Multiple sequence alignment - TraesCS5A01G418000

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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 TraesCS5A01G418000 chr5A 100.000 5068 0 0 1 5068 606156479 606161546 0.000000e+00 9359.0
1 TraesCS5A01G418000 chr5A 86.013 1194 123 29 2618 3794 430247472 430246306 0.000000e+00 1240.0
2 TraesCS5A01G418000 chr5A 94.714 227 12 0 2288 2514 430247852 430247626 2.240000e-93 353.0
3 TraesCS5A01G418000 chr5A 82.878 403 60 6 2105 2505 566632414 566632019 2.240000e-93 353.0
4 TraesCS5A01G418000 chr5B 90.475 3895 202 54 434 4233 595656196 595660016 0.000000e+00 4981.0
5 TraesCS5A01G418000 chr5B 88.077 1040 96 16 2691 3723 378815513 378816531 0.000000e+00 1208.0
6 TraesCS5A01G418000 chr5B 92.414 435 20 5 1 434 595655727 595656149 4.340000e-170 608.0
7 TraesCS5A01G418000 chr5B 94.348 230 13 0 2285 2514 378815067 378815296 2.240000e-93 353.0
8 TraesCS5A01G418000 chr5B 93.750 208 7 4 4860 5067 595660874 595661075 1.770000e-79 307.0
9 TraesCS5A01G418000 chr5B 86.268 284 24 6 4587 4864 595660643 595660917 1.380000e-75 294.0
10 TraesCS5A01G418000 chr5B 97.059 34 1 0 1367 1400 577225731 577225764 1.970000e-04 58.4
11 TraesCS5A01G418000 chr5D 94.571 1713 60 17 2618 4308 484573852 484575553 0.000000e+00 2617.0
12 TraesCS5A01G418000 chr5D 87.163 1114 108 21 2691 3791 326369110 326370201 0.000000e+00 1232.0
13 TraesCS5A01G418000 chr5D 90.435 690 31 11 1589 2271 484572438 484573099 0.000000e+00 876.0
14 TraesCS5A01G418000 chr5D 92.096 582 28 6 4487 5068 484576434 484576997 0.000000e+00 804.0
15 TraesCS5A01G418000 chr5D 92.324 482 26 4 2127 2598 484573105 484573585 0.000000e+00 675.0
16 TraesCS5A01G418000 chr5D 83.333 714 52 35 895 1584 484571667 484572337 9.390000e-167 597.0
17 TraesCS5A01G418000 chr5D 93.913 230 14 0 2285 2514 326368540 326368769 1.040000e-91 348.0
18 TraesCS5A01G418000 chr5D 83.978 181 23 4 513 693 484571224 484571398 8.730000e-38 169.0
19 TraesCS5A01G418000 chr5D 80.117 171 27 7 2024 2191 326368362 326368528 2.480000e-23 121.0
20 TraesCS5A01G418000 chr5D 89.333 75 8 0 4306 4380 484575855 484575929 1.500000e-15 95.3
21 TraesCS5A01G418000 chr5D 77.848 158 18 10 252 399 484571069 484571219 1.170000e-11 82.4
22 TraesCS5A01G418000 chr2B 84.431 501 68 6 3244 3740 55913159 55913653 7.630000e-133 484.0
23 TraesCS5A01G418000 chr2B 82.661 496 76 8 3246 3737 55923785 55924274 1.010000e-116 431.0
24 TraesCS5A01G418000 chr2B 79.701 468 70 17 3281 3740 40280557 40280107 1.060000e-81 315.0
25 TraesCS5A01G418000 chr2B 84.286 70 7 2 4311 4377 143807552 143807484 1.180000e-06 65.8
26 TraesCS5A01G418000 chr2A 83.400 500 74 7 3244 3739 36672845 36672351 5.980000e-124 455.0
27 TraesCS5A01G418000 chr2A 90.909 66 6 0 4309 4374 141506316 141506381 6.990000e-14 89.8
28 TraesCS5A01G418000 chr3B 85.464 399 34 10 1250 1634 242898204 242897816 1.320000e-105 394.0
29 TraesCS5A01G418000 chr4A 76.428 823 124 39 2043 2838 716529850 716529071 1.030000e-101 381.0
30 TraesCS5A01G418000 chr4A 81.023 469 73 9 2043 2504 594021820 594022279 4.820000e-95 359.0
31 TraesCS5A01G418000 chr1A 81.023 469 73 9 2043 2504 554113237 554112778 4.820000e-95 359.0
32 TraesCS5A01G418000 chr4B 84.906 106 7 5 2741 2841 626386895 626386996 1.160000e-16 99.0
33 TraesCS5A01G418000 chr6B 91.667 60 4 1 4306 4365 184636327 184636269 1.170000e-11 82.4
34 TraesCS5A01G418000 chr4D 90.909 55 5 0 4311 4365 481578760 481578814 1.960000e-09 75.0
35 TraesCS5A01G418000 chr2D 90.909 55 5 0 4311 4365 28425361 28425307 1.960000e-09 75.0
36 TraesCS5A01G418000 chr2D 91.304 46 4 0 4312 4357 14800370 14800325 4.240000e-06 63.9
37 TraesCS5A01G418000 chr1D 100.000 31 0 0 4310 4340 42514892 42514862 1.970000e-04 58.4
38 TraesCS5A01G418000 chr1D 100.000 31 0 0 4310 4340 459948327 459948297 1.970000e-04 58.4


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 TraesCS5A01G418000 chr5A 606156479 606161546 5067 False 9359.0000 9359 100.000000 1 5068 1 chr5A.!!$F1 5067
1 TraesCS5A01G418000 chr5A 430246306 430247852 1546 True 796.5000 1240 90.363500 2288 3794 2 chr5A.!!$R2 1506
2 TraesCS5A01G418000 chr5B 595655727 595661075 5348 False 1547.5000 4981 90.726750 1 5067 4 chr5B.!!$F3 5066
3 TraesCS5A01G418000 chr5B 378815067 378816531 1464 False 780.5000 1208 91.212500 2285 3723 2 chr5B.!!$F2 1438
4 TraesCS5A01G418000 chr5D 484571069 484576997 5928 False 739.4625 2617 87.989750 252 5068 8 chr5D.!!$F2 4816
5 TraesCS5A01G418000 chr5D 326368362 326370201 1839 False 567.0000 1232 87.064333 2024 3791 3 chr5D.!!$F1 1767
