Multiple sequence alignment - TraesCS2D01G101700

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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 TraesCS2D01G101700 chr2D 100.000 5349 0 0 1 5349 54867964 54873312 0.000000e+00 9878.0
1 TraesCS2D01G101700 chr2D 80.028 726 93 21 4152 4841 54874655 54875364 1.730000e-134 490.0
2 TraesCS2D01G101700 chr2D 93.774 257 12 3 5094 5349 54875985 54876238 3.020000e-102 383.0
3 TraesCS2D01G101700 chr2D 84.718 373 50 6 268 637 65684505 65684137 3.040000e-97 366.0
4 TraesCS2D01G101700 chr2D 97.143 35 1 0 2478 2512 54870380 54870414 5.790000e-05 60.2
5 TraesCS2D01G101700 chr2D 97.143 35 1 0 2417 2451 54870441 54870475 5.790000e-05 60.2
6 TraesCS2D01G101700 chr2B 91.124 3211 162 53 1624 4745 85643588 85646764 0.000000e+00 4237.0
7 TraesCS2D01G101700 chr2B 89.911 1239 58 22 612 1789 85642473 85643705 0.000000e+00 1533.0
8 TraesCS2D01G101700 chr2B 91.879 628 40 9 11 633 85641844 85642465 0.000000e+00 867.0
9 TraesCS2D01G101700 chr2B 81.103 725 86 28 4152 4841 85687622 85688330 2.840000e-147 532.0
10 TraesCS2D01G101700 chr2B 93.617 235 13 2 5115 5349 85695650 85695882 3.070000e-92 350.0
11 TraesCS2D01G101700 chr2B 97.500 40 1 0 1750 1789 85643546 85643585 9.610000e-08 69.4
12 TraesCS2D01G101700 chr2B 100.000 30 0 0 2478 2507 85644384 85644413 7.480000e-04 56.5
13 TraesCS2D01G101700 chr2B 100.000 29 0 0 5094 5122 85695544 85695572 3.000000e-03 54.7
14 TraesCS2D01G101700 chr2A 92.443 2567 124 34 2317 4840 55553483 55556022 0.000000e+00 3602.0
15 TraesCS2D01G101700 chr2A 93.220 1475 64 16 723 2172 55551943 55553406 0.000000e+00 2137.0
16 TraesCS2D01G101700 chr2A 94.758 248 12 1 5102 5349 55556897 55557143 8.400000e-103 385.0
17 TraesCS2D01G101700 chr2A 83.827 371 52 8 269 634 614575557 614575190 3.970000e-91 346.0
18 TraesCS2D01G101700 chr2A 83.378 373 54 8 267 633 748798015 748798385 6.640000e-89 339.0
19 TraesCS2D01G101700 chr2A 95.000 40 2 0 1750 1789 55552844 55552883 4.470000e-06 63.9
20 TraesCS2D01G101700 chr5A 83.871 372 53 7 267 633 350796138 350795769 1.100000e-91 348.0
21 TraesCS2D01G101700 chr5A 83.378 373 53 9 268 634 595159848 595160217 2.390000e-88 337.0
22 TraesCS2D01G101700 chr1A 83.784 370 53 7 269 633 48771962 48771595 1.430000e-90 344.0
23 TraesCS2D01G101700 chr1A 83.245 376 55 8 265 634 95433247 95432874 6.640000e-89 339.0
24 TraesCS2D01G101700 chr6A 83.558 371 55 6 269 634 196013198 196012829 5.130000e-90 342.0
25 TraesCS2D01G101700 chr7D 79.935 309 42 10 3564 3869 631923278 631922987 5.430000e-50 209.0
26 TraesCS2D01G101700 chr7D 80.000 170 26 4 16 181 439241670 439241835 9.410000e-23 119.0
27 TraesCS2D01G101700 chr4D 85.897 156 19 1 20 172 458264455 458264300 4.290000e-36 163.0
28 TraesCS2D01G101700 chr4D 80.380 158 25 6 16 171 43667704 43667857 1.220000e-21 115.0
29 TraesCS2D01G101700 chr4D 80.986 142 22 4 43 179 41718100 41718241 2.040000e-19 108.0
30 TraesCS2D01G101700 chr7A 84.431 167 20 5 10 171 4678709 4678874 5.550000e-35 159.0
31 TraesCS2D01G101700 chr5B 82.166 157 22 4 19 172 362839711 362839864 4.350000e-26 130.0
32 TraesCS2D01G101700 chr3A 80.337 178 25 8 1 174 706511945 706511774 5.620000e-25 126.0
33 TraesCS2D01G101700 chr1D 83.721 129 17 4 46 174 494304986 494305110 9.410000e-23 119.0


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 TraesCS2D01G101700 chr2D 54867964 54873312 5348 False 3332.800 9878 98.095333 1 5349 3 chr2D.!!$F1 5348
1 TraesCS2D01G101700 chr2D 54874655 54876238 1583 False 436.500 490 86.901000 4152 5349 2 chr2D.!!$F2 1197
2 TraesCS2D01G101700 chr2B 85641844 85646764 4920 False 1352.580 4237 94.082800 11 4745 5 chr2B.!!$F2 4734
3 TraesCS2D01G101700 chr2B 85687622 85688330 708 False 532.000 532 81.103000 4152 4841 1 chr2B.!!$F1 689
4 TraesCS2D01G101700 chr2A 55551943 55557143 5200 False 1546.975 3602 93.855250 723 5349 4 chr2A.!!$F2 4626

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
27 28 0.258484 TTGGATGCGGGGATGACAAT 59.742 50.000 0.00 0.0 0.00 2.71 F
703 755 0.468214 TTTGATCCCGGTGCCAAACA 60.468 50.000 0.00 0.0 0.00 2.83 F
754 806 1.121407 TCACCCACTGTCCCACTCTG 61.121 60.000 0.00 0.0 0.00 3.35 F
964 1030 1.294780 CCAGTCTGGCACTCTCCAC 59.705 63.158 5.79 0.0 30.26 4.02 F
2775 2952 0.907486 TGCTCTGCCTGAATGTAGCT 59.093 50.000 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1852 0.108520 GCCACTGCACATTCCCAATG 60.109 55.000 0.00 0.0 44.48 2.82 R
1789 1928 0.390340 ACATTGCTCTGATCGTGCGT 60.390 50.000 6.96 0.0 34.94 5.24 R
1922 2077 1.066303 GATAGCCACTGTCTCCGAGTG 59.934 57.143 0.00 0.0 40.55 3.51 R
2944 3147 1.115326 AACTGGGCAAAACCTCCTGC 61.115 55.000 0.00 0.0 39.10 4.85 R
4674 4916 3.236047 TCCAGCACACAGTAGGTCTTTA 58.764 45.455 0.00 0.0 0.00 1.85 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 0.258484 TTGGATGCGGGGATGACAAT 59.742 50.000 0.00 0.00 0.00 2.71
152 158 1.060937 GAGCGCTTTATGCCACACG 59.939 57.895 13.26 0.00 38.78 4.49
