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Table 2 Characterization of microsatellites in the P. monodon genomea

From: Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

Motif Unit Countsb # FESc % FESd Bases
(bp)e
Basesf Max
lengthg
Mean
lengthh
STD
lengthi
Mean
repeat no.j
RA
(%)k
RF
(%)l
A 1 159 158 0.76 7,467 0.07 376 46.96 35.63 46.96 0.81 1.88
AC 2 1153 1095 5.23 118,430 1.07 783 102.71 93.67 51.36 12.85 13.66
AG 2 1424 1395 6.67 198,119 1.78 763 139.13 104.88 69.56 21.50 16.87
AT 2 912 896 4.28 87,832 0.79 604 96.31 70.28 48.15 9.53 10.80
CG 2 91 91 0.43 3,995 0.04 142 43.90 10.94 21.95 0.43 1.08
AAC 3 125 114 0.54 10,390 0.09 457 83.12 65.03 27.71 1.13 1.48
AAG 3 265 255 1.22 27,823 0.25 720 104.99 111.32 35.00 3.02 3.14
AAT 3 915 881 4.21 130,973 1.18 751 143.14 121.98 47.71 14.21 10.84
ACC 3 111 108 0.52 7,814 0.07 584 70.40 77.28 23.47 0.85 1.32
ACG 3 69 67 0.32 5,163 0.05 184 74.83 32.98 24.94 0.56 0.82
ACT 3 182 181 0.86 13,809 0.12 659 75.87 72.91 25.29 1.50 2.16
AGC 3 169 163 0.78 8,098 0.07 159 47.92 19.98 15.97 0.88 2.00
AGG 3 333 321 1.53 25,140 0.23 422 75.50 68.45 25.17 2.73 3.95
ATC 3 545 536 2.56 50,116 0.45 596 91.96 66.43 30.65 5.44 6.46
CCG 3 68 55 0.26 5,940 0.05 564 87.35 140.92 29.12 0.64 0.806
AAAC 4 17 17 0.08 996 0.01 120 58.59 33.20 14.65 0.11 0.20
AAAG 4 89 88 0.42 7,128 0.06 249 80.09 31.49 20.02 0.77 1.05
AAAT 4 95 93 0.44 7,572 0.07 372 79.71 60.36 19.93 0.82 1.13
AAGC 4 9 9 0.04 707 0.01 348 78.56 101.09 19.64 0.08 0.11
AAGG 4 33 31 0.15 4,890 0.04 642 148.18 169.76 37.05 0.53 0.39
AATG 4 11 11 0.05 923 0.01 131 83.91 31.85 20.98 0.10 0.13
ACAG 4 46 46 0.22 7,787 0.07 639 169.28 155.00 42.32 0.85 0.55
ACAT 4 82 79 0.38 10,505 0.10 659 128.11 133.48 32.03 1.14 0.97
ACGC 4 18 18 0.09 1,250 0.01 140 69.44 33.17 17.36 0.14 0.21
ACGG 4 89 89 0.43 3,789 0.03 116 42.57 9.40 10.64 0.41 1.05
ACTC 4 34 34 0.16 5,470 0.05 727 160.88 157.78 40.22 0.59 0.40
AGAT 4 76 75 0.36 10,076 0.09 743 132.58 114.86 33.14 1.09 0.90
AGCC 4 134 134 0.64 17,294 0.16 330 129.06 43.55 32.26 1.88 1.59
AGCG 4 63 62 0.30 2,054 0.02 36 32.60 2.82 8.15 0.22 0.75
AGGC 4 62 62 0.30 5,970 0.05 415 96.29 71.97 24.07 0.65 0.74
AGGG 4 97 94 0.45 13,231 0.12 618 136.40 130.46 34.10 1.44 1.15
ATCC 4 6 6 0.03 432 0.00 170 72.00 57.96 18.00 0.05 0.07
CCCG 4 29 29 0.14 1,915 0.02 82 66.03 8.26 16.51 0.21 0.34
AAAAC 5 6 6 0.03 388 0.00 96 64.67 24.05 12.93 0.04 0.07
AAAAG 5 14 14 0.07 927 0.01 115 66.21 28.21 13.24 0.10 0.17
AAAAT 5 9 9 0.04 435 0.00 60 48.33 10.05 9.67 0.05 0.11
AACCT 5 131 126 0.60 41,414 0.37 705 316.14 205.30 63.23 4.49 1.55
AAGAG 5 24 24 0.11 3,946 0.04 676 164.42 167.47 32.88 0.43 0.28
AAGGG 5 12 12 0.06 1,930 0.02 414 160.83 143.66 32.17 0.21 0.14
AATAT 5 14 14 0.07 1,236 0.01 258 88.29 58.22 17.66 0.13 0.17
AGAGG 5 16 15 0.07 1,873 0.02 456 117.06 116.10 23.41 0.20 0.19
