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WormBase Tree Display for Sequence: Y60A3A

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Name Class

Y60A3ADNAY60A3A122592
SMapS_child (12)
StructureFromSourceCHROMOSOME_V
Overlap_rightY113G7A122480
Overlap_leftY116F11B
Clone_left_endY60A31
Y102G33623
Y113G747717
Y60A3A1
Clone_right_endY116F1147722
Y60A3122592
Y60A3A122592
DB_infoDatabaseEMBLNDB_ACAL117207
NDB_SVAL117207.1
Secondary_accessionAL021574
KeywordHTG
EMBL_dump_infoEMBL_dump_methodworm_EMBL-dump
OriginFrom_authorWilliams L
From_laboratoryHX
Date_directory990420
SpeciesCaenorhabditis elegans
StrainWBStrain00000001
VisibleCloneY60A3A
PropertiesGenomic_canonical
ChecksumMD5fab5f6521fe22b826a8c79652f04f634
StatusFinished20 Apr 1999 00:00:00
Submitted20 Apr 1999 00:00:00
Annotated21 Oct 1999 00:00:00
MapSequence-VEnds (2)
Interpolated_map_positionV24.1276
Assembly_tagsFinished Left14Y60A3A
Clone left end16Y60A3
36233628Y102G3
4771747722Y113G7
Warning2103321033
2985129851Y102G3 base diff
3562535625poss base diff
annotation2103221034First select a Feature -[ ] Unsure[X] Misc_featureThen select the text for the note(s) -[ ] Tandem repeat[ ] Single clone region[ ] Forced join[X] OtherAdd a comment here -Clone Y16F11 reads aTg at this point, but reads have been edited to the sequence of this clone.
2336623406
First select a Feature -
[ ] Unsure
[X] Misc_feature
Then select the text for the note(s) -
[ ] Tandem repeat
[X] Single clone region
[ ] Forced join
[ ] Other
Add a comment here -
Region contains only sonicated reads from subclone Y60A3_2e7.
3010529199First select a Feature -[ ] Unsure[X] Misc_featureThen select the text for the note(s) -[X] Tandem repeat[ ] Single clone region[ ] Forced join[ ] OtherAdd a comment here -Region contains a tandem repeat element which is 32bp long. There is some variation in the copies.
6437365119
First select a Feature -
[ ] Unsure
[X] Misc_feature
Then select the text for the note(s) -
[ ] Tandem repeat
[X] Single clone region
[ ] Forced join
[ ] Other
Add a comment here -
Region only contains sonicated reads from subclone vw64a10.
6516265196
First select a Feature -
[ ] Unsure
[X] Misc_feature
Then select the text for the note(s) -
[ ] Tandem repeat
[X] Single clone region
[ ] Forced join
[ ] Other
Add a comment here -
Region only contains sonicated reads from subclone vw64a10.
6527165348First select a Feature -[ ] Unsure[x] Misc_featureThen select the text for the note(s) -[ ] Tandem repeat[ ] Single clone region[ ] Forced join[x] OtherAdd a comment here -This region is the loop of an inverted repeat, the arms of which are approximately 2.7kb. Because the subclones used have an insert size of 1.5kb, orientation of this sequence is unconfirmed.
9878098821
First select a Feature -
[ ] Unsure
[x] Misc_feature
Then select the text for the note(s) -
[x] Tandem repeat
[ ] Single clone region
[ ] Forced join
[ ] Other
Add a comment here -
Suclones in this region show some rearangement.
Finisher comment2103221034
reads from Y116F11 read aTg
but both Y102G3 and Y60A3 read aCg
edited to majority
3562635624
Single subclone fron Y102G3 does
not have  the A.
6317263177single direction terms
6452164668single direction terms
8023080596Only reads from Y102G3 and F43A2
oligo2329123271
serial#= Y60A3.1
template=
sequence=CACATGGTTACATCATTTTTG
flags=
2346923486
serial#=Y60A3.2
template=
sequence=CTCGGAGCCAATTTTATC
flags=
comment2362723630clipped to allow join
2446324438?
2540325386?start of match with t08d2
2623826240?
2655126556cut back poss chimeric
2954929553
Some reads gttta
some reads gtcta
Therefore one set needs pulling out
4745747454Cipped read poss chimeric.
4795247957
Reads 3330, 2666 and 187 ttcttct 
the rest say....         tttttct
6042760428?
6360763613
 Some reads are calling gagaacc
and some are calling   gagcacc

Could be repeat left in situ for now !
6565165648End of vw64a10 sil
105338105331
Not sure about number of g and c's. 
Edited through by hand, moe work needs
doing.
117226117226?
cosmid vector2386023784
23788
2385723804
Direct Repeat2921529199
2975629725
3004230011
2991529884
2981929788
3001029979
2988329852
2997829947
3010530075
3007430043
Polymorphism3011830106breakpoint of repeat
Inverted Repeat4744547448
48361
4736447367
2226322376
2253122645
4645247368
6251365271
6534965349
6535068107
Clone right end4771747722Y116F11
122587122592Y60A3
compression6791967919
6269062699other arm has 9 t's at this point
6526165261
6526465264
6535565355
6535865358
6792067920other arm of repeat has 10 A's at this point
TeamLeader comment9877798831for john to check
Finished Right122589122592Y60A3A
repeat4564145486
4622545642
MethodGenomic_canonical