Multiple sequence alignment - TraesCS2A01G379400

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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 TraesCS2A01G379400 chr2A 100.000 8200 0 0 1 8200 622464532 622456333 0.000000e+00 15143.0
1 TraesCS2A01G379400 chr2A 88.089 764 90 1 3 766 205676980 205676218 0.000000e+00 905.0
2 TraesCS2A01G379400 chr2A 88.017 726 75 11 3490 4210 637461528 637460810 0.000000e+00 848.0
3 TraesCS2A01G379400 chr2A 90.152 396 39 0 2374 2769 622695655 622695260 4.390000e-142 516.0
4 TraesCS2A01G379400 chr2A 87.907 430 52 0 6771 7200 622694336 622693907 2.640000e-139 507.0
5 TraesCS2A01G379400 chr2A 90.217 368 33 3 991 1358 622697112 622696748 2.070000e-130 477.0
6 TraesCS2A01G379400 chr2A 81.728 602 70 25 6136 6708 622695212 622694622 4.480000e-127 466.0
7 TraesCS2A01G379400 chr2A 81.975 405 47 17 1621 2002 622696552 622696151 3.690000e-83 320.0
8 TraesCS2A01G379400 chr2D 95.849 1638 52 10 2003 3634 480137831 480136204 0.000000e+00 2634.0
9 TraesCS2A01G379400 chr2D 94.247 1495 60 16 5779 7270 480133842 480132371 0.000000e+00 2261.0
10 TraesCS2A01G379400 chr2D 96.727 825 24 1 4965 5786 480134695 480133871 0.000000e+00 1371.0
11 TraesCS2A01G379400 chr2D 94.881 547 12 3 3665 4210 480136211 480135680 0.000000e+00 841.0
12 TraesCS2A01G379400 chr2D 90.635 630 22 12 1418 2031 480138577 480137969 0.000000e+00 802.0
13 TraesCS2A01G379400 chr2D 84.081 691 73 15 7335 8022 480131990 480131334 4.180000e-177 632.0
14 TraesCS2A01G379400 chr2D 94.089 406 18 2 985 1387 480138978 480138576 5.440000e-171 612.0
15 TraesCS2A01G379400 chr2D 92.746 386 28 0 7815 8200 480131493 480131108 7.190000e-155 558.0
16 TraesCS2A01G379400 chr2D 89.095 431 47 0 6770 7200 480160611 480160181 3.370000e-148 536.0
17 TraesCS2A01G379400 chr2D 86.345 476 59 3 2346 2821 480161800 480161331 1.580000e-141 514.0
18 TraesCS2A01G379400 chr2D 89.891 366 34 3 991 1356 480162924 480162562 1.250000e-127 468.0
19 TraesCS2A01G379400 chr2D 91.640 311 24 2 3022 3332 46870532 46870224 5.880000e-116 429.0
20 TraesCS2A01G379400 chr2D 85.024 414 53 6 1618 2024 480162370 480161959 5.920000e-111 412.0
21 TraesCS2A01G379400 chr2D 88.053 226 20 4 5779 6001 46868268 46868047 2.270000e-65 261.0
22 TraesCS2A01G379400 chr2D 92.899 169 10 2 6416 6582 480161228 480161060 2.290000e-60 244.0
23 TraesCS2A01G379400 chr2D 88.350 206 18 3 7893 8093 190368693 190368489 8.220000e-60 243.0
24 TraesCS2A01G379400 chr2D 94.545 55 2 1 851 905 27884752 27884805 5.270000e-12 84.2
25 TraesCS2A01G379400 chr2B 95.146 1030 41 6 2003 3030 562981078 562980056 0.000000e+00 1616.0
26 TraesCS2A01G379400 chr2B 87.638 906 42 37 956 1827 562982432 562981563 0.000000e+00 989.0
27 TraesCS2A01G379400 chr2B 90.871 712 39 5 5996 6687 562980063 562979358 0.000000e+00 931.0
28 TraesCS2A01G379400 chr2B 89.377 706 50 8 7318 8023 562978313 562977633 0.000000e+00 865.0
29 TraesCS2A01G379400 chr2B 92.699 589 23 1 6729 7317 562979168 562978600 0.000000e+00 832.0
30 TraesCS2A01G379400 chr2B 93.798 387 22 2 7815 8200 562977793 562977408 1.530000e-161 580.0
31 TraesCS2A01G379400 chr2B 86.938 467 55 2 2346 2812 563026641 563026181 3.390000e-143 520.0
32 TraesCS2A01G379400 chr2B 88.194 432 49 2 6770 7200 563025353 563024923 1.580000e-141 514.0
33 TraesCS2A01G379400 chr2B 87.228 368 29 7 991 1358 563027694 563027345 3.560000e-108 403.0
34 TraesCS2A01G379400 chr2B 90.323 217 19 2 1645 1859 563027125 563026909 4.840000e-72 283.0
35 TraesCS2A01G379400 chr2B 92.308 169 11 2 6416 6582 563026034 563025866 1.060000e-58 239.0
36 TraesCS2A01G379400 chr2B 86.408 206 21 4 7893 8093 158359815 158360018 1.390000e-52 219.0
37 TraesCS2A01G379400 chr2B 85.965 114 14 2 5014 5126 787749109 787748997 4.020000e-23 121.0
38 TraesCS2A01G379400 chr7D 95.782 806 24 5 4207 5011 171329292 171328496 0.000000e+00 1291.0
39 TraesCS2A01G379400 chr7D 95.782 806 24 3 4207 5011 171336087 171335291 0.000000e+00 1291.0
40 TraesCS2A01G379400 chr7D 90.731 917 40 22 3329 4210 171330379 171329473 0.000000e+00 1181.0
41 TraesCS2A01G379400 chr7D 90.731 917 40 22 3329 4210 171337174 171336268 0.000000e+00 1181.0
42 TraesCS2A01G379400 chr7D 90.074 947 41 25 5101 5996 556308500 556309444 0.000000e+00 1179.0
43 TraesCS2A01G379400 chr7D 89.524 945 49 24 5101 5997 171328501 171327559 0.000000e+00 1151.0
44 TraesCS2A01G379400 chr7D 89.418 945 50 24 5101 5997 171335296 171334354 0.000000e+00 1146.0
45 TraesCS2A01G379400 chr7D 90.455 220 17 4 5779 5996 88606345 88606128 3.750000e-73 287.0
46 TraesCS2A01G379400 chr7D 89.873 79 4 4 826 901 7824535 7824458 1.880000e-16 99.0
47 TraesCS2A01G379400 chr7D 97.826 46 1 0 856 901 101395245 101395200 6.820000e-11 80.5
48 TraesCS2A01G379400 chr7A 94.601 815 34 2 4198 5011 78194444 78195249 0.000000e+00 1253.0
49 TraesCS2A01G379400 chr7A 92.642 299 21 1 3034 3332 218243802 218243505 5.880000e-116 429.0
50 TraesCS2A01G379400 chr7A 95.833 48 2 0 852 899 8775012 8775059 2.450000e-10 78.7
51 TraesCS2A01G379400 chr3B 94.417 806 34 3 4207 5011 386544302 386545097 0.000000e+00 1229.0
52 TraesCS2A01G379400 chr3B 91.104 888 40 17 3329 4210 315392917 315392063 0.000000e+00 1166.0
53 TraesCS2A01G379400 chr3B 90.312 898 46 7 3329 4210 386539278 386540150 0.000000e+00 1138.0
54 TraesCS2A01G379400 chr3B 92.040 804 53 4 4207 5009 275918618 275917825 0.000000e+00 1120.0
55 TraesCS2A01G379400 chr3B 92.899 676 42 6 5101 5775 275917828 275917158 0.000000e+00 977.0
56 TraesCS2A01G379400 chr3B 91.424 688 47 5 5101 5779 315389361 315388677 0.000000e+00 933.0
57 TraesCS2A01G379400 chr3B 88.991 218 22 2 5779 5995 315388641 315388425 1.360000e-67 268.0
58 TraesCS2A01G379400 chr3B 88.268 179 18 3 2049 2226 787347162 787347338 2.320000e-50 211.0
59 TraesCS2A01G379400 chr1A 96.054 735 19 3 4207 4940 30371667 30370942 0.000000e+00 1188.0
60 TraesCS2A01G379400 chr1A 96.054 735 19 3 4207 4940 30382527 30381802 0.000000e+00 1188.0
61 TraesCS2A01G379400 chr1A 92.878 688 32 7 5101 5777 30360381 30359700 0.000000e+00 983.0
62 TraesCS2A01G379400 chr1A 86.893 206 21 3 7893 8093 528934053 528933849 8.280000e-55 226.0
63 TraesCS2A01G379400 chr1A 89.759 166 14 3 2049 2213 13236946 13236783 8.340000e-50 209.0
64 TraesCS2A01G379400 chr1A 95.146 103 5 0 5008 5110 532672796 532672898 6.590000e-36 163.0
65 TraesCS2A01G379400 chr6A 89.554 919 51 17 3329 4210 429381942 429381032 0.000000e+00 1123.0
66 TraesCS2A01G379400 chr6A 88.171 727 73 12 3490 4210 34959840 34960559 0.000000e+00 854.0
67 TraesCS2A01G379400 chr6A 84.004 894 109 25 3330 4210 1953830 1952958 0.000000e+00 828.0
68 TraesCS2A01G379400 chr6A 81.664 769 130 11 3 766 12265264 12266026 5.400000e-176 628.0
69 TraesCS2A01G379400 chr6A 91.362 301 25 1 3032 3332 1956441 1956142 2.130000e-110 411.0
70 TraesCS2A01G379400 chr6A 85.976 164 19 1 3 166 611542715 611542556 1.090000e-38 172.0
71 TraesCS2A01G379400 chr3A 91.067 806 55 6 4207 5011 262528234 262527445 0.000000e+00 1074.0
72 TraesCS2A01G379400 chr3A 91.852 675 41 6 5101 5772 262527450 262526787 0.000000e+00 929.0
73 TraesCS2A01G379400 chr6D 89.118 873 48 23 5166 5995 6237671 6238539 0.000000e+00 1042.0
74 TraesCS2A01G379400 chr6D 88.835 206 17 3 7893 8093 86025809 86025605 1.770000e-61 248.0
75 TraesCS2A01G379400 chr6D 92.523 107 8 0 4999 5105 18672190 18672084 3.960000e-33 154.0
76 TraesCS2A01G379400 chr5A 88.104 807 92 2 4198 5003 23171753 23172556 0.000000e+00 955.0
