Multiple sequence alignment - TraesCS5B01G419000

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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 TraesCS5B01G419000 chr5B 100.000 5347 0 0 1 5347 594917810 594912464 0.000000e+00 9875.0
1 TraesCS5B01G419000 chr5B 100.000 29 0 0 2026 2054 594915756 594915728 3.000000e-03 54.7
2 TraesCS5B01G419000 chr5B 100.000 29 0 0 2055 2083 594915785 594915757 3.000000e-03 54.7
3 TraesCS5B01G419000 chr5A 93.946 2395 101 21 2057 4431 605226296 605223926 0.000000e+00 3579.0
4 TraesCS5B01G419000 chr5A 92.114 2067 131 24 1 2054 605228317 605226270 0.000000e+00 2885.0
5 TraesCS5B01G419000 chr5A 93.750 144 9 0 4678 4821 605223452 605223309 3.240000e-52 217.0
6 TraesCS5B01G419000 chr5A 89.844 128 10 3 4500 4627 605223891 605223767 1.540000e-35 161.0
7 TraesCS5B01G419000 chr5D 91.475 2041 109 34 2434 4431 483710496 483708478 0.000000e+00 2745.0
8 TraesCS5B01G419000 chr5D 92.675 1611 84 14 1 1595 483712782 483711190 0.000000e+00 2290.0
9 TraesCS5B01G419000 chr5D 89.598 423 35 7 1634 2054 483711188 483710773 3.670000e-146 529.0
10 TraesCS5B01G419000 chr5D 83.768 345 26 13 2055 2399 483710801 483710487 3.130000e-77 300.0
11 TraesCS5B01G419000 chr5D 86.784 227 24 3 5124 5345 483707830 483707605 1.150000e-61 248.0
12 TraesCS5B01G419000 chr5D 96.970 66 2 0 4474 4539 483708479 483708414 1.570000e-20 111.0
13 TraesCS5B01G419000 chr1B 77.778 225 19 16 2076 2278 654503874 654504089 5.660000e-20 110.0


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 TraesCS5B01G419000 chr5B 594912464 594917810 5346 True 3328.133333 9875 100.000000 1 5347 3 chr5B.!!$R1 5346
1 TraesCS5B01G419000 chr5A 605223309 605228317 5008 True 1710.500000 3579 92.413500 1 4821 4 chr5A.!!$R1 4820
2 TraesCS5B01G419000 chr5D 483707605 483712782 5177 True 1037.166667 2745 90.211667 1 5345 6 chr5D.!!$R1 5344

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
340 341 1.136147 GACGTACATGTCGCGGTCT 59.864 57.895 21.38 6.04 0.0 3.85 F
1939 1968 0.323302 TTGTCGACATTGCAGGCCTA 59.677 50.000 20.80 0.00 0.0 3.93 F
1982 2011 1.142474 GGTACCGGTTGTTCTTCGTG 58.858 55.000 15.04 0.00 0.0 4.35 F
3082 3142 1.630369 TGGCCAAACTAGCATCAGAGT 59.370 47.619 0.61 0.00 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2199 0.107263 TGCCTGAGAGCACAAACACA 60.107 50.0 0.00 0.00 38.0 3.72 R
3194 3255 0.538057 ACCTGGTGCACTCCACAATG 60.538 55.0 17.98 3.02 46.5 2.82 R
3280 3341 0.771127 AGTTGCCTAGCCCACTTTCA 59.229 50.0 0.00 0.00 0.0 2.69 R
4822 5175 0.675083 TCACAATGCCAGCAACCAAG 59.325 50.0 0.00 0.00 0.0 3.61 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
178 179 4.021925 GCTCCGAACAGCCCCACT 62.022 66.667 0.00 0.00 32.76 4.00
340 341 1.136147 GACGTACATGTCGCGGTCT 59.864 57.895 21.38 6.04 0.00 3.85
643 644 3.781770 GATGAGCCGCGTCTGGAGG 62.782 68.421 4.92 0.00 38.87 4.30
897 898 4.244802 GAGACGAGGCGAGGCGAG 62.245 72.222 0.00 0.00 0.00 5.03
934 940 5.473039 GCAGAAAATTGTGCTATGGACTTT 58.527 37.500 7.92 0.00 43.38 2.66
938 944 7.271223 CAGAAAATTGTGCTATGGACTTTAACG 59.729 37.037 0.00 0.00 0.00 3.18
967 973 1.153289 GCTCACGTGCCATCCATCT 60.153 57.895 11.67 0.00 0.00 2.90
1004 1010 1.154016 CGCTAGTCCCTCGTGTGTG 60.154 63.158 0.00 0.00 0.00 3.82
1005 1011 1.863662 CGCTAGTCCCTCGTGTGTGT 61.864 60.000 0.00 0.00 0.00 3.72
1006 1012 0.388649 GCTAGTCCCTCGTGTGTGTG 60.389 60.000 0.00 0.00 0.00 3.82
1011 1017 0.753848 TCCCTCGTGTGTGTGTCTCA 60.754 55.000 0.00 0.00 0.00 3.27
1157 1164 4.697756 TTGCCGTTGCCCTCCTCG 62.698 66.667 0.00 0.00 36.33 4.63
1273 1286 2.224137 CGAAGATTAGCATGAGCCTCCA 60.224 50.000 0.00 0.00 43.56 3.86
1350 1363 3.563808 TGTAAGTCACCAATTGAGCACAC 59.436 43.478 7.12 0.00 33.71 3.82
1365 1378 3.357079 CACACAGAACCCGCTGCC 61.357 66.667 0.00 0.00 39.51 4.85
1367 1380 2.281761 CACAGAACCCGCTGCCTT 60.282 61.111 0.00 0.00 39.51 4.35
1369 1382 1.021390 CACAGAACCCGCTGCCTTAG 61.021 60.000 0.00 0.00 39.51 2.18
1378 1391 3.442625 ACCCGCTGCCTTAGAATTAAAAC 59.557 43.478 0.00 0.00 0.00 2.43
1380 1393 4.879545 CCCGCTGCCTTAGAATTAAAACTA 59.120 41.667 0.00 0.00 0.00 2.24
1422 1436 1.068472 TCGTCTTTCCAGAGCTCGAAC 60.068 52.381 8.37 0.00 0.00 3.95
1431 1445 2.044252 AGCTCGAACTAGCCGGGA 60.044 61.111 2.18 0.00 43.86 5.14
1444 1458 1.643880 GCCGGGAGCAATGAAATTTG 58.356 50.000 2.18 0.00 42.97 2.32
1462 1490 2.760634 TGCTCCTTCTATTCGTGCAA 57.239 45.000 0.00 0.00 0.00 4.08
1473 1501 5.698832 TCTATTCGTGCAATGGTTTTTCTG 58.301 37.500 0.00 0.00 0.00 3.02
1522 1550 1.002315 GGGGCAATGTCACTGCATTTT 59.998 47.619 8.74 0.00 41.78 1.82
1542 1570 4.902443 TTAAGTGTTCGATGTTTTGCCA 57.098 36.364 0.00 0.00 0.00 4.92
1584 1612 8.527810 GTCCAAAGGTTGAAATGGTTAATATGA 58.472 33.333 0.00 0.00 34.50 2.15
1654 1682 4.340894 TTCACGCTCACTGCATAATTTC 57.659 40.909 0.00 0.00 43.06 2.17
1658 1686 3.372206 ACGCTCACTGCATAATTTCTGTC 59.628 43.478 0.00 0.00 43.06 3.51
1667 1695 3.853671 GCATAATTTCTGTCCTTGCAACG 59.146 43.478 0.00 0.00 0.00 4.10
1676 1704 1.133253 CCTTGCAACGATGACTGCG 59.867 57.895 0.00 0.00 41.63 5.18
1678 1706 0.451628 CTTGCAACGATGACTGCGTG 60.452 55.000 0.00 0.00 41.75 5.34
