Multiple sequence alignment - TraesCS3A01G528500

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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 TraesCS3A01G528500 chr3A 100.000 5165 0 0 1 5165 742444153 742438989 0.000000e+00 9539.0
1 TraesCS3A01G528500 chr3D 91.229 2839 137 53 123 2876 609089385 609086574 0.000000e+00 3760.0
2 TraesCS3A01G528500 chr3D 92.373 2229 115 26 2947 5164 609086572 609084388 0.000000e+00 3123.0
3 TraesCS3A01G528500 chr3B 88.088 2913 166 77 73 2876 819792492 819789652 0.000000e+00 3290.0
4 TraesCS3A01G528500 chr3B 90.799 2239 130 36 2947 5155 819789650 819787458 0.000000e+00 2924.0
5 TraesCS3A01G528500 chr2D 88.031 259 14 12 4834 5079 623474986 623474732 1.820000e-74 291.0
6 TraesCS3A01G528500 chr2D 83.562 292 29 11 3550 3837 623496454 623496178 6.640000e-64 255.0
7 TraesCS3A01G528500 chr2D 78.832 137 24 4 5006 5142 598308983 598308852 2.560000e-13 87.9
8 TraesCS3A01G528500 chr2D 76.136 176 24 12 4873 5041 642203691 642203527 5.550000e-10 76.8
9 TraesCS3A01G528500 chr2B 88.889 207 18 5 4131 4336 765484586 765484384 3.090000e-62 250.0
10 TraesCS3A01G528500 chr2B 75.812 277 46 11 4873 5143 799614132 799614393 2.530000e-23 121.0
11 TraesCS3A01G528500 chr4D 85.470 234 16 8 334 558 477874332 477874556 1.450000e-55 228.0
12 TraesCS3A01G528500 chr4D 92.373 118 7 2 128 244 477874112 477874228 3.200000e-37 167.0
13 TraesCS3A01G528500 chr2A 82.007 289 32 11 3550 3834 754708240 754707968 1.450000e-55 228.0
14 TraesCS3A01G528500 chr2A 77.143 210 36 9 4915 5118 766919390 766919187 1.520000e-20 111.0
15 TraesCS3A01G528500 chr2A 81.522 92 9 7 4828 4912 766973932 766973842 9.280000e-08 69.4
16 TraesCS3A01G528500 chr7B 81.863 204 17 13 398 597 207959625 207959438 2.490000e-33 154.0
17 TraesCS3A01G528500 chr7B 81.373 204 15 14 398 597 354697013 354696829 1.500000e-30 145.0
18 TraesCS3A01G528500 chr1B 80.882 204 19 13 398 597 488600567 488600380 5.390000e-30 143.0
19 TraesCS3A01G528500 chr6B 86.667 120 11 3 3984 4099 701866517 701866635 1.510000e-25 128.0
20 TraesCS3A01G528500 chr6B 72.785 316 74 10 1667 1979 701863856 701864162 4.260000e-16 97.1
21 TraesCS3A01G528500 chr6B 82.609 92 16 0 2543 2634 701864917 701865008 1.190000e-11 82.4
22 TraesCS3A01G528500 chr6A 84.746 118 13 3 3986 4099 606965203 606965319 4.230000e-21 113.0
23 TraesCS3A01G528500 chr6A 72.555 317 73 10 1667 1979 606962440 606962746 1.980000e-14 91.6
24 TraesCS3A01G528500 chr6D 73.354 319 67 14 1667 1979 460649431 460649737 9.150000e-18 102.0
25 TraesCS3A01G528500 chr6D 82.609 92 16 0 2543 2634 460650580 460650671 1.190000e-11 82.4


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 TraesCS3A01G528500 chr3A 742438989 742444153 5164 True 9539.0 9539 100.0000 1 5165 1 chr3A.!!$R1 5164
1 TraesCS3A01G528500 chr3D 609084388 609089385 4997 True 3441.5 3760 91.8010 123 5164 2 chr3D.!!$R1 5041
2 TraesCS3A01G528500 chr3B 819787458 819792492 5034 True 3107.0 3290 89.4435 73 5155 2 chr3B.!!$R1 5082

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
43 44 0.034059 CCGCTCGAATTATGCTCCCT 59.966 55.0 0.00 0.00 0.00 4.20 F
1855 1961 0.033894 TGCACTCATCCATGCACCAT 60.034 50.0 0.00 0.00 46.63 3.55 F
2293 2428 0.240945 ACGTTTACCTCGTACGGTGG 59.759 55.0 16.52 19.23 39.78 4.61 F
3162 3313 0.324091 CTGGGCAAAGCTCTTCCCAT 60.324 55.0 17.06 0.00 46.71 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2136 0.319469 GGTGGTGGAAAAATGTGGCG 60.319 55.000 0.0 0.0 0.00 5.69 R
2903 3054 0.535335 GCAGGGGAATCAGTCACGTA 59.465 55.000 0.0 0.0 0.00 3.57 R
3980 4144 1.070134 TCTTCCACTTGTCCTGGTTCG 59.930 52.381 0.0 0.0 0.00 3.95 R
4812 4993 0.250513 GGCAGAGGAGTGGTAACTGG 59.749 60.000 0.0 0.0 36.52 4.00 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
17 18 3.518068 GGATTTTGGCGGGCTCGG 61.518 66.667 8.71 0.00 36.79 4.63
35 36 2.504032 CAGGGGCCGCTCGAATTA 59.496 61.111 21.37 0.00 0.00 1.40
36 37 1.071471 CAGGGGCCGCTCGAATTAT 59.929 57.895 21.37 0.00 0.00 1.28
37 38 1.071471 AGGGGCCGCTCGAATTATG 59.929 57.895 18.22 0.00 0.00 1.90
38 39 2.617274 GGGGCCGCTCGAATTATGC 61.617 63.158 13.57 0.00 0.00 3.14
39 40 1.598130 GGGCCGCTCGAATTATGCT 60.598 57.895 0.00 0.00 0.00 3.79
40 41 1.569479 GGGCCGCTCGAATTATGCTC 61.569 60.000 0.00 0.00 0.00 4.26
41 42 1.569479 GGCCGCTCGAATTATGCTCC 61.569 60.000 0.00 0.00 0.00 4.70
42 43 1.569479 GCCGCTCGAATTATGCTCCC 61.569 60.000 0.00 0.00 0.00 4.30
43 44 0.034059 CCGCTCGAATTATGCTCCCT 59.966 55.000 0.00 0.00 0.00 4.20
44 45 1.423395 CGCTCGAATTATGCTCCCTC 58.577 55.000 0.00 0.00 0.00 4.30
45 46 1.802069 GCTCGAATTATGCTCCCTCC 58.198 55.000 0.00 0.00 0.00 4.30
