Multiple sequence alignment - TraesCS4A01G452400

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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 TraesCS4A01G452400 chr4A 100.000 2761 0 0 1 2761 717312250 717309490 0.000000e+00 5099
1 TraesCS4A01G452400 chr4A 100.000 2729 0 0 3029 5757 717309222 717306494 0.000000e+00 5040
2 TraesCS4A01G452400 chr4A 89.607 712 68 4 3251 3961 50232337 50233043 0.000000e+00 900
3 TraesCS4A01G452400 chr4A 90.141 284 23 3 5174 5456 664802276 664802555 1.180000e-96 364
4 TraesCS4A01G452400 chr4A 87.368 285 13 9 5474 5755 664802541 664802805 7.250000e-79 305
5 TraesCS4A01G452400 chr7A 93.129 2125 84 30 3042 5114 16018091 16015977 0.000000e+00 3059
6 TraesCS4A01G452400 chr7A 87.551 1221 72 44 1575 2761 16019306 16018132 0.000000e+00 1339
7 TraesCS4A01G452400 chr7A 89.845 965 54 18 641 1578 16023460 16022513 0.000000e+00 1199
8 TraesCS4A01G452400 chr7A 78.551 690 50 36 1 620 16024172 16023511 1.180000e-96 364
9 TraesCS4A01G452400 chr7A 82.540 315 21 17 5474 5757 16015662 16015351 4.460000e-61 246
10 TraesCS4A01G452400 chr7D 93.747 2015 78 21 3042 5022 16781414 16779414 0.000000e+00 2979
11 TraesCS4A01G452400 chr7D 85.733 2348 137 81 1 2203 16784575 16782281 0.000000e+00 2298
12 TraesCS4A01G452400 chr7D 90.343 642 60 2 3324 3964 744288 744928 0.000000e+00 841
13 TraesCS4A01G452400 chr7D 88.158 532 21 23 2235 2761 16781955 16781461 3.840000e-166 595
14 TraesCS4A01G452400 chr7D 82.911 316 19 16 5474 5757 16778697 16778385 9.580000e-63 252
15 TraesCS4A01G452400 chr3D 92.531 723 49 3 3251 3972 413347360 413346642 0.000000e+00 1031
16 TraesCS4A01G452400 chr3D 90.357 280 22 2 5174 5452 26348260 26347985 4.240000e-96 363
17 TraesCS4A01G452400 chr3D 86.755 151 10 7 5608 5755 539165479 539165622 5.970000e-35 159
18 TraesCS4A01G452400 chr6B 89.564 642 65 2 3324 3964 284281936 284282576 0.000000e+00 813
19 TraesCS4A01G452400 chr6B 91.197 284 20 2 5174 5456 546842946 546842667 1.170000e-101 381
20 TraesCS4A01G452400 chr6B 87.143 280 13 9 5474 5750 546842681 546842422 4.360000e-76 296
21 TraesCS4A01G452400 chr6B 83.957 187 16 6 2423 2609 388992491 388992319 3.570000e-37 167
22 TraesCS4A01G452400 chr3B 86.974 760 30 21 1968 2698 737695088 737694369 0.000000e+00 791
23 TraesCS4A01G452400 chr3B 93.069 404 26 2 3324 3726 238017989 238018391 1.790000e-164 590
24 TraesCS4A01G452400 chr3B 93.443 122 8 0 3843 3964 222545264 222545385 1.270000e-41 182
25 TraesCS4A01G452400 chr2B 86.711 760 32 28 1968 2698 60386578 60385859 0.000000e+00 780
26 TraesCS4A01G452400 chr2B 87.368 285 13 8 5474 5755 99485359 99485095 7.250000e-79 305
27 TraesCS4A01G452400 chr2B 79.755 163 13 9 2435 2595 302398926 302399070 3.670000e-17 100
28 TraesCS4A01G452400 chr6A 91.765 425 33 2 3341 3763 159243380 159242956 1.790000e-164 590
29 TraesCS4A01G452400 chr6A 87.170 265 13 7 2495 2759 94599208 94598965 1.220000e-71 281
30 TraesCS4A01G452400 chr6A 86.792 265 13 8 2495 2758 468736270 468736513 5.680000e-70 276
31 TraesCS4A01G452400 chr1B 92.603 365 26 1 3324 3687 50641605 50641241 1.840000e-144 523
32 TraesCS4A01G452400 chr1B 85.965 285 17 9 5474 5755 559761 560025 3.400000e-72 283
33 TraesCS4A01G452400 chr4B 91.197 284 20 2 5174 5456 439419201 439418922 1.170000e-101 381
34 TraesCS4A01G452400 chr4B 87.719 285 12 9 5474 5755 439418936 439418672 1.560000e-80 311
35 TraesCS4A01G452400 chr4D 91.429 280 19 2 5174 5452 47427376 47427651 4.210000e-101 379
36 TraesCS4A01G452400 chr4D 91.241 274 19 2 5180 5452 240093238 240092969 9.110000e-98 368
37 TraesCS4A01G452400 chr4D 85.430 151 12 7 5608 5755 240092968 240092825 1.290000e-31 148
38 TraesCS4A01G452400 chr1D 91.071 280 20 2 5174 5452 291339160 291339435 1.960000e-99 374
39 TraesCS4A01G452400 chr1D 86.755 151 10 7 5608 5755 454913715 454913572 5.970000e-35 159
40 TraesCS4A01G452400 chr2D 90.714 280 21 2 5174 5452 109535594 109535869 9.110000e-98 368
41 TraesCS4A01G452400 chr2D 90.714 280 21 2 5174 5452 620849162 620848887 9.110000e-98 368
42 TraesCS4A01G452400 chr2D 88.112 143 11 6 5617 5755 109535873 109536013 1.280000e-36 165
43 TraesCS4A01G452400 chr1A 87.266 267 13 7 2495 2761 51247280 51247525 9.440000e-73 285
44 TraesCS4A01G452400 chr1A 93.889 180 11 0 3042 3221 383539662 383539483 7.350000e-69 272
45 TraesCS4A01G452400 chr3A 95.000 180 9 0 3042 3221 13205506 13205327 3.400000e-72 283
46 TraesCS4A01G452400 chr3A 86.940 268 13 8 2495 2761 349330122 349329876 1.220000e-71 281
47 TraesCS4A01G452400 chr3A 86.891 267 14 7 2495 2761 538585864 538585619 4.390000e-71 279
48 TraesCS4A01G452400 chr3A 92.105 190 12 2 3032 3221 349329835 349329649 1.230000e-66 265
49 TraesCS4A01G452400 chr2A 86.940 268 13 9 2495 2761 138092656 138092902 1.220000e-71 281
50 TraesCS4A01G452400 chr2A 93.889 180 11 0 3042 3221 138092950 138093129 7.350000e-69 272
51 TraesCS4A01G452400 chr2A 93.889 180 11 0 3042 3221 284443043 284442864 7.350000e-69 272
52 TraesCS4A01G452400 chr5A 94.444 180 10 0 3042 3221 630445049 630445228 1.580000e-70 278
53 TraesCS4A01G452400 chr5A 86.567 268 14 8 2495 2761 62619307 62619553 5.680000e-70 276
54 TraesCS4A01G452400 chr5A 93.889 180 11 0 3042 3221 178108469 178108290 7.350000e-69 272
55 TraesCS4A01G452400 chr7B 83.039 283 13 13 5474 5755 396240014 396239766 2.090000e-54 224
56 TraesCS4A01G452400 chr5B 90.647 139 13 0 3832 3970 702404459 702404321 9.850000e-43 185


