Multiple sequence alignment - TraesCS1B01G108100

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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 TraesCS1B01G108100 chr1B 100.000 5336 0 0 1 5336 120394933 120400268 0.000000e+00 9854.0
1 TraesCS1B01G108100 chr1B 98.611 792 10 1 1 791 348477588 348478379 0.000000e+00 1400.0
2 TraesCS1B01G108100 chr1B 87.919 149 14 4 4865 5012 52057800 52057945 7.100000e-39 172.0
3 TraesCS1B01G108100 chr1B 100.000 35 0 0 1863 1897 120396631 120396665 1.240000e-06 65.8
4 TraesCS1B01G108100 chr1B 100.000 35 0 0 1699 1733 120396795 120396829 1.240000e-06 65.8
5 TraesCS1B01G108100 chr1D 96.130 2687 62 12 1918 4590 76788466 76791124 0.000000e+00 4348.0
6 TraesCS1B01G108100 chr1D 92.909 1100 47 14 786 1859 76787509 76788603 0.000000e+00 1570.0
7 TraesCS1B01G108100 chr1D 92.376 564 39 3 4470 5029 76791126 76791689 0.000000e+00 800.0
8 TraesCS1B01G108100 chr1D 100.000 35 0 0 1863 1897 76788441 76788475 1.240000e-06 65.8
9 TraesCS1B01G108100 chr1A 94.436 1959 81 10 3064 5017 108073061 108074996 0.000000e+00 2988.0
10 TraesCS1B01G108100 chr1A 97.368 1140 30 0 1918 3057 108071778 108072917 0.000000e+00 1940.0
11 TraesCS1B01G108100 chr1A 91.879 825 42 10 786 1586 108070545 108071368 0.000000e+00 1129.0
12 TraesCS1B01G108100 chr1A 95.899 317 10 1 1584 1897 108071471 108071787 1.330000e-140 510.0
13 TraesCS1B01G108100 chr1A 95.092 163 6 1 1699 1859 108071753 108071915 6.860000e-64 255.0
14 TraesCS1B01G108100 chr1A 88.889 153 16 1 4865 5017 321187632 321187481 2.540000e-43 187.0
15 TraesCS1B01G108100 chr1A 85.714 154 21 1 4864 5017 22251271 22251423 1.540000e-35 161.0
16 TraesCS1B01G108100 chr1A 86.869 99 12 1 1742 1840 549129975 549129878 5.650000e-20 110.0
17 TraesCS1B01G108100 chr1A 100.000 35 0 0 1863 1897 108071589 108071623 1.240000e-06 65.8
18 TraesCS1B01G108100 chr4A 99.489 783 4 0 1 783 607376953 607376171 0.000000e+00 1424.0
19 TraesCS1B01G108100 chr4A 90.196 153 12 3 4862 5013 556840529 556840379 4.220000e-46 196.0
20 TraesCS1B01G108100 chr7A 99.613 776 3 0 1 776 84756007 84756782 0.000000e+00 1417.0
21 TraesCS1B01G108100 chr3A 99.361 782 4 1 1 781 186709688 186708907 0.000000e+00 1415.0
22 TraesCS1B01G108100 chr3A 99.485 776 4 0 1 776 457933829 457934604 0.000000e+00 1411.0
23 TraesCS1B01G108100 chr5B 99.485 776 4 0 1 776 303238380 303237605 0.000000e+00 1411.0
24 TraesCS1B01G108100 chr5A 99.357 778 5 0 1 778 503870085 503870862 0.000000e+00 1410.0
25 TraesCS1B01G108100 chr2A 99.107 784 6 1 1 783 608903209 608903992 0.000000e+00 1408.0
26 TraesCS1B01G108100 chr2A 81.538 130 19 5 5094 5221 770924752 770924626 9.450000e-18 102.0
27 TraesCS1B01G108100 chr6B 99.356 776 5 0 1 776 640911349 640912124 0.000000e+00 1406.0
28 TraesCS1B01G108100 chr4D 90.667 150 11 3 4862 5010 43054313 43054460 4.220000e-46 196.0
29 TraesCS1B01G108100 chr4D 80.147 136 22 4 5092 5225 362196470 362196602 4.400000e-16 97.1
30 TraesCS1B01G108100 chr4B 89.241 158 12 5 4862 5017 57270361 57270515 5.450000e-45 193.0
31 TraesCS1B01G108100 chrUn 87.586 145 16 2 4872 5016 1946777 1946635 3.310000e-37 167.0
32 TraesCS1B01G108100 chrUn 80.714 140 19 7 5092 5231 63027968 63027837 9.450000e-18 102.0
33 TraesCS1B01G108100 chr7D 81.022 137 22 4 5090 5224 474009896 474009762 7.310000e-19 106.0
34 TraesCS1B01G108100 chr5D 90.411 73 7 0 5092 5164 448585571 448585643 4.400000e-16 97.1
35 TraesCS1B01G108100 chr6A 79.562 137 22 6 5092 5225 491581471 491581338 5.690000e-15 93.5
36 TraesCS1B01G108100 chr6A 84.043 94 15 0 5091 5184 68509039 68508946 2.050000e-14 91.6
37 TraesCS1B01G108100 chr2D 85.542 83 8 3 5006 5086 540811949 540811869 3.420000e-12 84.2
38 TraesCS1B01G108100 chr2B 78.195 133 21 7 5094 5223 334508754 334508881 1.590000e-10 78.7
39 TraesCS1B01G108100 chr6D 79.508 122 14 10 5092 5208 10759406 10759521 5.730000e-10 76.8


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 TraesCS1B01G108100 chr1B 120394933 120400268 5335 False 3328.533333 9854 100.00000 1 5336 3 chr1B.!!$F3 5335
1 TraesCS1B01G108100 chr1B 348477588 348478379 791 False 1400.000000 1400 98.61100 1 791 1 chr1B.!!$F2 790
2 TraesCS1B01G108100 chr1D 76787509 76791689 4180 False 1695.950000 4348 95.35375 786 5029 4 chr1D.!!$F1 4243
3 TraesCS1B01G108100 chr1A 108070545 108074996 4451 False 1147.966667 2988 95.77900 786 5017 6 chr1A.!!$F2 4231
4 TraesCS1B01G108100 chr4A 607376171 607376953 782 True 1424.000000 1424 99.48900 1 783 1 chr4A.!!$R2 782
5 TraesCS1B01G108100 chr7A 84756007 84756782 775 False 1417.000000 1417 99.61300 1 776 1 chr7A.!!$F1 775
6 TraesCS1B01G108100 chr3A 186708907 186709688 781 True 1415.000000 1415 99.36100 1 781 1 chr3A.!!$R1 780
7 TraesCS1B01G108100 chr3A 457933829 457934604 775 False 1411.000000 1411 99.48500 1 776 1 chr3A.!!$F1 775
8 TraesCS1B01G108100 chr5B 303237605 303238380 775 True 1411.000000 1411 99.48500 1 776 1 chr5B.!!$R1 775
9 TraesCS1B01G108100 chr5A 503870085 503870862 777 False 1410.000000 1410 99.35700 1 778 1 chr5A.!!$F1 777
