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TABLE S5.  List of duplications of non-repetitive DNA sequences present at breakpoint regions of inversions between D. melanogaster and D. yakuba. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12
 | D. melanogaster |  |  |  |  |  |  | D. yakuba
Inversion | First  Breakpoint Region |  | Second  Breakpoint Region |  | Third  Breakpoint Region |  |  | First  Breakpoint Region |  | Second  Breakpoint Region |  | Third  Breakpoint Region
Involving at least full or partial gene duplications
X(1) | CG14804-CG14817-CG14805 |  | CG32659-HDC18578-CG2577 |  | ─ |  |  | CG14804-CG14817-HDC18578-CG32659 |  | CG14805-CG14817-CG2577 |  | ─
 | [→           ←             →] |  | [→            →               →] |  |  |  |  | [→            ←             [NAME] |  | [[NAME]              →]
 |  |  |  |  |  |  |  | 473 |  | 453
2L(2) | CG31649-CG6081-CG10833 |  | CG16869-CG16870 |  | ─ |  |  | CG16869-CG6081-CG31649 |  | CG10833-CG6081-CG16870 |  | ─
 | [→            →           →] |  | [→            →] |  |  |  |  | [→             [NAME] |  | [[NAME]]
 |  |  |  |  |  |  |  | 1886 |  | 3062
2LR(5) | CG5818-CG4440 |  | CG11777-CG12891 † |  | ─ |  |  | CG11777-CG12891 *-CG5818 |  | CG12891-CG11777 *-CG4440 |  | ─
 | [[NAME]          →] |  | [→            ←] |  |  |  |  | [→            ←                 →] |  | [→            ←                 →]
 |  |  |  |  |  |  |  | 274 |  | 150
2L(6) | CG4580-CG4599 |  | CG15152-CG5758 |  | ─ |  |  | CG4580-CG4580(T)-2L(36A-B)-CG4580(T) *-CG5758-CG15152 |  | CG4599-2L(36A-B)-CG4580-CG4599(T)-CG5758 |  | ─
 | [→          →] |  | [→            →] |  |  |  |  | [→           →                     x                 →                ←            ←] |  | [[NAME][NAME]                 →]
 |  |  |  |  |  |  |  | 771-1109-1108-(123+46) |  | (1019+1103+604)-(309+515+485)-74
2LR(7) | CG2614-CG31678 † |  | CG8118-BcDNA:GM02923-CG30483 |  | ─ |  |  | CG2614-CG31678 *-CG30483-BcDNA:GM02923-CG8118 |  | CG31678-CG8118 *-BcDNA:GM02923-CG30483 |  | ─
 | [→          ←] |  | [→         [NAME] |  |  |  |  | [→           ←                 →            →                           ←] |  | [→            →               [NAME]
 |  |  |  |  |  |  |  | 754-618-847 |  | 323-865
2LR(8) | CG9331-CG31673-CG31674-CG9333 |  | CG12388-CG12387-CG12386-CG12385 |  | ─ |  |  | CG9333-CG31674 *-CG31673-CG12386 *-CG12388 |  | CG12385-CG12386-CG12387-CG9333 *-CG31674-CG31673-CG9331 |  | ─
 | [→          →             →            ←] |  | [[NAME] |  |  |  |  | [→          [NAME] |  | [→            →             →             →              [NAME]
 |  |  |  |  |  |  |  | 370-277-83 |  | 340
2R(10) | CG6518-HDC06835-CG6622 |  | CG30264-CG30272 |  | ─ |  |  | CG30264-CG6518 |  | CG6622-HDC06835-CG6518-CG30272 |  | ─
 | [→          →               →] |  | [→             →] |  |  |  |  | [→            ←] |  | [[NAME]→]
 |  |  |  |  |  |  |  |  |  | 240
2R(11) | CG4847-CG4853 |  | CG10972-HDC04083-CG10384 |  | ─ |  |  | CG4853-CG4847-HDC04083-CG10384 |  | CG10972-CG4866-CG4847 |  | ─
 | [→           →] |  | [→            →                →] |  |  |  |  | [[NAME] |  | [→            [NAME]
 |  |  |  |  |  |  |  | 282
3R(6) | CG2519-CG10390 |  | CG33333-CG14332 |  | ─ |  |  | CG2519-CG14332 |  | CG33333-CG14332-CG10390 |  | ─
 | [[NAME] |  | [→            ←] |  |  |  |  | [[NAME] |  | [→             →            ←]
 |  |  |  |  |  |  |  |  |  | 184
3R(7), 3R(8) | CG31286-CG1315 † |  | CG2708-HDC14862-pfd800-HDC12400-HDC14862-CG7918 |  | CG31176-HDC14860-HDC14861-HDC12400-pfd800-HDC14862-CG34034-CG5849 |  |  | CG31176-HDC14860-HDC14861-HDC14862-pfd800-HDC12400-CG2708 |  | CG1315-CG31286 *-CG34034 *-CG34034 *-CG34034(T) *-CG7918 |  | CG31286-CG31286(T) *-CG34034 *-CG5849
