Multiple sequence alignment - TraesCS7B01G203700

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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 TraesCS7B01G203700 chr7B 100.000 5807 0 0 1 5807 373182397 373176591 0.000000e+00 10724.0
1 TraesCS7B01G203700 chr7B 87.879 99 10 2 1533 1630 212411791 212411888 1.320000e-21 115.0
2 TraesCS7B01G203700 chr7A 95.187 5298 189 25 5 5270 426807699 426802436 0.000000e+00 8311.0
3 TraesCS7B01G203700 chr7A 88.710 372 31 5 5271 5641 426801216 426800855 1.480000e-120 444.0
4 TraesCS7B01G203700 chr7D 95.656 3867 113 23 1 3849 378498075 378494246 0.000000e+00 6159.0
5 TraesCS7B01G203700 chr7D 91.928 1115 56 17 4541 5641 378493703 378492609 0.000000e+00 1530.0
6 TraesCS7B01G203700 chr7D 96.768 557 7 6 3901 4452 378494248 378493698 0.000000e+00 918.0
7 TraesCS7B01G203700 chr7D 78.869 601 107 13 34 624 396135832 396136422 7.060000e-104 388.0
8 TraesCS7B01G203700 chr3D 81.655 447 76 6 20 462 560938239 560938683 3.310000e-97 366.0
9 TraesCS7B01G203700 chr3D 78.132 471 95 8 157 620 598487711 598488180 5.690000e-75 292.0
10 TraesCS7B01G203700 chr3D 91.489 47 4 0 18 64 598487636 598487682 1.350000e-06 65.8
11 TraesCS7B01G203700 chr2D 77.879 547 110 9 82 622 469369507 469368966 4.340000e-86 329.0
12 TraesCS7B01G203700 chr2D 84.000 100 15 1 1540 1638 296771675 296771576 1.720000e-15 95.3
13 TraesCS7B01G203700 chr2D 97.222 36 1 0 5638 5673 245329821 245329856 1.750000e-05 62.1
14 TraesCS7B01G203700 chr1B 76.068 585 119 15 46 622 192142023 192141452 9.520000e-73 285.0
15 TraesCS7B01G203700 chr1B 97.222 36 1 0 5638 5673 391140590 391140625 1.750000e-05 62.1
16 TraesCS7B01G203700 chr5B 77.851 456 90 11 177 626 589664811 589664361 7.410000e-69 272.0
17 TraesCS7B01G203700 chr5A 74.313 619 134 21 19 623 583689261 583689868 7.520000e-59 239.0
18 TraesCS7B01G203700 chr5A 84.906 106 15 1 1526 1630 180343710 180343815 7.960000e-19 106.0
19 TraesCS7B01G203700 chr2B 88.811 143 11 1 2786 2923 2619081 2618939 2.780000e-38 171.0
20 TraesCS7B01G203700 chr6D 85.577 104 12 3 1528 1630 1795697 1795798 7.960000e-19 106.0
21 TraesCS7B01G203700 chr4B 85.149 101 13 2 1531 1630 472388165 472388264 1.030000e-17 102.0
22 TraesCS7B01G203700 chr2A 84.466 103 15 1 1529 1630 139859800 139859698 3.700000e-17 100.0
23 TraesCS7B01G203700 chr2A 84.466 103 15 1 1529 1630 632618704 632618602 3.700000e-17 100.0
24 TraesCS7B01G203700 chr4D 81.148 122 14 9 1520 1638 465024429 465024314 8.010000e-14 89.8
25 TraesCS7B01G203700 chr3B 97.222 36 1 0 5638 5673 99363092 99363057 1.750000e-05 62.1
26 TraesCS7B01G203700 chr5D 92.308 39 3 0 5635 5673 232137397 232137435 8.130000e-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 TraesCS7B01G203700 chr7B 373176591 373182397 5806 True 10724.0 10724 100.0000 1 5807 1 chr7B.!!$R1 5806
1 TraesCS7B01G203700 chr7A 426800855 426807699 6844 True 4377.5 8311 91.9485 5 5641 2 chr7A.!!$R1 5636
2 TraesCS7B01G203700 chr7D 378492609 378498075 5466 True 2869.0 6159 94.7840 1 5641 3 chr7D.!!$R1 5640
3 TraesCS7B01G203700 chr7D 396135832 396136422 590 False 388.0 388 78.8690 34 624 1 chr7D.!!$F1 590
4 TraesCS7B01G203700 chr2D 469368966 469369507 541 True 329.0 329 77.8790 82 622 1 chr2D.!!$R2 540
5 TraesCS7B01G203700 chr1B 192141452 192142023 571 True 285.0 285 76.0680 46 622 1 chr1B.!!$R1 576
6 TraesCS7B01G203700 chr5A 583689261 583689868 607 False 239.0 239 74.3130 19 623 1 chr5A.!!$F2 604

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
419 429 0.403271 GTCCTATGGGGCATGAGCAT 59.597 55.000 0.00 0.0 44.61 3.79 F
1051 1064 0.476771 AAAACCTTCCTCCCGCTTCA 59.523 50.000 0.00 0.0 0.00 3.02 F
1168 1181 0.687354 TCCTTGCTTTCTCGAGGCTT 59.313 50.000 13.56 0.0 37.51 4.35 F
1188 1201 1.202842 TCCAAGAACGGGGGAAGAAAC 60.203 52.381 0.00 0.0 0.00 2.78 F
2420 2440 1.247567 GGCCGCATATGCCTGTTAAT 58.752 50.000 21.77 0.0 45.70 1.40 F
3001 3028 2.084546 GCGCTTCAACTTCCTATTGGT 58.915 47.619 0.00 0.0 34.23 3.67 F
4494 4539 1.068055 GCTTGTGATGGCTGTTTCAGG 60.068 52.381 0.00 0.0 31.21 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1250 1.891150 ACCCAAAATGCAGAGCAGAAG 59.109 47.619 0.00 0.0 43.65 2.85 R
2509 2529 2.691526 CACCTTTGCATGACCAGCATAT 59.308 45.455 0.00 0.0 42.33 1.78 R
3001 3028 2.742348 TCGGAACCAGCAGGAACTATA 58.258 47.619 0.35 0.0 36.02 1.31 R
3357 3390 4.217836 AGAGTCAATCATCACATGCACT 57.782 40.909 0.00 0.0 0.00 4.40 R
3829 3863 0.472925 TGGAACTGTGGCCTAGTGGA 60.473 55.000 12.97 0.0 34.57 4.02 R
4615 4660 0.668535 TGAGTGTCACAGACCGACAG 59.331 55.000 5.62 0.0 43.75 3.51 R
5503 6774 0.034198 TGTTGGAGCGAACCGATTGA 59.966 50.000 0.00 0.0 0.00 2.57 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
279 285 0.896479 TCGTGGGATTCAGTCGGTGA 60.896 55.000 0.00 0.00 0.00 4.02
