Multiple sequence alignment - TraesCS4B01G054400

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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 TraesCS4B01G054400 chr4B 100.000 5662 0 0 1 5662 43113755 43108094 0.000000e+00 10456.0
1 TraesCS4B01G054400 chr4B 89.796 98 8 2 2788 2885 22844126 22844031 2.140000e-24 124.0
2 TraesCS4B01G054400 chr4D 92.382 2809 149 30 2877 5654 30219032 30216258 0.000000e+00 3941.0
3 TraesCS4B01G054400 chr4D 89.422 1938 99 43 57 1961 30221794 30219930 0.000000e+00 2346.0
4 TraesCS4B01G054400 chr4D 87.844 872 63 20 1960 2795 30219895 30219031 0.000000e+00 983.0
5 TraesCS4B01G054400 chr4A 90.197 2836 188 44 1 2786 572829885 572832680 0.000000e+00 3615.0
6 TraesCS4B01G054400 chr4A 92.217 2544 134 38 2864 5362 572832681 572835205 0.000000e+00 3542.0
7 TraesCS4B01G054400 chr4A 88.293 205 10 6 5363 5553 572835241 572835445 3.410000e-57 233.0
8 TraesCS4B01G054400 chr4A 92.308 91 5 2 2789 2878 594030193 594030104 1.660000e-25 128.0
9 TraesCS4B01G054400 chr3A 93.478 92 6 0 2787 2878 507291581 507291490 2.750000e-28 137.0
10 TraesCS4B01G054400 chr3A 87.234 94 12 0 271 364 102107708 102107801 2.160000e-19 108.0
11 TraesCS4B01G054400 chr6D 92.941 85 6 0 2794 2878 142148799 142148715 2.140000e-24 124.0
12 TraesCS4B01G054400 chr6D 86.598 97 13 0 270 366 119139255 119139159 2.160000e-19 108.0
13 TraesCS4B01G054400 chr6D 88.506 87 10 0 271 357 348647287 348647201 7.760000e-19 106.0
14 TraesCS4B01G054400 chr6D 76.720 189 35 8 504 685 56934716 56934530 4.670000e-16 97.1
15 TraesCS4B01G054400 chr5A 92.045 88 7 0 2791 2878 59700795 59700882 2.140000e-24 124.0
16 TraesCS4B01G054400 chr3B 93.023 86 4 2 2794 2878 474402086 474402002 2.140000e-24 124.0
17 TraesCS4B01G054400 chr3B 97.674 43 1 0 271 313 168362914 168362956 2.190000e-09 75.0
18 TraesCS4B01G054400 chr3B 95.000 40 2 0 504 543 580887841 580887880 4.740000e-06 63.9
19 TraesCS4B01G054400 chr1D 92.135 89 6 1 2790 2878 216718719 216718806 2.140000e-24 124.0
20 TraesCS4B01G054400 chr1D 94.286 35 2 0 503 537 279521555 279521589 3.000000e-03 54.7
21 TraesCS4B01G054400 chr1A 92.135 89 6 1 2790 2878 277633037 277633124 2.140000e-24 124.0
22 TraesCS4B01G054400 chr7B 90.323 93 8 1 2794 2885 428965929 428965837 2.770000e-23 121.0
23 TraesCS4B01G054400 chr7B 96.774 31 1 0 507 537 464549286 464549256 1.000000e-02 52.8
24 TraesCS4B01G054400 chr6A 85.714 91 12 1 271 360 147303896 147303806 1.680000e-15 95.3
25 TraesCS4B01G054400 chr7A 88.732 71 6 2 272 341 36353289 36353220 1.010000e-12 86.1
26 TraesCS4B01G054400 chr6B 71.925 374 79 19 390 754 686862261 686862617 1.010000e-12 86.1
27 TraesCS4B01G054400 chr2D 71.756 393 83 22 380 756 54888986 54888606 1.010000e-12 86.1
28 TraesCS4B01G054400 chrUn 80.000 110 16 4 504 608 31703118 31703226 6.080000e-10 76.8
29 TraesCS4B01G054400 chrUn 95.238 42 2 0 272 313 28682597 28682556 3.660000e-07 67.6
30 TraesCS4B01G054400 chr2A 100.000 33 0 0 504 536 21557983 21557951 1.700000e-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 TraesCS4B01G054400 chr4B 43108094 43113755 5661 True 10456.000000 10456 100.000000 1 5662 1 chr4B.!!$R2 5661
1 TraesCS4B01G054400 chr4D 30216258 30221794 5536 True 2423.333333 3941 89.882667 57 5654 3 chr4D.!!$R1 5597
2 TraesCS4B01G054400 chr4A 572829885 572835445 5560 False 2463.333333 3615 90.235667 1 5553 3 chr4A.!!$F1 5552

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
943 989 0.609406 GACCCTTCCCTCCACAAAGC 60.609 60.000 0.0 0.0 0.00 3.51 F
1043 1101 1.229788 AGCAGCTTCCTCCTCCCTT 60.230 57.895 0.0 0.0 0.00 3.95 F
1885 1953 1.134401 CGTACAGCCTGATTGGTCCAT 60.134 52.381 0.0 0.0 38.35 3.41 F
3091 3233 0.884704 CCAACACAGTTCGGGGTCTG 60.885 60.000 0.0 0.0 37.65 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1939 0.179000 AGTCGATGGACCAATCAGGC 59.821 55.000 0.00 0.00 44.54 4.85 R
2172 2282 0.250209 CAACAGGACTCAGCAGCTGT 60.250 55.000 22.10 3.46 32.61 4.40 R
3472 3617 1.074405 ACTCATTGGCCTGTCACATGT 59.926 47.619 3.32 0.00 0.00 3.21 R
4687 4846 0.604578 CCAATGGGGCTGAACACAAG 59.395 55.000 0.00 0.00 0.00 3.16 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
85 86 7.499292 ACAAAATCCACAAATCAATGTCTTGA 58.501 30.769 4.58 0.00 45.15 3.02
185 189 4.152223 GCAACCACATAGCCAACATTTTTC 59.848 41.667 0.00 0.00 0.00 2.29
199 203 4.499183 ACATTTTTCGCTTTGTCCAAACA 58.501 34.783 0.00 0.00 0.00 2.83
267 271 7.278424 GCTCTTTGCTGCAAATTATTATTTCCA 59.722 33.333 26.18 1.55 38.95 3.53
268 272 9.321562 CTCTTTGCTGCAAATTATTATTTCCAT 57.678 29.630 26.18 0.00 32.70 3.41
295 299 6.939132 TCCAAAATAAGTGTCACGGTTTTA 57.061 33.333 12.46 1.77 0.00 1.52
400 414 9.462606 AAACGAAAAATGTCCTCCTAATAATCT 57.537 29.630 0.00 0.00 0.00 2.40
422 436 3.133901 TCGAGCTCAAATGCACCCTTATA 59.866 43.478 15.40 0.00 34.99 0.98
425 439 5.163663 CGAGCTCAAATGCACCCTTATAAAA 60.164 40.000 15.40 0.00 34.99 1.52