46 47 1.609320 GCTCGAATTATGCTCCCTCCC 60.609 57.143 0.00 0.00 0.00 4.30
47 48 0.679505 TCGAATTATGCTCCCTCCCG 59.320 55.000 0.00 0.00 0.00 5.14
48 49 0.320771 CGAATTATGCTCCCTCCCGG 60.321 60.000 0.00 0.00 0.00 5.73
49 50 1.056660 GAATTATGCTCCCTCCCGGA 58.943 55.000 0.73 0.00 38.83 5.14
50 51 1.630878 GAATTATGCTCCCTCCCGGAT 59.369 52.381 0.73 0.00 41.00 4.18
51 52 1.747444 ATTATGCTCCCTCCCGGATT 58.253 50.000 0.73 0.00 41.00 3.01
52 53 1.518367 TTATGCTCCCTCCCGGATTT 58.482 50.000 0.73 0.00 41.00 2.17
53 54 0.764890 TATGCTCCCTCCCGGATTTG 59.235 55.000 0.73 0.00 41.00 2.32
54 55 1.281925 ATGCTCCCTCCCGGATTTGT 61.282 55.000 0.73 0.00 41.00 2.83
55 56 1.303282 GCTCCCTCCCGGATTTGTT 59.697 57.895 0.73 0.00 41.00 2.83
56 57 0.323451 GCTCCCTCCCGGATTTGTTT 60.323 55.000 0.73 0.00 41.00 2.83
57 58 1.891011 GCTCCCTCCCGGATTTGTTTT 60.891 52.381 0.73 0.00 41.00 2.43
58 59 1.818674 CTCCCTCCCGGATTTGTTTTG 59.181 52.381 0.73 0.00 41.00 2.44
59 60 1.146152 TCCCTCCCGGATTTGTTTTGT 59.854 47.619 0.73 0.00 34.86 2.83
60 61 1.272212 CCCTCCCGGATTTGTTTTGTG 59.728 52.381 0.73 0.00 0.00 3.33
61 62 1.336795 CCTCCCGGATTTGTTTTGTGC 60.337 52.381 0.73 0.00 0.00 4.57
62 63 0.676736 TCCCGGATTTGTTTTGTGCC 59.323 50.000 0.73 0.00 0.00 5.01
63 64 0.320334 CCCGGATTTGTTTTGTGCCC 60.320 55.000 0.73 0.00 0.00 5.36
64 65 0.665972 CCGGATTTGTTTTGTGCCCG 60.666 55.000 0.00 0.00 35.68 6.13
65 66 0.665972 CGGATTTGTTTTGTGCCCGG 60.666 55.000 0.00 0.00 32.64 5.73
66 67 0.676736 GGATTTGTTTTGTGCCCGGA 59.323 50.000 0.73 0.00 0.00 5.14
67 68 1.275010 GGATTTGTTTTGTGCCCGGAT 59.725 47.619 0.73 0.00 0.00 4.18
68 69 2.289382 GGATTTGTTTTGTGCCCGGATT 60.289 45.455 0.73 0.00 0.00 3.01
69 70 2.517650 TTTGTTTTGTGCCCGGATTC 57.482 45.000 0.73 0.00 0.00 2.52
70 71 0.676736 TTGTTTTGTGCCCGGATTCC 59.323 50.000 0.73 0.00 0.00 3.01
101 102 0.239879 TCCGCGATTTGGTTTTCTGC 59.760 50.000 8.23 0.00 0.00 4.26
122 123 2.849646 CCGATTCCCCTCCCTCCC 60.850 72.222 0.00 0.00 0.00 4.30
124 125 2.849646 GATTCCCCTCCCTCCCGG 60.850 72.222 0.00 0.00 0.00 5.73
144 158 2.335712 GCTTGCTTCTTGACCCCGG 61.336 63.158 0.00 0.00 0.00 5.73
151 165 2.045340 CTTGACCCCGGCGGATTT 60.045 61.111 30.79 11.00 34.64 2.17
188 205 3.772636 CGATGCGGACACAGACAG 58.227 61.111 0.00 0.00 0.00 3.51
221 239 1.989706 TTTCAGACTTTTTCCCCCGG 58.010 50.000 0.00 0.00 0.00 5.73
236 254 2.202427 CGGGTTGAATTTCGCGGC 60.202 61.111 6.13 0.00 36.60 6.53
274 292 0.592754 GTCGCCTCTCCGATTCTTCG 60.593 60.000 0.00 0.00 45.08 3.79
328 346 0.108615 ATCGGGACTCTGTTCAAGCG 60.109 55.000 0.00 0.00 0.00 4.68
330 348 1.671742 GGGACTCTGTTCAAGCGGA 59.328 57.895 0.00 0.00 0.00 5.54
331 349 0.250513 GGGACTCTGTTCAAGCGGAT 59.749 55.000 0.00 0.00 0.00 4.18
332 350 1.339151 GGGACTCTGTTCAAGCGGATT 60.339 52.381 0.00 0.00 0.00 3.01
333 351 2.427506 GGACTCTGTTCAAGCGGATTT 58.572 47.619 0.00 0.00 0.00 2.17
402 453 6.916360 TTTTATTTCTGGATCTGTTTGGCT 57.084 33.333 0.00 0.00 0.00 4.75
403 454 6.916360 TTTATTTCTGGATCTGTTTGGCTT 57.084 33.333 0.00 0.00 0.00 4.35
404 455 4.796038 ATTTCTGGATCTGTTTGGCTTG 57.204 40.909 0.00 0.00 0.00 4.01
405 456 1.538047 TCTGGATCTGTTTGGCTTGC 58.462 50.000 0.00 0.00 0.00 4.01
465 528 9.585099 CAGCCAAAGAATTTTACTGCATAATAA 57.415 29.630 0.00 0.00 35.03 1.40
519 586 0.443869 CTGACCGCCAGATTTGTTCG 59.556 55.000 0.00 0.00 45.78 3.95
521 588 0.165944 GACCGCCAGATTTGTTCGTG 59.834 55.000 0.00 0.00 0.00 4.35
538 605 7.490962 TGTTCGTGTGTCTTTGATTTCTATT 57.509 32.000 0.00 0.00 0.00 1.73
540 617 7.855409 TGTTCGTGTGTCTTTGATTTCTATTTG 59.145 33.333 0.00 0.00 0.00 2.32
638 718 5.337788 GAGGTGATCTCACTCCCCTATAAT 58.662 45.833 9.98 0.00 45.73 1.28
683 763 1.151199 TCCCCTACTATGGCTATGGCA 59.849 52.381 2.58 0.00 43.52 4.92
700 789 1.004745 GGCAACTCCTCCTCCATCAAA 59.995 52.381 0.00 0.00 0.00 2.69
900 1000 1.398390 CCGTTTGAGCAATCAGTAGCC 59.602 52.381 0.00 0.00 0.00 3.93
955 1055 8.725148 GTTGCAGATAAAGCTTATATATGTGCT 58.275 33.333 26.34 8.03 43.11 4.40
1099 1199 5.621555 GCTCGGGTACATACACATTCGATAT 60.622 44.000 0.00 0.00 0.00 1.63
1122 1222 1.273609 TGTACTACCTGCCATGACCCT 60.274 52.381 0.00 0.00 0.00 4.34
1123 1223 1.139058 GTACTACCTGCCATGACCCTG 59.861 57.143 0.00 0.00 0.00 4.45
1132 1233 0.247185 CCATGACCCTGCGCAATTTT 59.753 50.000 13.05 0.00 0.00 1.82
1137 1238 2.088178 CCCTGCGCAATTTTCGTGC 61.088 57.895 13.05 0.00 40.32 5.34
1157 1260 6.309494 TCGTGCTGGATATTATGTATTAACGC 59.691 38.462 0.00 0.00 0.00 4.84
1164 1267 3.815856 TTATGTATTAACGCCCGGTGA 57.184 42.857 4.58 0.00 0.00 4.02
1202 1305 3.621958 GCTCAGCCAGGAGAAAGAAAGAT 60.622 47.826 0.00 0.00 37.05 2.40
