Multiple sequence alignment - TraesCS5A01G155900

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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 TraesCS5A01G155900 chr5A 100.000 4539 0 0 1 4539 334266152 334261614 0.000000e+00 8383.0
1 TraesCS5A01G155900 chr5A 98.569 1118 16 0 3422 4539 334249718 334248601 0.000000e+00 1977.0
2 TraesCS5A01G155900 chr5A 98.294 1114 18 1 3422 4534 376873238 376874351 0.000000e+00 1951.0
3 TraesCS5A01G155900 chr5A 86.181 948 111 18 3397 4336 292013175 292014110 0.000000e+00 1007.0
4 TraesCS5A01G155900 chr5A 88.000 175 21 0 2693 2867 275973092 275972918 1.650000e-49 207.0
5 TraesCS5A01G155900 chr5D 94.010 2504 128 13 187 2668 251065110 251062607 0.000000e+00 3773.0
6 TraesCS5A01G155900 chr5D 94.757 534 27 1 2887 3420 251062607 251062075 0.000000e+00 830.0
7 TraesCS5A01G155900 chr5D 94.059 202 12 0 1 202 251065365 251065164 1.590000e-79 307.0
8 TraesCS5A01G155900 chr5B 91.116 2724 180 27 1 2693 283625184 283622492 0.000000e+00 3633.0
9 TraesCS5A01G155900 chr5B 93.934 544 31 2 2879 3422 283622501 283621960 0.000000e+00 821.0
10 TraesCS5A01G155900 chr5B 87.709 179 20 2 2690 2867 95032371 95032194 1.650000e-49 207.0
11 TraesCS5A01G155900 chr4A 98.660 1119 14 1 3422 4539 502330930 502332048 0.000000e+00 1982.0
12 TraesCS5A01G155900 chr4A 97.950 1122 21 2 3420 4539 502317816 502318937 0.000000e+00 1943.0
13 TraesCS5A01G155900 chr4A 87.931 174 21 0 2694 2867 66741699 66741872 5.950000e-49 206.0
14 TraesCS5A01G155900 chr7A 98.213 1119 19 1 3422 4539 462937956 462936838 0.000000e+00 1954.0
15 TraesCS5A01G155900 chr7A 98.211 1118 19 1 3422 4539 534190545 534189429 0.000000e+00 1953.0
16 TraesCS5A01G155900 chr7A 98.122 1118 19 2 3422 4539 212320798 212321913 0.000000e+00 1947.0
17 TraesCS5A01G155900 chr7A 84.985 646 85 12 3399 4040 206078980 206079617 0.000000e+00 645.0
18 TraesCS5A01G155900 chr7A 88.571 175 20 0 2693 2867 268967683 268967509 3.560000e-51 213.0
19 TraesCS5A01G155900 chr7A 87.356 174 22 0 2694 2867 569977903 569977730 2.770000e-47 200.0
20 TraesCS5A01G155900 chr7A 85.443 158 23 0 1112 1269 177136164 177136321 1.010000e-36 165.0
21 TraesCS5A01G155900 chr7A 97.500 40 0 1 795 833 404465925 404465886 2.930000e-07 67.6
22 TraesCS5A01G155900 chr2A 98.122 1118 21 0 3422 4539 288650133 288651250 0.000000e+00 1949.0
23 TraesCS5A01G155900 chr2A 85.437 824 101 19 3405 4218 150606933 150606119 0.000000e+00 839.0
24 TraesCS5A01G155900 chr6A 98.122 1118 19 2 3418 4534 479866887 479868003 0.000000e+00 1947.0
25 TraesCS5A01G155900 chr6A 87.429 175 22 0 2693 2867 333512270 333512096 7.700000e-48 202.0
26 TraesCS5A01G155900 chr6A 85.535 159 23 0 1112 1270 520355710 520355552 2.810000e-37 167.0
27 TraesCS5A01G155900 chr3A 88.735 941 94 12 3401 4336 450789846 450790779 0.000000e+00 1140.0
28 TraesCS5A01G155900 chr3A 92.911 395 23 5 3405 3797 108011156 108010765 1.830000e-158 569.0
29 TraesCS5A01G155900 chr3A 89.017 173 18 1 2695 2867 617315817 617315646 3.560000e-51 213.0
30 TraesCS5A01G155900 chr7B 84.494 948 117 19 3405 4341 188924229 188923301 0.000000e+00 909.0
31 TraesCS5A01G155900 chr7B 85.443 158 23 0 1112 1269 140652907 140653064 1.010000e-36 165.0
32 TraesCS5A01G155900 chr4D 89.080 174 19 0 2694 2867 469626381 469626554 2.750000e-52 217.0
33 TraesCS5A01G155900 chr6B 87.931 174 21 0 2694 2867 232155917 232155744 5.950000e-49 206.0
34 TraesCS5A01G155900 chr6B 89.781 137 14 0 1134 1270 539727679 539727543 4.670000e-40 176.0
35 TraesCS5A01G155900 chr6D 89.051 137 15 0 1134 1270 358326135 358325999 2.170000e-38 171.0
36 TraesCS5A01G155900 chr6D 85.535 159 23 0 1112 1270 378379440 378379282 2.810000e-37 167.0
37 TraesCS5A01G155900 chr7D 85.443 158 23 0 1112 1269 174992614 174992771 1.010000e-36 165.0


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 TraesCS5A01G155900 chr5A 334261614 334266152 4538 True 8383.000000 8383 100.000000 1 4539 1 chr5A.!!$R3 4538
1 TraesCS5A01G155900 chr5A 334248601 334249718 1117 True 1977.000000 1977 98.569000 3422 4539 1 chr5A.!!$R2 1117
2 TraesCS5A01G155900 chr5A 376873238 376874351 1113 False 1951.000000 1951 98.294000 3422 4534 1 chr5A.!!$F2 1112
3 TraesCS5A01G155900 chr5A 292013175 292014110 935 False 1007.000000 1007 86.181000 3397 4336 1 chr5A.!!$F1 939
4 TraesCS5A01G155900 chr5D 251062075 251065365 3290 True 1636.666667 3773 94.275333 1 3420 3 chr5D.!!$R1 3419
5 TraesCS5A01G155900 chr5B 283621960 283625184 3224 True 2227.000000 3633 92.525000 1 3422 2 chr5B.!!$R2 3421
6 TraesCS5A01G155900 chr4A 502330930 502332048 1118 False 1982.000000 1982 98.660000 3422 4539 1 chr4A.!!$F3 1117
