Multiple sequence alignment - TraesCS7B01G139000

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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 TraesCS7B01G139000 chr7B 100.000 5746 0 0 1 5746 175192346 175198091 0.000000e+00 10611.0
1 TraesCS7B01G139000 chr7B 93.003 2358 113 19 412 2727 175722206 175719859 0.000000e+00 3393.0
2 TraesCS7B01G139000 chr7B 93.170 1962 100 15 791 2727 175614434 175612482 0.000000e+00 2850.0
3 TraesCS7B01G139000 chr7B 93.228 635 36 3 4421 5052 175612320 175611690 0.000000e+00 928.0
4 TraesCS7B01G139000 chr7B 88.720 461 32 5 5044 5484 175718989 175718529 3.910000e-151 545.0
5 TraesCS7B01G139000 chr7B 85.819 409 34 7 5044 5432 175611646 175611242 4.140000e-111 412.0
6 TraesCS7B01G139000 chr7B 89.262 298 9 5 518 792 175616051 175615754 9.160000e-93 351.0
7 TraesCS7B01G139000 chr7B 87.978 183 17 3 5568 5746 175298922 175298741 1.620000e-50 211.0
8 TraesCS7B01G139000 chr7B 96.491 114 3 1 285 397 175616528 175616415 2.730000e-43 187.0
9 TraesCS7B01G139000 chr7B 96.429 112 3 1 287 397 175722491 175722380 3.540000e-42 183.0
10 TraesCS7B01G139000 chr7B 96.226 106 4 0 4318 4423 685043922 685044027 2.130000e-39 174.0
11 TraesCS7B01G139000 chr7B 94.444 108 6 0 412 519 175616241 175616134 3.560000e-37 167.0
12 TraesCS7B01G139000 chr7B 93.043 115 7 1 4312 4425 316313680 316313794 3.560000e-37 167.0
13 TraesCS7B01G139000 chr7A 96.927 2213 60 5 518 2727 236349294 236351501 0.000000e+00 3703.0
14 TraesCS7B01G139000 chr7A 92.981 2365 106 26 412 2727 236079924 236082277 0.000000e+00 3393.0
15 TraesCS7B01G139000 chr7A 92.981 2365 106 26 412 2727 236323729 236326082 0.000000e+00 3393.0
16 TraesCS7B01G139000 chr7A 96.048 1594 56 4 1054 2646 236380877 236382464 0.000000e+00 2588.0
17 TraesCS7B01G139000 chr7A 95.852 1591 56 6 1054 2643 236355299 236356880 0.000000e+00 2564.0
18 TraesCS7B01G139000 chr7A 98.291 1346 20 2 2727 4071 641236674 641235331 0.000000e+00 2355.0
19 TraesCS7B01G139000 chr7A 98.414 1261 19 1 2844 4103 357349478 357348218 0.000000e+00 2217.0
20 TraesCS7B01G139000 chr7A 93.701 635 35 2 4421 5052 236082470 236083102 0.000000e+00 946.0
21 TraesCS7B01G139000 chr7A 93.448 641 33 3 4421 5052 236351693 236352333 0.000000e+00 942.0
22 TraesCS7B01G139000 chr7A 91.536 638 46 4 4421 5052 236377151 236377786 0.000000e+00 872.0
23 TraesCS7B01G139000 chr7A 90.439 638 53 5 4421 5052 236431143 236431778 0.000000e+00 833.0
24 TraesCS7B01G139000 chr7A 94.961 516 20 3 2132 2646 236448243 236448753 0.000000e+00 804.0
25 TraesCS7B01G139000 chr7A 90.614 586 47 5 4421 5000 236459082 236459665 0.000000e+00 771.0
26 TraesCS7B01G139000 chr7A 92.827 474 29 2 4421 4891 236326275 236326746 0.000000e+00 682.0
27 TraesCS7B01G139000 chr7A 90.337 445 34 8 5044 5484 236461593 236462032 4.990000e-160 575.0
28 TraesCS7B01G139000 chr7A 90.476 441 33 8 5048 5484 236431826 236432261 1.800000e-159 573.0
29 TraesCS7B01G139000 chr7A 89.888 445 36 8 5044 5484 236377830 236378269 1.080000e-156 564.0
30 TraesCS7B01G139000 chr7A 88.286 461 30 6 5044 5484 236083146 236083602 1.100000e-146 531.0
31 TraesCS7B01G139000 chr7A 89.841 315 25 5 5117 5427 236352840 236353151 1.160000e-106 398.0
32 TraesCS7B01G139000 chr7A 88.328 317 16 3 5044 5343 236328402 236328714 1.520000e-95 361.0
33 TraesCS7B01G139000 chr7A 96.209 211 7 1 4107 4316 236082260 236082470 1.530000e-90 344.0
34 TraesCS7B01G139000 chr7A 96.190 210 8 0 4107 4316 236376942 236377151 1.530000e-90 344.0
35 TraesCS7B01G139000 chr7A 92.369 249 5 1 285 519 236348932 236349180 5.510000e-90 342.0
36 TraesCS7B01G139000 chr7A 95.735 211 8 1 4107 4316 236326065 236326275 7.130000e-89 339.0
37 TraesCS7B01G139000 chr7A 95.714 210 9 0 4107 4316 236351484 236351693 7.130000e-89 339.0
38 TraesCS7B01G139000 chr7A 94.762 210 11 0 4107 4316 236458873 236459082 1.540000e-85 327.0
39 TraesCS7B01G139000 chr7A 92.857 210 11 1 4107 4316 236430938 236431143 9.360000e-78 302.0
40 TraesCS7B01G139000 chr7A 85.648 216 27 2 5534 5745 236379419 236379634 2.080000e-54 224.0
41 TraesCS7B01G139000 chr7A 95.614 114 4 1 285 397 236079632 236079745 1.270000e-41 182.0
42 TraesCS7B01G139000 chr7A 95.614 114 4 1 285 397 236323437 236323550 1.270000e-41 182.0
43 TraesCS7B01G139000 chr7A 82.243 214 24 6 5534 5745 236353833 236354034 7.650000e-39 172.0
44 TraesCS7B01G139000 chr7A 90.164 122 11 1 4305 4425 101275253 101275374 2.140000e-34 158.0
45 TraesCS7B01G139000 chr7A 96.739 92 3 0 2636 2727 236430864 236430955 2.770000e-33 154.0
46 TraesCS7B01G139000 chr7A 95.652 92 4 0 2636 2727 236458799 236458890 1.290000e-31 148.0
47 TraesCS7B01G139000 chr7A 96.053 76 3 0 5409 5484 236328717 236328792 2.170000e-24 124.0
48 TraesCS7B01G139000 chr7D 91.981 2494 137 25 285 2727 221296458 221298939 0.000000e+00 3439.0
49 TraesCS7B01G139000 chr7D 91.767 2502 150 21 285 2741 221697539 221695049 0.000000e+00 3428.0
50 TraesCS7B01G139000 chr7D 90.855 2176 128 24 414 2522 221685557 221687728 0.000000e+00 2850.0
51 TraesCS7B01G139000 chr7D 93.949 942 34 8 4421 5342 221694867 221693929 0.000000e+00 1402.0
52 TraesCS7B01G139000 chr7D 92.581 647 41 3 4409 5052 221583798 221584440 0.000000e+00 922.0
53 TraesCS7B01G139000 chr7D 92.117 647 44 4 4409 5052 221688237 221688879 0.000000e+00 905.0
54 TraesCS7B01G139000 chr7D 91.969 635 43 4 4421 5052 221299140 221299769 0.000000e+00 883.0
55 TraesCS7B01G139000 chr7D 91.892 444 11 6 412 832 221581112 221581553 1.070000e-166 597.0
56 TraesCS7B01G139000 chr7D 88.528 462 32 6 5044 5484 221299813 221300274 1.820000e-149 540.0
