Multiple sequence alignment - TraesCS1B01G283600

Loading Multiple Alignment...

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 TraesCS1B01G283600 chr1B 100.000 4060 0 0 1 4060 492359032 492354973 0.000000e+00 7498.0
1 TraesCS1B01G283600 chr1B 87.000 200 21 3 3476 3674 651884994 651884799 1.900000e-53 220.0
2 TraesCS1B01G283600 chr1D 88.916 3239 202 70 92 3255 368323412 368320256 0.000000e+00 3847.0
3 TraesCS1B01G283600 chr1D 87.246 2360 146 72 389 2672 369904535 369902255 0.000000e+00 2547.0
4 TraesCS1B01G283600 chr1D 89.455 550 33 8 2669 3195 369899932 369899385 0.000000e+00 671.0
5 TraesCS1B01G283600 chr1D 87.500 352 32 6 4 343 369904895 369904544 2.940000e-106 396.0
6 TraesCS1B01G283600 chr1D 92.254 142 7 1 3334 3475 368320168 368320031 8.900000e-47 198.0
7 TraesCS1B01G283600 chr1D 100.000 39 0 0 3383 3421 369899250 369899212 5.630000e-09 73.1
8 TraesCS1B01G283600 chr1A 85.089 1462 130 37 1000 2426 467259928 467258520 0.000000e+00 1411.0
9 TraesCS1B01G283600 chr1A 86.382 984 74 27 5 963 467260874 467259926 0.000000e+00 1020.0
10 TraesCS1B01G283600 chr1A 90.212 378 27 6 2880 3250 467258216 467257842 6.100000e-133 484.0
11 TraesCS1B01G283600 chr1A 90.278 288 21 6 1 283 468593632 468593347 1.780000e-98 370.0
12 TraesCS1B01G283600 chr1A 82.647 340 29 16 303 621 468593267 468592937 1.440000e-69 274.0
13 TraesCS1B01G283600 chr1A 83.654 312 21 14 2497 2808 467258493 467258212 2.410000e-67 267.0
14 TraesCS1B01G283600 chr1A 100.000 28 0 0 3383 3410 467257845 467257818 7.000000e-03 52.8
15 TraesCS1B01G283600 chr5A 91.003 389 33 2 3673 4060 674905200 674904813 1.290000e-144 523.0
16 TraesCS1B01G283600 chr5A 91.089 202 18 0 3476 3677 674823502 674823301 1.440000e-69 274.0
17 TraesCS1B01G283600 chr5A 90.547 201 19 0 3477 3677 674864260 674864060 2.410000e-67 267.0
18 TraesCS1B01G283600 chr5A 89.604 202 20 1 3477 3677 674905477 674905276 5.210000e-64 255.0
19 TraesCS1B01G283600 chr3D 88.740 373 41 1 3689 4060 31875790 31875418 4.780000e-124 455.0
20 TraesCS1B01G283600 chr3D 92.694 219 16 0 995 1213 484345581 484345799 2.360000e-82 316.0
21 TraesCS1B01G283600 chr3D 93.827 81 5 0 1300 1380 484345906 484345986 5.510000e-24 122.0
22 TraesCS1B01G283600 chr3D 89.474 76 7 1 1532 1607 484346249 484346323 1.200000e-15 95.3
23 TraesCS1B01G283600 chr6B 91.536 319 26 1 3743 4060 583588061 583588379 4.820000e-119 438.0
24 TraesCS1B01G283600 chr3A 86.595 373 49 1 3689 4060 688984497 688984869 1.050000e-110 411.0
25 TraesCS1B01G283600 chr3A 92.857 224 15 1 990 1213 627275625 627275847 1.410000e-84 324.0
26 TraesCS1B01G283600 chr3A 83.256 215 31 1 1000 1214 107617999 107617790 4.140000e-45 193.0
27 TraesCS1B01G283600 chr3A 84.328 134 20 1 1720 1853 627276529 627276661 3.290000e-26 130.0
28 TraesCS1B01G283600 chr3A 95.062 81 4 0 1300 1380 627275942 627276022 1.180000e-25 128.0
29 TraesCS1B01G283600 chr3A 88.732 71 8 0 1532 1602 627276288 627276358 2.010000e-13 87.9
30 TraesCS1B01G283600 chr6A 90.675 311 23 4 3712 4020 614001791 614001485 3.780000e-110 409.0
31 TraesCS1B01G283600 chr7D 86.595 373 45 5 3690 4060 71120329 71119960 1.360000e-109 407.0
32 TraesCS1B01G283600 chr2A 85.920 348 46 3 3715 4060 55869550 55869896 6.410000e-98 368.0
33 TraesCS1B01G283600 chr2B 84.615 377 49 3 3690 4060 44273597 44273224 2.310000e-97 366.0
34 TraesCS1B01G283600 chr5D 83.836 365 55 4 3698 4060 424916853 424916491 1.080000e-90 344.0
35 TraesCS1B01G283600 chr5D 83.721 215 29 2 1000 1214 10495639 10495431 8.900000e-47 198.0
36 TraesCS1B01G283600 chr5D 83.721 215 30 1 1000 1214 511490988 511490779 8.900000e-47 198.0
37 TraesCS1B01G283600 chr5D 100.000 28 0 0 3230 3257 338504733 338504760 7.000000e-03 52.8
38 TraesCS1B01G283600 chr3B 91.781 219 18 0 995 1213 647177884 647178102 5.100000e-79 305.0
39 TraesCS1B01G283600 chr3B 86.047 129 18 0 1728 1856 647178848 647178976 5.470000e-29 139.0
40 TraesCS1B01G283600 chr3B 91.089 101 6 3 1300 1400 647178235 647178332 2.550000e-27 134.0
41 TraesCS1B01G283600 chr3B 90.000 70 7 0 1532 1601 647178615 647178684 1.550000e-14 91.6
42 TraesCS1B01G283600 chr6D 87.065 201 19 7 3476 3674 465104932 465105127 1.900000e-53 220.0
43 TraesCS1B01G283600 chr6D 82.143 140 20 1 1074 1213 443355408 443355542 9.220000e-22 115.0
44 TraesCS1B01G283600 chr6D 94.737 57 3 0 1542 1598 468860022 468859966 5.590000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G283600 chr1B 492354973 492359032 4059 True 7498.000 7498 100.00000 1 4060 1 chr1B.!!$R1 4059
