Multiple sequence alignment - TraesCS3B01G148100

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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 TraesCS3B01G148100 chr3B 100.000 7652 0 0 1 7652 139416381 139408730 0.000000e+00 14131
1 TraesCS3B01G148100 chr3B 80.372 3276 542 66 1319 4529 622394951 622398190 0.000000e+00 2394
2 TraesCS3B01G148100 chr3B 84.211 323 50 1 4584 4906 622398558 622398879 5.760000e-81 313
3 TraesCS3B01G148100 chr3B 82.759 261 43 2 4963 5222 622399026 622399285 1.660000e-56 231
4 TraesCS3B01G148100 chr3B 93.333 90 5 1 5994 6082 817821050 817821139 1.730000e-26 132
5 TraesCS3B01G148100 chr3A 95.313 5078 182 22 333 5393 106441443 106436405 0.000000e+00 8008
6 TraesCS3B01G148100 chr3A 79.465 3287 525 92 1322 4529 610541296 610544511 0.000000e+00 2193
7 TraesCS3B01G148100 chr3A 86.881 1616 124 35 6083 7652 106435835 106434262 0.000000e+00 1729
8 TraesCS3B01G148100 chr3A 96.796 593 18 1 5404 5996 106436421 106435830 0.000000e+00 989
9 TraesCS3B01G148100 chr3A 80.943 488 79 8 5455 5942 610546224 610546697 2.610000e-99 374
10 TraesCS3B01G148100 chr3A 86.774 310 40 1 4597 4906 610545408 610545716 2.040000e-90 344
11 TraesCS3B01G148100 chr3A 77.778 468 84 17 6190 6644 610546770 610547230 3.520000e-68 270
12 TraesCS3B01G148100 chr3A 82.824 262 43 2 4963 5223 610545858 610546118 4.620000e-57 233
13 TraesCS3B01G148100 chr3A 95.238 105 3 2 67 171 106443129 106443027 1.710000e-36 165
14 TraesCS3B01G148100 chr3A 91.489 94 6 2 5994 6085 63069233 63069140 2.240000e-25 128
15 TraesCS3B01G148100 chr3A 92.222 90 6 1 5994 6082 740349458 740349547 8.060000e-25 126
16 TraesCS3B01G148100 chr3D 96.890 4469 116 9 932 5393 89904012 89899560 0.000000e+00 7461
17 TraesCS3B01G148100 chr3D 80.623 3277 529 68 1322 4529 468758883 468762122 0.000000e+00 2436
18 TraesCS3B01G148100 chr3D 87.549 1518 125 35 6166 7652 89898936 89897452 0.000000e+00 1698
19 TraesCS3B01G148100 chr3D 95.525 581 21 3 5411 5987 89899570 89898991 0.000000e+00 924
20 TraesCS3B01G148100 chr3D 83.732 418 38 10 398 814 89904455 89904067 1.210000e-97 368
21 TraesCS3B01G148100 chr3D 87.097 310 39 1 4597 4906 468762707 468763015 4.390000e-92 350
22 TraesCS3B01G148100 chr3D 82.759 261 43 2 4963 5222 468763156 468763415 1.660000e-56 231
23 TraesCS3B01G148100 chr3D 78.595 299 39 19 40 327 89904905 89904621 2.840000e-39 174
24 TraesCS3B01G148100 chr3D 93.333 90 5 1 5994 6082 608065333 608065422 1.730000e-26 132
25 TraesCS3B01G148100 chr4B 90.923 5145 317 71 887 5996 519051861 519046832 0.000000e+00 6776
26 TraesCS3B01G148100 chr4B 89.492 590 52 8 6144 6725 519046795 519046208 0.000000e+00 737
27 TraesCS3B01G148100 chr4D 91.616 4962 300 46 1059 5996 422085544 422080675 0.000000e+00 6752
28 TraesCS3B01G148100 chr4D 88.615 650 65 7 6081 6725 422080682 422080037 0.000000e+00 782
29 TraesCS3B01G148100 chr4D 86.486 259 17 5 1340 1595 418520802 418520559 1.270000e-67 268
30 TraesCS3B01G148100 chr4A 93.821 3512 190 15 1892 5389 41970252 41973750 0.000000e+00 5258
31 TraesCS3B01G148100 chr4A 85.923 888 60 17 1035 1897 41968234 41969081 0.000000e+00 887
32 TraesCS3B01G148100 chr4A 92.721 577 41 1 5422 5997 41973840 41974416 0.000000e+00 832
33 TraesCS3B01G148100 chr4A 89.362 611 51 9 6119 6719 41974410 41975016 0.000000e+00 756
34 TraesCS3B01G148100 chr4A 94.505 91 5 0 5994 6084 599610583 599610673 2.880000e-29 141
35 TraesCS3B01G148100 chr6D 85.276 1501 172 25 2830 4321 138806259 138804799 0.000000e+00 1502
36 TraesCS3B01G148100 chr6B 85.998 957 108 17 3450 4398 714810232 714811170 0.000000e+00 1002
37 TraesCS3B01G148100 chr1B 89.330 403 43 0 2827 3229 49437190 49437592 2.460000e-139 507
38 TraesCS3B01G148100 chr1B 78.683 319 65 3 5455 5772 545207897 545207581 7.780000e-50 209
39 TraesCS3B01G148100 chr7B 85.547 256 22 5 1340 1595 682958133 682957893 3.540000e-63 254
40 TraesCS3B01G148100 chr7B 93.258 89 5 1 5994 6082 587653472 587653385 6.230000e-26 130
41 TraesCS3B01G148100 chr1D 78.370 319 66 3 5455 5772 405366753 405366437 3.620000e-48 204
42 TraesCS3B01G148100 chr2D 77.287 317 68 4 5455 5769 534363925 534364239 4.720000e-42 183
43 TraesCS3B01G148100 chr7A 93.617 94 4 2 5994 6085 702619694 702619787 1.040000e-28 139
44 TraesCS3B01G148100 chr5A 93.258 89 5 1 5994 6082 237958509 237958422 6.230000e-26 130
45 TraesCS3B01G148100 chr5A 92.135 89 7 0 5994 6082 416144831 416144919 8.060000e-25 126


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 TraesCS3B01G148100 chr3B 139408730 139416381 7651 True 14131.000000 14131 100.000000 1 7652 1 chr3B.!!$R1 7651
1 TraesCS3B01G148100 chr3B 622394951 622399285 4334 False 979.333333 2394 82.447333 1319 5222 3 chr3B.!!$F2 3903
2 TraesCS3B01G148100 chr3A 106434262 106443129 8867 True 2722.750000 8008 93.557000 67 7652 4 chr3A.!!$R2 7585
3 TraesCS3B01G148100 chr3A 610541296 610547230 5934 False 682.800000 2193 81.556800 1322 6644 5 chr3A.!!$F2 5322
4 TraesCS3B01G148100 chr3D 89897452 89904905 7453 True 2125.000000 7461 88.458200 40 7652 5 chr3D.!!$R1 7612
5 TraesCS3B01G148100 chr3D 468758883 468763415 4532 False 1005.666667 2436 83.493000 1322 5222 3 chr3D.!!$F2 3900
