Multiple sequence alignment - TraesCS3D01G401500
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 | TraesCS3D01G401500 | chr3D | 100.000 | 3048 | 0 | 0 | 1 | 3048 | 516195253 | 516192206 | 0.000000e+00 | 5629.0 |
1 | TraesCS3D01G401500 | chr3D | 80.601 | 1098 | 128 | 51 | 1546 | 2575 | 515819222 | 515820302 | 0.000000e+00 | 769.0 |
2 | TraesCS3D01G401500 | chr3D | 82.114 | 492 | 47 | 21 | 1922 | 2378 | 515820931 | 515820446 | 1.710000e-102 | 383.0 |
3 | TraesCS3D01G401500 | chr3D | 94.444 | 36 | 1 | 1 | 2970 | 3005 | 515824797 | 515824831 | 2.000000e-03 | 54.7 |
4 | TraesCS3D01G401500 | chr3A | 92.851 | 1175 | 51 | 16 | 379 | 1525 | 651502939 | 651501770 | 0.000000e+00 | 1674.0 |
5 | TraesCS3D01G401500 | chr3A | 88.030 | 919 | 66 | 10 | 1542 | 2423 | 651501785 | 651500874 | 0.000000e+00 | 1048.0 |
6 | TraesCS3D01G401500 | chr3A | 81.232 | 1071 | 129 | 40 | 1546 | 2575 | 650195527 | 650196566 | 0.000000e+00 | 798.0 |
7 | TraesCS3D01G401500 | chr3A | 89.780 | 499 | 24 | 13 | 2568 | 3039 | 651500793 | 651500295 | 5.590000e-172 | 614.0 |
8 | TraesCS3D01G401500 | chr3A | 81.911 | 492 | 50 | 20 | 1922 | 2378 | 650197196 | 650196709 | 2.220000e-101 | 379.0 |
9 | TraesCS3D01G401500 | chr3A | 86.458 | 192 | 26 | 0 | 1332 | 1523 | 650195340 | 650195531 | 8.560000e-51 | 211.0 |
10 | TraesCS3D01G401500 | chr3A | 91.398 | 93 | 8 | 0 | 159 | 251 | 651503231 | 651503139 | 8.870000e-26 | 128.0 |
11 | TraesCS3D01G401500 | chr3A | 90.625 | 64 | 5 | 1 | 20 | 82 | 671738888 | 671738951 | 1.950000e-12 | 84.2 |
12 | TraesCS3D01G401500 | chr3A | 95.238 | 42 | 2 | 0 | 2420 | 2461 | 651500835 | 651500794 | 1.960000e-07 | 67.6 |
13 | TraesCS3D01G401500 | chr3A | 100.000 | 29 | 0 | 0 | 2977 | 3005 | 650197388 | 650197416 | 2.000000e-03 | 54.7 |
14 | TraesCS3D01G401500 | chr3B | 91.267 | 1042 | 60 | 16 | 498 | 1525 | 679624738 | 679623714 | 0.000000e+00 | 1391.0 |
15 | TraesCS3D01G401500 | chr3B | 93.303 | 657 | 14 | 4 | 2420 | 3048 | 679622774 | 679622120 | 0.000000e+00 | 942.0 |
16 | TraesCS3D01G401500 | chr3B | 90.964 | 664 | 54 | 4 | 1542 | 2200 | 679623729 | 679623067 | 0.000000e+00 | 889.0 |
17 | TraesCS3D01G401500 | chr3B | 79.955 | 1342 | 156 | 59 | 1302 | 2570 | 678711031 | 678712332 | 0.000000e+00 | 883.0 |
18 | TraesCS3D01G401500 | chr3B | 96.234 | 239 | 8 | 1 | 2185 | 2423 | 679623050 | 679622813 | 1.020000e-104 | 390.0 |
19 | TraesCS3D01G401500 | chr3B | 81.673 | 502 | 52 | 23 | 1913 | 2378 | 678712977 | 678712480 | 6.170000e-102 | 381.0 |
20 | TraesCS3D01G401500 | chr3B | 88.353 | 249 | 12 | 2 | 247 | 494 | 679625828 | 679625596 | 1.790000e-72 | 283.0 |
21 | TraesCS3D01G401500 | chr3B | 82.119 | 302 | 47 | 6 | 573 | 871 | 46026028 | 46025731 | 5.040000e-63 | 252.0 |
22 | TraesCS3D01G401500 | chr3B | 81.788 | 302 | 48 | 6 | 573 | 871 | 45962049 | 45961752 | 2.350000e-61 | 246.0 |
23 | TraesCS3D01G401500 | chr3B | 81.788 | 302 | 48 | 6 | 573 | 871 | 46012037 | 46011740 | 2.350000e-61 | 246.0 |
24 | TraesCS3D01G401500 | chr3B | 81.457 | 302 | 49 | 6 | 573 | 871 | 45782121 | 45781824 | 1.090000e-59 | 241.0 |
25 | TraesCS3D01G401500 | chr3B | 81.457 | 302 | 49 | 6 | 573 | 871 | 45879411 | 45879114 | 1.090000e-59 | 241.0 |
26 | TraesCS3D01G401500 | chr3B | 81.457 | 302 | 49 | 6 | 573 | 871 | 45945604 | 45945307 | 1.090000e-59 | 241.0 |
27 | TraesCS3D01G401500 | chr3B | 81.126 | 302 | 50 | 6 | 573 | 871 | 45827850 | 45827553 | 5.080000e-58 | 235.0 |
28 | TraesCS3D01G401500 | chr3B | 81.690 | 213 | 29 | 7 | 1253 | 1463 | 45758800 | 45759004 | 5.230000e-38 | 169.0 |
29 | TraesCS3D01G401500 | chr3B | 81.690 | 213 | 29 | 7 | 1253 | 1463 | 45962790 | 45962994 | 5.230000e-38 | 169.0 |
30 | TraesCS3D01G401500 | chr3B | 81.690 | 213 | 29 | 7 | 1253 | 1463 | 46012882 | 46013086 | 5.230000e-38 | 169.0 |
31 | TraesCS3D01G401500 | chr3B | 81.818 | 209 | 28 | 7 | 1253 | 1459 | 45924039 | 45924239 | 1.880000e-37 | 167.0 |
32 | TraesCS3D01G401500 | chr3B | 81.818 | 209 | 28 | 7 | 1253 | 1459 | 45974332 | 45974532 | 1.880000e-37 | 167.0 |
33 | TraesCS3D01G401500 | chr3B | 82.540 | 126 | 20 | 1 | 2607 | 2732 | 45768529 | 45768406 | 3.210000e-20 | 110.0 |
34 | TraesCS3D01G401500 | chr3B | 82.540 | 126 | 20 | 1 | 2607 | 2732 | 45838670 | 45838547 | 3.210000e-20 | 110.0 |
35 | TraesCS3D01G401500 | chr3B | 82.540 | 126 | 20 | 1 | 2607 | 2732 | 45875951 | 45875828 | 3.210000e-20 | 110.0 |
36 | TraesCS3D01G401500 | chr3B | 82.540 | 126 | 20 | 1 | 2607 | 2732 | 45890045 | 45889922 | 3.210000e-20 | 110.0 |
37 | TraesCS3D01G401500 | chr3B | 82.540 | 126 | 20 | 1 | 2607 | 2732 | 45933757 | 45933634 | 3.210000e-20 | 110.0 |
38 | TraesCS3D01G401500 | chr3B | 82.540 | 126 | 20 | 1 | 2607 | 2732 | 45983727 | 45983604 | 3.210000e-20 | 110.0 |
39 | TraesCS3D01G401500 | chr3B | 82.540 | 126 | 20 | 1 | 2607 | 2732 | 46022563 | 46022440 | 3.210000e-20 | 110.0 |
40 | TraesCS3D01G401500 | chr3B | 100.000 | 29 | 0 | 0 | 54 | 82 | 504655611 | 504655639 | 2.000000e-03 | 54.7 |
41 | TraesCS3D01G401500 | chr7A | 100.000 | 29 | 0 | 0 | 1711 | 1739 | 303967860 | 303967832 | 2.000000e-03 | 54.7 |