77 TraesCS2A01G379400 chr5A 91.362 301 25 1 3032 3332 544505842 544506141 2.130000e-110 411.0
78 TraesCS2A01G379400 chr5A 89.412 170 15 3 2049 2217 680718399 680718566 2.320000e-50 211.0
79 TraesCS2A01G379400 chr3D 90.574 679 52 9 5101 5776 192054299 192054968 0.000000e+00 889.0
80 TraesCS2A01G379400 chr3D 88.554 166 16 3 2049 2213 604843774 604843937 1.810000e-46 198.0
81 TraesCS2A01G379400 chr3D 94.000 50 3 0 850 899 518264127 518264176 8.830000e-10 76.8
82 TraesCS2A01G379400 chr3D 81.176 85 9 4 816 896 481569009 481569090 2.470000e-05 62.1
83 TraesCS2A01G379400 chr1D 92.173 626 33 6 5173 5786 288099329 288098708 0.000000e+00 870.0
84 TraesCS2A01G379400 chr1D 91.324 219 15 3 5779 5995 288098678 288098462 6.220000e-76 296.0
85 TraesCS2A01G379400 chr1D 92.661 109 6 2 5007 5113 420554541 420554649 1.100000e-33 156.0
86 TraesCS2A01G379400 chr5D 83.135 925 107 23 3330 4210 87166357 87165438 0.000000e+00 798.0
87 TraesCS2A01G379400 chr5D 82.199 764 135 1 3 766 363853144 363852382 0.000000e+00 656.0
88 TraesCS2A01G379400 chr5D 95.000 100 5 0 5008 5107 521371581 521371680 3.060000e-34 158.0
89 TraesCS2A01G379400 chr1B 84.479 844 91 25 3401 4210 551729900 551730737 0.000000e+00 797.0
90 TraesCS2A01G379400 chr1B 91.362 301 25 1 3032 3332 466927416 466927715 2.130000e-110 411.0
91 TraesCS2A01G379400 chr1B 94.286 105 5 1 5006 5109 359902046 359902150 8.520000e-35 159.0
92 TraesCS2A01G379400 chr1B 85.507 69 4 5 824 892 652294037 652293975 5.310000e-07 67.6
93 TraesCS2A01G379400 chr4A 80.779 770 135 11 3 766 732750465 732751227 2.550000e-164 590.0
94 TraesCS2A01G379400 chr4A 91.694 301 24 1 3032 3332 34863276 34862977 4.580000e-112 416.0
95 TraesCS2A01G379400 chr7B 79.740 770 142 13 3 766 23380076 23379315 5.600000e-151 545.0
96 TraesCS2A01G379400 chr7B 95.000 100 5 0 5008 5107 562993066 562993165 3.060000e-34 158.0
97 TraesCS2A01G379400 chr7B 92.661 109 7 1 4998 5106 34327085 34326978 1.100000e-33 156.0
98 TraesCS2A01G379400 chr4B 79.324 769 148 9 3 766 40904993 40905755 5.640000e-146 529.0
99 TraesCS2A01G379400 chr4B 91.362 301 25 1 3032 3332 42231421 42231122 2.130000e-110 411.0
100 TraesCS2A01G379400 chr4B 83.680 337 53 2 3 338 66628645 66628980 4.780000e-82 316.0
101 TraesCS2A01G379400 chrUn 83.163 588 78 7 186 766 466275107 466275680 1.220000e-142 518.0
102 TraesCS2A01G379400 chrUn 90.608 181 10 2 3 176 418276784 418276604 4.950000e-57 233.0
103 TraesCS2A01G379400 chrUn 88.701 177 16 4 2044 2217 97121101 97120926 6.450000e-51 213.0
104 TraesCS2A01G379400 chrUn 93.333 45 3 0 855 899 16525591 16525547 5.310000e-07 67.6
105 TraesCS2A01G379400 chr6B 92.593 297 21 1 3032 3328 538069580 538069285 7.610000e-115 425.0
106 TraesCS2A01G379400 chr6B 89.412 170 15 3 2049 2217 655756718 655756551 2.320000e-50 211.0
107 TraesCS2A01G379400 chr5B 84.545 220 32 2 7814 8032 546814111 546813893 4.980000e-52 217.0
108 TraesCS2A01G379400 chr5B 88.235 170 17 3 2049 2217 677578885 677578718 5.020000e-47 200.0
109 TraesCS2A01G379400 chr4D 97.521 121 2 1 1 121 451294564 451294683 1.080000e-48 206.0
110 TraesCS2A01G379400 chr4D 91.304 115 9 1 5001 5114 26254056 26253942 1.100000e-33 156.0
111 TraesCS2A01G379400 chr4D 97.826 46 1 0 856 901 466837185 466837230 6.820000e-11 80.5


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 TraesCS2A01G379400 chr2A 622456333 622464532 8199 True 15143.000000 15143 100.000000 1 8200 1 chr2A.!!$R2 8199
1 TraesCS2A01G379400 chr2A 205676218 205676980 762 True 905.000000 905 88.089000 3 766 1 chr2A.!!$R1 763
2 TraesCS2A01G379400 chr2A 637460810 637461528 718 True 848.000000 848 88.017000 3490 4210 1 chr2A.!!$R3 720
3 TraesCS2A01G379400 chr2A 622693907 622697112 3205 True 457.200000 516 86.395800 991 7200 5 chr2A.!!$R4 6209
4 TraesCS2A01G379400 chr2D 480131108 480138978 7870 True 1213.875000 2634 92.906875 985 8200 8 chr2D.!!$R3 7215
5 TraesCS2A01G379400 chr2D 480160181 480162924 2743 True 434.800000 536 88.650800 991 7200 5 chr2D.!!$R4 6209
6 TraesCS2A01G379400 chr2D 46868047 46870532 2485 True 345.000000 429 89.846500 3022 6001 2 chr2D.!!$R2 2979
7 TraesCS2A01G379400 chr2B 562977408 562982432 5024 True 968.833333 1616 91.588167 956 8200 6 chr2B.!!$R2 7244
8 TraesCS2A01G379400 chr2B 563024923 563027694 2771 True 391.800000 520 88.998200 991 7200 5 chr2B.!!$R3 6209
9 TraesCS2A01G379400 chr7D 171327559 171337174 9615 True 1206.833333 1291 91.994667 3329 5997 6 chr7D.!!$R4 2668
10 TraesCS2A01G379400 chr7D 556308500 556309444 944 False 1179.000000 1179 90.074000 5101 5996 1 chr7D.!!$F1 895
11 TraesCS2A01G379400 chr7A 78194444 78195249 805 False 1253.000000 1253 94.601000 4198 5011 1 chr7A.!!$F2 813
12 TraesCS2A01G379400 chr3B 386544302 386545097 795 False 1229.000000 1229 94.417000 4207 5011 1 chr3B.!!$F2 804
13 TraesCS2A01G379400 chr3B 386539278 386540150 872 False 1138.000000 1138 90.312000 3329 4210 1 chr3B.!!$F1 881
14 TraesCS2A01G379400 chr3B 275917158 275918618 1460 True 1048.500000 1120 92.469500 4207 5775 2 chr3B.!!$R1 1568
15 TraesCS2A01G379400 chr3B 315388425 315392917 4492 True 789.000000 1166 90.506333 3329 5995 3 chr3B.!!$R2 2666
16 TraesCS2A01G379400 chr1A 30370942 30371667 725 True 1188.000000 1188 96.054000 4207 4940 1 chr1A.!!$R3 733
17 TraesCS2A01G379400 chr1A 30381802 30382527 725 True 1188.000000 1188 96.054000 4207 4940 1 chr1A.!!$R4 733
18 TraesCS2A01G379400 chr1A 30359700 30360381 681 True 983.000000 983 92.878000 5101 5777 1 chr1A.!!$R2 676
19 TraesCS2A01G379400 chr6A 429381032 429381942 910 True 1123.000000 1123 89.554000 3329 4210 1 chr6A.!!$R1 881
20 TraesCS2A01G379400 chr6A 34959840 34960559 719 False 854.000000 854 88.171000 3490 4210 1 chr6A.!!$F2 720
21 TraesCS2A01G379400 chr6A 12265264 12266026 762 False 628.000000 628 81.664000 3 766 1 chr6A.!!$F1 763
22 TraesCS2A01G379400 chr6A 1952958 1956441 3483 True 619.500000 828 87.683000 3032 4210 2 chr6A.!!$R3 1178
23 TraesCS2A01G379400 chr3A 262526787 262528234 1447 True 1001.500000 1074 91.459500 4207 5772 2 chr3A.!!$R1 1565
24 TraesCS2A01G379400 chr6D 6237671 6238539 868 False 1042.000000 1042 89.118000 5166 5995 1 chr6D.!!$F1 829
25 TraesCS2A01G379400 chr5A 23171753 23172556 803 False 955.000000 955 88.104000 4198 5003 1 chr5A.!!$F1 805
26 TraesCS2A01G379400 chr3D 192054299 192054968 669 False 889.000000 889 90.574000 5101 5776 1 chr3D.!!$F1 675
27 TraesCS2A01G379400 chr1D 288098462 288099329 867 True 583.000000 870 91.748500 5173 5995 2 chr1D.!!$R1 822
28 TraesCS2A01G379400 chr5D 87165438 87166357 919 True 798.000000 798 83.135000 3330 4210 1 chr5D.!!$R1 880
29 TraesCS2A01G379400 chr5D 363852382 363853144 762 True 656.000000 656 82.199000 3 766 1 chr5D.!!$R2 763
30 TraesCS2A01G379400 chr1B 551729900 551730737 837 False 797.000000 797 84.479000 3401 4210 1 chr1B.!!$F3 809
31 TraesCS2A01G379400 chr4A 732750465 732751227 762 False 590.000000 590 80.779000 3 766 1 chr4A.!!$F1 763
32 TraesCS2A01G379400 chr7B 23379315 23380076 761 True 545.000000 545 79.740000 3 766 1 chr7B.!!$R1 763
33 TraesCS2A01G379400 chr4B 40904993 40905755 762 False 529.000000 529 79.324000 3 766 1 chr4B.!!$F1 763
34 TraesCS2A01G379400 chrUn 466275107 466275680 573 False 518.000000 518 83.163000 186 766 1 chrUn.!!$F1 580

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
953 961 0.179105 ACGGCACACTAACACGTTCA 60.179 50.000 0.00 0.00 33.54 3.18 F
