Multiple sequence alignment - TraesCS7D01G271100

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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 TraesCS7D01G271100 chr7D 100.000 3772 0 0 1 3772 258239271 258235500 0.000000e+00 6966.0
1 TraesCS7D01G271100 chr7D 91.156 147 12 1 3626 3772 614243856 614243711 8.260000e-47 198.0
2 TraesCS7D01G271100 chr7D 82.781 151 17 4 3083 3224 614245490 614245340 3.960000e-25 126.0
3 TraesCS7D01G271100 chr7B 96.132 1241 29 5 834 2056 237509876 237508637 0.000000e+00 2008.0
4 TraesCS7D01G271100 chr7B 94.094 1236 41 10 2043 3265 237508618 237507402 0.000000e+00 1849.0
5 TraesCS7D01G271100 chr7B 88.939 660 55 8 167 808 237514742 237514083 0.000000e+00 798.0
6 TraesCS7D01G271100 chr7B 95.604 91 4 0 3 93 237514975 237514885 3.040000e-31 147.0
7 TraesCS7D01G271100 chr7B 90.000 90 7 2 81 168 237514871 237514782 8.560000e-22 115.0
8 TraesCS7D01G271100 chr7B 85.149 101 5 1 3534 3624 237507351 237507251 1.120000e-15 95.3
9 TraesCS7D01G271100 chr7A 93.900 1295 45 7 834 2111 280072002 280070725 0.000000e+00 1923.0
10 TraesCS7D01G271100 chr7A 88.710 1240 79 35 2096 3298 280070710 280069495 0.000000e+00 1458.0
11 TraesCS7D01G271100 chr7A 86.295 664 62 15 167 813 280072932 280072281 0.000000e+00 695.0
12 TraesCS7D01G271100 chr7A 85.000 280 31 7 3503 3772 706281008 706280730 1.330000e-69 274.0
13 TraesCS7D01G271100 chr7A 85.427 199 28 1 3302 3499 353071898 353071700 4.940000e-49 206.0
14 TraesCS7D01G271100 chr7A 84.884 86 11 2 664 749 457854928 457854845 6.710000e-13 86.1
15 TraesCS7D01G271100 chr7A 93.182 44 2 1 125 168 706830061 706830019 3.150000e-06 63.9
16 TraesCS7D01G271100 chr5D 78.261 805 147 18 1221 2017 414810644 414809860 3.390000e-135 492.0
17 TraesCS7D01G271100 chr5D 76.592 628 119 17 2117 2740 414809776 414809173 1.690000e-83 320.0
18 TraesCS7D01G271100 chr5D 92.746 193 13 1 3304 3496 514563345 514563536 1.030000e-70 278.0
19 TraesCS7D01G271100 chr5B 78.288 806 139 22 1224 2017 500530020 500529239 1.580000e-133 486.0
20 TraesCS7D01G271100 chr5B 76.874 627 119 15 2117 2740 500529156 500528553 7.810000e-87 331.0
21 TraesCS7D01G271100 chr5B 89.362 141 15 0 3629 3769 258473219 258473079 1.080000e-40 178.0
22 TraesCS7D01G271100 chr1B 84.559 272 32 7 3504 3767 653814713 653814444 1.040000e-65 261.0
23 TraesCS7D01G271100 chr1B 88.360 189 22 0 3309 3497 453523013 453523201 1.050000e-55 228.0
24 TraesCS7D01G271100 chr1B 86.294 197 24 3 3302 3496 527770048 527769853 1.060000e-50 211.0
25 TraesCS7D01G271100 chr6A 83.871 279 33 3 3504 3772 574700632 574700356 4.840000e-64 255.0
26 TraesCS7D01G271100 chr6A 84.236 203 31 1 3298 3499 607089160 607089362 2.970000e-46 196.0
27 TraesCS7D01G271100 chr6A 84.236 203 31 1 3298 3499 607224346 607224548 2.970000e-46 196.0
28 TraesCS7D01G271100 chr6A 89.583 48 4 1 21 68 115937429 115937383 4.070000e-05 60.2
29 TraesCS7D01G271100 chr3A 85.204 196 28 1 3305 3499 308203806 308203611 2.300000e-47 200.0
30 TraesCS7D01G271100 chr3A 84.080 201 31 1 3300 3499 585158779 585158579 3.850000e-45 193.0
31 TraesCS7D01G271100 chr2D 85.859 198 16 7 3303 3499 613432833 613433019 2.300000e-47 200.0
32 TraesCS7D01G271100 chr2D 89.362 141 15 0 3629 3769 31756208 31756348 1.080000e-40 178.0
33 TraesCS7D01G271100 chr2D 81.395 86 15 1 664 749 577686940 577686856 6.760000e-08 69.4
34 TraesCS7D01G271100 chr3D 84.848 198 27 3 3304 3499 93390220 93390416 2.970000e-46 196.0
35 TraesCS7D01G271100 chr3D 88.194 144 17 0 3629 3772 49468012 49467869 5.010000e-39 172.0
36 TraesCS7D01G271100 chr3D 88.276 145 15 2 3629 3772 49473595 49473452 5.010000e-39 172.0
37 TraesCS7D01G271100 chr1D 89.510 143 15 0 3630 3772 481930062 481929920 8.320000e-42 182.0
38 TraesCS7D01G271100 chr6D 88.372 43 5 0 3586 3628 363243020 363242978 7.000000e-03 52.8


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 TraesCS7D01G271100 chr7D 258235500 258239271 3771 True 6966.000000 6966 100.000000 1 3772 1 chr7D.!!$R1 3771
1 TraesCS7D01G271100 chr7B 237507251 237509876 2625 True 1317.433333 2008 91.791667 834 3624 3 chr7B.!!$R1 2790
2 TraesCS7D01G271100 chr7B 237514083 237514975 892 True 353.333333 798 91.514333 3 808 3 chr7B.!!$R2 805
3 TraesCS7D01G271100 chr7A 280069495 280072932 3437 True 1358.666667 1923 89.635000 167 3298 3 chr7A.!!$R5 3131
4 TraesCS7D01G271100 chr5D 414809173 414810644 1471 True 406.000000 492 77.426500 1221 2740 2 chr5D.!!$R1 1519
5 TraesCS7D01G271100 chr5B 500528553 500530020 1467 True 408.500000 486 77.581000 1224 2740 2 chr5B.!!$R2 1516

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
489 565 0.736053 GGCTTGTCTCTCGATCGAGT 59.264 55.000 36.68 0.0 42.49 4.18 F
1716 2087 3.138798 TACGAGCTGGACGAGGCC 61.139 66.667 1.44 0.0 34.70 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 2117 1.642037 CGTAGCCTTCGTCGACCAGA 61.642 60.0 10.58 0.0 0.0 3.86 R
3328 3811 0.106669 GGGAGGAGGCGGCTTATTTT 60.107 55.0 14.76 0.0 0.0 1.82 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
61 62 4.177026 CTCGTGCTCTGCTTGTAACTATT 58.823 43.478 0.00 0.00 0.00 1.73