614 632 4.465886 TGAAGCACTTTTGTTTAGCCCTA 58.534 39.130 0.00 0.00 0.00 3.53
635 653 9.599866 GCCCTAAGCATTAAATAATGTTTTTCT 57.400 29.630 16.79 3.49 42.04 2.52
648 666 6.843069 AATGTTTTTCTCCACGGAAATTTG 57.157 33.333 0.00 0.00 35.51 2.32
655 677 3.016736 CTCCACGGAAATTTGCAGGTAT 58.983 45.455 10.49 0.00 0.00 2.73
687 709 8.563289 CATTTAACAATGTTTGCTGCAAAAAT 57.437 26.923 27.49 24.61 35.03 1.82
939 985 3.319198 GCGACCCTTCCCTCCACA 61.319 66.667 0.00 0.00 0.00 4.17
943 989 0.609406 GACCCTTCCCTCCACAAAGC 60.609 60.000 0.00 0.00 0.00 3.51
1043 1101 1.229788 AGCAGCTTCCTCCTCCCTT 60.230 57.895 0.00 0.00 0.00 3.95
1179 1237 4.479993 GGCTCGCAGCAGGTCCAT 62.480 66.667 9.78 0.00 44.75 3.41
1208 1267 2.335712 CCCTCTCCCAACGCTTTGC 61.336 63.158 0.00 0.00 0.00 3.68
1324 1390 4.177229 GCTCCTGCAACTCTCGTC 57.823 61.111 0.00 0.00 39.41 4.20
1352 1418 4.390264 GGTTCAGCCTAAAAGAACTCTGT 58.610 43.478 0.00 0.00 40.97 3.41
1435 1501 4.458295 CCATGTGATATTTGGATCTCCTGC 59.542 45.833 0.00 0.00 36.82 4.85
1454 1520 4.156008 CCTGCCCCTAAAATAATATCGTGC 59.844 45.833 0.00 0.00 0.00 5.34
1483 1551 5.946942 TCACTCTCTATTGCAGAATTCCT 57.053 39.130 0.65 0.00 31.12 3.36
1507 1575 6.638610 TCCTTTTCTGCATCAAAAAGTTCAA 58.361 32.000 19.42 7.13 39.66 2.69
1527 1595 3.027974 AGTTACTGAACTGTTCGCCTC 57.972 47.619 15.18 5.51 44.50 4.70
1572 1640 6.086222 CCCGTACATTTTTGTGATTCTCTTG 58.914 40.000 0.00 0.00 0.00 3.02
1610 1678 2.811431 CTCTTTGTTATGTGGGCGTCAA 59.189 45.455 0.00 0.00 0.00 3.18
1651 1719 6.119144 TCAAAGTGTTTGACTTGCTAGTTC 57.881 37.500 1.43 0.00 44.68 3.01
1682 1750 1.929836 GGTTAGCTCAGTGCAGATTCG 59.070 52.381 0.00 0.00 45.94 3.34
1707 1775 3.782443 CCCCTCCCGTACCACTGC 61.782 72.222 0.00 0.00 0.00 4.40
1765 1833 4.935808 AAAGCACTACTTTGGGTAGATTCG 59.064 41.667 9.39 0.00 47.00 3.34
1767 1835 8.971827 AAAGCACTACTTTGGGTAGATTCGGG 62.972 46.154 9.39 0.00 47.00 5.14
1779 1847 5.045872 GGTAGATTCGGGTACACAATACAC 58.954 45.833 0.00 0.00 0.00 2.90
1852 1920 4.341806 TGCACACTTCTGGAATTGTCAAAT 59.658 37.500 3.84 0.00 32.83 2.32
1871 1939 5.580691 TCAAATAAGGCTTCATGTCGTACAG 59.419 40.000 1.30 0.00 0.00 2.74
1885 1953 1.134401 CGTACAGCCTGATTGGTCCAT 60.134 52.381 0.00 0.00 38.35 3.41
1886 1954 2.565841 GTACAGCCTGATTGGTCCATC 58.434 52.381 0.00 0.00 38.35 3.51
2022 2127 6.010294 AGCTCAACATCTTGTCAGAAAATG 57.990 37.500 0.00 0.00 30.76 2.32
2063 2168 5.868454 TCATTCTCATGTTTCAACTCCAGA 58.132 37.500 0.00 0.00 0.00 3.86
2110 2216 5.184671 GGTTCTGGAAAGAAATGAAGCAGAT 59.815 40.000 0.00 0.00 35.85 2.90
2112 2218 7.094205 GGTTCTGGAAAGAAATGAAGCAGATTA 60.094 37.037 0.00 0.00 35.85 1.75
2172 2282 7.036829 CCATACATTCAGAACATTTTGATGCA 58.963 34.615 0.00 0.00 0.00 3.96
2228 2338 5.235850 TGGTACTTGCTCATTAGGAAACA 57.764 39.130 0.00 0.00 32.08 2.83
2237 2347 8.909708 TTGCTCATTAGGAAACAATAATTTCG 57.090 30.769 0.00 0.00 39.13 3.46
2238 2348 8.050778 TGCTCATTAGGAAACAATAATTTCGT 57.949 30.769 0.00 0.00 39.13 3.85
2265 2376 5.414360 TCTGAGATTCCATCTTCGTCTTTG 58.586 41.667 0.00 0.00 40.38 2.77
2269 2380 5.363939 AGATTCCATCTTCGTCTTTGGATC 58.636 41.667 0.00 0.00 38.04 3.36
2280 2391 4.094294 TCGTCTTTGGATCGCTAAATTTGG 59.906 41.667 0.00 0.00 0.00 3.28
2338 2456 2.929398 GCCTTTTAACAAATGATGCCCG 59.071 45.455 0.00 0.00 0.00 6.13
2349 2467 1.974265 TGATGCCCGTGAAGTTTCAA 58.026 45.000 0.00 0.00 39.21 2.69
2360 2478 3.003275 GTGAAGTTTCAATTGAGACGGCA 59.997 43.478 19.96 18.34 39.21 5.69
2373 2491 8.372521 CAATTGAGACGGCAAATTTGTATTAAC 58.627 33.333 19.03 8.35 0.00 2.01
2387 2505 5.755409 TGTATTAACCACACTCACTCCAT 57.245 39.130 0.00 0.00 0.00 3.41
2424 2542 3.562393 CCTGTCTTACTGAGGGACTGAGA 60.562 52.174 9.48 0.00 44.30 3.27
2440 2558 6.268847 GGGACTGAGATAGGTGATTCTACAAT 59.731 42.308 0.00 0.00 0.00 2.71
2455 2573 4.973168 TCTACAATTCACCTTGCTGAAGT 58.027 39.130 0.00 0.00 33.65 3.01
2468 2586 5.461078 CCTTGCTGAAGTCTTGTCAAATTTG 59.539 40.000 12.15 12.15 0.00 2.32
2470 2588 4.142204 TGCTGAAGTCTTGTCAAATTTGCA 60.142 37.500 13.54 11.56 0.00 4.08
2471 2589 4.805192 GCTGAAGTCTTGTCAAATTTGCAA 59.195 37.500 19.75 19.75 0.00 4.08
2472 2590 5.291614 GCTGAAGTCTTGTCAAATTTGCAAA 59.708 36.000 15.44 15.44 0.00 3.68
2473 2591 6.183360 GCTGAAGTCTTGTCAAATTTGCAAAA 60.183 34.615 17.19 11.23 0.00 2.44
2474 2592 7.623925 GCTGAAGTCTTGTCAAATTTGCAAAAA 60.624 33.333 17.19 3.73 0.00 1.94
2475 2593 7.741198 TGAAGTCTTGTCAAATTTGCAAAAAG 58.259 30.769 17.19 13.61 0.00 2.27
2476 2594 6.667007 AGTCTTGTCAAATTTGCAAAAAGG 57.333 33.333 17.19 8.37 0.00 3.11
2477 2595 5.585844 AGTCTTGTCAAATTTGCAAAAAGGG 59.414 36.000 17.19 6.57 0.00 3.95
2480 2598 6.656693 TCTTGTCAAATTTGCAAAAAGGGAAA 59.343 30.769 17.19 4.28 32.56 3.13
2481 2599 6.188400 TGTCAAATTTGCAAAAAGGGAAAC 57.812 33.333 17.19 8.80 30.75 2.78
2521 2654 6.613755 TTGTTTTAGTACAAGTCCAAGAGC 57.386 37.500 0.00 0.00 33.31 4.09