10 TraesCS1B01G108100 chr2A 608903209 608903992 783 False 1408.000000 1408 99.10700 1 783 1 chr2A.!!$F1 782
11 TraesCS1B01G108100 chr6B 640911349 640912124 775 False 1406.000000 1406 99.35600 1 776 1 chr6B.!!$F1 775

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
976 982 0.608640 CTTCCAGAACTACAGCCGGT 59.391 55.000 1.90 0.0 0.00 5.28 F
1148 1154 0.864455 GCCTCAATATCAGCAGCGTC 59.136 55.000 0.00 0.0 0.00 5.19 F
1209 1215 1.248101 TGATGTCGACGAGCAAGGGA 61.248 55.000 11.62 0.0 0.00 4.20 F
1444 1450 2.105128 CGCTGTGATCCGTCTCCC 59.895 66.667 0.00 0.0 0.00 4.30 F
2027 2162 2.259917 ACCATGTCACTCCTGATGTCA 58.740 47.619 0.00 0.0 0.00 3.58 F
3537 3810 2.578495 GAGCTTGACAACTTCATTGCG 58.422 47.619 0.00 0.0 42.62 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2142 2.235650 CTGACATCAGGAGTGACATGGT 59.764 50.000 0.00 0.0 40.2 3.55 R
2446 2582 3.066208 AGCCAGATCCCCATAGAGAAA 57.934 47.619 0.00 0.0 0.0 2.52 R
3081 3354 7.743104 AGCAATCGATAGTAGTTTCAAAGTTG 58.257 34.615 0.00 0.0 37.4 3.16 R
3398 3671 0.250234 TTGCTGCTCGTCTATGGCTT 59.750 50.000 0.00 0.0 0.0 4.35 R
3892 4165 1.071471 CCAACCTGCTCGAACCTGT 59.929 57.895 0.00 0.0 0.0 4.00 R
4593 4993 0.033504 CTGCTATTATGGTCCCGCGT 59.966 55.000 4.92 0.0 0.0 6.01 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
338 339 1.304254 TGTGTGTCCCAATGTTGACG 58.696 50.000 0.00 0.00 34.18 4.35
686 687 7.403813 TCATGACCATGAGATATCATCCCATAA 59.596 37.037 8.49 0.00 42.42 1.90
780 781 4.202030 GCACGGACACTTAGCTAGTATTCT 60.202 45.833 0.00 0.00 34.56 2.40
817 819 4.101448 GGCAGGCTGACGGTGGAT 62.101 66.667 20.86 0.00 0.00 3.41
865 867 2.618045 CCAACGGATGGTAAAAGCTCCT 60.618 50.000 0.00 0.00 44.85 3.69
888 890 3.699894 CTGCAGCCGGAGACCAGT 61.700 66.667 5.05 0.00 30.74 4.00
924 926 2.361230 GCCGCCTGCTAAACCCTT 60.361 61.111 0.00 0.00 36.87 3.95
938 940 2.076184 CCCTTCCCCATTCCGCCTA 61.076 63.158 0.00 0.00 0.00 3.93
970 976 1.295423 GCCGCCTTCCAGAACTACA 59.705 57.895 0.00 0.00 0.00 2.74
972 978 0.741221 CCGCCTTCCAGAACTACAGC 60.741 60.000 0.00 0.00 0.00 4.40
976 982 0.608640 CTTCCAGAACTACAGCCGGT 59.391 55.000 1.90 0.00 0.00 5.28
1038 1044 3.078836 CGCCGGACCCTCCCTAAA 61.079 66.667 5.05 0.00 31.13 1.85
1082 1088 2.509786 GTGCGCCCCGTCGATTAA 60.510 61.111 4.18 0.00 0.00 1.40
1143 1149 1.595109 CGCGGCCTCAATATCAGCA 60.595 57.895 0.00 0.00 0.00 4.41
1148 1154 0.864455 GCCTCAATATCAGCAGCGTC 59.136 55.000 0.00 0.00 0.00 5.19
1209 1215 1.248101 TGATGTCGACGAGCAAGGGA 61.248 55.000 11.62 0.00 0.00 4.20
1408 1414 4.228097 CGGCGAAATGCTCTGGCG 62.228 66.667 0.00 0.00 45.43 5.69
1444 1450 2.105128 CGCTGTGATCCGTCTCCC 59.895 66.667 0.00 0.00 0.00 4.30
1454 1481 2.833631 TCCGTCTCCCTTCTGTTTTC 57.166 50.000 0.00 0.00 0.00 2.29
1500 1527 4.662468 TTGCTCAATGTGTGGCTTTTTA 57.338 36.364 0.00 0.00 0.00 1.52
1511 1538 4.754618 GTGTGGCTTTTTAAAAGGGATTGG 59.245 41.667 17.68 0.00 0.00 3.16
1561 1588 4.229876 CGAAAGGGTGAGAAAAGCATTTC 58.770 43.478 6.30 6.30 44.34 2.17
1571 1598 6.145048 GTGAGAAAAGCATTTCCATTGTGAAG 59.855 38.462 10.64 0.00 44.96 3.02
1588 1720 8.908678 CATTGTGAAGTTTGTTCAGATGTATTG 58.091 33.333 0.00 0.00 0.00 1.90
1643 1775 3.691575 TGTTGGGACTTGACTTTGACAA 58.308 40.909 0.00 0.00 0.00 3.18
1658 1790 7.809331 TGACTTTGACAATCAAGATTATGTTGC 59.191 33.333 0.00 0.00 37.70 4.17
1660 1792 5.233957 TGACAATCAAGATTATGTTGCCG 57.766 39.130 0.00 0.00 0.00 5.69
1691 1826 5.747565 TGTTGAACTGAAATTAAGTCGCTG 58.252 37.500 0.00 0.00 0.00 5.18
1777 1912 3.803231 GCTAGCTCTCATCAGAACACATG 59.197 47.826 7.70 0.00 0.00 3.21
1874 2009 5.036737 CGCCTGTAAATGATTGTCAAATCC 58.963 41.667 0.00 0.00 41.40 3.01
1897 2032 8.492415 TCCAACTATATGCCTGTAAACTAGAT 57.508 34.615 0.00 0.00 0.00 1.98
1898 2033 8.934697 TCCAACTATATGCCTGTAAACTAGATT 58.065 33.333 0.00 0.00 0.00 2.40
1899 2034 9.561069 CCAACTATATGCCTGTAAACTAGATTT 57.439 33.333 0.00 0.00 0.00 2.17
2006 2141 6.113411 GCTAGAAAATTAAGTCCTGTGGCTA 58.887 40.000 0.00 0.00 0.00 3.93
2007 2142 6.598064 GCTAGAAAATTAAGTCCTGTGGCTAA 59.402 38.462 0.00 0.00 0.00 3.09
2027 2162 2.259917 ACCATGTCACTCCTGATGTCA 58.740 47.619 0.00 0.00 0.00 3.58
2038 2173 6.051074 CACTCCTGATGTCAGCACATAAATA 58.949 40.000 4.48 0.00 43.79 1.40
2083 2218 6.339587 TCACAAGTAAAAGGGCTAAAATGG 57.660 37.500 0.00 0.00 0.00 3.16
2446 2582 6.760440 ATTACTCACCTCATCATCCATTCT 57.240 37.500 0.00 0.00 0.00 2.40
2527 2663 8.764524 ACTCAACTTGTGTTATAGTCTTGATC 57.235 34.615 0.00 0.00 34.60 2.92
2855 2991 3.030291 AGTTTGCTGTGACAATTTCCCA 58.970 40.909 0.00 0.00 0.00 4.37
3215 3488 7.176690 GGGTATATTGTTGGCTTTATGCTATGT 59.823 37.037 0.00 0.00 42.39 2.29
3398 3671 3.589988 GAGTTGCCTCGAGATTCTTTCA 58.410 45.455 15.71 0.00 0.00 2.69
3494 3767 6.830873 ATTAAAAGAAGCAGATGTTGAGCT 57.169 33.333 0.00 0.00 41.03 4.09
3537 3810 2.578495 GAGCTTGACAACTTCATTGCG 58.422 47.619 0.00 0.00 42.62 4.85
3863 4136 4.534103 GGATAGAAGCCAGGGAAGATACAT 59.466 45.833 0.00 0.00 0.00 2.29
