Multiple sequence alignment - TraesCS5D01G194700

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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 TraesCS5D01G194700 chr5D 100.000 5383 0 0 1 5383 298690549 298695931 0.000000e+00 9941.0
1 TraesCS5D01G194700 chr5D 86.962 767 81 13 118 876 102021650 102020895 0.000000e+00 845.0
2 TraesCS5D01G194700 chr5D 79.478 268 48 6 4402 4666 259923723 259923986 3.310000e-42 183.0
3 TraesCS5D01G194700 chr5D 85.321 109 16 0 2128 2236 92464484 92464376 4.410000e-21 113.0
4 TraesCS5D01G194700 chr5D 100.000 35 0 0 2982 3016 298693496 298693530 1.250000e-06 65.8
5 TraesCS5D01G194700 chr5D 100.000 35 0 0 2948 2982 298693530 298693564 1.250000e-06 65.8
6 TraesCS5D01G194700 chr5A 90.650 2139 106 36 918 2982 400410665 400412783 0.000000e+00 2756.0
7 TraesCS5D01G194700 chr5A 87.398 2079 119 58 2378 4402 400501478 400499489 0.000000e+00 2255.0
8 TraesCS5D01G194700 chr5A 94.080 1419 57 10 918 2321 400502872 400501466 0.000000e+00 2130.0
9 TraesCS5D01G194700 chr5A 85.065 1453 104 57 2982 4399 400412749 400414123 0.000000e+00 1376.0
10 TraesCS5D01G194700 chr5A 81.210 628 110 8 4403 5027 341553866 341554488 2.890000e-137 499.0
11 TraesCS5D01G194700 chr5A 91.268 355 21 3 5037 5382 400425864 400426217 4.880000e-130 475.0
12 TraesCS5D01G194700 chr5A 91.579 285 9 7 4116 4399 400425609 400425879 3.930000e-101 379.0
13 TraesCS5D01G194700 chr5A 90.203 296 16 7 5036 5324 400414107 400414396 1.830000e-99 374.0
14 TraesCS5D01G194700 chr5A 89.735 302 18 7 5036 5330 400499508 400499213 1.830000e-99 374.0
15 TraesCS5D01G194700 chr5A 81.373 204 28 8 3542 3738 400412707 400412907 2.010000e-34 158.0
16 TraesCS5D01G194700 chr5A 79.730 222 35 8 2761 2982 150352719 150352508 9.340000e-33 152.0
17 TraesCS5D01G194700 chr5B 85.264 1459 112 44 2982 4399 339426584 339427980 0.000000e+00 1408.0
18 TraesCS5D01G194700 chr5B 93.295 701 24 11 918 1601 339424278 339424972 0.000000e+00 1013.0
19 TraesCS5D01G194700 chr5B 90.100 798 51 10 1636 2431 339424973 339425744 0.000000e+00 1011.0
20 TraesCS5D01G194700 chr5B 89.535 430 33 6 2450 2868 339425953 339426381 7.940000e-148 534.0
21 TraesCS5D01G194700 chr5B 93.156 263 15 2 5036 5296 339427964 339428225 3.040000e-102 383.0
22 TraesCS5D01G194700 chr5B 77.119 590 79 36 3336 3901 577020249 577020806 1.900000e-74 291.0
23 TraesCS5D01G194700 chr5B 90.991 111 8 2 2872 2982 339426510 339426618 1.210000e-31 148.0
24 TraesCS5D01G194700 chr5B 85.859 99 2 2 5286 5382 339428488 339428576 1.600000e-15 95.3
25 TraesCS5D01G194700 chr2B 92.334 887 28 16 3490 4360 98483993 98483131 0.000000e+00 1225.0
26 TraesCS5D01G194700 chr2B 89.139 801 75 9 113 906 14401672 14402467 0.000000e+00 987.0
27 TraesCS5D01G194700 chr2B 87.515 817 76 13 113 906 239464063 239463250 0.000000e+00 920.0
28 TraesCS5D01G194700 chr2B 88.486 634 72 1 4402 5035 63048444 63047812 0.000000e+00 765.0
29 TraesCS5D01G194700 chr2B 90.123 81 8 0 2599 2679 678198055 678197975 7.370000e-19 106.0
30 TraesCS5D01G194700 chr2B 90.909 77 7 0 2599 2675 677955900 677955976 2.650000e-18 104.0
31 TraesCS5D01G194700 chr7A 92.005 888 30 17 3490 4360 576477109 576477972 0.000000e+00 1208.0
32 TraesCS5D01G194700 chr7A 91.798 890 29 18 3490 4360 528226371 528225507 0.000000e+00 1199.0
33 TraesCS5D01G194700 chr7A 86.779 832 86 20 97 913 465272746 465271924 0.000000e+00 905.0
34 TraesCS5D01G194700 chr7A 86.224 813 92 15 115 913 46278445 46277639 0.000000e+00 863.0
35 TraesCS5D01G194700 chr7A 84.173 139 22 0 2115 2253 677871601 677871739 9.400000e-28 135.0
36 TraesCS5D01G194700 chr3B 91.901 889 31 16 3489 4360 712414652 712413788 0.000000e+00 1205.0
37 TraesCS5D01G194700 chr6A 91.206 887 38 15 3490 4360 549488453 549487591 0.000000e+00 1170.0
38 TraesCS5D01G194700 chr6A 94.787 633 30 2 4403 5035 23646424 23645795 0.000000e+00 983.0
39 TraesCS5D01G194700 chr6A 88.235 816 57 14 114 906 28316229 28315430 0.000000e+00 939.0
40 TraesCS5D01G194700 chr6A 95.904 293 10 2 4402 4694 68594568 68594278 1.750000e-129 473.0
41 TraesCS5D01G194700 chr6A 94.881 293 11 3 4402 4694 68564641 68564353 6.360000e-124 455.0
42 TraesCS5D01G194700 chr6A 75.325 539 130 3 4401 4938 409445774 409446310 6.920000e-64 255.0
43 TraesCS5D01G194700 chr6A 73.892 406 84 20 4403 4798 483990045 483989652 5.620000e-30 143.0
44 TraesCS5D01G194700 chr6A 86.239 109 15 0 2128 2236 107700901 107700793 9.470000e-23 119.0
45 TraesCS5D01G194700 chr4D 97.660 641 8 2 4401 5035 472920079 472920718 0.000000e+00 1094.0
46 TraesCS5D01G194700 chr4D 88.386 818 75 15 105 909 29617929 29617119 0.000000e+00 966.0
47 TraesCS5D01G194700 chr4D 75.367 341 79 5 4403 4741 37831818 37832155 5.580000e-35 159.0
48 TraesCS5D01G194700 chr4D 88.136 118 14 0 2128 2245 373933602 373933485 2.020000e-29 141.0
49 TraesCS5D01G194700 chr4D 87.179 117 15 0 2128 2244 373857823 373857707 3.380000e-27 134.0
50 TraesCS5D01G194700 chr6D 90.617 810 52 12 119 906 50960023 50959216 0.000000e+00 1053.0
51 TraesCS5D01G194700 chr6D 89.480 808 62 12 117 903 107596276 107597081 0.000000e+00 1000.0
52 TraesCS5D01G194700 chr6D 75.684 329 71 9 4401 4726 343561838 343561516 7.220000e-34 156.0
53 TraesCS5D01G194700 chr6D 74.613 323 69 12 4397 4714 295278081 295278395 4.380000e-26 130.0