57 TraesCS7B01G139000 chr7D 88.503 461 31 6 5044 5484 221688923 221689381 6.550000e-149 538.0
58 TraesCS7B01G139000 chr7D 88.069 461 33 6 5044 5484 221584484 221584942 1.420000e-145 527.0
59 TraesCS7B01G139000 chr7D 93.506 231 14 1 4107 4336 221687877 221688107 5.510000e-90 342.0
60 TraesCS7B01G139000 chr7D 92.857 224 14 2 4107 4328 221583437 221583660 2.000000e-84 324.0
61 TraesCS7B01G139000 chr7D 94.313 211 11 1 4107 4316 221695077 221694867 7.180000e-84 322.0
62 TraesCS7B01G139000 chr7D 94.241 191 10 1 4127 4316 221298950 221299140 2.030000e-74 291.0
63 TraesCS7B01G139000 chr7D 96.491 114 3 1 285 397 221685265 221685378 2.730000e-43 187.0
64 TraesCS7B01G139000 chr7D 92.373 118 7 2 4313 4428 356542870 356542753 3.560000e-37 167.0
65 TraesCS7B01G139000 chr7D 93.878 98 4 2 5646 5743 221823424 221823519 4.640000e-31 147.0
66 TraesCS7B01G139000 chr7D 94.545 55 3 0 5565 5619 221590660 221590606 1.030000e-12 86.1
67 TraesCS7B01G139000 chr7D 100.000 30 0 0 5652 5681 221590326 221590297 8.040000e-04 56.5
68 TraesCS7B01G139000 chr7D 100.000 30 0 0 5652 5681 221979221 221979250 8.040000e-04 56.5
69 TraesCS7B01G139000 chr5A 98.643 1253 15 2 2840 4090 598579693 598580945 0.000000e+00 2218.0
70 TraesCS7B01G139000 chr5A 98.414 1261 19 1 2844 4103 483275353 483276613 0.000000e+00 2217.0
71 TraesCS7B01G139000 chr5A 91.613 155 7 6 2695 2846 483273243 483273394 5.830000e-50 209.0
72 TraesCS7B01G139000 chr6A 98.414 1261 18 2 2844 4103 386107986 386109245 0.000000e+00 2217.0
73 TraesCS7B01G139000 chr6A 92.339 248 17 2 1 247 356291274 356291520 9.160000e-93 351.0
74 TraesCS7B01G139000 chr6A 94.286 105 6 0 4318 4422 558454893 558454789 1.660000e-35 161.0
75 TraesCS7B01G139000 chr6A 94.286 105 6 0 4318 4422 558458978 558458874 1.660000e-35 161.0
76 TraesCS7B01G139000 chr6A 94.286 105 6 0 4318 4422 558462298 558462194 1.660000e-35 161.0
77 TraesCS7B01G139000 chr1B 98.335 1261 20 1 2844 4103 574236886 574238146 0.000000e+00 2211.0
78 TraesCS7B01G139000 chr1B 96.947 131 4 0 2727 2857 512685226 512685356 2.700000e-53 220.0
79 TraesCS7B01G139000 chr1B 97.143 105 3 0 4318 4422 315353863 315353967 1.650000e-40 178.0
80 TraesCS7B01G139000 chr1B 94.444 108 6 0 4318 4425 159692173 159692066 3.560000e-37 167.0
81 TraesCS7B01G139000 chr1A 98.486 1255 17 2 2844 4096 22086705 22087959 0.000000e+00 2211.0
82 TraesCS7B01G139000 chr1A 96.241 133 1 2 2714 2846 491264678 491264806 1.250000e-51 215.0
83 TraesCS7B01G139000 chr1A 93.750 144 4 5 2706 2846 440787241 440787382 1.620000e-50 211.0
84 TraesCS7B01G139000 chr2B 98.332 1259 19 2 2847 4104 676548338 676549595 0.000000e+00 2207.0
85 TraesCS7B01G139000 chr2B 90.681 279 20 4 1 273 172985567 172985845 3.270000e-97 366.0
86 TraesCS7B01G139000 chr2B 95.139 144 4 3 2714 2857 465126464 465126604 2.080000e-54 224.0
87 TraesCS7B01G139000 chr1D 98.255 1261 20 2 2844 4103 247480052 247478793 0.000000e+00 2206.0
88 TraesCS7B01G139000 chr2D 94.239 243 10 2 1 239 637337557 637337315 9.100000e-98 368.0
89 TraesCS7B01G139000 chr2D 93.173 249 16 1 1 248 291910337 291910089 1.180000e-96 364.0
90 TraesCS7B01G139000 chr4A 93.416 243 14 2 1 242 553305552 553305311 5.470000e-95 359.0
91 TraesCS7B01G139000 chr4A 89.964 279 22 4 1 273 271088322 271088044 7.080000e-94 355.0
92 TraesCS7B01G139000 chr4A 90.637 267 20 3 1 264 211458532 211458796 3.290000e-92 350.0
93 TraesCS7B01G139000 chr6D 92.126 254 16 1 1 254 467669613 467669364 7.080000e-94 355.0
94 TraesCS7B01G139000 chr6D 95.238 105 5 0 4318 4422 271605273 271605377 3.560000e-37 167.0
95 TraesCS7B01G139000 chr3D 91.765 255 11 3 1 255 612665572 612665328 4.260000e-91 346.0
96 TraesCS7B01G139000 chr3D 94.737 114 5 1 4318 4430 42166759 42166646 5.920000e-40 176.0
97 TraesCS7B01G139000 chr3D 95.238 105 5 0 4318 4422 523325560 523325664 3.560000e-37 167.0
98 TraesCS7B01G139000 chr6B 95.673 208 6 1 2727 2931 222010427 222010220 1.190000e-86 331.0
99 TraesCS7B01G139000 chr6B 96.296 108 4 0 4318 4425 711763256 711763149 1.650000e-40 178.0
100 TraesCS7B01G139000 chr6B 96.190 105 4 0 4318 4422 1158251 1158147 7.650000e-39 172.0
101 TraesCS7B01G139000 chr6B 92.373 118 9 0 4306 4423 136521431 136521548 9.900000e-38 169.0
102 TraesCS7B01G139000 chr4D 99.206 126 1 0 2720 2845 12279464 12279339 1.610000e-55 228.0
103 TraesCS7B01G139000 chr4D 95.283 106 5 0 4318 4423 39410780 39410675 9.900000e-38 169.0
104 TraesCS7B01G139000 chr3B 97.674 129 2 1 2718 2846 796796869 796796996 2.700000e-53 220.0
105 TraesCS7B01G139000 chrUn 100.000 105 0 0 4318 4422 35885901 35885797 1.630000e-45 195.0
106 TraesCS7B01G139000 chrUn 92.793 111 8 0 4312 4422 138274132 138274242 1.660000e-35 161.0
107 TraesCS7B01G139000 chrUn 94.286 105 6 0 4318 4422 172121617 172121513 1.660000e-35 161.0
108 TraesCS7B01G139000 chrUn 93.396 106 7 0 4318 4423 37054872 37054977 2.140000e-34 158.0
109 TraesCS7B01G139000 chrUn 92.593 108 8 0 4315 4422 77508705 77508812 7.710000e-34 156.0
110 TraesCS7B01G139000 chrUn 91.892 111 9 0 4312 4422 138347993 138348103 7.710000e-34 156.0
111 TraesCS7B01G139000 chrUn 91.892 111 9 0 4312 4422 138417706 138417816 7.710000e-34 156.0
112 TraesCS7B01G139000 chrUn 91.892 111 9 0 4312 4422 138486772 138486882 7.710000e-34 156.0
113 TraesCS7B01G139000 chrUn 93.333 105 7 0 4318 4422 171110552 171110448 7.710000e-34 156.0
114 TraesCS7B01G139000 chrUn 91.892 111 9 0 4312 4422 312020781 312020891 7.710000e-34 156.0
115 TraesCS7B01G139000 chrUn 89.344 122 12 1 4312 4432 231397180 231397059 9.970000e-33 152.0
