Multiple sequence alignment - TraesCS7B01G239600

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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 TraesCS7B01G239600 chr7B 100.000 6198 0 0 1 6198 445667300 445661103 0.000000e+00 11446
1 TraesCS7B01G239600 chr7B 85.593 236 30 3 3940 4171 71072404 71072639 1.730000e-60 244
2 TraesCS7B01G239600 chr7D 92.701 5576 232 69 37 5525 428028726 428023239 0.000000e+00 7880
3 TraesCS7B01G239600 chr7D 91.793 792 59 6 3174 3964 431914101 431914887 0.000000e+00 1098
4 TraesCS7B01G239600 chr7D 85.502 269 23 12 5746 6012 428023058 428022804 3.680000e-67 267
5 TraesCS7B01G239600 chr7D 93.506 154 7 2 6048 6198 428022809 428022656 6.250000e-55 226
6 TraesCS7B01G239600 chr7D 92.800 125 8 1 5542 5666 428023189 428023066 4.940000e-41 180
7 TraesCS7B01G239600 chr7D 84.153 183 20 4 2981 3156 600897603 600897423 1.070000e-37 169
8 TraesCS7B01G239600 chr7D 82.632 190 26 4 2982 3164 497894383 497894572 1.790000e-35 161
9 TraesCS7B01G239600 chr7D 92.105 76 6 0 5659 5734 629185754 629185829 2.360000e-19 108
10 TraesCS7B01G239600 chr6B 87.718 1376 107 34 4183 5525 140846307 140847653 0.000000e+00 1548
11 TraesCS7B01G239600 chr6B 88.280 657 47 8 604 1245 140843674 140844315 0.000000e+00 760
12 TraesCS7B01G239600 chr6B 85.110 544 52 19 1415 1932 140844324 140844864 4.250000e-146 529
13 TraesCS7B01G239600 chr6B 86.214 486 47 15 1415 1884 219670428 219670909 5.540000e-140 508
14 TraesCS7B01G239600 chr6B 84.979 233 34 1 3940 4171 17007099 17007331 1.040000e-57 235
15 TraesCS7B01G239600 chr6B 88.136 118 13 1 2096 2212 140844963 140845080 8.380000e-29 139
16 TraesCS7B01G239600 chr6D 87.582 1377 105 35 4183 5525 65755584 65756928 0.000000e+00 1535
17 TraesCS7B01G239600 chr6D 91.923 780 61 2 3162 3940 160205166 160204388 0.000000e+00 1090
18 TraesCS7B01G239600 chr6D 88.696 575 35 12 610 1168 65753174 65753734 0.000000e+00 675
19 TraesCS7B01G239600 chr6D 85.575 513 64 8 1429 1932 65753799 65754310 4.250000e-146 529
20 TraesCS7B01G239600 chr6D 83.084 467 58 14 2360 2821 65754762 65755212 7.480000e-109 405
21 TraesCS7B01G239600 chr6D 93.056 72 5 0 5663 5734 273091448 273091519 8.500000e-19 106
22 TraesCS7B01G239600 chr6A 88.133 1264 90 31 4183 5415 82106744 82105510 0.000000e+00 1448
23 TraesCS7B01G239600 chr6A 87.386 658 46 17 614 1243 82109683 82109035 0.000000e+00 721
24 TraesCS7B01G239600 chr6A 80.261 613 86 19 2360 2960 82107353 82106764 4.440000e-116 429
25 TraesCS7B01G239600 chr7A 90.994 1077 64 19 4472 5525 504221545 504222611 0.000000e+00 1421
26 TraesCS7B01G239600 chr7A 82.275 1275 120 51 795 2038 504218770 504219969 0.000000e+00 1005
27 TraesCS7B01G239600 chr7A 89.319 543 49 4 2232 2773 504220675 504221209 0.000000e+00 673
28 TraesCS7B01G239600 chr7A 89.683 126 11 2 4335 4459 504221212 504221336 6.430000e-35 159
29 TraesCS7B01G239600 chr7A 85.593 118 13 4 2096 2211 504220220 504220335 3.030000e-23 121
30 TraesCS7B01G239600 chr5D 92.626 773 55 2 3163 3934 277251451 277252222 0.000000e+00 1110
31 TraesCS7B01G239600 chr5D 93.671 79 5 0 5659 5737 575039 575117 1.090000e-22 119
32 TraesCS7B01G239600 chr5D 89.024 82 9 0 5656 5737 461437305 461437224 1.100000e-17 102
33 TraesCS7B01G239600 chr3A 92.142 789 55 5 3156 3940 375017487 375018272 0.000000e+00 1107
34 TraesCS7B01G239600 chr3A 86.900 229 29 1 3942 4170 497657964 497657737 7.970000e-64 255
35 TraesCS7B01G239600 chr3A 92.105 76 6 0 5662 5737 714022261 714022186 2.360000e-19 108
36 TraesCS7B01G239600 chr2D 91.995 787 61 2 3156 3941 136426035 136426820 0.000000e+00 1103
37 TraesCS7B01G239600 chr2D 92.051 780 60 2 3162 3940 364092102 364091324 0.000000e+00 1096
38 TraesCS7B01G239600 chr2D 85.340 191 26 2 3983 4172 21657762 21657573 4.900000e-46 196
39 TraesCS7B01G239600 chr2D 92.208 77 6 0 5661 5737 650861483 650861407 6.570000e-20 110
40 TraesCS7B01G239600 chr1A 92.061 781 57 4 3156 3935 464808289 464809065 0.000000e+00 1094
41 TraesCS7B01G239600 chr1A 84.884 172 23 1 2996 3164 550956103 550956274 2.970000e-38 171
42 TraesCS7B01G239600 chr1A 92.105 76 5 1 5663 5737 313905941 313905866 8.500000e-19 106
43 TraesCS7B01G239600 chr1D 91.837 784 62 2 3156 3938 223523801 223524583 0.000000e+00 1092
44 TraesCS7B01G239600 chr4B 84.071 226 34 2 3945 4170 655123164 655122941 3.760000e-52 217
45 TraesCS7B01G239600 chrUn 87.634 186 22 1 3944 4128 61742529 61742344 1.350000e-51 215
46 TraesCS7B01G239600 chrUn 86.585 164 18 2 2996 3156 94876669 94876831 1.780000e-40 178
47 TraesCS7B01G239600 chr4D 87.634 186 22 1 3944 4128 499897986 499898171 1.350000e-51 215
48 TraesCS7B01G239600 chr1B 85.714 203 21 4 604 805 15712719 15712914 2.260000e-49 207
49 TraesCS7B01G239600 chr3D 83.256 215 30 5 3941 4152 2993806 2994017 6.340000e-45 193
50 TraesCS7B01G239600 chr3D 85.792 183 16 6 2980 3155 28377982 28378161 1.060000e-42 185
51 TraesCS7B01G239600 chr3D 93.056 72 5 0 5663 5734 465762250 465762321 8.500000e-19 106
52 TraesCS7B01G239600 chr4A 85.227 176 21 3 2996 3167 514415174 514415000 6.390000e-40 176
53 TraesCS7B01G239600 chr4A 84.615 182 19 5 2982 3156 43690483 43690304 8.260000e-39 172
54 TraesCS7B01G239600 chr2B 85.000 180 19 4 2982 3154 148039342 148039164 6.390000e-40 176
55 TraesCS7B01G239600 chr2B 92.105 76 6 0 5662 5737 779865598 779865673 2.360000e-19 108


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 TraesCS7B01G239600 chr7B 445661103 445667300 6197 True 11446.00 11446 100.00000 1 6198 1 chr7B.!!$R1 6197
