Multiple sequence alignment - TraesCS3B01G215700

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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 TraesCS3B01G215700 chr3B 100.000 5248 0 0 1 5248 256778829 256784076 0.000000e+00 9692.0
1 TraesCS3B01G215700 chr3B 84.762 420 53 8 1 413 377435231 377435646 1.360000e-110 411.0
2 TraesCS3B01G215700 chr3B 97.753 178 1 2 2471 2645 783212696 783212873 2.370000e-78 303.0
3 TraesCS3B01G215700 chr3B 86.170 94 10 3 1863 1956 684636622 684636712 1.200000e-16 99.0
4 TraesCS3B01G215700 chr3D 94.204 2657 78 19 2644 5248 178530388 178533020 0.000000e+00 3984.0
5 TraesCS3B01G215700 chr3D 95.670 993 23 5 880 1870 178528899 178529873 0.000000e+00 1578.0
6 TraesCS3B01G215700 chr3D 95.866 508 17 4 200 704 178527930 178528436 0.000000e+00 819.0
7 TraesCS3B01G215700 chr3D 93.385 514 15 6 1977 2483 178529888 178530389 0.000000e+00 743.0
8 TraesCS3B01G215700 chr3D 91.045 469 16 5 361 815 178528444 178528900 1.250000e-170 610.0
9 TraesCS3B01G215700 chr3D 97.403 77 2 0 1617 1693 274515932 274515856 1.190000e-26 132.0
10 TraesCS3B01G215700 chr3D 97.333 75 2 0 1616 1690 46481658 46481732 1.530000e-25 128.0
11 TraesCS3B01G215700 chr3A 92.766 2654 95 33 2644 5248 219795394 219797999 0.000000e+00 3747.0
12 TraesCS3B01G215700 chr3A 95.178 1659 49 12 836 2483 219793757 219795395 0.000000e+00 2591.0
13 TraesCS3B01G215700 chr3A 87.586 145 16 2 453 595 684327063 684326919 3.250000e-37 167.0
14 TraesCS3B01G215700 chr5D 83.914 603 65 12 1 596 110869521 110870098 9.940000e-152 547.0
15 TraesCS3B01G215700 chr5D 88.889 90 5 3 1869 1956 535136260 535136174 7.190000e-19 106.0
16 TraesCS3B01G215700 chr7D 82.638 599 81 14 3 595 428037659 428038240 4.690000e-140 508.0
17 TraesCS3B01G215700 chr7D 86.417 427 48 7 1 420 630509098 630508675 4.790000e-125 459.0
18 TraesCS3B01G215700 chr7D 85.480 427 48 10 1 420 630300570 630300151 2.900000e-117 433.0
19 TraesCS3B01G215700 chr7D 98.649 74 1 0 1617 1690 540843393 540843466 1.190000e-26 132.0
20 TraesCS3B01G215700 chr4D 81.664 589 85 14 1 581 463332818 463333391 7.960000e-128 468.0
21 TraesCS3B01G215700 chr4D 86.310 168 23 0 453 620 113574258 113574091 3.230000e-42 183.0
22 TraesCS3B01G215700 chr1D 85.439 467 37 11 4808 5248 452345388 452344927 1.720000e-124 457.0
23 TraesCS3B01G215700 chr1D 82.836 268 34 7 4993 5248 433519526 433519259 4.090000e-56 230.0
24 TraesCS3B01G215700 chr1D 98.649 74 1 0 1617 1690 218903633 218903706 1.190000e-26 132.0
25 TraesCS3B01G215700 chr5B 82.226 557 68 16 1 549 368491962 368491429 8.010000e-123 451.0
26 TraesCS3B01G215700 chr5B 97.222 180 2 3 2474 2652 283982431 283982254 8.540000e-78 302.0
27 TraesCS3B01G215700 chr5B 95.628 183 8 0 2480 2662 467042935 467042753 1.430000e-75 294.0
28 TraesCS3B01G215700 chr6D 81.593 565 82 12 24 581 11193731 11193182 1.040000e-121 448.0
29 TraesCS3B01G215700 chr6D 88.679 159 16 2 453 610 131683680 131683523 5.360000e-45 193.0
30 TraesCS3B01G215700 chr1A 82.885 520 66 15 21 538 243664665 243664167 3.730000e-121 446.0
31 TraesCS3B01G215700 chr1A 84.698 464 44 12 4808 5248 547258254 547257795 6.240000e-119 438.0
32 TraesCS3B01G215700 chr1A 82.609 276 34 9 4986 5248 532106040 532105766 1.140000e-56 231.0
33 TraesCS3B01G215700 chr5A 84.672 411 54 8 2 406 1397780 1398187 8.190000e-108 401.0
34 TraesCS3B01G215700 chr5A 84.783 92 11 1 1866 1957 688704962 688705050 7.240000e-14 89.8
35 TraesCS3B01G215700 chr1B 83.156 469 49 10 4806 5248 622183946 622184410 8.190000e-108 401.0
36 TraesCS3B01G215700 chr1B 99.412 170 1 0 2482 2651 442958085 442958254 5.100000e-80 309.0
37 TraesCS3B01G215700 chr1B 97.222 180 4 1 2470 2648 447321960 447322139 2.370000e-78 303.0
38 TraesCS3B01G215700 chr1B 82.734 278 30 12 4986 5248 585885088 585884814 1.140000e-56 231.0
39 TraesCS3B01G215700 chr1B 84.946 93 11 2 1866 1958 92616627 92616716 2.010000e-14 91.6
40 TraesCS3B01G215700 chr2A 99.408 169 1 0 2477 2645 113822290 113822458 1.840000e-79 307.0
41 TraesCS3B01G215700 chr2A 98.837 172 2 0 2482 2653 705822003 705821832 1.840000e-79 307.0
42 TraesCS3B01G215700 chr2A 85.276 163 20 4 454 613 180994366 180994205 1.170000e-36 165.0
43 TraesCS3B01G215700 chr7B 98.824 170 2 0 2482 2651 688929384 688929553 2.370000e-78 303.0
44 TraesCS3B01G215700 chr7B 82.184 174 29 2 423 595 468211544 468211372 1.180000e-31 148.0
45 TraesCS3B01G215700 chr7B 95.294 85 2 1 1618 1700 445663436 445663352 3.300000e-27 134.0