1405 1422 0.107703 TCTTATGGTCTGGCGCAAGG 60.108 55.000 12.96 0.00 38.28 3.61 F
1407 1424 0.392461 TTATGGTCTGGCGCAAGGTC 60.392 55.000 12.96 5.66 38.28 3.85 F
1428 1445 0.482887 AAGGTGTCCTTCCCCTTTGG 59.517 55.000 0.00 0.00 40.17 3.28 F
1484 1519 0.609957 TGGCAGCAGTCAATGGGAAG 60.610 55.000 0.00 0.00 0.00 3.46 F
1485 1520 0.610232 GGCAGCAGTCAATGGGAAGT 60.610 55.000 0.00 0.00 0.00 3.01 F
1489 1524 0.890683 GCAGTCAATGGGAAGTTGGG 59.109 55.000 0.00 0.00 0.00 4.12 F
2002 2329 1.072173 ACCCCAATGCTTTTCCTTTGC 59.928 47.619 0.00 0.00 0.00 3.68 F
3337 6535 1.719378 TCTCCCTCTCTCTGGTCCTTT 59.281 52.381 0.00 0.00 0.00 3.11 F
4378 7925 0.393077 AAGAACCAGGGACAGTCACG 59.607 55.000 2.17 0.00 0.00 4.35 F
5749 11121 0.324738 TTCTCGCCAGACAGGGAGAT 60.325 55.000 8.83 0.00 40.85 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 2185 0.103390 TTTTGTCTGACGACCTCGCA 59.897 50.000 2.98 0.00 44.43 5.10 R
3030 3888 0.167908 CCGCGCTTGCATTTTACTCA 59.832 50.000 5.56 0.00 39.07 3.41 R
3199 4057 1.153168 CGTGGGCCCTCGAATTGAT 60.153 57.895 37.00 0.00 35.30 2.57 R
3337 6535 7.044181 CCATTGTGACTGCTCTTAAGAAGATA 58.956 38.462 6.63 0.00 36.82 1.98 R
3905 7225 3.708451 TGAGTGATAGGCAGAAGGTACA 58.292 45.455 0.00 0.00 0.00 2.90 R
4156 7519 5.419788 ACTGTTACATGTCATTGGATGCATT 59.580 36.000 0.00 0.00 0.00 3.56 R
4240 7787 1.068127 CAAAATATCTGGCTGGCAGGC 59.932 52.381 31.94 31.94 41.77 4.85 R
4378 7925 0.960861 GGTTAGGGCAGGCTGTGTTC 60.961 60.000 17.16 0.00 0.00 3.18 R
5003 10305 0.337082 TGGGACGGAGGGAATACTGA 59.663 55.000 0.00 0.00 0.00 3.41 R
7046 19733 0.395312 AGTGGACCGAACCGACATTT 59.605 50.000 0.00 0.00 0.00 2.32 R
8139 21407 1.064946 CTCGCTCTCCTTAGTGGCG 59.935 63.158 0.00 0.00 42.56 5.69 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
121 122 3.118482 CGAAGCTTTGCAAAAATGACTCG 59.882 43.478 13.84 11.27 0.00 4.18
249 250 3.181290 CTCGACGCGCTTGCATGA 61.181 61.111 5.73 0.00 39.07 3.07
284 285 7.255942 CCATCAGTATTGATTTTTATCCACCCC 60.256 40.741 0.00 0.00 42.12 4.95
338 339 2.742116 GCGGGTATGCTCCCTTGGA 61.742 63.158 9.69 0.00 44.95 3.53
391 392 0.682852 TTCATCGACTGAACCGGGTT 59.317 50.000 13.26 13.26 38.97 4.11
410 411 4.145052 GGTTGAGGTCTCCTTTTTCATGT 58.855 43.478 0.00 0.00 31.76 3.21
416 417 6.430925 TGAGGTCTCCTTTTTCATGTGTAATG 59.569 38.462 0.00 0.00 31.76 1.90
488 489 4.326826 TGTCAGCTTCTGAAAACATAGGG 58.673 43.478 0.00 0.00 42.46 3.53
516 517 5.527214 CACAGAATATCCTTTCGCCATGTAA 59.473 40.000 0.00 0.00 0.00 2.41
520 521 1.281419 TCCTTTCGCCATGTAAGGGA 58.719 50.000 11.12 6.44 43.46 4.20
524 525 1.388547 TTCGCCATGTAAGGGAATGC 58.611 50.000 0.00 0.00 43.46 3.56
533 534 3.936564 TGTAAGGGAATGCAAATTTGGC 58.063 40.909 19.47 12.02 0.00 4.52
576 577 0.962356 CGCTGCATCCCAAAACCTCT 60.962 55.000 0.00 0.00 0.00 3.69
586 587 1.631405 CAAAACCTCTTGGCATGGGA 58.369 50.000 1.10 0.00 36.63 4.37
596 597 1.001641 GGCATGGGAGCAGTTCAGT 60.002 57.895 0.00 0.00 35.83 3.41
602 603 1.222113 GGAGCAGTTCAGTAGGGCC 59.778 63.158 0.00 0.00 0.00 5.80
613 614 1.142465 CAGTAGGGCCTGCATCAGATT 59.858 52.381 24.04 0.00 32.44 2.40
616 617 2.242882 AGGGCCTGCATCAGATTTTT 57.757 45.000 4.50 0.00 32.44 1.94
634 635 3.924918 TTTCTTCTCACCGAGACAGAG 57.075 47.619 0.00 0.00 38.51 3.35
656 664 2.276472 TGCACTTGCTGTTTGTTGAC 57.724 45.000 2.33 0.00 42.66 3.18
735 743 0.658897 AAACACACGTACTTTGGGCG 59.341 50.000 0.00 0.00 0.00 6.13
737 745 0.877213 ACACACGTACTTTGGGCGAC 60.877 55.000 0.00 0.00 0.00 5.19
755 763 2.996621 CGACACTTTAAGCTTCCAGAGG 59.003 50.000 0.00 1.42 0.00 3.69
762 770 1.722034 AAGCTTCCAGAGGTGAGACA 58.278 50.000 0.00 0.00 35.94 3.41
763 771 0.972883 AGCTTCCAGAGGTGAGACAC 59.027 55.000 0.00 0.00 34.08 3.67
764 772 0.681733 GCTTCCAGAGGTGAGACACA 59.318 55.000 0.00 0.00 35.86 3.72
765 773 1.277557 GCTTCCAGAGGTGAGACACAT 59.722 52.381 0.00 0.00 35.86 3.21
766 774 2.934364 GCTTCCAGAGGTGAGACACATG 60.934 54.545 0.00 0.00 35.86 3.21
767 775 2.015456 TCCAGAGGTGAGACACATGT 57.985 50.000 0.00 0.00 35.86 3.21
768 776 3.169512 TCCAGAGGTGAGACACATGTA 57.830 47.619 0.00 0.00 35.86 2.29
769 777 2.826128 TCCAGAGGTGAGACACATGTAC 59.174 50.000 0.00 0.00 35.86 2.90
770 778 2.828520 CCAGAGGTGAGACACATGTACT 59.171 50.000 0.00 0.61 35.86 2.73
771 779 3.119316 CCAGAGGTGAGACACATGTACTC 60.119 52.174 19.09 19.09 35.86 2.59
772 780 3.761218 CAGAGGTGAGACACATGTACTCT 59.239 47.826 23.35 15.81 35.86 3.24
773 781 4.219507 CAGAGGTGAGACACATGTACTCTT 59.780 45.833 23.35 14.12 35.86 2.85
774 782 4.835615 AGAGGTGAGACACATGTACTCTTT 59.164 41.667 23.35 13.88 35.86 2.52
775 783 4.887748 AGGTGAGACACATGTACTCTTTG 58.112 43.478 23.35 5.09 35.86 2.77
776 784 3.997021 GGTGAGACACATGTACTCTTTGG 59.003 47.826 23.35 4.42 35.86 3.28
777 785 4.503296 GGTGAGACACATGTACTCTTTGGT 60.503 45.833 23.35 7.20 35.86 3.67
778 786 4.449068 GTGAGACACATGTACTCTTTGGTG 59.551 45.833 23.35 0.00 34.08 4.17
779 787 4.343814 TGAGACACATGTACTCTTTGGTGA 59.656 41.667 23.35 7.49 0.00 4.02
780 788 5.012046 TGAGACACATGTACTCTTTGGTGAT 59.988 40.000 23.35 0.32 0.00 3.06
781 789 5.869579 AGACACATGTACTCTTTGGTGATT 58.130 37.500 0.00 0.00 0.00 2.57
782 790 5.702670 AGACACATGTACTCTTTGGTGATTG 59.297 40.000 0.00 0.00 0.00 2.67
783 791 5.376625 ACACATGTACTCTTTGGTGATTGT 58.623 37.500 0.00 0.00 0.00 2.71
784 792 5.827797 ACACATGTACTCTTTGGTGATTGTT 59.172 36.000 0.00 0.00 0.00 2.83
785 793 6.321181 ACACATGTACTCTTTGGTGATTGTTT 59.679 34.615 0.00 0.00 0.00 2.83
786 794 7.147915 ACACATGTACTCTTTGGTGATTGTTTT 60.148 33.333 0.00 0.00 0.00 2.43
787 795 8.349245 CACATGTACTCTTTGGTGATTGTTTTA 58.651 33.333 0.00 0.00 0.00 1.52
788 796 9.077885 ACATGTACTCTTTGGTGATTGTTTTAT 57.922 29.630 0.00 0.00 0.00 1.40
789 797 9.912634 CATGTACTCTTTGGTGATTGTTTTATT 57.087 29.630 0.00 0.00 0.00 1.40
810 818 6.879188 ATTTATAAAACATGGCGAAAACCG 57.121 33.333 1.21 0.00 42.21 4.44
811 819 3.926821 ATAAAACATGGCGAAAACCGT 57.073 38.095 0.00 0.00 41.15 4.83
812 820 2.588027 AAAACATGGCGAAAACCGTT 57.412 40.000 0.00 0.00 41.15 4.44
813 821 2.588027 AAACATGGCGAAAACCGTTT 57.412 40.000 0.00 0.00 41.15 3.60
814 822 2.588027 AACATGGCGAAAACCGTTTT 57.412 40.000 9.01 9.01 41.15 2.43
815 823 3.712091 AACATGGCGAAAACCGTTTTA 57.288 38.095 9.23 0.00 41.15 1.52
816 824 3.002708 ACATGGCGAAAACCGTTTTAC 57.997 42.857 9.23 5.18 41.15 2.01
817 825 1.973320 CATGGCGAAAACCGTTTTACG 59.027 47.619 9.23 14.17 42.11 3.18
818 826 1.012841 TGGCGAAAACCGTTTTACGT 58.987 45.000 19.95 0.00 40.58 3.57
819 827 2.205074 TGGCGAAAACCGTTTTACGTA 58.795 42.857 19.95 0.00 40.58 3.57
820 828 2.805099 TGGCGAAAACCGTTTTACGTAT 59.195 40.909 19.95 0.00 40.58 3.06
821 829 3.990469 TGGCGAAAACCGTTTTACGTATA 59.010 39.130 19.95 0.00 40.58 1.47
822 830 4.449068 TGGCGAAAACCGTTTTACGTATAA 59.551 37.500 19.95 0.00 40.58 0.98
823 831 5.050091 TGGCGAAAACCGTTTTACGTATAAA 60.050 36.000 19.95 0.00 40.58 1.40
824 832 6.020984 GGCGAAAACCGTTTTACGTATAAAT 58.979 36.000 19.95 0.00 40.58 1.40
825 833 6.022329 GGCGAAAACCGTTTTACGTATAAATG 60.022 38.462 19.95 5.90 40.58 2.32
826 834 6.519419 GCGAAAACCGTTTTACGTATAAATGT 59.481 34.615 19.95 0.00 40.58 2.71
827 835 7.059374 GCGAAAACCGTTTTACGTATAAATGTT 59.941 33.333 19.95 2.61 40.58 2.71
828 836 9.522454 CGAAAACCGTTTTACGTATAAATGTTA 57.478 29.630 9.23 0.00 40.58 2.41
832 840 8.185003 ACCGTTTTACGTATAAATGTTACTCC 57.815 34.615 0.00 0.00 40.58 3.85
833 841 7.277760 ACCGTTTTACGTATAAATGTTACTCCC 59.722 37.037 0.00 0.00 40.58 4.30