1 TraesCS1B01G283600 chr1D 368320031 368323412 3381 True 2022.500 3847 90.58500 92 3475 2 chr1D.!!$R1 3383
2 TraesCS1B01G283600 chr1D 369899212 369904895 5683 True 921.775 2547 91.05025 4 3421 4 chr1D.!!$R2 3417
3 TraesCS1B01G283600 chr1A 467257818 467260874 3056 True 646.960 1411 89.06740 5 3410 5 chr1A.!!$R1 3405
4 TraesCS1B01G283600 chr1A 468592937 468593632 695 True 322.000 370 86.46250 1 621 2 chr1A.!!$R2 620
5 TraesCS1B01G283600 chr5A 674904813 674905477 664 True 389.000 523 90.30350 3477 4060 2 chr5A.!!$R3 583

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
382 465 1.005097 AGCCCATGACATCAGCTCAAA 59.995 47.619 0.00 0.0 0.00 2.69 F
1390 1568 0.095245 CGCACCGTAATGCACTCTTG 59.905 55.000 0.00 0.0 46.47 3.02 F
2375 2619 0.036858 GGAAGGTGAGTGCCAGTCTC 60.037 60.000 0.53 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1714 0.435008 CGAAGCACACGCAGTACTTC 59.565 55.0 10.14 10.14 41.61 3.01 R
2597 2848 0.537188 CGAAGGAAGGAGGCTGCTAA 59.463 55.0 9.60 0.00 0.00 3.09 R
3953 6865 0.029567 CGCAGTCGGGACTAGATGAC 59.970 60.0 0.21 0.00 40.20 3.06 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 40 7.759433 TGTGTTCAATTCTGAAAAGAAAGGAAC 59.241 33.333 18.75 18.75 43.18 3.62
51 53 1.549203 AAGGAACCATGTGCATCCAC 58.451 50.000 4.66 0.00 42.40 4.02
111 114 2.034939 CAGCAAGCATTTCCAACAGTCA 59.965 45.455 0.00 0.00 0.00 3.41
112 115 2.694628 AGCAAGCATTTCCAACAGTCAA 59.305 40.909 0.00 0.00 0.00 3.18
137 140 5.285651 CAAACAACAACATTGGAACCGTAT 58.714 37.500 0.00 0.00 0.00 3.06
141 144 5.067936 ACAACAACATTGGAACCGTATCAAA 59.932 36.000 0.00 0.00 0.00 2.69
183 187 4.260170 AGATGAACTGGAATCTGCACTTC 58.740 43.478 0.00 0.00 31.89 3.01
227 238 2.941720 GCAACCAAATAGAGCCTCAGAG 59.058 50.000 0.00 0.00 0.00 3.35
228 239 3.369892 GCAACCAAATAGAGCCTCAGAGA 60.370 47.826 0.00 0.00 0.00 3.10
294 347 1.357137 TGATGGCCACTCCTACACAA 58.643 50.000 8.16 0.00 35.26 3.33
382 465 1.005097 AGCCCATGACATCAGCTCAAA 59.995 47.619 0.00 0.00 0.00 2.69
387 470 1.527034 TGACATCAGCTCAAAGTGCC 58.473 50.000 0.00 0.00 0.00 5.01
423 517 3.138283 CCAAGGCCAAGGTTATCTATCCA 59.862 47.826 5.01 0.00 0.00 3.41
504 608 1.075970 ACAGGGATGCTCGAGCCTA 60.076 57.895 33.23 17.53 41.18 3.93
526 630 9.008965 GCCTATTTCTTCTTCTTCTTCTTCTTT 57.991 33.333 0.00 0.00 0.00 2.52
621 739 3.927142 CGGCGTCCAGAGGAAATTATATC 59.073 47.826 0.00 0.00 31.38 1.63
658 784 1.303236 TCCTGGTCAAATGGGCACG 60.303 57.895 0.00 0.00 0.00 5.34
673 799 1.084370 GCACGAGCGCTTCCAGTAAT 61.084 55.000 13.26 0.00 0.00 1.89
678 804 3.187700 CGAGCGCTTCCAGTAATTAAGT 58.812 45.455 13.26 0.00 0.00 2.24
679 805 4.142315 ACGAGCGCTTCCAGTAATTAAGTA 60.142 41.667 13.26 0.00 0.00 2.24
680 806 4.441415 CGAGCGCTTCCAGTAATTAAGTAG 59.559 45.833 13.26 0.00 0.00 2.57
681 807 4.120589 AGCGCTTCCAGTAATTAAGTAGC 58.879 43.478 2.64 0.00 0.00 3.58
806 933 4.003788 CACGCCTCCCACCGACTT 62.004 66.667 0.00 0.00 0.00 3.01
807 934 3.692406 ACGCCTCCCACCGACTTC 61.692 66.667 0.00 0.00 0.00 3.01
829 960 1.518367 TCCGCCTATTTCAATCCCCT 58.482 50.000 0.00 0.00 0.00 4.79
864 995 1.536418 CCGCCTCCCATATCCCTCA 60.536 63.158 0.00 0.00 0.00 3.86
865 996 1.127567 CCGCCTCCCATATCCCTCAA 61.128 60.000 0.00 0.00 0.00 3.02
886 1017 2.838202 ACCATCTCTAACAACCATCCGT 59.162 45.455 0.00 0.00 0.00 4.69
915 1070 2.030457 GCAATCTGTTTGTATCCGTCGG 59.970 50.000 4.39 4.39 37.65 4.79
965 1125 2.167861 GTTGCTCGGCGGAGATCAC 61.168 63.158 24.11 12.55 43.27 3.06
1390 1568 0.095245 CGCACCGTAATGCACTCTTG 59.905 55.000 0.00 0.00 46.47 3.02
1395 1573 2.224185 ACCGTAATGCACTCTTGTCACA 60.224 45.455 0.00 0.00 0.00 3.58
1414 1598 3.110705 ACACTCCAGCACATATCTTCCT 58.889 45.455 0.00 0.00 0.00 3.36
1419 1603 3.643320 TCCAGCACATATCTTCCTGGTAG 59.357 47.826 5.05 0.00 42.77 3.18
1420 1604 3.389329 CCAGCACATATCTTCCTGGTAGT 59.611 47.826 0.00 0.00 38.55 2.73
1422 1606 4.100035 CAGCACATATCTTCCTGGTAGTGA 59.900 45.833 0.00 0.00 0.00 3.41
1424 1608 5.053145 GCACATATCTTCCTGGTAGTGAAG 58.947 45.833 0.00 0.00 39.44 3.02
1425 1609 5.395768 GCACATATCTTCCTGGTAGTGAAGT 60.396 44.000 0.00 0.00 39.19 3.01
1427 1611 7.632898 GCACATATCTTCCTGGTAGTGAAGTAA 60.633 40.741 0.00 0.00 39.19 2.24
1435 1619 4.630069 CCTGGTAGTGAAGTAAACAATCCG 59.370 45.833 0.00 0.00 0.00 4.18
1436 1620 5.217978 TGGTAGTGAAGTAAACAATCCGT 57.782 39.130 0.00 0.00 0.00 4.69
1440 1624 5.148651 AGTGAAGTAAACAATCCGTAGCT 57.851 39.130 0.00 0.00 0.00 3.32
1454 1639 4.279145 TCCGTAGCTAGGATCTGACTTTT 58.721 43.478 14.94 0.00 31.86 2.27