46 TraesCS3B01G215700 chr7B 95.588 68 3 0 1869 1936 428965845 428965912 5.560000e-20 110.0
47 TraesCS3B01G215700 chr7B 88.889 90 7 2 1868 1957 684403222 684403308 2.000000e-19 108.0
48 TraesCS3B01G215700 chr7B 87.500 88 8 3 1869 1956 44766164 44766248 1.200000e-16 99.0
49 TraesCS3B01G215700 chr6B 96.648 179 6 0 2472 2650 160917044 160917222 1.100000e-76 298.0
50 TraesCS3B01G215700 chr6B 98.649 74 1 0 1617 1690 20231027 20231100 1.190000e-26 132.0
51 TraesCS3B01G215700 chr7A 84.746 177 23 3 440 612 724969166 724968990 1.940000e-39 174.0
52 TraesCS3B01G215700 chr4A 97.468 79 1 1 1613 1690 302680115 302680193 3.300000e-27 134.0
53 TraesCS3B01G215700 chr2D 88.421 95 8 3 1862 1956 301762332 301762423 1.540000e-20 111.0


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 TraesCS3B01G215700 chr3B 256778829 256784076 5247 False 9692.0 9692 100.000 1 5248 1 chr3B.!!$F1 5247
1 TraesCS3B01G215700 chr3D 178527930 178533020 5090 False 1546.8 3984 94.034 200 5248 5 chr3D.!!$F2 5048
2 TraesCS3B01G215700 chr3A 219793757 219797999 4242 False 3169.0 3747 93.972 836 5248 2 chr3A.!!$F1 4412
3 TraesCS3B01G215700 chr5D 110869521 110870098 577 False 547.0 547 83.914 1 596 1 chr5D.!!$F1 595
4 TraesCS3B01G215700 chr7D 428037659 428038240 581 False 508.0 508 82.638 3 595 1 chr7D.!!$F1 592
5 TraesCS3B01G215700 chr4D 463332818 463333391 573 False 468.0 468 81.664 1 581 1 chr4D.!!$F1 580
6 TraesCS3B01G215700 chr5B 368491429 368491962 533 True 451.0 451 82.226 1 549 1 chr5B.!!$R2 548
7 TraesCS3B01G215700 chr6D 11193182 11193731 549 True 448.0 448 81.593 24 581 1 chr6D.!!$R1 557

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
668 1037 0.459078 TGTGTGCCATGTTGGTTGTG 59.541 50.0 0.00 0.0 40.46 3.33 F
2544 2938 0.528924 AAGTGACTACATACGGCGCA 59.471 50.0 10.83 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 3021 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.0 0.00 0.00 0.0 4.12 R
4505 4927 0.245539 TTGACGTGGGCTAGTACTGC 59.754 55.0 5.39 7.18 0.0 4.40 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
38 44 8.718102 AAAACTCGTATATCATAACTGCTTGT 57.282 30.769 0.00 0.00 0.00 3.16
54 60 3.181508 TGCTTGTGTGATCATGCATAACG 60.182 43.478 0.00 0.00 41.30 3.18
56 62 4.033932 GCTTGTGTGATCATGCATAACGTA 59.966 41.667 0.00 0.00 38.05 3.57
68 74 7.630026 TCATGCATAACGTAATCATTGAGAAC 58.370 34.615 0.00 0.00 0.00 3.01
71 77 6.752815 TGCATAACGTAATCATTGAGAACGTA 59.247 34.615 22.04 14.13 45.19 3.57
80 86 2.410785 TTGAGAACGTACGTGGACAG 57.589 50.000 23.57 0.00 0.00 3.51
114 120 3.571401 CACCTTCTATCATTTGATGGGCC 59.429 47.826 0.00 0.00 36.05 5.80
144 150 1.341482 TGCCGATGAGAAGAGAGGAGT 60.341 52.381 0.00 0.00 0.00 3.85
149 155 4.099266 CCGATGAGAAGAGAGGAGTGAATT 59.901 45.833 0.00 0.00 0.00 2.17
150 156 5.395103 CCGATGAGAAGAGAGGAGTGAATTT 60.395 44.000 0.00 0.00 0.00 1.82
152 158 5.157940 TGAGAAGAGAGGAGTGAATTTGG 57.842 43.478 0.00 0.00 0.00 3.28
161 167 4.331968 AGGAGTGAATTTGGCGTTTCATA 58.668 39.130 0.85 0.00 34.60 2.15
187 194 9.574516 AAAGGTGTACAATGAAATTAGAGACTT 57.425 29.630 0.00 0.00 32.46 3.01
193 200 9.088512 GTACAATGAAATTAGAGACTTCGATGT 57.911 33.333 3.22 3.22 32.46 3.06
230 237 6.644347 TCAGAAGGATTTGATGAAGGAGTAC 58.356 40.000 0.00 0.00 0.00 2.73
309 317 7.068955 GTGCAATAACCTTTTTGTATTTGTGC 58.931 34.615 0.00 0.00 0.00 4.57
665 1034 2.356665 TAGTGTGTGCCATGTTGGTT 57.643 45.000 0.00 0.00 40.46 3.67
668 1037 0.459078 TGTGTGCCATGTTGGTTGTG 59.541 50.000 0.00 0.00 40.46 3.33
698 1068 2.497675 ACCTATGCACTAGCCGGATATG 59.502 50.000 5.05 5.15 41.13 1.78
700 1070 3.055819 CCTATGCACTAGCCGGATATGTT 60.056 47.826 5.05 0.00 41.13 2.71
703 1073 3.616219 TGCACTAGCCGGATATGTTTTT 58.384 40.909 5.05 0.00 41.13 1.94
819 1201 6.301169 AGTTATTTTTCGAGAGGATCAGGT 57.699 37.500 0.00 0.00 37.82 4.00
820 1202 6.712276 AGTTATTTTTCGAGAGGATCAGGTT 58.288 36.000 0.00 0.00 37.82 3.50
821 1203 7.168905 AGTTATTTTTCGAGAGGATCAGGTTT 58.831 34.615 0.00 0.00 37.82 3.27
822 1204 7.665974 AGTTATTTTTCGAGAGGATCAGGTTTT 59.334 33.333 0.00 0.00 37.82 2.43
823 1205 6.901081 ATTTTTCGAGAGGATCAGGTTTTT 57.099 33.333 0.00 0.00 37.82 1.94
875 1257 8.515695 TTTTAGACATACTCGAGAGGAATACA 57.484 34.615 21.68 0.00 0.00 2.29
1214 1601 1.759459 GCCAGATTCTACCTCCCCCG 61.759 65.000 0.00 0.00 0.00 5.73
1233 1620 3.998672 GGTTCGCGACCTGTCCCA 61.999 66.667 9.15 0.00 45.55 4.37
1363 1750 2.751688 GCCGGTGGGGACAGTAAA 59.248 61.111 1.90 0.00 44.46 2.01
1525 1912 3.763360 TGTGGATGTAAAAATGGAGCTGG 59.237 43.478 0.00 0.00 0.00 4.85
1527 1914 4.016444 TGGATGTAAAAATGGAGCTGGTC 58.984 43.478 0.00 0.00 0.00 4.02