1 TraesCS7B01G239600 chr7D 428022656 428028726 6070 True 2138.25 7880 91.12725 37 6198 4 chr7D.!!$R2 6161
2 TraesCS7B01G239600 chr7D 431914101 431914887 786 False 1098.00 1098 91.79300 3174 3964 1 chr7D.!!$F1 790
3 TraesCS7B01G239600 chr6B 140843674 140847653 3979 False 744.00 1548 87.31100 604 5525 4 chr6B.!!$F3 4921
4 TraesCS7B01G239600 chr6D 160204388 160205166 778 True 1090.00 1090 91.92300 3162 3940 1 chr6D.!!$R1 778
5 TraesCS7B01G239600 chr6D 65753174 65756928 3754 False 786.00 1535 86.23425 610 5525 4 chr6D.!!$F2 4915
6 TraesCS7B01G239600 chr6A 82105510 82109683 4173 True 866.00 1448 85.26000 614 5415 3 chr6A.!!$R1 4801
7 TraesCS7B01G239600 chr7A 504218770 504222611 3841 False 675.80 1421 87.57280 795 5525 5 chr7A.!!$F1 4730
8 TraesCS7B01G239600 chr5D 277251451 277252222 771 False 1110.00 1110 92.62600 3163 3934 1 chr5D.!!$F2 771
9 TraesCS7B01G239600 chr3A 375017487 375018272 785 False 1107.00 1107 92.14200 3156 3940 1 chr3A.!!$F1 784
10 TraesCS7B01G239600 chr2D 136426035 136426820 785 False 1103.00 1103 91.99500 3156 3941 1 chr2D.!!$F1 785
11 TraesCS7B01G239600 chr2D 364091324 364092102 778 True 1096.00 1096 92.05100 3162 3940 1 chr2D.!!$R2 778
12 TraesCS7B01G239600 chr1A 464808289 464809065 776 False 1094.00 1094 92.06100 3156 3935 1 chr1A.!!$F1 779
13 TraesCS7B01G239600 chr1D 223523801 223524583 782 False 1092.00 1092 91.83700 3156 3938 1 chr1D.!!$F1 782

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
375 412 0.031178 ACGACTAAAGTTCGGCGTGT 59.969 50.000 6.85 0.0 0.00 4.49 F
1280 1362 1.929836 GGCGACAAAGAGCTACAGATG 59.070 52.381 0.00 0.0 0.00 2.90 F
1570 1665 0.615331 GGAGGCTGGTTCACATCTCA 59.385 55.000 0.00 0.0 33.55 3.27 F
3292 4701 1.067060 GGCACCTTTCGATATTTGGGC 59.933 52.381 0.00 0.0 0.00 5.36 F
4047 5458 0.532417 GCCACCAAACATTGCAAGCA 60.532 50.000 4.94 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1504 0.666913 CAGGTGGATAGCAGCAATGC 59.333 55.000 0.0 0.0 0.00 3.56 R
3003 4385 0.179043 TTTCTTGCGTGGGTGTAGCA 60.179 50.000 0.0 0.0 39.33 3.49 R
3350 4759 0.392863 TGGCACCACTTCATCCATCG 60.393 55.000 0.0 0.0 0.00 3.84 R
4671 6283 1.133668 GGATAGCAATCCCAGCAAGGT 60.134 52.381 0.0 0.0 45.37 3.50 R
6028 7705 0.248289 CGGTGGTCCTACAATCCGTT 59.752 55.000 0.0 0.0 34.38 4.44 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
26 27 8.484214 ACAATCACATACAGATATAGGAGTGT 57.516 34.615 0.00 0.00 31.68 3.55
27 28 8.928448 ACAATCACATACAGATATAGGAGTGTT 58.072 33.333 0.00 0.00 32.15 3.32
28 29 9.416794 CAATCACATACAGATATAGGAGTGTTC 57.583 37.037 0.00 0.00 0.00 3.18
29 30 8.948401 ATCACATACAGATATAGGAGTGTTCT 57.052 34.615 0.00 0.00 0.00 3.01
30 31 8.171164 TCACATACAGATATAGGAGTGTTCTG 57.829 38.462 0.00 0.00 39.70 3.02
31 32 7.231519 TCACATACAGATATAGGAGTGTTCTGG 59.768 40.741 0.00 0.00 38.46 3.86
32 33 7.231519 CACATACAGATATAGGAGTGTTCTGGA 59.768 40.741 0.00 0.00 38.46 3.86
33 34 7.231722 ACATACAGATATAGGAGTGTTCTGGAC 59.768 40.741 0.00 0.00 38.46 4.02
34 35 4.896482 ACAGATATAGGAGTGTTCTGGACC 59.104 45.833 0.00 0.00 38.46 4.46
35 36 4.282195 CAGATATAGGAGTGTTCTGGACCC 59.718 50.000 0.00 0.00 32.14 4.46
55 56 1.384191 GGGTGCCATGAAACCTCCT 59.616 57.895 14.25 0.00 36.64 3.69
57 58 1.215423 GGGTGCCATGAAACCTCCTAT 59.785 52.381 14.25 0.00 36.64 2.57
62 63 5.420739 GGTGCCATGAAACCTCCTATAAAAA 59.579 40.000 8.97 0.00 33.40 1.94
105 106 5.989477 TGTACCTCAAATCCAACTATCCAG 58.011 41.667 0.00 0.00 0.00 3.86
108 109 3.629398 CCTCAAATCCAACTATCCAGTGC 59.371 47.826 0.00 0.00 34.36 4.40
178 184 8.402472 TGGTGTTGTCTTGTAAATTCTAAACAG 58.598 33.333 0.00 0.00 0.00 3.16
180 186 7.378728 GTGTTGTCTTGTAAATTCTAAACAGCC 59.621 37.037 0.00 0.00 0.00 4.85
188 195 8.958175 TGTAAATTCTAAACAGCCGTATTTTG 57.042 30.769 0.00 0.00 0.00 2.44
194 201 4.483476 AAACAGCCGTATTTTGTCAGAC 57.517 40.909 0.00 0.00 0.00 3.51
205 212 7.117812 CCGTATTTTGTCAGACTTAGACACATT 59.882 37.037 1.31 0.00 44.95 2.71
210 217 5.289595 TGTCAGACTTAGACACATTGACAC 58.710 41.667 1.31 0.00 40.80 3.67
213 220 2.058798 ACTTAGACACATTGACACGCG 58.941 47.619 3.53 3.53 0.00 6.01
223 230 3.041351 GACACGCGTGCCACATGA 61.041 61.111 37.35 0.00 0.00 3.07
224 231 3.295228 GACACGCGTGCCACATGAC 62.295 63.158 37.35 15.07 0.00 3.06
240 247 8.839343 TGCCACATGACTAAACAATCTATATTG 58.161 33.333 0.00 0.00 46.66 1.90
245 252 9.017509 CATGACTAAACAATCTATATTGGCCAT 57.982 33.333 6.09 0.00 45.72 4.40
249 256 7.998383 ACTAAACAATCTATATTGGCCATGTGA 59.002 33.333 6.09 1.20 45.72 3.58
255 262 6.558771 TCTATATTGGCCATGTGAAATTCG 57.441 37.500 6.09 0.00 0.00 3.34
358 395 1.845266 ACATATGCGCAGAGAAGACG 58.155 50.000 18.32 0.38 0.00 4.18
363 400 0.879090 TGCGCAGAGAAGACGACTAA 59.121 50.000 5.66 0.00 0.00 2.24
371 408 2.916089 GAGAAGACGACTAAAGTTCGGC 59.084 50.000 0.00 0.00 34.70 5.54
375 412 0.031178 ACGACTAAAGTTCGGCGTGT 59.969 50.000 6.85 0.00 0.00 4.49
535 574 6.684897 TTTTTGGATGGTTTGGATTGATCT 57.315 33.333 0.00 0.00 0.00 2.75
671 718 3.402681 CCGCACATCCTCCCAGGT 61.403 66.667 0.00 0.00 36.53 4.00
778 826 4.003788 CCCCGTTGTCTCTGGCGT 62.004 66.667 0.00 0.00 0.00 5.68
1030 1102 4.823732 CCTGCCTAGCCCCTCCCA 62.824 72.222 0.00 0.00 0.00 4.37
1151 1232 3.881019 AACGACCCCCTGCTCTCGA 62.881 63.158 0.00 0.00 0.00 4.04
1172 1253 4.340263 GAGTTCAACCGTTTGACTTTGTC 58.660 43.478 0.00 0.00 41.64 3.18
1225 1306 3.808728 CAACTATAGCAGGCAAGCCTTA 58.191 45.455 11.67 2.71 45.70 2.69
1280 1362 1.929836 GGCGACAAAGAGCTACAGATG 59.070 52.381 0.00 0.00 0.00 2.90
1348 1430 4.690184 TCTGTAGACGAAAGCAACGATA 57.310 40.909 0.00 0.00 34.70 2.92