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 TraesCS4A01G452400 chr4A 717306494 717312250 5756 True 5069.5 5099 100.00000 1 5757 2 chr4A.!!$R1 5756
1 TraesCS4A01G452400 chr4A 50232337 50233043 706 False 900.0 900 89.60700 3251 3961 1 chr4A.!!$F1 710
2 TraesCS4A01G452400 chr4A 664802276 664802805 529 False 334.5 364 88.75450 5174 5755 2 chr4A.!!$F2 581
3 TraesCS4A01G452400 chr7A 16015351 16024172 8821 True 1241.4 3059 86.32320 1 5757 5 chr7A.!!$R1 5756
4 TraesCS4A01G452400 chr7D 16778385 16784575 6190 True 1531.0 2979 87.63725 1 5757 4 chr7D.!!$R1 5756
5 TraesCS4A01G452400 chr7D 744288 744928 640 False 841.0 841 90.34300 3324 3964 1 chr7D.!!$F1 640
6 TraesCS4A01G452400 chr3D 413346642 413347360 718 True 1031.0 1031 92.53100 3251 3972 1 chr3D.!!$R2 721
7 TraesCS4A01G452400 chr6B 284281936 284282576 640 False 813.0 813 89.56400 3324 3964 1 chr6B.!!$F1 640
8 TraesCS4A01G452400 chr6B 546842422 546842946 524 True 338.5 381 89.17000 5174 5750 2 chr6B.!!$R2 576
9 TraesCS4A01G452400 chr3B 737694369 737695088 719 True 791.0 791 86.97400 1968 2698 1 chr3B.!!$R1 730
10 TraesCS4A01G452400 chr2B 60385859 60386578 719 True 780.0 780 86.71100 1968 2698 1 chr2B.!!$R1 730
11 TraesCS4A01G452400 chr4B 439418672 439419201 529 True 346.0 381 89.45800 5174 5755 2 chr4B.!!$R1 581

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
94 98 0.104855 CATCCATCCGTGGTCGACAT 59.895 55.000 18.91 0.0 46.16 3.06 F
104 108 0.108851 TGGTCGACATCCATCACACG 60.109 55.000 18.91 0.0 0.00 4.49 F
1339 1490 0.032615 TTGGGGTGCTTTCTTGTGGT 60.033 50.000 0.00 0.0 0.00 4.16 F
1837 5222 0.035739 TTTACCCTGTCTGTTCGGGC 59.964 55.000 0.00 0.0 41.86 6.13 F
2241 5959 1.134189 GGGGGAGGATAAGGTCAAACG 60.134 57.143 0.00 0.0 0.00 3.60 F
3490 7243 0.178903 AGGTACCAGAGGCTGACCAA 60.179 55.000 15.94 0.0 39.06 3.67 F
4126 7895 0.036732 TGGCTGTGTTCCTGTCATCC 59.963 55.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1461 0.178990 AGCACCCCAAGAAACTGGAC 60.179 55.0 0.00 0.00 38.96 4.02 R
1573 1728 0.392193 GGCAGACACTGGGTGAGATG 60.392 60.0 4.62 1.95 36.96 2.90 R
3098 6838 1.098050 CAGTTAGCCAGCCATGAACC 58.902 55.0 0.00 0.00 0.00 3.62 R
3102 6842 1.381928 CCTGCAGTTAGCCAGCCATG 61.382 60.0 13.81 0.00 44.83 3.66 R
4126 7895 0.806868 AGATGCACATTGTGGCGAAG 59.193 50.0 18.05 0.00 33.64 3.79 R
4684 8453 0.031449 CCTTCTCGCCGATCCTCTTC 59.969 60.0 0.00 0.00 0.00 2.87 R
5040 8831 0.036010 AGGACAGGGCGATGAACAAG 60.036 55.0 0.00 0.00 0.00 3.16 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
24 25 4.644685 CCAACCCTAATCTTGTACCCATTG 59.355 45.833 0.00 0.00 0.00 2.82
51 55 2.612212 ACGCTACAACACTCCAAACTTG 59.388 45.455 0.00 0.00 0.00 3.16
82 86 2.910994 GCCAGCCAGCCATCCATC 60.911 66.667 0.00 0.00 0.00 3.51
83 87 2.203451 CCAGCCAGCCATCCATCC 60.203 66.667 0.00 0.00 0.00 3.51
84 88 2.593725 CAGCCAGCCATCCATCCG 60.594 66.667 0.00 0.00 0.00 4.18
88 92 2.591753 CAGCCATCCATCCGTGGT 59.408 61.111 0.00 0.00 46.16 4.16
89 93 1.524621 CAGCCATCCATCCGTGGTC 60.525 63.158 0.00 0.00 46.16 4.02
90 94 2.588877 GCCATCCATCCGTGGTCG 60.589 66.667 0.00 0.00 46.16 4.79
91 95 3.088941 GCCATCCATCCGTGGTCGA 62.089 63.158 0.00 0.00 46.16 4.20
92 96 1.227263 CCATCCATCCGTGGTCGAC 60.227 63.158 7.13 7.13 46.16 4.20
93 97 1.515487 CATCCATCCGTGGTCGACA 59.485 57.895 18.91 0.27 46.16 4.35
94 98 0.104855 CATCCATCCGTGGTCGACAT 59.895 55.000 18.91 0.00 46.16 3.06
104 108 0.108851 TGGTCGACATCCATCACACG 60.109 55.000 18.91 0.00 0.00 4.49
111 115 1.483827 ACATCCATCACACGATGCTCT 59.516 47.619 0.00 0.00 46.59 4.09
112 116 2.695147 ACATCCATCACACGATGCTCTA 59.305 45.455 0.00 0.00 46.59 2.43
113 117 2.871182 TCCATCACACGATGCTCTAC 57.129 50.000 0.00 0.00 46.59 2.59
114 118 1.409064 TCCATCACACGATGCTCTACC 59.591 52.381 0.00 0.00 46.59 3.18
115 119 1.136891 CCATCACACGATGCTCTACCA 59.863 52.381 0.00 0.00 46.59 3.25
132 136 0.594602 CCATACCATCAGCATTGCGG 59.405 55.000 2.38 2.21 0.00 5.69
152 156 3.423154 CACTCCGCTTTCACGCCC 61.423 66.667 0.00 0.00 0.00 6.13
163 167 4.308458 CACGCCCCTCGACACCAA 62.308 66.667 0.00 0.00 41.67 3.67
180 184 5.710984 ACACCAACAATTTACACGAAAACA 58.289 33.333 0.00 0.00 0.00 2.83
184 188 5.275510 CCAACAATTTACACGAAAACACACG 60.276 40.000 0.00 0.00 0.00 4.49
193 197 4.268405 ACACGAAAACACACGGTAAGTAAG 59.732 41.667 0.00 0.00 0.00 2.34
197 201 4.806342 AAACACACGGTAAGTAAGCAAG 57.194 40.909 0.00 0.00 0.00 4.01
198 202 2.140717 ACACACGGTAAGTAAGCAAGC 58.859 47.619 0.00 0.00 0.00 4.01
209 214 4.292186 AGTAAGCAAGCAAAGGAGATGA 57.708 40.909 0.00 0.00 0.00 2.92
225 230 6.928520 AGGAGATGAAAACAAAATCCATCAC 58.071 36.000 0.00 0.00 36.88 3.06
333 343 1.595093 CCATCCGCCCTCCAAACAAC 61.595 60.000 0.00 0.00 0.00 3.32
334 344 0.893270 CATCCGCCCTCCAAACAACA 60.893 55.000 0.00 0.00 0.00 3.33
337 347 1.007387 CGCCCTCCAAACAACAAGC 60.007 57.895 0.00 0.00 0.00 4.01
338 348 1.367471 GCCCTCCAAACAACAAGCC 59.633 57.895 0.00 0.00 0.00 4.35
339 349 2.049435 CCCTCCAAACAACAAGCCC 58.951 57.895 0.00 0.00 0.00 5.19
340 350 1.659794 CCTCCAAACAACAAGCCCG 59.340 57.895 0.00 0.00 0.00 6.13
341 351 1.007387 CTCCAAACAACAAGCCCGC 60.007 57.895 0.00 0.00 0.00 6.13
377 410 2.120940 TTGGGTCCCCGTAGCAGA 59.879 61.111 5.13 0.00 39.42 4.26
497 558 2.087857 AATCCGCCACCTTTTCCCCA 62.088 55.000 0.00 0.00 0.00 4.96
498 559 1.874299 ATCCGCCACCTTTTCCCCAT 61.874 55.000 0.00 0.00 0.00 4.00