1455 1640 4.098044 TCCGTAGCTAGGATCTGACTTTTG 59.902 45.833 14.94 0.00 31.86 2.44
1456 1641 4.142138 CCGTAGCTAGGATCTGACTTTTGT 60.142 45.833 14.94 0.00 0.00 2.83
1461 1646 2.508526 AGGATCTGACTTTTGTGTGCC 58.491 47.619 0.00 0.00 0.00 5.01
1462 1647 2.107204 AGGATCTGACTTTTGTGTGCCT 59.893 45.455 0.00 0.00 0.00 4.75
1463 1648 2.887152 GGATCTGACTTTTGTGTGCCTT 59.113 45.455 0.00 0.00 0.00 4.35
1464 1649 3.057946 GGATCTGACTTTTGTGTGCCTTC 60.058 47.826 0.00 0.00 0.00 3.46
1613 1799 0.872021 GACGGTAATGCGCTCCTCTG 60.872 60.000 9.73 4.77 0.00 3.35
1647 1833 3.576004 CAGAGCTGCTGCCTGTTC 58.424 61.111 7.01 9.32 40.80 3.18
1665 1851 0.963962 TCGACTGGTTCAGTACACCC 59.036 55.000 0.11 0.00 45.44 4.61
1671 1857 3.394606 ACTGGTTCAGTACACCCTTCAAT 59.605 43.478 0.00 0.00 43.46 2.57
1683 1870 5.074804 ACACCCTTCAATAACAAAGGTACC 58.925 41.667 2.73 2.73 40.43 3.34
1703 1890 5.443892 ACCATGTCTGCTGGTTACTCACC 62.444 52.174 0.00 0.00 44.67 4.02
1872 2075 7.660208 ACGGTAATTATGTTCCCTGATGTATTC 59.340 37.037 0.00 0.00 0.00 1.75
1881 2084 2.036475 CCCTGATGTATTCTCACTCCCG 59.964 54.545 0.00 0.00 0.00 5.14
1883 2086 3.491619 CCTGATGTATTCTCACTCCCGTG 60.492 52.174 0.00 0.00 42.59 4.94
1891 2094 2.872732 TCTCACTCCCGTGACTTTACT 58.127 47.619 0.00 0.00 44.85 2.24
1990 2193 3.308046 GCTTCACTCTTGATCCTTCCCTT 60.308 47.826 0.00 0.00 0.00 3.95
2048 2251 0.943673 TGATGCAGGTCACAACAACG 59.056 50.000 0.00 0.00 0.00 4.10
2051 2254 1.298339 GCAGGTCACAACAACGCAC 60.298 57.895 0.00 0.00 0.00 5.34
2053 2256 0.732571 CAGGTCACAACAACGCACTT 59.267 50.000 0.00 0.00 0.00 3.16
2054 2257 1.014352 AGGTCACAACAACGCACTTC 58.986 50.000 0.00 0.00 0.00 3.01
2092 2303 9.932207 ATTTATTCATTGATCTGCAACAAAAGA 57.068 25.926 0.00 4.45 39.78 2.52
2093 2304 8.746922 TTATTCATTGATCTGCAACAAAAGAC 57.253 30.769 0.00 0.00 39.78 3.01
2098 2309 4.645535 TGATCTGCAACAAAAGACTAGCT 58.354 39.130 0.00 0.00 0.00 3.32
2099 2310 4.453478 TGATCTGCAACAAAAGACTAGCTG 59.547 41.667 0.00 0.00 0.00 4.24
2119 2330 6.226787 AGCTGAAATCCTACTATATGTGTGC 58.773 40.000 0.00 0.00 0.00 4.57
2121 2332 6.708054 GCTGAAATCCTACTATATGTGTGCTT 59.292 38.462 0.00 0.00 0.00 3.91
2165 2376 7.995488 CAGATACCAAACAAAGGGAAGATCTAT 59.005 37.037 0.00 0.00 0.00 1.98
2221 2432 2.432444 GCCCACAGCAAAGTATGTACA 58.568 47.619 0.00 0.00 42.97 2.90
2222 2433 2.420022 GCCCACAGCAAAGTATGTACAG 59.580 50.000 0.33 0.00 42.97 2.74
2223 2434 3.674997 CCCACAGCAAAGTATGTACAGT 58.325 45.455 0.33 0.00 0.00 3.55
2225 2436 4.630069 CCCACAGCAAAGTATGTACAGTAC 59.370 45.833 0.33 3.49 0.00 2.73
2226 2437 5.479306 CCACAGCAAAGTATGTACAGTACT 58.521 41.667 12.07 6.90 33.98 2.73
2228 2439 7.094631 CCACAGCAAAGTATGTACAGTACTTA 58.905 38.462 20.99 7.20 40.49 2.24
2229 2440 7.063074 CCACAGCAAAGTATGTACAGTACTTAC 59.937 40.741 21.41 21.41 40.49 2.34
2231 2442 9.017509 ACAGCAAAGTATGTACAGTACTTACTA 57.982 33.333 27.51 5.22 44.18 1.82
2232 2443 9.504710 CAGCAAAGTATGTACAGTACTTACTAG 57.495 37.037 27.51 23.93 44.18 2.57
2233 2444 9.458727 AGCAAAGTATGTACAGTACTTACTAGA 57.541 33.333 27.51 3.98 44.18 2.43
2246 2457 9.509855 CAGTACTTACTAGATCACATTCAAGTC 57.490 37.037 0.00 0.00 34.13 3.01
2301 2541 0.109781 GCCAACATTGCAGGTACGTG 60.110 55.000 11.20 11.20 0.00 4.49
2375 2619 0.036858 GGAAGGTGAGTGCCAGTCTC 60.037 60.000 0.53 0.00 0.00 3.36
2397 2641 4.039609 TCTCAGCTGTTTCTCTGACATCAA 59.960 41.667 14.67 0.00 35.66 2.57
2438 2682 1.258445 AATTCAGCCCGACTCCGACT 61.258 55.000 0.00 0.00 38.22 4.18
2446 2690 2.997897 GACTCCGACTGCCCCTGT 60.998 66.667 0.00 0.00 0.00 4.00
2480 2724 8.586570 TGAACCAAATGATTTTGTCATGTTAC 57.413 30.769 0.00 0.00 46.80 2.50
2625 2876 2.389715 CTCCTTCCTTCGTGGTATCCT 58.610 52.381 0.00 0.00 37.07 3.24
2784 5362 2.827921 AGGCCACTGAATTCACCAAATC 59.172 45.455 5.01 0.32 0.00 2.17
2801 5379 5.779771 ACCAAATCCCTTTTTATCAGAGCAA 59.220 36.000 0.00 0.00 0.00 3.91
2812 5390 7.435068 TTTTATCAGAGCAACACTTTCTACC 57.565 36.000 0.00 0.00 0.00 3.18
2848 5426 2.591571 TCGTCTGATTCAGAGCATGG 57.408 50.000 16.62 4.80 41.46 3.66
2964 5542 0.811281 GGCCCTTGAAATCGTTCCTG 59.189 55.000 0.00 0.00 32.28 3.86
3070 5648 1.043673 ACCGCCTGATCTGAGTACCC 61.044 60.000 0.38 0.00 0.00 3.69
3088 5667 1.665679 CCCGAAGACACATACACATGC 59.334 52.381 0.00 0.00 35.39 4.06
3122 5723 0.316689 CGCGTTGTGACAAAACTCCC 60.317 55.000 0.00 0.00 0.00 4.30
3135 5736 6.106648 ACAAAACTCCCTAGGTAGTGTTAC 57.893 41.667 9.48 0.00 0.00 2.50
3136 5737 5.603813 ACAAAACTCCCTAGGTAGTGTTACA 59.396 40.000 9.48 0.00 0.00 2.41
3153 5754 6.155910 AGTGTTACATGGTGATTCTGAGATCT 59.844 38.462 0.00 0.00 0.00 2.75