2523 2656 6.296026 TGTTTTAGTACAAGTCCAAGAGCAT 58.704 36.000 0.00 0.00 0.00 3.79
2525 2658 2.704572 AGTACAAGTCCAAGAGCATGC 58.295 47.619 10.51 10.51 0.00 4.06
2541 2674 4.147321 AGCATGCCATATTGGTTTAGGAG 58.853 43.478 15.66 0.00 40.46 3.69
2569 2705 1.554595 CGCAACGCAAAAGCACTTG 59.445 52.632 0.00 0.00 0.00 3.16
2599 2735 8.057536 TGAAAAACAGTTTAGAGGCAAACTTA 57.942 30.769 0.00 0.00 44.40 2.24
2600 2736 8.691797 TGAAAAACAGTTTAGAGGCAAACTTAT 58.308 29.630 0.00 0.00 44.40 1.73
2601 2737 9.181805 GAAAAACAGTTTAGAGGCAAACTTATC 57.818 33.333 0.00 0.00 44.40 1.75
2666 2802 7.349598 ACATTCATTCACTTCTTATAGGCCTT 58.650 34.615 12.58 0.81 0.00 4.35
2669 2805 7.914427 TCATTCACTTCTTATAGGCCTTAGA 57.086 36.000 12.58 9.34 0.00 2.10
2768 2908 1.639298 GAGTCGTGGATTGGCTGTGC 61.639 60.000 0.00 0.00 0.00 4.57
2769 2909 1.965930 GTCGTGGATTGGCTGTGCA 60.966 57.895 0.00 0.00 0.00 4.57
2772 2912 1.514087 GTGGATTGGCTGTGCATGG 59.486 57.895 0.00 0.00 0.00 3.66
2807 2947 8.674925 AAAATATAATATACTCCCTCCGTCCA 57.325 34.615 0.00 0.00 0.00 4.02
2808 2948 8.674925 AAATATAATATACTCCCTCCGTCCAA 57.325 34.615 0.00 0.00 0.00 3.53
2809 2949 8.855804 AATATAATATACTCCCTCCGTCCAAT 57.144 34.615 0.00 0.00 0.00 3.16
2810 2950 9.947189 AATATAATATACTCCCTCCGTCCAATA 57.053 33.333 0.00 0.00 0.00 1.90
2811 2951 9.947189 ATATAATATACTCCCTCCGTCCAATAA 57.053 33.333 0.00 0.00 0.00 1.40
2812 2952 8.855804 ATAATATACTCCCTCCGTCCAATAAT 57.144 34.615 0.00 0.00 0.00 1.28
2813 2953 9.947189 ATAATATACTCCCTCCGTCCAATAATA 57.053 33.333 0.00 0.00 0.00 0.98
2814 2954 8.855804 AATATACTCCCTCCGTCCAATAATAT 57.144 34.615 0.00 0.00 0.00 1.28
2815 2955 9.947189 AATATACTCCCTCCGTCCAATAATATA 57.053 33.333 0.00 0.00 0.00 0.86
2816 2956 9.947189 ATATACTCCCTCCGTCCAATAATATAA 57.053 33.333 0.00 0.00 0.00 0.98
2817 2957 6.607004 ACTCCCTCCGTCCAATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
2818 2958 6.320518 ACTCCCTCCGTCCAATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
2819 2959 6.210984 ACTCCCTCCGTCCAATAATATAAGAC 59.789 42.308 0.00 0.00 0.00 3.01
2821 2961 5.047519 CCCTCCGTCCAATAATATAAGACGT 60.048 44.000 17.76 0.00 46.62 4.34
2822 2962 6.453092 CCTCCGTCCAATAATATAAGACGTT 58.547 40.000 17.76 0.00 46.62 3.99
2823 2963 6.927381 CCTCCGTCCAATAATATAAGACGTTT 59.073 38.462 17.76 0.00 46.62 3.60
2824 2964 7.440255 CCTCCGTCCAATAATATAAGACGTTTT 59.560 37.037 17.76 0.00 46.62 2.43
2825 2965 8.721019 TCCGTCCAATAATATAAGACGTTTTT 57.279 30.769 17.76 0.00 46.62 1.94
2826 2966 8.605746 TCCGTCCAATAATATAAGACGTTTTTG 58.394 33.333 17.76 7.53 46.62 2.44
2827 2967 7.375017 CCGTCCAATAATATAAGACGTTTTTGC 59.625 37.037 17.76 0.00 46.62 3.68
2828 2968 7.906010 CGTCCAATAATATAAGACGTTTTTGCA 59.094 33.333 13.54 0.00 43.89 4.08
2829 2969 9.562583 GTCCAATAATATAAGACGTTTTTGCAA 57.437 29.630 0.00 0.00 0.00 4.08
2830 2970 9.781834 TCCAATAATATAAGACGTTTTTGCAAG 57.218 29.630 0.00 0.00 0.00 4.01
2831 2971 8.531530 CCAATAATATAAGACGTTTTTGCAAGC 58.468 33.333 0.00 0.00 0.00 4.01
2832 2972 9.289303 CAATAATATAAGACGTTTTTGCAAGCT 57.711 29.630 0.00 0.00 0.00 3.74
2835 2975 8.841444 AATATAAGACGTTTTTGCAAGCTATG 57.159 30.769 0.00 0.00 0.00 2.23
2836 2976 4.568152 AAGACGTTTTTGCAAGCTATGT 57.432 36.364 0.00 0.68 0.00 2.29
2837 2977 4.568152 AGACGTTTTTGCAAGCTATGTT 57.432 36.364 0.00 0.00 0.00 2.71
2838 2978 4.290155 AGACGTTTTTGCAAGCTATGTTG 58.710 39.130 0.00 0.00 0.00 3.33
2839 2979 3.380142 ACGTTTTTGCAAGCTATGTTGG 58.620 40.909 0.00 0.00 0.00 3.77
2840 2980 2.155539 CGTTTTTGCAAGCTATGTTGGC 59.844 45.455 0.00 0.00 0.00 4.52
2841 2981 3.392882 GTTTTTGCAAGCTATGTTGGCT 58.607 40.909 0.00 0.00 42.31 4.75
2848 2988 3.749665 AAGCTATGTTGGCTTGCAAAA 57.250 38.095 0.00 0.00 46.53 2.44
2849 2989 3.749665 AGCTATGTTGGCTTGCAAAAA 57.250 38.095 0.00 0.00 36.56 1.94
2850 2990 3.392882 AGCTATGTTGGCTTGCAAAAAC 58.607 40.909 0.00 6.49 36.56 2.43
2851 2991 2.155539 GCTATGTTGGCTTGCAAAAACG 59.844 45.455 0.00 0.00 0.00 3.60
2852 2992 2.307934 ATGTTGGCTTGCAAAAACGT 57.692 40.000 0.00 4.53 0.00 3.99
2853 2993 1.634702 TGTTGGCTTGCAAAAACGTC 58.365 45.000 0.00 0.00 0.00 4.34
2854 2994 1.203523 TGTTGGCTTGCAAAAACGTCT 59.796 42.857 0.00 0.00 0.00 4.18
2855 2995 2.267426 GTTGGCTTGCAAAAACGTCTT 58.733 42.857 0.00 0.00 0.00 3.01
2856 2996 3.119459 TGTTGGCTTGCAAAAACGTCTTA 60.119 39.130 0.00 0.00 0.00 2.10
2857 2997 4.048504 GTTGGCTTGCAAAAACGTCTTAT 58.951 39.130 0.00 0.00 0.00 1.73
2858 2998 5.216648 GTTGGCTTGCAAAAACGTCTTATA 58.783 37.500 0.00 0.00 0.00 0.98
2859 2999 5.637006 TGGCTTGCAAAAACGTCTTATAT 57.363 34.783 0.00 0.00 0.00 0.86
2860 3000 6.019779 TGGCTTGCAAAAACGTCTTATATT 57.980 33.333 0.00 0.00 0.00 1.28
2861 3001 7.147143 TGGCTTGCAAAAACGTCTTATATTA 57.853 32.000 0.00 0.00 0.00 0.98
2862 3002 7.767261 TGGCTTGCAAAAACGTCTTATATTAT 58.233 30.769 0.00 0.00 0.00 1.28
2863 3003 7.700234 TGGCTTGCAAAAACGTCTTATATTATG 59.300 33.333 0.00 0.00 0.00 1.90