355 365 6.146898 CGTTTACAGGTTGAATTTTTCCGAT 58.853 36.000 0.00 0.00 0.00 4.18
356 366 6.304683 CGTTTACAGGTTGAATTTTTCCGATC 59.695 38.462 0.00 0.00 0.00 3.69
357 367 7.368059 GTTTACAGGTTGAATTTTTCCGATCT 58.632 34.615 0.00 0.00 0.00 2.75
358 368 8.508875 GTTTACAGGTTGAATTTTTCCGATCTA 58.491 33.333 0.00 0.00 0.00 1.98
361 371 6.659242 ACAGGTTGAATTTTTCCGATCTACAT 59.341 34.615 0.00 0.00 0.00 2.29
378 388 5.789521 TCTACATTTCTGTTCATCGGTGAA 58.210 37.500 7.11 7.11 41.89 3.18
419 429 0.403271 GTCCTATGGGGCATGAGCAT 59.597 55.000 0.00 0.00 44.61 3.79
471 481 3.401033 TTTGTCAGGCTTCGATGAAGA 57.599 42.857 10.58 0.00 41.71 2.87
946 959 4.040461 TCCCTCTGTTAACTTGAGACTTGG 59.960 45.833 22.05 16.59 0.00 3.61
1051 1064 0.476771 AAAACCTTCCTCCCGCTTCA 59.523 50.000 0.00 0.00 0.00 3.02
1168 1181 0.687354 TCCTTGCTTTCTCGAGGCTT 59.313 50.000 13.56 0.00 37.51 4.35
1188 1201 1.202842 TCCAAGAACGGGGGAAGAAAC 60.203 52.381 0.00 0.00 0.00 2.78
1197 1210 1.765727 GGGAAGAAACGGAGGGGTT 59.234 57.895 0.00 0.00 0.00 4.11
1218 1232 8.952278 GGGGTTGTTCAAGTTTTCTTTTAAAAT 58.048 29.630 0.09 0.00 38.17 1.82
1265 1280 5.876357 TCTGCATTTTGGGTAGTTAACTCT 58.124 37.500 12.39 0.00 0.00 3.24
1289 1304 5.412640 TGATTTTGCATGTGGAATGTGATC 58.587 37.500 0.00 0.00 0.00 2.92
1291 1306 2.812836 TGCATGTGGAATGTGATCCT 57.187 45.000 0.00 0.00 40.35 3.24
1295 1310 4.082081 TGCATGTGGAATGTGATCCTTTTC 60.082 41.667 0.00 0.00 40.35 2.29
1368 1383 1.838073 TTTCCTTCCTCTCCGTGGGC 61.838 60.000 0.00 0.00 0.00 5.36
1377 1392 2.092914 CCTCTCCGTGGGCTAAATCTTT 60.093 50.000 0.00 0.00 0.00 2.52
1404 1419 4.122776 GAGCTGGATCATTGTCGTGTAAT 58.877 43.478 0.00 0.00 0.00 1.89
1560 1575 8.210946 ACTATCTCCGATCCAAATTAATTGACA 58.789 33.333 0.39 0.00 41.85 3.58
1565 1580 5.163622 CCGATCCAAATTAATTGACACAGCT 60.164 40.000 0.39 0.00 41.85 4.24
1566 1581 6.324819 CGATCCAAATTAATTGACACAGCTT 58.675 36.000 0.39 0.00 41.85 3.74
1567 1582 6.808212 CGATCCAAATTAATTGACACAGCTTT 59.192 34.615 0.39 0.00 41.85 3.51
1568 1583 7.967854 CGATCCAAATTAATTGACACAGCTTTA 59.032 33.333 0.39 0.00 41.85 1.85
1569 1584 9.294030 GATCCAAATTAATTGACACAGCTTTAG 57.706 33.333 0.39 0.00 41.85 1.85
1570 1585 8.402798 TCCAAATTAATTGACACAGCTTTAGA 57.597 30.769 0.39 0.00 41.85 2.10
1571 1586 8.855110 TCCAAATTAATTGACACAGCTTTAGAA 58.145 29.630 0.39 0.00 41.85 2.10
1572 1587 9.643693 CCAAATTAATTGACACAGCTTTAGAAT 57.356 29.630 0.39 0.00 41.85 2.40
1646 1661 4.453819 GGGAGTATTGATTCATAGTGCTGC 59.546 45.833 0.00 0.00 0.00 5.25
1687 1702 9.429359 CCCTAAGACTAATGTAGCATCTTATTG 57.571 37.037 0.00 0.00 32.82 1.90
1691 1706 9.979578 AAGACTAATGTAGCATCTTATTGAGAG 57.020 33.333 0.00 0.00 37.93 3.20
1714 1729 9.998752 AGAGATATTAGGGTACTGCTATATTGT 57.001 33.333 0.00 0.00 0.00 2.71
1717 1732 9.099454 GATATTAGGGTACTGCTATATTGTTGC 57.901 37.037 0.00 0.00 0.00 4.17
1723 1738 3.595173 ACTGCTATATTGTTGCACGTGA 58.405 40.909 22.23 1.04 34.84 4.35
1781 1796 5.106157 CGGAAATACTCCTTTTTGAGCATGT 60.106 40.000 0.00 0.00 42.85 3.21
1783 1798 7.361713 CGGAAATACTCCTTTTTGAGCATGTTA 60.362 37.037 0.00 0.00 42.85 2.41
1920 1938 9.416794 CAGTATTCTAATACCATGAAGCTACAG 57.583 37.037 8.83 0.00 41.68 2.74
2213 2231 7.651808 CAATCAACACTGAAGGTAAGATGTTT 58.348 34.615 0.00 0.00 34.49 2.83
2218 2236 7.540474 ACACTGAAGGTAAGATGTTTCTAGA 57.460 36.000 0.00 0.00 0.00 2.43
2295 2314 4.744570 TCAGTTTCATGGTACTGATCGTC 58.255 43.478 20.10 0.00 44.20 4.20
2377 2396 3.542712 AATTTACACAAGACAGCAGCG 57.457 42.857 0.00 0.00 0.00 5.18
2420 2440 1.247567 GGCCGCATATGCCTGTTAAT 58.752 50.000 21.77 0.00 45.70 1.40
2509 2529 2.136298 TGGAGGTTGTTGAAACAGCA 57.864 45.000 11.40 0.00 41.24 4.41
2705 2725 7.872113 ATGAGGTATTGTTTTCATCTCCTTC 57.128 36.000 0.00 0.00 0.00 3.46
2728 2748 5.248248 TCCATATGTTTCTCACTGGACTGAA 59.752 40.000 1.24 0.00 36.74 3.02
2861 2888 4.275689 ACAACACACCACTGTCATGTATTG 59.724 41.667 9.33 9.33 28.75 1.90
2880 2907 6.605194 TGTATTGCAGGCCTGTCAAATTATTA 59.395 34.615 32.18 21.97 33.11 0.98
3001 3028 2.084546 GCGCTTCAACTTCCTATTGGT 58.915 47.619 0.00 0.00 34.23 3.67
3357 3390 5.077134 TCTGTACGTGTAGCTCTGTAGTA 57.923 43.478 0.00 0.00 0.00 1.82
3428 3461 8.369424 TGCTAGTCTGTGTTAAAACTTGGTATA 58.631 33.333 0.00 0.00 0.00 1.47
3561 3594 7.144722 TGTTTGTGATGTTTGGAGATCATAC 57.855 36.000 0.00 0.00 37.80 2.39
3801 3835 5.012239 TGCTTTAAAGATCCACTCATGCTT 58.988 37.500 19.48 0.00 0.00 3.91
3899 3933 5.353123 GCATCCCGTCTTCTGTTTTACATAA 59.647 40.000 0.00 0.00 0.00 1.90
4075 4109 8.917088 CCAATACAAATTTGAGGTGGATTATCT 58.083 33.333 24.64 0.00 31.81 1.98
4076 4110 9.740239 CAATACAAATTTGAGGTGGATTATCTG 57.260 33.333 24.64 6.94 0.00 2.90
4077 4111 6.212888 ACAAATTTGAGGTGGATTATCTGC 57.787 37.500 24.64 0.00 0.00 4.26
4078 4112 5.127682 ACAAATTTGAGGTGGATTATCTGCC 59.872 40.000 24.64 0.00 0.00 4.85