42 | TraesCS3D01G401500 | chr5A | 100.000 | 28 | 0 | 0 | 1715 | 1742 | 275080756 | 275080783 | 5.000000e-03 | 52.8 |
43 | TraesCS3D01G401500 | chr4D | 94.286 | 35 | 0 | 2 | 52 | 84 | 386751311 | 386751345 | 5.000000e-03 | 52.8 |
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 | TraesCS3D01G401500 | chr3D | 516192206 | 516195253 | 3047 | True | 5629.000000 | 5629 | 100.0000 | 1 | 3048 | 1 | chr3D.!!$R2 | 3047 |
1 | TraesCS3D01G401500 | chr3D | 515819222 | 515820302 | 1080 | False | 769.000000 | 769 | 80.6010 | 1546 | 2575 | 1 | chr3D.!!$F1 | 1029 |
2 | TraesCS3D01G401500 | chr3A | 651500295 | 651503231 | 2936 | True | 706.320000 | 1674 | 91.4594 | 159 | 3039 | 5 | chr3A.!!$R2 | 2880 |
3 | TraesCS3D01G401500 | chr3A | 650195340 | 650197416 | 2076 | False | 354.566667 | 798 | 89.2300 | 1332 | 3005 | 3 | chr3A.!!$F2 | 1673 |
4 | TraesCS3D01G401500 | chr3B | 678711031 | 678712332 | 1301 | False | 883.000000 | 883 | 79.9550 | 1302 | 2570 | 1 | chr3B.!!$F7 | 1268 |
5 | TraesCS3D01G401500 | chr3B | 679622120 | 679625828 | 3708 | True | 779.000000 | 1391 | 92.0242 | 247 | 3048 | 5 | chr3B.!!$R14 | 2801 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
77 | 78 | 0.320697 | AAACTTTCTCGGACGGAGGG | 59.679 | 55.0 | 9.88 | 4.26 | 43.34 | 4.3 | F |
1193 | 2133 | 0.103572 | GGTAGAAAGGCCGTATGCGA | 59.896 | 55.0 | 4.21 | 0.00 | 42.61 | 5.1 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1813 | 2789 | 0.106419 | TCCACTTTGGTTTCCGCCTT | 60.106 | 50.000 | 0.0 | 0.0 | 39.03 | 4.35 | R |
2048 | 3061 | 1.988107 | TCCACCAATCTTCCTGCTTCT | 59.012 | 47.619 | 0.0 | 0.0 | 0.00 | 2.85 | 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 |
---|---|---|---|---|---|---|---|---|---|
18 | 19 | 3.903876 | CACTATGTGTTGGCATCGC | 57.096 | 52.632 | 2.19 | 2.19 | 0.00 | 4.58 |
19 | 20 | 1.372582 | CACTATGTGTTGGCATCGCT | 58.627 | 50.000 | 10.19 | 0.00 | 0.00 | 4.93 |
20 | 21 | 1.739466 | CACTATGTGTTGGCATCGCTT | 59.261 | 47.619 | 10.19 | 6.69 | 0.00 | 4.68 |
21 | 22 | 2.935849 | CACTATGTGTTGGCATCGCTTA | 59.064 | 45.455 | 10.19 | 7.41 | 0.00 | 3.09 |
22 | 23 | 3.561310 | CACTATGTGTTGGCATCGCTTAT | 59.439 | 43.478 | 10.19 | 0.04 | 0.00 | 1.73 |
23 | 24 | 3.561310 | ACTATGTGTTGGCATCGCTTATG | 59.439 | 43.478 | 10.19 | 5.70 | 38.74 | 1.90 |
34 | 35 | 4.854361 | CATCGCTTATGCCAGATACATC | 57.146 | 45.455 | 0.00 | 0.00 | 35.36 | 3.06 |
35 | 36 | 3.319137 | TCGCTTATGCCAGATACATCC | 57.681 | 47.619 | 0.00 | 0.00 | 35.36 | 3.51 |
36 | 37 | 2.632512 | TCGCTTATGCCAGATACATCCA | 59.367 | 45.455 | 0.00 | 0.00 | 35.36 | 3.41 |
37 | 38 | 3.261643 | TCGCTTATGCCAGATACATCCAT | 59.738 | 43.478 | 0.00 | 0.00 | 35.36 | 3.41 |
38 | 39 | 4.005650 | CGCTTATGCCAGATACATCCATT | 58.994 | 43.478 | 0.00 | 0.00 | 35.36 | 3.16 |
39 | 40 | 4.456911 | CGCTTATGCCAGATACATCCATTT | 59.543 | 41.667 | 0.00 | 0.00 | 35.36 | 2.32 |
40 | 41 | 5.618418 | CGCTTATGCCAGATACATCCATTTG | 60.618 | 44.000 | 0.00 | 0.00 | 35.36 | 2.32 |
41 | 42 | 5.474532 | GCTTATGCCAGATACATCCATTTGA | 59.525 | 40.000 | 0.00 | 0.00 | 0.00 | 2.69 |
42 | 43 | 6.349115 | GCTTATGCCAGATACATCCATTTGAG | 60.349 | 42.308 | 0.00 | 0.00 | 0.00 | 3.02 |
43 | 44 | 3.824133 | TGCCAGATACATCCATTTGAGG | 58.176 | 45.455 | 0.00 | 0.00 | 0.00 | 3.86 |
44 | 45 | 3.152341 | GCCAGATACATCCATTTGAGGG | 58.848 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
45 | 46 | 3.181440 | GCCAGATACATCCATTTGAGGGA | 60.181 | 47.826 | 0.00 | 0.00 | 39.14 | 4.20 |
46 | 47 | 4.508047 | GCCAGATACATCCATTTGAGGGAT | 60.508 | 45.833 | 0.00 | 0.00 | 45.98 | 3.85 |
47 | 48 | 5.280676 | GCCAGATACATCCATTTGAGGGATA | 60.281 | 44.000 | 0.00 | 0.00 | 43.24 | 2.59 |
48 | 49 | 6.748045 | GCCAGATACATCCATTTGAGGGATAA | 60.748 | 42.308 | 0.00 | 0.00 | 43.24 | 1.75 |
49 | 50 | 7.233632 | CCAGATACATCCATTTGAGGGATAAA | 58.766 | 38.462 | 0.00 | 0.00 | 43.24 | 1.40 |
50 | 51 | 7.175641 | CCAGATACATCCATTTGAGGGATAAAC | 59.824 | 40.741 | 0.00 | 0.00 | 43.24 | 2.01 |
51 | 52 | 7.941238 | CAGATACATCCATTTGAGGGATAAACT | 59.059 | 37.037 | 0.00 | 0.00 | 43.24 | 2.66 |
52 | 53 | 8.506083 | AGATACATCCATTTGAGGGATAAACTT | 58.494 | 33.333 | 0.00 | 0.00 | 43.24 | 2.66 |
53 | 54 | 6.780457 | ACATCCATTTGAGGGATAAACTTG | 57.220 | 37.500 | 0.00 | 0.00 | 43.24 | 3.16 |
54 | 55 | 5.658190 | ACATCCATTTGAGGGATAAACTTGG | 59.342 | 40.000 | 0.00 | 0.00 | 43.24 | 3.61 |
55 | 56 | 4.609301 | TCCATTTGAGGGATAAACTTGGG | 58.391 | 43.478 | 0.00 | 0.00 | 0.00 | 4.12 |
56 | 57 | 4.293634 | TCCATTTGAGGGATAAACTTGGGA | 59.706 | 41.667 | 0.00 | 0.00 | 0.00 | 4.37 |
57 | 58 | 4.402474 | CCATTTGAGGGATAAACTTGGGAC | 59.598 | 45.833 | 0.00 | 0.00 | 0.00 | 4.46 |
58 | 59 | 4.733077 | TTTGAGGGATAAACTTGGGACA | 57.267 | 40.909 | 0.00 | 0.00 | 0.00 | 4.02 |
71 | 72 | 2.249844 | TGGGACAAACTTTCTCGGAC | 57.750 | 50.000 | 0.00 | 0.00 | 31.92 | 4.79 |
72 | 73 | 1.145803 | GGGACAAACTTTCTCGGACG | 58.854 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
73 | 74 | 1.145803 | GGACAAACTTTCTCGGACGG | 58.854 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
74 | 75 | 1.269936 | GGACAAACTTTCTCGGACGGA | 60.270 | 52.381 | 0.00 | 0.00 | 0.00 | 4.69 |