834 842 7.492344 CCGTTTTACGTATAAATGTTACTCCCT 59.508 37.037 0.00 0.00 40.58 4.20
835 843 8.534778 CGTTTTACGTATAAATGTTACTCCCTC 58.465 37.037 0.00 0.00 36.74 4.30
836 844 9.591792 GTTTTACGTATAAATGTTACTCCCTCT 57.408 33.333 0.00 0.00 30.33 3.69
837 845 9.590451 TTTTACGTATAAATGTTACTCCCTCTG 57.410 33.333 0.00 0.00 30.33 3.35
838 846 6.786967 ACGTATAAATGTTACTCCCTCTGT 57.213 37.500 0.00 0.00 0.00 3.41
839 847 6.570692 ACGTATAAATGTTACTCCCTCTGTG 58.429 40.000 0.00 0.00 0.00 3.66
840 848 6.379133 ACGTATAAATGTTACTCCCTCTGTGA 59.621 38.462 0.00 0.00 0.00 3.58
841 849 7.093640 ACGTATAAATGTTACTCCCTCTGTGAA 60.094 37.037 0.00 0.00 0.00 3.18
842 850 7.762615 CGTATAAATGTTACTCCCTCTGTGAAA 59.237 37.037 0.00 0.00 0.00 2.69
843 851 9.444600 GTATAAATGTTACTCCCTCTGTGAAAA 57.555 33.333 0.00 0.00 0.00 2.29
844 852 8.934023 ATAAATGTTACTCCCTCTGTGAAAAA 57.066 30.769 0.00 0.00 0.00 1.94
845 853 7.839680 AAATGTTACTCCCTCTGTGAAAAAT 57.160 32.000 0.00 0.00 0.00 1.82
846 854 8.934023 AAATGTTACTCCCTCTGTGAAAAATA 57.066 30.769 0.00 0.00 0.00 1.40
847 855 9.533831 AAATGTTACTCCCTCTGTGAAAAATAT 57.466 29.630 0.00 0.00 0.00 1.28
872 880 7.811117 ATAAGAGAGTAGTGATCTAAACGCT 57.189 36.000 0.00 0.00 0.00 5.07
873 881 6.518208 AAGAGAGTAGTGATCTAAACGCTT 57.482 37.500 0.00 0.00 0.00 4.68
874 882 6.518208 AGAGAGTAGTGATCTAAACGCTTT 57.482 37.500 0.00 0.00 0.00 3.51
875 883 6.926313 AGAGAGTAGTGATCTAAACGCTTTT 58.074 36.000 0.00 0.00 0.00 2.27
876 884 8.053026 AGAGAGTAGTGATCTAAACGCTTTTA 57.947 34.615 0.00 0.00 0.00 1.52
877 885 8.688151 AGAGAGTAGTGATCTAAACGCTTTTAT 58.312 33.333 0.00 0.00 0.00 1.40
878 886 9.947669 GAGAGTAGTGATCTAAACGCTTTTATA 57.052 33.333 0.00 0.00 0.00 0.98
892 900 7.186021 ACGCTTTTATATTTCATTACGGAGG 57.814 36.000 0.00 0.00 0.00 4.30
893 901 6.204108 ACGCTTTTATATTTCATTACGGAGGG 59.796 38.462 0.00 0.00 0.00 4.30
894 902 6.425721 CGCTTTTATATTTCATTACGGAGGGA 59.574 38.462 0.00 0.00 0.00 4.20
895 903 7.360101 CGCTTTTATATTTCATTACGGAGGGAG 60.360 40.741 0.00 0.00 0.00 4.30
896 904 7.444487 GCTTTTATATTTCATTACGGAGGGAGT 59.556 37.037 0.00 0.00 0.00 3.85
897 905 9.991906 CTTTTATATTTCATTACGGAGGGAGTA 57.008 33.333 0.00 0.00 0.00 2.59
898 906 9.991906 TTTTATATTTCATTACGGAGGGAGTAG 57.008 33.333 0.00 0.00 0.00 2.57
899 907 8.716674 TTATATTTCATTACGGAGGGAGTAGT 57.283 34.615 0.00 0.00 0.00 2.73
900 908 9.812347 TTATATTTCATTACGGAGGGAGTAGTA 57.188 33.333 0.00 0.00 0.00 1.82
901 909 8.896722 ATATTTCATTACGGAGGGAGTAGTAT 57.103 34.615 0.00 0.00 0.00 2.12
902 910 7.613551 ATTTCATTACGGAGGGAGTAGTATT 57.386 36.000 0.00 0.00 0.00 1.89
903 911 7.427989 TTTCATTACGGAGGGAGTAGTATTT 57.572 36.000 0.00 0.00 0.00 1.40
904 912 7.427989 TTCATTACGGAGGGAGTAGTATTTT 57.572 36.000 0.00 0.00 0.00 1.82
905 913 7.427989 TCATTACGGAGGGAGTAGTATTTTT 57.572 36.000 0.00 0.00 0.00 1.94
906 914 7.495055 TCATTACGGAGGGAGTAGTATTTTTC 58.505 38.462 0.00 0.00 0.00 2.29
907 915 7.343833 TCATTACGGAGGGAGTAGTATTTTTCT 59.656 37.037 0.00 0.00 0.00 2.52
908 916 7.486407 TTACGGAGGGAGTAGTATTTTTCTT 57.514 36.000 0.00 0.00 0.00 2.52
909 917 8.593945 TTACGGAGGGAGTAGTATTTTTCTTA 57.406 34.615 0.00 0.00 0.00 2.10
910 918 7.486407 ACGGAGGGAGTAGTATTTTTCTTAA 57.514 36.000 0.00 0.00 0.00 1.85
911 919 7.910584 ACGGAGGGAGTAGTATTTTTCTTAAA 58.089 34.615 0.00 0.00 0.00 1.52
912 920 7.821359 ACGGAGGGAGTAGTATTTTTCTTAAAC 59.179 37.037 0.00 0.00 0.00 2.01
913 921 8.039538 CGGAGGGAGTAGTATTTTTCTTAAACT 58.960 37.037 0.00 0.00 0.00 2.66
914 922 9.736414 GGAGGGAGTAGTATTTTTCTTAAACTT 57.264 33.333 0.00 0.00 0.00 2.66
916 924 9.516546 AGGGAGTAGTATTTTTCTTAAACTTGG 57.483 33.333 0.00 0.00 0.00 3.61
917 925 8.737175 GGGAGTAGTATTTTTCTTAAACTTGGG 58.263 37.037 0.00 0.00 0.00 4.12
918 926 9.293404 GGAGTAGTATTTTTCTTAAACTTGGGT 57.707 33.333 0.00 0.00 0.00 4.51
938 946 9.240159 CTTGGGTATAAATGTTATAAAAACGGC 57.760 33.333 0.00 0.00 0.00 5.68
939 947 8.289939 TGGGTATAAATGTTATAAAAACGGCA 57.710 30.769 0.00 0.00 0.00 5.69
940 948 8.189460 TGGGTATAAATGTTATAAAAACGGCAC 58.811 33.333 0.00 0.00 0.00 5.01
941 949 8.189460 GGGTATAAATGTTATAAAAACGGCACA 58.811 33.333 0.00 0.00 0.00 4.57
942 950 9.012448 GGTATAAATGTTATAAAAACGGCACAC 57.988 33.333 0.00 0.00 0.00 3.82
943 951 9.777575 GTATAAATGTTATAAAAACGGCACACT 57.222 29.630 0.00 0.00 0.00 3.55
946 954 8.510132 AAATGTTATAAAAACGGCACACTAAC 57.490 30.769 0.00 0.00 0.00 2.34
947 955 6.615264 TGTTATAAAAACGGCACACTAACA 57.385 33.333 0.00 0.00 0.00 2.41
948 956 6.428799 TGTTATAAAAACGGCACACTAACAC 58.571 36.000 0.00 0.00 0.00 3.32
949 957 2.461897 AAAAACGGCACACTAACACG 57.538 45.000 0.00 0.00 0.00 4.49
950 958 1.371595 AAAACGGCACACTAACACGT 58.628 45.000 0.00 0.00 39.74 4.49
951 959 3.068574 AACGGCACACTAACACGTT 57.931 47.368 0.00 0.00 42.17 3.99
952 960 0.932399 AACGGCACACTAACACGTTC 59.068 50.000 0.00 0.00 43.29 3.95
953 961 0.179105 ACGGCACACTAACACGTTCA 60.179 50.000 0.00 0.00 33.54 3.18
954 962 1.144969 CGGCACACTAACACGTTCAT 58.855 50.000 0.00 0.00 0.00 2.57
955 963 1.529438 CGGCACACTAACACGTTCATT 59.471 47.619 0.00 0.00 0.00 2.57
956 964 2.661709 CGGCACACTAACACGTTCATTG 60.662 50.000 0.00 0.00 0.00 2.82
957 965 2.289547 GGCACACTAACACGTTCATTGT 59.710 45.455 0.00 0.00 0.00 2.71
958 966 3.495377 GGCACACTAACACGTTCATTGTA 59.505 43.478 0.00 0.00 0.00 2.41
959 967 4.024725 GGCACACTAACACGTTCATTGTAA 60.025 41.667 0.00 0.00 0.00 2.41
960 968 5.503498 GCACACTAACACGTTCATTGTAAA 58.497 37.500 0.00 0.00 0.00 2.01
961 969 6.140110 GCACACTAACACGTTCATTGTAAAT 58.860 36.000 0.00 0.00 0.00 1.40
962 970 6.302313 GCACACTAACACGTTCATTGTAAATC 59.698 38.462 0.00 0.00 0.00 2.17
963 971 7.348956 CACACTAACACGTTCATTGTAAATCA 58.651 34.615 0.00 0.00 0.00 2.57
964 972 8.015087 CACACTAACACGTTCATTGTAAATCAT 58.985 33.333 0.00 0.00 0.00 2.45
965 973 9.210329 ACACTAACACGTTCATTGTAAATCATA 57.790 29.630 0.00 0.00 0.00 2.15
966 974 9.472995 CACTAACACGTTCATTGTAAATCATAC 57.527 33.333 0.00 0.00 0.00 2.39
967 975 9.431887 ACTAACACGTTCATTGTAAATCATACT 57.568 29.630 0.00 0.00 0.00 2.12
970 978 7.891782 ACACGTTCATTGTAAATCATACTACG 58.108 34.615 0.00 0.00 0.00 3.51
971 979 7.756272 ACACGTTCATTGTAAATCATACTACGA 59.244 33.333 0.00 0.00 0.00 3.43
972 980 8.588789 CACGTTCATTGTAAATCATACTACGAA 58.411 33.333 0.00 0.00 0.00 3.85
973 981 8.804743 ACGTTCATTGTAAATCATACTACGAAG 58.195 33.333 0.00 0.00 0.00 3.79
1010 1018 1.464687 CGCTCCGTCAATGAAAGCTTG 60.465 52.381 0.00 0.00 0.00 4.01
1188 1205 3.854669 CCGGAGCTCGCCTTCCAT 61.855 66.667 7.83 0.00 37.59 3.41
1405 1422 0.107703 TCTTATGGTCTGGCGCAAGG 60.108 55.000 12.96 0.00 38.28 3.61
1406 1423 0.392998 CTTATGGTCTGGCGCAAGGT 60.393 55.000 12.96 0.00 38.28 3.50
1407 1424 0.392461 TTATGGTCTGGCGCAAGGTC 60.392 55.000 12.96 5.66 38.28 3.85
1408 1425 2.252072 TATGGTCTGGCGCAAGGTCC 62.252 60.000 12.96 15.12 38.28 4.46
1409 1426 4.329545 GGTCTGGCGCAAGGTCCA 62.330 66.667 12.96 0.00 38.28 4.02
1410 1427 2.281484 GTCTGGCGCAAGGTCCAA 60.281 61.111 12.96 0.00 38.28 3.53
1428 1445 0.482887 AAGGTGTCCTTCCCCTTTGG 59.517 55.000 0.00 0.00 40.17 3.28
1484 1519 0.609957 TGGCAGCAGTCAATGGGAAG 60.610 55.000 0.00 0.00 0.00 3.46
1485 1520 0.610232 GGCAGCAGTCAATGGGAAGT 60.610 55.000 0.00 0.00 0.00 3.01
1486 1521 1.251251 GCAGCAGTCAATGGGAAGTT 58.749 50.000 0.00 0.00 0.00 2.66
1487 1522 1.068055 GCAGCAGTCAATGGGAAGTTG 60.068 52.381 0.00 0.00 0.00 3.16
1488 1523 1.542915 CAGCAGTCAATGGGAAGTTGG 59.457 52.381 0.00 0.00 0.00 3.77
1489 1524 0.890683 GCAGTCAATGGGAAGTTGGG 59.109 55.000 0.00 0.00 0.00 4.12
