Multiple sequence alignment - TraesCS2D01G333800

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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 TraesCS2D01G333800 chr2D 100.000 3719 0 0 1 3719 427447136 427443418 0.000000e+00 6868.0
1 TraesCS2D01G333800 chr2D 100.000 1568 0 0 4143 5710 427442994 427441427 0.000000e+00 2896.0
2 TraesCS2D01G333800 chr2D 84.606 825 117 5 2790 3612 611223928 611223112 0.000000e+00 811.0
3 TraesCS2D01G333800 chr2D 83.313 827 130 6 2788 3612 611233840 611233020 0.000000e+00 756.0
4 TraesCS2D01G333800 chr2D 83.902 615 85 12 4143 4757 611222840 611222240 4.960000e-160 575.0
5 TraesCS2D01G333800 chr2D 84.896 576 65 16 2232 2793 611234651 611234084 3.860000e-156 562.0
6 TraesCS2D01G333800 chr2D 84.642 573 55 18 2230 2793 611224726 611224178 1.810000e-149 540.0
7 TraesCS2D01G333800 chr2D 82.496 617 96 11 4143 4757 611232751 611232145 1.090000e-146 531.0
8 TraesCS2D01G333800 chr2D 78.103 580 91 25 4144 4710 427329059 427328503 9.170000e-88 335.0
9 TraesCS2D01G333800 chr2D 88.789 223 16 5 1529 1746 427335951 427335733 1.220000e-66 265.0
10 TraesCS2D01G333800 chr2D 84.074 270 37 5 900 1164 611236777 611236509 7.340000e-64 255.0
11 TraesCS2D01G333800 chr2D 87.615 218 25 2 2016 2231 611235119 611234902 9.500000e-63 252.0
12 TraesCS2D01G333800 chr2D 82.155 297 47 5 874 1164 611227195 611226899 3.420000e-62 250.0
13 TraesCS2D01G333800 chr2D 89.109 202 16 5 1591 1789 611226357 611226159 4.420000e-61 246.0
14 TraesCS2D01G333800 chr2D 88.835 206 15 4 1591 1789 611235989 611235785 4.420000e-61 246.0
15 TraesCS2D01G333800 chr2D 86.636 217 28 1 2016 2231 611225471 611225255 7.390000e-59 239.0
16 TraesCS2D01G333800 chr2D 78.763 372 27 28 1363 1710 427337288 427336945 9.700000e-48 202.0
17 TraesCS2D01G333800 chr2D 81.356 236 31 7 2113 2346 540221906 540221682 4.550000e-41 180.0
18 TraesCS2D01G333800 chr2A 94.506 1984 83 12 1644 3612 561023285 561025257 0.000000e+00 3037.0
19 TraesCS2D01G333800 chr2A 93.533 835 31 10 4881 5704 561082912 561083734 0.000000e+00 1221.0
20 TraesCS2D01G333800 chr2A 94.173 738 41 2 4143 4878 561025529 561026266 0.000000e+00 1123.0
21 TraesCS2D01G333800 chr2A 84.541 828 118 6 2788 3612 743562644 743561824 0.000000e+00 811.0
22 TraesCS2D01G333800 chr2A 83.313 809 124 10 2810 3612 743575348 743574545 0.000000e+00 736.0
23 TraesCS2D01G333800 chr2A 86.349 608 45 18 573 1169 561022160 561022740 3.760000e-176 628.0
24 TraesCS2D01G333800 chr2A 85.540 574 62 14 2233 2793 743576549 743575984 1.070000e-161 580.0
25 TraesCS2D01G333800 chr2A 85.294 578 61 16 2229 2793 743564761 743564195 4.960000e-160 575.0
26 TraesCS2D01G333800 chr2A 82.276 615 97 11 4145 4757 743574276 743573672 6.560000e-144 521.0
27 TraesCS2D01G333800 chr2A 76.857 579 102 25 4144 4710 561270066 561270624 1.200000e-76 298.0
28 TraesCS2D01G333800 chr2A 87.149 249 21 2 1257 1496 561022742 561022988 7.290000e-69 272.0
29 TraesCS2D01G333800 chr2A 88.182 220 22 3 1529 1745 561265035 561265253 5.680000e-65 259.0
30 TraesCS2D01G333800 chr2A 87.500 216 26 1 2016 2230 743565223 743565008 1.230000e-61 248.0
31 TraesCS2D01G333800 chr2A 88.038 209 23 2 2025 2231 743577005 743576797 4.420000e-61 246.0
32 TraesCS2D01G333800 chr2A 88.614 202 17 5 1591 1789 743566112 743565914 2.060000e-59 241.0
33 TraesCS2D01G333800 chr2A 81.544 298 47 6 875 1164 743568205 743567908 7.390000e-59 239.0
34 TraesCS2D01G333800 chr2A 84.274 248 36 2 920 1164 743578687 743578440 7.390000e-59 239.0
35 TraesCS2D01G333800 chr2A 73.893 655 114 44 2139 2764 561267965 561268591 5.800000e-50 209.0
36 TraesCS2D01G333800 chr2A 85.938 192 16 5 1592 1776 743577907 743577720 1.620000e-45 195.0
37 TraesCS2D01G333800 chr2A 96.491 114 4 0 1491 1604 561023171 561023284 7.550000e-44 189.0
38 TraesCS2D01G333800 chr2A 89.888 89 9 0 1168 1256 71661281 71661369 1.300000e-21 115.0
39 TraesCS2D01G333800 chr2A 87.500 96 11 1 1445 1540 561263374 561263468 6.050000e-20 110.0
40 TraesCS2D01G333800 chr2A 96.296 54 2 0 3666 3719 743574405 743574352 7.880000e-14 89.8
41 TraesCS2D01G333800 chr2B 89.713 1429 104 17 2216 3612 504322108 504320691 0.000000e+00 1784.0
42 TraesCS2D01G333800 chr2B 87.850 1177 94 25 22 1172 504325841 504324688 0.000000e+00 1336.0
43 TraesCS2D01G333800 chr2B 93.990 832 39 6 4881 5708 512487289 512486465 0.000000e+00 1249.0
44 TraesCS2D01G333800 chr2B 92.464 836 39 4 4881 5708 504319136 504318317 0.000000e+00 1173.0
45 TraesCS2D01G333800 chr2B 92.422 739 52 4 4143 4877 504320465 504319727 0.000000e+00 1051.0
46 TraesCS2D01G333800 chr2B 84.360 812 118 4 2803 3612 746110454 746109650 0.000000e+00 787.0
47 TraesCS2D01G333800 chr2B 82.027 829 123 11 2788 3612 746138419 746137613 0.000000e+00 682.0
48 TraesCS2D01G333800 chr2B 85.294 578 61 15 2230 2793 746111288 746110721 4.960000e-160 575.0
49 TraesCS2D01G333800 chr2B 84.775 578 63 19 2232 2793 746139228 746138660 1.800000e-154 556.0
50 TraesCS2D01G333800 chr2B 83.010 618 91 13 4143 4757 746137353 746136747 1.080000e-151 547.0
51 TraesCS2D01G333800 chr2B 82.764 615 92 12 4143 4757 746109378 746108778 2.340000e-148 536.0
52 TraesCS2D01G333800 chr2B 77.375 579 99 23 4144 4710 504199271 504198713 1.190000e-81 315.0
53 TraesCS2D01G333800 chr2B 93.617 188 11 1 1591 1777 504324417 504324230 4.360000e-71 279.0