3892 4165 7.657336 AGAGAACAAAAACAACAGAAGAACAA 58.343 30.769 0.00 0.00 0.00 2.83
3924 4197 4.164796 AGCAGGTTGGATGATGATACTGAA 59.835 41.667 0.00 0.00 0.00 3.02
3974 4247 2.487775 TGGCAGGGATAGTATGGTTGT 58.512 47.619 0.00 0.00 0.00 3.32
4025 4298 1.338674 ACATCCTCGGCGATTTGACAA 60.339 47.619 11.27 0.00 0.00 3.18
4037 4310 2.049077 TTTGACAACATGCGACATGC 57.951 45.000 16.43 4.69 46.70 4.06
4367 4643 1.350351 AGAACAGTCAAGCCTGCATCT 59.650 47.619 0.00 0.00 35.83 2.90
4369 4645 1.818642 ACAGTCAAGCCTGCATCTTC 58.181 50.000 0.00 0.00 35.83 2.87
4370 4646 1.093159 CAGTCAAGCCTGCATCTTCC 58.907 55.000 0.00 0.00 0.00 3.46
4371 4647 0.694771 AGTCAAGCCTGCATCTTCCA 59.305 50.000 0.00 0.00 0.00 3.53
4372 4648 1.284198 AGTCAAGCCTGCATCTTCCAT 59.716 47.619 0.00 0.00 0.00 3.41
4373 4649 1.404391 GTCAAGCCTGCATCTTCCATG 59.596 52.381 0.00 0.00 0.00 3.66
4374 4650 0.744874 CAAGCCTGCATCTTCCATGG 59.255 55.000 4.97 4.97 0.00 3.66
4375 4651 0.333993 AAGCCTGCATCTTCCATGGT 59.666 50.000 12.58 0.00 0.00 3.55
4376 4652 0.333993 AGCCTGCATCTTCCATGGTT 59.666 50.000 12.58 0.00 0.00 3.67
4377 4653 1.565759 AGCCTGCATCTTCCATGGTTA 59.434 47.619 12.58 0.03 0.00 2.85
4378 4654 1.678101 GCCTGCATCTTCCATGGTTAC 59.322 52.381 12.58 0.00 0.00 2.50
4392 4668 5.240623 TCCATGGTTACTGTTGTCACATTTC 59.759 40.000 12.58 0.00 30.39 2.17
4393 4669 5.460646 CATGGTTACTGTTGTCACATTTCC 58.539 41.667 0.00 0.00 30.39 3.13
4394 4670 4.787551 TGGTTACTGTTGTCACATTTCCT 58.212 39.130 0.00 0.00 30.39 3.36
4395 4671 4.819630 TGGTTACTGTTGTCACATTTCCTC 59.180 41.667 0.00 0.00 30.39 3.71
4396 4672 4.215613 GGTTACTGTTGTCACATTTCCTCC 59.784 45.833 0.00 0.00 30.39 4.30
4397 4673 3.576078 ACTGTTGTCACATTTCCTCCA 57.424 42.857 0.00 0.00 30.39 3.86
4398 4674 3.897239 ACTGTTGTCACATTTCCTCCAA 58.103 40.909 0.00 0.00 30.39 3.53
4399 4675 3.632145 ACTGTTGTCACATTTCCTCCAAC 59.368 43.478 0.00 0.00 34.32 3.77
4400 4676 2.616376 TGTTGTCACATTTCCTCCAACG 59.384 45.455 0.00 0.00 36.00 4.10
4401 4677 2.616842 GTTGTCACATTTCCTCCAACGT 59.383 45.455 0.00 0.00 0.00 3.99
4402 4678 2.217750 TGTCACATTTCCTCCAACGTG 58.782 47.619 0.00 0.00 0.00 4.49
4403 4679 2.218603 GTCACATTTCCTCCAACGTGT 58.781 47.619 0.00 0.00 0.00 4.49
4404 4680 2.616842 GTCACATTTCCTCCAACGTGTT 59.383 45.455 0.00 0.00 0.00 3.32
4405 4681 2.616376 TCACATTTCCTCCAACGTGTTG 59.384 45.455 5.76 5.76 40.13 3.33
4412 4688 1.153269 TCCAACGTGTTGCTGCAGA 60.153 52.632 20.43 0.00 39.16 4.26
4647 5050 2.622942 TGAATGTTGTCCTTGGCTGAAC 59.377 45.455 0.00 0.00 0.00 3.18
4655 5058 0.310854 CCTTGGCTGAACGTGTTTCC 59.689 55.000 0.00 0.00 32.58 3.13
4656 5059 1.308998 CTTGGCTGAACGTGTTTCCT 58.691 50.000 0.00 0.00 32.58 3.36
4662 5065 2.032808 GCTGAACGTGTTTCCTCAGTTC 60.033 50.000 12.81 0.28 40.90 3.01
4663 5066 3.458189 CTGAACGTGTTTCCTCAGTTCT 58.542 45.455 4.81 0.00 41.05 3.01
4728 5131 9.179552 CTCTTGTTATGAGATCATTCGTAAGAG 57.820 37.037 15.94 15.94 39.87 2.85
4838 5241 3.657398 TCATTCATTGGGATGCTCACT 57.343 42.857 0.00 0.00 33.14 3.41
4850 5255 2.177394 TGCTCACTAAACGCAATGGA 57.823 45.000 0.00 0.00 0.00 3.41
4857 5262 5.457140 TCACTAAACGCAATGGACATTTTC 58.543 37.500 0.00 0.00 0.00 2.29
4878 5283 4.975631 TCTTTTCCGTCCTGGTTTATTGA 58.024 39.130 0.00 0.00 39.52 2.57
4882 5287 3.112263 TCCGTCCTGGTTTATTGATCCT 58.888 45.455 0.00 0.00 39.52 3.24
4885 5290 4.384208 CCGTCCTGGTTTATTGATCCTCTT 60.384 45.833 0.00 0.00 0.00 2.85
4897 5302 8.786826 TTATTGATCCTCTTCGTATTTTGTGT 57.213 30.769 0.00 0.00 0.00 3.72
4977 5382 9.559732 TTATGTCATCTGGATTCGTATTTGAAT 57.440 29.630 0.00 0.00 41.16 2.57
5025 5432 6.621394 TGCTATGTATAACTTACTCCCTCCT 58.379 40.000 0.00 0.00 0.00 3.69
5031 5438 7.399634 TGTATAACTTACTCCCTCCTTTTTGG 58.600 38.462 0.00 0.00 37.10 3.28
5032 5439 4.808767 AACTTACTCCCTCCTTTTTGGT 57.191 40.909 0.00 0.00 37.07 3.67
5033 5440 4.808767 ACTTACTCCCTCCTTTTTGGTT 57.191 40.909 0.00 0.00 37.07 3.67
5034 5441 5.138758 ACTTACTCCCTCCTTTTTGGTTT 57.861 39.130 0.00 0.00 37.07 3.27
5035 5442 6.270219 ACTTACTCCCTCCTTTTTGGTTTA 57.730 37.500 0.00 0.00 37.07 2.01
5036 5443 6.860034 ACTTACTCCCTCCTTTTTGGTTTAT 58.140 36.000 0.00 0.00 37.07 1.40
5037 5444 7.302948 ACTTACTCCCTCCTTTTTGGTTTATT 58.697 34.615 0.00 0.00 37.07 1.40
5038 5445 8.450434 ACTTACTCCCTCCTTTTTGGTTTATTA 58.550 33.333 0.00 0.00 37.07 0.98
5039 5446 8.873186 TTACTCCCTCCTTTTTGGTTTATTAG 57.127 34.615 0.00 0.00 37.07 1.73
5040 5447 6.253758 ACTCCCTCCTTTTTGGTTTATTAGG 58.746 40.000 0.00 0.00 37.07 2.69
5041 5448 5.020795 TCCCTCCTTTTTGGTTTATTAGGC 58.979 41.667 0.00 0.00 37.07 3.93
5042 5449 5.023452 CCCTCCTTTTTGGTTTATTAGGCT 58.977 41.667 0.00 0.00 37.07 4.58
5043 5450 5.483937 CCCTCCTTTTTGGTTTATTAGGCTT 59.516 40.000 0.00 0.00 37.07 4.35
5044 5451 6.666113 CCCTCCTTTTTGGTTTATTAGGCTTA 59.334 38.462 0.00 0.00 37.07 3.09
5045 5452 7.344612 CCCTCCTTTTTGGTTTATTAGGCTTAT 59.655 37.037 0.00 0.00 37.07 1.73
5046 5453 8.414003 CCTCCTTTTTGGTTTATTAGGCTTATC 58.586 37.037 0.00 0.00 37.07 1.75
5047 5454 9.190317 CTCCTTTTTGGTTTATTAGGCTTATCT 57.810 33.333 0.00 0.00 37.07 1.98
