Multiple sequence alignment - TraesCS1D01G376900

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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 TraesCS1D01G376900 chr1D 100.000 5887 0 0 1 5887 453273107 453278993 0.000000e+00 10872.0
1 TraesCS1D01G376900 chr1D 91.026 78 5 1 5309 5384 453263463 453263540 2.900000e-18 104.0
2 TraesCS1D01G376900 chr1D 85.714 84 4 4 5183 5258 104427167 104427250 1.360000e-11 82.4
3 TraesCS1D01G376900 chr1B 94.821 5213 220 34 1 5188 623726474 623731661 0.000000e+00 8085.0
4 TraesCS1D01G376900 chr1B 89.498 219 12 7 5259 5467 623731670 623731887 3.500000e-67 267.0
5 TraesCS1D01G376900 chr1A 94.206 5247 209 42 1 5187 547963049 547968260 0.000000e+00 7917.0
6 TraesCS1D01G376900 chr1A 92.056 214 11 5 5259 5467 547968265 547968477 4.460000e-76 296.0
7 TraesCS1D01G376900 chr1A 88.742 151 14 3 5686 5834 547968925 547969074 1.300000e-41 182.0
8 TraesCS1D01G376900 chr1A 91.667 108 7 2 5579 5684 547968731 547968838 1.320000e-31 148.0
9 TraesCS1D01G376900 chr1A 86.486 74 8 2 5185 5258 24721261 24721190 4.890000e-11 80.5
10 TraesCS1D01G376900 chr1A 86.486 74 8 2 5185 5258 24734161 24734090 4.890000e-11 80.5
11 TraesCS1D01G376900 chr1A 93.478 46 2 1 5579 5624 489238963 489238919 3.810000e-07 67.6
12 TraesCS1D01G376900 chrUn 100.000 449 0 0 3534 3982 475776442 475775994 0.000000e+00 830.0
13 TraesCS1D01G376900 chr2B 89.474 76 5 2 5186 5258 111604635 111604710 6.280000e-15 93.5
14 TraesCS1D01G376900 chr2B 89.474 76 5 2 5186 5258 111604714 111604639 6.280000e-15 93.5
15 TraesCS1D01G376900 chr2B 87.671 73 7 2 5185 5257 521814622 521814552 3.780000e-12 84.2
16 TraesCS1D01G376900 chr5D 89.333 75 5 3 5186 5258 465200301 465200374 2.260000e-14 91.6
17 TraesCS1D01G376900 chr5D 88.000 75 6 3 5186 5258 465200378 465200305 1.050000e-12 86.1
18 TraesCS1D01G376900 chr5D 95.349 43 2 0 5579 5621 138468935 138468977 1.060000e-07 69.4
19 TraesCS1D01G376900 chr4B 89.189 74 6 2 5186 5258 171617721 171617649 2.260000e-14 91.6
20 TraesCS1D01G376900 chr4B 88.060 67 6 2 5501 5566 100321336 100321401 1.760000e-10 78.7
21 TraesCS1D01G376900 chr4B 85.714 70 9 1 5501 5570 43789529 43789461 8.180000e-09 73.1
22 TraesCS1D01G376900 chr3A 87.500 72 8 1 5498 5568 49871140 49871211 1.360000e-11 82.4
23 TraesCS1D01G376900 chr4D 88.060 67 7 1 5501 5566 459819036 459819102 1.760000e-10 78.7
24 TraesCS1D01G376900 chr7A 86.957 69 7 2 5501 5568 486318608 486318675 6.330000e-10 76.8
25 TraesCS1D01G376900 chr7A 86.957 69 7 2 5501 5568 496610017 496610084 6.330000e-10 76.8
26 TraesCS1D01G376900 chr7A 86.957 69 7 2 5501 5568 505172691 505172758 6.330000e-10 76.8
27 TraesCS1D01G376900 chr2D 86.957 69 7 2 5501 5568 487594922 487594989 6.330000e-10 76.8
28 TraesCS1D01G376900 chr2D 85.714 63 3 5 5563 5620 24978656 24978595 1.770000e-05 62.1
29 TraesCS1D01G376900 chr4A 85.714 70 9 1 5498 5566 677992310 677992379 8.180000e-09 73.1
30 TraesCS1D01G376900 chr6D 83.750 80 5 8 5563 5635 1795737 1795815 1.060000e-07 69.4
31 TraesCS1D01G376900 chr5A 95.349 43 2 0 5579 5621 184233284 184233242 1.060000e-07 69.4
32 TraesCS1D01G376900 chr5A 90.196 51 3 2 5579 5628 315267737 315267786 1.370000e-06 65.8
33 TraesCS1D01G376900 chr3D 87.719 57 6 1 5579 5635 174716506 174716451 1.370000e-06 65.8
34 TraesCS1D01G376900 chr6B 85.714 63 3 5 5563 5621 674946744 674946804 1.770000e-05 62.1


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 TraesCS1D01G376900 chr1D 453273107 453278993 5886 False 10872.00 10872 100.00000 1 5887 1 chr1D.!!$F3 5886
1 TraesCS1D01G376900 chr1B 623726474 623731887 5413 False 4176.00 8085 92.15950 1 5467 2 chr1B.!!$F1 5466
2 TraesCS1D01G376900 chr1A 547963049 547969074 6025 False 2135.75 7917 91.66775 1 5834 4 chr1A.!!$F1 5833

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
298 312 0.179056 CACCCAACGTGAACCAGTCT 60.179 55.0 0.00 0.00 46.20 3.24 F
299 313 0.179056 ACCCAACGTGAACCAGTCTG 60.179 55.0 0.00 0.00 0.00 3.51 F
361 375 0.523072 CTTCTCGTTAACCGGTCCGA 59.477 55.0 14.39 15.42 37.11 4.55 F
1643 1701 0.463833 GTAGAATTGCCACCGGGGAG 60.464 60.0 4.41 0.00 40.01 4.30 F
2179 2239 0.035630 AACTGCCTGAGAGTGATGCC 60.036 55.0 0.00 0.00 0.00 4.40 F
3188 3272 0.773644 AGCAGACATTGGTCAAGGGT 59.226 50.0 0.55 0.00 46.80 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 1556 0.035915 TTGGTCCGCGGATTCAATCA 60.036 50.000 33.58 18.69 0.00 2.57 R