7 TraesCS5A01G155900 chr4A 502317816 502318937 1121 False 1943.000000 1943 97.950000 3420 4539 1 chr4A.!!$F2 1119
8 TraesCS5A01G155900 chr7A 462936838 462937956 1118 True 1954.000000 1954 98.213000 3422 4539 1 chr7A.!!$R3 1117
9 TraesCS5A01G155900 chr7A 534189429 534190545 1116 True 1953.000000 1953 98.211000 3422 4539 1 chr7A.!!$R4 1117
10 TraesCS5A01G155900 chr7A 212320798 212321913 1115 False 1947.000000 1947 98.122000 3422 4539 1 chr7A.!!$F3 1117
11 TraesCS5A01G155900 chr7A 206078980 206079617 637 False 645.000000 645 84.985000 3399 4040 1 chr7A.!!$F2 641
12 TraesCS5A01G155900 chr2A 288650133 288651250 1117 False 1949.000000 1949 98.122000 3422 4539 1 chr2A.!!$F1 1117
13 TraesCS5A01G155900 chr2A 150606119 150606933 814 True 839.000000 839 85.437000 3405 4218 1 chr2A.!!$R1 813
14 TraesCS5A01G155900 chr6A 479866887 479868003 1116 False 1947.000000 1947 98.122000 3418 4534 1 chr6A.!!$F1 1116
15 TraesCS5A01G155900 chr3A 450789846 450790779 933 False 1140.000000 1140 88.735000 3401 4336 1 chr3A.!!$F1 935
16 TraesCS5A01G155900 chr7B 188923301 188924229 928 True 909.000000 909 84.494000 3405 4341 1 chr7B.!!$R1 936

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
492 578 0.106149 GGGGGCGATCGTATGTTTCT 59.894 55.0 17.81 0.00 0.00 2.52 F
1038 1135 0.600057 CAAACTCCAAGAGCAAGGCC 59.400 55.0 0.00 0.00 32.04 5.19 F
1425 1522 0.251077 CAAGCAGCCTTTCCCTGACT 60.251 55.0 0.00 0.00 32.03 3.41 F
1443 1540 0.321564 CTGCCTTTGGGTCATCGTCA 60.322 55.0 0.00 0.00 34.45 4.35 F
1737 1834 0.755686 GCGAGGAAGGAGATGATGGT 59.244 55.0 0.00 0.00 0.00 3.55 F
2736 2842 0.819582 GGAACTTATCGGTCGACCCA 59.180 55.0 28.52 17.72 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1522 0.327924 ATGACGATGACCCAAAGGCA 59.672 50.000 0.00 0.00 36.11 4.75 R
2717 2823 0.819582 TGGGTCGACCGATAAGTTCC 59.180 55.000 27.68 11.32 44.64 3.62 R
2821 2927 1.060713 CGCTTACTGTTGTCTGACCG 58.939 55.000 5.17 0.00 0.00 4.79 R
2822 2928 2.433868 TCGCTTACTGTTGTCTGACC 57.566 50.000 5.17 0.00 0.00 4.02 R
3338 3444 2.508526 CTAAGCACCCTGTTGAGCTTT 58.491 47.619 3.72 0.00 44.22 3.51 R
4346 4473 0.882042 CAGTCCTGAACACGCAGCTT 60.882 55.000 0.00 0.00 34.56 3.74 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
97 98 4.696479 ATCCCATAGCACTAGACCAAAG 57.304 45.455 0.00 0.00 0.00 2.77
124 125 5.415077 CACCTATACTCCATACTACCCTTCG 59.585 48.000 0.00 0.00 0.00 3.79
157 158 6.402222 GTGAGCTTCTTCTTCCTTTGATCTA 58.598 40.000 0.00 0.00 0.00 1.98
184 185 5.783360 TCACTTACTATTTCTCCCTTGTCCA 59.217 40.000 0.00 0.00 0.00 4.02
185 186 6.070767 TCACTTACTATTTCTCCCTTGTCCAG 60.071 42.308 0.00 0.00 0.00 3.86
217 287 0.238289 CCTCGTGCATGCGACTTTTT 59.762 50.000 14.09 0.00 36.80 1.94
227 297 7.306574 CGTGCATGCGACTTTTTCTAGATAATA 60.307 37.037 14.09 0.00 0.00 0.98
235 305 7.148787 CGACTTTTTCTAGATAATATCCCGCAC 60.149 40.741 0.00 0.00 0.00 5.34
252 322 2.026157 CTATCGCTCGCCGCAAGA 59.974 61.111 0.00 0.00 39.08 3.02
284 370 6.041069 AGCTAGCGATCTTCACTTTAATACCT 59.959 38.462 9.55 0.00 0.00 3.08
353 439 1.194547 CGTGTTCCTGTGTACATGCAC 59.805 52.381 0.00 2.11 39.65 4.57
432 518 7.763172 TGGTTTGTGTAATTTTGATGTTGTC 57.237 32.000 0.00 0.00 0.00 3.18
452 538 6.561737 TGTCGTATCAATTTTAGCAAACCA 57.438 33.333 0.00 0.00 0.00 3.67
480 566 2.317040 CTAGAACAATAGAGGGGGCGA 58.683 52.381 0.00 0.00 0.00 5.54
481 567 1.807814 AGAACAATAGAGGGGGCGAT 58.192 50.000 0.00 0.00 0.00 4.58
492 578 0.106149 GGGGGCGATCGTATGTTTCT 59.894 55.000 17.81 0.00 0.00 2.52
646 734 8.366401 TGCTTTGATTTATGAAAAGTTGGATCA 58.634 29.630 0.00 0.00 34.18 2.92
661 749 5.182760 AGTTGGATCAGATTTTGCAGTTCTC 59.817 40.000 0.00 0.00 0.00 2.87
786 875 9.495382 AGACTTTCAAGGAATCCTAATACTAGT 57.505 33.333 0.46 0.00 31.13 2.57
876 966 9.246670 TGATTAATTGAATCTGTTCTGTGGATT 57.753 29.630 0.00 0.00 43.90 3.01
886 976 7.206981 TCTGTTCTGTGGATTTGAGAATTTC 57.793 36.000 0.00 0.00 0.00 2.17
897 987 7.121759 TGGATTTGAGAATTTCAGACCTGATTC 59.878 37.037 0.01 3.36 39.64 2.52
899 989 9.388506 GATTTGAGAATTTCAGACCTGATTCTA 57.611 33.333 13.03 2.94 38.39 2.10
945 1042 5.970592 TGATTCTACATGTCTCACTCCTTG 58.029 41.667 0.00 0.00 0.00 3.61
964 1061 9.154632 ACTCCTTGGGATTAACAATTTAACTTT 57.845 29.630 0.00 0.00 29.77 2.66
1038 1135 0.600057 CAAACTCCAAGAGCAAGGCC 59.400 55.000 0.00 0.00 32.04 5.19
1089 1186 2.202810 GAGAAGAAGCCTCGGCCG 60.203 66.667 22.12 22.12 43.17 6.13
1248 1345 4.404098 AACGTCCCCATCGGTGGC 62.404 66.667 9.99 0.00 44.62 5.01
1325 1422 2.571216 CCTCGTCAGAACCCACGGT 61.571 63.158 0.00 0.00 37.65 4.83
1377 1474 1.228124 CTTTGCCAACGTCCTCCCA 60.228 57.895 0.00 0.00 0.00 4.37
1380 1477 2.112297 GCCAACGTCCTCCCAACA 59.888 61.111 0.00 0.00 0.00 3.33
