Multiple sequence alignment - TraesCS5A01G136100

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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 TraesCS5A01G136100 chr5A 100.000 5008 0 0 1 5008 307345307 307350314 0.000000e+00 9249.0
1 TraesCS5A01G136100 chr5A 87.109 256 27 5 3443 3695 456055929 456056181 8.210000e-73 285.0
2 TraesCS5A01G136100 chr5D 93.768 2744 79 23 2317 5008 228775007 228777710 0.000000e+00 4036.0
3 TraesCS5A01G136100 chr5D 95.839 1466 48 6 959 2420 228773551 228775007 0.000000e+00 2357.0
4 TraesCS5A01G136100 chr5B 91.637 1710 85 23 959 2644 254569676 254571351 0.000000e+00 2313.0
5 TraesCS5A01G136100 chr5B 92.199 846 34 12 4194 5008 254573173 254574017 0.000000e+00 1168.0
6 TraesCS5A01G136100 chr5B 87.924 1002 70 25 2461 3440 254571350 254572322 0.000000e+00 1133.0
7 TraesCS5A01G136100 chr5B 88.924 632 41 11 3503 4119 254572528 254573145 0.000000e+00 752.0
8 TraesCS5A01G136100 chr5B 78.396 1097 133 52 99 1144 254506096 254507139 7.120000e-173 617.0
9 TraesCS5A01G136100 chr5B 86.572 283 25 4 3158 3440 608323664 608323933 2.930000e-77 300.0
10 TraesCS5A01G136100 chr5B 86.667 255 29 4 3444 3695 608332722 608332974 1.370000e-70 278.0
11 TraesCS5A01G136100 chr5B 90.435 115 9 2 1 114 254504768 254504881 3.120000e-32 150.0
12 TraesCS5A01G136100 chr5B 85.256 156 11 4 1234 1383 254569897 254570046 3.120000e-32 150.0
13 TraesCS5A01G136100 chr4D 88.398 362 34 5 3074 3435 278186779 278186426 3.580000e-116 429.0
14 TraesCS5A01G136100 chr4D 86.392 316 30 10 1381 1685 111949795 111949482 2.890000e-87 333.0
15 TraesCS5A01G136100 chr4D 82.322 379 36 21 3021 3386 111948006 111947646 2.930000e-77 300.0
16 TraesCS5A01G136100 chr1B 87.834 337 31 7 3075 3409 113520018 113520346 2.190000e-103 387.0
17 TraesCS5A01G136100 chr1B 87.402 254 29 3 3443 3695 74127220 74127471 6.340000e-74 289.0
18 TraesCS5A01G136100 chr1B 86.873 259 29 4 3443 3698 629690792 629690536 8.210000e-73 285.0
19 TraesCS5A01G136100 chr4B 87.937 315 27 8 1381 1685 172523759 172523446 1.330000e-95 361.0
20 TraesCS5A01G136100 chr4B 80.902 377 45 20 3022 3387 172521999 172521639 6.390000e-69 272.0
21 TraesCS5A01G136100 chr4A 86.834 319 29 9 1376 1682 465327306 465327623 1.330000e-90 344.0
22 TraesCS5A01G136100 chr4A 82.292 384 37 21 3016 3386 465329328 465329693 2.270000e-78 303.0
23 TraesCS5A01G136100 chr4A 86.486 259 30 4 3443 3698 374493752 374493496 3.820000e-71 279.0
24 TraesCS5A01G136100 chr4A 86.100 259 31 4 3443 3698 27185428 27185172 1.780000e-69 274.0
25 TraesCS5A01G136100 chr2B 78.680 591 66 27 2864 3440 72605508 72604964 6.210000e-89 339.0
26 TraesCS5A01G136100 chr2B 86.572 283 25 3 3158 3440 70869346 70869615 2.930000e-77 300.0
27 TraesCS5A01G136100 chr2B 86.719 256 29 4 3443 3695 70869803 70870056 3.820000e-71 279.0
28 TraesCS5A01G136100 chr3B 87.633 283 22 3 3158 3440 345089219 345089488 2.910000e-82 316.0
29 TraesCS5A01G136100 chr3B 77.250 589 66 26 2864 3440 28063493 28062961 2.950000e-72 283.0
30 TraesCS5A01G136100 chr3B 79.688 128 13 5 3612 3728 455069292 455069417 4.160000e-11 80.5
31 TraesCS5A01G136100 chr3B 74.757 206 31 13 3030 3219 387432447 387432647 6.950000e-09 73.1
32 TraesCS5A01G136100 chr2A 87.109 256 28 4 3443 3695 713201563 713201816 8.210000e-73 285.0
33 TraesCS5A01G136100 chr3D 92.593 54 4 0 3030 3083 293809928 293809981 1.490000e-10 78.7


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 TraesCS5A01G136100 chr5A 307345307 307350314 5007 False 9249.0 9249 100.0000 1 5008 1 chr5A.!!$F1 5007
1 TraesCS5A01G136100 chr5D 228773551 228777710 4159 False 3196.5 4036 94.8035 959 5008 2 chr5D.!!$F1 4049
2 TraesCS5A01G136100 chr5B 254569676 254574017 4341 False 1103.2 2313 89.1880 959 5008 5 chr5B.!!$F4 4049
3 TraesCS5A01G136100 chr5B 254504768 254507139 2371 False 383.5 617 84.4155 1 1144 2 chr5B.!!$F3 1143
4 TraesCS5A01G136100 chr4D 111947646 111949795 2149 True 316.5 333 84.3570 1381 3386 2 chr4D.!!$R2 2005
5 TraesCS5A01G136100 chr4B 172521639 172523759 2120 True 316.5 361 84.4195 1381 3387 2 chr4B.!!$R1 2006
6 TraesCS5A01G136100 chr4A 465327306 465329693 2387 False 323.5 344 84.5630 1376 3386 2 chr4A.!!$F1 2010
7 TraesCS5A01G136100 chr2B 72604964 72605508 544 True 339.0 339 78.6800 2864 3440 1 chr2B.!!$R1 576
8 TraesCS5A01G136100 chr2B 70869346 70870056 710 False 289.5 300 86.6455 3158 3695 2 chr2B.!!$F1 537
9 TraesCS5A01G136100 chr3B 28062961 28063493 532 True 283.0 283 77.2500 2864 3440 1 chr3B.!!$R1 576

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