67 68 5.997746 TGCTCTGCTTGTAACTATTTTGAGT 59.002 36.000 0.00 0.00 0.00 3.41
79 80 6.128138 ACTATTTTGAGTGGGTTTAGAGCT 57.872 37.500 0.00 0.00 0.00 4.09
155 183 3.634448 CCACAACACAACATAAGAACCCA 59.366 43.478 0.00 0.00 0.00 4.51
156 184 4.499019 CCACAACACAACATAAGAACCCAC 60.499 45.833 0.00 0.00 0.00 4.61
157 185 4.338118 CACAACACAACATAAGAACCCACT 59.662 41.667 0.00 0.00 0.00 4.00
158 186 5.529430 CACAACACAACATAAGAACCCACTA 59.471 40.000 0.00 0.00 0.00 2.74
159 187 6.206634 CACAACACAACATAAGAACCCACTAT 59.793 38.462 0.00 0.00 0.00 2.12
160 188 7.389330 CACAACACAACATAAGAACCCACTATA 59.611 37.037 0.00 0.00 0.00 1.31
162 190 8.788806 CAACACAACATAAGAACCCACTATAAA 58.211 33.333 0.00 0.00 0.00 1.40
192 262 9.684702 TTATTCCCTACCAGATAAGGATTTAGT 57.315 33.333 0.00 0.00 34.58 2.24
195 265 9.510062 TTCCCTACCAGATAAGGATTTAGTAAA 57.490 33.333 0.00 0.00 34.58 2.01
231 301 7.114754 AGATCATGGATGAACTAGCAAGAAAA 58.885 34.615 0.00 0.00 38.03 2.29
325 398 8.458843 GCCTAACTTGTTATCAATCAAGCTTTA 58.541 33.333 0.00 0.00 43.05 1.85
469 545 1.888512 AGCCAATGTTGCGTCAAGATT 59.111 42.857 8.44 8.44 37.73 2.40
472 548 1.987770 CAATGTTGCGTCAAGATTGGC 59.012 47.619 22.76 0.00 45.28 4.52
489 565 0.736053 GGCTTGTCTCTCGATCGAGT 59.264 55.000 36.68 0.00 42.49 4.18
496 572 5.908916 TGTCTCTCGATCGAGTTACATAG 57.091 43.478 36.68 27.11 42.49 2.23
524 600 7.352079 AGTCATCCACTGTTCATTTCTTTTT 57.648 32.000 0.00 0.00 32.26 1.94
525 601 7.428826 AGTCATCCACTGTTCATTTCTTTTTC 58.571 34.615 0.00 0.00 32.26 2.29
547 623 4.946772 TCAGTCAATTTTGAACCACTCACA 59.053 37.500 0.00 0.00 39.21 3.58
575 651 5.086104 TCGAGCTTTTCTTACAGCCTTAT 57.914 39.130 0.00 0.00 36.62 1.73
657 733 7.506114 TCTTATCTTAAGCCCGTCATGTATTT 58.494 34.615 0.00 0.00 0.00 1.40
760 838 7.827236 TGTGGTGAGACAATTACTAATAAAGGG 59.173 37.037 0.00 0.00 0.00 3.95
762 840 8.387813 TGGTGAGACAATTACTAATAAAGGGTT 58.612 33.333 0.00 0.00 0.00 4.11
824 923 9.771534 CTTGTTATTTGATCAGGGGTTTAAAAA 57.228 29.630 0.00 0.00 0.00 1.94
1716 2087 3.138798 TACGAGCTGGACGAGGCC 61.139 66.667 1.44 0.00 34.70 5.19
1956 2327 1.734477 CTTCACCGACGTCCTGCTG 60.734 63.158 10.58 0.07 0.00 4.41
2049 2420 5.150683 CGCTTAAATGGAAAACACGAATGA 58.849 37.500 0.00 0.00 0.00 2.57
2057 2428 6.438259 TGGAAAACACGAATGAACACTTAA 57.562 33.333 0.00 0.00 0.00 1.85
2058 2429 6.853720 TGGAAAACACGAATGAACACTTAAA 58.146 32.000 0.00 0.00 0.00 1.52
2061 2460 9.113876 GGAAAACACGAATGAACACTTAAATAG 57.886 33.333 0.00 0.00 0.00 1.73
2446 2875 1.988015 CCATAACCCACGACCCAGT 59.012 57.895 0.00 0.00 0.00 4.00
2535 2964 2.262915 CCGGCGCTGAGTTCTCTT 59.737 61.111 20.25 0.00 0.00 2.85
2709 3138 0.321122 GGACTTGTCTGAGGTGCTGG 60.321 60.000 0.61 0.00 0.00 4.85
2900 3345 1.684983 TGCTACTACAATAGGTCCGGC 59.315 52.381 0.00 0.00 0.00 6.13
2955 3400 8.398665 GTTCTTAGCAGGGTAGATGTTTAATTG 58.601 37.037 0.00 0.00 0.00 2.32
3035 3509 5.306114 TGCTGCCTAGAGATGTACTACTA 57.694 43.478 0.00 0.00 0.00 1.82
3036 3510 5.064558 TGCTGCCTAGAGATGTACTACTAC 58.935 45.833 0.00 0.00 0.00 2.73
3088 3562 6.974932 ATGCAAGTATCAGTTGTGTTAGAG 57.025 37.500 0.00 0.00 31.33 2.43
3156 3630 3.305950 CCCATTTTTGTGCTTTGATCGGA 60.306 43.478 0.00 0.00 0.00 4.55
3161 3635 1.796796 GTGCTTTGATCGGAGGCAC 59.203 57.895 16.50 16.50 44.53 5.01
3188 3662 1.338020 ACTAACGTTCGGTTTCGGTCT 59.662 47.619 2.82 0.00 40.09 3.85
3193 3667 0.033090 GTTCGGTTTCGGTCTCTGGT 59.967 55.000 0.00 0.00 36.95 4.00
3218 3697 9.903682 GTTCCTTAGCACTATCACGTATATAAA 57.096 33.333 0.00 0.00 0.00 1.40
3259 3738 3.952323 GCATAGGTGAGATATACGGGCTA 59.048 47.826 0.00 0.00 0.00 3.93
3294 3777 5.031066 TCCTAACCACCGATCCATAAAAG 57.969 43.478 0.00 0.00 0.00 2.27
3298 3781 3.886123 ACCACCGATCCATAAAAGGAAG 58.114 45.455 0.00 0.00 41.92 3.46
3299 3782 3.265995 ACCACCGATCCATAAAAGGAAGT 59.734 43.478 0.00 0.00 41.92 3.01
3301 3784 4.261801 CACCGATCCATAAAAGGAAGTGT 58.738 43.478 0.00 0.00 41.92 3.55
3303 3786 5.878116 CACCGATCCATAAAAGGAAGTGTTA 59.122 40.000 0.00 0.00 41.92 2.41
3304 3787 6.037172 CACCGATCCATAAAAGGAAGTGTTAG 59.963 42.308 0.00 0.00 41.92 2.34
3305 3788 5.527582 CCGATCCATAAAAGGAAGTGTTAGG 59.472 44.000 0.00 0.00 41.92 2.69
3306 3789 5.527582 CGATCCATAAAAGGAAGTGTTAGGG 59.472 44.000 0.00 0.00 41.92 3.53
3307 3790 5.853572 TCCATAAAAGGAAGTGTTAGGGT 57.146 39.130 0.00 0.00 33.93 4.34
3308 3791 5.812286 TCCATAAAAGGAAGTGTTAGGGTC 58.188 41.667 0.00 0.00 33.93 4.46
3309 3792 5.311121 TCCATAAAAGGAAGTGTTAGGGTCA 59.689 40.000 0.00 0.00 33.93 4.02
3310 3793 5.648092 CCATAAAAGGAAGTGTTAGGGTCAG 59.352 44.000 0.00 0.00 0.00 3.51
3311 3794 4.790718 AAAAGGAAGTGTTAGGGTCAGT 57.209 40.909 0.00 0.00 0.00 3.41
3312 3795 4.790718 AAAGGAAGTGTTAGGGTCAGTT 57.209 40.909 0.00 0.00 0.00 3.16
3313 3796 4.790718 AAGGAAGTGTTAGGGTCAGTTT 57.209 40.909 0.00 0.00 0.00 2.66
3314 3797 4.790718 AGGAAGTGTTAGGGTCAGTTTT 57.209 40.909 0.00 0.00 0.00 2.43
3315 3798 5.125367 AGGAAGTGTTAGGGTCAGTTTTT 57.875 39.130 0.00 0.00 0.00 1.94
3346 3829 1.763968 AAAAATAAGCCGCCTCCTCC 58.236 50.000 0.00 0.00 0.00 4.30
3347 3830 0.106669 AAAATAAGCCGCCTCCTCCC 60.107 55.000 0.00 0.00 0.00 4.30