502 563 1.379843 CCACCTTTTCCCCATCCCG 60.380 63.158 0.00 0.00 0.00 5.14
503 564 1.379843 CACCTTTTCCCCATCCCGG 60.380 63.158 0.00 0.00 0.00 5.73
505 577 2.683475 CTTTTCCCCATCCCGGCT 59.317 61.111 0.00 0.00 0.00 5.52
506 578 1.000359 CTTTTCCCCATCCCGGCTT 60.000 57.895 0.00 0.00 0.00 4.35
509 581 1.794885 TTTCCCCATCCCGGCTTTCA 61.795 55.000 0.00 0.00 0.00 2.69
511 583 1.304879 CCCCATCCCGGCTTTCAAA 60.305 57.895 0.00 0.00 0.00 2.69
513 585 1.410932 CCCCATCCCGGCTTTCAAATA 60.411 52.381 0.00 0.00 0.00 1.40
515 587 1.333619 CCATCCCGGCTTTCAAATACG 59.666 52.381 0.00 0.00 0.00 3.06
527 599 1.136305 TCAAATACGCCCGAGAAGAGG 59.864 52.381 0.00 0.00 0.00 3.69
595 670 4.335647 CACCTTCCCGCAGCCACT 62.336 66.667 0.00 0.00 0.00 4.00
596 671 4.021925 ACCTTCCCGCAGCCACTC 62.022 66.667 0.00 0.00 0.00 3.51
597 672 3.710722 CCTTCCCGCAGCCACTCT 61.711 66.667 0.00 0.00 0.00 3.24
598 673 2.125350 CTTCCCGCAGCCACTCTC 60.125 66.667 0.00 0.00 0.00 3.20
599 674 2.604686 TTCCCGCAGCCACTCTCT 60.605 61.111 0.00 0.00 0.00 3.10
600 675 2.570582 CTTCCCGCAGCCACTCTCTC 62.571 65.000 0.00 0.00 0.00 3.20
993 1114 4.554036 GTGATGCCCGAGGAGCCC 62.554 72.222 0.00 0.00 0.00 5.19
1195 1322 7.605691 AGATGTCCATGTAAGAAGAAGAACAAG 59.394 37.037 0.00 0.00 0.00 3.16
1198 1325 7.388776 TGTCCATGTAAGAAGAAGAACAAGATG 59.611 37.037 0.00 0.00 0.00 2.90
1217 1344 2.641746 CCTCTCCCCACTCCCTCCT 61.642 68.421 0.00 0.00 0.00 3.69
1218 1345 1.075600 CTCTCCCCACTCCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
1219 1346 1.547755 TCTCCCCACTCCCTCCTCT 60.548 63.158 0.00 0.00 0.00 3.69
1222 1350 1.075600 CCCCACTCCCTCCTCTCTC 60.076 68.421 0.00 0.00 0.00 3.20
1228 1356 1.275002 ACTCCCTCCTCTCTCCTCTCT 60.275 57.143 0.00 0.00 0.00 3.10
1229 1357 1.852965 CTCCCTCCTCTCTCCTCTCTT 59.147 57.143 0.00 0.00 0.00 2.85
1233 1361 4.484270 TCCCTCCTCTCTCCTCTCTTAAAT 59.516 45.833 0.00 0.00 0.00 1.40
1234 1362 4.832823 CCCTCCTCTCTCCTCTCTTAAATC 59.167 50.000 0.00 0.00 0.00 2.17
1335 1486 2.695147 AGTTTCTTGGGGTGCTTTCTTG 59.305 45.455 0.00 0.00 0.00 3.02
1336 1487 2.430694 GTTTCTTGGGGTGCTTTCTTGT 59.569 45.455 0.00 0.00 0.00 3.16
1337 1488 1.691196 TCTTGGGGTGCTTTCTTGTG 58.309 50.000 0.00 0.00 0.00 3.33
1339 1490 0.032615 TTGGGGTGCTTTCTTGTGGT 60.033 50.000 0.00 0.00 0.00 4.16
1341 1492 1.119684 GGGGTGCTTTCTTGTGGTTT 58.880 50.000 0.00 0.00 0.00 3.27
1342 1493 1.484653 GGGGTGCTTTCTTGTGGTTTT 59.515 47.619 0.00 0.00 0.00 2.43
1343 1494 2.093181 GGGGTGCTTTCTTGTGGTTTTT 60.093 45.455 0.00 0.00 0.00 1.94
1344 1495 3.133183 GGGGTGCTTTCTTGTGGTTTTTA 59.867 43.478 0.00 0.00 0.00 1.52
1345 1496 4.368315 GGGTGCTTTCTTGTGGTTTTTAG 58.632 43.478 0.00 0.00 0.00 1.85
1346 1497 4.098807 GGGTGCTTTCTTGTGGTTTTTAGA 59.901 41.667 0.00 0.00 0.00 2.10
1347 1498 5.281727 GGTGCTTTCTTGTGGTTTTTAGAG 58.718 41.667 0.00 0.00 0.00 2.43
1348 1499 5.281727 GTGCTTTCTTGTGGTTTTTAGAGG 58.718 41.667 0.00 0.00 0.00 3.69
1349 1500 4.340950 TGCTTTCTTGTGGTTTTTAGAGGG 59.659 41.667 0.00 0.00 0.00 4.30
1350 1501 4.262036 GCTTTCTTGTGGTTTTTAGAGGGG 60.262 45.833 0.00 0.00 0.00 4.79
1351 1502 4.529716 TTCTTGTGGTTTTTAGAGGGGT 57.470 40.909 0.00 0.00 0.00 4.95
1352 1503 4.529716 TCTTGTGGTTTTTAGAGGGGTT 57.470 40.909 0.00 0.00 0.00 4.11
1382 1534 7.010738 ACACAGATTTGCAGATTTGTTTTCTTG 59.989 33.333 10.33 2.35 0.00 3.02
1411 1563 1.272807 TTTACCTCCCCTGTTCCTCG 58.727 55.000 0.00 0.00 0.00 4.63
1415 1567 1.219393 CTCCCCTGTTCCTCGCTTC 59.781 63.158 0.00 0.00 0.00 3.86
1426 1578 0.868406 CCTCGCTTCCACACAAGTTC 59.132 55.000 0.00 0.00 0.00 3.01
1427 1579 1.581934 CTCGCTTCCACACAAGTTCA 58.418 50.000 0.00 0.00 0.00 3.18
1470 1622 7.444299 AGCAAGCAAGAAAATAAAAATCCTCA 58.556 30.769 0.00 0.00 0.00 3.86
1503 1658 4.335416 TGGGAAGTAGCAATCTTTCCTTG 58.665 43.478 12.06 0.00 40.29 3.61
1522 1677 1.065782 TGCAGTTTTAGGGCTATGCGA 60.066 47.619 0.00 0.00 36.47 5.10
1531 1686 2.039418 AGGGCTATGCGACAGTGATTA 58.961 47.619 0.00 0.00 0.00 1.75
1538 1693 5.333645 GCTATGCGACAGTGATTATTCTTGG 60.334 44.000 0.00 0.00 0.00 3.61
1542 1697 4.033358 GCGACAGTGATTATTCTTGGAGTG 59.967 45.833 0.00 0.00 0.00 3.51
1573 1728 3.305398 TTTCCTCGAGAGCTTGTTCTC 57.695 47.619 15.71 4.70 40.16 2.87
1578 1733 3.489059 CCTCGAGAGCTTGTTCTCATCTC 60.489 52.174 15.71 0.00 43.02 2.75
1598 4964 0.188342 ACCCAGTGTCTGCCCAAAAT 59.812 50.000 0.00 0.00 0.00 1.82
1634 5004 3.191581 TGTTTTTGTCTGCAAACGAGGAA 59.808 39.130 0.00 0.00 43.47 3.36
1639 5009 1.129437 GTCTGCAAACGAGGAAGCATC 59.871 52.381 0.00 0.00 36.28 3.91
1640 5010 1.159285 CTGCAAACGAGGAAGCATCA 58.841 50.000 0.00 0.00 36.28 3.07
1641 5011 1.129998 CTGCAAACGAGGAAGCATCAG 59.870 52.381 0.00 0.00 36.28 2.90
1642 5012 0.179179 GCAAACGAGGAAGCATCAGC 60.179 55.000 0.00 0.00 42.56 4.26
1643 5013 1.159285 CAAACGAGGAAGCATCAGCA 58.841 50.000 0.00 0.00 45.49 4.41
1644 5014 1.741706 CAAACGAGGAAGCATCAGCAT 59.258 47.619 0.00 0.00 45.49 3.79
1676 5058 1.273327 CTTCCTTGCCTTGCGGATTTT 59.727 47.619 0.00 0.00 0.00 1.82
1821 5206 9.660180 TGTGTGCAAGTACAAGTATATGATTTA 57.340 29.630 0.00 0.00 31.36 1.40
1833 5218 9.046296 CAAGTATATGATTTACCCTGTCTGTTC 57.954 37.037 0.00 0.00 0.00 3.18
1837 5222 0.035739 TTTACCCTGTCTGTTCGGGC 59.964 55.000 0.00 0.00 41.86 6.13
1889 5276 3.982058 GCGACGAAAATACCTAGGAGATG 59.018 47.826 17.98 0.70 0.00 2.90
1890 5277 4.261489 GCGACGAAAATACCTAGGAGATGA 60.261 45.833 17.98 0.00 0.00 2.92
1935 5323 4.282957 TGATACCTCAGAGATTCCATGCTC 59.717 45.833 0.00 0.00 0.00 4.26