54 TraesCS5D01G194700 chr7D 88.971 816 66 13 113 906 75958725 75957912 0.000000e+00 987.0
55 TraesCS5D01G194700 chr7D 84.821 112 17 0 2125 2236 562425833 562425944 4.410000e-21 113.0
56 TraesCS5D01G194700 chr7D 83.333 120 20 0 2125 2244 562390011 562390130 1.580000e-20 111.0
57 TraesCS5D01G194700 chr7D 82.143 112 20 0 2125 2236 562424982 562425093 4.440000e-16 97.1
58 TraesCS5D01G194700 chr1D 89.012 810 68 11 114 906 452692110 452692915 0.000000e+00 983.0
59 TraesCS5D01G194700 chr1D 88.564 787 65 12 149 913 97542522 97543305 0.000000e+00 931.0
60 TraesCS5D01G194700 chr1D 88.774 775 60 15 104 855 123106092 123106862 0.000000e+00 924.0
61 TraesCS5D01G194700 chr1D 75.634 513 111 14 4400 4906 26282762 26282258 5.390000e-60 243.0
62 TraesCS5D01G194700 chr1D 75.904 249 48 11 4400 4642 463320030 463319788 3.410000e-22 117.0
63 TraesCS5D01G194700 chr1D 83.516 91 4 5 4241 4331 53404605 53404526 2.080000e-09 75.0
64 TraesCS5D01G194700 chr6B 92.179 716 23 16 3653 4360 242425468 242424778 0.000000e+00 981.0
65 TraesCS5D01G194700 chr6B 92.929 495 12 10 3868 4360 241094571 241095044 0.000000e+00 699.0
66 TraesCS5D01G194700 chr6B 86.120 634 87 1 4402 5035 89524714 89524082 0.000000e+00 682.0
67 TraesCS5D01G194700 chr6B 82.325 628 100 8 4402 5023 708969479 708970101 7.940000e-148 534.0
68 TraesCS5D01G194700 chr6B 79.903 617 111 11 4402 5010 6036177 6035566 1.780000e-119 440.0
69 TraesCS5D01G194700 chr6B 90.071 282 28 0 4401 4682 54238161 54237880 3.060000e-97 366.0
70 TraesCS5D01G194700 chr6B 87.755 147 18 0 4697 4843 54223332 54223478 7.170000e-39 172.0
71 TraesCS5D01G194700 chr6B 86.667 120 15 1 2128 2246 171805037 171804918 1.220000e-26 132.0
72 TraesCS5D01G194700 chr6B 86.555 119 15 1 2129 2246 171768301 171768183 4.380000e-26 130.0
73 TraesCS5D01G194700 chr3A 88.429 821 71 11 106 906 748453439 748452623 0.000000e+00 968.0
74 TraesCS5D01G194700 chr3A 80.000 225 33 10 2753 2976 425700572 425700785 7.220000e-34 156.0
75 TraesCS5D01G194700 chr4B 88.710 806 66 12 117 906 246320242 246321038 0.000000e+00 961.0
76 TraesCS5D01G194700 chr4B 85.563 755 64 20 3360 4096 232728125 232728852 0.000000e+00 749.0
77 TraesCS5D01G194700 chr4B 92.857 490 12 10 3873 4360 129045839 129045371 0.000000e+00 689.0
78 TraesCS5D01G194700 chr4B 88.136 118 14 0 2128 2245 460032090 460031973 2.020000e-29 141.0
79 TraesCS5D01G194700 chr4B 95.122 41 2 0 4026 4066 232728134 232728094 1.250000e-06 65.8
80 TraesCS5D01G194700 chr7B 87.697 634 77 1 4402 5035 66021112 66021744 0.000000e+00 737.0
81 TraesCS5D01G194700 chr1A 76.608 513 108 12 4400 4906 537359644 537359138 6.870000e-69 272.0
82 TraesCS5D01G194700 chr1A 75.538 511 113 12 4401 4906 494848053 494847550 1.940000e-59 241.0
83 TraesCS5D01G194700 chr1A 82.955 88 12 3 4401 4487 338611411 338611326 5.780000e-10 76.8
84 TraesCS5D01G194700 chr1A 82.979 94 4 8 4240 4332 53416236 53416154 2.080000e-09 75.0
85 TraesCS5D01G194700 chr2D 77.596 366 74 8 4400 4762 102911572 102911212 1.170000e-51 215.0
86 TraesCS5D01G194700 chr2D 77.727 220 38 9 2127 2345 642782382 642782591 2.040000e-24 124.0
87 TraesCS5D01G194700 chr2D 85.470 117 17 0 2127 2243 565862625 565862509 7.320000e-24 122.0
88 TraesCS5D01G194700 chr2D 92.405 79 6 0 2601 2679 565860998 565860920 4.410000e-21 113.0
89 TraesCS5D01G194700 chr2D 92.208 77 6 0 2599 2675 642783384 642783460 5.700000e-20 110.0
90 TraesCS5D01G194700 chr2D 90.000 80 8 0 2599 2678 565758780 565758701 2.650000e-18 104.0
91 TraesCS5D01G194700 chr4A 85.075 201 8 9 4161 4360 715474709 715474530 9.210000e-43 185.0
92 TraesCS5D01G194700 chr4A 88.430 121 14 0 2125 2245 90519138 90519258 4.340000e-31 147.0
93 TraesCS5D01G194700 chr4A 79.111 225 35 10 2753 2976 284000290 284000503 1.560000e-30 145.0
94 TraesCS5D01G194700 chr1B 86.667 120 16 0 2125 2244 651558032 651557913 3.380000e-27 134.0
95 TraesCS5D01G194700 chr1B 82.759 87 4 7 4240 4326 87965161 87965086 3.480000e-07 67.6
96 TraesCS5D01G194700 chr2A 93.151 73 5 0 2607 2679 706200532 706200460 2.050000e-19 108.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G194700 chr5D 298690549 298695931 5382 False 3357.533333 9941 100.000000 1 5383 3 chr5D.!!$F2 5382
1 TraesCS5D01G194700 chr5D 102020895 102021650 755 True 845.000000 845 86.962000 118 876 1 chr5D.!!$R2 758
2 TraesCS5D01G194700 chr5A 400499213 400502872 3659 True 1586.333333 2255 90.404333 918 5330 3 chr5A.!!$R2 4412
3 TraesCS5D01G194700 chr5A 400410665 400414396 3731 False 1166.000000 2756 86.822750 918 5324 4 chr5A.!!$F2 4406
4 TraesCS5D01G194700 chr5A 341553866 341554488 622 False 499.000000 499 81.210000 4403 5027 1 chr5A.!!$F1 624
5 TraesCS5D01G194700 chr5A 400425609 400426217 608 False 427.000000 475 91.423500 4116 5382 2 chr5A.!!$F3 1266
6 TraesCS5D01G194700 chr5B 339424278 339428576 4298 False 656.042857 1408 89.742857 918 5382 7 chr5B.!!$F2 4464
7 TraesCS5D01G194700 chr5B 577020249 577020806 557 False 291.000000 291 77.119000 3336 3901 1 chr5B.!!$F1 565
8 TraesCS5D01G194700 chr2B 98483131 98483993 862 True 1225.000000 1225 92.334000 3490 4360 1 chr2B.!!$R2 870
9 TraesCS5D01G194700 chr2B 14401672 14402467 795 False 987.000000 987 89.139000 113 906 1 chr2B.!!$F1 793