54 TraesCS2D01G333800 chr2B 89.950 199 14 5 1594 1789 746112907 746112712 9.500000e-63 252.0
55 TraesCS2D01G333800 chr2B 82.237 304 42 9 881 1174 746115997 746115696 9.500000e-63 252.0
56 TraesCS2D01G333800 chr2B 73.677 775 139 44 2025 2766 504201203 504200461 2.060000e-59 241.0
57 TraesCS2D01G333800 chr2B 86.636 217 28 1 2016 2231 746112031 746111815 7.390000e-59 239.0
58 TraesCS2D01G333800 chr2B 91.279 172 9 3 1610 1776 746140562 746140392 4.450000e-56 230.0
59 TraesCS2D01G333800 chr2B 87.255 204 19 7 2004 2206 504323906 504323709 5.760000e-55 226.0
60 TraesCS2D01G333800 chr2B 85.321 218 31 1 948 1164 746141332 746141115 2.070000e-54 224.0
61 TraesCS2D01G333800 chr2B 85.202 223 25 6 2016 2231 746139700 746139479 7.450000e-54 222.0
62 TraesCS2D01G333800 chr2B 94.118 119 5 2 1630 1746 504206204 504206086 4.550000e-41 180.0
63 TraesCS2D01G333800 chr2B 76.902 368 33 22 1362 1708 504208504 504208168 1.650000e-35 161.0
64 TraesCS2D01G333800 chr2B 93.519 108 7 0 3612 3719 504320658 504320551 1.650000e-35 161.0
65 TraesCS2D01G333800 chr2B 80.952 84 5 4 1502 1584 504324511 504324438 7.990000e-04 56.5
66 TraesCS2D01G333800 chr4A 85.141 249 31 5 2109 2354 37901851 37901606 3.420000e-62 250.0
67 TraesCS2D01G333800 chr5D 85.306 245 31 4 2109 2351 290662367 290662608 1.230000e-61 248.0
68 TraesCS2D01G333800 chr5B 86.550 171 18 5 2186 2354 650991853 650991686 3.510000e-42 183.0
69 TraesCS2D01G333800 chr5B 93.182 88 4 1 1169 1256 510889264 510889179 1.670000e-25 128.0
70 TraesCS2D01G333800 chr5B 92.222 90 5 1 1169 1256 664882949 664882860 6.010000e-25 126.0
71 TraesCS2D01G333800 chr4D 82.584 178 16 9 298 460 468897567 468897744 5.960000e-30 143.0
72 TraesCS2D01G333800 chr4D 78.049 123 25 2 245 367 104641704 104641824 6.130000e-10 76.8
73 TraesCS2D01G333800 chr3A 92.222 90 5 1 1169 1256 732768760 732768849 6.010000e-25 126.0
74 TraesCS2D01G333800 chr3A 92.222 90 5 1 1169 1256 732768849 732768760 6.010000e-25 126.0
75 TraesCS2D01G333800 chr3A 87.000 100 7 4 1165 1259 38429456 38429358 2.180000e-19 108.0
76 TraesCS2D01G333800 chr3B 90.110 91 5 1 1169 1259 130118020 130117934 1.300000e-21 115.0
77 TraesCS2D01G333800 chr4B 89.362 94 5 2 1168 1256 615554397 615554490 4.680000e-21 113.0
78 TraesCS2D01G333800 chr5A 89.011 91 8 1 1168 1256 653666214 653666124 1.680000e-20 111.0
79 TraesCS2D01G333800 chr6B 82.000 100 16 2 269 367 220069182 220069280 3.670000e-12 84.2
80 TraesCS2D01G333800 chr1B 76.667 180 21 14 59 235 662014662 662014823 4.740000e-11 80.5
81 TraesCS2D01G333800 chr7D 81.690 71 11 2 2681 2750 187106883 187106814 2.220000e-04 58.4
82 TraesCS2D01G333800 chr7B 88.889 45 5 0 2681 2725 329854554 329854510 7.990000e-04 56.5


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 TraesCS2D01G333800 chr2D 427441427 427447136 5709 True 4882.000000 6868 100.000000 1 5710 2 chr2D.!!$R4 5709
1 TraesCS2D01G333800 chr2D 611222240 611227195 4955 True 443.500000 811 85.175000 874 4757 6 chr2D.!!$R5 3883
2 TraesCS2D01G333800 chr2D 611232145 611236777 4632 True 433.666667 756 85.204833 900 4757 6 chr2D.!!$R6 3857
3 TraesCS2D01G333800 chr2D 427328503 427329059 556 True 335.000000 335 78.103000 4144 4710 1 chr2D.!!$R1 566
4 TraesCS2D01G333800 chr2D 427335733 427337288 1555 True 233.500000 265 83.776000 1363 1746 2 chr2D.!!$R3 383
5 TraesCS2D01G333800 chr2A 561082912 561083734 822 False 1221.000000 1221 93.533000 4881 5704 1 chr2A.!!$F2 823
6 TraesCS2D01G333800 chr2A 561022160 561026266 4106 False 1049.800000 3037 91.733600 573 4878 5 chr2A.!!$F3 4305
7 TraesCS2D01G333800 chr2A 743561824 743568205 6381 True 422.800000 811 85.498600 875 3612 5 chr2A.!!$R1 2737
8 TraesCS2D01G333800 chr2A 743573672 743578687 5015 True 372.400000 736 86.525000 920 4757 7 chr2A.!!$R2 3837
9 TraesCS2D01G333800 chr2A 561263374 561270624 7250 False 219.000000 298 81.608000 1445 4710 4 chr2A.!!$F4 3265
10 TraesCS2D01G333800 chr2B 512486465 512487289 824 True 1249.000000 1249 93.990000 4881 5708 1 chr2B.!!$R1 827
11 TraesCS2D01G333800 chr2B 504318317 504325841 7524 True 758.312500 1784 89.724000 22 5708 8 chr2B.!!$R4 5686
12 TraesCS2D01G333800 chr2B 746108778 746115997 7219 True 440.166667 787 85.206833 881 4757 6 chr2B.!!$R5 3876
13 TraesCS2D01G333800 chr2B 746136747 746141332 4585 True 410.166667 682 85.269000 948 4757 6 chr2B.!!$R6 3809
14 TraesCS2D01G333800 chr2B 504198713 504201203 2490 True 278.000000 315 75.526000 2025 4710 2 chr2B.!!$R2 2685

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
231 233 0.036306 GGGCTTCACCGGAGAGAAAA 59.964 55.000 9.46 0.00 40.62 2.29 F
1183 1226 0.172803 CTGTTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30 F
1184 1227 0.251297 TGTTACTCCCTCCGTTCGGA 60.251 55.000 13.34 13.34 0.00 4.55 F
1185 1228 0.890683 GTTACTCCCTCCGTTCGGAA 59.109 55.000 14.79 0.04 33.41 4.30 F
1196 1239 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19 F
1197 1240 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87 F
3184 15359 1.406180 CATCAATGAAATGCAGGCCGA 59.594 47.619 0.00 0.00 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1281 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 R
2976 15144 0.106268 TGCAGTTTGCCTTCTCCCAA 60.106 50.000 0.00 0.00 44.23 4.12 R
3159 15334 3.591023 CCTGCATTTCATTGATGTGCAA 58.409 40.909 20.18 9.84 44.20 4.08 R