186 192 9.663904 CTTATCATTTGGGTGTTTTATCGTATG 57.336 33.333 0.00 0.00 0.00 2.39
189 195 8.287439 TCATTTGGGTGTTTTATCGTATGAAT 57.713 30.769 0.00 0.00 0.00 2.57
237 243 9.561069 TTTAGACAATCCATATAGCTTTTCTCC 57.439 33.333 0.00 0.00 0.00 3.71
244 250 4.458295 CCATATAGCTTTTCTCCCATGCTG 59.542 45.833 0.00 0.00 35.47 4.41
271 277 5.412904 CGAGAGAAAAGGGCTAAAAATGAGT 59.587 40.000 0.00 0.00 0.00 3.41
279 285 2.952310 GGCTAAAAATGAGTAGGGCCTG 59.048 50.000 18.53 0.00 35.92 4.85
350 356 8.667076 AATTCAAACTTCCTGGATTCAAAAAG 57.333 30.769 0.00 0.00 0.00 2.27
351 357 7.416964 TTCAAACTTCCTGGATTCAAAAAGA 57.583 32.000 0.00 0.00 0.00 2.52
446 452 2.750948 TGCGACCTGTACAAAAGAGAC 58.249 47.619 0.00 0.00 0.00 3.36
474 480 5.028549 TCTGGACTTTGAGGATGAATAGC 57.971 43.478 0.00 0.00 0.00 2.97
496 502 1.962807 TCATGTGTGAAAAAGGCCCAG 59.037 47.619 0.00 0.00 0.00 4.45
583 589 2.267174 ATGCCTCCATGTATGTCTGC 57.733 50.000 0.00 0.00 0.00 4.26
627 633 9.252962 GGAAATGTAAAAATAGGCATTCTGATG 57.747 33.333 0.00 0.00 36.32 3.07
682 734 0.485543 TGGCCGATACCTATCCCTGA 59.514 55.000 0.00 0.00 0.00 3.86
703 755 0.468214 TTTGATCCCGGTGCCAAACA 60.468 50.000 0.00 0.00 0.00 2.83
754 806 1.121407 TCACCCACTGTCCCACTCTG 61.121 60.000 0.00 0.00 0.00 3.35
941 1002 2.676822 ACTTCGCCTCCTCGCTCA 60.677 61.111 0.00 0.00 0.00 4.26
945 1006 4.803426 CGCCTCCTCGCTCACACC 62.803 72.222 0.00 0.00 0.00 4.16
947 1008 3.775654 CCTCCTCGCTCACACCCC 61.776 72.222 0.00 0.00 0.00 4.95
948 1009 2.997315 CTCCTCGCTCACACCCCA 60.997 66.667 0.00 0.00 0.00 4.96
949 1010 2.997315 TCCTCGCTCACACCCCAG 60.997 66.667 0.00 0.00 0.00 4.45
950 1011 3.314331 CCTCGCTCACACCCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
952 1013 2.203640 TCGCTCACACCCCAGTCT 60.204 61.111 0.00 0.00 0.00 3.24
954 1015 2.348998 GCTCACACCCCAGTCTGG 59.651 66.667 12.40 12.40 37.25 3.86
956 1017 2.447572 TCACACCCCAGTCTGGCA 60.448 61.111 13.99 0.00 35.79 4.92
957 1018 2.281761 CACACCCCAGTCTGGCAC 60.282 66.667 13.99 0.00 35.79 5.01
964 1030 1.294780 CCAGTCTGGCACTCTCCAC 59.705 63.158 5.79 0.00 30.26 4.02
1455 1552 3.120385 CATTGCTGCCACTCGCGA 61.120 61.111 9.26 9.26 42.08 5.87
1817 1956 4.260661 CGATCAGAGCAATGTGAGGAAATG 60.261 45.833 0.00 0.00 0.00 2.32
1824 1963 1.647545 ATGTGAGGAAATGCACCGCG 61.648 55.000 0.00 0.00 34.19 6.46
1842 1981 3.865745 CCGCGTCATTCTTCAGTTTATCT 59.134 43.478 4.92 0.00 0.00 1.98
1871 2010 9.900710 CTTTAGTATACTCACTTGGCATACTAG 57.099 37.037 9.12 0.00 36.53 2.57
1922 2077 3.913089 ACCGATTCCTTCATTGTTTTGC 58.087 40.909 0.00 0.00 0.00 3.68
2034 2189 5.764686 TCCTACGAACAGTCTTACAGTGTTA 59.235 40.000 0.00 0.00 46.92 2.41
2081 2236 3.769300 GGTTTCCCAATCAAAGCTACCAT 59.231 43.478 0.00 0.00 0.00 3.55
2209 2372 3.044986 GCCTGTACATTGCGCAATTATG 58.955 45.455 32.13 24.58 0.00 1.90
2212 2375 4.438608 CCTGTACATTGCGCAATTATGTGT 60.439 41.667 32.13 27.84 39.31 3.72
2255 2418 5.796350 AGTCGTGCTGGTATGTTTTAATC 57.204 39.130 0.00 0.00 0.00 1.75
2264 2427 7.170658 TGCTGGTATGTTTTAATCTTTGTTTGC 59.829 33.333 0.00 0.00 0.00 3.68
2282 2445 1.002430 TGCTCTGTCAGTCAATGGGTC 59.998 52.381 0.00 0.00 0.00 4.46
2306 2469 2.079158 CATAGGAGCACCAGTGTTGTG 58.921 52.381 2.07 0.00 38.94 3.33
2341 2504 2.408271 TATTGACTTGCTCTGCCCAG 57.592 50.000 0.00 0.00 0.00 4.45
2459 2622 4.778579 AGACAATCCAGTCCATGATTCAG 58.221 43.478 0.00 0.00 39.34 3.02
2465 2632 3.041211 CCAGTCCATGATTCAGTCCCTA 58.959 50.000 0.00 0.00 0.00 3.53
2466 2633 3.181461 CCAGTCCATGATTCAGTCCCTAC 60.181 52.174 0.00 0.00 0.00 3.18
2472 2639 4.163078 CCATGATTCAGTCCCTACTTCAGT 59.837 45.833 0.00 0.00 31.97 3.41
2474 2641 6.127054 CCATGATTCAGTCCCTACTTCAGTAA 60.127 42.308 0.00 0.00 31.97 2.24
2475 2642 6.282199 TGATTCAGTCCCTACTTCAGTAAC 57.718 41.667 0.00 0.00 31.97 2.50
2477 2644 7.179966 TGATTCAGTCCCTACTTCAGTAACTA 58.820 38.462 0.00 0.00 31.97 2.24
2478 2645 7.339721 TGATTCAGTCCCTACTTCAGTAACTAG 59.660 40.741 0.00 0.00 31.97 2.57
2482 2649 5.595133 AGTCCCTACTTCAGTAACTAGATGC 59.405 44.000 0.00 0.00 29.00 3.91
2487 2655 7.199766 CCTACTTCAGTAACTAGATGCTTCAG 58.800 42.308 0.00 0.00 0.00 3.02
2490 2658 8.123639 ACTTCAGTAACTAGATGCTTCAGTAA 57.876 34.615 0.00 0.00 0.00 2.24
2491 2659 8.030106 ACTTCAGTAACTAGATGCTTCAGTAAC 58.970 37.037 0.00 0.00 0.00 2.50
2494 2662 8.894731 TCAGTAACTAGATGCTTCAGTAACTAG 58.105 37.037 0.00 7.41 35.11 2.57
2495 2663 8.894731 CAGTAACTAGATGCTTCAGTAACTAGA 58.105 37.037 13.71 0.00 33.77 2.43
2496 2664 9.116067 AGTAACTAGATGCTTCAGTAACTAGAG 57.884 37.037 13.71 0.00 33.77 2.43
2499 2667 8.671384 ACTAGATGCTTCAGTAACTAGAGTAG 57.329 38.462 13.71 0.00 33.77 2.57
2500 2668 8.487848 ACTAGATGCTTCAGTAACTAGAGTAGA 58.512 37.037 13.71 0.00 33.77 2.59
2501 2669 7.562454 AGATGCTTCAGTAACTAGAGTAGAC 57.438 40.000 0.00 0.00 0.00 2.59
2502 2670 7.113437 AGATGCTTCAGTAACTAGAGTAGACA 58.887 38.462 0.00 0.00 0.00 3.41
2503 2671 7.612244 AGATGCTTCAGTAACTAGAGTAGACAA 59.388 37.037 0.00 0.00 0.00 3.18
