Multiple sequence alignment - TraesCS6A01G420800

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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 TraesCS6A01G420800 chr6A 100.000 5929 0 0 1 5929 617340347 617346275 0.000000e+00 10949.0
1 TraesCS6A01G420800 chr6A 85.238 1050 121 13 4113 5140 617250191 617251228 0.000000e+00 1050.0
2 TraesCS6A01G420800 chr6A 82.857 1120 145 23 2112 3195 617248087 617249195 0.000000e+00 961.0
3 TraesCS6A01G420800 chr6A 86.747 664 77 8 4171 4829 617405074 617405731 0.000000e+00 728.0
4 TraesCS6A01G420800 chr6A 81.370 934 102 37 1102 2014 617246677 617247559 0.000000e+00 695.0
5 TraesCS6A01G420800 chr6A 88.956 498 42 9 3621 4109 617249662 617250155 2.360000e-168 603.0
6 TraesCS6A01G420800 chr6A 79.025 677 90 25 240 885 617244627 617245282 3.310000e-112 416.0
7 TraesCS6A01G420800 chr6A 87.328 363 39 6 2372 2730 617403235 617403594 5.530000e-110 409.0
8 TraesCS6A01G420800 chr6A 87.006 354 37 4 3194 3539 617249280 617249632 2.000000e-104 390.0
9 TraesCS6A01G420800 chr6A 76.067 773 144 19 2282 3044 617224615 617225356 1.210000e-96 364.0
10 TraesCS6A01G420800 chr6A 81.789 313 40 8 3559 3865 617404451 617404752 4.590000e-61 246.0
11 TraesCS6A01G420800 chr6A 91.195 159 14 0 1102 1260 617552444 617552602 3.600000e-52 217.0
12 TraesCS6A01G420800 chr6A 80.843 261 43 7 1511 1768 617553529 617553785 1.300000e-46 198.0
13 TraesCS6A01G420800 chr6A 80.176 227 32 8 3191 3413 617351308 617351525 2.210000e-34 158.0
14 TraesCS6A01G420800 chr6D 93.055 2750 125 19 808 3543 472492174 472489477 0.000000e+00 3960.0
15 TraesCS6A01G420800 chr6D 90.211 1328 115 10 4113 5437 472488842 472487527 0.000000e+00 1718.0
16 TraesCS6A01G420800 chr6D 89.863 582 44 8 3540 4113 472489447 472488873 0.000000e+00 734.0
17 TraesCS6A01G420800 chr6D 84.701 719 62 26 41 738 472492889 472492198 0.000000e+00 675.0
18 TraesCS6A01G420800 chr6D 92.453 159 12 0 1102 1260 472430057 472429899 1.660000e-55 228.0
19 TraesCS6A01G420800 chr6B 87.629 3476 295 79 2020 5437 717410025 717406627 0.000000e+00 3912.0
20 TraesCS6A01G420800 chr6B 83.478 1156 130 38 877 2006 717411845 717410725 0.000000e+00 1020.0
21 TraesCS6A01G420800 chr6B 83.610 482 52 14 5472 5929 717406552 717406074 1.530000e-115 427.0
22 TraesCS6A01G420800 chr6B 80.968 310 42 9 3178 3483 717139030 717138734 4.620000e-56 230.0
23 TraesCS6A01G420800 chr6B 92.453 159 12 0 1102 1260 717143097 717142939 1.660000e-55 228.0
24 TraesCS6A01G420800 chr6B 80.861 209 33 6 1526 1731 717141954 717141750 2.210000e-34 158.0
25 TraesCS6A01G420800 chr1A 88.638 1857 147 30 4113 5929 2662865 2661033 0.000000e+00 2202.0
26 TraesCS6A01G420800 chr1A 89.164 1532 125 25 2020 3543 2664983 2663485 0.000000e+00 1871.0
27 TraesCS6A01G420800 chr1A 90.787 1335 103 16 4113 5437 2633019 2631695 0.000000e+00 1766.0
28 TraesCS6A01G420800 chr1A 89.891 1098 82 15 926 2010 2667070 2665989 0.000000e+00 1386.0
29 TraesCS6A01G420800 chr1A 93.063 764 20 13 1840 2599 2634441 2633707 0.000000e+00 1086.0
30 TraesCS6A01G420800 chr1A 90.034 582 45 7 3540 4113 2633626 2633050 0.000000e+00 741.0
31 TraesCS6A01G420800 chr1A 84.470 689 66 17 65 729 2635504 2634833 5.010000e-180 641.0
32 TraesCS6A01G420800 chr1A 84.864 588 47 14 3540 4113 2663455 2662896 6.710000e-154 555.0
33 TraesCS6A01G420800 chr1A 94.570 221 10 2 1605 1823 2634650 2634430 2.050000e-89 340.0
34 TraesCS6A01G420800 chr1A 95.604 182 8 0 1393 1574 2634831 2634650 5.810000e-75 292.0
35 TraesCS6A01G420800 chr1A 84.146 328 22 9 525 829 2668775 2668455 2.090000e-74 291.0
36 TraesCS6A01G420800 chr1A 85.978 271 20 5 473 738 2667551 2667294 2.110000e-69 274.0
37 TraesCS6A01G420800 chr1A 81.855 248 36 8 1526 1768 2842727 2842484 3.620000e-47 200.0
38 TraesCS6A01G420800 chr1A 82.812 192 27 3 3263 3451 2839751 2839563 3.680000e-37 167.0
39 TraesCS6A01G420800 chr1A 81.325 166 16 2 1 152 2668942 2668778 2.900000e-23 121.0
40 TraesCS6A01G420800 chr1A 94.000 50 3 0 1 50 2635541 2635492 6.370000e-10 76.8
41 TraesCS6A01G420800 chr7D 83.954 349 48 4 3676 4017 194247650 194247997 1.590000e-85 327.0
42 TraesCS6A01G420800 chr7D 77.938 485 84 15 4557 5034 194248559 194249027 1.260000e-71 281.0
43 TraesCS6A01G420800 chr7D 78.610 374 59 17 1597 1965 194244153 194244510 1.660000e-55 228.0
44 TraesCS6A01G420800 chr7B 82.759 348 51 5 3676 4016 158172685 158173030 9.660000e-78 302.0
45 TraesCS6A01G420800 chr7B 77.834 397 64 17 1577 1965 158169341 158169721 2.150000e-54 224.0


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 TraesCS6A01G420800 chr6A 617340347 617346275 5928 False 10949.000000 10949 100.000000 1 5929 1 chr6A.!!$F2 5928
1 TraesCS6A01G420800 chr6A 617244627 617251228 6601 False 685.833333 1050 84.075333 240 5140 6 chr6A.!!$F4 4900
2 TraesCS6A01G420800 chr6A 617403235 617405731 2496 False 461.000000 728 85.288000 2372 4829 3 chr6A.!!$F5 2457
