Multiple sequence alignment - TraesCS2A01G387200

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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 TraesCS2A01G387200 chr2A 100.000 7377 0 0 1 7377 632955998 632948622 0.000000e+00 13623.0
1 TraesCS2A01G387200 chr2A 90.323 124 10 2 3005 3127 177665286 177665164 2.130000e-35 161.0
2 TraesCS2A01G387200 chr2A 86.567 134 14 4 3000 3130 177665193 177665325 2.150000e-30 145.0
3 TraesCS2A01G387200 chr2D 95.342 2662 87 18 6 2662 489413299 489410670 0.000000e+00 4194.0
4 TraesCS2A01G387200 chr2D 94.061 2172 86 16 3067 5208 489410062 489407904 0.000000e+00 3256.0
5 TraesCS2A01G387200 chr2D 92.068 1765 83 24 5649 7377 489407020 489405277 0.000000e+00 2431.0
6 TraesCS2A01G387200 chr2D 94.789 806 36 3 4845 5650 489407902 489407103 0.000000e+00 1251.0
7 TraesCS2A01G387200 chr2D 90.358 363 20 8 2664 3026 489410533 489410186 5.210000e-126 462.0
8 TraesCS2A01G387200 chr2D 95.652 46 1 1 2428 2472 83967087 83967042 1.030000e-08 73.1
9 TraesCS2A01G387200 chr2B 95.403 2393 81 13 276 2662 572794582 572792213 0.000000e+00 3783.0
10 TraesCS2A01G387200 chr2B 93.359 1822 86 15 3853 5660 572790824 572789024 0.000000e+00 2662.0
11 TraesCS2A01G387200 chr2B 92.452 1762 78 18 5652 7377 572788929 572787187 0.000000e+00 2466.0
12 TraesCS2A01G387200 chr2B 94.691 1036 34 10 2914 3931 572791854 572790822 0.000000e+00 1589.0
13 TraesCS2A01G387200 chr2B 90.909 253 18 2 3 251 572795021 572794770 1.190000e-87 335.0
14 TraesCS2A01G387200 chr2B 95.263 190 6 2 2664 2853 572792079 572791893 1.560000e-76 298.0
15 TraesCS2A01G387200 chr2B 81.786 280 34 13 4592 4863 692173772 692174042 1.250000e-52 219.0
16 TraesCS2A01G387200 chr2B 94.697 132 5 2 3797 3926 708794718 708794587 3.490000e-48 204.0
17 TraesCS2A01G387200 chr2B 82.692 208 20 11 5370 5570 133982314 133982512 3.540000e-38 171.0
18 TraesCS2A01G387200 chr2B 91.176 102 7 2 2986 3085 337084135 337084236 3.590000e-28 137.0
19 TraesCS2A01G387200 chr7B 84.848 264 32 5 4595 4851 191896075 191895813 7.340000e-65 259.0
20 TraesCS2A01G387200 chr7B 96.032 126 4 1 3797 3921 410845924 410845799 3.490000e-48 204.0
21 TraesCS2A01G387200 chr7B 92.593 135 10 0 3564 3698 493525847 493525981 2.100000e-45 195.0
22 TraesCS2A01G387200 chr7B 92.424 132 6 4 3571 3700 682239455 682239584 1.260000e-42 185.0
23 TraesCS2A01G387200 chr7B 100.000 31 0 0 4804 4834 97936638 97936608 2.870000e-04 58.4
24 TraesCS2A01G387200 chr1D 84.146 246 31 8 4596 4838 42983606 42983846 1.600000e-56 231.0
25 TraesCS2A01G387200 chr1D 90.741 54 4 1 2426 2478 305588318 305588265 3.690000e-08 71.3
26 TraesCS2A01G387200 chr1D 97.143 35 0 1 2428 2461 395625850 395625816 2.870000e-04 58.4
27 TraesCS2A01G387200 chr1D 92.683 41 2 1 2428 2467 395874274 395874234 2.870000e-04 58.4
28 TraesCS2A01G387200 chr6B 85.650 223 23 7 4636 4851 166590771 166590991 7.450000e-55 226.0
29 TraesCS2A01G387200 chr6B 82.609 184 25 7 2947 3127 149466968 149467147 9.910000e-34 156.0
30 TraesCS2A01G387200 chr5B 96.154 130 4 1 3797 3925 393581774 393581645 2.090000e-50 211.0
31 TraesCS2A01G387200 chr5B 96.063 127 4 1 3797 3922 309675157 309675031 9.700000e-49 206.0
32 TraesCS2A01G387200 chr5B 83.246 191 29 3 4595 4784 296438072 296438260 9.840000e-39 172.0
33 TraesCS2A01G387200 chr5B 93.269 104 5 2 2995 3096 140965917 140966020 1.280000e-32 152.0
34 TraesCS2A01G387200 chr3A 95.420 131 6 0 3570 3700 659015508 659015378 7.500000e-50 209.0
35 TraesCS2A01G387200 chr3A 94.656 131 6 1 3798 3927 601553399 601553529 1.260000e-47 202.0
36 TraesCS2A01G387200 chr3A 81.967 183 28 5 2947 3127 710277826 710278005 4.610000e-32 150.0
37 TraesCS2A01G387200 chr3A 92.500 40 3 0 3088 3127 212110295 212110334 2.870000e-04 58.4
38 TraesCS2A01G387200 chr3A 88.000 50 3 3 3087 3135 156206325 156206278 1.000000e-03 56.5
39 TraesCS2A01G387200 chr1B 96.032 126 4 1 3797 3921 159633665 159633540 3.490000e-48 204.0
40 TraesCS2A01G387200 chr1B 82.418 182 29 3 2947 3127 548535400 548535579 9.910000e-34 156.0
41 TraesCS2A01G387200 chr1B 91.304 46 3 1 2428 2472 420366100 420366055 2.220000e-05 62.1
42 TraesCS2A01G387200 chr5D 94.656 131 6 1 3571 3700 412263451 412263321 1.260000e-47 202.0
