Multiple sequence alignment - TraesCS4D01G155400
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 | TraesCS4D01G155400 | chr4D | 100.000 | 4243 | 0 | 0 | 1 | 4243 | 207362816 | 207367058 | 0 | 7836 |
1 | TraesCS4D01G155400 | chr5D | 95.717 | 4249 | 173 | 9 | 1 | 4243 | 503225672 | 503221427 | 0 | 6830 |
2 | TraesCS4D01G155400 | chr5D | 95.034 | 4249 | 200 | 10 | 1 | 4243 | 6196390 | 6192147 | 0 | 6667 |
3 | TraesCS4D01G155400 | chr3A | 95.670 | 4249 | 174 | 10 | 1 | 4243 | 66010169 | 66014413 | 0 | 6818 |
4 | TraesCS4D01G155400 | chr3A | 94.987 | 4249 | 204 | 9 | 1 | 4243 | 672902559 | 672906804 | 0 | 6658 |
5 | TraesCS4D01G155400 | chrUn | 95.504 | 4248 | 181 | 9 | 1 | 4243 | 216511154 | 216515396 | 0 | 6778 |
6 | TraesCS4D01G155400 | chrUn | 95.565 | 4239 | 178 | 9 | 10 | 4243 | 286272220 | 286267987 | 0 | 6778 |
7 | TraesCS4D01G155400 | chr3B | 95.154 | 4251 | 195 | 9 | 1 | 4243 | 201534483 | 201530236 | 0 | 6698 |
8 | TraesCS4D01G155400 | chr2B | 95.164 | 4239 | 194 | 11 | 10 | 4243 | 474915885 | 474911653 | 0 | 6682 |
9 | TraesCS4D01G155400 | chr1B | 95.471 | 3974 | 176 | 4 | 1 | 3972 | 633746444 | 633750415 | 0 | 6338 |
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 | TraesCS4D01G155400 | chr4D | 207362816 | 207367058 | 4242 | False | 7836 | 7836 | 100.000 | 1 | 4243 | 1 | chr4D.!!$F1 | 4242 |
1 | TraesCS4D01G155400 | chr5D | 503221427 | 503225672 | 4245 | True | 6830 | 6830 | 95.717 | 1 | 4243 | 1 | chr5D.!!$R2 | 4242 |
2 | TraesCS4D01G155400 | chr5D | 6192147 | 6196390 | 4243 | True | 6667 | 6667 | 95.034 | 1 | 4243 | 1 | chr5D.!!$R1 | 4242 |
3 | TraesCS4D01G155400 | chr3A | 66010169 | 66014413 | 4244 | False | 6818 | 6818 | 95.670 | 1 | 4243 | 1 | chr3A.!!$F1 | 4242 |
4 | TraesCS4D01G155400 | chr3A | 672902559 | 672906804 | 4245 | False | 6658 | 6658 | 94.987 | 1 | 4243 | 1 | chr3A.!!$F2 | 4242 |
5 | TraesCS4D01G155400 | chrUn | 216511154 | 216515396 | 4242 | False | 6778 | 6778 | 95.504 | 1 | 4243 | 1 | chrUn.!!$F1 | 4242 |
6 | TraesCS4D01G155400 | chrUn | 286267987 | 286272220 | 4233 | True | 6778 | 6778 | 95.565 | 10 | 4243 | 1 | chrUn.!!$R1 | 4233 |
7 | TraesCS4D01G155400 | chr3B | 201530236 | 201534483 | 4247 | True | 6698 | 6698 | 95.154 | 1 | 4243 | 1 | chr3B.!!$R1 | 4242 |
8 | TraesCS4D01G155400 | chr2B | 474911653 | 474915885 | 4232 | True | 6682 | 6682 | 95.164 | 10 | 4243 | 1 | chr2B.!!$R1 | 4233 |
9 | TraesCS4D01G155400 | chr1B | 633746444 | 633750415 | 3971 | False | 6338 | 6338 | 95.471 | 1 | 3972 | 1 | chr1B.!!$F1 | 3971 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
127 | 128 | 1.561542 | GCTTGGAGGGAGATCTTTCCA | 59.438 | 52.381 | 16.31 | 16.31 | 39.09 | 3.53 | F |
572 | 575 | 1.758122 | ATCCCAAAAGCATCCGGGC | 60.758 | 57.895 | 0.00 | 0.00 | 38.68 | 6.13 | F |
1735 | 1744 | 1.217942 | ACTTGGGTTTCAGCTTTCCCT | 59.782 | 47.619 | 11.80 | 0.00 | 40.48 | 4.20 | F |
1881 | 1891 | 0.750850 | ATGTTATCCCCACTCCGACG | 59.249 | 55.000 | 0.00 | 0.00 | 0.00 | 5.12 | F |