3348 3831 0.988678 AAATAAGCCGCCTCCTCCCT 60.989 55.000 0.00 0.00 0.00 4.20
3349 3832 1.411651 AATAAGCCGCCTCCTCCCTC 61.412 60.000 0.00 0.00 0.00 4.30
3354 3837 3.775654 CGCCTCCTCCCTCGCTTT 61.776 66.667 0.00 0.00 0.00 3.51
3355 3838 2.671682 GCCTCCTCCCTCGCTTTT 59.328 61.111 0.00 0.00 0.00 2.27
3356 3839 1.450491 GCCTCCTCCCTCGCTTTTC 60.450 63.158 0.00 0.00 0.00 2.29
3357 3840 1.222113 CCTCCTCCCTCGCTTTTCC 59.778 63.158 0.00 0.00 0.00 3.13
3358 3841 1.222113 CTCCTCCCTCGCTTTTCCC 59.778 63.158 0.00 0.00 0.00 3.97
3359 3842 1.537889 TCCTCCCTCGCTTTTCCCA 60.538 57.895 0.00 0.00 0.00 4.37
3360 3843 0.914417 TCCTCCCTCGCTTTTCCCAT 60.914 55.000 0.00 0.00 0.00 4.00
3361 3844 0.837272 CCTCCCTCGCTTTTCCCATA 59.163 55.000 0.00 0.00 0.00 2.74
3362 3845 1.211949 CCTCCCTCGCTTTTCCCATAA 59.788 52.381 0.00 0.00 0.00 1.90
3363 3846 2.565841 CTCCCTCGCTTTTCCCATAAG 58.434 52.381 0.00 0.00 0.00 1.73
3364 3847 1.025041 CCCTCGCTTTTCCCATAAGC 58.975 55.000 0.00 0.00 43.49 3.09
3365 3848 1.025041 CCTCGCTTTTCCCATAAGCC 58.975 55.000 0.00 0.00 43.93 4.35
3366 3849 1.681780 CCTCGCTTTTCCCATAAGCCA 60.682 52.381 0.00 0.00 43.93 4.75
3367 3850 2.301346 CTCGCTTTTCCCATAAGCCAT 58.699 47.619 0.00 0.00 43.93 4.40
3368 3851 2.689983 CTCGCTTTTCCCATAAGCCATT 59.310 45.455 0.00 0.00 43.93 3.16
3369 3852 3.882888 CTCGCTTTTCCCATAAGCCATTA 59.117 43.478 0.00 0.00 43.93 1.90
3370 3853 3.882888 TCGCTTTTCCCATAAGCCATTAG 59.117 43.478 0.00 0.00 43.93 1.73
3371 3854 3.550842 CGCTTTTCCCATAAGCCATTAGC 60.551 47.826 0.00 0.00 43.93 3.09
3397 3880 9.512435 CATCATTTATTGAGGCTTTTGAACTAG 57.488 33.333 0.00 0.00 37.89 2.57
3398 3881 8.635765 TCATTTATTGAGGCTTTTGAACTAGT 57.364 30.769 0.00 0.00 0.00 2.57
3399 3882 9.077885 TCATTTATTGAGGCTTTTGAACTAGTT 57.922 29.630 8.13 8.13 0.00 2.24
3403 3886 9.733556 TTATTGAGGCTTTTGAACTAGTTATGA 57.266 29.630 8.42 0.00 0.00 2.15
3404 3887 7.672983 TTGAGGCTTTTGAACTAGTTATGAG 57.327 36.000 8.42 5.84 0.00 2.90
3405 3888 7.004555 TGAGGCTTTTGAACTAGTTATGAGA 57.995 36.000 8.42 0.00 0.00 3.27
3406 3889 7.624549 TGAGGCTTTTGAACTAGTTATGAGAT 58.375 34.615 8.42 0.00 0.00 2.75
3407 3890 8.758829 TGAGGCTTTTGAACTAGTTATGAGATA 58.241 33.333 8.42 0.00 0.00 1.98
3408 3891 9.601217 GAGGCTTTTGAACTAGTTATGAGATAA 57.399 33.333 8.42 0.00 0.00 1.75
3409 3892 9.384764 AGGCTTTTGAACTAGTTATGAGATAAC 57.615 33.333 8.42 0.00 44.18 1.89
3436 3919 8.837788 AATTTAGAAGCCTCAAATTCTTTTGG 57.162 30.769 0.00 0.00 42.10 3.28
3437 3920 4.879197 AGAAGCCTCAAATTCTTTTGGG 57.121 40.909 0.00 0.00 42.06 4.12
3438 3921 4.482990 AGAAGCCTCAAATTCTTTTGGGA 58.517 39.130 0.00 0.00 44.68 4.37
3439 3922 5.089434 AGAAGCCTCAAATTCTTTTGGGAT 58.911 37.500 0.00 0.00 44.68 3.85
3440 3923 5.186603 AGAAGCCTCAAATTCTTTTGGGATC 59.813 40.000 0.00 0.00 44.68 3.36
3441 3924 4.419282 AGCCTCAAATTCTTTTGGGATCA 58.581 39.130 0.00 0.00 44.68 2.92
3442 3925 4.840115 AGCCTCAAATTCTTTTGGGATCAA 59.160 37.500 0.00 0.00 44.68 2.57
3443 3926 4.931601 GCCTCAAATTCTTTTGGGATCAAC 59.068 41.667 0.00 0.00 44.68 3.18
3444 3927 5.279657 GCCTCAAATTCTTTTGGGATCAACT 60.280 40.000 0.00 0.00 44.68 3.16
3445 3928 6.742363 GCCTCAAATTCTTTTGGGATCAACTT 60.742 38.462 0.00 0.00 44.68 2.66
3446 3929 7.525360 GCCTCAAATTCTTTTGGGATCAACTTA 60.525 37.037 0.00 0.00 44.68 2.24
3447 3930 8.534496 CCTCAAATTCTTTTGGGATCAACTTAT 58.466 33.333 0.00 0.00 44.68 1.73
3448 3931 9.933723 CTCAAATTCTTTTGGGATCAACTTATT 57.066 29.630 0.00 0.00 44.68 1.40
3469 3952 4.569719 TTTTTAAGCTGGGGAGAGGTAG 57.430 45.455 0.00 0.00 0.00 3.18
3470 3953 1.497161 TTAAGCTGGGGAGAGGTAGC 58.503 55.000 0.00 0.00 36.45 3.58
3471 3954 3.114390 AGCTGGGGAGAGGTAGCT 58.886 61.111 0.00 0.00 41.38 3.32
3472 3955 1.394151 AGCTGGGGAGAGGTAGCTT 59.606 57.895 0.00 0.00 43.49 3.74
3473 3956 0.637195 AGCTGGGGAGAGGTAGCTTA 59.363 55.000 0.00 0.00 43.49 3.09
3474 3957 1.221781 AGCTGGGGAGAGGTAGCTTAT 59.778 52.381 0.00 0.00 43.49 1.73
3475 3958 2.050918 GCTGGGGAGAGGTAGCTTATT 58.949 52.381 0.00 0.00 33.53 1.40
3476 3959 2.439880 GCTGGGGAGAGGTAGCTTATTT 59.560 50.000 0.00 0.00 33.53 1.40
3477 3960 3.745797 GCTGGGGAGAGGTAGCTTATTTG 60.746 52.174 0.00 0.00 33.53 2.32
3478 3961 3.456277 CTGGGGAGAGGTAGCTTATTTGT 59.544 47.826 0.00 0.00 0.00 2.83
3479 3962 3.850173 TGGGGAGAGGTAGCTTATTTGTT 59.150 43.478 0.00 0.00 0.00 2.83
3480 3963 5.034200 TGGGGAGAGGTAGCTTATTTGTTA 58.966 41.667 0.00 0.00 0.00 2.41
3481 3964 5.489637 TGGGGAGAGGTAGCTTATTTGTTAA 59.510 40.000 0.00 0.00 0.00 2.01
3482 3965 6.056236 GGGGAGAGGTAGCTTATTTGTTAAG 58.944 44.000 0.00 0.00 40.34 1.85
3490 3973 3.859411 CTTATTTGTTAAGCCGCCCAA 57.141 42.857 0.00 0.00 31.37 4.12
3491 3974 4.181309 CTTATTTGTTAAGCCGCCCAAA 57.819 40.909 0.00 0.00 31.37 3.28
3492 3975 4.561105 CTTATTTGTTAAGCCGCCCAAAA 58.439 39.130 0.00 0.00 31.37 2.44
3493 3976 2.981859 TTTGTTAAGCCGCCCAAAAA 57.018 40.000 0.00 0.00 0.00 1.94
3515 3998 7.849322 AAAAATGGTTAAAAGGGCTAGAAGA 57.151 32.000 0.00 0.00 0.00 2.87
3517 4000 4.296621 TGGTTAAAAGGGCTAGAAGACC 57.703 45.455 0.00 0.00 46.64 3.85
3528 4011 1.669779 CTAGAAGACCGTCTACCACCG 59.330 57.143 0.26 0.00 0.00 4.94