1636 2023 1.831736 TGGGTTTCAGCTCTAGCCTAC 59.168 52.381 0.00 0.00 43.38 3.18
1650 2037 1.497286 AGCCTACCCCAACTTGTTTGA 59.503 47.619 0.00 0.00 37.39 2.69
1690 2077 6.040247 TGTTGTTGTTGTTGTTGTTGTTGTA 58.960 32.000 0.00 0.00 0.00 2.41
1764 2151 8.102047 TCTATAGGAAATTACTCCTCTCCTACG 58.898 40.741 1.79 0.00 42.53 3.51
1765 2152 3.637694 AGGAAATTACTCCTCTCCTACGC 59.362 47.826 0.00 0.00 42.53 4.42
1806 2193 7.978099 AAATTTTGATTAGATGCTTACCCCT 57.022 32.000 0.00 0.00 0.00 4.79
1807 2194 7.978099 AATTTTGATTAGATGCTTACCCCTT 57.022 32.000 0.00 0.00 0.00 3.95
1808 2195 7.978099 ATTTTGATTAGATGCTTACCCCTTT 57.022 32.000 0.00 0.00 0.00 3.11
1809 2196 7.404671 TTTTGATTAGATGCTTACCCCTTTC 57.595 36.000 0.00 0.00 0.00 2.62
1810 2197 5.975988 TGATTAGATGCTTACCCCTTTCT 57.024 39.130 0.00 0.00 0.00 2.52
1811 2198 6.327386 TGATTAGATGCTTACCCCTTTCTT 57.673 37.500 0.00 0.00 0.00 2.52
1978 2365 4.711355 AGCATGCTTTAGGCCAAAAGAATA 59.289 37.500 16.30 0.00 38.50 1.75
2114 2503 1.821216 TGGAGAAAAGGTTCATCCGC 58.179 50.000 0.00 0.00 41.99 5.54
2225 2614 3.023119 TGGGGTGCATGATGTATTCAAC 58.977 45.455 0.00 0.00 38.03 3.18
2352 2741 5.838531 TTGGTCACCGAAAAACATTTACT 57.161 34.783 0.00 0.00 0.00 2.24
2353 2742 5.838531 TGGTCACCGAAAAACATTTACTT 57.161 34.783 0.00 0.00 0.00 2.24
2354 2743 6.939132 TGGTCACCGAAAAACATTTACTTA 57.061 33.333 0.00 0.00 0.00 2.24
2355 2744 7.513371 TGGTCACCGAAAAACATTTACTTAT 57.487 32.000 0.00 0.00 0.00 1.73
2356 2745 7.942990 TGGTCACCGAAAAACATTTACTTATT 58.057 30.769 0.00 0.00 0.00 1.40
2357 2746 9.064706 TGGTCACCGAAAAACATTTACTTATTA 57.935 29.630 0.00 0.00 0.00 0.98
2479 2873 1.462616 AAGCAGCACCGCATTCATTA 58.537 45.000 0.00 0.00 0.00 1.90
2481 2875 2.026641 AGCAGCACCGCATTCATTATT 58.973 42.857 0.00 0.00 0.00 1.40
2482 2876 3.213506 AGCAGCACCGCATTCATTATTA 58.786 40.909 0.00 0.00 0.00 0.98
2483 2877 3.003689 AGCAGCACCGCATTCATTATTAC 59.996 43.478 0.00 0.00 0.00 1.89
2484 2878 3.003689 GCAGCACCGCATTCATTATTACT 59.996 43.478 0.00 0.00 0.00 2.24
2485 2879 4.776743 CAGCACCGCATTCATTATTACTC 58.223 43.478 0.00 0.00 0.00 2.59
2486 2880 3.815401 AGCACCGCATTCATTATTACTCC 59.185 43.478 0.00 0.00 0.00 3.85
2487 2881 3.058224 GCACCGCATTCATTATTACTCCC 60.058 47.826 0.00 0.00 0.00 4.30
2488 2882 4.389374 CACCGCATTCATTATTACTCCCT 58.611 43.478 0.00 0.00 0.00 4.20
2489 2883 4.452455 CACCGCATTCATTATTACTCCCTC 59.548 45.833 0.00 0.00 0.00 4.30
2490 2884 4.003648 CCGCATTCATTATTACTCCCTCC 58.996 47.826 0.00 0.00 0.00 4.30
2491 2885 3.679980 CGCATTCATTATTACTCCCTCCG 59.320 47.826 0.00 0.00 0.00 4.63
2492 2886 4.642429 GCATTCATTATTACTCCCTCCGT 58.358 43.478 0.00 0.00 0.00 4.69
2493 2887 5.063880 GCATTCATTATTACTCCCTCCGTT 58.936 41.667 0.00 0.00 0.00 4.44
2494 2888 5.179555 GCATTCATTATTACTCCCTCCGTTC 59.820 44.000 0.00 0.00 0.00 3.95
2495 2889 4.950205 TCATTATTACTCCCTCCGTTCC 57.050 45.455 0.00 0.00 0.00 3.62
2496 2890 4.553678 TCATTATTACTCCCTCCGTTCCT 58.446 43.478 0.00 0.00 0.00 3.36
2497 2891 5.708544 TCATTATTACTCCCTCCGTTCCTA 58.291 41.667 0.00 0.00 0.00 2.94
2498 2892 6.138263 TCATTATTACTCCCTCCGTTCCTAA 58.862 40.000 0.00 0.00 0.00 2.69
2499 2893 6.612456 TCATTATTACTCCCTCCGTTCCTAAA 59.388 38.462 0.00 0.00 0.00 1.85
2500 2894 7.291651 TCATTATTACTCCCTCCGTTCCTAAAT 59.708 37.037 0.00 0.00 0.00 1.40
2501 2895 8.591072 CATTATTACTCCCTCCGTTCCTAAATA 58.409 37.037 0.00 0.00 0.00 1.40
2502 2896 5.859205 TTACTCCCTCCGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
2503 2897 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2504 2898 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2505 2899 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2506 2900 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2507 2901 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2508 2902 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
2509 2903 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2510 2904 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2511 2905 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
2512 2906 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
2513 2907 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
2514 2908 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
2515 2909 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
2516 2910 9.291664 CGTTCCTAAATACTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
2526 2920 8.964476 ACTTGTCTTTCTAGAGATTTCAACAA 57.036 30.769 0.00 0.00 0.00 2.83