1691 1719 2.228822 GACTGCGTGATGGAATGGTTTT 59.771 45.455 0.00 0.00 0.00 2.43
1736 1765 7.496529 GCAATTGGCATATACTTACTTCTCA 57.503 36.000 7.72 0.00 43.97 3.27
1737 1766 8.103948 GCAATTGGCATATACTTACTTCTCAT 57.896 34.615 7.72 0.00 43.97 2.90
1738 1767 8.019669 GCAATTGGCATATACTTACTTCTCATG 58.980 37.037 7.72 0.00 43.97 3.07
1744 1773 9.077674 GGCATATACTTACTTCTCATGATAACG 57.922 37.037 0.00 0.00 0.00 3.18
1764 1793 3.799035 CGAAATGTGAGTTCGTTTCTGG 58.201 45.455 0.00 0.00 42.23 3.86
1768 1797 3.469008 TGTGAGTTCGTTTCTGGATGT 57.531 42.857 0.00 0.00 0.00 3.06
1813 1842 2.158914 CCAAGCTGCAAACTTTCCCTTT 60.159 45.455 1.02 0.00 0.00 3.11
1837 1866 2.962421 CACCATAAACCCAAACACTGGT 59.038 45.455 0.00 0.00 44.76 4.00
1846 1875 1.078072 AAACACTGGTGTCGTGGCA 60.078 52.632 6.84 0.00 44.13 4.92
1865 1894 0.830648 AATTCCCGATCCTCGCTTGA 59.169 50.000 0.00 0.00 38.82 3.02
1879 1908 1.003972 CGCTTGAACGTGCTCTCAAAA 60.004 47.619 0.00 0.00 31.41 2.44
1939 1968 0.323302 TTGTCGACATTGCAGGCCTA 59.677 50.000 20.80 0.00 0.00 3.93
1975 2004 1.725803 AAGGAGAGGTACCGGTTGTT 58.274 50.000 15.04 0.00 0.00 2.83
1982 2011 1.142474 GGTACCGGTTGTTCTTCGTG 58.858 55.000 15.04 0.00 0.00 4.35
1988 2017 4.630111 ACCGGTTGTTCTTCGTGTTATTA 58.370 39.130 0.00 0.00 0.00 0.98
1990 2019 4.687483 CCGGTTGTTCTTCGTGTTATTACT 59.313 41.667 0.00 0.00 0.00 2.24
1991 2020 5.389098 CCGGTTGTTCTTCGTGTTATTACTG 60.389 44.000 0.00 0.00 0.00 2.74
1992 2021 5.403166 CGGTTGTTCTTCGTGTTATTACTGA 59.597 40.000 0.00 0.00 0.00 3.41
2016 2045 2.347755 CAGCACAGAACATGTCGATGAG 59.652 50.000 0.00 0.00 41.41 2.90
2026 2055 5.095691 ACATGTCGATGAGTGTTTTTCAC 57.904 39.130 0.00 0.00 38.85 3.18
2147 2176 6.098409 ACATCCGTGAAGTGGATTCTATACTT 59.902 38.462 0.00 0.00 43.76 2.24
2235 2271 5.316327 AGCTTTGCATCTTTTTACTAGCC 57.684 39.130 0.00 0.00 0.00 3.93
2370 2407 6.366315 TGTAGTTGTACAATGTTGGAACAC 57.634 37.500 12.26 0.00 36.62 3.32
2436 2473 1.723608 TTGGTCCTTGTTGTGCTGCG 61.724 55.000 0.00 0.00 0.00 5.18
2651 2689 8.723365 TGATCTTGAACAGGTAATATAATGGGT 58.277 33.333 0.00 0.00 0.00 4.51
2673 2728 6.184789 GGTGAGGGATTTAAGTGTGGATTTA 58.815 40.000 0.00 0.00 0.00 1.40
2677 2732 9.983024 TGAGGGATTTAAGTGTGGATTTATTTA 57.017 29.630 0.00 0.00 0.00 1.40
2712 2768 8.810652 TGTTCATACTTAACCAAGAATTTTGC 57.189 30.769 0.00 0.00 35.60 3.68
2813 2873 9.685828 GGTAAGTAAGATATTCACAAGCTCTAG 57.314 37.037 0.00 0.00 0.00 2.43
3082 3142 1.630369 TGGCCAAACTAGCATCAGAGT 59.370 47.619 0.61 0.00 0.00 3.24
3085 3145 2.159462 GCCAAACTAGCATCAGAGTTGC 60.159 50.000 0.00 0.00 36.05 4.17
3133 3193 6.070538 AGCTCAGGTTTGTGATAAGTGATACT 60.071 38.462 0.00 0.00 0.00 2.12
3144 3204 8.190784 TGTGATAAGTGATACTATATGCATCGG 58.809 37.037 0.19 0.00 0.00 4.18
3157 3217 4.586017 ATGCATCGGCCTAGGCATTAGG 62.586 54.545 34.09 20.49 43.86 2.69
3241 3302 4.022242 GCTGAACTGTCTGAACTACCACTA 60.022 45.833 0.00 0.00 0.00 2.74
3280 3341 8.814038 AATACCTAAATTCTCTTGATGTTGCT 57.186 30.769 0.00 0.00 0.00 3.91
3420 3481 6.944862 AGCTGTTGATCCTAACTTTCAAATCT 59.055 34.615 0.00 0.00 31.66 2.40
3491 3552 6.252015 CAGGTTTTATTCGCATTCTCACAATG 59.748 38.462 0.00 0.00 0.00 2.82
3534 3595 0.609131 CCGTGGGAACTGCCTTCATT 60.609 55.000 0.00 0.00 36.66 2.57
3583 3644 8.684386 TTTGACTATGTTTTGTCTTGGATGTA 57.316 30.769 0.00 0.00 34.57 2.29
3688 3749 5.482526 TGTAAGTATCAGGGTTCTGTGCTAA 59.517 40.000 0.00 0.00 41.59 3.09
3691 3752 6.163135 AGTATCAGGGTTCTGTGCTAATAC 57.837 41.667 0.00 0.00 41.59 1.89
3693 3754 7.067421 AGTATCAGGGTTCTGTGCTAATACTA 58.933 38.462 0.00 0.00 41.59 1.82
3700 3761 6.869388 GGGTTCTGTGCTAATACTAAGATAGC 59.131 42.308 0.00 0.00 41.84 2.97
3702 3763 7.596995 GGTTCTGTGCTAATACTAAGATAGCTG 59.403 40.741 0.00 0.00 41.97 4.24
3705 3766 6.997655 TGTGCTAATACTAAGATAGCTGCAT 58.002 36.000 1.02 0.00 41.97 3.96
3720 3781 5.710513 AGCTGCATGTTCTTTTCATGTAA 57.289 34.783 1.02 0.00 42.94 2.41
3722 3783 7.395190 AGCTGCATGTTCTTTTCATGTAATA 57.605 32.000 1.02 0.00 42.94 0.98
3727 3788 8.629158 TGCATGTTCTTTTCATGTAATATACCC 58.371 33.333 7.55 0.00 42.94 3.69
3735 3806 8.436046 TTTTCATGTAATATACCCGGTGTTAC 57.564 34.615 0.00 7.67 0.00 2.50
3748 3819 7.160547 ACCCGGTGTTACTTTAATAATTTGG 57.839 36.000 0.00 0.00 0.00 3.28
3803 3874 1.006688 GATTTTGTTGCGGCGGGTT 60.007 52.632 9.78 0.00 0.00 4.11
3805 3876 2.428960 ATTTTGTTGCGGCGGGTTCC 62.429 55.000 9.78 0.00 0.00 3.62
3858 3929 9.878599 GGTAACAATATGTGCACTTATATGAAC 57.121 33.333 21.65 19.97 0.00 3.18
3894 3970 5.948992 AGAGATAAAGCACACAAGGAAAC 57.051 39.130 0.00 0.00 0.00 2.78
3895 3971 4.452455 AGAGATAAAGCACACAAGGAAACG 59.548 41.667 0.00 0.00 0.00 3.60
3897 3973 5.302360 AGATAAAGCACACAAGGAAACGTA 58.698 37.500 0.00 0.00 0.00 3.57
3908 3984 8.901748 CACACAAGGAAACGTATTTATTTCTTG 58.098 33.333 13.89 13.89 35.55 3.02
3909 3985 8.626526 ACACAAGGAAACGTATTTATTTCTTGT 58.373 29.630 14.95 14.95 37.04 3.16
3917 3993 8.480643 AACGTATTTATTTCTTGTCCTCTCTG 57.519 34.615 0.00 0.00 0.00 3.35
3947 4023 1.827792 TGAGGTTGGAAGGGAAGGAA 58.172 50.000 0.00 0.00 0.00 3.36
3983 4059 1.539929 GGAGATGTCATGCTCTTCCGG 60.540 57.143 0.00 0.00 0.00 5.14
4005 4081 5.277779 CGGTTCAATGTGTGACAACAATACT 60.278 40.000 0.00 0.00 38.27 2.12