4079 4113 4.803329 ATTTGAGGTGGATTATCTGCCT 57.197 40.909 7.55 7.55 0.00 4.75
4080 4114 4.591321 TTTGAGGTGGATTATCTGCCTT 57.409 40.909 8.80 0.00 0.00 4.35
4204 4244 5.450818 AGCACTGGAGATAATTGGGTTAA 57.549 39.130 0.00 0.00 0.00 2.01
4480 4525 2.033801 CACCTCTTTCACTTGGCTTGTG 59.966 50.000 4.51 4.51 36.82 3.33
4494 4539 1.068055 GCTTGTGATGGCTGTTTCAGG 60.068 52.381 0.00 0.00 31.21 3.86
4524 4569 5.710646 TCTTGAATCTGGACCTAGAGCTAT 58.289 41.667 0.00 0.00 0.00 2.97
4525 4570 5.772672 TCTTGAATCTGGACCTAGAGCTATC 59.227 44.000 0.00 0.00 0.00 2.08
4563 4608 7.893124 AAATTAATTGCATCTCATGACTCCT 57.107 32.000 0.39 0.00 0.00 3.69
4576 4621 1.907255 TGACTCCTCTCACTCTACGGA 59.093 52.381 0.00 0.00 0.00 4.69
4593 4638 4.602340 ACGGACTCACTTTGTAGATTGT 57.398 40.909 0.00 0.00 0.00 2.71
4621 4666 8.928270 AGTTGAGTAATAATTACTTCTGTCGG 57.072 34.615 0.00 0.00 46.01 4.79
4625 4670 8.188799 TGAGTAATAATTACTTCTGTCGGTCTG 58.811 37.037 0.00 0.00 46.01 3.51
4634 4679 0.668535 CTGTCGGTCTGTGACACTCA 59.331 55.000 7.20 0.00 41.20 3.41
4672 4717 7.633193 TTCTTGCAGGTAAAACAAGTAAAGA 57.367 32.000 0.00 0.00 41.22 2.52
4922 4968 6.449635 TGCACTGTAAAAATGTGTCTTCTT 57.550 33.333 0.00 0.00 34.52 2.52
5040 5086 3.650461 AGTGAGGCTTCCTTCTCTTCTTT 59.350 43.478 0.00 0.00 31.76 2.52
5063 5109 3.243301 GCATGGAAGTACAATGCAGATGG 60.243 47.826 14.32 0.00 38.08 3.51
5077 5123 6.630444 ATGCAGATGGAATGTTAAGCTTAG 57.370 37.500 6.24 0.00 0.00 2.18
5129 5175 1.412343 GTGGCCTTTGAACACCATGTT 59.588 47.619 3.32 0.00 44.37 2.71
5190 5237 8.866970 TTGATTGCATAATCTAGGCATCATTA 57.133 30.769 0.35 0.00 45.52 1.90
5203 5250 9.135189 TCTAGGCATCATTACAAAATAAGCAAT 57.865 29.630 0.00 0.00 0.00 3.56
5205 5252 7.558604 AGGCATCATTACAAAATAAGCAATGT 58.441 30.769 0.00 0.00 0.00 2.71
5206 5253 8.042515 AGGCATCATTACAAAATAAGCAATGTT 58.957 29.630 0.00 0.00 0.00 2.71
5207 5254 9.311916 GGCATCATTACAAAATAAGCAATGTTA 57.688 29.630 0.00 0.00 0.00 2.41
5252 5303 8.254508 ACTAAATGTGGACTATGAGAAACTCTC 58.745 37.037 0.00 0.00 43.65 3.20
5299 6569 8.934023 ACATTTCACTAAAACTCCCAAGATAA 57.066 30.769 0.00 0.00 0.00 1.75
5314 6584 7.402054 TCCCAAGATAAAGATAACAAAGCTCA 58.598 34.615 0.00 0.00 0.00 4.26
5316 6586 7.192232 CCAAGATAAAGATAACAAAGCTCAGC 58.808 38.462 0.00 0.00 0.00 4.26
5323 6593 8.792830 AAAGATAACAAAGCTCAGCTATGTTA 57.207 30.769 0.00 3.61 38.25 2.41
5330 6600 6.430925 ACAAAGCTCAGCTATGTTAACATTGA 59.569 34.615 27.21 21.75 38.25 2.57
5333 6603 5.583854 AGCTCAGCTATGTTAACATTGACAG 59.416 40.000 27.21 18.94 36.99 3.51
5349 6619 9.685276 AACATTGACAGATGAAATTCCATAGTA 57.315 29.630 0.00 0.00 0.00 1.82
5366 6636 6.761242 TCCATAGTAATCAATTTGTCTGGTCG 59.239 38.462 0.00 0.00 0.00 4.79
5392 6662 2.046285 GGCACGCTAGGGTTTGCAT 61.046 57.895 19.62 0.00 36.66 3.96
5426 6696 1.143073 GTGGGACCTCAACCAACTCTT 59.857 52.381 0.00 0.00 38.73 2.85
5427 6697 1.850345 TGGGACCTCAACCAACTCTTT 59.150 47.619 0.00 0.00 32.89 2.52
5428 6698 2.243736 TGGGACCTCAACCAACTCTTTT 59.756 45.455 0.00 0.00 32.89 2.27
5429 6699 3.296854 GGGACCTCAACCAACTCTTTTT 58.703 45.455 0.00 0.00 0.00 1.94
5483 6754 5.817296 TGAATACATACATGCAACCTCAGAC 59.183 40.000 0.00 0.00 0.00 3.51
5514 6785 4.331443 TGGATAATGTTGTCAATCGGTTCG 59.669 41.667 0.00 0.00 0.00 3.95
5516 6787 1.808411 ATGTTGTCAATCGGTTCGCT 58.192 45.000 0.00 0.00 0.00 4.93
5535 6806 6.567687 TCGCTCCAACATCTCAAATTTAAA 57.432 33.333 0.00 0.00 0.00 1.52
5543 6814 8.479280 CCAACATCTCAAATTTAAAACAACTCG 58.521 33.333 0.00 0.00 0.00 4.18
5548 6819 8.835467 TCTCAAATTTAAAACAACTCGTCTTG 57.165 30.769 0.00 0.00 0.00 3.02
5565 6836 5.989168 TCGTCTTGCAATTCTCTCAACTAAA 59.011 36.000 0.00 0.00 0.00 1.85
5570 6842 6.228273 TGCAATTCTCTCAACTAAAAGACG 57.772 37.500 0.00 0.00 0.00 4.18
5641 6913 8.880750 GGACAAAAGTGAACCACTATCTAATAC 58.119 37.037 0.00 0.00 44.62 1.89
5642 6914 9.654663 GACAAAAGTGAACCACTATCTAATACT 57.345 33.333 0.00 0.00 44.62 2.12
5643 6915 9.654663 ACAAAAGTGAACCACTATCTAATACTC 57.345 33.333 0.00 0.00 44.62 2.59
5644 6916 9.099454 CAAAAGTGAACCACTATCTAATACTCC 57.901 37.037 0.00 0.00 44.62 3.85
5645 6917 6.980416 AGTGAACCACTATCTAATACTCCC 57.020 41.667 0.00 0.00 43.46 4.30
5646 6918 6.684538 AGTGAACCACTATCTAATACTCCCT 58.315 40.000 0.00 0.00 43.46 4.20
5647 6919 6.778559 AGTGAACCACTATCTAATACTCCCTC 59.221 42.308 0.00 0.00 43.46 4.30
5648 6920 6.778559 GTGAACCACTATCTAATACTCCCTCT 59.221 42.308 0.00 0.00 0.00 3.69
5649 6921 6.778069 TGAACCACTATCTAATACTCCCTCTG 59.222 42.308 0.00 0.00 0.00 3.35
5650 6922 6.282568 ACCACTATCTAATACTCCCTCTGT 57.717 41.667 0.00 0.00 0.00 3.41
5651 6923 6.308566 ACCACTATCTAATACTCCCTCTGTC 58.691 44.000 0.00 0.00 0.00 3.51
5652 6924 5.712917 CCACTATCTAATACTCCCTCTGTCC 59.287 48.000 0.00 0.00 0.00 4.02
