Multiple sequence alignment - TraesCS2D01G396500
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 | TraesCS2D01G396500 | chr2D | 100.000 | 6315 | 0 | 0 | 1 | 6315 | 507757204 | 507750890 | 0.000000e+00 | 11662.0 |
1 | TraesCS2D01G396500 | chr2A | 94.545 | 3831 | 119 | 28 | 1019 | 4812 | 652295233 | 652291456 | 0.000000e+00 | 5834.0 |
2 | TraesCS2D01G396500 | chr2A | 96.571 | 1458 | 41 | 3 | 4866 | 6315 | 652291303 | 652289847 | 0.000000e+00 | 2407.0 |
3 | TraesCS2D01G396500 | chr2A | 86.126 | 764 | 69 | 16 | 5 | 756 | 652298766 | 652298028 | 0.000000e+00 | 789.0 |
4 | TraesCS2D01G396500 | chr2A | 85.766 | 274 | 20 | 8 | 779 | 1034 | 652297699 | 652297427 | 8.070000e-69 | 272.0 |
5 | TraesCS2D01G396500 | chr2A | 94.118 | 68 | 4 | 0 | 4480 | 4547 | 652291831 | 652291764 | 3.110000e-18 | 104.0 |
6 | TraesCS2D01G396500 | chr2B | 95.934 | 1451 | 55 | 2 | 4866 | 6315 | 596413341 | 596411894 | 0.000000e+00 | 2350.0 |
7 | TraesCS2D01G396500 | chr2B | 95.043 | 807 | 28 | 6 | 4010 | 4812 | 596414291 | 596413493 | 0.000000e+00 | 1258.0 |
8 | TraesCS2D01G396500 | chr2B | 92.343 | 875 | 32 | 10 | 765 | 1635 | 596418044 | 596417201 | 0.000000e+00 | 1212.0 |
9 | TraesCS2D01G396500 | chr2B | 91.057 | 861 | 64 | 9 | 2376 | 3229 | 596416183 | 596415329 | 0.000000e+00 | 1151.0 |
10 | TraesCS2D01G396500 | chr2B | 95.296 | 574 | 21 | 3 | 3233 | 3806 | 596415262 | 596414695 | 0.000000e+00 | 905.0 |
11 | TraesCS2D01G396500 | chr2B | 87.059 | 255 | 24 | 8 | 1705 | 1957 | 596417011 | 596416764 | 4.820000e-71 | 279.0 |
12 | TraesCS2D01G396500 | chr2B | 92.073 | 164 | 13 | 0 | 2212 | 2375 | 596416423 | 596416260 | 1.370000e-56 | 231.0 |
13 | TraesCS2D01G396500 | chr2B | 88.827 | 179 | 6 | 5 | 3800 | 3970 | 596414465 | 596414293 | 2.310000e-49 | 207.0 |
14 | TraesCS2D01G396500 | chr2B | 96.610 | 59 | 1 | 1 | 4810 | 4868 | 596413452 | 596413395 | 5.210000e-16 | 97.1 |
15 | TraesCS2D01G396500 | chr6D | 76.667 | 360 | 74 | 9 | 5899 | 6253 | 427568677 | 427569031 | 2.320000e-44 | 191.0 |
16 | TraesCS2D01G396500 | chr7A | 87.970 | 133 | 15 | 1 | 4927 | 5058 | 65461566 | 65461698 | 8.480000e-34 | 156.0 |
17 | TraesCS2D01G396500 | chr7A | 76.923 | 221 | 41 | 8 | 6027 | 6242 | 556299832 | 556299617 | 4.000000e-22 | 117.0 |
18 | TraesCS2D01G396500 | chr7A | 87.037 | 54 | 7 | 0 | 6198 | 6251 | 33606899 | 33606952 | 1.900000e-05 | 62.1 |
19 | TraesCS2D01G396500 | chr4D | 74.595 | 370 | 67 | 24 | 5899 | 6253 | 387756775 | 387756418 | 3.070000e-28 | 137.0 |
20 | TraesCS2D01G396500 | chr7B | 78.281 | 221 | 38 | 8 | 6027 | 6242 | 517394351 | 517394136 | 3.970000e-27 | 134.0 |
21 | TraesCS2D01G396500 | chr7D | 77.376 | 221 | 40 | 8 | 6027 | 6242 | 489114706 | 489114491 | 8.600000e-24 | 122.0 |
22 | TraesCS2D01G396500 | chr6B | 77.193 | 228 | 40 | 11 | 6032 | 6253 | 219571081 | 219570860 | 8.600000e-24 | 122.0 |
23 | TraesCS2D01G396500 | chr6A | 81.481 | 135 | 23 | 2 | 6026 | 6159 | 156751569 | 156751702 | 6.690000e-20 | 110.0 |
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.
query | scaffold | start | end | length | rev.comp | avg.bitscore | max.bitscore | avg.percent.identical | query.start | query.end | num_hsp | groupid | homo_length | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | TraesCS2D01G396500 | chr2D | 507750890 | 507757204 | 6314 | True | 11662.000000 | 11662 | 100.000000 | 1 | 6315 | 1 | chr2D.!!$R1 | 6314 |
1 | TraesCS2D01G396500 | chr2A | 652289847 | 652295233 | 5386 | True | 2781.666667 | 5834 | 95.078000 | 1019 | 6315 | 3 | chr2A.!!$R1 | 5296 |
2 | TraesCS2D01G396500 | chr2A | 652297427 | 652298766 | 1339 | True | 530.500000 | 789 | 85.946000 | 5 | 1034 | 2 | chr2A.!!$R2 | 1029 |
3 | TraesCS2D01G396500 | chr2B | 596411894 | 596418044 | 6150 | True | 854.455556 | 2350 | 92.693556 | 765 | 6315 | 9 | chr2B.!!$R1 | 5550 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
125 | 127 | 0.250513 | ATCCTGAGGGCGTTGAAGTC | 59.749 | 55.000 | 0.00 | 0.00 | 0.00 | 3.01 | F |
1268 | 1619 | 0.257616 | CCTCCTCGTCCTCCTCTTCT | 59.742 | 60.000 | 0.00 | 0.00 | 0.00 | 2.85 | F |
1706 | 2071 | 0.931005 | GTACGATGGCTGCTGTTAGC | 59.069 | 55.000 | 0.00 | 0.00 | 42.82 | 3.09 | F |
3257 | 4146 | 0.251742 | TTAAGCTGCAACATGCCCCT | 60.252 | 50.000 | 1.02 | 0.00 | 44.23 | 4.79 | F |