1425 1522 0.251077 CAAGCAGCCTTTCCCTGACT 60.251 55.000 0.00 0.00 32.03 3.41
1443 1540 0.321564 CTGCCTTTGGGTCATCGTCA 60.322 55.000 0.00 0.00 34.45 4.35
1488 1585 3.299977 CCTGGTGGGACGACGTCA 61.300 66.667 27.77 7.81 37.23 4.35
1512 1609 1.255667 TAGACGTGTTGAGAGGGGGC 61.256 60.000 0.00 0.00 0.00 5.80
1577 1674 1.632018 TACTATGGTGGGCCTGCCAC 61.632 60.000 19.73 11.00 37.62 5.01
1647 1744 2.046023 CCAGGTCCGATGCAGCAA 60.046 61.111 1.53 0.00 0.00 3.91
1653 1750 1.002257 TCCGATGCAGCAACATGGT 60.002 52.632 1.53 0.00 0.00 3.55
1686 1783 2.311542 TGGTGGAAATGGAATAGGTGCT 59.688 45.455 0.00 0.00 0.00 4.40
1734 1831 1.047002 CTGGCGAGGAAGGAGATGAT 58.953 55.000 0.00 0.00 0.00 2.45
1737 1834 0.755686 GCGAGGAAGGAGATGATGGT 59.244 55.000 0.00 0.00 0.00 3.55
1739 1836 2.288518 GCGAGGAAGGAGATGATGGTAC 60.289 54.545 0.00 0.00 0.00 3.34
1793 1890 1.907807 TTGGCAATGGTGGAGGTGC 60.908 57.895 0.00 0.00 36.24 5.01
1860 1957 1.269448 GTGACGATGGGCAACAACAAT 59.731 47.619 0.00 0.00 39.74 2.71
1887 1984 6.451393 ACACAACAACAACAATAACAACAGT 58.549 32.000 0.00 0.00 0.00 3.55
1890 1987 5.004922 ACAACAACAATAACAACAGTGGG 57.995 39.130 0.00 0.00 0.00 4.61
1910 2007 1.067635 GGGTGATGACAACAATGGTGC 60.068 52.381 0.00 0.00 35.07 5.01
1976 2073 1.376466 GGCAGAGCCTCCTCAACAA 59.624 57.895 0.00 0.00 46.69 2.83
1999 2096 2.240667 AGCTCCCTGATGTAAGTGCAAT 59.759 45.455 0.00 0.00 0.00 3.56
2047 2144 4.202556 TGAATTGGAGAAGTGGGTCAATCA 60.203 41.667 0.00 0.00 0.00 2.57
2185 2287 1.980844 GTGTGTCATTTGCGATGCTTG 59.019 47.619 0.00 0.00 0.00 4.01
2311 2413 6.195600 AGTTAGTTTACCCACTGATCCAAA 57.804 37.500 0.00 0.00 0.00 3.28
2371 2473 6.183360 CCTCATTTGTAGAAACACTAGCCATG 60.183 42.308 0.00 0.00 34.61 3.66
2515 2620 2.290071 CGTCCACCAAAGAGGGTACAAT 60.290 50.000 0.00 0.00 43.89 2.71
2612 2718 1.784525 GGGTCTTGTGACTCTTGTCG 58.215 55.000 0.00 0.00 45.70 4.35
2624 2730 4.215965 GACTCTTGTCGATCGAGCTAATC 58.784 47.826 20.09 6.11 33.15 1.75
2631 2737 2.095008 TCGATCGAGCTAATCCATGAGC 60.095 50.000 15.15 0.00 39.08 4.26
2683 2789 5.310451 TGATAGGCTTACGAAGGTTTTGTT 58.690 37.500 0.00 0.00 0.00 2.83
2684 2790 3.982576 AGGCTTACGAAGGTTTTGTTG 57.017 42.857 0.00 0.00 0.00 3.33
2685 2791 2.621526 AGGCTTACGAAGGTTTTGTTGG 59.378 45.455 0.00 0.00 0.00 3.77
2686 2792 2.359848 GGCTTACGAAGGTTTTGTTGGT 59.640 45.455 0.00 0.00 0.00 3.67
2687 2793 3.181484 GGCTTACGAAGGTTTTGTTGGTT 60.181 43.478 0.00 0.00 0.00 3.67
2688 2794 4.039703 GCTTACGAAGGTTTTGTTGGTTC 58.960 43.478 0.00 0.00 0.00 3.62
2689 2795 4.201980 GCTTACGAAGGTTTTGTTGGTTCT 60.202 41.667 0.00 0.00 0.00 3.01
2690 2796 5.677852 GCTTACGAAGGTTTTGTTGGTTCTT 60.678 40.000 0.00 0.00 0.00 2.52
2691 2797 4.365899 ACGAAGGTTTTGTTGGTTCTTC 57.634 40.909 0.00 0.00 0.00 2.87
2692 2798 3.129813 ACGAAGGTTTTGTTGGTTCTTCC 59.870 43.478 0.00 0.00 0.00 3.46
2693 2799 3.490249 CGAAGGTTTTGTTGGTTCTTCCC 60.490 47.826 0.00 0.00 34.77 3.97
2694 2800 3.108847 AGGTTTTGTTGGTTCTTCCCA 57.891 42.857 0.00 0.00 34.77 4.37
2695 2801 3.445987 AGGTTTTGTTGGTTCTTCCCAA 58.554 40.909 0.00 0.00 42.16 4.12
2696 2802 4.037222 AGGTTTTGTTGGTTCTTCCCAAT 58.963 39.130 0.00 0.00 45.79 3.16
2697 2803 4.126437 GGTTTTGTTGGTTCTTCCCAATG 58.874 43.478 0.00 0.00 45.79 2.82
2698 2804 4.383661 GGTTTTGTTGGTTCTTCCCAATGT 60.384 41.667 0.00 0.00 45.79 2.71
2699 2805 5.182487 GTTTTGTTGGTTCTTCCCAATGTT 58.818 37.500 0.00 0.00 45.79 2.71
2700 2806 4.399004 TTGTTGGTTCTTCCCAATGTTG 57.601 40.909 0.00 0.00 45.79 3.33
2701 2807 2.697751 TGTTGGTTCTTCCCAATGTTGG 59.302 45.455 4.77 4.77 45.79 3.77
2711 2817 2.276732 CCAATGTTGGGGATATCGCT 57.723 50.000 18.21 0.00 44.70 4.93
2712 2818 2.586425 CCAATGTTGGGGATATCGCTT 58.414 47.619 18.21 2.96 44.70 4.68
2713 2819 3.750371 CCAATGTTGGGGATATCGCTTA 58.250 45.455 18.21 6.48 44.70 3.09
2714 2820 4.335416 CCAATGTTGGGGATATCGCTTAT 58.665 43.478 18.21 6.34 44.70 1.73
2715 2821 4.766891 CCAATGTTGGGGATATCGCTTATT 59.233 41.667 18.21 10.99 44.70 1.40
2716 2822 5.943416 CCAATGTTGGGGATATCGCTTATTA 59.057 40.000 18.21 3.85 44.70 0.98
2717 2823 6.094048 CCAATGTTGGGGATATCGCTTATTAG 59.906 42.308 18.21 5.08 44.70 1.73
2718 2824 5.160607 TGTTGGGGATATCGCTTATTAGG 57.839 43.478 18.21 0.00 0.00 2.69
2719 2825 4.841813 TGTTGGGGATATCGCTTATTAGGA 59.158 41.667 18.21 0.00 0.00 2.94
2720 2826 5.308497 TGTTGGGGATATCGCTTATTAGGAA 59.692 40.000 18.21 0.00 0.00 3.36
2721 2827 5.416271 TGGGGATATCGCTTATTAGGAAC 57.584 43.478 18.21 0.00 0.00 3.62
2722 2828 5.091552 TGGGGATATCGCTTATTAGGAACT 58.908 41.667 18.21 0.00 46.37 3.01
2723 2829 5.546499 TGGGGATATCGCTTATTAGGAACTT 59.454 40.000 18.21 0.00 41.75 2.66