10 TraesCS5D01G194700 chr2B 239463250 239464063 813 True 920.000000 920 87.515000 113 906 1 chr2B.!!$R3 793
11 TraesCS5D01G194700 chr2B 63047812 63048444 632 True 765.000000 765 88.486000 4402 5035 1 chr2B.!!$R1 633
12 TraesCS5D01G194700 chr7A 576477109 576477972 863 False 1208.000000 1208 92.005000 3490 4360 1 chr7A.!!$F1 870
13 TraesCS5D01G194700 chr7A 528225507 528226371 864 True 1199.000000 1199 91.798000 3490 4360 1 chr7A.!!$R3 870
14 TraesCS5D01G194700 chr7A 465271924 465272746 822 True 905.000000 905 86.779000 97 913 1 chr7A.!!$R2 816
15 TraesCS5D01G194700 chr7A 46277639 46278445 806 True 863.000000 863 86.224000 115 913 1 chr7A.!!$R1 798
16 TraesCS5D01G194700 chr3B 712413788 712414652 864 True 1205.000000 1205 91.901000 3489 4360 1 chr3B.!!$R1 871
17 TraesCS5D01G194700 chr6A 549487591 549488453 862 True 1170.000000 1170 91.206000 3490 4360 1 chr6A.!!$R7 870
18 TraesCS5D01G194700 chr6A 23645795 23646424 629 True 983.000000 983 94.787000 4403 5035 1 chr6A.!!$R1 632
19 TraesCS5D01G194700 chr6A 28315430 28316229 799 True 939.000000 939 88.235000 114 906 1 chr6A.!!$R2 792
20 TraesCS5D01G194700 chr6A 409445774 409446310 536 False 255.000000 255 75.325000 4401 4938 1 chr6A.!!$F1 537
21 TraesCS5D01G194700 chr4D 472920079 472920718 639 False 1094.000000 1094 97.660000 4401 5035 1 chr4D.!!$F2 634
22 TraesCS5D01G194700 chr4D 29617119 29617929 810 True 966.000000 966 88.386000 105 909 1 chr4D.!!$R1 804
23 TraesCS5D01G194700 chr6D 50959216 50960023 807 True 1053.000000 1053 90.617000 119 906 1 chr6D.!!$R1 787
24 TraesCS5D01G194700 chr6D 107596276 107597081 805 False 1000.000000 1000 89.480000 117 903 1 chr6D.!!$F1 786
25 TraesCS5D01G194700 chr7D 75957912 75958725 813 True 987.000000 987 88.971000 113 906 1 chr7D.!!$R1 793
26 TraesCS5D01G194700 chr1D 452692110 452692915 805 False 983.000000 983 89.012000 114 906 1 chr1D.!!$F3 792
27 TraesCS5D01G194700 chr1D 97542522 97543305 783 False 931.000000 931 88.564000 149 913 1 chr1D.!!$F1 764
28 TraesCS5D01G194700 chr1D 123106092 123106862 770 False 924.000000 924 88.774000 104 855 1 chr1D.!!$F2 751
29 TraesCS5D01G194700 chr1D 26282258 26282762 504 True 243.000000 243 75.634000 4400 4906 1 chr1D.!!$R1 506
30 TraesCS5D01G194700 chr6B 242424778 242425468 690 True 981.000000 981 92.179000 3653 4360 1 chr6B.!!$R6 707
31 TraesCS5D01G194700 chr6B 89524082 89524714 632 True 682.000000 682 86.120000 4402 5035 1 chr6B.!!$R3 633
32 TraesCS5D01G194700 chr6B 708969479 708970101 622 False 534.000000 534 82.325000 4402 5023 1 chr6B.!!$F3 621
33 TraesCS5D01G194700 chr6B 6035566 6036177 611 True 440.000000 440 79.903000 4402 5010 1 chr6B.!!$R1 608
34 TraesCS5D01G194700 chr3A 748452623 748453439 816 True 968.000000 968 88.429000 106 906 1 chr3A.!!$R1 800
35 TraesCS5D01G194700 chr4B 246320242 246321038 796 False 961.000000 961 88.710000 117 906 1 chr4B.!!$F2 789
36 TraesCS5D01G194700 chr4B 232728125 232728852 727 False 749.000000 749 85.563000 3360 4096 1 chr4B.!!$F1 736
37 TraesCS5D01G194700 chr7B 66021112 66021744 632 False 737.000000 737 87.697000 4402 5035 1 chr7B.!!$F1 633
38 TraesCS5D01G194700 chr1A 537359138 537359644 506 True 272.000000 272 76.608000 4400 4906 1 chr1A.!!$R4 506
39 TraesCS5D01G194700 chr1A 494847550 494848053 503 True 241.000000 241 75.538000 4401 4906 1 chr1A.!!$R3 505

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
172 173 1.077501 CCCACACGCCTCCATCATT 60.078 57.895 0.00 0.00 0.00 2.57 F
1507 1609 0.040246 GTCGATCGGTCCTCGGAATC 60.040 60.000 16.41 0.00 39.77 2.52 F
2345 2461 0.179089 AGCTCATCTGCCGCAAGTAG 60.179 55.000 0.00 0.00 0.00 2.57 F
2399 2515 0.308684 AGTTCATGCACGTGCTGTTG 59.691 50.000 37.59 29.67 42.66 3.33 F
2972 3446 0.318120 GCCCTGTCCATGTTGTTTGG 59.682 55.000 0.00 0.00 35.45 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2198 0.904865 AGTCCATCAAGCGGGAGACA 60.905 55.0 0.00 0.0 32.85 3.41 R
2365 2481 0.037232 GAACTTGACCAGACGAGGGG 60.037 60.0 0.00 0.0 0.00 4.79 R
3240 3730 0.976641 ACTGTTGCAGAATCGGGAGA 59.023 50.0 2.91 0.0 38.10 3.71 R
3350 3845 1.950828 GACAGCATCCATCAGGTGAG 58.049 55.0 0.00 0.0 37.04 3.51 R
4715 5305 0.036022 GCAGAAGTTGGTGCTCTCCT 59.964 55.0 0.38 0.0 36.71 3.69 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
21 22 2.878406 CCGTGTGGGATTAATGATGTCC 59.122 50.000 0.00 0.00 38.47 4.02
22 23 3.433598 CCGTGTGGGATTAATGATGTCCT 60.434 47.826 0.00 0.00 38.47 3.85
23 24 3.809832 CGTGTGGGATTAATGATGTCCTC 59.190 47.826 0.00 0.00 32.55 3.71
24 25 4.443457 CGTGTGGGATTAATGATGTCCTCT 60.443 45.833 0.00 0.00 32.55 3.69
25 26 4.818546 GTGTGGGATTAATGATGTCCTCTG 59.181 45.833 0.00 0.00 32.55 3.35
26 27 4.721274 TGTGGGATTAATGATGTCCTCTGA 59.279 41.667 0.00 0.00 32.55 3.27
27 28 5.370584 TGTGGGATTAATGATGTCCTCTGAT 59.629 40.000 0.00 0.00 32.55 2.90
28 29 5.936956 GTGGGATTAATGATGTCCTCTGATC 59.063 44.000 0.00 0.00 32.55 2.92
29 30 5.848369 TGGGATTAATGATGTCCTCTGATCT 59.152 40.000 0.00 0.00 32.55 2.75
30 31 6.171921 GGGATTAATGATGTCCTCTGATCTG 58.828 44.000 0.00 0.00 32.55 2.90
31 32 6.171921 GGATTAATGATGTCCTCTGATCTGG 58.828 44.000 0.00 0.00 0.00 3.86
32 33 6.013898 GGATTAATGATGTCCTCTGATCTGGA 60.014 42.308 0.00 0.00 0.00 3.86
42 43 7.156876 GTCCTCTGATCTGGACTATCATTAG 57.843 44.000 18.97 0.29 46.65 1.73
