Multiple sequence alignment - TraesCS2A01G136500
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 | TraesCS2A01G136500 | chr2A | 100.000 | 4703 | 0 | 0 | 1 | 4703 | 82214443 | 82209741 | 0.000000e+00 | 8685.0 |
1 | TraesCS2A01G136500 | chr2A | 85.660 | 1827 | 215 | 31 | 1939 | 3745 | 83784097 | 83785896 | 0.000000e+00 | 1879.0 |
2 | TraesCS2A01G136500 | chr2A | 91.781 | 73 | 6 | 0 | 3972 | 4044 | 2716884 | 2716812 | 8.330000e-18 | 102.0 |
3 | TraesCS2A01G136500 | chr2A | 100.000 | 47 | 0 | 0 | 3700 | 3746 | 82210697 | 82210651 | 2.330000e-13 | 87.9 |
4 | TraesCS2A01G136500 | chr2A | 100.000 | 47 | 0 | 0 | 3747 | 3793 | 82210744 | 82210698 | 2.330000e-13 | 87.9 |
5 | TraesCS2A01G136500 | chr2A | 75.676 | 185 | 27 | 11 | 3747 | 3930 | 83785851 | 83786018 | 5.050000e-10 | 76.8 |
6 | TraesCS2A01G136500 | chr2D | 95.870 | 3341 | 105 | 19 | 1384 | 4703 | 82109052 | 82105724 | 0.000000e+00 | 5374.0 |
7 | TraesCS2A01G136500 | chr2D | 85.418 | 1831 | 213 | 31 | 1937 | 3745 | 83101687 | 83103485 | 0.000000e+00 | 1853.0 |
8 | TraesCS2A01G136500 | chr2D | 91.204 | 739 | 35 | 15 | 606 | 1319 | 82110009 | 82109276 | 0.000000e+00 | 977.0 |
9 | TraesCS2A01G136500 | chr2D | 100.000 | 47 | 0 | 0 | 3700 | 3746 | 82106684 | 82106638 | 2.330000e-13 | 87.9 |
10 | TraesCS2A01G136500 | chr2D | 100.000 | 47 | 0 | 0 | 3747 | 3793 | 82106731 | 82106685 | 2.330000e-13 | 87.9 |
11 | TraesCS2A01G136500 | chr2B | 94.267 | 1814 | 92 | 5 | 1937 | 3746 | 133849065 | 133847260 | 0.000000e+00 | 2763.0 |
12 | TraesCS2A01G136500 | chr2B | 86.341 | 1823 | 224 | 17 | 1942 | 3745 | 134778775 | 134780591 | 0.000000e+00 | 1964.0 |
13 | TraesCS2A01G136500 | chr2B | 88.860 | 772 | 46 | 15 | 592 | 1332 | 133851042 | 133850280 | 0.000000e+00 | 913.0 |
14 | TraesCS2A01G136500 | chr2B | 91.050 | 581 | 39 | 9 | 1366 | 1940 | 133850082 | 133849509 | 0.000000e+00 | 773.0 |
15 | TraesCS2A01G136500 | chr2B | 86.286 | 525 | 48 | 13 | 4180 | 4703 | 133846836 | 133846335 | 2.470000e-152 | 549.0 |
16 | TraesCS2A01G136500 | chr2B | 86.374 | 433 | 42 | 7 | 3753 | 4178 | 133847294 | 133846872 | 1.540000e-124 | 457.0 |
17 | TraesCS2A01G136500 | chr2B | 87.433 | 374 | 35 | 7 | 1573 | 1940 | 134778342 | 134778709 | 2.020000e-113 | 420.0 |
18 | TraesCS2A01G136500 | chr2B | 91.304 | 46 | 4 | 0 | 3747 | 3792 | 134780546 | 134780591 | 3.930000e-06 | 63.9 |
19 | TraesCS2A01G136500 | chr1D | 90.909 | 517 | 34 | 8 | 82 | 594 | 206085469 | 206085976 | 0.000000e+00 | 682.0 |
20 | TraesCS2A01G136500 | chr1D | 90.909 | 517 | 33 | 9 | 82 | 594 | 247838285 | 247837779 | 0.000000e+00 | 682.0 |
21 | TraesCS2A01G136500 | chr1D | 85.542 | 83 | 12 | 0 | 3972 | 4054 | 253346937 | 253346855 | 2.330000e-13 | 87.9 |
22 | TraesCS2A01G136500 | chr1B | 90.385 | 520 | 38 | 7 | 79 | 594 | 629847960 | 629847449 | 0.000000e+00 | 673.0 |
23 | TraesCS2A01G136500 | chr5A | 90.504 | 516 | 37 | 7 | 82 | 594 | 547116561 | 547116055 | 0.000000e+00 | 671.0 |
24 | TraesCS2A01G136500 | chr1A | 90.076 | 524 | 38 | 9 | 76 | 594 | 98495251 | 98494737 | 0.000000e+00 | 667.0 |
25 | TraesCS2A01G136500 | chr6D | 90.310 | 516 | 38 | 7 | 82 | 594 | 159786282 | 159785776 | 0.000000e+00 | 665.0 |
26 | TraesCS2A01G136500 | chr5D | 90.116 | 516 | 39 | 7 | 82 | 594 | 424878178 | 424878684 | 0.000000e+00 | 660.0 |
27 | TraesCS2A01G136500 | chr4A | 90.116 | 516 | 39 | 7 | 82 | 594 | 724240797 | 724240291 | 0.000000e+00 | 660.0 |
28 | TraesCS2A01G136500 | chr3D | 90.116 | 516 | 39 | 7 | 82 | 594 | 288314474 | 288314980 | 0.000000e+00 | 660.0 |
29 | TraesCS2A01G136500 | chr7D | 77.807 | 374 | 76 | 7 | 1987 | 2356 | 578721247 | 578721617 | 1.700000e-54 | 224.0 |
30 | TraesCS2A01G136500 | chr7D | 90.278 | 72 | 7 | 0 | 3983 | 4054 | 413234090 | 413234019 | 1.390000e-15 | 95.3 |
31 | TraesCS2A01G136500 | chr7B | 77.807 | 374 | 76 | 7 | 1987 | 2356 | 642480137 | 642480507 | 1.700000e-54 | 224.0 |
32 | TraesCS2A01G136500 | chr7B | 88.158 | 76 | 9 | 0 | 3981 | 4056 | 713284352 | 713284277 | 1.800000e-14 | 91.6 |
33 | TraesCS2A01G136500 | chr6A | 88.462 | 78 | 8 | 1 | 3981 | 4057 | 609314524 | 609314447 | 5.010000e-15 | 93.5 |
34 | TraesCS2A01G136500 | chr7A | 85.057 | 87 | 13 | 0 | 3968 | 4054 | 124795775 | 124795689 | 6.480000e-14 | 89.8 |
35 | TraesCS2A01G136500 | chr4B | 88.000 | 75 | 8 | 1 | 3980 | 4054 | 563210536 | 563210609 | 2.330000e-13 | 87.9 |
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 | TraesCS2A01G136500 | chr2A | 82209741 | 82214443 | 4702 | True | 2953.600000 | 8685 | 100.000000 | 1 | 4703 | 3 | chr2A.!!$R2 | 4702 |
