% of Identical Nucleotides Background conservation. % of Identical Nucleotides Background conservation AG GT
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1 80 % of Identical Nucleotides Background conservation Hsap/Ggal Ggal/Mmus Ggal/Rnor Hsap/Mmus Hsap/Rnor Mmus/Rnor AG GT % of Identical Nucleotides Background conservation
2 6% Size fraction of all interspersed repeats 5% 4% 3% 2% 1% DNA transposons LTR elements LINEs 0% Substitution level compared to consensus sequences
3 Distribution of CR1 and L1 insertion sizes Number of L1 inserts of certain length length of LINE insert (bp) L1 CR1
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6 SINFRUP SINFRUP Gg_ADHX Hs_ADHX SINFRUP SINFRUP Fr_ At_ ADH2 Hs_ADH2 ADH2 STRCA 791 Gg_ADH2P 900 Hs_ADH6 Gg_ADHa Gg_ADHb 973 Gg_ADHc Gg_ADH1/ Hs_ADHA Hs_ADHB Hs_ADHG Hs_ADH7 0.1
7 A: MTRILTAFKVVRTLKTGFGFTNVTAHQKWKFSRPGIRLLSVKAQTAHIVLEDGTKMKGYS MTRILTACKVMKTLKGRLEFCKVSA-DHWSFWRSGTRLLSIKAQTANLVLEDGTKMKGYS FGHPSSVAGEVVFNTGLGGYPEAITDPAYKGQILTMANPIIGNGGAPDTTALDELGLSKY FGYPSSTAGEVVFNTGISGYTEALTDPSYKGQILTLANPVVGNGGVPDTAALDEIGLRRF LESNGIKVSGLLVLDYSKDYNHWLATKSLGQWLQEEKVPAIYGVDTRMLTKIIRDKGTML LESDGIKVSGLLVLDYSNEYSHWQAARSLGEWLQEEKVPALYGVDTRMLSKLIRDKGTVL GKIEFEGQPVDFVDPNKQNLIAEVSTKDVKVYGKGNPTKVVAVDCGIKNNVIRLLVKRGA GKIEFEGQPTEFADPNKQNLIAEVSTKELRIAEGDYCFRMILMDCEVSLNLVLDTEGQGA EVHLVPWNHDFTKMEYDGILIAGGPGNPALAEPLIQNVRKILESDRKEPLFGISTGNLIT EVHLVPWDHDFTSMEYDGLIISGGPGDPMKAQEVIQNVRKVLESNRPEPLFGIGMGNLIT GLAAGAKTYKMSMANRGQNQPVLNITNKQAFITAQNHGYALDN-TLPAGWKPLFVNVNDQ GIAAGATSYRMQMANRGQNQPVLNTLSGQAVITAQNHAYAIDSSTLPPGWRPLFVNANDQ TNEGIMHESKPFFAVQFHPEVTPGPIDTEYLFDSFFSLIKKGKATTITSVLPKPALVASR TNEGIMHETRPIFTAQFYPDANPGPTDTEFLFDSFISLVKRGKGTTIASVLPKAGATASR VEVSKVLILGSGGLSIGQAGEFDYSGSQAVKAMKEENVKTVLMNPNIASVQTNEVGLKQA VEVSKVLILGSGGLSIGQAGEFDYSGSQAVKALKEENVKIVLMNPNIASVQTNETGLKQA DTVYFLPITPQFVTEVIKAEQPDGLILGMGGQTALNCGVELFKRGVLKEYGVKVLGTSVE DAVYFLPITPQFVTEVIKAEHPDGLILGMGGQTALNCGVELFKQGVLQQYGVKVLGTSVE SIMATEDRQLFSDKLNEINEKIAPSFAVESIEDALKAADTIGYPVMIRSAYALGGLGSGI SIMATEDRKLFSDKLMELNEKIAPSFAVESIEDALEAAEKISYPVMIRSAYALGGLGSGV CPNRETLMDLSTKAFAMTNQILVEKSVTGWKEIEYEVVRDADDNCVTVCNMENVDAMGVH CTDKESLLDLGTKAFAVTKQILVEKSVVGWKEIEYEVVRDAADNCIAVCNMENIDAMGVH TGDSVVVAPAQTLSNAEFQMLRRTSINVVRHLGIVGECNIQFALHPTSMEYCIIEVNARL TGDSVVVAPSQTLTNEEFQMLRDRAIKVVRYLDIVGECNIQFALHPTSLEYYIIEVNARL SRSSALASKATGYPLAFIAAKIALGIPLPEIKNVVSGKTSACFEPSLDYMVTKIPRWDLD SRSSALASKATGYPLAFIAAKIALGIPLPEIKNVVTGKTSAYFEPSLDYVVTKIPRWDLD