4006 4082 5.914635 GGTTCAATGTGTGACAACAATACTG 59.085 40.000 0.00 0.00 38.27 2.74
4018 4094 6.127758 TGACAACAATACTGTGCAAGAAGTTT 60.128 34.615 3.55 0.00 35.37 2.66
4021 4097 6.449635 ACAATACTGTGCAAGAAGTTTCAA 57.550 33.333 3.55 0.00 33.30 2.69
4048 4124 8.114290 GCTTTATTCAACTCGAATTTCATACGA 58.886 33.333 0.00 0.00 41.83 3.43
4074 4150 4.751767 ACAAGGCAAGACAAAATTTGGA 57.248 36.364 10.71 0.00 34.12 3.53
4111 4187 4.771590 TGTCTTTGAGGCATCAATTGTC 57.228 40.909 15.42 9.26 44.75 3.18
4115 4191 4.773674 TCTTTGAGGCATCAATTGTCCATT 59.226 37.500 15.42 0.00 44.75 3.16
4118 4194 6.602410 TTGAGGCATCAATTGTCCATTTAA 57.398 33.333 10.22 0.00 40.54 1.52
4190 4267 8.763049 TGTAACATATGCAGATACTTGATAGC 57.237 34.615 1.58 0.00 0.00 2.97
4300 4378 9.458374 AGTAATCCATTTTTGAAGTAACAAACG 57.542 29.630 0.00 0.00 39.08 3.60
4328 4407 6.393990 GGAGAGTGTCCTACTGCAATATATG 58.606 44.000 0.00 0.00 42.99 1.78
4353 4432 8.579006 TGAAGACAAAAGTTATCTGCAAATCAT 58.421 29.630 0.00 0.00 0.00 2.45
4389 4468 2.366167 CCAGGAGGGACCCAGGAG 60.366 72.222 14.60 0.00 40.01 3.69
4394 4473 0.397394 GGAGGGACCCAGGAGTCTAC 60.397 65.000 14.60 0.00 36.95 2.59
4416 4495 8.768397 TCTACAACTCCAATATACTCCAACATT 58.232 33.333 0.00 0.00 0.00 2.71
4458 4537 7.800155 TTATTGTGTGAGTGTGAAATTCTGA 57.200 32.000 0.00 0.00 0.00 3.27
4459 4538 6.698008 ATTGTGTGAGTGTGAAATTCTGAA 57.302 33.333 0.00 0.00 0.00 3.02
4460 4539 6.698008 TTGTGTGAGTGTGAAATTCTGAAT 57.302 33.333 0.00 0.00 0.00 2.57
4461 4540 6.698008 TGTGTGAGTGTGAAATTCTGAATT 57.302 33.333 9.76 9.76 0.00 2.17
4462 4541 7.800155 TGTGTGAGTGTGAAATTCTGAATTA 57.200 32.000 15.45 0.00 0.00 1.40
4463 4542 8.219546 TGTGTGAGTGTGAAATTCTGAATTAA 57.780 30.769 15.45 5.37 0.00 1.40
4464 4543 8.849168 TGTGTGAGTGTGAAATTCTGAATTAAT 58.151 29.630 15.45 1.70 0.00 1.40
4465 4544 9.334693 GTGTGAGTGTGAAATTCTGAATTAATC 57.665 33.333 15.45 11.03 0.00 1.75
4466 4545 8.514594 TGTGAGTGTGAAATTCTGAATTAATCC 58.485 33.333 15.45 6.85 0.00 3.01
4467 4546 7.970614 GTGAGTGTGAAATTCTGAATTAATCCC 59.029 37.037 15.45 3.71 0.00 3.85
4468 4547 7.669304 TGAGTGTGAAATTCTGAATTAATCCCA 59.331 33.333 15.45 6.07 0.00 4.37
4469 4548 8.059798 AGTGTGAAATTCTGAATTAATCCCAG 57.940 34.615 15.45 10.10 0.00 4.45
4470 4549 7.123247 AGTGTGAAATTCTGAATTAATCCCAGG 59.877 37.037 15.45 0.00 0.00 4.45
4471 4550 7.122650 GTGTGAAATTCTGAATTAATCCCAGGA 59.877 37.037 15.45 8.79 0.00 3.86
4472 4551 7.340232 TGTGAAATTCTGAATTAATCCCAGGAG 59.660 37.037 15.45 0.00 0.00 3.69
4508 4597 3.811497 ACTTCGGTGTGCTTAAAGTTACC 59.189 43.478 0.00 0.00 0.00 2.85
4535 4624 9.905713 TCTAAGATTGCCTCATTTTATGTTACT 57.094 29.630 0.00 0.00 0.00 2.24
4550 4639 8.702408 TTTATGTTACTTGAAAATTGTCGTCG 57.298 30.769 0.00 0.00 0.00 5.12
4551 4640 5.721876 TGTTACTTGAAAATTGTCGTCGT 57.278 34.783 0.00 0.00 0.00 4.34
4552 4641 5.730269 TGTTACTTGAAAATTGTCGTCGTC 58.270 37.500 0.00 0.00 0.00 4.20
4553 4642 3.499072 ACTTGAAAATTGTCGTCGTCG 57.501 42.857 0.00 0.00 38.55 5.12
4554 4643 3.117794 ACTTGAAAATTGTCGTCGTCGA 58.882 40.909 0.00 0.00 44.12 4.20
4598 4687 7.560368 ACCTTTTCTCATGTATAGAAGGACAG 58.440 38.462 17.85 5.87 34.59 3.51
4670 4961 5.880332 TGCAATCTATTTTGGAGTACCTCAC 59.120 40.000 0.00 0.00 37.04 3.51
4671 4962 6.116126 GCAATCTATTTTGGAGTACCTCACT 58.884 40.000 0.00 0.00 41.47 3.41
4672 4963 7.093068 TGCAATCTATTTTGGAGTACCTCACTA 60.093 37.037 0.00 0.00 37.72 2.74
4674 4965 9.482627 CAATCTATTTTGGAGTACCTCACTATC 57.517 37.037 0.00 0.00 37.72 2.08
4675 4966 8.783660 ATCTATTTTGGAGTACCTCACTATCA 57.216 34.615 0.00 0.00 37.72 2.15
4686 5039 8.325421 AGTACCTCACTATCACAGTATATTCG 57.675 38.462 0.00 0.00 34.98 3.34
4689 5042 7.877003 ACCTCACTATCACAGTATATTCGAAG 58.123 38.462 3.35 0.00 34.98 3.79
4763 5116 3.118408 GGGAACACATACACCATAGCAGA 60.118 47.826 0.00 0.00 0.00 4.26
4813 5166 0.249489 CGGGCCTAGGTGAGAAATCG 60.249 60.000 11.31 0.00 0.00 3.34
4821 5174 2.086869 AGGTGAGAAATCGCCATGTTG 58.913 47.619 10.26 0.00 42.44 3.33
4822 5175 1.468054 GGTGAGAAATCGCCATGTTGC 60.468 52.381 3.01 0.00 39.90 4.17
4823 5176 1.470098 GTGAGAAATCGCCATGTTGCT 59.530 47.619 0.00 0.00 0.00 3.91
4824 5177 2.095059 GTGAGAAATCGCCATGTTGCTT 60.095 45.455 0.00 0.00 0.00 3.91
4825 5178 2.095110 TGAGAAATCGCCATGTTGCTTG 60.095 45.455 0.00 0.00 0.00 4.01
4826 5179 1.203052 AGAAATCGCCATGTTGCTTGG 59.797 47.619 0.00 0.00 37.31 3.61
4827 5180 0.968405 AAATCGCCATGTTGCTTGGT 59.032 45.000 0.00 0.00 36.57 3.67
4828 5181 0.968405 AATCGCCATGTTGCTTGGTT 59.032 45.000 0.00 0.00 36.57 3.67
4829 5182 0.244450 ATCGCCATGTTGCTTGGTTG 59.756 50.000 0.00 0.00 36.57 3.77
4830 5183 2.023223 CGCCATGTTGCTTGGTTGC 61.023 57.895 0.00 0.00 36.57 4.17
4831 5184 1.368579 GCCATGTTGCTTGGTTGCT 59.631 52.632 0.00 0.00 36.57 3.91
4832 5185 0.947180 GCCATGTTGCTTGGTTGCTG 60.947 55.000 0.00 0.00 36.57 4.41
4833 5186 0.320073 CCATGTTGCTTGGTTGCTGG 60.320 55.000 0.00 0.00 0.00 4.85
4834 5187 0.947180 CATGTTGCTTGGTTGCTGGC 60.947 55.000 0.00 0.00 0.00 4.85
4835 5188 1.401318 ATGTTGCTTGGTTGCTGGCA 61.401 50.000 0.00 0.00 0.00 4.92
4836 5189 1.368579 GTTGCTTGGTTGCTGGCAT 59.631 52.632 0.00 0.00 34.59 4.40