1947 5335 2.437359 ATGCTCCCTCGCTTGCAC 60.437 61.111 0.00 0.00 38.29 4.57
2039 5427 6.466885 TTTTGGTCCTAGACTACTAGATGC 57.533 41.667 0.00 0.00 46.34 3.91
2040 5428 4.790718 TGGTCCTAGACTACTAGATGCA 57.209 45.455 0.00 0.00 46.34 3.96
2066 5466 2.289532 GCTCAGTGAGGAGGCCACT 61.290 63.158 21.54 1.49 44.92 4.00
2083 5500 6.260663 AGGCCACTTCCCATTATTTTCTTTA 58.739 36.000 5.01 0.00 0.00 1.85
2121 5539 8.727100 ATATTATTTCCCCAGGATTTTTCTCC 57.273 34.615 0.00 0.00 35.37 3.71
2241 5959 1.134189 GGGGGAGGATAAGGTCAAACG 60.134 57.143 0.00 0.00 0.00 3.60
2251 5969 3.336138 AAGGTCAAACGAGAGATTCCC 57.664 47.619 0.00 0.00 0.00 3.97
2252 5970 2.257207 AGGTCAAACGAGAGATTCCCA 58.743 47.619 0.00 0.00 0.00 4.37
2253 5971 2.637872 AGGTCAAACGAGAGATTCCCAA 59.362 45.455 0.00 0.00 0.00 4.12
2444 6171 1.269778 GCCTCTGAACCAAAACTTGCC 60.270 52.381 0.00 0.00 0.00 4.52
2500 6227 7.527568 AGATACTGCTACTCCAAATACTACC 57.472 40.000 0.00 0.00 0.00 3.18
2504 6231 5.127356 ACTGCTACTCCAAATACTACCACTC 59.873 44.000 0.00 0.00 0.00 3.51
2506 6233 4.202233 GCTACTCCAAATACTACCACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
2539 6276 9.598517 TTTCATTTCAAAGTTCAAAATGCTACT 57.401 25.926 13.95 0.00 39.24 2.57
2541 6278 9.897744 TCATTTCAAAGTTCAAAATGCTACTAG 57.102 29.630 13.95 0.00 39.24 2.57
2542 6279 9.683069 CATTTCAAAGTTCAAAATGCTACTAGT 57.317 29.630 0.00 0.00 34.65 2.57
2545 6282 9.555727 TTCAAAGTTCAAAATGCTACTAGTACT 57.444 29.630 0.00 0.00 0.00 2.73
2546 6283 8.988934 TCAAAGTTCAAAATGCTACTAGTACTG 58.011 33.333 5.39 0.00 0.00 2.74
2547 6284 8.988934 CAAAGTTCAAAATGCTACTAGTACTGA 58.011 33.333 5.39 0.00 0.00 3.41
2548 6285 9.726438 AAAGTTCAAAATGCTACTAGTACTGAT 57.274 29.630 5.39 0.00 0.00 2.90
2549 6286 8.709386 AGTTCAAAATGCTACTAGTACTGATG 57.291 34.615 5.39 0.00 0.00 3.07
2550 6287 8.531982 AGTTCAAAATGCTACTAGTACTGATGA 58.468 33.333 5.39 0.00 0.00 2.92
2551 6288 8.596380 GTTCAAAATGCTACTAGTACTGATGAC 58.404 37.037 5.39 0.00 0.00 3.06
2552 6289 7.836842 TCAAAATGCTACTAGTACTGATGACA 58.163 34.615 5.39 0.00 0.00 3.58
2554 6291 7.646548 AAATGCTACTAGTACTGATGACAGA 57.353 36.000 5.39 0.00 46.03 3.41
2555 6292 7.831691 AATGCTACTAGTACTGATGACAGAT 57.168 36.000 5.39 0.00 46.03 2.90
2611 6351 5.096443 AGGAGAGGAGAAAAATAGCAGTG 57.904 43.478 0.00 0.00 0.00 3.66
2620 6360 5.203528 AGAAAAATAGCAGTGGCCATGTAT 58.796 37.500 9.72 0.64 42.56 2.29
2621 6361 4.924305 AAAATAGCAGTGGCCATGTATG 57.076 40.909 9.72 7.31 42.56 2.39
2666 6406 6.164425 AGGGTGATGGATAGATCTAGTGAT 57.836 41.667 8.70 0.00 35.26 3.06
2667 6407 5.957168 AGGGTGATGGATAGATCTAGTGATG 59.043 44.000 8.70 0.00 32.19 3.07
2668 6408 5.954752 GGGTGATGGATAGATCTAGTGATGA 59.045 44.000 8.70 0.00 32.19 2.92
2698 6438 3.799281 TGCTTTTGTCCCACTTTTGAG 57.201 42.857 0.00 0.00 0.00 3.02
2721 6461 2.087646 GACCAAGGAAATGAGTGCTCC 58.912 52.381 0.00 0.00 0.00 4.70
3131 6871 0.698238 TAACTGCAGGTCCAGCCAAT 59.302 50.000 19.93 0.00 40.61 3.16
3147 6887 2.718563 CCAATTGGTAGGTGGGTGTAC 58.281 52.381 16.90 0.00 0.00 2.90
3151 6891 1.281419 TGGTAGGTGGGTGTACATGG 58.719 55.000 0.00 0.00 0.00 3.66
3241 6981 1.698506 TCAACATTGACACCCCAACC 58.301 50.000 0.00 0.00 31.01 3.77
3337 7089 5.770162 AGTTTTAACTAGGCTGAAATGTGCT 59.230 36.000 0.00 0.00 37.52 4.40
3345 7097 4.620982 AGGCTGAAATGTGCTTGTTTTAC 58.379 39.130 0.00 0.00 0.00 2.01
3350 7102 5.596845 TGAAATGTGCTTGTTTTACCTTCC 58.403 37.500 0.00 0.00 0.00 3.46
3369 7121 5.652014 CCTTCCCAGCATTGTTGTTCTTATA 59.348 40.000 0.00 0.00 0.00 0.98
3490 7243 0.178903 AGGTACCAGAGGCTGACCAA 60.179 55.000 15.94 0.00 39.06 3.67
3502 7255 1.200020 GCTGACCAAGTACACCATTGC 59.800 52.381 0.00 0.00 0.00 3.56
3593 7346 3.775654 CCGCTCCTCACCCAGGTC 61.776 72.222 0.00 0.00 43.95 3.85
3791 7547 2.109799 CTGATGATCCGCGGCCTT 59.890 61.111 23.51 12.81 0.00 4.35
4059 7815 0.798776 CGCATTCGAGCCAAACTTCT 59.201 50.000 0.00 0.00 38.10 2.85
4111 7880 2.613696 TACCCACAGGCCATGGCT 60.614 61.111 34.70 18.82 41.60 4.75
4126 7895 0.036732 TGGCTGTGTTCCTGTCATCC 59.963 55.000 0.00 0.00 0.00 3.51
4306 8075 4.175489 GTCCGCATGCAGCTGCTG 62.175 66.667 36.61 29.93 42.61 4.41
4637 8406 0.453282 CTTCGGCAATGTCAGCAACG 60.453 55.000 0.00 0.00 0.00 4.10
4684 8453 1.153289 CAAGGGCATGGAGGACGAG 60.153 63.158 0.00 0.00 0.00 4.18
4762 8531 3.531059 CAGGGGGAGGGTATGATTGATA 58.469 50.000 0.00 0.00 0.00 2.15
4763 8532 3.264450 CAGGGGGAGGGTATGATTGATAC 59.736 52.174 0.00 0.00 36.87 2.24
4764 8533 3.115962 AGGGGGAGGGTATGATTGATACA 60.116 47.826 0.00 0.00 39.08 2.29
4765 8534 3.852578 GGGGGAGGGTATGATTGATACAT 59.147 47.826 0.00 0.00 39.08 2.29
4767 8536 5.222337 GGGGGAGGGTATGATTGATACATTT 60.222 44.000 0.00 0.00 39.08 2.32
4768 8537 5.946377 GGGGAGGGTATGATTGATACATTTC 59.054 44.000 0.00 0.00 39.08 2.17
4769 8538 6.467194 GGGGAGGGTATGATTGATACATTTCA 60.467 42.308 0.00 0.00 39.08 2.69
4770 8539 7.177878 GGGAGGGTATGATTGATACATTTCAT 58.822 38.462 0.00 0.00 39.08 2.57
4771 8540 7.121759 GGGAGGGTATGATTGATACATTTCATG 59.878 40.741 0.00 0.00 39.08 3.07
4772 8541 7.121759 GGAGGGTATGATTGATACATTTCATGG 59.878 40.741 0.00 0.00 39.08 3.66
4773 8542 7.529555 AGGGTATGATTGATACATTTCATGGT 58.470 34.615 0.00 0.00 39.08 3.55
4774 8543 8.006564 AGGGTATGATTGATACATTTCATGGTT 58.993 33.333 0.00 0.00 39.08 3.67
4777 8546 7.664552 ATGATTGATACATTTCATGGTTGGT 57.335 32.000 0.00 0.00 33.60 3.67
4781 8550 5.083122 TGATACATTTCATGGTTGGTTGGT 58.917 37.500 0.00 0.00 33.60 3.67
