Nicely display longer alignments over multiple lines

[Xyaneon]

From the class notes website:

For extra credit on Homework Assignment 3, add numbers to make longer alignments more readable something like this:

$ ruby semi-global.rb acalifornia2009.fasta acalifornia2009m1.fasta
Alignment 1
Sequence 1 0001 TAGATATTAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCG
                            ||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0001 ____________ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCG

Sequence 1 0061 TCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTGGAAAGTGTCTTTGCAGGAAAGAAC
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0049 TCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTGGAAAGTGTCTTTGCAGGAAAGAAC

Sequence 1 0121 ACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCTTGTCACCTCTGACT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0109 ACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCTTGTCACCTCTGACT

Sequence 1 0181 AAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0169 AAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGT

Sequence 1 0241 AGACGCTTTGTCCAAAATGCCCTAAATGGGAATGGGGACCCGAACAACATGGATAGAGCA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0229 AGACGCTTTGTCCAAAATGCCCTAAATGGGAATGGGGACCCGAACAACATGGATAGAGCA

Sequence 1 0301 GTTAAACTATACAAGAAGCTCAAAAGAGAAATAACGTTCCATGGGGCCAAGGAGGTGTCA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0289 GTTAAACTATACAAGAAGCTCAAAAGAGAAATAACGTTCCATGGGGCCAAGGAGGTGTCA

Sequence 1 0361 CTAAGCTATTCAACTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGGATGGGA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0349 CTAAGCTATTCAACTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGGATGGGA

Sequence 1 0421 ACAGTGACCACAGAAGCTGCTTTTGGTCTAGTGTGTGCCACTTGTGAACAGATTGCTGAT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0409 ACAGTGACCACAGAAGCTGCTTTTGGTCTAGTGTGTGCCACTTGTGAACAGATTGCTGAT

Sequence 1 0481 TCACAGCATCGGTCTCACAGACAGATGGCTACTACCACCAATCCACTAATCAGGCATGAA
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0469 TCACAGCATCGGTCTCACAGACAGATGGCTACTACCACCAATCCACTAATCAGGCATGAA

Sequence 1 0541 AACAGAATGGTGCTGGCTAGCACTACGGCAAAGGCTATGGAACAGATGGCTGGATCGAGT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0529 AACAGAATGGTGCTGGCTAGCACTACGGCAAAGGCTATGGAACAGATGGCTGGATCGAGT

Sequence 1 0601 GAACAGGCAGCGGAGGCCATGGAGGTTGCTAATCAGACTAGGCAGATGGTACATGCAATG
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0589 GAACAGGCAGCGGAGGCCATGGAGGTTGCTAATCAGACTAGGCAGATGGTACATGCAATG

Sequence 1 0661 AGAACTATTGGGACTCATCCTAGCTCCAGTGCTGGTCTGAAAGATGACCTTCTTGAAAAT
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence 2 0649 AGAACTATTGGGACTCATCCTAGCTCCAGTGCTGGTCTGAAAGATGACCTTCTTGAAAAT

Sequence 1 0721 TTGCAGGCCTACCAGAAGCGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGT
                |||||||||||||||||||||||||||||||||||||||||||||||||||         
Sequence 2 0709 TTGCAGGCCTACCAGAAGCGAATGGGAGTGCAGATGCAGCGATTCAAGTGA_________

Sequence 1 0781 CATTGCAGCAAATATCATTGGGATCTTGCACCTGATATTGTGGATTACTGATCGTCTTTT

Sequence 2 0760 ____________________________________________________________

Sequence 1 0841 TTTCAAATGTATTTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGG

Sequence 2 0760 ____________________________________________________________

Sequence 1 0901 AGTGCCTGAGTCCATGAGGGAAGAATATCAACAGGAACAGCAGAGTGCTGTGGATGTTGA

Sequence 2 0760 ____________________________________________________________

Sequence 1 0961 CGATGGTCATTTTGTCAACATAGAGCTAGAGTAAAAAACTAC

Sequence 2 0760 __________________________________________

[Xyaneon]

No longer targeted for the due date, since we're past that now.