75 | 76 | 2.059541 | GACAAACTTTCTCGGACGGAG | 58.940 | 52.381 | 3.68 | 3.68 | 44.58 | 4.63 |
76 | 77 | 1.270147 | ACAAACTTTCTCGGACGGAGG | 60.270 | 52.381 | 9.88 | 0.00 | 43.34 | 4.30 |
77 | 78 | 0.320697 | AAACTTTCTCGGACGGAGGG | 59.679 | 55.000 | 9.88 | 4.26 | 43.34 | 4.30 |
78 | 79 | 0.541296 | AACTTTCTCGGACGGAGGGA | 60.541 | 55.000 | 9.88 | 0.00 | 43.34 | 4.20 |
79 | 80 | 0.966370 | ACTTTCTCGGACGGAGGGAG | 60.966 | 60.000 | 9.88 | 10.00 | 43.34 | 4.30 |
80 | 81 | 0.966370 | CTTTCTCGGACGGAGGGAGT | 60.966 | 60.000 | 9.88 | 0.00 | 43.34 | 3.85 |
81 | 82 | 0.329261 | TTTCTCGGACGGAGGGAGTA | 59.671 | 55.000 | 9.88 | 0.00 | 43.34 | 2.59 |
82 | 83 | 0.393537 | TTCTCGGACGGAGGGAGTAC | 60.394 | 60.000 | 9.88 | 0.00 | 43.34 | 2.73 |
83 | 84 | 1.077930 | CTCGGACGGAGGGAGTACA | 60.078 | 63.158 | 2.13 | 0.00 | 39.22 | 2.90 |
84 | 85 | 0.465824 | CTCGGACGGAGGGAGTACAT | 60.466 | 60.000 | 2.13 | 0.00 | 39.22 | 2.29 |
85 | 86 | 0.750546 | TCGGACGGAGGGAGTACATG | 60.751 | 60.000 | 0.00 | 0.00 | 0.00 | 3.21 |
86 | 87 | 1.035932 | CGGACGGAGGGAGTACATGT | 61.036 | 60.000 | 2.69 | 2.69 | 0.00 | 3.21 |
87 | 88 | 1.192428 | GGACGGAGGGAGTACATGTT | 58.808 | 55.000 | 2.30 | 0.00 | 0.00 | 2.71 |
88 | 89 | 2.381911 | GGACGGAGGGAGTACATGTTA | 58.618 | 52.381 | 2.30 | 0.00 | 0.00 | 2.41 |
89 | 90 | 2.762327 | GGACGGAGGGAGTACATGTTAA | 59.238 | 50.000 | 2.30 | 0.00 | 0.00 | 2.01 |
90 | 91 | 3.429960 | GGACGGAGGGAGTACATGTTAAC | 60.430 | 52.174 | 2.30 | 0.00 | 0.00 | 2.01 |
91 | 92 | 3.167485 | ACGGAGGGAGTACATGTTAACA | 58.833 | 45.455 | 11.41 | 11.41 | 0.00 | 2.41 |
92 | 93 | 3.579586 | ACGGAGGGAGTACATGTTAACAA | 59.420 | 43.478 | 13.23 | 0.00 | 0.00 | 2.83 |
93 | 94 | 3.930848 | CGGAGGGAGTACATGTTAACAAC | 59.069 | 47.826 | 13.23 | 6.59 | 0.00 | 3.32 |
94 | 95 | 4.259356 | GGAGGGAGTACATGTTAACAACC | 58.741 | 47.826 | 13.23 | 9.05 | 0.00 | 3.77 |
95 | 96 | 4.263156 | GGAGGGAGTACATGTTAACAACCA | 60.263 | 45.833 | 13.23 | 0.00 | 0.00 | 3.67 |
96 | 97 | 5.497474 | GAGGGAGTACATGTTAACAACCAT | 58.503 | 41.667 | 13.23 | 7.18 | 0.00 | 3.55 |
97 | 98 | 5.887754 | AGGGAGTACATGTTAACAACCATT | 58.112 | 37.500 | 13.23 | 0.00 | 0.00 | 3.16 |
98 | 99 | 6.311735 | AGGGAGTACATGTTAACAACCATTT | 58.688 | 36.000 | 13.23 | 0.00 | 0.00 | 2.32 |
99 | 100 | 6.208599 | AGGGAGTACATGTTAACAACCATTTG | 59.791 | 38.462 | 13.23 | 7.70 | 38.83 | 2.32 |
100 | 101 | 5.861787 | GGAGTACATGTTAACAACCATTTGC | 59.138 | 40.000 | 13.23 | 0.00 | 36.00 | 3.68 |
101 | 102 | 6.398234 | AGTACATGTTAACAACCATTTGCA | 57.602 | 33.333 | 13.23 | 0.00 | 36.00 | 4.08 |
102 | 103 | 6.810911 | AGTACATGTTAACAACCATTTGCAA | 58.189 | 32.000 | 13.23 | 0.00 | 36.00 | 4.08 |
103 | 104 | 5.982465 | ACATGTTAACAACCATTTGCAAC | 57.018 | 34.783 | 13.23 | 0.00 | 36.00 | 4.17 |
104 | 105 | 4.505922 | ACATGTTAACAACCATTTGCAACG | 59.494 | 37.500 | 13.23 | 0.00 | 35.29 | 4.10 |
105 | 106 | 4.111375 | TGTTAACAACCATTTGCAACGT | 57.889 | 36.364 | 5.64 | 0.00 | 35.29 | 3.99 |
106 | 107 | 4.106197 | TGTTAACAACCATTTGCAACGTC | 58.894 | 39.130 | 5.64 | 0.00 | 35.29 | 4.34 |
107 | 108 | 2.949451 | AACAACCATTTGCAACGTCA | 57.051 | 40.000 | 0.00 | 0.00 | 36.00 | 4.35 |
108 | 109 | 2.949451 | ACAACCATTTGCAACGTCAA | 57.051 | 40.000 | 0.00 | 0.00 | 36.00 | 3.18 |
109 | 110 | 2.808244 | ACAACCATTTGCAACGTCAAG | 58.192 | 42.857 | 0.00 | 0.00 | 36.00 | 3.02 |
110 | 111 | 1.522258 | CAACCATTTGCAACGTCAAGC | 59.478 | 47.619 | 0.00 | 0.00 | 0.00 | 4.01 |
111 | 112 | 0.743688 | ACCATTTGCAACGTCAAGCA | 59.256 | 45.000 | 0.00 | 6.23 | 39.32 | 3.91 |
112 | 113 | 1.269206 | ACCATTTGCAACGTCAAGCAG | 60.269 | 47.619 | 0.00 | 2.80 | 42.39 | 4.24 |
113 | 114 | 1.269206 | CCATTTGCAACGTCAAGCAGT | 60.269 | 47.619 | 0.00 | 2.34 | 42.39 | 4.40 |
114 | 115 | 2.462889 | CATTTGCAACGTCAAGCAGTT | 58.537 | 42.857 | 0.00 | 1.05 | 42.39 | 3.16 |
115 | 116 | 2.187351 | TTTGCAACGTCAAGCAGTTC | 57.813 | 45.000 | 0.00 | 0.00 | 42.39 | 3.01 |
116 | 117 | 1.090728 | TTGCAACGTCAAGCAGTTCA | 58.909 | 45.000 | 9.68 | 0.00 | 42.39 | 3.18 |
117 | 118 | 0.376852 | TGCAACGTCAAGCAGTTCAC | 59.623 | 50.000 | 6.23 | 0.00 | 35.51 | 3.18 |
118 | 119 | 0.376852 | GCAACGTCAAGCAGTTCACA | 59.623 | 50.000 | 0.00 | 0.00 | 0.00 | 3.58 |
119 | 120 | 1.202132 | GCAACGTCAAGCAGTTCACAA | 60.202 | 47.619 | 0.00 | 0.00 | 0.00 | 3.33 |
120 | 121 | 2.730715 | GCAACGTCAAGCAGTTCACAAA | 60.731 | 45.455 | 0.00 | 0.00 | 0.00 | 2.83 |
121 | 122 | 3.100817 | CAACGTCAAGCAGTTCACAAAG | 58.899 | 45.455 | 0.00 | 0.00 | 0.00 | 2.77 |
122 | 123 | 2.627945 | ACGTCAAGCAGTTCACAAAGA | 58.372 | 42.857 | 0.00 | 0.00 | 0.00 | 2.52 |
123 | 124 | 3.206150 | ACGTCAAGCAGTTCACAAAGAT | 58.794 | 40.909 | 0.00 | 0.00 | 0.00 | 2.40 |
124 | 125 | 3.002656 | ACGTCAAGCAGTTCACAAAGATG | 59.997 | 43.478 | 0.00 | 0.00 | 0.00 | 2.90 |
125 | 126 | 3.303406 | GTCAAGCAGTTCACAAAGATGC | 58.697 | 45.455 | 0.00 | 0.00 | 37.15 | 3.91 |
129 | 130 | 4.660789 | AGCAGTTCACAAAGATGCTTTT | 57.339 | 36.364 | 0.00 | 0.00 | 44.47 | 2.27 |
130 | 131 | 5.014808 | AGCAGTTCACAAAGATGCTTTTT | 57.985 | 34.783 | 0.00 | 0.00 | 44.47 | 1.94 |
