Multiple sequence alignment - TraesCS5B01G052900

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 TraesCS5B01G052900 chr5B 100.000 3523 0 0 1 3523 57683395 57686917 0.000000e+00 6506.0
1 TraesCS5B01G052900 chr5B 81.182 914 137 24 1 900 338955367 338956259 0.000000e+00 702.0
2 TraesCS5B01G052900 chr5B 92.523 428 32 0 3095 3522 57696303 57696730 6.460000e-172 614.0
3 TraesCS5B01G052900 chr5B 88.200 500 50 9 2182 2678 540322612 540322119 3.920000e-164 588.0
4 TraesCS5B01G052900 chr5B 97.872 47 1 0 2682 2728 540321853 540321807 8.110000e-12 82.4
5 TraesCS5B01G052900 chr3D 91.348 1491 83 8 2047 3523 324421083 324419625 0.000000e+00 1997.0
6 TraesCS5B01G052900 chr3D 96.040 808 32 0 894 1701 324422288 324421481 0.000000e+00 1315.0
7 TraesCS5B01G052900 chr3D 91.907 729 55 2 974 1701 324397904 324397179 0.000000e+00 1016.0
8 TraesCS5B01G052900 chr3D 85.336 907 95 20 1 902 324423888 324423015 0.000000e+00 904.0
9 TraesCS5B01G052900 chr3D 87.484 775 81 12 942 1706 324393631 324392863 0.000000e+00 880.0
10 TraesCS5B01G052900 chr3D 84.199 924 98 28 1 913 120105282 120104396 0.000000e+00 854.0
11 TraesCS5B01G052900 chr3D 88.800 500 41 8 2182 2678 324392257 324391770 1.810000e-167 599.0
12 TraesCS5B01G052900 chr3D 84.749 518 62 12 406 909 141671231 141670717 1.460000e-138 503.0
13 TraesCS5B01G052900 chr3D 86.937 444 41 3 3095 3523 324413643 324413202 1.900000e-132 483.0
14 TraesCS5B01G052900 chr3D 92.647 272 19 1 2818 3088 324391462 324391191 1.190000e-104 390.0
15 TraesCS5B01G052900 chr3D 80.328 427 63 16 3095 3503 497520170 497519747 1.590000e-78 303.0
16 TraesCS5B01G052900 chr3D 79.091 440 72 17 3095 3523 313050194 313050624 5.760000e-73 285.0
17 TraesCS5B01G052900 chr3D 93.443 183 9 1 1701 1880 324421338 324421156 5.800000e-68 268.0
18 TraesCS5B01G052900 chr3D 87.709 179 16 5 1701 1879 324392734 324392562 1.660000e-48 204.0
19 TraesCS5B01G052900 chr3D 83.784 185 10 8 1701 1880 324397036 324396867 1.310000e-34 158.0
20 TraesCS5B01G052900 chr3D 88.889 63 7 0 3200 3262 260053014 260052952 1.050000e-10 78.7
21 TraesCS5B01G052900 chr3A 89.330 1284 65 24 1701 2977 437891751 437890533 0.000000e+00 1546.0
22 TraesCS5B01G052900 chr3A 94.865 779 40 0 923 1701 437892671 437891893 0.000000e+00 1218.0
23 TraesCS5B01G052900 chr3A 91.329 715 59 1 987 1701 437661243 437660532 0.000000e+00 974.0
24 TraesCS5B01G052900 chr3A 91.329 715 59 1 987 1701 437876334 437875623 0.000000e+00 974.0
25 TraesCS5B01G052900 chr3A 85.355 915 106 17 1 909 437930963 437930071 0.000000e+00 922.0
26 TraesCS5B01G052900 chr3A 86.979 768 89 6 939 1699 437870892 437870129 0.000000e+00 854.0
27 TraesCS5B01G052900 chr3A 86.589 768 92 6 939 1699 437649562 437648799 0.000000e+00 837.0
28 TraesCS5B01G052900 chr3A 89.980 499 37 7 2182 2678 437648150 437647663 1.780000e-177 632.0
29 TraesCS5B01G052900 chr3A 86.637 449 38 6 3095 3523 437884487 437884041 8.850000e-131 477.0
30 TraesCS5B01G052900 chr3A 87.019 416 39 11 2182 2591 437869448 437869042 4.150000e-124 455.0
31 TraesCS5B01G052900 chr3A 86.701 391 39 4 3145 3523 437890532 437890143 4.200000e-114 422.0
32 TraesCS5B01G052900 chr3A 90.809 272 24 1 2818 3088 437647352 437647081 2.580000e-96 363.0
33 TraesCS5B01G052900 chr3A 91.045 268 23 1 2818 3084 437868761 437868494 9.300000e-96 361.0
34 TraesCS5B01G052900 chr3A 85.490 255 34 3 605 856 611695340 611695086 2.700000e-66 263.0
35 TraesCS5B01G052900 chr3A 91.351 185 11 2 1701 1880 437660389 437660205 7.550000e-62 248.0
36 TraesCS5B01G052900 chr3A 90.270 185 9 3 1701 1880 437875480 437875300 2.110000e-57 233.0
37 TraesCS5B01G052900 chr3A 94.667 75 4 0 3101 3175 437671123 437671049 2.220000e-22 117.0
38 TraesCS5B01G052900 chr3B 90.112 1163 87 18 1936 3091 424576364 424577505 0.000000e+00 1485.0
39 TraesCS5B01G052900 chr3B 92.535 777 47 5 928 1701 424575277 424576045 0.000000e+00 1103.0
40 TraesCS5B01G052900 chr3B 91.602 774 51 3 939 1701 424738773 424739543 0.000000e+00 1057.0
41 TraesCS5B01G052900 chr3B 87.193 773 83 12 939 1701 424784137 424784903 0.000000e+00 865.0
42 TraesCS5B01G052900 chr3B 80.109 920 143 33 1 907 465653544 465654436 0.000000e+00 649.0
43 TraesCS5B01G052900 chr3B 89.178 499 41 5 2182 2678 424785968 424786455 8.360000e-171 610.0
44 TraesCS5B01G052900 chr3B 82.946 516 53 17 1701 2184 424785041 424785553 1.940000e-117 433.0
45 TraesCS5B01G052900 chr3B 90.441 272 25 1 2818 3088 424786768 424787039 1.200000e-94 357.0
46 TraesCS5B01G052900 chr3B 88.797 241 21 5 1936 2172 424785681 424785919 1.240000e-74 291.0