3184 15359 0.325671 TCCGATCTTCCCCTTCTGCT 60.326 55.000 0.00 0.00 0.00 4.24 R
3278 15453 4.898829 TTACCATCCAAGCATGAATTCG 57.101 40.909 0.00 0.00 0.00 3.34 R
3353 15529 3.616956 TTCTTGGCGAGATCAATCTGT 57.383 42.857 5.02 0.00 37.25 3.41 R
5047 17997 0.315251 TCAGCTGGATAATCTCGCCG 59.685 55.000 15.13 0.00 0.00 6.46 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
17 18 4.513519 TGCTATCCAAAGGACGCG 57.486 55.556 3.53 3.53 35.22 6.01
18 19 1.813753 TGCTATCCAAAGGACGCGC 60.814 57.895 5.73 0.00 35.22 6.86
19 20 1.813753 GCTATCCAAAGGACGCGCA 60.814 57.895 5.73 0.00 32.98 6.09
20 21 2.006772 CTATCCAAAGGACGCGCAC 58.993 57.895 5.73 0.00 32.98 5.34
36 37 0.103208 GCACGGGTGACTCCTATGAG 59.897 60.000 2.38 0.00 44.62 2.90
50 51 2.232208 CCTATGAGTCGCTATGCCATGA 59.768 50.000 0.00 0.00 0.00 3.07
56 57 1.146930 CGCTATGCCATGACCCAGT 59.853 57.895 0.00 0.00 0.00 4.00
60 61 1.212688 CTATGCCATGACCCAGTCCAA 59.787 52.381 0.00 0.00 0.00 3.53
85 86 8.492673 AATTAGCTAAATGTCAGTCGATTGAA 57.507 30.769 12.63 3.97 0.00 2.69
103 105 9.364989 TCGATTGAATTTAAATTTGGGTCAATC 57.635 29.630 25.75 25.75 34.56 2.67
104 106 9.149225 CGATTGAATTTAAATTTGGGTCAATCA 57.851 29.630 29.82 15.86 35.99 2.57
118 120 5.048782 TGGGTCAATCAATTTTGAGAGTTCG 60.049 40.000 0.00 0.00 41.08 3.95
119 121 4.853743 GGTCAATCAATTTTGAGAGTTCGC 59.146 41.667 0.00 0.00 41.08 4.70
120 122 4.853743 GTCAATCAATTTTGAGAGTTCGCC 59.146 41.667 0.00 0.00 41.08 5.54
143 145 0.608640 GTGAGCCGGAGAGAAGGAAA 59.391 55.000 5.05 0.00 0.00 3.13
163 165 0.458716 GAGAAGAAAGGGGCTCGTCG 60.459 60.000 0.00 0.00 0.00 5.12
190 192 5.983540 GGCAACCCCATATCTATCTTAGAG 58.016 45.833 0.00 0.00 38.38 2.43
191 193 5.423886 GCAACCCCATATCTATCTTAGAGC 58.576 45.833 0.00 0.00 38.38 4.09
202 204 5.636123 TCTATCTTAGAGCTTAGGGTGAGG 58.364 45.833 0.00 0.00 0.00 3.86
203 205 4.544564 ATCTTAGAGCTTAGGGTGAGGA 57.455 45.455 0.00 0.00 0.00 3.71
207 209 0.971447 GAGCTTAGGGTGAGGACGGT 60.971 60.000 0.00 0.00 0.00 4.83
214 216 4.016706 GTGAGGACGGTGGTGGGG 62.017 72.222 0.00 0.00 0.00 4.96
219 221 3.948719 GACGGTGGTGGGGCTTCA 61.949 66.667 0.00 0.00 0.00 3.02
227 229 3.003173 TGGGGCTTCACCGGAGAG 61.003 66.667 9.46 3.50 40.62 3.20
231 233 0.036306 GGGCTTCACCGGAGAGAAAA 59.964 55.000 9.46 0.00 40.62 2.29
232 234 1.544759 GGGCTTCACCGGAGAGAAAAA 60.545 52.381 9.46 0.00 40.62 1.94
246 248 4.870190 AAAAACAGACGCGGGAGT 57.130 50.000 12.47 1.76 0.00 3.85
258 268 3.866582 GGGAGTGATGGCCGAGGG 61.867 72.222 0.00 0.00 0.00 4.30
377 387 3.646715 CCGGTGGCCTGGGAAGAA 61.647 66.667 3.32 0.00 0.00 2.52
378 388 2.045926 CGGTGGCCTGGGAAGAAG 60.046 66.667 3.32 0.00 0.00 2.85
379 389 2.592993 CGGTGGCCTGGGAAGAAGA 61.593 63.158 3.32 0.00 0.00 2.87
380 390 1.767692 GGTGGCCTGGGAAGAAGAA 59.232 57.895 3.32 0.00 0.00 2.52
384 394 0.679321 GGCCTGGGAAGAAGAAGCTG 60.679 60.000 0.00 0.00 0.00 4.24
396 406 3.906846 AGAAGAAGCTGGAGGAAGAAGAA 59.093 43.478 0.00 0.00 0.00 2.52
397 407 4.349342 AGAAGAAGCTGGAGGAAGAAGAAA 59.651 41.667 0.00 0.00 0.00 2.52
408 418 0.540597 AAGAAGAAAGGCTGCCACCC 60.541 55.000 22.65 8.73 0.00 4.61
430 440 1.031571 TTGATCTGCATCCAACGGCC 61.032 55.000 0.00 0.00 0.00 6.13
432 442 1.718757 GATCTGCATCCAACGGCCAC 61.719 60.000 2.24 0.00 0.00 5.01
441 451 1.154488 CAACGGCCACAAACGATCG 60.154 57.895 14.88 14.88 0.00 3.69
463 473 4.143200 CGACCGACTCAAATTCGAAATTCA 60.143 41.667 0.00 0.00 38.85 2.57
464 474 5.613795 CGACCGACTCAAATTCGAAATTCAA 60.614 40.000 0.00 0.00 38.85 2.69
510 521 1.144503 CCCAGCCCTCTGATTAAGCAT 59.855 52.381 0.00 0.00 42.95 3.79
512 523 2.621998 CCAGCCCTCTGATTAAGCATTG 59.378 50.000 0.00 0.00 42.95 2.82
524 535 9.764363 TCTGATTAAGCATTGTACTAATACAGG 57.236 33.333 0.00 0.00 42.29 4.00
547 558 1.338674 CGAGAAATGTGCACCCTACCA 60.339 52.381 15.69 0.00 0.00 3.25
603 614 1.356624 GTGTATTGGCTGATGCGGC 59.643 57.895 0.00 0.00 40.82 6.53
647 664 0.529833 GCTGCAGCTAGTCAGTCAGA 59.470 55.000 31.33 0.00 38.21 3.27
687 704 1.589993 CACAGCTACCGATCCGCAG 60.590 63.158 0.00 0.00 0.00 5.18
739 766 1.592064 TGCGAGCAATTCAACACAGA 58.408 45.000 0.00 0.00 0.00 3.41
741 768 1.722751 GCGAGCAATTCAACACAGACG 60.723 52.381 0.00 0.00 0.00 4.18
746 773 2.146342 CAATTCAACACAGACGGAGCT 58.854 47.619 0.00 0.00 0.00 4.09
758 785 2.932234 CGGAGCTTGTGTCGTCCCT 61.932 63.158 0.00 0.00 0.00 4.20
771 798 3.215151 GTCGTCCCTATCACTCTGATCA 58.785 50.000 0.00 0.00 38.26 2.92
772 799 3.632604 GTCGTCCCTATCACTCTGATCAA 59.367 47.826 0.00 0.00 38.26 2.57
773 800 4.098044 GTCGTCCCTATCACTCTGATCAAA 59.902 45.833 0.00 0.00 38.26 2.69
774 801 4.098044 TCGTCCCTATCACTCTGATCAAAC 59.902 45.833 0.00 0.00 38.26 2.93
775 802 4.142160 CGTCCCTATCACTCTGATCAAACA 60.142 45.833 0.00 0.00 38.26 2.83
859 889 3.876309 AAACACTACACATGGTTCCCT 57.124 42.857 0.00 0.00 0.00 4.20
860 890 2.859165 ACACTACACATGGTTCCCTG 57.141 50.000 0.00 0.00 0.00 4.45
861 891 1.271379 ACACTACACATGGTTCCCTGC 60.271 52.381 0.00 0.00 0.00 4.85
862 892 0.328258 ACTACACATGGTTCCCTGCC 59.672 55.000 0.00 0.00 0.00 4.85
863 893 0.327924 CTACACATGGTTCCCTGCCA 59.672 55.000 0.00 0.00 40.68 4.92
864 894 0.998928 TACACATGGTTCCCTGCCAT 59.001 50.000 0.00 0.00 46.77 4.40
885 915 2.836372 TGTGCCATCTCATCTCAGAAGT 59.164 45.455 0.00 0.00 0.00 3.01
933 964 3.865164 TCTGCTAAATATGCACACAGACG 59.135 43.478 0.00 0.00 36.37 4.18
961 1000 1.507140 TATAGGTGGTGCCAAGGGAG 58.493 55.000 0.00 0.00 40.61 4.30