1392 1475 5.177327 GTGTGGTTTATTTGCCAGTTTGATG 59.823 40.000 0.00 0.00 35.14 3.07
1393 1476 5.163364 TGTGGTTTATTTGCCAGTTTGATGT 60.163 36.000 0.00 0.00 35.14 3.06
1394 1477 6.040955 TGTGGTTTATTTGCCAGTTTGATGTA 59.959 34.615 0.00 0.00 35.14 2.29
1421 1504 4.525912 AAATTAGGTTTCCAAGCTGCAG 57.474 40.909 10.11 10.11 39.97 4.41
1510 1593 2.543641 GCATGCTGCTTGGGTTAATTC 58.456 47.619 11.37 0.00 40.96 2.17
1570 1665 0.615331 GGAGGCTGGTTCACATCTCA 59.385 55.000 0.00 0.00 33.55 3.27
1747 1842 4.060205 GGTTTGTTAGAACGCAGAAGGTA 58.940 43.478 0.00 0.00 0.00 3.08
1813 1909 8.738645 ACCAATAGGAATTTCAGATGTAGAAC 57.261 34.615 0.00 0.00 38.69 3.01
1936 2051 7.877003 TGAGAGCTTAAGAGATAAGATAACCG 58.123 38.462 6.67 0.00 40.24 4.44
1954 2080 2.092429 ACCGGCAGTCATGTATGGAATT 60.092 45.455 0.00 0.00 0.00 2.17
1965 2091 6.919662 GTCATGTATGGAATTGTGGCATAAAG 59.080 38.462 0.00 0.00 0.00 1.85
1988 2117 7.129457 AGCATTATACACAGATGAAGGAGAA 57.871 36.000 0.00 0.00 0.00 2.87
2044 2176 9.308000 TCATAACTTGATTGTTAAATCTTGGGT 57.692 29.630 0.63 0.00 42.40 4.51
2110 2440 7.201785 CCAGTATTAATCGGCCTGTTAACAAAT 60.202 37.037 10.03 6.46 0.00 2.32
2163 2494 9.674068 TTACCAATATGTACATGTGCTTTTCTA 57.326 29.630 18.81 0.00 0.00 2.10
2258 3233 8.860088 GGGATTTGCAGTTATTTGGTAGAATAT 58.140 33.333 0.00 0.00 0.00 1.28
2327 3303 7.919690 TCTCATTTGATATTTGATCGGTTCAC 58.080 34.615 0.00 0.00 32.84 3.18
2438 3583 8.863086 TCAATGAAAATTCTGAATTTGTCTCCT 58.137 29.630 24.51 11.11 40.05 3.69
2676 3836 8.330466 TCTCGTATTGTAATTTGTCCATGTTT 57.670 30.769 0.00 0.00 0.00 2.83
2683 3843 6.904498 TGTAATTTGTCCATGTTTCGTTAGG 58.096 36.000 0.00 0.00 0.00 2.69
2727 3887 7.041167 CGGGCAAATCAATAGTAAATCTGATCA 60.041 37.037 0.00 0.00 0.00 2.92
2807 3971 7.010830 CAGATATTAATATGCCCTCATGTGTCG 59.989 40.741 12.74 0.00 34.22 4.35
2825 3989 6.267817 TGTGTCGACCTAGGATTTTTATACG 58.732 40.000 17.98 6.74 0.00 3.06
2828 3992 5.628606 GTCGACCTAGGATTTTTATACGCTC 59.371 44.000 17.98 0.00 0.00 5.03
2915 4285 2.338785 GCTCAAAGCTCAGCACCCC 61.339 63.158 0.00 0.00 38.45 4.95
2949 4331 1.917872 TGCACCCGCCTAGAATTTTT 58.082 45.000 0.00 0.00 37.32 1.94
2957 4339 1.745653 GCCTAGAATTTTTCTGCCGCT 59.254 47.619 0.00 0.00 40.94 5.52
2965 4347 6.963796 AGAATTTTTCTGCCGCTTCATATAG 58.036 36.000 0.00 0.00 38.91 1.31
2967 4349 6.942532 ATTTTTCTGCCGCTTCATATAGAA 57.057 33.333 0.00 0.00 34.41 2.10
2988 4370 3.034635 AGGTCTTGACTCTTGAGTGTGT 58.965 45.455 8.11 0.00 0.00 3.72
3084 4484 7.121168 GTGGGAATGATCAACAAATGTTAGAGA 59.879 37.037 0.00 0.00 36.32 3.10
3213 4613 2.147958 GTACATGAGGTGCGGTTTCAA 58.852 47.619 0.00 0.00 0.00 2.69
3242 4651 1.545706 GCACGAGGAGGAGGAGGTTT 61.546 60.000 0.00 0.00 0.00 3.27
3273 4682 2.352805 GGTGGTGCCTGAGAAGGG 59.647 66.667 0.00 0.00 0.00 3.95
3292 4701 1.067060 GGCACCTTTCGATATTTGGGC 59.933 52.381 0.00 0.00 0.00 5.36
3320 4729 2.641321 CTGCAGAAGGATGGGGATATCA 59.359 50.000 8.42 0.00 0.00 2.15
3350 4759 2.091541 TGAACCATCGAATCAAAGCCC 58.908 47.619 0.00 0.00 0.00 5.19
3396 4805 3.262660 TCTGGCATTCTCTGTGACAAGAT 59.737 43.478 0.00 0.00 33.42 2.40
3398 4807 2.681848 GGCATTCTCTGTGACAAGATGG 59.318 50.000 0.00 0.00 0.00 3.51
3435 4845 8.714906 AGCTAAAAGGCAAGTTCTATAGGATAA 58.285 33.333 0.00 0.00 34.17 1.75
3560 4970 1.450211 CCACACAAGGAAGGACCGT 59.550 57.895 0.00 0.00 44.74 4.83
3767 5178 7.164803 GGAGGAGTCCATAAAGAAAGATATGG 58.835 42.308 12.86 5.63 46.56 2.74
4022 5433 5.854010 TTGTATAGAGCTTCTCGGATGTT 57.146 39.130 0.00 0.00 35.36 2.71
4028 5439 4.446371 AGAGCTTCTCGGATGTTATTTGG 58.554 43.478 0.00 0.00 35.36 3.28
4047 5458 0.532417 GCCACCAAACATTGCAAGCA 60.532 50.000 4.94 0.00 0.00 3.91
4048 5459 1.878948 GCCACCAAACATTGCAAGCAT 60.879 47.619 4.94 0.00 0.00 3.79
4049 5460 2.070783 CCACCAAACATTGCAAGCATC 58.929 47.619 4.94 0.00 0.00 3.91
4050 5461 2.289195 CCACCAAACATTGCAAGCATCT 60.289 45.455 4.94 0.00 0.00 2.90
4051 5462 2.991190 CACCAAACATTGCAAGCATCTC 59.009 45.455 4.94 0.00 0.00 2.75
4052 5463 2.895404 ACCAAACATTGCAAGCATCTCT 59.105 40.909 4.94 0.00 0.00 3.10
4053 5464 4.081406 ACCAAACATTGCAAGCATCTCTA 58.919 39.130 4.94 0.00 0.00 2.43
4054 5465 4.523943 ACCAAACATTGCAAGCATCTCTAA 59.476 37.500 4.94 0.00 0.00 2.10
4055 5466 4.860907 CCAAACATTGCAAGCATCTCTAAC 59.139 41.667 4.94 0.00 0.00 2.34
4056 5467 5.463286 CAAACATTGCAAGCATCTCTAACA 58.537 37.500 4.94 0.00 0.00 2.41
4081 5492 6.416631 TTGTTGATGATCATTCCCACAAAA 57.583 33.333 10.14 1.33 0.00 2.44
4180 5591 4.278419 CCACTACTTTCCCAAAAGGTCTTG 59.722 45.833 3.24 0.00 45.15 3.02
4247 5658 8.008513 TGTCACTCACTTTAGACTTCTAACTT 57.991 34.615 0.00 0.00 38.09 2.66
4443 5858 8.685838 TGTCTTGCTAAAGTTACCAGTTAAAT 57.314 30.769 0.00 0.00 34.78 1.40
4460 5876 5.784906 AGTTAAATGGGGAATGTTGATTGGT 59.215 36.000 0.00 0.00 0.00 3.67
4461 5877 4.556592 AAATGGGGAATGTTGATTGGTG 57.443 40.909 0.00 0.00 0.00 4.17
4466 5883 5.832221 TGGGGAATGTTGATTGGTGTAATA 58.168 37.500 0.00 0.00 0.00 0.98
4624 6236 4.261994 GGCTTTAGCAAGGAAACATTGACA 60.262 41.667 3.88 0.00 44.36 3.58
4671 6283 2.815503 TCGTGACGGACATAACTGAAGA 59.184 45.455 4.70 0.00 0.00 2.87
5035 6647 0.461961 GGTCGATCCTGCTAAGTGCT 59.538 55.000 0.00 0.00 43.37 4.40
5143 6755 1.093972 CACGCAACCTATTGGCATCA 58.906 50.000 0.00 0.00 36.23 3.07
5238 6852 5.118990 GTGCAGCTTTTGATATCTCCTGTA 58.881 41.667 3.98 0.86 0.00 2.74
5239 6853 5.236047 GTGCAGCTTTTGATATCTCCTGTAG 59.764 44.000 3.98 0.00 0.00 2.74
5240 6854 4.754114 GCAGCTTTTGATATCTCCTGTAGG 59.246 45.833 3.98 0.00 0.00 3.18
5241 6855 4.754114 CAGCTTTTGATATCTCCTGTAGGC 59.246 45.833 3.98 0.00 34.44 3.93
