Multiple sequence alignment - TraesCS4B01G221800

Loading Multiple Alignment...

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 TraesCS4B01G221800 chr4B 100.000 3554 0 0 1 3554 466060930 466057377 0.000000e+00 6564.0
1 TraesCS4B01G221800 chr4B 85.326 184 23 4 3274 3454 104813105 104812923 1.680000e-43 187.0
2 TraesCS4B01G221800 chr4D 95.164 2316 80 15 483 2786 379260895 379258600 0.000000e+00 3627.0
3 TraesCS4B01G221800 chr4D 89.904 416 28 10 1 411 379261694 379261288 1.130000e-144 523.0
4 TraesCS4B01G221800 chr4D 88.095 462 26 15 2820 3272 379258494 379258053 4.070000e-144 521.0
5 TraesCS4B01G221800 chr4D 85.930 199 23 5 3268 3463 84999558 84999362 1.290000e-49 207.0
6 TraesCS4B01G221800 chr4D 84.270 89 9 4 683 770 208558579 208558663 8.180000e-12 82.4
7 TraesCS4B01G221800 chr4A 94.337 1960 83 12 873 2805 85568682 85570640 0.000000e+00 2979.0
8 TraesCS4B01G221800 chr4A 86.364 242 14 7 2805 3039 85570769 85570998 2.740000e-61 246.0
9 TraesCS4B01G221800 chr6B 88.281 640 60 10 203 837 602204129 602204758 0.000000e+00 752.0
10 TraesCS4B01G221800 chr6B 84.492 187 26 3 3274 3458 162605184 162605369 7.840000e-42 182.0
11 TraesCS4B01G221800 chr2D 88.108 185 20 2 3276 3459 52224357 52224540 5.970000e-53 219.0
12 TraesCS4B01G221800 chr2D 76.948 308 44 15 1240 1547 26327151 26326871 2.210000e-32 150.0
13 TraesCS4B01G221800 chr2D 77.626 219 26 15 1237 1455 26035952 26036147 1.040000e-20 111.0
14 TraesCS4B01G221800 chr2D 100.000 29 0 0 72 100 48180095 48180067 2.000000e-03 54.7
15 TraesCS4B01G221800 chr5B 86.813 182 23 1 3274 3454 107198326 107198507 6.020000e-48 202.0
16 TraesCS4B01G221800 chr5B 79.078 282 50 9 1504 1779 554808832 554808554 6.060000e-43 185.0
17 TraesCS4B01G221800 chr5B 87.838 74 8 1 683 756 438219962 438219890 6.320000e-13 86.1
18 TraesCS4B01G221800 chr2B 85.075 201 26 4 3265 3463 764141761 764141959 6.020000e-48 202.0
19 TraesCS4B01G221800 chr3B 87.079 178 19 2 3282 3458 256728198 256728024 7.780000e-47 198.0
20 TraesCS4B01G221800 chr1B 86.339 183 23 2 3274 3455 481325158 481324977 7.780000e-47 198.0
21 TraesCS4B01G221800 chr1B 85.714 182 23 3 3274 3453 32992047 32992227 4.680000e-44 189.0
22 TraesCS4B01G221800 chr5A 78.547 289 53 9 1504 1786 573086443 573086158 7.840000e-42 182.0
23 TraesCS4B01G221800 chr2A 78.531 177 21 10 1323 1494 28212859 28213023 2.260000e-17 100.0
24 TraesCS4B01G221800 chr2A 79.825 114 17 4 682 792 445714985 445714875 1.060000e-10 78.7
25 TraesCS4B01G221800 chr5D 89.041 73 8 0 683 755 223960508 223960580 1.360000e-14 91.6
26 TraesCS4B01G221800 chr5D 79.630 108 17 4 683 789 322389139 322389036 4.920000e-09 73.1
27 TraesCS4B01G221800 chrUn 83.333 96 16 0 12 107 79434925 79434830 4.890000e-14 89.8
28 TraesCS4B01G221800 chrUn 83.333 96 16 0 12 107 369070454 369070359 4.890000e-14 89.8
29 TraesCS4B01G221800 chrUn 74.820 139 27 5 6 138 40740640 40740776 4.960000e-04 56.5
30 TraesCS4B01G221800 chrUn 74.820 139 27 5 6 138 40747265 40747129 4.960000e-04 56.5
31 TraesCS4B01G221800 chrUn 74.820 139 27 5 6 138 303400194 303400330 4.960000e-04 56.5
32 TraesCS4B01G221800 chr7A 87.671 73 9 0 683 755 209158217 209158289 6.320000e-13 86.1
33 TraesCS4B01G221800 chr7A 86.765 68 9 0 688 755 498590286 498590353 3.800000e-10 76.8
34 TraesCS4B01G221800 chr3D 79.817 109 18 3 683 790 309080994 309081099 3.800000e-10 76.8
35 TraesCS4B01G221800 chr3A 89.796 49 3 2 6 53 694532509 694532556 1.070000e-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 TraesCS4B01G221800 chr4B 466057377 466060930 3553 True 6564.0 6564 100.000000 1 3554 1 chr4B.!!$R2 3553
1 TraesCS4B01G221800 chr4D 379258053 379261694 3641 True 1557.0 3627 91.054333 1 3272 3 chr4D.!!$R2 3271
2 TraesCS4B01G221800 chr4A 85568682 85570998 2316 False 1612.5 2979 90.350500 873 3039 2 chr4A.!!$F1 2166
3 TraesCS4B01G221800 chr6B 602204129 602204758 629 False 752.0 752 88.281000 203 837 1 chr6B.!!$F2 634

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
107 108 0.108186 TGATGTGGCGGCTTAGTCTG 60.108 55.0 11.43 0.00 0.00 3.51 F
161 164 0.109458 GTGAGTATGTGTCCGCGTCA 60.109 55.0 4.92 0.46 0.00 4.35 F
444 450 0.114168 CCATCCCTCCAAACAACCCA 59.886 55.0 0.00 0.00 0.00 4.51 F
541 868 0.254178 ATCATCTCGGCTTGGTGCTT 59.746 50.0 0.00 0.00 42.39 3.91 F
2508 2852 0.252479 AGCTGATGAGTTGGAGCCAG 59.748 55.0 0.00 0.00 31.43 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2192 0.608582 AGAAGCACGACGGTAGGAGT 60.609 55.000 0.00 0.0 0.00 3.85 R
1899 2237 3.304764 CTCCTTCGCGTCGACGTCA 62.305 63.158 35.48 21.4 42.22 4.35 R
2193 2531 4.527583 CTCTCGAGCAGCCTGCCC 62.528 72.222 14.25 0.0 46.52 5.36 R
2512 2856 0.035439 TTGGTCTTCTTGGATCGGCC 60.035 55.000 0.00 0.0 37.10 6.13 R
3533 4058 0.471191 TGTATGATGCAGAGGCTGGG 59.529 55.000 0.00 0.0 41.91 4.45 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