116 TraesCS7B01G139000 chrUn 87.023 131 15 2 4294 4422 260324604 260324734 4.640000e-31 147.0
117 TraesCS7B01G139000 chr4B 97.222 108 3 0 4318 4425 483271060 483271167 3.540000e-42 183.0
118 TraesCS7B01G139000 chr4B 93.805 113 6 1 4318 4429 489652862 489652974 9.900000e-38 169.0
119 TraesCS7B01G139000 chr4B 92.857 112 8 0 4311 4422 274388395 274388506 4.610000e-36 163.0
120 TraesCS7B01G139000 chr5B 97.143 105 3 0 4318 4422 381026294 381026190 1.650000e-40 178.0
121 TraesCS7B01G139000 chr5B 97.143 105 3 0 4318 4422 665971386 665971282 1.650000e-40 178.0
122 TraesCS7B01G139000 chr5D 95.238 105 5 0 4318 4422 554363620 554363516 3.560000e-37 167.0
123 TraesCS7B01G139000 chr5D 90.598 117 10 1 4318 4433 544700489 544700373 2.770000e-33 154.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G139000 chr7B 175192346 175198091 5745 False 10611.000000 10611 100.000000 1 5746 1 chr7B.!!$F1 5745
1 TraesCS7B01G139000 chr7B 175718529 175722491 3962 True 1373.666667 3393 92.717333 287 5484 3 chr7B.!!$R3 5197
2 TraesCS7B01G139000 chr7B 175611242 175616528 5286 True 815.833333 2850 92.069000 285 5432 6 chr7B.!!$R2 5147
3 TraesCS7B01G139000 chr7A 641235331 641236674 1343 True 2355.000000 2355 98.291000 2727 4071 1 chr7A.!!$R2 1344
4 TraesCS7B01G139000 chr7A 357348218 357349478 1260 True 2217.000000 2217 98.414000 2844 4103 1 chr7A.!!$R1 1259
5 TraesCS7B01G139000 chr7A 236348932 236356880 7948 False 1208.571429 3703 92.342000 285 5745 7 chr7A.!!$F5 5460
6 TraesCS7B01G139000 chr7A 236079632 236083602 3970 False 1079.200000 3393 93.358200 285 5484 5 chr7A.!!$F3 5199
7 TraesCS7B01G139000 chr7A 236376942 236382464 5522 False 918.400000 2588 91.862000 1054 5745 5 chr7A.!!$F6 4691
8 TraesCS7B01G139000 chr7A 236323437 236328792 5355 False 846.833333 3393 93.589667 285 5484 6 chr7A.!!$F4 5199
9 TraesCS7B01G139000 chr7A 236448243 236448753 510 False 804.000000 804 94.961000 2132 2646 1 chr7A.!!$F2 514
10 TraesCS7B01G139000 chr7A 236430864 236432261 1397 False 465.500000 833 92.627750 2636 5484 4 chr7A.!!$F7 2848
11 TraesCS7B01G139000 chr7A 236458799 236462032 3233 False 455.250000 771 92.841250 2636 5484 4 chr7A.!!$F8 2848
12 TraesCS7B01G139000 chr7D 221693929 221697539 3610 True 1717.333333 3428 93.343000 285 5342 3 chr7D.!!$R3 5057
13 TraesCS7B01G139000 chr7D 221296458 221300274 3816 False 1288.250000 3439 91.679750 285 5484 4 chr7D.!!$F3 5199
14 TraesCS7B01G139000 chr7D 221685265 221689381 4116 False 964.400000 2850 92.294400 285 5484 5 chr7D.!!$F5 5199
15 TraesCS7B01G139000 chr7D 221581112 221584942 3830 False 592.500000 922 91.349750 412 5484 4 chr7D.!!$F4 5072
16 TraesCS7B01G139000 chr5A 598579693 598580945 1252 False 2218.000000 2218 98.643000 2840 4090 1 chr5A.!!$F1 1250
17 TraesCS7B01G139000 chr5A 483273243 483276613 3370 False 1213.000000 2217 95.013500 2695 4103 2 chr5A.!!$F2 1408
18 TraesCS7B01G139000 chr6A 386107986 386109245 1259 False 2217.000000 2217 98.414000 2844 4103 1 chr6A.!!$F2 1259
19 TraesCS7B01G139000 chr1B 574236886 574238146 1260 False 2211.000000 2211 98.335000 2844 4103 1 chr1B.!!$F3 1259
20 TraesCS7B01G139000 chr1A 22086705 22087959 1254 False 2211.000000 2211 98.486000 2844 4096 1 chr1A.!!$F1 1252
21 TraesCS7B01G139000 chr2B 676548338 676549595 1257 False 2207.000000 2207 98.332000 2847 4104 1 chr2B.!!$F3 1257
22 TraesCS7B01G139000 chr1D 247478793 247480052 1259 True 2206.000000 2206 98.255000 2844 4103 1 chr1D.!!$R1 1259

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
792 1097 0.036875 AGTAGCCTTTGTGCTCACCC 59.963 55.000 0.0 0.0 41.68 4.61 F
793 1098 0.036875 GTAGCCTTTGTGCTCACCCT 59.963 55.000 0.0 0.0 41.68 4.34 F
2172 5082 0.987294 ACAACCCAGACTATGCTGCT 59.013 50.000 0.0 0.0 34.56 4.24 F
2232 5142 1.683011 CCTCCAAATTGCCCTCGTCAT 60.683 52.381 0.0 0.0 0.00 3.06 F
3536 8427 1.998315 CTTCTGGCATTCTCTGTGACG 59.002 52.381 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2722 5651 2.093181 ACAACATAGGCGGAGTTATGCA 60.093 45.455 0.00 0.0 32.97 3.96 R
2723 5652 2.544267 GACAACATAGGCGGAGTTATGC 59.456 50.000 0.00 0.0 32.97 3.14 R
4153 9057 0.178903 AGAAGTCACCCACCTGGCTA 60.179 55.000 0.00 0.0 37.83 3.93 R
4180 9084 5.636903 AGGAGTGGTGCTATAATCAACAT 57.363 39.130 0.00 0.0 33.28 2.71 R
5134 13869 0.027586 CTATGGGCTTGCGCGTTTAC 59.972 55.000 8.43 0.0 36.88 2.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.919348 TTTTACGGCGATTGTATATTTTCTTAC 57.081 29.630 16.62 0.00 0.00 2.34
50 51 5.978919 ACGGCGATTGTATATTTTCTTACGA 59.021 36.000 16.62 0.00 0.00 3.43
51 52 6.643770 ACGGCGATTGTATATTTTCTTACGAT 59.356 34.615 16.62 0.00 0.00 3.73
52 53 7.148853 ACGGCGATTGTATATTTTCTTACGATC 60.149 37.037 16.62 0.00 36.50 3.69
53 54 7.061905 CGGCGATTGTATATTTTCTTACGATCT 59.938 37.037 0.00 0.00 37.20 2.75
54 55 9.350357 GGCGATTGTATATTTTCTTACGATCTA 57.650 33.333 0.00 0.00 37.20 1.98
104 105 8.944212 ACTTACGAAACATAAAATTACAGTGC 57.056 30.769 0.00 0.00 0.00 4.40
105 106 8.561212 ACTTACGAAACATAAAATTACAGTGCA 58.439 29.630 0.00 0.00 0.00 4.57
107 108 9.900710 TTACGAAACATAAAATTACAGTGCATT 57.099 25.926 0.00 0.00 0.00 3.56
108 109 8.226543 ACGAAACATAAAATTACAGTGCATTG 57.773 30.769 7.79 7.79 0.00 2.82
109 110 7.328249 ACGAAACATAAAATTACAGTGCATTGG 59.672 33.333 14.25 0.00 0.00 3.16
110 111 7.328249 CGAAACATAAAATTACAGTGCATTGGT 59.672 33.333 14.25 3.71 0.00 3.67
111 112 7.887996 AACATAAAATTACAGTGCATTGGTG 57.112 32.000 14.25 0.61 0.00 4.17
112 113 6.397272 ACATAAAATTACAGTGCATTGGTGG 58.603 36.000 14.25 0.00 0.00 4.61
113 114 4.953940 AAAATTACAGTGCATTGGTGGT 57.046 36.364 14.25 0.00 0.00 4.16
114 115 7.177568 ACATAAAATTACAGTGCATTGGTGGTA 59.822 33.333 14.25 0.00 0.00 3.25