4782 8551 5.541868 TGATACATTTCATGGTTGGTTGGTT 59.458 36.000 0.00 0.00 33.60 3.67
4783 8552 4.070630 ACATTTCATGGTTGGTTGGTTG 57.929 40.909 0.00 0.00 33.60 3.77
4792 8561 3.777522 TGGTTGGTTGGTTGGAAAGATTT 59.222 39.130 0.00 0.00 0.00 2.17
4798 8567 4.202253 GGTTGGTTGGAAAGATTTCTTGCT 60.202 41.667 5.37 0.00 37.35 3.91
4799 8568 5.010617 GGTTGGTTGGAAAGATTTCTTGCTA 59.989 40.000 5.37 0.00 37.35 3.49
4849 8623 7.180229 TGTGAGAGGGTATGATTTGTTCTTCTA 59.820 37.037 0.00 0.00 0.00 2.10
5009 8790 8.878769 GTTGTTAAATTCTTTTGCTTGGAAGAA 58.121 29.630 1.55 1.55 43.64 2.52
5028 8809 7.040478 TGGAAGAAAGACAATTGTAACTGATGG 60.040 37.037 11.95 0.00 0.00 3.51
5029 8810 7.040409 GGAAGAAAGACAATTGTAACTGATGGT 60.040 37.037 11.95 0.00 0.00 3.55
5030 8811 7.206981 AGAAAGACAATTGTAACTGATGGTG 57.793 36.000 11.95 0.00 0.00 4.17
5031 8812 6.998074 AGAAAGACAATTGTAACTGATGGTGA 59.002 34.615 11.95 0.00 0.00 4.02
5032 8813 7.667219 AGAAAGACAATTGTAACTGATGGTGAT 59.333 33.333 11.95 0.00 0.00 3.06
5033 8814 8.862325 AAAGACAATTGTAACTGATGGTGATA 57.138 30.769 11.95 0.00 0.00 2.15
5034 8815 9.466497 AAAGACAATTGTAACTGATGGTGATAT 57.534 29.630 11.95 0.00 0.00 1.63
5035 8816 8.442632 AGACAATTGTAACTGATGGTGATATG 57.557 34.615 11.95 0.00 0.00 1.78
5036 8817 7.500227 AGACAATTGTAACTGATGGTGATATGG 59.500 37.037 11.95 0.00 0.00 2.74
5040 8831 5.680619 TGTAACTGATGGTGATATGGTTCC 58.319 41.667 0.00 0.00 0.00 3.62
5054 8845 0.322546 GGTTCCTTGTTCATCGCCCT 60.323 55.000 0.00 0.00 0.00 5.19
5056 8847 0.400213 TTCCTTGTTCATCGCCCTGT 59.600 50.000 0.00 0.00 0.00 4.00
5059 8850 0.036010 CTTGTTCATCGCCCTGTCCT 60.036 55.000 0.00 0.00 0.00 3.85
5061 8852 1.153349 GTTCATCGCCCTGTCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
5062 8853 2.367202 TTCATCGCCCTGTCCTCCC 61.367 63.158 0.00 0.00 0.00 4.30
5063 8854 2.765807 CATCGCCCTGTCCTCCCT 60.766 66.667 0.00 0.00 0.00 4.20
5064 8855 2.765807 ATCGCCCTGTCCTCCCTG 60.766 66.667 0.00 0.00 0.00 4.45
5065 8856 3.317436 ATCGCCCTGTCCTCCCTGA 62.317 63.158 0.00 0.00 0.00 3.86
5066 8857 2.822643 ATCGCCCTGTCCTCCCTGAA 62.823 60.000 0.00 0.00 0.00 3.02
5067 8858 2.592993 CGCCCTGTCCTCCCTGAAA 61.593 63.158 0.00 0.00 0.00 2.69
5068 8859 1.767692 GCCCTGTCCTCCCTGAAAA 59.232 57.895 0.00 0.00 0.00 2.29
5069 8860 0.112412 GCCCTGTCCTCCCTGAAAAA 59.888 55.000 0.00 0.00 0.00 1.94
5118 9182 9.773328 ATTTATGTCGAAAATGTGATTGTGTAG 57.227 29.630 0.00 0.00 0.00 2.74
5119 9183 8.541133 TTATGTCGAAAATGTGATTGTGTAGA 57.459 30.769 0.00 0.00 0.00 2.59
5122 9186 6.073819 TGTCGAAAATGTGATTGTGTAGAGTG 60.074 38.462 0.00 0.00 0.00 3.51
5162 9226 1.471684 CAATCTGCCTGGTGCTTCTTC 59.528 52.381 0.00 0.00 42.00 2.87
5163 9227 0.990374 ATCTGCCTGGTGCTTCTTCT 59.010 50.000 0.00 0.00 42.00 2.85
5164 9228 0.767375 TCTGCCTGGTGCTTCTTCTT 59.233 50.000 0.00 0.00 42.00 2.52
5178 9242 6.924060 GTGCTTCTTCTTTCACTCTAGTACAA 59.076 38.462 0.00 0.00 0.00 2.41
5204 9268 5.006649 GGAACTTTGTTTTGGTTCATTCTGC 59.993 40.000 0.00 0.00 40.48 4.26
5209 9273 5.987777 TGTTTTGGTTCATTCTGCAAATG 57.012 34.783 12.59 12.59 0.00 2.32
5299 9392 2.095059 GCAAACACAGGACCATGTCATC 60.095 50.000 2.12 0.00 33.68 2.92
5304 9397 3.203716 CACAGGACCATGTCATCATCAG 58.796 50.000 0.00 0.00 33.68 2.90
5319 9413 2.846206 TCATCAGGGCACTCCACTAATT 59.154 45.455 0.00 0.00 38.24 1.40
5449 9544 2.477845 GCCCCTTGCAAATTGTTGAT 57.522 45.000 0.00 0.00 40.77 2.57
5450 9545 2.078392 GCCCCTTGCAAATTGTTGATG 58.922 47.619 0.00 0.00 40.77 3.07
5451 9546 2.078392 CCCCTTGCAAATTGTTGATGC 58.922 47.619 0.00 0.00 36.83 3.91
5452 9547 2.289819 CCCCTTGCAAATTGTTGATGCT 60.290 45.455 0.00 0.00 40.66 3.79
5453 9548 3.055963 CCCCTTGCAAATTGTTGATGCTA 60.056 43.478 0.00 0.00 40.66 3.49
5454 9549 4.563168 CCCCTTGCAAATTGTTGATGCTAA 60.563 41.667 0.00 0.00 40.66 3.09
5455 9550 5.180271 CCCTTGCAAATTGTTGATGCTAAT 58.820 37.500 0.00 0.00 40.66 1.73
5456 9551 5.644636 CCCTTGCAAATTGTTGATGCTAATT 59.355 36.000 0.00 0.00 40.66 1.40
5457 9552 6.149807 CCCTTGCAAATTGTTGATGCTAATTT 59.850 34.615 0.00 0.00 40.66 1.82
5458 9553 7.308710 CCCTTGCAAATTGTTGATGCTAATTTT 60.309 33.333 0.00 0.00 40.66 1.82
5459 9554 8.077386 CCTTGCAAATTGTTGATGCTAATTTTT 58.923 29.630 0.00 0.00 40.66 1.94
5525 9620 2.520260 GGGTGGATGCATCTGGGC 60.520 66.667 25.28 9.96 0.00 5.36
5620 9744 4.481930 TTGCACTACACATTGTACTTGC 57.518 40.909 0.00 7.70 37.32 4.01
5621 9745 3.471680 TGCACTACACATTGTACTTGCA 58.528 40.909 11.37 11.37 41.10 4.08
5622 9746 4.071423 TGCACTACACATTGTACTTGCAT 58.929 39.130 11.37 0.00 39.73 3.96
5623 9747 4.518590 TGCACTACACATTGTACTTGCATT 59.481 37.500 11.37 0.00 39.73 3.56
5624 9748 4.853196 GCACTACACATTGTACTTGCATTG 59.147 41.667 9.06 0.00 37.02 2.82
5641 9765 4.408270 TGCATTGCACCCCATATGTTTAAT 59.592 37.500 7.38 0.00 31.71 1.40
5650 9776 4.971924 CCCCATATGTTTAATCCCCCAAAA 59.028 41.667 1.24 0.00 0.00 2.44
5751 9883 0.657840 GAACCTGACACACACTGCAC 59.342 55.000 0.00 0.00 0.00 4.57
5755 9887 1.311859 CTGACACACACTGCACCATT 58.688 50.000 0.00 0.00 0.00 3.16
5756 9888 1.677576 CTGACACACACTGCACCATTT 59.322 47.619 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.347320 GAGTGTTGTAGCGTACAGGC 58.653 55.000 0.00 0.00 40.24 4.85
51 55 2.289565 GGCTGGCAAAGAGTGTATACC 58.710 52.381 0.00 0.00 0.00 2.73
82 86 0.806102 GTGATGGATGTCGACCACGG 60.806 60.000 14.12 0.00 40.36 4.94
83 87 0.108851 TGTGATGGATGTCGACCACG 60.109 55.000 14.12 0.00 40.36 4.94
84 88 1.359848 GTGTGATGGATGTCGACCAC 58.640 55.000 14.12 12.77 40.36 4.16
