Schema for ucscRetroAli5
  Database: hg19    Primary Table: ucscRetroAli5    Row Count: 13,742   Data last updated: 2013-03-12
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2032int(10) unsigned range Number of bases that match that aren't repeats
misMatches 25int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName AK021903.1-1varchar(255) values Query sequence name
qSize 2057int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2057int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 249250621int(10) unsigned range Target sequence size
tStart 87548int(10) unsigned range Alignment start position in target
tEnd 89605int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 2057,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 87548,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg19.ucscRetroCds5.id (via ucscRetroAli5.qName)
      hg19.ucscRetroExpressed5.name (via ucscRetroAli5.qName)
      hg19.ucscRetroInfo5.name (via ucscRetroAli5.qName)
      hg19.ucscRetroOrtho5.name (via ucscRetroAli5.qName)
      hg19.ucscRetroSeq5.acc (via ucscRetroAli5.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585203225000000-AK021903.1-1205702057chr1249250621875488960512057,0,87548,
732588471000000+NM_015125.3-1547305471chr12492506211310671348364732,28,87,12,246,220,35,95,33,67,112,59,176,7,93,79,92,61,27,112,149,233,21,47,56,7,9,7,7,8,12,11,28,12,6,36,66,53,45,52,22,11,9, ...0,33,70,160,188,435,655,690,788,847,914,1034,1094,1278,1286,1380,1461,1554,1617,1644,1757,4198,4432,4454,4502,4558,4565,4574,458 ...131067,131099,131127,131214,131226,131472,131693,131733,131828,131861,131929,132041,132100,132276,132283,132376,132455,132547,13 ...
58648043000000-AK130965.1-15382538chr1249250621228262228787623,47,48,290,86,29,0,29,77,128,418,507,228262,228285,228332,228380,228672,228758,
58662624000000-AK021903.1-3205701614chr12492506212355162361662198,452,443,1605,235516,235714,
5872404000000+AK302511.1-142066342972chr1249250621321020321264211,233,342,739,321020,321031,
587419131000000-BC018677.1-41161156724chr12492506213214383220241620,40,7,14,32,6,104,33,17,85,35,8,60,23,53,13,437,457,501,509,523,557,563,669,702,719,805,840,848,909,939,992,321438,321473,321513,321520,321535,321567,321578,321682,321716,321734,321819,321859,321869,321929,321952,322011,
587167098000000+BC054485.1-3021382252073chr12492506213265843284121336,31,23,20,30,11,13,7,27,4,12,169,1385,225,268,299,322,358,389,400,413,420,447,457,470,688,326584,326620,326662,326689,326709,326739,326766,326785,326812,326842,326846,326858,327027,
5872595464000000-NM_015125.3-2547305471chr124925062132851733228246404,17,40,18,8,34,52,45,53,66,36,6,12,28,11,12,8,7,7,9,7,56,47,21,233,149,112,27,61,92,79,93,7,176,59,112,67,33,95,35,220,246,12 ...2,418,443,483,501,509,543,598,644,698,772,808,814,826,854,865,877,885,892,899,908,915,972,1020,1042,3567,3717,3829,3858,3920,401 ...328517,328921,328938,329218,329281,329318,329365,329417,329462,329515,329581,329643,329652,329719,329786,329829,329848,329876,32 ...
58737855000000-AK308843.1-113600448chr1249250621379128379568587,124,128,54,40,912,1005,1129,1266,1320,379128,379215,379342,379470,379528,
58843536000000+AK312123.1-24842478chr1249250621470895471368529,86,152,188,16,2,34,120,273,462,470895,470924,471012,471164,471352,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.