Multiple sequence alignment - TraesCS4B01G102900

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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 TraesCS4B01G102900 chr4B 100.000 3422 0 0 1 3422 109054053 109050632 0.000000e+00 6320.0
1 TraesCS4B01G102900 chr4B 94.554 202 8 2 1 199 64711497 64711296 3.320000e-80 309.0
2 TraesCS4B01G102900 chr4D 92.702 2494 162 13 932 3417 76625059 76622578 0.000000e+00 3579.0
3 TraesCS4B01G102900 chr4D 95.336 1844 78 4 922 2764 77016794 77018630 0.000000e+00 2922.0
4 TraesCS4B01G102900 chr4D 86.767 665 80 8 2759 3418 77022882 77023543 0.000000e+00 734.0
5 TraesCS4B01G102900 chr4D 93.627 204 11 2 1 202 24794842 24794639 1.540000e-78 303.0
6 TraesCS4B01G102900 chr4D 90.741 216 20 0 191 406 77016131 77016346 4.320000e-74 289.0
7 TraesCS4B01G102900 chr4D 85.662 272 34 4 404 670 403293452 403293181 7.230000e-72 281.0
8 TraesCS4B01G102900 chr4D 97.368 76 2 0 755 830 77016712 77016787 2.770000e-26 130.0
9 TraesCS4B01G102900 chr4A 95.047 1716 77 4 937 2651 511036913 511038621 0.000000e+00 2691.0
10 TraesCS4B01G102900 chr4A 85.996 457 62 2 2894 3349 511077593 511078048 3.970000e-134 488.0
11 TraesCS4B01G102900 chr4A 83.925 479 48 11 267 740 511035841 511036295 6.780000e-117 431.0
12 TraesCS4B01G102900 chr4A 83.333 456 66 6 2894 3349 511048267 511048712 2.460000e-111 412.0
13 TraesCS4B01G102900 chr4A 87.978 183 20 2 2759 2939 511077420 511077602 7.440000e-52 215.0
14 TraesCS4B01G102900 chr4A 96.491 57 1 1 191 247 511035795 511035850 3.640000e-15 93.5
15 TraesCS4B01G102900 chr7B 96.354 192 6 1 1 191 413072075 413071884 7.130000e-82 315.0
16 TraesCS4B01G102900 chr7B 93.659 205 9 4 1 202 103864545 103864342 1.540000e-78 303.0
17 TraesCS4B01G102900 chr7B 84.892 278 37 2 404 676 111212372 111212095 3.360000e-70 276.0
18 TraesCS4B01G102900 chr6B 95.897 195 7 1 1 194 480743725 480743531 7.130000e-82 315.0
19 TraesCS4B01G102900 chr5B 95.897 195 7 1 1 194 330367556 330367362 7.130000e-82 315.0
20 TraesCS4B01G102900 chr5B 96.335 191 6 1 1 190 299723445 299723635 2.560000e-81 313.0
21 TraesCS4B01G102900 chr5B 83.630 281 38 7 396 670 179244365 179244643 1.220000e-64 257.0
22 TraesCS4B01G102900 chr5D 94.500 200 8 3 1 199 1206001 1205804 4.290000e-79 305.0
23 TraesCS4B01G102900 chr2D 93.627 204 11 2 1 202 517206662 517206459 1.540000e-78 303.0
24 TraesCS4B01G102900 chrUn 85.609 271 33 5 406 670 62222262 62222532 2.600000e-71 279.0
25 TraesCS4B01G102900 chr2B 85.609 271 33 4 406 670 207722384 207722114 2.600000e-71 279.0
26 TraesCS4B01G102900 chr2B 85.769 260 31 4 417 670 218295000 218295259 1.570000e-68 270.0
27 TraesCS4B01G102900 chr7A 84.982 273 35 5 404 670 661943114 661942842 4.350000e-69 272.0
28 TraesCS4B01G102900 chr3B 85.393 267 34 4 404 666 812616235 812616500 4.350000e-69 272.0
29 TraesCS4B01G102900 chr1B 84.307 274 37 5 403 670 168972272 168971999 2.620000e-66 263.0


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 TraesCS4B01G102900 chr4B 109050632 109054053 3421 True 6320.000000 6320 100.000000 1 3422 1 chr4B.!!$R2 3421
1 TraesCS4B01G102900 chr4D 76622578 76625059 2481 True 3579.000000 3579 92.702000 932 3417 1 chr4D.!!$R2 2485
2 TraesCS4B01G102900 chr4D 77016131 77018630 2499 False 1113.666667 2922 94.481667 191 2764 3 chr4D.!!$F2 2573
3 TraesCS4B01G102900 chr4D 77022882 77023543 661 False 734.000000 734 86.767000 2759 3418 1 chr4D.!!$F1 659
4 TraesCS4B01G102900 chr4A 511035795 511038621 2826 False 1071.833333 2691 91.821000 191 2651 3 chr4A.!!$F2 2460
5 TraesCS4B01G102900 chr4A 511077420 511078048 628 False 351.500000 488 86.987000 2759 3349 2 chr4A.!!$F3 590

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
912 1740 0.109781 CTCCAAATCCCAAACGCGTG 60.110 55.0 14.98 0.0 0.0 5.34 F
2277 3105 0.035152 TTGGTGCTCAGCAATCCGAT 60.035 50.0 0.00 0.0 43.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 3228 0.323178 AAGGAATGGCAGAGCTGTGG 60.323 55.0 13.44 0.0 0.0 4.17 R
3213 4087 0.252742 GAGAGAAAGGGGGAGGGACA 60.253 60.0 0.00 0.0 0.0 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.938563 ATCATCTTTGATTAACGAGCTAGTC 57.061 36.000 0.00 0.00 39.64 2.59
34 35 6.863275 TCATCTTTGATTAACGAGCTAGTCA 58.137 36.000 0.00 0.00 0.00 3.41
35 36 7.320399 TCATCTTTGATTAACGAGCTAGTCAA 58.680 34.615 0.00 0.00 0.00 3.18
36 37 7.817478 TCATCTTTGATTAACGAGCTAGTCAAA 59.183 33.333 0.00 5.76 36.02 2.69
37 38 8.607459 CATCTTTGATTAACGAGCTAGTCAAAT 58.393 33.333 10.50 8.83 37.08 2.32
38 39 9.817809 ATCTTTGATTAACGAGCTAGTCAAATA 57.182 29.630 10.50 5.98 37.08 1.40
39 40 9.302345 TCTTTGATTAACGAGCTAGTCAAATAG 57.698 33.333 10.50 5.19 37.08 1.73
40 41 9.302345 CTTTGATTAACGAGCTAGTCAAATAGA 57.698 33.333 10.50 1.29 37.08 1.98
41 42 8.858003 TTGATTAACGAGCTAGTCAAATAGAG 57.142 34.615 0.00 0.00 28.07 2.43
42 43 7.426410 TGATTAACGAGCTAGTCAAATAGAGG 58.574 38.462 0.00 0.00 0.00 3.69
43 44 3.719173 ACGAGCTAGTCAAATAGAGGC 57.281 47.619 0.00 0.00 0.00 4.70
44 45 3.024547 ACGAGCTAGTCAAATAGAGGCA 58.975 45.455 0.00 0.00 0.00 4.75