143 1374 0.172578 CATGGTCAGCATTGCCACTG 59.827 55.000 4.70 0.0 34.71 3.66 F
203 1434 0.179145 ATCGACAACCACGATCCGTC 60.179 55.000 0.00 0.0 45.32 4.79 F
1716 3015 0.179111 CTACGCGCATCCTTCTTCCA 60.179 55.000 5.73 0.0 0.00 3.53 F
1718 3017 0.392998 ACGCGCATCCTTCTTCCATT 60.393 50.000 5.73 0.0 0.00 3.16 F
1761 3060 0.526524 GTAGCTGCGATCTTGCGACT 60.527 55.000 0.00 0.0 37.81 4.18 F
2745 5135 1.475930 GGCCTGATGCTCTCCCTTTAC 60.476 57.143 0.00 0.0 40.92 2.01 F
3844 6726 2.831685 ATGTTCTGTACTTCACCGCA 57.168 45.000 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 2338 0.469144 GTAGCCTCCTCCTCCTCCTG 60.469 65.000 0.00 0.00 0.00 3.86 R
1734 3033 0.924090 GATCGCAGCTACACGGAAAG 59.076 55.000 3.50 0.00 0.00 2.62 R
2706 4917 2.741228 GCCACAAATTCAAACTGTGCCA 60.741 45.455 2.29 0.00 39.30 4.92 R
2895 5429 2.930826 ACTGGAATGTGAAAGACGGT 57.069 45.000 0.00 0.00 0.00 4.83 R
2941 5480 4.322804 GCAATGCTGAATTCGAAGTTTCAG 59.677 41.667 26.45 26.45 44.87 3.02 R
3907 6789 0.181587 TGAAAGTTGCAGACCCGGAA 59.818 50.000 0.73 0.00 0.00 4.30 R
4961 7893 0.104304 AGACCGTTCTCAACACGCTT 59.896 50.000 0.00 0.00 36.27 4.68 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
33 34 8.716674 TCTAGTCTTTAGGGTTTTAGTCTTGA 57.283 34.615 0.00 0.00 0.00 3.02
36 37 6.704937 AGTCTTTAGGGTTTTAGTCTTGAACG 59.295 38.462 0.00 0.00 0.00 3.95
43 44 3.441496 TTTAGTCTTGAACGTGACGGT 57.559 42.857 10.66 0.68 38.16 4.83
44 45 2.693797 TAGTCTTGAACGTGACGGTC 57.306 50.000 17.25 17.25 44.56 4.79
45 46 1.030457 AGTCTTGAACGTGACGGTCT 58.970 50.000 24.28 0.00 44.60 3.85
50 51 1.212229 GAACGTGACGGTCTCCCTC 59.788 63.158 16.80 0.00 40.75 4.30
65 66 7.776030 ACGGTCTCCCTCTACATCTATATATTG 59.224 40.741 0.00 0.00 0.00 1.90
90 91 4.330250 ACTGGATGCCTGTGAATATATGC 58.670 43.478 0.00 0.00 34.44 3.14
114 115 6.661377 GCCTGTTGTATCCTATCATCTCTCTA 59.339 42.308 0.00 0.00 0.00 2.43
124 1355 6.544197 TCCTATCATCTCTCTACACACAAGAC 59.456 42.308 0.00 0.00 0.00 3.01
126 1357 6.788598 ATCATCTCTCTACACACAAGACAT 57.211 37.500 0.00 0.00 0.00 3.06
127 1358 5.958955 TCATCTCTCTACACACAAGACATG 58.041 41.667 0.00 0.00 0.00 3.21
128 1359 4.790765 TCTCTCTACACACAAGACATGG 57.209 45.455 0.00 0.00 0.00 3.66
133 1364 1.597742 ACACACAAGACATGGTCAGC 58.402 50.000 0.00 0.00 34.60 4.26
143 1374 0.172578 CATGGTCAGCATTGCCACTG 59.827 55.000 4.70 0.00 34.71 3.66
145 1376 2.570181 GTCAGCATTGCCACTGCC 59.430 61.111 4.70 0.00 40.56 4.85
156 1387 1.443407 CCACTGCCACCGAGATAGG 59.557 63.158 0.00 0.00 37.30 2.57
171 1402 0.839946 ATAGGCCGAAGCAATGGAGT 59.160 50.000 0.00 0.00 42.56 3.85
180 1411 4.155826 CCGAAGCAATGGAGTACAATCAAA 59.844 41.667 0.00 0.00 0.00 2.69
195 1426 1.504359 TCAAACGGATCGACAACCAC 58.496 50.000 0.00 0.00 0.00 4.16
201 1432 4.806571 ATCGACAACCACGATCCG 57.193 55.556 0.00 0.00 45.32 4.18
202 1433 1.888018 ATCGACAACCACGATCCGT 59.112 52.632 0.00 0.00 45.32 4.69
203 1434 0.179145 ATCGACAACCACGATCCGTC 60.179 55.000 0.00 0.00 45.32 4.79
212 1443 4.463597 CGATCCGTCGGACGAAAA 57.536 55.556 30.33 15.94 46.05 2.29
242 1473 3.007290 AGTGATGGTCATATCGTCCATGG 59.993 47.826 4.97 4.97 42.74 3.66
245 1476 4.591072 TGATGGTCATATCGTCCATGGTAA 59.409 41.667 12.58 0.00 42.74 2.85
246 1477 4.330944 TGGTCATATCGTCCATGGTAAC 57.669 45.455 12.58 2.13 0.00 2.50
266 1497 4.412796 ACCACACCATGACAGAGATATG 57.587 45.455 0.00 0.00 0.00 1.78
303 1534 6.228273 TCAAGATTTTGACATCGAGAACAC 57.772 37.500 0.00 0.00 38.37 3.32
315 1546 7.272731 TGACATCGAGAACACGTATCTAAAAAG 59.727 37.037 3.25 0.00 34.70 2.27
316 1547 7.310664 ACATCGAGAACACGTATCTAAAAAGA 58.689 34.615 3.25 0.79 34.70 2.52
371 1603 7.839907 TGAATTACTCTTTCCATCCCAAAATG 58.160 34.615 0.00 0.00 0.00 2.32
372 1604 7.454380 TGAATTACTCTTTCCATCCCAAAATGT 59.546 33.333 0.00 0.00 0.00 2.71
375 1607 4.524328 ACTCTTTCCATCCCAAAATGTGTC 59.476 41.667 0.00 0.00 0.00 3.67
377 1609 5.147032 TCTTTCCATCCCAAAATGTGTCTT 58.853 37.500 0.00 0.00 0.00 3.01
379 1611 4.870123 TCCATCCCAAAATGTGTCTTTG 57.130 40.909 0.00 0.00 34.24 2.77
381 1613 4.280677 TCCATCCCAAAATGTGTCTTTGAC 59.719 41.667 0.00 0.00 36.12 3.18
382 1614 4.281688 CCATCCCAAAATGTGTCTTTGACT 59.718 41.667 0.00 0.00 36.12 3.41
385 1617 7.432869 CATCCCAAAATGTGTCTTTGACTTTA 58.567 34.615 0.00 0.00 36.12 1.85
386 1618 7.595819 TCCCAAAATGTGTCTTTGACTTTAT 57.404 32.000 0.00 0.00 36.12 1.40
387 1619 8.017418 TCCCAAAATGTGTCTTTGACTTTATT 57.983 30.769 0.00 0.00 36.12 1.40
388 1620 9.137459 TCCCAAAATGTGTCTTTGACTTTATTA 57.863 29.630 0.00 0.00 36.12 0.98
389 1621 9.191995 CCCAAAATGTGTCTTTGACTTTATTAC 57.808 33.333 0.00 0.00 36.12 1.89