2527 2921 9.050601 ACTTGTCTTTCTAGAGATTTCAACAAG 57.949 33.333 18.42 18.42 32.73 3.16
2528 2922 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2529 2923 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2530 2924 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2531 2925 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2532 2926 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2533 2927 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2534 2928 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2535 2929 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2536 2930 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2538 2932 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2539 2933 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2540 2934 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2541 2935 3.581755 TCAACAAGTGACTACATACGGC 58.418 45.455 0.00 0.00 0.00 5.68
2542 2936 2.273370 ACAAGTGACTACATACGGCG 57.727 50.000 4.80 4.80 0.00 6.46
2543 2937 0.921347 CAAGTGACTACATACGGCGC 59.079 55.000 6.90 0.00 0.00 6.53
2544 2938 0.528924 AAGTGACTACATACGGCGCA 59.471 50.000 10.83 0.00 0.00 6.09
2545 2939 0.528924 AGTGACTACATACGGCGCAA 59.471 50.000 10.83 0.00 0.00 4.85
2546 2940 1.067425 AGTGACTACATACGGCGCAAA 60.067 47.619 10.83 0.00 0.00 3.68
2547 2941 1.727880 GTGACTACATACGGCGCAAAA 59.272 47.619 10.83 0.00 0.00 2.44
2548 2942 2.350498 GTGACTACATACGGCGCAAAAT 59.650 45.455 10.83 0.00 0.00 1.82
2549 2943 2.350192 TGACTACATACGGCGCAAAATG 59.650 45.455 10.83 11.57 0.00 2.32
2550 2944 2.605818 GACTACATACGGCGCAAAATGA 59.394 45.455 10.83 0.00 0.00 2.57
2551 2945 2.607635 ACTACATACGGCGCAAAATGAG 59.392 45.455 10.83 10.39 0.00 2.90
2552 2946 1.448985 ACATACGGCGCAAAATGAGT 58.551 45.000 10.83 0.00 0.00 3.41
2553 2947 1.130373 ACATACGGCGCAAAATGAGTG 59.870 47.619 10.83 0.00 0.00 3.51
2554 2948 1.396648 CATACGGCGCAAAATGAGTGA 59.603 47.619 10.83 0.00 0.00 3.41
2555 2949 1.514003 TACGGCGCAAAATGAGTGAA 58.486 45.000 10.83 0.00 0.00 3.18
2556 2950 0.881118 ACGGCGCAAAATGAGTGAAT 59.119 45.000 10.83 0.00 0.00 2.57
2557 2951 1.135689 ACGGCGCAAAATGAGTGAATC 60.136 47.619 10.83 0.00 0.00 2.52
2558 2952 1.131126 CGGCGCAAAATGAGTGAATCT 59.869 47.619 10.83 0.00 0.00 2.40
2559 2953 2.351418 CGGCGCAAAATGAGTGAATCTA 59.649 45.455 10.83 0.00 0.00 1.98
2560 2954 3.685058 GGCGCAAAATGAGTGAATCTAC 58.315 45.455 10.83 0.00 0.00 2.59
2561 2955 3.126858 GGCGCAAAATGAGTGAATCTACA 59.873 43.478 10.83 0.00 0.00 2.74
2562 2956 4.091424 GCGCAAAATGAGTGAATCTACAC 58.909 43.478 0.30 0.00 40.60 2.90
2600 2994 4.944048 CATACATCCGTATGTTGAGTCCA 58.056 43.478 0.00 0.00 46.70 4.02
2601 2995 5.541845 CATACATCCGTATGTTGAGTCCAT 58.458 41.667 0.00 0.00 46.70 3.41
2602 2996 4.487714 ACATCCGTATGTTGAGTCCATT 57.512 40.909 0.00 0.00 44.07 3.16
2603 2997 4.843728 ACATCCGTATGTTGAGTCCATTT 58.156 39.130 0.00 0.00 44.07 2.32
2604 2998 5.984725 ACATCCGTATGTTGAGTCCATTTA 58.015 37.500 0.00 0.00 44.07 1.40
2605 2999 6.411376 ACATCCGTATGTTGAGTCCATTTAA 58.589 36.000 0.00 0.00 44.07 1.52
2606 3000 6.882140 ACATCCGTATGTTGAGTCCATTTAAA 59.118 34.615 0.00 0.00 44.07 1.52
2607 3001 7.392113 ACATCCGTATGTTGAGTCCATTTAAAA 59.608 33.333 0.00 0.00 44.07 1.52
2608 3002 7.931578 TCCGTATGTTGAGTCCATTTAAAAT 57.068 32.000 0.00 0.00 0.00 1.82
2609 3003 7.757526 TCCGTATGTTGAGTCCATTTAAAATG 58.242 34.615 0.00 0.00 0.00 2.32
2610 3004 6.472163 CCGTATGTTGAGTCCATTTAAAATGC 59.528 38.462 0.00 0.00 0.00 3.56
2611 3005 6.472163 CGTATGTTGAGTCCATTTAAAATGCC 59.528 38.462 0.00 0.00 0.00 4.40
2612 3006 6.610075 ATGTTGAGTCCATTTAAAATGCCT 57.390 33.333 0.00 0.00 0.00 4.75
2613 3007 7.716799 ATGTTGAGTCCATTTAAAATGCCTA 57.283 32.000 0.00 0.00 0.00 3.93
2614 3008 7.156876 TGTTGAGTCCATTTAAAATGCCTAG 57.843 36.000 0.00 0.00 0.00 3.02
2615 3009 6.945435 TGTTGAGTCCATTTAAAATGCCTAGA 59.055 34.615 0.00 0.00 0.00 2.43
2616 3010 7.450014 TGTTGAGTCCATTTAAAATGCCTAGAA 59.550 33.333 0.00 0.00 0.00 2.10
2617 3011 8.303876 GTTGAGTCCATTTAAAATGCCTAGAAA 58.696 33.333 0.00 0.00 0.00 2.52
2618 3012 8.055279 TGAGTCCATTTAAAATGCCTAGAAAG 57.945 34.615 0.00 0.00 0.00 2.62
2619 3013 7.888021 TGAGTCCATTTAAAATGCCTAGAAAGA 59.112 33.333 0.00 0.00 0.00 2.52
2620 3014 8.056407 AGTCCATTTAAAATGCCTAGAAAGAC 57.944 34.615 0.00 0.00 0.00 3.01
2621 3015 7.669722 AGTCCATTTAAAATGCCTAGAAAGACA 59.330 33.333 0.00 0.00 0.00 3.41
2622 3016 8.303876 GTCCATTTAAAATGCCTAGAAAGACAA 58.696 33.333 0.00 0.00 0.00 3.18
2623 3017 8.522830 TCCATTTAAAATGCCTAGAAAGACAAG 58.477 33.333 0.00 0.00 0.00 3.16