5653 6925 6.468066 CCACTATCTAATACTCCCTCTGTCCT 60.468 46.154 0.00 0.00 0.00 3.85
5654 6926 7.257089 CCACTATCTAATACTCCCTCTGTCCTA 60.257 44.444 0.00 0.00 0.00 2.94
5655 6927 8.164733 CACTATCTAATACTCCCTCTGTCCTAA 58.835 40.741 0.00 0.00 0.00 2.69
5656 6928 8.734763 ACTATCTAATACTCCCTCTGTCCTAAA 58.265 37.037 0.00 0.00 0.00 1.85
5657 6929 9.589461 CTATCTAATACTCCCTCTGTCCTAAAA 57.411 37.037 0.00 0.00 0.00 1.52
5659 6931 8.855804 TCTAATACTCCCTCTGTCCTAAAATT 57.144 34.615 0.00 0.00 0.00 1.82
5660 6932 8.925338 TCTAATACTCCCTCTGTCCTAAAATTC 58.075 37.037 0.00 0.00 0.00 2.17
5661 6933 7.757242 AATACTCCCTCTGTCCTAAAATTCT 57.243 36.000 0.00 0.00 0.00 2.40
5662 6934 7.757242 ATACTCCCTCTGTCCTAAAATTCTT 57.243 36.000 0.00 0.00 0.00 2.52
5663 6935 5.810095 ACTCCCTCTGTCCTAAAATTCTTG 58.190 41.667 0.00 0.00 0.00 3.02
5664 6936 5.310857 ACTCCCTCTGTCCTAAAATTCTTGT 59.689 40.000 0.00 0.00 0.00 3.16
5665 6937 6.183361 ACTCCCTCTGTCCTAAAATTCTTGTT 60.183 38.462 0.00 0.00 0.00 2.83
5666 6938 6.610830 TCCCTCTGTCCTAAAATTCTTGTTT 58.389 36.000 0.00 0.00 0.00 2.83
5667 6939 7.066781 TCCCTCTGTCCTAAAATTCTTGTTTT 58.933 34.615 0.00 0.00 35.60 2.43
5668 6940 8.221944 TCCCTCTGTCCTAAAATTCTTGTTTTA 58.778 33.333 0.00 0.00 33.62 1.52
5669 6941 8.515414 CCCTCTGTCCTAAAATTCTTGTTTTAG 58.485 37.037 10.61 10.61 45.04 1.85
5670 6942 9.284968 CCTCTGTCCTAAAATTCTTGTTTTAGA 57.715 33.333 16.53 2.54 46.89 2.10
5693 6965 8.572855 AGATTCTAAGACAAGAATTTTGGGAG 57.427 34.615 0.99 0.00 44.38 4.30
5694 6966 7.613411 AGATTCTAAGACAAGAATTTTGGGAGG 59.387 37.037 0.99 0.00 44.38 4.30
5695 6967 5.570320 TCTAAGACAAGAATTTTGGGAGGG 58.430 41.667 5.68 0.00 0.00 4.30
5696 6968 4.469469 AAGACAAGAATTTTGGGAGGGA 57.531 40.909 5.68 0.00 0.00 4.20
5697 6969 4.039603 AGACAAGAATTTTGGGAGGGAG 57.960 45.455 5.68 0.00 0.00 4.30
5698 6970 3.092301 GACAAGAATTTTGGGAGGGAGG 58.908 50.000 5.68 0.00 0.00 4.30
5699 6971 2.450886 ACAAGAATTTTGGGAGGGAGGT 59.549 45.455 5.68 0.00 0.00 3.85
5700 6972 3.660669 ACAAGAATTTTGGGAGGGAGGTA 59.339 43.478 5.68 0.00 0.00 3.08
5701 6973 4.107311 ACAAGAATTTTGGGAGGGAGGTAA 59.893 41.667 5.68 0.00 0.00 2.85
5702 6974 5.222547 ACAAGAATTTTGGGAGGGAGGTAAT 60.223 40.000 5.68 0.00 0.00 1.89
5703 6975 6.011096 ACAAGAATTTTGGGAGGGAGGTAATA 60.011 38.462 5.68 0.00 0.00 0.98
5704 6976 6.865651 AGAATTTTGGGAGGGAGGTAATAT 57.134 37.500 0.00 0.00 0.00 1.28
5705 6977 7.964730 AGAATTTTGGGAGGGAGGTAATATA 57.035 36.000 0.00 0.00 0.00 0.86
5706 6978 8.539856 AGAATTTTGGGAGGGAGGTAATATAT 57.460 34.615 0.00 0.00 0.00 0.86
5707 6979 9.643778 AGAATTTTGGGAGGGAGGTAATATATA 57.356 33.333 0.00 0.00 0.00 0.86
5708 6980 9.682465 GAATTTTGGGAGGGAGGTAATATATAC 57.318 37.037 0.00 0.00 0.00 1.47
5709 6981 7.578458 TTTTGGGAGGGAGGTAATATATACC 57.422 40.000 0.00 0.00 37.86 2.73
5721 6993 7.859540 AGGTAATATATACCTACGAGCAGAGA 58.140 38.462 5.38 0.00 45.47 3.10
5722 6994 7.988599 AGGTAATATATACCTACGAGCAGAGAG 59.011 40.741 5.38 0.00 45.47 3.20
5723 6995 7.227116 GGTAATATATACCTACGAGCAGAGAGG 59.773 44.444 0.00 0.00 34.82 3.69
5724 6996 4.644163 ATATACCTACGAGCAGAGAGGT 57.356 45.455 12.34 12.34 40.80 3.85
5725 6997 2.039818 TACCTACGAGCAGAGAGGTG 57.960 55.000 15.31 0.00 39.12 4.00
5726 6998 0.328592 ACCTACGAGCAGAGAGGTGA 59.671 55.000 0.00 0.00 37.98 4.02
5727 6999 1.271982 ACCTACGAGCAGAGAGGTGAA 60.272 52.381 0.00 0.00 37.98 3.18
5728 7000 2.028130 CCTACGAGCAGAGAGGTGAAT 58.972 52.381 0.00 0.00 0.00 2.57
5729 7001 2.034053 CCTACGAGCAGAGAGGTGAATC 59.966 54.545 0.00 0.00 0.00 2.52
5730 7002 0.820871 ACGAGCAGAGAGGTGAATCC 59.179 55.000 0.00 0.00 0.00 3.01
5731 7003 0.820226 CGAGCAGAGAGGTGAATCCA 59.180 55.000 0.00 0.00 39.02 3.41
5732 7004 1.470632 CGAGCAGAGAGGTGAATCCAC 60.471 57.143 0.00 0.00 42.46 4.02
5746 7018 6.949352 GTGAATCCACCAAATATCTGATGT 57.051 37.500 0.00 0.00 37.33 3.06
5747 7019 7.338800 GTGAATCCACCAAATATCTGATGTT 57.661 36.000 0.00 0.00 37.33 2.71
5748 7020 7.420800 GTGAATCCACCAAATATCTGATGTTC 58.579 38.462 0.00 0.00 37.33 3.18
5749 7021 7.067372 GTGAATCCACCAAATATCTGATGTTCA 59.933 37.037 0.00 0.00 37.33 3.18
5750 7022 7.781219 TGAATCCACCAAATATCTGATGTTCAT 59.219 33.333 0.00 0.00 0.00 2.57
5751 7023 7.756395 ATCCACCAAATATCTGATGTTCATC 57.244 36.000 0.00 5.91 0.00 2.92
5752 7024 6.903516 TCCACCAAATATCTGATGTTCATCT 58.096 36.000 12.94 0.00 0.00 2.90
5753 7025 7.348815 TCCACCAAATATCTGATGTTCATCTT 58.651 34.615 12.94 2.75 0.00 2.40
5754 7026 7.500227 TCCACCAAATATCTGATGTTCATCTTC 59.500 37.037 12.94 0.00 0.00 2.87
5755 7027 7.283807 CCACCAAATATCTGATGTTCATCTTCA 59.716 37.037 12.94 0.00 0.00 3.02
5756 7028 8.680001 CACCAAATATCTGATGTTCATCTTCAA 58.320 33.333 12.94 0.00 31.43 2.69
5757 7029 9.417561 ACCAAATATCTGATGTTCATCTTCAAT 57.582 29.630 12.94 5.25 31.43 2.57
5758 7030 9.894783 CCAAATATCTGATGTTCATCTTCAATC 57.105 33.333 12.94 0.00 31.43 2.67