40 41 1.613925 TCGTTCAGTGGGAAGAGACAG 59.386 52.381 0.00 0.00 35.82 3.51
45 46 0.827925 AGTGGGAAGAGACAGTCGCA 60.828 55.000 7.09 0.00 34.66 5.10
66 67 2.860009 TCGACTACGGAGATGCCTATT 58.140 47.619 0.00 0.00 40.21 1.73
71 72 5.335740 CGACTACGGAGATGCCTATTGTAAT 60.336 44.000 0.00 0.00 35.72 1.89
83 84 9.837525 GATGCCTATTGTAATTTCATCAATCTC 57.162 33.333 0.00 0.00 34.35 2.75
95 96 8.942338 ATTTCATCAATCTCAAAATGATGTGG 57.058 30.769 12.98 0.00 46.61 4.17
99 100 0.810648 TCTCAAAATGATGTGGCGGC 59.189 50.000 0.00 0.00 0.00 6.53
104 105 2.128771 AAATGATGTGGCGGCTTAGT 57.871 45.000 11.43 0.00 0.00 2.24
105 106 1.668419 AATGATGTGGCGGCTTAGTC 58.332 50.000 11.43 3.98 0.00 2.59
106 107 0.833287 ATGATGTGGCGGCTTAGTCT 59.167 50.000 11.43 0.00 0.00 3.24
107 108 0.108186 TGATGTGGCGGCTTAGTCTG 60.108 55.000 11.43 0.00 0.00 3.51
108 109 0.175760 GATGTGGCGGCTTAGTCTGA 59.824 55.000 11.43 0.00 0.00 3.27
109 110 0.833287 ATGTGGCGGCTTAGTCTGAT 59.167 50.000 11.43 0.00 0.00 2.90
110 111 0.108186 TGTGGCGGCTTAGTCTGATG 60.108 55.000 11.43 0.00 0.00 3.07
111 112 1.153369 TGGCGGCTTAGTCTGATGC 60.153 57.895 11.43 0.00 0.00 3.91
161 164 0.109458 GTGAGTATGTGTCCGCGTCA 60.109 55.000 4.92 0.46 0.00 4.35
281 285 3.307762 CCCTTTTTACCTCTCCACCTCTG 60.308 52.174 0.00 0.00 0.00 3.35
339 343 0.389391 CACCGGCCGAAGTGATATCT 59.611 55.000 30.73 0.00 36.01 1.98
350 354 3.066208 AGTGATATCTCCCACCACCAT 57.934 47.619 3.98 0.00 34.00 3.55
384 389 4.379243 CACGTTGGCTCGCTCCCT 62.379 66.667 0.00 0.00 0.00 4.20
392 397 2.818132 CTCGCTCCCTTGCCCTAG 59.182 66.667 0.00 0.00 0.00 3.02
400 405 4.899239 CTTGCCCTAGCCTCGCGG 62.899 72.222 6.13 0.00 38.69 6.46
408 413 2.381665 CTAGCCTCGCGGTCTCTTCG 62.382 65.000 6.13 0.00 0.00 3.79
415 420 3.744719 CGGTCTCTTCGCCGGTCA 61.745 66.667 1.90 0.00 43.85 4.02
416 421 2.893398 GGTCTCTTCGCCGGTCAT 59.107 61.111 1.90 0.00 0.00 3.06
417 422 1.227002 GGTCTCTTCGCCGGTCATC 60.227 63.158 1.90 0.00 0.00 2.92
418 423 1.586564 GTCTCTTCGCCGGTCATCG 60.587 63.158 1.90 0.00 38.88 3.84
419 424 2.956964 CTCTTCGCCGGTCATCGC 60.957 66.667 1.90 0.00 37.59 4.58
420 425 4.508128 TCTTCGCCGGTCATCGCC 62.508 66.667 1.90 0.00 37.59 5.54
444 450 0.114168 CCATCCCTCCAAACAACCCA 59.886 55.000 0.00 0.00 0.00 4.51
448 454 1.354368 TCCCTCCAAACAACCCATCTC 59.646 52.381 0.00 0.00 0.00 2.75
465 471 0.460987 CTCCTCCAGCATTGACGACC 60.461 60.000 0.00 0.00 0.00 4.79
466 472 1.450312 CCTCCAGCATTGACGACCC 60.450 63.158 0.00 0.00 0.00 4.46
496 823 0.320374 CGCACTTGTCAACCCTCCTA 59.680 55.000 0.00 0.00 0.00 2.94
498 825 1.939838 GCACTTGTCAACCCTCCTACG 60.940 57.143 0.00 0.00 0.00 3.51
519 846 3.370231 TCGGTGTCGCAGCTAGCA 61.370 61.111 18.83 0.00 46.13 3.49
539 866 0.462581 TCATCATCTCGGCTTGGTGC 60.463 55.000 0.00 0.00 41.94 5.01
541 868 0.254178 ATCATCTCGGCTTGGTGCTT 59.746 50.000 0.00 0.00 42.39 3.91
578 905 5.187576 CCATAACCACTGACCCATGAAAAAT 59.812 40.000 0.00 0.00 0.00 1.82
632 963 5.751243 AATACAGACAATTTACGCCCATC 57.249 39.130 0.00 0.00 0.00 3.51
668 999 9.075678 CCATTTCTTATTGGCAGATATTCTCTT 57.924 33.333 0.00 0.00 29.16 2.85
728 1059 6.093633 ACGGATGTATCTAAAGACTTTTTGGC 59.906 38.462 5.61 0.00 0.00 4.52
729 1060 6.487103 GGATGTATCTAAAGACTTTTTGGCG 58.513 40.000 5.61 0.00 0.00 5.69
742 1073 6.879458 AGACTTTTTGGCGTTAGATACATTCT 59.121 34.615 0.00 0.00 38.57 2.40
743 1074 8.038944 AGACTTTTTGGCGTTAGATACATTCTA 58.961 33.333 0.00 0.00 35.79 2.10
942 1276 2.785540 TTATAACCCCAACCCGTCAC 57.214 50.000 0.00 0.00 0.00 3.67
998 1336 3.522731 CCCTCTCACTCTCGCCGG 61.523 72.222 0.00 0.00 0.00 6.13
1092 1430 1.822425 TTTCCCCACACTTCCCACTA 58.178 50.000 0.00 0.00 0.00 2.74
1287 1625 4.363990 CACTGGACGCACCTCGCT 62.364 66.667 1.15 0.00 43.23 4.93
1470 1808 2.052690 CGATCCCTCCCGTGTCTGT 61.053 63.158 0.00 0.00 0.00 3.41
1488 1826 4.477975 CACGTCCTCGCCGAGTCC 62.478 72.222 13.83 1.76 41.18 3.85
1680 2018 1.506718 CGAGGTGTTGCTCGCTCTA 59.493 57.895 0.00 0.00 36.29 2.43
1689 2027 1.956297 TGCTCGCTCTAGAGTACCTC 58.044 55.000 20.75 7.69 40.26 3.85
1835 2173 3.058160 GCAGGTGCGGCAACAGAT 61.058 61.111 21.65 0.00 0.00 2.90
2193 2531 1.739562 GCAGCTCAAGGACCTCGTG 60.740 63.158 0.00 0.00 0.00 4.35
2504 2848 0.725686 CGCAAGCTGATGAGTTGGAG 59.274 55.000 0.00 0.00 0.00 3.86
2508 2852 0.252479 AGCTGATGAGTTGGAGCCAG 59.748 55.000 0.00 0.00 31.43 4.85
2512 2856 0.179936 GATGAGTTGGAGCCAGGAGG 59.820 60.000 0.00 0.00 38.23 4.30
2588 2938 0.522286 TTTTGCTGCGTGTGTTCGTG 60.522 50.000 0.00 0.00 0.00 4.35
2624 2981 3.181497 GGTTCGTGGCGTGTATAGACTAA 60.181 47.826 0.00 0.00 0.00 2.24
2662 3020 0.747255 ATCGATCGAGGAGGTTGTGG 59.253 55.000 23.84 0.00 0.00 4.17
2676 3039 2.041405 GTGGGGAGGAGGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
2685 3048 2.761767 GAGGAGGAGGAGGTTTGTAGTC 59.238 54.545 0.00 0.00 0.00 2.59
2783 3151 5.200483 TCCCTTGTTCACTGAGATTTGTTT 58.800 37.500 0.00 0.00 0.00 2.83