43 44 6.719370 GTCCTCTGATCTGGACTATCATTAGT 59.281 42.308 18.97 0.00 46.65 2.24
44 45 7.885922 GTCCTCTGATCTGGACTATCATTAGTA 59.114 40.741 18.97 0.00 46.65 1.82
45 46 8.448816 TCCTCTGATCTGGACTATCATTAGTAA 58.551 37.037 0.00 0.00 38.81 2.24
46 47 8.519526 CCTCTGATCTGGACTATCATTAGTAAC 58.480 40.741 0.00 0.00 38.81 2.50
47 48 8.100508 TCTGATCTGGACTATCATTAGTAACG 57.899 38.462 0.00 0.00 38.81 3.18
48 49 7.937394 TCTGATCTGGACTATCATTAGTAACGA 59.063 37.037 0.00 0.00 38.81 3.85
49 50 8.459911 TGATCTGGACTATCATTAGTAACGAA 57.540 34.615 0.00 0.00 38.81 3.85
50 51 8.350722 TGATCTGGACTATCATTAGTAACGAAC 58.649 37.037 0.00 0.00 38.81 3.95
51 52 7.876936 TCTGGACTATCATTAGTAACGAACT 57.123 36.000 0.00 0.00 38.81 3.01
52 53 8.289939 TCTGGACTATCATTAGTAACGAACTT 57.710 34.615 0.00 0.00 38.81 2.66
53 54 8.188799 TCTGGACTATCATTAGTAACGAACTTG 58.811 37.037 0.00 0.00 38.81 3.16
54 55 8.058667 TGGACTATCATTAGTAACGAACTTGA 57.941 34.615 0.00 0.00 38.81 3.02
55 56 8.692710 TGGACTATCATTAGTAACGAACTTGAT 58.307 33.333 11.69 11.69 38.81 2.57
56 57 8.969267 GGACTATCATTAGTAACGAACTTGATG 58.031 37.037 14.56 12.20 38.81 3.07
57 58 8.354011 ACTATCATTAGTAACGAACTTGATGC 57.646 34.615 14.56 0.00 36.67 3.91
58 59 8.198109 ACTATCATTAGTAACGAACTTGATGCT 58.802 33.333 14.56 8.68 36.67 3.79
59 60 6.647212 TCATTAGTAACGAACTTGATGCTG 57.353 37.500 0.00 0.00 39.80 4.41
60 61 6.163476 TCATTAGTAACGAACTTGATGCTGT 58.837 36.000 0.00 0.00 39.80 4.40
61 62 6.649141 TCATTAGTAACGAACTTGATGCTGTT 59.351 34.615 0.00 0.00 39.80 3.16
62 63 7.815549 TCATTAGTAACGAACTTGATGCTGTTA 59.184 33.333 0.00 0.00 39.80 2.41
63 64 7.949903 TTAGTAACGAACTTGATGCTGTTAA 57.050 32.000 0.00 0.00 39.80 2.01
64 65 8.542497 TTAGTAACGAACTTGATGCTGTTAAT 57.458 30.769 0.00 0.00 39.80 1.40
65 66 7.435068 AGTAACGAACTTGATGCTGTTAATT 57.565 32.000 0.00 0.00 33.35 1.40
66 67 8.542497 AGTAACGAACTTGATGCTGTTAATTA 57.458 30.769 0.00 0.00 33.35 1.40
67 68 8.995220 AGTAACGAACTTGATGCTGTTAATTAA 58.005 29.630 0.00 0.00 33.35 1.40
68 69 9.769093 GTAACGAACTTGATGCTGTTAATTAAT 57.231 29.630 0.31 0.00 0.00 1.40
172 173 1.077501 CCCACACGCCTCCATCATT 60.078 57.895 0.00 0.00 0.00 2.57
195 196 4.985413 ACTCATTTTGCCACGTATGAATG 58.015 39.130 0.00 0.00 0.00 2.67
318 322 7.507672 GTCTCGACGAGATCTTCAAAATTAA 57.492 36.000 28.81 0.00 40.98 1.40
378 388 5.490159 CCCAAAAGTTGCCATGATGTTTAT 58.510 37.500 0.00 0.00 0.00 1.40
404 414 4.698304 TGTAGTTGCCATAGTGCTTAAACC 59.302 41.667 0.00 0.00 0.00 3.27
405 415 3.761897 AGTTGCCATAGTGCTTAAACCA 58.238 40.909 0.00 0.00 0.00 3.67
406 416 4.344104 AGTTGCCATAGTGCTTAAACCAT 58.656 39.130 0.00 0.00 0.00 3.55
407 417 4.158394 AGTTGCCATAGTGCTTAAACCATG 59.842 41.667 0.00 0.00 0.00 3.66
408 418 3.023119 TGCCATAGTGCTTAAACCATGG 58.977 45.455 11.19 11.19 40.91 3.66
409 419 3.715628 CCATAGTGCTTAAACCATGGC 57.284 47.619 13.04 0.00 33.49 4.40
441 469 9.935241 TTGTAGAGCATGGCAATTTTAATTTTA 57.065 25.926 0.00 0.00 0.00 1.52
688 722 2.897326 AGACATGGCAACTTTTAACCCC 59.103 45.455 0.00 0.00 37.61 4.95
906 956 2.596553 TTTGACTCCCGCCACACGTT 62.597 55.000 0.00 0.00 41.42 3.99
907 957 1.746322 TTGACTCCCGCCACACGTTA 61.746 55.000 0.00 0.00 41.42 3.18
908 958 1.445582 GACTCCCGCCACACGTTAG 60.446 63.158 0.00 0.00 41.42 2.34
909 959 2.813908 CTCCCGCCACACGTTAGC 60.814 66.667 0.00 0.00 41.42 3.09
931 981 4.968181 GCGTTGTCCTAAAGAAAACACTTC 59.032 41.667 0.00 0.00 42.15 3.01
1367 1464 1.336609 ACGACAAGGAAGGTAGCGAAC 60.337 52.381 0.00 0.00 0.00 3.95
1445 1547 4.140599 CTCCTTCTGCTCGCCGCT 62.141 66.667 0.00 0.00 40.11 5.52
1507 1609 0.040246 GTCGATCGGTCCTCGGAATC 60.040 60.000 16.41 0.00 39.77 2.52
1603 1705 2.422276 AACATTTCTCTGCGTTTGCC 57.578 45.000 0.00 0.00 41.78 4.52
1628 1737 2.811317 CTTGCTCGCTGTCGGGAC 60.811 66.667 0.00 0.00 38.83 4.46
1695 1804 4.105486 GCTTGTTTTGCTCTTCGTTTTCT 58.895 39.130 0.00 0.00 0.00 2.52
1751 1860 3.904136 AGGAACATTTCTCTGCGTTTG 57.096 42.857 0.00 0.00 0.00 2.93
1877 1990 1.462670 GCACTCAAGCTAGCTTCACAC 59.537 52.381 27.08 11.95 33.42 3.82
1942 2055 3.802685 AGTTAGATCGGCTTGCGTTTATC 59.197 43.478 0.00 0.00 0.00 1.75
1968 2081 4.537135 TCCTAATAAGTGATGGGATCGC 57.463 45.455 2.14 2.14 40.02 4.58
1971 2084 4.466370 CCTAATAAGTGATGGGATCGCCTA 59.534 45.833 7.38 0.00 40.59 3.93
2031 2146 5.734855 ATTTGAACTCGATTTGGATACCG 57.265 39.130 0.00 0.00 0.00 4.02
2053 2168 5.220548 CCGAATCTAACTGCTGTTCATCTTG 60.221 44.000 12.67 1.16 37.59 3.02
2082 2198 6.756221 AGTGTTGGTCGTTCTCTAATTACTT 58.244 36.000 0.00 0.00 0.00 2.24
2147 2263 1.368950 GGATCAGCAGCGCCTCATA 59.631 57.895 2.29 0.00 0.00 2.15
2181 2297 1.672356 CTGGAAGAAGGCCACACGG 60.672 63.158 5.01 0.00 34.07 4.94
2323 2439 1.448540 CCCTCAAGTACAGGCAGCG 60.449 63.158 0.00 0.00 0.00 5.18
2345 2461 0.179089 AGCTCATCTGCCGCAAGTAG 60.179 55.000 0.00 0.00 0.00 2.57
2364 2480 1.599240 GCCCCTGAATCGATGCCTC 60.599 63.158 0.00 0.00 0.00 4.70
2365 2481 1.072159 CCCCTGAATCGATGCCTCC 59.928 63.158 0.00 0.00 0.00 4.30
2389 2505 1.069978 TCGTCTGGTCAAGTTCATGCA 59.930 47.619 0.00 0.00 0.00 3.96
2390 2506 1.195448 CGTCTGGTCAAGTTCATGCAC 59.805 52.381 0.00 0.00 0.00 4.57
2399 2515 0.308684 AGTTCATGCACGTGCTGTTG 59.691 50.000 37.59 29.67 42.66 3.33
2431 2558 5.170021 GGTTGCTATGAGCTATCTCTGATG 58.830 45.833 0.00 0.00 42.97 3.07
2432 2559 5.279406 GGTTGCTATGAGCTATCTCTGATGT 60.279 44.000 0.00 0.00 42.97 3.06