3258 | 4147 | 0.251742 | TAAGCTGCAACATGCCCCTT | 60.252 | 50.000 | 1.02 | 5.12 | 44.23 | 3.95 | F |
4492 | 5627 | 2.227036 | AGGTCCACTTGGGCTCCAG | 61.227 | 63.158 | 0.00 | 0.00 | 40.38 | 3.86 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1689 | 2054 | 0.036010 | AAGCTAACAGCAGCCATCGT | 60.036 | 50.000 | 0.38 | 0.0 | 45.56 | 3.73 | R |
2834 | 3660 | 2.088423 | AGAAAAGGCACACACAAACGA | 58.912 | 42.857 | 0.00 | 0.0 | 0.00 | 3.85 | R |
3331 | 4220 | 3.693085 | ACTAAACATGGCAGCAATCAGAG | 59.307 | 43.478 | 0.00 | 0.0 | 0.00 | 3.35 | R |
4912 | 6148 | 0.260230 | TCACCAAGGGGCTGTTTCAA | 59.740 | 50.000 | 0.00 | 0.0 | 37.90 | 2.69 | R |
4959 | 6195 | 1.160137 | CTGAAAACTGGGCTTCTCCG | 58.840 | 55.000 | 0.00 | 0.0 | 34.94 | 4.63 | R |
5421 | 6664 | 0.460459 | GTTCTGCCTTAGTCGAGGGC | 60.460 | 60.000 | 10.50 | 10.5 | 45.45 | 5.19 | 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 |
---|---|---|---|---|---|---|---|---|---|
30 | 31 | 2.124860 | ACCGCCGCAATCCTAACC | 60.125 | 61.111 | 0.00 | 0.00 | 0.00 | 2.85 |
34 | 35 | 1.076995 | GCCGCAATCCTAACCCCTT | 60.077 | 57.895 | 0.00 | 0.00 | 0.00 | 3.95 |
38 | 39 | 1.064685 | CGCAATCCTAACCCCTTCCTT | 60.065 | 52.381 | 0.00 | 0.00 | 0.00 | 3.36 |
41 | 42 | 3.952323 | GCAATCCTAACCCCTTCCTTTAC | 59.048 | 47.826 | 0.00 | 0.00 | 0.00 | 2.01 |
55 | 57 | 3.140623 | TCCTTTACGCACCAAAACCTAC | 58.859 | 45.455 | 0.00 | 0.00 | 0.00 | 3.18 |
57 | 59 | 4.040217 | TCCTTTACGCACCAAAACCTACTA | 59.960 | 41.667 | 0.00 | 0.00 | 0.00 | 1.82 |
70 | 72 | 6.717997 | CCAAAACCTACTATTTTACACCACCT | 59.282 | 38.462 | 0.00 | 0.00 | 0.00 | 4.00 |
78 | 80 | 7.220890 | ACTATTTTACACCACCTAATCCCAT | 57.779 | 36.000 | 0.00 | 0.00 | 0.00 | 4.00 |
83 | 85 | 2.637872 | ACACCACCTAATCCCATATCGG | 59.362 | 50.000 | 0.00 | 0.00 | 0.00 | 4.18 |
86 | 88 | 2.615493 | CCACCTAATCCCATATCGGTGC | 60.615 | 54.545 | 0.00 | 0.00 | 40.32 | 5.01 |
87 | 89 | 2.303022 | CACCTAATCCCATATCGGTGCT | 59.697 | 50.000 | 0.00 | 0.00 | 35.96 | 4.40 |
88 | 90 | 2.567615 | ACCTAATCCCATATCGGTGCTC | 59.432 | 50.000 | 0.00 | 0.00 | 0.00 | 4.26 |
109 | 111 | 1.202533 | CCTCACATCCACACGGTATCC | 60.203 | 57.143 | 0.00 | 0.00 | 0.00 | 2.59 |
110 | 112 | 1.757118 | CTCACATCCACACGGTATCCT | 59.243 | 52.381 | 0.00 | 0.00 | 0.00 | 3.24 |
125 | 127 | 0.250513 | ATCCTGAGGGCGTTGAAGTC | 59.749 | 55.000 | 0.00 | 0.00 | 0.00 | 3.01 |
126 | 128 | 1.738099 | CCTGAGGGCGTTGAAGTCG | 60.738 | 63.158 | 0.00 | 0.00 | 0.00 | 4.18 |
127 | 129 | 1.738099 | CTGAGGGCGTTGAAGTCGG | 60.738 | 63.158 | 0.00 | 0.00 | 0.00 | 4.79 |
128 | 130 | 2.434359 | GAGGGCGTTGAAGTCGGG | 60.434 | 66.667 | 0.00 | 0.00 | 0.00 | 5.14 |
129 | 131 | 4.699522 | AGGGCGTTGAAGTCGGGC | 62.700 | 66.667 | 0.00 | 0.00 | 0.00 | 6.13 |
132 | 134 | 3.479269 | GCGTTGAAGTCGGGCGAG | 61.479 | 66.667 | 0.00 | 0.00 | 0.00 | 5.03 |
133 | 135 | 2.809601 | CGTTGAAGTCGGGCGAGG | 60.810 | 66.667 | 0.00 | 0.00 | 0.00 | 4.63 |
134 | 136 | 2.434359 | GTTGAAGTCGGGCGAGGG | 60.434 | 66.667 | 0.00 | 0.00 | 0.00 | 4.30 |
186 | 188 | 2.094338 | CAGAGGAAATGAAAGCCTTGCC | 60.094 | 50.000 | 0.00 | 0.00 | 30.70 | 4.52 |
196 | 198 | 2.811542 | AAGCCTTGCCTTCGCCTCTC | 62.812 | 60.000 | 0.00 | 0.00 | 0.00 | 3.20 |
212 | 214 | 2.280628 | CTCTCAACCGCCTTTATCACC | 58.719 | 52.381 | 0.00 | 0.00 | 0.00 | 4.02 |
246 | 248 | 6.604735 | AACATATATGCTCGAGTTTTGGTC | 57.395 | 37.500 | 15.13 | 0.00 | 0.00 | 4.02 |
254 | 256 | 4.213270 | TGCTCGAGTTTTGGTCTTTACATG | 59.787 | 41.667 | 15.13 | 0.00 | 0.00 | 3.21 |
255 | 257 | 4.712763 | CTCGAGTTTTGGTCTTTACATGC | 58.287 | 43.478 | 3.62 | 0.00 | 0.00 | 4.06 |
266 | 268 | 4.380867 | GGTCTTTACATGCTTGGTTGGATG | 60.381 | 45.833 | 4.44 | 0.00 | 40.80 | 3.51 |
286 | 288 | 5.707764 | GGATGTAATTAGAGGAAGGGAATGC | 59.292 | 44.000 | 0.00 | 0.00 | 0.00 | 3.56 |
297 | 299 | 3.563479 | GGAAGGGAATGCAAACTTAGGGA | 60.563 | 47.826 | 0.00 | 0.00 | 0.00 | 4.20 |
298 | 300 | 4.281657 | GAAGGGAATGCAAACTTAGGGAT | 58.718 | 43.478 | 0.00 | 0.00 | 0.00 | 3.85 |
303 | 313 | 5.598417 | GGGAATGCAAACTTAGGGATTACAT | 59.402 | 40.000 | 0.00 | 0.00 | 28.16 | 2.29 |
307 | 317 | 5.565509 | TGCAAACTTAGGGATTACATGACA | 58.434 | 37.500 | 0.00 | 0.00 | 0.00 | 3.58 |