2864 3004 7.913297 GGCTTGCAAAAACGTCTTATATTATGA 59.087 33.333 0.00 0.00 0.00 2.15
2865 3005 8.947940 GCTTGCAAAAACGTCTTATATTATGAG 58.052 33.333 0.00 0.00 0.00 2.90
2923 3064 4.396166 GGGATTGTGACCTTACATTCAGTG 59.604 45.833 0.00 0.00 34.35 3.66
2928 3069 5.302360 TGTGACCTTACATTCAGTGGTTAC 58.698 41.667 0.00 0.00 34.96 2.50
2931 3072 4.964593 ACCTTACATTCAGTGGTTACGTT 58.035 39.130 0.00 0.00 0.00 3.99
2932 3073 4.753107 ACCTTACATTCAGTGGTTACGTTG 59.247 41.667 0.00 0.00 0.00 4.10
3091 3233 0.884704 CCAACACAGTTCGGGGTCTG 60.885 60.000 0.00 0.00 37.65 3.51
3133 3275 2.565841 ACTGGAATAATTGGAGCTCGC 58.434 47.619 7.83 1.18 0.00 5.03
3151 3293 1.690219 GCGGAGATGATGACCAGGGT 61.690 60.000 0.00 0.00 0.00 4.34
3184 3326 4.275936 GTCAACAACATGAGCTTTAGTGGT 59.724 41.667 0.00 0.00 0.00 4.16
3400 3542 2.148768 CTCCAGGTAACCCGTTGTTTC 58.851 52.381 0.00 0.00 38.42 2.78
3408 3550 2.413310 ACCCGTTGTTTCACTCAGTT 57.587 45.000 0.00 0.00 0.00 3.16
3458 3603 7.928307 TTTCTCTCAACAATCCTAATCTTGG 57.072 36.000 0.00 0.00 0.00 3.61
3459 3604 6.874278 TCTCTCAACAATCCTAATCTTGGA 57.126 37.500 0.00 0.00 38.06 3.53
3460 3605 6.644347 TCTCTCAACAATCCTAATCTTGGAC 58.356 40.000 0.00 0.00 36.30 4.02
3465 3610 5.762179 ACAATCCTAATCTTGGACTCACA 57.238 39.130 0.00 0.00 36.30 3.58
3471 3616 6.778821 TCCTAATCTTGGACTCACAATTTGA 58.221 36.000 2.79 0.00 0.00 2.69
3472 3617 7.230747 TCCTAATCTTGGACTCACAATTTGAA 58.769 34.615 2.79 0.00 32.21 2.69
3567 3712 2.031769 ACAATCTGTGCACACATGTTCG 60.032 45.455 17.42 4.36 41.01 3.95
3647 3792 7.396540 ACCTTTTTCATCATTGGATACTGAC 57.603 36.000 0.00 0.00 37.61 3.51
3689 3834 5.301551 TGTGAGATATGCACAACAAAACCTT 59.698 36.000 5.72 0.00 42.75 3.50
3822 3967 9.985318 CAGTTGATTTTTATTTGCAAAAACAGA 57.015 25.926 17.19 3.25 39.49 3.41
3838 3983 9.087424 GCAAAAACAGACAGATTTAGTTTCTTT 57.913 29.630 0.00 0.00 31.80 2.52
3840 3985 8.634475 AAAACAGACAGATTTAGTTTCTTTGC 57.366 30.769 0.00 0.00 31.80 3.68
4027 4172 6.775594 ATAGAAGGGGTAAATTCAAACTGC 57.224 37.500 0.00 0.00 0.00 4.40
4037 4182 7.071414 GGTAAATTCAAACTGCAAAGCAAATC 58.929 34.615 0.00 0.00 38.41 2.17
4039 4184 4.405116 TTCAAACTGCAAAGCAAATCCT 57.595 36.364 0.00 0.00 38.41 3.24
4040 4185 4.405116 TCAAACTGCAAAGCAAATCCTT 57.595 36.364 0.00 0.00 38.41 3.36
4043 4188 5.294060 TCAAACTGCAAAGCAAATCCTTTTC 59.706 36.000 0.00 0.00 38.41 2.29
4045 4190 5.027293 ACTGCAAAGCAAATCCTTTTCTT 57.973 34.783 0.00 0.00 38.41 2.52
4056 4201 8.043113 AGCAAATCCTTTTCTTTTTCTTTCTGT 58.957 29.630 0.00 0.00 0.00 3.41
4067 4212 7.826690 TCTTTTTCTTTCTGTAGCAAACTGTT 58.173 30.769 0.00 0.00 0.00 3.16
4068 4213 7.754924 TCTTTTTCTTTCTGTAGCAAACTGTTG 59.245 33.333 0.00 0.00 37.83 3.33
4081 4226 4.696455 CAAACTGTTGATGGCCTTCTTTT 58.304 39.130 18.67 8.08 36.83 2.27
4083 4228 3.565307 ACTGTTGATGGCCTTCTTTTCA 58.435 40.909 18.67 11.17 0.00 2.69
4091 4246 4.396357 TGGCCTTCTTTTCATTCCCTTA 57.604 40.909 3.32 0.00 0.00 2.69
4101 4256 8.181904 TCTTTTCATTCCCTTATTATGCATCC 57.818 34.615 0.19 0.00 0.00 3.51
4108 4263 8.906867 CATTCCCTTATTATGCATCCGATATTT 58.093 33.333 0.19 0.00 0.00 1.40
4109 4264 7.864108 TCCCTTATTATGCATCCGATATTTG 57.136 36.000 0.19 0.00 0.00 2.32
4113 4268 8.393366 CCTTATTATGCATCCGATATTTGTCTG 58.607 37.037 0.19 0.00 0.00 3.51
4288 4444 3.107601 TCTCTCCATCTTCCGACCAATT 58.892 45.455 0.00 0.00 0.00 2.32
4337 4496 2.936202 ACCAGCATGTATTTGCCTAGG 58.064 47.619 3.67 3.67 43.83 3.02
4367 4526 5.139727 AGAGAGATGCTAGCAGTAGTTGAT 58.860 41.667 23.89 2.85 0.00 2.57
4384 4543 5.809001 AGTTGATCCTGATTCAGCTTGTAA 58.191 37.500 8.23 0.00 0.00 2.41
4415 4574 2.139323 ATGATCTGTGCATGCAGGTT 57.861 45.000 23.41 11.96 37.12 3.50
4445 4604 2.512896 GCCATCGGGGAGAGCAAT 59.487 61.111 0.00 0.00 40.01 3.56
4457 4616 3.459378 GAGCAATGCGGTGGATGCG 62.459 63.158 0.00 0.00 43.39 4.73
4775 4934 0.823356 ATGCGTGTATGGGAATGGGC 60.823 55.000 0.00 0.00 0.00 5.36
4806 4965 2.133281 TGATGATTTGCTGGAGGTGG 57.867 50.000 0.00 0.00 0.00 4.61
4811 4970 2.295885 GATTTGCTGGAGGTGGATGAG 58.704 52.381 0.00 0.00 0.00 2.90
4875 5034 5.853282 GTGTCTGAATTTGAATTTGACTCGG 59.147 40.000 16.66 2.13 35.34 4.63
4906 5065 8.656849 CAAACATCTGACTGTGGTATACTAAAC 58.343 37.037 2.25 0.37 0.00 2.01
4946 5120 8.076178 GTCATTTTTATTATTGGGACCTCATCG 58.924 37.037 0.00 0.00 0.00 3.84
4981 5155 6.457528 GGTTCCTGCGATTTCATAAAGAAGAG 60.458 42.308 0.00 0.00 37.57 2.85
4995 5169 5.916661 AAAGAAGAGTATAGTTGGCTCGA 57.083 39.130 0.00 0.00 34.69 4.04
5025 5199 0.750249 AAACCAGGCCGAAAACCAAG 59.250 50.000 0.00 0.00 0.00 3.61
5111 5297 6.597262 AAAAAGATAAAACCAACAAAGCCG 57.403 33.333 0.00 0.00 0.00 5.52
5112 5298 3.297830 AGATAAAACCAACAAAGCCGC 57.702 42.857 0.00 0.00 0.00 6.53
5113 5299 2.029380 AGATAAAACCAACAAAGCCGCC 60.029 45.455 0.00 0.00 0.00 6.13
5150 5336 2.360350 CTCCACCGCCAACATGCT 60.360 61.111 0.00 0.00 0.00 3.79
5151 5337 1.973281 CTCCACCGCCAACATGCTT 60.973 57.895 0.00 0.00 0.00 3.91
