Multiple sequence alignment - TraesCS5B01G203400

Loading Multiple Alignment...

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 TraesCS5B01G203400 chr5B 100.000 4325 0 0 1 4325 369638712 369634388 0.000000e+00 7987.0
1 TraesCS5B01G203400 chr5B 89.744 195 20 0 4131 4325 655452822 655452628 2.580000e-62 250.0
2 TraesCS5B01G203400 chr5D 90.949 4143 170 65 88 4133 319507696 319503662 0.000000e+00 5384.0
3 TraesCS5B01G203400 chr5D 91.304 46 3 1 38 83 319507811 319507767 1.300000e-05 62.1
4 TraesCS5B01G203400 chr5A 87.685 3784 209 119 86 3736 414753450 414757109 0.000000e+00 4169.0
5 TraesCS5B01G203400 chr5A 85.449 323 23 11 3828 4127 414757173 414757494 9.030000e-82 315.0
6 TraesCS5B01G203400 chr7D 85.575 818 80 24 1620 2423 624903514 624902721 0.000000e+00 822.0
7 TraesCS5B01G203400 chr3A 93.264 193 13 0 4133 4325 738686200 738686392 7.080000e-73 285.0
8 TraesCS5B01G203400 chr1D 92.784 194 13 1 4133 4325 372438973 372439166 3.290000e-71 279.0


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 TraesCS5B01G203400 chr5B 369634388 369638712 4324 True 7987.00 7987 100.0000 1 4325 1 chr5B.!!$R1 4324
1 TraesCS5B01G203400 chr5D 319503662 319507811 4149 True 2723.05 5384 91.1265 38 4133 2 chr5D.!!$R1 4095
2 TraesCS5B01G203400 chr5A 414753450 414757494 4044 False 2242.00 4169 86.5670 86 4127 2 chr5A.!!$F1 4041
3 TraesCS5B01G203400 chr7D 624902721 624903514 793 True 822.00 822 85.5750 1620 2423 1 chr7D.!!$R1 803

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
776 910 0.107214 ACGAGAGAGAGAGAGGCAGG 60.107 60.0 0.00 0.0 0.00 4.85 F
777 911 0.180171 CGAGAGAGAGAGAGGCAGGA 59.820 60.0 0.00 0.0 0.00 3.86 F
1344 1547 0.196118 TTTCAGTTCCCTCCCCTCCT 59.804 55.0 0.00 0.0 0.00 3.69 F
3201 3453 0.040425 GAAGCGCCAACGACAACAAT 60.040 50.0 2.29 0.0 43.93 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2384 0.457166 CAGCCACCGCATTGTTCATG 60.457 55.000 0.00 0.00 37.52 3.07 R
2701 2952 1.202114 GATTTTGGCACTGCGGAATCA 59.798 47.619 0.00 0.00 0.00 2.57 R
3216 3468 0.829333 AGAAGGCGATCTCTGTGCAT 59.171 50.000 0.00 0.00 0.00 3.96 R
4197 4530 0.034089 ATTTGGCTAGGGACACTGCC 60.034 55.000 10.28 10.28 41.14 4.85 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
21 22 3.515330 AACAAATCCTGCAGCATAAGC 57.485 42.857 8.66 0.00 42.56 3.09
22 23 2.449464 ACAAATCCTGCAGCATAAGCA 58.551 42.857 8.66 0.00 45.49 3.91
23 24 2.827322 ACAAATCCTGCAGCATAAGCAA 59.173 40.909 8.66 0.00 45.49 3.91
24 25 3.119245 ACAAATCCTGCAGCATAAGCAAG 60.119 43.478 8.66 0.00 45.49 4.01
25 26 2.431954 ATCCTGCAGCATAAGCAAGT 57.568 45.000 8.66 0.00 45.49 3.16
26 27 3.565764 ATCCTGCAGCATAAGCAAGTA 57.434 42.857 8.66 0.00 45.49 2.24
27 28 2.632377 TCCTGCAGCATAAGCAAGTAC 58.368 47.619 8.66 0.00 45.49 2.73
28 29 1.672881 CCTGCAGCATAAGCAAGTACC 59.327 52.381 8.66 0.00 45.49 3.34
29 30 2.358957 CTGCAGCATAAGCAAGTACCA 58.641 47.619 0.00 0.00 45.49 3.25
30 31 2.083774 TGCAGCATAAGCAAGTACCAC 58.916 47.619 0.00 0.00 45.49 4.16
31 32 2.083774 GCAGCATAAGCAAGTACCACA 58.916 47.619 0.00 0.00 45.49 4.17
32 33 2.684881 GCAGCATAAGCAAGTACCACAT 59.315 45.455 0.00 0.00 45.49 3.21
33 34 3.876914 GCAGCATAAGCAAGTACCACATA 59.123 43.478 0.00 0.00 45.49 2.29
34 35 4.516698 GCAGCATAAGCAAGTACCACATAT 59.483 41.667 0.00 0.00 45.49 1.78
35 36 5.700832 GCAGCATAAGCAAGTACCACATATA 59.299 40.000 0.00 0.00 45.49 0.86
36 37 6.128445 GCAGCATAAGCAAGTACCACATATAG 60.128 42.308 0.00 0.00 45.49 1.31
37 38 7.154656 CAGCATAAGCAAGTACCACATATAGA 58.845 38.462 0.00 0.00 45.49 1.98
38 39 7.657354 CAGCATAAGCAAGTACCACATATAGAA 59.343 37.037 0.00 0.00 45.49 2.10
39 40 8.210946 AGCATAAGCAAGTACCACATATAGAAA 58.789 33.333 0.00 0.00 45.49 2.52
40 41 8.836413 GCATAAGCAAGTACCACATATAGAAAA 58.164 33.333 0.00 0.00 41.58 2.29
83 84 0.332293 TGGCACATGGTCATGGTCAT 59.668 50.000 14.49 0.00 42.91 3.06
84 85 0.742505 GGCACATGGTCATGGTCATG 59.257 55.000 20.12 20.12 44.42 3.07
90 156 1.766494 TGGTCATGGTCATGGCAATC 58.234 50.000 16.06 1.53 44.79 2.67
133 202 2.200373 AAAAGGAACATCACGGGAGG 57.800 50.000 0.00 0.00 0.00 4.30
570 688 1.376037 GCCACACCTTTCCTCTCGG 60.376 63.158 0.00 0.00 0.00 4.63
581 699 4.811557 CCTTTCCTCTCGGTTGATTATCAC 59.188 45.833 0.00 0.00 0.00 3.06
606 730 9.005777 ACTCGGTTTTGCTTGTTTATTTATCTA 57.994 29.630 0.00 0.00 0.00 1.98
657 783 1.227263 CTGCCACCCGATCTAACCG 60.227 63.158 0.00 0.00 0.00 4.44
770 904 6.014925 AGCAGTATACATACGAGAGAGAGAGA 60.015 42.308 5.50 0.00 38.28 3.10
772 906 6.811665 CAGTATACATACGAGAGAGAGAGAGG 59.188 46.154 5.50 0.00 38.28 3.69
773 907 2.846193 ACATACGAGAGAGAGAGAGGC 58.154 52.381 0.00 0.00 0.00 4.70
774 908 2.171659 ACATACGAGAGAGAGAGAGGCA 59.828 50.000 0.00 0.00 0.00 4.75
