BAC T2H3 encodes a genomic repeat residing from position 22035 to 23281. This repeat is also found in BACs F26C24, F23F1 and F6I18, thus the copy number is at least 4. As the alignment below demonstrates, this repeat consists of two regions separated by a spacer element. The two repeated regions are highly conserved, while the spacer region appears variable. The table below lists the other sequences found to contain this repeat, with the position and strand noted.

        1                                                         60
  T2H3  CAGTCCAACACATCGAAGCACACAAGTT...GCTAAATTGGTCCGA.TTAGTCTTAGAGC
F26C24  ~~~~ATTACACGTATTTTCCAACATGTTTCCGACAAGTTAATCTAACATATAGTTAGGGC
 F23F1  ~~~~CTTTCGAATCTAAATTAGGAAGAT...CCGTA..TGAGCAAA.AAGTACTTAGGGT
 F6I18  ~~~~~~~CCATATGCATAATGCAATGCAAATGGGTAAGTAGTC..AGTTAAACTAAGGGC

        61                                                       120
  T2H3  TTGATTGGTTCTCCCTCTGTCACCCGCAAACGCTGCGTTTGCGGGTGGTAGCAGTTGTTA
F26C24  TTGATTAGTTCTCCCTCTGCCACCCGCAAACGCAGCGTTTGCGGGTGGTAGCGGTTGTTA
 F23F1  TTGATTGGTTCTCCCTCTGTCACCCGCAAACGCTGCGTTTGCAGGTGGTAGCGGTTATTA
 F6I18  TTGATTGGTTCTCCCTCTGCCACCCGCAAACGCAGCGTTTGCGGGTGGTAGCGGTTGTTA

        121                                                      180
  T2H3  GCGTTTGACACCAATCATAAAAACCGTTAGATACCGCTTTGGACCGCTCGAAATCGCCAT
F26C24  GCGATTGGCACCAATCATAGAAACCGCTCGATACCGCTTTGGACCGCTCGAAATCGCCAG
 F23F1  GCGGTTGGCACTAATCATAGAAACCGCTAGATATCGCTTTGTACCGCTCGAAATCGCCAG
 F6I18  GCGATTGGCACCAATCATATAAACCGCTAGATATCGCTTTGGACCGCTCGAAATCGCCAG

        181                                                      240
  T2H3  ATTTTAAAAGTTCCTTCCCGCAAGCGTTTGCGGTTGCGGGCGGTAGCGGTTAGGTTAATT 
F26C24  ATTTCAAAAGCTCATTCCCGCAAGCGTTTGCGGTTGCGGGCGGTAGCGGTTAGGTTAAAT 
 F23F1  ATTTCAAAAGCTCCTTCCCGCAAGCGTTTGCGGTTGCGGGCGGTAGCGGTTAGATTAAAA
 F6I18  ATTTCAAAAGCTCCTTCCCGCAAGCGTTTGCGGTTGCGGGCGGTAGCGGTTAGGTTAAAA 

        241                                                      300
  T2H3  TTT.......TTTTTTAATTAACTAAAATAATTATGTCTTCCACCCAAACCCTATATATC 
F26C24  TTTTTTATTATTTTTTAATTAATTAAAATAATCATGTCTTTCACCCAAACCCTATATATC 
 F23F1  ATAATAATAA....TTAATTAATTAAAATAATTATGTCTTCCACCCAAACCCTATA...C
 F6I18  AAAAAATTATTTTTATAATTAATTAAAATAATTATATTTTCCACCCAAACCCTATATATC 

        301                                                      360
  T2H3  TTATTCTTATCAGAAAATCC...TAATCAATATATTGAAACCCTATTCTCTCAATTATGG 
F26C24  TTATTCTTATTAGAAAACCC...TAATCAATATATTGTAACCCTATTCTCTCAATTATGG 
 F23F1  TTATTCTTATCAGAAAACCC...TAATCAA.....TGAAACCCTATTCTCTCAATTATGG
 F6I18  TTATTCTTATTAGAAAACTCTAATAATTAATATATTGTAACTCTATTCTCTCAATTATGG 

        361                                                      420
  T2H3  CATCTACCCAAACTAACGAAAATCAAAATCAAAATCAAGAATCAAACGTAAGTATGATCT 
F26C24  CATCCACCCAAACAGAGGAAAATTAAAATCAAAATCAAGAATCAAACGTAAGTATGATCT 
 F23F1  CATCCACCCAAACTGACAAAAATCAAAGTCAAAATCAAGAATCAAACGTAAGTATGATCT
 F6I18  CATCCACCCAAACGGATAAAAATTAAAATCAAAATCAATAATCAAAAGTAAGTATCATAT 

        421                                                      480
  T2H3  ATCCTTTCATCCATTCATTAGCTAGTGTAATTCTCTGAGTATTTTATGGCATCGTCATTT 
F26C24  ........ATCCATTCATTAGCTAGTGTAATTCTCTGAGTATTTCATGGCATCGTTGTTT 
 F23F1  ATCCTTTCATCCATTCATTAGCTAGTGTAATTCTCGGAATATTTCATGGCATCGT..TTT
 F6I18  ATTCGTTCATCCATTCACGACC...................................... 