2724 2830 6.727231 TGGGGATATCGCTTATTAGGAACTTA 59.273 38.462 18.21 0.00 41.75 2.24
2725 2831 7.402071 TGGGGATATCGCTTATTAGGAACTTAT 59.598 37.037 18.21 0.00 41.75 1.73
2726 2832 7.927092 GGGGATATCGCTTATTAGGAACTTATC 59.073 40.741 18.21 0.00 41.75 1.75
2727 2833 7.648510 GGGATATCGCTTATTAGGAACTTATCG 59.351 40.741 12.31 0.00 41.75 2.92
2728 2834 7.648510 GGATATCGCTTATTAGGAACTTATCGG 59.351 40.741 0.00 0.00 41.75 4.18
2729 2835 5.779529 TCGCTTATTAGGAACTTATCGGT 57.220 39.130 0.00 0.00 41.75 4.69
2730 2836 5.766222 TCGCTTATTAGGAACTTATCGGTC 58.234 41.667 0.00 0.00 41.75 4.79
2731 2837 4.615961 CGCTTATTAGGAACTTATCGGTCG 59.384 45.833 0.00 0.00 41.75 4.79
2732 2838 5.561532 CGCTTATTAGGAACTTATCGGTCGA 60.562 44.000 0.00 0.00 41.75 4.20
2733 2839 5.628606 GCTTATTAGGAACTTATCGGTCGAC 59.371 44.000 7.13 7.13 41.75 4.20
2734 2840 4.581077 ATTAGGAACTTATCGGTCGACC 57.419 45.455 25.28 25.28 41.75 4.79
2735 2841 1.109609 AGGAACTTATCGGTCGACCC 58.890 55.000 28.52 11.63 27.25 4.46
2736 2842 0.819582 GGAACTTATCGGTCGACCCA 59.180 55.000 28.52 17.72 0.00 4.51
2737 2843 1.205417 GGAACTTATCGGTCGACCCAA 59.795 52.381 28.52 17.41 0.00 4.12
2738 2844 2.159000 GGAACTTATCGGTCGACCCAAT 60.159 50.000 28.52 22.68 0.00 3.16
2739 2845 3.068590 GGAACTTATCGGTCGACCCAATA 59.931 47.826 28.52 21.68 0.00 1.90
2740 2846 4.262335 GGAACTTATCGGTCGACCCAATAT 60.262 45.833 28.52 18.00 0.00 1.28
2741 2847 5.047802 GGAACTTATCGGTCGACCCAATATA 60.048 44.000 28.52 17.05 0.00 0.86
2742 2848 6.409524 AACTTATCGGTCGACCCAATATAA 57.590 37.500 28.52 21.99 0.00 0.98
2743 2849 6.409524 ACTTATCGGTCGACCCAATATAAA 57.590 37.500 28.52 12.22 0.00 1.40
2744 2850 6.453092 ACTTATCGGTCGACCCAATATAAAG 58.547 40.000 28.52 21.06 0.00 1.85
2745 2851 3.738830 TCGGTCGACCCAATATAAAGG 57.261 47.619 28.52 10.55 0.00 3.11
2755 2861 5.638596 CCCAATATAAAGGGTAAATCGGC 57.361 43.478 4.98 0.00 40.34 5.54
2756 2862 4.461431 CCCAATATAAAGGGTAAATCGGCC 59.539 45.833 0.00 0.00 40.34 6.13
2757 2863 5.074115 CCAATATAAAGGGTAAATCGGCCA 58.926 41.667 2.24 0.00 0.00 5.36
2758 2864 5.183140 CCAATATAAAGGGTAAATCGGCCAG 59.817 44.000 2.24 0.00 0.00 4.85
2759 2865 3.945640 ATAAAGGGTAAATCGGCCAGT 57.054 42.857 2.24 0.00 0.00 4.00
2760 2866 2.597578 AAAGGGTAAATCGGCCAGTT 57.402 45.000 2.24 0.00 0.00 3.16
2761 2867 2.597578 AAGGGTAAATCGGCCAGTTT 57.402 45.000 2.24 5.51 0.00 2.66
2762 2868 3.724732 AAGGGTAAATCGGCCAGTTTA 57.275 42.857 2.24 4.40 0.00 2.01
2763 2869 3.945640 AGGGTAAATCGGCCAGTTTAT 57.054 42.857 2.24 0.00 0.00 1.40
2764 2870 3.816994 AGGGTAAATCGGCCAGTTTATC 58.183 45.455 2.24 7.54 0.00 1.75
2765 2871 2.546789 GGGTAAATCGGCCAGTTTATCG 59.453 50.000 2.24 0.00 0.00 2.92
2766 2872 3.460103 GGTAAATCGGCCAGTTTATCGA 58.540 45.455 2.24 0.00 36.07 3.59
2767 2873 3.246936 GGTAAATCGGCCAGTTTATCGAC 59.753 47.826 2.24 0.00 34.40 4.20
2768 2874 2.684001 AATCGGCCAGTTTATCGACA 57.316 45.000 2.24 0.00 34.40 4.35
2769 2875 2.910688 ATCGGCCAGTTTATCGACAT 57.089 45.000 2.24 0.00 34.40 3.06
2770 2876 4.330944 AATCGGCCAGTTTATCGACATA 57.669 40.909 2.24 0.00 34.40 2.29
2771 2877 4.537135 ATCGGCCAGTTTATCGACATAT 57.463 40.909 2.24 0.00 34.40 1.78
2772 2878 3.909430 TCGGCCAGTTTATCGACATATC 58.091 45.455 2.24 0.00 0.00 1.63
2787 2893 5.688348 GACATATCGACTGATTTATCGCC 57.312 43.478 3.96 0.00 38.24 5.54
2788 2894 5.134202 ACATATCGACTGATTTATCGCCA 57.866 39.130 3.96 0.00 38.24 5.69
2789 2895 5.724328 ACATATCGACTGATTTATCGCCAT 58.276 37.500 3.96 0.00 38.24 4.40
2790 2896 6.863275 ACATATCGACTGATTTATCGCCATA 58.137 36.000 3.96 0.00 38.24 2.74
2791 2897 7.492524 ACATATCGACTGATTTATCGCCATAT 58.507 34.615 3.96 0.00 38.24 1.78
2792 2898 7.649705 ACATATCGACTGATTTATCGCCATATC 59.350 37.037 3.96 0.00 38.24 1.63
2793 2899 5.644977 TCGACTGATTTATCGCCATATCT 57.355 39.130 0.00 0.00 38.24 1.98
2794 2900 6.025749 TCGACTGATTTATCGCCATATCTT 57.974 37.500 0.00 0.00 38.24 2.40
2795 2901 6.093404 TCGACTGATTTATCGCCATATCTTC 58.907 40.000 0.00 0.00 38.24 2.87
2796 2902 6.071896 TCGACTGATTTATCGCCATATCTTCT 60.072 38.462 0.00 0.00 38.24 2.85
2797 2903 7.120726 TCGACTGATTTATCGCCATATCTTCTA 59.879 37.037 0.00 0.00 38.24 2.10
2798 2904 7.755373 CGACTGATTTATCGCCATATCTTCTAA 59.245 37.037 0.00 0.00 0.00 2.10
2799 2905 9.593134 GACTGATTTATCGCCATATCTTCTAAT 57.407 33.333 0.00 0.00 0.00 1.73
2807 2913 7.818997 TCGCCATATCTTCTAATATATCCGT 57.181 36.000 0.00 0.00 0.00 4.69
2808 2914 7.872881 TCGCCATATCTTCTAATATATCCGTC 58.127 38.462 0.00 0.00 0.00 4.79
2809 2915 6.797513 CGCCATATCTTCTAATATATCCGTCG 59.202 42.308 0.00 0.00 0.00 5.12
2810 2916 7.307811 CGCCATATCTTCTAATATATCCGTCGA 60.308 40.741 0.00 0.00 0.00 4.20
2811 2917 8.516234 GCCATATCTTCTAATATATCCGTCGAT 58.484 37.037 0.00 0.00 0.00 3.59
