Multiple sequence alignment - TraesCS4B01G004700

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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 TraesCS4B01G004700 chr4B 100.000 8328 0 0 1 8328 3329187 3320860 0.000000e+00 15380.0
1 TraesCS4B01G004700 chr7A 96.832 2809 83 4 4922 7727 28824510 28821705 0.000000e+00 4689.0
2 TraesCS4B01G004700 chr7A 96.262 2809 80 7 4922 7727 28988111 28985325 0.000000e+00 4582.0
3 TraesCS4B01G004700 chr7A 96.120 2809 89 6 4922 7727 28865639 28862848 0.000000e+00 4566.0
4 TraesCS4B01G004700 chr7A 96.048 2809 92 5 4922 7727 28935616 28932824 0.000000e+00 4554.0
5 TraesCS4B01G004700 chr7A 96.787 2708 85 2 1 2707 28874792 28872086 0.000000e+00 4518.0
6 TraesCS4B01G004700 chr7A 96.718 2712 83 5 1 2707 28944773 28942063 0.000000e+00 4510.0
7 TraesCS4B01G004700 chr7A 96.455 2708 95 1 1 2707 28833631 28830924 0.000000e+00 4468.0
8 TraesCS4B01G004700 chr7A 96.676 1775 51 4 5956 7727 28893565 28891796 0.000000e+00 2944.0
9 TraesCS4B01G004700 chr7A 93.681 1171 72 2 2687 3856 28872067 28870898 0.000000e+00 1751.0
10 TraesCS4B01G004700 chr7A 93.612 1174 73 2 2684 3856 28900974 28899802 0.000000e+00 1751.0
11 TraesCS4B01G004700 chr7A 93.526 1174 74 2 2684 3856 28942047 28940875 0.000000e+00 1746.0
12 TraesCS4B01G004700 chr7A 93.441 1174 75 2 2684 3856 28830908 28829736 0.000000e+00 1740.0
13 TraesCS4B01G004700 chr7A 92.845 1174 81 3 2684 3856 28994554 28993383 0.000000e+00 1700.0
14 TraesCS4B01G004700 chr7A 94.698 943 36 2 4922 5864 28894540 28893612 0.000000e+00 1452.0
15 TraesCS4B01G004700 chr7A 94.766 363 17 1 7869 8231 28821640 28821280 1.570000e-156 564.0
16 TraesCS4B01G004700 chr7A 94.215 363 19 1 7869 8231 28985260 28984900 3.400000e-153 553.0
17 TraesCS4B01G004700 chr7A 91.460 363 19 2 7869 8231 28891731 28891381 9.720000e-134 488.0
18 TraesCS4B01G004700 chr7A 93.255 341 7 4 3841 4167 28899779 28899441 9.720000e-134 488.0
19 TraesCS4B01G004700 chr7A 91.460 363 19 2 7869 8231 28932759 28932409 9.720000e-134 488.0
20 TraesCS4B01G004700 chr7A 92.962 341 8 4 3841 4167 28940852 28940514 4.520000e-132 483.0
21 TraesCS4B01G004700 chr7A 92.962 341 8 4 3841 4167 28993360 28993022 4.520000e-132 483.0
22 TraesCS4B01G004700 chr7A 93.134 335 8 3 3847 4167 28870870 28870537 2.100000e-130 477.0
23 TraesCS4B01G004700 chr7A 92.330 339 10 4 3841 4165 28829713 28829377 1.270000e-127 468.0
24 TraesCS4B01G004700 chr7A 94.366 142 8 0 4164 4305 28989239 28989098 1.410000e-52 219.0
25 TraesCS4B01G004700 chr7A 93.662 142 9 0 4164 4305 28825520 28825379 6.550000e-51 213.0
26 TraesCS4B01G004700 chr7A 98.291 117 1 1 4685 4801 28894971 28894856 3.940000e-48 204.0
27 TraesCS4B01G004700 chr7A 98.291 117 1 1 4685 4801 28936047 28935932 3.940000e-48 204.0
28 TraesCS4B01G004700 chr7A 98.291 117 1 1 4685 4801 28988543 28988428 3.940000e-48 204.0
29 TraesCS4B01G004700 chr7A 97.436 117 2 1 4685 4801 28866070 28865955 1.830000e-46 198.0
30 TraesCS4B01G004700 chr7A 98.795 83 1 0 8246 8328 28862258 28862176 1.870000e-31 148.0
31 TraesCS4B01G004700 chr7A 98.795 83 1 0 8246 8328 28891206 28891124 1.870000e-31 148.0
32 TraesCS4B01G004700 chr7A 98.795 83 1 0 8246 8328 28932234 28932152 1.870000e-31 148.0
33 TraesCS4B01G004700 chr7A 97.590 83 2 0 8246 8328 28821105 28821023 8.710000e-30 143.0
34 TraesCS4B01G004700 chr7A 97.590 83 2 0 8246 8328 28984725 28984643 8.710000e-30 143.0
35 TraesCS4B01G004700 chr7A 92.135 89 4 2 4805 4893 28894731 28894646 1.140000e-23 122.0
36 TraesCS4B01G004700 chr7A 100.000 31 0 0 4892 4922 263171947 263171917 3.250000e-04 58.4
37 TraesCS4B01G004700 chrUn 96.894 2801 81 4 4925 7722 330029303 330032100 0.000000e+00 4686.0
38 TraesCS4B01G004700 chrUn 96.823 2801 83 4 4925 7722 330026405 330029202 0.000000e+00 4674.0
39 TraesCS4B01G004700 chrUn 96.573 2714 86 5 1 2707 290158902 290156189 0.000000e+00 4490.0
40 TraesCS4B01G004700 chrUn 96.669 1531 44 5 6200 7727 241301508 241299982 0.000000e+00 2538.0
41 TraesCS4B01G004700 chrUn 96.669 1531 44 5 6200 7727 317311742 317310216 0.000000e+00 2538.0
42 TraesCS4B01G004700 chrUn 96.757 1141 36 1 5058 6198 434496562 434495423 0.000000e+00 1901.0
43 TraesCS4B01G004700 chrUn 93.526 1174 72 4 2684 3856 290150381 290149211 0.000000e+00 1744.0
44 TraesCS4B01G004700 chrUn 93.526 1174 72 4 2684 3856 290156173 290155003 0.000000e+00 1744.0
45 TraesCS4B01G004700 chrUn 93.526 1174 72 4 2684 3856 344779990 344781160 0.000000e+00 1744.0
46 TraesCS4B01G004700 chrUn 93.441 1174 75 2 2684 3856 375529606 375530778 0.000000e+00 1740.0
47 TraesCS4B01G004700 chrUn 97.062 885 26 0 4925 5809 461961560 461962444 0.000000e+00 1491.0
48 TraesCS4B01G004700 chrUn 91.874 443 32 2 4252 4690 38159019 38159461 4.270000e-172 616.0
49 TraesCS4B01G004700 chrUn 94.490 363 18 1 7869 8231 241299917 241299557 7.300000e-155 558.0
50 TraesCS4B01G004700 chrUn 94.490 363 18 1 7869 8231 317310151 317309791 7.300000e-155 558.0
51 TraesCS4B01G004700 chrUn 93.169 366 23 1 7866 8231 235338233 235338596 3.420000e-148 536.0
52 TraesCS4B01G004700 chrUn 93.388 363 21 2 7869 8231 333415682 333415323 1.230000e-147 534.0
53 TraesCS4B01G004700 chrUn 92.375 341 10 4 3841 4167 290149188 290148850 9.780000e-129 472.0
54 TraesCS4B01G004700 chrUn 92.375 341 10 9 3841 4167 290154980 290154642 9.780000e-129 472.0
55 TraesCS4B01G004700 chrUn 92.375 341 10 9 3841 4167 344781183 344781521 9.780000e-129 472.0
56 TraesCS4B01G004700 chrUn 91.765 340 11 6 3841 4167 316054497 316054832 2.740000e-124 457.0
57 TraesCS4B01G004700 chrUn 91.471 340 12 6 3841 4167 314357561 314357896 1.270000e-122 451.0