2504 2672 7.704578 TGCTTCAGTAACTAGAGTAGACAAT 57.295 36.000 0.00 0.00 0.00 2.71
2507 2675 7.148052 GCTTCAGTAACTAGAGTAGACAATCCA 60.148 40.741 0.00 0.00 0.00 3.41
2508 2676 8.824756 TTCAGTAACTAGAGTAGACAATCCAT 57.175 34.615 0.00 0.00 0.00 3.41
2523 2697 4.403432 ACAATCCATTCCCTGCTTGTTATG 59.597 41.667 0.00 0.00 29.79 1.90
2586 2760 6.392625 TGTTATGGTGCAGAGAGTACTATC 57.607 41.667 9.56 9.56 35.72 2.08
2649 2826 4.924305 ACGGACACTCTAAAGTTGTACA 57.076 40.909 0.00 0.00 31.71 2.90
2670 2847 6.992063 ACAATTTGTTTGTTTAATGTGGCA 57.008 29.167 0.00 0.00 46.51 4.92
2684 2861 9.072294 GTTTAATGTGGCAATATGTACTGTTTC 57.928 33.333 0.00 0.00 0.00 2.78
2711 2888 5.690464 ATCTTTCACTGAATGAGGTAGCT 57.310 39.130 11.74 0.00 38.99 3.32
2722 2899 3.026707 TGAGGTAGCTACAGGCACATA 57.973 47.619 24.75 0.18 44.79 2.29
2771 2948 7.148120 GCATATATATTTGCTCTGCCTGAATGT 60.148 37.037 17.79 0.00 35.95 2.71
2772 2949 9.387257 CATATATATTTGCTCTGCCTGAATGTA 57.613 33.333 0.00 0.00 0.00 2.29
2773 2950 7.918536 ATATATTTGCTCTGCCTGAATGTAG 57.081 36.000 0.00 0.00 0.00 2.74
2774 2951 1.742761 TTGCTCTGCCTGAATGTAGC 58.257 50.000 0.00 0.00 0.00 3.58
2775 2952 0.907486 TGCTCTGCCTGAATGTAGCT 59.093 50.000 0.00 0.00 0.00 3.32
2776 2953 2.110578 TGCTCTGCCTGAATGTAGCTA 58.889 47.619 0.00 0.00 0.00 3.32
2777 2954 2.159043 TGCTCTGCCTGAATGTAGCTAC 60.159 50.000 17.30 17.30 0.00 3.58
2778 2955 2.159043 GCTCTGCCTGAATGTAGCTACA 60.159 50.000 27.91 27.91 40.98 2.74
2779 2956 3.715495 CTCTGCCTGAATGTAGCTACAG 58.285 50.000 29.05 17.26 39.92 2.74
2780 2957 3.099905 TCTGCCTGAATGTAGCTACAGT 58.900 45.455 29.05 27.44 39.92 3.55
2781 2958 4.278310 TCTGCCTGAATGTAGCTACAGTA 58.722 43.478 29.05 17.24 39.92 2.74
2782 2959 4.339530 TCTGCCTGAATGTAGCTACAGTAG 59.660 45.833 29.05 23.74 39.92 2.57
2783 2960 3.384789 TGCCTGAATGTAGCTACAGTAGG 59.615 47.826 30.63 30.63 39.92 3.18
2784 2961 3.800604 GCCTGAATGTAGCTACAGTAGGC 60.801 52.174 36.66 36.66 44.91 3.93
2785 2962 3.384789 CCTGAATGTAGCTACAGTAGGCA 59.615 47.826 29.05 19.83 39.92 4.75
2786 2963 4.141937 CCTGAATGTAGCTACAGTAGGCAA 60.142 45.833 29.05 11.49 39.92 4.52
2787 2964 5.011090 TGAATGTAGCTACAGTAGGCAAG 57.989 43.478 29.05 0.00 39.92 4.01
2862 3065 3.990369 ACTACAGTAGGCTACCCAATCA 58.010 45.455 20.67 0.60 0.00 2.57
2943 3146 6.834168 TCTAAACCCCATCTCAATTTCAAC 57.166 37.500 0.00 0.00 0.00 3.18
2944 3147 4.519540 AAACCCCATCTCAATTTCAACG 57.480 40.909 0.00 0.00 0.00 4.10
3113 3316 6.092122 CGAGGTTTGTTAGCTATCAATGTCAA 59.908 38.462 16.08 0.90 33.94 3.18
3165 3368 7.814587 TGATACATCAGTAGTTGCTATACATGC 59.185 37.037 0.00 0.00 32.86 4.06
3172 3375 4.311816 AGTTGCTATACATGCATTTGCC 57.688 40.909 0.00 0.00 40.34 4.52
3199 3402 2.906389 AGGCTGACTACATTTGTCTCCA 59.094 45.455 0.00 0.00 35.63 3.86
3572 3775 8.877808 TGTTCAGAGTACAGCAAATATATCTG 57.122 34.615 0.00 0.00 35.40 2.90
3667 3870 5.586155 ATTCTCGTCTTCCTCCTATCCTA 57.414 43.478 0.00 0.00 0.00 2.94
3668 3871 4.354893 TCTCGTCTTCCTCCTATCCTAC 57.645 50.000 0.00 0.00 0.00 3.18
3669 3872 3.975312 TCTCGTCTTCCTCCTATCCTACT 59.025 47.826 0.00 0.00 0.00 2.57
3811 4014 7.553881 AGCATAAGAGCGTGTATTGTTATTT 57.446 32.000 0.00 0.00 40.15 1.40
3854 4057 2.350899 TCAAATTGCAATGCTGGACG 57.649 45.000 13.82 0.00 0.00 4.79
3869 4072 3.058224 GCTGGACGCTTACATTTTTCTGT 60.058 43.478 0.00 0.00 35.14 3.41
4052 4277 2.836667 TCCCTATCCCTTTACGTGGTT 58.163 47.619 0.00 0.00 0.00 3.67
4055 4280 3.135895 CCCTATCCCTTTACGTGGTTGAT 59.864 47.826 0.00 0.00 0.00 2.57
4059 4284 5.638596 ATCCCTTTACGTGGTTGATTTTC 57.361 39.130 0.00 0.00 0.00 2.29
4060 4285 4.721132 TCCCTTTACGTGGTTGATTTTCT 58.279 39.130 0.00 0.00 0.00 2.52
4063 4288 6.771749 TCCCTTTACGTGGTTGATTTTCTTTA 59.228 34.615 0.00 0.00 0.00 1.85
4115 4343 3.817647 AGCTTGATTTTCTGTCTGTGACC 59.182 43.478 0.00 0.00 0.00 4.02
4189 4418 2.360801 TGTAGTTTCTTGTGCTTTGCCC 59.639 45.455 0.00 0.00 0.00 5.36
4267 4502 6.414732 TGTATGTGGAGCAAAATAGCTTACT 58.585 36.000 0.00 0.00 46.75 2.24
4405 4646 0.187851 ATACTCCCTCCGTCCCGAAT 59.812 55.000 0.00 0.00 0.00 3.34
4450 4691 7.572814 TCAGGATCACATGTATGGACATTTTA 58.427 34.615 0.00 0.00 44.18 1.52
4526 4768 7.964011 GTGTAAGTAGTAAGTTGTTTTTGCACA 59.036 33.333 0.00 0.00 32.58 4.57
4722 4964 0.470766 ACGGTAAGCCACCTTTGTGA 59.529 50.000 3.76 0.00 46.19 3.58
4774 5265 9.865321 ATTTCATTTTTGTTCTCACAGGATATG 57.135 29.630 0.00 0.00 33.22 1.78
4777 5268 8.859090 TCATTTTTGTTCTCACAGGATATGTTT 58.141 29.630 0.00 0.00 41.41 2.83
4786 5277 6.551975 TCTCACAGGATATGTTTACCGGATAA 59.448 38.462 9.46 0.00 41.41 1.75
4819 5311 9.491675 AGATTTGAACAATATCACAAAAATGCA 57.508 25.926 0.00 0.00 36.19 3.96
4825 5317 8.428186 AACAATATCACAAAAATGCATCATCC 57.572 30.769 0.00 0.00 0.00 3.51
4830 5322 5.856156 TCACAAAAATGCATCATCCAAACT 58.144 33.333 0.00 0.00 0.00 2.66
4831 5323 6.289834 TCACAAAAATGCATCATCCAAACTT 58.710 32.000 0.00 0.00 0.00 2.66
4841 5333 3.831323 TCATCCAAACTTCTCCTTGCAA 58.169 40.909 0.00 0.00 0.00 4.08
