Multiple sequence alignment - TraesCS1D01G120100

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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 TraesCS1D01G120100 chr1D 100.000 3512 0 0 1 3512 118509480 118512991 0.000000e+00 6486.0
1 TraesCS1D01G120100 chr1D 89.862 217 20 2 3297 3512 325705360 325705145 9.600000e-71 278.0
2 TraesCS1D01G120100 chr1B 96.688 1993 46 11 745 2726 180405569 180407552 0.000000e+00 3297.0
3 TraesCS1D01G120100 chr1B 87.967 723 71 5 3 719 180403989 180404701 0.000000e+00 839.0
4 TraesCS1D01G120100 chr1B 89.066 439 38 7 2863 3297 180411758 180412190 1.430000e-148 536.0
5 TraesCS1D01G120100 chr1A 94.323 2149 75 13 819 2928 130149030 130151170 0.000000e+00 3249.0
6 TraesCS1D01G120100 chr1A 91.026 312 27 1 2987 3297 130151358 130151669 1.510000e-113 420.0
7 TraesCS1D01G120100 chr3D 72.776 1484 284 88 1045 2491 75962138 75963538 3.290000e-105 392.0
8 TraesCS1D01G120100 chr3D 77.487 382 76 8 2116 2491 75947852 75948229 1.640000e-53 220.0
9 TraesCS1D01G120100 chr7B 79.566 553 99 8 183 723 707963344 707963894 1.980000e-102 383.0
10 TraesCS1D01G120100 chr7B 78.756 579 104 11 158 724 632802861 632802290 1.540000e-98 370.0
11 TraesCS1D01G120100 chr7B 78.339 554 99 16 185 723 736089192 736088645 4.340000e-89 339.0
12 TraesCS1D01G120100 chr2D 78.856 577 104 10 157 720 575827298 575827869 1.190000e-99 374.0
13 TraesCS1D01G120100 chr2D 90.367 218 19 2 3296 3512 439285401 439285185 5.740000e-73 285.0
14 TraesCS1D01G120100 chr5D 79.061 554 96 14 183 723 477991423 477991969 2.580000e-96 363.0
15 TraesCS1D01G120100 chr5D 78.481 553 104 8 183 723 481520402 481519853 7.220000e-92 348.0
16 TraesCS1D01G120100 chr5B 78.237 556 100 13 183 722 618466514 618467064 1.560000e-88 337.0
17 TraesCS1D01G120100 chr5B 77.838 555 103 17 183 723 446012911 446012363 3.380000e-85 326.0
18 TraesCS1D01G120100 chr5B 90.367 218 18 3 3297 3512 208861657 208861873 2.060000e-72 283.0
19 TraesCS1D01G120100 chr5B 89.862 217 21 1 3297 3512 286076099 286076315 9.600000e-71 278.0
20 TraesCS1D01G120100 chr4A 91.284 218 18 1 3296 3512 344044430 344044647 2.650000e-76 296.0
21 TraesCS1D01G120100 chr7D 90.826 218 17 3 3297 3512 236859895 236859679 4.440000e-74 289.0
22 TraesCS1D01G120100 chr3A 90.323 217 20 1 3297 3512 207773650 207773866 2.060000e-72 283.0
23 TraesCS1D01G120100 chr3A 78.820 373 70 7 2123 2491 90365158 90365525 3.500000e-60 243.0
24 TraesCS1D01G120100 chr3A 77.632 380 76 7 2116 2491 90294357 90294731 4.560000e-54 222.0
25 TraesCS1D01G120100 chr6D 90.323 217 18 3 3298 3512 338690615 338690400 7.420000e-72 281.0
26 TraesCS1D01G120100 chr6D 75.000 192 46 2 1856 2046 3038167 3037977 1.740000e-13 87.9
27 TraesCS1D01G120100 chr6D 89.231 65 7 0 1045 1109 3040175 3040111 8.080000e-12 82.4
28 TraesCS1D01G120100 chr6D 86.207 58 5 3 3218 3274 68072351 68072296 3.790000e-05 60.2
29 TraesCS1D01G120100 chr4D 89.862 217 21 1 3297 3512 343017046 343017262 9.600000e-71 278.0
30 TraesCS1D01G120100 chr2B 88.532 218 19 3 2420 2635 135790028 135790241 3.480000e-65 259.0
31 TraesCS1D01G120100 chr3B 77.895 380 75 7 2116 2491 123034374 123034748 9.810000e-56 228.0
32 TraesCS1D01G120100 chr3B 81.641 256 47 0 2116 2371 122827322 122827577 2.750000e-51 213.0
33 TraesCS1D01G120100 chr7A 80.000 255 42 8 2127 2378 543432112 543432360 2.790000e-41 180.0
34 TraesCS1D01G120100 chr6B 71.429 483 86 40 1045 1513 6213362 6212918 2.910000e-11 80.5


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 TraesCS1D01G120100 chr1D 118509480 118512991 3511 False 6486.0 6486 100.0000 1 3512 1 chr1D.!!$F1 3511
1 TraesCS1D01G120100 chr1B 180403989 180407552 3563 False 2068.0 3297 92.3275 3 2726 2 chr1B.!!$F2 2723
2 TraesCS1D01G120100 chr1A 130149030 130151669 2639 False 1834.5 3249 92.6745 819 3297 2 chr1A.!!$F1 2478
3 TraesCS1D01G120100 chr3D 75962138 75963538 1400 False 392.0 392 72.7760 1045 2491 1 chr3D.!!$F2 1446
4 TraesCS1D01G120100 chr7B 707963344 707963894 550 False 383.0 383 79.5660 183 723 1 chr7B.!!$F1 540
5 TraesCS1D01G120100 chr7B 632802290 632802861 571 True 370.0 370 78.7560 158 724 1 chr7B.!!$R1 566
6 TraesCS1D01G120100 chr7B 736088645 736089192 547 True 339.0 339 78.3390 185 723 1 chr7B.!!$R2 538
7 TraesCS1D01G120100 chr2D 575827298 575827869 571 False 374.0 374 78.8560 157 720 1 chr2D.!!$F1 563
8 TraesCS1D01G120100 chr5D 477991423 477991969 546 False 363.0 363 79.0610 183 723 1 chr5D.!!$F1 540
9 TraesCS1D01G120100 chr5D 481519853 481520402 549 True 348.0 348 78.4810 183 723 1 chr5D.!!$R1 540
10 TraesCS1D01G120100 chr5B 618466514 618467064 550 False 337.0 337 78.2370 183 722 1 chr5B.!!$F3 539
11 TraesCS1D01G120100 chr5B 446012363 446012911 548 True 326.0 326 77.8380 183 723 1 chr5B.!!$R1 540

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
742 1595 0.107214 ACAATCCACGTGCATAGGGG 60.107 55.0 10.91 7.07 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2687 3608 0.31904 CATACATCGCCCTGTCCTCG 60.319 60.0 0.0 0.0 0.0 4.63 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
27 28 2.455032 TGAAAATTTTCACGCACGTGG 58.545 42.857 26.01 10.05 45.43 4.94
142 144 0.535553 GGCACCACCGACCTAACAAA 60.536 55.000 0.00 0.00 0.00 2.83
149 151 3.992427 CCACCGACCTAACAAAACTAGAC 59.008 47.826 0.00 0.00 0.00 2.59