5242 6856 4.657969 AGCTTTTGATATCTCCTGTAGGCT 59.342 41.667 3.98 0.00 34.44 4.58
5243 6857 4.754114 GCTTTTGATATCTCCTGTAGGCTG 59.246 45.833 3.98 0.00 34.44 4.85
5244 6858 5.686124 GCTTTTGATATCTCCTGTAGGCTGT 60.686 44.000 3.98 0.00 34.44 4.40
5245 6859 6.463049 GCTTTTGATATCTCCTGTAGGCTGTA 60.463 42.308 3.98 0.00 34.44 2.74
5287 6901 3.192001 TGTTCTCATTTTGCATGGAGAGC 59.808 43.478 11.59 11.59 37.66 4.09
5334 6970 5.775195 TCAGTGGAGATTAGACAAAGACAGA 59.225 40.000 0.00 0.00 0.00 3.41
5403 7044 2.164422 GCCCAGAAGCATGTTTCTTACC 59.836 50.000 20.80 9.03 35.28 2.85
5416 7057 9.248291 GCATGTTTCTTACCCATGTAAATTATG 57.752 33.333 0.00 0.00 38.53 1.90
5427 7068 5.333035 CCATGTAAATTATGTACGCGTGAGG 60.333 44.000 24.59 0.00 0.00 3.86
5434 7075 8.821147 AAATTATGTACGCGTGAGGATAATTA 57.179 30.769 24.59 0.00 0.00 1.40
5458 7099 4.524714 CCTCATCGTGTATAGAATCACCCT 59.475 45.833 0.00 0.00 0.00 4.34
5532 7174 8.747538 AATTCCTTGGTATATCTTTGTGTACC 57.252 34.615 0.00 0.00 37.65 3.34
5533 7175 6.877668 TCCTTGGTATATCTTTGTGTACCA 57.122 37.500 0.00 0.00 43.45 3.25
5537 7179 9.219603 CCTTGGTATATCTTTGTGTACCATATG 57.780 37.037 4.16 0.00 44.25 1.78
5539 7181 9.554395 TTGGTATATCTTTGTGTACCATATGTG 57.446 33.333 1.24 0.00 44.25 3.21
5540 7182 7.659799 TGGTATATCTTTGTGTACCATATGTGC 59.340 37.037 1.24 0.00 41.08 4.57
5554 7229 0.179084 ATGTGCACGGACCTATTCGG 60.179 55.000 13.13 0.00 39.35 4.30
5576 7251 4.637977 GGTTCAAGGGAATCTGATGAGTTC 59.362 45.833 0.00 0.00 35.05 3.01
5577 7252 5.495640 GTTCAAGGGAATCTGATGAGTTCT 58.504 41.667 0.00 0.00 35.05 3.01
5579 7254 4.080695 TCAAGGGAATCTGATGAGTTCTGG 60.081 45.833 0.00 0.00 0.00 3.86
5581 7256 3.710677 AGGGAATCTGATGAGTTCTGGAG 59.289 47.826 0.00 0.00 0.00 3.86
5582 7257 3.454082 GGGAATCTGATGAGTTCTGGAGT 59.546 47.826 0.00 0.00 0.00 3.85
5583 7258 4.080638 GGGAATCTGATGAGTTCTGGAGTT 60.081 45.833 0.00 0.00 0.00 3.01
5592 7267 5.060662 TGAGTTCTGGAGTTATTGTCTCG 57.939 43.478 0.00 0.00 33.26 4.04
5628 7303 2.616842 GGAGTTTGTTTCGCTTTCAGGA 59.383 45.455 0.00 0.00 0.00 3.86
5666 7341 3.278574 TGTTGCTGTGAGCTAGTTTGTT 58.721 40.909 0.00 0.00 42.97 2.83
5668 7343 3.475566 TGCTGTGAGCTAGTTTGTTCT 57.524 42.857 0.00 0.00 42.97 3.01
5669 7344 3.393800 TGCTGTGAGCTAGTTTGTTCTC 58.606 45.455 0.00 0.00 42.97 2.87
5670 7345 3.070159 TGCTGTGAGCTAGTTTGTTCTCT 59.930 43.478 0.00 0.00 42.97 3.10
5671 7346 3.431572 GCTGTGAGCTAGTTTGTTCTCTG 59.568 47.826 0.00 0.00 38.45 3.35
5672 7347 4.626042 CTGTGAGCTAGTTTGTTCTCTGT 58.374 43.478 0.00 0.00 0.00 3.41
5673 7348 5.023533 TGTGAGCTAGTTTGTTCTCTGTT 57.976 39.130 0.00 0.00 0.00 3.16
5674 7349 5.428253 TGTGAGCTAGTTTGTTCTCTGTTT 58.572 37.500 0.00 0.00 0.00 2.83
5675 7350 5.294306 TGTGAGCTAGTTTGTTCTCTGTTTG 59.706 40.000 0.00 0.00 0.00 2.93
5676 7351 5.294552 GTGAGCTAGTTTGTTCTCTGTTTGT 59.705 40.000 0.00 0.00 0.00 2.83
5677 7352 6.479001 GTGAGCTAGTTTGTTCTCTGTTTGTA 59.521 38.462 0.00 0.00 0.00 2.41
5678 7353 7.011109 GTGAGCTAGTTTGTTCTCTGTTTGTAA 59.989 37.037 0.00 0.00 0.00 2.41
5679 7354 7.551262 TGAGCTAGTTTGTTCTCTGTTTGTAAA 59.449 33.333 0.00 0.00 0.00 2.01
5680 7355 7.694886 AGCTAGTTTGTTCTCTGTTTGTAAAC 58.305 34.615 0.65 0.65 39.33 2.01
5681 7356 7.553044 AGCTAGTTTGTTCTCTGTTTGTAAACT 59.447 33.333 8.74 0.00 39.59 2.66
5682 7357 8.823818 GCTAGTTTGTTCTCTGTTTGTAAACTA 58.176 33.333 8.74 0.00 39.59 2.24
5783 7458 3.070018 CCGATTTATAGAGCTGGGCAAG 58.930 50.000 0.00 0.00 0.00 4.01
5796 7471 3.344515 CTGGGCAAGGTCTTTAACTACC 58.655 50.000 0.00 0.00 35.91 3.18
5852 7527 8.296713 TCAGCTAGCTAAACAATAAACCAAAAG 58.703 33.333 18.86 0.00 0.00 2.27
5854 7529 9.025041 AGCTAGCTAAACAATAAACCAAAAGAT 57.975 29.630 17.69 0.00 0.00 2.40
5890 7567 7.121382 TGAGCCTGATCTTCTGGAATTATTTT 58.879 34.615 4.78 0.00 37.65 1.82
5892 7569 7.352738 AGCCTGATCTTCTGGAATTATTTTCT 58.647 34.615 4.78 0.00 37.65 2.52
5928 7605 1.816074 GATGGCAAACAACCGGTCTA 58.184 50.000 8.04 0.00 0.00 2.59
5931 7608 2.376109 TGGCAAACAACCGGTCTAAAA 58.624 42.857 8.04 0.00 0.00 1.52
5955 7632 5.934402 AAATGATGAGTCCCTAGTACGTT 57.066 39.130 0.00 0.00 0.00 3.99
5956 7633 5.934402 AATGATGAGTCCCTAGTACGTTT 57.066 39.130 0.00 0.00 0.00 3.60
5957 7634 7.414222 AAATGATGAGTCCCTAGTACGTTTA 57.586 36.000 0.00 0.00 0.00 2.01
5958 7635 7.598759 AATGATGAGTCCCTAGTACGTTTAT 57.401 36.000 0.00 0.00 0.00 1.40
5959 7636 6.387041 TGATGAGTCCCTAGTACGTTTATG 57.613 41.667 0.00 0.00 0.00 1.90
5960 7637 5.889853 TGATGAGTCCCTAGTACGTTTATGT 59.110 40.000 0.00 0.00 0.00 2.29
5961 7638 7.056006 TGATGAGTCCCTAGTACGTTTATGTA 58.944 38.462 0.00 0.00 0.00 2.29
5962 7639 6.932356 TGAGTCCCTAGTACGTTTATGTAG 57.068 41.667 0.00 0.00 0.00 2.74
5963 7640 6.418101 TGAGTCCCTAGTACGTTTATGTAGT 58.582 40.000 0.00 0.00 32.84 2.73
5964 7641 6.886459 TGAGTCCCTAGTACGTTTATGTAGTT 59.114 38.462 0.00 0.00 30.80 2.24
5965 7642 7.394359 TGAGTCCCTAGTACGTTTATGTAGTTT 59.606 37.037 0.00 0.00 30.80 2.66
5966 7643 7.766283 AGTCCCTAGTACGTTTATGTAGTTTC 58.234 38.462 0.00 0.00 30.80 2.78
5967 7644 7.394359 AGTCCCTAGTACGTTTATGTAGTTTCA 59.606 37.037 0.00 0.00 30.80 2.69
5968 7645 7.699812 GTCCCTAGTACGTTTATGTAGTTTCAG 59.300 40.741 0.00 0.00 30.80 3.02
5992 7669 2.800544 CGTGTTGACAACCAGTTCCTAG 59.199 50.000 15.59 0.00 0.00 3.02
5993 7670 3.740141 CGTGTTGACAACCAGTTCCTAGT 60.740 47.826 15.59 0.00 0.00 2.57
5994 7671 4.500205 CGTGTTGACAACCAGTTCCTAGTA 60.500 45.833 15.59 0.00 0.00 1.82
5995 7672 4.748600 GTGTTGACAACCAGTTCCTAGTAC 59.251 45.833 15.59 0.00 0.00 2.73
5996 7673 3.928727 TGACAACCAGTTCCTAGTACG 57.071 47.619 0.00 0.00 0.00 3.67