3 TraesCS6A01G420800 chr6A 617224615 617225356 741 False 364.000000 364 76.067000 2282 3044 1 chr6A.!!$F1 762
4 TraesCS6A01G420800 chr6A 617552444 617553785 1341 False 207.500000 217 86.019000 1102 1768 2 chr6A.!!$F6 666
5 TraesCS6A01G420800 chr6D 472487527 472492889 5362 True 1771.750000 3960 89.457500 41 5437 4 chr6D.!!$R2 5396
6 TraesCS6A01G420800 chr6B 717406074 717411845 5771 True 1786.333333 3912 84.905667 877 5929 3 chr6B.!!$R2 5052
7 TraesCS6A01G420800 chr6B 717138734 717143097 4363 True 205.333333 230 84.760667 1102 3483 3 chr6B.!!$R1 2381
8 TraesCS6A01G420800 chr1A 2661033 2668942 7909 True 957.142857 2202 86.286571 1 5929 7 chr1A.!!$R2 5928
9 TraesCS6A01G420800 chr1A 2631695 2635541 3846 True 706.114286 1766 91.789714 1 5437 7 chr1A.!!$R1 5436
10 TraesCS6A01G420800 chr7D 194244153 194249027 4874 False 278.666667 327 80.167333 1597 5034 3 chr7D.!!$F1 3437
11 TraesCS6A01G420800 chr7B 158169341 158173030 3689 False 263.000000 302 80.296500 1577 4016 2 chr7B.!!$F1 2439

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
232 233 0.179000 AAGATGACATCGGAGGCACC 59.821 55.000 9.77 0.0 0.00 5.01 F
963 3056 0.756070 GTACTCCTCCCTTCCTCCGG 60.756 65.000 0.00 0.0 0.00 5.14 F
1496 3654 0.109153 AATCACAGTCAGGTGCTGCA 59.891 50.000 0.00 0.0 38.66 4.41 F
1865 4931 0.170339 GTGGGCGGTTTACTTGCATC 59.830 55.000 0.00 0.0 0.00 3.91 F
2885 8296 1.205064 CTCACCTGCGAAAAGTGCG 59.795 57.895 0.00 0.0 34.24 5.34 F
4574 10645 1.898472 TGATGATAGCCTAGCTGAGCC 59.102 52.381 0.00 0.0 40.10 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 3295 0.032117 TCGGTGAGTCCCTGGATGAT 60.032 55.000 0.00 0.00 0.00 2.45 R
2885 8296 0.398318 ACCACAGTTCAGAAGGCTCC 59.602 55.000 0.00 0.00 0.00 4.70 R
3438 9160 3.605486 GCTTTTCAGCGCTCACTTTAATG 59.395 43.478 7.13 0.00 35.91 1.90 R
3850 9686 1.538047 AATCATGTGTGCGCCTTTCT 58.462 45.000 4.18 0.00 0.00 2.52 R
4607 10678 0.108138 GGTGACCTCATCAGGGTTCG 60.108 60.000 0.00 0.00 45.53 3.95 R
5734 11873 0.362512 GACGCGTTCTTCAAGCTACG 59.637 55.000 15.53 7.34 37.09 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.733443 GGCAAGTTCACCATTTTGACT 57.267 42.857 0.00 0.00 0.00 3.41
21 22 3.642705 GGCAAGTTCACCATTTTGACTC 58.357 45.455 0.00 0.00 0.00 3.36
22 23 3.300009 GCAAGTTCACCATTTTGACTCG 58.700 45.455 0.00 0.00 0.00 4.18
23 24 3.243068 GCAAGTTCACCATTTTGACTCGT 60.243 43.478 0.00 0.00 0.00 4.18
25 26 5.679906 CAAGTTCACCATTTTGACTCGTAG 58.320 41.667 0.00 0.00 0.00 3.51
26 27 4.315803 AGTTCACCATTTTGACTCGTAGG 58.684 43.478 0.00 0.00 0.00 3.18
28 29 1.393539 CACCATTTTGACTCGTAGGCG 59.606 52.381 0.00 0.00 39.92 5.52
29 30 1.274167 ACCATTTTGACTCGTAGGCGA 59.726 47.619 0.00 0.00 45.79 5.54
30 31 1.659098 CCATTTTGACTCGTAGGCGAC 59.341 52.381 0.00 0.00 42.81 5.19
48 49 1.226379 CGCTAAAACTGCCGGCATG 60.226 57.895 32.87 25.18 0.00 4.06
62 63 2.467826 GCATGAAGGCCACGAGAGC 61.468 63.158 5.01 0.00 0.00 4.09
65 66 2.507324 GAAGGCCACGAGAGCGAC 60.507 66.667 5.01 0.00 41.64 5.19
66 67 2.992114 AAGGCCACGAGAGCGACT 60.992 61.111 5.01 0.00 41.64 4.18
67 68 3.288308 AAGGCCACGAGAGCGACTG 62.288 63.158 5.01 0.00 41.64 3.51
68 69 4.803426 GGCCACGAGAGCGACTGG 62.803 72.222 0.00 0.00 41.64 4.00
108 109 4.326478 AGGGACCCCTTCCTAGGA 57.674 61.111 7.62 7.62 45.70 2.94
110 111 1.074395 GGGACCCCTTCCTAGGAGG 60.074 68.421 13.96 13.96 45.05 4.30
111 112 1.074395 GGACCCCTTCCTAGGAGGG 60.074 68.421 29.15 29.15 45.05 4.30
133 134 4.803426 GCACAGCGTCTCCCGGAG 62.803 72.222 8.30 8.30 36.94 4.63
148 149 2.278330 GGAGGTTGGCCAGCAAAGG 61.278 63.158 22.07 0.00 37.19 3.11
158 159 2.753043 AGCAAAGGCCCAGCATCG 60.753 61.111 13.36 0.00 42.56 3.84
159 160 2.751436 GCAAAGGCCCAGCATCGA 60.751 61.111 0.00 0.00 0.00 3.59
160 161 3.056313 GCAAAGGCCCAGCATCGAC 62.056 63.158 0.00 0.00 0.00 4.20
162 163 1.675641 AAAGGCCCAGCATCGACAC 60.676 57.895 0.00 0.00 0.00 3.67
163 164 3.958147 AAGGCCCAGCATCGACACG 62.958 63.158 0.00 0.00 0.00 4.49
166 167 2.887568 CCCAGCATCGACACGCTC 60.888 66.667 3.00 0.00 35.96 5.03
167 168 2.182791 CCAGCATCGACACGCTCT 59.817 61.111 3.00 0.00 35.96 4.09
168 169 2.163390 CCAGCATCGACACGCTCTG 61.163 63.158 3.00 0.00 35.96 3.35
169 170 1.153958 CAGCATCGACACGCTCTGA 60.154 57.895 3.00 0.00 35.96 3.27
172 173 0.803768 GCATCGACACGCTCTGACAT 60.804 55.000 0.00 0.00 0.00 3.06
173 174 0.919300 CATCGACACGCTCTGACATG 59.081 55.000 0.00 0.00 0.00 3.21
174 175 0.811281 ATCGACACGCTCTGACATGA 59.189 50.000 0.00 0.00 0.00 3.07
176 177 1.195347 CGACACGCTCTGACATGATC 58.805 55.000 0.00 0.00 0.00 2.92
178 179 2.191802 GACACGCTCTGACATGATCTG 58.808 52.381 0.00 0.00 0.00 2.90
179 180 1.547820 ACACGCTCTGACATGATCTGT 59.452 47.619 0.00 0.00 42.15 3.41
192 193 6.535963 ACATGATCTGTCATAGTCAACTGA 57.464 37.500 0.00 0.00 43.14 3.41
193 194 6.939622 ACATGATCTGTCATAGTCAACTGAA 58.060 36.000 0.00 0.00 43.14 3.02