1490 1525 1.547675 GCAGTCAATGGGAAGTTGGGA 60.548 52.381 0.00 0.00 0.00 4.37
1491 1526 2.875296 CAGTCAATGGGAAGTTGGGAA 58.125 47.619 0.00 0.00 0.00 3.97
1520 1555 5.600898 TGTCTCGGGGAGTATGAAATTATGA 59.399 40.000 0.00 0.00 0.00 2.15
1522 1557 7.162082 GTCTCGGGGAGTATGAAATTATGAAT 58.838 38.462 0.00 0.00 0.00 2.57
1583 1618 7.744087 AGTTTGCTGTAAATAATGTGACTGA 57.256 32.000 0.00 0.00 0.00 3.41
1590 1625 5.699001 TGTAAATAATGTGACTGACGCTTGT 59.301 36.000 0.00 0.00 0.00 3.16
1595 1630 8.487313 AATAATGTGACTGACGCTTGTTATTA 57.513 30.769 0.00 0.00 0.00 0.98
1781 1835 2.034066 CTCCTGGGAGCGGCAAAA 59.966 61.111 1.45 0.00 35.31 2.44
1841 2146 6.313905 GTGCTTGCTTATAGTTCTGCTCTAAA 59.686 38.462 0.00 0.00 0.00 1.85
1874 2185 8.403236 GGAATTTAGTACTTCAGTTGTGTTTGT 58.597 33.333 0.00 0.00 0.00 2.83
1904 2217 5.869888 GTCGTCAGACAAAATACTTGATCCT 59.130 40.000 0.41 0.00 46.32 3.24
1908 2221 7.556844 GTCAGACAAAATACTTGATCCTCCTA 58.443 38.462 0.00 0.00 0.00 2.94
1967 2294 8.819974 CATTTGCTAATTCTCTTGTTGTTTGTT 58.180 29.630 0.00 0.00 0.00 2.83
2002 2329 1.072173 ACCCCAATGCTTTTCCTTTGC 59.928 47.619 0.00 0.00 0.00 3.68
2174 2823 4.023279 TGTGTGCTCATTGTGTTTGTATCC 60.023 41.667 0.00 0.00 0.00 2.59
2181 2830 6.770785 GCTCATTGTGTTTGTATCCCCTTATA 59.229 38.462 0.00 0.00 0.00 0.98
2451 3274 2.350804 GCTGGTGCATCGCATATGATAG 59.649 50.000 6.97 0.00 41.91 2.08
2822 3680 2.066262 ACAAAAGTCTATGTCGCACGG 58.934 47.619 0.00 0.00 0.00 4.94
2891 3749 2.863740 CAGTCACAAAACAGAGCACGTA 59.136 45.455 0.00 0.00 0.00 3.57
2993 3851 2.771943 TCTCCCCTGTTGCTTATGGTAG 59.228 50.000 0.00 0.00 0.00 3.18
3030 3888 9.914131 GAAGGAAACAAATGCTAATAGTTTCTT 57.086 29.630 13.79 5.90 44.41 2.52
3072 3930 6.204882 CGGTCCTAATTCTTTTCTGAAAGTGT 59.795 38.462 2.75 0.00 42.32 3.55
3202 4061 3.834013 TTTGACCGCCGCCACATCA 62.834 57.895 0.00 0.00 0.00 3.07
3337 6535 1.719378 TCTCCCTCTCTCTGGTCCTTT 59.281 52.381 0.00 0.00 0.00 3.11
3658 6929 5.425217 TGTATTTCTTCCAGTCTGCCTCATA 59.575 40.000 0.00 0.00 0.00 2.15
3739 7011 2.997986 CAAAGTTTTGATGCAGATGCCC 59.002 45.455 1.72 0.00 40.55 5.36
4001 7363 7.504238 TGTTTAGAAACCACTTCCATGTAACAT 59.496 33.333 2.80 0.00 38.11 2.71
4156 7519 5.552870 AGCAAGTAAGAAACCTCTCTTGA 57.447 39.130 0.00 0.00 36.34 3.02
4240 7787 2.937149 CTGCTCTGAATGTCTCCACATG 59.063 50.000 0.00 0.00 42.89 3.21
4378 7925 0.393077 AAGAACCAGGGACAGTCACG 59.607 55.000 2.17 0.00 0.00 4.35
4666 8222 5.032327 TGCAGCTCATCAGATTCATAGTT 57.968 39.130 0.00 0.00 0.00 2.24
4686 8242 2.664402 ACTGTCCTGCTCCAATTTGT 57.336 45.000 0.00 0.00 0.00 2.83
4725 8281 3.499338 TGCTCAAATTTGTCATCCACCT 58.501 40.909 17.47 0.00 0.00 4.00
4812 10113 3.306571 CCACTCACTGTCATCACTGTCAT 60.307 47.826 0.00 0.00 32.63 3.06
4813 10114 3.925299 CACTCACTGTCATCACTGTCATC 59.075 47.826 0.00 0.00 32.63 2.92
4814 10115 3.575687 ACTCACTGTCATCACTGTCATCA 59.424 43.478 0.00 0.00 32.63 3.07
4815 10116 3.917988 TCACTGTCATCACTGTCATCAC 58.082 45.455 0.00 0.00 32.63 3.06
4816 10117 3.575687 TCACTGTCATCACTGTCATCACT 59.424 43.478 0.00 0.00 32.63 3.41
4817 10118 3.678548 CACTGTCATCACTGTCATCACTG 59.321 47.826 0.00 0.00 32.63 3.66
4818 10119 3.323115 ACTGTCATCACTGTCATCACTGT 59.677 43.478 0.00 0.00 35.17 3.55
4819 10120 3.917988 TGTCATCACTGTCATCACTGTC 58.082 45.455 0.00 0.00 32.63 3.51
4820 10121 3.321682 TGTCATCACTGTCATCACTGTCA 59.678 43.478 0.00 0.00 32.63 3.58
5003 10305 2.859951 ACCTAGGACTGCCCCTAATTT 58.140 47.619 17.98 0.00 38.26 1.82
5019 10321 5.298347 CCTAATTTCAGTATTCCCTCCGTC 58.702 45.833 0.00 0.00 0.00 4.79
5021 10323 1.492764 TTCAGTATTCCCTCCGTCCC 58.507 55.000 0.00 0.00 0.00 4.46
5022 10324 0.337082 TCAGTATTCCCTCCGTCCCA 59.663 55.000 0.00 0.00 0.00 4.37
5024 10326 1.557832 CAGTATTCCCTCCGTCCCAAA 59.442 52.381 0.00 0.00 0.00 3.28
5038 10394 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
5077 10433 8.138365 TGCACTAAAGTTAGTACAAAGTTGAG 57.862 34.615 3.46 0.00 41.82 3.02
5080 10436 9.309516 CACTAAAGTTAGTACAAAGTTGAGACA 57.690 33.333 3.46 0.00 41.82 3.41
5093 10449 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
5095 10451 3.071479 TGAGACACTTATTTTGGGACGC 58.929 45.455 0.00 0.00 0.00 5.19
5097 10453 3.074412 AGACACTTATTTTGGGACGCAG 58.926 45.455 0.00 0.00 0.00 5.18
5350 10707 9.832445 AAATGTACTTCGATTGGTCACTATATT 57.168 29.630 0.00 0.00 0.00 1.28
5631 10996 2.519780 GAGGATCTCCGGGTCGCT 60.520 66.667 0.00 0.00 42.08 4.93
5642 11007 1.898154 GGGTCGCTGTAGATGTGGT 59.102 57.895 0.00 0.00 0.00 4.16
5653 11018 1.885049 AGATGTGGTGCCATCCTAGT 58.115 50.000 0.00 0.00 41.79 2.57
5749 11121 0.324738 TTCTCGCCAGACAGGGAGAT 60.325 55.000 8.83 0.00 40.85 2.75
5826 18030 3.260100 CCTGGGCCCTCTGGTGTT 61.260 66.667 25.70 0.00 0.00 3.32
5984 18189 2.109425 AAGAATTAGGACCGCGCTTT 57.891 45.000 5.56 0.00 0.00 3.51
5985 18190 2.109425 AGAATTAGGACCGCGCTTTT 57.891 45.000 5.56 0.00 0.00 2.27
6115 18320 7.216973 AGTCTGGATTAAGTATTAGCCTACG 57.783 40.000 0.00 0.00 30.85 3.51
6197 18402 7.044181 TGAAAGGCTACTCTAGTGATGATTTG 58.956 38.462 0.00 0.00 0.00 2.32
6301 18506 3.307975 CCATTCCACTGGATGTCTTCAGT 60.308 47.826 0.00 0.00 44.12 3.41
6302 18507 3.685139 TTCCACTGGATGTCTTCAGTC 57.315 47.619 0.00 0.00 41.71 3.51
6303 18508 2.608623 TCCACTGGATGTCTTCAGTCA 58.391 47.619 0.00 0.00 41.71 3.41
6304 18509 2.564504 TCCACTGGATGTCTTCAGTCAG 59.435 50.000 0.00 0.00 41.71 3.51
6305 18510 2.301296 CCACTGGATGTCTTCAGTCAGT 59.699 50.000 0.00 0.00 41.71 3.41
6315 18520 8.301002 GGATGTCTTCAGTCAGTTAGTATATCC 58.699 40.741 0.00 0.00 0.00 2.59
6654 18968 6.818142 ACCTTCAATTTTGTTTTTCTGTGAGG 59.182 34.615 0.00 0.00 0.00 3.86
6656 18970 7.223387 CCTTCAATTTTGTTTTTCTGTGAGGAG 59.777 37.037 0.00 0.00 0.00 3.69
6733 19346 8.147058 ACTTAGACATCAGGACATGCTTATTAG 58.853 37.037 0.00 0.00 0.00 1.73
6787 19474 9.716531 CTGTATCATCCTGAATAAATGCTCTTA 57.283 33.333 0.00 0.00 0.00 2.10
6894 19581 1.107945 TCCTGCCGTCGTCAATGATA 58.892 50.000 0.00 0.00 0.00 2.15
6941 19628 1.114722 TGGGCAGAAGTTTGCTTGGG 61.115 55.000 9.05 0.00 43.57 4.12
7016 19703 4.228824 TCTACCAACAGTTAGTTCCTGGT 58.771 43.478 0.00 0.00 40.87 4.00
7046 19733 9.621629 ATGTTTGGTATCGGTATTAGAAATGAA 57.378 29.630 0.00 0.00 0.00 2.57
7094 19781 0.108329 ACCCGCATTTCTTCGTCGAT 60.108 50.000 0.00 0.00 0.00 3.59
7209 19896 2.363788 TTCGCTGTAATGCTCTTCGT 57.636 45.000 0.00 0.00 0.00 3.85
7210 19897 2.363788 TCGCTGTAATGCTCTTCGTT 57.636 45.000 0.00 0.00 0.00 3.85
7312 20244 5.918426 TTCAAGGCTCAAATGCATATTCA 57.082 34.783 0.00 0.00 34.04 2.57
7328 20546 5.566826 GCATATTCATCAGGCTCAAATGCAT 60.567 40.000 0.00 0.00 37.67 3.96
7332 20550 5.700722 TCATCAGGCTCAAATGCATATTC 57.299 39.130 0.00 0.00 34.04 1.75
7333 20551 5.134661 TCATCAGGCTCAAATGCATATTCA 58.865 37.500 0.00 0.00 34.04 2.57
7363 20581 3.440522 GCAGATTTGTTGGAGTTAGACCC 59.559 47.826 0.00 0.00 0.00 4.46
7440 20658 9.720667 ATGTGATAAAAATGACATACATGTTCG 57.279 29.630 2.30 0.00 41.95 3.95
7505 20725 6.349300 CATTGACAAGCCCAATAGTACTACT 58.651 40.000 4.31 0.00 33.35 2.57
7506 20726 7.418597 CCATTGACAAGCCCAATAGTACTACTA 60.419 40.741 4.31 0.00 34.82 1.82
7507 20727 6.461110 TGACAAGCCCAATAGTACTACTAC 57.539 41.667 4.31 0.00 32.84 2.73
7508 20728 5.953548 TGACAAGCCCAATAGTACTACTACA 59.046 40.000 4.31 0.00 32.84 2.74
7509 20729 6.127535 TGACAAGCCCAATAGTACTACTACAC 60.128 42.308 4.31 0.00 32.84 2.90
7511 20731 6.211986 ACAAGCCCAATAGTACTACTACACAA 59.788 38.462 4.31 0.00 32.84 3.33
7512 20732 6.862469 AGCCCAATAGTACTACTACACAAA 57.138 37.500 4.31 0.00 32.84 2.83
