Multiple sequence alignment - TraesCS7A01G508200

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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 TraesCS7A01G508200 chr7A 100.000 3123 0 0 1 3123 696019817 696016695 0.000000e+00 5768.0
1 TraesCS7A01G508200 chr7A 89.277 429 44 2 2695 3123 91624646 91624220 1.270000e-148 536.0
2 TraesCS7A01G508200 chr7A 92.453 212 13 2 2914 3123 118334613 118334403 1.820000e-77 300.0
3 TraesCS7A01G508200 chr7A 76.972 469 62 29 2695 3123 509725207 509725669 3.130000e-55 226.0
4 TraesCS7A01G508200 chr7A 100.000 71 0 0 267 337 696019487 696019417 7.030000e-27 132.0
5 TraesCS7A01G508200 chr7A 100.000 71 0 0 331 401 696019551 696019481 7.030000e-27 132.0
6 TraesCS7A01G508200 chr7D 95.232 2370 74 16 331 2695 603357274 603354939 0.000000e+00 3714.0
7 TraesCS7A01G508200 chr7D 85.226 819 104 11 1886 2695 603284273 603283463 0.000000e+00 826.0
8 TraesCS7A01G508200 chr7D 96.439 337 12 0 1 337 603357540 603357204 9.780000e-155 556.0
9 TraesCS7A01G508200 chr7D 84.450 418 38 7 2716 3123 138039553 138039953 1.360000e-103 387.0
10 TraesCS7A01G508200 chr7D 80.631 444 63 21 2696 3123 165480796 165480360 3.890000e-84 322.0
11 TraesCS7A01G508200 chr7D 87.864 206 24 1 1696 1901 603292122 603291918 1.120000e-59 241.0
12 TraesCS7A01G508200 chr7D 76.010 421 77 17 1375 1780 603269242 603268831 2.460000e-46 196.0
13 TraesCS7A01G508200 chr7B 94.934 2211 73 7 345 2555 684459746 684457575 0.000000e+00 3426.0
14 TraesCS7A01G508200 chr7B 95.181 249 12 0 1 249 684459994 684459746 8.120000e-106 394.0
15 TraesCS7A01G508200 chr7B 95.890 146 3 2 2550 2695 684457166 684457024 1.870000e-57 233.0
16 TraesCS7A01G508200 chr7B 94.737 57 3 0 281 337 684459746 684459690 4.290000e-14 89.8
17 TraesCS7A01G508200 chr5D 88.903 1568 152 17 803 2356 416068137 416066578 0.000000e+00 1912.0
18 TraesCS7A01G508200 chr5A 88.205 1543 159 19 803 2330 528559573 528558039 0.000000e+00 1820.0
19 TraesCS7A01G508200 chr5A 88.000 400 47 1 333 732 528560084 528559686 3.650000e-129 472.0
20 TraesCS7A01G508200 chr5A 82.822 326 53 3 13 337 528560339 528560016 3.940000e-74 289.0
21 TraesCS7A01G508200 chr5B 85.736 652 75 15 1718 2356 502498948 502498302 0.000000e+00 673.0
22 TraesCS7A01G508200 chr5B 78.846 260 39 11 493 752 502499577 502499334 8.960000e-36 161.0
23 TraesCS7A01G508200 chr3D 79.914 463 61 21 2690 3123 501791534 501791993 8.410000e-81 311.0
24 TraesCS7A01G508200 chr3D 88.372 172 14 2 2958 3123 517006998 517006827 5.280000e-48 202.0
25 TraesCS7A01G508200 chr6A 90.000 190 19 0 2934 3123 556658123 556657934 2.410000e-61 246.0
26 TraesCS7A01G508200 chr6A 86.441 118 15 1 2695 2812 62130969 62131085 9.090000e-26 128.0
27 TraesCS7A01G508200 chr3A 90.361 166 16 0 2958 3123 670554201 670554036 5.240000e-53 219.0
28 TraesCS7A01G508200 chr3A 85.366 164 23 1 2714 2876 26047838 26047675 5.360000e-38 169.0
29 TraesCS7A01G508200 chr6D 88.333 180 13 5 2951 3123 47078845 47079023 3.160000e-50 209.0
30 TraesCS7A01G508200 chr2D 88.372 172 14 3 2958 3123 375356231 375356402 5.280000e-48 202.0
31 TraesCS7A01G508200 chr4A 82.682 179 25 4 2695 2872 620626463 620626636 1.500000e-33 154.0
32 TraesCS7A01G508200 chr1B 87.273 55 5 2 841 893 60251279 60251225 9.350000e-06 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 TraesCS7A01G508200 chr7A 696016695 696019817 3122 True 2010.666667 5768 100.000000 1 3123 3 chr7A.!!$R3 3122
1 TraesCS7A01G508200 chr7D 603354939 603357540 2601 True 2135.000000 3714 95.835500 1 2695 2 chr7D.!!$R5 2694
2 TraesCS7A01G508200 chr7D 603283463 603284273 810 True 826.000000 826 85.226000 1886 2695 1 chr7D.!!$R3 809
3 TraesCS7A01G508200 chr7B 684457024 684459994 2970 True 1035.700000 3426 95.185500 1 2695 4 chr7B.!!$R1 2694
4 TraesCS7A01G508200 chr5D 416066578 416068137 1559 True 1912.000000 1912 88.903000 803 2356 1 chr5D.!!$R1 1553
5 TraesCS7A01G508200 chr5A 528558039 528560339 2300 True 860.333333 1820 86.342333 13 2330 3 chr5A.!!$R1 2317
6 TraesCS7A01G508200 chr5B 502498302 502499577 1275 True 417.000000 673 82.291000 493 2356 2 chr5B.!!$R1 1863

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
355 357 0.261991 TCCCATTCTACCCGCTCTCT 59.738 55.0 0.0 0.0 0.00 3.10 F
360 362 0.467659 TTCTACCCGCTCTCTAGCCC 60.468 60.0 0.0 0.0 46.68 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2137 3.084786 AGCTTCCATAACTTTGGCAGAC 58.915 45.455 0.0 0.0 32.41 3.51 R
2127 2200 3.128764 TCATTAGCAGTCAGTAGTGTCGG 59.871 47.826 0.0 0.0 0.00 4.79 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
53 54 1.133637 ACCACTATGGCACCACAACAA 60.134 47.619 0.00 0.00 42.67 2.83
66 67 6.072175 GGCACCACAACAAGTCTTATATGAAA 60.072 38.462 0.00 0.00 0.00 2.69
304 306 1.671261 CGCTCTCTAGCCCATGCATAC 60.671 57.143 0.00 0.00 46.68 2.39
305 307 1.338579 GCTCTCTAGCCCATGCATACC 60.339 57.143 0.00 0.00 43.40 2.73
306 308 2.255406 CTCTCTAGCCCATGCATACCT 58.745 52.381 0.00 0.00 41.13 3.08
307 309 1.973515 TCTCTAGCCCATGCATACCTG 59.026 52.381 0.00 0.00 41.13 4.00
316 318 2.280865 GCATACCTGCCTACCGCC 60.281 66.667 0.00 0.00 42.88 6.13
317 319 2.029073 CATACCTGCCTACCGCCG 59.971 66.667 0.00 0.00 36.24 6.46
318 320 3.925090 ATACCTGCCTACCGCCGC 61.925 66.667 0.00 0.00 36.24 6.53