115 116 6.412362 AAAATTACAGTGCATTGGTGGTAA 57.588 33.333 14.25 3.55 0.00 2.85
117 118 6.412362 AATTACAGTGCATTGGTGGTAAAA 57.588 33.333 14.25 0.00 0.00 1.52
118 119 6.603940 ATTACAGTGCATTGGTGGTAAAAT 57.396 33.333 14.25 0.00 0.00 1.82
119 120 7.710676 ATTACAGTGCATTGGTGGTAAAATA 57.289 32.000 14.25 0.00 0.00 1.40
120 121 5.643379 ACAGTGCATTGGTGGTAAAATAG 57.357 39.130 14.25 0.00 0.00 1.73
121 122 5.076873 ACAGTGCATTGGTGGTAAAATAGT 58.923 37.500 14.25 0.00 0.00 2.12
122 123 5.048083 ACAGTGCATTGGTGGTAAAATAGTG 60.048 40.000 14.25 0.00 0.00 2.74
124 125 3.766591 TGCATTGGTGGTAAAATAGTGGG 59.233 43.478 0.00 0.00 0.00 4.61
125 126 3.132111 GCATTGGTGGTAAAATAGTGGGG 59.868 47.826 0.00 0.00 0.00 4.96
126 127 3.459710 TTGGTGGTAAAATAGTGGGGG 57.540 47.619 0.00 0.00 0.00 5.40
128 129 2.041891 TGGTGGTAAAATAGTGGGGGTG 59.958 50.000 0.00 0.00 0.00 4.61
129 130 2.309458 GGTGGTAAAATAGTGGGGGTGA 59.691 50.000 0.00 0.00 0.00 4.02
130 131 3.245336 GGTGGTAAAATAGTGGGGGTGAA 60.245 47.826 0.00 0.00 0.00 3.18
133 134 4.354387 TGGTAAAATAGTGGGGGTGAAGAA 59.646 41.667 0.00 0.00 0.00 2.52
134 135 5.015817 TGGTAAAATAGTGGGGGTGAAGAAT 59.984 40.000 0.00 0.00 0.00 2.40
135 136 6.217900 TGGTAAAATAGTGGGGGTGAAGAATA 59.782 38.462 0.00 0.00 0.00 1.75
136 137 7.120716 GGTAAAATAGTGGGGGTGAAGAATAA 58.879 38.462 0.00 0.00 0.00 1.40
137 138 7.067859 GGTAAAATAGTGGGGGTGAAGAATAAC 59.932 40.741 0.00 0.00 0.00 1.89
140 141 7.707467 AATAGTGGGGGTGAAGAATAACTAT 57.293 36.000 0.00 0.00 32.43 2.12
141 142 7.707467 ATAGTGGGGGTGAAGAATAACTATT 57.293 36.000 0.00 0.00 0.00 1.73
142 143 6.002653 AGTGGGGGTGAAGAATAACTATTC 57.997 41.667 1.83 1.83 41.78 1.75
143 144 5.104067 AGTGGGGGTGAAGAATAACTATTCC 60.104 44.000 5.95 0.00 42.29 3.01
144 145 5.043762 TGGGGGTGAAGAATAACTATTCCT 58.956 41.667 5.95 0.00 42.29 3.36
145 146 5.132144 TGGGGGTGAAGAATAACTATTCCTC 59.868 44.000 5.95 4.07 42.29 3.71
150 151 6.884472 TGAAGAATAACTATTCCTCACCCA 57.116 37.500 6.65 0.00 42.29 4.51
151 152 6.889198 TGAAGAATAACTATTCCTCACCCAG 58.111 40.000 6.65 0.00 42.29 4.45
152 153 5.896073 AGAATAACTATTCCTCACCCAGG 57.104 43.478 5.95 0.00 42.29 4.45
153 154 4.660771 AGAATAACTATTCCTCACCCAGGG 59.339 45.833 2.85 2.85 43.67 4.45
155 156 5.687706 GAATAACTATTCCTCACCCAGGGTG 60.688 48.000 31.06 31.06 43.50 4.61
156 157 7.827072 GAATAACTATTCCTCACCCAGGGTGA 61.827 46.154 35.32 35.32 45.54 4.02
157 158 9.736671 GAATAACTATTCCTCACCCAGGGTGAC 62.737 48.148 34.62 17.53 44.45 3.67
164 165 3.393854 ACCCAGGGTGACGAATAGT 57.606 52.632 11.70 0.00 32.98 2.12
555 836 7.990886 AGTTATGTCCTTACTTTTGTGAACTGA 59.009 33.333 0.00 0.00 0.00 3.41
560 841 6.417930 GTCCTTACTTTTGTGAACTGAATTGC 59.582 38.462 0.00 0.00 0.00 3.56
626 929 6.672266 TCTAGCCTAGGGATCTAAAACATG 57.328 41.667 11.72 0.00 0.00 3.21
792 1097 0.036875 AGTAGCCTTTGTGCTCACCC 59.963 55.000 0.00 0.00 41.68 4.61
793 1098 0.036875 GTAGCCTTTGTGCTCACCCT 59.963 55.000 0.00 0.00 41.68 4.34
863 2520 5.225129 CGTTCACGTTTCTTTTGTTTCTCTG 59.775 40.000 0.00 0.00 34.11 3.35
1439 4323 4.259970 CGCTGATGTGTGAGTATTACTTGC 60.260 45.833 0.00 0.00 0.00 4.01
1495 4379 8.031277 CCAGCTTTTTGTATTTATTTCTGAGCT 58.969 33.333 0.00 0.00 36.14 4.09
1662 4550 4.836125 ATATAAAAGGATGTGCTTGCCG 57.164 40.909 0.00 0.00 0.00 5.69
1786 4676 9.791820 GTTGAAAGGTAAGCTAACTTTTGTTTA 57.208 29.630 10.39 0.00 45.18 2.01
1993 4903 1.591703 GCTTAGCTTTGTTGGGGCC 59.408 57.895 0.00 0.00 0.00 5.80
2172 5082 0.987294 ACAACCCAGACTATGCTGCT 59.013 50.000 0.00 0.00 34.56 4.24
2232 5142 1.683011 CCTCCAAATTGCCCTCGTCAT 60.683 52.381 0.00 0.00 0.00 3.06
2323 5236 4.082026 GCTAAATGAATTGCTGGTTGGACT 60.082 41.667 0.00 0.00 0.00 3.85
2342 5255 4.951094 GGACTAGCCTCTCTCTTCTGTTTA 59.049 45.833 0.00 0.00 0.00 2.01
2426 5340 3.745975 TCAACTGAGAATGCGTTACAAGG 59.254 43.478 0.00 0.00 0.00 3.61
2427 5341 2.076863 ACTGAGAATGCGTTACAAGGC 58.923 47.619 0.00 0.00 40.04 4.35
2725 5654 9.890629 AAACTATATGAGAGTTCTGTTAATGCA 57.109 29.630 0.00 0.00 36.10 3.96
2788 5717 2.554563 GGGTAAAGGAGGAGGGTTGTA 58.445 52.381 0.00 0.00 0.00 2.41
3536 8427 1.998315 CTTCTGGCATTCTCTGTGACG 59.002 52.381 0.00 0.00 0.00 4.35
3571 8462 7.147976 CACAAAAGCTAAAAGGCAAGTTCTAT 58.852 34.615 0.00 0.00 34.17 1.98
3576 8467 7.142995 AGCTAAAAGGCAAGTTCTATAGGAT 57.857 36.000 0.00 0.00 34.17 3.24
3650 8542 3.120649 GCGACATGTTCAACAGTTAGGTC 60.121 47.826 0.00 0.00 0.00 3.85
3977 8869 2.239402 TGGAAGCTTGCTATCCATGTGA 59.761 45.455 19.34 0.00 38.30 3.58
4103 8997 6.128282 TGTTGTTGTTGTTGTTGTTGTTGTTT 60.128 30.769 0.00 0.00 0.00 2.83
4104 8998 5.799960 TGTTGTTGTTGTTGTTGTTGTTTG 58.200 33.333 0.00 0.00 0.00 2.93
4105 8999 5.351465 TGTTGTTGTTGTTGTTGTTGTTTGT 59.649 32.000 0.00 0.00 0.00 2.83
4112 9006 7.203910 TGTTGTTGTTGTTGTTTGTAGAGTTT 58.796 30.769 0.00 0.00 0.00 2.66
4153 9057 9.823647 GCCTATATATAGTTGCATAACACAGAT 57.176 33.333 16.78 0.00 39.30 2.90
4316 9220 3.126514 GTGATGTCTGCTGTTTCCATCTG 59.873 47.826 0.00 0.00 34.44 2.90
4318 9222 1.072806 TGTCTGCTGTTTCCATCTGCT 59.927 47.619 0.00 0.00 0.00 4.24
4329 9233 1.227089 CATCTGCTCCCTCCGTTCG 60.227 63.158 0.00 0.00 0.00 3.95
4330 9234 2.427245 ATCTGCTCCCTCCGTTCGG 61.427 63.158 4.74 4.74 0.00 4.30
4336 9240 1.538419 GCTCCCTCCGTTCGGAAATAG 60.538 57.143 14.79 12.07 33.41 1.73
4337 9241 1.755380 CTCCCTCCGTTCGGAAATAGT 59.245 52.381 14.79 0.00 33.41 2.12
4338 9242 2.167900 CTCCCTCCGTTCGGAAATAGTT 59.832 50.000 14.79 0.00 33.41 2.24
4342 9246 3.581755 CTCCGTTCGGAAATAGTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
4345 9249 4.390603 TCCGTTCGGAAATAGTTGTCATTG 59.609 41.667 11.66 0.00 0.00 2.82