2784 3152 5.656416 TCCCTTGTTCACTGAGATTTGTTTT 59.344 36.000 0.00 0.00 0.00 2.43
2785 3153 5.979517 CCCTTGTTCACTGAGATTTGTTTTC 59.020 40.000 0.00 0.00 0.00 2.29
2786 3154 5.979517 CCTTGTTCACTGAGATTTGTTTTCC 59.020 40.000 0.00 0.00 0.00 3.13
2787 3155 6.183360 CCTTGTTCACTGAGATTTGTTTTCCT 60.183 38.462 0.00 0.00 0.00 3.36
2808 3176 7.798596 TCCTTTCTCATAACGGTACTAGTAG 57.201 40.000 1.87 0.00 0.00 2.57
2811 3179 8.127954 CCTTTCTCATAACGGTACTAGTAGTTC 58.872 40.741 8.40 3.00 0.00 3.01
2812 3180 8.798859 TTTCTCATAACGGTACTAGTAGTTCT 57.201 34.615 8.40 0.00 0.00 3.01
2813 3181 8.798859 TTCTCATAACGGTACTAGTAGTTCTT 57.201 34.615 8.40 0.00 0.00 2.52
2814 3182 8.798859 TCTCATAACGGTACTAGTAGTTCTTT 57.201 34.615 8.40 4.57 0.00 2.52
2815 3183 9.890629 TCTCATAACGGTACTAGTAGTTCTTTA 57.109 33.333 8.40 6.47 0.00 1.85
2817 3185 8.616076 TCATAACGGTACTAGTAGTTCTTTAGC 58.384 37.037 8.40 0.00 0.00 3.09
2839 3352 6.070656 AGCGGTAGTATATTACAGTGGGTTA 58.929 40.000 7.60 0.00 0.00 2.85
2840 3353 6.208204 AGCGGTAGTATATTACAGTGGGTTAG 59.792 42.308 7.60 0.00 0.00 2.34
2929 3442 4.574828 TCTTTGACCAACAACAAGTAGAGC 59.425 41.667 0.00 0.00 38.29 4.09
2971 3487 7.061441 CACTGTGTATTGAATTTGAACATCTGC 59.939 37.037 0.00 0.00 0.00 4.26
2973 3489 5.003778 GTGTATTGAATTTGAACATCTGCGC 59.996 40.000 0.00 0.00 0.00 6.09
2974 3490 2.634982 TGAATTTGAACATCTGCGCC 57.365 45.000 4.18 0.00 0.00 6.53
2975 3491 2.161855 TGAATTTGAACATCTGCGCCT 58.838 42.857 4.18 0.00 0.00 5.52
2976 3492 2.095110 TGAATTTGAACATCTGCGCCTG 60.095 45.455 4.18 2.06 0.00 4.85
2977 3493 0.171903 ATTTGAACATCTGCGCCTGC 59.828 50.000 4.18 0.00 43.20 4.85
3071 3590 2.024590 GCCCATGCCATGCCTTTCTC 62.025 60.000 0.00 0.00 0.00 2.87
3098 3617 0.036765 TGCACTGTACGGGTTGATCC 60.037 55.000 6.65 0.00 0.00 3.36
3112 3631 4.443621 GGTTGATCCCTACTTTAGTCTGC 58.556 47.826 0.00 0.00 0.00 4.26
3113 3632 4.162509 GGTTGATCCCTACTTTAGTCTGCT 59.837 45.833 0.00 0.00 0.00 4.24
3114 3633 5.363005 GGTTGATCCCTACTTTAGTCTGCTA 59.637 44.000 0.00 0.00 0.00 3.49
3115 3634 6.042208 GGTTGATCCCTACTTTAGTCTGCTAT 59.958 42.308 0.00 0.00 0.00 2.97
3116 3635 7.232941 GGTTGATCCCTACTTTAGTCTGCTATA 59.767 40.741 0.00 0.00 0.00 1.31
3117 3636 8.639761 GTTGATCCCTACTTTAGTCTGCTATAA 58.360 37.037 0.00 0.00 0.00 0.98
3118 3637 8.410673 TGATCCCTACTTTAGTCTGCTATAAG 57.589 38.462 0.00 0.00 0.00 1.73
3120 3639 9.517868 GATCCCTACTTTAGTCTGCTATAAGTA 57.482 37.037 0.00 0.00 34.11 2.24
3152 3671 6.611613 TCCAGAGAATTAACAGTGTCTCAT 57.388 37.500 10.54 0.00 39.20 2.90
3154 3673 6.211384 TCCAGAGAATTAACAGTGTCTCATCA 59.789 38.462 10.54 0.00 39.20 3.07
3155 3674 7.046652 CCAGAGAATTAACAGTGTCTCATCAT 58.953 38.462 10.54 0.00 39.20 2.45
3156 3675 7.224362 CCAGAGAATTAACAGTGTCTCATCATC 59.776 40.741 10.54 0.00 39.20 2.92
3157 3676 7.980662 CAGAGAATTAACAGTGTCTCATCATCT 59.019 37.037 10.54 3.12 39.20 2.90
3158 3677 9.194972 AGAGAATTAACAGTGTCTCATCATCTA 57.805 33.333 10.54 0.00 39.20 1.98
3159 3678 9.809096 GAGAATTAACAGTGTCTCATCATCTAA 57.191 33.333 0.00 0.00 37.15 2.10
3160 3679 9.593134 AGAATTAACAGTGTCTCATCATCTAAC 57.407 33.333 0.00 0.00 0.00 2.34
3161 3680 9.593134 GAATTAACAGTGTCTCATCATCTAACT 57.407 33.333 0.00 0.00 0.00 2.24
3162 3681 9.950496 AATTAACAGTGTCTCATCATCTAACTT 57.050 29.630 0.00 0.00 0.00 2.66
3163 3682 8.988064 TTAACAGTGTCTCATCATCTAACTTC 57.012 34.615 0.00 0.00 0.00 3.01
3167 3686 6.756074 CAGTGTCTCATCATCTAACTTCTTCC 59.244 42.308 0.00 0.00 0.00 3.46
3172 3691 7.768120 GTCTCATCATCTAACTTCTTCCACAAT 59.232 37.037 0.00 0.00 0.00 2.71
3174 3693 9.605275 CTCATCATCTAACTTCTTCCACAATTA 57.395 33.333 0.00 0.00 0.00 1.40
3203 3722 9.613428 TTTATACGATGATTCTTCATGAAACCT 57.387 29.630 9.88 0.00 42.73 3.50
3205 3724 4.568359 ACGATGATTCTTCATGAAACCTCG 59.432 41.667 9.88 15.22 44.47 4.63
3217 3736 0.038526 AAACCTCGCACGTCAGTAGG 60.039 55.000 0.00 0.00 0.00 3.18
3224 3743 1.065551 CGCACGTCAGTAGGATGATCA 59.934 52.381 0.00 0.00 36.34 2.92
3226 3745 2.860735 GCACGTCAGTAGGATGATCAAC 59.139 50.000 0.00 0.00 36.34 3.18
3241 3760 4.450976 TGATCAACCAGATTTGATACCCG 58.549 43.478 0.00 0.00 44.59 5.28
3244 3763 5.110814 TCAACCAGATTTGATACCCGATT 57.889 39.130 0.00 0.00 30.29 3.34
3291 3816 6.817765 TTTTTGGTGTGATTAGGACTCATC 57.182 37.500 0.00 0.00 0.00 2.92
3292 3817 5.762179 TTTGGTGTGATTAGGACTCATCT 57.238 39.130 0.00 0.00 0.00 2.90
3293 3818 6.867519 TTTGGTGTGATTAGGACTCATCTA 57.132 37.500 0.00 0.00 0.00 1.98
3294 3819 6.471233 TTGGTGTGATTAGGACTCATCTAG 57.529 41.667 0.00 0.00 0.00 2.43
3295 3820 5.766590 TGGTGTGATTAGGACTCATCTAGA 58.233 41.667 0.00 0.00 0.00 2.43
3296 3821 6.377080 TGGTGTGATTAGGACTCATCTAGAT 58.623 40.000 0.00 0.00 0.00 1.98
3297 3822 6.266330 TGGTGTGATTAGGACTCATCTAGATG 59.734 42.308 24.32 24.32 40.09 2.90
3298 3823 6.266558 GGTGTGATTAGGACTCATCTAGATGT 59.733 42.308 27.80 13.30 39.72 3.06
3299 3824 7.144661 GTGTGATTAGGACTCATCTAGATGTG 58.855 42.308 27.80 26.80 39.72 3.21