7513 20733 6.637657 AGCCCAATAGTACTACTACACAAAC 58.362 40.000 4.31 0.00 32.84 2.93
7514 20734 6.211986 AGCCCAATAGTACTACTACACAAACA 59.788 38.462 4.31 0.00 32.84 2.83
7515 20735 6.312180 GCCCAATAGTACTACTACACAAACAC 59.688 42.308 4.31 0.00 32.84 3.32
7516 20736 7.380536 CCCAATAGTACTACTACACAAACACA 58.619 38.462 4.31 0.00 32.84 3.72
7517 20737 7.874016 CCCAATAGTACTACTACACAAACACAA 59.126 37.037 4.31 0.00 32.84 3.33
7518 20738 9.263538 CCAATAGTACTACTACACAAACACAAA 57.736 33.333 4.31 0.00 32.84 2.83
7520 20740 9.820725 AATAGTACTACTACACAAACACAAACA 57.179 29.630 4.31 0.00 32.84 2.83
7521 20741 7.529880 AGTACTACTACACAAACACAAACAC 57.470 36.000 0.00 0.00 0.00 3.32
7522 20742 7.098477 AGTACTACTACACAAACACAAACACA 58.902 34.615 0.00 0.00 0.00 3.72
7523 20743 6.804770 ACTACTACACAAACACAAACACAA 57.195 33.333 0.00 0.00 0.00 3.33
7524 20744 7.204496 ACTACTACACAAACACAAACACAAA 57.796 32.000 0.00 0.00 0.00 2.83
7525 20745 7.649973 ACTACTACACAAACACAAACACAAAA 58.350 30.769 0.00 0.00 0.00 2.44
7531 20751 7.305474 ACACAAACACAAACACAAAAACAAAA 58.695 26.923 0.00 0.00 0.00 2.44
7569 20789 1.000717 ACCGCACAATGTAAACAAGCC 60.001 47.619 0.00 0.00 0.00 4.35
7573 20793 0.239879 ACAATGTAAACAAGCCGGCG 59.760 50.000 23.20 10.77 0.00 6.46
7627 20847 7.894376 AGTAAACATTGCCAAAATCATTGAG 57.106 32.000 0.00 0.00 0.00 3.02
7644 20864 3.920231 TGAGCCAGCATTGTAGATTCT 57.080 42.857 0.00 0.00 0.00 2.40
7694 20914 4.351054 AAGGAGGTGGCGCAAGGG 62.351 66.667 10.83 0.00 38.28 3.95
7936 21204 1.914764 GGGTACCGTGAACTGGGGA 60.915 63.158 5.65 0.00 40.86 4.81
7939 21207 0.668401 GTACCGTGAACTGGGGAACG 60.668 60.000 0.00 0.00 35.85 3.95
7941 21209 3.047877 CGTGAACTGGGGAACGGC 61.048 66.667 0.00 0.00 32.55 5.68
7992 21260 2.665185 GACCTGCGGTGTGGTGAC 60.665 66.667 4.94 0.00 35.25 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.090052 GTGGTGGCGCCTATCTTGAC 61.090 60.000 29.70 15.38 38.35 3.18
87 88 3.431572 GCAAAGCTTCGAGGCTATGATAG 59.568 47.826 23.37 9.91 42.24 2.08
89 90 2.216898 GCAAAGCTTCGAGGCTATGAT 58.783 47.619 23.37 3.79 42.24 2.45
121 122 1.279840 GCACTTGCTGTTCGTGACC 59.720 57.895 0.00 0.00 38.21 4.02
153 154 4.614535 GCCGTATACAGGTATTACAGACCG 60.615 50.000 3.32 0.00 42.21 4.79
193 194 4.758674 TGGCTAAATCATCTATTGCTCTGC 59.241 41.667 0.00 0.00 0.00 4.26
210 211 1.205460 GGAGTTGGAGGGGTGGCTAA 61.205 60.000 0.00 0.00 0.00 3.09
244 245 7.502120 AATACTGATGGAAGTATTGTCATGC 57.498 36.000 8.42 0.00 46.64 4.06
284 285 2.981302 TGGCGTCCACCTGATGAG 59.019 61.111 0.00 0.00 31.07 2.90
302 303 1.752694 CACCTTGCCGGGTTATGGG 60.753 63.158 2.18 0.00 37.52 4.00
325 326 3.434167 GCTTGATCTTCCAAGGGAGCATA 60.434 47.826 0.00 0.00 42.73 3.14
338 339 4.546829 ACATTTGGCATTGCTTGATCTT 57.453 36.364 8.82 0.00 0.00 2.40
391 392 4.437682 ACACATGAAAAAGGAGACCTCA 57.562 40.909 0.00 0.00 30.89 3.86
454 455 0.694771 AGCTGACAGGGCAAAGATGA 59.305 50.000 4.26 0.00 0.00 2.92
488 489 3.309954 GGCGAAAGGATATTCTGTGTGAC 59.690 47.826 0.00 0.00 0.00 3.67
516 517 0.249955 CGGCCAAATTTGCATTCCCT 59.750 50.000 12.92 0.00 0.00 4.20
520 521 4.130118 TGTTAAACGGCCAAATTTGCATT 58.870 34.783 12.92 5.30 0.00 3.56
524 525 4.310769 TGGATGTTAAACGGCCAAATTTG 58.689 39.130 11.40 11.40 0.00 2.32
533 534 3.426963 CGGATTGGTTGGATGTTAAACGG 60.427 47.826 0.00 0.00 0.00 4.44
576 577 0.609957 CTGAACTGCTCCCATGCCAA 60.610 55.000 0.00 0.00 0.00 4.52
586 587 1.986413 CAGGCCCTACTGAACTGCT 59.014 57.895 0.00 0.00 40.97 4.24
596 597 3.053395 AGAAAAATCTGATGCAGGCCCTA 60.053 43.478 0.00 0.00 31.51 3.53
602 603 5.638783 GGTGAGAAGAAAAATCTGATGCAG 58.361 41.667 0.00 0.00 0.00 4.41
613 614 3.637229 ACTCTGTCTCGGTGAGAAGAAAA 59.363 43.478 0.00 0.00 40.59 2.29
616 617 2.570415 ACTCTGTCTCGGTGAGAAGA 57.430 50.000 0.00 3.96 40.59 2.87
634 635 2.992543 TCAACAAACAGCAAGTGCAAAC 59.007 40.909 6.00 0.00 45.16 2.93
656 664 7.821652 AGAGTACATTGAGGTATCGACATATG 58.178 38.462 0.00 0.00 0.00 1.78
735 743 3.748568 CACCTCTGGAAGCTTAAAGTGTC 59.251 47.826 0.00 0.00 0.00 3.67
737 745 3.999663 CTCACCTCTGGAAGCTTAAAGTG 59.000 47.826 0.00 2.16 0.00 3.16
755 763 4.449068 CACCAAAGAGTACATGTGTCTCAC 59.551 45.833 24.40 10.54 34.56 3.51
762 770 6.959639 AAACAATCACCAAAGAGTACATGT 57.040 33.333 2.69 2.69 0.00 3.21
763 771 9.912634 AATAAAACAATCACCAAAGAGTACATG 57.087 29.630 0.00 0.00 0.00 3.21
784 792 8.861101 CGGTTTTCGCCATGTTTTATAAATAAA 58.139 29.630 0.00 0.00 0.00 1.40
785 793 8.027771 ACGGTTTTCGCCATGTTTTATAAATAA 58.972 29.630 0.00 0.00 43.89 1.40
786 794 7.536855 ACGGTTTTCGCCATGTTTTATAAATA 58.463 30.769 0.00 0.00 43.89 1.40
787 795 6.391537 ACGGTTTTCGCCATGTTTTATAAAT 58.608 32.000 0.00 0.00 43.89 1.40
788 796 5.770417 ACGGTTTTCGCCATGTTTTATAAA 58.230 33.333 0.00 0.00 43.89 1.40
789 797 5.373981 ACGGTTTTCGCCATGTTTTATAA 57.626 34.783 0.00 0.00 43.89 0.98
790 798 5.373981 AACGGTTTTCGCCATGTTTTATA 57.626 34.783 0.00 0.00 43.89 0.98
791 799 3.926821 ACGGTTTTCGCCATGTTTTAT 57.073 38.095 0.00 0.00 43.89 1.40
792 800 3.712091 AACGGTTTTCGCCATGTTTTA 57.288 38.095 0.00 0.00 43.89 1.52
793 801 2.588027 AACGGTTTTCGCCATGTTTT 57.412 40.000 0.00 0.00 43.89 2.43
794 802 2.588027 AAACGGTTTTCGCCATGTTT 57.412 40.000 0.00 0.00 43.89 2.83
795 803 2.588027 AAAACGGTTTTCGCCATGTT 57.412 40.000 12.86 0.00 43.89 2.71
796 804 2.602694 CGTAAAACGGTTTTCGCCATGT 60.603 45.455 21.09 0.00 43.89 3.21
797 805 1.973320 CGTAAAACGGTTTTCGCCATG 59.027 47.619 21.09 6.86 43.89 3.66
798 806 2.319241 CGTAAAACGGTTTTCGCCAT 57.681 45.000 21.09 0.48 43.89 4.40
799 807 3.821881 CGTAAAACGGTTTTCGCCA 57.178 47.368 21.09 2.44 43.89 5.69
810 818 9.591792 AGAGGGAGTAACATTTATACGTAAAAC 57.408 33.333 0.00 0.00 33.76 2.43
811 819 9.590451 CAGAGGGAGTAACATTTATACGTAAAA 57.410 33.333 0.00 2.51 33.76 1.52
812 820 8.752187 ACAGAGGGAGTAACATTTATACGTAAA 58.248 33.333 0.00 0.00 34.50 2.01
813 821 8.192774 CACAGAGGGAGTAACATTTATACGTAA 58.807 37.037 0.00 0.00 0.00 3.18
814 822 7.557358 TCACAGAGGGAGTAACATTTATACGTA 59.443 37.037 0.00 0.00 0.00 3.57
815 823 6.379133 TCACAGAGGGAGTAACATTTATACGT 59.621 38.462 0.00 0.00 0.00 3.57
816 824 6.802608 TCACAGAGGGAGTAACATTTATACG 58.197 40.000 0.00 0.00 0.00 3.06
817 825 9.444600 TTTTCACAGAGGGAGTAACATTTATAC 57.555 33.333 0.00 0.00 0.00 1.47
819 827 8.934023 TTTTTCACAGAGGGAGTAACATTTAT 57.066 30.769 0.00 0.00 0.00 1.40
820 828 8.934023 ATTTTTCACAGAGGGAGTAACATTTA 57.066 30.769 0.00 0.00 0.00 1.40
821 829 7.839680 ATTTTTCACAGAGGGAGTAACATTT 57.160 32.000 0.00 0.00 0.00 2.32
846 854 9.509956 AGCGTTTAGATCACTACTCTCTTATAT 57.490 33.333 0.00 0.00 0.00 0.86
847 855 8.905660 AGCGTTTAGATCACTACTCTCTTATA 57.094 34.615 0.00 0.00 0.00 0.98
848 856 7.811117 AGCGTTTAGATCACTACTCTCTTAT 57.189 36.000 0.00 0.00 0.00 1.73
849 857 7.627298 AAGCGTTTAGATCACTACTCTCTTA 57.373 36.000 0.00 0.00 0.00 2.10
850 858 6.518208 AAGCGTTTAGATCACTACTCTCTT 57.482 37.500 0.00 0.00 0.00 2.85
851 859 6.518208 AAAGCGTTTAGATCACTACTCTCT 57.482 37.500 0.00 0.00 0.00 3.10
852 860 8.859517 ATAAAAGCGTTTAGATCACTACTCTC 57.140 34.615 10.55 0.00 32.76 3.20
866 874 8.126700 CCTCCGTAATGAAATATAAAAGCGTTT 58.873 33.333 2.53 2.53 0.00 3.60
867 875 7.255001 CCCTCCGTAATGAAATATAAAAGCGTT 60.255 37.037 0.00 0.00 0.00 4.84
868 876 6.204108 CCCTCCGTAATGAAATATAAAAGCGT 59.796 38.462 0.00 0.00 0.00 5.07
869 877 6.425721 TCCCTCCGTAATGAAATATAAAAGCG 59.574 38.462 0.00 0.00 0.00 4.68
870 878 7.444487 ACTCCCTCCGTAATGAAATATAAAAGC 59.556 37.037 0.00 0.00 0.00 3.51
871 879 8.904099 ACTCCCTCCGTAATGAAATATAAAAG 57.096 34.615 0.00 0.00 0.00 2.27