58 TraesCS4B01G004700 chrUn 98.291 117 1 1 4685 4801 469655638 469655523 3.940000e-48 204.0
59 TraesCS4B01G004700 chrUn 97.436 117 2 1 4685 4801 324331957 324332072 1.830000e-46 198.0
60 TraesCS4B01G004700 chrUn 97.436 117 2 1 4685 4801 324335111 324335226 1.830000e-46 198.0
61 TraesCS4B01G004700 chrUn 97.436 117 2 1 4685 4801 340810744 340810629 1.830000e-46 198.0
62 TraesCS4B01G004700 chrUn 98.795 83 1 0 8246 8328 241299382 241299300 1.870000e-31 148.0
63 TraesCS4B01G004700 chrUn 97.590 83 2 0 8246 8328 317309616 317309534 8.710000e-30 143.0
64 TraesCS4B01G004700 chr5A 96.831 2714 74 3 1 2707 13085422 13082714 0.000000e+00 4525.0
65 TraesCS4B01G004700 chr5A 100.000 41 0 0 4853 4893 321019547 321019507 8.960000e-10 76.8
66 TraesCS4B01G004700 chr5A 100.000 41 0 0 4853 4893 692389908 692389868 8.960000e-10 76.8
67 TraesCS4B01G004700 chr2B 96.347 2710 94 5 1 2707 788181421 788184128 0.000000e+00 4451.0
68 TraesCS4B01G004700 chr2B 96.317 2715 87 5 1 2707 788176559 788179268 0.000000e+00 4447.0
69 TraesCS4B01G004700 chr2B 94.309 861 37 2 3841 4690 788185331 788186190 0.000000e+00 1308.0
70 TraesCS4B01G004700 chr2B 83.229 799 119 11 5789 6575 392029991 392030786 0.000000e+00 719.0
71 TraesCS4B01G004700 chr2B 94.142 478 14 2 4919 5396 788186835 788187298 0.000000e+00 715.0
72 TraesCS4B01G004700 chr2B 92.627 434 29 1 4260 4690 655821647 655821214 9.180000e-174 621.0
73 TraesCS4B01G004700 chr2B 91.874 443 32 2 4252 4690 663911951 663912393 4.270000e-172 616.0
74 TraesCS4B01G004700 chr2B 91.781 219 18 0 4035 4253 392028119 392028337 1.050000e-78 305.0
75 TraesCS4B01G004700 chr2B 93.605 172 8 2 7716 7884 540428425 540428254 3.860000e-63 254.0
76 TraesCS4B01G004700 chr2B 96.000 150 5 1 3841 3990 788180472 788180620 8.350000e-60 243.0
77 TraesCS4B01G004700 chr2B 96.581 117 4 0 4685 4801 788186403 788186519 2.370000e-45 195.0
78 TraesCS4B01G004700 chr2B 90.625 96 7 1 4800 4893 788186637 788186732 8.780000e-25 126.0
79 TraesCS4B01G004700 chr2B 93.103 87 2 1 8246 8328 788199831 788199917 3.160000e-24 124.0
80 TraesCS4B01G004700 chr1D 93.547 2464 149 5 1 2462 415600192 415602647 0.000000e+00 3661.0
81 TraesCS4B01G004700 chr1D 84.959 605 85 3 5788 6387 415605119 415605722 7.150000e-170 608.0
82 TraesCS4B01G004700 chr1D 93.529 170 9 1 7714 7881 59324841 59324672 1.390000e-62 252.0
83 TraesCS4B01G004700 chr1D 93.529 170 9 1 7714 7881 91416035 91415866 1.390000e-62 252.0
84 TraesCS4B01G004700 chr6D 93.274 2468 157 4 1 2467 450185706 450183247 0.000000e+00 3629.0
85 TraesCS4B01G004700 chr6D 92.099 443 31 2 4252 4690 149394282 149394724 9.180000e-174 621.0
86 TraesCS4B01G004700 chr6D 82.153 353 27 13 5314 5665 450180338 450180021 3.830000e-68 270.0
87 TraesCS4B01G004700 chr6D 100.000 31 0 0 4894 4924 56208479 56208449 3.250000e-04 58.4
88 TraesCS4B01G004700 chr6D 100.000 31 0 0 4892 4922 462080017 462080047 3.250000e-04 58.4
89 TraesCS4B01G004700 chr6D 100.000 29 0 0 4894 4922 158232864 158232892 4.000000e-03 54.7
90 TraesCS4B01G004700 chr3B 92.551 443 29 2 4252 4690 822389797 822390239 4.240000e-177 632.0
91 TraesCS4B01G004700 chr3B 92.325 443 30 2 4252 4690 822425705 822426147 1.970000e-175 627.0
92 TraesCS4B01G004700 chr3B 92.325 443 30 2 4252 4690 822505560 822506002 1.970000e-175 627.0
93 TraesCS4B01G004700 chr3D 91.874 443 32 2 4252 4690 177338806 177338364 4.270000e-172 616.0
94 TraesCS4B01G004700 chr5D 85.033 608 85 3 5788 6390 127930521 127929915 1.540000e-171 614.0
95 TraesCS4B01G004700 chr5D 84.758 433 30 13 5234 5665 127931195 127930798 1.300000e-107 401.0
96 TraesCS4B01G004700 chr5D 93.902 82 5 0 4172 4253 510558674 510558755 3.160000e-24 124.0
97 TraesCS4B01G004700 chr3A 95.082 366 18 0 7866 8231 574288062 574288427 2.020000e-160 577.0
98 TraesCS4B01G004700 chr3A 90.331 362 35 0 7876 8237 65458609 65458248 7.560000e-130 475.0
99 TraesCS4B01G004700 chr3A 97.590 83 2 0 8246 8328 574288602 574288684 8.710000e-30 143.0
100 TraesCS4B01G004700 chr3A 100.000 41 0 0 4853 4893 13273438 13273478 8.960000e-10 76.8
101 TraesCS4B01G004700 chr2D 86.788 439 56 2 5790 6227 622817353 622817790 9.720000e-134 488.0
102 TraesCS4B01G004700 chr2D 100.000 41 0 0 4853 4893 129159508 129159468 8.960000e-10 76.8
103 TraesCS4B01G004700 chr2D 100.000 29 0 0 4894 4922 93092930 93092958 4.000000e-03 54.7
104 TraesCS4B01G004700 chr2D 100.000 29 0 0 4894 4922 131679583 131679611 4.000000e-03 54.7
105 TraesCS4B01G004700 chr7D 84.527 433 31 13 5234 5665 340190801 340191198 6.060000e-106 396.0
106 TraesCS4B01G004700 chr7D 84.065 433 33 13 5234 5665 449486310 449485913 1.310000e-102 385.0
107 TraesCS4B01G004700 chr7D 90.763 249 23 0 4005 4253 449487038 449486790 4.820000e-87 333.0
108 TraesCS4B01G004700 chr7D 94.872 78 4 0 4176 4253 574096036 574095959 1.140000e-23 122.0
109 TraesCS4B01G004700 chr1A 93.103 174 10 1 7709 7880 491136160 491136333 3.860000e-63 254.0
110 TraesCS4B01G004700 chr1A 97.674 43 1 0 4851 4893 486943007 486943049 3.220000e-09 75.0
111 TraesCS4B01G004700 chr1A 100.000 33 0 0 4890 4922 533264086 533264054 2.510000e-05 62.1
112 TraesCS4B01G004700 chr1A 100.000 29 0 0 4894 4922 8266867 8266839 4.000000e-03 54.7
113 TraesCS4B01G004700 chr1A 100.000 29 0 0 4894 4922 566633854 566633882 4.000000e-03 54.7
114 TraesCS4B01G004700 chr4D 93.529 170 9 1 7714 7881 35997378 35997209 1.390000e-62 252.0
115 TraesCS4B01G004700 chr4D 93.529 170 9 1 7714 7881 94994898 94994729 1.390000e-62 252.0
116 TraesCS4B01G004700 chr4D 93.529 170 9 1 7714 7881 179764024 179763855 1.390000e-62 252.0
117 TraesCS4B01G004700 chr4D 93.529 170 9 1 7714 7881 458445328 458445159 1.390000e-62 252.0