169 171 1.882623 CTGAAAAGTCACTTGGCTCCC 59.117 52.381 0.00 0.00 0.00 4.30
233 235 3.255149 CACCTTTTGAGCTGAGCTTGATT 59.745 43.478 9.00 0.00 39.88 2.57
247 249 4.785301 AGCTTGATTTGGCTCTATTGCTA 58.215 39.130 0.00 0.00 32.98 3.49
253 255 8.696043 TTGATTTGGCTCTATTGCTAATATGT 57.304 30.769 0.00 0.00 33.62 2.29
357 359 3.767673 ACGCCATCAAACTCTAGACCTAA 59.232 43.478 0.00 0.00 0.00 2.69
426 429 2.989253 GAACCCCAAACCCCGCAG 60.989 66.667 0.00 0.00 0.00 5.18
439 442 0.686789 CCCGCAGATGATCCACCATA 59.313 55.000 0.00 0.00 0.00 2.74
558 567 2.285083 CGAAGAAACAACTCCACCACA 58.715 47.619 0.00 0.00 0.00 4.17
561 570 3.644966 AGAAACAACTCCACCACAAGA 57.355 42.857 0.00 0.00 0.00 3.02
568 577 0.606401 CTCCACCACAAGAATGCCGT 60.606 55.000 0.00 0.00 0.00 5.68
591 600 3.259064 GCTGCCACGTCATTCTTACTTA 58.741 45.455 0.00 0.00 0.00 2.24
685 705 2.970639 CACTCCCATCACCGTCGT 59.029 61.111 0.00 0.00 0.00 4.34
706 726 3.604627 GTCGAAGTCAAGACGATGAAGAC 59.395 47.826 0.00 0.00 38.27 3.01
708 728 3.611766 CGAAGTCAAGACGATGAAGACCA 60.612 47.826 0.00 0.00 36.20 4.02
713 735 5.007724 AGTCAAGACGATGAAGACCAAAAAC 59.992 40.000 0.00 0.00 36.20 2.43
728 1581 7.937649 AGACCAAAAACCTAAACTACACAATC 58.062 34.615 0.00 0.00 0.00 2.67
732 1585 5.934935 AAACCTAAACTACACAATCCACG 57.065 39.130 0.00 0.00 0.00 4.94
740 1593 1.737838 ACACAATCCACGTGCATAGG 58.262 50.000 10.91 0.00 37.93 2.57
741 1594 1.016627 CACAATCCACGTGCATAGGG 58.983 55.000 10.91 0.00 0.00 3.53
742 1595 0.107214 ACAATCCACGTGCATAGGGG 60.107 55.000 10.91 7.07 0.00 4.79
743 1596 0.819259 CAATCCACGTGCATAGGGGG 60.819 60.000 10.91 5.55 36.57 5.40
744 1597 1.279025 AATCCACGTGCATAGGGGGT 61.279 55.000 10.91 3.56 36.62 4.95
745 1598 1.696097 ATCCACGTGCATAGGGGGTC 61.696 60.000 10.91 0.00 36.62 4.46
746 1599 2.202878 CACGTGCATAGGGGGTCG 60.203 66.667 0.82 0.00 0.00 4.79
800 1665 3.441290 CGGCGAACGGACTCTCCT 61.441 66.667 0.00 0.00 39.42 3.69
803 1668 1.064458 GCGAACGGACTCTCCTAGC 59.936 63.158 0.00 0.00 33.30 3.42
805 1670 1.728672 GAACGGACTCTCCTAGCGG 59.271 63.158 0.00 0.00 33.30 5.52
806 1671 2.339100 GAACGGACTCTCCTAGCGGC 62.339 65.000 0.00 0.00 33.30 6.53
809 1674 3.597728 GACTCTCCTAGCGGCGGG 61.598 72.222 9.78 0.71 0.00 6.13
810 1675 4.124943 ACTCTCCTAGCGGCGGGA 62.125 66.667 9.78 14.83 0.00 5.14
948 1814 2.671682 GCTCCCACTTCCACTCCC 59.328 66.667 0.00 0.00 0.00 4.30
951 1817 0.543749 CTCCCACTTCCACTCCCATC 59.456 60.000 0.00 0.00 0.00 3.51
1722 2600 2.364448 GACTCCGAGAAGCCCCCT 60.364 66.667 1.33 0.00 0.00 4.79
1749 2627 2.372690 CCTCGCCAACACGTTCGAG 61.373 63.158 11.87 11.87 45.50 4.04
1777 2655 2.816958 CTGATGCGCTGGCTTCGT 60.817 61.111 9.73 0.00 44.06 3.85
2016 2900 0.834687 AGTCCAACAGGCCGTTCCTA 60.835 55.000 9.57 0.00 45.52 2.94
2061 2945 1.218316 GGACAAGGACGAAGGCGAT 59.782 57.895 0.00 0.00 41.64 4.58
2379 3290 0.033503 TGAGGAGGTGCGTGGAGATA 60.034 55.000 0.00 0.00 0.00 1.98
2574 3491 2.895372 GAGTGTAATGCCGCGGGG 60.895 66.667 29.38 15.40 0.00 5.73
2663 3580 2.732366 CTTATCGTGTCCGGATGTCTG 58.268 52.381 7.81 0.00 33.95 3.51
2752 3698 9.569122 ACTAGCTTTGTTTGTCTAAAAAGGATA 57.431 29.630 0.00 0.00 0.00 2.59
2787 3733 3.498397 CGTACTTTGATGCACTCCAAGTT 59.502 43.478 15.58 4.53 39.73 2.66
2799 3745 4.518970 GCACTCCAAGTTGGTTCTTAATCA 59.481 41.667 21.35 0.00 39.03 2.57
2807 3753 6.668541 AGTTGGTTCTTAATCATGTCATCG 57.331 37.500 0.00 0.00 0.00 3.84
2810 3756 4.080582 TGGTTCTTAATCATGTCATCGGGT 60.081 41.667 0.00 0.00 0.00 5.28
2818 3764 4.590850 TCATGTCATCGGGTGATAGAAG 57.409 45.455 0.00 0.00 39.48 2.85
2823 3769 1.681793 CATCGGGTGATAGAAGGTCGT 59.318 52.381 0.00 0.00 32.18 4.34
2828 3774 3.370061 CGGGTGATAGAAGGTCGTTTTTC 59.630 47.826 0.00 0.00 0.00 2.29
2849 3795 9.748708 TTTTTCCTAATGCACATCTAAATATGC 57.251 29.630 0.00 0.00 38.59 3.14
2852 3798 9.791801 TTCCTAATGCACATCTAAATATGCTAA 57.208 29.630 0.00 0.00 38.90 3.09
2853 3799 9.440773 TCCTAATGCACATCTAAATATGCTAAG 57.559 33.333 0.00 0.00 38.90 2.18
2854 3800 9.224267 CCTAATGCACATCTAAATATGCTAAGT 57.776 33.333 0.00 0.00 38.90 2.24
2858 3804 8.818141 TGCACATCTAAATATGCTAAGTCTAC 57.182 34.615 0.00 0.00 38.90 2.59
2865 3823 2.586258 ATGCTAAGTCTACAGCCGTG 57.414 50.000 4.39 0.00 36.95 4.94
2871 3829 0.038159 AGTCTACAGCCGTGCACTTC 60.038 55.000 16.19 6.18 0.00 3.01
2878 3836 2.908073 GCCGTGCACTTCAAGTGGG 61.908 63.158 19.35 12.65 46.01 4.61
2879 3837 1.525995 CCGTGCACTTCAAGTGGGT 60.526 57.895 19.35 0.00 46.01 4.51
2880 3838 1.101049 CCGTGCACTTCAAGTGGGTT 61.101 55.000 19.35 0.00 46.01 4.11
2881 3839 0.307760 CGTGCACTTCAAGTGGGTTC 59.692 55.000 19.35 2.89 46.01 3.62
2882 3840 1.680338 GTGCACTTCAAGTGGGTTCT 58.320 50.000 19.35 0.00 46.01 3.01
2883 3841 2.024414 GTGCACTTCAAGTGGGTTCTT 58.976 47.619 19.35 0.00 46.01 2.52
2884 3842 2.427095 GTGCACTTCAAGTGGGTTCTTT 59.573 45.455 19.35 0.00 46.01 2.52
2885 3843 3.630312 GTGCACTTCAAGTGGGTTCTTTA 59.370 43.478 19.35 0.00 46.01 1.85
2886 3844 4.097286 GTGCACTTCAAGTGGGTTCTTTAA 59.903 41.667 19.35 0.00 46.01 1.52
2887 3845 4.338118 TGCACTTCAAGTGGGTTCTTTAAG 59.662 41.667 19.35 0.00 46.01 1.85
2914 3872 2.189499 CAGCAAGCTATTCCGGCCC 61.189 63.158 0.00 0.00 0.00 5.80
2915 3873 2.193248 GCAAGCTATTCCGGCCCT 59.807 61.111 0.00 0.00 0.00 5.19
2920 3878 3.335579 CAAGCTATTCCGGCCCTTATAC 58.664 50.000 0.00 0.00 0.00 1.47