872 880 9.991906 CTACTCCCTCCGTAATGAAATATAAAA 57.008 33.333 0.00 0.00 0.00 1.52
873 881 9.151177 ACTACTCCCTCCGTAATGAAATATAAA 57.849 33.333 0.00 0.00 0.00 1.40
874 882 8.716674 ACTACTCCCTCCGTAATGAAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
875 883 9.986157 ATACTACTCCCTCCGTAATGAAATATA 57.014 33.333 0.00 0.00 0.00 0.86
876 884 8.896722 ATACTACTCCCTCCGTAATGAAATAT 57.103 34.615 0.00 0.00 0.00 1.28
877 885 8.716674 AATACTACTCCCTCCGTAATGAAATA 57.283 34.615 0.00 0.00 0.00 1.40
878 886 7.613551 AATACTACTCCCTCCGTAATGAAAT 57.386 36.000 0.00 0.00 0.00 2.17
879 887 7.427989 AAATACTACTCCCTCCGTAATGAAA 57.572 36.000 0.00 0.00 0.00 2.69
880 888 7.427989 AAAATACTACTCCCTCCGTAATGAA 57.572 36.000 0.00 0.00 0.00 2.57
881 889 7.343833 AGAAAAATACTACTCCCTCCGTAATGA 59.656 37.037 0.00 0.00 0.00 2.57
882 890 7.498443 AGAAAAATACTACTCCCTCCGTAATG 58.502 38.462 0.00 0.00 0.00 1.90
883 891 7.672122 AGAAAAATACTACTCCCTCCGTAAT 57.328 36.000 0.00 0.00 0.00 1.89
884 892 7.486407 AAGAAAAATACTACTCCCTCCGTAA 57.514 36.000 0.00 0.00 0.00 3.18
885 893 8.593945 TTAAGAAAAATACTACTCCCTCCGTA 57.406 34.615 0.00 0.00 0.00 4.02
886 894 7.486407 TTAAGAAAAATACTACTCCCTCCGT 57.514 36.000 0.00 0.00 0.00 4.69
887 895 8.039538 AGTTTAAGAAAAATACTACTCCCTCCG 58.960 37.037 0.00 0.00 0.00 4.63
888 896 9.736414 AAGTTTAAGAAAAATACTACTCCCTCC 57.264 33.333 0.00 0.00 0.00 4.30
890 898 9.516546 CCAAGTTTAAGAAAAATACTACTCCCT 57.483 33.333 0.00 0.00 0.00 4.20
891 899 8.737175 CCCAAGTTTAAGAAAAATACTACTCCC 58.263 37.037 0.00 0.00 0.00 4.30
892 900 9.293404 ACCCAAGTTTAAGAAAAATACTACTCC 57.707 33.333 0.00 0.00 0.00 3.85
912 920 9.240159 GCCGTTTTTATAACATTTATACCCAAG 57.760 33.333 0.00 0.00 0.00 3.61
913 921 8.746530 TGCCGTTTTTATAACATTTATACCCAA 58.253 29.630 0.00 0.00 0.00 4.12
914 922 8.189460 GTGCCGTTTTTATAACATTTATACCCA 58.811 33.333 0.00 0.00 0.00 4.51
915 923 8.189460 TGTGCCGTTTTTATAACATTTATACCC 58.811 33.333 0.00 0.00 0.00 3.69
916 924 9.012448 GTGTGCCGTTTTTATAACATTTATACC 57.988 33.333 0.00 0.00 0.00 2.73
917 925 9.777575 AGTGTGCCGTTTTTATAACATTTATAC 57.222 29.630 0.00 0.00 0.00 1.47
920 928 9.609950 GTTAGTGTGCCGTTTTTATAACATTTA 57.390 29.630 0.00 0.00 0.00 1.40
921 929 8.136165 TGTTAGTGTGCCGTTTTTATAACATTT 58.864 29.630 0.00 0.00 29.56 2.32
922 930 7.592164 GTGTTAGTGTGCCGTTTTTATAACATT 59.408 33.333 0.00 0.00 35.20 2.71
923 931 7.079475 GTGTTAGTGTGCCGTTTTTATAACAT 58.921 34.615 0.00 0.00 35.20 2.71
924 932 6.428799 GTGTTAGTGTGCCGTTTTTATAACA 58.571 36.000 0.00 0.00 31.46 2.41
925 933 5.561125 CGTGTTAGTGTGCCGTTTTTATAAC 59.439 40.000 0.00 0.00 0.00 1.89
926 934 5.236047 ACGTGTTAGTGTGCCGTTTTTATAA 59.764 36.000 0.00 0.00 0.00 0.98
927 935 4.749099 ACGTGTTAGTGTGCCGTTTTTATA 59.251 37.500 0.00 0.00 0.00 0.98
928 936 3.560896 ACGTGTTAGTGTGCCGTTTTTAT 59.439 39.130 0.00 0.00 0.00 1.40
929 937 2.935201 ACGTGTTAGTGTGCCGTTTTTA 59.065 40.909 0.00 0.00 0.00 1.52
930 938 1.738908 ACGTGTTAGTGTGCCGTTTTT 59.261 42.857 0.00 0.00 0.00 1.94
931 939 1.371595 ACGTGTTAGTGTGCCGTTTT 58.628 45.000 0.00 0.00 0.00 2.43
932 940 1.328374 GAACGTGTTAGTGTGCCGTTT 59.672 47.619 0.00 0.00 41.31 3.60
933 941 0.932399 GAACGTGTTAGTGTGCCGTT 59.068 50.000 0.00 0.00 43.61 4.44
934 942 0.179105 TGAACGTGTTAGTGTGCCGT 60.179 50.000 0.00 0.00 0.00 5.68
935 943 1.144969 ATGAACGTGTTAGTGTGCCG 58.855 50.000 0.00 0.00 0.00 5.69
936 944 2.289547 ACAATGAACGTGTTAGTGTGCC 59.710 45.455 0.00 0.00 0.00 5.01
937 945 3.602390 ACAATGAACGTGTTAGTGTGC 57.398 42.857 0.00 0.00 0.00 4.57
938 946 7.348956 TGATTTACAATGAACGTGTTAGTGTG 58.651 34.615 9.38 0.00 0.00 3.82
939 947 7.485418 TGATTTACAATGAACGTGTTAGTGT 57.515 32.000 0.00 0.00 0.00 3.55
940 948 9.472995 GTATGATTTACAATGAACGTGTTAGTG 57.527 33.333 0.00 0.00 0.00 2.74
941 949 9.431887 AGTATGATTTACAATGAACGTGTTAGT 57.568 29.630 0.00 0.00 0.00 2.24
944 952 8.377681 CGTAGTATGATTTACAATGAACGTGTT 58.622 33.333 0.00 0.00 0.00 3.32
945 953 7.756272 TCGTAGTATGATTTACAATGAACGTGT 59.244 33.333 0.00 0.00 32.13 4.49
946 954 8.110970 TCGTAGTATGATTTACAATGAACGTG 57.889 34.615 0.00 0.00 32.13 4.49
947 955 8.692110 TTCGTAGTATGATTTACAATGAACGT 57.308 30.769 0.00 0.00 32.13 3.99
948 956 8.804743 ACTTCGTAGTATGATTTACAATGAACG 58.195 33.333 0.00 0.00 31.21 3.95
959 967 9.790389 CTGTCTCTTTTACTTCGTAGTATGATT 57.210 33.333 2.52 0.00 36.76 2.57
960 968 9.175312 TCTGTCTCTTTTACTTCGTAGTATGAT 57.825 33.333 2.52 0.00 36.76 2.45
961 969 8.449397 GTCTGTCTCTTTTACTTCGTAGTATGA 58.551 37.037 2.52 2.31 36.76 2.15
962 970 7.425882 CGTCTGTCTCTTTTACTTCGTAGTATG 59.574 40.741 2.52 0.00 36.76 2.39
963 971 7.462731 CGTCTGTCTCTTTTACTTCGTAGTAT 58.537 38.462 2.52 0.00 36.76 2.12
964 972 6.619446 GCGTCTGTCTCTTTTACTTCGTAGTA 60.619 42.308 0.00 0.00 35.78 1.82
965 973 5.687828 CGTCTGTCTCTTTTACTTCGTAGT 58.312 41.667 0.00 0.00 38.44 2.73
966 974 4.554200 GCGTCTGTCTCTTTTACTTCGTAG 59.446 45.833 0.00 0.00 0.00 3.51
967 975 4.470462 GCGTCTGTCTCTTTTACTTCGTA 58.530 43.478 0.00 0.00 0.00 3.43
968 976 3.306818 GCGTCTGTCTCTTTTACTTCGT 58.693 45.455 0.00 0.00 0.00 3.85
969 977 2.662156 GGCGTCTGTCTCTTTTACTTCG 59.338 50.000 0.00 0.00 0.00 3.79
970 978 2.662156 CGGCGTCTGTCTCTTTTACTTC 59.338 50.000 0.00 0.00 0.00 3.01
971 979 2.673833 CGGCGTCTGTCTCTTTTACTT 58.326 47.619 0.00 0.00 0.00 2.24
972 980 1.669211 GCGGCGTCTGTCTCTTTTACT 60.669 52.381 9.37 0.00 0.00 2.24
973 981 0.714439 GCGGCGTCTGTCTCTTTTAC 59.286 55.000 9.37 0.00 0.00 2.01
974 982 0.601558 AGCGGCGTCTGTCTCTTTTA 59.398 50.000 9.37 0.00 0.00 1.52
975 983 0.667792 GAGCGGCGTCTGTCTCTTTT 60.668 55.000 9.37 0.00 0.00 2.27
976 984 1.080434 GAGCGGCGTCTGTCTCTTT 60.080 57.895 9.37 0.00 0.00 2.52
977 985 2.569134 GAGCGGCGTCTGTCTCTT 59.431 61.111 9.37 0.00 0.00 2.85
978 986 3.444805 GGAGCGGCGTCTGTCTCT 61.445 66.667 9.37 0.00 0.00 3.10
979 987 4.838486 CGGAGCGGCGTCTGTCTC 62.838 72.222 9.37 5.80 0.00 3.36
983 991 3.989698 ATTGACGGAGCGGCGTCTG 62.990 63.158 9.37 12.34 37.93 3.51
1010 1018 1.603739 GTCAAGTGGAAGGTGGGGC 60.604 63.158 0.00 0.00 0.00 5.80
1182 1199 2.401766 GGTGCGGTGCTCATGGAAG 61.402 63.158 0.00 0.00 0.00 3.46
1220 1237 3.307108 CCCCTAGCCGCTCTAGCC 61.307 72.222 0.00 0.00 42.73 3.93
1224 1241 1.761271 GGTAACCCCTAGCCGCTCT 60.761 63.158 0.00 0.00 0.00 4.09
1405 1422 1.379146 GGGGAAGGACACCTTGGAC 59.621 63.158 7.81 0.00 44.82 4.02
1406 1423 3.916184 GGGGAAGGACACCTTGGA 58.084 61.111 7.81 0.00 44.82 3.53
1428 1445 1.538419 GCCAGATTACCGGAGTAGCAC 60.538 57.143 9.46 0.00 0.00 4.40
1484 1519 0.602905 CCGAGACACCAGTTCCCAAC 60.603 60.000 0.00 0.00 0.00 3.77
1485 1520 1.752198 CCGAGACACCAGTTCCCAA 59.248 57.895 0.00 0.00 0.00 4.12
1486 1521 2.214216 CCCGAGACACCAGTTCCCA 61.214 63.158 0.00 0.00 0.00 4.37
1487 1522 2.663196 CCCGAGACACCAGTTCCC 59.337 66.667 0.00 0.00 0.00 3.97
1488 1523 1.889530 CTCCCCGAGACACCAGTTCC 61.890 65.000 0.00 0.00 0.00 3.62
1489 1524 1.186267 ACTCCCCGAGACACCAGTTC 61.186 60.000 0.00 0.00 33.32 3.01
1490 1525 0.113776 TACTCCCCGAGACACCAGTT 59.886 55.000 0.00 0.00 33.32 3.16
1491 1526 0.335361 ATACTCCCCGAGACACCAGT 59.665 55.000 0.00 0.00 33.32 4.00
1520 1555 3.767673 TCAGTAGTACCGCTCCAGAAATT 59.232 43.478 0.00 0.00 0.00 1.82
1522 1557 2.799017 TCAGTAGTACCGCTCCAGAAA 58.201 47.619 0.00 0.00 0.00 2.52
1583 1618 3.744426 ACGAGCAAACTAATAACAAGCGT 59.256 39.130 0.00 0.00 0.00 5.07
1590 1625 8.887036 ATGTGATCATACGAGCAAACTAATAA 57.113 30.769 0.00 0.00 39.75 1.40
1595 1630 5.292834 CAGAATGTGATCATACGAGCAAACT 59.707 40.000 0.00 0.00 39.75 2.66
