Multiple sequence alignment - TraesCS2D01G305500

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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 TraesCS2D01G305500 chr2D 100.000 8542 0 0 1 8542 391281407 391272866 0.000000e+00 15775
1 TraesCS2D01G305500 chr2D 97.170 106 3 0 8424 8529 394299066 394299171 6.810000e-41 180
2 TraesCS2D01G305500 chr2D 96.226 106 4 0 8424 8529 227201155 227201260 3.170000e-39 174
3 TraesCS2D01G305500 chr2D 96.226 106 4 0 8424 8529 466862164 466862059 3.170000e-39 174
4 TraesCS2D01G305500 chr2D 96.226 106 4 0 8424 8529 488634055 488633950 3.170000e-39 174
5 TraesCS2D01G305500 chr2B 97.296 3883 79 13 2794 6673 462893070 462889211 0.000000e+00 6565
6 TraesCS2D01G305500 chr2B 95.462 1785 60 13 6656 8431 462888195 462886423 0.000000e+00 2828
7 TraesCS2D01G305500 chr2B 96.670 991 26 5 980 1965 462895157 462894169 0.000000e+00 1640
8 TraesCS2D01G305500 chr2B 96.882 834 24 2 1966 2799 462894042 462893211 0.000000e+00 1395
9 TraesCS2D01G305500 chr2B 86.404 456 25 10 369 811 462895877 462895446 1.680000e-126 464
10 TraesCS2D01G305500 chr2B 83.660 306 48 2 1 305 462896341 462896037 3.900000e-73 287
11 TraesCS2D01G305500 chr2B 91.525 118 8 2 8412 8529 770333796 770333911 2.470000e-35 161
12 TraesCS2D01G305500 chr2A 94.156 3097 107 24 515 3568 527922132 527919067 0.000000e+00 4649
13 TraesCS2D01G305500 chr2A 97.066 2147 35 12 3911 6051 527919060 527916936 0.000000e+00 3591
14 TraesCS2D01G305500 chr2A 96.528 1325 32 6 6825 8144 527913240 527911925 0.000000e+00 2180
15 TraesCS2D01G305500 chr2A 96.114 669 18 4 6046 6713 527914359 527913698 0.000000e+00 1085
16 TraesCS2D01G305500 chr2A 92.333 300 20 1 8127 8426 527904293 527903997 2.850000e-114 424
17 TraesCS2D01G305500 chr2A 93.413 167 7 2 352 514 527922640 527922474 2.380000e-60 244
18 TraesCS2D01G305500 chr2A 98.374 123 1 1 6693 6814 527913515 527913393 1.870000e-51 215
19 TraesCS2D01G305500 chr2A 97.458 118 1 1 1 118 527924768 527924653 5.230000e-47 200
20 TraesCS2D01G305500 chr2A 95.413 109 5 0 8421 8529 530256349 530256457 3.170000e-39 174
21 TraesCS2D01G305500 chr4D 97.087 103 3 0 8427 8529 250267931 250268033 3.170000e-39 174
22 TraesCS2D01G305500 chr7B 90.698 129 12 0 6486 6614 533773486 533773358 1.140000e-38 172
23 TraesCS2D01G305500 chr5A 95.283 106 5 0 8424 8529 367376390 367376495 1.470000e-37 169
24 TraesCS2D01G305500 chr5A 89.565 115 12 0 6501 6615 417902713 417902827 6.910000e-31 147
25 TraesCS2D01G305500 chr1B 93.043 115 6 2 8416 8529 372934745 372934632 5.300000e-37 167
26 TraesCS2D01G305500 chr7A 88.372 129 15 0 6486 6614 573430961 573430833 1.150000e-33 156
27 TraesCS2D01G305500 chrUn 88.189 127 15 0 6488 6614 24221055 24221181 1.490000e-32 152
28 TraesCS2D01G305500 chr4A 87.786 131 14 2 6484 6613 564893776 564893647 1.490000e-32 152
29 TraesCS2D01G305500 chr3B 88.983 118 12 1 6498 6615 433271464 433271348 2.490000e-30 145
30 TraesCS2D01G305500 chr3A 85.385 130 19 0 6485 6614 12747903 12748032 1.500000e-27 135


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 TraesCS2D01G305500 chr2D 391272866 391281407 8541 True 15775.000000 15775 100.000000 1 8542 1 chr2D.!!$R1 8541
1 TraesCS2D01G305500 chr2B 462886423 462896341 9918 True 2196.500000 6565 92.729000 1 8431 6 chr2B.!!$R1 8430
2 TraesCS2D01G305500 chr2A 527911925 527924768 12843 True 1737.714286 4649 96.158429 1 8144 7 chr2A.!!$R2 8143

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
367 2162 0.106335 TAAAACTCGCGGTTGGGTGA 59.894 50.000 6.13 0.0 38.29 4.02 F
761 2950 0.969894 ACTCGCAGGCAGTAACTTCT 59.030 50.000 0.00 0.0 0.00 2.85 F
2547 5003 0.533531 CACTGCTTGCTCACAGTCCA 60.534 55.000 3.54 0.0 45.15 4.02 F
2898 5500 2.170166 TGATTGAATGTCTTGGGGTGC 58.830 47.619 0.00 0.0 0.00 5.01 F
3581 6183 3.162666 TGAGAACAGAATCCACCTACGT 58.837 45.455 0.00 0.0 0.00 3.57 F
4841 7443 0.040646 TTCTGCTCCCTTCCCTACGA 59.959 55.000 0.00 0.0 0.00 3.43 F
5124 7731 0.595588 TTAGTTGTGTTGGCATGGCG 59.404 50.000 15.27 0.0 0.00 5.69 F
6190 11381 6.012658 TGAAAAATGCTAGACCATTGTGTC 57.987 37.500 0.00 0.0 35.70 3.67 F
7139 13709 4.578105 CCTCGAGGTACTTAAATACTCCGT 59.422 45.833 24.04 0.0 41.55 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 3809 0.393808 GAGTAAGCCGCAATTCCCCA 60.394 55.000 0.00 0.0 0.00 4.96 R
2713 5170 0.394565 AGCGCATCCCATACTTCTCC 59.605 55.000 11.47 0.0 0.00 3.71 R
3781 6383 2.816087 CCTGGTGAACCTTGTGAGAATG 59.184 50.000 0.37 0.0 36.82 2.67 R
4841 7443 0.608130 TGCTACGCACAGAGAATGGT 59.392 50.000 0.00 0.0 31.71 3.55 R
5124 7731 1.153958 GCCAGCGAATGCCAAAGTC 60.154 57.895 0.00 0.0 44.31 3.01 R
6649 11841 1.439543 AGTGACCCTCTCTTTGGCTT 58.560 50.000 0.00 0.0 0.00 4.35 R
6650 11842 1.439543 AAGTGACCCTCTCTTTGGCT 58.560 50.000 0.00 0.0 26.81 4.75 R
7384 13956 1.153168 CAGGGATCCGGCATTCGTT 60.153 57.895 5.45 0.0 37.11 3.85 R
8248 14827 0.388778 TGCAATGCAATGAAGCCGTG 60.389 50.000 5.01 0.0 34.76 4.94 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
114 115 7.281100 GCATTTATAGTGGTCTATATCCTTGCC 59.719 40.741 0.00 0.00 38.45 4.52
184 1770 5.369833 AGTACATACGCTCATAGACTCACT 58.630 41.667 0.00 0.00 0.00 3.41