5048 5455 9.541884 TCCTTTTTGGTTTATTAGGCTTATCTT 57.458 29.630 0.00 0.00 37.07 2.40
5100 5507 8.831715 AAGCCTTATTTTCACTTGGTTTATTG 57.168 30.769 0.00 0.00 0.00 1.90
5101 5508 7.386059 AGCCTTATTTTCACTTGGTTTATTGG 58.614 34.615 0.00 0.00 0.00 3.16
5102 5509 6.092122 GCCTTATTTTCACTTGGTTTATTGGC 59.908 38.462 0.00 0.00 0.00 4.52
5103 5510 6.593770 CCTTATTTTCACTTGGTTTATTGGCC 59.406 38.462 0.00 0.00 0.00 5.36
5104 5511 4.344359 TTTTCACTTGGTTTATTGGCCC 57.656 40.909 0.00 0.00 0.00 5.80
5105 5512 2.990740 TCACTTGGTTTATTGGCCCT 57.009 45.000 0.00 0.00 0.00 5.19
5106 5513 2.802719 TCACTTGGTTTATTGGCCCTC 58.197 47.619 0.00 0.00 0.00 4.30
5107 5514 2.378547 TCACTTGGTTTATTGGCCCTCT 59.621 45.455 0.00 0.00 0.00 3.69
5108 5515 3.165071 CACTTGGTTTATTGGCCCTCTT 58.835 45.455 0.00 0.00 0.00 2.85
5109 5516 3.578282 CACTTGGTTTATTGGCCCTCTTT 59.422 43.478 0.00 0.00 0.00 2.52
5110 5517 3.578282 ACTTGGTTTATTGGCCCTCTTTG 59.422 43.478 0.00 0.00 0.00 2.77
5111 5518 3.252554 TGGTTTATTGGCCCTCTTTGT 57.747 42.857 0.00 0.00 0.00 2.83
5112 5519 4.390129 TGGTTTATTGGCCCTCTTTGTA 57.610 40.909 0.00 0.00 0.00 2.41
5113 5520 4.941713 TGGTTTATTGGCCCTCTTTGTAT 58.058 39.130 0.00 0.00 0.00 2.29
5114 5521 5.337788 TGGTTTATTGGCCCTCTTTGTATT 58.662 37.500 0.00 0.00 0.00 1.89
5115 5522 5.782845 TGGTTTATTGGCCCTCTTTGTATTT 59.217 36.000 0.00 0.00 0.00 1.40
5116 5523 6.271159 TGGTTTATTGGCCCTCTTTGTATTTT 59.729 34.615 0.00 0.00 0.00 1.82
5117 5524 6.593770 GGTTTATTGGCCCTCTTTGTATTTTG 59.406 38.462 0.00 0.00 0.00 2.44
5118 5525 6.926630 TTATTGGCCCTCTTTGTATTTTGT 57.073 33.333 0.00 0.00 0.00 2.83
5119 5526 4.599047 TTGGCCCTCTTTGTATTTTGTG 57.401 40.909 0.00 0.00 0.00 3.33
5120 5527 2.298729 TGGCCCTCTTTGTATTTTGTGC 59.701 45.455 0.00 0.00 0.00 4.57
5121 5528 2.353704 GGCCCTCTTTGTATTTTGTGCC 60.354 50.000 0.00 0.00 0.00 5.01
5122 5529 2.298729 GCCCTCTTTGTATTTTGTGCCA 59.701 45.455 0.00 0.00 0.00 4.92
5123 5530 3.244044 GCCCTCTTTGTATTTTGTGCCAA 60.244 43.478 0.00 0.00 0.00 4.52
5124 5531 4.742138 GCCCTCTTTGTATTTTGTGCCAAA 60.742 41.667 0.00 0.00 0.00 3.28
5125 5532 5.550290 CCCTCTTTGTATTTTGTGCCAAAT 58.450 37.500 1.89 0.00 0.00 2.32
5126 5533 5.997129 CCCTCTTTGTATTTTGTGCCAAATT 59.003 36.000 1.89 2.10 0.00 1.82
5127 5534 6.486320 CCCTCTTTGTATTTTGTGCCAAATTT 59.514 34.615 1.89 0.00 0.00 1.82
5128 5535 7.013178 CCCTCTTTGTATTTTGTGCCAAATTTT 59.987 33.333 1.89 0.00 0.00 1.82
5129 5536 7.856894 CCTCTTTGTATTTTGTGCCAAATTTTG 59.143 33.333 1.99 1.99 0.00 2.44
5130 5537 8.498054 TCTTTGTATTTTGTGCCAAATTTTGA 57.502 26.923 10.72 0.00 0.00 2.69
5131 5538 9.118300 TCTTTGTATTTTGTGCCAAATTTTGAT 57.882 25.926 10.72 0.00 0.00 2.57
5132 5539 9.384682 CTTTGTATTTTGTGCCAAATTTTGATC 57.615 29.630 10.72 3.09 0.00 2.92
5133 5540 7.114882 TGTATTTTGTGCCAAATTTTGATCG 57.885 32.000 10.72 0.00 0.00 3.69
5134 5541 6.703607 TGTATTTTGTGCCAAATTTTGATCGT 59.296 30.769 10.72 0.00 0.00 3.73
5135 5542 7.867909 TGTATTTTGTGCCAAATTTTGATCGTA 59.132 29.630 10.72 0.00 0.00 3.43
5136 5543 7.721286 ATTTTGTGCCAAATTTTGATCGTAA 57.279 28.000 10.72 0.00 0.00 3.18
5137 5544 7.539712 TTTTGTGCCAAATTTTGATCGTAAA 57.460 28.000 10.72 3.46 0.00 2.01
5138 5545 7.721286 TTTGTGCCAAATTTTGATCGTAAAT 57.279 28.000 10.72 1.02 0.00 1.40
5139 5546 7.721286 TTGTGCCAAATTTTGATCGTAAATT 57.279 28.000 10.72 10.79 36.91 1.82
5140 5547 7.721286 TGTGCCAAATTTTGATCGTAAATTT 57.279 28.000 18.21 18.21 42.72 1.82
5141 5548 8.818141 TGTGCCAAATTTTGATCGTAAATTTA 57.182 26.923 21.18 10.62 41.03 1.40
5142 5549 9.261180 TGTGCCAAATTTTGATCGTAAATTTAA 57.739 25.926 21.18 12.70 41.03 1.52
5143 5550 9.523730 GTGCCAAATTTTGATCGTAAATTTAAC 57.476 29.630 21.18 17.72 41.03 2.01
5144 5551 9.482627 TGCCAAATTTTGATCGTAAATTTAACT 57.517 25.926 21.18 6.44 41.03 2.24
5165 5572 6.267496 ACTAACAAACTGTTAATCCATGGC 57.733 37.500 6.96 0.00 41.70 4.40
5166 5573 5.772672 ACTAACAAACTGTTAATCCATGGCA 59.227 36.000 6.96 0.00 41.70 4.92
5167 5574 5.743636 AACAAACTGTTAATCCATGGCAT 57.256 34.783 6.96 0.00 39.09 4.40
5168 5575 6.849085 AACAAACTGTTAATCCATGGCATA 57.151 33.333 6.96 0.00 39.09 3.14
5169 5576 6.207691 ACAAACTGTTAATCCATGGCATAC 57.792 37.500 6.96 3.08 0.00 2.39
5170 5577 5.714333 ACAAACTGTTAATCCATGGCATACA 59.286 36.000 6.96 7.66 0.00 2.29
5171 5578 6.210385 ACAAACTGTTAATCCATGGCATACAA 59.790 34.615 6.96 0.00 0.00 2.41
5172 5579 6.849085 AACTGTTAATCCATGGCATACAAA 57.151 33.333 6.96 0.00 0.00 2.83
5173 5580 6.849085 ACTGTTAATCCATGGCATACAAAA 57.151 33.333 6.96 0.00 0.00 2.44
5174 5581 7.422465 ACTGTTAATCCATGGCATACAAAAT 57.578 32.000 6.96 0.00 0.00 1.82
5175 5582 7.850193 ACTGTTAATCCATGGCATACAAAATT 58.150 30.769 6.96 1.39 0.00 1.82
5176 5583 8.976353 ACTGTTAATCCATGGCATACAAAATTA 58.024 29.630 6.96 0.34 0.00 1.40
5177 5584 9.985730 CTGTTAATCCATGGCATACAAAATTAT 57.014 29.630 6.96 0.00 0.00 1.28
5178 5585 9.761504 TGTTAATCCATGGCATACAAAATTATG 57.238 29.630 6.96 0.00 33.25 1.90
5179 5586 9.762933 GTTAATCCATGGCATACAAAATTATGT 57.237 29.630 6.96 0.00 37.32 2.29
5180 5587 9.979578 TTAATCCATGGCATACAAAATTATGTC 57.020 29.630 6.96 0.00 35.06 3.06