118 TraesCS4B01G004700 chr4D 93.529 170 9 1 7714 7881 479717925 479717756 1.390000e-62 252.0
119 TraesCS4B01G004700 chr6B 97.727 44 1 0 4850 4893 603759193 603759236 8.960000e-10 76.8
120 TraesCS4B01G004700 chr4A 100.000 41 0 0 4853 4893 738865947 738865987 8.960000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G004700 chr4B 3320860 3329187 8327 True 15380.000000 15380 100.000000 1 8328 1 chr4B.!!$R1 8327
1 TraesCS4B01G004700 chr7A 28870537 28874792 4255 True 2248.666667 4518 94.534000 1 4167 3 chr7A.!!$R4 4166
2 TraesCS4B01G004700 chr7A 28940514 28944773 4259 True 2246.333333 4510 94.402000 1 4167 3 chr7A.!!$R8 4166
3 TraesCS4B01G004700 chr7A 28821023 28833631 12608 True 1755.000000 4689 95.010857 1 8328 7 chr7A.!!$R2 8327
4 TraesCS4B01G004700 chr7A 28862176 28866070 3894 True 1637.333333 4566 97.450333 4685 8328 3 chr7A.!!$R3 3643
5 TraesCS4B01G004700 chr7A 28932152 28936047 3895 True 1348.500000 4554 96.148500 4685 8328 4 chr7A.!!$R7 3643
6 TraesCS4B01G004700 chr7A 28984643 28994554 9911 True 1126.285714 4582 95.218714 2684 8328 7 chr7A.!!$R9 5644
7 TraesCS4B01G004700 chr7A 28899441 28900974 1533 True 1119.500000 1751 93.433500 2684 4167 2 chr7A.!!$R6 1483
8 TraesCS4B01G004700 chr7A 28891124 28894971 3847 True 893.000000 2944 95.342500 4685 8328 6 chr7A.!!$R5 3643
9 TraesCS4B01G004700 chrUn 330026405 330032100 5695 False 4680.000000 4686 96.858500 4925 7722 2 chrUn.!!$F8 2797
10 TraesCS4B01G004700 chrUn 290154642 290158902 4260 True 2235.333333 4490 94.158000 1 4167 3 chrUn.!!$R7 4166
11 TraesCS4B01G004700 chrUn 434495423 434496562 1139 True 1901.000000 1901 96.757000 5058 6198 1 chrUn.!!$R3 1140
12 TraesCS4B01G004700 chrUn 375529606 375530778 1172 False 1740.000000 1740 93.441000 2684 3856 1 chrUn.!!$F5 1172
13 TraesCS4B01G004700 chrUn 461961560 461962444 884 False 1491.000000 1491 97.062000 4925 5809 1 chrUn.!!$F6 884
14 TraesCS4B01G004700 chrUn 290148850 290150381 1531 True 1108.000000 1744 92.950500 2684 4167 2 chrUn.!!$R6 1483
15 TraesCS4B01G004700 chrUn 344779990 344781521 1531 False 1108.000000 1744 92.950500 2684 4167 2 chrUn.!!$F9 1483
16 TraesCS4B01G004700 chrUn 241299300 241301508 2208 True 1081.333333 2538 96.651333 6200 8328 3 chrUn.!!$R5 2128
17 TraesCS4B01G004700 chrUn 317309534 317311742 2208 True 1079.666667 2538 96.249667 6200 8328 3 chrUn.!!$R8 2128
18 TraesCS4B01G004700 chr5A 13082714 13085422 2708 True 4525.000000 4525 96.831000 1 2707 1 chr5A.!!$R1 2706
19 TraesCS4B01G004700 chr2B 788176559 788187298 10739 False 1640.714286 4451 94.903000 1 5396 7 chr2B.!!$F4 5395
20 TraesCS4B01G004700 chr2B 392028119 392030786 2667 False 512.000000 719 87.505000 4035 6575 2 chr2B.!!$F3 2540
21 TraesCS4B01G004700 chr1D 415600192 415605722 5530 False 2134.500000 3661 89.253000 1 6387 2 chr1D.!!$F1 6386
22 TraesCS4B01G004700 chr6D 450180021 450185706 5685 True 1949.500000 3629 87.713500 1 5665 2 chr6D.!!$R2 5664
23 TraesCS4B01G004700 chr5D 127929915 127931195 1280 True 507.500000 614 84.895500 5234 6390 2 chr5D.!!$R1 1156
24 TraesCS4B01G004700 chr3A 574288062 574288684 622 False 360.000000 577 96.336000 7866 8328 2 chr3A.!!$F2 462
25 TraesCS4B01G004700 chr7D 449485913 449487038 1125 True 359.000000 385 87.414000 4005 5665 2 chr7D.!!$R2 1660

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
407 412 1.362717 CGGGCCTTACGTCATCGAT 59.637 57.895 0.84 0.00 40.62 3.59 F
1790 6659 1.464189 GGAATTCTTGCGACGTCTTGC 60.464 52.381 14.70 11.21 0.00 4.01 F
2970 8247 0.253610 TTTGTGGTGAGGACGTTGGT 59.746 50.000 0.00 0.00 0.00 3.67 F
4323 18980 0.107643 TGTGTTCCATCTCCGTTGCA 59.892 50.000 0.00 0.00 0.00 4.08 F
6213 24834 0.172578 CGAGCGTGGTAAGATGGACA 59.827 55.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 7095 2.168326 TTGTGCACATGATCGACAGT 57.832 45.000 22.39 0.00 0.00 3.55 R
3052 8363 0.253160 ACCTCCTATCCAACTGGCCA 60.253 55.000 4.71 4.71 34.44 5.36 R
4915 20310 0.175760 TGGGCGTGAGACAAGCTATC 59.824 55.000 9.13 0.00 45.40 2.08 R
6228 24849 1.373497 GCTCCATATCCGCACGAGG 60.373 63.158 0.00 0.00 0.00 4.63 R
7859 26484 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12 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
127 128 6.151144 CGGACTCAATTTAGGGAAAATCAAGT 59.849 38.462 0.00 0.00 36.76 3.16
165 166 4.768968 AGCCAGGAAATATGCATACCATTC 59.231 41.667 8.99 13.18 35.34 2.67
407 412 1.362717 CGGGCCTTACGTCATCGAT 59.637 57.895 0.84 0.00 40.62 3.59
529 534 2.093764 AGTGCAGCCTCATAGTCTTCAC 60.094 50.000 0.00 0.00 0.00 3.18
602 607 2.365293 GGTCCAACTCCTTGTTTTGCAT 59.635 45.455 0.00 0.00 36.63 3.96
838 843 7.626084 TCACCTAGGGATCTTAATTCCTGTAAA 59.374 37.037 14.81 0.00 41.43 2.01
911 916 7.015877 TGTTGTAGTATCACTTACCTGGAGTTT 59.984 37.037 0.00 0.00 0.00 2.66
931 936 5.132144 AGTTTCCTTTTGAGGTCTCCAACTA 59.868 40.000 0.00 0.00 0.00 2.24
1154 1159 7.509141 TCTGCATAAAAGAAATGTCAACTCA 57.491 32.000 0.00 0.00 0.00 3.41
1667 6536 4.989168 ACTAGTGTTGTAGCACTTACTTGC 59.011 41.667 6.69 0.00 46.45 4.01
1790 6659 1.464189 GGAATTCTTGCGACGTCTTGC 60.464 52.381 14.70 11.21 0.00 4.01
1854 6723 4.204012 GGGTGCTAACATAGTGCCAATAA 58.796 43.478 0.00 0.00 0.00 1.40
1871 6740 5.692654 GCCAATAACATACAAAACAAACCGT 59.307 36.000 0.00 0.00 0.00 4.83
1979 6848 7.535489 AACGCTTAACAGGTTTACATCTATC 57.465 36.000 0.00 0.00 0.00 2.08
2216 7095 3.560453 CCTTTTGGTGGTCGGGATCTAAA 60.560 47.826 0.00 0.00 34.07 1.85
2232 7111 4.186856 TCTAAACTGTCGATCATGTGCA 57.813 40.909 0.00 0.00 0.00 4.57
2267 7146 4.686554 GGTGAGCACGATAACCTCATATTC 59.313 45.833 0.00 0.00 37.85 1.75
2289 7168 2.349817 GCATGTTTCACACTGAGTTCCG 60.350 50.000 0.00 0.00 0.00 4.30
2296 7175 1.002468 CACACTGAGTTCCGCCAAAAG 60.002 52.381 0.00 0.00 0.00 2.27