348 350 4.003614 CCCCCTCCCATTCTACCC 57.996 66.667 0.00 0.00 0.00 3.69
349 351 2.147387 CCCCCTCCCATTCTACCCG 61.147 68.421 0.00 0.00 0.00 5.28
350 352 2.819284 CCCCTCCCATTCTACCCGC 61.819 68.421 0.00 0.00 0.00 6.13
351 353 1.766461 CCCTCCCATTCTACCCGCT 60.766 63.158 0.00 0.00 0.00 5.52
352 354 1.749033 CCTCCCATTCTACCCGCTC 59.251 63.158 0.00 0.00 0.00 5.03
353 355 0.760945 CCTCCCATTCTACCCGCTCT 60.761 60.000 0.00 0.00 0.00 4.09
354 356 0.676736 CTCCCATTCTACCCGCTCTC 59.323 60.000 0.00 0.00 0.00 3.20
355 357 0.261991 TCCCATTCTACCCGCTCTCT 59.738 55.000 0.00 0.00 0.00 3.10
356 358 1.497716 TCCCATTCTACCCGCTCTCTA 59.502 52.381 0.00 0.00 0.00 2.43
357 359 1.889829 CCCATTCTACCCGCTCTCTAG 59.110 57.143 0.00 0.00 0.00 2.43
358 360 1.271102 CCATTCTACCCGCTCTCTAGC 59.729 57.143 0.00 0.00 45.86 3.42
359 361 1.271102 CATTCTACCCGCTCTCTAGCC 59.729 57.143 0.00 0.00 46.68 3.93
360 362 0.467659 TTCTACCCGCTCTCTAGCCC 60.468 60.000 0.00 0.00 46.68 5.19
361 363 1.152735 CTACCCGCTCTCTAGCCCA 60.153 63.158 0.00 0.00 46.68 5.36
362 364 0.540830 CTACCCGCTCTCTAGCCCAT 60.541 60.000 0.00 0.00 46.68 4.00
363 365 0.827925 TACCCGCTCTCTAGCCCATG 60.828 60.000 0.00 0.00 46.68 3.66
364 366 2.030262 CCGCTCTCTAGCCCATGC 59.970 66.667 0.00 0.00 46.68 4.06
365 367 2.800541 CCGCTCTCTAGCCCATGCA 61.801 63.158 0.00 0.00 46.68 3.96
366 368 1.370437 CGCTCTCTAGCCCATGCAT 59.630 57.895 0.00 0.00 46.68 3.96
367 369 0.605083 CGCTCTCTAGCCCATGCATA 59.395 55.000 0.00 0.00 46.68 3.14
560 562 5.093849 TCTGGTTAGGCTTGTTACCATAC 57.906 43.478 9.81 0.00 39.74 2.39
766 769 5.740513 GCTTATAGGCAAGAAGGACACCTAG 60.741 48.000 1.27 0.00 36.48 3.02
784 787 7.354312 ACACCTAGGATGGTATTAAGCAAAAT 58.646 34.615 17.98 0.00 38.45 1.82
906 968 4.162509 ACCCCTTAGTGTGCTTATCTTCTC 59.837 45.833 0.00 0.00 0.00 2.87
927 989 7.004555 TCTCCGGTGAGCATATAATACAAAT 57.995 36.000 0.00 0.00 38.58 2.32
1946 2016 2.760159 GCCGCGCTTCAATGGCTAA 61.760 57.895 13.63 0.00 44.16 3.09
2067 2137 3.585862 CAATACCATATTCCGTCGGGAG 58.414 50.000 12.29 0.00 44.98 4.30
2099 2169 5.819991 AGTTATGGAAGCTTGATCTTTCCA 58.180 37.500 2.10 17.61 32.21 3.53
2127 2200 6.494893 TCATTTTGATAGTTGGTAGCACAC 57.505 37.500 0.00 0.00 0.00 3.82
2432 2525 5.541868 TGAATAAAATGCTTCTGTTTGGGGA 59.458 36.000 0.00 0.00 0.00 4.81
2489 2582 0.533755 GAGGGAGATGATTGGTGGCG 60.534 60.000 0.00 0.00 0.00 5.69
2506 2599 2.694760 CGCTGAGCCTTTGAAGGGC 61.695 63.158 10.70 10.70 46.56 5.19
2565 3072 1.284785 TCTCATCCATTGGTGAACCCC 59.715 52.381 1.86 0.00 34.29 4.95
2566 3073 1.005805 CTCATCCATTGGTGAACCCCA 59.994 52.381 1.86 0.00 34.29 4.96
2637 3148 4.291249 TCTTAGGGGCAGTCAAATAAGGTT 59.709 41.667 0.00 0.00 0.00 3.50
2695 3208 6.535508 GCCTATAACTTCTAGGTTGTTGTCAG 59.464 42.308 2.96 0.00 38.42 3.51
2696 3209 7.578955 GCCTATAACTTCTAGGTTGTTGTCAGA 60.579 40.741 2.96 0.00 38.42 3.27
2697 3210 7.976734 CCTATAACTTCTAGGTTGTTGTCAGAG 59.023 40.741 0.00 0.00 32.60 3.35
2698 3211 3.996480 ACTTCTAGGTTGTTGTCAGAGC 58.004 45.455 0.00 0.00 0.00 4.09
2699 3212 3.388024 ACTTCTAGGTTGTTGTCAGAGCA 59.612 43.478 0.00 0.00 0.00 4.26
2700 3213 4.040952 ACTTCTAGGTTGTTGTCAGAGCAT 59.959 41.667 0.00 0.00 0.00 3.79
2701 3214 4.193826 TCTAGGTTGTTGTCAGAGCATC 57.806 45.455 0.00 0.00 0.00 3.91
2713 3226 1.796796 GAGCATCTTCAACACCCGC 59.203 57.895 0.00 0.00 0.00 6.13
2714 3227 1.970917 GAGCATCTTCAACACCCGCG 61.971 60.000 0.00 0.00 0.00 6.46
2715 3228 2.480555 CATCTTCAACACCCGCGC 59.519 61.111 0.00 0.00 0.00 6.86
2716 3229 2.746277 ATCTTCAACACCCGCGCC 60.746 61.111 0.00 0.00 0.00 6.53
2717 3230 3.545124 ATCTTCAACACCCGCGCCA 62.545 57.895 0.00 0.00 0.00 5.69
2718 3231 3.283684 CTTCAACACCCGCGCCAA 61.284 61.111 0.00 0.00 0.00 4.52
2719 3232 3.536498 CTTCAACACCCGCGCCAAC 62.536 63.158 0.00 0.00 0.00 3.77
2735 3248 3.407657 ACGCACCGCACGTTAAAA 58.592 50.000 0.00 0.00 41.93 1.52
2736 3249 1.277440 ACGCACCGCACGTTAAAAG 59.723 52.632 0.00 0.00 41.93 2.27
2737 3250 1.277440 CGCACCGCACGTTAAAAGT 59.723 52.632 0.00 0.00 0.00 2.66
2738 3251 0.720173 CGCACCGCACGTTAAAAGTC 60.720 55.000 0.00 0.00 0.00 3.01
2739 3252 0.305313 GCACCGCACGTTAAAAGTCA 59.695 50.000 0.00 0.00 0.00 3.41
2740 3253 1.659211 GCACCGCACGTTAAAAGTCAG 60.659 52.381 0.00 0.00 0.00 3.51
2741 3254 1.862201 CACCGCACGTTAAAAGTCAGA 59.138 47.619 0.00 0.00 0.00 3.27
2742 3255 2.285756 CACCGCACGTTAAAAGTCAGAA 59.714 45.455 0.00 0.00 0.00 3.02
2743 3256 3.059188 CACCGCACGTTAAAAGTCAGAAT 60.059 43.478 0.00 0.00 0.00 2.40
2744 3257 4.150980 CACCGCACGTTAAAAGTCAGAATA 59.849 41.667 0.00 0.00 0.00 1.75
2745 3258 4.151157 ACCGCACGTTAAAAGTCAGAATAC 59.849 41.667 0.00 0.00 0.00 1.89
2746 3259 4.150980 CCGCACGTTAAAAGTCAGAATACA 59.849 41.667 0.00 0.00 0.00 2.29
2747 3260 5.305812 CGCACGTTAAAAGTCAGAATACAG 58.694 41.667 0.00 0.00 0.00 2.74
2748 3261 5.080068 GCACGTTAAAAGTCAGAATACAGC 58.920 41.667 0.00 0.00 0.00 4.40
2749 3262 5.305812 CACGTTAAAAGTCAGAATACAGCG 58.694 41.667 0.00 0.00 0.00 5.18
2750 3263 4.143179 ACGTTAAAAGTCAGAATACAGCGC 60.143 41.667 0.00 0.00 0.00 5.92
2751 3264 4.648970 GTTAAAAGTCAGAATACAGCGCC 58.351 43.478 2.29 0.00 0.00 6.53
2752 3265 1.359848 AAAGTCAGAATACAGCGCCG 58.640 50.000 2.29 0.00 0.00 6.46
2753 3266 0.460284 AAGTCAGAATACAGCGCCGG 60.460 55.000 2.29 0.00 0.00 6.13
2754 3267 1.141019 GTCAGAATACAGCGCCGGA 59.859 57.895 5.05 0.00 0.00 5.14