47 TraesCS5B01G052900 chr3B 75.307 733 95 39 202 913 802691609 802690942 4.480000e-69 272.0
48 TraesCS5B01G052900 chr3B 92.432 185 9 2 1701 1880 424739686 424739870 3.490000e-65 259.0
49 TraesCS5B01G052900 chr3B 92.308 182 11 1 1701 1879 424576186 424576367 4.510000e-64 255.0
50 TraesCS5B01G052900 chr3B 76.940 451 90 11 2 446 507282922 507283364 9.770000e-61 244.0
51 TraesCS5B01G052900 chr3B 90.164 122 12 0 1758 1879 424785563 424785684 3.640000e-35 159.0
52 TraesCS5B01G052900 chr3B 95.556 45 2 0 2682 2726 424786722 424786766 4.880000e-09 73.1
53 TraesCS5B01G052900 chr6B 84.551 835 89 22 1 829 584912839 584912039 0.000000e+00 791.0
54 TraesCS5B01G052900 chr6B 78.926 745 111 24 172 907 244856085 244855378 6.890000e-127 464.0
55 TraesCS5B01G052900 chr4D 87.463 678 69 9 1 677 309496333 309496995 0.000000e+00 767.0
56 TraesCS5B01G052900 chr1A 80.895 916 119 35 1 909 474445109 474444243 0.000000e+00 671.0
57 TraesCS5B01G052900 chr1A 86.697 218 24 5 694 907 287538523 287538739 1.630000e-58 237.0
58 TraesCS5B01G052900 chr1A 90.625 64 4 2 1882 1945 109577151 109577212 2.250000e-12 84.2
59 TraesCS5B01G052900 chr7D 80.326 920 140 28 1 909 538494859 538495748 0.000000e+00 658.0
60 TraesCS5B01G052900 chr7D 85.931 462 62 3 1 461 250316715 250316256 1.140000e-134 490.0
61 TraesCS5B01G052900 chr7D 79.043 439 78 10 3095 3523 140728710 140728276 4.450000e-74 289.0
62 TraesCS5B01G052900 chr7D 94.737 57 3 0 1882 1938 34234315 34234259 4.840000e-14 89.8
63 TraesCS5B01G052900 chr5D 85.021 474 64 6 406 874 46715452 46714981 3.180000e-130 475.0
64 TraesCS5B01G052900 chr5D 79.372 446 72 15 3095 3523 138874326 138874768 2.660000e-76 296.0
65 TraesCS5B01G052900 chr5D 79.954 439 59 21 477 907 470749390 470749807 2.660000e-76 296.0
66 TraesCS5B01G052900 chr5D 93.103 58 4 0 3199 3256 226314064 226314121 6.270000e-13 86.1
67 TraesCS5B01G052900 chr5D 90.625 64 4 2 1877 1938 298145759 298145822 2.250000e-12 84.2
68 TraesCS5B01G052900 chr2D 81.701 623 67 29 300 910 607602792 607603379 3.180000e-130 475.0
69 TraesCS5B01G052900 chr2D 91.667 60 3 1 1885 1942 422773736 422773677 8.110000e-12 82.4
70 TraesCS5B01G052900 chr2D 88.889 63 7 0 3200 3262 322176866 322176804 1.050000e-10 78.7
71 TraesCS5B01G052900 chr7A 76.825 863 159 32 1 848 680560659 680561495 6.940000e-122 448.0
72 TraesCS5B01G052900 chr7A 82.407 432 59 11 408 834 675137203 675136784 9.300000e-96 361.0
73 TraesCS5B01G052900 chr7A 72.683 410 91 17 3095 3493 472187763 472187364 2.220000e-22 117.0
74 TraesCS5B01G052900 chr7A 88.406 69 5 2 1873 1940 83786107 83786041 2.920000e-11 80.5
75 TraesCS5B01G052900 chr1D 90.132 304 29 1 400 703 480938265 480938567 9.170000e-106 394.0
76 TraesCS5B01G052900 chr1D 80.872 298 45 12 619 910 278526592 278526883 1.270000e-54 224.0
77 TraesCS5B01G052900 chr1D 94.737 57 2 1 1882 1938 48193822 48193877 1.740000e-13 87.9
78 TraesCS5B01G052900 chr5A 81.720 279 39 11 636 907 601261591 601261864 4.580000e-54 222.0
79 TraesCS5B01G052900 chr4A 83.613 238 26 11 680 909 8590933 8590701 9.910000e-51 211.0
80 TraesCS5B01G052900 chr4A 75.446 448 90 15 3093 3523 238189801 238190245 2.140000e-47 200.0
81 TraesCS5B01G052900 chr7B 74.483 435 86 18 3095 3523 375165235 375165650 7.820000e-37 165.0
82 TraesCS5B01G052900 chr7B 93.443 61 3 1 1882 1941 196390833 196390893 4.840000e-14 89.8
83 TraesCS5B01G052900 chr6A 94.737 57 3 0 1882 1938 594732744 594732800 4.840000e-14 89.8
84 TraesCS5B01G052900 chr4B 100.000 28 0 0 2733 2760 555341008 555340981 6.000000e-03 52.8


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 TraesCS5B01G052900 chr5B 57683395 57686917 3522 False 6506.000000 6506 100.000000 1 3523 1 chr5B.!!$F1 3522
1 TraesCS5B01G052900 chr5B 338955367 338956259 892 False 702.000000 702 81.182000 1 900 1 chr5B.!!$F3 899
2 TraesCS5B01G052900 chr5B 540321807 540322612 805 True 335.200000 588 93.036000 2182 2728 2 chr5B.!!$R1 546
3 TraesCS5B01G052900 chr3D 324419625 324423888 4263 True 1121.000000 1997 91.541750 1 3523 4 chr3D.!!$R7 3522
4 TraesCS5B01G052900 chr3D 120104396 120105282 886 True 854.000000 854 84.199000 1 913 1 chr3D.!!$R1 912
5 TraesCS5B01G052900 chr3D 324391191 324397904 6713 True 541.166667 1016 88.721833 942 3088 6 chr3D.!!$R6 2146
6 TraesCS5B01G052900 chr3D 141670717 141671231 514 True 503.000000 503 84.749000 406 909 1 chr3D.!!$R2 503
7 TraesCS5B01G052900 chr3A 437890143 437892671 2528 True 1062.000000 1546 90.298667 923 3523 3 chr3A.!!$R9 2600
8 TraesCS5B01G052900 chr3A 437930071 437930963 892 True 922.000000 922 85.355000 1 909 1 chr3A.!!$R3 908