195 196 5.724328 TGATCTGTCATAGTCAACTGAACC 58.276 41.667 0.00 0.00 0.00 3.62
196 197 5.481824 TGATCTGTCATAGTCAACTGAACCT 59.518 40.000 0.00 0.00 0.00 3.50
198 199 6.911250 TCTGTCATAGTCAACTGAACCTTA 57.089 37.500 0.00 0.00 0.00 2.69
199 200 7.297936 TCTGTCATAGTCAACTGAACCTTAA 57.702 36.000 0.00 0.00 0.00 1.85
200 201 7.152645 TCTGTCATAGTCAACTGAACCTTAAC 58.847 38.462 0.00 0.00 0.00 2.01
203 204 8.644216 TGTCATAGTCAACTGAACCTTAACTTA 58.356 33.333 0.00 0.00 0.00 2.24
204 205 8.923683 GTCATAGTCAACTGAACCTTAACTTAC 58.076 37.037 0.00 0.00 0.00 2.34
205 206 8.092687 TCATAGTCAACTGAACCTTAACTTACC 58.907 37.037 0.00 0.00 0.00 2.85
208 209 6.556116 AGTCAACTGAACCTTAACTTACCCTA 59.444 38.462 0.00 0.00 0.00 3.53
209 210 6.648310 GTCAACTGAACCTTAACTTACCCTAC 59.352 42.308 0.00 0.00 0.00 3.18
210 211 6.556116 TCAACTGAACCTTAACTTACCCTACT 59.444 38.462 0.00 0.00 0.00 2.57
211 212 6.356186 ACTGAACCTTAACTTACCCTACTG 57.644 41.667 0.00 0.00 0.00 2.74
212 213 5.247792 ACTGAACCTTAACTTACCCTACTGG 59.752 44.000 0.00 0.00 41.37 4.00
213 214 5.405279 TGAACCTTAACTTACCCTACTGGA 58.595 41.667 0.00 0.00 38.00 3.86
214 215 5.845614 TGAACCTTAACTTACCCTACTGGAA 59.154 40.000 0.00 0.00 38.00 3.53
215 216 6.013984 TGAACCTTAACTTACCCTACTGGAAG 60.014 42.308 0.00 0.00 42.29 3.46
216 217 5.658474 ACCTTAACTTACCCTACTGGAAGA 58.342 41.667 0.00 0.00 37.43 2.87
217 218 6.269974 ACCTTAACTTACCCTACTGGAAGAT 58.730 40.000 0.00 0.00 37.43 2.40
218 219 6.156429 ACCTTAACTTACCCTACTGGAAGATG 59.844 42.308 0.00 0.00 37.43 2.90
219 220 6.383147 CCTTAACTTACCCTACTGGAAGATGA 59.617 42.308 0.00 0.00 37.43 2.92
221 222 4.684724 ACTTACCCTACTGGAAGATGACA 58.315 43.478 0.00 0.00 37.43 3.58
222 223 5.281314 ACTTACCCTACTGGAAGATGACAT 58.719 41.667 0.00 0.00 37.43 3.06
223 224 5.364157 ACTTACCCTACTGGAAGATGACATC 59.636 44.000 7.39 7.39 37.43 3.06
224 225 2.695666 ACCCTACTGGAAGATGACATCG 59.304 50.000 9.77 0.00 37.43 3.84
226 227 2.959030 CCTACTGGAAGATGACATCGGA 59.041 50.000 9.77 0.00 37.43 4.55
227 228 3.005261 CCTACTGGAAGATGACATCGGAG 59.995 52.174 9.77 7.05 37.43 4.63
228 229 1.759445 ACTGGAAGATGACATCGGAGG 59.241 52.381 9.77 3.92 37.43 4.30
230 231 0.465705 GGAAGATGACATCGGAGGCA 59.534 55.000 9.77 0.00 0.00 4.75
231 232 1.576356 GAAGATGACATCGGAGGCAC 58.424 55.000 9.77 0.00 0.00 5.01
232 233 0.179000 AAGATGACATCGGAGGCACC 59.821 55.000 9.77 0.00 0.00 5.01
241 242 2.652530 GGAGGCACCGTAACACGA 59.347 61.111 0.00 0.00 46.05 4.35
242 243 1.005867 GGAGGCACCGTAACACGAA 60.006 57.895 0.00 0.00 46.05 3.85
243 244 1.012486 GGAGGCACCGTAACACGAAG 61.012 60.000 0.00 0.00 46.05 3.79
244 245 1.005394 AGGCACCGTAACACGAAGG 60.005 57.895 0.00 0.00 46.05 3.46
245 246 2.674084 GGCACCGTAACACGAAGGC 61.674 63.158 0.00 1.17 46.05 4.35
246 247 1.957186 GCACCGTAACACGAAGGCA 60.957 57.895 0.00 0.00 46.05 4.75
248 249 1.301165 ACCGTAACACGAAGGCACC 60.301 57.895 0.00 0.00 46.05 5.01
293 1406 5.235186 CCATAATTCTTGCACTAGTTCCTCG 59.765 44.000 0.00 0.00 0.00 4.63
307 1423 5.986501 AGTTCCTCGTTAGTCTTCATCTT 57.013 39.130 0.00 0.00 0.00 2.40
371 1487 1.748122 GTCGCCGGAGAGGACTACA 60.748 63.158 8.65 0.00 45.00 2.74
405 1521 1.672363 CAACTGCTCTGTGCTGAACAA 59.328 47.619 14.17 0.00 42.27 2.83
424 2312 3.204158 ACAACATGCACCTTATCCCCATA 59.796 43.478 0.00 0.00 0.00 2.74
437 2326 1.029947 CCCCATAACAGACGGCCAAC 61.030 60.000 2.24 0.00 0.00 3.77
554 2489 4.504916 CCTCTCTCCGTGCCGCAG 62.505 72.222 0.00 0.00 0.00 5.18
606 2541 3.630312 CGTTCCAAGGGAAGAAAAAGTGA 59.370 43.478 0.00 0.00 42.88 3.41
612 2547 4.536295 AGGGAAGAAAAAGTGAAAGGGA 57.464 40.909 0.00 0.00 0.00 4.20
616 2551 5.047731 GGGAAGAAAAAGTGAAAGGGAGATG 60.048 44.000 0.00 0.00 0.00 2.90
618 2553 5.066913 AGAAAAAGTGAAAGGGAGATGGT 57.933 39.130 0.00 0.00 0.00 3.55
631 2566 1.077716 GATGGTGGTACAGGGTGCC 60.078 63.158 0.00 0.00 41.80 5.01
632 2567 2.869503 GATGGTGGTACAGGGTGCCG 62.870 65.000 0.00 0.00 41.19 5.69
633 2568 4.404098 GGTGGTACAGGGTGCCGG 62.404 72.222 0.00 0.00 41.19 6.13
634 2569 4.404098 GTGGTACAGGGTGCCGGG 62.404 72.222 2.18 0.00 41.19 5.73
635 2570 4.642488 TGGTACAGGGTGCCGGGA 62.642 66.667 2.18 0.00 41.19 5.14
636 2571 4.091939 GGTACAGGGTGCCGGGAC 62.092 72.222 19.24 19.24 31.68 4.46
677 2646 4.521062 CTTCAGCGGCGGGGAGAG 62.521 72.222 9.78 0.00 0.00 3.20
684 2653 4.779733 GGCGGGGAGAGTGGGAGA 62.780 72.222 0.00 0.00 0.00 3.71
685 2654 3.151022 GCGGGGAGAGTGGGAGAG 61.151 72.222 0.00 0.00 0.00 3.20
801 2821 2.033194 GCCTACTGTCCACGTTGGC 61.033 63.158 9.77 9.77 43.73 4.52
854 2879 4.072088 GTCGGCCGCGTGAGTTTG 62.072 66.667 23.51 0.00 0.00 2.93
859 2884 1.741770 GCCGCGTGAGTTTGGATCT 60.742 57.895 4.92 0.00 0.00 2.75
863 2922 1.126846 CGCGTGAGTTTGGATCTCAAC 59.873 52.381 0.00 0.00 42.42 3.18
871 2930 5.163205 TGAGTTTGGATCTCAACAAGGAAGA 60.163 40.000 9.37 0.00 38.71 2.87
883 2942 1.537202 CAAGGAAGAAAAGGCCGACAG 59.463 52.381 0.00 0.00 0.00 3.51