1354 1460 1.964290 GCTGAGCAGTGTGATGACGC 61.964 60.000 0.00 0.00 0.00 5.19
1384 1490 0.883833 AAAAGCATTGCCGTGGAGAG 59.116 50.000 4.70 0.00 0.00 3.20
1476 1582 2.293955 TCGACACGAAATGGTACTGACA 59.706 45.455 0.00 0.00 31.06 3.58
1775 1881 3.637273 GACCGCAACACCTCCCCT 61.637 66.667 0.00 0.00 0.00 4.79
1855 1961 0.033894 TGCACTCATCCATGCACCAT 60.034 50.000 0.00 0.00 46.63 3.55
1889 1995 5.568685 AGAGCTATATGCCACAGTATACG 57.431 43.478 0.00 0.00 44.23 3.06
1981 2087 6.043243 GGAGAGATGTCCAATAAAGGTATGGA 59.957 42.308 0.00 0.00 36.51 3.41
2028 2134 2.484417 CGCTTCTCCACAGGCTTCATAT 60.484 50.000 0.00 0.00 0.00 1.78
2030 2136 3.563390 GCTTCTCCACAGGCTTCATATTC 59.437 47.826 0.00 0.00 0.00 1.75
2056 2188 5.642919 CCACATTTTTCCACCACCATTATTG 59.357 40.000 0.00 0.00 0.00 1.90
2097 2229 4.644685 TGCAGGAATTGGACTAAATAAGGC 59.355 41.667 0.00 0.00 0.00 4.35
2098 2230 4.889995 GCAGGAATTGGACTAAATAAGGCT 59.110 41.667 0.00 0.00 31.67 4.58
2099 2231 6.062095 GCAGGAATTGGACTAAATAAGGCTA 58.938 40.000 0.00 0.00 31.67 3.93
2100 2232 6.717084 GCAGGAATTGGACTAAATAAGGCTAT 59.283 38.462 0.00 0.00 31.67 2.97
2102 2234 8.571336 CAGGAATTGGACTAAATAAGGCTATTG 58.429 37.037 0.00 0.00 31.67 1.90
2139 2274 8.718102 TCAACTAGGTAGCAAGCTAAATTTAG 57.282 34.615 19.08 19.08 35.36 1.85
2195 2330 4.843220 ACAAAGAGCAATGTTCAAGAGG 57.157 40.909 0.00 0.00 0.00 3.69
2293 2428 0.240945 ACGTTTACCTCGTACGGTGG 59.759 55.000 16.52 19.23 39.78 4.61
2372 2507 8.278639 TGATAGCCTCAATCCTTATTTTGGTAA 58.721 33.333 0.00 0.00 0.00 2.85
2481 2616 7.715249 TCTGAGGACTACAATGGTATATTTTGC 59.285 37.037 0.00 0.00 0.00 3.68
2524 2665 5.907207 TCTTCGTTAGCATGAGAGCTTATT 58.093 37.500 0.00 0.00 43.70 1.40
2525 2666 5.750547 TCTTCGTTAGCATGAGAGCTTATTG 59.249 40.000 0.00 0.00 43.70 1.90
2529 2670 7.210174 TCGTTAGCATGAGAGCTTATTGTATT 58.790 34.615 0.00 0.00 43.70 1.89
2530 2671 7.382488 TCGTTAGCATGAGAGCTTATTGTATTC 59.618 37.037 0.00 0.00 43.70 1.75
2532 2673 5.312079 AGCATGAGAGCTTATTGTATTCCC 58.688 41.667 0.00 0.00 43.70 3.97
2533 2674 4.457257 GCATGAGAGCTTATTGTATTCCCC 59.543 45.833 0.00 0.00 0.00 4.81
2534 2675 4.706842 TGAGAGCTTATTGTATTCCCCC 57.293 45.455 0.00 0.00 0.00 5.40
2651 2798 7.497773 AGGTAAATACTGGCTTCTAGAAGTT 57.502 36.000 28.72 17.48 40.45 2.66
2654 2801 9.662947 GGTAAATACTGGCTTCTAGAAGTTAAA 57.337 33.333 28.72 14.34 40.45 1.52
2657 2804 9.740710 AAATACTGGCTTCTAGAAGTTAAATGT 57.259 29.630 28.72 20.49 40.45 2.71
2661 2808 7.502561 ACTGGCTTCTAGAAGTTAAATGTTTGT 59.497 33.333 28.72 13.02 40.45 2.83
2684 2831 9.926158 TTGTTGATATTGCATTAGAAATTGTGT 57.074 25.926 0.00 0.00 0.00 3.72
2695 2842 9.749490 GCATTAGAAATTGTGTTTGATGAAATG 57.251 29.630 0.00 0.00 0.00 2.32
2723 2873 5.402398 ACAGTTCTTTGAACTCTGTTTTGC 58.598 37.500 9.67 0.00 36.17 3.68
2763 2914 8.757982 AGTTCTGTCATAATTAAGGAATGCAT 57.242 30.769 0.00 0.00 0.00 3.96
2779 2930 7.048512 AGGAATGCATAAGTTACTTCCTGTAC 58.951 38.462 12.10 0.00 40.63 2.90
2790 2941 2.300437 ACTTCCTGTACTTGCTGAGTCC 59.700 50.000 0.00 0.00 39.86 3.85
2797 2948 1.428869 ACTTGCTGAGTCCAGAGGTT 58.571 50.000 0.00 0.00 43.02 3.50
2804 2955 3.680196 GCTGAGTCCAGAGGTTATGGTTC 60.680 52.174 0.00 0.00 43.02 3.62
2805 2956 3.515502 CTGAGTCCAGAGGTTATGGTTCA 59.484 47.826 0.00 0.00 43.02 3.18
2810 2961 6.314917 AGTCCAGAGGTTATGGTTCAATTTT 58.685 36.000 0.00 0.00 39.01 1.82
2852 3003 7.744715 CGGAACTAATTCATTACACAGTGAAAC 59.255 37.037 7.81 0.00 37.82 2.78
2876 3027 6.483640 ACTTGTCCTCTCATGACAGTTTTAAC 59.516 38.462 0.00 0.00 43.14 2.01
2877 3028 4.988540 TGTCCTCTCATGACAGTTTTAACG 59.011 41.667 0.00 0.00 37.80 3.18
2878 3029 4.989168 GTCCTCTCATGACAGTTTTAACGT 59.011 41.667 0.00 0.00 32.91 3.99
2879 3030 5.465724 GTCCTCTCATGACAGTTTTAACGTT 59.534 40.000 5.88 5.88 32.91 3.99
2880 3031 6.018180 GTCCTCTCATGACAGTTTTAACGTTT 60.018 38.462 5.91 0.00 32.91 3.60
2881 3032 6.540914 TCCTCTCATGACAGTTTTAACGTTTT 59.459 34.615 5.91 0.00 0.00 2.43
2882 3033 6.851330 CCTCTCATGACAGTTTTAACGTTTTC 59.149 38.462 5.91 0.00 0.00 2.29
2883 3034 7.254795 CCTCTCATGACAGTTTTAACGTTTTCT 60.255 37.037 5.91 0.00 0.00 2.52
2884 3035 7.981142 TCTCATGACAGTTTTAACGTTTTCTT 58.019 30.769 5.91 0.00 0.00 2.52
2885 3036 8.455682 TCTCATGACAGTTTTAACGTTTTCTTT 58.544 29.630 5.91 0.00 0.00 2.52
2886 3037 8.609478 TCATGACAGTTTTAACGTTTTCTTTC 57.391 30.769 5.91 3.90 0.00 2.62
2887 3038 8.455682 TCATGACAGTTTTAACGTTTTCTTTCT 58.544 29.630 5.91 0.00 0.00 2.52
2888 3039 9.710979 CATGACAGTTTTAACGTTTTCTTTCTA 57.289 29.630 5.91 0.00 0.00 2.10
2890 3041 9.925268 TGACAGTTTTAACGTTTTCTTTCTATC 57.075 29.630 5.91 0.00 0.00 2.08
2910 3061 9.784680 TTCTATCTAGAATTTCTTGTACGTGAC 57.215 33.333 3.86 0.00 37.40 3.67