5160 5346 1.538047 CCAACATGCTTGCTACCTGT 58.462 50.000 0.00 0.00 0.00 4.00
5197 5383 4.536765 TCAAGAAGGAAGAATAATGCCCC 58.463 43.478 0.00 0.00 0.00 5.80
5226 5412 3.147595 TCTCCGGCATCGACCCTG 61.148 66.667 0.00 0.00 39.00 4.45
5265 5451 2.561037 CCCAGAAACCGCCCACAAC 61.561 63.158 0.00 0.00 0.00 3.32
5273 5459 4.335647 CGCCCACAACTCCCTGCT 62.336 66.667 0.00 0.00 0.00 4.24
5301 5487 2.039831 ATAGGGCCCGATGGTGGT 60.040 61.111 17.77 0.00 0.00 4.16
5303 5489 1.286305 ATAGGGCCCGATGGTGGTTT 61.286 55.000 17.77 0.00 0.00 3.27
5311 5497 3.132111 GCCCGATGGTGGTTTGATATTTT 59.868 43.478 0.00 0.00 0.00 1.82
5329 5516 7.556275 TGATATTTTGCCACTTTTAGTAGAGGG 59.444 37.037 0.00 0.00 0.00 4.30
5337 5524 5.469084 CCACTTTTAGTAGAGGGTTTGACAC 59.531 44.000 0.00 0.00 0.00 3.67
5348 5535 1.473278 GGTTTGACACGGTTTTCACCA 59.527 47.619 0.00 0.00 44.53 4.17
5407 5638 8.017418 TGTTGTGTAGAAAATTGGAAGGAAAT 57.983 30.769 0.00 0.00 0.00 2.17
5555 5792 3.874392 ACTTTTAATCCATGCACCTGC 57.126 42.857 0.00 0.00 42.50 4.85
5557 5794 2.121291 TTTAATCCATGCACCTGCGA 57.879 45.000 0.00 0.00 45.83 5.10
5564 5801 2.103941 TCCATGCACCTGCGAATACATA 59.896 45.455 0.00 0.00 45.83 2.29
5566 5803 3.125829 CCATGCACCTGCGAATACATATC 59.874 47.826 0.00 0.00 45.83 1.63
5571 5808 5.696270 TGCACCTGCGAATACATATCTAAAG 59.304 40.000 0.00 0.00 45.83 1.85
5639 5877 7.488792 GCAGTTGCATCAATAAAATCACACATA 59.511 33.333 0.00 0.00 41.59 2.29
5660 5898 2.399396 AAAATGCAACGACAACGAGG 57.601 45.000 0.00 0.00 42.66 4.63
5661 5899 1.305201 AAATGCAACGACAACGAGGT 58.695 45.000 0.00 0.00 42.66 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 4.584638 TGTGGATTTTGTAGGCCTACAT 57.415 40.909 39.32 27.92 44.54 2.29
51 52 4.374689 TTGTGGATTTTGTAGGCCTACA 57.625 40.909 36.63 36.63 43.61 2.74
52 53 5.417580 TGATTTGTGGATTTTGTAGGCCTAC 59.582 40.000 32.37 32.37 36.63 3.18
53 54 5.575157 TGATTTGTGGATTTTGTAGGCCTA 58.425 37.500 8.91 8.91 0.00 3.93
54 55 4.415596 TGATTTGTGGATTTTGTAGGCCT 58.584 39.130 11.78 11.78 0.00 5.19
55 56 4.799564 TGATTTGTGGATTTTGTAGGCC 57.200 40.909 0.00 0.00 0.00 5.19
85 86 9.995003 TTTGGCAATTTAGAAAATATGACTTGT 57.005 25.926 0.00 0.00 0.00 3.16
99 100 4.942852 TGTCCACAAGTTTGGCAATTTAG 58.057 39.130 0.00 0.00 36.48 1.85
169 170 4.685628 ACAAAGCGAAAAATGTTGGCTATG 59.314 37.500 0.00 0.00 32.82 2.23
267 271 5.710099 ACCGTGACACTTATTTTGGATCAAT 59.290 36.000 3.68 0.00 0.00 2.57
268 272 5.067273 ACCGTGACACTTATTTTGGATCAA 58.933 37.500 3.68 0.00 0.00 2.57
340 344 6.884836 ACAAAATACTACTCCCTTCAATCCAC 59.115 38.462 0.00 0.00 0.00 4.02
346 350 5.007682 GGCAACAAAATACTACTCCCTTCA 58.992 41.667 0.00 0.00 0.00 3.02
400 414 0.036732 AAGGGTGCATTTGAGCTCGA 59.963 50.000 9.64 3.88 34.99 4.04
480 494 9.107177 TGCAGCCATACAAAAATATAAAAATGG 57.893 29.630 0.00 0.00 36.53 3.16
608 626 9.599866 GAAAAACATTATTTAATGCTTAGGGCT 57.400 29.630 9.65 0.00 45.24 5.19
614 632 9.139174 CGTGGAGAAAAACATTATTTAATGCTT 57.861 29.630 9.65 2.43 45.24 3.91
623 641 7.117667 GCAAATTTCCGTGGAGAAAAACATTAT 59.882 33.333 0.00 0.00 39.11 1.28
624 642 6.422400 GCAAATTTCCGTGGAGAAAAACATTA 59.578 34.615 0.00 0.00 39.11 1.90
626 644 4.749598 GCAAATTTCCGTGGAGAAAAACAT 59.250 37.500 0.00 0.00 39.11 2.71
627 645 4.116238 GCAAATTTCCGTGGAGAAAAACA 58.884 39.130 0.00 0.00 39.11 2.83
628 646 4.116238 TGCAAATTTCCGTGGAGAAAAAC 58.884 39.130 0.00 0.00 39.11 2.43
635 653 2.570415 TACCTGCAAATTTCCGTGGA 57.430 45.000 0.00 0.00 0.00 4.02
636 654 2.491693 ACATACCTGCAAATTTCCGTGG 59.508 45.455 0.00 0.00 0.00 4.94
648 666 8.841444 CATTGTTAAATGTTCTACATACCTGC 57.159 34.615 0.00 0.00 37.97 4.85
726 769 7.548097 TCAAATGCACCTTTGTAAACAGTAAA 58.452 30.769 11.50 0.00 37.39 2.01
727 770 7.101652 TCAAATGCACCTTTGTAAACAGTAA 57.898 32.000 11.50 0.00 37.39 2.24
728 771 6.701145 TCAAATGCACCTTTGTAAACAGTA 57.299 33.333 11.50 0.00 37.39 2.74
729 772 5.590530 TCAAATGCACCTTTGTAAACAGT 57.409 34.783 11.50 0.00 37.39 3.55
730 773 4.445385 GCTCAAATGCACCTTTGTAAACAG 59.555 41.667 11.50 4.13 37.39 3.16
731 774 4.099266 AGCTCAAATGCACCTTTGTAAACA 59.901 37.500 11.50 0.00 37.39 2.83
732 775 4.620982 AGCTCAAATGCACCTTTGTAAAC 58.379 39.130 11.50 2.39 37.39 2.01
733 776 4.556501 CGAGCTCAAATGCACCTTTGTAAA 60.557 41.667 15.40 0.00 37.39 2.01
734 777 3.058293 CGAGCTCAAATGCACCTTTGTAA 60.058 43.478 15.40 0.00 37.39 2.41
735 778 2.483877 CGAGCTCAAATGCACCTTTGTA 59.516 45.455 15.40 0.60 37.39 2.41
736 779 1.267806 CGAGCTCAAATGCACCTTTGT 59.732 47.619 15.40 0.00 37.39 2.83
737 780 1.536766 TCGAGCTCAAATGCACCTTTG 59.463 47.619 15.40 6.46 37.44 2.77
738 781 1.896220 TCGAGCTCAAATGCACCTTT 58.104 45.000 15.40 0.00 34.99 3.11
739 782 1.896220 TTCGAGCTCAAATGCACCTT 58.104 45.000 15.40 0.00 34.99 3.50
982 1029 4.111053 GGTTTCCTCTCCGGGGCC 62.111 72.222 0.00 0.00 0.00 5.80
1179 1237 1.392534 GGAGAGGGAAGGGTCAGGA 59.607 63.158 0.00 0.00 0.00 3.86
1217 1276 1.593469 CTCTAGCGAGACGAATCACGA 59.407 52.381 0.00 0.00 40.92 4.35