390 1622 8.901748 CCAAAATGTGTCTTTGACTTTATTACG 58.098 33.333 0.00 0.00 36.12 3.18
393 1626 7.956420 ATGTGTCTTTGACTTTATTACGACA 57.044 32.000 0.00 0.00 33.15 4.35
399 1632 9.737025 GTCTTTGACTTTATTACGACATTGTAC 57.263 33.333 0.00 0.00 0.00 2.90
441 1687 7.734942 ACAAAATTGAGACATGTATTTTGGGT 58.265 30.769 29.99 17.83 45.43 4.51
442 1688 8.210265 ACAAAATTGAGACATGTATTTTGGGTT 58.790 29.630 29.99 17.37 45.43 4.11
443 1689 8.711457 CAAAATTGAGACATGTATTTTGGGTTC 58.289 33.333 24.39 2.27 41.13 3.62
444 1690 5.975693 TTGAGACATGTATTTTGGGTTCC 57.024 39.130 0.00 0.00 0.00 3.62
445 1691 5.255397 TGAGACATGTATTTTGGGTTCCT 57.745 39.130 0.00 0.00 0.00 3.36
446 1692 6.381498 TGAGACATGTATTTTGGGTTCCTA 57.619 37.500 0.00 0.00 0.00 2.94
447 1693 6.177610 TGAGACATGTATTTTGGGTTCCTAC 58.822 40.000 0.00 0.00 0.00 3.18
448 1694 6.012858 TGAGACATGTATTTTGGGTTCCTACT 60.013 38.462 0.00 0.00 0.00 2.57
449 1695 6.790319 AGACATGTATTTTGGGTTCCTACTT 58.210 36.000 0.00 0.00 0.00 2.24
451 1697 6.548321 ACATGTATTTTGGGTTCCTACTTGA 58.452 36.000 0.00 0.00 0.00 3.02
452 1698 6.433093 ACATGTATTTTGGGTTCCTACTTGAC 59.567 38.462 0.00 0.00 0.00 3.18
453 1699 5.942961 TGTATTTTGGGTTCCTACTTGACA 58.057 37.500 0.00 0.00 0.00 3.58
468 1720 4.130118 ACTTGACAACTTGACAGGTCATC 58.870 43.478 2.52 0.00 39.73 2.92
471 1723 3.876914 TGACAACTTGACAGGTCATCAAC 59.123 43.478 2.52 0.00 39.64 3.18
472 1724 2.872245 ACAACTTGACAGGTCATCAACG 59.128 45.455 2.52 0.00 39.64 4.10
473 1725 2.872245 CAACTTGACAGGTCATCAACGT 59.128 45.455 2.52 0.00 39.64 3.99
474 1726 3.194005 ACTTGACAGGTCATCAACGTT 57.806 42.857 2.52 0.00 39.64 3.99
475 1727 3.541632 ACTTGACAGGTCATCAACGTTT 58.458 40.909 0.00 0.00 39.64 3.60
476 1728 3.945285 ACTTGACAGGTCATCAACGTTTT 59.055 39.130 0.00 0.00 39.64 2.43
477 1729 4.398044 ACTTGACAGGTCATCAACGTTTTT 59.602 37.500 0.00 0.00 39.64 1.94
478 1730 4.285807 TGACAGGTCATCAACGTTTTTG 57.714 40.909 0.00 0.00 34.14 2.44
479 1731 3.692101 TGACAGGTCATCAACGTTTTTGT 59.308 39.130 0.00 0.00 34.14 2.83
483 1735 5.575218 ACAGGTCATCAACGTTTTTGTTTTC 59.425 36.000 0.00 0.00 0.00 2.29
492 1744 4.160594 ACGTTTTTGTTTTCCTTGTCGAC 58.839 39.130 9.11 9.11 0.00 4.20
494 1746 5.122082 ACGTTTTTGTTTTCCTTGTCGACTA 59.878 36.000 17.92 8.49 0.00 2.59
510 1762 1.402613 GACTAGGCCTCGTGTTCTCTC 59.597 57.143 15.82 0.00 0.00 3.20
555 1807 3.755628 GTCCGCTGCCCACGTAGA 61.756 66.667 0.00 0.00 0.00 2.59
556 1808 3.755628 TCCGCTGCCCACGTAGAC 61.756 66.667 0.00 0.00 0.00 2.59
567 1819 2.099831 CGTAGACGTCGGAGCACC 59.900 66.667 10.46 0.00 34.11 5.01
585 1837 1.514553 CAGCATGGCGAGAGAGACA 59.485 57.895 0.00 0.00 0.00 3.41
587 1839 1.882167 GCATGGCGAGAGAGACAGC 60.882 63.158 0.00 0.00 0.00 4.40
590 1842 4.200283 GGCGAGAGAGACAGCGGG 62.200 72.222 0.00 0.00 0.00 6.13
593 1845 4.200283 GAGAGAGACAGCGGGCCG 62.200 72.222 24.35 24.35 0.00 6.13
613 1865 2.045045 TGAATTCGCAGCCCCTGG 60.045 61.111 0.04 0.00 31.21 4.45
617 1869 2.552231 AATTCGCAGCCCCTGGTACC 62.552 60.000 4.43 4.43 31.21 3.34
629 1881 1.610967 TGGTACCGGCAGATCACCA 60.611 57.895 7.57 2.71 36.94 4.17
633 1885 0.616395 TACCGGCAGATCACCAGGAA 60.616 55.000 0.00 0.00 0.00 3.36
634 1886 1.153289 CCGGCAGATCACCAGGAAG 60.153 63.158 0.00 0.00 0.00 3.46
635 1887 1.153289 CGGCAGATCACCAGGAAGG 60.153 63.158 0.00 0.00 45.67 3.46
636 1888 1.617018 CGGCAGATCACCAGGAAGGA 61.617 60.000 0.00 0.00 41.22 3.36
637 1889 0.620556 GGCAGATCACCAGGAAGGAA 59.379 55.000 0.00 0.00 41.22 3.36
638 1890 1.004745 GGCAGATCACCAGGAAGGAAA 59.995 52.381 0.00 0.00 41.22 3.13
639 1891 2.363683 GCAGATCACCAGGAAGGAAAG 58.636 52.381 0.00 0.00 41.22 2.62
640 1892 2.026822 GCAGATCACCAGGAAGGAAAGA 60.027 50.000 0.00 0.00 41.22 2.52
658 1910 4.992381 AAGACGAGAAGAAATGAAACCG 57.008 40.909 0.00 0.00 0.00 4.44
685 1943 2.046892 CCACCTGGACGCTTCCTG 60.047 66.667 11.01 9.91 43.31 3.86
695 1953 4.357279 GCTTCCTGCCTGCCCACT 62.357 66.667 0.00 0.00 35.15 4.00
700 1958 2.434884 CTGCCTGCCCACTGTACG 60.435 66.667 0.00 0.00 0.00 3.67
708 1966 3.306225 CCTGCCCACTGTACGTTACTTAA 60.306 47.826 0.00 0.00 0.00 1.85
711 1969 3.588955 CCCACTGTACGTTACTTAACCC 58.411 50.000 0.00 0.00 32.69 4.11
714 1972 2.231235 ACTGTACGTTACTTAACCCGGG 59.769 50.000 22.25 22.25 32.69 5.73
715 1973 2.491693 CTGTACGTTACTTAACCCGGGA 59.508 50.000 32.02 1.07 32.69 5.14
716 1974 2.230266 TGTACGTTACTTAACCCGGGAC 59.770 50.000 32.02 12.37 32.69 4.46
850 2117 2.288825 TGTCGAGAGTCACCAAATCCAC 60.289 50.000 0.00 0.00 0.00 4.02
852 2119 1.079503 GAGAGTCACCAAATCCACGC 58.920 55.000 0.00 0.00 0.00 5.34
860 2127 4.722700 AAATCCACGCTGCCCGCT 62.723 61.111 0.00 0.00 41.76 5.52