775 909 2.613026 TACGAGAGAGAGAGAGGCAG 57.387 55.000 0.00 0.00 0.00 4.85
776 910 0.107214 ACGAGAGAGAGAGAGGCAGG 60.107 60.000 0.00 0.00 0.00 4.85
777 911 0.180171 CGAGAGAGAGAGAGGCAGGA 59.820 60.000 0.00 0.00 0.00 3.86
778 912 1.408127 CGAGAGAGAGAGAGGCAGGAA 60.408 57.143 0.00 0.00 0.00 3.36
786 920 0.254462 GAGAGGCAGGAAGGGAAAGG 59.746 60.000 0.00 0.00 0.00 3.11
787 921 1.379176 GAGGCAGGAAGGGAAAGGC 60.379 63.158 0.00 0.00 0.00 4.35
790 924 1.380302 GCAGGAAGGGAAAGGCAGA 59.620 57.895 0.00 0.00 0.00 4.26
810 944 2.993853 GGTCAAGGCTGGGAGAGG 59.006 66.667 0.00 0.00 0.00 3.69
812 946 1.613630 GTCAAGGCTGGGAGAGGGA 60.614 63.158 0.00 0.00 0.00 4.20
859 1009 0.596577 TCGTTCGTTCACAGAGGAGG 59.403 55.000 0.00 0.00 0.00 4.30
860 1010 0.596577 CGTTCGTTCACAGAGGAGGA 59.403 55.000 0.00 0.00 0.00 3.71
862 1012 1.614413 GTTCGTTCACAGAGGAGGAGT 59.386 52.381 0.00 0.00 0.00 3.85
869 1019 2.158370 TCACAGAGGAGGAGTGGTGTTA 60.158 50.000 0.00 0.00 34.17 2.41
919 1071 2.692741 GGTTCAGGGGAGGGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
920 1072 2.692741 GTTCAGGGGAGGGGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
921 1073 4.038804 TTCAGGGGAGGGGAGGGG 62.039 72.222 0.00 0.00 0.00 4.79
1110 1272 4.030913 CCACCAGAAAGGAGTCAGGTATA 58.969 47.826 0.00 0.00 41.22 1.47
1113 1275 5.892119 CACCAGAAAGGAGTCAGGTATACTA 59.108 44.000 2.25 0.00 41.22 1.82
1133 1296 1.290134 CTACTGCCCTCCCCTTTCTT 58.710 55.000 0.00 0.00 0.00 2.52
1177 1349 0.811616 AATCTCGGGATTGACAGCGC 60.812 55.000 10.42 0.00 40.30 5.92
1219 1392 1.864176 CGCGCCCGTAGTTTTTCTT 59.136 52.632 0.00 0.00 0.00 2.52
1230 1433 2.505405 AGTTTTTCTTTCCCGCTCTCC 58.495 47.619 0.00 0.00 0.00 3.71
1278 1481 1.153086 GTCTGCCCGCCTGATTCAT 60.153 57.895 0.00 0.00 0.00 2.57
1291 1494 1.442526 GATTCATCTGCTGGCGGTGG 61.443 60.000 0.00 0.00 0.00 4.61
1292 1495 4.783621 TCATCTGCTGGCGGTGGC 62.784 66.667 0.00 0.00 38.90 5.01
1344 1547 0.196118 TTTCAGTTCCCTCCCCTCCT 59.804 55.000 0.00 0.00 0.00 3.69
1356 1559 3.383223 CTCCCCTCCTCATCTTCTTCTT 58.617 50.000 0.00 0.00 0.00 2.52
1373 1576 4.098807 TCTTCTTTTGTTTTCGGGAAAGGG 59.901 41.667 0.00 0.00 31.69 3.95
1465 1678 1.078848 CGCTTCTGGTTCCAGGGAG 60.079 63.158 17.37 15.59 35.01 4.30
1468 1681 1.541368 TTCTGGTTCCAGGGAGGGG 60.541 63.158 17.37 0.00 38.24 4.79
1575 1788 3.486263 CGGATCCGTGCCTGTTTC 58.514 61.111 26.35 0.00 34.35 2.78
1576 1789 2.452813 CGGATCCGTGCCTGTTTCG 61.453 63.158 26.35 0.00 34.35 3.46
1577 1790 2.750888 GGATCCGTGCCTGTTTCGC 61.751 63.158 0.00 0.00 0.00 4.70
1578 1791 1.741770 GATCCGTGCCTGTTTCGCT 60.742 57.895 0.00 0.00 0.00 4.93
1579 1792 1.298859 GATCCGTGCCTGTTTCGCTT 61.299 55.000 0.00 0.00 0.00 4.68
1580 1793 1.298859 ATCCGTGCCTGTTTCGCTTC 61.299 55.000 0.00 0.00 0.00 3.86
1581 1794 1.961277 CCGTGCCTGTTTCGCTTCT 60.961 57.895 0.00 0.00 0.00 2.85
1649 1878 4.626042 GAGAATTGTCTCTGTGTCTGTGT 58.374 43.478 0.00 0.00 45.99 3.72
1650 1879 4.626042 AGAATTGTCTCTGTGTCTGTGTC 58.374 43.478 0.00 0.00 0.00 3.67
1651 1880 4.343526 AGAATTGTCTCTGTGTCTGTGTCT 59.656 41.667 0.00 0.00 0.00 3.41
1652 1881 3.443099 TTGTCTCTGTGTCTGTGTCTG 57.557 47.619 0.00 0.00 0.00 3.51
1653 1882 2.379005 TGTCTCTGTGTCTGTGTCTGT 58.621 47.619 0.00 0.00 0.00 3.41
1654 1883 3.551846 TGTCTCTGTGTCTGTGTCTGTA 58.448 45.455 0.00 0.00 0.00 2.74
1694 1923 4.741239 GGGGGAGGAGGAGTGCCA 62.741 72.222 0.00 0.00 36.29 4.92
1760 1989 0.904865 TCATGTCCTTCAGGTCGGCT 60.905 55.000 0.00 0.00 36.34 5.52
1901 2133 3.129871 TGCCAGTTTTGCTAATTGTTGC 58.870 40.909 0.00 0.00 0.00 4.17
1941 2174 1.996191 GAGATCGTTTGGTGCTGAGAC 59.004 52.381 0.00 0.00 0.00 3.36
1997 2230 1.966451 GCTTACGGTGTGCAGCCTT 60.966 57.895 5.79 0.00 0.00 4.35
2146 2384 2.226602 TTAAACAACCGCCTTTTGCC 57.773 45.000 0.00 0.00 36.24 4.52
2231 2469 6.366877 CCCTGTTTGATTTGCAGAAAATACTG 59.633 38.462 0.00 0.00 38.64 2.74
2250 2488 5.924475 ACTGTCTGTAAAATCCAACTTCG 57.076 39.130 0.00 0.00 0.00 3.79
2258 2496 7.444183 TCTGTAAAATCCAACTTCGAACTGAAT 59.556 33.333 0.00 0.00 35.63 2.57
2479 2730 2.019984 CAGGAGCTTATGTTCTTGGCC 58.980 52.381 0.00 0.00 29.38 5.36
2554 2805 2.779506 ACCTTTTTCACTCCGGCTAAG 58.220 47.619 0.00 0.00 0.00 2.18
2557 2808 2.561478 TTTTCACTCCGGCTAAGCTT 57.439 45.000 3.48 3.48 0.00 3.74
2560 2811 2.125512 ACTCCGGCTAAGCTTGCG 60.126 61.111 9.86 0.82 0.00 4.85
2641 2892 0.390209 CTTTGCCGGCCATTTCCAAG 60.390 55.000 26.77 10.34 0.00 3.61
2701 2952 1.905215 AGCACATCTAGCTCCAACACT 59.095 47.619 0.00 0.00 38.01 3.55
2740 2991 1.771854 TCTTCAGGCCAGTTGGTTGTA 59.228 47.619 5.01 0.00 37.57 2.41
2749 3000 1.420138 CAGTTGGTTGTACCTCCCACT 59.580 52.381 4.93 4.93 39.58 4.00
2774 3025 1.434622 GCCCTCGTCGTCGACTCATA 61.435 60.000 22.18 5.32 41.35 2.15