1 | TraesCS2A01G136500 | chr2A | 83784097 | 83786018 | 1921 | False | 977.900000 | 1879 | 80.668000 | 1939 | 3930 | 2 | chr2A.!!$F1 | 1991 |
2 | TraesCS2A01G136500 | chr2D | 83101687 | 83103485 | 1798 | False | 1853.000000 | 1853 | 85.418000 | 1937 | 3745 | 1 | chr2D.!!$F1 | 1808 |
3 | TraesCS2A01G136500 | chr2D | 82105724 | 82110009 | 4285 | True | 1631.700000 | 5374 | 96.768500 | 606 | 4703 | 4 | chr2D.!!$R1 | 4097 |
4 | TraesCS2A01G136500 | chr2B | 133846335 | 133851042 | 4707 | True | 1091.000000 | 2763 | 89.367400 | 592 | 4703 | 5 | chr2B.!!$R1 | 4111 |
5 | TraesCS2A01G136500 | chr2B | 134778342 | 134780591 | 2249 | False | 815.966667 | 1964 | 88.359333 | 1573 | 3792 | 3 | chr2B.!!$F1 | 2219 |
6 | TraesCS2A01G136500 | chr1D | 206085469 | 206085976 | 507 | False | 682.000000 | 682 | 90.909000 | 82 | 594 | 1 | chr1D.!!$F1 | 512 |
7 | TraesCS2A01G136500 | chr1D | 247837779 | 247838285 | 506 | True | 682.000000 | 682 | 90.909000 | 82 | 594 | 1 | chr1D.!!$R1 | 512 |
8 | TraesCS2A01G136500 | chr1B | 629847449 | 629847960 | 511 | True | 673.000000 | 673 | 90.385000 | 79 | 594 | 1 | chr1B.!!$R1 | 515 |
9 | TraesCS2A01G136500 | chr5A | 547116055 | 547116561 | 506 | True | 671.000000 | 671 | 90.504000 | 82 | 594 | 1 | chr5A.!!$R1 | 512 |
10 | TraesCS2A01G136500 | chr1A | 98494737 | 98495251 | 514 | True | 667.000000 | 667 | 90.076000 | 76 | 594 | 1 | chr1A.!!$R1 | 518 |
11 | TraesCS2A01G136500 | chr6D | 159785776 | 159786282 | 506 | True | 665.000000 | 665 | 90.310000 | 82 | 594 | 1 | chr6D.!!$R1 | 512 |
12 | TraesCS2A01G136500 | chr5D | 424878178 | 424878684 | 506 | False | 660.000000 | 660 | 90.116000 | 82 | 594 | 1 | chr5D.!!$F1 | 512 |
13 | TraesCS2A01G136500 | chr4A | 724240291 | 724240797 | 506 | True | 660.000000 | 660 | 90.116000 | 82 | 594 | 1 | chr4A.!!$R1 | 512 |
14 | TraesCS2A01G136500 | chr3D | 288314474 | 288314980 | 506 | False | 660.000000 | 660 | 90.116000 | 82 | 594 | 1 | chr3D.!!$F1 | 512 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
23 | 24 | 0.522626 | CAACATCATCTTGCGCACCA | 59.477 | 50.000 | 11.12 | 0.00 | 0.00 | 4.17 | F |
1044 | 1092 | 0.176680 | CGGCAATCCTACTCAGCAGT | 59.823 | 55.000 | 0.00 | 0.00 | 36.55 | 4.40 | F |
1652 | 1917 | 0.533755 | GCTTGTGTGCAGAGGTCAGT | 60.534 | 55.000 | 0.00 | 0.00 | 0.00 | 3.41 | F |
2286 | 3001 | 1.616374 | TGAGTACATGCACGAGGAACA | 59.384 | 47.619 | 0.00 | 0.00 | 0.00 | 3.18 | F |
3291 | 4023 | 1.269998 | GCGGGAAGATAGCACGTCTAT | 59.730 | 52.381 | 7.09 | 7.09 | 40.59 | 1.98 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1122 | 1179 | 1.476845 | TAGCTTCCGTGGCAGGTGAA | 61.477 | 55.000 | 6.43 | 8.34 | 0.00 | 3.18 | R |
2534 | 3260 | 0.038526 | CCCGACACACCTGTACAGAC | 60.039 | 60.000 | 24.68 | 7.15 | 0.00 | 3.51 | R |
3291 | 4023 | 1.134753 | GAATGCGGCAATGTCATCCAA | 59.865 | 47.619 | 6.82 | 0.00 | 0.00 | 3.53 | R |
3399 | 4134 | 2.951642 | CCCGCCCTGCATATTTATATGG | 59.048 | 50.000 | 10.78 | 0.00 | 40.31 | 2.74 | R |
4612 | 5406 | 0.322322 | ATGCGTACAAACCCCTTCGA | 59.678 | 50.000 | 0.00 | 0.00 | 0.00 | 3.71 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
21 | 22 | 2.645411 | GCAACATCATCTTGCGCAC | 58.355 | 52.632 | 11.12 | 0.00 | 35.04 | 5.34 |
22 | 23 | 0.799534 | GCAACATCATCTTGCGCACC | 60.800 | 55.000 | 11.12 | 0.00 | 35.04 | 5.01 |
23 | 24 | 0.522626 | CAACATCATCTTGCGCACCA | 59.477 | 50.000 | 11.12 | 0.00 | 0.00 | 4.17 |
24 | 25 | 0.523072 | AACATCATCTTGCGCACCAC | 59.477 | 50.000 | 11.12 | 0.00 | 0.00 | 4.16 |
34 | 35 | 2.954868 | CGCACCACGCTCGGTATC | 60.955 | 66.667 | 0.00 | 0.00 | 37.07 | 2.24 |
35 | 36 | 2.954868 | GCACCACGCTCGGTATCG | 60.955 | 66.667 | 0.00 | 0.00 | 37.07 | 2.92 |
36 | 37 | 2.278596 | CACCACGCTCGGTATCGG | 60.279 | 66.667 | 0.00 | 0.00 | 37.07 | 4.18 |
37 | 38 | 3.524606 | ACCACGCTCGGTATCGGG | 61.525 | 66.667 | 0.00 | 0.00 | 37.57 | 5.14 |
38 | 39 | 4.280494 | CCACGCTCGGTATCGGGG | 62.280 | 72.222 | 0.00 | 0.00 | 43.31 | 5.73 |
41 | 42 | 2.595463 | CGCTCGGTATCGGGGGTA | 60.595 | 66.667 | 3.76 | 0.00 | 43.62 | 3.69 |
42 | 43 | 1.975407 | CGCTCGGTATCGGGGGTAT | 60.975 | 63.158 | 3.76 | 0.00 | 43.62 | 2.73 |
43 | 44 | 0.677731 | CGCTCGGTATCGGGGGTATA | 60.678 | 60.000 | 3.76 | 0.00 | 43.62 | 1.47 |
44 | 45 | 1.772836 | GCTCGGTATCGGGGGTATAT | 58.227 | 55.000 | 0.00 | 0.00 | 37.35 | 0.86 |
45 | 46 | 1.407979 | GCTCGGTATCGGGGGTATATG | 59.592 | 57.143 | 0.00 | 0.00 | 37.35 | 1.78 |
46 | 47 | 2.947243 | GCTCGGTATCGGGGGTATATGA | 60.947 | 54.545 | 0.00 | 0.00 | 37.35 | 2.15 |
47 | 48 | 3.563223 | CTCGGTATCGGGGGTATATGAT | 58.437 | 50.000 | 0.00 | 0.00 | 36.95 | 2.45 |
48 | 49 | 3.293337 | TCGGTATCGGGGGTATATGATG | 58.707 | 50.000 | 0.00 | 0.00 | 36.95 | 3.07 |
