<apex:page controller="CustomPaginationController" sidebar="false">

//I added this
<apex:includeScript value="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js" />
<script type="text/javascript">
    $ = jQuery.noConflict();
    function Select1stAccounts(chk, contactId, Account.Name)
        {
            alert( '1' );
            var lstAccounts = $('input[id$="lstAccounts"]');
            var selectedlstAccounts = lstAccounts.val();
            
            if (chk.checked == true)
            {
                alert( '2A' );
                if (selectedlstAccounts == '')
                {
                    alert( '2A1' );
                    selectedlstAccounts = lstAccounts;
                } 
                else
                {
                    alert( '2A2' );
                    selectedlstAccounts = selectedlstAccounts + ',' + lstAccounts;
                }
            }
            else 
            {
                alert( '2B' );
                var accountIndex = selectedlstAccounts.indexOf(contactId);
                var accountToRemove = '';

                if (selectedlstAccounts.length == lstAccounts.length) {
                    accountToRemove = lstAccounts;
                }
                else {
                    if (accountIndex == 0){
                        accountToRemove = lstAccounts+ ',';
                    }
                    else{
                        accountToRemove = ',' + lstAccounts;
                    }
                }
            
                selectedlstAccounts = selectedlstAccounts.replace(accountToRemove, '');
            }
            alert( 'B' );
            lstAccounts.val(selectedlstAccounts);
            alert (lstAccounts.val());
    }
</script>
//Orignal Code
    <apex:form >
        <apex:inputHidden value="{!selectedlstAccounts}" id="lstAccountsIds"/>
        <apex:pageBlock >
            <apex:pageMessages ></apex:pageMessages>
            <apex:pageBlockButtons >
                <apex:commandButton action="{!Search}" value="Search" />
            </apex:pageBlockButtons>
            
            <apex:pageblockSection >
                <apex:inputText value="{!acc.Name}" label="Name"/> 
                
            </apex:pageblockSection>
        </apex:pageBlock>
        <apex:pageBlock id="resultId" rendered="{!if(lstAccount != null && lstAccount.size > 0, true,false )}">
            <apex:pageBlockButtons >
                <div style="text-align:right"> 
                  Total Records Found: {!Con.resultSize}  
      <apex:image url="/img/search_prevarrow_disabled.gif" styleClass="prevArrow" rendered="{!NOT(Con.HasPrevious)}"/>  
      <apex:image url="/img/search_prevarrow.gif" title="Previous Page" styleClass="prevArrow" rendered="{!Con.HasPrevious}"/>  
      <apex:commandLink action="{!Previous}" title="Previous Page" value="Previous Page" rendered="{!Con.HasPrevious}"/>  
      <apex:outputPanel styleClass="pShowLess noLink" style="color:grey" rendered="{!NOT(Con.HasPrevious)}">Previous Page</apex:outputPanel>           
      <apex:outputPanel styleClass="pShowLess noLink" style="color:grey" rendered="{!NOT(Con.HasNext)}">Next Page</apex:outputPanel>           
      <apex:commandLink title="Next Page" value="Next Page" rendered="{!Con.HasNext}" action="{!Next}"/>&nbsp;  
      <apex:image url="/img/search_nextarrow.gif" title="Next Page" styleClass="nextArrow" rendered="{!Con.HasNext}"/>  
      <apex:image url="/img/search_nextarrow_disabled.gif" rendered="{!NOT(Con.HasNext)}"/> 
      <img src="/s.gif" title="Last Page" alt="Last Page" class="last"/>         
                </div>
            </apex:pageBlockButtons>                
            <apex:pageBlockSection columns="1">
                <apex:pageBlockTable value="{!lstAccount}" var="acc" >
                <apex:column headerValue="Select" width="100px;">
                    <apex:inputCheckbox onclick="javascript:SelectAccounts(this, '{!acc.Id}');"/>
                    </apex:column>
                    <apex:column value="{!acc.Name}"/>
                    <apex:column value="{!acc.Account.Name}"/>
                    <apex:column value="{!acc.Cargo__c}"/>
                </apex:PageblockTable>
                <apex:commandButton value="Add Target" action="{!addTargets}"/>
            </apex:pageBlockSection>
        </apex:pageBlock>
    </apex:form>
</apex:page>

public with sharing class CustomPaginationController 
{

    public Contact acc {get;set;}   
    public ApexPages.StandardSetController con{get; set;} 
    public CustomPaginationController ()
    {
       acc = new Contact();
       lstAccount = new List<Contact>();
    }
    public List<Contact> lstAccount 
    {  
        get  
        {  
            if(con != null)  
                return (List<Contact>)con.getRecords();  
            else  
                return null ;  
        }  
        set;
    }  
    
    
    //added by me to test
     public PageReference addTarget() {
        //system.debug('sssssssss');
        List<Contact> lstAccountsIds = selectedlstAccounts.split(',');
        List<Target__c> lstAccount = new List<Target__c>();
        //system.debug('rrrrrrr');
        for (string s : lstAccountsIds )
        {
      //system.debug('lstAccountsIds: ' + lstAccountsIds);
            system.debug('s: ' + s);
            system.debug('Name: ' + accountMap.get(s).Name);
            Target__c newtarget = new Target__c (Target__c = lstAccount, Name = lstAccountsMap.get(s).Name); 
            Target.add(newtarget);
        }
        //system.debug('yyyyyyy');
        if (Target.size() > 0)
        {
            //system.debug('ppppppp');
            insert lstAccount;
        }
        string strPageRef = '"javascript:window.close();"';
        return new PageReference(strPageRef);
    }   
    
    
    public PageReference Search()
    {
        String query= '';
        String strFilter = '';
        if(acc.Name != null && (acc.Name ).trim() !='')
        {
           strFilter  = strFilter  +  ' where Name Like \''+acc.Name+'%\'' ;
        }
        if(acc.Account.Name != null && (acc.Account.Name).trim() !='' )
        {
            strFilter  = strFilter  +  ' where Name Like \''+acc.Account.Name+'%\'' ;
           
        }
        if(strFilter != '')
        {
            query = 'Select name ,id, Account.Name, Cargo__c from Contact '+strFilter+ ' limit 1000';
            System.debug('Query ---->'+ query );
            con = new ApexPages.StandardSetController(Database.getQueryLocator(query)); 
            con.setPageSize(10);
        }
        else
        {
        }
       return null;
    }
    public Boolean hasNext  
    {  
        get  
        {  
            return con.getHasNext();  
        }  
        set;  
    }  
    public Boolean hasPrevious  
    {  
        get  
        {  
            return con.getHasPrevious();  
        }  
        set;  
    }  
    public Integer pageNumber  
    {  
        get  
        {  
            return con.getPageNumber();  
        }  
        set;  
    }  
    public void previous()  
    {  
        con.previous();  
    }  
    public void next()  
    {  
        con.next();  
    }  
   
}