2778 3029 0.372679 TCGTCGTCGACTCATACTGC 59.627 55.000 22.18 0.00 41.35 4.40
3040 3291 4.323417 TCCGAGTGTTGCAGAACATTTAT 58.677 39.130 0.00 0.00 43.95 1.40
3045 3296 6.566564 CGAGTGTTGCAGAACATTTATCAGTT 60.567 38.462 0.00 0.00 43.95 3.16
3109 3360 5.464722 GCTGATATTCATCATGTCTTCGTGT 59.535 40.000 0.00 0.00 40.40 4.49
3110 3361 6.346439 GCTGATATTCATCATGTCTTCGTGTC 60.346 42.308 0.00 0.00 40.40 3.67
3112 3363 7.267857 TGATATTCATCATGTCTTCGTGTCTT 58.732 34.615 0.00 0.00 36.22 3.01
3113 3364 7.436376 TGATATTCATCATGTCTTCGTGTCTTC 59.564 37.037 0.00 0.00 36.22 2.87
3170 3422 1.965754 AAGAGCCCGATGGAGAGCAC 61.966 60.000 0.00 0.00 0.00 4.40
3201 3453 0.040425 GAAGCGCCAACGACAACAAT 60.040 50.000 2.29 0.00 43.93 2.71
3216 3468 4.910195 ACAACAATAGCAAGTCCTCATCA 58.090 39.130 0.00 0.00 0.00 3.07
3261 3513 1.446792 CCATGAAGAGTCGCTGCGT 60.447 57.895 22.48 2.86 0.00 5.24
3344 3597 3.832490 TGATCCGATATGATCTTCCGGTT 59.168 43.478 16.53 11.38 41.42 4.44
3378 3631 1.754803 ACCATGATGGCTGATGCAAAG 59.245 47.619 12.25 0.00 42.67 2.77
3504 3780 9.877178 TTTATGATGTGTTTTGTTTTGGTTAGT 57.123 25.926 0.00 0.00 0.00 2.24
3677 3958 6.687081 TTATAGGCTTACAAATTTCCACCG 57.313 37.500 0.00 0.00 0.00 4.94
3729 4011 8.581578 TCTTGTTCTTCTGTTTTTACCAACTTT 58.418 29.630 0.00 0.00 0.00 2.66
3752 4034 1.063616 CAGGAGCTTCATGATGTTGCG 59.936 52.381 10.05 3.35 27.97 4.85
3766 4048 0.308993 GTTGCGTGCTTGAGCTCTTT 59.691 50.000 16.19 0.00 42.66 2.52
3767 4049 0.588252 TTGCGTGCTTGAGCTCTTTC 59.412 50.000 16.19 4.09 42.66 2.62
3784 4066 3.905678 CCGGGCGCTCTGGTCTAG 61.906 72.222 5.36 0.00 37.13 2.43
3785 4067 3.141488 CGGGCGCTCTGGTCTAGT 61.141 66.667 5.36 0.00 0.00 2.57
3791 4073 1.676529 GCGCTCTGGTCTAGTACATCA 59.323 52.381 0.00 0.00 0.00 3.07
3796 4078 4.201970 GCTCTGGTCTAGTACATCACTGAC 60.202 50.000 0.00 0.00 38.24 3.51
3801 4083 4.219944 GGTCTAGTACATCACTGACCACAA 59.780 45.833 15.23 0.00 45.37 3.33
3819 4101 2.030007 ACAATTGTGCACAATAGCGCTT 60.030 40.909 37.92 23.19 45.06 4.68
3820 4102 2.267188 ATTGTGCACAATAGCGCTTG 57.733 45.000 37.29 12.18 44.09 4.01
3823 4105 1.303236 TGCACAATAGCGCTTGGGT 60.303 52.632 18.68 8.65 37.31 4.51
3833 4121 3.393089 AGCGCTTGGGTGAATATCTAG 57.607 47.619 2.64 0.00 0.00 2.43
3838 4126 4.271049 CGCTTGGGTGAATATCTAGTTGTG 59.729 45.833 0.00 0.00 0.00 3.33
3904 4192 1.746615 CACCACCGGCATCCTGAAG 60.747 63.158 0.00 0.00 0.00 3.02
4023 4350 5.591067 TCTCCGTTGGTTGTTTTATTTCTGT 59.409 36.000 0.00 0.00 0.00 3.41
4127 4460 2.829120 GCCCCCAAATTGCTTGTACTAA 59.171 45.455 0.00 0.00 32.65 2.24
4128 4461 3.368013 GCCCCCAAATTGCTTGTACTAAC 60.368 47.826 0.00 0.00 32.65 2.34
4129 4462 4.086457 CCCCCAAATTGCTTGTACTAACT 58.914 43.478 0.00 0.00 32.65 2.24
4130 4463 5.258051 CCCCCAAATTGCTTGTACTAACTA 58.742 41.667 0.00 0.00 32.65 2.24
4131 4464 5.357032 CCCCCAAATTGCTTGTACTAACTAG 59.643 44.000 0.00 0.00 32.65 2.57
4132 4465 5.944007 CCCCAAATTGCTTGTACTAACTAGT 59.056 40.000 0.00 0.00 34.92 2.57
4133 4466 6.433093 CCCCAAATTGCTTGTACTAACTAGTT 59.567 38.462 13.68 13.68 33.62 2.24
4134 4467 7.039993 CCCCAAATTGCTTGTACTAACTAGTTT 60.040 37.037 14.49 0.00 33.62 2.66
4135 4468 8.357402 CCCAAATTGCTTGTACTAACTAGTTTT 58.643 33.333 14.49 4.06 33.62 2.43
4136 4469 9.744468 CCAAATTGCTTGTACTAACTAGTTTTT 57.256 29.630 14.49 3.68 33.62 1.94
4165 4498 8.005192 ACGAGTAACTAGGGACTTTATTAAGG 57.995 38.462 0.00 0.00 41.75 2.69
4166 4499 7.836183 ACGAGTAACTAGGGACTTTATTAAGGA 59.164 37.037 0.00 0.00 41.75 3.36
4167 4500 8.351461 CGAGTAACTAGGGACTTTATTAAGGAG 58.649 40.741 0.00 0.00 41.75 3.69
4168 4501 9.199645 GAGTAACTAGGGACTTTATTAAGGAGT 57.800 37.037 0.00 0.00 41.75 3.85
4169 4502 8.979534 AGTAACTAGGGACTTTATTAAGGAGTG 58.020 37.037 0.00 0.00 41.75 3.51
4170 4503 8.975295 GTAACTAGGGACTTTATTAAGGAGTGA 58.025 37.037 0.00 0.00 41.75 3.41
4171 4504 8.625467 AACTAGGGACTTTATTAAGGAGTGAT 57.375 34.615 0.00 0.00 41.75 3.06
4172 4505 9.725206 AACTAGGGACTTTATTAAGGAGTGATA 57.275 33.333 0.00 0.00 41.75 2.15
4173 4506 9.725206 ACTAGGGACTTTATTAAGGAGTGATAA 57.275 33.333 0.00 0.00 41.75 1.75
4176 4509 9.225682 AGGGACTTTATTAAGGAGTGATAATCA 57.774 33.333 0.00 0.00 35.61 2.57
4177 4510 9.847224 GGGACTTTATTAAGGAGTGATAATCAA 57.153 33.333 0.00 0.00 35.61 2.57
4180 4513 9.326413 ACTTTATTAAGGAGTGATAATCAACGG 57.674 33.333 0.00 0.00 35.61 4.44
4181 4514 9.542462 CTTTATTAAGGAGTGATAATCAACGGA 57.458 33.333 0.00 0.00 0.00 4.69
4182 4515 9.893634 TTTATTAAGGAGTGATAATCAACGGAA 57.106 29.630 0.00 0.00 0.00 4.30
4185 4518 8.882415 TTAAGGAGTGATAATCAACGGAATAC 57.118 34.615 0.00 0.00 0.00 1.89
4186 4519 6.479972 AGGAGTGATAATCAACGGAATACA 57.520 37.500 0.00 0.00 0.00 2.29