87 91 1.854743 CATCGTGTGATGGATGTCGAC 59.145 52.381 9.11 9.11 46.76 4.20
88 92 2.208326 CATCGTGTGATGGATGTCGA 57.792 50.000 0.00 0.00 46.76 4.20
104 108 3.007290 TGCTGATGGTATGGTAGAGCATC 59.993 47.826 8.26 8.26 46.98 3.91
111 115 2.493035 CGCAATGCTGATGGTATGGTA 58.507 47.619 2.94 0.00 0.00 3.25
112 116 1.311859 CGCAATGCTGATGGTATGGT 58.688 50.000 2.94 0.00 0.00 3.55
113 117 0.594602 CCGCAATGCTGATGGTATGG 59.405 55.000 2.94 0.00 0.00 2.74
114 118 1.311859 ACCGCAATGCTGATGGTATG 58.688 50.000 3.13 0.00 32.71 2.39
115 119 1.949525 GAACCGCAATGCTGATGGTAT 59.050 47.619 3.13 0.00 33.17 2.73
132 136 1.204312 GCGTGAAAGCGGAGTGAAC 59.796 57.895 0.00 0.00 0.00 3.18
152 156 3.363575 CGTGTAAATTGTTGGTGTCGAGG 60.364 47.826 0.00 0.00 0.00 4.63
163 167 4.142643 ACCGTGTGTTTTCGTGTAAATTGT 60.143 37.500 0.00 0.00 0.00 2.71
180 184 2.536761 TGCTTGCTTACTTACCGTGT 57.463 45.000 0.00 0.00 0.00 4.49
184 188 4.324267 TCTCCTTTGCTTGCTTACTTACC 58.676 43.478 0.00 0.00 0.00 2.85
193 197 3.981211 TGTTTTCATCTCCTTTGCTTGC 58.019 40.909 0.00 0.00 0.00 4.01
197 201 5.990996 TGGATTTTGTTTTCATCTCCTTTGC 59.009 36.000 0.00 0.00 0.00 3.68
198 202 7.874016 TGATGGATTTTGTTTTCATCTCCTTTG 59.126 33.333 0.00 0.00 36.24 2.77
225 230 3.190535 GGTGCACCTACAATTGTACCAAG 59.809 47.826 29.12 6.66 45.17 3.61
234 239 1.346395 TGACTTCGGTGCACCTACAAT 59.654 47.619 32.28 14.65 0.00 2.71
243 248 1.225855 TGAACATGTGACTTCGGTGC 58.774 50.000 0.00 0.00 0.00 5.01
314 324 1.304052 TTGTTTGGAGGGCGGATGG 60.304 57.895 0.00 0.00 0.00 3.51
322 332 1.659794 CGGGCTTGTTGTTTGGAGG 59.340 57.895 0.00 0.00 0.00 4.30
350 367 2.117423 GGACCCAACCCAACCCAG 59.883 66.667 0.00 0.00 0.00 4.45
377 410 2.095438 TTATGGGGGCGTGGGGTTTT 62.095 55.000 0.00 0.00 0.00 2.43
429 462 0.661020 GGTAGAGAGAGAGAGTGCGC 59.339 60.000 0.00 0.00 0.00 6.09
497 558 1.021968 GCGTATTTGAAAGCCGGGAT 58.978 50.000 2.18 0.00 0.00 3.85
498 559 1.027792 GGCGTATTTGAAAGCCGGGA 61.028 55.000 2.18 0.00 40.17 5.14
503 564 1.365699 TCTCGGGCGTATTTGAAAGC 58.634 50.000 0.00 0.00 0.00 3.51
505 577 3.259064 CTCTTCTCGGGCGTATTTGAAA 58.741 45.455 0.00 0.00 0.00 2.69
506 578 2.418197 CCTCTTCTCGGGCGTATTTGAA 60.418 50.000 0.00 0.00 0.00 2.69
509 581 1.409427 CTCCTCTTCTCGGGCGTATTT 59.591 52.381 0.00 0.00 0.00 1.40
511 583 0.183014 TCTCCTCTTCTCGGGCGTAT 59.817 55.000 0.00 0.00 0.00 3.06
513 585 1.751162 CTCTCCTCTTCTCGGGCGT 60.751 63.158 0.00 0.00 0.00 5.68
515 587 0.106918 TCTCTCTCCTCTTCTCGGGC 60.107 60.000 0.00 0.00 0.00 6.13
527 599 1.411074 GGGTTCCTCCTCCTCTCTCTC 60.411 61.905 0.00 0.00 36.25 3.20
595 670 3.741075 GCGTGATGAGAGAGAGAGAGAGA 60.741 52.174 0.00 0.00 0.00 3.10
596 671 2.545526 GCGTGATGAGAGAGAGAGAGAG 59.454 54.545 0.00 0.00 0.00 3.20
597 672 2.093235 TGCGTGATGAGAGAGAGAGAGA 60.093 50.000 0.00 0.00 0.00 3.10
598 673 2.032054 GTGCGTGATGAGAGAGAGAGAG 59.968 54.545 0.00 0.00 0.00 3.20
599 674 2.013400 GTGCGTGATGAGAGAGAGAGA 58.987 52.381 0.00 0.00 0.00 3.10
600 675 1.742268 TGTGCGTGATGAGAGAGAGAG 59.258 52.381 0.00 0.00 0.00 3.20
1195 1322 2.447714 GGGAGTGGGGAGAGGCATC 61.448 68.421 0.00 0.00 0.00 3.91
1198 1325 2.766229 GAGGGAGTGGGGAGAGGC 60.766 72.222 0.00 0.00 0.00 4.70
1248 1376 0.465460 AGAAACGGCCAAGAACTGCA 60.465 50.000 2.24 0.00 0.00 4.41
1250 1378 1.676006 ACAAGAAACGGCCAAGAACTG 59.324 47.619 2.24 0.00 0.00 3.16
1310 1461 0.178990 AGCACCCCAAGAAACTGGAC 60.179 55.000 0.00 0.00 38.96 4.02
1335 1486 3.319972 GTGGAAACCCCTCTAAAAACCAC 59.680 47.826 0.00 0.00 38.40 4.16
1336 1487 3.052793 TGTGGAAACCCCTCTAAAAACCA 60.053 43.478 0.00 0.00 35.38 3.67
1337 1488 3.319972 GTGTGGAAACCCCTCTAAAAACC 59.680 47.826 0.00 0.00 35.38 3.27
1339 1490 4.079672 TCTGTGTGGAAACCCCTCTAAAAA 60.080 41.667 0.00 0.00 35.38 1.94
1341 1492 3.050089 TCTGTGTGGAAACCCCTCTAAA 58.950 45.455 0.00 0.00 35.38 1.85
1342 1493 2.696775 TCTGTGTGGAAACCCCTCTAA 58.303 47.619 0.00 0.00 35.38 2.10
1343 1494 2.409064 TCTGTGTGGAAACCCCTCTA 57.591 50.000 0.00 0.00 35.38 2.43
1344 1495 1.747444 ATCTGTGTGGAAACCCCTCT 58.253 50.000 0.00 0.00 35.38 3.69
1345 1496 2.558359 CAAATCTGTGTGGAAACCCCTC 59.442 50.000 0.00 0.00 35.38 4.30
1346 1497 2.597455 CAAATCTGTGTGGAAACCCCT 58.403 47.619 0.00 0.00 35.38 4.79
1347 1498 1.000843 GCAAATCTGTGTGGAAACCCC 59.999 52.381 0.00 0.00 0.00 4.95
1348 1499 1.686052 TGCAAATCTGTGTGGAAACCC 59.314 47.619 0.00 0.00 0.00 4.11
1349 1500 2.622942 TCTGCAAATCTGTGTGGAAACC 59.377 45.455 0.00 0.00 0.00 3.27
1350 1501 3.988379 TCTGCAAATCTGTGTGGAAAC 57.012 42.857 0.00 0.00 0.00 2.78
1351 1502 5.163426 ACAAATCTGCAAATCTGTGTGGAAA 60.163 36.000 0.00 0.00 0.00 3.13
1352 1503 4.341806 ACAAATCTGCAAATCTGTGTGGAA 59.658 37.500 0.00 0.00 0.00 3.53
1382 1534 4.018688 ACAGGGGAGGTAAAATACAGGAAC 60.019 45.833 0.00 0.00 0.00 3.62
1395 1547 3.003763 GCGAGGAACAGGGGAGGT 61.004 66.667 0.00 0.00 0.00 3.85
1411 1563 1.269257 GGCTTGAACTTGTGTGGAAGC 60.269 52.381 0.00 0.00 39.02 3.86
1415 1567 1.679139 TCTGGCTTGAACTTGTGTGG 58.321 50.000 0.00 0.00 0.00 4.17
1426 1578 2.942710 CTTGTGAGCAAATCTGGCTTG 58.057 47.619 0.00 0.00 42.78 4.01
1491 1646 5.473039 CCCTAAAACTGCAAGGAAAGATTG 58.527 41.667 2.79 0.00 39.30 2.67
1503 1658 1.330829 GTCGCATAGCCCTAAAACTGC 59.669 52.381 0.00 0.00 0.00 4.40
1522 1677 5.171339 AGCACTCCAAGAATAATCACTGT 57.829 39.130 0.00 0.00 0.00 3.55
1531 1686 5.700402 AATAGTGGTAGCACTCCAAGAAT 57.300 39.130 29.64 14.51 36.68 2.40
1538 1693 4.113354 CGAGGAAAATAGTGGTAGCACTC 58.887 47.826 29.64 15.61 36.68 3.51