2911 3062 9.175312 TCTATCTAGAATTTCTTGTACGTGACT 57.825 33.333 3.86 0.00 0.00 3.41
2912 3063 9.227490 CTATCTAGAATTTCTTGTACGTGACTG 57.773 37.037 3.86 0.00 0.00 3.51
2913 3064 7.210718 TCTAGAATTTCTTGTACGTGACTGA 57.789 36.000 3.86 0.00 0.00 3.41
2914 3065 7.827701 TCTAGAATTTCTTGTACGTGACTGAT 58.172 34.615 3.86 0.00 0.00 2.90
2915 3066 8.304596 TCTAGAATTTCTTGTACGTGACTGATT 58.695 33.333 3.86 0.00 0.00 2.57
2916 3067 7.352719 AGAATTTCTTGTACGTGACTGATTC 57.647 36.000 0.00 0.00 0.00 2.52
2917 3068 6.369065 AGAATTTCTTGTACGTGACTGATTCC 59.631 38.462 0.00 0.00 0.00 3.01
2918 3069 3.587797 TCTTGTACGTGACTGATTCCC 57.412 47.619 0.00 0.00 0.00 3.97
2919 3070 2.232941 TCTTGTACGTGACTGATTCCCC 59.767 50.000 0.00 0.00 0.00 4.81
2920 3071 1.933021 TGTACGTGACTGATTCCCCT 58.067 50.000 0.00 0.00 0.00 4.79
2921 3072 1.548719 TGTACGTGACTGATTCCCCTG 59.451 52.381 0.00 0.00 0.00 4.45
2922 3073 0.535335 TACGTGACTGATTCCCCTGC 59.465 55.000 0.00 0.00 0.00 4.85
2923 3074 1.296392 CGTGACTGATTCCCCTGCA 59.704 57.895 0.00 0.00 0.00 4.41
2924 3075 0.742281 CGTGACTGATTCCCCTGCAG 60.742 60.000 6.78 6.78 35.81 4.41
2925 3076 0.615331 GTGACTGATTCCCCTGCAGA 59.385 55.000 17.39 0.00 33.94 4.26
2926 3077 1.211457 GTGACTGATTCCCCTGCAGAT 59.789 52.381 17.39 0.00 33.94 2.90
2927 3078 2.435805 GTGACTGATTCCCCTGCAGATA 59.564 50.000 17.39 0.00 33.94 1.98
2928 3079 3.114606 TGACTGATTCCCCTGCAGATAA 58.885 45.455 17.39 6.55 33.94 1.75
2929 3080 3.718434 TGACTGATTCCCCTGCAGATAAT 59.282 43.478 17.39 11.35 33.94 1.28
2930 3081 4.907269 TGACTGATTCCCCTGCAGATAATA 59.093 41.667 17.39 0.00 33.94 0.98
2931 3082 5.549228 TGACTGATTCCCCTGCAGATAATAT 59.451 40.000 17.39 1.50 33.94 1.28
2932 3083 6.044754 TGACTGATTCCCCTGCAGATAATATT 59.955 38.462 17.39 0.00 33.94 1.28
2933 3084 7.237471 TGACTGATTCCCCTGCAGATAATATTA 59.763 37.037 17.39 0.00 33.94 0.98
2934 3085 7.398024 ACTGATTCCCCTGCAGATAATATTAC 58.602 38.462 17.39 1.00 33.94 1.89
2935 3086 6.721318 TGATTCCCCTGCAGATAATATTACC 58.279 40.000 17.39 0.67 0.00 2.85
2936 3087 6.505344 TGATTCCCCTGCAGATAATATTACCT 59.495 38.462 17.39 0.00 0.00 3.08
2937 3088 6.780198 TTCCCCTGCAGATAATATTACCTT 57.220 37.500 17.39 0.00 0.00 3.50
2938 3089 6.374417 TCCCCTGCAGATAATATTACCTTC 57.626 41.667 17.39 0.00 0.00 3.46
2939 3090 6.091555 TCCCCTGCAGATAATATTACCTTCT 58.908 40.000 17.39 0.00 0.00 2.85
2940 3091 6.562608 TCCCCTGCAGATAATATTACCTTCTT 59.437 38.462 17.39 0.00 0.00 2.52
2941 3092 7.737607 TCCCCTGCAGATAATATTACCTTCTTA 59.262 37.037 17.39 0.00 0.00 2.10
2942 3093 8.552296 CCCCTGCAGATAATATTACCTTCTTAT 58.448 37.037 17.39 0.00 0.00 1.73
2943 3094 9.388506 CCCTGCAGATAATATTACCTTCTTATG 57.611 37.037 17.39 0.00 0.00 1.90
2953 3104 6.636454 ATTACCTTCTTATGAGTGTTCCCA 57.364 37.500 0.00 0.00 0.00 4.37
2955 3106 4.911390 ACCTTCTTATGAGTGTTCCCAAG 58.089 43.478 0.00 0.00 0.00 3.61
2965 3116 9.832445 TTATGAGTGTTCCCAAGTAATATTCTC 57.168 33.333 0.00 0.00 0.00 2.87
2974 3125 7.338710 TCCCAAGTAATATTCTCCACTTTCTG 58.661 38.462 0.00 0.00 0.00 3.02
2982 3133 4.873746 TTCTCCACTTTCTGTACAGAGG 57.126 45.455 23.97 20.95 38.88 3.69
3030 3181 2.002018 TTGAAAGTGGCCTCCGGGTT 62.002 55.000 3.32 0.00 34.45 4.11
3152 3303 1.067354 GGAATGTGAAGCTGGGCAAAG 60.067 52.381 0.00 0.00 0.00 2.77
3161 3312 1.075482 CTGGGCAAAGCTCTTCCCA 59.925 57.895 16.16 16.16 45.87 4.37
3162 3313 0.324091 CTGGGCAAAGCTCTTCCCAT 60.324 55.000 17.06 0.00 46.71 4.00
3222 3373 3.635373 CAGATGCCATGAAACCATTAGCT 59.365 43.478 0.00 0.00 0.00 3.32
3253 3404 9.463443 AAGGCATAATAAAATTATTTCTCGTGC 57.537 29.630 3.91 7.24 35.20 5.34
3254 3405 8.850156 AGGCATAATAAAATTATTTCTCGTGCT 58.150 29.630 3.91 0.00 35.20 4.40
3264 3415 9.463443 AAATTATTTCTCGTGCTTTTATATGGC 57.537 29.630 0.00 0.00 0.00 4.40
3304 3455 6.132791 GACAATTGTCAAGATGCATCTGAT 57.867 37.500 29.34 12.60 44.18 2.90
3316 3467 9.926158 CAAGATGCATCTGATAGTTTCTATAGT 57.074 33.333 29.34 5.29 37.19 2.12
3433 3584 2.306512 AGACCAAGGCCGGTTATAACAA 59.693 45.455 17.16 0.00 40.22 2.83
3500 3651 7.352079 ACATGGTTCTGTTCATTCTCTTTTT 57.648 32.000 0.00 0.00 0.00 1.94
3506 3657 7.759433 GGTTCTGTTCATTCTCTTTTTGAAACA 59.241 33.333 0.00 0.00 31.66 2.83
3509 3660 8.522830 TCTGTTCATTCTCTTTTTGAAACAACT 58.477 29.630 0.00 0.00 31.66 3.16
3626 3777 0.742990 CCGCTATTGGGCAAAGACGA 60.743 55.000 0.00 0.00 0.00 4.20
3653 3804 1.380302 GCCCTTCTCCTTGCCTGAA 59.620 57.895 0.00 0.00 0.00 3.02
3674 3825 0.545309 TGGAGGCACTAGTGGAAGCT 60.545 55.000 23.95 0.43 41.55 3.74
3677 3828 1.002544 GAGGCACTAGTGGAAGCTGTT 59.997 52.381 23.95 0.70 41.55 3.16