4845 5337 5.200368 TCCAAACTTCTCCTTGCAATTTC 57.800 39.130 0.00 0.00 0.00 2.17
4846 5338 4.895297 TCCAAACTTCTCCTTGCAATTTCT 59.105 37.500 0.00 0.00 0.00 2.52
4847 5339 6.068010 TCCAAACTTCTCCTTGCAATTTCTA 58.932 36.000 0.00 0.00 0.00 2.10
4848 5340 6.721208 TCCAAACTTCTCCTTGCAATTTCTAT 59.279 34.615 0.00 0.00 0.00 1.98
4849 5341 7.888021 TCCAAACTTCTCCTTGCAATTTCTATA 59.112 33.333 0.00 0.00 0.00 1.31
4850 5342 8.522830 CCAAACTTCTCCTTGCAATTTCTATAA 58.477 33.333 0.00 0.00 0.00 0.98
4880 5660 4.713321 ACTCCAAGCTTTAATTGGCATGAT 59.287 37.500 0.00 0.00 45.69 2.45
4881 5661 5.163478 ACTCCAAGCTTTAATTGGCATGATC 60.163 40.000 0.00 0.00 45.69 2.92
4882 5662 4.046462 CCAAGCTTTAATTGGCATGATCG 58.954 43.478 0.00 0.00 40.74 3.69
4883 5663 3.360249 AGCTTTAATTGGCATGATCGC 57.640 42.857 0.00 0.00 0.00 4.58
4886 5666 2.753989 TTAATTGGCATGATCGCACG 57.246 45.000 0.00 0.00 0.00 5.34
4890 5671 1.946745 TTGGCATGATCGCACGAATA 58.053 45.000 0.00 0.00 0.00 1.75
4896 5677 2.363788 TGATCGCACGAATATAGGCC 57.636 50.000 0.00 0.00 0.00 5.19
4898 5679 1.993370 GATCGCACGAATATAGGCCAC 59.007 52.381 5.01 0.00 0.00 5.01
4899 5680 0.032952 TCGCACGAATATAGGCCACC 59.967 55.000 5.01 0.00 0.00 4.61
4917 5698 3.066760 CCACCTGTTGAAACTTTCTGACC 59.933 47.826 3.22 0.00 0.00 4.02
4918 5699 3.694072 CACCTGTTGAAACTTTCTGACCA 59.306 43.478 3.22 0.00 0.00 4.02
4927 5708 5.067674 TGAAACTTTCTGACCATCAAACAGG 59.932 40.000 3.22 0.00 33.19 4.00
4928 5709 2.887152 ACTTTCTGACCATCAAACAGGC 59.113 45.455 0.00 0.00 33.19 4.85
4929 5710 2.957402 TTCTGACCATCAAACAGGCT 57.043 45.000 0.00 0.00 33.19 4.58
4930 5711 4.202461 ACTTTCTGACCATCAAACAGGCTA 60.202 41.667 0.00 0.00 33.19 3.93
4931 5712 4.365514 TTCTGACCATCAAACAGGCTAA 57.634 40.909 0.00 0.00 33.19 3.09
4932 5713 3.674997 TCTGACCATCAAACAGGCTAAC 58.325 45.455 0.00 0.00 33.19 2.34
4933 5714 3.327757 TCTGACCATCAAACAGGCTAACT 59.672 43.478 0.00 0.00 33.19 2.24
4946 5727 5.757850 CAGGCTAACTGTTGAAACTTTCT 57.242 39.130 2.69 0.00 42.42 2.52
4947 5728 5.514279 CAGGCTAACTGTTGAAACTTTCTG 58.486 41.667 2.69 0.00 42.42 3.02
4948 5729 5.296780 CAGGCTAACTGTTGAAACTTTCTGA 59.703 40.000 2.69 0.00 42.42 3.27
4949 5730 5.885912 AGGCTAACTGTTGAAACTTTCTGAA 59.114 36.000 2.69 0.00 0.00 3.02
4950 5731 5.971792 GGCTAACTGTTGAAACTTTCTGAAC 59.028 40.000 2.69 1.40 0.00 3.18
4951 5732 5.677178 GCTAACTGTTGAAACTTTCTGAACG 59.323 40.000 2.69 0.00 0.00 3.95
4952 5733 5.622770 AACTGTTGAAACTTTCTGAACGT 57.377 34.783 3.22 0.00 0.00 3.99
4953 5734 5.217895 ACTGTTGAAACTTTCTGAACGTC 57.782 39.130 0.00 0.00 0.00 4.34
4954 5735 4.935808 ACTGTTGAAACTTTCTGAACGTCT 59.064 37.500 0.00 0.00 0.00 4.18
4955 5736 5.163854 ACTGTTGAAACTTTCTGAACGTCTG 60.164 40.000 0.00 0.00 0.00 3.51
4956 5737 4.693566 TGTTGAAACTTTCTGAACGTCTGT 59.306 37.500 0.00 0.00 0.00 3.41
4957 5738 5.180492 TGTTGAAACTTTCTGAACGTCTGTT 59.820 36.000 0.00 0.00 42.23 3.16
4958 5739 6.369340 TGTTGAAACTTTCTGAACGTCTGTTA 59.631 34.615 0.00 0.00 38.78 2.41
4959 5740 6.583912 TGAAACTTTCTGAACGTCTGTTAG 57.416 37.500 0.00 0.00 38.78 2.34
4962 5743 6.980051 AACTTTCTGAACGTCTGTTAGTTT 57.020 33.333 0.00 0.00 38.78 2.66
4970 5751 9.100554 TCTGAACGTCTGTTAGTTTAATTTTCA 57.899 29.630 0.00 0.00 38.78 2.69
4971 5752 9.878599 CTGAACGTCTGTTAGTTTAATTTTCAT 57.121 29.630 0.00 0.00 38.78 2.57
4987 5768 7.832503 AATTTTCATTAATTTCCGCTTGGAG 57.167 32.000 0.00 0.00 44.35 3.86
4988 5769 6.582677 TTTTCATTAATTTCCGCTTGGAGA 57.417 33.333 0.00 0.00 44.35 3.71
4989 5770 6.773976 TTTCATTAATTTCCGCTTGGAGAT 57.226 33.333 0.00 0.00 44.35 2.75
4990 5771 5.756195 TCATTAATTTCCGCTTGGAGATG 57.244 39.130 0.00 0.00 44.35 2.90
4991 5772 5.436175 TCATTAATTTCCGCTTGGAGATGA 58.564 37.500 0.00 0.00 44.35 2.92
4992 5773 6.064060 TCATTAATTTCCGCTTGGAGATGAT 58.936 36.000 0.00 0.00 44.35 2.45
4993 5774 6.547141 TCATTAATTTCCGCTTGGAGATGATT 59.453 34.615 0.00 0.00 44.35 2.57
4994 5775 6.773976 TTAATTTCCGCTTGGAGATGATTT 57.226 33.333 0.00 0.00 44.35 2.17
4995 5776 7.873719 TTAATTTCCGCTTGGAGATGATTTA 57.126 32.000 0.00 0.00 44.35 1.40
4996 5777 6.773976 AATTTCCGCTTGGAGATGATTTAA 57.226 33.333 0.00 0.00 44.35 1.52
4997 5778 6.773976 ATTTCCGCTTGGAGATGATTTAAA 57.226 33.333 0.00 0.00 44.35 1.52
4998 5779 5.560966 TTCCGCTTGGAGATGATTTAAAC 57.439 39.130 0.00 0.00 44.35 2.01
4999 5780 4.843728 TCCGCTTGGAGATGATTTAAACT 58.156 39.130 0.00 0.00 36.65 2.66
5000 5781 5.253330 TCCGCTTGGAGATGATTTAAACTT 58.747 37.500 0.00 0.00 36.65 2.66
5001 5782 6.411376 TCCGCTTGGAGATGATTTAAACTTA 58.589 36.000 0.00 0.00 36.65 2.24
5002 5783 6.882140 TCCGCTTGGAGATGATTTAAACTTAA 59.118 34.615 0.00 0.00 36.65 1.85
5003 5784 7.065803 TCCGCTTGGAGATGATTTAAACTTAAG 59.934 37.037 0.00 0.00 36.65 1.85
5004 5785 7.148239 CCGCTTGGAGATGATTTAAACTTAAGT 60.148 37.037 1.12 1.12 33.02 2.24
5005 5786 7.905493 CGCTTGGAGATGATTTAAACTTAAGTC 59.095 37.037 8.95 0.00 32.10 3.01
5006 5787 7.905493 GCTTGGAGATGATTTAAACTTAAGTCG 59.095 37.037 8.95 0.00 33.58 4.18