1964 | 1974 | 1.165270 | CAGGGTCCGGAACAATGAAC | 58.835 | 55.000 | 23.64 | 1.83 | 0.00 | 3.18 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1725 | 1734 | 0.332972 | AAAGGGGCTAGGGAAAGCTG | 59.667 | 55.0 | 0.00 | 0.0 | 42.37 | 4.24 | R |
1865 | 1875 | 1.108776 | CTTCGTCGGAGTGGGGATAA | 58.891 | 55.0 | 0.00 | 0.0 | 0.00 | 1.75 | R |
2970 | 2981 | 0.037975 | GCTTGCCATCCACACCAAAG | 60.038 | 55.0 | 0.00 | 0.0 | 0.00 | 2.77 | R |
3014 | 3025 | 0.179142 | GAACGCTCGTAAGGAGTCCC | 60.179 | 60.0 | 5.25 | 0.0 | 45.03 | 4.46 | R |
3564 | 3575 | 1.103398 | GCCCAAAGAGGCGCATATGT | 61.103 | 55.0 | 10.83 | 0.0 | 44.57 | 2.29 | 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 |
---|---|---|---|---|---|---|---|---|---|
50 | 51 | 9.575783 | GAGTAAATAGAATTCCATACTCGATCC | 57.424 | 37.037 | 15.69 | 2.22 | 32.62 | 3.36 |
127 | 128 | 1.561542 | GCTTGGAGGGAGATCTTTCCA | 59.438 | 52.381 | 16.31 | 16.31 | 39.09 | 3.53 |
130 | 131 | 4.459330 | CTTGGAGGGAGATCTTTCCAATC | 58.541 | 47.826 | 25.19 | 13.64 | 45.70 | 2.67 |
145 | 147 | 1.765314 | CCAATCCTTCGAGATCCACCT | 59.235 | 52.381 | 0.00 | 0.00 | 0.00 | 4.00 |
226 | 229 | 4.911390 | ACGGATTCTTGAACCTCTTTCAT | 58.089 | 39.130 | 0.00 | 0.00 | 43.99 | 2.57 |
227 | 230 | 6.049955 | ACGGATTCTTGAACCTCTTTCATA | 57.950 | 37.500 | 0.00 | 0.00 | 43.99 | 2.15 |
292 | 295 | 6.935741 | ATCCGATCCAATTTTTCGTAATCA | 57.064 | 33.333 | 0.00 | 0.00 | 0.00 | 2.57 |
407 | 410 | 6.564328 | ACAAAAGACAGAAACAAATCCACTC | 58.436 | 36.000 | 0.00 | 0.00 | 0.00 | 3.51 |
418 | 421 | 6.783708 | AACAAATCCACTCTTGGTTTTACA | 57.216 | 33.333 | 0.50 | 0.00 | 41.16 | 2.41 |
451 | 454 | 6.572167 | ACGTAGAGTAACTCCCAATATAGC | 57.428 | 41.667 | 0.00 | 0.00 | 0.00 | 2.97 |
460 | 463 | 9.614792 | AGTAACTCCCAATATAGCAGTAAAAAG | 57.385 | 33.333 | 0.00 | 0.00 | 0.00 | 2.27 |
464 | 467 | 7.775561 | ACTCCCAATATAGCAGTAAAAAGAAGG | 59.224 | 37.037 | 0.00 | 0.00 | 0.00 | 3.46 |
466 | 469 | 6.321181 | CCCAATATAGCAGTAAAAAGAAGGCA | 59.679 | 38.462 | 0.00 | 0.00 | 0.00 | 4.75 |
513 | 516 | 7.041712 | GGAAAGTTCCGATTGAAATAGGATCTC | 60.042 | 40.741 | 13.10 | 5.63 | 38.48 | 2.75 |
565 | 568 | 5.127031 | GGTTATTAGAAGCATCCCAAAAGCA | 59.873 | 40.000 | 0.00 | 0.00 | 0.00 | 3.91 |
572 | 575 | 1.758122 | ATCCCAAAAGCATCCGGGC | 60.758 | 57.895 | 0.00 | 0.00 | 38.68 | 6.13 |
634 | 639 | 2.440599 | CAAAGGGAGTGGGGGTGG | 59.559 | 66.667 | 0.00 | 0.00 | 0.00 | 4.61 |
673 | 678 | 2.625314 | CGACTCATAGAATGGCAGAGGA | 59.375 | 50.000 | 0.00 | 0.00 | 0.00 | 3.71 |
687 | 692 | 4.716784 | TGGCAGAGGAAAATAGAGCTCTTA | 59.283 | 41.667 | 23.84 | 8.44 | 0.00 | 2.10 |
740 | 745 | 7.010160 | TCTATGTATGTAGACACATGGATCCA | 58.990 | 38.462 | 18.88 | 18.88 | 45.17 | 3.41 |
745 | 750 | 5.276461 | TGTAGACACATGGATCCATACAC | 57.724 | 43.478 | 26.87 | 17.09 | 34.91 | 2.90 |
753 | 758 | 2.957474 | TGGATCCATACACCTCGATCA | 58.043 | 47.619 | 11.44 | 0.00 | 34.14 | 2.92 |
782 | 787 | 7.552050 | AGAATCAATAGAAGGAGAATCGGAT | 57.448 | 36.000 | 0.00 | 0.00 | 34.37 | 4.18 |