3750 3903 2.997485 GACACAAGGTCATTGCTTCC 57.003 50.000 0.00 0.00 46.19 3.46
3783 3936 0.773644 ATGTTGGCCTCTTGGTCTGT 59.226 50.000 3.32 0.00 39.11 3.41
3853 4006 6.249192 TGATCATAGGACCTATGTCGATCTT 58.751 40.000 31.69 14.72 42.92 2.40
3871 4024 7.167136 GTCGATCTTAAGGTAATTCAGTAACCG 59.833 40.741 1.85 0.00 38.37 4.44
4014 4178 1.148273 GAAGACCCTGGTGCACACA 59.852 57.895 20.43 13.12 0.00 3.72
4143 4307 0.538057 CAGGCAAGGCTTCAGGACAA 60.538 55.000 0.00 0.00 0.00 3.18
4145 4309 1.583477 GCAAGGCTTCAGGACAAGC 59.417 57.895 0.00 0.00 46.99 4.01
4174 4338 2.308570 TCCAGCTGCTAAAGGAAATCCA 59.691 45.455 8.66 0.00 38.89 3.41
4183 4347 2.744352 AAGGAAATCCATCTCTGCCC 57.256 50.000 1.67 0.00 38.89 5.36
4221 4388 9.495572 AGAGGAAAACTGATACTCTGTAAAAAG 57.504 33.333 0.00 0.00 37.16 2.27
4274 4441 9.567776 TTCTGTATTTATTCCAAAACTCACAGA 57.432 29.630 0.00 0.00 35.44 3.41
4350 4523 7.342284 TCTTTCCTCTGTCGGTTAATAAGAGAT 59.658 37.037 0.00 0.00 37.20 2.75
4511 4684 6.500684 AGTAATTACACTGTCTTGCATTGG 57.499 37.500 17.65 0.00 32.74 3.16
4603 4778 3.643792 CCCTTGTGGTTGGATTTGGTAAA 59.356 43.478 0.00 0.00 0.00 2.01
4711 4891 3.655615 AGGTGTTAAACTGTCCCAACA 57.344 42.857 0.00 0.00 0.00 3.33
4800 4981 2.201927 GCCCATTAGCCCAACAAGG 58.798 57.895 0.00 0.00 37.03 3.61
4808 4989 2.564721 GCCCAACAAGGTCCAGCAC 61.565 63.158 0.00 0.00 34.66 4.40
4810 4991 0.468029 CCCAACAAGGTCCAGCACTT 60.468 55.000 0.00 0.00 34.66 3.16
4811 4992 1.202879 CCCAACAAGGTCCAGCACTTA 60.203 52.381 0.00 0.00 34.66 2.24
4812 4993 1.880027 CCAACAAGGTCCAGCACTTAC 59.120 52.381 0.00 0.00 0.00 2.34
5051 5232 1.375396 CCTGTTCGACCGAATGCCA 60.375 57.895 8.14 1.56 36.45 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.518068 CCGAGCCCGCCAAAATCC 61.518 66.667 0.00 0.00 0.00 3.01
1 2 4.193334 GCCGAGCCCGCCAAAATC 62.193 66.667 0.00 0.00 0.00 2.17
17 18 3.750373 TAATTCGAGCGGCCCCTGC 62.750 63.158 0.00 0.00 0.00 4.85
18 19 1.071471 ATAATTCGAGCGGCCCCTG 59.929 57.895 0.00 0.00 0.00 4.45
19 20 1.071471 CATAATTCGAGCGGCCCCT 59.929 57.895 0.00 0.00 0.00 4.79
20 21 2.617274 GCATAATTCGAGCGGCCCC 61.617 63.158 0.00 0.00 0.00 5.80
21 22 1.569479 GAGCATAATTCGAGCGGCCC 61.569 60.000 0.00 0.00 0.00 5.80
22 23 1.569479 GGAGCATAATTCGAGCGGCC 61.569 60.000 0.00 0.00 0.00 6.13
23 24 1.569479 GGGAGCATAATTCGAGCGGC 61.569 60.000 0.00 0.00 0.00 6.53
24 25 0.034059 AGGGAGCATAATTCGAGCGG 59.966 55.000 0.00 0.00 0.00 5.52
25 26 1.423395 GAGGGAGCATAATTCGAGCG 58.577 55.000 0.00 0.00 0.00 5.03
26 27 1.609320 GGGAGGGAGCATAATTCGAGC 60.609 57.143 0.00 0.00 0.00 5.03
27 28 1.337260 CGGGAGGGAGCATAATTCGAG 60.337 57.143 0.00 0.00 0.00 4.04
28 29 0.679505 CGGGAGGGAGCATAATTCGA 59.320 55.000 0.00 0.00 0.00 3.71
29 30 3.217242 CGGGAGGGAGCATAATTCG 57.783 57.895 0.00 0.00 0.00 3.34
42 43 1.336795 GGCACAAAACAAATCCGGGAG 60.337 52.381 0.00 0.00 0.00 4.30
43 44 0.676736 GGCACAAAACAAATCCGGGA 59.323 50.000 0.00 0.00 0.00 5.14
44 45 0.320334 GGGCACAAAACAAATCCGGG 60.320 55.000 0.00 0.00 0.00 5.73
45 46 0.665972 CGGGCACAAAACAAATCCGG 60.666 55.000 0.00 0.00 33.27 5.14
46 47 0.665972 CCGGGCACAAAACAAATCCG 60.666 55.000 0.00 0.00 36.23 4.18
47 48 0.676736 TCCGGGCACAAAACAAATCC 59.323 50.000 0.00 0.00 0.00 3.01
48 49 2.741759 ATCCGGGCACAAAACAAATC 57.258 45.000 0.00 0.00 0.00 2.17
49 50 2.289382 GGAATCCGGGCACAAAACAAAT 60.289 45.455 0.00 0.00 0.00 2.32
50 51 1.069358 GGAATCCGGGCACAAAACAAA 59.931 47.619 0.00 0.00 0.00 2.83
51 52 0.676736 GGAATCCGGGCACAAAACAA 59.323 50.000 0.00 0.00 0.00 2.83
52 53 1.519751 CGGAATCCGGGCACAAAACA 61.520 55.000 14.91 0.00 44.15 2.83
53 54 1.211709 CGGAATCCGGGCACAAAAC 59.788 57.895 14.91 0.00 44.15 2.43
54 55 3.674906 CGGAATCCGGGCACAAAA 58.325 55.556 14.91 0.00 44.15 2.44
64 65 1.464997 GGAGCATAATTCGCGGAATCC 59.535 52.381 6.13 0.00 30.29 3.01
65 66 1.126846 CGGAGCATAATTCGCGGAATC 59.873 52.381 6.13 0.00 30.29 2.52
66 67 1.148310 CGGAGCATAATTCGCGGAAT 58.852 50.000 6.13 1.73 33.25 3.01
67 68 2.600388 CGGAGCATAATTCGCGGAA 58.400 52.632 6.13 0.00 0.00 4.30
68 69 4.336581 CGGAGCATAATTCGCGGA 57.663 55.556 6.13 0.00 0.00 5.54
118 119 3.273788 AAGAAGCAAGCCCCGGGAG 62.274 63.158 26.32 13.96 0.00 4.30
119 120 3.256960 AAGAAGCAAGCCCCGGGA 61.257 61.111 26.32 0.00 0.00 5.14
122 123 2.335712 GGTCAAGAAGCAAGCCCCG 61.336 63.158 0.00 0.00 0.00 5.73
124 125 1.979155 GGGGTCAAGAAGCAAGCCC 60.979 63.158 0.00 0.00 43.01 5.19
125 126 2.335712 CGGGGTCAAGAAGCAAGCC 61.336 63.158 0.00 0.00 0.00 4.35
126 127 2.335712 CCGGGGTCAAGAAGCAAGC 61.336 63.158 0.00 0.00 0.00 4.01
151 165 3.923864 ACGCAACAGGACGGAGCA 61.924 61.111 0.00 0.00 0.00 4.26
191 208 4.861102 AAAGTCTGAAATGGGCAAGAAG 57.139 40.909 0.00 0.00 0.00 2.85