45 46 3.639094 ACGAGCTAGTCAAATAGAGGCAT 59.361 43.478 0.00 0.00 0.00 4.40
46 47 4.827835 ACGAGCTAGTCAAATAGAGGCATA 59.172 41.667 0.00 0.00 0.00 3.14
47 48 5.157781 CGAGCTAGTCAAATAGAGGCATAC 58.842 45.833 0.00 0.00 0.00 2.39
48 49 5.048364 CGAGCTAGTCAAATAGAGGCATACT 60.048 44.000 0.00 0.00 0.00 2.12
49 50 6.149640 CGAGCTAGTCAAATAGAGGCATACTA 59.850 42.308 0.00 0.00 0.00 1.82
50 51 7.461182 AGCTAGTCAAATAGAGGCATACTAG 57.539 40.000 0.00 0.00 38.50 2.57
51 52 6.435904 AGCTAGTCAAATAGAGGCATACTAGG 59.564 42.308 0.00 0.00 36.85 3.02
52 53 6.350612 GCTAGTCAAATAGAGGCATACTAGGG 60.351 46.154 0.00 0.00 36.85 3.53
53 54 5.716979 AGTCAAATAGAGGCATACTAGGGA 58.283 41.667 0.00 0.00 0.00 4.20
54 55 5.540719 AGTCAAATAGAGGCATACTAGGGAC 59.459 44.000 0.00 0.00 0.00 4.46
55 56 5.304614 GTCAAATAGAGGCATACTAGGGACA 59.695 44.000 0.00 0.00 0.00 4.02
56 57 5.903010 TCAAATAGAGGCATACTAGGGACAA 59.097 40.000 0.00 0.00 0.00 3.18
57 58 6.558775 TCAAATAGAGGCATACTAGGGACAAT 59.441 38.462 0.00 0.00 0.00 2.71
58 59 7.733047 TCAAATAGAGGCATACTAGGGACAATA 59.267 37.037 0.00 0.00 0.00 1.90
59 60 8.543774 CAAATAGAGGCATACTAGGGACAATAT 58.456 37.037 0.00 0.00 0.00 1.28
60 61 7.667575 ATAGAGGCATACTAGGGACAATATG 57.332 40.000 0.00 0.00 0.00 1.78
61 62 5.407049 AGAGGCATACTAGGGACAATATGT 58.593 41.667 0.00 0.00 0.00 2.29
62 63 5.846714 AGAGGCATACTAGGGACAATATGTT 59.153 40.000 0.00 0.00 0.00 2.71
63 64 6.330250 AGAGGCATACTAGGGACAATATGTTT 59.670 38.462 0.00 0.00 0.00 2.83
64 65 6.911308 AGGCATACTAGGGACAATATGTTTT 58.089 36.000 0.00 0.00 0.00 2.43
65 66 6.772716 AGGCATACTAGGGACAATATGTTTTG 59.227 38.462 0.00 0.00 0.00 2.44
66 67 6.546034 GGCATACTAGGGACAATATGTTTTGT 59.454 38.462 0.00 0.00 42.37 2.83
84 85 8.389779 TGTTTTGTCTATGTATTCACACATGT 57.610 30.769 0.00 0.00 39.46 3.21
85 86 9.495572 TGTTTTGTCTATGTATTCACACATGTA 57.504 29.630 0.00 0.00 39.46 2.29
86 87 9.755064 GTTTTGTCTATGTATTCACACATGTAC 57.245 33.333 0.00 0.00 39.46 2.90
87 88 9.719355 TTTTGTCTATGTATTCACACATGTACT 57.281 29.630 0.00 0.00 39.46 2.73
96 97 8.705134 TGTATTCACACATGTACTAAGTTTTCG 58.295 33.333 0.00 0.00 0.00 3.46
97 98 6.533819 TTCACACATGTACTAAGTTTTCGG 57.466 37.500 0.00 0.00 0.00 4.30
98 99 5.603596 TCACACATGTACTAAGTTTTCGGT 58.396 37.500 0.00 0.00 0.00 4.69
99 100 6.050432 TCACACATGTACTAAGTTTTCGGTT 58.950 36.000 0.00 0.00 0.00 4.44
100 101 7.208777 TCACACATGTACTAAGTTTTCGGTTA 58.791 34.615 0.00 0.00 0.00 2.85
101 102 7.710044 TCACACATGTACTAAGTTTTCGGTTAA 59.290 33.333 0.00 0.00 0.00 2.01
102 103 8.500773 CACACATGTACTAAGTTTTCGGTTAAT 58.499 33.333 0.00 0.00 0.00 1.40
103 104 9.709495 ACACATGTACTAAGTTTTCGGTTAATA 57.291 29.630 0.00 0.00 0.00 0.98
104 105 9.962759 CACATGTACTAAGTTTTCGGTTAATAC 57.037 33.333 0.00 0.00 0.00 1.89
105 106 9.709495 ACATGTACTAAGTTTTCGGTTAATACA 57.291 29.630 0.00 0.00 0.00 2.29
114 115 8.556213 AGTTTTCGGTTAATACAATTCTAGCA 57.444 30.769 0.00 0.00 0.00 3.49
115 116 9.174166 AGTTTTCGGTTAATACAATTCTAGCAT 57.826 29.630 0.00 0.00 0.00 3.79
116 117 9.221775 GTTTTCGGTTAATACAATTCTAGCATG 57.778 33.333 0.00 0.00 0.00 4.06
117 118 8.725405 TTTCGGTTAATACAATTCTAGCATGA 57.275 30.769 0.00 0.00 0.00 3.07
118 119 8.725405 TTCGGTTAATACAATTCTAGCATGAA 57.275 30.769 0.00 0.00 0.00 2.57
119 120 8.902540 TCGGTTAATACAATTCTAGCATGAAT 57.097 30.769 0.00 0.00 38.19 2.57
120 121 9.990360 TCGGTTAATACAATTCTAGCATGAATA 57.010 29.630 0.00 0.00 35.82 1.75
178 179 6.969993 AACTTTATTGTTGCCTTTAGGACA 57.030 33.333 0.00 0.00 37.39 4.02
179 180 7.539034 AACTTTATTGTTGCCTTTAGGACAT 57.461 32.000 0.00 0.00 37.39 3.06
180 181 8.644374 AACTTTATTGTTGCCTTTAGGACATA 57.356 30.769 0.00 0.00 37.39 2.29
181 182 8.823220 ACTTTATTGTTGCCTTTAGGACATAT 57.177 30.769 0.00 0.00 37.39 1.78
182 183 9.255029 ACTTTATTGTTGCCTTTAGGACATATT 57.745 29.630 0.00 0.00 37.39 1.28
185 186 6.524101 TTGTTGCCTTTAGGACATATTTCC 57.476 37.500 0.00 0.00 37.39 3.13
187 188 6.252995 TGTTGCCTTTAGGACATATTTCCTT 58.747 36.000 15.55 1.08 44.22 3.36
188 189 6.377146 TGTTGCCTTTAGGACATATTTCCTTC 59.623 38.462 15.55 2.34 44.22 3.46
189 190 6.073447 TGCCTTTAGGACATATTTCCTTCA 57.927 37.500 15.55 0.98 44.22 3.02
190 191 5.885912 TGCCTTTAGGACATATTTCCTTCAC 59.114 40.000 15.55 3.18 44.22 3.18
191 192 6.122964 GCCTTTAGGACATATTTCCTTCACT 58.877 40.000 15.55 0.00 44.22 3.41
192 193 6.261158 GCCTTTAGGACATATTTCCTTCACTC 59.739 42.308 15.55 0.62 44.22 3.51
193 194 7.569240 CCTTTAGGACATATTTCCTTCACTCT 58.431 38.462 15.55 0.00 44.22 3.24
194 195 8.049721 CCTTTAGGACATATTTCCTTCACTCTT 58.950 37.037 15.55 0.00 44.22 2.85
239 240 4.280677 CAGCTGAAATCCCTGTTTTTACCA 59.719 41.667 8.42 0.00 0.00 3.25
245 246 7.796054 TGAAATCCCTGTTTTTACCATTTTCA 58.204 30.769 0.00 0.00 0.00 2.69
246 247 8.267894 TGAAATCCCTGTTTTTACCATTTTCAA 58.732 29.630 0.00 0.00 0.00 2.69
247 248 8.445275 AAATCCCTGTTTTTACCATTTTCAAC 57.555 30.769 0.00 0.00 0.00 3.18
361 362 5.182760 CCTACCTAGACACGTCAAACTTACT 59.817 44.000 0.00 0.00 0.00 2.24
418 419 3.064207 CACGCGTTAGGGCATGTATAAT 58.936 45.455 10.22 0.00 0.00 1.28