4837 5190 0.249996 GTTGCTTGGTTGCTGGCATT 60.250 50.000 0.00 0.00 34.59 3.56
4838 5191 0.249953 TTGCTTGGTTGCTGGCATTG 60.250 50.000 0.00 0.00 34.59 2.82
4839 5192 1.368579 GCTTGGTTGCTGGCATTGT 59.631 52.632 0.00 0.00 0.00 2.71
4840 5193 0.947180 GCTTGGTTGCTGGCATTGTG 60.947 55.000 0.00 0.00 0.00 3.33
4841 5194 0.675083 CTTGGTTGCTGGCATTGTGA 59.325 50.000 0.00 0.00 0.00 3.58
4842 5195 1.068895 CTTGGTTGCTGGCATTGTGAA 59.931 47.619 0.00 0.00 0.00 3.18
4843 5196 1.340088 TGGTTGCTGGCATTGTGAAT 58.660 45.000 0.00 0.00 0.00 2.57
4844 5197 1.001068 TGGTTGCTGGCATTGTGAATG 59.999 47.619 0.00 0.00 41.85 2.67
4856 5209 5.171147 CATTGTGAATGCCTCTTCTCATC 57.829 43.478 0.00 0.00 31.06 2.92
4857 5210 4.564782 TTGTGAATGCCTCTTCTCATCT 57.435 40.909 0.00 0.00 31.06 2.90
4858 5211 4.564782 TGTGAATGCCTCTTCTCATCTT 57.435 40.909 0.00 0.00 0.00 2.40
4859 5212 5.682234 TGTGAATGCCTCTTCTCATCTTA 57.318 39.130 0.00 0.00 0.00 2.10
4860 5213 5.423015 TGTGAATGCCTCTTCTCATCTTAC 58.577 41.667 0.00 0.00 0.00 2.34
4861 5214 4.813697 GTGAATGCCTCTTCTCATCTTACC 59.186 45.833 0.00 0.00 0.00 2.85
4862 5215 4.471025 TGAATGCCTCTTCTCATCTTACCA 59.529 41.667 0.00 0.00 0.00 3.25
4863 5216 3.895232 TGCCTCTTCTCATCTTACCAC 57.105 47.619 0.00 0.00 0.00 4.16
4864 5217 3.173151 TGCCTCTTCTCATCTTACCACA 58.827 45.455 0.00 0.00 0.00 4.17
4865 5218 3.776969 TGCCTCTTCTCATCTTACCACAT 59.223 43.478 0.00 0.00 0.00 3.21
4866 5219 4.225942 TGCCTCTTCTCATCTTACCACATT 59.774 41.667 0.00 0.00 0.00 2.71
4867 5220 4.574013 GCCTCTTCTCATCTTACCACATTG 59.426 45.833 0.00 0.00 0.00 2.82
4868 5221 5.627735 GCCTCTTCTCATCTTACCACATTGA 60.628 44.000 0.00 0.00 0.00 2.57
4927 5280 7.397892 TCGATAATCCAATCTACTCCTCATC 57.602 40.000 0.00 0.00 0.00 2.92
4930 5283 7.543868 CGATAATCCAATCTACTCCTCATCAAC 59.456 40.741 0.00 0.00 0.00 3.18
4936 5289 7.345653 TCCAATCTACTCCTCATCAACAGTAAT 59.654 37.037 0.00 0.00 0.00 1.89
4940 5293 9.965902 ATCTACTCCTCATCAACAGTAATTTTT 57.034 29.630 0.00 0.00 0.00 1.94
4942 5295 6.681777 ACTCCTCATCAACAGTAATTTTTGC 58.318 36.000 0.00 0.00 0.00 3.68
4952 5314 9.474920 TCAACAGTAATTTTTGCAGAAAATAGG 57.525 29.630 6.49 1.55 31.07 2.57
4953 5315 8.711457 CAACAGTAATTTTTGCAGAAAATAGGG 58.289 33.333 6.49 1.23 31.07 3.53
4954 5316 7.386059 ACAGTAATTTTTGCAGAAAATAGGGG 58.614 34.615 6.49 6.77 31.07 4.79
4958 5320 5.896073 TTTTTGCAGAAAATAGGGGGAAA 57.104 34.783 0.00 0.00 31.07 3.13
4959 5321 5.896073 TTTTGCAGAAAATAGGGGGAAAA 57.104 34.783 0.00 0.00 0.00 2.29
4960 5322 5.896073 TTTGCAGAAAATAGGGGGAAAAA 57.104 34.783 0.00 0.00 0.00 1.94
4970 5332 3.490060 AGGGGGAAAAATTAGCACCAT 57.510 42.857 0.00 0.00 0.00 3.55
4975 5337 4.898861 GGGGAAAAATTAGCACCATGGATA 59.101 41.667 21.47 5.33 0.00 2.59
4978 5340 6.098266 GGGAAAAATTAGCACCATGGATACTT 59.902 38.462 21.47 6.01 37.61 2.24
4980 5342 7.363793 GGAAAAATTAGCACCATGGATACTTGT 60.364 37.037 21.47 1.45 40.00 3.16
5016 5378 5.106987 GCATGGAAATTTGTGTGGTCATTTC 60.107 40.000 0.00 0.00 0.00 2.17
5019 5381 5.221422 TGGAAATTTGTGTGGTCATTTCTCC 60.221 40.000 0.00 0.00 0.00 3.71
5020 5382 5.221422 GGAAATTTGTGTGGTCATTTCTCCA 60.221 40.000 0.00 0.00 0.00 3.86
5025 5387 4.665451 TGTGTGGTCATTTCTCCATGAAT 58.335 39.130 0.00 0.00 34.89 2.57
5029 5391 6.587608 GTGTGGTCATTTCTCCATGAATTTTC 59.412 38.462 0.00 0.00 34.89 2.29
5042 5404 5.105228 CCATGAATTTTCCCATAGCACACTT 60.105 40.000 0.00 0.00 0.00 3.16
5046 5408 2.787473 TTCCCATAGCACACTTGAGG 57.213 50.000 0.00 0.00 0.00 3.86
5053 5415 2.376808 AGCACACTTGAGGATCTTCG 57.623 50.000 0.00 0.00 34.92 3.79
5061 5423 2.559698 TGAGGATCTTCGGTGCAAAA 57.440 45.000 0.00 0.00 34.92 2.44
5062 5424 2.857483 TGAGGATCTTCGGTGCAAAAA 58.143 42.857 0.00 0.00 34.92 1.94
5089 5451 7.805700 ACAAACAGATGTTTTTCAACCTTTTG 58.194 30.769 8.19 0.00 45.07 2.44
5090 5452 7.659390 ACAAACAGATGTTTTTCAACCTTTTGA 59.341 29.630 8.19 0.00 45.07 2.69
5091 5453 8.502387 CAAACAGATGTTTTTCAACCTTTTGAA 58.498 29.630 8.19 0.00 45.29 2.69
5122 5496 4.082274 TGTTCATGTCAGCGCAATTTAG 57.918 40.909 11.47 0.00 0.00 1.85
5148 5837 6.231211 ACCATCACTACTAACTTCACAAAGG 58.769 40.000 0.00 0.00 36.78 3.11
5224 5918 4.464008 TCAGGTTTTCTGTCTTGCAATCT 58.536 39.130 0.00 0.00 43.76 2.40
5260 5954 5.679638 GCCACCAACAATAGTTTGATCATCC 60.680 44.000 0.00 0.00 35.28 3.51
5265 5959 7.148018 ACCAACAATAGTTTGATCATCCATCAC 60.148 37.037 0.00 0.00 41.56 3.06
5266 5960 7.067859 CCAACAATAGTTTGATCATCCATCACT 59.932 37.037 0.00 0.00 41.56 3.41
5269 5963 9.857656 ACAATAGTTTGATCATCCATCACTAAT 57.142 29.630 0.00 0.00 41.56 1.73
5309 6003 2.009774 CTCCTAACTCAAATGCCACCG 58.990 52.381 0.00 0.00 0.00 4.94
5329 6023 2.154462 GCATTATGCGCATAACCCTCT 58.846 47.619 37.61 22.77 36.24 3.69
5340 6034 5.230942 CGCATAACCCTCTTCATAAGTAGG 58.769 45.833 0.00 0.00 0.00 3.18
5345 6039 6.713731 AACCCTCTTCATAAGTAGGGAAAA 57.286 37.500 21.21 0.00 43.19 2.29
5346 6040 6.910259 ACCCTCTTCATAAGTAGGGAAAAT 57.090 37.500 21.21 5.72 43.19 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.483188 GGTGAAGTATGGGTTAGAGCCG 60.483 54.545 0.00 0.00 38.98 5.52
64 65 2.435586 CTCTCCGGGTTGCAGCTG 60.436 66.667 10.11 10.11 0.00 4.24
76 77 1.220477 GGAGGCTGACTTGCTCTCC 59.780 63.158 0.00 0.00 40.45 3.71