2928 3886 3.034343 GCCCTTATACGTCCGCGC 61.034 66.667 0.00 0.00 42.83 6.86
2930 3888 1.947642 CCCTTATACGTCCGCGCAC 60.948 63.158 8.75 0.00 42.83 5.34
2933 3891 1.477030 CTTATACGTCCGCGCACACC 61.477 60.000 8.75 0.00 42.83 4.16
2942 3900 4.107051 GCGCACACCACTGGATGC 62.107 66.667 0.30 15.31 35.90 3.91
2945 3903 2.680913 GCACACCACTGGATGCGTC 61.681 63.158 0.71 0.00 31.44 5.19
2948 3906 2.046892 ACCACTGGATGCGTCTGC 60.047 61.111 5.77 0.00 43.20 4.26
2958 3916 3.106407 GCGTCTGCGGACACTGAC 61.106 66.667 24.91 5.32 42.21 3.51
2959 3917 2.645567 CGTCTGCGGACACTGACT 59.354 61.111 24.91 0.00 42.21 3.41
2960 3918 1.873863 CGTCTGCGGACACTGACTA 59.126 57.895 24.91 0.00 42.21 2.59
2961 3919 0.454620 CGTCTGCGGACACTGACTAC 60.455 60.000 24.91 0.00 42.21 2.73
2962 3920 0.882474 GTCTGCGGACACTGACTACT 59.118 55.000 21.02 0.00 41.75 2.57
2963 3921 0.881796 TCTGCGGACACTGACTACTG 59.118 55.000 0.00 0.00 0.00 2.74
2964 3922 0.881796 CTGCGGACACTGACTACTGA 59.118 55.000 0.00 0.00 0.00 3.41
2965 3923 0.596577 TGCGGACACTGACTACTGAC 59.403 55.000 0.00 0.00 0.00 3.51
2967 3925 1.401670 GCGGACACTGACTACTGACTG 60.402 57.143 0.00 0.00 0.00 3.51
2968 3926 2.152016 CGGACACTGACTACTGACTGA 58.848 52.381 0.00 0.00 0.00 3.41
2970 3928 3.181505 CGGACACTGACTACTGACTGATC 60.182 52.174 0.00 0.00 0.00 2.92
2971 3929 3.759086 GGACACTGACTACTGACTGATCA 59.241 47.826 0.00 0.00 0.00 2.92
2972 3930 4.218635 GGACACTGACTACTGACTGATCAA 59.781 45.833 0.00 0.00 33.30 2.57
2973 3931 5.105554 GGACACTGACTACTGACTGATCAAT 60.106 44.000 0.00 0.00 33.30 2.57
2974 3932 5.960113 ACACTGACTACTGACTGATCAATC 58.040 41.667 0.00 0.00 33.30 2.67
2976 3934 5.126869 CACTGACTACTGACTGATCAATCCT 59.873 44.000 1.00 0.00 33.30 3.24
2977 3935 5.359576 ACTGACTACTGACTGATCAATCCTC 59.640 44.000 1.00 0.00 33.30 3.71
2979 3937 5.716703 TGACTACTGACTGATCAATCCTCAA 59.283 40.000 1.00 0.00 33.30 3.02
2980 3938 6.211384 TGACTACTGACTGATCAATCCTCAAA 59.789 38.462 1.00 0.00 33.30 2.69
2981 3939 7.093156 TGACTACTGACTGATCAATCCTCAAAT 60.093 37.037 1.00 0.00 33.30 2.32
2982 3940 7.046652 ACTACTGACTGATCAATCCTCAAATG 58.953 38.462 1.00 0.00 33.30 2.32
2983 3941 4.639310 ACTGACTGATCAATCCTCAAATGC 59.361 41.667 1.00 0.00 33.30 3.56
2985 3943 4.880120 TGACTGATCAATCCTCAAATGCTC 59.120 41.667 1.00 0.00 0.00 4.26
3021 4108 6.586344 CACCTCATGTCACCTAAATCTACAT 58.414 40.000 0.00 0.00 0.00 2.29
3026 4113 9.770097 CTCATGTCACCTAAATCTACATTATGT 57.230 33.333 2.58 2.58 0.00 2.29
3071 4159 9.675464 ACTATCGATGAAACCTAAAATAAACCA 57.325 29.630 8.54 0.00 0.00 3.67
3093 4181 8.553459 ACCATATAGATCATCAACGAAATTCC 57.447 34.615 0.00 0.00 0.00 3.01
3094 4182 8.156820 ACCATATAGATCATCAACGAAATTCCA 58.843 33.333 0.00 0.00 0.00 3.53
3139 4227 3.261981 ACCAGCCGGTAGTTAATTCAG 57.738 47.619 1.90 0.00 46.71 3.02
3165 4253 8.970691 ATCAAAATACACAGTTTAAGCATCAC 57.029 30.769 0.00 0.00 0.00 3.06
3194 4282 2.098117 CCGGCAAATGGACAGAGATTTC 59.902 50.000 0.00 0.00 0.00 2.17
3239 4327 1.467678 CGAAGATGGAGAGGGCCGAT 61.468 60.000 0.00 0.00 0.00 4.18
3247 4335 1.587547 GAGAGGGCCGATGAATTCAC 58.412 55.000 11.07 4.22 0.00 3.18
3258 4346 3.600388 GATGAATTCACCACTTCCTCGT 58.400 45.455 11.07 0.00 0.00 4.18
3271 4359 2.434359 CTCGTCGGTCCTTTGCCC 60.434 66.667 0.00 0.00 0.00 5.36
3274 4362 1.186917 TCGTCGGTCCTTTGCCCTTA 61.187 55.000 0.00 0.00 0.00 2.69
3276 4364 1.137479 CGTCGGTCCTTTGCCCTTATA 59.863 52.381 0.00 0.00 0.00 0.98
3286 4374 2.670019 TGCCCTTATAGTAGAGCGGA 57.330 50.000 0.00 0.00 0.00 5.54
3297 4385 1.413077 GTAGAGCGGATGTAGCCCTTT 59.587 52.381 0.00 0.00 34.64 3.11
3298 4386 0.179000 AGAGCGGATGTAGCCCTTTG 59.821 55.000 0.00 0.00 34.64 2.77
3299 4387 0.178068 GAGCGGATGTAGCCCTTTGA 59.822 55.000 0.00 0.00 34.64 2.69
3300 4388 0.618458 AGCGGATGTAGCCCTTTGAA 59.382 50.000 0.00 0.00 34.64 2.69
3301 4389 1.004277 AGCGGATGTAGCCCTTTGAAA 59.996 47.619 0.00 0.00 34.64 2.69
3302 4390 1.401905 GCGGATGTAGCCCTTTGAAAG 59.598 52.381 0.00 0.00 0.00 2.62
3303 4391 2.711542 CGGATGTAGCCCTTTGAAAGT 58.288 47.619 4.02 0.00 0.00 2.66
3304 4392 2.420022 CGGATGTAGCCCTTTGAAAGTG 59.580 50.000 4.02 0.00 0.00 3.16
3305 4393 2.164422 GGATGTAGCCCTTTGAAAGTGC 59.836 50.000 4.15 4.15 31.56 4.40
3306 4394 2.356665 TGTAGCCCTTTGAAAGTGCA 57.643 45.000 14.47 0.00 34.07 4.57
3307 4395 2.660572 TGTAGCCCTTTGAAAGTGCAA 58.339 42.857 14.47 0.00 34.07 4.08
3308 4396 3.230134 TGTAGCCCTTTGAAAGTGCAAT 58.770 40.909 14.47 0.00 34.07 3.56
3309 4397 3.640967 TGTAGCCCTTTGAAAGTGCAATT 59.359 39.130 14.47 0.00 34.07 2.32
3310 4398 4.830046 TGTAGCCCTTTGAAAGTGCAATTA 59.170 37.500 14.47 0.00 34.07 1.40
3311 4399 4.953940 AGCCCTTTGAAAGTGCAATTAA 57.046 36.364 14.47 0.00 34.07 1.40
3312 4400 5.488262 AGCCCTTTGAAAGTGCAATTAAT 57.512 34.783 14.47 0.00 34.07 1.40
3313 4401 5.482006 AGCCCTTTGAAAGTGCAATTAATC 58.518 37.500 14.47 0.00 34.07 1.75
3314 4402 5.246883 AGCCCTTTGAAAGTGCAATTAATCT 59.753 36.000 14.47 0.00 34.07 2.40
3315 4403 5.578336 GCCCTTTGAAAGTGCAATTAATCTC 59.422 40.000 7.51 0.00 31.77 2.75
3316 4404 6.101997 CCCTTTGAAAGTGCAATTAATCTCC 58.898 40.000 0.00 0.00 0.00 3.71
3317 4405 6.101997 CCTTTGAAAGTGCAATTAATCTCCC 58.898 40.000 0.00 0.00 0.00 4.30
3318 4406 4.963276 TGAAAGTGCAATTAATCTCCCG 57.037 40.909 0.00 0.00 0.00 5.14
3319 4407 4.584874 TGAAAGTGCAATTAATCTCCCGA 58.415 39.130 0.00 0.00 0.00 5.14