2566 7627 5.535030 AGTTTTGGATTAAGTTGACCTCACC 59.465 40.000 0.00 0.00 0.00 4.02
2747 7990 2.566570 TACGACAGTTGCTGGGCGA 61.567 57.895 16.21 0.00 37.05 5.54
2775 8018 7.877097 CCAATTTTGATTGTCCACCTAATTCAA 59.123 33.333 0.00 0.00 0.00 2.69
2835 8078 5.163804 GCACGTTCCAACATAATCATGTACA 60.164 40.000 0.00 0.00 44.83 2.90
2967 8244 1.399089 CGTTTTTGTGGTGAGGACGTT 59.601 47.619 0.00 0.00 0.00 3.99
2970 8247 0.253610 TTTGTGGTGAGGACGTTGGT 59.746 50.000 0.00 0.00 0.00 3.67
3006 8309 0.460284 TTTGGAGGAGAAGATCGCGC 60.460 55.000 0.00 0.00 0.00 6.86
3287 9006 4.390264 AGCACTGCTACTCACTATATCGA 58.610 43.478 0.21 0.00 36.99 3.59
3364 9083 0.694444 GCCTCCCTCCTTCCCATACA 60.694 60.000 0.00 0.00 0.00 2.29
3367 9086 1.139058 CTCCCTCCTTCCCATACAACG 59.861 57.143 0.00 0.00 0.00 4.10
3377 9096 0.391395 CCATACAACGTACGCCCCAA 60.391 55.000 16.72 0.00 0.00 4.12
3428 9147 0.179092 GGGTTCGTCCGGTTCCTATG 60.179 60.000 0.00 0.00 37.00 2.23
3546 9265 4.011517 GGCCGGACGACAGGGAAA 62.012 66.667 5.05 0.00 32.13 3.13
3607 9333 2.050144 GCCCCCTGATCTTGATCTGTA 58.950 52.381 11.31 0.00 0.00 2.74
3608 9334 2.641815 GCCCCCTGATCTTGATCTGTAT 59.358 50.000 11.31 0.00 0.00 2.29
3644 9842 1.144565 CTCTGGCGTCGCAATCTCTG 61.145 60.000 20.50 5.32 0.00 3.35
3785 9992 4.603535 GGGGTGGCCACTTGCAGT 62.604 66.667 33.91 0.00 43.89 4.40
3884 10128 1.871039 CTCAACCAAACACACCCTACG 59.129 52.381 0.00 0.00 0.00 3.51
4206 18863 1.893801 GCCATCCGCTACAGGTAGTAT 59.106 52.381 8.16 0.00 35.65 2.12
4235 18892 4.499357 CCATGGCTCTTTACGTCTAGTACC 60.499 50.000 0.00 0.00 34.56 3.34
4258 18915 1.315690 GGTCATCCGGATACTCGTCA 58.684 55.000 18.63 0.00 0.00 4.35
4274 18931 4.866486 ACTCGTCAACGTAAACTTTTCACT 59.134 37.500 2.09 0.00 40.80 3.41
4284 18941 4.900635 AAACTTTTCACTGCGATCTGTT 57.099 36.364 0.00 0.00 0.00 3.16
4302 18959 3.843240 CGAGCGCGAACCTTCAGC 61.843 66.667 12.10 0.00 40.82 4.26
4303 18960 2.433318 GAGCGCGAACCTTCAGCT 60.433 61.111 12.10 0.00 41.42 4.24
4304 18961 2.029844 GAGCGCGAACCTTCAGCTT 61.030 57.895 12.10 0.00 39.71 3.74
4305 18962 2.174349 GCGCGAACCTTCAGCTTG 59.826 61.111 12.10 0.00 0.00 4.01
4306 18963 2.607892 GCGCGAACCTTCAGCTTGT 61.608 57.895 12.10 0.00 0.00 3.16
4307 18964 1.205064 CGCGAACCTTCAGCTTGTG 59.795 57.895 0.00 0.00 0.00 3.33
4308 18965 1.498865 CGCGAACCTTCAGCTTGTGT 61.499 55.000 0.00 0.00 0.00 3.72
4309 18966 0.663153 GCGAACCTTCAGCTTGTGTT 59.337 50.000 0.00 0.00 0.00 3.32
4310 18967 1.334149 GCGAACCTTCAGCTTGTGTTC 60.334 52.381 0.00 0.00 33.66 3.18
4311 18968 1.264288 CGAACCTTCAGCTTGTGTTCC 59.736 52.381 8.69 0.00 33.48 3.62
4312 18969 2.297701 GAACCTTCAGCTTGTGTTCCA 58.702 47.619 0.00 0.00 31.41 3.53
4313 18970 2.664402 ACCTTCAGCTTGTGTTCCAT 57.336 45.000 0.00 0.00 0.00 3.41
4314 18971 2.508526 ACCTTCAGCTTGTGTTCCATC 58.491 47.619 0.00 0.00 0.00 3.51
4315 18972 2.107204 ACCTTCAGCTTGTGTTCCATCT 59.893 45.455 0.00 0.00 0.00 2.90
4316 18973 2.746362 CCTTCAGCTTGTGTTCCATCTC 59.254 50.000 0.00 0.00 0.00 2.75
4317 18974 2.479566 TCAGCTTGTGTTCCATCTCC 57.520 50.000 0.00 0.00 0.00 3.71
4318 18975 1.081892 CAGCTTGTGTTCCATCTCCG 58.918 55.000 0.00 0.00 0.00 4.63
4319 18976 0.687354 AGCTTGTGTTCCATCTCCGT 59.313 50.000 0.00 0.00 0.00 4.69
4320 18977 1.072331 AGCTTGTGTTCCATCTCCGTT 59.928 47.619 0.00 0.00 0.00 4.44
4321 18978 1.197721 GCTTGTGTTCCATCTCCGTTG 59.802 52.381 0.00 0.00 0.00 4.10
4322 18979 1.197721 CTTGTGTTCCATCTCCGTTGC 59.802 52.381 0.00 0.00 0.00 4.17
4323 18980 0.107643 TGTGTTCCATCTCCGTTGCA 59.892 50.000 0.00 0.00 0.00 4.08
4324 18981 0.798776 GTGTTCCATCTCCGTTGCAG 59.201 55.000 0.00 0.00 0.00 4.41
4325 18982 0.955428 TGTTCCATCTCCGTTGCAGC 60.955 55.000 0.00 0.00 0.00 5.25
4326 18983 1.377202 TTCCATCTCCGTTGCAGCC 60.377 57.895 0.00 0.00 0.00 4.85
4327 18984 1.841302 TTCCATCTCCGTTGCAGCCT 61.841 55.000 0.00 0.00 0.00 4.58
4328 18985 1.377725 CCATCTCCGTTGCAGCCTT 60.378 57.895 0.00 0.00 0.00 4.35
4329 18986 1.372087 CCATCTCCGTTGCAGCCTTC 61.372 60.000 0.00 0.00 0.00 3.46
4330 18987 0.674581 CATCTCCGTTGCAGCCTTCA 60.675 55.000 0.00 0.00 0.00 3.02
4331 18988 0.392193 ATCTCCGTTGCAGCCTTCAG 60.392 55.000 0.00 0.00 0.00 3.02
4372 19059 2.329379 CGCCATCTTTAGATCGTAGGC 58.671 52.381 8.16 8.16 36.86 3.93
4393 19080 3.741075 GCGAATGACCCACATGTATCTCA 60.741 47.826 0.00 0.00 39.39 3.27
4564 19504 3.167485 ACCAAGAACCCGTCACATACTA 58.833 45.455 0.00 0.00 0.00 1.82
4651 19591 5.333568 GCGTAGAAGTTAACGTGTCCAAATT 60.334 40.000 0.00 0.00 41.10 1.82
4813 20204 4.414852 CTTGCTGCCAAATACATACACAC 58.585 43.478 0.00 0.00 0.00 3.82
4815 20206 2.675844 GCTGCCAAATACATACACACGA 59.324 45.455 0.00 0.00 0.00 4.35
4817 20208 4.727734 GCTGCCAAATACATACACACGAAG 60.728 45.833 0.00 0.00 0.00 3.79
4851 20246 6.448207 AGGCTGCTTAATTGATTTCTTCTC 57.552 37.500 0.00 0.00 0.00 2.87
4907 20302 7.759489 TGATCAATATTATAGGTGGCCAAAC 57.241 36.000 7.24 3.12 0.00 2.93
4908 20303 6.429692 TGATCAATATTATAGGTGGCCAAACG 59.570 38.462 7.24 0.00 0.00 3.60
4910 20305 2.358322 ATTATAGGTGGCCAAACGGG 57.642 50.000 7.24 0.00 40.85 5.28
4919 20314 2.203153 CCAAACGGGCCGGGATAG 60.203 66.667 31.78 14.48 0.00 2.08
4928 20400 1.686325 GGCCGGGATAGCTTGTCTCA 61.686 60.000 2.18 0.00 0.00 3.27
4934 20406 0.175760 GATAGCTTGTCTCACGCCCA 59.824 55.000 0.00 0.00 28.47 5.36
4964 20436 0.403271 AGGAGCATGCTGGAAACTGT 59.597 50.000 28.27 0.00 32.93 3.55
4965 20437 0.524862 GGAGCATGCTGGAAACTGTG 59.475 55.000 28.27 0.00 0.00 3.66
5289 20780 6.153000 CCATATAGTACTTACGAGCCCAATCT 59.847 42.308 0.00 0.00 0.00 2.40
5403 20894 0.904865 TCGGGAGCAGTTCATCAGGT 60.905 55.000 0.00 0.00 0.00 4.00
5446 20937 2.750637 GCGACGTCCTCTCCTCCA 60.751 66.667 10.58 0.00 0.00 3.86