49 | 50 | 3.053470 | TCGGTATCGGGGGTATATGATGA | 60.053 | 47.826 | 0.00 | 0.00 | 36.95 | 2.92 |
50 | 51 | 3.067742 | CGGTATCGGGGGTATATGATGAC | 59.932 | 52.174 | 0.00 | 0.00 | 0.00 | 3.06 |
51 | 52 | 3.067742 | GGTATCGGGGGTATATGATGACG | 59.932 | 52.174 | 0.00 | 0.00 | 0.00 | 4.35 |
52 | 53 | 2.297698 | TCGGGGGTATATGATGACGT | 57.702 | 50.000 | 0.00 | 0.00 | 0.00 | 4.34 |
53 | 54 | 1.890489 | TCGGGGGTATATGATGACGTG | 59.110 | 52.381 | 0.00 | 0.00 | 0.00 | 4.49 |
54 | 55 | 1.671850 | CGGGGGTATATGATGACGTGC | 60.672 | 57.143 | 0.00 | 0.00 | 0.00 | 5.34 |
55 | 56 | 1.623811 | GGGGGTATATGATGACGTGCT | 59.376 | 52.381 | 0.00 | 0.00 | 0.00 | 4.40 |
56 | 57 | 2.353803 | GGGGGTATATGATGACGTGCTC | 60.354 | 54.545 | 0.00 | 0.00 | 0.00 | 4.26 |
57 | 58 | 2.353803 | GGGGTATATGATGACGTGCTCC | 60.354 | 54.545 | 0.00 | 0.00 | 0.00 | 4.70 |
58 | 59 | 2.299013 | GGGTATATGATGACGTGCTCCA | 59.701 | 50.000 | 0.00 | 0.00 | 0.00 | 3.86 |
59 | 60 | 3.318017 | GGTATATGATGACGTGCTCCAC | 58.682 | 50.000 | 0.00 | 0.00 | 0.00 | 4.02 |
60 | 61 | 3.243737 | GGTATATGATGACGTGCTCCACA | 60.244 | 47.826 | 0.00 | 0.00 | 33.40 | 4.17 |
61 | 62 | 3.541996 | ATATGATGACGTGCTCCACAA | 57.458 | 42.857 | 0.00 | 0.00 | 33.40 | 3.33 |
62 | 63 | 2.408271 | ATGATGACGTGCTCCACAAT | 57.592 | 45.000 | 0.00 | 0.00 | 33.40 | 2.71 |
63 | 64 | 2.183478 | TGATGACGTGCTCCACAATT | 57.817 | 45.000 | 0.00 | 0.00 | 33.40 | 2.32 |
64 | 65 | 2.503331 | TGATGACGTGCTCCACAATTT | 58.497 | 42.857 | 0.00 | 0.00 | 33.40 | 1.82 |
65 | 66 | 2.884012 | TGATGACGTGCTCCACAATTTT | 59.116 | 40.909 | 0.00 | 0.00 | 33.40 | 1.82 |
66 | 67 | 2.772568 | TGACGTGCTCCACAATTTTG | 57.227 | 45.000 | 0.00 | 0.00 | 33.40 | 2.44 |
67 | 68 | 2.020720 | TGACGTGCTCCACAATTTTGT | 58.979 | 42.857 | 0.00 | 0.00 | 43.36 | 2.83 |
68 | 69 | 2.032799 | TGACGTGCTCCACAATTTTGTC | 59.967 | 45.455 | 0.00 | 0.00 | 39.91 | 3.18 |
69 | 70 | 2.290641 | GACGTGCTCCACAATTTTGTCT | 59.709 | 45.455 | 0.00 | 0.00 | 39.91 | 3.41 |
70 | 71 | 2.033299 | ACGTGCTCCACAATTTTGTCTG | 59.967 | 45.455 | 0.00 | 0.00 | 39.91 | 3.51 |
71 | 72 | 2.605338 | CGTGCTCCACAATTTTGTCTGG | 60.605 | 50.000 | 0.00 | 0.00 | 39.91 | 3.86 |
72 | 73 | 1.962807 | TGCTCCACAATTTTGTCTGGG | 59.037 | 47.619 | 0.00 | 0.00 | 39.91 | 4.45 |
73 | 74 | 1.337167 | GCTCCACAATTTTGTCTGGGC | 60.337 | 52.381 | 0.00 | 0.00 | 39.91 | 5.36 |
74 | 75 | 1.962807 | CTCCACAATTTTGTCTGGGCA | 59.037 | 47.619 | 0.00 | 0.00 | 39.91 | 5.36 |
94 | 98 | 8.810652 | TGGGCAATAATATTTTTCGATAAAGC | 57.189 | 30.769 | 7.13 | 3.29 | 0.00 | 3.51 |
106 | 110 | 7.728580 | TTTTCGATAAAGCGCGATTTTATTT | 57.271 | 28.000 | 28.45 | 10.56 | 36.31 | 1.40 |
192 | 198 | 3.127533 | GGATGCACACAGCCGGAC | 61.128 | 66.667 | 5.05 | 0.00 | 43.70 | 4.79 |
193 | 199 | 2.046892 | GATGCACACAGCCGGACT | 60.047 | 61.111 | 5.05 | 0.00 | 44.83 | 3.85 |
194 | 200 | 1.218047 | GATGCACACAGCCGGACTA | 59.782 | 57.895 | 5.05 | 0.00 | 44.83 | 2.59 |
195 | 201 | 0.807667 | GATGCACACAGCCGGACTAG | 60.808 | 60.000 | 5.05 | 0.75 | 44.83 | 2.57 |
196 | 202 | 2.125512 | GCACACAGCCGGACTAGG | 60.126 | 66.667 | 5.05 | 0.00 | 37.23 | 3.02 |
230 | 236 | 4.976987 | TGACAACCAGAAGAAAACGAAAC | 58.023 | 39.130 | 0.00 | 0.00 | 0.00 | 2.78 |
250 | 257 | 3.616219 | ACCAGCAAATCGGCAATAGTAA | 58.384 | 40.909 | 0.00 | 0.00 | 35.83 | 2.24 |
387 | 394 | 2.034053 | ACACCGCATTGAACAACGATTT | 59.966 | 40.909 | 0.00 | 0.00 | 0.00 | 2.17 |
402 | 409 | 4.471904 | ACGATTTGACCTCTGCTCATTA | 57.528 | 40.909 | 0.00 | 0.00 | 0.00 | 1.90 |
453 | 460 | 1.812571 | ACAACGGAAAATAGCCTGCAG | 59.187 | 47.619 | 6.78 | 6.78 | 0.00 | 4.41 |
528 | 535 | 4.618460 | CGACCATAATAAGGCATACGCTCT | 60.618 | 45.833 | 0.00 | 0.00 | 38.60 | 4.09 |
541 | 548 | 4.262079 | GCATACGCTCTCACCCTTAATAGT | 60.262 | 45.833 | 0.00 | 0.00 | 34.30 | 2.12 |
550 | 557 | 7.121315 | GCTCTCACCCTTAATAGTGTTTTGAAT | 59.879 | 37.037 | 5.26 | 0.00 | 35.45 | 2.57 |
573 | 581 | 6.563222 | TCTATTTAAAAACCGTCCAACCAG | 57.437 | 37.500 | 0.00 | 0.00 | 0.00 | 4.00 |
589 | 597 | 5.835819 | TCCAACCAGTGACCAAAAATATTGA | 59.164 | 36.000 | 0.00 | 0.00 | 0.00 | 2.57 |
669 | 683 | 2.426024 | TCGCTATACTTGGTCCTGTCAC | 59.574 | 50.000 | 0.00 | 0.00 | 0.00 | 3.67 |
670 | 684 | 2.165641 | CGCTATACTTGGTCCTGTCACA | 59.834 | 50.000 | 0.00 | 0.00 | 0.00 | 3.58 |
754 | 779 | 4.168291 | CCGCTCTTGGCCCTCTCC | 62.168 | 72.222 | 0.00 | 0.00 | 37.74 | 3.71 |
755 | 780 | 4.168291 | CGCTCTTGGCCCTCTCCC | 62.168 | 72.222 | 0.00 | 0.00 | 37.74 | 4.30 |
775 | 800 | 1.234821 | CCAACGCTGGCTGAAAAGTA | 58.765 | 50.000 | 0.00 | 0.00 | 35.39 | 2.24 |
778 | 803 | 0.804989 | ACGCTGGCTGAAAAGTATGC | 59.195 | 50.000 | 0.00 | 0.00 | 0.00 | 3.14 |