2624 3018 8.306761 CCATTTAAAATGCCTAGAAAGACAAGT 58.693 33.333 0.00 0.00 0.00 3.16
2630 3024 7.396540 AATGCCTAGAAAGACAAGTATTTGG 57.603 36.000 2.81 0.00 38.66 3.28
2631 3025 5.253330 TGCCTAGAAAGACAAGTATTTGGG 58.747 41.667 2.81 0.00 38.66 4.12
2632 3026 5.013704 TGCCTAGAAAGACAAGTATTTGGGA 59.986 40.000 2.81 0.00 38.66 4.37
2633 3027 5.944007 GCCTAGAAAGACAAGTATTTGGGAA 59.056 40.000 2.81 0.00 38.66 3.97
2634 3028 6.127980 GCCTAGAAAGACAAGTATTTGGGAAC 60.128 42.308 2.81 0.00 38.66 3.62
2635 3029 5.941948 AGAAAGACAAGTATTTGGGAACG 57.058 39.130 2.81 0.00 38.66 3.95
2636 3030 4.760204 AGAAAGACAAGTATTTGGGAACGG 59.240 41.667 2.81 0.00 38.66 4.44
2637 3031 4.360951 AAGACAAGTATTTGGGAACGGA 57.639 40.909 2.81 0.00 38.66 4.69
2638 3032 3.939066 AGACAAGTATTTGGGAACGGAG 58.061 45.455 2.81 0.00 38.66 4.63
2639 3033 3.007635 GACAAGTATTTGGGAACGGAGG 58.992 50.000 2.81 0.00 38.66 4.30
2640 3034 2.290705 ACAAGTATTTGGGAACGGAGGG 60.291 50.000 2.81 0.00 38.66 4.30
2641 3035 1.961133 AGTATTTGGGAACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
2642 3036 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
2651 3045 2.566279 GGAACGGAGGGAGTAGAAGTTT 59.434 50.000 0.00 0.00 0.00 2.66
2673 3067 2.700897 ACCAGATATACCCTCAGTGTGC 59.299 50.000 0.00 0.00 0.00 4.57
2952 3346 9.720769 TTTTCATTACTTTACTTAGTGGAGGAG 57.279 33.333 0.00 0.00 0.00 3.69
3095 3496 5.048434 TCGCTCAGTATACTGGATTCATCTG 60.048 44.000 28.33 11.26 43.91 2.90
3112 3513 6.656632 TCATCTGAACTGATGTCTATACCC 57.343 41.667 16.81 0.00 43.03 3.69
3204 3605 3.269381 TGCTTTCCCCTTGGTATTCTCAT 59.731 43.478 0.00 0.00 0.00 2.90
3304 3705 4.261405 CGTTTGTGGGCTTTTGAGTTATGA 60.261 41.667 0.00 0.00 0.00 2.15
3347 3748 7.339721 TGTTTAGTTATGGACCTTTGTTTGTGA 59.660 33.333 0.00 0.00 0.00 3.58
3580 3981 5.804639 TCTTCAGCTTAGCCTTGAAATGTA 58.195 37.500 9.58 0.00 31.11 2.29
3644 4048 3.432378 TCTCAGTCACCTAGGTTCCTTC 58.568 50.000 13.15 1.15 0.00 3.46
3710 4114 4.689071 AGCACATGCACATAATCCATTTG 58.311 39.130 6.64 0.00 45.16 2.32
3809 4228 4.261801 ACACCATGTGAACTAGTTATGGC 58.738 43.478 25.90 9.67 41.50 4.40
4080 4499 7.392953 TGTTCATGTACTTTTCATAGGAATGCA 59.607 33.333 4.01 0.00 32.76 3.96
4191 4610 6.831976 AGCTGGGATATTTCTAGTTAAGGTG 58.168 40.000 0.00 0.00 0.00 4.00
4214 4633 1.134580 TGTTTGGGTGTTTGTGCCATG 60.135 47.619 0.00 0.00 0.00 3.66
4440 4861 4.365514 TGAATTGTCCTGTAAAGCTGGA 57.634 40.909 0.00 0.00 42.01 3.86
4454 4875 5.505181 AAAGCTGGAGGAGATAAAACAGA 57.495 39.130 0.00 0.00 0.00 3.41
4455 4876 5.505181 AAGCTGGAGGAGATAAAACAGAA 57.495 39.130 0.00 0.00 0.00 3.02
4487 4908 2.485814 GGACAAATCAGTCAGCCTTCAC 59.514 50.000 0.00 0.00 40.29 3.18
4500 4922 2.431771 TTCACGGCATCGGACACG 60.432 61.111 0.00 0.00 41.39 4.49
4505 4927 2.106332 GGCATCGGACACGGTAGG 59.894 66.667 0.00 0.00 41.39 3.18
4508 4930 1.226974 CATCGGACACGGTAGGCAG 60.227 63.158 0.00 0.00 41.39 4.85
4511 4933 1.138247 CGGACACGGTAGGCAGTAC 59.862 63.158 0.00 0.00 36.18 2.73
4541 4979 6.537301 CCACGTCAAAACCTTAGCAGATATAA 59.463 38.462 0.00 0.00 0.00 0.98
4589 5027 3.375642 GCTCAGCCAAAAGAACAGAAAC 58.624 45.455 0.00 0.00 0.00 2.78
4600 5048 4.639135 AGAACAGAAACAGGTGCTTTTC 57.361 40.909 0.00 0.00 32.76 2.29
4717 5165 0.872388 GTGTTTCATCCGACACACCC 59.128 55.000 1.35 0.00 43.88 4.61
4877 5326 5.112686 GGATCTGGATACGATAAGCCAATC 58.887 45.833 0.00 0.00 42.51 2.67
4929 5378 1.796017 TCCCGGTATCAGTTGGCATA 58.204 50.000 0.00 0.00 0.00 3.14
5057 5524 2.340337 GCTGCAACTTAATGCCCAAAG 58.660 47.619 0.00 0.00 45.83 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 20 6.801575 TCACACAAGCAGTTATGATATACGA 58.198 36.000 0.00 0.00 0.00 3.43
29 35 2.232399 TGCATGATCACACAAGCAGTT 58.768 42.857 0.00 0.00 31.53 3.16
38 44 7.226325 TCAATGATTACGTTATGCATGATCACA 59.774 33.333 10.16 0.00 0.00 3.58
54 60 5.004156 GTCCACGTACGTTCTCAATGATTAC 59.996 44.000 20.23 1.83 0.00 1.89
56 62 3.924686 GTCCACGTACGTTCTCAATGATT 59.075 43.478 20.23 0.00 0.00 2.57
68 74 3.770263 TCTAAATCCTGTCCACGTACG 57.230 47.619 15.01 15.01 0.00 3.67
70 76 6.406177 GGTGTAATCTAAATCCTGTCCACGTA 60.406 42.308 0.00 0.00 0.00 3.57
71 77 5.416947 GTGTAATCTAAATCCTGTCCACGT 58.583 41.667 0.00 0.00 0.00 4.49
114 120 5.532557 TCTTCTCATCGGCATAACACATAG 58.467 41.667 0.00 0.00 0.00 2.23
144 150 5.221342 ACACCTTTATGAAACGCCAAATTCA 60.221 36.000 0.00 0.00 39.66 2.57
149 155 4.135306 TGTACACCTTTATGAAACGCCAA 58.865 39.130 0.00 0.00 0.00 4.52
150 156 3.741249 TGTACACCTTTATGAAACGCCA 58.259 40.909 0.00 0.00 0.00 5.69
152 158 5.933790 TCATTGTACACCTTTATGAAACGC 58.066 37.500 4.98 0.00 0.00 4.84