43 TraesCS2A01G387200 chr7D 92.593 135 10 0 3564 3698 469842393 469842527 2.100000e-45 195.0
44 TraesCS2A01G387200 chr7D 86.111 180 19 3 4669 4842 209588057 209588236 9.770000e-44 189.0
45 TraesCS2A01G387200 chr7D 87.324 71 7 2 2928 2998 71362835 71362903 6.140000e-11 80.5
46 TraesCS2A01G387200 chr7D 95.238 42 1 1 2428 2468 573982329 573982288 1.720000e-06 65.8
47 TraesCS2A01G387200 chr4A 93.798 129 8 0 3570 3698 60654158 60654286 2.100000e-45 195.0
48 TraesCS2A01G387200 chr4A 92.308 104 8 0 2990 3093 428159989 428159886 1.660000e-31 148.0
49 TraesCS2A01G387200 chr3D 92.424 132 9 1 3570 3700 524713715 524713584 3.510000e-43 187.0
50 TraesCS2A01G387200 chr7A 85.165 182 25 2 4595 4776 635079080 635078901 1.260000e-42 185.0
51 TraesCS2A01G387200 chr7A 86.885 61 6 2 2936 2996 717088928 717088986 4.780000e-07 67.6
52 TraesCS2A01G387200 chr6D 82.199 191 30 4 4595 4784 402325061 402325248 2.130000e-35 161.0
53 TraesCS2A01G387200 chr6D 90.000 50 5 0 2943 2992 58701949 58701998 1.720000e-06 65.8
54 TraesCS2A01G387200 chr1A 98.889 90 1 0 3005 3094 527083930 527084019 2.130000e-35 161.0
55 TraesCS2A01G387200 chr1A 93.617 47 3 0 2946 2992 83823656 83823610 3.690000e-08 71.3
56 TraesCS2A01G387200 chr1A 90.741 54 4 1 2426 2478 384333747 384333694 3.690000e-08 71.3
57 TraesCS2A01G387200 chr5A 95.960 99 2 2 2992 3090 393474478 393474382 7.660000e-35 159.0
58 TraesCS2A01G387200 chr3B 89.474 114 8 3 2979 3090 53239778 53239889 2.770000e-29 141.0
59 TraesCS2A01G387200 chr6A 91.304 46 3 1 2428 2472 427446051 427446096 2.220000e-05 62.1


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 TraesCS2A01G387200 chr2A 632948622 632955998 7376 True 13623.0 13623 100.0000 1 7377 1 chr2A.!!$R2 7376
1 TraesCS2A01G387200 chr2D 489405277 489413299 8022 True 2318.8 4194 93.3236 6 7377 5 chr2D.!!$R2 7371
2 TraesCS2A01G387200 chr2B 572787187 572795021 7834 True 1855.5 3783 93.6795 3 7377 6 chr2B.!!$R2 7374

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
344 512 0.035739 TCCTCCTTGTGCGTAAACCC 59.964 55.0 0.0 0.0 0.00 4.11 F
2045 2226 0.116143 AGAGGAGACAAGGGAGCAGT 59.884 55.0 0.0 0.0 0.00 4.40 F
2672 2988 1.206878 ATACCTGACAGCTCATGCCA 58.793 50.0 0.0 0.0 40.80 4.92 F
4115 4609 0.609662 ATGGCATGGGCAAACTGTTC 59.390 50.0 0.0 0.0 42.43 3.18 F
5297 6171 1.048160 CAAACCCTGCCAACCCTGTT 61.048 55.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2269 0.040646 TCCGAAGTCCTTCTGGCCTA 59.959 55.000 3.32 0.00 37.44 3.93 R
3818 4234 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26 R
4290 4795 1.152567 CAAGTGGGGTCTGGCCAAA 60.153 57.895 7.01 0.00 39.65 3.28 R
5309 6183 0.312729 GTGAAAATCCAAACCGCGGT 59.687 50.000 28.70 28.70 0.00 5.68 R
7260 8280 0.034198 TAGTGGTTAACAGCGCTGCA 59.966 50.000 36.28 22.66 41.41 4.41 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
26 27 2.555757 GCAGTTGGAGCTCTTTTGACAT 59.444 45.455 14.64 0.00 0.00 3.06
51 56 2.615493 GGACATGTCGGAGAATGTTGGT 60.615 50.000 19.33 0.00 39.69 3.67
63 68 0.597568 ATGTTGGTGGCACATGTTCG 59.402 50.000 20.82 0.00 44.52 3.95
85 90 4.636249 GCCTACCTATGGATGTCTTCTTG 58.364 47.826 0.00 0.00 0.00 3.02
99 104 8.919661 GGATGTCTTCTTGTTTTGAATGAAATC 58.080 33.333 0.00 0.00 0.00 2.17
125 130 9.575783 CTTAGCAACTCTCCTACTAACTTTTAG 57.424 37.037 0.00 0.00 0.00 1.85
183 188 2.988570 TGTCCTAAAACACACAACGGT 58.011 42.857 0.00 0.00 0.00 4.83
244 249 2.593026 GTCTCTCCTATGGGACTGAGG 58.407 57.143 12.64 0.00 35.70 3.86
260 265 0.547954 GAGGAAAGACACCCCCTCCT 60.548 60.000 0.00 0.00 39.33 3.69
271 276 1.133809 CCCCCTCCTCCTTGTCACAA 61.134 60.000 0.00 0.00 0.00 3.33
322 490 0.598065 AACAATGCTTCTGTTCCGGC 59.402 50.000 0.00 0.00 31.29 6.13
325 493 0.889186 AATGCTTCTGTTCCGGCGTT 60.889 50.000 6.01 0.00 0.00 4.84
335 503 2.725203 TTCCGGCGTTCCTCCTTGTG 62.725 60.000 6.01 0.00 0.00 3.33
344 512 0.035739 TCCTCCTTGTGCGTAAACCC 59.964 55.000 0.00 0.00 0.00 4.11
348 516 0.596082 CCTTGTGCGTAAACCCCAAG 59.404 55.000 0.00 0.00 33.88 3.61
407 575 6.073331 ACCGCCAATTCAACACAATTATTTTG 60.073 34.615 0.00 0.00 0.00 2.44
408 576 6.305639 CGCCAATTCAACACAATTATTTTGG 58.694 36.000 0.00 0.00 35.36 3.28
409 577 6.610456 GCCAATTCAACACAATTATTTTGGG 58.390 36.000 0.00 0.00 33.38 4.12