4346 9250 4.390603 CCGTTCGGAAATAGTTGTCATTGA 59.609 41.667 5.19 0.00 0.00 2.57
4348 9252 6.367421 CGTTCGGAAATAGTTGTCATTGAAA 58.633 36.000 0.00 0.00 0.00 2.69
4349 9253 7.021196 CGTTCGGAAATAGTTGTCATTGAAAT 58.979 34.615 0.00 0.00 0.00 2.17
4350 9254 7.007367 CGTTCGGAAATAGTTGTCATTGAAATG 59.993 37.037 0.00 0.00 37.75 2.32
4351 9255 6.851609 TCGGAAATAGTTGTCATTGAAATGG 58.148 36.000 3.31 0.00 37.03 3.16
4352 9256 6.657117 TCGGAAATAGTTGTCATTGAAATGGA 59.343 34.615 3.31 0.00 37.03 3.41
4354 9258 7.433131 CGGAAATAGTTGTCATTGAAATGGATG 59.567 37.037 3.31 0.00 37.03 3.51
4355 9259 8.253113 GGAAATAGTTGTCATTGAAATGGATGT 58.747 33.333 3.31 0.00 37.03 3.06
4359 9263 6.248433 AGTTGTCATTGAAATGGATGTACCT 58.752 36.000 3.31 0.00 39.86 3.08
4362 9266 7.194112 TGTCATTGAAATGGATGTACCTAGA 57.806 36.000 3.31 0.00 39.86 2.43
4363 9267 7.805163 TGTCATTGAAATGGATGTACCTAGAT 58.195 34.615 3.31 0.00 39.86 1.98
4364 9268 7.716560 TGTCATTGAAATGGATGTACCTAGATG 59.283 37.037 3.31 0.00 39.86 2.90
4365 9269 7.716998 GTCATTGAAATGGATGTACCTAGATGT 59.283 37.037 3.31 0.00 39.86 3.06
4366 9270 8.933653 TCATTGAAATGGATGTACCTAGATGTA 58.066 33.333 3.31 0.00 39.86 2.29
4367 9271 9.730705 CATTGAAATGGATGTACCTAGATGTAT 57.269 33.333 0.00 0.00 39.86 2.29
4398 9359 9.383519 GTTCTAGATACATCCATTTTGAAGACA 57.616 33.333 0.00 0.00 0.00 3.41
4399 9360 9.958180 TTCTAGATACATCCATTTTGAAGACAA 57.042 29.630 0.00 0.00 0.00 3.18
4400 9361 9.605275 TCTAGATACATCCATTTTGAAGACAAG 57.395 33.333 0.00 0.00 37.32 3.16
4403 9364 9.739276 AGATACATCCATTTTGAAGACAAGTAA 57.261 29.630 0.00 0.00 37.32 2.24
4407 9368 8.306761 ACATCCATTTTGAAGACAAGTAATTCC 58.693 33.333 0.00 0.00 37.32 3.01
4412 9373 5.585500 TTGAAGACAAGTAATTCCGAACG 57.415 39.130 0.00 0.00 0.00 3.95
4557 9522 5.711506 TCTGTGCAACCATCTGATAATTTGT 59.288 36.000 0.00 0.00 34.36 2.83
4558 9523 5.953183 TGTGCAACCATCTGATAATTTGTC 58.047 37.500 0.00 0.00 34.36 3.18
4569 9538 9.447040 CATCTGATAATTTGTCACACATGATTC 57.553 33.333 0.00 0.00 37.14 2.52
4683 9652 6.820656 AGAAGCCAATCTTGTAACTCACATAG 59.179 38.462 0.00 0.00 36.90 2.23
4715 9684 5.952947 ACTAGCTCTACAAGTACCAGTGATT 59.047 40.000 0.00 0.00 0.00 2.57
4834 9842 7.377928 GCTATTTTGCTGCATTATCTTACTGTG 59.622 37.037 1.84 0.00 0.00 3.66
4883 9891 2.159282 CCCTTATGTCGTACGTTGCTCT 60.159 50.000 16.05 0.00 0.00 4.09
4962 11423 9.783256 GTTGTTGTAGAAAGTTATTGAAACTGT 57.217 29.630 0.00 0.00 0.00 3.55
4994 13287 1.112113 ACCTCACTCTGTTCGTGTGT 58.888 50.000 0.00 0.00 38.09 3.72
5046 13391 6.025896 GTGTGTTGCACATCATAATCTCTTG 58.974 40.000 5.22 0.00 46.32 3.02
5134 13869 4.646960 TCATGTTTATGTGACGAATTGCG 58.353 39.130 0.00 0.00 39.60 4.85
5209 13946 6.569179 ATGACAAAAGCCGTTAAACTATGT 57.431 33.333 0.00 0.00 0.00 2.29
5306 14078 2.363683 GAAAGAGTGAGCCCCATTCTG 58.636 52.381 3.14 0.00 40.44 3.02
5343 14115 8.611757 GTTTACAAACTGGCATGAGAAAATTTT 58.388 29.630 2.28 2.28 36.03 1.82
5349 14121 5.244626 ACTGGCATGAGAAAATTTTAGCTGT 59.755 36.000 2.75 4.90 0.00 4.40
5350 14122 6.100404 TGGCATGAGAAAATTTTAGCTGTT 57.900 33.333 2.75 0.00 0.00 3.16
5382 14156 8.253113 CCTTTATTAGCCTGACATGACAAAATT 58.747 33.333 0.00 0.00 0.00 1.82
5388 14162 5.049167 GCCTGACATGACAAAATTTCACAA 58.951 37.500 0.00 0.00 0.00 3.33
5407 14183 0.834687 ACGACCTCTGGTTAAGGGCA 60.835 55.000 0.00 0.00 42.62 5.36
5410 14186 0.541863 ACCTCTGGTTAAGGGCATCG 59.458 55.000 0.00 0.00 38.29 3.84
5485 14398 7.507616 AGGTCAAATAAACCTTGTACCAATTGA 59.492 33.333 7.12 0.00 44.93 2.57
5487 14400 7.812669 GTCAAATAAACCTTGTACCAATTGAGG 59.187 37.037 7.12 7.80 0.00 3.86
5489 14402 4.463050 AAACCTTGTACCAATTGAGGGA 57.537 40.909 7.12 0.00 0.00 4.20
5491 14404 5.789574 AACCTTGTACCAATTGAGGGATA 57.210 39.130 7.12 0.00 0.00 2.59
5492 14405 5.112129 ACCTTGTACCAATTGAGGGATAC 57.888 43.478 7.12 2.47 0.00 2.24
5493 14406 4.538490 ACCTTGTACCAATTGAGGGATACA 59.462 41.667 7.12 4.93 39.74 2.29
5494 14407 5.014755 ACCTTGTACCAATTGAGGGATACAA 59.985 40.000 7.12 11.57 39.74 2.41
5495 14408 5.357032 CCTTGTACCAATTGAGGGATACAAC 59.643 44.000 7.12 0.00 39.74 3.32
5497 14410 5.496556 TGTACCAATTGAGGGATACAACAG 58.503 41.667 7.12 0.00 39.74 3.16
5498 14411 4.927267 ACCAATTGAGGGATACAACAGA 57.073 40.909 7.12 0.00 39.74 3.41
5499 14412 4.589908 ACCAATTGAGGGATACAACAGAC 58.410 43.478 7.12 0.00 39.74 3.51
5502 14415 5.106157 CCAATTGAGGGATACAACAGACAAC 60.106 44.000 7.12 0.00 39.74 3.32
5503 14416 4.974645 TTGAGGGATACAACAGACAACT 57.025 40.909 0.00 0.00 39.74 3.16
5504 14417 6.620877 ATTGAGGGATACAACAGACAACTA 57.379 37.500 0.00 0.00 39.74 2.24
5505 14418 5.661056 TGAGGGATACAACAGACAACTAG 57.339 43.478 0.00 0.00 39.74 2.57
5506 14419 5.084519 TGAGGGATACAACAGACAACTAGT 58.915 41.667 0.00 0.00 39.74 2.57
5507 14420 6.250711 TGAGGGATACAACAGACAACTAGTA 58.749 40.000 0.00 0.00 39.74 1.82
5508 14421 6.377429 TGAGGGATACAACAGACAACTAGTAG 59.623 42.308 0.00 0.00 39.74 2.57
5509 14422 5.127356 AGGGATACAACAGACAACTAGTAGC 59.873 44.000 0.00 0.00 39.74 3.58
5511 14424 5.805994 GGATACAACAGACAACTAGTAGCAC 59.194 44.000 0.00 0.00 0.00 4.40
5512 14425 4.939052 ACAACAGACAACTAGTAGCACT 57.061 40.909 0.00 0.00 0.00 4.40
5513 14426 5.277857 ACAACAGACAACTAGTAGCACTT 57.722 39.130 0.00 0.00 0.00 3.16
5516 14429 8.118976 ACAACAGACAACTAGTAGCACTTATA 57.881 34.615 0.00 0.00 0.00 0.98
5517 14430 8.027771 ACAACAGACAACTAGTAGCACTTATAC 58.972 37.037 0.00 0.00 0.00 1.47
5518 14431 7.698506 ACAGACAACTAGTAGCACTTATACA 57.301 36.000 0.00 0.00 0.00 2.29
5519 14432 8.294954 ACAGACAACTAGTAGCACTTATACAT 57.705 34.615 0.00 0.00 0.00 2.29
5520 14433 8.750298 ACAGACAACTAGTAGCACTTATACATT 58.250 33.333 0.00 0.00 0.00 2.71