6 TraesCS3B01G148100 chr4B 519046208 519051861 5653 True 3756.500000 6776 90.207500 887 6725 2 chr4B.!!$R1 5838
7 TraesCS3B01G148100 chr4D 422080037 422085544 5507 True 3767.000000 6752 90.115500 1059 6725 2 chr4D.!!$R2 5666
8 TraesCS3B01G148100 chr4A 41968234 41975016 6782 False 1933.250000 5258 90.456750 1035 6719 4 chr4A.!!$F2 5684
9 TraesCS3B01G148100 chr6D 138804799 138806259 1460 True 1502.000000 1502 85.276000 2830 4321 1 chr6D.!!$R1 1491
10 TraesCS3B01G148100 chr6B 714810232 714811170 938 False 1002.000000 1002 85.998000 3450 4398 1 chr6B.!!$F1 948

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
330 808 0.110778 CGATCATCATGAAGCTGCGC 60.111 55.000 0.00 0.0 0.00 6.09 F
761 2190 0.179018 CCGATCCATCCTTGGTTCCC 60.179 60.000 0.00 0.0 44.06 3.97 F
1761 3258 0.417437 TCACCTTCTCCTGGATGGGA 59.583 55.000 14.01 0.0 41.83 4.37 F
3207 5898 0.472471 GGGTCCTTGAGTGGTGTTCA 59.528 55.000 0.00 0.0 0.00 3.18 F
3937 6706 1.982958 GGGTTCTGGGTCTACTGGAAA 59.017 52.381 0.00 0.0 0.00 3.13 F
4129 6906 0.533978 TGGCTGTTGCAAGTTCGCTA 60.534 50.000 0.00 0.0 41.91 4.26 F
6049 9878 1.270550 AGCTGAATGGAAAGTTTGGCG 59.729 47.619 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
1812 3309 0.612744 TGTCGGCATGATCAAGGTCA 59.387 50.000 0.00 0.00 0.00 4.02 R
2238 4914 0.807275 TGTTGATCATCTCGCCGCTG 60.807 55.000 0.00 0.00 0.00 5.18 R
3524 6246 2.758979 AGCTGAAGGCAGGAATTCAATG 59.241 45.455 7.93 6.66 44.79 2.82 R
4129 6906 1.779092 AGTGCCCTTATGAGGATGCAT 59.221 47.619 4.80 0.00 46.74 3.96 R
4951 8689 1.831106 AGCCCATATCAAGTCACGTCA 59.169 47.619 0.00 0.00 0.00 4.35 R
6051 9880 0.171455 AACAACAAAAGGCGCACGAA 59.829 45.000 10.83 0.00 0.00 3.85 R
7482 11387 1.037030 TCAAATCCGATGGCCCAAGC 61.037 55.000 0.00 0.00 38.76 4.01 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
24 25 7.786178 CTCGATGAACCCTCACAAAAATATA 57.214 36.000 0.00 0.00 33.30 0.86
25 26 8.208718 CTCGATGAACCCTCACAAAAATATAA 57.791 34.615 0.00 0.00 33.30 0.98
61 62 4.919677 AAAAACAAGCGAAAACCTGTTG 57.080 36.364 0.00 0.00 0.00 3.33
62 63 3.586100 AAACAAGCGAAAACCTGTTGT 57.414 38.095 0.00 0.00 32.75 3.32
63 64 4.705337 AAACAAGCGAAAACCTGTTGTA 57.295 36.364 0.00 0.00 31.19 2.41
64 65 4.911514 AACAAGCGAAAACCTGTTGTAT 57.088 36.364 0.00 0.00 31.19 2.29
65 66 4.911514 ACAAGCGAAAACCTGTTGTATT 57.088 36.364 0.00 0.00 29.63 1.89
189 658 3.746492 AGATGAACCGACTTCCTTTTTCG 59.254 43.478 0.00 0.00 0.00 3.46
200 669 4.753107 ACTTCCTTTTTCGCGATTACAAGA 59.247 37.500 10.88 0.00 0.00 3.02
201 670 4.921470 TCCTTTTTCGCGATTACAAGAG 57.079 40.909 10.88 5.70 0.00 2.85
202 671 3.124636 TCCTTTTTCGCGATTACAAGAGC 59.875 43.478 10.88 0.00 0.00 4.09
209 678 0.532862 CGATTACAAGAGCGGGGCAT 60.533 55.000 0.00 0.00 0.00 4.40
226 695 1.060122 GCATACGCTACGTTCACCAAC 59.940 52.381 0.00 0.00 41.54 3.77
228 697 2.505628 TACGCTACGTTCACCAACAA 57.494 45.000 0.00 0.00 41.54 2.83
262 736 4.973168 AGATGTTGCTGGACTTAACTTGA 58.027 39.130 0.00 0.00 0.00 3.02
263 737 5.376625 AGATGTTGCTGGACTTAACTTGAA 58.623 37.500 0.00 0.00 0.00 2.69
264 742 5.471456 AGATGTTGCTGGACTTAACTTGAAG 59.529 40.000 0.00 0.00 0.00 3.02
270 748 6.119536 TGCTGGACTTAACTTGAAGAAAAGA 58.880 36.000 14.78 0.00 0.00 2.52
283 761 6.506500 TGAAGAAAAGAAGATGCAAGGATC 57.493 37.500 0.00 0.00 0.00 3.36
288 766 1.562942 AGAAGATGCAAGGATCCTGCA 59.437 47.619 29.13 29.13 43.04 4.41
304 782 3.196469 TCCTGCAGGACTTGTTATCTCTG 59.804 47.826 32.00 0.00 39.78 3.35
330 808 0.110778 CGATCATCATGAAGCTGCGC 60.111 55.000 0.00 0.00 0.00 6.09
331 809 0.942252 GATCATCATGAAGCTGCGCA 59.058 50.000 10.98 10.98 0.00 6.09
338 1764 1.938577 CATGAAGCTGCGCATACTCTT 59.061 47.619 12.24 12.17 0.00 2.85
339 1765 1.362768 TGAAGCTGCGCATACTCTTG 58.637 50.000 12.24 0.00 0.00 3.02
373 1799 4.079253 AGGAAAAATTACGCACAGTCCAT 58.921 39.130 0.00 0.00 0.00 3.41
374 1800 5.250200 AGGAAAAATTACGCACAGTCCATA 58.750 37.500 0.00 0.00 0.00 2.74
375 1801 5.885912 AGGAAAAATTACGCACAGTCCATAT 59.114 36.000 0.00 0.00 0.00 1.78
376 1802 7.051623 AGGAAAAATTACGCACAGTCCATATA 58.948 34.615 0.00 0.00 0.00 0.86
377 1803 7.719633 AGGAAAAATTACGCACAGTCCATATAT 59.280 33.333 0.00 0.00 0.00 0.86
391 1817 8.368668 ACAGTCCATATATTAGTAAACTGAGGC 58.631 37.037 13.13 0.00 37.06 4.70
403 1829 7.360575 AGTAAACTGAGGCAATAGTTAAACG 57.639 36.000 0.00 0.00 36.19 3.60
441 1867 2.729882 GCTACGGTAATAACAGGATGCG 59.270 50.000 0.00 0.00 42.53 4.73
442 1868 2.973694 ACGGTAATAACAGGATGCGT 57.026 45.000 0.00 0.00 42.53 5.24
444 1870 3.709987 ACGGTAATAACAGGATGCGTAC 58.290 45.455 0.00 0.00 42.53 3.67
445 1871 3.382546 ACGGTAATAACAGGATGCGTACT 59.617 43.478 0.00 0.00 42.53 2.73
446 1872 4.580167 ACGGTAATAACAGGATGCGTACTA 59.420 41.667 0.00 0.00 42.53 1.82
448 1874 5.278169 CGGTAATAACAGGATGCGTACTACT 60.278 44.000 0.00 0.00 42.53 2.57
449 1875 6.073058 CGGTAATAACAGGATGCGTACTACTA 60.073 42.308 0.00 0.00 42.53 1.82
450 1876 7.303998 GGTAATAACAGGATGCGTACTACTAG 58.696 42.308 0.00 0.00 42.53 2.57
452 1878 8.993121 GTAATAACAGGATGCGTACTACTAGTA 58.007 37.037 1.89 1.89 42.53 1.82
453 1879 5.747951 AACAGGATGCGTACTACTAGTAC 57.252 43.478 14.27 14.27 42.98 2.73