787 | 792 | 7.831753 | TCAATAGAAGGAGAATCGGATGATAC | 58.168 | 38.462 | 0.00 | 0.00 | 34.37 | 2.24 |
794 | 799 | 5.011533 | AGGAGAATCGGATGATACCTTTCTG | 59.988 | 44.000 | 0.00 | 0.00 | 33.45 | 3.02 |
795 | 800 | 5.011125 | GGAGAATCGGATGATACCTTTCTGA | 59.989 | 44.000 | 0.00 | 0.00 | 33.45 | 3.27 |
853 | 858 | 8.829373 | AAAATCATTATCAACTAAGCCCTCTT | 57.171 | 30.769 | 0.00 | 0.00 | 36.35 | 2.85 |
937 | 943 | 4.041691 | ACCTATTCATGGGGATTCCGTAAG | 59.958 | 45.833 | 0.00 | 0.00 | 38.76 | 2.34 |
965 | 971 | 7.212976 | TCCCATTTCAAAAATCGAAACAATCA | 58.787 | 30.769 | 0.00 | 0.00 | 35.31 | 2.57 |
967 | 973 | 7.384660 | CCCATTTCAAAAATCGAAACAATCAGA | 59.615 | 33.333 | 0.00 | 0.00 | 35.31 | 3.27 |
975 | 981 | 8.925161 | AAAATCGAAACAATCAGAACTTTTCA | 57.075 | 26.923 | 0.00 | 0.00 | 0.00 | 2.69 |
976 | 982 | 9.533253 | AAAATCGAAACAATCAGAACTTTTCAT | 57.467 | 25.926 | 0.00 | 0.00 | 0.00 | 2.57 |
1188 | 1194 | 9.790344 | AAAGATAGACCTTGGATCTATTTCATG | 57.210 | 33.333 | 10.70 | 0.00 | 39.09 | 3.07 |
1197 | 1203 | 7.201767 | CCTTGGATCTATTTCATGTCTTCAACC | 60.202 | 40.741 | 0.00 | 0.00 | 0.00 | 3.77 |
1218 | 1224 | 9.727859 | TCAACCAGTTTAGTAATAAGCATAACA | 57.272 | 29.630 | 0.00 | 0.00 | 0.00 | 2.41 |
1455 | 1461 | 9.386010 | TGTGGTGCTAACGATTTAATAACTATT | 57.614 | 29.630 | 0.00 | 0.00 | 0.00 | 1.73 |
1499 | 1505 | 8.786826 | TTCAGTTTATGTTCCTACCTATTGTG | 57.213 | 34.615 | 0.00 | 0.00 | 0.00 | 3.33 |
1532 | 1538 | 5.457140 | CAAGAGAGATCTACGGTCTAATGC | 58.543 | 45.833 | 0.00 | 0.00 | 0.00 | 3.56 |
1542 | 1548 | 2.626743 | ACGGTCTAATGCGGCTACTATT | 59.373 | 45.455 | 0.00 | 0.00 | 0.00 | 1.73 |
1618 | 1624 | 3.326521 | TGGCTATATGGTTCATCTGGGT | 58.673 | 45.455 | 0.00 | 0.00 | 0.00 | 4.51 |
1628 | 1637 | 2.366916 | GTTCATCTGGGTGGAGATCGAT | 59.633 | 50.000 | 0.00 | 0.00 | 29.72 | 3.59 |
1629 | 1638 | 2.682594 | TCATCTGGGTGGAGATCGATT | 58.317 | 47.619 | 0.00 | 0.00 | 29.72 | 3.34 |
1643 | 1652 | 8.450964 | GTGGAGATCGATTTTCAAGAAATTGTA | 58.549 | 33.333 | 0.00 | 0.00 | 0.00 | 2.41 |
1656 | 1665 | 7.735500 | TCAAGAAATTGTAAACGGTCTTATCG | 58.264 | 34.615 | 0.00 | 0.00 | 0.00 | 2.92 |
1690 | 1699 | 9.719355 | AATGTATAACTCCCCAAAAATTTCAAC | 57.281 | 29.630 | 0.00 | 0.00 | 0.00 | 3.18 |
1725 | 1734 | 3.764237 | TCACTGTAGGACTTGGGTTTC | 57.236 | 47.619 | 0.00 | 0.00 | 0.00 | 2.78 |
1735 | 1744 | 1.217942 | ACTTGGGTTTCAGCTTTCCCT | 59.782 | 47.619 | 11.80 | 0.00 | 40.48 | 4.20 |
1820 | 1830 | 9.791781 | TTCCTACCTCTATATCTATCTCTGAGA | 57.208 | 37.037 | 10.23 | 10.23 | 0.00 | 3.27 |
1834 | 1844 | 5.047566 | TCTCTGAGATGTTTGGGTTTTGA | 57.952 | 39.130 | 2.58 | 0.00 | 0.00 | 2.69 |
1835 | 1845 | 5.634118 | TCTCTGAGATGTTTGGGTTTTGAT | 58.366 | 37.500 | 2.58 | 0.00 | 0.00 | 2.57 |
1846 | 1856 | 8.251383 | TGTTTGGGTTTTGATAAACTCCATAA | 57.749 | 30.769 | 9.95 | 6.72 | 42.88 | 1.90 |
1865 | 1875 | 9.388506 | CTCCATAAACATGTAGAAGAGAAATGT | 57.611 | 33.333 | 0.00 | 0.00 | 32.99 | 2.71 |
1881 | 1891 | 0.750850 | ATGTTATCCCCACTCCGACG | 59.249 | 55.000 | 0.00 | 0.00 | 0.00 | 5.12 |