3300 3825 7.013750 GTGTGATTAGGACTCATCTAGATGTGA 59.986 40.741 31.51 16.50 39.72 3.58
3301 3826 7.013750 TGTGATTAGGACTCATCTAGATGTGAC 59.986 40.741 31.51 26.28 39.72 3.67
3302 3827 7.013750 GTGATTAGGACTCATCTAGATGTGACA 59.986 40.741 31.51 14.63 39.72 3.58
3303 3828 7.727634 TGATTAGGACTCATCTAGATGTGACAT 59.272 37.037 31.51 26.18 39.72 3.06
3304 3829 9.237187 GATTAGGACTCATCTAGATGTGACATA 57.763 37.037 31.51 25.36 39.72 2.29
3305 3830 8.996651 TTAGGACTCATCTAGATGTGACATAA 57.003 34.615 31.51 28.22 39.72 1.90
3306 3831 7.283625 AGGACTCATCTAGATGTGACATAAC 57.716 40.000 31.51 17.19 39.72 1.89
3307 3832 7.066142 AGGACTCATCTAGATGTGACATAACT 58.934 38.462 31.51 18.63 39.72 2.24
3308 3833 8.221251 AGGACTCATCTAGATGTGACATAACTA 58.779 37.037 31.51 11.24 39.72 2.24
3309 3834 9.019656 GGACTCATCTAGATGTGACATAACTAT 57.980 37.037 31.51 13.01 39.72 2.12
3310 3835 9.838975 GACTCATCTAGATGTGACATAACTATG 57.161 37.037 31.51 7.64 39.72 2.23
3311 3836 9.360901 ACTCATCTAGATGTGACATAACTATGT 57.639 33.333 31.51 9.95 42.86 2.29
3345 3870 9.783081 AAGTATGACATCATATAACATCAGCAA 57.217 29.630 4.93 0.00 40.53 3.91
3346 3871 9.783081 AGTATGACATCATATAACATCAGCAAA 57.217 29.630 4.93 0.00 40.53 3.68
3418 3943 7.534723 TGGTAAACTAGTTAGATGTGACACT 57.465 36.000 8.92 0.00 0.00 3.55
3419 3944 7.600065 TGGTAAACTAGTTAGATGTGACACTC 58.400 38.462 8.92 2.31 0.00 3.51
3420 3945 7.450634 TGGTAAACTAGTTAGATGTGACACTCT 59.549 37.037 8.92 9.48 0.00 3.24
3421 3946 8.305317 GGTAAACTAGTTAGATGTGACACTCTT 58.695 37.037 8.92 0.00 0.00 2.85
3426 3951 9.915629 ACTAGTTAGATGTGACACTCTTAAAAG 57.084 33.333 7.20 6.45 0.00 2.27
3428 3953 8.819643 AGTTAGATGTGACACTCTTAAAAGAC 57.180 34.615 7.20 0.00 0.00 3.01
3429 3954 7.595502 AGTTAGATGTGACACTCTTAAAAGACG 59.404 37.037 7.20 0.00 0.00 4.18
3430 3955 4.686554 AGATGTGACACTCTTAAAAGACGC 59.313 41.667 7.20 0.00 0.00 5.19
3431 3956 3.128349 TGTGACACTCTTAAAAGACGCC 58.872 45.455 7.20 0.00 0.00 5.68
3432 3957 3.181469 TGTGACACTCTTAAAAGACGCCT 60.181 43.478 7.20 0.00 0.00 5.52
3433 3958 4.038282 TGTGACACTCTTAAAAGACGCCTA 59.962 41.667 7.20 0.00 0.00 3.93
3434 3959 4.621886 GTGACACTCTTAAAAGACGCCTAG 59.378 45.833 0.00 0.00 0.00 3.02
3435 3960 4.521639 TGACACTCTTAAAAGACGCCTAGA 59.478 41.667 0.00 0.00 0.00 2.43
3436 3961 5.185249 TGACACTCTTAAAAGACGCCTAGAT 59.815 40.000 0.00 0.00 0.00 1.98
3437 3962 5.411781 ACACTCTTAAAAGACGCCTAGATG 58.588 41.667 0.00 0.00 0.00 2.90
3438 3963 5.047235 ACACTCTTAAAAGACGCCTAGATGT 60.047 40.000 0.00 0.00 0.00 3.06
3439 3964 5.289675 CACTCTTAAAAGACGCCTAGATGTG 59.710 44.000 0.00 0.00 0.00 3.21
3440 3965 5.185249 ACTCTTAAAAGACGCCTAGATGTGA 59.815 40.000 0.00 0.00 0.00 3.58
3441 3966 6.032956 TCTTAAAAGACGCCTAGATGTGAA 57.967 37.500 0.00 0.00 0.00 3.18
3442 3967 6.640518 TCTTAAAAGACGCCTAGATGTGAAT 58.359 36.000 0.00 0.00 0.00 2.57
3443 3968 7.103641 TCTTAAAAGACGCCTAGATGTGAATT 58.896 34.615 0.00 0.00 0.00 2.17
3444 3969 8.255206 TCTTAAAAGACGCCTAGATGTGAATTA 58.745 33.333 0.00 0.00 0.00 1.40
3445 3970 6.910536 AAAAGACGCCTAGATGTGAATTAG 57.089 37.500 0.00 0.00 0.00 1.73
3446 3971 5.599999 AAGACGCCTAGATGTGAATTAGT 57.400 39.130 0.00 0.00 0.00 2.24
3447 3972 5.189659 AGACGCCTAGATGTGAATTAGTC 57.810 43.478 0.00 0.00 0.00 2.59
3448 3973 4.645136 AGACGCCTAGATGTGAATTAGTCA 59.355 41.667 0.00 0.00 0.00 3.41
3449 3974 5.303078 AGACGCCTAGATGTGAATTAGTCAT 59.697 40.000 0.00 0.00 38.90 3.06
3450 3975 5.918608 ACGCCTAGATGTGAATTAGTCATT 58.081 37.500 0.00 0.00 38.90 2.57
3451 3976 5.986135 ACGCCTAGATGTGAATTAGTCATTC 59.014 40.000 0.00 0.00 41.76 2.67
3452 3977 6.183360 ACGCCTAGATGTGAATTAGTCATTCT 60.183 38.462 0.00 4.18 41.91 2.40
3453 3978 6.145209 CGCCTAGATGTGAATTAGTCATTCTG 59.855 42.308 7.87 1.08 41.91 3.02
3454 3979 6.989169 GCCTAGATGTGAATTAGTCATTCTGT 59.011 38.462 7.87 0.00 41.91 3.41
3455 3980 8.144478 GCCTAGATGTGAATTAGTCATTCTGTA 58.856 37.037 7.87 0.00 41.91 2.74
3485 4010 9.938280 TTTTACTATTCATATAGGATTCACGGG 57.062 33.333 0.00 0.00 38.45 5.28
3486 4011 5.978814 ACTATTCATATAGGATTCACGGGC 58.021 41.667 0.00 0.00 38.45 6.13
3487 4012 4.908601 ATTCATATAGGATTCACGGGCA 57.091 40.909 0.00 0.00 0.00 5.36
3488 4013 3.678056 TCATATAGGATTCACGGGCAC 57.322 47.619 0.00 0.00 0.00 5.01
3489 4014 7.126233 CTATTCATATAGGATTCACGGGCACC 61.126 46.154 0.00 0.00 36.53 5.01
3490 4015 9.936805 CTATTCATATAGGATTCACGGGCACCC 62.937 48.148 0.00 0.00 36.53 4.61
3503 4028 1.673168 GGCACCCAAGAGCTTCTATG 58.327 55.000 0.00 0.00 0.00 2.23
3504 4029 1.020437 GCACCCAAGAGCTTCTATGC 58.980 55.000 0.00 0.00 0.00 3.14
3505 4030 1.679944 GCACCCAAGAGCTTCTATGCA 60.680 52.381 0.00 0.00 34.99 3.96
3506 4031 2.715046 CACCCAAGAGCTTCTATGCAA 58.285 47.619 0.00 0.00 34.99 4.08
3507 4032 3.285484 CACCCAAGAGCTTCTATGCAAT 58.715 45.455 0.00 0.00 34.99 3.56
3508 4033 3.698040 CACCCAAGAGCTTCTATGCAATT 59.302 43.478 0.00 0.00 34.99 2.32