3181 5782 2.769663 TGGCCTCGATGTAACAATACCT 59.230 45.455 3.32 0.00 0.00 3.08
3220 5904 8.978564 TTTGACATATTGCACGTCATTTTAAT 57.021 26.923 7.92 0.00 39.29 1.40
3251 5937 8.258850 TCCCCTGTAAAGAAATATAAGATCGT 57.741 34.615 0.00 0.00 0.00 3.73
3252 5938 8.711170 TCCCCTGTAAAGAAATATAAGATCGTT 58.289 33.333 0.00 0.00 0.00 3.85
3253 5939 9.338622 CCCCTGTAAAGAAATATAAGATCGTTT 57.661 33.333 0.00 0.00 0.00 3.60
3316 6002 6.593268 ACTTCTTTACAGAGGAAGTACTCC 57.407 41.667 0.00 0.00 44.98 3.85
3333 6019 3.728385 CTCCAAGAGAGGGGAACAATT 57.272 47.619 0.00 0.00 39.13 2.32
3334 6020 3.615155 CTCCAAGAGAGGGGAACAATTC 58.385 50.000 0.00 0.00 39.13 2.17
3335 6021 3.260205 TCCAAGAGAGGGGAACAATTCT 58.740 45.455 0.00 0.00 0.00 2.40
3336 6022 4.435137 TCCAAGAGAGGGGAACAATTCTA 58.565 43.478 0.00 0.00 0.00 2.10
3337 6023 4.849810 TCCAAGAGAGGGGAACAATTCTAA 59.150 41.667 0.00 0.00 0.00 2.10
3338 6024 4.944317 CCAAGAGAGGGGAACAATTCTAAC 59.056 45.833 0.00 0.00 0.00 2.34
3339 6025 5.514834 CCAAGAGAGGGGAACAATTCTAACA 60.515 44.000 0.00 0.00 0.00 2.41
3340 6026 5.843019 AGAGAGGGGAACAATTCTAACAA 57.157 39.130 0.00 0.00 0.00 2.83
3341 6027 5.810095 AGAGAGGGGAACAATTCTAACAAG 58.190 41.667 0.00 0.00 0.00 3.16
3342 6028 5.310857 AGAGAGGGGAACAATTCTAACAAGT 59.689 40.000 0.00 0.00 0.00 3.16
3343 6029 5.316987 AGAGGGGAACAATTCTAACAAGTG 58.683 41.667 0.00 0.00 0.00 3.16
3344 6030 5.073144 AGAGGGGAACAATTCTAACAAGTGA 59.927 40.000 0.00 0.00 0.00 3.41
3345 6031 5.892348 AGGGGAACAATTCTAACAAGTGAT 58.108 37.500 0.00 0.00 0.00 3.06
3346 6032 5.946377 AGGGGAACAATTCTAACAAGTGATC 59.054 40.000 0.00 0.00 0.00 2.92
3347 6033 5.163754 GGGGAACAATTCTAACAAGTGATCG 60.164 44.000 0.00 0.00 0.00 3.69
3348 6034 5.642063 GGGAACAATTCTAACAAGTGATCGA 59.358 40.000 0.00 0.00 0.00 3.59
3349 6035 6.316390 GGGAACAATTCTAACAAGTGATCGAT 59.684 38.462 0.00 0.00 0.00 3.59
3350 6036 7.148239 GGGAACAATTCTAACAAGTGATCGATT 60.148 37.037 0.00 0.00 0.00 3.34
3351 6037 7.693951 GGAACAATTCTAACAAGTGATCGATTG 59.306 37.037 0.00 7.88 0.00 2.67
3352 6038 7.076842 ACAATTCTAACAAGTGATCGATTGG 57.923 36.000 0.00 0.00 0.00 3.16
3353 6039 6.094048 ACAATTCTAACAAGTGATCGATTGGG 59.906 38.462 0.00 4.76 0.00 4.12
3354 6040 4.819105 TCTAACAAGTGATCGATTGGGT 57.181 40.909 0.00 4.73 0.00 4.51
3355 6041 5.160607 TCTAACAAGTGATCGATTGGGTT 57.839 39.130 0.00 3.51 0.00 4.11
3356 6042 5.556915 TCTAACAAGTGATCGATTGGGTTT 58.443 37.500 0.00 3.22 0.00 3.27
3357 6043 6.001460 TCTAACAAGTGATCGATTGGGTTTT 58.999 36.000 0.00 2.95 0.00 2.43
3358 6044 4.503741 ACAAGTGATCGATTGGGTTTTG 57.496 40.909 0.00 2.38 0.00 2.44
3359 6045 4.141287 ACAAGTGATCGATTGGGTTTTGA 58.859 39.130 0.00 0.00 0.00 2.69
3360 6046 4.023193 ACAAGTGATCGATTGGGTTTTGAC 60.023 41.667 0.00 0.00 0.00 3.18
3361 6047 3.081804 AGTGATCGATTGGGTTTTGACC 58.918 45.455 0.00 0.00 0.00 4.02
3362 6048 2.817258 GTGATCGATTGGGTTTTGACCA 59.183 45.455 0.00 0.00 35.88 4.02
3372 6058 6.901081 TTGGGTTTTGACCAAATTTTGTTT 57.099 29.167 8.26 0.00 44.52 2.83
3373 6059 6.901081 TGGGTTTTGACCAAATTTTGTTTT 57.099 29.167 8.26 0.00 34.44 2.43
3374 6060 6.681777 TGGGTTTTGACCAAATTTTGTTTTG 58.318 32.000 8.26 0.00 34.44 2.44
3375 6061 5.574830 GGGTTTTGACCAAATTTTGTTTTGC 59.425 36.000 8.26 0.00 35.67 3.68
3376 6062 6.152379 GGTTTTGACCAAATTTTGTTTTGCA 58.848 32.000 8.26 0.00 35.67 4.08
3377 6063 6.088749 GGTTTTGACCAAATTTTGTTTTGCAC 59.911 34.615 8.26 0.00 35.67 4.57
3378 6064 6.566197 TTTGACCAAATTTTGTTTTGCACT 57.434 29.167 8.26 0.00 35.67 4.40
3379 6065 6.566197 TTGACCAAATTTTGTTTTGCACTT 57.434 29.167 8.26 0.00 35.67 3.16
3380 6066 6.175712 TGACCAAATTTTGTTTTGCACTTC 57.824 33.333 8.26 0.00 35.67 3.01
3381 6067 5.123027 TGACCAAATTTTGTTTTGCACTTCC 59.877 36.000 8.26 0.00 35.67 3.46
3421 6252 3.944015 CCTTACTTTTCTCTCATGGCTGG 59.056 47.826 0.00 0.00 0.00 4.85
3442 6273 2.231964 GCAGCCAAGATCAATTCCAACA 59.768 45.455 0.00 0.00 0.00 3.33
3443 6274 3.118884 GCAGCCAAGATCAATTCCAACAT 60.119 43.478 0.00 0.00 0.00 2.71
3444 6275 4.098349 GCAGCCAAGATCAATTCCAACATA 59.902 41.667 0.00 0.00 0.00 2.29
3445 6276 5.221382 GCAGCCAAGATCAATTCCAACATAT 60.221 40.000 0.00 0.00 0.00 1.78
3477 6308 7.320443 TGTAGTTCATCATTATCAACAAGCC 57.680 36.000 0.00 0.00 0.00 4.35
3478 6309 5.841957 AGTTCATCATTATCAACAAGCCC 57.158 39.130 0.00 0.00 0.00 5.19
3479 6310 4.646492 AGTTCATCATTATCAACAAGCCCC 59.354 41.667 0.00 0.00 0.00 5.80
3480 6311 3.565307 TCATCATTATCAACAAGCCCCC 58.435 45.455 0.00 0.00 0.00 5.40