455 1881 4.132336 CAGGATGCGTACTACTAGTACCA 58.868 47.826 17.29 15.87 46.27 3.25
456 1882 4.024218 CAGGATGCGTACTACTAGTACCAC 60.024 50.000 17.29 11.83 46.27 4.16
457 1883 3.879295 GGATGCGTACTACTAGTACCACA 59.121 47.826 17.29 15.84 46.27 4.17
458 1884 4.518211 GGATGCGTACTACTAGTACCACAT 59.482 45.833 19.92 19.92 46.27 3.21
505 1932 5.105635 ACCACCTTTTATTATCTCGTCGTCA 60.106 40.000 0.00 0.00 0.00 4.35
507 1934 5.459107 CACCTTTTATTATCTCGTCGTCAGG 59.541 44.000 0.00 0.00 0.00 3.86
513 1940 2.080286 ATCTCGTCGTCAGGTTTTGG 57.920 50.000 0.00 0.00 0.00 3.28
522 1949 2.486548 CGTCAGGTTTTGGGAAGGAGAA 60.487 50.000 0.00 0.00 0.00 2.87
623 2051 4.794648 CGGGCCGGGATTCTGCAA 62.795 66.667 20.56 0.00 0.00 4.08
702 2131 3.972276 CCGCCACCACCAAAACCG 61.972 66.667 0.00 0.00 0.00 4.44
741 2170 3.670629 CTCCCACCTCCGCTCTCCT 62.671 68.421 0.00 0.00 0.00 3.69
749 2178 2.519541 CCGCTCTCCTCCGATCCA 60.520 66.667 0.00 0.00 0.00 3.41
750 2179 1.905843 CCGCTCTCCTCCGATCCAT 60.906 63.158 0.00 0.00 0.00 3.41
752 2181 1.872197 CGCTCTCCTCCGATCCATCC 61.872 65.000 0.00 0.00 0.00 3.51
754 2183 2.008242 CTCTCCTCCGATCCATCCTT 57.992 55.000 0.00 0.00 0.00 3.36
755 2184 1.617850 CTCTCCTCCGATCCATCCTTG 59.382 57.143 0.00 0.00 0.00 3.61
756 2185 0.683973 CTCCTCCGATCCATCCTTGG 59.316 60.000 0.00 0.00 45.15 3.61
758 2187 0.839946 CCTCCGATCCATCCTTGGTT 59.160 55.000 0.00 0.00 44.06 3.67
759 2188 1.202698 CCTCCGATCCATCCTTGGTTC 60.203 57.143 0.00 0.00 44.06 3.62
760 2189 0.837272 TCCGATCCATCCTTGGTTCC 59.163 55.000 0.00 0.00 44.06 3.62
761 2190 0.179018 CCGATCCATCCTTGGTTCCC 60.179 60.000 0.00 0.00 44.06 3.97
762 2191 0.179018 CGATCCATCCTTGGTTCCCC 60.179 60.000 0.00 0.00 44.06 4.81
763 2192 0.926293 GATCCATCCTTGGTTCCCCA 59.074 55.000 0.00 0.00 44.06 4.96
764 2193 1.500736 GATCCATCCTTGGTTCCCCAT 59.499 52.381 0.00 0.00 44.06 4.00
765 2194 1.392407 TCCATCCTTGGTTCCCCATT 58.608 50.000 0.00 0.00 44.06 3.16
812 2241 2.605295 TGGGTGGGTAGGGACACG 60.605 66.667 0.00 0.00 38.46 4.49
813 2242 3.396570 GGGTGGGTAGGGACACGG 61.397 72.222 0.00 0.00 38.46 4.94
814 2243 4.091939 GGTGGGTAGGGACACGGC 62.092 72.222 0.00 0.00 38.46 5.68
815 2244 4.091939 GTGGGTAGGGACACGGCC 62.092 72.222 0.00 0.00 0.00 6.13
916 2355 1.964891 TCGCCGTCACGACTCTTCT 60.965 57.895 0.00 0.00 37.09 2.85
919 2367 1.507174 CCGTCACGACTCTTCTCCC 59.493 63.158 0.00 0.00 0.00 4.30
952 2400 0.533951 GCCCGGTCCCCTATATAACG 59.466 60.000 0.00 0.00 0.00 3.18
1233 2706 4.003788 CGGTGGGGACAGTTCGCT 62.004 66.667 0.00 0.00 44.46 4.93
1305 2778 1.881602 GCTCGTCTCGTGGTACCTT 59.118 57.895 14.36 0.00 0.00 3.50
1314 2787 1.758280 TCGTGGTACCTTGACAACAGT 59.242 47.619 14.36 0.00 0.00 3.55
1318 2791 1.476110 GGTACCTTGACAACAGTGGCA 60.476 52.381 4.06 0.00 42.77 4.92
1319 2792 1.602377 GTACCTTGACAACAGTGGCAC 59.398 52.381 10.29 10.29 44.76 5.01
1320 2793 0.751643 ACCTTGACAACAGTGGCACC 60.752 55.000 15.27 0.00 44.76 5.01
1506 2982 2.124487 CTCCTCTCCGTCCTCGCT 60.124 66.667 0.00 0.00 35.54 4.93
1595 3071 2.125912 CGTTGAGGTCCTCGCAGG 60.126 66.667 14.34 5.42 36.46 4.85
1629 3114 3.056328 GCCGGGTTCTCTGCCAAC 61.056 66.667 2.18 0.00 0.00 3.77
1761 3258 0.417437 TCACCTTCTCCTGGATGGGA 59.583 55.000 14.01 0.00 41.83 4.37
2219 4895 1.336632 GGGCTCTCTCTGTCCAGCAT 61.337 60.000 0.00 0.00 33.22 3.79
2238 4914 3.655810 CTCCAGACAGAGCCGCACC 62.656 68.421 0.00 0.00 0.00 5.01
2971 5647 2.554032 ACGCTGAAGGACCTGAATTTTG 59.446 45.455 0.00 0.00 0.00 2.44
2985 5674 3.638160 TGAATTTTGAAGCTCAGCAAGGT 59.362 39.130 0.00 0.00 37.29 3.50
3207 5898 0.472471 GGGTCCTTGAGTGGTGTTCA 59.528 55.000 0.00 0.00 0.00 3.18
3288 5979 2.791347 TAAATCTTAGTGGCGGGCAA 57.209 45.000 5.57 0.00 0.00 4.52
3354 6045 6.260714 CCGACATCTATTTGTTTGATGATCCA 59.739 38.462 8.86 0.00 39.17 3.41
3524 6246 3.498397 CAGTGGTTTATGTCACTCACCAC 59.502 47.826 16.55 16.55 41.71 4.16
3766 6523 4.097437 ACAGCATTGGATGTGATTGATGTC 59.903 41.667 0.00 0.00 43.13 3.06
3843 6612 8.092521 TCAGCTGAAGAGAAAGATAAACAAAG 57.907 34.615 15.67 0.00 0.00 2.77
3854 6623 6.463995 AAGATAAACAAAGTGGCAAAGACA 57.536 33.333 0.00 0.00 0.00 3.41
3937 6706 1.982958 GGGTTCTGGGTCTACTGGAAA 59.017 52.381 0.00 0.00 0.00 3.13
4129 6906 0.533978 TGGCTGTTGCAAGTTCGCTA 60.534 50.000 0.00 0.00 41.91 4.26
4451 7235 5.475564 ACAACTAGTTGGAATTATTGCGGTT 59.524 36.000 33.11 9.65 44.45 4.44
4508 7292 5.598416 TCGTTCCTGTGATCATTATCTGT 57.402 39.130 0.00 0.00 32.93 3.41
4582 7369 2.977405 CTGCAAGTTCAGCACCTTAC 57.023 50.000 0.00 0.00 37.02 2.34
4951 8689 9.439500 TTTATACCAAGTAACGTTAGCAGATTT 57.561 29.630 8.60 0.00 0.00 2.17
5185 8923 1.451387 CCCCATAACTGGCCGTCAC 60.451 63.158 0.00 0.00 41.64 3.67
5229 8967 5.475909 TGACGTCCATGTAAGTACTCTTTCT 59.524 40.000 14.12 0.00 35.36 2.52
5230 8968 6.015688 TGACGTCCATGTAAGTACTCTTTCTT 60.016 38.462 14.12 0.00 35.36 2.52
5280 9018 6.822676 TCTCCTTTTCTTTTACCGTGTTGTTA 59.177 34.615 0.00 0.00 0.00 2.41
5296 9034 7.008266 CCGTGTTGTTATGCAGAAATTTCATAC 59.992 37.037 19.99 9.17 0.00 2.39
5314 9052 6.012658 TCATACTTTTTGCCATTGTGAGTC 57.987 37.500 0.00 0.00 0.00 3.36
5361 9099 5.010112 TGGGAAACGAATTGTAAATTCAGCA 59.990 36.000 11.97 0.00 0.00 4.41
5394 9132 9.928236 CAAATGAAAAATAACCAATTTGTTCGT 57.072 25.926 0.00 0.00 37.85 3.85
