Multiple sequence alignment - TraesCS7B01G193900

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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 TraesCS7B01G193900 chr7B 100.000 2969 0 0 1 2969 333128260 333131228 0.000000e+00 5483.0
1 TraesCS7B01G193900 chr7D 91.578 2066 83 29 809 2824 188873932 188875956 0.000000e+00 2767.0
2 TraesCS7B01G193900 chr7D 84.075 584 76 12 242 816 188829788 188830363 5.600000e-152 547.0
3 TraesCS7B01G193900 chr7D 92.593 108 8 0 2855 2962 188875951 188876058 3.960000e-34 156.0
4 TraesCS7B01G193900 chr7D 83.146 178 20 5 81 250 188828819 188828994 1.430000e-33 154.0
5 TraesCS7B01G193900 chr7D 100.000 31 0 0 2092 2122 188876624 188876654 1.150000e-04 58.4
6 TraesCS7B01G193900 chr7A 90.420 1858 83 36 612 2419 195218603 195216791 0.000000e+00 2357.0
7 TraesCS7B01G193900 chr7A 87.097 341 21 13 2507 2824 195215103 195214763 6.050000e-97 364.0
8 TraesCS7B01G193900 chr6B 77.063 824 139 42 956 1745 549193280 549194087 2.110000e-116 429.0
9 TraesCS7B01G193900 chr6B 75.796 471 91 18 1262 1728 48552037 48552488 1.790000e-52 217.0
10 TraesCS7B01G193900 chr6D 76.950 846 133 49 956 1761 364226907 364227730 2.740000e-115 425.0
11 TraesCS7B01G193900 chr6D 75.796 471 91 18 1262 1728 26351124 26351575 1.790000e-52 217.0
12 TraesCS7B01G193900 chr6A 75.650 961 164 58 956 1874 505247775 505246843 5.920000e-112 414.0
13 TraesCS7B01G193900 chr4A 75.435 460 90 14 1258 1716 649428486 649428923 5.020000e-48 202.0
14 TraesCS7B01G193900 chr4B 75.053 469 92 21 1265 1728 653583 653135 8.400000e-46 195.0


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 TraesCS7B01G193900 chr7B 333128260 333131228 2968 False 5483.0 5483 100.000000 1 2969 1 chr7B.!!$F1 2968
1 TraesCS7B01G193900 chr7D 188873932 188876654 2722 False 993.8 2767 94.723667 809 2962 3 chr7D.!!$F2 2153
2 TraesCS7B01G193900 chr7D 188828819 188830363 1544 False 350.5 547 83.610500 81 816 2 chr7D.!!$F1 735
3 TraesCS7B01G193900 chr7A 195214763 195218603 3840 True 1360.5 2357 88.758500 612 2824 2 chr7A.!!$R1 2212
4 TraesCS7B01G193900 chr6B 549193280 549194087 807 False 429.0 429 77.063000 956 1745 1 chr6B.!!$F2 789
5 TraesCS7B01G193900 chr6D 364226907 364227730 823 False 425.0 425 76.950000 956 1761 1 chr6D.!!$F2 805
6 TraesCS7B01G193900 chr6A 505246843 505247775 932 True 414.0 414 75.650000 956 1874 1 chr6A.!!$R1 918

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
344 1155 0.323725 GGCAAATCAAGGGGCTCTGA 60.324 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2904 0.108804 GATCGACCGCAGTTCCTTCA 60.109 55.0 0.0 0.0 0.0 3.02 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
21 22 4.416505 CAAGATGACTTTTGTGCTCCTC 57.583 45.455 0.00 0.00 33.70 3.71
22 23 3.777106 AGATGACTTTTGTGCTCCTCA 57.223 42.857 0.00 0.00 0.00 3.86
23 24 4.090761 AGATGACTTTTGTGCTCCTCAA 57.909 40.909 0.00 0.00 0.00 3.02
24 25 3.817647 AGATGACTTTTGTGCTCCTCAAC 59.182 43.478 0.00 0.00 0.00 3.18
25 26 2.297701 TGACTTTTGTGCTCCTCAACC 58.702 47.619 0.00 0.00 0.00 3.77
26 27 2.297701 GACTTTTGTGCTCCTCAACCA 58.702 47.619 0.00 0.00 0.00 3.67
27 28 2.024414 ACTTTTGTGCTCCTCAACCAC 58.976 47.619 0.00 0.00 0.00 4.16
28 29 2.023673 CTTTTGTGCTCCTCAACCACA 58.976 47.619 0.00 0.00 37.67 4.17
29 30 2.136298 TTTGTGCTCCTCAACCACAA 57.864 45.000 1.70 1.70 44.84 3.33
30 31 2.363306 TTGTGCTCCTCAACCACAAT 57.637 45.000 1.70 0.00 42.56 2.71
31 32 1.608055 TGTGCTCCTCAACCACAATG 58.392 50.000 0.00 0.00 36.62 2.82
32 33 1.133823 TGTGCTCCTCAACCACAATGT 60.134 47.619 0.00 0.00 36.62 2.71
33 34 2.105649 TGTGCTCCTCAACCACAATGTA 59.894 45.455 0.00 0.00 36.62 2.29
34 35 3.244875 TGTGCTCCTCAACCACAATGTAT 60.245 43.478 0.00 0.00 36.62 2.29
35 36 3.758554 GTGCTCCTCAACCACAATGTATT 59.241 43.478 0.00 0.00 0.00 1.89
36 37 4.941263 GTGCTCCTCAACCACAATGTATTA 59.059 41.667 0.00 0.00 0.00 0.98
37 38 5.590259 GTGCTCCTCAACCACAATGTATTAT 59.410 40.000 0.00 0.00 0.00 1.28
38 39 5.822519 TGCTCCTCAACCACAATGTATTATC 59.177 40.000 0.00 0.00 0.00 1.75
39 40 5.050091 GCTCCTCAACCACAATGTATTATCG 60.050 44.000 0.00 0.00 0.00 2.92
40 41 5.364778 TCCTCAACCACAATGTATTATCGG 58.635 41.667 0.00 0.00 0.00 4.18
41 42 5.104693 TCCTCAACCACAATGTATTATCGGT 60.105 40.000 0.00 0.00 0.00 4.69
42 43 5.007626 CCTCAACCACAATGTATTATCGGTG 59.992 44.000 0.00 0.00 0.00 4.94
43 44 5.735766 TCAACCACAATGTATTATCGGTGA 58.264 37.500 0.00 0.00 0.00 4.02
44 45 5.815222 TCAACCACAATGTATTATCGGTGAG 59.185 40.000 0.00 0.00 0.00 3.51
45 46 5.607939 ACCACAATGTATTATCGGTGAGA 57.392 39.130 0.00 0.00 0.00 3.27
46 47 5.984725 ACCACAATGTATTATCGGTGAGAA 58.015 37.500 0.00 0.00 0.00 2.87
47 48 5.815740 ACCACAATGTATTATCGGTGAGAAC 59.184 40.000 0.00 0.00 0.00 3.01
48 49 5.815222 CCACAATGTATTATCGGTGAGAACA 59.185 40.000 0.00 0.00 0.00 3.18
49 50 6.315144 CCACAATGTATTATCGGTGAGAACAA 59.685 38.462 0.00 0.00 0.00 2.83
50 51 7.148323 CCACAATGTATTATCGGTGAGAACAAA 60.148 37.037 0.00 0.00 0.00 2.83