4187 4520 6.884832 AGGAGTGATAATCAACGGAATACAA 58.115 36.000 0.00 0.00 0.00 2.41
4188 4521 7.335627 AGGAGTGATAATCAACGGAATACAAA 58.664 34.615 0.00 0.00 0.00 2.83
4189 4522 7.993183 AGGAGTGATAATCAACGGAATACAAAT 59.007 33.333 0.00 0.00 0.00 2.32
4190 4523 9.268268 GGAGTGATAATCAACGGAATACAAATA 57.732 33.333 0.00 0.00 0.00 1.40
4198 4531 7.315247 TCAACGGAATACAAATAATGTCTGG 57.685 36.000 0.00 0.00 42.70 3.86
4199 4532 5.751243 ACGGAATACAAATAATGTCTGGC 57.249 39.130 0.00 0.00 42.70 4.85
4200 4533 5.189928 ACGGAATACAAATAATGTCTGGCA 58.810 37.500 0.00 0.00 42.70 4.92
4201 4534 5.296780 ACGGAATACAAATAATGTCTGGCAG 59.703 40.000 8.58 8.58 42.70 4.85
4202 4535 5.296780 CGGAATACAAATAATGTCTGGCAGT 59.703 40.000 15.27 0.00 42.70 4.40
4203 4536 6.498304 GGAATACAAATAATGTCTGGCAGTG 58.502 40.000 15.27 5.16 42.70 3.66
4204 4537 6.095440 GGAATACAAATAATGTCTGGCAGTGT 59.905 38.462 15.27 11.04 42.70 3.55
4205 4538 6.683974 ATACAAATAATGTCTGGCAGTGTC 57.316 37.500 15.27 7.22 42.70 3.67
4206 4539 3.758554 ACAAATAATGTCTGGCAGTGTCC 59.241 43.478 15.27 2.06 37.96 4.02
4207 4540 2.717639 ATAATGTCTGGCAGTGTCCC 57.282 50.000 15.27 0.00 0.00 4.46
4208 4541 1.656587 TAATGTCTGGCAGTGTCCCT 58.343 50.000 15.27 0.00 0.00 4.20
4209 4542 1.656587 AATGTCTGGCAGTGTCCCTA 58.343 50.000 15.27 0.00 0.00 3.53
4210 4543 1.198713 ATGTCTGGCAGTGTCCCTAG 58.801 55.000 15.27 0.00 0.00 3.02
4211 4544 1.219393 GTCTGGCAGTGTCCCTAGC 59.781 63.158 15.27 0.00 0.00 3.42
4214 4547 3.077907 GGCAGTGTCCCTAGCCAA 58.922 61.111 0.00 0.00 46.26 4.52
4215 4548 1.378762 GGCAGTGTCCCTAGCCAAA 59.621 57.895 0.00 0.00 46.26 3.28
4216 4549 0.034089 GGCAGTGTCCCTAGCCAAAT 60.034 55.000 0.00 0.00 46.26 2.32
4217 4550 1.211949 GGCAGTGTCCCTAGCCAAATA 59.788 52.381 0.00 0.00 46.26 1.40
4218 4551 2.158608 GGCAGTGTCCCTAGCCAAATAT 60.159 50.000 0.00 0.00 46.26 1.28
4219 4552 2.880890 GCAGTGTCCCTAGCCAAATATG 59.119 50.000 0.00 0.00 0.00 1.78
4220 4553 3.433598 GCAGTGTCCCTAGCCAAATATGA 60.434 47.826 0.00 0.00 0.00 2.15
4221 4554 4.130118 CAGTGTCCCTAGCCAAATATGAC 58.870 47.826 0.00 0.00 0.00 3.06
4222 4555 3.131396 GTGTCCCTAGCCAAATATGACG 58.869 50.000 0.00 0.00 0.00 4.35
4223 4556 3.035363 TGTCCCTAGCCAAATATGACGA 58.965 45.455 0.00 0.00 0.00 4.20
4224 4557 3.181469 TGTCCCTAGCCAAATATGACGAC 60.181 47.826 0.00 0.00 0.00 4.34
4225 4558 2.367567 TCCCTAGCCAAATATGACGACC 59.632 50.000 0.00 0.00 0.00 4.79
4226 4559 2.368875 CCCTAGCCAAATATGACGACCT 59.631 50.000 0.00 0.00 0.00 3.85
4227 4560 3.576982 CCCTAGCCAAATATGACGACCTA 59.423 47.826 0.00 0.00 0.00 3.08
4228 4561 4.557205 CCTAGCCAAATATGACGACCTAC 58.443 47.826 0.00 0.00 0.00 3.18
4238 4571 3.501396 CGACCTACGGGAAGCGTA 58.499 61.111 0.00 0.00 38.46 4.42
4239 4572 1.354506 CGACCTACGGGAAGCGTAG 59.645 63.158 0.00 0.00 39.04 3.51
4240 4573 1.091771 CGACCTACGGGAAGCGTAGA 61.092 60.000 3.62 0.00 41.05 2.59
4241 4574 1.316651 GACCTACGGGAAGCGTAGAT 58.683 55.000 3.62 0.00 41.05 1.98
4242 4575 1.001597 GACCTACGGGAAGCGTAGATG 60.002 57.143 3.62 0.00 41.05 2.90
4243 4576 0.318784 CCTACGGGAAGCGTAGATGC 60.319 60.000 3.62 0.00 41.05 3.91
4244 4577 0.384309 CTACGGGAAGCGTAGATGCA 59.616 55.000 0.00 0.00 41.05 3.96
4245 4578 0.384309 TACGGGAAGCGTAGATGCAG 59.616 55.000 0.00 0.00 37.31 4.41
4246 4579 2.240500 CGGGAAGCGTAGATGCAGC 61.241 63.158 0.00 0.00 37.31 5.25
4247 4580 1.144936 GGGAAGCGTAGATGCAGCT 59.855 57.895 10.44 10.44 43.90 4.24
4252 4585 1.813513 AGCGTAGATGCAGCTTTTGT 58.186 45.000 11.02 0.00 38.13 2.83
4253 4586 2.154462 AGCGTAGATGCAGCTTTTGTT 58.846 42.857 11.02 0.00 38.13 2.83
4254 4587 3.334691 AGCGTAGATGCAGCTTTTGTTA 58.665 40.909 11.02 0.00 38.13 2.41
4255 4588 3.372206 AGCGTAGATGCAGCTTTTGTTAG 59.628 43.478 11.02 0.00 38.13 2.34
4256 4589 3.674423 CGTAGATGCAGCTTTTGTTAGC 58.326 45.455 11.02 0.00 41.53 3.09
4257 4590 2.907910 AGATGCAGCTTTTGTTAGCG 57.092 45.000 0.00 0.00 45.82 4.26
4258 4591 1.135575 AGATGCAGCTTTTGTTAGCGC 60.136 47.619 0.00 0.00 45.82 5.92
4259 4592 0.597568 ATGCAGCTTTTGTTAGCGCA 59.402 45.000 11.47 14.01 46.36 6.09
4260 4593 0.597568 TGCAGCTTTTGTTAGCGCAT 59.402 45.000 11.47 0.00 45.82 4.73
4261 4594 0.986992 GCAGCTTTTGTTAGCGCATG 59.013 50.000 11.47 0.00 45.82 4.06
4262 4595 1.666888 GCAGCTTTTGTTAGCGCATGT 60.667 47.619 11.47 0.00 45.82 3.21
4263 4596 1.980844 CAGCTTTTGTTAGCGCATGTG 59.019 47.619 11.47 0.66 45.82 3.21
4264 4597 0.710017 GCTTTTGTTAGCGCATGTGC 59.290 50.000 23.64 23.64 37.78 4.57
4266 4599 2.664916 CTTTTGTTAGCGCATGTGCTT 58.335 42.857 36.33 21.01 44.46 3.91
4267 4600 2.791383 TTTGTTAGCGCATGTGCTTT 57.209 40.000 36.33 18.00 44.46 3.51
4268 4601 3.906014 TTTGTTAGCGCATGTGCTTTA 57.094 38.095 36.33 22.54 44.46 1.85
4269 4602 3.906014 TTGTTAGCGCATGTGCTTTAA 57.094 38.095 36.33 23.48 44.46 1.52