451 452 4.082523 ATGTGGGCCCACTCGTCG 62.083 66.667 45.89 0.00 46.30 5.12
456 457 1.380302 GTCAAGATGTGGGCCCACT 59.620 57.895 45.89 34.07 46.30 4.00
604 605 3.755628 ATGTACGTCCTGGCGCGT 61.756 61.111 8.43 17.28 44.02 6.01
889 890 1.448013 GTTTTCCCTCCTCGCCTCG 60.448 63.158 0.00 0.00 0.00 4.63
891 892 1.889530 CTCGTTTTCCCTCCTCGCCT 61.890 60.000 0.00 0.00 0.00 5.52
892 893 1.448013 CTCGTTTTCCCTCCTCGCC 60.448 63.158 0.00 0.00 0.00 5.54
894 895 1.448013 GCCTCGTTTTCCCTCCTCG 60.448 63.158 0.00 0.00 0.00 4.63
896 897 0.836400 TCTGCCTCGTTTTCCCTCCT 60.836 55.000 0.00 0.00 0.00 3.69
897 898 0.036306 TTCTGCCTCGTTTTCCCTCC 59.964 55.000 0.00 0.00 0.00 4.30
898 899 1.892209 TTTCTGCCTCGTTTTCCCTC 58.108 50.000 0.00 0.00 0.00 4.30
899 900 2.358322 TTTTCTGCCTCGTTTTCCCT 57.642 45.000 0.00 0.00 0.00 4.20
900 901 3.243737 ACAATTTTCTGCCTCGTTTTCCC 60.244 43.478 0.00 0.00 0.00 3.97
903 904 3.123050 GCACAATTTTCTGCCTCGTTTT 58.877 40.909 0.00 0.00 0.00 2.43
967 973 3.250280 AGCGCGAGATAGAACGATAGAAA 59.750 43.478 12.10 0.00 41.38 2.52
1004 1010 1.154073 GGAGCGTACGGTGAGACAC 60.154 63.158 26.54 8.91 0.00 3.67
1005 1011 1.303074 AGGAGCGTACGGTGAGACA 60.303 57.895 26.54 0.00 0.00 3.41
1006 1012 1.136984 CAGGAGCGTACGGTGAGAC 59.863 63.158 26.54 10.09 0.00 3.36
1088 1095 4.303993 AACCCCACGAACGGACGG 62.304 66.667 8.20 0.00 37.61 4.79
1089 1096 2.735857 GAACCCCACGAACGGACG 60.736 66.667 0.00 2.26 39.31 4.79
1090 1097 1.957695 GTGAACCCCACGAACGGAC 60.958 63.158 0.00 0.00 35.86 4.79
1091 1098 2.422591 GTGAACCCCACGAACGGA 59.577 61.111 0.00 0.00 35.86 4.69
1350 1363 1.003839 TAAGGCAGCGGGTTCTGTG 60.004 57.895 0.00 0.00 36.49 3.66
1365 1378 8.033626 ACGGACAGGAGTAGTTTTAATTCTAAG 58.966 37.037 0.00 0.00 0.00 2.18
1367 1380 7.177216 TCACGGACAGGAGTAGTTTTAATTCTA 59.823 37.037 0.00 0.00 0.00 2.10
1369 1382 6.161381 TCACGGACAGGAGTAGTTTTAATTC 58.839 40.000 0.00 0.00 0.00 2.17
1378 1391 1.746220 CCTTCTCACGGACAGGAGTAG 59.254 57.143 0.00 0.00 32.93 2.57
1380 1393 0.112606 TCCTTCTCACGGACAGGAGT 59.887 55.000 0.00 0.00 32.01 3.85
1422 1436 1.972872 ATTTCATTGCTCCCGGCTAG 58.027 50.000 0.00 0.00 42.39 3.42
1444 1458 2.289002 CCATTGCACGAATAGAAGGAGC 59.711 50.000 0.00 0.00 0.00 4.70
1462 1490 4.396166 CGCTTCATCTACCAGAAAAACCAT 59.604 41.667 0.00 0.00 0.00 3.55
1473 1501 0.736325 ACACGCACGCTTCATCTACC 60.736 55.000 0.00 0.00 0.00 3.18
1522 1550 3.880490 AGTGGCAAAACATCGAACACTTA 59.120 39.130 0.00 0.00 34.36 2.24
1542 1570 2.447443 TGGACGACAGCATCTCTAAGT 58.553 47.619 0.00 0.00 0.00 2.24
1584 1612 7.503566 TCATCAAAACTCTCTTCAAGTTCCAAT 59.496 33.333 0.00 0.00 35.96 3.16
1654 1682 1.462283 CAGTCATCGTTGCAAGGACAG 59.538 52.381 23.02 17.93 0.00 3.51
1658 1686 1.133253 CGCAGTCATCGTTGCAAGG 59.867 57.895 12.91 12.91 40.28 3.61
1667 1695 1.600957 CCATTCCATCACGCAGTCATC 59.399 52.381 0.00 0.00 41.61 2.92
1676 1704 6.183360 GCGAAACATAAAAACCATTCCATCAC 60.183 38.462 0.00 0.00 0.00 3.06
1678 1706 5.866633 TGCGAAACATAAAAACCATTCCATC 59.133 36.000 0.00 0.00 0.00 3.51
1691 1719 4.155644 TGCATCTCACATTGCGAAACATAA 59.844 37.500 0.00 0.00 41.80 1.90
1726 1755 9.087424 TCACATTTCGTTATCATGAGAAGTAAG 57.913 33.333 2.29 0.00 0.00 2.34
1730 1759 7.531280 ACTCACATTTCGTTATCATGAGAAG 57.469 36.000 2.29 0.00 36.45 2.85
1731 1760 7.201435 CGAACTCACATTTCGTTATCATGAGAA 60.201 37.037 0.09 0.00 40.77 2.87
1732 1761 6.253512 CGAACTCACATTTCGTTATCATGAGA 59.746 38.462 0.09 0.00 40.77 3.27
1734 1763 6.331170 CGAACTCACATTTCGTTATCATGA 57.669 37.500 0.00 0.00 40.77 3.07
1744 1773 5.049405 ACATCCAGAAACGAACTCACATTTC 60.049 40.000 0.00 0.00 0.00 2.17
1763 1792 7.654022 TCCCATTTTCAACCTAATAACATCC 57.346 36.000 0.00 0.00 0.00 3.51
1764 1793 8.197439 CCTTCCCATTTTCAACCTAATAACATC 58.803 37.037 0.00 0.00 0.00 3.06
1768 1797 5.423931 GGCCTTCCCATTTTCAACCTAATAA 59.576 40.000 0.00 0.00 0.00 1.40
1813 1842 3.034635 AGTGTTTGGGTTTATGGTGCAA 58.965 40.909 0.00 0.00 0.00 4.08
1837 1866 0.742990 GATCGGGAATTGCCACGACA 60.743 55.000 16.96 0.00 40.48 4.35
1865 1894 4.829064 TGCTTAATTTTGAGAGCACGTT 57.171 36.364 0.00 0.00 39.97 3.99
1879 1908 2.744202 CGTCTGCTTGGACTTGCTTAAT 59.256 45.455 0.00 0.00 34.38 1.40
1939 1968 1.959282 CCTTTGCTTGCTCCTTTGACT 59.041 47.619 0.00 0.00 0.00 3.41
1975 2004 4.566759 GCTGCATCAGTAATAACACGAAGA 59.433 41.667 0.00 0.00 33.43 2.87
1982 2011 5.122239 TGTTCTGTGCTGCATCAGTAATAAC 59.878 40.000 22.42 19.65 33.43 1.89
1988 2017 1.810755 CATGTTCTGTGCTGCATCAGT 59.189 47.619 22.42 8.66 33.43 3.41
1990 2019 1.808343 GACATGTTCTGTGCTGCATCA 59.192 47.619 5.27 5.20 38.54 3.07
1991 2020 1.201998 CGACATGTTCTGTGCTGCATC 60.202 52.381 5.27 0.09 38.54 3.91
1992 2021 0.800631 CGACATGTTCTGTGCTGCAT 59.199 50.000 5.27 0.00 38.54 3.96
2167 2196 1.068748 CCTGAGAGCACAAACACATGC 60.069 52.381 0.00 0.00 42.39 4.06
2168 2197 1.068748 GCCTGAGAGCACAAACACATG 60.069 52.381 0.00 0.00 0.00 3.21
2169 2198 1.242076 GCCTGAGAGCACAAACACAT 58.758 50.000 0.00 0.00 0.00 3.21
2170 2199 0.107263 TGCCTGAGAGCACAAACACA 60.107 50.000 0.00 0.00 38.00 3.72
2214 2249 4.098416 CGGCTAGTAAAAAGATGCAAAGC 58.902 43.478 0.00 0.00 0.00 3.51