200 1786 4.503910 ACTCACTCTTATAAATGCACGCA 58.496 39.130 0.00 0.00 0.00 5.24
202 1788 6.280643 ACTCACTCTTATAAATGCACGCATA 58.719 36.000 4.68 0.00 35.31 3.14
212 1798 2.522638 GCACGCATACGCACCCTAC 61.523 63.158 0.00 0.00 45.53 3.18
227 1813 1.213296 CCTACCCCTATGCACACCTT 58.787 55.000 0.00 0.00 0.00 3.50
229 1815 1.141053 CTACCCCTATGCACACCTTCC 59.859 57.143 0.00 0.00 0.00 3.46
234 1820 2.569059 CCTATGCACACCTTCCAGATG 58.431 52.381 0.00 0.00 0.00 2.90
239 1825 1.883638 GCACACCTTCCAGATGCTGAA 60.884 52.381 0.00 0.00 32.44 3.02
240 1826 2.507484 CACACCTTCCAGATGCTGAAA 58.493 47.619 0.00 0.00 32.44 2.69
269 1855 7.258441 CAGGTTATCTTGAGATTGACGAAGTA 58.742 38.462 0.00 0.00 37.04 2.24
285 1871 5.680619 ACGAAGTATCCATAAATGCCTTCA 58.319 37.500 0.00 0.00 41.94 3.02
288 1874 7.936847 ACGAAGTATCCATAAATGCCTTCATAA 59.063 33.333 0.00 0.00 41.94 1.90
295 1881 5.408299 CCATAAATGCCTTCATAATCGACGA 59.592 40.000 0.00 0.00 31.46 4.20
305 1891 6.255670 CCTTCATAATCGACGAAAATGTCTCA 59.744 38.462 17.35 2.01 36.71 3.27
307 1893 7.770801 TCATAATCGACGAAAATGTCTCATT 57.229 32.000 17.35 1.69 36.71 2.57
308 1894 7.841486 TCATAATCGACGAAAATGTCTCATTC 58.159 34.615 17.35 0.00 36.71 2.67
310 1896 3.920446 TCGACGAAAATGTCTCATTCCA 58.080 40.909 0.00 0.00 36.71 3.53
312 1898 3.181520 CGACGAAAATGTCTCATTCCACC 60.182 47.826 0.00 0.00 36.71 4.61
321 1911 0.652592 CTCATTCCACCGAACATCGC 59.347 55.000 0.00 0.00 38.82 4.58
355 2150 5.966742 AATTCAGGCCAAGTCTAAAACTC 57.033 39.130 5.01 0.00 37.17 3.01
367 2162 0.106335 TAAAACTCGCGGTTGGGTGA 59.894 50.000 6.13 0.00 38.29 4.02
430 2225 2.200092 TGCCCCACCAAACTTCCC 59.800 61.111 0.00 0.00 0.00 3.97
446 2241 4.445545 CCGCGAGCGCCAAAACTC 62.446 66.667 8.23 0.00 37.98 3.01
447 2242 4.445545 CGCGAGCGCCAAAACTCC 62.446 66.667 2.29 0.00 37.98 3.85
448 2243 3.353836 GCGAGCGCCAAAACTCCA 61.354 61.111 2.29 0.00 34.56 3.86
449 2244 2.556287 CGAGCGCCAAAACTCCAC 59.444 61.111 2.29 0.00 0.00 4.02
450 2245 2.250939 CGAGCGCCAAAACTCCACA 61.251 57.895 2.29 0.00 0.00 4.17
451 2246 1.282875 GAGCGCCAAAACTCCACAC 59.717 57.895 2.29 0.00 0.00 3.82
452 2247 2.130073 GAGCGCCAAAACTCCACACC 62.130 60.000 2.29 0.00 0.00 4.16
453 2248 2.485795 GCGCCAAAACTCCACACCA 61.486 57.895 0.00 0.00 0.00 4.17
454 2249 1.358759 CGCCAAAACTCCACACCAC 59.641 57.895 0.00 0.00 0.00 4.16
455 2250 1.739667 GCCAAAACTCCACACCACC 59.260 57.895 0.00 0.00 0.00 4.61
456 2251 2.029743 CCAAAACTCCACACCACCG 58.970 57.895 0.00 0.00 0.00 4.94
538 2696 2.125912 GCTCACGATCACGCACCT 60.126 61.111 0.00 0.00 43.96 4.00
539 2697 2.447887 GCTCACGATCACGCACCTG 61.448 63.158 0.00 0.00 43.96 4.00
540 2698 1.807165 CTCACGATCACGCACCTGG 60.807 63.158 0.00 0.00 43.96 4.45
541 2699 3.490759 CACGATCACGCACCTGGC 61.491 66.667 0.00 0.00 43.96 4.85
542 2700 3.695606 ACGATCACGCACCTGGCT 61.696 61.111 0.00 0.00 43.96 4.75
543 2701 2.887568 CGATCACGCACCTGGCTC 60.888 66.667 0.00 0.00 41.67 4.70
544 2702 2.887568 GATCACGCACCTGGCTCG 60.888 66.667 6.64 6.64 41.67 5.03
655 2829 1.956170 CACTGACAGCACGGACCAC 60.956 63.158 1.25 0.00 0.00 4.16
761 2950 0.969894 ACTCGCAGGCAGTAACTTCT 59.030 50.000 0.00 0.00 0.00 2.85
852 3046 3.440127 CACTCTTCTTTCTCCTCCTCCT 58.560 50.000 0.00 0.00 0.00 3.69
1244 3557 2.512974 CCCGGTGCCCGTGATTAC 60.513 66.667 11.85 0.00 46.80 1.89
1356 3669 2.098770 GGATCACCACGTGTCTAGGTAC 59.901 54.545 15.65 0.00 34.79 3.34
1386 3699 1.610624 CGCCCGATGGTTATGGCTTAT 60.611 52.381 0.00 0.00 41.80 1.73
1406 3719 2.270257 TGCGAATTTGCTGCAGCCT 61.270 52.632 34.64 17.34 41.18 4.58
1407 3720 1.804326 GCGAATTTGCTGCAGCCTG 60.804 57.895 34.64 18.27 41.18 4.85
1459 3772 1.670791 TTCACGTTTGGGGTGAAGTC 58.329 50.000 3.44 0.00 46.33 3.01
1461 3774 1.227734 ACGTTTGGGGTGAAGTCGG 60.228 57.895 0.00 0.00 0.00 4.79
1494 3809 4.648762 TGGGTGACACTGTGATTGAATTTT 59.351 37.500 15.86 0.00 0.00 1.82
1703 4019 3.944650 GCCACTTCATTTGTTTTTGGGTT 59.055 39.130 0.00 0.00 0.00 4.11
2037 4493 5.083533 TGTTGATGGTTCTTTGTTGCTTT 57.916 34.783 0.00 0.00 0.00 3.51
2470 4926 1.219213 ACCTCTACCTCCATCTCCCAG 59.781 57.143 0.00 0.00 0.00 4.45
2496 4952 3.251484 TGTTCACCTCTTCCTCCATCTT 58.749 45.455 0.00 0.00 0.00 2.40
2528 4984 0.676736 CGCCTCTTCCTACATCTCCC 59.323 60.000 0.00 0.00 0.00 4.30
2547 5003 0.533531 CACTGCTTGCTCACAGTCCA 60.534 55.000 3.54 0.00 45.15 4.02
2554 5010 2.636647 TGCTCACAGTCCAAATCACA 57.363 45.000 0.00 0.00 0.00 3.58
2625 5081 8.974060 TTACCTTGGATTTAACAGGTATCATC 57.026 34.615 0.00 0.00 32.75 2.92
2667 5124 6.201425 GCATCATTTGCGGTTTGATTATCATT 59.799 34.615 0.00 0.00 42.54 2.57
2689 5146 7.546316 TCATTTGGAACTCAATGCATTAATGTG 59.454 33.333 12.53 7.64 34.98 3.21
2716 5173 9.701098 TTATTATACGCTACAAAACCTATGGAG 57.299 33.333 0.00 0.00 0.00 3.86
2729 5186 3.584848 ACCTATGGAGAAGTATGGGATGC 59.415 47.826 0.00 0.00 0.00 3.91
2898 5500 2.170166 TGATTGAATGTCTTGGGGTGC 58.830 47.619 0.00 0.00 0.00 5.01
3092 5694 5.865085 ACTTACTTGTCTTTCTATGCACCA 58.135 37.500 0.00 0.00 0.00 4.17
3406 6008 5.658634 TCTCATGCACATAGAGGTAAAGTCT 59.341 40.000 0.00 0.00 0.00 3.24
3411 6013 5.360144 TGCACATAGAGGTAAAGTCTAGTCC 59.640 44.000 0.00 0.00 30.04 3.85