1952 | 1962 | 2.755103 | CAATTTAGGTGAAGCAGGGTCC | 59.245 | 50.000 | 0.00 | 0.00 | 0.00 | 4.46 |
1964 | 1974 | 1.165270 | CAGGGTCCGGAACAATGAAC | 58.835 | 55.000 | 23.64 | 1.83 | 0.00 | 3.18 |
2029 | 2039 | 5.012354 | ACGGGTAGTTCCTACAAAGAATCAA | 59.988 | 40.000 | 4.01 | 0.00 | 38.58 | 2.57 |
2076 | 2086 | 8.243289 | TGAATTATCGATGTACATGCTACATG | 57.757 | 34.615 | 14.43 | 6.03 | 38.18 | 3.21 |
2183 | 2193 | 4.989279 | ATTGGGAACGAATCAAATCAGG | 57.011 | 40.909 | 0.00 | 0.00 | 0.00 | 3.86 |
2185 | 2195 | 3.343617 | TGGGAACGAATCAAATCAGGTC | 58.656 | 45.455 | 0.00 | 0.00 | 0.00 | 3.85 |
2207 | 2217 | 6.091034 | GGTCGTTCTATTTCTCAACCTTTCTC | 59.909 | 42.308 | 0.00 | 0.00 | 0.00 | 2.87 |
2338 | 2348 | 9.933723 | AAATCGATTTTGAAAAAGAATGGATCT | 57.066 | 25.926 | 17.60 | 0.00 | 41.32 | 2.75 |
2350 | 2360 | 8.738645 | AAAAGAATGGATCTGGTCTTATACAC | 57.261 | 34.615 | 0.00 | 0.00 | 38.79 | 2.90 |
2353 | 2363 | 6.384015 | AGAATGGATCTGGTCTTATACACACA | 59.616 | 38.462 | 0.00 | 0.00 | 36.88 | 3.72 |
2419 | 2429 | 1.480789 | TATCACTTAGGAGCCGTGCA | 58.519 | 50.000 | 0.00 | 0.00 | 0.00 | 4.57 |
2457 | 2467 | 3.612479 | GCACGGTTTTGCATGAGAGAAAT | 60.612 | 43.478 | 0.00 | 0.00 | 42.49 | 2.17 |
2491 | 2501 | 3.196685 | CCTCTTTTCGAATCTGACTCCCT | 59.803 | 47.826 | 0.00 | 0.00 | 0.00 | 4.20 |
2606 | 2616 | 6.845758 | TCAAATGAATGGCATCTTCTTCTT | 57.154 | 33.333 | 0.00 | 0.00 | 35.78 | 2.52 |
2607 | 2617 | 6.860080 | TCAAATGAATGGCATCTTCTTCTTC | 58.140 | 36.000 | 0.00 | 0.00 | 35.78 | 2.87 |
2613 | 2623 | 4.952262 | TGGCATCTTCTTCTTCAAATCG | 57.048 | 40.909 | 0.00 | 0.00 | 0.00 | 3.34 |
2642 | 2652 | 5.659440 | TTCTTAGCATGATTTTGGGGAAC | 57.341 | 39.130 | 0.00 | 0.00 | 0.00 | 3.62 |
2700 | 2710 | 3.557054 | GCTTGCATATTCGTCCATAGGGA | 60.557 | 47.826 | 0.00 | 0.00 | 42.29 | 4.20 |
2714 | 2724 | 6.448369 | TCCATAGGGAAAATCGGATATGTT | 57.552 | 37.500 | 0.00 | 0.00 | 41.32 | 2.71 |
2742 | 2752 | 6.817765 | TTGGAATAATTGTTGGAGACTCAC | 57.182 | 37.500 | 4.53 | 0.00 | 0.00 | 3.51 |
2832 | 2842 | 8.236585 | TGCTTGCATTGTATTATTTGGTCTAT | 57.763 | 30.769 | 0.00 | 0.00 | 0.00 | 1.98 |
2843 | 2853 | 3.615224 | TTTGGTCTATGTACCGGAACC | 57.385 | 47.619 | 9.46 | 4.34 | 42.91 | 3.62 |
2918 | 2929 | 5.596361 | TCTCTCTTTAGCCCTATGTCTCTTG | 59.404 | 44.000 | 0.00 | 0.00 | 0.00 | 3.02 |
2970 | 2981 | 7.522901 | GGTTTCTTCGGAAAACTCTATCTAC | 57.477 | 40.000 | 5.55 | 0.00 | 45.35 | 2.59 |
2972 | 2983 | 7.818446 | GGTTTCTTCGGAAAACTCTATCTACTT | 59.182 | 37.037 | 5.55 | 0.00 | 45.35 | 2.24 |
3012 | 3023 | 5.221126 | GCAGGCCTATATTTCTTGGTTTCAG | 60.221 | 44.000 | 3.98 | 0.00 | 0.00 | 3.02 |
3014 | 3025 | 5.888161 | AGGCCTATATTTCTTGGTTTCAGTG | 59.112 | 40.000 | 1.29 | 0.00 | 0.00 | 3.66 |
3109 | 3120 | 4.099419 | CCAAGAAATAACCCCTTATGTGCC | 59.901 | 45.833 | 0.00 | 0.00 | 0.00 | 5.01 |
3182 | 3193 | 5.596836 | TGACTGTATGTGTGATAGCATCA | 57.403 | 39.130 | 0.00 | 0.00 | 36.84 | 3.07 |
3212 | 3223 | 4.525487 | CCAGGAATATCAATGAACCCCATG | 59.475 | 45.833 | 0.00 | 0.00 | 35.24 | 3.66 |