1542 1697 4.612943 CTCTCGAGGAAAATAGTGGTAGC 58.387 47.826 13.56 0.00 0.00 3.58
1560 1715 3.520569 GGTGAGATGAGAACAAGCTCTC 58.479 50.000 0.00 0.00 41.98 3.20
1573 1728 0.392193 GGCAGACACTGGGTGAGATG 60.392 60.000 4.62 1.95 36.96 2.90
1578 1733 0.754957 TTTTGGGCAGACACTGGGTG 60.755 55.000 0.00 0.00 39.75 4.61
1676 5058 4.342665 AGGAGAAACGGCCAAAACAAATTA 59.657 37.500 2.24 0.00 0.00 1.40
1779 5164 3.124297 GCACACAGTAGCAGAAAGATGAC 59.876 47.826 0.00 0.00 0.00 3.06
1821 5206 4.003788 CGCCCGAACAGACAGGGT 62.004 66.667 1.46 0.00 46.69 4.34
1837 5222 0.934496 CAATATACGCACCCACACCG 59.066 55.000 0.00 0.00 0.00 4.94
1889 5276 3.917380 CGACGCATCCTATCATTTCTCTC 59.083 47.826 0.00 0.00 0.00 3.20
1890 5277 3.319405 ACGACGCATCCTATCATTTCTCT 59.681 43.478 0.00 0.00 0.00 3.10
1935 5323 2.826777 AATGGAGGTGCAAGCGAGGG 62.827 60.000 0.00 0.00 40.95 4.30
1947 5335 6.233434 TGCTTGCTACTGATAATAATGGAGG 58.767 40.000 0.00 0.00 0.00 4.30
2088 5505 7.401060 TCCTGGGGAAATAATATTTAGCTGA 57.599 36.000 0.00 0.00 0.00 4.26
2121 5539 9.122779 GTGTAGGTAGATATAACTATAGGCAGG 57.877 40.741 4.43 0.00 0.00 4.85
2177 5595 3.085947 TCAGCAGGGCAGGGCTAG 61.086 66.667 0.00 0.00 38.56 3.42
2221 5646 1.134189 CGTTTGACCTTATCCTCCCCC 60.134 57.143 0.00 0.00 0.00 5.40
2222 5647 1.835531 TCGTTTGACCTTATCCTCCCC 59.164 52.381 0.00 0.00 0.00 4.81
2223 5648 2.764572 TCTCGTTTGACCTTATCCTCCC 59.235 50.000 0.00 0.00 0.00 4.30
2224 5649 3.700038 TCTCTCGTTTGACCTTATCCTCC 59.300 47.826 0.00 0.00 0.00 4.30
2225 5650 4.985538 TCTCTCGTTTGACCTTATCCTC 57.014 45.455 0.00 0.00 0.00 3.71
2226 5651 5.163395 GGAATCTCTCGTTTGACCTTATCCT 60.163 44.000 0.00 0.00 0.00 3.24
2227 5652 5.051153 GGAATCTCTCGTTTGACCTTATCC 58.949 45.833 0.00 0.00 0.00 2.59
2251 5969 3.305516 GGCAGGCACCCTTGGTTG 61.306 66.667 0.00 0.00 31.02 3.77
2252 5970 3.511610 AGGCAGGCACCCTTGGTT 61.512 61.111 0.00 0.00 31.02 3.67
2253 5971 4.290622 CAGGCAGGCACCCTTGGT 62.291 66.667 0.00 0.00 35.62 3.67
2444 6171 2.623878 ATCTGAAGCAGAGCATGGAG 57.376 50.000 3.36 0.00 44.08 3.86
2500 6227 6.573664 TTGAAATGAAATACAGTGGGAGTG 57.426 37.500 0.00 0.00 0.00 3.51
2504 6231 7.432869 TGAACTTTGAAATGAAATACAGTGGG 58.567 34.615 0.00 0.00 0.00 4.61
2541 6278 8.734386 AGGAAATGAAAAATCTGTCATCAGTAC 58.266 33.333 0.00 0.00 41.91 2.73
2542 6279 8.868522 AGGAAATGAAAAATCTGTCATCAGTA 57.131 30.769 0.00 0.00 41.91 2.74
2543 6280 7.771927 AGGAAATGAAAAATCTGTCATCAGT 57.228 32.000 0.00 0.00 41.91 3.41
2544 6281 9.731819 CATAGGAAATGAAAAATCTGTCATCAG 57.268 33.333 0.00 0.00 42.54 2.90
2545 6282 9.465199 TCATAGGAAATGAAAAATCTGTCATCA 57.535 29.630 0.00 0.00 33.31 3.07
2546 6283 9.947669 CTCATAGGAAATGAAAAATCTGTCATC 57.052 33.333 0.00 0.00 33.31 2.92
2547 6284 9.471702 ACTCATAGGAAATGAAAAATCTGTCAT 57.528 29.630 0.00 0.00 36.00 3.06
2548 6285 8.733458 CACTCATAGGAAATGAAAAATCTGTCA 58.267 33.333 0.00 0.00 0.00 3.58
2549 6286 8.950210 TCACTCATAGGAAATGAAAAATCTGTC 58.050 33.333 0.00 0.00 0.00 3.51
2550 6287 8.868522 TCACTCATAGGAAATGAAAAATCTGT 57.131 30.769 0.00 0.00 0.00 3.41
2551 6288 9.731819 CATCACTCATAGGAAATGAAAAATCTG 57.268 33.333 0.00 0.00 0.00 2.90
2552 6289 9.471702 ACATCACTCATAGGAAATGAAAAATCT 57.528 29.630 2.27 0.00 0.00 2.40
2666 6406 3.253188 GGACAAAAGCAATGCAGTACTCA 59.747 43.478 8.35 0.00 0.00 3.41
2667 6407 3.366374 GGGACAAAAGCAATGCAGTACTC 60.366 47.826 8.35 0.00 0.00 2.59
2668 6408 2.558359 GGGACAAAAGCAATGCAGTACT 59.442 45.455 8.35 0.00 0.00 2.73
2698 6438 2.087646 GCACTCATTTCCTTGGTCCTC 58.912 52.381 0.00 0.00 0.00 3.71
3028 6768 3.421844 GTTATCACCACCCTCTTTTGCT 58.578 45.455 0.00 0.00 0.00 3.91
3029 6769 2.492088 GGTTATCACCACCCTCTTTTGC 59.508 50.000 0.00 0.00 43.61 3.68
3038 6778 6.238925 GCATAATTACAAGGGTTATCACCACC 60.239 42.308 0.00 0.00 46.43 4.61
3039 6779 6.320164 TGCATAATTACAAGGGTTATCACCAC 59.680 38.462 0.00 0.00 46.43 4.16
3040 6780 6.320164 GTGCATAATTACAAGGGTTATCACCA 59.680 38.462 0.00 0.00 46.43 4.17
3081 6821 7.614494 CCATGAACCATCAATTTTTCTAGGTT 58.386 34.615 0.00 0.00 39.49 3.50
3087 6827 4.632688 CCAGCCATGAACCATCAATTTTTC 59.367 41.667 0.00 0.00 39.49 2.29
3096 6836 1.285962 AGTTAGCCAGCCATGAACCAT 59.714 47.619 0.00 0.00 0.00 3.55
3098 6838 1.098050 CAGTTAGCCAGCCATGAACC 58.902 55.000 0.00 0.00 0.00 3.62
3102 6842 1.381928 CCTGCAGTTAGCCAGCCATG 61.382 60.000 13.81 0.00 44.83 3.66
3131 6871 1.631388 CCATGTACACCCACCTACCAA 59.369 52.381 0.00 0.00 0.00 3.67
3147 6887 2.224113 GGCCCTATGCAATTCAACCATG 60.224 50.000 0.00 0.00 43.89 3.66
3151 6891 2.497273 AGTTGGCCCTATGCAATTCAAC 59.503 45.455 0.00 0.59 43.89 3.18
3241 6981 7.149569 AGATGAACTCATTACACAATTGTGG 57.850 36.000 35.20 21.68 42.49 4.17
3337 7089 3.964031 ACAATGCTGGGAAGGTAAAACAA 59.036 39.130 0.00 0.00 0.00 2.83
3345 7097 2.242043 AGAACAACAATGCTGGGAAGG 58.758 47.619 0.00 0.00 0.00 3.46
3350 7102 7.645340 GCAAGTATATAAGAACAACAATGCTGG 59.355 37.037 0.00 0.00 0.00 4.85
3490 7243 3.181461 GCTAGAGATGGCAATGGTGTACT 60.181 47.826 0.00 0.00 0.00 2.73
3502 7255 2.036992 GACATGTGGGAGCTAGAGATGG 59.963 54.545 1.15 0.00 0.00 3.51
3797 7553 2.046023 TGCTTGCCCGAGTCATGG 60.046 61.111 0.00 0.00 0.00 3.66
3890 7646 1.063649 CATGAACGCAGCCATGAGC 59.936 57.895 4.54 0.00 41.99 4.26
4059 7815 1.148310 GCGTACTTGAGCTTGCTGAA 58.852 50.000 0.00 0.00 0.00 3.02
4111 7880 1.608025 GCGAAGGATGACAGGAACACA 60.608 52.381 0.00 0.00 0.00 3.72
4126 7895 0.806868 AGATGCACATTGTGGCGAAG 59.193 50.000 18.05 0.00 33.64 3.79