1643 1701 0.038310 AAGCACCCTGTTAGCCTTCC 59.962 55.000 0.00 0.00 0.00 3.46 R
1754 1812 0.178767 CTGATCCATTGAGCCCGTCA 59.821 55.000 0.00 0.00 0.00 4.35 R
2743 2824 1.617850 CCTGCAAATACAAGCCCACAA 59.382 47.619 0.00 0.00 0.00 3.33 R
3982 4066 2.889512 TGGAAGCTCTCTCCACAAGTA 58.110 47.619 1.25 0.00 0.00 2.24 R
4898 4983 0.329261 TCAGAATGGCTTGGGAGGTG 59.671 55.000 0.00 0.00 36.16 4.00 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
64 66 2.856000 AGGGAGCACAAGGCCAGT 60.856 61.111 5.01 0.00 46.50 4.00
75 77 4.122776 CACAAGGCCAGTATCTACATCAC 58.877 47.826 5.01 0.00 0.00 3.06
129 131 7.732996 TCATGATATGATTCTTCTCTCTTGCA 58.267 34.615 0.00 0.00 33.59 4.08
133 135 8.093307 TGATATGATTCTTCTCTCTTGCATACC 58.907 37.037 0.00 0.00 0.00 2.73
141 143 6.556495 TCTTCTCTCTTGCATACCCTTGATAT 59.444 38.462 0.00 0.00 0.00 1.63
148 150 9.160496 CTCTTGCATACCCTTGATATATTCTTC 57.840 37.037 0.00 0.00 0.00 2.87
154 156 3.009033 CCCTTGATATATTCTTCGGGGCA 59.991 47.826 0.00 0.00 0.00 5.36
175 177 1.202203 GCGCACATACCATTGCATTG 58.798 50.000 0.30 1.49 38.76 2.82
193 195 8.830201 TTGCATTGCAAAATAGTAAAACTGAT 57.170 26.923 21.24 0.00 45.96 2.90
202 204 9.449719 CAAAATAGTAAAACTGATCCACCTAGT 57.550 33.333 0.00 0.00 0.00 2.57
246 248 1.443802 GCAAGCCGGCTAATCTATCC 58.556 55.000 33.07 0.00 0.00 2.59
292 306 4.322385 GCGCCACCCAACGTGAAC 62.322 66.667 0.00 0.00 46.20 3.18
293 307 3.656045 CGCCACCCAACGTGAACC 61.656 66.667 0.00 0.00 46.20 3.62
294 308 2.517402 GCCACCCAACGTGAACCA 60.517 61.111 0.00 0.00 46.20 3.67
295 309 2.551912 GCCACCCAACGTGAACCAG 61.552 63.158 0.00 0.00 46.20 4.00
296 310 1.153046 CCACCCAACGTGAACCAGT 60.153 57.895 0.00 0.00 46.20 4.00
297 311 1.164041 CCACCCAACGTGAACCAGTC 61.164 60.000 0.00 0.00 46.20 3.51
298 312 0.179056 CACCCAACGTGAACCAGTCT 60.179 55.000 0.00 0.00 46.20 3.24
299 313 0.179056 ACCCAACGTGAACCAGTCTG 60.179 55.000 0.00 0.00 0.00 3.51
300 314 0.884704 CCCAACGTGAACCAGTCTGG 60.885 60.000 17.88 17.88 45.02 3.86
301 315 0.884704 CCAACGTGAACCAGTCTGGG 60.885 60.000 23.06 7.16 43.37 4.45
311 325 3.237268 ACCAGTCTGGGCACAAAAATA 57.763 42.857 23.06 0.00 43.37 1.40
321 335 2.165641 GGCACAAAAATAGGCCACTACC 59.834 50.000 5.01 0.00 45.70 3.18
361 375 0.523072 CTTCTCGTTAACCGGTCCGA 59.477 55.000 14.39 15.42 37.11 4.55
378 392 2.125512 ACGCTTGATGCTCGGTCC 60.126 61.111 0.00 0.00 40.11 4.46
466 480 2.030628 GCTCCTAACTAGCGCCTTCTAG 60.031 54.545 2.29 1.02 41.31 2.43
535 549 2.520741 CCGGCCCAACAACAAGGT 60.521 61.111 0.00 0.00 0.00 3.50
557 572 2.725815 GCTTGTTCACAACGCGCC 60.726 61.111 5.73 0.00 0.00 6.53
605 622 6.645415 AGTTAATCGATCGACTGTTGACTTTT 59.355 34.615 22.06 9.15 0.00 2.27
606 623 5.924475 AATCGATCGACTGTTGACTTTTT 57.076 34.783 22.06 2.98 0.00 1.94
607 624 4.708868 TCGATCGACTGTTGACTTTTTG 57.291 40.909 15.15 0.00 0.00 2.44
608 625 4.364860 TCGATCGACTGTTGACTTTTTGA 58.635 39.130 15.15 0.00 0.00 2.69
609 626 4.988540 TCGATCGACTGTTGACTTTTTGAT 59.011 37.500 15.15 0.00 0.00 2.57
610 627 6.153756 TCGATCGACTGTTGACTTTTTGATA 58.846 36.000 15.15 0.00 0.00 2.15
611 628 6.643360 TCGATCGACTGTTGACTTTTTGATAA 59.357 34.615 15.15 0.00 0.00 1.75
759 777 7.095229 GCAAACTCCAAAAAGTTCAAGAGTTTT 60.095 33.333 11.99 0.00 46.79 2.43
783 801 5.782893 AAGAAATGTTCACGGGATTTGAA 57.217 34.783 0.00 0.00 0.00 2.69
785 803 6.155475 AGAAATGTTCACGGGATTTGAAAA 57.845 33.333 0.00 0.00 34.78 2.29
899 939 3.199071 TCCAAAAAGCGAAGGCCTATCTA 59.801 43.478 5.16 0.00 41.24 1.98
969 1010 2.048127 AGCGAGGTTTGACGAGCC 60.048 61.111 0.00 0.00 0.00 4.70
993 1034 2.108425 AGAGGGGAAAACCAAGAACTCC 59.892 50.000 0.00 0.00 42.91 3.85
1105 1146 2.178235 GTCGCGCTTAACCCCATCC 61.178 63.158 5.56 0.00 0.00 3.51
1158 1216 3.242673 CGAGATCTGAGGCATTTTCTTGC 60.243 47.826 0.00 0.00 42.01 4.01
1181 1239 2.997986 ACTGCGGTTCTTACGGTATTTG 59.002 45.455 0.00 0.00 0.00 2.32
1223 1281 3.502572 GGATTTGCCTGCCGAGAC 58.497 61.111 0.00 0.00 0.00 3.36
1246 1304 6.236017 CTGCGAGTCAGGTTAATGTTTTTA 57.764 37.500 0.00 0.00 39.15 1.52
1282 1340 3.161450 TACAGGGGCCGGAGATGC 61.161 66.667 5.05 0.00 0.00 3.91
1295 1353 3.388308 CGGAGATGCTCATGGACTTTAG 58.612 50.000 0.00 0.00 31.08 1.85
1363 1421 2.489938 AAATGCGCTTCCTCTGGTAA 57.510 45.000 9.73 0.00 0.00 2.85
1459 1517 0.679505 CTGAAGGAACCTGTCGGTGA 59.320 55.000 0.00 0.00 44.73 4.02
1498 1556 2.017049 GCTCCATGTAGCCAACGATTT 58.983 47.619 0.00 0.00 36.45 2.17
1529 1587 0.872388 CGGACCAAGGTGTGCTTTAC 59.128 55.000 0.00 0.00 0.00 2.01
