Blat Alignment ID Query Source Id Number of Spans 5 Prime Gap (size) > 10bp 3 Prime Gap (size) > 10bp
Internal Gap1..N > 5bp
(query gap size)[Genomic Interval](genomic gap size)
*note1: "--" for no 5 or 3 prime query gap, "1" for query gap falling into genomic sequence gap, "0" for query gap not falling into genomic sequence gap
*note2: for 5 or 3 prime query gap, look 10 times gapsize away on genomic sequence for genomic sequence gaps
inconsistent alignments for NM_030641
10887253 NM_030641 3 (0) -- (1408) 1  
inconsistent alignments for NM_025045
10887212 NM_025045 9 (2) -- (20) 0 (133)[1413](0) 0
inconsistent alignments for NM_025013
10887244 NM_025013 10 (0) -- (108) 0  
inconsistent alignments for NM_023004
10887133 NM_023004 1 (20) 0 (0) --  
inconsistent alignments for NM_021974
10886974 NM_021974 4 (20) 0 (0) --  
inconsistent alignments for NM_021574
10887101 NM_021574 9 (3646) 1 (7) --  
10887103 NM_021574 5 (4025) 1 (7) -- (6)[7](0) 0 : (26)[31](0) 0
10887099 NM_021574 9 (3646) 1 (7) --  
10887100 NM_021574 9 (3646) 1 (7) --  
10887098 NM_021574 11 (3474) 1 (7) --  
10887096 NM_021574 35 (0) -- (7) -- (6)[5](0) 0
10887102 NM_021574 12 (3646) 1 (7) -- (12)[1067](0) 0
10887097 NM_021574 13 (3474) 1 (7) --  
inconsistent alignments for NM_021115
10886613 NM_021115 13 (0) -- (203) 0  
inconsistent alignments for NM_021076
10887139 NM_021076 6 (0) -- (0) -- (18)[0](0) 0 : (12)[6](0) 0
inconsistent alignments for NM_019103
10886969 NM_019103 5 (105) 0 (0) --  
inconsistent alignments for NM_017834
10886816 NM_017834 4 (1357) 1 (166) 0 (14)[15](0) 0
10886815 NM_017834 1 (0) -- (139) 0  
10886817 NM_017834 4 (1354) 0 (57) 0 (171)[0](0) 0
inconsistent alignments for NM_017584
10886991 NM_017584 9 (14) 0 (0) --  
inconsistent alignments for NM_017424
10886999 NM_017424 10 (0) -- (1577) 1  
inconsistent alignments for NM_017414
10886753 NM_017414 12 (39) 1 (29) 0  
10886758 NM_017414 2 (1275) 1 (29) 0  
10886755 NM_017414 2 (1275) 0 (29) 0  
10886756 NM_017414 8 (359) 0 (647) 0  
10886757 NM_017414 2 (1275) 1 (29) 0  
10886754 NM_017414 2 (1275) 0 (29) 0  
inconsistent alignments for NM_016449
10886746 NM_016449 1 (0) -- (42) 0  
10886745 NM_016449 8 (0) -- (93) 0 (42)[38](0) 0 : (8)[20](0) 0 : (6)[0](0) 0 : (19)[20](0) 0 : (11)[5](0) 0 : (20)[52](0) 0
inconsistent alignments for NM_015703
10886694 NM_015703 18 (0) -- (126) 0  
10886693 NM_015703 23 (0) -- (11) 0 (7)[2](0) 0 : (10)[0](0) 0 : (8)[1578](0) 0
inconsistent alignments for NM_015366
10886688 NM_015366 12 (67) 0 (0) --  
inconsistent alignments for NM_014678
10886679 NM_014678 16 (1477) 1 (0) --  
inconsistent alignments for NM_014338
10887261 NM_014338 7 (21) 1 (0) --  
inconsistent alignments for NM_014337
10886625 NM_014337 20 (14) 0 (1) --  
inconsistent alignments for NM_013986
10887084 NM_013986 14 (67) 0 (0) --  
inconsistent alignments for NM_013298
10886667 NM_013298 1 (117) 0 (20) 0  
inconsistent alignments for NM_007068
10886603 NM_007068 15 (19) 0 (0) --  
inconsistent alignments for NM_007061
10886607 NM_007061 9 (1) -- (0) --  
inconsistent alignments for NM_006932