3530 4013 2.554074 GAAGACCGTCTACCACCGCC 62.554 65.000 0.26 0.00 0.00 6.13
3531 4014 4.487412 GACCGTCTACCACCGCCG 62.487 72.222 0.00 0.00 0.00 6.46
3548 4031 1.146930 CGGCCACCATATCAGTGCT 59.853 57.895 2.24 0.00 33.75 4.40
3624 4117 1.892819 CGAGGGCCATGTCAGTGACT 61.893 60.000 23.29 7.08 33.15 3.41
3625 4118 0.107945 GAGGGCCATGTCAGTGACTC 60.108 60.000 23.29 7.66 33.15 3.36
3626 4119 0.546267 AGGGCCATGTCAGTGACTCT 60.546 55.000 23.29 8.77 33.15 3.24
3627 4120 0.107945 GGGCCATGTCAGTGACTCTC 60.108 60.000 23.29 10.09 33.15 3.20
3628 4121 0.107945 GGCCATGTCAGTGACTCTCC 60.108 60.000 23.29 14.68 33.15 3.71
3629 4122 0.107945 GCCATGTCAGTGACTCTCCC 60.108 60.000 23.29 5.48 33.15 4.30
3630 4123 1.566211 CCATGTCAGTGACTCTCCCT 58.434 55.000 23.29 0.00 33.15 4.20
3631 4124 1.206610 CCATGTCAGTGACTCTCCCTG 59.793 57.143 23.29 10.88 33.15 4.45
3632 4125 0.901124 ATGTCAGTGACTCTCCCTGC 59.099 55.000 23.29 0.00 33.15 4.85
3633 4126 0.178950 TGTCAGTGACTCTCCCTGCT 60.179 55.000 23.29 0.00 33.15 4.24
3634 4127 0.246086 GTCAGTGACTCTCCCTGCTG 59.754 60.000 16.26 0.00 0.00 4.41
3635 4128 1.079266 CAGTGACTCTCCCTGCTGC 60.079 63.158 0.00 0.00 0.00 5.25
3636 4129 2.267324 GTGACTCTCCCTGCTGCC 59.733 66.667 0.00 0.00 0.00 4.85
3637 4130 2.203832 TGACTCTCCCTGCTGCCA 60.204 61.111 0.00 0.00 0.00 4.92
3638 4131 1.614525 TGACTCTCCCTGCTGCCAT 60.615 57.895 0.00 0.00 0.00 4.40
3639 4132 1.145819 GACTCTCCCTGCTGCCATC 59.854 63.158 0.00 0.00 0.00 3.51
3640 4133 1.306825 ACTCTCCCTGCTGCCATCT 60.307 57.895 0.00 0.00 0.00 2.90
3641 4134 0.031716 ACTCTCCCTGCTGCCATCTA 60.032 55.000 0.00 0.00 0.00 1.98
3642 4135 1.350071 CTCTCCCTGCTGCCATCTAT 58.650 55.000 0.00 0.00 0.00 1.98
3643 4136 1.002201 CTCTCCCTGCTGCCATCTATG 59.998 57.143 0.00 0.00 0.00 2.23
3644 4137 0.763652 CTCCCTGCTGCCATCTATGT 59.236 55.000 0.00 0.00 0.00 2.29
3645 4138 0.761187 TCCCTGCTGCCATCTATGTC 59.239 55.000 0.00 0.00 0.00 3.06
3646 4139 0.471191 CCCTGCTGCCATCTATGTCA 59.529 55.000 0.00 0.00 0.00 3.58
3647 4140 1.590932 CCTGCTGCCATCTATGTCAC 58.409 55.000 0.00 0.00 0.00 3.67
3648 4141 1.590932 CTGCTGCCATCTATGTCACC 58.409 55.000 0.00 0.00 0.00 4.02
3649 4142 0.181114 TGCTGCCATCTATGTCACCC 59.819 55.000 0.00 0.00 0.00 4.61
3650 4143 0.181114 GCTGCCATCTATGTCACCCA 59.819 55.000 0.00 0.00 0.00 4.51
3651 4144 1.813092 GCTGCCATCTATGTCACCCAG 60.813 57.143 0.00 0.00 0.00 4.45
3652 4145 0.839277 TGCCATCTATGTCACCCAGG 59.161 55.000 0.00 0.00 0.00 4.45
3653 4146 0.839946 GCCATCTATGTCACCCAGGT 59.160 55.000 0.00 0.00 0.00 4.00
3654 4147 1.475751 GCCATCTATGTCACCCAGGTG 60.476 57.143 10.73 10.73 46.64 4.00
3655 4148 1.141657 CCATCTATGTCACCCAGGTGG 59.858 57.143 16.63 0.00 45.43 4.61
3665 4158 4.290622 CCAGGTGGTGCTGCCCTT 62.291 66.667 0.00 0.00 36.04 3.95
3666 4159 2.674380 CAGGTGGTGCTGCCCTTC 60.674 66.667 0.00 0.00 36.04 3.46
3667 4160 2.856000 AGGTGGTGCTGCCCTTCT 60.856 61.111 0.00 0.00 36.04 2.85
3668 4161 2.116125 GGTGGTGCTGCCCTTCTT 59.884 61.111 0.00 0.00 36.04 2.52
3669 4162 1.973812 GGTGGTGCTGCCCTTCTTC 60.974 63.158 0.00 0.00 36.04 2.87
3670 4163 1.973812 GTGGTGCTGCCCTTCTTCC 60.974 63.158 0.00 0.00 36.04 3.46
3671 4164 2.156098 TGGTGCTGCCCTTCTTCCT 61.156 57.895 0.00 0.00 36.04 3.36
3672 4165 1.377856 GGTGCTGCCCTTCTTCCTC 60.378 63.158 0.00 0.00 0.00 3.71
3673 4166 1.743252 GTGCTGCCCTTCTTCCTCG 60.743 63.158 0.00 0.00 0.00 4.63
3674 4167 1.913262 TGCTGCCCTTCTTCCTCGA 60.913 57.895 0.00 0.00 0.00 4.04
3675 4168 1.448717 GCTGCCCTTCTTCCTCGAC 60.449 63.158 0.00 0.00 0.00 4.20
3676 4169 1.219393 CTGCCCTTCTTCCTCGACC 59.781 63.158 0.00 0.00 0.00 4.79
3677 4170 1.535444 TGCCCTTCTTCCTCGACCA 60.535 57.895 0.00 0.00 0.00 4.02
3678 4171 0.909610 TGCCCTTCTTCCTCGACCAT 60.910 55.000 0.00 0.00 0.00 3.55
3679 4172 0.462759 GCCCTTCTTCCTCGACCATG 60.463 60.000 0.00 0.00 0.00 3.66
3680 4173 0.462759 CCCTTCTTCCTCGACCATGC 60.463 60.000 0.00 0.00 0.00 4.06
3681 4174 0.462759 CCTTCTTCCTCGACCATGCC 60.463 60.000 0.00 0.00 0.00 4.40
3682 4175 0.539051 CTTCTTCCTCGACCATGCCT 59.461 55.000 0.00 0.00 0.00 4.75
3683 4176 0.984230 TTCTTCCTCGACCATGCCTT 59.016 50.000 0.00 0.00 0.00 4.35
3684 4177 0.984230 TCTTCCTCGACCATGCCTTT 59.016 50.000 0.00 0.00 0.00 3.11
3685 4178 2.184533 TCTTCCTCGACCATGCCTTTA 58.815 47.619 0.00 0.00 0.00 1.85
3686 4179 2.093658 TCTTCCTCGACCATGCCTTTAC 60.094 50.000 0.00 0.00 0.00 2.01
3687 4180 1.568504 TCCTCGACCATGCCTTTACT 58.431 50.000 0.00 0.00 0.00 2.24
3688 4181 1.207089 TCCTCGACCATGCCTTTACTG 59.793 52.381 0.00 0.00 0.00 2.74
3689 4182 1.009829 CTCGACCATGCCTTTACTGC 58.990 55.000 0.00 0.00 0.00 4.40
3690 4183 0.392461 TCGACCATGCCTTTACTGCC 60.392 55.000 0.00 0.00 0.00 4.85
3691 4184 1.705337 CGACCATGCCTTTACTGCCG 61.705 60.000 0.00 0.00 0.00 5.69
3692 4185 1.376609 GACCATGCCTTTACTGCCGG 61.377 60.000 0.00 0.00 0.00 6.13
3693 4186 1.077787 CCATGCCTTTACTGCCGGA 60.078 57.895 5.05 0.00 0.00 5.14
3694 4187 1.097547 CCATGCCTTTACTGCCGGAG 61.098 60.000 5.05 1.84 0.00 4.63
3695 4188 0.107703 CATGCCTTTACTGCCGGAGA 60.108 55.000 5.05 0.00 0.00 3.71