51 52 7.904977 CACAATGTATTATCGGTGAGAACAAAG 59.095 37.037 0.00 0.00 0.00 2.77
52 53 7.065803 ACAATGTATTATCGGTGAGAACAAAGG 59.934 37.037 0.00 0.00 0.00 3.11
53 54 6.045072 TGTATTATCGGTGAGAACAAAGGT 57.955 37.500 0.00 0.00 0.00 3.50
54 55 6.103997 TGTATTATCGGTGAGAACAAAGGTC 58.896 40.000 0.00 0.00 0.00 3.85
55 56 4.610605 TTATCGGTGAGAACAAAGGTCA 57.389 40.909 0.00 0.00 0.00 4.02
56 57 3.703001 ATCGGTGAGAACAAAGGTCAT 57.297 42.857 0.00 0.00 0.00 3.06
57 58 3.040147 TCGGTGAGAACAAAGGTCATC 57.960 47.619 0.00 0.00 0.00 2.92
58 59 2.632996 TCGGTGAGAACAAAGGTCATCT 59.367 45.455 0.00 0.00 0.00 2.90
59 60 2.738846 CGGTGAGAACAAAGGTCATCTG 59.261 50.000 0.00 0.00 0.00 2.90
60 61 3.554960 CGGTGAGAACAAAGGTCATCTGA 60.555 47.826 0.00 0.00 0.00 3.27
61 62 4.583871 GGTGAGAACAAAGGTCATCTGAT 58.416 43.478 0.00 0.00 0.00 2.90
62 63 4.633565 GGTGAGAACAAAGGTCATCTGATC 59.366 45.833 0.00 0.00 0.00 2.92
63 64 5.240891 GTGAGAACAAAGGTCATCTGATCA 58.759 41.667 0.00 0.00 0.00 2.92
64 65 5.121454 GTGAGAACAAAGGTCATCTGATCAC 59.879 44.000 0.00 0.00 0.00 3.06
65 66 4.248859 AGAACAAAGGTCATCTGATCACG 58.751 43.478 0.00 0.00 0.00 4.35
66 67 3.685139 ACAAAGGTCATCTGATCACGT 57.315 42.857 0.00 0.00 0.00 4.49
67 68 3.589988 ACAAAGGTCATCTGATCACGTC 58.410 45.455 0.00 0.00 0.00 4.34
68 69 3.006859 ACAAAGGTCATCTGATCACGTCA 59.993 43.478 0.00 0.00 35.05 4.35
69 70 4.186926 CAAAGGTCATCTGATCACGTCAT 58.813 43.478 0.00 0.00 35.97 3.06
70 71 5.105351 ACAAAGGTCATCTGATCACGTCATA 60.105 40.000 0.00 0.00 35.97 2.15
71 72 4.844998 AGGTCATCTGATCACGTCATAG 57.155 45.455 0.00 0.00 35.97 2.23
72 73 4.464947 AGGTCATCTGATCACGTCATAGA 58.535 43.478 0.00 0.00 35.97 1.98
73 74 4.518590 AGGTCATCTGATCACGTCATAGAG 59.481 45.833 0.00 0.00 35.97 2.43
74 75 4.320861 GGTCATCTGATCACGTCATAGAGG 60.321 50.000 0.00 0.00 35.97 3.69
75 76 3.254411 TCATCTGATCACGTCATAGAGGC 59.746 47.826 0.00 0.00 35.97 4.70
76 77 2.654863 TCTGATCACGTCATAGAGGCA 58.345 47.619 0.00 0.00 35.97 4.75
77 78 3.023832 TCTGATCACGTCATAGAGGCAA 58.976 45.455 0.00 0.00 35.97 4.52
78 79 3.447229 TCTGATCACGTCATAGAGGCAAA 59.553 43.478 0.00 0.00 35.97 3.68
79 80 3.785486 TGATCACGTCATAGAGGCAAAG 58.215 45.455 0.00 0.00 0.00 2.77
87 88 6.425114 CACGTCATAGAGGCAAAGCTATATTT 59.575 38.462 0.00 0.00 0.00 1.40
89 90 6.646653 CGTCATAGAGGCAAAGCTATATTTCA 59.353 38.462 0.00 0.00 0.00 2.69
93 94 5.945310 AGAGGCAAAGCTATATTTCATCCA 58.055 37.500 0.00 0.00 0.00 3.41
96 97 5.533903 AGGCAAAGCTATATTTCATCCACAG 59.466 40.000 0.00 0.00 0.00 3.66
97 98 5.532406 GGCAAAGCTATATTTCATCCACAGA 59.468 40.000 0.00 0.00 0.00 3.41
99 100 7.255730 GGCAAAGCTATATTTCATCCACAGATT 60.256 37.037 0.00 0.00 0.00 2.40
100 101 7.806960 GCAAAGCTATATTTCATCCACAGATTC 59.193 37.037 0.00 0.00 0.00 2.52
101 102 7.664082 AAGCTATATTTCATCCACAGATTCG 57.336 36.000 0.00 0.00 0.00 3.34
111 112 1.229428 CACAGATTCGGTGCAACTGT 58.771 50.000 0.00 0.00 45.64 3.55
113 114 2.033299 CACAGATTCGGTGCAACTGTTT 59.967 45.455 0.00 0.00 45.64 2.83
118 119 2.254546 TCGGTGCAACTGTTTCATCT 57.745 45.000 0.00 0.00 45.64 2.90
120 121 1.136252 CGGTGCAACTGTTTCATCTCG 60.136 52.381 0.00 1.72 38.78 4.04
129 130 6.363473 CAACTGTTTCATCTCGGTTTTAGTC 58.637 40.000 0.00 0.00 31.82 2.59
139 140 4.342951 TCTCGGTTTTAGTCTTTGTCCTCA 59.657 41.667 0.00 0.00 0.00 3.86
144 145 1.263356 TAGTCTTTGTCCTCACGGGG 58.737 55.000 0.00 0.00 35.33 5.73
154 155 1.521681 CTCACGGGGCCGATCTTTC 60.522 63.158 0.00 0.00 42.83 2.62
155 156 2.238847 CTCACGGGGCCGATCTTTCA 62.239 60.000 0.00 0.00 42.83 2.69
159 160 0.463654 CGGGGCCGATCTTTCAATCA 60.464 55.000 0.00 0.00 42.83 2.57
169 170 6.310197 CCGATCTTTCAATCAGTTGAGTTTC 58.690 40.000 0.00 0.00 44.62 2.78
174 175 8.731275 TCTTTCAATCAGTTGAGTTTCTGTTA 57.269 30.769 0.00 0.00 44.62 2.41
199 206 5.293324 GGGTGTCTTTTTGTTGGTTTGATTC 59.707 40.000 0.00 0.00 0.00 2.52
200 207 6.106003 GGTGTCTTTTTGTTGGTTTGATTCT 58.894 36.000 0.00 0.00 0.00 2.40
212 221 7.118971 TGTTGGTTTGATTCTTTTTGAAGTTGG 59.881 33.333 0.00 0.00 38.18 3.77
253 1064 4.876107 ACGGTGAAGATTTTGCGATTCTAT 59.124 37.500 0.00 0.00 0.00 1.98
258 1069 5.470098 TGAAGATTTTGCGATTCTATAGCCC 59.530 40.000 0.00 0.00 0.00 5.19
259 1070 3.997021 AGATTTTGCGATTCTATAGCCCG 59.003 43.478 0.00 0.00 0.00 6.13
262 1073 3.442996 GCGATTCTATAGCCCGCAT 57.557 52.632 20.38 0.17 44.55 4.73
265 1076 2.094417 GCGATTCTATAGCCCGCATTTC 59.906 50.000 20.38 0.73 44.55 2.17
271 1082 0.468029 ATAGCCCGCATTTCCAAGGG 60.468 55.000 0.00 0.00 46.44 3.95
287 1098 1.358152 AGGGTTCATCCTCGACCAAA 58.642 50.000 0.00 0.00 35.11 3.28
296 1107 2.950433 TCCTCGACCAAATACGTTCAC 58.050 47.619 0.00 0.00 0.00 3.18
298 1109 2.921754 CCTCGACCAAATACGTTCACTC 59.078 50.000 0.00 0.00 0.00 3.51
301 1112 4.232221 TCGACCAAATACGTTCACTCTTC 58.768 43.478 0.00 0.00 0.00 2.87
303 1114 4.143389 CGACCAAATACGTTCACTCTTCAC 60.143 45.833 0.00 0.00 0.00 3.18
306 1117 3.655276 AATACGTTCACTCTTCACGGT 57.345 42.857 0.00 0.00 38.26 4.83
334 1145 4.970860 TCTTTTTGGATGGGCAAATCAA 57.029 36.364 2.38 0.00 0.00 2.57