2823 2929 9.894783 AATATATCCGTCGATTTATCTTATCGG 57.105 33.333 0.00 0.00 43.73 4.18
2824 2930 5.640189 ATCCGTCGATTTATCTTATCGGT 57.360 39.130 0.00 0.00 43.73 4.69
2825 2931 5.039480 TCCGTCGATTTATCTTATCGGTC 57.961 43.478 0.00 0.00 43.73 4.79
2826 2932 4.516321 TCCGTCGATTTATCTTATCGGTCA 59.484 41.667 0.00 0.00 43.73 4.02
2827 2933 4.852104 CCGTCGATTTATCTTATCGGTCAG 59.148 45.833 0.00 0.00 43.73 3.51
2828 2934 5.334646 CCGTCGATTTATCTTATCGGTCAGA 60.335 44.000 0.00 0.00 43.73 3.27
2829 2935 5.564504 CGTCGATTTATCTTATCGGTCAGAC 59.435 44.000 0.00 0.00 43.73 3.51
2830 2936 6.436261 GTCGATTTATCTTATCGGTCAGACA 58.564 40.000 2.17 0.00 43.73 3.41
2831 2937 6.916387 GTCGATTTATCTTATCGGTCAGACAA 59.084 38.462 2.17 0.00 43.73 3.18
2832 2938 6.916387 TCGATTTATCTTATCGGTCAGACAAC 59.084 38.462 2.17 0.00 43.73 3.32
2833 2939 6.695713 CGATTTATCTTATCGGTCAGACAACA 59.304 38.462 2.17 0.00 40.78 3.33
2834 2940 7.096436 CGATTTATCTTATCGGTCAGACAACAG 60.096 40.741 2.17 0.00 40.78 3.16
2835 2941 6.525578 TTATCTTATCGGTCAGACAACAGT 57.474 37.500 2.17 0.00 0.00 3.55
2836 2942 7.634671 TTATCTTATCGGTCAGACAACAGTA 57.365 36.000 2.17 0.00 0.00 2.74
2837 2943 5.970317 TCTTATCGGTCAGACAACAGTAA 57.030 39.130 2.17 0.00 0.00 2.24
2838 2944 5.950883 TCTTATCGGTCAGACAACAGTAAG 58.049 41.667 2.17 4.03 0.00 2.34
2839 2945 2.433868 TCGGTCAGACAACAGTAAGC 57.566 50.000 2.17 0.00 0.00 3.09
2840 2946 1.060713 CGGTCAGACAACAGTAAGCG 58.939 55.000 2.17 0.00 0.00 4.68
2841 2947 1.335597 CGGTCAGACAACAGTAAGCGA 60.336 52.381 2.17 0.00 0.00 4.93
2842 2948 2.671351 CGGTCAGACAACAGTAAGCGAT 60.671 50.000 2.17 0.00 0.00 4.58
2843 2949 3.427098 CGGTCAGACAACAGTAAGCGATA 60.427 47.826 2.17 0.00 0.00 2.92
2844 2950 4.491676 GGTCAGACAACAGTAAGCGATAA 58.508 43.478 2.17 0.00 0.00 1.75
2845 2951 4.927425 GGTCAGACAACAGTAAGCGATAAA 59.073 41.667 2.17 0.00 0.00 1.40
2846 2952 5.581085 GGTCAGACAACAGTAAGCGATAAAT 59.419 40.000 2.17 0.00 0.00 1.40
2847 2953 6.237861 GGTCAGACAACAGTAAGCGATAAATC 60.238 42.308 2.17 0.00 0.00 2.17
2848 2954 6.310467 GTCAGACAACAGTAAGCGATAAATCA 59.690 38.462 0.00 0.00 0.00 2.57
2849 2955 6.531594 TCAGACAACAGTAAGCGATAAATCAG 59.468 38.462 0.00 0.00 0.00 2.90
2850 2956 5.292101 AGACAACAGTAAGCGATAAATCAGC 59.708 40.000 0.00 0.00 0.00 4.26
2851 2957 4.332819 ACAACAGTAAGCGATAAATCAGCC 59.667 41.667 0.00 0.00 0.00 4.85
2852 2958 4.137116 ACAGTAAGCGATAAATCAGCCA 57.863 40.909 0.00 0.00 0.00 4.75
2853 2959 4.513442 ACAGTAAGCGATAAATCAGCCAA 58.487 39.130 0.00 0.00 0.00 4.52
2854 2960 5.126067 ACAGTAAGCGATAAATCAGCCAAT 58.874 37.500 0.00 0.00 0.00 3.16
2855 2961 5.590259 ACAGTAAGCGATAAATCAGCCAATT 59.410 36.000 0.00 0.00 0.00 2.32
2856 2962 6.095440 ACAGTAAGCGATAAATCAGCCAATTT 59.905 34.615 0.00 0.25 33.54 1.82
2857 2963 7.282224 ACAGTAAGCGATAAATCAGCCAATTTA 59.718 33.333 4.19 4.19 35.99 1.40
2858 2964 8.292448 CAGTAAGCGATAAATCAGCCAATTTAT 58.708 33.333 11.68 11.68 41.99 1.40
2859 2965 8.507249 AGTAAGCGATAAATCAGCCAATTTATC 58.493 33.333 20.96 20.96 46.11 1.75
2870 2976 9.911788 AATCAGCCAATTTATCGGAATATATCT 57.088 29.630 0.00 0.00 0.00 1.98
2871 2977 9.911788 ATCAGCCAATTTATCGGAATATATCTT 57.088 29.630 0.00 0.00 0.00 2.40
2872 2978 9.166173 TCAGCCAATTTATCGGAATATATCTTG 57.834 33.333 0.00 0.00 0.00 3.02
2873 2979 9.166173 CAGCCAATTTATCGGAATATATCTTGA 57.834 33.333 0.00 0.00 0.00 3.02
2874 2980 9.739276 AGCCAATTTATCGGAATATATCTTGAA 57.261 29.630 0.00 0.00 0.00 2.69
2947 3053 5.254339 AGAAAACTTGAAAGGTTGCTCTG 57.746 39.130 0.00 0.00 36.94 3.35
3185 3291 3.788227 AAGGTTGATAAGGTGCACTCA 57.212 42.857 17.98 9.70 0.00 3.41
3196 3302 4.090761 AGGTGCACTCATCTTTCAAAGA 57.909 40.909 17.98 1.30 42.69 2.52
3214 3320 3.425162 AGAATTTTGGAGGAGCGACTT 57.575 42.857 0.00 0.00 0.00 3.01
3245 3351 6.299805 TCGGGCTTATTCATGAGCTATATT 57.700 37.500 4.84 0.00 39.17 1.28
3246 3352 6.108687 TCGGGCTTATTCATGAGCTATATTG 58.891 40.000 4.84 0.00 39.17 1.90
3261 3367 7.292356 TGAGCTATATTGTTTGATTCCCTAGGA 59.708 37.037 11.48 0.00 0.00 2.94
3331 3437 5.043248 GCATGCATGTTTGTTAGGGTATTC 58.957 41.667 26.79 1.51 0.00 1.75
3338 3444 7.870445 GCATGTTTGTTAGGGTATTCTTTTCAA 59.130 33.333 0.00 0.00 0.00 2.69
3347 3453 6.749139 AGGGTATTCTTTTCAAAAGCTCAAC 58.251 36.000 4.87 1.32 0.00 3.18
3357 3463 2.622942 CAAAAGCTCAACAGGGTGCTTA 59.377 45.455 0.00 0.00 43.80 3.09
3380 3486 9.787532 CTTAGCTAGCATCTCTATCATTAAGAC 57.212 37.037 18.83 0.00 0.00 3.01
3563 3675 3.056821 CGGTTTCACTACCAGAGATGACA 60.057 47.826 0.00 0.00 38.12 3.58
3892 4009 5.251764 CCATGAGAGTTTGAAATCTGACCT 58.748 41.667 0.00 0.00 32.87 3.85