1530 1588 1.542547 CGGACCAAGGTGTGCTTTACT 60.543 52.381 0.00 0.00 0.00 2.24
1563 1621 5.119694 TGGTTTTGGGAAAATTTACACTGC 58.880 37.500 0.00 0.00 32.22 4.40
1585 1643 7.708752 ACTGCACTCTAAAGATATAAGTCTTGC 59.291 37.037 0.00 0.00 38.41 4.01
1588 1646 7.096394 GCACTCTAAAGATATAAGTCTTGCGAC 60.096 40.741 0.00 0.00 38.41 5.19
1592 1650 4.491234 AGATATAAGTCTTGCGACCTCG 57.509 45.455 0.00 0.00 41.16 4.63
1634 1692 5.630680 CACATGAACTGTTTGTAGAATTGCC 59.369 40.000 0.00 0.00 35.29 4.52
1643 1701 0.463833 GTAGAATTGCCACCGGGGAG 60.464 60.000 4.41 0.00 40.01 4.30
1677 1735 2.147150 GTGCTTTCTGAGACCACTTCC 58.853 52.381 0.00 0.00 0.00 3.46
1689 1747 2.351276 ACTTCCGGTGATGGTGCC 59.649 61.111 0.00 0.00 0.00 5.01
1713 1771 1.299976 GAAGGGTGGCGACCTGATT 59.700 57.895 18.11 10.17 42.66 2.57
1754 1812 1.039856 GCACAAGATGGTGGTTTGGT 58.960 50.000 0.00 0.00 39.19 3.67
1771 1829 0.815615 GGTGACGGGCTCAATGGATC 60.816 60.000 0.00 0.00 0.00 3.36
1907 1966 1.491668 TAATCTCTTGTAGCGCCCCA 58.508 50.000 2.29 0.00 0.00 4.96
1951 2010 0.179073 ACATCCACTAGCATCCGCAC 60.179 55.000 0.00 0.00 42.27 5.34
2032 2091 1.737793 CGGTGGAAAGCAAGTATCACC 59.262 52.381 0.00 0.00 40.68 4.02
2073 2132 7.010830 CAGATCCACAAGAACATACATACACAG 59.989 40.741 0.00 0.00 0.00 3.66
2124 2183 5.741388 GGATACAATTCAAGCGTCATTCT 57.259 39.130 0.00 0.00 0.00 2.40
2179 2239 0.035630 AACTGCCTGAGAGTGATGCC 60.036 55.000 0.00 0.00 0.00 4.40
2194 2254 1.713005 ATGCCGGATCCATTGAGCCT 61.713 55.000 13.41 0.00 45.19 4.58
2231 2291 2.261671 GCGGCTTCGGTCTTCAGA 59.738 61.111 0.00 0.00 0.00 3.27
2256 2316 2.266055 GCTCCTAGCACCGCACTT 59.734 61.111 0.00 0.00 41.89 3.16
2330 2390 4.794648 TGGCGATTTGGCTCGGGG 62.795 66.667 0.00 0.00 45.14 5.73
2386 2446 2.258591 CCGGACGGTCTGACACAG 59.741 66.667 18.40 3.08 0.00 3.66
2413 2473 1.002773 GGTGTGTATTCGGGGTCACTT 59.997 52.381 0.00 0.00 0.00 3.16
2730 2811 6.682113 GCAGTCATGATTTCTTGCCACATAAT 60.682 38.462 0.00 0.00 0.00 1.28
3032 3113 3.033659 TCCAAGGACTCTGATCTACCC 57.966 52.381 0.00 0.00 0.00 3.69
3188 3272 0.773644 AGCAGACATTGGTCAAGGGT 59.226 50.000 0.55 0.00 46.80 4.34
3386 3470 4.842531 TTCATTGGATCCTAGTCAGCAA 57.157 40.909 14.23 0.00 0.00 3.91
3982 4066 4.385310 GGGAAGGTTAATGGTGCTGTAGAT 60.385 45.833 0.00 0.00 0.00 1.98
4422 4506 8.902540 AATCTCTCAACACTTGTATTGTACAA 57.097 30.769 11.41 11.41 45.66 2.41
4429 4513 7.906010 TCAACACTTGTATTGTACAAAGTTTCG 59.094 33.333 13.23 2.90 46.90 3.46
4447 4531 2.870175 TCGAAATTTGTGGGGACATGT 58.130 42.857 0.00 0.00 46.14 3.21
4574 4658 5.852005 TGTCATTTGTTGTTTTCTTTTGCG 58.148 33.333 0.00 0.00 0.00 4.85
4619 4704 7.088905 GTCAACTTTTGATGCAGAATGAAGAT 58.911 34.615 0.00 0.00 42.47 2.40
4624 4709 6.387041 TTTGATGCAGAATGAAGATGGATC 57.613 37.500 0.00 0.00 40.84 3.36
4740 4825 2.229792 ACAACCCACATGTAAGCAGTG 58.770 47.619 0.00 0.00 0.00 3.66
4898 4983 0.674895 ATCCGTGAAGCAAGACCAGC 60.675 55.000 0.00 0.00 0.00 4.85
4960 5045 8.194769 AGTTCAGTGTTTGATTTATTTTTCGGT 58.805 29.630 0.00 0.00 35.27 4.69
4999 5084 3.211045 GTTTGTGGAGAAGGTTGTAGCA 58.789 45.455 0.00 0.00 0.00 3.49
5037 5124 5.656859 GCCAGTAGGGGAAAATAAATTCTGT 59.343 40.000 0.00 0.00 37.04 3.41
5188 5279 2.303311 GGGTTCAAGCCTCACTTCTACT 59.697 50.000 0.00 0.00 36.04 2.57
5189 5280 3.591023 GGTTCAAGCCTCACTTCTACTC 58.409 50.000 0.00 0.00 36.04 2.59
5190 5281 3.591023 GTTCAAGCCTCACTTCTACTCC 58.409 50.000 0.00 0.00 36.04 3.85
5191 5282 2.180276 TCAAGCCTCACTTCTACTCCC 58.820 52.381 0.00 0.00 36.04 4.30
5194 5285 1.116308 GCCTCACTTCTACTCCCTCC 58.884 60.000 0.00 0.00 0.00 4.30
5195 5286 1.394618 CCTCACTTCTACTCCCTCCG 58.605 60.000 0.00 0.00 0.00 4.63
5196 5287 1.341187 CCTCACTTCTACTCCCTCCGT 60.341 57.143 0.00 0.00 0.00 4.69
5197 5288 2.018515 CTCACTTCTACTCCCTCCGTC 58.981 57.143 0.00 0.00 0.00 4.79
5198 5289 1.104630 CACTTCTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
5199 5290 0.702902 ACTTCTACTCCCTCCGTCCA 59.297 55.000 0.00 0.00 0.00 4.02
5200 5291 1.076677 ACTTCTACTCCCTCCGTCCAA 59.923 52.381 0.00 0.00 0.00 3.53
5201 5292 2.292323 ACTTCTACTCCCTCCGTCCAAT 60.292 50.000 0.00 0.00 0.00 3.16
5202 5293 3.053095 ACTTCTACTCCCTCCGTCCAATA 60.053 47.826 0.00 0.00 0.00 1.90
5203 5294 3.675348 TCTACTCCCTCCGTCCAATAA 57.325 47.619 0.00 0.00 0.00 1.40
5204 5295 4.194678 TCTACTCCCTCCGTCCAATAAT 57.805 45.455 0.00 0.00 0.00 1.28
5205 5296 3.895656 TCTACTCCCTCCGTCCAATAATG 59.104 47.826 0.00 0.00 0.00 1.90