420 421 3.243941 ACGCGTTAGGGCATGTATAATGA 60.244 43.478 5.58 0.00 0.00 2.57
431 432 9.532494 AGGGCATGTATAATGATGCTATTTTAA 57.468 29.630 0.00 0.00 43.77 1.52
464 465 4.989875 AGGATAAATGATGAGGTGGAGG 57.010 45.455 0.00 0.00 0.00 4.30
465 466 4.310740 AGGATAAATGATGAGGTGGAGGT 58.689 43.478 0.00 0.00 0.00 3.85
476 477 0.528470 GGTGGAGGTGAGAGAACTCG 59.472 60.000 0.00 0.00 45.25 4.18
480 481 3.255149 GTGGAGGTGAGAGAACTCGTAAA 59.745 47.826 0.00 0.00 45.25 2.01
559 560 8.664798 CAATATGTCTCATCACGTTTTTAGGAA 58.335 33.333 0.00 0.00 0.00 3.36
561 562 6.480524 TGTCTCATCACGTTTTTAGGAATG 57.519 37.500 0.00 0.00 0.00 2.67
562 563 6.227522 TGTCTCATCACGTTTTTAGGAATGA 58.772 36.000 0.00 0.00 0.00 2.57
604 605 9.533831 AAGGTTAAAAGATGAACCATTGTAGAT 57.466 29.630 6.57 0.00 46.41 1.98
605 606 9.533831 AGGTTAAAAGATGAACCATTGTAGATT 57.466 29.630 6.57 0.00 46.41 2.40
666 671 5.179045 ACTACCTTATCAACCATCGTACG 57.821 43.478 9.53 9.53 0.00 3.67
670 675 3.444916 CTTATCAACCATCGTACGTGCT 58.555 45.455 16.05 0.00 0.00 4.40
671 676 2.380084 ATCAACCATCGTACGTGCTT 57.620 45.000 16.05 4.13 0.00 3.91
675 680 4.056740 TCAACCATCGTACGTGCTTTTAA 58.943 39.130 16.05 0.00 0.00 1.52
682 687 2.567067 GTACGTGCTTTTAAACGCCAG 58.433 47.619 13.49 9.81 43.49 4.85
685 690 1.399727 CGTGCTTTTAAACGCCAGGAG 60.400 52.381 13.49 0.00 32.40 3.69
702 707 3.741344 CAGGAGGTGACGTTTGTTCTTAG 59.259 47.826 0.00 0.00 0.00 2.18
734 739 3.269347 CGGCCATAGCGTTTCCGG 61.269 66.667 2.24 0.00 41.24 5.14
746 751 2.265683 CGTTTCCGGTAAAGCTAGGAC 58.734 52.381 0.00 0.00 31.69 3.85
748 753 3.259902 GTTTCCGGTAAAGCTAGGACTG 58.740 50.000 0.00 0.00 31.69 3.51
749 754 0.822164 TCCGGTAAAGCTAGGACTGC 59.178 55.000 0.00 0.00 0.00 4.40
750 755 0.179081 CCGGTAAAGCTAGGACTGCC 60.179 60.000 0.00 0.00 0.00 4.85
751 756 0.535335 CGGTAAAGCTAGGACTGCCA 59.465 55.000 0.00 0.00 36.29 4.92
752 757 1.066430 CGGTAAAGCTAGGACTGCCAA 60.066 52.381 0.00 0.00 36.29 4.52
831 1659 7.420184 AAATGGTTAAATTGTGCTAAAGTGC 57.580 32.000 0.00 0.00 0.00 4.40
835 1663 5.293560 GTTAAATTGTGCTAAAGTGCCCAA 58.706 37.500 0.00 0.00 35.08 4.12
836 1664 3.385193 AATTGTGCTAAAGTGCCCAAC 57.615 42.857 0.00 0.00 33.59 3.77
837 1665 0.665835 TTGTGCTAAAGTGCCCAACG 59.334 50.000 0.00 0.00 0.00 4.10
838 1666 1.169661 TGTGCTAAAGTGCCCAACGG 61.170 55.000 0.00 0.00 0.00 4.44
861 1689 6.785337 GGGGGTTATATTTTGTGCTAAAGT 57.215 37.500 0.00 0.00 0.00 2.66
862 1690 7.177832 GGGGGTTATATTTTGTGCTAAAGTT 57.822 36.000 0.00 0.00 0.00 2.66
863 1691 8.296211 GGGGGTTATATTTTGTGCTAAAGTTA 57.704 34.615 0.00 0.00 0.00 2.24
864 1692 8.192774 GGGGGTTATATTTTGTGCTAAAGTTAC 58.807 37.037 0.00 0.00 0.00 2.50
865 1693 8.192774 GGGGTTATATTTTGTGCTAAAGTTACC 58.807 37.037 0.00 0.00 0.00 2.85
866 1694 7.911727 GGGTTATATTTTGTGCTAAAGTTACCG 59.088 37.037 0.00 0.00 0.00 4.02
867 1695 8.667463 GGTTATATTTTGTGCTAAAGTTACCGA 58.333 33.333 0.00 0.00 0.00 4.69
872 1700 7.687005 TTTTGTGCTAAAGTTACCGAAAATG 57.313 32.000 0.00 0.00 0.00 2.32
873 1701 5.365403 TGTGCTAAAGTTACCGAAAATGG 57.635 39.130 0.00 0.00 0.00 3.16
874 1702 4.822896 TGTGCTAAAGTTACCGAAAATGGT 59.177 37.500 0.00 0.00 46.26 3.55
875 1703 5.151389 GTGCTAAAGTTACCGAAAATGGTG 58.849 41.667 0.00 0.00 43.68 4.17
876 1704 5.049267 GTGCTAAAGTTACCGAAAATGGTGA 60.049 40.000 0.00 0.00 43.68 4.02
877 1705 5.531659 TGCTAAAGTTACCGAAAATGGTGAA 59.468 36.000 0.00 0.00 43.68 3.18
878 1706 6.039493 TGCTAAAGTTACCGAAAATGGTGAAA 59.961 34.615 0.00 0.00 43.68 2.69
879 1707 6.919115 GCTAAAGTTACCGAAAATGGTGAAAA 59.081 34.615 0.00 0.00 43.68 2.29
880 1708 7.096353 GCTAAAGTTACCGAAAATGGTGAAAAC 60.096 37.037 0.00 0.00 43.68 2.43
881 1709 5.838531 AGTTACCGAAAATGGTGAAAACA 57.161 34.783 0.00 0.00 43.68 2.83
882 1710 5.827666 AGTTACCGAAAATGGTGAAAACAG 58.172 37.500 0.00 0.00 43.68 3.16
883 1711 5.358725 AGTTACCGAAAATGGTGAAAACAGT 59.641 36.000 0.00 0.00 43.68 3.55
884 1712 4.040445 ACCGAAAATGGTGAAAACAGTG 57.960 40.909 0.00 0.00 41.85 3.66
885 1713 3.697045 ACCGAAAATGGTGAAAACAGTGA 59.303 39.130 0.00 0.00 41.85 3.41
886 1714 4.340950 ACCGAAAATGGTGAAAACAGTGAT 59.659 37.500 0.00 0.00 41.85 3.06
887 1715 5.163457 ACCGAAAATGGTGAAAACAGTGATT 60.163 36.000 0.00 0.00 41.85 2.57
888 1716 5.752955 CCGAAAATGGTGAAAACAGTGATTT 59.247 36.000 0.00 0.00 0.00 2.17
889 1717 6.257630 CCGAAAATGGTGAAAACAGTGATTTT 59.742 34.615 0.00 0.00 34.46 1.82
890 1718 7.118724 CGAAAATGGTGAAAACAGTGATTTTG 58.881 34.615 0.00 0.00 31.90 2.44
891 1719 6.923928 AAATGGTGAAAACAGTGATTTTGG 57.076 33.333 0.00 0.00 31.90 3.28
892 1720 3.791245 TGGTGAAAACAGTGATTTTGGC 58.209 40.909 0.00 0.00 31.90 4.52
893 1721 3.130633 GGTGAAAACAGTGATTTTGGCC 58.869 45.455 0.00 0.00 31.90 5.36
894 1722 3.181466 GGTGAAAACAGTGATTTTGGCCT 60.181 43.478 3.32 0.00 31.90 5.19
895 1723 4.051237 GTGAAAACAGTGATTTTGGCCTC 58.949 43.478 3.32 0.00 31.90 4.70
896 1724 3.069443 TGAAAACAGTGATTTTGGCCTCC 59.931 43.478 3.32 0.00 31.90 4.30
897 1725 2.380064 AACAGTGATTTTGGCCTCCA 57.620 45.000 3.32 0.00 0.00 3.86
