[Genome] differences between MAF and 2bit

[Pavel Sumazin]

I obtained a few coordinates from the mouse genome from the 17 
vertebrate MAF files (mm8 is in the alignment) and attempted to retrieve 
flanking sequence from mm8.2bit
While the sequence information exists in the MAF files, it appears to be 
missing from the 2bit file.  Is this a known phenomena?  Is there a 
reason for this?
I am including the problematic regions below.

Thanks,
Pavel

----------------------------------

chr10:1580222-1595222
chr10:1617696-1632696
chr10:1622371-1637371
chr10:1628386-1643386
chr10:1719750-1734750
chr10:1720947-1735947
chr10:1723502-1738502
chr10:1836299-1851299
chr10:1845002-1860002
chr10:1867826-1882826
chr10:1914649-1929649
chr10:1975021-1990021
chr10:1975369-1990369
chr10:1993795-2008795
chr10:2015417-2030417
chr10:2042729-2057729
chr10:2043929-2058929
chr10:2047326-2062326
chr10:2047391-2062391
chr10:2051919-2066919
chr10:2101210-2116210
chr10:2131846-2146846
chr10:2141109-2156109
chr10:2178724-2193724
chr10:2214138-2229138
chr10:2220258-2235258
chr10:2243283-2258283
chr10:2248703-2263703
chr10:2288675-2303675
chr10:2309814-2324814
chr10:2329785-2344785
chr10:2331482-2346482
chr10:2450934-2465934
chr10:2492728-2507728
chr10:2511309-2526309
chr10:260893-275893
chr10:2680359-2695359
chr10:2794156-2809156
chr10:2809478-2824478
chr10:2874457-2889457
chr10:2874934-2889934
chr10:2880224-2895224
chr10:2920094-2935094
chr10:377837-392837
chr10:932728-947728
chr1:177616-192616
chr1:1984125-1999125
chr1:2010530-2025530
chr1:2081239-2096239
chr1:2111890-2126890
chr12:1152309-1167309
chr1:2184304-2199304
chr1:2498693-2513693
chr1:2848074-2863074
chr13:0-9435
chr13:1092860-1107860
chr13:11089088-11104088
chr13:1501341-1516341
chr13:1503859-1518859
chr13:2206584-2221584
chr13:22310-37310
chr13:2454751-2469751
chr13:691196-706196
chr1:393253-408253
chr1:537375-552375
chr1:541851-556851
chr17:2039786-2054786
chr18:1317598-1332598
chr18:1456739-1471739
chr18:1693472-1708472
chr18:44383-59383
chr2:176101878-176116878
chr2:176330068-176345068
chr3:0-1684
chr3:1568344-1583344
chr3:15714271-15729271
chr3:1854827-1869827
chr3:1885230-1900230
chr3:1915118-1930118
chr4:1025555-1040555
chr4:1084758-1099758
chr4:1097824-1112824
chr4:1208593-1223593
chr4:121881029-121896029
chr4:1272011-1287011
chr4:1503025-1518025
chr4:1534100-1549100
chr4:154290-169290
chr4:160073-175073
chr4:160278-175278
chr4:178279-193279
chr4:1879861-1894861
chr4:212494-227494
chr4:2162246-2177246
chr4:2163680-2178680
chr4:2195773-2210773
chr4:2209048-2224048
chr4:2688384-2703384
chr4:279208-294208
chr4:282080-297080
chr4:301592-316592
chr4:311723-326723
chr4:31762137-31777137
chr4:326964-341964
chr4:396249-411249
chr4:436992-451992
chr4:517689-532689
chr4:521117-536117
chr4:611893-626893
chr4:809490-824490
chr4:825296-840296
chr5:68503-83503
chr7:0-2353
chr7:1461315-1476315
chr7:1486950-1501950
chr7:25797-40797
chr7:369833-384833
chr7:408919-423919
chr7:466426-481426
chr7:727175-742175
chr7:883844-898844
chr7:901622-916622
chr8:1573442-1588442
chr8:20223847-20238847
chr8:21592558-21607558
chr8:457261-472261
chr8:58243751-58258751
chr8:58248362-58263362
chr8:58277430-58292430
chr8:58301692-58316692
chrX:1010247-1025247
chrX:1523464-1538464
chrX:1524856-1539856
chrX:2814671-2829671
chrX:2866971-2881971
chrX:2933212-2948212
chrX:3611925-3626925
chrX:3808426-3823426
chrX:3811419-3826419
chrX:877279-892279
chrX:893084-908084
chrX:896646-911646