9 TraesCS5B01G052900 chr3A 437660205 437661243 1038 True 611.000000 974 91.340000 987 1880 2 chr3A.!!$R6 893
10 TraesCS5B01G052900 chr3A 437647081 437649562 2481 True 610.666667 837 89.126000 939 3088 3 chr3A.!!$R5 2149
11 TraesCS5B01G052900 chr3A 437875300 437876334 1034 True 603.500000 974 90.799500 987 1880 2 chr3A.!!$R8 893
12 TraesCS5B01G052900 chr3A 437868494 437870892 2398 True 556.666667 854 88.347667 939 3084 3 chr3A.!!$R7 2145
13 TraesCS5B01G052900 chr3B 424575277 424577505 2228 False 947.666667 1485 91.651667 928 3091 3 chr3B.!!$F3 2163
14 TraesCS5B01G052900 chr3B 424738773 424739870 1097 False 658.000000 1057 92.017000 939 1880 2 chr3B.!!$F4 941
15 TraesCS5B01G052900 chr3B 465653544 465654436 892 False 649.000000 649 80.109000 1 907 1 chr3B.!!$F1 906
16 TraesCS5B01G052900 chr3B 424784137 424787039 2902 False 398.300000 865 89.182143 939 3088 7 chr3B.!!$F5 2149
17 TraesCS5B01G052900 chr3B 802690942 802691609 667 True 272.000000 272 75.307000 202 913 1 chr3B.!!$R1 711
18 TraesCS5B01G052900 chr6B 584912039 584912839 800 True 791.000000 791 84.551000 1 829 1 chr6B.!!$R2 828
19 TraesCS5B01G052900 chr6B 244855378 244856085 707 True 464.000000 464 78.926000 172 907 1 chr6B.!!$R1 735
20 TraesCS5B01G052900 chr4D 309496333 309496995 662 False 767.000000 767 87.463000 1 677 1 chr4D.!!$F1 676
21 TraesCS5B01G052900 chr1A 474444243 474445109 866 True 671.000000 671 80.895000 1 909 1 chr1A.!!$R1 908
22 TraesCS5B01G052900 chr7D 538494859 538495748 889 False 658.000000 658 80.326000 1 909 1 chr7D.!!$F1 908
23 TraesCS5B01G052900 chr2D 607602792 607603379 587 False 475.000000 475 81.701000 300 910 1 chr2D.!!$F1 610
24 TraesCS5B01G052900 chr7A 680560659 680561495 836 False 448.000000 448 76.825000 1 848 1 chr7A.!!$F1 847

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
116 117 0.034198 TGTGATTCAACGCCGGAAGA 59.966 50.0 5.05 0.0 0.00 2.87 F
613 688 0.036732 AGCCAGCGGAAGAAATGTGA 59.963 50.0 0.00 0.0 0.00 3.58 F
614 689 0.449388 GCCAGCGGAAGAAATGTGAG 59.551 55.0 0.00 0.0 0.00 3.51 F
1567 2428 0.672401 GGATTTCGACAAGGCCGACA 60.672 55.0 0.00 0.0 35.61 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 2428 0.394565 AGCTTGTCAAGAGTCGCCTT 59.605 50.0 16.99 0.00 0.0 4.35 R
1934 7346 0.470766 TGGGTCGGCTGTTTTGTACT 59.529 50.0 0.00 0.00 0.0 2.73 R
1936 7348 0.470766 AGTGGGTCGGCTGTTTTGTA 59.529 50.0 0.00 0.00 0.0 2.41 R
3455 9305 0.247460 CATCAGAGAAGCACCGGTGA 59.753 55.0 38.30 15.05 0.0 4.02 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 39 4.388469 CGGCGGAATTTTTGATGTTTGAAT 59.612 37.500 0.00 0.00 0.00 2.57
99 100 1.261480 ATGTCCGCTCTCTCAGTTGT 58.739 50.000 0.00 0.00 0.00 3.32
116 117 0.034198 TGTGATTCAACGCCGGAAGA 59.966 50.000 5.05 0.00 0.00 2.87
210 224 0.106469 CTCCTCCTCCTCATCGGACA 60.106 60.000 0.00 0.00 36.69 4.02
282 297 0.108851 GCCCATTTTGTACCTTGGCG 60.109 55.000 0.00 0.00 0.00 5.69
305 320 3.294493 TTGAACAGCTTGCGGGCC 61.294 61.111 0.00 0.00 0.00 5.80
440 475 1.393603 TGCTGGTGAGGATCTAGACG 58.606 55.000 0.00 0.00 34.92 4.18
563 620 2.045926 GAGGTGGAGGCGTTGCAT 60.046 61.111 0.00 0.00 0.00 3.96
568 625 1.090052 GTGGAGGCGTTGCATAGGAC 61.090 60.000 0.00 0.00 0.00 3.85
578 635 2.819608 GTTGCATAGGACATGTTGTGGT 59.180 45.455 0.00 0.00 0.00 4.16
609 684 0.326264 ACAGAGCCAGCGGAAGAAAT 59.674 50.000 0.00 0.00 0.00 2.17
610 685 0.731417 CAGAGCCAGCGGAAGAAATG 59.269 55.000 0.00 0.00 0.00 2.32
611 686 0.326264 AGAGCCAGCGGAAGAAATGT 59.674 50.000 0.00 0.00 0.00 2.71
612 687 0.449388 GAGCCAGCGGAAGAAATGTG 59.551 55.000 0.00 0.00 0.00 3.21
613 688 0.036732 AGCCAGCGGAAGAAATGTGA 59.963 50.000 0.00 0.00 0.00 3.58
614 689 0.449388 GCCAGCGGAAGAAATGTGAG 59.551 55.000 0.00 0.00 0.00 3.51
615 690 1.089920 CCAGCGGAAGAAATGTGAGG 58.910 55.000 0.00 0.00 0.00 3.86
616 691 1.611673 CCAGCGGAAGAAATGTGAGGT 60.612 52.381 0.00 0.00 0.00 3.85
617 692 1.466167 CAGCGGAAGAAATGTGAGGTG 59.534 52.381 0.00 0.00 0.00 4.00
794 895 2.361104 GAAATGGGTCGGCAGGCA 60.361 61.111 0.00 0.00 0.00 4.75
860 961 3.509137 TTTTCTGTCCGCGCCGACT 62.509 57.895 25.39 0.00 33.70 4.18
888 991 3.192922 CCCGCGGACGAAATGGTC 61.193 66.667 30.73 0.00 43.93 4.02
934 1774 3.548668 CGCTTATTGTGTTTGATGGCATG 59.451 43.478 3.81 0.00 0.00 4.06
935 1775 4.497300 GCTTATTGTGTTTGATGGCATGT 58.503 39.130 3.81 0.00 0.00 3.21
1100 1961 4.124351 CCGTGCCCTCGAACGCTA 62.124 66.667 1.87 0.00 38.46 4.26
1230 2091 0.752658 CCATGGATCTCGGCACTGTA 59.247 55.000 5.56 0.00 0.00 2.74
1459 2320 1.220206 CTCAAGGATGAGCTGCCGT 59.780 57.895 0.00 0.00 46.11 5.68
1524 2385 0.986019 ACATAGGCGGGTGGATCCAA 60.986 55.000 18.20 0.00 38.11 3.53