5461 9286 7.575414 TTAACTTGTCAAATTTCTGCAGGTA 57.425 32.000 15.13 2.15 0.00 3.08
5769 9594 1.543802 CGATCAGATCTGGGAGGTAGC 59.456 57.143 22.42 4.02 0.00 3.58
5813 9638 6.525121 TTCTTGTCAGTCGTCAAATACTTG 57.475 37.500 0.00 0.00 0.00 3.16
5815 9640 2.729360 TGTCAGTCGTCAAATACTTGCG 59.271 45.455 0.00 0.00 35.06 4.85
6006 9835 9.995003 TGAAACTTAATTTGCTTTGTAATCCAT 57.005 25.926 0.00 0.00 0.00 3.41
6008 9837 7.832503 ACTTAATTTGCTTTGTAATCCATGC 57.167 32.000 0.00 0.00 0.00 4.06
6009 9838 7.614494 ACTTAATTTGCTTTGTAATCCATGCT 58.386 30.769 0.00 0.00 0.00 3.79
6010 9839 7.546667 ACTTAATTTGCTTTGTAATCCATGCTG 59.453 33.333 0.00 0.00 0.00 4.41
6011 9840 4.870123 TTTGCTTTGTAATCCATGCTGT 57.130 36.364 0.00 0.00 0.00 4.40
6012 9841 5.973899 TTTGCTTTGTAATCCATGCTGTA 57.026 34.783 0.00 0.00 0.00 2.74
6013 9842 6.528537 TTTGCTTTGTAATCCATGCTGTAT 57.471 33.333 0.00 0.00 0.00 2.29
6014 9843 5.503662 TGCTTTGTAATCCATGCTGTATG 57.496 39.130 0.00 0.00 36.50 2.39
6015 9844 4.949238 TGCTTTGTAATCCATGCTGTATGT 59.051 37.500 5.04 0.00 34.87 2.29
6016 9845 5.066375 TGCTTTGTAATCCATGCTGTATGTC 59.934 40.000 5.04 0.00 34.87 3.06
6017 9846 5.733226 TTTGTAATCCATGCTGTATGTCG 57.267 39.130 5.04 0.00 34.87 4.35
6018 9847 3.130633 TGTAATCCATGCTGTATGTCGC 58.869 45.455 5.04 0.00 34.87 5.19
6019 9848 2.627515 AATCCATGCTGTATGTCGCT 57.372 45.000 5.04 0.00 34.87 4.93
6020 9849 3.751479 AATCCATGCTGTATGTCGCTA 57.249 42.857 5.04 0.00 34.87 4.26
6021 9850 3.969287 ATCCATGCTGTATGTCGCTAT 57.031 42.857 5.04 0.00 34.87 2.97
6022 9851 3.751479 TCCATGCTGTATGTCGCTATT 57.249 42.857 5.04 0.00 34.87 1.73
6023 9852 3.392882 TCCATGCTGTATGTCGCTATTG 58.607 45.455 5.04 0.00 34.87 1.90
6024 9853 3.069443 TCCATGCTGTATGTCGCTATTGA 59.931 43.478 5.04 0.00 34.87 2.57
6025 9854 3.431233 CCATGCTGTATGTCGCTATTGAG 59.569 47.826 5.04 0.00 34.87 3.02
6026 9855 2.473816 TGCTGTATGTCGCTATTGAGC 58.526 47.619 0.00 0.00 46.00 4.26
6027 9856 5.326283 CATGCTGTATGTCGCTATTGAGCT 61.326 45.833 0.00 0.00 38.02 4.09
6028 9857 7.298182 CATGCTGTATGTCGCTATTGAGCTG 62.298 48.000 0.00 0.00 38.02 4.24
6037 9866 3.881780 GCTATTGAGCTGAGCTGAATG 57.118 47.619 25.80 17.10 41.98 2.67
6038 9867 2.548904 GCTATTGAGCTGAGCTGAATGG 59.451 50.000 25.80 23.74 41.98 3.16
6039 9868 3.743584 GCTATTGAGCTGAGCTGAATGGA 60.744 47.826 28.06 10.82 41.42 3.41
6040 9869 2.865119 TTGAGCTGAGCTGAATGGAA 57.135 45.000 13.71 0.00 39.88 3.53
6041 9870 2.865119 TGAGCTGAGCTGAATGGAAA 57.135 45.000 13.71 0.00 39.88 3.13
6042 9871 2.708051 TGAGCTGAGCTGAATGGAAAG 58.292 47.619 13.71 0.00 39.88 2.62
6043 9872 2.039480 TGAGCTGAGCTGAATGGAAAGT 59.961 45.455 13.71 0.00 39.88 2.66
6044 9873 3.080319 GAGCTGAGCTGAATGGAAAGTT 58.920 45.455 13.71 0.00 39.88 2.66
6045 9874 3.494332 AGCTGAGCTGAATGGAAAGTTT 58.506 40.909 5.97 0.00 37.57 2.66
6046 9875 3.255149 AGCTGAGCTGAATGGAAAGTTTG 59.745 43.478 5.97 0.00 37.57 2.93
6047 9876 3.613432 GCTGAGCTGAATGGAAAGTTTGG 60.613 47.826 0.00 0.00 0.00 3.28
6048 9877 2.297033 TGAGCTGAATGGAAAGTTTGGC 59.703 45.455 0.00 0.00 0.00 4.52
6049 9878 1.270550 AGCTGAATGGAAAGTTTGGCG 59.729 47.619 0.00 0.00 0.00 5.69
6050 9879 1.701704 CTGAATGGAAAGTTTGGCGC 58.298 50.000 0.00 0.00 0.00 6.53
6051 9880 1.270550 CTGAATGGAAAGTTTGGCGCT 59.729 47.619 7.64 0.00 0.00 5.92
6052 9881 1.686052 TGAATGGAAAGTTTGGCGCTT 59.314 42.857 7.64 0.00 0.00 4.68
6053 9882 2.288152 TGAATGGAAAGTTTGGCGCTTC 60.288 45.455 7.64 1.15 0.00 3.86
6054 9883 0.240945 ATGGAAAGTTTGGCGCTTCG 59.759 50.000 7.64 0.00 0.00 3.79
6055 9884 1.098712 TGGAAAGTTTGGCGCTTCGT 61.099 50.000 7.64 0.00 0.00 3.85
6056 9885 0.660300 GGAAAGTTTGGCGCTTCGTG 60.660 55.000 7.64 0.00 0.00 4.35
6057 9886 1.268778 GAAAGTTTGGCGCTTCGTGC 61.269 55.000 7.64 0.00 38.45 5.34
6066 9895 2.331451 GCTTCGTGCGCCTTTTGT 59.669 55.556 4.18 0.00 0.00 2.83
6067 9896 1.299089 GCTTCGTGCGCCTTTTGTT 60.299 52.632 4.18 0.00 0.00 2.83
6068 9897 1.539776 GCTTCGTGCGCCTTTTGTTG 61.540 55.000 4.18 0.00 0.00 3.33
6069 9898 0.248458 CTTCGTGCGCCTTTTGTTGT 60.248 50.000 4.18 0.00 0.00 3.32
6070 9899 0.171455 TTCGTGCGCCTTTTGTTGTT 59.829 45.000 4.18 0.00 0.00 2.83
6071 9900 1.015109 TCGTGCGCCTTTTGTTGTTA 58.985 45.000 4.18 0.00 0.00 2.41
6072 9901 1.400846 TCGTGCGCCTTTTGTTGTTAA 59.599 42.857 4.18 0.00 0.00 2.01
6073 9902 2.159421 TCGTGCGCCTTTTGTTGTTAAA 60.159 40.909 4.18 0.00 0.00 1.52
6074 9903 2.599082 CGTGCGCCTTTTGTTGTTAAAA 59.401 40.909 4.18 0.00 0.00 1.52
6075 9904 3.060895 CGTGCGCCTTTTGTTGTTAAAAA 59.939 39.130 4.18 0.00 0.00 1.94
6114 9944 4.635765 CGTTCACACATTTCCCAGTATCAT 59.364 41.667 0.00 0.00 0.00 2.45
6153 9983 7.298122 AGATTTGAAAACTATAACACGTGCTG 58.702 34.615 17.22 3.92 0.00 4.41
6160 9990 1.238439 ATAACACGTGCTGCTGCTTT 58.762 45.000 17.22 1.96 40.48 3.51
6531 10380 1.299541 CTGTTGGTCTGACAAACGCT 58.700 50.000 20.07 0.00 31.17 5.07
6537 10387 2.243957 TCTGACAAACGCTGTGCCG 61.244 57.895 0.00 0.00 38.84 5.69
6633 10484 0.108992 TTGTGGCGGAGTACACGATC 60.109 55.000 13.23 5.74 39.60 3.69
6646 10497 3.308008 CGATCAGAGCGACGCACG 61.308 66.667 23.70 12.11 45.66 5.34
6673 10524 2.103094 CCAACGAATAGATCCTCCAGCA 59.897 50.000 0.00 0.00 0.00 4.41