884 2943 1.056660 AGGAAGAAAAGGCCGACAGA 58.943 50.000 0.00 0.00 0.00 3.41
898 2957 2.482336 CCGACAGAGATCGATTCGAGAT 59.518 50.000 15.98 5.26 45.13 2.75
956 3049 2.658489 TCTGGTAAGGTACTCCTCCCTT 59.342 50.000 0.00 0.00 44.35 3.95
963 3056 0.756070 GTACTCCTCCCTTCCTCCGG 60.756 65.000 0.00 0.00 0.00 5.14
1001 3094 4.207891 TCTCCAGTCTTGTAATGCTTCC 57.792 45.455 0.00 0.00 0.00 3.46
1021 3114 2.353889 CCTCAAATCGAATCTGCTGTGG 59.646 50.000 0.00 0.00 0.00 4.17
1133 3253 2.579201 CGGAGGTCGCCAAGATGT 59.421 61.111 0.00 0.00 0.00 3.06
1134 3254 1.079127 CGGAGGTCGCCAAGATGTT 60.079 57.895 0.00 0.00 0.00 2.71
1175 3295 4.738998 CCATGCCCAAGCGTCCCA 62.739 66.667 0.00 0.00 44.31 4.37
1251 3371 1.305046 AGGTCCCCGTCCAGTACAG 60.305 63.158 0.00 0.00 0.00 2.74
1496 3654 0.109153 AATCACAGTCAGGTGCTGCA 59.891 50.000 0.00 0.00 38.66 4.41
1663 4644 1.133976 CAGGGAATGCCTCTTCGGATT 60.134 52.381 0.00 0.00 33.16 3.01
1697 4678 2.099756 AGCTTGAAGCAAAGTCACCAAC 59.900 45.455 20.45 0.00 45.56 3.77
1786 4834 4.701765 TGTCACATTTGGTCCATTTTTGG 58.298 39.130 0.00 0.00 0.00 3.28
1865 4931 0.170339 GTGGGCGGTTTACTTGCATC 59.830 55.000 0.00 0.00 0.00 3.91
1999 5070 6.245890 AGATCTGAATTCTAGAAACAGGGG 57.754 41.667 27.30 14.03 33.20 4.79
2001 5072 6.445139 AGATCTGAATTCTAGAAACAGGGGAA 59.555 38.462 27.30 16.82 33.20 3.97
2002 5073 5.805728 TCTGAATTCTAGAAACAGGGGAAC 58.194 41.667 27.30 9.19 33.20 3.62
2007 7163 7.563556 TGAATTCTAGAAACAGGGGAACTTTTT 59.436 33.333 9.71 0.00 32.00 1.94
2018 7177 8.313944 ACAGGGGAACTTTTTATAAAACAAGT 57.686 30.769 10.18 9.37 37.24 3.16
2546 7917 3.562182 TGCGTTCTCTCCCATGTATAGA 58.438 45.455 0.00 0.00 0.00 1.98
2708 8103 4.098960 TCCTTACTGATTACTAAGCCGGTG 59.901 45.833 1.90 0.00 0.00 4.94
2746 8145 8.517878 CAGAATATTTATGTAATTCCTGGCAGG 58.482 37.037 28.01 28.01 36.46 4.85
2748 8147 2.254546 TATGTAATTCCTGGCAGGCG 57.745 50.000 29.02 6.54 34.61 5.52
2755 8155 2.436646 CCTGGCAGGCGGTTACAG 60.437 66.667 22.68 0.00 0.00 2.74
2885 8296 1.205064 CTCACCTGCGAAAAGTGCG 59.795 57.895 0.00 0.00 34.24 5.34
3054 8482 9.924650 TCTATTCCTTGTTTGTCTAGACTTTAC 57.075 33.333 23.01 17.00 0.00 2.01
3315 9034 7.970384 TGATTTGACCATTTATTAGTCGTGTC 58.030 34.615 0.00 0.00 33.09 3.67
3316 9035 6.730960 TTTGACCATTTATTAGTCGTGTCC 57.269 37.500 0.00 0.00 33.09 4.02
3515 9289 9.178758 GGATAGTCCAACTTTCATCAAATAAGT 57.821 33.333 1.07 0.00 36.28 2.24
3604 9424 8.915057 AGACAATATCATACTCAAATTGGAGG 57.085 34.615 14.48 0.00 39.27 4.30
3740 9575 7.269316 TGTGAGTTAGTTGTCTTGTAATGTGA 58.731 34.615 0.00 0.00 0.00 3.58
3804 9640 3.213206 TCTGTGCTGAATTGAACAGGT 57.787 42.857 4.49 0.00 42.44 4.00
3850 9686 7.509141 TTTTGATGCTCATGTTCTTGAAGTA 57.491 32.000 0.00 0.00 0.00 2.24
3977 9930 5.043248 GTGCATGCATTTATTCTGGTTACC 58.957 41.667 25.64 0.38 0.00 2.85
3990 9943 3.071312 TCTGGTTACCGTGTTACACCATT 59.929 43.478 10.10 0.00 36.91 3.16
3991 9944 3.139850 TGGTTACCGTGTTACACCATTG 58.860 45.455 10.10 0.00 32.38 2.82
4045 10030 7.880160 TTGCCTGCACATAGAGTTATATTTT 57.120 32.000 0.00 0.00 0.00 1.82
4135 10153 6.647334 TGGTTTTCTTCTTCATAACATGCA 57.353 33.333 0.00 0.00 0.00 3.96
4144 10162 4.823442 TCTTCATAACATGCATGGACATCC 59.177 41.667 29.41 0.00 0.00 3.51
4160 10180 4.281941 GGACATCCATACATGAGTAGCTCA 59.718 45.833 0.00 1.06 39.34 4.26
4175 10195 1.985159 AGCTCACCATGGTCCTTTGTA 59.015 47.619 16.53 0.00 0.00 2.41
4235 10264 6.279882 CAAACTTACTTTGGCATTTCCTTGA 58.720 36.000 0.00 0.00 36.35 3.02
4266 10295 5.804944 TTCCAATCTGCAATTTCTTTGGA 57.195 34.783 0.00 0.00 40.49 3.53
4307 10336 8.905660 ATCTGAATGTTCAAGGAAGATAGATG 57.094 34.615 0.00 0.00 36.64 2.90
4375 10409 7.716998 AGCCAATTATCTTACCATGTAGTCAAG 59.283 37.037 0.00 0.00 0.00 3.02
4432 10469 8.408601 GCTTGTTTCTATGATGTTTACCATGAT 58.591 33.333 0.00 0.00 32.56 2.45
4494 10532 6.480524 TTTATTTTCACGTGACAGGAGATG 57.519 37.500 19.90 0.00 0.00 2.90
4574 10645 1.898472 TGATGATAGCCTAGCTGAGCC 59.102 52.381 0.00 0.00 40.10 4.70
4607 10678 4.744795 AGTCACACAAGAGGATGGATAC 57.255 45.455 0.00 0.00 0.00 2.24
4635 10706 0.836400 ATGAGGTCACCGTGGTTCCT 60.836 55.000 11.01 11.01 34.28 3.36
4636 10707 1.004918 GAGGTCACCGTGGTTCCTG 60.005 63.158 14.75 0.00 32.65 3.86
4658 10729 1.315257 CCACCAAATCAAGGAGGGCG 61.315 60.000 0.00 0.00 33.74 6.13
4837 10909 2.669391 CGCTTCCCTGTGCATTTCTTTC 60.669 50.000 0.00 0.00 0.00 2.62
5061 11145 3.679389 AGGTCTAGACAGGCACAATTTG 58.321 45.455 23.91 0.00 0.00 2.32
5083 11168 0.169230 AAACAAAGAACGCGCACACA 59.831 45.000 5.73 0.00 0.00 3.72
5103 11188 3.567164 ACACACCAGAAGATTTCTTGCAG 59.433 43.478 0.00 0.00 38.11 4.41
5110 11202 5.048224 CCAGAAGATTTCTTGCAGATTGTGT 60.048 40.000 0.00 0.00 38.11 3.72
5209 11306 4.447724 ACCTACATAAAGCGATATGTTGCG 59.552 41.667 18.43 13.55 42.40 4.85
5244 11341 4.728772 CCAATACATGGCATCTAGGGAAA 58.271 43.478 0.00 0.00 43.80 3.13
5262 11360 2.086054 AAGACAAGTCATGGTCGCTC 57.914 50.000 2.72 0.00 39.01 5.03