2755 3268 0.249489 GTCAGAATACAGCGCCGGAT 60.249 55.000 5.05 0.00 0.00 4.18
2756 3269 0.464036 TCAGAATACAGCGCCGGATT 59.536 50.000 5.05 0.61 0.00 3.01
2757 3270 1.684450 TCAGAATACAGCGCCGGATTA 59.316 47.619 5.05 0.00 0.00 1.75
2758 3271 2.061773 CAGAATACAGCGCCGGATTAG 58.938 52.381 5.05 0.00 0.00 1.73
2759 3272 0.790814 GAATACAGCGCCGGATTAGC 59.209 55.000 5.05 4.30 0.00 3.09
2760 3273 0.602905 AATACAGCGCCGGATTAGCC 60.603 55.000 5.05 0.00 0.00 3.93
2761 3274 1.754380 ATACAGCGCCGGATTAGCCA 61.754 55.000 5.05 0.00 35.94 4.75
2762 3275 2.363711 TACAGCGCCGGATTAGCCAG 62.364 60.000 5.05 3.00 35.94 4.85
2763 3276 4.918201 AGCGCCGGATTAGCCAGC 62.918 66.667 5.05 0.00 36.68 4.85
2764 3277 4.918201 GCGCCGGATTAGCCAGCT 62.918 66.667 5.05 0.00 37.96 4.24
2765 3278 2.203070 CGCCGGATTAGCCAGCTT 60.203 61.111 5.05 0.00 37.96 3.74
2766 3279 1.819632 CGCCGGATTAGCCAGCTTT 60.820 57.895 5.05 0.00 37.96 3.51
2767 3280 1.376609 CGCCGGATTAGCCAGCTTTT 61.377 55.000 5.05 0.00 37.96 2.27
2768 3281 0.101219 GCCGGATTAGCCAGCTTTTG 59.899 55.000 5.05 0.00 37.09 2.44
2792 3305 4.099170 GCAGTGCGCTGGCTTCAG 62.099 66.667 27.56 1.60 42.78 3.02
2810 3323 2.179517 CGGCCGCCGCAAATTAAA 59.820 55.556 20.79 0.00 41.17 1.52
2811 3324 1.871789 CGGCCGCCGCAAATTAAAG 60.872 57.895 20.79 0.00 41.17 1.85
2812 3325 2.164663 GGCCGCCGCAAATTAAAGC 61.165 57.895 0.00 0.00 36.38 3.51
2813 3326 1.445238 GCCGCCGCAAATTAAAGCA 60.445 52.632 0.00 0.00 34.03 3.91
2814 3327 1.682867 GCCGCCGCAAATTAAAGCAC 61.683 55.000 0.00 0.00 34.03 4.40
2815 3328 1.402479 CCGCCGCAAATTAAAGCACG 61.402 55.000 0.00 0.00 0.00 5.34
2816 3329 0.727793 CGCCGCAAATTAAAGCACGT 60.728 50.000 0.00 0.00 0.00 4.49
2817 3330 0.981956 GCCGCAAATTAAAGCACGTC 59.018 50.000 0.00 0.00 0.00 4.34
2818 3331 1.613270 CCGCAAATTAAAGCACGTCC 58.387 50.000 0.00 0.00 0.00 4.79
2819 3332 1.246970 CGCAAATTAAAGCACGTCCG 58.753 50.000 0.00 0.00 0.00 4.79
2820 3333 1.136197 CGCAAATTAAAGCACGTCCGA 60.136 47.619 0.00 0.00 0.00 4.55
2821 3334 2.505866 GCAAATTAAAGCACGTCCGAG 58.494 47.619 0.00 0.00 0.00 4.63
2822 3335 2.505866 CAAATTAAAGCACGTCCGAGC 58.494 47.619 0.72 0.72 0.00 5.03
2823 3336 1.084289 AATTAAAGCACGTCCGAGCC 58.916 50.000 5.51 0.00 32.18 4.70
2824 3337 1.082117 ATTAAAGCACGTCCGAGCCG 61.082 55.000 5.51 0.00 32.18 5.52
2832 3345 4.373116 GTCCGAGCCGCTCCAACA 62.373 66.667 14.85 0.00 0.00 3.33
2833 3346 3.621805 TCCGAGCCGCTCCAACAA 61.622 61.111 14.85 0.00 0.00 2.83
2834 3347 3.121030 CCGAGCCGCTCCAACAAG 61.121 66.667 14.85 0.00 0.00 3.16
2835 3348 2.357517 CGAGCCGCTCCAACAAGT 60.358 61.111 14.85 0.00 0.00 3.16
2836 3349 2.671177 CGAGCCGCTCCAACAAGTG 61.671 63.158 14.85 0.00 0.00 3.16
2850 3363 6.076981 CCAACAAGTGGGCTATATTTCATC 57.923 41.667 0.00 0.00 44.64 2.92
2851 3364 5.829924 CCAACAAGTGGGCTATATTTCATCT 59.170 40.000 0.00 0.00 44.64 2.90
2852 3365 6.238842 CCAACAAGTGGGCTATATTTCATCTG 60.239 42.308 0.00 0.00 44.64 2.90
2853 3366 6.006275 ACAAGTGGGCTATATTTCATCTGT 57.994 37.500 0.00 0.00 0.00 3.41
2854 3367 6.426587 ACAAGTGGGCTATATTTCATCTGTT 58.573 36.000 0.00 0.00 0.00 3.16
2855 3368 6.891908 ACAAGTGGGCTATATTTCATCTGTTT 59.108 34.615 0.00 0.00 0.00 2.83
2856 3369 7.397192 ACAAGTGGGCTATATTTCATCTGTTTT 59.603 33.333 0.00 0.00 0.00 2.43
2857 3370 7.961326 AGTGGGCTATATTTCATCTGTTTTT 57.039 32.000 0.00 0.00 0.00 1.94
2908 3421 9.804758 AAAATGAGTAGATAGTTTTCTCCTACG 57.195 33.333 0.00 0.00 39.23 3.51
2909 3422 6.939132 TGAGTAGATAGTTTTCTCCTACGG 57.061 41.667 0.00 0.00 39.23 4.02
2910 3423 6.421485 TGAGTAGATAGTTTTCTCCTACGGT 58.579 40.000 0.00 0.00 39.23 4.83
2911 3424 7.568349 TGAGTAGATAGTTTTCTCCTACGGTA 58.432 38.462 0.00 0.00 39.23 4.02
2912 3425 7.714377 TGAGTAGATAGTTTTCTCCTACGGTAG 59.286 40.741 8.22 8.22 39.23 3.18
2913 3426 7.800092 AGTAGATAGTTTTCTCCTACGGTAGA 58.200 38.462 16.59 0.00 39.23 2.59
2914 3427 8.439172 AGTAGATAGTTTTCTCCTACGGTAGAT 58.561 37.037 16.59 0.00 39.23 1.98
2915 3428 9.717942 GTAGATAGTTTTCTCCTACGGTAGATA 57.282 37.037 16.59 3.69 31.65 1.98
2916 3429 8.851541 AGATAGTTTTCTCCTACGGTAGATAG 57.148 38.462 16.59 12.63 0.00 2.08
2917 3430 8.439172 AGATAGTTTTCTCCTACGGTAGATAGT 58.561 37.037 16.59 0.00 0.00 2.12
2918 3431 8.993404 ATAGTTTTCTCCTACGGTAGATAGTT 57.007 34.615 16.59 0.00 0.00 2.24
2919 3432 7.332213 AGTTTTCTCCTACGGTAGATAGTTC 57.668 40.000 16.59 2.30 0.00 3.01
2920 3433 6.888632 AGTTTTCTCCTACGGTAGATAGTTCA 59.111 38.462 16.59 1.30 0.00 3.18
2921 3434 7.560626 AGTTTTCTCCTACGGTAGATAGTTCAT 59.439 37.037 16.59 0.00 0.00 2.57
2922 3435 8.844244 GTTTTCTCCTACGGTAGATAGTTCATA 58.156 37.037 16.59 0.00 0.00 2.15
2923 3436 8.618702 TTTCTCCTACGGTAGATAGTTCATAG 57.381 38.462 16.59 0.00 0.00 2.23
2924 3437 7.313740 TCTCCTACGGTAGATAGTTCATAGT 57.686 40.000 16.59 0.00 0.00 2.12
2925 3438 7.743749 TCTCCTACGGTAGATAGTTCATAGTT 58.256 38.462 16.59 0.00 0.00 2.24
2926 3439 7.877097 TCTCCTACGGTAGATAGTTCATAGTTC 59.123 40.741 16.59 0.00 0.00 3.01
2927 3440 6.648310 TCCTACGGTAGATAGTTCATAGTTCG 59.352 42.308 16.59 0.00 0.00 3.95
2928 3441 6.426328 CCTACGGTAGATAGTTCATAGTTCGT 59.574 42.308 16.59 0.00 0.00 3.85
2929 3442 6.297694 ACGGTAGATAGTTCATAGTTCGTC 57.702 41.667 0.00 0.00 0.00 4.20
2930 3443 5.238214 ACGGTAGATAGTTCATAGTTCGTCC 59.762 44.000 0.00 0.00 0.00 4.79
