running...
Interspersed Repeat Masking Based on Protein Similarity

Details
http://www.repeatmasker.org/RepeatProteinMask.html#database


also
rmOutToGFF3.pl - A utility to convert RM *.out files to gff version 3 files. - Robert Hubley. 




-

random few that includes some of 12

http://www.repeatmasker.org/tmp/9de6af614bae5c8e3a34e05c827144b8.html






Repeat Protein Mask Results.html




v032 sees between 20k and 25k (149 seqs)

Request number -1 submited to the rmcluster queue.

Your request has been queued. Once execution finishes you will find your results here: a5975fd0be55b5192cf89fe6669716a6.html



-----

Your request has been queued. Once execution finishes you will find your results here: 12ee2bb493ddce5c02a86351bfd5d802.html




Repeat Protein Mask Results_1.html


v032  sans BAC plus removing ~127k bp of séquence got file length to suitable for analysis

File analyzed =
cgigas_alpha_v032sansBAC.fa



Repeat Annotation Based on Matches to Transposable Element Proteins

Request number -1 submited to the rmcluster queue.

Your request has been queued. Once execution finishes you will find your results here: 3c130a42981749014438a3d51272517f.html

RepeatProteinMask Completed 04-May-2012 19:58:20 PDT

Identifying Simple and Low Complexity Repeats...(masking turned off)
   - TRF         : 133
   - RepeatMasker: 1225
Masking Repeat Proteins...
   - Protein Hits = 70
Done!
2618.14user 52.27system 7:40.97elapsed 579%CPU (0avgtext+0avgdata 1392976maxresident)k
0inputs+0outputs (0major+10868014minor)pagefaults 0swaps
Masked Sequence 
pValue      Score Method   SeqID              Begin    End        Repeat             Type               Begin    End     
1.40e-15       21 WUBlastX Contig_139160_v03 12605    12673    - BEL-14_CQ       LTR/Pao             1674     1696
1.30e-75       80 WUBlastX Contig_139160_v03 13251    13628    - BEL24_DR        LTR/Pao             1373     1515
2.10e-156     141 WUBlastX Contig_139160_v03 13335    13583    - BEL-1_XT        LTR/Pao             1584     1669
8.00e-163     250 WUBlastX Contig_139160_v03 13489    13935    - BEL1_DR         LTR/Pao             1209     1356
1.30e-185     277 WUBlastX Contig_139160_v03 13558    13944    - BEL-5_XT        LTR/Pao             1404     1532
2.80e-168     120 WUBlastX Contig_139160_v03 13945    14157    - BEL33_DR        LTR/Pao             1114     1178
2.60e-207     129 WUBlastX Contig_139160_v03 13990    14157    - BEL-2_XT        LTR/Pao             1103     1157
2.70e-187     863 WUBlastX Contig_139160_v03 14166    15797    - BEL36_DR        LTR/Pao              494     1051
2.70e-187     337 WUBlastX Contig_139160_v03 15739    16881    - BEL36_DR        LTR/Pao              131      514
2.70e-173     400 WUBlastX Contig_139160_v03 15787    16590    - BEL-1_XT        LTR/Pao              483      764
1.60e-171      20 WUBlastX Contig_139160_v03 16925    17110    - BEL11_DR        LTR/Pao               13       73
8.20e-01       23 WUBlastX Contig_146443_v03 5616     5789     - MdoERV1_pol     LTR/ERV1             569      625
3.40e-38      345 WUBlastX Contig_151235_v03 225      872      + DIRS-26_NV_pol  LTR/Ngaro            321      530
2.60e-33      247 WUBlastX Contig_151235_v03 934      1749     + LvNgaro1_yr     LTR/Ngaro             31      301