161 167 9.574516 AAGTCTCTAATTTCATTGTACACCTTT 57.425 29.630 0.00 0.00 0.00 3.11
187 194 1.992667 GAAGTTGATCGTGCACATCGA 59.007 47.619 18.64 14.87 41.45 3.59
193 200 2.037121 TCCTTCTGAAGTTGATCGTGCA 59.963 45.455 15.72 0.00 0.00 4.57
230 237 4.807304 GCTATTTTGCCATGTCATTTCCAG 59.193 41.667 0.00 0.00 0.00 3.86
309 317 5.716094 TCAAATCCACAAGATCAAATGCAG 58.284 37.500 0.00 0.00 32.47 4.41
607 975 3.572584 CAAAGTCAAAGATGCCAAGAGC 58.427 45.455 0.00 0.00 44.14 4.09
608 976 3.255149 AGCAAAGTCAAAGATGCCAAGAG 59.745 43.478 0.00 0.00 39.59 2.85
609 977 3.225104 AGCAAAGTCAAAGATGCCAAGA 58.775 40.909 0.00 0.00 39.59 3.02
610 978 3.655276 AGCAAAGTCAAAGATGCCAAG 57.345 42.857 0.00 0.00 39.59 3.61
665 1034 3.694043 TGCATAGGTAGAAAGCACACA 57.306 42.857 0.00 0.00 0.00 3.72
747 1129 1.676006 ACTGAGTGTTGGCTTTTTCGG 59.324 47.619 0.00 0.00 0.00 4.30
821 1203 8.564574 ACGTATTCATCTCAAGTTTGCTAAAAA 58.435 29.630 0.00 0.00 0.00 1.94
822 1204 8.094798 ACGTATTCATCTCAAGTTTGCTAAAA 57.905 30.769 0.00 0.00 0.00 1.52
823 1205 7.667043 ACGTATTCATCTCAAGTTTGCTAAA 57.333 32.000 0.00 0.00 0.00 1.85
824 1206 7.667043 AACGTATTCATCTCAAGTTTGCTAA 57.333 32.000 0.00 0.00 0.00 3.09
825 1207 7.667043 AAACGTATTCATCTCAAGTTTGCTA 57.333 32.000 0.00 0.00 0.00 3.49
826 1208 6.560253 AAACGTATTCATCTCAAGTTTGCT 57.440 33.333 0.00 0.00 0.00 3.91
827 1209 7.623268 AAAAACGTATTCATCTCAAGTTTGC 57.377 32.000 0.00 0.00 31.77 3.68
854 1236 6.065374 ACATGTATTCCTCTCGAGTATGTCT 58.935 40.000 13.13 0.00 0.00 3.41
855 1237 6.320494 ACATGTATTCCTCTCGAGTATGTC 57.680 41.667 13.13 0.00 0.00 3.06
856 1238 9.168451 CTATACATGTATTCCTCTCGAGTATGT 57.832 37.037 22.90 12.42 0.00 2.29
859 1241 7.395617 AGCTATACATGTATTCCTCTCGAGTA 58.604 38.462 22.90 0.44 0.00 2.59
875 1257 5.716703 ACCAAAGAAAAGGCAAGCTATACAT 59.283 36.000 0.00 0.00 0.00 2.29
918 1302 1.944024 TGGGCTCGTACTGTTGTTTTG 59.056 47.619 0.00 0.00 0.00 2.44
1233 1620 4.162040 AGCTCTAAACCATAAGCAGCAT 57.838 40.909 0.00 0.00 37.22 3.79
1363 1750 2.531942 GGGTCCCAGTTCCCCAGT 60.532 66.667 1.78 0.00 38.37 4.00
1594 1981 1.705186 ACAAGTTGGGGCAGTCTGTAT 59.295 47.619 7.96 0.00 0.00 2.29
1636 2023 4.278419 CCTTTAGTCTCAAACAAGTTGGGG 59.722 45.833 7.96 0.00 38.37 4.96
1650 2037 5.185056 ACAACAACAACAAAGCCTTTAGTCT 59.815 36.000 0.00 0.00 0.00 3.24
1690 2077 5.934625 CAGAAGGCAGTCTGTATTTTGTACT 59.065 40.000 9.41 0.00 40.22 2.73
1811 2198 9.423061 CCTCAACAAAAAGAAAGAAAGAAAGAA 57.577 29.630 0.00 0.00 0.00 2.52
1946 2333 2.435805 CCTAAAGCATGCTACTCCCTCA 59.564 50.000 23.00 0.00 0.00 3.86
1978 2365 5.365619 ACGGATGTAGTTTTCACAGAAGTT 58.634 37.500 0.00 0.00 0.00 2.66
1998 2387 6.984474 TCTTTGCTCTGTAAAATAGGATACGG 59.016 38.462 0.00 0.00 46.39 4.02
2225 2614 2.470362 CGAGCCAGCTCCAGCAATG 61.470 63.158 13.83 0.00 45.16 2.82
2479 2873 6.141790 AGTATTTAGGAACGGAGGGAGTAAT 58.858 40.000 0.00 0.00 0.00 1.89
2481 2875 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
2482 2876 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
2483 2877 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2484 2878 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2485 2879 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2486 2880 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2487 2881 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
2488 2882 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
2489 2883 8.248945 TCTAGAAAGACAAGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
2490 2884 9.291664 CTCTAGAAAGACAAGTATTTAGGAACG 57.708 37.037 0.00 0.00 0.00 3.95
2501 2895 8.964476 TTGTTGAAATCTCTAGAAAGACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2502 2896 9.050601 ACTTGTTGAAATCTCTAGAAAGACAAG 57.949 33.333 17.75 17.75 33.18 3.16
2503 2897 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2504 2898 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2505 2899 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2506 2900 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2507 2901 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2508 2902 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2509 2903 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2510 2904 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2511 2905 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2512 2906 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2513 2907 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2514 2908 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2515 2909 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2516 2910 6.672357 GCCGTATGTAGTCACTTGTTGAAATC 60.672 42.308 0.00 0.00 35.39 2.17