5181 5588 7.600231 ATCCATGGCATACAAAATTATGTCA 57.400 32.000 6.96 0.22 45.68 3.58
5187 5594 7.845037 TGGCATACAAAATTATGTCATTTGGA 58.155 30.769 0.00 0.00 38.79 3.53
5188 5595 8.484575 TGGCATACAAAATTATGTCATTTGGAT 58.515 29.630 0.00 0.00 38.79 3.41
5189 5596 9.328845 GGCATACAAAATTATGTCATTTGGATT 57.671 29.630 0.00 0.00 35.85 3.01
5201 5608 7.757941 TGTCATTTGGATTTGTATCTGAACA 57.242 32.000 0.00 0.00 0.00 3.18
5202 5609 8.352137 TGTCATTTGGATTTGTATCTGAACAT 57.648 30.769 0.00 0.00 0.00 2.71
5203 5610 9.460019 TGTCATTTGGATTTGTATCTGAACATA 57.540 29.630 0.00 0.00 0.00 2.29
5204 5611 9.941664 GTCATTTGGATTTGTATCTGAACATAG 57.058 33.333 0.00 0.00 0.00 2.23
5205 5612 9.685276 TCATTTGGATTTGTATCTGAACATAGT 57.315 29.630 0.00 0.00 0.00 2.12
5209 5616 9.739276 TTGGATTTGTATCTGAACATAGTTTCT 57.261 29.630 0.00 0.00 0.00 2.52
5253 5660 8.863872 ATGTATAATTTATTCCCTCCTTTCCG 57.136 34.615 0.00 0.00 0.00 4.30
5254 5661 7.228590 TGTATAATTTATTCCCTCCTTTCCGG 58.771 38.462 0.00 0.00 0.00 5.14
5255 5662 4.603094 AATTTATTCCCTCCTTTCCGGT 57.397 40.909 0.00 0.00 0.00 5.28
5256 5663 4.603094 ATTTATTCCCTCCTTTCCGGTT 57.397 40.909 0.00 0.00 0.00 4.44
5257 5664 4.391683 TTTATTCCCTCCTTTCCGGTTT 57.608 40.909 0.00 0.00 0.00 3.27
5258 5665 5.517620 TTTATTCCCTCCTTTCCGGTTTA 57.482 39.130 0.00 0.00 0.00 2.01
5259 5666 5.720486 TTATTCCCTCCTTTCCGGTTTAT 57.280 39.130 0.00 0.00 0.00 1.40
5260 5667 4.603094 ATTCCCTCCTTTCCGGTTTATT 57.397 40.909 0.00 0.00 0.00 1.40
5261 5668 5.720486 ATTCCCTCCTTTCCGGTTTATTA 57.280 39.130 0.00 0.00 0.00 0.98
5262 5669 4.765813 TCCCTCCTTTCCGGTTTATTAG 57.234 45.455 0.00 0.00 0.00 1.73
5263 5670 4.106324 TCCCTCCTTTCCGGTTTATTAGT 58.894 43.478 0.00 0.00 0.00 2.24
5264 5671 4.162888 TCCCTCCTTTCCGGTTTATTAGTC 59.837 45.833 0.00 0.00 0.00 2.59
5265 5672 4.449131 CCTCCTTTCCGGTTTATTAGTCC 58.551 47.826 0.00 0.00 0.00 3.85
5266 5673 4.449131 CTCCTTTCCGGTTTATTAGTCCC 58.551 47.826 0.00 0.00 0.00 4.46
5267 5674 3.845398 TCCTTTCCGGTTTATTAGTCCCA 59.155 43.478 0.00 0.00 0.00 4.37
5268 5675 4.475747 TCCTTTCCGGTTTATTAGTCCCAT 59.524 41.667 0.00 0.00 0.00 4.00
5269 5676 4.820173 CCTTTCCGGTTTATTAGTCCCATC 59.180 45.833 0.00 0.00 0.00 3.51
5270 5677 5.397559 CCTTTCCGGTTTATTAGTCCCATCT 60.398 44.000 0.00 0.00 0.00 2.90
5271 5678 4.950205 TCCGGTTTATTAGTCCCATCTC 57.050 45.455 0.00 0.00 0.00 2.75
5272 5679 4.291792 TCCGGTTTATTAGTCCCATCTCA 58.708 43.478 0.00 0.00 0.00 3.27
5273 5680 4.905456 TCCGGTTTATTAGTCCCATCTCAT 59.095 41.667 0.00 0.00 0.00 2.90
5274 5681 5.368523 TCCGGTTTATTAGTCCCATCTCATT 59.631 40.000 0.00 0.00 0.00 2.57
5275 5682 6.062095 CCGGTTTATTAGTCCCATCTCATTT 58.938 40.000 0.00 0.00 0.00 2.32
5276 5683 6.546034 CCGGTTTATTAGTCCCATCTCATTTT 59.454 38.462 0.00 0.00 0.00 1.82
5277 5684 7.255139 CCGGTTTATTAGTCCCATCTCATTTTC 60.255 40.741 0.00 0.00 0.00 2.29
5278 5685 7.499232 CGGTTTATTAGTCCCATCTCATTTTCT 59.501 37.037 0.00 0.00 0.00 2.52
5279 5686 9.190317 GGTTTATTAGTCCCATCTCATTTTCTT 57.810 33.333 0.00 0.00 0.00 2.52
5281 5688 8.752005 TTATTAGTCCCATCTCATTTTCTTGG 57.248 34.615 0.00 0.00 0.00 3.61
5282 5689 4.664688 AGTCCCATCTCATTTTCTTGGT 57.335 40.909 0.00 0.00 0.00 3.67
5283 5690 5.003096 AGTCCCATCTCATTTTCTTGGTT 57.997 39.130 0.00 0.00 0.00 3.67
5284 5691 5.397360 AGTCCCATCTCATTTTCTTGGTTT 58.603 37.500 0.00 0.00 0.00 3.27
5285 5692 5.840693 AGTCCCATCTCATTTTCTTGGTTTT 59.159 36.000 0.00 0.00 0.00 2.43
5286 5693 6.327365 AGTCCCATCTCATTTTCTTGGTTTTT 59.673 34.615 0.00 0.00 0.00 1.94
5322 5729 8.477419 AGTCTTATTTTCATTTCTTTCCACCA 57.523 30.769 0.00 0.00 0.00 4.17
5323 5730 9.093458 AGTCTTATTTTCATTTCTTTCCACCAT 57.907 29.630 0.00 0.00 0.00 3.55
5331 5738 9.487790 TTTCATTTCTTTCCACCATATTTTCAC 57.512 29.630 0.00 0.00 0.00 3.18
5332 5739 8.187913 TCATTTCTTTCCACCATATTTTCACA 57.812 30.769 0.00 0.00 0.00 3.58
5333 5740 8.814931 TCATTTCTTTCCACCATATTTTCACAT 58.185 29.630 0.00 0.00 0.00 3.21
5334 5741 9.439500 CATTTCTTTCCACCATATTTTCACATT 57.561 29.630 0.00 0.00 0.00 2.71
5335 5742 9.657419 ATTTCTTTCCACCATATTTTCACATTC 57.343 29.630 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
338 339 8.575649 TCCAAGACAATCTTTTTATACCTTCC 57.424 34.615 0.00 0.00 33.78 3.46
565 566 0.033796 CCTTCTCCCACCATGCATGT 60.034 55.000 24.58 10.59 0.00 3.21
686 687 6.064060 TGACATGAGAGTCAAAGGTCATTTT 58.936 36.000 0.00 0.00 44.92 1.82
780 781 5.194432 TGCCAGTTGGTTGTAAGAAACTAA 58.806 37.500 0.00 0.00 37.57 2.24
817 819 2.523168 TGTCCACGTGGAGGAGCA 60.523 61.111 37.04 27.01 46.49 4.26
888 890 3.708544 CGGGCGGTAAACCCTGGA 61.709 66.667 0.00 0.00 46.04 3.86
924 926 1.682451 CGAGTTAGGCGGAATGGGGA 61.682 60.000 0.00 0.00 0.00 4.81
1035 1041 0.736325 GCGACGAAGAGGCTGCTTTA 60.736 55.000 0.00 0.00 0.00 1.85
1038 1044 3.349481 GAGCGACGAAGAGGCTGCT 62.349 63.158 0.00 0.00 39.30 4.24
1209 1215 1.748122 CTTGCTCCGCATGCTCCTT 60.748 57.895 17.13 0.00 38.76 3.36
1284 1290 0.440371 GCTTCTTTCGGAGCTTGACG 59.560 55.000 0.00 0.00 0.00 4.35