3481 6312 2.051334 TCATTATCAACAAGCCCCCG 57.949 50.000 0.00 0.00 0.00 5.73
3482 6313 0.385390 CATTATCAACAAGCCCCCGC 59.615 55.000 0.00 0.00 0.00 6.13
3483 6314 1.101049 ATTATCAACAAGCCCCCGCG 61.101 55.000 0.00 0.00 41.18 6.46
3555 6386 1.926426 CGCCCTTCCCCTGATTCCTT 61.926 60.000 0.00 0.00 0.00 3.36
3559 6390 1.925959 CCTTCCCCTGATTCCTTCCTT 59.074 52.381 0.00 0.00 0.00 3.36
3609 6440 4.680237 CTGGCCAACCGACAGCGA 62.680 66.667 7.01 0.00 40.82 4.93
3633 6464 1.760480 GAGGTGCTCTCCTCCTCCC 60.760 68.421 6.71 0.00 44.72 4.30
3634 6465 2.236959 GAGGTGCTCTCCTCCTCCCT 62.237 65.000 6.71 0.00 44.72 4.20
3639 6471 1.757423 GCTCTCCTCCTCCCTGCATC 61.757 65.000 0.00 0.00 0.00 3.91
3646 6478 1.457643 CCTCCCTGCATCGGGTCTA 60.458 63.158 10.68 0.00 44.95 2.59
3745 6656 1.361271 GACGACAGGTCCAACGACA 59.639 57.895 8.83 0.00 41.13 4.35
3771 6682 3.942439 GGCACCCGATCTAGGCCC 61.942 72.222 0.00 0.00 38.70 5.80
3813 6724 2.862536 CACTTGCTGATCTCATGTACCG 59.137 50.000 0.00 0.00 0.00 4.02
3817 6728 1.269831 GCTGATCTCATGTACCGTCCC 60.270 57.143 0.00 0.00 0.00 4.46
3820 6731 1.001597 GATCTCATGTACCGTCCCGTC 60.002 57.143 0.00 0.00 0.00 4.79
3830 6741 2.877691 GTCCCGTCAATGGCTTGC 59.122 61.111 0.00 0.00 32.11 4.01
3833 6744 2.180017 CCGTCAATGGCTTGCTGC 59.820 61.111 0.00 0.00 41.94 5.25
3843 6754 2.123982 CTTGCTGCCCCTGGGATC 60.124 66.667 16.20 6.14 37.50 3.36
3847 6758 3.866582 CTGCCCCTGGGATCGACC 61.867 72.222 16.20 0.00 37.50 4.79
3925 6837 2.520982 CCGGAGATGGTCGGCCTA 60.521 66.667 7.97 0.00 39.78 3.93
3945 6857 0.322546 AGGCTGGGTTGTCGGATTTC 60.323 55.000 0.00 0.00 0.00 2.17
3994 6906 2.111999 TTGGGGAGACAGAGTTGCCG 62.112 60.000 0.00 0.00 0.00 5.69
4012 6924 3.792716 GGTGAAAACCGAGCCAATG 57.207 52.632 0.00 0.00 0.00 2.82
4034 6946 4.398598 GCGATGGCGGCGTTTTGT 62.399 61.111 9.37 0.00 38.16 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 0.609957 ACCTGTGTGGATGCACATGG 60.610 55.000 27.85 27.85 46.65 3.66
58 60 6.265196 TCAAATAACTGAAGTTGCCAATCACT 59.735 34.615 5.95 0.00 38.90 3.41
111 114 4.257731 GGTTCCAATGTTGTTGTTTGGTT 58.742 39.130 0.00 0.00 40.62 3.67
112 115 3.677424 CGGTTCCAATGTTGTTGTTTGGT 60.677 43.478 0.00 0.00 40.62 3.67
137 140 6.763355 TCCGGGATTGAAAATTTGAATTTGA 58.237 32.000 0.00 0.00 38.53 2.69
141 144 6.380846 TCATCTCCGGGATTGAAAATTTGAAT 59.619 34.615 0.00 0.00 31.27 2.57
183 187 5.706916 CAGGAATTGAATTGGTCTGAACTG 58.293 41.667 0.00 0.00 0.00 3.16
227 238 5.905181 CAGCAACAAATGTTTGCAGAAAATC 59.095 36.000 16.98 0.00 41.79 2.17
228 239 5.585445 TCAGCAACAAATGTTTGCAGAAAAT 59.415 32.000 16.98 0.00 41.79 1.82
294 347 2.686405 CCATACATGATGCAACAGCTGT 59.314 45.455 15.25 15.25 33.79 4.40
382 465 2.555547 GGCAACAAGAAGCGGCACT 61.556 57.895 1.45 0.00 0.00 4.40
387 470 3.442441 TTGGGGCAACAAGAAGCG 58.558 55.556 0.00 0.00 39.74 4.68
423 517 8.734386 CAAAGAAGTGGCATTAAAGTAGAGAAT 58.266 33.333 0.00 0.00 0.00 2.40
455 553 4.678509 TGCATTCGGTTGACTAATGAAC 57.321 40.909 11.36 0.00 33.38 3.18
504 608 9.401058 TGACAAAGAAGAAGAAGAAGAAGAAAT 57.599 29.630 0.00 0.00 0.00 2.17
607 722 7.674348 TCCGGTGATACTGATATAATTTCCTCT 59.326 37.037 0.00 0.00 0.00 3.69
621 739 3.637229 AGGACAATACTCCGGTGATACTG 59.363 47.826 11.17 4.57 35.20 2.74
637 763 0.187117 TGCCCATTTGACCAGGACAA 59.813 50.000 0.00 0.00 0.00 3.18
658 784 4.209495 GCTACTTAATTACTGGAAGCGCTC 59.791 45.833 12.06 4.06 37.60 5.03
673 799 2.781681 GGAGCAACTGGGCTACTTAA 57.218 50.000 0.00 0.00 45.99 1.85
678 804 1.995626 GGGAGGAGCAACTGGGCTA 60.996 63.158 0.00 0.00 45.99 3.93
680 806 2.900671 GATGGGAGGAGCAACTGGGC 62.901 65.000 0.00 0.00 0.00 5.36
681 807 1.225704 GATGGGAGGAGCAACTGGG 59.774 63.158 0.00 0.00 0.00 4.45
803 930 3.713826 TTGAAATAGGCGGAAGGAAGT 57.286 42.857 0.00 0.00 0.00 3.01
804 931 3.565902 GGATTGAAATAGGCGGAAGGAAG 59.434 47.826 0.00 0.00 0.00 3.46
805 932 3.551846 GGATTGAAATAGGCGGAAGGAA 58.448 45.455 0.00 0.00 0.00 3.36
806 933 2.158667 GGGATTGAAATAGGCGGAAGGA 60.159 50.000 0.00 0.00 0.00 3.36
807 934 2.230660 GGGATTGAAATAGGCGGAAGG 58.769 52.381 0.00 0.00 0.00 3.46
864 995 3.263425 ACGGATGGTTGTTAGAGATGGTT 59.737 43.478 0.00 0.00 0.00 3.67
865 996 2.838202 ACGGATGGTTGTTAGAGATGGT 59.162 45.455 0.00 0.00 0.00 3.55
886 1017 1.530419 AAACAGATTGCACCGCCCA 60.530 52.632 0.00 0.00 0.00 5.36
987 1147 3.685835 CGTGGTCCATCCTCTCTTCTCTA 60.686 52.174 0.00 0.00 37.07 2.43
1390 1568 3.533606 AGATATGTGCTGGAGTGTGAC 57.466 47.619 0.00 0.00 0.00 3.67
1395 1573 3.834489 CAGGAAGATATGTGCTGGAGT 57.166 47.619 0.00 0.00 31.32 3.85
1414 1598 5.217978 ACGGATTGTTTACTTCACTACCA 57.782 39.130 0.00 0.00 0.00 3.25