3696 4189 0.107654 ATGCCTTTACTGCCGGAGAC 60.108 55.000 5.05 0.00 0.00 3.36
3697 4190 1.449778 GCCTTTACTGCCGGAGACC 60.450 63.158 5.05 0.00 0.00 3.85
3698 4191 1.221021 CCTTTACTGCCGGAGACCC 59.779 63.158 5.05 0.00 0.00 4.46
3699 4192 1.221021 CTTTACTGCCGGAGACCCC 59.779 63.158 5.05 0.00 0.00 4.95
3700 4193 1.536907 TTTACTGCCGGAGACCCCA 60.537 57.895 5.05 0.00 34.14 4.96
3701 4194 1.128809 TTTACTGCCGGAGACCCCAA 61.129 55.000 5.05 0.00 34.14 4.12
3702 4195 1.550130 TTACTGCCGGAGACCCCAAG 61.550 60.000 5.05 0.00 34.14 3.61
3703 4196 4.101448 CTGCCGGAGACCCCAAGG 62.101 72.222 5.05 0.00 40.04 3.61
3713 4206 3.072468 CCCCAAGGTGCAGCCATG 61.072 66.667 13.29 12.10 40.61 3.66
3729 4222 3.350833 GCCATGGGCTATCTTCTATTGG 58.649 50.000 15.13 0.00 46.69 3.16
3730 4223 3.245052 GCCATGGGCTATCTTCTATTGGT 60.245 47.826 15.13 0.00 46.69 3.67
3731 4224 4.583871 CCATGGGCTATCTTCTATTGGTC 58.416 47.826 2.85 0.00 0.00 4.02
3732 4225 4.566488 CCATGGGCTATCTTCTATTGGTCC 60.566 50.000 2.85 0.00 0.00 4.46
3733 4226 2.979678 TGGGCTATCTTCTATTGGTCCC 59.020 50.000 0.00 0.00 0.00 4.46
3734 4227 3.252351 GGGCTATCTTCTATTGGTCCCT 58.748 50.000 0.00 0.00 0.00 4.20
3735 4228 3.008485 GGGCTATCTTCTATTGGTCCCTG 59.992 52.174 0.00 0.00 0.00 4.45
3736 4229 3.558109 GGCTATCTTCTATTGGTCCCTGC 60.558 52.174 0.00 0.00 0.00 4.85
3737 4230 3.558109 GCTATCTTCTATTGGTCCCTGCC 60.558 52.174 0.00 0.00 0.00 4.85
3738 4231 1.965414 TCTTCTATTGGTCCCTGCCA 58.035 50.000 0.00 0.00 36.62 4.92
3743 4236 4.841441 TTGGTCCCTGCCAATCAC 57.159 55.556 0.00 0.00 42.98 3.06
3744 4237 1.303236 TTGGTCCCTGCCAATCACG 60.303 57.895 0.00 0.00 42.98 4.35
3745 4238 2.438434 GGTCCCTGCCAATCACGG 60.438 66.667 0.00 0.00 0.00 4.94
3746 4239 2.351276 GTCCCTGCCAATCACGGT 59.649 61.111 0.00 0.00 0.00 4.83
3747 4240 1.303317 GTCCCTGCCAATCACGGTT 60.303 57.895 0.00 0.00 0.00 4.44
3748 4241 0.035820 GTCCCTGCCAATCACGGTTA 60.036 55.000 0.00 0.00 0.00 2.85
3749 4242 0.251916 TCCCTGCCAATCACGGTTAG 59.748 55.000 0.00 0.00 0.00 2.34
3750 4243 0.035439 CCCTGCCAATCACGGTTAGT 60.035 55.000 0.00 0.00 0.00 2.24
3751 4244 1.369625 CCTGCCAATCACGGTTAGTC 58.630 55.000 0.00 0.00 0.00 2.59
3752 4245 1.338674 CCTGCCAATCACGGTTAGTCA 60.339 52.381 0.00 0.00 0.00 3.41
3753 4246 1.732259 CTGCCAATCACGGTTAGTCAC 59.268 52.381 0.00 0.00 0.00 3.67
3754 4247 1.346395 TGCCAATCACGGTTAGTCACT 59.654 47.619 0.00 0.00 0.00 3.41
3755 4248 2.563620 TGCCAATCACGGTTAGTCACTA 59.436 45.455 0.00 0.00 0.00 2.74
3756 4249 2.928116 GCCAATCACGGTTAGTCACTAC 59.072 50.000 0.00 0.00 0.00 2.73
3757 4250 3.368116 GCCAATCACGGTTAGTCACTACT 60.368 47.826 0.00 0.00 39.91 2.57
3758 4251 4.142315 GCCAATCACGGTTAGTCACTACTA 60.142 45.833 0.00 0.00 37.15 1.82
3759 4252 5.451520 GCCAATCACGGTTAGTCACTACTAT 60.452 44.000 0.00 0.00 38.02 2.12
3760 4253 6.570692 CCAATCACGGTTAGTCACTACTATT 58.429 40.000 0.00 0.00 38.02 1.73
3761 4254 7.039882 CCAATCACGGTTAGTCACTACTATTT 58.960 38.462 0.00 0.00 38.02 1.40
3762 4255 7.548075 CCAATCACGGTTAGTCACTACTATTTT 59.452 37.037 0.00 0.00 38.02 1.82
3763 4256 8.380644 CAATCACGGTTAGTCACTACTATTTTG 58.619 37.037 0.00 0.00 38.02 2.44
3764 4257 5.865552 TCACGGTTAGTCACTACTATTTTGC 59.134 40.000 0.00 0.00 38.02 3.68
3765 4258 5.636121 CACGGTTAGTCACTACTATTTTGCA 59.364 40.000 0.00 0.00 38.02 4.08
3766 4259 6.312918 CACGGTTAGTCACTACTATTTTGCAT 59.687 38.462 0.00 0.00 38.02 3.96
3767 4260 7.490079 CACGGTTAGTCACTACTATTTTGCATA 59.510 37.037 0.00 0.00 38.02 3.14
3768 4261 8.036575 ACGGTTAGTCACTACTATTTTGCATAA 58.963 33.333 0.00 0.00 38.02 1.90
3769 4262 8.875803 CGGTTAGTCACTACTATTTTGCATAAA 58.124 33.333 0.00 0.00 38.02 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.170998 ACTTGATCTTACGTTTCGTTGAAATCT 59.829 33.333 0.00 0.00 41.54 2.40
1 2 7.288672 ACTTGATCTTACGTTTCGTTGAAATC 58.711 34.615 0.00 1.22 41.54 2.17
15 16 8.989653 AGCTACTTTCTACAACTTGATCTTAC 57.010 34.615 0.00 0.00 0.00 2.34
61 62 8.161425 ACTTATTTAGCTCTAAACCCACTCAAA 58.839 33.333 4.39 0.00 37.80 2.69
200 270 6.723052 TGCTAGTTCATCCATGATCTCTGATA 59.277 38.462 0.00 0.00 37.80 2.15
274 346 8.557029 GCTTTAATAGCCGTGTGTTAAATATCT 58.443 33.333 0.00 0.00 44.48 1.98
311 384 7.609056 AGCAGAAACATTAAAGCTTGATTGAT 58.391 30.769 11.85 0.00 0.00 2.57
443 519 2.393768 CGCAACATTGGCTCGCTCT 61.394 57.895 0.00 0.00 0.00 4.09
444 520 2.099062 CGCAACATTGGCTCGCTC 59.901 61.111 0.00 0.00 0.00 5.03
448 524 0.874390 TCTTGACGCAACATTGGCTC 59.126 50.000 0.00 0.00 0.00 4.70
469 545 0.735471 CTCGATCGAGAGACAAGCCA 59.265 55.000 36.13 1.73 46.97 4.75
472 548 4.601621 TGTAACTCGATCGAGAGACAAG 57.398 45.455 42.97 21.87 46.97 3.16
489 565 7.614192 TGAACAGTGGATGACTACTCTATGTAA 59.386 37.037 0.00 0.00 35.71 2.41
496 572 6.402222 AGAAATGAACAGTGGATGACTACTC 58.598 40.000 0.00 0.00 35.71 2.59
524 600 4.946772 TGTGAGTGGTTCAAAATTGACTGA 59.053 37.500 0.00 0.00 37.61 3.41
525 601 5.247507 TGTGAGTGGTTCAAAATTGACTG 57.752 39.130 0.00 0.00 37.61 3.51
547 623 3.866449 CTGTAAGAAAAGCTCGAGGGCTT 60.866 47.826 15.58 10.45 45.88 4.35
566 642 1.977854 TGTCTGTGTGGATAAGGCTGT 59.022 47.619 0.00 0.00 0.00 4.40