5759 7031 9.894783 CAAATATCTGATGTTCATCTTCAATCC 57.105 33.333 12.94 0.00 31.43 3.01
5760 7032 9.863650 AAATATCTGATGTTCATCTTCAATCCT 57.136 29.630 12.94 0.00 31.43 3.24
5770 7042 8.623903 TGTTCATCTTCAATCCTATATTTGTGC 58.376 33.333 0.00 0.00 0.00 4.57
5771 7043 8.844244 GTTCATCTTCAATCCTATATTTGTGCT 58.156 33.333 0.00 0.00 0.00 4.40
5781 7053 8.798859 ATCCTATATTTGTGCTATCATGAACC 57.201 34.615 0.00 0.00 0.00 3.62
5782 7054 7.168219 TCCTATATTTGTGCTATCATGAACCC 58.832 38.462 0.00 0.00 0.00 4.11
5783 7055 6.942005 CCTATATTTGTGCTATCATGAACCCA 59.058 38.462 0.00 0.00 0.00 4.51
5784 7056 4.989279 ATTTGTGCTATCATGAACCCAC 57.011 40.909 0.00 7.70 0.00 4.61
5785 7057 2.418368 TGTGCTATCATGAACCCACC 57.582 50.000 15.81 0.00 0.00 4.61
5786 7058 1.632920 TGTGCTATCATGAACCCACCA 59.367 47.619 15.81 1.81 0.00 4.17
5787 7059 2.017049 GTGCTATCATGAACCCACCAC 58.983 52.381 0.00 0.00 0.00 4.16
5788 7060 1.632920 TGCTATCATGAACCCACCACA 59.367 47.619 0.00 0.00 0.00 4.17
5789 7061 2.241941 TGCTATCATGAACCCACCACAT 59.758 45.455 0.00 0.00 0.00 3.21
5790 7062 2.620115 GCTATCATGAACCCACCACATG 59.380 50.000 0.00 0.00 41.55 3.21
5792 7064 2.198827 TCATGAACCCACCACATGAC 57.801 50.000 0.00 0.00 43.17 3.06
5793 7065 1.704628 TCATGAACCCACCACATGACT 59.295 47.619 0.00 0.00 43.17 3.41
5794 7066 2.108075 TCATGAACCCACCACATGACTT 59.892 45.455 0.00 0.00 43.17 3.01
5795 7067 2.270352 TGAACCCACCACATGACTTC 57.730 50.000 0.00 0.00 0.00 3.01
5796 7068 1.774254 TGAACCCACCACATGACTTCT 59.226 47.619 0.00 0.00 0.00 2.85
5797 7069 2.154462 GAACCCACCACATGACTTCTG 58.846 52.381 0.00 0.00 0.00 3.02
5798 7070 1.434188 ACCCACCACATGACTTCTGA 58.566 50.000 0.00 0.00 0.00 3.27
5799 7071 1.349026 ACCCACCACATGACTTCTGAG 59.651 52.381 0.00 0.00 0.00 3.35
5800 7072 1.446907 CCACCACATGACTTCTGAGC 58.553 55.000 0.00 0.00 0.00 4.26
5801 7073 1.271001 CCACCACATGACTTCTGAGCA 60.271 52.381 0.00 0.00 0.00 4.26
5802 7074 2.497138 CACCACATGACTTCTGAGCAA 58.503 47.619 0.00 0.00 0.00 3.91
5803 7075 2.880268 CACCACATGACTTCTGAGCAAA 59.120 45.455 0.00 0.00 0.00 3.68
5804 7076 2.880890 ACCACATGACTTCTGAGCAAAC 59.119 45.455 0.00 0.00 0.00 2.93
5805 7077 2.227388 CCACATGACTTCTGAGCAAACC 59.773 50.000 0.00 0.00 0.00 3.27
5806 7078 3.144506 CACATGACTTCTGAGCAAACCT 58.855 45.455 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.321996 GAGACAAGGCGAAGACCCTT 59.678 55.000 0.00 0.00 43.29 3.95
69 71 4.154347 GCCCTCTCACCGGCAGAG 62.154 72.222 19.92 19.92 45.01 3.35
111 116 7.681939 TGACACAAATTCTAATCAACCCTAC 57.318 36.000 0.00 0.00 0.00 3.18
355 365 5.400066 TCACCGATGAACAGAAATGTAGA 57.600 39.130 0.00 0.00 0.00 2.59
356 366 5.063944 CCTTCACCGATGAACAGAAATGTAG 59.936 44.000 0.00 0.00 40.01 2.74
357 367 4.935205 CCTTCACCGATGAACAGAAATGTA 59.065 41.667 0.00 0.00 40.01 2.29
358 368 3.753272 CCTTCACCGATGAACAGAAATGT 59.247 43.478 0.00 0.00 40.01 2.71
361 371 3.485463 ACCTTCACCGATGAACAGAAA 57.515 42.857 0.00 0.00 40.01 2.52
378 388 0.318955 GCGCATCAAAACAGCAACCT 60.319 50.000 0.30 0.00 0.00 3.50
419 429 1.315690 AGACAGTCGGAAAGTCGTCA 58.684 50.000 0.00 0.00 37.36 4.35
478 488 2.631696 GAAATCGCACCGCCGTCATG 62.632 60.000 0.00 0.00 0.00 3.07
623 636 8.977505 GCTTAATCAGTGAGAACATATCTTCTC 58.022 37.037 12.42 12.42 44.52 2.87
665 678 1.886542 GTTCATGTGGGTTTGGACTCC 59.113 52.381 0.00 0.00 0.00 3.85
929 942 3.714798 ACCTCCCAAGTCTCAAGTTAACA 59.285 43.478 8.61 0.00 0.00 2.41
946 959 1.556911 TCCAGATCAAGAAGCACCTCC 59.443 52.381 0.00 0.00 0.00 4.30
1051 1064 3.577805 ACAACAAGGAACAGGCTTAGT 57.422 42.857 0.00 0.00 0.00 2.24
1057 1070 4.559862 AGGAGATACAACAAGGAACAGG 57.440 45.455 0.00 0.00 0.00 4.00
1113 1126 2.125912 CGCTCCAGTTCCCACTCG 60.126 66.667 0.00 0.00 0.00 4.18
1168 1181 1.142060 TTTCTTCCCCCGTTCTTGGA 58.858 50.000 0.00 0.00 0.00 3.53
1188 1201 1.687563 AAACTTGAACAACCCCTCCG 58.312 50.000 0.00 0.00 0.00 4.63
1218 1232 4.020662 GCAGAAGAGGAAGAGAGGAGAAAA 60.021 45.833 0.00 0.00 0.00 2.29
1219 1233 3.513515 GCAGAAGAGGAAGAGAGGAGAAA 59.486 47.826 0.00 0.00 0.00 2.52
1230 1245 3.430042 AAATGCAGAGCAGAAGAGGAA 57.570 42.857 0.00 0.00 43.65 3.36
1232 1247 2.163815 CCAAAATGCAGAGCAGAAGAGG 59.836 50.000 0.00 0.00 43.65 3.69
1235 1250 1.891150 ACCCAAAATGCAGAGCAGAAG 59.109 47.619 0.00 0.00 43.65 2.85
1265 1280 5.211174 TCACATTCCACATGCAAAATCAA 57.789 34.783 0.00 0.00 0.00 2.57
1289 1304 4.072839 GTGGTAGAAAGTCTGGGAAAAGG 58.927 47.826 0.00 0.00 0.00 3.11
1291 1306 5.512576 GCTAGTGGTAGAAAGTCTGGGAAAA 60.513 44.000 0.00 0.00 0.00 2.29
1295 1310 3.100671 AGCTAGTGGTAGAAAGTCTGGG 58.899 50.000 0.00 0.00 0.00 4.45
1368 1383 8.632906 ATGATCCAGCTCCATTAAAGATTTAG 57.367 34.615 0.00 0.00 0.00 1.85
1377 1392 3.134623 ACGACAATGATCCAGCTCCATTA 59.865 43.478 0.00 0.00 0.00 1.90
1404 1419 9.574458 TTGTAATGAAAACTTGAAAATTCGTGA 57.426 25.926 0.00 0.00 0.00 4.35