310 | 320 | 7.498900 | TGCAAACTTAGGGATTACATGACATAG | 59.501 | 37.037 | 0.00 | 0.00 | 0.00 | 2.23 |
336 | 346 | 6.710744 | AGTCACCTGTGGTTTTAGATAGTTTG | 59.289 | 38.462 | 0.00 | 0.00 | 31.02 | 2.93 |
382 | 392 | 3.257624 | GGGAGTTTAGAGTCGAACTTCCA | 59.742 | 47.826 | 24.08 | 0.00 | 46.49 | 3.53 |
414 | 424 | 1.884235 | CAGTGAAGTGGTGGGAACTC | 58.116 | 55.000 | 0.00 | 0.00 | 0.00 | 3.01 |
416 | 426 | 0.391597 | GTGAAGTGGTGGGAACTCGA | 59.608 | 55.000 | 0.00 | 0.00 | 0.00 | 4.04 |
424 | 434 | 1.407025 | GGTGGGAACTCGAAGGGAATC | 60.407 | 57.143 | 0.00 | 0.00 | 0.00 | 2.52 |
441 | 451 | 4.035675 | GGGAATCGATTCACATGGAACTTC | 59.964 | 45.833 | 32.92 | 14.94 | 39.94 | 3.01 |
482 | 492 | 6.825610 | AGAATAAATGTCTCCTCAGATGGTC | 58.174 | 40.000 | 0.00 | 0.00 | 0.00 | 4.02 |
489 | 499 | 3.769844 | GTCTCCTCAGATGGTCAAACCTA | 59.230 | 47.826 | 0.00 | 0.00 | 39.58 | 3.08 |
555 | 566 | 7.955185 | AGATCTATCCACTTCTAATCTCACCAT | 59.045 | 37.037 | 0.00 | 0.00 | 0.00 | 3.55 |
556 | 567 | 9.249053 | GATCTATCCACTTCTAATCTCACCATA | 57.751 | 37.037 | 0.00 | 0.00 | 0.00 | 2.74 |
565 | 576 | 8.646900 | ACTTCTAATCTCACCATAATTCTCTCC | 58.353 | 37.037 | 0.00 | 0.00 | 0.00 | 3.71 |
573 | 584 | 7.841729 | TCTCACCATAATTCTCTCCTAACTCTT | 59.158 | 37.037 | 0.00 | 0.00 | 0.00 | 2.85 |
593 | 604 | 8.115490 | ACTCTTATTCATCTTCCCAAAAGTTG | 57.885 | 34.615 | 0.00 | 0.00 | 0.00 | 3.16 |
594 | 605 | 7.725844 | ACTCTTATTCATCTTCCCAAAAGTTGT | 59.274 | 33.333 | 0.00 | 0.00 | 0.00 | 3.32 |
601 | 612 | 5.576447 | TCTTCCCAAAAGTTGTCAAACTC | 57.424 | 39.130 | 0.00 | 0.00 | 46.15 | 3.01 |
631 | 644 | 8.905850 | TCATTGTCGTGTCCTTATACAACTATA | 58.094 | 33.333 | 0.00 | 0.00 | 33.27 | 1.31 |
639 | 652 | 6.097270 | TGTCCTTATACAACTATACAAGGCGT | 59.903 | 38.462 | 0.00 | 0.00 | 0.00 | 5.68 |
640 | 653 | 7.285172 | TGTCCTTATACAACTATACAAGGCGTA | 59.715 | 37.037 | 0.00 | 0.00 | 0.00 | 4.42 |
641 | 654 | 8.137437 | GTCCTTATACAACTATACAAGGCGTAA | 58.863 | 37.037 | 0.00 | 0.00 | 32.59 | 3.18 |
642 | 655 | 8.863086 | TCCTTATACAACTATACAAGGCGTAAT | 58.137 | 33.333 | 0.00 | 0.00 | 32.59 | 1.89 |
643 | 656 | 9.485206 | CCTTATACAACTATACAAGGCGTAATT | 57.515 | 33.333 | 0.00 | 0.00 | 32.59 | 1.40 |
647 | 660 | 5.756833 | ACAACTATACAAGGCGTAATTAGGC | 59.243 | 40.000 | 19.46 | 19.46 | 32.59 | 3.93 |
656 | 669 | 4.400036 | GGCGTAATTAGGCCGAAATTAG | 57.600 | 45.455 | 28.09 | 16.15 | 45.77 | 1.73 |
669 | 682 | 5.613358 | CCGAAATTAGGCCTATCATTGAC | 57.387 | 43.478 | 14.74 | 8.52 | 0.00 | 3.18 |
670 | 683 | 4.455877 | CCGAAATTAGGCCTATCATTGACC | 59.544 | 45.833 | 14.74 | 4.30 | 0.00 | 4.02 |
673 | 686 | 6.263168 | CGAAATTAGGCCTATCATTGACCTTT | 59.737 | 38.462 | 14.74 | 2.97 | 31.79 | 3.11 |
708 | 721 | 7.846644 | CTCTGATGAGCTTGTATTTTCTTCT | 57.153 | 36.000 | 0.00 | 0.00 | 33.12 | 2.85 |
709 | 722 | 7.606858 | TCTGATGAGCTTGTATTTTCTTCTG | 57.393 | 36.000 | 0.00 | 0.00 | 0.00 | 3.02 |
725 | 738 | 5.298989 | TCTTCTGGTACACTTTGGCTTTA | 57.701 | 39.130 | 0.00 | 0.00 | 0.00 | 1.85 |
727 | 740 | 6.123651 | TCTTCTGGTACACTTTGGCTTTAAA | 58.876 | 36.000 | 0.00 | 0.00 | 0.00 | 1.52 |
730 | 743 | 4.538738 | TGGTACACTTTGGCTTTAAACCT | 58.461 | 39.130 | 0.00 | 0.00 | 0.00 | 3.50 |
731 | 744 | 4.339814 | TGGTACACTTTGGCTTTAAACCTG | 59.660 | 41.667 | 0.00 | 2.26 | 0.00 | 4.00 |
733 | 746 | 4.918810 | ACACTTTGGCTTTAAACCTGAG | 57.081 | 40.909 | 7.89 | 7.75 | 0.00 | 3.35 |
743 | 756 | 4.462834 | GCTTTAAACCTGAGGGCTTTACAT | 59.537 | 41.667 | 2.38 | 0.00 | 35.63 | 2.29 |
748 | 761 | 3.185455 | ACCTGAGGGCTTTACATCTCTT | 58.815 | 45.455 | 2.38 | 0.00 | 35.63 | 2.85 |
903 | 1245 | 1.313091 | GGTTGCGGATTTCAGTCCCC | 61.313 | 60.000 | 0.00 | 0.00 | 34.67 | 4.81 |
904 | 1246 | 0.608035 | GTTGCGGATTTCAGTCCCCA | 60.608 | 55.000 | 0.00 | 0.00 | 34.67 | 4.96 |
905 | 1247 | 0.608035 | TTGCGGATTTCAGTCCCCAC | 60.608 | 55.000 | 0.00 | 0.00 | 34.67 | 4.61 |
906 | 1248 | 1.749258 | GCGGATTTCAGTCCCCACC | 60.749 | 63.158 | 0.00 | 0.00 | 34.67 | 4.61 |
907 | 1249 | 1.077716 | CGGATTTCAGTCCCCACCC | 60.078 | 63.158 | 0.00 | 0.00 | 34.67 | 4.61 |
1268 | 1619 | 0.257616 | CCTCCTCGTCCTCCTCTTCT | 59.742 | 60.000 | 0.00 | 0.00 | 0.00 | 2.85 |
1537 | 1888 | 6.040278 | TGTGATTCTACTAGAGCAGGAAGATG | 59.960 | 42.308 | 0.00 | 0.00 | 0.00 | 2.90 |
1584 | 1935 | 6.812879 | TGAGAGATTACGTAACTGACTCAA | 57.187 | 37.500 | 22.10 | 13.82 | 0.00 | 3.02 |