6674 10525 3.432186 CCAACGAATAGATCCTCCAGCAA 60.432 47.826 0.00 0.00 0.00 3.91
6675 10526 4.191544 CAACGAATAGATCCTCCAGCAAA 58.808 43.478 0.00 0.00 0.00 3.68
6684 10535 3.744940 TCCTCCAGCAAATTCTTCCAT 57.255 42.857 0.00 0.00 0.00 3.41
6769 10633 1.203287 TGTGAAGTGCTCTCGGATCTG 59.797 52.381 0.00 0.00 0.00 2.90
6813 10677 1.127213 CGCGCACGGTAACTTTACATT 59.873 47.619 8.75 0.00 35.37 2.71
6851 10719 2.298163 TGAAGGTGGTTAAGAGTCGGTC 59.702 50.000 0.00 0.00 0.00 4.79
6891 10759 7.758528 TGAAGAAAGTAGTTCGTTAAGGATAGC 59.241 37.037 0.00 0.00 41.52 2.97
6904 10777 2.551270 AGGATAGCAAGACCTGAACCA 58.449 47.619 0.00 0.00 32.39 3.67
6916 10789 3.767673 GACCTGAACCATGGTAGTAGTCA 59.232 47.826 20.12 16.50 36.59 3.41
6991 10864 4.932146 TGATGATGTACTGTGTGATACCG 58.068 43.478 0.00 0.00 0.00 4.02
7004 10877 7.444183 ACTGTGTGATACCGGGATAAATAAATG 59.556 37.037 6.32 0.00 0.00 2.32
7005 10878 7.510407 TGTGTGATACCGGGATAAATAAATGA 58.490 34.615 6.32 0.00 0.00 2.57
7006 10879 7.993758 TGTGTGATACCGGGATAAATAAATGAA 59.006 33.333 6.32 0.00 0.00 2.57
7007 10880 8.504005 GTGTGATACCGGGATAAATAAATGAAG 58.496 37.037 6.32 0.00 0.00 3.02
7008 10881 8.215050 TGTGATACCGGGATAAATAAATGAAGT 58.785 33.333 6.32 0.00 0.00 3.01
7009 10882 8.504005 GTGATACCGGGATAAATAAATGAAGTG 58.496 37.037 6.32 0.00 0.00 3.16
7017 10890 7.342026 GGGATAAATAAATGAAGTGGAAGTGGT 59.658 37.037 0.00 0.00 0.00 4.16
7065 10938 2.043227 CCCTCCCTGACTGTTCCTATC 58.957 57.143 0.00 0.00 0.00 2.08
7092 10965 2.200337 GGGTCTGTGTTGGGTTGGC 61.200 63.158 0.00 0.00 0.00 4.52
7120 10993 1.689984 TGCCAAGCATGAACAGAACA 58.310 45.000 0.00 0.00 31.71 3.18
7129 11002 1.082756 GAACAGAACAGCCGTTGCG 60.083 57.895 0.00 0.00 44.33 4.85
7169 11043 4.460382 TGTCATTCTTTTTCCCTCTGCATC 59.540 41.667 0.00 0.00 0.00 3.91
7204 11078 3.552875 TCCTCTACAATACCTCCTCACG 58.447 50.000 0.00 0.00 0.00 4.35
7216 11090 0.175760 TCCTCACGGTGCAGCTTATC 59.824 55.000 14.92 0.00 0.00 1.75
7219 11107 0.108186 TCACGGTGCAGCTTATCCTG 60.108 55.000 14.92 0.00 35.93 3.86
7241 11129 4.058124 GCATCAGGCAATCGTAAGTCATA 58.942 43.478 0.00 0.00 43.97 2.15
7242 11130 4.692625 GCATCAGGCAATCGTAAGTCATAT 59.307 41.667 0.00 0.00 43.97 1.78
7243 11131 5.869344 GCATCAGGCAATCGTAAGTCATATA 59.131 40.000 0.00 0.00 43.97 0.86
7244 11132 6.183360 GCATCAGGCAATCGTAAGTCATATAC 60.183 42.308 0.00 0.00 43.97 1.47
7245 11133 6.399639 TCAGGCAATCGTAAGTCATATACA 57.600 37.500 0.00 0.00 39.48 2.29
7278 11166 2.227388 GCTGTTCTGAATTCAGTGGTGG 59.773 50.000 29.80 19.10 44.12 4.61
7293 11181 4.082408 CAGTGGTGGATTCGTCAGTAACTA 60.082 45.833 0.00 0.00 0.00 2.24
7311 11199 6.942576 AGTAACTACTTGCATTTTCAGGACAT 59.057 34.615 0.00 0.00 31.13 3.06
7334 11222 4.150897 TGTTCTTTGACTAAGCACAGGT 57.849 40.909 0.00 0.00 35.50 4.00
7359 11247 1.955778 CCTTTGGCTGATTCACACACA 59.044 47.619 0.00 0.00 0.00 3.72
7361 11249 3.366679 CCTTTGGCTGATTCACACACATC 60.367 47.826 0.00 0.00 0.00 3.06
7362 11250 2.565046 TGGCTGATTCACACACATCA 57.435 45.000 0.00 0.00 0.00 3.07
7363 11251 2.153645 TGGCTGATTCACACACATCAC 58.846 47.619 0.00 0.00 0.00 3.06
7364 11252 1.470098 GGCTGATTCACACACATCACC 59.530 52.381 0.00 0.00 0.00 4.02
7365 11253 2.153645 GCTGATTCACACACATCACCA 58.846 47.619 0.00 0.00 0.00 4.17
7366 11254 2.553602 GCTGATTCACACACATCACCAA 59.446 45.455 0.00 0.00 0.00 3.67
7368 11256 3.549794 TGATTCACACACATCACCAACA 58.450 40.909 0.00 0.00 0.00 3.33
7369 11257 3.950395 TGATTCACACACATCACCAACAA 59.050 39.130 0.00 0.00 0.00 2.83
7371 11259 4.998671 TTCACACACATCACCAACAATT 57.001 36.364 0.00 0.00 0.00 2.32
7374 11262 4.159321 TCACACACATCACCAACAATTTGT 59.841 37.500 0.00 0.00 0.00 2.83
7386 11283 7.279758 TCACCAACAATTTGTCAAAGAAAATCC 59.720 33.333 1.83 0.00 0.00 3.01
7389 11286 7.280652 CCAACAATTTGTCAAAGAAAATCCAGT 59.719 33.333 1.83 0.00 0.00 4.00
7427 11324 0.106868 TTGCCTCCCATCATCTGCTG 60.107 55.000 0.00 0.00 0.00 4.41
7428 11325 0.984432 TGCCTCCCATCATCTGCTGA 60.984 55.000 0.00 0.00 38.53 4.26
7430 11327 1.202903 GCCTCCCATCATCTGCTGAAT 60.203 52.381 0.00 0.00 37.44 2.57
7431 11328 2.752154 GCCTCCCATCATCTGCTGAATT 60.752 50.000 0.00 0.00 37.44 2.17
7436 11333 3.815962 CCCATCATCTGCTGAATTCTGAG 59.184 47.826 15.79 10.00 37.44 3.35
7439 11336 2.237893 TCATCTGCTGAATTCTGAGCCA 59.762 45.455 15.79 4.16 34.04 4.75
7448 11345 0.459237 ATTCTGAGCCACTCGAAGCG 60.459 55.000 0.00 0.00 32.35 4.68
7466 11363 1.078426 GGCTGCGCCTCCTTTTAGA 60.078 57.895 4.18 0.00 46.69 2.10
7468 11365 0.448197 GCTGCGCCTCCTTTTAGAAC 59.552 55.000 4.18 0.00 0.00 3.01
7469 11366 1.087501 CTGCGCCTCCTTTTAGAACC 58.912 55.000 4.18 0.00 0.00 3.62
7470 11367 0.672401 TGCGCCTCCTTTTAGAACCG 60.672 55.000 4.18 0.00 0.00 4.44
7482 11387 5.517054 CCTTTTAGAACCGAGAGAGATTTCG 59.483 44.000 0.00 0.00 36.62 3.46
7563 11468 1.841663 GCGACCAGCTTTGCGAAGAA 61.842 55.000 18.32 0.00 44.04 2.52
7573 11478 3.383761 CTTTGCGAAGAAGCCAAATTGT 58.616 40.909 8.08 0.00 34.71 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.683974 ATATTTTTGTGAGGGTTCATCGAG 57.316 37.500 0.00 0.00 35.39 4.04
1 2 8.568676 TTTATATTTTTGTGAGGGTTCATCGA 57.431 30.769 0.00 0.00 35.39 3.59
40 41 4.311606 ACAACAGGTTTTCGCTTGTTTTT 58.688 34.783 0.00 0.00 0.00 1.94