221 239 1.063412 GAACGCCGCGAAATTCAACC 61.063 55.000 21.79 0.00 0.00 3.77
236 254 0.796312 CCACGGAACATCCAAGAACG 59.204 55.000 0.00 0.00 35.91 3.95
396 447 4.877378 AATTCTGAATCAGCAAGCCAAA 57.123 36.364 5.18 0.00 0.00 3.28
397 448 4.561938 CCAAATTCTGAATCAGCAAGCCAA 60.562 41.667 5.18 0.00 0.00 4.52
398 449 3.056393 CCAAATTCTGAATCAGCAAGCCA 60.056 43.478 5.18 0.00 0.00 4.75
399 450 3.518590 CCAAATTCTGAATCAGCAAGCC 58.481 45.455 5.18 0.00 0.00 4.35
400 451 2.928116 GCCAAATTCTGAATCAGCAAGC 59.072 45.455 5.18 0.00 0.00 4.01
402 453 4.322198 GGAAGCCAAATTCTGAATCAGCAA 60.322 41.667 5.18 1.73 0.00 3.91
403 454 3.194116 GGAAGCCAAATTCTGAATCAGCA 59.806 43.478 5.18 0.00 0.00 4.41
404 455 3.446516 AGGAAGCCAAATTCTGAATCAGC 59.553 43.478 5.18 7.16 0.00 4.26
405 456 5.047519 ACAAGGAAGCCAAATTCTGAATCAG 60.048 40.000 3.38 3.38 0.00 2.90
519 586 7.434897 TGCAACAAATAGAAATCAAAGACACAC 59.565 33.333 0.00 0.00 0.00 3.82
521 588 7.862372 TCTGCAACAAATAGAAATCAAAGACAC 59.138 33.333 0.00 0.00 0.00 3.67
538 605 4.358851 CTTTTCATCGGTTTCTGCAACAA 58.641 39.130 0.00 0.00 37.07 2.83
540 617 3.004315 TCCTTTTCATCGGTTTCTGCAAC 59.996 43.478 0.00 0.00 34.18 4.17
638 718 2.193127 ACGGTGGAGATTGATTGGGTA 58.807 47.619 0.00 0.00 0.00 3.69
683 763 2.040412 GTGGTTTGATGGAGGAGGAGTT 59.960 50.000 0.00 0.00 0.00 3.01
895 995 0.105039 CAGTGAGGATTCCCGGCTAC 59.895 60.000 0.00 0.00 37.58 3.58
900 1000 2.159099 TCGAATTCAGTGAGGATTCCCG 60.159 50.000 6.22 3.29 37.58 5.14
955 1055 1.144969 CTTTCGCAGGCAGTAAACGA 58.855 50.000 0.00 0.00 0.00 3.85
1099 1199 2.108168 GTCATGGCAGGTAGTACAGGA 58.892 52.381 2.06 0.00 0.00 3.86
1122 1222 1.371512 CCAGCACGAAAATTGCGCA 60.372 52.632 5.66 5.66 45.15 6.09
1123 1223 0.456653 ATCCAGCACGAAAATTGCGC 60.457 50.000 0.00 0.00 45.15 6.09
1132 1233 6.309494 GCGTTAATACATAATATCCAGCACGA 59.691 38.462 0.00 0.00 0.00 4.35
1137 1238 5.522460 CCGGGCGTTAATACATAATATCCAG 59.478 44.000 0.00 0.00 0.00 3.86
1157 1260 1.149174 CCCCTGAATCATCACCGGG 59.851 63.158 6.32 0.00 39.63 5.73
1164 1267 1.281867 TGAGCGTTTCCCCTGAATCAT 59.718 47.619 0.00 0.00 0.00 2.45
1184 1287 3.843027 TCTCATCTTTCTTTCTCCTGGCT 59.157 43.478 0.00 0.00 0.00 4.75
1202 1305 3.081061 CAAATCAAACGGGGACATCTCA 58.919 45.455 0.00 0.00 0.00 3.27
1354 1460 1.926511 AATGCTTTTGAGCGGCGGAG 61.927 55.000 9.78 0.00 37.69 4.63
1384 1490 0.464452 ACCAGAACCCGCTATACAGC 59.536 55.000 0.00 0.00 44.90 4.40
1775 1881 1.171549 TCGCTTCAGCATGGCACAAA 61.172 50.000 0.00 0.00 42.21 2.83
1855 1961 7.829211 GTGGCATATAGCTCTTATTATTTCCCA 59.171 37.037 0.00 0.00 44.79 4.37
1889 1995 1.267121 TCCTTATCCTGCTATCGCCC 58.733 55.000 0.00 0.00 34.43 6.13
1981 2087 7.839680 AAGGTTAACTTTGTGATGAGGATTT 57.160 32.000 5.42 0.00 35.35 2.17
2028 2134 1.067821 GTGGTGGAAAAATGTGGCGAA 59.932 47.619 0.00 0.00 0.00 4.70
2030 2136 0.319469 GGTGGTGGAAAAATGTGGCG 60.319 55.000 0.00 0.00 0.00 5.69
2056 2188 5.588648 TCCTGCAATATTTAGTTAGTGCCAC 59.411 40.000 2.02 0.00 41.25 5.01
2060 2192 8.902806 TCCAATTCCTGCAATATTTAGTTAGTG 58.097 33.333 0.00 0.00 0.00 2.74
2293 2428 3.930229 TCTGTGCAATGTACCAATCGTAC 59.070 43.478 0.00 0.00 46.53 3.67
2372 2507 5.652452 AGCGGCATTTTCTTTTAGGAAGTAT 59.348 36.000 1.45 0.00 0.00 2.12
2493 2632 7.382488 GCTCTCATGCTAACGAAGAATATAACA 59.618 37.037 0.00 0.00 0.00 2.41
2494 2633 7.596995 AGCTCTCATGCTAACGAAGAATATAAC 59.403 37.037 0.00 0.00 42.10 1.89
2498 2637 5.521906 AGCTCTCATGCTAACGAAGAATA 57.478 39.130 0.00 0.00 42.10 1.75
2501 2640 3.876274 AAGCTCTCATGCTAACGAAGA 57.124 42.857 0.00 0.00 43.24 2.87
2508 2647 6.467677 GGGAATACAATAAGCTCTCATGCTA 58.532 40.000 0.00 0.00 43.24 3.49
2513 2652 4.706842 GGGGGAATACAATAAGCTCTCA 57.293 45.455 0.00 0.00 0.00 3.27
2532 2673 3.258372 GCTTAACTGAAAAAGGAAGGGGG 59.742 47.826 0.00 0.00 0.00 5.40
2533 2674 4.152647 AGCTTAACTGAAAAAGGAAGGGG 58.847 43.478 0.00 0.00 0.00 4.79
2534 2675 6.715264 TCTTAGCTTAACTGAAAAAGGAAGGG 59.285 38.462 0.00 0.00 0.00 3.95
2535 2676 7.745620 TCTTAGCTTAACTGAAAAAGGAAGG 57.254 36.000 0.00 0.00 0.00 3.46
2536 2677 9.833182 GATTCTTAGCTTAACTGAAAAAGGAAG 57.167 33.333 0.00 0.00 0.00 3.46
2545 2687 9.155975 GAATGACTTGATTCTTAGCTTAACTGA 57.844 33.333 0.00 0.00 30.79 3.41
2674 2821 6.762187 TGCACATTTCATCAAACACAATTTCT 59.238 30.769 0.00 0.00 0.00 2.52
2675 2822 6.946165 TGCACATTTCATCAAACACAATTTC 58.054 32.000 0.00 0.00 0.00 2.17
2676 2823 6.922247 TGCACATTTCATCAAACACAATTT 57.078 29.167 0.00 0.00 0.00 1.82
2679 2826 5.173664 TGTTGCACATTTCATCAAACACAA 58.826 33.333 0.00 0.00 0.00 3.33
2684 2831 5.904941 AGAACTGTTGCACATTTCATCAAA 58.095 33.333 16.01 0.00 39.38 2.69