2931 3444 5.614231 CGGTAGATAGTTCATAGTTCGTCCG 60.614 48.000 0.00 0.00 0.00 4.79
2932 3445 5.468072 GGTAGATAGTTCATAGTTCGTCCGA 59.532 44.000 0.00 0.00 0.00 4.55
2933 3446 6.017605 GGTAGATAGTTCATAGTTCGTCCGAA 60.018 42.308 0.00 0.00 0.00 4.30
2947 3460 3.279183 CGAACTCGGACTCTGCCT 58.721 61.111 0.00 0.00 35.37 4.75
2948 3461 1.153939 CGAACTCGGACTCTGCCTG 60.154 63.158 0.00 0.00 35.37 4.85
2949 3462 1.446966 GAACTCGGACTCTGCCTGC 60.447 63.158 0.00 0.00 0.00 4.85
2950 3463 1.882989 GAACTCGGACTCTGCCTGCT 61.883 60.000 0.00 0.00 0.00 4.24
2951 3464 1.476007 AACTCGGACTCTGCCTGCTT 61.476 55.000 0.00 0.00 0.00 3.91
2952 3465 1.153667 CTCGGACTCTGCCTGCTTC 60.154 63.158 0.00 0.00 0.00 3.86
2953 3466 1.603236 CTCGGACTCTGCCTGCTTCT 61.603 60.000 0.00 0.00 0.00 2.85
2954 3467 0.323451 TCGGACTCTGCCTGCTTCTA 60.323 55.000 0.00 0.00 0.00 2.10
2955 3468 0.179124 CGGACTCTGCCTGCTTCTAC 60.179 60.000 0.00 0.00 0.00 2.59
2956 3469 0.898320 GGACTCTGCCTGCTTCTACA 59.102 55.000 0.00 0.00 0.00 2.74
2957 3470 1.276421 GGACTCTGCCTGCTTCTACAA 59.724 52.381 0.00 0.00 0.00 2.41
2958 3471 2.093235 GGACTCTGCCTGCTTCTACAAT 60.093 50.000 0.00 0.00 0.00 2.71
2959 3472 3.133003 GGACTCTGCCTGCTTCTACAATA 59.867 47.826 0.00 0.00 0.00 1.90
2960 3473 4.367450 GACTCTGCCTGCTTCTACAATAG 58.633 47.826 0.00 0.00 0.00 1.73
2961 3474 3.129871 CTCTGCCTGCTTCTACAATAGC 58.870 50.000 0.00 0.00 37.89 2.97
2962 3475 2.158900 TCTGCCTGCTTCTACAATAGCC 60.159 50.000 0.00 0.00 36.56 3.93
2963 3476 1.839994 TGCCTGCTTCTACAATAGCCT 59.160 47.619 0.00 0.00 36.56 4.58
2964 3477 3.038280 TGCCTGCTTCTACAATAGCCTA 58.962 45.455 0.00 0.00 36.56 3.93
2965 3478 3.181465 TGCCTGCTTCTACAATAGCCTAC 60.181 47.826 0.00 0.00 36.56 3.18
2966 3479 3.070302 GCCTGCTTCTACAATAGCCTACT 59.930 47.826 0.00 0.00 36.56 2.57
2967 3480 4.443598 GCCTGCTTCTACAATAGCCTACTT 60.444 45.833 0.00 0.00 36.56 2.24
2968 3481 5.293560 CCTGCTTCTACAATAGCCTACTTC 58.706 45.833 0.00 0.00 36.56 3.01
2969 3482 5.069781 CCTGCTTCTACAATAGCCTACTTCT 59.930 44.000 0.00 0.00 36.56 2.85
2970 3483 6.265649 CCTGCTTCTACAATAGCCTACTTCTA 59.734 42.308 0.00 0.00 36.56 2.10
2971 3484 7.039363 CCTGCTTCTACAATAGCCTACTTCTAT 60.039 40.741 0.00 0.00 36.56 1.98
2972 3485 7.661968 TGCTTCTACAATAGCCTACTTCTATG 58.338 38.462 0.00 0.00 36.56 2.23
2973 3486 7.505923 TGCTTCTACAATAGCCTACTTCTATGA 59.494 37.037 0.00 0.00 36.56 2.15
2974 3487 8.527810 GCTTCTACAATAGCCTACTTCTATGAT 58.472 37.037 0.00 0.00 0.00 2.45
3014 3527 7.542534 AAACTAGTACTACTCATCTGACTCG 57.457 40.000 0.00 0.00 0.00 4.18
3015 3528 5.603596 ACTAGTACTACTCATCTGACTCGG 58.396 45.833 0.00 0.00 0.00 4.63
3016 3529 4.757019 AGTACTACTCATCTGACTCGGA 57.243 45.455 0.00 0.00 0.00 4.55
3017 3530 4.444536 AGTACTACTCATCTGACTCGGAC 58.555 47.826 0.00 0.00 0.00 4.79
3018 3531 3.637911 ACTACTCATCTGACTCGGACT 57.362 47.619 0.00 0.00 0.00 3.85
3019 3532 3.537580 ACTACTCATCTGACTCGGACTC 58.462 50.000 0.00 0.00 0.00 3.36
3020 3533 2.799126 ACTCATCTGACTCGGACTCT 57.201 50.000 0.00 0.00 0.00 3.24
3021 3534 2.639065 ACTCATCTGACTCGGACTCTC 58.361 52.381 0.00 0.00 0.00 3.20
3022 3535 2.238646 ACTCATCTGACTCGGACTCTCT 59.761 50.000 0.00 0.00 0.00 3.10
3023 3536 2.872245 CTCATCTGACTCGGACTCTCTC 59.128 54.545 0.00 0.00 0.00 3.20
3024 3537 2.503765 TCATCTGACTCGGACTCTCTCT 59.496 50.000 0.00 0.00 0.00 3.10
3025 3538 2.684001 TCTGACTCGGACTCTCTCTC 57.316 55.000 0.00 0.00 0.00 3.20
3026 3539 1.134936 TCTGACTCGGACTCTCTCTCG 60.135 57.143 0.00 0.00 0.00 4.04
3027 3540 0.108089 TGACTCGGACTCTCTCTCGG 60.108 60.000 0.00 0.00 0.00 4.63
3028 3541 0.108041 GACTCGGACTCTCTCTCGGT 60.108 60.000 0.00 0.00 0.00 4.69
3029 3542 0.391927 ACTCGGACTCTCTCTCGGTG 60.392 60.000 0.00 0.00 0.00 4.94
3030 3543 0.108089 CTCGGACTCTCTCTCGGTGA 60.108 60.000 0.00 0.00 0.00 4.02
3031 3544 0.542333 TCGGACTCTCTCTCGGTGAT 59.458 55.000 0.00 0.00 0.00 3.06
3032 3545 0.660488 CGGACTCTCTCTCGGTGATG 59.340 60.000 0.00 0.00 0.00 3.07
3033 3546 1.757682 GGACTCTCTCTCGGTGATGT 58.242 55.000 0.00 0.00 0.00 3.06
3034 3547 2.096248 GGACTCTCTCTCGGTGATGTT 58.904 52.381 0.00 0.00 0.00 2.71
3035 3548 2.098443 GGACTCTCTCTCGGTGATGTTC 59.902 54.545 0.00 0.00 0.00 3.18
3036 3549 3.013921 GACTCTCTCTCGGTGATGTTCT 58.986 50.000 0.00 0.00 0.00 3.01
3037 3550 3.013921 ACTCTCTCTCGGTGATGTTCTC 58.986 50.000 0.00 0.00 0.00 2.87
3038 3551 2.010497 TCTCTCTCGGTGATGTTCTCG 58.990 52.381 0.00 0.00 0.00 4.04
3039 3552 1.740585 CTCTCTCGGTGATGTTCTCGT 59.259 52.381 0.00 0.00 0.00 4.18
3040 3553 1.738350 TCTCTCGGTGATGTTCTCGTC 59.262 52.381 0.00 0.00 0.00 4.20
3041 3554 0.809385 TCTCGGTGATGTTCTCGTCC 59.191 55.000 0.00 0.00 0.00 4.79
3042 3555 0.523546 CTCGGTGATGTTCTCGTCCG 60.524 60.000 0.00 0.00 41.90 4.79
3043 3556 0.956902 TCGGTGATGTTCTCGTCCGA 60.957 55.000 0.00 0.00 44.67 4.55
3044 3557 0.797249 CGGTGATGTTCTCGTCCGAC 60.797 60.000 0.00 0.00 42.61 4.79
3045 3558 0.797249 GGTGATGTTCTCGTCCGACG 60.797 60.000 14.94 14.94 44.19 5.12
3046 3559 0.109873 GTGATGTTCTCGTCCGACGT 60.110 55.000 19.89 0.00 43.14 4.34
3047 3560 0.167470 TGATGTTCTCGTCCGACGTC 59.833 55.000 19.89 5.18 43.14 4.34
3048 3561 0.447011 GATGTTCTCGTCCGACGTCT 59.553 55.000 19.89 0.93 43.14 4.18
3049 3562 0.168348 ATGTTCTCGTCCGACGTCTG 59.832 55.000 19.89 7.40 43.14 3.51