41 42 3.920446 ACAACAGGTTTTCGCTTGTTTT 58.080 36.364 0.00 0.00 0.00 2.43
42 43 3.586100 ACAACAGGTTTTCGCTTGTTT 57.414 38.095 0.00 0.00 0.00 2.83
43 44 4.911514 ATACAACAGGTTTTCGCTTGTT 57.088 36.364 0.00 0.00 0.00 2.83
44 45 4.097286 ACAATACAACAGGTTTTCGCTTGT 59.903 37.500 0.00 0.00 0.00 3.16
45 46 4.606961 ACAATACAACAGGTTTTCGCTTG 58.393 39.130 0.00 0.00 0.00 4.01
46 47 4.911514 ACAATACAACAGGTTTTCGCTT 57.088 36.364 0.00 0.00 0.00 4.68
47 48 5.061179 ACTACAATACAACAGGTTTTCGCT 58.939 37.500 0.00 0.00 0.00 4.93
48 49 5.352643 ACTACAATACAACAGGTTTTCGC 57.647 39.130 0.00 0.00 0.00 4.70
49 50 7.410800 TGTACTACAATACAACAGGTTTTCG 57.589 36.000 0.00 0.00 32.07 3.46
53 54 9.781633 TGTAAATGTACTACAATACAACAGGTT 57.218 29.630 12.46 0.00 38.53 3.50
54 55 9.431887 CTGTAAATGTACTACAATACAACAGGT 57.568 33.333 14.42 0.00 37.57 4.00
55 56 9.647797 TCTGTAAATGTACTACAATACAACAGG 57.352 33.333 14.42 7.37 39.61 4.00
88 89 1.542547 CCCAGCTTTGTCGGTTGTACT 60.543 52.381 0.00 0.00 0.00 2.73
90 91 0.887387 GCCCAGCTTTGTCGGTTGTA 60.887 55.000 0.00 0.00 0.00 2.41
172 173 0.584876 CGCGAAAAAGGAAGTCGGTT 59.415 50.000 0.00 0.00 35.35 4.44
175 644 2.875080 AATCGCGAAAAAGGAAGTCG 57.125 45.000 15.24 0.00 37.82 4.18
189 658 2.534903 GCCCCGCTCTTGTAATCGC 61.535 63.158 0.00 0.00 0.00 4.58
202 671 1.947642 GAACGTAGCGTATGCCCCG 60.948 63.158 12.71 12.71 44.31 5.73
209 678 2.396601 CTTGTTGGTGAACGTAGCGTA 58.603 47.619 0.00 0.00 39.99 4.42
226 695 3.304928 GCAACATCTTTGTCTCCACCTTG 60.305 47.826 0.00 0.00 34.06 3.61
228 697 2.107204 AGCAACATCTTTGTCTCCACCT 59.893 45.455 0.00 0.00 34.06 4.00
235 709 5.239525 AGTTAAGTCCAGCAACATCTTTGTC 59.760 40.000 0.00 0.00 34.06 3.18
262 736 5.418209 CAGGATCCTTGCATCTTCTTTTCTT 59.582 40.000 13.00 0.00 0.00 2.52
263 737 4.948621 CAGGATCCTTGCATCTTCTTTTCT 59.051 41.667 13.00 0.00 0.00 2.52
264 742 4.439837 GCAGGATCCTTGCATCTTCTTTTC 60.440 45.833 23.33 0.00 0.00 2.29
270 748 1.409802 CCTGCAGGATCCTTGCATCTT 60.410 52.381 29.88 0.21 37.95 2.40
283 761 3.529533 CAGAGATAACAAGTCCTGCAGG 58.470 50.000 27.87 27.87 0.00 4.85
288 766 3.840666 TCAAGCCAGAGATAACAAGTCCT 59.159 43.478 0.00 0.00 0.00 3.85
304 782 2.032204 GCTTCATGATGATCGTCAAGCC 60.032 50.000 21.10 7.50 0.00 4.35
347 1773 5.751509 GGACTGTGCGTAATTTTTCCTTTTT 59.248 36.000 0.00 0.00 0.00 1.94
348 1774 5.163499 TGGACTGTGCGTAATTTTTCCTTTT 60.163 36.000 0.00 0.00 0.00 2.27
352 1778 3.907894 TGGACTGTGCGTAATTTTTCC 57.092 42.857 0.00 0.00 0.00 3.13
359 1785 9.467258 GTTTACTAATATATGGACTGTGCGTAA 57.533 33.333 5.32 0.00 0.00 3.18
361 1787 7.652105 CAGTTTACTAATATATGGACTGTGCGT 59.348 37.037 0.00 0.00 0.00 5.24
377 1803 8.928733 CGTTTAACTATTGCCTCAGTTTACTAA 58.071 33.333 0.00 0.00 36.44 2.24
380 1806 7.355332 TCGTTTAACTATTGCCTCAGTTTAC 57.645 36.000 0.00 0.23 36.44 2.01
396 1822 6.567891 GCCCAGATATAATGGCTTCGTTTAAC 60.568 42.308 1.53 0.00 40.77 2.01
400 1826 3.412386 GCCCAGATATAATGGCTTCGTT 58.588 45.455 1.53 0.00 40.77 3.85
442 1868 7.701539 TTTCCGAAATGTGGTACTAGTAGTA 57.298 36.000 5.90 5.90 0.00 1.82
444 1870 8.488651 AATTTTCCGAAATGTGGTACTAGTAG 57.511 34.615 1.87 0.00 35.69 2.57
445 1871 7.550196 GGAATTTTCCGAAATGTGGTACTAGTA 59.450 37.037 0.00 0.00 37.65 1.82
446 1872 6.373495 GGAATTTTCCGAAATGTGGTACTAGT 59.627 38.462 0.00 0.00 37.65 2.57
448 1874 6.746745 GGAATTTTCCGAAATGTGGTACTA 57.253 37.500 0.00 0.00 37.65 1.82
449 1875 5.638596 GGAATTTTCCGAAATGTGGTACT 57.361 39.130 0.00 0.00 37.65 2.73
505 1932 7.419750 GGTTTAAAATTCTCCTTCCCAAAACCT 60.420 37.037 0.00 0.00 39.20 3.50
507 1934 6.422701 CGGTTTAAAATTCTCCTTCCCAAAAC 59.577 38.462 0.00 0.00 0.00 2.43
513 1940 4.022676 TGCACGGTTTAAAATTCTCCTTCC 60.023 41.667 0.00 0.00 0.00 3.46
522 1949 7.822822 AGTATCTTCTACTGCACGGTTTAAAAT 59.177 33.333 0.00 0.00 0.00 1.82
579 2006 1.353076 GGGGTTTTGACTACGCTACG 58.647 55.000 0.00 0.00 0.00 3.51
580 2007 1.353076 CGGGGTTTTGACTACGCTAC 58.647 55.000 0.00 0.00 0.00 3.58
581 2008 0.247185 CCGGGGTTTTGACTACGCTA 59.753 55.000 0.00 0.00 0.00 4.26
582 2009 1.004200 CCGGGGTTTTGACTACGCT 60.004 57.895 0.00 0.00 0.00 5.07
587 2014 4.653888 CCGGCCGGGGTTTTGACT 62.654 66.667 37.42 0.00 0.00 3.41
623 2051 2.799917 GCGGCAGTCGAGATAAATGAGT 60.800 50.000 0.00 0.00 42.43 3.41
702 2131 6.325596 GGAGAGGTGAGTAAATCAAAATTGC 58.674 40.000 0.00 0.00 40.43 3.56
756 2185 1.923586 GGAGGGGAGAATGGGGAAC 59.076 63.158 0.00 0.00 0.00 3.62
758 2187 2.040884 CGGAGGGGAGAATGGGGA 60.041 66.667 0.00 0.00 0.00 4.81
759 2188 2.366972 ACGGAGGGGAGAATGGGG 60.367 66.667 0.00 0.00 0.00 4.96
760 2189 2.797278 CGACGGAGGGGAGAATGGG 61.797 68.421 0.00 0.00 0.00 4.00
761 2190 2.815308 CGACGGAGGGGAGAATGG 59.185 66.667 0.00 0.00 0.00 3.16
762 2191 2.107141 GCGACGGAGGGGAGAATG 59.893 66.667 0.00 0.00 0.00 2.67
763 2192 3.528370 CGCGACGGAGGGGAGAAT 61.528 66.667 0.00 0.00 0.00 2.40
1166 2633 2.436646 CTGATTCCTTGCCGCGGT 60.437 61.111 28.70 3.94 0.00 5.68
1193 2663 3.785859 GGATGCCACCGCCTCTCA 61.786 66.667 0.00 0.00 30.95 3.27
1280 2753 1.632948 CCACGAGACGAGCGAGTACA 61.633 60.000 0.00 0.00 0.00 2.90
1305 2778 2.203139 CCGGTGCCACTGTTGTCA 60.203 61.111 2.45 0.00 0.00 3.58
1812 3309 0.612744 TGTCGGCATGATCAAGGTCA 59.387 50.000 0.00 0.00 0.00 4.02