1226 1285 1.071568 GCGTACGTACTCTAGCGAGAC 60.072 57.143 22.55 0.00 39.74 3.36
1320 1386 2.649034 GCTGAACCCACGAGACGA 59.351 61.111 0.00 0.00 0.00 4.20
1321 1387 1.592400 TAGGCTGAACCCACGAGACG 61.592 60.000 0.00 0.00 40.58 4.18
1322 1388 0.606604 TTAGGCTGAACCCACGAGAC 59.393 55.000 0.00 0.00 40.58 3.36
1323 1389 1.344065 TTTAGGCTGAACCCACGAGA 58.656 50.000 0.00 0.00 40.58 4.04
1324 1390 2.076863 CTTTTAGGCTGAACCCACGAG 58.923 52.381 0.00 0.00 40.58 4.18
1352 1418 3.804325 CGCAGTTTTCTTCTGAGAGTGAA 59.196 43.478 0.00 0.00 35.36 3.18
1435 1501 7.565680 AGGATAGCACGATATTATTTTAGGGG 58.434 38.462 0.00 0.00 0.00 4.79
1454 1520 6.647334 TCTGCAATAGAGAGTGAAGGATAG 57.353 41.667 0.00 0.00 26.42 2.08
1483 1551 6.219417 TGAACTTTTTGATGCAGAAAAGGA 57.781 33.333 24.47 12.96 43.63 3.36
1527 1595 2.159240 GGAAGCCCGCTGATTTTTAAGG 60.159 50.000 0.00 0.00 0.00 2.69
1572 1640 6.569780 ACAAAGAGGGTCACAAAAATAACAC 58.430 36.000 0.00 0.00 0.00 3.32
1610 1678 9.566432 ACACTTTGAAGAATACTGAAGAATCTT 57.434 29.630 0.00 0.00 33.28 2.40
1651 1719 0.681243 GAGCTAACCCCCAAAGCCAG 60.681 60.000 0.00 0.00 36.92 4.85
1688 1756 2.284405 AGTGGTACGGGAGGGGTG 60.284 66.667 0.00 0.00 0.00 4.61
1689 1757 2.284405 CAGTGGTACGGGAGGGGT 60.284 66.667 0.00 0.00 0.00 4.95
1690 1758 3.782443 GCAGTGGTACGGGAGGGG 61.782 72.222 0.00 0.00 0.00 4.79
1691 1759 3.000819 TGCAGTGGTACGGGAGGG 61.001 66.667 0.00 0.00 0.00 4.30
1692 1760 2.227089 GACTGCAGTGGTACGGGAGG 62.227 65.000 27.27 0.00 36.20 4.30
1693 1761 1.215647 GACTGCAGTGGTACGGGAG 59.784 63.158 27.27 0.00 37.71 4.30
1707 1775 4.313282 TGAATTCAGTGCAGAGAAGACTG 58.687 43.478 3.38 0.00 38.79 3.51
1765 1833 8.138365 CACAACATATAGTGTATTGTGTACCC 57.862 38.462 7.14 0.00 41.45 3.69
1779 1847 8.641155 CAACAATGAAAGCAACACAACATATAG 58.359 33.333 0.00 0.00 0.00 1.31
1852 1920 2.888594 GCTGTACGACATGAAGCCTTA 58.111 47.619 0.00 0.00 0.00 2.69
1871 1939 0.179000 AGTCGATGGACCAATCAGGC 59.821 55.000 0.00 0.00 44.54 4.85
1885 1953 6.888632 AGACCTAACTCAAATAACCTAGTCGA 59.111 38.462 0.00 0.00 0.00 4.20
1886 1954 7.098074 AGACCTAACTCAAATAACCTAGTCG 57.902 40.000 0.00 0.00 0.00 4.18
1939 2007 4.838986 ACTAGGTGATAGTGACAAGGTGTT 59.161 41.667 0.00 0.00 43.35 3.32
1940 2008 4.417437 ACTAGGTGATAGTGACAAGGTGT 58.583 43.478 0.00 0.00 43.35 4.16
1998 2103 6.040166 ACATTTTCTGACAAGATGTTGAGCTT 59.960 34.615 9.96 0.00 37.10 3.74
1999 2104 5.533903 ACATTTTCTGACAAGATGTTGAGCT 59.466 36.000 9.96 0.00 37.10 4.09
2022 2127 8.775527 TGAGAATGAGACACTATAACTATCGAC 58.224 37.037 0.00 0.00 0.00 4.20
2063 2168 8.655935 ACCTCTTTTCTGTTTCATAATTGGAT 57.344 30.769 0.00 0.00 0.00 3.41
2110 2216 6.943146 TGTATCAAGGTACCACAAAAGCATAA 59.057 34.615 15.94 0.00 0.00 1.90
2112 2218 5.321102 TGTATCAAGGTACCACAAAAGCAT 58.679 37.500 15.94 0.00 0.00 3.79
2121 2230 9.391006 GTCTTAAAATGATGTATCAAGGTACCA 57.609 33.333 15.94 0.00 40.69 3.25
2122 2231 8.837389 GGTCTTAAAATGATGTATCAAGGTACC 58.163 37.037 2.73 2.73 40.69 3.34
2150 2260 6.979465 TGTGCATCAAAATGTTCTGAATGTA 58.021 32.000 0.00 0.00 35.18 2.29
2172 2282 0.250209 CAACAGGACTCAGCAGCTGT 60.250 55.000 22.10 3.46 32.61 4.40
2228 2338 8.737168 TGGAATCTCAGAATCACGAAATTATT 57.263 30.769 0.00 0.00 0.00 1.40
2265 2376 5.376854 ACATATGCCAAATTTAGCGATCC 57.623 39.130 1.58 0.00 0.00 3.36
2269 2380 8.801715 AGAAAATACATATGCCAAATTTAGCG 57.198 30.769 1.58 0.00 0.00 4.26
2328 2446 2.513753 TGAAACTTCACGGGCATCATT 58.486 42.857 0.00 0.00 31.01 2.57
2338 2456 3.003275 TGCCGTCTCAATTGAAACTTCAC 59.997 43.478 9.88 0.00 36.83 3.18
2349 2467 7.033185 GGTTAATACAAATTTGCCGTCTCAAT 58.967 34.615 18.12 0.00 0.00 2.57
2360 2478 7.504238 TGGAGTGAGTGTGGTTAATACAAATTT 59.496 33.333 0.00 0.00 0.00 1.82
2373 2491 4.743057 TTGATAGATGGAGTGAGTGTGG 57.257 45.455 0.00 0.00 0.00 4.17
2440 2558 3.206150 GACAAGACTTCAGCAAGGTGAA 58.794 45.455 13.33 13.33 35.16 3.18
2455 2573 5.738909 TCCCTTTTTGCAAATTTGACAAGA 58.261 33.333 22.31 15.86 0.00 3.02
2468 2586 6.036577 TGATATTGAGGTTTCCCTTTTTGC 57.963 37.500 0.00 0.00 42.86 3.68
2470 2588 8.670521 AGAATGATATTGAGGTTTCCCTTTTT 57.329 30.769 0.00 0.00 42.86 1.94
2471 2589 8.670521 AAGAATGATATTGAGGTTTCCCTTTT 57.329 30.769 0.00 0.00 42.86 2.27
2472 2590 8.118600 AGAAGAATGATATTGAGGTTTCCCTTT 58.881 33.333 0.00 0.00 42.86 3.11
2473 2591 7.646884 AGAAGAATGATATTGAGGTTTCCCTT 58.353 34.615 0.00 0.00 42.86 3.95
2474 2592 7.218314 AGAAGAATGATATTGAGGTTTCCCT 57.782 36.000 0.00 0.00 46.66 4.20
2475 2593 7.340487 ACAAGAAGAATGATATTGAGGTTTCCC 59.660 37.037 0.00 0.00 0.00 3.97
2476 2594 8.286191 ACAAGAAGAATGATATTGAGGTTTCC 57.714 34.615 0.00 0.00 0.00 3.13
2521 2654 4.473444 ACCTCCTAAACCAATATGGCATG 58.527 43.478 10.98 0.00 42.67 4.06
2523 2656 4.724798 ACTACCTCCTAAACCAATATGGCA 59.275 41.667 0.00 0.00 42.67 4.92
2525 2658 7.311109 GGGATACTACCTCCTAAACCAATATGG 60.311 44.444 0.00 0.00 36.93 2.74