3529 6131 5.066375 TGCCTTGTCTCATAACACATATTGC 59.934 40.000 0.00 0.00 0.00 3.56
3581 6183 3.162666 TGAGAACAGAATCCACCTACGT 58.837 45.455 0.00 0.00 0.00 3.57
3625 6227 5.333568 GCGGTAATTAGGTTGCCTTTATACG 60.334 44.000 0.00 0.00 40.14 3.06
3678 6280 7.366513 TGAAACGATTTCATTCTGCATAAACA 58.633 30.769 8.47 0.00 44.21 2.83
3679 6281 7.538334 TGAAACGATTTCATTCTGCATAAACAG 59.462 33.333 8.47 0.00 44.21 3.16
3682 6284 8.039603 ACGATTTCATTCTGCATAAACAGTTA 57.960 30.769 0.00 0.00 38.84 2.24
3683 6285 8.511321 ACGATTTCATTCTGCATAAACAGTTAA 58.489 29.630 0.00 0.00 38.84 2.01
3684 6286 9.003112 CGATTTCATTCTGCATAAACAGTTAAG 57.997 33.333 0.00 0.00 38.84 1.85
3693 6295 9.764363 TCTGCATAAACAGTTAAGATATAGGTG 57.236 33.333 0.00 0.00 38.84 4.00
3694 6296 8.902540 TGCATAAACAGTTAAGATATAGGTGG 57.097 34.615 0.00 0.00 0.00 4.61
3695 6297 7.444183 TGCATAAACAGTTAAGATATAGGTGGC 59.556 37.037 0.00 0.00 0.00 5.01
3696 6298 7.444183 GCATAAACAGTTAAGATATAGGTGGCA 59.556 37.037 0.00 0.00 0.00 4.92
3697 6299 9.337396 CATAAACAGTTAAGATATAGGTGGCAA 57.663 33.333 0.00 0.00 0.00 4.52
3698 6300 7.865706 AAACAGTTAAGATATAGGTGGCAAG 57.134 36.000 0.00 0.00 0.00 4.01
3713 6315 5.307976 AGGTGGCAAGTCATAGCTTATATGA 59.692 40.000 0.00 0.00 0.00 2.15
3808 6410 3.636300 TCACAAGGTTCACCAGGATTTTG 59.364 43.478 0.00 0.00 38.89 2.44
3849 6451 7.822161 AGAAATGCTTGGCAATATATACACA 57.178 32.000 0.00 0.00 43.62 3.72
3850 6452 8.236585 AGAAATGCTTGGCAATATATACACAA 57.763 30.769 0.00 0.00 43.62 3.33
3851 6453 8.863086 AGAAATGCTTGGCAATATATACACAAT 58.137 29.630 0.00 0.00 43.62 2.71
3854 6456 7.822161 TGCTTGGCAATATATACACAATCTT 57.178 32.000 0.00 0.00 34.76 2.40
4298 6900 4.713553 TGGACATGCTTCTGTTTGACTTA 58.286 39.130 0.00 0.00 0.00 2.24
4354 6956 7.010460 GGCTTGCATATGTTTTACTCCATTTTC 59.990 37.037 4.29 0.00 0.00 2.29
4495 7097 6.892456 TGTACCTTCTCTTACAGACTGATGAT 59.108 38.462 10.08 0.00 0.00 2.45
4595 7197 5.086104 ACCTGTGATTCGCAGTTATACTT 57.914 39.130 22.21 0.00 39.99 2.24
4668 7270 8.082852 CCACAGGTAGTATACAGCTTGTATAAG 58.917 40.741 5.50 0.00 44.57 1.73
4841 7443 0.040646 TTCTGCTCCCTTCCCTACGA 59.959 55.000 0.00 0.00 0.00 3.43
5050 7656 1.340991 TGCTGGCAATTCTTCCCTACC 60.341 52.381 0.00 0.00 0.00 3.18
5070 7676 2.305343 CCCATGGCAATTTTTCCTTCCA 59.695 45.455 6.09 0.00 0.00 3.53
5124 7731 0.595588 TTAGTTGTGTTGGCATGGCG 59.404 50.000 15.27 0.00 0.00 5.69
5999 8608 7.604657 TTCCCAATAAGAAGATAGAGGACTC 57.395 40.000 0.00 0.00 0.00 3.36
6190 11381 6.012658 TGAAAAATGCTAGACCATTGTGTC 57.987 37.500 0.00 0.00 35.70 3.67
6557 11748 9.787435 TGGATGTATCTAACACTAAAACTTGTT 57.213 29.630 0.00 0.00 42.09 2.83
6968 13538 5.065914 TGCTCCATTTATGCTATCTGTTCC 58.934 41.667 0.00 0.00 0.00 3.62
7139 13709 4.578105 CCTCGAGGTACTTAAATACTCCGT 59.422 45.833 24.04 0.00 41.55 4.69
7140 13710 5.760253 CCTCGAGGTACTTAAATACTCCGTA 59.240 44.000 24.04 0.00 41.55 4.02
7141 13711 6.293135 CCTCGAGGTACTTAAATACTCCGTAC 60.293 46.154 24.04 0.00 41.55 3.67
7142 13712 6.349300 TCGAGGTACTTAAATACTCCGTACT 58.651 40.000 0.00 0.00 41.55 2.73
7143 13713 6.823689 TCGAGGTACTTAAATACTCCGTACTT 59.176 38.462 0.00 0.00 41.55 2.24
7144 13714 7.011482 TCGAGGTACTTAAATACTCCGTACTTC 59.989 40.741 0.00 0.00 41.55 3.01
7145 13715 7.201644 CGAGGTACTTAAATACTCCGTACTTCA 60.202 40.741 0.00 0.00 41.55 3.02
7384 13956 0.320050 TACGCACTGAATCAGGCACA 59.680 50.000 15.38 3.28 35.51 4.57
7430 14002 1.270826 GGCTCCTTGAAACTCCAAAGC 59.729 52.381 0.00 0.00 32.16 3.51
7472 14044 3.059120 GGTTCTAAGCGTCTTTTGTGGAC 60.059 47.826 0.00 0.00 0.00 4.02
7557 14129 2.010497 TGTAGCTTTGTGTTGCGACAA 58.990 42.857 8.77 0.00 40.65 3.18
7560 14132 0.179150 GCTTTGTGTTGCGACAACCA 60.179 50.000 8.77 0.17 37.57 3.67
7803 14377 6.695713 GGTACAACATTGGAGAAAAAGTGAAC 59.304 38.462 0.00 0.00 0.00 3.18
7833 14407 1.619827 CTGAAATGGTGTGGGTGCATT 59.380 47.619 0.00 0.00 0.00 3.56
7899 14474 7.421599 TGATGTTTAAATTCAAGTCGAAAGCA 58.578 30.769 0.00 0.00 37.12 3.91
7900 14475 8.081633 TGATGTTTAAATTCAAGTCGAAAGCAT 58.918 29.630 0.00 0.00 37.12 3.79
7948 14524 3.495001 CGGAGGACAGTTGTTTCTTTCTC 59.505 47.826 0.00 0.00 0.00 2.87
7956 14532 5.063564 ACAGTTGTTTCTTTCTCGACAGTTC 59.936 40.000 0.00 0.00 0.00 3.01
7994 14572 5.234972 CCTTGACCAAAGTTTCTTGCATTTC 59.765 40.000 0.00 0.00 33.66 2.17
8011 14589 4.328983 GCATTTCTCATTTGATGCAACCAG 59.671 41.667 0.00 0.00 43.23 4.00
8172 14751 9.046296 TGCACCGATAATTACAAATTTTGTTTT 57.954 25.926 19.15 14.96 42.22 2.43
8173 14752 9.523730 GCACCGATAATTACAAATTTTGTTTTC 57.476 29.630 19.15 6.49 42.22 2.29
8213 14792 1.352083 AGACAGGCTTGGCTTAGTGA 58.648 50.000 0.00 0.00 40.86 3.41
8224 14803 5.412904 GCTTGGCTTAGTGATGAAGTACTTT 59.587 40.000 10.02 0.00 0.00 2.66
8249 14828 2.575532 CAAGAGCTCCTTGGTTTGACA 58.424 47.619 10.93 0.00 46.54 3.58
8250 14829 2.262423 AGAGCTCCTTGGTTTGACAC 57.738 50.000 10.93 0.00 0.00 3.67
8269 14849 0.388778 CGGCTTCATTGCATTGCACA 60.389 50.000 11.66 3.45 38.71 4.57
8289 14869 1.559682 AGTGCATGTGTAGGGTAAGGG 59.440 52.381 0.00 0.00 0.00 3.95
8290 14870 0.254747 TGCATGTGTAGGGTAAGGGC 59.745 55.000 0.00 0.00 0.00 5.19
8316 14896 4.218852 CCTCGTATAATCCTTCCTCAGACC 59.781 50.000 0.00 0.00 0.00 3.85