6000 7677 5.027293 ACAACCAGTTCCTAGTACGTTTT 57.973 39.130 0.00 0.00 0.00 2.43
6021 7698 4.876701 TGCGTTGCAGAAGGAGTT 57.123 50.000 0.00 0.00 33.32 3.01
6022 7699 2.320215 TGCGTTGCAGAAGGAGTTG 58.680 52.632 0.00 0.00 33.32 3.16
6023 7700 0.463654 TGCGTTGCAGAAGGAGTTGT 60.464 50.000 0.00 0.00 33.32 3.32
6024 7701 1.202592 TGCGTTGCAGAAGGAGTTGTA 60.203 47.619 0.00 0.00 33.32 2.41
6025 7702 1.871039 GCGTTGCAGAAGGAGTTGTAA 59.129 47.619 0.00 0.00 0.00 2.41
6026 7703 2.289547 GCGTTGCAGAAGGAGTTGTAAA 59.710 45.455 0.00 0.00 0.00 2.01
6027 7704 6.262433 TGCGTTGCAGAAGGAGTTGTAAAC 62.262 45.833 0.00 0.00 39.79 2.01
6046 7723 1.734163 CAACGGATTGTAGGACCACC 58.266 55.000 0.00 0.00 0.00 4.61
6072 7749 2.233305 TCCGTTAGGAAAGAGAGCCT 57.767 50.000 0.00 0.00 45.12 4.58
6074 7751 1.137282 CCGTTAGGAAAGAGAGCCTCC 59.863 57.143 0.00 0.00 41.02 4.30
6075 7752 1.202313 CGTTAGGAAAGAGAGCCTCCG 60.202 57.143 0.00 0.00 35.73 4.63
6076 7753 1.826096 GTTAGGAAAGAGAGCCTCCGT 59.174 52.381 0.00 0.00 35.73 4.69
6077 7754 2.233305 TAGGAAAGAGAGCCTCCGTT 57.767 50.000 0.00 0.00 35.73 4.44
6119 7799 4.431809 AGCTGATCGTTTGAATCTCTCTG 58.568 43.478 0.00 0.00 0.00 3.35
6132 7812 2.603021 TCTCTCTGAGAACTGGTTGCT 58.397 47.619 8.95 0.00 35.59 3.91
6137 7817 0.469494 TGAGAACTGGTTGCTCTGCA 59.531 50.000 0.00 0.00 36.47 4.41
6155 7835 6.147492 GCTCTGCACTAAAGGAGATATGAATG 59.853 42.308 2.78 0.00 35.36 2.67
6187 7867 1.799916 GCATAACGCGGGTGCAAAC 60.800 57.895 22.05 0.00 42.97 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.928448 ACACTCCTATATCTGTATGTGATTGTT 58.072 33.333 0.00 0.00 0.00 2.83
1 2 8.484214 ACACTCCTATATCTGTATGTGATTGT 57.516 34.615 0.00 0.00 0.00 2.71
2 3 9.416794 GAACACTCCTATATCTGTATGTGATTG 57.583 37.037 0.00 0.00 0.00 2.67
3 4 9.373450 AGAACACTCCTATATCTGTATGTGATT 57.627 33.333 0.00 0.00 0.00 2.57
4 5 8.801299 CAGAACACTCCTATATCTGTATGTGAT 58.199 37.037 0.00 0.00 34.29 3.06
5 6 7.231519 CCAGAACACTCCTATATCTGTATGTGA 59.768 40.741 0.00 0.00 36.61 3.58
6 7 7.231519 TCCAGAACACTCCTATATCTGTATGTG 59.768 40.741 0.00 0.00 36.61 3.21
7 8 7.231722 GTCCAGAACACTCCTATATCTGTATGT 59.768 40.741 0.00 0.00 36.61 2.29
8 9 7.309499 GGTCCAGAACACTCCTATATCTGTATG 60.309 44.444 0.00 0.00 36.61 2.39
9 10 6.722129 GGTCCAGAACACTCCTATATCTGTAT 59.278 42.308 0.00 0.00 36.61 2.29
10 11 6.069331 GGTCCAGAACACTCCTATATCTGTA 58.931 44.000 0.00 0.00 36.61 2.74
11 12 4.896482 GGTCCAGAACACTCCTATATCTGT 59.104 45.833 0.00 0.00 36.61 3.41
12 13 4.282195 GGGTCCAGAACACTCCTATATCTG 59.718 50.000 0.00 0.00 37.77 2.90
13 14 4.171044 AGGGTCCAGAACACTCCTATATCT 59.829 45.833 0.00 0.00 36.74 1.98
14 15 4.282195 CAGGGTCCAGAACACTCCTATATC 59.718 50.000 0.00 0.00 40.69 1.63
15 16 4.227197 CAGGGTCCAGAACACTCCTATAT 58.773 47.826 0.00 0.00 40.69 0.86
16 17 3.630054 CCAGGGTCCAGAACACTCCTATA 60.630 52.174 0.00 0.00 40.69 1.31
17 18 2.472029 CAGGGTCCAGAACACTCCTAT 58.528 52.381 0.00 0.00 40.69 2.57
18 19 1.552486 CCAGGGTCCAGAACACTCCTA 60.552 57.143 0.00 0.00 40.69 2.94
19 20 0.838122 CCAGGGTCCAGAACACTCCT 60.838 60.000 0.00 0.00 40.69 3.69
20 21 1.679898 CCAGGGTCCAGAACACTCC 59.320 63.158 0.00 0.00 40.69 3.85
21 22 1.128188 ACCCAGGGTCCAGAACACTC 61.128 60.000 4.76 0.00 40.69 3.51
22 23 1.073706 ACCCAGGGTCCAGAACACT 60.074 57.895 4.76 0.00 44.77 3.55
23 24 1.073199 CACCCAGGGTCCAGAACAC 59.927 63.158 8.79 0.00 31.02 3.32
24 25 2.829384 GCACCCAGGGTCCAGAACA 61.829 63.158 8.79 0.00 31.02 3.18
25 26 2.034221 GCACCCAGGGTCCAGAAC 59.966 66.667 8.79 0.00 31.02 3.01
26 27 3.256960 GGCACCCAGGGTCCAGAA 61.257 66.667 8.79 0.00 31.02 3.02
27 28 3.889525 ATGGCACCCAGGGTCCAGA 62.890 63.158 25.52 10.98 36.73 3.86
28 29 3.341629 ATGGCACCCAGGGTCCAG 61.342 66.667 25.52 11.81 36.73 3.86
29 30 3.660571 CATGGCACCCAGGGTCCA 61.661 66.667 24.41 24.41 36.75 4.02
30 31 2.439553 TTTCATGGCACCCAGGGTCC 62.440 60.000 8.79 13.92 36.75 4.46
31 32 1.076549 TTTCATGGCACCCAGGGTC 59.923 57.895 8.79 3.65 36.75 4.46
32 33 1.228862 GTTTCATGGCACCCAGGGT 60.229 57.895 4.76 4.76 36.75 4.34
33 34 1.984026 GGTTTCATGGCACCCAGGG 60.984 63.158 2.85 2.85 36.75 4.45
34 35 0.967380 GAGGTTTCATGGCACCCAGG 60.967 60.000 9.86 0.00 36.75 4.45
35 36 0.967380 GGAGGTTTCATGGCACCCAG 60.967 60.000 9.86 0.00 36.75 4.45
62 63 6.708502 GGTACAAATGCCCAACTTATTTTTGT 59.291 34.615 0.00 0.00 38.77 2.83
69 70 4.374689 TGAGGTACAAATGCCCAACTTA 57.625 40.909 0.00 0.00 0.00 2.24
156 157 6.577427 CGGCTGTTTAGAATTTACAAGACAAC 59.423 38.462 0.00 0.00 0.00 3.32
158 159 5.761234 ACGGCTGTTTAGAATTTACAAGACA 59.239 36.000 0.00 0.00 0.00 3.41
159 160 6.237313 ACGGCTGTTTAGAATTTACAAGAC 57.763 37.500 0.00 0.00 0.00 3.01
160 161 8.556213 AATACGGCTGTTTAGAATTTACAAGA 57.444 30.769 1.99 0.00 0.00 3.02
161 162 9.620660 AAAATACGGCTGTTTAGAATTTACAAG 57.379 29.630 1.99 0.00 0.00 3.16
163 164 8.569641 ACAAAATACGGCTGTTTAGAATTTACA 58.430 29.630 1.99 0.00 0.00 2.41
178 184 4.927425 TGTCTAAGTCTGACAAAATACGGC 59.073 41.667 10.88 0.00 40.89 5.68
180 186 7.582435 ATGTGTCTAAGTCTGACAAAATACG 57.418 36.000 10.88 0.00 44.63 3.06
188 195 4.383052 CGTGTCAATGTGTCTAAGTCTGAC 59.617 45.833 0.00 0.00 33.85 3.51
194 201 2.058798 ACGCGTGTCAATGTGTCTAAG 58.941 47.619 12.93 0.00 29.94 2.18
210 217 0.179225 GTTTAGTCATGTGGCACGCG 60.179 55.000 13.77 3.53 45.01 6.01
213 220 6.683974 ATAGATTGTTTAGTCATGTGGCAC 57.316 37.500 11.55 11.55 0.00 5.01
223 230 7.998383 TCACATGGCCAATATAGATTGTTTAGT 59.002 33.333 10.96 0.00 40.87 2.24
224 231 8.394971 TCACATGGCCAATATAGATTGTTTAG 57.605 34.615 10.96 0.00 40.87 1.85