4270 4603 3.906014 TGTTAGCGCATGTGCTTTAAA 57.094 38.095 36.33 22.77 44.46 1.52
4271 4604 4.230314 TGTTAGCGCATGTGCTTTAAAA 57.770 36.364 36.33 22.42 44.46 1.52
4272 4605 4.804108 TGTTAGCGCATGTGCTTTAAAAT 58.196 34.783 36.33 15.03 44.46 1.82
4273 4606 5.226396 TGTTAGCGCATGTGCTTTAAAATT 58.774 33.333 36.33 14.29 44.46 1.82
4274 4607 6.382608 TGTTAGCGCATGTGCTTTAAAATTA 58.617 32.000 36.33 15.12 44.46 1.40
4275 4608 7.032580 TGTTAGCGCATGTGCTTTAAAATTAT 58.967 30.769 36.33 12.83 44.46 1.28
4276 4609 7.543868 TGTTAGCGCATGTGCTTTAAAATTATT 59.456 29.630 36.33 12.31 44.46 1.40
4277 4610 6.966435 AGCGCATGTGCTTTAAAATTATTT 57.034 29.167 27.71 1.21 44.46 1.40
4278 4611 7.363205 AGCGCATGTGCTTTAAAATTATTTT 57.637 28.000 27.71 8.07 44.46 1.82
4279 4612 7.455447 AGCGCATGTGCTTTAAAATTATTTTC 58.545 30.769 27.71 0.00 44.46 2.29
4280 4613 7.331687 AGCGCATGTGCTTTAAAATTATTTTCT 59.668 29.630 27.71 0.00 44.46 2.52
4281 4614 7.956943 GCGCATGTGCTTTAAAATTATTTTCTT 59.043 29.630 23.77 0.00 39.32 2.52
4282 4615 9.810231 CGCATGTGCTTTAAAATTATTTTCTTT 57.190 25.926 6.17 0.00 39.32 2.52
4310 4643 7.962934 TTCAAATTTGAACTTGACGTAGTTG 57.037 32.000 26.01 0.00 41.36 3.16
4311 4644 7.310072 TCAAATTTGAACTTGACGTAGTTGA 57.690 32.000 18.45 0.00 38.43 3.18
4312 4645 7.753659 TCAAATTTGAACTTGACGTAGTTGAA 58.246 30.769 18.45 3.90 38.43 2.69
4313 4646 7.694784 TCAAATTTGAACTTGACGTAGTTGAAC 59.305 33.333 18.45 0.00 38.43 3.18
4323 4656 4.254402 ACGTAGTTGAACTCCCTTCTTC 57.746 45.455 0.00 0.00 37.78 2.87
4324 4657 3.896272 ACGTAGTTGAACTCCCTTCTTCT 59.104 43.478 0.00 0.00 37.78 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.119245 ACTTGCTTATGCTGCAGGATTTG 60.119 43.478 26.52 18.68 41.71 2.32
4 5 3.094572 ACTTGCTTATGCTGCAGGATTT 58.905 40.909 26.52 6.27 41.71 2.17
5 6 2.731572 ACTTGCTTATGCTGCAGGATT 58.268 42.857 26.52 10.43 41.71 3.01
6 7 2.431954 ACTTGCTTATGCTGCAGGAT 57.568 45.000 24.79 24.79 41.71 3.24
7 8 2.632377 GTACTTGCTTATGCTGCAGGA 58.368 47.619 17.12 14.45 41.71 3.86
8 9 1.672881 GGTACTTGCTTATGCTGCAGG 59.327 52.381 17.12 0.00 41.71 4.85
9 10 2.096496 GTGGTACTTGCTTATGCTGCAG 59.904 50.000 10.11 10.11 41.71 4.41
10 11 2.083774 GTGGTACTTGCTTATGCTGCA 58.916 47.619 4.13 4.13 40.48 4.41
11 12 2.083774 TGTGGTACTTGCTTATGCTGC 58.916 47.619 1.96 0.00 40.48 5.25
12 13 7.154656 TCTATATGTGGTACTTGCTTATGCTG 58.845 38.462 1.96 0.00 40.48 4.41
13 14 7.303182 TCTATATGTGGTACTTGCTTATGCT 57.697 36.000 1.96 0.00 40.48 3.79
14 15 7.962964 TTCTATATGTGGTACTTGCTTATGC 57.037 36.000 0.00 0.00 40.20 3.14
18 19 9.515226 TTTCTTTTCTATATGTGGTACTTGCTT 57.485 29.630 0.00 0.00 0.00 3.91
19 20 9.515226 TTTTCTTTTCTATATGTGGTACTTGCT 57.485 29.630 0.00 0.00 0.00 3.91
47 48 1.471327 GCCATGTGCGCACCATATTTT 60.471 47.619 35.72 10.38 0.00 1.82
51 52 2.045536 TGCCATGTGCGCACCATA 60.046 55.556 35.72 19.66 45.60 2.74
80 81 8.192774 GTCTGATGATTAAAAAGATTGCCATGA 58.807 33.333 0.00 0.00 0.00 3.07
83 84 7.315142 GTGTCTGATGATTAAAAAGATTGCCA 58.685 34.615 0.00 0.00 0.00 4.92
84 85 6.470235 CGTGTCTGATGATTAAAAAGATTGCC 59.530 38.462 0.00 0.00 0.00 4.52
90 156 7.621832 TTTTGCGTGTCTGATGATTAAAAAG 57.378 32.000 0.00 0.00 0.00 2.27
202 285 4.908687 AAGACCACGTGCTGCGCA 62.909 61.111 10.98 10.98 46.11 6.09
242 325 3.995506 CTGTGGGCCCGTGGGATTC 62.996 68.421 19.37 0.31 37.50 2.52
273 356 0.263765 ATTACTAGGTGGGGAGCGGA 59.736 55.000 0.00 0.00 0.00 5.54
287 370 1.403780 GGTCACACGAGCCGAATTACT 60.404 52.381 1.50 0.00 33.34 2.24
408 509 3.046087 CACTGCCACTGACAGCCG 61.046 66.667 1.25 0.00 38.79 5.52
570 688 5.296813 AGCAAAACCGAGTGATAATCAAC 57.703 39.130 0.00 0.00 0.00 3.18
641 767 2.588034 GCGGTTAGATCGGGTGGC 60.588 66.667 0.00 0.00 0.00 5.01
657 783 3.798889 GCTTATTTATTTTCGGCCCAGGC 60.799 47.826 0.00 0.00 41.06 4.85
720 854 0.835941 ACTCCTCCTAGCCAAGCATG 59.164 55.000 0.00 0.00 0.00 4.06
722 856 1.007238 AGTACTCCTCCTAGCCAAGCA 59.993 52.381 0.00 0.00 0.00 3.91
731 865 0.707616 ACTGCTCCAGTACTCCTCCT 59.292 55.000 0.00 0.00 43.46 3.69
732 866 2.438800 TACTGCTCCAGTACTCCTCC 57.561 55.000 0.00 0.00 43.46 4.30
770 904 2.147433 CTGCCTTTCCCTTCCTGCCT 62.147 60.000 0.00 0.00 0.00 4.75
772 906 0.679321 CTCTGCCTTTCCCTTCCTGC 60.679 60.000 0.00 0.00 0.00 4.85
773 907 0.679321 GCTCTGCCTTTCCCTTCCTG 60.679 60.000 0.00 0.00 0.00 3.86
774 908 1.688211 GCTCTGCCTTTCCCTTCCT 59.312 57.895 0.00 0.00 0.00 3.36
775 909 1.746991 CGCTCTGCCTTTCCCTTCC 60.747 63.158 0.00 0.00 0.00 3.46
776 910 1.746991 CCGCTCTGCCTTTCCCTTC 60.747 63.158 0.00 0.00 0.00 3.46
777 911 2.352805 CCGCTCTGCCTTTCCCTT 59.647 61.111 0.00 0.00 0.00 3.95
778 912 2.930562 ACCGCTCTGCCTTTCCCT 60.931 61.111 0.00 0.00 0.00 4.20