2517 2911 5.121768 GCCGTATGTAGTCACTTGTTGAAAT 59.878 40.000 0.00 0.00 35.39 2.17
2518 2912 4.449743 GCCGTATGTAGTCACTTGTTGAAA 59.550 41.667 0.00 0.00 35.39 2.69
2519 2913 3.991773 GCCGTATGTAGTCACTTGTTGAA 59.008 43.478 0.00 0.00 35.39 2.69
2520 2914 3.581755 GCCGTATGTAGTCACTTGTTGA 58.418 45.455 0.00 0.00 0.00 3.18
2521 2915 2.344441 CGCCGTATGTAGTCACTTGTTG 59.656 50.000 0.00 0.00 0.00 3.33
2522 2916 2.602878 CGCCGTATGTAGTCACTTGTT 58.397 47.619 0.00 0.00 0.00 2.83
2523 2917 1.734707 GCGCCGTATGTAGTCACTTGT 60.735 52.381 0.00 0.00 0.00 3.16
2524 2918 0.921347 GCGCCGTATGTAGTCACTTG 59.079 55.000 0.00 0.00 0.00 3.16
2525 2919 0.528924 TGCGCCGTATGTAGTCACTT 59.471 50.000 4.18 0.00 0.00 3.16
2526 2920 0.528924 TTGCGCCGTATGTAGTCACT 59.471 50.000 4.18 0.00 0.00 3.41
2527 2921 1.352114 TTTGCGCCGTATGTAGTCAC 58.648 50.000 4.18 0.00 0.00 3.67
2528 2922 2.081725 TTTTGCGCCGTATGTAGTCA 57.918 45.000 4.18 0.00 0.00 3.41
2529 2923 2.605818 TCATTTTGCGCCGTATGTAGTC 59.394 45.455 4.18 0.00 0.00 2.59
2530 2924 2.607635 CTCATTTTGCGCCGTATGTAGT 59.392 45.455 4.18 0.00 0.00 2.73
2531 2925 2.607635 ACTCATTTTGCGCCGTATGTAG 59.392 45.455 4.18 7.56 0.00 2.74
2532 2926 2.350192 CACTCATTTTGCGCCGTATGTA 59.650 45.455 4.18 0.00 0.00 2.29
2533 2927 1.130373 CACTCATTTTGCGCCGTATGT 59.870 47.619 4.18 0.00 0.00 2.29
2534 2928 1.396648 TCACTCATTTTGCGCCGTATG 59.603 47.619 4.18 5.63 0.00 2.39
2535 2929 1.732941 TCACTCATTTTGCGCCGTAT 58.267 45.000 4.18 0.00 0.00 3.06
2536 2930 1.514003 TTCACTCATTTTGCGCCGTA 58.486 45.000 4.18 0.00 0.00 4.02
2537 2931 0.881118 ATTCACTCATTTTGCGCCGT 59.119 45.000 4.18 0.00 0.00 5.68
2538 2932 1.131126 AGATTCACTCATTTTGCGCCG 59.869 47.619 4.18 0.00 0.00 6.46
2539 2933 2.927553 AGATTCACTCATTTTGCGCC 57.072 45.000 4.18 0.00 0.00 6.53
2540 2934 4.091424 GTGTAGATTCACTCATTTTGCGC 58.909 43.478 0.00 0.00 35.68 6.09
2541 2935 5.536554 AGTGTAGATTCACTCATTTTGCG 57.463 39.130 0.00 0.00 44.07 4.85
2542 2936 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
2579 2973 5.808366 ATGGACTCAACATACGGATGTAT 57.192 39.130 15.10 0.00 45.93 2.29
2580 2974 5.607939 AATGGACTCAACATACGGATGTA 57.392 39.130 15.10 0.00 45.93 2.29
2582 2976 6.918892 TTAAATGGACTCAACATACGGATG 57.081 37.500 5.94 5.94 39.16 3.51
2583 2977 7.931578 TTTTAAATGGACTCAACATACGGAT 57.068 32.000 0.00 0.00 0.00 4.18
2584 2978 7.627513 GCATTTTAAATGGACTCAACATACGGA 60.628 37.037 17.89 0.00 0.00 4.69
2585 2979 6.472163 GCATTTTAAATGGACTCAACATACGG 59.528 38.462 17.89 0.00 0.00 4.02
2586 2980 6.472163 GGCATTTTAAATGGACTCAACATACG 59.528 38.462 17.89 0.00 0.00 3.06
2587 2981 7.547227 AGGCATTTTAAATGGACTCAACATAC 58.453 34.615 17.89 0.00 0.00 2.39
2588 2982 7.716799 AGGCATTTTAAATGGACTCAACATA 57.283 32.000 17.89 0.00 0.00 2.29
2589 2983 6.610075 AGGCATTTTAAATGGACTCAACAT 57.390 33.333 17.89 0.00 0.00 2.71
2590 2984 6.945435 TCTAGGCATTTTAAATGGACTCAACA 59.055 34.615 17.89 0.00 0.00 3.33
2591 2985 7.391148 TCTAGGCATTTTAAATGGACTCAAC 57.609 36.000 17.89 1.13 0.00 3.18
2592 2986 8.415950 TTTCTAGGCATTTTAAATGGACTCAA 57.584 30.769 17.89 2.83 0.00 3.02
2593 2987 7.888021 TCTTTCTAGGCATTTTAAATGGACTCA 59.112 33.333 17.89 0.00 0.00 3.41
2594 2988 8.184848 GTCTTTCTAGGCATTTTAAATGGACTC 58.815 37.037 17.89 2.75 0.00 3.36
2595 2989 7.669722 TGTCTTTCTAGGCATTTTAAATGGACT 59.330 33.333 17.89 9.51 29.10 3.85
2596 2990 7.826690 TGTCTTTCTAGGCATTTTAAATGGAC 58.173 34.615 17.89 13.56 29.10 4.02
2597 2991 8.415950 TTGTCTTTCTAGGCATTTTAAATGGA 57.584 30.769 17.89 5.27 35.56 3.41
2598 2992 8.306761 ACTTGTCTTTCTAGGCATTTTAAATGG 58.693 33.333 17.89 3.11 35.56 3.16
2604 2998 8.306761 CCAAATACTTGTCTTTCTAGGCATTTT 58.693 33.333 0.00 0.00 35.56 1.82
2605 2999 7.093771 CCCAAATACTTGTCTTTCTAGGCATTT 60.094 37.037 0.00 0.00 35.56 2.32
2606 3000 6.378280 CCCAAATACTTGTCTTTCTAGGCATT 59.622 38.462 0.00 0.00 35.56 3.56
2607 3001 5.888161 CCCAAATACTTGTCTTTCTAGGCAT 59.112 40.000 0.00 0.00 35.56 4.40
2608 3002 5.013704 TCCCAAATACTTGTCTTTCTAGGCA 59.986 40.000 0.00 0.00 33.22 4.75
2609 3003 5.497474 TCCCAAATACTTGTCTTTCTAGGC 58.503 41.667 0.00 0.00 0.00 3.93
2610 3004 6.092259 CGTTCCCAAATACTTGTCTTTCTAGG 59.908 42.308 0.00 0.00 0.00 3.02
2611 3005 6.092259 CCGTTCCCAAATACTTGTCTTTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
2612 3006 5.935789 CCGTTCCCAAATACTTGTCTTTCTA 59.064 40.000 0.00 0.00 0.00 2.10
2613 3007 4.760204 CCGTTCCCAAATACTTGTCTTTCT 59.240 41.667 0.00 0.00 0.00 2.52
