!head /Volumes/web/cnidarian/LT_L6_4000_C1q.fasta
>L6_4000_C1q - CCATACCTCTCCACTTCTTCCTCTTTCCCTTTACAATTTTTATTTTTTTTAAATAATAAAGTGATGATTTATTTAT TGGTTAAAGAGGAAAATCCTCACATCACAGAATGGTGCTGTCCTCACACAGGGAAGAGCAGGAAGCCACTGAAGGT GTTGTGGTTATCATGGCTATCATGGAGACCCTGGTCTTCAGGGAGACGAAGGTAGACCACATCCTCCTTCTCCAGC TCTAGTGTCAACGCATTAGATATGTACTGCCAACCCCCAACTGTATTTCTTTCTACATTATATAGAACTCTTTGAT TATTGTGAAACATCATGATGCCCATGAGTTGTGGGTGGCGGGATGACATGGCCGTGAATCTGAAGAAGTAGACTCC TTTCACTGATGCTGTGAAGATGCCTGCATCAGAGGAGAAATAGAGTGATATCAGCACTGTCTGTCTCATGTTGCTG TAGCTTTAATGTTTTTAACAAATAAACTCAGCAAAAAAAGAAATGTCCCTTTTCAGGACCCTGTCTTTCAAAGATA ATTCGTAAAAATCCAAATAACTTCACAGATCTTCATTTTAAAGGGTTTAAACACTGTTTCCCATGCTTCTTCAATG AACCATAAACAATTAATGAACATGCACCTGTGGAACGGTCGTTAAGACACTAACAGCTTACAGACGGTAGGCAGTT
!head /Volumes/web/cnidarian/LT_S7_4000_C1q.fasta
>S7_4000_C1q - CCATACCTCTCCACTTCTTCCTCTTTCCCTTTACAATTTTTATTTTTTTTAAATAATAAAGTGATGATTTATTTAT TGGTTAAAGAGGAAAATCCTCACATCACAGAATGGTGCTGTCCTCACACAGGGAAGAGCAGGAAGCCACTGAAGGT GTTGTGGTTATCATGGCTATCATGGAGACCCTGGTCTTCAGGGAGACGAAGGTAGACCACATCCTCCTTCTCCAGC TCTAGTGTCAACGCATTAGATATGTACTGCCAACCCCCAACTGTATTTCTTTCTACATTATATAGAACTCTTTGAT TATTGTGAAACATCATGATGCCCATGAGTTGTGGGTGGCGGGATGACATGGCCGTGAATCTGAAGAAGTAGACTCC TTTCACTGATGCTGTGAAGATGCCTGCATCAGAGGAGAAATAGAGTGATATCAGCACTGTCTGTCTCATGTTGCTG TAGCTGGAATGTTTTTAACAAATAAACTCAGCAAAAAAAGAAATGTCCCTTTTCAGGACCCTGTCTTTCAAAGATA ATTCGTAAAAATCCAAATAACTTCACAGATCTTCATTTTAAAGGGTTTAAACACTGTTTCCCATGCTTCTTCAATG AACCATAAACAATTAATGAACATGCACCTGTGGAACGGTCGTTAAGACACTAACAGCTTACAGACGGTAGGCAGTT
#This is in reverse order 3' to 5'.
#The line marked C1q is the lean cDNA and the one marked Contig1S7cDNA is the siscowet cDNA
#you see it misses some of the sequence present in the lean cDNA at about 3125 to 3145.
#They are both being compared to the siscowet genomic sequence.
!head /Volumes/web/cnidarian/LT_C1q_align.txt
10 20 30 40 50 60 70 80 90 100 Contig_1 CCATACCTCTCCACTTCTTCCTCTTTCCCTTTACAATTTTTATTTTTTTTAAATAATAAAGTGATGATTTATTTATTGGTTAAAGAGGAAAATCCTCACA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Consensus: CCATACCTCTCCACTTCTTCCTCTTTCCCTTTACAATTTTTATTTTTTTTAAATAATAAAGTGATGATTTATTTATTGGTTAAAGAGGAAAATCCTCACA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C1q CCATACCTCTCCACTTCTTCCTCTTTCCCTTTACAATTTTTATTTTTTTTAAATAATAAAGTGATGATTTATTTATTGGTTAAAGAGGAAAATCCTCACA Contig1S7cDNA CCATACCTCTCCACTTCTTCCTCTTTCCCTTTACAATTTTTATTTTTTTTAAATAATAAAGTGATGATTTATTTATTGGTTAAAGAGGAAAATCCTCACA S7 4000 C1q CCATACCTCTCCACTTCTTCCTCTTTCCCTTTACAATTTTTATTTTTTTTAAATAATAAAGTGATGATTTATTTATTGGTTAAAGAGGAAAATCCTCACA 110 120 130 140 150 160 170 180 190 200