1442 1457 5.997746 CAGGAGAAAAGTTTGTGACCATAGA 59.002 40.000 0.00 0.00 0.00 1.98
1523 1538 6.598457 TGGATCGGAGATAGTACTATACTTGC 59.402 42.308 15.42 8.70 45.12 4.01
1576 1591 7.680113 GCCACTTTAGTACAACTTTGCACTAAA 60.680 37.037 19.50 19.50 46.64 1.85
1577 1592 6.238538 GCCACTTTAGTACAACTTTGCACTAA 60.239 38.462 9.74 9.74 42.33 2.24
1582 1597 3.002965 ACGCCACTTTAGTACAACTTTGC 59.997 43.478 0.00 0.00 0.00 3.68
1600 1615 3.314080 TCCGATCCAAATTAATTGACGCC 59.686 43.478 0.39 0.00 41.85 5.68
1691 1706 9.099454 GCAACAATATAGCAGTACCCTAATATC 57.901 37.037 0.00 0.00 0.00 1.63
1708 1723 5.716094 TGTAGTACTCACGTGCAACAATAT 58.284 37.500 11.67 0.00 35.74 1.28
1709 1724 5.123805 TGTAGTACTCACGTGCAACAATA 57.876 39.130 11.67 0.00 35.74 1.90
1710 1725 3.985008 TGTAGTACTCACGTGCAACAAT 58.015 40.909 11.67 0.00 35.74 2.71
1711 1726 3.439895 TGTAGTACTCACGTGCAACAA 57.560 42.857 11.67 0.00 35.74 2.83
1712 1727 3.653539 ATGTAGTACTCACGTGCAACA 57.346 42.857 11.67 8.57 35.74 3.33
1713 1728 5.632347 ACTTAATGTAGTACTCACGTGCAAC 59.368 40.000 11.67 8.60 0.00 4.17
1714 1729 5.775686 ACTTAATGTAGTACTCACGTGCAA 58.224 37.500 11.67 0.00 0.00 4.08
1715 1730 5.381174 ACTTAATGTAGTACTCACGTGCA 57.619 39.130 11.67 0.89 0.00 4.57
1716 1731 6.701432 AAACTTAATGTAGTACTCACGTGC 57.299 37.500 11.67 0.00 0.00 5.34
1717 1732 8.289440 TGAAAACTTAATGTAGTACTCACGTG 57.711 34.615 9.94 9.94 0.00 4.49
1729 1744 8.034804 GCCCATGTTAAGATGAAAACTTAATGT 58.965 33.333 13.90 0.00 42.06 2.71
1747 1762 2.365582 GAGTATTTCCGTGCCCATGTT 58.634 47.619 0.00 0.00 0.00 2.71
1781 1796 7.896811 TGAGAGCAAGATCTAAAGTCAACTAA 58.103 34.615 0.00 0.00 0.00 2.24
1783 1798 6.352016 TGAGAGCAAGATCTAAAGTCAACT 57.648 37.500 0.00 0.00 0.00 3.16
2265 2283 5.124457 CAGTACCATGAAACTGAAAGGGATG 59.876 44.000 17.69 0.00 44.79 3.51
2295 2314 9.605275 TCTCAATGGATAATGACAGAAACTAAG 57.395 33.333 0.00 0.00 0.00 2.18
2377 2396 9.663904 GCCAATTAAAAACAGAAGGAATTTTTC 57.336 29.630 0.00 0.00 36.95 2.29
2429 2449 3.754965 TCAAAAGCACTCAGGTAGCAAT 58.245 40.909 0.00 0.00 0.00 3.56
2509 2529 2.691526 CACCTTTGCATGACCAGCATAT 59.308 45.455 0.00 0.00 42.33 1.78
2705 2725 5.089970 TCAGTCCAGTGAGAAACATATGG 57.910 43.478 7.80 0.00 38.64 2.74
2728 2748 4.881850 CAGAAAGTGAAACAGGTTACCAGT 59.118 41.667 3.51 0.00 41.43 4.00
2861 2888 8.792633 TGTATATTAATAATTTGACAGGCCTGC 58.207 33.333 33.06 24.14 0.00 4.85
2880 2907 9.726438 GGGTACTGATGCTTCTATTTGTATATT 57.274 33.333 0.88 0.00 0.00 1.28
3001 3028 2.742348 TCGGAACCAGCAGGAACTATA 58.258 47.619 0.35 0.00 36.02 1.31
3357 3390 4.217836 AGAGTCAATCATCACATGCACT 57.782 40.909 0.00 0.00 0.00 4.40
3428 3461 7.016858 TCCACAAGGTTGTCTAACTAGGTTATT 59.983 37.037 0.00 0.00 39.91 1.40
3561 3594 6.032775 CGCTCTTGCTGTTGTTTTGTATTATG 59.967 38.462 0.00 0.00 36.97 1.90
3628 3661 4.277672 CCATGAGCATTTCTGTAATCCCAG 59.722 45.833 0.00 0.00 0.00 4.45
3801 3835 5.471556 TCGTCAACCAATAAGAGGTAACA 57.528 39.130 0.00 0.00 38.76 2.41
3829 3863 0.472925 TGGAACTGTGGCCTAGTGGA 60.473 55.000 12.97 0.00 34.57 4.02
3881 3915 7.277981 AGCTATGGTTATGTAAAACAGAAGACG 59.722 37.037 0.00 0.00 29.06 4.18
4075 4109 5.418840 GGATTTTTCTCTGGTGATAAAGGCA 59.581 40.000 0.00 0.00 0.00 4.75
4076 4110 5.654209 AGGATTTTTCTCTGGTGATAAAGGC 59.346 40.000 0.00 0.00 0.00 4.35
4077 4111 8.678199 GTTAGGATTTTTCTCTGGTGATAAAGG 58.322 37.037 0.00 0.00 0.00 3.11
4078 4112 9.454859 AGTTAGGATTTTTCTCTGGTGATAAAG 57.545 33.333 0.00 0.00 0.00 1.85
4079 4113 9.807921 AAGTTAGGATTTTTCTCTGGTGATAAA 57.192 29.630 0.00 0.00 0.00 1.40
4080 4114 9.231297 CAAGTTAGGATTTTTCTCTGGTGATAA 57.769 33.333 0.00 0.00 0.00 1.75
4204 4244 2.376855 CCAAGAAACTCCCCTTTCCTCT 59.623 50.000 0.00 0.00 31.44 3.69
4480 4525 1.941999 GCCTGCCTGAAACAGCCATC 61.942 60.000 0.00 0.00 33.65 3.51
4494 4539 1.674962 GTCCAGATTCAAGATGCCTGC 59.325 52.381 0.00 0.00 0.00 4.85
4563 4608 3.420300 AAGTGAGTCCGTAGAGTGAGA 57.580 47.619 0.00 0.00 0.00 3.27
4576 4621 7.047891 TCAACTCAACAATCTACAAAGTGAGT 58.952 34.615 0.00 0.00 35.90 3.41
4613 4658 1.337071 GAGTGTCACAGACCGACAGAA 59.663 52.381 5.62 0.00 43.75 3.02
4615 4660 0.668535 TGAGTGTCACAGACCGACAG 59.331 55.000 5.62 0.00 43.75 3.51
4621 4666 3.002246 TCGCAAAATTGAGTGTCACAGAC 59.998 43.478 5.62 0.00 0.00 3.51
4625 4670 2.032799 TGGTCGCAAAATTGAGTGTCAC 59.967 45.455 0.00 0.00 0.00 3.67
4634 4679 3.726607 TGCAAGAAATGGTCGCAAAATT 58.273 36.364 0.00 0.00 0.00 1.82
4922 4968 9.189156 CTTAAGAGAATGGGTGAAAATAATGGA 57.811 33.333 0.00 0.00 0.00 3.41
5040 5086 3.070476 TCTGCATTGTACTTCCATGCA 57.930 42.857 16.51 16.51 44.71 3.96
5203 5250 5.172687 TGTGGTCCATTGAGCTAATAACA 57.827 39.130 0.00 0.00 39.75 2.41
5205 5252 5.815581 AGTTGTGGTCCATTGAGCTAATAA 58.184 37.500 0.00 0.00 39.75 1.40