2433 2560 5.388408 TGCTATGAGCTATCTCTGATGTG 57.612 43.478 0.00 0.00 42.97 3.21
2434 2561 4.175516 GCTATGAGCTATCTCTGATGTGC 58.824 47.826 0.00 0.00 40.03 4.57
2467 2784 5.705441 GCCAACTAATTAGCAGTGGCATATA 59.295 40.000 31.40 0.00 43.25 0.86
2499 2816 4.637483 AACATTTCCTTGTCATATGCCG 57.363 40.909 0.00 0.00 0.00 5.69
2501 2818 3.627577 ACATTTCCTTGTCATATGCCGAC 59.372 43.478 0.00 0.00 0.00 4.79
2502 2819 3.342377 TTTCCTTGTCATATGCCGACA 57.658 42.857 0.00 0.00 41.53 4.35
2522 2854 5.565259 CGACAAACTCTCATGTTTTGCATAC 59.435 40.000 0.00 0.00 37.98 2.39
2530 2862 7.223582 ACTCTCATGTTTTGCATACGAAGATAG 59.776 37.037 0.00 0.00 35.74 2.08
2708 3043 5.180492 CCTTAACTGCGACCTATTGTTTTGA 59.820 40.000 0.00 0.00 0.00 2.69
2735 3073 3.766545 TCTTTCATGCTTGGCCTTACTT 58.233 40.909 3.32 0.00 0.00 2.24
2737 3075 2.584835 TCATGCTTGGCCTTACTTGT 57.415 45.000 3.32 0.00 0.00 3.16
2741 3079 2.504367 TGCTTGGCCTTACTTGTCTTC 58.496 47.619 3.32 0.00 0.00 2.87
2754 3092 7.115520 CCTTACTTGTCTTCATATATGCTGTCG 59.884 40.741 7.92 0.00 0.00 4.35
2776 3114 1.262950 TGCATGTTCTTGGTTTCGTCG 59.737 47.619 0.00 0.00 0.00 5.12
2790 3128 1.136984 CGTCGTACCTCAGTCAGCC 59.863 63.158 0.00 0.00 0.00 4.85
2868 3214 6.899393 TGCTTGTTTCAGAGTTATTGGAAT 57.101 33.333 0.00 0.00 0.00 3.01
2870 3216 6.489700 TGCTTGTTTCAGAGTTATTGGAATGA 59.510 34.615 0.00 0.00 0.00 2.57
2907 3380 9.169468 CAATTTACAAATAATGGCGCTTACTAG 57.831 33.333 7.64 0.00 0.00 2.57
2913 3386 6.540438 AATAATGGCGCTTACTAGGCTATA 57.460 37.500 7.64 0.00 0.00 1.31
2914 3387 6.732896 ATAATGGCGCTTACTAGGCTATAT 57.267 37.500 7.64 0.00 0.00 0.86
2915 3388 7.834881 ATAATGGCGCTTACTAGGCTATATA 57.165 36.000 7.64 0.00 0.00 0.86
2918 3391 5.014858 TGGCGCTTACTAGGCTATATAGTT 58.985 41.667 7.64 3.35 35.20 2.24
2959 3433 4.215109 GGTCACCATAAATATTGCCCTGT 58.785 43.478 0.00 0.00 0.00 4.00
2960 3434 4.278419 GGTCACCATAAATATTGCCCTGTC 59.722 45.833 0.00 0.00 0.00 3.51
2961 3435 4.278419 GTCACCATAAATATTGCCCTGTCC 59.722 45.833 0.00 0.00 0.00 4.02
2962 3436 4.079500 TCACCATAAATATTGCCCTGTCCA 60.080 41.667 0.00 0.00 0.00 4.02
2963 3437 4.834496 CACCATAAATATTGCCCTGTCCAT 59.166 41.667 0.00 0.00 0.00 3.41
2964 3438 4.834496 ACCATAAATATTGCCCTGTCCATG 59.166 41.667 0.00 0.00 0.00 3.66
2965 3439 4.834496 CCATAAATATTGCCCTGTCCATGT 59.166 41.667 0.00 0.00 0.00 3.21
2966 3440 5.305128 CCATAAATATTGCCCTGTCCATGTT 59.695 40.000 0.00 0.00 0.00 2.71
2967 3441 4.741321 AAATATTGCCCTGTCCATGTTG 57.259 40.909 0.00 0.00 0.00 3.33
2968 3442 2.897271 TATTGCCCTGTCCATGTTGT 57.103 45.000 0.00 0.00 0.00 3.32
2969 3443 2.014010 ATTGCCCTGTCCATGTTGTT 57.986 45.000 0.00 0.00 0.00 2.83
2970 3444 1.786937 TTGCCCTGTCCATGTTGTTT 58.213 45.000 0.00 0.00 0.00 2.83
2971 3445 1.039068 TGCCCTGTCCATGTTGTTTG 58.961 50.000 0.00 0.00 0.00 2.93
2972 3446 0.318120 GCCCTGTCCATGTTGTTTGG 59.682 55.000 0.00 0.00 35.45 3.28
2973 3447 0.318120 CCCTGTCCATGTTGTTTGGC 59.682 55.000 0.00 0.00 34.06 4.52
2974 3448 1.331214 CCTGTCCATGTTGTTTGGCT 58.669 50.000 0.00 0.00 34.06 4.75
2975 3449 1.270550 CCTGTCCATGTTGTTTGGCTC 59.729 52.381 0.00 0.00 34.06 4.70
2976 3450 2.233271 CTGTCCATGTTGTTTGGCTCT 58.767 47.619 0.00 0.00 34.06 4.09
2977 3451 3.411446 CTGTCCATGTTGTTTGGCTCTA 58.589 45.455 0.00 0.00 34.06 2.43
2978 3452 3.411446 TGTCCATGTTGTTTGGCTCTAG 58.589 45.455 0.00 0.00 34.06 2.43
2979 3453 3.181445 TGTCCATGTTGTTTGGCTCTAGT 60.181 43.478 0.00 0.00 34.06 2.57
2980 3454 3.437049 GTCCATGTTGTTTGGCTCTAGTC 59.563 47.826 0.00 0.00 34.06 2.59
2981 3455 3.072330 TCCATGTTGTTTGGCTCTAGTCA 59.928 43.478 0.00 0.00 34.06 3.41
2982 3456 3.820467 CCATGTTGTTTGGCTCTAGTCAA 59.180 43.478 0.00 0.00 37.94 3.18
2983 3457 4.460382 CCATGTTGTTTGGCTCTAGTCAAT 59.540 41.667 0.00 0.00 39.61 2.57
2984 3458 5.647658 CCATGTTGTTTGGCTCTAGTCAATA 59.352 40.000 0.00 0.00 39.61 1.90
2985 3459 6.319658 CCATGTTGTTTGGCTCTAGTCAATAT 59.680 38.462 0.00 0.00 39.61 1.28
2986 3460 7.148018 CCATGTTGTTTGGCTCTAGTCAATATT 60.148 37.037 0.00 0.00 39.61 1.28
2987 3461 7.144722 TGTTGTTTGGCTCTAGTCAATATTG 57.855 36.000 9.29 9.29 39.61 1.90
2988 3462 5.818136 TGTTTGGCTCTAGTCAATATTGC 57.182 39.130 10.76 6.21 39.61 3.56
3001 3475 3.700539 TCAATATTGCCCTGTCCATGTTG 59.299 43.478 10.76 0.00 0.00 3.33
3048 3530 1.597742 CACCTTGTGTGGGTCTTCTG 58.402 55.000 0.00 0.00 41.52 3.02
3056 3538 2.808543 GTGTGGGTCTTCTGTGATCAAC 59.191 50.000 0.00 0.00 0.00 3.18
3114 3596 5.633830 AAATATGCCAAGTCAGTTCACTG 57.366 39.130 0.02 0.02 45.08 3.66
3124 3606 1.400142 TCAGTTCACTGGTGTTTTGCG 59.600 47.619 7.11 0.00 43.91 4.85
3130 3612 3.206964 TCACTGGTGTTTTGCGTCAATA 58.793 40.909 0.53 0.00 0.00 1.90
3135 3617 5.351465 ACTGGTGTTTTGCGTCAATATAGAG 59.649 40.000 0.00 0.00 0.00 2.43
3175 3660 7.064728 AGCTTACTACTACAGCTTTGTTTATGC 59.935 37.037 0.00 0.00 41.24 3.14
3181 3666 5.647658 ACTACAGCTTTGTTTATGCTATGCA 59.352 36.000 0.00 0.00 44.86 3.96
3223 3713 7.441157 TGTTTTGTACTGTTCTCTGTATTCTGG 59.559 37.037 0.00 0.00 32.34 3.86
3238 3728 1.191489 TCTGGTGTGCGGAATCCTCA 61.191 55.000 0.00 0.00 0.00 3.86
3240 3730 0.327924 TGGTGTGCGGAATCCTCAAT 59.672 50.000 0.00 0.00 0.00 2.57
3271 3761 0.661187 GCAACAGTGTGTGCAATCGG 60.661 55.000 19.18 0.00 0.00 4.18
3279 3769 1.277842 TGTGTGCAATCGGGTGATACT 59.722 47.619 0.00 0.00 33.40 2.12