3050 3563 1.162181 TGTTCTCGTCCGACGTCTGT 61.162 55.000 19.89 0.00 43.14 3.41
3051 3564 0.725118 GTTCTCGTCCGACGTCTGTG 60.725 60.000 19.89 4.94 43.14 3.66
3052 3565 2.453773 TTCTCGTCCGACGTCTGTGC 62.454 60.000 19.89 4.35 43.14 4.57
3053 3566 4.379143 TCGTCCGACGTCTGTGCG 62.379 66.667 19.89 15.28 43.14 5.34
3055 3568 2.557805 GTCCGACGTCTGTGCGTA 59.442 61.111 14.70 0.00 45.79 4.42
3056 3569 1.511464 GTCCGACGTCTGTGCGTAG 60.511 63.158 14.70 0.00 45.79 3.51
3058 3571 2.874780 CGACGTCTGTGCGTAGGC 60.875 66.667 14.70 0.00 45.79 3.93
3061 3574 2.874780 CGTCTGTGCGTAGGCGTC 60.875 66.667 5.93 0.00 44.10 5.19
3062 3575 2.257371 GTCTGTGCGTAGGCGTCA 59.743 61.111 2.53 4.18 44.10 4.35
3063 3576 1.372499 GTCTGTGCGTAGGCGTCAA 60.372 57.895 2.53 0.00 44.10 3.18
3064 3577 1.080772 TCTGTGCGTAGGCGTCAAG 60.081 57.895 2.53 0.00 44.10 3.02
3065 3578 1.080772 CTGTGCGTAGGCGTCAAGA 60.081 57.895 2.53 0.00 44.10 3.02
3066 3579 0.666274 CTGTGCGTAGGCGTCAAGAA 60.666 55.000 2.53 0.00 44.10 2.52
3067 3580 0.249531 TGTGCGTAGGCGTCAAGAAA 60.250 50.000 2.53 0.00 44.10 2.52
3068 3581 0.163146 GTGCGTAGGCGTCAAGAAAC 59.837 55.000 2.53 0.00 44.10 2.78
3069 3582 0.947180 TGCGTAGGCGTCAAGAAACC 60.947 55.000 2.53 0.00 44.10 3.27
3070 3583 1.952266 GCGTAGGCGTCAAGAAACCG 61.952 60.000 0.00 0.00 40.81 4.44
3071 3584 1.785951 GTAGGCGTCAAGAAACCGC 59.214 57.895 0.00 0.00 46.28 5.68
3072 3585 0.669625 GTAGGCGTCAAGAAACCGCT 60.670 55.000 0.00 0.00 46.23 5.52
3073 3586 0.389426 TAGGCGTCAAGAAACCGCTC 60.389 55.000 0.00 0.00 46.23 5.03
3074 3587 2.470286 GCGTCAAGAAACCGCTCG 59.530 61.111 0.00 0.00 43.81 5.03
3075 3588 2.308039 GCGTCAAGAAACCGCTCGT 61.308 57.895 0.00 0.00 43.81 4.18
3076 3589 1.773496 CGTCAAGAAACCGCTCGTC 59.227 57.895 0.00 0.00 0.00 4.20
3077 3590 1.773496 GTCAAGAAACCGCTCGTCG 59.227 57.895 0.00 0.00 38.08 5.12
3078 3591 2.019951 TCAAGAAACCGCTCGTCGC 61.020 57.895 0.00 0.00 36.73 5.19
3079 3592 2.737376 AAGAAACCGCTCGTCGCC 60.737 61.111 0.00 0.00 36.73 5.54
3087 3600 4.539881 GCTCGTCGCCGGAGTCTC 62.540 72.222 5.05 0.00 33.95 3.36
3088 3601 3.125573 CTCGTCGCCGGAGTCTCA 61.126 66.667 5.05 0.00 33.95 3.27
3089 3602 3.102107 CTCGTCGCCGGAGTCTCAG 62.102 68.421 5.05 0.00 33.95 3.35
3090 3603 4.180946 CGTCGCCGGAGTCTCAGG 62.181 72.222 14.22 14.22 34.70 3.86
3091 3604 2.750637 GTCGCCGGAGTCTCAGGA 60.751 66.667 21.82 0.00 33.29 3.86
3092 3605 2.438614 TCGCCGGAGTCTCAGGAG 60.439 66.667 21.82 18.35 33.29 3.69
3093 3606 3.522731 CGCCGGAGTCTCAGGAGG 61.523 72.222 21.82 9.26 33.29 4.30
3094 3607 2.043852 GCCGGAGTCTCAGGAGGA 60.044 66.667 21.82 0.00 33.29 3.71
3095 3608 2.419739 GCCGGAGTCTCAGGAGGAC 61.420 68.421 21.82 1.25 33.29 3.85
3096 3609 2.115911 CCGGAGTCTCAGGAGGACG 61.116 68.421 13.37 0.00 38.58 4.79
3097 3610 2.766400 CGGAGTCTCAGGAGGACGC 61.766 68.421 1.47 0.00 38.58 5.19
3098 3611 1.679305 GGAGTCTCAGGAGGACGCA 60.679 63.158 1.47 0.00 38.58 5.24
3099 3612 1.040339 GGAGTCTCAGGAGGACGCAT 61.040 60.000 1.47 0.00 38.58 4.73
3100 3613 0.383949 GAGTCTCAGGAGGACGCATC 59.616 60.000 0.00 0.00 38.58 3.91
3101 3614 0.033601 AGTCTCAGGAGGACGCATCT 60.034 55.000 0.00 0.00 38.58 2.90
3102 3615 0.383949 GTCTCAGGAGGACGCATCTC 59.616 60.000 0.00 0.00 0.00 2.75
3107 3620 1.663173 GGAGGACGCATCTCCTAGC 59.337 63.158 10.81 0.00 45.46 3.42
3113 3626 3.853712 GCATCTCCTAGCGCGATG 58.146 61.111 12.10 15.31 38.02 3.84
3114 3627 1.006805 GCATCTCCTAGCGCGATGT 60.007 57.895 12.10 0.00 37.46 3.06
3115 3628 0.598680 GCATCTCCTAGCGCGATGTT 60.599 55.000 12.10 0.00 37.46 2.71
3116 3629 1.135046 CATCTCCTAGCGCGATGTTG 58.865 55.000 12.10 0.00 32.07 3.33
3117 3630 0.747255 ATCTCCTAGCGCGATGTTGT 59.253 50.000 12.10 0.00 0.00 3.32
3118 3631 1.385528 TCTCCTAGCGCGATGTTGTA 58.614 50.000 12.10 0.00 0.00 2.41
3119 3632 1.954382 TCTCCTAGCGCGATGTTGTAT 59.046 47.619 12.10 0.00 0.00 2.29
3120 3633 2.361119 TCTCCTAGCGCGATGTTGTATT 59.639 45.455 12.10 0.00 0.00 1.89
3121 3634 3.123804 CTCCTAGCGCGATGTTGTATTT 58.876 45.455 12.10 0.00 0.00 1.40
3122 3635 4.037089 TCTCCTAGCGCGATGTTGTATTTA 59.963 41.667 12.10 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 9.209175 GTTATCGGAAGCATTTCATATAAGACT 57.791 33.333 0.00 0.00 34.90 3.24
66 67 2.427095 GGCTTTTGGTTATCGGAAGCAT 59.573 45.455 8.42 0.00 43.28 3.79
229 231 3.936453 GCCACACACGAAGGAATAACATA 59.064 43.478 0.00 0.00 0.00 2.29
331 333 2.147387 CGGGTAGAATGGGAGGGGG 61.147 68.421 0.00 0.00 0.00 5.40
332 334 2.819284 GCGGGTAGAATGGGAGGGG 61.819 68.421 0.00 0.00 0.00 4.79
333 335 1.759459 GAGCGGGTAGAATGGGAGGG 61.759 65.000 0.00 0.00 0.00 4.30
334 336 0.760945 AGAGCGGGTAGAATGGGAGG 60.761 60.000 0.00 0.00 0.00 4.30
335 337 0.676736 GAGAGCGGGTAGAATGGGAG 59.323 60.000 0.00 0.00 0.00 4.30
336 338 0.261991 AGAGAGCGGGTAGAATGGGA 59.738 55.000 0.00 0.00 0.00 4.37
337 339 1.889829 CTAGAGAGCGGGTAGAATGGG 59.110 57.143 0.00 0.00 0.00 4.00
338 340 1.271102 GCTAGAGAGCGGGTAGAATGG 59.729 57.143 0.00 0.00 39.39 3.16
339 341 2.715737 GCTAGAGAGCGGGTAGAATG 57.284 55.000 0.00 0.00 39.39 2.67
350 352 2.028294 CAGGTATGCATGGGCTAGAGAG 60.028 54.545 10.16 0.00 41.91 3.20
351 353 1.973515 CAGGTATGCATGGGCTAGAGA 59.026 52.381 10.16 0.00 41.91 3.10
352 354 2.469274 CAGGTATGCATGGGCTAGAG 57.531 55.000 10.16 0.00 41.91 2.43
364 366 2.029073 CGGCGGTAGGCAGGTATG 59.971 66.667 0.00 0.00 46.16 2.39