3572 | 3583 | 8.450964 | CCTATTCTTATTTGGGTAACATATGCG | 58.549 | 37.037 | 1.58 | 0.00 | 39.74 | 4.73 |
3617 | 3628 | 9.261180 | GAATCGAGAAATTGGATTGTACATCTA | 57.739 | 33.333 | 0.00 | 0.00 | 34.78 | 1.98 |
3672 | 3683 | 9.352191 | GATACATATAAGGTGTCCTACGGATAT | 57.648 | 37.037 | 0.00 | 0.00 | 32.73 | 1.63 |
3716 | 3727 | 4.148838 | GTCTGACTCAGGCCTATATGACT | 58.851 | 47.826 | 3.98 | 0.00 | 28.61 | 3.41 |
3721 | 3732 | 4.745351 | ACTCAGGCCTATATGACTGATCA | 58.255 | 43.478 | 13.31 | 0.00 | 39.06 | 2.92 |
3840 | 3851 | 6.406370 | CCTTGATAGTGAAATGGTAGACACA | 58.594 | 40.000 | 0.00 | 0.00 | 35.97 | 3.72 |
3844 | 3855 | 4.537135 | AGTGAAATGGTAGACACACGAT | 57.463 | 40.909 | 0.00 | 0.00 | 35.97 | 3.73 |
3865 | 3876 | 5.062183 | CGATACTCAAAATCTCGTGCTGAAA | 59.938 | 40.000 | 0.00 | 0.00 | 0.00 | 2.69 |
4003 | 4014 | 3.133183 | GTCCTTAACCATCTCCCTGAGAC | 59.867 | 52.174 | 0.00 | 0.00 | 41.76 | 3.36 |
4030 | 4041 | 9.569122 | AAGTAGACAGTAAAAGCCAAAATAGAA | 57.431 | 29.630 | 0.00 | 0.00 | 0.00 | 2.10 |
4095 | 4107 | 7.182060 | AGGAGATAATAAAGAACCCAAAGCAA | 58.818 | 34.615 | 0.00 | 0.00 | 0.00 | 3.91 |
4099 | 4111 | 7.765819 | AGATAATAAAGAACCCAAAGCAAATGC | 59.234 | 33.333 | 0.00 | 0.00 | 42.49 | 3.56 |
4132 | 4144 | 4.265073 | CAAGGGTGGTCTTAAGAATCCAG | 58.735 | 47.826 | 13.66 | 1.06 | 0.00 | 3.86 |
4138 | 4150 | 5.046231 | GGTGGTCTTAAGAATCCAGAAGAGT | 60.046 | 44.000 | 13.66 | 0.00 | 0.00 | 3.24 |
4162 | 4174 | 9.360901 | AGTTTGCTCAGAAGAGATAGATGTATA | 57.639 | 33.333 | 0.00 | 0.00 | 44.98 | 1.47 |
4170 | 4182 | 8.865090 | CAGAAGAGATAGATGTATACCAACCTT | 58.135 | 37.037 | 0.00 | 0.00 | 0.00 | 3.50 |
4180 | 4192 | 9.838339 | AGATGTATACCAACCTTATTTTCTCAG | 57.162 | 33.333 | 0.00 | 0.00 | 0.00 | 3.35 |
4182 | 4194 | 7.924541 | TGTATACCAACCTTATTTTCTCAGGT | 58.075 | 34.615 | 0.00 | 0.00 | 43.17 | 4.00 |
4230 | 4243 | 3.345508 | AAAGTGACTACGAATTCCCCC | 57.654 | 47.619 | 0.00 | 0.00 | 0.00 | 5.40 |
4238 | 4251 | 3.824443 | ACTACGAATTCCCCCTTTTGTTG | 59.176 | 43.478 | 0.00 | 0.00 | 0.00 | 3.33 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
31 | 32 | 7.410991 | TCTATGGGATCGAGTATGGAATTCTA | 58.589 | 38.462 | 5.23 | 0.00 | 0.00 | 2.10 |
50 | 51 | 7.621285 | TCCACAGAATTCTATAGGGATCTATGG | 59.379 | 40.741 | 7.86 | 15.23 | 36.87 | 2.74 |
127 | 128 | 4.030913 | TGTAAGGTGGATCTCGAAGGATT | 58.969 | 43.478 | 0.00 | 0.00 | 0.00 | 3.01 |
130 | 131 | 3.887621 | TTGTAAGGTGGATCTCGAAGG | 57.112 | 47.619 | 0.00 | 0.00 | 0.00 | 3.46 |
145 | 147 | 5.087323 | TGGCTTTTTGACCCCATATTGTAA | 58.913 | 37.500 | 0.00 | 0.00 | 0.00 | 2.41 |
171 | 173 | 9.796120 | TTTATAAGGGCGAAAATCACTTATTTG | 57.204 | 29.630 | 3.26 | 0.00 | 37.85 | 2.32 |
186 | 189 | 8.132995 | AGAATCCGTTTTATTTTTATAAGGGCG | 58.867 | 33.333 | 0.00 | 0.00 | 0.00 | 6.13 |
200 | 203 | 6.768861 | TGAAAGAGGTTCAAGAATCCGTTTTA | 59.231 | 34.615 | 0.00 | 0.00 | 43.43 | 1.52 |
226 | 229 | 4.335594 | CAGTACCTCGATGTGACATGAGTA | 59.664 | 45.833 | 1.23 | 0.00 | 0.00 | 2.59 |
227 | 230 | 3.129462 | CAGTACCTCGATGTGACATGAGT | 59.871 | 47.826 | 1.23 | 0.00 | 0.00 | 3.41 |