6 TraesCS5A01G418000 chr4A 716529071 716529850 779 True 381.0000 381 76.428000 2043 2838 1 chr4A.!!$R1 795

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
427 438 0.036388 GTCCGAGCAAATCCCACAGA 60.036 55.000 0.00 0.0 0.00 3.41 F
1171 1361 0.105039 GGGTATCGTCTTCCTGGCTG 59.895 60.000 0.00 0.0 0.00 4.85 F
1371 1568 0.109597 CCATGGACGCTGTTGCTTTC 60.110 55.000 5.56 0.0 36.97 2.62 F
1995 2333 0.107361 ACGGCACCCCTACAATAAGC 60.107 55.000 0.00 0.0 0.00 3.09 F
2121 2471 0.515564 CCGAGTTACACGCAAAAGGG 59.484 55.000 0.00 0.0 0.00 3.95 F
3206 4149 1.280421 AGGATGGAGCTGGTTGAAGTC 59.720 52.381 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1554 0.040958 CACAGGAAAGCAACAGCGTC 60.041 55.0 0.00 0.0 0.0 5.19 R
1976 2314 0.107361 GCTTATTGTAGGGGTGCCGT 60.107 55.0 0.00 0.0 0.0 5.68 R
3095 4038 0.930310 CTGTGCACACGAATATCCGG 59.070 55.0 17.42 0.0 0.0 5.14 R
3892 4845 2.164422 CACAGATGCAGAAGTCCGTAGA 59.836 50.0 0.00 0.0 0.0 2.59 R
3897 4850 2.740981 CTCAACACAGATGCAGAAGTCC 59.259 50.0 0.00 0.0 0.0 3.85 R
4807 6626 0.039256 GCATGCCGTTCAGCTTCAAA 60.039 50.0 6.36 0.0 0.0 2.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.049405 GGTTTGACATAAGTTCCACAGTGAG 60.049 44.000 0.62 0.00 0.00 3.51
25 26 5.545063 TTGACATAAGTTCCACAGTGAGA 57.455 39.130 0.62 0.00 0.00 3.27
43 44 7.663081 ACAGTGAGATGACTTTGATGTTTATGT 59.337 33.333 0.00 0.00 0.00 2.29
44 45 8.509690 CAGTGAGATGACTTTGATGTTTATGTT 58.490 33.333 0.00 0.00 0.00 2.71
45 46 9.071276 AGTGAGATGACTTTGATGTTTATGTTT 57.929 29.630 0.00 0.00 0.00 2.83
116 118 5.533482 TCATCAACCGGTGGTAAAATTTTG 58.467 37.500 8.52 0.00 33.12 2.44
134 136 6.560253 ATTTTGTATGACCAGTGACTGTTC 57.440 37.500 12.15 7.58 0.00 3.18
198 200 2.047560 ACTTTACCGGCGCAGGTC 60.048 61.111 35.52 2.84 44.68 3.85
250 252 1.872952 CATGTTCTGGTCAACTGCGAA 59.127 47.619 0.00 0.00 0.00 4.70
270 272 5.050972 GCGAAGAGTAGGATTTATTTGTCCG 60.051 44.000 0.00 0.00 39.54 4.79
369 371 4.632153 CCGCACTAGTAAATAATCCAGCT 58.368 43.478 0.00 0.00 0.00 4.24
370 372 5.779922 CCGCACTAGTAAATAATCCAGCTA 58.220 41.667 0.00 0.00 0.00 3.32
371 373 5.864474 CCGCACTAGTAAATAATCCAGCTAG 59.136 44.000 0.00 0.00 34.00 3.42
372 374 5.346281 CGCACTAGTAAATAATCCAGCTAGC 59.654 44.000 6.62 6.62 31.77 3.42
408 419 4.217754 TCCGGTTTCATTTTCTTTGTCG 57.782 40.909 0.00 0.00 0.00 4.35
418 429 1.942677 TTCTTTGTCGTCCGAGCAAA 58.057 45.000 13.00 13.00 0.00 3.68
419 430 2.163818 TCTTTGTCGTCCGAGCAAAT 57.836 45.000 13.62 0.00 32.61 2.32
421 432 1.128692 CTTTGTCGTCCGAGCAAATCC 59.871 52.381 13.62 0.00 32.61 3.01
425 436 1.375396 CGTCCGAGCAAATCCCACA 60.375 57.895 0.00 0.00 0.00 4.17
426 437 1.361668 CGTCCGAGCAAATCCCACAG 61.362 60.000 0.00 0.00 0.00 3.66
427 438 0.036388 GTCCGAGCAAATCCCACAGA 60.036 55.000 0.00 0.00 0.00 3.41
439 450 2.806434 TCCCACAGATTTCATGGTTGG 58.194 47.619 0.00 0.00 0.00 3.77
440 451 2.109834 TCCCACAGATTTCATGGTTGGT 59.890 45.455 0.00 0.00 0.00 3.67
453 511 1.423541 TGGTTGGTACTCTGGTGCATT 59.576 47.619 0.00 0.00 0.00 3.56
469 527 1.845266 CATTCTGTGCTATCGCTCGT 58.155 50.000 0.00 0.00 36.97 4.18
474 532 1.600013 CTGTGCTATCGCTCGTCTACT 59.400 52.381 0.00 0.00 36.97 2.57
603 664 7.065216 TGATTTACTTGAGAAAGATGAAGCG 57.935 36.000 0.00 0.00 0.00 4.68
618 679 2.758423 TGAAGCGTCTGCCTAAGATACA 59.242 45.455 0.31 0.00 44.31 2.29
936 1098 3.252284 AGGATAGGCCGGCCCATG 61.252 66.667 41.72 0.00 43.43 3.66
996 1165 2.583024 AGTAGGACGTATAGAGCCCC 57.417 55.000 0.00 0.00 0.00 5.80
1033 1213 3.781307 CGGGACCGGCATCTTCCA 61.781 66.667 0.00 0.00 35.56 3.53
1035 1215 2.668632 GGACCGGCATCTTCCACA 59.331 61.111 0.00 0.00 0.00 4.17
1133 1315 4.704103 TCCTCGCCTGTGCTCCCT 62.704 66.667 0.00 0.00 34.43 4.20
1168 1358 1.070758 CCATGGGTATCGTCTTCCTGG 59.929 57.143 2.85 0.00 0.00 4.45
1169 1359 0.759346 ATGGGTATCGTCTTCCTGGC 59.241 55.000 0.00 0.00 0.00 4.85
1170 1360 0.325296 TGGGTATCGTCTTCCTGGCT 60.325 55.000 0.00 0.00 0.00 4.75
1171 1361 0.105039 GGGTATCGTCTTCCTGGCTG 59.895 60.000 0.00 0.00 0.00 4.85
1172 1362 0.530870 GGTATCGTCTTCCTGGCTGC 60.531 60.000 0.00 0.00 0.00 5.25
1173 1363 0.175760 GTATCGTCTTCCTGGCTGCA 59.824 55.000 0.50 0.00 0.00 4.41
1174 1364 0.901827 TATCGTCTTCCTGGCTGCAA 59.098 50.000 0.50 0.00 0.00 4.08
1175 1365 0.254178 ATCGTCTTCCTGGCTGCAAT 59.746 50.000 0.50 0.00 0.00 3.56
1176 1366 0.901827 TCGTCTTCCTGGCTGCAATA 59.098 50.000 0.50 0.00 0.00 1.90
1177 1367 1.134699 TCGTCTTCCTGGCTGCAATAG 60.135 52.381 0.50 0.00 0.00 1.73
1287 1480 6.955963 CACTGTTTTATTCTGTATCTTCGTGC 59.044 38.462 0.00 0.00 0.00 5.34