5520 21012 6.368779 ACCAAACTGTATGTACACCTATGT 57.631 37.500 0.00 0.00 43.30 2.29
5672 21164 6.881065 ACTACTTTCTCTAAATTGCATGCTCA 59.119 34.615 20.33 5.88 0.00 4.26
5675 21167 8.461249 ACTTTCTCTAAATTGCATGCTCATAT 57.539 30.769 20.33 4.39 0.00 1.78
5681 21173 8.315391 TCTAAATTGCATGCTCATATGTCTAC 57.685 34.615 20.33 0.00 0.00 2.59
5850 24471 3.491619 GGACAAGAATATGCAGCGAGAGA 60.492 47.826 0.00 0.00 0.00 3.10
5860 24481 0.732571 CAGCGAGAGAGAGAGGTGAC 59.267 60.000 0.00 0.00 34.41 3.67
5945 24566 0.612744 TGGAACAGATGATGACGGCA 59.387 50.000 0.00 0.00 0.00 5.69
5966 24587 2.512286 CGTGCAGCCGTGGATCAT 60.512 61.111 0.00 0.00 0.00 2.45
6079 24700 5.715279 AGATGGAATTCAATATCATGCAGGG 59.285 40.000 7.93 0.00 0.00 4.45
6136 24757 3.369471 CGTAAGGACATGGATCACAAGGT 60.369 47.826 0.00 0.00 0.00 3.50
6184 24805 1.230635 AATATGATGCAGGACCGCGC 61.231 55.000 0.00 0.00 33.35 6.86
6213 24834 0.172578 CGAGCGTGGTAAGATGGACA 59.827 55.000 0.00 0.00 0.00 4.02
6228 24849 6.140303 AGATGGACATCAATACAATGCAAC 57.860 37.500 14.16 0.00 40.22 4.17
6267 24888 3.843510 GCGAAAGTTACAACAAGACCGTG 60.844 47.826 0.00 0.00 0.00 4.94
6404 25029 2.381109 CGCAGGAGCAATCTGTCTG 58.619 57.895 0.00 0.00 42.27 3.51
6427 25052 0.987294 AGCACCTCTACAGGCACAAT 59.013 50.000 0.00 0.00 45.05 2.71
6563 25188 0.172578 CGTACACCGGAGCAATCTGA 59.827 55.000 9.46 0.00 0.00 3.27
6814 25439 1.405821 GGAGACCTGGTATGACGACAG 59.594 57.143 0.00 0.00 0.00 3.51
6866 25491 6.806249 CAGCTAATGGAGAAAAATTTGCGTTA 59.194 34.615 0.00 0.00 38.83 3.18
7220 25845 0.677288 TGGGTACAAGGATATCGGCG 59.323 55.000 0.00 0.00 0.00 6.46
7280 25905 7.150783 AGGAAGAAACTTGCAGATAACAATC 57.849 36.000 5.88 0.00 0.00 2.67
7493 26118 4.484236 TGTTGCTCAATTTTTAGATGCCG 58.516 39.130 0.00 0.00 0.00 5.69
7582 26207 3.958704 TCACGCAACAGTTTGGTTATTG 58.041 40.909 0.00 0.00 32.81 1.90
7602 26227 4.906065 TGCTGATGCTTTAGCTTATTGG 57.094 40.909 15.89 0.00 42.66 3.16
7706 26331 3.424703 AGATGCTTTTGTATGGCAGTGT 58.575 40.909 0.00 0.00 39.38 3.55
7727 26352 7.551617 CAGTGTTTAATAATTACTCCCTCCGTT 59.448 37.037 0.00 0.00 0.00 4.44
7728 26353 7.767659 AGTGTTTAATAATTACTCCCTCCGTTC 59.232 37.037 0.00 0.00 0.00 3.95
7729 26354 7.011763 GTGTTTAATAATTACTCCCTCCGTTCC 59.988 40.741 0.00 0.00 0.00 3.62
7731 26356 1.961133 AATTACTCCCTCCGTTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
7737 26362 2.850568 ACTCCCTCCGTTCCCAAATATT 59.149 45.455 0.00 0.00 0.00 1.28
7738 26363 3.268595 ACTCCCTCCGTTCCCAAATATTT 59.731 43.478 0.00 0.00 0.00 1.40
7740 26365 3.010808 TCCCTCCGTTCCCAAATATTTGT 59.989 43.478 23.24 0.00 36.45 2.83
7741 26366 3.380320 CCCTCCGTTCCCAAATATTTGTC 59.620 47.826 23.24 11.68 36.45 3.18
7742 26367 4.270008 CCTCCGTTCCCAAATATTTGTCT 58.730 43.478 23.24 0.00 36.45 3.41
7743 26368 4.705023 CCTCCGTTCCCAAATATTTGTCTT 59.295 41.667 23.24 0.00 36.45 3.01
7745 26370 6.376018 CCTCCGTTCCCAAATATTTGTCTTTA 59.624 38.462 23.24 4.73 36.45 1.85
7772 26397 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
7773 26398 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
7774 26399 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
7775 26400 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
7776 26401 5.456548 TCAACAAGTGACTACATACGGAA 57.543 39.130 0.00 0.00 0.00 4.30
7777 26402 5.224888 TCAACAAGTGACTACATACGGAAC 58.775 41.667 0.00 0.00 0.00 3.62
7779 26404 5.204409 ACAAGTGACTACATACGGAACAA 57.796 39.130 0.00 0.00 0.00 2.83
7781 26406 6.050432 ACAAGTGACTACATACGGAACAAAA 58.950 36.000 0.00 0.00 0.00 2.44
7783 26408 6.721571 AGTGACTACATACGGAACAAAATG 57.278 37.500 0.00 0.00 0.00 2.32
7784 26409 6.460781 AGTGACTACATACGGAACAAAATGA 58.539 36.000 0.00 0.00 0.00 2.57
7785 26410 6.590292 AGTGACTACATACGGAACAAAATGAG 59.410 38.462 0.00 0.00 0.00 2.90
7787 26412 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
7790 26415 5.305585 ACATACGGAACAAAATGAGTGAGT 58.694 37.500 0.00 0.00 0.00 3.41
7791 26416 5.408604 ACATACGGAACAAAATGAGTGAGTC 59.591 40.000 0.00 0.00 0.00 3.36
7792 26417 4.073293 ACGGAACAAAATGAGTGAGTCT 57.927 40.909 0.00 0.00 0.00 3.24
7793 26418 5.209818 ACGGAACAAAATGAGTGAGTCTA 57.790 39.130 0.00 0.00 0.00 2.59
7794 26419 4.989168 ACGGAACAAAATGAGTGAGTCTAC 59.011 41.667 0.00 0.00 0.00 2.59
7795 26420 4.988540 CGGAACAAAATGAGTGAGTCTACA 59.011 41.667 0.00 0.00 0.00 2.74
7796 26421 5.107453 CGGAACAAAATGAGTGAGTCTACAC 60.107 44.000 0.00 0.00 40.60 2.90
7834 26459 4.438148 CATACATCCGTATGTTGTGTCCA 58.562 43.478 0.00 0.00 46.70 4.02
7835 26460 3.627395 ACATCCGTATGTTGTGTCCAT 57.373 42.857 0.00 0.00 44.07 3.41
7836 26461 3.950397 ACATCCGTATGTTGTGTCCATT 58.050 40.909 0.00 0.00 44.07 3.16
7837 26462 4.331968 ACATCCGTATGTTGTGTCCATTT 58.668 39.130 0.00 0.00 44.07 2.32
7838 26463 4.155826 ACATCCGTATGTTGTGTCCATTTG 59.844 41.667 0.00 0.00 44.07 2.32
7839 26464 3.078097 TCCGTATGTTGTGTCCATTTGG 58.922 45.455 0.00 0.00 0.00 3.28
7840 26465 3.078097 CCGTATGTTGTGTCCATTTGGA 58.922 45.455 0.00 0.00 43.08 3.53
7853 26478 5.857471 TCCATTTGGAATGCCTAGAAATG 57.143 39.130 6.93 6.93 42.18 2.32
7854 26479 4.099881 TCCATTTGGAATGCCTAGAAATGC 59.900 41.667 8.05 0.00 42.18 3.56
7855 26480 4.141892 CCATTTGGAATGCCTAGAAATGCA 60.142 41.667 8.05 0.00 35.40 3.96
7857 26482 6.239373 CCATTTGGAATGCCTAGAAATGCATA 60.239 38.462 0.00 0.00 46.97 3.14
7858 26483 6.982160 TTTGGAATGCCTAGAAATGCATAT 57.018 33.333 0.00 0.00 46.97 1.78
7859 26484 6.982160 TTGGAATGCCTAGAAATGCATATT 57.018 33.333 0.00 0.00 46.97 1.28
7860 26485 6.982160 TGGAATGCCTAGAAATGCATATTT 57.018 33.333 0.00 0.00 46.97 1.40
7861 26486 6.751157 TGGAATGCCTAGAAATGCATATTTG 58.249 36.000 0.00 0.00 46.97 2.32
7862 26487 6.161381 GGAATGCCTAGAAATGCATATTTGG 58.839 40.000 0.00 0.31 46.97 3.28