2614 3008 4.758165 TCCGTTCCCAAATACTTGTCTTTC 59.242 41.667 0.00 0.00 0.00 2.62
2615 3009 4.721132 TCCGTTCCCAAATACTTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
2616 3010 4.324267 CTCCGTTCCCAAATACTTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2617 3011 3.307480 CCTCCGTTCCCAAATACTTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2618 3012 3.007635 CCTCCGTTCCCAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
2619 3013 2.290705 CCCTCCGTTCCCAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
2620 3014 2.026636 TCCCTCCGTTCCCAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
2621 3015 2.238898 CTCCCTCCGTTCCCAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
2622 3016 1.838077 CTCCCTCCGTTCCCAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
2623 3017 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
2624 3018 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2625 3019 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
2626 3020 1.203212 TCTACTCCCTCCGTTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
2627 3021 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
2628 3022 0.410663 TTCTACTCCCTCCGTTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
2629 3023 1.112950 CTTCTACTCCCTCCGTTCCC 58.887 60.000 0.00 0.00 0.00 3.97
2630 3024 1.849977 ACTTCTACTCCCTCCGTTCC 58.150 55.000 0.00 0.00 0.00 3.62
2631 3025 3.957591 AAACTTCTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 0.00 3.95
2632 3026 3.513119 GGTAAACTTCTACTCCCTCCGTT 59.487 47.826 0.00 0.00 0.00 4.44
2633 3027 3.095332 GGTAAACTTCTACTCCCTCCGT 58.905 50.000 0.00 0.00 0.00 4.69
2634 3028 3.094572 TGGTAAACTTCTACTCCCTCCG 58.905 50.000 0.00 0.00 0.00 4.63
2635 3029 4.351127 TCTGGTAAACTTCTACTCCCTCC 58.649 47.826 0.00 0.00 0.00 4.30
2636 3030 7.842887 ATATCTGGTAAACTTCTACTCCCTC 57.157 40.000 0.00 0.00 0.00 4.30
2637 3031 7.729431 GGTATATCTGGTAAACTTCTACTCCCT 59.271 40.741 0.00 0.00 0.00 4.20
2638 3032 7.039152 GGGTATATCTGGTAAACTTCTACTCCC 60.039 44.444 0.00 0.00 0.00 4.30
2639 3033 7.729431 AGGGTATATCTGGTAAACTTCTACTCC 59.271 40.741 0.00 0.00 0.00 3.85
2640 3034 8.709272 AGGGTATATCTGGTAAACTTCTACTC 57.291 38.462 0.00 0.00 0.00 2.59
2641 3035 8.287350 TGAGGGTATATCTGGTAAACTTCTACT 58.713 37.037 0.00 0.00 0.00 2.57
2642 3036 8.474710 TGAGGGTATATCTGGTAAACTTCTAC 57.525 38.462 0.00 0.00 0.00 2.59
2651 3045 3.895656 GCACACTGAGGGTATATCTGGTA 59.104 47.826 0.00 0.00 0.00 3.25
2734 3128 8.570488 GTGATAACTGATAATTTCATCATGGCA 58.430 33.333 0.00 0.00 34.50 4.92
2818 3212 2.052782 ATCATCAAACGTTAGGGGCC 57.947 50.000 0.00 0.00 0.00 5.80
3095 3496 5.737635 GCACTGAGGGTATAGACATCAGTTC 60.738 48.000 19.29 13.77 45.08 3.01
3204 3605 8.523915 TGATAACCACTAAAAGTATACGGAGA 57.476 34.615 0.00 0.00 0.00 3.71
3304 3705 1.567357 ACAGCCCACAAACAAAGGTT 58.433 45.000 0.00 0.00 39.43 3.50
3347 3748 3.264450 AGCAGGTCCATAACTAAACAGCT 59.736 43.478 0.00 0.00 0.00 4.24
3710 4114 7.786178 TGCTTATGTCAAGATGGTTGTATAC 57.214 36.000 0.00 0.00 0.00 1.47
4080 4499 6.322712 TGCCATTACCACTTCAAAAAGTAACT 59.677 34.615 0.00 0.00 43.99 2.24
4156 4575 1.289160 ATCCCAGCTCCAGCAAGTAA 58.711 50.000 0.48 0.00 45.16 2.24
4191 4610 0.809636 GCACAAACACCCAAACAGGC 60.810 55.000 0.00 0.00 35.39 4.85
4214 4633 5.408909 CACAATGCTGATCATAGAGGTCATC 59.591 44.000 0.00 0.00 34.33 2.92
4454 4875 7.725251 TGACTGATTTGTCCAAATTTTAGCTT 58.275 30.769 6.70 0.00 40.77 3.74
4455 4876 7.288810 TGACTGATTTGTCCAAATTTTAGCT 57.711 32.000 6.70 0.00 40.77 3.32
4487 4908 2.278596 CTACCGTGTCCGATGCCG 60.279 66.667 0.00 0.00 35.63 5.69
4505 4927 0.245539 TTGACGTGGGCTAGTACTGC 59.754 55.000 5.39 7.18 0.00 4.40
4508 4930 2.071540 GGTTTTGACGTGGGCTAGTAC 58.928 52.381 0.00 0.00 0.00 2.73
4511 4933 1.892209 AAGGTTTTGACGTGGGCTAG 58.108 50.000 0.00 0.00 0.00 3.42
4541 4979 8.749354 CAAAGTTAAGCCTAACCAAATATTCCT 58.251 33.333 1.48 0.00 38.59 3.36
4585 5023 3.692791 AAGACGAAAAGCACCTGTTTC 57.307 42.857 0.00 0.00 0.00 2.78
4589 5027 3.555518 GCTTAAAGACGAAAAGCACCTG 58.444 45.455 0.00 0.00 43.98 4.00
4600 5048 5.458779 CCTTTTGAAGTTTGGCTTAAAGACG 59.541 40.000 0.00 0.00 35.96 4.18
4717 5165 2.876079 GCACTTCAGTCCTTAACCCTGG 60.876 54.545 0.00 0.00 0.00 4.45
4724 5172 3.935993 GGCTGCACTTCAGTCCTTA 57.064 52.632 0.50 0.00 44.66 2.69
4777 5225 6.942532 TGTTTCAAACTCAGTTGCTCTTAT 57.057 33.333 1.10 0.00 0.00 1.73
5057 5524 8.715088 ACGATGTTAGTTAAATTGTGGTACTTC 58.285 33.333 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.