RFHGTSSRIGSSMKSVGEVMAIGRTFEESFQKALRMCHPSIEGFTPRLPMNKEWPSNLDL RFQGTSNQIGSSMKSVGEVMAIGRTFEESFQKALRMCHPSIDGFTSHLPMNKAWPAIADL RKELSEPSSTRIYAIAKAIDDNMSLDEIEKLTYIDKWFLYKMRDILNMEKTLKGLNSESM QKELSEPSSTRIYAMAKALENGVPVDVIHKLTAIDKWFLCKMRSIVNMEKILKEVKHEEI TEETLKRAKEIGFSDKQISKCLGLTEAQTRELRLKKNIHPWVKQIDTLAAEYPSVTNYLY PEETLRKAKQMGFSDRQIGKCLGLTEVQCRQLRLRKNVVPWVKKIDTLAAEYPAVTNYLY
8 VTYNGQEHDVNFDDHGMMVLGCGPYHIGSSVEFDWCAVSSIRTLRQLGKKTVVVNCNPET VTYNGQEHDIKFDDCGVMVLGCGPYHIGSSVEFDWCAVSSIRTLRQLGNKTVVVNCNPET VSTDFDECDKLYFEELSLERILDIYHQEACGGCIISVGGQIPNNLAVPLYKNGVKIMGTS VSTDFDECDRLYFEEMSLERILDIYQYEGCSGCIISVGGQIPNNLAVPLHQSGVKIFGTH PLQIDRAEDRSIFSAVLDELKVAQAPWKAVNTLNEALEFAKSVDYPCLLRPSYVLSGSAM PLQINRAEDRSIFSAVLDELHVAQAPWKAVSTLVDAVEFAGSVSYPCLLRPSYVLSGSAM NVVFSEDEMKKFLEEATRVSQEHPVVLTKFVEGAREVEMDAVGKDGRVISHAISEHVEDA NVVFTEEEMKKFLVEATRVSQDHPVVLTKFIEDAREVEMDAVAKAGRVIAHAVSEHVEDA GVHSGDATLMLPTQTISQGAIEKVKDATRKIAKAFAISGPFNVQFLVKGNDVLVIECNLR GVHSGDATLILPTQTISQGALEKVKSATKKIANAFAISGPFNVQFLVRGNNVLVIECNLR ASRSFPFVSKTLGVDFIDVATKVMIGENVDEKHLPTLDHPIIPADYVAIKAPMFSWPRLR ASRSFPFVSKTLGVDFIDVATKVMIGKEVNESSLPTLEHPIIPSKYIGIKAPVFSWSRLR DADPILRCEMASTGEVACFGEGIHTAFLKAMLSTGFKIPQKGILIGIQQSFRPRFLGVAE DADPVLRCEMASTGEVACFGEDVYSAFQKAMLATGFTFPKQGILIGIQKSFRPKFLGVAE QLHNEGFKLFATEATSDWLNANNVPATPVAWPSQEGQNPSLSSIRKLIRDGSIDLVINLP LLYGKGFKLYATEATSDWLNANGIPADPVAWPSQESLSPSLPPVRRLIRDGKIDLVINLP NNNTKFVHDNYVIRRTAVDSGIPLLTNFQVTKLFAEAVQKSRKVDSKSLFHYRQYSAGKAA NSNTKFVHDNYVIRRMAIDSGIALLTNYQVTKLFAEAIKYSGKLDSKSLFHYRQFDKGDAA
9 B: Thymus Spleen Bursa Skin Leg Muscle Ovary Liver Brain Genomic 100bp marker
10 Chromosome length (Mb) Z W Chromosome number 40
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12 Z a. Fraction of windows all macro inter micro sex b GC content (%) GC content (%) en chromosome c. 75 GC content (%) Y X chromosome
13 Fraction of 2 Mbp window comprised by interspersed repeats chr1 chr2 chr3 chr Position along chromosome (Mbp)
14 4p arm DAPI-dull 4q arm DAPI-bright DAPI-dull microchrom 4p cen interstitial telomere
15 /automnt/raid0/raid0/home/ext29/rat31/parasight/ chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr16 chr17 chr18 chr19 chr20 chr21 chr22 chr chr24 chr26 chr27 chr chr32 chre22c19w28 chre26c13 chre50c23 chre64 chrm chrw chrz