984 1024 1.709147 CTGACGCTGCAACATAGCCC 61.709 60.000 0.00 0.00 37.90 5.19
988 1029 2.779033 GCTGCAACATAGCCCCTGC 61.779 63.158 0.00 0.00 35.15 4.85
999 1042 2.273449 CCCCTGCCATCACTCCAC 59.727 66.667 0.00 0.00 0.00 4.02
1168 1211 0.468226 TCAGGTTTCCACTCGCTGTT 59.532 50.000 0.00 0.00 0.00 3.16
1169 1212 1.689813 TCAGGTTTCCACTCGCTGTTA 59.310 47.619 0.00 0.00 0.00 2.41
1170 1213 1.798813 CAGGTTTCCACTCGCTGTTAC 59.201 52.381 0.00 0.00 0.00 2.50
1171 1214 1.692519 AGGTTTCCACTCGCTGTTACT 59.307 47.619 0.00 0.00 0.00 2.24
1172 1215 2.067013 GGTTTCCACTCGCTGTTACTC 58.933 52.381 0.00 0.00 0.00 2.59
1173 1216 2.067013 GTTTCCACTCGCTGTTACTCC 58.933 52.381 0.00 0.00 0.00 3.85
1174 1217 0.606604 TTCCACTCGCTGTTACTCCC 59.393 55.000 0.00 0.00 0.00 4.30
1175 1218 0.251653 TCCACTCGCTGTTACTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
1176 1219 0.173708 CCACTCGCTGTTACTCCCTC 59.826 60.000 0.00 0.00 0.00 4.30
1177 1220 0.173708 CACTCGCTGTTACTCCCTCC 59.826 60.000 0.00 0.00 0.00 4.30
1178 1221 1.313812 ACTCGCTGTTACTCCCTCCG 61.314 60.000 0.00 0.00 0.00 4.63
1179 1222 1.303888 TCGCTGTTACTCCCTCCGT 60.304 57.895 0.00 0.00 0.00 4.69
1180 1223 0.896940 TCGCTGTTACTCCCTCCGTT 60.897 55.000 0.00 0.00 0.00 4.44
1181 1224 0.458025 CGCTGTTACTCCCTCCGTTC 60.458 60.000 0.00 0.00 0.00 3.95
1182 1225 0.458025 GCTGTTACTCCCTCCGTTCG 60.458 60.000 0.00 0.00 0.00 3.95
1183 1226 0.172803 CTGTTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
1184 1227 0.251297 TGTTACTCCCTCCGTTCGGA 60.251 55.000 13.34 13.34 0.00 4.55
1185 1228 0.890683 GTTACTCCCTCCGTTCGGAA 59.109 55.000 14.79 0.04 33.41 4.30
1186 1229 1.479730 GTTACTCCCTCCGTTCGGAAT 59.520 52.381 14.79 2.09 33.41 3.01
1187 1230 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
1188 1231 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1189 1232 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1190 1233 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1191 1234 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1192 1235 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1193 1236 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1194 1237 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1195 1238 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
1196 1239 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
1197 1240 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
1198 1241 1.987770 GTTCGGAATTACTTGTCGCGA 59.012 47.619 3.71 3.71 0.00 5.87
1199 1242 2.350899 TCGGAATTACTTGTCGCGAA 57.649 45.000 12.06 0.00 0.00 4.70
1200 1243 2.674954 TCGGAATTACTTGTCGCGAAA 58.325 42.857 12.06 0.54 0.00 3.46
1201 1244 3.058450 TCGGAATTACTTGTCGCGAAAA 58.942 40.909 12.06 12.01 0.00 2.29
1202 1245 3.680937 TCGGAATTACTTGTCGCGAAAAT 59.319 39.130 13.05 5.74 0.00 1.82
1203 1246 3.778718 CGGAATTACTTGTCGCGAAAATG 59.221 43.478 13.05 9.32 0.00 2.32
1204 1247 4.095610 GGAATTACTTGTCGCGAAAATGG 58.904 43.478 13.05 4.35 0.00 3.16
1205 1248 4.142773 GGAATTACTTGTCGCGAAAATGGA 60.143 41.667 13.05 0.56 0.00 3.41
1206 1249 5.448632 GGAATTACTTGTCGCGAAAATGGAT 60.449 40.000 13.05 3.91 0.00 3.41
1207 1250 2.900122 ACTTGTCGCGAAAATGGATG 57.100 45.000 13.05 2.76 0.00 3.51
1208 1251 2.151202 ACTTGTCGCGAAAATGGATGT 58.849 42.857 13.05 3.46 0.00 3.06
1209 1252 3.331150 ACTTGTCGCGAAAATGGATGTA 58.669 40.909 13.05 0.00 0.00 2.29
1210 1253 3.938963 ACTTGTCGCGAAAATGGATGTAT 59.061 39.130 13.05 0.00 0.00 2.29
1211 1254 4.034048 ACTTGTCGCGAAAATGGATGTATC 59.966 41.667 13.05 0.00 0.00 2.24
1212 1255 3.792401 TGTCGCGAAAATGGATGTATCT 58.208 40.909 12.06 0.00 0.00 1.98
1213 1256 4.939271 TGTCGCGAAAATGGATGTATCTA 58.061 39.130 12.06 0.00 0.00 1.98
1214 1257 4.982295 TGTCGCGAAAATGGATGTATCTAG 59.018 41.667 12.06 0.00 0.00 2.43
1215 1258 5.220381 GTCGCGAAAATGGATGTATCTAGA 58.780 41.667 12.06 0.00 0.00 2.43
1216 1259 5.117287 GTCGCGAAAATGGATGTATCTAGAC 59.883 44.000 12.06 0.00 0.00 2.59
1217 1260 4.088638 CGCGAAAATGGATGTATCTAGACG 59.911 45.833 0.00 0.00 0.00 4.18
1218 1261 4.982916 GCGAAAATGGATGTATCTAGACGT 59.017 41.667 0.00 0.00 0.00 4.34
1219 1262 5.117287 GCGAAAATGGATGTATCTAGACGTC 59.883 44.000 7.70 7.70 35.04 4.34
1227 1270 6.677027 GATGTATCTAGACGTCCATTTTCG 57.323 41.667 13.01 0.00 30.39 3.46
1228 1271 5.823209 TGTATCTAGACGTCCATTTTCGA 57.177 39.130 13.01 0.00 0.00 3.71
1229 1272 5.817988 TGTATCTAGACGTCCATTTTCGAG 58.182 41.667 13.01 0.00 0.00 4.04
1230 1273 5.587443 TGTATCTAGACGTCCATTTTCGAGA 59.413 40.000 13.01 3.05 0.00 4.04
1231 1274 4.617808 TCTAGACGTCCATTTTCGAGAG 57.382 45.455 13.01 0.00 0.00 3.20
1232 1275 4.259356 TCTAGACGTCCATTTTCGAGAGA 58.741 43.478 13.01 0.00 39.20 3.10
1246 1289 4.012319 TCGAGAGAAGTAATTCCGAACG 57.988 45.455 0.00 1.81 37.03 3.95
1247 1290 3.106672 CGAGAGAAGTAATTCCGAACGG 58.893 50.000 6.94 6.94 0.00 4.44
1248 1291 3.181503 CGAGAGAAGTAATTCCGAACGGA 60.182 47.826 12.04 12.04 43.52 4.69
1249 1292 4.352887 GAGAGAAGTAATTCCGAACGGAG 58.647 47.826 15.34 0.00 46.06 4.63
1250 1293 3.130693 AGAGAAGTAATTCCGAACGGAGG 59.869 47.826 15.34 0.00 46.06 4.30
1251 1294 2.167900 AGAAGTAATTCCGAACGGAGGG 59.832 50.000 15.34 0.00 46.06 4.30
1252 1295 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1253 1296 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1271 1315 3.817647 GGGAGTACTTCATTGATCCATGC 59.182 47.826 2.92 0.00 0.00 4.06