1890 4563 1.603739 GGTGAACTTGGGGCCAGAC 60.604 63.158 4.39 0.00 0.00 3.51
1977 4650 1.279271 GTGGCCAGGTTGTAGATGAGT 59.721 52.381 5.11 0.00 0.00 3.41
2219 4895 2.283173 TGCGGCTCTGTCTGGAGA 60.283 61.111 0.00 0.00 35.52 3.71
2238 4914 0.807275 TGTTGATCATCTCGCCGCTG 60.807 55.000 0.00 0.00 0.00 5.18
3207 5898 6.229733 CAAGATCTCCAAGTCTTTCTTCAGT 58.770 40.000 0.00 0.00 32.60 3.41
3288 5979 3.956848 GGGCTATCTGAATCCTTTGCTTT 59.043 43.478 0.00 0.00 0.00 3.51
3354 6045 3.403277 GCATCGACTGCGCTGAAT 58.597 55.556 21.92 8.32 41.97 2.57
3524 6246 2.758979 AGCTGAAGGCAGGAATTCAATG 59.241 45.455 7.93 6.66 44.79 2.82
3629 6384 9.635404 CCCACCTTTCATTACCTACATATAAAA 57.365 33.333 0.00 0.00 0.00 1.52
3630 6385 9.005318 TCCCACCTTTCATTACCTACATATAAA 57.995 33.333 0.00 0.00 0.00 1.40
3633 6388 6.849697 TCTCCCACCTTTCATTACCTACATAT 59.150 38.462 0.00 0.00 0.00 1.78
3766 6523 0.461548 TCTCACTGCCTCCATTAGCG 59.538 55.000 0.00 0.00 0.00 4.26
3843 6612 0.028902 GTCACCGTTGTCTTTGCCAC 59.971 55.000 0.00 0.00 0.00 5.01
3854 6623 1.485066 ACTCTGAACCTTGTCACCGTT 59.515 47.619 0.00 0.00 0.00 4.44
3937 6706 2.745152 GCCGTAAGCCAATGTGAGGTAT 60.745 50.000 0.00 0.00 34.35 2.73
3976 6745 3.961480 AGTAGCTGTGCTATCAACACA 57.039 42.857 0.00 0.00 43.30 3.72
4129 6906 1.779092 AGTGCCCTTATGAGGATGCAT 59.221 47.619 4.80 0.00 46.74 3.96
4415 7199 8.877864 TTCCAACTAGTTGTATGATGGAAAAT 57.122 30.769 29.05 0.00 41.19 1.82
4451 7235 2.366590 CTGCCATGCTACCTGAGACATA 59.633 50.000 0.00 0.00 0.00 2.29
4556 7343 4.342092 AGGTGCTGAACTTGCAGTTAAAAT 59.658 37.500 2.17 0.00 38.80 1.82
4570 7357 7.507277 AGATGATAGATGTAGTAAGGTGCTGAA 59.493 37.037 0.00 0.00 0.00 3.02
4582 7369 3.367327 GCGCTGCAAGATGATAGATGTAG 59.633 47.826 0.00 0.00 34.07 2.74
4933 8671 4.986659 ACGTCAAATCTGCTAACGTTACTT 59.013 37.500 3.29 0.00 43.36 2.24
4951 8689 1.831106 AGCCCATATCAAGTCACGTCA 59.169 47.619 0.00 0.00 0.00 4.35
5185 8923 2.417933 CACGAAGCTGAATTTCTCCCTG 59.582 50.000 0.00 0.00 0.00 4.45
5280 9018 6.935771 TGGCAAAAAGTATGAAATTTCTGCAT 59.064 30.769 18.64 7.76 0.00 3.96
5296 9034 4.685924 AGTTGACTCACAATGGCAAAAAG 58.314 39.130 0.00 0.00 40.76 2.27
5314 9052 7.443575 CCCATCAGACTGGATTTCTAATAGTTG 59.556 40.741 1.81 0.00 38.69 3.16
5430 9253 9.195411 GCAGAAATTTGACAAGTTAATGATGAA 57.805 29.630 0.00 0.00 0.00 2.57
5432 9255 8.523523 TGCAGAAATTTGACAAGTTAATGATG 57.476 30.769 0.00 2.45 0.00 3.07
5436 9259 7.054491 ACCTGCAGAAATTTGACAAGTTAAT 57.946 32.000 17.39 0.00 0.00 1.40
5461 9286 5.636903 ATGGTAGTTGTGGAGCATATCTT 57.363 39.130 0.00 0.00 32.20 2.40
5769 9594 2.975410 TGAAGCATGTGAAAGCGAAG 57.025 45.000 0.00 0.00 35.48 3.79
5813 9638 7.615455 TCCAAGAGGTTCTCGACTATTTCGC 62.615 48.000 0.00 0.00 41.07 4.70
5815 9640 5.326200 TCCAAGAGGTTCTCGACTATTTC 57.674 43.478 0.00 0.00 35.36 2.17
5996 9825 3.559655 GCGACATACAGCATGGATTACAA 59.440 43.478 0.00 0.00 34.52 2.41
5999 9828 3.751479 AGCGACATACAGCATGGATTA 57.249 42.857 0.00 0.00 34.52 1.75
6003 9832 3.392882 TCAATAGCGACATACAGCATGG 58.607 45.455 0.00 0.00 43.62 3.66
6006 9835 2.473816 GCTCAATAGCGACATACAGCA 58.526 47.619 0.00 0.00 39.39 4.41
6018 9847 4.069300 TCCATTCAGCTCAGCTCAATAG 57.931 45.455 0.00 0.00 36.40 1.73
6019 9848 4.492494 TTCCATTCAGCTCAGCTCAATA 57.508 40.909 0.00 0.00 36.40 1.90
6020 9849 3.361281 TTCCATTCAGCTCAGCTCAAT 57.639 42.857 0.00 0.00 36.40 2.57
6021 9850 2.865119 TTCCATTCAGCTCAGCTCAA 57.135 45.000 0.00 0.00 36.40 3.02
6022 9851 2.039480 ACTTTCCATTCAGCTCAGCTCA 59.961 45.455 0.00 0.00 36.40 4.26
6023 9852 2.709213 ACTTTCCATTCAGCTCAGCTC 58.291 47.619 0.00 0.00 36.40 4.09
6024 9853 2.875094 ACTTTCCATTCAGCTCAGCT 57.125 45.000 0.00 0.00 40.77 4.24
6025 9854 3.572584 CAAACTTTCCATTCAGCTCAGC 58.427 45.455 0.00 0.00 0.00 4.26
6026 9855 3.613432 GCCAAACTTTCCATTCAGCTCAG 60.613 47.826 0.00 0.00 0.00 3.35
6027 9856 2.297033 GCCAAACTTTCCATTCAGCTCA 59.703 45.455 0.00 0.00 0.00 4.26
6028 9857 2.669391 CGCCAAACTTTCCATTCAGCTC 60.669 50.000 0.00 0.00 0.00 4.09
6029 9858 1.270550 CGCCAAACTTTCCATTCAGCT 59.729 47.619 0.00 0.00 0.00 4.24
6030 9859 1.701704 CGCCAAACTTTCCATTCAGC 58.298 50.000 0.00 0.00 0.00 4.26
6031 9860 1.270550 AGCGCCAAACTTTCCATTCAG 59.729 47.619 2.29 0.00 0.00 3.02
6032 9861 1.327303 AGCGCCAAACTTTCCATTCA 58.673 45.000 2.29 0.00 0.00 2.57
6033 9862 2.328473 GAAGCGCCAAACTTTCCATTC 58.672 47.619 2.29 0.00 0.00 2.67
6034 9863 1.335872 CGAAGCGCCAAACTTTCCATT 60.336 47.619 2.29 0.00 0.00 3.16
6035 9864 0.240945 CGAAGCGCCAAACTTTCCAT 59.759 50.000 2.29 0.00 0.00 3.41
6036 9865 1.098712 ACGAAGCGCCAAACTTTCCA 61.099 50.000 2.29 0.00 0.00 3.53
6037 9866 0.660300 CACGAAGCGCCAAACTTTCC 60.660 55.000 2.29 0.00 0.00 3.13
6038 9867 1.268778 GCACGAAGCGCCAAACTTTC 61.269 55.000 2.29 0.00 0.00 2.62
6039 9868 1.299089 GCACGAAGCGCCAAACTTT 60.299 52.632 2.29 0.00 0.00 2.66
6040 9869 2.331451 GCACGAAGCGCCAAACTT 59.669 55.556 2.29 0.00 0.00 2.66
6049 9878 1.299089 AACAAAAGGCGCACGAAGC 60.299 52.632 10.83 0.00 40.87 3.86
6050 9879 0.248458 ACAACAAAAGGCGCACGAAG 60.248 50.000 10.83 0.00 0.00 3.79
6051 9880 0.171455 AACAACAAAAGGCGCACGAA 59.829 45.000 10.83 0.00 0.00 3.85