5283 11382 2.043227 GGGCTAGGCTGTTGAGACTAT 58.957 52.381 16.80 0.00 39.26 2.12
5359 11458 6.596621 TCGTCAATCCCAATATGGTAAATCA 58.403 36.000 0.00 0.00 35.17 2.57
5400 11499 1.671054 GGTGCAAGTAAGCTCGGCA 60.671 57.895 0.00 0.00 34.14 5.69
5420 11519 3.128349 CACCATAGTATACGCCACAACC 58.872 50.000 0.00 0.00 0.00 3.77
5426 11525 2.833338 AGTATACGCCACAACCACCTAA 59.167 45.455 0.00 0.00 0.00 2.69
5437 11536 0.537188 ACCACCTAATGACTCGGCTG 59.463 55.000 0.00 0.00 0.00 4.85
5439 11538 0.537188 CACCTAATGACTCGGCTGGT 59.463 55.000 0.00 0.00 0.00 4.00
5440 11539 0.537188 ACCTAATGACTCGGCTGGTG 59.463 55.000 0.00 0.00 0.00 4.17
5465 11591 0.037303 CCCAGTGATGAGGCACACTT 59.963 55.000 0.00 0.00 43.52 3.16
5470 11609 1.741706 GTGATGAGGCACACTTGATGG 59.258 52.381 0.00 0.00 38.63 3.51
5475 11614 1.303561 GGCACACTTGATGGCCTGA 60.304 57.895 3.32 0.00 39.98 3.86
5500 11639 7.450074 AGTGAAATGAAAGTGTGTATAGGTGA 58.550 34.615 0.00 0.00 0.00 4.02
5524 11663 3.206964 TCGGTGCATGTGTTACTTTGAA 58.793 40.909 0.00 0.00 0.00 2.69
5531 11670 4.757149 GCATGTGTTACTTTGAAGAGGAGT 59.243 41.667 0.00 0.00 0.00 3.85
5532 11671 5.239525 GCATGTGTTACTTTGAAGAGGAGTT 59.760 40.000 0.00 0.00 0.00 3.01
5534 11673 5.741011 TGTGTTACTTTGAAGAGGAGTTGT 58.259 37.500 0.00 0.00 0.00 3.32
5630 11769 1.671328 CCGAGAACGCTGATCTGTAGA 59.329 52.381 1.27 0.00 38.29 2.59
5635 11774 2.656560 ACGCTGATCTGTAGAACCAC 57.343 50.000 1.27 0.00 0.00 4.16
5645 11784 5.661056 TCTGTAGAACCACGATGAAGAAT 57.339 39.130 0.00 0.00 0.00 2.40
5718 11857 0.247736 GGCTGTGGATCTCGACAAGT 59.752 55.000 0.00 0.00 34.26 3.16
5727 11866 1.822506 TCTCGACAAGTGATCCGTCT 58.177 50.000 0.00 0.00 0.00 4.18
5734 11873 2.069273 CAAGTGATCCGTCTGTGAACC 58.931 52.381 0.00 0.00 0.00 3.62
5743 11882 1.335597 CGTCTGTGAACCGTAGCTTGA 60.336 52.381 0.00 0.00 0.00 3.02
5744 11883 2.750948 GTCTGTGAACCGTAGCTTGAA 58.249 47.619 0.00 0.00 0.00 2.69
5763 11926 3.459378 GAACGCGTCGGCCGATCTA 62.459 63.158 33.58 5.39 39.56 1.98
5783 11946 1.596752 TCATGTGGTTTGTCGCGCT 60.597 52.632 5.56 0.00 0.00 5.92
5784 11947 1.163420 TCATGTGGTTTGTCGCGCTT 61.163 50.000 5.56 0.00 0.00 4.68
5851 12014 2.158711 GGCATGATCATCACCTTCTCCA 60.159 50.000 4.86 0.00 0.00 3.86
5852 12015 3.139850 GCATGATCATCACCTTCTCCAG 58.860 50.000 4.86 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.120304 GCCTACGAGTCAAAATGGTGAAC 60.120 47.826 0.00 0.00 0.00 3.18
22 23 0.369248 GCAGTTTTAGCGTCGCCTAC 59.631 55.000 14.86 7.04 0.00 3.18
23 24 0.738412 GGCAGTTTTAGCGTCGCCTA 60.738 55.000 14.86 2.89 36.58 3.93
25 26 2.479198 GGCAGTTTTAGCGTCGCC 59.521 61.111 14.86 0.00 0.00 5.54
26 27 2.095843 CGGCAGTTTTAGCGTCGC 59.904 61.111 9.80 9.80 0.00 5.19
28 29 1.644786 ATGCCGGCAGTTTTAGCGTC 61.645 55.000 35.36 0.00 0.00 5.19
29 30 1.674322 ATGCCGGCAGTTTTAGCGT 60.674 52.632 35.36 11.90 0.00 5.07
30 31 1.226379 CATGCCGGCAGTTTTAGCG 60.226 57.895 35.36 11.01 0.00 4.26
31 32 0.525761 TTCATGCCGGCAGTTTTAGC 59.474 50.000 35.36 0.64 0.00 3.09
32 33 1.133025 CCTTCATGCCGGCAGTTTTAG 59.867 52.381 35.36 23.74 0.00 1.85
33 34 1.173043 CCTTCATGCCGGCAGTTTTA 58.827 50.000 35.36 16.30 0.00 1.52
34 35 1.966762 CCTTCATGCCGGCAGTTTT 59.033 52.632 35.36 15.81 0.00 2.43
36 37 3.064324 GCCTTCATGCCGGCAGTT 61.064 61.111 35.36 17.12 45.59 3.16
48 49 2.507324 GTCGCTCTCGTGGCCTTC 60.507 66.667 3.32 0.00 36.96 3.46
93 94 1.074395 CCCTCCTAGGAAGGGGTCC 60.074 68.421 27.02 0.00 42.59 4.46
94 95 4.730917 CCCTCCTAGGAAGGGGTC 57.269 66.667 27.02 0.00 42.59 4.46
98 99 2.448736 GGGCCCCTCCTAGGAAGG 60.449 72.222 18.55 18.55 45.21 3.46
99 100 2.844839 CGGGCCCCTCCTAGGAAG 60.845 72.222 18.66 6.68 37.67 3.46
118 119 4.680537 ACCTCCGGGAGACGCTGT 62.681 66.667 25.60 11.13 42.52 4.40
119 120 3.382832 AACCTCCGGGAGACGCTG 61.383 66.667 25.60 10.46 42.52 5.18
120 121 3.382832 CAACCTCCGGGAGACGCT 61.383 66.667 25.60 3.62 42.52 5.07
121 122 4.452733 CCAACCTCCGGGAGACGC 62.453 72.222 25.60 0.00 42.52 5.19
122 123 4.452733 GCCAACCTCCGGGAGACG 62.453 72.222 25.60 11.94 43.80 4.18
123 124 4.097361 GGCCAACCTCCGGGAGAC 62.097 72.222 25.60 8.72 36.25 3.36
124 125 4.649705 TGGCCAACCTCCGGGAGA 62.650 66.667 25.60 0.00 36.63 3.71
125 126 4.101448 CTGGCCAACCTCCGGGAG 62.101 72.222 17.41 17.41 36.63 4.30
129 130 2.597217 TTTGCTGGCCAACCTCCG 60.597 61.111 7.01 0.00 36.63 4.63
130 131 2.278330 CCTTTGCTGGCCAACCTCC 61.278 63.158 7.01 0.00 36.63 4.30
132 133 2.919328 GCCTTTGCTGGCCAACCT 60.919 61.111 7.01 0.00 46.82 3.50
140 141 2.890371 GATGCTGGGCCTTTGCTG 59.110 61.111 4.53 0.00 37.74 4.41
141 142 2.753043 CGATGCTGGGCCTTTGCT 60.753 61.111 4.53 0.00 37.74 3.91
145 146 2.045926 GTGTCGATGCTGGGCCTT 60.046 61.111 4.53 0.00 0.00 4.35
149 150 2.887568 GAGCGTGTCGATGCTGGG 60.888 66.667 13.49 0.00 44.95 4.45
150 151 2.163390 CAGAGCGTGTCGATGCTGG 61.163 63.158 13.49 3.59 44.95 4.85
153 154 0.803768 ATGTCAGAGCGTGTCGATGC 60.804 55.000 0.00 0.00 0.00 3.91