1585 | 1936 | 6.609533 | TGAGAGATTACGTAACTGACTCAAC | 58.390 | 40.000 | 22.10 | 18.12 | 0.00 | 3.18 |
1614 | 1965 | 2.028748 | GTGCTTGAGATGTGGGCAATTT | 60.029 | 45.455 | 0.00 | 0.00 | 34.65 | 1.82 |
1654 | 2012 | 5.886474 | GCTCTAGGTTTAAATTAGTTGGCCT | 59.114 | 40.000 | 3.32 | 0.00 | 0.00 | 5.19 |
1657 | 2015 | 7.043565 | TCTAGGTTTAAATTAGTTGGCCTACG | 58.956 | 38.462 | 11.80 | 0.00 | 0.00 | 3.51 |
1670 | 2035 | 1.353076 | GCCTACGGTGTTTCTAACGG | 58.647 | 55.000 | 0.00 | 0.00 | 0.00 | 4.44 |
1689 | 2054 | 2.810164 | GGTGCCCAATTAGGTTTGGTA | 58.190 | 47.619 | 2.81 | 0.00 | 43.92 | 3.25 |
1705 | 2070 | 1.134818 | TGGTACGATGGCTGCTGTTAG | 60.135 | 52.381 | 0.00 | 0.00 | 0.00 | 2.34 |
1706 | 2071 | 0.931005 | GTACGATGGCTGCTGTTAGC | 59.069 | 55.000 | 0.00 | 0.00 | 42.82 | 3.09 |
1806 | 2276 | 2.380084 | TTGGGAGTTACAGCGATCAC | 57.620 | 50.000 | 0.00 | 0.00 | 0.00 | 3.06 |
1807 | 2277 | 1.262417 | TGGGAGTTACAGCGATCACA | 58.738 | 50.000 | 0.00 | 0.00 | 0.00 | 3.58 |
1842 | 2312 | 6.863126 | AGCTATTAGTGTGTTTGCATCAAAAC | 59.137 | 34.615 | 0.00 | 0.00 | 39.90 | 2.43 |
1905 | 2375 | 4.196971 | GCGGAGGTTTGATGTATTAGGTT | 58.803 | 43.478 | 0.00 | 0.00 | 0.00 | 3.50 |
1983 | 2464 | 7.684937 | ATGATCTGCCAAAGCTTAGATAATC | 57.315 | 36.000 | 9.02 | 5.42 | 40.80 | 1.75 |
1984 | 2465 | 6.000219 | TGATCTGCCAAAGCTTAGATAATCC | 59.000 | 40.000 | 9.02 | 0.00 | 40.80 | 3.01 |
2005 | 2490 | 4.044191 | TCCATAGATATCGAAGGACCAGGA | 59.956 | 45.833 | 5.78 | 0.00 | 0.00 | 3.86 |
2053 | 2538 | 8.348285 | AGCTATTCTCTCTCATACCAACTATC | 57.652 | 38.462 | 0.00 | 0.00 | 0.00 | 2.08 |
2064 | 2549 | 7.824289 | TCTCATACCAACTATCTGTTTTTCAGG | 59.176 | 37.037 | 0.00 | 0.00 | 43.76 | 3.86 |
2116 | 2601 | 4.875544 | GCTTTACGCCATTACTTGATGA | 57.124 | 40.909 | 0.00 | 0.00 | 0.00 | 2.92 |
2156 | 2641 | 1.605451 | GGGTAAAGTGGTGGGGCAC | 60.605 | 63.158 | 0.00 | 0.00 | 0.00 | 5.01 |
2197 | 2682 | 5.547465 | TCCCTTAACTGTACATGACTTGTG | 58.453 | 41.667 | 0.00 | 0.00 | 39.48 | 3.33 |
2309 | 3053 | 1.518431 | CCCCATCCCCAAGGTTTCCT | 61.518 | 60.000 | 0.00 | 0.00 | 33.87 | 3.36 |
2320 | 3064 | 6.387220 | TCCCCAAGGTTTCCTTTTTGAATTTA | 59.613 | 34.615 | 0.00 | 0.00 | 41.69 | 1.40 |
2438 | 3258 | 1.614996 | TGCTGTTACATGGGGTTGTG | 58.385 | 50.000 | 0.00 | 0.00 | 0.00 | 3.33 |
2449 | 3269 | 1.216678 | TGGGGTTGTGTTTCCTCACAT | 59.783 | 47.619 | 0.47 | 0.00 | 45.73 | 3.21 |
2521 | 3341 | 9.485206 | GACTTAGGAAATTAGTTGTACTGTTCA | 57.515 | 33.333 | 0.00 | 0.00 | 0.00 | 3.18 |
2587 | 3407 | 8.931568 | GGAACTAATACTAAAATGGTCTCCCTA | 58.068 | 37.037 | 0.00 | 0.00 | 0.00 | 3.53 |
2672 | 3494 | 4.400845 | CTGCACATTTCTTTGAGATGTCG | 58.599 | 43.478 | 1.50 | 0.76 | 35.63 | 4.35 |
2673 | 3495 | 3.166657 | GCACATTTCTTTGAGATGTCGC | 58.833 | 45.455 | 1.50 | 5.71 | 35.63 | 5.19 |
2708 | 3534 | 9.672086 | TCAGTGCAAACAATTATTTAACAGTAC | 57.328 | 29.630 | 0.00 | 0.00 | 0.00 | 2.73 |
2887 | 3713 | 4.274147 | TCCTGTTGGTTTTAAAGACTGCA | 58.726 | 39.130 | 0.00 | 0.00 | 34.23 | 4.41 |
2933 | 3759 | 6.432783 | ACATCGAAGTGGATTTGAATAACCAA | 59.567 | 34.615 | 0.00 | 0.00 | 34.88 | 3.67 |
3107 | 3933 | 6.986250 | TCATATCAGCCTACTAACACAGATG | 58.014 | 40.000 | 0.00 | 0.00 | 0.00 | 2.90 |
3256 | 4145 | 0.607620 | TTTAAGCTGCAACATGCCCC | 59.392 | 50.000 | 1.02 | 0.00 | 44.23 | 5.80 |
3257 | 4146 | 0.251742 | TTAAGCTGCAACATGCCCCT | 60.252 | 50.000 | 1.02 | 0.00 | 44.23 | 4.79 |
3258 | 4147 | 0.251742 | TAAGCTGCAACATGCCCCTT | 60.252 | 50.000 | 1.02 | 5.12 | 44.23 | 3.95 |
3331 | 4220 | 7.278135 | TGGCAAATGCTATCATAGATCTATCC | 58.722 | 38.462 | 12.50 | 6.95 | 41.70 | 2.59 |
3343 | 4232 | 4.540359 | AGATCTATCCTCTGATTGCTGC | 57.460 | 45.455 | 0.00 | 0.00 | 32.18 | 5.25 |
3503 | 4392 | 6.152661 | CCAAGTTAACATGGAATTGGCTAGAA | 59.847 | 38.462 | 22.56 | 0.00 | 36.89 | 2.10 |
3678 | 4567 | 6.486657 | ACTGCAGCGGTTGATAAATTATGTAT | 59.513 | 34.615 | 15.27 | 0.00 | 0.00 | 2.29 |
3798 | 4687 | 6.934645 | TGGGGTCGATTCTTTATGATATTGTC | 59.065 | 38.462 | 0.00 | 0.00 | 0.00 | 3.18 |
3823 | 4948 | 9.378551 | TCGTATTACAATTTAGAAAGTCATGCT | 57.621 | 29.630 | 0.00 | 0.00 | 0.00 | 3.79 |
3842 | 4967 | 6.379417 | TCATGCTTTCTCAGAGAAGATAGTGA | 59.621 | 38.462 | 12.74 | 11.51 | 35.37 | 3.41 |