7863 26488 5.733620 ATGCCTAGAAATGCATATTTGGG 57.266 39.130 0.00 0.80 45.89 4.12
7864 26489 4.802307 TGCCTAGAAATGCATATTTGGGA 58.198 39.130 0.00 0.00 36.66 4.37
7865 26490 5.207354 TGCCTAGAAATGCATATTTGGGAA 58.793 37.500 0.00 0.00 36.66 3.97
7866 26491 5.068987 TGCCTAGAAATGCATATTTGGGAAC 59.931 40.000 0.00 0.00 36.66 3.62
7867 26492 5.762045 CCTAGAAATGCATATTTGGGAACG 58.238 41.667 0.00 0.00 36.66 3.95
7882 26507 2.826725 GGGAACGGAGGGAGTAGATATG 59.173 54.545 0.00 0.00 0.00 1.78
7908 26533 6.773638 AGTGTCATATTGTCTGGAGAACTTT 58.226 36.000 0.00 0.00 0.00 2.66
7948 26573 2.008329 AGTAACAACGCGTTTGGTTCA 58.992 42.857 25.22 12.88 39.84 3.18
7975 26610 2.680913 CCGCGGCTTTTGACTCCAG 61.681 63.158 14.67 0.00 0.00 3.86
7978 26613 1.166531 GCGGCTTTTGACTCCAGTGT 61.167 55.000 0.00 0.00 0.00 3.55
7994 26629 5.374921 TCCAGTGTATTCCAAAACCGTAAA 58.625 37.500 0.00 0.00 0.00 2.01
8009 26644 8.861101 CAAAACCGTAAAGTTGTATTTGTTTCA 58.139 29.630 0.00 0.00 0.00 2.69
8077 26712 0.965866 ACTGAAGACGCCCAGATCGA 60.966 55.000 0.00 0.00 34.65 3.59
8092 26727 4.337555 CCAGATCGAAGCTGATTGGAAAAT 59.662 41.667 17.32 0.00 35.39 1.82
8115 26750 1.518056 AACACATCTGCGCCAACCAG 61.518 55.000 4.18 0.00 0.00 4.00
8131 26766 2.737376 AGACGAAGCGCGGTTTCC 60.737 61.111 25.80 16.15 46.49 3.13
8231 26866 8.880750 GGATATGTACTGTAAAAACTCCAGAAC 58.119 37.037 0.00 0.00 0.00 3.01
8232 26867 9.654663 GATATGTACTGTAAAAACTCCAGAACT 57.345 33.333 0.00 0.00 0.00 3.01
8233 26868 7.964604 ATGTACTGTAAAAACTCCAGAACTC 57.035 36.000 0.00 0.00 0.00 3.01
8237 26872 6.415573 ACTGTAAAAACTCCAGAACTCTTGT 58.584 36.000 0.00 0.00 0.00 3.16
8238 26873 7.562135 ACTGTAAAAACTCCAGAACTCTTGTA 58.438 34.615 0.00 0.00 0.00 2.41
8239 26874 8.211629 ACTGTAAAAACTCCAGAACTCTTGTAT 58.788 33.333 0.00 0.00 0.00 2.29
8240 26875 8.603242 TGTAAAAACTCCAGAACTCTTGTATC 57.397 34.615 0.00 0.00 0.00 2.24
8241 26876 8.429641 TGTAAAAACTCCAGAACTCTTGTATCT 58.570 33.333 0.00 0.00 0.00 1.98
8242 26877 7.971183 AAAAACTCCAGAACTCTTGTATCTC 57.029 36.000 0.00 0.00 0.00 2.75
8243 26878 6.672266 AAACTCCAGAACTCTTGTATCTCA 57.328 37.500 0.00 0.00 0.00 3.27
8290 27085 8.818141 TCTACAACTCTTGTATCTCACTTTTG 57.182 34.615 0.00 0.00 44.46 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 5.336213 GCAGAATGGTATGCATATTTCCTGG 60.336 44.000 10.16 7.72 41.77 4.45
165 166 3.479006 CAACGAAATTTGTAGGACGCAG 58.521 45.455 0.00 0.00 0.00 5.18
202 203 2.101917 CCAATGGGATGCAAAAGCCTAG 59.898 50.000 0.00 0.00 33.53 3.02
204 205 0.906775 CCAATGGGATGCAAAAGCCT 59.093 50.000 0.00 0.00 33.53 4.58
365 366 7.326305 CCGTATACTGCAATCTACATCAAGTAC 59.674 40.741 0.56 0.00 0.00 2.73
407 412 7.039784 AGCCAAATGTTAGCAAACTATTCTTCA 60.040 33.333 0.00 0.00 36.51 3.02
602 607 2.092646 ACACCTAGTGCAAAACCTGTGA 60.093 45.455 8.69 0.00 36.98 3.58
911 916 3.326880 GGTAGTTGGAGACCTCAAAAGGA 59.673 47.826 0.00 0.00 46.67 3.36
1667 6536 5.877012 TCTACAAGGAAATCTAGCTTTGCTG 59.123 40.000 12.97 9.93 40.10 4.41
1790 6659 3.119990 ACGCCAAATATTTCGTCCTTGTG 60.120 43.478 8.63 0.00 0.00 3.33
1854 6723 5.529430 TCATCAGACGGTTTGTTTTGTATGT 59.471 36.000 0.00 0.00 0.00 2.29
2216 7095 2.168326 TTGTGCACATGATCGACAGT 57.832 45.000 22.39 0.00 0.00 3.55
2289 7168 4.082026 ACACATATTTCAGGCTCTTTTGGC 60.082 41.667 0.00 0.00 0.00 4.52
2296 7175 5.133221 ACCCATTACACATATTTCAGGCTC 58.867 41.667 0.00 0.00 0.00 4.70
2381 7261 2.371841 ACAGAATTGCCACTACCAGACA 59.628 45.455 0.00 0.00 0.00 3.41
2707 7839 2.356313 CACAGGAACGTCGCTGCT 60.356 61.111 0.00 0.00 0.00 4.24
2714 7885 1.165907 TCGTACGTCCACAGGAACGT 61.166 55.000 16.05 14.57 40.42 3.99
2747 7990 7.738437 ATTAGGTGGACAATCAAAATTGGAT 57.262 32.000 3.45 0.00 45.48 3.41
2775 8018 3.834799 GTACCGCCCGCAGCTACT 61.835 66.667 0.00 0.00 40.39 2.57
2835 8078 4.006319 GCTCTTGTCATCTAAACAGGCTT 58.994 43.478 0.00 0.00 0.00 4.35
2951 8227 0.253610 ACCAACGTCCTCACCACAAA 59.746 50.000 0.00 0.00 0.00 2.83
2953 8229 1.145156 CACCAACGTCCTCACCACA 59.855 57.895 0.00 0.00 0.00 4.17
2967 8244 1.676968 CCAGTCCCATCGAACACCA 59.323 57.895 0.00 0.00 0.00 4.17
2970 8247 0.400213 AAAGCCAGTCCCATCGAACA 59.600 50.000 0.00 0.00 0.00 3.18
3052 8363 0.253160 ACCTCCTATCCAACTGGCCA 60.253 55.000 4.71 4.71 34.44 5.36
3102 8413 2.052104 CCATCGGCCCTTCCAAACC 61.052 63.158 0.00 0.00 34.01 3.27
3125 8436 7.606456 AGAATTGGATTAACACTTATCACGTGT 59.394 33.333 16.51 5.66 46.77 4.49
3364 9083 2.281692 GGGTTTGGGGCGTACGTT 60.282 61.111 17.90 0.00 0.00 3.99
3367 9086 2.857575 CTACCGGGTTTGGGGCGTAC 62.858 65.000 4.31 0.00 0.00 3.67
3428 9147 2.159179 ACTAAACATGGGAATGGGCC 57.841 50.000 0.00 0.00 0.00 5.80
3593 9319 4.163427 GGAGGGGATACAGATCAAGATCA 58.837 47.826 12.21 0.00 40.22 2.92
3644 9842 0.676736 GGAGAGACGATGGGGATGAC 59.323 60.000 0.00 0.00 0.00 3.06
3748 9947 0.394216 TACTAGGTCGCCGCCAGTTA 60.394 55.000 0.00 0.00 0.00 2.24
3884 10128 3.056536 TCATTCACTGCTCAGGAGTACAC 60.057 47.826 0.00 0.00 0.00 2.90
4206 18863 1.403647 CGTAAAGAGCCATGGTCGTGA 60.404 52.381 14.67 0.00 35.00 4.35
4235 18892 1.067565 CGAGTATCCGGATGACCCATG 60.068 57.143 27.55 6.34 34.14 3.66
4258 18915 4.510340 AGATCGCAGTGAAAAGTTTACGTT 59.490 37.500 0.00 0.00 0.00 3.99
4284 18941 2.126463 CTGAAGGTTCGCGCTCGA 60.126 61.111 5.56 0.00 43.89 4.04
4307 18964 1.648467 GGCTGCAACGGAGATGGAAC 61.648 60.000 0.50 0.00 26.60 3.62
4308 18965 1.377202 GGCTGCAACGGAGATGGAA 60.377 57.895 0.50 0.00 26.60 3.53
4309 18966 1.841302 AAGGCTGCAACGGAGATGGA 61.841 55.000 0.50 0.00 0.00 3.41
4310 18967 1.372087 GAAGGCTGCAACGGAGATGG 61.372 60.000 0.50 0.00 0.00 3.51
4311 18968 0.674581 TGAAGGCTGCAACGGAGATG 60.675 55.000 0.50 0.00 0.00 2.90
4312 18969 0.392193 CTGAAGGCTGCAACGGAGAT 60.392 55.000 0.50 0.00 0.00 2.75