3.30e-131      38 WUBlastX Contig_151235_v03 2882     3478     + BEL-5_XT        LTR/Pao              105      300
1.50e-211    1364 WUBlastX Contig_151235_v03 2975     6067     + BEL36_DR        LTR/Pao               20     1051
2.70e-228     129 WUBlastX Contig_151235_v03 6076     6243     + BEL-2_XT        LTR/Pao             1103     1157
6.60e-147     120 WUBlastX Contig_151235_v03 6076     6288     + BEL33_DR        LTR/Pao             1114     1178
3.30e-156     277 WUBlastX Contig_151235_v03 6298     6723     + BEL-1_XT        LTR/Pao             1466     1608
7.00e-90       80 WUBlastX Contig_151235_v03 6605     6982     + BEL24_DR        LTR/Pao             1373     1515
2.80e-139     141 WUBlastX Contig_151235_v03 6650     6898     + BEL-1_XT        LTR/Pao             1584     1669
1.40e-15       21 WUBlastX Contig_151235_v03 7560     7628     + BEL-14_CQ       LTR/Pao             1674     1696
8.80e-01       25 WUBlastX Contig_155776_v03 22064    22306    + RTEX-5_BF_pol   LINE/RTE-X          1099     1174
1.00e+00       41 WUBlastX Contig_155776_v03 22205    22306    + RTEX-1_SP_pol   LINE/RTE-X          1090     1123
8.70e-01       21 WUBlastX Contig_156887_v03 15372    15521    - ORTE-6_AAe      LINE/RTE-BovB       1461     1511
1.00e+00       26 WUBlastX Contig_15868_v032 22222    22353    - Neptune1_Ren_po LINE/Penelope        587      631
2.40e-15       22 WUBlastX Contig_166839_v03 807      926      - DIRS-26_NV_pol  LTR/Ngaro            443      482
2.40e-15       67 WUBlastX Contig_166839_v03 1009     1260     - DIRS-26_NV_pol  LTR/Ngaro            331      419
1.20e-12       76 WUBlastX Contig_166839_v03 1075     1260     - SpNgaro1_pol    LTR/Ngaro            406      467
2.40e-15       27 WUBlastX Contig_166839_v03 1334     1738     - DIRS-26_NV_pol  LTR/Ngaro            171      306
1.10e-13       98 WUBlastX Contig_166839_v03 1358     1690     - LvNgaro1_pol    LTR/Ngaro            259      373
1.20e-01       48 WUBlastX Contig_166839_v03 13788    14087    - DIRS-1_SP_yr    LTR/Ngaro            214      315
7.60e-18       26 WUBlastX Contig_166839_v03 14265    14468    - DIRS-1_SP_pol   LTR/Ngaro            452      518
1.30e-16       25 WUBlastX Contig_166839_v03 14524    14628    - LvNgaro1_pol    LTR/Ngaro            497      529
7.60e-18       88 WUBlastX Contig_166839_v03 14755    15036    - DIRS-1_SP_pol   LTR/Ngaro            244      341
2.30e-16       22 WUBlastX Contig_166839_v03 15054    15086    - SpNgaro1_pol    LTR/Ngaro            322      332
2.30e-16       67 WUBlastX Contig_166839_v03 15119    15748    - SpNgaro1_pol    LTR/Ngaro             88      309
1.80e-06       58 WUBlastX Contig_166982_v03 13035    13811    - CR1-16_HM_pol   LINE/L2               54      330
0.00e+00     1372 WUBlastX Contig_166982_v03 13155    15677    - Helentron5      RC/Helitron         2145     2986
0.00e+00     1618 WUBlastX Contig_166982_v03 15649    17748    - Helitron-2_SP   RC/Helitron         1835     2526
0.00e+00      459 WUBlastX Contig_166982_v03 17753    19603    - Helentron5      RC/Helitron          839     1443
8.80e-38      276 WUBlastX Contig_166982_v03 19232    20590    - Helentron5      RC/Helitron          256      706