898 1726 2.380064 ACAGTGATTTTGGCCTCCAA 57.620 45.000 3.32 0.00 42.29 3.53
905 1733 3.880174 TTTGGCCTCCAAATCCCAA 57.120 47.368 3.32 0.00 46.92 4.12
906 1734 2.109229 TTTGGCCTCCAAATCCCAAA 57.891 45.000 3.32 0.00 46.92 3.28
907 1735 1.347062 TTGGCCTCCAAATCCCAAAC 58.653 50.000 3.32 0.00 40.92 2.93
908 1736 0.897863 TGGCCTCCAAATCCCAAACG 60.898 55.000 3.32 0.00 0.00 3.60
909 1737 1.215382 GCCTCCAAATCCCAAACGC 59.785 57.895 0.00 0.00 0.00 4.84
910 1738 1.506262 CCTCCAAATCCCAAACGCG 59.494 57.895 3.53 3.53 0.00 6.01
911 1739 1.241315 CCTCCAAATCCCAAACGCGT 61.241 55.000 5.58 5.58 0.00 6.01
912 1740 0.109781 CTCCAAATCCCAAACGCGTG 60.110 55.000 14.98 0.00 0.00 5.34
913 1741 1.732683 CCAAATCCCAAACGCGTGC 60.733 57.895 14.98 0.00 0.00 5.34
914 1742 1.007964 CAAATCCCAAACGCGTGCA 60.008 52.632 14.98 0.00 0.00 4.57
915 1743 0.388391 CAAATCCCAAACGCGTGCAT 60.388 50.000 14.98 0.00 0.00 3.96
916 1744 1.135546 CAAATCCCAAACGCGTGCATA 60.136 47.619 14.98 0.00 0.00 3.14
917 1745 1.388547 AATCCCAAACGCGTGCATAT 58.611 45.000 14.98 0.00 0.00 1.78
918 1746 1.388547 ATCCCAAACGCGTGCATATT 58.611 45.000 14.98 0.00 0.00 1.28
919 1747 1.169577 TCCCAAACGCGTGCATATTT 58.830 45.000 14.98 0.00 0.00 1.40
920 1748 1.135546 TCCCAAACGCGTGCATATTTG 60.136 47.619 14.98 12.61 32.89 2.32
929 1757 5.101628 ACGCGTGCATATTTGATTTGATTT 58.898 33.333 12.93 0.00 0.00 2.17
1313 2141 4.394712 CTCCGGACCAGCCACCAC 62.395 72.222 0.00 0.00 35.94 4.16
1431 2259 1.719780 CGTGACGCTTCTAAGGTGTTC 59.280 52.381 0.00 0.00 0.00 3.18
1491 2319 0.824595 TGCTTGATGTGCTGTGCCTT 60.825 50.000 0.00 0.00 0.00 4.35
1613 2441 2.202987 CTGGGATGCTGTCGAGGC 60.203 66.667 3.64 3.64 0.00 4.70
1680 2508 1.300931 GTTGGTCAGCGTGCTCTCA 60.301 57.895 0.00 0.00 0.00 3.27
1724 2552 4.796495 GGGGCTTGCGGTCGGAAT 62.796 66.667 0.00 0.00 0.00 3.01
1809 2637 5.196341 TGATCGACATGTATGGGAAGTAC 57.804 43.478 0.00 0.00 0.00 2.73
1836 2664 0.250467 TTGACTGTTGCAGGAGAGCC 60.250 55.000 1.29 0.00 35.51 4.70
1879 2707 1.555075 AGGTCTGTACGTGGAATGCAT 59.445 47.619 0.00 0.00 0.00 3.96
1980 2808 2.352960 GCCGAACCAGATCACATTTCTC 59.647 50.000 0.00 0.00 0.00 2.87
2070 2898 3.901222 TGACTGAATACAAGGTGACTCCA 59.099 43.478 0.00 0.00 42.68 3.86
2161 2989 1.609320 GGATAGAGCGGATGCCCTTTC 60.609 57.143 0.00 0.00 44.31 2.62
2263 3091 2.480419 CGAAAACTAGTGGCTCTTGGTG 59.520 50.000 0.00 0.00 0.00 4.17
2277 3105 0.035152 TTGGTGCTCAGCAATCCGAT 60.035 50.000 0.00 0.00 43.00 4.18
2282 3110 0.811616 GCTCAGCAATCCGATCGGTT 60.812 55.000 32.15 22.54 36.47 4.44
2343 3171 3.567797 GCTGCGACGAGAATGGGC 61.568 66.667 0.00 0.00 0.00 5.36
2400 3228 2.949644 AGGGCAAAGTAGTGTTGTGTTC 59.050 45.455 0.00 0.00 0.00 3.18
2416 3244 0.807496 GTTCCACAGCTCTGCCATTC 59.193 55.000 0.00 0.00 0.00 2.67
2437 3265 6.920569 TTCCTTGACTAGAGTTTGTTTGTC 57.079 37.500 0.00 0.00 0.00 3.18
2496 3325 7.159372 TCTCATGACTTGTACCTTAGGAAAAC 58.841 38.462 4.77 0.61 0.00 2.43
2521 3353 7.032580 CACTAAACCACATCTTGTTGTTCAAA 58.967 34.615 0.00 0.00 35.52 2.69
2522 3354 7.543868 CACTAAACCACATCTTGTTGTTCAAAA 59.456 33.333 0.00 0.00 35.52 2.44
2597 3429 0.098200 GCGCCCGTTACCTTTGATTC 59.902 55.000 0.00 0.00 0.00 2.52
2651 3483 3.671433 GCACAGAATTGTAGTGGCATGTG 60.671 47.826 7.51 7.51 39.73 3.21
2653 3485 3.753272 ACAGAATTGTAGTGGCATGTGTC 59.247 43.478 0.00 0.00 35.25 3.67
2654 3486 3.002791 AGAATTGTAGTGGCATGTGTCG 58.997 45.455 0.00 0.00 0.00 4.35
2655 3487 1.737838 ATTGTAGTGGCATGTGTCGG 58.262 50.000 0.00 0.00 0.00 4.79
2656 3488 0.394938 TTGTAGTGGCATGTGTCGGT 59.605 50.000 0.00 0.00 0.00 4.69
2657 3489 0.320334 TGTAGTGGCATGTGTCGGTG 60.320 55.000 0.00 0.00 0.00 4.94
2751 3583 4.336433 TCTTTGCAAGAGGTTTGAGTGAAG 59.664 41.667 0.00 0.00 32.71 3.02
2753 3585 1.882623 GCAAGAGGTTTGAGTGAAGGG 59.117 52.381 0.00 0.00 0.00 3.95
2815 3648 8.857098 AGAAAAATATCCACAGGATTCATCATG 58.143 33.333 3.55 0.00 39.79 3.07
2838 3671 6.638610 TGCAAATCAAACAACCAATATAGGG 58.361 36.000 0.00 0.00 0.00 3.53
2874 3707 9.764363 AAAATCTTTTAAATCAAAGAGTCCCAC 57.236 29.630 2.60 0.00 44.21 4.61
2877 3712 6.264518 TCTTTTAAATCAAAGAGTCCCACACC 59.735 38.462 0.00 0.00 37.77 4.16
2889 3724 2.556622 GTCCCACACCGATGACAAAAAT 59.443 45.455 0.00 0.00 0.00 1.82
2894 3729 4.562394 CCACACCGATGACAAAAATATTGC 59.438 41.667 0.00 0.00 0.00 3.56
2910 3782 8.753497 AAAATATTGCCCAGTTTAACCAAAAA 57.247 26.923 0.00 0.00 0.00 1.94
2911 3783 7.977789 AATATTGCCCAGTTTAACCAAAAAG 57.022 32.000 0.00 0.00 0.00 2.27
2912 3784 5.622346 ATTGCCCAGTTTAACCAAAAAGA 57.378 34.783 0.00 0.00 0.00 2.52
2932 3805 4.798574 AGAAAAAGAAATACAAGCAGCCG 58.201 39.130 0.00 0.00 0.00 5.52
2956 3829 1.482182 TGATATGCGTGCAGTTCTCCT 59.518 47.619 0.00 0.00 0.00 3.69
3019 3892 3.229276 TCAAAATGCCGCTAACCATTG 57.771 42.857 0.00 0.00 32.40 2.82
3045 3918 1.525077 TGGTCCGGACACTTTGTGC 60.525 57.895 34.40 15.78 36.98 4.57
3117 3990 2.158726 TCCTGCAAACCGGAAGTAAAGT 60.159 45.455 9.46 0.00 0.00 2.66
3213 4087 2.843113 AGAGCCCTGCTTTTATCACTCT 59.157 45.455 0.00 0.00 39.88 3.24
3220 4094 4.187694 CTGCTTTTATCACTCTGTCCCTC 58.812 47.826 0.00 0.00 0.00 4.30