3847 | 4972 | 7.416664 | GCTTTCTCAGAGAAGATAGTGATGTCT | 60.417 | 40.741 | 12.74 | 0.00 | 35.37 | 3.41 |
3999 | 5132 | 4.440250 | GCGCTGTCTATCTCTGTTTCCTAA | 60.440 | 45.833 | 0.00 | 0.00 | 0.00 | 2.69 |
4100 | 5234 | 3.328505 | AGGCATATTGTTTTGCAGTTGC | 58.671 | 40.909 | 0.00 | 0.00 | 40.66 | 4.17 |
4378 | 5513 | 5.647658 | TGCGATTCTTTTGAACCTGTATCAT | 59.352 | 36.000 | 0.00 | 0.00 | 41.77 | 2.45 |
4455 | 5590 | 7.551262 | CACCTATCGCTAGACTAGATCTGTTAT | 59.449 | 40.741 | 13.91 | 0.00 | 38.49 | 1.89 |
4456 | 5591 | 8.104566 | ACCTATCGCTAGACTAGATCTGTTATT | 58.895 | 37.037 | 13.91 | 0.00 | 38.49 | 1.40 |
4457 | 5592 | 9.602568 | CCTATCGCTAGACTAGATCTGTTATTA | 57.397 | 37.037 | 13.91 | 0.00 | 38.49 | 0.98 |
4492 | 5627 | 2.227036 | AGGTCCACTTGGGCTCCAG | 61.227 | 63.158 | 0.00 | 0.00 | 40.38 | 3.86 |
4612 | 5747 | 5.473504 | ACAATGACCAGATTCACCAAACTAC | 59.526 | 40.000 | 0.00 | 0.00 | 0.00 | 2.73 |
4829 | 6009 | 2.897326 | GGTAACCATCCTGTTTTTGGCT | 59.103 | 45.455 | 0.00 | 0.00 | 33.66 | 4.75 |
4959 | 6195 | 4.452795 | GGAACACTAGAAGCTGGAGAAAAC | 59.547 | 45.833 | 0.00 | 0.00 | 0.00 | 2.43 |
5139 | 6375 | 1.576451 | GCACATGCGATGGTGTCACA | 61.576 | 55.000 | 5.12 | 0.00 | 37.35 | 3.58 |
5165 | 6401 | 1.531578 | GGAATCGAGCTAAATTCGCCC | 59.468 | 52.381 | 12.15 | 0.00 | 37.94 | 6.13 |
5176 | 6412 | 2.044123 | AATTCGCCCTGATGGAGTTC | 57.956 | 50.000 | 0.00 | 0.00 | 35.07 | 3.01 |
5180 | 6416 | 1.617018 | CGCCCTGATGGAGTTCTCCA | 61.617 | 60.000 | 21.55 | 21.55 | 44.85 | 3.86 |
5195 | 6431 | 4.248842 | CCACACCGCTGGGTCACA | 62.249 | 66.667 | 0.00 | 0.00 | 46.01 | 3.58 |
5336 | 6579 | 1.734465 | CTTTCTTCCGGCAAGTGCTAG | 59.266 | 52.381 | 0.00 | 0.00 | 41.70 | 3.42 |
5345 | 6588 | 0.603707 | GCAAGTGCTAGTCCTGTGCA | 60.604 | 55.000 | 0.00 | 0.00 | 38.21 | 4.57 |
5391 | 6634 | 2.565391 | TCATCAACCTCGCTTACCAAGA | 59.435 | 45.455 | 0.00 | 0.00 | 0.00 | 3.02 |
5396 | 6639 | 1.519455 | CTCGCTTACCAAGAGGCCG | 60.519 | 63.158 | 0.00 | 0.00 | 39.06 | 6.13 |
5421 | 6664 | 2.438075 | GCTGCTTCTGCTCCCAGG | 60.438 | 66.667 | 0.00 | 0.00 | 39.61 | 4.45 |
5433 | 6677 | 1.381327 | TCCCAGGCCCTCGACTAAG | 60.381 | 63.158 | 0.00 | 0.00 | 0.00 | 2.18 |
5576 | 6820 | 3.672295 | GAGCGGCCTTGGTCCTCAG | 62.672 | 68.421 | 0.00 | 0.00 | 0.00 | 3.35 |
5848 | 7092 | 3.909086 | AAGCCCTTGAGCTGCGTCC | 62.909 | 63.158 | 0.00 | 0.00 | 44.11 | 4.79 |
6279 | 7523 | 2.532199 | TAGTTTGGCCCCCGGGAA | 60.532 | 61.111 | 26.32 | 4.79 | 37.50 | 3.97 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
16 | 17 | 1.076995 | AAGGGGTTAGGATTGCGGC | 60.077 | 57.895 | 0.00 | 0.00 | 0.00 | 6.53 |
18 | 19 | 0.546598 | AGGAAGGGGTTAGGATTGCG | 59.453 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
21 | 22 | 3.371273 | GCGTAAAGGAAGGGGTTAGGATT | 60.371 | 47.826 | 0.00 | 0.00 | 0.00 | 3.01 |
30 | 31 | 1.611519 | TTTGGTGCGTAAAGGAAGGG | 58.388 | 50.000 | 0.00 | 0.00 | 0.00 | 3.95 |
34 | 35 | 2.351706 | AGGTTTTGGTGCGTAAAGGA | 57.648 | 45.000 | 0.00 | 0.00 | 0.00 | 3.36 |
38 | 39 | 6.880942 | AAAATAGTAGGTTTTGGTGCGTAA | 57.119 | 33.333 | 0.00 | 0.00 | 0.00 | 3.18 |
41 | 42 | 6.081693 | GTGTAAAATAGTAGGTTTTGGTGCG | 58.918 | 40.000 | 0.00 | 0.00 | 31.71 | 5.34 |
55 | 57 | 9.449719 | GATATGGGATTAGGTGGTGTAAAATAG | 57.550 | 37.037 | 0.00 | 0.00 | 0.00 | 1.73 |
57 | 59 | 6.940298 | CGATATGGGATTAGGTGGTGTAAAAT | 59.060 | 38.462 | 0.00 | 0.00 | 0.00 | 1.82 |
70 | 72 | 1.906574 | GGGAGCACCGATATGGGATTA | 59.093 | 52.381 | 11.20 | 0.00 | 44.64 | 1.75 |
78 | 80 | 1.040646 | GATGTGAGGGAGCACCGATA | 58.959 | 55.000 | 0.00 | 0.00 | 46.96 | 2.92 |
83 | 85 | 0.674895 | GTGTGGATGTGAGGGAGCAC | 60.675 | 60.000 | 0.00 | 0.00 | 39.22 | 4.40 |
86 | 88 | 1.219124 | CCGTGTGGATGTGAGGGAG | 59.781 | 63.158 | 0.00 | 0.00 | 37.49 | 4.30 |
87 | 89 | 0.251877 | TACCGTGTGGATGTGAGGGA | 60.252 | 55.000 | 0.00 | 0.00 | 39.21 | 4.20 |
88 | 90 | 0.830648 | ATACCGTGTGGATGTGAGGG | 59.169 | 55.000 | 0.00 | 0.00 | 39.21 | 4.30 |
109 | 111 | 1.738099 | CCGACTTCAACGCCCTCAG | 60.738 | 63.158 | 0.00 | 0.00 | 0.00 | 3.35 |
110 | 112 | 2.342279 | CCGACTTCAACGCCCTCA | 59.658 | 61.111 | 0.00 | 0.00 | 0.00 | 3.86 |
143 | 145 | 4.217035 | CGTCATCGGGATTGGCAA | 57.783 | 55.556 | 0.68 | 0.68 | 0.00 | 4.52 |
161 | 163 | 1.747924 | GGCTTTCATTTCCTCTGCTCC | 59.252 | 52.381 | 0.00 | 0.00 | 0.00 | 4.70 |