151 | 152 | 4.708726 | TTTTGTTTTGGTTTTGCATGGG | 57.291 | 36.364 | 0.00 | 0.00 | 0.00 | 4.00 |
152 | 153 | 1.673168 | TGTTTTGGTTTTGCATGGGC | 58.327 | 45.000 | 0.00 | 0.00 | 41.68 | 5.36 |
189 | 190 | 2.296471 | TGAGGAAGAACGGTCAGAAGTC | 59.704 | 50.000 | 1.87 | 0.00 | 0.00 | 3.01 |
191 | 192 | 1.343465 | GGAAGAACGGTCAGAAGTCCA | 59.657 | 52.381 | 1.87 | 0.00 | 0.00 | 4.02 |
218 | 219 | 5.584253 | ACTGTGAATGTATTCGTAGCTCT | 57.416 | 39.130 | 0.00 | 0.00 | 39.62 | 4.09 |
229 | 230 | 2.562635 | TCGTAGCTCTCGCTTGTATCT | 58.437 | 47.619 | 0.00 | 0.00 | 46.47 | 1.98 |
242 | 243 | 5.577164 | TCGCTTGTATCTTTCTTGTAGCTTC | 59.423 | 40.000 | 0.00 | 0.00 | 0.00 | 3.86 |
264 | 300 | 5.924356 | TCACTTGTAAATCAGGTTGACTCA | 58.076 | 37.500 | 0.00 | 0.00 | 34.09 | 3.41 |
307 | 343 | 0.815734 | GCTGCAACATCTCCATGCTT | 59.184 | 50.000 | 0.00 | 0.00 | 40.66 | 3.91 |
351 | 388 | 3.820467 | CAGGCCAATCTGTTAACAGTCAA | 59.180 | 43.478 | 29.83 | 15.32 | 44.12 | 3.18 |
374 | 411 | 1.153066 | TCACGTCCAGCCAAGCAAA | 60.153 | 52.632 | 0.00 | 0.00 | 0.00 | 3.68 |
377 | 414 | 1.039856 | ACGTCCAGCCAAGCAAATTT | 58.960 | 45.000 | 0.00 | 0.00 | 0.00 | 1.82 |
435 | 509 | 2.761809 | AGAGACAGCTTGAGATGGGAT | 58.238 | 47.619 | 1.02 | 0.00 | 35.42 | 3.85 |
443 | 517 | 1.213678 | CTTGAGATGGGATGCCTCCAA | 59.786 | 52.381 | 10.44 | 0.00 | 44.08 | 3.53 |
494 | 568 | 3.895656 | AGGAAAAACTTTACTGCCTTCCC | 59.104 | 43.478 | 0.00 | 0.00 | 32.89 | 3.97 |
495 | 569 | 3.639561 | GGAAAAACTTTACTGCCTTCCCA | 59.360 | 43.478 | 0.00 | 0.00 | 0.00 | 4.37 |
496 | 570 | 4.100344 | GGAAAAACTTTACTGCCTTCCCAA | 59.900 | 41.667 | 0.00 | 0.00 | 0.00 | 4.12 |
497 | 571 | 5.395879 | GGAAAAACTTTACTGCCTTCCCAAA | 60.396 | 40.000 | 0.00 | 0.00 | 0.00 | 3.28 |
498 | 572 | 5.887214 | AAAACTTTACTGCCTTCCCAAAT | 57.113 | 34.783 | 0.00 | 0.00 | 0.00 | 2.32 |
499 | 573 | 5.887214 | AAACTTTACTGCCTTCCCAAATT | 57.113 | 34.783 | 0.00 | 0.00 | 0.00 | 1.82 |
500 | 574 | 5.887214 | AACTTTACTGCCTTCCCAAATTT | 57.113 | 34.783 | 0.00 | 0.00 | 0.00 | 1.82 |
502 | 576 | 4.653801 | ACTTTACTGCCTTCCCAAATTTGT | 59.346 | 37.500 | 16.73 | 0.00 | 0.00 | 2.83 |
503 | 577 | 5.130311 | ACTTTACTGCCTTCCCAAATTTGTT | 59.870 | 36.000 | 16.73 | 0.00 | 0.00 | 2.83 |
504 | 578 | 5.622346 | TTACTGCCTTCCCAAATTTGTTT | 57.378 | 34.783 | 16.73 | 0.00 | 0.00 | 2.83 |
507 | 581 | 3.983741 | TGCCTTCCCAAATTTGTTTACG | 58.016 | 40.909 | 16.73 | 1.25 | 0.00 | 3.18 |
552 | 1482 | 1.031029 | ACGGAGGGAGAGCGTAGAAC | 61.031 | 60.000 | 0.00 | 0.00 | 0.00 | 3.01 |
627 | 1559 | 0.755698 | GGATCCGGGTGCTCTGTAGA | 60.756 | 60.000 | 0.00 | 0.00 | 0.00 | 2.59 |
853 | 1785 | 1.160137 | GGCATTGCCGGATCATCTAC | 58.840 | 55.000 | 12.82 | 0.00 | 39.62 | 2.59 |
982 | 1916 | 2.208431 | GATGCAGGATCCTCGTTTCTG | 58.792 | 52.381 | 12.69 | 0.18 | 0.00 | 3.02 |
1050 | 1984 | 2.510238 | AAGATGCGCTGCTCGGAC | 60.510 | 61.111 | 9.73 | 0.00 | 42.53 | 4.79 |
1182 | 2122 | 5.665459 | AGGATCGATTCTGTTGGTAGAAAG | 58.335 | 41.667 | 5.09 | 0.00 | 39.87 | 2.62 |
1185 | 2125 | 2.678336 | CGATTCTGTTGGTAGAAAGGCC | 59.322 | 50.000 | 0.00 | 0.00 | 39.87 | 5.19 |
1186 | 2126 | 2.178912 | TTCTGTTGGTAGAAAGGCCG | 57.821 | 50.000 | 0.00 | 0.00 | 33.96 | 6.13 |
1193 | 2133 | 0.103572 | GGTAGAAAGGCCGTATGCGA | 59.896 | 55.000 | 4.21 | 0.00 | 42.61 | 5.10 |
1224 | 2166 | 1.887320 | CGTTGCAATTCTGTGCTAGC | 58.113 | 50.000 | 8.10 | 8.10 | 45.17 | 3.42 |
1265 | 2209 | 6.564709 | TTTCTGTGATGTTTCTTGAGATGG | 57.435 | 37.500 | 0.00 | 0.00 | 0.00 | 3.51 |
1286 | 2230 | 6.399639 | TGGTTTCTTGTTCTGGGTAATTTC | 57.600 | 37.500 | 0.00 | 0.00 | 0.00 | 2.17 |
1294 | 2238 | 5.636123 | TGTTCTGGGTAATTTCTGCCTTAA | 58.364 | 37.500 | 0.00 | 0.00 | 0.00 | 1.85 |
1295 | 2239 | 6.071984 | TGTTCTGGGTAATTTCTGCCTTAAA | 58.928 | 36.000 | 0.00 | 0.00 | 0.00 | 1.52 |
1296 | 2240 | 6.723977 | TGTTCTGGGTAATTTCTGCCTTAAAT | 59.276 | 34.615 | 0.00 | 0.00 | 0.00 | 1.40 |
1414 | 2359 | 5.102953 | TCATCCAATCCCTGAACTAGTTG | 57.897 | 43.478 | 14.14 | 0.00 | 0.00 | 3.16 |
1426 | 2371 | 4.523083 | TGAACTAGTTGACATTATGGGGC | 58.477 | 43.478 | 14.14 | 0.00 | 0.00 | 5.80 |
1512 | 2476 | 5.869753 | TTTTAGATTGCAGCAGAGAGAAC | 57.130 | 39.130 | 0.00 | 0.00 | 0.00 | 3.01 |
1513 | 2477 | 2.399916 | AGATTGCAGCAGAGAGAACC | 57.600 | 50.000 | 0.00 | 0.00 | 0.00 | 3.62 |
1514 | 2478 | 1.907936 | AGATTGCAGCAGAGAGAACCT | 59.092 | 47.619 | 0.00 | 0.00 | 0.00 | 3.50 |
1515 | 2479 | 2.008329 | GATTGCAGCAGAGAGAACCTG | 58.992 | 52.381 | 0.00 | 0.00 | 34.88 | 4.00 |
1516 | 2480 | 1.051008 | TTGCAGCAGAGAGAACCTGA | 58.949 | 50.000 | 0.00 | 0.00 | 33.65 | 3.86 |
1517 | 2481 | 1.273759 | TGCAGCAGAGAGAACCTGAT | 58.726 | 50.000 | 0.00 | 0.00 | 33.65 | 2.90 |
1518 | 2482 | 1.206610 | TGCAGCAGAGAGAACCTGATC | 59.793 | 52.381 | 0.00 | 0.00 | 33.65 | 2.92 |
1519 | 2483 | 1.481772 | GCAGCAGAGAGAACCTGATCT | 59.518 | 52.381 | 0.00 | 0.00 | 33.65 | 2.75 |
1520 | 2484 | 2.739287 | GCAGCAGAGAGAACCTGATCTG | 60.739 | 54.545 | 0.00 | 0.00 | 41.68 | 2.90 |
1521 | 2485 | 2.759535 | CAGCAGAGAGAACCTGATCTGA | 59.240 | 50.000 | 5.28 | 0.00 | 41.35 | 3.27 |