4014 4134 1.888512 GGTTGGCTGCTCAGATTTCAA 59.111 47.619 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.214545 CCAGATGTTTAAACACTACCGCAA 59.785 41.667 22.78 0.00 42.51 4.85
97 98 6.313324 AGGGTAGTATGGAGTATAGGTGTTC 58.687 44.000 0.00 0.00 0.00 3.18
124 125 2.147150 GAAGAAGCTCACCAGGTGAAC 58.853 52.381 23.11 18.71 42.26 3.18
157 158 8.652290 GGACAAGGGAGAAATAGTAAGTGATAT 58.348 37.037 0.00 0.00 0.00 1.63
169 170 2.646798 AGAAGCTGGACAAGGGAGAAAT 59.353 45.455 0.00 0.00 0.00 2.17
180 181 3.595173 GAGGAAGAAGAAGAAGCTGGAC 58.405 50.000 0.00 0.00 0.00 4.02
182 183 2.028567 ACGAGGAAGAAGAAGAAGCTGG 60.029 50.000 0.00 0.00 0.00 4.85
184 185 2.611722 GCACGAGGAAGAAGAAGAAGCT 60.612 50.000 0.00 0.00 0.00 3.74
185 186 1.729517 GCACGAGGAAGAAGAAGAAGC 59.270 52.381 0.00 0.00 0.00 3.86
217 287 5.238868 GCGATAGTGCGGGATATTATCTAGA 59.761 44.000 0.00 0.00 39.35 2.43
227 297 2.645567 CGAGCGATAGTGCGGGAT 59.354 61.111 0.00 0.00 40.67 3.85
284 370 2.093869 GCCCGTGGTTAGATCTACAACA 60.094 50.000 0.67 0.43 0.00 3.33
323 409 1.400494 ACAGGAACACGCAAACAAGAC 59.600 47.619 0.00 0.00 0.00 3.01
432 518 5.732647 CGAGTGGTTTGCTAAAATTGATACG 59.267 40.000 0.00 0.00 0.00 3.06
452 538 4.822896 CCCTCTATTGTTCTAGCTACGAGT 59.177 45.833 0.00 0.00 0.00 4.18
480 566 7.145323 CCCTTTTCAAAACAGAAACATACGAT 58.855 34.615 0.00 0.00 37.24 3.73
481 567 6.460399 CCCCTTTTCAAAACAGAAACATACGA 60.460 38.462 0.00 0.00 37.24 3.43
492 578 6.013812 CCTGGAAATATCCCCTTTTCAAAACA 60.014 38.462 0.00 0.00 45.95 2.83
638 726 5.182760 AGAGAACTGCAAAATCTGATCCAAC 59.817 40.000 0.69 0.00 0.00 3.77
646 734 7.765695 TGGATAAAAGAGAACTGCAAAATCT 57.234 32.000 0.00 0.00 0.00 2.40
727 815 4.279145 TCTCCTAGTTACTAACCAGGCAG 58.721 47.826 8.21 7.25 39.73 4.85
762 851 9.268282 TCACTAGTATTAGGATTCCTTGAAAGT 57.732 33.333 11.25 5.12 34.61 2.66
786 875 7.691993 AATAAGCTTCCTTTCCCTATACTCA 57.308 36.000 0.00 0.00 32.47 3.41
793 882 6.936279 GCTTAAAAATAAGCTTCCTTTCCCT 58.064 36.000 0.00 0.00 46.49 4.20
868 958 5.709164 AGGTCTGAAATTCTCAAATCCACAG 59.291 40.000 0.00 0.00 32.17 3.66
870 960 5.707298 TCAGGTCTGAAATTCTCAAATCCAC 59.293 40.000 0.00 0.00 36.53 4.02
876 966 7.679783 TGTAGAATCAGGTCTGAAATTCTCAA 58.320 34.615 15.83 7.15 43.58 3.02
886 976 7.335171 TCAAAATGTCATGTAGAATCAGGTCTG 59.665 37.037 0.00 0.00 0.00 3.51
897 987 9.345517 CATTGGTTAACTCAAAATGTCATGTAG 57.654 33.333 5.42 0.00 0.00 2.74
899 989 7.950512 TCATTGGTTAACTCAAAATGTCATGT 58.049 30.769 5.42 0.00 31.63 3.21
1089 1186 0.676151 CCACCTTCTGCTCTGGCTTC 60.676 60.000 0.00 0.00 39.59 3.86
1314 1411 0.889186 GCATGACAACCGTGGGTTCT 60.889 55.000 0.00 0.00 43.05 3.01
1325 1422 3.700970 TCGAGGGCGGCATGACAA 61.701 61.111 12.47 0.00 38.28 3.18
1335 1432 4.767255 CCTGTGCAGGTCGAGGGC 62.767 72.222 9.96 0.00 43.61 5.19
1377 1474 6.265196 TCTCAAAACCAGCAGACATAAATGTT 59.735 34.615 0.00 0.00 41.95 2.71
1380 1477 7.363268 GGAATCTCAAAACCAGCAGACATAAAT 60.363 37.037 0.00 0.00 0.00 1.40
1425 1522 0.327924 ATGACGATGACCCAAAGGCA 59.672 50.000 0.00 0.00 36.11 4.75
1461 1558 3.826282 CCACCAGGGGACATCACT 58.174 61.111 0.00 0.00 0.00 3.41
1488 1585 3.195825 CCCCTCTCAACACGTCTAGAAAT 59.804 47.826 0.00 0.00 0.00 2.17
1512 1609 1.094073 CATCAAGAAGCCCTCCTGCG 61.094 60.000 0.00 0.00 36.02 5.18
1577 1674 1.617322 CATCCCAATGCCTGATCCAG 58.383 55.000 0.00 0.00 0.00 3.86
1613 1710 0.897401 TGGAATGCCAAATGACGCCA 60.897 50.000 0.00 0.00 42.49 5.69
1647 1744 1.339055 CCAACCACGAGATCACCATGT 60.339 52.381 0.00 0.00 0.00 3.21
1653 1750 1.052617 TTCCACCAACCACGAGATCA 58.947 50.000 0.00 0.00 0.00 2.92
1686 1783 4.082081 CCCTGAAATATTGAAGCAGTTGCA 60.082 41.667 6.90 0.00 45.16 4.08
1793 1890 1.740380 CGCCTCCTGATACAACACCAG 60.740 57.143 0.00 0.00 0.00 4.00
1860 1957 9.723447 CTGTTGTTATTGTTGTTGTTGTGTATA 57.277 29.630 0.00 0.00 0.00 1.47
1882 1979 0.850100 TTGTCATCACCCCCACTGTT 59.150 50.000 0.00 0.00 0.00 3.16
1887 1984 1.549722 CCATTGTTGTCATCACCCCCA 60.550 52.381 0.00 0.00 0.00 4.96
1890 1987 1.067635 GCACCATTGTTGTCATCACCC 60.068 52.381 0.00 0.00 0.00 4.61
1910 2007 1.338337 AGTAGCAATCCCTCGATGACG 59.662 52.381 0.00 0.00 41.26 4.35
1976 2073 1.065854 GCACTTACATCAGGGAGCTGT 60.066 52.381 0.00 0.00 0.00 4.40
1999 2096 5.898120 TGACCTCCATTTCCCATTTTCTTA 58.102 37.500 0.00 0.00 0.00 2.10
2047 2144 8.779354 AGAAGCGATGAAACTAGTAAGAAAAT 57.221 30.769 0.00 0.00 0.00 1.82
2292 2394 4.447138 TGTTTGGATCAGTGGGTAAACT 57.553 40.909 0.00 0.00 0.00 2.66
2371 2473 6.827586 TGTTATAACCCACAAAAGACCATC 57.172 37.500 13.01 0.00 0.00 3.51
2612 2718 3.591196 AGCTCATGGATTAGCTCGATC 57.409 47.619 0.93 0.00 45.92 3.69
2624 2730 7.338800 AGAAAACAAATGGTATAGCTCATGG 57.661 36.000 3.20 0.00 0.00 3.66
2672 2778 3.449377 TGGGAAGAACCAACAAAACCTTC 59.551 43.478 0.00 0.00 41.20 3.46