365 367 3.925090 GCGGCGGTAGGCAGGTAT 61.925 66.667 9.78 0.00 46.16 2.73
522 524 6.918022 CCTAACCAGAAGACACAAATCAAAAC 59.082 38.462 0.00 0.00 0.00 2.43
528 530 4.373156 AGCCTAACCAGAAGACACAAAT 57.627 40.909 0.00 0.00 0.00 2.32
650 653 5.127031 GCAAGTCCAAACATGGGTACATAAT 59.873 40.000 0.00 0.00 34.99 1.28
754 757 6.741801 GCTTAATACCATCCTAGGTGTCCTTC 60.742 46.154 9.08 0.00 43.14 3.46
906 968 8.492673 ACATATTTGTATTATATGCTCACCGG 57.507 34.615 0.00 0.00 38.81 5.28
962 1024 6.000840 GGGTTGCAAGGATAAAAATGGAAAA 58.999 36.000 0.00 0.00 0.00 2.29
1495 1561 6.602009 ACAAGTTGTTCTGTAAGTAAAGGCTT 59.398 34.615 1.64 0.00 33.76 4.35
1497 1563 6.373186 ACAAGTTGTTCTGTAAGTAAAGGC 57.627 37.500 1.64 0.00 33.76 4.35
1946 2016 3.938334 GACAAGTTGTTTGCACCCAAAAT 59.062 39.130 10.45 0.00 42.19 1.82
2067 2137 3.084786 AGCTTCCATAACTTTGGCAGAC 58.915 45.455 0.00 0.00 32.41 3.51
2127 2200 3.128764 TCATTAGCAGTCAGTAGTGTCGG 59.871 47.826 0.00 0.00 0.00 4.79
2442 2535 2.905996 ATTTCCGGGAGCAGCCACA 61.906 57.895 0.00 0.00 38.95 4.17
2499 2592 7.014518 CCATGAACTTATCATTTATGCCCTTCA 59.985 37.037 0.00 0.00 46.85 3.02
2506 2599 9.669353 GTTAGCACCATGAACTTATCATTTATG 57.331 33.333 0.00 0.00 46.85 1.90
2637 3148 4.514585 AGCGGGCCAACACCACAA 62.515 61.111 4.39 0.00 0.00 3.33
2695 3208 1.796796 GCGGGTGTTGAAGATGCTC 59.203 57.895 0.00 0.00 0.00 4.26
2696 3209 2.034879 CGCGGGTGTTGAAGATGCT 61.035 57.895 0.00 0.00 0.00 3.79
2697 3210 2.480555 CGCGGGTGTTGAAGATGC 59.519 61.111 0.00 0.00 0.00 3.91
2698 3211 2.480555 GCGCGGGTGTTGAAGATG 59.519 61.111 8.83 0.00 0.00 2.90
2699 3212 2.746277 GGCGCGGGTGTTGAAGAT 60.746 61.111 8.83 0.00 0.00 2.40
2700 3213 3.758973 TTGGCGCGGGTGTTGAAGA 62.759 57.895 8.83 0.00 0.00 2.87
2701 3214 3.283684 TTGGCGCGGGTGTTGAAG 61.284 61.111 8.83 0.00 0.00 3.02
2702 3215 3.587933 GTTGGCGCGGGTGTTGAA 61.588 61.111 8.83 0.00 0.00 2.69
2718 3231 1.277440 CTTTTAACGTGCGGTGCGT 59.723 52.632 0.00 0.00 45.07 5.24
2719 3232 0.720173 GACTTTTAACGTGCGGTGCG 60.720 55.000 0.00 0.00 0.00 5.34
2720 3233 0.305313 TGACTTTTAACGTGCGGTGC 59.695 50.000 0.00 0.00 0.00 5.01
2721 3234 1.862201 TCTGACTTTTAACGTGCGGTG 59.138 47.619 0.00 0.00 0.00 4.94
2722 3235 2.228138 TCTGACTTTTAACGTGCGGT 57.772 45.000 0.00 0.00 0.00 5.68
2723 3236 3.806316 ATTCTGACTTTTAACGTGCGG 57.194 42.857 0.00 0.00 0.00 5.69
2724 3237 5.258685 TGTATTCTGACTTTTAACGTGCG 57.741 39.130 0.00 0.00 0.00 5.34
2725 3238 5.080068 GCTGTATTCTGACTTTTAACGTGC 58.920 41.667 0.00 0.00 0.00 5.34
2726 3239 5.305812 CGCTGTATTCTGACTTTTAACGTG 58.694 41.667 0.00 0.00 0.00 4.49
2727 3240 4.143179 GCGCTGTATTCTGACTTTTAACGT 60.143 41.667 0.00 0.00 0.00 3.99
2728 3241 4.323751 GCGCTGTATTCTGACTTTTAACG 58.676 43.478 0.00 0.00 0.00 3.18
2729 3242 4.648970 GGCGCTGTATTCTGACTTTTAAC 58.351 43.478 7.64 0.00 0.00 2.01
2730 3243 3.369756 CGGCGCTGTATTCTGACTTTTAA 59.630 43.478 8.45 0.00 0.00 1.52
2731 3244 2.927477 CGGCGCTGTATTCTGACTTTTA 59.073 45.455 8.45 0.00 0.00 1.52
2732 3245 1.732259 CGGCGCTGTATTCTGACTTTT 59.268 47.619 8.45 0.00 0.00 2.27
2733 3246 1.359848 CGGCGCTGTATTCTGACTTT 58.640 50.000 8.45 0.00 0.00 2.66
2734 3247 0.460284 CCGGCGCTGTATTCTGACTT 60.460 55.000 16.49 0.00 0.00 3.01
2735 3248 1.141881 CCGGCGCTGTATTCTGACT 59.858 57.895 16.49 0.00 0.00 3.41
2736 3249 0.249489 ATCCGGCGCTGTATTCTGAC 60.249 55.000 16.49 0.00 0.00 3.51
2737 3250 0.464036 AATCCGGCGCTGTATTCTGA 59.536 50.000 16.49 4.12 0.00 3.27
2738 3251 2.061773 CTAATCCGGCGCTGTATTCTG 58.938 52.381 16.49 4.42 0.00 3.02
2739 3252 1.605712 GCTAATCCGGCGCTGTATTCT 60.606 52.381 16.49 0.00 0.00 2.40
2740 3253 0.790814 GCTAATCCGGCGCTGTATTC 59.209 55.000 16.49 0.00 0.00 1.75
2741 3254 0.602905 GGCTAATCCGGCGCTGTATT 60.603 55.000 16.49 14.07 0.00 1.89
2742 3255 1.004918 GGCTAATCCGGCGCTGTAT 60.005 57.895 16.49 0.76 0.00 2.29
2743 3256 2.363711 CTGGCTAATCCGGCGCTGTA 62.364 60.000 16.49 0.00 37.80 2.74
2744 3257 3.740128 CTGGCTAATCCGGCGCTGT 62.740 63.158 16.49 0.00 37.80 4.40
2745 3258 2.969238 CTGGCTAATCCGGCGCTG 60.969 66.667 9.96 9.96 37.80 5.18
2750 3263 0.101219 GCAAAAGCTGGCTAATCCGG 59.899 55.000 0.00 0.00 44.43 5.14
2751 3264 0.810648 TGCAAAAGCTGGCTAATCCG 59.189 50.000 6.80 0.00 37.80 4.18
2752 3265 1.468054 CGTGCAAAAGCTGGCTAATCC 60.468 52.381 6.80 0.00 0.00 3.01
2753 3266 1.900237 CGTGCAAAAGCTGGCTAATC 58.100 50.000 6.80 0.00 0.00 1.75
2754 3267 0.109132 GCGTGCAAAAGCTGGCTAAT 60.109 50.000 6.80 0.00 0.00 1.73
2755 3268 1.285641 GCGTGCAAAAGCTGGCTAA 59.714 52.632 6.80 0.00 0.00 3.09
2756 3269 2.953821 GCGTGCAAAAGCTGGCTA 59.046 55.556 6.80 0.00 0.00 3.93
2757 3270 4.332637 CGCGTGCAAAAGCTGGCT 62.333 61.111 0.00 0.00 0.00 4.75
2775 3288 4.099170 CTGAAGCCAGCGCACTGC 62.099 66.667 11.47 9.17 43.02 4.40
2794 3307 2.164663 GCTTTAATTTGCGGCGGCC 61.165 57.895 14.25 9.54 38.85 6.13
2795 3308 1.445238 TGCTTTAATTTGCGGCGGC 60.445 52.632 9.78 9.68 40.52 6.53
2796 3309 1.402479 CGTGCTTTAATTTGCGGCGG 61.402 55.000 9.78 0.00 0.00 6.13
2797 3310 0.727793 ACGTGCTTTAATTTGCGGCG 60.728 50.000 0.51 0.51 36.69 6.46
2798 3311 0.981956 GACGTGCTTTAATTTGCGGC 59.018 50.000 0.00 0.00 0.00 6.53
2799 3312 1.613270 GGACGTGCTTTAATTTGCGG 58.387 50.000 0.00 0.00 0.00 5.69
2800 3313 1.136197 TCGGACGTGCTTTAATTTGCG 60.136 47.619 5.27 0.00 0.00 4.85