4306 8075 1.227973 GAGGGCGATGATGAACCCC 60.228 63.158 0.00 0.00 43.96 4.95
4684 8453 0.031449 CCTTCTCGCCGATCCTCTTC 59.969 60.000 0.00 0.00 0.00 2.87
4762 8531 3.181456 CCAACCAACCAACCATGAAATGT 60.181 43.478 0.00 0.00 44.81 2.71
4763 8532 3.070734 TCCAACCAACCAACCATGAAATG 59.929 43.478 0.00 0.00 46.21 2.32
4764 8533 3.312890 TCCAACCAACCAACCATGAAAT 58.687 40.909 0.00 0.00 0.00 2.17
4765 8534 2.752030 TCCAACCAACCAACCATGAAA 58.248 42.857 0.00 0.00 0.00 2.69
4767 8536 2.461300 TTCCAACCAACCAACCATGA 57.539 45.000 0.00 0.00 0.00 3.07
4768 8537 2.697751 TCTTTCCAACCAACCAACCATG 59.302 45.455 0.00 0.00 0.00 3.66
4769 8538 3.039252 TCTTTCCAACCAACCAACCAT 57.961 42.857 0.00 0.00 0.00 3.55
4770 8539 2.534042 TCTTTCCAACCAACCAACCA 57.466 45.000 0.00 0.00 0.00 3.67
4771 8540 4.100963 AGAAATCTTTCCAACCAACCAACC 59.899 41.667 0.00 0.00 37.92 3.77
4772 8541 5.276461 AGAAATCTTTCCAACCAACCAAC 57.724 39.130 0.00 0.00 37.92 3.77
4773 8542 5.669477 CAAGAAATCTTTCCAACCAACCAA 58.331 37.500 0.00 0.00 37.92 3.67
4774 8543 4.442753 GCAAGAAATCTTTCCAACCAACCA 60.443 41.667 0.00 0.00 37.92 3.67
4777 8546 5.010617 GGTAGCAAGAAATCTTTCCAACCAA 59.989 40.000 8.86 0.00 37.92 3.67
4781 8550 6.267471 ACAATGGTAGCAAGAAATCTTTCCAA 59.733 34.615 0.00 0.00 37.92 3.53
4782 8551 5.774690 ACAATGGTAGCAAGAAATCTTTCCA 59.225 36.000 0.00 1.72 37.92 3.53
4783 8552 6.272822 ACAATGGTAGCAAGAAATCTTTCC 57.727 37.500 0.00 0.00 37.92 3.13
4814 8587 0.532862 ACCCTCTCACAAGCACAACG 60.533 55.000 0.00 0.00 0.00 4.10
5009 8790 8.896744 CATATCACCATCAGTTACAATTGTCTT 58.103 33.333 15.85 0.00 0.00 3.01
5028 8809 4.260784 GCGATGAACAAGGAACCATATCAC 60.261 45.833 0.00 0.00 0.00 3.06
5029 8810 3.876914 GCGATGAACAAGGAACCATATCA 59.123 43.478 0.00 0.00 0.00 2.15
5030 8811 3.251004 GGCGATGAACAAGGAACCATATC 59.749 47.826 0.00 0.00 0.00 1.63
5031 8812 3.214328 GGCGATGAACAAGGAACCATAT 58.786 45.455 0.00 0.00 0.00 1.78
5032 8813 2.639065 GGCGATGAACAAGGAACCATA 58.361 47.619 0.00 0.00 0.00 2.74
5033 8814 1.463674 GGCGATGAACAAGGAACCAT 58.536 50.000 0.00 0.00 0.00 3.55
5034 8815 0.608035 GGGCGATGAACAAGGAACCA 60.608 55.000 0.00 0.00 0.00 3.67
5035 8816 0.322546 AGGGCGATGAACAAGGAACC 60.323 55.000 0.00 0.00 0.00 3.62
5036 8817 0.804989 CAGGGCGATGAACAAGGAAC 59.195 55.000 0.00 0.00 0.00 3.62
5040 8831 0.036010 AGGACAGGGCGATGAACAAG 60.036 55.000 0.00 0.00 0.00 3.16
5054 8845 4.080863 GCTAGAGATTTTTCAGGGAGGACA 60.081 45.833 0.00 0.00 0.00 4.02
5056 8847 4.104086 TGCTAGAGATTTTTCAGGGAGGA 58.896 43.478 0.00 0.00 0.00 3.71
5059 8850 4.532126 TGACTGCTAGAGATTTTTCAGGGA 59.468 41.667 0.00 0.00 0.00 4.20
5061 8852 5.220815 GCATGACTGCTAGAGATTTTTCAGG 60.221 44.000 0.00 0.00 45.32 3.86
5062 8853 5.808403 GCATGACTGCTAGAGATTTTTCAG 58.192 41.667 0.00 0.00 45.32 3.02
5063 8854 5.808042 GCATGACTGCTAGAGATTTTTCA 57.192 39.130 0.00 0.00 45.32 2.69
5118 9182 6.978080 TGCACCAGAAGTTTTTATTTTCACTC 59.022 34.615 0.00 0.00 0.00 3.51
5119 9183 6.872920 TGCACCAGAAGTTTTTATTTTCACT 58.127 32.000 0.00 0.00 0.00 3.41
5122 9186 8.490355 CAGATTGCACCAGAAGTTTTTATTTTC 58.510 33.333 0.00 0.00 0.00 2.29
5162 9226 8.552034 CAAAGTTCCTTTGTACTAGAGTGAAAG 58.448 37.037 8.25 8.18 43.85 2.62
5163 9227 8.433421 CAAAGTTCCTTTGTACTAGAGTGAAA 57.567 34.615 8.25 0.00 43.85 2.69
5178 9242 6.818142 CAGAATGAACCAAAACAAAGTTCCTT 59.182 34.615 0.00 0.00 39.69 3.36
5204 9268 4.707030 TTCCAGAATAGCAGCACATTTG 57.293 40.909 0.00 0.00 0.00 2.32
5209 9273 3.119708 CCAAGTTTCCAGAATAGCAGCAC 60.120 47.826 0.00 0.00 0.00 4.40
5216 9280 6.126863 ACACTCATCCAAGTTTCCAGAATA 57.873 37.500 0.00 0.00 0.00 1.75
5299 9392 3.287867 AATTAGTGGAGTGCCCTGATG 57.712 47.619 0.00 0.00 35.38 3.07
5331 9425 3.947196 TGTGCCCTGATAATGATGTGTTC 59.053 43.478 0.00 0.00 0.00 3.18
5458 9553 9.545105 AGCATCAACAATATTTTTCACAAGAAA 57.455 25.926 0.00 0.00 41.78 2.52
5465 9560 9.585099 GGTCATTAGCATCAACAATATTTTTCA 57.415 29.630 0.00 0.00 0.00 2.69
5466 9561 9.807649 AGGTCATTAGCATCAACAATATTTTTC 57.192 29.630 0.00 0.00 0.00 2.29
5468 9563 9.807649 GAAGGTCATTAGCATCAACAATATTTT 57.192 29.630 0.00 0.00 0.00 1.82
5469 9564 8.416329 GGAAGGTCATTAGCATCAACAATATTT 58.584 33.333 0.00 0.00 0.00 1.40
5470 9565 7.560991 TGGAAGGTCATTAGCATCAACAATATT 59.439 33.333 0.00 0.00 0.00 1.28
5471 9566 7.013655 GTGGAAGGTCATTAGCATCAACAATAT 59.986 37.037 0.00 0.00 27.69 1.28
5472 9567 6.318648 GTGGAAGGTCATTAGCATCAACAATA 59.681 38.462 0.00 0.00 27.69 1.90
5473 9568 5.126061 GTGGAAGGTCATTAGCATCAACAAT 59.874 40.000 0.00 0.00 27.69 2.71
5474 9569 4.458989 GTGGAAGGTCATTAGCATCAACAA 59.541 41.667 0.00 0.00 27.69 2.83
5620 9744 5.511202 GGGATTAAACATATGGGGTGCAATG 60.511 44.000 7.80 0.00 0.00 2.82
5621 9745 4.592778 GGGATTAAACATATGGGGTGCAAT 59.407 41.667 7.80 0.00 0.00 3.56
5622 9746 3.964031 GGGATTAAACATATGGGGTGCAA 59.036 43.478 7.80 0.00 0.00 4.08
5623 9747 3.571590 GGGATTAAACATATGGGGTGCA 58.428 45.455 7.80 0.00 0.00 4.57
5624 9748 2.897326 GGGGATTAAACATATGGGGTGC 59.103 50.000 7.80 0.00 0.00 5.01
5650 9776 4.103153 TCTCAGTCCTTCTGGTGATTGTTT 59.897 41.667 0.00 0.00 43.76 2.83
5653 9779 3.969287 TCTCAGTCCTTCTGGTGATTG 57.031 47.619 0.00 0.00 43.76 2.67
5654 9780 6.627087 TTTATCTCAGTCCTTCTGGTGATT 57.373 37.500 0.00 0.00 43.76 2.57
5691 9821 5.988561 AGAACAGAGCTTTCTTCAAGTACAG 59.011 40.000 0.00 0.00 34.56 2.74


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

AutoCloner maintained by Alex Coulton.