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Sequence 202 Supplemental page

     

    Table S1. Sequence Composition

    # Output from 'compseq'
    #
    # The Expected frequencies are calculated on the (false) assumption that every
    # word has equal frequency.
    #
    # The input sequences are:
    # seq202

    Word size 2
    Total count 399999

    # Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency
    #
    AA 31849  0.0796227 0.0625000 1.2739632
    AC 21103  0.0527576 0.0625000 0.8441221
    AG 26402  0.0660052 0.0625000 1.0560826
    AT 25797  0.0644927 0.0625000 1.0318826
    CA 26297  0.0657427 0.0625000 1.0518826
    CC 24105  0.0602627 0.0625000 0.9642024
    CG 17360  0.0434001 0.0625000 0.6944017
    CT 25666  0.0641652 0.0625000 1.0266426
    GA 26356  0.0658902 0.0625000 1.0542426
    GC 22385  0.0559626 0.0625000 0.8954022
    GG 25716  0.0642902 0.0625000 1.0286426
    GT 21197  0.0529926 0.0625000 0.8478821
    TA 20650  0.0516251 0.0625000 0.8260021
    TC 25838  0.0645952 0.0625000 1.0335226
    TG 26177  0.0654427 0.0625000 1.0470826
    TT 31081  0.0777027 0.0625000 1.2432431

    Other 2020  0.0050500 0.0000000 10000000000.0000000

    Table S2: Location of Undefined Sequences

     

    Ns length start Segment length Ns length start Segment length
    100 65422 65421 100 197596 2291
    100 108625 43103 100 200217 2521
    100 124836 16111 100 202442 2125
    100 130039 5103 100 212754 10212
    100 140852 10713 100 257537 44683
    100 149977 9025 100 262479 4842
    100 166575 16498 100 275591 13012
    100 167670 995 100 352904 77213
    100 192682 24912 100 353975 971
    100 195205 2423 100 360474 6399

    Last segment length is 39427.

    Table S3: CpG analysis  

    CPGPLOT islands of unusual CG composition
    seq202 from 1 to 400000

         Observed/Expected ratio > 0.60
         Percent C + Percent G > 50.00
         Length > 200

     Length 802 (49..850)

     Length 1506 (925..2430)

     Length 1112 (2481..3592)

     Length 1143 (3602..4744)

     Length 603 (4845..5447)

     Length 1202 (5472..6673)

     Length 978 (6751..7728)

     Length 1051 (7757..8807)

     Length 241 (8913..9153)

     Length 224 (9159..9382)

     Length 1059 (9441..10499)

     Length 854 (10684..11537)

     Length 1434 (11586..13019)

     Length 477 (13053..13529)

     Length 1107 (13769..14875)

     Length 254 (14928..15181)

     Length 2394 (15183..17576)

     Length 1203 (17598..18800)

     Length 384 (18872..19255)

     Length 232 (19262..19493)

     Length 1171 (19573..20743)

     Length 227 (20772..20998)

     Length 543 (21063..21605)

     Length 367 (21791..22157)

     Length 681 (22169..22849)

     Length 729 (22911..23639)

     Length 1071 (23689..24759)

     Length 942 (24793..25734)

     Length 1153 (25811..26963)

     Length 305 (27042..27346)

     Length 236 (27663..27898)

     Length 272 (28467..28738)

     Length 1099 (29519..30617)

     Length 2699 (30642..33340)

     Length 1009 (33451..34459)

     Length 1854 (34736..36589)

     Length 801 (36681..37481)

     Length 287 (37585..37871)

     Length 1470 (38074..39543)

     Length 2079 (39584..41662)

     Length 1149 (41758..42906)

     Length 227 (46694..46920)

     Length 467 (47041..47507)

     Length 317 (47512..47828)

     Length 735 (47940..48674)

     Length 316 (49944..50259)

     Length 224 (50759..50982)

     Length 426 (51103..51528)

     Length 209 (55996..56204)

     Length 208 (59138..59345)

     Length 205 (59839..60043)

     Length 522 (69829..70350)

     Length 846 (70395..71240)

     Length 1058 (71295..72352)

     Length 725 (79924..80648)

     Length 1155 (83702..84856)

     Length 204 (85119..85322)

     Length 626 (88155..88780)

     Length 426 (89495..89920)

     Length 219 (90055..90273)

     Length 329 (91552..91880)

     Length 279 (94953..95231)

     Length 493 (95777..96269)

     Length 287 (101365..101651)

     Length 273 (111267..111539)

     Length 268 (113378..113645)

     Length 493 (113672..114164)

     Length 486 (121404..121889)

     Length 262 (124549..124810)

     Length 278 (125083..125360)

     Length 868 (127207..128074)

     Length 414 (128865..129278)

     Length 278 (137379..137656)

     Length 879 (139488..140366)

     Length 879 (147252..148130)

     Length 282 (150766..151047)

     Length 366 (153019..153384)

     Length 325 (157707..158031)

     Length 330 (158613..158942)

     Length 341 (165674..166014)

     Length 338 (168524..168861)

     Length 324 (170480..170803)

     Length 243 (172788..173030)

     Length 1001 (173040..174040)

     Length 729 (191359..192087)