786 920 3.123620 CAGCCTTGACCGCTCTGC 61.124 66.667 0.00 0.00 33.17 4.26
787 921 2.435586 CCAGCCTTGACCGCTCTG 60.436 66.667 0.00 0.00 33.17 3.35
790 924 3.710722 CTCCCAGCCTTGACCGCT 61.711 66.667 0.00 0.00 36.91 5.52
810 944 1.791103 CGACGATGCTCTCCCTCTCC 61.791 65.000 0.00 0.00 0.00 3.71
812 946 1.077357 ACGACGATGCTCTCCCTCT 60.077 57.895 0.00 0.00 0.00 3.69
859 1009 2.558795 TCTCTCACTGCTAACACCACTC 59.441 50.000 0.00 0.00 0.00 3.51
860 1010 2.560542 CTCTCTCACTGCTAACACCACT 59.439 50.000 0.00 0.00 0.00 4.00
862 1012 2.558795 GACTCTCTCACTGCTAACACCA 59.441 50.000 0.00 0.00 0.00 4.17
869 1019 1.354031 TCCTCTGACTCTCTCACTGCT 59.646 52.381 0.00 0.00 0.00 4.24
919 1071 0.903454 TCGTTTCTCACTCCCCTCCC 60.903 60.000 0.00 0.00 0.00 4.30
920 1072 0.974383 TTCGTTTCTCACTCCCCTCC 59.026 55.000 0.00 0.00 0.00 4.30
921 1073 2.833631 TTTCGTTTCTCACTCCCCTC 57.166 50.000 0.00 0.00 0.00 4.30
1110 1272 0.717196 AAGGGGAGGGCAGTAGTAGT 59.283 55.000 0.00 0.00 0.00 2.73
1113 1275 0.119358 AGAAAGGGGAGGGCAGTAGT 59.881 55.000 0.00 0.00 0.00 2.73
1133 1296 2.038269 GCCGAACTCGCCCAAATCA 61.038 57.895 0.00 0.00 38.18 2.57
1153 1325 2.604914 CTGTCAATCCCGAGATTCGTTG 59.395 50.000 0.00 0.00 40.89 4.10
1202 1375 1.400629 GGAAAGAAAAACTACGGGCGC 60.401 52.381 0.00 0.00 0.00 6.53
1207 1380 3.064931 AGAGCGGGAAAGAAAAACTACG 58.935 45.455 0.00 0.00 0.00 3.51
1213 1386 0.768622 TGGGAGAGCGGGAAAGAAAA 59.231 50.000 0.00 0.00 0.00 2.29
1215 1388 0.541863 GATGGGAGAGCGGGAAAGAA 59.458 55.000 0.00 0.00 0.00 2.52
1219 1392 2.363795 ACGATGGGAGAGCGGGAA 60.364 61.111 0.00 0.00 37.96 3.97
1312 1515 3.187432 GGAACTGAAAGAAAGGCGAGAAG 59.813 47.826 0.00 0.00 37.43 2.85
1344 1547 5.825679 TCCCGAAAACAAAAGAAGAAGATGA 59.174 36.000 0.00 0.00 0.00 2.92
1356 1559 2.312390 CTCCCCTTTCCCGAAAACAAA 58.688 47.619 0.00 0.00 0.00 2.83
1373 1576 1.300697 CCCATACCTAACGCGCTCC 60.301 63.158 5.73 0.00 0.00 4.70
1449 1662 1.566298 CCCCTCCCTGGAACCAGAAG 61.566 65.000 20.79 16.18 46.30 2.85
1465 1678 1.749258 GATTTGGCGTGTCTCCCCC 60.749 63.158 0.00 0.00 0.00 5.40
1468 1681 1.468914 GGAAAGATTTGGCGTGTCTCC 59.531 52.381 0.00 0.00 0.00 3.71
1566 1779 1.654220 GCAAGAAGCGAAACAGGCA 59.346 52.632 0.00 0.00 0.00 4.75
1567 1780 4.541020 GCAAGAAGCGAAACAGGC 57.459 55.556 0.00 0.00 0.00 4.85
1739 1968 0.608130 CCGACCTGAAGGACATGACA 59.392 55.000 2.62 0.00 38.94 3.58
1901 2133 0.510790 TGCACAACATAACGAGCACG 59.489 50.000 0.76 0.76 45.75 5.34
1941 2174 3.974835 TACTGCACGCTGCCATGGG 62.975 63.158 15.13 0.00 44.23 4.00
2109 2345 3.901797 AACGGGCTACCAGCAGCAC 62.902 63.158 0.00 0.00 44.75 4.40
2146 2384 0.457166 CAGCCACCGCATTGTTCATG 60.457 55.000 0.00 0.00 37.52 3.07
2231 2469 6.202188 TCAGTTCGAAGTTGGATTTTACAGAC 59.798 38.462 1.81 0.00 0.00 3.51
2262 2504 6.833041 TGTCCCTTCACAAATAAGACAAGTA 58.167 36.000 0.00 0.00 0.00 2.24
2278 2523 2.115291 GGCTTCGGCATGTCCCTTC 61.115 63.158 0.00 0.00 43.96 3.46
2402 2652 3.676873 GCCAGCAAACCTAAATGACATGG 60.677 47.826 0.00 0.00 0.00 3.66
2557 2808 4.704833 GAAGCCTCAGGTGCCGCA 62.705 66.667 0.00 0.00 0.00 5.69
2560 2811 2.360475 GGTGAAGCCTCAGGTGCC 60.360 66.667 0.00 0.00 30.14 5.01
2641 2892 1.202568 TGAGACATGATGGACATCGGC 60.203 52.381 0.00 0.00 40.63 5.54
2701 2952 1.202114 GATTTTGGCACTGCGGAATCA 59.798 47.619 0.00 0.00 0.00 2.57
2740 2991 1.306226 GGGCTGACTAGTGGGAGGT 60.306 63.158 0.00 0.00 0.00 3.85
2749 3000 2.104859 CGACGACGAGGGCTGACTA 61.105 63.158 0.00 0.00 42.66 2.59
2886 3137 6.233434 ACATCAATACATCATCCAGCGTATT 58.767 36.000 0.00 0.00 35.47 1.89
3040 3291 9.745880 GCTATGTTATGTAGCTAAGTTAACTGA 57.254 33.333 9.34 0.00 41.00 3.41
3045 3296 8.246430 ACAGGCTATGTTATGTAGCTAAGTTA 57.754 34.615 0.00 0.00 39.96 2.24
3060 3311 7.164122 CCTATGATCACAAATACAGGCTATGT 58.836 38.462 0.00 0.90 46.45 2.29
3109 3360 4.083961 CGTAGTCGTCACTCTGAAAGAAGA 60.084 45.833 0.00 0.00 46.34 2.87
3110 3361 4.152526 CGTAGTCGTCACTCTGAAAGAAG 58.847 47.826 0.00 0.00 46.34 2.85
3112 3363 2.483106 CCGTAGTCGTCACTCTGAAAGA 59.517 50.000 0.00 0.00 37.02 2.52
3113 3364 2.852748 CCGTAGTCGTCACTCTGAAAG 58.147 52.381 0.00 0.00 33.62 2.62
3201 3453 2.236893 TGTGCATGATGAGGACTTGCTA 59.763 45.455 0.00 0.00 38.58 3.49
3216 3468 0.829333 AGAAGGCGATCTCTGTGCAT 59.171 50.000 0.00 0.00 0.00 3.96
3303 3555 6.590292 CGGATCAGATGTGTAGTTTTGTACTT 59.410 38.462 0.00 0.00 38.33 2.24
3344 3597 5.379187 CCATCATGGTTGAATCTATGGACA 58.621 41.667 0.00 0.00 34.96 4.02
3378 3631 5.181690 TGGATGCAAAATCTTATTACGGC 57.818 39.130 0.00 0.00 0.00 5.68
3504 3780 1.164411 CCAGCATTACAGGTTGCGAA 58.836 50.000 0.00 0.00 43.61 4.70
3677 3958 0.663153 AACAGAGCTTTGCAACCGAC 59.337 50.000 3.74 0.00 0.00 4.79
3729 4011 3.691118 GCAACATCATGAAGCTCCTGTAA 59.309 43.478 0.00 0.00 0.00 2.41