1500 1527 4.263025 GGCAAAACATCTCCAATCCCTTTT 60.263 41.667 0.00 0.00 0.00 2.27
1511 1538 4.092383 GCATTGACAATGGCAAAACATCTC 59.908 41.667 25.64 4.67 39.31 2.75
1561 1588 5.835257 ACATCTGAACAAACTTCACAATGG 58.165 37.500 0.00 0.00 0.00 3.16
1571 1598 9.844790 TTGATTCATCAATACATCTGAACAAAC 57.155 29.630 0.00 0.00 41.51 2.93
1643 1775 2.174639 TCCCCGGCAACATAATCTTGAT 59.825 45.455 0.00 0.00 0.00 2.57
1658 1790 0.951558 CAGTTCAACAAAGTCCCCGG 59.048 55.000 0.00 0.00 0.00 5.73
1660 1792 4.937201 ATTTCAGTTCAACAAAGTCCCC 57.063 40.909 0.00 0.00 0.00 4.81
1777 1912 6.757478 ACTTAAATTTCTAGCGGAGTTAGCTC 59.243 38.462 0.00 0.00 44.79 4.09
1941 2076 8.186163 TGTTTTGATGAGAGCTAGCATTTATTG 58.814 33.333 18.83 0.00 0.00 1.90
1948 2083 4.006780 TGTGTTTTGATGAGAGCTAGCA 57.993 40.909 18.83 0.00 0.00 3.49
1950 2085 5.220624 GCTGATGTGTTTTGATGAGAGCTAG 60.221 44.000 0.00 0.00 0.00 3.42
2006 2141 2.639347 TGACATCAGGAGTGACATGGTT 59.361 45.455 0.00 0.00 34.75 3.67
2007 2142 2.235650 CTGACATCAGGAGTGACATGGT 59.764 50.000 0.00 0.00 40.20 3.55
2027 2162 5.093849 ACGGTGGTAACTATTTATGTGCT 57.906 39.130 0.00 0.00 37.61 4.40
2038 2173 4.612264 AAACATACAGACGGTGGTAACT 57.388 40.909 0.00 0.00 37.61 2.24
2291 2427 7.282901 TGCTTCAATGCAGCAACTAGATAATTA 59.717 33.333 4.87 0.00 44.42 1.40
2389 2525 3.777106 AGGACTTTGTGCAGATCAAGA 57.223 42.857 2.54 0.00 0.00 3.02
2446 2582 3.066208 AGCCAGATCCCCATAGAGAAA 57.934 47.619 0.00 0.00 0.00 2.52
3066 3339 9.116067 GTTTCAAAGTTGCATACATATAGGGTA 57.884 33.333 0.00 0.00 0.00 3.69
3081 3354 7.743104 AGCAATCGATAGTAGTTTCAAAGTTG 58.257 34.615 0.00 0.00 37.40 3.16
3207 3480 9.388506 GATAGCAAACTCCATTATACATAGCAT 57.611 33.333 0.00 0.00 0.00 3.79
3215 3488 9.338968 AGGATAAGGATAGCAAACTCCATTATA 57.661 33.333 0.00 0.00 33.75 0.98
3398 3671 0.250234 TTGCTGCTCGTCTATGGCTT 59.750 50.000 0.00 0.00 0.00 4.35
3494 3767 1.610363 CTGGTCGCTATCCTCAGCTA 58.390 55.000 0.00 0.00 39.51 3.32
3537 3810 4.701765 TCTCTGCTGCATTCTCTATTTCC 58.298 43.478 1.31 0.00 0.00 3.13
3863 4136 6.878923 TCTTCTGTTGTTTTTGTTCTCTCTCA 59.121 34.615 0.00 0.00 0.00 3.27
3892 4165 1.071471 CCAACCTGCTCGAACCTGT 59.929 57.895 0.00 0.00 0.00 4.00
3924 4197 2.729479 CCAGTCCTCGCCTGATGCT 61.729 63.158 0.00 0.00 38.05 3.79
3974 4247 1.205655 CATGCCTCTCCTTGTCGAAGA 59.794 52.381 0.00 0.00 0.00 2.87
4025 4298 1.520120 CTCCTCGCATGTCGCATGT 60.520 57.895 17.22 0.00 42.60 3.21
4037 4310 0.173708 GTGCCTGGAACTACTCCTCG 59.826 60.000 0.00 0.00 45.64 4.63
4101 4374 3.678056 ACACTAACTGCATTCTTCGGA 57.322 42.857 0.00 0.00 0.00 4.55
4104 4377 6.545504 TCAGAAACACTAACTGCATTCTTC 57.454 37.500 0.00 0.00 30.53 2.87
4252 4525 0.527817 CAGTTGTCGCCGGTATCCTC 60.528 60.000 1.90 0.00 0.00 3.71
4253 4526 1.515954 CAGTTGTCGCCGGTATCCT 59.484 57.895 1.90 0.00 0.00 3.24
4254 4527 1.520787 CCAGTTGTCGCCGGTATCC 60.521 63.158 1.90 0.00 0.00 2.59
4367 4643 4.157849 TGTGACAACAGTAACCATGGAA 57.842 40.909 21.47 2.58 0.00 3.53
4369 4645 5.452078 AAATGTGACAACAGTAACCATGG 57.548 39.130 11.19 11.19 40.39 3.66
4370 4646 5.241506 AGGAAATGTGACAACAGTAACCATG 59.758 40.000 0.00 0.00 40.39 3.66
4371 4647 5.385198 AGGAAATGTGACAACAGTAACCAT 58.615 37.500 0.00 0.00 40.39 3.55
4372 4648 4.787551 AGGAAATGTGACAACAGTAACCA 58.212 39.130 0.00 0.00 40.39 3.67
4373 4649 4.215613 GGAGGAAATGTGACAACAGTAACC 59.784 45.833 0.00 0.00 40.39 2.85
4374 4650 4.819630 TGGAGGAAATGTGACAACAGTAAC 59.180 41.667 0.00 0.00 40.39 2.50
4375 4651 5.042463 TGGAGGAAATGTGACAACAGTAA 57.958 39.130 0.00 0.00 40.39 2.24
4376 4652 4.698201 TGGAGGAAATGTGACAACAGTA 57.302 40.909 0.00 0.00 40.39 2.74
4377 4653 3.576078 TGGAGGAAATGTGACAACAGT 57.424 42.857 0.00 0.00 40.39 3.55
4378 4654 3.303990 CGTTGGAGGAAATGTGACAACAG 60.304 47.826 0.00 0.00 40.39 3.16
4392 4668 2.121564 CTGCAGCAACACGTTGGAGG 62.122 60.000 11.64 0.00 40.05 4.30
4393 4669 1.159713 TCTGCAGCAACACGTTGGAG 61.160 55.000 9.47 0.00 44.21 3.86
4394 4670 0.746204 TTCTGCAGCAACACGTTGGA 60.746 50.000 9.47 0.00 40.74 3.53
4395 4671 0.100325 TTTCTGCAGCAACACGTTGG 59.900 50.000 9.47 0.00 40.74 3.77
4396 4672 1.847999 CTTTTCTGCAGCAACACGTTG 59.152 47.619 9.47 5.53 43.14 4.10
4397 4673 1.742831 TCTTTTCTGCAGCAACACGTT 59.257 42.857 9.47 0.00 0.00 3.99
4398 4674 1.331756 CTCTTTTCTGCAGCAACACGT 59.668 47.619 9.47 0.00 0.00 4.49
4399 4675 1.331756 ACTCTTTTCTGCAGCAACACG 59.668 47.619 9.47 0.00 0.00 4.49
4400 4676 3.366719 GAACTCTTTTCTGCAGCAACAC 58.633 45.455 9.47 0.00 0.00 3.32
4401 4677 2.032054 CGAACTCTTTTCTGCAGCAACA 59.968 45.455 9.47 0.00 0.00 3.33
4402 4678 2.032178 ACGAACTCTTTTCTGCAGCAAC 59.968 45.455 9.47 0.00 0.00 4.17
4403 4679 2.288666 ACGAACTCTTTTCTGCAGCAA 58.711 42.857 9.47 0.30 0.00 3.91
4404 4680 1.953559 ACGAACTCTTTTCTGCAGCA 58.046 45.000 9.47 0.00 0.00 4.41
4405 4681 2.287915 TCAACGAACTCTTTTCTGCAGC 59.712 45.455 9.47 0.00 0.00 5.25
4412 4688 4.965119 AACAAGCTCAACGAACTCTTTT 57.035 36.364 0.00 0.00 0.00 2.27
4475 4751 3.117625 AGCATGATGTCAGGTGGAATCAT 60.118 43.478 0.00 0.00 39.71 2.45
4566 4966 0.882042 CAACTGGCAGACTGCTTCGT 60.882 55.000 25.92 16.92 44.28 3.85