3286 3776 0.467474 ATCGGGTGATACTCCGCTCA 60.467 55.000 0.00 0.00 45.31 4.26
3314 3809 4.944962 TTTCAATCACTTGTAGATGCCG 57.055 40.909 0.00 0.00 33.87 5.69
3325 3820 5.585047 ACTTGTAGATGCCGACTTTAATTCC 59.415 40.000 0.00 0.00 0.00 3.01
3329 3824 5.505173 AGATGCCGACTTTAATTCCATTG 57.495 39.130 0.00 0.00 0.00 2.82
3330 3825 4.949856 AGATGCCGACTTTAATTCCATTGT 59.050 37.500 0.00 0.00 0.00 2.71
3332 3827 4.804108 TGCCGACTTTAATTCCATTGTTG 58.196 39.130 0.00 0.00 0.00 3.33
3333 3828 4.520874 TGCCGACTTTAATTCCATTGTTGA 59.479 37.500 0.00 0.00 0.00 3.18
3334 3829 5.010112 TGCCGACTTTAATTCCATTGTTGAA 59.990 36.000 0.00 0.00 0.00 2.69
3335 3830 5.923684 GCCGACTTTAATTCCATTGTTGAAA 59.076 36.000 0.00 0.00 0.00 2.69
3350 3845 8.702438 CCATTGTTGAAATGTCACTTGTTTATC 58.298 33.333 0.00 0.00 31.90 1.75
3352 3847 9.683069 ATTGTTGAAATGTCACTTGTTTATCTC 57.317 29.630 0.00 0.00 31.90 2.75
3364 3859 6.037940 CACTTGTTTATCTCACCTGATGGATG 59.962 42.308 0.00 0.00 37.04 3.51
3383 3878 2.241160 TGCTGTCCATGCATGTTCTTT 58.759 42.857 24.58 0.00 35.31 2.52
3454 3951 9.970395 TTTTTCATCATCCATATCTGTTTATGC 57.030 29.630 0.00 0.00 0.00 3.14
3455 3952 6.973229 TCATCATCCATATCTGTTTATGCG 57.027 37.500 0.00 0.00 0.00 4.73
3475 3986 6.854496 TGCGTGTTTCAGAGTTATTTAAGT 57.146 33.333 0.00 0.00 0.00 2.24
3512 4034 8.562892 CCATTTTAGACACATAATGGAGCTAAG 58.437 37.037 6.83 0.00 46.35 2.18
3736 4278 3.750652 TGTTTTGCATCAATCTGACGCTA 59.249 39.130 0.00 0.00 36.42 4.26
3847 4402 0.660488 CTGAGTCGTCGATCTCCCAG 59.340 60.000 16.83 9.00 0.00 4.45
4194 4754 1.140852 TCCCTATGGATTCCTGTTGCG 59.859 52.381 3.95 0.00 35.03 4.85
4314 4889 6.825721 GGTTCTGTTCTGTTGGAATAGATGAT 59.174 38.462 5.85 0.00 46.40 2.45
4364 4939 0.317854 GCACCTTGGTTCAGTTTCGC 60.318 55.000 0.00 0.00 0.00 4.70
4388 4971 6.405731 GCCCAATTGTTAGCATTCTGTTATGA 60.406 38.462 4.43 0.00 0.00 2.15
4397 4980 4.768968 AGCATTCTGTTATGAGCCAAGTTT 59.231 37.500 0.00 0.00 0.00 2.66
4398 4981 5.244626 AGCATTCTGTTATGAGCCAAGTTTT 59.755 36.000 0.00 0.00 0.00 2.43
4525 5108 5.447279 GGTGCTGTCATTCGGTAAACATAAG 60.447 44.000 0.00 0.00 0.00 1.73
4715 5305 1.760613 AGTCTGTTTCGAAGACCACCA 59.239 47.619 11.27 0.00 44.27 4.17
4951 5551 6.406177 CCTGCCATTTGCTATATGTTTTCTGT 60.406 38.462 0.00 0.00 42.00 3.41
5035 5635 2.100197 TCTGTCACAGGAATCGGTAGG 58.900 52.381 4.57 0.00 31.51 3.18
5036 5636 1.825474 CTGTCACAGGAATCGGTAGGT 59.175 52.381 0.00 0.00 0.00 3.08
5041 5641 4.098960 GTCACAGGAATCGGTAGGTTATGA 59.901 45.833 0.00 0.00 0.00 2.15
5046 5646 3.008049 GGAATCGGTAGGTTATGAGCCAT 59.992 47.826 0.00 0.00 0.00 4.40
5090 5698 2.206750 TGTTTCTCTGTTCCGGTTTCG 58.793 47.619 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.808728 AGGACATCATTAATCCCACACG 58.191 45.455 0.00 0.00 32.47 4.49
8 9 7.002250 TCCAGATCAGAGGACATCATTAATC 57.998 40.000 0.00 0.00 0.00 1.75
19 20 6.857848 ACTAATGATAGTCCAGATCAGAGGA 58.142 40.000 0.00 0.00 37.90 3.71
20 21 8.519526 GTTACTAATGATAGTCCAGATCAGAGG 58.480 40.741 0.00 0.00 41.49 3.69
21 22 8.233868 CGTTACTAATGATAGTCCAGATCAGAG 58.766 40.741 0.00 0.00 41.49 3.35
22 23 7.937394 TCGTTACTAATGATAGTCCAGATCAGA 59.063 37.037 0.00 0.00 41.49 3.27
23 24 8.100508 TCGTTACTAATGATAGTCCAGATCAG 57.899 38.462 0.00 0.00 41.49 2.90
24 25 8.350722 GTTCGTTACTAATGATAGTCCAGATCA 58.649 37.037 0.00 0.00 41.49 2.92
25 26 8.569641 AGTTCGTTACTAATGATAGTCCAGATC 58.430 37.037 0.00 0.00 41.49 2.75
26 27 8.466617 AGTTCGTTACTAATGATAGTCCAGAT 57.533 34.615 0.00 0.00 41.49 2.90
27 28 7.876936 AGTTCGTTACTAATGATAGTCCAGA 57.123 36.000 0.00 0.00 41.49 3.86
28 29 8.188799 TCAAGTTCGTTACTAATGATAGTCCAG 58.811 37.037 0.00 0.00 41.49 3.86
29 30 8.058667 TCAAGTTCGTTACTAATGATAGTCCA 57.941 34.615 0.00 0.00 41.49 4.02
30 31 8.969267 CATCAAGTTCGTTACTAATGATAGTCC 58.031 37.037 7.06 0.00 41.49 3.85
31 32 8.480853 GCATCAAGTTCGTTACTAATGATAGTC 58.519 37.037 14.12 0.00 41.49 2.59
32 33 8.198109 AGCATCAAGTTCGTTACTAATGATAGT 58.802 33.333 14.12 0.00 44.53 2.12
33 34 8.483218 CAGCATCAAGTTCGTTACTAATGATAG 58.517 37.037 14.12 8.44 33.86 2.08
34 35 7.979537 ACAGCATCAAGTTCGTTACTAATGATA 59.020 33.333 14.12 0.00 33.86 2.15
35 36 6.818644 ACAGCATCAAGTTCGTTACTAATGAT 59.181 34.615 14.12 9.20 35.61 2.45
36 37 6.163476 ACAGCATCAAGTTCGTTACTAATGA 58.837 36.000 14.12 7.87 35.54 2.57
37 38 6.408858 ACAGCATCAAGTTCGTTACTAATG 57.591 37.500 0.00 9.35 35.54 1.90
38 39 8.542497 TTAACAGCATCAAGTTCGTTACTAAT 57.458 30.769 0.00 0.00 35.54 1.73
39 40 7.949903 TTAACAGCATCAAGTTCGTTACTAA 57.050 32.000 0.00 0.00 35.54 2.24
40 41 8.542497 AATTAACAGCATCAAGTTCGTTACTA 57.458 30.769 0.00 0.00 35.54 1.82
41 42 7.435068 AATTAACAGCATCAAGTTCGTTACT 57.565 32.000 0.00 0.00 39.32 2.24
42 43 9.769093 ATTAATTAACAGCATCAAGTTCGTTAC 57.231 29.630 0.00 0.00 0.00 2.50
172 173 5.065859 CCATTCATACGTGGCAAAATGAGTA 59.934 40.000 0.00 0.00 30.53 2.59
274 278 6.009115 AGACGGATTTAATGGTGAAAACAC 57.991 37.500 0.00 0.00 0.00 3.32
318 322 4.398044 GTCGAAACATATCAACATGGGGTT 59.602 41.667 0.00 0.00 41.47 4.11
378 388 4.819105 AAGCACTATGGCAACTACAGTA 57.181 40.909 0.00 0.00 35.83 2.74
404 414 4.569162 CCATGCTCTACAAAAATTGCCATG 59.431 41.667 0.00 0.00 0.00 3.66
405 415 4.761975 CCATGCTCTACAAAAATTGCCAT 58.238 39.130 0.00 0.00 0.00 4.40
406 416 3.617045 GCCATGCTCTACAAAAATTGCCA 60.617 43.478 0.00 0.00 0.00 4.92
407 417 2.931969 GCCATGCTCTACAAAAATTGCC 59.068 45.455 0.00 0.00 0.00 4.52