8329 14909 2.363680 CCTCAGACCCAGCTAGTATGTG 59.636 54.545 9.70 7.78 0.00 3.21
8357 14937 1.355720 AGCACTGGTCTGCCCTTTTAT 59.644 47.619 0.00 0.00 37.96 1.40
8431 15011 9.915629 GAATTTTAGCTAGCTAGTATTAGAGCA 57.084 33.333 23.03 3.09 41.36 4.26
8433 15013 9.868277 ATTTTAGCTAGCTAGTATTAGAGCATG 57.132 33.333 23.03 0.00 41.36 4.06
8434 15014 5.913137 AGCTAGCTAGTATTAGAGCATGG 57.087 43.478 17.69 0.00 41.36 3.66
8435 15015 5.329399 AGCTAGCTAGTATTAGAGCATGGT 58.671 41.667 17.69 0.00 41.36 3.55
8436 15016 5.777732 AGCTAGCTAGTATTAGAGCATGGTT 59.222 40.000 17.69 0.00 41.36 3.67
8437 15017 6.948886 AGCTAGCTAGTATTAGAGCATGGTTA 59.051 38.462 17.69 0.00 41.36 2.85
8438 15018 7.451877 AGCTAGCTAGTATTAGAGCATGGTTAA 59.548 37.037 17.69 0.68 41.36 2.01
8439 15019 8.254508 GCTAGCTAGTATTAGAGCATGGTTAAT 58.745 37.037 21.62 7.97 41.36 1.40
8452 15032 8.986991 AGAGCATGGTTAATAATATAGCTAGCT 58.013 33.333 23.12 23.12 0.00 3.32
8453 15033 8.954950 AGCATGGTTAATAATATAGCTAGCTG 57.045 34.615 27.68 6.30 0.00 4.24
8454 15034 8.762645 AGCATGGTTAATAATATAGCTAGCTGA 58.237 33.333 27.68 15.23 0.00 4.26
8455 15035 9.553064 GCATGGTTAATAATATAGCTAGCTGAT 57.447 33.333 27.68 16.84 0.00 2.90
8458 15038 7.987458 TGGTTAATAATATAGCTAGCTGATGGC 59.013 37.037 27.68 6.64 42.19 4.40
8470 15050 2.417719 GCTGATGGCTATAAGGAACCG 58.582 52.381 0.00 0.00 38.06 4.44
8471 15051 2.417719 CTGATGGCTATAAGGAACCGC 58.582 52.381 0.00 0.00 0.00 5.68
8472 15052 1.071699 TGATGGCTATAAGGAACCGCC 59.928 52.381 0.00 0.00 41.06 6.13
8474 15054 1.136828 TGGCTATAAGGAACCGCCAT 58.863 50.000 5.53 0.00 45.08 4.40
8475 15055 1.202758 TGGCTATAAGGAACCGCCATG 60.203 52.381 5.53 0.00 45.08 3.66
8476 15056 1.202770 GGCTATAAGGAACCGCCATGT 60.203 52.381 0.00 0.00 40.41 3.21
8477 15057 2.143925 GCTATAAGGAACCGCCATGTC 58.856 52.381 0.00 0.00 40.02 3.06
8478 15058 2.484770 GCTATAAGGAACCGCCATGTCA 60.485 50.000 0.00 0.00 40.02 3.58
8479 15059 3.807209 GCTATAAGGAACCGCCATGTCAT 60.807 47.826 0.00 0.00 40.02 3.06
8480 15060 2.325583 TAAGGAACCGCCATGTCATC 57.674 50.000 0.00 0.00 40.02 2.92
8481 15061 0.620556 AAGGAACCGCCATGTCATCT 59.379 50.000 0.00 0.00 40.02 2.90
8482 15062 1.496060 AGGAACCGCCATGTCATCTA 58.504 50.000 0.00 0.00 40.02 1.98
8483 15063 2.050144 AGGAACCGCCATGTCATCTAT 58.950 47.619 0.00 0.00 40.02 1.98
8484 15064 3.239449 AGGAACCGCCATGTCATCTATA 58.761 45.455 0.00 0.00 40.02 1.31
8485 15065 3.259374 AGGAACCGCCATGTCATCTATAG 59.741 47.826 0.00 0.00 40.02 1.31
8486 15066 2.751166 ACCGCCATGTCATCTATAGC 57.249 50.000 0.00 0.00 0.00 2.97
8487 15067 1.276421 ACCGCCATGTCATCTATAGCC 59.724 52.381 0.00 0.00 0.00 3.93
8488 15068 1.276138 CCGCCATGTCATCTATAGCCA 59.724 52.381 0.00 0.00 0.00 4.75
8489 15069 2.093288 CCGCCATGTCATCTATAGCCAT 60.093 50.000 0.00 0.00 0.00 4.40
8490 15070 3.193263 CGCCATGTCATCTATAGCCATC 58.807 50.000 0.00 0.00 0.00 3.51
8491 15071 3.368739 CGCCATGTCATCTATAGCCATCA 60.369 47.826 0.00 0.00 0.00 3.07
8492 15072 4.682589 CGCCATGTCATCTATAGCCATCAT 60.683 45.833 0.00 0.00 0.00 2.45
8493 15073 4.815308 GCCATGTCATCTATAGCCATCATC 59.185 45.833 0.00 0.00 0.00 2.92
8494 15074 5.396548 GCCATGTCATCTATAGCCATCATCT 60.397 44.000 0.00 0.00 0.00 2.90
8495 15075 6.183360 GCCATGTCATCTATAGCCATCATCTA 60.183 42.308 0.00 0.00 0.00 1.98
8496 15076 7.208777 CCATGTCATCTATAGCCATCATCTAC 58.791 42.308 0.00 0.00 0.00 2.59
8497 15077 7.147776 CCATGTCATCTATAGCCATCATCTACA 60.148 40.741 0.00 0.00 0.00 2.74
8498 15078 7.968014 TGTCATCTATAGCCATCATCTACAT 57.032 36.000 0.00 0.00 0.00 2.29
8499 15079 7.779073 TGTCATCTATAGCCATCATCTACATG 58.221 38.462 0.00 0.00 0.00 3.21
8500 15080 6.700960 GTCATCTATAGCCATCATCTACATGC 59.299 42.308 0.00 0.00 0.00 4.06
8501 15081 6.381994 TCATCTATAGCCATCATCTACATGCA 59.618 38.462 0.00 0.00 0.00 3.96
8502 15082 5.970592 TCTATAGCCATCATCTACATGCAC 58.029 41.667 0.00 0.00 0.00 4.57
8503 15083 4.904895 ATAGCCATCATCTACATGCACT 57.095 40.909 0.00 0.00 0.00 4.40
8504 15084 3.123157 AGCCATCATCTACATGCACTC 57.877 47.619 0.00 0.00 0.00 3.51
8505 15085 2.436911 AGCCATCATCTACATGCACTCA 59.563 45.455 0.00 0.00 0.00 3.41
8506 15086 3.072622 AGCCATCATCTACATGCACTCAT 59.927 43.478 0.00 0.00 0.00 2.90
8507 15087 4.285260 AGCCATCATCTACATGCACTCATA 59.715 41.667 0.00 0.00 0.00 2.15
8508 15088 4.391216 GCCATCATCTACATGCACTCATAC 59.609 45.833 0.00 0.00 0.00 2.39
8509 15089 5.544650 CCATCATCTACATGCACTCATACA 58.455 41.667 0.00 0.00 0.00 2.29
8510 15090 5.993441 CCATCATCTACATGCACTCATACAA 59.007 40.000 0.00 0.00 0.00 2.41
8511 15091 6.653740 CCATCATCTACATGCACTCATACAAT 59.346 38.462 0.00 0.00 0.00 2.71
8512 15092 7.820872 CCATCATCTACATGCACTCATACAATA 59.179 37.037 0.00 0.00 0.00 1.90
8513 15093 9.211485 CATCATCTACATGCACTCATACAATAA 57.789 33.333 0.00 0.00 0.00 1.40
8514 15094 9.955102 ATCATCTACATGCACTCATACAATAAT 57.045 29.630 0.00 0.00 0.00 1.28
8515 15095 9.211485 TCATCTACATGCACTCATACAATAATG 57.789 33.333 0.00 0.00 0.00 1.90
8516 15096 8.996271 CATCTACATGCACTCATACAATAATGT 58.004 33.333 0.00 0.00 43.74 2.71
8517 15097 8.369218 TCTACATGCACTCATACAATAATGTG 57.631 34.615 0.00 0.00 40.84 3.21