5206 5297 2.478292 ACTCCCTCCGTCCAATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
5207 5298 3.649843 ACTCCCTCCGTCCAATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
5208 5299 4.035112 ACTCCCTCCGTCCAATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
5209 5300 4.472108 ACTCCCTCCGTCCAATAATGTAAA 59.528 41.667 0.00 0.00 0.00 2.01
5210 5301 5.045432 ACTCCCTCCGTCCAATAATGTAAAA 60.045 40.000 0.00 0.00 0.00 1.52
5211 5302 5.187687 TCCCTCCGTCCAATAATGTAAAAC 58.812 41.667 0.00 0.00 0.00 2.43
5212 5303 4.337274 CCCTCCGTCCAATAATGTAAAACC 59.663 45.833 0.00 0.00 0.00 3.27
5213 5304 5.190677 CCTCCGTCCAATAATGTAAAACCT 58.809 41.667 0.00 0.00 0.00 3.50
5214 5305 5.650703 CCTCCGTCCAATAATGTAAAACCTT 59.349 40.000 0.00 0.00 0.00 3.50
5215 5306 6.152154 CCTCCGTCCAATAATGTAAAACCTTT 59.848 38.462 0.00 0.00 0.00 3.11
5216 5307 7.309560 CCTCCGTCCAATAATGTAAAACCTTTT 60.310 37.037 0.00 0.00 0.00 2.27
5217 5308 7.953752 TCCGTCCAATAATGTAAAACCTTTTT 58.046 30.769 0.00 0.00 0.00 1.94
5218 5309 7.868415 TCCGTCCAATAATGTAAAACCTTTTTG 59.132 33.333 0.00 0.00 0.00 2.44
5219 5310 7.654116 CCGTCCAATAATGTAAAACCTTTTTGT 59.346 33.333 0.00 0.00 0.00 2.83
5220 5311 8.696175 CGTCCAATAATGTAAAACCTTTTTGTC 58.304 33.333 0.00 0.00 0.00 3.18
5221 5312 9.535878 GTCCAATAATGTAAAACCTTTTTGTCA 57.464 29.630 0.00 0.00 0.00 3.58
5222 5313 9.535878 TCCAATAATGTAAAACCTTTTTGTCAC 57.464 29.630 0.00 0.00 0.00 3.67
5223 5314 9.541143 CCAATAATGTAAAACCTTTTTGTCACT 57.459 29.630 0.00 0.00 0.00 3.41
5227 5318 8.474006 AATGTAAAACCTTTTTGTCACTTGAC 57.526 30.769 2.19 2.19 44.97 3.18
5254 5345 5.623956 AATGTCTTACATTATGGGACGGA 57.376 39.130 3.51 0.00 46.11 4.69
5255 5346 4.665833 TGTCTTACATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
5256 5347 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
5257 5348 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
5282 5373 3.788227 AATTGGTGCCTAGTTGACAGA 57.212 42.857 0.00 0.00 0.00 3.41
5384 5484 6.417258 TCTCATCTTATGTCCAATTTGCAGA 58.583 36.000 0.00 0.00 0.00 4.26
5402 5502 3.370366 GCAGAGATATAGAGCAATTGCCG 59.630 47.826 26.45 6.04 43.38 5.69
5409 5509 1.010350 GAGCAATTGCCGCATCTCG 60.010 57.895 26.45 0.00 43.38 4.04
5456 5557 9.594478 TTCTTATTTCAATACACTCAATCGCTA 57.406 29.630 0.00 0.00 0.00 4.26
5473 5616 8.445493 TCAATCGCTAAATATCATGCATACTTG 58.555 33.333 0.00 0.00 0.00 3.16
5480 5623 7.986085 AAATATCATGCATACTTGGTACTCC 57.014 36.000 0.00 0.00 0.00 3.85
5481 5624 3.452755 TCATGCATACTTGGTACTCCG 57.547 47.619 0.00 0.00 36.30 4.63
5484 5640 3.688694 TGCATACTTGGTACTCCGTTT 57.311 42.857 0.00 0.00 36.30 3.60
5496 5652 8.652810 TTGGTACTCCGTTTCTAAATATAAGC 57.347 34.615 0.00 0.00 36.30 3.09
5500 5656 9.322773 GTACTCCGTTTCTAAATATAAGCCTTT 57.677 33.333 0.00 0.00 0.00 3.11
5524 5747 3.999046 TGCTCTGCATGTACTCCATATG 58.001 45.455 0.00 0.00 31.71 1.78
5525 5748 3.642848 TGCTCTGCATGTACTCCATATGA 59.357 43.478 3.65 0.00 31.71 2.15
5530 5753 7.572724 GCTCTGCATGTACTCCATATGAAAATC 60.573 40.741 3.65 0.00 30.71 2.17
5561 5786 9.931210 AAAAGATTTATATTTAGGAACGAAGCG 57.069 29.630 0.00 0.00 0.00 4.68
5579 5804 7.256286 ACGAAGCGAGTACAATTCTTATACTT 58.744 34.615 0.00 0.00 29.25 2.24
5580 5805 7.220300 ACGAAGCGAGTACAATTCTTATACTTG 59.780 37.037 0.00 0.00 34.62 3.16
5581 5806 7.220300 CGAAGCGAGTACAATTCTTATACTTGT 59.780 37.037 0.00 0.00 34.19 3.16
5582 5807 7.988904 AGCGAGTACAATTCTTATACTTGTC 57.011 36.000 0.00 0.00 34.19 3.18
5588 5830 9.819267 AGTACAATTCTTATACTTGTCCTAAGC 57.181 33.333 0.00 0.00 35.00 3.09
5595 5837 0.666577 ACTTGTCCTAAGCGTGCGTC 60.667 55.000 0.00 0.00 0.00 5.19
5603 5845 3.936453 TCCTAAGCGTGCGTCAATTAATT 59.064 39.130 0.00 0.00 0.00 1.40
5609 5851 3.482110 GCGTGCGTCAATTAATTTGGATC 59.518 43.478 0.00 0.00 35.92 3.36
5611 5853 4.035017 GTGCGTCAATTAATTTGGATCGG 58.965 43.478 0.00 0.00 35.92 4.18
5721 6050 5.744490 AGTACAATACAAAGACAAACACGC 58.256 37.500 0.00 0.00 0.00 5.34
5722 6051 4.893424 ACAATACAAAGACAAACACGCT 57.107 36.364 0.00 0.00 0.00 5.07
5723 6052 4.597079 ACAATACAAAGACAAACACGCTG 58.403 39.130 0.00 0.00 0.00 5.18
5724 6053 4.334203 ACAATACAAAGACAAACACGCTGA 59.666 37.500 0.00 0.00 0.00 4.26
5726 6055 3.131240 ACAAAGACAAACACGCTGAAC 57.869 42.857 0.00 0.00 0.00 3.18
5727 6056 2.159435 ACAAAGACAAACACGCTGAACC 60.159 45.455 0.00 0.00 0.00 3.62
5729 6058 1.967319 AGACAAACACGCTGAACCAT 58.033 45.000 0.00 0.00 0.00 3.55