154 155 0.919300 CATGTCAGAGCGTGTCGATG 59.081 55.000 0.00 0.00 0.00 3.84
155 156 0.811281 TCATGTCAGAGCGTGTCGAT 59.189 50.000 0.00 0.00 0.00 3.59
158 159 2.191802 CAGATCATGTCAGAGCGTGTC 58.808 52.381 0.00 0.00 0.00 3.67
159 160 1.547820 ACAGATCATGTCAGAGCGTGT 59.452 47.619 0.00 0.00 37.75 4.49
160 161 2.290531 ACAGATCATGTCAGAGCGTG 57.709 50.000 0.00 0.00 37.75 5.34
169 170 6.535963 TCAGTTGACTATGACAGATCATGT 57.464 37.500 0.00 0.00 45.54 3.21
172 173 5.481824 AGGTTCAGTTGACTATGACAGATCA 59.518 40.000 0.00 0.00 39.83 2.92
173 174 5.971763 AGGTTCAGTTGACTATGACAGATC 58.028 41.667 0.00 0.00 0.00 2.75
174 175 6.365970 AAGGTTCAGTTGACTATGACAGAT 57.634 37.500 0.00 0.00 0.00 2.90
176 177 7.155328 AGTTAAGGTTCAGTTGACTATGACAG 58.845 38.462 0.00 0.00 0.00 3.51
178 179 7.964604 AAGTTAAGGTTCAGTTGACTATGAC 57.035 36.000 0.00 0.00 0.00 3.06
179 180 8.092687 GGTAAGTTAAGGTTCAGTTGACTATGA 58.907 37.037 0.00 0.00 0.00 2.15
181 182 7.237055 AGGGTAAGTTAAGGTTCAGTTGACTAT 59.763 37.037 0.00 0.00 0.00 2.12
182 183 6.556116 AGGGTAAGTTAAGGTTCAGTTGACTA 59.444 38.462 0.00 0.00 0.00 2.59
183 184 5.368816 AGGGTAAGTTAAGGTTCAGTTGACT 59.631 40.000 0.00 0.00 0.00 3.41
184 185 5.618236 AGGGTAAGTTAAGGTTCAGTTGAC 58.382 41.667 0.00 0.00 0.00 3.18
185 186 5.899631 AGGGTAAGTTAAGGTTCAGTTGA 57.100 39.130 0.00 0.00 0.00 3.18
186 187 6.649557 CAGTAGGGTAAGTTAAGGTTCAGTTG 59.350 42.308 0.00 0.00 0.00 3.16
188 189 5.247792 CCAGTAGGGTAAGTTAAGGTTCAGT 59.752 44.000 0.00 0.00 0.00 3.41
189 190 5.482878 TCCAGTAGGGTAAGTTAAGGTTCAG 59.517 44.000 0.00 0.00 38.11 3.02
190 191 5.405279 TCCAGTAGGGTAAGTTAAGGTTCA 58.595 41.667 0.00 0.00 38.11 3.18
191 192 6.212187 TCTTCCAGTAGGGTAAGTTAAGGTTC 59.788 42.308 0.00 0.00 38.11 3.62
192 193 6.086775 TCTTCCAGTAGGGTAAGTTAAGGTT 58.913 40.000 0.00 0.00 38.11 3.50
193 194 5.658474 TCTTCCAGTAGGGTAAGTTAAGGT 58.342 41.667 0.00 0.00 38.11 3.50
195 196 7.093465 TGTCATCTTCCAGTAGGGTAAGTTAAG 60.093 40.741 0.00 0.00 38.11 1.85
196 197 6.727231 TGTCATCTTCCAGTAGGGTAAGTTAA 59.273 38.462 0.00 0.00 38.11 2.01
198 199 5.091552 TGTCATCTTCCAGTAGGGTAAGTT 58.908 41.667 0.00 0.00 38.11 2.66
199 200 4.684724 TGTCATCTTCCAGTAGGGTAAGT 58.315 43.478 0.00 0.00 38.11 2.24
200 201 5.508153 CGATGTCATCTTCCAGTAGGGTAAG 60.508 48.000 11.04 0.00 38.11 2.34
203 204 2.695666 CGATGTCATCTTCCAGTAGGGT 59.304 50.000 11.04 0.00 38.11 4.34
204 205 2.036475 CCGATGTCATCTTCCAGTAGGG 59.964 54.545 11.04 0.00 34.83 3.53
205 206 2.959030 TCCGATGTCATCTTCCAGTAGG 59.041 50.000 11.04 2.53 0.00 3.18
208 209 1.759445 CCTCCGATGTCATCTTCCAGT 59.241 52.381 11.04 0.00 0.00 4.00
209 210 1.539929 GCCTCCGATGTCATCTTCCAG 60.540 57.143 11.04 1.72 0.00 3.86
210 211 0.465705 GCCTCCGATGTCATCTTCCA 59.534 55.000 11.04 0.00 0.00 3.53
211 212 0.465705 TGCCTCCGATGTCATCTTCC 59.534 55.000 11.04 0.00 0.00 3.46
212 213 1.576356 GTGCCTCCGATGTCATCTTC 58.424 55.000 11.04 0.00 0.00 2.87
213 214 0.179000 GGTGCCTCCGATGTCATCTT 59.821 55.000 11.04 0.00 0.00 2.40
214 215 1.826024 GGTGCCTCCGATGTCATCT 59.174 57.895 11.04 0.00 0.00 2.90
215 216 4.445699 GGTGCCTCCGATGTCATC 57.554 61.111 2.43 2.43 0.00 2.92
224 225 1.005867 TTCGTGTTACGGTGCCTCC 60.006 57.895 1.24 0.00 42.81 4.30
226 227 1.005394 CCTTCGTGTTACGGTGCCT 60.005 57.895 1.24 0.00 42.81 4.75
227 228 2.674084 GCCTTCGTGTTACGGTGCC 61.674 63.158 1.24 0.00 42.81 5.01
228 229 1.957186 TGCCTTCGTGTTACGGTGC 60.957 57.895 1.24 3.23 42.81 5.01
230 231 1.301165 GGTGCCTTCGTGTTACGGT 60.301 57.895 1.24 0.00 42.81 4.83
231 232 2.377310 CGGTGCCTTCGTGTTACGG 61.377 63.158 1.24 0.00 42.81 4.02
232 233 0.940519 TTCGGTGCCTTCGTGTTACG 60.941 55.000 0.00 0.00 44.19 3.18
234 235 0.320073 CCTTCGGTGCCTTCGTGTTA 60.320 55.000 0.00 0.00 0.00 2.41
235 236 1.597027 CCTTCGGTGCCTTCGTGTT 60.597 57.895 0.00 0.00 0.00 3.32
236 237 2.030562 CCTTCGGTGCCTTCGTGT 59.969 61.111 0.00 0.00 0.00 4.49
237 238 2.742372 CCCTTCGGTGCCTTCGTG 60.742 66.667 0.00 0.00 0.00 4.35
238 239 2.920912 TCCCTTCGGTGCCTTCGT 60.921 61.111 0.00 0.00 0.00 3.85
239 240 2.125512 CTCCCTTCGGTGCCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
241 242 4.035102 GCCTCCCTTCGGTGCCTT 62.035 66.667 0.00 0.00 0.00 4.35
244 245 3.645268 ATTGGCCTCCCTTCGGTGC 62.645 63.158 3.32 0.00 0.00 5.01
245 246 1.750399 CATTGGCCTCCCTTCGGTG 60.750 63.158 3.32 0.00 0.00 4.94
246 247 2.198304 GACATTGGCCTCCCTTCGGT 62.198 60.000 3.32 0.00 0.00 4.69
248 249 1.452108 GGACATTGGCCTCCCTTCG 60.452 63.158 3.32 0.00 0.00 3.79
293 1406 4.564769 CAGCCGAGAAAGATGAAGACTAAC 59.435 45.833 0.00 0.00 0.00 2.34
326 1442 3.992406 GAGGATGATGGCCCCTCA 58.008 61.111 17.46 12.84 44.42 3.86
405 1521 3.204158 TGTTATGGGGATAAGGTGCATGT 59.796 43.478 0.00 0.00 0.00 3.21
437 2326 5.648092 AGGATCTAATTCCAGGTTCAAAACG 59.352 40.000 0.00 0.00 38.32 3.60
439 2328 5.880332 CGAGGATCTAATTCCAGGTTCAAAA 59.120 40.000 0.00 0.00 38.32 2.44