1292 1343 2.818130 TAGCGTAGGTCGTTGGTTTT 57.182 45.000 0.00 0.00 42.13 2.43
1311 1362 5.971792 GGTTTTCTTTCTTAGTTCAGCACAC 59.028 40.000 0.00 0.00 0.00 3.82
1315 1366 6.545504 TCTTTCTTAGTTCAGCACACATTC 57.454 37.500 0.00 0.00 0.00 2.67
1327 1415 7.036996 TCAGCACACATTCTTTGTATGAAAA 57.963 32.000 0.00 0.00 34.53 2.29
1457 1561 5.121298 GTCCGGAATTAGTAACAAGTTGGAC 59.879 44.000 5.23 4.99 34.84 4.02
1587 6945 8.970859 ATCTGGTCTCCTCTTACAATTATTTG 57.029 34.615 0.00 0.00 38.86 2.32
1589 6947 8.260818 TCTGGTCTCCTCTTACAATTATTTGAG 58.739 37.037 4.42 0.00 36.64 3.02
1766 7146 2.188837 TCTTCTACACGCAGCGTATG 57.811 50.000 22.49 12.32 38.32 2.39
1845 7244 5.045286 AGGGAGTGAGAGCAACAGAAATTAT 60.045 40.000 0.00 0.00 0.00 1.28
1846 7245 5.649831 GGGAGTGAGAGCAACAGAAATTATT 59.350 40.000 0.00 0.00 0.00 1.40
1847 7246 6.404074 GGGAGTGAGAGCAACAGAAATTATTG 60.404 42.308 0.00 0.00 0.00 1.90
1984 9766 8.610896 CCAGCAAAGTAATTTTCATTTCAAACA 58.389 29.630 0.00 0.00 0.00 2.83
2307 12298 2.365582 GGAATGGACGCATACAGGTTT 58.634 47.619 0.00 0.00 0.00 3.27
2346 12337 9.347240 ACAAGAATTCTTCCAGGTATGATATTG 57.653 33.333 17.91 4.60 33.11 1.90
2479 12502 8.093307 TCTTAATGCATGATAGATGGAACTCTC 58.907 37.037 0.00 0.00 0.00 3.20
2576 12601 8.592998 GGTCGTCTAACTGTCAGTATTTAATTG 58.407 37.037 5.77 0.00 0.00 2.32
2577 12602 9.136952 GTCGTCTAACTGTCAGTATTTAATTGT 57.863 33.333 5.77 0.00 0.00 2.71
2608 12633 4.989279 ATCCAATGTACCAAACTGCATC 57.011 40.909 0.00 0.00 0.00 3.91
2827 14995 4.314740 TGCAAAATAACCAACTGACACC 57.685 40.909 0.00 0.00 0.00 4.16
3159 15334 6.290605 TCATCCATGAACGTGATTGATATGT 58.709 36.000 0.00 0.00 33.08 2.29
3184 15359 1.406180 CATCAATGAAATGCAGGCCGA 59.594 47.619 0.00 0.00 0.00 5.54
3366 15542 9.958234 TCTAGAAAAGAATACAGATTGATCTCG 57.042 33.333 0.00 0.00 34.22 4.04
3427 15606 0.547553 GAGGAGACTACCCCGAGAGT 59.452 60.000 0.00 0.00 44.43 3.24
3439 15618 6.837568 ACTACCCCGAGAGTATGAAAGAATTA 59.162 38.462 0.00 0.00 0.00 1.40
3442 15621 6.837568 ACCCCGAGAGTATGAAAGAATTAGTA 59.162 38.462 0.00 0.00 0.00 1.82
3492 15671 4.437682 AACAGTCTGAATTGGTGAAGGA 57.562 40.909 6.91 0.00 0.00 3.36
3608 15787 2.096013 GCTCAAGCAAATCTTACCGGTC 59.904 50.000 12.40 0.00 41.59 4.79
3648 15901 6.071391 CCAGCCTAACAATGTTAAGGAAATGT 60.071 38.462 18.94 0.00 0.00 2.71
3688 16016 4.057406 TGCTAACATTGCCCAATTATGC 57.943 40.909 0.00 0.00 0.00 3.14
4318 16650 4.469657 AGCAACCAGGTTCAAACTTATCA 58.530 39.130 0.12 0.00 0.00 2.15
4452 16789 0.543277 CCTTGATGCCCTGCTGAGTA 59.457 55.000 0.00 0.00 0.00 2.59
4464 16801 2.164422 CTGCTGAGTACGATCAGGTCAA 59.836 50.000 12.58 0.00 45.66 3.18
4474 16811 2.417924 CGATCAGGTCAAAGCTAGCACT 60.418 50.000 18.83 0.00 0.00 4.40
4640 16993 3.408634 CTTCGGGTTACACTTTGTGGAT 58.591 45.455 2.72 0.00 37.94 3.41
4715 17068 5.743117 AGGTTCCTCAAGAGATGATTTCAG 58.257 41.667 0.00 0.00 37.44 3.02
4761 17114 9.970395 GAGAAATTATGGATGCATTGTATTTGA 57.030 29.630 4.56 0.00 0.00 2.69
4774 17130 7.230510 TGCATTGTATTTGAGGTTTACTTCAGT 59.769 33.333 0.00 0.00 33.43 3.41
4779 17135 3.947910 TGAGGTTTACTTCAGTACCCG 57.052 47.619 0.00 0.00 29.05 5.28
4785 17141 6.226052 AGGTTTACTTCAGTACCCGTTTTAG 58.774 40.000 0.00 0.00 29.05 1.85
4835 17191 1.115467 CCTTCGTATGTGAGAGGCCT 58.885 55.000 3.86 3.86 0.00 5.19
4836 17192 1.202463 CCTTCGTATGTGAGAGGCCTG 60.202 57.143 12.00 0.00 0.00 4.85
4855 17212 5.874810 GGCCTGTTTGGAATAAAGGAATTTC 59.125 40.000 0.00 0.00 38.35 2.17
5031 17981 4.202121 GCTGCCTTCATGATCACATCAATT 60.202 41.667 0.00 0.00 43.50 2.32
5049 17999 6.494893 TCAATTCAGTTGACTAATTTCCGG 57.505 37.500 0.00 0.00 41.79 5.14
5056 18006 3.536956 TGACTAATTTCCGGCGAGATT 57.463 42.857 9.30 7.99 0.00 2.40
5067 18017 1.067283 CGGCGAGATTATCCAGCTGAT 60.067 52.381 17.39 9.50 36.38 2.90
5071 18021 4.060900 GCGAGATTATCCAGCTGATTTGA 58.939 43.478 17.39 3.73 34.76 2.69
5075 18025 6.292757 CGAGATTATCCAGCTGATTTGAACTG 60.293 42.308 17.39 0.00 34.76 3.16
5091 18041 4.507710 TGAACTGCCTACAAATAGCTGAG 58.492 43.478 0.00 0.00 0.00 3.35
5094 18044 2.871022 CTGCCTACAAATAGCTGAGCAG 59.129 50.000 7.39 0.00 40.33 4.24
5117 18067 4.794246 GCATTCTCTGTTACTCACTCGTAC 59.206 45.833 0.00 0.00 0.00 3.67
5124 18074 3.058708 TGTTACTCACTCGTACCAGTTCG 60.059 47.826 0.00 0.00 0.00 3.95
5129 18079 1.395954 CACTCGTACCAGTTCGATCGA 59.604 52.381 15.15 15.15 35.57 3.59
5138 18096 3.119137 ACCAGTTCGATCGATCAACATGA 60.119 43.478 27.30 15.70 0.00 3.07
5591 18551 0.884704 GCAACAAGCTGACCGGAAGA 60.885 55.000 9.46 0.00 41.15 2.87
5654 18614 3.423154 GCCTCGAACAACCGCCTG 61.423 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.813753 GCGCGTCCTTTGGATAGCA 60.814 57.895 8.43 0.00 37.82 3.49
1 2 1.813753 TGCGCGTCCTTTGGATAGC 60.814 57.895 8.43 6.86 35.80 2.97
2 3 1.752501 CGTGCGCGTCCTTTGGATAG 61.753 60.000 12.43 0.00 32.73 2.08
3 4 1.807981 CGTGCGCGTCCTTTGGATA 60.808 57.895 12.43 0.00 32.73 2.59
15 16 3.077519 ATAGGAGTCACCCGTGCGC 62.078 63.158 0.00 0.00 40.05 6.09
16 17 1.226974 CATAGGAGTCACCCGTGCG 60.227 63.158 0.00 0.00 40.05 5.34
17 18 0.103208 CTCATAGGAGTCACCCGTGC 59.897 60.000 0.00 0.00 40.05 5.34
36 37 0.882042 CTGGGTCATGGCATAGCGAC 60.882 60.000 0.00 3.61 0.00 5.19
50 51 5.580022 ACATTTAGCTAATTTGGACTGGGT 58.420 37.500 7.08 0.00 0.00 4.51
56 57 6.403049 TCGACTGACATTTAGCTAATTTGGA 58.597 36.000 7.08 0.00 0.00 3.53
60 61 8.492673 TTCAATCGACTGACATTTAGCTAATT 57.507 30.769 7.08 0.48 0.00 1.40