5731 6060 3.472652 AGACAAACACGCTGAACCATTA 58.527 40.909 0.00 0.00 0.00 1.90
5732 6061 3.250040 AGACAAACACGCTGAACCATTAC 59.750 43.478 0.00 0.00 0.00 1.89
5733 6062 2.946329 ACAAACACGCTGAACCATTACA 59.054 40.909 0.00 0.00 0.00 2.41
5740 6069 3.502211 ACGCTGAACCATTACAAAAGAGG 59.498 43.478 0.00 0.00 0.00 3.69
5751 6080 8.576442 ACCATTACAAAAGAGGTGAATAAACAG 58.424 33.333 0.00 0.00 0.00 3.16
5776 6105 9.860898 AGTTATGAATAAGTGGATTTCTTTTGC 57.139 29.630 0.00 0.00 0.00 3.68
5802 6131 2.126951 CCTTTTGCAAGGGCTGTGT 58.873 52.632 0.00 0.00 45.63 3.72
5819 6148 4.063967 TGACCTCGCGCCATCGTT 62.064 61.111 0.00 0.00 38.14 3.85
5820 6149 3.554692 GACCTCGCGCCATCGTTG 61.555 66.667 0.00 0.00 38.14 4.10
5834 6164 2.749280 TCGTTGCATGTCTGACTGAT 57.251 45.000 9.51 0.00 0.00 2.90
5835 6165 2.610433 TCGTTGCATGTCTGACTGATC 58.390 47.619 9.51 0.00 0.00 2.92
5836 6166 1.322637 CGTTGCATGTCTGACTGATCG 59.677 52.381 9.51 3.41 0.00 3.69
5837 6167 2.341257 GTTGCATGTCTGACTGATCGT 58.659 47.619 9.51 0.00 0.00 3.73
5838 6168 2.000429 TGCATGTCTGACTGATCGTG 58.000 50.000 9.51 0.00 0.00 4.35
5839 6169 0.649475 GCATGTCTGACTGATCGTGC 59.351 55.000 9.51 1.70 34.36 5.34
5840 6170 1.284657 CATGTCTGACTGATCGTGCC 58.715 55.000 9.51 0.00 0.00 5.01
5841 6171 0.179127 ATGTCTGACTGATCGTGCCG 60.179 55.000 9.51 0.00 0.00 5.69
5842 6172 2.161486 GTCTGACTGATCGTGCCGC 61.161 63.158 0.00 0.00 0.00 6.53
5843 6173 2.887568 CTGACTGATCGTGCCGCC 60.888 66.667 0.00 0.00 0.00 6.13
5844 6174 4.794439 TGACTGATCGTGCCGCCG 62.794 66.667 0.00 0.00 0.00 6.46
5856 6186 3.716006 CCGCCGCAAGACACACTG 61.716 66.667 0.00 0.00 43.02 3.66
5857 6187 2.967076 CGCCGCAAGACACACTGT 60.967 61.111 0.00 0.00 43.02 3.55
5858 6188 2.534019 CGCCGCAAGACACACTGTT 61.534 57.895 0.00 0.00 43.02 3.16
5859 6189 1.727467 GCCGCAAGACACACTGTTT 59.273 52.632 0.00 0.00 43.02 2.83
5860 6190 0.317020 GCCGCAAGACACACTGTTTC 60.317 55.000 0.00 0.00 43.02 2.78
5861 6191 1.299541 CCGCAAGACACACTGTTTCT 58.700 50.000 0.00 0.00 43.02 2.52
5862 6192 1.670811 CCGCAAGACACACTGTTTCTT 59.329 47.619 4.96 4.96 43.02 2.52
5863 6193 2.286418 CCGCAAGACACACTGTTTCTTC 60.286 50.000 7.49 3.61 43.02 2.87
5864 6194 2.609459 CGCAAGACACACTGTTTCTTCT 59.391 45.455 7.49 0.00 43.02 2.85
5865 6195 3.302740 CGCAAGACACACTGTTTCTTCTC 60.303 47.826 7.49 3.27 43.02 2.87
5866 6196 3.302740 GCAAGACACACTGTTTCTTCTCG 60.303 47.826 7.49 0.08 31.31 4.04
5867 6197 2.474816 AGACACACTGTTTCTTCTCGC 58.525 47.619 0.00 0.00 0.00 5.03
5868 6198 2.159099 AGACACACTGTTTCTTCTCGCA 60.159 45.455 0.00 0.00 0.00 5.10
5869 6199 1.933853 ACACACTGTTTCTTCTCGCAC 59.066 47.619 0.00 0.00 0.00 5.34
5870 6200 2.205074 CACACTGTTTCTTCTCGCACT 58.795 47.619 0.00 0.00 0.00 4.40
5871 6201 2.033407 CACACTGTTTCTTCTCGCACTG 60.033 50.000 0.00 0.00 0.00 3.66
5872 6202 2.159099 ACACTGTTTCTTCTCGCACTGA 60.159 45.455 0.00 0.00 0.00 3.41
5873 6203 2.474359 CACTGTTTCTTCTCGCACTGAG 59.526 50.000 0.00 0.00 46.72 3.35
5884 6214 3.126001 TCGCACTGAGATGGTTTTTCT 57.874 42.857 0.00 0.00 0.00 2.52
5885 6215 3.476552 TCGCACTGAGATGGTTTTTCTT 58.523 40.909 0.00 0.00 0.00 2.52
5886 6216 3.250762 TCGCACTGAGATGGTTTTTCTTG 59.749 43.478 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.471617 CAGCCCTCCCGATTCTGATT 59.528 55.000 0.00 0.00 0.00 2.57
129 131 5.104485 GCCCCGAAGAATATATCAAGGGTAT 60.104 44.000 0.00 0.00 36.87 2.73
133 135 4.286297 TGCCCCGAAGAATATATCAAGG 57.714 45.455 0.00 0.00 0.00 3.61
141 143 1.891919 GCGCATGCCCCGAAGAATA 60.892 57.895 13.15 0.00 33.98 1.75
148 150 3.952675 GTATGTGCGCATGCCCCG 61.953 66.667 22.84 0.00 41.78 5.73
154 156 1.034356 ATGCAATGGTATGTGCGCAT 58.966 45.000 15.91 18.22 43.93 4.73
175 177 7.158099 AGGTGGATCAGTTTTACTATTTTGC 57.842 36.000 0.00 0.00 0.00 3.68
202 204 2.956132 TCAAATCACTTTGGAAGGCCA 58.044 42.857 5.01 0.00 41.74 5.36
290 304 1.859302 TTTTTGTGCCCAGACTGGTT 58.141 45.000 20.24 0.00 35.17 3.67
291 305 2.086610 ATTTTTGTGCCCAGACTGGT 57.913 45.000 20.24 0.00 35.17 4.00
292 306 2.493278 CCTATTTTTGTGCCCAGACTGG 59.507 50.000 15.15 15.15 37.25 4.00
293 307 2.094545 GCCTATTTTTGTGCCCAGACTG 60.095 50.000 0.00 0.00 0.00 3.51
294 308 2.171003 GCCTATTTTTGTGCCCAGACT 58.829 47.619 0.00 0.00 0.00 3.24
295 309 1.204704 GGCCTATTTTTGTGCCCAGAC 59.795 52.381 0.00 0.00 37.94 3.51
296 310 1.203112 TGGCCTATTTTTGTGCCCAGA 60.203 47.619 3.32 0.00 43.35 3.86
297 311 1.066929 GTGGCCTATTTTTGTGCCCAG 60.067 52.381 3.32 0.00 43.35 4.45