10886604 NM_006932 26 (8) -- (35) 0 (19)[17](0) 0
inconsistent alignments for NM_006487
10887066 NM_006487 14 (0) -- (642) 1  
inconsistent alignments for NM_006485
10887064 NM_006485 15 (0) -- (48) 0  
inconsistent alignments for NM_005974
10886568 NM_005974 14 (479) 0 (0) --  
10886567 NM_005974 15 (1009) 1 (0) -- (11)[0](0) 0 : (23)[9](0) 0 : (27)[0](0) 0
inconsistent alignments for NM_005675
10887012 NM_005675 6 (48) 0 (13) 0  
10887013 NM_005675 7 (48) 0 (6) --  
inconsistent alignments for NM_005659
10886564 NM_005659 12 (10) -- (0) -- (107)[3682](0) 0
inconsistent alignments for NM_005243
10887057 NM_005243 18 (55) 0 (16) 0  
inconsistent alignments for NM_005137
10887015 NM_005137 11 (0) -- (0) -- (18)[0](0) 0
inconsistent alignments for NM_005080
10886475 NM_005080 12 (0) -- (25) 1 (14)[0](2350) 1
inconsistent alignments for NM_004981
10886474 NM_004981 1 (57) 1 (10) --  
inconsistent alignments for NM_004782
10886448 NM_004782 5 (0) -- (14) 0  
inconsistent alignments for NM_004327
10887093 NM_004327 8 (3670) 1 (0) --  
10887095 NM_004327 4 (4049) 1 (0) -- (6)[7](0) 0 : (26)[31](0) 0
10887091 NM_004327 8 (3670) 1 (0) --  
10887092 NM_004327 8 (3670) 1 (0) --  
10887090 NM_004327 10 (3497) 1 (0) --  
10887088 NM_004327 27 (35) 0 (0) --  
10887094 NM_004327 11 (3670) 1 (0) -- (12)[1067](0) 0
10887089 NM_004327 12 (3497) 1 (0) --  
inconsistent alignments for NM_004173
10886437 NM_004173 7 (38) 0 (0) --  
inconsistent alignments for NM_003935
10886404 NM_003935 17 (14) 1 (0) --  
10886405 NM_003935 1 (2218) 1 (0) --  
inconsistent alignments for NM_003932
10887019 NM_003932 13 (19) 0 (0) --  
inconsistent alignments for NM_003753
10886398 NM_003753 15 (13) 0 (19) 0  
inconsistent alignments for NM_003426
10886407 NM_003426 10 (0) -- (0) --  
inconsistent alignments for NM_003312
10886373 NM_003312 4 (20) 0 (20) 0  
inconsistent alignments for NM_003073
10886355 NM_003073 9 (0) -- (297) 0  
inconsistent alignments for NM_002872
10886388 NM_002872 7 (0) -- (174) 0  
inconsistent alignments for NM_002745
10886352 NM_002745 13 (132) 0 (7) --  
inconsistent alignments for NM_001952
10887104 NM_001952 3 (0) -- (0) -- (22)[0](0) 0 : (76)[0](0) 0
10887106 NM_001952 3 (0) -- (0) -- (76)[0](0) 0 : (22)[0](0) 0
10887105 NM_001952 3 (0) -- (0) -- (22)[0](0) 0 : (76)[0](0) 0
inconsistent alignments for NM_001894
10886345 NM_001894 9 (9) -- (26) 1  
inconsistent alignments for NM_001886
10887113 NM_001886 7 (22) 0 (0) --  
inconsistent alignments for NM_001585
10886300 NM_001585 4 (0) -- (1642) 0  
inconsistent alignments for NM_001429
10886318 NM_001429 52 (1) -- (0) -- (19)[0](0) 0
inconsistent alignments for NM_001197
10886314 NM_001197 7 (293) 0 (13) 0  
inconsistent alignments for NM_001127
10886298 NM_001127 22 (18) 0 (0) --  
inconsistent alignments for NM_001098
10886306 NM_001098 13 (0) -- (11) 0 (69)[105](0) 0 : (19)[9](0) 0 : (134)[9](0) 0
10886305 NM_001098 19 (0) -- (11) 0  
inconsistent alignments for NM_000496
10887115 NM_000496 6 (0) -- (7) -- (7)[8](0) 0
10887116 NM_000496 6 (185) 0 (7) -- (14)[10](0) 0