240 247 6.420604 CCATTAATTACGAATTTCACATGGCC 59.579 38.462 0.00 0.00 32.38 5.36
245 252 7.430793 CGATTGCCATTAATTACGAATTTCACA 59.569 33.333 0.00 0.00 32.38 3.58
346 383 3.204597 ACTTTAGTCGTCTTCTCTGCG 57.795 47.619 0.00 0.00 0.00 5.18
358 395 2.913590 GTCTACACGCCGAACTTTAGTC 59.086 50.000 0.00 0.00 0.00 2.59
363 400 2.066262 CATTGTCTACACGCCGAACTT 58.934 47.619 0.00 0.00 0.00 2.66
371 408 2.143122 ACACCTTGCATTGTCTACACG 58.857 47.619 0.00 0.00 0.00 4.49
574 613 7.181569 TGATATCGATGCATGTATCCCTAAA 57.818 36.000 16.92 0.80 0.00 1.85
586 625 2.867975 CTGTGCAGTTGATATCGATGCA 59.132 45.455 19.51 19.51 44.10 3.96
588 627 3.246936 CACCTGTGCAGTTGATATCGATG 59.753 47.826 8.54 0.00 0.00 3.84
591 630 2.892374 TCACCTGTGCAGTTGATATCG 58.108 47.619 0.00 0.00 0.00 2.92
778 826 2.667418 GAGGCAAGAGAGGCTGCA 59.333 61.111 0.50 0.00 45.32 4.41
934 991 1.599606 GAAGGCACGAGAGCTCAGGA 61.600 60.000 17.77 0.00 34.17 3.86
1039 1120 1.683418 GGTGGGAGCCTAACCCTACG 61.683 65.000 0.00 0.00 46.82 3.51
1151 1232 4.007659 AGACAAAGTCAAACGGTTGAACT 58.992 39.130 19.26 14.33 45.29 3.01
1172 1253 1.154016 CACGACCGGCTACACAGAG 60.154 63.158 0.00 0.00 0.00 3.35
1245 1326 1.370414 CGCCAAACTCCACAAAGCG 60.370 57.895 0.00 0.00 35.82 4.68
1270 1352 1.468224 CGACTCGCAACATCTGTAGCT 60.468 52.381 0.00 0.00 0.00 3.32
1280 1362 2.279918 ACCCACACGACTCGCAAC 60.280 61.111 0.00 0.00 0.00 4.17
1348 1430 6.544931 CCACACATATCCAAGTGAATGAATCT 59.455 38.462 0.00 0.00 39.03 2.40
1393 1476 8.899771 GCAGCTTGGAAACCTAATTTAATACTA 58.100 33.333 0.00 0.00 0.00 1.82
1394 1477 7.396055 TGCAGCTTGGAAACCTAATTTAATACT 59.604 33.333 0.00 0.00 0.00 2.12
1402 1485 1.821136 GCTGCAGCTTGGAAACCTAAT 59.179 47.619 31.33 0.00 38.21 1.73
1421 1504 0.666913 CAGGTGGATAGCAGCAATGC 59.333 55.000 0.00 0.00 0.00 3.56
1510 1593 2.393764 AGCACGCGAAAAAGAAAATGG 58.606 42.857 15.93 0.00 0.00 3.16
1618 1713 3.444742 CCTGCTCATTGTATTTGAAGCCA 59.555 43.478 0.00 0.00 0.00 4.75
1705 1800 7.728532 ACAAACCAGTCTCCCTTTACATAATTT 59.271 33.333 0.00 0.00 0.00 1.82
1747 1842 6.211184 TGGAATGCAGAAAATAAACCAGACAT 59.789 34.615 0.00 0.00 0.00 3.06
1834 1939 9.830975 ATTGTATTACACACACTATGCTTCATA 57.169 29.630 0.00 0.00 36.69 2.15
1878 1984 6.291377 TGAAGTGAGCAACTGAACTTAGAAT 58.709 36.000 0.00 0.00 39.81 2.40
1936 2051 3.067180 CCACAATTCCATACATGACTGCC 59.933 47.826 0.00 0.00 0.00 4.85
1954 2080 6.118852 TCTGTGTATAATGCTTTATGCCACA 58.881 36.000 23.28 23.28 42.00 4.17
1965 2091 7.976135 ATTCTCCTTCATCTGTGTATAATGC 57.024 36.000 0.00 0.00 0.00 3.56
1988 2117 8.405531 CAAATTGGATAACGGAGTATCACAAAT 58.594 33.333 5.68 0.00 45.00 2.32
2039 2171 3.762823 ACAAACTTGAAAACCGTACCCAA 59.237 39.130 0.00 0.00 0.00 4.12
2044 2176 8.550376 GTTCAGTATACAAACTTGAAAACCGTA 58.450 33.333 5.50 0.00 0.00 4.02
2148 2479 6.230472 ACACAGACATAGAAAAGCACATGTA 58.770 36.000 0.00 0.00 31.94 2.29
2163 2494 2.653726 TGACTGGCAAAACACAGACAT 58.346 42.857 0.00 0.00 35.20 3.06
2224 2576 7.068103 CCAAATAACTGCAAATCCCATAGTACA 59.932 37.037 0.00 0.00 0.00 2.90
2225 2577 7.068226 ACCAAATAACTGCAAATCCCATAGTAC 59.932 37.037 0.00 0.00 0.00 2.73
2228 2580 6.469782 ACCAAATAACTGCAAATCCCATAG 57.530 37.500 0.00 0.00 0.00 2.23
2229 2581 7.350382 TCTACCAAATAACTGCAAATCCCATA 58.650 34.615 0.00 0.00 0.00 2.74
2230 2582 6.194235 TCTACCAAATAACTGCAAATCCCAT 58.806 36.000 0.00 0.00 0.00 4.00
2309 3285 2.538037 CGCGTGAACCGATCAAATATCA 59.462 45.455 0.00 0.00 40.50 2.15
2327 3303 4.262045 GGCACTAAACAAAATATGAACGCG 59.738 41.667 3.53 3.53 0.00 6.01
2458 3603 8.374743 TCATTCCGAAATCTGGATATTGTATCA 58.625 33.333 0.03 0.00 34.91 2.15
2461 3606 6.650807 GCTCATTCCGAAATCTGGATATTGTA 59.349 38.462 0.00 0.00 34.91 2.41
2499 3644 4.526650 GGGTAATTGTTTGTCCAGTCCAAT 59.473 41.667 0.00 0.00 0.00 3.16
2676 3836 5.182950 TGTCCGTATACAGAAAACCTAACGA 59.817 40.000 3.32 0.00 0.00 3.85
2683 3843 2.925563 CCCGTGTCCGTATACAGAAAAC 59.074 50.000 3.32 0.00 0.00 2.43
2727 3887 7.797121 AATCACATGGGTTAGGAATCTTTTT 57.203 32.000 0.00 0.00 0.00 1.94
2735 3895 6.636454 AAGAAGTAATCACATGGGTTAGGA 57.364 37.500 0.00 0.00 0.00 2.94
2738 3898 7.235079 TCCAAAAGAAGTAATCACATGGGTTA 58.765 34.615 0.00 0.00 30.98 2.85
2807 3971 5.766222 TCGAGCGTATAAAAATCCTAGGTC 58.234 41.667 9.08 0.00 0.00 3.85
2825 3989 6.793349 TGTAACTTATAAGACTTCCTCGAGC 58.207 40.000 19.38 0.00 0.00 5.03
2828 3992 8.752766 TTGTTGTAACTTATAAGACTTCCTCG 57.247 34.615 19.38 0.00 0.00 4.63
2893 4263 1.335689 GGTGCTGAGCTTTGAGCAAAG 60.336 52.381 16.51 16.51 46.49 2.77
2894 4264 0.670162 GGTGCTGAGCTTTGAGCAAA 59.330 50.000 15.29 0.00 46.49 3.68
2915 4285 1.079197 TGCATAGCACGTCCCACAG 60.079 57.895 0.00 0.00 31.71 3.66
2957 4339 8.595362 TCAAGAGTCAAGACCTTCTATATGAA 57.405 34.615 0.00 0.00 0.00 2.57
2965 4347 4.054671 CACACTCAAGAGTCAAGACCTTC 58.945 47.826 0.00 0.00 40.20 3.46
2967 4349 3.034635 ACACACTCAAGAGTCAAGACCT 58.965 45.455 0.00 0.00 40.20 3.85
2968 4350 3.460857 ACACACTCAAGAGTCAAGACC 57.539 47.619 0.00 0.00 40.20 3.85
3003 4385 0.179043 TTTCTTGCGTGGGTGTAGCA 60.179 50.000 0.00 0.00 39.33 3.49
3084 4484 0.465287 CCACCAAACTTTGCAAGCCT 59.535 50.000 0.00 0.00 0.00 4.58
3138 4538 5.139435 TGAGTCATTTCGAGTGATCTTGT 57.861 39.130 5.96 0.00 0.00 3.16
3139 4539 6.471976 TTTGAGTCATTTCGAGTGATCTTG 57.528 37.500 5.96 0.00 0.00 3.02
3141 4541 5.641209 CCTTTTGAGTCATTTCGAGTGATCT 59.359 40.000 5.96 5.64 0.00 2.75
3142 4542 5.409826 ACCTTTTGAGTCATTTCGAGTGATC 59.590 40.000 5.96 5.92 0.00 2.92
3144 4544 4.703897 ACCTTTTGAGTCATTTCGAGTGA 58.296 39.130 0.00 0.00 0.00 3.41