4593 4993 0.033504 CTGCTATTATGGTCCCGCGT 59.966 55.000 4.92 0.00 0.00 6.01
4598 4998 2.972713 TGACCTCCTGCTATTATGGTCC 59.027 50.000 0.00 0.00 42.15 4.46
4647 5050 5.326200 ACCTATAGAACTGAGGAAACACG 57.674 43.478 0.00 0.00 34.24 4.49
4655 5058 3.570550 CCCCTTCGACCTATAGAACTGAG 59.429 52.174 0.00 0.00 0.00 3.35
4656 5059 3.053095 ACCCCTTCGACCTATAGAACTGA 60.053 47.826 0.00 0.00 0.00 3.41
4662 5065 2.240279 CCAGACCCCTTCGACCTATAG 58.760 57.143 0.00 0.00 0.00 1.31
4663 5066 1.572415 ACCAGACCCCTTCGACCTATA 59.428 52.381 0.00 0.00 0.00 1.31
4750 5153 7.486647 CCTTCAAATATTTCTATGTGCAAGCT 58.513 34.615 0.00 0.00 0.00 3.74
4763 5166 3.840078 ACAAGCAGGGCCTTCAAATATTT 59.160 39.130 1.32 0.00 0.00 1.40
4795 5198 6.929049 TGAATGAGTAAACTTATATGCCTCGG 59.071 38.462 0.00 0.00 0.00 4.63
4807 5210 7.417116 GCATCCCAATGAATGAATGAGTAAACT 60.417 37.037 0.76 0.00 34.61 2.66
4838 5241 6.422400 GGAAAAGAAAATGTCCATTGCGTTTA 59.578 34.615 0.00 0.00 0.00 2.01
4850 5255 3.562182 ACCAGGACGGAAAAGAAAATGT 58.438 40.909 0.00 0.00 38.63 2.71
4857 5262 5.163652 GGATCAATAAACCAGGACGGAAAAG 60.164 44.000 0.00 0.00 38.63 2.27
4878 5283 7.687941 ATTTGACACAAAATACGAAGAGGAT 57.312 32.000 0.00 0.00 0.00 3.24
4882 5287 9.743057 ATCAAAATTTGACACAAAATACGAAGA 57.257 25.926 10.91 0.00 43.48 2.87
4885 5290 9.689976 ATGATCAAAATTTGACACAAAATACGA 57.310 25.926 10.91 0.00 43.48 3.43
4950 5355 8.956533 TCAAATACGAATCCAGATGACATAAA 57.043 30.769 0.00 0.00 0.00 1.40
5074 5481 9.921637 CAATAAACCAAGTGAAAATAAGGCTTA 57.078 29.630 9.79 9.79 0.00 3.09
5075 5482 7.877612 CCAATAAACCAAGTGAAAATAAGGCTT 59.122 33.333 4.58 4.58 0.00 4.35
5076 5483 7.386059 CCAATAAACCAAGTGAAAATAAGGCT 58.614 34.615 0.00 0.00 0.00 4.58
5077 5484 6.092122 GCCAATAAACCAAGTGAAAATAAGGC 59.908 38.462 0.00 0.00 0.00 4.35
5078 5485 6.593770 GGCCAATAAACCAAGTGAAAATAAGG 59.406 38.462 0.00 0.00 0.00 2.69
5079 5486 6.593770 GGGCCAATAAACCAAGTGAAAATAAG 59.406 38.462 4.39 0.00 0.00 1.73
5080 5487 6.271159 AGGGCCAATAAACCAAGTGAAAATAA 59.729 34.615 6.18 0.00 0.00 1.40
5081 5488 5.782845 AGGGCCAATAAACCAAGTGAAAATA 59.217 36.000 6.18 0.00 0.00 1.40
5082 5489 4.597075 AGGGCCAATAAACCAAGTGAAAAT 59.403 37.500 6.18 0.00 0.00 1.82
5083 5490 3.970640 AGGGCCAATAAACCAAGTGAAAA 59.029 39.130 6.18 0.00 0.00 2.29
5084 5491 3.576550 GAGGGCCAATAAACCAAGTGAAA 59.423 43.478 6.18 0.00 0.00 2.69
5085 5492 3.161866 GAGGGCCAATAAACCAAGTGAA 58.838 45.455 6.18 0.00 0.00 3.18
5086 5493 2.378547 AGAGGGCCAATAAACCAAGTGA 59.621 45.455 6.18 0.00 0.00 3.41
5087 5494 2.807676 AGAGGGCCAATAAACCAAGTG 58.192 47.619 6.18 0.00 0.00 3.16
5088 5495 3.542969 AAGAGGGCCAATAAACCAAGT 57.457 42.857 6.18 0.00 0.00 3.16
5089 5496 3.578282 ACAAAGAGGGCCAATAAACCAAG 59.422 43.478 6.18 0.00 0.00 3.61
5090 5497 3.582164 ACAAAGAGGGCCAATAAACCAA 58.418 40.909 6.18 0.00 0.00 3.67
5091 5498 3.252554 ACAAAGAGGGCCAATAAACCA 57.747 42.857 6.18 0.00 0.00 3.67
5092 5499 5.932619 AATACAAAGAGGGCCAATAAACC 57.067 39.130 6.18 0.00 0.00 3.27
5093 5500 7.117667 CACAAAATACAAAGAGGGCCAATAAAC 59.882 37.037 6.18 0.00 0.00 2.01
5094 5501 7.158021 CACAAAATACAAAGAGGGCCAATAAA 58.842 34.615 6.18 0.00 0.00 1.40
5095 5502 6.696411 CACAAAATACAAAGAGGGCCAATAA 58.304 36.000 6.18 0.00 0.00 1.40
5096 5503 5.337169 GCACAAAATACAAAGAGGGCCAATA 60.337 40.000 6.18 0.00 0.00 1.90
5097 5504 4.563374 GCACAAAATACAAAGAGGGCCAAT 60.563 41.667 6.18 0.00 0.00 3.16
5098 5505 3.244044 GCACAAAATACAAAGAGGGCCAA 60.244 43.478 6.18 0.00 0.00 4.52
5099 5506 2.298729 GCACAAAATACAAAGAGGGCCA 59.701 45.455 6.18 0.00 0.00 5.36
5100 5507 2.353704 GGCACAAAATACAAAGAGGGCC 60.354 50.000 0.00 0.00 0.00 5.80
5101 5508 2.298729 TGGCACAAAATACAAAGAGGGC 59.701 45.455 0.00 0.00 31.92 5.19
5116 5523 7.721286 AAATTTACGATCAAAATTTGGCACA 57.279 28.000 19.87 0.00 42.19 4.57
5117 5524 9.523730 GTTAAATTTACGATCAAAATTTGGCAC 57.476 29.630 24.87 18.36 43.10 5.01
5118 5525 9.482627 AGTTAAATTTACGATCAAAATTTGGCA 57.517 25.926 24.87 12.19 43.10 4.92
5139 5546 8.301002 GCCATGGATTAACAGTTTGTTAGTTAA 58.699 33.333 18.40 0.00 42.93 2.01
5140 5547 7.448777 TGCCATGGATTAACAGTTTGTTAGTTA 59.551 33.333 18.40 0.00 42.93 2.24
5141 5548 6.266558 TGCCATGGATTAACAGTTTGTTAGTT 59.733 34.615 18.40 0.00 42.93 2.24
5142 5549 5.772672 TGCCATGGATTAACAGTTTGTTAGT 59.227 36.000 18.40 0.06 42.93 2.24
5143 5550 6.266168 TGCCATGGATTAACAGTTTGTTAG 57.734 37.500 18.40 0.00 42.93 2.34
5144 5551 6.849085 ATGCCATGGATTAACAGTTTGTTA 57.151 33.333 18.40 0.00 41.45 2.41
5145 5552 5.743636 ATGCCATGGATTAACAGTTTGTT 57.256 34.783 18.40 0.00 43.88 2.83
5146 5553 5.714333 TGTATGCCATGGATTAACAGTTTGT 59.286 36.000 18.40 0.00 0.00 2.83
5147 5554 6.206395 TGTATGCCATGGATTAACAGTTTG 57.794 37.500 18.40 0.00 0.00 2.93
5148 5555 6.849085 TTGTATGCCATGGATTAACAGTTT 57.151 33.333 18.40 0.00 0.00 2.66
5149 5556 6.849085 TTTGTATGCCATGGATTAACAGTT 57.151 33.333 18.40 0.00 0.00 3.16
5150 5557 6.849085 TTTTGTATGCCATGGATTAACAGT 57.151 33.333 18.40 0.00 0.00 3.55
5151 5558 9.985730 ATAATTTTGTATGCCATGGATTAACAG 57.014 29.630 18.40 0.00 0.00 3.16
