This is a table summary from running Repeat Masker on the caribou
genome sequence. The last three rows of SINE elements and the last row
of DNA elements are added manually, from counting using a python
program. Some of the percentage such as SINE may not add up due to the
unidentified SINE elements which were not labelled as any of the sub-
categories. The specific parameter was as follows: -pa 16 -species
cow, which means it was analyzed with respect to the documented cow
repetitive elements. The algorithm Cross_Match is implemented.
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file name: caribou_21Dec2016_247Nf.fasta
sequences: 4699
total length: 2205150215 bp (2189511821 bp excl N/X-runs)
GC level: 41.44 %
bases masked: 872085469 bp ( 39.55 %)
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number of length percentage
elements* occupied of sequence
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SINEs: 1631712 311437191 bp 14.12 %
Alu/B1 1 58 bp 0.00 %
MIRs 394551 56912390 bp 2.58 %
BovA 767983 132973230 bp 6.03 %
t-RNA Glu 194442 32002890 bp 1.45 %
others - 89529099 bp 4.06 %
LINEs: 927164 393815394 bp 17.86 %
LINE1 504103 249829470 bp 11.33 %
LINE2 233961 62395704 bp 2.83 %
L3/CR1 33842 6909977 bp 0.31 %
RTE 154947 74610417 bp 3.38 %
LTR elements: 278299 87109634 bp 3.95 %
ERVL 63965 24053666 bp 1.09 %
ERVL-MaLRs 113986 36511920 bp 1.66 %
ERV_classI 61420 22323619 bp 1.01 %
ERV_classII 1082 400649 bp 0.02 %
DNA elements: 218551 48621090 bp 2.20 %
hAT-Charlie 120963 20018542 bp 0.91 %
TcMar-Tigger 23784 5964768 bp 0.27 %
MER1_Type 6728757 bp 0.30 %
Unclassified: 4853 920572 bp 0.04 %
Total interspersed repeats: 841903881 bp 38.18 %
Small RNA: 86119 6463508 bp 0.29 %
Satellites: 906 653122 bp 0.03 %
Simple repeats: 252451 11563720 bp 0.52 %
Low complexity: 299525 11760696 bp 0.53 %
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* most repeats fragmented by insertions or deletions
have been counted as one element
The query species was assumed to be bos taurus
RepeatMasker version open-3.2.6 , default mode
run with cross_match version 0.990329
RepBase Update 20080801, RM database version 20080801