337 1148 1.570803 TTGGATGGGCAAATCAAGGG 58.429 50.000 2.38 0.00 0.00 3.95
338 1149 0.325484 TGGATGGGCAAATCAAGGGG 60.325 55.000 2.38 0.00 0.00 4.79
339 1150 1.689243 GGATGGGCAAATCAAGGGGC 61.689 60.000 2.38 0.00 0.00 5.80
340 1151 0.688749 GATGGGCAAATCAAGGGGCT 60.689 55.000 0.00 0.00 0.00 5.19
341 1152 0.688749 ATGGGCAAATCAAGGGGCTC 60.689 55.000 0.00 0.00 0.00 4.70
342 1153 1.000866 GGGCAAATCAAGGGGCTCT 59.999 57.895 0.00 0.00 0.00 4.09
343 1154 1.325476 GGGCAAATCAAGGGGCTCTG 61.325 60.000 0.00 0.00 0.00 3.35
344 1155 0.323725 GGCAAATCAAGGGGCTCTGA 60.324 55.000 0.00 0.00 0.00 3.27
345 1156 1.687368 GGCAAATCAAGGGGCTCTGAT 60.687 52.381 0.00 0.00 0.00 2.90
346 1157 2.423373 GGCAAATCAAGGGGCTCTGATA 60.423 50.000 0.00 0.00 0.00 2.15
347 1158 2.620585 GCAAATCAAGGGGCTCTGATAC 59.379 50.000 0.00 0.00 0.00 2.24
348 1159 3.686691 GCAAATCAAGGGGCTCTGATACT 60.687 47.826 0.00 0.00 0.00 2.12
349 1160 4.530875 CAAATCAAGGGGCTCTGATACTT 58.469 43.478 0.00 0.00 0.00 2.24
352 1163 4.222124 TCAAGGGGCTCTGATACTTTTC 57.778 45.455 0.00 0.00 0.00 2.29
357 1168 3.190874 GGGCTCTGATACTTTTCTGTCG 58.809 50.000 0.00 0.00 0.00 4.35
361 1172 5.452077 GGCTCTGATACTTTTCTGTCGGTAT 60.452 44.000 0.00 0.00 0.00 2.73
369 1180 5.855045 ACTTTTCTGTCGGTATTCAAGTCT 58.145 37.500 0.00 0.00 0.00 3.24
371 1182 3.232213 TCTGTCGGTATTCAAGTCTGC 57.768 47.619 0.00 0.00 0.00 4.26
383 1194 2.361119 TCAAGTCTGCGTACAAGTGACT 59.639 45.455 0.00 0.00 39.35 3.41
389 1200 4.090066 GTCTGCGTACAAGTGACTATGTTG 59.910 45.833 5.91 0.00 0.00 3.33
391 1202 3.985279 TGCGTACAAGTGACTATGTTGAC 59.015 43.478 5.91 0.50 0.00 3.18
401 1212 7.997773 AGTGACTATGTTGACACTCTAGTTA 57.002 36.000 0.00 0.00 38.21 2.24
407 1218 9.998106 ACTATGTTGACACTCTAGTTAAATTGT 57.002 29.630 0.00 0.00 0.00 2.71
412 1223 7.884816 TGACACTCTAGTTAAATTGTAGTGC 57.115 36.000 12.69 8.81 37.06 4.40
419 1230 8.685838 TCTAGTTAAATTGTAGTGCCTTTGTT 57.314 30.769 0.00 0.00 0.00 2.83
420 1231 9.127277 TCTAGTTAAATTGTAGTGCCTTTGTTT 57.873 29.630 0.00 0.00 0.00 2.83
424 1235 9.738832 GTTAAATTGTAGTGCCTTTGTTTAAGA 57.261 29.630 0.00 0.00 35.80 2.10
425 1236 9.959749 TTAAATTGTAGTGCCTTTGTTTAAGAG 57.040 29.630 0.00 0.00 35.80 2.85
441 1252 8.516811 TGTTTAAGAGTTGAGTAGATTTCGTC 57.483 34.615 0.00 0.00 0.00 4.20
444 1255 8.967552 TTAAGAGTTGAGTAGATTTCGTCTTC 57.032 34.615 0.00 0.00 38.42 2.87
450 1261 7.497909 AGTTGAGTAGATTTCGTCTTCCAAAAA 59.502 33.333 0.00 0.00 38.42 1.94
475 1286 2.942804 TCACAAGAAGGTGCATCCAAA 58.057 42.857 0.00 0.00 38.66 3.28
476 1287 2.886523 TCACAAGAAGGTGCATCCAAAG 59.113 45.455 0.00 0.00 38.66 2.77
477 1288 2.624838 CACAAGAAGGTGCATCCAAAGT 59.375 45.455 0.00 0.00 39.02 2.66
480 1291 5.047802 CACAAGAAGGTGCATCCAAAGTATT 60.048 40.000 0.00 0.00 39.02 1.89
481 1292 5.539955 ACAAGAAGGTGCATCCAAAGTATTT 59.460 36.000 0.00 0.00 40.26 1.40
482 1293 5.904362 AGAAGGTGCATCCAAAGTATTTC 57.096 39.130 0.00 0.00 35.03 2.17
483 1294 5.324409 AGAAGGTGCATCCAAAGTATTTCA 58.676 37.500 0.00 0.00 35.03 2.69
486 1297 6.212888 AGGTGCATCCAAAGTATTTCATTC 57.787 37.500 0.00 0.00 35.03 2.67
487 1298 5.954150 AGGTGCATCCAAAGTATTTCATTCT 59.046 36.000 0.00 0.00 35.03 2.40
489 1300 7.615365 AGGTGCATCCAAAGTATTTCATTCTAA 59.385 33.333 0.00 0.00 35.03 2.10
531 1342 3.535280 TGTGCACACTCTGTTCACTAA 57.465 42.857 17.42 0.00 43.29 2.24
556 1368 3.708563 AGACATTTGACACCAAAACCG 57.291 42.857 0.00 0.00 44.49 4.44
566 1378 4.035792 TGACACCAAAACCGTCTTACATTG 59.964 41.667 0.00 0.00 0.00 2.82
567 1379 3.316868 ACACCAAAACCGTCTTACATTGG 59.683 43.478 0.00 0.00 42.29 3.16
572 1384 4.823790 AAACCGTCTTACATTGGTGAAC 57.176 40.909 0.00 0.00 34.26 3.18
576 1388 3.679980 CCGTCTTACATTGGTGAACAGAG 59.320 47.826 0.00 0.00 0.00 3.35
582 1394 6.722590 TCTTACATTGGTGAACAGAGGTAGTA 59.277 38.462 0.00 0.00 0.00 1.82
636 1448 5.695816 CACCTGTAATGGTTTTCATGTTTGG 59.304 40.000 0.00 0.00 38.45 3.28
733 1545 1.815021 GCTGGGCTTGGCATTTTGTTT 60.815 47.619 0.00 0.00 0.00 2.83
781 1598 4.424711 GGCCTGCCCGGTCATTGA 62.425 66.667 0.00 0.00 37.34 2.57
821 1638 2.107366 TGTTCCTCATCGATAGCCACA 58.893 47.619 0.00 0.00 0.00 4.17
862 1679 2.638354 CCTACGGCCACGGTACACA 61.638 63.158 2.24 0.00 46.48 3.72
863 1680 1.444895 CTACGGCCACGGTACACAC 60.445 63.158 2.24 0.00 46.48 3.82
865 1682 2.144833 TACGGCCACGGTACACACTG 62.145 60.000 2.24 0.00 46.48 3.66
866 1683 2.738480 GGCCACGGTACACACTGA 59.262 61.111 0.00 0.00 34.87 3.41
867 1684 1.666872 GGCCACGGTACACACTGAC 60.667 63.158 0.00 0.00 34.87 3.51
868 1685 1.068417 GCCACGGTACACACTGACA 59.932 57.895 0.00 0.00 34.87 3.58
869 1686 1.219522 GCCACGGTACACACTGACAC 61.220 60.000 0.00 0.00 34.87 3.67
870 1687 0.387929 CCACGGTACACACTGACACT 59.612 55.000 0.00 0.00 34.87 3.55
871 1688 1.610038 CCACGGTACACACTGACACTA 59.390 52.381 0.00 0.00 34.87 2.74
872 1689 2.230508 CCACGGTACACACTGACACTAT 59.769 50.000 0.00 0.00 34.87 2.12
873 1690 3.305813 CCACGGTACACACTGACACTATT 60.306 47.826 0.00 0.00 34.87 1.73