8518 15098 6.381481 ACATGCACTCATACAATAATGTGG 57.619 37.500 0.00 0.00 40.84 4.17
8519 15099 5.300034 ACATGCACTCATACAATAATGTGGG 59.700 40.000 0.00 0.00 40.84 4.61
8520 15100 3.631686 TGCACTCATACAATAATGTGGGC 59.368 43.478 6.26 6.26 45.55 5.36
8521 15101 3.885297 GCACTCATACAATAATGTGGGCT 59.115 43.478 6.02 0.00 43.25 5.19
8522 15102 5.063204 GCACTCATACAATAATGTGGGCTA 58.937 41.667 6.02 0.00 43.25 3.93
8523 15103 5.707298 GCACTCATACAATAATGTGGGCTAT 59.293 40.000 6.02 0.00 43.25 2.97
8524 15104 6.878923 GCACTCATACAATAATGTGGGCTATA 59.121 38.462 6.02 0.00 43.25 1.31
8525 15105 7.390440 GCACTCATACAATAATGTGGGCTATAA 59.610 37.037 6.02 0.00 43.25 0.98
8526 15106 8.939929 CACTCATACAATAATGTGGGCTATAAG 58.060 37.037 0.00 0.00 40.84 1.73
8527 15107 8.103305 ACTCATACAATAATGTGGGCTATAAGG 58.897 37.037 0.00 0.00 40.84 2.69
8528 15108 7.984475 TCATACAATAATGTGGGCTATAAGGT 58.016 34.615 0.00 0.00 40.84 3.50
8529 15109 7.882791 TCATACAATAATGTGGGCTATAAGGTG 59.117 37.037 0.00 0.00 40.84 4.00
8530 15110 5.385198 ACAATAATGTGGGCTATAAGGTGG 58.615 41.667 0.00 0.00 38.69 4.61
8531 15111 5.133660 ACAATAATGTGGGCTATAAGGTGGA 59.866 40.000 0.00 0.00 38.69 4.02
8532 15112 6.183361 ACAATAATGTGGGCTATAAGGTGGAT 60.183 38.462 0.00 0.00 38.69 3.41
8533 15113 3.795688 ATGTGGGCTATAAGGTGGATG 57.204 47.619 0.00 0.00 0.00 3.51
8534 15114 2.487775 TGTGGGCTATAAGGTGGATGT 58.512 47.619 0.00 0.00 0.00 3.06
8535 15115 2.172505 TGTGGGCTATAAGGTGGATGTG 59.827 50.000 0.00 0.00 0.00 3.21
8536 15116 1.774254 TGGGCTATAAGGTGGATGTGG 59.226 52.381 0.00 0.00 0.00 4.17
8537 15117 2.054799 GGGCTATAAGGTGGATGTGGA 58.945 52.381 0.00 0.00 0.00 4.02
8538 15118 2.039084 GGGCTATAAGGTGGATGTGGAG 59.961 54.545 0.00 0.00 0.00 3.86
8539 15119 2.706190 GGCTATAAGGTGGATGTGGAGT 59.294 50.000 0.00 0.00 0.00 3.85
8540 15120 3.136626 GGCTATAAGGTGGATGTGGAGTT 59.863 47.826 0.00 0.00 0.00 3.01
8541 15121 4.385310 GGCTATAAGGTGGATGTGGAGTTT 60.385 45.833 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 8.592105 TTTCTCAAATTCTTAAAATGCCACAG 57.408 30.769 0.00 0.00 0.00 3.66
172 1758 7.862873 CGTGCATTTATAAGAGTGAGTCTATGA 59.137 37.037 0.00 0.00 32.65 2.15
177 1763 4.566759 TGCGTGCATTTATAAGAGTGAGTC 59.433 41.667 0.00 0.00 0.00 3.36
184 1770 4.383774 GCGTATGCGTGCATTTATAAGA 57.616 40.909 13.20 0.00 40.81 2.10
200 1786 1.640917 CATAGGGGTAGGGTGCGTAT 58.359 55.000 0.00 0.00 0.00 3.06
202 1788 2.440817 GCATAGGGGTAGGGTGCGT 61.441 63.158 0.00 0.00 0.00 5.24
212 1798 0.107017 CTGGAAGGTGTGCATAGGGG 60.107 60.000 0.00 0.00 0.00 4.79
227 1813 0.674581 CTGCCGTTTCAGCATCTGGA 60.675 55.000 0.00 0.00 40.04 3.86
229 1815 0.957395 ACCTGCCGTTTCAGCATCTG 60.957 55.000 0.00 0.00 40.04 2.90
234 1820 1.739067 AGATAACCTGCCGTTTCAGC 58.261 50.000 0.00 0.00 35.79 4.26
239 1825 3.914426 ATCTCAAGATAACCTGCCGTT 57.086 42.857 0.00 0.00 38.57 4.44
240 1826 3.197766 TCAATCTCAAGATAACCTGCCGT 59.802 43.478 0.00 0.00 33.73 5.68
246 1832 7.382759 GGATACTTCGTCAATCTCAAGATAACC 59.617 40.741 0.00 0.00 33.73 2.85
249 1835 7.582667 TGGATACTTCGTCAATCTCAAGATA 57.417 36.000 0.00 0.00 33.28 1.98
269 1855 6.092670 CGTCGATTATGAAGGCATTTATGGAT 59.907 38.462 0.00 0.00 35.94 3.41
279 1865 5.006746 AGACATTTTCGTCGATTATGAAGGC 59.993 40.000 18.51 8.68 40.98 4.35
285 1871 6.761242 TGGAATGAGACATTTTCGTCGATTAT 59.239 34.615 0.00 0.00 40.98 1.28
288 1874 4.330074 GTGGAATGAGACATTTTCGTCGAT 59.670 41.667 0.00 0.00 40.98 3.59
295 1881 4.141287 TGTTCGGTGGAATGAGACATTTT 58.859 39.130 0.00 0.00 34.05 1.82
305 1891 0.322098 TTGGCGATGTTCGGTGGAAT 60.322 50.000 0.00 0.00 40.84 3.01
307 1893 0.535328 TTTTGGCGATGTTCGGTGGA 60.535 50.000 0.00 0.00 40.84 4.02
308 1894 0.312416 TTTTTGGCGATGTTCGGTGG 59.688 50.000 0.00 0.00 40.84 4.61
330 1920 7.148239 CGAGTTTTAGACTTGGCCTGAATTTAT 60.148 37.037 3.32 0.00 39.19 1.40
335 1925 3.399330 CGAGTTTTAGACTTGGCCTGAA 58.601 45.455 3.32 0.00 39.19 3.02
339 1952 0.442699 CGCGAGTTTTAGACTTGGCC 59.557 55.000 0.00 0.00 39.75 5.36
355 2150 4.715523 ACCCATCACCCAACCGCG 62.716 66.667 0.00 0.00 0.00 6.46
367 2162 2.048222 CGCTGACGTGTCACCCAT 60.048 61.111 0.00 0.00 35.46 4.00
430 2225 4.445545 GGAGTTTTGGCGCTCGCG 62.446 66.667 7.64 6.98 43.06 5.87
439 2234 1.358759 GCGGTGGTGTGGAGTTTTG 59.641 57.895 0.00 0.00 0.00 2.44
440 2235 1.077357 TGCGGTGGTGTGGAGTTTT 60.077 52.632 0.00 0.00 0.00 2.43
441 2236 1.822186 GTGCGGTGGTGTGGAGTTT 60.822 57.895 0.00 0.00 0.00 2.66
442 2237 2.203153 GTGCGGTGGTGTGGAGTT 60.203 61.111 0.00 0.00 0.00 3.01
443 2238 4.250305 GGTGCGGTGGTGTGGAGT 62.250 66.667 0.00 0.00 0.00 3.85
444 2239 4.248842 TGGTGCGGTGGTGTGGAG 62.249 66.667 0.00 0.00 0.00 3.86
445 2240 4.555709 GTGGTGCGGTGGTGTGGA 62.556 66.667 0.00 0.00 0.00 4.02
446 2241 2.463589 ATAGTGGTGCGGTGGTGTGG 62.464 60.000 0.00 0.00 0.00 4.17
447 2242 1.003839 ATAGTGGTGCGGTGGTGTG 60.004 57.895 0.00 0.00 0.00 3.82
448 2243 1.295423 GATAGTGGTGCGGTGGTGT 59.705 57.895 0.00 0.00 0.00 4.16
449 2244 1.449601 GGATAGTGGTGCGGTGGTG 60.450 63.158 0.00 0.00 0.00 4.17
450 2245 1.271840 ATGGATAGTGGTGCGGTGGT 61.272 55.000 0.00 0.00 0.00 4.16
451 2246 0.532862 GATGGATAGTGGTGCGGTGG 60.533 60.000 0.00 0.00 0.00 4.61