1333 1530 9.921637 ATTCAGAATCCTATCTATTTCGAGTTC 57.078 33.333 0.00 0.00 0.00 3.01
1352 1549 2.639065 TCCTTTTATGCCATGTCCGTC 58.361 47.619 0.00 0.00 0.00 4.79
1353 1550 1.676006 CCTTTTATGCCATGTCCGTCC 59.324 52.381 0.00 0.00 0.00 4.79
1354 1551 2.364632 CTTTTATGCCATGTCCGTCCA 58.635 47.619 0.00 0.00 0.00 4.02
1355 1552 2.727123 TTTATGCCATGTCCGTCCAT 57.273 45.000 0.00 0.00 0.00 3.41
1356 1553 1.965935 TTATGCCATGTCCGTCCATG 58.034 50.000 4.93 4.93 41.52 3.66
1367 1564 2.870372 GTCCATGGACGCTGTTGC 59.130 61.111 28.52 3.94 35.30 4.17
1368 1565 1.672356 GTCCATGGACGCTGTTGCT 60.672 57.895 28.52 0.00 35.30 3.91
1369 1566 1.073025 TCCATGGACGCTGTTGCTT 59.927 52.632 11.44 0.00 36.97 3.91
1370 1567 0.537143 TCCATGGACGCTGTTGCTTT 60.537 50.000 11.44 0.00 36.97 3.51
1371 1568 0.109597 CCATGGACGCTGTTGCTTTC 60.110 55.000 5.56 0.00 36.97 2.62
1372 1569 0.109597 CATGGACGCTGTTGCTTTCC 60.110 55.000 0.00 0.00 38.66 3.13
1373 1570 0.250901 ATGGACGCTGTTGCTTTCCT 60.251 50.000 0.00 0.00 38.85 3.36
1457 1675 4.084328 GGACGCATTCACAGCATAATACTC 60.084 45.833 0.00 0.00 0.00 2.59
1461 1679 4.818546 GCATTCACAGCATAATACTCTGGT 59.181 41.667 0.00 0.00 32.42 4.00
1467 1685 2.430694 AGCATAATACTCTGGTGACGCA 59.569 45.455 0.00 0.00 0.00 5.24
1484 1702 2.256174 CGCATGCCTCTGTTTGAAATG 58.744 47.619 13.15 0.00 0.00 2.32
1487 1705 3.430895 GCATGCCTCTGTTTGAAATGTTG 59.569 43.478 6.36 0.00 0.00 3.33
1488 1706 4.796946 GCATGCCTCTGTTTGAAATGTTGA 60.797 41.667 6.36 0.00 0.00 3.18
1498 1722 6.272318 TGTTTGAAATGTTGATGGACTTGTC 58.728 36.000 0.00 0.00 0.00 3.18
1526 1750 5.584251 TGTTATTATGCATGCTTCGTTCTGA 59.416 36.000 20.33 0.00 0.00 3.27
1528 1752 5.762825 ATTATGCATGCTTCGTTCTGAAT 57.237 34.783 20.33 4.59 35.63 2.57
1530 1754 3.206034 TGCATGCTTCGTTCTGAATTG 57.794 42.857 20.33 0.00 35.63 2.32
1565 1792 3.076621 TCAGCCATGCTCAAAGTTACAG 58.923 45.455 0.00 0.00 36.40 2.74
1569 1796 3.568538 CCATGCTCAAAGTTACAGTTGC 58.431 45.455 0.00 0.00 0.00 4.17
1578 1805 6.288294 TCAAAGTTACAGTTGCTATCACAGT 58.712 36.000 0.00 0.00 0.00 3.55
1585 1812 5.414360 ACAGTTGCTATCACAGTCATGTAG 58.586 41.667 0.00 0.00 37.65 2.74
1586 1813 4.807834 CAGTTGCTATCACAGTCATGTAGG 59.192 45.833 0.00 0.00 37.65 3.18
1601 1924 9.490379 CAGTCATGTAGGTATAATTTCCTTACC 57.510 37.037 0.00 0.00 36.45 2.85
1605 1928 9.847224 CATGTAGGTATAATTTCCTTACCAGTT 57.153 33.333 0.00 0.00 38.27 3.16
1695 2024 9.856488 TCATCTAGACGCTAATTTATTATGTCC 57.144 33.333 0.00 0.00 32.45 4.02
1833 2166 2.720758 CGAACTCCTCAAGCACGCG 61.721 63.158 3.53 3.53 0.00 6.01
1890 2223 5.939764 AGCTTTCTTTTTCTTTGACCCTT 57.060 34.783 0.00 0.00 0.00 3.95
1953 2291 0.865769 CAGTACCAGAAACACACCGC 59.134 55.000 0.00 0.00 0.00 5.68
1958 2296 1.966451 CAGAAACACACCGCCTCCC 60.966 63.158 0.00 0.00 0.00 4.30
1959 2297 3.047877 GAAACACACCGCCTCCCG 61.048 66.667 0.00 0.00 0.00 5.14
1960 2298 3.819877 GAAACACACCGCCTCCCGT 62.820 63.158 0.00 0.00 34.38 5.28
1976 2314 6.017770 CGCCTCCCGTTGAATTATTATAAACA 60.018 38.462 0.00 0.00 0.00 2.83
1995 2333 0.107361 ACGGCACCCCTACAATAAGC 60.107 55.000 0.00 0.00 0.00 3.09
2086 2429 3.807622 TAGTTTCAACTAGTGTGCTGCAC 59.192 43.478 25.15 25.15 42.93 4.57
2121 2471 0.515564 CCGAGTTACACGCAAAAGGG 59.484 55.000 0.00 0.00 0.00 3.95
2131 2481 1.367471 GCAAAAGGGTTGGCCAGAC 59.633 57.895 5.11 7.55 36.17 3.51
2150 2500 6.932356 CAGACTTTCTGGCACATGTTATAT 57.068 37.500 0.00 0.00 40.71 0.86
2151 2501 6.722301 CAGACTTTCTGGCACATGTTATATG 58.278 40.000 0.00 0.00 40.71 1.78
2152 2502 5.297776 AGACTTTCTGGCACATGTTATATGC 59.702 40.000 0.00 0.00 38.20 3.14
2153 2503 5.195940 ACTTTCTGGCACATGTTATATGCT 58.804 37.500 0.00 0.00 38.20 3.79
2154 2504 5.653769 ACTTTCTGGCACATGTTATATGCTT 59.346 36.000 0.00 0.00 38.20 3.91
2254 2616 8.548721 ACAAGAAACTATAAATAGCATGTACGC 58.451 33.333 0.00 0.00 33.68 4.42
2271 2633 2.140717 ACGCGTTTCTTTTCGATTCCT 58.859 42.857 5.58 0.00 0.00 3.36
2272 2634 2.096417 ACGCGTTTCTTTTCGATTCCTG 60.096 45.455 5.58 0.00 0.00 3.86
2333 2846 7.285566 AGAATGGCAAGAAGATGCTTATTCTA 58.714 34.615 20.10 0.00 46.12 2.10
2552 3205 5.353938 TGTGTAAGTGGTGAGACTTGTTAC 58.646 41.667 0.00 0.00 36.80 2.50
2598 3254 4.300189 ACTGATGATCGCAGAAGTAGAC 57.700 45.455 18.84 0.00 43.58 2.59
2616 3520 2.430332 AGACTGAGCTAGGCAATGACTC 59.570 50.000 0.00 0.00 36.64 3.36
2644 3570 8.352201 TCTGAAACTTTTTCCATGTCTGTTATG 58.648 33.333 0.00 0.00 0.00 1.90
2649 3575 5.957842 TTTTCCATGTCTGTTATGGTGAC 57.042 39.130 0.00 0.00 44.35 3.67
2652 3578 3.055167 TCCATGTCTGTTATGGTGACCTG 60.055 47.826 2.11 0.00 44.35 4.00