1419 1603 5.519206 CCTAGCTACGGATTGTTTACTTCAC 59.481 44.000 3.82 0.00 0.00 3.18
1420 1604 5.419788 TCCTAGCTACGGATTGTTTACTTCA 59.580 40.000 7.59 0.00 0.00 3.02
1422 1606 5.927281 TCCTAGCTACGGATTGTTTACTT 57.073 39.130 7.59 0.00 0.00 2.24
1424 1608 5.921408 CAGATCCTAGCTACGGATTGTTTAC 59.079 44.000 19.51 10.18 41.24 2.01
1425 1609 5.831525 TCAGATCCTAGCTACGGATTGTTTA 59.168 40.000 19.51 7.40 41.24 2.01
1427 1611 4.038162 GTCAGATCCTAGCTACGGATTGTT 59.962 45.833 19.51 10.32 41.24 2.83
1435 1619 5.578727 CACACAAAAGTCAGATCCTAGCTAC 59.421 44.000 0.00 0.00 0.00 3.58
1436 1620 5.724328 CACACAAAAGTCAGATCCTAGCTA 58.276 41.667 0.00 0.00 0.00 3.32
1440 1624 3.327757 AGGCACACAAAAGTCAGATCCTA 59.672 43.478 0.00 0.00 0.00 2.94
1454 1639 2.179547 CACACTGCGAAGGCACACA 61.180 57.895 0.00 0.00 46.21 3.72
1455 1640 2.105960 GACACACTGCGAAGGCACAC 62.106 60.000 0.00 0.00 46.21 3.82
1456 1641 1.887242 GACACACTGCGAAGGCACA 60.887 57.895 0.00 0.00 46.21 4.57
1461 1646 1.007271 ACGAGGACACACTGCGAAG 60.007 57.895 0.00 0.00 0.00 3.79
1462 1647 1.299850 CACGAGGACACACTGCGAA 60.300 57.895 0.00 0.00 0.00 4.70
1463 1648 2.335011 CACGAGGACACACTGCGA 59.665 61.111 0.00 0.00 0.00 5.10
1464 1649 2.016704 GACACGAGGACACACTGCG 61.017 63.158 0.00 0.00 0.00 5.18
1528 1714 0.435008 CGAAGCACACGCAGTACTTC 59.565 55.000 10.14 10.14 41.61 3.01
1613 1799 1.886585 TGCTCGGAGAAGCAGAGTC 59.113 57.895 9.69 0.00 40.44 3.36
1647 1833 0.966920 AGGGTGTACTGAACCAGTCG 59.033 55.000 2.55 0.00 41.21 4.18
1665 1851 7.530010 CAGACATGGTACCTTTGTTATTGAAG 58.470 38.462 14.36 0.00 0.00 3.02
1671 1857 4.323417 CAGCAGACATGGTACCTTTGTTA 58.677 43.478 14.36 0.00 34.74 2.41
1881 2084 3.323979 TGAAGAGGTGGGAGTAAAGTCAC 59.676 47.826 0.00 0.00 0.00 3.67
1883 2086 4.383226 GGATGAAGAGGTGGGAGTAAAGTC 60.383 50.000 0.00 0.00 0.00 3.01
1891 2094 4.227197 GAATCTAGGATGAAGAGGTGGGA 58.773 47.826 0.00 0.00 0.00 4.37
1951 2154 0.675522 AGCCATTAACACCGTTCCCG 60.676 55.000 0.00 0.00 0.00 5.14
1963 2166 5.431765 GAAGGATCAAGAGTGAAGCCATTA 58.568 41.667 0.00 0.00 37.30 1.90
1990 2193 3.208570 TGGGTAAGTATGAACTCCCCA 57.791 47.619 10.36 10.36 38.31 4.96
2043 2246 6.431198 TTTTAGAAAGAAGAAGTGCGTTGT 57.569 33.333 0.00 0.00 0.00 3.32
2075 2283 5.049198 CAGCTAGTCTTTTGTTGCAGATCAA 60.049 40.000 0.00 0.00 0.00 2.57
2092 2303 8.580720 CACACATATAGTAGGATTTCAGCTAGT 58.419 37.037 0.00 0.00 0.00 2.57
2093 2304 7.543868 GCACACATATAGTAGGATTTCAGCTAG 59.456 40.741 0.00 0.00 0.00 3.42
2098 2309 9.542462 GTTAAGCACACATATAGTAGGATTTCA 57.458 33.333 0.00 0.00 0.00 2.69
2099 2310 9.765795 AGTTAAGCACACATATAGTAGGATTTC 57.234 33.333 0.00 0.00 0.00 2.17
2119 2330 4.816385 TCTGCACAACCAAGAAGAGTTAAG 59.184 41.667 0.00 0.00 0.00 1.85
2121 2332 4.415881 TCTGCACAACCAAGAAGAGTTA 57.584 40.909 0.00 0.00 0.00 2.24
2165 2376 1.803334 CGTTCCCTTCATTGACCGAA 58.197 50.000 0.00 0.00 0.00 4.30
2221 2432 8.688151 GGACTTGAATGTGATCTAGTAAGTACT 58.312 37.037 0.00 0.00 35.91 2.73
2222 2433 8.467598 TGGACTTGAATGTGATCTAGTAAGTAC 58.532 37.037 0.00 0.00 35.91 2.73
2223 2434 8.467598 GTGGACTTGAATGTGATCTAGTAAGTA 58.532 37.037 0.00 0.00 35.91 2.24
2225 2436 7.323420 TGTGGACTTGAATGTGATCTAGTAAG 58.677 38.462 0.00 0.00 35.91 2.34
2226 2437 7.239763 TGTGGACTTGAATGTGATCTAGTAA 57.760 36.000 0.00 0.00 35.91 2.24
2228 2439 5.745312 TGTGGACTTGAATGTGATCTAGT 57.255 39.130 0.00 0.00 37.96 2.57
2229 2440 6.427853 TGTTTGTGGACTTGAATGTGATCTAG 59.572 38.462 0.00 0.00 0.00 2.43
2231 2442 5.132502 TGTTTGTGGACTTGAATGTGATCT 58.867 37.500 0.00 0.00 0.00 2.75
2232 2443 5.437289 TGTTTGTGGACTTGAATGTGATC 57.563 39.130 0.00 0.00 0.00 2.92
2233 2444 5.535783 TGATGTTTGTGGACTTGAATGTGAT 59.464 36.000 0.00 0.00 0.00 3.06
2236 2447 4.644234 TGTGATGTTTGTGGACTTGAATGT 59.356 37.500 0.00 0.00 0.00 2.71
2238 2449 4.279169 CCTGTGATGTTTGTGGACTTGAAT 59.721 41.667 0.00 0.00 0.00 2.57
2246 2457 3.213506 TGACTTCCTGTGATGTTTGTGG 58.786 45.455 0.00 0.00 0.00 4.17
2301 2541 1.004745 TGGGGAAACTTGCATCTCTCC 59.995 52.381 0.00 0.00 0.00 3.71
2375 2619 3.922910 TGATGTCAGAGAAACAGCTGAG 58.077 45.455 23.35 0.00 41.42 3.35
2397 2641 1.947456 GCTGTGGAAGAGTTTCGGTTT 59.053 47.619 0.00 0.00 33.98 3.27
2461 2705 7.083858 CGTGGAGTAACATGACAAAATCATTT 58.916 34.615 0.00 0.00 46.54 2.32
2597 2848 0.537188 CGAAGGAAGGAGGCTGCTAA 59.463 55.000 9.60 0.00 0.00 3.09
2598 2849 0.614979 ACGAAGGAAGGAGGCTGCTA 60.615 55.000 9.60 0.00 0.00 3.49
2599 2850 1.915769 ACGAAGGAAGGAGGCTGCT 60.916 57.895 1.28 1.28 0.00 4.24