452 2247 0.532862 GGATGGATAGTGGTGCGGTG 60.533 60.000 0.00 0.00 0.00 4.94
453 2248 0.980754 TGGATGGATAGTGGTGCGGT 60.981 55.000 0.00 0.00 0.00 5.68
454 2249 0.532862 GTGGATGGATAGTGGTGCGG 60.533 60.000 0.00 0.00 0.00 5.69
455 2250 0.875908 CGTGGATGGATAGTGGTGCG 60.876 60.000 0.00 0.00 0.00 5.34
456 2251 0.464036 TCGTGGATGGATAGTGGTGC 59.536 55.000 0.00 0.00 0.00 5.01
605 2767 1.304962 GATGCCGGGGGAGGTTTTT 60.305 57.895 2.18 0.00 0.00 1.94
606 2768 2.359011 GATGCCGGGGGAGGTTTT 59.641 61.111 2.18 0.00 0.00 2.43
684 2871 4.704833 ACGTGCGGCTGATGGCTT 62.705 61.111 0.00 0.00 41.46 4.35
926 3122 3.024356 AGAGGGGAGCGGAGGAGA 61.024 66.667 0.00 0.00 0.00 3.71
1244 3557 4.235762 CGCATAGTGGGTCCGGGG 62.236 72.222 0.00 0.00 0.00 5.73
1406 3719 2.527624 AGGGCAGCAGACTCCACA 60.528 61.111 0.00 0.00 0.00 4.17
1407 3720 2.046507 CAGGGCAGCAGACTCCAC 60.047 66.667 0.00 0.00 0.00 4.02
1459 3772 0.804989 GTCACCCAAATTCAGCTCCG 59.195 55.000 0.00 0.00 0.00 4.63
1461 3774 2.227388 CAGTGTCACCCAAATTCAGCTC 59.773 50.000 0.00 0.00 0.00 4.09
1494 3809 0.393808 GAGTAAGCCGCAATTCCCCA 60.394 55.000 0.00 0.00 0.00 4.96
1797 4115 4.386652 TCTGCATCCGACTAAAACGTAAAC 59.613 41.667 0.00 0.00 0.00 2.01
2037 4493 2.107031 CCATGGACCTGGAGATTATGCA 59.893 50.000 5.56 0.00 38.69 3.96
2470 4926 2.147150 GAGGAAGAGGTGAACAAGCAC 58.853 52.381 0.00 0.00 38.05 4.40
2496 4952 3.596066 GAGGCGAGCAAGCAGTGGA 62.596 63.158 5.80 0.00 39.27 4.02
2528 4984 0.533531 TGGACTGTGAGCAAGCAGTG 60.534 55.000 10.94 0.00 44.89 3.66
2564 5020 5.494706 TGTTCCACTCCCTAATAATTTCCCT 59.505 40.000 0.00 0.00 0.00 4.20
2571 5027 4.953579 GCCAAATGTTCCACTCCCTAATAA 59.046 41.667 0.00 0.00 0.00 1.40
2643 5099 7.703298 AATGATAATCAAACCGCAAATGATG 57.297 32.000 0.00 0.00 34.21 3.07
2648 5104 6.030548 TCCAAATGATAATCAAACCGCAAA 57.969 33.333 0.00 0.00 0.00 3.68
2654 5111 8.598075 GCATTGAGTTCCAAATGATAATCAAAC 58.402 33.333 0.00 0.00 38.43 2.93
2667 5124 6.343716 ACACATTAATGCATTGAGTTCCAA 57.656 33.333 22.27 6.60 39.41 3.53
2689 5146 9.480053 TCCATAGGTTTTGTAGCGTATAATAAC 57.520 33.333 0.00 0.00 0.00 1.89
2698 5155 4.504858 ACTTCTCCATAGGTTTTGTAGCG 58.495 43.478 0.00 0.00 0.00 4.26
2713 5170 0.394565 AGCGCATCCCATACTTCTCC 59.605 55.000 11.47 0.00 0.00 3.71
2716 5173 4.275936 ACAATTTAGCGCATCCCATACTTC 59.724 41.667 11.47 0.00 0.00 3.01
2729 5186 8.826710 TCTACTGGAATATTGAACAATTTAGCG 58.173 33.333 5.37 0.00 32.50 4.26
2898 5500 2.094026 GCCTTCCCAAACATTTAGGCAG 60.094 50.000 9.90 0.00 45.73 4.85
3092 5694 2.556622 CAGGCAAGGAAAATACCGTTGT 59.443 45.455 0.00 0.00 34.73 3.32
3109 5711 5.587289 TGTTGTTCAGTCAATTAAACAGGC 58.413 37.500 0.00 0.00 33.54 4.85
3306 5908 0.982852 TCTCACGAGCCCATCCCATT 60.983 55.000 0.00 0.00 0.00 3.16
3406 6008 4.360951 AAACTGAATTTCCCACGGACTA 57.639 40.909 0.00 0.00 0.00 2.59
3411 6013 7.198306 ACTTTAGTAAACTGAATTTCCCACG 57.802 36.000 0.00 0.00 0.00 4.94
3607 6209 8.999431 CATATGTTCGTATAAAGGCAACCTAAT 58.001 33.333 0.00 0.00 31.13 1.73
3658 6260 8.894409 TTAACTGTTTATGCAGAATGAAATCG 57.106 30.769 0.00 0.00 39.69 3.34
3673 6275 8.545472 ACTTGCCACCTATATCTTAACTGTTTA 58.455 33.333 0.00 0.00 0.00 2.01
3678 6280 6.808321 TGACTTGCCACCTATATCTTAACT 57.192 37.500 0.00 0.00 0.00 2.24
3679 6281 7.332182 GCTATGACTTGCCACCTATATCTTAAC 59.668 40.741 0.00 0.00 0.00 2.01
3682 6284 5.545723 AGCTATGACTTGCCACCTATATCTT 59.454 40.000 0.00 0.00 0.00 2.40
3683 6285 5.090139 AGCTATGACTTGCCACCTATATCT 58.910 41.667 0.00 0.00 0.00 1.98
3684 6286 5.413309 AGCTATGACTTGCCACCTATATC 57.587 43.478 0.00 0.00 0.00 1.63
3685 6287 5.832539 AAGCTATGACTTGCCACCTATAT 57.167 39.130 0.00 0.00 0.00 0.86
3686 6288 6.935240 ATAAGCTATGACTTGCCACCTATA 57.065 37.500 0.00 0.00 0.00 1.31
3687 6289 5.832539 ATAAGCTATGACTTGCCACCTAT 57.167 39.130 0.00 0.00 0.00 2.57
3688 6290 6.496911 TCATATAAGCTATGACTTGCCACCTA 59.503 38.462 0.00 0.00 0.00 3.08
3689 6291 5.307976 TCATATAAGCTATGACTTGCCACCT 59.692 40.000 0.00 0.00 0.00 4.00
3690 6292 5.551233 TCATATAAGCTATGACTTGCCACC 58.449 41.667 0.00 0.00 0.00 4.61
3691 6293 6.402983 GCATCATATAAGCTATGACTTGCCAC 60.403 42.308 10.51 0.00 35.52 5.01
3692 6294 5.645067 GCATCATATAAGCTATGACTTGCCA 59.355 40.000 10.51 0.00 35.52 4.92
3693 6295 5.879223 AGCATCATATAAGCTATGACTTGCC 59.121 40.000 15.28 3.91 39.17 4.52
3694 6296 6.981762 AGCATCATATAAGCTATGACTTGC 57.018 37.500 12.60 12.60 38.89 4.01
3695 6297 9.866798 TCTAAGCATCATATAAGCTATGACTTG 57.133 33.333 0.00 0.00 37.70 3.16
3697 6299 9.253832 ACTCTAAGCATCATATAAGCTATGACT 57.746 33.333 0.00 0.00 37.70 3.41
3698 6300 9.868277 AACTCTAAGCATCATATAAGCTATGAC 57.132 33.333 0.00 0.00 37.70 3.06
3713 6315 4.580167 TGTCAAAACAGCAACTCTAAGCAT 59.420 37.500 0.00 0.00 0.00 3.79
3767 6369 4.263462 TGTGAGAATGAGTAACCTGGCATT 60.263 41.667 0.00 0.00 33.97 3.56
3781 6383 2.816087 CCTGGTGAACCTTGTGAGAATG 59.184 50.000 0.37 0.00 36.82 2.67
3849 6451 9.649167 CAGAAATTCAGGAAATTGCTAAAGATT 57.351 29.630 0.00 0.00 40.71 2.40
3850 6452 8.810041 ACAGAAATTCAGGAAATTGCTAAAGAT 58.190 29.630 0.00 0.00 40.71 2.40
3851 6453 8.181904 ACAGAAATTCAGGAAATTGCTAAAGA 57.818 30.769 0.00 0.00 40.71 2.52
3854 6456 6.721208 AGGACAGAAATTCAGGAAATTGCTAA 59.279 34.615 0.00 0.00 40.71 3.09