298 312 0.972883 GTGGCCTATTTTTGTGCCCA 59.027 50.000 3.32 0.00 43.35 5.36
299 313 1.266178 AGTGGCCTATTTTTGTGCCC 58.734 50.000 3.32 0.00 43.35 5.36
300 314 2.165641 GGTAGTGGCCTATTTTTGTGCC 59.834 50.000 3.32 0.00 44.27 5.01
301 315 3.089284 AGGTAGTGGCCTATTTTTGTGC 58.911 45.455 3.32 0.00 37.04 4.57
311 325 2.375174 TCAATTTGTGAGGTAGTGGCCT 59.625 45.455 3.32 0.00 42.53 5.19
378 392 1.922135 CTTGATGGGTCGGGTTTGCG 61.922 60.000 0.00 0.00 0.00 4.85
471 485 2.432146 TGAATCCTTACTCAGCGCAGAT 59.568 45.455 11.47 0.00 0.00 2.90
472 486 1.824852 TGAATCCTTACTCAGCGCAGA 59.175 47.619 11.47 6.15 0.00 4.26
473 487 2.200067 CTGAATCCTTACTCAGCGCAG 58.800 52.381 11.47 0.00 33.17 5.18
535 549 0.376852 GCGTTGTGAACAAGCTGTCA 59.623 50.000 0.00 0.00 36.39 3.58
545 560 3.641986 GAACCGGCGCGTTGTGAA 61.642 61.111 16.44 0.00 0.00 3.18
759 777 6.885952 TCAAATCCCGTGAACATTTCTTTA 57.114 33.333 0.00 0.00 0.00 1.85
767 785 6.341316 TGAAAATTTTCAAATCCCGTGAACA 58.659 32.000 27.22 3.50 43.62 3.18
854 873 1.379642 GCTTGCCTGCTCCGCTATTT 61.380 55.000 0.00 0.00 0.00 1.40
855 874 1.821332 GCTTGCCTGCTCCGCTATT 60.821 57.895 0.00 0.00 0.00 1.73
856 875 2.203126 GCTTGCCTGCTCCGCTAT 60.203 61.111 0.00 0.00 0.00 2.97
857 876 4.473520 GGCTTGCCTGCTCCGCTA 62.474 66.667 4.11 0.00 0.00 4.26
899 939 5.298527 CGGGTTTCTAGAAGGAAGTGTTTTT 59.701 40.000 5.12 0.00 0.00 1.94
969 1010 2.552743 GTTCTTGGTTTTCCCCTCTTCG 59.447 50.000 0.00 0.00 39.73 3.79
1029 1070 1.152943 CGTCGGGATCAGGAGGAGA 60.153 63.158 0.00 0.00 0.00 3.71
1158 1216 0.244450 TACCGTAAGAACCGCAGTGG 59.756 55.000 0.00 0.00 42.81 4.00
1181 1239 2.456000 TCTGCAAGAAATCCGACGC 58.544 52.632 0.00 0.00 42.31 5.19
1223 1281 4.749245 AAAACATTAACCTGACTCGCAG 57.251 40.909 0.00 0.00 44.49 5.18
1238 1296 9.513906 CCAAAACCCAAAATCCTATAAAAACAT 57.486 29.630 0.00 0.00 0.00 2.71
1246 1304 5.719563 CCTGTACCAAAACCCAAAATCCTAT 59.280 40.000 0.00 0.00 0.00 2.57
1282 1340 6.884280 AAAGAAACCACTAAAGTCCATGAG 57.116 37.500 0.00 0.00 0.00 2.90
1295 1353 4.749598 CCTGCCAAAACATAAAGAAACCAC 59.250 41.667 0.00 0.00 0.00 4.16
1459 1517 1.135721 GCGGTTCCTCCACTAATACGT 59.864 52.381 0.00 0.00 35.57 3.57
1485 1543 5.273944 GGATTCAATCAAATCGTTGGCTAC 58.726 41.667 0.00 0.00 36.66 3.58
1498 1556 0.035915 TTGGTCCGCGGATTCAATCA 60.036 50.000 33.58 18.69 0.00 2.57
1537 1595 6.821160 CAGTGTAAATTTTCCCAAAACCAAGT 59.179 34.615 0.00 0.00 32.37 3.16
1588 1646 3.262420 CAAACCATCTAAGGACACGAGG 58.738 50.000 0.00 0.00 0.00 4.63
1592 1650 3.146066 TGTGCAAACCATCTAAGGACAC 58.854 45.455 0.00 0.00 0.00 3.67
1634 1692 1.993391 TTAGCCTTCCTCCCCGGTG 60.993 63.158 0.00 0.00 0.00 4.94
1643 1701 0.038310 AAGCACCCTGTTAGCCTTCC 59.962 55.000 0.00 0.00 0.00 3.46
1689 1747 1.087771 GGTCGCCACCCTTCAATACG 61.088 60.000 0.00 0.00 36.54 3.06
1713 1771 1.227823 CCGCCTTGTCACTTGGTCA 60.228 57.895 0.00 0.00 0.00 4.02
1754 1812 0.178767 CTGATCCATTGAGCCCGTCA 59.821 55.000 0.00 0.00 0.00 4.35
1771 1829 0.954449 CCTGTGTGCTTCTCCTGCTG 60.954 60.000 0.00 0.00 0.00 4.41
1907 1966 1.050988 ATCTGCATAGTGCCGGTCCT 61.051 55.000 1.90 1.16 44.23 3.85
1915 1974 4.244066 GGATGTGCTAGATCTGCATAGTG 58.756 47.826 18.55 0.00 42.69 2.74
1951 2010 3.921021 GTGGCGTCTTAGGATCGATATTG 59.079 47.826 0.00 0.00 0.00 1.90
2073 2132 7.431084 TCGTTAAATTTGACTCTTTGAAGTTGC 59.569 33.333 10.92 0.00 0.00 4.17
2111 2170 3.242518 CGTGTTCTAGAATGACGCTTGA 58.757 45.455 20.45 0.00 0.00 3.02
2116 2175 2.666508 CCCAACGTGTTCTAGAATGACG 59.333 50.000 26.25 26.25 36.05 4.35
2124 2183 1.071814 GGTGGCCCAACGTGTTCTA 59.928 57.895 0.00 0.00 0.00 2.10
2168 2228 0.683973 ATGGATCCGGCATCACTCTC 59.316 55.000 7.39 0.45 32.33 3.20
2179 2239 0.877649 CGACAGGCTCAATGGATCCG 60.878 60.000 7.39 0.00 34.44 4.18
2194 2254 1.004560 CAAGCTCAAGCCCTCGACA 60.005 57.895 0.00 0.00 43.38 4.35
2255 2315 1.682849 CTGGATGACACCCCGGAAA 59.317 57.895 0.73 0.00 0.00 3.13
2256 2316 2.297895 CCTGGATGACACCCCGGAA 61.298 63.158 0.73 0.00 0.00 4.30
2330 2390 1.289066 GAAAAAGCCGCTTGGACCC 59.711 57.895 6.34 0.00 33.02 4.46
2385 2445 2.612746 AATACACACCGGGCCCCT 60.613 61.111 18.66 0.00 0.00 4.79
2386 2446 2.124445 GAATACACACCGGGCCCC 60.124 66.667 18.66 0.00 0.00 5.80
2413 2473 4.148079 TGCTTGGTGGTATCATCAAAACA 58.852 39.130 2.73 1.86 42.72 2.83
2708 2789 7.760794 TGAAATTATGTGGCAAGAAATCATGAC 59.239 33.333 0.00 0.00 0.00 3.06
2730 2811 6.825610 ACAAGCCCACAAAATTTAGATGAAA 58.174 32.000 0.00 0.00 0.00 2.69
2743 2824 1.617850 CCTGCAAATACAAGCCCACAA 59.382 47.619 0.00 0.00 0.00 3.33