4313 18970 1.004560 CTGAAGGCTGCAACGGAGA 60.005 57.895 0.50 0.00 0.00 3.71
4314 18971 2.684843 GCTGAAGGCTGCAACGGAG 61.685 63.158 0.50 0.00 38.66 4.63
4315 18972 2.669569 GCTGAAGGCTGCAACGGA 60.670 61.111 0.50 0.00 38.66 4.69
4325 18982 1.517242 AGCGTTCAAGAAGCTGAAGG 58.483 50.000 0.00 0.00 41.79 3.46
4326 18983 2.545526 TGAAGCGTTCAAGAAGCTGAAG 59.454 45.455 0.00 0.00 41.53 3.02
4327 18984 2.560504 TGAAGCGTTCAAGAAGCTGAA 58.439 42.857 0.00 0.00 41.53 3.02
4328 18985 2.238942 TGAAGCGTTCAAGAAGCTGA 57.761 45.000 0.00 0.00 41.53 4.26
4372 19059 4.058721 TGAGATACATGTGGGTCATTCG 57.941 45.455 9.11 0.00 34.09 3.34
4393 19080 6.017192 TCTTCCTTGTGGTAGATGACTACTT 58.983 40.000 0.00 0.00 45.70 2.24
4564 19504 4.516698 GCCATTTATCGACCATGTTGATCT 59.483 41.667 0.30 0.00 37.74 2.75
4651 19591 2.700722 TCGTGGTTATGGCATGCTAA 57.299 45.000 18.92 6.47 0.00 3.09
4813 20204 0.320771 AGCCTACTTGTGTGCCTTCG 60.321 55.000 0.00 0.00 0.00 3.79
4815 20206 0.890996 GCAGCCTACTTGTGTGCCTT 60.891 55.000 0.00 0.00 0.00 4.35
4817 20208 0.890996 AAGCAGCCTACTTGTGTGCC 60.891 55.000 0.00 0.00 34.56 5.01
4857 20252 3.904800 TGAGAGTGTGTTTGGACTCAA 57.095 42.857 0.00 0.00 41.01 3.02
4858 20253 4.422073 AATGAGAGTGTGTTTGGACTCA 57.578 40.909 0.00 0.00 41.01 3.41
4859 20254 7.173218 TCAATAAATGAGAGTGTGTTTGGACTC 59.827 37.037 0.00 0.00 39.18 3.36
4902 20297 2.203153 CTATCCCGGCCCGTTTGG 60.203 66.667 0.85 0.00 37.09 3.28
4903 20298 2.886730 AAGCTATCCCGGCCCGTTTG 62.887 60.000 0.85 0.00 0.00 2.93
4904 20299 2.676265 AAGCTATCCCGGCCCGTTT 61.676 57.895 0.85 0.00 0.00 3.60
4905 20300 3.087906 AAGCTATCCCGGCCCGTT 61.088 61.111 0.85 0.00 0.00 4.44
4907 20302 3.809374 GACAAGCTATCCCGGCCCG 62.809 68.421 0.00 0.00 0.00 6.13
4908 20303 2.111251 GACAAGCTATCCCGGCCC 59.889 66.667 0.00 0.00 0.00 5.80
4910 20305 0.530870 GTGAGACAAGCTATCCCGGC 60.531 60.000 0.00 0.00 0.00 6.13
4911 20306 0.249073 CGTGAGACAAGCTATCCCGG 60.249 60.000 0.00 0.00 0.00 5.73
4912 20307 0.872021 GCGTGAGACAAGCTATCCCG 60.872 60.000 0.00 0.00 36.06 5.14
4914 20309 0.530870 GGGCGTGAGACAAGCTATCC 60.531 60.000 9.13 0.09 45.40 2.59
4915 20310 0.175760 TGGGCGTGAGACAAGCTATC 59.824 55.000 9.13 0.00 45.40 2.08
4917 20312 0.175760 GATGGGCGTGAGACAAGCTA 59.824 55.000 9.13 1.09 45.40 3.32
4919 20314 2.456119 CGATGGGCGTGAGACAAGC 61.456 63.158 0.00 0.00 45.40 4.01
4928 20400 0.179073 CCTTCATCTTCGATGGGCGT 60.179 55.000 4.21 0.00 41.80 5.68
4934 20406 2.104451 AGCATGCTCCTTCATCTTCGAT 59.896 45.455 16.30 0.00 0.00 3.59
4964 20436 3.729108 AGAGATCATCTCCCAAGGTTCA 58.271 45.455 11.33 0.00 44.42 3.18
4965 20437 4.769345 AAGAGATCATCTCCCAAGGTTC 57.231 45.455 11.33 0.00 44.42 3.62
5493 20985 3.566322 GGTGTACATACAGTTTGGTTGCA 59.434 43.478 0.00 0.00 36.78 4.08
5520 21012 7.860649 TTACTACTAAGAGGGAAGGAAACAA 57.139 36.000 0.00 0.00 0.00 2.83
5672 21164 4.590647 ACTGCTATGTGCCAGTAGACATAT 59.409 41.667 0.00 0.00 42.00 1.78
5675 21167 2.179427 ACTGCTATGTGCCAGTAGACA 58.821 47.619 0.00 0.00 42.00 3.41
5681 21173 1.405463 TCTCGTACTGCTATGTGCCAG 59.595 52.381 0.00 0.00 42.00 4.85
5850 24471 1.410004 TTGTTGTCCGTCACCTCTCT 58.590 50.000 0.00 0.00 0.00 3.10
5860 24481 3.138304 TCCAGTTTCAGATTGTTGTCCG 58.862 45.455 0.00 0.00 0.00 4.79
5966 24587 5.508567 TCATCATGGAAATGCTTCAACCTA 58.491 37.500 0.00 0.00 32.75 3.08
6079 24700 3.195698 GATCCCTGTTCGCACGCC 61.196 66.667 0.00 0.00 0.00 5.68
6184 24805 1.515088 CCACGCTCGAGCTGTACAG 60.515 63.158 32.88 18.93 39.32 2.74
6213 24834 3.181497 GCACGAGGTTGCATTGTATTGAT 60.181 43.478 0.00 0.00 42.49 2.57
6228 24849 1.373497 GCTCCATATCCGCACGAGG 60.373 63.158 0.00 0.00 0.00 4.63
6267 24888 4.689612 TGGCCTTGTAATCTAGATCACC 57.310 45.455 5.51 0.00 0.00 4.02
6320 24941 2.196749 CTACTAGCACGGTCTTGCATG 58.803 52.381 2.44 0.00 45.62 4.06
6404 25029 0.826715 TGCCTGTAGAGGTGCTGATC 59.173 55.000 7.90 0.00 42.15 2.92
6427 25052 2.501723 GCTTTGGTCTAGGGATGTCTCA 59.498 50.000 0.00 0.00 0.00 3.27
6563 25188 3.681835 GCGGAGGTGGTGACGAGT 61.682 66.667 0.00 0.00 0.00 4.18
6814 25439 0.250597 ACCTTGCCGGGTTCAACTAC 60.251 55.000 2.18 0.00 35.89 2.73
6866 25491 2.755208 GCTTTCCCTTTGTACCCTTGGT 60.755 50.000 0.00 0.00 40.16 3.67
6942 25567 3.548745 TCTACATCATGTTGGCCTGAG 57.451 47.619 3.32 0.00 0.00 3.35
7024 25649 2.118313 TGTGCATCATCTGAGGTTGG 57.882 50.000 0.00 0.00 0.00 3.77
7179 25804 5.923114 CCACACGAATATATGTCTTCCTCAG 59.077 44.000 0.00 0.00 0.00 3.35
7220 25845 1.048601 TATTCGCCCATGTCCCTCTC 58.951 55.000 0.00 0.00 0.00 3.20
7280 25905 3.429085 CGAAATCCAATGCTTTCTTCGG 58.571 45.455 0.00 0.00 32.65 4.30
7392 26017 7.773489 TGAAGTGATTGTTGGATGGAAAATA 57.227 32.000 0.00 0.00 0.00 1.40
7582 26207 3.885297 TCCCAATAAGCTAAAGCATCAGC 59.115 43.478 4.54 0.00 45.16 4.26
7602 26227 5.277828 GCCGTATGACAGATTATTTGGTTCC 60.278 44.000 0.00 0.00 0.00 3.62
7611 26236 6.040504 ACACAGAATAGCCGTATGACAGATTA 59.959 38.462 0.00 0.00 0.00 1.75
7619 26244 5.597806 TCCTTTACACAGAATAGCCGTATG 58.402 41.667 0.00 0.00 0.00 2.39
7706 26331 6.158344 TGGGAACGGAGGGAGTAATTATTAAA 59.842 38.462 0.00 0.00 0.00 1.52
7738 26363 9.996554 TCACTTGTTGAAATCTCTATAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
7750 26375 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
7751 26376 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
7752 26377 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
7753 26378 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
7755 26380 4.986034 TGTTCCGTATGTAGTCACTTGTTG 59.014 41.667 0.00 0.00 0.00 3.33
7756 26381 5.204409 TGTTCCGTATGTAGTCACTTGTT 57.796 39.130 0.00 0.00 0.00 2.83
7757 26382 4.859304 TGTTCCGTATGTAGTCACTTGT 57.141 40.909 0.00 0.00 0.00 3.16