1567 2428 0.672401 GGATTTCGACAAGGCCGACA 60.672 55.000 0.00 0.00 35.61 4.35
1594 2455 2.171448 ACTCTTGACAAGCTTGAGTGGT 59.829 45.455 32.50 18.02 36.74 4.16
1610 2471 2.510238 GTTGCTCGCTCTCGCCAT 60.510 61.111 0.00 0.00 35.26 4.40
1680 2542 2.676632 TGGGCAGCATAATTTTGCAG 57.323 45.000 20.75 14.73 45.23 4.41
1755 2788 9.051679 CGTCATTTTGGAATTGGTAGTGATATA 57.948 33.333 0.00 0.00 0.00 0.86
1809 2844 6.039159 TGCATTGTTGATACAAGAAGTTGTCA 59.961 34.615 0.00 0.00 43.88 3.58
1831 2866 6.698766 GTCAAAGAAGTTCAGTTTCATGCATT 59.301 34.615 5.50 0.00 0.00 3.56
1832 2867 7.223387 GTCAAAGAAGTTCAGTTTCATGCATTT 59.777 33.333 5.50 0.00 0.00 2.32
1882 7294 5.928976 TGATGCTGCATAAATGGTACTACT 58.071 37.500 16.23 0.00 0.00 2.57
1883 7295 5.991606 TGATGCTGCATAAATGGTACTACTC 59.008 40.000 16.23 0.00 0.00 2.59
1884 7296 4.703897 TGCTGCATAAATGGTACTACTCC 58.296 43.478 0.00 0.00 0.00 3.85
1885 7297 3.741344 GCTGCATAAATGGTACTACTCCG 59.259 47.826 0.00 0.00 0.00 4.63
1887 7299 4.940463 TGCATAAATGGTACTACTCCGTC 58.060 43.478 0.00 0.00 0.00 4.79
1888 7300 4.202182 TGCATAAATGGTACTACTCCGTCC 60.202 45.833 0.00 0.00 0.00 4.79
1890 7302 2.537633 AATGGTACTACTCCGTCCCA 57.462 50.000 0.00 0.00 0.00 4.37
1891 7303 2.769602 ATGGTACTACTCCGTCCCAT 57.230 50.000 0.00 0.00 0.00 4.00
1892 7304 3.889859 ATGGTACTACTCCGTCCCATA 57.110 47.619 0.00 0.00 31.14 2.74
1893 7305 3.668141 TGGTACTACTCCGTCCCATAA 57.332 47.619 0.00 0.00 0.00 1.90
1894 7306 4.188937 TGGTACTACTCCGTCCCATAAT 57.811 45.455 0.00 0.00 0.00 1.28
1895 7307 5.323382 TGGTACTACTCCGTCCCATAATA 57.677 43.478 0.00 0.00 0.00 0.98
1896 7308 5.895807 TGGTACTACTCCGTCCCATAATAT 58.104 41.667 0.00 0.00 0.00 1.28
1897 7309 7.031415 TGGTACTACTCCGTCCCATAATATA 57.969 40.000 0.00 0.00 0.00 0.86
1898 7310 7.469343 TGGTACTACTCCGTCCCATAATATAA 58.531 38.462 0.00 0.00 0.00 0.98
1899 7311 7.613022 TGGTACTACTCCGTCCCATAATATAAG 59.387 40.741 0.00 0.00 0.00 1.73
1900 7312 7.831193 GGTACTACTCCGTCCCATAATATAAGA 59.169 40.741 0.00 0.00 0.00 2.10
1901 7313 7.941431 ACTACTCCGTCCCATAATATAAGAG 57.059 40.000 0.00 0.00 0.00 2.85
1902 7314 5.662674 ACTCCGTCCCATAATATAAGAGC 57.337 43.478 0.00 0.00 0.00 4.09
1903 7315 4.158025 ACTCCGTCCCATAATATAAGAGCG 59.842 45.833 0.00 0.00 0.00 5.03
1904 7316 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
1905 7317 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
1906 7318 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
1907 7319 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
1908 7320 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
1909 7321 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
1910 7322 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
1911 7323 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
1912 7324 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
1913 7325 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
1914 7326 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
1915 7327 9.988350 CATAATATAAGAGCGTTTTTGACACTT 57.012 29.630 0.00 0.00 0.00 3.16
1923 7335 9.988350 AAGAGCGTTTTTGACACTTATATTATG 57.012 29.630 0.00 0.00 0.00 1.90
1924 7336 9.378551 AGAGCGTTTTTGACACTTATATTATGA 57.621 29.630 0.00 0.00 0.00 2.15
1925 7337 9.638300 GAGCGTTTTTGACACTTATATTATGAG 57.362 33.333 0.00 0.00 0.00 2.90
1926 7338 9.378551 AGCGTTTTTGACACTTATATTATGAGA 57.621 29.630 2.71 0.00 0.00 3.27
1927 7339 9.422196 GCGTTTTTGACACTTATATTATGAGAC 57.578 33.333 2.71 0.00 0.00 3.36
1928 7340 9.619727 CGTTTTTGACACTTATATTATGAGACG 57.380 33.333 2.71 0.00 0.00 4.18
1929 7341 9.422196 GTTTTTGACACTTATATTATGAGACGC 57.578 33.333 2.71 0.00 0.00 5.19
1930 7342 8.710835 TTTTGACACTTATATTATGAGACGCA 57.289 30.769 2.71 0.00 0.00 5.24
1931 7343 7.930513 TTGACACTTATATTATGAGACGCAG 57.069 36.000 2.71 0.00 0.00 5.18
1932 7344 6.447162 TGACACTTATATTATGAGACGCAGG 58.553 40.000 2.71 0.00 0.00 4.85
1933 7345 5.784177 ACACTTATATTATGAGACGCAGGG 58.216 41.667 2.71 0.00 0.00 4.45
1934 7346 5.538813 ACACTTATATTATGAGACGCAGGGA 59.461 40.000 2.71 0.00 0.00 4.20
1935 7347 6.096036 CACTTATATTATGAGACGCAGGGAG 58.904 44.000 2.71 0.00 0.00 4.30
1936 7348 5.775701 ACTTATATTATGAGACGCAGGGAGT 59.224 40.000 2.71 0.00 0.00 3.85
1937 7349 6.946583 ACTTATATTATGAGACGCAGGGAGTA 59.053 38.462 2.71 0.00 0.00 2.59
1938 7350 5.646577 ATATTATGAGACGCAGGGAGTAC 57.353 43.478 0.00 0.00 0.00 2.73
1939 7351 2.430248 TATGAGACGCAGGGAGTACA 57.570 50.000 0.00 0.00 0.00 2.90
1940 7352 1.557099 ATGAGACGCAGGGAGTACAA 58.443 50.000 0.00 0.00 0.00 2.41
1941 7353 1.334160 TGAGACGCAGGGAGTACAAA 58.666 50.000 0.00 0.00 0.00 2.83
1942 7354 1.689813 TGAGACGCAGGGAGTACAAAA 59.310 47.619 0.00 0.00 0.00 2.44