918 1735 1.993369 GCGCTGGCCAGAAATACCAC 61.993 60.000 37.21 14.63 0.00 4.16
926 1743 1.134367 CCAGAAATACCACGCGAGAGA 59.866 52.381 15.93 0.00 0.00 3.10
1325 2189 1.368950 CGCCCATCATCGTGATCCT 59.631 57.895 0.00 0.00 34.28 3.24
1340 2204 3.953775 CCTGGACAGCCCCAACGT 61.954 66.667 0.00 0.00 35.47 3.99
1524 2391 2.360350 CTCGTTGCCACCCTGCAT 60.360 61.111 0.00 0.00 41.70 3.96
1548 2415 1.135257 CAGTTCGAGATCCTGTCGCTT 60.135 52.381 0.00 0.00 37.35 4.68
1716 2583 1.516386 CAATGCCGTCTACGAGCGT 60.516 57.895 3.65 0.00 43.02 5.07
1917 2784 1.408822 GGGAATGTTGGGAGCTACCAG 60.409 57.143 19.46 0.00 42.47 4.00
2017 2903 6.451393 GTCGCATCAGAATTACTAGGAGATT 58.549 40.000 0.00 0.00 0.00 2.40
2018 2904 6.926272 GTCGCATCAGAATTACTAGGAGATTT 59.074 38.462 0.00 0.00 0.00 2.17
2023 2909 9.270640 CATCAGAATTACTAGGAGATTTGAAGG 57.729 37.037 0.00 0.00 0.00 3.46
2030 2916 2.704572 AGGAGATTTGAAGGAACTGCG 58.295 47.619 0.00 0.00 36.15 5.18
2031 2917 1.740025 GGAGATTTGAAGGAACTGCGG 59.260 52.381 0.00 0.00 36.15 5.69
2148 3034 3.003897 GGTCAACGCATTTTGTGGACTAA 59.996 43.478 1.13 0.00 39.70 2.24
2149 3035 4.219033 GTCAACGCATTTTGTGGACTAAG 58.781 43.478 0.00 0.00 37.32 2.18
2150 3036 3.880490 TCAACGCATTTTGTGGACTAAGT 59.120 39.130 0.00 0.00 30.87 2.24
2154 3040 6.380095 ACGCATTTTGTGGACTAAGTTTTA 57.620 33.333 0.00 0.00 30.87 1.52
2155 3041 6.435428 ACGCATTTTGTGGACTAAGTTTTAG 58.565 36.000 0.00 0.00 30.87 1.85
2156 3042 6.261381 ACGCATTTTGTGGACTAAGTTTTAGA 59.739 34.615 3.04 0.00 30.87 2.10
2157 3043 6.577427 CGCATTTTGTGGACTAAGTTTTAGAC 59.423 38.462 3.04 0.00 0.00 2.59
2158 3044 7.519970 CGCATTTTGTGGACTAAGTTTTAGACT 60.520 37.037 3.04 0.00 41.47 3.24
2187 3075 6.644347 AGTACTCATGTCGGAAAAATCTCAT 58.356 36.000 0.00 0.00 0.00 2.90
2188 3076 7.782049 AGTACTCATGTCGGAAAAATCTCATA 58.218 34.615 0.00 0.00 0.00 2.15
2189 3077 6.910536 ACTCATGTCGGAAAAATCTCATAC 57.089 37.500 0.00 0.00 0.00 2.39
2198 3086 5.107453 CGGAAAAATCTCATACTACATCGCC 60.107 44.000 0.00 0.00 0.00 5.54
2378 3289 6.787085 AATTTTCAGTTCGACCTTCTACTG 57.213 37.500 6.37 6.37 39.41 2.74
2379 3290 5.524971 TTTTCAGTTCGACCTTCTACTGA 57.475 39.130 10.55 10.55 43.69 3.41
2386 3300 3.285484 TCGACCTTCTACTGATACACCC 58.715 50.000 0.00 0.00 0.00 4.61
2428 3343 5.957842 ATGAAAGCATGGTTAAAACTCGA 57.042 34.783 11.15 0.00 32.31 4.04
2437 3352 4.190772 TGGTTAAAACTCGAAACGACCTT 58.809 39.130 0.00 0.00 0.00 3.50
2439 3354 5.814705 TGGTTAAAACTCGAAACGACCTTTA 59.185 36.000 0.00 0.00 0.00 1.85
2440 3355 6.018832 TGGTTAAAACTCGAAACGACCTTTAG 60.019 38.462 0.00 0.00 0.00 1.85
2441 3356 6.357980 GTTAAAACTCGAAACGACCTTTAGG 58.642 40.000 0.00 0.00 42.17 2.69
2476 3391 3.053831 AGGTGTATTCCGGTCTTTGTG 57.946 47.619 0.00 0.00 0.00 3.33
2482 3397 1.301423 TTCCGGTCTTTGTGTTTCCG 58.699 50.000 0.00 0.00 40.72 4.30
2502 5036 0.514255 CTGCATGTGTCACTTGGTCG 59.486 55.000 17.78 0.00 0.00 4.79
2512 5051 2.096218 GTCACTTGGTCGTGAGCAATTC 60.096 50.000 14.15 3.38 46.12 2.17
2527 5066 2.094854 GCAATTCCCTGCTTCTGTTCAG 60.095 50.000 0.00 0.00 39.34 3.02
2534 5073 2.360165 CCTGCTTCTGTTCAGTTTTGCT 59.640 45.455 0.00 0.00 0.00 3.91
2548 5087 3.318275 AGTTTTGCTACTGTCGACTCTGA 59.682 43.478 17.92 0.00 0.00 3.27
2606 5146 1.523758 AGGGTCTGCGACAATTTCAC 58.476 50.000 10.14 0.00 33.68 3.18
2644 5202 1.808945 CAGCCTACTCCACTTTGCAAG 59.191 52.381 0.00 0.00 0.00 4.01
2704 5263 3.579151 GTCCCTAGTCCTCTGTTTTGTCT 59.421 47.826 0.00 0.00 0.00 3.41
2707 5266 4.202367 CCCTAGTCCTCTGTTTTGTCTGTT 60.202 45.833 0.00 0.00 0.00 3.16
2723 5282 3.127030 GTCTGTTAGTAATGCCAGGTTGC 59.873 47.826 0.00 0.00 0.00 4.17
2725 5284 2.081462 GTTAGTAATGCCAGGTTGCGT 58.919 47.619 0.00 0.00 0.00 5.24
2750 5309 0.998928 TAGATCCTTTTGGCAGCCCA 59.001 50.000 9.64 0.00 40.06 5.36
2812 5371 2.033424 GGGAGCCTAAATCAAATCGTGC 59.967 50.000 0.00 0.00 0.00 5.34
2814 5373 3.242870 GGAGCCTAAATCAAATCGTGCAG 60.243 47.826 0.00 0.00 0.00 4.41
2815 5374 3.347216 AGCCTAAATCAAATCGTGCAGT 58.653 40.909 0.00 0.00 0.00 4.40
2817 5376 4.332819 AGCCTAAATCAAATCGTGCAGTAC 59.667 41.667 0.00 0.00 0.00 2.73
2819 5378 5.727791 GCCTAAATCAAATCGTGCAGTACTG 60.728 44.000 18.93 18.93 0.00 2.74
2820 5379 5.351465 CCTAAATCAAATCGTGCAGTACTGT 59.649 40.000 23.44 0.64 0.00 3.55
2821 5380 6.533723 CCTAAATCAAATCGTGCAGTACTGTA 59.466 38.462 23.44 17.20 0.00 2.74
2822 5381 6.985188 AAATCAAATCGTGCAGTACTGTAT 57.015 33.333 23.44 9.92 0.00 2.29
2827 5386 8.126871 TCAAATCGTGCAGTACTGTATTATTC 57.873 34.615 23.44 6.59 0.00 1.75
2828 5387 7.762159 TCAAATCGTGCAGTACTGTATTATTCA 59.238 33.333 23.44 8.69 0.00 2.57
2829 5388 7.700322 AATCGTGCAGTACTGTATTATTCAG 57.300 36.000 23.44 6.96 38.68 3.02
2830 5389 5.588240 TCGTGCAGTACTGTATTATTCAGG 58.412 41.667 23.44 15.39 37.25 3.86
2831 5390 4.209288 CGTGCAGTACTGTATTATTCAGGC 59.791 45.833 23.44 5.66 37.25 4.85
2832 5391 5.116180 GTGCAGTACTGTATTATTCAGGCA 58.884 41.667 23.44 8.25 37.25 4.75