407 | 410 | 6.378582 | ACGTATTGCTTGATGTAAAACCAAG | 58.621 | 36.000 | 0.00 | 0.00 | 40.00 | 3.61 |
418 | 421 | 6.461231 | GGGAGTTACTCTACGTATTGCTTGAT | 60.461 | 42.308 | 12.41 | 0.00 | 0.00 | 2.57 |
513 | 516 | 1.000938 | GGCAAGTGCTCTTCCTTGTTG | 60.001 | 52.381 | 2.85 | 0.00 | 40.13 | 3.33 |
565 | 568 | 1.303317 | GCCATATTTCGGCCCGGAT | 60.303 | 57.895 | 0.73 | 0.17 | 44.22 | 4.18 |
572 | 575 | 8.702163 | AACTTAATTTGAAAGCCATATTTCGG | 57.298 | 30.769 | 0.00 | 0.00 | 41.21 | 4.30 |
673 | 678 | 8.324163 | ACGAAAATGTGTAAGAGCTCTATTTT | 57.676 | 30.769 | 24.32 | 24.32 | 0.00 | 1.82 |
687 | 692 | 6.976088 | TGTTCATGGATTAACGAAAATGTGT | 58.024 | 32.000 | 0.00 | 0.00 | 0.00 | 3.72 |
740 | 745 | 6.878317 | TGATTCTTTTCTGATCGAGGTGTAT | 58.122 | 36.000 | 0.00 | 0.00 | 0.00 | 2.29 |
745 | 750 | 8.654230 | TTCTATTGATTCTTTTCTGATCGAGG | 57.346 | 34.615 | 0.00 | 0.00 | 0.00 | 4.63 |
753 | 758 | 9.323985 | CGATTCTCCTTCTATTGATTCTTTTCT | 57.676 | 33.333 | 0.00 | 0.00 | 0.00 | 2.52 |
782 | 787 | 9.712305 | TTTTTGTTTGTTTTCAGAAAGGTATCA | 57.288 | 25.926 | 0.00 | 0.00 | 0.00 | 2.15 |
826 | 831 | 9.920946 | AGAGGGCTTAGTTGATAATGATTTTTA | 57.079 | 29.630 | 0.00 | 0.00 | 0.00 | 1.52 |
828 | 833 | 8.689972 | CAAGAGGGCTTAGTTGATAATGATTTT | 58.310 | 33.333 | 0.00 | 0.00 | 31.81 | 1.82 |
853 | 858 | 5.435686 | TCTTATTCTTAAGCAAGCCCTCA | 57.564 | 39.130 | 0.00 | 0.00 | 35.72 | 3.86 |
937 | 943 | 8.527567 | TTGTTTCGATTTTTGAAATGGGATAC | 57.472 | 30.769 | 0.00 | 0.00 | 37.62 | 2.24 |
965 | 971 | 6.888632 | ACTGCATCCAATCTATGAAAAGTTCT | 59.111 | 34.615 | 0.00 | 0.00 | 0.00 | 3.01 |
967 | 973 | 7.472334 | AACTGCATCCAATCTATGAAAAGTT | 57.528 | 32.000 | 0.00 | 0.00 | 0.00 | 2.66 |
976 | 982 | 9.276590 | CATGAATTAGTAACTGCATCCAATCTA | 57.723 | 33.333 | 0.00 | 0.00 | 0.00 | 1.98 |
1137 | 1143 | 8.737168 | TTTTATCAGAGGTTGAATCGATCATT | 57.263 | 30.769 | 0.00 | 0.00 | 39.77 | 2.57 |
1177 | 1183 | 8.641498 | AAACTGGTTGAAGACATGAAATAGAT | 57.359 | 30.769 | 0.00 | 0.00 | 0.00 | 1.98 |
1188 | 1194 | 8.319143 | TGCTTATTACTAAACTGGTTGAAGAC | 57.681 | 34.615 | 0.00 | 0.00 | 0.00 | 3.01 |
1197 | 1203 | 9.174166 | AGGGTTGTTATGCTTATTACTAAACTG | 57.826 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
1218 | 1224 | 3.112263 | TCTCCATCGGAACAATAGGGTT | 58.888 | 45.455 | 0.00 | 0.00 | 0.00 | 4.11 |
1219 | 1225 | 2.700897 | CTCTCCATCGGAACAATAGGGT | 59.299 | 50.000 | 0.00 | 0.00 | 0.00 | 4.34 |
1357 | 1363 | 9.113838 | CTCTGTTATAGCCATTTCTGTACATTT | 57.886 | 33.333 | 0.00 | 0.00 | 0.00 | 2.32 |
1455 | 1461 | 5.827797 | ACTGAAACATTCTGGAGCTACAAAA | 59.172 | 36.000 | 0.00 | 0.00 | 33.45 | 2.44 |
1542 | 1548 | 6.436027 | TGCCCAACCCATGAGTAAATATTTA | 58.564 | 36.000 | 3.71 | 3.71 | 0.00 | 1.40 |
1561 | 1567 | 2.092753 | CCAGAATAGAAGAGCTTGCCCA | 60.093 | 50.000 | 0.00 | 0.00 | 0.00 | 5.36 |
1618 | 1624 | 7.452880 | ACAATTTCTTGAAAATCGATCTCCA | 57.547 | 32.000 | 0.00 | 0.00 | 36.20 | 3.86 |
1629 | 1638 | 9.887406 | GATAAGACCGTTTACAATTTCTTGAAA | 57.113 | 29.630 | 0.00 | 0.00 | 36.20 | 2.69 |