2235 2271 2.489329 AGTTGAGAAACATGGGAATGCG 59.511 45.455 0.00 0.00 0.00 4.73
2390 2427 5.593909 CCCATTAATGAATAACAGTGCCAGA 59.406 40.000 17.23 0.00 0.00 3.86
2651 2689 8.893563 AAATAAATCCACACTTAAATCCCTCA 57.106 30.769 0.00 0.00 0.00 3.86
2712 2768 9.545105 AATCTCTTCTCTATCTGCAGTATTTTG 57.455 33.333 14.67 1.58 0.00 2.44
2813 2873 9.638239 TCAAGAACAAAACCTATCAAATAATGC 57.362 29.630 0.00 0.00 0.00 3.56
3082 3142 2.523245 TGTAACCATGCCAGATTGCAA 58.477 42.857 0.00 0.00 45.84 4.08
3085 3145 6.638096 TGATATTGTAACCATGCCAGATTG 57.362 37.500 0.00 0.00 0.00 2.67
3133 3193 1.567357 TGCCTAGGCCGATGCATATA 58.433 50.000 30.81 5.05 41.09 0.86
3192 3253 1.321474 CTGGTGCACTCCACAATGTT 58.679 50.000 17.98 0.00 46.50 2.71
3194 3255 0.538057 ACCTGGTGCACTCCACAATG 60.538 55.000 17.98 3.02 46.50 2.82
3200 3261 1.302832 CCTCAACCTGGTGCACTCC 60.303 63.158 17.98 0.70 0.00 3.85
3280 3341 0.771127 AGTTGCCTAGCCCACTTTCA 59.229 50.000 0.00 0.00 0.00 2.69
3429 3490 4.949856 AGCTTTTGTTTCCTGACAAAGAGA 59.050 37.500 3.77 0.00 46.60 3.10
3432 3493 4.567959 CCAAGCTTTTGTTTCCTGACAAAG 59.432 41.667 0.00 0.00 46.60 2.77
3498 3559 8.460428 GTTCCCACGGTAATTGAAATAATACAA 58.540 33.333 0.00 0.00 0.00 2.41
3516 3577 1.247567 AAATGAAGGCAGTTCCCACG 58.752 50.000 0.00 0.00 33.75 4.94
3534 3595 1.550327 TGTCCACACAGTGCCAAAAA 58.450 45.000 0.00 0.00 31.34 1.94
3539 3600 1.102978 AACTTTGTCCACACAGTGCC 58.897 50.000 0.00 0.00 37.02 5.01
3544 3605 5.650266 ACATAGTCAAAACTTTGTCCACACA 59.350 36.000 2.30 0.00 41.93 3.72
3548 3609 7.607250 ACAAAACATAGTCAAAACTTTGTCCA 58.393 30.769 2.30 0.00 43.96 4.02
3550 3611 8.911247 AGACAAAACATAGTCAAAACTTTGTC 57.089 30.769 14.00 14.00 43.96 3.18
3679 3740 6.265422 TGCAGCTATCTTAGTATTAGCACAGA 59.735 38.462 11.66 0.00 36.33 3.41
3688 3749 8.970859 AAAAGAACATGCAGCTATCTTAGTAT 57.029 30.769 7.10 0.00 30.56 2.12
3691 3752 7.312657 TGAAAAGAACATGCAGCTATCTTAG 57.687 36.000 7.10 0.00 30.56 2.18
3693 3754 6.152323 ACATGAAAAGAACATGCAGCTATCTT 59.848 34.615 0.00 0.00 45.95 2.40
3700 3761 9.669353 GGTATATTACATGAAAAGAACATGCAG 57.331 33.333 0.00 0.00 45.95 4.41
3702 3763 7.803189 CGGGTATATTACATGAAAAGAACATGC 59.197 37.037 0.00 0.00 45.95 4.06
3705 3766 7.281324 CACCGGGTATATTACATGAAAAGAACA 59.719 37.037 6.32 0.00 0.00 3.18
3722 3783 8.905850 CCAAATTATTAAAGTAACACCGGGTAT 58.094 33.333 6.32 0.00 0.00 2.73
3727 3788 7.201282 CGTTGCCAAATTATTAAAGTAACACCG 60.201 37.037 0.00 0.00 0.00 4.94
3735 3806 6.153067 TGTGACCGTTGCCAAATTATTAAAG 58.847 36.000 0.00 0.00 0.00 1.85
3864 3935 7.602644 CCTTGTGTGCTTTATCTCTAACACTAA 59.397 37.037 5.47 0.00 38.90 2.24
3869 3945 7.298854 GTTTCCTTGTGTGCTTTATCTCTAAC 58.701 38.462 0.00 0.00 0.00 2.34
3878 3954 4.911514 AATACGTTTCCTTGTGTGCTTT 57.088 36.364 0.00 0.00 0.00 3.51
3894 3970 7.759886 TCACAGAGAGGACAAGAAATAAATACG 59.240 37.037 0.00 0.00 0.00 3.06
3895 3971 8.874816 GTCACAGAGAGGACAAGAAATAAATAC 58.125 37.037 0.00 0.00 34.22 1.89
3897 3973 7.605691 CAGTCACAGAGAGGACAAGAAATAAAT 59.394 37.037 0.00 0.00 36.50 1.40
3908 3984 1.252175 TCTGCAGTCACAGAGAGGAC 58.748 55.000 14.67 0.00 41.72 3.85
3909 3985 3.753787 TCTGCAGTCACAGAGAGGA 57.246 52.632 14.67 0.00 41.72 3.71
3917 3993 1.002430 TCCAACCTCATCTGCAGTCAC 59.998 52.381 14.67 0.00 0.00 3.67
3947 4023 6.043590 TGACATCTCCTTCCTGCACAATATAT 59.956 38.462 0.00 0.00 0.00 0.86
3983 4059 6.414694 CACAGTATTGTTGTCACACATTGAAC 59.585 38.462 0.00 0.00 33.18 3.18
4005 4081 4.454728 AAAGCTTGAAACTTCTTGCACA 57.545 36.364 0.00 0.00 0.00 4.57
4006 4082 6.697019 TGAATAAAGCTTGAAACTTCTTGCAC 59.303 34.615 0.00 0.00 0.00 4.57
4018 4094 7.870826 TGAAATTCGAGTTGAATAAAGCTTGA 58.129 30.769 6.02 0.00 46.65 3.02
4021 4097 8.116753 CGTATGAAATTCGAGTTGAATAAAGCT 58.883 33.333 6.02 0.00 46.65 3.74
4048 4124 6.538381 CCAAATTTTGTCTTGCCTTGTAAGTT 59.462 34.615 8.26 0.00 0.00 2.66
4074 4150 7.555554 CCTCAAAGACAAATTCTGATGGTCTAT 59.444 37.037 0.00 0.00 37.82 1.98
4087 4163 6.105397 ACAATTGATGCCTCAAAGACAAAT 57.895 33.333 13.59 0.00 44.29 2.32
4185 4262 5.545588 TCCAAGTTATGATGCAGAGCTATC 58.454 41.667 0.00 0.00 0.00 2.08
4188 4265 3.920231 TCCAAGTTATGATGCAGAGCT 57.080 42.857 0.00 0.00 0.00 4.09
4190 4267 4.970711 AGGATCCAAGTTATGATGCAGAG 58.029 43.478 15.82 0.00 0.00 3.35
4275 4353 8.696175 CCGTTTGTTACTTCAAAAATGGATTAC 58.304 33.333 0.00 0.00 38.71 1.89
4276 4354 8.414778 ACCGTTTGTTACTTCAAAAATGGATTA 58.585 29.630 11.21 0.00 38.71 1.75
4277 4355 7.269316 ACCGTTTGTTACTTCAAAAATGGATT 58.731 30.769 11.21 0.00 38.71 3.01
4282 4360 7.499895 TCTCCTACCGTTTGTTACTTCAAAAAT 59.500 33.333 0.00 0.00 38.71 1.82
4328 4407 8.976986 ATGATTTGCAGATAACTTTTGTCTTC 57.023 30.769 0.00 0.00 0.00 2.87
4379 4458 1.939980 AGTTGTAGACTCCTGGGTCC 58.060 55.000 10.50 0.00 36.95 4.46
4388 4467 7.399191 TGTTGGAGTATATTGGAGTTGTAGACT 59.601 37.037 0.00 0.00 42.70 3.24
4389 4468 7.553334 TGTTGGAGTATATTGGAGTTGTAGAC 58.447 38.462 0.00 0.00 0.00 2.59
4394 4473 8.279970 TCAAATGTTGGAGTATATTGGAGTTG 57.720 34.615 0.00 0.00 0.00 3.16
4432 4511 9.500785 TCAGAATTTCACACTCACACAATAATA 57.499 29.630 0.00 0.00 0.00 0.98
4433 4512 8.394971 TCAGAATTTCACACTCACACAATAAT 57.605 30.769 0.00 0.00 0.00 1.28