3240 4115 1.342819 CCCCCTTTCTCTCTATCTGCG 59.657 57.143 0.00 0.00 0.00 5.18
3253 4128 2.130272 ATCTGCGTAGTCTGAGACCA 57.870 50.000 9.33 0.00 32.18 4.02
3257 4132 1.281899 GCGTAGTCTGAGACCAATGC 58.718 55.000 9.33 11.07 32.18 3.56
3304 4179 3.081409 GGCCTTGCCGGACCTCTA 61.081 66.667 5.05 0.00 39.62 2.43
3318 4193 0.112606 CCTCTACCGCTCCCTGGATA 59.887 60.000 0.00 0.00 0.00 2.59
3338 4213 7.066781 TGGATATAGACTAACCACATGTCTCA 58.933 38.462 0.00 0.00 40.86 3.27
3355 4230 3.057946 GTCTCAAAGCCATGGTCAAGTTC 60.058 47.826 14.67 0.00 0.00 3.01
3361 4236 1.369625 CCATGGTCAAGTTCGCTACC 58.630 55.000 2.57 0.00 0.00 3.18
3366 4241 2.818274 CAAGTTCGCTACCGGGGC 60.818 66.667 6.32 9.20 34.56 5.80
3387 4266 0.666374 GTCAAGGTGTTTGAACCGGG 59.334 55.000 6.32 0.00 46.85 5.73
3408 4287 3.071167 GGGTACTTGAGAGAACCAACTGT 59.929 47.826 0.00 0.00 33.46 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.863275 TGACTAGCTCGTTAATCAAAGATGA 58.137 36.000 0.00 0.00 40.57 2.92
11 12 7.525688 TTGACTAGCTCGTTAATCAAAGATG 57.474 36.000 0.00 0.00 0.00 2.90
12 13 8.723942 ATTTGACTAGCTCGTTAATCAAAGAT 57.276 30.769 0.00 0.00 38.89 2.40
13 14 9.302345 CTATTTGACTAGCTCGTTAATCAAAGA 57.698 33.333 0.00 0.00 38.89 2.52
14 15 9.302345 TCTATTTGACTAGCTCGTTAATCAAAG 57.698 33.333 0.00 0.00 38.89 2.77
15 16 9.302345 CTCTATTTGACTAGCTCGTTAATCAAA 57.698 33.333 0.00 0.00 39.58 2.69
16 17 7.921214 CCTCTATTTGACTAGCTCGTTAATCAA 59.079 37.037 0.00 0.00 0.00 2.57
17 18 7.426410 CCTCTATTTGACTAGCTCGTTAATCA 58.574 38.462 0.00 0.00 0.00 2.57
18 19 6.363896 GCCTCTATTTGACTAGCTCGTTAATC 59.636 42.308 0.00 0.00 0.00 1.75
19 20 6.183360 TGCCTCTATTTGACTAGCTCGTTAAT 60.183 38.462 0.00 0.00 0.00 1.40
20 21 5.126545 TGCCTCTATTTGACTAGCTCGTTAA 59.873 40.000 0.00 0.00 0.00 2.01
21 22 4.643334 TGCCTCTATTTGACTAGCTCGTTA 59.357 41.667 0.00 0.00 0.00 3.18
22 23 3.447586 TGCCTCTATTTGACTAGCTCGTT 59.552 43.478 0.00 0.00 0.00 3.85
23 24 3.024547 TGCCTCTATTTGACTAGCTCGT 58.975 45.455 0.00 0.00 0.00 4.18
24 25 3.717400 TGCCTCTATTTGACTAGCTCG 57.283 47.619 0.00 0.00 0.00 5.03
25 26 6.339587 AGTATGCCTCTATTTGACTAGCTC 57.660 41.667 0.00 0.00 0.00 4.09
26 27 6.435904 CCTAGTATGCCTCTATTTGACTAGCT 59.564 42.308 0.00 0.00 35.60 3.32
27 28 6.350612 CCCTAGTATGCCTCTATTTGACTAGC 60.351 46.154 0.00 0.00 35.60 3.42
28 29 6.948886 TCCCTAGTATGCCTCTATTTGACTAG 59.051 42.308 0.00 0.00 36.32 2.57
29 30 6.720288 GTCCCTAGTATGCCTCTATTTGACTA 59.280 42.308 0.00 0.00 0.00 2.59
30 31 5.540719 GTCCCTAGTATGCCTCTATTTGACT 59.459 44.000 0.00 0.00 0.00 3.41
31 32 5.304614 TGTCCCTAGTATGCCTCTATTTGAC 59.695 44.000 0.00 0.00 0.00 3.18
32 33 5.464069 TGTCCCTAGTATGCCTCTATTTGA 58.536 41.667 0.00 0.00 0.00 2.69
33 34 5.808366 TGTCCCTAGTATGCCTCTATTTG 57.192 43.478 0.00 0.00 0.00 2.32
34 35 8.543774 CATATTGTCCCTAGTATGCCTCTATTT 58.456 37.037 0.00 0.00 0.00 1.40
35 36 7.680310 ACATATTGTCCCTAGTATGCCTCTATT 59.320 37.037 0.00 0.00 0.00 1.73
36 37 7.192628 ACATATTGTCCCTAGTATGCCTCTAT 58.807 38.462 0.00 0.00 0.00 1.98
37 38 6.562228 ACATATTGTCCCTAGTATGCCTCTA 58.438 40.000 0.00 0.00 0.00 2.43
38 39 5.407049 ACATATTGTCCCTAGTATGCCTCT 58.593 41.667 0.00 0.00 0.00 3.69
39 40 5.746990 ACATATTGTCCCTAGTATGCCTC 57.253 43.478 0.00 0.00 0.00 4.70
40 41 6.515512 AAACATATTGTCCCTAGTATGCCT 57.484 37.500 0.00 0.00 0.00 4.75
41 42 6.546034 ACAAAACATATTGTCCCTAGTATGCC 59.454 38.462 0.00 0.00 39.23 4.40
42 43 7.568199 ACAAAACATATTGTCCCTAGTATGC 57.432 36.000 0.00 0.00 39.23 3.14
58 59 9.013229 ACATGTGTGAATACATAGACAAAACAT 57.987 29.630 0.00 0.00 39.17 2.71
59 60 8.389779 ACATGTGTGAATACATAGACAAAACA 57.610 30.769 0.00 0.00 39.17 2.83
60 61 9.755064 GTACATGTGTGAATACATAGACAAAAC 57.245 33.333 9.11 0.00 39.17 2.43
61 62 9.719355 AGTACATGTGTGAATACATAGACAAAA 57.281 29.630 9.11 0.00 39.17 2.44
70 71 8.705134 CGAAAACTTAGTACATGTGTGAATACA 58.295 33.333 9.11 0.00 34.63 2.29
71 72 8.166706 CCGAAAACTTAGTACATGTGTGAATAC 58.833 37.037 9.11 0.00 0.00 1.89
72 73 7.874016 ACCGAAAACTTAGTACATGTGTGAATA 59.126 33.333 9.11 0.00 0.00 1.75
73 74 6.708949 ACCGAAAACTTAGTACATGTGTGAAT 59.291 34.615 9.11 0.00 0.00 2.57
74 75 6.050432 ACCGAAAACTTAGTACATGTGTGAA 58.950 36.000 9.11 0.00 0.00 3.18
75 76 5.603596 ACCGAAAACTTAGTACATGTGTGA 58.396 37.500 9.11 0.00 0.00 3.58
76 77 5.917541 ACCGAAAACTTAGTACATGTGTG 57.082 39.130 9.11 0.00 0.00 3.82
77 78 8.611654 ATTAACCGAAAACTTAGTACATGTGT 57.388 30.769 9.11 0.00 0.00 3.72
78 79 9.962759 GTATTAACCGAAAACTTAGTACATGTG 57.037 33.333 9.11 0.00 0.00 3.21
79 80 9.709495 TGTATTAACCGAAAACTTAGTACATGT 57.291 29.630 2.69 2.69 0.00 3.21
88 89 9.005777 TGCTAGAATTGTATTAACCGAAAACTT 57.994 29.630 0.00 0.00 0.00 2.66
89 90 8.556213 TGCTAGAATTGTATTAACCGAAAACT 57.444 30.769 0.00 0.00 0.00 2.66
90 91 9.221775 CATGCTAGAATTGTATTAACCGAAAAC 57.778 33.333 0.00 0.00 0.00 2.43
91 92 9.168451 TCATGCTAGAATTGTATTAACCGAAAA 57.832 29.630 0.00 0.00 0.00 2.29
92 93 8.725405 TCATGCTAGAATTGTATTAACCGAAA 57.275 30.769 0.00 0.00 0.00 3.46