3145 4545 5.424121 AACCTTTTGAGTCATTTCGAGTG 57.576 39.130 0.00 0.00 0.00 3.51
3146 4546 6.451064 AAAACCTTTTGAGTCATTTCGAGT 57.549 33.333 0.00 0.00 0.00 4.18
3147 4547 7.798982 GTCTAAAACCTTTTGAGTCATTTCGAG 59.201 37.037 0.00 0.00 0.00 4.04
3148 4548 7.497909 AGTCTAAAACCTTTTGAGTCATTTCGA 59.502 33.333 0.00 0.00 0.00 3.71
3149 4549 7.639945 AGTCTAAAACCTTTTGAGTCATTTCG 58.360 34.615 0.00 0.00 0.00 3.46
3152 4552 9.628500 ACTAAGTCTAAAACCTTTTGAGTCATT 57.372 29.630 0.00 0.00 0.00 2.57
3154 4554 9.760077 CTACTAAGTCTAAAACCTTTTGAGTCA 57.240 33.333 0.00 0.00 0.00 3.41
3213 4613 2.709934 TCCTCCTCGTGCCTAGTAGTAT 59.290 50.000 0.00 0.00 0.00 2.12
3266 4675 2.981859 TATCGAAAGGTGCCCTTCTC 57.018 50.000 6.91 6.54 43.92 2.87
3273 4682 2.024414 AGCCCAAATATCGAAAGGTGC 58.976 47.619 0.00 0.00 0.00 5.01
3292 4701 1.676529 CCATCCTTCTGCAGCATTGAG 59.323 52.381 9.47 1.60 0.00 3.02
3350 4759 0.392863 TGGCACCACTTCATCCATCG 60.393 55.000 0.00 0.00 0.00 3.84
3396 4805 1.781786 TTTAGCTTTTGTGGCACCCA 58.218 45.000 16.26 0.00 0.00 4.51
3398 4807 2.754472 CCTTTTAGCTTTTGTGGCACC 58.246 47.619 16.26 0.00 0.00 5.01
3498 4908 1.754803 CATCTCCGCCACACCTAACTA 59.245 52.381 0.00 0.00 0.00 2.24
3560 4970 3.746940 TCGTATATCATCACTCCGGACA 58.253 45.455 0.00 0.00 0.00 4.02
3568 4978 7.121463 ACCCAACTCTATCTCGTATATCATCAC 59.879 40.741 0.00 0.00 0.00 3.06
4005 5416 5.601662 CCAAATAACATCCGAGAAGCTCTA 58.398 41.667 0.00 0.00 0.00 2.43
4015 5426 1.468985 TGGTGGCCAAATAACATCCG 58.531 50.000 7.24 0.00 0.00 4.18
4028 5439 0.532417 TGCTTGCAATGTTTGGTGGC 60.532 50.000 0.00 0.00 0.00 5.01
4041 5452 5.702865 TCAACAAATGTTAGAGATGCTTGC 58.297 37.500 0.00 0.00 36.32 4.01
4048 5459 8.896744 GGAATGATCATCAACAAATGTTAGAGA 58.103 33.333 9.06 0.00 36.32 3.10
4049 5460 8.133627 GGGAATGATCATCAACAAATGTTAGAG 58.866 37.037 9.06 0.00 36.32 2.43
4050 5461 7.614974 TGGGAATGATCATCAACAAATGTTAGA 59.385 33.333 9.06 0.49 36.32 2.10
4051 5462 7.703621 GTGGGAATGATCATCAACAAATGTTAG 59.296 37.037 9.06 0.00 36.32 2.34
4052 5463 7.178097 TGTGGGAATGATCATCAACAAATGTTA 59.822 33.333 9.06 0.00 36.32 2.41
4053 5464 6.014413 TGTGGGAATGATCATCAACAAATGTT 60.014 34.615 9.06 0.00 39.12 2.71
4054 5465 5.481122 TGTGGGAATGATCATCAACAAATGT 59.519 36.000 9.06 0.00 0.00 2.71
4055 5466 5.968254 TGTGGGAATGATCATCAACAAATG 58.032 37.500 9.06 0.00 0.00 2.32
4056 5467 6.608539 TTGTGGGAATGATCATCAACAAAT 57.391 33.333 9.06 0.00 0.00 2.32
4110 5521 1.265905 CTACACCCACGCAAGAAAACC 59.734 52.381 0.00 0.00 43.62 3.27
4180 5591 4.196971 GTTGTGTTGTCCCATATCCCTAC 58.803 47.826 0.00 0.00 0.00 3.18
4247 5658 5.818857 GGTTGTGACTTTAGTTCCACACTAA 59.181 40.000 4.46 0.00 44.86 2.24
4333 5744 5.404946 AGCACATGCATCATAACTTGTTTC 58.595 37.500 6.64 0.00 45.16 2.78
4337 5748 4.035909 TGCTAGCACATGCATCATAACTTG 59.964 41.667 14.93 0.00 45.16 3.16
4443 5858 2.692709 ACACCAATCAACATTCCCCA 57.307 45.000 0.00 0.00 0.00 4.96
4466 5883 9.593134 CAAATCTATGTAAACTGCTAAGAGACT 57.407 33.333 0.00 0.00 0.00 3.24
4624 6236 2.814805 ATAATGCTTGGCCTCTGTGT 57.185 45.000 3.32 0.00 0.00 3.72
4671 6283 1.133668 GGATAGCAATCCCAGCAAGGT 60.134 52.381 0.00 0.00 45.37 3.50
5287 6901 4.583871 ACATCCCTTTGTTAGCTTCTCTG 58.416 43.478 0.00 0.00 0.00 3.35
5334 6970 9.238368 TGACCCTATACAAAAATCTTCGAAAAT 57.762 29.630 0.00 0.00 0.00 1.82
5403 7044 5.333035 CCTCACGCGTACATAATTTACATGG 60.333 44.000 13.44 0.00 0.00 3.66
5416 7057 4.234530 AGGTAATTATCCTCACGCGTAC 57.765 45.455 13.44 1.44 0.00 3.67
5434 7075 4.281182 GGGTGATTCTATACACGATGAGGT 59.719 45.833 0.00 0.00 37.82 3.85
5528 7170 1.138266 AGGTCCGTGCACATATGGTAC 59.862 52.381 18.64 9.45 0.00 3.34
5529 7171 1.491668 AGGTCCGTGCACATATGGTA 58.508 50.000 18.64 0.00 0.00 3.25
5531 7173 2.839486 ATAGGTCCGTGCACATATGG 57.161 50.000 18.64 9.99 0.00 2.74
5532 7174 2.731451 CGAATAGGTCCGTGCACATATG 59.269 50.000 18.64 0.00 0.00 1.78
5533 7175 2.288825 CCGAATAGGTCCGTGCACATAT 60.289 50.000 18.64 3.89 34.51 1.78
5537 7179 4.104143 CCGAATAGGTCCGTGCAC 57.896 61.111 6.82 6.82 34.51 4.57
5554 7229 5.353678 CAGAACTCATCAGATTCCCTTGAAC 59.646 44.000 0.00 0.00 32.13 3.18
5576 7251 2.561733 TCGCGAGACAATAACTCCAG 57.438 50.000 3.71 0.00 33.31 3.86
5577 7252 3.520290 AATCGCGAGACAATAACTCCA 57.480 42.857 16.66 0.00 46.97 3.86
5579 7254 5.896974 GCTAAAAATCGCGAGACAATAACTC 59.103 40.000 16.66 0.00 46.97 3.01
5581 7256 5.796813 AGCTAAAAATCGCGAGACAATAAC 58.203 37.500 16.66 0.27 46.97 1.89
5582 7257 5.810587 AGAGCTAAAAATCGCGAGACAATAA 59.189 36.000 16.66 0.00 46.97 1.40
5583 7258 5.232202 CAGAGCTAAAAATCGCGAGACAATA 59.768 40.000 16.66 3.18 46.97 1.90
5592 7267 4.083271 ACAAACTCCAGAGCTAAAAATCGC 60.083 41.667 0.00 0.00 0.00 4.58
5628 7303 6.015180 ACAGCAACAATTCATATGGTTTCAGT 60.015 34.615 2.13 0.00 0.00 3.41
5727 7402 9.976511 GCCACTGTACAGTACTCAATTAATATA 57.023 33.333 27.48 0.00 40.20 0.86
5728 7403 8.482943 TGCCACTGTACAGTACTCAATTAATAT 58.517 33.333 27.48 0.00 40.20 1.28
5729 7404 7.842982 TGCCACTGTACAGTACTCAATTAATA 58.157 34.615 27.48 2.23 40.20 0.98
5730 7405 6.707290 TGCCACTGTACAGTACTCAATTAAT 58.293 36.000 27.48 0.00 40.20 1.40
5731 7406 6.014925 TCTGCCACTGTACAGTACTCAATTAA 60.015 38.462 27.48 5.50 40.20 1.40
5732 7407 5.479027 TCTGCCACTGTACAGTACTCAATTA 59.521 40.000 27.48 10.88 40.20 1.40
5733 7408 4.283467 TCTGCCACTGTACAGTACTCAATT 59.717 41.667 27.48 0.00 40.20 2.32
5734 7409 3.832490 TCTGCCACTGTACAGTACTCAAT 59.168 43.478 27.48 0.76 40.20 2.57
5735 7410 3.227614 TCTGCCACTGTACAGTACTCAA 58.772 45.455 27.48 11.22 40.20 3.02
5736 7411 2.820197 CTCTGCCACTGTACAGTACTCA 59.180 50.000 27.48 21.46 40.20 3.41