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20 Hsa1 Hsa2 Hsa3 Hsa4 Hsa5 Hsa6 Hsa7 Hsa8 Hsa9 Hsa10 Gga1 Gga2 Gga3 Gga4 Gga5 Gga6 Gga7 Gga8 Gga9 Gga X Y W Z Gga21 Gga22 Gga23 Gga24 Gga26 Gga27 Gga28 Gga32 GgaW GgaZ E22C19W28 E26C13 Gga11 Gga12 Gga13 Gga14 Gga15 Gga16 Gga17 Gga18 Gga19 Gga20 Hsa11 Hsa12 Hsa13 Hsa14 Hsa15 Hsa16 Hsa17 Hsa18 Hsa19 Hsa20 Hsa21 Hsa22 HsaX
21 Macro synteny en 4 (1178) 3 (1267) 6 (549) 5 (931) 8 (561) 7 (561) 10 (421) 20 (361) 1 (2080) 13 (352) 17 (313) 9 (463) 2 (1432) 11 (304) 19 (332) 28 (181) 12 (369) 14 (518) 15 (374) 18 (217) 21 (231) Z (369) 24 (185) 23 (212) 26 (185) 27 (116) W (45) 32 (60) 22 (49) E26C13 (14) 16 (22) E22C19W28 (5) Un (2870) first line: shared orthologs (random expectation); second: number of synteny blocks (random expectation); color marks over-/under- representation of orthologs (p-value<1%) 4 (849) 6 (1113) 10 (839) 14 (709) 1 (2165) 2 (1455) 15 (679) 20 (636) 12 (1088) 5 (1008) 9 (844) 3 (1138) 8 (788) 16 (946) 17 (1222) 19 (1377) 11 (1415) 13 (377) X (869) 7 (1063) 22 (528) 18 (306) 21 (261) DR51 (2) Y (110) 461 (31) 36 (2) 7 (9) 3 (0) 2 (76) 1 (6) 414 (39) 15 (2) 79 (45) 7 (2) 3 (16) 43 (5) 5 (0) 9 (1) 2 (0) 3 (0) 6 (90) 1 (5) 349 (14) 38 (1) 16 (54) 3 (6) 75 (37) 2 (4) 9 (13) 2 (1) 18 (75) 8 (8) 334 (18) 1 4 (10) 126 (73) 8 (7) 376 (32) 16 (3) 46 (120) 9 (12) 9 (83) 1 (8) 4 (30) 1 (3) 148 (13) 12 (1) 128 (12) 20 (1) 84 (10) 6 (1) 2 (2) 5 (55) 2 (2) 30 (3) 6 (0) 12 (0) 3 (0) E50C23 (2) Number of inter-chromosomal relations: 84 (16 on diagonal) 29 (49) 4 (4) 225 (53) 22 (4) 321 (23) 19 (2) 2 (17) 45 (87) 1 (7) 89 (19) 1 6 (21) 3 (1) 8 (2) 64 (166) 16 (120) 20 (16) 5 (10) 63 (18) 6 (2) 273 (8) 3 2 (7) 7 (41) 3 (5) 7 (57) 3 (7) 11 (20) 2 (2) 27 (21) 5 (2) 226 (6) 20 (0) 34 (8) 4 (0) 6 (0) 2 (49) 1 (5) 2 (28) 2 (16) 344 (62) 21 (4) 221 (10) 24 (1) 156 (11) 7 (0) 29 (86) 8 (6) 46 (42) 7 (5) 128 (10) 12 (1) 28 (1) 2 (0) 19 (84) 6 (10) 25 (22) 4 (2) 104 (83) 11 (9) 199 (7) 16 (0) 220 (18) 22 (2) 16 (32) 4 (3) 17 (8) 2 (1) 83 (8) 12 (1) 12 (65) 3 (7) 146 (57) 15 (6) 213 (14) 29 (1) 7 (115) 3 (13) 38 (25) 7 (1) 43 (27) 5 (2) 230 (30) 11 (2) 173 (6) 25 (1) 7 (7) 2 (0) 18 (1) 47 (62) 4 (4) 163 (11) 25 (1) 26 (63) 8 (10) 179 (10) 2 30 (15) 3 (2) 146 (6) 17 (0) 60 (3) 13 (0) 24 (88) 9 (11) 27 (2) (25) 8 (4) 24 (35) 1 (3) 223 (26) 24 (2) 102 (58) 9 (6) 120 (5) 10 (0) 15 (80) 6 (8) 231 (27) 10 (1) 174 (19) 32 (2) 114 (33) 5 (4) 149 (56) 14 (5) 204 (38) 15 (3) 48 (9) 8 (0) 77 (14) 8 (1) 4 (78) 2 (7) 146 (28) 6 (2) 96 (5) 13 (0) 2 (39) 1 (3) 120 (12) 12 (1) 11 (4) 2 (3) 23 (25) 5 (3) 13 (3) 2 (0) 105 (14) 4 (0) 6 (3) 2 (0) 21:10:33