883 2152 1.593787 CGATCCCCCATCCTCATCG 59.406 63.158 0.00 0.00 0.00 3.84
937 2206 2.032681 AGCCAGCCTTCACCGTTC 59.967 61.111 0.00 0.00 0.00 3.95
944 2213 0.385598 GCCTTCACCGTTCGAAAAGC 60.386 55.000 0.00 0.00 0.00 3.51
945 2214 1.226746 CCTTCACCGTTCGAAAAGCT 58.773 50.000 0.00 0.00 0.00 3.74
946 2215 1.602377 CCTTCACCGTTCGAAAAGCTT 59.398 47.619 0.00 0.00 0.00 3.74
947 2216 2.349532 CCTTCACCGTTCGAAAAGCTTC 60.350 50.000 0.00 0.00 0.00 3.86
948 2217 1.223187 TCACCGTTCGAAAAGCTTCC 58.777 50.000 0.00 0.00 0.00 3.46
949 2218 0.237498 CACCGTTCGAAAAGCTTCCC 59.763 55.000 0.00 0.00 0.00 3.97
950 2219 0.887836 ACCGTTCGAAAAGCTTCCCC 60.888 55.000 0.00 0.00 0.00 4.81
1001 2285 2.440247 CACCCAATTCCCCGAGCC 60.440 66.667 0.00 0.00 0.00 4.70
1716 3015 0.179111 CTACGCGCATCCTTCTTCCA 60.179 55.000 5.73 0.00 0.00 3.53
1718 3017 0.392998 ACGCGCATCCTTCTTCCATT 60.393 50.000 5.73 0.00 0.00 3.16
1732 3031 0.694444 TCCATTCTAGCACCCCCTCC 60.694 60.000 0.00 0.00 0.00 4.30
1733 3032 1.447643 CATTCTAGCACCCCCTCCG 59.552 63.158 0.00 0.00 0.00 4.63
1734 3033 2.444256 ATTCTAGCACCCCCTCCGC 61.444 63.158 0.00 0.00 0.00 5.54
1758 3057 1.633171 GTGTAGCTGCGATCTTGCG 59.367 57.895 0.00 0.00 37.81 4.85
1761 3060 0.526524 GTAGCTGCGATCTTGCGACT 60.527 55.000 0.00 0.00 37.81 4.18
2035 3695 8.494433 TGCTATTTGAGACAGTAAATTCCCTAT 58.506 33.333 0.00 0.00 0.00 2.57
2183 3843 6.602179 TGAGCACTTCTTGTTCATAAATTCG 58.398 36.000 0.00 0.00 40.27 3.34
2226 3886 5.184479 AGCCGATGTTCTAGTTGTAACACTA 59.816 40.000 0.00 0.00 38.35 2.74
2264 3924 3.295973 TGCTTTGGCCTTTACTCAAACT 58.704 40.909 3.32 0.00 37.74 2.66
2436 4199 8.879342 ATGACACTTGAAATAGTATGAGCTAC 57.121 34.615 0.00 0.00 0.00 3.58
2488 4258 5.638596 ACGGATGTTGATTAAAAAGGACC 57.361 39.130 0.00 0.00 0.00 4.46
2632 4630 3.727726 TCTGTTTGCGATGAAACTCTGA 58.272 40.909 0.00 0.00 36.86 3.27
2735 4946 1.927487 TGAATTTGTGGCCTGATGCT 58.073 45.000 3.32 0.00 40.92 3.79
2745 5135 1.475930 GGCCTGATGCTCTCCCTTTAC 60.476 57.143 0.00 0.00 40.92 2.01
2761 5151 4.412207 CCTTTACGCTTGATTTTGGTAGC 58.588 43.478 0.00 0.00 0.00 3.58
2861 5395 4.985538 TGGAGCTTCCACAATTACTTCTT 58.014 39.130 1.25 0.00 42.67 2.52
2895 5429 9.726438 TGATCGATCTGAACTCTAATATCAGTA 57.274 33.333 25.02 0.00 41.04 2.74
2909 5443 8.692710 TCTAATATCAGTACCGTCTTTCACATT 58.307 33.333 0.00 0.00 0.00 2.71
3415 6083 7.510549 TGGCTAATTATTCCAGATAAACAGC 57.489 36.000 3.27 0.00 0.00 4.40
3539 6409 3.253188 TCAATTGTCTGTAACTTGCTGGC 59.747 43.478 5.13 0.00 0.00 4.85
3730 6612 9.856162 TTGGTTTATAACAGTCCTAACTCTTTT 57.144 29.630 0.00 0.00 31.71 2.27
3731 6613 9.280174 TGGTTTATAACAGTCCTAACTCTTTTG 57.720 33.333 0.00 0.00 31.71 2.44
3741 6623 7.812669 CAGTCCTAACTCTTTTGTTTGTTTGTT 59.187 33.333 0.00 0.00 31.71 2.83
3743 6625 8.432359 GTCCTAACTCTTTTGTTTGTTTGTTTG 58.568 33.333 0.00 0.00 0.00 2.93
3744 6626 8.145122 TCCTAACTCTTTTGTTTGTTTGTTTGT 58.855 29.630 0.00 0.00 0.00 2.83
3745 6627 8.769891 CCTAACTCTTTTGTTTGTTTGTTTGTT 58.230 29.630 0.00 0.00 0.00 2.83
3747 6629 8.833976 AACTCTTTTGTTTGTTTGTTTGTTTG 57.166 26.923 0.00 0.00 0.00 2.93
3748 6630 7.980062 ACTCTTTTGTTTGTTTGTTTGTTTGT 58.020 26.923 0.00 0.00 0.00 2.83
3749 6631 8.454894 ACTCTTTTGTTTGTTTGTTTGTTTGTT 58.545 25.926 0.00 0.00 0.00 2.83
3750 6632 9.283420 CTCTTTTGTTTGTTTGTTTGTTTGTTT 57.717 25.926 0.00 0.00 0.00 2.83
3751 6633 9.065871 TCTTTTGTTTGTTTGTTTGTTTGTTTG 57.934 25.926 0.00 0.00 0.00 2.93
3752 6634 8.742554 TTTTGTTTGTTTGTTTGTTTGTTTGT 57.257 23.077 0.00 0.00 0.00 2.83
3753 6635 7.954906 TTGTTTGTTTGTTTGTTTGTTTGTC 57.045 28.000 0.00 0.00 0.00 3.18
3797 6679 6.548622 CAGTCAAGGTATTTCCCATCATCATT 59.451 38.462 0.00 0.00 36.75 2.57
3798 6680 6.548622 AGTCAAGGTATTTCCCATCATCATTG 59.451 38.462 0.00 0.00 36.75 2.82
3799 6681 6.322201 GTCAAGGTATTTCCCATCATCATTGT 59.678 38.462 0.00 0.00 36.75 2.71
3800 6682 7.502226 GTCAAGGTATTTCCCATCATCATTGTA 59.498 37.037 0.00 0.00 36.75 2.41
3835 6717 9.296400 ACAAACAAACACATTAATGTTCTGTAC 57.704 29.630 18.50 0.00 42.01 2.90
3844 6726 2.831685 ATGTTCTGTACTTCACCGCA 57.168 45.000 0.00 0.00 0.00 5.69
3907 6789 3.840666 TCAAGGAGAAGGACACAGCTTAT 59.159 43.478 0.00 0.00 0.00 1.73
4022 6904 3.290710 AGCTTTGAGTGTGTTGTTCCAT 58.709 40.909 0.00 0.00 0.00 3.41
4023 6905 3.067180 AGCTTTGAGTGTGTTGTTCCATG 59.933 43.478 0.00 0.00 0.00 3.66
4032 6917 3.181505 TGTGTTGTTCCATGTGTCGAAAC 60.182 43.478 0.00 0.00 0.00 2.78
4042 6927 4.286910 CATGTGTCGAAACGTTTTTCCAT 58.713 39.130 15.89 10.17 38.35 3.41
4059 6944 2.232941 TCCATCGGAGGTGTAGTTTGTC 59.767 50.000 0.00 0.00 0.00 3.18
