FNIP repeats
These sequences are coding for FNIP repeats (Source: Pandit - PF05725). Magnolia classifies them as protein coding sequences and predicts the correct reading frame for each sequence.
Magnolia multiple alignment of nucleic sequences
Q8T126_DICDI/754-797 TTTAATCAACCTTTAAAACTTGGT---GTAATTCCTGATTCTTGTACTTTTATTCAATTT
Q8SSW4_DICDI/189-234 TTCAATCAATCTTTAAAAGGTAAT---TGGCTATCATCAAATATTAAATCATTGAAATTT
Q8T126_DICDI/514-556 CATTCGAAATCTTTAAAACCAAGA---GATATACCAAAGAGTATCATTCATTTACAATTA
Q8MP78_DICDI/367-412 TTTAATCAACCATTTGATCAAGATAATATATTACCATCAACATTAACTCATTTAATATTA
Q8T126_DICDI/754-797 GGTTCACAATTTAAT---CAATCATTAGAACCAATG------GTTATACCATCATCAGTT
Q8SSW4_DICDI/189-234 GGTAATGAATTCAGT---CAACCAATTAGTGACATTAATAATTTTTTACCAAAATCATTA
Q8T126_DICDI/514-556 CCA---AATTATAAT---TTAAAAATTCGTAGAAATTCA------ATACCTGATCAAACA
Q8MP78_DICDI/367-412 AATAATAATTATTCAATTGAAAATTTATTAAAAATTAAA------TTACCAATTTCATTA
Q8T126_DICDI/754-797 AAAGAATTAATATTTGGTTCACAA
Q8SSW4_DICDI/189-234 ACATCATTAAATTTACCATCAAAA
Q8T126_DICDI/514-556 AAATTCTTAATATTAGGTTCTGAT
Q8MP78_DICDI/367-412 ACATTTTTATCACTATCAAAAAAT
Magnolia multiple alignment for predicted amino-acid sequences
Q8T126_DICDI/754-797 FNQPLKLG-VIPDSCTFIQFGSQFN-QSLEPM--VIPSSVKELIFGSQ
Q8SSW4_DICDI/189-234 FNQSLKGN-WLSSNIKSLKFGNEFS-QPISDINNFLPKSLTSLNLPSK
Q8T126_DICDI/514-556 HSKSLKPR-DIPKSIIHLQLP-NYN-LKIRRNS--IPDQTKFLILGSD
Q8MP78_DICDI/367-412 FNQPFDQDNILPSTLTHLILNNNYSIENLLKIK--LPISLTFLSLSKN
Reference hand-curated multiple alignment (Pandit)
Q8T126_DICDI/754-797 FNQP-LKLGVIPDSCTFIQF-GSQFN-QSLE--PMVIPSSVKELIFGSQ
Q8SSW4_DICDI/189-234 FNQS-LKGNWLSSNIKSLKF-GNEFS-QPISDINNFLPKSLTSLNLPSK
Q8T126_DICDI/514-556 HSKS-LKPRDIPKSIIHLQL--PNYN-LKIR--RNSIPDQTKFLILGSD
Q8MP78_DICDI/367-412 FNQPFDQDNILPSTLTHLIL-NNNYSiENLL--KIKLPISLTFLSLSKN
ClustalW alignment of nucleic sequences
Q8T126_DICDI/754-797 --TTTAATCAACCTTTAAAACTTGGTGTAATTCCTGATTCTTGTACTTTTATTCA-----
Q8SSW4_DICDI/189-234 --TTCAATCAATC-TTTAA----AAGGTAATTGGCTATCATCAAATATTAAATCATTGAA
Q8T126_DICDI/514-556 CATTCGA--AATCTTTAAAACC-AAGAGATATACCAAAGAGTAT-CATTCATTTAC----
Q8MP78_DICDI/367-412 --TTTAATCAACCATTTGATC--AAGATAATATATTACCATCAA-CATTAACTCATTTAA
Q8T126_DICDI/754-797 -ATTTGGTTCACA----ATTTAATCAATCATTAGAACCAATGGTTAT---ACCATCATCA
Q8SSW4_DICDI/189-234 -ATTTGGTAATGAATTCAGTCAACCAATTAGTGACATTAATAATTTT-TTACCAAAATCA
Q8T126_DICDI/514-556 -AATTACCAAATT-----ATAATTTAAAAATT--CGTAGAAATTCAA--TACCTGATCAA
Q8MP78_DICDI/367-412 TATTAAATAATAA--TTATTCAATTGAAAATT--TATTAAAAATTAAATTACCAATTTCA
Q8T126_DICDI/754-797 GTTAAAGAATTAATATTTGGTTCACAA---
Q8SSW4_DICDI/189-234 TTAACATCATTAAATTTACCATCAAAA---
Q8T126_DICDI/514-556 ACAAAATTCTTAATATTAGGTTCTGAT---
Q8MP78_DICDI/367-412 TTAACATTTTTA---TCACTATCAAAAAAT
Transfer RNAs
This data set contains five tRNA sequences. It comes from Bralibase II, tRNA 13. Magnolia classifies these sequences as non-coding RNA genes, and provides a multiple alignment that is very similar to the hand-curated structural alignment. In contrast, ClustalW produces a mutliple alignment which is not compatible with the secondary structure, especially regarding the first sequence (X61674).