491 659 2.489938 ATAATGGTTGACACGCACCT 57.510 45.000 0.00 0.00 0.00 4.00
492 660 3.620427 ATAATGGTTGACACGCACCTA 57.380 42.857 0.00 0.00 0.00 3.08
493 661 1.519408 AATGGTTGACACGCACCTAC 58.481 50.000 0.00 0.00 0.00 3.18
494 662 0.685097 ATGGTTGACACGCACCTACT 59.315 50.000 0.00 0.00 0.00 2.57
495 663 0.249699 TGGTTGACACGCACCTACTG 60.250 55.000 0.00 0.00 0.00 2.74
499 667 1.612676 TGACACGCACCTACTGTACT 58.387 50.000 0.00 0.00 0.00 2.73
520 688 1.630369 TGGCTGGCTGTACTCTTTGAT 59.370 47.619 2.00 0.00 0.00 2.57
534 702 5.295950 ACTCTTTGATCCGAATGCTCATAG 58.704 41.667 0.00 0.00 0.00 2.23
535 703 5.163364 ACTCTTTGATCCGAATGCTCATAGT 60.163 40.000 0.00 0.00 0.00 2.12
536 704 6.040955 ACTCTTTGATCCGAATGCTCATAGTA 59.959 38.462 0.00 0.00 0.00 1.82
545 713 6.266786 TCCGAATGCTCATAGTACTAATCCAA 59.733 38.462 6.70 0.00 0.00 3.53
553 721 9.174166 GCTCATAGTACTAATCCAAAAGGAAAA 57.826 33.333 6.70 0.00 0.00 2.29
637 806 8.991243 TTGTACGAGCAAAATAATACAGTAGT 57.009 30.769 0.00 0.00 0.00 2.73
639 808 9.507280 TGTACGAGCAAAATAATACAGTAGTAC 57.493 33.333 0.00 0.00 31.96 2.73
640 809 9.727627 GTACGAGCAAAATAATACAGTAGTACT 57.272 33.333 0.00 0.00 31.96 2.73
642 811 9.727627 ACGAGCAAAATAATACAGTAGTACTAC 57.272 33.333 23.03 23.03 36.35 2.73
643 812 9.947669 CGAGCAAAATAATACAGTAGTACTACT 57.052 33.333 26.61 26.61 46.52 2.57
676 845 2.656192 TTTAGTTTTGTCGTGAGCGC 57.344 45.000 0.00 0.00 38.14 5.92
763 932 8.970859 ATCCTTAATCCTCACAGATAAACAAG 57.029 34.615 0.00 0.00 0.00 3.16
786 955 3.607370 GACTCAACTCCCCCGGCAC 62.607 68.421 0.00 0.00 0.00 5.01
1431 1612 3.307906 TACACCACGCTCCGCCTT 61.308 61.111 0.00 0.00 0.00 4.35
1467 1648 2.676822 TTCCGTCTCCTCTGCGCT 60.677 61.111 9.73 0.00 0.00 5.92
1567 1748 3.423154 GCTCCCACCGCTTCGTTG 61.423 66.667 0.00 0.00 0.00 4.10
1587 1768 3.948719 GTTGACACCCAGCCCGGA 61.949 66.667 0.73 0.00 36.56 5.14
1734 1915 1.183030 TCCCTTCTTCGCTCACGGAA 61.183 55.000 0.00 0.00 40.63 4.30
2045 2226 0.116143 AGAGGAGACAAGGGAGCAGT 59.884 55.000 0.00 0.00 0.00 4.40
2220 2401 7.094508 TGTGTTTATGCTTCAAGTTGAAAGA 57.905 32.000 18.55 8.87 35.73 2.52
2235 2416 5.987347 AGTTGAAAGATTGGATTTTGCTGTG 59.013 36.000 0.00 0.00 0.00 3.66
2251 2432 6.839124 TTGCTGTGGTTGAGAATATTCAAT 57.161 33.333 17.56 0.00 39.13 2.57
2252 2433 6.839124 TGCTGTGGTTGAGAATATTCAATT 57.161 33.333 17.56 0.00 39.13 2.32
2257 2438 8.213518 TGTGGTTGAGAATATTCAATTAGAGC 57.786 34.615 17.56 7.20 39.13 4.09
2461 2642 9.479549 ACTAAAACCATGACAAGAATATGGAAT 57.520 29.630 9.28 0.00 43.15 3.01
2627 2808 7.996385 GGTTGTTCAACCTGTAGCAATTATAT 58.004 34.615 22.68 0.00 39.71 0.86
2636 2817 9.654919 AACCTGTAGCAATTATATTGGGTATTT 57.345 29.630 1.99 0.00 0.00 1.40
2651 2832 3.072211 GGTATTTGGCCTTATACTCGGC 58.928 50.000 20.18 0.00 45.55 5.54
2653 2834 4.020839 GGTATTTGGCCTTATACTCGGCTA 60.021 45.833 20.18 0.00 45.57 3.93
2657 2838 3.094572 TGGCCTTATACTCGGCTATACC 58.905 50.000 3.32 0.00 45.57 2.73
2662 2843 5.008331 CCTTATACTCGGCTATACCTGACA 58.992 45.833 0.00 0.00 35.61 3.58
2672 2988 1.206878 ATACCTGACAGCTCATGCCA 58.793 50.000 0.00 0.00 40.80 4.92
2706 3022 9.844257 TTGGAACCAAAATTTAATCTTTGTGAT 57.156 25.926 3.62 0.00 32.97 3.06
2735 3051 3.846360 ACTATAACAGCGACCACACTTC 58.154 45.455 0.00 0.00 0.00 3.01
2783 3099 7.154435 TGTAATAGTTGTCAGTCCAGAGTAC 57.846 40.000 0.00 0.00 0.00 2.73
2805 3121 9.796180 AGTACCCACACAATTACTTTTATTACA 57.204 29.630 0.00 0.00 0.00 2.41
2973 3289 7.016268 ACTCCCTCTGTCTAAAAATAAGTGTCA 59.984 37.037 0.00 0.00 0.00 3.58
3052 3368 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
3097 3496 9.681062 TTTCTTTATGGAGGGAGTACTAAATTG 57.319 33.333 0.00 0.00 0.00 2.32
3139 3538 3.586892 GAGGGAGTAGTTTGGAAGTTCG 58.413 50.000 0.00 0.00 0.00 3.95
3157 3556 7.849515 GGAAGTTCGAAGTTAACTTTTGTACTG 59.150 37.037 21.40 6.84 44.94 2.74
3267 3669 3.325716 TGAAACACCCTTGTACTCCTACC 59.674 47.826 0.00 0.00 33.55 3.18
3542 3946 4.370364 TTTTGCTCTTTGGTTCTCACAC 57.630 40.909 0.00 0.00 0.00 3.82
3612 4028 8.779354 ATTAGTTGTCTTGGATTTGTCTAGAC 57.221 34.615 16.32 16.32 36.61 2.59
3808 4224 6.701400 CCAACAATTTTAACAAGTCCTGGAAG 59.299 38.462 0.00 0.00 0.00 3.46
3818 4234 0.676151 GTCCTGGAAGCAGCCTCTTG 60.676 60.000 0.00 0.00 0.00 3.02