3509 4034 3.950395 ACCCAAGAGCTTCTATGCAATTC 59.050 43.478 0.00 0.00 34.99 2.17
3510 4035 4.205587 CCCAAGAGCTTCTATGCAATTCT 58.794 43.478 0.00 0.00 34.99 2.40
3511 4036 4.643784 CCCAAGAGCTTCTATGCAATTCTT 59.356 41.667 0.00 0.00 34.99 2.52
3512 4037 5.126707 CCCAAGAGCTTCTATGCAATTCTTT 59.873 40.000 0.00 0.00 34.99 2.52
3513 4038 6.350780 CCCAAGAGCTTCTATGCAATTCTTTT 60.351 38.462 0.00 0.00 34.99 2.27
3514 4039 6.750963 CCAAGAGCTTCTATGCAATTCTTTTC 59.249 38.462 0.00 0.00 34.99 2.29
3515 4040 7.362747 CCAAGAGCTTCTATGCAATTCTTTTCT 60.363 37.037 0.00 0.00 34.99 2.52
3516 4041 7.700022 AGAGCTTCTATGCAATTCTTTTCTT 57.300 32.000 0.00 0.00 34.99 2.52
3517 4042 8.120140 AGAGCTTCTATGCAATTCTTTTCTTT 57.880 30.769 0.00 0.00 34.99 2.52
3518 4043 8.583296 AGAGCTTCTATGCAATTCTTTTCTTTT 58.417 29.630 0.00 0.00 34.99 2.27
3519 4044 8.754230 AGCTTCTATGCAATTCTTTTCTTTTC 57.246 30.769 0.00 0.00 34.99 2.29
3520 4045 7.540055 AGCTTCTATGCAATTCTTTTCTTTTCG 59.460 33.333 0.00 0.00 34.99 3.46
3521 4046 7.538678 GCTTCTATGCAATTCTTTTCTTTTCGA 59.461 33.333 0.00 0.00 0.00 3.71
3522 4047 9.398170 CTTCTATGCAATTCTTTTCTTTTCGAA 57.602 29.630 0.00 0.00 0.00 3.71
3523 4048 8.955061 TCTATGCAATTCTTTTCTTTTCGAAG 57.045 30.769 0.00 0.00 32.21 3.79
3524 4049 8.783093 TCTATGCAATTCTTTTCTTTTCGAAGA 58.217 29.630 0.00 0.00 32.21 2.87
3525 4050 7.864307 ATGCAATTCTTTTCTTTTCGAAGAG 57.136 32.000 9.36 9.36 38.43 2.85
3526 4051 6.208644 TGCAATTCTTTTCTTTTCGAAGAGG 58.791 36.000 15.04 0.21 38.43 3.69
3527 4052 5.631096 GCAATTCTTTTCTTTTCGAAGAGGG 59.369 40.000 15.04 4.71 38.43 4.30
3528 4053 5.966742 ATTCTTTTCTTTTCGAAGAGGGG 57.033 39.130 15.04 4.41 38.43 4.79
3529 4054 4.699925 TCTTTTCTTTTCGAAGAGGGGA 57.300 40.909 15.04 6.36 38.43 4.81
3530 4055 5.242795 TCTTTTCTTTTCGAAGAGGGGAT 57.757 39.130 15.04 0.00 38.43 3.85
3531 4056 6.368779 TCTTTTCTTTTCGAAGAGGGGATA 57.631 37.500 15.04 0.00 38.43 2.59
3532 4057 6.775708 TCTTTTCTTTTCGAAGAGGGGATAA 58.224 36.000 15.04 0.00 38.43 1.75
3533 4058 6.653740 TCTTTTCTTTTCGAAGAGGGGATAAC 59.346 38.462 15.04 0.00 38.43 1.89
3534 4059 4.482952 TCTTTTCGAAGAGGGGATAACC 57.517 45.455 15.04 0.00 38.43 2.85
3535 4060 5.805424 TTTCTTTTCGAAGAGGGGATAACCC 60.805 44.000 15.04 0.00 45.99 4.11
3544 4069 4.887615 GGATAACCCAGCCTCTGC 57.112 61.111 0.00 0.00 37.95 4.26
3545 4070 1.915228 GGATAACCCAGCCTCTGCA 59.085 57.895 0.00 0.00 41.13 4.41
3546 4071 0.475906 GGATAACCCAGCCTCTGCAT 59.524 55.000 0.00 0.00 41.13 3.96
3547 4072 1.544314 GGATAACCCAGCCTCTGCATC 60.544 57.143 0.00 0.00 41.13 3.91
3548 4073 1.141657 GATAACCCAGCCTCTGCATCA 59.858 52.381 0.00 0.00 41.13 3.07
3549 4074 1.216064 TAACCCAGCCTCTGCATCAT 58.784 50.000 0.00 0.00 41.13 2.45
3550 4075 1.216064 AACCCAGCCTCTGCATCATA 58.784 50.000 0.00 0.00 41.13 2.15
3551 4076 0.471617 ACCCAGCCTCTGCATCATAC 59.528 55.000 0.00 0.00 41.13 2.39
3552 4077 0.471191 CCCAGCCTCTGCATCATACA 59.529 55.000 0.00 0.00 41.13 2.29
3553 4078 1.134007 CCCAGCCTCTGCATCATACAA 60.134 52.381 0.00 0.00 41.13 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.223187 ACGAACATCGCCGAAAAGTT 58.777 45.000 0.00 0.00 45.12 2.66
11 12 1.416049 CACTGAACGAACATCGCCG 59.584 57.895 0.00 0.00 45.12 6.46
12 13 1.635663 CCCACTGAACGAACATCGCC 61.636 60.000 0.00 0.00 45.12 5.54
45 46 2.563261 TAGGCATCTCCGTAGTCGAT 57.437 50.000 0.00 0.00 40.77 3.59
71 72 6.814644 GCCACATCATTTTGAGATTGATGAAA 59.185 34.615 16.55 0.00 43.75 2.69
83 84 2.164219 ACTAAGCCGCCACATCATTTTG 59.836 45.455 0.00 0.00 0.00 2.44
86 87 1.210478 AGACTAAGCCGCCACATCATT 59.790 47.619 0.00 0.00 0.00 2.57
95 96 0.179100 TGAGCATCAGACTAAGCCGC 60.179 55.000 0.00 0.00 42.56 6.53
107 108 1.490574 ACCCTACCTCTGTGAGCATC 58.509 55.000 0.00 0.00 0.00 3.91
108 109 1.556911 CAACCCTACCTCTGTGAGCAT 59.443 52.381 0.00 0.00 0.00 3.79
109 110 0.976641 CAACCCTACCTCTGTGAGCA 59.023 55.000 0.00 0.00 0.00 4.26
110 111 0.977395 ACAACCCTACCTCTGTGAGC 59.023 55.000 0.00 0.00 0.00 4.26
111 112 1.971357 ACACAACCCTACCTCTGTGAG 59.029 52.381 7.97 0.00 41.35 3.51
254 258 4.263771 GGTGGAGAGGTAAAAAGGGATTGA 60.264 45.833 0.00 0.00 0.00 2.57
260 264 3.328050 ACAGAGGTGGAGAGGTAAAAAGG 59.672 47.826 0.00 0.00 0.00 3.11
281 285 4.666532 GTGGCGCGTGCTGACAAC 62.667 66.667 21.89 8.06 42.25 3.32
304 308 1.377202 GTGATGGCGTGTGGGTCAT 60.377 57.895 0.00 0.00 34.32 3.06
332 336 3.059051 TGATGGTGGTGGGAGATATCA 57.941 47.619 5.32 0.00 0.00 2.15
339 343 0.331278 GTTGGATGATGGTGGTGGGA 59.669 55.000 0.00 0.00 0.00 4.37
350 354 2.170397 ACGTGATGGCTATGTTGGATGA 59.830 45.455 0.00 0.00 0.00 2.92
400 405 1.586564 CGATGACCGGCGAAGAGAC 60.587 63.158 9.30 0.00 33.91 3.36
414 419 2.111878 GGGATGGTCAGGGCGATG 59.888 66.667 0.00 0.00 0.00 3.84
415 420 2.040464 AGGGATGGTCAGGGCGAT 60.040 61.111 0.00 0.00 0.00 4.58
416 421 2.764128 GAGGGATGGTCAGGGCGA 60.764 66.667 0.00 0.00 0.00 5.54
417 422 3.866582 GGAGGGATGGTCAGGGCG 61.867 72.222 0.00 0.00 0.00 6.13