4298 6900 8.257306 TGAGAGGAAAAGCAACAAAATACTTTT 58.743 29.630 0.00 0.00 43.15 2.27
4354 6956 5.450453 TCAGGATAGAAGAGTACAGGAAGG 58.550 45.833 0.00 0.00 0.00 3.46
4595 7197 2.807967 CAAGACCAGCGAGAATTTGACA 59.192 45.455 0.00 0.00 0.00 3.58
4841 7443 0.608130 TGCTACGCACAGAGAATGGT 59.392 50.000 0.00 0.00 31.71 3.55
5050 7656 3.699411 TGGAAGGAAAAATTGCCATGG 57.301 42.857 7.63 7.63 0.00 3.66
5070 7676 4.584638 TTGTTAGGGACTTGCCATGTAT 57.415 40.909 0.00 0.00 41.75 2.29
5124 7731 1.153958 GCCAGCGAATGCCAAAGTC 60.154 57.895 0.00 0.00 44.31 3.01
5133 7740 2.019984 GGAGAGAAATTGCCAGCGAAT 58.980 47.619 0.00 0.00 0.00 3.34
5814 8421 3.165071 ACAAAAGGATGGTCCATCAACC 58.835 45.455 29.07 15.63 42.13 3.77
5999 8608 4.503007 CACATCGATTTGAGGTACCGTAAG 59.497 45.833 5.61 0.00 40.19 2.34
6497 11688 7.728532 ACAAACCTAAGACAAGTAATTTGGGAT 59.271 33.333 0.00 0.00 41.25 3.85
6531 11722 9.787435 AACAAGTTTTAGTGTTAGATACATCCA 57.213 29.630 0.00 0.00 39.39 3.41
6584 11775 4.685924 TCCGTCCCGAATTATTTGTCTAC 58.314 43.478 0.00 0.00 0.00 2.59
6649 11841 1.439543 AGTGACCCTCTCTTTGGCTT 58.560 50.000 0.00 0.00 0.00 4.35
6650 11842 1.439543 AAGTGACCCTCTCTTTGGCT 58.560 50.000 0.00 0.00 26.81 4.75
6651 11843 3.636153 ATAAGTGACCCTCTCTTTGGC 57.364 47.619 0.00 0.00 33.02 4.52
6652 11844 8.024145 ACTATAATAAGTGACCCTCTCTTTGG 57.976 38.462 0.00 0.00 33.02 3.28
6738 13164 8.433421 TTCTAGCTATTTCTTAAATTGGTCCG 57.567 34.615 0.00 0.00 36.20 4.79
6968 13538 2.557920 AAGGAGTGTGAGCTTTCAGG 57.442 50.000 0.00 0.00 0.00 3.86
7136 13706 2.496070 TGAGGATGGAAGTGAAGTACGG 59.504 50.000 0.00 0.00 0.00 4.02
7139 13709 6.655003 GTGAAAATGAGGATGGAAGTGAAGTA 59.345 38.462 0.00 0.00 0.00 2.24
7140 13710 5.474876 GTGAAAATGAGGATGGAAGTGAAGT 59.525 40.000 0.00 0.00 0.00 3.01
7141 13711 5.105997 GGTGAAAATGAGGATGGAAGTGAAG 60.106 44.000 0.00 0.00 0.00 3.02
7142 13712 4.766891 GGTGAAAATGAGGATGGAAGTGAA 59.233 41.667 0.00 0.00 0.00 3.18
7143 13713 4.335416 GGTGAAAATGAGGATGGAAGTGA 58.665 43.478 0.00 0.00 0.00 3.41
7144 13714 3.445096 GGGTGAAAATGAGGATGGAAGTG 59.555 47.826 0.00 0.00 0.00 3.16
7145 13715 3.334881 AGGGTGAAAATGAGGATGGAAGT 59.665 43.478 0.00 0.00 0.00 3.01
7384 13956 1.153168 CAGGGATCCGGCATTCGTT 60.153 57.895 5.45 0.00 37.11 3.85
7472 14044 2.997986 GGTGCATTTTTCATGCTGAAGG 59.002 45.455 8.22 0.00 44.79 3.46
7557 14129 5.417894 TCGACTGTACAGTAAATCAGATGGT 59.582 40.000 27.98 1.65 42.66 3.55
7560 14132 7.545965 CCTTTTCGACTGTACAGTAAATCAGAT 59.454 37.037 27.98 2.28 42.66 2.90
7803 14377 6.934645 ACCCACACCATTTCAGAATATATACG 59.065 38.462 0.00 0.00 0.00 3.06
7833 14407 4.208746 ACCATGTTTCGGTTACAGGAAAA 58.791 39.130 3.13 0.00 34.26 2.29
7882 14457 5.830912 TGTCAATGCTTTCGACTTGAATTT 58.169 33.333 12.59 0.00 36.22 1.82
7883 14458 5.437289 TGTCAATGCTTTCGACTTGAATT 57.563 34.783 12.59 0.00 36.22 2.17
7925 14501 3.118371 AGAAAGAAACAACTGTCCTCCGT 60.118 43.478 0.00 0.00 0.00 4.69
7948 14524 2.078849 TATGTGTGCCAGAACTGTCG 57.921 50.000 1.18 0.00 0.00 4.35
7956 14532 2.684881 GGTCAAGGATTATGTGTGCCAG 59.315 50.000 0.00 0.00 0.00 4.85
7994 14572 4.022589 AGTTGTCTGGTTGCATCAAATGAG 60.023 41.667 0.00 0.00 0.00 2.90
8179 14758 9.832445 CCAAGCCTGTCTTTAAATAAGATAGTA 57.168 33.333 9.44 0.00 34.81 1.82
8180 14759 7.283354 GCCAAGCCTGTCTTTAAATAAGATAGT 59.717 37.037 9.44 0.00 34.81 2.12
8181 14760 7.500559 AGCCAAGCCTGTCTTTAAATAAGATAG 59.499 37.037 0.00 0.00 35.91 2.08
8185 14764 5.904362 AGCCAAGCCTGTCTTTAAATAAG 57.096 39.130 0.00 0.00 31.27 1.73
8207 14786 6.428083 TGGTGGAAAGTACTTCATCACTAA 57.572 37.500 23.12 15.12 35.55 2.24
8213 14792 4.042187 AGCTCTTGGTGGAAAGTACTTCAT 59.958 41.667 8.95 0.00 35.55 2.57
8241 14820 1.930371 GCAATGAAGCCGTGTCAAACC 60.930 52.381 0.00 0.00 0.00 3.27
8243 14822 1.028130 TGCAATGAAGCCGTGTCAAA 58.972 45.000 0.00 0.00 0.00 2.69
8246 14825 1.621107 CAATGCAATGAAGCCGTGTC 58.379 50.000 0.00 0.00 0.00 3.67
8247 14826 0.388907 GCAATGCAATGAAGCCGTGT 60.389 50.000 5.79 0.00 0.00 4.49
8248 14827 0.388778 TGCAATGCAATGAAGCCGTG 60.389 50.000 5.01 0.00 34.76 4.94
8249 14828 0.388907 GTGCAATGCAATGAAGCCGT 60.389 50.000 10.44 0.00 41.47 5.68
8250 14829 0.388778 TGTGCAATGCAATGAAGCCG 60.389 50.000 10.44 0.00 41.47 5.52
8269 14849 1.559682 CCCTTACCCTACACATGCACT 59.440 52.381 0.00 0.00 0.00 4.40
8289 14869 2.300437 AGGAAGGATTATACGAGGCAGC 59.700 50.000 0.00 0.00 0.00 5.25
8290 14870 3.574396 TGAGGAAGGATTATACGAGGCAG 59.426 47.826 0.00 0.00 0.00 4.85
8316 14896 5.285651 GCTAGAAACTCACATACTAGCTGG 58.714 45.833 14.51 0.00 46.79 4.85
8329 14909 2.342179 GCAGACCAGTGCTAGAAACTC 58.658 52.381 0.00 0.00 40.54 3.01
8432 15012 7.987458 GCCATCAGCTAGCTATATTATTAACCA 59.013 37.037 18.86 0.00 38.99 3.67
8433 15013 8.371770 GCCATCAGCTAGCTATATTATTAACC 57.628 38.462 18.86 0.00 38.99 2.85
8450 15030 2.417719 CGGTTCCTTATAGCCATCAGC 58.582 52.381 0.00 0.00 44.25 4.26
8451 15031 2.417719 GCGGTTCCTTATAGCCATCAG 58.582 52.381 0.00 0.00 0.00 2.90
8452 15032 1.071699 GGCGGTTCCTTATAGCCATCA 59.928 52.381 0.00 0.00 46.48 3.07
8453 15033 1.809684 GGCGGTTCCTTATAGCCATC 58.190 55.000 0.00 0.00 46.48 3.51
8457 15037 2.143925 GACATGGCGGTTCCTTATAGC 58.856 52.381 0.00 0.00 35.26 2.97