2688 2835 5.904941 TCAAAGAACTGTTGCACATTTCAT 58.095 33.333 16.01 6.68 39.38 2.57
2695 2842 4.142600 ACAGAGTTCAAAGAACTGTTGCAC 60.143 41.667 16.33 2.20 38.41 4.57
2763 2914 6.267014 ACTCAGCAAGTACAGGAAGTAACTTA 59.733 38.462 0.00 0.00 36.07 2.24
2779 2930 3.529533 CATAACCTCTGGACTCAGCAAG 58.470 50.000 0.00 0.00 40.69 4.01
2817 2968 9.602568 TGTAATGAATTAGTTCCGTTGCTTATA 57.397 29.630 0.00 0.00 33.26 0.98
2818 2969 8.395633 GTGTAATGAATTAGTTCCGTTGCTTAT 58.604 33.333 0.00 0.00 33.26 1.73
2827 2978 8.784043 AGTTTCACTGTGTAATGAATTAGTTCC 58.216 33.333 7.79 0.00 34.87 3.62
2832 2983 8.564574 GGACAAGTTTCACTGTGTAATGAATTA 58.435 33.333 7.79 0.00 34.87 1.40
2852 3003 6.346919 CGTTAAAACTGTCATGAGAGGACAAG 60.347 42.308 22.62 5.47 44.04 3.16
2859 3010 7.548196 AGAAAACGTTAAAACTGTCATGAGA 57.452 32.000 0.00 0.00 0.00 3.27
2884 3035 9.784680 GTCACGTACAAGAAATTCTAGATAGAA 57.215 33.333 4.84 4.84 45.43 2.10
2885 3036 9.175312 AGTCACGTACAAGAAATTCTAGATAGA 57.825 33.333 0.00 0.00 0.00 1.98
2886 3037 9.227490 CAGTCACGTACAAGAAATTCTAGATAG 57.773 37.037 0.00 0.00 0.00 2.08
2887 3038 8.953313 TCAGTCACGTACAAGAAATTCTAGATA 58.047 33.333 0.00 0.00 0.00 1.98
2888 3039 7.827701 TCAGTCACGTACAAGAAATTCTAGAT 58.172 34.615 0.00 0.00 0.00 1.98
2889 3040 7.210718 TCAGTCACGTACAAGAAATTCTAGA 57.789 36.000 0.00 0.00 0.00 2.43
2890 3041 8.467402 AATCAGTCACGTACAAGAAATTCTAG 57.533 34.615 0.00 0.00 0.00 2.43
2891 3042 7.544566 GGAATCAGTCACGTACAAGAAATTCTA 59.455 37.037 0.00 0.00 0.00 2.10
2892 3043 6.369065 GGAATCAGTCACGTACAAGAAATTCT 59.631 38.462 0.00 0.00 0.00 2.40
2893 3044 6.402226 GGGAATCAGTCACGTACAAGAAATTC 60.402 42.308 0.00 1.57 0.00 2.17
2894 3045 5.411669 GGGAATCAGTCACGTACAAGAAATT 59.588 40.000 0.00 0.00 0.00 1.82
2895 3046 4.935808 GGGAATCAGTCACGTACAAGAAAT 59.064 41.667 0.00 0.00 0.00 2.17
2896 3047 4.312443 GGGAATCAGTCACGTACAAGAAA 58.688 43.478 0.00 0.00 0.00 2.52
2897 3048 3.306502 GGGGAATCAGTCACGTACAAGAA 60.307 47.826 0.00 0.00 0.00 2.52
2898 3049 2.232941 GGGGAATCAGTCACGTACAAGA 59.767 50.000 0.00 0.00 0.00 3.02
2899 3050 2.233922 AGGGGAATCAGTCACGTACAAG 59.766 50.000 0.00 0.00 0.00 3.16
2900 3051 2.028476 CAGGGGAATCAGTCACGTACAA 60.028 50.000 0.00 0.00 0.00 2.41
2901 3052 1.548719 CAGGGGAATCAGTCACGTACA 59.451 52.381 0.00 0.00 0.00 2.90
2902 3053 1.739371 GCAGGGGAATCAGTCACGTAC 60.739 57.143 0.00 0.00 0.00 3.67
2903 3054 0.535335 GCAGGGGAATCAGTCACGTA 59.465 55.000 0.00 0.00 0.00 3.57
2904 3055 1.296715 GCAGGGGAATCAGTCACGT 59.703 57.895 0.00 0.00 0.00 4.49
2905 3056 0.742281 CTGCAGGGGAATCAGTCACG 60.742 60.000 5.57 0.00 0.00 4.35
2906 3057 0.615331 TCTGCAGGGGAATCAGTCAC 59.385 55.000 15.13 0.00 0.00 3.67
2907 3058 1.588239 ATCTGCAGGGGAATCAGTCA 58.412 50.000 15.13 0.00 0.00 3.41
2908 3059 3.845781 TTATCTGCAGGGGAATCAGTC 57.154 47.619 15.13 0.00 0.00 3.51
2909 3060 6.460103 AATATTATCTGCAGGGGAATCAGT 57.540 37.500 15.13 0.00 0.00 3.41
2910 3061 6.825721 GGTAATATTATCTGCAGGGGAATCAG 59.174 42.308 15.13 0.00 0.00 2.90
2911 3062 6.505344 AGGTAATATTATCTGCAGGGGAATCA 59.495 38.462 15.13 0.00 0.00 2.57
2912 3063 6.963322 AGGTAATATTATCTGCAGGGGAATC 58.037 40.000 15.13 0.00 0.00 2.52
2913 3064 6.977244 AGGTAATATTATCTGCAGGGGAAT 57.023 37.500 15.13 12.94 0.00 3.01
2914 3065 6.562608 AGAAGGTAATATTATCTGCAGGGGAA 59.437 38.462 15.13 6.10 0.00 3.97
2915 3066 6.091555 AGAAGGTAATATTATCTGCAGGGGA 58.908 40.000 15.13 0.00 0.00 4.81
2916 3067 6.380079 AGAAGGTAATATTATCTGCAGGGG 57.620 41.667 15.13 0.00 0.00 4.79
2917 3068 9.388506 CATAAGAAGGTAATATTATCTGCAGGG 57.611 37.037 15.13 0.00 0.00 4.45
2927 3078 8.778059 TGGGAACACTCATAAGAAGGTAATATT 58.222 33.333 0.00 0.00 33.40 1.28
2928 3079 8.331931 TGGGAACACTCATAAGAAGGTAATAT 57.668 34.615 0.00 0.00 33.40 1.28
2929 3080 7.743116 TGGGAACACTCATAAGAAGGTAATA 57.257 36.000 0.00 0.00 33.40 0.98
2930 3081 6.636454 TGGGAACACTCATAAGAAGGTAAT 57.364 37.500 0.00 0.00 33.40 1.89
2931 3082 6.043938 ACTTGGGAACACTCATAAGAAGGTAA 59.956 38.462 0.00 0.00 42.67 2.85
2932 3083 5.546499 ACTTGGGAACACTCATAAGAAGGTA 59.454 40.000 0.00 0.00 42.67 3.08
2933 3084 4.351111 ACTTGGGAACACTCATAAGAAGGT 59.649 41.667 0.00 0.00 42.67 3.50
2934 3085 4.911390 ACTTGGGAACACTCATAAGAAGG 58.089 43.478 0.00 0.00 42.67 3.46
2935 3086 9.838339 ATATTACTTGGGAACACTCATAAGAAG 57.162 33.333 0.00 0.00 42.67 2.85
2937 3088 9.832445 GAATATTACTTGGGAACACTCATAAGA 57.168 33.333 0.00 0.00 42.67 2.10
2938 3089 9.838339 AGAATATTACTTGGGAACACTCATAAG 57.162 33.333 0.00 0.00 42.67 1.73
2939 3090 9.832445 GAGAATATTACTTGGGAACACTCATAA 57.168 33.333 0.00 0.00 42.67 1.90
2940 3091 8.429641 GGAGAATATTACTTGGGAACACTCATA 58.570 37.037 0.00 0.00 42.67 2.15