408 418 3.587923 TGCCATGCTCTACAAAAATTGC 58.412 40.909 0.00 0.00 0.00 3.56
409 419 6.730960 AATTGCCATGCTCTACAAAAATTG 57.269 33.333 0.00 0.00 0.00 2.32
441 469 7.830697 TCAAAGTACTGGAATTGTCATCATCAT 59.169 33.333 0.00 0.00 0.00 2.45
450 479 5.630121 TCATGGTCAAAGTACTGGAATTGT 58.370 37.500 0.00 0.00 0.00 2.71
536 566 5.927281 AGAAACTAGATTTGCCATGCATT 57.073 34.783 0.00 0.00 38.76 3.56
860 909 2.627945 CACACGCCCTATAACACACAT 58.372 47.619 0.00 0.00 0.00 3.21
906 956 5.362263 AGTGTTTTCTTTAGGACAACGCTA 58.638 37.500 7.49 0.00 46.83 4.26
907 957 4.196971 AGTGTTTTCTTTAGGACAACGCT 58.803 39.130 4.06 4.06 45.14 5.07
908 958 4.547406 AGTGTTTTCTTTAGGACAACGC 57.453 40.909 0.00 0.00 42.23 4.84
909 959 6.359480 AGAAGTGTTTTCTTTAGGACAACG 57.641 37.500 0.00 0.00 37.41 4.10
910 960 6.238676 GGGAGAAGTGTTTTCTTTAGGACAAC 60.239 42.308 0.00 0.00 35.76 3.32
911 961 5.826208 GGGAGAAGTGTTTTCTTTAGGACAA 59.174 40.000 0.00 0.00 0.00 3.18
912 962 5.374071 GGGAGAAGTGTTTTCTTTAGGACA 58.626 41.667 0.00 0.00 0.00 4.02
913 963 4.760715 GGGGAGAAGTGTTTTCTTTAGGAC 59.239 45.833 0.00 0.00 0.00 3.85
914 964 4.414182 TGGGGAGAAGTGTTTTCTTTAGGA 59.586 41.667 0.00 0.00 0.00 2.94
915 965 4.725490 TGGGGAGAAGTGTTTTCTTTAGG 58.275 43.478 0.00 0.00 0.00 2.69
916 966 5.621193 TCTGGGGAGAAGTGTTTTCTTTAG 58.379 41.667 0.00 0.00 0.00 1.85
931 981 3.492309 CGATGATTTCACTCTCTGGGGAG 60.492 52.174 0.00 0.00 40.73 4.30
1320 1417 3.554692 CCTTGACGTCGGCGATGC 61.555 66.667 27.66 19.98 42.00 3.91
1367 1464 1.825281 GATGAGAGGCGGGGAGATGG 61.825 65.000 0.00 0.00 0.00 3.51
1507 1609 2.025359 GATCGAAACAAGCGCCTCCG 62.025 60.000 2.29 0.00 37.57 4.63
1569 1671 6.985645 AGAGAAATGTTTCTAGCTAGCATCTG 59.014 38.462 18.83 3.76 46.84 2.90
1751 1860 1.705256 TCTACCAATCGAACACGCAC 58.295 50.000 0.00 0.00 0.00 5.34
1848 1961 1.132640 GCTTGAGTGCTTAACGCGG 59.867 57.895 12.47 0.00 43.27 6.46
1877 1990 4.036734 CGGGTCAAACATGGAATCTATTGG 59.963 45.833 0.00 0.00 0.00 3.16
1942 2055 6.425114 CGATCCCATCACTTATTAGGAAACTG 59.575 42.308 0.00 0.00 43.88 3.16
1968 2081 2.485814 GCAGGTTGCTGAAGAAAGTAGG 59.514 50.000 0.00 0.00 40.96 3.18
2031 2146 6.974932 TCAAGATGAACAGCAGTTAGATTC 57.025 37.500 0.00 0.00 38.30 2.52
2053 2168 7.829378 ATTAGAGAACGACCAACACTAATTC 57.171 36.000 0.00 0.00 0.00 2.17
2082 2198 0.904865 AGTCCATCAAGCGGGAGACA 60.905 55.000 0.00 0.00 32.85 3.41
2147 2263 1.748122 CAGCTGCTTCCCTGCGAAT 60.748 57.895 0.00 0.00 42.57 3.34
2181 2297 0.036765 TGGATGTTGTAGTCCGCCAC 60.037 55.000 0.00 0.00 37.32 5.01
2261 2377 2.126603 GGTGGGTAGGTTCCCCCT 59.873 66.667 0.00 0.00 46.48 4.79
2323 2439 0.654683 CTTGCGGCAGATGAGCTTAC 59.345 55.000 1.67 0.00 34.17 2.34
2345 2461 2.595754 GGCATCGATTCAGGGGCC 60.596 66.667 6.45 6.45 0.00 5.80
2364 2480 1.481056 AACTTGACCAGACGAGGGGG 61.481 60.000 0.00 0.00 0.00 5.40
2365 2481 0.037232 GAACTTGACCAGACGAGGGG 60.037 60.000 0.00 0.00 0.00 4.79
2389 2505 1.095228 CACACCTTCCAACAGCACGT 61.095 55.000 0.00 0.00 0.00 4.49
2390 2506 1.648720 CACACCTTCCAACAGCACG 59.351 57.895 0.00 0.00 0.00 5.34
2399 2515 2.359900 CTCATAGCAACCACACCTTCC 58.640 52.381 0.00 0.00 0.00 3.46
2431 2558 4.766404 ATTAGTTGGCAACTACAAGCAC 57.234 40.909 33.50 5.84 45.35 4.40
2432 2559 5.106317 GCTAATTAGTTGGCAACTACAAGCA 60.106 40.000 34.81 25.33 45.35 3.91
2433 2560 5.106317 TGCTAATTAGTTGGCAACTACAAGC 60.106 40.000 34.08 34.08 46.92 4.01
2434 2561 6.494893 TGCTAATTAGTTGGCAACTACAAG 57.505 37.500 33.50 28.29 46.92 3.16
2467 2784 6.540914 TGACAAGGAAATGTTTAAGAGTCGTT 59.459 34.615 0.00 0.00 32.57 3.85
2499 2816 5.565259 CGTATGCAAAACATGAGAGTTTGTC 59.435 40.000 0.00 2.57 40.60 3.18
2501 2818 5.688823 TCGTATGCAAAACATGAGAGTTTG 58.311 37.500 0.00 5.72 40.60 2.93
2502 2819 5.940192 TCGTATGCAAAACATGAGAGTTT 57.060 34.783 0.00 0.00 43.13 2.66
2503 2820 5.700832 TCTTCGTATGCAAAACATGAGAGTT 59.299 36.000 0.00 0.00 40.06 3.01
2522 2854 3.759418 TGCTTCTGAACGACTATCTTCG 58.241 45.455 0.00 0.00 44.87 3.79
2530 2862 4.204978 CACACAAAATTGCTTCTGAACGAC 59.795 41.667 0.00 0.00 0.00 4.34
2536 2868 4.508492 TGATTGCACACAAAATTGCTTCTG 59.492 37.500 0.00 0.00 39.77 3.02
2708 3043 4.737578 AGGCCAAGCATGAAAGATGATAT 58.262 39.130 5.01 0.00 0.00 1.63
2735 3073 4.925646 GCATCGACAGCATATATGAAGACA 59.074 41.667 17.10 0.00 0.00 3.41
2737 3075 5.138125 TGCATCGACAGCATATATGAAGA 57.862 39.130 17.10 7.52 37.02 2.87
2754 3092 3.492313 GACGAAACCAAGAACATGCATC 58.508 45.455 0.00 0.00 0.00 3.91
2776 3114 7.830201 ACACTATATATAGGCTGACTGAGGTAC 59.170 40.741 21.20 0.00 34.69 3.34
2823 3169 5.618863 GCATCATAACAAAACACCGTGATGA 60.619 40.000 14.52 2.54 42.30 2.92
2898 3371 7.591165 TGAACAACTATATAGCCTAGTAAGCG 58.409 38.462 9.78 0.00 34.64 4.68
2907 3380 7.520614 GCCAAGAACATGAACAACTATATAGCC 60.521 40.741 9.78 0.00 0.00 3.93
2913 3386 4.666512 AGGCCAAGAACATGAACAACTAT 58.333 39.130 5.01 0.00 0.00 2.12
2914 3387 4.098914 AGGCCAAGAACATGAACAACTA 57.901 40.909 5.01 0.00 0.00 2.24
2915 3388 2.949447 AGGCCAAGAACATGAACAACT 58.051 42.857 5.01 0.00 0.00 3.16
2918 3391 1.962807 CCAAGGCCAAGAACATGAACA 59.037 47.619 5.01 0.00 0.00 3.18
2959 3433 3.072330 TGACTAGAGCCAAACAACATGGA 59.928 43.478 0.00 0.00 40.56 3.41
2960 3434 3.411446 TGACTAGAGCCAAACAACATGG 58.589 45.455 0.00 0.00 41.08 3.66
2961 3435 5.633830 ATTGACTAGAGCCAAACAACATG 57.366 39.130 0.00 0.00 0.00 3.21