2625 2876 4.202253 ACATGGATAAGCGTAATCAGCTGA 60.202 41.667 20.79 20.79 45.31 4.26
2759 5337 2.107378 TGGTGAATTCAGTGGCCTTACA 59.893 45.455 8.80 0.00 0.00 2.41
2784 5362 5.712152 AAGTGTTGCTCTGATAAAAAGGG 57.288 39.130 0.00 0.00 0.00 3.95
2801 5379 6.156256 TGGCATAGTATCAAGGTAGAAAGTGT 59.844 38.462 0.00 0.00 0.00 3.55
2964 5542 2.360801 GAGACCTCTGGTGTATCTCAGC 59.639 54.545 0.00 0.00 43.90 4.26
3070 5648 3.305361 CAGAGCATGTGTATGTGTCTTCG 59.695 47.826 0.00 0.00 36.65 3.79
3122 5723 6.980978 CAGAATCACCATGTAACACTACCTAG 59.019 42.308 0.00 0.00 0.00 3.02
3135 5736 5.878669 TGACAAAGATCTCAGAATCACCATG 59.121 40.000 0.00 0.00 0.00 3.66
3136 5737 6.058553 TGACAAAGATCTCAGAATCACCAT 57.941 37.500 0.00 0.00 0.00 3.55
3153 5754 3.006940 GTTACATCGAGGCCATGACAAA 58.993 45.455 5.01 0.00 0.00 2.83
3227 5911 8.904099 AACGATCTTATATTTCTTTACAGGGG 57.096 34.615 0.00 0.00 0.00 4.79
3292 5978 7.236529 TGGAGTACTTCCTCTGTAAAGAAGTA 58.763 38.462 0.00 7.55 46.32 2.24
3294 5980 6.591750 TGGAGTACTTCCTCTGTAAAGAAG 57.408 41.667 0.00 0.00 46.92 2.85
3295 5981 6.781014 TCTTGGAGTACTTCCTCTGTAAAGAA 59.219 38.462 0.00 0.00 46.92 2.52
3296 5982 6.312529 TCTTGGAGTACTTCCTCTGTAAAGA 58.687 40.000 0.00 0.00 46.92 2.52
3297 5983 6.434652 TCTCTTGGAGTACTTCCTCTGTAAAG 59.565 42.308 0.00 0.00 46.92 1.85
3298 5984 6.312529 TCTCTTGGAGTACTTCCTCTGTAAA 58.687 40.000 0.00 0.00 46.92 2.01
3299 5985 5.888901 TCTCTTGGAGTACTTCCTCTGTAA 58.111 41.667 0.00 0.00 46.92 2.41
3300 5986 5.502079 CTCTCTTGGAGTACTTCCTCTGTA 58.498 45.833 0.00 0.00 46.92 2.74
3301 5987 4.340617 CTCTCTTGGAGTACTTCCTCTGT 58.659 47.826 0.00 0.00 46.92 3.41
3302 5988 3.699038 CCTCTCTTGGAGTACTTCCTCTG 59.301 52.174 0.00 0.00 46.92 3.35
3303 5989 3.309556 CCCTCTCTTGGAGTACTTCCTCT 60.310 52.174 0.00 0.00 46.92 3.69
3304 5990 3.028130 CCCTCTCTTGGAGTACTTCCTC 58.972 54.545 0.00 0.00 46.92 3.71
3305 5991 2.292587 CCCCTCTCTTGGAGTACTTCCT 60.293 54.545 0.00 0.00 46.92 3.36
3306 5992 2.112190 CCCCTCTCTTGGAGTACTTCC 58.888 57.143 0.00 1.65 46.98 3.46
3307 5993 3.103080 TCCCCTCTCTTGGAGTACTTC 57.897 52.381 0.00 0.00 40.30 3.01
3308 5994 3.174779 GTTCCCCTCTCTTGGAGTACTT 58.825 50.000 0.00 0.00 40.30 2.24
3309 5995 2.111972 TGTTCCCCTCTCTTGGAGTACT 59.888 50.000 0.00 0.00 40.30 2.73
3310 5996 2.537143 TGTTCCCCTCTCTTGGAGTAC 58.463 52.381 0.00 0.00 40.30 2.73
3311 5997 3.269592 TTGTTCCCCTCTCTTGGAGTA 57.730 47.619 0.00 0.00 40.30 2.59
3312 5998 2.118403 TTGTTCCCCTCTCTTGGAGT 57.882 50.000 0.00 0.00 40.30 3.85
3313 5999 3.265479 AGAATTGTTCCCCTCTCTTGGAG 59.735 47.826 0.00 0.00 41.51 3.86
3314 6000 3.260205 AGAATTGTTCCCCTCTCTTGGA 58.740 45.455 0.00 0.00 0.00 3.53
3315 6001 3.728385 AGAATTGTTCCCCTCTCTTGG 57.272 47.619 0.00 0.00 0.00 3.61
3316 6002 5.560724 TGTTAGAATTGTTCCCCTCTCTTG 58.439 41.667 0.00 0.00 0.00 3.02
3317 6003 5.843019 TGTTAGAATTGTTCCCCTCTCTT 57.157 39.130 0.00 0.00 0.00 2.85
3318 6004 5.310857 ACTTGTTAGAATTGTTCCCCTCTCT 59.689 40.000 0.00 0.00 0.00 3.10
3319 6005 5.412904 CACTTGTTAGAATTGTTCCCCTCTC 59.587 44.000 0.00 0.00 0.00 3.20
3320 6006 5.073144 TCACTTGTTAGAATTGTTCCCCTCT 59.927 40.000 0.00 0.00 0.00 3.69
3321 6007 5.313712 TCACTTGTTAGAATTGTTCCCCTC 58.686 41.667 0.00 0.00 0.00 4.30
3322 6008 5.319043 TCACTTGTTAGAATTGTTCCCCT 57.681 39.130 0.00 0.00 0.00 4.79
3323 6009 5.163754 CGATCACTTGTTAGAATTGTTCCCC 60.164 44.000 0.00 0.00 0.00 4.81
3324 6010 5.642063 TCGATCACTTGTTAGAATTGTTCCC 59.358 40.000 0.00 0.00 0.00 3.97
3325 6011 6.721571 TCGATCACTTGTTAGAATTGTTCC 57.278 37.500 0.00 0.00 0.00 3.62
3326 6012 7.693951 CCAATCGATCACTTGTTAGAATTGTTC 59.306 37.037 0.00 0.00 0.00 3.18
3327 6013 7.362056 CCCAATCGATCACTTGTTAGAATTGTT 60.362 37.037 0.00 0.00 0.00 2.83
3328 6014 6.094048 CCCAATCGATCACTTGTTAGAATTGT 59.906 38.462 0.00 0.00 0.00 2.71
3329 6015 6.094048 ACCCAATCGATCACTTGTTAGAATTG 59.906 38.462 0.00 0.00 0.00 2.32
3330 6016 6.180472 ACCCAATCGATCACTTGTTAGAATT 58.820 36.000 0.00 0.00 0.00 2.17
3331 6017 5.745227 ACCCAATCGATCACTTGTTAGAAT 58.255 37.500 0.00 0.00 0.00 2.40
3332 6018 5.160607 ACCCAATCGATCACTTGTTAGAA 57.839 39.130 0.00 0.00 0.00 2.10
3333 6019 4.819105 ACCCAATCGATCACTTGTTAGA 57.181 40.909 0.00 0.00 0.00 2.10
3334 6020 5.880054 AAACCCAATCGATCACTTGTTAG 57.120 39.130 0.00 0.00 0.00 2.34
3335 6021 5.765677 TCAAAACCCAATCGATCACTTGTTA 59.234 36.000 0.00 0.00 0.00 2.41
3336 6022 4.582656 TCAAAACCCAATCGATCACTTGTT 59.417 37.500 0.00 0.00 0.00 2.83
3337 6023 4.023193 GTCAAAACCCAATCGATCACTTGT 60.023 41.667 0.00 0.00 0.00 3.16