3320 4408 5.192927 TGAAAGTGCAATTAATCTCCCGAT 58.807 37.500 0.00 0.00 0.00 4.18
3321 4409 5.066375 TGAAAGTGCAATTAATCTCCCGATG 59.934 40.000 0.00 0.00 0.00 3.84
3322 4410 3.480470 AGTGCAATTAATCTCCCGATGG 58.520 45.455 0.00 0.00 0.00 3.51
3323 4411 3.117888 AGTGCAATTAATCTCCCGATGGT 60.118 43.478 0.00 0.00 0.00 3.55
3324 4412 3.632145 GTGCAATTAATCTCCCGATGGTT 59.368 43.478 0.00 0.00 0.00 3.67
3325 4413 4.097892 GTGCAATTAATCTCCCGATGGTTT 59.902 41.667 0.00 0.00 0.00 3.27
3326 4414 4.709397 TGCAATTAATCTCCCGATGGTTTT 59.291 37.500 0.00 0.00 0.00 2.43
3327 4415 5.043248 GCAATTAATCTCCCGATGGTTTTG 58.957 41.667 0.00 0.00 0.00 2.44
3328 4416 5.163561 GCAATTAATCTCCCGATGGTTTTGA 60.164 40.000 0.00 0.00 0.00 2.69
3329 4417 6.461509 GCAATTAATCTCCCGATGGTTTTGAT 60.462 38.462 0.00 0.00 0.00 2.57
3330 4418 7.255451 GCAATTAATCTCCCGATGGTTTTGATA 60.255 37.037 0.00 0.00 0.00 2.15
3331 4419 8.629158 CAATTAATCTCCCGATGGTTTTGATAA 58.371 33.333 0.00 0.00 0.00 1.75
3332 4420 8.940397 ATTAATCTCCCGATGGTTTTGATAAT 57.060 30.769 0.00 0.00 0.00 1.28
3333 4421 8.760980 TTAATCTCCCGATGGTTTTGATAATT 57.239 30.769 0.00 0.00 0.00 1.40
3334 4422 6.884280 ATCTCCCGATGGTTTTGATAATTC 57.116 37.500 0.00 0.00 0.00 2.17
3335 4423 6.001449 TCTCCCGATGGTTTTGATAATTCT 57.999 37.500 0.00 0.00 0.00 2.40
3336 4424 7.131907 TCTCCCGATGGTTTTGATAATTCTA 57.868 36.000 0.00 0.00 0.00 2.10
3337 4425 7.570132 TCTCCCGATGGTTTTGATAATTCTAA 58.430 34.615 0.00 0.00 0.00 2.10
3338 4426 7.497909 TCTCCCGATGGTTTTGATAATTCTAAC 59.502 37.037 0.00 0.00 0.00 2.34
3339 4427 7.113437 TCCCGATGGTTTTGATAATTCTAACA 58.887 34.615 0.00 0.00 0.00 2.41
3340 4428 7.612244 TCCCGATGGTTTTGATAATTCTAACAA 59.388 33.333 0.00 0.00 0.00 2.83
3341 4429 8.413229 CCCGATGGTTTTGATAATTCTAACAAT 58.587 33.333 0.00 0.00 0.00 2.71
3379 4467 9.478768 TGAACTAATATTCGTTCAAGTGTAACA 57.521 29.630 25.17 6.93 44.47 2.41
3385 4473 9.607285 AATATTCGTTCAAGTGTAACATTTCAC 57.393 29.630 0.00 0.00 41.43 3.18
3386 4474 6.424176 TTCGTTCAAGTGTAACATTTCACA 57.576 33.333 4.49 0.00 41.43 3.58
3387 4475 6.424176 TCGTTCAAGTGTAACATTTCACAA 57.576 33.333 4.49 0.00 41.43 3.33
3388 4476 6.843208 TCGTTCAAGTGTAACATTTCACAAA 58.157 32.000 4.49 0.00 41.43 2.83
3389 4477 6.964370 TCGTTCAAGTGTAACATTTCACAAAG 59.036 34.615 4.49 0.00 41.43 2.77
3390 4478 6.745450 CGTTCAAGTGTAACATTTCACAAAGT 59.255 34.615 4.49 0.00 41.43 2.66
3391 4479 7.272515 CGTTCAAGTGTAACATTTCACAAAGTT 59.727 33.333 4.49 0.00 41.43 2.66
3392 4480 8.583765 GTTCAAGTGTAACATTTCACAAAGTTC 58.416 33.333 4.49 0.00 41.43 3.01
3393 4481 7.821652 TCAAGTGTAACATTTCACAAAGTTCA 58.178 30.769 4.49 0.00 41.43 3.18
3394 4482 8.300286 TCAAGTGTAACATTTCACAAAGTTCAA 58.700 29.630 4.49 0.00 41.43 2.69
3395 4483 9.086336 CAAGTGTAACATTTCACAAAGTTCAAT 57.914 29.630 4.49 0.00 41.43 2.57
3396 4484 8.633075 AGTGTAACATTTCACAAAGTTCAATG 57.367 30.769 4.49 0.00 41.43 2.82
3397 4485 8.465999 AGTGTAACATTTCACAAAGTTCAATGA 58.534 29.630 4.49 0.00 41.43 2.57
3398 4486 9.081997 GTGTAACATTTCACAAAGTTCAATGAA 57.918 29.630 0.00 0.00 36.32 2.57
3399 4487 9.814899 TGTAACATTTCACAAAGTTCAATGAAT 57.185 25.926 0.00 0.00 31.45 2.57
3401 4489 7.718272 ACATTTCACAAAGTTCAATGAATGG 57.282 32.000 0.00 0.00 31.45 3.16
3402 4490 6.203338 ACATTTCACAAAGTTCAATGAATGGC 59.797 34.615 0.00 0.00 31.45 4.40
3403 4491 4.933505 TCACAAAGTTCAATGAATGGCA 57.066 36.364 0.00 0.00 0.00 4.92
3404 4492 5.471556 TCACAAAGTTCAATGAATGGCAT 57.528 34.783 0.00 0.00 39.43 4.40
3405 4493 5.231702 TCACAAAGTTCAATGAATGGCATG 58.768 37.500 0.00 0.00 37.28 4.06
3406 4494 4.390603 CACAAAGTTCAATGAATGGCATGG 59.609 41.667 0.00 0.00 37.28 3.66
3407 4495 2.973694 AGTTCAATGAATGGCATGGC 57.026 45.000 13.29 13.29 37.28 4.40
3408 4496 2.181125 AGTTCAATGAATGGCATGGCA 58.819 42.857 25.52 25.52 37.28 4.92
3409 4497 2.769663 AGTTCAATGAATGGCATGGCAT 59.230 40.909 27.75 27.75 37.28 4.40
3410 4498 2.869801 GTTCAATGAATGGCATGGCATG 59.130 45.455 32.77 22.99 37.28 4.06
3411 4499 1.414550 TCAATGAATGGCATGGCATGG 59.585 47.619 32.77 19.71 37.28 3.66
3412 4500 1.414550 CAATGAATGGCATGGCATGGA 59.585 47.619 32.77 22.53 37.28 3.41
3413 4501 1.045407 ATGAATGGCATGGCATGGAC 58.955 50.000 32.77 25.04 35.42 4.02
3414 4502 0.032912 TGAATGGCATGGCATGGACT 60.033 50.000 32.77 18.78 0.00 3.85
3415 4503 1.214923 TGAATGGCATGGCATGGACTA 59.785 47.619 32.77 15.72 0.00 2.59
3416 4504 1.884579 GAATGGCATGGCATGGACTAG 59.115 52.381 32.77 2.65 0.00 2.57
3417 4505 1.142936 ATGGCATGGCATGGACTAGA 58.857 50.000 31.78 3.09 0.00 2.43
3418 4506 0.471191 TGGCATGGCATGGACTAGAG 59.529 55.000 27.48 1.12 0.00 2.43
3419 4507 0.761187 GGCATGGCATGGACTAGAGA 59.239 55.000 27.48 0.00 0.00 3.10
3420 4508 1.350351 GGCATGGCATGGACTAGAGAT 59.650 52.381 27.48 0.00 0.00 2.75
3421 4509 2.424557 GCATGGCATGGACTAGAGATG 58.575 52.381 27.48 0.60 0.00 2.90
3422 4510 2.224475 GCATGGCATGGACTAGAGATGT 60.224 50.000 27.48 0.00 0.00 3.06
3423 4511 3.400255 CATGGCATGGACTAGAGATGTG 58.600 50.000 19.80 0.00 0.00 3.21
3424 4512 1.764723 TGGCATGGACTAGAGATGTGG 59.235 52.381 0.00 0.00 0.00 4.17
3425 4513 2.042464 GGCATGGACTAGAGATGTGGA 58.958 52.381 0.00 0.00 0.00 4.02
3426 4514 2.224161 GGCATGGACTAGAGATGTGGAC 60.224 54.545 0.00 0.00 0.00 4.02
3427 4515 2.697751 GCATGGACTAGAGATGTGGACT 59.302 50.000 0.00 0.00 0.00 3.85
3428 4516 3.243704 GCATGGACTAGAGATGTGGACTC 60.244 52.174 0.00 0.00 34.95 3.36