1841 2146 8.504005 CAACTGAAGTACTAAATTCCGTGAAAT 58.496 33.333 0.00 0.00 0.00 2.17
1874 2185 0.103390 TTTTGTCTGACGACCTCGCA 59.897 50.000 2.98 0.00 44.43 5.10
1904 2217 3.689872 AACTGGAGAGCCTACATAGGA 57.310 47.619 9.25 0.00 46.63 2.94
1908 2221 5.700402 ACATAAAACTGGAGAGCCTACAT 57.300 39.130 0.00 0.00 34.31 2.29
1973 2300 5.279960 GGAAAAGCATTGGGGTTGTATTCTT 60.280 40.000 0.00 0.00 37.28 2.52
2102 2749 1.140804 GCCAACACCAACACACACC 59.859 57.895 0.00 0.00 0.00 4.16
2147 2796 0.183492 ACACAATGAGCACACACCCT 59.817 50.000 0.00 0.00 0.00 4.34
2181 2830 8.734386 GTGGATTCTATTCACTCAAAATGAAGT 58.266 33.333 0.00 0.00 39.36 3.01
2226 2876 1.957177 TCATCCTACTTAGCTGAGCGG 59.043 52.381 5.23 6.75 0.00 5.52
2228 2878 2.695666 TGGTCATCCTACTTAGCTGAGC 59.304 50.000 5.23 0.00 34.93 4.26
2273 2925 7.745620 ACTTCTGACAATTTCCGATTTAGTT 57.254 32.000 0.00 0.00 0.00 2.24
2377 3200 1.475280 TCACCGTTCCCTTCGTCATAG 59.525 52.381 0.00 0.00 0.00 2.23
2441 3264 7.712639 TCAAGAACACCTTCTTCTATCATATGC 59.287 37.037 0.00 0.00 43.70 3.14
2451 3274 4.137543 ACACCATCAAGAACACCTTCTTC 58.862 43.478 0.00 0.00 43.70 2.87
2822 3680 2.161855 TGGCATGATCCACTGTGTTTC 58.838 47.619 7.08 3.89 0.00 2.78
2993 3851 6.363357 GCATTTGTTTCCTTCAACTGATACAC 59.637 38.462 0.00 0.00 30.59 2.90
3030 3888 0.167908 CCGCGCTTGCATTTTACTCA 59.832 50.000 5.56 0.00 39.07 3.41
3072 3930 5.947663 TGAAAGAATTAGGACCCAAGTGAA 58.052 37.500 0.00 0.00 0.00 3.18
3199 4057 1.153168 CGTGGGCCCTCGAATTGAT 60.153 57.895 37.00 0.00 35.30 2.57
3337 6535 7.044181 CCATTGTGACTGCTCTTAAGAAGATA 58.956 38.462 6.63 0.00 36.82 1.98
3905 7225 3.708451 TGAGTGATAGGCAGAAGGTACA 58.292 45.455 0.00 0.00 0.00 2.90
4156 7519 5.419788 ACTGTTACATGTCATTGGATGCATT 59.580 36.000 0.00 0.00 0.00 3.56
4240 7787 1.068127 CAAAATATCTGGCTGGCAGGC 59.932 52.381 31.94 31.94 41.77 4.85
4378 7925 0.960861 GGTTAGGGCAGGCTGTGTTC 60.961 60.000 17.16 0.00 0.00 3.18
4666 8222 3.788227 ACAAATTGGAGCAGGACAGTA 57.212 42.857 0.00 0.00 0.00 2.74
4812 10113 5.449041 GCAATGAAAAAGACAGTGACAGTGA 60.449 40.000 17.24 0.00 35.76 3.41
4813 10114 4.736793 GCAATGAAAAAGACAGTGACAGTG 59.263 41.667 8.80 8.80 35.76 3.66
4814 10115 4.398988 TGCAATGAAAAAGACAGTGACAGT 59.601 37.500 0.00 0.00 35.76 3.55
4815 10116 4.923893 TGCAATGAAAAAGACAGTGACAG 58.076 39.130 0.00 0.00 35.76 3.51
4816 10117 4.979943 TGCAATGAAAAAGACAGTGACA 57.020 36.364 0.00 0.00 35.76 3.58
4817 10118 6.833342 ATTTGCAATGAAAAAGACAGTGAC 57.167 33.333 0.00 0.00 35.76 3.67
4818 10119 7.765360 AGAAATTTGCAATGAAAAAGACAGTGA 59.235 29.630 0.00 0.00 35.76 3.41
4819 10120 7.912383 AGAAATTTGCAATGAAAAAGACAGTG 58.088 30.769 0.00 0.00 36.60 3.66
4820 10121 8.496707 AAGAAATTTGCAATGAAAAAGACAGT 57.503 26.923 0.00 0.00 0.00 3.55
5003 10305 0.337082 TGGGACGGAGGGAATACTGA 59.663 55.000 0.00 0.00 0.00 3.41
5019 10321 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
5021 10323 9.424319 TCTACTAAGCTTGAGACACTTATTTTG 57.576 33.333 9.86 0.00 0.00 2.44
5022 10324 9.998106 TTCTACTAAGCTTGAGACACTTATTTT 57.002 29.630 9.86 0.00 0.00 1.82
5024 10326 8.808092 AGTTCTACTAAGCTTGAGACACTTATT 58.192 33.333 9.86 0.00 0.00 1.40
5077 10433 2.161609 CCTGCGTCCCAAAATAAGTGTC 59.838 50.000 0.00 0.00 0.00 3.67
5080 10436 1.353022 TCCCTGCGTCCCAAAATAAGT 59.647 47.619 0.00 0.00 0.00 2.24
5093 10449 3.132289 TCCTCAGTTTAATACTCCCTGCG 59.868 47.826 0.00 0.00 33.85 5.18
5095 10451 5.659079 AGTCTCCTCAGTTTAATACTCCCTG 59.341 44.000 0.00 0.00 33.85 4.45
5097 10453 6.547930 AAGTCTCCTCAGTTTAATACTCCC 57.452 41.667 0.00 0.00 33.85 4.30
5631 10996 1.583556 AGGATGGCACCACATCTACA 58.416 50.000 8.48 0.00 45.11 2.74
5642 11007 2.900273 GGCGACACTAGGATGGCA 59.100 61.111 0.00 0.00 0.00 4.92
5685 11056 0.907230 GCTCCAGTGAGAAGAGGGGT 60.907 60.000 0.00 0.00 41.42 4.95
5749 11121 2.124996 CTTCCCCACCCCTCTCCA 59.875 66.667 0.00 0.00 0.00 3.86
5826 18030 0.531974 GCTTTGACCAGTCCACGTCA 60.532 55.000 0.00 0.00 37.23 4.35
5946 18151 7.630242 ATTCTTTTCTGAAAGTGTCACTTGA 57.370 32.000 18.84 9.29 42.32 3.02
6151 18356 6.553953 TCAGGTGCCTACTCAATATGTTTA 57.446 37.500 0.00 0.00 0.00 2.01
6197 18402 3.181483 CCAAGCTGTTGATTTCCCATAGC 60.181 47.826 0.00 0.00 35.46 2.97
6301 18506 8.117813 TGAATGTATGCGGATATACTAACTGA 57.882 34.615 0.00 0.00 35.16 3.41
6302 18507 8.648097 GTTGAATGTATGCGGATATACTAACTG 58.352 37.037 0.00 0.00 35.16 3.16
6303 18508 8.585881 AGTTGAATGTATGCGGATATACTAACT 58.414 33.333 0.00 6.58 35.16 2.24
6304 18509 8.758633 AGTTGAATGTATGCGGATATACTAAC 57.241 34.615 0.00 4.55 35.16 2.34
6315 18520 5.357257 AGGTAGGTTAGTTGAATGTATGCG 58.643 41.667 0.00 0.00 0.00 4.73
6654 18968 3.504134 TCCTAGTGATATGAAGCGCTCTC 59.496 47.826 12.06 11.52 33.11 3.20
6656 18970 3.832276 CTCCTAGTGATATGAAGCGCTC 58.168 50.000 12.06 4.99 33.11 5.03
6733 19346 4.278058 GTCGTACCGATAGTAAAGCTGTC 58.722 47.826 0.00 0.00 38.42 3.51
6753 19440 3.521560 TCAGGATGATACAGTTTGCGTC 58.478 45.455 0.00 0.00 42.56 5.19
6787 19474 3.838903 CCCTTCTACTACCTGGAACAAGT 59.161 47.826 0.00 0.93 38.70 3.16
6941 19628 1.973812 GGGCTTCACCTTGTCTGGC 60.974 63.158 0.00 0.00 39.10 4.85
7016 19703 9.887629 TTTCTAATACCGATACCAAACATAACA 57.112 29.630 0.00 0.00 0.00 2.41
7046 19733 0.395312 AGTGGACCGAACCGACATTT 59.605 50.000 0.00 0.00 0.00 2.32
7049 19736 1.529948 AGAGTGGACCGAACCGACA 60.530 57.895 0.00 0.00 0.00 4.35
7312 20244 5.773176 TGATGAATATGCATTTGAGCCTGAT 59.227 36.000 3.54 0.00 0.00 2.90
7328 20546 6.095860 CCAACAAATCTGCCTTCTGATGAATA 59.904 38.462 0.00 0.00 32.23 1.75
7332 20550 3.760151 TCCAACAAATCTGCCTTCTGATG 59.240 43.478 0.00 0.00 32.23 3.07
7333 20551 4.015084 CTCCAACAAATCTGCCTTCTGAT 58.985 43.478 0.00 0.00 33.07 2.90
7363 20581 2.848858 GCATTAGCCCGCCATGTGG 61.849 63.158 0.00 0.00 34.43 4.17
7505 20725 7.534085 TTGTTTTTGTGTTTGTGTTTGTGTA 57.466 28.000 0.00 0.00 0.00 2.90
7506 20726 6.422776 TTGTTTTTGTGTTTGTGTTTGTGT 57.577 29.167 0.00 0.00 0.00 3.72
7507 20727 7.725610 TTTTGTTTTTGTGTTTGTGTTTGTG 57.274 28.000 0.00 0.00 0.00 3.33
7508 20728 7.807907 TGTTTTTGTTTTTGTGTTTGTGTTTGT 59.192 25.926 0.00 0.00 0.00 2.83
7509 20729 8.161754 TGTTTTTGTTTTTGTGTTTGTGTTTG 57.838 26.923 0.00 0.00 0.00 2.93
7511 20731 8.742554 TTTGTTTTTGTTTTTGTGTTTGTGTT 57.257 23.077 0.00 0.00 0.00 3.32
7512 20732 8.742554 TTTTGTTTTTGTTTTTGTGTTTGTGT 57.257 23.077 0.00 0.00 0.00 3.72
7513 20733 9.453087 GTTTTTGTTTTTGTTTTTGTGTTTGTG 57.547 25.926 0.00 0.00 0.00 3.33
7514 20734 9.191995 TGTTTTTGTTTTTGTTTTTGTGTTTGT 57.808 22.222 0.00 0.00 0.00 2.83
7525 20745 9.900710 GGTTCCTATTTTGTTTTTGTTTTTGTT 57.099 25.926 0.00 0.00 0.00 2.83
7531 20751 5.292345 GTGCGGTTCCTATTTTGTTTTTGTT 59.708 36.000 0.00 0.00 0.00 2.83
7569 20789 2.401990 GCCATTTACCGTTCGCCG 59.598 61.111 0.00 0.00 0.00 6.46
7573 20793 4.181309 TGATTTTGGCCATTTACCGTTC 57.819 40.909 6.09 0.00 0.00 3.95
7627 20847 1.262683 GCGAGAATCTACAATGCTGGC 59.737 52.381 0.00 0.00 0.00 4.85
7694 20914 2.175811 GAACGTGCCGATGCCAAC 59.824 61.111 0.00 0.00 36.33 3.77
7695 20915 2.281139 TGAACGTGCCGATGCCAA 60.281 55.556 0.00 0.00 36.33 4.52
7753 20973 4.507869 CCTGCAATTCCATCCATCTCCATA 60.508 45.833 0.00 0.00 0.00 2.74
7921 21189 1.667151 CGTTCCCCAGTTCACGGTA 59.333 57.895 0.00 0.00 0.00 4.02
8139 21407 1.064946 CTCGCTCTCCTTAGTGGCG 59.935 63.158 0.00 0.00 42.56 5.69
8143 21411 1.758906 GGCCCTCGCTCTCCTTAGT 60.759 63.158 0.00 0.00 34.44 2.24


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

AutoCloner maintained by Alex Coulton.