1522 | 2486 | 3.385433 | CAGCAGAGAGAACCTGATCTGAT | 59.615 | 47.826 | 5.28 | 0.00 | 41.35 | 2.90 |
1523 | 2487 | 3.638160 | AGCAGAGAGAACCTGATCTGATC | 59.362 | 47.826 | 10.72 | 10.72 | 41.35 | 2.92 |
1524 | 2488 | 3.638160 | GCAGAGAGAACCTGATCTGATCT | 59.362 | 47.826 | 17.82 | 4.60 | 41.35 | 2.75 |
1525 | 2489 | 4.099881 | GCAGAGAGAACCTGATCTGATCTT | 59.900 | 45.833 | 17.82 | 4.93 | 41.35 | 2.40 |
1526 | 2490 | 5.395546 | GCAGAGAGAACCTGATCTGATCTTT | 60.396 | 44.000 | 17.82 | 8.84 | 41.35 | 2.52 |
1527 | 2491 | 6.642430 | CAGAGAGAACCTGATCTGATCTTTT | 58.358 | 40.000 | 17.82 | 8.53 | 41.35 | 2.27 |
1528 | 2492 | 7.104939 | CAGAGAGAACCTGATCTGATCTTTTT | 58.895 | 38.462 | 17.82 | 8.21 | 41.35 | 1.94 |
1641 | 2613 | 0.855598 | AAGGGATGGCAGCATGGTAT | 59.144 | 50.000 | 4.64 | 0.00 | 35.86 | 2.73 |
1648 | 2620 | 2.786777 | TGGCAGCATGGTATCATCATC | 58.213 | 47.619 | 0.00 | 0.00 | 35.86 | 2.92 |
1786 | 2758 | 3.937706 | CTGCTCCTAAACATGTCTCCAAG | 59.062 | 47.826 | 0.00 | 0.00 | 0.00 | 3.61 |
1813 | 2789 | 3.118702 | TGAAACGTTGGTTGGACAGTAGA | 60.119 | 43.478 | 0.00 | 0.00 | 36.25 | 2.59 |
1892 | 2875 | 0.185175 | AACCACTGACCCCAAGAACC | 59.815 | 55.000 | 0.00 | 0.00 | 0.00 | 3.62 |
1913 | 2923 | 1.732259 | CTGTACCCAGCAATTCGACAC | 59.268 | 52.381 | 0.00 | 0.00 | 0.00 | 3.67 |
1965 | 2975 | 1.679680 | CCCAGCATCATTCATGACACC | 59.320 | 52.381 | 0.00 | 0.00 | 40.03 | 4.16 |
1993 | 3003 | 3.884350 | ATGATGCTTGCTGCCGCG | 61.884 | 61.111 | 0.00 | 0.00 | 42.00 | 6.46 |
2048 | 3061 | 4.074970 | GGACTCTGAAAAGAAGCCATGAA | 58.925 | 43.478 | 0.00 | 0.00 | 0.00 | 2.57 |
2260 | 3349 | 3.579709 | GATGATATGATGCCGAGACGTT | 58.420 | 45.455 | 0.00 | 0.00 | 0.00 | 3.99 |
2293 | 3386 | 2.101209 | AAAAGTTGCACGTCTCCGCG | 62.101 | 55.000 | 0.00 | 0.00 | 37.70 | 6.46 |
2368 | 3461 | 3.553917 | TGATAATGTGAATGTACACGCCG | 59.446 | 43.478 | 0.00 | 0.00 | 42.86 | 6.46 |
2379 | 3472 | 3.377439 | TGTACACGCCGCTATAAGAATG | 58.623 | 45.455 | 0.00 | 0.00 | 0.00 | 2.67 |
2421 | 3514 | 3.678072 | CGTACTTCGGTGACATTGACATT | 59.322 | 43.478 | 0.00 | 0.00 | 35.71 | 2.71 |
2422 | 3515 | 4.434198 | CGTACTTCGGTGACATTGACATTG | 60.434 | 45.833 | 0.00 | 0.00 | 35.71 | 2.82 |
2475 | 3611 | 7.155328 | GGCCATGGACTATATATATGCTACAC | 58.845 | 42.308 | 18.40 | 0.00 | 0.00 | 2.90 |
2504 | 3640 | 9.574516 | AGTTAATAACTTATCTAGCCCCAAATG | 57.425 | 33.333 | 0.00 | 0.00 | 39.04 | 2.32 |
2557 | 3693 | 5.991606 | CAGAGTGAGTGGAAAGTTCAACATA | 59.008 | 40.000 | 1.52 | 0.00 | 33.44 | 2.29 |
2952 | 4621 | 1.955778 | TCAGTTGCCAACTTGTCATGG | 59.044 | 47.619 | 7.51 | 0.00 | 40.46 | 3.66 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
0 | 1 | 1.372582 | AGCGATGCCAACACATAGTG | 58.627 | 50.000 | 0.00 | 0.00 | 39.75 | 2.74 |
1 | 2 | 2.113860 | AAGCGATGCCAACACATAGT | 57.886 | 45.000 | 0.00 | 0.00 | 0.00 | 2.12 |
2 | 3 | 4.137849 | CATAAGCGATGCCAACACATAG | 57.862 | 45.455 | 0.00 | 0.00 | 0.00 | 2.23 |
13 | 14 | 3.620374 | GGATGTATCTGGCATAAGCGATG | 59.380 | 47.826 | 0.00 | 0.00 | 43.41 | 3.84 |
14 | 15 | 3.261643 | TGGATGTATCTGGCATAAGCGAT | 59.738 | 43.478 | 0.00 | 0.00 | 43.41 | 4.58 |
15 | 16 | 2.632512 | TGGATGTATCTGGCATAAGCGA | 59.367 | 45.455 | 0.00 | 0.00 | 43.41 | 4.93 |
16 | 17 | 3.044235 | TGGATGTATCTGGCATAAGCG | 57.956 | 47.619 | 0.00 | 0.00 | 43.41 | 4.68 |
17 | 18 | 5.474532 | TCAAATGGATGTATCTGGCATAAGC | 59.525 | 40.000 | 0.00 | 0.00 | 41.10 | 3.09 |
18 | 19 | 6.150641 | CCTCAAATGGATGTATCTGGCATAAG | 59.849 | 42.308 | 0.00 | 0.00 | 0.00 | 1.73 |
19 | 20 | 6.005823 | CCTCAAATGGATGTATCTGGCATAA | 58.994 | 40.000 | 0.00 | 0.00 | 0.00 | 1.90 |
20 | 21 | 5.515359 | CCCTCAAATGGATGTATCTGGCATA | 60.515 | 44.000 | 0.00 | 0.00 | 0.00 | 3.14 |
21 | 22 | 4.404640 | CCTCAAATGGATGTATCTGGCAT | 58.595 | 43.478 | 0.00 | 0.00 | 0.00 | 4.40 |
22 | 23 | 3.435457 | CCCTCAAATGGATGTATCTGGCA | 60.435 | 47.826 | 0.00 | 0.00 | 0.00 | 4.92 |
23 | 24 | 3.152341 | CCCTCAAATGGATGTATCTGGC | 58.848 | 50.000 | 0.00 | 0.00 | 0.00 | 4.85 |
24 | 25 | 4.712051 | TCCCTCAAATGGATGTATCTGG | 57.288 | 45.455 | 0.00 | 0.00 | 0.00 | 3.86 |
25 | 26 | 7.941238 | AGTTTATCCCTCAAATGGATGTATCTG | 59.059 | 37.037 | 2.10 | 0.00 | 42.57 | 2.90 |
26 | 27 | 8.050316 | AGTTTATCCCTCAAATGGATGTATCT | 57.950 | 34.615 | 2.10 | 0.00 | 42.57 | 1.98 |
27 | 28 | 8.571336 | CAAGTTTATCCCTCAAATGGATGTATC | 58.429 | 37.037 | 2.10 | 0.00 | 42.57 | 2.24 |
28 | 29 | 7.506938 | CCAAGTTTATCCCTCAAATGGATGTAT | 59.493 | 37.037 | 2.10 | 0.00 | 42.57 | 2.29 |
29 | 30 | 6.833416 | CCAAGTTTATCCCTCAAATGGATGTA | 59.167 | 38.462 | 2.10 | 0.00 | 42.57 | 2.29 |
30 | 31 | 5.658190 | CCAAGTTTATCCCTCAAATGGATGT | 59.342 | 40.000 | 2.10 | 0.00 | 42.57 | 3.06 |
31 | 32 | 5.069516 | CCCAAGTTTATCCCTCAAATGGATG | 59.930 | 44.000 | 2.10 | 0.00 | 42.57 | 3.51 |
32 | 33 | 5.043432 | TCCCAAGTTTATCCCTCAAATGGAT | 60.043 | 40.000 | 0.00 | 0.00 | 44.71 | 3.41 |
33 | 34 | 4.293634 | TCCCAAGTTTATCCCTCAAATGGA | 59.706 | 41.667 | 0.00 | 0.00 | 36.05 | 3.41 |
34 | 35 | 4.402474 | GTCCCAAGTTTATCCCTCAAATGG | 59.598 | 45.833 | 0.00 | 0.00 | 0.00 | 3.16 |
35 | 36 | 5.016173 | TGTCCCAAGTTTATCCCTCAAATG | 58.984 | 41.667 | 0.00 | 0.00 | 0.00 | 2.32 |