8458 15038 3.469008 TGACATGGCGGTTCCTTATAG 57.531 47.619 0.00 0.00 35.26 1.31
8459 15039 3.646162 AGATGACATGGCGGTTCCTTATA 59.354 43.478 0.00 0.00 35.26 0.98
8460 15040 2.439507 AGATGACATGGCGGTTCCTTAT 59.560 45.455 0.00 0.00 35.26 1.73
8461 15041 1.837439 AGATGACATGGCGGTTCCTTA 59.163 47.619 0.00 0.00 35.26 2.69
8462 15042 0.620556 AGATGACATGGCGGTTCCTT 59.379 50.000 0.00 0.00 35.26 3.36
8463 15043 1.496060 TAGATGACATGGCGGTTCCT 58.504 50.000 0.00 0.00 35.26 3.36
8464 15044 2.550830 ATAGATGACATGGCGGTTCC 57.449 50.000 0.00 0.00 0.00 3.62
8465 15045 2.996621 GCTATAGATGACATGGCGGTTC 59.003 50.000 3.21 0.00 0.00 3.62
8466 15046 2.289694 GGCTATAGATGACATGGCGGTT 60.290 50.000 3.21 0.00 31.17 4.44
8467 15047 1.276421 GGCTATAGATGACATGGCGGT 59.724 52.381 3.21 0.00 31.17 5.68
8468 15048 1.276138 TGGCTATAGATGACATGGCGG 59.724 52.381 3.21 0.00 31.17 6.13
8469 15049 2.749280 TGGCTATAGATGACATGGCG 57.251 50.000 3.21 0.00 31.17 5.69
8470 15050 4.212143 TGATGGCTATAGATGACATGGC 57.788 45.455 3.21 0.00 0.00 4.40
8471 15051 6.236558 AGATGATGGCTATAGATGACATGG 57.763 41.667 3.21 0.00 0.00 3.66
8472 15052 7.779073 TGTAGATGATGGCTATAGATGACATG 58.221 38.462 3.21 0.00 0.00 3.21
8473 15053 7.968014 TGTAGATGATGGCTATAGATGACAT 57.032 36.000 3.21 3.55 0.00 3.06
8474 15054 7.632245 GCATGTAGATGATGGCTATAGATGACA 60.632 40.741 3.21 0.00 0.00 3.58
8475 15055 6.700960 GCATGTAGATGATGGCTATAGATGAC 59.299 42.308 3.21 0.00 0.00 3.06
8476 15056 6.381994 TGCATGTAGATGATGGCTATAGATGA 59.618 38.462 3.21 0.00 0.00 2.92
8477 15057 6.479331 GTGCATGTAGATGATGGCTATAGATG 59.521 42.308 3.21 0.00 0.00 2.90
8478 15058 6.383436 AGTGCATGTAGATGATGGCTATAGAT 59.617 38.462 3.21 0.00 0.00 1.98
8479 15059 5.718607 AGTGCATGTAGATGATGGCTATAGA 59.281 40.000 3.21 0.00 0.00 1.98
8480 15060 5.975282 AGTGCATGTAGATGATGGCTATAG 58.025 41.667 3.61 0.00 0.00 1.31
8481 15061 5.481473 TGAGTGCATGTAGATGATGGCTATA 59.519 40.000 3.61 0.00 0.00 1.31
8482 15062 4.285260 TGAGTGCATGTAGATGATGGCTAT 59.715 41.667 3.61 0.00 0.00 2.97
8483 15063 3.642848 TGAGTGCATGTAGATGATGGCTA 59.357 43.478 3.61 0.00 0.00 3.93
8484 15064 2.436911 TGAGTGCATGTAGATGATGGCT 59.563 45.455 3.61 0.00 0.00 4.75
8485 15065 2.842457 TGAGTGCATGTAGATGATGGC 58.158 47.619 3.61 0.00 0.00 4.40
8486 15066 5.544650 TGTATGAGTGCATGTAGATGATGG 58.455 41.667 3.61 0.00 35.94 3.51
8487 15067 7.668525 ATTGTATGAGTGCATGTAGATGATG 57.331 36.000 3.61 0.00 35.94 3.07
8488 15068 9.955102 ATTATTGTATGAGTGCATGTAGATGAT 57.045 29.630 3.61 0.00 35.94 2.45
8489 15069 9.211485 CATTATTGTATGAGTGCATGTAGATGA 57.789 33.333 3.61 0.00 35.94 2.92
8490 15070 8.996271 ACATTATTGTATGAGTGCATGTAGATG 58.004 33.333 0.00 0.00 35.94 2.90
8491 15071 8.996271 CACATTATTGTATGAGTGCATGTAGAT 58.004 33.333 0.00 0.00 35.94 1.98
8492 15072 7.442062 CCACATTATTGTATGAGTGCATGTAGA 59.558 37.037 0.00 0.00 35.94 2.59
8493 15073 7.308169 CCCACATTATTGTATGAGTGCATGTAG 60.308 40.741 0.00 0.00 35.94 2.74
8494 15074 6.486320 CCCACATTATTGTATGAGTGCATGTA 59.514 38.462 0.00 0.00 35.94 2.29
8495 15075 5.300034 CCCACATTATTGTATGAGTGCATGT 59.700 40.000 0.00 0.00 35.94 3.21
8496 15076 5.765176 CCCACATTATTGTATGAGTGCATG 58.235 41.667 0.00 0.00 35.94 4.06
8497 15077 4.279169 GCCCACATTATTGTATGAGTGCAT 59.721 41.667 0.00 0.00 38.54 3.96
8498 15078 3.631686 GCCCACATTATTGTATGAGTGCA 59.368 43.478 0.00 0.00 33.76 4.57
8499 15079 3.885297 AGCCCACATTATTGTATGAGTGC 59.115 43.478 0.00 0.00 33.76 4.40
8500 15080 8.846943 TTATAGCCCACATTATTGTATGAGTG 57.153 34.615 0.00 0.00 33.76 3.51
8501 15081 8.103305 CCTTATAGCCCACATTATTGTATGAGT 58.897 37.037 0.00 0.00 33.76 3.41
8502 15082 8.103305 ACCTTATAGCCCACATTATTGTATGAG 58.897 37.037 0.00 0.00 33.76 2.90
8503 15083 7.882791 CACCTTATAGCCCACATTATTGTATGA 59.117 37.037 0.00 0.00 33.76 2.15
8504 15084 7.121168 CCACCTTATAGCCCACATTATTGTATG 59.879 40.741 0.00 0.00 33.76 2.39
8505 15085 7.018149 TCCACCTTATAGCCCACATTATTGTAT 59.982 37.037 0.00 0.00 33.76 2.29
8506 15086 6.330514 TCCACCTTATAGCCCACATTATTGTA 59.669 38.462 0.00 0.00 33.76 2.41
8507 15087 5.133660 TCCACCTTATAGCCCACATTATTGT 59.866 40.000 0.00 0.00 36.15 2.71
8508 15088 5.630121 TCCACCTTATAGCCCACATTATTG 58.370 41.667 0.00 0.00 0.00 1.90
8509 15089 5.922960 TCCACCTTATAGCCCACATTATT 57.077 39.130 0.00 0.00 0.00 1.40
8510 15090 5.313240 ACATCCACCTTATAGCCCACATTAT 59.687 40.000 0.00 0.00 0.00 1.28
8511 15091 4.663120 ACATCCACCTTATAGCCCACATTA 59.337 41.667 0.00 0.00 0.00 1.90
8512 15092 3.463329 ACATCCACCTTATAGCCCACATT 59.537 43.478 0.00 0.00 0.00 2.71
8513 15093 3.056080 ACATCCACCTTATAGCCCACAT 58.944 45.455 0.00 0.00 0.00 3.21
8514 15094 2.172505 CACATCCACCTTATAGCCCACA 59.827 50.000 0.00 0.00 0.00 4.17
8515 15095 2.487265 CCACATCCACCTTATAGCCCAC 60.487 54.545 0.00 0.00 0.00 4.61
8516 15096 1.774254 CCACATCCACCTTATAGCCCA 59.226 52.381 0.00 0.00 0.00 5.36
8517 15097 2.039084 CTCCACATCCACCTTATAGCCC 59.961 54.545 0.00 0.00 0.00 5.19
8518 15098 2.706190 ACTCCACATCCACCTTATAGCC 59.294 50.000 0.00 0.00 0.00 3.93
8519 15099 4.423625 AACTCCACATCCACCTTATAGC 57.576 45.455 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.