3752 4034 1.301677 CCCGGAAAGAGCTCAAGCAC 61.302 60.000 17.77 0.88 45.16 4.40
3766 4048 4.435970 TAGACCAGAGCGCCCGGA 62.436 66.667 13.75 0.00 0.00 5.14
3767 4049 3.905678 CTAGACCAGAGCGCCCGG 61.906 72.222 2.29 4.48 0.00 5.73
3784 4066 4.613622 GCACAATTGTGGTCAGTGATGTAC 60.614 45.833 33.56 13.04 45.72 2.90
3785 4067 3.501828 GCACAATTGTGGTCAGTGATGTA 59.498 43.478 33.56 0.00 45.72 2.29
3791 4073 1.761449 TGTGCACAATTGTGGTCAGT 58.239 45.000 33.56 0.00 45.72 3.41
3796 4078 2.252747 CGCTATTGTGCACAATTGTGG 58.747 47.619 41.08 30.03 43.48 4.17
3819 4101 5.905331 AGATCCACAACTAGATATTCACCCA 59.095 40.000 0.00 0.00 0.00 4.51
3820 4102 6.183361 ACAGATCCACAACTAGATATTCACCC 60.183 42.308 0.00 0.00 0.00 4.61
3823 4105 7.904558 AGACAGATCCACAACTAGATATTCA 57.095 36.000 0.00 0.00 0.00 2.57
3833 4121 3.677424 GCTGACCTAGACAGATCCACAAC 60.677 52.174 16.98 0.00 37.54 3.32
3838 4126 2.100584 CAGTGCTGACCTAGACAGATCC 59.899 54.545 16.98 6.83 37.54 3.36
3889 4177 1.656652 CTAACTTCAGGATGCCGGTG 58.343 55.000 1.90 0.00 34.76 4.94
3901 4189 4.911514 TCAAGCAAAACCACCTAACTTC 57.088 40.909 0.00 0.00 0.00 3.01
3904 4192 4.803613 CAGTTTCAAGCAAAACCACCTAAC 59.196 41.667 5.95 0.00 39.46 2.34
3989 4289 9.990360 AAAACAACCAACGGAGAATAAAATAAT 57.010 25.926 0.00 0.00 0.00 1.28
4023 4350 2.832643 TCGGTGTATCTGGGAGGTTA 57.167 50.000 0.00 0.00 0.00 2.85
4139 4472 9.125026 CCTTAATAAAGTCCCTAGTTACTCGTA 57.875 37.037 0.00 0.00 0.00 3.43
4140 4473 7.836183 TCCTTAATAAAGTCCCTAGTTACTCGT 59.164 37.037 0.00 0.00 0.00 4.18
4141 4474 8.230472 TCCTTAATAAAGTCCCTAGTTACTCG 57.770 38.462 0.00 0.00 0.00 4.18
4142 4475 9.199645 ACTCCTTAATAAAGTCCCTAGTTACTC 57.800 37.037 0.00 0.00 0.00 2.59
4143 4476 8.979534 CACTCCTTAATAAAGTCCCTAGTTACT 58.020 37.037 0.00 0.00 0.00 2.24
4144 4477 8.975295 TCACTCCTTAATAAAGTCCCTAGTTAC 58.025 37.037 0.00 0.00 0.00 2.50
4145 4478 9.725206 ATCACTCCTTAATAAAGTCCCTAGTTA 57.275 33.333 0.00 0.00 0.00 2.24
4146 4479 8.625467 ATCACTCCTTAATAAAGTCCCTAGTT 57.375 34.615 0.00 0.00 0.00 2.24
4147 4480 9.725206 TTATCACTCCTTAATAAAGTCCCTAGT 57.275 33.333 0.00 0.00 0.00 2.57
4150 4483 9.225682 TGATTATCACTCCTTAATAAAGTCCCT 57.774 33.333 0.00 0.00 0.00 4.20
4151 4484 9.847224 TTGATTATCACTCCTTAATAAAGTCCC 57.153 33.333 0.00 0.00 0.00 4.46
4154 4487 9.326413 CCGTTGATTATCACTCCTTAATAAAGT 57.674 33.333 0.00 0.00 0.00 2.66
4155 4488 9.542462 TCCGTTGATTATCACTCCTTAATAAAG 57.458 33.333 0.00 0.00 0.00 1.85
4156 4489 9.893634 TTCCGTTGATTATCACTCCTTAATAAA 57.106 29.630 0.00 0.00 0.00 1.40
4159 4492 9.490379 GTATTCCGTTGATTATCACTCCTTAAT 57.510 33.333 0.00 0.00 0.00 1.40
4160 4493 8.479689 TGTATTCCGTTGATTATCACTCCTTAA 58.520 33.333 0.00 0.00 0.00 1.85
4161 4494 8.014070 TGTATTCCGTTGATTATCACTCCTTA 57.986 34.615 0.00 0.00 0.00 2.69
4162 4495 6.884832 TGTATTCCGTTGATTATCACTCCTT 58.115 36.000 0.00 0.00 0.00 3.36
4163 4496 6.479972 TGTATTCCGTTGATTATCACTCCT 57.520 37.500 0.00 0.00 0.00 3.69
4164 4497 7.548196 TTTGTATTCCGTTGATTATCACTCC 57.452 36.000 0.00 0.00 0.00 3.85
4172 4505 8.405531 CCAGACATTATTTGTATTCCGTTGATT 58.594 33.333 0.00 0.00 39.18 2.57
4173 4506 7.468631 GCCAGACATTATTTGTATTCCGTTGAT 60.469 37.037 0.00 0.00 39.18 2.57
4174 4507 6.183360 GCCAGACATTATTTGTATTCCGTTGA 60.183 38.462 0.00 0.00 39.18 3.18
4175 4508 5.971202 GCCAGACATTATTTGTATTCCGTTG 59.029 40.000 0.00 0.00 39.18 4.10
4176 4509 5.650266 TGCCAGACATTATTTGTATTCCGTT 59.350 36.000 0.00 0.00 39.18 4.44
4177 4510 5.189928 TGCCAGACATTATTTGTATTCCGT 58.810 37.500 0.00 0.00 39.18 4.69
4178 4511 5.296780 ACTGCCAGACATTATTTGTATTCCG 59.703 40.000 0.00 0.00 39.18 4.30
4179 4512 6.095440 ACACTGCCAGACATTATTTGTATTCC 59.905 38.462 0.00 0.00 39.18 3.01
4180 4513 7.088589 ACACTGCCAGACATTATTTGTATTC 57.911 36.000 0.00 0.00 39.18 1.75
4181 4514 6.095440 GGACACTGCCAGACATTATTTGTATT 59.905 38.462 0.00 0.00 39.18 1.89
4182 4515 5.590259 GGACACTGCCAGACATTATTTGTAT 59.410 40.000 0.00 0.00 39.18 2.29
4183 4516 4.941263 GGACACTGCCAGACATTATTTGTA 59.059 41.667 0.00 0.00 39.18 2.41
4184 4517 3.758554 GGACACTGCCAGACATTATTTGT 59.241 43.478 0.00 0.00 42.79 2.83
4185 4518 3.129287 GGGACACTGCCAGACATTATTTG 59.871 47.826 0.00 0.00 0.00 2.32
4186 4519 3.010584 AGGGACACTGCCAGACATTATTT 59.989 43.478 0.00 0.00 0.00 1.40
4187 4520 2.578021 AGGGACACTGCCAGACATTATT 59.422 45.455 0.00 0.00 0.00 1.40
4188 4521 2.200081 AGGGACACTGCCAGACATTAT 58.800 47.619 0.00 0.00 0.00 1.28
4189 4522 1.656587 AGGGACACTGCCAGACATTA 58.343 50.000 0.00 0.00 0.00 1.90
4190 4523 1.556911 CTAGGGACACTGCCAGACATT 59.443 52.381 0.00 0.00 0.00 2.71
4191 4524 1.198713 CTAGGGACACTGCCAGACAT 58.801 55.000 0.00 0.00 0.00 3.06