3429 4517 3.019799 TGGACTAGAGATGTGGACTCC 57.980 52.381 0.00 0.00 35.27 3.85
3430 4518 2.583101 TGGACTAGAGATGTGGACTCCT 59.417 50.000 0.00 0.00 35.27 3.69
3431 4519 3.219281 GGACTAGAGATGTGGACTCCTC 58.781 54.545 0.00 0.00 35.27 3.71
3432 4520 3.372133 GGACTAGAGATGTGGACTCCTCA 60.372 52.174 0.00 2.30 35.27 3.86
3433 4521 4.274147 GACTAGAGATGTGGACTCCTCAA 58.726 47.826 3.95 0.00 35.27 3.02
3434 4522 4.678256 ACTAGAGATGTGGACTCCTCAAA 58.322 43.478 3.95 0.00 35.27 2.69
3435 4523 5.087323 ACTAGAGATGTGGACTCCTCAAAA 58.913 41.667 3.95 0.00 35.27 2.44
3436 4524 4.550076 AGAGATGTGGACTCCTCAAAAG 57.450 45.455 3.95 0.00 35.27 2.27
3437 4525 3.262915 AGAGATGTGGACTCCTCAAAAGG 59.737 47.826 3.95 0.00 44.89 3.11
3438 4526 2.087646 GATGTGGACTCCTCAAAAGGC 58.912 52.381 3.95 0.00 43.02 4.35
3439 4527 1.140312 TGTGGACTCCTCAAAAGGCT 58.860 50.000 0.00 0.00 43.02 4.58
3440 4528 2.334977 TGTGGACTCCTCAAAAGGCTA 58.665 47.619 0.00 0.00 43.02 3.93
3441 4529 2.708861 TGTGGACTCCTCAAAAGGCTAA 59.291 45.455 0.00 0.00 43.02 3.09
3442 4530 3.244561 TGTGGACTCCTCAAAAGGCTAAG 60.245 47.826 0.00 0.00 43.02 2.18
3443 4531 2.305927 TGGACTCCTCAAAAGGCTAAGG 59.694 50.000 0.00 0.00 43.02 2.69
3444 4532 2.356227 GGACTCCTCAAAAGGCTAAGGG 60.356 54.545 0.00 0.00 43.02 3.95
3445 4533 1.004862 ACTCCTCAAAAGGCTAAGGGC 59.995 52.381 0.00 0.00 43.02 5.19
3446 4534 1.004745 CTCCTCAAAAGGCTAAGGGCA 59.995 52.381 0.00 0.00 43.02 5.36
3447 4535 1.177401 CCTCAAAAGGCTAAGGGCAC 58.823 55.000 0.00 0.00 44.01 5.01
3448 4536 1.547675 CCTCAAAAGGCTAAGGGCACA 60.548 52.381 0.00 0.00 44.01 4.57
3449 4537 2.450476 CTCAAAAGGCTAAGGGCACAT 58.550 47.619 0.00 0.00 44.01 3.21
3450 4538 3.620488 CTCAAAAGGCTAAGGGCACATA 58.380 45.455 0.00 0.00 44.01 2.29
3451 4539 4.210331 CTCAAAAGGCTAAGGGCACATAT 58.790 43.478 0.00 0.00 44.01 1.78
3452 4540 4.609301 TCAAAAGGCTAAGGGCACATATT 58.391 39.130 0.00 0.00 44.01 1.28
3453 4541 4.402155 TCAAAAGGCTAAGGGCACATATTG 59.598 41.667 0.00 0.00 44.01 1.90
3454 4542 2.664402 AGGCTAAGGGCACATATTGG 57.336 50.000 0.00 0.00 44.01 3.16
3466 4554 5.921004 GCACATATTGGCAAAAGTTCAAA 57.079 34.783 3.01 0.00 0.00 2.69
3467 4555 6.297694 GCACATATTGGCAAAAGTTCAAAA 57.702 33.333 3.01 0.00 0.00 2.44
3468 4556 6.135400 GCACATATTGGCAAAAGTTCAAAAC 58.865 36.000 3.01 0.00 0.00 2.43
3469 4557 6.018016 GCACATATTGGCAAAAGTTCAAAACT 60.018 34.615 3.01 0.00 45.46 2.66
3470 4558 7.566709 CACATATTGGCAAAAGTTCAAAACTC 58.433 34.615 3.01 0.00 41.91 3.01
3471 4559 7.439056 CACATATTGGCAAAAGTTCAAAACTCT 59.561 33.333 3.01 0.00 41.91 3.24
3472 4560 7.986889 ACATATTGGCAAAAGTTCAAAACTCTT 59.013 29.630 3.01 0.00 41.91 2.85
3473 4561 6.908870 ATTGGCAAAAGTTCAAAACTCTTC 57.091 33.333 3.01 0.00 41.91 2.87
3474 4562 5.398603 TGGCAAAAGTTCAAAACTCTTCA 57.601 34.783 0.00 0.00 41.91 3.02
3475 4563 5.976458 TGGCAAAAGTTCAAAACTCTTCAT 58.024 33.333 0.00 0.00 41.91 2.57
3476 4564 6.405538 TGGCAAAAGTTCAAAACTCTTCATT 58.594 32.000 0.00 0.00 41.91 2.57
3477 4565 6.878389 TGGCAAAAGTTCAAAACTCTTCATTT 59.122 30.769 0.00 0.00 41.91 2.32
3478 4566 7.064490 TGGCAAAAGTTCAAAACTCTTCATTTC 59.936 33.333 0.00 0.00 41.91 2.17
3479 4567 7.278646 GGCAAAAGTTCAAAACTCTTCATTTCT 59.721 33.333 0.00 0.00 41.91 2.52
3480 4568 9.301153 GCAAAAGTTCAAAACTCTTCATTTCTA 57.699 29.630 0.00 0.00 41.91 2.10
3506 4594 8.728337 TTTTAGAGATCCAAGATCACATTGAG 57.272 34.615 7.30 0.00 0.00 3.02
3507 4595 5.954153 AGAGATCCAAGATCACATTGAGT 57.046 39.130 7.30 0.00 0.00 3.41
3508 4596 6.310764 AGAGATCCAAGATCACATTGAGTT 57.689 37.500 7.30 0.00 0.00 3.01
3509 4597 6.347696 AGAGATCCAAGATCACATTGAGTTC 58.652 40.000 7.30 0.00 0.00 3.01
3510 4598 6.058553 AGATCCAAGATCACATTGAGTTCA 57.941 37.500 7.30 0.00 0.00 3.18
3511 4599 6.660800 AGATCCAAGATCACATTGAGTTCAT 58.339 36.000 7.30 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 99 3.559069 CCTGGACTCATATGCACCATTT 58.441 45.455 12.98 0.00 0.00 2.32
100 102 0.181114 GCCTGGACTCATATGCACCA 59.819 55.000 0.00 12.32 0.00 4.17
107 109 2.134287 GCCGGAGCCTGGACTCATA 61.134 63.158 5.05 0.00 38.50 2.15
149 151 1.882623 GGGAGCCAAGTGACTTTTCAG 59.117 52.381 0.00 0.00 30.10 3.02
169 171 2.260154 TGGCTGTTGCGATGGTGTG 61.260 57.895 0.00 0.00 40.82 3.82
202 204 3.679389 AGCTCAAAAGGTGATTCGTCAT 58.321 40.909 0.00 0.00 35.07 3.06
217 219 1.542915 GCCAAATCAAGCTCAGCTCAA 59.457 47.619 0.00 0.00 38.25 3.02
233 235 7.009179 AGCTACATATTAGCAATAGAGCCAA 57.991 36.000 15.00 0.00 42.68 4.52
273 275 1.474077 GATTTGACTTTGGCGAGCCAT 59.526 47.619 18.32 2.66 46.64 4.40
357 359 2.478894 CGTTTTAGTCGTGCAAGGATGT 59.521 45.455 0.00 0.00 31.14 3.06
426 429 5.125097 GGCATCTGAAATATGGTGGATCATC 59.875 44.000 0.00 0.00 0.00 2.92
439 442 1.789078 GCATCGGCGGCATCTGAAAT 61.789 55.000 10.53 0.00 0.00 2.17
544 552 2.362077 GCATTCTTGTGGTGGAGTTGTT 59.638 45.455 0.00 0.00 0.00 2.83
558 567 3.127533 GGCAGCGACGGCATTCTT 61.128 61.111 0.00 0.00 43.41 2.52
568 577 0.245266 TAAGAATGACGTGGCAGCGA 59.755 50.000 14.63 0.00 35.59 4.93
685 705 3.366070 GGTCTTCATCGTCTTGACTTCGA 60.366 47.826 0.00 0.00 37.96 3.71
704 724 7.143340 GGATTGTGTAGTTTAGGTTTTTGGTC 58.857 38.462 0.00 0.00 0.00 4.02
706 726 6.921307 GTGGATTGTGTAGTTTAGGTTTTTGG 59.079 38.462 0.00 0.00 0.00 3.28
708 728 6.319405 ACGTGGATTGTGTAGTTTAGGTTTTT 59.681 34.615 0.00 0.00 0.00 1.94