5036 5818 2.316108 AACCAAATGTGGGTTCTGGAC 58.684 47.619 6.92 0.00 45.31 4.02
5051 5893 1.301401 GGACTTGCACACCGCTACA 60.301 57.895 0.00 0.00 43.06 2.74
5055 5897 0.391661 CTTGCACACCGCTACATCCT 60.392 55.000 0.00 0.00 43.06 3.24
5059 5901 1.808411 CACACCGCTACATCCTTGTT 58.192 50.000 0.00 0.00 37.28 2.83
5062 5904 2.151202 CACCGCTACATCCTTGTTGTT 58.849 47.619 0.00 0.00 37.28 2.83
5064 5906 2.812011 ACCGCTACATCCTTGTTGTTTC 59.188 45.455 0.00 0.00 37.28 2.78
5065 5907 2.161609 CCGCTACATCCTTGTTGTTTCC 59.838 50.000 0.00 0.00 37.28 3.13
5068 5910 4.092968 CGCTACATCCTTGTTGTTTCCTAC 59.907 45.833 0.00 0.00 37.28 3.18
5071 5913 3.813166 ACATCCTTGTTGTTTCCTACGTG 59.187 43.478 0.00 0.00 29.55 4.49
5073 5915 2.171027 TCCTTGTTGTTTCCTACGTGGT 59.829 45.455 0.00 0.00 37.07 4.16
5075 5917 3.002965 CCTTGTTGTTTCCTACGTGGTTC 59.997 47.826 0.00 0.00 37.07 3.62
5076 5918 3.263489 TGTTGTTTCCTACGTGGTTCA 57.737 42.857 0.00 0.00 37.07 3.18
5083 5925 6.231951 TGTTTCCTACGTGGTTCAAATCATA 58.768 36.000 0.00 0.00 37.07 2.15
5084 5926 6.148150 TGTTTCCTACGTGGTTCAAATCATAC 59.852 38.462 0.00 0.00 37.07 2.39
5085 5927 5.670792 TCCTACGTGGTTCAAATCATACT 57.329 39.130 0.00 0.00 37.07 2.12
5086 5928 6.045072 TCCTACGTGGTTCAAATCATACTT 57.955 37.500 0.00 0.00 37.07 2.24
5088 5930 7.613585 TCCTACGTGGTTCAAATCATACTTAA 58.386 34.615 0.00 0.00 37.07 1.85
5089 5931 8.095792 TCCTACGTGGTTCAAATCATACTTAAA 58.904 33.333 0.00 0.00 37.07 1.52
5090 5932 8.173130 CCTACGTGGTTCAAATCATACTTAAAC 58.827 37.037 0.00 0.00 0.00 2.01
5091 5933 6.595794 ACGTGGTTCAAATCATACTTAAACG 58.404 36.000 0.00 0.00 0.00 3.60
5092 5934 6.424509 ACGTGGTTCAAATCATACTTAAACGA 59.575 34.615 0.00 0.00 0.00 3.85
5095 6006 9.061610 GTGGTTCAAATCATACTTAAACGATTG 57.938 33.333 0.00 0.00 0.00 2.67
5140 6051 4.560128 TGTAGCTTTCAGTACTCTGCAAG 58.440 43.478 0.00 3.94 43.91 4.01
5239 6150 4.494855 GCATATGCTGAGTTTTCGGACTTC 60.495 45.833 20.64 0.00 38.21 3.01
5257 6168 7.501225 TCGGACTTCTTAACTTCCTTGAAAAAT 59.499 33.333 0.00 0.00 0.00 1.82
5258 6169 8.135529 CGGACTTCTTAACTTCCTTGAAAAATT 58.864 33.333 0.00 0.00 0.00 1.82
5295 6208 4.065789 AGAAAAATGAGGACACCGAAGTC 58.934 43.478 0.00 0.00 37.80 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.053865 CCCGCATCCAACTTGCCAT 61.054 57.895 0.00 0.00 36.75 4.40
1 2 2.676121 CCCGCATCCAACTTGCCA 60.676 61.111 0.00 0.00 36.75 4.92
2 3 3.451894 CCCCGCATCCAACTTGCC 61.452 66.667 0.00 0.00 36.75 4.52
3 4 1.754234 ATCCCCGCATCCAACTTGC 60.754 57.895 0.00 0.00 36.74 4.01
4 5 0.394216 TCATCCCCGCATCCAACTTG 60.394 55.000 0.00 0.00 0.00 3.16
5 6 0.394352 GTCATCCCCGCATCCAACTT 60.394 55.000 0.00 0.00 0.00 2.66
6 7 1.224592 GTCATCCCCGCATCCAACT 59.775 57.895 0.00 0.00 0.00 3.16
7 8 0.679640 TTGTCATCCCCGCATCCAAC 60.680 55.000 0.00 0.00 0.00 3.77
9 10 0.258484 AATTGTCATCCCCGCATCCA 59.742 50.000 0.00 0.00 0.00 3.41
27 28 4.367450 GTTGCCATGCTTGACAACTAAAA 58.633 39.130 19.93 0.00 39.39 1.52
152 158 4.518970 ACACCCAAATGATAAGTGTCACAC 59.481 41.667 0.00 0.00 37.05 3.82
165 171 8.405531 AGATTCATACGATAAAACACCCAAATG 58.594 33.333 0.00 0.00 0.00 2.32
217 223 6.349944 GCATGGGAGAAAAGCTATATGGATTG 60.350 42.308 0.00 0.00 0.00 2.67
237 243 1.664659 CTTTTCTCTCGAGCAGCATGG 59.335 52.381 7.81 0.00 35.86 3.66
244 250 2.674796 TTAGCCCTTTTCTCTCGAGC 57.325 50.000 7.81 0.00 0.00 5.03
271 277 2.589157 CGGTCACCAACAGGCCCTA 61.589 63.158 0.00 0.00 0.00 3.53
279 285 1.021390 CATGGAGCTCGGTCACCAAC 61.021 60.000 7.83 0.00 36.00 3.77
314 320 8.619546 CCAGGAAGTTTGAATTTTGCATTTAAA 58.380 29.630 0.00 0.00 0.00 1.52
315 321 7.989741 TCCAGGAAGTTTGAATTTTGCATTTAA 59.010 29.630 0.00 0.00 0.00 1.52
316 322 7.504403 TCCAGGAAGTTTGAATTTTGCATTTA 58.496 30.769 0.00 0.00 0.00 1.40
321 327 5.990996 TGAATCCAGGAAGTTTGAATTTTGC 59.009 36.000 0.00 0.00 0.00 3.68
446 452 6.579666 TCATCCTCAAAGTCCAGAATTTTG 57.420 37.500 0.00 0.00 34.07 2.44
474 480 2.299582 TGGGCCTTTTTCACACATGATG 59.700 45.455 4.53 0.00 33.85 3.07
509 515 6.839124 ATACATTGAAATGAAGGCTGTGAA 57.161 33.333 9.94 0.00 39.67 3.18
510 516 6.839124 AATACATTGAAATGAAGGCTGTGA 57.161 33.333 9.94 0.00 39.67 3.58
511 517 7.385752 ACAAAATACATTGAAATGAAGGCTGTG 59.614 33.333 9.94 2.46 39.67 3.66
513 519 7.894376 ACAAAATACATTGAAATGAAGGCTG 57.106 32.000 9.94 4.46 39.67 4.85
514 520 8.370182 AGAACAAAATACATTGAAATGAAGGCT 58.630 29.630 9.94 0.00 39.67 4.58
515 521 8.437742 CAGAACAAAATACATTGAAATGAAGGC 58.562 33.333 9.94 0.00 39.67 4.35
601 607 9.252962 CATCAGAATGCCTATTTTTACATTTCC 57.747 33.333 0.00 0.00 33.07 3.13
627 633 8.477256 TGATACCCATTTCCTGATTTCAAAATC 58.523 33.333 8.25 8.25 43.91 2.17
641 677 1.692411 GGGCCTGTGATACCCATTTC 58.308 55.000 0.84 0.00 43.64 2.17
648 684 4.963878 CCAGTGGGCCTGTGATAC 57.036 61.111 4.53 0.00 39.74 2.24
661 697 0.487772 AGGGATAGGTATCGGCCAGT 59.512 55.000 2.24 0.00 33.52 4.00
682 734 0.178975 TTTGGCACCGGGATCAAAGT 60.179 50.000 6.32 0.00 0.00 2.66
716 768 2.025898 GAGGTGAGAGTGGTAGTAGGC 58.974 57.143 0.00 0.00 0.00 3.93