3032 3113 5.151297 ACATTTGGGAGCCATACTTTTTG 57.849 39.130 0.00 0.00 31.53 2.44
3188 3272 3.076621 GCAATCATCCTGTGTCTGTTCA 58.923 45.455 0.00 0.00 0.00 3.18
3386 3470 3.611025 TTCTCCTGGTTTGGGAATTGT 57.389 42.857 0.00 0.00 31.92 2.71
3532 3616 4.271049 ACGTTGCATGTTATCTATCAGCAC 59.729 41.667 0.00 0.00 0.00 4.40
3982 4066 2.889512 TGGAAGCTCTCTCCACAAGTA 58.110 47.619 1.25 0.00 0.00 2.24
4422 4506 3.702045 TGTCCCCACAAATTTCGAAACTT 59.298 39.130 13.81 5.60 0.00 2.66
4429 4513 5.010282 AGTAGACATGTCCCCACAAATTTC 58.990 41.667 22.21 0.00 35.64 2.17
4447 4531 5.728637 TCTCTCATCTTTTGCACAGTAGA 57.271 39.130 0.00 0.00 0.00 2.59
4619 4704 2.917933 CCAAGTTTCCATAGCGATCCA 58.082 47.619 0.00 0.00 0.00 3.41
4624 4709 1.398390 GAGTGCCAAGTTTCCATAGCG 59.602 52.381 0.00 0.00 0.00 4.26
4898 4983 0.329261 TCAGAATGGCTTGGGAGGTG 59.671 55.000 0.00 0.00 36.16 4.00
4999 5084 4.141620 CCCTACTGGCATGTAATCTCAACT 60.142 45.833 0.00 0.00 0.00 3.16
5037 5124 4.928615 GCATGCCAAAAAGTATTTGCACTA 59.071 37.500 6.36 0.00 39.02 2.74
5156 5244 1.946283 GCTTGAACCCTGCCTGACTAC 60.946 57.143 0.00 0.00 0.00 2.73
5188 5279 5.187687 GTTTTACATTATTGGACGGAGGGA 58.812 41.667 0.00 0.00 0.00 4.20
5189 5280 4.337274 GGTTTTACATTATTGGACGGAGGG 59.663 45.833 0.00 0.00 0.00 4.30
5190 5281 5.190677 AGGTTTTACATTATTGGACGGAGG 58.809 41.667 0.00 0.00 0.00 4.30
5191 5282 6.753107 AAGGTTTTACATTATTGGACGGAG 57.247 37.500 0.00 0.00 0.00 4.63
5194 5285 8.582433 ACAAAAAGGTTTTACATTATTGGACG 57.418 30.769 0.00 0.00 0.00 4.79
5195 5286 9.535878 TGACAAAAAGGTTTTACATTATTGGAC 57.464 29.630 0.00 0.00 0.00 4.02
5196 5287 9.535878 GTGACAAAAAGGTTTTACATTATTGGA 57.464 29.630 0.00 0.00 0.00 3.53
5197 5288 9.541143 AGTGACAAAAAGGTTTTACATTATTGG 57.459 29.630 0.00 0.00 0.00 3.16
5201 5292 9.575783 GTCAAGTGACAAAAAGGTTTTACATTA 57.424 29.630 6.57 0.00 44.18 1.90
5202 5293 8.474006 GTCAAGTGACAAAAAGGTTTTACATT 57.526 30.769 6.57 0.00 44.18 2.71
5229 5320 6.887545 TCCGTCCCATAATGTAAGACATTTTT 59.112 34.615 9.92 0.00 45.80 1.94
5230 5321 6.419791 TCCGTCCCATAATGTAAGACATTTT 58.580 36.000 9.92 0.33 45.80 1.82
5231 5322 5.996644 TCCGTCCCATAATGTAAGACATTT 58.003 37.500 9.92 0.00 45.80 2.32
5233 5324 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
5234 5325 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
5235 5326 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
5236 5327 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
5237 5328 2.704065 ACCCTCCGTCCCATAATGTAAG 59.296 50.000 0.00 0.00 0.00 2.34
5238 5329 2.766736 ACCCTCCGTCCCATAATGTAA 58.233 47.619 0.00 0.00 0.00 2.41
5239 5330 2.482414 ACCCTCCGTCCCATAATGTA 57.518 50.000 0.00 0.00 0.00 2.29
5240 5331 1.591768 AACCCTCCGTCCCATAATGT 58.408 50.000 0.00 0.00 0.00 2.71
5241 5332 3.849563 TTAACCCTCCGTCCCATAATG 57.150 47.619 0.00 0.00 0.00 1.90
5242 5333 4.866327 TTTTAACCCTCCGTCCCATAAT 57.134 40.909 0.00 0.00 0.00 1.28
5243 5334 4.866327 ATTTTAACCCTCCGTCCCATAA 57.134 40.909 0.00 0.00 0.00 1.90
5244 5335 4.528920 CAATTTTAACCCTCCGTCCCATA 58.471 43.478 0.00 0.00 0.00 2.74
5245 5336 3.361786 CAATTTTAACCCTCCGTCCCAT 58.638 45.455 0.00 0.00 0.00 4.00
5246 5337 2.555670 CCAATTTTAACCCTCCGTCCCA 60.556 50.000 0.00 0.00 0.00 4.37
5247 5338 2.097036 CCAATTTTAACCCTCCGTCCC 58.903 52.381 0.00 0.00 0.00 4.46
5248 5339 2.490509 CACCAATTTTAACCCTCCGTCC 59.509 50.000 0.00 0.00 0.00 4.79
5249 5340 2.094906 GCACCAATTTTAACCCTCCGTC 60.095 50.000 0.00 0.00 0.00 4.79
5250 5341 1.890489 GCACCAATTTTAACCCTCCGT 59.110 47.619 0.00 0.00 0.00 4.69
5251 5342 1.203758 GGCACCAATTTTAACCCTCCG 59.796 52.381 0.00 0.00 0.00 4.63
5252 5343 2.536066 AGGCACCAATTTTAACCCTCC 58.464 47.619 0.00 0.00 0.00 4.30
5253 5344 4.341487 ACTAGGCACCAATTTTAACCCTC 58.659 43.478 0.00 0.00 0.00 4.30
5254 5345 4.397919 ACTAGGCACCAATTTTAACCCT 57.602 40.909 0.00 0.00 0.00 4.34
5255 5346 4.525100 TCAACTAGGCACCAATTTTAACCC 59.475 41.667 0.00 0.00 0.00 4.11
5256 5347 5.010213 TGTCAACTAGGCACCAATTTTAACC 59.990 40.000 0.00 0.00 0.00 2.85
5257 5348 6.016610 TCTGTCAACTAGGCACCAATTTTAAC 60.017 38.462 0.00 0.00 0.00 2.01
5291 5382 7.704271 AGAAGCCAAGTACTTAAAGAAAACAC 58.296 34.615 8.04 0.00 0.00 3.32
5295 5386 7.875327 ACAAGAAGCCAAGTACTTAAAGAAA 57.125 32.000 8.04 0.00 0.00 2.52
5298 5389 8.379457 ACTAACAAGAAGCCAAGTACTTAAAG 57.621 34.615 8.04 1.50 0.00 1.85
5384 5484 3.407424 TGCGGCAATTGCTCTATATCT 57.593 42.857 28.42 0.00 41.70 1.98