2833 5392 5.235186 GTGCAGTACTGTATTATTCAGGCAG 59.765 44.000 23.44 0.00 37.25 4.85
2834 5393 5.104941 TGCAGTACTGTATTATTCAGGCAGT 60.105 40.000 23.44 0.00 42.25 4.40
2835 5394 6.097696 TGCAGTACTGTATTATTCAGGCAGTA 59.902 38.462 23.44 0.00 40.39 2.74
2836 5395 6.984474 GCAGTACTGTATTATTCAGGCAGTAA 59.016 38.462 23.44 0.00 42.10 2.24
2837 5396 7.494625 GCAGTACTGTATTATTCAGGCAGTAAA 59.505 37.037 23.44 0.00 42.10 2.01
2838 5397 8.818057 CAGTACTGTATTATTCAGGCAGTAAAC 58.182 37.037 15.06 0.00 42.10 2.01
2839 5398 8.537016 AGTACTGTATTATTCAGGCAGTAAACA 58.463 33.333 0.00 0.00 42.10 2.83
2840 5399 7.849804 ACTGTATTATTCAGGCAGTAAACAG 57.150 36.000 4.00 0.00 38.46 3.16
2841 5400 6.823689 ACTGTATTATTCAGGCAGTAAACAGG 59.176 38.462 4.00 0.00 38.46 4.00
2842 5401 5.588648 TGTATTATTCAGGCAGTAAACAGGC 59.411 40.000 0.00 0.00 0.00 4.85
2843 5402 2.887151 ATTCAGGCAGTAAACAGGCT 57.113 45.000 0.00 0.00 38.76 4.58
2844 5403 5.429681 TTATTCAGGCAGTAAACAGGCTA 57.570 39.130 1.28 0.00 36.17 3.93
2845 5404 3.334583 TTCAGGCAGTAAACAGGCTAG 57.665 47.619 1.28 0.00 36.17 3.42
2846 5405 1.066143 TCAGGCAGTAAACAGGCTAGC 60.066 52.381 6.04 6.04 36.17 3.42
2847 5406 0.253327 AGGCAGTAAACAGGCTAGCC 59.747 55.000 27.19 27.19 36.54 3.93
2869 5428 6.586082 AGCCTGAACTTGTATTTTTAAATGCG 59.414 34.615 0.00 0.00 34.29 4.73
2875 5434 6.894828 ACTTGTATTTTTAAATGCGTCGTCT 58.105 32.000 0.00 0.00 34.29 4.18
2955 5514 7.451255 TCATGTTGGAGTAATCAAATTTGGAGT 59.549 33.333 17.90 6.97 0.00 3.85
2962 5521 9.668497 GGAGTAATCAAATTTGGAGTAGTACTT 57.332 33.333 17.90 3.53 0.00 2.24
2968 5527 8.697846 TCAAATTTGGAGTAGTACTTCATACG 57.302 34.615 17.90 1.35 32.87 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.817084 TGAGGAGCACAAAAGTCATCTTG 59.183 43.478 0.00 0.00 33.79 3.02
1 2 4.090761 TGAGGAGCACAAAAGTCATCTT 57.909 40.909 0.00 0.00 35.14 2.40
3 4 3.057946 GGTTGAGGAGCACAAAAGTCATC 60.058 47.826 0.00 0.00 0.00 2.92
4 5 2.887152 GGTTGAGGAGCACAAAAGTCAT 59.113 45.455 0.00 0.00 0.00 3.06
6 7 2.297701 TGGTTGAGGAGCACAAAAGTC 58.702 47.619 0.00 0.00 0.00 3.01
7 8 2.435372 TGGTTGAGGAGCACAAAAGT 57.565 45.000 0.00 0.00 0.00 2.66
14 15 3.719268 ATACATTGTGGTTGAGGAGCA 57.281 42.857 0.00 0.00 0.00 4.26
15 16 5.050091 CGATAATACATTGTGGTTGAGGAGC 60.050 44.000 0.00 0.00 0.00 4.70
16 17 5.466728 CCGATAATACATTGTGGTTGAGGAG 59.533 44.000 0.00 0.00 0.00 3.69
17 18 5.104693 ACCGATAATACATTGTGGTTGAGGA 60.105 40.000 0.00 0.00 0.00 3.71
18 19 5.007626 CACCGATAATACATTGTGGTTGAGG 59.992 44.000 0.00 0.00 0.00 3.86
19 20 5.815222 TCACCGATAATACATTGTGGTTGAG 59.185 40.000 0.00 0.00 0.00 3.02
20 21 5.735766 TCACCGATAATACATTGTGGTTGA 58.264 37.500 0.00 0.00 0.00 3.18
21 22 5.815222 TCTCACCGATAATACATTGTGGTTG 59.185 40.000 0.00 0.00 0.00 3.77
22 23 5.984725 TCTCACCGATAATACATTGTGGTT 58.015 37.500 0.00 0.00 0.00 3.67
23 24 5.607939 TCTCACCGATAATACATTGTGGT 57.392 39.130 0.00 0.00 0.00 4.16
24 25 5.815222 TGTTCTCACCGATAATACATTGTGG 59.185 40.000 0.00 0.00 0.00 4.17
25 26 6.902224 TGTTCTCACCGATAATACATTGTG 57.098 37.500 0.00 0.00 0.00 3.33
26 27 7.065803 CCTTTGTTCTCACCGATAATACATTGT 59.934 37.037 0.00 0.00 0.00 2.71
27 28 7.065803 ACCTTTGTTCTCACCGATAATACATTG 59.934 37.037 0.00 0.00 0.00 2.82
28 29 7.110155 ACCTTTGTTCTCACCGATAATACATT 58.890 34.615 0.00 0.00 0.00 2.71
29 30 6.650120 ACCTTTGTTCTCACCGATAATACAT 58.350 36.000 0.00 0.00 0.00 2.29
30 31 6.045072 ACCTTTGTTCTCACCGATAATACA 57.955 37.500 0.00 0.00 0.00 2.29
31 32 6.103997 TGACCTTTGTTCTCACCGATAATAC 58.896 40.000 0.00 0.00 0.00 1.89
32 33 6.288941 TGACCTTTGTTCTCACCGATAATA 57.711 37.500 0.00 0.00 0.00 0.98
33 34 5.160607 TGACCTTTGTTCTCACCGATAAT 57.839 39.130 0.00 0.00 0.00 1.28
34 35 4.610605 TGACCTTTGTTCTCACCGATAA 57.389 40.909 0.00 0.00 0.00 1.75
35 36 4.466370 AGATGACCTTTGTTCTCACCGATA 59.534 41.667 0.00 0.00 0.00 2.92
36 37 3.261897 AGATGACCTTTGTTCTCACCGAT 59.738 43.478 0.00 0.00 0.00 4.18
37 38 2.632996 AGATGACCTTTGTTCTCACCGA 59.367 45.455 0.00 0.00 0.00 4.69
38 39 2.738846 CAGATGACCTTTGTTCTCACCG 59.261 50.000 0.00 0.00 0.00 4.94
39 40 4.008074 TCAGATGACCTTTGTTCTCACC 57.992 45.455 0.00 0.00 0.00 4.02
40 41 5.121454 GTGATCAGATGACCTTTGTTCTCAC 59.879 44.000 0.00 0.00 0.00 3.51
41 42 5.240891 GTGATCAGATGACCTTTGTTCTCA 58.759 41.667 0.00 0.00 0.00 3.27
42 43 4.328440 CGTGATCAGATGACCTTTGTTCTC 59.672 45.833 0.00 0.00 0.00 2.87
43 44 4.248859 CGTGATCAGATGACCTTTGTTCT 58.751 43.478 0.00 0.00 0.00 3.01
44 45 3.997021 ACGTGATCAGATGACCTTTGTTC 59.003 43.478 0.00 0.00 0.00 3.18
45 46 3.997021 GACGTGATCAGATGACCTTTGTT 59.003 43.478 0.00 0.00 0.00 2.83
46 47 3.006859 TGACGTGATCAGATGACCTTTGT 59.993 43.478 0.00 0.00 31.91 2.83
47 48 3.588955 TGACGTGATCAGATGACCTTTG 58.411 45.455 0.00 0.00 31.91 2.77
48 49 3.961480 TGACGTGATCAGATGACCTTT 57.039 42.857 0.00 0.00 31.91 3.11
49 50 4.889995 TCTATGACGTGATCAGATGACCTT 59.110 41.667 0.00 0.00 41.91 3.50
50 51 4.464947 TCTATGACGTGATCAGATGACCT 58.535 43.478 0.00 0.00 41.91 3.85
51 52 4.320861 CCTCTATGACGTGATCAGATGACC 60.321 50.000 0.00 0.00 41.91 4.02