        481                                                      540
  T2H3  TATTTATTTTGTA.TTTTTTTGAGTTTTTTGATTGAATACATGTTTTGATTTGTTTTCTC 
F26C24  TTTTTATTTTGTATTTTTTTTTAGTTTTTTAATTGAATACATGTTTCGATTTGTTTTCTC 
 F23F1  TTTTTATTTTGTT.GTTTTTTAAGTTTTTTGATTGAATACATGTTTTGATTTGTTTTCTC
 F6I18  .....AGTTTGATTTTTTTTTGAGTT.................................. 

        541                                                      600
  T2H3  GATTAGAAAATTATTTGGTCAGACGAGATGACCCGTTTCTTGTTAG.............. 
F26C24  AATTAGAAAATCATTTGGTCAGACGAGATGACCCGTTTCTTGTTAGAACTGATAACCCTA 
 F23F1  GATTAGAAAATCATTTGGTCAAACGAGACCACATTTGCGTTACTTCAACGGGTTATTGTG
 F6I18  ............................................................ 

        601                                                      660
  T2H3  ............................................................ 
F26C24  GAGAAACAAGCTGGAAATTATAGAGGCAAAAGTTTGATTGAGAAAGGAAAAGAAAATGTT 
 F23F1  GAGAAATAAACGGAAGAATGCA.................AAGACCCCAAAATCAGATTTC
 F6I18  ............................................................ 

        661                                                      720
  T2H3  ............................................................ 
F26C24  CTTGTGAAATTTAAAAAACGATTTCCAATAACCTTAAATTGGAACAAAGTTAAGAACAGA 
 F23F1  TAAGTGATGTTCAAAAAGAAA.......................................
 F6I18  ............................................................ 

        721                                                      780
  T2H3  ............................................................ 
F26C24  CTTGATACTTTAAAGAAGCAATACGAAATCTATCGTAAAATCATTTTTTGGGTCAACTGG 
 F23F1  ............................................................
 F6I18  ............................................................ 

        781                                                      840
  T2H3  ............................................................ 
F26C24  TCTCGGAACTAATCAAAGGACAGGAAGTCTTGATGCCCCTGATCATTGGTGGAAAGATAA 
 F23F1  ............................................................
 F6I18  ............................................................ 

        841                                                      900
  T2H3  ............................................................ 
F26C24  AATTAAGGTATGTTATCACATATGTATATGTTAATTTCTTATTTTATATTCTTATTTTGA 
 F23F1  .............................................ATATTCTTAAGAATA
 F6I18  ............................................................ 

        901                                                      960
  T2H3  ............................................................ 
F26C24  TTGGCTTTTGTTTTTGGTTTATTGGGCTTATCCTGAAGCTGCTAAACTTCGGTCGCATCC 
 F23F1  TTAACGTT....................................................
 F6I18  ............................................................ 

        961                                                     1020
  T2H3  ............................................................ 
F26C24  ACTGCGGTTTATACCACTTCTTGATGTAGTCTTCCGAGATGAAACTGTTGTCGTTGAAGA 
 F23F1  ............................................................
 F6I18  ............................................................ 

        1021                                                    1080
  T2H3  ............................................................ 
F26C24  GTCATGGCAACCAAGACGTGGTGTACATCGTCGTGCTCCAGTACTGGACTTAAGCGACAG 
 F23F1  ............................................................
 F6I18  ............................................................ 

        1081                                                    1140
  T2H3  ............................................................ 
F26C24  TGAATGTCCAAACAATAATGGAGATGAGAGAGAAGATCTGATGCAAAATCGTGAACGTGA 
 F23F1  ............................................................
 F6I18  ............................................................ 

        1141                                                    1200
  T2H3  ............................................................ 
F26C24  TCATATGAGACCACCAACCCCAGATTGGATGTCACAAACCCCGATGGAAAATTCTCCAAC 
 F23F1  ............................................................
 F6I18  ............................................................ 

        1201                                                    1260
  T2H3  ............................................................ 
F26C24  TTCAGCTAACTCGGATCCGCCATTTGCATCACAAGAGAGATCTTCCACACACACTCAAGT 
 F23F1  ............................................................
 F6I18  ............................................................ 

        1261                                                    1320
  T2H3  ............................................................ 
F26C24  GAAAAATGTAAGCAGGAACAGAAAGCGTAAACAAAATCCAGCAGACTCGACGCTCGACCG 
 F23F1  ............................................................
 F6I18  ............................................................ 