5550 14901 6.653320 ACTGTCAAAATAAATAGCTTCACCGA 59.347 34.615 0.00 0.00 0.00 4.69
5555 14906 4.706842 ATAAATAGCTTCACCGACCCAT 57.293 40.909 0.00 0.00 0.00 4.00
5556 14907 5.818678 ATAAATAGCTTCACCGACCCATA 57.181 39.130 0.00 0.00 0.00 2.74
5560 14911 5.818678 ATAGCTTCACCGACCCATAATTA 57.181 39.130 0.00 0.00 0.00 1.40
5597 14948 0.035439 TCGGCCCATGAGGAGAAAAC 60.035 55.000 0.00 0.00 38.24 2.43
5601 14952 1.821136 GCCCATGAGGAGAAAACAAGG 59.179 52.381 0.00 0.00 38.24 3.61
5607 14958 4.771114 TGAGGAGAAAACAAGGAACTCA 57.229 40.909 0.00 0.00 38.49 3.41
5608 14959 5.310409 TGAGGAGAAAACAAGGAACTCAT 57.690 39.130 0.00 0.00 38.49 2.90
5616 14967 7.386059 AGAAAACAAGGAACTCATTTTGTTGT 58.614 30.769 2.63 0.00 41.43 3.32
5619 14970 6.136541 ACAAGGAACTCATTTTGTTGTCTC 57.863 37.500 0.00 0.00 38.49 3.36
5625 14976 5.560966 ACTCATTTTGTTGTCTCGTTTGT 57.439 34.783 0.00 0.00 0.00 2.83
5628 14979 6.537301 ACTCATTTTGTTGTCTCGTTTGTAGA 59.463 34.615 0.00 0.00 0.00 2.59
5629 14980 7.065324 ACTCATTTTGTTGTCTCGTTTGTAGAA 59.935 33.333 0.00 0.00 0.00 2.10
5631 14982 8.067784 TCATTTTGTTGTCTCGTTTGTAGAATC 58.932 33.333 0.00 0.00 0.00 2.52
5632 14983 5.570262 TTGTTGTCTCGTTTGTAGAATCG 57.430 39.130 0.00 0.00 0.00 3.34
5634 14985 2.247637 TGTCTCGTTTGTAGAATCGCG 58.752 47.619 0.00 0.00 0.00 5.87
5635 14986 2.095617 TGTCTCGTTTGTAGAATCGCGA 60.096 45.455 13.09 13.09 0.00 5.87
5639 14990 4.043761 TCGTTTGTAGAATCGCGAAAAC 57.956 40.909 15.24 16.77 0.00 2.43
5641 14992 3.592383 CGTTTGTAGAATCGCGAAAACAC 59.408 43.478 23.72 16.17 0.00 3.32
5642 14993 3.427516 TTGTAGAATCGCGAAAACACG 57.572 42.857 15.24 0.00 0.00 4.49
5643 14994 1.722464 TGTAGAATCGCGAAAACACGG 59.278 47.619 15.24 0.00 0.00 4.94
5644 14995 1.723003 GTAGAATCGCGAAAACACGGT 59.277 47.619 15.24 0.00 0.00 4.83
5645 14996 2.068837 AGAATCGCGAAAACACGGTA 57.931 45.000 15.24 0.00 0.00 4.02
5646 14997 2.406130 AGAATCGCGAAAACACGGTAA 58.594 42.857 15.24 0.00 0.00 2.85
5647 14998 2.156310 AGAATCGCGAAAACACGGTAAC 59.844 45.455 15.24 0.00 0.00 2.50
5723 15074 3.070018 GCTGAATTCGGATATGGAGTGG 58.930 50.000 18.72 0.00 0.00 4.00
5745 15096 3.060895 GCGCCAATATATAGCTTCGACAC 59.939 47.826 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.919348 GTAAGAAAATATACAATCGCCGTAAAA 57.081 29.630 0.00 0.00 0.00 1.52
78 79 9.389570 GCACTGTAATTTTATGTTTCGTAAGTT 57.610 29.630 0.00 0.00 39.48 2.66
79 80 8.561212 TGCACTGTAATTTTATGTTTCGTAAGT 58.439 29.630 0.00 0.00 39.48 2.24
80 81 8.942669 TGCACTGTAATTTTATGTTTCGTAAG 57.057 30.769 0.00 0.00 0.00 2.34
84 85 7.328249 ACCAATGCACTGTAATTTTATGTTTCG 59.672 33.333 0.00 0.00 0.00 3.46
85 86 8.434661 CACCAATGCACTGTAATTTTATGTTTC 58.565 33.333 0.00 0.00 0.00 2.78
86 87 7.387397 CCACCAATGCACTGTAATTTTATGTTT 59.613 33.333 0.00 0.00 0.00 2.83
87 88 6.873076 CCACCAATGCACTGTAATTTTATGTT 59.127 34.615 0.00 0.00 0.00 2.71
90 91 6.603940 ACCACCAATGCACTGTAATTTTAT 57.396 33.333 0.00 0.00 0.00 1.40
91 92 7.526142 TTACCACCAATGCACTGTAATTTTA 57.474 32.000 0.00 0.00 0.00 1.52
92 93 4.953940 ACCACCAATGCACTGTAATTTT 57.046 36.364 0.00 0.00 0.00 1.82
93 94 6.412362 TTTACCACCAATGCACTGTAATTT 57.588 33.333 0.00 0.00 0.00 1.82
94 95 6.412362 TTTTACCACCAATGCACTGTAATT 57.588 33.333 0.00 0.00 0.00 1.40
95 96 6.603940 ATTTTACCACCAATGCACTGTAAT 57.396 33.333 0.00 0.00 0.00 1.89
97 98 6.150307 CACTATTTTACCACCAATGCACTGTA 59.850 38.462 0.00 0.00 0.00 2.74
98 99 5.048083 CACTATTTTACCACCAATGCACTGT 60.048 40.000 0.00 0.00 0.00 3.55
99 100 5.401550 CACTATTTTACCACCAATGCACTG 58.598 41.667 0.00 0.00 0.00 3.66
100 101 4.462483 CCACTATTTTACCACCAATGCACT 59.538 41.667 0.00 0.00 0.00 4.40
101 102 4.381505 CCCACTATTTTACCACCAATGCAC 60.382 45.833 0.00 0.00 0.00 4.57
102 103 3.766591 CCCACTATTTTACCACCAATGCA 59.233 43.478 0.00 0.00 0.00 3.96
103 104 3.132111 CCCCACTATTTTACCACCAATGC 59.868 47.826 0.00 0.00 0.00 3.56
104 105 3.704061 CCCCCACTATTTTACCACCAATG 59.296 47.826 0.00 0.00 0.00 2.82
105 106 3.338519 ACCCCCACTATTTTACCACCAAT 59.661 43.478 0.00 0.00 0.00 3.16
107 108 2.041891 CACCCCCACTATTTTACCACCA 59.958 50.000 0.00 0.00 0.00 4.17
108 109 2.309458 TCACCCCCACTATTTTACCACC 59.691 50.000 0.00 0.00 0.00 4.61
109 110 3.724732 TCACCCCCACTATTTTACCAC 57.275 47.619 0.00 0.00 0.00 4.16
110 111 3.917629 TCTTCACCCCCACTATTTTACCA 59.082 43.478 0.00 0.00 0.00 3.25
111 112 4.579647 TCTTCACCCCCACTATTTTACC 57.420 45.455 0.00 0.00 0.00 2.85
112 113 7.832685 AGTTATTCTTCACCCCCACTATTTTAC 59.167 37.037 0.00 0.00 0.00 2.01
113 114 7.935405 AGTTATTCTTCACCCCCACTATTTTA 58.065 34.615 0.00 0.00 0.00 1.52
114 115 6.800890 AGTTATTCTTCACCCCCACTATTTT 58.199 36.000 0.00 0.00 0.00 1.82
115 116 6.402981 AGTTATTCTTCACCCCCACTATTT 57.597 37.500 0.00 0.00 0.00 1.40
117 118 7.202195 GGAATAGTTATTCTTCACCCCCACTAT 60.202 40.741 10.71 0.00 41.33 2.12
118 119 6.100714 GGAATAGTTATTCTTCACCCCCACTA 59.899 42.308 10.71 0.00 41.33 2.74
119 120 5.104067 GGAATAGTTATTCTTCACCCCCACT 60.104 44.000 10.71 0.00 41.33 4.00
120 121 5.104067 AGGAATAGTTATTCTTCACCCCCAC 60.104 44.000 10.71 0.00 41.33 4.61
121 122 5.043762 AGGAATAGTTATTCTTCACCCCCA 58.956 41.667 10.71 0.00 41.33 4.96
122 123 5.132144 TGAGGAATAGTTATTCTTCACCCCC 59.868 44.000 17.60 0.23 46.85 5.40
128 129 6.292150 CCTGGGTGAGGAATAGTTATTCTTC 58.708 44.000 13.90 13.90 46.33 2.87
129 130 5.132816 CCCTGGGTGAGGAATAGTTATTCTT 59.867 44.000 3.97 4.41 46.33 2.52
130 131 4.660771 CCCTGGGTGAGGAATAGTTATTCT 59.339 45.833 3.97 0.00 46.33 2.40
133 134 4.022359 ACCCTGGGTGAGGAATAGTTAT 57.978 45.455 19.82 0.00 46.33 1.89
134 135 3.502051 ACCCTGGGTGAGGAATAGTTA 57.498 47.619 19.82 0.00 46.33 2.24