4434 4513 7.800155 TCAGAATTTCACACTCACACAATAA 57.200 32.000 0.00 0.00 0.00 1.40
4435 4514 7.800155 TTCAGAATTTCACACTCACACAATA 57.200 32.000 0.00 0.00 0.00 1.90
4436 4515 6.698008 TTCAGAATTTCACACTCACACAAT 57.302 33.333 0.00 0.00 0.00 2.71
4437 4516 6.698008 ATTCAGAATTTCACACTCACACAA 57.302 33.333 0.00 0.00 0.00 3.33
4438 4517 6.698008 AATTCAGAATTTCACACTCACACA 57.302 33.333 2.20 0.00 0.00 3.72
4439 4518 9.334693 GATTAATTCAGAATTTCACACTCACAC 57.665 33.333 13.71 0.00 32.38 3.82
4440 4519 8.514594 GGATTAATTCAGAATTTCACACTCACA 58.485 33.333 13.71 0.00 32.38 3.58
4441 4520 7.970614 GGGATTAATTCAGAATTTCACACTCAC 59.029 37.037 13.71 0.00 32.38 3.51
4442 4521 7.669304 TGGGATTAATTCAGAATTTCACACTCA 59.331 33.333 13.71 5.49 32.38 3.41
4443 4522 8.055279 TGGGATTAATTCAGAATTTCACACTC 57.945 34.615 13.71 0.36 32.38 3.51
4444 4523 7.123247 CCTGGGATTAATTCAGAATTTCACACT 59.877 37.037 13.71 0.00 32.38 3.55
4445 4524 7.122650 TCCTGGGATTAATTCAGAATTTCACAC 59.877 37.037 13.71 7.28 32.38 3.82
4446 4525 7.181361 TCCTGGGATTAATTCAGAATTTCACA 58.819 34.615 13.71 11.99 32.38 3.58
4447 4526 7.340487 ACTCCTGGGATTAATTCAGAATTTCAC 59.660 37.037 13.71 8.10 32.38 3.18
4448 4527 7.413446 ACTCCTGGGATTAATTCAGAATTTCA 58.587 34.615 13.71 2.18 32.38 2.69
4449 4528 7.888250 ACTCCTGGGATTAATTCAGAATTTC 57.112 36.000 13.71 6.39 32.38 2.17
4450 4529 7.780271 GGTACTCCTGGGATTAATTCAGAATTT 59.220 37.037 13.71 0.00 32.38 1.82
4451 4530 7.290813 GGTACTCCTGGGATTAATTCAGAATT 58.709 38.462 13.06 13.06 34.90 2.17
4452 4531 6.183361 GGGTACTCCTGGGATTAATTCAGAAT 60.183 42.308 16.53 0.00 0.00 2.40
4453 4532 5.132144 GGGTACTCCTGGGATTAATTCAGAA 59.868 44.000 16.53 0.00 0.00 3.02
4454 4533 4.658901 GGGTACTCCTGGGATTAATTCAGA 59.341 45.833 16.53 2.08 0.00 3.27
4455 4534 4.202472 GGGGTACTCCTGGGATTAATTCAG 60.202 50.000 3.84 10.86 35.33 3.02
4456 4535 3.720002 GGGGTACTCCTGGGATTAATTCA 59.280 47.826 3.84 0.00 35.33 2.57
4457 4536 3.074094 GGGGGTACTCCTGGGATTAATTC 59.926 52.174 12.68 0.00 35.33 2.17
4458 4537 3.061369 GGGGGTACTCCTGGGATTAATT 58.939 50.000 12.68 0.00 35.33 1.40
4459 4538 2.255649 AGGGGGTACTCCTGGGATTAAT 59.744 50.000 12.68 0.00 32.53 1.40
4460 4539 1.660430 AGGGGGTACTCCTGGGATTAA 59.340 52.381 12.68 0.00 32.53 1.40
4461 4540 1.336347 AGGGGGTACTCCTGGGATTA 58.664 55.000 12.68 0.00 32.53 1.75
4462 4541 1.336347 TAGGGGGTACTCCTGGGATT 58.664 55.000 12.68 0.00 35.92 3.01
4463 4542 1.336347 TTAGGGGGTACTCCTGGGAT 58.664 55.000 12.68 0.00 35.92 3.85
4464 4543 1.103811 TTTAGGGGGTACTCCTGGGA 58.896 55.000 12.68 0.00 35.92 4.37
4465 4544 1.774856 CATTTAGGGGGTACTCCTGGG 59.225 57.143 12.68 0.00 35.92 4.45
4466 4545 2.438392 GTCATTTAGGGGGTACTCCTGG 59.562 54.545 12.68 2.87 35.92 4.45
4467 4546 3.385115 AGTCATTTAGGGGGTACTCCTG 58.615 50.000 12.68 1.13 35.92 3.86
4468 4547 3.797671 AGTCATTTAGGGGGTACTCCT 57.202 47.619 12.68 12.16 38.36 3.69
4469 4548 3.181468 CGAAGTCATTTAGGGGGTACTCC 60.181 52.174 1.90 1.90 0.00 3.85
4470 4549 3.181468 CCGAAGTCATTTAGGGGGTACTC 60.181 52.174 0.00 0.00 0.00 2.59
4471 4550 2.770232 CCGAAGTCATTTAGGGGGTACT 59.230 50.000 0.00 0.00 0.00 2.73
4472 4551 2.502947 ACCGAAGTCATTTAGGGGGTAC 59.497 50.000 0.00 0.00 36.00 3.34
4535 4624 2.473609 CCTCGACGACGACAATTTTCAA 59.526 45.455 5.75 0.00 43.81 2.69
4547 4636 1.935933 ATGTAAATGGCCTCGACGAC 58.064 50.000 3.32 0.00 0.00 4.34
4550 4639 7.012989 AGGTTATAAAATGTAAATGGCCTCGAC 59.987 37.037 3.32 0.00 0.00 4.20
4551 4640 7.057894 AGGTTATAAAATGTAAATGGCCTCGA 58.942 34.615 3.32 0.00 0.00 4.04
4552 4641 7.272037 AGGTTATAAAATGTAAATGGCCTCG 57.728 36.000 3.32 0.00 0.00 4.63
4553 4642 9.884636 AAAAGGTTATAAAATGTAAATGGCCTC 57.115 29.630 3.32 0.00 0.00 4.70
4554 4643 9.884636 GAAAAGGTTATAAAATGTAAATGGCCT 57.115 29.630 3.32 0.00 0.00 5.19
4641 4932 9.646522 AGGTACTCCAAAATAGATTGCATATTT 57.353 29.630 0.00 0.00 34.97 1.40
4686 5039 8.443937 GTGTGTTGTACCAATTTATCTCTCTTC 58.556 37.037 0.00 0.00 0.00 2.87
4689 5042 7.172532 TGTGTGTGTTGTACCAATTTATCTCTC 59.827 37.037 0.00 0.00 0.00 3.20
4730 5083 3.795688 ATGTGTTCCCACTTCTCATGT 57.204 42.857 0.00 0.00 42.34 3.21
4763 5116 4.186856 CCCGTGGCACAAAAGATATTTT 57.813 40.909 19.09 0.00 44.16 1.82
4793 5146 0.831307 GATTTCTCACCTAGGCCCGT 59.169 55.000 9.30 0.00 0.00 5.28
4813 5166 0.947180 CAGCAACCAAGCAACATGGC 60.947 55.000 0.00 0.00 41.89 4.40
4821 5174 0.947180 CACAATGCCAGCAACCAAGC 60.947 55.000 0.00 0.00 0.00 4.01
4822 5175 0.675083 TCACAATGCCAGCAACCAAG 59.325 50.000 0.00 0.00 0.00 3.61
4823 5176 1.117994 TTCACAATGCCAGCAACCAA 58.882 45.000 0.00 0.00 0.00 3.67
4824 5177 1.001068 CATTCACAATGCCAGCAACCA 59.999 47.619 0.00 0.00 31.20 3.67
4825 5178 1.717194 CATTCACAATGCCAGCAACC 58.283 50.000 0.00 0.00 31.20 3.77
4834 5187 4.882427 AGATGAGAAGAGGCATTCACAATG 59.118 41.667 6.67 0.00 41.85 2.82
4835 5188 5.113446 AGATGAGAAGAGGCATTCACAAT 57.887 39.130 6.67 0.00 34.24 2.71
4836 5189 4.564782 AGATGAGAAGAGGCATTCACAA 57.435 40.909 6.67 0.00 34.24 3.33
4837 5190 4.564782 AAGATGAGAAGAGGCATTCACA 57.435 40.909 5.39 5.39 34.88 3.58
4838 5191 4.813697 GGTAAGATGAGAAGAGGCATTCAC 59.186 45.833 5.44 0.22 0.00 3.18
4839 5192 4.471025 TGGTAAGATGAGAAGAGGCATTCA 59.529 41.667 5.44 0.00 0.00 2.57