3861 4277 2.676342 CGTACAATAGACCCAAAGTGGC 59.324 50.000 0.00 0.00 35.79 5.01
4011 4505 8.792633 ACTACATTTAATTGTTAGAGCTTGCAA 58.207 29.630 8.20 0.00 0.00 4.08
4080 4574 4.755123 ACATGGTGAAAGTTAGTGTACTGC 59.245 41.667 0.00 0.00 0.00 4.40
4081 4575 4.409718 TGGTGAAAGTTAGTGTACTGCA 57.590 40.909 0.00 0.00 0.00 4.41
4115 4609 0.609662 ATGGCATGGGCAAACTGTTC 59.390 50.000 0.00 0.00 42.43 3.18
4132 4626 4.449068 ACTGTTCGCTGTTCAATTCTAGTG 59.551 41.667 0.00 0.00 0.00 2.74
4313 4818 1.228245 CCAGACCCCACTTGGTGTG 60.228 63.158 0.66 0.66 46.44 3.82
4448 4953 5.440610 AGTAGCATAAAATGGAGGAAGGTG 58.559 41.667 0.00 0.00 0.00 4.00
4576 5084 8.365399 GCAATGTGCATAGTAGAACATAGTAA 57.635 34.615 0.00 0.00 44.26 2.24
4614 5122 5.959618 ATTACTCCCTCCGTTTCTTTTTG 57.040 39.130 0.00 0.00 0.00 2.44
4630 5138 5.537188 TCTTTTTGCTCCGCACATAAAATT 58.463 33.333 0.00 0.00 38.71 1.82
4753 5261 8.997621 AATGCATCTAATGATATTGATTTGGC 57.002 30.769 0.00 0.00 0.00 4.52
4771 5279 7.492994 TGATTTGGCATTGTGAATGTTGATATG 59.507 33.333 0.00 0.00 41.01 1.78
4801 5309 8.613482 TCAGATAAACAACGTCAAACATGTTTA 58.387 29.630 22.87 18.24 46.31 2.01
4802 5310 8.678510 CAGATAAACAACGTCAAACATGTTTAC 58.321 33.333 22.87 18.24 45.57 2.01
4929 5437 8.436200 CAGAGTGTACTTAGTAAAAGCAATGTC 58.564 37.037 0.00 0.00 0.00 3.06
4943 5451 6.913873 AAGCAATGTCCAATATTTGATTGC 57.086 33.333 15.19 15.19 43.28 3.56
4954 5462 7.914871 TCCAATATTTGATTGCAGACGTTTATG 59.085 33.333 0.00 0.00 0.00 1.90
5133 5641 4.244862 GCCATTGTGAAGGTTATTTGTGG 58.755 43.478 0.00 0.00 0.00 4.17
5242 6115 4.683832 GCCGATGTAGTTACTCTCACATT 58.316 43.478 1.44 0.00 31.94 2.71
5262 6135 6.425114 CACATTTATTTATCTCCCAGTCCTCG 59.575 42.308 0.00 0.00 0.00 4.63
5297 6171 1.048160 CAAACCCTGCCAACCCTGTT 61.048 55.000 0.00 0.00 0.00 3.16
5309 6183 2.019807 ACCCTGTTTCCTCGGAAGTA 57.980 50.000 0.00 0.00 35.38 2.24
5311 6185 1.066358 CCCTGTTTCCTCGGAAGTACC 60.066 57.143 0.00 0.00 35.38 3.34
5455 6330 6.341316 TCTTGGTCATTACTCTTATCACAGC 58.659 40.000 0.00 0.00 0.00 4.40
5533 6408 2.417651 CCCAACCATTGCAACAGCATAG 60.418 50.000 0.00 0.00 38.23 2.23
5672 6647 4.580995 AGTACTGTACTACTGGCTATGCAG 59.419 45.833 18.42 0.00 37.23 4.41
5683 6658 9.035890 ACTACTGGCTATGCAGTATTAATATCA 57.964 33.333 0.00 0.00 33.96 2.15
5706 6681 1.195115 CTGAATTCCCTGGTCTCCGA 58.805 55.000 2.27 0.00 0.00 4.55
5725 6700 1.185618 AGAGGCTGCTCGTGGTGTAA 61.186 55.000 0.00 0.00 0.00 2.41
5762 6737 8.830741 AGATCTCTCATCCTTTTCTTTTCCTTA 58.169 33.333 0.00 0.00 0.00 2.69
5780 6755 0.894835 TACGCTGAGATGGCACTGAA 59.105 50.000 0.00 0.00 0.00 3.02
5844 6819 5.689835 TGGCATAGTTGTGCTCCATATTTA 58.310 37.500 0.95 0.00 44.45 1.40
5845 6820 5.530915 TGGCATAGTTGTGCTCCATATTTAC 59.469 40.000 0.95 0.00 44.45 2.01
5847 6822 6.207417 GGCATAGTTGTGCTCCATATTTACAT 59.793 38.462 0.95 0.00 44.45 2.29
5848 6823 7.301054 GCATAGTTGTGCTCCATATTTACATC 58.699 38.462 0.00 0.00 41.82 3.06
5849 6824 7.041167 GCATAGTTGTGCTCCATATTTACATCA 60.041 37.037 0.00 0.00 41.82 3.07
5850 6825 9.006839 CATAGTTGTGCTCCATATTTACATCAT 57.993 33.333 0.00 0.00 0.00 2.45
5896 6881 9.801873 CGTTGTATTATTGAAAAAGATGGGAAT 57.198 29.630 0.00 0.00 0.00 3.01
5923 6911 3.974871 TTGCCTTACGAAAAGGAACAC 57.025 42.857 20.66 7.33 39.81 3.32
6252 7240 3.622630 AGTCTAACACTGTAGCCTCGAT 58.377 45.455 0.00 0.00 32.26 3.59
6340 7328 3.363844 GAGACTGCTGTCCGGGAGC 62.364 68.421 18.96 16.94 43.91 4.70
6377 7365 1.739338 CTCGCCGGAGAAGCCATAGT 61.739 60.000 9.83 0.00 43.27 2.12
6409 7397 6.598753 TTCCTTGTTTCTCTTAACTTCACG 57.401 37.500 0.00 0.00 0.00 4.35
6416 7404 2.036217 TCTCTTAACTTCACGCCGGAAA 59.964 45.455 5.05 0.00 0.00 3.13
6427 7415 1.482593 ACGCCGGAAAATCAGATCTCT 59.517 47.619 5.05 0.00 0.00 3.10
6482 7472 1.003108 GTTTTGTTGGGGCGTTTGTG 58.997 50.000 0.00 0.00 0.00 3.33
6545 7535 4.346418 AGATACAGGCCTCGATTGATTTCT 59.654 41.667 0.00 0.00 0.00 2.52
6584 7577 3.195825 CGTCATTCTTGAACCCTAGGACT 59.804 47.826 11.48 0.00 32.48 3.85
6596 7589 1.410004 CTAGGACTGTTATCCCGCCA 58.590 55.000 0.00 0.00 39.91 5.69
6670 7668 2.820037 GCCTTGGCCGTAGTGCTC 60.820 66.667 0.00 0.00 0.00 4.26
6762 7770 4.794278 TGTTAAGTATTGCGAGGACTGA 57.206 40.909 0.00 0.00 0.00 3.41
6780 7788 6.889722 AGGACTGATTCGGATTTATTTTTCCA 59.110 34.615 0.00 0.00 31.99 3.53