36 | 37 | 5.269554 | TGTCCCAAGTTTATCCCTCAAAT | 57.730 | 39.130 | 0.00 | 0.00 | 0.00 | 2.32 |
37 | 38 | 4.733077 | TGTCCCAAGTTTATCCCTCAAA | 57.267 | 40.909 | 0.00 | 0.00 | 0.00 | 2.69 |
38 | 39 | 4.733077 | TTGTCCCAAGTTTATCCCTCAA | 57.267 | 40.909 | 0.00 | 0.00 | 0.00 | 3.02 |
39 | 40 | 4.105697 | AGTTTGTCCCAAGTTTATCCCTCA | 59.894 | 41.667 | 0.00 | 0.00 | 0.00 | 3.86 |
40 | 41 | 4.663334 | AGTTTGTCCCAAGTTTATCCCTC | 58.337 | 43.478 | 0.00 | 0.00 | 0.00 | 4.30 |
41 | 42 | 4.741928 | AGTTTGTCCCAAGTTTATCCCT | 57.258 | 40.909 | 0.00 | 0.00 | 0.00 | 4.20 |
42 | 43 | 5.538813 | AGAAAGTTTGTCCCAAGTTTATCCC | 59.461 | 40.000 | 0.00 | 0.00 | 0.00 | 3.85 |
43 | 44 | 6.567891 | CGAGAAAGTTTGTCCCAAGTTTATCC | 60.568 | 42.308 | 7.14 | 0.00 | 30.13 | 2.59 |
44 | 45 | 6.371389 | CGAGAAAGTTTGTCCCAAGTTTATC | 58.629 | 40.000 | 7.14 | 0.00 | 0.00 | 1.75 |
45 | 46 | 5.240844 | CCGAGAAAGTTTGTCCCAAGTTTAT | 59.759 | 40.000 | 7.14 | 0.00 | 0.00 | 1.40 |
46 | 47 | 4.577283 | CCGAGAAAGTTTGTCCCAAGTTTA | 59.423 | 41.667 | 7.14 | 0.00 | 0.00 | 2.01 |
47 | 48 | 3.380320 | CCGAGAAAGTTTGTCCCAAGTTT | 59.620 | 43.478 | 7.14 | 0.00 | 0.00 | 2.66 |
48 | 49 | 2.949644 | CCGAGAAAGTTTGTCCCAAGTT | 59.050 | 45.455 | 7.14 | 0.00 | 0.00 | 2.66 |
49 | 50 | 2.171870 | TCCGAGAAAGTTTGTCCCAAGT | 59.828 | 45.455 | 7.14 | 0.00 | 0.00 | 3.16 |
50 | 51 | 2.548480 | GTCCGAGAAAGTTTGTCCCAAG | 59.452 | 50.000 | 7.14 | 0.00 | 0.00 | 3.61 |
51 | 52 | 2.567985 | GTCCGAGAAAGTTTGTCCCAA | 58.432 | 47.619 | 7.14 | 0.00 | 0.00 | 4.12 |
52 | 53 | 1.539496 | CGTCCGAGAAAGTTTGTCCCA | 60.539 | 52.381 | 7.14 | 0.00 | 0.00 | 4.37 |
53 | 54 | 1.145803 | CGTCCGAGAAAGTTTGTCCC | 58.854 | 55.000 | 7.14 | 0.00 | 0.00 | 4.46 |
54 | 55 | 1.145803 | CCGTCCGAGAAAGTTTGTCC | 58.854 | 55.000 | 7.14 | 0.00 | 0.00 | 4.02 |
55 | 56 | 2.059541 | CTCCGTCCGAGAAAGTTTGTC | 58.940 | 52.381 | 2.68 | 2.68 | 41.63 | 3.18 |
56 | 57 | 1.270147 | CCTCCGTCCGAGAAAGTTTGT | 60.270 | 52.381 | 0.00 | 0.00 | 41.63 | 2.83 |
57 | 58 | 1.429463 | CCTCCGTCCGAGAAAGTTTG | 58.571 | 55.000 | 0.00 | 0.00 | 41.63 | 2.93 |
58 | 59 | 0.320697 | CCCTCCGTCCGAGAAAGTTT | 59.679 | 55.000 | 0.00 | 0.00 | 41.63 | 2.66 |
59 | 60 | 0.541296 | TCCCTCCGTCCGAGAAAGTT | 60.541 | 55.000 | 0.00 | 0.00 | 41.63 | 2.66 |
60 | 61 | 0.966370 | CTCCCTCCGTCCGAGAAAGT | 60.966 | 60.000 | 0.00 | 0.00 | 41.63 | 2.66 |
61 | 62 | 0.966370 | ACTCCCTCCGTCCGAGAAAG | 60.966 | 60.000 | 0.00 | 0.00 | 41.63 | 2.62 |
62 | 63 | 0.329261 | TACTCCCTCCGTCCGAGAAA | 59.671 | 55.000 | 0.00 | 0.00 | 41.63 | 2.52 |
63 | 64 | 0.393537 | GTACTCCCTCCGTCCGAGAA | 60.394 | 60.000 | 0.00 | 0.00 | 41.63 | 2.87 |
64 | 65 | 1.222936 | GTACTCCCTCCGTCCGAGA | 59.777 | 63.158 | 0.00 | 0.00 | 41.63 | 4.04 |
65 | 66 | 0.465824 | ATGTACTCCCTCCGTCCGAG | 60.466 | 60.000 | 0.00 | 0.00 | 38.46 | 4.63 |
66 | 67 | 0.750546 | CATGTACTCCCTCCGTCCGA | 60.751 | 60.000 | 0.00 | 0.00 | 0.00 | 4.55 |
67 | 68 | 1.035932 | ACATGTACTCCCTCCGTCCG | 61.036 | 60.000 | 0.00 | 0.00 | 0.00 | 4.79 |
68 | 69 | 1.192428 | AACATGTACTCCCTCCGTCC | 58.808 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
69 | 70 | 3.194116 | TGTTAACATGTACTCCCTCCGTC | 59.806 | 47.826 | 3.59 | 0.00 | 0.00 | 4.79 |
70 | 71 | 3.167485 | TGTTAACATGTACTCCCTCCGT | 58.833 | 45.455 | 3.59 | 0.00 | 0.00 | 4.69 |
71 | 72 | 3.880047 | TGTTAACATGTACTCCCTCCG | 57.120 | 47.619 | 3.59 | 0.00 | 0.00 | 4.63 |
72 | 73 | 4.259356 | GGTTGTTAACATGTACTCCCTCC | 58.741 | 47.826 | 9.56 | 0.00 | 0.00 | 4.30 |
73 | 74 | 4.901868 | TGGTTGTTAACATGTACTCCCTC | 58.098 | 43.478 | 9.56 | 0.00 | 0.00 | 4.30 |
74 | 75 | 4.986054 | TGGTTGTTAACATGTACTCCCT | 57.014 | 40.909 | 9.56 | 0.00 | 0.00 | 4.20 |
75 | 76 | 6.386654 | CAAATGGTTGTTAACATGTACTCCC | 58.613 | 40.000 | 9.56 | 0.00 | 0.00 | 4.30 |
76 | 77 | 5.861787 | GCAAATGGTTGTTAACATGTACTCC | 59.138 | 40.000 | 9.56 | 6.37 | 37.06 | 3.85 |
77 | 78 | 6.442952 | TGCAAATGGTTGTTAACATGTACTC | 58.557 | 36.000 | 9.56 | 0.63 | 37.06 | 2.59 |
78 | 79 | 6.398234 | TGCAAATGGTTGTTAACATGTACT | 57.602 | 33.333 | 9.56 | 0.00 | 37.06 | 2.73 |
79 | 80 | 6.345408 | CGTTGCAAATGGTTGTTAACATGTAC | 60.345 | 38.462 | 9.56 | 4.72 | 37.06 | 2.90 |
80 | 81 | 5.687730 | CGTTGCAAATGGTTGTTAACATGTA | 59.312 | 36.000 | 9.56 | 0.09 | 37.06 | 2.29 |
81 | 82 | 4.505922 | CGTTGCAAATGGTTGTTAACATGT | 59.494 | 37.500 | 9.56 | 0.00 | 37.06 | 3.21 |
82 | 83 | 4.505922 | ACGTTGCAAATGGTTGTTAACATG | 59.494 | 37.500 | 9.56 | 4.71 | 37.08 | 3.21 |
83 | 84 | 4.688021 | ACGTTGCAAATGGTTGTTAACAT | 58.312 | 34.783 | 9.56 | 0.00 | 37.08 | 2.71 |
84 | 85 | 4.106197 | GACGTTGCAAATGGTTGTTAACA | 58.894 | 39.130 | 3.59 | 3.59 | 37.08 | 2.41 |
85 | 86 | 4.106197 | TGACGTTGCAAATGGTTGTTAAC | 58.894 | 39.130 | 0.00 | 0.00 | 37.08 | 2.01 |
86 | 87 | 4.371855 | TGACGTTGCAAATGGTTGTTAA | 57.628 | 36.364 | 0.00 | 0.00 | 37.08 | 2.01 |
87 | 88 | 4.355437 | CTTGACGTTGCAAATGGTTGTTA | 58.645 | 39.130 | 0.00 | 0.00 | 37.08 | 2.41 |
88 | 89 | 2.949451 | TGACGTTGCAAATGGTTGTT | 57.051 | 40.000 | 0.00 | 0.00 | 37.08 | 2.83 |
89 | 90 | 2.808244 | CTTGACGTTGCAAATGGTTGT | 58.192 | 42.857 | 0.00 | 0.00 | 37.08 | 3.32 |