Reference structural alignment
X61674.1-10 GGAGAGATGGCTGAGT-GGACTAAAGCGGCGGATTGCTAATCCGTT-GTACAATT
Y00430.1-24 GGGGGTGTAGCTCAGT-GGT--AGAGCGCATGCTTTGCATGTATGAG--------
X12977.1-94 GCGCCCGTAGCTCAGCTGGAT-AGAGCGCTGCCCTCCGGAGGCAGAG--------
X54300.1-29 GGGTTATTAGCTCAGTTGGTT-AGAGCACACCCCTGATAAGGGTGAG--------
AJ271079.2- TCCTCAGTAGCTCAGT-GGT--AGAGCGGTCGGCTGTTAACCGATTG--------
X61674.1-10 TTTTTGTAC--CGAGGGTTCGAATCCCTCTCTTTCCG
Y00430.1-24 ---------GTCTTGGGTTCAATCCCCAGCATCTCCA
X12977.1-94 ---------GTCACAGGTTCGAATCCTGTCGGGCGCA
X54300.1-29 ---------GTCCCTGGTTCAAATCCAGGATAACCCA
AJ271079.2- ---------GTCGTAGGTTCGAATCCTACTTGGGGAG
Magnolia alignment
X61674.1-10 --GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCGTTGTACAATT
Y00430.1-24 GGGGG-TG-TAGCTCAG-TGG-TAGAGCGCATGCTTTGCATGTATGAGG----T-
X12977.1-94 GCGCC-CG-TAGCTCAGCTGGATAGAGCGCTGCCCTCCGGAGGCAGAGG----T-
X54300.1-29 GGGTT-AT-TAGCTCAGTTGGTTAGAGCACACCCCTGATAAGGGTGAGG----T-
AJ271079.2- TCCTC-AG-TAGCTCAG-TGG-TAGAGCGGTCGGCTGTTAACCGATTGG----T-
((((( (((((( ))))))
X61674.1-10 TTTTTGTACCGAGGGTTCGAATCCCTC---TCTTTCCG
Y00430.1-24 --------C-TTGGGTTC-AATCCCCAGCATCT--CCA
X12977.1-94 --------C-ACAGGTTCGAATCCTG-TCGGGC--GCA
X54300.1-29 --------C-CCTGGTTCAAATCCAGG-ATAAC--CCA
AJ271079.2- --------C-GTAGGTTCGAATCCTAC-TTGGG--GAG
((((( ))))) ))) ))
ClustalW alignment
X61674.1-10 GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCGTTGTACAATTTT
Y00430.1-24 GGGGGTGTAGCTCAGT--GGTAGAGCGCATGCTTTGCATGTATGAGGTCTTGGGT
X12977.1-94 GCGCCCGTAGCTCAGCTGGATAGAGCGCTGCCCTCCGGAGGCAGAGGTCACAGGT
X54300.1-29 GGGTTATTAGCTCAGTTGGTTAGAGCACACCCCTGATAAGGGTGAGGTCCCTGGT
AJ271079.2- TCCTCAGTAGCTCAGT--GGTAGAGCGGTCGGCTGTTAACCGATTGGTCGTAGGT
X61674.1-10 TTTGTACCGAGGGTTCGAATCCCTCTCTTTCCG
Y00430.1-24 TCAATCCCCAGCATCTCCA--------------
X12977.1-94 TCGAATCCTGTCGGGCGCA--------------
X54300.1-29 TCAAATCCAGGATAACCCA--------------
AJ271079.2- TCGAATCCTACTTGGGGAG--------------