2693 2799 5.964958 AATAAGCGATATCCCCAACATTG 57.035 39.130 0.00 0.00 0.00 2.82
2694 2800 6.012858 TCCTAATAAGCGATATCCCCAACATT 60.013 38.462 0.00 0.00 0.00 2.71
2695 2801 5.487488 TCCTAATAAGCGATATCCCCAACAT 59.513 40.000 0.00 0.00 0.00 2.71
2696 2802 4.841813 TCCTAATAAGCGATATCCCCAACA 59.158 41.667 0.00 0.00 0.00 3.33
2697 2803 5.416271 TCCTAATAAGCGATATCCCCAAC 57.584 43.478 0.00 0.00 0.00 3.77
2698 2804 5.546499 AGTTCCTAATAAGCGATATCCCCAA 59.454 40.000 0.00 0.00 0.00 4.12
2699 2805 5.091552 AGTTCCTAATAAGCGATATCCCCA 58.908 41.667 0.00 0.00 0.00 4.96
2700 2806 5.678955 AGTTCCTAATAAGCGATATCCCC 57.321 43.478 0.00 0.00 0.00 4.81
2701 2807 7.648510 CGATAAGTTCCTAATAAGCGATATCCC 59.351 40.741 0.00 0.00 0.00 3.85
2702 2808 7.648510 CCGATAAGTTCCTAATAAGCGATATCC 59.351 40.741 0.00 0.00 0.00 2.59
2703 2809 8.189460 ACCGATAAGTTCCTAATAAGCGATATC 58.811 37.037 0.00 0.00 0.00 1.63
2704 2810 8.064336 ACCGATAAGTTCCTAATAAGCGATAT 57.936 34.615 0.00 0.00 0.00 1.63
2705 2811 7.458409 ACCGATAAGTTCCTAATAAGCGATA 57.542 36.000 0.00 0.00 0.00 2.92
2706 2812 6.342338 ACCGATAAGTTCCTAATAAGCGAT 57.658 37.500 0.00 0.00 0.00 4.58
2707 2813 5.561532 CGACCGATAAGTTCCTAATAAGCGA 60.562 44.000 0.00 0.00 0.00 4.93
2708 2814 4.615961 CGACCGATAAGTTCCTAATAAGCG 59.384 45.833 0.00 0.00 0.00 4.68
2709 2815 5.628606 GTCGACCGATAAGTTCCTAATAAGC 59.371 44.000 3.51 0.00 0.00 3.09
2710 2816 6.148264 GGTCGACCGATAAGTTCCTAATAAG 58.852 44.000 20.85 0.00 0.00 1.73
2711 2817 5.010012 GGGTCGACCGATAAGTTCCTAATAA 59.990 44.000 27.68 0.00 36.71 1.40
2712 2818 4.520492 GGGTCGACCGATAAGTTCCTAATA 59.480 45.833 27.68 0.00 36.71 0.98
2713 2819 3.320256 GGGTCGACCGATAAGTTCCTAAT 59.680 47.826 27.68 0.00 36.71 1.73
2714 2820 2.689983 GGGTCGACCGATAAGTTCCTAA 59.310 50.000 27.68 0.00 36.71 2.69
2715 2821 2.301346 GGGTCGACCGATAAGTTCCTA 58.699 52.381 27.68 0.00 36.71 2.94
2716 2822 1.109609 GGGTCGACCGATAAGTTCCT 58.890 55.000 27.68 0.00 36.71 3.36
2717 2823 0.819582 TGGGTCGACCGATAAGTTCC 59.180 55.000 27.68 11.32 44.64 3.62
2718 2824 2.660189 TTGGGTCGACCGATAAGTTC 57.340 50.000 27.68 12.04 44.64 3.01
2719 2825 4.950205 ATATTGGGTCGACCGATAAGTT 57.050 40.909 27.68 10.98 46.42 2.66
2720 2826 6.409524 TTTATATTGGGTCGACCGATAAGT 57.590 37.500 27.68 15.53 46.42 2.24
2721 2827 5.867716 CCTTTATATTGGGTCGACCGATAAG 59.132 44.000 27.68 20.51 46.42 1.73
2722 2828 5.279607 CCCTTTATATTGGGTCGACCGATAA 60.280 44.000 27.68 22.06 46.42 1.75
2724 2830 3.007614 CCCTTTATATTGGGTCGACCGAT 59.992 47.826 27.68 23.99 45.71 4.18
2725 2831 2.366266 CCCTTTATATTGGGTCGACCGA 59.634 50.000 27.68 22.29 44.64 4.69
2726 2832 2.762745 CCCTTTATATTGGGTCGACCG 58.237 52.381 27.68 10.69 44.64 4.79
2734 2840 5.074115 TGGCCGATTTACCCTTTATATTGG 58.926 41.667 0.00 0.00 0.00 3.16
2735 2841 5.768164 ACTGGCCGATTTACCCTTTATATTG 59.232 40.000 0.00 0.00 0.00 1.90
2736 2842 5.948842 ACTGGCCGATTTACCCTTTATATT 58.051 37.500 0.00 0.00 0.00 1.28
2737 2843 5.578157 ACTGGCCGATTTACCCTTTATAT 57.422 39.130 0.00 0.00 0.00 0.86
2738 2844 5.376756 AACTGGCCGATTTACCCTTTATA 57.623 39.130 0.00 0.00 0.00 0.98
2739 2845 3.945640 ACTGGCCGATTTACCCTTTAT 57.054 42.857 0.00 0.00 0.00 1.40
2740 2846 3.724732 AACTGGCCGATTTACCCTTTA 57.275 42.857 0.00 0.00 0.00 1.85
2741 2847 2.597578 AACTGGCCGATTTACCCTTT 57.402 45.000 0.00 0.00 0.00 3.11
2742 2848 2.597578 AAACTGGCCGATTTACCCTT 57.402 45.000 0.00 0.00 0.00 3.95
2743 2849 3.743269 CGATAAACTGGCCGATTTACCCT 60.743 47.826 12.18 0.00 0.00 4.34
2744 2850 2.546789 CGATAAACTGGCCGATTTACCC 59.453 50.000 12.18 7.63 0.00 3.69
2745 2851 3.246936 GTCGATAAACTGGCCGATTTACC 59.753 47.826 12.18 3.60 33.47 2.85
2746 2852 3.866910 TGTCGATAAACTGGCCGATTTAC 59.133 43.478 12.18 4.81 33.47 2.01
2747 2853 4.126208 TGTCGATAAACTGGCCGATTTA 57.874 40.909 12.29 12.29 33.47 1.40
2748 2854 2.980568 TGTCGATAAACTGGCCGATTT 58.019 42.857 8.88 8.88 33.47 2.17
2749 2855 2.684001 TGTCGATAAACTGGCCGATT 57.316 45.000 0.00 0.00 33.47 3.34
2750 2856 2.910688 ATGTCGATAAACTGGCCGAT 57.089 45.000 0.00 0.00 33.47 4.18
2751 2857 3.909430 GATATGTCGATAAACTGGCCGA 58.091 45.455 0.00 0.00 0.00 5.54
2765 2871 5.161358 TGGCGATAAATCAGTCGATATGTC 58.839 41.667 0.00 0.00 40.11 3.06
2766 2872 5.134202 TGGCGATAAATCAGTCGATATGT 57.866 39.130 0.00 0.00 40.11 2.29
2767 2873 7.864882 AGATATGGCGATAAATCAGTCGATATG 59.135 37.037 0.00 0.00 40.11 1.78
2768 2874 7.946207 AGATATGGCGATAAATCAGTCGATAT 58.054 34.615 0.00 0.00 40.11 1.63
2769 2875 7.334844 AGATATGGCGATAAATCAGTCGATA 57.665 36.000 0.00 0.00 40.11 2.92
2770 2876 6.214191 AGATATGGCGATAAATCAGTCGAT 57.786 37.500 0.00 0.00 40.11 3.59
2771 2877 5.644977 AGATATGGCGATAAATCAGTCGA 57.355 39.130 0.00 0.00 40.11 4.20