801 | 826 | 2.122783 | TGTTTCGGCCCTCAAATAGG | 57.877 | 50.000 | 0.00 | 0.00 | 46.09 | 2.57 |
802 | 827 | 1.353022 | TGTTTCGGCCCTCAAATAGGT | 59.647 | 47.619 | 0.00 | 0.00 | 44.90 | 3.08 |
805 | 830 | 0.988832 | TCGGCCCTCAAATAGGTTGT | 59.011 | 50.000 | 0.00 | 0.00 | 44.90 | 3.32 |
809 | 834 | 1.202348 | GCCCTCAAATAGGTTGTGCAC | 59.798 | 52.381 | 10.75 | 10.75 | 44.90 | 4.57 |
839 | 868 | 2.500098 | GCCCTCAGATAGTGTGTGGTAA | 59.500 | 50.000 | 0.00 | 0.00 | 0.00 | 2.85 |
840 | 869 | 3.134804 | GCCCTCAGATAGTGTGTGGTAAT | 59.865 | 47.826 | 0.00 | 0.00 | 0.00 | 1.89 |
841 | 870 | 4.697514 | CCCTCAGATAGTGTGTGGTAATG | 58.302 | 47.826 | 0.00 | 0.00 | 0.00 | 1.90 |
842 | 871 | 4.443457 | CCCTCAGATAGTGTGTGGTAATGG | 60.443 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
843 | 872 | 4.162320 | CCTCAGATAGTGTGTGGTAATGGT | 59.838 | 45.833 | 0.00 | 0.00 | 0.00 | 3.55 |
844 | 873 | 5.362717 | CCTCAGATAGTGTGTGGTAATGGTA | 59.637 | 44.000 | 0.00 | 0.00 | 0.00 | 3.25 |
845 | 874 | 6.042093 | CCTCAGATAGTGTGTGGTAATGGTAT | 59.958 | 42.308 | 0.00 | 0.00 | 0.00 | 2.73 |
969 | 1017 | 1.665916 | CCAGTGTCACAGGCTCACG | 60.666 | 63.158 | 5.62 | 0.00 | 37.20 | 4.35 |
984 | 1032 | 2.726760 | GCTCACGAGTCACAACTAACAG | 59.273 | 50.000 | 0.00 | 0.00 | 35.28 | 3.16 |
996 | 1044 | 8.085296 | AGTCACAACTAACAGAGAGTTCATTAG | 58.915 | 37.037 | 0.00 | 0.00 | 41.64 | 1.73 |
1044 | 1092 | 0.176680 | CGGCAATCCTACTCAGCAGT | 59.823 | 55.000 | 0.00 | 0.00 | 36.55 | 4.40 |
1122 | 1179 | 0.613012 | GCTTTCCCCATGTCCAAGCT | 60.613 | 55.000 | 8.25 | 0.00 | 37.47 | 3.74 |
1308 | 1365 | 2.292569 | GCAGGTATACGCTAGTGCTACA | 59.707 | 50.000 | 14.89 | 0.00 | 36.97 | 2.74 |
1309 | 1366 | 3.057456 | GCAGGTATACGCTAGTGCTACAT | 60.057 | 47.826 | 14.89 | 7.96 | 36.97 | 2.29 |
1310 | 1367 | 4.155462 | GCAGGTATACGCTAGTGCTACATA | 59.845 | 45.833 | 14.89 | 2.60 | 36.97 | 2.29 |
1321 | 1378 | 9.121658 | ACGCTAGTGCTACATATGTACATATAT | 57.878 | 33.333 | 24.50 | 18.07 | 36.97 | 0.86 |
1347 | 1404 | 6.617782 | TTTGCTTTATCAATTCCCAATCCA | 57.382 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
1348 | 1405 | 6.811634 | TTGCTTTATCAATTCCCAATCCAT | 57.188 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
1349 | 1406 | 6.164417 | TGCTTTATCAATTCCCAATCCATG | 57.836 | 37.500 | 0.00 | 0.00 | 0.00 | 3.66 |
1356 | 1566 | 6.224665 | TCAATTCCCAATCCATGTTTCATC | 57.775 | 37.500 | 0.00 | 0.00 | 0.00 | 2.92 |
1373 | 1594 | 8.065473 | TGTTTCATCATTATGGTTTGCTACAT | 57.935 | 30.769 | 0.00 | 0.00 | 33.61 | 2.29 |
1382 | 1603 | 3.681593 | TGGTTTGCTACATCACTAACCC | 58.318 | 45.455 | 0.00 | 0.00 | 39.84 | 4.11 |
1402 | 1654 | 5.018809 | ACCCAGATACTTGTTTCATTGCAT | 58.981 | 37.500 | 0.00 | 0.00 | 0.00 | 3.96 |
1407 | 1659 | 9.590451 | CCAGATACTTGTTTCATTGCATTATTT | 57.410 | 29.630 | 0.00 | 0.00 | 0.00 | 1.40 |
1461 | 1713 | 1.904287 | TGCCGTTTCAGCTATTTGGT | 58.096 | 45.000 | 0.00 | 0.00 | 0.00 | 3.67 |
1465 | 1717 | 2.811431 | CCGTTTCAGCTATTTGGTGTCA | 59.189 | 45.455 | 0.00 | 0.00 | 43.97 | 3.58 |
1469 | 1721 | 5.562696 | CGTTTCAGCTATTTGGTGTCATGTT | 60.563 | 40.000 | 0.00 | 0.00 | 43.97 | 2.71 |
1474 | 1728 | 4.943705 | AGCTATTTGGTGTCATGTTGTAGG | 59.056 | 41.667 | 0.00 | 0.00 | 0.00 | 3.18 |
1475 | 1729 | 4.438744 | GCTATTTGGTGTCATGTTGTAGGC | 60.439 | 45.833 | 0.00 | 0.00 | 0.00 | 3.93 |
1568 | 1827 | 5.715439 | ATTCCTGGACAATCTAATCCACA | 57.285 | 39.130 | 0.00 | 0.00 | 40.17 | 4.17 |
1622 | 1887 | 6.243216 | TCGTTAACCCCAGCTAATTAATCT | 57.757 | 37.500 | 0.00 | 0.00 | 0.00 | 2.40 |
1635 | 1900 | 5.391310 | GCTAATTAATCTATGCATGCACGCT | 60.391 | 40.000 | 25.37 | 10.39 | 0.00 | 5.07 |
1652 | 1917 | 0.533755 | GCTTGTGTGCAGAGGTCAGT | 60.534 | 55.000 | 0.00 | 0.00 | 0.00 | 3.41 |
1664 | 1929 | 4.333926 | GCAGAGGTCAGTAAAATGGATGAC | 59.666 | 45.833 | 0.00 | 0.00 | 41.03 | 3.06 |
1802 | 2067 | 7.876068 | TCACTTTAAGAAACAGGTTGATATCGT | 59.124 | 33.333 | 0.00 | 0.00 | 0.00 | 3.73 |
2216 | 2931 | 2.616842 | CAAGTTAAACGTGCCCTTCACT | 59.383 | 45.455 | 0.00 | 0.00 | 43.46 | 3.41 |
2224 | 2939 | 2.303600 | ACGTGCCCTTCACTTACCATTA | 59.696 | 45.455 | 0.00 | 0.00 | 43.46 | 1.90 |
2286 | 3001 | 1.616374 | TGAGTACATGCACGAGGAACA | 59.384 | 47.619 | 0.00 | 0.00 | 0.00 | 3.18 |
2408 | 3123 | 8.251750 | TGTTATACTCAACTACACAATGAAGC | 57.748 | 34.615 | 0.00 | 0.00 | 0.00 | 3.86 |
2534 | 3260 | 2.510064 | TACTTTAGGTGGTGGCGCGG | 62.510 | 60.000 | 8.83 | 0.00 | 0.00 | 6.46 |
2604 | 3330 | 1.749063 | GGTTACCTTTGGTGCTATGCC | 59.251 | 52.381 | 0.00 | 0.00 | 36.19 | 4.40 |
2729 | 3455 | 5.547465 | TGAGGAATGTCGACAACTAAATGT | 58.453 | 37.500 | 24.13 | 0.00 | 35.90 | 2.71 |