713 735 3.124636 GCACGTGGATTGTGTAGTTTAGG 59.875 47.826 18.88 0.00 39.53 2.69
728 1581 2.189521 GACCCCCTATGCACGTGG 59.810 66.667 18.88 0.00 0.00 4.94
732 1585 3.757248 CTGGCGACCCCCTATGCAC 62.757 68.421 0.00 0.00 0.00 4.57
803 1668 1.747745 CTAAAAACCCCTCCCGCCG 60.748 63.158 0.00 0.00 0.00 6.46
805 1670 1.022982 CGACTAAAAACCCCTCCCGC 61.023 60.000 0.00 0.00 0.00 6.13
806 1671 0.392060 CCGACTAAAAACCCCTCCCG 60.392 60.000 0.00 0.00 0.00 5.14
809 1674 1.022982 CGGCCGACTAAAAACCCCTC 61.023 60.000 24.07 0.00 0.00 4.30
810 1675 1.002990 CGGCCGACTAAAAACCCCT 60.003 57.895 24.07 0.00 0.00 4.79
813 1678 1.673337 AGGCGGCCGACTAAAAACC 60.673 57.895 37.50 19.69 0.00 3.27
814 1679 0.952010 TCAGGCGGCCGACTAAAAAC 60.952 55.000 37.66 10.35 0.00 2.43
896 1762 2.897271 TTCTACCAGTACCGGTACCA 57.103 50.000 35.52 19.91 40.67 3.25
948 1814 1.970917 GCGCTTTGACACGAGGGATG 61.971 60.000 0.00 0.00 0.00 3.51
951 1817 3.777925 CGCGCTTTGACACGAGGG 61.778 66.667 5.56 0.00 0.00 4.30
971 1837 0.685097 TAACTCGAGCAAGCTTGGGT 59.315 50.000 27.10 9.03 42.66 4.51
1722 2600 1.233950 TGTTGGCGAGGACGTACGTA 61.234 55.000 22.87 0.00 41.98 3.57
1777 2655 1.289066 CTTCGACGTGAGGCCTCAA 59.711 57.895 36.66 18.71 41.85 3.02
2016 2900 0.981183 TGTCTTTCCGTAGCACCCAT 59.019 50.000 0.00 0.00 0.00 4.00
2061 2945 1.667154 CGAGGAGTCCCTTGATCGCA 61.667 60.000 5.25 0.00 45.27 5.10
2121 3011 2.435663 CACTCCACCACCATGCCA 59.564 61.111 0.00 0.00 0.00 4.92
2460 3371 4.067512 TCCCTCAGGCTCCGCTCT 62.068 66.667 0.00 0.00 0.00 4.09
2574 3491 2.048603 GGCAGGGCAGTCACAATCC 61.049 63.158 0.00 0.00 0.00 3.01
2663 3580 4.623595 GTCTTGAGAATGACCGAAAGAGAC 59.376 45.833 0.00 0.00 0.00 3.36
2687 3608 0.319040 CATACATCGCCCTGTCCTCG 60.319 60.000 0.00 0.00 0.00 4.63
2748 3694 1.680338 ACGGCTGCATTTTCCTATCC 58.320 50.000 0.50 0.00 0.00 2.59
2752 3698 2.200373 AAGTACGGCTGCATTTTCCT 57.800 45.000 0.50 0.00 0.00 3.36
2758 3704 0.734889 GCATCAAAGTACGGCTGCAT 59.265 50.000 0.50 0.00 0.00 3.96
2787 3733 4.080582 ACCCGATGACATGATTAAGAACCA 60.081 41.667 0.00 0.00 0.00 3.67
2799 3745 3.309296 ACCTTCTATCACCCGATGACAT 58.691 45.455 0.00 0.00 41.24 3.06
2807 3753 3.688185 GGAAAAACGACCTTCTATCACCC 59.312 47.826 0.00 0.00 0.00 4.61
2810 3756 6.315393 GCATTAGGAAAAACGACCTTCTATCA 59.685 38.462 0.00 0.00 37.68 2.15
2818 3764 3.907894 TGTGCATTAGGAAAAACGACC 57.092 42.857 0.00 0.00 0.00 4.79
2823 3769 9.748708 GCATATTTAGATGTGCATTAGGAAAAA 57.251 29.630 9.69 0.00 46.19 1.94
2849 3795 1.202582 AGTGCACGGCTGTAGACTTAG 59.797 52.381 12.01 0.00 0.00 2.18
2852 3798 0.038159 GAAGTGCACGGCTGTAGACT 60.038 55.000 12.01 0.00 0.00 3.24
2853 3799 0.319555 TGAAGTGCACGGCTGTAGAC 60.320 55.000 12.01 0.00 0.00 2.59
2854 3800 0.391228 TTGAAGTGCACGGCTGTAGA 59.609 50.000 12.01 0.00 0.00 2.59
2855 3801 0.792640 CTTGAAGTGCACGGCTGTAG 59.207 55.000 12.01 1.94 0.00 2.74
2858 3804 1.280746 CACTTGAAGTGCACGGCTG 59.719 57.895 12.89 4.86 39.62 4.85
2865 3823 4.578928 TCTTAAAGAACCCACTTGAAGTGC 59.421 41.667 19.45 6.21 44.63 4.40
2871 3829 5.006386 AGATGCTCTTAAAGAACCCACTTG 58.994 41.667 0.00 0.00 0.00 3.16
2878 3836 6.674278 GCTTGCTGTAGATGCTCTTAAAGAAC 60.674 42.308 0.00 0.00 0.00 3.01
2879 3837 5.352569 GCTTGCTGTAGATGCTCTTAAAGAA 59.647 40.000 0.00 0.00 0.00 2.52
2880 3838 4.872691 GCTTGCTGTAGATGCTCTTAAAGA 59.127 41.667 0.00 0.00 0.00 2.52
2881 3839 4.874966 AGCTTGCTGTAGATGCTCTTAAAG 59.125 41.667 0.00 0.00 0.00 1.85
2882 3840 4.836825 AGCTTGCTGTAGATGCTCTTAAA 58.163 39.130 0.00 0.00 0.00 1.52
2883 3841 4.478206 AGCTTGCTGTAGATGCTCTTAA 57.522 40.909 0.00 0.00 0.00 1.85
2884 3842 5.798125 ATAGCTTGCTGTAGATGCTCTTA 57.202 39.130 5.26 0.00 35.47 2.10
2885 3843 4.686191 ATAGCTTGCTGTAGATGCTCTT 57.314 40.909 5.26 0.00 35.47 2.85
2886 3844 4.502950 GGAATAGCTTGCTGTAGATGCTCT 60.503 45.833 5.26 0.00 35.47 4.09
2887 3845 3.745458 GGAATAGCTTGCTGTAGATGCTC 59.255 47.826 5.26 0.00 35.47 4.26
2914 3872 1.477030 GGTGTGCGCGGACGTATAAG 61.477 60.000 25.71 0.00 42.83 1.73
2915 3873 1.516821 GGTGTGCGCGGACGTATAA 60.517 57.895 25.71 4.80 42.83 0.98
2928 3886 1.004560 AGACGCATCCAGTGGTGTG 60.005 57.895 18.12 18.12 0.00 3.82
2930 3888 2.393768 GCAGACGCATCCAGTGGTG 61.394 63.158 9.54 8.15 38.36 4.17
2933 3891 3.190849 CCGCAGACGCATCCAGTG 61.191 66.667 0.00 0.00 38.40 3.66
2936 3894 3.690280 TGTCCGCAGACGCATCCA 61.690 61.111 0.00 0.00 46.74 3.41
2942 3900 0.454620 GTAGTCAGTGTCCGCAGACG 60.455 60.000 0.00 0.00 46.74 4.18
2945 3903 0.881796 TCAGTAGTCAGTGTCCGCAG 59.118 55.000 0.00 0.00 0.00 5.18
2948 3906 2.152016 TCAGTCAGTAGTCAGTGTCCG 58.848 52.381 0.00 0.00 0.00 4.79
2949 3907 3.759086 TGATCAGTCAGTAGTCAGTGTCC 59.241 47.826 0.00 0.00 0.00 4.02
2950 3908 5.378292 TTGATCAGTCAGTAGTCAGTGTC 57.622 43.478 0.00 0.00 35.39 3.67
2951 3909 5.105554 GGATTGATCAGTCAGTAGTCAGTGT 60.106 44.000 18.70 0.00 35.39 3.55
2954 3912 5.359292 TGAGGATTGATCAGTCAGTAGTCAG 59.641 44.000 18.70 0.00 35.39 3.51
2955 3913 5.264395 TGAGGATTGATCAGTCAGTAGTCA 58.736 41.667 18.70 10.25 35.39 3.41
2957 3915 6.611613 TTTGAGGATTGATCAGTCAGTAGT 57.388 37.500 18.70 0.00 35.39 2.73
2958 3916 6.018098 GCATTTGAGGATTGATCAGTCAGTAG 60.018 42.308 18.70 4.31 35.39 2.57
2959 3917 5.819379 GCATTTGAGGATTGATCAGTCAGTA 59.181 40.000 18.70 2.61 35.39 2.74
2960 3918 4.639310 GCATTTGAGGATTGATCAGTCAGT 59.361 41.667 18.70 6.32 35.39 3.41
