| Lineups found Starting lineup changes since last game |
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| July 2012 |
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| Coach Kreis since 03-May-07 |
| M.1 | 31-Jul | away | Heredia | | 1-0 | 4-3-1-2 | |
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| August 2012 |
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 01-Aug to 01-Sep Olave L hamstring strain |
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 19-Aug to 21-Aug Borchers Red card 7/31 vs. Herediano |
| M.2 | 21-Aug | | Tauro | | 2-0 | 4-3-1-2 | In:W Siriboe, Mansally, P Júnior, Out:Olave, Borchers, Espi'la, |
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| 22-Aug to 06-Sep Mansally L knee MCL sprain |
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| 22-Aug to 24-Aug Espíndola R groin tightness |
| September 2012 |
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| 02-Sep to 06-Sep Wingert Yellow Card accumulation |
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| 02-Sep to 11-Sep Beckerman International duty |
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| 02-Sep to 11-Sep Johnson, Will (1987) International duty |
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| 02-Sep to 11-Sep Saborío International duty |
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| 07-Sep to 18-Sep Beckerman Red card 8/21 vs. Tauro |
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| 17-Sep to 09-Oct Watson Siriboe R adductor strain |
| M.4 | 18-Sep | away | Tauro | | 0-1 | 4-3-1-2 | In:Olave, Borchers, Steele, Espi'la, Out:W Siriboe, Mansally, Beckerman, P Júnior, |
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| 19-Sep to 22-Sep Saborío R shoulder sprain |
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| 23-Sep to 29-Sep Olave Yellow Card accumulation |
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| 27-Sep to 17-Oct Grabavoy R quad strain |
| October 2012 |
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| 04-Oct to 06-Oct Johnson, Will (1987) birth of child |
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| 08-Oct to 17-Oct Saborío International duty |
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| 08-Oct to 17-Oct Johnson, Will (1987) International duty |
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| 11-Oct to 17-Oct Watson Siriboe R leg strain |
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| 18-Oct to 27-Oct Olave L quad strain |
| M.6 | 23-Oct | | Heredia | | 0-0 | 4-3-1-2 | In:Schuler, Gil, Beckerman, P Júnior, Out:Olave, Steele, Grabavoy, Saborío, |
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| 24-Oct to 08-Nov Schuler, C R quad strain |
| March 2013 |
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| 07-Nov to 08-Nov Wingert aggravated leg muscle |
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| 01-Dec to 13-Apr Wingert R foot fracture |
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 03-Dec to 03-Dec Braun, J Joining Toronto FC for 2013 season |
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| 03-Dec to 03-Dec Olave Joining New York Red Bulls for 2013 season |
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| 03-Dec to 03-Dec Espíndola Joining New York Red Bulls for 2013 season |
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| 03-Dec to 03-Dec Johnson, Will (1987) Joining Portland Timbers for 2013 season |
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| 16-Jan to 16-Mar Borchers L quadriceps surgery |
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| 04-Feb to 23-Mar Morales, Javier (1980) R knee menisectomy |
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 27-Feb to 03-Mar Gil, Luis Returned to Club |
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| 01-Mar to 09-Mar Braun, J concussion |
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| 02-Mar to 09-Mar Grabavoy family matter |
| April 2013 |
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| 14-Mar to 16-Mar Mansally MLS Disciplinary Committee decision |
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| 15-Mar to 13-Apr Viana, D R quad strain |
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| 17-Mar to 25-Mar Johnson, Will (1987) International duty |
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| 18-Mar to 26-Mar Rimando International duty |
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| 18-Mar to 26-Mar Beltran International duty |
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| 18-Mar to 26-Mar Beckerman International duty |
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| 18-Mar to 26-Mar Saborío International duty |
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| 18-Mar to 24-Mar Mansally International duty |
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| 24-Mar to 30-Mar Álvarez, Y Red card 3/23 vs. FC Dallas |
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| 27-Mar to 07-Apr Espíndola L hamstring Injury |
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| 27-Mar to 30-Mar Saborío R knee swelling |
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| 12-Apr to 13-Apr Velásquez, S R hand fracture |
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| 14-Apr to 20-Apr Beckerman dislocated rib |
| May 2013 |
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| Color References: GK, DF, DM, MF, FW , Unknown Pos |