169 | 171 | 2.672195 | CGAAGGCAAGGCTTTCATTTCC | 60.672 | 50.000 | 10.35 | 0.00 | 43.32 | 3.13 |
186 | 188 | 2.788191 | AAGGCGGTTGAGAGGCGAAG | 62.788 | 60.000 | 0.00 | 0.00 | 38.03 | 3.79 |
196 | 198 | 1.094785 | CAGGGTGATAAAGGCGGTTG | 58.905 | 55.000 | 0.00 | 0.00 | 0.00 | 3.77 |
212 | 214 | 6.319911 | TCGAGCATATATGTTAGGATCTCAGG | 59.680 | 42.308 | 14.14 | 0.40 | 0.00 | 3.86 |
246 | 248 | 4.789012 | ACATCCAACCAAGCATGTAAAG | 57.211 | 40.909 | 0.00 | 0.00 | 0.00 | 1.85 |
254 | 256 | 5.437060 | TCCTCTAATTACATCCAACCAAGC | 58.563 | 41.667 | 0.00 | 0.00 | 0.00 | 4.01 |
255 | 257 | 6.543831 | CCTTCCTCTAATTACATCCAACCAAG | 59.456 | 42.308 | 0.00 | 0.00 | 0.00 | 3.61 |
266 | 268 | 6.603599 | AGTTTGCATTCCCTTCCTCTAATTAC | 59.396 | 38.462 | 0.00 | 0.00 | 0.00 | 1.89 |
286 | 288 | 9.265901 | CTCTATGTCATGTAATCCCTAAGTTTG | 57.734 | 37.037 | 0.00 | 0.00 | 0.00 | 2.93 |
307 | 317 | 6.875972 | ATCTAAAACCACAGGTGACTCTAT | 57.124 | 37.500 | 0.00 | 0.00 | 40.21 | 1.98 |
310 | 320 | 6.038997 | ACTATCTAAAACCACAGGTGACTC | 57.961 | 41.667 | 0.00 | 0.00 | 40.21 | 3.36 |
317 | 327 | 8.166422 | AGTTTCCAAACTATCTAAAACCACAG | 57.834 | 34.615 | 2.74 | 0.00 | 46.75 | 3.66 |
336 | 346 | 4.999311 | ACCCGTTATCACTTGTAAGTTTCC | 59.001 | 41.667 | 0.00 | 0.00 | 37.08 | 3.13 |
355 | 365 | 0.172803 | CGACTCTAAACTCCCACCCG | 59.827 | 60.000 | 0.00 | 0.00 | 0.00 | 5.28 |
382 | 392 | 4.460382 | CCACTTCACTGCTAATGAAATGGT | 59.540 | 41.667 | 13.89 | 2.01 | 44.62 | 3.55 |
414 | 424 | 2.545526 | CCATGTGAATCGATTCCCTTCG | 59.454 | 50.000 | 30.16 | 16.81 | 40.46 | 3.79 |
416 | 426 | 3.931907 | TCCATGTGAATCGATTCCCTT | 57.068 | 42.857 | 30.16 | 17.34 | 35.97 | 3.95 |
424 | 434 | 7.201530 | GGTTAGTAAGAAGTTCCATGTGAATCG | 60.202 | 40.741 | 0.00 | 0.00 | 34.90 | 3.34 |
464 | 474 | 4.566488 | GGTTTGACCATCTGAGGAGACATT | 60.566 | 45.833 | 0.00 | 0.00 | 38.42 | 2.71 |
529 | 540 | 7.301420 | TGGTGAGATTAGAAGTGGATAGATCT | 58.699 | 38.462 | 0.00 | 0.00 | 0.00 | 2.75 |
530 | 541 | 7.531857 | TGGTGAGATTAGAAGTGGATAGATC | 57.468 | 40.000 | 0.00 | 0.00 | 0.00 | 2.75 |
532 | 543 | 9.607333 | ATTATGGTGAGATTAGAAGTGGATAGA | 57.393 | 33.333 | 0.00 | 0.00 | 0.00 | 1.98 |
536 | 547 | 8.324191 | AGAATTATGGTGAGATTAGAAGTGGA | 57.676 | 34.615 | 0.00 | 0.00 | 0.00 | 4.02 |
565 | 576 | 9.454859 | ACTTTTGGGAAGATGAATAAGAGTTAG | 57.545 | 33.333 | 0.00 | 0.00 | 0.00 | 2.34 |
573 | 584 | 7.831691 | TTGACAACTTTTGGGAAGATGAATA | 57.168 | 32.000 | 3.53 | 0.00 | 34.12 | 1.75 |
593 | 604 | 2.538449 | ACGACAATGACACGAGTTTGAC | 59.462 | 45.455 | 4.70 | 0.00 | 0.00 | 3.18 |
594 | 605 | 2.538037 | CACGACAATGACACGAGTTTGA | 59.462 | 45.455 | 4.70 | 0.00 | 0.00 | 2.69 |
601 | 612 | 1.497991 | AAGGACACGACAATGACACG | 58.502 | 50.000 | 0.00 | 0.00 | 0.00 | 4.49 |
631 | 644 | 0.538118 | TCGGCCTAATTACGCCTTGT | 59.462 | 50.000 | 19.29 | 0.00 | 43.38 | 3.16 |
646 | 659 | 4.072131 | TCAATGATAGGCCTAATTTCGGC | 58.928 | 43.478 | 18.42 | 9.34 | 46.83 | 5.54 |
647 | 660 | 4.455877 | GGTCAATGATAGGCCTAATTTCGG | 59.544 | 45.833 | 18.42 | 5.50 | 0.00 | 4.30 |
648 | 661 | 5.308825 | AGGTCAATGATAGGCCTAATTTCG | 58.691 | 41.667 | 18.42 | 6.05 | 0.00 | 3.46 |
649 | 662 | 7.588497 | AAAGGTCAATGATAGGCCTAATTTC | 57.412 | 36.000 | 18.42 | 10.84 | 0.00 | 2.17 |
687 | 700 | 6.240894 | ACCAGAAGAAAATACAAGCTCATCA | 58.759 | 36.000 | 0.00 | 0.00 | 0.00 | 3.07 |
690 | 703 | 6.426937 | GTGTACCAGAAGAAAATACAAGCTCA | 59.573 | 38.462 | 0.00 | 0.00 | 0.00 | 4.26 |
691 | 704 | 6.651225 | AGTGTACCAGAAGAAAATACAAGCTC | 59.349 | 38.462 | 0.00 | 0.00 | 0.00 | 4.09 |
708 | 721 | 4.339814 | CAGGTTTAAAGCCAAAGTGTACCA | 59.660 | 41.667 | 13.60 | 0.00 | 0.00 | 3.25 |
709 | 722 | 4.581409 | TCAGGTTTAAAGCCAAAGTGTACC | 59.419 | 41.667 | 13.60 | 0.00 | 0.00 | 3.34 |
727 | 740 | 2.839228 | AGAGATGTAAAGCCCTCAGGT | 58.161 | 47.619 | 0.00 | 0.00 | 34.57 | 4.00 |
730 | 743 | 6.560003 | TCATTAAGAGATGTAAAGCCCTCA | 57.440 | 37.500 | 0.00 | 0.00 | 0.00 | 3.86 |
731 | 744 | 8.457238 | AAATCATTAAGAGATGTAAAGCCCTC | 57.543 | 34.615 | 0.00 | 0.00 | 0.00 | 4.30 |
772 | 795 | 8.284435 | TCCTCCTCAATTTCATTAAGGAATCAT | 58.716 | 33.333 | 3.00 | 0.00 | 35.77 | 2.45 |
774 | 797 | 8.525290 | TTCCTCCTCAATTTCATTAAGGAATC | 57.475 | 34.615 | 3.00 | 0.00 | 36.89 | 2.52 |