6790 7798 8.566260 TCGGATTTATTTTTCCACTTTCGTTAA 58.434 29.630 0.00 0.00 31.99 2.01
6800 7808 3.619929 CCACTTTCGTTAATAACCTCCGG 59.380 47.826 0.00 0.00 0.00 5.14
6801 7809 4.497300 CACTTTCGTTAATAACCTCCGGA 58.503 43.478 2.93 2.93 0.00 5.14
6823 7834 2.063156 TGTTGGATTTGCATGCGTTC 57.937 45.000 14.09 9.36 0.00 3.95
6893 7904 0.469144 TTTGCCACTGGGGAAGAACC 60.469 55.000 0.00 0.00 45.93 3.62
6899 7910 1.279271 CACTGGGGAAGAACCGAAGAT 59.721 52.381 0.00 0.00 40.11 2.40
6934 7945 9.458374 GCTTGCATAAGTTTCAAGTTTTACTAA 57.542 29.630 11.37 0.00 39.36 2.24
7022 8034 2.871633 GGAATTTGCACAAAAGTGGTGG 59.128 45.455 0.00 0.00 36.76 4.61
7023 8035 3.431486 GGAATTTGCACAAAAGTGGTGGA 60.431 43.478 0.00 0.00 36.76 4.02
7024 8036 4.379652 GAATTTGCACAAAAGTGGTGGAT 58.620 39.130 0.00 0.00 36.47 3.41
7025 8037 2.886862 TTGCACAAAAGTGGTGGATG 57.113 45.000 0.00 0.00 36.47 3.51
7026 8038 1.774110 TGCACAAAAGTGGTGGATGT 58.226 45.000 0.00 0.00 36.76 3.06
7027 8039 2.106566 TGCACAAAAGTGGTGGATGTT 58.893 42.857 0.00 0.00 36.76 2.71
7028 8040 2.499289 TGCACAAAAGTGGTGGATGTTT 59.501 40.909 0.00 0.00 36.76 2.83
7043 8062 3.983344 GGATGTTTGGCATATCAAATCGC 59.017 43.478 0.00 0.00 38.64 4.58
7106 8125 2.031807 CGATATCGTCGTCCAGTCAGTT 59.968 50.000 17.06 0.00 45.19 3.16
7107 8126 3.487042 CGATATCGTCGTCCAGTCAGTTT 60.487 47.826 17.06 0.00 45.19 2.66
7134 8153 2.843730 TGACTAGATTTGGGCTAAGGCA 59.156 45.455 0.00 0.00 40.87 4.75
7150 8169 2.357517 CACGGCCGCAAGAACTCT 60.358 61.111 28.58 0.00 43.02 3.24
7151 8170 1.961277 CACGGCCGCAAGAACTCTT 60.961 57.895 28.58 0.00 43.02 2.85
7153 8172 0.034337 ACGGCCGCAAGAACTCTTAA 59.966 50.000 28.58 0.00 43.02 1.85
7154 8173 0.442699 CGGCCGCAAGAACTCTTAAC 59.557 55.000 14.67 0.00 43.02 2.01
7155 8174 1.809684 GGCCGCAAGAACTCTTAACT 58.190 50.000 0.00 0.00 43.02 2.24
7156 8175 1.464997 GGCCGCAAGAACTCTTAACTG 59.535 52.381 0.00 0.00 43.02 3.16
7157 8176 1.135944 GCCGCAAGAACTCTTAACTGC 60.136 52.381 0.00 0.00 43.02 4.40
7158 8177 2.143122 CCGCAAGAACTCTTAACTGCA 58.857 47.619 2.92 0.00 43.02 4.41
7159 8178 2.096218 CCGCAAGAACTCTTAACTGCAC 60.096 50.000 2.92 0.00 43.02 4.57
7167 8186 2.628657 ACTCTTAACTGCACTTCCTCGT 59.371 45.455 0.00 0.00 0.00 4.18
7209 8229 2.931512 AGCAAGACGTAGCTTCTCTC 57.068 50.000 0.00 0.00 38.01 3.20
7219 8239 3.060098 CGTAGCTTCTCTCGAGCAAAAAG 59.940 47.826 7.81 9.21 42.56 2.27
7259 8279 4.946478 ATCCTAGGATTTCCTCGTTCTG 57.054 45.455 19.18 0.00 44.77 3.02
7260 8280 3.709587 TCCTAGGATTTCCTCGTTCTGT 58.290 45.455 7.62 0.00 44.77 3.41
7273 8294 0.586319 GTTCTGTGCAGCGCTGTTAA 59.414 50.000 35.80 20.59 0.00 2.01
7287 8308 3.190535 CGCTGTTAACCACTAAGCCATTT 59.809 43.478 2.48 0.00 0.00 2.32
7308 8329 9.450807 CCATTTTCAAGTTTGTGTTAAGACTAG 57.549 33.333 4.21 0.00 0.00 2.57
7312 8333 8.882415 TTCAAGTTTGTGTTAAGACTAGTAGG 57.118 34.615 4.21 0.00 0.00 3.18
7357 8383 1.269778 GCTTGGTTTCCACTGGCTTTC 60.270 52.381 0.00 0.00 30.78 2.62
7359 8385 1.691196 TGGTTTCCACTGGCTTTCTG 58.309 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.038426 ACATTCTCCGACATGTCCAACA 59.962 45.455 20.03 1.27 0.00 3.33
42 43 2.676076 GAACATGTGCCACCAACATTC 58.324 47.619 0.00 0.00 0.00 2.67
63 68 4.101741 ACAAGAAGACATCCATAGGTAGGC 59.898 45.833 0.00 0.00 0.00 3.93
85 90 9.122613 GAGAGTTGCTAAGATTTCATTCAAAAC 57.877 33.333 0.00 0.00 0.00 2.43
99 104 9.575783 CTAAAAGTTAGTAGGAGAGTTGCTAAG 57.424 37.037 0.00 0.00 0.00 2.18
146 151 8.792830 TTTAGGACACCATAGACTTACCATAT 57.207 34.615 0.00 0.00 0.00 1.78
216 221 2.489985 CCCATAGGAGAGACGTGGATCT 60.490 54.545 0.00 0.00 33.47 2.75
244 249 0.547954 AGGAGGAGGGGGTGTCTTTC 60.548 60.000 0.00 0.00 0.00 2.62
260 265 4.728772 AGATTGTTGGATTGTGACAAGGA 58.271 39.130 3.74 0.00 36.80 3.36
271 276 9.631257 AAAAGAAAATGGAAAAGATTGTTGGAT 57.369 25.926 0.00 0.00 0.00 3.41
322 490 1.193874 GTTTACGCACAAGGAGGAACG 59.806 52.381 0.00 0.00 0.00 3.95
325 493 0.035739 GGGTTTACGCACAAGGAGGA 59.964 55.000 0.00 0.00 0.00 3.71
361 529 7.067129 GGCGGTTTAATCTTCTTTTTCTCCTAT 59.933 37.037 0.00 0.00 0.00 2.57
362 530 6.373495 GGCGGTTTAATCTTCTTTTTCTCCTA 59.627 38.462 0.00 0.00 0.00 2.94
363 531 5.183331 GGCGGTTTAATCTTCTTTTTCTCCT 59.817 40.000 0.00 0.00 0.00 3.69
364 532 5.048294 TGGCGGTTTAATCTTCTTTTTCTCC 60.048 40.000 0.00 0.00 0.00 3.71