575 651 0.254462 TTGCCTTGTGTCTGTGTGGA 59.746 50.000 0.00 0.00 0.00 4.02
644 720 5.872617 TGTCTTCTAACAAATACATGACGGG 59.127 40.000 0.00 0.00 0.00 5.28
676 752 9.136952 ACGAAGAAATAACTCATTGTACAGTAC 57.863 33.333 3.49 3.49 0.00 2.73
764 842 9.657419 CAATTAAAGAAAAGGCATGTCCTATTT 57.343 29.630 8.81 10.69 46.94 1.40
765 843 8.815912 ACAATTAAAGAAAAGGCATGTCCTATT 58.184 29.630 8.81 4.29 46.94 1.73
827 926 6.761242 CGGAGTCCATGTAAAGTGATAAATGA 59.239 38.462 10.49 0.00 0.00 2.57
828 927 6.511767 GCGGAGTCCATGTAAAGTGATAAATG 60.512 42.308 10.49 0.00 0.00 2.32
830 929 4.873827 GCGGAGTCCATGTAAAGTGATAAA 59.126 41.667 10.49 0.00 0.00 1.40
832 931 3.181469 GGCGGAGTCCATGTAAAGTGATA 60.181 47.826 10.49 0.00 0.00 2.15
1142 1507 4.767255 CACCCTGAGACGCCCAGC 62.767 72.222 0.00 0.00 0.00 4.85
1578 1946 2.124570 GCATCCACCATCTGGCGT 60.125 61.111 0.00 0.00 40.39 5.68
1746 2117 1.642037 CGTAGCCTTCGTCGACCAGA 61.642 60.000 10.58 0.00 0.00 3.86
1870 2241 1.960040 ATGATCCTGCCGACGAAGCA 61.960 55.000 0.00 0.00 38.82 3.91
1956 2327 3.706373 TCGCTGCCTTGGAGGGAC 61.706 66.667 0.00 0.00 37.94 4.46
2049 2420 8.840321 GGACACATGCATATCTATTTAAGTGTT 58.160 33.333 11.81 0.00 36.71 3.32
2058 2429 9.755804 CTAATTATCGGACACATGCATATCTAT 57.244 33.333 0.00 0.00 0.00 1.98
2061 2460 6.536582 AGCTAATTATCGGACACATGCATATC 59.463 38.462 0.00 0.00 0.00 1.63
2446 2875 4.308458 CCGGCTTGTCCCACACGA 62.308 66.667 0.00 0.00 0.00 4.35
2618 3047 2.398554 CGTGGCAACCCAGAATCCG 61.399 63.158 0.00 0.00 43.18 4.18
2694 3123 3.160585 CCCCAGCACCTCAGACAA 58.839 61.111 0.00 0.00 0.00 3.18
2709 3138 1.448540 CCATCTCACACGACAGCCC 60.449 63.158 0.00 0.00 0.00 5.19
2900 3345 0.108804 CAGCAGTACACGTACCAGGG 60.109 60.000 3.73 0.00 36.75 4.45
2955 3400 5.411977 TCCTGATAGTAGCTCATAACTACGC 59.588 44.000 0.00 0.00 43.86 4.42
2967 3441 4.399618 TCACACTCACTTCCTGATAGTAGC 59.600 45.833 0.00 0.00 0.00 3.58
3088 3562 4.377431 GGTCAATGACAACGTGAGATCAAC 60.377 45.833 15.86 0.00 33.68 3.18
3156 3630 0.816421 ACGTTAGTTTTGGCGTGCCT 60.816 50.000 12.84 0.00 36.16 4.75
3161 3635 0.582960 ACCGAACGTTAGTTTTGGCG 59.417 50.000 0.00 0.00 41.34 5.69
3188 3662 3.130516 CGTGATAGTGCTAAGGAACCAGA 59.869 47.826 0.00 0.00 0.00 3.86
3218 3697 5.689383 ATGCAAATGTGTACGTTCTCTTT 57.311 34.783 0.00 0.00 0.00 2.52
3259 3738 1.552719 GGTTAGGAGTCTGTGGGGTCT 60.553 57.143 0.00 0.00 0.00 3.85
3265 3744 1.254026 TCGGTGGTTAGGAGTCTGTG 58.746 55.000 0.00 0.00 0.00 3.66
3267 3746 1.409427 GGATCGGTGGTTAGGAGTCTG 59.591 57.143 0.00 0.00 0.00 3.51
3327 3810 1.685180 GGGAGGAGGCGGCTTATTTTT 60.685 52.381 14.76 0.00 0.00 1.94
3328 3811 0.106669 GGGAGGAGGCGGCTTATTTT 60.107 55.000 14.76 0.00 0.00 1.82
3329 3812 0.988678 AGGGAGGAGGCGGCTTATTT 60.989 55.000 14.76 0.00 0.00 1.40
3330 3813 1.384643 AGGGAGGAGGCGGCTTATT 60.385 57.895 14.76 1.09 0.00 1.40
3331 3814 1.839296 GAGGGAGGAGGCGGCTTAT 60.839 63.158 14.76 4.47 0.00 1.73
3332 3815 2.444140 GAGGGAGGAGGCGGCTTA 60.444 66.667 14.76 0.00 0.00 3.09
3337 3820 3.316573 AAAAGCGAGGGAGGAGGCG 62.317 63.158 0.00 0.00 0.00 5.52
3338 3821 1.450491 GAAAAGCGAGGGAGGAGGC 60.450 63.158 0.00 0.00 0.00 4.70
3339 3822 1.222113 GGAAAAGCGAGGGAGGAGG 59.778 63.158 0.00 0.00 0.00 4.30
3340 3823 1.222113 GGGAAAAGCGAGGGAGGAG 59.778 63.158 0.00 0.00 0.00 3.69
3341 3824 0.914417 ATGGGAAAAGCGAGGGAGGA 60.914 55.000 0.00 0.00 0.00 3.71
3342 3825 0.837272 TATGGGAAAAGCGAGGGAGG 59.163 55.000 0.00 0.00 0.00 4.30
3343 3826 2.565841 CTTATGGGAAAAGCGAGGGAG 58.434 52.381 0.00 0.00 0.00 4.30
3344 3827 1.408266 GCTTATGGGAAAAGCGAGGGA 60.408 52.381 0.00 0.00 39.92 4.20
3345 3828 1.025041 GCTTATGGGAAAAGCGAGGG 58.975 55.000 0.00 0.00 39.92 4.30
3350 3833 3.384467 TGCTAATGGCTTATGGGAAAAGC 59.616 43.478 0.00 0.00 46.90 3.51
3351 3834 5.302568 TGATGCTAATGGCTTATGGGAAAAG 59.697 40.000 0.00 0.00 42.39 2.27
3352 3835 5.207354 TGATGCTAATGGCTTATGGGAAAA 58.793 37.500 0.00 0.00 42.39 2.29
3353 3836 4.802307 TGATGCTAATGGCTTATGGGAAA 58.198 39.130 0.00 0.00 42.39 3.13
3354 3837 4.451891 TGATGCTAATGGCTTATGGGAA 57.548 40.909 0.00 0.00 42.39 3.97
3355 3838 4.662966 ATGATGCTAATGGCTTATGGGA 57.337 40.909 0.00 0.00 42.39 4.37
3356 3839 5.733620 AAATGATGCTAATGGCTTATGGG 57.266 39.130 0.00 0.00 42.39 4.00
3357 3840 8.525316 TCAATAAATGATGCTAATGGCTTATGG 58.475 33.333 0.00 0.00 35.92 2.74
3358 3841 9.569167 CTCAATAAATGATGCTAATGGCTTATG 57.431 33.333 0.00 0.00 37.44 1.90
3359 3842 8.746530 CCTCAATAAATGATGCTAATGGCTTAT 58.253 33.333 0.00 0.00 37.44 1.73
3360 3843 7.309377 GCCTCAATAAATGATGCTAATGGCTTA 60.309 37.037 0.00 0.00 43.81 3.09
3361 3844 6.517864 GCCTCAATAAATGATGCTAATGGCTT 60.518 38.462 0.00 0.00 43.81 4.35
3362 3845 5.047519 GCCTCAATAAATGATGCTAATGGCT 60.048 40.000 0.00 0.00 43.81 4.75
3363 3846 5.166398 GCCTCAATAAATGATGCTAATGGC 58.834 41.667 0.00 0.00 43.81 4.40
3370 3853 6.815142 AGTTCAAAAGCCTCAATAAATGATGC 59.185 34.615 0.00 0.00 46.49 3.91
3371 3854 9.512435 CTAGTTCAAAAGCCTCAATAAATGATG 57.488 33.333 0.00 0.00 37.44 3.07
3372 3855 9.247861 ACTAGTTCAAAAGCCTCAATAAATGAT 57.752 29.630 0.00 0.00 37.44 2.45
3373 3856 8.635765 ACTAGTTCAAAAGCCTCAATAAATGA 57.364 30.769 0.00 0.00 36.38 2.57