5206 5253 5.435686 AGTTGTGGTCCATTGAGCTAATA 57.564 39.130 0.00 0.00 39.75 0.98
5207 5254 4.307032 AGTTGTGGTCCATTGAGCTAAT 57.693 40.909 0.00 0.00 39.75 1.73
5252 5303 8.627487 ATGTACATTAATGGTGCATAAAAACG 57.373 30.769 19.37 0.00 39.34 3.60
5314 6584 8.565896 TTTCATCTGTCAATGTTAACATAGCT 57.434 30.769 21.07 3.45 35.10 3.32
5323 6593 8.585471 ACTATGGAATTTCATCTGTCAATGTT 57.415 30.769 1.37 0.00 0.00 2.71
5349 6619 2.095059 GCTGCGACCAGACAAATTGATT 60.095 45.455 0.00 0.00 41.77 2.57
5385 6655 4.445385 CACAAAGTTGGAAGCTATGCAAAC 59.555 41.667 0.00 0.21 41.36 2.93
5392 6662 2.488347 GGTCCCACAAAGTTGGAAGCTA 60.488 50.000 0.00 0.00 39.24 3.32
5452 6722 6.912591 GGTTGCATGTATGTATTCAGCTTTAC 59.087 38.462 0.00 0.00 0.00 2.01
5453 6723 6.828273 AGGTTGCATGTATGTATTCAGCTTTA 59.172 34.615 0.00 0.00 0.00 1.85
5454 6724 5.653769 AGGTTGCATGTATGTATTCAGCTTT 59.346 36.000 0.00 0.00 0.00 3.51
5459 6730 5.817296 GTCTGAGGTTGCATGTATGTATTCA 59.183 40.000 0.00 0.00 0.00 2.57
5463 6734 3.517500 TGGTCTGAGGTTGCATGTATGTA 59.482 43.478 0.00 0.00 0.00 2.29
5465 6736 2.989909 TGGTCTGAGGTTGCATGTATG 58.010 47.619 0.00 0.00 0.00 2.39
5503 6774 0.034198 TGTTGGAGCGAACCGATTGA 59.966 50.000 0.00 0.00 0.00 2.57
5508 6779 0.389817 TGAGATGTTGGAGCGAACCG 60.390 55.000 0.00 0.00 0.00 4.44
5514 6785 7.945033 TGTTTTAAATTTGAGATGTTGGAGC 57.055 32.000 0.00 0.00 0.00 4.70
5516 6787 9.528018 GAGTTGTTTTAAATTTGAGATGTTGGA 57.472 29.630 0.00 0.00 0.00 3.53
5535 6806 4.130118 AGAGAATTGCAAGACGAGTTGTT 58.870 39.130 4.94 0.00 0.00 2.83
5543 6814 7.800847 GTCTTTTAGTTGAGAGAATTGCAAGAC 59.199 37.037 4.94 1.13 31.34 3.01
5548 6819 6.467723 TCGTCTTTTAGTTGAGAGAATTGC 57.532 37.500 0.00 0.00 0.00 3.56
5641 6913 5.810095 ACAAGAATTTTAGGACAGAGGGAG 58.190 41.667 0.00 0.00 0.00 4.30
5642 6914 5.843019 ACAAGAATTTTAGGACAGAGGGA 57.157 39.130 0.00 0.00 0.00 4.20
5643 6915 6.901081 AAACAAGAATTTTAGGACAGAGGG 57.099 37.500 0.00 0.00 0.00 4.30
5644 6916 9.284968 TCTAAAACAAGAATTTTAGGACAGAGG 57.715 33.333 14.74 0.00 45.87 3.69
5667 6939 9.672673 CTCCCAAAATTCTTGTCTTAGAATCTA 57.327 33.333 0.00 0.00 42.53 1.98
5668 6940 7.613411 CCTCCCAAAATTCTTGTCTTAGAATCT 59.387 37.037 0.00 0.00 42.53 2.40
5669 6941 7.148000 CCCTCCCAAAATTCTTGTCTTAGAATC 60.148 40.741 0.00 0.00 42.53 2.52
5670 6942 6.665248 CCCTCCCAAAATTCTTGTCTTAGAAT 59.335 38.462 0.00 0.00 44.62 2.40
5671 6943 6.010219 CCCTCCCAAAATTCTTGTCTTAGAA 58.990 40.000 0.00 0.00 38.43 2.10
5672 6944 5.312178 TCCCTCCCAAAATTCTTGTCTTAGA 59.688 40.000 0.00 0.00 0.00 2.10
5673 6945 5.570320 TCCCTCCCAAAATTCTTGTCTTAG 58.430 41.667 0.00 0.00 0.00 2.18
5674 6946 5.516591 CCTCCCTCCCAAAATTCTTGTCTTA 60.517 44.000 0.00 0.00 0.00 2.10
5675 6947 4.411013 CTCCCTCCCAAAATTCTTGTCTT 58.589 43.478 0.00 0.00 0.00 3.01
5676 6948 3.245407 CCTCCCTCCCAAAATTCTTGTCT 60.245 47.826 0.00 0.00 0.00 3.41
5677 6949 3.092301 CCTCCCTCCCAAAATTCTTGTC 58.908 50.000 0.00 0.00 0.00 3.18
5678 6950 2.450886 ACCTCCCTCCCAAAATTCTTGT 59.549 45.455 0.00 0.00 0.00 3.16
5679 6951 3.175438 ACCTCCCTCCCAAAATTCTTG 57.825 47.619 0.00 0.00 0.00 3.02
5680 6952 5.552430 ATTACCTCCCTCCCAAAATTCTT 57.448 39.130 0.00 0.00 0.00 2.52
5681 6953 6.865651 ATATTACCTCCCTCCCAAAATTCT 57.134 37.500 0.00 0.00 0.00 2.40
5682 6954 9.682465 GTATATATTACCTCCCTCCCAAAATTC 57.318 37.037 0.00 0.00 0.00 2.17
5683 6955 8.621073 GGTATATATTACCTCCCTCCCAAAATT 58.379 37.037 0.00 0.00 34.82 1.82
5684 6956 7.973549 AGGTATATATTACCTCCCTCCCAAAAT 59.026 37.037 9.53 0.00 44.10 1.82
5685 6957 7.326248 AGGTATATATTACCTCCCTCCCAAAA 58.674 38.462 9.53 0.00 44.10 2.44
5686 6958 6.893396 AGGTATATATTACCTCCCTCCCAAA 58.107 40.000 9.53 0.00 44.10 3.28
5687 6959 6.509633 AGGTATATATTACCTCCCTCCCAA 57.490 41.667 9.53 0.00 44.10 4.12
5688 6960 6.354213 CGTAGGTATATATTACCTCCCTCCCA 60.354 46.154 15.60 0.76 44.10 4.37
5689 6961 6.067350 CGTAGGTATATATTACCTCCCTCCC 58.933 48.000 15.60 0.00 44.10 4.30
5690 6962 6.904626 TCGTAGGTATATATTACCTCCCTCC 58.095 44.000 15.60 4.89 44.10 4.30
5691 6963 6.486320 GCTCGTAGGTATATATTACCTCCCTC 59.514 46.154 15.60 8.09 44.10 4.30
5692 6964 6.069206 TGCTCGTAGGTATATATTACCTCCCT 60.069 42.308 15.60 0.00 44.10 4.20
5693 6965 6.125029 TGCTCGTAGGTATATATTACCTCCC 58.875 44.000 15.60 9.74 44.10 4.30
5694 6966 7.052873 TCTGCTCGTAGGTATATATTACCTCC 58.947 42.308 15.60 7.72 44.10 4.30
5695 6967 7.986320 TCTCTGCTCGTAGGTATATATTACCTC 59.014 40.741 15.60 9.62 44.10 3.85
5697 6969 7.227116 CCTCTCTGCTCGTAGGTATATATTACC 59.773 44.444 0.00 6.16 37.86 2.85
5698 6970 7.769970 ACCTCTCTGCTCGTAGGTATATATTAC 59.230 40.741 0.00 0.00 40.57 1.89
5699 6971 7.769507 CACCTCTCTGCTCGTAGGTATATATTA 59.230 40.741 0.00 0.00 40.39 0.98
5700 6972 6.600032 CACCTCTCTGCTCGTAGGTATATATT 59.400 42.308 0.00 0.00 40.39 1.28
5701 6973 6.070136 TCACCTCTCTGCTCGTAGGTATATAT 60.070 42.308 0.00 0.00 40.39 0.86