1943 7355 2.067013 GAGACGCAGGGAGTACAAAAC 58.933 52.381 0.00 0.00 0.00 2.43
1944 7356 1.414919 AGACGCAGGGAGTACAAAACA 59.585 47.619 0.00 0.00 0.00 2.83
1945 7357 1.798813 GACGCAGGGAGTACAAAACAG 59.201 52.381 0.00 0.00 0.00 3.16
1964 7376 4.337060 CGACCCACTCACGCGACA 62.337 66.667 15.93 0.00 0.00 4.35
2044 7458 2.221299 CGTGAGGGTGGAGGGGAAA 61.221 63.158 0.00 0.00 0.00 3.13
2080 7496 2.351350 GGAATTAGTTGTGGTTGTGGCG 60.351 50.000 0.00 0.00 0.00 5.69
2125 7549 7.362662 TGCAGTTAGTTCTGTCAATTTCAATC 58.637 34.615 0.00 0.00 37.70 2.67
2147 7571 4.219070 TCAGGGTTTTCATGCTCTTGATTG 59.781 41.667 0.00 0.00 0.00 2.67
2164 7590 8.311395 TCTTGATTGATCTCTGTAACTGGTAT 57.689 34.615 0.00 0.00 0.00 2.73
2265 7793 9.770097 TTTGATAGATTGCTCTGTTAGGATTAG 57.230 33.333 0.00 0.00 32.66 1.73
2349 7878 2.261037 TGCAATGTAAGCAATGACGC 57.739 45.000 0.00 0.00 39.39 5.19
2381 7913 4.949238 TCACTTGGAAATACATCACCATGG 59.051 41.667 11.19 11.19 33.82 3.66
2440 7974 3.695606 GCAGTGCCGTCCTCTGGA 61.696 66.667 2.85 0.00 35.97 3.86
2498 8039 0.764890 CTGGGTTGAGTGAGTGGGAA 59.235 55.000 0.00 0.00 0.00 3.97
2531 8072 1.203237 AGAGAGGGGTGACATGAGTGT 60.203 52.381 0.00 0.00 42.49 3.55
2560 8101 1.278127 GATTTGGGGACGAGAGGAACA 59.722 52.381 0.00 0.00 0.00 3.18
2562 8103 0.178944 TTGGGGACGAGAGGAACAGA 60.179 55.000 0.00 0.00 0.00 3.41
2608 8149 5.579047 TCAATTTGAGAATTTAGGGCCAGA 58.421 37.500 6.18 0.00 33.25 3.86
2621 8190 2.106166 AGGGCCAGATGCTATTCTGAAG 59.894 50.000 6.18 0.69 44.88 3.02
2622 8191 2.105477 GGGCCAGATGCTATTCTGAAGA 59.895 50.000 4.39 0.00 44.88 2.87
2623 8192 3.244840 GGGCCAGATGCTATTCTGAAGAT 60.245 47.826 4.39 0.00 44.88 2.40
2624 8193 4.396522 GGCCAGATGCTATTCTGAAGATT 58.603 43.478 0.00 0.00 44.88 2.40
2625 8194 5.513788 GGGCCAGATGCTATTCTGAAGATTA 60.514 44.000 4.39 0.00 44.88 1.75
2626 8195 6.000219 GGCCAGATGCTATTCTGAAGATTAA 59.000 40.000 0.00 0.00 44.88 1.40
2627 8196 6.488006 GGCCAGATGCTATTCTGAAGATTAAA 59.512 38.462 0.00 0.00 44.88 1.52
2628 8197 7.176340 GGCCAGATGCTATTCTGAAGATTAAAT 59.824 37.037 0.00 0.00 44.88 1.40
2629 8198 8.021973 GCCAGATGCTATTCTGAAGATTAAATG 58.978 37.037 11.81 0.00 44.88 2.32
2630 8199 9.281371 CCAGATGCTATTCTGAAGATTAAATGA 57.719 33.333 11.81 0.00 44.88 2.57
2639 8208 8.743085 TTCTGAAGATTAAATGATCAAGGAGG 57.257 34.615 0.00 0.00 0.00 4.30
2640 8209 8.094284 TCTGAAGATTAAATGATCAAGGAGGA 57.906 34.615 0.00 0.00 0.00 3.71
2641 8210 7.989741 TCTGAAGATTAAATGATCAAGGAGGAC 59.010 37.037 0.00 0.00 0.00 3.85
2642 8211 7.056635 TGAAGATTAAATGATCAAGGAGGACC 58.943 38.462 0.00 0.00 0.00 4.46
2643 8212 6.581388 AGATTAAATGATCAAGGAGGACCA 57.419 37.500 0.00 0.00 38.94 4.02
2644 8213 6.973642 AGATTAAATGATCAAGGAGGACCAA 58.026 36.000 0.00 0.00 38.94 3.67
2645 8214 7.413446 AGATTAAATGATCAAGGAGGACCAAA 58.587 34.615 0.00 0.00 38.94 3.28
2646 8215 8.063770 AGATTAAATGATCAAGGAGGACCAAAT 58.936 33.333 0.00 0.00 38.94 2.32
2647 8216 8.613922 ATTAAATGATCAAGGAGGACCAAATT 57.386 30.769 0.00 0.00 38.94 1.82
2648 8217 9.713684 ATTAAATGATCAAGGAGGACCAAATTA 57.286 29.630 0.00 0.00 38.94 1.40
2649 8218 7.651027 AAATGATCAAGGAGGACCAAATTAG 57.349 36.000 0.00 0.00 38.94 1.73
2947 8785 7.343357 TGGGATTTCACCTATTAGATTTCGTT 58.657 34.615 0.00 0.00 0.00 3.85
2951 8789 6.995511 TTCACCTATTAGATTTCGTTTGGG 57.004 37.500 0.00 0.00 0.00 4.12
2952 8790 6.057321 TCACCTATTAGATTTCGTTTGGGT 57.943 37.500 0.00 0.00 0.00 4.51
2967 8805 0.038166 TGGGTGAACCAGATTGGCTC 59.962 55.000 1.16 0.00 46.80 4.70
3037 8875 8.231692 TCATCAAGGAGTTGTTTGTTTTGATA 57.768 30.769 0.00 0.00 33.45 2.15
3048 8886 7.397892 TGTTTGTTTTGATAGTTGGAGTTCA 57.602 32.000 0.00 0.00 0.00 3.18
3091 8929 1.933853 GTAGCTAATTGGACGGTGCAG 59.066 52.381 1.81 0.00 0.00 4.41
3098 8936 4.314440 GGACGGTGCAGGCTGTCA 62.314 66.667 17.16 11.74 44.33 3.58
3111 8949 1.213926 GGCTGTCAGGGGATTGATTCT 59.786 52.381 1.14 0.00 0.00 2.40
3116 8954 2.172293 GTCAGGGGATTGATTCTGAGCT 59.828 50.000 0.00 0.00 37.00 4.09
3118 8956 3.389329 TCAGGGGATTGATTCTGAGCTAC 59.611 47.826 0.00 0.00 33.07 3.58
3160 8998 1.628846 GTTTGAGTTCTAGGGGCCTGA 59.371 52.381 0.84 0.00 0.00 3.86
3181 9019 0.883153 TTTGCGTCTACGAGGCTACA 59.117 50.000 6.71 0.00 42.87 2.74
3182 9020 1.100510 TTGCGTCTACGAGGCTACAT 58.899 50.000 6.71 0.00 42.87 2.29
3193 9031 1.500474 AGGCTACATGCTAGGCTTGA 58.500 50.000 18.94 0.00 46.48 3.02
3232 9070 3.175710 AGGTTCGGGCCACCTTGT 61.176 61.111 9.71 0.00 42.45 3.16
3234 9072 2.112297 GTTCGGGCCACCTTGTGA 59.888 61.111 4.39 0.00 35.23 3.58
3239 9077 1.024579 CGGGCCACCTTGTGATGTAC 61.025 60.000 4.39 0.00 35.23 2.90