4119 7004 1.272147 ACCCTGGAGATTGGAAACTGC 60.272 52.381 0.00 0.00 0.00 4.40
4120 7005 1.467920 CCTGGAGATTGGAAACTGCC 58.532 55.000 0.00 0.00 0.00 4.85
4121 7006 1.005215 CCTGGAGATTGGAAACTGCCT 59.995 52.381 0.00 0.00 0.00 4.75
4122 7007 2.239654 CCTGGAGATTGGAAACTGCCTA 59.760 50.000 0.00 0.00 0.00 3.93
4127 7028 4.446889 GGAGATTGGAAACTGCCTATGGAT 60.447 45.833 0.00 0.00 0.00 3.41
4151 7052 3.648339 TTGGAACTCTGAAAATGCTGC 57.352 42.857 0.00 0.00 0.00 5.25
4164 7065 2.354305 GCTGCCGCATATGCTTGC 60.354 61.111 24.56 24.38 39.32 4.01
4169 7070 0.883814 GCCGCATATGCTTGCTCTCT 60.884 55.000 24.56 0.00 40.54 3.10
4170 7071 1.590932 CCGCATATGCTTGCTCTCTT 58.409 50.000 24.56 0.00 40.54 2.85
4171 7072 1.945394 CCGCATATGCTTGCTCTCTTT 59.055 47.619 24.56 0.00 40.54 2.52
4189 7090 4.536364 CTTTCTTCGCTGAAAGTTGTCA 57.464 40.909 16.53 0.00 44.53 3.58
4209 7110 5.241506 TGTCATTTTCAGTGAGATTGGGTTC 59.758 40.000 5.90 0.00 0.00 3.62
4261 7165 8.642908 AGGCTTAGTTCAAAATTTGTTTACAC 57.357 30.769 5.56 0.00 0.00 2.90
4438 7349 1.413445 TGCAGCACCAAAAAGCAATCT 59.587 42.857 0.00 0.00 31.42 2.40
4503 7429 4.247258 CAGAGCCAAAATAGCAAATGCAA 58.753 39.130 8.28 0.00 45.16 4.08
4575 7504 0.373716 CGAGCGGCTTGTAACCATTC 59.626 55.000 2.97 0.00 0.00 2.67
4590 7519 2.432510 ACCATTCGGACTTCCAGAGATC 59.567 50.000 0.00 0.00 35.59 2.75
4596 7525 1.760029 GGACTTCCAGAGATCTCACCC 59.240 57.143 24.39 10.08 35.64 4.61
4605 7534 4.372656 CAGAGATCTCACCCGATTTAACC 58.627 47.826 24.39 0.00 0.00 2.85
4747 7676 0.611200 CACCTGGAATACCACCGTCA 59.389 55.000 0.00 0.00 41.77 4.35
4779 7708 0.322456 CGAGGAAGACCCAATTGCCA 60.322 55.000 0.00 0.00 37.41 4.92
4867 7796 4.986034 ACAACATCGTCGAAAGTACATTGA 59.014 37.500 0.00 0.00 0.00 2.57
4885 7814 4.742438 TTGACATTAGTTCGCCAGTTTC 57.258 40.909 0.00 0.00 0.00 2.78
4907 7836 7.591006 TTCGAACAAGGATGTAAATGACTAC 57.409 36.000 0.00 0.00 39.40 2.73
4915 7847 6.779860 AGGATGTAAATGACTACAAGGTGTT 58.220 36.000 0.00 0.00 35.48 3.32
4946 7878 1.102154 CACTCACCTGGCAAAACACA 58.898 50.000 0.00 0.00 0.00 3.72
4961 7893 7.014711 TGGCAAAACACAAAGGAGTTGAATATA 59.985 33.333 0.00 0.00 39.87 0.86
4991 7923 1.279271 AGAACGGTCTTGGAATCTGGG 59.721 52.381 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.666577 GGGAGACCGTCACGTTCAAG 60.667 60.000 0.00 0.00 43.64 3.02
43 44 7.561722 GTGCCAATATATAGATGTAGAGGGAGA 59.438 40.741 0.00 0.00 0.00 3.71
44 45 7.563188 AGTGCCAATATATAGATGTAGAGGGAG 59.437 40.741 0.00 0.00 0.00 4.30
45 46 7.343057 CAGTGCCAATATATAGATGTAGAGGGA 59.657 40.741 0.00 0.00 0.00 4.20
50 51 8.883954 CATCCAGTGCCAATATATAGATGTAG 57.116 38.462 0.00 0.00 0.00 2.74
77 78 7.164122 AGGATACAACAGGCATATATTCACAG 58.836 38.462 0.00 0.00 41.41 3.66
88 89 5.150715 AGAGATGATAGGATACAACAGGCA 58.849 41.667 0.00 0.00 41.41 4.75
89 90 5.480073 AGAGAGATGATAGGATACAACAGGC 59.520 44.000 0.00 0.00 41.41 4.85
90 91 7.667635 TGTAGAGAGATGATAGGATACAACAGG 59.332 40.741 0.00 0.00 41.41 4.00
114 115 1.134128 TGCTGACCATGTCTTGTGTGT 60.134 47.619 0.00 0.00 33.15 3.72
124 1355 0.172578 CAGTGGCAATGCTGACCATG 59.827 55.000 4.82 0.00 34.87 3.66
126 1357 2.270257 GCAGTGGCAATGCTGACCA 61.270 57.895 30.43 0.00 40.59 4.02
127 1358 2.570181 GCAGTGGCAATGCTGACC 59.430 61.111 30.43 3.11 40.59 4.02
128 1359 2.270257 TGGCAGTGGCAATGCTGAC 61.270 57.895 34.65 21.17 43.35 3.51
133 1364 2.672651 TCGGTGGCAGTGGCAATG 60.673 61.111 22.39 16.30 43.71 2.82
143 1374 2.701163 CTTCGGCCTATCTCGGTGGC 62.701 65.000 0.00 0.00 45.42 5.01
145 1376 1.300233 GCTTCGGCCTATCTCGGTG 60.300 63.158 0.00 0.00 34.32 4.94
156 1387 1.448985 TTGTACTCCATTGCTTCGGC 58.551 50.000 0.00 0.00 42.19 5.54
171 1402 3.680937 GGTTGTCGATCCGTTTGATTGTA 59.319 43.478 0.00 0.00 36.40 2.41
180 1411 1.888018 ATCGTGGTTGTCGATCCGT 59.112 52.632 0.00 0.00 43.12 4.69
225 1456 3.070446 GGTTACCATGGACGATATGACCA 59.930 47.826 21.47 0.00 46.39 4.02
226 1457 3.070446 TGGTTACCATGGACGATATGACC 59.930 47.826 21.47 11.64 0.00 4.02
242 1473 3.678056 TCTCTGTCATGGTGTGGTTAC 57.322 47.619 0.00 0.00 0.00 2.50
245 1476 4.033009 TCATATCTCTGTCATGGTGTGGT 58.967 43.478 0.00 0.00 0.00 4.16
246 1477 4.629092 CTCATATCTCTGTCATGGTGTGG 58.371 47.826 0.00 0.00 0.00 4.17
286 1517 5.466819 AGATACGTGTTCTCGATGTCAAAA 58.533 37.500 0.00 0.00 34.70 2.44
289 1520 5.806366 TTAGATACGTGTTCTCGATGTCA 57.194 39.130 0.00 0.00 34.70 3.58
290 1521 7.484007 TCTTTTTAGATACGTGTTCTCGATGTC 59.516 37.037 0.00 0.00 34.70 3.06
291 1522 7.310664 TCTTTTTAGATACGTGTTCTCGATGT 58.689 34.615 0.00 0.00 34.70 3.06
347 1579 7.761249 CACATTTTGGGATGGAAAGAGTAATTC 59.239 37.037 0.00 0.00 0.00 2.17
