252197 AATAAGGTGAGGTGGACGGC 59.748 55.000 0.00 0.00 0.00 5.68
1005 1398 2.518349 ACGTTGGGGTGCACCTTG 60.518 61.111 33.91 20.62 40.03 3.61
1746 2163 2.518349 CTTGTTGCCGTGTGGGGT 60.518 61.111 0.00 0.00 35.78 4.95
1747 2164 3.294493 CCTTGTTGCCGTGTGGGG 61.294 66.667 0.00 0.00 35.78 4.96
1779 2196 1.852626 AGGTGGGGCCAGTAGCTTT 60.853 57.895 4.39 0.00 43.05 3.51
1888 2305 2.423446 CATCCAGCCTCCGTAGCC 59.577 66.667 0.00 0.00 0.00 3.93
1914 2331 6.006449 ACCGTATATACACCGATTCCTAAGT 58.994 40.000 13.22 0.00 0.00 2.24
1936 2353 2.262423 ACAAGTTTCAGAGGCTGACC 57.738 50.000 0.00 0.00 40.46 4.02
1966 2385 9.424319 AGATCCATGTACATAGTATTTTTAGCG 57.576 33.333 8.32 0.00 0.00 4.26
2030 2450 0.104304 GATGCCCTTACACGATCGGT 59.896 55.000 20.98 16.20 0.00 4.69
2046 2466 0.673644 AAGGGTCGGCGTTCAAGATG 60.674 55.000 6.85 0.00 0.00 2.90
2052 2472 0.321034 AGGTTTAAGGGTCGGCGTTC 60.321 55.000 6.85 1.15 0.00 3.95
2065 2485 4.314522 TTGGAAGGATGCATGAGGTTTA 57.685 40.909 2.46 0.00 0.00 2.01
2073 2493 1.927487 TGCAGTTTGGAAGGATGCAT 58.073 45.000 0.00 0.00 41.65 3.96
2083 2503 2.541588 CGGTTTGAAGAGTGCAGTTTGG 60.542 50.000 0.00 0.00 0.00 3.28
2085 2505 1.065551 GCGGTTTGAAGAGTGCAGTTT 59.934 47.619 0.00 0.00 0.00 2.66
2089 2509 0.812014 TTCGCGGTTTGAAGAGTGCA 60.812 50.000 6.13 0.00 0.00 4.57
2095 2515 0.240945 ATGGCTTTCGCGGTTTGAAG 59.759 50.000 6.13 4.60 36.88 3.02
2098 2518 1.154035 GGATGGCTTTCGCGGTTTG 60.154 57.895 6.13 0.00 36.88 2.93
2099 2519 1.175983 TTGGATGGCTTTCGCGGTTT 61.176 50.000 6.13 0.00 36.88 3.27
2107 2527 2.489329 CAGAATCACGTTGGATGGCTTT 59.511 45.455 0.00 0.00 0.00 3.51
2134 2554 3.460103 ACGTTCAAACCGTGTTGTAGAT 58.540 40.909 0.00 0.00 37.12 1.98
2137 2557 3.779759 AGTACGTTCAAACCGTGTTGTA 58.220 40.909 0.00 0.00 39.22 2.41
2172 2592 4.074970 CAAAGCTCCCATGTTTGTCTACT 58.925 43.478 0.00 0.00 0.00 2.57
2236 2658 3.590574 GGAGGGTTTGGGTGGGCT 61.591 66.667 0.00 0.00 0.00 5.19
2255 2680 1.007734 GAACACGCACTGACGAGGA 60.008 57.895 0.00 0.00 36.70 3.71
2298 2723 1.742900 CGCGCTCTACAACGACATGG 61.743 60.000 5.56 0.00 0.00 3.66
2342 2767 1.609210 TGAGAGGTCATGTCCGCCA 60.609 57.895 8.96 4.81 0.00 5.69
2350 2775 1.901085 GAAGGCGGTGAGAGGTCAT 59.099 57.895 0.00 0.00 34.36 3.06
2351 2776 2.636412 CGAAGGCGGTGAGAGGTCA 61.636 63.158 0.00 0.00 0.00 4.02
2423 2848 1.501292 CGGCATTGAACATGCACGA 59.499 52.632 8.96 0.00 46.21 4.35
2429 2854 0.036388 ACGTCTCCGGCATTGAACAT 60.036 50.000 0.00 0.00 38.78 2.71
2456 2881 6.827251 GTGGTATATATCTGTCCCATCTCGTA 59.173 42.308 0.00 0.00 0.00 3.43
2501 2926 0.178301 TTAATGGCGGCATACGGACA 59.822 50.000 26.05 3.69 44.51 4.02
2602 3032 2.432628 CCGAGTGTGGTCGCCTTC 60.433 66.667 0.00 0.00 38.69 3.46
2609 3039 1.817447 GTAGACTTAGCCGAGTGTGGT 59.183 52.381 0.00 0.00 0.00 4.16
2616 3047 2.490903 GTTGTGGAGTAGACTTAGCCGA 59.509 50.000 0.00 0.00 0.00 5.54
2624 3055 2.143925 GGCTTGTGTTGTGGAGTAGAC 58.856 52.381 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.