135 136 2.361085 ACCCTGGGTGAGGAATAGTT 57.639 50.000 19.82 0.00 46.33 2.24
272 273 9.952030 CATGGTAATCTATCTCTACTCTCTACA 57.048 37.037 0.00 0.00 0.00 2.74
273 274 8.889717 GCATGGTAATCTATCTCTACTCTCTAC 58.110 40.741 0.00 0.00 0.00 2.59
275 276 7.698912 AGCATGGTAATCTATCTCTACTCTCT 58.301 38.462 0.00 0.00 0.00 3.10
276 277 7.938140 AGCATGGTAATCTATCTCTACTCTC 57.062 40.000 0.00 0.00 0.00 3.20
277 278 8.052748 CCTAGCATGGTAATCTATCTCTACTCT 58.947 40.741 6.04 0.00 0.00 3.24
278 279 7.284489 CCCTAGCATGGTAATCTATCTCTACTC 59.716 44.444 6.04 0.00 0.00 2.59
279 280 7.122715 CCCTAGCATGGTAATCTATCTCTACT 58.877 42.308 6.04 0.00 0.00 2.57
280 281 6.183360 GCCCTAGCATGGTAATCTATCTCTAC 60.183 46.154 6.04 0.00 39.53 2.59
282 283 4.714308 GCCCTAGCATGGTAATCTATCTCT 59.286 45.833 6.04 0.00 39.53 3.10
283 284 4.714308 AGCCCTAGCATGGTAATCTATCTC 59.286 45.833 6.04 0.00 43.56 2.75
555 836 2.291800 ACTAGTTGGGGCATCAGCAATT 60.292 45.455 0.00 0.00 44.61 2.32
560 841 2.171237 TCATCACTAGTTGGGGCATCAG 59.829 50.000 0.00 0.00 0.00 2.90
792 1097 4.763793 ACCACCATGAACATGAAAAGAGAG 59.236 41.667 15.21 0.33 41.20 3.20
793 1098 4.520111 CACCACCATGAACATGAAAAGAGA 59.480 41.667 15.21 0.00 41.20 3.10
863 2520 2.224257 TGGGAAAGGCAAAATGCTTGAC 60.224 45.455 2.00 0.00 44.28 3.18
993 2650 6.299805 ACCTTGTCAGCTAACATATCTTGA 57.700 37.500 0.00 0.00 0.00 3.02
1439 4323 7.378461 ACAAATTAACTACGATGTTGTGCAAAG 59.622 33.333 0.00 0.00 0.00 2.77
1495 4379 7.589587 CGTTAGAAAACAACTGCAACATCATTA 59.410 33.333 0.00 0.00 35.16 1.90
1581 4465 9.301153 GGTTAACCATTGATCAAATATGAACAC 57.699 33.333 20.12 3.27 35.71 3.32
1662 4550 9.472361 AATAGTCATACAATACATACACGGAAC 57.528 33.333 0.00 0.00 0.00 3.62
1786 4676 8.524487 AGTAACGATATTGAAGAGAAGTTGACT 58.476 33.333 0.00 0.00 0.00 3.41
1841 4733 9.230122 TCAACATGCTAGATGAATGAAAAACTA 57.770 29.630 0.00 0.00 35.24 2.24
1927 4819 6.166279 TGAGCAATTGAGGTAGTGAAAGTAG 58.834 40.000 10.34 0.00 0.00 2.57
1946 4838 2.815503 CTGGTTGTGTGATCATTGAGCA 59.184 45.455 0.00 0.00 0.00 4.26
1993 4903 6.314896 AGAACAGGCGAGATTTCTGAAAATAG 59.685 38.462 6.95 1.36 35.21 1.73
2232 5142 5.620206 TCAGTTGGTTCAATAAGCTCTGAA 58.380 37.500 0.00 0.00 39.37 3.02
2323 5236 6.665992 TGTTTAAACAGAAGAGAGAGGCTA 57.334 37.500 17.01 0.00 34.30 3.93
2426 5340 8.488651 AGTACCACAATATTAAAGTACACAGC 57.511 34.615 16.93 0.00 34.03 4.40
2605 5526 6.855763 TTGCCATCCAATTTACAGAAATCT 57.144 33.333 0.00 0.00 34.01 2.40
2606 5527 6.313658 GGTTTGCCATCCAATTTACAGAAATC 59.686 38.462 0.00 0.00 32.57 2.17
2699 5627 9.890629 TGCATTAACAGAACTCTCATATAGTTT 57.109 29.630 0.00 0.00 37.31 2.66
2712 5641 4.495844 GGCGGAGTTATGCATTAACAGAAC 60.496 45.833 3.54 1.59 42.30 3.01
2713 5642 3.625764 GGCGGAGTTATGCATTAACAGAA 59.374 43.478 3.54 0.00 42.30 3.02
2714 5643 3.118408 AGGCGGAGTTATGCATTAACAGA 60.118 43.478 3.54 0.00 42.30 3.41
2715 5644 3.206150 AGGCGGAGTTATGCATTAACAG 58.794 45.455 3.54 5.05 42.30 3.16
2716 5645 3.275617 AGGCGGAGTTATGCATTAACA 57.724 42.857 3.54 0.00 42.30 2.41
2717 5646 4.755123 ACATAGGCGGAGTTATGCATTAAC 59.245 41.667 3.54 7.66 40.50 2.01
2718 5647 4.968259 ACATAGGCGGAGTTATGCATTAA 58.032 39.130 3.54 0.00 32.97 1.40
2719 5648 4.617253 ACATAGGCGGAGTTATGCATTA 57.383 40.909 3.54 0.00 32.97 1.90
2720 5649 3.492102 ACATAGGCGGAGTTATGCATT 57.508 42.857 3.54 0.00 32.97 3.56
2721 5650 3.141398 CAACATAGGCGGAGTTATGCAT 58.859 45.455 3.79 3.79 32.97 3.96
2722 5651 2.093181 ACAACATAGGCGGAGTTATGCA 60.093 45.455 0.00 0.00 32.97 3.96
2723 5652 2.544267 GACAACATAGGCGGAGTTATGC 59.456 50.000 0.00 0.00 32.97 3.14
2724 5653 4.051922 GAGACAACATAGGCGGAGTTATG 58.948 47.826 0.00 0.00 34.83 1.90
2725 5654 3.704566 TGAGACAACATAGGCGGAGTTAT 59.295 43.478 0.00 0.00 0.00 1.89
3101 7991 6.015350 GTCCTATCTTAATCGGGAAGTCATCA 60.015 42.308 0.00 0.00 0.00 3.07
3261 8151 8.711170 CCATAACTCTAACTTCCTATTTACCCA 58.289 37.037 0.00 0.00 0.00 4.51
3536 8427 1.889545 AGCTTTTGTGGCACTCTCTC 58.110 50.000 19.83 5.50 0.00 3.20
3571 8462 2.428925 GGGTCGAACCGCCATCCTA 61.429 63.158 2.28 0.00 39.83 2.94
3650 8542 0.530650 AACATACGCATCTCCGCCAG 60.531 55.000 0.00 0.00 0.00 4.85
4103 8997 6.380995 CAGCATGCATTAACAAAACTCTACA 58.619 36.000 21.98 0.00 0.00 2.74
4104 8998 6.859715 CAGCATGCATTAACAAAACTCTAC 57.140 37.500 21.98 0.00 0.00 2.59
4153 9057 0.178903 AGAAGTCACCCACCTGGCTA 60.179 55.000 0.00 0.00 37.83 3.93
4180 9084 5.636903 AGGAGTGGTGCTATAATCAACAT 57.363 39.130 0.00 0.00 33.28 2.71
4316 9220 0.462789 TATTTCCGAACGGAGGGAGC 59.537 55.000 15.34 0.00 46.06 4.70
4318 9222 1.856629 ACTATTTCCGAACGGAGGGA 58.143 50.000 15.34 7.17 46.06 4.20
4329 9233 8.253113 ACATCCATTTCAATGACAACTATTTCC 58.747 33.333 0.81 0.00 38.70 3.13
4336 9240 6.515272 AGGTACATCCATTTCAATGACAAC 57.485 37.500 0.81 0.00 38.70 3.32
4337 9241 7.629157 TCTAGGTACATCCATTTCAATGACAA 58.371 34.615 0.81 0.00 38.70 3.18
4338 9242 7.194112 TCTAGGTACATCCATTTCAATGACA 57.806 36.000 0.81 0.00 38.70 3.58
4372 9276 9.383519 TGTCTTCAAAATGGATGTATCTAGAAC 57.616 33.333 0.00 0.00 0.00 3.01
4373 9277 9.958180 TTGTCTTCAAAATGGATGTATCTAGAA 57.042 29.630 0.00 0.00 0.00 2.10
4389 9327 5.049954 CCGTTCGGAATTACTTGTCTTCAAA 60.050 40.000 5.19 0.00 32.87 2.69
4391 9329 3.991773 CCGTTCGGAATTACTTGTCTTCA 59.008 43.478 5.19 0.00 0.00 3.02
4392 9330 4.240096 TCCGTTCGGAATTACTTGTCTTC 58.760 43.478 11.66 0.00 0.00 2.87
4398 9359 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
4399 9360 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4400 9361 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4403 9364 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
4406 9367 2.305009 ACTAATACTCCCTCCGTTCGG 58.695 52.381 4.74 4.74 0.00 4.30