2886 3823 2.044555 GGCGCCTAAACTTGGGACC 61.045 63.158 22.15 0.00 0.00 4.46
3001 3940 9.982651 GAGAGGTGTGCATCTTTATATAAGTTA 57.017 33.333 0.00 0.00 35.71 2.24
3005 3944 9.982651 GGTGTGCATCTTTATATAAGTTAGAGA 57.017 33.333 0.00 0.00 0.00 3.10
3015 3954 8.880991 TTATATAAGTTAGAGAGTAGGGCAGG 57.119 38.462 0.00 0.00 0.00 4.85
3040 3982 8.926092 GGATAATCCCTTGAGCTTAATTTAGT 57.074 34.615 0.00 0.00 0.00 2.24
3206 4149 1.280421 AGGATGGAGCTGGTTGAAGTC 59.720 52.381 0.00 0.00 0.00 3.01
3209 4152 1.371558 GGAGCTGGTTGAAGTCGGT 59.628 57.895 0.00 0.00 0.00 4.69
3703 4650 4.097892 GTGAAGCCAAGAAAAACAAGGAGA 59.902 41.667 0.00 0.00 0.00 3.71
3705 4652 5.363580 TGAAGCCAAGAAAAACAAGGAGAAT 59.636 36.000 0.00 0.00 0.00 2.40
3799 4752 1.963515 AGGATTTTTGGTGCACCTGAC 59.036 47.619 34.75 19.12 36.82 3.51
3829 4782 1.604604 GCTGTGTTAAGCCAACTGGA 58.395 50.000 0.00 0.00 38.05 3.86
3892 4845 4.276678 GTCTTTTTAGGCCGTAAAACCTGT 59.723 41.667 15.44 0.00 39.79 4.00
3897 4850 1.067354 AGGCCGTAAAACCTGTCTACG 60.067 52.381 0.00 5.41 38.47 3.51
3913 4866 2.164422 TCTACGGACTTCTGCATCTGTG 59.836 50.000 9.33 1.43 35.95 3.66
4019 4973 8.486210 TGTTGTTAGTCCTTGATATTAGCTGAT 58.514 33.333 0.00 0.00 0.00 2.90
4021 4975 8.484214 TGTTAGTCCTTGATATTAGCTGATCT 57.516 34.615 0.00 0.00 0.00 2.75
4073 5027 3.096092 TCTGGTTACCATGGCCATTTTC 58.904 45.455 17.92 5.10 30.82 2.29
4107 5066 5.007626 TCTGTATATCCTGCATTTTTGTCGC 59.992 40.000 0.00 0.00 0.00 5.19
4361 5689 8.410673 TGTTTTGGGCATTTTAGTATGAACTA 57.589 30.769 0.00 0.00 37.15 2.24
4365 5693 7.801716 TGGGCATTTTAGTATGAACTACATC 57.198 36.000 0.00 0.00 37.94 3.06
4367 5695 6.073222 GGGCATTTTAGTATGAACTACATCCG 60.073 42.308 0.00 0.00 37.94 4.18
4374 5702 4.580995 AGTATGAACTACATCCGGACTGAG 59.419 45.833 6.12 6.53 40.07 3.35
4380 5708 0.749649 ACATCCGGACTGAGATGAGC 59.250 55.000 6.12 0.00 42.04 4.26
4381 5709 0.749049 CATCCGGACTGAGATGAGCA 59.251 55.000 6.12 0.00 42.04 4.26
4382 5710 1.137675 CATCCGGACTGAGATGAGCAA 59.862 52.381 6.12 0.00 42.04 3.91
4383 5711 1.489481 TCCGGACTGAGATGAGCAAT 58.511 50.000 0.00 0.00 0.00 3.56
4385 5713 1.579698 CGGACTGAGATGAGCAATGG 58.420 55.000 0.00 0.00 0.00 3.16
4386 5714 1.307097 GGACTGAGATGAGCAATGGC 58.693 55.000 0.00 0.00 41.61 4.40
4387 5715 1.407851 GGACTGAGATGAGCAATGGCA 60.408 52.381 0.00 0.00 44.61 4.92
4388 5716 2.362736 GACTGAGATGAGCAATGGCAA 58.637 47.619 0.00 0.00 44.61 4.52
4389 5717 2.950309 GACTGAGATGAGCAATGGCAAT 59.050 45.455 0.00 0.00 44.61 3.56
4390 5718 2.688446 ACTGAGATGAGCAATGGCAATG 59.312 45.455 0.00 0.00 44.61 2.82
4391 5719 2.688446 CTGAGATGAGCAATGGCAATGT 59.312 45.455 4.21 0.00 44.61 2.71
4392 5720 3.881089 CTGAGATGAGCAATGGCAATGTA 59.119 43.478 4.21 0.00 44.61 2.29
4393 5721 3.881089 TGAGATGAGCAATGGCAATGTAG 59.119 43.478 4.21 0.00 44.61 2.74
4394 5722 3.220110 AGATGAGCAATGGCAATGTAGG 58.780 45.455 4.21 0.00 44.61 3.18
4395 5723 1.766494 TGAGCAATGGCAATGTAGGG 58.234 50.000 4.21 0.00 44.61 3.53
4396 5724 1.284491 TGAGCAATGGCAATGTAGGGA 59.716 47.619 4.21 0.00 44.61 4.20
4397 5725 1.952296 GAGCAATGGCAATGTAGGGAG 59.048 52.381 4.21 0.00 44.61 4.30
4398 5726 1.285962 AGCAATGGCAATGTAGGGAGT 59.714 47.619 4.21 0.00 44.61 3.85
4399 5727 2.102578 GCAATGGCAATGTAGGGAGTT 58.897 47.619 4.21 0.00 40.72 3.01
4400 5728 2.159198 GCAATGGCAATGTAGGGAGTTG 60.159 50.000 4.21 0.00 40.72 3.16
4401 5729 3.355378 CAATGGCAATGTAGGGAGTTGA 58.645 45.455 0.00 0.00 0.00 3.18
4402 5730 2.489938 TGGCAATGTAGGGAGTTGAC 57.510 50.000 0.00 0.00 0.00 3.18
4403 5731 1.004277 TGGCAATGTAGGGAGTTGACC 59.996 52.381 0.00 0.00 29.73 4.02
4404 5732 1.282157 GGCAATGTAGGGAGTTGACCT 59.718 52.381 0.00 0.00 42.15 3.85
4405 5733 2.290960 GGCAATGTAGGGAGTTGACCTT 60.291 50.000 0.00 0.00 39.54 3.50
4406 5734 2.749621 GCAATGTAGGGAGTTGACCTTG 59.250 50.000 0.00 0.00 39.54 3.61
4407 5735 3.810743 GCAATGTAGGGAGTTGACCTTGT 60.811 47.826 0.00 0.00 39.54 3.16
4408 5736 4.564821 GCAATGTAGGGAGTTGACCTTGTA 60.565 45.833 0.00 0.00 39.54 2.41
4409 5737 5.178797 CAATGTAGGGAGTTGACCTTGTAG 58.821 45.833 0.00 0.00 39.54 2.74
4410 5738 3.170717 TGTAGGGAGTTGACCTTGTAGG 58.829 50.000 0.00 0.00 42.49 3.18
4411 5739 1.657804 AGGGAGTTGACCTTGTAGGG 58.342 55.000 0.00 0.00 40.58 3.53
4412 5740 1.132495 AGGGAGTTGACCTTGTAGGGT 60.132 52.381 0.00 0.00 40.58 4.34
4413 5741 1.703513 GGGAGTTGACCTTGTAGGGTT 59.296 52.381 0.00 0.00 40.58 4.11
4414 5742 2.107726 GGGAGTTGACCTTGTAGGGTTT 59.892 50.000 0.00 0.00 40.58 3.27
4415 5743 3.436035 GGGAGTTGACCTTGTAGGGTTTT 60.436 47.826 0.00 0.00 40.58 2.43