3252 9090 5.202746 TGTGATGTACTACCCTACTCCTT 57.797 43.478 0.00 0.00 0.00 3.36
3281 9119 6.223120 GTTGTATTTTGCTTGTGGGAAGAAT 58.777 36.000 0.00 0.00 0.00 2.40
3287 9125 2.297033 TGCTTGTGGGAAGAATTCTTGC 59.703 45.455 26.52 26.52 46.56 4.01
3293 9131 3.950395 GTGGGAAGAATTCTTGCAGCTAT 59.050 43.478 32.42 6.86 46.56 2.97
3298 9136 6.204495 GGGAAGAATTCTTGCAGCTATAAGAG 59.796 42.308 32.42 0.00 46.56 2.85
3331 9181 1.002502 GGGCGCTAGGGTTTGAGTT 60.003 57.895 7.64 0.00 0.00 3.01
3365 9215 1.043116 CATCCTCTCTACGGTGGCCA 61.043 60.000 0.00 0.00 0.00 5.36
3385 9235 2.100916 CACCCTATCCCTTATATCGGCG 59.899 54.545 0.00 0.00 0.00 6.46
3402 9252 3.342477 GCCTTGGGCCTCTTCCCT 61.342 66.667 4.53 0.00 46.67 4.20
3427 9277 0.397957 TATGAGCGGGAAGGGCTACA 60.398 55.000 0.00 0.00 41.72 2.74
3448 9298 1.078709 CAGCGAGGCAATTCGAAAGA 58.921 50.000 0.00 0.00 43.03 2.52
3455 9305 2.039084 AGGCAATTCGAAAGAGGACAGT 59.961 45.455 0.00 0.00 43.69 3.55
3457 9307 3.067106 GCAATTCGAAAGAGGACAGTCA 58.933 45.455 0.00 0.00 43.69 3.41
3470 9320 1.115930 ACAGTCACCGGTGCTTCTCT 61.116 55.000 30.25 17.67 0.00 3.10
3473 9323 0.247736 GTCACCGGTGCTTCTCTGAT 59.752 55.000 30.25 0.00 0.00 2.90
3498 9348 0.598065 GTGGTCTTCGCCTGCAAAAT 59.402 50.000 0.00 0.00 0.00 1.82
3505 9355 3.316588 TCTTCGCCTGCAAAATGTGTTAA 59.683 39.130 0.00 0.00 0.00 2.01
3514 9364 3.121113 GCAAAATGTGTTAACCATGACGC 59.879 43.478 2.48 6.23 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.038618 AAATTCCGCCGCTGTTTTCC 60.039 50.000 0.00 0.00 0.00 3.13
13 14 0.887933 ACATCAAAAATTCCGCCGCT 59.112 45.000 0.00 0.00 0.00 5.52
38 39 3.757493 ACTTTGACACAACAAACCCGTTA 59.243 39.130 0.00 0.00 36.11 3.18
99 100 1.368641 CATCTTCCGGCGTTGAATCA 58.631 50.000 6.01 0.00 0.00 2.57
148 162 1.656587 TCACCACCTCAATAGCCAGT 58.343 50.000 0.00 0.00 0.00 4.00
210 224 3.616956 TTGCGACTCTGATGATTCCTT 57.383 42.857 0.00 0.00 0.00 3.36
264 278 1.540267 TCGCCAAGGTACAAAATGGG 58.460 50.000 0.00 0.00 33.45 4.00
305 320 2.604373 GCTGATCGTCTCCTTCATCGAG 60.604 54.545 0.00 0.00 35.85 4.04
563 620 0.321210 CGGCACCACAACATGTCCTA 60.321 55.000 0.00 0.00 0.00 2.94
568 625 3.271706 CTGCCGGCACCACAACATG 62.272 63.158 29.03 8.86 0.00 3.21
578 635 4.383861 CTCTGTCAGCTGCCGGCA 62.384 66.667 30.59 30.59 44.79 5.69
599 656 1.197721 CACACCTCACATTTCTTCCGC 59.802 52.381 0.00 0.00 0.00 5.54
630 705 1.006102 CAGCCTCCTTCGTCGTTGT 60.006 57.895 0.00 0.00 0.00 3.32
632 707 2.657237 CCAGCCTCCTTCGTCGTT 59.343 61.111 0.00 0.00 0.00 3.85
741 839 1.209127 GATTTGTGTTGGCCGGACG 59.791 57.895 5.05 0.00 0.00 4.79
750 849 4.562552 CCCATTTTTAGCCGGATTTGTGTT 60.563 41.667 5.05 0.00 0.00 3.32
753 852 2.093711 GCCCATTTTTAGCCGGATTTGT 60.094 45.455 5.05 0.00 0.00 2.83
794 895 0.315869 CACGCGTCTGCTTTTCGTTT 60.316 50.000 9.86 0.00 39.65 3.60
887 990 3.876589 GAGCAACTCCAACGGGCGA 62.877 63.158 0.00 0.00 0.00 5.54
888 991 2.501223 TAGAGCAACTCCAACGGGCG 62.501 60.000 0.00 0.00 0.00 6.13
889 992 0.321298 TTAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
934 1774 1.969589 AAACCACGAATCCGGCCAC 60.970 57.895 2.24 0.00 40.78 5.01
935 1775 1.969064 CAAACCACGAATCCGGCCA 60.969 57.895 2.24 0.00 40.78 5.36
1177 2038 0.810016 GAGAGGTAGTCGCGGAGTTT 59.190 55.000 6.13 0.00 0.00 2.66
1430 2291 1.144503 CATCCTTGAGCCTTGCCCTAT 59.855 52.381 0.00 0.00 0.00 2.57
1459 2320 4.641645 CAAGTCCACCGGCAGCCA 62.642 66.667 13.30 0.00 0.00 4.75
1524 2385 0.916358 CAACCCTCCCATCCACCTCT 60.916 60.000 0.00 0.00 0.00 3.69
1567 2428 0.394565 AGCTTGTCAAGAGTCGCCTT 59.605 50.000 16.99 0.00 0.00 4.35
1610 2471 6.351881 GGACACAATAGTTACCTTCCTGATGA 60.352 42.308 0.00 0.00 0.00 2.92
1680 2542 0.675633 ACAAGATTGCCACCAAGCAC 59.324 50.000 0.00 0.00 43.97 4.40
1755 2788 1.425066 TCCCAGAAAGGCAGTGTGAAT 59.575 47.619 0.00 0.00 35.39 2.57
1756 2789 0.843309 TCCCAGAAAGGCAGTGTGAA 59.157 50.000 0.00 0.00 35.39 3.18
1809 2844 8.416329 ACTAAATGCATGAAACTGAACTTCTTT 58.584 29.630 0.00 0.00 0.00 2.52
1882 7294 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
1883 7295 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
1884 7296 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
1885 7297 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
1887 7299 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
1888 7300 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
1901 7313 9.422196 GTCTCATAATATAAGTGTCAAAAACGC 57.578 33.333 0.00 0.00 38.74 4.84
1902 7314 9.619727 CGTCTCATAATATAAGTGTCAAAAACG 57.380 33.333 0.00 0.00 0.00 3.60
1903 7315 9.422196 GCGTCTCATAATATAAGTGTCAAAAAC 57.578 33.333 0.00 0.00 0.00 2.43
1904 7316 9.157104 TGCGTCTCATAATATAAGTGTCAAAAA 57.843 29.630 0.00 0.00 0.00 1.94