103 105 1.804151 TCCGGCGAACTCTCAAAATTG 59.196 47.619 9.30 0.00 0.00 2.32
104 106 2.076863 CTCCGGCGAACTCTCAAAATT 58.923 47.619 9.30 0.00 0.00 1.82
110 112 1.137825 CTCACTCCGGCGAACTCTC 59.862 63.158 9.30 0.00 0.00 3.20
111 113 2.995872 GCTCACTCCGGCGAACTCT 61.996 63.158 9.30 0.00 0.00 3.24
135 137 3.245087 GCCCCTTTCTTCTCTTTCCTTCT 60.245 47.826 0.00 0.00 0.00 2.85
143 145 0.899019 GACGAGCCCCTTTCTTCTCT 59.101 55.000 0.00 0.00 0.00 3.10
163 165 1.742308 TAGATATGGGGTTGCCCTCC 58.258 55.000 4.02 0.00 44.66 4.30
175 177 8.815565 TCACCCTAAGCTCTAAGATAGATATG 57.184 38.462 0.00 0.00 33.66 1.78
176 178 8.058847 CCTCACCCTAAGCTCTAAGATAGATAT 58.941 40.741 0.00 0.00 33.66 1.63
190 192 1.218316 CACCGTCCTCACCCTAAGC 59.782 63.158 0.00 0.00 0.00 3.09
191 193 0.903454 ACCACCGTCCTCACCCTAAG 60.903 60.000 0.00 0.00 0.00 2.18
202 204 3.948719 TGAAGCCCCACCACCGTC 61.949 66.667 0.00 0.00 0.00 4.79
203 205 4.265056 GTGAAGCCCCACCACCGT 62.265 66.667 0.00 0.00 0.00 4.83
231 233 0.670546 CATCACTCCCGCGTCTGTTT 60.671 55.000 4.92 0.00 0.00 2.83
232 234 1.079819 CATCACTCCCGCGTCTGTT 60.080 57.895 4.92 0.00 0.00 3.16
233 235 2.573869 CATCACTCCCGCGTCTGT 59.426 61.111 4.92 0.00 0.00 3.41
234 236 2.202797 CCATCACTCCCGCGTCTG 60.203 66.667 4.92 0.00 0.00 3.51
235 237 4.148825 GCCATCACTCCCGCGTCT 62.149 66.667 4.92 0.00 0.00 4.18
239 241 4.899239 CTCGGCCATCACTCCCGC 62.899 72.222 2.24 0.00 41.68 6.13
240 242 4.227134 CCTCGGCCATCACTCCCG 62.227 72.222 2.24 0.00 43.21 5.14
263 273 2.666812 CCCACCACCGGTCTTACC 59.333 66.667 2.59 0.00 31.02 2.85
265 275 1.611261 CTCCCCACCACCGGTCTTA 60.611 63.158 2.59 0.00 31.02 2.10
335 345 4.814294 GCCTGCGACCACTACCCG 62.814 72.222 0.00 0.00 0.00 5.28
336 346 4.814294 CGCCTGCGACCACTACCC 62.814 72.222 5.43 0.00 42.83 3.69
340 350 4.250305 AAACCGCCTGCGACCACT 62.250 61.111 13.94 0.00 42.83 4.00
364 374 1.136329 AGCTTCTTCTTCCCAGGCCA 61.136 55.000 5.01 0.00 0.00 5.36
376 386 4.506448 CCTTTCTTCTTCCTCCAGCTTCTT 60.506 45.833 0.00 0.00 0.00 2.52
377 387 3.008923 CCTTTCTTCTTCCTCCAGCTTCT 59.991 47.826 0.00 0.00 0.00 2.85
378 388 3.342719 CCTTTCTTCTTCCTCCAGCTTC 58.657 50.000 0.00 0.00 0.00 3.86
379 389 2.554124 GCCTTTCTTCTTCCTCCAGCTT 60.554 50.000 0.00 0.00 0.00 3.74
380 390 1.004161 GCCTTTCTTCTTCCTCCAGCT 59.996 52.381 0.00 0.00 0.00 4.24
384 394 1.458398 GCAGCCTTTCTTCTTCCTCC 58.542 55.000 0.00 0.00 0.00 4.30
396 406 2.713531 ATCAAACGGGTGGCAGCCTT 62.714 55.000 30.90 21.25 32.48 4.35
397 407 3.210012 ATCAAACGGGTGGCAGCCT 62.210 57.895 30.90 16.63 32.48 4.58
430 440 0.982673 GAGTCGGTCGATCGTTTGTG 59.017 55.000 19.01 2.34 0.00 3.33
432 442 1.693467 TTGAGTCGGTCGATCGTTTG 58.307 50.000 19.01 5.97 0.00 2.93
441 451 5.277601 TGAATTTCGAATTTGAGTCGGTC 57.722 39.130 9.85 0.00 39.01 4.79
463 473 1.557099 TGGCTACACCTGAGTCGATT 58.443 50.000 0.00 0.00 40.22 3.34
464 474 1.781786 ATGGCTACACCTGAGTCGAT 58.218 50.000 0.00 0.00 40.22 3.59
510 521 5.648178 TTCTCGTGCCTGTATTAGTACAA 57.352 39.130 0.00 0.00 40.16 2.41
512 523 6.019801 CACATTTCTCGTGCCTGTATTAGTAC 60.020 42.308 0.00 0.00 0.00 2.73
547 558 3.034635 ACGTCTGCCCTGAGATTAGATT 58.965 45.455 0.00 0.00 0.00 2.40
675 692 1.447140 GTGTTGCTGCGGATCGGTA 60.447 57.895 0.00 0.00 0.00 4.02
687 704 7.042335 AGAGAACTGGTGTATAATAGTGTTGC 58.958 38.462 0.00 0.00 0.00 4.17
739 766 2.338984 GGACGACACAAGCTCCGT 59.661 61.111 0.00 0.00 38.01 4.69
741 768 0.824759 ATAGGGACGACACAAGCTCC 59.175 55.000 0.00 0.00 0.00 4.70
746 773 2.492088 CAGAGTGATAGGGACGACACAA 59.508 50.000 0.00 0.00 35.97 3.33
771 798 2.092968 TGGAACTGCTGTCTCTGTGTTT 60.093 45.455 0.00 0.00 0.00 2.83
772 799 1.486310 TGGAACTGCTGTCTCTGTGTT 59.514 47.619 0.00 0.00 0.00 3.32
773 800 1.123077 TGGAACTGCTGTCTCTGTGT 58.877 50.000 0.00 0.00 0.00 3.72
774 801 2.245159 TTGGAACTGCTGTCTCTGTG 57.755 50.000 0.00 0.00 0.00 3.66
775 802 3.281727 TTTTGGAACTGCTGTCTCTGT 57.718 42.857 0.00 0.00 0.00 3.41
865 895 3.540314 ACTTCTGAGATGAGATGGCAC 57.460 47.619 2.06 0.00 0.00 5.01
926 957 2.094494 CCTATATAGGCCTGCGTCTGTG 60.094 54.545 17.99 0.00 36.53 3.66
965 1004 1.709147 GGGCTATGTTGCAGCGTCAG 61.709 60.000 0.00 0.00 40.05 3.51
984 1024 0.750546 CCATGTGGAGTGATGGCAGG 60.751 60.000 0.00 0.00 37.39 4.85
988 1029 1.381928 GCAGCCATGTGGAGTGATGG 61.382 60.000 2.55 0.00 41.95 3.51
1015 1058 4.767255 GAGGACAGCCGGCACCAG 62.767 72.222 31.54 17.63 39.96 4.00
1168 1211 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
1169 1212 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1170 1213 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1171 1214 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1172 1215 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1173 1216 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1174 1217 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
1175 1218 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
1176 1219 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
1177 1220 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
1178 1221 1.987770 TCGCGACAAGTAATTCCGAAC 59.012 47.619 3.71 0.00 0.00 3.95
1179 1222 2.350899 TCGCGACAAGTAATTCCGAA 57.649 45.000 3.71 0.00 0.00 4.30
1180 1223 2.350899 TTCGCGACAAGTAATTCCGA 57.649 45.000 9.15 0.00 0.00 4.55
1181 1224 3.443054 TTTTCGCGACAAGTAATTCCG 57.557 42.857 9.15 0.00 0.00 4.30
1182 1225 4.095610 CCATTTTCGCGACAAGTAATTCC 58.904 43.478 9.15 0.00 0.00 3.01