350 1582 6.074648 ACACATTTTGGGATGGAAAGAGTAA 58.925 36.000 0.00 0.00 0.00 2.24
353 1585 4.768968 AGACACATTTTGGGATGGAAAGAG 59.231 41.667 0.00 0.00 0.00 2.85
355 1587 5.473066 AAGACACATTTTGGGATGGAAAG 57.527 39.130 0.00 0.00 0.00 2.62
356 1588 5.365025 TCAAAGACACATTTTGGGATGGAAA 59.635 36.000 0.00 0.00 36.44 3.13
357 1589 4.898265 TCAAAGACACATTTTGGGATGGAA 59.102 37.500 0.00 0.00 36.44 3.53
364 1596 8.901748 CGTAATAAAGTCAAAGACACATTTTGG 58.098 33.333 0.00 0.00 36.44 3.28
371 1603 8.280497 ACAATGTCGTAATAAAGTCAAAGACAC 58.720 33.333 0.00 0.00 39.68 3.67
372 1604 8.373048 ACAATGTCGTAATAAAGTCAAAGACA 57.627 30.769 0.00 0.00 40.86 3.41
417 1650 8.606040 AACCCAAAATACATGTCTCAATTTTG 57.394 30.769 24.81 24.81 43.77 2.44
421 1654 6.256053 AGGAACCCAAAATACATGTCTCAAT 58.744 36.000 0.00 0.00 0.00 2.57
441 1687 4.163458 ACCTGTCAAGTTGTCAAGTAGGAA 59.837 41.667 12.17 0.00 0.00 3.36
442 1688 3.709653 ACCTGTCAAGTTGTCAAGTAGGA 59.290 43.478 12.17 3.14 0.00 2.94
443 1689 4.058817 GACCTGTCAAGTTGTCAAGTAGG 58.941 47.826 2.11 3.94 0.00 3.18
444 1690 4.693283 TGACCTGTCAAGTTGTCAAGTAG 58.307 43.478 2.11 0.00 36.53 2.57
445 1691 4.746535 TGACCTGTCAAGTTGTCAAGTA 57.253 40.909 2.11 0.00 36.53 2.24
446 1692 3.627395 TGACCTGTCAAGTTGTCAAGT 57.373 42.857 4.34 4.34 36.53 3.16
447 1693 4.129380 TGATGACCTGTCAAGTTGTCAAG 58.871 43.478 3.79 0.00 43.58 3.02
448 1694 4.149511 TGATGACCTGTCAAGTTGTCAA 57.850 40.909 3.79 0.00 43.58 3.18
449 1695 3.836365 TGATGACCTGTCAAGTTGTCA 57.164 42.857 3.79 2.50 43.58 3.58
451 1697 2.872245 CGTTGATGACCTGTCAAGTTGT 59.128 45.455 3.79 0.00 43.58 3.32
452 1698 2.872245 ACGTTGATGACCTGTCAAGTTG 59.128 45.455 3.79 0.00 43.58 3.16
453 1699 3.194005 ACGTTGATGACCTGTCAAGTT 57.806 42.857 3.79 0.00 43.58 2.66
468 1720 4.617645 TCGACAAGGAAAACAAAAACGTTG 59.382 37.500 0.00 0.00 35.31 4.10
471 1723 4.408694 AGTCGACAAGGAAAACAAAAACG 58.591 39.130 19.50 0.00 0.00 3.60
472 1724 5.969435 CCTAGTCGACAAGGAAAACAAAAAC 59.031 40.000 19.50 0.00 34.58 2.43
473 1725 5.449451 GCCTAGTCGACAAGGAAAACAAAAA 60.449 40.000 19.50 0.00 34.58 1.94
474 1726 4.035909 GCCTAGTCGACAAGGAAAACAAAA 59.964 41.667 19.50 0.00 34.58 2.44
475 1727 3.562557 GCCTAGTCGACAAGGAAAACAAA 59.437 43.478 19.50 0.00 34.58 2.83
476 1728 3.135994 GCCTAGTCGACAAGGAAAACAA 58.864 45.455 19.50 0.00 34.58 2.83
477 1729 2.549349 GGCCTAGTCGACAAGGAAAACA 60.549 50.000 19.50 0.00 34.58 2.83
478 1730 2.074576 GGCCTAGTCGACAAGGAAAAC 58.925 52.381 19.50 0.00 34.58 2.43
479 1731 1.975680 AGGCCTAGTCGACAAGGAAAA 59.024 47.619 19.50 0.00 34.58 2.29
483 1735 1.313812 ACGAGGCCTAGTCGACAAGG 61.314 60.000 19.50 6.88 39.92 3.61
492 1744 0.378962 CGAGAGAACACGAGGCCTAG 59.621 60.000 4.42 8.81 32.29 3.02
494 1746 2.995872 GCGAGAGAACACGAGGCCT 61.996 63.158 3.86 3.86 32.29 5.19
555 1807 3.695606 ATGCTGGTGCTCCGACGT 61.696 61.111 0.00 0.00 40.48 4.34
556 1808 3.190849 CATGCTGGTGCTCCGACG 61.191 66.667 0.00 0.00 40.48 5.12
557 1809 2.821366 CCATGCTGGTGCTCCGAC 60.821 66.667 0.00 0.00 40.48 4.79
558 1810 4.783621 GCCATGCTGGTGCTCCGA 62.784 66.667 0.00 0.00 40.46 4.55
566 1818 1.227205 GTCTCTCTCGCCATGCTGG 60.227 63.158 0.00 0.00 41.55 4.85
567 1819 0.528033 CTGTCTCTCTCGCCATGCTG 60.528 60.000 0.00 0.00 0.00 4.41
585 1837 2.125106 GAATTCAGACGGCCCGCT 60.125 61.111 1.23 0.00 0.00 5.52
587 1839 3.564027 GCGAATTCAGACGGCCCG 61.564 66.667 0.00 0.00 0.00 6.13
590 1842 2.401195 GCTGCGAATTCAGACGGC 59.599 61.111 6.22 7.17 36.19 5.68
593 1845 1.078143 AGGGGCTGCGAATTCAGAC 60.078 57.895 6.22 0.00 41.37 3.51
613 1865 1.144057 CCTGGTGATCTGCCGGTAC 59.856 63.158 1.90 0.00 0.00 3.34
617 1869 1.153289 CCTTCCTGGTGATCTGCCG 60.153 63.158 0.00 0.00 0.00 5.69
620 1872 3.604582 GTCTTTCCTTCCTGGTGATCTG 58.395 50.000 0.00 0.00 37.07 2.90
629 1881 4.957684 TTTCTTCTCGTCTTTCCTTCCT 57.042 40.909 0.00 0.00 0.00 3.36
633 1885 5.470437 GGTTTCATTTCTTCTCGTCTTTCCT 59.530 40.000 0.00 0.00 0.00 3.36
634 1886 5.614887 CGGTTTCATTTCTTCTCGTCTTTCC 60.615 44.000 0.00 0.00 0.00 3.13
635 1887 5.374898 CGGTTTCATTTCTTCTCGTCTTTC 58.625 41.667 0.00 0.00 0.00 2.62
636 1888 4.319549 GCGGTTTCATTTCTTCTCGTCTTT 60.320 41.667 0.00 0.00 0.00 2.52
637 1889 3.186613 GCGGTTTCATTTCTTCTCGTCTT 59.813 43.478 0.00 0.00 0.00 3.01
638 1890 2.737252 GCGGTTTCATTTCTTCTCGTCT 59.263 45.455 0.00 0.00 0.00 4.18
639 1891 2.472397 CGCGGTTTCATTTCTTCTCGTC 60.472 50.000 0.00 0.00 0.00 4.20
640 1892 1.459592 CGCGGTTTCATTTCTTCTCGT 59.540 47.619 0.00 0.00 0.00 4.18
683 1941 2.434884 CGTACAGTGGGCAGGCAG 60.435 66.667 0.00 0.00 0.00 4.85