6052 9881 1.015109 TAACAACAAAAGGCGCACGA 58.985 45.000 10.83 0.00 0.00 4.35
6053 9882 1.828832 TTAACAACAAAAGGCGCACG 58.171 45.000 10.83 0.00 0.00 5.34
6054 9883 4.585619 TTTTTAACAACAAAAGGCGCAC 57.414 36.364 10.83 0.00 0.00 5.34
6073 9902 8.487176 GTGTGAACGATGAGCAAATTTATTTTT 58.513 29.630 0.00 0.00 0.00 1.94
6074 9903 7.651304 TGTGTGAACGATGAGCAAATTTATTTT 59.349 29.630 0.00 0.00 0.00 1.82
6075 9904 7.144661 TGTGTGAACGATGAGCAAATTTATTT 58.855 30.769 0.00 0.00 0.00 1.40
6077 9906 6.252967 TGTGTGAACGATGAGCAAATTTAT 57.747 33.333 0.00 0.00 0.00 1.40
6079 9908 4.566545 TGTGTGAACGATGAGCAAATTT 57.433 36.364 0.00 0.00 0.00 1.82
6114 9944 7.995488 AGTTTTCAAATCTTGGAAGAGAAGAGA 59.005 33.333 0.00 0.00 38.66 3.10
6164 9994 8.992073 AGGCAAAATAACATGATTTTTCAGTTC 58.008 29.630 0.00 0.00 36.99 3.01
6531 10380 0.179076 CACCTGCATAGATCGGCACA 60.179 55.000 5.78 0.00 35.86 4.57
6537 10387 0.882042 CGGCCACACCTGCATAGATC 60.882 60.000 2.24 0.00 35.61 2.75
6621 10472 1.015109 TCGCTCTGATCGTGTACTCC 58.985 55.000 0.55 0.00 0.00 3.85
6659 10510 5.133322 TGGAAGAATTTGCTGGAGGATCTAT 59.867 40.000 0.00 0.00 33.73 1.98
6661 10512 3.267812 TGGAAGAATTTGCTGGAGGATCT 59.732 43.478 0.00 0.00 33.73 2.75
6673 10524 2.493278 CCTCAACGGCATGGAAGAATTT 59.507 45.455 0.00 0.00 0.00 1.82
6674 10525 2.094675 CCTCAACGGCATGGAAGAATT 58.905 47.619 0.00 0.00 0.00 2.17
6675 10526 1.755179 CCTCAACGGCATGGAAGAAT 58.245 50.000 0.00 0.00 0.00 2.40
6769 10633 2.281208 TAGCACCAACACCGTGGC 60.281 61.111 3.03 0.00 43.00 5.01
6813 10677 3.891366 CCTTCAGCCTTTTCCTTCAGAAA 59.109 43.478 0.00 0.00 42.82 2.52
6891 10759 3.703001 ACTACCATGGTTCAGGTCTTG 57.297 47.619 25.38 0.00 39.31 3.02
6904 10777 5.125097 CCGTAAAGTGAGTGACTACTACCAT 59.875 44.000 0.00 0.00 37.25 3.55
6916 10789 1.291272 GGTCCGCCGTAAAGTGAGT 59.709 57.895 0.00 0.00 0.00 3.41
6991 10864 7.342026 ACCACTTCCACTTCATTTATTTATCCC 59.658 37.037 0.00 0.00 0.00 3.85
7004 10877 4.023963 GCTAAACTGAACCACTTCCACTTC 60.024 45.833 0.00 0.00 0.00 3.01
7005 10878 3.883489 GCTAAACTGAACCACTTCCACTT 59.117 43.478 0.00 0.00 0.00 3.16
7006 10879 3.118038 TGCTAAACTGAACCACTTCCACT 60.118 43.478 0.00 0.00 0.00 4.00
7007 10880 3.003378 GTGCTAAACTGAACCACTTCCAC 59.997 47.826 0.00 0.00 0.00 4.02
7008 10881 3.118038 AGTGCTAAACTGAACCACTTCCA 60.118 43.478 0.00 0.00 37.88 3.53
7009 10882 3.477530 AGTGCTAAACTGAACCACTTCC 58.522 45.455 0.00 0.00 37.88 3.46
7065 10938 2.677836 CCAACACAGACCCACAATATCG 59.322 50.000 0.00 0.00 0.00 2.92
7129 11002 7.875971 AGAATGACAGAATTTACAAGAACACC 58.124 34.615 0.00 0.00 0.00 4.16
7169 11043 5.947228 TGTAGAGGAATTTGACTTGCAAG 57.053 39.130 24.84 24.84 37.87 4.01
7219 11107 2.279741 TGACTTACGATTGCCTGATGC 58.720 47.619 0.00 0.00 41.77 3.91
7231 11119 6.427242 TGAGGAGCTACTGTATATGACTTACG 59.573 42.308 0.99 0.00 0.00 3.18
7278 11166 6.648725 AATGCAAGTAGTTACTGACGAATC 57.351 37.500 0.00 0.00 36.50 2.52
7293 11181 4.147321 ACAGATGTCCTGAAAATGCAAGT 58.853 39.130 0.00 0.00 45.78 3.16
7353 11241 4.159321 TGACAAATTGTTGGTGATGTGTGT 59.841 37.500 0.00 0.00 39.22 3.72
7355 11243 4.998671 TGACAAATTGTTGGTGATGTGT 57.001 36.364 0.00 0.00 39.22 3.72
7359 11247 8.735692 ATTTTCTTTGACAAATTGTTGGTGAT 57.264 26.923 0.00 0.00 39.22 3.06
7361 11249 7.065563 TGGATTTTCTTTGACAAATTGTTGGTG 59.934 33.333 0.00 0.00 39.22 4.17
7362 11250 7.108847 TGGATTTTCTTTGACAAATTGTTGGT 58.891 30.769 0.00 0.00 39.22 3.67
7363 11251 7.280652 ACTGGATTTTCTTTGACAAATTGTTGG 59.719 33.333 0.00 0.00 39.22 3.77
7364 11252 8.200364 ACTGGATTTTCTTTGACAAATTGTTG 57.800 30.769 0.00 0.00 40.84 3.33
7365 11253 8.040132 TGACTGGATTTTCTTTGACAAATTGTT 58.960 29.630 0.00 0.00 0.00 2.83
7366 11254 7.555087 TGACTGGATTTTCTTTGACAAATTGT 58.445 30.769 0.00 0.00 0.00 2.71
7368 11256 9.617523 ATTTGACTGGATTTTCTTTGACAAATT 57.382 25.926 0.05 0.00 32.78 1.82
7386 11283 7.538678 GGCAACAGTGTTTCTATTATTTGACTG 59.461 37.037 5.57 0.00 36.48 3.51
7389 11286 7.094377 GGAGGCAACAGTGTTTCTATTATTTGA 60.094 37.037 5.57 0.00 41.41 2.69
7404 11301 1.064906 CAGATGATGGGAGGCAACAGT 60.065 52.381 0.00 0.00 41.41 3.55
7427 11324 1.663135 GCTTCGAGTGGCTCAGAATTC 59.337 52.381 0.00 0.00 0.00 2.17
7428 11325 1.731720 GCTTCGAGTGGCTCAGAATT 58.268 50.000 0.00 0.00 0.00 2.17
7430 11327 1.080501 CGCTTCGAGTGGCTCAGAA 60.081 57.895 5.77 1.47 0.00 3.02
7431 11328 2.568612 CGCTTCGAGTGGCTCAGA 59.431 61.111 5.77 0.00 0.00 3.27
7461 11358 4.158025 AGCGAAATCTCTCTCGGTTCTAAA 59.842 41.667 0.00 0.00 42.68 1.85
7462 11359 3.695060 AGCGAAATCTCTCTCGGTTCTAA 59.305 43.478 0.00 0.00 42.68 2.10
7463 11360 3.280295 AGCGAAATCTCTCTCGGTTCTA 58.720 45.455 0.00 0.00 42.68 2.10
7464 11361 2.096248 AGCGAAATCTCTCTCGGTTCT 58.904 47.619 0.00 0.00 42.68 3.01
7468 11365 1.565305 CCAAGCGAAATCTCTCTCGG 58.435 55.000 0.00 0.00 35.60 4.63
7469 11366 1.565305 CCCAAGCGAAATCTCTCTCG 58.435 55.000 0.00 0.00 38.11 4.04
7470 11367 1.294857 GCCCAAGCGAAATCTCTCTC 58.705 55.000 0.00 0.00 0.00 3.20
7482 11387 1.037030 TCAAATCCGATGGCCCAAGC 61.037 55.000 0.00 0.00 38.76 4.01
7563 11468 2.159382 CTCCACCGTTACAATTTGGCT 58.841 47.619 0.78 0.00 0.00 4.75
7573 11478 4.030314 TCTCTTCTCTTCTCCACCGTTA 57.970 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.