93 94 8.725405 TTCATGCTAGAATTGTATTAACCGAA 57.275 30.769 0.00 0.00 0.00 4.30
94 95 8.902540 ATTCATGCTAGAATTGTATTAACCGA 57.097 30.769 0.00 0.00 34.70 4.69
152 153 9.084533 TGTCCTAAAGGCAACAATAAAGTTATT 57.915 29.630 0.00 0.00 41.41 1.40
153 154 8.644374 TGTCCTAAAGGCAACAATAAAGTTAT 57.356 30.769 0.00 0.00 41.41 1.89
154 155 8.644374 ATGTCCTAAAGGCAACAATAAAGTTA 57.356 30.769 0.00 0.00 41.41 2.24
155 156 6.969993 TGTCCTAAAGGCAACAATAAAGTT 57.030 33.333 0.00 0.00 41.41 2.66
156 157 8.823220 ATATGTCCTAAAGGCAACAATAAAGT 57.177 30.769 0.00 0.00 41.41 2.66
159 160 8.691797 GGAAATATGTCCTAAAGGCAACAATAA 58.308 33.333 4.48 0.00 34.78 1.40
160 161 8.058847 AGGAAATATGTCCTAAAGGCAACAATA 58.941 33.333 13.25 0.00 46.69 1.90
161 162 6.897413 AGGAAATATGTCCTAAAGGCAACAAT 59.103 34.615 13.25 0.00 46.69 2.71
162 163 6.252995 AGGAAATATGTCCTAAAGGCAACAA 58.747 36.000 13.25 0.00 46.69 2.83
163 164 5.826643 AGGAAATATGTCCTAAAGGCAACA 58.173 37.500 13.25 0.00 46.69 3.33
174 175 6.173339 TGACAAGAGTGAAGGAAATATGTCC 58.827 40.000 3.38 3.38 35.10 4.02
175 176 7.335422 ACATGACAAGAGTGAAGGAAATATGTC 59.665 37.037 0.00 0.00 36.19 3.06
176 177 7.120285 CACATGACAAGAGTGAAGGAAATATGT 59.880 37.037 0.00 0.00 35.33 2.29
177 178 7.335171 TCACATGACAAGAGTGAAGGAAATATG 59.665 37.037 0.00 0.00 39.15 1.78
178 179 7.397221 TCACATGACAAGAGTGAAGGAAATAT 58.603 34.615 0.00 0.00 39.15 1.28
179 180 6.768483 TCACATGACAAGAGTGAAGGAAATA 58.232 36.000 0.00 0.00 39.15 1.40
180 181 5.624159 TCACATGACAAGAGTGAAGGAAAT 58.376 37.500 0.00 0.00 39.15 2.17
181 182 5.034852 TCACATGACAAGAGTGAAGGAAA 57.965 39.130 0.00 0.00 39.15 3.13
182 183 4.687901 TCACATGACAAGAGTGAAGGAA 57.312 40.909 0.00 0.00 39.15 3.36
183 184 4.572909 CATCACATGACAAGAGTGAAGGA 58.427 43.478 0.00 0.00 44.47 3.36
184 185 3.126514 GCATCACATGACAAGAGTGAAGG 59.873 47.826 0.00 8.70 44.47 3.46
185 186 3.749609 TGCATCACATGACAAGAGTGAAG 59.250 43.478 0.00 8.93 44.47 3.02
186 187 3.742385 TGCATCACATGACAAGAGTGAA 58.258 40.909 0.00 0.00 44.47 3.18
187 188 3.405823 TGCATCACATGACAAGAGTGA 57.594 42.857 0.00 10.06 45.26 3.41
188 189 3.064958 GGATGCATCACATGACAAGAGTG 59.935 47.826 27.25 0.00 39.84 3.51
189 190 3.276857 GGATGCATCACATGACAAGAGT 58.723 45.455 27.25 0.00 39.84 3.24
190 191 3.275999 TGGATGCATCACATGACAAGAG 58.724 45.455 27.25 0.00 39.84 2.85
191 192 3.353370 TGGATGCATCACATGACAAGA 57.647 42.857 27.25 0.00 39.84 3.02
192 193 4.443913 TTTGGATGCATCACATGACAAG 57.556 40.909 27.25 0.00 39.84 3.16
193 194 4.142116 GGATTTGGATGCATCACATGACAA 60.142 41.667 27.25 17.36 39.84 3.18
194 195 3.382227 GGATTTGGATGCATCACATGACA 59.618 43.478 27.25 12.47 39.84 3.58
239 240 9.160496 TCATTTTGTGCTAAAGTTGTTGAAAAT 57.840 25.926 0.00 0.00 0.00 1.82
245 246 9.816354 AATAGTTCATTTTGTGCTAAAGTTGTT 57.184 25.926 0.00 0.00 0.00 2.83
246 247 9.816354 AAATAGTTCATTTTGTGCTAAAGTTGT 57.184 25.926 0.00 0.00 32.74 3.32
317 318 6.915843 GGTAGGACATAAACGCCATAATTTTG 59.084 38.462 0.00 0.00 0.00 2.44
328 329 4.095483 ACGTGTCTAGGTAGGACATAAACG 59.905 45.833 0.00 0.00 44.04 3.60
418 419 9.317936 CTACATGTCACTCTTAAAATAGCATCA 57.682 33.333 0.00 0.00 0.00 3.07
420 421 8.486210 TCCTACATGTCACTCTTAAAATAGCAT 58.514 33.333 0.00 0.00 0.00 3.79
431 432 8.255111 TCATCATTTATCCTACATGTCACTCT 57.745 34.615 0.00 0.00 0.00 3.24
437 438 6.329986 TCCACCTCATCATTTATCCTACATGT 59.670 38.462 2.69 2.69 0.00 3.21
440 441 5.307976 CCTCCACCTCATCATTTATCCTACA 59.692 44.000 0.00 0.00 0.00 2.74
521 522 8.427276 TGATGAGACATATTGTGCTAAGAGATT 58.573 33.333 0.00 0.00 0.00 2.40
528 529 5.262588 ACGTGATGAGACATATTGTGCTA 57.737 39.130 0.00 0.00 0.00 3.49
529 530 4.128925 ACGTGATGAGACATATTGTGCT 57.871 40.909 0.00 0.00 0.00 4.40
530 531 4.864916 AACGTGATGAGACATATTGTGC 57.135 40.909 0.00 0.00 0.00 4.57
531 532 7.904977 CCTAAAAACGTGATGAGACATATTGTG 59.095 37.037 0.00 0.00 0.00 3.33
545 546 9.715121 AATAACTAGTCATTCCTAAAAACGTGA 57.285 29.630 0.00 0.00 0.00 4.35
640 641 7.063780 CGTACGATGGTTGATAAGGTAGTTTTT 59.936 37.037 10.44 0.00 0.00 1.94
661 666 1.070710 TGGCGTTTAAAAGCACGTACG 60.071 47.619 24.23 15.01 38.70 3.67
666 671 1.068541 CCTCCTGGCGTTTAAAAGCAC 60.069 52.381 24.23 15.25 35.00 4.40
670 675 2.223745 GTCACCTCCTGGCGTTTAAAA 58.776 47.619 0.00 0.00 36.63 1.52
671 676 1.874739 CGTCACCTCCTGGCGTTTAAA 60.875 52.381 0.00 0.00 43.37 1.52
682 687 3.064931 CCTAAGAACAAACGTCACCTCC 58.935 50.000 0.00 0.00 0.00 4.30
685 690 1.534163 GCCCTAAGAACAAACGTCACC 59.466 52.381 0.00 0.00 0.00 4.02
715 720 3.406559 GGAAACGCTATGGCCGTC 58.593 61.111 0.00 0.00 34.44 4.79
734 739 3.676093 AGTTTGGCAGTCCTAGCTTTAC 58.324 45.455 0.00 0.00 0.00 2.01
740 745 3.600388 CAGGTAAGTTTGGCAGTCCTAG 58.400 50.000 0.00 0.00 0.00 3.02
741 746 2.290071 GCAGGTAAGTTTGGCAGTCCTA 60.290 50.000 0.00 0.00 0.00 2.94
742 747 1.545651 GCAGGTAAGTTTGGCAGTCCT 60.546 52.381 0.00 0.00 0.00 3.85
746 751 0.951558 AACGCAGGTAAGTTTGGCAG 59.048 50.000 0.00 0.00 0.00 4.85
748 753 0.663269 GCAACGCAGGTAAGTTTGGC 60.663 55.000 0.00 0.00 0.00 4.52
749 754 0.385473 CGCAACGCAGGTAAGTTTGG 60.385 55.000 0.00 0.00 0.00 3.28