685 1943 1.017701 GTAACGTACAGTGGGCAGGC 61.018 60.000 0.00 0.00 0.00 4.85
693 1951 2.231235 CCCGGGTTAAGTAACGTACAGT 59.769 50.000 14.18 0.00 37.07 3.55
694 1952 2.491693 TCCCGGGTTAAGTAACGTACAG 59.508 50.000 22.86 0.00 37.07 2.74
695 1953 2.230266 GTCCCGGGTTAAGTAACGTACA 59.770 50.000 22.86 0.00 37.07 2.90
700 1958 1.000843 ACACGTCCCGGGTTAAGTAAC 59.999 52.381 22.86 8.42 42.45 2.50
714 1972 3.336566 CGGGTTGGGAAACACGTC 58.663 61.111 5.13 0.00 43.97 4.34
717 1975 3.299977 GGGCGGGTTGGGAAACAC 61.300 66.667 0.00 0.00 0.00 3.32
718 1976 2.873557 TTTGGGCGGGTTGGGAAACA 62.874 55.000 0.00 0.00 0.00 2.83
719 1977 1.687297 TTTTGGGCGGGTTGGGAAAC 61.687 55.000 0.00 0.00 0.00 2.78
721 1979 1.382695 TTTTTGGGCGGGTTGGGAA 60.383 52.632 0.00 0.00 0.00 3.97
722 1980 2.282446 TTTTTGGGCGGGTTGGGA 59.718 55.556 0.00 0.00 0.00 4.37
742 2000 3.063725 TGACACGTTCCGGTAAGTTTTTG 59.936 43.478 0.00 0.00 0.00 2.44
743 2001 3.269178 TGACACGTTCCGGTAAGTTTTT 58.731 40.909 0.00 0.00 0.00 1.94
744 2002 2.867975 CTGACACGTTCCGGTAAGTTTT 59.132 45.455 0.00 0.00 0.00 2.43
745 2003 2.476821 CTGACACGTTCCGGTAAGTTT 58.523 47.619 0.00 0.00 0.00 2.66
747 2005 0.316204 CCTGACACGTTCCGGTAAGT 59.684 55.000 0.00 0.00 0.00 2.24
748 2006 0.389426 CCCTGACACGTTCCGGTAAG 60.389 60.000 0.00 0.00 0.00 2.34
749 2007 0.827089 TCCCTGACACGTTCCGGTAA 60.827 55.000 0.00 0.00 0.00 2.85
750 2008 1.228521 TCCCTGACACGTTCCGGTA 60.229 57.895 0.00 0.00 0.00 4.02
751 2009 2.522436 TCCCTGACACGTTCCGGT 60.522 61.111 0.00 0.00 0.00 5.28
754 2012 1.372623 GTCGTCCCTGACACGTTCC 60.373 63.158 0.00 0.00 38.75 3.62
793 2051 1.335324 GCCATGCGTATCTTGGATTGC 60.335 52.381 0.00 0.00 41.25 3.56
797 2055 0.179048 CAGGCCATGCGTATCTTGGA 60.179 55.000 5.01 0.00 41.25 3.53
818 2084 1.004277 CTCTCGACAAGTCACCACGC 61.004 60.000 0.72 0.00 0.00 5.34
820 2086 1.337071 TGACTCTCGACAAGTCACCAC 59.663 52.381 17.73 0.00 46.15 4.16
863 2130 1.539869 ATGAGGATGGGGGATCGGG 60.540 63.158 0.00 0.00 30.87 5.14
864 2131 1.892819 CGATGAGGATGGGGGATCGG 61.893 65.000 0.00 0.00 33.82 4.18
866 2133 1.298014 GCGATGAGGATGGGGGATC 59.702 63.158 0.00 0.00 0.00 3.36
867 2134 0.843782 ATGCGATGAGGATGGGGGAT 60.844 55.000 0.00 0.00 0.00 3.85
868 2135 0.178906 TATGCGATGAGGATGGGGGA 60.179 55.000 0.00 0.00 31.61 4.81
871 2138 3.885297 AGTTTTTATGCGATGAGGATGGG 59.115 43.478 0.00 0.00 31.61 4.00
874 2141 4.336433 CACCAGTTTTTATGCGATGAGGAT 59.664 41.667 0.00 0.00 34.41 3.24
875 2142 3.689161 CACCAGTTTTTATGCGATGAGGA 59.311 43.478 0.00 0.00 0.00 3.71
883 2152 1.402325 GGGTCGCACCAGTTTTTATGC 60.402 52.381 7.49 0.00 41.02 3.14
918 2187 3.850098 AACGGTGAAGGCTGGCTGG 62.850 63.158 3.84 0.00 0.00 4.85
919 2188 2.281761 AACGGTGAAGGCTGGCTG 60.282 61.111 3.84 0.00 0.00 4.85
920 2189 2.032681 GAACGGTGAAGGCTGGCT 59.967 61.111 0.00 0.00 0.00 4.75
921 2190 3.423154 CGAACGGTGAAGGCTGGC 61.423 66.667 0.00 0.00 0.00 4.85
922 2191 0.882927 TTTCGAACGGTGAAGGCTGG 60.883 55.000 0.00 0.00 0.00 4.85
923 2192 0.941542 TTTTCGAACGGTGAAGGCTG 59.058 50.000 0.00 0.00 0.00 4.85
937 2206 1.616159 TTCCTTGGGGAAGCTTTTCG 58.384 50.000 0.00 0.00 45.72 3.46
946 2215 1.591768 GAGGTGGTATTCCTTGGGGA 58.408 55.000 0.00 0.00 40.36 4.81
947 2216 0.180406 CGAGGTGGTATTCCTTGGGG 59.820 60.000 0.00 0.00 35.20 4.96
948 2217 0.463833 GCGAGGTGGTATTCCTTGGG 60.464 60.000 0.00 0.00 37.06 4.12
949 2218 0.463833 GGCGAGGTGGTATTCCTTGG 60.464 60.000 0.00 0.00 37.06 3.61
950 2219 0.810031 CGGCGAGGTGGTATTCCTTG 60.810 60.000 0.00 0.00 38.97 3.61
1053 2337 2.305314 TAGCCTCCTCCTCCTCCTGC 62.305 65.000 0.00 0.00 0.00 4.85
1054 2338 0.469144 GTAGCCTCCTCCTCCTCCTG 60.469 65.000 0.00 0.00 0.00 3.86
1055 2339 1.935191 GTAGCCTCCTCCTCCTCCT 59.065 63.158 0.00 0.00 0.00 3.69
1232 2522 2.040606 TAGGACTGGGGCTGGGAC 59.959 66.667 0.00 0.00 0.00 4.46
1716 3015 2.444256 GCGGAGGGGGTGCTAGAAT 61.444 63.158 0.00 0.00 0.00 2.40
1718 3017 3.618855 AAGCGGAGGGGGTGCTAGA 62.619 63.158 0.00 0.00 38.17 2.43
1732 3031 2.778679 GCAGCTACACGGAAAGCG 59.221 61.111 0.00 0.00 43.63 4.68
1733 3032 1.084370 ATCGCAGCTACACGGAAAGC 61.084 55.000 3.50 0.00 39.08 3.51
1734 3033 0.924090 GATCGCAGCTACACGGAAAG 59.076 55.000 3.50 0.00 0.00 2.62
1775 3074 4.518970 CCGAAATCTTTCTCCACAGGAAAA 59.481 41.667 1.56 0.00 35.07 2.29
1776 3075 4.072131 CCGAAATCTTTCTCCACAGGAAA 58.928 43.478 1.56 0.00 35.07 3.13
1777 3076 3.072476 ACCGAAATCTTTCTCCACAGGAA 59.928 43.478 1.56 0.00 35.07 3.36
1778 3077 2.637872 ACCGAAATCTTTCTCCACAGGA 59.362 45.455 1.56 0.00 35.07 3.86
1792 3091 2.566913 TGTGCACTGTTGTACCGAAAT 58.433 42.857 19.41 0.00 37.53 2.17