1643 | 1652 | 6.592607 | ACATTTGTGTATCGATAAGACCGTTT | 59.407 | 34.615 | 6.72 | 0.00 | 0.00 | 3.60 |
1656 | 1665 | 8.514330 | TTTGGGGAGTTATACATTTGTGTATC | 57.486 | 34.615 | 4.49 | 0.00 | 36.50 | 2.24 |
1680 | 1689 | 9.807649 | GATGGATATAAGTGCAGTTGAAATTTT | 57.192 | 29.630 | 17.21 | 0.00 | 0.00 | 1.82 |
1681 | 1690 | 8.970020 | TGATGGATATAAGTGCAGTTGAAATTT | 58.030 | 29.630 | 17.21 | 0.00 | 0.00 | 1.82 |
1690 | 1699 | 6.015095 | TCCTACAGTGATGGATATAAGTGCAG | 60.015 | 42.308 | 0.00 | 0.00 | 0.00 | 4.41 |
1725 | 1734 | 0.332972 | AAAGGGGCTAGGGAAAGCTG | 59.667 | 55.000 | 0.00 | 0.00 | 42.37 | 4.24 |
1735 | 1744 | 4.141251 | GGAGTCCATTATGAAAAGGGGCTA | 60.141 | 45.833 | 3.60 | 0.00 | 0.00 | 3.93 |
1820 | 1830 | 6.739331 | TGGAGTTTATCAAAACCCAAACAT | 57.261 | 33.333 | 8.04 | 0.00 | 45.11 | 2.71 |
1846 | 1856 | 7.775561 | GGGGATAACATTTCTCTTCTACATGTT | 59.224 | 37.037 | 2.30 | 0.00 | 40.38 | 2.71 |
1865 | 1875 | 1.108776 | CTTCGTCGGAGTGGGGATAA | 58.891 | 55.000 | 0.00 | 0.00 | 0.00 | 1.75 |
1936 | 1946 | 1.987855 | CCGGACCCTGCTTCACCTA | 60.988 | 63.158 | 0.00 | 0.00 | 0.00 | 3.08 |
1952 | 1962 | 6.683974 | ATCATAAAGAGGTTCATTGTTCCG | 57.316 | 37.500 | 0.00 | 0.00 | 0.00 | 4.30 |
2066 | 2076 | 2.292267 | GAGAACCCACCATGTAGCATG | 58.708 | 52.381 | 2.38 | 2.38 | 0.00 | 4.06 |
2076 | 2086 | 1.909302 | TCTGAAGGATGAGAACCCACC | 59.091 | 52.381 | 0.00 | 0.00 | 0.00 | 4.61 |
2183 | 2193 | 6.645415 | TGAGAAAGGTTGAGAAATAGAACGAC | 59.355 | 38.462 | 0.00 | 0.00 | 0.00 | 4.34 |
2185 | 2195 | 6.647067 | AGTGAGAAAGGTTGAGAAATAGAACG | 59.353 | 38.462 | 0.00 | 0.00 | 0.00 | 3.95 |
2337 | 2347 | 3.442625 | TCCTCGTGTGTGTATAAGACCAG | 59.557 | 47.826 | 0.00 | 0.00 | 0.00 | 4.00 |
2338 | 2348 | 3.423749 | TCCTCGTGTGTGTATAAGACCA | 58.576 | 45.455 | 0.00 | 0.00 | 0.00 | 4.02 |
2350 | 2360 | 5.682943 | TTTTTGATTACCTTCCTCGTGTG | 57.317 | 39.130 | 0.00 | 0.00 | 0.00 | 3.82 |
2419 | 2429 | 3.005554 | CCGTGCATGAGACTTTCATCTT | 58.994 | 45.455 | 7.72 | 0.00 | 44.76 | 2.40 |
2480 | 2490 | 1.360852 | ACTGGAGTGAGGGAGTCAGAT | 59.639 | 52.381 | 0.00 | 0.00 | 35.13 | 2.90 |
2491 | 2501 | 2.158957 | AGAAAAGCAACGACTGGAGTGA | 60.159 | 45.455 | 0.00 | 0.00 | 0.00 | 3.41 |
2588 | 2598 | 6.403964 | CGATTTGAAGAAGAAGATGCCATTCA | 60.404 | 38.462 | 0.00 | 0.00 | 0.00 | 2.57 |
2642 | 2652 | 5.163713 | GCTTGTTTGAGTAATAGCAAGGAGG | 60.164 | 44.000 | 0.00 | 0.00 | 35.31 | 4.30 |
2742 | 2752 | 5.582689 | ATCATGCTTGCATATCCATCATG | 57.417 | 39.130 | 7.84 | 4.03 | 32.28 | 3.07 |
2799 | 2809 | 9.492973 | AAATAATACAATGCAAGCAAAAGTTCT | 57.507 | 25.926 | 0.00 | 0.00 | 0.00 | 3.01 |
2832 | 2842 | 3.734597 | CGAATGTTATCGGTTCCGGTACA | 60.735 | 47.826 | 13.64 | 12.33 | 39.12 | 2.90 |
2843 | 2853 | 5.863935 | TCCTGCATAATCTCGAATGTTATCG | 59.136 | 40.000 | 0.00 | 0.00 | 44.04 | 2.92 |
2918 | 2929 | 3.973458 | GGAAGGCCTCCTAGGGAC | 58.027 | 66.667 | 5.23 | 0.00 | 41.61 | 4.46 |
2970 | 2981 | 0.037975 | GCTTGCCATCCACACCAAAG | 60.038 | 55.000 | 0.00 | 0.00 | 0.00 | 2.77 |