2961 3919 4.882427 AGCATTTGAGGATTGATCAGTCAG 59.118 41.667 18.70 2.36 35.39 3.51
2962 3920 4.851843 AGCATTTGAGGATTGATCAGTCA 58.148 39.130 18.70 7.61 0.00 3.41
2963 3921 4.275443 GGAGCATTTGAGGATTGATCAGTC 59.725 45.833 9.63 9.63 0.00 3.51
2964 3922 4.205587 GGAGCATTTGAGGATTGATCAGT 58.794 43.478 0.00 0.00 0.00 3.41
2965 3923 3.568853 GGGAGCATTTGAGGATTGATCAG 59.431 47.826 0.00 0.00 0.00 2.90
2967 3925 2.551459 CGGGAGCATTTGAGGATTGATC 59.449 50.000 0.00 0.00 0.00 2.92
2968 3926 2.579873 CGGGAGCATTTGAGGATTGAT 58.420 47.619 0.00 0.00 0.00 2.57
2993 4080 1.644509 TAGGTGACATGAGGTGCACT 58.355 50.000 17.98 2.27 36.08 4.40
2999 4086 9.212641 CATAATGTAGATTTAGGTGACATGAGG 57.787 37.037 0.00 0.00 31.29 3.86
3069 4157 8.552083 TGGAATTTCGTTGATGATCTATATGG 57.448 34.615 0.00 0.00 0.00 2.74
3121 4209 4.693283 TGATCTGAATTAACTACCGGCTG 58.307 43.478 0.00 0.00 0.00 4.85
3139 4227 9.065871 GTGATGCTTAAACTGTGTATTTTGATC 57.934 33.333 0.00 0.00 0.00 2.92
3159 4247 3.044059 GCCGGCTGAACTGTGATGC 62.044 63.158 22.15 0.00 0.00 3.91
3165 4253 1.213537 CCATTTGCCGGCTGAACTG 59.786 57.895 29.70 17.87 0.00 3.16
3214 4302 2.876079 GCCCTCTCCATCTTCGTTTTGT 60.876 50.000 0.00 0.00 0.00 2.83
3221 4309 0.034616 CATCGGCCCTCTCCATCTTC 59.965 60.000 0.00 0.00 0.00 2.87
3227 4315 0.469917 TGAATTCATCGGCCCTCTCC 59.530 55.000 3.38 0.00 0.00 3.71
3239 4327 2.609491 CGACGAGGAAGTGGTGAATTCA 60.609 50.000 3.38 3.38 0.00 2.57
3247 4335 1.533469 AAGGACCGACGAGGAAGTGG 61.533 60.000 8.56 0.00 45.00 4.00
3271 4359 4.096682 GGGCTACATCCGCTCTACTATAAG 59.903 50.000 0.00 0.00 0.00 1.73
3274 4362 2.041891 AGGGCTACATCCGCTCTACTAT 59.958 50.000 0.00 0.00 36.19 2.12
3276 4364 0.186386 AGGGCTACATCCGCTCTACT 59.814 55.000 0.00 0.00 36.19 2.57
3297 4385 4.584874 TCGGGAGATTAATTGCACTTTCA 58.415 39.130 0.00 0.00 0.00 2.69
3312 4400 6.001449 AGAATTATCAAAACCATCGGGAGA 57.999 37.500 0.00 0.00 46.90 3.71
3313 4401 7.282224 TGTTAGAATTATCAAAACCATCGGGAG 59.718 37.037 0.00 0.00 38.05 4.30
3314 4402 7.113437 TGTTAGAATTATCAAAACCATCGGGA 58.887 34.615 0.00 0.00 38.05 5.14
3315 4403 7.328277 TGTTAGAATTATCAAAACCATCGGG 57.672 36.000 0.00 0.00 41.29 5.14
3359 4447 9.607285 GTGAAATGTTACACTTGAACGAATATT 57.393 29.630 0.00 0.00 34.65 1.28
3360 4448 8.779303 TGTGAAATGTTACACTTGAACGAATAT 58.221 29.630 0.00 0.00 37.81 1.28
3361 4449 8.144155 TGTGAAATGTTACACTTGAACGAATA 57.856 30.769 0.00 0.00 37.81 1.75
3362 4450 7.022055 TGTGAAATGTTACACTTGAACGAAT 57.978 32.000 0.00 0.00 37.81 3.34
3363 4451 6.424176 TGTGAAATGTTACACTTGAACGAA 57.576 33.333 0.00 0.00 37.81 3.85
3364 4452 6.424176 TTGTGAAATGTTACACTTGAACGA 57.576 33.333 0.00 0.00 37.81 3.85
3365 4453 6.745450 ACTTTGTGAAATGTTACACTTGAACG 59.255 34.615 0.00 0.00 37.81 3.95
3366 4454 8.460831 AACTTTGTGAAATGTTACACTTGAAC 57.539 30.769 0.00 0.00 37.81 3.18
3367 4455 8.300286 TGAACTTTGTGAAATGTTACACTTGAA 58.700 29.630 0.00 0.00 37.81 2.69
3368 4456 7.821652 TGAACTTTGTGAAATGTTACACTTGA 58.178 30.769 0.00 0.00 37.81 3.02
3369 4457 8.459521 TTGAACTTTGTGAAATGTTACACTTG 57.540 30.769 0.00 0.00 37.81 3.16
3370 4458 9.086336 CATTGAACTTTGTGAAATGTTACACTT 57.914 29.630 0.00 0.00 37.81 3.16
3371 4459 8.465999 TCATTGAACTTTGTGAAATGTTACACT 58.534 29.630 0.00 0.00 37.81 3.55
3372 4460 8.627487 TCATTGAACTTTGTGAAATGTTACAC 57.373 30.769 0.00 0.00 37.51 2.90
3373 4461 9.814899 ATTCATTGAACTTTGTGAAATGTTACA 57.185 25.926 0.15 0.00 34.62 2.41
3375 4463 9.258826 CCATTCATTGAACTTTGTGAAATGTTA 57.741 29.630 0.15 0.00 34.62 2.41
3376 4464 7.254863 GCCATTCATTGAACTTTGTGAAATGTT 60.255 33.333 0.15 0.00 34.62 2.71
3377 4465 6.203338 GCCATTCATTGAACTTTGTGAAATGT 59.797 34.615 0.15 0.00 34.62 2.71
3378 4466 6.203145 TGCCATTCATTGAACTTTGTGAAATG 59.797 34.615 0.15 0.00 34.62 2.32
3379 4467 6.289834 TGCCATTCATTGAACTTTGTGAAAT 58.710 32.000 0.15 0.00 34.62 2.17
3380 4468 5.668471 TGCCATTCATTGAACTTTGTGAAA 58.332 33.333 0.15 0.00 34.62 2.69
3381 4469 5.273674 TGCCATTCATTGAACTTTGTGAA 57.726 34.783 0.15 0.00 35.33 3.18
3382 4470 4.933505 TGCCATTCATTGAACTTTGTGA 57.066 36.364 0.15 0.00 0.00 3.58
3383 4471 4.390603 CCATGCCATTCATTGAACTTTGTG 59.609 41.667 0.15 0.00 31.79 3.33
3384 4472 4.571919 CCATGCCATTCATTGAACTTTGT 58.428 39.130 0.15 0.00 31.79 2.83
3385 4473 3.372822 GCCATGCCATTCATTGAACTTTG 59.627 43.478 0.15 0.00 31.79 2.77
3386 4474 3.008157 TGCCATGCCATTCATTGAACTTT 59.992 39.130 0.15 0.00 31.79 2.66
3387 4475 2.568062 TGCCATGCCATTCATTGAACTT 59.432 40.909 0.15 0.00 31.79 2.66
3388 4476 2.181125 TGCCATGCCATTCATTGAACT 58.819 42.857 0.15 0.00 31.79 3.01
3389 4477 2.676632 TGCCATGCCATTCATTGAAC 57.323 45.000 0.15 0.00 31.79 3.18
3390 4478 2.158885 CCATGCCATGCCATTCATTGAA 60.159 45.455 0.75 0.75 31.79 2.69
3391 4479 1.414550 CCATGCCATGCCATTCATTGA 59.585 47.619 0.00 0.00 31.79 2.57
3392 4480 1.414550 TCCATGCCATGCCATTCATTG 59.585 47.619 0.00 0.00 31.79 2.82
3393 4481 1.414919 GTCCATGCCATGCCATTCATT 59.585 47.619 0.00 0.00 31.79 2.57
3394 4482 1.045407 GTCCATGCCATGCCATTCAT 58.955 50.000 0.00 0.00 35.31 2.57
3395 4483 0.032912 AGTCCATGCCATGCCATTCA 60.033 50.000 0.00 0.00 0.00 2.57
3396 4484 1.884579 CTAGTCCATGCCATGCCATTC 59.115 52.381 0.00 0.00 0.00 2.67
3397 4485 1.496001 TCTAGTCCATGCCATGCCATT 59.504 47.619 0.00 0.00 0.00 3.16
3398 4486 1.073444 CTCTAGTCCATGCCATGCCAT 59.927 52.381 0.00 0.00 0.00 4.40