2830 | 3561 | 4.338012 | TGTCATGGACTGATTTTCATGCT | 58.662 | 39.130 | 0.00 | 0.00 | 37.49 | 3.79 |
3291 | 4023 | 1.269998 | GCGGGAAGATAGCACGTCTAT | 59.730 | 52.381 | 7.09 | 7.09 | 40.59 | 1.98 |
3370 | 4102 | 8.927675 | AACTATAACAACTCAACCACCAATAA | 57.072 | 30.769 | 0.00 | 0.00 | 0.00 | 1.40 |
3399 | 4134 | 9.953697 | ACTCAAGATAATGTATCTAACTTCGAC | 57.046 | 33.333 | 0.00 | 0.00 | 44.44 | 4.20 |
3561 | 4296 | 3.930336 | TCAAGCTCACTTCGAACATCAT | 58.070 | 40.909 | 0.00 | 0.00 | 32.29 | 2.45 |
3625 | 4360 | 4.944619 | AGCATGCTAGTGTTCTATGCTA | 57.055 | 40.909 | 21.21 | 0.00 | 37.88 | 3.49 |
3937 | 4678 | 1.066430 | AGTTGTGTGTCTCCACGTTGT | 60.066 | 47.619 | 0.00 | 0.00 | 44.92 | 3.32 |
3938 | 4679 | 1.735571 | GTTGTGTGTCTCCACGTTGTT | 59.264 | 47.619 | 0.00 | 0.00 | 44.92 | 2.83 |
3939 | 4680 | 1.364721 | TGTGTGTCTCCACGTTGTTG | 58.635 | 50.000 | 0.00 | 0.00 | 44.92 | 3.33 |
3976 | 4727 | 6.389869 | TCTCTCTCTCTCTCTCTTAATCCCTT | 59.610 | 42.308 | 0.00 | 0.00 | 0.00 | 3.95 |
3978 | 4729 | 6.159575 | TCTCTCTCTCTCTCTTAATCCCTTCA | 59.840 | 42.308 | 0.00 | 0.00 | 0.00 | 3.02 |
4119 | 4877 | 4.701171 | CGGCCAAAACCCAACTATTAAGTA | 59.299 | 41.667 | 2.24 | 0.00 | 33.75 | 2.24 |
4345 | 5137 | 3.916989 | ACCAAGGAGGGATACAAGAAACT | 59.083 | 43.478 | 0.00 | 0.00 | 43.89 | 2.66 |
4388 | 5180 | 2.101415 | TCAGACTATTCCACCGATGCAG | 59.899 | 50.000 | 0.00 | 0.00 | 0.00 | 4.41 |
4389 | 5181 | 2.101415 | CAGACTATTCCACCGATGCAGA | 59.899 | 50.000 | 0.00 | 0.00 | 0.00 | 4.26 |
4394 | 5187 | 2.559698 | TTCCACCGATGCAGAAGAAA | 57.440 | 45.000 | 0.00 | 0.00 | 0.00 | 2.52 |
4478 | 5272 | 9.825972 | AATTACGTACACAGAAATCTCATTTTG | 57.174 | 29.630 | 0.00 | 0.00 | 31.47 | 2.44 |
4479 | 5273 | 6.861065 | ACGTACACAGAAATCTCATTTTGT | 57.139 | 33.333 | 0.00 | 0.00 | 31.47 | 2.83 |
4612 | 5406 | 0.253327 | GTGAGGCCCGGAGAAGAAAT | 59.747 | 55.000 | 0.73 | 0.00 | 0.00 | 2.17 |
4651 | 5445 | 0.459489 | GTGAGGCAAAACTGTTGGCA | 59.541 | 50.000 | 14.10 | 0.00 | 46.01 | 4.92 |
4653 | 5447 | 0.598419 | GAGGCAAAACTGTTGGCAGC | 60.598 | 55.000 | 14.10 | 0.00 | 46.30 | 5.25 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
0 | 1 | 0.524816 | GCGCAAGATGATGTTGCTGG | 60.525 | 55.000 | 22.34 | 10.90 | 46.73 | 4.85 |
1 | 2 | 0.169451 | TGCGCAAGATGATGTTGCTG | 59.831 | 50.000 | 22.34 | 16.84 | 46.73 | 4.41 |
2 | 3 | 0.169672 | GTGCGCAAGATGATGTTGCT | 59.830 | 50.000 | 22.34 | 0.00 | 46.73 | 3.91 |
3 | 4 | 0.799534 | GGTGCGCAAGATGATGTTGC | 60.800 | 55.000 | 14.00 | 16.36 | 45.68 | 4.17 |
4 | 5 | 0.522626 | TGGTGCGCAAGATGATGTTG | 59.477 | 50.000 | 14.00 | 0.00 | 43.02 | 3.33 |
5 | 6 | 0.523072 | GTGGTGCGCAAGATGATGTT | 59.477 | 50.000 | 14.00 | 0.00 | 43.02 | 2.71 |
6 | 7 | 1.638388 | CGTGGTGCGCAAGATGATGT | 61.638 | 55.000 | 14.00 | 0.00 | 43.02 | 3.06 |
7 | 8 | 1.061411 | CGTGGTGCGCAAGATGATG | 59.939 | 57.895 | 14.00 | 0.00 | 43.02 | 3.07 |
8 | 9 | 3.489731 | CGTGGTGCGCAAGATGAT | 58.510 | 55.556 | 14.00 | 0.00 | 43.02 | 2.45 |
18 | 19 | 2.954868 | CGATACCGAGCGTGGTGC | 60.955 | 66.667 | 12.54 | 4.57 | 43.68 | 5.01 |
19 | 20 | 2.278596 | CCGATACCGAGCGTGGTG | 60.279 | 66.667 | 12.54 | 0.00 | 43.68 | 4.17 |
20 | 21 | 3.524606 | CCCGATACCGAGCGTGGT | 61.525 | 66.667 | 8.04 | 8.04 | 46.26 | 4.16 |
21 | 22 | 4.280494 | CCCCGATACCGAGCGTGG | 62.280 | 72.222 | 0.00 | 0.00 | 38.22 | 4.94 |
22 | 23 | 4.280494 | CCCCCGATACCGAGCGTG | 62.280 | 72.222 | 0.00 | 0.00 | 38.22 | 5.34 |
23 | 24 | 2.703675 | ATACCCCCGATACCGAGCGT | 62.704 | 60.000 | 0.00 | 0.00 | 38.22 | 5.07 |
24 | 25 | 0.677731 | TATACCCCCGATACCGAGCG | 60.678 | 60.000 | 0.00 | 0.00 | 38.22 | 5.03 |
25 | 26 | 1.407979 | CATATACCCCCGATACCGAGC | 59.592 | 57.143 | 0.00 | 0.00 | 38.22 | 5.03 |
26 | 27 | 3.008835 | TCATATACCCCCGATACCGAG | 57.991 | 52.381 | 0.00 | 0.00 | 38.22 | 4.63 |
27 | 28 | 3.053470 | TCATCATATACCCCCGATACCGA | 60.053 | 47.826 | 0.00 | 0.00 | 38.22 | 4.69 |
28 | 29 | 3.067742 | GTCATCATATACCCCCGATACCG | 59.932 | 52.174 | 0.00 | 0.00 | 0.00 | 4.02 |
29 | 30 | 3.067742 | CGTCATCATATACCCCCGATACC | 59.932 | 52.174 | 0.00 | 0.00 | 0.00 | 2.73 |
30 | 31 | 3.698040 | ACGTCATCATATACCCCCGATAC | 59.302 | 47.826 | 0.00 | 0.00 | 0.00 | 2.24 |
31 | 32 | 3.697542 | CACGTCATCATATACCCCCGATA | 59.302 | 47.826 | 0.00 | 0.00 | 0.00 | 2.92 |
32 | 33 | 2.496070 | CACGTCATCATATACCCCCGAT | 59.504 | 50.000 | 0.00 | 0.00 | 0.00 | 4.18 |
33 | 34 | 1.890489 | CACGTCATCATATACCCCCGA | 59.110 | 52.381 | 0.00 | 0.00 | 0.00 | 5.14 |
34 | 35 | 1.671850 | GCACGTCATCATATACCCCCG | 60.672 | 57.143 | 0.00 | 0.00 | 0.00 | 5.73 |
35 | 36 | 1.623811 | AGCACGTCATCATATACCCCC | 59.376 | 52.381 | 0.00 | 0.00 | 0.00 | 5.40 |