4416 5744 4.212716 GGAGTTGACCTTGTAGGGTTTTT 58.787 43.478 0.00 0.00 40.58 1.94
4417 5745 5.379187 GGAGTTGACCTTGTAGGGTTTTTA 58.621 41.667 0.00 0.00 40.58 1.52
4418 5746 5.472478 GGAGTTGACCTTGTAGGGTTTTTAG 59.528 44.000 0.00 0.00 40.58 1.85
4419 5747 6.256643 AGTTGACCTTGTAGGGTTTTTAGA 57.743 37.500 0.00 0.00 40.58 2.10
4420 5748 6.665695 AGTTGACCTTGTAGGGTTTTTAGAA 58.334 36.000 0.00 0.00 40.58 2.10
4421 5749 6.771267 AGTTGACCTTGTAGGGTTTTTAGAAG 59.229 38.462 0.00 0.00 40.58 2.85
4422 5750 6.256643 TGACCTTGTAGGGTTTTTAGAAGT 57.743 37.500 0.00 0.00 40.58 3.01
4423 5751 6.665695 TGACCTTGTAGGGTTTTTAGAAGTT 58.334 36.000 0.00 0.00 40.58 2.66
4424 5752 6.544564 TGACCTTGTAGGGTTTTTAGAAGTTG 59.455 38.462 0.00 0.00 40.58 3.16
4425 5753 6.665695 ACCTTGTAGGGTTTTTAGAAGTTGA 58.334 36.000 0.00 0.00 40.58 3.18
4439 5767 7.624360 TTAGAAGTTGATGAACAAACACACT 57.376 32.000 0.00 0.00 40.36 3.55
4447 5775 8.921670 GTTGATGAACAAACACACTAAAACTTT 58.078 29.630 0.00 0.00 40.36 2.66
4449 5777 9.134734 TGATGAACAAACACACTAAAACTTTTC 57.865 29.630 0.00 0.00 0.00 2.29
4451 5779 9.651913 ATGAACAAACACACTAAAACTTTTCAT 57.348 25.926 0.00 0.00 0.00 2.57
4452 5780 9.482627 TGAACAAACACACTAAAACTTTTCATT 57.517 25.926 0.00 0.00 0.00 2.57
4480 5808 4.942765 GTGTAGCTCACGTGTCAAAATAC 58.057 43.478 16.51 11.21 37.31 1.89
4481 5809 4.446385 GTGTAGCTCACGTGTCAAAATACA 59.554 41.667 16.51 13.39 37.31 2.29
4482 5810 5.120208 GTGTAGCTCACGTGTCAAAATACAT 59.880 40.000 16.51 0.00 37.31 2.29
4483 5811 6.309494 GTGTAGCTCACGTGTCAAAATACATA 59.691 38.462 16.51 0.00 37.31 2.29
4520 6333 5.971895 TTTTGAATTTTGCTGCTTCTGTC 57.028 34.783 0.00 0.00 0.00 3.51
4528 6341 0.392729 GCTGCTTCTGTCTGGAGCAT 60.393 55.000 12.69 0.00 45.03 3.79
4533 6346 3.254166 TGCTTCTGTCTGGAGCATTTTTC 59.746 43.478 8.56 0.00 0.00 2.29
4570 6383 3.056628 GCAGTGCAGGTGCTAGTAG 57.943 57.895 11.09 0.00 42.66 2.57
4572 6385 0.534412 CAGTGCAGGTGCTAGTAGCT 59.466 55.000 22.34 6.73 42.97 3.32
4609 6422 7.554476 GTGAAAAGATTCTGGGCTTATACTCTT 59.446 37.037 0.00 0.00 36.48 2.85
4645 6458 2.092968 GGTCAGGTGATTGATGCCACTA 60.093 50.000 0.00 0.00 33.99 2.74
4648 6461 4.641989 GTCAGGTGATTGATGCCACTATTT 59.358 41.667 0.00 0.00 33.99 1.40
4649 6462 5.126061 GTCAGGTGATTGATGCCACTATTTT 59.874 40.000 0.00 0.00 33.99 1.82
4853 6672 2.348998 GGATGCCTCCCGCCATAG 59.651 66.667 0.00 0.00 35.28 2.23
4854 6673 2.348998 GATGCCTCCCGCCATAGG 59.651 66.667 0.00 0.00 36.24 2.57
5026 6869 2.031465 TTCGGGAACAGCGGGAAC 59.969 61.111 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.624697 TTGCTAAACATAAACATCAAAGTCATC 57.375 29.630 0.00 0.00 0.00 2.92
58 59 8.458843 CCATTAAAGTTATACCACCTCACAAAG 58.541 37.037 0.00 0.00 0.00 2.77
73 74 7.609960 TGATGATGCAAAAGCCATTAAAGTTA 58.390 30.769 0.00 0.00 0.00 2.24
134 136 0.249238 GAGAGCTCACATACCTGCGG 60.249 60.000 17.77 0.00 0.00 5.69
174 176 0.373716 GCGCCGGTAAAGTCATTCAG 59.626 55.000 1.90 0.00 0.00 3.02
204 206 4.390909 CCGTAGAAAATAAACTTCCGCACT 59.609 41.667 0.00 0.00 0.00 4.40
216 218 5.116180 CCAGAACATGCTCCGTAGAAAATA 58.884 41.667 0.00 0.00 0.00 1.40
219 221 2.301870 ACCAGAACATGCTCCGTAGAAA 59.698 45.455 0.00 0.00 0.00 2.52
250 252 5.661759 AGACCGGACAAATAAATCCTACTCT 59.338 40.000 9.46 0.00 32.33 3.24
270 272 2.028112 TGACACAATGAGCTACCAGACC 60.028 50.000 0.00 0.00 0.00 3.85
339 341 0.970640 TTACTAGTGCGGCCAAGTCA 59.029 50.000 5.39 0.00 0.00 3.41
408 419 0.036388 TCTGTGGGATTTGCTCGGAC 60.036 55.000 0.00 0.00 0.00 4.79
418 429 3.245730 ACCAACCATGAAATCTGTGGGAT 60.246 43.478 0.00 0.00 37.33 3.85
419 430 2.109834 ACCAACCATGAAATCTGTGGGA 59.890 45.455 0.00 0.00 37.33 4.37
421 432 4.335416 AGTACCAACCATGAAATCTGTGG 58.665 43.478 0.00 4.55 38.96 4.17
425 436 4.289672 ACCAGAGTACCAACCATGAAATCT 59.710 41.667 0.00 0.00 0.00 2.40
426 437 4.396166 CACCAGAGTACCAACCATGAAATC 59.604 45.833 0.00 0.00 0.00 2.17
427 438 4.335416 CACCAGAGTACCAACCATGAAAT 58.665 43.478 0.00 0.00 0.00 2.17
430 441 1.003118 GCACCAGAGTACCAACCATGA 59.997 52.381 0.00 0.00 0.00 3.07
431 442 1.271325 TGCACCAGAGTACCAACCATG 60.271 52.381 0.00 0.00 0.00 3.66
432 443 1.064003 TGCACCAGAGTACCAACCAT 58.936 50.000 0.00 0.00 0.00 3.55
433 444 1.064003 ATGCACCAGAGTACCAACCA 58.936 50.000 0.00 0.00 0.00 3.67
434 445 2.084546 GAATGCACCAGAGTACCAACC 58.915 52.381 0.00 0.00 0.00 3.77
438 449 2.350522 CACAGAATGCACCAGAGTACC 58.649 52.381 0.00 0.00 42.53 3.34
461 519 4.650754 ACCAAATAAGTAGACGAGCGAT 57.349 40.909 0.00 0.00 0.00 4.58
529 590 9.282247 CAGAAATTCAAGAATTAAATCTCCACG 57.718 33.333 8.34 0.00 39.88 4.94