3.20e-67      500 WUBlastX Contig_193349_v03 14088    15047    - Tc1_FR2_tp      DNA/TcMar-Tc1         17      341
2.00e-02       24 WUBlastX Contig_29087_v032 19560    19889    + Tx1-10_BF_pol   LINE/L1-Tx1         1032     1145
1.10e-01       50 WUBlastX Contig_29087_v032 19614    19889    + Tx1-16_BF_pol   LINE/L1-Tx1         1071     1163
3.80e-01       45 WUBlastX Contig_29791_v032 25040    25159    + Gypsy16_CR_pol  LTR/Gypsy            491      530
9.80e-01       28 WUBlastX Contig_36179_v032 9795     10295    - HATw-2_BF       DNA/hAT-hATw         154      318
5.20e-01       31 WUBlastX Contig_54493_v032 15203    15475    - Helitron-2_SP   RC/Helitron         1934     2026
1.50e-03       21 WUBlastX Contig_54493_v032 17620    17802    - Gypsy1-SM_gag   LTR/Gypsy            141      200
4.40e-27       89 WUBlastX Contig_64118_v032 3        233      + 48139970_Ame    DNA/hAT              741      817
1.30e-07       43 WUBlastX Contig_64118_v032 800      955      + 48139970_Ame    DNA/hAT             1010     1061
2.00e-17       26 WUBlastX Contig_64118_v032 1083     1214     + 48139970_Ame    DNA/hAT              964     1006
1.30e-23       58 WUBlastX Contig_64118_v032 1662     1841     + 48139970_Ame    DNA/hAT              912      971
4.40e-27       38 WUBlastX Contig_64118_v032 2339     2464     + 48139970_Ame    DNA/hAT              927      971
4.40e-27       67 WUBlastX Contig_64118_v032 2707     2967     + 48139970_Ame    DNA/hAT              979     1069
6.50e-170    1607 WUBlastX Contig_65550_v032 15854    16873    - IS5_tp          DNA/IS                 1      340
2.40e-02       25 WUBlastX Contig_70442_v032 19411    19566    - RTEX-6_BF_pol   LINE/RTE-X          1089     1143
3.20e-01       41 WUBlastX Contig_70442_v032 19471    19578    - RTEX-2_NV_pol   LINE/RTE-X          1073     1108
7.90e-01       22 WUBlastX Contig_70442_v032 19580    19738    - RTEX-4_BF_pol   LINE/RTE-X          1046     1095
9.90e-01       22 WUBlastX Contig_8130_v032  4462     4512     + Helentron5      RC/Helitron          383      399
3.90e-01       21 WUBlastX Contig_83771_v032 13026    13562    + CR1-2_BF_pol    LINE/CR1             802      980
1.30e-04       73 WUBlastX Contig_83771_v032 13074    13481    + CR1-2_NV_pol    LINE/CR1             786      930
2.60e-04       47 WUBlastX Contig_83771_v032 13517    13945    + CR1-12_BF_pol   LINE/CR1             916     1048
2.90e-03       51 WUBlastX Contig_83771_v032 13532    13666    + CR1-21_NV_pol   LINE/CR1             950      991
9.80e-01       28 WUBlastX Contig_90720_v032 13063    13563    + HATw-2_BF       DNA/hAT-hATw         154      318
4.10e-03       65 WUBlastX Contig_96982_v032 3165     3320     - RTE-19_BF_pol   LINE/RTE-BovB        693      744
4.20e-02       66 WUBlastX Contig_96982_v032 3168     3293     - RTE-7_NV        LINE/RTE-BovB        959     1001
9.98e-01       25 WUBlastX Contig_96982_v032 18865    19392    + TABARE_p1       LTR/Gypsy             30      201
1.00e-07       82 WUBlastX Contig_98668_v032 2795     3259     - HAT6-1_NV_tp    DNA/hAT-Blackja      469      628
1.20e-09      119 WUBlastX Contig_99930_v032 27160    27489    + Tx1-9_BF_pol    LINE/L1-Tx1         1052     1170