36 | 37 | 2.353803 | GGAGCACGTCATCATATACCCC | 60.354 | 54.545 | 0.00 | 0.00 | 0.00 | 4.95 |
37 | 38 | 2.299013 | TGGAGCACGTCATCATATACCC | 59.701 | 50.000 | 0.00 | 0.00 | 0.00 | 3.69 |
38 | 39 | 3.243737 | TGTGGAGCACGTCATCATATACC | 60.244 | 47.826 | 0.00 | 0.00 | 37.14 | 2.73 |
39 | 40 | 3.977427 | TGTGGAGCACGTCATCATATAC | 58.023 | 45.455 | 0.00 | 0.00 | 37.14 | 1.47 |
40 | 41 | 4.664150 | TTGTGGAGCACGTCATCATATA | 57.336 | 40.909 | 0.00 | 0.00 | 37.14 | 0.86 |
41 | 42 | 3.541996 | TTGTGGAGCACGTCATCATAT | 57.458 | 42.857 | 0.00 | 0.00 | 37.14 | 1.78 |
42 | 43 | 3.541996 | ATTGTGGAGCACGTCATCATA | 57.458 | 42.857 | 0.00 | 0.00 | 37.14 | 2.15 |
43 | 44 | 2.408271 | ATTGTGGAGCACGTCATCAT | 57.592 | 45.000 | 0.00 | 0.00 | 37.14 | 2.45 |
44 | 45 | 2.183478 | AATTGTGGAGCACGTCATCA | 57.817 | 45.000 | 0.00 | 0.00 | 37.14 | 3.07 |
45 | 46 | 3.236816 | CAAAATTGTGGAGCACGTCATC | 58.763 | 45.455 | 0.00 | 0.00 | 37.14 | 2.92 |
46 | 47 | 2.622942 | ACAAAATTGTGGAGCACGTCAT | 59.377 | 40.909 | 0.00 | 0.00 | 40.49 | 3.06 |
47 | 48 | 2.020720 | ACAAAATTGTGGAGCACGTCA | 58.979 | 42.857 | 0.00 | 0.00 | 40.49 | 4.35 |
48 | 49 | 2.290641 | AGACAAAATTGTGGAGCACGTC | 59.709 | 45.455 | 3.05 | 0.00 | 42.43 | 4.34 |
49 | 50 | 2.033299 | CAGACAAAATTGTGGAGCACGT | 59.967 | 45.455 | 3.05 | 0.00 | 42.43 | 4.49 |
50 | 51 | 2.605338 | CCAGACAAAATTGTGGAGCACG | 60.605 | 50.000 | 3.05 | 0.00 | 42.43 | 5.34 |
51 | 52 | 2.288395 | CCCAGACAAAATTGTGGAGCAC | 60.288 | 50.000 | 3.05 | 0.00 | 42.43 | 4.40 |
52 | 53 | 1.962807 | CCCAGACAAAATTGTGGAGCA | 59.037 | 47.619 | 3.05 | 0.00 | 42.43 | 4.26 |
53 | 54 | 1.337167 | GCCCAGACAAAATTGTGGAGC | 60.337 | 52.381 | 3.05 | 2.86 | 42.43 | 4.70 |
54 | 55 | 1.962807 | TGCCCAGACAAAATTGTGGAG | 59.037 | 47.619 | 3.05 | 0.00 | 42.43 | 3.86 |
55 | 56 | 2.079170 | TGCCCAGACAAAATTGTGGA | 57.921 | 45.000 | 3.05 | 0.00 | 42.43 | 4.02 |
56 | 57 | 2.906691 | TTGCCCAGACAAAATTGTGG | 57.093 | 45.000 | 3.05 | 0.38 | 42.43 | 4.17 |
57 | 58 | 8.721019 | AATATTATTGCCCAGACAAAATTGTG | 57.279 | 30.769 | 3.05 | 0.00 | 42.43 | 3.33 |
58 | 59 | 9.737844 | AAAATATTATTGCCCAGACAAAATTGT | 57.262 | 25.926 | 0.00 | 0.00 | 45.65 | 2.71 |
61 | 62 | 9.097257 | CGAAAAATATTATTGCCCAGACAAAAT | 57.903 | 29.630 | 0.00 | 0.00 | 32.27 | 1.82 |
62 | 63 | 8.307483 | TCGAAAAATATTATTGCCCAGACAAAA | 58.693 | 29.630 | 0.00 | 0.00 | 32.27 | 2.44 |
63 | 64 | 7.831753 | TCGAAAAATATTATTGCCCAGACAAA | 58.168 | 30.769 | 0.00 | 0.00 | 32.27 | 2.83 |
64 | 65 | 7.397892 | TCGAAAAATATTATTGCCCAGACAA | 57.602 | 32.000 | 0.00 | 0.00 | 0.00 | 3.18 |
65 | 66 | 7.581213 | ATCGAAAAATATTATTGCCCAGACA | 57.419 | 32.000 | 0.00 | 0.00 | 0.00 | 3.41 |
66 | 67 | 9.959749 | TTTATCGAAAAATATTATTGCCCAGAC | 57.040 | 29.630 | 0.00 | 0.00 | 0.00 | 3.51 |
68 | 69 | 8.915654 | GCTTTATCGAAAAATATTATTGCCCAG | 58.084 | 33.333 | 0.00 | 0.00 | 0.00 | 4.45 |
69 | 70 | 7.593273 | CGCTTTATCGAAAAATATTATTGCCCA | 59.407 | 33.333 | 0.00 | 0.00 | 0.00 | 5.36 |
70 | 71 | 7.410407 | GCGCTTTATCGAAAAATATTATTGCCC | 60.410 | 37.037 | 0.00 | 0.00 | 0.00 | 5.36 |
71 | 72 | 7.437124 | GCGCTTTATCGAAAAATATTATTGCC | 58.563 | 34.615 | 0.00 | 0.00 | 0.00 | 4.52 |
72 | 73 | 7.059033 | TCGCGCTTTATCGAAAAATATTATTGC | 59.941 | 33.333 | 5.56 | 0.00 | 0.00 | 3.56 |
73 | 74 | 8.416998 | TCGCGCTTTATCGAAAAATATTATTG | 57.583 | 30.769 | 5.56 | 0.00 | 0.00 | 1.90 |
74 | 75 | 9.607285 | AATCGCGCTTTATCGAAAAATATTATT | 57.393 | 25.926 | 5.56 | 0.00 | 38.28 | 1.40 |
94 | 98 | 8.461398 | GCTACATTTTGAGTAAATAAAATCGCG | 58.539 | 33.333 | 0.00 | 0.00 | 35.07 | 5.87 |
106 | 110 | 6.472016 | TCCACTTGATGCTACATTTTGAGTA | 58.528 | 36.000 | 0.00 | 0.00 | 0.00 | 2.59 |
138 | 143 | 3.319689 | TCGGGTGTTGCTCGATCATAATA | 59.680 | 43.478 | 0.00 | 0.00 | 46.45 | 0.98 |
147 | 152 | 2.432628 | GAGGTCGGGTGTTGCTCG | 60.433 | 66.667 | 0.00 | 0.00 | 43.78 | 5.03 |
148 | 153 | 1.374758 | CAGAGGTCGGGTGTTGCTC | 60.375 | 63.158 | 0.00 | 0.00 | 0.00 | 4.26 |
149 | 154 | 2.743718 | CAGAGGTCGGGTGTTGCT | 59.256 | 61.111 | 0.00 | 0.00 | 0.00 | 3.91 |
190 | 196 | 3.067833 | GTCAGACTTTTGGTGCCTAGTC | 58.932 | 50.000 | 0.00 | 0.00 | 37.79 | 2.59 |
192 | 198 | 3.126001 | TGTCAGACTTTTGGTGCCTAG | 57.874 | 47.619 | 1.31 | 0.00 | 0.00 | 3.02 |
193 | 199 | 3.211045 | GTTGTCAGACTTTTGGTGCCTA | 58.789 | 45.455 | 1.31 | 0.00 | 0.00 | 3.93 |
194 | 200 | 2.024414 | GTTGTCAGACTTTTGGTGCCT | 58.976 | 47.619 | 1.31 | 0.00 | 0.00 | 4.75 |
195 | 201 | 1.067060 | GGTTGTCAGACTTTTGGTGCC | 59.933 | 52.381 | 1.31 | 0.00 | 0.00 | 5.01 |
196 | 202 | 1.748493 | TGGTTGTCAGACTTTTGGTGC | 59.252 | 47.619 | 1.31 | 0.00 | 0.00 | 5.01 |