2962 3436 7.629222 GCAATATTGACTAGAGCCAAACAACAT 60.629 37.037 19.73 0.00 0.00 2.71
2963 3437 6.349280 GCAATATTGACTAGAGCCAAACAACA 60.349 38.462 19.73 0.00 0.00 3.33
2964 3438 6.030228 GCAATATTGACTAGAGCCAAACAAC 58.970 40.000 19.73 0.00 0.00 3.32
2965 3439 5.125417 GGCAATATTGACTAGAGCCAAACAA 59.875 40.000 19.73 0.00 40.29 2.83
2966 3440 4.640201 GGCAATATTGACTAGAGCCAAACA 59.360 41.667 19.73 0.00 40.29 2.83
2967 3441 4.036852 GGGCAATATTGACTAGAGCCAAAC 59.963 45.833 20.60 0.00 42.26 2.93
2968 3442 4.079787 AGGGCAATATTGACTAGAGCCAAA 60.080 41.667 20.60 0.00 42.26 3.28
2969 3443 3.459598 AGGGCAATATTGACTAGAGCCAA 59.540 43.478 20.60 0.00 42.26 4.52
2970 3444 3.048600 AGGGCAATATTGACTAGAGCCA 58.951 45.455 20.60 0.00 42.26 4.75
2971 3445 3.181450 ACAGGGCAATATTGACTAGAGCC 60.181 47.826 20.60 11.21 36.14 4.70
2972 3446 4.061596 GACAGGGCAATATTGACTAGAGC 58.938 47.826 20.60 3.90 36.14 4.09
2973 3447 4.101585 TGGACAGGGCAATATTGACTAGAG 59.898 45.833 20.60 10.47 36.14 2.43
2974 3448 4.037222 TGGACAGGGCAATATTGACTAGA 58.963 43.478 20.60 0.00 36.14 2.43
2975 3449 4.422073 TGGACAGGGCAATATTGACTAG 57.578 45.455 20.60 15.05 36.14 2.57
2976 3450 4.165950 ACATGGACAGGGCAATATTGACTA 59.834 41.667 20.60 2.89 36.14 2.59
2977 3451 3.053395 ACATGGACAGGGCAATATTGACT 60.053 43.478 20.60 13.25 36.14 3.41
2978 3452 3.290710 ACATGGACAGGGCAATATTGAC 58.709 45.455 19.73 16.63 34.70 3.18
2979 3453 3.668141 ACATGGACAGGGCAATATTGA 57.332 42.857 19.73 0.00 0.00 2.57
2980 3454 3.448301 ACAACATGGACAGGGCAATATTG 59.552 43.478 11.27 11.27 0.00 1.90
2981 3455 3.711863 ACAACATGGACAGGGCAATATT 58.288 40.909 0.00 0.00 0.00 1.28
2982 3456 3.386932 ACAACATGGACAGGGCAATAT 57.613 42.857 0.00 0.00 0.00 1.28
2983 3457 2.897271 ACAACATGGACAGGGCAATA 57.103 45.000 0.00 0.00 0.00 1.90
2984 3458 2.014010 AACAACATGGACAGGGCAAT 57.986 45.000 0.00 0.00 0.00 3.56
2985 3459 1.411977 CAAACAACATGGACAGGGCAA 59.588 47.619 0.00 0.00 0.00 4.52
2986 3460 1.039068 CAAACAACATGGACAGGGCA 58.961 50.000 0.00 0.00 0.00 5.36
2987 3461 0.318120 CCAAACAACATGGACAGGGC 59.682 55.000 0.00 0.00 40.56 5.19
2988 3462 0.318120 GCCAAACAACATGGACAGGG 59.682 55.000 0.00 0.00 40.56 4.45
3001 3475 4.253685 TGCTACAATGACTAGAGCCAAAC 58.746 43.478 0.00 0.00 31.98 2.93
3056 3538 9.406828 CAGGCATCATGAGATTGTTTAATTATG 57.593 33.333 0.09 0.00 30.20 1.90
3114 3596 5.796350 ACTCTATATTGACGCAAAACACC 57.204 39.130 0.00 0.00 0.00 4.16
3124 3606 8.582657 TCCCTTAGCATCTACTCTATATTGAC 57.417 38.462 0.00 0.00 0.00 3.18
3201 3691 6.041637 ACACCAGAATACAGAGAACAGTACAA 59.958 38.462 0.00 0.00 0.00 2.41
3223 3713 1.936547 GAGATTGAGGATTCCGCACAC 59.063 52.381 8.81 6.32 32.04 3.82
3240 3730 0.976641 ACTGTTGCAGAATCGGGAGA 59.023 50.000 2.91 0.00 38.10 3.71
3271 3761 3.413327 TCTCTATGAGCGGAGTATCACC 58.587 50.000 0.00 0.00 36.25 4.02
3279 3769 5.069648 AGTGATTGAAATCTCTATGAGCGGA 59.930 40.000 5.95 0.00 37.45 5.54
3286 3776 9.270640 GCATCTACAAGTGATTGAAATCTCTAT 57.729 33.333 7.77 3.67 38.05 1.98
3314 3809 9.474920 TGACATTTCAACAATGGAATTAAAGTC 57.525 29.630 0.00 0.00 32.11 3.01
3325 3820 9.467258 AGATAAACAAGTGACATTTCAACAATG 57.533 29.630 0.00 0.00 31.90 2.82
3329 3824 7.591426 GGTGAGATAAACAAGTGACATTTCAAC 59.409 37.037 0.00 0.00 31.90 3.18
3330 3825 7.502226 AGGTGAGATAAACAAGTGACATTTCAA 59.498 33.333 0.00 0.00 31.90 2.69
3332 3827 7.173218 TCAGGTGAGATAAACAAGTGACATTTC 59.827 37.037 0.00 0.00 0.00 2.17
3333 3828 6.998074 TCAGGTGAGATAAACAAGTGACATTT 59.002 34.615 0.00 0.00 0.00 2.32
3334 3829 6.533730 TCAGGTGAGATAAACAAGTGACATT 58.466 36.000 0.00 0.00 0.00 2.71
3335 3830 6.114187 TCAGGTGAGATAAACAAGTGACAT 57.886 37.500 0.00 0.00 0.00 3.06
3350 3845 1.950828 GACAGCATCCATCAGGTGAG 58.049 55.000 0.00 0.00 37.04 3.51
3364 3859 2.029649 ACAAAGAACATGCATGGACAGC 60.030 45.455 29.41 13.66 0.00 4.40
3736 4278 7.328277 CAGAGCTGTAGTAGTTATCTCTGTT 57.672 40.000 0.00 0.00 40.43 3.16
3776 4323 8.100791 ACAGCACAAATAGTATAACTGAAGGAA 58.899 33.333 0.00 0.00 0.00 3.36
3790 4337 4.248859 AGAGCAGTACACAGCACAAATAG 58.751 43.478 0.00 0.00 0.00 1.73
3847 4402 2.633657 CACACACTGCTGCGGAAC 59.366 61.111 16.72 0.00 0.00 3.62
4194 4754 2.749621 GGTCATCAACAGAACCCATGAC 59.250 50.000 0.00 0.00 41.73 3.06
4364 4939 7.099266 TCATAACAGAATGCTAACAATTGGG 57.901 36.000 10.83 0.83 42.53 4.12
4525 5108 4.939509 TGAATTAGCTAAAGTTGGTCGC 57.060 40.909 10.85 0.00 0.00 5.19
4715 5305 0.036022 GCAGAAGTTGGTGCTCTCCT 59.964 55.000 0.38 0.00 36.71 3.69
4951 5551 2.266554 CTCTTTTGTGCGCAACCAAAA 58.733 42.857 27.16 27.16 33.82 2.44
5035 5635 5.163513 CAGGAACAAAACATGGCTCATAAC 58.836 41.667 0.00 0.00 0.00 1.89
5036 5636 4.832266 ACAGGAACAAAACATGGCTCATAA 59.168 37.500 0.00 0.00 0.00 1.90
5041 5641 4.218417 GTCATACAGGAACAAAACATGGCT 59.782 41.667 0.00 0.00 0.00 4.75
5046 5646 4.447138 AGGGTCATACAGGAACAAAACA 57.553 40.909 0.00 0.00 0.00 2.83
5090 5698 6.039382 AGTTCAACAACCTGAATAACTCAACC 59.961 38.462 0.00 0.00 37.63 3.77
5099 5707 1.963515 GGCCAGTTCAACAACCTGAAT 59.036 47.619 0.00 0.00 37.63 2.57
5100 5708 1.398692 GGCCAGTTCAACAACCTGAA 58.601 50.000 0.00 0.00 32.22 3.02
5260 5874 6.810888 ATGTGTGAACAAAAAGATCGTTTG 57.189 33.333 18.08 18.08 40.95 2.93


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

AutoCloner maintained by Alex Coulton.