7758 26383 6.533819 TTTTGTTCCGTATGTAGTCACTTG 57.466 37.500 0.00 0.00 0.00 3.16
7759 26384 6.932400 TCATTTTGTTCCGTATGTAGTCACTT 59.068 34.615 0.00 0.00 0.00 3.16
7765 26390 6.590292 ACTCACTCATTTTGTTCCGTATGTAG 59.410 38.462 0.00 0.00 0.00 2.74
7766 26391 6.460781 ACTCACTCATTTTGTTCCGTATGTA 58.539 36.000 0.00 0.00 0.00 2.29
7767 26392 5.305585 ACTCACTCATTTTGTTCCGTATGT 58.694 37.500 0.00 0.00 0.00 2.29
7768 26393 5.639506 AGACTCACTCATTTTGTTCCGTATG 59.360 40.000 0.00 0.00 0.00 2.39
7770 26395 5.209818 AGACTCACTCATTTTGTTCCGTA 57.790 39.130 0.00 0.00 0.00 4.02
7771 26396 4.073293 AGACTCACTCATTTTGTTCCGT 57.927 40.909 0.00 0.00 0.00 4.69
7772 26397 4.988540 TGTAGACTCACTCATTTTGTTCCG 59.011 41.667 0.00 0.00 0.00 4.30
7773 26398 5.992217 AGTGTAGACTCACTCATTTTGTTCC 59.008 40.000 0.00 0.00 44.07 3.62
7813 26438 4.746535 TGGACACAACATACGGATGTAT 57.253 40.909 15.10 2.23 45.93 2.29
7814 26439 4.746535 ATGGACACAACATACGGATGTA 57.253 40.909 15.10 0.00 45.93 2.29
7815 26440 6.831899 CCAAATGGACACAACATACGGATGT 61.832 44.000 7.68 7.68 42.42 3.06
7816 26441 4.438608 CCAAATGGACACAACATACGGATG 60.439 45.833 5.94 5.94 36.84 3.51
7817 26442 3.694072 CCAAATGGACACAACATACGGAT 59.306 43.478 0.00 0.00 37.39 4.18
7818 26443 3.078097 CCAAATGGACACAACATACGGA 58.922 45.455 0.00 0.00 37.39 4.69
7819 26444 3.078097 TCCAAATGGACACAACATACGG 58.922 45.455 0.00 0.00 39.78 4.02
7820 26445 4.757799 TTCCAAATGGACACAACATACG 57.242 40.909 0.54 0.00 45.39 3.06
7821 26446 4.864247 GCATTCCAAATGGACACAACATAC 59.136 41.667 0.54 0.00 45.39 2.39
7822 26447 4.081752 GGCATTCCAAATGGACACAACATA 60.082 41.667 0.54 0.00 45.39 2.29
7823 26448 3.306919 GGCATTCCAAATGGACACAACAT 60.307 43.478 0.54 0.00 45.39 2.71
7824 26449 2.036992 GGCATTCCAAATGGACACAACA 59.963 45.455 0.54 0.00 45.39 3.33
7825 26450 2.299867 AGGCATTCCAAATGGACACAAC 59.700 45.455 0.54 0.00 45.39 3.32
7826 26451 2.607499 AGGCATTCCAAATGGACACAA 58.393 42.857 0.54 0.00 45.39 3.33
7827 26452 2.307496 AGGCATTCCAAATGGACACA 57.693 45.000 0.54 0.00 45.39 3.72
7828 26453 3.620488 TCTAGGCATTCCAAATGGACAC 58.380 45.455 0.54 0.00 45.39 3.67
7829 26454 4.314522 TTCTAGGCATTCCAAATGGACA 57.685 40.909 0.54 0.00 45.39 4.02
7830 26455 5.594926 CATTTCTAGGCATTCCAAATGGAC 58.405 41.667 0.54 0.00 45.39 4.02
7831 26456 4.099881 GCATTTCTAGGCATTCCAAATGGA 59.900 41.667 0.00 0.00 43.73 3.41
7832 26457 4.141892 TGCATTTCTAGGCATTCCAAATGG 60.142 41.667 10.88 0.00 35.91 3.16
7833 26458 5.013568 TGCATTTCTAGGCATTCCAAATG 57.986 39.130 6.48 6.48 35.91 2.32
7842 26467 4.802307 TCCCAAATATGCATTTCTAGGCA 58.198 39.130 3.54 0.00 46.15 4.75
7843 26468 5.532557 GTTCCCAAATATGCATTTCTAGGC 58.467 41.667 3.54 0.00 31.82 3.93
7844 26469 5.278463 CCGTTCCCAAATATGCATTTCTAGG 60.278 44.000 3.54 1.12 31.82 3.02
7845 26470 5.530915 TCCGTTCCCAAATATGCATTTCTAG 59.469 40.000 3.54 0.00 31.82 2.43
7846 26471 5.441500 TCCGTTCCCAAATATGCATTTCTA 58.558 37.500 3.54 0.00 31.82 2.10
7847 26472 4.277476 TCCGTTCCCAAATATGCATTTCT 58.723 39.130 3.54 0.00 31.82 2.52
7848 26473 4.499696 CCTCCGTTCCCAAATATGCATTTC 60.500 45.833 3.54 0.00 31.82 2.17
7849 26474 3.384467 CCTCCGTTCCCAAATATGCATTT 59.616 43.478 3.54 0.00 34.60 2.32
7850 26475 2.958355 CCTCCGTTCCCAAATATGCATT 59.042 45.455 3.54 0.00 0.00 3.56
7851 26476 2.586425 CCTCCGTTCCCAAATATGCAT 58.414 47.619 3.79 3.79 0.00 3.96
7852 26477 1.409521 CCCTCCGTTCCCAAATATGCA 60.410 52.381 0.00 0.00 0.00 3.96
7853 26478 1.133915 TCCCTCCGTTCCCAAATATGC 60.134 52.381 0.00 0.00 0.00 3.14
7854 26479 2.172717 ACTCCCTCCGTTCCCAAATATG 59.827 50.000 0.00 0.00 0.00 1.78
7855 26480 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
7856 26481 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
7857 26482 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
7858 26483 1.203212 TCTACTCCCTCCGTTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
7859 26484 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
7860 26485 0.635009 ATCTACTCCCTCCGTTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
7861 26486 2.671896 TATCTACTCCCTCCGTTCCC 57.328 55.000 0.00 0.00 0.00 3.97
7862 26487 3.764218 TCATATCTACTCCCTCCGTTCC 58.236 50.000 0.00 0.00 0.00 3.62
7863 26488 4.828387 ACTTCATATCTACTCCCTCCGTTC 59.172 45.833 0.00 0.00 0.00 3.95
7864 26489 4.585162 CACTTCATATCTACTCCCTCCGTT 59.415 45.833 0.00 0.00 0.00 4.44
7865 26490 4.145807 CACTTCATATCTACTCCCTCCGT 58.854 47.826 0.00 0.00 0.00 4.69
7866 26491 4.145807 ACACTTCATATCTACTCCCTCCG 58.854 47.826 0.00 0.00 0.00 4.63
7867 26492 5.141182 TGACACTTCATATCTACTCCCTCC 58.859 45.833 0.00 0.00 0.00 4.30
7882 26507 6.402222 AGTTCTCCAGACAATATGACACTTC 58.598 40.000 0.00 0.00 0.00 3.01
7966 26591 4.825085 GGTTTTGGAATACACTGGAGTCAA 59.175 41.667 0.00 0.00 0.00 3.18
7975 26610 6.497437 ACAACTTTACGGTTTTGGAATACAC 58.503 36.000 0.00 0.00 0.00 2.90
7978 26613 9.680315 CAAATACAACTTTACGGTTTTGGAATA 57.320 29.630 0.00 0.00 0.00 1.75
7994 26629 5.493133 TTGCGAGTGAAACAAATACAACT 57.507 34.783 0.00 0.00 41.43 3.16
8077 26712 3.903090 TGTTCCCATTTTCCAATCAGCTT 59.097 39.130 0.00 0.00 0.00 3.74
8092 26727 2.359850 GGCGCAGATGTGTTCCCA 60.360 61.111 10.83 0.00 0.00 4.37
8115 26750 3.011760 CTGGAAACCGCGCTTCGTC 62.012 63.158 5.56 0.00 36.19 4.20
8131 26766 8.997621 TTGTAGCCTAGACACTAATTTAACTG 57.002 34.615 0.00 0.00 0.00 3.16
8239 26874 9.959721 AACAAAGCTATCCTTATAAAAGTGAGA 57.040 29.630 0.00 0.00 32.20 3.27
8241 26876 9.959721 AGAACAAAGCTATCCTTATAAAAGTGA 57.040 29.630 0.00 0.00 32.20 3.41
8290 27085 5.741982 GCGGTTGATTTATGTTTGGACATAC 59.258 40.000 0.00 0.00 45.81 2.39


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

AutoCloner maintained by Alex Coulton.