725 777 0.319728 CAGTGGGTGAGGTGAGAGTG 59.680 60.000 0.00 0.00 0.00 3.51
754 806 3.255379 GTTCGAGGGCGTGCGATC 61.255 66.667 0.00 0.00 38.98 3.69
861 922 2.418976 GGCTTGTTAGTTTCGGGTGATC 59.581 50.000 0.00 0.00 0.00 2.92
941 1002 2.448542 AGTGCCAGACTGGGGTGT 60.449 61.111 23.09 0.00 38.19 4.16
945 1006 1.915266 TGGAGAGTGCCAGACTGGG 60.915 63.158 23.09 5.16 38.19 4.45
947 1008 1.294780 GGTGGAGAGTGCCAGACTG 59.705 63.158 0.00 0.00 38.95 3.51
948 1009 1.915769 GGGTGGAGAGTGCCAGACT 60.916 63.158 0.00 0.00 38.95 3.24
949 1010 2.665603 GGGTGGAGAGTGCCAGAC 59.334 66.667 0.00 0.00 38.95 3.51
950 1011 2.607750 GGGGTGGAGAGTGCCAGA 60.608 66.667 0.00 0.00 38.95 3.86
952 1013 3.249189 GTGGGGTGGAGAGTGCCA 61.249 66.667 0.00 0.00 35.02 4.92
956 1017 4.954118 TGGCGTGGGGTGGAGAGT 62.954 66.667 0.00 0.00 0.00 3.24
957 1018 4.394712 GTGGCGTGGGGTGGAGAG 62.395 72.222 0.00 0.00 0.00 3.20
983 1050 1.369625 CATGGAAGAGCGGTGGTTAC 58.630 55.000 0.00 0.00 0.00 2.50
1671 1768 2.401766 CCACTGCGCATTCCCAGTC 61.402 63.158 12.24 0.00 40.12 3.51
1713 1852 0.108520 GCCACTGCACATTCCCAATG 60.109 55.000 0.00 0.00 44.48 2.82
1714 1853 0.542467 TGCCACTGCACATTCCCAAT 60.542 50.000 0.00 0.00 44.23 3.16
1715 1854 1.152589 TGCCACTGCACATTCCCAA 60.153 52.632 0.00 0.00 44.23 4.12
1743 1882 3.451894 CCAATTGCCGGCACCTCC 61.452 66.667 32.95 0.00 0.00 4.30
1751 1890 0.458889 CTGCACATTCCCAATTGCCG 60.459 55.000 0.00 0.00 33.86 5.69
1752 1891 0.609662 ACTGCACATTCCCAATTGCC 59.390 50.000 0.00 0.00 33.86 4.52
1753 1892 1.673626 CCACTGCACATTCCCAATTGC 60.674 52.381 0.00 0.00 35.45 3.56
1754 1893 1.673626 GCCACTGCACATTCCCAATTG 60.674 52.381 0.00 0.00 37.47 2.32
1755 1894 0.609662 GCCACTGCACATTCCCAATT 59.390 50.000 0.00 0.00 37.47 2.32
1789 1928 0.390340 ACATTGCTCTGATCGTGCGT 60.390 50.000 6.96 0.00 34.94 5.24
1817 1956 1.291877 ACTGAAGAATGACGCGGTGC 61.292 55.000 12.47 0.00 0.00 5.01
1824 1963 9.766277 CTAAAGCAAGATAAACTGAAGAATGAC 57.234 33.333 0.00 0.00 0.00 3.06
1842 1981 5.800296 TGCCAAGTGAGTATACTAAAGCAA 58.200 37.500 5.09 0.00 31.41 3.91
1922 2077 1.066303 GATAGCCACTGTCTCCGAGTG 59.934 57.143 0.00 0.00 40.55 3.51
2034 2189 5.313712 AGTAGGTTCATCCGAAACAACATT 58.686 37.500 0.00 0.00 41.66 2.71
2081 2236 4.223032 GGTTCCTCCTCTCTGTAAACATCA 59.777 45.833 0.00 0.00 0.00 3.07
2233 2396 5.488341 AGATTAAAACATACCAGCACGACT 58.512 37.500 0.00 0.00 0.00 4.18
2255 2418 4.621068 TTGACTGACAGAGCAAACAAAG 57.379 40.909 10.08 0.00 0.00 2.77
2264 2427 1.404717 CGGACCCATTGACTGACAGAG 60.405 57.143 10.08 0.00 0.00 3.35
2282 2445 2.109799 CTGGTGCTCCTATGGCGG 59.890 66.667 6.34 0.00 34.23 6.13
2306 2469 7.519008 GCAAGTCAATATGCTGATGGTACTTAC 60.519 40.741 0.00 0.00 39.46 2.34
2371 2534 8.443160 TGATTCGTTTTGCATTTCTAGTCTAAG 58.557 33.333 0.00 0.00 0.00 2.18
2459 2622 5.595133 AGCATCTAGTTACTGAAGTAGGGAC 59.405 44.000 0.00 0.00 38.60 4.46
2465 2632 6.597832 ACTGAAGCATCTAGTTACTGAAGT 57.402 37.500 0.00 0.00 0.00 3.01
2466 2633 8.247562 AGTTACTGAAGCATCTAGTTACTGAAG 58.752 37.037 10.29 0.00 34.27 3.02
2474 2641 8.487848 TCTACTCTAGTTACTGAAGCATCTAGT 58.512 37.037 0.00 0.00 0.00 2.57
2475 2642 8.770828 GTCTACTCTAGTTACTGAAGCATCTAG 58.229 40.741 0.00 0.00 0.00 2.43
2477 2644 7.113437 TGTCTACTCTAGTTACTGAAGCATCT 58.887 38.462 0.00 0.00 0.00 2.90
2478 2645 7.323049 TGTCTACTCTAGTTACTGAAGCATC 57.677 40.000 0.00 0.00 0.00 3.91
2482 2649 8.282455 TGGATTGTCTACTCTAGTTACTGAAG 57.718 38.462 0.00 0.00 0.00 3.02
2487 2655 7.288158 AGGGAATGGATTGTCTACTCTAGTTAC 59.712 40.741 0.00 0.00 0.00 2.50
2490 2658 5.600484 CAGGGAATGGATTGTCTACTCTAGT 59.400 44.000 0.00 0.00 0.00 2.57
2491 2659 5.510520 GCAGGGAATGGATTGTCTACTCTAG 60.511 48.000 0.00 0.00 0.00 2.43
2494 2662 3.135530 AGCAGGGAATGGATTGTCTACTC 59.864 47.826 0.00 0.00 0.00 2.59
2495 2663 3.118531 AGCAGGGAATGGATTGTCTACT 58.881 45.455 0.00 0.00 0.00 2.57
2496 2664 3.567478 AGCAGGGAATGGATTGTCTAC 57.433 47.619 0.00 0.00 0.00 2.59
2499 2667 2.450476 ACAAGCAGGGAATGGATTGTC 58.550 47.619 0.00 0.00 39.17 3.18
2500 2668 2.610438 ACAAGCAGGGAATGGATTGT 57.390 45.000 0.00 0.00 38.66 2.71
2501 2669 4.403432 ACATAACAAGCAGGGAATGGATTG 59.597 41.667 0.00 0.00 36.54 2.67
2502 2670 4.613437 ACATAACAAGCAGGGAATGGATT 58.387 39.130 0.00 0.00 0.00 3.01
2503 2671 4.255510 ACATAACAAGCAGGGAATGGAT 57.744 40.909 0.00 0.00 0.00 3.41
2504 2672 3.737559 ACATAACAAGCAGGGAATGGA 57.262 42.857 0.00 0.00 0.00 3.41
2507 2675 4.406456 TGTGAACATAACAAGCAGGGAAT 58.594 39.130 0.00 0.00 0.00 3.01
2508 2676 3.826524 TGTGAACATAACAAGCAGGGAA 58.173 40.909 0.00 0.00 0.00 3.97
2523 2697 4.843728 TGAGATGGGGTTTAGATGTGAAC 58.156 43.478 0.00 0.00 0.00 3.18
2586 2760 7.606349 TGTAGCAATATATAGGTTGAGCTGAG 58.394 38.462 0.00 0.00 32.70 3.35
2684 2861 8.394121 GCTACCTCATTCAGTGAAAGATTAAAG 58.606 37.037 10.14 7.40 36.14 1.85
2722 2899 6.765989 TGCAGATGTGTAGTTAGAAAACACTT 59.234 34.615 6.41 0.38 43.09 3.16
2771 2948 3.427573 TGTGTCTTGCCTACTGTAGCTA 58.572 45.455 9.35 0.00 0.00 3.32