52 53 4.793071 CCTCTATGACGTGATCAGATGAC 58.207 47.826 0.00 0.00 41.91 3.06
53 54 3.254411 GCCTCTATGACGTGATCAGATGA 59.746 47.826 0.00 0.00 41.91 2.92
54 55 3.005155 TGCCTCTATGACGTGATCAGATG 59.995 47.826 0.00 0.00 41.91 2.90
55 56 3.225940 TGCCTCTATGACGTGATCAGAT 58.774 45.455 0.00 0.00 41.91 2.90
56 57 2.654863 TGCCTCTATGACGTGATCAGA 58.345 47.619 0.00 0.00 41.91 3.27
57 58 3.443099 TTGCCTCTATGACGTGATCAG 57.557 47.619 0.00 0.00 41.91 2.90
58 59 3.785486 CTTTGCCTCTATGACGTGATCA 58.215 45.455 0.00 0.00 43.13 2.92
59 60 2.541762 GCTTTGCCTCTATGACGTGATC 59.458 50.000 0.00 0.00 0.00 2.92
60 61 2.169352 AGCTTTGCCTCTATGACGTGAT 59.831 45.455 0.00 0.00 0.00 3.06
61 62 1.550524 AGCTTTGCCTCTATGACGTGA 59.449 47.619 0.00 0.00 0.00 4.35
62 63 2.015736 AGCTTTGCCTCTATGACGTG 57.984 50.000 0.00 0.00 0.00 4.49
63 64 5.730296 ATATAGCTTTGCCTCTATGACGT 57.270 39.130 0.00 0.00 0.00 4.34
64 65 6.646653 TGAAATATAGCTTTGCCTCTATGACG 59.353 38.462 0.00 0.00 0.00 4.35
65 66 7.969536 TGAAATATAGCTTTGCCTCTATGAC 57.030 36.000 0.00 0.00 0.00 3.06
66 67 7.826252 GGATGAAATATAGCTTTGCCTCTATGA 59.174 37.037 0.00 0.00 0.00 2.15
67 68 7.609146 TGGATGAAATATAGCTTTGCCTCTATG 59.391 37.037 0.00 0.00 0.00 2.23
68 69 7.609532 GTGGATGAAATATAGCTTTGCCTCTAT 59.390 37.037 0.00 0.00 0.00 1.98
69 70 6.936900 GTGGATGAAATATAGCTTTGCCTCTA 59.063 38.462 0.00 0.00 0.00 2.43
70 71 5.767168 GTGGATGAAATATAGCTTTGCCTCT 59.233 40.000 0.00 0.00 0.00 3.69
71 72 5.532406 TGTGGATGAAATATAGCTTTGCCTC 59.468 40.000 0.00 0.00 0.00 4.70
72 73 5.448654 TGTGGATGAAATATAGCTTTGCCT 58.551 37.500 0.00 0.00 0.00 4.75
73 74 5.532406 TCTGTGGATGAAATATAGCTTTGCC 59.468 40.000 0.00 0.00 0.00 4.52
74 75 6.624352 TCTGTGGATGAAATATAGCTTTGC 57.376 37.500 0.00 0.00 0.00 3.68
75 76 8.013947 CGAATCTGTGGATGAAATATAGCTTTG 58.986 37.037 0.00 0.00 31.75 2.77
76 77 7.173907 CCGAATCTGTGGATGAAATATAGCTTT 59.826 37.037 0.00 0.00 31.75 3.51
77 78 6.652481 CCGAATCTGTGGATGAAATATAGCTT 59.348 38.462 0.00 0.00 31.75 3.74
78 79 6.169094 CCGAATCTGTGGATGAAATATAGCT 58.831 40.000 0.00 0.00 31.75 3.32
79 80 5.934625 ACCGAATCTGTGGATGAAATATAGC 59.065 40.000 0.00 0.00 31.75 2.97
87 88 0.612744 TGCACCGAATCTGTGGATGA 59.387 50.000 6.92 0.00 34.27 2.92
89 90 1.003580 AGTTGCACCGAATCTGTGGAT 59.996 47.619 6.92 0.00 33.92 3.41
93 94 1.967319 AACAGTTGCACCGAATCTGT 58.033 45.000 0.00 0.00 40.40 3.41
96 97 3.189287 AGATGAAACAGTTGCACCGAATC 59.811 43.478 0.00 0.00 0.00 2.52
97 98 3.149196 AGATGAAACAGTTGCACCGAAT 58.851 40.909 0.00 0.00 0.00 3.34
99 100 2.143122 GAGATGAAACAGTTGCACCGA 58.857 47.619 0.00 0.00 0.00 4.69
100 101 1.136252 CGAGATGAAACAGTTGCACCG 60.136 52.381 0.00 0.00 0.00 4.94
101 102 1.197721 CCGAGATGAAACAGTTGCACC 59.802 52.381 0.00 0.00 0.00 5.01
110 111 6.956047 ACAAAGACTAAAACCGAGATGAAAC 58.044 36.000 0.00 0.00 0.00 2.78
111 112 6.204108 GGACAAAGACTAAAACCGAGATGAAA 59.796 38.462 0.00 0.00 0.00 2.69
113 114 5.011738 AGGACAAAGACTAAAACCGAGATGA 59.988 40.000 0.00 0.00 0.00 2.92
118 119 4.374399 GTGAGGACAAAGACTAAAACCGA 58.626 43.478 0.00 0.00 0.00 4.69
120 121 4.727235 CGTGAGGACAAAGACTAAAACC 57.273 45.455 0.00 0.00 0.00 3.27
139 140 0.463833 GATTGAAAGATCGGCCCCGT 60.464 55.000 6.61 0.00 40.74 5.28
144 145 3.686726 ACTCAACTGATTGAAAGATCGGC 59.313 43.478 0.00 0.00 44.28 5.54
154 155 5.765182 ACCCTAACAGAAACTCAACTGATTG 59.235 40.000 0.00 0.00 37.54 2.67
155 156 5.765182 CACCCTAACAGAAACTCAACTGATT 59.235 40.000 0.00 0.00 37.54 2.57
159 160 4.409247 AGACACCCTAACAGAAACTCAACT 59.591 41.667 0.00 0.00 0.00 3.16
169 170 4.401202 ACCAACAAAAAGACACCCTAACAG 59.599 41.667 0.00 0.00 0.00 3.16
174 175 3.835395 TCAAACCAACAAAAAGACACCCT 59.165 39.130 0.00 0.00 0.00 4.34
212 221 5.007430 TCACCGTAATATCGAGTGAAGTCTC 59.993 44.000 0.00 0.00 37.72 3.36
219 228 7.337718 CAAAATCTTCACCGTAATATCGAGTG 58.662 38.462 0.00 0.00 35.25 3.51
253 1064 1.077068 CCCTTGGAAATGCGGGCTA 60.077 57.895 0.00 0.00 0.00 3.93
258 1069 1.134946 GGATGAACCCTTGGAAATGCG 59.865 52.381 0.00 0.00 0.00 4.73
259 1070 2.428530 GAGGATGAACCCTTGGAAATGC 59.571 50.000 0.00 0.00 40.05 3.56
262 1073 1.982226 TCGAGGATGAACCCTTGGAAA 59.018 47.619 0.00 0.00 38.11 3.13
265 1076 0.107654 GGTCGAGGATGAACCCTTGG 60.108 60.000 0.00 0.00 38.11 3.61
271 1082 3.518590 ACGTATTTGGTCGAGGATGAAC 58.481 45.455 0.00 0.00 0.00 3.18
287 1098 3.655276 AACCGTGAAGAGTGAACGTAT 57.345 42.857 0.00 0.00 35.59 3.06
296 1107 5.438761 AAAAGATGGAAAACCGTGAAGAG 57.561 39.130 0.00 0.00 0.00 2.85
298 1109 4.744631 CCAAAAAGATGGAAAACCGTGAAG 59.255 41.667 0.00 0.00 43.54 3.02
301 1112 4.314740 TCCAAAAAGATGGAAAACCGTG 57.685 40.909 0.00 0.00 46.36 4.94
328 1139 4.870021 AAGTATCAGAGCCCCTTGATTT 57.130 40.909 0.00 0.00 0.00 2.17
334 1145 3.185455 ACAGAAAAGTATCAGAGCCCCT 58.815 45.455 0.00 0.00 0.00 4.79
337 1148 3.190874 CCGACAGAAAAGTATCAGAGCC 58.809 50.000 0.00 0.00 0.00 4.70
338 1149 3.851098 ACCGACAGAAAAGTATCAGAGC 58.149 45.455 0.00 0.00 0.00 4.09