2541 2674 0.460635 TTGCGTTGCGGGATACTACC 60.461 55.000 0.00 0.00 0.00 3.18
2569 2705 4.681483 GCCTCTAAACTGTTTTTCATGTGC 59.319 41.667 11.48 2.72 0.00 4.57
2677 2813 7.823745 AATACATTGTTCTTCAGTCCAGTTT 57.176 32.000 0.00 0.00 0.00 2.66
2735 2875 6.585695 TCCACGACTCTTAAGAAATAGTGT 57.414 37.500 19.48 9.57 0.00 3.55
2793 2933 7.395489 GTCTTATATTATTGGACGGAGGGAGTA 59.605 40.741 0.00 0.00 0.00 2.59
2794 2934 6.210984 GTCTTATATTATTGGACGGAGGGAGT 59.789 42.308 0.00 0.00 0.00 3.85
2795 2935 6.625300 CGTCTTATATTATTGGACGGAGGGAG 60.625 46.154 16.41 0.00 43.69 4.30
2796 2936 5.184479 CGTCTTATATTATTGGACGGAGGGA 59.816 44.000 16.41 0.00 43.69 4.20
2797 2937 5.408356 CGTCTTATATTATTGGACGGAGGG 58.592 45.833 16.41 0.00 43.69 4.30
2803 2943 9.562583 TTGCAAAAACGTCTTATATTATTGGAC 57.437 29.630 0.00 0.00 0.00 4.02
2804 2944 9.781834 CTTGCAAAAACGTCTTATATTATTGGA 57.218 29.630 0.00 0.00 0.00 3.53
2805 2945 8.531530 GCTTGCAAAAACGTCTTATATTATTGG 58.468 33.333 0.00 0.00 0.00 3.16
2806 2946 9.289303 AGCTTGCAAAAACGTCTTATATTATTG 57.711 29.630 0.00 0.00 0.00 1.90
2809 2949 9.929722 CATAGCTTGCAAAAACGTCTTATATTA 57.070 29.630 0.00 0.00 0.00 0.98
2810 2950 8.458843 ACATAGCTTGCAAAAACGTCTTATATT 58.541 29.630 0.00 0.00 0.00 1.28
2811 2951 7.985476 ACATAGCTTGCAAAAACGTCTTATAT 58.015 30.769 0.00 0.00 0.00 0.86
2812 2952 7.372451 ACATAGCTTGCAAAAACGTCTTATA 57.628 32.000 0.00 0.00 0.00 0.98
2813 2953 6.254281 ACATAGCTTGCAAAAACGTCTTAT 57.746 33.333 0.00 0.00 0.00 1.73
2814 2954 5.682943 ACATAGCTTGCAAAAACGTCTTA 57.317 34.783 0.00 0.00 0.00 2.10
2815 2955 4.568152 ACATAGCTTGCAAAAACGTCTT 57.432 36.364 0.00 0.00 0.00 3.01
2816 2956 4.290155 CAACATAGCTTGCAAAAACGTCT 58.710 39.130 0.00 0.00 0.00 4.18
2817 2957 3.425193 CCAACATAGCTTGCAAAAACGTC 59.575 43.478 0.00 0.00 0.00 4.34
2818 2958 3.380142 CCAACATAGCTTGCAAAAACGT 58.620 40.909 0.00 0.00 0.00 3.99
2819 2959 2.155539 GCCAACATAGCTTGCAAAAACG 59.844 45.455 0.00 0.00 0.00 3.60
2820 2960 3.392882 AGCCAACATAGCTTGCAAAAAC 58.607 40.909 0.00 0.00 37.24 2.43
2821 2961 3.749665 AGCCAACATAGCTTGCAAAAA 57.250 38.095 0.00 0.00 37.24 1.94
2829 2969 3.392882 GTTTTTGCAAGCCAACATAGCT 58.607 40.909 0.00 0.00 44.19 3.32
2830 2970 2.155539 CGTTTTTGCAAGCCAACATAGC 59.844 45.455 14.85 0.00 31.97 2.97
2831 2971 3.380142 ACGTTTTTGCAAGCCAACATAG 58.620 40.909 14.85 5.25 31.97 2.23
2832 2972 3.067461 AGACGTTTTTGCAAGCCAACATA 59.933 39.130 14.85 0.00 31.97 2.29
2833 2973 2.159114 AGACGTTTTTGCAAGCCAACAT 60.159 40.909 14.85 3.64 31.97 2.71
2834 2974 1.203523 AGACGTTTTTGCAAGCCAACA 59.796 42.857 14.85 0.00 31.97 3.33
2835 2975 1.921243 AGACGTTTTTGCAAGCCAAC 58.079 45.000 0.00 3.84 31.97 3.77
2836 2976 2.663826 AAGACGTTTTTGCAAGCCAA 57.336 40.000 0.00 0.00 0.00 4.52
2837 2977 5.637006 ATATAAGACGTTTTTGCAAGCCA 57.363 34.783 0.00 0.00 0.00 4.75
2838 2978 7.913297 TCATAATATAAGACGTTTTTGCAAGCC 59.087 33.333 0.00 0.00 0.00 4.35
2839 2979 8.835467 TCATAATATAAGACGTTTTTGCAAGC 57.165 30.769 0.00 0.00 0.00 4.01
2843 2983 9.599322 CCATCTCATAATATAAGACGTTTTTGC 57.401 33.333 0.00 0.00 0.00 3.68
2846 2986 9.712305 CCTCCATCTCATAATATAAGACGTTTT 57.288 33.333 0.00 0.00 0.00 2.43
2847 2987 8.314751 CCCTCCATCTCATAATATAAGACGTTT 58.685 37.037 0.00 0.00 0.00 3.60
2848 2988 7.674348 TCCCTCCATCTCATAATATAAGACGTT 59.326 37.037 0.00 0.00 0.00 3.99
2849 2989 7.182760 TCCCTCCATCTCATAATATAAGACGT 58.817 38.462 0.00 0.00 0.00 4.34
2850 2990 7.340743 ACTCCCTCCATCTCATAATATAAGACG 59.659 40.741 0.00 0.00 0.00 4.18
2851 2991 8.602472 ACTCCCTCCATCTCATAATATAAGAC 57.398 38.462 0.00 0.00 0.00 3.01
2855 2995 9.480861 CAGTTACTCCCTCCATCTCATAATATA 57.519 37.037 0.00 0.00 0.00 0.86
2856 2996 8.180165 TCAGTTACTCCCTCCATCTCATAATAT 58.820 37.037 0.00 0.00 0.00 1.28
2857 2997 7.535738 TCAGTTACTCCCTCCATCTCATAATA 58.464 38.462 0.00 0.00 0.00 0.98
2858 2998 6.385443 TCAGTTACTCCCTCCATCTCATAAT 58.615 40.000 0.00 0.00 0.00 1.28
2859 2999 5.777449 TCAGTTACTCCCTCCATCTCATAA 58.223 41.667 0.00 0.00 0.00 1.90
2860 3000 5.403558 TCAGTTACTCCCTCCATCTCATA 57.596 43.478 0.00 0.00 0.00 2.15
2861 3001 4.271807 TCAGTTACTCCCTCCATCTCAT 57.728 45.455 0.00 0.00 0.00 2.90
2862 3002 3.757947 TCAGTTACTCCCTCCATCTCA 57.242 47.619 0.00 0.00 0.00 3.27
2863 3003 5.186797 CCATATCAGTTACTCCCTCCATCTC 59.813 48.000 0.00 0.00 0.00 2.75
2864 3004 5.090139 CCATATCAGTTACTCCCTCCATCT 58.910 45.833 0.00 0.00 0.00 2.90
2865 3005 4.323104 GCCATATCAGTTACTCCCTCCATC 60.323 50.000 0.00 0.00 0.00 3.51
2866 3006 3.584848 GCCATATCAGTTACTCCCTCCAT 59.415 47.826 0.00 0.00 0.00 3.41
2867 3007 2.972713 GCCATATCAGTTACTCCCTCCA 59.027 50.000 0.00 0.00 0.00 3.86
2868 3008 2.972713 TGCCATATCAGTTACTCCCTCC 59.027 50.000 0.00 0.00 0.00 4.30
2923 3064 8.563289 TTGTCAAATAAATTCACAACGTAACC 57.437 30.769 0.00 0.00 0.00 2.85
3091 3233 3.620488 TGATATCCCAAAACCAGCTGAC 58.380 45.455 17.39 0.00 0.00 3.51