22 Macro synteny first line: shared orthologs (random expectation); second: number of synteny blocks (random expectation); color marks over-/under- representation of orthologs (p-value<1%) 1 (2165) 14 (709) X (869) 20 (636) 17 (1222) 19 (1377) 2 (1455) 6 (1113) 16 (946) 4 (849) 5 (1008) 11 (1415) 3 (1138) 12 (1088) 18 (306) 8 (788) 13 (377) 7 (1063) 10 (839) 9 (844) 22 (528) 15 (679) 21 (261) Y (110) DR51 (2) Mouse 4 (1499) 12 (852) X (1116) 2 (2058) 11 (1877) 7 (2003) 1 (1504) 17 (1157) 8 (1189) 5 (1478) 13 (1012) 19 (795) 16 (811) 10 (1205) 18 (628) 15 (953) 14 (898) 3 (1237) 6 (1282) 9 (1394) 596 (93) 16 (3) 27 (117) 4 (3) 429 (93) 12 (3) 36 (74) 1 (2) 23 (92) 1 (3) 16 (63) 2 (2) 3 (50) 2 (56) 422 (77) 12 (2) 5 (80) 1 (2) 356 (17) 9 (0) 151 (18) 6 (0) 483 (21) 42 (1) 2 (28) 1 (2) 445 (36) (70) 31 (2) Number of inter-chromosomal relations: 113 (17 on diagonal) 430 (68) 22 (3) 80 (39) 5 (1) 166 (40) 6 (1) 113 (41) 4 (1) 60 (47) 4 (2) 81 (32) 8 (1) 189 (77) 11 (4) 56 (71) 2 (3) 2 (75) 1 (3) 382 (56) 16 (2) 85 (43) 4 (2) 50 (55) 1 (2) 7 (45) 1 (2) 11 (23) 81 (48) 4 (2) 40 (46) 2 (2) 35 (46) 4 (2) 326 (35) (31) 8 (1) 194 (37) 8 (1) 3 (27) 53 (43) 2 (2) 6 (49) 157 (52) 9 (2) 113 (30) 3 (1) 298 (31) 8 (1) 81 (21) 4 (0) 93 (27) 6 (1) 303 (33) 8 (1) 153 (28) 9 (1) 18 (29) 3 (1) 150 (51) 9 (2) 7 (41) 2 (2) 14 (31) 3 (1) 255 (27) 15 (1) 185 (17) 5 (0) 77 (26) 5 (1) 170 (84) 13 (3) 344 (81) 18 (3) 252 (32) 4 (1) 255 (57) 7 (2) 10 (40) 239 (28) 13 (1) 84 (31) 7 (1) 118 (42) 7 (2) 134 (44) 7 (2) 280 (48) 8 (2) 189 (48) 5 (1) 4 (26) 258 (39) 7 (1) 157 (31) 3 (0) 204 (41) 10 (1) 17 (12) 23 (9) 2 (0) 165 (5) 8 (0) 53 (30) 3 (1) 45 (30) 2 (1) 106 (24) 12 (1) 3 (20) 6 (16) 187 (19) 6 (1) 77 (18) 3 (1) 28 (25) 3 (1) 9 (15) 47 (12) 4 (0) 35 (15) 146 (9) 12 (0) 20 (12) 53 (23) 5 (1) 43 (50) 4 (2) 296 (40) 17 (2) 21 (27) 253 (34) 7 (1) 10 (37) 3 (2) 88 (48) 4 (2) 71 (46) 2 (2) 4 (27) 17 (23) 3 (1) 207 (18) 5 (0) 78 (28) 3 (1) 21 (14) 4 (0) 82 (21) 5 (1) 17 (30) 2 (1) 236 (34) 15 (2) 215 (47) 12 (3) 55 (23) 5 (1) 64 (18) 5 (1) 47 (24) 5 (15) 20 (19) 3 (1) 46 (10) 5 (0) 25 (15) 4 (0) 175 (12) 5 (0) 13 (17) 140 (36) 2 (1) 112 (35) 12 (1) 196 (25) 7 (1) 18 (6) 93 (4) 3 (0) 36 (7) 2 (0)
23
24 69.46 cen * /
25 A. B. Chromosome length (cm) Recombination rate (cm/mb) Chromosome length (Mb) Chromosome length (Mb)
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