5152 5559 9.761504 CATAATTTTGTATGCCATGGATTAACA 57.238 29.630 18.40 10.63 0.00 2.41
5153 5560 9.762933 ACATAATTTTGTATGCCATGGATTAAC 57.237 29.630 18.40 7.95 35.26 2.01
5154 5561 9.979578 GACATAATTTTGTATGCCATGGATTAA 57.020 29.630 18.40 0.00 35.26 1.40
5155 5562 9.140874 TGACATAATTTTGTATGCCATGGATTA 57.859 29.630 18.40 8.28 35.26 1.75
5156 5563 8.020777 TGACATAATTTTGTATGCCATGGATT 57.979 30.769 18.40 6.09 35.26 3.01
5157 5564 7.600231 TGACATAATTTTGTATGCCATGGAT 57.400 32.000 18.40 8.90 35.26 3.41
5158 5565 7.600231 ATGACATAATTTTGTATGCCATGGA 57.400 32.000 18.40 0.31 34.45 3.41
5159 5566 8.552865 CAAATGACATAATTTTGTATGCCATGG 58.447 33.333 7.63 7.63 35.50 3.66
5160 5567 8.552865 CCAAATGACATAATTTTGTATGCCATG 58.447 33.333 1.22 0.00 35.50 3.66
5161 5568 8.484575 TCCAAATGACATAATTTTGTATGCCAT 58.515 29.630 1.22 0.00 36.48 4.40
5162 5569 7.845037 TCCAAATGACATAATTTTGTATGCCA 58.155 30.769 1.22 0.00 35.26 4.92
5163 5570 8.891671 ATCCAAATGACATAATTTTGTATGCC 57.108 30.769 1.22 0.00 35.26 4.40
5175 5582 9.460019 TGTTCAGATACAAATCCAAATGACATA 57.540 29.630 0.00 0.00 31.98 2.29
5176 5583 8.352137 TGTTCAGATACAAATCCAAATGACAT 57.648 30.769 0.00 0.00 31.98 3.06
5177 5584 7.757941 TGTTCAGATACAAATCCAAATGACA 57.242 32.000 0.00 0.00 31.98 3.58
5178 5585 9.941664 CTATGTTCAGATACAAATCCAAATGAC 57.058 33.333 0.00 0.00 31.98 3.06
5179 5586 9.685276 ACTATGTTCAGATACAAATCCAAATGA 57.315 29.630 0.00 0.00 31.98 2.57
5183 5590 9.739276 AGAAACTATGTTCAGATACAAATCCAA 57.261 29.630 0.00 0.00 31.98 3.53
5227 5634 9.953565 CGGAAAGGAGGGAATAAATTATACATA 57.046 33.333 0.00 0.00 0.00 2.29
5228 5635 7.888546 CCGGAAAGGAGGGAATAAATTATACAT 59.111 37.037 0.00 0.00 45.00 2.29
5229 5636 7.147266 ACCGGAAAGGAGGGAATAAATTATACA 60.147 37.037 9.46 0.00 45.00 2.29
5230 5637 7.229308 ACCGGAAAGGAGGGAATAAATTATAC 58.771 38.462 9.46 0.00 45.00 1.47
5231 5638 7.396906 ACCGGAAAGGAGGGAATAAATTATA 57.603 36.000 9.46 0.00 45.00 0.98
5232 5639 6.275692 ACCGGAAAGGAGGGAATAAATTAT 57.724 37.500 9.46 0.00 45.00 1.28
5233 5640 5.720486 ACCGGAAAGGAGGGAATAAATTA 57.280 39.130 9.46 0.00 45.00 1.40
5234 5641 4.603094 ACCGGAAAGGAGGGAATAAATT 57.397 40.909 9.46 0.00 45.00 1.82
5235 5642 4.603094 AACCGGAAAGGAGGGAATAAAT 57.397 40.909 9.46 0.00 45.00 1.40
5236 5643 4.391683 AAACCGGAAAGGAGGGAATAAA 57.608 40.909 9.46 0.00 45.00 1.40
5237 5644 5.720486 ATAAACCGGAAAGGAGGGAATAA 57.280 39.130 9.46 0.00 45.00 1.40
5238 5645 5.720486 AATAAACCGGAAAGGAGGGAATA 57.280 39.130 9.46 0.00 45.00 1.75
5239 5646 4.603094 AATAAACCGGAAAGGAGGGAAT 57.397 40.909 9.46 0.00 45.00 3.01
5240 5647 4.537288 ACTAATAAACCGGAAAGGAGGGAA 59.463 41.667 9.46 0.00 45.00 3.97
5241 5648 4.106324 ACTAATAAACCGGAAAGGAGGGA 58.894 43.478 9.46 0.00 45.00 4.20
5242 5649 4.449131 GACTAATAAACCGGAAAGGAGGG 58.551 47.826 9.46 0.00 45.00 4.30
5243 5650 4.449131 GGACTAATAAACCGGAAAGGAGG 58.551 47.826 9.46 0.00 45.00 4.30
5244 5651 4.080751 TGGGACTAATAAACCGGAAAGGAG 60.081 45.833 9.46 0.00 45.00 3.69
5245 5652 3.845398 TGGGACTAATAAACCGGAAAGGA 59.155 43.478 9.46 0.00 45.00 3.36
5247 5654 5.681639 AGATGGGACTAATAAACCGGAAAG 58.318 41.667 9.46 0.00 0.00 2.62
5248 5655 5.190132 TGAGATGGGACTAATAAACCGGAAA 59.810 40.000 9.46 0.00 0.00 3.13
5249 5656 4.717778 TGAGATGGGACTAATAAACCGGAA 59.282 41.667 9.46 0.00 0.00 4.30
5250 5657 4.291792 TGAGATGGGACTAATAAACCGGA 58.708 43.478 9.46 0.00 0.00 5.14
5251 5658 4.682778 TGAGATGGGACTAATAAACCGG 57.317 45.455 0.00 0.00 0.00 5.28
5252 5659 7.499232 AGAAAATGAGATGGGACTAATAAACCG 59.501 37.037 0.00 0.00 0.00 4.44
5253 5660 8.753497 AGAAAATGAGATGGGACTAATAAACC 57.247 34.615 0.00 0.00 0.00 3.27
5255 5662 9.189156 CCAAGAAAATGAGATGGGACTAATAAA 57.811 33.333 0.00 0.00 0.00 1.40
5256 5663 8.336235 ACCAAGAAAATGAGATGGGACTAATAA 58.664 33.333 0.00 0.00 35.44 1.40
5257 5664 7.872138 ACCAAGAAAATGAGATGGGACTAATA 58.128 34.615 0.00 0.00 35.44 0.98
5258 5665 6.735556 ACCAAGAAAATGAGATGGGACTAAT 58.264 36.000 0.00 0.00 35.44 1.73
5259 5666 6.139679 ACCAAGAAAATGAGATGGGACTAA 57.860 37.500 0.00 0.00 35.44 2.24
5260 5667 5.779241 ACCAAGAAAATGAGATGGGACTA 57.221 39.130 0.00 0.00 35.44 2.59
5261 5668 4.664688 ACCAAGAAAATGAGATGGGACT 57.335 40.909 0.00 0.00 35.44 3.85
5262 5669 5.728637 AAACCAAGAAAATGAGATGGGAC 57.271 39.130 0.00 0.00 35.44 4.46
5263 5670 6.745794 AAAAACCAAGAAAATGAGATGGGA 57.254 33.333 0.00 0.00 35.44 4.37
5296 5703 8.923270 TGGTGGAAAGAAATGAAAATAAGACTT 58.077 29.630 0.00 0.00 0.00 3.01
5297 5704 8.477419 TGGTGGAAAGAAATGAAAATAAGACT 57.523 30.769 0.00 0.00 0.00 3.24
5305 5712 9.487790 GTGAAAATATGGTGGAAAGAAATGAAA 57.512 29.630 0.00 0.00 0.00 2.69
5306 5713 8.646004 TGTGAAAATATGGTGGAAAGAAATGAA 58.354 29.630 0.00 0.00 0.00 2.57
5307 5714 8.187913 TGTGAAAATATGGTGGAAAGAAATGA 57.812 30.769 0.00 0.00 0.00 2.57
5308 5715 9.439500 AATGTGAAAATATGGTGGAAAGAAATG 57.561 29.630 0.00 0.00 0.00 2.32
5309 5716 9.657419 GAATGTGAAAATATGGTGGAAAGAAAT 57.343 29.630 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.