226 | 232 | 2.368655 | ATTGCCGATTTGCTGGTTTC | 57.631 | 45.000 | 0.00 | 0.00 | 0.00 | 2.78 |
230 | 236 | 4.096382 | ACTTTACTATTGCCGATTTGCTGG | 59.904 | 41.667 | 0.00 | 0.00 | 0.00 | 4.85 |
250 | 257 | 4.441634 | GCACAATGTCGGTCTATAGGACTT | 60.442 | 45.833 | 0.00 | 0.00 | 43.97 | 3.01 |
329 | 336 | 2.574824 | AGGTGGCTACGGAGGTTTTTAT | 59.425 | 45.455 | 0.00 | 0.00 | 0.00 | 1.40 |
373 | 380 | 4.320494 | GCAGAGGTCAAATCGTTGTTCAAT | 60.320 | 41.667 | 0.00 | 0.00 | 36.07 | 2.57 |
402 | 409 | 5.185828 | TCGCTTCATATGTGGTCTATGCTAT | 59.814 | 40.000 | 1.90 | 0.00 | 0.00 | 2.97 |
453 | 460 | 8.816640 | TTTTAATGACAAAAATGCTTCTCCTC | 57.183 | 30.769 | 0.00 | 0.00 | 0.00 | 3.71 |
495 | 502 | 4.213482 | CCTTATTATGGTCGCTTTGGCTAC | 59.787 | 45.833 | 0.00 | 0.00 | 36.09 | 3.58 |
541 | 548 | 9.465985 | GGACGGTTTTTAAATAGATTCAAAACA | 57.534 | 29.630 | 16.75 | 0.00 | 36.04 | 2.83 |
550 | 557 | 6.016943 | CACTGGTTGGACGGTTTTTAAATAGA | 60.017 | 38.462 | 0.00 | 0.00 | 0.00 | 1.98 |
560 | 568 | 1.147600 | GGTCACTGGTTGGACGGTT | 59.852 | 57.895 | 0.00 | 0.00 | 34.87 | 4.44 |
573 | 581 | 6.074569 | CGTTGGTTGTCAATATTTTTGGTCAC | 60.075 | 38.462 | 0.00 | 0.00 | 37.73 | 3.67 |
669 | 683 | 3.183754 | TGAACGTACAACTGTGTCACTG | 58.816 | 45.455 | 8.21 | 8.21 | 39.30 | 3.66 |
670 | 684 | 3.513680 | TGAACGTACAACTGTGTCACT | 57.486 | 42.857 | 4.27 | 0.00 | 39.30 | 3.41 |
678 | 692 | 4.613944 | TGTTTCTCGATGAACGTACAACT | 58.386 | 39.130 | 0.00 | 0.00 | 43.13 | 3.16 |
709 | 731 | 4.443034 | GGTGTCAGCTCCGTTTTCCTATAT | 60.443 | 45.833 | 0.00 | 0.00 | 0.00 | 0.86 |
721 | 745 | 4.459089 | GGCTCGGGTGTCAGCTCC | 62.459 | 72.222 | 1.41 | 0.00 | 35.82 | 4.70 |
722 | 746 | 4.803426 | CGGCTCGGGTGTCAGCTC | 62.803 | 72.222 | 1.41 | 0.00 | 35.82 | 4.09 |
754 | 779 | 2.146073 | CTTTTCAGCCAGCGTTGGGG | 62.146 | 60.000 | 20.66 | 0.00 | 45.16 | 4.96 |
755 | 780 | 1.286880 | CTTTTCAGCCAGCGTTGGG | 59.713 | 57.895 | 20.66 | 4.24 | 45.16 | 4.12 |
775 | 800 | 1.228552 | AGGGCCGAAACAAGTGCAT | 60.229 | 52.632 | 0.00 | 0.00 | 0.00 | 3.96 |
778 | 803 | 1.028905 | TTTGAGGGCCGAAACAAGTG | 58.971 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
801 | 826 | 2.037121 | AGGGCCAAAATAAGTGCACAAC | 59.963 | 45.455 | 21.04 | 0.00 | 0.00 | 3.32 |
802 | 827 | 2.298729 | GAGGGCCAAAATAAGTGCACAA | 59.701 | 45.455 | 21.04 | 7.03 | 0.00 | 3.33 |
805 | 830 | 2.170166 | CTGAGGGCCAAAATAAGTGCA | 58.830 | 47.619 | 6.18 | 0.00 | 0.00 | 4.57 |
809 | 834 | 5.297776 | CACACTATCTGAGGGCCAAAATAAG | 59.702 | 44.000 | 6.18 | 0.00 | 27.73 | 1.73 |
839 | 868 | 2.032550 | CGTGACCTCGAACGTATACCAT | 59.967 | 50.000 | 0.00 | 0.00 | 35.13 | 3.55 |
840 | 869 | 1.398041 | CGTGACCTCGAACGTATACCA | 59.602 | 52.381 | 0.00 | 0.00 | 35.13 | 3.25 |
841 | 870 | 1.268234 | CCGTGACCTCGAACGTATACC | 60.268 | 57.143 | 6.62 | 0.00 | 38.11 | 2.73 |
842 | 871 | 1.398390 | ACCGTGACCTCGAACGTATAC | 59.602 | 52.381 | 6.62 | 0.00 | 38.11 | 1.47 |
843 | 872 | 1.737838 | ACCGTGACCTCGAACGTATA | 58.262 | 50.000 | 6.62 | 0.00 | 38.11 | 1.47 |
844 | 873 | 0.883833 | AACCGTGACCTCGAACGTAT | 59.116 | 50.000 | 6.62 | 0.00 | 38.11 | 3.06 |
845 | 874 | 0.238289 | GAACCGTGACCTCGAACGTA | 59.762 | 55.000 | 6.62 | 0.00 | 38.11 | 3.57 |
969 | 1017 | 5.833082 | TGAACTCTCTGTTAGTTGTGACTC | 58.167 | 41.667 | 0.00 | 0.00 | 39.30 | 3.36 |
984 | 1032 | 4.630111 | CTGCCATCCTCTAATGAACTCTC | 58.370 | 47.826 | 0.00 | 0.00 | 0.00 | 3.20 |
996 | 1044 | 0.391661 | TCAAACTCGCTGCCATCCTC | 60.392 | 55.000 | 0.00 | 0.00 | 0.00 | 3.71 |
1044 | 1092 | 2.068821 | GGCAGATGAGGAGCAGGGA | 61.069 | 63.158 | 0.00 | 0.00 | 0.00 | 4.20 |
1053 | 1101 | 1.879380 | CGAGAGGAGTAGGCAGATGAG | 59.121 | 57.143 | 0.00 | 0.00 | 0.00 | 2.90 |
1122 | 1179 | 1.476845 | TAGCTTCCGTGGCAGGTGAA | 61.477 | 55.000 | 6.43 | 8.34 | 0.00 | 3.18 |
1147 | 1204 | 3.299340 | TTCGTGTTCAACTCTAGAGGC | 57.701 | 47.619 | 23.50 | 8.71 | 0.00 | 4.70 |
1325 | 1382 | 6.156602 | ACATGGATTGGGAATTGATAAAGCAA | 59.843 | 34.615 | 0.00 | 0.00 | 0.00 | 3.91 |
1332 | 1389 | 6.384595 | TGATGAAACATGGATTGGGAATTGAT | 59.615 | 34.615 | 0.00 | 0.00 | 0.00 | 2.57 |
1333 | 1390 | 5.720520 | TGATGAAACATGGATTGGGAATTGA | 59.279 | 36.000 | 0.00 | 0.00 | 0.00 | 2.57 |
1334 | 1391 | 5.979993 | TGATGAAACATGGATTGGGAATTG | 58.020 | 37.500 | 0.00 | 0.00 | 0.00 | 2.32 |
1335 | 1392 | 6.818281 | ATGATGAAACATGGATTGGGAATT | 57.182 | 33.333 | 0.00 | 0.00 | 0.00 | 2.17 |
1336 | 1393 | 6.818281 | AATGATGAAACATGGATTGGGAAT | 57.182 | 33.333 | 0.00 | 0.00 | 0.00 | 3.01 |
1338 | 1395 | 6.268158 | CCATAATGATGAAACATGGATTGGGA | 59.732 | 38.462 | 0.00 | 0.00 | 38.77 | 4.37 |
1339 | 1396 | 6.042322 | ACCATAATGATGAAACATGGATTGGG | 59.958 | 38.462 | 5.94 | 0.00 | 38.77 | 4.12 |