339 1150 7.258441 TGAATACCGACAGAAAAGTATCAGAG 58.742 38.462 0.00 0.00 0.00 3.35
340 1151 7.165460 TGAATACCGACAGAAAAGTATCAGA 57.835 36.000 0.00 0.00 0.00 3.27
341 1152 7.545965 ACTTGAATACCGACAGAAAAGTATCAG 59.454 37.037 0.00 0.00 0.00 2.90
342 1153 7.383687 ACTTGAATACCGACAGAAAAGTATCA 58.616 34.615 0.00 0.00 0.00 2.15
343 1154 7.760340 AGACTTGAATACCGACAGAAAAGTATC 59.240 37.037 0.00 0.00 0.00 2.24
344 1155 7.545965 CAGACTTGAATACCGACAGAAAAGTAT 59.454 37.037 0.00 0.00 0.00 2.12
345 1156 6.866770 CAGACTTGAATACCGACAGAAAAGTA 59.133 38.462 0.00 0.00 0.00 2.24
346 1157 5.696724 CAGACTTGAATACCGACAGAAAAGT 59.303 40.000 0.00 0.00 0.00 2.66
347 1158 5.389935 GCAGACTTGAATACCGACAGAAAAG 60.390 44.000 0.00 0.00 0.00 2.27
348 1159 4.451096 GCAGACTTGAATACCGACAGAAAA 59.549 41.667 0.00 0.00 0.00 2.29
349 1160 3.994392 GCAGACTTGAATACCGACAGAAA 59.006 43.478 0.00 0.00 0.00 2.52
352 1163 1.920574 CGCAGACTTGAATACCGACAG 59.079 52.381 0.00 0.00 0.00 3.51
357 1168 4.091509 CACTTGTACGCAGACTTGAATACC 59.908 45.833 0.00 0.00 0.00 2.73
361 1172 3.120792 GTCACTTGTACGCAGACTTGAA 58.879 45.455 0.00 0.00 0.00 2.69
369 1180 3.985279 GTCAACATAGTCACTTGTACGCA 59.015 43.478 0.00 0.00 0.00 5.24
371 1182 5.220381 AGTGTCAACATAGTCACTTGTACG 58.780 41.667 0.00 0.00 37.81 3.67
389 1200 7.097834 AGGCACTACAATTTAACTAGAGTGTC 58.902 38.462 0.00 0.00 38.12 3.67
391 1202 7.907214 AAGGCACTACAATTTAACTAGAGTG 57.093 36.000 0.00 0.00 38.49 3.51
401 1212 8.007405 ACTCTTAAACAAAGGCACTACAATTT 57.993 30.769 0.00 0.00 38.49 1.82
407 1218 6.354130 ACTCAACTCTTAAACAAAGGCACTA 58.646 36.000 0.00 0.00 38.49 2.74
419 1230 8.027771 GGAAGACGAAATCTACTCAACTCTTAA 58.972 37.037 0.00 0.00 36.27 1.85
420 1231 7.176165 TGGAAGACGAAATCTACTCAACTCTTA 59.824 37.037 0.00 0.00 36.27 2.10
424 1235 5.723672 TGGAAGACGAAATCTACTCAACT 57.276 39.130 0.00 0.00 36.27 3.16
425 1236 6.780706 TTTGGAAGACGAAATCTACTCAAC 57.219 37.500 0.00 0.00 36.27 3.18
450 1261 5.263599 TGGATGCACCTTCTTGTGAATATT 58.736 37.500 0.00 0.00 34.53 1.28
451 1262 4.858850 TGGATGCACCTTCTTGTGAATAT 58.141 39.130 0.00 0.00 34.53 1.28
456 1267 2.624838 ACTTTGGATGCACCTTCTTGTG 59.375 45.455 0.00 0.00 39.86 3.33
457 1268 2.949447 ACTTTGGATGCACCTTCTTGT 58.051 42.857 0.00 0.00 39.86 3.16
501 1312 8.575589 TGAACAGAGTGTGCACAAATATATTTT 58.424 29.630 23.59 7.44 29.08 1.82
514 1325 5.926542 TCTTACATTAGTGAACAGAGTGTGC 59.073 40.000 0.00 0.00 0.00 4.57
531 1342 6.512297 GGTTTTGGTGTCAAATGTCTTACAT 58.488 36.000 0.00 0.00 41.84 2.29
556 1368 4.642429 ACCTCTGTTCACCAATGTAAGAC 58.358 43.478 0.00 0.00 0.00 3.01
591 1403 8.964772 CAGGTGAAATTCTTTGGATCTAAGATT 58.035 33.333 10.31 5.96 32.09 2.40
597 1409 7.123247 CCATTACAGGTGAAATTCTTTGGATCT 59.877 37.037 0.00 0.00 0.00 2.75
607 1419 7.734942 ACATGAAAACCATTACAGGTGAAATT 58.265 30.769 0.00 0.00 42.25 1.82
612 1424 5.695816 CCAAACATGAAAACCATTACAGGTG 59.304 40.000 0.00 0.00 42.25 4.00
679 1491 8.967218 CATGAAAATGGCTATTTTGGTAATACG 58.033 33.333 23.53 2.18 44.35 3.06
733 1545 3.302344 GGCCTTGCAAAGCCCGAA 61.302 61.111 25.94 0.00 44.44 4.30
775 1592 0.175760 GCGCTAGACCAGGTCAATGA 59.824 55.000 22.31 3.04 34.60 2.57
778 1595 0.898326 TCAGCGCTAGACCAGGTCAA 60.898 55.000 22.31 0.00 34.60 3.18
781 1598 1.776662 TATTCAGCGCTAGACCAGGT 58.223 50.000 10.99 0.00 0.00 4.00
821 1638 0.832135 TGGAGTTTGGAGCCGAGACT 60.832 55.000 0.00 0.00 0.00 3.24
862 1679 4.339247 ACAAGCAAAAGCAATAGTGTCAGT 59.661 37.500 0.00 0.00 0.00 3.41
863 1680 4.678287 CACAAGCAAAAGCAATAGTGTCAG 59.322 41.667 0.00 0.00 0.00 3.51
865 1682 3.426525 GCACAAGCAAAAGCAATAGTGTC 59.573 43.478 0.00 0.00 41.58 3.67
866 1683 3.383761 GCACAAGCAAAAGCAATAGTGT 58.616 40.909 0.00 0.00 41.58 3.55
867 1684 2.406024 CGCACAAGCAAAAGCAATAGTG 59.594 45.455 0.00 0.00 42.27 2.74
868 1685 2.607771 CCGCACAAGCAAAAGCAATAGT 60.608 45.455 0.00 0.00 42.27 2.12
869 1686 1.987770 CCGCACAAGCAAAAGCAATAG 59.012 47.619 0.00 0.00 42.27 1.73
870 1687 1.934399 GCCGCACAAGCAAAAGCAATA 60.934 47.619 0.00 0.00 42.27 1.90
871 1688 1.223417 GCCGCACAAGCAAAAGCAAT 61.223 50.000 0.00 0.00 42.27 3.56
872 1689 1.882167 GCCGCACAAGCAAAAGCAA 60.882 52.632 0.00 0.00 42.27 3.91
873 1690 2.279385 GCCGCACAAGCAAAAGCA 60.279 55.556 0.00 0.00 42.27 3.91
918 1735 1.010574 CGCCTTCTAGTCTCTCGCG 60.011 63.158 0.00 0.00 0.00 5.87
926 1743 0.614979 TTGAGCCTCCGCCTTCTAGT 60.615 55.000 0.00 0.00 34.57 2.57
1325 2189 2.951475 GAACACGTTGGGGCTGTCCA 62.951 60.000 0.00 0.00 37.22 4.02
1340 2204 0.984230 GAGGATGTGGGAGTGGAACA 59.016 55.000 0.00 0.00 41.43 3.18
1524 2391 0.904865 ACAGGATCTCGAACTGCCCA 60.905 55.000 6.13 0.00 35.70 5.36
1766 2633 2.498726 CTTCTCCCTGCGCCTCTC 59.501 66.667 4.18 0.00 0.00 3.20
2017 2903 0.320374 ATCGACCGCAGTTCCTTCAA 59.680 50.000 0.00 0.00 0.00 2.69
2018 2904 0.108804 GATCGACCGCAGTTCCTTCA 60.109 55.000 0.00 0.00 0.00 3.02
2023 2909 0.388649 ACAGTGATCGACCGCAGTTC 60.389 55.000 0.00 0.00 0.00 3.01
2030 2916 1.726853 CTTTCCCACAGTGATCGACC 58.273 55.000 0.62 0.00 0.00 4.79