418 423 1.863155 TTTGGAGGGATGGTCAGGGC 61.863 60.000 0.00 0.00 0.00 5.19
419 424 0.034089 GTTTGGAGGGATGGTCAGGG 60.034 60.000 0.00 0.00 0.00 4.45
420 425 0.698238 TGTTTGGAGGGATGGTCAGG 59.302 55.000 0.00 0.00 0.00 3.86
422 427 1.203001 GGTTGTTTGGAGGGATGGTCA 60.203 52.381 0.00 0.00 0.00 4.02
423 428 1.545841 GGTTGTTTGGAGGGATGGTC 58.454 55.000 0.00 0.00 0.00 4.02
444 450 1.137872 GTCGTCAATGCTGGAGGAGAT 59.862 52.381 0.00 0.00 30.64 2.75
448 454 1.450312 GGGTCGTCAATGCTGGAGG 60.450 63.158 0.00 0.00 0.00 4.30
473 479 1.071814 GGGTTGACAAGTGCGGGTA 59.928 57.895 0.00 0.00 0.00 3.69
519 846 1.813092 GCACCAAGCCGAGATGATGAT 60.813 52.381 0.00 0.00 37.23 2.45
539 866 3.126831 GTTATGGGACTGAGATGCGAAG 58.873 50.000 0.00 0.00 0.00 3.79
541 868 1.412710 GGTTATGGGACTGAGATGCGA 59.587 52.381 0.00 0.00 0.00 5.10
632 963 0.679640 TAAGAAATGGCGCCAGGTGG 60.680 55.000 35.36 0.00 38.53 4.61
706 1037 7.073342 ACGCCAAAAAGTCTTTAGATACATC 57.927 36.000 0.00 0.00 0.00 3.06
716 1047 7.390718 AGAATGTATCTAACGCCAAAAAGTCTT 59.609 33.333 0.00 0.00 36.32 3.01
773 1104 6.256975 CGATCCGATCTATTACCTCTGTCTAG 59.743 46.154 6.81 0.00 0.00 2.43
856 1190 1.660167 GGAACCGTATGGGCAAGTAC 58.340 55.000 5.82 0.00 40.62 2.73
857 1191 0.176219 CGGAACCGTATGGGCAAGTA 59.824 55.000 5.82 0.00 40.62 2.24
858 1192 1.078708 CGGAACCGTATGGGCAAGT 60.079 57.895 5.82 0.00 40.62 3.16
942 1276 2.036958 TGTTTGGAGTCTGTGTGTGG 57.963 50.000 0.00 0.00 0.00 4.17
998 1336 4.120331 GGTGCGGTGCTTCCATGC 62.120 66.667 0.00 0.00 35.57 4.06
1059 1397 1.064389 GGGGAAATGTCAGAGAAGGGG 60.064 57.143 0.00 0.00 0.00 4.79
1061 1399 2.040278 TGTGGGGAAATGTCAGAGAAGG 59.960 50.000 0.00 0.00 0.00 3.46
1119 1457 2.024751 GGAGGTGAAGGAGAGGTCTAGT 60.025 54.545 0.00 0.00 0.00 2.57
1122 1460 0.787084 TGGAGGTGAAGGAGAGGTCT 59.213 55.000 0.00 0.00 0.00 3.85
1470 1808 3.429141 GACTCGGCGAGGACGTGA 61.429 66.667 36.81 0.64 41.98 4.35
1644 1982 4.452733 GCGGCGTAGAACCTGGCT 62.453 66.667 9.37 0.00 0.00 4.75
1669 2007 2.421751 AGGTACTCTAGAGCGAGCAA 57.578 50.000 19.97 0.00 34.35 3.91
1680 2018 1.306642 CGAGCACGTGGAGGTACTCT 61.307 60.000 18.88 2.39 44.35 3.24
1854 2192 0.608582 AGAAGCACGACGGTAGGAGT 60.609 55.000 0.00 0.00 0.00 3.85
1899 2237 3.304764 CTCCTTCGCGTCGACGTCA 62.305 63.158 35.48 21.40 42.22 4.35
2193 2531 4.527583 CTCTCGAGCAGCCTGCCC 62.528 72.222 14.25 0.00 46.52 5.36
2469 2813 4.653888 CGGAAAACCCCCTGCCGT 62.654 66.667 0.00 0.00 37.35 5.68
2508 2852 1.147153 CTTCTTGGATCGGCCCTCC 59.853 63.158 11.39 11.39 34.97 4.30
2512 2856 0.035439 TTGGTCTTCTTGGATCGGCC 60.035 55.000 0.00 0.00 37.10 6.13
2588 2938 3.937079 CCACGAACCCTAACCAGATTAAC 59.063 47.826 0.00 0.00 0.00 2.01
2624 2981 0.970937 TCGCGATCCCTTCCACTCTT 60.971 55.000 3.71 0.00 0.00 2.85
2651 3009 1.229658 CTCCTCCCCACAACCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
2652 3010 2.301738 CCTCCTCCCCACAACCTCC 61.302 68.421 0.00 0.00 0.00 4.30
2657 3015 1.081092 CTCCTCCTCCTCCCCACAA 59.919 63.158 0.00 0.00 0.00 3.33
2662 3020 0.547954 ACAAACCTCCTCCTCCTCCC 60.548 60.000 0.00 0.00 0.00 4.30
2676 3039 6.308282 CCTCGATCTTTGTACAGACTACAAAC 59.692 42.308 0.00 0.00 41.00 2.93
2685 3048 2.561733 TCGCCTCGATCTTTGTACAG 57.438 50.000 0.00 0.00 0.00 2.74
2783 3151 7.831193 ACTACTAGTACCGTTATGAGAAAGGAA 59.169 37.037 0.00 0.00 0.00 3.36
2784 3152 7.341805 ACTACTAGTACCGTTATGAGAAAGGA 58.658 38.462 0.00 0.00 0.00 3.36
2785 3153 7.565323 ACTACTAGTACCGTTATGAGAAAGG 57.435 40.000 0.00 0.00 0.00 3.11
2786 3154 8.891720 AGAACTACTAGTACCGTTATGAGAAAG 58.108 37.037 7.34 0.00 0.00 2.62
2787 3155 8.798859 AGAACTACTAGTACCGTTATGAGAAA 57.201 34.615 7.34 0.00 0.00 2.52
2808 3176 9.178427 CACTGTAATATACTACCGCTAAAGAAC 57.822 37.037 0.00 0.00 0.00 3.01
2811 3179 7.088905 CCCACTGTAATATACTACCGCTAAAG 58.911 42.308 0.00 0.00 0.00 1.85
2812 3180 6.550854 ACCCACTGTAATATACTACCGCTAAA 59.449 38.462 0.00 0.00 0.00 1.85
2813 3181 6.070656 ACCCACTGTAATATACTACCGCTAA 58.929 40.000 0.00 0.00 0.00 3.09
2814 3182 5.634118 ACCCACTGTAATATACTACCGCTA 58.366 41.667 0.00 0.00 0.00 4.26
2815 3183 4.477249 ACCCACTGTAATATACTACCGCT 58.523 43.478 0.00 0.00 0.00 5.52
2816 3184 4.861102 ACCCACTGTAATATACTACCGC 57.139 45.455 0.00 0.00 0.00 5.68
2817 3185 7.446625 AGACTAACCCACTGTAATATACTACCG 59.553 40.741 0.00 0.00 0.00 4.02
2839 3352 3.505386 ACTGGTCAATCTGTCAGAGACT 58.495 45.455 17.27 0.46 31.75 3.24
2840 3353 3.951775 ACTGGTCAATCTGTCAGAGAC 57.048 47.619 8.82 10.63 31.75 3.36
2929 3442 5.111989 ACACAGTGTTCAAGATATCGGATG 58.888 41.667 0.00 0.00 0.00 3.51
2992 3508 8.553459 TGTTCAGAAGAGGAAATGTTAGAATC 57.447 34.615 0.00 0.00 0.00 2.52
3071 3590 2.739704 CGTACAGTGCATGTGGGCG 61.740 63.158 10.77 7.30 43.80 6.13
3136 3655 9.950496 AAGTTAGATGATGAGACACTGTTAATT 57.050 29.630 0.00 0.00 0.00 1.40
3181 3700 5.748630 CGAGGTTTCATGAAGAATCATCGTA 59.251 40.000 19.88 0.04 46.65 3.43