5737 7412 2.416162 GCTCTGCCACTGTACAGTACTC 60.416 54.545 27.48 18.44 40.20 2.59
5738 7413 1.546476 GCTCTGCCACTGTACAGTACT 59.454 52.381 27.48 3.18 40.20 2.73
5739 7414 1.997669 GCTCTGCCACTGTACAGTAC 58.002 55.000 27.48 21.68 40.20 2.73
5796 7471 2.159653 GCAAACGCTAGTCCAAGTGATG 60.160 50.000 0.00 0.00 0.00 3.07
5812 7487 3.243002 GCTAGCTGATTCCATGAGCAAAC 60.243 47.826 7.70 0.00 42.27 2.93
5864 7541 3.842007 ATTCCAGAAGATCAGGCTCAG 57.158 47.619 0.00 0.00 0.00 3.35
5865 7542 5.901413 ATAATTCCAGAAGATCAGGCTCA 57.099 39.130 0.00 0.00 0.00 4.26
5931 7608 6.295719 ACGTACTAGGGACTCATCATTTTT 57.704 37.500 0.00 0.00 41.75 1.94
5936 7613 5.889853 ACATAAACGTACTAGGGACTCATCA 59.110 40.000 0.00 0.00 41.75 3.07
5937 7614 6.388435 ACATAAACGTACTAGGGACTCATC 57.612 41.667 0.00 0.00 41.75 2.92
5938 7615 7.059156 ACTACATAAACGTACTAGGGACTCAT 58.941 38.462 0.00 0.00 41.75 2.90
5939 7616 6.418101 ACTACATAAACGTACTAGGGACTCA 58.582 40.000 0.00 0.00 41.75 3.41
5940 7617 6.934048 ACTACATAAACGTACTAGGGACTC 57.066 41.667 0.00 0.00 41.75 3.36
5942 7619 7.538575 TGAAACTACATAAACGTACTAGGGAC 58.461 38.462 0.00 0.00 0.00 4.46
5943 7620 7.394359 ACTGAAACTACATAAACGTACTAGGGA 59.606 37.037 0.00 0.00 0.00 4.20
5945 7622 8.976986 AACTGAAACTACATAAACGTACTAGG 57.023 34.615 0.00 0.00 0.00 3.02
5946 7623 8.783251 CGAACTGAAACTACATAAACGTACTAG 58.217 37.037 0.00 0.00 0.00 2.57
5947 7624 8.289618 ACGAACTGAAACTACATAAACGTACTA 58.710 33.333 0.00 0.00 0.00 1.82
5949 7626 7.096477 ACACGAACTGAAACTACATAAACGTAC 60.096 37.037 0.00 0.00 0.00 3.67
5951 7628 5.750067 ACACGAACTGAAACTACATAAACGT 59.250 36.000 0.00 0.00 0.00 3.99
5953 7630 7.581600 GTCAACACGAACTGAAACTACATAAAC 59.418 37.037 0.00 0.00 0.00 2.01
5955 7632 6.757478 TGTCAACACGAACTGAAACTACATAA 59.243 34.615 0.00 0.00 0.00 1.90
5956 7633 6.274579 TGTCAACACGAACTGAAACTACATA 58.725 36.000 0.00 0.00 0.00 2.29
5957 7634 5.113383 TGTCAACACGAACTGAAACTACAT 58.887 37.500 0.00 0.00 0.00 2.29
5958 7635 4.496360 TGTCAACACGAACTGAAACTACA 58.504 39.130 0.00 0.00 0.00 2.74
5959 7636 5.253335 GTTGTCAACACGAACTGAAACTAC 58.747 41.667 10.93 0.00 0.00 2.73
5960 7637 4.330620 GGTTGTCAACACGAACTGAAACTA 59.669 41.667 17.29 0.00 0.00 2.24
5961 7638 3.126343 GGTTGTCAACACGAACTGAAACT 59.874 43.478 17.29 0.00 0.00 2.66
5962 7639 3.120130 TGGTTGTCAACACGAACTGAAAC 60.120 43.478 17.29 0.00 0.00 2.78
5963 7640 3.075148 TGGTTGTCAACACGAACTGAAA 58.925 40.909 17.29 0.00 0.00 2.69
5964 7641 2.675844 CTGGTTGTCAACACGAACTGAA 59.324 45.455 17.29 0.00 0.00 3.02
5965 7642 2.276201 CTGGTTGTCAACACGAACTGA 58.724 47.619 17.29 0.00 0.00 3.41
5966 7643 2.006888 ACTGGTTGTCAACACGAACTG 58.993 47.619 17.29 6.23 0.00 3.16
5967 7644 2.396590 ACTGGTTGTCAACACGAACT 57.603 45.000 17.29 0.00 0.00 3.01
5968 7645 2.223180 GGAACTGGTTGTCAACACGAAC 60.223 50.000 17.29 5.66 0.00 3.95
6004 7681 0.463654 ACAACTCCTTCTGCAACGCA 60.464 50.000 0.00 0.00 36.92 5.24
6005 7682 1.508632 TACAACTCCTTCTGCAACGC 58.491 50.000 0.00 0.00 0.00 4.84
6006 7683 3.311322 TGTTTACAACTCCTTCTGCAACG 59.689 43.478 0.00 0.00 0.00 4.10
6007 7684 4.893424 TGTTTACAACTCCTTCTGCAAC 57.107 40.909 0.00 0.00 0.00 4.17
6019 7696 5.334337 GGTCCTACAATCCGTTGTTTACAAC 60.334 44.000 14.24 14.24 46.07 3.32
6020 7697 4.756135 GGTCCTACAATCCGTTGTTTACAA 59.244 41.667 0.00 0.00 46.07 2.41
6021 7698 4.202336 TGGTCCTACAATCCGTTGTTTACA 60.202 41.667 0.00 0.00 46.07 2.41
6022 7699 4.152938 GTGGTCCTACAATCCGTTGTTTAC 59.847 45.833 0.00 0.00 46.07 2.01
6023 7700 4.317488 GTGGTCCTACAATCCGTTGTTTA 58.683 43.478 0.00 0.00 46.07 2.01
6024 7701 3.143728 GTGGTCCTACAATCCGTTGTTT 58.856 45.455 0.00 0.00 46.07 2.83
6025 7702 2.551504 GGTGGTCCTACAATCCGTTGTT 60.552 50.000 0.00 0.00 46.07 2.83
6027 7704 1.734163 GGTGGTCCTACAATCCGTTG 58.266 55.000 0.00 0.00 41.20 4.10
6028 7705 0.248289 CGGTGGTCCTACAATCCGTT 59.752 55.000 0.00 0.00 34.38 4.44
6029 7706 1.895238 CGGTGGTCCTACAATCCGT 59.105 57.895 0.00 0.00 34.38 4.69
6030 7707 1.520787 GCGGTGGTCCTACAATCCG 60.521 63.158 0.00 0.00 40.72 4.18
6031 7708 0.252197 AAGCGGTGGTCCTACAATCC 59.748 55.000 0.00 0.00 0.00 3.01
6032 7709 1.369625 CAAGCGGTGGTCCTACAATC 58.630 55.000 0.00 0.00 0.00 2.67
6033 7710 0.676782 GCAAGCGGTGGTCCTACAAT 60.677 55.000 0.00 0.00 0.00 2.71
6034 7711 1.302192 GCAAGCGGTGGTCCTACAA 60.302 57.895 0.00 0.00 0.00 2.41
6035 7712 2.214216 AGCAAGCGGTGGTCCTACA 61.214 57.895 0.00 0.00 29.87 2.74
6036 7713 2.663196 AGCAAGCGGTGGTCCTAC 59.337 61.111 0.00 0.00 29.87 3.18
6041 7718 2.781595 CTAACGGAGCAAGCGGTGGT 62.782 60.000 0.00 0.00 41.89 4.16
6042 7719 2.047655 TAACGGAGCAAGCGGTGG 60.048 61.111 0.00 0.00 0.00 4.61
6043 7720 2.100631 CCTAACGGAGCAAGCGGTG 61.101 63.158 0.00 0.00 0.00 4.94
6044 7721 1.823169 TTCCTAACGGAGCAAGCGGT 61.823 55.000 0.00 0.00 41.25 5.68
6045 7722 0.672401 TTTCCTAACGGAGCAAGCGG 60.672 55.000 0.00 0.00 41.25 5.52
6046 7723 0.721718 CTTTCCTAACGGAGCAAGCG 59.278 55.000 0.00 0.00 41.25 4.68
6092 7772 4.573900 AGATTCAAACGATCAGCTCAGTT 58.426 39.130 0.00 0.00 0.00 3.16
6096 7776 4.503734 CAGAGAGATTCAAACGATCAGCTC 59.496 45.833 0.00 0.00 32.25 4.09
6119 7799 0.871057 GTGCAGAGCAACCAGTTCTC 59.129 55.000 0.00 3.31 41.47 2.87
6132 7812 5.994054 GCATTCATATCTCCTTTAGTGCAGA 59.006 40.000 0.00 0.00 0.00 4.26
6137 7817 5.760253 CCAACGCATTCATATCTCCTTTAGT 59.240 40.000 0.00 0.00 0.00 2.24
6155 7835 2.393764 GTTATGCCATTATGCCAACGC 58.606 47.619 0.00 0.00 0.00 4.84


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

AutoCloner maintained by Alex Coulton.