4840 5193 4.813697 GTGGTAAGATGAGAAGAGGCATTC 59.186 45.833 0.00 0.00 0.00 2.67
4841 5194 4.225942 TGTGGTAAGATGAGAAGAGGCATT 59.774 41.667 0.00 0.00 0.00 3.56
4842 5195 3.776969 TGTGGTAAGATGAGAAGAGGCAT 59.223 43.478 0.00 0.00 0.00 4.40
4843 5196 3.173151 TGTGGTAAGATGAGAAGAGGCA 58.827 45.455 0.00 0.00 0.00 4.75
4844 5197 3.895232 TGTGGTAAGATGAGAAGAGGC 57.105 47.619 0.00 0.00 0.00 4.70
4845 5198 5.982356 TCAATGTGGTAAGATGAGAAGAGG 58.018 41.667 0.00 0.00 0.00 3.69
4846 5199 8.396390 CAAATCAATGTGGTAAGATGAGAAGAG 58.604 37.037 0.00 0.00 0.00 2.85
4847 5200 8.102676 TCAAATCAATGTGGTAAGATGAGAAGA 58.897 33.333 0.00 0.00 0.00 2.87
4848 5201 8.272545 TCAAATCAATGTGGTAAGATGAGAAG 57.727 34.615 0.00 0.00 0.00 2.85
4849 5202 8.812513 ATCAAATCAATGTGGTAAGATGAGAA 57.187 30.769 0.00 0.00 0.00 2.87
4852 5205 9.850198 TGATATCAAATCAATGTGGTAAGATGA 57.150 29.630 1.98 0.00 0.00 2.92
4853 5206 9.888878 GTGATATCAAATCAATGTGGTAAGATG 57.111 33.333 7.07 0.00 0.00 2.90
4854 5207 9.631257 TGTGATATCAAATCAATGTGGTAAGAT 57.369 29.630 7.07 0.00 0.00 2.40
4855 5208 9.460019 TTGTGATATCAAATCAATGTGGTAAGA 57.540 29.630 7.07 0.00 0.00 2.10
4885 5238 9.964253 GATTATCGATTGTGATGATGTGTATTC 57.036 33.333 1.71 0.00 0.00 1.75
4899 5252 7.233553 TGAGGAGTAGATTGGATTATCGATTGT 59.766 37.037 1.71 0.00 0.00 2.71
4927 5280 8.711457 CCCTATTTTCTGCAAAAATTACTGTTG 58.289 33.333 18.28 0.00 35.10 3.33
4930 5283 6.818142 CCCCCTATTTTCTGCAAAAATTACTG 59.182 38.462 18.28 10.46 35.10 2.74
4936 5289 5.896073 TTTCCCCCTATTTTCTGCAAAAA 57.104 34.783 8.54 8.54 35.10 1.94
4940 5293 6.351796 GCTAATTTTTCCCCCTATTTTCTGCA 60.352 38.462 0.00 0.00 0.00 4.41
4942 5295 7.041721 GTGCTAATTTTTCCCCCTATTTTCTG 58.958 38.462 0.00 0.00 0.00 3.02
4951 5313 2.170397 CCATGGTGCTAATTTTTCCCCC 59.830 50.000 2.57 0.00 0.00 5.40
4952 5314 3.103742 TCCATGGTGCTAATTTTTCCCC 58.896 45.455 12.58 0.00 0.00 4.81
4953 5315 5.598417 AGTATCCATGGTGCTAATTTTTCCC 59.402 40.000 12.58 0.00 0.00 3.97
4954 5316 6.715347 AGTATCCATGGTGCTAATTTTTCC 57.285 37.500 12.58 0.00 0.00 3.13
4958 5320 5.951747 ACACAAGTATCCATGGTGCTAATTT 59.048 36.000 12.58 0.00 32.89 1.82
4959 5321 5.357878 CACACAAGTATCCATGGTGCTAATT 59.642 40.000 12.58 5.26 32.89 1.40
4960 5322 4.883585 CACACAAGTATCCATGGTGCTAAT 59.116 41.667 12.58 0.00 32.89 1.73
4970 5332 3.169908 TCCTAGCACACACAAGTATCCA 58.830 45.455 0.00 0.00 0.00 3.41
4975 5337 3.614399 GCTCCTAGCACACACAAGT 57.386 52.632 0.00 0.00 41.89 3.16
4997 5359 5.841810 TGGAGAAATGACCACACAAATTTC 58.158 37.500 0.00 0.00 38.65 2.17
5004 5366 5.649782 AATTCATGGAGAAATGACCACAC 57.350 39.130 0.00 0.00 40.22 3.82
5005 5367 6.295236 GGAAAATTCATGGAGAAATGACCACA 60.295 38.462 0.00 0.00 40.22 4.17
5016 5378 4.646040 TGTGCTATGGGAAAATTCATGGAG 59.354 41.667 0.00 0.00 0.00 3.86
5019 5381 5.587388 AGTGTGCTATGGGAAAATTCATG 57.413 39.130 0.00 0.00 0.00 3.07
5020 5382 5.716228 TCAAGTGTGCTATGGGAAAATTCAT 59.284 36.000 0.00 0.00 0.00 2.57
5025 5387 3.073798 TCCTCAAGTGTGCTATGGGAAAA 59.926 43.478 0.00 0.00 0.00 2.29
5029 5391 2.437281 AGATCCTCAAGTGTGCTATGGG 59.563 50.000 0.00 0.00 0.00 4.00
5042 5404 2.559698 TTTTGCACCGAAGATCCTCA 57.440 45.000 0.00 0.00 0.00 3.86
5063 5425 7.977789 AAAGGTTGAAAAACATCTGTTTGTT 57.022 28.000 8.94 6.14 46.47 2.83
5064 5426 7.659390 TCAAAAGGTTGAAAAACATCTGTTTGT 59.341 29.630 8.94 3.68 42.18 2.83
5065 5427 8.027440 TCAAAAGGTTGAAAAACATCTGTTTG 57.973 30.769 8.94 0.00 42.18 2.93
5091 5453 5.502220 GCGCTGACATGAACAATTTGTTTTT 60.502 36.000 15.54 4.49 41.28 1.94
5092 5454 4.025813 GCGCTGACATGAACAATTTGTTTT 60.026 37.500 15.54 4.82 41.28 2.43
5096 5458 2.663808 TGCGCTGACATGAACAATTTG 58.336 42.857 9.73 0.00 0.00 2.32
5097 5459 3.367992 TTGCGCTGACATGAACAATTT 57.632 38.095 9.73 0.00 0.00 1.82
5108 5482 3.126858 TGATGGTTCTAAATTGCGCTGAC 59.873 43.478 9.73 0.00 0.00 3.51
5109 5483 3.126858 GTGATGGTTCTAAATTGCGCTGA 59.873 43.478 9.73 0.00 0.00 4.26
5111 5485 3.347216 AGTGATGGTTCTAAATTGCGCT 58.653 40.909 9.73 0.00 0.00 5.92
5113 5487 7.277981 AGTTAGTAGTGATGGTTCTAAATTGCG 59.722 37.037 0.00 0.00 0.00 4.85
5122 5496 7.095187 CCTTTGTGAAGTTAGTAGTGATGGTTC 60.095 40.741 0.00 0.00 0.00 3.62
5199 5888 2.886523 TGCAAGACAGAAAACCTGATGG 59.113 45.455 0.00 0.00 45.78 3.51
5211 5905 3.842732 TGCATCAAGATTGCAAGACAG 57.157 42.857 4.94 0.00 35.46 3.51
5224 5918 1.340889 GTTGGTGGCTTCTTGCATCAA 59.659 47.619 0.00 0.00 45.15 2.57
5233 5927 4.846779 TCAAACTATTGTTGGTGGCTTC 57.153 40.909 0.00 0.00 37.79 3.86
5290 5984 1.948611 GCGGTGGCATTTGAGTTAGGA 60.949 52.381 0.00 0.00 39.62 2.94
5309 6003 2.154462 AGAGGGTTATGCGCATAATGC 58.846 47.619 37.35 27.26 40.69 3.56
5312 6006 3.552132 TGAAGAGGGTTATGCGCATAA 57.448 42.857 33.26 33.26 0.00 1.90
5313 6007 3.769739 ATGAAGAGGGTTATGCGCATA 57.230 42.857 25.78 25.78 0.00 3.14
5316 6010 3.467803 ACTTATGAAGAGGGTTATGCGC 58.532 45.455 0.00 0.00 0.00 6.09
5318 6012 5.307196 TCCCTACTTATGAAGAGGGTTATGC 59.693 44.000 16.65 0.00 42.15 3.14
5321 6015 7.817910 TTTTCCCTACTTATGAAGAGGGTTA 57.182 36.000 16.65 8.80 42.15 2.85


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

AutoCloner maintained by Alex Coulton.