1183 1226 4.965062 TCCATTTTCGCGACAAGTAATTC 58.035 39.130 9.15 0.00 0.00 2.17
1184 1227 5.106317 ACATCCATTTTCGCGACAAGTAATT 60.106 36.000 9.15 0.00 0.00 1.40
1185 1228 4.394920 ACATCCATTTTCGCGACAAGTAAT 59.605 37.500 9.15 0.42 0.00 1.89
1186 1229 3.749088 ACATCCATTTTCGCGACAAGTAA 59.251 39.130 9.15 0.00 0.00 2.24
1187 1230 3.331150 ACATCCATTTTCGCGACAAGTA 58.669 40.909 9.15 0.00 0.00 2.24
1188 1231 2.151202 ACATCCATTTTCGCGACAAGT 58.849 42.857 9.15 0.00 0.00 3.16
1189 1232 2.900122 ACATCCATTTTCGCGACAAG 57.100 45.000 9.15 2.84 0.00 3.16
1190 1233 4.188462 AGATACATCCATTTTCGCGACAA 58.812 39.130 9.15 9.93 0.00 3.18
1191 1234 3.792401 AGATACATCCATTTTCGCGACA 58.208 40.909 9.15 0.00 0.00 4.35
1192 1235 5.117287 GTCTAGATACATCCATTTTCGCGAC 59.883 44.000 9.15 0.00 0.00 5.19
1193 1236 5.220381 GTCTAGATACATCCATTTTCGCGA 58.780 41.667 3.71 3.71 0.00 5.87
1194 1237 4.088638 CGTCTAGATACATCCATTTTCGCG 59.911 45.833 0.00 0.00 0.00 5.87
1195 1238 4.982916 ACGTCTAGATACATCCATTTTCGC 59.017 41.667 0.00 0.00 0.00 4.70
1196 1239 5.629849 GGACGTCTAGATACATCCATTTTCG 59.370 44.000 16.46 0.00 0.00 3.46
1197 1240 6.513180 TGGACGTCTAGATACATCCATTTTC 58.487 40.000 16.46 0.00 31.30 2.29
1198 1241 6.479972 TGGACGTCTAGATACATCCATTTT 57.520 37.500 16.46 0.00 31.30 1.82
1199 1242 6.672266 ATGGACGTCTAGATACATCCATTT 57.328 37.500 16.46 5.19 42.93 2.32
1200 1243 6.672266 AATGGACGTCTAGATACATCCATT 57.328 37.500 23.63 23.63 46.96 3.16
1201 1244 6.672266 AAATGGACGTCTAGATACATCCAT 57.328 37.500 16.46 17.69 46.51 3.41
1202 1245 6.479972 AAAATGGACGTCTAGATACATCCA 57.520 37.500 16.46 15.48 40.39 3.41
1203 1246 5.629849 CGAAAATGGACGTCTAGATACATCC 59.370 44.000 16.46 1.79 0.00 3.51
1204 1247 6.436261 TCGAAAATGGACGTCTAGATACATC 58.564 40.000 16.46 3.12 0.00 3.06
1205 1248 6.262496 TCTCGAAAATGGACGTCTAGATACAT 59.738 38.462 16.46 6.21 0.00 2.29
1206 1249 5.587443 TCTCGAAAATGGACGTCTAGATACA 59.413 40.000 16.46 3.81 0.00 2.29
1207 1250 6.018098 TCTCTCGAAAATGGACGTCTAGATAC 60.018 42.308 16.46 0.00 0.00 2.24
1208 1251 6.053650 TCTCTCGAAAATGGACGTCTAGATA 58.946 40.000 16.46 0.00 0.00 1.98
1209 1252 4.882427 TCTCTCGAAAATGGACGTCTAGAT 59.118 41.667 16.46 0.00 0.00 1.98
1210 1253 4.259356 TCTCTCGAAAATGGACGTCTAGA 58.741 43.478 16.46 1.47 0.00 2.43
1211 1254 4.617808 TCTCTCGAAAATGGACGTCTAG 57.382 45.455 16.46 0.00 0.00 2.43
1212 1255 4.458295 ACTTCTCTCGAAAATGGACGTCTA 59.542 41.667 16.46 10.40 0.00 2.59
1213 1256 3.256136 ACTTCTCTCGAAAATGGACGTCT 59.744 43.478 16.46 0.00 0.00 4.18
1214 1257 3.576648 ACTTCTCTCGAAAATGGACGTC 58.423 45.455 7.13 7.13 0.00 4.34
1215 1258 3.662247 ACTTCTCTCGAAAATGGACGT 57.338 42.857 0.00 0.00 0.00 4.34
1216 1259 6.237861 GGAATTACTTCTCTCGAAAATGGACG 60.238 42.308 0.00 0.00 0.00 4.79
1217 1260 6.237861 CGGAATTACTTCTCTCGAAAATGGAC 60.238 42.308 0.00 0.00 0.00 4.02
1218 1261 5.810587 CGGAATTACTTCTCTCGAAAATGGA 59.189 40.000 0.00 0.00 0.00 3.41
1219 1262 5.810587 TCGGAATTACTTCTCTCGAAAATGG 59.189 40.000 0.00 0.00 0.00 3.16
1220 1263 6.887376 TCGGAATTACTTCTCTCGAAAATG 57.113 37.500 0.00 0.00 0.00 2.32
1221 1264 6.034683 CGTTCGGAATTACTTCTCTCGAAAAT 59.965 38.462 6.86 0.00 35.68 1.82
1222 1265 5.344128 CGTTCGGAATTACTTCTCTCGAAAA 59.656 40.000 6.86 0.00 35.68 2.29
1223 1266 4.855388 CGTTCGGAATTACTTCTCTCGAAA 59.145 41.667 6.86 0.00 35.68 3.46
1224 1267 4.409570 CGTTCGGAATTACTTCTCTCGAA 58.590 43.478 0.00 0.00 33.28 3.71
1225 1268 3.181503 CCGTTCGGAATTACTTCTCTCGA 60.182 47.826 5.19 0.00 0.00 4.04
1226 1269 3.106672 CCGTTCGGAATTACTTCTCTCG 58.893 50.000 5.19 0.00 0.00 4.04
1227 1270 4.352887 CTCCGTTCGGAATTACTTCTCTC 58.647 47.826 14.79 0.00 33.41 3.20
1228 1271 3.130693 CCTCCGTTCGGAATTACTTCTCT 59.869 47.826 14.79 0.00 33.41 3.10
1229 1272 3.445857 CCTCCGTTCGGAATTACTTCTC 58.554 50.000 14.79 0.00 33.41 2.87
1230 1273 2.167900 CCCTCCGTTCGGAATTACTTCT 59.832 50.000 14.79 0.00 33.41 2.85
1231 1274 2.167075 TCCCTCCGTTCGGAATTACTTC 59.833 50.000 14.79 0.00 33.41 3.01
1232 1275 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1233 1276 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1234 1277 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1235 1278 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1236 1279 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
1237 1280 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
1238 1281 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
1239 1282 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
1240 1283 0.455005 GAAGTACTCCCTCCGTTCGG 59.545 60.000 4.74 4.74 0.00 4.30
1241 1284 1.171308 TGAAGTACTCCCTCCGTTCG 58.829 55.000 0.00 0.00 0.00 3.95
1242 1285 3.194968 TCAATGAAGTACTCCCTCCGTTC 59.805 47.826 0.00 0.00 0.00 3.95
1243 1286 3.170717 TCAATGAAGTACTCCCTCCGTT 58.829 45.455 0.00 0.00 0.00 4.44
1244 1287 2.816411 TCAATGAAGTACTCCCTCCGT 58.184 47.619 0.00 0.00 0.00 4.69
1245 1288 3.243907 GGATCAATGAAGTACTCCCTCCG 60.244 52.174 0.00 0.00 0.00 4.63
1246 1289 3.711704 TGGATCAATGAAGTACTCCCTCC 59.288 47.826 0.00 0.00 0.00 4.30
1247 1290 5.303971 CATGGATCAATGAAGTACTCCCTC 58.696 45.833 3.76 0.00 0.00 4.30
1248 1291 4.445448 GCATGGATCAATGAAGTACTCCCT 60.445 45.833 14.66 0.00 0.00 4.20
1249 1292 3.817647 GCATGGATCAATGAAGTACTCCC 59.182 47.826 14.66 0.00 0.00 4.30
1250 1293 4.454678 TGCATGGATCAATGAAGTACTCC 58.545 43.478 14.66 0.00 0.00 3.85