980 | 1323 | 4.393371 | GGCTGTTCCAGTAGAATTCAGAAC | 59.607 | 45.833 | 8.44 | 11.89 | 36.69 | 3.01 |
1174 | 1519 | 3.767044 | GAGGGGGAGGAGGAGGAGC | 62.767 | 73.684 | 0.00 | 0.00 | 0.00 | 4.70 |
1316 | 1667 | 2.841988 | GGGGCAGAGAGATCGGCT | 60.842 | 66.667 | 0.68 | 0.00 | 0.00 | 5.52 |
1507 | 1858 | 5.301551 | CCTGCTCTAGTAGAATCACAGACAT | 59.698 | 44.000 | 15.55 | 0.00 | 0.00 | 3.06 |
1510 | 1861 | 5.117406 | TCCTGCTCTAGTAGAATCACAGA | 57.883 | 43.478 | 15.55 | 6.76 | 0.00 | 3.41 |
1526 | 1877 | 1.493871 | CCTCCCAATCATCTTCCTGCT | 59.506 | 52.381 | 0.00 | 0.00 | 0.00 | 4.24 |
1537 | 1888 | 2.409570 | ACTAGTAAGGCCCTCCCAATC | 58.590 | 52.381 | 0.00 | 0.00 | 35.39 | 2.67 |
1577 | 1928 | 3.213206 | AGCACCAATTGAGTTGAGTCA | 57.787 | 42.857 | 7.12 | 0.00 | 40.37 | 3.41 |
1580 | 1931 | 4.156664 | CTCAAGCACCAATTGAGTTGAG | 57.843 | 45.455 | 7.12 | 13.98 | 45.58 | 3.02 |
1614 | 1965 | 9.569122 | AAACCTAGAGCAATGTTCTTTTAACTA | 57.431 | 29.630 | 4.66 | 0.00 | 0.00 | 2.24 |
1654 | 2012 | 1.605202 | GGCACCGTTAGAAACACCGTA | 60.605 | 52.381 | 0.00 | 0.00 | 0.00 | 4.02 |
1657 | 2015 | 2.250646 | GGGCACCGTTAGAAACACC | 58.749 | 57.895 | 0.00 | 0.00 | 40.86 | 4.16 |
1689 | 2054 | 0.036010 | AAGCTAACAGCAGCCATCGT | 60.036 | 50.000 | 0.38 | 0.00 | 45.56 | 3.73 |
1705 | 2070 | 4.760204 | ACGATATACCCAGGCAATAAAAGC | 59.240 | 41.667 | 0.00 | 0.00 | 0.00 | 3.51 |
1706 | 2071 | 6.877611 | AACGATATACCCAGGCAATAAAAG | 57.122 | 37.500 | 0.00 | 0.00 | 0.00 | 2.27 |
1846 | 2316 | 9.407380 | ACCATTACATTCAACATGCTAATAAGA | 57.593 | 29.630 | 0.00 | 0.00 | 0.00 | 2.10 |
1905 | 2375 | 4.515191 | GTGAACACAGCAGTCCTTTTGATA | 59.485 | 41.667 | 0.00 | 0.00 | 0.00 | 2.15 |
1983 | 2464 | 4.344978 | TCCTGGTCCTTCGATATCTATGG | 58.655 | 47.826 | 0.34 | 2.13 | 0.00 | 2.74 |
1984 | 2465 | 5.257262 | TCTCCTGGTCCTTCGATATCTATG | 58.743 | 45.833 | 0.34 | 0.00 | 0.00 | 2.23 |
2005 | 2490 | 0.114954 | TTGGGCATTTGGGCTCTTCT | 59.885 | 50.000 | 0.00 | 0.00 | 42.84 | 2.85 |
2053 | 2538 | 8.099364 | TCTCAAAGTATTAGCCTGAAAAACAG | 57.901 | 34.615 | 0.00 | 0.00 | 45.36 | 3.16 |
2113 | 2598 | 9.533253 | CCAACTTTCTGTACTGAAAATTTTCAT | 57.467 | 29.630 | 28.86 | 21.21 | 45.26 | 2.57 |
2114 | 2599 | 7.978975 | CCCAACTTTCTGTACTGAAAATTTTCA | 59.021 | 33.333 | 27.39 | 27.39 | 44.31 | 2.69 |
2115 | 2600 | 7.979537 | ACCCAACTTTCTGTACTGAAAATTTTC | 59.020 | 33.333 | 23.09 | 21.60 | 35.79 | 2.29 |
2116 | 2601 | 7.847096 | ACCCAACTTTCTGTACTGAAAATTTT | 58.153 | 30.769 | 23.09 | 15.50 | 35.79 | 1.82 |
2309 | 3053 | 9.558396 | AGCACCTCATTTCAATAAATTCAAAAA | 57.442 | 25.926 | 0.00 | 0.00 | 32.87 | 1.94 |
2320 | 3064 | 5.688807 | AGCAGTATAGCACCTCATTTCAAT | 58.311 | 37.500 | 0.00 | 0.00 | 36.85 | 2.57 |
2325 | 3069 | 4.202264 | GGTGTAGCAGTATAGCACCTCATT | 60.202 | 45.833 | 0.00 | 0.00 | 44.35 | 2.57 |
2438 | 3258 | 3.434940 | ACCCCACTTATGTGAGGAAAC | 57.565 | 47.619 | 15.13 | 0.00 | 43.77 | 2.78 |
2449 | 3269 | 9.819267 | CTTATTAAAACAAAACAACCCCACTTA | 57.181 | 29.630 | 0.00 | 0.00 | 0.00 | 2.24 |
2672 | 3494 | 3.968649 | TGTTTGCACTGAGAAATCAAGC | 58.031 | 40.909 | 0.00 | 0.00 | 0.00 | 4.01 |
2673 | 3495 | 8.752766 | ATAATTGTTTGCACTGAGAAATCAAG | 57.247 | 30.769 | 0.00 | 0.00 | 0.00 | 3.02 |
2708 | 3534 | 4.994852 | TCGGTCTTCAGACATACAAAAAGG | 59.005 | 41.667 | 9.18 | 0.00 | 46.47 | 3.11 |
2720 | 3546 | 3.599343 | CACCATGAATTCGGTCTTCAGA | 58.401 | 45.455 | 2.32 | 0.00 | 36.16 | 3.27 |
2834 | 3660 | 2.088423 | AGAAAAGGCACACACAAACGA | 58.912 | 42.857 | 0.00 | 0.00 | 0.00 | 3.85 |
2843 | 3669 | 6.323739 | AGGAAATAGTTGAAAGAAAAGGCACA | 59.676 | 34.615 | 0.00 | 0.00 | 0.00 | 4.57 |
2887 | 3713 | 9.314321 | CGATGTTTTGTATTCCTGTAGTAAGAT | 57.686 | 33.333 | 0.00 | 0.00 | 0.00 | 2.40 |
2933 | 3759 | 4.009002 | GAGACCCACGAACTCTAACTACT | 58.991 | 47.826 | 0.00 | 0.00 | 0.00 | 2.57 |
3107 | 3933 | 9.372369 | ACAGAGCATTAGAGATTTTACACTAAC | 57.628 | 33.333 | 0.00 | 0.00 | 0.00 | 2.34 |
3111 | 3937 | 6.531948 | ACGACAGAGCATTAGAGATTTTACAC | 59.468 | 38.462 | 0.00 | 0.00 | 0.00 | 2.90 |
3168 | 3994 | 9.307121 | CAGTTGTAGGAATGAAAGTCTAGTATG | 57.693 | 37.037 | 0.00 | 0.00 | 0.00 | 2.39 |
3256 | 4145 | 6.036953 | GCCAGATAACAGAATGAGTTCAGAAG | 59.963 | 42.308 | 0.00 | 0.00 | 39.69 | 2.85 |