750 755 0.306533 ACGCAACGCAGGTAAGTTTG 59.693 50.000 0.00 0.00 0.00 2.93
751 756 1.018910 AACGCAACGCAGGTAAGTTT 58.981 45.000 0.00 0.00 0.00 2.66
752 757 0.306533 CAACGCAACGCAGGTAAGTT 59.693 50.000 0.00 0.00 0.00 2.66
810 1638 4.262249 GGGCACTTTAGCACAATTTAACCA 60.262 41.667 0.00 0.00 38.00 3.67
838 1666 6.785337 ACTTTAGCACAAAATATAACCCCC 57.215 37.500 0.00 0.00 0.00 5.40
839 1667 8.192774 GGTAACTTTAGCACAAAATATAACCCC 58.807 37.037 0.00 0.00 0.00 4.95
840 1668 7.911727 CGGTAACTTTAGCACAAAATATAACCC 59.088 37.037 0.00 0.00 0.00 4.11
841 1669 8.667463 TCGGTAACTTTAGCACAAAATATAACC 58.333 33.333 0.00 0.00 0.00 2.85
846 1674 9.400638 CATTTTCGGTAACTTTAGCACAAAATA 57.599 29.630 12.82 0.00 34.69 1.40
847 1675 7.383843 CCATTTTCGGTAACTTTAGCACAAAAT 59.616 33.333 9.78 9.78 35.67 1.82
848 1676 6.697892 CCATTTTCGGTAACTTTAGCACAAAA 59.302 34.615 7.17 7.17 32.17 2.44
849 1677 6.183360 ACCATTTTCGGTAACTTTAGCACAAA 60.183 34.615 0.00 0.00 37.57 2.83
850 1678 5.299782 ACCATTTTCGGTAACTTTAGCACAA 59.700 36.000 0.00 0.00 37.57 3.33
851 1679 4.822896 ACCATTTTCGGTAACTTTAGCACA 59.177 37.500 0.00 0.00 37.57 4.57
852 1680 5.049267 TCACCATTTTCGGTAACTTTAGCAC 60.049 40.000 0.00 0.00 37.07 4.40
853 1681 5.064558 TCACCATTTTCGGTAACTTTAGCA 58.935 37.500 0.00 0.00 37.07 3.49
854 1682 5.616488 TCACCATTTTCGGTAACTTTAGC 57.384 39.130 0.00 0.00 37.07 3.09
855 1683 7.916450 TGTTTTCACCATTTTCGGTAACTTTAG 59.084 33.333 0.00 0.00 37.07 1.85
856 1684 7.769220 TGTTTTCACCATTTTCGGTAACTTTA 58.231 30.769 0.00 0.00 37.07 1.85
857 1685 6.631962 TGTTTTCACCATTTTCGGTAACTTT 58.368 32.000 0.00 0.00 37.07 2.66
858 1686 6.127563 ACTGTTTTCACCATTTTCGGTAACTT 60.128 34.615 0.00 0.00 37.07 2.66
859 1687 5.358725 ACTGTTTTCACCATTTTCGGTAACT 59.641 36.000 0.00 0.00 37.07 2.24
860 1688 5.457473 CACTGTTTTCACCATTTTCGGTAAC 59.543 40.000 0.00 0.00 37.07 2.50
861 1689 5.357314 TCACTGTTTTCACCATTTTCGGTAA 59.643 36.000 0.00 0.00 37.07 2.85
862 1690 4.882427 TCACTGTTTTCACCATTTTCGGTA 59.118 37.500 0.00 0.00 37.07 4.02
863 1691 3.697045 TCACTGTTTTCACCATTTTCGGT 59.303 39.130 0.00 0.00 41.07 4.69
864 1692 4.300189 TCACTGTTTTCACCATTTTCGG 57.700 40.909 0.00 0.00 0.00 4.30
865 1693 6.826893 AAATCACTGTTTTCACCATTTTCG 57.173 33.333 0.00 0.00 0.00 3.46
866 1694 7.408910 CCAAAATCACTGTTTTCACCATTTTC 58.591 34.615 0.00 0.00 0.00 2.29
867 1695 6.183360 GCCAAAATCACTGTTTTCACCATTTT 60.183 34.615 0.00 0.00 0.00 1.82
868 1696 5.296531 GCCAAAATCACTGTTTTCACCATTT 59.703 36.000 0.00 0.00 0.00 2.32
869 1697 4.815846 GCCAAAATCACTGTTTTCACCATT 59.184 37.500 0.00 0.00 0.00 3.16
870 1698 4.379652 GCCAAAATCACTGTTTTCACCAT 58.620 39.130 0.00 0.00 0.00 3.55
871 1699 3.431486 GGCCAAAATCACTGTTTTCACCA 60.431 43.478 0.00 0.00 0.00 4.17
872 1700 3.130633 GGCCAAAATCACTGTTTTCACC 58.869 45.455 0.00 0.00 0.00 4.02
873 1701 4.051237 GAGGCCAAAATCACTGTTTTCAC 58.949 43.478 5.01 0.00 0.00 3.18
874 1702 3.069443 GGAGGCCAAAATCACTGTTTTCA 59.931 43.478 5.01 0.00 0.00 2.69
875 1703 3.069443 TGGAGGCCAAAATCACTGTTTTC 59.931 43.478 5.01 0.00 0.00 2.29
876 1704 3.037549 TGGAGGCCAAAATCACTGTTTT 58.962 40.909 5.01 0.00 0.00 2.43
877 1705 2.676748 TGGAGGCCAAAATCACTGTTT 58.323 42.857 5.01 0.00 0.00 2.83
878 1706 2.380064 TGGAGGCCAAAATCACTGTT 57.620 45.000 5.01 0.00 0.00 3.16
879 1707 2.380064 TTGGAGGCCAAAATCACTGT 57.620 45.000 5.01 0.00 40.92 3.55
888 1716 1.347062 GTTTGGGATTTGGAGGCCAA 58.653 50.000 5.01 0.00 42.29 4.52
889 1717 0.897863 CGTTTGGGATTTGGAGGCCA 60.898 55.000 5.01 0.00 0.00 5.36
890 1718 1.890174 CGTTTGGGATTTGGAGGCC 59.110 57.895 0.00 0.00 0.00 5.19
891 1719 1.215382 GCGTTTGGGATTTGGAGGC 59.785 57.895 0.00 0.00 0.00 4.70
892 1720 1.241315 ACGCGTTTGGGATTTGGAGG 61.241 55.000 5.58 0.00 0.00 4.30
893 1721 0.109781 CACGCGTTTGGGATTTGGAG 60.110 55.000 10.22 0.00 0.00 3.86
894 1722 1.953017 CACGCGTTTGGGATTTGGA 59.047 52.632 10.22 0.00 0.00 3.53
895 1723 1.732683 GCACGCGTTTGGGATTTGG 60.733 57.895 10.22 0.00 0.00 3.28
896 1724 0.388391 ATGCACGCGTTTGGGATTTG 60.388 50.000 10.22 0.00 0.00 2.32
897 1725 1.169577 TATGCACGCGTTTGGGATTT 58.830 45.000 10.22 0.00 0.00 2.17
898 1726 1.388547 ATATGCACGCGTTTGGGATT 58.611 45.000 10.22 0.00 0.00 3.01
899 1727 1.388547 AATATGCACGCGTTTGGGAT 58.611 45.000 10.22 8.32 0.00 3.85
900 1728 1.135546 CAAATATGCACGCGTTTGGGA 60.136 47.619 10.22 0.00 0.00 4.37
901 1729 1.135546 TCAAATATGCACGCGTTTGGG 60.136 47.619 10.22 0.00 33.55 4.12
902 1730 2.254918 TCAAATATGCACGCGTTTGG 57.745 45.000 10.22 0.00 33.55 3.28
903 1731 4.323070 TCAAATCAAATATGCACGCGTTTG 59.677 37.500 10.22 11.23 33.91 2.93
904 1732 4.480541 TCAAATCAAATATGCACGCGTTT 58.519 34.783 10.22 0.00 0.00 3.60
905 1733 4.090138 TCAAATCAAATATGCACGCGTT 57.910 36.364 10.22 0.00 0.00 4.84
906 1734 3.755965 TCAAATCAAATATGCACGCGT 57.244 38.095 5.58 5.58 0.00 6.01
907 1735 5.229678 TCAAATCAAATCAAATATGCACGCG 59.770 36.000 3.53 3.53 0.00 6.01
908 1736 6.572153 TCAAATCAAATCAAATATGCACGC 57.428 33.333 0.00 0.00 0.00 5.34