2035 3695 7.339212 CCATGATGAACAAGGTTAAACAGGATA 59.661 37.037 0.00 0.00 33.27 2.59
2183 3843 7.652300 TCGGCTATCACACAAAATACATATC 57.348 36.000 0.00 0.00 0.00 1.63
2322 3982 2.167693 TCTAAACACCATAGCCACGGAG 59.832 50.000 0.00 0.00 0.00 4.63
2409 4172 6.699204 AGCTCATACTATTTCAAGTGTCATCG 59.301 38.462 0.00 0.00 0.00 3.84
2467 4237 5.183140 ACTGGTCCTTTTTAATCAACATCCG 59.817 40.000 0.00 0.00 0.00 4.18
2657 4656 5.353394 TGACTTACATACCAAGTGGATCC 57.647 43.478 4.20 4.20 36.38 3.36
2706 4917 2.741228 GCCACAAATTCAAACTGTGCCA 60.741 45.455 2.29 0.00 39.30 4.92
2735 4946 3.756434 CCAAAATCAAGCGTAAAGGGAGA 59.244 43.478 0.00 0.00 0.00 3.71
2745 5135 3.559238 ACTTGCTACCAAAATCAAGCG 57.441 42.857 0.00 0.00 39.45 4.68
2861 5395 7.867305 AGAGTTCAGATCGATCAAGTAGTTA 57.133 36.000 26.47 0.76 0.00 2.24
2873 5407 7.095144 ACGGTACTGATATTAGAGTTCAGATCG 60.095 40.741 9.17 8.39 39.36 3.69
2895 5429 2.930826 ACTGGAATGTGAAAGACGGT 57.069 45.000 0.00 0.00 0.00 4.83
2941 5480 4.322804 GCAATGCTGAATTCGAAGTTTCAG 59.677 41.667 26.45 26.45 44.87 3.02
3448 6318 9.232473 GAACAAATAAAGTTGAAGTCCCTAGAT 57.768 33.333 0.00 0.00 32.59 1.98
3730 6612 7.308782 AGACAAACAAACAAACAAACAAACA 57.691 28.000 0.00 0.00 0.00 2.83
3731 6613 9.312146 CATAGACAAACAAACAAACAAACAAAC 57.688 29.630 0.00 0.00 0.00 2.93
3734 6616 6.646653 TGCATAGACAAACAAACAAACAAACA 59.353 30.769 0.00 0.00 0.00 2.83
3735 6617 7.054855 TGCATAGACAAACAAACAAACAAAC 57.945 32.000 0.00 0.00 0.00 2.93
3741 6623 4.400884 ACACCTGCATAGACAAACAAACAA 59.599 37.500 0.00 0.00 0.00 2.83
3743 6625 4.568152 ACACCTGCATAGACAAACAAAC 57.432 40.909 0.00 0.00 0.00 2.93
3744 6626 4.930963 CAACACCTGCATAGACAAACAAA 58.069 39.130 0.00 0.00 0.00 2.83
3745 6627 4.566545 CAACACCTGCATAGACAAACAA 57.433 40.909 0.00 0.00 0.00 2.83
3835 6717 3.252215 TGAAACCAATTAGTGCGGTGAAG 59.748 43.478 0.00 0.00 31.94 3.02
3844 6726 8.047310 CCCTACAGAAGTATGAAACCAATTAGT 58.953 37.037 0.00 0.00 0.00 2.24
3907 6789 0.181587 TGAAAGTTGCAGACCCGGAA 59.818 50.000 0.73 0.00 0.00 4.30
3976 6858 3.746492 GTCTTTGTATTGAACTGCGGAGT 59.254 43.478 2.68 2.68 0.00 3.85
3981 6863 4.453819 AGCTCAGTCTTTGTATTGAACTGC 59.546 41.667 0.00 0.00 0.00 4.40
4022 6904 3.544440 CGATGGAAAAACGTTTCGACACA 60.544 43.478 15.01 9.73 43.56 3.72
4023 6905 2.962191 CGATGGAAAAACGTTTCGACAC 59.038 45.455 15.01 4.31 43.56 3.67
4032 6917 1.519408 ACACCTCCGATGGAAAAACG 58.481 50.000 0.73 0.00 0.00 3.60
4042 6927 2.589720 TCAGACAAACTACACCTCCGA 58.410 47.619 0.00 0.00 0.00 4.55
4059 6944 3.727079 GCAGCAACATCACTCGAATTCAG 60.727 47.826 6.22 4.96 0.00 3.02
4119 7004 4.080356 TCAGAGTTCCAAACCATCCATAGG 60.080 45.833 0.00 0.00 0.00 2.57
4120 7005 5.102953 TCAGAGTTCCAAACCATCCATAG 57.897 43.478 0.00 0.00 0.00 2.23
4121 7006 5.512942 TTCAGAGTTCCAAACCATCCATA 57.487 39.130 0.00 0.00 0.00 2.74
4122 7007 4.387026 TTCAGAGTTCCAAACCATCCAT 57.613 40.909 0.00 0.00 0.00 3.41
4127 7028 3.960102 AGCATTTTCAGAGTTCCAAACCA 59.040 39.130 0.00 0.00 0.00 3.67
4169 7070 5.499139 AATGACAACTTTCAGCGAAGAAA 57.501 34.783 4.84 0.00 36.21 2.52
4170 7071 5.499139 AAATGACAACTTTCAGCGAAGAA 57.501 34.783 4.84 0.00 0.00 2.52
4171 7072 5.065859 TGAAAATGACAACTTTCAGCGAAGA 59.934 36.000 10.49 0.00 36.79 2.87
4189 7090 5.634118 TCAGAACCCAATCTCACTGAAAAT 58.366 37.500 0.00 0.00 32.66 1.82
4261 7165 9.942850 ATTTCAGGTTAATTTAGGTTTGATTGG 57.057 29.630 0.00 0.00 0.00 3.16
4376 7286 2.292845 GGCTTGAGAATCCTATTGCTGC 59.707 50.000 0.00 0.00 0.00 5.25
4575 7504 1.407258 GGTGAGATCTCTGGAAGTCCG 59.593 57.143 22.95 0.00 39.43 4.79
4590 7519 2.389962 TTCCGGTTAAATCGGGTGAG 57.610 50.000 15.64 0.00 46.78 3.51
4596 7525 3.126171 TGAAGTGCATTCCGGTTAAATCG 59.874 43.478 0.00 0.00 37.08 3.34
4605 7534 3.201290 AGCTATCTTGAAGTGCATTCCG 58.799 45.455 0.00 0.00 37.08 4.30
4710 7639 2.932614 GGTGGTGATCATCGAGTTTCTG 59.067 50.000 0.00 0.00 0.00 3.02
4747 7676 1.411612 CTTCCTCGGGGTAATAAGCGT 59.588 52.381 0.00 0.00 0.00 5.07
4779 7708 1.821216 ACATTTTCCGCGGTCTCATT 58.179 45.000 27.15 3.95 0.00 2.57
4867 7796 3.034721 TCGAAACTGGCGAACTAATGT 57.965 42.857 0.00 0.00 34.45 2.71
4885 7814 6.961359 TGTAGTCATTTACATCCTTGTTCG 57.039 37.500 0.00 0.00 37.28 3.95
4892 7821 7.174253 TGAAACACCTTGTAGTCATTTACATCC 59.826 37.037 0.00 0.00 33.81 3.51
4915 7847 2.815503 CAGGTGAGTGATGCATTGTGAA 59.184 45.455 0.00 0.00 0.00 3.18
4946 7878 6.653320 TCAACACGCTTATATTCAACTCCTTT 59.347 34.615 0.00 0.00 0.00 3.11
4961 7893 0.104304 AGACCGTTCTCAACACGCTT 59.896 50.000 0.00 0.00 36.27 4.68


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

AutoCloner maintained by Alex Coulton.