365 533 6.009115 TGGCGGTTTAATCTTCTTTTTCTC 57.991 37.500 0.00 0.00 0.00 2.87
366 534 6.399639 TTGGCGGTTTAATCTTCTTTTTCT 57.600 33.333 0.00 0.00 0.00 2.52
367 535 7.383843 TGAATTGGCGGTTTAATCTTCTTTTTC 59.616 33.333 0.00 0.00 0.00 2.29
383 551 6.305639 CAAAATAATTGTGTTGAATTGGCGG 58.694 36.000 0.00 0.00 0.00 6.13
407 575 4.082787 TCGAAGTGAATGCAAGAAAATCCC 60.083 41.667 0.00 0.00 0.00 3.85
408 576 5.046910 TCGAAGTGAATGCAAGAAAATCC 57.953 39.130 0.00 0.00 0.00 3.01
409 577 6.373779 TCTTCGAAGTGAATGCAAGAAAATC 58.626 36.000 23.85 0.00 35.63 2.17
491 659 1.348064 ACAGCCAGCCAAGTACAGTA 58.652 50.000 0.00 0.00 0.00 2.74
492 660 1.002087 GTACAGCCAGCCAAGTACAGT 59.998 52.381 10.79 0.00 37.40 3.55
493 661 1.276421 AGTACAGCCAGCCAAGTACAG 59.724 52.381 15.48 0.00 39.33 2.74
494 662 1.275291 GAGTACAGCCAGCCAAGTACA 59.725 52.381 15.48 0.00 39.33 2.90
495 663 1.550976 AGAGTACAGCCAGCCAAGTAC 59.449 52.381 0.00 8.67 37.65 2.73
499 667 1.419762 TCAAAGAGTACAGCCAGCCAA 59.580 47.619 0.00 0.00 0.00 4.52
520 688 5.773176 TGGATTAGTACTATGAGCATTCGGA 59.227 40.000 2.79 0.00 0.00 4.55
557 725 7.893124 TGGTGGAGGATTAGTTTACTACTAG 57.107 40.000 0.00 0.00 40.35 2.57
558 726 8.063153 TCATGGTGGAGGATTAGTTTACTACTA 58.937 37.037 0.00 0.00 38.33 1.82
559 727 6.901300 TCATGGTGGAGGATTAGTTTACTACT 59.099 38.462 0.00 0.00 41.04 2.57
560 728 7.069578 TCTCATGGTGGAGGATTAGTTTACTAC 59.930 40.741 0.00 0.00 35.58 2.73
561 729 7.130099 TCTCATGGTGGAGGATTAGTTTACTA 58.870 38.462 0.00 0.00 35.58 1.82
562 730 5.964477 TCTCATGGTGGAGGATTAGTTTACT 59.036 40.000 0.00 0.00 35.58 2.24
563 731 6.235231 TCTCATGGTGGAGGATTAGTTTAC 57.765 41.667 0.00 0.00 35.58 2.01
564 732 6.443849 AGTTCTCATGGTGGAGGATTAGTTTA 59.556 38.462 0.00 0.00 35.58 2.01
565 733 5.251700 AGTTCTCATGGTGGAGGATTAGTTT 59.748 40.000 0.00 0.00 35.58 2.66
614 783 9.727627 AGTACTACTGTATTATTTTGCTCGTAC 57.272 33.333 0.00 0.00 0.00 3.67
644 813 9.628746 ACGACAAAACTAAAACAAAATGTTACT 57.371 25.926 0.00 0.00 40.14 2.24
645 814 9.664826 CACGACAAAACTAAAACAAAATGTTAC 57.335 29.630 0.00 0.00 40.14 2.50
646 815 9.622004 TCACGACAAAACTAAAACAAAATGTTA 57.378 25.926 0.00 0.00 40.14 2.41
647 816 8.522178 TCACGACAAAACTAAAACAAAATGTT 57.478 26.923 0.00 0.00 43.41 2.71
648 817 7.201401 GCTCACGACAAAACTAAAACAAAATGT 60.201 33.333 0.00 0.00 0.00 2.71
676 845 6.092670 GTGTCGTCATGATGGGATTATTATGG 59.907 42.308 14.91 0.00 0.00 2.74
763 932 4.097361 GGGGAGTTGAGTCCGGGC 62.097 72.222 0.00 0.00 37.50 6.13
786 955 1.273327 GGTTGGAGTTGCAGATTTGGG 59.727 52.381 0.00 0.00 0.00 4.12
1305 1486 4.131088 GCGACCGTCCACCTCTCC 62.131 72.222 0.00 0.00 0.00 3.71
1446 1627 1.513622 GCAGAGGAGACGGAAGACC 59.486 63.158 0.00 0.00 0.00 3.85
2045 2226 2.409064 TGGGGACTCTTGTGAACCTA 57.591 50.000 0.00 0.00 0.00 3.08
2088 2269 0.040646 TCCGAAGTCCTTCTGGCCTA 59.959 55.000 3.32 0.00 37.44 3.93
2220 2401 3.896888 TCTCAACCACAGCAAAATCCAAT 59.103 39.130 0.00 0.00 0.00 3.16
2235 2416 7.859875 GCTTGCTCTAATTGAATATTCTCAACC 59.140 37.037 16.24 0.00 38.12 3.77
2251 2432 3.904136 GCTGAAAACAGCTTGCTCTAA 57.096 42.857 13.83 0.00 44.31 2.10
2272 2453 7.490657 TTCTTAACCCTTCAGCATAGTAGAA 57.509 36.000 0.00 0.00 0.00 2.10
2391 2572 8.643324 ACTAACTCTTAACCCTTCAGCATATAG 58.357 37.037 0.00 0.00 0.00 1.31
2461 2642 4.600111 ACTACCAAACAAATACTCCCTCCA 59.400 41.667 0.00 0.00 0.00 3.86
2614 2795 7.039363 GGCCAAATACCCAATATAATTGCTACA 60.039 37.037 0.00 0.00 0.00 2.74
2627 2808 4.445162 CCGAGTATAAGGCCAAATACCCAA 60.445 45.833 18.83 0.00 30.35 4.12
2651 2832 2.366590 TGGCATGAGCTGTCAGGTATAG 59.633 50.000 4.12 0.00 41.70 1.31
2653 2834 1.134280 GTGGCATGAGCTGTCAGGTAT 60.134 52.381 4.12 0.00 40.99 2.73
2657 2838 1.645704 GCTGTGGCATGAGCTGTCAG 61.646 60.000 12.75 0.00 40.99 3.51
2672 2988 9.435688 GATTAAATTTTGGTTCCAAATAGCTGT 57.564 29.630 16.25 0.00 36.09 4.40
2706 3022 5.049954 GTGGTCGCTGTTATAGTTCAACAAA 60.050 40.000 0.00 0.00 35.57 2.83
2716 3032 3.762288 AGAGAAGTGTGGTCGCTGTTATA 59.238 43.478 0.00 0.00 34.40 0.98
2735 3051 3.001414 CTCCACTCACTGCAATTGAGAG 58.999 50.000 24.95 18.74 42.81 3.20
2783 3099 6.745450 CGCTGTAATAAAAGTAATTGTGTGGG 59.255 38.462 0.00 0.00 0.00 4.61
2804 3120 2.148916 TGGTACACAGAACTTCGCTG 57.851 50.000 0.00 0.00 39.26 5.18