1340 | 1397 | 7.058023 | ACCATAATGATGAAACATGGATTGG | 57.942 | 36.000 | 5.94 | 0.00 | 38.77 | 3.16 |
1342 | 1399 | 7.496591 | GCAAACCATAATGATGAAACATGGATT | 59.503 | 33.333 | 5.94 | 0.00 | 38.77 | 3.01 |
1345 | 1402 | 6.342906 | AGCAAACCATAATGATGAAACATGG | 58.657 | 36.000 | 0.00 | 0.00 | 41.60 | 3.66 |
1347 | 1404 | 8.065473 | TGTAGCAAACCATAATGATGAAACAT | 57.935 | 30.769 | 0.00 | 0.00 | 34.73 | 2.71 |
1348 | 1405 | 7.459795 | TGTAGCAAACCATAATGATGAAACA | 57.540 | 32.000 | 0.00 | 0.00 | 34.73 | 2.83 |
1349 | 1406 | 8.190122 | TGATGTAGCAAACCATAATGATGAAAC | 58.810 | 33.333 | 0.00 | 0.00 | 34.73 | 2.78 |
1356 | 1566 | 7.417612 | GGTTAGTGATGTAGCAAACCATAATG | 58.582 | 38.462 | 0.00 | 0.00 | 37.05 | 1.90 |
1373 | 1594 | 6.428083 | TGAAACAAGTATCTGGGTTAGTGA | 57.572 | 37.500 | 0.00 | 0.00 | 0.00 | 3.41 |
1428 | 1680 | 9.502091 | AGCTGAAACGGCATATATTATTTCTAA | 57.498 | 29.630 | 5.39 | 0.00 | 38.37 | 2.10 |
1430 | 1682 | 7.986085 | AGCTGAAACGGCATATATTATTTCT | 57.014 | 32.000 | 5.39 | 0.00 | 38.37 | 2.52 |
1434 | 1686 | 8.677300 | CCAAATAGCTGAAACGGCATATATTAT | 58.323 | 33.333 | 0.00 | 0.00 | 38.37 | 1.28 |
1435 | 1687 | 7.663905 | ACCAAATAGCTGAAACGGCATATATTA | 59.336 | 33.333 | 0.00 | 0.00 | 38.37 | 0.98 |
1444 | 1696 | 2.811431 | TGACACCAAATAGCTGAAACGG | 59.189 | 45.455 | 0.00 | 0.00 | 0.00 | 4.44 |
1461 | 1713 | 4.455533 | GTCAGAAATGCCTACAACATGACA | 59.544 | 41.667 | 0.00 | 0.00 | 0.00 | 3.58 |
1465 | 1717 | 7.886629 | ATAATGTCAGAAATGCCTACAACAT | 57.113 | 32.000 | 0.00 | 0.00 | 0.00 | 2.71 |
1544 | 1803 | 6.830912 | TGTGGATTAGATTGTCCAGGAATAG | 58.169 | 40.000 | 0.00 | 0.00 | 44.71 | 1.73 |
1635 | 1900 | 3.552132 | TTTACTGACCTCTGCACACAA | 57.448 | 42.857 | 0.00 | 0.00 | 0.00 | 3.33 |
1652 | 1917 | 4.397103 | CAGCTCTTGCAGTCATCCATTTTA | 59.603 | 41.667 | 0.00 | 0.00 | 42.74 | 1.52 |
1664 | 1929 | 7.325660 | TCCTTTAATTTATCAGCTCTTGCAG | 57.674 | 36.000 | 0.00 | 0.00 | 42.74 | 4.41 |
1802 | 2067 | 9.613428 | ATTCATCCTCGATAATTTGACTTAACA | 57.387 | 29.630 | 0.00 | 0.00 | 0.00 | 2.41 |
2026 | 2741 | 3.933861 | TCTTTCCTAAAGCTCCCATCC | 57.066 | 47.619 | 0.00 | 0.00 | 38.39 | 3.51 |
2216 | 2931 | 7.039363 | CCTTTTCAATGTCCTTGGTAATGGTAA | 60.039 | 37.037 | 0.00 | 0.00 | 35.43 | 2.85 |
2224 | 2939 | 2.965147 | CACCCTTTTCAATGTCCTTGGT | 59.035 | 45.455 | 0.00 | 0.00 | 35.43 | 3.67 |
2286 | 3001 | 5.044846 | AGCTCCAATAGAGTTGGGTTATGTT | 60.045 | 40.000 | 6.95 | 0.00 | 45.21 | 2.71 |
2383 | 3098 | 8.094548 | AGCTTCATTGTGTAGTTGAGTATAACA | 58.905 | 33.333 | 0.00 | 0.00 | 33.02 | 2.41 |
2408 | 3123 | 6.032094 | GGCATGCATTTTATATCGATTCCAG | 58.968 | 40.000 | 21.36 | 0.00 | 0.00 | 3.86 |
2534 | 3260 | 0.038526 | CCCGACACACCTGTACAGAC | 60.039 | 60.000 | 24.68 | 7.15 | 0.00 | 3.51 |
2604 | 3330 | 7.642669 | ACGCAAATTCTTTCTCATGGTATATG | 58.357 | 34.615 | 0.00 | 0.00 | 0.00 | 1.78 |
2729 | 3455 | 3.964031 | ACTTTCAAACCTTTGTATGGCCA | 59.036 | 39.130 | 8.56 | 8.56 | 39.18 | 5.36 |
2830 | 3561 | 6.014012 | TCCCATCTACATGTCGGATTACATA | 58.986 | 40.000 | 0.00 | 0.00 | 38.01 | 2.29 |
3291 | 4023 | 1.134753 | GAATGCGGCAATGTCATCCAA | 59.865 | 47.619 | 6.82 | 0.00 | 0.00 | 3.53 |
3370 | 4102 | 9.757227 | GAAGTTAGATACATTATCTTGAGTGCT | 57.243 | 33.333 | 1.13 | 0.00 | 42.70 | 4.40 |
3399 | 4134 | 2.951642 | CCCGCCCTGCATATTTATATGG | 59.048 | 50.000 | 10.78 | 0.00 | 40.31 | 2.74 |
3625 | 4360 | 5.163163 | TGCTGAAGGTATATGCATCTTTCCT | 60.163 | 40.000 | 0.19 | 4.62 | 0.00 | 3.36 |
3937 | 4678 | 3.776969 | AGAGAGAGAGAGAGAGAGAGCAA | 59.223 | 47.826 | 0.00 | 0.00 | 0.00 | 3.91 |
3938 | 4679 | 3.378512 | AGAGAGAGAGAGAGAGAGAGCA | 58.621 | 50.000 | 0.00 | 0.00 | 0.00 | 4.26 |
3939 | 4680 | 3.640967 | AGAGAGAGAGAGAGAGAGAGAGC | 59.359 | 52.174 | 0.00 | 0.00 | 0.00 | 4.09 |
4141 | 4899 | 5.631481 | GCAGGGATAAAATACTCCACTTGGA | 60.631 | 44.000 | 0.00 | 0.00 | 43.08 | 3.53 |
4345 | 5137 | 4.314121 | ACCTAATTACAACCGCGTGTTTA | 58.686 | 39.130 | 7.72 | 1.52 | 34.00 | 2.01 |
4424 | 5217 | 7.711772 | TCTCTTGAAAACCATTTCTACGTACAA | 59.288 | 33.333 | 0.00 | 0.00 | 44.32 | 2.41 |
4478 | 5272 | 0.946221 | CACTCAGAGGTGCACCGAAC | 60.946 | 60.000 | 29.68 | 23.12 | 42.08 | 3.95 |
4479 | 5273 | 1.367471 | CACTCAGAGGTGCACCGAA | 59.633 | 57.895 | 29.68 | 15.19 | 42.08 | 4.30 |
4612 | 5406 | 0.322322 | ATGCGTACAAACCCCTTCGA | 59.678 | 50.000 | 0.00 | 0.00 | 0.00 | 3.71 |
4651 | 5445 | 6.035758 | GCGTACAAAAGCAAGTAACTATAGCT | 59.964 | 38.462 | 0.00 | 0.00 | 37.08 | 3.32 |
4653 | 5447 | 7.285783 | TGCGTACAAAAGCAAGTAACTATAG | 57.714 | 36.000 | 0.00 | 0.00 | 40.78 | 1.31 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.