3399 4487 0.471191 CTCTAGTCCATGCCATGCCA 59.529 55.000 0.00 0.00 0.00 4.92
3400 4488 0.761187 TCTCTAGTCCATGCCATGCC 59.239 55.000 0.00 0.00 0.00 4.40
3401 4489 2.224475 ACATCTCTAGTCCATGCCATGC 60.224 50.000 0.00 0.00 0.00 4.06
3402 4490 3.400255 CACATCTCTAGTCCATGCCATG 58.600 50.000 0.00 0.00 0.00 3.66
3403 4491 2.371179 CCACATCTCTAGTCCATGCCAT 59.629 50.000 0.00 0.00 0.00 4.40
3404 4492 1.764723 CCACATCTCTAGTCCATGCCA 59.235 52.381 0.00 0.00 0.00 4.92
3405 4493 2.042464 TCCACATCTCTAGTCCATGCC 58.958 52.381 0.00 0.00 0.00 4.40
3406 4494 2.697751 AGTCCACATCTCTAGTCCATGC 59.302 50.000 0.00 0.00 0.00 4.06
3407 4495 3.320541 GGAGTCCACATCTCTAGTCCATG 59.679 52.174 3.60 0.00 32.63 3.66
3408 4496 3.206412 AGGAGTCCACATCTCTAGTCCAT 59.794 47.826 12.86 0.00 34.45 3.41
3409 4497 2.583101 AGGAGTCCACATCTCTAGTCCA 59.417 50.000 12.86 0.00 34.45 4.02
3410 4498 3.219281 GAGGAGTCCACATCTCTAGTCC 58.781 54.545 12.86 0.00 33.06 3.85
3411 4499 3.892284 TGAGGAGTCCACATCTCTAGTC 58.108 50.000 12.86 0.00 33.06 2.59
3412 4500 4.323569 TTGAGGAGTCCACATCTCTAGT 57.676 45.455 12.86 0.00 33.06 2.57
3413 4501 5.395103 CCTTTTGAGGAGTCCACATCTCTAG 60.395 48.000 12.86 4.80 33.06 2.43
3414 4502 4.467795 CCTTTTGAGGAGTCCACATCTCTA 59.532 45.833 12.86 0.00 33.06 2.43
3415 4503 3.262915 CCTTTTGAGGAGTCCACATCTCT 59.737 47.826 12.86 0.00 33.06 3.10
3416 4504 3.604582 CCTTTTGAGGAGTCCACATCTC 58.395 50.000 12.86 0.00 0.00 2.75
3417 4505 2.290577 GCCTTTTGAGGAGTCCACATCT 60.291 50.000 12.86 0.00 0.00 2.90
3418 4506 2.087646 GCCTTTTGAGGAGTCCACATC 58.912 52.381 12.86 0.41 0.00 3.06
3419 4507 1.707427 AGCCTTTTGAGGAGTCCACAT 59.293 47.619 12.86 0.00 0.00 3.21
3420 4508 1.140312 AGCCTTTTGAGGAGTCCACA 58.860 50.000 12.86 8.86 0.00 4.17
3421 4509 3.339141 CTTAGCCTTTTGAGGAGTCCAC 58.661 50.000 12.86 5.67 0.00 4.02
3422 4510 2.305927 CCTTAGCCTTTTGAGGAGTCCA 59.694 50.000 12.86 0.00 0.00 4.02
3423 4511 2.356227 CCCTTAGCCTTTTGAGGAGTCC 60.356 54.545 0.00 0.00 0.00 3.85
3424 4512 2.941860 GCCCTTAGCCTTTTGAGGAGTC 60.942 54.545 0.00 0.00 34.35 3.36
3425 4513 1.004862 GCCCTTAGCCTTTTGAGGAGT 59.995 52.381 0.00 0.00 34.35 3.85
3426 4514 1.004745 TGCCCTTAGCCTTTTGAGGAG 59.995 52.381 0.00 0.00 42.71 3.69
3427 4515 1.072266 TGCCCTTAGCCTTTTGAGGA 58.928 50.000 0.00 0.00 42.71 3.71
3428 4516 1.177401 GTGCCCTTAGCCTTTTGAGG 58.823 55.000 0.00 0.00 42.71 3.86
3429 4517 1.909700 TGTGCCCTTAGCCTTTTGAG 58.090 50.000 0.00 0.00 42.71 3.02
3430 4518 2.603075 ATGTGCCCTTAGCCTTTTGA 57.397 45.000 0.00 0.00 42.71 2.69
3431 4519 4.441913 CCAATATGTGCCCTTAGCCTTTTG 60.442 45.833 0.00 0.00 42.71 2.44
3432 4520 3.706086 CCAATATGTGCCCTTAGCCTTTT 59.294 43.478 0.00 0.00 42.71 2.27
3433 4521 3.299503 CCAATATGTGCCCTTAGCCTTT 58.700 45.455 0.00 0.00 42.71 3.11
3434 4522 2.949447 CCAATATGTGCCCTTAGCCTT 58.051 47.619 0.00 0.00 42.71 4.35
3435 4523 1.479389 GCCAATATGTGCCCTTAGCCT 60.479 52.381 0.00 0.00 42.71 4.58
3436 4524 0.961753 GCCAATATGTGCCCTTAGCC 59.038 55.000 0.00 0.00 42.71 3.93
3437 4525 1.691196 TGCCAATATGTGCCCTTAGC 58.309 50.000 0.00 0.00 44.14 3.09
3438 4526 4.160252 ACTTTTGCCAATATGTGCCCTTAG 59.840 41.667 0.00 0.00 0.00 2.18
3439 4527 4.093011 ACTTTTGCCAATATGTGCCCTTA 58.907 39.130 0.00 0.00 0.00 2.69
3440 4528 2.905736 ACTTTTGCCAATATGTGCCCTT 59.094 40.909 0.00 0.00 0.00 3.95
3441 4529 2.539302 ACTTTTGCCAATATGTGCCCT 58.461 42.857 0.00 0.00 0.00 5.19
3442 4530 3.261580 GAACTTTTGCCAATATGTGCCC 58.738 45.455 0.00 0.00 0.00 5.36
3443 4531 3.924144 TGAACTTTTGCCAATATGTGCC 58.076 40.909 0.00 0.00 0.00 5.01
3444 4532 5.921004 TTTGAACTTTTGCCAATATGTGC 57.079 34.783 0.00 0.00 0.00 4.57
3445 4533 7.439056 AGAGTTTTGAACTTTTGCCAATATGTG 59.561 33.333 0.00 0.00 43.03 3.21
3446 4534 7.500141 AGAGTTTTGAACTTTTGCCAATATGT 58.500 30.769 0.00 0.00 43.03 2.29
3447 4535 7.951530 AGAGTTTTGAACTTTTGCCAATATG 57.048 32.000 0.00 0.00 43.03 1.78
3448 4536 8.203485 TGAAGAGTTTTGAACTTTTGCCAATAT 58.797 29.630 1.89 0.00 43.03 1.28
3449 4537 7.551585 TGAAGAGTTTTGAACTTTTGCCAATA 58.448 30.769 1.89 0.00 43.03 1.90
3450 4538 6.405538 TGAAGAGTTTTGAACTTTTGCCAAT 58.594 32.000 1.89 0.00 43.03 3.16
3451 4539 5.788450 TGAAGAGTTTTGAACTTTTGCCAA 58.212 33.333 1.89 0.00 43.03 4.52
3452 4540 5.398603 TGAAGAGTTTTGAACTTTTGCCA 57.601 34.783 1.89 0.00 43.03 4.92
3453 4541 6.908870 AATGAAGAGTTTTGAACTTTTGCC 57.091 33.333 1.89 0.00 43.03 4.52
3454 4542 8.189709 AGAAATGAAGAGTTTTGAACTTTTGC 57.810 30.769 1.89 0.00 43.03 3.68
3480 4568 9.339850 CTCAATGTGATCTTGGATCTCTAAAAT 57.660 33.333 8.66 0.00 0.00 1.82
3481 4569 8.324306 ACTCAATGTGATCTTGGATCTCTAAAA 58.676 33.333 8.66 0.00 0.00 1.52
3482 4570 7.855375 ACTCAATGTGATCTTGGATCTCTAAA 58.145 34.615 8.66 0.00 0.00 1.85
3483 4571 7.429374 ACTCAATGTGATCTTGGATCTCTAA 57.571 36.000 8.66 0.00 0.00 2.10
3484 4572 7.124750 TGAACTCAATGTGATCTTGGATCTCTA 59.875 37.037 8.66 0.00 0.00 2.43
3485 4573 5.954153 ACTCAATGTGATCTTGGATCTCT 57.046 39.130 8.66 0.00 0.00 3.10
3486 4574 6.111382 TGAACTCAATGTGATCTTGGATCTC 58.889 40.000 8.66 6.01 0.00 2.75
3487 4575 6.058553 TGAACTCAATGTGATCTTGGATCT 57.941 37.500 8.66 0.00 0.00 2.75
3488 4576 6.939132 ATGAACTCAATGTGATCTTGGATC 57.061 37.500 0.00 1.04 0.00 3.36


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

AutoCloner maintained by Alex Coulton.