3377 3860 9.733556 TCATAACTAGTTCAAAAGCCTCAATAA 57.266 29.630 12.39 0.00 0.00 1.40
3378 3861 9.383519 CTCATAACTAGTTCAAAAGCCTCAATA 57.616 33.333 12.39 0.00 0.00 1.90
3379 3862 8.103305 TCTCATAACTAGTTCAAAAGCCTCAAT 58.897 33.333 12.39 0.00 0.00 2.57
3380 3863 7.450074 TCTCATAACTAGTTCAAAAGCCTCAA 58.550 34.615 12.39 0.00 0.00 3.02
3381 3864 7.004555 TCTCATAACTAGTTCAAAAGCCTCA 57.995 36.000 12.39 0.00 0.00 3.86
3382 3865 9.601217 TTATCTCATAACTAGTTCAAAAGCCTC 57.399 33.333 12.39 0.00 0.00 4.70
3383 3866 9.384764 GTTATCTCATAACTAGTTCAAAAGCCT 57.615 33.333 12.39 0.79 41.40 4.58
3448 3931 3.308188 GCTACCTCTCCCCAGCTTAAAAA 60.308 47.826 0.00 0.00 0.00 1.94
3449 3932 2.238898 GCTACCTCTCCCCAGCTTAAAA 59.761 50.000 0.00 0.00 0.00 1.52
3450 3933 1.838077 GCTACCTCTCCCCAGCTTAAA 59.162 52.381 0.00 0.00 0.00 1.52
3451 3934 1.008449 AGCTACCTCTCCCCAGCTTAA 59.992 52.381 0.00 0.00 41.50 1.85
3452 3935 0.637195 AGCTACCTCTCCCCAGCTTA 59.363 55.000 0.00 0.00 41.50 3.09
3453 3936 0.252927 AAGCTACCTCTCCCCAGCTT 60.253 55.000 1.97 1.97 46.69 3.74
3454 3937 0.637195 TAAGCTACCTCTCCCCAGCT 59.363 55.000 0.00 0.00 46.05 4.24
3455 3938 1.723288 ATAAGCTACCTCTCCCCAGC 58.277 55.000 0.00 0.00 0.00 4.85
3456 3939 3.456277 ACAAATAAGCTACCTCTCCCCAG 59.544 47.826 0.00 0.00 0.00 4.45
3457 3940 3.460825 ACAAATAAGCTACCTCTCCCCA 58.539 45.455 0.00 0.00 0.00 4.96
3458 3941 4.505324 AACAAATAAGCTACCTCTCCCC 57.495 45.455 0.00 0.00 0.00 4.81
3470 3953 3.859411 TTGGGCGGCTTAACAAATAAG 57.141 42.857 9.56 0.00 43.32 1.73
3471 3954 4.602340 TTTTGGGCGGCTTAACAAATAA 57.398 36.364 9.56 0.00 33.40 1.40
3472 3955 4.602340 TTTTTGGGCGGCTTAACAAATA 57.398 36.364 9.56 3.34 33.40 1.40
3473 3956 3.477210 TTTTTGGGCGGCTTAACAAAT 57.523 38.095 9.56 0.00 33.40 2.32
3474 3957 2.981859 TTTTTGGGCGGCTTAACAAA 57.018 40.000 9.56 7.99 0.00 2.83
3491 3974 7.256190 GGTCTTCTAGCCCTTTTAACCATTTTT 60.256 37.037 0.00 0.00 0.00 1.94
3492 3975 6.210784 GGTCTTCTAGCCCTTTTAACCATTTT 59.789 38.462 0.00 0.00 0.00 1.82
3493 3976 5.715279 GGTCTTCTAGCCCTTTTAACCATTT 59.285 40.000 0.00 0.00 0.00 2.32
3494 3977 5.262009 GGTCTTCTAGCCCTTTTAACCATT 58.738 41.667 0.00 0.00 0.00 3.16
3495 3978 4.625564 CGGTCTTCTAGCCCTTTTAACCAT 60.626 45.833 0.00 0.00 0.00 3.55
3496 3979 3.307199 CGGTCTTCTAGCCCTTTTAACCA 60.307 47.826 0.00 0.00 0.00 3.67
3497 3980 3.268330 CGGTCTTCTAGCCCTTTTAACC 58.732 50.000 0.00 0.00 0.00 2.85
3498 3981 3.931468 GACGGTCTTCTAGCCCTTTTAAC 59.069 47.826 0.00 0.00 0.00 2.01
3499 3982 3.836562 AGACGGTCTTCTAGCCCTTTTAA 59.163 43.478 4.45 0.00 0.00 1.52
3500 3983 3.438183 AGACGGTCTTCTAGCCCTTTTA 58.562 45.455 4.45 0.00 0.00 1.52
3501 3984 2.258109 AGACGGTCTTCTAGCCCTTTT 58.742 47.619 4.45 0.00 0.00 2.27
3528 4011 1.893808 CACTGATATGGTGGCCGGC 60.894 63.158 21.18 21.18 0.00 6.13
3530 4013 1.146930 AGCACTGATATGGTGGCCG 59.853 57.895 0.00 0.00 35.47 6.13
3531 4014 2.711711 CAGCACTGATATGGTGGCC 58.288 57.895 0.00 0.00 42.99 5.36
3534 4017 1.162181 CCGCCAGCACTGATATGGTG 61.162 60.000 0.00 0.00 45.64 4.17
3535 4018 1.146930 CCGCCAGCACTGATATGGT 59.853 57.895 0.00 0.00 36.43 3.55
3536 4019 2.256591 GCCGCCAGCACTGATATGG 61.257 63.158 0.00 0.00 42.97 2.74
3537 4020 3.337619 GCCGCCAGCACTGATATG 58.662 61.111 0.00 0.00 42.97 1.78
3574 4057 1.908619 TGGTGGAGATAAAGCAGCTGA 59.091 47.619 20.43 0.00 0.00 4.26
3575 4058 2.408271 TGGTGGAGATAAAGCAGCTG 57.592 50.000 10.11 10.11 0.00 4.24
3576 4059 2.716217 GTTGGTGGAGATAAAGCAGCT 58.284 47.619 0.00 0.00 0.00 4.24
3577 4060 1.398390 CGTTGGTGGAGATAAAGCAGC 59.602 52.381 0.00 0.00 0.00 5.25
3579 4062 1.626321 TCCGTTGGTGGAGATAAAGCA 59.374 47.619 0.00 0.00 33.05 3.91
3580 4063 2.396590 TCCGTTGGTGGAGATAAAGC 57.603 50.000 0.00 0.00 33.05 3.51
3581 4064 3.206150 CCATCCGTTGGTGGAGATAAAG 58.794 50.000 0.00 0.00 42.45 1.85
3582 4065 3.275617 CCATCCGTTGGTGGAGATAAA 57.724 47.619 0.00 0.00 42.45 1.40
3624 4117 1.054231 CATAGATGGCAGCAGGGAGA 58.946 55.000 5.19 0.00 0.00 3.71
3625 4118 0.763652 ACATAGATGGCAGCAGGGAG 59.236 55.000 5.19 0.00 0.00 4.30
3626 4119 0.761187 GACATAGATGGCAGCAGGGA 59.239 55.000 5.19 0.00 35.34 4.20
3627 4120 0.471191 TGACATAGATGGCAGCAGGG 59.529 55.000 5.19 0.00 41.84 4.45
3633 4126 0.839277 CCTGGGTGACATAGATGGCA 59.161 55.000 0.00 0.00 45.19 4.92
3634 4127 0.839946 ACCTGGGTGACATAGATGGC 59.160 55.000 0.00 0.00 35.98 4.40
3648 4141 4.290622 AAGGGCAGCACCACCTGG 62.291 66.667 0.00 0.00 42.05 4.45
3649 4142 2.674380 GAAGGGCAGCACCACCTG 60.674 66.667 0.00 0.00 42.05 4.00
3650 4143 2.417558 GAAGAAGGGCAGCACCACCT 62.418 60.000 0.00 0.00 42.05 4.00
3651 4144 1.973812 GAAGAAGGGCAGCACCACC 60.974 63.158 0.00 0.00 42.05 4.61
3652 4145 1.973812 GGAAGAAGGGCAGCACCAC 60.974 63.158 0.00 0.00 42.05 4.16
3653 4146 2.129555 GAGGAAGAAGGGCAGCACCA 62.130 60.000 0.00 0.00 42.05 4.17
3654 4147 1.377856 GAGGAAGAAGGGCAGCACC 60.378 63.158 0.00 0.00 37.93 5.01
3655 4148 1.743252 CGAGGAAGAAGGGCAGCAC 60.743 63.158 0.00 0.00 0.00 4.40
3656 4149 1.913262 TCGAGGAAGAAGGGCAGCA 60.913 57.895 0.00 0.00 0.00 4.41