909 1737 9.416058 CAAATCAAATCAAATCAAATATGCACG 57.584 29.630 0.00 0.00 0.00 5.34
920 1748 9.476761 GCGGTAAAAATCAAATCAAATCAAATC 57.523 29.630 0.00 0.00 0.00 2.17
929 1757 2.416162 GCCGGCGGTAAAAATCAAATCA 60.416 45.455 28.82 0.00 0.00 2.57
973 1801 3.771160 GGAAGCCGGCGAGAGGAA 61.771 66.667 23.20 0.00 0.00 3.36
1258 2086 2.430367 GGAAGGGAACGTGTGGCT 59.570 61.111 0.00 0.00 0.00 4.75
1431 2259 3.508840 GGGCTGGCCATTTCGTCG 61.509 66.667 16.34 0.00 37.98 5.12
1613 2441 3.509967 GTGTACCAAAAATCCCCTGAAGG 59.490 47.826 0.00 0.00 0.00 3.46
1652 2480 4.308458 TGACCAACGTGGCCTCCG 62.308 66.667 3.32 9.27 42.67 4.63
1680 2508 1.342174 CCATCCAAGTTTGCACAAGCT 59.658 47.619 0.00 0.00 42.74 3.74
1722 2550 0.732571 CATAAGCGTGAACGGCCATT 59.267 50.000 2.24 0.00 40.23 3.16
1724 2552 1.004320 ACATAAGCGTGAACGGCCA 60.004 52.632 2.24 0.00 40.23 5.36
1809 2637 1.165907 TGCAACAGTCAAGCTTCCCG 61.166 55.000 0.00 0.00 0.00 5.14
1836 2664 5.111989 TCCTTCTCGCATACAATCTGAAAG 58.888 41.667 0.00 0.00 0.00 2.62
1965 2793 3.176552 AGAGCGAGAAATGTGATCTGG 57.823 47.619 0.00 0.00 0.00 3.86
1980 2808 1.702886 CACAACCTGTCAGTAGAGCG 58.297 55.000 0.00 0.00 0.00 5.03
2070 2898 3.835978 CACATCCATAATGGGCCATCATT 59.164 43.478 21.48 7.90 39.90 2.57
2121 2949 3.137176 TCCTCTCAATGGCCTCCATAAAG 59.863 47.826 3.32 0.78 44.40 1.85
2238 3066 1.359459 GAGCCACTAGTTTTCGCCCG 61.359 60.000 0.00 0.00 0.00 6.13
2263 3091 0.811616 AACCGATCGGATTGCTGAGC 60.812 55.000 39.55 0.00 38.96 4.26
2277 3105 4.819105 ATTCCTGATAGTCACAAACCGA 57.181 40.909 0.00 0.00 0.00 4.69
2343 3171 1.890979 GGCCTCATGCATCACCTCG 60.891 63.158 0.00 0.00 43.89 4.63
2400 3228 0.323178 AAGGAATGGCAGAGCTGTGG 60.323 55.000 13.44 0.00 0.00 4.17
2416 3244 4.318831 GCGACAAACAAACTCTAGTCAAGG 60.319 45.833 0.00 0.00 0.00 3.61
2437 3265 2.813754 TCCCAGAAGAGAAATGTTTGCG 59.186 45.455 0.00 0.00 0.00 4.85
2443 3271 3.195825 ACGGTAGTCCCAGAAGAGAAATG 59.804 47.826 0.00 0.00 0.00 2.32
2447 3275 2.561419 CAAACGGTAGTCCCAGAAGAGA 59.439 50.000 0.00 0.00 0.00 3.10
2496 3325 6.130298 TGAACAACAAGATGTGGTTTAGTG 57.870 37.500 4.84 0.00 44.06 2.74
2563 3395 1.135315 GCGCACGATGCAGTGAATT 59.865 52.632 10.09 0.00 45.36 2.17
2581 3413 1.444836 TGCGAATCAAAGGTAACGGG 58.555 50.000 0.00 0.00 46.39 5.28
2582 3414 2.739913 TCTTGCGAATCAAAGGTAACGG 59.260 45.455 0.00 0.00 46.39 4.44
2583 3415 4.600012 ATCTTGCGAATCAAAGGTAACG 57.400 40.909 0.00 0.00 46.39 3.18
2614 3446 7.665559 ACAATTCTGTGCTTTTCCTAATACTGA 59.334 33.333 0.00 0.00 33.30 3.41
2651 3483 8.696175 CAAAATTTTATAGGTTTTGACACCGAC 58.304 33.333 2.44 0.00 42.47 4.79
2653 3485 8.582433 ACAAAATTTTATAGGTTTTGACACCG 57.418 30.769 18.29 0.00 42.47 4.94
2753 3585 9.744468 ATTGCGGTACATTTAATAGGAATTTTC 57.256 29.630 0.00 0.00 0.00 2.29
2815 3648 6.872920 TCCCTATATTGGTTGTTTGATTTGC 58.127 36.000 2.42 0.00 0.00 3.68
2873 3706 4.381505 GGGCAATATTTTTGTCATCGGTGT 60.382 41.667 0.00 0.00 0.00 4.16
2874 3707 4.111916 GGGCAATATTTTTGTCATCGGTG 58.888 43.478 0.00 0.00 0.00 4.94
2877 3712 4.997565 ACTGGGCAATATTTTTGTCATCG 58.002 39.130 0.00 0.00 0.00 3.84
2889 3724 6.732896 TCTTTTTGGTTAAACTGGGCAATA 57.267 33.333 0.00 0.00 0.00 1.90
2894 3729 8.554835 TTCTTTTTCTTTTTGGTTAAACTGGG 57.445 30.769 0.00 0.00 0.00 4.45
2910 3782 4.518970 TCGGCTGCTTGTATTTCTTTTTCT 59.481 37.500 0.00 0.00 0.00 2.52
2911 3783 4.794169 TCGGCTGCTTGTATTTCTTTTTC 58.206 39.130 0.00 0.00 0.00 2.29
2912 3784 4.321230 CCTCGGCTGCTTGTATTTCTTTTT 60.321 41.667 0.00 0.00 0.00 1.94
2922 3795 0.833287 ATATCACCTCGGCTGCTTGT 59.167 50.000 0.00 0.00 0.00 3.16
2932 3805 1.594862 GAACTGCACGCATATCACCTC 59.405 52.381 0.00 0.00 0.00 3.85
2956 3829 5.261216 CCTTAGGGATTGGAGCTAAACAAA 58.739 41.667 2.59 0.00 33.58 2.83
3045 3918 4.137872 ACGTACGGCGGTGGATGG 62.138 66.667 21.06 0.00 46.52 3.51
3117 3990 3.918253 ATCCGCAAAGCTCCGCCAA 62.918 57.895 2.00 0.00 0.00 4.52
3170 4043 1.045911 GTGGTTTTTGGCTGGGTCCA 61.046 55.000 0.00 0.00 0.00 4.02
3213 4087 0.252742 GAGAGAAAGGGGGAGGGACA 60.253 60.000 0.00 0.00 0.00 4.02
3220 4094 1.342819 CGCAGATAGAGAGAAAGGGGG 59.657 57.143 0.00 0.00 0.00 5.40
3240 4115 1.927895 CGGCATTGGTCTCAGACTAC 58.072 55.000 4.40 0.00 32.47 2.73
3253 4128 3.910914 TTGGTGTAGCGGCGGCATT 62.911 57.895 19.21 0.80 43.41 3.56
3257 4132 4.690719 TGGTTGGTGTAGCGGCGG 62.691 66.667 9.78 0.00 0.00 6.13
3303 4178 2.648304 AGTCTATATCCAGGGAGCGGTA 59.352 50.000 0.00 0.00 0.00 4.02
3304 4179 1.429687 AGTCTATATCCAGGGAGCGGT 59.570 52.381 0.00 0.00 0.00 5.68
3318 4193 6.109359 GCTTTGAGACATGTGGTTAGTCTAT 58.891 40.000 1.15 0.00 42.29 1.98
3338 4213 0.598065 GCGAACTTGACCATGGCTTT 59.402 50.000 13.04 0.00 0.00 3.51
3361 4236 4.636435 AACACCTTGACCGCCCCG 62.636 66.667 0.00 0.00 0.00 5.73
3366 4241 0.306533 CGGTTCAAACACCTTGACCG 59.693 55.000 11.35 11.35 43.90 4.79
3385 4264 2.638363 AGTTGGTTCTCTCAAGTACCCC 59.362 50.000 0.00 0.00 41.12 4.95
3387 4266 4.308265 GACAGTTGGTTCTCTCAAGTACC 58.692 47.826 0.00 0.00 41.92 3.34


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

AutoCloner maintained by Alex Coulton.