2801 3314 2.505866 CTCGGACGTGCTTTAATTTGC 58.494 47.619 5.27 0.00 0.00 3.68
2802 3315 2.505866 GCTCGGACGTGCTTTAATTTG 58.494 47.619 5.27 0.00 0.00 2.32
2803 3316 1.467342 GGCTCGGACGTGCTTTAATTT 59.533 47.619 16.66 0.00 35.28 1.82
2804 3317 1.084289 GGCTCGGACGTGCTTTAATT 58.916 50.000 16.66 0.00 35.28 1.40
2805 3318 1.082117 CGGCTCGGACGTGCTTTAAT 61.082 55.000 16.66 0.00 35.28 1.40
2806 3319 1.735198 CGGCTCGGACGTGCTTTAA 60.735 57.895 16.66 0.00 35.28 1.52
2807 3320 2.126228 CGGCTCGGACGTGCTTTA 60.126 61.111 16.66 0.00 35.28 1.85
2815 3328 3.876589 TTGTTGGAGCGGCTCGGAC 62.877 63.158 22.63 21.50 0.00 4.79
2816 3329 3.589654 CTTGTTGGAGCGGCTCGGA 62.590 63.158 22.63 11.42 0.00 4.55
2817 3330 3.121030 CTTGTTGGAGCGGCTCGG 61.121 66.667 22.63 5.78 0.00 4.63
2818 3331 2.357517 ACTTGTTGGAGCGGCTCG 60.358 61.111 22.63 10.86 0.00 5.03
2819 3332 3.257933 CACTTGTTGGAGCGGCTC 58.742 61.111 21.57 21.57 0.00 4.70
2827 3340 5.829924 AGATGAAATATAGCCCACTTGTTGG 59.170 40.000 0.00 0.00 46.47 3.77
2828 3341 6.319658 ACAGATGAAATATAGCCCACTTGTTG 59.680 38.462 0.00 0.00 0.00 3.33
2829 3342 6.426587 ACAGATGAAATATAGCCCACTTGTT 58.573 36.000 0.00 0.00 0.00 2.83
2830 3343 6.006275 ACAGATGAAATATAGCCCACTTGT 57.994 37.500 0.00 0.00 0.00 3.16
2831 3344 6.949352 AACAGATGAAATATAGCCCACTTG 57.051 37.500 0.00 0.00 0.00 3.16
2832 3345 7.961326 AAAACAGATGAAATATAGCCCACTT 57.039 32.000 0.00 0.00 0.00 3.16
2833 3346 7.961326 AAAAACAGATGAAATATAGCCCACT 57.039 32.000 0.00 0.00 0.00 4.00
2882 3395 9.804758 CGTAGGAGAAAACTATCTACTCATTTT 57.195 33.333 0.00 0.00 39.90 1.82
2904 3417 7.359933 GGACGAACTATGAACTATCTACCGTAG 60.360 44.444 0.00 0.00 0.00 3.51
2905 3418 6.425114 GGACGAACTATGAACTATCTACCGTA 59.575 42.308 0.00 0.00 0.00 4.02
2906 3419 5.238214 GGACGAACTATGAACTATCTACCGT 59.762 44.000 0.00 0.00 0.00 4.83
2907 3420 5.614231 CGGACGAACTATGAACTATCTACCG 60.614 48.000 0.00 0.00 0.00 4.02
2908 3421 5.468072 TCGGACGAACTATGAACTATCTACC 59.532 44.000 0.00 0.00 0.00 3.18
2909 3422 6.536731 TCGGACGAACTATGAACTATCTAC 57.463 41.667 0.00 0.00 0.00 2.59
2930 3443 1.153939 CAGGCAGAGTCCGAGTTCG 60.154 63.158 0.00 0.00 39.44 3.95
2931 3444 1.446966 GCAGGCAGAGTCCGAGTTC 60.447 63.158 0.00 0.00 0.00 3.01
2932 3445 1.476007 AAGCAGGCAGAGTCCGAGTT 61.476 55.000 0.00 0.00 0.00 3.01
2933 3446 1.882989 GAAGCAGGCAGAGTCCGAGT 61.883 60.000 0.00 0.00 0.00 4.18
2934 3447 1.153667 GAAGCAGGCAGAGTCCGAG 60.154 63.158 0.00 0.00 0.00 4.63
2935 3448 0.323451 TAGAAGCAGGCAGAGTCCGA 60.323 55.000 0.00 0.00 0.00 4.55
2936 3449 0.179124 GTAGAAGCAGGCAGAGTCCG 60.179 60.000 0.00 0.00 0.00 4.79
2937 3450 0.898320 TGTAGAAGCAGGCAGAGTCC 59.102 55.000 0.00 0.00 0.00 3.85
2938 3451 2.751166 TTGTAGAAGCAGGCAGAGTC 57.249 50.000 0.00 0.00 0.00 3.36
2939 3452 3.431486 GCTATTGTAGAAGCAGGCAGAGT 60.431 47.826 0.00 0.00 38.63 3.24
2940 3453 3.129871 GCTATTGTAGAAGCAGGCAGAG 58.870 50.000 0.00 0.00 38.63 3.35
2941 3454 2.158900 GGCTATTGTAGAAGCAGGCAGA 60.159 50.000 5.91 0.00 40.61 4.26
2942 3455 2.158842 AGGCTATTGTAGAAGCAGGCAG 60.159 50.000 11.41 0.00 40.61 4.85
2943 3456 1.839994 AGGCTATTGTAGAAGCAGGCA 59.160 47.619 11.41 0.00 40.61 4.75
2944 3457 2.629336 AGGCTATTGTAGAAGCAGGC 57.371 50.000 0.00 3.32 40.61 4.85
2945 3458 4.946478 AGTAGGCTATTGTAGAAGCAGG 57.054 45.455 0.00 0.00 40.61 4.85
2946 3459 6.155475 AGAAGTAGGCTATTGTAGAAGCAG 57.845 41.667 0.00 0.00 40.61 4.24
2947 3460 7.505923 TCATAGAAGTAGGCTATTGTAGAAGCA 59.494 37.037 0.00 0.00 40.61 3.91
2948 3461 7.887381 TCATAGAAGTAGGCTATTGTAGAAGC 58.113 38.462 0.00 0.00 38.03 3.86
2988 3501 8.452534 CGAGTCAGATGAGTAGTACTAGTTTTT 58.547 37.037 11.56 0.46 0.00 1.94
2989 3502 7.066043 CCGAGTCAGATGAGTAGTACTAGTTTT 59.934 40.741 11.56 2.81 0.00 2.43
2990 3503 6.539464 CCGAGTCAGATGAGTAGTACTAGTTT 59.461 42.308 11.56 3.15 0.00 2.66
2991 3504 6.050432 CCGAGTCAGATGAGTAGTACTAGTT 58.950 44.000 11.56 0.00 0.00 2.24
2992 3505 5.363292 TCCGAGTCAGATGAGTAGTACTAGT 59.637 44.000 10.09 10.09 0.00 2.57
2993 3506 5.693104 GTCCGAGTCAGATGAGTAGTACTAG 59.307 48.000 1.87 0.00 0.00 2.57
2994 3507 5.363292 AGTCCGAGTCAGATGAGTAGTACTA 59.637 44.000 1.88 0.00 0.00 1.82
2995 3508 4.162698 AGTCCGAGTCAGATGAGTAGTACT 59.837 45.833 1.37 1.37 0.00 2.73
2996 3509 4.444536 AGTCCGAGTCAGATGAGTAGTAC 58.555 47.826 0.00 0.00 0.00 2.73
2997 3510 4.406326 AGAGTCCGAGTCAGATGAGTAGTA 59.594 45.833 6.01 0.00 0.00 1.82
2998 3511 3.199071 AGAGTCCGAGTCAGATGAGTAGT 59.801 47.826 6.01 0.00 0.00 2.73
2999 3512 3.804036 AGAGTCCGAGTCAGATGAGTAG 58.196 50.000 6.01 0.00 0.00 2.57
3000 3513 3.452990 AGAGAGTCCGAGTCAGATGAGTA 59.547 47.826 6.01 0.00 0.00 2.59
3001 3514 2.238646 AGAGAGTCCGAGTCAGATGAGT 59.761 50.000 6.01 0.00 0.00 3.41
3002 3515 2.872245 GAGAGAGTCCGAGTCAGATGAG 59.128 54.545 6.01 0.00 0.00 2.90
3003 3516 2.503765 AGAGAGAGTCCGAGTCAGATGA 59.496 50.000 6.01 0.00 0.00 2.92
3004 3517 2.872245 GAGAGAGAGTCCGAGTCAGATG 59.128 54.545 6.01 0.00 0.00 2.90
3005 3518 2.483013 CGAGAGAGAGTCCGAGTCAGAT 60.483 54.545 6.01 0.00 0.00 2.90
3006 3519 1.134936 CGAGAGAGAGTCCGAGTCAGA 60.135 57.143 6.01 0.00 0.00 3.27
3007 3520 1.286501 CGAGAGAGAGTCCGAGTCAG 58.713 60.000 6.01 0.00 0.00 3.51
3008 3521 0.108089 CCGAGAGAGAGTCCGAGTCA 60.108 60.000 6.01 0.00 0.00 3.41
3009 3522 0.108041 ACCGAGAGAGAGTCCGAGTC 60.108 60.000 0.00 0.00 0.00 3.36