3186 3705 3.436704 GTGCGAGGTTTCATGAAGAATCA 59.563 43.478 8.41 1.32 40.57 2.57
3202 3721 0.733150 TCATCCTACTGACGTGCGAG 59.267 55.000 0.00 0.00 0.00 5.03
3203 3722 1.333931 GATCATCCTACTGACGTGCGA 59.666 52.381 0.00 0.00 0.00 5.10
3205 3724 2.860735 GTTGATCATCCTACTGACGTGC 59.139 50.000 0.00 0.00 0.00 5.34
3217 3736 5.180117 CGGGTATCAAATCTGGTTGATCATC 59.820 44.000 0.00 0.00 43.24 2.92
3224 3743 6.850752 AAAAATCGGGTATCAAATCTGGTT 57.149 33.333 0.00 0.00 0.00 3.67
3272 3797 5.766590 TCTAGATGAGTCCTAATCACACCA 58.233 41.667 0.00 0.00 0.00 4.17
3273 3798 6.266558 ACATCTAGATGAGTCCTAATCACACC 59.733 42.308 34.16 0.00 41.20 4.16
3274 3799 7.013750 TCACATCTAGATGAGTCCTAATCACAC 59.986 40.741 34.16 0.00 41.20 3.82
3275 3800 7.013750 GTCACATCTAGATGAGTCCTAATCACA 59.986 40.741 34.16 8.00 41.20 3.58
3276 3801 7.013750 TGTCACATCTAGATGAGTCCTAATCAC 59.986 40.741 34.16 19.10 41.20 3.06
3277 3802 7.062957 TGTCACATCTAGATGAGTCCTAATCA 58.937 38.462 34.16 17.19 41.20 2.57
3278 3803 7.517614 TGTCACATCTAGATGAGTCCTAATC 57.482 40.000 34.16 15.37 41.20 1.75
3279 3804 9.593565 TTATGTCACATCTAGATGAGTCCTAAT 57.406 33.333 34.16 19.85 41.20 1.73
3280 3805 8.851145 GTTATGTCACATCTAGATGAGTCCTAA 58.149 37.037 34.16 22.91 41.20 2.69
3281 3806 8.221251 AGTTATGTCACATCTAGATGAGTCCTA 58.779 37.037 34.16 19.40 41.20 2.94
3282 3807 7.066142 AGTTATGTCACATCTAGATGAGTCCT 58.934 38.462 34.16 20.26 41.20 3.85
3283 3808 7.283625 AGTTATGTCACATCTAGATGAGTCC 57.716 40.000 34.16 21.59 41.20 3.85
3284 3809 9.838975 CATAGTTATGTCACATCTAGATGAGTC 57.161 37.037 34.16 24.57 41.20 3.36
3285 3810 9.360901 ACATAGTTATGTCACATCTAGATGAGT 57.639 33.333 34.16 17.35 42.96 3.41
3319 3844 9.783081 TTGCTGATGTTATATGATGTCATACTT 57.217 29.630 4.93 0.00 41.15 2.24
3320 3845 9.783081 TTTGCTGATGTTATATGATGTCATACT 57.217 29.630 4.93 0.00 41.15 2.12
3392 3917 9.251440 AGTGTCACATCTAACTAGTTTACCATA 57.749 33.333 14.49 0.00 0.00 2.74
3393 3918 8.135382 AGTGTCACATCTAACTAGTTTACCAT 57.865 34.615 14.49 0.00 0.00 3.55
3394 3919 7.450634 AGAGTGTCACATCTAACTAGTTTACCA 59.549 37.037 14.49 0.00 0.00 3.25
3395 3920 7.828712 AGAGTGTCACATCTAACTAGTTTACC 58.171 38.462 14.49 0.00 0.00 2.85
3400 3925 9.915629 CTTTTAAGAGTGTCACATCTAACTAGT 57.084 33.333 5.62 0.00 0.00 2.57
3402 3927 9.909644 GTCTTTTAAGAGTGTCACATCTAACTA 57.090 33.333 5.62 0.00 35.32 2.24
3403 3928 7.595502 CGTCTTTTAAGAGTGTCACATCTAACT 59.404 37.037 5.62 0.00 35.32 2.24
3404 3929 7.619571 GCGTCTTTTAAGAGTGTCACATCTAAC 60.620 40.741 5.62 0.00 35.32 2.34
3405 3930 6.365247 GCGTCTTTTAAGAGTGTCACATCTAA 59.635 38.462 5.62 0.00 35.32 2.10
3406 3931 5.862323 GCGTCTTTTAAGAGTGTCACATCTA 59.138 40.000 5.62 0.00 35.32 1.98
3407 3932 4.686554 GCGTCTTTTAAGAGTGTCACATCT 59.313 41.667 5.62 2.68 35.32 2.90
3408 3933 4.143094 GGCGTCTTTTAAGAGTGTCACATC 60.143 45.833 5.62 0.30 35.32 3.06
3409 3934 3.746492 GGCGTCTTTTAAGAGTGTCACAT 59.254 43.478 5.62 0.00 35.32 3.21
3410 3935 3.128349 GGCGTCTTTTAAGAGTGTCACA 58.872 45.455 5.62 0.00 35.32 3.58
3411 3936 3.391049 AGGCGTCTTTTAAGAGTGTCAC 58.609 45.455 0.00 0.00 35.32 3.67
3412 3937 3.746045 AGGCGTCTTTTAAGAGTGTCA 57.254 42.857 0.00 0.00 35.32 3.58
3413 3938 5.056894 TCTAGGCGTCTTTTAAGAGTGTC 57.943 43.478 0.00 0.00 35.32 3.67
3414 3939 5.047235 ACATCTAGGCGTCTTTTAAGAGTGT 60.047 40.000 0.00 0.00 35.32 3.55
3415 3940 5.289675 CACATCTAGGCGTCTTTTAAGAGTG 59.710 44.000 0.00 0.00 35.32 3.51
3416 3941 5.185249 TCACATCTAGGCGTCTTTTAAGAGT 59.815 40.000 0.00 0.00 35.32 3.24
3417 3942 5.651530 TCACATCTAGGCGTCTTTTAAGAG 58.348 41.667 0.00 0.00 35.32 2.85
3418 3943 5.654603 TCACATCTAGGCGTCTTTTAAGA 57.345 39.130 0.00 0.00 0.00 2.10
3419 3944 6.910536 ATTCACATCTAGGCGTCTTTTAAG 57.089 37.500 0.00 0.00 0.00 1.85
3420 3945 8.038944 ACTAATTCACATCTAGGCGTCTTTTAA 58.961 33.333 0.00 0.00 0.00 1.52
3421 3946 7.553334 ACTAATTCACATCTAGGCGTCTTTTA 58.447 34.615 0.00 0.00 0.00 1.52
3422 3947 6.407202 ACTAATTCACATCTAGGCGTCTTTT 58.593 36.000 0.00 0.00 0.00 2.27
3423 3948 5.978814 ACTAATTCACATCTAGGCGTCTTT 58.021 37.500 0.00 0.00 0.00 2.52
3424 3949 5.127194 TGACTAATTCACATCTAGGCGTCTT 59.873 40.000 0.00 0.00 0.00 3.01
3425 3950 4.645136 TGACTAATTCACATCTAGGCGTCT 59.355 41.667 0.00 0.00 0.00 4.18
3426 3951 4.933330 TGACTAATTCACATCTAGGCGTC 58.067 43.478 0.00 0.00 0.00 5.19
3427 3952 5.537300 ATGACTAATTCACATCTAGGCGT 57.463 39.130 0.00 0.00 36.92 5.68
3428 3953 6.145209 CAGAATGACTAATTCACATCTAGGCG 59.855 42.308 1.30 0.00 46.21 5.52
3429 3954 6.989169 ACAGAATGACTAATTCACATCTAGGC 59.011 38.462 1.30 0.00 46.21 3.93
3459 3984 9.938280 CCCGTGAATCCTATATGAATAGTAAAA 57.062 33.333 0.00 0.00 34.36 1.52
3460 3985 8.038944 GCCCGTGAATCCTATATGAATAGTAAA 58.961 37.037 0.00 0.00 34.36 2.01
3461 3986 7.179516 TGCCCGTGAATCCTATATGAATAGTAA 59.820 37.037 0.00 0.00 34.36 2.24
3462 3987 6.666113 TGCCCGTGAATCCTATATGAATAGTA 59.334 38.462 0.00 0.00 34.36 1.82