        1321                                                    1380
  T2H3  ............................................................ 
F26C24  TATTGCTGCGACTATGAAAAAAATTTGAGTTGGAGATGTGTTAAAAATCGTTTGGATATC 
 F23F1  ..............TGGAAAAAATTTGAGTTGGAGATGTGTTAAAAATCGTTTGGATATC
 F6I18  ...............................GGAGATGTGTTATAAATCGTTTGGATATC 

        1381                                                    1440
  T2H3  .......AACTTTATCATATGTATAGAGGCAATCCGGAAAACCCACGAGTTCAACGTTAT 
F26C24  TTGAAGAAACTTTATCATATGTATAGAGGCAATCCGGAAAACCCGCGAGTTCAACGTTAT 
 F23F1  TTGAAGAAACTTTATCATATGTATAGAGGCAATCCGGAAAACCCGCGAGTTCAACGTTAT
 F6I18  TTGAAGAAACTTTATTATATGTATAGAGGCAATCTGGAAAATCCGCGAGTTCAACGTTAT 

        1441                                                    1500
  T2H3  TTACAGTTTATTACACTACTTGATGCAATTTTTGGTGATGTACCAAATGCATAAAGTACT 
F26C24  TTACAGTTTATCACACTACTTGATGCAATTTTTGGTGATGTACCAAATGCATAAAGTATT 
 F23F1  TTACAGTTTATCACACTACTTGATGCAATTTTTGGTGATGTACCAAATGCATAAAGTATT
 F6I18  TTACAGTTTATCACACTATTTGATGTAATTTTTGGTGATGTACCAAATGCATAAAGTATT 

        1501                                                    1560
  T2H3  AAGCTTTTTCTTACAAAATTTATTTATTTTTGAATTTAATGTTTTATTTATGGTTTTAAT 
F26C24  AAGTTTTTTCTTACAAAATTTATTTATTTTTGAATTTAATATTTTATTTATGGTTTTAAT 
 F23F1  AAGCTTTTTCTTACAAAATTTATTTATTTTTGAATTTTCAGTTTTATTTATGGTTTTAAT
 F6I18  AAGCTTTTTCTTGCAAAATTTATTTATTTTTGAATTTAATGTTTTATTTACGGTTTTAAT 

        1561                                                    1620
  T2H3  TATTAAGCATGTTTAATTTTTCTAATATTATCAATTTATCATAATAATATATTGTATTTT 
F26C24  TATTAAGCATGTTTAATTTTTCTAATATTATCAATTTATCATAATAATATATTGTATTTT 
 F23F1  TATTAAGTATGTTTAATTTTTCAAATATTATCAATTTATCATAATAATATATTGTATTTT
 F6I18  TTTTAATTATATTTAATTTTTCTAATATTATGAATTTATCATAATAATATATTATATTTT 

        1621                                                    1680
  T2H3  ..TTTCTTTTACTAGTAATATATTATATTTATTTTGGTTATTTTTTATTTAATTACTATC 
F26C24  TCTTTCTTTTAATAGTAATATATTATATTTATTTTGG...TTTTTTATTTAATTACTATC 
 F23F1  ..TTTCTTTTAATAGTAATATATTATATTTATTTTGGTTATTTTTTATTTAATTACTATC
 F6I18  TCTTTCTTTTAATAGTAATATATTATATTTATTTTGGTTTATTTTTGTTTAATTACTATC 

        1681                                                    1740
  T2H3  GCACCCGCTGGTTTACCAATCATAAAACTCCCGCAAACGCACTCATTATCAAACGCTCAA 
F26C24  GCACCTGCTGGTTTACCAGTCATAAAACTCCCGCAAACGCACTCATTATCAAACGCTCAA 
 F23F1  GCACCCGCTGGTTTATCAGTCATAAAACTCCCGCAAACGCACCTATTACCAAACGCTCAA
 F6I18  ACACCCGCTGGTTTACCAGTCATAAAACTCCCGCAAACGCACCCATTATCAAACGTTCAA 

        1741                                                    1800
  T2H3  CCAGTCGTTCAAAACACTTGATAACGCTTGAAACCGCAACCGCCTGTTTCCGCAAACTCC 
F26C24  CCAGTCGTTCAAAACGCTTGATAACGCTTAAAACCGCAACCGTCCGTTTCCGCAAACTCC 
 F23F1  CCAGTCGTTCAAAACACTTGATAACGCTTGAAACCGCAACCGCCCGTTTCCGCAAACTCC
 F6I18  CCAGTCGTTCAAAACGTTTGATAACGCTTGAAACTGCAACCGCCAGTTTCCGCAAACTTC 

        1801                                                    1860
  T2H3  CGCAACCGCAACCGCATCCGCTGCGTTTAAACCAGTCAGGCCCTTATTTGTTAGAGACAT 
F26C24  CGCAACCGCAACCGCACCCACTGCGTTTAAACCAGTCAGGCCCTAAGTTTGTTCA..... 
 F23F1  CGCAACCGCAACCGCACCCGCTGCGTTTAAACCAGTCAGGCCCTTAGATTCCTATTAGCA
 F6I18  CGCAACCATAACCGCACCCGCTGCATTTTAATCCGTCAGGCCCTAAAAAAATTAA..TCA 

        1861                               1899
  T2H3  CCGAACTTTTAAAAGTTAAAACTGATATGCTTG~~~~~~
F26C24  .TTGTCTTTAAAAATTTGGCTATTTTGTGCATATTCACT
 F23F1  ACACGGCGACGATTAAGAGTACTTGCATAGACTCCCACA
 F6I18  CTAGGCCGTTAATCCCTATCCGTAATACGAAACAC~~~~

written 3 Sep 98
Larry Parnell