2772 2878 6.096036 AGAAGATATGGCGATAAATCAGTCG 58.904 40.000 0.00 0.00 40.62 4.18
2773 2879 8.988064 TTAGAAGATATGGCGATAAATCAGTC 57.012 34.615 0.00 0.00 0.00 3.51
2781 2887 9.516546 ACGGATATATTAGAAGATATGGCGATA 57.483 33.333 0.00 0.00 0.00 2.92
2782 2888 8.410673 ACGGATATATTAGAAGATATGGCGAT 57.589 34.615 0.00 0.00 0.00 4.58
2783 2889 7.307811 CGACGGATATATTAGAAGATATGGCGA 60.308 40.741 0.00 0.00 0.00 5.54
2784 2890 6.797513 CGACGGATATATTAGAAGATATGGCG 59.202 42.308 0.00 0.00 0.00 5.69
2785 2891 7.872881 TCGACGGATATATTAGAAGATATGGC 58.127 38.462 0.00 0.00 0.00 4.40
2808 2914 6.695713 TGTTGTCTGACCGATAAGATAAATCG 59.304 38.462 5.17 0.00 44.51 3.34
2809 2915 7.707035 ACTGTTGTCTGACCGATAAGATAAATC 59.293 37.037 5.17 0.00 0.00 2.17
2810 2916 7.556844 ACTGTTGTCTGACCGATAAGATAAAT 58.443 34.615 5.17 0.00 0.00 1.40
2811 2917 6.931838 ACTGTTGTCTGACCGATAAGATAAA 58.068 36.000 5.17 0.00 0.00 1.40
2812 2918 6.525578 ACTGTTGTCTGACCGATAAGATAA 57.474 37.500 5.17 0.00 0.00 1.75
2813 2919 7.634671 TTACTGTTGTCTGACCGATAAGATA 57.365 36.000 5.17 0.00 0.00 1.98
2814 2920 6.525578 TTACTGTTGTCTGACCGATAAGAT 57.474 37.500 5.17 0.00 0.00 2.40
2815 2921 5.621555 GCTTACTGTTGTCTGACCGATAAGA 60.622 44.000 5.17 0.00 0.00 2.10
2816 2922 4.563184 GCTTACTGTTGTCTGACCGATAAG 59.437 45.833 5.17 7.47 0.00 1.73
2817 2923 4.491676 GCTTACTGTTGTCTGACCGATAA 58.508 43.478 5.17 0.00 0.00 1.75
2818 2924 3.427098 CGCTTACTGTTGTCTGACCGATA 60.427 47.826 5.17 0.00 0.00 2.92
2819 2925 2.671351 CGCTTACTGTTGTCTGACCGAT 60.671 50.000 5.17 0.00 0.00 4.18
2820 2926 1.335597 CGCTTACTGTTGTCTGACCGA 60.336 52.381 5.17 0.00 0.00 4.69
2821 2927 1.060713 CGCTTACTGTTGTCTGACCG 58.939 55.000 5.17 0.00 0.00 4.79
2822 2928 2.433868 TCGCTTACTGTTGTCTGACC 57.566 50.000 5.17 0.00 0.00 4.02
2823 2929 6.310467 TGATTTATCGCTTACTGTTGTCTGAC 59.690 38.462 0.00 0.00 0.00 3.51
2824 2930 6.394809 TGATTTATCGCTTACTGTTGTCTGA 58.605 36.000 0.00 0.00 0.00 3.27
2825 2931 6.647212 TGATTTATCGCTTACTGTTGTCTG 57.353 37.500 0.00 0.00 0.00 3.51
2826 2932 5.292101 GCTGATTTATCGCTTACTGTTGTCT 59.708 40.000 0.00 0.00 0.00 3.41
2827 2933 5.493735 GCTGATTTATCGCTTACTGTTGTC 58.506 41.667 0.00 0.00 0.00 3.18
2828 2934 4.332819 GGCTGATTTATCGCTTACTGTTGT 59.667 41.667 0.00 0.00 0.00 3.32
2829 2935 4.332543 TGGCTGATTTATCGCTTACTGTTG 59.667 41.667 0.00 0.00 0.00 3.33
2830 2936 4.513442 TGGCTGATTTATCGCTTACTGTT 58.487 39.130 0.00 0.00 0.00 3.16
2831 2937 4.137116 TGGCTGATTTATCGCTTACTGT 57.863 40.909 0.00 0.00 0.00 3.55
2832 2938 5.679734 ATTGGCTGATTTATCGCTTACTG 57.320 39.130 0.00 0.00 0.00 2.74
2833 2939 6.699575 AAATTGGCTGATTTATCGCTTACT 57.300 33.333 0.00 0.00 0.00 2.24
2834 2940 8.660968 GATAAATTGGCTGATTTATCGCTTAC 57.339 34.615 20.51 7.56 43.49 2.34
2844 2950 9.911788 AGATATATTCCGATAAATTGGCTGATT 57.088 29.630 0.00 0.00 0.00 2.57
2845 2951 9.911788 AAGATATATTCCGATAAATTGGCTGAT 57.088 29.630 0.00 0.00 0.00 2.90
2846 2952 9.166173 CAAGATATATTCCGATAAATTGGCTGA 57.834 33.333 0.00 0.00 0.00 4.26
2847 2953 9.166173 TCAAGATATATTCCGATAAATTGGCTG 57.834 33.333 0.00 0.00 0.00 4.85
2848 2954 9.739276 TTCAAGATATATTCCGATAAATTGGCT 57.261 29.630 0.00 0.00 0.00 4.75
2857 2963 9.877178 GAACCACTATTCAAGATATATTCCGAT 57.123 33.333 0.00 0.00 0.00 4.18
2858 2964 9.090103 AGAACCACTATTCAAGATATATTCCGA 57.910 33.333 0.00 0.00 0.00 4.55
2859 2965 9.712305 AAGAACCACTATTCAAGATATATTCCG 57.288 33.333 0.00 0.00 0.00 4.30
2947 3053 5.841957 ACCTTGATGATGGAAATGCTAAC 57.158 39.130 0.00 0.00 0.00 2.34
3113 3219 4.468765 AGAGTGTGTGAGATGGAGAATG 57.531 45.455 0.00 0.00 0.00 2.67
3118 3224 4.040339 TGCTTTAAGAGTGTGTGAGATGGA 59.960 41.667 0.00 0.00 0.00 3.41
3185 3291 6.571150 CGCTCCTCCAAAATTCTTTGAAAGAT 60.571 38.462 8.64 0.00 44.03 2.40
3196 3302 2.554032 CACAAGTCGCTCCTCCAAAATT 59.446 45.455 0.00 0.00 0.00 1.82
3214 3320 3.552132 TGAATAAGCCCGATTAGCACA 57.448 42.857 0.00 0.00 0.00 4.57
3245 3351 7.936301 CCAAAAATTTTCCTAGGGAATCAAACA 59.064 33.333 9.46 0.00 41.71 2.83
3246 3352 7.936847 ACCAAAAATTTTCCTAGGGAATCAAAC 59.063 33.333 9.46 0.00 41.71 2.93
3331 3437 4.114794 CACCCTGTTGAGCTTTTGAAAAG 58.885 43.478 13.09 13.09 0.00 2.27
3338 3444 2.508526 CTAAGCACCCTGTTGAGCTTT 58.491 47.619 3.72 0.00 44.22 3.51
3357 3463 6.657117 TCGTCTTAATGATAGAGATGCTAGCT 59.343 38.462 17.23 0.83 36.46 3.32
3753 3870 6.544928 TTAGGCATCACTTCAGTCATTCTA 57.455 37.500 0.00 0.00 0.00 2.10
3892 4009 2.167693 AGGAACTGACACGTGTCTCAAA 59.832 45.455 39.62 24.03 44.99 2.69
4346 4473 0.882042 CAGTCCTGAACACGCAGCTT 60.882 55.000 0.00 0.00 34.56 3.74


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

AutoCloner maintained by Alex Coulton.