495 2404 0.522626 TGCTCGTGGATTGCAATGTG 59.477 50.000 18.59 4.49 33.48 3.21
499 2408 2.279741 GATAGTGCTCGTGGATTGCAA 58.720 47.619 0.00 0.00 38.50 4.08
606 2541 1.916181 CCTGTACCACCATCTCCCTTT 59.084 52.381 0.00 0.00 0.00 3.11
612 2547 1.562672 GGCACCCTGTACCACCATCT 61.563 60.000 0.00 0.00 0.00 2.90
616 2551 4.404098 CCGGCACCCTGTACCACC 62.404 72.222 0.00 0.00 0.00 4.61
618 2553 4.642488 TCCCGGCACCCTGTACCA 62.642 66.667 0.00 0.00 0.00 3.25
631 2566 1.671054 AGTTTGCCATGTCGTCCCG 60.671 57.895 0.00 0.00 0.00 5.14
632 2567 1.875963 CAGTTTGCCATGTCGTCCC 59.124 57.895 0.00 0.00 0.00 4.46
633 2568 1.210155 GCAGTTTGCCATGTCGTCC 59.790 57.895 0.00 0.00 37.42 4.79
634 2569 4.847255 GCAGTTTGCCATGTCGTC 57.153 55.556 0.00 0.00 37.42 4.20
643 2578 0.675633 AAGTGGTGATGGCAGTTTGC 59.324 50.000 0.00 0.00 44.08 3.68
673 2642 1.939769 GACCACGCTCTCCCACTCTC 61.940 65.000 0.00 0.00 0.00 3.20
674 2643 1.979693 GACCACGCTCTCCCACTCT 60.980 63.158 0.00 0.00 0.00 3.24
675 2644 2.276116 TGACCACGCTCTCCCACTC 61.276 63.158 0.00 0.00 0.00 3.51
676 2645 2.203640 TGACCACGCTCTCCCACT 60.204 61.111 0.00 0.00 0.00 4.00
677 2646 2.048127 GTGACCACGCTCTCCCAC 60.048 66.667 0.00 0.00 0.00 4.61
678 2647 2.523168 TGTGACCACGCTCTCCCA 60.523 61.111 0.00 0.00 0.00 4.37
679 2648 2.262915 CTGTGACCACGCTCTCCC 59.737 66.667 0.00 0.00 0.00 4.30
680 2649 2.433318 GCTGTGACCACGCTCTCC 60.433 66.667 8.80 0.00 0.00 3.71
681 2650 1.735920 CTGCTGTGACCACGCTCTC 60.736 63.158 14.34 0.00 33.98 3.20
682 2651 2.341543 CTGCTGTGACCACGCTCT 59.658 61.111 14.34 0.00 33.98 4.09
683 2652 2.029666 ACTGCTGTGACCACGCTC 59.970 61.111 14.34 0.88 33.98 5.03
684 2653 2.280389 CACTGCTGTGACCACGCT 60.280 61.111 18.08 0.00 46.55 5.07
685 2654 1.714899 AAACACTGCTGTGACCACGC 61.715 55.000 27.99 9.03 46.55 5.34
812 2832 1.237285 CCCTTTTGGTGCTCCTCACG 61.237 60.000 6.34 0.00 46.56 4.35
851 2876 6.040842 CCTTTTCTTCCTTGTTGAGATCCAAA 59.959 38.462 0.00 0.00 36.36 3.28
852 2877 5.536161 CCTTTTCTTCCTTGTTGAGATCCAA 59.464 40.000 0.00 0.00 0.00 3.53
854 2879 4.082517 GCCTTTTCTTCCTTGTTGAGATCC 60.083 45.833 0.00 0.00 0.00 3.36
859 2884 1.953686 CGGCCTTTTCTTCCTTGTTGA 59.046 47.619 0.00 0.00 0.00 3.18
863 2922 1.537202 CTGTCGGCCTTTTCTTCCTTG 59.463 52.381 0.00 0.00 0.00 3.61
871 2930 0.895530 TCGATCTCTGTCGGCCTTTT 59.104 50.000 0.00 0.00 41.74 2.27
883 2942 4.792702 CAGTATGCATCTCGAATCGATCTC 59.207 45.833 5.59 0.00 34.61 2.75
884 2943 4.217334 ACAGTATGCATCTCGAATCGATCT 59.783 41.667 5.59 0.00 42.53 2.75
898 2957 2.289010 CCTGTGTCTGTGACAGTATGCA 60.289 50.000 12.93 7.03 43.57 3.96
963 3056 3.198635 TGGAGATGGAGAACAGATTGGAC 59.801 47.826 0.00 0.00 0.00 4.02
1001 3094 3.005554 ACCACAGCAGATTCGATTTGAG 58.994 45.455 0.00 0.00 0.00 3.02
1175 3295 0.032117 TCGGTGAGTCCCTGGATGAT 60.032 55.000 0.00 0.00 0.00 2.45
1251 3371 0.034337 TCTTGGGCAACGTACCTGAC 59.966 55.000 7.42 0.00 37.60 3.51
1446 3604 1.492993 GGGCAAGAGGACTGAACCCT 61.493 60.000 0.00 0.00 36.57 4.34
1496 3654 8.655935 ATTCTCAATAAAAGGGAATGAACAGT 57.344 30.769 0.00 0.00 0.00 3.55
1565 4544 4.149396 CGGTCGGTTACAACAAGTTAGAAG 59.851 45.833 0.00 0.00 0.00 2.85
1575 4554 1.569708 TGTGTTCGGTCGGTTACAAC 58.430 50.000 0.00 0.00 0.00 3.32
1651 4632 2.115291 GGCCACAATCCGAAGAGGC 61.115 63.158 0.00 0.00 40.77 4.70
1663 4644 3.177884 AAGCTGGACCAGGCCACA 61.178 61.111 23.09 0.00 33.52 4.17
1865 4931 7.436080 GGTCATGCATGTAAAATAGAATGGTTG 59.564 37.037 25.43 0.00 0.00 3.77
1989 5060 8.983789 TGTTTTATAAAAAGTTCCCCTGTTTCT 58.016 29.630 12.14 0.00 32.66 2.52
2012 7171 9.502091 TCTGAAACAATGCTACTATTACTTGTT 57.498 29.630 0.00 0.00 38.17 2.83
2035 7194 5.130292 ACAAGGATGCAAAGTGATTTCTG 57.870 39.130 0.00 0.00 0.00 3.02
2690 8084 5.609533 AATACACCGGCTTAGTAATCAGT 57.390 39.130 0.00 0.00 0.00 3.41
2691 8086 6.920569 AAAATACACCGGCTTAGTAATCAG 57.079 37.500 0.00 0.00 0.00 2.90
2692 8087 6.480981 GCTAAAATACACCGGCTTAGTAATCA 59.519 38.462 0.00 0.00 0.00 2.57
2732 8131 0.679960 AACCGCCTGCCAGGAATTAC 60.680 55.000 16.85 0.00 37.67 1.89
2746 8145 1.235724 AAAAGCCAGACTGTAACCGC 58.764 50.000 0.93 0.00 0.00 5.68
2885 8296 0.398318 ACCACAGTTCAGAAGGCTCC 59.602 55.000 0.00 0.00 0.00 4.70
3054 8482 6.246420 AGCACAATTCTTAAGCACTACTTG 57.754 37.500 0.00 0.00 39.58 3.16
3128 8590 4.413087 GCATATAAGATGCATGCTGAAGC 58.587 43.478 20.33 0.71 44.00 3.86
3315 9034 6.808212 GTGATTTTACAGTCATTTGGTCATGG 59.192 38.462 0.00 0.00 0.00 3.66
3316 9035 6.808212 GGTGATTTTACAGTCATTTGGTCATG 59.192 38.462 0.00 0.00 0.00 3.07
3438 9160 3.605486 GCTTTTCAGCGCTCACTTTAATG 59.395 43.478 7.13 0.00 35.91 1.90
3494 9267 6.803807 GCAGACTTATTTGATGAAAGTTGGAC 59.196 38.462 0.00 0.00 33.72 4.02
3515 9289 9.778741 CTCCAACATTAGTATTTATTAGGCAGA 57.221 33.333 0.00 0.00 0.00 4.26
3604 9424 5.254901 TCCTTACTCCGGCTCTCTATAATC 58.745 45.833 0.00 0.00 0.00 1.75
3772 9608 8.579006 TCAATTCAGCACAGAAATGTTTATTCT 58.421 29.630 0.00 0.00 37.62 2.40