2941 3092 7.092444 TGGAGAATATTACTTGGGAACACTCAT 60.092 37.037 0.00 0.00 42.67 2.90
2942 3093 6.214615 TGGAGAATATTACTTGGGAACACTCA 59.785 38.462 0.00 0.00 42.67 3.41
2943 3094 6.539103 GTGGAGAATATTACTTGGGAACACTC 59.461 42.308 0.00 0.00 42.67 3.51
2944 3095 6.215636 AGTGGAGAATATTACTTGGGAACACT 59.784 38.462 0.00 0.00 42.67 3.55
2945 3096 6.415573 AGTGGAGAATATTACTTGGGAACAC 58.584 40.000 0.00 0.00 42.67 3.32
2953 3104 9.877178 CTGTACAGAAAGTGGAGAATATTACTT 57.123 33.333 18.45 0.00 35.06 2.24
2955 3106 9.522804 CTCTGTACAGAAAGTGGAGAATATTAC 57.477 37.037 25.14 0.00 36.94 1.89
2965 3116 3.919216 CAGTCCTCTGTACAGAAAGTGG 58.081 50.000 25.14 21.48 36.94 4.00
2982 3133 6.385033 ACTAGTAACAACGTCCATTACAGTC 58.615 40.000 15.06 0.00 32.33 3.51
3030 3181 5.110814 TCTTTCCTTGAAGAAGAACACCA 57.889 39.130 0.00 0.00 32.95 4.17
3161 3312 2.022035 TCCTCTGGTATTCTGACCCCAT 60.022 50.000 0.00 0.00 38.89 4.00
3162 3313 1.364678 TCCTCTGGTATTCTGACCCCA 59.635 52.381 0.00 0.00 38.89 4.96
3240 3391 8.165239 TGCCATATAAAAGCACGAGAAATAAT 57.835 30.769 0.00 0.00 0.00 1.28
3243 3394 5.590259 ACTGCCATATAAAAGCACGAGAAAT 59.410 36.000 0.00 0.00 32.06 2.17
3249 3400 4.562394 CCAAAACTGCCATATAAAAGCACG 59.438 41.667 0.00 0.00 32.06 5.34
3253 3404 8.527810 TCCTAAACCAAAACTGCCATATAAAAG 58.472 33.333 0.00 0.00 0.00 2.27
3254 3405 8.423906 TCCTAAACCAAAACTGCCATATAAAA 57.576 30.769 0.00 0.00 0.00 1.52
3264 3415 7.264947 ACAATTGTCTTCCTAAACCAAAACTG 58.735 34.615 4.92 0.00 0.00 3.16
3304 3455 8.451748 CAGAGCGCACATATACTATAGAAACTA 58.548 37.037 11.47 0.00 0.00 2.24
3315 3466 1.423395 GCTCCAGAGCGCACATATAC 58.577 55.000 11.47 0.00 45.29 1.47
3316 3467 3.894257 GCTCCAGAGCGCACATATA 57.106 52.632 11.47 0.00 45.29 0.86
3317 3468 4.766970 GCTCCAGAGCGCACATAT 57.233 55.556 11.47 0.00 45.29 1.78
3662 3813 3.733337 CTGTTCAACAGCTTCCACTAGT 58.267 45.455 4.15 0.00 39.62 2.57
3674 3825 2.023673 CCTGTTCCAAGCTGTTCAACA 58.976 47.619 0.00 0.00 0.00 3.33
3677 3828 2.575532 CTTCCTGTTCCAAGCTGTTCA 58.424 47.619 0.00 0.00 0.00 3.18
3783 3936 1.476110 CGTCCCTCCACCTGAACAAAA 60.476 52.381 0.00 0.00 0.00 2.44
3853 4006 4.186159 GCTGCGGTTACTGAATTACCTTA 58.814 43.478 0.00 0.00 0.00 2.69
3890 4043 9.325150 CAGAAAGAAATAAAAAGCAATGCAATG 57.675 29.630 8.35 0.00 0.00 2.82
3980 4144 1.070134 TCTTCCACTTGTCCTGGTTCG 59.930 52.381 0.00 0.00 0.00 3.95
4163 4327 2.584498 AGGGCAGAGATGGATTTCCTTT 59.416 45.455 0.00 0.00 36.82 3.11
4174 4338 2.903871 TAGGCAGGCAGGGCAGAGAT 62.904 60.000 0.00 0.00 35.46 2.75
4183 4347 1.198713 TTTCCTCTCTAGGCAGGCAG 58.801 55.000 0.00 0.00 43.31 4.85
4300 4473 1.681327 CCTGGCCTGAGCAGCAAAT 60.681 57.895 11.88 0.00 42.56 2.32
4350 4523 1.470098 GTCGAGACCAGGCGTTTAGTA 59.530 52.381 0.00 0.00 0.00 1.82
4489 4662 6.149474 ACTCCAATGCAAGACAGTGTAATTAC 59.851 38.462 8.75 8.75 42.83 1.89
4491 4664 5.072741 ACTCCAATGCAAGACAGTGTAATT 58.927 37.500 0.00 0.00 42.83 1.40
4494 4667 3.769739 ACTCCAATGCAAGACAGTGTA 57.230 42.857 0.00 0.00 42.83 2.90
4525 4698 5.897377 AAACAATAATCCGGTTTCTCTGG 57.103 39.130 0.00 0.00 43.70 3.86
4576 4749 4.384647 CCAAATCCAACCACAAGGGAAAAA 60.385 41.667 0.00 0.00 41.15 1.94
4581 4754 1.715785 ACCAAATCCAACCACAAGGG 58.284 50.000 0.00 0.00 44.81 3.95
4626 4801 7.722285 AGCAACTACTGTACCATTTCCTAAAAA 59.278 33.333 0.00 0.00 0.00 1.94
4627 4802 7.228590 AGCAACTACTGTACCATTTCCTAAAA 58.771 34.615 0.00 0.00 0.00 1.52
4628 4803 6.775708 AGCAACTACTGTACCATTTCCTAAA 58.224 36.000 0.00 0.00 0.00 1.85
4691 4871 3.655615 TGTTGGGACAGTTTAACACCT 57.344 42.857 0.00 0.00 42.39 4.00
4692 4872 4.929819 ATTGTTGGGACAGTTTAACACC 57.070 40.909 0.00 0.00 42.39 4.16
4799 4980 2.614734 GGTAACTGGTAAGTGCTGGACC 60.615 54.545 0.00 0.00 36.51 4.46
4800 4981 2.038033 TGGTAACTGGTAAGTGCTGGAC 59.962 50.000 0.00 0.00 36.51 4.02
4808 4989 3.368531 GCAGAGGAGTGGTAACTGGTAAG 60.369 52.174 0.00 0.00 36.52 2.34
4810 4991 2.176889 GCAGAGGAGTGGTAACTGGTA 58.823 52.381 0.00 0.00 36.52 3.25
4811 4992 0.977395 GCAGAGGAGTGGTAACTGGT 59.023 55.000 0.00 0.00 36.52 4.00
4812 4993 0.250513 GGCAGAGGAGTGGTAACTGG 59.749 60.000 0.00 0.00 36.52 4.00
4877 5058 1.674764 CGAGGCATGAGAGGAGCAGT 61.675 60.000 0.00 0.00 0.00 4.40
5045 5226 4.684134 AGGTTGCGGCCTGGCATT 62.684 61.111 22.05 0.00 43.52 3.56
5051 5232 4.070552 GAGACGAGGTTGCGGCCT 62.071 66.667 0.00 0.00 41.12 5.19
5057 5238 2.982130 CCCCAGGAGACGAGGTTG 59.018 66.667 0.00 0.00 0.00 3.77
5146 5327 3.853330 CATCGTTGTCGGCGGCAG 61.853 66.667 15.90 3.97 37.69 4.85


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

AutoCloner maintained by Alex Coulton.