603 664 6.745159 TCTATCGATGTATCTTAGGCAGAC 57.255 41.667 8.54 0.00 32.83 3.51
647 708 9.775854 TTTTGAAACACATGACCATTCATTTAT 57.224 25.926 0.00 0.00 40.79 1.40
802 900 7.974482 TTTCGTTTTTACTTTTCCCCAAAAA 57.026 28.000 0.00 0.00 35.56 1.94
998 1167 2.504244 GAGACGACGGTTGGCGAG 60.504 66.667 0.00 0.00 0.00 5.03
999 1168 4.047059 GGAGACGACGGTTGGCGA 62.047 66.667 0.00 0.00 0.00 5.54
1106 1288 1.247567 CAGGCGAGGAACAAACCAAT 58.752 50.000 0.00 0.00 0.00 3.16
1133 1315 5.853572 ACCCATGGAGTTAAGGTAAAAGA 57.146 39.130 15.22 0.00 0.00 2.52
1168 1358 0.659957 GCACTGGCTACTATTGCAGC 59.340 55.000 0.00 0.00 36.96 5.25
1223 1413 6.455360 TTCTACATCATCAATTTTCCAGGC 57.545 37.500 0.00 0.00 0.00 4.85
1316 1513 8.713271 GCATAAAAGGAACTCGAAATAGATAGG 58.287 37.037 0.00 0.00 38.49 2.57
1333 1530 1.676006 GGACGGACATGGCATAAAAGG 59.324 52.381 0.00 0.00 0.00 3.11
1352 1549 0.109597 GAAAGCAACAGCGTCCATGG 60.110 55.000 4.97 4.97 0.00 3.66
1353 1550 0.109597 GGAAAGCAACAGCGTCCATG 60.110 55.000 7.93 0.00 37.32 3.66
1354 1551 0.250901 AGGAAAGCAACAGCGTCCAT 60.251 50.000 13.27 0.31 38.83 3.41
1355 1552 1.148273 AGGAAAGCAACAGCGTCCA 59.852 52.632 13.27 0.00 38.83 4.02
1356 1553 1.166531 ACAGGAAAGCAACAGCGTCC 61.167 55.000 0.00 0.00 37.51 4.79
1357 1554 0.040958 CACAGGAAAGCAACAGCGTC 60.041 55.000 0.00 0.00 0.00 5.19
1358 1555 1.447317 CCACAGGAAAGCAACAGCGT 61.447 55.000 0.00 0.00 0.00 5.07
1359 1556 1.165907 TCCACAGGAAAGCAACAGCG 61.166 55.000 0.00 0.00 0.00 5.18
1360 1557 1.000938 CTTCCACAGGAAAGCAACAGC 60.001 52.381 0.00 0.00 41.54 4.40
1437 1655 4.084171 CCAGAGTATTATGCTGTGAATGCG 60.084 45.833 8.86 0.00 29.89 4.73
1457 1675 2.104859 CAGAGGCATGCGTCACCAG 61.105 63.158 34.49 20.48 33.73 4.00
1461 1679 0.250252 TCAAACAGAGGCATGCGTCA 60.250 50.000 34.49 15.72 33.73 4.35
1467 1685 5.475719 CATCAACATTTCAAACAGAGGCAT 58.524 37.500 0.00 0.00 0.00 4.40
1484 1702 4.900635 AACAACAGACAAGTCCATCAAC 57.099 40.909 0.00 0.00 0.00 3.18
1487 1705 7.148255 TGCATAATAACAACAGACAAGTCCATC 60.148 37.037 0.00 0.00 0.00 3.51
1488 1706 6.658816 TGCATAATAACAACAGACAAGTCCAT 59.341 34.615 0.00 0.00 0.00 3.41
1498 1722 5.572211 ACGAAGCATGCATAATAACAACAG 58.428 37.500 21.98 0.00 0.00 3.16
1536 1760 3.650281 TGAGCATGGCTGAATTTCCTA 57.350 42.857 0.00 0.00 39.88 2.94
1539 1763 4.184079 ACTTTGAGCATGGCTGAATTTC 57.816 40.909 0.00 0.00 39.88 2.17
1542 1766 4.081406 TGTAACTTTGAGCATGGCTGAAT 58.919 39.130 0.00 0.00 39.88 2.57
1543 1767 3.485394 TGTAACTTTGAGCATGGCTGAA 58.515 40.909 0.00 0.00 39.88 3.02
1544 1768 3.076621 CTGTAACTTTGAGCATGGCTGA 58.923 45.455 0.00 0.00 39.88 4.26
1548 1775 3.254166 AGCAACTGTAACTTTGAGCATGG 59.746 43.478 0.00 0.00 0.00 3.66
1565 1792 4.759782 ACCTACATGACTGTGATAGCAAC 58.240 43.478 0.00 0.00 36.79 4.17
1578 1805 9.220906 ACTGGTAAGGAAATTATACCTACATGA 57.779 33.333 0.00 0.00 39.84 3.07
1601 1924 8.764524 AATCAAAGAAGCTGTACTAGTAACTG 57.235 34.615 3.61 4.89 0.00 3.16
1606 1929 8.035984 GGAACTAATCAAAGAAGCTGTACTAGT 58.964 37.037 0.00 0.00 0.00 2.57
1607 1930 8.254508 AGGAACTAATCAAAGAAGCTGTACTAG 58.745 37.037 0.00 0.00 36.02 2.57
1608 1931 8.135382 AGGAACTAATCAAAGAAGCTGTACTA 57.865 34.615 0.00 0.00 36.02 1.82
1695 2024 4.433186 TGCTTTTAAACCATCCATGTCG 57.567 40.909 0.00 0.00 0.00 4.35
1759 2092 3.552875 CCACCATCTTGCTCATCTGATT 58.447 45.455 0.00 0.00 0.00 2.57
1760 2093 2.748798 GCCACCATCTTGCTCATCTGAT 60.749 50.000 0.00 0.00 0.00 2.90
1806 2139 3.941657 GAGGAGTTCGCGCTTGGCT 62.942 63.158 5.56 0.00 40.44 4.75
1860 2193 8.323854 GTCAAAGAAAAAGAAAGCTTGACATTC 58.676 33.333 0.00 2.05 33.79 2.67
1861 2194 7.278646 GGTCAAAGAAAAAGAAAGCTTGACATT 59.721 33.333 0.00 0.00 33.79 2.71
1862 2195 6.758416 GGTCAAAGAAAAAGAAAGCTTGACAT 59.242 34.615 0.00 0.00 33.79 3.06
1863 2196 6.099341 GGTCAAAGAAAAAGAAAGCTTGACA 58.901 36.000 0.00 0.00 33.79 3.58
1864 2197 5.520288 GGGTCAAAGAAAAAGAAAGCTTGAC 59.480 40.000 0.00 0.00 33.79 3.18
1865 2198 5.422012 AGGGTCAAAGAAAAAGAAAGCTTGA 59.578 36.000 0.00 0.00 33.79 3.02
1866 2199 5.664457 AGGGTCAAAGAAAAAGAAAGCTTG 58.336 37.500 0.00 0.00 33.79 4.01
1867 2200 5.939764 AGGGTCAAAGAAAAAGAAAGCTT 57.060 34.783 0.00 0.00 35.37 3.74
1868 2201 5.939764 AAGGGTCAAAGAAAAAGAAAGCT 57.060 34.783 0.00 0.00 0.00 3.74
1869 2202 6.985188 AAAAGGGTCAAAGAAAAAGAAAGC 57.015 33.333 0.00 0.00 0.00 3.51
1909 2242 9.388506 TGCAAATTAAACTGAAGGAAATTTTGA 57.611 25.926 0.00 0.00 29.66 2.69
1953 2291 7.349711 CGTGTTTATAATAATTCAACGGGAGG 58.650 38.462 0.00 0.00 0.00 4.30
1958 2296 6.412653 GGTGCCGTGTTTATAATAATTCAACG 59.587 38.462 0.00 0.00 0.00 4.10