90 | 91 | 1.522258 | GCTTGACGTTGCAAATGGTTG | 59.478 | 47.619 | 0.00 | 0.00 | 37.08 | 3.77 |
91 | 92 | 1.135915 | TGCTTGACGTTGCAAATGGTT | 59.864 | 42.857 | 0.00 | 0.00 | 37.08 | 3.67 |
92 | 93 | 0.743688 | TGCTTGACGTTGCAAATGGT | 59.256 | 45.000 | 0.00 | 0.00 | 37.08 | 3.55 |
93 | 94 | 1.269206 | ACTGCTTGACGTTGCAAATGG | 60.269 | 47.619 | 0.00 | 0.00 | 38.81 | 3.16 |
94 | 95 | 2.124011 | ACTGCTTGACGTTGCAAATG | 57.876 | 45.000 | 0.00 | 0.00 | 38.81 | 2.32 |
95 | 96 | 2.098934 | TGAACTGCTTGACGTTGCAAAT | 59.901 | 40.909 | 0.00 | 0.00 | 38.81 | 2.32 |
96 | 97 | 1.470494 | TGAACTGCTTGACGTTGCAAA | 59.530 | 42.857 | 0.00 | 0.00 | 38.81 | 3.68 |
97 | 98 | 1.090728 | TGAACTGCTTGACGTTGCAA | 58.909 | 45.000 | 11.71 | 0.00 | 38.81 | 4.08 |
98 | 99 | 0.376852 | GTGAACTGCTTGACGTTGCA | 59.623 | 50.000 | 10.49 | 10.49 | 37.63 | 4.08 |
99 | 100 | 0.376852 | TGTGAACTGCTTGACGTTGC | 59.623 | 50.000 | 0.00 | 0.00 | 0.00 | 4.17 |
100 | 101 | 2.823196 | TTGTGAACTGCTTGACGTTG | 57.177 | 45.000 | 0.00 | 0.00 | 0.00 | 4.10 |
101 | 102 | 3.006940 | TCTTTGTGAACTGCTTGACGTT | 58.993 | 40.909 | 0.00 | 0.00 | 0.00 | 3.99 |
102 | 103 | 2.627945 | TCTTTGTGAACTGCTTGACGT | 58.372 | 42.857 | 0.00 | 0.00 | 0.00 | 4.34 |
103 | 104 | 3.548587 | CATCTTTGTGAACTGCTTGACG | 58.451 | 45.455 | 0.00 | 0.00 | 0.00 | 4.35 |
104 | 105 | 3.004106 | AGCATCTTTGTGAACTGCTTGAC | 59.996 | 43.478 | 0.00 | 0.00 | 40.08 | 3.18 |
105 | 106 | 3.216800 | AGCATCTTTGTGAACTGCTTGA | 58.783 | 40.909 | 0.00 | 0.00 | 40.08 | 3.02 |
106 | 107 | 3.637998 | AGCATCTTTGTGAACTGCTTG | 57.362 | 42.857 | 0.00 | 0.00 | 40.08 | 4.01 |
108 | 109 | 4.660789 | AAAAGCATCTTTGTGAACTGCT | 57.339 | 36.364 | 0.00 | 0.00 | 44.62 | 4.24 |
129 | 130 | 4.619160 | GCCCATGCAAAACCAAAACAAAAA | 60.619 | 37.500 | 0.00 | 0.00 | 37.47 | 1.94 |
130 | 131 | 3.119352 | GCCCATGCAAAACCAAAACAAAA | 60.119 | 39.130 | 0.00 | 0.00 | 37.47 | 2.44 |
131 | 132 | 2.424956 | GCCCATGCAAAACCAAAACAAA | 59.575 | 40.909 | 0.00 | 0.00 | 37.47 | 2.83 |
132 | 133 | 2.019984 | GCCCATGCAAAACCAAAACAA | 58.980 | 42.857 | 0.00 | 0.00 | 37.47 | 2.83 |
133 | 134 | 1.065199 | TGCCCATGCAAAACCAAAACA | 60.065 | 42.857 | 0.00 | 0.00 | 46.66 | 2.83 |
134 | 135 | 1.673168 | TGCCCATGCAAAACCAAAAC | 58.327 | 45.000 | 0.00 | 0.00 | 46.66 | 2.43 |
145 | 146 | 4.392940 | AGTAATTATCTCTGTGCCCATGC | 58.607 | 43.478 | 0.00 | 0.00 | 38.26 | 4.06 |
146 | 147 | 6.057533 | TCAAGTAATTATCTCTGTGCCCATG | 58.942 | 40.000 | 0.00 | 0.00 | 0.00 | 3.66 |
147 | 148 | 6.252599 | TCAAGTAATTATCTCTGTGCCCAT | 57.747 | 37.500 | 0.00 | 0.00 | 0.00 | 4.00 |
148 | 149 | 5.396772 | CCTCAAGTAATTATCTCTGTGCCCA | 60.397 | 44.000 | 0.00 | 0.00 | 0.00 | 5.36 |
149 | 150 | 5.059833 | CCTCAAGTAATTATCTCTGTGCCC | 58.940 | 45.833 | 0.00 | 0.00 | 0.00 | 5.36 |
150 | 151 | 5.918608 | TCCTCAAGTAATTATCTCTGTGCC | 58.081 | 41.667 | 0.00 | 0.00 | 0.00 | 5.01 |
151 | 152 | 7.268586 | TCTTCCTCAAGTAATTATCTCTGTGC | 58.731 | 38.462 | 0.00 | 0.00 | 0.00 | 4.57 |
152 | 153 | 9.092876 | GTTCTTCCTCAAGTAATTATCTCTGTG | 57.907 | 37.037 | 0.00 | 0.00 | 0.00 | 3.66 |
153 | 154 | 7.976734 | CGTTCTTCCTCAAGTAATTATCTCTGT | 59.023 | 37.037 | 0.00 | 0.00 | 0.00 | 3.41 |
154 | 155 | 7.436673 | CCGTTCTTCCTCAAGTAATTATCTCTG | 59.563 | 40.741 | 0.00 | 0.00 | 0.00 | 3.35 |
155 | 156 | 7.124448 | ACCGTTCTTCCTCAAGTAATTATCTCT | 59.876 | 37.037 | 0.00 | 0.00 | 0.00 | 3.10 |
156 | 157 | 7.266400 | ACCGTTCTTCCTCAAGTAATTATCTC | 58.734 | 38.462 | 0.00 | 0.00 | 0.00 | 2.75 |
157 | 158 | 7.093465 | TGACCGTTCTTCCTCAAGTAATTATCT | 60.093 | 37.037 | 0.00 | 0.00 | 0.00 | 1.98 |
191 | 192 | 6.034591 | GCTACGAATACATTCACAGTACTGT | 58.965 | 40.000 | 22.95 | 22.95 | 46.17 | 3.55 |
218 | 219 | 5.073311 | AGCTACAAGAAAGATACAAGCGA | 57.927 | 39.130 | 0.00 | 0.00 | 34.01 | 4.93 |
229 | 230 | 8.445275 | TGATTTACAAGTGAAGCTACAAGAAA | 57.555 | 30.769 | 0.00 | 0.00 | 0.00 | 2.52 |
242 | 243 | 6.618287 | TTGAGTCAACCTGATTTACAAGTG | 57.382 | 37.500 | 0.08 | 0.00 | 0.00 | 3.16 |
275 | 311 | 1.134946 | GTTGCAGCACACCTTCTTGTT | 59.865 | 47.619 | 0.00 | 0.00 | 0.00 | 2.83 |
283 | 319 | 0.890542 | TGGAGATGTTGCAGCACACC | 60.891 | 55.000 | 5.00 | 10.16 | 0.00 | 4.16 |
307 | 343 | 7.044798 | CCTGAACCAACAAAATTACTGGAAAA | 58.955 | 34.615 | 0.00 | 0.00 | 32.97 | 2.29 |
351 | 388 | 0.036952 | CTTGGCTGGACGTGACAGAT | 60.037 | 55.000 | 18.20 | 0.00 | 38.20 | 2.90 |
374 | 411 | 7.978975 | CGGGTGTTAATTGATATGGACAAAAAT | 59.021 | 33.333 | 0.00 | 0.00 | 0.00 | 1.82 |
377 | 414 | 6.181190 | TCGGGTGTTAATTGATATGGACAAA | 58.819 | 36.000 | 0.00 | 0.00 | 0.00 | 2.83 |
443 | 517 | 5.984926 | TCGTTTCGTACCAACAAATTAGAGT | 59.015 | 36.000 | 4.04 | 0.00 | 0.00 | 3.24 |
494 | 568 | 9.026074 | ACAGTGGTATTTTCGTAAACAAATTTG | 57.974 | 29.630 | 16.67 | 16.67 | 0.00 | 2.32 |
498 | 572 | 9.719279 | CTTTACAGTGGTATTTTCGTAAACAAA | 57.281 | 29.630 | 0.00 | 0.00 | 0.00 | 2.83 |
499 | 573 | 7.856894 | GCTTTACAGTGGTATTTTCGTAAACAA | 59.143 | 33.333 | 0.00 | 0.00 | 0.00 | 2.83 |
500 | 574 | 7.012138 | TGCTTTACAGTGGTATTTTCGTAAACA | 59.988 | 33.333 | 0.00 | 0.00 | 0.00 | 2.83 |