4192 4525 1.544825 GCTAGGGACACTGCCAGACA 61.545 60.000 0.00 0.00 0.00 3.41
4193 4526 1.219393 GCTAGGGACACTGCCAGAC 59.781 63.158 0.00 0.00 0.00 3.51
4194 4527 1.990060 GGCTAGGGACACTGCCAGA 60.990 63.158 11.84 0.00 40.73 3.86
4195 4528 1.841302 TTGGCTAGGGACACTGCCAG 61.841 60.000 16.91 0.00 46.57 4.85
4196 4529 1.422977 TTTGGCTAGGGACACTGCCA 61.423 55.000 14.56 14.56 45.40 4.92
4197 4530 0.034089 ATTTGGCTAGGGACACTGCC 60.034 55.000 10.28 10.28 41.14 4.85
4198 4531 2.710096 TATTTGGCTAGGGACACTGC 57.290 50.000 0.00 0.00 0.00 4.40
4199 4532 4.130118 GTCATATTTGGCTAGGGACACTG 58.870 47.826 0.00 0.00 0.00 3.66
4200 4533 3.181465 CGTCATATTTGGCTAGGGACACT 60.181 47.826 0.00 0.00 0.00 3.55
4201 4534 3.131396 CGTCATATTTGGCTAGGGACAC 58.869 50.000 0.00 0.00 0.00 3.67
4202 4535 3.035363 TCGTCATATTTGGCTAGGGACA 58.965 45.455 0.00 0.00 0.00 4.02
4203 4536 3.391049 GTCGTCATATTTGGCTAGGGAC 58.609 50.000 0.00 0.00 0.00 4.46
4204 4537 2.367567 GGTCGTCATATTTGGCTAGGGA 59.632 50.000 0.00 0.00 0.00 4.20
4205 4538 2.368875 AGGTCGTCATATTTGGCTAGGG 59.631 50.000 0.00 0.00 0.00 3.53
4206 4539 3.753294 AGGTCGTCATATTTGGCTAGG 57.247 47.619 0.00 0.00 0.00 3.02
4207 4540 4.227538 CGTAGGTCGTCATATTTGGCTAG 58.772 47.826 0.00 0.00 34.52 3.42
4208 4541 4.233123 CGTAGGTCGTCATATTTGGCTA 57.767 45.455 0.00 0.00 34.52 3.93
4209 4542 3.093717 CGTAGGTCGTCATATTTGGCT 57.906 47.619 0.00 0.00 34.52 4.75
4228 4561 2.240500 GCTGCATCTACGCTTCCCG 61.241 63.158 0.00 0.00 44.21 5.14
4229 4562 0.462759 AAGCTGCATCTACGCTTCCC 60.463 55.000 1.02 0.00 39.62 3.97
4230 4563 1.373570 AAAGCTGCATCTACGCTTCC 58.626 50.000 10.20 0.00 42.65 3.46
4231 4564 2.160417 ACAAAAGCTGCATCTACGCTTC 59.840 45.455 10.20 0.00 42.65 3.86
4232 4565 2.154462 ACAAAAGCTGCATCTACGCTT 58.846 42.857 1.02 4.42 45.13 4.68
4233 4566 1.813513 ACAAAAGCTGCATCTACGCT 58.186 45.000 1.02 0.00 35.09 5.07
4234 4567 2.619013 AACAAAAGCTGCATCTACGC 57.381 45.000 1.02 0.00 0.00 4.42
4235 4568 3.674423 GCTAACAAAAGCTGCATCTACG 58.326 45.455 1.02 0.00 39.50 3.51
4236 4569 3.674423 CGCTAACAAAAGCTGCATCTAC 58.326 45.455 1.02 0.00 40.49 2.59
4237 4570 2.095853 GCGCTAACAAAAGCTGCATCTA 59.904 45.455 0.00 0.00 40.49 1.98
4238 4571 1.135575 GCGCTAACAAAAGCTGCATCT 60.136 47.619 0.00 0.00 40.49 2.90
4239 4572 1.262882 GCGCTAACAAAAGCTGCATC 58.737 50.000 0.00 0.00 40.49 3.91
4240 4573 0.597568 TGCGCTAACAAAAGCTGCAT 59.402 45.000 9.73 0.00 42.62 3.96
4241 4574 2.028936 TGCGCTAACAAAAGCTGCA 58.971 47.368 9.73 9.95 44.05 4.41
4242 4575 0.986992 CATGCGCTAACAAAAGCTGC 59.013 50.000 9.73 0.00 40.49 5.25
4243 4576 1.980844 CACATGCGCTAACAAAAGCTG 59.019 47.619 9.73 0.00 40.49 4.24
4244 4577 1.666888 GCACATGCGCTAACAAAAGCT 60.667 47.619 9.73 0.00 40.49 3.74
4245 4578 0.710017 GCACATGCGCTAACAAAAGC 59.290 50.000 9.73 0.00 39.21 3.51
4253 4586 8.591312 GAAAATAATTTTAAAGCACATGCGCTA 58.409 29.630 8.98 0.00 38.45 4.26
4254 4587 7.331687 AGAAAATAATTTTAAAGCACATGCGCT 59.668 29.630 9.73 1.41 38.45 5.92
4255 4588 7.455447 AGAAAATAATTTTAAAGCACATGCGC 58.545 30.769 0.00 0.00 38.45 6.09
4256 4589 9.810231 AAAGAAAATAATTTTAAAGCACATGCG 57.190 25.926 0.00 0.00 38.45 4.73
4286 4619 7.753659 TCAACTACGTCAAGTTCAAATTTGAA 58.246 30.769 26.01 26.01 44.31 2.69
4287 4620 7.310072 TCAACTACGTCAAGTTCAAATTTGA 57.690 32.000 16.91 16.91 37.61 2.69
4288 4621 7.696453 AGTTCAACTACGTCAAGTTCAAATTTG 59.304 33.333 12.15 12.15 37.61 2.32
4289 4622 7.758495 AGTTCAACTACGTCAAGTTCAAATTT 58.242 30.769 0.65 0.00 37.61 1.82
4290 4623 7.316544 AGTTCAACTACGTCAAGTTCAAATT 57.683 32.000 0.65 0.00 37.61 1.82
4291 4624 6.018180 GGAGTTCAACTACGTCAAGTTCAAAT 60.018 38.462 0.65 0.00 37.61 2.32
4292 4625 5.292589 GGAGTTCAACTACGTCAAGTTCAAA 59.707 40.000 0.65 0.00 37.61 2.69
4293 4626 4.807304 GGAGTTCAACTACGTCAAGTTCAA 59.193 41.667 0.65 0.00 37.61 2.69
4294 4627 4.365723 GGAGTTCAACTACGTCAAGTTCA 58.634 43.478 0.65 0.00 37.61 3.18
4295 4628 3.739810 GGGAGTTCAACTACGTCAAGTTC 59.260 47.826 0.65 0.00 37.61 3.01
4296 4629 3.387050 AGGGAGTTCAACTACGTCAAGTT 59.613 43.478 0.00 0.00 40.33 2.66
4297 4630 2.963782 AGGGAGTTCAACTACGTCAAGT 59.036 45.455 0.00 0.00 26.61 3.16
4298 4631 3.662247 AGGGAGTTCAACTACGTCAAG 57.338 47.619 0.00 0.00 26.61 3.02
4299 4632 3.640029 AGAAGGGAGTTCAACTACGTCAA 59.360 43.478 0.00 0.00 37.67 3.18
4300 4633 3.228453 AGAAGGGAGTTCAACTACGTCA 58.772 45.455 0.00 0.00 37.67 4.35
4301 4634 3.938289 AGAAGGGAGTTCAACTACGTC 57.062 47.619 0.00 0.00 37.67 4.34
4302 4635 3.896272 AGAAGAAGGGAGTTCAACTACGT 59.104 43.478 0.00 0.00 37.67 3.57
4303 4636 4.522722 AGAAGAAGGGAGTTCAACTACG 57.477 45.455 0.00 0.00 37.67 3.51


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

AutoCloner maintained by Alex Coulton.