1959 2297 6.693978 GGGTGCCGTGTTTATAATAATTCAAC 59.306 38.462 0.00 0.00 0.00 3.18
1960 2298 6.183360 GGGGTGCCGTGTTTATAATAATTCAA 60.183 38.462 0.00 0.00 0.00 2.69
1976 2314 0.107361 GCTTATTGTAGGGGTGCCGT 60.107 55.000 0.00 0.00 0.00 5.68
1995 2333 8.064222 GGACACACAAGATAATGATGATTTACG 58.936 37.037 0.00 0.00 0.00 3.18
2086 2429 1.674322 CGGCCCCAAAGTACACTGG 60.674 63.158 0.00 6.32 0.00 4.00
2131 2481 5.762825 AGCATATAACATGTGCCAGAAAG 57.237 39.130 0.00 0.00 46.99 2.62
2151 2501 3.859386 GCAAGTGGTTATATGCACAAAGC 59.141 43.478 0.00 0.00 45.96 3.51
2152 2502 5.058149 TGCAAGTGGTTATATGCACAAAG 57.942 39.130 0.00 0.00 43.32 2.77
2239 2601 6.411630 AAAGAAACGCGTACATGCTATTTA 57.588 33.333 14.46 0.00 0.00 1.40
2246 2608 3.427516 TCGAAAAGAAACGCGTACATG 57.572 42.857 14.46 0.00 0.00 3.21
2254 2616 6.310467 TCTGATACAGGAATCGAAAAGAAACG 59.690 38.462 0.00 0.00 31.51 3.60
2271 2633 6.286240 ACATTAGAGCAACAGTCTGATACA 57.714 37.500 6.91 0.00 0.00 2.29
2272 2634 7.118390 ACAAACATTAGAGCAACAGTCTGATAC 59.882 37.037 6.91 0.00 0.00 2.24
2333 2846 4.040461 ACTGTGCTAGTCTTTGTACCATGT 59.960 41.667 0.00 0.00 33.17 3.21
2352 2865 2.032894 CGAGCACATCGTTCAAAACTGT 60.033 45.455 0.00 0.00 46.62 3.55
2586 3239 2.032799 CCTAGCTCAGTCTACTTCTGCG 59.967 54.545 0.00 0.00 33.48 5.18
2587 3240 2.223711 GCCTAGCTCAGTCTACTTCTGC 60.224 54.545 0.00 0.00 33.48 4.26
2598 3254 2.975732 TGAGTCATTGCCTAGCTCAG 57.024 50.000 0.00 0.00 33.05 3.35
2616 3520 6.742109 ACAGACATGGAAAAAGTTTCAGATG 58.258 36.000 0.00 6.71 0.00 2.90
3001 3940 3.503227 GGATTATCCCTGCCCTACTCTCT 60.503 52.174 0.00 0.00 0.00 3.10
3015 3954 8.926092 ACTAAATTAAGCTCAAGGGATTATCC 57.074 34.615 1.91 1.91 35.23 2.59
3095 4038 0.930310 CTGTGCACACGAATATCCGG 59.070 55.000 17.42 0.00 0.00 5.14
3209 4152 2.915869 ACTACCAGGTCCATTGAAGGA 58.084 47.619 0.00 0.00 34.64 3.36
3633 4580 4.854399 TGTCGCTTGTTAAGGTCAATTTG 58.146 39.130 0.00 0.00 0.00 2.32
3703 4650 5.281727 GTTGACCTTTTGCTTCTTCGAATT 58.718 37.500 0.00 0.00 0.00 2.17
3705 4652 3.066203 GGTTGACCTTTTGCTTCTTCGAA 59.934 43.478 0.00 0.00 0.00 3.71
3829 4782 3.136626 AGCTCAACCTAACAAGTTGGTCT 59.863 43.478 7.96 0.00 43.83 3.85
3892 4845 2.164422 CACAGATGCAGAAGTCCGTAGA 59.836 50.000 0.00 0.00 0.00 2.59
3897 4850 2.740981 CTCAACACAGATGCAGAAGTCC 59.259 50.000 0.00 0.00 0.00 3.85
3913 4866 4.987912 GTCTGATAGATAAGCTGCCTCAAC 59.012 45.833 0.00 0.00 0.00 3.18
4019 4973 6.290294 TGTCATCTCAACAATCATCTCAGA 57.710 37.500 0.00 0.00 0.00 3.27
4021 4975 5.820947 CCATGTCATCTCAACAATCATCTCA 59.179 40.000 0.00 0.00 0.00 3.27
4073 5027 8.618702 ATGCAGGATATACAGATTCAGAAAAG 57.381 34.615 0.00 0.00 0.00 2.27
4134 5093 5.380043 CATATTCACAGGGCTACAGGATTT 58.620 41.667 0.00 0.00 0.00 2.17
4297 5321 4.421948 GAAGGGAGTACTACATTGACACG 58.578 47.826 10.30 0.00 0.00 4.49
4343 5671 6.073222 CCGGATGTAGTTCATACTAAAATGCC 60.073 42.308 0.00 0.00 38.55 4.40
4344 5672 6.704493 TCCGGATGTAGTTCATACTAAAATGC 59.296 38.462 0.00 0.00 38.55 3.56
4346 5674 7.926555 CAGTCCGGATGTAGTTCATACTAAAAT 59.073 37.037 7.81 0.00 38.55 1.82
4349 5677 6.124340 TCAGTCCGGATGTAGTTCATACTAA 58.876 40.000 7.81 0.00 38.55 2.24
4361 5689 0.749649 GCTCATCTCAGTCCGGATGT 59.250 55.000 7.81 0.00 39.93 3.06
4365 5693 1.579698 CATTGCTCATCTCAGTCCGG 58.420 55.000 0.00 0.00 0.00 5.14
4367 5695 1.307097 GCCATTGCTCATCTCAGTCC 58.693 55.000 0.00 0.00 33.53 3.85
4374 5702 2.295349 CCCTACATTGCCATTGCTCATC 59.705 50.000 0.00 0.00 38.71 2.92
4380 5708 3.129287 GTCAACTCCCTACATTGCCATTG 59.871 47.826 0.00 0.00 0.00 2.82
4381 5709 3.356290 GTCAACTCCCTACATTGCCATT 58.644 45.455 0.00 0.00 0.00 3.16
4382 5710 2.357154 GGTCAACTCCCTACATTGCCAT 60.357 50.000 0.00 0.00 0.00 4.40
4383 5711 1.004277 GGTCAACTCCCTACATTGCCA 59.996 52.381 0.00 0.00 0.00 4.92
4385 5713 2.749621 CAAGGTCAACTCCCTACATTGC 59.250 50.000 0.00 0.00 29.59 3.56
4386 5714 4.021102 ACAAGGTCAACTCCCTACATTG 57.979 45.455 0.00 0.00 39.92 2.82
4387 5715 4.225267 CCTACAAGGTCAACTCCCTACATT 59.775 45.833 0.00 0.00 0.00 2.71
4388 5716 3.775316 CCTACAAGGTCAACTCCCTACAT 59.225 47.826 0.00 0.00 0.00 2.29
4389 5717 3.170717 CCTACAAGGTCAACTCCCTACA 58.829 50.000 0.00 0.00 0.00 2.74
4390 5718 2.500504 CCCTACAAGGTCAACTCCCTAC 59.499 54.545 0.00 0.00 31.93 3.18
4391 5719 2.113052 ACCCTACAAGGTCAACTCCCTA 59.887 50.000 0.00 0.00 33.81 3.53
4392 5720 1.132495 ACCCTACAAGGTCAACTCCCT 60.132 52.381 0.00 0.00 33.81 4.20
4393 5721 1.359168 ACCCTACAAGGTCAACTCCC 58.641 55.000 0.00 0.00 33.81 4.30
4394 5722 3.503800 AAACCCTACAAGGTCAACTCC 57.496 47.619 0.00 0.00 40.05 3.85