1251 1294 6.128336 GCTATGCATGGATCAATGAAGTACTC 60.128 42.308 14.66 0.00 0.00 2.59
1252 1295 5.704515 GCTATGCATGGATCAATGAAGTACT 59.295 40.000 14.66 0.00 0.00 2.73
1253 1296 5.390251 CGCTATGCATGGATCAATGAAGTAC 60.390 44.000 14.66 0.00 0.00 2.73
1271 1315 2.288961 AACCAACGACCTACGCTATG 57.711 50.000 0.00 0.00 46.94 2.23
1292 1343 6.291377 AGAATGTGTGCTGAACTAAGAAAGA 58.709 36.000 0.00 0.00 0.00 2.52
1315 1366 8.606727 GCTTATGCTACAGTTTTCATACAAAG 57.393 34.615 0.00 0.00 36.03 2.77
1355 1443 5.691896 TGATCGTATTCCTAAGAGAGTCCA 58.308 41.667 0.00 0.00 0.00 4.02
1897 9640 9.959749 GTCAACAGAACTAAAAATTTGGACATA 57.040 29.630 0.00 0.00 0.00 2.29
1916 9659 3.679389 AGAATGGCCTAGTTGTCAACAG 58.321 45.455 17.78 11.99 0.00 3.16
1984 9766 6.181206 AGAAAAAGGCTACTCTGAACTTCT 57.819 37.500 0.00 0.00 0.00 2.85
2392 12385 5.292589 GGAAATGGCAAGATAGTGCAAAATG 59.707 40.000 0.00 0.00 46.81 2.32
2479 12502 1.070134 TCTCGGTTGACTCCACCTTTG 59.930 52.381 0.00 0.00 0.00 2.77
2587 12612 3.378112 CGATGCAGTTTGGTACATTGGAT 59.622 43.478 0.00 0.00 39.30 3.41
2588 12613 2.746904 CGATGCAGTTTGGTACATTGGA 59.253 45.455 0.00 0.00 39.30 3.53
2608 12633 6.316140 TGATGAAATAAAGGACCTGATGTTCG 59.684 38.462 0.00 0.00 0.00 3.95
2653 12697 5.045869 GCACCCCTGCAGGTATATAAAGATA 60.046 44.000 30.63 0.00 43.62 1.98
2827 14995 3.745975 TCTTTGTAGTCATTTCTGCACCG 59.254 43.478 0.00 0.00 30.51 4.94
2976 15144 0.106268 TGCAGTTTGCCTTCTCCCAA 60.106 50.000 0.00 0.00 44.23 4.12
3159 15334 3.591023 CCTGCATTTCATTGATGTGCAA 58.409 40.909 20.18 9.84 44.20 4.08
3184 15359 0.325671 TCCGATCTTCCCCTTCTGCT 60.326 55.000 0.00 0.00 0.00 4.24
3278 15453 4.898829 TTACCATCCAAGCATGAATTCG 57.101 40.909 0.00 0.00 0.00 3.34
3353 15529 3.616956 TTCTTGGCGAGATCAATCTGT 57.383 42.857 5.02 0.00 37.25 3.41
3366 15542 5.324784 CCTACAGGGTTTTTATTCTTGGC 57.675 43.478 0.00 0.00 0.00 4.52
3427 15606 8.755977 AGACGGTTTCCTACTAATTCTTTCATA 58.244 33.333 0.00 0.00 0.00 2.15
3439 15618 1.590147 CGGCAGACGGTTTCCTACT 59.410 57.895 0.00 0.00 39.42 2.57
3442 15621 3.883744 CTGCGGCAGACGGTTTCCT 62.884 63.158 25.33 0.00 44.51 3.36
3492 15671 7.121759 AGTTGATTCCAATGAAGTCGAATGAAT 59.878 33.333 0.00 0.00 34.39 2.57
3595 15774 4.566987 GAGAACACTGACCGGTAAGATTT 58.433 43.478 26.69 16.69 0.00 2.17
3608 15787 0.040958 GCTGGCAAACGAGAACACTG 60.041 55.000 0.00 0.00 0.00 3.66
3648 15901 5.523438 AGCATGTTTTTCTAAAACCGGAA 57.477 34.783 9.46 0.00 0.00 4.30
3652 15905 8.009409 GCAATGTTAGCATGTTTTTCTAAAACC 58.991 33.333 11.30 0.00 35.15 3.27
3688 16016 1.535462 GACACCATTTCGAACACCTGG 59.465 52.381 0.00 5.55 0.00 4.45
4352 16686 1.960417 TGTTGTTGGCTTCATCGACA 58.040 45.000 0.00 0.00 34.08 4.35
4452 16789 1.550524 TGCTAGCTTTGACCTGATCGT 59.449 47.619 17.23 0.00 0.00 3.73
4464 16801 8.678199 GGATTATAAAAGTCAAAGTGCTAGCTT 58.322 33.333 17.23 0.00 0.00 3.74
4485 16822 8.321353 AGTTGATGTCTTGACATAGTTGGATTA 58.679 33.333 15.21 0.00 0.00 1.75
4640 16993 2.484065 CCGCTTCCGACCATGGTTATAA 60.484 50.000 20.85 12.14 36.29 0.98
4715 17068 4.929808 TCTCGCTGGTTTCTAGTTGATTTC 59.070 41.667 0.00 0.00 0.00 2.17
4761 17114 4.694760 AAACGGGTACTGAAGTAAACCT 57.305 40.909 9.51 0.00 38.67 3.50
4774 17130 5.593502 ACCAATGTTTCAACTAAAACGGGTA 59.406 36.000 7.90 0.00 41.12 3.69
4779 17135 6.801575 TCTCCACCAATGTTTCAACTAAAAC 58.198 36.000 0.00 0.00 39.16 2.43
4785 17141 7.708752 TGTTTTAATCTCCACCAATGTTTCAAC 59.291 33.333 0.00 0.00 0.00 3.18
4830 17186 3.825908 TCCTTTATTCCAAACAGGCCT 57.174 42.857 0.00 0.00 37.29 5.19
4835 17191 6.090483 TGCGAAATTCCTTTATTCCAAACA 57.910 33.333 0.00 0.00 0.00 2.83
4836 17192 5.576774 CCTGCGAAATTCCTTTATTCCAAAC 59.423 40.000 0.00 0.00 0.00 2.93
4855 17212 5.756195 TTCATTCCTATGAAATTCCTGCG 57.244 39.130 0.00 0.00 45.38 5.18
4878 17235 8.959705 TCTGAGTCTATCTACATCGACTAAAA 57.040 34.615 0.00 0.00 35.65 1.52
5031 17981 2.028839 TCGCCGGAAATTAGTCAACTGA 60.029 45.455 5.05 0.00 0.00 3.41
5041 17991 3.403038 CTGGATAATCTCGCCGGAAATT 58.597 45.455 5.05 0.56 0.00 1.82
5046 17996 0.668706 CAGCTGGATAATCTCGCCGG 60.669 60.000 5.57 0.00 0.00 6.13
5047 17997 0.315251 TCAGCTGGATAATCTCGCCG 59.685 55.000 15.13 0.00 0.00 6.46
5049 17999 4.060900 TCAAATCAGCTGGATAATCTCGC 58.939 43.478 15.13 0.00 34.28 5.03
5056 18006 3.054139 AGGCAGTTCAAATCAGCTGGATA 60.054 43.478 15.13 0.00 34.28 2.59
5067 18017 5.312895 TCAGCTATTTGTAGGCAGTTCAAA 58.687 37.500 0.00 0.00 35.92 2.69
5071 18021 3.274288 GCTCAGCTATTTGTAGGCAGTT 58.726 45.455 0.00 0.00 0.00 3.16
5091 18041 3.594134 AGTGAGTAACAGAGAATGCTGC 58.406 45.455 0.00 0.00 39.51 5.25
5094 18044 3.839293 ACGAGTGAGTAACAGAGAATGC 58.161 45.455 0.00 0.00 0.00 3.56
5117 18067 3.243877 GTCATGTTGATCGATCGAACTGG 59.756 47.826 23.50 21.14 0.00 4.00
5124 18074 3.063997 GTGGTTGGTCATGTTGATCGATC 59.936 47.826 18.72 18.72 27.66 3.69
5129 18079 2.270352 ACGTGGTTGGTCATGTTGAT 57.730 45.000 0.00 0.00 33.52 2.57
5138 18096 0.393808 AGAAGTGCAACGTGGTTGGT 60.394 50.000 10.19 0.00 45.86 3.67
5208 18168 3.057337 CGTCCGGAAGTCTGGGTT 58.943 61.111 5.23 0.00 42.72 4.11
5213 18173 2.035940 AGGAGCGTCCGGAAGTCT 59.964 61.111 18.88 15.37 42.75 3.24
5546 18506 1.079750 GCTGACGGAGGTGAGGTTC 60.080 63.158 0.00 0.00 0.00 3.62
5591 18551 2.285368 TGGAGCGACCTGGGGATT 60.285 61.111 0.00 0.00 39.86 3.01


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

AutoCloner maintained by Alex Coulton.