1905 7317 8.710835 TGCGTCTCATAATATAAGTGTCAAAA 57.289 30.769 0.00 0.00 0.00 2.44
1906 7318 7.438160 CCTGCGTCTCATAATATAAGTGTCAAA 59.562 37.037 0.00 0.00 0.00 2.69
1907 7319 6.923508 CCTGCGTCTCATAATATAAGTGTCAA 59.076 38.462 0.00 0.00 0.00 3.18
1908 7320 6.447162 CCTGCGTCTCATAATATAAGTGTCA 58.553 40.000 0.00 0.00 0.00 3.58
1909 7321 5.864474 CCCTGCGTCTCATAATATAAGTGTC 59.136 44.000 0.00 0.00 0.00 3.67
1910 7322 5.538813 TCCCTGCGTCTCATAATATAAGTGT 59.461 40.000 0.00 0.00 0.00 3.55
1911 7323 6.025749 TCCCTGCGTCTCATAATATAAGTG 57.974 41.667 0.00 0.00 0.00 3.16
1912 7324 5.775701 ACTCCCTGCGTCTCATAATATAAGT 59.224 40.000 0.00 0.00 0.00 2.24
1913 7325 6.274157 ACTCCCTGCGTCTCATAATATAAG 57.726 41.667 0.00 0.00 0.00 1.73
1914 7326 6.717997 TGTACTCCCTGCGTCTCATAATATAA 59.282 38.462 0.00 0.00 0.00 0.98
1915 7327 6.243148 TGTACTCCCTGCGTCTCATAATATA 58.757 40.000 0.00 0.00 0.00 0.86
1916 7328 5.077564 TGTACTCCCTGCGTCTCATAATAT 58.922 41.667 0.00 0.00 0.00 1.28
1917 7329 4.466827 TGTACTCCCTGCGTCTCATAATA 58.533 43.478 0.00 0.00 0.00 0.98
1918 7330 3.296854 TGTACTCCCTGCGTCTCATAAT 58.703 45.455 0.00 0.00 0.00 1.28
1919 7331 2.730382 TGTACTCCCTGCGTCTCATAA 58.270 47.619 0.00 0.00 0.00 1.90
1920 7332 2.430248 TGTACTCCCTGCGTCTCATA 57.570 50.000 0.00 0.00 0.00 2.15
1921 7333 1.557099 TTGTACTCCCTGCGTCTCAT 58.443 50.000 0.00 0.00 0.00 2.90
1922 7334 1.334160 TTTGTACTCCCTGCGTCTCA 58.666 50.000 0.00 0.00 0.00 3.27
1923 7335 2.067013 GTTTTGTACTCCCTGCGTCTC 58.933 52.381 0.00 0.00 0.00 3.36
1924 7336 1.414919 TGTTTTGTACTCCCTGCGTCT 59.585 47.619 0.00 0.00 0.00 4.18
1925 7337 1.798813 CTGTTTTGTACTCCCTGCGTC 59.201 52.381 0.00 0.00 0.00 5.19
1926 7338 1.878953 CTGTTTTGTACTCCCTGCGT 58.121 50.000 0.00 0.00 0.00 5.24
1927 7339 0.517316 GCTGTTTTGTACTCCCTGCG 59.483 55.000 0.00 0.00 0.00 5.18
1928 7340 0.881796 GGCTGTTTTGTACTCCCTGC 59.118 55.000 0.00 0.00 0.00 4.85
1929 7341 1.156736 CGGCTGTTTTGTACTCCCTG 58.843 55.000 0.00 0.00 0.00 4.45
1930 7342 1.053424 TCGGCTGTTTTGTACTCCCT 58.947 50.000 0.00 0.00 0.00 4.20
1931 7343 1.154197 GTCGGCTGTTTTGTACTCCC 58.846 55.000 0.00 0.00 0.00 4.30
1932 7344 1.154197 GGTCGGCTGTTTTGTACTCC 58.846 55.000 0.00 0.00 0.00 3.85
1933 7345 1.154197 GGGTCGGCTGTTTTGTACTC 58.846 55.000 0.00 0.00 0.00 2.59
1934 7346 0.470766 TGGGTCGGCTGTTTTGTACT 59.529 50.000 0.00 0.00 0.00 2.73
1935 7347 0.589708 GTGGGTCGGCTGTTTTGTAC 59.410 55.000 0.00 0.00 0.00 2.90
1936 7348 0.470766 AGTGGGTCGGCTGTTTTGTA 59.529 50.000 0.00 0.00 0.00 2.41
1937 7349 0.818040 GAGTGGGTCGGCTGTTTTGT 60.818 55.000 0.00 0.00 0.00 2.83
1938 7350 0.817634 TGAGTGGGTCGGCTGTTTTG 60.818 55.000 0.00 0.00 0.00 2.44
1939 7351 0.818040 GTGAGTGGGTCGGCTGTTTT 60.818 55.000 0.00 0.00 0.00 2.43
1940 7352 1.227853 GTGAGTGGGTCGGCTGTTT 60.228 57.895 0.00 0.00 0.00 2.83
1941 7353 2.426023 GTGAGTGGGTCGGCTGTT 59.574 61.111 0.00 0.00 0.00 3.16
1942 7354 3.991051 CGTGAGTGGGTCGGCTGT 61.991 66.667 0.00 0.00 0.00 4.40
2034 7447 0.698238 CACACATCCTTTCCCCTCCA 59.302 55.000 0.00 0.00 0.00 3.86
2044 7458 2.202236 ATTCCGGCTGCACACATCCT 62.202 55.000 0.50 0.00 29.36 3.24
2107 7531 5.388654 ACCCTGATTGAAATTGACAGAACT 58.611 37.500 0.00 0.00 0.00 3.01
2125 7549 4.219070 TCAATCAAGAGCATGAAAACCCTG 59.781 41.667 0.00 0.00 32.06 4.45
2147 7571 6.702282 GCCACTAAATACCAGTTACAGAGATC 59.298 42.308 0.00 0.00 0.00 2.75
2164 7590 3.997762 ACTACGAATGTGTGCCACTAAA 58.002 40.909 0.00 0.00 35.11 1.85
2347 7876 2.084610 TCCAAGTGAACTGATGAGCG 57.915 50.000 0.00 0.00 0.00 5.03
2349 7878 7.335171 TGATGTATTTCCAAGTGAACTGATGAG 59.665 37.037 0.00 0.00 31.05 2.90
2459 8000 1.893808 GATGACGCCATGGCCGAAT 60.894 57.895 30.79 20.28 37.98 3.34
2475 8016 0.987294 CACTCACTCAACCCAGGGAT 59.013 55.000 14.54 0.00 0.00 3.85
2498 8039 1.577736 CCTCTCTCACATGTCCCCTT 58.422 55.000 0.00 0.00 0.00 3.95
2531 8072 2.227757 TCCCCAAATCCAGCGGTGA 61.228 57.895 17.83 2.44 0.00 4.02
2533 8074 2.355115 GTCCCCAAATCCAGCGGT 59.645 61.111 0.00 0.00 0.00 5.68
2560 8101 4.202202 CGTCAAATCCCTAGCTCAATCTCT 60.202 45.833 0.00 0.00 0.00 3.10
2562 8103 3.742640 GCGTCAAATCCCTAGCTCAATCT 60.743 47.826 0.00 0.00 0.00 2.40
2621 8190 7.645058 TTTGGTCCTCCTTGATCATTTAATC 57.355 36.000 0.00 0.00 34.23 1.75
2622 8191 8.613922 AATTTGGTCCTCCTTGATCATTTAAT 57.386 30.769 0.00 0.00 34.23 1.40
2623 8192 9.189156 CTAATTTGGTCCTCCTTGATCATTTAA 57.811 33.333 0.00 0.00 34.23 1.52
2624 8193 8.336235 ACTAATTTGGTCCTCCTTGATCATTTA 58.664 33.333 0.00 0.00 34.23 1.40
2625 8194 7.184862 ACTAATTTGGTCCTCCTTGATCATTT 58.815 34.615 0.00 0.00 34.23 2.32