3133 3275 1.704641 TACCCTGGTCATCATCTCCG 58.295 55.000 0.00 0.00 0.00 4.63
3184 3326 5.425217 TGCCCTTAATCTTGTGAGATCTACA 59.575 40.000 0.00 0.00 41.78 2.74
3441 3586 5.939883 TGTGAGTCCAAGATTAGGATTGTTG 59.060 40.000 0.00 0.00 37.52 3.33
3465 3610 2.964464 TGGCCTGTCACATGTTCAAATT 59.036 40.909 3.32 0.00 0.00 1.82
3471 3616 2.165167 CTCATTGGCCTGTCACATGTT 58.835 47.619 3.32 0.00 0.00 2.71
3472 3617 1.074405 ACTCATTGGCCTGTCACATGT 59.926 47.619 3.32 0.00 0.00 3.21
3567 3712 3.266510 TCCGGGCAGCAATATATGATC 57.733 47.619 0.00 0.00 0.00 2.92
3647 3792 1.968017 AACCAGCCACTGCATCACG 60.968 57.895 0.00 0.00 41.13 4.35
3689 3834 5.279859 CCTGATAGCCTCAATAATCTGAGCA 60.280 44.000 0.00 0.00 41.36 4.26
3838 3983 5.163591 CCATCTGCACAAATGAGATAAAGCA 60.164 40.000 1.48 0.00 0.00 3.91
3840 3985 6.446781 ACCATCTGCACAAATGAGATAAAG 57.553 37.500 1.48 0.00 0.00 1.85
3852 3997 2.027073 GTCGCGAACCATCTGCACA 61.027 57.895 12.06 0.00 0.00 4.57
4009 4154 4.503123 GCTTTGCAGTTTGAATTTACCCCT 60.503 41.667 0.00 0.00 0.00 4.79
4037 4182 8.595533 GTTTGCTACAGAAAGAAAAAGAAAAGG 58.404 33.333 0.00 0.00 0.00 3.11
4039 4184 9.139174 CAGTTTGCTACAGAAAGAAAAAGAAAA 57.861 29.630 0.00 0.00 0.00 2.29
4040 4185 8.303876 ACAGTTTGCTACAGAAAGAAAAAGAAA 58.696 29.630 0.00 0.00 0.00 2.52
4043 4188 7.754924 TCAACAGTTTGCTACAGAAAGAAAAAG 59.245 33.333 0.00 0.00 32.17 2.27
4045 4190 7.151999 TCAACAGTTTGCTACAGAAAGAAAA 57.848 32.000 0.00 0.00 32.17 2.29
4056 4201 2.584835 AGGCCATCAACAGTTTGCTA 57.415 45.000 5.01 0.00 32.17 3.49
4067 4212 3.099141 GGGAATGAAAAGAAGGCCATCA 58.901 45.455 11.19 2.47 0.00 3.07
4068 4213 3.369175 AGGGAATGAAAAGAAGGCCATC 58.631 45.455 5.01 1.19 0.00 3.51
4081 4226 5.497464 TCGGATGCATAATAAGGGAATGA 57.503 39.130 0.00 0.00 0.00 2.57
4083 4228 8.906867 CAAATATCGGATGCATAATAAGGGAAT 58.093 33.333 0.00 0.00 0.00 3.01
4091 4246 6.712095 ACACAGACAAATATCGGATGCATAAT 59.288 34.615 0.00 0.00 0.00 1.28
4101 4256 3.181517 CCTGCACACACAGACAAATATCG 60.182 47.826 0.00 0.00 40.25 2.92
4108 4263 2.043604 CTCCCCTGCACACACAGACA 62.044 60.000 0.00 0.00 40.25 3.41
4109 4264 1.302033 CTCCCCTGCACACACAGAC 60.302 63.158 0.00 0.00 40.25 3.51
4273 4429 2.614057 GGCTGTAATTGGTCGGAAGATG 59.386 50.000 0.00 0.00 45.19 2.90
4288 4444 2.632377 GCACTCTATTGCTTGGCTGTA 58.368 47.619 0.00 0.00 39.59 2.74
4331 4490 3.465871 CATCTCTCTTTTGCTCCTAGGC 58.534 50.000 2.96 0.00 0.00 3.93
4337 4496 3.529533 TGCTAGCATCTCTCTTTTGCTC 58.470 45.455 14.93 0.00 45.09 4.26
4384 4543 2.753452 CACAGATCATTTGGCTCAGCTT 59.247 45.455 0.00 0.00 0.00 3.74
4387 4546 2.089201 TGCACAGATCATTTGGCTCAG 58.911 47.619 0.00 0.00 0.00 3.35
4415 4574 3.918253 GATGGCCGGCACCTGAACA 62.918 63.158 30.85 15.69 0.00 3.18
4686 4845 1.331214 CAATGGGGCTGAACACAAGT 58.669 50.000 0.00 0.00 0.00 3.16
4687 4846 0.604578 CCAATGGGGCTGAACACAAG 59.395 55.000 0.00 0.00 0.00 3.16
4775 4934 3.431856 CAAATCATCATCAACGTGCCTG 58.568 45.455 0.00 0.00 0.00 4.85
4811 4970 9.565213 CACATCAGTTCTTTTTCATTTATCTCC 57.435 33.333 0.00 0.00 0.00 3.71
4875 5034 5.695851 ACCACAGTCAGATGTTTGAATTC 57.304 39.130 0.00 0.00 0.00 2.17
4946 5120 1.677637 CGCAGGAACCCTACCCTCTC 61.678 65.000 0.00 0.00 29.64 3.20
4995 5169 7.706100 TTTCGGCCTGGTTTTACTTATAAAT 57.294 32.000 0.00 0.00 30.33 1.40
5025 5199 4.630894 TCAATCAAGTTGTTGTGTGGTC 57.369 40.909 2.11 0.00 38.95 4.02
5160 5346 1.945354 CTTGAAGGCGTCTCGGGCTA 61.945 60.000 1.41 0.00 42.70 3.93
5163 5349 0.737715 CTTCTTGAAGGCGTCTCGGG 60.738 60.000 1.41 0.00 0.00 5.14
5165 5351 0.243907 TCCTTCTTGAAGGCGTCTCG 59.756 55.000 21.16 0.51 39.80 4.04
5197 5383 1.592669 CCGGAGACAATAGCGCCTG 60.593 63.158 2.29 1.21 0.00 4.85
5203 5389 1.603172 GGTCGATGCCGGAGACAATAG 60.603 57.143 5.05 0.00 36.68 1.73
5205 5391 1.144057 GGTCGATGCCGGAGACAAT 59.856 57.895 5.05 0.00 36.68 2.71
5207 5393 3.458163 GGGTCGATGCCGGAGACA 61.458 66.667 5.05 0.00 36.68 3.41
5226 5412 3.312697 GGTGAAAGTTCTATTGATCGGCC 59.687 47.826 0.00 0.00 0.00 6.13
5265 5451 1.001641 CCCAAGGTTCAGCAGGGAG 60.002 63.158 0.00 0.00 42.25 4.30
5273 5459 1.286305 GGGCCCTATCCCAAGGTTCA 61.286 60.000 17.04 0.00 45.82 3.18
5303 5489 7.556275 CCCTCTACTAAAAGTGGCAAAATATCA 59.444 37.037 0.00 0.00 0.00 2.15
5311 5497 4.103469 TCAAACCCTCTACTAAAAGTGGCA 59.897 41.667 0.00 0.00 0.00 4.92
5329 5516 2.478879 CCTGGTGAAAACCGTGTCAAAC 60.479 50.000 0.00 0.00 0.00 2.93
5337 5524 1.671845 TCGAAAACCTGGTGAAAACCG 59.328 47.619 0.00 0.00 0.00 4.44
5407 5638 6.567687 TTTGGCTTCAATCGACTTAATTGA 57.432 33.333 0.00 0.00 40.44 2.57
5452 5689 0.535780 TTGCACTCTGGAAGCACTGG 60.536 55.000 0.00 0.00 38.11 4.00
5461 5698 0.240145 TACGTCGTCTTGCACTCTGG 59.760 55.000 0.00 0.00 0.00 3.86
5464 5701 1.269166 CCATACGTCGTCTTGCACTC 58.731 55.000 0.00 0.00 0.00 3.51
5644 5882 4.771127 ACCTCGTTGTCGTTGCAT 57.229 50.000 0.00 0.00 38.33 3.96


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

AutoCloner maintained by Alex Coulton.