AGGCG 5 25 25 0.12 922 0.01 37 36.88 0.60 7.38 0.10 0.30
AGGGG 5 20 20 0.10 1,884 0.02 215 94.20 53.84 18.84 0.20 0.24
AAAAAG 6 13 13 0.06 1,703 0.02 437 131.00 119.28 21.83 0.19 0.15
AAAAAT 6 9 9 0.04 452 0.00 62 50.22 16.36 8.37 0.05 0.11
AAACAC 6 6 6 0.03 425 0.00 133 70.83 32.20 11.81 0.05 0.07
AAAGAG 6 26 26 0.12 4,633 0.04 705 178.19 156.46 29.70 0.50 0.31
AAATAT 6 6 4 0.02 184 0.00 59 30.67 16.68 5.11 0.02 0.07
AAATGG 6 6 3 0.01 218 0.00 79 36.33 23.55 6.06 0.02 0.07
AACAAT 6 7 7 0.03 625 0.01 119 89.29 22.26 14.88 0.07 0.08
AACAGC 6 25 25 0.12 1,052 0.01 55 42.08 5.61 7.01 0.11 0.30
AAGAGC 6 8 8 0.04 352 0.00 44 44.00 0.00 7.33 0.04 0.10
AAGAGG 6 30 30 0.14 4,223 0.04 554 140.77 124.39 23.46 0.46 0.36
AAGGAG 6 28 28 0.13 3,377 0.03 318 120.61 85.98 20.10 0.37 0.33
AAGGGG 6 23 23 0.11 2,123 0.02 195 92.30 55.98 15.38 0.23 0.27
AATATT 6 7 7 0.03 370 0.00 98 52.86 30.56 8.81 0.04 0.08
AATGAT 6 45 41 0.20 5,325 0.05 453 118.33 107.96 19.72 0.58 0.53
ACACAT 6 16 16 0.08 2,716 0.02 714 169.75 190.21 28.29 0.30 0.19
ACACGC 6 14 14 0.07 1,056 0.01 136 75.43 32.56 12.57 0.12 0.17
ACACTC 6 10 10 0.05 972 0.01 172 97.20 46.96 16.20 0.11 0.12
ACAGAG 6 13 13 0.06 2,486 0.02 733 191.23 196.79 31.87 0.27 0.15
ACATAT 6 15 13 0.06 1,737 0.02 367 115.80 104.02 19.30 0.19 0.18
ACCATC 6 11 11 0.05 852 0.01 203 77.45 66.27 12.91 0.09 0.13
ACCTCC 6 8 8 0.04 587 0.01 150 73.38 50.83 12.23 0.06 0.10
ACGATG 6 9 9 0.04 424 0.00 86 47.11 22.13 7.85 0.05 0.11
ACTCTC 6 6 6 0.03 752 0.01 229 125.33 84.80 20.89 0.08 0.07
AGAGGG 6 49 49 0.23 7,856 0.07 702 160.33 138.90 26.72 0.85 0.58
AGCCGC 6 10 10 0.05 642 0.01 175 64.20 43.00 10.70 0.07 0.12
AGGATG 6 6 6 0.03 929 0.01 509 154.83 181.98 25.81 0.10 0.07
AGGGGG 6 19 19 0.09 2,064 0.02 321 108.63 73.56 18.11 0.22 0.23
CCCCCG 6 66 25 0.12 838 0.01 58 12.70 5.66 2.12 0.09 0.78
  1. a The characterization of microsatellites in P. monodon FESs is accomplished in terms of the occurring hitsb, the number of occurred FESsc, the percentage frequency of repeats in terms of the total number of FES analyzedd, the amount of repeats in terms of nucleotide lengthe and as a percentagef of total sequence (11,114,786 bp) analyzed, the maximum lengthg, the standard deviationi about the microsatellite mean lengthh, the mean repeat numberj, the relative abundancek, and the relative frequencyl. In total, seventy-one microsatellite types have 6 hits in the 20,926 FESs; the remaining 91 microsatellite types with 1~5 hits were omitted.
  2. kThe relative abundance (RA) is the base-pairs comprised by each repeat class [Bases (bp)e] divided by the total length of all microsatellites (921,720 bp) ×100.
  3. l The relative frequency (RF) is the hits of each repeat class [Countsb] divided by the total hits of all microsatellites (8,441 hits) ×100.