502 | 576 | 7.227116 | AGTGCTTTACAGTGGTATTTTCGTAAA | 59.773 | 33.333 | 0.00 | 0.00 | 0.00 | 2.01 |
503 | 577 | 6.707161 | AGTGCTTTACAGTGGTATTTTCGTAA | 59.293 | 34.615 | 0.00 | 0.00 | 0.00 | 3.18 |
504 | 578 | 6.225318 | AGTGCTTTACAGTGGTATTTTCGTA | 58.775 | 36.000 | 0.00 | 0.00 | 0.00 | 3.43 |
507 | 581 | 6.966021 | TCAAGTGCTTTACAGTGGTATTTTC | 58.034 | 36.000 | 0.00 | 0.00 | 30.18 | 2.29 |
523 | 1452 | 1.115467 | CTCCCTCCGTATCAAGTGCT | 58.885 | 55.000 | 0.00 | 0.00 | 0.00 | 4.40 |
552 | 1482 | 4.878971 | TGTAATGTATCCATTCGTTGGTGG | 59.121 | 41.667 | 6.97 | 0.54 | 46.52 | 4.61 |
627 | 1559 | 4.881850 | CCTGGAATTATCAACGGCTACTTT | 59.118 | 41.667 | 0.00 | 0.00 | 0.00 | 2.66 |
853 | 1785 | 3.151022 | GGAGAGGAGGGCTGACGG | 61.151 | 72.222 | 0.00 | 0.00 | 0.00 | 4.79 |
982 | 1916 | 3.119955 | GCCATCTACAAAAGTTTCGACCC | 60.120 | 47.826 | 0.00 | 0.00 | 0.00 | 4.46 |
1050 | 1984 | 0.863538 | CTGAATCGTCGGACAGCGAG | 60.864 | 60.000 | 9.10 | 0.00 | 40.56 | 5.03 |
1130 | 2070 | 4.230657 | GAGAATTCGACAGGATCATACCG | 58.769 | 47.826 | 0.00 | 0.00 | 34.73 | 4.02 |
1182 | 2122 | 3.123621 | CAGAAGATAAATCGCATACGGCC | 59.876 | 47.826 | 0.00 | 0.00 | 40.31 | 6.13 |
1185 | 2125 | 3.425525 | ACGCAGAAGATAAATCGCATACG | 59.574 | 43.478 | 0.00 | 0.00 | 42.01 | 3.06 |
1186 | 2126 | 4.974103 | ACGCAGAAGATAAATCGCATAC | 57.026 | 40.909 | 0.00 | 0.00 | 0.00 | 2.39 |
1193 | 2133 | 6.032094 | CAGAATTGCAACGCAGAAGATAAAT | 58.968 | 36.000 | 0.00 | 0.00 | 40.61 | 1.40 |
1265 | 2209 | 5.920840 | GCAGAAATTACCCAGAACAAGAAAC | 59.079 | 40.000 | 0.00 | 0.00 | 0.00 | 2.78 |
1384 | 2329 | 6.154021 | AGTTCAGGGATTGGATGAAAATTCAG | 59.846 | 38.462 | 1.98 | 0.00 | 41.08 | 3.02 |
1414 | 2359 | 4.021544 | TGAGTTGTTTTGCCCCATAATGTC | 60.022 | 41.667 | 0.00 | 0.00 | 0.00 | 3.06 |
1426 | 2371 | 7.543868 | TGTCTATTGGTTTTGTGAGTTGTTTTG | 59.456 | 33.333 | 0.00 | 0.00 | 0.00 | 2.44 |
1533 | 2497 | 2.466846 | TCAGATCAGGTTCCATTCGGA | 58.533 | 47.619 | 0.00 | 0.00 | 40.60 | 4.55 |
1534 | 2498 | 2.988010 | TCAGATCAGGTTCCATTCGG | 57.012 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
1535 | 2499 | 4.056740 | CAGATCAGATCAGGTTCCATTCG | 58.943 | 47.826 | 13.14 | 0.00 | 0.00 | 3.34 |
1536 | 2500 | 5.033589 | ACAGATCAGATCAGGTTCCATTC | 57.966 | 43.478 | 13.14 | 0.00 | 0.00 | 2.67 |
1537 | 2501 | 5.426509 | TGTACAGATCAGATCAGGTTCCATT | 59.573 | 40.000 | 13.14 | 0.00 | 0.00 | 3.16 |
1538 | 2502 | 4.964897 | TGTACAGATCAGATCAGGTTCCAT | 59.035 | 41.667 | 13.14 | 0.00 | 0.00 | 3.41 |
1539 | 2503 | 4.352893 | TGTACAGATCAGATCAGGTTCCA | 58.647 | 43.478 | 13.14 | 7.80 | 0.00 | 3.53 |
1540 | 2504 | 5.105146 | AGTTGTACAGATCAGATCAGGTTCC | 60.105 | 44.000 | 13.14 | 5.70 | 0.00 | 3.62 |
1541 | 2505 | 5.971763 | AGTTGTACAGATCAGATCAGGTTC | 58.028 | 41.667 | 13.14 | 8.59 | 0.00 | 3.62 |
1542 | 2506 | 7.563188 | AGATAGTTGTACAGATCAGATCAGGTT | 59.437 | 37.037 | 13.14 | 0.00 | 0.00 | 3.50 |
1543 | 2507 | 7.066142 | AGATAGTTGTACAGATCAGATCAGGT | 58.934 | 38.462 | 13.14 | 12.07 | 0.00 | 4.00 |
1584 | 2550 | 2.970974 | GAACCTTGTGCGCTCTGCC | 61.971 | 63.158 | 9.73 | 0.00 | 45.60 | 4.85 |
1621 | 2587 | 1.517238 | TACCATGCTGCCATCCCTTA | 58.483 | 50.000 | 0.00 | 0.00 | 0.00 | 2.69 |
1641 | 2613 | 3.586100 | TTCTGTTTCCGTCGATGATGA | 57.414 | 42.857 | 6.11 | 0.00 | 0.00 | 2.92 |
1648 | 2620 | 1.860676 | TCCAGTTTCTGTTTCCGTCG | 58.139 | 50.000 | 0.00 | 0.00 | 0.00 | 5.12 |
1786 | 2758 | 0.666374 | CCAACCAACGTTTCACCTCC | 59.334 | 55.000 | 0.00 | 0.00 | 0.00 | 4.30 |
1813 | 2789 | 0.106419 | TCCACTTTGGTTTCCGCCTT | 60.106 | 50.000 | 0.00 | 0.00 | 39.03 | 4.35 |
1864 | 2845 | 0.827507 | GGTCAGTGGTTGTGGCCATT | 60.828 | 55.000 | 9.72 | 0.00 | 41.08 | 3.16 |
1892 | 2875 | 1.338674 | TGTCGAATTGCTGGGTACAGG | 60.339 | 52.381 | 0.00 | 0.00 | 45.04 | 4.00 |
1913 | 2923 | 4.202040 | TGCACTGTTTTCATCAGAACCTTG | 60.202 | 41.667 | 0.00 | 0.00 | 36.81 | 3.61 |
1965 | 2975 | 2.159421 | GCAAGCATCATGTCCACAAGAG | 60.159 | 50.000 | 0.00 | 0.00 | 0.00 | 2.85 |
2008 | 3018 | 3.011517 | TTGGCCTGCTCCTCCTCC | 61.012 | 66.667 | 3.32 | 0.00 | 0.00 | 4.30 |
2009 | 3019 | 2.588989 | CTTGGCCTGCTCCTCCTC | 59.411 | 66.667 | 3.32 | 0.00 | 0.00 | 3.71 |
2048 | 3061 | 1.988107 | TCCACCAATCTTCCTGCTTCT | 59.012 | 47.619 | 0.00 | 0.00 | 0.00 | 2.85 |
2260 | 3349 | 4.274705 | TGCAACTTTTAGCATTCAACGAGA | 59.725 | 37.500 | 0.00 | 0.00 | 35.51 | 4.04 |
2293 | 3386 | 6.266103 | AGAGGAGAGATCATGAGAGAAATGAC | 59.734 | 42.308 | 0.09 | 0.00 | 36.89 | 3.06 |
2379 | 3472 | 7.818642 | AGTACGCACTTACAGATCTATAATCC | 58.181 | 38.462 | 0.00 | 0.00 | 0.00 | 3.01 |
2421 | 3514 | 4.400529 | TGCTTATGAATCGGCTAAGTCA | 57.599 | 40.909 | 0.00 | 0.00 | 0.00 | 3.41 |
2422 | 3515 | 4.752101 | ACATGCTTATGAATCGGCTAAGTC | 59.248 | 41.667 | 0.00 | 0.00 | 0.00 | 3.01 |
2504 | 3640 | 2.338577 | ATGGCATGGCAGTCTTCTAC | 57.661 | 50.000 | 27.02 | 0.00 | 0.00 | 2.59 |
2575 | 3711 | 6.109359 | ACTAGTTGCCTGAAATCATACAGAC | 58.891 | 40.000 | 0.00 | 0.00 | 36.38 | 3.51 |
2975 | 4645 | 3.609103 | CACCAGTTGCACAAGAACTAC | 57.391 | 47.619 | 0.00 | 0.00 | 32.27 | 2.73 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.