2972 | 2983 | 1.152589 | TGCTTGCCATCCACACCAA | 60.153 | 52.632 | 0.00 | 0.00 | 0.00 | 3.67 |
3012 | 3023 | 1.139095 | CGCTCGTAAGGAGTCCCAC | 59.861 | 63.158 | 5.25 | 3.34 | 45.03 | 4.61 |
3014 | 3025 | 0.179142 | GAACGCTCGTAAGGAGTCCC | 60.179 | 60.000 | 5.25 | 0.00 | 45.03 | 4.46 |
3078 | 3089 | 4.077108 | GGGGTTATTTCTTGGTTTCGTCT | 58.923 | 43.478 | 0.00 | 0.00 | 0.00 | 4.18 |
3182 | 3193 | 8.164070 | GGGTTCATTGATATTCCTGGTATAGTT | 58.836 | 37.037 | 0.00 | 0.00 | 0.00 | 2.24 |
3212 | 3223 | 2.223665 | GGTATCCTGAGCAATTGCAAGC | 60.224 | 50.000 | 30.89 | 19.59 | 45.16 | 4.01 |
3328 | 3339 | 9.726438 | GATTATAAGTTCATAACCCTAGCACAT | 57.274 | 33.333 | 0.00 | 0.00 | 0.00 | 3.21 |
3329 | 3340 | 8.710239 | TGATTATAAGTTCATAACCCTAGCACA | 58.290 | 33.333 | 0.00 | 0.00 | 0.00 | 4.57 |
3331 | 3342 | 9.725019 | CATGATTATAAGTTCATAACCCTAGCA | 57.275 | 33.333 | 2.05 | 0.00 | 31.50 | 3.49 |
3392 | 3403 | 2.355756 | GTGCACGGTCTAGTTCGGTATA | 59.644 | 50.000 | 0.00 | 0.00 | 0.00 | 1.47 |
3402 | 3413 | 6.811954 | TCATAATAAGAATGTGCACGGTCTA | 58.188 | 36.000 | 19.17 | 7.22 | 0.00 | 2.59 |
3564 | 3575 | 1.103398 | GCCCAAAGAGGCGCATATGT | 61.103 | 55.000 | 10.83 | 0.00 | 44.57 | 2.29 |
3672 | 3683 | 5.953183 | ACATCAAATAGCTTCGATTTGCAA | 58.047 | 33.333 | 13.39 | 0.00 | 41.86 | 4.08 |
3716 | 3727 | 6.878317 | AGTCTTGGAGTATTTCGATTGATCA | 58.122 | 36.000 | 0.00 | 0.00 | 0.00 | 2.92 |
3721 | 3732 | 5.420409 | GTGGAGTCTTGGAGTATTTCGATT | 58.580 | 41.667 | 0.00 | 0.00 | 0.00 | 3.34 |
3823 | 3834 | 4.537135 | ATCGTGTGTCTACCATTTCACT | 57.463 | 40.909 | 0.00 | 0.00 | 0.00 | 3.41 |
3840 | 3851 | 3.859961 | CAGCACGAGATTTTGAGTATCGT | 59.140 | 43.478 | 0.00 | 0.00 | 46.63 | 3.73 |
3844 | 3855 | 5.334105 | GCTTTTCAGCACGAGATTTTGAGTA | 60.334 | 40.000 | 0.00 | 0.00 | 46.49 | 2.59 |
3865 | 3876 | 1.289380 | GACTCGAACCTCCACGCTT | 59.711 | 57.895 | 0.00 | 0.00 | 0.00 | 4.68 |
3959 | 3970 | 3.476552 | CTCAGAAGATAGAGGAGAGCGT | 58.523 | 50.000 | 0.00 | 0.00 | 0.00 | 5.07 |
4003 | 4014 | 8.999431 | TCTATTTTGGCTTTTACTGTCTACTTG | 58.001 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
4045 | 4056 | 5.057149 | CGAGGGATTTTTAGGATCGTTCAT | 58.943 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
4095 | 4107 | 2.780010 | ACCCTTGCACTAGGATAGCATT | 59.220 | 45.455 | 5.98 | 0.00 | 44.39 | 3.56 |
4099 | 4111 | 2.103263 | GACCACCCTTGCACTAGGATAG | 59.897 | 54.545 | 5.98 | 0.00 | 46.50 | 2.08 |
4107 | 4119 | 2.561478 | TCTTAAGACCACCCTTGCAC | 57.439 | 50.000 | 0.00 | 0.00 | 0.00 | 4.57 |
4132 | 4144 | 6.862209 | TCTATCTCTTCTGAGCAAACTCTTC | 58.138 | 40.000 | 0.00 | 0.00 | 43.85 | 2.87 |
4138 | 4150 | 8.580720 | GGTATACATCTATCTCTTCTGAGCAAA | 58.419 | 37.037 | 5.01 | 0.00 | 40.03 | 3.68 |
4162 | 4174 | 5.061721 | ACACCTGAGAAAATAAGGTTGGT | 57.938 | 39.130 | 0.00 | 0.00 | 41.65 | 3.67 |
4201 | 4214 | 4.659111 | TCGTAGTCACTTTTTCCTGTCA | 57.341 | 40.909 | 0.00 | 0.00 | 0.00 | 3.58 |
![](/static/images/cyverse_long.png)
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.