3010 3523 0.391927 CACCGAGAGAGAGTCCGAGT 60.392 60.000 0.00 0.00 0.00 4.18
3011 3524 0.108089 TCACCGAGAGAGAGTCCGAG 60.108 60.000 0.00 0.00 0.00 4.63
3012 3525 0.542333 ATCACCGAGAGAGAGTCCGA 59.458 55.000 0.00 0.00 0.00 4.55
3013 3526 0.660488 CATCACCGAGAGAGAGTCCG 59.340 60.000 0.00 0.00 0.00 4.79
3014 3527 1.757682 ACATCACCGAGAGAGAGTCC 58.242 55.000 0.00 0.00 0.00 3.85
3015 3528 3.013921 AGAACATCACCGAGAGAGAGTC 58.986 50.000 0.00 0.00 0.00 3.36
3016 3529 3.013921 GAGAACATCACCGAGAGAGAGT 58.986 50.000 0.00 0.00 0.00 3.24
3017 3530 2.031560 CGAGAACATCACCGAGAGAGAG 59.968 54.545 0.00 0.00 0.00 3.20
3018 3531 2.010497 CGAGAACATCACCGAGAGAGA 58.990 52.381 0.00 0.00 0.00 3.10
3019 3532 1.740585 ACGAGAACATCACCGAGAGAG 59.259 52.381 0.00 0.00 0.00 3.20
3020 3533 1.738350 GACGAGAACATCACCGAGAGA 59.262 52.381 0.00 0.00 0.00 3.10
3021 3534 1.202200 GGACGAGAACATCACCGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
3022 3535 0.809385 GGACGAGAACATCACCGAGA 59.191 55.000 0.00 0.00 0.00 4.04
3023 3536 0.523546 CGGACGAGAACATCACCGAG 60.524 60.000 0.00 0.00 44.84 4.63
3024 3537 0.956902 TCGGACGAGAACATCACCGA 60.957 55.000 0.00 0.00 46.76 4.69
3025 3538 0.797249 GTCGGACGAGAACATCACCG 60.797 60.000 0.00 0.00 44.01 4.94
3026 3539 0.797249 CGTCGGACGAGAACATCACC 60.797 60.000 25.29 0.00 46.05 4.02
3027 3540 0.109873 ACGTCGGACGAGAACATCAC 60.110 55.000 34.40 0.00 46.05 3.06
3028 3541 0.167470 GACGTCGGACGAGAACATCA 59.833 55.000 34.40 0.00 46.05 3.07
3029 3542 0.447011 AGACGTCGGACGAGAACATC 59.553 55.000 34.40 20.45 46.05 3.06
3030 3543 0.168348 CAGACGTCGGACGAGAACAT 59.832 55.000 34.40 13.02 46.05 2.71
3031 3544 1.162181 ACAGACGTCGGACGAGAACA 61.162 55.000 34.40 0.00 46.05 3.18
3032 3545 0.725118 CACAGACGTCGGACGAGAAC 60.725 60.000 34.40 20.93 46.05 3.01
3033 3546 1.572941 CACAGACGTCGGACGAGAA 59.427 57.895 34.40 0.00 46.05 2.87
3034 3547 2.962827 GCACAGACGTCGGACGAGA 61.963 63.158 34.40 0.00 46.05 4.04
3035 3548 2.502080 GCACAGACGTCGGACGAG 60.502 66.667 34.40 24.02 46.05 4.18
3036 3549 4.379143 CGCACAGACGTCGGACGA 62.379 66.667 34.40 0.00 46.05 4.20
3037 3550 3.299304 TACGCACAGACGTCGGACG 62.299 63.158 27.33 27.33 44.43 4.79
3038 3551 1.511464 CTACGCACAGACGTCGGAC 60.511 63.158 22.71 12.28 44.43 4.79
3039 3552 2.865308 CTACGCACAGACGTCGGA 59.135 61.111 22.71 0.00 44.43 4.55
3040 3553 2.202440 CCTACGCACAGACGTCGG 60.202 66.667 14.42 14.42 44.43 4.79
3041 3554 2.874780 GCCTACGCACAGACGTCG 60.875 66.667 10.46 7.86 44.43 5.12
3042 3555 2.874780 CGCCTACGCACAGACGTC 60.875 66.667 7.70 7.70 44.43 4.34
3044 3557 2.874780 GACGCCTACGCACAGACG 60.875 66.667 0.00 0.00 45.53 4.18
3045 3558 1.344942 CTTGACGCCTACGCACAGAC 61.345 60.000 0.00 0.00 45.53 3.51
3046 3559 1.080772 CTTGACGCCTACGCACAGA 60.081 57.895 0.00 0.00 45.53 3.41
3047 3560 0.666274 TTCTTGACGCCTACGCACAG 60.666 55.000 0.00 0.00 45.53 3.66
3048 3561 0.249531 TTTCTTGACGCCTACGCACA 60.250 50.000 0.00 0.00 45.53 4.57
3049 3562 0.163146 GTTTCTTGACGCCTACGCAC 59.837 55.000 0.00 0.00 45.53 5.34
3050 3563 0.947180 GGTTTCTTGACGCCTACGCA 60.947 55.000 0.00 0.00 45.53 5.24
3051 3564 1.785951 GGTTTCTTGACGCCTACGC 59.214 57.895 0.00 0.00 45.53 4.42
3052 3565 1.952266 GCGGTTTCTTGACGCCTACG 61.952 60.000 0.00 0.00 46.92 3.51
3053 3566 1.785951 GCGGTTTCTTGACGCCTAC 59.214 57.895 0.00 0.00 46.92 3.18
3054 3567 4.272100 GCGGTTTCTTGACGCCTA 57.728 55.556 0.00 0.00 46.92 3.93
3058 3571 1.773496 GACGAGCGGTTTCTTGACG 59.227 57.895 0.00 0.00 0.00 4.35
3059 3572 1.773496 CGACGAGCGGTTTCTTGAC 59.227 57.895 0.00 0.00 36.03 3.18
3060 3573 2.019951 GCGACGAGCGGTTTCTTGA 61.020 57.895 0.00 0.00 41.29 3.02
3061 3574 2.470286 GCGACGAGCGGTTTCTTG 59.530 61.111 0.00 0.00 41.29 3.02
3074 3587 2.750637 TCCTGAGACTCCGGCGAC 60.751 66.667 9.30 0.00 0.00 5.19
3075 3588 2.438614 CTCCTGAGACTCCGGCGA 60.439 66.667 9.30 0.00 0.00 5.54
3076 3589 3.522731 CCTCCTGAGACTCCGGCG 61.523 72.222 8.01 0.00 0.00 6.46
3077 3590 2.043852 TCCTCCTGAGACTCCGGC 60.044 66.667 8.01 0.00 0.00 6.13
3078 3591 2.115911 CGTCCTCCTGAGACTCCGG 61.116 68.421 6.58 6.58 0.00 5.14
3079 3592 2.766400 GCGTCCTCCTGAGACTCCG 61.766 68.421 0.00 0.00 0.00 4.63
3080 3593 1.040339 ATGCGTCCTCCTGAGACTCC 61.040 60.000 0.00 0.00 0.00 3.85
3081 3594 0.383949 GATGCGTCCTCCTGAGACTC 59.616 60.000 0.00 0.00 0.00 3.36
3082 3595 0.033601 AGATGCGTCCTCCTGAGACT 60.034 55.000 1.23 0.00 0.00 3.24
3083 3596 0.383949 GAGATGCGTCCTCCTGAGAC 59.616 60.000 1.23 0.00 0.00 3.36
3084 3597 0.753479 GGAGATGCGTCCTCCTGAGA 60.753 60.000 13.94 0.00 45.18 3.27
3085 3598 1.739049 GGAGATGCGTCCTCCTGAG 59.261 63.158 13.94 0.00 45.18 3.35
3086 3599 3.941081 GGAGATGCGTCCTCCTGA 58.059 61.111 13.94 0.00 45.18 3.86
3089 3602 1.663173 GCTAGGAGATGCGTCCTCC 59.337 63.158 13.55 13.55 44.25 4.30
3090 3603 1.284408 CGCTAGGAGATGCGTCCTC 59.716 63.158 1.23 0.00 44.25 3.71
3096 3609 3.853712 CATCGCGCTAGGAGATGC 58.146 61.111 5.56 0.00 44.22 3.91
3098 3611 0.747255 ACAACATCGCGCTAGGAGAT 59.253 50.000 5.56 0.00 35.35 2.75
3099 3612 1.385528 TACAACATCGCGCTAGGAGA 58.614 50.000 5.56 0.00 0.00 3.71
3100 3613 2.423926 ATACAACATCGCGCTAGGAG 57.576 50.000 5.56 0.00 0.00 3.69
3101 3614 2.882927 AATACAACATCGCGCTAGGA 57.117 45.000 5.56 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.