3463 3988 5.483937 TGCCCGTGAATCCTATATGAATAGT 59.516 40.000 0.00 0.00 34.36 2.12
3464 3989 5.812642 GTGCCCGTGAATCCTATATGAATAG 59.187 44.000 0.00 0.00 35.73 1.73
3465 3990 5.338056 GGTGCCCGTGAATCCTATATGAATA 60.338 44.000 0.00 0.00 0.00 1.75
3466 3991 4.565652 GGTGCCCGTGAATCCTATATGAAT 60.566 45.833 0.00 0.00 0.00 2.57
3467 3992 3.244422 GGTGCCCGTGAATCCTATATGAA 60.244 47.826 0.00 0.00 0.00 2.57
3468 3993 2.301870 GGTGCCCGTGAATCCTATATGA 59.698 50.000 0.00 0.00 0.00 2.15
3469 3994 2.615493 GGGTGCCCGTGAATCCTATATG 60.615 54.545 0.00 0.00 0.00 1.78
3470 3995 1.628846 GGGTGCCCGTGAATCCTATAT 59.371 52.381 0.00 0.00 0.00 0.86
3471 3996 1.053424 GGGTGCCCGTGAATCCTATA 58.947 55.000 0.00 0.00 0.00 1.31
3472 3997 0.986019 TGGGTGCCCGTGAATCCTAT 60.986 55.000 2.44 0.00 39.42 2.57
3473 3998 1.202099 TTGGGTGCCCGTGAATCCTA 61.202 55.000 2.44 0.00 39.42 2.94
3474 3999 2.484287 CTTGGGTGCCCGTGAATCCT 62.484 60.000 2.44 0.00 39.42 3.24
3475 4000 2.034999 TTGGGTGCCCGTGAATCC 59.965 61.111 2.44 0.00 39.42 3.01
3476 4001 1.002624 TCTTGGGTGCCCGTGAATC 60.003 57.895 2.44 0.00 39.42 2.52
3477 4002 1.002134 CTCTTGGGTGCCCGTGAAT 60.002 57.895 2.44 0.00 39.42 2.57
3478 4003 2.429930 CTCTTGGGTGCCCGTGAA 59.570 61.111 2.44 0.00 39.42 3.18
3479 4004 4.329545 GCTCTTGGGTGCCCGTGA 62.330 66.667 2.44 2.70 39.42 4.35
3480 4005 3.850098 AAGCTCTTGGGTGCCCGTG 62.850 63.158 2.44 0.00 39.42 4.94
3481 4006 3.553095 GAAGCTCTTGGGTGCCCGT 62.553 63.158 2.44 0.00 39.42 5.28
3482 4007 1.899437 TAGAAGCTCTTGGGTGCCCG 61.899 60.000 2.44 0.00 39.42 6.13
3483 4008 0.548510 ATAGAAGCTCTTGGGTGCCC 59.451 55.000 0.00 0.00 32.98 5.36
3484 4009 1.673168 CATAGAAGCTCTTGGGTGCC 58.327 55.000 0.00 0.00 32.98 5.01
3485 4010 1.020437 GCATAGAAGCTCTTGGGTGC 58.980 55.000 0.00 0.00 0.00 5.01
3486 4011 2.408271 TGCATAGAAGCTCTTGGGTG 57.592 50.000 0.00 0.00 34.99 4.61
3487 4012 3.659183 ATTGCATAGAAGCTCTTGGGT 57.341 42.857 0.00 0.00 34.99 4.51
3488 4013 4.205587 AGAATTGCATAGAAGCTCTTGGG 58.794 43.478 0.00 0.00 34.99 4.12
3489 4014 5.831702 AAGAATTGCATAGAAGCTCTTGG 57.168 39.130 0.00 0.00 34.99 3.61
3490 4015 7.536855 AGAAAAGAATTGCATAGAAGCTCTTG 58.463 34.615 0.00 0.00 30.11 3.02
3491 4016 7.700022 AGAAAAGAATTGCATAGAAGCTCTT 57.300 32.000 0.00 0.00 30.64 2.85
3492 4017 7.700022 AAGAAAAGAATTGCATAGAAGCTCT 57.300 32.000 0.00 0.00 34.99 4.09
3493 4018 8.754230 AAAAGAAAAGAATTGCATAGAAGCTC 57.246 30.769 0.00 0.00 34.99 4.09
3494 4019 7.540055 CGAAAAGAAAAGAATTGCATAGAAGCT 59.460 33.333 0.00 0.00 34.99 3.74
3495 4020 7.538678 TCGAAAAGAAAAGAATTGCATAGAAGC 59.461 33.333 0.00 0.00 0.00 3.86
3496 4021 8.955061 TCGAAAAGAAAAGAATTGCATAGAAG 57.045 30.769 0.00 0.00 0.00 2.85
3497 4022 9.398170 CTTCGAAAAGAAAAGAATTGCATAGAA 57.602 29.630 0.00 0.00 38.57 2.10
3498 4023 8.783093 TCTTCGAAAAGAAAAGAATTGCATAGA 58.217 29.630 0.00 0.00 38.58 1.98
3499 4024 8.955061 TCTTCGAAAAGAAAAGAATTGCATAG 57.045 30.769 0.00 0.00 38.58 2.23
3500 4025 8.023128 CCTCTTCGAAAAGAAAAGAATTGCATA 58.977 33.333 0.00 0.00 40.95 3.14
3501 4026 6.865205 CCTCTTCGAAAAGAAAAGAATTGCAT 59.135 34.615 0.00 0.00 40.95 3.96
3502 4027 6.208644 CCTCTTCGAAAAGAAAAGAATTGCA 58.791 36.000 0.00 0.00 40.95 4.08
3503 4028 5.631096 CCCTCTTCGAAAAGAAAAGAATTGC 59.369 40.000 0.00 0.00 40.95 3.56
3504 4029 6.016276 TCCCCTCTTCGAAAAGAAAAGAATTG 60.016 38.462 0.00 0.00 40.95 2.32
3505 4030 6.068670 TCCCCTCTTCGAAAAGAAAAGAATT 58.931 36.000 0.00 0.00 40.95 2.17
3506 4031 5.631119 TCCCCTCTTCGAAAAGAAAAGAAT 58.369 37.500 0.00 0.00 40.95 2.40
3507 4032 5.043737 TCCCCTCTTCGAAAAGAAAAGAA 57.956 39.130 0.00 0.00 40.95 2.52
3508 4033 4.699925 TCCCCTCTTCGAAAAGAAAAGA 57.300 40.909 0.00 0.00 40.95 2.52
3509 4034 6.127980 GGTTATCCCCTCTTCGAAAAGAAAAG 60.128 42.308 0.00 0.00 40.95 2.27
3510 4035 5.708697 GGTTATCCCCTCTTCGAAAAGAAAA 59.291 40.000 0.00 0.00 40.95 2.29
3511 4036 5.250982 GGTTATCCCCTCTTCGAAAAGAAA 58.749 41.667 0.00 0.00 40.95 2.52
3512 4037 4.840271 GGTTATCCCCTCTTCGAAAAGAA 58.160 43.478 0.00 0.00 40.95 2.52
3513 4038 4.482952 GGTTATCCCCTCTTCGAAAAGA 57.517 45.455 0.00 0.00 39.22 2.52
3526 4051 1.635817 TGCAGAGGCTGGGTTATCCC 61.636 60.000 1.42 1.42 45.56 3.85
3527 4052 0.475906 ATGCAGAGGCTGGGTTATCC 59.524 55.000 0.00 0.00 41.91 2.59
3528 4053 1.141657 TGATGCAGAGGCTGGGTTATC 59.858 52.381 0.00 0.00 41.91 1.75
3529 4054 1.216064 TGATGCAGAGGCTGGGTTAT 58.784 50.000 0.00 0.00 41.91 1.89
3530 4055 1.216064 ATGATGCAGAGGCTGGGTTA 58.784 50.000 0.00 0.00 41.91 2.85
3531 4056 1.133976 GTATGATGCAGAGGCTGGGTT 60.134 52.381 0.00 0.00 41.91 4.11
3532 4057 0.471617 GTATGATGCAGAGGCTGGGT 59.528 55.000 0.00 0.00 41.91 4.51
3533 4058 0.471191 TGTATGATGCAGAGGCTGGG 59.529 55.000 0.00 0.00 41.91 4.45
3534 4059 2.336945 TTGTATGATGCAGAGGCTGG 57.663 50.000 0.00 0.00 41.91 4.85


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

AutoCloner maintained by Alex Coulton.