3338 6024 4.475944 GTCAAAACCCAATCGATCACTTG 58.524 43.478 0.00 0.00 0.00 3.16
3339 6025 3.506067 GGTCAAAACCCAATCGATCACTT 59.494 43.478 0.00 0.00 39.93 3.16
3340 6026 3.081804 GGTCAAAACCCAATCGATCACT 58.918 45.455 0.00 0.00 39.93 3.41
3341 6027 2.817258 TGGTCAAAACCCAATCGATCAC 59.183 45.455 0.00 0.00 45.83 3.06
3342 6028 3.147553 TGGTCAAAACCCAATCGATCA 57.852 42.857 0.00 0.00 45.83 2.92
3343 6029 4.513198 TTTGGTCAAAACCCAATCGATC 57.487 40.909 0.00 0.00 45.83 3.69
3344 6030 5.482163 AATTTGGTCAAAACCCAATCGAT 57.518 34.783 0.00 0.00 45.83 3.59
3345 6031 4.946478 AATTTGGTCAAAACCCAATCGA 57.054 36.364 0.00 0.00 45.83 3.59
3346 6032 5.295540 ACAAAATTTGGTCAAAACCCAATCG 59.704 36.000 10.71 0.00 45.83 3.34
3347 6033 6.691754 ACAAAATTTGGTCAAAACCCAATC 57.308 33.333 10.71 0.00 45.83 2.67
3348 6034 7.473735 AAACAAAATTTGGTCAAAACCCAAT 57.526 28.000 10.71 0.00 45.83 3.16
3349 6035 6.901081 AAACAAAATTTGGTCAAAACCCAA 57.099 29.167 10.71 0.00 45.83 4.12
3350 6036 6.681777 CAAAACAAAATTTGGTCAAAACCCA 58.318 32.000 10.71 0.00 45.83 4.51
3351 6037 5.574830 GCAAAACAAAATTTGGTCAAAACCC 59.425 36.000 10.71 0.00 45.83 4.11
3352 6038 6.088749 GTGCAAAACAAAATTTGGTCAAAACC 59.911 34.615 10.71 0.00 46.66 3.27
3353 6039 6.860539 AGTGCAAAACAAAATTTGGTCAAAAC 59.139 30.769 10.71 1.73 39.99 2.43
3354 6040 6.974965 AGTGCAAAACAAAATTTGGTCAAAA 58.025 28.000 10.71 0.00 39.99 2.44
3355 6041 6.566197 AGTGCAAAACAAAATTTGGTCAAA 57.434 29.167 10.71 0.00 39.99 2.69
3356 6042 6.348868 GGAAGTGCAAAACAAAATTTGGTCAA 60.349 34.615 10.71 0.00 39.99 3.18
3357 6043 5.123027 GGAAGTGCAAAACAAAATTTGGTCA 59.877 36.000 10.71 0.00 39.99 4.02
3358 6044 5.568482 GGAAGTGCAAAACAAAATTTGGTC 58.432 37.500 10.71 0.00 39.99 4.02
3359 6045 4.094146 CGGAAGTGCAAAACAAAATTTGGT 59.906 37.500 10.71 0.00 39.99 3.67
3360 6046 4.331168 TCGGAAGTGCAAAACAAAATTTGG 59.669 37.500 10.71 0.00 39.99 3.28
3361 6047 5.462034 TCGGAAGTGCAAAACAAAATTTG 57.538 34.783 3.89 3.89 42.01 2.32
3362 6048 5.814705 TGATCGGAAGTGCAAAACAAAATTT 59.185 32.000 0.00 0.00 0.00 1.82
3363 6049 5.234116 GTGATCGGAAGTGCAAAACAAAATT 59.766 36.000 0.00 0.00 0.00 1.82
3364 6050 4.744631 GTGATCGGAAGTGCAAAACAAAAT 59.255 37.500 0.00 0.00 0.00 1.82
3365 6051 4.109050 GTGATCGGAAGTGCAAAACAAAA 58.891 39.130 0.00 0.00 0.00 2.44
3366 6052 3.701241 GTGATCGGAAGTGCAAAACAAA 58.299 40.909 0.00 0.00 0.00 2.83
3367 6053 2.286713 CGTGATCGGAAGTGCAAAACAA 60.287 45.455 0.00 0.00 0.00 2.83
3368 6054 1.262950 CGTGATCGGAAGTGCAAAACA 59.737 47.619 0.00 0.00 0.00 2.83
3369 6055 1.950472 CGTGATCGGAAGTGCAAAAC 58.050 50.000 0.00 0.00 0.00 2.43
3381 6067 2.125673 GGGTGTGGTCCGTGATCG 60.126 66.667 0.00 0.00 0.00 3.69
3421 6252 2.231964 TGTTGGAATTGATCTTGGCTGC 59.768 45.455 0.00 0.00 0.00 5.25
3538 6369 0.553333 GGAAGGAATCAGGGGAAGGG 59.447 60.000 0.00 0.00 0.00 3.95
3546 6377 2.622436 GGTGACGAAGGAAGGAATCAG 58.378 52.381 0.00 0.00 0.00 2.90
3588 6419 3.850098 CTGTCGGTTGGCCAGGCTT 62.850 63.158 12.43 0.00 34.09 4.35
3602 6433 4.148825 ACCTCCGCCATCGCTGTC 62.149 66.667 0.00 0.00 0.00 3.51
3633 6464 0.319728 CCCATCTAGACCCGATGCAG 59.680 60.000 0.00 0.00 37.52 4.41
3634 6465 1.121407 CCCCATCTAGACCCGATGCA 61.121 60.000 0.00 0.00 37.52 3.96
3639 6471 3.616721 CCGCCCCATCTAGACCCG 61.617 72.222 0.00 0.00 0.00 5.28
3720 6631 4.773117 GACCTGTCGTCGTCCGCC 62.773 72.222 0.00 0.00 36.19 6.13
3771 6682 2.124570 CCCACCGAAGCCCATCTG 60.125 66.667 0.00 0.00 0.00 2.90
3813 6724 1.675641 AGCAAGCCATTGACGGGAC 60.676 57.895 0.00 0.00 38.83 4.46
3830 6741 3.866582 GGTCGATCCCAGGGGCAG 61.867 72.222 5.33 0.00 34.68 4.85
3843 6754 2.796651 CCCTCGAGTTACGGGTCG 59.203 66.667 12.31 0.00 41.44 4.79
3847 6758 2.101770 GACGCCCTCGAGTTACGG 59.898 66.667 19.00 11.41 42.82 4.02
3848 6759 2.277120 CGACGCCCTCGAGTTACG 60.277 66.667 12.31 13.86 46.14 3.18
3850 6761 3.136123 CCCGACGCCCTCGAGTTA 61.136 66.667 12.31 0.00 46.14 2.24
3901 6813 3.447025 GACCATCTCCGGCGAAGGG 62.447 68.421 19.20 15.68 0.00 3.95
3909 6821 1.364171 CTTAGGCCGACCATCTCCG 59.636 63.158 0.00 0.00 39.06 4.63
3925 6837 0.112412 AAATCCGACAACCCAGCCTT 59.888 50.000 0.00 0.00 0.00 4.35
3945 6857 1.889829 GGGACTAGATGACGGATCTGG 59.110 57.143 6.47 8.50 43.67 3.86
3953 6865 0.029567 CGCAGTCGGGACTAGATGAC 59.970 60.000 0.21 0.00 40.20 3.06
3956 6868 0.107116 ACTCGCAGTCGGGACTAGAT 60.107 55.000 0.21 0.00 40.20 1.98
3994 6906 0.243636 CCATTGGCTCGGTTTTCACC 59.756 55.000 0.00 0.00 40.16 4.02


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

AutoCloner maintained by Alex Coulton.