4395 5723 6.293698 TCTAAAAACCCTACAAGGTCAACTC 58.706 40.000 0.00 0.00 40.05 3.01
4396 5724 6.256643 TCTAAAAACCCTACAAGGTCAACT 57.743 37.500 0.00 0.00 40.05 3.16
4397 5725 6.544931 ACTTCTAAAAACCCTACAAGGTCAAC 59.455 38.462 0.00 0.00 40.05 3.18
4398 5726 6.665695 ACTTCTAAAAACCCTACAAGGTCAA 58.334 36.000 0.00 0.00 40.05 3.18
4399 5727 6.256643 ACTTCTAAAAACCCTACAAGGTCA 57.743 37.500 0.00 0.00 40.05 4.02
4400 5728 6.769341 TCAACTTCTAAAAACCCTACAAGGTC 59.231 38.462 0.00 0.00 40.05 3.85
4401 5729 6.665695 TCAACTTCTAAAAACCCTACAAGGT 58.334 36.000 0.00 0.00 44.00 3.50
4402 5730 7.447238 TCATCAACTTCTAAAAACCCTACAAGG 59.553 37.037 0.00 0.00 34.30 3.61
4403 5731 8.391075 TCATCAACTTCTAAAAACCCTACAAG 57.609 34.615 0.00 0.00 0.00 3.16
4404 5732 8.626526 GTTCATCAACTTCTAAAAACCCTACAA 58.373 33.333 0.00 0.00 0.00 2.41
4405 5733 7.776030 TGTTCATCAACTTCTAAAAACCCTACA 59.224 33.333 0.00 0.00 33.17 2.74
4406 5734 8.161699 TGTTCATCAACTTCTAAAAACCCTAC 57.838 34.615 0.00 0.00 33.17 3.18
4407 5735 8.754991 TTGTTCATCAACTTCTAAAAACCCTA 57.245 30.769 0.00 0.00 33.17 3.53
4408 5736 7.654022 TTGTTCATCAACTTCTAAAAACCCT 57.346 32.000 0.00 0.00 33.17 4.34
4409 5737 7.762159 TGTTTGTTCATCAACTTCTAAAAACCC 59.238 33.333 0.00 0.00 35.61 4.11
4410 5738 8.592155 GTGTTTGTTCATCAACTTCTAAAAACC 58.408 33.333 0.00 0.00 35.61 3.27
4411 5739 9.134734 TGTGTTTGTTCATCAACTTCTAAAAAC 57.865 29.630 0.00 0.00 35.61 2.43
4412 5740 9.134734 GTGTGTTTGTTCATCAACTTCTAAAAA 57.865 29.630 0.00 0.00 35.61 1.94
4413 5741 8.519526 AGTGTGTTTGTTCATCAACTTCTAAAA 58.480 29.630 0.00 0.00 35.61 1.52
4414 5742 8.050778 AGTGTGTTTGTTCATCAACTTCTAAA 57.949 30.769 0.00 0.00 35.61 1.85
4415 5743 7.624360 AGTGTGTTTGTTCATCAACTTCTAA 57.376 32.000 0.00 0.00 35.61 2.10
4416 5744 8.725405 TTAGTGTGTTTGTTCATCAACTTCTA 57.275 30.769 0.00 0.00 35.61 2.10
4417 5745 7.624360 TTAGTGTGTTTGTTCATCAACTTCT 57.376 32.000 0.00 0.00 35.61 2.85
4418 5746 8.583765 GTTTTAGTGTGTTTGTTCATCAACTTC 58.416 33.333 0.00 0.00 35.61 3.01
4419 5747 8.303876 AGTTTTAGTGTGTTTGTTCATCAACTT 58.696 29.630 0.00 0.00 35.61 2.66
4420 5748 7.826690 AGTTTTAGTGTGTTTGTTCATCAACT 58.173 30.769 0.00 0.00 35.61 3.16
4421 5749 8.460831 AAGTTTTAGTGTGTTTGTTCATCAAC 57.539 30.769 0.00 0.00 35.61 3.18
4422 5750 9.482627 AAAAGTTTTAGTGTGTTTGTTCATCAA 57.517 25.926 0.00 0.00 0.00 2.57
4423 5751 9.134734 GAAAAGTTTTAGTGTGTTTGTTCATCA 57.865 29.630 0.00 0.00 0.00 3.07
4424 5752 9.134734 TGAAAAGTTTTAGTGTGTTTGTTCATC 57.865 29.630 0.00 0.00 0.00 2.92
4425 5753 9.651913 ATGAAAAGTTTTAGTGTGTTTGTTCAT 57.348 25.926 0.00 0.00 0.00 2.57
4460 5788 5.779806 ATGTATTTTGACACGTGAGCTAC 57.220 39.130 25.01 13.86 30.52 3.58
4461 5789 5.513849 CGTATGTATTTTGACACGTGAGCTA 59.486 40.000 25.01 7.87 30.52 3.32
4463 5791 4.325204 TCGTATGTATTTTGACACGTGAGC 59.675 41.667 25.01 14.17 30.52 4.26
4464 5792 6.384178 TTCGTATGTATTTTGACACGTGAG 57.616 37.500 25.01 0.00 30.52 3.51
4465 5793 6.954616 ATTCGTATGTATTTTGACACGTGA 57.045 33.333 25.01 0.00 30.52 4.35
4466 5794 7.012943 ACAATTCGTATGTATTTTGACACGTG 58.987 34.615 15.48 15.48 30.52 4.49
4467 5795 7.124347 ACAATTCGTATGTATTTTGACACGT 57.876 32.000 0.00 0.00 30.52 4.49
4468 5796 7.742525 TGAACAATTCGTATGTATTTTGACACG 59.257 33.333 0.00 0.00 30.52 4.49
4469 5797 8.942669 TGAACAATTCGTATGTATTTTGACAC 57.057 30.769 0.00 0.00 30.52 3.67
4470 5798 9.767684 GATGAACAATTCGTATGTATTTTGACA 57.232 29.630 0.00 0.00 0.00 3.58
4479 5807 9.859427 ATTCAAAATGATGAACAATTCGTATGT 57.141 25.926 0.00 0.00 41.78 2.29
4483 5811 9.866936 CAAAATTCAAAATGATGAACAATTCGT 57.133 25.926 0.00 0.00 41.78 3.85
4520 6333 3.928727 TTGCTCTGAAAAATGCTCCAG 57.071 42.857 0.00 0.00 0.00 3.86
4550 6363 1.751351 CTACTAGCACCTGCACTGCTA 59.249 52.381 16.84 16.84 43.37 3.49
4559 6372 5.455040 CCAGTAGTAGTAGCTACTAGCACCT 60.455 48.000 29.74 24.09 46.18 4.00
4570 6383 7.489757 CAGAATCTTTTCACCAGTAGTAGTAGC 59.510 40.741 0.00 0.00 34.08 3.58
4572 6385 7.093465 CCCAGAATCTTTTCACCAGTAGTAGTA 60.093 40.741 0.00 0.00 34.08 1.82
4582 6395 6.122964 AGTATAAGCCCAGAATCTTTTCACC 58.877 40.000 0.00 0.00 34.08 4.02
4585 6398 7.012799 CCAAGAGTATAAGCCCAGAATCTTTTC 59.987 40.741 0.00 0.00 0.00 2.29
4614 6427 2.532715 ACCTGACCTGGGTGCCAT 60.533 61.111 0.00 0.00 35.51 4.40
4645 6458 5.705400 TGACAAGGAAGGAAGGAGAAAAAT 58.295 37.500 0.00 0.00 0.00 1.82
4648 6461 3.716872 ACTGACAAGGAAGGAAGGAGAAA 59.283 43.478 0.00 0.00 0.00 2.52
4649 6462 3.071602 CACTGACAAGGAAGGAAGGAGAA 59.928 47.826 0.00 0.00 0.00 2.87
4807 6626 0.039256 GCATGCCGTTCAGCTTCAAA 60.039 50.000 6.36 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.