4407 9368 5.936956 AGTATACTAATACTCCCTCCGTTCG 59.063 44.000 2.75 0.00 44.05 3.95
4412 9373 6.912951 TGCAAGTATACTAATACTCCCTCC 57.087 41.667 5.65 0.00 46.17 4.30
4557 9522 8.940768 TCAGATAAATAACGAATCATGTGTGA 57.059 30.769 0.00 0.00 39.04 3.58
4558 9523 9.590088 CATCAGATAAATAACGAATCATGTGTG 57.410 33.333 0.00 0.00 0.00 3.82
4569 9538 5.410746 AGAGCATGCCATCAGATAAATAACG 59.589 40.000 15.66 0.00 0.00 3.18
4669 9638 4.988540 GTGTCACTGCTATGTGAGTTACAA 59.011 41.667 7.75 0.00 46.09 2.41
4683 9652 3.057174 ACTTGTAGAGCTAGTGTCACTGC 60.057 47.826 16.03 15.70 32.18 4.40
4834 9842 5.074584 AGCTTAGCTAAGGTAGAACACAC 57.925 43.478 31.46 12.97 41.72 3.82
4883 9891 1.644509 TCTCAGTTCCAGCCAAGCTA 58.355 50.000 0.00 0.00 36.40 3.32
4962 11423 6.533730 ACAGAGTGAGGTAAAATCAATGTGA 58.466 36.000 7.41 0.00 38.01 3.58
5134 13869 0.027586 CTATGGGCTTGCGCGTTTAC 59.972 55.000 8.43 0.00 36.88 2.01
5268 14039 8.600625 CACTCTTTCCATGAAATGCATTTTATG 58.399 33.333 33.77 33.77 44.97 1.90
5306 14078 5.915196 GCCAGTTTGTAAACTCTTTGATCAC 59.085 40.000 7.02 0.00 45.65 3.06
5349 14121 4.261801 GTCAGGCTAATAAAGGTGCAGAA 58.738 43.478 0.00 0.00 0.00 3.02
5350 14122 3.263170 TGTCAGGCTAATAAAGGTGCAGA 59.737 43.478 0.00 0.00 0.00 4.26
5382 14156 3.493699 CCTTAACCAGAGGTCGTTGTGAA 60.494 47.826 0.00 0.00 33.12 3.18
5388 14162 0.834687 TGCCCTTAACCAGAGGTCGT 60.835 55.000 0.00 0.00 33.12 4.34
5407 14183 2.496899 AAGACTTGCCATCCAACGAT 57.503 45.000 0.00 0.00 0.00 3.73
5410 14186 4.072131 TCTTGTAAGACTTGCCATCCAAC 58.928 43.478 0.00 0.00 0.00 3.77
5485 14398 5.127356 GCTACTAGTTGTCTGTTGTATCCCT 59.873 44.000 0.00 0.00 0.00 4.20
5487 14400 5.805994 GTGCTACTAGTTGTCTGTTGTATCC 59.194 44.000 0.00 0.00 0.00 2.59
5489 14402 6.591750 AGTGCTACTAGTTGTCTGTTGTAT 57.408 37.500 0.00 0.00 0.00 2.29
5491 14404 4.939052 AGTGCTACTAGTTGTCTGTTGT 57.061 40.909 0.00 0.00 0.00 3.32
5492 14405 8.027189 TGTATAAGTGCTACTAGTTGTCTGTTG 58.973 37.037 0.00 0.00 0.00 3.33
5493 14406 8.118976 TGTATAAGTGCTACTAGTTGTCTGTT 57.881 34.615 0.00 0.00 0.00 3.16
5494 14407 7.698506 TGTATAAGTGCTACTAGTTGTCTGT 57.301 36.000 0.00 0.00 0.00 3.41
5524 14437 7.174253 TCGGTGAAGCTATTTATTTTGACAGTT 59.826 33.333 0.00 0.00 0.00 3.16
5525 14438 6.653320 TCGGTGAAGCTATTTATTTTGACAGT 59.347 34.615 0.00 0.00 0.00 3.55
5526 14439 6.961554 GTCGGTGAAGCTATTTATTTTGACAG 59.038 38.462 0.00 0.00 0.00 3.51
5527 14440 6.128117 GGTCGGTGAAGCTATTTATTTTGACA 60.128 38.462 0.00 0.00 0.00 3.58
5528 14441 6.255950 GGTCGGTGAAGCTATTTATTTTGAC 58.744 40.000 0.00 0.00 0.00 3.18
5529 14442 5.355910 GGGTCGGTGAAGCTATTTATTTTGA 59.644 40.000 0.00 0.00 0.00 2.69
5532 14445 4.850680 TGGGTCGGTGAAGCTATTTATTT 58.149 39.130 0.00 0.00 0.00 1.40
5537 14888 4.706842 ATTATGGGTCGGTGAAGCTATT 57.293 40.909 0.00 0.00 0.00 1.73
5550 14901 0.831966 TGCGGTCGGTAATTATGGGT 59.168 50.000 0.00 0.00 0.00 4.51
5555 14906 1.144496 GGCCTGCGGTCGGTAATTA 59.856 57.895 0.00 0.00 0.00 1.40
5556 14907 2.124860 GGCCTGCGGTCGGTAATT 60.125 61.111 0.00 0.00 0.00 1.40
5575 14926 1.198094 TTCTCCTCATGGGCCGAACA 61.198 55.000 0.00 0.00 34.39 3.18
5577 14928 0.695924 TTTTCTCCTCATGGGCCGAA 59.304 50.000 0.00 0.00 34.39 4.30
5578 14929 0.035439 GTTTTCTCCTCATGGGCCGA 60.035 55.000 0.00 0.00 34.39 5.54
5580 14931 1.821136 CTTGTTTTCTCCTCATGGGCC 59.179 52.381 0.00 0.00 34.39 5.80
5583 14934 4.401925 AGTTCCTTGTTTTCTCCTCATGG 58.598 43.478 0.00 0.00 0.00 3.66
5584 14935 5.065914 TGAGTTCCTTGTTTTCTCCTCATG 58.934 41.667 0.00 0.00 0.00 3.07
5585 14936 5.310409 TGAGTTCCTTGTTTTCTCCTCAT 57.690 39.130 0.00 0.00 0.00 2.90
5586 14937 4.771114 TGAGTTCCTTGTTTTCTCCTCA 57.229 40.909 0.00 0.00 0.00 3.86
5587 14938 6.641169 AAATGAGTTCCTTGTTTTCTCCTC 57.359 37.500 0.00 0.00 0.00 3.71
5597 14948 5.207768 CGAGACAACAAAATGAGTTCCTTG 58.792 41.667 0.00 0.00 0.00 3.61
5601 14952 6.027749 ACAAACGAGACAACAAAATGAGTTC 58.972 36.000 0.00 0.00 0.00 3.01
5607 14958 7.069569 CGATTCTACAAACGAGACAACAAAAT 58.930 34.615 0.00 0.00 29.57 1.82
5608 14959 6.415702 CGATTCTACAAACGAGACAACAAAA 58.584 36.000 0.00 0.00 29.57 2.44
5616 14967 2.905959 TCGCGATTCTACAAACGAGA 57.094 45.000 3.71 0.00 34.94 4.04
5619 14970 3.592383 GTGTTTTCGCGATTCTACAAACG 59.408 43.478 20.57 0.00 0.00 3.60
5632 14983 1.439201 GCCGTTACCGTGTTTTCGC 60.439 57.895 0.00 0.00 0.00 4.70
5634 14985 0.662085 TTGGCCGTTACCGTGTTTTC 59.338 50.000 0.00 0.00 0.00 2.29
5635 14986 0.381445 GTTGGCCGTTACCGTGTTTT 59.619 50.000 0.00 0.00 0.00 2.43
5639 14990 1.572447 CAAGTTGGCCGTTACCGTG 59.428 57.895 0.00 0.00 0.00 4.94
5641 14992 1.296056 CTCCAAGTTGGCCGTTACCG 61.296 60.000 17.68 0.00 37.47 4.02
5642 14993 1.583495 GCTCCAAGTTGGCCGTTACC 61.583 60.000 17.68 0.00 37.47 2.85
5643 14994 0.605589 AGCTCCAAGTTGGCCGTTAC 60.606 55.000 17.68 2.67 37.47 2.50
5644 14995 0.605319 CAGCTCCAAGTTGGCCGTTA 60.605 55.000 17.68 0.00 37.47 3.18
5645 14996 1.898574 CAGCTCCAAGTTGGCCGTT 60.899 57.895 17.68 5.84 37.47 4.44
5646 14997 2.281761 CAGCTCCAAGTTGGCCGT 60.282 61.111 17.68 0.36 37.47 5.68
5647 14998 0.962356 ATTCAGCTCCAAGTTGGCCG 60.962 55.000 17.68 11.39 37.47 6.13
5648 14999 1.203287 GAATTCAGCTCCAAGTTGGCC 59.797 52.381 17.68 10.36 37.47 5.36
5654 15005 2.099141 TGTCCGAATTCAGCTCCAAG 57.901 50.000 6.22 0.00 0.00 3.61
5689 15040 4.178540 CGAATTCAGCTCCAATTTGCATT 58.821 39.130 6.22 0.00 0.00 3.56
5690 15041 3.429822 CCGAATTCAGCTCCAATTTGCAT 60.430 43.478 6.22 0.00 0.00 3.96
5697 15048 3.390967 TCCATATCCGAATTCAGCTCCAA 59.609 43.478 6.22 0.00 0.00 3.53
5723 15074 3.060895 GTGTCGAAGCTATATATTGGCGC 59.939 47.826 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.