2945 3261 9.047947 ACACTTATTTTTAGACAGAGGGAGTAT 57.952 33.333 0.00 0.00 0.00 2.12
2997 3313 7.844493 TCTTTACAGAGGGAGTACAACTTTA 57.156 36.000 0.00 0.00 0.00 1.85
3062 3378 8.379331 ACTCCCTCCATAAAGAAATATAAGAGC 58.621 37.037 0.00 0.00 0.00 4.09
3079 3478 5.308497 TGTTGTCAATTTAGTACTCCCTCCA 59.692 40.000 0.00 0.00 0.00 3.86
3097 3496 3.816523 TCCGTCCCAAAATAAGTGTTGTC 59.183 43.478 0.00 0.00 0.00 3.18
3240 3640 6.607019 AGGAGTACAAGGGTGTTTCAATAAA 58.393 36.000 0.00 0.00 39.30 1.40
3518 3922 4.202141 TGTGAGAACCAAAGAGCAAAATGG 60.202 41.667 0.00 0.00 38.91 3.16
3542 3946 6.662414 TTTAGTAAGAATCAGCCAATGACG 57.338 37.500 0.00 0.00 41.91 4.35
3612 4028 3.965292 ACGTGTCTAGATACATCCGTG 57.035 47.619 18.39 4.75 32.78 4.94
3643 4059 9.570468 TTAGATTTGTCTAGATACGGATGTACT 57.430 33.333 0.00 0.00 32.26 2.73
3715 4131 7.492344 CCCTAATACCAAATGAAAATGCAAGAC 59.508 37.037 0.00 0.00 0.00 3.01
3818 4234 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
3861 4277 3.400054 GTCTGGGGAAGGGTCCGG 61.400 72.222 0.00 0.00 46.04 5.14
4042 4536 6.918892 TCACCATGTATAGAATTTTGACCG 57.081 37.500 0.00 0.00 0.00 4.79
4074 4568 4.585879 TGGTCTTAAAATCCCTGCAGTAC 58.414 43.478 13.81 0.00 0.00 2.73
4080 4574 3.364549 TGCCATGGTCTTAAAATCCCTG 58.635 45.455 14.67 0.00 0.00 4.45
4081 4575 3.756082 TGCCATGGTCTTAAAATCCCT 57.244 42.857 14.67 0.00 0.00 4.20
4115 4609 6.706055 TTCTTACACTAGAATTGAACAGCG 57.294 37.500 0.00 0.00 0.00 5.18
4290 4795 1.152567 CAAGTGGGGTCTGGCCAAA 60.153 57.895 7.01 0.00 39.65 3.28
4448 4953 5.636543 CAGCTCAGGGATTTGAAAAACAATC 59.363 40.000 0.00 0.00 38.36 2.67
4576 5084 9.668497 GAGGGAGTAATATGTTTTTCTTACAGT 57.332 33.333 0.00 0.00 0.00 3.55
4583 5091 6.997239 AACGGAGGGAGTAATATGTTTTTC 57.003 37.500 0.00 0.00 0.00 2.29
4630 5138 5.804692 TTGCGAAGTTTGACTTTAGACAA 57.195 34.783 0.00 0.00 38.80 3.18
4753 5261 9.628746 TCTGAAAACATATCAACATTCACAATG 57.371 29.630 0.00 0.00 44.48 2.82
4771 5279 7.728580 TGTTTGACGTTGTTTATCTGAAAAC 57.271 32.000 0.00 7.87 39.35 2.43
4786 5294 5.821516 TTGAAGGTAAACATGTTTGACGT 57.178 34.783 29.72 20.39 34.23 4.34
4787 5295 6.030849 TGTTTGAAGGTAAACATGTTTGACG 58.969 36.000 29.72 0.00 43.46 4.35
4929 5437 7.701924 ACATAAACGTCTGCAATCAAATATTGG 59.298 33.333 0.00 0.00 0.00 3.16
4943 5451 7.292292 TGAAATTCGGTAAACATAAACGTCTG 58.708 34.615 0.00 0.00 0.00 3.51
4954 5462 8.601476 CATAGTAGTTCCTGAAATTCGGTAAAC 58.399 37.037 0.73 5.37 0.00 2.01
5177 6050 9.806203 CATAATTTAACCAAGAATGCTCAATCA 57.194 29.630 0.00 0.00 0.00 2.57
5208 6081 3.395702 ATCGGCGTACCCTTGGCA 61.396 61.111 6.85 0.00 0.00 4.92
5242 6115 7.008332 TCATACGAGGACTGGGAGATAAATAA 58.992 38.462 0.00 0.00 0.00 1.40
5262 6135 4.526650 AGGGTTTGTGGATTTTGGTCATAC 59.473 41.667 0.00 0.00 0.00 2.39
5309 6183 0.312729 GTGAAAATCCAAACCGCGGT 59.687 50.000 28.70 28.70 0.00 5.68
5311 6185 0.388006 GGGTGAAAATCCAAACCGCG 60.388 55.000 0.00 0.00 33.24 6.46
5371 6246 4.463891 AGTGCCTTTATGCAATTGTTAGCT 59.536 37.500 7.40 0.00 44.11 3.32
5474 6349 5.068329 CACCAAAAGCTCCTTTTCTTTCTCT 59.932 40.000 0.28 0.00 41.05 3.10
5475 6350 5.163509 ACACCAAAAGCTCCTTTTCTTTCTC 60.164 40.000 0.28 0.00 41.05 2.87
5476 6351 4.711846 ACACCAAAAGCTCCTTTTCTTTCT 59.288 37.500 0.28 0.00 41.05 2.52
5477 6352 4.805719 CACACCAAAAGCTCCTTTTCTTTC 59.194 41.667 0.28 0.00 41.05 2.62
5478 6353 4.466015 TCACACCAAAAGCTCCTTTTCTTT 59.534 37.500 0.28 0.00 41.05 2.52
5479 6354 4.023291 TCACACCAAAAGCTCCTTTTCTT 58.977 39.130 0.28 0.00 41.05 2.52
5533 6408 9.143631 CATTGTCAAACCTTGAAATATTCCTTC 57.856 33.333 0.00 0.00 42.15 3.46
5630 6505 8.873144 ACAGTACTAGTATTTAACAAACAGGGA 58.127 33.333 5.75 0.00 0.00 4.20
5672 6647 9.442047 CAGGGAATTCAGGTCTGATATTAATAC 57.558 37.037 7.93 0.00 39.64 1.89
5706 6681 1.185618 TTACACCACGAGCAGCCTCT 61.186 55.000 0.00 0.00 35.90 3.69
5725 6700 7.673641 AGGATGAGAGATCTTCACATTAGTT 57.326 36.000 0.00 0.00 37.26 2.24
5762 6737 0.671781 GTTCAGTGCCATCTCAGCGT 60.672 55.000 0.00 0.00 0.00 5.07
5844 6819 7.496591 GGTCAATGAAATTTGCCATTATGATGT 59.503 33.333 0.00 0.00 31.22 3.06
5845 6820 7.306925 CGGTCAATGAAATTTGCCATTATGATG 60.307 37.037 0.00 0.00 31.22 3.07
5847 6822 6.041511 CGGTCAATGAAATTTGCCATTATGA 58.958 36.000 0.00 0.00 31.22 2.15