2772 2949 2.248248 TGTGTCTTGCCTACTGTAGCT 58.752 47.619 9.35 0.00 0.00 3.32
2773 2950 2.743636 TGTGTCTTGCCTACTGTAGC 57.256 50.000 9.35 5.92 0.00 3.58
2774 2951 4.814234 TGTTTTGTGTCTTGCCTACTGTAG 59.186 41.667 7.87 7.87 0.00 2.74
2775 2952 4.771903 TGTTTTGTGTCTTGCCTACTGTA 58.228 39.130 0.00 0.00 0.00 2.74
2776 2953 3.616219 TGTTTTGTGTCTTGCCTACTGT 58.384 40.909 0.00 0.00 0.00 3.55
2777 2954 4.630894 TTGTTTTGTGTCTTGCCTACTG 57.369 40.909 0.00 0.00 0.00 2.74
2778 2955 5.359576 TGATTTGTTTTGTGTCTTGCCTACT 59.640 36.000 0.00 0.00 0.00 2.57
2779 2956 5.587289 TGATTTGTTTTGTGTCTTGCCTAC 58.413 37.500 0.00 0.00 0.00 3.18
2780 2957 5.843673 TGATTTGTTTTGTGTCTTGCCTA 57.156 34.783 0.00 0.00 0.00 3.93
2781 2958 4.734398 TGATTTGTTTTGTGTCTTGCCT 57.266 36.364 0.00 0.00 0.00 4.75
2782 2959 5.108517 TCTTGATTTGTTTTGTGTCTTGCC 58.891 37.500 0.00 0.00 0.00 4.52
2783 2960 6.531240 TCTTCTTGATTTGTTTTGTGTCTTGC 59.469 34.615 0.00 0.00 0.00 4.01
2784 2961 8.638685 ATCTTCTTGATTTGTTTTGTGTCTTG 57.361 30.769 0.00 0.00 29.59 3.02
2822 3025 2.948979 AGTTACTGGAGCATCTCTCTCG 59.051 50.000 0.00 0.00 41.60 4.04
2943 3146 2.597217 TGGGCAAAACCTCCTGCG 60.597 61.111 0.00 0.00 39.55 5.18
2944 3147 1.115326 AACTGGGCAAAACCTCCTGC 61.115 55.000 0.00 0.00 39.10 4.85
3113 3316 6.142817 CACAAAACTGAAAGCGCTAAGTAAT 58.857 36.000 12.05 5.37 37.60 1.89
3172 3375 5.028549 ACAAATGTAGTCAGCCTGGATAG 57.971 43.478 0.00 0.00 0.00 2.08
3235 3438 9.482627 AGGATCAAAAAGATTATCTAGTTAGCG 57.517 33.333 0.00 0.00 37.00 4.26
3439 3642 7.591795 GTGACAGGAGTACATCTTACATTATCG 59.408 40.741 0.00 0.00 0.00 2.92
3572 3775 7.277760 AGCCAAAACAATGAGTTAACAAAGAAC 59.722 33.333 8.61 0.00 40.26 3.01
3667 3870 5.872070 GCTCATAAACTTCTACTTGCTGAGT 59.128 40.000 0.00 0.00 42.55 3.41
3668 3871 5.871524 TGCTCATAAACTTCTACTTGCTGAG 59.128 40.000 0.00 0.00 0.00 3.35
3669 3872 5.793817 TGCTCATAAACTTCTACTTGCTGA 58.206 37.500 0.00 0.00 0.00 4.26
3823 4026 8.472413 AGCATTGCAATTTGATCTATAACACTT 58.528 29.630 9.83 0.00 0.00 3.16
3869 4072 5.875224 TCAGTTCACAGGGAAAATATGTCA 58.125 37.500 0.00 0.00 37.23 3.58
4115 4343 5.473504 ACCCAGTTATCTTAACTGTTTGCTG 59.526 40.000 20.25 8.51 44.52 4.41
4405 4646 8.740123 TCCTGAAGTGAAATTACAACAGTTAA 57.260 30.769 0.00 0.00 0.00 2.01
4583 4825 5.870978 GCAAATGCAACTAGGATCAACAATT 59.129 36.000 0.00 0.00 41.59 2.32
4588 4830 8.518430 TTATAAGCAAATGCAACTAGGATCAA 57.482 30.769 8.28 0.00 45.16 2.57
4674 4916 3.236047 TCCAGCACACAGTAGGTCTTTA 58.764 45.455 0.00 0.00 0.00 1.85
4722 4964 8.747538 AATAGTGTTACAAACCTCAAGAGTTT 57.252 30.769 0.00 0.00 0.00 2.66
4749 4991 8.859090 ACATATCCTGTGAGAACAAAAATGAAA 58.141 29.630 0.00 0.00 36.48 2.69
4774 5265 9.321562 TCAAATCTGAATAGTTATCCGGTAAAC 57.678 33.333 0.00 7.48 0.00 2.01
4777 5268 8.479689 TGTTCAAATCTGAATAGTTATCCGGTA 58.520 33.333 0.00 0.00 43.39 4.02
4779 5270 7.786178 TGTTCAAATCTGAATAGTTATCCGG 57.214 36.000 0.00 0.00 43.39 5.14
4806 5297 6.469410 AGTTTGGATGATGCATTTTTGTGAT 58.531 32.000 0.00 0.00 0.00 3.06
4819 5311 4.038271 TGCAAGGAGAAGTTTGGATGAT 57.962 40.909 0.00 0.00 0.00 2.45
4849 5341 9.599866 GCCAATTAAAGCTTGGAGTAATAAATT 57.400 29.630 9.98 0.00 44.95 1.82
4850 5342 8.757877 TGCCAATTAAAGCTTGGAGTAATAAAT 58.242 29.630 9.98 0.00 44.95 1.40
4851 5343 8.128322 TGCCAATTAAAGCTTGGAGTAATAAA 57.872 30.769 9.98 0.00 44.95 1.40
4852 5344 7.710676 TGCCAATTAAAGCTTGGAGTAATAA 57.289 32.000 9.98 0.00 44.95 1.40
4855 5635 5.714333 TCATGCCAATTAAAGCTTGGAGTAA 59.286 36.000 9.98 0.00 44.95 2.24
4859 5639 4.202040 CGATCATGCCAATTAAAGCTTGGA 60.202 41.667 9.98 0.00 44.95 3.53
4860 5640 4.046462 CGATCATGCCAATTAAAGCTTGG 58.954 43.478 0.00 0.00 44.94 3.61
4868 5648 1.946745 TCGTGCGATCATGCCAATTA 58.053 45.000 0.00 0.00 0.00 1.40
4880 5660 0.032952 GGTGGCCTATATTCGTGCGA 59.967 55.000 3.32 0.00 0.00 5.10
4881 5661 0.033504 AGGTGGCCTATATTCGTGCG 59.966 55.000 3.32 0.00 28.47 5.34
4882 5662 1.202651 ACAGGTGGCCTATATTCGTGC 60.203 52.381 3.32 0.00 29.64 5.34
4883 5663 2.872245 CAACAGGTGGCCTATATTCGTG 59.128 50.000 3.32 2.48 29.64 4.35
4886 5666 5.193679 AGTTTCAACAGGTGGCCTATATTC 58.806 41.667 3.32 0.00 29.64 1.75
4890 5671 3.525800 AAGTTTCAACAGGTGGCCTAT 57.474 42.857 3.32 0.00 29.64 2.57
4896 5677 3.694072 TGGTCAGAAAGTTTCAACAGGTG 59.306 43.478 17.65 6.21 0.00 4.00
4898 5679 4.580167 TGATGGTCAGAAAGTTTCAACAGG 59.420 41.667 17.65 2.35 0.00 4.00
4899 5680 5.756195 TGATGGTCAGAAAGTTTCAACAG 57.244 39.130 17.65 4.97 0.00 3.16
4927 5708 5.677178 CGTTCAGAAAGTTTCAACAGTTAGC 59.323 40.000 17.65 0.00 0.00 3.09
4928 5709 6.772078 ACGTTCAGAAAGTTTCAACAGTTAG 58.228 36.000 17.65 4.38 0.00 2.34
4929 5710 6.592607 AGACGTTCAGAAAGTTTCAACAGTTA 59.407 34.615 17.65 0.00 0.00 2.24
4930 5711 5.411669 AGACGTTCAGAAAGTTTCAACAGTT 59.588 36.000 17.65 2.33 0.00 3.16
4931 5712 4.935808 AGACGTTCAGAAAGTTTCAACAGT 59.064 37.500 17.65 14.12 0.00 3.55
4932 5713 5.163854 ACAGACGTTCAGAAAGTTTCAACAG 60.164 40.000 17.65 11.68 0.00 3.16