5702 6974 5.247792 TCACCTCTCTGCTCGTAGGTATATA 59.752 44.000 0.00 0.00 40.39 0.86
5703 6975 4.041815 TCACCTCTCTGCTCGTAGGTATAT 59.958 45.833 0.00 0.00 40.39 0.86
5704 6976 3.390311 TCACCTCTCTGCTCGTAGGTATA 59.610 47.826 0.00 0.00 40.39 1.47
5705 6977 2.172930 TCACCTCTCTGCTCGTAGGTAT 59.827 50.000 0.00 0.00 40.39 2.73
5706 6978 1.558294 TCACCTCTCTGCTCGTAGGTA 59.442 52.381 0.00 0.00 40.39 3.08
5707 6979 0.328592 TCACCTCTCTGCTCGTAGGT 59.671 55.000 0.00 0.00 43.15 3.08
5708 6980 1.464734 TTCACCTCTCTGCTCGTAGG 58.535 55.000 0.00 0.00 35.14 3.18
5709 6981 2.034053 GGATTCACCTCTCTGCTCGTAG 59.966 54.545 0.00 0.00 35.41 3.51
5710 6982 2.025155 GGATTCACCTCTCTGCTCGTA 58.975 52.381 0.00 0.00 35.41 3.43
5711 6983 0.820871 GGATTCACCTCTCTGCTCGT 59.179 55.000 0.00 0.00 35.41 4.18
5712 6984 0.820226 TGGATTCACCTCTCTGCTCG 59.180 55.000 0.00 0.00 39.86 5.03
5713 6985 2.307934 GTGGATTCACCTCTCTGCTC 57.692 55.000 0.00 0.00 37.92 4.26
5723 6995 6.949352 ACATCAGATATTTGGTGGATTCAC 57.051 37.500 10.95 0.00 42.91 3.18
5724 6996 7.118060 TGAACATCAGATATTTGGTGGATTCA 58.882 34.615 10.95 9.24 33.41 2.57
5725 6997 7.572523 TGAACATCAGATATTTGGTGGATTC 57.427 36.000 10.95 7.06 33.41 2.52
5726 6998 8.003044 AGATGAACATCAGATATTTGGTGGATT 58.997 33.333 10.95 0.00 40.22 3.01
5727 6999 7.524290 AGATGAACATCAGATATTTGGTGGAT 58.476 34.615 10.95 0.00 40.22 3.41
5728 7000 6.903516 AGATGAACATCAGATATTTGGTGGA 58.096 36.000 10.95 0.00 40.22 4.02
5729 7001 7.283807 TGAAGATGAACATCAGATATTTGGTGG 59.716 37.037 10.95 0.00 40.22 4.61
5730 7002 8.217131 TGAAGATGAACATCAGATATTTGGTG 57.783 34.615 15.63 4.99 40.22 4.17
5731 7003 8.812513 TTGAAGATGAACATCAGATATTTGGT 57.187 30.769 15.63 0.00 40.22 3.67
5732 7004 9.894783 GATTGAAGATGAACATCAGATATTTGG 57.105 33.333 15.63 0.00 40.22 3.28
5733 7005 9.894783 GGATTGAAGATGAACATCAGATATTTG 57.105 33.333 15.63 0.00 40.22 2.32
5734 7006 9.863650 AGGATTGAAGATGAACATCAGATATTT 57.136 29.630 15.63 1.92 40.22 1.40
5744 7016 8.623903 GCACAAATATAGGATTGAAGATGAACA 58.376 33.333 3.50 0.00 0.00 3.18
5745 7017 8.844244 AGCACAAATATAGGATTGAAGATGAAC 58.156 33.333 3.50 0.00 0.00 3.18
5746 7018 8.985315 AGCACAAATATAGGATTGAAGATGAA 57.015 30.769 3.50 0.00 0.00 2.57
5755 7027 9.236006 GGTTCATGATAGCACAAATATAGGATT 57.764 33.333 0.00 0.00 0.00 3.01
5756 7028 7.831193 GGGTTCATGATAGCACAAATATAGGAT 59.169 37.037 0.00 0.00 0.00 3.24
5757 7029 7.168219 GGGTTCATGATAGCACAAATATAGGA 58.832 38.462 0.00 0.00 0.00 2.94
5758 7030 6.942005 TGGGTTCATGATAGCACAAATATAGG 59.058 38.462 0.00 0.00 0.00 2.57
5759 7031 7.094634 GGTGGGTTCATGATAGCACAAATATAG 60.095 40.741 0.00 0.00 0.00 1.31
5760 7032 6.714810 GGTGGGTTCATGATAGCACAAATATA 59.285 38.462 0.00 0.00 0.00 0.86
5761 7033 5.536161 GGTGGGTTCATGATAGCACAAATAT 59.464 40.000 0.00 0.00 0.00 1.28
5762 7034 4.887071 GGTGGGTTCATGATAGCACAAATA 59.113 41.667 0.00 0.00 0.00 1.40
5763 7035 3.701040 GGTGGGTTCATGATAGCACAAAT 59.299 43.478 0.00 0.00 0.00 2.32
5764 7036 3.088532 GGTGGGTTCATGATAGCACAAA 58.911 45.455 0.00 0.00 0.00 2.83
5765 7037 2.040947 TGGTGGGTTCATGATAGCACAA 59.959 45.455 0.00 0.00 0.00 3.33
5766 7038 1.632920 TGGTGGGTTCATGATAGCACA 59.367 47.619 0.00 0.00 0.00 4.57
5767 7039 2.017049 GTGGTGGGTTCATGATAGCAC 58.983 52.381 0.00 6.33 33.45 4.40
5768 7040 1.632920 TGTGGTGGGTTCATGATAGCA 59.367 47.619 0.00 0.00 0.00 3.49
5769 7041 2.418368 TGTGGTGGGTTCATGATAGC 57.582 50.000 0.00 0.00 0.00 2.97
5770 7042 3.879295 GTCATGTGGTGGGTTCATGATAG 59.121 47.826 9.65 0.00 45.79 2.08
5771 7043 3.523157 AGTCATGTGGTGGGTTCATGATA 59.477 43.478 9.65 0.00 45.79 2.15
5772 7044 2.309755 AGTCATGTGGTGGGTTCATGAT 59.690 45.455 9.65 0.00 45.79 2.45
5773 7045 1.704628 AGTCATGTGGTGGGTTCATGA 59.295 47.619 0.00 0.00 43.36 3.07
5774 7046 2.205022 AGTCATGTGGTGGGTTCATG 57.795 50.000 0.00 0.00 39.87 3.07
5775 7047 2.376518 AGAAGTCATGTGGTGGGTTCAT 59.623 45.455 0.00 0.00 0.00 2.57
5776 7048 1.774254 AGAAGTCATGTGGTGGGTTCA 59.226 47.619 0.00 0.00 0.00 3.18
5777 7049 2.154462 CAGAAGTCATGTGGTGGGTTC 58.846 52.381 0.00 0.00 0.00 3.62
5778 7050 1.774254 TCAGAAGTCATGTGGTGGGTT 59.226 47.619 0.00 0.00 0.00 4.11
5779 7051 1.349026 CTCAGAAGTCATGTGGTGGGT 59.651 52.381 0.00 0.00 0.00 4.51
5780 7052 1.947678 GCTCAGAAGTCATGTGGTGGG 60.948 57.143 0.00 0.00 0.00 4.61
5781 7053 1.271001 TGCTCAGAAGTCATGTGGTGG 60.271 52.381 0.00 0.00 0.00 4.61
5782 7054 2.174363 TGCTCAGAAGTCATGTGGTG 57.826 50.000 0.00 0.00 0.00 4.17
5783 7055 2.880890 GTTTGCTCAGAAGTCATGTGGT 59.119 45.455 0.00 0.00 0.00 4.16
5784 7056 2.227388 GGTTTGCTCAGAAGTCATGTGG 59.773 50.000 0.00 0.00 0.00 4.17
5785 7057 3.144506 AGGTTTGCTCAGAAGTCATGTG 58.855 45.455 0.00 0.00 0.00 3.21
5786 7058 3.498774 AGGTTTGCTCAGAAGTCATGT 57.501 42.857 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.