 | [→            ←] |  | [→          →               →         →                →                →] |  | [[NAME]               ←              [NAME] |  |  | [[NAME]               →               ←               [NAME] |  | [→           ←                 →                   →                →                      →] |  | [→            →                       ←                  →]
 |  |  | 5491+1723 |  | 7746 |  |  |  |  | 663-1419-369-373 |  | 1045-1153
3R(10), 3R(11) | CG31211-CG31366 |  | CG3028-CG9925-CG3041 |  | CG14899-CG14900 |  |  | CG14900-3R(88A)-CG9925-CG31366 |  | CG3028-3R(88A) *-CG9925-CG14899 |  | CG3041-CG31211
 | [→            ←] |  | [→          [NAME]] |  | [[NAME] |  |  | [→            x                 [NAME] |  | [→           x                ←            →] |  | [[NAME]
 |  |  |  |  |  |  |  | 221 |  | 294-143
3R(12) | CG31142-CG5289 † |  | CG11504-CG7908 |  | ─ |  |  | CG31142-CG11504 |  | CG5289-CG31142-CG11504-CG7908 |  | ─
 | [→            ←] |  | [→            →] |  |  |  |  | [→            ←] |  | [→          [NAME]→]
 |  |  |  |  |  |  |  |  |  | 165-148
Involving solely duplications of non-coding sequences
X(5) | CG2186-CG2157 |  | CG9578-CG9579 † |  | ─ |  |  | CG2157-X(9F5)-CG9578 |  | CG2186-X(9F5)-CG9579 |  | ─
 | [→           →] |  | [→          ←] |  |  |  |  | [[NAME] |  | [→          x           ←]
 |  |  |  |  |  |  |  | 549 |  | 783
X(6) | CG1697-CG2247 |  | CG13012-CG13010 |  | ─ |  |  | CG13012-X(15A)-CG1697 |  | CG2247-X(15A) *-CG13010 |  | ─
 | [→          ←] |  | [[NAME] |  |  |  |  | [[NAME] |  | [→          x               ←]
 |  |  |  |  |  |  |  | 340 |  | 279
2L(1) | CG3036-CG2837 |  | CG7233-CG7231 |  | ─ |  |  | CG3036-2L(25B1-2)-CG7233 |  | CG2837-2L(25B1-2)-CG7231 |  | ─
 | [→          ←] |  | [[NAME]          →] |  |  |  |  | [→          x                   →] |  | [→          x                   →]
 |  |  |  |  |  |  |  | 256 |  | 229
2LR(4) | CG15274-CG4182 |  | CG12110-CG9397 |  | ─ |  |  | CG15274-2L(35B8) *-CG9397 |  | CG4182-2L(35B8) *-CG12110 |  | ─
 | [→            →] |  | [→            →] |  |  |  |  | [→             x                 →] |  | [[NAME]←]
 |  |  |  |  |  |  |  | (1654+779) |  | (1114+349+835)
2R(9) | CG16801-CG8166 |  | CG13504-CG6741 |  | ─ |  |  | CG16801-2R(51F)-2R(58C-D)-CG13504 |  | CG8166-2R(51F)-2R(58C-D)-CG6741 |  | ─
 | [→            →] |  | [[NAME]] |  |  |  |  | [→             x            x                 →] |  | [[NAME]                  →]
 |  |  |  |  |  |  |  | 850-(217+228) |  | 753-(228+215)
Protein-coding genes adjacent to breakpoints appear from left to right according to their order from the telomere of the X Chromosome to the telomere of the chromosomal arm 3R for each species. Putatitve transcribed sequences between reference protein-coding genes are also shown.
Full or partial copies of  coding sequences and putative transcribed regions that are duplicated, red (underlined if GENSCAN predicts a complete ORF); duplicated non-coding sequences, blue (the cytological location in D. melanogaster where they derive from in indicated).  Genes that probably result from transposition events, green.
The orientation of coding and putatively transcribed regions is indicated by arrows, 3'-5'.  The size (bp) of the duplicated fragments is shown in the third row of each inversion.  If a duplicate is present in several pieces, their size appears in brackets.
The case of the inversion 2LR(8) involves the duplication of multiple protein-coding genes at its corresponding co-occurrent breakpoint regions.  Due to this, all relevant genes are shown.
(T), copies derived from tandem duplication events.
* Verified by sequencing.
† 3' overlapping genes.