4933 5714 4.693566 ACAGACGTTCAGAAAGTTTCAACA 59.306 37.500 17.65 0.00 0.00 3.33
4934 5715 5.217895 ACAGACGTTCAGAAAGTTTCAAC 57.782 39.130 17.65 12.35 0.00 3.18
4935 5716 5.873179 AACAGACGTTCAGAAAGTTTCAA 57.127 34.783 17.65 1.51 0.00 2.69
4936 5717 6.103997 ACTAACAGACGTTCAGAAAGTTTCA 58.896 36.000 17.65 0.00 36.52 2.69
4937 5718 6.585389 ACTAACAGACGTTCAGAAAGTTTC 57.415 37.500 7.57 7.57 36.52 2.78
4938 5719 6.980051 AACTAACAGACGTTCAGAAAGTTT 57.020 33.333 3.04 0.00 36.52 2.66
4939 5720 6.980051 AAACTAACAGACGTTCAGAAAGTT 57.020 33.333 3.04 0.00 36.52 2.66
4940 5721 8.658499 ATTAAACTAACAGACGTTCAGAAAGT 57.342 30.769 0.81 0.81 36.52 2.66
4941 5722 9.931210 AAATTAAACTAACAGACGTTCAGAAAG 57.069 29.630 0.00 0.00 36.52 2.62
4943 5724 9.925268 GAAAATTAAACTAACAGACGTTCAGAA 57.075 29.630 0.00 0.00 36.52 3.02
4944 5725 9.100554 TGAAAATTAAACTAACAGACGTTCAGA 57.899 29.630 0.00 0.00 36.52 3.27
4945 5726 9.878599 ATGAAAATTAAACTAACAGACGTTCAG 57.121 29.630 0.00 0.00 36.52 3.02
4959 5740 9.753669 CCAAGCGGAAATTAATGAAAATTAAAC 57.246 29.630 0.00 0.00 30.78 2.01
4962 5743 8.744652 TCTCCAAGCGGAAATTAATGAAAATTA 58.255 29.630 0.00 0.00 42.21 1.40
4968 5749 5.436175 TCATCTCCAAGCGGAAATTAATGA 58.564 37.500 0.00 0.00 42.21 2.57
4970 5751 6.966534 AATCATCTCCAAGCGGAAATTAAT 57.033 33.333 0.00 0.00 42.21 1.40
4971 5752 6.773976 AAATCATCTCCAAGCGGAAATTAA 57.226 33.333 0.00 0.00 42.21 1.40
4973 5754 6.773976 TTAAATCATCTCCAAGCGGAAATT 57.226 33.333 0.00 0.00 42.21 1.82
4978 5759 5.567138 AAGTTTAAATCATCTCCAAGCGG 57.433 39.130 0.00 0.00 0.00 5.52
4979 5760 7.752695 ACTTAAGTTTAAATCATCTCCAAGCG 58.247 34.615 1.12 0.00 0.00 4.68
4980 5761 7.905493 CGACTTAAGTTTAAATCATCTCCAAGC 59.095 37.037 10.02 0.00 0.00 4.01
4989 5770 9.100554 TGAAACTCACGACTTAAGTTTAAATCA 57.899 29.630 10.02 5.13 41.86 2.57
4990 5771 9.925268 TTGAAACTCACGACTTAAGTTTAAATC 57.075 29.630 10.02 2.76 41.86 2.17
4992 5773 9.545611 GTTTGAAACTCACGACTTAAGTTTAAA 57.454 29.630 10.02 0.00 41.86 1.52
4993 5774 8.177013 GGTTTGAAACTCACGACTTAAGTTTAA 58.823 33.333 10.02 0.00 41.86 1.52
4994 5775 7.333921 TGGTTTGAAACTCACGACTTAAGTTTA 59.666 33.333 10.02 0.00 41.86 2.01
4995 5776 6.149807 TGGTTTGAAACTCACGACTTAAGTTT 59.850 34.615 10.02 0.00 43.84 2.66
4996 5777 5.644636 TGGTTTGAAACTCACGACTTAAGTT 59.355 36.000 10.02 0.00 34.81 2.66
4997 5778 5.180271 TGGTTTGAAACTCACGACTTAAGT 58.820 37.500 8.13 8.13 0.00 2.24
4998 5779 5.728351 TGGTTTGAAACTCACGACTTAAG 57.272 39.130 8.09 0.00 0.00 1.85
4999 5780 6.497785 TTTGGTTTGAAACTCACGACTTAA 57.502 33.333 8.09 0.00 0.00 1.85
5000 5781 6.094325 ACATTTGGTTTGAAACTCACGACTTA 59.906 34.615 8.09 0.00 0.00 2.24
5001 5782 5.105917 ACATTTGGTTTGAAACTCACGACTT 60.106 36.000 8.09 0.00 0.00 3.01
5002 5783 4.398044 ACATTTGGTTTGAAACTCACGACT 59.602 37.500 8.09 0.00 0.00 4.18
5003 5784 4.499040 CACATTTGGTTTGAAACTCACGAC 59.501 41.667 8.09 0.00 0.00 4.34
5004 5785 4.439426 CCACATTTGGTTTGAAACTCACGA 60.439 41.667 8.09 0.00 38.23 4.35
5005 5786 3.796178 CCACATTTGGTTTGAAACTCACG 59.204 43.478 8.09 0.00 38.23 4.35
5006 5787 4.119136 CCCACATTTGGTTTGAAACTCAC 58.881 43.478 8.09 0.00 42.10 3.51
5027 5808 1.507141 CGGTGTGCAAGTCCAGAACC 61.507 60.000 0.00 0.00 0.00 3.62
5051 5893 3.181448 ACCACGTAGGAAACAACAAGGAT 60.181 43.478 10.46 0.00 41.22 3.24
5055 5897 3.607741 TGAACCACGTAGGAAACAACAA 58.392 40.909 10.46 0.00 41.22 2.83
5059 5901 4.452825 TGATTTGAACCACGTAGGAAACA 58.547 39.130 10.46 5.27 41.22 2.83
5062 5904 6.045072 AGTATGATTTGAACCACGTAGGAA 57.955 37.500 10.46 0.00 41.22 3.36
5064 5906 7.837202 TTAAGTATGATTTGAACCACGTAGG 57.163 36.000 0.00 0.00 45.67 3.18
5065 5907 7.896274 CGTTTAAGTATGATTTGAACCACGTAG 59.104 37.037 0.00 0.00 0.00 3.51
5068 5910 6.823531 TCGTTTAAGTATGATTTGAACCACG 58.176 36.000 0.00 0.00 0.00 4.94
5083 5925 5.730550 TCCTGCTCATACAATCGTTTAAGT 58.269 37.500 0.00 0.00 0.00 2.24
5084 5926 6.851222 ATCCTGCTCATACAATCGTTTAAG 57.149 37.500 0.00 0.00 0.00 1.85
5085 5927 7.415095 CCAAATCCTGCTCATACAATCGTTTAA 60.415 37.037 0.00 0.00 0.00 1.52
5086 5928 6.038161 CCAAATCCTGCTCATACAATCGTTTA 59.962 38.462 0.00 0.00 0.00 2.01
5088 5930 4.336433 CCAAATCCTGCTCATACAATCGTT 59.664 41.667 0.00 0.00 0.00 3.85
5089 5931 3.879295 CCAAATCCTGCTCATACAATCGT 59.121 43.478 0.00 0.00 0.00 3.73
5090 5932 3.879295 ACCAAATCCTGCTCATACAATCG 59.121 43.478 0.00 0.00 0.00 3.34
5091 5933 5.450965 CCAACCAAATCCTGCTCATACAATC 60.451 44.000 0.00 0.00 0.00 2.67
5092 5934 4.403432 CCAACCAAATCCTGCTCATACAAT 59.597 41.667 0.00 0.00 0.00 2.71
5095 6006 2.689983 CCCAACCAAATCCTGCTCATAC 59.310 50.000 0.00 0.00 0.00 2.39
5140 6051 3.118629 TCAGATGTTCTGGTGTCCATAGC 60.119 47.826 4.78 0.00 44.39 2.97
5258 6169 9.426837 CCTCATTTTTCTTGCTTCATGATTTAA 57.573 29.630 0.00 0.00 0.00 1.52
5262 6175 6.209986 TGTCCTCATTTTTCTTGCTTCATGAT 59.790 34.615 0.00 0.00 0.00 2.45
5295 6208 1.453155 ACAACAGGATTTAGCTGCCG 58.547 50.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.