5445 5546 7.821359 AGTATGCATGATATTTAGCGATTGAGT 59.179 33.333 10.16 0.00 0.00 3.41
5456 5557 6.650807 CGGAGTACCAAGTATGCATGATATTT 59.349 38.462 10.16 0.00 35.59 1.40
5473 5616 7.440198 AGGCTTATATTTAGAAACGGAGTACC 58.560 38.462 0.00 0.00 45.00 3.34
5500 5656 3.138884 TGGAGTACATGCAGAGCAAAA 57.861 42.857 0.00 0.00 43.62 2.44
5503 5659 3.642848 TCATATGGAGTACATGCAGAGCA 59.357 43.478 2.13 0.00 44.86 4.26
5504 5660 4.263018 TCATATGGAGTACATGCAGAGC 57.737 45.455 2.13 0.00 40.82 4.09
5505 5661 7.660617 AGATTTTCATATGGAGTACATGCAGAG 59.339 37.037 2.13 0.00 40.82 3.35
5506 5662 7.512130 AGATTTTCATATGGAGTACATGCAGA 58.488 34.615 2.13 0.00 40.82 4.26
5507 5663 7.660617 AGAGATTTTCATATGGAGTACATGCAG 59.339 37.037 2.13 0.00 40.82 4.41
5509 5665 7.976135 AGAGATTTTCATATGGAGTACATGC 57.024 36.000 2.13 0.00 40.82 4.06
5541 5764 8.190122 TGTACTCGCTTCGTTCCTAAATATAAA 58.810 33.333 0.00 0.00 0.00 1.40
5542 5765 7.706159 TGTACTCGCTTCGTTCCTAAATATAA 58.294 34.615 0.00 0.00 0.00 0.98
5552 5777 4.905412 AAGAATTGTACTCGCTTCGTTC 57.095 40.909 0.00 0.00 0.00 3.95
5579 5804 0.037697 ATTGACGCACGCTTAGGACA 60.038 50.000 0.00 0.00 0.00 4.02
5580 5805 1.076332 AATTGACGCACGCTTAGGAC 58.924 50.000 0.00 0.00 0.00 3.85
5581 5806 2.658373 TAATTGACGCACGCTTAGGA 57.342 45.000 0.00 0.00 0.00 2.94
5582 5807 3.944422 ATTAATTGACGCACGCTTAGG 57.056 42.857 0.00 0.00 0.00 2.69
5588 5830 3.718864 CGATCCAAATTAATTGACGCACG 59.281 43.478 0.39 1.28 41.85 5.34
5595 5837 5.133221 ACTCCCTCCGATCCAAATTAATTG 58.867 41.667 0.39 0.00 38.84 2.32
5603 5845 2.471815 ATGTACTCCCTCCGATCCAA 57.528 50.000 0.00 0.00 0.00 3.53
5609 5851 6.821665 TCAAATAGAAAAATGTACTCCCTCCG 59.178 38.462 0.00 0.00 0.00 4.63
5721 6050 6.633500 TTCACCTCTTTTGTAATGGTTCAG 57.367 37.500 0.00 0.00 0.00 3.02
5722 6051 8.698973 TTATTCACCTCTTTTGTAATGGTTCA 57.301 30.769 0.00 0.00 0.00 3.18
5723 6052 9.406828 GTTTATTCACCTCTTTTGTAATGGTTC 57.593 33.333 0.00 0.00 0.00 3.62
5724 6053 8.919145 TGTTTATTCACCTCTTTTGTAATGGTT 58.081 29.630 0.00 0.00 0.00 3.67
5726 6055 8.576442 ACTGTTTATTCACCTCTTTTGTAATGG 58.424 33.333 0.00 0.00 0.00 3.16
5727 6056 9.965824 AACTGTTTATTCACCTCTTTTGTAATG 57.034 29.630 0.00 0.00 0.00 1.90
5731 6060 9.349713 TCATAACTGTTTATTCACCTCTTTTGT 57.650 29.630 0.00 0.00 0.00 2.83
5751 6080 9.638239 TGCAAAAGAAATCCACTTATTCATAAC 57.362 29.630 0.00 0.00 0.00 1.89
5758 6087 5.726980 TGCTGCAAAAGAAATCCACTTAT 57.273 34.783 0.00 0.00 0.00 1.73
5797 6126 3.939837 ATGGCGCGAGGTCACACAG 62.940 63.158 12.10 0.00 29.38 3.66
5799 6128 3.188786 GATGGCGCGAGGTCACAC 61.189 66.667 12.10 0.00 29.38 3.82
5800 6129 4.794439 CGATGGCGCGAGGTCACA 62.794 66.667 12.10 0.00 29.38 3.58
5801 6130 4.796231 ACGATGGCGCGAGGTCAC 62.796 66.667 12.10 0.00 42.48 3.67
5802 6131 4.063967 AACGATGGCGCGAGGTCA 62.064 61.111 12.10 1.74 42.48 4.02
5819 6148 2.000429 CACGATCAGTCAGACATGCA 58.000 50.000 2.66 0.00 0.00 3.96
5820 6149 0.649475 GCACGATCAGTCAGACATGC 59.351 55.000 2.66 0.00 0.00 4.06
5839 6169 3.716006 CAGTGTGTCTTGCGGCGG 61.716 66.667 9.78 0.00 0.00 6.13
5840 6170 2.047151 AAACAGTGTGTCTTGCGGCG 62.047 55.000 0.51 0.51 0.00 6.46
5841 6171 0.317020 GAAACAGTGTGTCTTGCGGC 60.317 55.000 6.17 0.00 0.00 6.53
5842 6172 1.299541 AGAAACAGTGTGTCTTGCGG 58.700 50.000 10.38 0.00 22.60 5.69
5843 6173 2.609459 AGAAGAAACAGTGTGTCTTGCG 59.391 45.455 29.47 0.00 39.87 4.85
5844 6174 3.302740 CGAGAAGAAACAGTGTGTCTTGC 60.303 47.826 29.47 19.96 39.87 4.01
5845 6175 3.302740 GCGAGAAGAAACAGTGTGTCTTG 60.303 47.826 29.47 17.70 39.87 3.02
5846 6176 2.866762 GCGAGAAGAAACAGTGTGTCTT 59.133 45.455 25.68 25.68 42.15 3.01
5847 6177 2.159099 TGCGAGAAGAAACAGTGTGTCT 60.159 45.455 10.38 10.38 30.36 3.41
5848 6178 2.033662 GTGCGAGAAGAAACAGTGTGTC 60.034 50.000 5.19 5.19 0.00 3.67
5849 6179 1.933853 GTGCGAGAAGAAACAGTGTGT 59.066 47.619 0.00 0.00 0.00 3.72
5850 6180 2.033407 CAGTGCGAGAAGAAACAGTGTG 60.033 50.000 0.00 0.00 0.00 3.82
5851 6181 2.159099 TCAGTGCGAGAAGAAACAGTGT 60.159 45.455 0.00 0.00 35.45 3.55
5852 6182 2.473816 TCAGTGCGAGAAGAAACAGTG 58.526 47.619 0.00 0.00 35.29 3.66
5853 6183 2.748605 CTCAGTGCGAGAAGAAACAGT 58.251 47.619 0.00 0.00 45.45 3.55
5863 6193 3.070018 AGAAAAACCATCTCAGTGCGAG 58.930 45.455 0.00 0.00 43.80 5.03
5864 6194 3.126001 AGAAAAACCATCTCAGTGCGA 57.874 42.857 0.00 0.00 0.00 5.10
5865 6195 3.558505 CAAGAAAAACCATCTCAGTGCG 58.441 45.455 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.