5848 6823 5.811613 ACGGTCAATGAAATTTGCCATTATG 59.188 36.000 0.00 0.00 31.22 1.90
5849 6824 5.976458 ACGGTCAATGAAATTTGCCATTAT 58.024 33.333 0.00 0.00 31.22 1.28
5850 6825 5.398603 ACGGTCAATGAAATTTGCCATTA 57.601 34.783 0.00 0.00 31.22 1.90
5868 6853 7.394923 TCCCATCTTTTTCAATAATACAACGGT 59.605 33.333 0.00 0.00 0.00 4.83
5900 6885 5.103687 GTGTTCCTTTTCGTAAGGCAAAAA 58.896 37.500 12.37 2.08 37.34 1.94
5901 6886 4.158025 TGTGTTCCTTTTCGTAAGGCAAAA 59.842 37.500 12.37 2.36 37.34 2.44
5923 6911 6.539826 TGAACACAGCATGATAATACTCCTTG 59.460 38.462 0.00 0.00 39.69 3.61
6252 7240 1.613437 TGCGAGACATGACAGAACTGA 59.387 47.619 8.87 0.00 0.00 3.41
6340 7328 0.387878 AGTCACGCTCTTTCGCTCTG 60.388 55.000 0.00 0.00 0.00 3.35
6377 7365 8.621286 GTTAAGAGAAACAAGGAAAGAATGACA 58.379 33.333 0.00 0.00 0.00 3.58
6409 7397 5.235401 GTCTTAAGAGATCTGATTTTCCGGC 59.765 44.000 5.12 0.00 33.70 6.13
6416 7404 7.555087 CCTGTTCTGTCTTAAGAGATCTGATT 58.445 38.462 5.12 0.00 33.70 2.57
6427 7415 2.040278 AGCATGGCCTGTTCTGTCTTAA 59.960 45.455 3.32 0.00 0.00 1.85
6545 7535 2.543802 CGAGAGATACGCCCTCGCA 61.544 63.158 0.00 0.00 42.34 5.10
6584 7577 3.637911 ATAAACAGTGGCGGGATAACA 57.362 42.857 0.00 0.00 0.00 2.41
6596 7589 8.150945 CCAGGTATACAAGAGCATATAAACAGT 58.849 37.037 5.01 0.00 0.00 3.55
6680 7678 8.384365 CAGTTACATATAATTTACACACGCACA 58.616 33.333 0.00 0.00 0.00 4.57
6711 7709 6.127479 TGTTTACTGAACAGTTTGGCTTCAAT 60.127 34.615 12.66 0.00 43.13 2.57
6712 7710 5.184096 TGTTTACTGAACAGTTTGGCTTCAA 59.816 36.000 12.66 0.00 43.13 2.69
6762 7770 7.599171 ACGAAAGTGGAAAAATAAATCCGAAT 58.401 30.769 0.00 0.00 46.97 3.34
6795 7803 2.230992 TGCAAATCCAACATTTCCGGAG 59.769 45.455 3.34 0.00 30.84 4.63
6800 7808 2.995258 ACGCATGCAAATCCAACATTTC 59.005 40.909 19.57 0.00 0.00 2.17
6801 7809 3.042871 ACGCATGCAAATCCAACATTT 57.957 38.095 19.57 0.00 0.00 2.32
6823 7834 7.165812 CACAAACCATCTGTTTTCGTTTCTAAG 59.834 37.037 0.00 0.00 44.80 2.18
6836 7847 3.558931 TCAGACACACAAACCATCTGT 57.441 42.857 0.00 0.00 38.35 3.41
6846 7857 6.101650 ACAAGTCTCATTATCAGACACACA 57.898 37.500 0.00 0.00 42.51 3.72
6893 7904 1.812922 AAGCTGCGAGGCATCTTCG 60.813 57.895 0.00 0.00 40.29 3.79
6934 7945 4.297664 ACCTTAATTCCCCTCCCATTCTTT 59.702 41.667 0.00 0.00 0.00 2.52
7022 8034 3.665409 CGCGATTTGATATGCCAAACATC 59.335 43.478 0.00 0.00 40.38 3.06
7023 8035 3.066621 ACGCGATTTGATATGCCAAACAT 59.933 39.130 15.93 0.00 43.18 2.71
7024 8036 2.421775 ACGCGATTTGATATGCCAAACA 59.578 40.909 15.93 0.00 38.65 2.83
7025 8037 2.783284 CACGCGATTTGATATGCCAAAC 59.217 45.455 15.93 0.00 38.65 2.93
7026 8038 2.794282 GCACGCGATTTGATATGCCAAA 60.794 45.455 15.93 0.00 39.93 3.28
7027 8039 1.268488 GCACGCGATTTGATATGCCAA 60.268 47.619 15.93 0.00 0.00 4.52
7028 8040 0.307453 GCACGCGATTTGATATGCCA 59.693 50.000 15.93 0.00 0.00 4.92
7043 8062 1.586028 CTGGGAAAATGGGTGCACG 59.414 57.895 11.45 0.00 0.00 5.34
7106 8125 7.993183 CCTTAGCCCAAATCTAGTCATAGAAAA 59.007 37.037 0.00 0.00 41.36 2.29
7107 8126 7.509546 CCTTAGCCCAAATCTAGTCATAGAAA 58.490 38.462 0.00 0.00 41.36 2.52
7134 8153 0.034337 TTAAGAGTTCTTGCGGCCGT 59.966 50.000 28.70 3.94 37.40 5.68
7157 8176 1.803519 GCTCTCGCACGAGGAAGTG 60.804 63.158 19.09 6.83 44.47 3.16
7158 8177 0.677098 TAGCTCTCGCACGAGGAAGT 60.677 55.000 19.09 5.51 42.20 3.01
7159 8178 0.665835 ATAGCTCTCGCACGAGGAAG 59.334 55.000 19.09 11.52 42.20 3.46
7209 8229 2.870372 CGCTCCCCTTTTTGCTCG 59.130 61.111 0.00 0.00 0.00 5.03
7259 8279 1.082104 GTGGTTAACAGCGCTGCAC 60.082 57.895 36.28 28.75 0.00 4.57
7260 8280 0.034198 TAGTGGTTAACAGCGCTGCA 59.966 50.000 36.28 22.66 41.41 4.41
7273 8294 5.128663 ACAAACTTGAAAATGGCTTAGTGGT 59.871 36.000 0.00 0.00 0.00 4.16
7287 8308 7.929785 CCCTACTAGTCTTAACACAAACTTGAA 59.070 37.037 0.00 0.00 0.00 2.69
7308 8329 0.248289 TCAAGTTGGTAGCGCCCTAC 59.752 55.000 2.29 6.47 42.60 3.18
7309 8330 0.978151 TTCAAGTTGGTAGCGCCCTA 59.022 50.000 2.29 0.00 36.04 3.53
7310 8331 0.321653 CTTCAAGTTGGTAGCGCCCT 60.322 55.000 2.29 0.00 36.04 5.19
7311 8332 1.305930 CCTTCAAGTTGGTAGCGCCC 61.306 60.000 2.29 0.00 36.04 6.13
7312 8333 0.321298 TCCTTCAAGTTGGTAGCGCC 60.321 55.000 2.29 0.00 37.90 6.53


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

AutoCloner maintained by Alex Coulton.