     Length 250 (203733..203982)

     Length 215 (210782..210996)

     Length 447 (211371..211817)

     Length 211 (212454..212664)

     Length 211 (213364..213574)

     Length 250 (213920..214169)

     Length 277 (214210..214486)

     Length 425 (219984..220408)

     Length 327 (222563..222889)

     Length 373 (226594..226966)

     Length 398 (231738..232135)

     Length 768 (239845..240612)

     Length 1948 (240635..242582)

     Length 213 (247048..247260)

     Length 519 (247368..247886)

     Length 403 (247939..248341)

     Length 1702 (248435..250136)

     Length 1517 (250214..251730)

     Length 569 (251737..252305)

     Length 308 (252329..252636)

     Length 608 (252866..253473)

     Length 587 (253864..254450)

     Length 239 (255046..255284)

     Length 285 (256514..256798)

     Length 858 (258511..259368)

     Length 265 (261133..261397)

     Length 893 (267613..268505)

     Length 279 (275693..275971)

     Length 265 (277738..278002)

     Length 870 (285173..286042)

     Length 726 (286197..286922)

     Length 508 (287249..287756)

     Length 214 (287763..287976)

     Length 345 (288039..288383)

     Length 1354 (288421..289774)

     Length 1136 (289781..290916)

     Length 531 (291001..291531)

     Length 411 (291572..291982)

     Length 519 (300291..300809)

     Length 336 (301077..301412)

     Length 271 (302350..302620)

     Length 1389 (305688..307076)

     Length 1031 (316320..317350)

     Length 216 (320889..321104)

     Length 1042 (324693..325734)

     Length 1033 (329562..330594)

     Length 1518 (331124..332641)

     Length 774 (336283..337056)

     Length 310 (337087..337396)

     Length 753 (337408..338160)

     Length 1411 (338195..339605)

     Length 300 (346170..346469)

     Length 235 (346621..346855)

     Length 736 (348517..349252)

     Length 218 (349546..349763)

     Length 475 (350319..350793)

     Length 772 (353015..353786)

     Length 431 (360029..360459)

     Length 889 (360579..361467)

     Length 632 (366224..366855)

     Length 1037 (367306..368342)

     Length 256 (368631..368886)

     Length 261 (369134..369394)

     Length 323 (369556..369878)

     Length 333 (369885..370217)

     Length 438 (370228..370665)

     Length 536 (373132..373667)

     Length 231 (387571..387801)

     Length 210 (388891..389100)

     Length 1710 (394841..396550)

     Length 303 (397736..398038)

     Length 219 (398109..398327)

     Length 780 (398378..399157)

     Length 748 (399197..399944)

    Table S4: Retroelement and Transposon Analysis

     

    ==================================================
    file name: RM2sequpload_1292012739  
    sequences:             1
    total length:     400000 bp  (398000 bp excl N/X-runs)
    GC level:         47.51 %
    bases masked:     340252 bp ( 85.06 %)
    ==================================================
                   number of      length   percentage
                   elements*    occupied  of sequence
    --------------------------------------------------
    Retroelements          113       336728 bp   84.18 %
       SINEs:                0            0 bp    0.00 %
       Penelope              0            0 bp    0.00 %
       LINEs:                5         3457 bp    0.86 %
        CRE/SLACS            0            0 bp    0.00 %
         L2/CR1/Rex          0            0 bp    0.00 %
         R1/LOA/Jockey       0            0 bp    0.00 %
         R2/R4/NeSL          0            0 bp    0.00 %
         RTE/Bov-B           0            0 bp    0.00 %
         L1/CIN4             5         3457 bp    0.86 %
       LTR elements:       108       333271 bp   83.32 %
         BEL/Pao             0            0 bp    0.00 %
         Ty1/Copia          52       102738 bp   25.68 %
         Gypsy/DIRS1        50       228994 bp   57.25 %
           Retroviral        0            0 bp    0.00 %
    
    DNA transposons         14         2434 bp    0.61 %
       hobo-Activator        6         1303 bp    0.33 %
       Tc1-IS630-Pogo        3          469 bp    0.12 %
       En-Spm                0            0 bp    0.00 %
       MuDR-IS905            0            0 bp    0.00 %
       PiggyBac              0            0 bp    0.00 %
       Tourist/Harbinger     3          504 bp    0.13 %
       Other (Mirage,        0            0 bp    0.00 %
        P-element, Transib)
    
    Rolling-circles          0            0 bp    0.00 %
    
    Unclassified:            0            0 bp    0.00 %
    
    Total interspersed repeats:      339162 bp   84.79 %
    
    
    Small RNA:               0            0 bp    0.00 %
    
    Satellites:              0            0 bp    0.00 %
    Simple repeats:          7          439 bp    0.11 %
    Low complexity:         16          651 bp    0.16 %
    ==================================================
    
    * most repeats fragmented by insertions or deletions
      have been counted as one element
                                                          
    
    The query species was assumed to be zea           
    RepeatMasker version open-3.2.9 , default mode
                                       
    run with blastp version 3.0SE-AB [2009-10-30] [linux26-x64-I32LPF64 2009-10-30T17:06:09]
    RepBase Update 20090604, RM database version 20090604
    
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