3804 9640 2.269940 AGAGGGCCTGCTCTTTTCTTA 58.730 47.619 12.95 0.00 0.00 2.10
3850 9686 1.538047 AATCATGTGTGCGCCTTTCT 58.462 45.000 4.18 0.00 0.00 2.52
3990 9943 3.030291 GCCCCAATTATGACATCCAACA 58.970 45.455 0.00 0.00 0.00 3.33
3991 9944 3.299503 AGCCCCAATTATGACATCCAAC 58.700 45.455 0.00 0.00 0.00 3.77
4062 10047 5.694006 AGTTGTCATCAAGTTCTTTCTCGAG 59.306 40.000 5.93 5.93 33.97 4.04
4135 10153 7.430102 TGAGCTACTCATGTATGGATGTCCAT 61.430 42.308 17.91 17.91 45.83 3.41
4144 10162 4.202295 ACCATGGTGAGCTACTCATGTATG 60.202 45.833 18.99 6.24 42.73 2.39
4148 10166 2.484417 GGACCATGGTGAGCTACTCATG 60.484 54.545 25.52 12.86 42.73 3.07
4175 10195 4.380791 ACTAGGATGGGTTTAATGGGTCT 58.619 43.478 0.00 0.00 0.00 3.85
4225 10254 9.095065 GATTGGAAATGAAATCTCAAGGAAATG 57.905 33.333 0.00 0.00 34.49 2.32
4235 10264 8.319146 AGAAATTGCAGATTGGAAATGAAATCT 58.681 29.630 0.00 0.00 42.51 2.40
4307 10336 3.350219 TCTGCACTGTTATTCTTCCCC 57.650 47.619 0.00 0.00 0.00 4.81
4349 10381 7.136822 TGACTACATGGTAAGATAATTGGCT 57.863 36.000 0.00 0.00 0.00 4.75
4375 10409 3.188460 TCACTCTGCGCTTTCCATTTTAC 59.812 43.478 9.73 0.00 0.00 2.01
4381 10415 0.321346 TCATCACTCTGCGCTTTCCA 59.679 50.000 9.73 0.00 0.00 3.53
4574 10645 3.673746 TGTGTGACTTTTGAGCTTTCG 57.326 42.857 0.00 0.00 0.00 3.46
4590 10661 3.118738 GGTTCGTATCCATCCTCTTGTGT 60.119 47.826 0.00 0.00 0.00 3.72
4607 10678 0.108138 GGTGACCTCATCAGGGTTCG 60.108 60.000 0.00 0.00 45.53 3.95
4635 10706 0.251742 CTCCTTGATTTGGTGGGCCA 60.252 55.000 0.00 0.00 44.38 5.36
4636 10707 0.972471 CCTCCTTGATTTGGTGGGCC 60.972 60.000 0.00 0.00 35.29 5.80
4658 10729 2.467826 GCAGCCAGCTTGTCGGATC 61.468 63.158 0.00 0.00 41.15 3.36
5061 11145 2.212466 GTGTGCGCGTTCTTTGTTTTAC 59.788 45.455 8.43 0.00 0.00 2.01
5083 11168 4.090761 TCTGCAAGAAATCTTCTGGTGT 57.909 40.909 0.00 0.00 42.31 4.16
5103 11188 3.811722 TGAAGATGCGTGAACACAATC 57.188 42.857 5.80 7.42 0.00 2.67
5110 11202 5.877564 TGTACCATAAATGAAGATGCGTGAA 59.122 36.000 0.00 0.00 0.00 3.18
5159 11252 9.974980 CAACCTTTGGTGTTTAATTTATGTACT 57.025 29.630 0.00 0.00 35.34 2.73
5200 11293 4.574828 GGTCATAAGGTCAACGCAACATAT 59.425 41.667 0.00 0.00 0.00 1.78
5209 11306 6.377327 CCATGTATTGGTCATAAGGTCAAC 57.623 41.667 0.00 0.00 40.99 3.18
5244 11341 0.109086 CGAGCGACCATGACTTGTCT 60.109 55.000 0.00 0.00 0.00 3.41
5262 11360 1.153549 GTCTCAACAGCCTAGCCCG 60.154 63.158 0.00 0.00 0.00 6.13
5283 11382 1.764571 AACTGCACCTAGCCCACGAA 61.765 55.000 0.00 0.00 44.83 3.85
5359 11458 3.290948 TTCACCCTGTTTGTAGCAAGT 57.709 42.857 0.00 0.00 0.00 3.16
5400 11499 2.767394 TGGTTGTGGCGTATACTATGGT 59.233 45.455 0.56 0.00 0.00 3.55
5420 11519 0.537188 ACCAGCCGAGTCATTAGGTG 59.463 55.000 0.00 0.00 0.00 4.00
5426 11525 0.904649 TCATTCACCAGCCGAGTCAT 59.095 50.000 0.00 0.00 0.00 3.06
5437 11536 2.636830 CTCATCACTGGGTCATTCACC 58.363 52.381 0.00 0.00 45.97 4.02
5439 11538 1.065199 GCCTCATCACTGGGTCATTCA 60.065 52.381 0.00 0.00 0.00 2.57
5440 11539 1.065199 TGCCTCATCACTGGGTCATTC 60.065 52.381 0.00 0.00 0.00 2.67
5465 11591 3.438216 TTCATTTCACTCAGGCCATCA 57.562 42.857 5.01 0.00 0.00 3.07
5470 11609 3.316308 ACACACTTTCATTTCACTCAGGC 59.684 43.478 0.00 0.00 0.00 4.85
5475 11614 7.450074 TCACCTATACACACTTTCATTTCACT 58.550 34.615 0.00 0.00 0.00 3.41
5500 11639 4.277174 TCAAAGTAACACATGCACCGAATT 59.723 37.500 0.00 0.00 0.00 2.17
5524 11663 3.558746 CCATCAGCTCAAACAACTCCTCT 60.559 47.826 0.00 0.00 0.00 3.69
5531 11670 1.171549 TGCGCCATCAGCTCAAACAA 61.172 50.000 4.18 0.00 40.39 2.83
5532 11671 1.600356 TGCGCCATCAGCTCAAACA 60.600 52.632 4.18 0.00 40.39 2.83
5534 11673 1.579964 CTGTGCGCCATCAGCTCAAA 61.580 55.000 4.18 0.00 38.09 2.69
5614 11753 2.924290 GTGGTTCTACAGATCAGCGTTC 59.076 50.000 0.00 0.00 0.00 3.95
5630 11769 2.684881 GGATGCATTCTTCATCGTGGTT 59.315 45.455 0.00 0.00 40.80 3.67
5697 11836 1.532604 TTGTCGAGATCCACAGCCGT 61.533 55.000 0.00 0.00 0.00 5.68
5718 11857 1.471287 CTACGGTTCACAGACGGATCA 59.529 52.381 0.00 0.00 0.00 2.92
5727 11866 3.128349 GTTCTTCAAGCTACGGTTCACA 58.872 45.455 0.00 0.00 0.00 3.58
5734 11873 0.362512 GACGCGTTCTTCAAGCTACG 59.637 55.000 15.53 7.34 37.09 3.51
5743 11882 4.430765 ATCGGCCGACGCGTTCTT 62.431 61.111 33.75 9.32 43.86 2.52
5744 11883 4.849329 GATCGGCCGACGCGTTCT 62.849 66.667 33.75 13.48 43.86 3.01
5763 11926 1.841663 GCGCGACAAACCACATGACT 61.842 55.000 12.10 0.00 0.00 3.41
5783 11946 3.986277 GAGGTGTACTTCCTCGACAAAA 58.014 45.455 17.23 0.00 41.36 2.44
5784 11947 3.655276 GAGGTGTACTTCCTCGACAAA 57.345 47.619 17.23 0.00 41.36 2.83
5851 12014 1.202879 TGGCCACGTTTTCCTCAATCT 60.203 47.619 0.00 0.00 0.00 2.40
5852 12015 1.068541 GTGGCCACGTTTTCCTCAATC 60.069 52.381 22.49 0.00 0.00 2.67
5896 12059 2.094659 CAGTCGAAACCGCGAGCAT 61.095 57.895 8.23 0.00 41.49 3.79


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

AutoCloner maintained by Alex Coulton.