2626 8195 6.735556 ACTAATTTGGTCCTCCTTGATCATT 58.264 36.000 0.00 0.00 34.23 2.57
2627 8196 6.332976 ACTAATTTGGTCCTCCTTGATCAT 57.667 37.500 0.00 0.00 34.23 2.45
2628 8197 5.779241 ACTAATTTGGTCCTCCTTGATCA 57.221 39.130 0.00 0.00 34.23 2.92
2629 8198 7.339482 ACTTACTAATTTGGTCCTCCTTGATC 58.661 38.462 0.00 0.00 34.23 2.92
2630 8199 7.272144 ACTTACTAATTTGGTCCTCCTTGAT 57.728 36.000 0.00 0.00 34.23 2.57
2631 8200 6.697641 ACTTACTAATTTGGTCCTCCTTGA 57.302 37.500 0.00 0.00 34.23 3.02
2632 8201 6.715264 ACAACTTACTAATTTGGTCCTCCTTG 59.285 38.462 4.45 0.00 34.23 3.61
2633 8202 6.849151 ACAACTTACTAATTTGGTCCTCCTT 58.151 36.000 4.45 0.00 34.23 3.36
2634 8203 6.449830 ACAACTTACTAATTTGGTCCTCCT 57.550 37.500 4.45 0.00 34.23 3.69
2635 8204 7.881751 AGTTACAACTTACTAATTTGGTCCTCC 59.118 37.037 4.45 0.00 35.21 4.30
2636 8205 8.718734 CAGTTACAACTTACTAATTTGGTCCTC 58.281 37.037 4.45 0.00 37.08 3.71
2637 8206 7.174426 GCAGTTACAACTTACTAATTTGGTCCT 59.826 37.037 4.45 0.00 37.08 3.85
2638 8207 7.040961 TGCAGTTACAACTTACTAATTTGGTCC 60.041 37.037 4.45 0.00 37.08 4.46
2639 8208 7.867752 TGCAGTTACAACTTACTAATTTGGTC 58.132 34.615 4.45 0.00 37.08 4.02
2640 8209 7.811117 TGCAGTTACAACTTACTAATTTGGT 57.189 32.000 4.45 0.00 37.08 3.67
2641 8210 8.349983 ACTTGCAGTTACAACTTACTAATTTGG 58.650 33.333 4.45 0.00 37.08 3.28
2642 8211 9.730420 AACTTGCAGTTACAACTTACTAATTTG 57.270 29.630 0.44 0.00 36.52 2.32
2645 8214 9.946165 GAAAACTTGCAGTTACAACTTACTAAT 57.054 29.630 2.60 0.00 37.47 1.73
2646 8215 8.948145 TGAAAACTTGCAGTTACAACTTACTAA 58.052 29.630 2.60 0.00 37.47 2.24
2647 8216 8.495361 TGAAAACTTGCAGTTACAACTTACTA 57.505 30.769 2.60 0.00 37.47 1.82
2648 8217 7.385778 TGAAAACTTGCAGTTACAACTTACT 57.614 32.000 2.60 0.00 37.47 2.24
2649 8218 8.455598 TTTGAAAACTTGCAGTTACAACTTAC 57.544 30.769 14.40 0.00 37.47 2.34
2947 8785 0.482446 AGCCAATCTGGTTCACCCAA 59.518 50.000 0.00 0.00 44.65 4.12
2967 8805 1.952296 GCTATTGGCAGGATGAACTGG 59.048 52.381 0.00 0.00 39.69 4.00
3037 8875 3.554934 TCACAAAGCATGAACTCCAACT 58.445 40.909 0.00 0.00 0.00 3.16
3048 8886 1.474077 GCGGGAAGAATCACAAAGCAT 59.526 47.619 0.00 0.00 0.00 3.79
3091 8929 1.213926 AGAATCAATCCCCTGACAGCC 59.786 52.381 0.00 0.00 0.00 4.85
3098 8936 2.366916 CGTAGCTCAGAATCAATCCCCT 59.633 50.000 0.00 0.00 0.00 4.79
3111 8949 0.539986 GGTGGATTTCCCGTAGCTCA 59.460 55.000 0.00 0.00 37.93 4.26
3116 8954 2.516906 GGTTTTGGTGGATTTCCCGTA 58.483 47.619 0.00 0.00 37.93 4.02
3118 8956 0.606096 GGGTTTTGGTGGATTTCCCG 59.394 55.000 0.00 0.00 37.93 5.14
3143 8981 0.413832 AGTCAGGCCCCTAGAACTCA 59.586 55.000 0.00 0.00 0.00 3.41
3147 8985 0.328258 GCAAAGTCAGGCCCCTAGAA 59.672 55.000 0.00 0.00 0.00 2.10
3160 8998 1.135460 GTAGCCTCGTAGACGCAAAGT 60.135 52.381 0.00 0.00 40.93 2.66
3181 9019 1.550524 TGTCTTCGTCAAGCCTAGCAT 59.449 47.619 0.00 0.00 0.00 3.79
3182 9020 0.966179 TGTCTTCGTCAAGCCTAGCA 59.034 50.000 0.00 0.00 0.00 3.49
3190 9028 0.682852 AATCCCCGTGTCTTCGTCAA 59.317 50.000 0.00 0.00 0.00 3.18
3193 9031 1.066645 GGTAAATCCCCGTGTCTTCGT 60.067 52.381 0.00 0.00 0.00 3.85
3227 9065 4.341520 GGAGTAGGGTAGTACATCACAAGG 59.658 50.000 2.06 0.00 0.00 3.61
3232 9070 5.728937 AGAAGGAGTAGGGTAGTACATCA 57.271 43.478 2.06 0.00 0.00 3.07
3234 9072 5.209659 CCAAGAAGGAGTAGGGTAGTACAT 58.790 45.833 2.06 0.00 41.22 2.29
3239 9077 3.838903 ACAACCAAGAAGGAGTAGGGTAG 59.161 47.826 0.00 0.00 41.22 3.18
3252 9090 4.202202 CCCACAAGCAAAATACAACCAAGA 60.202 41.667 0.00 0.00 0.00 3.02
3281 9119 3.181461 GGCTCCTCTTATAGCTGCAAGAA 60.181 47.826 1.02 0.34 38.80 2.52
3287 9125 1.543802 CTCCGGCTCCTCTTATAGCTG 59.456 57.143 0.00 0.00 43.41 4.24
3331 9181 0.914417 GGATGGGTTCCTCACCTCCA 60.914 60.000 0.00 0.00 46.38 3.86
3365 9215 2.385803 CGCCGATATAAGGGATAGGGT 58.614 52.381 0.00 0.00 0.00 4.34
3370 9220 1.066143 CAAGGCGCCGATATAAGGGAT 60.066 52.381 23.20 0.00 0.00 3.85
3402 9252 2.930950 CCCTTCCCGCTCATATTTTCA 58.069 47.619 0.00 0.00 0.00 2.69
3427 9277 1.197721 CTTTCGAATTGCCTCGCTGTT 59.802 47.619 0.00 0.00 38.73 3.16
3434 9284 2.039084 ACTGTCCTCTTTCGAATTGCCT 59.961 45.455 0.00 0.00 0.00 4.75
3448 9298 2.100879 GAAGCACCGGTGACTGTCCT 62.101 60.000 38.30 20.81 0.00 3.85
3455 9305 0.247460 CATCAGAGAAGCACCGGTGA 59.753 55.000 38.30 15.05 0.00 4.02
3457 9307 0.976641 TTCATCAGAGAAGCACCGGT 59.023 50.000 0.00 0.00 0.00 5.28
3470 9320 1.610624 GGCGAAGACCACCTTTCATCA 60.611 52.381 0.00 0.00 34.68 3.07
3473 9323 0.250295 CAGGCGAAGACCACCTTTCA 60.250 55.000 0.00 0.00 31.70 2.69
3498 9348 1.570347 GGCGCGTCATGGTTAACACA 61.570 55.000 5.47 3.64 0.00 3.72


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

AutoCloner maintained by Alex Coulton.