2031 2917 1.079503 GCTTTCCCACAGTGATCGAC 58.920 55.000 0.62 0.00 0.00 4.20
2090 2976 3.181497 GCATTGCATACTCCACAAATCGT 60.181 43.478 3.15 0.00 0.00 3.73
2150 3036 9.199982 CCGACATGAGTACTAAAAAGTCTAAAA 57.800 33.333 0.00 0.00 0.00 1.52
2154 3040 6.585695 TCCGACATGAGTACTAAAAAGTCT 57.414 37.500 0.00 0.00 0.00 3.24
2155 3041 7.647907 TTTCCGACATGAGTACTAAAAAGTC 57.352 36.000 0.00 0.00 0.00 3.01
2156 3042 8.441312 TTTTTCCGACATGAGTACTAAAAAGT 57.559 30.769 0.00 0.00 0.00 2.66
2157 3043 9.543018 GATTTTTCCGACATGAGTACTAAAAAG 57.457 33.333 0.00 0.00 31.15 2.27
2158 3044 9.280174 AGATTTTTCCGACATGAGTACTAAAAA 57.720 29.630 0.00 9.77 31.67 1.94
2187 3075 5.469084 CACTGATACACTAGGCGATGTAGTA 59.531 44.000 0.00 0.00 34.88 1.82
2188 3076 4.276183 CACTGATACACTAGGCGATGTAGT 59.724 45.833 0.00 0.00 34.88 2.73
2189 3077 4.276183 ACACTGATACACTAGGCGATGTAG 59.724 45.833 0.00 0.00 34.88 2.74
2198 3086 4.357018 TCTTGCGACACTGATACACTAG 57.643 45.455 0.00 0.00 0.00 2.57
2386 3300 7.559590 TTCATTTTGTTAAATTGTTGTGGGG 57.440 32.000 0.00 0.00 31.63 4.96
2437 3352 0.810426 TTGCGTTGCGTGACACCTAA 60.810 50.000 0.00 0.00 0.00 2.69
2439 3354 2.512745 TTGCGTTGCGTGACACCT 60.513 55.556 0.00 0.00 0.00 4.00
2440 3355 2.052237 CTTGCGTTGCGTGACACC 60.052 61.111 0.00 0.00 0.00 4.16
2441 3356 2.052237 CCTTGCGTTGCGTGACAC 60.052 61.111 0.00 0.00 0.00 3.67
2442 3357 2.512745 ACCTTGCGTTGCGTGACA 60.513 55.556 0.00 0.00 0.00 3.58
2443 3358 1.492319 TACACCTTGCGTTGCGTGAC 61.492 55.000 2.99 0.00 0.00 3.67
2462 3377 1.877443 CGGAAACACAAAGACCGGAAT 59.123 47.619 9.46 0.00 39.92 3.01
2476 3391 0.385974 GTGACACATGCAGCGGAAAC 60.386 55.000 0.00 0.00 0.00 2.78
2482 3397 0.239347 GACCAAGTGACACATGCAGC 59.761 55.000 8.59 0.00 0.00 5.25
2512 5051 2.544486 GCAAAACTGAACAGAAGCAGGG 60.544 50.000 8.87 0.00 36.47 4.45
2527 5066 3.639538 TCAGAGTCGACAGTAGCAAAAC 58.360 45.455 19.50 0.00 0.00 2.43
2534 5073 5.944599 ACTCCTTAATTCAGAGTCGACAGTA 59.055 40.000 19.50 1.37 36.06 2.74
2548 5087 4.030913 TCCTGACCGATCACTCCTTAATT 58.969 43.478 0.00 0.00 0.00 1.40
2644 5202 4.593634 TCTTTTTCTATAGGGGAGGCTAGC 59.406 45.833 6.04 6.04 0.00 3.42
2704 5263 2.080693 CGCAACCTGGCATTACTAACA 58.919 47.619 0.00 0.00 0.00 2.41
2707 5266 2.027561 AGAACGCAACCTGGCATTACTA 60.028 45.455 0.00 0.00 0.00 1.82
2723 5282 3.198872 GCCAAAAGGATCTAGGAGAACG 58.801 50.000 0.00 0.00 0.00 3.95
2725 5284 3.370953 GCTGCCAAAAGGATCTAGGAGAA 60.371 47.826 0.00 0.00 0.00 2.87
2750 5309 2.675423 TGGAGCTCGTACCACGCT 60.675 61.111 7.83 0.00 42.21 5.07
2808 5367 4.209288 GCCTGAATAATACAGTACTGCACG 59.791 45.833 22.90 6.02 34.04 5.34
2812 5371 8.818057 GTTTACTGCCTGAATAATACAGTACTG 58.182 37.037 21.44 21.44 41.99 2.74
2814 5373 8.712285 TGTTTACTGCCTGAATAATACAGTAC 57.288 34.615 0.00 0.00 41.99 2.73
2815 5374 7.985184 CCTGTTTACTGCCTGAATAATACAGTA 59.015 37.037 0.00 0.00 41.56 2.74
2817 5376 6.238484 GCCTGTTTACTGCCTGAATAATACAG 60.238 42.308 0.00 0.00 35.43 2.74
2819 5378 5.823045 AGCCTGTTTACTGCCTGAATAATAC 59.177 40.000 0.00 0.00 0.00 1.89
2820 5379 6.001449 AGCCTGTTTACTGCCTGAATAATA 57.999 37.500 0.00 0.00 0.00 0.98
2821 5380 4.860022 AGCCTGTTTACTGCCTGAATAAT 58.140 39.130 0.00 0.00 0.00 1.28
2822 5381 4.301072 AGCCTGTTTACTGCCTGAATAA 57.699 40.909 0.00 0.00 0.00 1.40
2827 5386 1.373570 GCTAGCCTGTTTACTGCCTG 58.626 55.000 2.29 0.00 0.00 4.85
2828 5387 0.253327 GGCTAGCCTGTTTACTGCCT 59.747 55.000 27.17 0.00 36.32 4.75
2829 5388 0.253327 AGGCTAGCCTGTTTACTGCC 59.747 55.000 35.59 4.04 46.22 4.85
2830 5389 3.863407 AGGCTAGCCTGTTTACTGC 57.137 52.632 35.59 3.64 46.22 4.40
2840 5399 5.644977 AAAAATACAAGTTCAGGCTAGCC 57.355 39.130 27.19 27.19 0.00 3.93
2841 5400 9.076596 CATTTAAAAATACAAGTTCAGGCTAGC 57.923 33.333 6.04 6.04 0.00 3.42
2842 5401 9.076596 GCATTTAAAAATACAAGTTCAGGCTAG 57.923 33.333 0.00 0.00 0.00 3.42
2843 5402 7.753132 CGCATTTAAAAATACAAGTTCAGGCTA 59.247 33.333 0.00 0.00 0.00 3.93
2844 5403 6.586082 CGCATTTAAAAATACAAGTTCAGGCT 59.414 34.615 0.00 0.00 0.00 4.58
2845 5404 6.364976 ACGCATTTAAAAATACAAGTTCAGGC 59.635 34.615 0.00 0.00 0.00 4.85
2846 5405 7.201232 CGACGCATTTAAAAATACAAGTTCAGG 60.201 37.037 0.00 0.00 0.00 3.86
2847 5406 7.322699 ACGACGCATTTAAAAATACAAGTTCAG 59.677 33.333 0.00 0.00 0.00 3.02
2848 5407 7.133513 ACGACGCATTTAAAAATACAAGTTCA 58.866 30.769 0.00 0.00 0.00 3.18
2849 5408 7.532884 AGACGACGCATTTAAAAATACAAGTTC 59.467 33.333 0.00 0.00 0.00 3.01
2850 5409 7.357303 AGACGACGCATTTAAAAATACAAGTT 58.643 30.769 0.00 0.00 0.00 2.66
2851 5410 6.894828 AGACGACGCATTTAAAAATACAAGT 58.105 32.000 0.00 0.00 0.00 3.16
2852 5411 9.144085 GATAGACGACGCATTTAAAAATACAAG 57.856 33.333 0.00 0.00 0.00 3.16
2853 5412 8.875803 AGATAGACGACGCATTTAAAAATACAA 58.124 29.630 0.00 0.00 0.00 2.41
2924 5483 8.731275 AATTTGATTACTCCAACATGATCGTA 57.269 30.769 0.00 0.00 0.00 3.43


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

AutoCloner maintained by Alex Coulton.