3257 | 4146 | 5.877012 | GCCAGATAACAGAATGAGTTCAGAA | 59.123 | 40.000 | 0.00 | 0.00 | 39.69 | 3.02 |
3258 | 4147 | 5.046376 | TGCCAGATAACAGAATGAGTTCAGA | 60.046 | 40.000 | 0.00 | 0.00 | 39.69 | 3.27 |
3331 | 4220 | 3.693085 | ACTAAACATGGCAGCAATCAGAG | 59.307 | 43.478 | 0.00 | 0.00 | 0.00 | 3.35 |
3343 | 4232 | 4.930963 | TGCAGAACACAAACTAAACATGG | 58.069 | 39.130 | 0.00 | 0.00 | 0.00 | 3.66 |
3503 | 4392 | 5.763876 | AGACCACTAAAAGTAGCCTCAAT | 57.236 | 39.130 | 0.00 | 0.00 | 0.00 | 2.57 |
3678 | 4567 | 9.345254 | TCCATTTATCCCATGTTATCATAGGTA | 57.655 | 33.333 | 0.00 | 0.00 | 35.04 | 3.08 |
3798 | 4687 | 9.988350 | AAGCATGACTTTCTAAATTGTAATACG | 57.012 | 29.630 | 0.00 | 0.00 | 33.71 | 3.06 |
3823 | 4948 | 7.953005 | AGACATCACTATCTTCTCTGAGAAA | 57.047 | 36.000 | 19.73 | 11.79 | 33.19 | 2.52 |
3842 | 4967 | 7.603180 | TGTGGATGTAAGAAGCTATAGACAT | 57.397 | 36.000 | 3.21 | 3.05 | 0.00 | 3.06 |
3847 | 4972 | 7.948357 | ACGTAATGTGGATGTAAGAAGCTATA | 58.052 | 34.615 | 0.00 | 0.00 | 0.00 | 1.31 |
3999 | 5132 | 5.431731 | TGAATAATAGACACCAGGGACCATT | 59.568 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
4039 | 5172 | 3.698539 | TCAGTTTGTTCAATTGTCTGGCA | 59.301 | 39.130 | 5.13 | 0.00 | 0.00 | 4.92 |
4100 | 5234 | 6.623486 | TGACCAAATATGAAGAACTGCATTG | 58.377 | 36.000 | 0.32 | 0.00 | 0.00 | 2.82 |
4209 | 5343 | 7.541783 | TGTTTTAGATCAGCACATTTATGTTGC | 59.458 | 33.333 | 0.00 | 8.34 | 39.39 | 4.17 |
4240 | 5374 | 0.731417 | CTGGATAGTGTTGCTGCTGC | 59.269 | 55.000 | 8.89 | 8.89 | 40.20 | 5.25 |
4347 | 5481 | 4.026062 | GGTTCAAAAGAATCGCAACCAAAC | 60.026 | 41.667 | 0.00 | 0.00 | 34.57 | 2.93 |
4388 | 5523 | 9.262358 | GCCCAAGTTATCTCTTTATTACTGTAG | 57.738 | 37.037 | 0.00 | 0.00 | 0.00 | 2.74 |
4389 | 5524 | 8.989131 | AGCCCAAGTTATCTCTTTATTACTGTA | 58.011 | 33.333 | 0.00 | 0.00 | 0.00 | 2.74 |
4390 | 5525 | 7.862675 | AGCCCAAGTTATCTCTTTATTACTGT | 58.137 | 34.615 | 0.00 | 0.00 | 0.00 | 3.55 |
4391 | 5526 | 8.207545 | AGAGCCCAAGTTATCTCTTTATTACTG | 58.792 | 37.037 | 0.00 | 0.00 | 32.44 | 2.74 |
4492 | 5627 | 5.008118 | GTCTAGCAATAGGTGATTTTGGCTC | 59.992 | 44.000 | 0.00 | 0.00 | 29.64 | 4.70 |
4612 | 5747 | 5.969435 | CAGTGTGTCAATATTTGCAGCTATG | 59.031 | 40.000 | 0.00 | 0.00 | 0.00 | 2.23 |
4827 | 6007 | 5.803020 | ATTTAAAGGATCGAACACTCAGC | 57.197 | 39.130 | 0.00 | 0.00 | 0.00 | 4.26 |
4829 | 6009 | 7.444183 | AGAACAATTTAAAGGATCGAACACTCA | 59.556 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
4868 | 6048 | 4.223923 | ACTTGCTGCTGAACCTCTATACTT | 59.776 | 41.667 | 0.00 | 0.00 | 0.00 | 2.24 |
4869 | 6049 | 3.772025 | ACTTGCTGCTGAACCTCTATACT | 59.228 | 43.478 | 0.00 | 0.00 | 0.00 | 2.12 |
4870 | 6050 | 4.130286 | ACTTGCTGCTGAACCTCTATAC | 57.870 | 45.455 | 0.00 | 0.00 | 0.00 | 1.47 |
4871 | 6051 | 4.826274 | AACTTGCTGCTGAACCTCTATA | 57.174 | 40.909 | 0.00 | 0.00 | 0.00 | 1.31 |
4912 | 6148 | 0.260230 | TCACCAAGGGGCTGTTTCAA | 59.740 | 50.000 | 0.00 | 0.00 | 37.90 | 2.69 |
4959 | 6195 | 1.160137 | CTGAAAACTGGGCTTCTCCG | 58.840 | 55.000 | 0.00 | 0.00 | 34.94 | 4.63 |
5094 | 6330 | 3.396260 | TTCTTGTAGTTCTCCCCAACG | 57.604 | 47.619 | 0.00 | 0.00 | 0.00 | 4.10 |
5139 | 6375 | 5.733373 | GCGAATTTAGCTCGATTCCCAAATT | 60.733 | 40.000 | 13.42 | 7.54 | 38.61 | 1.82 |
5176 | 6412 | 3.625897 | TGACCCAGCGGTGTGGAG | 61.626 | 66.667 | 23.30 | 8.86 | 44.88 | 3.86 |
5180 | 6416 | 4.250305 | GGTGTGACCCAGCGGTGT | 62.250 | 66.667 | 14.40 | 0.00 | 44.88 | 4.16 |
5195 | 6431 | 4.720046 | TGTGTGTGTACAACATATTGGGT | 58.280 | 39.130 | 0.00 | 0.00 | 41.97 | 4.51 |
5336 | 6579 | 3.054503 | CAGCCAGCTGCACAGGAC | 61.055 | 66.667 | 8.66 | 0.00 | 44.83 | 3.85 |
5421 | 6664 | 0.460459 | GTTCTGCCTTAGTCGAGGGC | 60.460 | 60.000 | 10.50 | 10.50 | 45.45 | 5.19 |
5433 | 6677 | 3.846360 | AGTACTGTATCGTTGTTCTGCC | 58.154 | 45.455 | 0.00 | 0.00 | 0.00 | 4.85 |
5576 | 6820 | 1.067071 | AGCTCGCCTACAAGGTTACAC | 60.067 | 52.381 | 0.00 | 0.00 | 37.80 | 2.90 |
5746 | 6990 | 1.227089 | CCATCTCCGCCGTCTTCAG | 60.227 | 63.158 | 0.00 | 0.00 | 0.00 | 3.02 |
5877 | 7121 | 1.927487 | TTGGGCAGAACGAGTACCTA | 58.073 | 50.000 | 0.00 | 0.00 | 0.00 | 3.08 |
6279 | 7523 | 4.719369 | GTGGTCGCCGCGTTCTCT | 62.719 | 66.667 | 13.39 | 0.00 | 0.00 | 3.10 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.