3657 4150 1.448717 GTCGAGGAAGAAGGGCAGC 60.449 63.158 0.00 0.00 0.00 5.25
3658 4151 1.219393 GGTCGAGGAAGAAGGGCAG 59.781 63.158 0.00 0.00 0.00 4.85
3659 4152 0.909610 ATGGTCGAGGAAGAAGGGCA 60.910 55.000 0.00 0.00 0.00 5.36
3660 4153 0.462759 CATGGTCGAGGAAGAAGGGC 60.463 60.000 0.00 0.00 0.00 5.19
3661 4154 0.462759 GCATGGTCGAGGAAGAAGGG 60.463 60.000 0.00 0.00 0.00 3.95
3662 4155 0.462759 GGCATGGTCGAGGAAGAAGG 60.463 60.000 0.00 0.00 0.00 3.46
3663 4156 0.539051 AGGCATGGTCGAGGAAGAAG 59.461 55.000 0.00 0.00 0.00 2.85
3664 4157 0.984230 AAGGCATGGTCGAGGAAGAA 59.016 50.000 0.00 0.00 0.00 2.52
3665 4158 0.984230 AAAGGCATGGTCGAGGAAGA 59.016 50.000 0.00 0.00 0.00 2.87
3666 4159 2.093447 AGTAAAGGCATGGTCGAGGAAG 60.093 50.000 0.00 0.00 0.00 3.46
3667 4160 1.906574 AGTAAAGGCATGGTCGAGGAA 59.093 47.619 0.00 0.00 0.00 3.36
3668 4161 1.207089 CAGTAAAGGCATGGTCGAGGA 59.793 52.381 0.00 0.00 0.00 3.71
3669 4162 1.656652 CAGTAAAGGCATGGTCGAGG 58.343 55.000 0.00 0.00 0.00 4.63
3670 4163 1.009829 GCAGTAAAGGCATGGTCGAG 58.990 55.000 0.00 0.00 0.00 4.04
3671 4164 0.392461 GGCAGTAAAGGCATGGTCGA 60.392 55.000 0.00 0.00 0.00 4.20
3672 4165 1.705337 CGGCAGTAAAGGCATGGTCG 61.705 60.000 0.00 0.00 0.00 4.79
3673 4166 1.376609 CCGGCAGTAAAGGCATGGTC 61.377 60.000 0.00 0.00 0.00 4.02
3674 4167 1.378514 CCGGCAGTAAAGGCATGGT 60.379 57.895 0.00 0.00 0.00 3.55
3675 4168 1.077787 TCCGGCAGTAAAGGCATGG 60.078 57.895 0.00 0.00 0.00 3.66
3676 4169 0.107703 TCTCCGGCAGTAAAGGCATG 60.108 55.000 0.00 0.00 0.00 4.06
3677 4170 0.107654 GTCTCCGGCAGTAAAGGCAT 60.108 55.000 0.00 0.00 0.00 4.40
3678 4171 1.295423 GTCTCCGGCAGTAAAGGCA 59.705 57.895 0.00 0.00 0.00 4.75
3679 4172 1.449778 GGTCTCCGGCAGTAAAGGC 60.450 63.158 0.00 0.00 0.00 4.35
3680 4173 1.221021 GGGTCTCCGGCAGTAAAGG 59.779 63.158 0.00 0.00 0.00 3.11
3681 4174 1.221021 GGGGTCTCCGGCAGTAAAG 59.779 63.158 0.00 0.00 0.00 1.85
3682 4175 1.128809 TTGGGGTCTCCGGCAGTAAA 61.129 55.000 0.00 0.00 38.76 2.01
3683 4176 1.536907 TTGGGGTCTCCGGCAGTAA 60.537 57.895 0.00 0.00 38.76 2.24
3684 4177 1.987855 CTTGGGGTCTCCGGCAGTA 60.988 63.158 0.00 0.00 38.76 2.74
3685 4178 3.322466 CTTGGGGTCTCCGGCAGT 61.322 66.667 0.00 0.00 38.76 4.40
3686 4179 4.101448 CCTTGGGGTCTCCGGCAG 62.101 72.222 0.00 0.00 38.76 4.85
3687 4180 4.974438 ACCTTGGGGTCTCCGGCA 62.974 66.667 0.00 0.00 43.38 5.69
3688 4181 4.410400 CACCTTGGGGTCTCCGGC 62.410 72.222 0.00 0.00 45.41 6.13
3689 4182 4.410400 GCACCTTGGGGTCTCCGG 62.410 72.222 0.00 0.00 45.41 5.14
3690 4183 3.612247 CTGCACCTTGGGGTCTCCG 62.612 68.421 0.00 0.00 45.41 4.63
3691 4184 2.352805 CTGCACCTTGGGGTCTCC 59.647 66.667 0.00 0.00 45.41 3.71
3692 4185 2.360475 GCTGCACCTTGGGGTCTC 60.360 66.667 0.00 0.00 45.41 3.36
3693 4186 3.971702 GGCTGCACCTTGGGGTCT 61.972 66.667 0.50 0.00 45.41 3.85
3694 4187 3.590466 ATGGCTGCACCTTGGGGTC 62.590 63.158 0.50 0.00 45.41 4.46
3696 4189 3.072468 CATGGCTGCACCTTGGGG 61.072 66.667 0.50 0.00 39.42 4.96
3699 4192 3.766691 GCCCATGGCTGCACCTTG 61.767 66.667 6.09 11.70 46.69 3.61
3709 4202 4.566488 GGACCAATAGAAGATAGCCCATGG 60.566 50.000 4.14 4.14 0.00 3.66
3710 4203 4.566488 GGGACCAATAGAAGATAGCCCATG 60.566 50.000 0.00 0.00 33.28 3.66
3711 4204 3.589288 GGGACCAATAGAAGATAGCCCAT 59.411 47.826 0.00 0.00 33.28 4.00
3712 4205 2.979678 GGGACCAATAGAAGATAGCCCA 59.020 50.000 0.00 0.00 33.28 5.36
3713 4206 3.008485 CAGGGACCAATAGAAGATAGCCC 59.992 52.174 0.00 0.00 0.00 5.19
3714 4207 3.558109 GCAGGGACCAATAGAAGATAGCC 60.558 52.174 0.00 0.00 0.00 3.93
3715 4208 3.558109 GGCAGGGACCAATAGAAGATAGC 60.558 52.174 0.00 0.00 0.00 2.97
3716 4209 3.648067 TGGCAGGGACCAATAGAAGATAG 59.352 47.826 0.00 0.00 36.55 2.08
3717 4210 3.664320 TGGCAGGGACCAATAGAAGATA 58.336 45.455 0.00 0.00 36.55 1.98
3718 4211 2.492025 TGGCAGGGACCAATAGAAGAT 58.508 47.619 0.00 0.00 36.55 2.40
3719 4212 1.965414 TGGCAGGGACCAATAGAAGA 58.035 50.000 0.00 0.00 36.55 2.87
3720 4213 2.806945 TTGGCAGGGACCAATAGAAG 57.193 50.000 0.00 0.00 44.80 2.85
3727 4220 2.350895 CGTGATTGGCAGGGACCA 59.649 61.111 0.00 0.00 38.16 4.02
3732 4225 1.338674 TGACTAACCGTGATTGGCAGG 60.339 52.381 0.00 0.00 0.00 4.85
3733 4226 1.732259 GTGACTAACCGTGATTGGCAG 59.268 52.381 0.00 0.00 0.00 4.85
3734 4227 1.346395 AGTGACTAACCGTGATTGGCA 59.654 47.619 0.00 0.00 0.00 4.92
3735 4228 2.094762 AGTGACTAACCGTGATTGGC 57.905 50.000 0.00 0.00 0.00 4.52
3736 4229 4.451629 AGTAGTGACTAACCGTGATTGG 57.548 45.455 0.00 0.00 32.65 3.16
3737 4230 8.380644 CAAAATAGTAGTGACTAACCGTGATTG 58.619 37.037 0.00 0.00 41.53 2.67
3738 4231 7.064253 GCAAAATAGTAGTGACTAACCGTGATT 59.936 37.037 0.00 0.00 41.53 2.57
3739 4232 6.534079 GCAAAATAGTAGTGACTAACCGTGAT 59.466 38.462 0.00 0.00 41.53 3.06
3740 4233 5.865552 GCAAAATAGTAGTGACTAACCGTGA 59.134 40.000 0.00 0.00 41.53 4.35
3741 4234 5.636121 TGCAAAATAGTAGTGACTAACCGTG 59.364 40.000 0.00 0.00 41.53 4.94
3742 4235 5.786311 TGCAAAATAGTAGTGACTAACCGT 58.214 37.500 0.00 0.00 41.53 4.83
3743 4236 6.903883 ATGCAAAATAGTAGTGACTAACCG 57.096 37.500 0.00 0.00 41.53 4.44


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

AutoCloner maintained by Alex Coulton.